bluuebunny/crossref_metadata_2025_split huggingface dataset:
The Effects of Selenium Supplementation on Glucose Metabolism and Lipid Profiles Among Patients with Metabolic Diseases: A Systematic Review and Meta-Analysis of Randomized Controlled Trials
Authors: Tabrizi Reza , Akbari Maryam , Moosazadeh Mahmood , Lankarani Kamran , Heydari Seyed , Kolahdooz Fariba , Mohammadi Ali , Shabani Azade , Badehnoosh Bita , Jamilian Mehri , Assarian Amin , Asemi Zatollah 
Published: October 2017

AbstractThis systematic review and meta-analysis of randomized controlled trials (RCTs) was conducted to summarize the effect of selenium administration on glucose metabolism and lipid profiles among patients with diseases related to metabolic syndrome (MetS). We searched the following databases up to May 2017: MEDLINE, EMBASE, Web of Science, and Cochrane Central Register of Controlled Trials. The relevant data were extracted and assessed for quality of the studies according to the Cochrane risk of bias tool. Data were pooled using the inverse variance method and expressed as standardized mean difference (MDs) with 95% confidence intervals (95% CI). Five studies were included in the meta-analyses. The results showed that selenium supplementation significantly reduced insulin levels (SMD −0.42; 95% CI, −0.83 to −0.01) and increased quantitative insulin sensitivity check index (QUICKI) (SMD 0.83; 95% CI, 0.58 to 1.09). Selenium supplementation had no beneficial effects on other glucose homeostasis parameters, such as fasting plasma glucose (FPG) (SMD −0.29; 95% CI, −0.73 to 0.15), homeostasis model assessment of insulin resistance (HOMA-IR) (SMD −0.80; 95% CI, −1.58 to −0.03), and lipid profiles, such as triglycerides (SMD −0.42; 95% CI, −0.83 to −0.01), VLDL- (SMD −0.42; 95% CI, −0.83 to −0.01), total- (SMD −0.42; 95% CI, −0.83 to −0.01), LDL- (SMD 0.02; 95% CI, −0.20 to 0.24), and HDL-cholesterol (SMD 0.16; 95% CI, −0.06 to −0.38). Overall, this meta-analysis showed that selenium administration may lead to an improvement in insulin and QUICKI, but did not affect FPG, HOMA-IR, and lipid profiles.
The Anti-Inflammatory Potential of Mimosa caesalpiniifolia Following Experimental Colitis: Role of COX-2 and TNF-Alpha Expression
Authors: Silva Marcelo , Vilegas Wagner , da Silva Marcelo , Paiotti Ana , Pastrelo Mauricio , Ruiz Pedro , de Moura Carolina , Oshima Celina , Ribeiro Daniel 
Published: October 2017

AbstractThe aim of this study was to evaluate the preventive and/or protective action of Mimosa caesalpiniifolia (M. caesalpiniifolia) following experimental colitis in rats. The rats were randomized into ten groups (n=10 per group), as follows: G1 – Sham group:; G2 – TNBS group; G3, G4 –colitis and treated with hydroalcoholic extract of M. caesalpiniifolia 250 mg/kg/day after and before/after inducing colitis, respectively; G5, G6 – colitis and treated with hydroalcoholic extract of M. caesalpiniifolia at 125 mg/kg/day after and before/after inducing colitis respectively; G7,G8 – colitis and treated with ethylacetate fraction of M. caesalpiniifolia at 50 mg/kg/day after and before/after inducing colitis, respectively; G9,G10 – colitis and treated with ethylacetate fraction of M. caesalpiniifolia at 50 mg/kg/day after and before/after inducing colitis, respectively. Rats treated with hydroalcoholic extract of M. caesalpiniifolia for both doses showed lower tissue damage in the distal colon. Ethylacetate fraction was effective at the highest dose only when administrated after inducing colitis. A downregulation of COX-2 was detected to rats suffering colitis and treated with M. caesalpiniifolia at high dose. On the other hand, TNF-alpha immunoexpression decreased in groups treated with M. caesalpiniifolia at low dose after inducing colitis. In summary, our results suggest that M. caesalpiniifolia attenuated the lesions of the colon, reduced inflammation, and modulates the expression of COX-2 and TNF-α during chronic colitis induced by TNBS when using for therapeutic purposes on a dose-dependent manner.
Inhibition of DAI-dependent necroptosis by the Z-DNA binding domain of the vaccinia virus innate immune evasion protein, E3
Authors: Koehler Heather , Cotsmire Samantha , Langland Jeffrey , Kibler Karen V. , Kalman Daniel , Upton Jason W. , Mocarski Edward S. , Jacobs Bertram L. 
Published: October 2017

