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  • 1
    Online Resource
    Online Resource
    Proceedings of the National Academy of Sciences ; 2015
    In:  Proceedings of the National Academy of Sciences Vol. 112, No. 47 ( 2015-11-24), p. 14670-14675
    In: Proceedings of the National Academy of Sciences, Proceedings of the National Academy of Sciences, Vol. 112, No. 47 ( 2015-11-24), p. 14670-14675
    Abstract: Noninvasive prenatal testing (NIPT) using sequencing of fetal cell-free DNA from maternal plasma has enabled accurate prenatal diagnosis of aneuploidy and become increasingly accepted in clinical practice. We investigated whether NIPT using semiconductor sequencing platform (SSP) could reliably detect subchromosomal deletions/duplications in women carrying high-risk fetuses. We first showed that increasing concentration of abnormal DNA and sequencing depth improved detection. Subsequently, we analyzed plasma from 1,456 pregnant women to develop a method for estimating fetal DNA concentration based on the size distribution of DNA fragments. Finally, we collected plasma from 1,476 pregnant women with fetal structural abnormalities detected on ultrasound who also underwent an invasive diagnostic procedure. We used SSP of maternal plasma DNA to detect subchromosomal abnormalities and validated our results with array comparative genomic hybridization (aCGH). With 3.5 million reads, SSP detected 56 of 78 (71.8%) subchromosomal abnormalities detected by aCGH. With increased sequencing depth up to 10 million reads and restriction of the size of abnormalities to more than 1 Mb, sensitivity improved to 69 of 73 (94.5%). Of 55 false-positive samples, 35 were caused by deletions/duplications present in maternal DNA, indicating the necessity of a validation test to exclude maternal karyotype abnormalities. This study shows that detection of fetal subchromosomal abnormalities is a viable extension of NIPT based on SSP. Although we focused on the application of cell-free DNA sequencing for NIPT, we believe that this method has broader applications for genetic diagnosis, such as analysis of circulating tumor DNA for detection of cancer.
    Type of Medium: Online Resource
    ISSN: 0027-8424 , 1091-6490
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    Language: English
    Publisher: Proceedings of the National Academy of Sciences
    Publication Date: 2015
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  • 2
    In: Proceedings of the National Academy of Sciences, Proceedings of the National Academy of Sciences, Vol. 117, No. 5 ( 2020-02-04), p. 2560-2569
    Abstract: De novo mutations (DNMs), or mutations that appear in an individual despite not being seen in their parents, are an important source of genetic variation whose impact is relevant to studies of human evolution, genetics, and disease. Utilizing high-coverage whole-genome sequencing data as part of the Trans-Omics for Precision Medicine (TOPMed) Program, we called 93,325 single-nucleotide DNMs across 1,465 trios from an array of diverse human populations, and used them to directly estimate and analyze DNM counts, rates, and spectra. We find a significant positive correlation between local recombination rate and local DNM rate, and that DNM rate explains a substantial portion (8.98 to 34.92%, depending on the model) of the genome-wide variation in population-level genetic variation from 41K unrelated TOPMed samples. Genome-wide heterozygosity does correlate with DNM rate, but only explains 〈 1% of variation. While we are underpowered to see small differences, we do not find significant differences in DNM rate between individuals of European, African, and Latino ancestry, nor across ancestrally distinct segments within admixed individuals. However, we did find significantly fewer DNMs in Amish individuals, even when compared with other Europeans, and even after accounting for parental age and sequencing center. Specifically, we found significant reductions in the number of C→A and T→C mutations in the Amish, which seem to underpin their overall reduction in DNMs. Finally, we calculated near-zero estimates of narrow sense heritability ( h 2 ), which suggest that variation in DNM rate is significantly shaped by nonadditive genetic effects and the environment.
