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Reply to Steinman and Wang: Involvement of the p150 isoform of the RNA editing enzyme ADAR1 in embryonic lethality [Letters (Online Only)] (2011)

Ward, S. V., George, C. X., Samuel, C. E., Oldstone, M. B. A.

National Academy of Sciences

In: PNAS - Proceedings of the National Academy of Sciences

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Publication Date: 2011-06-15

Description: In their letter, Steinman and Wang (1) raise the possibility that p110 expression may be affected by specific gene targeting of the p150 isoform of adenosine deaminase 1 (ADAR1), similar to the concerns raised in the letter by Matthaei et al. (2). Although Steinman and Wang acknowledge that the levels of the constitutive exon 1B-containing transcript encoding the p110 isoform of ADAR1 were similar in both p150+/− and p150−/− MEF cells derived from gene-targeted embryos compared with MEF cells derived from WT embryos as shown in our article (3), they suggest that protein expression may have been affected as a...

Keywords: Letters

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Reply to Romero and Agrawal: Unpacking the specific links between biodiversity, ecosystem services, and social diversity is an essential first step [Letters (Online Only)] (2011)

Diaz, S., Quetier, F., Trainor, S. F., Caceres, D. M.

National Academy of Sciences

In: PNAS - Proceedings of the National Academy of Sciences

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Publication Date: 2011-06-08

Description: Romero and Agrawal (1) question the usefulness of our framework to link functional diversity with social actor strategies (2), arguing that it oversimplifies the complexity of the social dimensions of socioecological systems. We agree on the crucial importance of such dimensions, and we repeatedly highlighted this in our article, as is obvious from figure 1, the text, and the examples. While focusing on functional diversity, ecosystem services, and their role in different social actor strategies, we situated these in a broader setting that can be analyzed with the tools and concepts of social sciences, including institutional analyses.Rather than replacing major...

Keywords: Letters, Sustainability Science

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Algal ice-binding proteins change the structure of sea ice [Letters (Online Only)] (2011)

Raymond, J. A.

National Academy of Sciences

In: PNAS - Proceedings of the National Academy of Sciences

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Publication Date: 2011-06-15

Description: Krembs et al. (1) reported that extracellular polymeric substances (EPS) produced by a sea ice diatom, Melosira, created convoluted ice-pore morphologies in sea ice, potentially increasing its habitability and primary productivity. The activity was reduced by heat treatment and glycosidase treatments, suggesting that a glycoprotein was involved. Based on our previous work (2), it is very likely that the active substance is an ice-binding protein (IBP).All sea ice diatoms examined so far secrete similar ∼25 kDa IBPs that bind to ice, distorting its shape as it grows (2). Similar proteins are found in ice-adapted bacteria and fungi (3) and even...

Keywords: Letters

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ADAR1 isoform involvement in embryonic lethality [Letters (Online Only)] (2011)

Steinman, R. A., Wang, Q.

National Academy of Sciences

In: PNAS - Proceedings of the National Academy of Sciences

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Publication Date: 2011-06-15

Description: Letters to the editor recently published in PNAS (1, 2) challenged and defended a claim made on a recent article (3). Matthaei et al. (1) questioned whether the animal model used by Ward et al. (3) was adequate to support their claim that the P150 isoform of the RNA editing enzyme adenosine deaminase 1 (ADAR1) is required for embryogenesis. We believe the question remains open and present data indicating that a more complete assessment of ADAR1 isoform protein expression in the model of Ward et al. (3) is necessary to draw firm conclusions from it.In mammalian cells, the two major...

Keywords: Letters

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Long-term correlations in European socioeconomic conditions create a bias to conclusion that an invasion debt occurs [Letters (Online Only)] (2011)

Keller, R. P., Springborn, M.

National Academy of Sciences

In: PNAS - Proceedings of the National Academy of Sciences

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Publication Date: 2011-06-22

Description: Essl et al. (1) tested whether historical socioeconomic conditions have created an invasion debt in Europe (i.e., a suite of nonnative species that have not yet been discovered but whose establishment has been determined by previous socioeconomic conditions). Essl et al. (1) tested this theory by asking whether the cumulative numbers of nonnative species presently established in 28 European countries were more closely correlated to socioeconomic conditions in the year 1900 or 2000. In this letter, we describe a flaw in their logic that biases the analysis to concluding that an invasion debt does occur.Essl et al. (1) modeled the...

Keywords: Letters, Sustainability Science

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Policy perils of ignoring uncertainty in oil palm research [Letters (Online Only)] (2011)

Paoli, G. D., Carlson, K. M., Hooijer, A., Page, S. E., Curran, L. M., Wells, P. L., Morrison, R., Jauhiainen, J., Pittman, A. M., Gilbert, D., Lawrence, D.

National Academy of Sciences

In: PNAS - Proceedings of the National Academy of Sciences

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Publication Date: 2011-06-22

Description: Success of the emerging Low Emissions Development paradigm in Southeast Asia depends on mitigating impacts of oil palm (OP) expansion on carbon-dense ecosystems, especially tropical peatlands. To this end, Koh et al. (1) mapped OP planted before 2002 across Peninsular Malaysia, Sumatra, and Borneo to estimate emissions and biodiversity losses from peatland conversion (≈880,000 ha). Unfortunately, emissions scenarios are oversimplified, remote-sensing (RS) methods are unsuitable for OP monitoring, and recommendations for peatland restoration are overstated.The article risks misinforming national and international climate change policies under development.Koh et al. overestimated emissions from aboveground biomass (AGB) conversion to OP (136 million MgC)...

Keywords: Letters, Sustainability Science

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Reply to Mulrooney et al.: Accepting lower precision radiocarbon dates results in longer colonization chronologies for East Polynesia [Letters (Online Only)] (2011)

Wilmshurst, J. M., Hunt, T. L., Lipo, C. P., Anderson, A. J.

National Academy of Sciences

In: PNAS - Proceedings of the National Academy of Sciences

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Publication Date: 2011-06-08

Description: Mulrooney et al. (1) draw attention to a problem with our table S1 (2), which was unfortunately corrupted in transfer to PNAS (and has since been corrected). The actual database used for our analyses was free of errors (as their reanalysis has shown), thus, our results and conclusions remain unchanged (2).The letter by Mulrooney et al. (1) raises three issues:i) They believe our criteria for classifying dates by accuracy and precision are overly strict (1). However, relaxing standards of acceptance reduces their reliability. Our top down approach (2) may be conservative but results in high-precision, reliable chronologies that can be...

Keywords: Letters

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Building interdisciplinary frameworks: The importance of institutions, scale, and politics [Letters (Online Only)] (2011)

Romero, C., Agrawal, A.

National Academy of Sciences

In: PNAS - Proceedings of the National Academy of Sciences

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Publication Date: 2011-06-08

Description: Díaz et al. (1) proposed an “interdisciplinary framework for the analysis of relationships between functional diversity, ecosystem services, and human actions.” Their framework addresses the linkages between land uses and ecosystem service (ES) provision to inform decisions by relevant parties. We welcome the development and practical application of tools for analyzing the complexity of social-ecological systems (SESs), but there are fundamental gaps in the oversimplified framework of Díaz et al. (1). These flaws obscure critical aspects of the functioning of SESs, preclude their improved understanding, and thereby undermine the goal of fruitful scientific analysis.In particular, the proposed local-level framework does...

Keywords: Letters, Sustainability Science

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High-precision dating of colonization and settlement in East Polynesia [Letters (Online Only)] (2011)

Mulrooney, M. A., Bickler, S. H., Allen, M. S., Ladefoged, T. N.

National Academy of Sciences

In: PNAS - Proceedings of the National Academy of Sciences

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Publication Date: 2011-06-08

Description: Wilmshurst et al. (1) proposed recent and rapid colonization of East Polynesia based on analysis of 1,434 radiocarbon determinations. We commend the development of rigorous and replicable radiocarbon protocols that emphasize accuracy and precision, but we found (i) inaccuracies in their originally published supplementary data table, (ii) problems with their criteria for exclusion and inclusion of valid colonization estimators (i.e., Class 1 dates), and (iii) biases in their statistical analysis.Our review of their originally published 207 Class 1 dates identified 112 incorrectly reported 14C laboratory numbers and 123 misreported conventional radiocarbon ages, with 110 of these reported as at least...

Keywords: Letters

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Reply to Paoli et al.: Explicit consideration of model uncertainties [Letters (Online Only)] (2011)

Koh, L. P., Miettinen, J., Liew, S. C., Ghazoul, J.

National Academy of Sciences

In: PNAS - Proceedings of the National Academy of Sciences

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Publication Date: 2011-06-22

Description: Paoli et al. (1) raise some interesting criticisms of our article (2), but we think that they misinterpret important elements of our study, ignore our consideration of model uncertainties, and fail to recognize the wider significance of our work.We presented a framework for quantifying the impacts of oil-palm expansion on biodiversity and carbon stocks. We did so by combining a unique remote-sensing methodology with a unique species-area model and recently published carbon flux estimates. We also explicitly accounted for and presented uncertainties in all model projections. We estimated that the conversion of peatswamp forests to large-scale, closed canopy oil-palm plantations...

Keywords: Letters, Sustainability Science

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Reply to Keller and Springborn: No doubt about invasion debt [Letters (Online Only)] (2011)

Essl, F., Dullinger, S., Rabitsch, W., Hulme, P. E., Hulber, K., Jarosik, V., Kleinbauer, I., Krausmann, F., Kuhn, I., Nentwig, W., Vila, M., Genovesi, P., Gherardi, F., Desprez-Loustau, M.-L., Roques, A., Pysek, P.

National Academy of Sciences

In: PNAS - Proceedings of the National Academy of Sciences

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Publication Date: 2011-06-22

Description: We recently showed (1) that, for a wide range of taxa, the current numbers of established alien species in 28 European countries were generally more closely related to socioeconomic indicators from the year 1900 than 2000. Thus, the establishment of alien species seemed to lag considerably behind one of the main drivers of alien species introductions (2). We concluded that current high socioeconomic activity could result in considerable additional accumulation of alien species in the future, a phenomenon that we have called invasion debt.Keller and Springborn (3) suggest that cumulative numbers of established alien species would be better explained by...

Keywords: Letters, Sustainability Science

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Replies to Shen, Chen et al., and Yi and Zhou: Linear regression analysis misses effects of winter temperature on Tibetan vegetation [Letters (Online Only)] (2011)

Luedeling, E., Yu, H., Xu, J.

National Academy of Sciences

In: PNAS - Proceedings of the National Academy of Sciences

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Publication Date: 2011-05-11

Description: We are happy to see that our article (1) has stirred some interest, and we thank the authors of the three letters for their valuable comments (2–4).Shen (2) writes that linear regression could not detect a clear relationship between winter temperatures and beginning of growing season (BGS). This is not surprising. As has been shown many times, the primary driver of spring phenology is spring temperature, and this effect overlays smaller effects of temperature during other parts of the year. To tease such minor effects out of our dataset, we used partial least squares regression, which analyzed the impacts of...