Significance
The host interferon system is a potent antiviral system, responsible for protecting vertebrate organisms against virus infection. In this paper we demonstrate that the N terminus of the vaccinia virus innate immune evasion protein, E3, is necessary to inhibit the action of interferon. Interferon-treated cells infected with virus encoding an E3 deleted of the N-terminal domain die rapidly. This death is dependent on the host RIPK3 protein, which is a mediator of programmed necrotic death, and on DAI, which is a sensor of virus infection. Since both E3 and DAI contain Z-DNA binding domains, we hypothesize that the cellular DAI virus sensor and the viral antiinterferon E3 protein compete for binding to a vaccinia virus-induced Z-nucleic acid, pathogen-associated molecular pattern.
Kinship and familiarity mitigate costs of social conflict between Seychelles warbler neighbors
Authors: Bebbington Kat , Kingma Sjouke A. , Fairfield Eleanor A. , Dugdale Hannah L. , Komdeur Jan , Spurgin Lewis G. , Richardson David S. 
Published: October 2017

Significance
In nature, animals must compete with their neighbors for access to limited resources. Since conflict over resources can be extremely costly in terms of time, energy, and reproductive success, investigating how individuals resolve conflict is crucial to understanding the evolution of social behaviors. In the Seychelles warbler, we demonstrate two mechanisms by which individuals minimize costs of conflict and show the benefits individuals gain from doing so. Birds that live near relatives or familiar individuals invest less energy in defending and maintaining territory borders and also show less aging-related signs of physiological damage. Our results suggest that conflict between neighbors can be mitigated by kin-selected benefits of sharing resources with relatives but also through direct mutual benefits of cooperation.
PrimPol is required for replication reinitiation after mtDNA damage
Authors: Torregrosa-Muñumer Rubén , Forslund Josefin M. E. , Goffart Steffi , Pfeiffer Annika , Stojkovič Gorazd , Carvalho Gustavo , Al-Furoukh Natalie , Blanco Luis , Wanrooij Sjoerd , Pohjoismäki Jaakko L. O. 
Published: October 2017

Significance
Failure to maintain mtDNA integrity can lead to a wide variety of neuromuscular disorders. Despite its central role in the development of these disorders, many mechanistic details of mtDNA maintenance are still unclear. In the present work, we have studied the role of PrimPol, an unusual primase-polymerase, in mammalian mtDNA maintenance. We report here that PrimPol is specifically required for replication reinitiation after DNA damage. PrimPol synthesizes DNA primers on an ssDNA template, which can be elongated by the mitochondrial replicative polymerase γ, a solution to reprime replication beyond DNA lesions and to facilitate lagging-strand replication. Our findings show that PrimPol has biological relevance for mtDNA maintenance.
Geophysical potential for wind energy over the open oceans
Authors: Possner Anna , Caldeira Ken 
Published: October 2017

Significance
Wind speeds over open ocean areas are often higher than those in the windiest areas over land, which has motivated a quest to develop technologies that could harvest wind energy in deep water environments. However, it remains unclear whether these open ocean wind speeds are higher because of lack of surface drag or whether a greater downward transport of kinetic energy may be sustained in open ocean environments. Focusing on the North Atlantic region, we provide evidence that there is potential for greater downward transport of kinetic energy in the overlying atmosphere. As a result, wind power generation over some ocean areas can exceed power generation on land by a factor of three or more.
Maladaptive DNA repair is the ultimate contributor to the death of trimethoprim-treated cells under aerobic and anaerobic conditions
Authors: Giroux Xavier , Su Wei-Lin , Bredeche Marie-Florence , Matic Ivan 
Published: October 2017

