bluuebunny/crossref_metadata_2025_split huggingface dataset:
The effects of terlipressin and direct portacaval shunting on liver hemodynamics following 80% hepatectomy in the pig
Authors: Hammond John S. , Godtliebsen Fred , Steigen Sonja , Guha I. Neil , Wyatt Judy , Revhaug Arthur , Lobo Dileep N. , Mortensen Kim E. 
Published: January 2019

Abstract
Liver failure is the major cause of death following liver resection. Post-resection portal venous pressure (PVP) predicts liver failure, is implicated in its pathogenesis, and when PVP is reduced, rates of liver dysfunction decrease. The aim of the present study was to characterize the hemodynamic, biochemical, and histological changes induced by 80% hepatectomy in non-cirrhotic pigs and determine if terlipressin or direct portacaval shunting can modulate these effects. Pigs were randomized (n=8/group) to undergo 80% hepatectomy alone (control); terlipressin (2 mg bolus + 0.5–1 mg/h) + 80% hepatectomy; or portacaval shunt (PCS) + 80% hepatectomy, and were maintained under terminal anesthesia for 8 h. The primary outcome was changed in PVP. Secondary outcomes included portal venous flow (PVF), hepatic arterial flow (HAF), and biochemical and histological markers of liver injury. Hepatectomy increased PVP (9.3 ± 0.4 mmHg pre-hepatectomy compared with 13.0 ± 0.8 mmHg post-hepatectomy, P&lt;0.0001) and PVF/g liver (1.2 ± 0.2 compared with 6.0 ± 0.6 ml/min/g, P&lt;0.0001) and decreased HAF (70.8 ± 5.0 compared with 41.8 ± 5.7 ml/min, P=0.002). Terlipressin and PCS reduced PVP (terlipressin = 10.4 ± 0.8 mmHg, P=0.046 and PCS = 8.3 ± 1.2 mmHg, P=0.025) and PVF (control = 869.0 ± 36.1 ml/min compared with terlipressin = 565.6 ± 25.7 ml/min, P&lt;0.0001 and PCS = 488.4 ± 106.4 ml/min, P=0.002) compared with control. Treatment with terlipressin increased HAF (73.2 ± 11.3 ml/min) compared with control (40.3 ± 6.3 ml/min, P=0.026). The results of the present study suggest that terlipressin and PCS may have a role in the prevention and treatment of post-resection liver failure.
Digital hybrid current mode control for DC–DC converters
Authors: Ugur Abdulkerim , Yilmaz Murat 
Published: January 2019

A digital hybrid current mode (HCM) control technique which combines peak current and average current mode (ACM) control methods is studied. The proposed controller consists of three control loops, an analogue fast current loop, a digital slow current loop and an outer voltage loop. For the control method, both continuous and discrete‐time models are built. Similarly, a continuous‐time model for ACM control is provided for comparison. For both control techniques, a compensator design method is proposed. The control methods are implemented on a 6 W synchronous buck converter with a mixed‐signal ARM‐based microcontroller. Controller models are verified with the frequency response measurements of the inner and outer loops. In digital HCM control, higher DC gain and phase margin is achieved with the same gain margin compared to digital ACM control. Furthermore, the transient responses of the systems are analysed. When the outer voltage loop is open, 30% faster dynamic response is measured by the digital HCM method. With voltage compensation, comparable dynamic response on the output voltage is achieved without inductor current overshooting by the digital HCM control.
Serum Lipids and Risk of Rapid Renal Function Decline in Treated Hypertensive Adults With Normal Renal Function
Authors: Zhang Xianglin , Wang Binyan , Yang Juan , Wang Jiancheng , Yu Yaren , Jiang Chongfei , Xie Liling , Song Yun , Zhong Biyan , Li Youbao , Liang Min , Wang Guobao , Li Jianping , Zhang Yan , Huo Yong , Xu Xiping , Qin Xianhui 
Published: January 2019

Abstract

BACKGROUND
We aim to evaluate the effect of different lipids parameters, including triglycerides (TG), high-density lipoprotein cholesterol (HDL-C), the TG to HDL-C (TG:HDL-C) ratio, total cholesterol (TC), and low-density lipoprotein cholesterol (LDL-C), on the risk of rapid renal function decline and examine any possible effect modifiers in general hypertensive patients with normal renal function.