Keywords: Letters

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Delayed spring phenology on the Tibetan Plateau may also be attributable to other factors than winter and spring warming [Letters (Online Only)] (2011)

Chen, H., Zhu, Q., Wu, N., Wang, Y., Peng, C.-H.

National Academy of Sciences

In: PNAS - Proceedings of the National Academy of Sciences

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Publication Date: 2011-05-11

Description: In their recent paper “Winter and spring warming result in delayed spring phenology on the Tibetan Plateau,” Yu et al. (1) reported an interesting but unexpected result that spring phenology initiated retreating in the mid-1990s, despite continued warming for grasslands (both steppe and meadow) on the Tibetan Plateau, and shortening the length of the growing season of the steppe together with an advancing end. Although we have not observed the same phenomenon in our own many years of field studies on the eastern edge of the Tibetan Plateau, we believed that there were indeed some complicated yet poorly understood dynamics...

Keywords: Letters

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Guanylyl cyclase activity in plants? [Letters (Online Only)] (2011)

Ashton, A. R.

National Academy of Sciences

In: PNAS - Proceedings of the National Academy of Sciences

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Publication Date: 2011-05-11

Description: Cyclic nucleotides have defined signal transduction roles in animals, fungi, and other diverse eukaryote kingdoms. However, the situation in plants is still not clear after more than 3 decades of investigations reporting evidence for and against a regulatory role for cyclic nucleotides in higher plants. No sequenced higher plant genome contains homologs of the nucleotidyl cyclase genes that are recognizable in diverse eukaryotic kingdoms, including, curiously, the Chlorophyta phylum of the Viridiplantae kingdom. The report of Qi et al. (1) is a recent example of claims that recombinant plant proteins (or their fragments) from diverse protein families have guanylyl cyclase...

Keywords: Letters

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Increasing contamination might have delayed spring phenology on the Tibetan Plateau [Letters (Online Only)] (2011)

Yi, S., Zhou, Z.

National Academy of Sciences

In: PNAS - Proceedings of the National Academy of Sciences

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Publication Date: 2011-05-11

Description: Using the National Aeronautics and Space Administration (NASA) Global Inventory, Monitoring, and Modeling Studies (GIMMS) Normalized Difference Vegetation Index (NDVI) dataset (1982–2006), Yu et al. (1) found that the trend of advancing spring phenology for alpine steppe and meadow was reversed around 2000, despite the increasing air temperature over the Tibetan Plateau. This phenomenon cannot be explained by changes in precipitation or snow melt. They speculated that the lack of fulfillment of a chilling requirement caused by warming winters could be the reason. This might have significant implications for the ecosystem and economy of the Tibetan Plateau. However, we offer...

Keywords: Letters

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Spring phenology was not consistently related to winter warming on the Tibetan Plateau [Letters (Online Only)] (2011)

Shen, M.

National Academy of Sciences

In: PNAS - Proceedings of the National Academy of Sciences

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Publication Date: 2011-05-11

Description: Yu et al. (1) reported that the beginning of vegetation growing season (BGS) of the alpine steppe and meadow on the Tibetan Plateau was delayed since the mid-1990s under warming winter and spring (1). They wrote that “this delay appeared to be related to later fulfillment of chilling requirements,” and they suggested that “continued warming may strengthen this effect or even reverse the advancing trend in spring phenology” (1).This idea was proposed earlier for phenology of some species (2) and was tested on the alpine vegetations at the regional level. Using this idea, if winter warming continues and spring warming...

Keywords: Letters

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Information content and word frequency in natural language: Word length matters [Letters (Online Only)] (2011)

Reilly, J., Kean, J.

National Academy of Sciences

In: PNAS - Proceedings of the National Academy of Sciences

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Publication Date: 2011-05-18

Description: For centuries, scientists have attempted to uncover commonalities that underlie the structure of human languages (1). In a recent issue of PNAS, Piantadosi et al. (2) reported an exciting finding with respect to one unique type of language universal. The authors empirically demonstrated that word length strongly correlated with information content across 11 distinct natural languages. This finding is remarkable in that it directly contravenes Zipf's principle of least effort, which holds that language optimizes communication by spontaneously truncating words as a function of their relative frequency (e.g., television → TV). Simply stated, more frequent words tend to be shorter,...

Keywords: Letters

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Reply to McPherron et al.: Doubting Dikika is about data, not paradigms [Letters (Online Only)] (2011)

Dominguez-Rodrigo, M., Pickering, T. R., Bunn, H. T.

National Academy of Sciences

In: PNAS - Proceedings of the National Academy of Sciences

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Publication Date: 2011-05-25

Description: We critiqued the claim that bone surface marks on two ∼3.4 Ma fossils from Dikika (Ethiopia) are the earliest evidence of hominin butchery damage (1) by (i) providing a detailed argument showing site- and assemblage-level weaknesses for the claim and (ii) matching those marks morphologically to marks produced on modern bones by trampling in coarse-grained sedimentary substrates, similar to those of the Dikika site (2). The letter by McPherron et al. (3), responding to our critique, completely ignores these substantive issues and, instead, seeks to disqualify our assessment by arguing that we are unwilling to accept a paradigm shift. McPherron...

Keywords: Letters

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Tool-marked bones from before the Oldowan change the paradigm [Letters (Online Only)] (2011)

Mc; Pherron, S. P., Alemseged, Z., Marean, C., Wynn, J. G., Reed, D., Geraads, D., Bobe, R., Bearat, H.

National Academy of Sciences

In: PNAS - Proceedings of the National Academy of Sciences

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Publication Date: 2011-05-25

Description: Domínguez-Rodrigo et al. (1) critiqued our paper (2), which provided the earliest evidence for stone tool use and animal tissue consumption as evidenced by bones bearing tool-induced marks found at DIK-55 (Dikika, Ethiopia) and dated to 3.39 Ma. Applying a configurational approach, they questioned the bones’ context and without examining or conducting new analysis on the original fossils, argued that all of the Dikika marks resulted from trampling, because a small subset of these marks superficially resembled a small subset of experimentally trampled specimens. Furthermore, they argued (1) that stone tool use and meat consumption before the current consensus dates...

Keywords: Letters

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Reply to Lee: Spatial sorting, assortative mating, and natural selection [Letters (Online Only)] (2011)

Shine, R., Brown, G. P., Phillips, B. L.

National Academy of Sciences

In: PNAS - Proceedings of the National Academy of Sciences

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Publication Date: 2011-08-03

Description: Lee (1) suggests that spatial sorting will be important only under limited circumstances, that it may often affect traits also subject to natural selection, and that it will enhance the effectiveness of selection by increasing phenotypic variance via positive assortative mating. These points build on the arguments advanced in our original paper, and we broadly agree with him.First, Lee (1) suggests that spatial sorting has only transitory effects. This is certainly true in the case of continuous range expansion (which must stop eventually). However, empirical and theoretical evidence suggests that spatial sorting also may occur continuously at stable range edges...

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Reply to Ferrarini: Strengths and weaknesses of simple competition models [Letters (Online Only)] (2011)

Allesina, S., Levine, J. M.

National Academy of Sciences

In: PNAS - Proceedings of the National Academy of Sciences

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Publication Date: 2011-08-03

Description: In our work (1), we showed how a largely overlooked mechanism of coexistence based on intransitive competitive relations could be widespread in nature and improve our understanding of biodiversity maintenance. We outlined the basic mechanism, providing a simplified model that can be expanded in several directions. In his comment, Ferrarini (2) raises four points that he believes weaken our approach. Here, we show that these arise from a misunderstanding of our framework, and it is not clear that any of these points would change our fundamental results.First, he stresses how our approach is rooted in zero-sum dynamics and focuses exclusively...

Keywords: Letters

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Reply to Hettinger: Olfaction is a physical and a chemical sense in Drosophila [Letters (Online Only)] (2011)

Franco, M. I., Turin, L., Mershin, A., Skoulakis, E. M. C.

National Academy of Sciences

In: PNAS - Proceedings of the National Academy of Sciences

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Publication Date: 2011-08-03

Description: We would like to thank Dr. Hettinger (1) for his positive comment on our results showing that flies can discriminate isotopes by smell and are capable of cross-learning between odorants sharing a molecular vibration. Our article (2) demonstrated the presence of a physical (vibrational) component to odor character necessitating a vibration-sensing mechanism, the nature of which was not addressed experimentally and remains to be elucidated. We suggest that it likely involves inelastic electron tunneling, because this is consistent with our experimental data and with Brookes et al. (3), who have shown that an inelastic tunneling mechanism in olfaction is physically...

Keywords: Letters

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Ancient starch: Cooked or just old? [Letters (Online Only)] (2011)

Collins, M. J., Copeland, L.

National Academy of Sciences

In: PNAS - Proceedings of the National Academy of Sciences

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Publication Date: 2011-06-01

Description: Henry et al. (1) argued for greater sophistication in Neanderthal diets on the basis of the identification of ancient starch granules, some of which—according to changes in morphology—displayed “clear evidence of cooking.” Despite the emphasis on morphology and morphological change, there is no attempt to apply any statistical rigor to their morphology-based identifications (cf. ref. 2); nor is there any attempt to independently confirm that any of the observed structures are indeed composed of starch. Biochemical tests, such as digestion with Bacillus licheniformis 1,4-α-d-glucan-glucanohydrolase (3), can confirm the presence of starch and may give some insight into diagenesis. Similar characterization...

Keywords: Letters

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What about European alvarezsauroids? [Letters (Online Only)] (2011)

Dyke, G. J., Naish, D.

National Academy of Sciences

In: PNAS - Proceedings of the National Academy of Sciences

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Publication Date: 2011-06-01

Description: Xu et al. (1) reported the alvarezsauroid Linhenykus monodactylus from Inner Mongolia, a confirmed monodactyl Mesozoic dinosaur. Xu et al.’s (1) phylogenetic hypothesis for Linhenykus suggests that it is sister to a clade that includes all other Cretaceous Laurasian alvarezsauroids. On this basis, Xu et al. (1) discussed the paleobiogeographic history of Alvarezsauroidea, concluding that the lineage originated in Asia and then spread via successive dispersal events to South and North America [the earliest known record of this lineage is from the Jurassic of China (2)].Although there is little doubt that Linhenykus is important and interesting from both phylogenetic and...

Keywords: Letters

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Reply to Dyke and Naish: European alvarezsauroids do not change the picture [Letters (Online Only)] (2011)

Xu, X., Sullivan, C., Pittman, M., Choiniere, J. N., Hone, D., Upchurch, P., Tan, Q., Xiao, D., Tan, L., Han, F.

National Academy of Sciences

In: PNAS - Proceedings of the National Academy of Sciences

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Publication Date: 2011-06-01

Description: Dyke and Naish (1) draw attention to three points that they consider to be “serious shortcomings” of our recent paper on a monodactyl nonavian dinosaur (2). Here, we respond to each point in turn.Our paleobiogeographic hypothesis was based strictly on the phylogenetic tree we recovered (2), which did not include the European alvarezsauroid Heptasteornis because of the extremely fragmentary nature of the known material (3). However, we did include this taxon in a section of our paper (albeit in the SI Appendix) dealing with the biogeography of the Alvarezsauroidea, and even discussed its possible systematic position (2). Because it is...

