bluuebunny/crossref_metadata_2025_split huggingface dataset:
A new mechanism for dendritic pattern formation in dense systems
Authors: Oikawa Noriko , Kurita Rei 
Published: June 2016

AbstractPatterns are often formed when particles cluster: Since patterns reflect the connectivity of different types of material, the emergence of patterns affects the physical and chemical properties of systems and shares a close relationship to their macroscopic functions. A radial dendritic pattern (RDP) is observed in many systems such as snow crystals, polymer crystals and biological systems. Although most of these systems are considered as dense particle suspensions, the mechanism of RDP formation in dense particle systems is not yet understood. It should be noted that the diffusion limited aggregation model is not applicable to RDP formation in dense systems, but in dilute particle systems. Here, we propose a simple model that exhibits RDP formation in a dense particle system. The model potential for the inter-particle interaction is composed of two parts, a repulsive and an attractive force. The repulsive force is applied to all the particles all the time and the attractive force is exerted only among particles inside a circular domain, which expands at a certain speed as a wave front propagating from a preselected centre. It is found that an RDP is formed if the velocity of the wave front that triggers the attractive interaction is of the same order of magnitude as the time scale defined by the aggregation speed.
Two different mechanisms mediate chemotaxis to inorganic phosphate in Pseudomonas aeruginosa
Authors: Rico-Jiménez Miriam , Reyes-Darias Jose Antonio , Ortega Álvaro , Díez Peña Ana Isabel , Morel Bertrand , Krell Tino 
Published: June 2016

AbstractInorganic phosphate (Pi) is a central signaling molecule that modulates virulence in various pathogens. In Pseudomonas aeruginosa, low Pi concentrations induce transcriptional alterations that increase virulence. Also, under low Pi levels, P. aeruginosa exhibits Pi chemotaxis—a process mediated by the two non-paralogous receptors CtpH and CtpL. Here we show that the two receptors operate via different mechanisms. We demonstrate that the ligand binding domain (LBD) of CtpH but not CtpL binds Pi directly. We identify the periplasmic ligand binding protein PstS as the protein that binds in its Pi loaded state to CtpL, resulting in receptor stimulation. PstS forms part of the Pi transporter and has thus a double function in Pi transport and chemotaxis. The affinity of Pi for CtpH was modest whereas that for PstS very high, which may explain why CtpH and CtpL mediate chemotaxis to high and low Pi concentrations, respectively. The pstS/ctpH double mutant was almost devoid of Pi taxis, indicating that PstS is the only CtpL Pi-shuttle. Chemotaxis mechanisms based on indirect ligand recognition were unambiguously identified in enterobacteria. The discovery of a similar mechanism in a different bacterial order, involving a different chemoreceptor type and chemoeffector suggests that such systems are widespread.
Degradation of dyes using crude extract and a thermostable and pH-stable laccase isolated from Pleurotus nebrodensis
Authors: Yuan Xianghe , Tian Guoting , Zhao Yongchang , Zhao Liyan , Wang Hexiang , Ng Tzi Bun 
Published: June 2016

Three laccase isoenzymes (Lac1, Lac2 and Lac3) have been purified to homogeneity from Pleurotus nebrodensis in our previous study. Lac2 was shown to be the dominant isoform, capable of oxidizing the majority of laccase substrates and manifesting good thermostability and pH stability. Hence, Lac2 was selected to decolourize structurally different dyes and the colour removal efficiencies of Lac2 and the crude extract of P. nebrodensis were compared. By monitoring the λmax of the reaction system during the course of biotransformation, clear hypsochromic shifts were observed for most of the dyes examined, illustrating that at least one peak disappeared as a result of laccase treatment. In general, Lac2 was more efficient within a short time (1 h) and the crude extract, in general, could achieve similar or even higher efficiency when the duration of treatment was extended to 24 h. Malachite green (MG) was chosen to study the detoxifying potential of Lac2, because of the relatively simple structure and high toxicity of the dye towards microorganisms. The toxicity of MG towards both bacteria (Bacillus subtilis, Bacillus licheniformis, Pseudomonas fluorescens and Escherichia coli) and fungi (Fusarium graminearum and Trichoderma harzianum) was dramatically decreased and the potential mechanism was estimated by GC–MS as to remove four methyl groups firstly and the two newly formed amine groups would be degraded or polymerized further. The present study facilitates an understanding of the application of P. nebrodensis laccases and furnishes evidence for the safety of their utilization in the treatment of wastewater emanating from textile industries.
Zoledronic Acid Improves Bone Quality in the Streptozotocin-Induced Diabetes Rat through Affecting the Expression of the Osteoblast-Regulating Transcription Factors
Authors: Cui M. , Yu L.-Z , Zhang N. , Wang L.-J. , Sun J. , Cong J. 
Published: June 2016

