bluuebunny/crossref_metadata_2025_split huggingface dataset:
Th17 cells give rise to Th1 cells that are required for the pathogenesis of colitis
Authors: Harbour Stacey N. , Maynard Craig L. , Zindl Carlene L. , Schoeb Trenton R. , Weaver Casey T. 
Published: May 2015

SignificanceThe Th17 subset of CD4+T cells are important in the pathogenesis of inflammatory bowel disease (IBD), but the mechanisms of their actions, particularly the role of the development of IFN-γ–producing progeny of Th17 cells (Th1-like cells), are incompletely understood. Here, we show in a mouse model of Th17-driven IBD that transition of Th17 precursors to Th1-like cells is absolutely required for disease, because Th17 cells deficient in IFN-γ fail to induce intestinal inflammation. This transition is dependent on the transcription factors T-bet and, to a lesser extent, Stat4. These findings are relevant for clinical strategies that target IBD and suggest that focusing on both the Th17 and Th1-like arms of disease may be beneficial in therapy design.
Virus-induced translational arrest through 4EBP1/2-dependent decay of 5′-TOP mRNAs restricts viral infection
Authors: Hopkins Kaycie C. , Tartell Michael A. , Herrmann Christin , Hackett Brent A. , Taschuk Frances , Panda Debasis , Menghani Sanjay V. , Sabin Leah R. , Cherry Sara 
Published: May 2015

Significance
Rift Valley fever virus (RVFV), a mosquito-transmitted bunyavirus, blocks the two common methods of antiviral translational shutdown, PKR and type I interferon. However, it has previously been shown that RVFV infection halts protein production in infected human cells. Here, we demonstrate that RVFV is restricted by a previously unknown mechanism of antiviral translational shutdown, wherein 5′-terminal oligopyrimidine (5′-TOP) mRNAs encoding the core translational machinery are selectively degraded by the RNA decapping enzyme NUDT16 during RVFV infection, and that this decay is triggered in response to mTOR attenuation via the translational repressor 4EBP1/2 axis. We present a previously unknown mechanism for translational shutdown in response to viral infection and identify mTOR attenuation as a potential therapeutic target against bunyaviral infection.
The messenger RNA decapping and recapping pathway in
Trypanosoma
Authors: Ignatochkina Anna V. , Takagi Yuko , Liu Yancheng , Nagata Kyosuke , Ho C. Kiong 
Published: May 2015

Significance
The 5′ end of eukaryotic mRNA is capped and methylated to protect mRNA from degradation and enhance protein synthesis. However, the cap can be removed from mRNA by decapping. We identified a recapping enzyme with 5′-monophosphate RNA kinase activity from trypanosome and provide evidence that decapped transcripts can be recapped to regenerate translatable mRNA. The kinase activity is dependent on mRNA leader sequence and is stimulated by hypermethylation found in the trypanosome mRNA. We also identify a trypanosome decapping enzyme that removes cap structure from the mRNA, but is less active on hypermethylated capped mRNA. These results suggest that hypermethylated cap structure can influence certain transcripts to be preferentially decapped or recapped during the parasite life cycle.
Kinetically coupled folding of a single HIV-1 glycoprotein 41 complex in viral membrane fusion and inhibition
Authors: Jiao Junyi , Rebane Aleksander A. , Ma Lu , Gao Ying , Zhang Yongli 
Published: May 2015

Significance
Enveloped viruses infect cells via fusion of viral and host cell membranes mediated by highly conserved fusion proteins. HIV-1 glycoprotein 41 (gp41) represents a family of fusion proteins with similar structures and fusion mechanisms. They couple their energetic folding to draw two membranes close for fusion, forming trimers of helical hairpins. Yet, the energy release, force generation, and kinetics associated with folding of these proteins are poorly quantified. We found that gp41 hairpins fold sequentially but in a kinetically coupled manner and that an anti-HIV drug blocked gp41 folding by a new mechanism. As major proteins on viral surfaces, fusion proteins are primary targets for vaccine development and fusion inhibitors to intervene in major infectious diseases such as AIDS, Ebola, and influenza.
Temperate and lytic bacteriophages programmed to sensitize and kill antibiotic-resistant bacteria
Authors: Yosef Ido , Manor Miriam , Kiro Ruth , Qimron Udi 
Published: May 2015