    Type of Medium: Online Resource
    ISSN: 0027-8424 , 1091-6490
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    Language: English
    Publisher: Proceedings of the National Academy of Sciences
    Publication Date: 2020
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  • 3
    Online Resource
    Online Resource
    American Association for the Advancement of Science (AAAS) ; 2021
    In:  Science Vol. 371, No. 6536 ( 2021-03-26), p. 1374-1378
    In: Science, American Association for the Advancement of Science (AAAS), Vol. 371, No. 6536 ( 2021-03-26), p. 1374-1378
    Abstract: The COVID-19 pandemic caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) continually poses serious threats to global public health. The main protease (M pro ) of SARS-CoV-2 plays a central role in viral replication. We designed and synthesized 32 new bicycloproline-containing M pro inhibitors derived from either boceprevir or telaprevir, both of which are approved antivirals. All compounds inhibited SARS-CoV-2 M pro activity in vitro, with 50% inhibitory concentration values ranging from 7.6 to 748.5 nM. The cocrystal structure of M pro in complex with MI-23, one of the most potent compounds, revealed its interaction mode. Two compounds (MI-09 and MI-30) showed excellent antiviral activity in cell-based assays. In a transgenic mouse model of SARS-CoV-2 infection, oral or intraperitoneal treatment with MI-09 or MI-30 significantly reduced lung viral loads and lung lesions. Both also displayed good pharmacokinetic properties and safety in rats.
    Type of Medium: Online Resource
    ISSN: 0036-8075 , 1095-9203
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    Language: English
    Publisher: American Association for the Advancement of Science (AAAS)
    Publication Date: 2021
    detail.hit.zdb_id: 128410-1
    detail.hit.zdb_id: 2066996-3
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  • 4
    In: Science, American Association for the Advancement of Science (AAAS), Vol. 340, No. 6140 ( 2013-06-28), p. 1555-1559
    Abstract: Permeability controls fluid flow in fault zones and is a proxy for rock damage after an earthquake. We used the tidal response of water level in a deep borehole to track permeability for 18 months in the damage zone of the causative fault of the 2008 moment magnitude 7.9 Wenchuan earthquake. The unusually high measured hydraulic diffusivity of 2.4 × 10 −2 square meters per second implies a major role for water circulation in the fault zone. For most of the observation period, the permeability decreased rapidly as the fault healed. The trend was interrupted by abrupt permeability increases attributable to shaking from remote earthquakes. These direct measurements of the fault zone reveal a process of punctuated recovery as healing and damage interact in the aftermath of a major earthquake.
    Type of Medium: Online Resource
    ISSN: 0036-8075 , 1095-9203
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    Language: English
    Publisher: American Association for the Advancement of Science (AAAS)
    Publication Date: 2013
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  • 5
    Online Resource
    Online Resource
    Association for Computing Machinery (ACM) ; 2010
    In:  ACM Transactions on Asian Language Information Processing Vol. 9, No. 2 ( 2010-06), p. 1-32
    In: ACM Transactions on Asian Language Information Processing, Association for Computing Machinery (ACM), Vol. 9, No. 2 ( 2010-06), p. 1-32
    Abstract: Chinese word segmentation is an active area in Chinese language processing though it is suffering from the argument about what precisely is a word in Chinese. Based on corpus-based segmentation standard, we launched this study. In detail, we regard Chinese word segmentation as a character-based tagging problem. We show that there has been a potent trend of using a character-based tagging approach in this field. In particular, learning from segmented corpus with or without additional linguistic resources is treated in a unified way in which the only difference depends on how the feature template set is selected. It differs from existing work in that both feature template selection and tag set selection are considered in our approach, instead of the previous feature template focus only technique. We show that there is a significant performance difference as different tag sets are selected. This is especially applied to a six-tag set, which is good enough for most current segmented corpora. The linguistic meaning of a tag set is also discussed. Our results show that a simple learning system with six n -gram feature templates and a six-tag set can obtain competitive performance in the cases of learning only from a training corpus. In cases when additional linguistic resources are available, an ensemble learning technique, assistant segmenter, is proposed and its effectiveness is verified. Assistant segmenter is also proven to be an effective method as segmentation standard adaptation that outperforms existing ones. Based on the proposed approach, our system provides state-of-the-art performance in all 12 corpora of three international Chinese word segmentation bakeoffs.
