bluuebunny/crossref_metadata_2025_split huggingface dataset:
Satellite gravity gradient grids for geophysics
Authors: Bouman Johannes , Ebbing Jörg , Fuchs Martin , Sebera Josef , Lieb Verena , Szwillus Wolfgang , Haagmans Roger , Novak Pavel 
Published: February 2016

AbstractThe Gravity field and steady-state Ocean Circulation Explorer (GOCE) satellite aimed at determining the Earth’s mean gravity field. GOCE delivered gravity gradients containing directional information, which are complicated to use because of their error characteristics and because they are given in a rotating instrument frame indirectly related to the Earth. We compute gravity gradients in grids at 225 km and 255 km altitude above the reference ellipsoid corresponding to the GOCE nominal and lower orbit phases respectively and find that the grids may contain additional high-frequency content compared with GOCE-based global models. We discuss the gradient sensitivity for crustal depth slices using a 3D lithospheric model of the North-East Atlantic region, which shows that the depth sensitivity differs from gradient to gradient. In addition, the relative signal power for the individual gradient component changes comparing the 225 km and 255 km grids, implying that using all components at different heights reduces parameter uncertainties in geophysical modelling. Furthermore, since gravity gradients contain complementary information to gravity, we foresee the use of the grids in a wide range of applications from lithospheric modelling to studies on dynamic topography and glacial isostatic adjustment, to bedrock geometry determination under ice sheets.
An integrated platform for large-scale data collection and precise perturbation of live Drosophila embryos
Authors: Levario Thomas J. , Zhao Charles , Rouse Tel , Shvartsman Stanislav Y. , Lu Hang 
Published: February 2016

AbstractUnderstanding the fundamental principles governing embryogenesis is a key goal of developmental biology. Direct observation of embryogenesis via in vivo live imaging is vital to understanding embryogenesis; yet, tedious sample preparation makes it difficult to acquire large-scale imaging data that is often required to overcome experimental and biological noises for quantitative studies. Furthermore, it is often difficult and sometimes impossible, to incorporate environmental perturbation for understanding developmental responses to external stimuli. To address this issue, we have developed a method for high-throughput imaging of live embryos, delivering precise environmental perturbations and unbiased data extraction. This platform includes an optimized microfluidic device specifically for live embryos and also for precise perturbations in the microenvironment of the developing embryos. In addition, we developed software for simple, yet accurate, automated segmentation of fluorescent images and automated data extraction. Using a quantitative assessment we find that embryos develop normally within the microfluidic device. Finally, we show an application of the high-throughput assay for monitoring developmental responses to external stimuli: anoxia-induced developmental arrest in Drosophila embryos. With slight modifications, the method developed in this work can be applied to many other models of development and other stimulus-response behaviors during development.
Real-time kinetics of electrogenic Na+ transport by rhodopsin from the marine flavobacterium Dokdonia sp. PRO95
Authors: Bogachev Alexander V. , Bertsova Yulia V. , Verkhovskaya Marina L. , Mamedov Mahir D. , Skulachev Vladimir P. 
Published: February 2016

AbstractDiscovery of the light-driven sodium-motive pump Na+-rhodopsin (NaR) has initiated studies of the molecular mechanism of this novel membrane-linked energy transducer. In this paper, we investigated the photocycle of NaR from the marine flavobacterium Dokdonia sp. PRO95 and identified electrogenic and Na+-dependent steps of this cycle. We found that the NaR photocycle is composed of at least four steps: NaR519 + hv → K585 → (L450↔M495) → O585 → NaR519. The third step is the only step that depends on the Na+ concentration inside right-side-out NaR-containing proteoliposomes, indicating that this step is coupled with Na+ binding to NaR. For steps 2, 3, and 4, the values of the rate constants are 4×104 s–1, 4.7 × 103 M–1 s–1, and 150 s–1, respectively. These steps contributed 15, 15, and 70% of the total membrane electric potential (Δψ ~ 200 mV) generated by a single turnover of NaR incorporated into liposomes and attached to phospholipid-impregnated collodion film. On the basis of these observations, a mechanism of light-driven Na+ pumping by NaR is suggested.
Temporal retinal transcriptome and systems biology analysis identifies key pathways and hub genes in Staphylococcus aureus endophthalmitis
Authors: Rajamani Deepa , Singh Pawan Kumar , Rottmann Bruce G. , Singh Natasha , Bhasin Manoj K. , Kumar Ashok 
Published: February 2016

