bluuebunny/crossref_metadata_2025_split huggingface dataset:
Evolution and convergence of the patterns of international scientific collaboration
Authors: Coccia Mario , Wang Lili 
Published: February 2016

Significance
The evolution of the patterns of international scientific collaboration plays an important role in the social construction of science to design efficient research policies and to support the production of knowledge. However, in studies of science, little is known about how patterns of international research collaboration for fields of science have evolved in the past four decades. This study shows, for the first time to our knowledge, starting from pioneering results described by literature in the 1970s and 1990s, that the long-run patterns of international scientific collaboration are generating a convergence between applied and basic fields. This convergence of collaboration patterns across research fields might be one of contributing factors that supports the evolution of scientific disciplines.
Ribbon curling via stress relaxation in thin polymer films
Authors: Prior Chris , Moussou Julien , Chakrabarti Buddhapriya , Jensen Oliver E. , Juel Anne 
Published: February 2016

Significance
The forming of thin film structures through differential stress relaxation is an important engineering design tool to create flexible objects such as rolls, spirals, and origamis. We exploit the everyday process inspired from gift wrapping of curling an initially straight ribbon by pulling it over a blade to probe the mechanical shear response of thin polymer sheets. Experiments show that curling occurs over a limited range of loads applied to the ribbon, with the curl radius reaching a maximum at intermediate loads. A theoretical model reveals several patterns of irreversible yielding across the ribbon, and the dependence of curl radius on pulling speed shows that stress relaxes dynamically as the ribbon passes over the blade.
Charge of a quasiparticle in a superconductor
Authors: Ronen Yuval , Cohen Yonatan , Kang Jung-Hyun , Haim Arbel , Rieder Maria-Theresa , Heiblum Moty , Mahalu Diana , Shtrikman Hadas 
Published: February 2016

Significance
The charge of the quasiparticles in superconductors was never, to our knowledge, directly measured. Here, we used our experience and sensitive techniques in measuring the fractional excitations in the fractional quantum Hall effect via quantum shot noise, to measure the tunneling quasiparticles in a 1D superconductor–insulator–superconductor Josephson junction, and find their charge to be significantly less than that of an electron.
Force sensing by the vascular protein von Willebrand factor is tuned by a strong intermonomer interaction
Authors: Müller Jochen P. , Mielke Salomé , Löf Achim , Obser Tobias , Beer Christof , Bruetzel Linda K. , Pippig Diana A. , Vanderlinden Willem , Lipfert Jan , Schneppenheim Reinhard , Benoit Martin 
Published: February 2016

Significance
Excessive blood loss at a site of vascular injury is prevented by recruitment of platelets to the injured vessel wall and the formation of a platelet plug. Under elevated shear flow conditions, these processes are critically mediated by the large plasma glycoprotein von Willebrand factor (VWF). Remarkably, VWF’s activation for hemostasis correlates with its abrupt elongation at sufficiently high shear rates. In this study, we have discovered a strong intermonomer interaction in VWF that is expected to tune VWF’s ability to sense hydrodynamic forces in the bloodstream. Our data will help to comprehend the force-induced activation of VWF and provide clues for understanding clotting disorders, such as von Willebrand disease and thrombosis, at the single-molecule level.
Diminished viral replication and compartmentalization of hepatitis C virus in hepatocellular carcinoma tissue
Authors: Harouaka Djamila , Engle Ronald E. , Wollenberg Kurt , Diaz Giacomo , Tice Ashley B. , Zamboni Fausto , Govindarajan Sugantha , Alter Harvey , Kleiner David E. , Farci Patrizia 
Published: February 2016

