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  • 1
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    A significant effect of the TSPY1 copy number on spermatogenesis efficiency and the phenotypic expression of the gr/gr deletion (2013)
    Oxford University Press
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    Publication Date: 2013-03-23
    Description: AZFc deletions cause a significant phenotypic heterogeneity with respect to spermatogenesis; however, the reason for this is poorly understood. Recently, testis-specific protein Y-encoded 1 ( TSPY1 ) copy number variation (CNV) was determined to be a potential genetic modifier of spermatogenesis. We performed a large-scale cohort study to investigate the effect of TSPY1 CNV on spermatogenesis and to elucidate the possible contribution of TSPY1 genetic variation to the phenotypic expression of AZFc deletions. Haplogrouping of the Y-chromosome and quantification of the TSPY1 copy number were performed in 2272 Han Chinese males with different spermatogenic statuses (704 males with the b2/b4 or gr/gr deletion and 1568 non- AZFc -deleted males). Our data revealed that the TSPY1 copy number distributions were significantly different among non- AZFc -deleted males with different spermatogenic phenotypes. Lower sperm production and an elevated risk of spermatogenic failure were observed in males with fewer than 21 TSPY1 copies and in those with more than 55 copies relative to men with 21–35 copies. Similar results were observed in males with the gr/gr deletion. These findings indicate that TSPY1 CNV affects an individual's susceptibility to spermatogenic failure by modulating the efficiency of spermatogenesis and strongly suggest that there is a significant quantity effect of the TSPY1 copy number on the phenotypic expression of the gr/gr deletion. To our knowledge, this CNV is the first independent genetic factor that has been clearly observed to influence the spermatogenic status of gr/gr deletion carriers. A combined genetic analysis of the TSPY1 copy number and the gr/gr deletion could inform the clinical counselling of infertile couples.
    Print ISSN: 0964-6906
    Electronic ISSN: 1460-2083
    Topics: Biology , Medicine
    Published by Oxford University Press
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  • 2
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    Magnetostratigraphy of the middle-upper Jurassic sedimentary sequences at Yanshiping, Qiangtang Basin, China (2016)
    Oxford University Press
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    Publication Date: 2016-07-29
    Description: A series of important geological events occurred in the Tibetan Plateau area during the Jurassic, such as the collision of the Lhasa and Qiangtang Terranes, the closure of the Meso-Tethyan Ocean, the opening of the Neo-Tethyan Ocean and the cessation of the mega-monsoon. The ~3000 m thick Jurassic sedimentary sequence in the Qiangtang Basin on the central Tibetan Plateau, which is called the Yanshiping (YSP) Group, recorded these geological events. However, the chronology of the sequence is surprisingly poorly constrained. Here, we perform a detailed palaeomagnetic analysis on the ~1060 m thick middle and upper portions of the YSP Group (the Xiali and Suowa Formations) in the YSP section of the eastern Qiangtang Basin. Three bivalve zones at stratigraphic intervals of ~40–140, 640–800 and 940–1040 m are identified, which yield a Bathonian–Callovian age for the Lower Xiali Fm., a Callovian–Oxfordian age for the Lower Suowa Fm. and an Oxfordian–Kimmeridgian age for the Upper Suowa Fm. A total of 544 oriented palaeomagnetic samples were collected from the section. By combining thermal and alternating field demagnetizations, clear characteristic remanent magnetization (ChRM) directions are isolated for most of the samples. The robust ChRM directions pass fold and reversals tests, which support the primary nature of the ChRMs and yield a palaeopole at 76.8°N/297.2°E (dp = 2.2°, dm = 3.7°). A total of 27 normal and 26 reversed polarity zones were successfully recorded in the section. Combined with fossil age constraints, results suggest that the section is plausibly composed of a Callovian-Early Kimmeridgian age sedimentary sequence.
    Keywords: Geomagnetism, Rock Magnetism and Palaeomagnetism
    Print ISSN: 0956-540X
    Electronic ISSN: 1365-246X
    Topics: Geosciences
    Published by Oxford University Press on behalf of The Deutsche Geophysikalische Gesellschaft (DGG) and the Royal Astronomical Society (RAS).
