bluuebunny/crossref_metadata_2025_split huggingface dataset:
DeepMSA: constructing deep multiple sequence alignment to improve contact prediction and fold-recognition for distant-homology proteins
Authors: Zhang Chengxin , Zheng Wei , Mortuza S M , Li Yang , Zhang Yang 
Published: November 2019

Abstract

Motivation
The success of genome sequencing techniques has resulted in rapid explosion of protein sequences. Collections of multiple homologous sequences can provide critical information to the modeling of structure and function of unknown proteins. There are however no standard and efficient pipeline available for sensitive multiple sequence alignment (MSA) collection. This is particularly challenging when large whole-genome and metagenome databases are involved.

Results
We developed DeepMSA, a new open-source method for sensitive MSA construction, which has homologous sequences and alignments created from multi-sources of whole-genome and metagenome databases through complementary hidden Markov model algorithms. The practical usefulness of the pipeline was examined in three large-scale benchmark experiments based on 614 non-redundant proteins. First, DeepMSA was utilized to generate MSAs for residue-level contact prediction by six coevolution and deep learning-based programs, which resulted in an accuracy increase in long-range contacts by up to 24.4% compared to the default programs. Next, multiple threading programs are performed for homologous structure identification, where the average TM-score of the template alignments has over 7.5% increases with the use of the new DeepMSA profiles. Finally, DeepMSA was used for secondary structure prediction and resulted in statistically significant improvements in the Q3 accuracy. It is noted that all these improvements were achieved without re-training the parameters and neural-network models, demonstrating the robustness and general usefulness of the DeepMSA in protein structural bioinformatics applications, especially for targets without homologous templates in the PDB library.

Availability and implementation
https://zhanglab.ccmb.med.umich.edu/DeepMSA/.

Supplementary information
Supplementary data are available at Bioinformatics online.
Robust empirical Bayes small area estimation with density power divergence
Authors: Sugasawa S 
Published: November 2019

Summary
A two-stage normal hierarchical model called the Fay–Herriot model and the empirical Bayes estimator are widely used to obtain indirect and model-based estimates of means in small areas. However, the performance of the empirical Bayes estimator can be poor when the assumed normal distribution is misspecified. This article presents a simple modification that makes use of density power divergence and proposes a new robust empirical Bayes small area estimator. The mean squared error and estimated mean squared error of the proposed estimator are derived based on the asymptotic properties of the robust estimator of the model parameters. We investigate the numerical performance of the proposed method through simulations and an application to survey data.
Regulation of cell–cell adhesion in prostate cancer cells by microRNA-96 through upregulation of E-Cadherin and EpCAM
Authors: Voss Gjendine , Haflidadóttir Benedikta S , Järemo Helena , Persson Margareta , Catela Ivkovic Tina , Wikström Pernilla , Ceder Yvonne 
Published: November 2019

Abstract
Prostate cancer is one of the most common cancers in men, yet the biology behind lethal disease progression and bone metastasis is poorly understood. In this study, we found elevated levels of microRNA-96 (miR-96) in prostate cancer bone metastasis samples. To determine the molecular mechanisms by which miR-96 deregulation contributes to metastatic progression, we performed an Argonaute2-immunoprecipitation assay, in which mRNAs associated with cell–cell interaction were enriched. The expression of two cell adhesion molecules, E-Cadherin and EpCAM, was upregulated by miR-96, and potential targets sites were identified in the coding sequences of their mRNAs. We further showed that miR-96 enhanced cell–cell adhesion between prostate cancer cells as well as their ability to bind to osteoblasts. Our findings suggest that increased levels of miR-96 give prostate cancer cells an advantage at forming metastases in the bone microenvironment due to increased cell–cell interaction. We propose that miR-96 promotes bone metastasis in prostate cancer patients by facilitating the outgrowth of macroscopic tumours in the bone.
Reporting From the Whites of Their Eyes: How Whiteness as Neoliberalism Promotes Racism in the News Coverage of “All Lives Matter”
Authors: Kil Sang Hea 
Published: November 2019

