bluuebunny/crossref_metadata_2025_split huggingface dataset:
ISOGlyP: de novo prediction of isoform-specific mucin-type O-glycosylation
Authors: Mohl Jonathon E , Gerken Thomas A , Leung Ming-Ying 
Published: July 2020

Abstract
Mucin-type O-glycosylation is one of the most common posttranslational modifications of proteins. The abnormal expression of various polypeptide GalNAc-transferases (GalNAc-Ts) which initiate and define sites of O-glycosylation are linked to many cancers and other diseases. Current O-glycosyation prediction programs utilize O-glycoproteomics data obtained without regard to the transferase isoform (s) responsible for the glycosylation. With 20 different GalNAc-Ts in humans, having an ability to predict and interpret O-glycosylation sites in terms of specific GalNAc-T isoforms is invaluable.
To fill this gap, ISOGlyP (Isoform-Specific O-Glycosylation Prediction) has been developed. Using position-specific enhancement values generated based on GalNAc-T isoform-specific amino acid preferences, ISOGlyP predicts the propensity that a site would be glycosylated by a specific transferase. ISOGlyP gave an overall prediction accuracy of 70% against in vivo data, which is comparable to that of the NetOGlyc4.0 predictor. Additionally, ISOGlyP can identify the known effects of long- and short-range prior glycosylation and can generate potential peptide sequences selectively glycosylated by specific isoforms.
ISOGlyP is freely available for use at ISOGlyP.utep.edu. The code is also available on GitHub (https://github.com/jonmohl/ISOGlyP).
Interferon-Induced Macrophage-Derived Exosomes Mediate Antiviral Activity Against Hepatitis B Virus Through miR-574-5p
Authors: Wu Wenyu , Wu Di , Yan Weiming , Wang Yongli , You Jie , Wan Xiaoyang , Xi Dong , Luo Xiaoping , Han Meifang , Ning Qin 
Published: July 2020

Abstract

Background
Interferon alfa (IFN-α) has been proved effective in treating chronic hepatitis B (CHB), owing to its ability to suppress hepatitis B surface antigen and hepatitis B virus (HBV) covalently closed circular DNA. However, the underlying mechanisms are unclear.

Methods
We investigated the antiviral activities of exosomes from responders and nonresponders to pegylated IFN-α (PegIFN-α) as well as the supernatants of IFN-α–treated macrophages derived from THP-1 (the human leukemia monocyte cell line). Then the expression profiles of exosomal microRNAs (miRNAs) were analyzed using miRNA sequencing. The luciferase reporter assay was used to locate the binding position of HBV genomic sequence targeted by the identified miRNA.

Results
Exosomes from PegIFN-α–treated patients, particularly responders, as well as the supernatants of IFN-α–treated macrophages exhibited anti-HBV activities, as manifested by the suppression of hepatitis B surface antigen, hepatitis B e antigen, HBV DNA, and covalently closed circular DNA levels in HBV-related cell lines. PegIFN-α treatment up-regulated exosomal hsa-miR-193a-5p, hsa-miR-25-5p, and hsa-miR-574-5p, which could partially inhibit HBV replication and transcription, and hsa-miR-574-5p reduced pregenomic RNA and polymerase messenger RNA levels by binding to the 2750–2757 position of the HBV genomic sequence.

Conclusions
Exosomes can transfer IFN-α–related miRNAs from macrophages to HBV-infected hepatocytes, and they exhibit antiviral activities against HBV replication and expression.
Why International Organizations Commit to Liberal Norms
Authors: Tallberg Jonas , Lundgren Magnus , Sommerer Thomas , Squatrito Theresa 
Published: July 2020

AbstractRecent decades have witnessed the emergence and spread of a broad range of liberal norms in global governance, among them sustainable development, gender equality, and human security. While existing scholarship tells us a lot about the trajectories of particular norms, we know much less about the broader patterns and sources of commitments to liberal norms by international organizations (IOs). This article offers the first comparative large-N analysis of such commitments, building on a unique dataset on IO policy decisions over the time period 1980–2015. Distinguishing between deep norm commitment and shallow norm recognition, the analysis produces several novel findings. We establish that IOs’ deeper commitments to liberal norms primarily are driven by internal conditions: democratic memberships and institutional designs more conducive to norm entrepreneurship. In contrast, legitimacy standards in the external environment of IOs, often invoked in existing research, mainly account for shallower recognition or “talk” of norms.
Digestibility of amino acids and concentrations of metabolizable energy and net energy are greater in high-shear dry soybean expellers than in soybean meal when fed to growing pigs
Authors: Rodriguez Diego A , Lee Su A , Stein Hans H 
Published: July 2020

