bluuebunny/crossref_metadata_2025_split huggingface dataset:
CTLA-4 controls follicular helper T-cell differentiation by regulating the strength of CD28 engagement
Authors: Wang Chun Jing , Heuts Frank , Ovcinnikovs Vitalijs , Wardzinski Lukasz , Bowers Chantelle , Schmidt Emily M. , Kogimtzis Alexandros , Kenefeck Rupert , Sansom David M. , Walker Lucy S. K. 
Published: December 2014

SignificanceThe inhibitory protein cytotoxic T-lymphocyte-associated antigen-4 (CTLA-4) is recognized as a crucial regulator of autoimmunity, but its precise mechanism of action is not yet fully understood. CTLA-4 can down-regulate expression of the costimulatory ligands CD80 and CD86 on antigen presenting cells, thereby reducing T-cell CD28 engagement. Here we demonstrate that quantitative changes in the level of CD28 engagement have functional consequences for T-cell differentiation toward follicular helper T cells (TFHs). These findings link CTLA-4 control of T-cell responses with the generation of high-affinity class-switched antibody responses. This generates an advanced conceptual framework for understanding the linked nature of CTLA-4 and CD28 functions and the role of this pathway in influencing autoimmunity.
Immunological consequences of intragenus conservation ofMycobacterium tuberculosisT-cell epitopes
Authors: Lindestam Arlehamn Cecilia S. , Paul Sinu , Mele Federico , Huang Charlie , Greenbaum Jason A. , Vita Randi , Sidney John , Peters Bjoern , Sallusto Federica , Sette Alessandro 
Published: December 2014

SignificanceMycobacterium tuberculosis(MTB) infection is one of the most common diseases worldwide. TheMycobacteriaare a large bacterial family that includes MTB and nontuberculous mycobacteria commonly found in the environment (NTMs). We have shown that non–MTB-infected and non–bacillus Calmette–Guerin-vaccinated individuals nevertheless react to MTB-derived sequences. This reactivity can be explained by conservation of the epitope sequence in NTMs. Thus, the widespread exposure to various species ofMycobacteriainfluences reactivity to MTB and NTMs. We identified epitopes that are found only in NTMs, allowing dissociation of MTB- versus NTM-specific reactivity. These epitopes, in conjunction with epitopes specific to latent MTB infection, will provide a novel tool to study host–pathogen dynamics in the context of the design and evaluation of MTB vaccines and diagnostics.
Oxidation-driven surface dynamics on NiAl(100)
Authors: Qin Hailang , Chen Xidong , Li Liang , Sutter Peter W. , Zhou Guangwen 
Published: December 2014

Significance
Oxidation of metals involves the reaction of oxygen with the metallic substrate, requiring sources or sinks of substrate atoms. This study provides direct evidence that atomic steps serve as the sources of Al surface atoms for aluminum oxide growth in the oxidation of NiAl(100), which results in coordinated migration and bunching of steps that progressively impedes the oxide growth. Comparison with the oxidation of NiAl(110) that exhibits unimpeded oxide film growth over substrate steps suggests that whenever steps are the source of atoms used for oxide growth they limit the oxidation process; when atoms are supplied from the bulk, the oxidation rate is not limited by the motion of surface steps.
Plasmonic photonic crystals realized through DNA-programmable assembly
Authors: Park Daniel J. , Zhang Chuan , Ku Jessie C. , Zhou Yu , Schatz George C. , Mirkin Chad A. 
Published: December 2014

Significance
DNA-programmable methods provide unprecedented control over the assembly of nanoparticles into complex structures, including superlattices with deliberately tailorable compositions, crystal symmetries, lattice constants, and crystal habits. In principle, such bottom-up approaches can be used to assemble interesting photonic structures, including ones containing quantum dots and metal nanoparticles. Herein we show that we can tune the interaction between light and the collective electronic modes of gold nanoparticles by independently adjusting lattice constants and gold nanoparticle diameters. This opens up exciting possibilities for tuning the interaction between light and highly organized collections of particles at the nanoscale for applications ranging from lasers to quantum electrodynamics to biosensing. The structures reported herein are the first devices to our knowledge prepared by DNA guided colloidal crystallization.
Spatiotemporal variations of seismicity before major earthquakes in the Japanese area and their relation with the epicentral locations
Authors: Sarlis Nicholas V. , Skordas Efthimios S. , Varotsos Panayiotis A. , Nagao Toshiyasu , Kamogawa Masashi , Uyeda Seiya 
Published: December 2014