METHODS
A total of 12,549 hypertensive patients with estimated glomerular filtration rate (eGFR) ≥60 ml/min/1.73 m2 in the renal sub-study of the China Stroke Primary Prevention Trial were included in the analyses. The primary outcome was rapid renal function decline, defined as an average decline in eGFR ≥ 5 ml/min/1.73 m2 per year.

RESULTS
The median treatment duration was 4.4 years. After the full adjustment for TC, TG, HDL-C, and other major covariates, a significantly higher risk of rapid renal function decline was found in participants with higher TG [≥150 vs. &lt;150 mg/dl, 7.7% vs. 5.5%; odds ratios (OR): 1.27; 95% confidence interval (CI): 1.06–1.51], higher TG:HDL-C ratio [≥2.7 (median) vs. &lt;2.7, 7.7% vs. 5.0%; OR: 1.39; 95% CI: 1.14–1.71), lower TC (≥200 vs. &lt;200 mg/dl, 6.0% vs. 7.0%; OR: 0.79; 95% CI: 0.67–0.93), or lower LDL-C levels (≥130 vs. &lt;130 mg/dl, 6.1% vs. 7.0%; OR: 0.79; 95% CI: 0.67–0.94). Moreover, the increased risk of the primary outcome associated with elevated TG was particularly evident among individuals with lower total homocysteine levels [&lt;12.4 (median) vs. ≥ 12.4 μmol/l, P interaction = 0.036].

CONCLUSIONS
Higher TG and TG:HDL-C ratio were independent risk factors for rapid renal function decline in hypertensive adults with normal renal function.
Use of a physician order entry system to identify opportunities for intravenous to oral levofloxacin conversion
Authors: Glemaud Indy 
Published: January 2019

Abstract
Experience with a program for identifying, through a physician order entry system, potentially inappropriate use of expensive intravenous (i.v.) drugs, including levofloxacin, is described.
The program identifies patients who are receiving i.v. levofloxacin and simultaneously receiving oral medications or an oral diet. A computerized report of such patients is printed every morning at the hospital and distributed to pharmacists according to their nursing station assignments. The pharmacists document their daily interventions to encourage switching from i.v. to oral therapy, and data are compiled and posted at the end of each month. From January 1 through September 30, 1999, the first 10 months of the program, the cost per day of levofloxacin therapy per patient decreased substantially.
The program helped the institution decrease the number of patients receiving i.v. levofloxacin.
Dynamic changes in ABA content in water-stressed Populus nigra: effects on carbon fixation and soluble carbohydrates
Authors: Brunetti Cecilia , Gori Antonella , Marino Giovanni , Latini Paolo , Sobolev Anatoly P , Nardini Andrea , Haworth Matthew , Giovannelli Alessio , Capitani Donatella , Loreto Francesco , Taylor Gail , Mugnozza Giuseppe Scarascia , Harfouche Antoine , Centritto Mauro 
Published: January 2019

AbstractBackground and AimsHydraulic and chemical signals operate in tandem to regulate systemic plant responses to drought. Transport of abscisic acid (ABA) through the xylem and phloem from the root to shoot has been suggested to serve as the main signal of water deficit. There is evidence that ABA and its ABA-glycosyl-ester (ABA-GE) are also formed in leaves and stems through the chloroplastic 2-C-methylerythritol-5-phosphate (MEP) pathway. This study aimed to evaluate how hormonal and hydraulic signals contribute to optimize stomatal (gs), mesophyll (gm) and leaf hydraulic (Kleaf) conductance under well-watered and water-stressed conditions in Populus nigra (black poplar) plants. In addition, we assessed possible relationships between ABA and soluble carbohydrates within the leaf and stem.MethodsPlants were subjected to three water treatments: well-watered (WW), moderate stress (WS1) and severe stress (WS2). This experimental set-up enabled a time-course analysis of the response to water deficit at the physiological [leaf gas exchange, plant water relations, (Kleaf)], biochemical (ABA and its metabolite/catabolite quantification in xylem sap, leaves, wood, bark and roots) and molecular (gene expression of ABA biosynthesis) levels.Key ResultsOur results showed strong coordination between gs, gm and Kleaf under water stress, which reduced transpiration and increased intrinsic water use efficiency (WUEint). Analysis of gene expression of 9-cis-epoxycarotenoid dioxygenase (NCED) and ABA content in different tissues showed a general up-regulation of the biosynthesis of this hormone and its finely-tuned catabolism in response to water stress. Significant linear relationships were found between soluble carbohydrates and ABA contents in both leaves and stems, suggesting a putative function for this hormone in carbohydrate mobilization under severe water stress.ConclusionsThis study demonstrates the tight regulation of the photosynthetic machinery by levels of ABA in different plants organs on a daily basis in both well-watered and water stress conditions to optimize WUEint and coordinate whole plant acclimation responses to drought.
polyDFEv2.0: testing for invariance of the distribution of fitness effects within and across species
Authors: Tataru Paula , Bataillon Thomas 
Published: January 2019