Keywords: Letters

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Reply to Collins and Copeland: Spontaneous gelatinization not supported by evidence [Letters (Online Only)] (2011)

Henry, A. G., Brooks, A. S., Piperno, D. R.

National Academy of Sciences

In: PNAS - Proceedings of the National Academy of Sciences

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Publication Date: 2011-06-01

Description: We thank Collins and Copeland (1) for raising the point that a better understanding of starch granule behavior in archaeological settings would be useful. However, we disagree with their assessment that the cooked starch granules we observed on Neanderthal teeth (2) were an effect of diagenesis.To estimate the effect of aging on starch granules, they apply an equation that is used to describe thermal gelatinization of a starch/water system, and we believe their application is not appropriate for predictions about archaeological specimens. Their activation energy estimate derives from experiments in which starches are heated to gelatinization temperatures (≈50–80 °C), far...

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Reply to Grinsted et al.: Estimating land subsidence in North Carolina [Letters (Online Only)] (2011)

Kemp, A. C., Horton, B. P., Donnelly, J. P., Mann, M. E., Vermeer, M., Rahmstorf, S.

National Academy of Sciences

In: PNAS - Proceedings of the National Academy of Sciences

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Publication Date: 2011-10-05

Description: Reconstructions and observations of relative sea level (RSL) must be corrected for vertical land movements from glacial isostatic adjustment (GIA) to facilitate comparisons among regions and identify deviations from background rates. Late Holocene (past 2 ka) GIA rates are estimated from geological data and permanent global positioning system (GPS) stations or predicted from GIA models. We used a linear trend fitted to the regional, compaction-free, RSL reconstructions compiled by Engelhart et al. (1) for the past 2 ka (excluding data since AD 1900) as a GIA estimate. Similarly, GIA models also attribute all RSL changes during the past 2 ka...

Keywords: Letters, Sustainability Science

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Comment on the subsidence adjustment applied to the Kemp et al. proxy of North Carolina relative sea level [Letters (Online Only)] (2011)

Grinsted, A., Jevrejeva, S., Moore, J. C.

National Academy of Sciences

In: PNAS - Proceedings of the National Academy of Sciences

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Publication Date: 2011-10-05

Description: Kemp et al. (1) presented a new salt-marsh proxy record of relative sea level (RSL) from North Carolina (NCRSL). The salt marsh is slowly subsiding as a result of glacial isostatic adjustment (GIA), and the NCRSL record needs to be adjusted to remove this vertical land movement from the sea level record. Kemp et al. (1) corrected for a constant subsidence rate of approximately 1 mm/y. This is a “geologic” estimate based on sea level index points, which are determined from linear fits to data from other North American RSL proxy records. Thus, the geologic method implicitly assumes that the...

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Potential effects of the APOE ϵ2 allele and of family history of Alzheimer's disease on brain amyloid-{beta} in normal elderly [Letters (Online Only)] (2011)

Pomara, N., Bruno, D.

National Academy of Sciences

In: PNAS - Proceedings of the National Academy of Sciences

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Publication Date: 2011-11-09

Description: Cirrito et al. (1) provided compelling data from investigations in PS1/APP double-transgenic mice that acute and chronic pharmacological manipulations of serotonin signaling were associated with significant reductions in brain interstitial fluid amyloid-β (Aβ) levels and plaque load, respectively. More importantly, they also reported that cognitively intact elderly individuals with a retrospectively obtained history of antidepressant treatment with serotonin reuptake inhibitor (SSRI) drugs, within the past 5 y, showed less brain amyloid load as quantified by PET-Pittsburgh Compound B (PIB) than controls without such a history. In addition, longer duration of SSRI treatment was associated with lower Aβ levels. The authors...

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Reply to Pomara and Bruno: Need for prospective, randomized clinical trial [Letters (Online Only)] (2011)

Sheline, Y. I., Cirrito, J. R.

National Academy of Sciences

In: PNAS - Proceedings of the National Academy of Sciences

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Publication Date: 2011-11-09

Description: Thank you for giving us an opportunity to reply to the letter to the editor by Pomara and Bruno (1) requesting clarification about the APOE ε2 allele and family history status of the antidepressant-treated group vs. untreated group in our paper in PNAS (2). As pointed out in the letter, there is work describing protective effects of APOE ε2 allele status and higher risk with a family history of Alzheimer's disease. These indeed are potentially important covariates. We did not include APOE ε2 status in the paper because of the small number of individuals in our study sample with this...

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Density minimum in supercooled confined water [Letters (Online Only)] (2011)

Soper, A. K.

National Academy of Sciences

In: PNAS - Proceedings of the National Academy of Sciences

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Publication Date: 2011-11-23

Description: Recent papers in PNAS, here labeled I (1) and II (2), have proposed that when water confined in the porous silica matrix MCM-41-S with a 15-Å pore diameter is supercooled, it reaches a density minimum at around 200 K. The evidence for this assertion is based on the observed intensity of the (100) Bragg diffraction peak, which arises from the hexagonal arrangement of the cylindrical pores, as a function of temperature. In I, it is further found that the density profile as function of temperature shows significant hysteresis between heating and cooling at different pressures. Both results are used to...

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Reply to Soper: Density measurement of confined water with neutron scattering [Letters (Online Only)] (2011)

Zhang, Y., Faraone, A., Kamitakahara, W. A., Liu, K.–H., Mou, C.–Y., Leao, J. B., Chang, S., Chen, S.–H.

National Academy of Sciences

In: PNAS - Proceedings of the National Academy of Sciences

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Publication Date: 2011-11-23

Description: This is a response to Soper's two comments (1) regarding our papers (2, 3) in PNAS that (a) the distribution of water across the pores is not uniform and (b) the majority of water may reside outside the pores. Here, we show that we have given proper consideration to both issues and have reconfirmed the validity of our method and conclusion as elaborated in the following.The possibility that layering effects across the pores may introduce errors in associating the (100) interchannel peak height with density is not a new idea (reference 3 in ref. 1), and it has already been...

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Which of satellite- or model-based estimates is closer to reality for aerosol indirect forcing? [Letters (Online Only)] (2011)

Quaas, J., Boucher, O., Bellouin, N., Kinne, S.

National Academy of Sciences

In: PNAS - Proceedings of the National Academy of Sciences

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Publication Date: 2011-11-16

Description: In their contribution to PNAS, Penner et al. (1) used a climate model to estimate the radiative forcing by the aerosol first indirect effect (cloud albedo effect) in two different ways: first, by deriving a statistical relationship between the logarithm of cloud droplet number concentration, ln Nc, and the logarithm of aerosol optical depth, ln AOD (or the logarithm of the aerosol index, ln AI) for present-day and preindustrial aerosol fields, a method that was applied earlier to satellite data (2), and, second, by computing the radiative flux perturbation between two simulations with and without anthropogenic aerosol sources. They find...

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Reply to Quaas et al.: Can satellites be used to estimate indirect climate forcing by aerosols? [Letters (Online Only)] (2011)

Penner, J. E., Zhou, C., Xu, L., Wang, M.

National Academy of Sciences

In: PNAS - Proceedings of the National Academy of Sciences

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Publication Date: 2011-11-16

Description: We welcome the comments by Quaas et al. (1). In our paper (2), we used a model to show that the methods used to estimate indirect aerosol forcing using satellite data, especially those based on relating the slope of present-day (PD) drop number (Nc) to aerosol optical depth (AOD), underestimate the forcing calculated when both PD and preindustrial (PI) data are available.i) Quaas et al. (1) claim that studies that adjust tunable parameters in models to fit PD slopes do not suffer from the issues that we pointed out in our paper (2). However, our results show that the evolution...

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Are exploited fish populations stable? [Letters (Online Only)] (2011)

Sugihara, G., Beddington, J., Hsieh, C.-h., Deyle, E., Fogarty, M., Glaser, S. M., Hewitt, R., Hollowed, A., May, R. M., Munch, S. B., Perretti, C., Rosenberg, A. A., Sandin, S., Ye, H.

National Academy of Sciences

In: PNAS - Proceedings of the National Academy of Sciences

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Publication Date: 2011-11-30

Description: Shelton and Mangel (1) examined patterns of variability in fish populations and concluded that the higher stock variability observed in exploited species results from heightened effects of stochastic forcing in the supposed absence of nonlinear dynamics. In contrast, Anderson et al. (2) found that higher variability in these stocks is attributable to amplified nonlinear behavior in noisy ecological systems under exploitation. Here, we reconcile these apparently conflicting views and demonstrate that stochasticity of demographic parameters directly enhances nonlinearity (2–4), thus challenging assessments of stability based on statistical fits to noise-free models.Shelton and Mangel (1) concluded that fish populations are stable...

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Reply to Sugihara et al: The biology of variability in fish populations [Letters (Online Only)] (2011)

Shelton, A. O., Mangel, M.

National Academy of Sciences

In: PNAS - Proceedings of the National Academy of Sciences

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Publication Date: 2011-11-30

Description: Sugihara et al. (1) ask, “Are exploited fish populations stable?” and conclude that they are not. We concur. However, we do not concur that Shelton and Mangel (2) “conclude that fish populations are stable…” or that “higher stock variability observed in exploited species results from heightened effects of stochastic forcing in the supposed absence of nonlinear dynamics” (1).We (2) started from the observation that many natural populations of fish fluctuate in abundance. By using available data from a diverse range of species, we showed that single deterministic nonlinear dynamics are very unlikely to drive the variability of natural populations. This...

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Reply to Weinshall-Margel and Shapard: Extraneous factors in judicial decisions persist [Letters (Online Only)] (2011)

Danziger, S., Levav, J., Avnaim-Pesso, L.

National Academy of Sciences

In: PNAS - Proceedings of the National Academy of Sciences

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Publication Date: 2011-10-19

Description: Shapard and Weinshall-Margel (1) elucidate several critiques of our article, “Extraneous factors in judicial decisions” (2), in which we report a greater likelihood of judicial ruling in favor of a prisoner at the beginning of the work day or after a food break than later in a sequence of cases. They argue that two interlinked factors jointly produce our results: (i) all prisoners from one prison are seen before a break is taken, and (ii) all prisoners without representation are seen at the end of each decision session, prior to the breaks.The data fail to support their assertions. We recoded...

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Reply to Skoyles: Misplaced assumptions of perfect human prosociality [Letters (Online Only)] (2011)

Horner, V., Carter, J. D., Suchak, M., de Waal, F. B. M.

National Academy of Sciences

In: PNAS - Proceedings of the National Academy of Sciences

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Publication Date: 2011-10-19

Description: In his letter (1), the author argues against prosocial tendencies in chimpanzees because the chimpanzees in our study (2) failed to select the prosocial option all of the time. Instead, he suggests that they show evidence for “mean-spirited” motivations, because any deviation from a perfectly prosocial score must indicate purposeful withholding of benefits for the partner. However, behavioral studies are not conducted in a vacuum, informed by hypothetical analogies. Our study involved real participants in a social environment in which they express myriad conflicting motivations, inhibitions, distractions, emotions, and preexisting social “baggage” brought with them into an experimental setting. Before...

