bluuebunny/crossref_metadata_2025_split huggingface dataset:
Escherichia coli of sequence type 3835 carrying blaNDM-1, blaCTX-M-15, blaCMY-42 and blaSHV-12
Authors: Feng Yu , Yang Ping , Xie Yi , Wang Xiaohui , McNally Alan , Zong Zhiyong 
Published: July 2015

AbstractNew Delhi metallo-β-lactamase (NDM) represents a serious challenge for treatment and public health. A carbapenem-resistant Escherichia coli clinical strain WCHEC13-8 was subjected to antimicrobial susceptibility tests, whole genome sequencing and conjugation experiments. It was resistant to imipenem (MIC, >256 μg/ml) and meropenem (MIC, 128 μg/ml) and belonged to ST3835. blaNDM-1 was the only carbapenemase gene detected. Strain WCHEC13-8 also had a plasmid-borne AmpC gene (blaCMY-42) and two extended-spectrum β-lactamase genes (blaCTX-M-15 and blaSHV-12). blaNDM-1 and blaSHV-12 were carried by a 54-kb IncX3 self-transmissible plasmid, which is identical to plasmid pNDM-HF727 from Enterobacter cloacae. blaCMY-42 was carried by a 64-kb IncI1 plasmid and blaCTX-M-15 was located on a 141-kb plasmid with multiple F replicons (replicon type: F36:A4:B1). blaCMY-42 was in a complicated context and the mobilisation of blaCMY-42 was due to the transposition of ISEcp1 by misidentifying its right-end boundary. Genetic context of blaNDM-1 in strain WCHEC13-8 was closely related to those on IncX3 plasmids in various Enterobacteriaceae species in China. In conclusion, a multidrug-resistant ST3835 E. coli clinical strain carrying blaNDM-1, blaCTX-M-15, blaCMY-42 and blaSHV-12 was identified. IncX3 plasmids may be making a significant contribution to the dissemination of blaNDM among Enterobacteriaceae in China.
On the importance of sensor height variation for detection of magnetic labels by magnetoresistive sensors
Authors: Henriksen Anders Dahl , Wang Shan Xiang , Hansen Mikkel Fougt 
Published: July 2015

AbstractMagnetoresistive sensors are widely used for biosensing by detecting the signal from magnetic labels bound to a functionalized area that usually covers the entire sensor structure. Magnetic labels magnetized by a homogeneous applied magnetic field weaken and strengthen the applied field when they are over and outside the sensor area, respectively and the detailed origin of the sensor signal in experimental studies has not been clarified. We systematically analyze the signal from both a single sensor stripe and an array of sensor stripes as function of the geometrical parameters of the sensor stripes as well as the distribution of magnetic labels over the stripes. We show that the signal from sensor stripes with a uniform protective coating, contrary to conventional wisdom in the field, is usually dominated by the contribution from magnetic labels between the sensor stripes rather than by the labels on top of the sensor stripes because these are at a lower height. We therefore propose a shift of paradigm to maximize the signal due to magnetic labels between sensor stripes. Guidelines for this optimization are provided and illustrated for an experimental case from the literature.
Yindanxinnaotong, a Chinese compound medicine, synergistically attenuatesatherosclerosis progress
Authors: Cheng Long , Pan Guo-feng , Zhang Xiao-dong , Wang Jian-lu , Wang Wan-dan , Zhang Jian-yong , Wang Hui , Liang Ri-xin , Sun Xiao-bo 
Published: July 2015

Abstract
Yindanxinnaotong (YD), a traditional Chinese medicine, has been introduced toclinical medicine for more than a decade, while its pharmacological properties arestill not to be well addressed. This report aimed to explore theanti-atherosclerosis properties and underlying mechanisms of YD. We initiallyperformed a computational prediction based on a network pharmacology simulation,which clued YD exerted synergistically anti-atherosclerosis properties by vascularendothelium protection, lipid-lowering, anti-inflammation and anti-oxidation. Theseoutcomes were then validated in atherosclerosis rats. The experiments providedevidences indicating YD’s contribution in this study included, (1)significantly reduced the severity of atherosclerosis, inhibited reconstruction ofthe artery wall and regulated the lipid profile; (2) enhanced antioxidant power,strengthened the activity of antioxidant enzymes and decreased malondialdhydelevels; (3) significantly increased the viability of umbilical vein endothelialcells exposed to oxidative stress due to pretreatment with YD; (4) significantlyreduced the level of pro-inflammatory cytokines; (5) significantly down-regulatedNF-kB/p65 and up-regulated IkB in the YD-treated groups. Overall, these resultsdemonstrated that YD intervention relieves atherosclerosis through regulatinglipids, reducing lipid particle deposition in the endothelial layer of artery,enhancing antioxidant power and repressing inflammation activity by inhibiting thenuclear factor-kappa B signal pathway.
Control of the wrinkle structure on surface-reformed poly(dimethylsiloxane) via ion-beam bombardment
Authors: Park Hong-Gyu , Jeong Hae-Chang , Jung Yoon Ho , Seo Dae-Shik 
Published: July 2015