    Type of Medium: Online Resource
    ISSN: 1530-0226 , 1558-3430
    Language: English
    Publisher: Association for Computing Machinery (ACM)
    Publication Date: 2010
    detail.hit.zdb_id: 2820615-0
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  • 6
    Online Resource
    Online Resource
    Proceedings of the National Academy of Sciences ; 2017
    In:  Proceedings of the National Academy of Sciences Vol. 114, No. 36 ( 2017-09-05)
    In: Proceedings of the National Academy of Sciences, Proceedings of the National Academy of Sciences, Vol. 114, No. 36 ( 2017-09-05)
    Abstract: Severe fever with thrombocytopenia syndrome virus (SFTSV) and Rift Valley fever virus (RVFV) are two arthropod-borne phleboviruses in the Bunyaviridae family, which cause severe illness in humans and animals. Glycoprotein N (Gn) is one of the envelope proteins on the virus surface and is a major antigenic component. Despite its importance for virus entry and fusion, the molecular features of the phleboviruse Gn were unknown. Here, we present the crystal structures of the Gn head domain from both SFTSV and RVFV, which display a similar compact triangular shape overall, while the three subdomains (domains I, II, and III) making up the Gn head display different arrangements. Ten cysteines in the Gn stem region are conserved among phleboviruses, four of which are responsible for Gn dimerization, as revealed in this study, and they are highly conserved for all members in Bunyaviridae . Therefore, we propose an anchoring mode on the viral surface. The complex structure of the SFTSV Gn head and human neutralizing antibody MAb 4–5 reveals that helices α6 in subdomain III is the key component for neutralization. Importantly, the structure indicates that domain III is an ideal region recognized by specific neutralizing antibodies, while domain II is probably recognized by broadly neutralizing antibodies. Collectively, Gn is a desirable vaccine target, and our data provide a molecular basis for the rational design of vaccines against the diseases caused by phleboviruses and a model for bunyavirus Gn embedding on the viral surface.
    Type of Medium: Online Resource
    ISSN: 0027-8424 , 1091-6490
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    Language: English
    Publisher: Proceedings of the National Academy of Sciences
    Publication Date: 2017
    detail.hit.zdb_id: 209104-5
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  • 7
    In: Brain, Oxford University Press (OUP), Vol. 143, No. 1 ( 2020-01-01), p. 222-233
    Abstract: Essential tremor is one of the most common movement disorders. Despite its high prevalence and heritability, the genetic aetiology of essential tremor remains elusive. Up to now, only a few genes/loci have been identified, but these genes have not been replicated in other essential tremor families or cohorts. Here we report a genetic study in a cohort of 197 Chinese pedigrees clinically diagnosed with essential tremor. Using a comprehensive strategy combining linkage analysis, whole-exome sequencing, long-read whole-genome sequencing, repeat-primed polymerase chain reaction and GC-rich polymerase chain reaction, we identified an abnormal GGC repeat expansion in the 5′ region of the NOTCH2NLC gene that co-segregated with disease in 11 essential tremor families (5.58%) from our cohort. Clinically, probands that had an abnormal GGC repeat expansion were found to have more severe tremor phenotypes, lower activities of daily living ability. Obvious genetic anticipation was also detected in these 11 essential tremor-positive families. These results indicate that abnormal GGC repeat expansion in the 5′ region of NOTCH2NLC gene is associated with essential tremor, and provide strong evidence that essential tremor is a family of diseases with high clinical and genetic heterogeneities.