Abstract

Summary
Distribution of fitness effects (DFE) of mutations can be inferred from site frequency spectrum (SFS) data. There is mounting interest to determine whether distinct genomic regions and/or species share a common DFE, or whether evidence exists for differences among them. polyDFEv2.0 fits multiple SFS datasets at once and provides likelihood ratio tests for DFE invariance across datasets. Simulations show that testing for DFE invariance across genomic regions within a species requires models accounting for distinct sources of heterogeneity (chance and genuine difference in DFE) underlying differences in SFS data in these regions. Not accounting for this will result in the spurious detection of DFE differences.

Availability and Implementation
polyDFEv2.0 is implemented in C and is accompanied by a series of R functions that facilitate post-processing of the output. It is available as source code and compiled binaries under a GNU General Public License v3.0 from https://github.com/paula-tataru/polyDFE.

Supplementary information
Supplementary data are available at Bioinformatics online.
Preparing for the future: integrating spatial ecology into ecosystem-based management
Authors: Lowerre-Barbieri Susan K , Catalán Ignacio A , Frugård Opdal Anders , Jørgensen Christian 
Published: January 2019

AbstractMarine resource management is shifting from optimizing single species yield to redefining sustainable fisheries within the context of managing ocean use and ecosystem health. In this introductory article to the theme set, “Plugging spatial ecology into ecosystem-based management (EBM)” we conduct an informal horizon scan with leaders in EBM research to identify three rapidly evolving areas that will be game changers in integrating spatial ecology into EBM. These are: (1) new data streams from fishers, genomics, and technological advances in remote sensing and bio-logging; (2) increased analytical power through “Big Data” and artificial intelligence; and (3) better integration of social dimensions into management. We address each of these areas by first imagining capacity in 20 years from now, and then highlighting emerging efforts to get us there, drawing on articles in this theme set, other scientific literature, and presentations/discussions from the symposium on “Linkages between spatial ecology and sustainable fisheries” held at the ICES Annual Science Conference in September 2017.
Case Report and Literature Review of Nodular Hidradenoma, a Rare Adnexal Tumor That Mimics Breast Carcinoma, in a 20-Year-Old Woman
Authors: Jaitly Vanya , Jahan-Tigh Richard , Belousova Tatiana , Zhu Hui , Brown Robert , Saluja Karan 
Published: January 2019

Abstract
Nodular hidradenoma is an uncommon cutaneous adnexal tumor arising from sweat glands. In the skin, it usually presents as a solitary dermal nodule; excision is curative in most cases. In rare instances, it may present as a breast mass and can mimic breast carcinoma clinically and radiologically, causing diagnostic dilemmas for the treating physician and pathologist. Herein, we discuss a case of nodular hidradenoma in a 20-year-old Hispanic woman as a rapidly growing mass in the breast that mimicked breast carcinoma. We discuss the rare presentation of this uncommon tumor and the differential diagnosis of this entity, as well as the results of our literature review on the topic.
A century after introduction: variability in Cepaea hortensis (Müller, 1774) in Sibiu, central Romania
Authors: Gheoca Voichița , Benedek Ana Maria , Cameron Robert A D , Stroia Radu Camil 
Published: January 2019