Abstract
Aims To evaluate the short term effect of zoledronic acid on bone remodeling in the streptozotocin induced diabetes rats.
Materials and Methods Diabetes was induced by an injection of streptozotocin (60 mg/kg). The rats were treated with zoledronic acid (0.1 mg/kg) at the onset of diabetes (Z-I group) and 2 weeks later (Z-II group). Rats were sacrificed at the 1, 2, 3, 4 and 5 weeks after the onset of diabetes. Real–time PCR and western blot were performed to detect the expression of the following osteogenic gene mRNAs and their proteins: bone morphogenetic proteins 2 (BMP2), Runx2, Osterix and Noggin. The bone mineral density (BMD) and the mechanical resistance test was measured.
Results BMP2, Runx2 and Osterix mRNA and protein expression in group D had regulated down, while Noggin expression increased. Z-I treatment could reverse the results. However group Z-II showed only a transient reversing effect. On the 5th week in group D, the BMD decreased, the bone trabecular distance increased, while the trabecular thickness and bone trabecular volume were reduced, the biomechanics index decreased significantly. Zoledronic acid treatment restored these alterations.
Conclusions Zoledronic acid administered in the early stage of the diabetes could prevent the osteopenia. The underlying mechanisms might be that zoledronic acid treatment reversed the effect of diabetes on the expression of osteoblast-regulating transcription factors: BMP2, Runx2 and Osterix.
Salinity of deep groundwater in California: Water quantity, quality, and protection
Authors: Kang Mary , Jackson Robert B. 
Published: June 2016

Significance
Groundwater withdrawals are increasing across the United States, particularly in California, which faces a growing population and prolonged drought. Deep groundwater aquifers provide an alternative source of fresh and saline water that can be useable with desalination and/or treatment. In the Central Valley alone, fresh groundwater volumes can be increased almost threefold, and useable groundwater volumes can be increased fourfold if we extend depths to 3,000 m. However, some of these deep groundwater resources are vulnerable to contamination from oil/gas and other human activities. Our findings provide the first estimates, to our knowledge, of underground sources of drinking water depths and volumes in California and show the need to better characterize and protect deep groundwater aquifers.
Bacterial lipids activate, synergize, and inhibit a developmental switch in choanoflagellates
Authors: Woznica Arielle , Cantley Alexandra M. , Beemelmanns Christine , Freinkman Elizaveta , Clardy Jon , King Nicole 
Published: June 2016

Significance
Bacterial symbionts profoundly influence the biology of their animal hosts, yet complex interactions between animals and their resident bacteria often make it challenging to characterize the molecules and mechanisms. Simple model systems can reveal fundamental processes underlying interactions between eukaryotes and their associated microbial communities and provide insight into how bacteria regulate animal biology. In this study we isolate and characterize bacterial molecules that regulate multicellular development in the closest living relatives of animals, the choanoflagellate. We find that multiple bacterially derived lipids converge to activate, enhance, and inhibit choanoflagellate multicellular development.
Analysis of tandem gene copies in maize chromosomal regions reconstructed from long sequence reads
Authors: Dong Jiaqiang , Feng Yaping , Kumar Dibyendu , Zhang Wei , Zhu Tingting , Luo Ming-Cheng , Messing Joachim 
Published: June 2016

Significance
Gene copy number variation plays an important role in genome evolution and the penetrance of phenotype variations within a species. We have applied new sequencing and physical mapping strategies to obtain long chromosomal regions from a single DNA preparation in each method that comprise tandem repeated gene copies interspersed with transposable elements that comprise about 85% of the genome. This approach should reduce the time and cost to study haplotype variation of complex genomes like those from mammalian and plant species.
Predicting the Stability of Endangered Stonecats in the LaPlatte River, Vermont
Authors: Puchala Elizabeth A. , Parrish Donna L. , Donovan Therese M. 
Published: June 2016