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Reply to Sharp et al.: Host species sampling bias and Plasmodium falciparum origin paradigm shifts [Letters (Online Only)] (2011)

Prugnolle, F., Durand, P., Ollomo, B., Ayala, F. J., Renaud, F.

National Academy of Sciences

In: PNAS - Proceedings of the National Academy of Sciences

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Publication Date: 2011-10-26

Description: We thank Sharp et al. (1) for their comments, but we disagree. The results of Prugnolle et al. (2) did not disprove that human Plasmodium falciparum has a gorilla origin but brought that conclusion into question, which is what we asserted (and yes, a single isolate in a single monkey species is enough to question it).Current data can be accounted for by the hypothesis of a gorilla origin of human P. falciparum, but there are alternatives (reviewed in ref. 3). These alternative hypotheses need to be considered and tested. The available data could be biased or incomplete. Liu et al.'s...

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Reply to Davies: Hydraulic fracturing remains a possible mechanism for observed methane contamination of drinking water [Letters (Online Only)] (2011)

Jackson, R. B., Osborn, S. G., Vengosh, A., Warner, N. R.

National Academy of Sciences

In: PNAS - Proceedings of the National Academy of Sciences

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Publication Date: 2011-10-26

Description: Davies (1) agrees that methane contamination of drinking water has occurred in aquifers overlying the Marcellus formation but asserts that we prematurely ascribed its cause to hydraulic fracturing (2). We respond briefly, noting that we carefully avoided ascribing any mechanism and suggested some additional research (2) for the important need that Davies (1) identifies—to understand the mechanism of contamination better. Comments about sampling procedures and methane seeps are in refs. 3 and 4.Our paper discussed three mechanisms for stray gas migration (2). One was physical displacement of gas-rich water up from the shale formation, which we dismissed as “unlikely” (2)....

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Flexible strategies, forgiveness, and the evolution of generosity in one-shot encounters [Letters (Online Only)] (2011)

Mc; Nally, L., Tanner, C. J.

National Academy of Sciences

In: PNAS - Proceedings of the National Academy of Sciences

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Publication Date: 2011-11-02

Description: By using agent-based simulations, Delton and colleagues (1) suggested in PNAS that cooperation by humans in one-shot interactions could have evolved as a byproduct of selection for reciprocity when it is uncertain if interactions will be repeated. We believe their work should be commended both for the novelty of the hypothesis proposed and the explicit cognitive framework in which the model is posed, providing new insight into an important interdisciplinary problem. However, as a result of the authors’ focus on decision-making in the first round of interaction, the possibility of subsequent strategy updating is ignored and, as a result, only...

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Reply to Saba and Orzechowski and Schon: Methane contamination of drinking water accompanying gas-well drilling and hydraulic fracturing [Letters (Online Only)] (2011)

Osborn, S. G., Vengosh, A., Warner, N. R., Jackson, R. B.

National Academy of Sciences

In: PNAS - Proceedings of the National Academy of Sciences

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Publication Date: 2011-09-14

Description: Two letters by Saba and Orzechowski (1) and Schon (2) address our research linking elevated methane and ethane concentrations to shale-gas drilling and hydraulic fracturing (3). We respond briefly here and point readers to a supplementary document for more details (4).An assertion, and misconception, in both letters is that, because we found small amounts of mixed biogenic and thermogenic gas in 85% of groundwater samples, the thermogenic gas we observed near shale-gas wells occurred naturally. What we showed instead (figures 3 and 4 of ref. 3) was that drinking water was more likely to have high methane and ethane concentrations...

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Lack of data to support a relationship between methane contamination of drinking water wells and hydraulic fracturing [Letters (Online Only)] (2011)

Saba, T., Orzechowski, M.

National Academy of Sciences

In: PNAS - Proceedings of the National Academy of Sciences

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Publication Date: 2011-09-14

Description: Osborn et al. (1) sampled 68 water wells located in upstate New York (Genesee formation) and northeast Pennsylvania (Catskill and Lockhaven formations). The study opined that there is systematic evidence of increased concentrations of thermogenic methane in water wells near active gas extraction areas compared with water wells outside active gas extraction areas. Average methane concentrations were 19.2 and 1.1 mg L−1 for active and nonactive areas, respectively. By using isotope analysis, the study concluded that the thermogenic methane in the water wells is consistent with Marcellus shale gases.However, the Genesee data show that average methane concentrations in nonactive area...

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Hydraulic fracturing not responsible for methane migration [Letters (Online Only)] (2011)

Schon, S. C.

National Academy of Sciences

In: PNAS - Proceedings of the National Academy of Sciences

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Publication Date: 2011-09-14

Description: Although Osborn et al. (1) provided important geochemical measurements of dissolved methane in a portion of the Appalachian basin, their report does not fully appreciate the geologic history of this region and misrepresents potential risks of modern drilling and completion techniques used to develop shale-gas resources. The fear that hydraulic fracturing is responsible for methane migration from the Marcellus shale into shallow groundwater is contrasted by direct observations in microseismic studies that even the longest fractures induced by the hydraulic fracturing process remain thousands of feet below groundwater resources (2).The Marcellus is a Devonian-age (∼390 Ma) black shale and the...

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Reply to Godfrey et al.: Outside the box [Letters (Online Only)] (2011)

Cerling, T. E., Mbua, E., Kirera, F. M., Manthi, F. K., Grine, F. E., Leakey, M. G., Sponheimer, M., Uno, K. T., Lee-Thorp, J.

National Academy of Sciences

In: PNAS - Proceedings of the National Academy of Sciences

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Publication Date: 2011-09-21

Description: We thank Godfrey et al. (1) for their comments comparing the possible diet of Hadropithecus with that of Paranthropus boisei (2, 3). We wrote: “Indeed, the only known haplorrhine primate with a similar carbon isotope composition is the extinct grass-eating baboon Theropithecus oswaldi,” which explicitly excluded Hadropithecus and other Malagasy strepsirrhine primates from the comparison as they are only very distantly related to modern apes and humans. Molecular and morphological approaches indicate that the strepsirrhine-haplorrhine divergence occurred before the Eocene (4, 5).Although certain morphological convergences between the taxa may exist, it is far from certain that this implies similar diets....

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Overlooked factors in the analysis of parole decisions [Letters (Online Only)] (2011)

Weinshall-Margel, K., Shapard, J.

National Academy of Sciences

In: PNAS - Proceedings of the National Academy of Sciences

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Publication Date: 2011-10-19

Description: Danziger et al. (1) concluded that meal breaks taken by Israeli parole boards influence the boards’ decisions. This conclusion depends on the order of cases being random or at least exogenous to the timing of meal breaks. We examined data provided by the authors and obtained additional data from 12 hearing days (n = 227 decisions).* We also interviewed three attorneys, a parole panel judge, and five personnel at Israeli Prison Services and Court Management, learning that case ordering is not random and that several factors contribute to the downward trend in prisoner success between meal breaks. The most important...

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Chimpanzees make mean-spirited, not prosocial, choices [Letters (Online Only)] (2011)

Skoyles, J. R.

National Academy of Sciences

In: PNAS - Proceedings of the National Academy of Sciences

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Publication Date: 2011-10-19

Description: Horner et al. (1) argued that chimpanzees “overwhelmingly” favor “prosocial choices” in preference to “selfish” ones. However, their findings are better interpreted as evidence that chimpanzees make “mean-spirited” decisions.Consider a situation that transposes their experimental setup into a human context. A flight attendant of an airline provides refreshments for passengers in paired seats by giving one of them a bucket of colored tokens. This passenger then picks one of two colored token types to hand to the attendant. One color results in this passenger and the adjacent one both receiving a piece of banana wrapped in paper (self-and-other token), whereas...

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Reply to McNally and Tanner: Generosity evolves when cooperative decisions must be made under uncertainty [Letters (Online Only)] (2011)

Delton, A. W., Krasnow, M. M., Cosmides, L., Tooby, J.

National Academy of Sciences

In: PNAS - Proceedings of the National Academy of Sciences

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Publication Date: 2011-11-02

Description: We thank McNally and Tanner (1) for their considered critique of our article (2). Our article addressed the puzzle of why humans, in one-shot interactions, often choose to incur costs to allocate benefits to others, with no possibility of recouping these losses (i.e., “irrational” generosity) (2). This empirical pattern challenges standard models of economic and evolutionary rationality, and has prompted the development of ever-more-cumbersome explanations (e.g., group selection, gene–culture coevolution, cultural group selection)—models fragilely dependent on many hard-to-verify assumptions. In our article, we demonstrated that the well-documented selective regime of direct reciprocity produces agents willing to cooperate in apparently one-shot...

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Methane contamination of drinking water caused by hydraulic fracturing remains unproven [Letters (Online Only)] (2011)

Davies, R. J.

National Academy of Sciences

In: PNAS - Proceedings of the National Academy of Sciences

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Publication Date: 2011-10-26

Description: Shale gas extraction involves the drilling of organic-rich, low-permeability shale and then stimulation of hydraulic fractures that allows gas to be produced. Methane in aquifers located above the shale strata, for instance, in Pennsylvania, United States, has been attributed by some to be the result of contamination caused by the hydraulic fracturing process. The work by Osborn et al. (1) described geochemical data from 68 drinking water wells in northeastern Pennsylvania and upstate New York and evaluated whether the aquifers that the water wells penetrated were contaminated with thermogenic methane sourced from the underlying Marcellus and Utica shale formations. The...

Keywords: Letters

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Is the p150 isoform of the RNA editing enzyme Adenosine Deaminase 1 really responsible for embryonic lethality? [Letters (Online Only)] (2011)

Matthaei, K. I., Frese, M., Hill, C. E.

National Academy of Sciences

In: PNAS - Proceedings of the National Academy of Sciences

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Publication Date: 2011-03-23

Description: We read with interest the manuscript by Ward et al. (1) in PNAS in which selective disruption of the p150 isoform, but not the p110 isoform, of the RNA editing enzyme Adenosine Deaminase 1 (ADAR1) was reported to cause early embryonic lethality.ADAR1 exists in two molecular weight isoforms: a long protein of 150 kDa (p150), which is expressed from an interferon-inducible promoter using a translational start site in exon 1A, and a short form of 110 kDa (p110), which is expressed from two constitutive promoters using exon 1B or 1C and an alternative translational start site in exon 2. Both...

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Oxytocin and intergroup relations: Goodwill is not a fixed pie [Letters (Online Only)] (2011)

Chen, F. S., Kumsta, R., Heinrichs, M.