AbstractWe investigated the surface reformation of poly(dimethylsiloxane) (PDMS) elastomers by means of ion beam bombardment for fabricating wrinkle structures. Oxidation on the PDMS surface formed a silica-like outer layer that interacted with the inner PDMS layer, leading to the formation of wrinkle structures that minimized the combined bending energy of the outer layer and stretching energy of the inner layer. In addition, we controlled the amplitude and period of the wrinkle structures by adjusting the PDMS annealing temperature. As the PDMS annealing temperature was increased, the amplitude and period of the wrinkles formed by IB irradiation changed from 604.35 to 69.01 nm and from 3.07 to 0.80 μm, respectively.
Ancestry, admixture and fitness in Colombian genomes
Authors: Rishishwar Lavanya , Conley Andrew B. , Wigington Charles H. , Wang Lu , Valderrama-Aguirre Augusto , King Jordan I. 
Published: July 2015

AbstractThe human dimension of the Columbian Exchange entailed substantial genetic admixture between ancestral source populations from Africa, the Americas and Europe, which had evolved separately for many thousands of years. We sought to address the implications of the creation of admixed American genomes, containing novel allelic combinations, for human health and fitness via analysis of an admixed Colombian population from Medellin. Colombian genomes from Medellin show a wide range of three-way admixture contributions from ancestral source populations. The primary ancestry component for the population is European (average = 74.6%, range = 45.0%–96.7%), followed by Native American (average = 18.1%, range = 2.1%–33.3%) and African (average = 7.3%, range = 0.2%–38.6%). Locus-specific patterns of ancestry were evaluated to search for genomic regions that are enriched across the population for particular ancestry contributions. Adaptive and innate immune system related genes and pathways are particularly over-represented among ancestry-enriched segments, including genes (HLA-BandMAPK10) that are involved in defense against endemic pathogens such as malaria. Genes that encode functions related to skin pigmentation (SCL4A5) and cutaneous glands (EDAR) are also found in regions with anomalous ancestry patterns. These results suggest the possibility that ancestry-specific loci were differentially retained in the modern admixed Colombian population based on their utility in the New World environment.
Fertile fathoms: Deep reproductive refugia for threatened shallow corals
Authors: Holstein Daniel M. , Smith Tyler B. , Gyory Joanna , Paris Claire B. 
Published: July 2015

AbstractThe persistence of natural metapopulations may depend on subpopulations that exist at the edges of species ranges, removed from anthropogenic stress. Mesophotic coral ecosystems (30–150 m) are buffered from disturbance by depth and distance and are potentially massive reservoirs of coral diversity and fecundity; yet we know little about the reproductive capabilities of their constituent species and the potential for these marginal environments to influence patterns of coral reef persistence. We investigated the reproductive performance of the threatened depth-generalist coralOrbicella faveolataover the extent of its vertical range to assess mesophotic contributions to regional larval pools. Over equal habitat area, mesophotic coral populations were found to produce over an order of magnitude more eggs than nearby shallow populations. Positive changes with depth in both population abundance and polyp fecundity contributed to this discrepancy. Relative larval pool contributions of deeper living corals will likely increase as shallow habitats further degrade due to climate change and local habitat degradation. This is a compelling example of the potential for marginal habitat to be critical to metapopulation persistence as reproductive refugia.
An advanced fragment analysis-based individualized subtype classification of pediatric acute lymphoblastic leukemia
Authors: Zhang Han , Cheng Hao , Wang Qingqing , Zeng Xianping , Chen Yanfen , Yan Jin , Sun Yanran , Zhao Xiaoxi , Li Weijing , Gao Chao , Gong Wenyu , Li Bei , Zhang Ruidong , Nan Li , Wu Yong , Bao Shilai , Han Jing-Dong J. , Zheng Huyong 
Published: July 2015