Abstract
Soybean expellers may be produced by dry extrusion and mechanical oil pressing of soybeans, but there is limited information about the nutritional value of expellers produced via this procedure. Therefore, 2 experiments were conducted to test the hypothesis that standardized ileal digestibility (SID) of CP and amino acids (AA), apparent total tract digestibility (ATTD) of energy and total dietary fiber (TDF), and concentrations of DE, ME, and NE are greater in soybean expellers than in soybean meal (SBM) when fed to growing pigs. Pigs were the offspring of Line 359 boars mated to Camborough females (Pig Improvement Company, Hendersonville, TN). In experiment 1, nine growing barrows (initial BW: 55.98 kg ± 13.75 kg) with T-cannulas installed in the distal ileum were allotted to 1 of 3 diets using a triplicated 3 × 3 Latin square design with 3 periods. Two diets were formulated to contain 35% soybean expellers or 33% SBM as the sole source of AA. A N-free diet was used to determine basal endogenous losses of AA. Ileal digesta were collected on days 6 and 7 of each 7-d period. Results indicated that the SID of most indispensable and dispensable AA were greater (P &lt; 0.05) or tended (P &lt; 0.10) to be greater in soybean expellers than in SBM. In experiment 2, a corn-based diet and 2 diets based on corn and each of the 2 soybean products were formulated. Twenty-four growing barrows (initial BW: 44.88 kg ± 2.17 kg) were allotted to 1 of the 3 diets with 8 pigs per diet. Urine and fecal samples were collected for 4 d after 5 d of adaptation. Results indicated that the ATTD of energy and TDF was not different between soybean expellers and SBM, but the ATTD of TDF in the 2 soybean products was greater (P &lt; 0.05) than in corn. Concentrations of DE and ME in soybean expellers were greater (P &lt; 0.05) compared with corn or SBM. Soybean expellers had greater (P &lt; 0.05) calculated NE compared with SBM, but there was no difference in NE between corn and soybean expellers. In conclusion, values for SID of most AA and DE, ME, and NE in soybean expellers were greater than in SBM.
A new family and superfamily for the southern giant crab of Australia, Pseudocarcinus gigas (Lamarck, 1818) (Decapoda: Brachyura)
Authors: Ng Peter K L , Davie Peter J F 
Published: July 2020

AbstractThe Australian southern giant crab, Pseudocarcinus gigas (Lamarck, 1818), has traditionally been placed in the families Oziidae Dana, 1851 or Menippidae Ortmann, 1893 (superfamily Eriphioidea MacLeay, 1838). Previous genetic studies questioned the validity of this classification as the molecular markers placed it far from all eriphioid lineages. A morphological re-examination of P. gigas shows that it possesses a suite of unusual characters in the structure of the antennae, antennules, epistome, carapace, pereopods, thoracic sternum, and vulvae that show it is different from other Eriphioidea as well as all other extant heterotremes, confirming the genetic results. A new family, Pseudocarcinidae, and a new superfamily, Pseudocarcinoidea, both monotypic, are here established for P. gigas.
Comparing fitness measures and the influence of age of first reproduction in Columbian ground squirrels
Authors: Rubach Kristin K , Dobson F Stephen , Zinner Bertram , Murie Jan O , Viblanc Vincent A 
Published: July 2020