National Academy of Sciences

In: PNAS - Proceedings of the National Academy of Sciences

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Publication Date: 2011-03-30

Description: De Dreu et al. (1) presented a set of experiments exploring the effects of the neuropeptide oxytocin on implicit associations and moral reasoning about in-group and out-group members. Although their experiments were cleverly designed, their data did not clearly support their interpretation that oxytocin promotes human “ethnocentrism” (1).Oxytocin has been shown to mediate social stress buffering and attachment behaviors in many mammalian species (2). In humans, oxytocin decreases stress and anxiety responses (e.g., attenuated hypothalamic-pituitary-adrenal axis and amygdala reactivity) and promotes various aspects of complex social cognition and social behavior, including trust and emotion recognition (3, 4). De Dreu et...

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Reply to Hudgens et al.: Bald eagles, no-analog ecological scenarios, and conservation strategies on the Channel Islands [Letters (Online Only)] (2011)

Newsome, S. D., Collins, P. W., Rick, T. C., Guthrie, D. A., Erlandson, J. M., Fogel, M. L.

National Academy of Sciences

In: PNAS - Proceedings of the National Academy of Sciences

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Publication Date: 2011-02-23

Description: Hudgens et al. (1) raise two issues with our interpretation of past bald eagle diets on the Channel Islands (CI). First, they provide an alternative explanation for the terrestrial isotopic signatures of Pleistocene bald eagles from the CI, suggesting that they regularly fed on pygmy mammoth carrion (1). Although this explanation is plausible, it is not more parsimonious than the one that we provided (2). Movement data of reintroduced bald eagles show evidence of dispersal from the CI to the mainland, and in some cases, individuals return to the islands after using inland habitats across western North America (3). Such...

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Ghost prey and missing conflicts: Reinterpreting the implications of bald eagle diet composition on the California Channel Islands [Letters (Online Only)] (2011)

Hudgens, B. R., Coonan, T. J., Faulkner, K. R., Garcelon, D. K.

National Academy of Sciences

In: PNAS - Proceedings of the National Academy of Sciences

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Publication Date: 2011-02-23

Description: The study by Newsome et al. (1) presented an approach to evaluating the historic ecological role of bald eagles (Haliaeetus leucocephalus) on the California Channel Islands (CI). Unfortunately, they ignore an alternative explanation for some of their data and overinterpret their results, leading to conclusions that are not the most parsimonious (1).First, Newsome et al. (1) incorrectly dismissed two prehistoric eagles with a stable isotope signature, suggesting “heavy reliance on terrestrial prey” as “migrants from the mainland.” They do so by arguing that large terrestrial prey would not have been available to resident CI eagles when their specimens were preserved....

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Benefits of tropical crops for food security [Letters (Online Only)] (2011)

Vermeulen, S. J., Wollenberg, E. K.

National Academy of Sciences

In: PNAS - Proceedings of the National Academy of Sciences

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Publication Date: 2011-03-02

Description: West et al.’s recent paper (1) compared tradeoffs of carbon and crop production in temperate and tropical zones. We welcome the empirical evidence in support of agricultural intensification rather than extensification. We strongly caution against the implicit conclusion that food production might need to be concentrated in the temperate zone, however. First, this has implications for food security. People vulnerable to food insecurity live largely in low-income tropical countries and depend predominantly on local agriculture both for food supplies and to provide the livelihoods that underpin food security (2). Second, as the maps of West et al. (1) show, there...

Keywords: Letters, Sustainability Science

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Reply to Butterfield: The Devonian radiation of large predatory fish coincided with elevated atmospheric oxygen levels [Letters (Online Only)] (2011)

Dahl, T. W., Hammarlund, E. U., Anbar, A. D., Bond, D. P. G., Gill, B. C., Gordon, G. W., Knoll, A. H., Canfield, D. E.

National Academy of Sciences

In: PNAS - Proceedings of the National Academy of Sciences

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Publication Date: 2011-03-02

Description: We welcome this opportunity to clarify the conclusions and implications of our recent publication in PNAS. Butterfield (1) raises four issues regarding the oxygenation of the Paleozoic Earth's surface and its correlation to animal evolution. Our geochemical and paleontological data supported ocean oxygenation in the Silurian-Early Devonian (2), a critical transition in Earth history that influenced biogeochemical cycles and biological systems.First, Butterfield suggests that evidence of charcoal in late Silurian rocks is incompatible with our claim that the earlier Paleozoic atmosphere had oxygen levels below 50% PAL (present-day atmospheric level). This counterargument rests on the assumption that the “fire window”...

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Was the Devonian radiation of large predatory fish a consequence of rising atmospheric oxygen concentration? [Letters (Online Only)] (2011)

Butterfield, N. J.

National Academy of Sciences

In: PNAS - Proceedings of the National Academy of Sciences

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Publication Date: 2011-03-02

Description: On the basis of a Mo-based geochemical proxy calibrated to the fossil record of fish, Dahl et al. argued that oxygen levels in the early Paleozoic were 15–50% of present atmospheric levels (PAL) and probably no more than a few percent PAL for the previous 2 billion years (1). It is an interesting result, but the study raised a number of issues.First, it is difficult to reconcile 15–50% PAL oxygen with the presence of Silurian charcoal, when ≈62% PAL oxygen is necessary to sustain wildfire (2).Second, the correlation between the Devonian radiation of large predatory fish and modeled oxygen rise...

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Reply to Vermeulen and Wollenberg: Distinguishing food security and crop yields [Letters (Online Only)] (2011)

West, P. C., Gibbs, H. K., Monfreda, C., Wagner, J., Barford, C., Carpenter, S. R., Foley, J.

National Academy of Sciences

In: PNAS - Proceedings of the National Academy of Sciences

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Publication Date: 2011-03-02

Description: Vermeulen and Wollenberg (1) caution against interpreting our recent paper (2) as a call to concentrate food production in temperate areas. We did not intend our research to be interpreted as such. As Vermeulen and Wollenberg state, even very low yields can play an extremely important role in providing food security, particularly in low-income tropical countries. We agree that it is important to make the distinction between yields and food security.As noted in our paper, the tradeoff between carbon and crop yields that results from expanding croplands is particularly strong in the tropics, where natural ecosystems generally store a lot...

Keywords: Letters, Sustainability Science

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Reply to Seth et al.: DNAX accessory molecule-1 (DNAM-1) plays an important role in alloreactive CD8+ T cells responsible for the exacerbation of acute graft-versus-host disease [Biological Sciences] (2011)

Nabekura, T., Shibuya, K., Shibuya, A.

National Academy of Sciences

In: PNAS - Proceedings of the National Academy of Sciences

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Publication Date: 2011-03-09

Description: We appreciate the comments of Seth et al. (1), because they provide an important finding that is supplementary to our paper (2). They show that recipient mice deficient in CD155 (Cd155−/− mice), a ligand for DNAM-1 (DNAX accessory molecule-1, CD226), exhibited shorter rather than longer survival than WT mice after bone marrow transplantation (BMT) with full MHC disparity. They also show that donor CD4+, but not CD8+, T cells were responsible for the poor survival of the recipient Cd155−/− mice, suggesting that the interaction of CD155 on recipient organs with the receptor ligand on donor CD4+ T cells protects recipient...

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The teleost agouti-related protein 2 gene is an ohnolog gone missing from the tetrapod genome [Letters (Online Only)] (2011)

Braasch, I., Postlethwait, J. H.

National Academy of Sciences

In: PNAS - Proceedings of the National Academy of Sciences

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Publication Date: 2011-03-30

Description: A central question in evolutionary genomics is how morphological differences between taxa arise from differences in gene repertoire. Answers require rigorous orthology assignments. Recent work (1) illuminated the mechanism of background adaptation in teleost fishes by investigating the function of agouti-related protein 2 (agrp2), a gene so far found only in teleosts.Agouti family proteins antagonize melanocortin receptors, function in energy homeostasis, and regulate pigmentation. The authors (1) proposed a neurocrine axis in which zebrafish Agrp2 is expressed exclusively in the pineal gland, where it binds to the melanocortin 1 receptor and thereby, controls expression of melanin-concentrating hormones; this causes melanosome...

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Reply to Braasch and Postlethwait: Evolutionary origin of the teleost A2 agouti genes (agouti signaling protein 2 and agouti-related protein 2) remains unclear [Letters (Online Only)] (2011)

Schioth, H. B., Vastermark, A., Cone, R. D.

National Academy of Sciences

In: PNAS - Proceedings of the National Academy of Sciences

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Publication Date: 2011-03-30

Description: Tetrapods express one agouti gene [agouti signaling protein (asip)] in the skin regulating pigmentation and a second [agouti-related protein (agrp)] in the brain regulating energy homeostasis. In contrast, most teleosts have four genes encoding agouti-type proteins. Braasch and Postlethwait (1) present an analysis of the evolutionary history of agouti genes in teleosts, reordering the phylogenetic tree proposed previously (2) and proposing a nomenclature change. However, gene nomenclature derives mainly from functional or sequence properties and not from evolutionary predictions. Furthermore, inclusion of an ancient agouti sequence from the elephant shark provides an additional interpretation of the phylogeny (Fig. 1).pnas;108/13/E49/FIG01F1fig01Fig. 1Phylogeny...

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Reply to Chen et al.: Perhaps goodwill is unlimited but oxytocin-induced goodwill is not [Letters (Online Only)] (2011)

De Dreu, C. K. W., Greer, L. L., Van Kleef, G. A., Shalvi, S., Handgraaf, M. J. J.

National Academy of Sciences

In: PNAS - Proceedings of the National Academy of Sciences

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Publication Date: 2011-03-30

Description: Chen et al. (1) raise several issues with the data and interpretations published in De Dreu et al. (2). We appreciate their constructive remarks. Here, we address their concerns and explain why our data do, in fact, show that oxytocin promotes human ethnocentrism.For starters, Chen et al. (1) believe we oversimplify past work by referring to oxytocin as an “indiscriminate love drug” (1). Although one may take issue with the catchy wording, the view of oxytocin as motivating general prosocial tendencies still dominates the scholarly literatures: “oxytocin is not only the moral molecule, but also a primary element of the...

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2,4-Dichlorophenoxyacetic acid (2,4-D)-resistant crops and the potential for evolution of 2,4-D-resistant weeds [Biological Sciences] (2011)

Egan, J. F., Maxwell, B. D., Mortensen, D. A., Ryan, M. R., Smith, R. G.

National Academy of Sciences

In: PNAS - Proceedings of the National Academy of Sciences

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Publication Date: 2011-03-16

Description: In their recent article, we feel that Wright et al. (1) misrepresented the potential for 2,4-dichlorophenoxyacetic acid (2,4-D)–resistant weeds in 2,4-D–resistant cropping systems and exaggerated the sustainability of their approach to addressing glyphosate-resistant weed problems in agriculture.Wright et al. (1) announced the development by Dow AgroSciences of transgenes in corn, soybean, and cotton that will confer metabolic resistance in these crops to the herbicide 2,4-D. They promoted this technology as a solution to the epidemic of glyphosate-resistant weeds caused by overuse of the herbicide glyphosate in glyphosate-resistant crops. In addressing the obvious criticism that their technology will enable a similar...

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Reply to Matthaei et al.: The p150 isoform of the RNA editing enzyme Adenosine Deaminase 1 is required for embryogenesis [Letters (Online Only)] (2011)

Ward, S. V., George, C. X., Samuel, C. E., Oldstone, M. B.