AbstractBacterial endophthalmitis remains a devastating inflammatory condition associated with permanent vision loss. Hence, assessing the host response in this disease may provide new targets for intervention. Using a mouse model ofStaphylococcus aureus(SA) endophthalmitis and performing retinal transcriptome analysis, we discovered progressive changes in the expression of 1,234 genes. Gene ontology (GO) and pathway analyses revealed the major pathways impacted in endophthalmitis includes: metabolism, inflammatory/immune, antimicrobial, cell trafficking, and lipid biosynthesis. Among the immune/inflammation pathways, JAK/Stat and IL-17A signaling were the most significantly affected. Interactive network-based analyses identified 13 focus hub genes (IL-6, IL-1β, CXCL2, STAT3, NUPR1, Jun, CSF1, CYR61, CEBPB, IGF-1, EGFR1, SPP1, and TGM2) within these important pathways. The expression of hub genes confirmed by qRT-PCR, ELISA (IL-6, IL-1β, and CXCL2), and Western blot or immunostaining (CEBP, STAT3, NUPR1, and IGF1) showed strong correlation with transcriptome data. Since TLR2 plays an important role in SA endophthalmitis, counter regulation analysis of TLR2 ligand pretreated retina or the use of retinas from TLR2 knockout mice showed the down-regulation of inflammatory regulatory genes. Collectively, our study provides, for the first time, a comprehensive analysis of the transcriptomic response and identifies key pathways regulating retinal innate responses in staphylococcal endophthalmitis.
New statistical approach to interpret power transformer frequency response analysis: non‐parametric statistical methods
Authors: Behjat Vahid , Mahvi Mojtaba , Rahimpour Ebrahim 
Published: February 2016

The frequency response analysis (FRA) test has been recognised as one of the sensitive tools for detecting electrical and mechanical faults inside power transformers. However, there is still no universally systematic interpretation technique for these tests. Many research efforts have employed different statistical criteria in order to aid the interpretative capability of the FRA, but it is shown that the methods used so far are based on parametric statistics, which need a set of assumptions about the normality, randomness and statistical independence of FRA data. Therefore, this study aims to propose some non‐parametric statistical methods which are based on explicitly weaker assumptions than such classical parametric methods. The proposed statistical methods are applied to the experimental FRA measurements obtained from two test objects: a three phase distribution transformer (35/0.4 kV, 100 kVA) to study the winding interturn fault and a two winding transformer (1.2 MVA, 10 kV) for the study of radial deformation. The non‐parametric statistical methods, namely Spearman correlation coefficient, Wilcoxon signed rank test and Friedman test are used to compare FRA traces. It was found through this research work that the applied non‐parametric methods can effectively reflect the differences between compared FRA data and diagnose the fault.
Binding interactions of the peripheral stalk subunit isoforms from human V-ATPase
Authors: Rahman Suhaila , Yamato Ichiro , Saijo Shinya , Mizutani Kenji , Takamuku Yuuki , Ishizuka-Katsura Yoshiko , Ohsawa Noboru , Terada Takaho , Shirouzu Mikako , Yokoyama Shigeyuki , Murata Takeshi 
Published: February 2016

AbstractThe mammalian peripheral stalk subunits of the vacuolar-type H+-ATPases (V-ATPases) possess several isoforms (C1, C2, E1, E2, G1, G2, G3, a1, a2, a3, and a4), which may play significant role in regulating ATPase assembly and disassembly in different tissues. To better understand the structure and function of V-ATPase, we expressed and purified several isoforms of the human V-ATPase peripheral stalk: E1G1, E1G2, E1G3, E2G1, E2G2, E2G3, C1, C2, H, a1NT, and a2NT. Here, we investigated and characterized the isoforms of the peripheral stalk region of human V-ATPase with respect to their affinity and kinetics in different combination. We found that different isoforms interacted in a similar manner with the isoforms of other subunits. The differences in binding affinities among isoforms were minor from our in vitro studies. However, such minor differences from the binding interaction among isoforms might provide valuable information for the future structural-functional studies of this holoenzyme.
Tumor cell-derived secretory factor downregulates Semaphorin-3a in osteoblasts by activating mammalian target of rapamycin pathway
Authors: Yamada Daisuke , Kawahara Kohichi , Ozaki Masanobu , Maeda Takehiko 
Published: February 2016