Abstract
This study evaluates how “all lives matter” (ALM) has advanced Whiteness in the news. Critical race theory’s critique of liberalism’s embrace of race-neutral racism is applied to the journalistic practice of objectivity. Racialized reporting is considered “fair” through the race-neutral journalistic practice of objectivity that mystifies the Whiteness of the news industry. Neoliberalism, a project of liberalism, creates structural racism that impacts society and the newsroom, where regulatory changes help to vertically integrate the media market. This media oligarchy threatens democratic principles, distorts racial reality, and advances Whiteness and its supremacy. Critical discourse analysis method was used on select, major, U.S. newspapers to reveal ALM’s three discursive strategies: (a) co-optation of Black social justice work; (b) fear of Black power or “blue”/police power; and (c) equating ALM with White power. Theoretical significance reflects that Whiteness as neoliberalism owns all, is all, and flattens all differences. The recommendation for resistance is color-conscious, intersectional journalism.
STAT3-miR-17/20 signalling axis plays a critical role in attenuating myocardial infarction following rapamycin treatment in diabetic mice
Authors: Samidurai Arun , Roh Sean K , Prakash Meeta , Durrant David , Salloum Fadi N , Kukreja Rakesh C , Das Anindita 
Published: November 2019

Abstract

Aims
Deregulation of mTOR (mammalian target of rapamycin) signalling occurs in diabetes, which exacerbates injury following myocardial infarction (MI). We therefore investigated the infarct-limiting effect of chronic treatment with rapamycin (RAPA, mTOR inhibitor) in diabetic mice following myocardial ischaemia/reperfusion (I/R) injury and delineated the potential protective mechanism.

Methods and results
Adult male diabetic (db/db) or wild-type (WT) (C57) mice were treated with RAPA (0.25 mg/kg/day, intraperitoneal) or vehicle (5% DMSO) for 28 days. The hearts from treated mice were subjected to global I/R in Langendorff mode. Cardiomyocytes, isolated from treated mice, were subjected to simulated ischaemia/reoxygenation (SI/RO) to assess necrosis and apoptosis. Myocardial infarct size was increased in diabetic heart following I/R as compared to WT. Likewise, enhanced necrosis and apoptosis were observed in isolated cardiomyocytes of diabetic mice following SI/RO. Treatment with RAPA reduced infarct size as well as cardiomyocyte necrosis and apoptosis of diabetes and WT mice. RAPA increased STAT3 phosphorylation and miRNA-17/20a expression in diabetic hearts. In addition, RAPA restored AKT phosphorylation (target of mTORC2) but suppressed S6 phosphorylation (target of mTORC1) following I/R injury. RAPA-induced cardioprotection against I/R injury as well as the induction of miR-17/20a and AKT phosphorylation were abolished in cardiac-specific STAT3-deficient diabetic mice, without alteration of S6 phosphorylation. The infarct-limiting effect of RAPA was obliterated in cardiac-specific miRNA-17-92-deficient diabetic mice. The post-I/R restoration of phosphorylation of STAT3 and AKT with RAPA were also abolished in miRNA-17-92-deficient diabetic mice. Additionally, RAPA suppressed the pro-apoptotic prolyl hydroxylase (Egln3/PHD3), a target of miRNA-17/20a in diabetic hearts, which was abrogated in miRNA-17-92-deficient diabetic mice.

Conclusion
Induction of STAT3-miRNA-17-92 signalling axis plays a critical role in attenuating MI in RAPA-treated diabetic mice. Our study indicates that chronic treatment with RAPA might be a promising pharmacological intervention for attenuating MI and improving prognosis in diabetic patients.
ChIPSummitDB: a ChIP-seq-based database of human transcription factor binding sites and the topological arrangements of the proteins bound to them
Authors: Czipa Erik , Schiller Mátyás , Nagy Tibor , Kontra Levente , Steiner László , Koller Júlia , Pálné-Szén Orsolya , Barta Endre 
Published: November 2019

AbstractChIP-seq reveals genomic regions where proteins, e.g. transcription factors (TFs) interact with DNA. A substantial fraction of these regions, however, do not contain the cognate binding site for the TF of interest. This phenomenon might be explained by protein–protein interactions and co-precipitation of interacting gene regulatory elements. We uniformly processed 3727 human ChIP-seq data sets and determined the cistrome of 292 TFs, as well as the distances between the TF binding motif centers and the ChIP-seq peak summits. ChIPSummitDB enables the analysis of ChIP-seq data using multiple approaches. The 292 cistromes and corresponding ChIP-seq peak sets can be browsed in GenomeView. Overlapping SNPs can be inspected in dbSNPView. Most importantly, the MotifView and PairShiftView pages show the average distance between motif centers and overlapping ChIP-seq peak summits and distance distributions thereof, respectively. In addition to providing a comprehensive human TF binding site collection, the ChIPSummitDB database and web interface allows for the examination of the topological arrangement of TF complexes genome-wide. ChIPSummitDB is freely accessible at http://summit.med.unideb.hu/summitdb/. The database will be regularly updated and extended with the newly available human and mouse ChIP-seq data sets.
Role of non-PTS dependent glucose permease (GlcU) in maintaining the fitness cost during acquisition of nisin resistance by Enterococcus faecalis
Authors: Kumar Sandeep , Narayan Kapil Singh , Shandilya Shruti , Sood Shiv Kumar , Kapila Suman 
Published: November 2019