Abstract
The timing of life-history traits may have strong influences on the evolution of life cycles and on population demography. This is especially true of the age at which females first reproduce (Cole’s principle). We examined whether the age at which females first reproduce influences fitness in Columbian ground squirrels (Urocitellus columbianus), for which females varied in the age at which they initially produce weaned offspring, from ages 1 through 5 years. With 148 females with complete known life spans in a 28-year data set, we examined four fitness measures: individual fitness (λ ind), individual fitness relative to the pattern of growth of the population (λ rel), lifetime reproductive success (LRS), and LRS relative to the total LRS for each female’s cohort (LRSrel). These metrics were calculated for offspring produced at the time of weaning and offspring that survived to emerge after their first hibernation period. Individual fitness (λ ind) was significantly associated with population growth during a female’s lifetime (λ Leslie; R2 = 0.523, P &lt; 0.0001), indicating the need to adjust individual fitness for demonstrated changes in population growth and thus producing a relative individual fitness index (λ rel). We regressed λ rel on age at first reproduction, and found significant selection favoring earlier reproductive success (β ± SE = −0.20 ± 0.06; R2 = 0.306, P &lt; 0.0001). When using an earlier (offspring at weaning) versus later (those that survived their first hibernation) measure of fecundity, we found that the latter introduced considerable variation, likely environmental, into the estimate of selection. This greatly weakened the regression of relative fitness on the age at first successful reproduction. LRS and LRSrel exhibited nonsignificant changes with age at first reproduction. Finally, those females that reproduced successfully at younger ages had similar litter sizes but significantly shorter life spans than females that matured when older, perhaps reflecting costs to early reproduction.
High-resolution VLA low radio frequency observations of the Perseus cluster: radio lobes, mini-halo, and bent-jet radio galaxies
Authors: Gendron-Marsolais M , Hlavacek-Larrondo J , van Weeren R J , Rudnick L , Clarke T E , Sebastian B , Mroczkowski T , Fabian A C , Blundell K M , Sheldahl E , Nyland K , Sanders J S , Peters W M , Intema H T 
Published: July 2020

ABSTRACT
We present the first high-resolution 230–470 MHz map of the Perseus cluster obtained with the Karl G. Jansky Very Large Array. The high dynamic range and resolution achieved have allowed the identification of previously unknown structures in this nearby galaxy cluster. New hints of sub-structures appear in the inner radio lobes of the brightest cluster galaxy NGC 1275. The spurs of radio emission extending into the outer X-ray cavities, inflated by past nuclear outbursts, are seen for the first time at these frequencies, consistent with spectral aging. Beyond NGC 1275, we also analyse complex radio sources harboured in the cluster. Two new distinct, narrowly collimated jets are visible in IC 310, consistent with a highly projected narrow-angle tail radio galaxy infalling into the cluster. We show how this is in agreement with its blazar-like behaviour, implying that blazars and bent-jet radio galaxies are not mutually exclusive. We report the presence of filamentary structures across the entire tail of NGC 1265, including two new pairs of long filaments in the faintest bent extension of the tail. Such filaments have been seen in other cluster radio sources such as relics and radio lobes, indicating that there may be a fundamental connection between all these radio structures. We resolve the very narrow and straight tail of CR 15 without indication of double jets, so that the interpretation of such head–tail sources is yet unclear. Finally, we note that only the brightest western parts of the mini-halo remain, near NGC 1272 and its bent double jets.
On the distribution of fluxes of gamma-ray blazars: hints for a stochastic process?
Authors: Tavecchio F , Bonnoli G , Galanti G 
Published: July 2020

ABSTRACT
We examine a model for the observed temporal variability of powerful blazars in the γ-ray band in which the dynamics is described in terms of a stochastic differential equation, including the contribution of a deterministic drift and a stochastic term. The form of the equation is motivated by the current astrophysical framework, accepting that jets are powered through the extraction of the rotational energy of the central supermassive black hole mediated by magnetic fields supported by a so-called magnetically arrested accretion disc. We apply the model to the γ-ray light curves of several bright blazars and we infer the parameters suitable to describe them. In particular, we examine the differential distribution of fluxes (dN/dFγ) and we show that the predicted probability density function for the assumed stochastic equation naturally reproduces the observed power-law shape at large fluxes $\mathrm{ d}N/\mathrm{ d}F_{\gamma } \propto F_{\gamma }^{-\alpha }$ with α &gt; 2.
Alignment and quantification of ChIP-exo crosslinking patterns reveal the spatial organization of protein–DNA complexes
Authors: Yamada Naomi , Rossi Matthew J , Farrell Nina , Pugh B Franklin , Mahony Shaun 
Published: July 2020