Significance
It was recently found that a few months before major earthquakes, the seismicity in the entire Japanese region exhibits a characteristic change. This change, however, can be identified when seismic data are analyzed in a new time domain termed “natural time.” By dividing the Japanese region into small areas, we find that some small areas show the characteristic change almost simultaneously with the large area and such small areas are clustered within a few hundred kilometers from the actual epicenter of the related major earthquake. This phenomenon may serve for forecasting the epicenter of a future major earthquake.
Controlled analysis of nanoparticle charge on mucosal and systemic antibody responses following pulmonary immunization
Authors: Fromen Catherine A. , Robbins Gregory R. , Shen Tammy W. , Kai Marc P. , Ting Jenny P. Y. , DeSimone Joseph M. 
Published: December 2014

Significance
To our knowledge, no other nano-based vaccine delivery platform has directly assessed the effects of nanoparticle charge on pulmonary vaccination without affecting other physio/chemical particle characteristics and/or antigen loading. The Particle Replication in Non-Wetting Templates nanoparticle fabrication process is unique in that it allows for isolation of charge as the sole variable in these studies while maintaining all other physical and chemical parameters constant. We find that positively charged nanoparticles induce robust mucosal and systemic antibody responses following pulmonary administration, whereas negatively charged nanoparticles fail to do so. Therefore, our studies underscore the importance of considering nanoparticle charge as a critical design parameter when generating pulmonary-based vaccines and may have implications for particulate vaccination through other routes of administration.
Lunapark stabilizes nascent three-way junctions in the endoplasmic reticulum
Authors: Chen Shuliang , Desai Tanvi , McNew James A. , Gerard Patrick , Novick Peter J. , Ferro-Novick Susan 
Published: December 2014

Significance
In this study, we have identified an important role of mammalian Lnp1 (mLnp1) in stabilizing nascent three-way ER junctions. When new junctions acquire mLnp1, they tend to remain stable within the ER network, whereas the nascent junctions that fail to acquire mLnp1 preferentially undergo ring closure. Our findings provide insights into the function of mLnp1.
The global distribution of diet breadth in insect herbivores
Authors: Forister Matthew L. , Novotny Vojtech , Panorska Anna K. , Baje Leontine , Basset Yves , Butterill Philip T. , Cizek Lukas , Coley Phyllis D. , Dem Francesca , Diniz Ivone R. , Drozd Pavel , Fox Mark , Glassmire Andrea E. , Hazen Rebecca , Hrcek Jan , Jahner Joshua P. , Kaman Ondrej , Kozubowski Tomasz J. , Kursar Thomas A. , Lewis Owen T. , Lill John , Marquis Robert J. , Miller Scott E. , Morais Helena C. , Murakami Masashi , Nickel Herbert , Pardikes Nicholas A. , Ricklefs Robert E. , Singer Michael S. , Smilanich Angela M. , Stireman John O. , Villamarín-Cortez Santiago , Vodka Stepan , Volf Martin , Wagner David L. , Walla Thomas , Weiblen George D. , Dyer Lee A. 
Published: December 2014

Significance
Dietary specialization determines an organism’s resource base as well as impacts on host or prey species. There are important basic and applied reasons to ask why some animals have narrow diets and others are more generalized, and if different regions of the Earth support more specialized interactions. We investigated site-specific host records for more than 7,500 species of insect herbivores. Although host specialists predominate, the proportion of specialists is affected by the diversity of hosts and shifts globally, supporting predictions of more exclusive tropical interactions. These results not only affect our understanding of the ecology of food webs, but also have implications for how they respond to environmental change, as well as for ecosystem management and restoration.
Optogenetic activation of cholinergic neurons in the PPT or LDT induces REM sleep
Authors: Van Dort Christa J. , Zachs Daniel P. , Kenny Jonathan D. , Zheng Shu , Goldblum Rebecca R. , Gelwan Noah A. , Ramos Daniel M. , Nolan Michael A. , Wang Karen , Weng Feng-Ju , Lin Yingxi , Wilson Matthew A. , Brown Emery N. 
Published: December 2014