ABSTRACT
Nisin is used for food preservation due to its antibacterial activity. However, some bacteria survive under the prevailing conditions owing to the acquisition of resistance. This study aimed to characterize nisin-resistant Enterococcus faecalis isolated from raw buffalo milk and investigate their fitness cost. FE-SEM, biofilm and cytochrome c assay were used for characterization. Growth kinetics, HPLC, qPCR and western blotting were performed to confer their fitness cost. Results revealed that nisin-resistant E. faecalis were morphologically different from sensitive strain and internalize more glucose. However, no significant difference was observed in the growth pattern of the resistant strain compared to that of the sensitive strain. A non-phosphotransferase glucose permease (GlcU) was found to be associated with enhanced glucose uptake. Conversely, Mpt, a major phosphotransferase system responsible for glucose uptake, did not play any role, as confirmed by gene expression studies and western blot analysis of HPr protein. The phosphorylation of His-15 residue of HPr phosphoprotein was reduced, while that of the Ser-46 residue increased with progression in nisin resistance, indicating that it may be involved in the regulation of pathogenicity. In conclusion, resistance imposes a significant fitness cost and GlcU plays a key role in maintaining the fitness cost in nisin-resistant variants.
Playing Analog Games Is Associated With Reduced Declines in Cognitive Function: A 68-Year Longitudinal Cohort Study
Authors: Altschul Drew M , Deary Ian J 
Published: November 2019

Abstract

Objectives
Playing analog games may be associated with better cognitive function but, to date, these studies have not had extensive longitudinal follow-up. Our goal was to examine the association between playing games and change in cognitive function from age 11 to age 70, and from age 70 to 79.

Method
Participants were 1,091 nonclinical, independent, community-dwelling individuals all born in 1936 and residing in Scotland. General cognitive function was assessed at ages 11 and 70, and hierarchical domains were assessed at ages 70, 73, 76, and 79 using a comprehensive cognitive battery of 14 tests. Games playing behaviors were assessed at ages 70 and 76. All models controlled for early life cognitive function, education, social class, sex, activity levels, and health issues. All analyses were preregistered.

Results
Higher frequency of playing games was associated with higher cognitive function at age 70, controlling for age 11 cognitive function, and the majority of this association could not be explained by control variables. Playing more games was also associated with less general cognitive decline from age 70 to age 79, and in particularly, less decline in memory ability. Increased games playing between 70 and 76 was associated with less decline in cognitive speed.

Discussion
Playing games were associated with less relative cognitive decline from age 11 to age 70, and less cognitive decline from age 70 to 79. Controlling for age 11 cognitive function and other confounders, these findings suggest that playing more games is linked to reduced lifetime decline in cognitive function.
Joint estimate of the co-seismic 2011 Tohoku earthquake fault slip and post-seismic viscoelastic relaxation by GRACE data inversion
Authors: Cambiotti G 
Published: November 2019

SUMMARY
Satellite-derived gravity data offer a novel perspective for understanding the physics of megathrust earthquakes at subduction zones. Nonetheless, their temporal resolution and observational errors make it difficult to discern the different phases of the seismic cycle, as the elastostatic deformation (co-seismic) and the stress relaxation by viscous flow (post-seismic). To overcome these difficulties and to take advantage of the physical constraints on the temporal evolution and on the spatial pattern of the earthquake-induced gravity disturbances, we have jointly estimated the fault slip of the 2011 Tohoku earthquake and the rheological stratification by means of a Bayesian inversion of GRACE data time series and within the framework of spherically symmetric self-gravitating compressible viscoelastic Earth models. This approach, in addition to improve the exploitation of satellite-derived gravity data, allows us (i) to constrain the fault slip taking advantage of information from both the co- and post-seismic signatures and (ii) to investigate the trade-off between the fault slip and the shallow rheological stratification. In this respect, it can be used to improve the modelling of crustal displacements from GPS data, even if their higher accuracy and temporal resolution allow to discriminate well the co-seismic signature from the others.
The Incidence and Prevalence of Anxiety, Depression, and Post-traumatic Stress Disorder in a National Cohort of US Veterans With Inflammatory Bowel Disease
Authors: Thakur Elyse R , Sansgiry Shubhada , Kramer Jennifer R , Waljee Akbar K , Gaidos Jill K , Feagins Linda A , Govani Shail M , Dindo Lilian , El-Serag Hashem B , Hou Jason K 
Published: November 2019