National Academy of Sciences

In: PNAS - Proceedings of the National Academy of Sciences

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Publication Date: 2011-03-23

Description: Matthaei et al. (1) raise the possibility that specific targeting of the p150 isoform of the RNA editing enzyme Adenosine Deaminase 1 (ADAR1) may have resulted in the generation of a hypomorph of the p110 isoform, thereby generating a functional double deletion similar to previous Adar1 gene disruptions (2, 3). On this basis, they question our conclusion that the p150 isoform of ADAR1 is required for embryogenesis. Specifically, Matthaei et al. call into question the results reported in figure 1E of our article (4), which supported the conclusion that expression of the exon 1B-containing transcript encoding the p110 isoform is...

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Reply to Parsons: Many tumor types follow the monoclonal model of tumor initiation [Letters (Online Only)] (2011)

Cheng, Y.-K., Beroukhim, R., Levine, R. L., Mellinghoff, I. K., Michor, F.

National Academy of Sciences

In: PNAS - Proceedings of the National Academy of Sciences

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Publication Date: 2011-02-02

Description: We agree that some cancers may primarily have a polyclonal origin that results in genetically heterogeneous tumors. Retracing the Evolutionary Steps in Cancer (RESIC), as currently implemented (1), is not applicable to these cases. Depending on the source of heterogeneity, we are considering several refinements to our algorithm. Should this heterogeneity arise from interactions between separate cell populations, as in the polyclonal colorectal cancer example by Parsons (2), we will remove the independence assumption of cell niches. However, such modification requires information on the mechanisms, frequency, and strength of interniche interactions, which is not currently available. Without this knowledge, any...

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Monoclonal tumor origin is an underlying misconception of the RESIC approach [Letters (Online Only)] (2011)

Parsons, B. L.

National Academy of Sciences

In: PNAS - Proceedings of the National Academy of Sciences

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Publication Date: 2011-02-02

Description: Attolini et al. (1) recently reported a computational approach named retracing the evolutionary steps in cancer (RESIC), the purpose of which is to “deduce the temporal sequence of genetic events during tumorigenesis from cross-sectional data of tumors at their fully transformed stage” (1). The authors (1) indicated that they chose colon cancer as a model in which to validate their approach because there is an “established sequence of genetic events during the multistep process of colon carcinogenesis” (1). The basic premise underlying the RESIC approach (that initial events can be ordered based on the frequency of events in fully transformed...

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Reply to Quistorff and Grunnet: Dysfunctional mitochondria, brain lactate, and lactate dehydrogenase isoforms [Letters (Online Only)] (2011)

Ross, J. M., Coppotelli, G., Olson, L.

National Academy of Sciences

In: PNAS - Proceedings of the National Academy of Sciences

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Publication Date: 2011-02-16

Description: Quistorff and Grunnet (1), on theoretical grounds, question our suggested explanation of the pathologically increased lactate levels that we reported in prematurely aging mtDNA mutator and normally aging mice (2). A clarification of the chain of events based on our experimental data is, therefore, warranted. The primary cause of lactate pathology in mtDNA mutator mice is precisely known: a mutation drastically decreasing the proofreading function of the catalytic subunit of Polγ. This leads to progressive increase of mtDNA mutation frequency in mitochondria of all cells and premature-aging phenotypes (3). Accumulating mtDNA mutations causes respiratory chain dysfunction, shown by cytochrome c...

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Promising antiapoptotic effects of helix B-surface peptide (HBSP) for treatment of heart diseases [Letters (Online Only)] (2011)

Abdelwahid, E., Smith, G.

National Academy of Sciences

In: PNAS - Proceedings of the National Academy of Sciences

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Publication Date: 2011-02-09

Description: We read with great interest the recent paper in PNAS by Ueba et al. (1) concerning the cardioprotection by helix B-surface peptide (HBSP), a nonerythropoietic, tissue-protective peptide mimicking the 3D structure of erythropoietin. The authors showed that HBSP protects cardiomyocytes from apoptosis in vitro and in vivo. Cardioprotection by HBSP presented in the paper was fascinating and complements other works concerning cardiomyocyte survival by erythropoietin (EPO) alternatives. The authors analyzed the effects of HBSP on cardiomyocyte apoptosis by using TUNEL and annexin V. The authors also attempted to analyze HBSP signaling in cell survival. Their conclusion that HBSP protects cardiomyocytes...

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Reply to Abdelwahid and Smith: The effect on cardiomyocytes of helix B-surface peptide (HBSP), a peptide with cell-protective but not erythropoietic activities of erythropoietin [Letters (Online Only)] (2011)

Kawakami, M., Ueba, H., Brines, M., Yamin, M., Umemoto, T., Ako, J., Momomura, S.-i., Cerami, A.

National Academy of Sciences

In: PNAS - Proceedings of the National Academy of Sciences

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Publication Date: 2011-02-09

Description: We thank Abdelwahid and Smith (1) for their interest and comments concerning our studies of the cardioprotective effects of a peptide designed to mimic the 3D surface structure of a portion of helix B [helix B-surface peptide (HBSP)] of erythropoietin (EPO) (2). This peptide has been shown to have similar tissue protective and regenerative activities as EPO, but lacks hematopoietic effects (3). On the basis of a variety of evidence (4), we believe different EPO receptor isoforms are responsible for these differences. In the study (2), a combination of in vivo and in vitro experiments were performed that confirmed antiapoptotic...

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High brain lactate is not caused by a shift in the lactate dehydrogenase A/B ratio [Letters (Online Only)] (2011)

Quistorff, B., Grunnet, N.

National Academy of Sciences

In: PNAS - Proceedings of the National Academy of Sciences

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Publication Date: 2011-02-16

Description: In their paper, Ross et al. (1) suggested that high brain lactate is a marker of aging and that this lactate accumulation is explained by a shift in the lactate dehydrogenase (LDH) isoenzyme pattern also found to be associated with aging. Although the brain lactate increase with age is highly interesting, the suggested explanation may be problematic.LDH is a tetramere of two proteins M and H (products of the Ldh-A and Ldh-B genes, respectively). Therefore, the LDH enzyme presents with five isoenzymes: M4, MH3, M2H2, M3H, and H4. The M-dominated isoenzymes have different kinetic properties (Km and Vmax values) than...

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Different adiabatic quantum optimization algorithms for the NP-complete exact cover problem [Letters (Online Only)] (2011)

Choi, V.

National Academy of Sciences

In: PNAS - Proceedings of the National Academy of Sciences

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Publication Date: 2011-02-16

Description: Altshuler et al. (1) claim that adiabatic quantum optimization (AQO) fails for random instances of the NP-complete exact cover 3 (EC3) problem. They showed that a specific AQO algorithm failed for random instances of EC3 because of Anderson localization (AL).For any problem, there are three components (initial Hamiltonian, problem Hamiltonian, and evolution path) specifying an AQO algorithm. A different component (particularly a different problem Hamiltonian) gives a different AQO algorithm for the same problem. It is incorrect to conclude from the failure of one specific AQO algorithm that all algorithms fail for the same problem. In this letter, we describe...

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Implications of allometry [Letters (Online Only)] (2011)

Skole, D. L., Samek, J. H., Smalligan, M. J.

National Academy of Sciences

In: PNAS - Proceedings of the National Academy of Sciences

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Publication Date: 2011-01-26

Description: The thoughtful paper by Asner et al. (1) needs clarification. A major conclusion is that light detection and ranging (LiDAR)-based sampling combined with an allometric model of tree biomass that uses height measurements is significantly better than simply using the Intergovernmental Panel on Climate Change Tier 1 prescribed forest carbon values (2) for a given area [395 teragrams (Tg) or 1012 grams carbon (C) vs. 587 Tg C]. We are not convinced.First, the authors (1) biased the IPCC estimate upwards (i) by not stratifying the study site with existing vegetation cover maps (Ministerio del Ambiente or Global Land Cover 2000)...

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Reply to Skole et al.: Regarding high-resolution carbon stocks and emissions in the Amazon [Letters (Online Only)] (2011)

Asner, G. P., Mascaro, J., Clark, J. K., Powell, G.

National Academy of Sciences

In: PNAS - Proceedings of the National Academy of Sciences

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Publication Date: 2011-01-26

Description: Skole et al. (1) claim that we do not make a case for high-resolution carbon stock and emissions mapping in tropical forests. Specifically, they argue that (i) our Intergovernmental Panel on Climate Change (IPCC) Tier 1 estimates for the Peruvian Amazon study are biased, (ii) our plot-level carbon estimates used to calibrate airborne Light Detection and Ranging (LiDAR) are flawed, and (iii) our regional mapping of carbon stocks is low compared with a their estimate using field data from a previous local-scale study. However, their critique is based on misstatements about our methods and a misunderstanding of carbon stock variation...

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Reply to Nikiforovich et al.: Restoration of the loop regions of G-protein-coupled receptors [Letters (Online Only)] (2011)

Goldfeld, D. A., Zhu, K., Beuming, T., Friesner, R. A.

National Academy of Sciences

In: PNAS - Proceedings of the National Academy of Sciences

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Publication Date: 2011-07-27

Description: We agree with Nikiforovich et al. that the protocol we used in our G-protein–coupled receptor (GPCR) loop calculations (1) differed in some of its details from the protocol they used in their earlier work (2). Our objective in demonstrating that we could restore loops in GPCR crystal structures in good agreement with X-ray crystallographic data was to show that our energy model and sampling algorithms were able to take on this specific task with reasonably good accuracy. We view these capabilities as a necessary, but not sufficient, condition for actually predicting GPCR loops in a realistic application, such as homology...

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Reply to Sandgathe et al.: Neandertal use of fire [Letters (Online Only)] (2011)

Roebroeks, W., Villa, P.

National Academy of Sciences

In: PNAS - Proceedings of the National Academy of Sciences

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Publication Date: 2011-07-20

Description: Sandgathe et al. (1) agree that fire was not a requisite technology for hominin expansion into northern latitudes, but they suggest that habitual use of fire appeared later than stated in our paper (2), only near the end of the Late Pleistocene. They stress that, despite the growing number of Neandertal sites with solid evidence for fire use, there is also a large number of sites without such evidence (1). Based primarily on their extrapolation of data from two recently excavated Middle Paleolithic sites in the Dordogne (France), they argue that the sequences from many Neandertal sites associated with cold...

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Reply to Guedj et al.: Early transient increase of hepatitis C virus viral load in genotype 1 and 2 infections, and the use of mathematical modeling [Letters (Online Only)] (2011)

Hsu, C.-S., Chen, H.-C., Jeng, J., Kao, J.-H., Chen, D.-S.

National Academy of Sciences

In: PNAS - Proceedings of the National Academy of Sciences

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Publication Date: 2011-07-20

Description: We appreciate the comments of Guedj et al. (1) on our paper addressing the association of IL28B gene variations with mathematical modeling of viral kinetics in patients with chronic hepatitis C treated with pegylated IFN plus ribavirin therapy (2). Regarding the distribution of the blips among hepatitis C virus (HCV) genotypes, we not only found a lower virion production rate but earlier blips among patients with HCV genotype 2 infection than those with genotype 1 infection. The time for the observed maximal viral load and the estimated time for maximal viral load were significantly different between these two genotypes (genotype...