AbstractPediatric acute lymphoblastic leukemia (ALL) is the most common neoplasm and one of the primary causes of death in children. Its treatment is highly dependent on the correct classification of subtype. Previously, we developed a microarray-based subtype classifier based on the relative expression levels of 62 marker genes, which can predict 7 different ALL subtypes with an accuracy as high as 97% in completely independent samples. Because the classifier is based on gene expression rank values rather than actual values, the classifier enables an individualized diagnosis, without the need to reference the background distribution of the marker genes in a large number of other samples and also enables cross platform application. Here, we demonstrate that the classifier can be extended from a microarray-based technology to a multiplex qPCR-based technology using the same set of marker genes as the advanced fragment analysis (AFA). Compared to microarray assays, the new assay system makes the convenient, low cost and individualized subtype diagnosis of pediatric ALL a reality and is clinically applicable, particularly in developing countries.
Formation of the ether lipids archaetidylglycerol and archaetidylethanolamine in Escherichia coli
Authors: Caforio Antonella , Jain Samta , Fodran Peter , Siliakus Melvin , Minnaard Adriaan J. , van der Oost John , Driessen Arnold J.M. 
Published: July 2015

In archaea, the membrane phospholipids consist of isoprenoid hydrocarbon chains that are ether-linked to a sn-glycerol1-phosphate backbone. This unique structure is believed to be vital for the adaptation of these micro-organisms to extreme environments, but it also reflects an evolutionary marker that distinguishes archaea from bacteria and eukaryotes. CDP–archaeol is the central precursor for polar head group attachment. We examined various bacterial enzymes involved in the attachment of L-serine and glycerol as polar head groups for their promiscuity in recognizing CDP–archaeol as a substrate. Using a combination of mutated bacterial and archaeal enzymes, archaetidylethanolamine (AE) and archaetidylglycerol (AG) could be produced in vitro using nine purified enzymes while starting from simple building blocks. The ether lipid pathway constituted by a set of archaeal and bacterial enzymes was introduced into Escherichia coli, which resulted in the biosynthesis of AE and AG. This is a further step in the reprogramming of E. coli for ether lipid biosynthesis.
Insights into G-quadruplex specific recognition by the DEAH-box helicase RHAU: Solution structure of a peptide–quadruplex complex
Authors: Heddi Brahim , Cheong Vee Vee , Martadinata Herry , Phan Anh Tuân 
Published: July 2015

Significance
G-quadruplexes (G4) are four-stranded nucleic acid structures implicated in important biological processes. Interaction between G4 and proteins is essential for the cellular functions of G4. The DEAH (Asp-Glu-Ala-His) box RNA helicase associated with AU-rich element (RHAU) (also named DHX36 or G4R1) specifically binds and unwinds G4 structures. The structure of an 18-aa peptide, identified as the G4-binding domain of RHAU, was solved in the complex with a G4 by NMR spectroscopy. The structure of the complex explains how RHAU specifically recognizes G4 structures and suggests a strategy for G4 recognition by proteins.
Global trends in infectious diseases at the wildlife–livestock interface
Authors: Wiethoelter Anke K. , Beltrán-Alcrudo Daniel , Kock Richard , Mor Siobhan M. 
Published: July 2015

SignificanceInfectious diseases at the wildlife–livestock interface threaten the health and well-being of wildlife, livestock, and human populations, and contribute to significant economic losses to each sector. No studies have sought to characterize the diseases and animals involved on a global level. Using a scoping review framework we show that 10 diseases—mostly zoonoses—have accounted for half of the published research in this area over the past century. We show that relatively few interfaces can be considered important from a disease ecology perspective. These findings suggest that surveillance and research strategies that target specific wildlife–livestock interfaces may yield the greatest return in investment.
Hypoxia-induced force increase (HIFI) is a novel mechanism underlying the strengthening of labor contractions, produced by hypoxic stresses
Authors: Alotaibi Mohammed , Arrowsmith Sarah , Wray Susan 
Published: July 2015