Abstract
We found that conditioned medium derived from Lewis Lung Carcinoma cells down-regulated Semaphorin3a (Sema3a) mRNA expression and increased the activity of mammalian target of rapamycin complex 1 (mTORC1) in osteoblast-like MC3T3-E1 cells. Furthermore, mTORC1 inhibition with rapamycin counteracted the effect of conditioned media on Sema3a mRNA expression. These results suggest that tumor cells decrease Sema3a mRNA expression in osteoblast in an mTORC1-dependent manner.
Overexpression of ACC gene from oleaginous yeast Lipomyces starkeyi enhanced the lipid accumulation in Saccharomyces cerevisiae with increased levels of glycerol 3-phosphate substrates
Authors: Wang Jiancai , Xu Ronghua , Wang Ruling , Haque Mohammad Enamul , Liu Aizhong 
Published: February 2016

Abstract
The conversion of acetyl-CoA to malonyl-CoA by acetyl-CoA carboxylase (ACC) is the rate-limiting step in fatty acid biosynthesis. In this study, a gene coding for ACC was isolated and characterized from an oleaginous yeast, Lipomyces starkeyi. Real-time quantitative PCR (qPCR) analysis of L. starkeyi acetyl-CoA carboxylase gene (LsACC1) showed that the expression levels were upregulated with the fast accumulation of lipids. The LsACC1 was co-overexpressed with the glycerol 3-phosphate dehydrogenase gene (GPD1), which regulates lipids biosynthesis by supplying another substrates glycerol 3-phosphate for storage lipid assembly, in the non-oleaginous yeast Saccharomyces cerevisiae. Further, the S. cerevisiae acetyl-CoA carboxylase (ScACC1) was transferred with GPD1 and its function was analyzed in comparison with LsACC1. The results showed that overexpressed LsACC1 and GPD1 resulted in a 63% increase in S. cerevisiae. This study gives new data in understanding of the molecular mechanisms underlying the regulation of fatty acids and lipid biosynthesis in yeasts.
Biophysics of food perception
Authors: Burbidge Adam S , Le Révérend Benjamin J D 
Published: February 2016

Abstract
In this article, we present food perception across a range of time and length scales as well as across the disciplines of physics, chemistry and biology. We achieve the objective of the article by presenting food from a material science angle as well as presenting the physiology of food perception that enables humans to probe materials in terms of aroma, taste and texture. We highlight that by using simple physical concepts, one can also decipher the mechanisms of transport that link food structure with perception physiology and define the regime in which physiology operates. Most importantly, we emphasise the notion that food/consumer interaction operates across the biological fluid interface grouped under the terminology of mucus, acting as a transfer fluid for taste, aroma and pressure between food and dedicated receptors.
The tuning of light-matter coupling and dichroism in graphene for enhanced absorption: Implications for graphene-based optical absorption devices
Authors: Rakheja Shaloo , Sengupta Parijat 
Published: February 2016

Abstract
The inter-band optical absorption in graphene characterized by its fine-structure constant has a universal value of 2.3% independent of the material parameters. However, for several graphene-based photonic applications, enhanced optical absorption is highly desired. In this work, we quantify the tunability of optical absorption in graphene via the Fermi level, angle of incidence of the incident polarized light, and the dielectric constants of the surrounding dielectric media in which graphene is embedded. The influence of impurities adsorbed on the surface of graphene on the Lorentzian broadening of the spectral function of the density of states is analytically evaluated within the equilibrium Green’s function formalism. In all the cases, we find that absorption of light graphene embedded in dielectric medium is significantly higher than 2.3%. We also compute the differential absorption of right and left circularly-polarized light in graphene that is uniaxially and optically strained. The preferential absorption or circular dichroism is investigated for armchair and zigzag strain and the interplay of k-space and velocity anisotropy is examined. Finally, we relate circular dichroism to the Berry curvature of gapped graphene and explain the connection to parameters that define the underlying Hamiltonian.
Sex Differences in Risk Factors and Natural History of Oral Human Papillomavirus Infection
Authors: D'Souza Gypsyamber , Wentz Alicia , Kluz Nicole , Zhang Yuehan , Sugar Elizabeth , Youngfellow Renee M. , Guo Yingshi , Xiao Weihong , Gillison Maura L. 
Published: February 2016