SignificanceHepatocellular carcinoma (HCC) associated with hepatitis C virus (HCV) infection is the fastest-rising cause of cancer-related death in the United States. The level of intratumor HCV replication and the molecular interactions between virus and tumor remain elusive, however. Here we demonstrate that the ability of HCV to replicate in HCC is severely hampered despite unchanged miR122 expression. Surprisingly, we found that livers containing HCC harbor a more diverse viral population than that seen in cirrhotic livers without HCC. Tracking of individual variants demonstrated changes in quasispecies distribution between tumor and nontumorous areas, suggesting viral compartmentalization within the tumor. These insights into the interplay between HCV and HCC call for further investigation of whether malignant hepatocytes express or lack factors that restrict HCV entry or negatively affect viral replication.
Oyster reproduction is affected by exposure to polystyrene microplastics
Authors: Sussarellu Rossana , Suquet Marc , Thomas Yoann , Lambert Christophe , Fabioux Caroline , Pernet Marie Eve Julie , Le Goïc Nelly , Quillien Virgile , Mingant Christian , Epelboin Yanouk , Corporeau Charlotte , Guyomarch Julien , Robbens Johan , Paul-Pont Ika , Soudant Philippe , Huvet Arnaud 
Published: February 2016

Significance
Plastics are a contaminant of emerging concern accumulating in marine ecosystems. Plastics tend to break down into small particles, called microplastics, which also enter the marine environment directly as fragments from a variety of sources, including cosmetics, clothing, and industrial processes. Given their ubiquitous nature and small dimensions, the ingestion and impact of microplastics on marine life are a cause for concern, notably for filter feeders. Oysters were exposed to polystyrene microparticles, which were shown to interfere with energy uptake and allocation, reproduction, and offspring performance. A drop in energy allocation played a major role in this reproductive impairment. This study provides ground-breaking data on microplastic impacts in an invertebrate model, helping to predict ecological impact in marine ecosystems.
Programmable polyproteams built using twin peptide superglues
Authors: Veggiani Gianluca , Nakamura Tomohiko , Brenner Michael D. , Gayet Raphaël V. , Yan Jun , Robinson Carol V. , Howarth Mark 
Published: February 2016

SignificanceMany biological events depend on proteins working together as a team. Here we establish how to program team formation, covalently linking protein modules step by step. We split a domain fromStreptococcus pneumoniaeto form a peptide and protein pair, SnoopTag and SnoopCatcher, which form an isopeptide bond when mixed together. SnoopTag/SnoopCatcher reacted with each other but not with an alternative peptide/protein pair, SpyTag/SpyCatcher. We formed polyprotein chains by alternating SpyTag reaction with SnoopTag reaction. Cellular signaling often relies on integrated activation of different receptors, so we built polyprotein teams to stimulate Death Receptor and Growth Factor receptors, finding an optimal combination for cell-death induction in cancer cells. Programmable “polyproteams” provide a simple route to investigate or harness biological teamwork.
Enhanced stability of tristetraprolin mRNA protects mice against immune-mediated inflammatory pathologies
Authors: Patial Sonika , Curtis Alan D. , Lai Wi S. , Stumpo Deborah J. , Hill Georgette D. , Flake Gordon P. , Mannie Mark D. , Blackshear Perry J. 
Published: February 2016

Significance
Inflammation is involved in the pathogenesis of many chronic diseases. Many deleterious effects of inflammation are mediated through increased production of proinflammatory mediators, known as cytokines and chemokines. Many current therapies for these diseases involve blocking single proinflammatory mediators, such as TNF, using parenteral administration of recombinant binding proteins. We demonstrate here that a genetic modification in the mouse that increases the expression of an endogenous antiinflammatory protein, tristetraprolin (TTP), results in protection against mouse models for several human inflammatory diseases, including rheumatoid arthritis, psoriasis, and multiple sclerosis, presumably by decreasing the production of proinflammatory cytokines. Our results suggest that increasing TTP expression may be an effective therapeutic strategy in the treatment of certain inflammatory diseases.
Structure-based analysis of the molecular interactions between acyltransferase and acyl carrier protein in vicenistatin biosynthesis
Authors: Miyanaga Akimasa , Iwasawa Shohei , Shinohara Yuji , Kudo Fumitaka , Eguchi Tadashi 
Published: February 2016