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Understanding the nature of early HCV RNA blips and the use of mathematical modeling of viral kinetics during IFN-based therapy [Letters (Online Only)] (2011)

Guedj, J., Dahari, H., Perelson, A. S.

National Academy of Sciences

In: PNAS - Proceedings of the National Academy of Sciences

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Publication Date: 2011-07-20

Description: In PNAS, Hsu et al. (1) observed an early transient increase (here, termed a blip) in hepatitis C virus (HCV) viral load in 92 out of 145 Taiwanese patients with chronic hepatitis C treated with pegylated IFN-α (IFN) and ribavirin and found that these blips were significantly associated with the outcome of therapy [i.e., sustained virologic response (SVR)]. Further, they sought to explain the origin and time of these blips using a version of a well-studied mathematical model of HCV infection and treatment (2) in a nonstandard way. Although these blips are interesting, several concerns need to be raised before...

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Does casein kinase II phosphorylation of Maf1 trigger RNA polymerase III activation? [Letters (Online Only)] (2011)

Willis, I. M., Moir, R. D., Lee, J.

National Academy of Sciences

In: PNAS - Proceedings of the National Academy of Sciences

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Publication Date: 2011-07-20

Description: The recent study of Graczyk et al. (1) reported a role for casein kinase II (CK2) phosphorylation of Maf1 during the reactivation of RNA polymerase III (Pol III) transcription that occurs as cells transition from repressive to favorable growth conditions. This is a potentially important finding. However, the preceding conclusion remains in question because of two concerns that allow alternative explanations for the data.Using the differential mobility of Maf1 in one-dimensional SDS gels, Graczyk et al. (1) reported changes in Maf1 phosphorylation upon conditional or pharmacological inhibition of CK2. However, prior work has established that these same changes in the...

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Difference between restoring and predicting 3D structures of the loops in G-protein-coupled receptors by molecular modeling [Letters (Online Only)] (2011)

Nikiforovich, G. V., Taylor, C. M., Marshall, G. R., Baranski, T. J.

National Academy of Sciences

In: PNAS - Proceedings of the National Academy of Sciences

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Publication Date: 2011-07-27

Description: Goldfeld et al. (1) presented modeling results on restoring 3D structures of the intra- and extracellular loops in bovine rhodopsin (bRh), human A2A adenosine receptor (A2Ar), turkey β1-adrenergic receptor (β1AR), and human β2-adrenergic receptor (β2AR). In all cases, the lowest energy conformers of the loops matched the corresponding X-ray structures with excellent rmsd values. The extracellular loops for the same receptors were modeled in our article previously (2) with the use of a much less sophisticated modeling procedure. Goldfeld et al. (1) emphasized substantially better accuracy of reproducing the X-ray structures of the loops, especially larger loops, in their study...

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Can the functional MRI responses to physical pain really tell us why social re&jnodot;ection "hurts"? [Letters (Online Only)] (2011)

Iannetti, G. D., Mouraux, A.

National Academy of Sciences

In: PNAS - Proceedings of the National Academy of Sciences

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Publication Date: 2011-07-27

Description: We read with great interest the recent PNAS report by Kross et al. (1). In this study, the authors selected a population of volunteers who recently experienced an unwanted breakup of their love relationship, and used functional MRI (fMRI) to record the brain responses elicited by (i) observing a photograph of their ex-partner as they think about being rejected and (ii) receiving actual nociceptive somatosensory simulation. Based on the observation of an “overlap between social rejection and physical pain[...] areas”, assumed to “support the sensory components of physical pain (secondary somatosensory cortex; dorsal posterior insula)”, they conclude that their “results...

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Reply to Iannetti and Mouraux: What functional MRI responses to physical pain tell us about why social re&jnodot;ection "hurts" [Letters (Online Only)] (2011)

Kross, E., Berman, M. G., Mischel, W., Smith, E. E., Wager, T. D.

National Academy of Sciences

In: PNAS - Proceedings of the National Academy of Sciences

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Publication Date: 2011-07-27

Description: We recently reported that having participants who experienced an unwanted breakup view a photograph of their ex-partner as they thought about being rejected activated portions of the operculoinsular cortex strongly implicated in physical pain—the dorsal posterior insula (dpINS) and OP1 (the most caudal area of the parietal operculum). The same regions were also activated when participants experienced physical pain (1).These findings were notable for two reasons. First, a wealth of data suggest that these regions, in particular dpINS, support physical pain sensation. As Craig noted recently, “the dorsal posterior insula contains the primary cortical sensory representation of temperature and pain...

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Reply to Willis et al.: Casein kinase II phosphorylation of Maf1 triggers RNA polymerase III activation [Letters (Online Only)] (2011)

Boguta, M., Graczyk, D.

National Academy of Sciences

In: PNAS - Proceedings of the National Academy of Sciences

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Publication Date: 2011-07-20

Description: We recently reported (1) that casein kinase II (CK2)-mediated phosphorylation of Maf1 stimulates polymerase III (Pol III) transcription upon transfer of yeast from repressive conditions in glycerol medium to medium with glucose. Willis et al. (2) have taken issue with our conclusion that Maf1 is a target for CK2 and brought to our attention the possibility that activation of Pol III in our experimental conditions may be mediated by PKA or Sch9 kinases independent of any involvement of CK2.In response to Willis's objection, we note the following: first, the CK2 phosphoacceptor sites in Maf1 were determined by mass spectrometry, mutated...

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Timing of the appearance of habitual fire use [Letters (Online Only)] (2011)

Sandgathe, D. M., Dibble, H. L., Goldberg, P., McPherron, S. P., Turq, A., Niven, L., Hodgkins, J.

National Academy of Sciences

In: PNAS - Proceedings of the National Academy of Sciences

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Publication Date: 2011-07-20

Description: Using a number of Middle and Late Pleistocene sites with good evidence for fire, Roebroeks and Villa (1) argued that the habitual use of fire did not become part of hominin technological repertoires until the latter half of the Middle Pleistocene. We are pleased to see other researchers taking a more critical view of the nature and quality of the available evidence for early fire use and questioning what seems to be a long-held assumption that the earliest evidence for fire use marks the point at which it becomes inextricably part of hominin adaptations (2, 3). We agree that the...

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Fragile-to-strong crossover in supercooled liquids remains elusive [Letters (Online Only)] (2011)

Elmatad, Y. S.

National Academy of Sciences

In: PNAS - Proceedings of the National Academy of Sciences

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Publication Date: 2011-06-30

Description: Transport properties of glass-forming liquids change markedly around an onset temperature To. For temperatures T 〉 To, these properties depend little on T, whereas for T 〈 To these properties are super-Arrhenius—varying faster than exponentially in 1/T. Upon lowering temperature significantly further, theory (1) predicts that reversible transport in a supercooled liquid, if it can be observed, will ultimately cross over from super-Arrhenius to Arrhenius temperature variation. However, this so-called “fragile-to-strong” (FS) crossover at a temperature Tx 〈 To has proved difficult to observe because most bulk fluids fall out of equilibrium at a glass transition temperature Tg that is...

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Reply to Elmatad: Supercooled viscous liquids display a fragile-to-strong dynamic crossover [Letters (Online Only)] (2011)

Mallamace, F., Corsaro, C., Chen, S.-H., Stanley, H. E.

National Academy of Sciences

In: PNAS - Proceedings of the National Academy of Sciences

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Publication Date: 2011-06-30

Description: Theory predicts a fragile-to-strong (FS) dynamic crossover temperature Tx in supercooled liquids but, contrary to what is reported in ref. 1, Tx must be 〉Tg (2), where Tg is the glass transition temperature. Ref. 4 of ref. 1 hypothesizes that a parabolic form is valid in a range To 〉 T 〉 Tx, where To is defined as an onset temperature that marks the crossover from normal liquid behavior to supercooled liquid behavior. A second paper by the same authors (ref. 5 of ref. 1) proposes the range of the hypothesized parabolic behavior can be extended to cover T

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Cerebral vasculopathy is a common feature in Aicardi-Goutieres syndrome associated with SAMHD1 mutations [Letters (Online Only)] (2011)

du Moulin, M., Nurnberg, P., Crow, Y. J., Rutsch, F.

National Academy of Sciences

In: PNAS - Proceedings of the National Academy of Sciences

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Publication Date: 2011-06-30

Description: In their recent interesting paper, Xin et al. (1) described an autosomal recessive condition in 14 individuals of Old Order Amish ancestry characterized by cerebral vasculopathy and early onset stroke. The affected patients presented a heterogeneous phenotype, including variable developmental disability, irritability in infancy, chilblain lesions, glaucoma, and arthritis. Through genome-wide homozygosity mapping and candidate gene sequencing, the authors identified the homozygous mutation c.1411-2A 〉 G in SAMHD1 being associated with this entity. Additionally, they detected this mutation in 3 of 44 patients with developmental delay (phenotypes not further described). Although mutations in SAMHD1 have been found to be disease-causing...

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Reply to du Moulin et al.: Cerebral vasculopathy is a common hallmark in individuals with SAMHD1 mutations [Letters (Online Only)] (2011)

Xin, B., Li, W., Bright, A., Hinze, C., Wang, H.

National Academy of Sciences

In: PNAS - Proceedings of the National Academy of Sciences

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Publication Date: 2011-06-30

Description: In their Letter to the Editor, du Moulin et al. (1) speculate that the autosomal recessive condition we described in Old Order Amish (2) might be Aicardi–Goutières syndrome (AGS). They suggest head computed tomography (CT) and cerebrospinal fluid (CSF) studies to confirm this suspicion. The clinical data in our patients, however, do not support their assumption, and we disagree with the approaches they propose.As we reported previously (2), the condition associated with mutations in the SAMHD1 gene was highly heterogeneous and its diagnosis was very challenging. Most patients went through an extensive workup by numerous pediatric subspecialists at major medical...

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Susceptibility of coral-disease models [Letters (Online Only)] (2011)

Jordan-Garza, A. G., Muller, E. M., Burman, S. G., van Woesik, R.

National Academy of Sciences

In: PNAS - Proceedings of the National Academy of Sciences

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Publication Date: 2011-05-18

Description: The scarcity of empirical data on marine diseases highlights the need for epidemiological models that explain patterns and processes. Yakob and Mumby (1) used a generic susceptible-infected model to describe the prevalence of white plague type II disease on a coral population (Dichocoenia stokesii). They compared their model with the metapopulation model of Sokolow et al. (2). Yakob and Mumby (1) stated that rapid population turnover explained the observed oscillations in disease prevalence. Previous marine-disease models have largely ignored life-history traits. Indeed, systems subjected to high return periods of stress can be dominated by weedy species with rapid turnover rates....

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Reply to Reilly and Kean: Clarifications on word length and information content [Letters (Online Only)] (2011)

Piantadosi, S. T., Tily, H., Gibson, E.