AbstractStonecatsNoturus flavusin Vermont conform to a rare distribution pattern (as designated by Rabinowitz 1981) because their known distribution within the state is limited to the LaPlatte and Missisquoi rivers. We focused on Stonecats in the LaPlatte River to predict the stability of the population. During 2012–2014, we captured Stonecats via backpack electrofishing; fish were PIT‐tagged (>90 mm TL) and marked with visible implant elastomer. Among the 1,671 Stonecats that were captured, 1,252 were PIT‐tagged. Only 156 (12%) of the PIT‐tagged fish were recaptured, and only 22 of those individuals were recaptured more than once. The Pradel model in Program MARK was used to estimate apparent survival (Φ) and seniority, which were used to derive the rate of population change (λ) for the Stonecat encounter histories we studied. We examined a total of 64 models in our candidate set, with the following covariates: TL at first capture, maximum temperature, season, maximum discharge, and area sampled. Survival estimates were highest in the spring (range of daily Φ = 0.9993–0.9995) and increased with greater TL at first capture. We also estimated increases in capture probability with increasing area sampled. We derived an annual λ of 0.9794, which indicates a slightly decreasing population. However, our λ estimate contained uncertainty that was likely increased due to the low recapture rates. Additional years of data could increase the accuracy of the λ estimate. In the meantime, we have provided insight into Stonecat population parameters that were otherwise unknown.Received December 22, 2015; accepted March 1, 2016 Published online June 29, 2016
Money, migration and masculinity among artisanal miners in Katanga (DR Congo)
Authors: Cuvelier Jeroen 
Published: June 2016

ABSTRACT
The Katangese artisanal mining sector has grown spectacularly since the late 1990s. Faced with political instability and economic crisis, tens of thousands of men have moved to the mining areas in order to find new sources of income. This article offers a detailed ethnographic description of how male migrant workers experience and cope with the challenging realities of life on the mines against the backdrop of recent changes in Katanga’s political economy. More specifically, it examines the relationship between money, migration and masculinity through an extended case study of a money dispute among a group of artisanal miners working in the Kalabi mine near Lwambo, a small town situated 20 kilometres north of Likasi. It is found that the conspicuous consumption of money plays a vital role in the mining subculture; that credit and debt dominate life on the mines; and that artisanal mining has given rise to significant changes in gender relations and household organisation.
Structural distinctions of fast and slow bacterial luciferases revealed by phylogenetic analysis
Authors: Deeva Anna A. , Temlyakova Evgenia A. , Sorokin Anatoly A. , Nemtseva Elena V. , Kratasyuk Valentina A. 
Published: June 2016

Abstract
Motivation: Bacterial luciferases are heterodimeric enzymes that catalyze a chemical reaction, so called bioluminescence, which causes light emission in bacteria. Bioluminescence is vastly used as a reporter system in research tools and commercial developments. However, the details of the mechanisms that stabilize and transform the reaction intermediates as well as differences in the enzymatic kinetics amongst different bacterial luciferases remain to be elucidated.
Results: Amino acid sequences alignments for 21 bacterial luciferases (both α- and β-subunits) were analyzed. For α-subunit, containing the enzyme active center, 48 polymorphic amino acid positions were identified. According to them, the sequences fell into two distinct groups known as slow and fast based on the decay rate of the bioluminescence reaction. The differences in the enzyme active site induced by structural polymorphism are analyzed.
Availability and implementation: Three-dimensional models of Photobacterium leiognathi luciferase and Vibrio harveyi luciferase (with reconstructed mobile loop) are freely available at PMDB database: PM0080525 and PM0080526, respectively.
Contact: adeeva@sfu-kras.ru
Supplementary information: Supplementary data are available at Bioinformatics online.
Nonparametric binary instrumental variable analysis of competing risks data
Authors: Richardson Amy , Hudgens Michael G. , Fine Jason P. , Brookhart M. Alan 
Published: June 2016