Significance
Antibiotic resistance of pathogens is a growing concern to human health, reviving interest in phage therapy. This therapy uses phages (natural bacterial enemies) to kill pathogens. However, it encounters many obstacles such as delivery barriers into the tissues and bacterial resistance to phages. Here, we use phages for delivering a programmable DNA nuclease, clustered regularly interspaced short palindromic repeats (CRISPR)–CRISPR-associated (Cas), to reverse antibiotic resistance and eliminate the transfer of resistance between strains. This approach combines CRISPR-Cas delivery with lytic phage selection of antibiotic-sensitized bacteria. The strategy may reduce the prevalence of antibiotic-resistant bacteria in treated surfaces and on skin of medical personnel, as it uses phages in a unique way that overcomes many of the hurdles encountered by phage therapy.
Pds5 regulators segregate cohesion and condensation pathways in
Saccharomyces cerevisiae
Authors: Tong Kevin , Skibbens Robert V. 
Published: May 2015

Significance
Chromosomes are replicated during S phase to produce sister chromatids that remain tethered together by protein complexes termed cohesins. In preparation for mitosis, sister chromatids condense into discrete, compact chromosomes, a process that also requires cohesins. At anaphase onset, cohesins are inactivated, allowing each chromatid to segregate away from its sister and into newly forming daughter cells. The requirement for cohesin in both cohesion and condensation suggests that these pathways are intimately coupled. Here, we identify cohesin regulators through which cohesin functions for the first time can be isolated from one another. These regulations will be critical for elucidating post-translation modifications through which cohesin roles in chromatin metabolism can be studied in isolation.
Rodent reservoirs of future zoonotic diseases
Authors: Han Barbara A. , Schmidt John Paul , Bowden Sarah E. , Drake John M. 
Published: May 2015

SignificanceForecasting reservoirs of zoonotic disease is a pressing public health priority. We apply machine learning to datasets describing the biological, ecological, and life history traits of rodents, which collectively carry a disproportionate number of zoonotic pathogens. We identify particular rodent species predicted to be novel zoonotic reservoirs and geographic regions from which new emerging pathogens are most likely to arise. We also describe trait profiles—complexes of biological features—that distinguish reservoirs from nonreservoirs. Generally, the most permissive rodent reservoirs display a fast-paced life history strategy, maximizing near-term fitness by having many altricial young that begin reproduction early and reproduce frequently. These findings may constitute an important lead in guiding the search for novel disease reservoirs in the wild.
Gradual decline in mobility with the adoption of food production in Europe
Authors: Ruff Christopher B. , Holt Brigitte , Niskanen Markku , Sladek Vladimir , Berner Margit , Garofalo Evan , Garvin Heather M. , Hora Martin , Junno Juho-Antti , Schuplerova Eliska , Vilkama Rosa , Whittey Erin 
Published: May 2015

Significance
Declining mobility levels following the Pleistocene had profound effects on human demography, social organization, and health, but the exact timing and pace of this critical change are unknown. Here we examine direct evidence for changing mobility levels from limb bone structural characteristics in a large sample of European skeletons spanning the past 30,000 y. Our results show that mobility first declined during the Neolithic, at the onset of food production, but that the decline was gradual, continuing for several thousand years as agriculture intensified. No change in relative limb strength occurred during the past 2,000 y. Thus, the more gracile modern human skeleton is a result of increased sedentism tied to food production, not subsequent mechanization and industrialization.
Laser printing hierarchical structures with the aid of controlled capillary-driven self-assembly
Authors: Hu Yanlei , Lao Zhaoxin , Cumming Benjamin P. , Wu Dong , Li Jiawen , Liang Haiyi , Chu Jiaru , Huang Wenhao , Gu Min 
Published: May 2015

Significance
We propose a strategy to realize designable hierarchical functional structures via laser printing capillary-assisted self-assembly (LPCS). Ultrafast laser printing is applied for building unit blocks and capillary force is finely tuned as driving force. Diverse structures are successfully fabricated by controlling the spatial arrangements, heights, diameters of pillars, and the evaporation process. The ability of these LPCS structures to selectively trap and release microobjects suggests enormous potential applications in the fields of chemistry, biomedicine, and microfluidic engineering.
Retinal waves regulate afferent terminal targeting in the early visual pathway
Authors: Failor Samuel , Chapman Barbara , Cheng Hwai-Jong 
Published: May 2015