    Type of Medium: Online Resource
    ISSN: 0006-8950 , 1460-2156
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    Language: English
    Publisher: Oxford University Press (OUP)
    Publication Date: 2020
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  • 8
    Online Resource
    Online Resource
    Proceedings of the National Academy of Sciences ; 2016
    In:  Proceedings of the National Academy of Sciences Vol. 113, No. 19 ( 2016-05-10), p. 5293-5298
    In: Proceedings of the National Academy of Sciences, Proceedings of the National Academy of Sciences, Vol. 113, No. 19 ( 2016-05-10), p. 5293-5298
    Abstract: Cyclic stretch is an important inducer of vascular smooth muscle cell (VSMC) proliferation, which is crucial in vascular remodeling during hypertension. However, the molecular mechanism remains unclear. We studied the effects of emerin and lamin A/C, two important nuclear envelope proteins, on VSMC proliferation in hypertension and the underlying mechano-mechanisms. In common carotid artery of hypertensive rats in vivo and in cultured cells subjected to high (15%) cyclic stretch in vitro, VSMC proliferation was increased significantly, and the expression of emerin and lamin A/C was repressed compared with normotensive or normal (5%) cyclic stretch controls. Using targeted siRNA to mimic the repressed expression of emerin or lamin A/C induced by 15% stretch, we found that VSMC proliferation was enhanced under static and 5%-stretch conditions. Overexpression of emerin or lamin A/C reversed VSMC proliferation induced by 15% stretch. Hence, emerin and lamin A/C play critical roles in suppressing VSMC hyperproliferation induced by hyperstretch. ChIP-on-chip and MOTIF analyses showed that the DNAs binding with emerin contain three transcription factor motifs: CCNGGA, CCMGCC, and ABTTCCG; DNAs binding with lamin A/C contain the motifs CVGGAA, GCCGCYGC, and DAAGAAA. Protein/DNA array proved that altered emerin or lamin A/C expression modulated the activation of various transcription factors. Furthermore, accelerating local expression of emerin or lamin A/C reversed cell proliferation in the carotid artery of hypertensive rats in vivo. Our findings establish the pathogenetic role of emerin and lamin A/C repression in stretch-induced VSMC proliferation and suggest mechanobiological mechanism underlying this process that involves the sequence-specific binding of emerin and lamin A/C to specific transcription factor motifs.
    Type of Medium: Online Resource
    ISSN: 0027-8424 , 1091-6490
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    Language: English
    Publisher: Proceedings of the National Academy of Sciences
    Publication Date: 2016
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  • 9
    Online Resource
    Online Resource
    Proceedings of the National Academy of Sciences ; 2013
    In:  Proceedings of the National Academy of Sciences Vol. 110, No. 9 ( 2013-02-26)
    In: Proceedings of the National Academy of Sciences, Proceedings of the National Academy of Sciences, Vol. 110, No. 9 ( 2013-02-26)
    Abstract: In the present study, we found that the level of BMP4 in human white adipose tissue is inversely associated with fat mass. Mice with overexpressed or absent BMP4 in white adipose tissue revealed that BMP4 induces brown fat-like changes in white adipose tissue in addition to altering metabolism and insulin sensitivity. Therefore, we showed that BMP4-mediated expression of PGC1α proceeds through the p38/MAPK/ATF2 pathway ( Fig. P1 ). These findings indicate that manipulation of BMP4 expression in white adipose tissue may serve as a therapeutic target for the prevention and/or treatment of obesity and its metabolic complications. We then explored the molecular mechanism of BMP4-induced brown adipose-like changes in white adipose tissue and found that peroxisome proliferator-activated receptor γ coactivator α (PGC1α) was the key regulator during the program. We further demonstrated that activation of the p38/MAPK/activating transcription factor 2 (ATF2) pathway and PGC1α expression by BMP4 play an important role in the induction of white adipose tissue into brown adipose-like tissue. Two mouse models were used in the present study: the BMP4 transgenic mouse in which BMP4 was specifically overexpressed and a knockout mouse in which BMP4 was specifically knocked out in adipose tissue. We assessed the phenotype of adipose tissue and the systematical metabolic alteration in these mice. Our findings revealed that the forced expression of BMP4 in white adipose tissue promotes the acquisition of brown fat-like characteristics, including decreased adipocyte size and lipid droplets, increased mitochondrial biogenesis, and the increased expression of fatty acid-oxidizing genes. Changes in adipose tissue resulted in a systematical increase in basal respiratory rate, increased insulin sensitivity, and decreased blood fat. Similarly, cell culture experiments