SignificanceRapid eye movement (REM) sleep is a critical component of restful sleep, yet the mechanisms that control REM sleep are incompletely understood. Brainstem cholinergic neurons have been implicated in REM sleep regulation, but heterogeneous cell types in the area have made it difficult to determine the specific role of each population, leading to a debate about the importance of cholinergic neurons. Therefore, we selectively activated brainstem cholinergic neurons to determine their role in REM sleep regulation. We found that activation of cholinergic neurons during non-REM sleep increased the number of REM sleep episodes but not REM sleep duration. Our data demonstrate that brainstem cholinergic neurons are important modulators of REM sleep and clarify their role in REM sleep initiation.
Crystal structure refinement withSHELXL
Authors: Sheldrick George M. 
Published: December 2014

The improvements in the crystal structure refinement programSHELXLhave been closely coupled with the development and increasing importance of the CIF (Crystallographic Information Framework) format for validating and archiving crystal structures. An important simplification is that now only one file in CIF format (for convenience, referred to simply as `a CIF') containing embedded reflection data andSHELXLinstructions is needed for a complete structure archive; the programSHREDCIFcan be used to extract the .hkl and .ins files required for further refinement withSHELXL. Recent developments inSHELXLfacilitate refinement against neutron diffraction data, the treatment of H atoms, the determination of absolute structure, the input of partial structure factors and the refinement of twinned and disordered structures.SHELXLis available free to academics for the Windows, Linux and Mac OS X operating systems, and is particularly suitable for multiple-core processors.
Paraneoplastic pemphigus: Two cases of intra‐abdominal malignancy presenting solely as treatment refractory oral ulceration
Authors: Kelly Shane , Schifter Mark , Fulcher David A. , Lin Ming‐Wei 
Published: December 2014

AbstractTwo patients with initial diagnoses of oral lichen planus and pemphigus vulgaris presented with refractory oral mucosal blistering. Subsequent positive serology results for paraneoplastic pemphigus led to the discovery of occult intra‐abdominal malignancies in both, unicentric Castleman's and non‐Hodgkin's lymphoma. The diagnosis of paraneoplastic pemphigus should be considered in patients with recalcitrant oral ulceration, even in the absence of clinical features of malignancy.
A novel sister clade to the enterobacteria microviruses (family Microviridae) identified in methane seep sediments
Authors: Bryson Samuel Joseph , Thurber Andrew R. , Correa Adrienne M. S. , Orphan Victoria J. , Vega Thurber Rebecca 
Published: December 2014

SummaryMethane seep microbial communities perform a key ecosystem service by consuming the greenhouse gas methane prior to its release into the hydrosphere, minimizing the impact of marine methane sources on our climate. Although previous studies have examined the ecology and biochemistry of these communities, none has examined viral assemblages associated with these habitats. We employed virus particle purification, genome amplification, pyrosequencing and gene/genome reconstruction and annotation on two metagenomic libraries, one prepared for ssDNA and the other for all DNA, to identify the viral community in a methane seep. Similarity analysis of these libraries (raw and assembled) revealed a community dominated by phages, with a significant proportion of similarities to the Microviridae family of ssDNA phages. We define these viruses as the Eel River Basin Microviridae (ERBM). Assembly and comparison of 21 ERBM closed circular genomes identified five as members of a novel sister clade to the Microvirus genus of Enterobacteria phages. Comparisons among other metagenomes and these Microviridae major‐capsid sequences indicated that this clade of phages is currently unique to the Eel River Basin sediments. Given this ERBM clade's relationship to the Microviridae genus Microvirus, we define this sister clade as the candidate genus Pequeñovirus.
Diversity and distribution of unicellular opisthokonts along the European coast analysed using high‐throughput sequencing
Authors: del Campo Javier , Mallo Diego , Massana Ramon , de Vargas Colomban , Richards Thomas A. , Ruiz‐Trillo Iñaki 
Published: December 2014