Significance
Acyltransferases (ATs) are responsible for the selection and incorporation of acyl building blocks in the biosynthesis of various polyketide natural products. Proper protein–protein interactions between AT and cognate acyl carrier protein (ACP) are critical for the functional transfer of acyl groups. However, the ACP recognition mechanism has remained elusive because the structural determination of an AT–ACP complex is hampered by the weak and transient interactions between them. Herein, we describe the first crystal structure of the AT–ACP complex. To stabilize the weak protein–protein interaction sufficiently for analysis, we prepared a covalent AT–ACP complex using a cross-linking reagent for crystallization. The determined AT–ACP complex structure provides detailed mechanistic insights into ACP recognition by AT.
Sensor histidine kinase is a β-lactam receptor and induces resistance to β-lactam antibiotics
Authors: Li Lu , Wang Qiyao , Zhang Hui , Yang Minjun , Khan Mazhar I. , Zhou Xiaohui 
Published: February 2016

Significance
Bacteria can produce β-lactamases, enzymes that destroy β-lactam antibiotics and thereby resist these potent antibiotics that target cell wall synthesis. Production of β-lactamases is often controlled by β-lactam-induced perturbations in the cell wall. Here, we have identified a new mechanism controlling β-lactamase production. We found a signaling system in which a membrane-associated histidine kinase directly binds β-lactams, triggering the expression of a β-lactamase and resistance to β-lactam antibiotics. Direct sensing of β-lactam antibiotics may enable sufficiently rapid induction of β-lactamase to degrade β-lactam antibiotics before the integrity of the cell wall is disturbed.
In vivo imaging identifies temporal signature of D1 and D2 medium spiny neurons in cocaine reward
Authors: Calipari Erin S. , Bagot Rosemary C. , Purushothaman Immanuel , Davidson Thomas J. , Yorgason Jordan T. , Peña Catherine J. , Walker Deena M. , Pirpinias Stephen T. , Guise Kevin G. , Ramakrishnan Charu , Deisseroth Karl , Nestler Eric J. 
Published: February 2016

Significance
Strong associations between cocaine and the environmental contexts where cocaine is administered are thought to drive relapse. The nucleus accumbens (NAc) encodes these cue–reward associations, and here we determined how cocaine alters the ability of cells in NAc to respond to drug-associated environmental stimuli to drive drug seeking. Using fiber photometry calcium imaging we define the specific population of cells, dopamine D1 receptor-expressing neurons, that encodes information about drug associations and show that these cells can be manipulated to attenuate the strength of drug associations and prevent relapse. Together, these data define a basic circuit mechanism underlying drug–context associations and suggest that pharmacotherapeutic agents aimed at D1-type neurons may help to promote sustained abstinence in cocaine abusers.
Ligase I and ligase III mediate the DNA double-strand break ligation in alternative end-joining
Authors: Lu Guangqing , Duan Jinzhi , Shu Sheng , Wang Xuxiang , Gao Linlin , Guo Jing , Zhang Yu 
Published: February 2016

Significance
DNA repair is not only extremely important for the genome stability in normal cells but also extensively involved in carcinogenesis and evolution. DNA double-strand breaks (DSBs), one of the most harmful types of DNA damage, are repaired mainly by homologous repair (HR) and nonhomologous end-joining (NHEJ). Although the components of NHEJ have been studied extensively in last two decades, in cells deficient for core classic NHEJ factors, significant DSB end-joining activities have been observed in various situations, suggesting the existence of the alternative end-joining (A-EJ) activities. Here, we dissected the roles of DNA ligases in mediating the last step of A-EJ. The results suggested the existence of multiple DNA ligase-containing complexes in A-EJ.
Breakdown of interdependent directed networks
Authors: Liu Xueming , Stanley H. Eugene , Gao Jianxi 
Published: February 2016