Abstract
The ChIP-exo assay precisely delineates protein–DNA crosslinking patterns by combining chromatin immunoprecipitation with 5′ to 3′ exonuclease digestion. Within a regulatory complex, the physical distance of a regulatory protein to DNA affects crosslinking efficiencies. Therefore, the spatial organization of a protein–DNA complex could potentially be inferred by analyzing how crosslinking signatures vary between its subunits. Here, we present a computational framework that aligns ChIP-exo crosslinking patterns from multiple proteins across a set of coordinately bound regulatory regions, and which detects and quantifies protein–DNA crosslinking events within the aligned profiles. By producing consistent measurements of protein–DNA crosslinking strengths across multiple proteins, our approach enables characterization of relative spatial organization within a regulatory complex. Applying our approach to collections of ChIP-exo data, we demonstrate that it can recover aspects of regulatory complex spatial organization at yeast ribosomal protein genes and yeast tRNA genes. We also demonstrate the ability to quantify changes in protein–DNA complex organization across conditions by applying our approach to analyze Drosophila Pol II transcriptional components. Our results suggest that principled analyses of ChIP-exo crosslinking patterns enable inference of spatial organization within protein–DNA complexes.
Decoding the epitranscriptional landscape from native RNA sequences
Authors: Jenjaroenpun Piroon , Wongsurawat Thidathip , Wadley Taylor D , Wassenaar Trudy M , Liu Jun , Dai Qing , Wanchai Visanu , Akel Nisreen S , Jamshidi-Parsian Azemat , Franco Aime T , Boysen Gunnar , Jennings Michael L , Ussery David W , He Chuan , Nookaew Intawat 
Published: July 2020

Abstract
Traditional epitranscriptomics relies on capturing a single RNA modification by antibody or chemical treatment, combined with short-read sequencing to identify its transcriptomic location. This approach is labor-intensive and may introduce experimental artifacts. Direct sequencing of native RNA using Oxford Nanopore Technologies (ONT) can allow for directly detecting the RNA base modifications, although these modifications might appear as sequencing errors. The percent Error of Specific Bases (%ESB) was higher for native RNA than unmodified RNA, which enabled the detection of ribonucleotide modification sites. Based on the %ESB differences, we developed a bioinformatic tool, epitranscriptional landscape inferring from glitches of ONT signals (ELIGOS), that is based on various types of synthetic modified RNA and applied to rRNA and mRNA. ELIGOS is able to accurately predict known classes of RNA methylation sites (AUC &gt; 0.93) in rRNAs from Escherichiacoli, yeast, and human cells, using either unmodified in vitro transcription RNA or a background error model, which mimics the systematic error of direct RNA sequencing as the reference. The well-known DRACH/RRACH motif was localized and identified, consistent with previous studies, using differential analysis of ELIGOS to study the impact of RNA m6A methyltransferase by comparing wild type and knockouts in yeast and mouse cells. Lastly, the DRACH motif could also be identified in the mRNA of three human cell lines. The mRNA modification identified by ELIGOS is at the level of individual base resolution. In summary, we have developed a bioinformatic software package to uncover native RNA modifications.
Giant Fusiform and Dolichoectatic Aneurysms of the Basilar Trunk and Vertebrobasilar Junction—Clinicopathological and Surgical Outcome
Authors: Nakatomi Hirofumi , Kiyofuji Satoshi , Ono Hideaki , Tanaka Minoru , Kamiyama Hiroyasu , Takizawa Katsumi , Imai Hideaki , Saito Nobuhito , Shiokawa Yoshiaki , Morita Akio , Flemming Kelly D , Link Michael J 
Published: July 2020

Abstract

BACKGROUND
Giant fusiform and dolichoectatic aneurysms of the basilar trunk and vertebrobasilar junction (BTVBJ-GFDA) are extremely difficult to treat.

OBJECTIVE
To evaluate factors influencing survival and outcome of BTVBJ-GFDA by performing a retrospective multicenter cohort study.

METHODS
A total of 32 patients with BTVBJ-GFDA were included in this study. Clinicopathological characteristics, treatment measures, and outcomes were collected from medical records and imaging studies. Autopsy and histological findings of the aneurysm and adjacent brain tissue were also obtained in 9 cases.