Summary
In both observational studies and randomized trials with noncompliance, unmeasured confounding may exist which may bias treatment effect estimates. Instrumental variables (IV) are a popular technique for addressing such confounding, enabling consistent estimation of causal effects. This paper proposes nonparametric IV estimators for censored time to event data that may be subject to competing risks. A simple, plug-in estimator is introduced using nonparametric estimators of the cumulative incidence function, with confidence intervals derived using asymptotic theory. To provide an overall test of the treatment effect, an integrated weighted difference statistic is suggested, which is applicable to data with and without competing risks. Simulation studies demonstrate that the methods perform well with realistic samples sizes. The methods are applied to assess the effect of infant or maternal antiretroviral therapy on transmission of HIV from mother to child via breastfeeding using data from a large, recently completed randomized trial in Malawi where noncompliance with assigned treatment may confound treatment effect estimates.
Seismological investigation of the 2016 January 6 North Korean underground nuclear test
Authors: Zhao Lian-Feng , Xie Xiao-Bi , Wang Wei-Min , Hao Jin-Lai , Yao Zhen-Xing 
Published: June 2016

AbstractSeismology plays an important role in characterizing potential underground nuclear tests. Using broad-band digital seismic data from Northeast China, South Korea and Japan, we investigated the properties of the recent seismic event occurred in North Korea on 2016 January 6. Using a relative location method and choosing the previous 2006 explosion as the master event, the 2016 event was located within the North Korean nuclear test site, with its epicentre at latitude 41.3003°N and longitude 129.0678°E, approximately 900 m north and 500 m west of the previous event on 2013 February 12. Based on the error ellipse, the relocation uncertainty was approximately 70 m. Using the P/S spectral ratios, including Pg/Lg, Pn/Lg and Pn/Sn, as the discriminants, we identify the 2016 event as an explosion rather than an earthquake. The body-wave magnitude calculated from regional wave Lg is mb(Lg) equal to 4.7 ± 0.2. Adopting an empirical magnitude–yield relation, and assuming that the explosion is fully coupled and detonated at a normally scaled depth, we find that the seismic yield is about 4 kt, with the uncertainties allowing a range from 2 to 8 kt.
The Shifting Nature of Work and Its Implications
Authors: Walton Michael J 
Published: June 2016

Abstract
Employment is a critical feature of modern society. The nature of employment not only determines the operation of the economy and economic and business prosperity but also determines the quality of individuals’ lives. In that respect, work is both an economic transaction and central to human life and dignity. There has been a seismic shift in how employment manifests in twenty-first-century Western economies. Rapid growth in non-standard forms of employment, and the corresponding decline of the standard employment contract, has resulted in a less stable and more fragmented labour market. Flexibility may benefit a worker who can operate successfully as a ‘free agent in a boundary-less workplace’. However, others may become stuck in enclaves, unable to access permanent work and having little bargaining power. This raises the prospect of the existence of a ‘dual labour market’, where workers are separated into primary and secondary markets. Those engaged in the primary market will have job security and opportunities for advancement, while those in secondary markets will become increasingly vulnerable. Regulatory systems based upon traditional models of employment are ill-equipped to deal with the challenges these developments pose for modern economies.
Comparative efficacy of telavancin and daptomycin in experimental
endocarditis due to multi-clonotype MRSA strains
Authors: Xiong Yan Q. , Abdelhady Wessam , Tang Chieh ‘Genna’ , Bayer Arnold S. 
Published: June 2016

Abstract

Background
MRSA strains of clonal complexes (CCs) 5, 8, 30 and 45 are leading causes of complicated endovascular infections associated with suboptimal clinical outcomes. Telavancin is a novel anti-MRSA agent that both inhibits bacterial cell wall synthesis and disrupts membranes by depolarization.

Methods
In this study, we compared the in vitro susceptibility and in vivo efficacy of telavancin versus daptomycin in an experimental rabbit infective endocarditis (IE) model caused by four MRSA strains representing each of the above CC types.

Results
All study strains were susceptible to telavancin (MICs of ≤0.12 mg/L) and daptomycin (MICs of ≤0.5 mg/L). In vitro time–kill analyses revealed that supra-MIC levels of telavancin were effective at preventing regrowth at 24 h of incubation. In the IE animal model for all CC types, treatment with telavancin produced significantly greater reductions in MRSA counts as compared with daptomycin-treated animals in all target tissues. Moreover, telavancin-treated animals had a significantly higher percentage of sterile tissue cultures versus daptomycin-treated animals (e.g. 78%–100% versus 0% sterile vegetations and 100% versus 0%–11% sterile kidneys and spleen, in the telavancin- and daptomycin-treated animals, respectively).