SummaryThe opisthokonts are one of the major super groups of eukaryotes. It comprises two major clades: (i) the Metazoa and their unicellular relatives and (ii) the Fungi and their unicellular relatives. There is, however, little knowledge of the role of opisthokont microbes in many natural environments, especially among non‐metazoan and non‐fungal opisthokonts. Here, we begin to address this gap by analysing high‐throughput 18S rDNA and 18S rRNA sequencing data from different European coastal sites, sampled at different size fractions and depths. In particular, we analyse the diversity and abundance of choanoflagellates, filastereans, ichthyosporeans, nucleariids, corallochytreans and their related lineages. Our results show the great diversity of choanoflagellates in coastal waters as well as a relevant representation of the ichthyosporeans and the uncultured marine opisthokonts (MAOP). Furthermore, we describe a new lineage of marine fonticulids (MAFO) that appears to be abundant in sediments. Taken together, our work points to a greater potential ecological role for unicellular opisthokonts than previously appreciated in marine environments, both in water column and sediments, and also provides evidence of novel opisthokont phylogenetic lineages. This study highlights the importance of high‐throughput sequencing approaches to unravel the diversity and distribution of both known and novel eukaryotic lineages.
A holistic view of polyhydroxyalkanoate metabolism in Pseudomonas putida
Authors: Prieto Auxiliadora , Escapa Isabel F. , Martínez Virginia , Dinjaski Nina , Herencias Cristina , de la Peña Fernando , Tarazona Natalia , Revelles Olga 
Published: December 2014

SummaryPolyhydroxyalkanoate (PHA) metabolism has been traditionally considered as a futile cycle involved in carbon and energy storage. The use of cutting‐edge technologies linked to systems biology has improved our understanding of the interaction between bacterial physiology, PHA metabolism and other cell functions in model bacteria such as Pseudomonas putida KT2440. PHA granules or carbonosomes are supramolecular complexes of biopolyester and proteins that are essential for granule segregation during cell division, and for the functioning of the PHA metabolic route as a continuous cycle. The simultaneous activities of PHA synthase and depolymerase ensure the carbon flow to the transient demand for metabolic intermediates to balance the storage and use of carbon and energy. PHA cycle also determines the number and size of bacterial cells. The importance of PHAs as nutrients for members of the microbial community different to those that produce them is illustrated here via examples of bacterial predators such as Bdellovibrio bacteriovorus that prey on PHA producers and produces specific extra‐cellular depolymerases. PHA hydrolysis confers Bdellovibrio ecological advantages in terms of motility and predation efficiency, demonstrating the importance of PHA producers predation in population dynamics. Metabolic modulation strategies for broadening the portfolio of PHAs are summarized and their properties are compiled.
Lethal Laryngopyocele
Authors: Byard Roger W. , Gilbert John D. 
Published: December 2014

AbstractA 44‐year‐old man collapsed after complaining of difficulty breathing. Layer dissection of the neck at autopsy revealed a large mixed internal and external laryngopyocele occluding the upper airway. It contained 30 mls of yellow‐gray pus. Mechanisms of death in laryngoceles involve obstruction of the opening into the larynx resulting in accumulation of mucus or air within the sac causing airway occlusion. Once infection supervenes, deaths in laryngopyocoeles result either from accumulated pus causing airway occlusion from a mass effect (as in the current case) or the discharge of pus into the airway causing death from aspiration. Sudden death in laryngopyoceles is a very rare event that requires careful dissection at autopsy to demonstrate the characteristics of the underlying lesion and the possible mechanism of death. Laryngopyocele should be considered in the differential diagnosis of natural conditions causing acute, potentially lethal, upper airway obstruction.
Exogenous Lipoid Pneumonia as a Contributory Factor in a Drug‐related Death
Authors: Moreau Emilie , Rérolle Camille , Deveaux Marc , Paraf François , Saint‐Martin Pauline 
Published: December 2014

AbstractPostmortem investigation often reveals various conditions, which may or may not have played a part in the death of the individual. The case of a 32‐year‐old woman is reported, with a long history of drug addiction. She was found dead in her bed. The autopsy revealed diffuse pulmonary edema with congestion of the lungs, brain, liver, and spleen. Microscopic examination of the lungs showed multiple intra‐alveolar and interstitial foamy macrophages and extracellular fat droplets surrounded by polynuclear giant cells. Death was attributed to acute polydrug intoxication. As microscopic examination had revealed severe pulmonary lesions, lipoid pneumonia was considered as a contributing factor to death. Lipoid pneumonia is an uncommon entity with the characteristic radiograph features and histologic findings of alveoli filled with vacuolated, lipid‐laden histiocytes. It can be either exogenous or endogenous in cause, based on the source of the lipid. Exogenous lipoid pneumonia usually results from aspiration or inhalation of fat‐like material, such as mineral oil or petroleum‐based lubricants and decongestants, resulting in pulmonary inflammatory reactions.
Child Suicide in the North of Portugal
Authors: Mendes Ricardo , Santos Sara , Taveira Francisco , Dinis‐Oliveira Ricardo Jorge , Santos Agostinho , Magalhães Teresa 
Published: December 2014