Abstract
Oral human papillomavirus genotype 16 (HPV16) infection causes oropharyngeal squamous cell carcinoma (SCC), and the prevalence of oropharyngeal SCC is higher among men than women in the United States. In a cohort study of oral HPV infection among 409 individuals aged 18–25 years, the risk among men but not among women significantly increased as the number of recent (ie, within the prior 3 months) oral sex partners increased (Pinteraction = .05). In contrast, the risk among women but not among men significantly decreased as the lifetime number of vaginal sex partners increased (Pinteraction = .037). Men were also significantly less likely than women to clear oral HPV infection. Our data contribute to understanding sex differences in risk for HPV-positive oropharyngeal SCC.
Clinical Trials Registration.  NCT00994019.
The Psychologist as Managerial Coach
Authors: Lowman Rodney L. 
Published: February 2016

Abstract
This article addresses executive coaching as an area of practice and research by psychologists. As an emerging area associated both with psychology and other professional groups, coaching has rapidly expanded despite a modest body of literature available in support for its efficacy so far. Coaching clearly enjoys a large market demand, and in turn there is an abundance of coaches providing services. This article covers issues associated with defining coaching, identifying the competencies apparently needed for professional practice in this area, and some of the evidence for coaching’s effectiveness (efficacy). It also identifies some of the ethical issues raised in this practice area (coaching ethics) including expectations of science- and evidence-based practice, boundaries of competence, informed consent, multiple relationships, and confidentiality.
Third Wave Variationism
Authors: Eckert Penelope 
Published: February 2016

Abstract
This article traces the development of the most recent approach to the study of sociolinguistic variation and considers the theoretical issues it raises. This field has moved through three waves of analytic practice. The first focused on the spread of linguistic change, finding robust correlations between linguistic variables and macrosocial categories across large populations. The second wave took an ethnographic turn, examining the relation between variation and local social dynamics. The third wave focuses on the indexical nature of sociolinguistic variation and on the stylistic practice in which variables gain their meaning. This approach differs from earlier practice in its focus on social meaning and speaker agency, and on the role of stylistic practice in social change and the construction of social distinctions.
Public Order Policing and Liberal Democracy
Authors: de Lint Willem 
Published: February 2016

AbstractThis article argues that public order police developed in relative autonomy from government. It accounts for the genesis of that autonomy and its significance in support of the opportunity to contest liberal rule. The argument developed is that it is from their relative insulation from public and private authorities that police draw power in liberal democracies. Understanding public order policing, it follows, requires an appreciation of how that power interacts with ideological expression. Current public order mobilizations considered more or less in favor of this account are reviewed, and an argument in favor of the pluralist account is provided.
Group-Based Trajectory Modeling
Authors: Jennings Wesley G. , Meade Caitlyn 
Published: February 2016

AbstractThis article explores group-based trajectory modeling as a methodological design for studying criminal behavior. Originally developed by Nagin and Land (1993) as a nonparametric, nested, mixed Poisson model, group-based trajectory modeling is a statistical methodology that uses longitudinal data to understand trajectories as a criminological endeavor. Its objective is to determine whether the age–crime curve of criminal offending found at the societal level also applies to the individual level and whether an individual’s criminal career can be modeled without including the structural elements of career onset, desistance, or dormancy. This article begins with a historical background on how group-based trajectory modeling was developed and goes on to discuss how it is implemented in the field of criminology. It also considers the methodological and substantive applications of group-based trajectory modeling, along with its advantages and disadvantages. Finally, it outlines directions for future research on group-based trajectory modeling.
Adolescent Idiopathic Scoliosis Thoracic Volume Modeling: The Effect of Surgical Correction
Authors: Wozniczka Jennifer K. , Ledonio Charles G. T. , Polly David W. , Rosenstein Benjamin E. , Nuckley David J. 
Published: February 2016

Background:
Scoliosis has been shown to have detrimental effects on pulmonary function, traditionally measured by pulmonary function tests, which is theorized to be correlated to the distortion of the spine and thorax. The changes in thoracic volume with surgical correction have not been well quantified. This study seeks to define the effect of surgical correction on thoracic volume in patients with adolescent idiopathic scoliosis.