Conclusions
These results suggest that telavancin exhibits significantly greater efficacies versus daptomycin in treating experimental IE caused by MRSA clinical isolates across four common CC types.
Eligibility requirements for advanced health informatics certification
Authors: Gadd Cynthia S , Williamson Jeffrey J , Steen Elaine B , Andriole Katherine P , Delaney Connie , Gumpper Karl , LaVenture Martin , Rosendale Doug , Sittig Dean F , Thyvalikakath Thankam , Turner Peggy , Fridsma Douglas B 
Published: June 2016

Abstract
AMIA is leading the effort to strengthen the health informatics profession by creating an advanced health informatics certification (AHIC) for individuals whose informatics work directly impacts the practice of health care, public health, or personal health. The AMIA Board of Directors has endorsed a set of proposed AHIC eligibility requirements that will be presented to the future AHIC certifying entity for adoption. These requirements specifically establish who will be eligible to sit for the AHIC examination and more generally signal the depth and breadth of knowledge and experience expected from certified individuals. They also inform the development of the accreditation process and provide guidance to graduate health informatics programs as well as individuals interested in pursuing AHIC. AHIC eligibility will be determined by practice focus, education in primary field and health informatics, and significant health informatics experience.
V346 Normae: first post-outburst observations of an FU Orionis star
Authors: Kraus S. , Caratti o Garatti A. , Garcia-Lopez R. , Kreplin A. , Aarnio A. , Monnier J. D. , Naylor T. , Weigelt G. 
Published: June 2016

Abstract
During their formation phase, stars gain most of their mass in violent episodic accretion events, such as observed in FU Orionis (FUor) and EXor stars. V346 Normae is a well-studied FUor that underwent a strong outburst beginning around 1980. Here, we report on photometric and spectroscopic observations, which show that the visual/near-infrared brightness has decreased dramatically between the 1990s and 2010 (ΔR ≈ 10.9 mag, ΔJ ≈ 7.8 mag and ΔK ≈ 5.8 mag). The spectral properties of this fading event cannot be explained by variable extinction alone, but indicate a drop in accretion rate by two to three orders of magnitude. This is the first time that a member of the FUor class has been observed to switch to a very low accretion phase. Remarkably, in the last few years (2011–2015) V346 Nor has brightened again at all near-infrared wavelengths, indicating the onset of a new outburst event. The observed behaviour might be consistent with the clustered luminosity bursts that have been predicted by recent gravitational instability and fragmentation models for the early stages of protostellar evolution. Given V346 Nor's unique characteristics (concerning outburst duration, repetition frequency and spectroscopic diagnostics), our results also highlight the need to revisit the FUor/EXor classification scheme.
Inset of Unilateral Dual Microvascular Breast Reconstruction Using Nonabdominal Free Tissue Transfer
Authors: Buescher Teresa M. , Andry Danielle , Brown Travis , Vargo James , Nazir Naiman , Andrews Brian T. 
Published: June 2016

Background:
Large breasted patients are difficult to reconstruct using free tissue transfer after mastectomy when abdominal tissue is inadequate. For these, two unilateral free flaps may be required. This study reviews the authors’ experience using transverse upper gracilis and profunda artery perforator flaps.

Methods:
Through retrospective chart review, subjects were divided into three groups based on vascular anastomotic orientation: group 1, thoracodorsal and internal mammary; group 2, noncrossed internal mammary; and group 3, crossed internal mammary. Statistical comparison determined differences between groups for peri-operative “take-backs” and flap survival.

Results:
Twenty-one subjects underwent 42 free tissue transfers for unilateral breast reconstruction. Perioperative complications requiring return to the operating room occurred as follows for each group: group 1, two of four flaps (50 percent); group 2, two of two flaps (100 percent); and group 3, two of 36 flaps (5.5 percent). Long-term flap survival was as follows: group 1, three of four flaps (75 percent); group 2, zero of two flaps (0 percent); and group 3, 36 of 36 flaps (100 percent). Both the incidence of perioperative complications (p = 0.0011) and flap survival (p = 0.0008) were statistically significant in the three groups.

Conclusions:
Use of double free tissue transfer consisting of transverse upper gracilis or profunda artery perforator flaps is a feasible option for unilateral autologous breast reconstruction. In the authors’ experience, horizontal inset with crossed pedicles to the internal mammary system is the safest and most reliable technique for flap and pedicle inset.