AbstractSuicide in children is a rare finding and is probably motivated by acts of impulsiveness. This study aims to contribute to the characterization of child suicide in a forensic perspective in the Portuguese population. Data of forensic autopsies from 2004 to 2012 related to suicide victims under 18 years were reviewed. A total of 17 cases, with a male predominance (64.7%) and a mean age of 15.24 ± 1.348 for both genders, were registered. The leading suicide method was hanging (35.3%), and a suicide note was found in 41.2%. Psychological autopsy proved to be useful in promoting a better understanding of these incidents and their antecedents. This study also offers useful information, namely the implied risk factors, for future programs of suicide research and prevention.
An autotrophic H2‐oxidizing, nitrate‐respiring, Tc(VII)‐reducing Acidovorax sp. isolated from a subsurface oxic‐anoxic transition zone
Authors: Lee Ji‐Hoon , Fredrickson James K. , Plymale Andrew E. , Dohnalkova Alice C. , Resch Charles T. , McKinley James P. , Shi Liang 
Published: December 2014

SummaryIncreasing concentrations of H2 with depth were observed across a geologic unconformity and associated redox transition zone in the subsurface at the Hanford Site in south‐central Washington, USA. An opposing gradient characterized by decreasing O2 and nitrate concentrations was consistent with microbial‐catalysed biogeochemical processes. Sterile sand was incubated in situ within a multilevel sampler placed across the redox transition zone to evaluate the potential for Tc(VII) reduction and for enrichment of H2‐oxidizing denitrifiers capable of reducing Tc(VII). H2‐driven TcO4− reduction was detected in sand incubated at all depths but was strongest in material from a depth of 17.1 m. Acidovorax spp. were isolated from H2‐nitrate enrichments from colonized sand from 15.1 m, with one representative, strain JHL‐9, subsequently characterized. JHL‐9 grew on acetate with either O2 or nitrate as electron acceptor (data not shown) and on medium with bicarbonate, H2 and nitrate. JHL‐9 also reduced pertechnetate (TcO4−) under denitrifying conditions with H2 as the electron donor. H2‐oxidizing Acidovorax spp. in the subsurface at Hanford and other locations may contribute to the maintenance of subsurface redox gradients and offer the potential for Tc(VII) reduction.
Glutamatergic and neurometabolic alterations in chronic cocaine users measured with 1H‐magnetic resonance spectroscopy
Authors: Hulka Lea M. , Scheidegger Milan , Vonmoos Matthias , Preller Katrin H. , Baumgartner Markus R. , Herdener Marcus , Seifritz Erich , Henning Anke , Quednow Boris B. 
Published: December 2014

AbstractCocaine addiction is a chronically relapsing disorder that is associated with harmful consequences. Relapses occur frequently and effective pharmacotherapies are currently sparse. Preclinical studies suggest that altered glutamatergic signaling is crucial for the maintenance of cocaine self‐administration. However, the translational validity of these models is currently unknown. Therefore, we investigated potential differences of glutamate, glutamine and further metabolite levels in the pregenual anterior cingulate cortex (pgACC) and the right dorsolateral prefrontal cortex (rDLPFC) of chronic cocaine users and controls using the PRior knOwledge FITting 2.0 tool in combination with two‐dimensional J‐resolved single‐voxel 1H‐magnetic resonance spectroscopy at 3T and voxel tissue composition and relaxation correction. Glutamate and glutamine levels did not differ between cocaine users and controls, but higher weekly cocaine use and higher cocaine hair concentrations were associated with lower glutamine/creatine ratios in the pgACC. Interestingly, cocaine users exhibited higher glucose/total creatine ratios than controls in the pgACC and higher choline/creatine ratios in the pgACC and rDLPFC. These results imply that cocaine use is associated with altered cortical glucose metabolism and membrane turnover. Finally, cocaine use over the past 6 months appears to decrease cortical glutamine levels indicating changes in glutamate cycling.