Significance
Antibiotic resistance leads to substantial mortality and morbidity and significant economic cost because it seriously undermines our ability to treat bacterial infections. Therefore, a better understanding of the effect of antibiotics on bacteria is needed to increase the effectiveness of treatments and slow the emergence of resistance. The bactericidal effects of antibiotics are triggered by target-specific interactions, but there is growing evidence that an important part of their cytotoxicity results from metabolic disturbances induced by treatment. In this article, we report that the perturbation of DNA replication by a wide-spectrum antibiotic, trimethoprim, affects bacterial metabolism, which provokes the production of genotoxic agents and DNA damage, whose processing ultimately contributes to cell death under both aerobic and anaerobic conditions.
Human SHMT inhibitors reveal defective glycine import as a targetable metabolic vulnerability of diffuse large B-cell lymphoma
Authors: Ducker Gregory S. , Ghergurovich Jonathan M. , Mainolfi Nello , Suri Vipin , Jeong Stephanie K. , Hsin-Jung Li Sophia , Friedman Adam , Manfredi Mark G. , Gitai Zemer , Kim Hahn , Rabinowitz Joshua D. 
Published: October 2017

Significance
Enzymes of the folate cycle are among the most consistently overexpressed proteins in cancer. Whereas multiple clinical agents inhibit thymidylate synthase, no current drugs target the incorporation of one-carbon into folates via serine hydroxymethyltransferase (SHMT). Using genetics, we show that cancer cells require SHMT to generate tumors. We then describe small-molecule SHMT inhibitors, and show that they block the growth of many human cancer cells, with B-cell lymphomas particularly sensitive to SHMT inhibition. We find that this sensitivity arises from the lymphomas’ inability to import the amino acid glycine, which is made as a byproduct of the SHMT reaction. Thus, B-cell lymphomas have an intrinsic defect in amino acid import, which causes a therapeutically targetable metabolic vulnerability.
Visual perception as retrospective Bayesian decoding from high- to low-level features
Authors: Ding Stephanie , Cueva Christopher J. , Tsodyks Misha , Qian Ning 
Published: October 2017

Significance
The nature of perceptual decoding remains an open, fundamental question. Many studies assume that decoding follows the same low- to high-level hierarchy of encoding, yet this assumption was never rigorously tested. We performed such a test, which refutes the assumption to the extent that absolute and relative/ordinal orientations are features of different levels. Additionally, the backward aftereffect we discovered cannot be explained by the efficient-coding theories of adaptation. Finally, we proposed a new theory that explains our data as retrospective Bayesian decoding from high to low levels in working memory. This decoding hierarchy is justified by considering memory stability/distortion of high/low-level features. Thus, our work rejects the currently dominant decoding scheme and offers a framework that integrates perceptual decoding and working memory.
Intragenic DNA methylation and BORIS-mediated cancer-specific splicing contribute to the Warburg effect
Authors: Singh Smriti , Narayanan Sathiya Pandi , Biswas Kajal , Gupta Amit , Ahuja Neha , Yadav Sandhya , Panday Rajendra Kumar , Samaiya Atul , Sharan Shyam K. , Shukla Sanjeev 
Published: October 2017

Significance
Recent advances in cancer epigenetics have shown the involvement of epigenetic abnormalities in the initiation and progression of cancer, but their role in cancer-specific aberrant splicing is not clear. The identification of upstream epigenetic regulators of cancer-specific splicing will enable us to therapeutically target aberrant splicing and provide an approach to cancer therapy. Here we have demonstrated a mechanism of intragenic DNA methylation-mediated regulation of alternative splicing by Brother of Regulator of Imprinted Sites (BORIS), which can contribute to breast cancer tumorigenesis by favoring the Warburg effect. The reversal of the Warburg effect was achieved by the inhibition of DNA methylation or down-regulation of BORIS, which may serve as a useful approach to inhibit the growth of breast cancer cells.
Molecular photoswitches mediating the strain-driven disassembly of supramolecular tubules
Authors: Fredy Jean W. , Méndez-Ardoy Alejandro , Kwangmettatam Supaporn , Bochicchio Davide , Matt Benjamin , Stuart Marc C. A. , Huskens Jurriaan , Katsonis Nathalie , Pavan Giovanni M. , Kudernac Tibor 
Published: October 2017

Significance
Developing molecular machines has been a leading goal for scientists, but to be practically valuable their mechanically relevant motion must be decoupled from the Brownian storm that dominates in solution. The disassembly of cellular tubules operates by the switching of the shapes of the building blocks, ultimately pulling sets of chromosomes apart. Here, we show that artificial photoswitches can be incorporated within supramolecular microtubules and that individual switching events lead to conversion of light into elastic energy that can be stored, accumulated, and subsequently released to produce a mechanical effect. The work paves the way toward fully artificial supramolecular machines that convert molecular motion into sophisticated operation modes, at length scales that are typically the realm of living matter.
Spatial organization of a model 15-member human gut microbiota established in gnotobiotic mice
Authors: Mark Welch Jessica L. , Hasegawa Yuko , McNulty Nathan P. , Gordon Jeffrey I. , Borisy Gary G. 
Published: October 2017