Abstract

Background
Patients with inflammatory bowel disease (IBD) are more susceptible to mental health problems than the general population; however, temporal trends in psychiatric diagnoses’ incidence or prevalence in the United States are lacking. We sought to identify these trends among patients with IBD using national Veterans Heath Administration data.

Methods
We ascertained the presence of anxiety, depression, or posttraumatic stress disorder among veterans with IBD (ulcerative colitis or Crohn’s disease) during fiscal years 2000–2015. Patients with prior anxiety, depression, or posttraumatic stress disorder before their first Veterans Health Administration IBD encounter were excluded to form the study cohort. We calculated annual prevalence, incidence rates, and age standardized and stratified by gender using a direct standardization method.

Results
We identified 60,086 IBD patients (93.9% male). The prevalence of anxiety, depression, and/or posttraumatic stress disorder increased from 10.8 per 100 with IBD in 2001 to 38 per 100 with IBD in 2015; 19,595 (32.6%) patients had a new anxiety, depression, and/or posttraumatic stress disorder diagnosis during the study period. The annual incidence rates of these mental health problems went from 6.1 per 100 with IBD in 2001 to 3.6 per 100 in 2015. This trend was largely driven by decline in depression.

Conclusions
The prevalence of anxiety, depression, and posttraumatic stress disorder is high among US veterans with IBD and increasing, given the chronicity of IBD and psychological diagnoses. Incidence, particularly depression, appears to be declining. Confirmation and reasons for this encouraging trend are needed.
Hatching Asynchrony in Oviraptorid Dinosaurs Sheds Light on Their Unique Nesting Biology
Authors: Yang T -R , Engler T , Lallensack J N , Samathi A , Makowska M , Schillinger B 
Published: November 2019

SynopsisDinosaur nesting biology has been an intriguing research topic, though dinosaur behaviors were relatively less illuminated because of the constraints of the fossil record. For instance, hatching asynchrony, where eggs in a single clutch hatch at different times, is unique to modern neoavian birds but was also suggested to be present in oviraptorid dinosaurs based on a possible partial clutch of four embryo-containing eggs from Mongolia. Unfortunately, unequivocal evidence for the origination of these eggs from a single clutch is lacking. Here we report a new, better preserved partial oviraptorid clutch with three embryo-containing eggs—a single egg (Egg I) and a pair (Egg II/III)—from the Late Cretaceous Nanxiong Group of Jiangxi Province, China. Geopetal features indicate that the pair of eggs was laid prior to the single egg. Neutron tomographic images in combination with osteological features indicate that the embryo of the single egg is less developed than those of the paired eggs. Eggshell histology suggests that the embryo-induced erosion in the paired eggs is markedly more pronounced than in the single egg, providing a new line of evidence for hatching asynchrony. The inferred hatching asynchrony in combination with previously surmised thermoregulatory incubation and communal nesting behaviors very likely suggests that oviraptorid dinosaurs presented a unique reproductive biology lacking modern analogs, which is contrary to the predominant view that their reproductive biology was intermediate between that of modern crocodiles and birds.
Clinical Management of the Microbiome in Irritable Bowel Syndrome
Authors: Andrews Christopher N , Sidani Sacha , Marshall John K 
Published: November 2019

Abstract

Background
A growing body of evidence suggests that dysbiosis contributes to the onset and symptomatology of irritable bowel syndrome (IBS) and other functional bowel disorders. Changes to the gastrointestinal microbiome may contribute to the underlying pathophysiology of IBS.

Methods
The present review summarizes the potential effects of microbiome changes on GI transit, intestinal barrier function, immune dysregulation and inflammation, gut–brain interactions and neuropsychiatric function.