Significance
Spontaneous neural activity is known to play a role in the maturation of nascent neural circuitry. Here we show for the first time a role for early spontaneous correlated retinal activity (i.e., retinal waves) in regulating the laminar targeting and functional development of the retinogeniculate pathway in the monocular condition—a condition where intereye competition and eye-specific segregation are not present. These findings demonstrate the importance of intraeye competition in early visual pathway circuit development. Our results provide a revision to the model of retinogeniculate development and to our general understanding of how neural activity guides the establishment of proper connectivity in the developing brain.
Subcortical barrelette-like and barreloid-like structures in the prosimian galago (
Otolemur garnetti
)
Authors: Sawyer Eva Kille , Liao Chia-Chi , Qi Hui-Xin , Balaram Pooja , Matrov Denis , Kaas Jon H. 
Published: May 2015

Significance
Nearly all mammals have tactile hairs. Distinct modular representations of the vibrissae within the central nervous system have been found in five mammalian orders (Marsupialia, Carnivora, Eulipotyphla, Lagomorpha, Rodentia). This work documents vibrissae-related modules in a sixth order: Primata. The presence of subcortical barrel-like modules in the prosimian galagos suggests broad similarities in the processing of sensory information among rodents and primates. Additionally, the thalamic “galagounculus” appears to show the representation of the entire body surface with unusual clarity.
Predictive information in a sensory population
Authors: Palmer Stephanie E. , Marre Olivier , Berry Michael J. , Bialek William 
Published: May 2015

Significance
Prediction is an essential part of life. However, are we really “good” at making predictions? More specifically, are pieces of our brain close to being optimal predictors? To assess the efficiency of prediction, we need to measure the information that neurons carry about the future of our sensory experiences. We show how to do this, at least in simplified contexts, and find that groups of neurons in the retina indeed are close to maximally efficient at separating predictive information from the nonpredictive background. Efficient coding of predictive information is a principle that can be applied at every stage of neural computation.
GABARAPs regulate PI4P-dependent autophagosome:lysosome fusion
Authors: Wang Hanzhi , Sun Hui-Qiao , Zhu Xiaohui , Zhang Li , Albanesi Joseph , Levine Beth , Yin Helen 
Published: May 2015

Significance
Autophagy is an essential homeostatic process that is critically important for maintaining health and that is dysregulated in multiple devastating diseases. The steps in the final stages of autophagy that culminate in autophagosome:lysosome fusion are not well understood. The γ-aminobutyric acid receptor-associated protein (GABARAP) family of Atg8 (autophagy-related 8) proteins has been implicated in autophagosome maturation. Here we report that phosphatidylinositol 4-kinase IIα (PI4KIIα), a lipid kinase that generates phosphatidylinositol 4-phosphate (PI4P) and binds GABARAPs, is recruited to autophagosomes by GABARAPs. Furthermore, PI4P generation by PI4KIIα, but not by PI4KIIIβ, another major mammalian PI4K, promotes autophagosome fusion with lysosomes. Our results establish for the first time to our knowledge that PI4KIIα is a specific downstream effector of GABARAP and that PI4P has a key role in the final stage of autophagy.
AMCase is a crucial regulator of type 2 immune responses to inhaled house dust mites
Authors: Kim Lark Kyun , Morita Rimpei , Kobayashi Yasushi , Eisenbarth Stephanie C. , Lee Chun Geun , Elias Jack , Eynon Elizabeth E. , Flavell Richard A. 
Published: May 2015

SignificanceMillions of people are affected by asthma and that number is growing. A clear understanding of how the disease develops is lacking. The immune responses to inhaled allergens like house dust mite (HDM) provide much of the basis of asthma. Acidic mammalian chitinase (AMCase) is an enzyme that degrades chitin, a major structural polymer in the exoskeleton of HDM. By the use of a newly generated enzymatically dead AMCase knockin mouse, we found that AMCase enzymatic activity is of critical importance in the control of type 2 immune responses to inhaled HDM. This discovery may help the understanding of the mechanisms that govern the development of chitin-related asthma and allergy and may lead to new therapeutic strategies in these disorders.
Preparation of proteoglycan from salmon nasal cartilage under nondenaturing conditions
Authors: Tatara Yota , Suto Shinichiro , Sasaki Yoshitaka , Endo Masahiko 
Published: May 2015