Significance
Spatial structure is postulated to have a powerful influence on establishing and sustaining the signaling and metabolic exchanges that define relationships among members of the gut microbiota and host. However, information about gut community spatial structure is limited. Simultaneous imaging of components of a 15-member model human gut bacterial community over a range of spatial scales in gnotobiotic mice revealed that the colon is better conceptualized as an incompletely mixed bioreactor, rather than having sharply stratified luminal and mucosal compartments. Identifying host and microbial factors that constrain the ability of community members to establish sizeable single or oligotaxon agglomerations should yield new insights about how “micro”-scale mixing defines community function.
Big data modeling to predict platelet usage and minimize wastage in a tertiary care system
Authors: Guan Leying , Tian Xiaoying , Gombar Saurabh , Zemek Allison J. , Krishnan Gomathi , Scott Robert , Narasimhan Balasubramanian , Tibshirani Robert J. , Pham Tho D. 
Published: October 2017

SignificanceIn modern hospital systems where complicated, severely ill patient populations are the norm, there is currently no reliable way to forecast the use of perishable medical resources to enable a smart and economic way to deliver optimal patient care. We here demonstrate a statistical model using hospital patient data to quantitatively forecast, days in advance, the need for platelet transfusions. This approach can be leveraged to significantly decrease platelet wastage, and, if adopted nationwide, would save approximately 80 million dollars per year. We believe our approach can be generalized to all other aspects of patient care involving timely delivery of perishable medical resources.
Perceiving social interactions in the posterior superior temporal sulcus
Authors: Isik Leyla , Koldewyn Kami , Beeler David , Kanwisher Nancy 
Published: October 2017

Significance
Humans spend a large percentage of their time perceiving the appearance, actions, and intentions of others, and extensive previous research has identified multiple brain regions engaged in these functions. However, social life depends on the ability to understand not just individuals, but also groups and their interactions. Here we show that a specific region of the posterior superior temporal sulcus responds strongly and selectively when viewing social interactions between two other agents. This region also contains information about whether the interaction is positive (helping) or negative (hindering), and may underlie our ability to perceive, understand, and navigate within our social world.
Transcription factor ISX mediates the cross talk between diet and immunity
Authors: Widjaja-Adhi Made Airanthi K. , Palczewski Grzegorz , Dale Kali , Knauss Elizabeth A. , Kelly Mary E. , Golczak Marcin , Levine Alan D. , von Lintig Johannes 
Published: October 2017

SignificanceThe intestine is the major entrance site for nutrients, electrolytes, and water while constituting an effective barrier against toxins, antigens, and enteric flora. Hence, the intestinal mucosa harbors one of the largest populations of lymphocytes in the body. Nutrients such as vitamin A have been recognized to influence gut homing and differentiation of these cells. We identified the ISX protein as a critical molecular mediator of this cross talk between diet and immunity. This transcription factor regulates vitamin A production from dietary precursor molecules. Loss of this control in mice disrupts vitamin A homeostasis and impairs immunity. Reported genetic polymorphisms in theIsxgene have been associated with inflammatory disorders in humans, indicating that our findings in mice have clinical implications.
Molecular Cloning, Characterization, and Expression Analysis of Cathepsin A in the Chinese Giant Salamander Andrias davidianus
Authors: Zhang Qihuan , Han Panpan , Huang Bei , Wang Zisheng , Qiao Guo , Wang Puze , Qi Zhitao 
Published: October 2017