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  • 3
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    A new bound constraints method for 3-D potential field data inversion using Lagrangian multipliers (2015)
    Oxford University Press
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    Publication Date: 2015-02-19
    Description: In this paper, we present a method for incorporating prior geological information into potential field data inversion problem. As opposed to the traditional inverse algorithm, our proposed method takes full advantage of prior geological information as a constraint and thus obtains a new objective function for inversion by adding Lagrangian multipliers and slack variables to the traditional inversion method. These additional parameters can be easily solved during iterations. We used both synthetic and observed data sets to test the stability and validity of the proposed method. Our results using synthetic gravity data show that our new method predicts depth and density anomalies more efficiently and accurately than the traditional inversion method that does not include prior geological constraints. Then using observed gravity data in the Three Gorges area and geological constraint information, we obtained the density distribution of the upper and middle crust in this area thus revealing its geological structure. These results confirm the proposed method's validity and indicate its potential application for magnetism data inversion and exploration of geological structures.
    Keywords: Gravity, Geodesy and Tides
    Print ISSN: 0956-540X
    Electronic ISSN: 1365-246X
    Topics: Geosciences
    Published by Oxford University Press on behalf of The Deutsche Geophysikalische Gesellschaft (DGG) and the Royal Astronomical Society (RAS).
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  • 4
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    Attribute-Based Oblivious Access Control (2012)
    Oxford University Press
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    Publication Date: 2012-10-02
    Description: In an attribute-based system (ABS), users are identified by various attributes, instead of their identities. Since its seminal introduction, the attribute-based mechanism has attracted a lot of attention. However, current ABS schemes have a number of drawbacks: (i) the communication cost is linear in the number of the required attributes; (ii) the computation cost is linear in the number of the required attributes and (iii) there are no efficient verification algorithms for the secret keys. These drawbacks limit the use of ABS in practice. In this paper, we propose an attribute-based oblivious access control (ABOAC) scheme to address these problems, where only the receiver whose attributes satisfy the access policies can obtain services obliviously. As a result, the receiver does not release anything about the contents of the selected services and his attributes to the sender, and even the number and supersets of his attributes are protected. The sender only knows the number of the services selected by the authorized receiver. Notably, the costs of computation and communication are constant and independent of the number of required attributes. While, in the prior comparable schemes, both the costs of computation and communication are linear in the required attributes. Therefore, our ABOAC scheme provides a novel and elegant solution to protect user's privacy in the systems where both the bandwidth and the computing capability are limited, such as wireless sensor and actor networks, mobile ad hoc networks, etc..
    Print ISSN: 0010-4620
    Electronic ISSN: 1460-2067
    Topics: Computer Science
    Published by Oxford University Press
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  • 5
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    Robust expression of vault RNAs induced by influenza A virus plays a critical role in suppression of PKR-mediated innate immunity (2015)
    Oxford University Press
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    Publication Date: 2015-12-02
    Description: Protein kinase R (PKR) is a vital component of host innate immunity against viral infection. However, the mechanism underlying inactivation of PKR by influenza A virus (IAV) remains elusive. Here, we found that vault RNAs (vtRNAs) were greatly induced in A549 cells and mouse lungs after infection with IAV. The viral NS1 protein was shown to be the inducer triggering the upregulation of vtRNAs. Importantly, silencing vtRNA in A549 cells significantly inhibited IAV replication, whereas overexpression of vtRNAs markedly promoted the viral replication. Furthermore, in vivo studies showed that disrupting vtRNA expression in mice significantly decreased IAV replication in infected lungs. The vtRNA knockdown animals exhibited significantly enhanced resistance to IAV infection, as evidenced by attenuated acute lung injury and spleen atrophy and consequently increased survival rates. Interestingly, vtRNAs promoted viral replication through repressing the activation of PKR and the subsequent antiviral interferon response. In addition, increased expression of vtRNAs was required for efficient suppression of PKR by NS1 during IAV infection. Moreover, vtRNAs were also significantly upregulated by infections of several other viruses and involved in the inactivation of PKR signaling by these viruses. These results reveal a novel mechanism by which some viruses circumvent PKR-mediated innate immunity.