National Academy of Sciences

In: PNAS - Proceedings of the National Academy of Sciences

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Publication Date: 2011-05-18

Description: First, we disagree with Reilly and Kean (1) that our results on word length (2) contradicted Zipf's principle of least effort. Our findings were in the same spirit, except that we measured effort in a more principled way than Zipf could have (2). Assigning word length by information content is least effort under an assumption of a superlinear relationship between effort and information content (3), and it is optimal under a desire to stay just under the channel capacity of linguistic systems (4).Reilly and Kean (1) bring up the important issue of how we quantified information content (2). In one...

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Reply to Jordan-Garza et al.: Demographic dynamism as an additional mechanism of coral disease resistance [Letters (Online Only)] (2011)

Yakob, L., Mumby, P. J.

National Academy of Sciences

In: PNAS - Proceedings of the National Academy of Sciences

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Publication Date: 2011-05-18

Description: We thank Jordan-Garza et al. (1) for their interest in our study (2). Contrary to their assertion, which was not supported by the cited study, recruitment can increase after coral mortality because of an easing of space limitation (3). Mass mortality of adults throughout a metapopulation could, in principle, deplete recruitment, but such limitation has not been demonstrated. We note the observation of stifled recruitment after the first epizootic in the population of Dichocoenia stokesii. It is not the rate at which recruits colonize empty space that drives the population turnover in our model, however. Population turnover is a function...

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Women's underrepresentation in science: The role of language and laws [Letters (Online Only)] (2011)

Drago, R.

National Academy of Sciences

In: PNAS - Proceedings of the National Academy of Sciences

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Publication Date: 2011-05-25

Description: Ceci and Williams (1) concluded that women's underrepresentation in science is not attributable to sex discrimination. They instead discussed causal factors, such as women preferring people as opposed to mathematically oriented fields, women's lesser abilities at the top of the mathematics performance distribution, and women's preferences for the performance of child care.The authors ignored the long-term increase in sex segregation within the sciences: Between 1977 and 2009, the percentage of women receiving doctorates in the life sciences, of all women's science (including engineering) doctorates, rose from 65% to 74%. Men left those same fields, with the percentage of life science...

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Reply to Ashton: The putative guanylyl cyclase domain of AtPepR1 and similar plant receptors [Letters (Online Only)] (2011)

Berkowitz, G. A., Gehring, C., Irving, H. R., Kwezi, L.

National Academy of Sciences

In: PNAS - Proceedings of the National Academy of Sciences

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Publication Date: 2011-05-11

Description: We recently showed (1) that peptide ligand binding to a plant leucine-rich-repeat receptor-like kinase (LRR-RLK) (AtPepR1) initiates pathogen defense signaling cascades through elevation of cytosolic Ca2+. We provided indirect evidence consistent with AtPepR1 signaling through cytosolic guanylyl cyclase (GC) activity as follows. Receptor signaling required a cyclic nucleotide activated Ca2+ channel. Exogenous lipophilic cGMP activated channel-dependent Ca2+ elevation. Expression of the putative GC domain of the AtPepR1 receptor (“AtPepR1-GC”) in Escherichia coli increased cell cGMP levels. Affinity-purified AtPepR1-GC had a level of GC activity in vitro equal to that of other plant proteins with a similar putative GC domain (2).Ashton...

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Further evidence for old radiations originating at the northern edge of the Australian plate [Letters (Online Only)] (2011)

Oliver, P. M.

National Academy of Sciences

In: PNAS - Proceedings of the National Academy of Sciences

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Publication Date: 2011-05-18

Description: With respect to Jønsson et al. (1) and their discussion of the geographic origin of basal lineages within the core Corvoidea, I would like to highlight relevant evidence from recent phylogenetic studies of other Australasian vertebrate lineages. These have identified at least five other lineages with distributions centered or restricted to the islands to the northern edge of the Australian plate and east of the Asian plate that potentially date back to at least the Miocence: Ceratobatrachid frogs (endemic radiation ≈30 Mya) (2), two lineages of blindsnakes [Acutothyphlops and Pacific Rhamphothyphlops (both endemic clades ≈20–30 Mya)] (3), and two lineages...

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Reply to Drago: Culture and history are important in understanding the low number of women [Letters (Online Only)] (2011)

Ceci, S. J., Williams, W. M.

National Academy of Sciences

In: PNAS - Proceedings of the National Academy of Sciences

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Publication Date: 2011-05-25

Description: Drago (1) makes a number of good points about the need to consider historical trends and culture in understanding women's underrepresentation in math-intensive fields. We agree with some of these points and have no position on others. Nevertheless, we want to point out that the main point—that we should consider historical and cultural influences in sex segregation—is something that we have done consistently in our publications on this topic, including this one (2–4). In online SI Text accompanying our article, we reiterated a point we have made in numerous past articles, namely, that sex cannot be considered in isolation from...

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Reply to Frederick et al.: Anchoring effects on energy perceptions [Letters (Online Only)] (2011)

Attari, S. Z., De; Kay, M. L., Davidson, C. I., de Bruin, W. B.

National Academy of Sciences

In: PNAS - Proceedings of the National Academy of Sciences

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Publication Date: 2011-02-23

Description: Both our study (1) and the follow-up described by Frederick et al. (2) indicate that people know relatively little about how much energy is used by different devices and appliances. In our view, the additional data strengthen rather than weaken our original conclusions.It is well known that numerical judgments are subject to anchoring effects, with initial values having substantial influence on final answers (3). In our article, we noted that the compressed range of respondents’ energy estimates “almost certainly resulted from an anchoring bias in which the reference point provided in the task served as an anchor for participants’ estimates,...

Keywords: Letters, Sustainability Science

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Characterizing perceptions of energy consumption [Letters (Online Only)] (2011)

Frederick, S. W., Meyer, A. B., Mochon, D.

National Academy of Sciences

In: PNAS - Proceedings of the National Academy of Sciences

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Publication Date: 2011-02-23

Description: The adoption of energy-saving technologies is presumably deterred by underestimates of energy use and by corresponding underestimates of the difference between more- and less-efficient appliances. Thus, it is easy to grasp the potential policy significance of a recent study (1) concluding that Americans underestimate energy use by a factor of 2.8.However, the apparent precision of that statistic belies its arbitrary origins. By manipulating just two experimental details (the provided numeric referent and the units in which judgments were rendered), we show that one can readily reach qualitatively different conclusions.For the study in question (1), respondents were first told that a...

Keywords: Letters, Sustainability Science

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Regarding Anderegg et al. and climate change credibility [Letters (Online Only)] (2011)

Bodenstein, L.

National Academy of Sciences

In: PNAS - Proceedings of the National Academy of Sciences

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Publication Date: 2011-01-04

Description: The study by Anderegg et al. (1) employed suspect methodology that treated publication metrics as a surrogate for expertise. Credentialed scientists, having devoted much of their careers to a certain area, with multiple relevant peer-reviewed publications, should be deemed core experts, notwithstanding that others are more or less prolific in print or that their views stand in the minority. In the climate change (CC) controversy, a priori, one expects that the much larger and more “politically correct” side would excel in certain publication metrics. They continue to cite each other's work in an upward spiral of self-affirmation. The authors' treatment...

Keywords: Letters

Print ISSN: 0027-8424

Electronic ISSN: 1091-6490

Topics: Biology , Medicine , Natural Sciences in General

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It is not necessarily YY1--the frequently forgotten Yin-Yang-2 transcription factor [Letters (Online Only)] (2011)

Klar, M.

National Academy of Sciences

In: PNAS - Proceedings of the National Academy of Sciences

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Publication Date: 2011-01-04

Description: de Nigris et al. (1) performed an interesting study on the functional implication of YY1 in the VEGF regulatory network, leading to a rationale for using YY1 as a therapeutic target molecule in cancer therapy. However, considering the application of YY1 for antiangiogenic treatment bears a fundamental risk because the observed effects are not necessarily specific for YY1: the YY1 antibody (C-20, sc-281, Santa Cruz Biotechnology) used for (chromatin-) immunoprecipitation experiments and Western blotting does not detect exclusively YY1 but also the highly homologous YY2 transcription factor, as previously shown (2). Notably, increasing evidence is given that YY2 is regulated...

Keywords: Letters

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Reply to Bodenstein: Contextual data about the relative scale of opposing scientific communities [Letters (Online Only)] (2011)

Anderegg, W. R. L., Prall, J. W., Harold, J.

National Academy of Sciences

In: PNAS - Proceedings of the National Academy of Sciences

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Publication Date: 2011-01-04

Description: The letter by Bodenstein (1) takes issue with several semantic distinctions and the value of measuring expert agreement and credentials in our recent study (2). Bodenstein's (1) comments suggest a disagreement with the mere practice of analyzing expert perspectives and credentials. He raises many speculative points without offering data, which we have addressed elsewhere (3). We stand by the analysis presented in our study.Bodenstein (1) suggests that our study takes an ad hominem approach of “truth by majority rule” that bypasses the merits of evaluating the scientific data. This misunderstands our study's framing and stands in direct contrast to two...

Keywords: Letters

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Reply to Klar: Key role of YY1 in neoangiogenesis [Letters (Online Only)] (2011)

de Nigris, F., Crudele, V., Giovane, A., Casamassimi, A., Garban, H. J., Marquez-Garban, D. C., Hayashi, T., Ignarro, L. J., Napoli, C.

National Academy of Sciences

In: PNAS - Proceedings of the National Academy of Sciences

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Publication Date: 2011-01-04

Description: In our study (1), we investigated the role of YY1 and described a potential molecular mechanism of cross-talk between YY1 and the VEGF network. YY1 binds hypoxia-inducible factor-1α on VEGF regulatory region. The specific silencing of YY1 reduced VEGF transcription by approximately 20%, the availability of active VEGF protein via AKT, and neoangiogenesis (1). Klar (2) brings to our attention the possibility that these effects also may be mediated by the homolog protein YY2. First, we consider that proteins that play a critical role in the cell occur often in multiple distinct homologous forms but not necessarily with redundant functions....

Keywords: Letters

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Lamprey endocrinology is not ancestral [Letters (Online Only)] (2011)

Thornton, J. W., Carroll, S. M.

National Academy of Sciences

In: PNAS - Proceedings of the National Academy of Sciences

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Publication Date: 2011-01-12

Description: The report of Close et al. (1) in PNAS concerning corticosteroid signaling in the lamprey Petromyzon marinus elucidates interesting issues in comparative endocrinology. It does not, however, support the authors’ claim that the ancestral corticosteroid receptor was specifically activated by the glucocorticoid 11-deoxycortisol (S) and that sensitivity to mineralocorticoids and other corticosteroids is evolutionarily derived.Close et al. (1) reported that lamprey produce S and deoxycorticosterone (DOC) when treated with pituitary hormones; exogenous S triggers vertebrate-like mineralocorticoid and glucocorticoid responses. These data suggest that S, DOC, or their metabolites function in lamprey in a vertebrate-like endocrinological axis.Close et al. (1) made...

Keywords: Letters

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