Abstract
Cathepsin A (CTSA) is serine carboxypeptidase, an important protease in the lysosome. In this study, the full complementary DNA (cDNA) sequence of CTSA in Chinese giant salamanders Andrias davidianus was cloned, and its sequence features were analyzed. Tissue expression patterns of CTSA in healthy and Aeromonas hydrophila-infected salamanders were also investigated. The full cDNA sequence of salamander CTSA was 1,620 base pairs in length, encoding 472 amino acids. Salamander CTSA shared high sequence identities with other vertebrates’ CTSAs, ranging from 62.7% to 68.9%. In healthy salamanders, CTSA was highly expressed in spleen, followed by brain, intestine, and stomach. After A. hydrophila infection, salamander CTSA was significantly upregulated in lung, heart, muscle, and kidney; was downregulated in liver, spleen, and intestine; and exhibited no significant changes in stomach and skin, indicating that salamander CTSA might play defense roles in multiple tissues during bacterial infection. These results provide a solid basis for further study of the immune function of amphibian CTSA.
Received September 18, 2016; accepted June 18, 2017 Published online October 9, 2017
Long‐term effects of acoustic reafference training (ART)
Authors: Pizzera Alexandra , Hohmann Tanja , Streese Lukas , Habbig Anja , Raab Markus 
Published: October 2017

AbstractIn sport visual feedback is often used to enhance performance, mostly neglecting the auditory modality. However, athletes produce natural sounds when they move (acoustic reafferences) which they perceive and use to control their movements. We examined the short‐ and long‐term effects of a training intervention on a complex movement by using acoustic reafferences. Natural step sounds produced during hurdling were recorded and played back to the participants immediately before each trial, with an increase (fast group), decrease (slow group), or no manipulation (control group) in the tempo. All groups increased their hurdling performance regarding overall running time, with the slow group showing the best performance development. After a 10‐week retention, the fast and slow group further increased performance, whereas the control group declined. The repeated experience with acoustic information associated with the rhythmic pattern of hurdling may have helped developing a cognitive representation of that movement, especially regarding long‐term effects.
Deciphering programs of transcriptional regulation by combined deconvolution of multiple omics layers
Authors: Hüebschmann Daniel , Kurzawa Nils , Steinhauser Sebastian , Rentzsch Philipp , Krämer Stephen , Andresen Carolin , Park Jeongbin , Eils Roland , Schlesner Matthias , Herrmann Carl 
Published: October 2017

AbstractMetazoans are crucially dependent on multiple layers of gene regulatory mechanisms which allow them to control gene expression across developmental stages, tissues and cell types. Multiple recent research consortia have aimed to generate comprehensive datasets to profile the activity of these cell type- and condition-specific regulatory landscapes across many different cell lines and primary cells. However, extraction of genes or regulatory elements specific to certain entities from these datasets remains challenging. We here propose a novel method based on non-negative matrix factorization for disentangling and associating huge multi-assay datasets including chromatin accessibility and gene expression data. Taking advantage of implementations of NMF algorithms in the GPU CUDA environment full datasets composed of tens of thousands of genes as well as hundreds of samples can be processed without the need for prior feature selection to reduce the input size. Applying this framework to multiple layers of genomic data derived from human blood cells we unravel mechanisms of regulation of cell type-specific expression in T-cells and monocytes.
Many rare genetic variants have unrecognized large-effect disruptions to exon recognition
Authors: Cheung Rocky , Insigne Kimberly D. , Yao David , Burghard Christina P. , Jones Eric M. , Goodman Daniel B. , Kosuri Sriram 
Published: October 2017

AbstractAny individual’s genome contains ∼4-5 million genetic variants that differ from reference, and understanding how these variants give rise to trait diversity and disease susceptibility is a central goal of human genetics1. A vast majority (96-99%) of an individual’s variants are common, though at a population level the overwhelming majority of variants are rare2–5. Because of their scarcity in an individual’s genome, rare variants that play important roles in complex traits are likely to have large functional effects6,7. Mutations that cause an exon to be skipped can have severe functional consequences on gene function, and many known disease-causing mutations reduce or eliminate exon recognition8. Here we explore the extent to which rare genetic variation in humans results in near complete loss of exon recognition. We developed a Multiplexed Functional Assay of Splicing using Sort-seq (MFASS) that allows us to measure exon inclusion in thousands of human exons and surrounding intronic sequence simultaneously. We assayed 27,733 extant variants in the Exome Aggregation Consortium (ExAC)9within or adjacent to 2,339 human exons, and found that 3.8% (1,050) of the variants, almost all of which were extremely rare, led to large-effect defects in exon recognition. Importantly, we find that 83% of these splice-disrupting variants (SDVs) are located outside of canonical splice sites, are distributed evenly across distinct exonic and intronic regions, and are difficult to predicta priori. Our results indicate that loss of exon recognition is an important and underappreciated means by which rare variants exert large functional effects, and that MFASS enables their empirical assessment for splicing defects at scale.