Methods:
Images were obtained from adolescents with idiopathic scoliosis enrolled in a multicenter database (Prospective Pediatric Scoliosis Study). A convenience sample of patients with Lenke type 1 curves with a complete data set meeting specific parameters was used. Blender v2.63a software was used to construct a 3-dimensional (3D) computational model of the spine from 2-dimensional calibrated radiographs. To accomplish this, the 3D thorax model was deformed to match the calibrated radiographs. The thorax volume was then calculated in cubic centimeters using Mimics v15 software.

Results:
The results using this computational modeling technique demonstrated that surgical correction resulted in decreased curve measurement as determined by Cobb method, and increased postoperative thoracic volume as expected. Thoracic volume significantly increased by a mean of 567 mm3 (P<0.001). The percent change in thoracic volume after surgical correction averaged 40% (range, 3% to 87%). The smaller the baseline volume, the greater the change in volume postoperatively (r=–0.86).
Evaluation of postoperative data demonstrated that spinal curve measurement as determined by Cobb method was significantly reduced from a mean of 69 degrees (range, 50 to 96 degrees) preoperatively to 27 degrees (range, 13 to 33 degrees) postoperatively (P<0.001).

Conclusions:
This pilot study demonstrates methodologic plausibility for measuring 3D changes in thoracic volumes using 2-dimensional imaging. This is an assessment of the novel modeling technique, to be used in larger future studies to assess clinical significance.

Level of Evidence:
Level 3—retrospective comparison of prospectively collected data.
Use of Biotelemetry to Define Physiology-Based Deterioration Thresholds in a Murine Cecal Ligation and Puncture Model of Sepsis
Authors: Lewis Anthony J. , Yuan Du , Zhang Xianghong , Angus Derek C. , Rosengart Matthew R. , Seymour Christopher W. 
Published: February 2016

Objectives:
Murine models of critical illness are commonly used to test new therapeutic interventions. However, these interventions are often administered at fixed time intervals after the insult, perhaps ignoring the inherent variability in magnitude and temporality of the host response. We propose to use wireless biotelemetry monitoring to define and validate criteria for acute deterioration and generate a physiology-based murine cecal ligation and puncture model that is more similar to the conduct of human trials of sepsis.

Design:
Laboratory and animal research.

Setting:
University basic science laboratory.

Subjects:
Male C57BL/6 mice.

Interventions:
Mice underwent cecal ligation and puncture, and an HD-X11 wireless telemetry monitor (Data Sciences International) was implanted that enabled continuous, real-time measurement of heart rate, core temperature, and mobility. We performed a population-based analysis to determine threshold criteria that met face validity for acute physiologic deterioration. We assessed construct validity by temporally matching mice that met these acute physiologic deterioration thresholds with mice that had not yet met deterioration threshold. We analyzed matched blood samples for blood gas, inflammatory cytokine concentration, cystatin C, and alanine aminotransferase.

Measurements and Main Results:
We observed that a 10% reduction in both heart rate and temperature sustained for greater than or equal to 10 minutes defined acute physiologic deterioration. There was significant variability in the time to reach acute deterioration threshold across mice, ranging from 339 to 529 minutes after cecal ligation and puncture. We found adequate construct validity, as mice that met criteria for acute deterioration had significantly worse shock, systemic inflammation (elevated tumor necrosis factor-α, p = 0.003; interleukin-6, p = 0.01; interleukin-10, p = 0.005), and acute kidney injury when compared with mice that had not yet met acute deterioration criteria.

Conclusions:
We defined a murine threshold for acute physiologic deterioration after cecal ligation and puncture that has adequate face and construct validity. This model may enable a more physiology-based model for evaluation of novel therapeutics in critical illness.