Abstract
Salmon nasal cartilage was micronized in ethanol using a rotor–stator homogenizer for the high yield of proteoglycan extraction. This procedure also brought about depressing the degradation of proteoglycan and the contamination of collagens. Proteoglycan was extracted by 4 M magnesium chloride and isolated by anion-exchange chromatography. The gel filtration HPLC and the antibody reactivity showed that the core protein was intact.
Possible role of NAD-dependent glyceraldehyde-3-phosphate dehydrogenase in growth promotion of Arabidopsis seedlings by low levels of selenium
Authors: Takeda Toru , Fukui Yuki 
Published: May 2015

Abstract
We explored functional significance of selenium (Se) in Arabidopsis physiology. Se at very low concentrations in cultivation exerted a considerable positive effect on Arabidopsis growth with no indication of oxidative stress, whereas Se at higher concentrations significantly suppressed the growth and brought serious oxidative damage. Respiration, ATP levels, and the activity of NAD-dependent glyceraldehyde-3-phosphate dehydrogenase (NAD-GAPDH) were enhanced in Arabidopsis grown in the medium containing 1.0 μM Se. Addition of an inhibitor of glutathione (GSH) synthesis to the medium abolished both of the Se-dependent growth promotion and NAD-GAPDH up-regulation. Assay of NAD-GAPDH purified from seedlings subjected to Se interventions raised the possibility of a direct connection between the activity of this enzyme and Arabidopsis growth. These results reveal that trace amounts of Se accelerate Arabidopsis growth, and suggest that this pro-growth effect of Se arises enhancing mitochondrial performance in a GSH-dependent manner, in which NAD-GAPDH may serve as a key regulator.
Geometric Satake, Springer correspondence, and small representations II
Authors: Achar Pramod , Henderson Anthony , Riche Simon 
Published: May 2015

For a split reductive group scheme

G
ˇ

\check G

over a commutative ring

k
\Bbbk

with Weyl group

W
W

, there is an important functor

R
e
p

(

G
ˇ

,
k
)
→

R
e
p

(
W
,
k
)

{\mathsf {Rep}}(\check G,\Bbbk )\to {\mathsf {Rep}}(W,\Bbbk )

defined by taking the zero weight space. We prove that the restriction of this functor to the subcategory of small representations has an alternative geometric description, in terms of the affine Grassmannian and the nilpotent cone of the Langlands dual group

G
G

. The translation from representation theory to geometry is via the Satake equivalence and the Springer correspondence. This generalizes the result for the

k
=

C

\Bbbk =\mathbb {C}

case proved by the first two authors, and also provides a better explanation than in the earlier paper, since the current proof is uniform across all types.
Associations of Reducing Sedentary Time With Vascular Function and Insulin Sensitivity in Older Sedentary Adults
Authors: Suboc Tisha B. , Knabel Daniel , Strath Scott J. , Dharmashankar Kodlipet , Coulliard Allison , Malik Mobin , Haak Kristoph , Widlansky Michael E. 
Published: May 2015

Abstract

BACKGROUND
We previously reported increased moderate-intensity (3–6 metabolic equivalents (METs)) physical activity (PA) reverses aging-associated vascular endothelial dysfunction, a surrogate marker of cardiovascular risk. Whether reductions in sedentary time alone contribute to this improvement is unknown.

METHODS
Data from 96 adults (aged ≥50 years) enrolled in a randomized control trial evaluating a 12-week intervention to increase PA in sedentary individuals were analyzed. Amount and intensity of activity were measured pre- and post-intervention by step count and accelerometry. Subjects were divided into 3 categories based on change in sedentary activity (&lt;1. 5 METs): (i) ≥5% reduction in sedentary time, (ii) 0–4.99% reduction, and (iii) increase sedentary time. Vascular endothelial function was measured by brachial artery flow-mediated dilation (FMD%) pre- and post-intervention.

RESULTS
Sedentary time decreased overall ( P = 0.001), with a 101-minute decrease in category 1 ( N = 27, P &lt; 0.001), a 42-minute decrease in category 2 ( N = 29, P = 0.003), and a 44-minute increase in category 3 ( N = 40, P = 0.02). While FMD% increased in the entire study population ( P = 0.008) over 12 weeks, no differences were observed between the categories ( P = 0.73). In category 1, FMD% improvement was associated achievement of ≥20 minutes/day of moderate intensity PA in bouts ≥ 10 minutes in length.