revealed that treatment with BMP4 during 3T3-L1 adipocyte differentiation leads to a gene-expression profile similar to that of brown fat cells. More importantly, overexpression of BMP4 in white adipose tissue improves insulin sensitivity and protects against diet-induced obesity and diabetes. Conversely, BMP4-deficient mice exhibit enlarged white adipocyte morphology, increased blood fat, and impaired insulin sensitivity. These results reveal an interesting role for BMP4 in the regulation of adipogenesis and metabolism. White adipose tissue stores energy in the form of triglycerides. However, the increases in cell division or cell size (i.e., hyperplasia and hypertrophy, respectively) of adipocytes that accompany the excessive accumulation of body fat are associated with insulin resistance, type 2 diabetes, and an inflammatory response ( 1 ). In contrast, brown adipose tissue dissipates energy as heat by means of mitochondrial uncoupling protein 1. Promotion of brown adipose tissue activity helps prevent genetic obesity in rodents ( 2 ). Recent studies have identified metabolically active fat cells, known as “brite” (brown-in-white) or “beige” adipocytes, in white fat deposits in both mice and humans ( 3 ). The number of active brown adipose tissue cells is inversely correlated with BMI in humans ( 4 ). Therefore, the identification of factors that induce brown-like fat cells in white adipose tissue could suggest an approach to preventing and/or treating obesity and its metabolic complications. We previously found that BMP4 induces multipotent C3H10T1/2 stem cells to become preadipocytes ( 5 ). Our present findings reveal that the level of BMP4 in human white adipose tissue is inversely associated with BMI, and we explore whether BMP4 regulates the terminal differentiation and metabolic function of adipocytes. Two types of fat storage cells, known as “adipocytes,” coordinately regulate energy balance in humans and other mammals. White adipocytes are specialized to store energy, whereas brown adipocytes produce heat. Promotion of brown adipocyte activity in white adipose tissue helps prevent obesity and its metabolic complications. Bone morphogenetic protein 4 (BMP4) is a member of the bone morphogenetic protein family, which is part of the TGF-β superfamily. BMP4 is essential for embryonic formation and is involved in the development of tissues such as bone and muscle, teeth, and neurons. In the present study, we found that the level of BMP4 in human white adipose tissue is inversely associated with body mass index (BMI). The BMP4 protein also was shown to induce brown adipose tissue-like changes in white adipose tissue, and to increase glucose and energy expenditure in mice models.
    Type of Medium: Online Resource
    ISSN: 0027-8424 , 1091-6490
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    Language: English
    Publisher: Proceedings of the National Academy of Sciences
    Publication Date: 2013
    detail.hit.zdb_id: 209104-5
    detail.hit.zdb_id: 1461794-8
    SSG: 11
    SSG: 12
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  • 10
    Online Resource
    Online Resource
    Proceedings of the National Academy of Sciences ; 2015
    In:  Proceedings of the National Academy of Sciences Vol. 112, No. 4 ( 2015-01-27), p. 1095-1100
    In: Proceedings of the National Academy of Sciences, Proceedings of the National Academy of Sciences, Vol. 112, No. 4 ( 2015-01-27), p. 1095-1100
    Abstract: The Tibetan hulless barley ( Hordeum vulgare L. var. nudum ), also called “Qingke” in Chinese and “ Ne ” in Tibetan, is the staple food for Tibetans and an important livestock feed in the Tibetan Plateau. The diploid nature and adaptation to diverse environments of the highland give it unique resources for genetic research and crop improvement. Here we produced a 3.89-Gb draft assembly of Tibetan hulless barley with 36,151 predicted protein-coding genes. Comparative analyses revealed the divergence times and synteny between barley and other representative Poaceae genomes. The expansion of the gene family related to stress responses was found in Tibetan hulless barley. Resequencing of 10 barley accessions uncovered high levels of genetic variation in Tibetan wild barley and genetic divergence between Tibetan and non-Tibetan barley genomes. Selective sweep analyses demonstrate adaptive correlations of genes under selection with extensive environmental variables. Our results not only construct a genomic framework for crop improvement but also provide evolutionary insights of highland adaptation of Tibetan hulless barley.
    Type of Medium: Online Resource
    ISSN: 0027-8424 , 1091-6490
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    Language: English
    Publisher: Proceedings of the National Academy of Sciences
    Publication Date: 2015
    detail.hit.zdb_id: 209104-5
    detail.hit.zdb_id: 1461794-8
    SSG: 11
    SSG: 12
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