    Print ISSN: 0305-1048
    Electronic ISSN: 1362-4962
    Topics: Biology
    Published by Oxford University Press
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  • 6
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    A genome-wide association study identifies polymorphisms in the HLA-DR region associated with non-response to hepatitis B vaccination in Chinese Han populations (2014)
    Oxford University Press
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    Publication Date: 2014-03-20
    Description: Vaccination against hepatitis B virus is an effective and routine practice that can prevent infection. However, 5–10% of healthy adults fail to produce protective levels of antibody against the hepatitis B vaccination. It has been reported that host genetic variants might affect the immune response to hepatitis B vaccination. Here, we reported a genome-wide association study in a Chinese Han population consisting of 108 primary high-responders and 77 booster non-responders to hepatitis B vaccination using the Illumina HumanOmniExpress Beadchip. We identified 21 SNPs at 6p21.32 were significantly associated with non-response to booster hepatitis B vaccination ( P -value 〈1 x 10 –6 ). The most significant SNP in the region was rs477515, located ~12 kb upstream of the HLA-DRB1 gene. Its P- value (4.81 x 10 –8 ) exceeded the Bonferroni-corrected genome-wide significance threshold. Four tagging SNPs (rs477515, rs28366298, rs3763316 and rs13204672) that capture genetic information of these 21 SNPs were validated in three additional Chinese Han populations, consisting of 1336 primary high-responders and 420 primary non-responders. The four SNPs continued to show significant associations with non-response to hepatitis B vaccination ( P -combined = 3.98 x 10 –13 – 1.42 x 10 –8 ). Further analysis showed that the rs477515 was independently associated with non-response to hepatitis B vaccination with correction for other three SNPs in our GWAS and the known hepatitis B vaccine immunity associated SNP in previous GWAS. Our findings suggest that the rs477515 was an independent marker associated with non-response to hepatitis B vaccination and HLA-DR region might be a critical susceptibility locus of hepatitis B vaccine-induced immunity.
    Print ISSN: 0964-6906
    Electronic ISSN: 1460-2083
    Topics: Biology , Medicine
    Published by Oxford University Press
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  • 7
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    Attribute-Based Data Transfer with Filtering Scheme in Cloud Computing (2014)
    Oxford University Press
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    Publication Date: 2014-03-27
    Description: Data transfer is a transmission of data over a point-to-point or point-to-multipoint communication channel. To protect the confidentiality of the transferred data, public-key cryptography has been introduced in data transfer schemes (DTSs). Unfortunately, there exist some drawbacks in the current DTSs. First, the sender must know who the real receivers are. This is undesirable in a system where the number of the users is very large, such as cloud computing. In practice, the sender only knows some descriptive attributes of the receivers. Secondly, the receiver cannot be guaranteed to only receive messages from the legal senders. Therefore, it remains an elusive and challenging research problem on how to design a DTS scheme where the sender can send messages to the unknown receivers and the receiver can filter out false messages according to the described attributes. In this paper, we propose an attribute-based data transfer with filtering (ABDTF) scheme to address these problems. In our proposed scheme, the receiver can publish an access structure so that only the users whose attributes satisfy this access structure can send messages to him. Furthermore, the sender can encrypt a message under a set of attributes such that only the users who hold these attributes can obtain the message. In particular, we provide an efficient filtering algorithm for the receiver to resist the denial-of-service attacks. Notably, we propose the formal definition and security models for ABDTF schemes. To the best of our knowledge, it is the first time that a provable ABDTF scheme is proposed. Hence, this work provides a new research approach to ABDTF schemes.