Results
A multimodal approach to IBS management is recommended in accordance with current Canadian guidelines. Pharmacologic treatments are advised to target the presumed underlying pathophysiological mechanism, such as dysregulation of GI transit, peristalsis, intestinal barrier function and pain signalling. The management plan for IBS may also include treatments directed at dysbiosis, including dietary modification and use of probiotics, which may promote the growth of beneficial bacteria, affect intestinal gas production and modulate the immune response; and the administration of periodic short courses of a nonsystemic antibiotic such as rifaximin, which may re-establish microbiota diversity and improve IBS symptoms.

Conclusion
Dysregulated host–microbiome interactions are complex and the use of microbiome-directed therapies will necessarily be empiric in individual patients. A management algorithm comprising microbiome- and nonmicrobiome-directed therapies is proposed.
Experimental validation of a 2D–3D conversion method for estimation of multiple 3D characteristics of discrete elements
Authors: Ueda Takao 
Published: November 2019

Abstract
Accurate assessment of three-dimensional (3D) characteristics, such as the shape and size distribution, of discrete elements (e.g. particles, granules, grains, voids, crystals, cells and fibers) is required in various fields. But generally, in practice, two-dimensional (2D) instead of 3D assessment is conducted due to limitations in time, cost or measurement technology (as in microscopic observation of discrete elements). In this study, experimental validation was conducted for a 2D–3D conversion method, developed in 2018, which estimates multiple 3D parameters based on 2D counterparts, using an x-ray computed tomography analysis of silica sand. Six 3D parameters (volume, surface area, long-axis length, sphericity and long/middle and long/short axis ratios) were successfully estimated based on five measured 2D parameters (sectional area, perimeter, long-axis length, circularity and long/short axis ratio).
Survey of period variations of superhumps in SU UMa-type dwarf novae. X. The tenth year (2017)
Authors: Kato Taichi , Isogai Keisuke , Wakamatsu Yasuyuki , Hambsch Franz-Josef , Itoh Hiroshi , Tordai Tamás , Vanmunster Tonny , Dubovsky Pavol A , Kudzej Igor , Medulka Tomáš , Kimura Mariko , Ohnishi Ryuhei , Monard Berto , Pavlenko Elena P , Antonyuk Kirill A , Pit Nikolaj V , Antonyuk Oksana I , Babina Julia V , Baklanov Aleksei V , Sosnovskij Aleksei A , Pickard Roger D , Miller Ian , Maeda Yutaka , de Miguel Enrique , Brincat Stephen M , Licchelli Domenico , Cook Lewis M , Shugarov Sergey Yu , Zaostrojnykh Anna M , Chochol Drahomir , Golysheva Polina , Katysheva Natalia , Zubareva Alexandra M , Stone Geoff , Kasai Kiyoshi , Starr Peter , Littlefield Colin , Kiyota Seiichiro , Andreev Maksim V , Sergeev Alexandr V , Ruiz Javier , Myers Gordon , Simon Andrii O , Vasylenko Volodymyr V , Soldán Francisco , Ögmen Yenal , Nakajima Kazuhiro , Nelson Peter , Masi Gianluca , Menzies Kenneth , Sabo Richard , Bolt Greg , Dvorak Shawn , Stanek Krzysztof Z , Shields Joseph V , Kochanek Christopher S , Holoien Thomas W-S , Shappee Benjamin , Prieto José L , Kojima Tadashi , Nishimura Hideo , Kaneko Shizuo , Fujikawa Shigehisa , Stubbings Rod , Muyllaert Eddy , Poyner Gary , Moriyama Masayuki , Maehara Hiroyuki , Schmeer Patrick , Denisenko Denis 
Published: November 2019

AbstractContinuing the project described by Kato et al. (2009, PASJ, 61, S395), we collected times of superhump maxima for 102 SU UMa-type dwarf novae observed mainly during the 2017 season, and characterized these objects. WZ Sge-type stars identified in this study are PT And, ASASSN-17ei, ASASSN-17el, ASASSN-17es, ASASSN-17fn, ASASSN-17fz, ASASSN-17hw, ASASSN-17kd, ASASSN-17la, PNV J20205397$+$2508145, and TCP J00332502$-$3518565. We obtained new mass ratios for seven objects using growing superhumps (stage A). ASASSN-17gf is an EI Psc-type object below the period minimum. CRTS J080941.3$+$171528 and DDE 51 are objects in the period gap, and both showed a long-lasting phase of stage A superhumps. We also summarize the recent advances in understanding of SU UMa-type and WZ Sge-type dwarf novae.