Significance
Parturition requires strong uterine contractions. A longstanding enigma has been how contractions strengthen despite also causing transient ischemia as they occlude uterine blood vessels. Here we demonstrate a hitherto undescribed mechanism whereby in an adaptation at labor, brief hypoxia in uterine muscle, stimulates the contractile activity. We have named this hypoxia-induced force increase, or HIFI. We identify the underlying mechanism, which involves adenosine and prostaglandin and a rise in intracellular calcium, and show it is present in animal and human uterus, but only close to delivery. We speculate that aberrations in this powerful mechanism could underlie contractions being triggered too early (preterm labor) or if HIFI is deficient, weak contractions, and thus poor and unsuccessful term labors.
The Xist RNA-PRC2 complex at 20-nm resolution reveals a low Xist stoichiometry and suggests a hit-and-run mechanism in mouse cells
Authors: Sunwoo Hongjae , Wu John Y. , Lee Jeannie T. 
Published: July 2015

Significance
X-chromosome inactivation (XCI) is initiated by the long noncoding RNA Xist. Here we view Xist RNA and the Xi at 20-nm resolution using STochastic Optical Reconstruction Microscopy (STORM) and observe dynamics at the single-cell level not predicted by epigenomic analysis. Only 50–100 Xist molecules and ∼50 PRC2 foci are observed per Xi, contrasting with the chromosome-wide “coat” observed by deep sequencing and conventional microscopy. Xist knock-off experiments enable visualization of dissociation and relocalization dynamics, and support a functional tethering of Xist and PRC2. Thus, Xist-PRC2 complexes are less numerous than expected, implying that the Xist-PRC2 complexes methylate nucleosomes in a hit-and-run model.
Heterogeneous binding of the SH3 client protein to the DnaK molecular chaperone
Authors: Lee Jung Ho , Zhang Dongyu , Hughes Christopher , Okuno Yusuke , Sekhar Ashok , Cavagnero Silvia 
Published: July 2015

Significance
Heat shock protein 70 (Hsp70) molecular chaperones play key roles in protein folding and other cellular processes. The effect of Hsp70 on the conformation of its substrate proteins is still largely unknown. This study unveils, for the first time to our knowledge, the effect of the bacterial Hsp70 chaperone DnaK on the structure of the full-length substrate protein SRC homology 3 domain (SH3). We show that multiple largely unstructured conformations of SH3, distinct from the protein’s unfolded state, interact with DnaK. The bound client protein shares a flexible N terminus and multiple slowly interconverting conformations in different parts of the sequence. In all, there is significant structural and dynamical heterogeneity. This result is important because it reveals that proteins may undergo conformational sampling while chaperone-bound.
Complex dynamics of synergistic coinfections on realistically clustered networks
Authors: Hébert-Dufresne Laurent , Althouse Benjamin M. 
Published: July 2015

SignificanceConcurrent infection with multiple pathogens is an important factor for human disease. For example, rates ofStreptococcus pneumoniaecarriage (a leading cause of pneumonia) in children under five years can exceed 80%, and coinfection with other respiratory infections (e.g., influenza) can increase mortality drastically; despite this, examination of interacting coinfections on realistic human contact structures remains an understudied problem in epidemiology and network science. Here we show that clustering of contacts, which usually hinders disease spread, can speed up spread of both diseases by keeping synergistic infections together and that a microscopic change in transmission rates can cause a macroscopic change in expected epidemic size, such that clustered networks can sustain diseases that would otherwise die in random networks.
Ubl4A is required for insulin-induced Akt plasma membrane translocation through promotion of Arp2/3-dependent actin branching
Authors: Zhao Yu , Lin Yuting , Zhang Honghong , Mañas Adriana , Tang Wenwen , Zhang Yuzhu , Wu Dianqing , Lin Anning , Xiang Jialing 
Published: July 2015

Significance
The signal-induced Akt membrane recruitment is a crucial step for its activation, but the underlying mechanism is incompletely understood. We show that ubiquitin-like protein 4A (Ubl4A) is required for insulin-induced Akt membrane translocation through direct promotion of actin-related protein 2 and 3 (Arp2/3)-dependent actin branching, thereby ensuring glycogen synthesis for neonatal survival. As a novel Arp2/3-binding protein, Ubl4A may play important roles in the translocation of other actin-binding molecules controlled by a similar mechanism, as well as a broad range of cellular functions related to the actin branching network.
Protein tyrosine phosphatase SAP-1 protects against colitis through regulation of CEACAM20 in the intestinal epithelium
Authors: Murata Yoji , Kotani Takenori , Supriatna Yana , Kitamura Yasuaki , Imada Shinya , Kawahara Kohichi , Nishio Miki , Daniwijaya Edwin Widyanto , Sadakata Hisanobu , Kusakari Shinya , Mori Munemasa , Kanazawa Yoshitake , Saito Yasuyuki , Okawa Katsuya , Takeda-Morishita Mariko , Okazawa Hideki , Ohnishi Hiroshi , Azuma Takeshi , Suzuki Akira , Matozaki Takashi 
Published: July 2015