    Print ISSN: 0010-4620
    Electronic ISSN: 1460-2067
    Topics: Computer Science
    Published by Oxford University Press
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  • 8
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    Giant Pandas Are Not an Evolutionary cul-de-sac: Evidence from Multidisciplinary Research (2014)
    Oxford University Press
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    Publication Date: 2014-12-20
    Description: The giant panda ( Ailuropoda melanoleuca ) is one of the world’s most endangered mammals and remains threatened by environmental and anthropogenic pressure. It is commonly argued that giant pandas are an evolutionary cul-de-sac because of their specialized bamboo diet, phylogenetic changes in body size, small population, low genetic diversity, and low reproductive rate. This notion is incorrect, arose from a poor understanding or appreciation of giant panda biology, and is in need of correction. In this review, we summarize research across morphology, ecology, and genetics to dispel the idea, once and for all, that giant pandas are evolutionary dead-end. The latest and most advanced research shows that giant pandas are successful animals highly adapted to a specialized bamboo diet via morphological, ecological, and genetic adaptations and coadaptation of gut microbiota. We also debunk misconceptions around population size, population growth rate, and genetic variation. During their evolutionary history spanning 8 My, giant pandas have survived diet specialization, massive bamboo flowering and die off, and rapid climate oscillations. Now, they are suffering from enormous human interference. Fortunately, continued conservation effort is greatly reducing impacts from anthropogenic interference and allowing giant panda populations and habitat to recover. Previous ideas of a giant panda evolutionary cul-de-sac resulted from an unsystematic and unsophisticated understanding of their biology and it is time to shed this baggage and focus on the survival and maintenance of this high-profile species.
    Print ISSN: 0737-4038
    Electronic ISSN: 1537-1719
    Topics: Biology
    Published by Oxford University Press
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  • 9
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    New astrometric observations of Triton in 2007-2009 (2014)
    Oxford University Press
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    Publication Date: 2014-04-20
    Description: Astrometric positions of the Neptunian satellite Triton with a visual magnitude of 13.5 were obtained during three successive oppositions in 2007, 2008 and 2009. A total of 1095 new observed positions of Triton were collected during 46 nights of observations, involving eight missions and three telescopes. We compared our observations to the best ephemerides of Triton available now. This comparison has shown that our observations present a high level of accuracy as they provide standard deviations of residuals hardly higher than 50 mas and mean residuals lower than 30 mas, corresponding to about only 500 km in the position of the very distant satellite Triton. Moreover, we have compared most of the different planetary ephemerides of Neptune available now as well as two recent orbit models of Triton. These new comparisons have clearly shown the differences between all of these ephemerides which can be significant and that are presented in this work.
    Print ISSN: 0035-8711
    Electronic ISSN: 1365-2966
    Topics: Physics
    Published by Oxford University Press
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  • 10
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    Revealing the architecture of genetic and epigenetic regulation: a maximum likelihood model (2014)
    Oxford University Press
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    Publication Date: 2014-11-20
    Description: Gene expression is modulated by multiple mechanisms, including genetic and/or epigenetic regulation, and associated with the processes of cellular differentiation and morphogenesis. Single nucleotide polymorphisms (SNPs) and DNA methylation play important roles in regulating gene expression. In this study, we focused on revealing the relationship between SNPs, DNA methylation and gene expression in two human populations genome-wide through proposing four regulation patterns and developed maximum likelihood estimate models. Using simulated data with different correlation coefficients between any two traits, the power of our approach showed a favourable performance and relative stability. In all, 6733 SNP–CpG-gene pairs including 957 genes were obtained in Northern European ancestry (CEU) population. As the results showed, SNPs and DNA methylation had approximately the same effect on expression regulation of 49% genes, which was termed cooperative/antagonistic regulation pattern. Less than 30% of genes are controlled only by one of the factors (SNP/DNA methylation). The others showed SNPs that affect methylation have no consequent effects or crosstalk regulation on gene expression. Similar result was shown in Yourba (YRI) population. Specific genes were inferred using the different mechanisms of gene regulation involved in complex diseases by combining literature. This approach provides a method to comprehensively assess regulation patterns of gene expression in the whole genome.
    Print ISSN: 1467-5463
    Electronic ISSN: 1477-4054
    Topics: Biology , Computer Science
    Published by Oxford University Press
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