RESULTS
A total of 11 patients did not undergo surgery, of whom 10 died; 3 from progressive brainstem compression, 4 from subarachnoid hemorrhage, 2 from brainstem infarction, and 1 from associated atherosclerotic disease. The remaining 21 patients underwent a surgical treatment, consisting of immediately proximal parent artery occlusion, remotely proximal parent artery occlusion, clip reconstruction, and distal bypass and achieved significantly longer overall survival compared with those who received conservative therapy (adjusted hazard ratio 1.508, 95% CI 1.058-2.148, P = .02). Histological examination of the aneurysms demonstrated staged clots, open lumen, and intrathrombotic channels with endothelial lining. The patients younger than 45 yr of age showed statistically longer survival than those equal and older than 45 yr (P = .03).

CONCLUSION
Surgical intervention achieved greater survival than conservative management in BTVBJ-GFDA. Narrow ideal treatment window of the blood flow within the aneurysm to maintain sufficient but not excess supply should be targeted based on the hemodynamics of both the posterior communicating arteries and perforating vessel collaterals.
Out of the West: Formation of a Permanent Plague Reservoir in South-Central Germany (1349–1356) and its Implications
Authors: Slavin Philip 
Published: July 2020

Abstract
This article deals with the origins and spread of the second outbreak of fourteenth-century plague pandemic, the pestis secunda, which swept over West Eurasia and North Africa between 1356 and 1366. Unlike the Black Death, its immediate predecessor, which seems to have originated in Central Asia, the pestis secunda emerged in Central Germany, most likely in the Frankfurt region, in summer 1356. Having seeded its new reservoir, the plague radiated from Central Germany, a landlocked region, into other parts of West Eurasia and North Africa, via inland routes. The inland mode of transmission is at odds with the geographic spread of the Black Death, whereby the plague arrived in West Eurasian and North African ports via maritime trade routes. To appreciate the appearance of the Central Germany plague reservoir in the early 1350s, the wider ecological, climatic and socio-economic context of the Frankfurt region is scrutinized, on the basis of textual, palaeoclimatic and palaeogenetic evidence. Although beyond the remit of this article, it argues that the Central German reservoir may have become the origin of recurrent late-medieval and early-modern plague outbreaks.
Social optimism biases are associated with cortical thickness
Authors: Moser Dominik Andreas , Dricu Mihai , Wiest Roland , Schüpbach Laurent , Aue Tatjana 
Published: July 2020

Abstract
Optimism biases denote the tendency to see future desirable events as being more likely to happen to oneself than undesirable events. Such biases are important for mental health and may extend to other individuals or social groups (social optimism biases). However, little is known about whether social optimism biases relate to brain structure. Using sparse canonical correlation analysis, we associated cortical thickness (assessed by magnetic resonance imaging) with measures of social and personal optimism bias, trait optimism and related concepts. We identified a defensive self-enhancement dimension that associated significantly and reliably with the cortical thickness of the insula and inferior frontal cortex. This self-enhancement dimension included unfavorable biases toward unpopular out-groups and indicators of personal optimism and pessimism. A shared biological substrate underlying future expectancies that subserves the promotion of the self and the denigration of unpopular out-groups may render society-wide efforts to counteract stereotyping particularly difficult: such efforts may hinder the establishment of adaptive personal optimism biases.
Attentional conditions differentially affect early, intermediate and late neural responses to fearful and neutral faces
Authors: Schindler Sebastian , Bruchmann Maximilian , Steinweg Anna-Lena , Moeck Robert , Straube Thomas 
Published: July 2020

AbstractThe processing of fearful facial expressions is prioritized by the human brain. This priority is maintained across various information processing stages as evident in early, intermediate and late components of event-related potentials (ERPs). However, emotional modulations are inconsistently reported for these different processing stages. In this pre-registered study, we investigated how feature-based attention differentially affects ERPs to fearful and neutral faces in 40 participants. The tasks required the participants to discriminate either the orientation of lines overlaid onto the face, the sex of the face or the face’s emotional expression, increasing attention to emotion-related features. We found main effects of emotion for the N170, early posterior negativity (EPN) and late positive potential (LPP). While N170 emotional modulations were task-independent, interactions of emotion and task were observed for the EPN and LPP. While EPN emotion effects were found in the sex and emotion tasks, the LPP emotion effect was mainly driven by the emotion task. This study shows that early responses to fearful faces are task-independent (N170) and likely based on low-level and configural information while during later processing stages, attention to the face (EPN) or—more specifically—to the face’s emotional expression (LPP) is crucial for reliable amplified processing of emotional faces.