SignificanceMuch attention has been recently paid to the role of intestinal epithelial cells in the homeostatic regulation of intestinal immunity. Here we show that ablation of stomach-cancer–associated protein tyrosine phosphatase 1 (SAP-1) markedly increased the severity of colitis in interleukin (IL)-10–deficient mice, suggesting that SAP-1 protects against colitis in a cooperative manner with IL-10. We also identify carcinoembryonic antigen-related cell adhesion molecule (CEACAM) 20, an intestinal microvilli-specific membrane protein, as a dephosphorylation target for SAP-1. Indeed, tyrosine phosphorylation of CEACAM20 promotes the binding of spleen tyrosine kinase (Syk) and activation of nuclear factor-κB (NF-κB), thereby inducing production of chemokines such as IL-8. Thus, we propose a mechanism by SAP-1 and CEACAM20 in the intestinal epithelium for regulation of the intestinal immunity.
Top-down modulation in the infant brain: Learning-induced expectations rapidly affect the sensory cortex at 6 months
Authors: Emberson Lauren L. , Richards John E. , Aslin Richard N. 
Published: July 2015

SignificanceAlthough infants are excellent learners, it is unclear whether infants use neural strategies similar to those of adults to track changes in their environment. One adult neural strategy is to use feedback connections to modulate sensory cortices based on their expectations. The current study provides, to our knowledge, the first evidence that the fundamental architecture required for sensory feedback is already in place in infancy. This top-down modulation is especially impressive because the study employs an audiovisual task that requires the flexible use of long-range neural connections, and the infant brain is dominated by short-range neural connections with weak (e.g., unmyelinated) long-range connections. These results suggest that learners can use sophisticated top-down feedback neural strategies from an early age.
Erlotinib protects against LPS-induced Endotoxicity because TLR4 needs EGFR to signal
Authors: De Sarmishtha , Zhou Hao , DeSantis David , Croniger Colleen M. , Li Xiaoxia , Stark George R. 
Published: July 2015

Significance
The activation of nuclear factor κB (NFκB) in the normal inflammatory response is rapidly down regulated, whereas constitutive NFκB activation is a hallmark of cancer. We now reveal cross signaling between EGF receptor (EGFR) and Toll-like receptor 4 (TLR4). NFκB activation in response to EGF requires, in addition to EGFR, TLR4 and two downstream proteins. Conversely, EGFR is required for TLR4-mediated activation of NFκB in response to lipopolysaccharide (LPS). The LYN proto-oncogene (LYN) is required for NFκB activation in response to either ligand. In mice, the EGFR inhibitor erlotinib greatly reduces both cytokine expression and endotoxicity in response to LPS, suggesting that EGFR inhibitors may find use in treating septic shock.
Small-molecule enhancers of autophagy modulate cellular disease phenotypes suggested by human genetics
Authors: Kuo Szu-Yu , Castoreno Adam B. , Aldrich Leslie N. , Lassen Kara G. , Goel Gautam , Dančík Vlado , Kuballa Petric , Latorre Isabel , Conway Kara L. , Sarkar Sovan , Maetzel Dorothea , Jaenisch Rudolf , Clemons Paul A. , Schreiber Stuart L. , Shamji Alykhan F. , Xavier Ramnik J. 
Published: July 2015

Significance
Given the importance of autophagy in a number of human diseases, we have identified small-molecule modulators of autophagy that affect disease-associated phenotypes in relevant cell types. BRD5631 and related compounds can serve as tools for studying how autophagy regulates immune pathways, and for evaluating the therapeutic potential of modulating autophagy in a variety of disease contexts. Deeper investigation into their mechanisms of action may reveal proteins and pathways that could serve as relevant targets for future therapeutic discovery.