Significance
Real-world complex systems interact with one another, and these interactions increase the probability of catastrophic failure. Using interdependent networks to model these phenomena helps understand a system’s robustness and enables design of more robust infrastructures. Previous research has been limited to an idealized case where each layer is undirected, but almost all real-world networks are directed and exhibit in-degree and out-degree correlations. Therefore, we develop a general theoretical framework for analyzing the breakdown of interdependent directed networks with, or without, in-degree and out-degree correlations, and apply it to real-world international trade networks. Surprisingly, we find that the robustness of interdependent heterogeneous networks increases, whereas that of interdependent homogeneous networks with strong coupling strengths decreases with in-degree and out-degree correlations.
MHC class II super-enhancer increases surface expression of HLA-DR and HLA-DQ and affects cytokine production in autoimmune vitiligo
Authors: Cavalli Giulio , Hayashi Masahiro , Jin Ying , Yorgov Daniel , Santorico Stephanie A. , Holcomb Cherie , Rastrou Melinda , Erlich Henry , Tengesdal Isak W. , Dagna Lorenzo , Neff C. Preston , Palmer Brent E. , Spritz Richard A. , Dinarello Charles A. 
Published: February 2016

SignificanceVitiligo is a classic autoimmune disease genetically associated with SNPs in the MHC class II region. To date, the impact of HLA molecules on autoimmunity has focused on structural diversity of antigen presentation. Here, we describe the properties of a 47-nucleotide high-risk haplotype of three SNPs within an intergenic “super-enhancer” located between theHLA-DRB1andHLA-DQA1genes, localized by a genome-wide association study of 2,853 subjects with vitiligo. Monocytes from healthy subjects homozygous for the high-risk haplotype have increased surface expression of HLA-DR and -DQ, and peripheral blood mononuclear cells from high-risk subjects produce more IL-1β and IFN-γ upon engagement of dectin-1, mannose, and Toll-like receptors. This study underscores the importance of transcriptional regulation ofHLAgenes to the risk of developing an autoimmune disease.
Enterovirus D68 receptor requirements unveiled by haploid genetics
Authors: Baggen Jim , Thibaut Hendrik Jan , Staring Jacqueline , Jae Lucas T. , Liu Yue , Guo Hongbo , Slager Jasper J. , de Bruin Jost W. , van Vliet Arno L. W. , Blomen Vincent A. , Overduin Pieter , Sheng Ju , de Haan Cornelis A. M. , de Vries Erik , Meijer Adam , Rossmann Michael G. , Brummelkamp Thijn R. , van Kuppeveld Frank J. M. 
Published: February 2016

Significance
Enterovirus D68 (EV-D68) is an emerging pathogen that recently caused a large outbreak of severe respiratory disease in the United States and is associated with cases of paralysis. Little is known about EV-D68 host factor requirements. Here, using a genome-wide knockout approach, we identified several genes in sialic acid (Sia) biology as being essential for infection. We also showed that not only α2,6-linked Sia, which mainly occurs in the upper respiratory tract, but also α2,3-linked Sia, which mainly occurs in the lower respiratory tract, can serve as the receptor. Moreover, we identified recent EV-D68 isolates that can use an alternative, nonsialylated receptor. Our findings are essential to understand tropism and pathogenesis of EV-D68 as well as the potential of using Sia-targeting inhibitors to treat EV-D68 infections.
Aminoacyl β-naphthylamides as substrates and modulators of AcrB multidrug efflux pump
Authors: Kinana Alfred D. , Vargiu Attilio V. , May Thithiwat , Nikaido Hiroshi 
Published: February 2016

SignificanceResistance-nodulation division family efflux pumps, exemplified by AcrB ofEscherichia coli, play an important role in multidrug resistance of Gram-negative bacteria by actively pumping out a very wide range of antimicrobial agents. Yet it is unclear with how much affinity and with how much rate this pumping process works, except for our earlier studies on cephalosporins and penicillins. Here we succeeded in determining these parameters for the earliest-discovered inhibitor Phenylalanyl-argenine β-naphthylamide and its relatives, and examined the binding of these compounds to AcrB binding sites by docking and molecular dynamics simulations. The results suggest how an inhibitor, even when it is itself pumped out, can reduce the pumping of other substrates.
Asymmetric ecological conditions favor Red-Queen type of continued evolution over stasis
Authors: Nordbotten Jan Martin , Stenseth Nils C. 
Published: February 2016