CONCLUSIONS
Reductions of up to 100 minutes of sedentary time per day over 12 weeks was not significantly associated with improved vascular endothelial function in older adults. FMD% was significantly higher among those with lower sedentary behavior and concomitant moderate-intensity PA of ≥20 minutes/day in bouts.
TRAL: tandem repeat annotation library
Authors: Schaper Elke , Korsunsky Alexander , Pečerska Jūlija , Messina Antonio , Murri Riccardo , Stockinger Heinz , Zoller Stefan , Xenarios Ioannis , Anisimova Maria 
Published: May 2015

Abstract
Motivation: Currently, more than 40 sequence tandem repeat detectors are published, providing heterogeneous, partly complementary, partly conflicting results.
Results: We present TRAL, a tandem repeat annotation library that allows running and parsing of various detection outputs, clustering of redundant or overlapping annotations, several statistical frameworks for filtering false positive annotations, and importantly a tandem repeat annotation and refinement module based on circular profile hidden Markov models (cpHMMs). Using TRAL, we evaluated the performance of a multi-step tandem repeat annotation workflow on 547 085 sequences in UniProtKB/Swiss-Prot. The researcher can use these results to predict run-times for specific datasets, and to choose annotation complexity accordingly.
Availability and implementation: TRAL is an open-source Python 3 library and is available, together with documentation and tutorials via http://www.vital-it.ch/software/tral.
Contact: elke.schaper@isb-sib.ch
IMSEQ—a fast and error aware approach to immunogenetic sequence analysis
Authors: Kuchenbecker Leon , Nienen Mikalai , Hecht Jochen , Neumann Avidan U. , Babel Nina , Reinert Knut , Robinson Peter N. 
Published: May 2015

Abstract
Motivation: Recombined T- and B-cell receptor repertoires are increasingly being studied using next generation sequencing (NGS) in order to interrogate the repertoire composition as well as changes in the distribution of receptor clones under different physiological and disease states. This type of analysis requires efficient and unambiguous clonotype assignment to a large number of NGS read sequences, including the identification of the incorporated V and J gene segments and the CDR3 sequence. Current tools have deficits with respect to performance, accuracy and documentation of their underlying algorithms and usage.
Results: We present IMSEQ, a method to derive clonotype repertoires from NGS data with sophisticated routines for handling errors stemming from PCR and sequencing artefacts. The application can handle different kinds of input data originating from single- or paired-end sequencing in different configurations and is generic regarding the species and gene of interest. We have carefully evaluated our method with simulated and real world data and show that IMSEQ is superior to other tools with respect to its clonotyping as well as standalone error correction and runtime performance.
Availability and implementation: IMSEQ was implemented in C++ using the SeqAn library for efficient sequence analysis. It is freely available under the GPLv2 open source license and can be downloaded at www.imtools.org.
Supplementary information: Supplementary data are available at Bioinformatics online.
Contact: lkuchenb@inf.fu-berlin.de or peter.robinson@charite.de
Between Classicism and Modernity: Éric Rohmer on Urban Change
Authors: Schmid Marion 
Published: May 2015

Abstract

A director at the crossroads of the arts, Éric Rohmer took a keen interest in the urban transformations France underwent in the course of the twentieth century, in particular the post-war
villes nouvelles
project launched by the Gaullist government in 1965. In a programmatic article on the relationship between cinema and architecture, followed by a series of television documentaries from the 1960s and 1970s, as well as two feature films —
Les Nuits de la pleine lune
(1984) and
L
'
Ami de mon amie
(1987) — the director interrogates the new types of urban living proposed by progressive architects and town planners. Focusing on the intersection between his theoretical writings, his little-known documentaries, and his fictional work, this article assesses Rohmer's ambivalent attitude towards modern architecture in the wider context of the tension between classicism and modernity evidenced in his aesthetics and creative practice. As cautious of the functional modernism of a Le Corbusier as he is of postmodern housing schemes, the director offers a probing reflection on the relationship between the built environment and lived experience, framed by a broader questioning of cinema's place among its more established sister arts.