Significance
The work presented here demonstrates analytically for the very first time (to our knowledge) that, within a very general theoretical framework, both Red-Queen type of continuous evolution and evolutionary stasis may be the outcomes of ecological interactions within a multispecies ecological community. Whether or not evolution will cease or continue in an abiotically stable environment (i.e., where there are only biotic forces) has been an unsettled problem within evolutionary biology. Our contribution specifies the ecological conditions for which Red-Queen type of continuous evolution and stasis will result. The new and general eco-evolutionary model provides a profoundly new basis for further theoretical and empirical work within the field of coevolution within multispecies ecological systems.
Multiplexed autoantigen microarrays identify HLA as a key driver of anti-desmoglein and -non-desmoglein reactivities in pemphigus
Authors: Sajda Thomas , Hazelton Julian , Patel Milan , Seiffert-Sinha Kristina , Steinman Lawrence , Robinson William , Haab Brian B. , Sinha Animesh A. 
Published: February 2016

SignificanceAlthough the pathogenicity of autoantibodies (autoAbs) targeting the desmosomal cadherins desmoglein (Dsg) 3 and 1 is well established in pemphigus vulgaris (PV), the disease relevance of other autoAbs remains an area of intense research. By using disease-specific protein microarrays to characterize the autoAb response in PV, we identified Dsg and non-Dsg antigens as primary targets of patient autoAbs. Additionally, we found that healthy first- or second-degree relatives of patients with PV, specifically those expressing HLA DRB1*0402 or DQB1*0503 (PV susceptibility alleles) exhibit patterns of autoreactivity similar to that of patients with PV. These findings suggest a potential role for non-Dsg autoAbs in disease pathogenesis and implicate HLA as a primary driver of autoAb specificity in PV.
Common BRAF(V600E)-directed pathway mediates widespread epigenetic silencing in colorectal cancer and melanoma
Authors: Fang Minggang , Hutchinson Lloyd , Deng April , Green Michael R. 
Published: February 2016

Significance
In many cancers, specific genes affecting cellular growth control are hypermethylated and transcriptionally repressed, a phenomenon known as epigenetic silencing. However, the mechanistic basis of epigenetic silencing is not well understood. One model, called the “instructive model,” posits that epigenetic silencing occurs through a specific pathway, comprising a defined set of components, initiated by an oncoprotein. We have previously shown that in colorectal cancer, B-Raf proto-oncogene (BRAF) directs widespread promoter methylation and epigenetic silencing by up-regulating the transcriptional repressor v-maf avian musculoaponeurotic fibrosarcoma oncogene homolog G (MAFG), which, in turn, recruits a set of corepressors, resulting in transcriptional repression. Here, we show that this same BRAF-directed pathway also mediates widespread epigenetic silencing in melanoma. Our results provide strong support for the instructive model of oncoprotein-directed epigenetic silencing.
TLR4/MD-2 activation by a synthetic agonist with no similarity to LPS
Authors: Wang Ying , Su Lijing , Morin Matthew D. , Jones Brian T. , Whitby Landon R. , Surakattula Murali M. R. P. , Huang Hua , Shi Hexin , Choi Jin Huk , Wang Kuan-wen , Moresco Eva Marie Y. , Berger Michael , Zhan Xiaoming , Zhang Hong , Boger Dale L. , Beutler Bruce 
Published: February 2016

Significance
The Toll-like receptor 4 (TLR4)/myeloid differentiation factor 2 (MD-2) complex recognizes lipopolysaccharide (LPS) on Gram-negative bacteria to induce an innate immune response. Neoseptins, chemically synthesized peptidomimetics that bind and activate the mouse TLR4 (mTLR4)/MD-2 complex independent of LPS, were discovered through unbiased screening and reverse genetic studies, and improved by chemical modification. NMR and X-ray crystallography of the TLR4/MD-2/Neoseptin-3 complex determined the mechanism by which Neoseptin-3 activates mTLR4/MD-2 and triggers myeloid differentiation primary response gene 88- and Toll-interleukin 1 receptor domain-containing adaptor inducing IFN-beta-dependent signaling. Neoseptin-3 binds as a dimer within the hydrophobic pocket of MD-2, contacting residues distinct from those contacted by LPS or lipid A, yet triggering a conformational change very similar to that elicited by LPS or lipid A. Natural peptides might conceivably produce similar effects.