AbstractThe polymorphic land snail Cepaea hortensis was introduced to the city of Sibiu, central Romania, in the first decade of the 20th century and has spread widely across the city. A total of 97 locations were examined in 2017 across the city to determine the habitat preferences and variation in shell size, shape, colour and banding polymorphism of C. hortensis, and to relate these to the same features in the likely source population from Mannheim, Germany, and the first established population in Sibiu. We found that C. hortensis was largely restricted to sites with some woody vegetation cover and showed a marked preference for abandoned and overgrown private gardens. Mean adult shell size in present-day populations was almost always smaller than in both the presumed population of origin from Germany and the first recorded population from Sibiu. Populations showed a wide range of variation in frequencies of shell colours and banding morphs. This variation was not related to habitat or cover, and there was no evident geographical structure in the patterns. Comparisons with a smaller-scale sampling in 2004/5 showed that some populations had gone extinct, some remained stable and in some morph frequencies had changed drastically, but in no consistent direction. These results are similar to those obtained for the related species C. nemoralis in comparable circumstances, but differ from those obtained from regions where C. hortensis is long established and where habitats have been stable. The patterns we observed most likely reflect the effect of passive dispersal by humans, genetic drift and founder effects.
Osteomyelitis Risk Factors Related to Combat Trauma Open Femur Fractures: A Case–Control Analysis
Authors: Lewandowski Louis R. , Potter Benjamin K. , Murray Clinton K. , Petfield Joseph , Stinner Daniel J. , Krauss Margot , Weintrob Amy C. , Tribble David R. ,   the Trauma Infectious Disease Outcomes Study Group
Published: January 2019

Objectives:
To identify the risk factors for osteomyelitis development in US military personnel with combat-related, open femur fractures?

Design:
Retrospective observational case–control study.

Setting:
US military regional hospital in Germany and tertiary care hospitals in United States (2003–2009).

Patients/Participants:
One hundred three patients with open femur fractures who met diagnostic osteomyelitis criteria (medical record review verification) were classified as cases. Sixty-four patients with open femur fractures who did not meet osteomyelitis diagnostic criteria were included as controls.

Main Outcome Measurements:
The main outcome measurements were multivariable odds ratios (ORs) and 95% confidence interval (CI).

Results:
Among patients with surgical implants, osteomyelitis cases had significantly longer time to definitive orthopaedic surgery compared with controls (median: 21 vs. 13 days). Independent predictors for osteomyelitis risk were Gustilo–Anderson classification (transfemoral amputation OR: 19.3; CI: 3.0–123.0) and Orthopaedic Trauma Association Open Fracture Classification for muscle loss (OR: 5.7; CI: 1.3–25.1) and dead muscle (OR: 32.9; CI: 5.4–199.1). Being injured between 2003 and 2006, antibiotic bead use, and foreign body plus implant(s) at fracture site were also risk factors.

Conclusions:
Patients with open femur fractures resulting in significant muscle damage have the highest osteomyelitis risk. Foreign body contamination was only significant when an implant was present. Increased risk with antibiotic bead use is likely a surrogate for clinical suspicion of contamination with complex wounds. The timeframe association is likely due to changing trauma system patterns around 2006–2007 (eg, increased negative pressure wound therapy, reduced high-pressure irrigation, decreased crystalloid use, and delayed definitive internal fixations).

Level of Evidence:
Prognostic Level III. See Instructions for Authors for a complete description of levels of evidence.
CSynth: A Dynamic Modelling and Visualisation Tool for 3D Chromatin Structure
Authors: Todd Stephen , Todd Peter , McGowan Simon J. , Hughes James R. , Kakui Yasutaka , Leymarie Frederic Fol , Latham William , Taylor Stephen 
Published: January 2019

AbstractThe 3D structure of chromatin in the nucleus is important for gene expression and regulation. Chromosomal conformation capture techniques, such as Hi-C, generate large amounts of data showing interaction points on the genome but these are hard to interpret using standard tools. We have developed CSynth, a high performance 3D genome browser and real time chromatin restraint-based modeller to visualise dynamic and interactive models of chromatin capture data. CSynth does its calculations in the GPU hence is much faster than existing modelling software to infer and visualise the chromatin structure which also allow real-time interaction with the modelling parameters. It also allows straightforward comparison of interaction data and the results of third party 3D modelling outputs. In addition we include an option to view and manipulate these complicated structures using Virtual Reality (VR) allowing scientists to immerse themselves in the models for further understanding. This VR component has also proven to be a valuable teaching and public engagement tool. CSynth is web based and available to use at http://csynth.org.
Functional dissection of Alzheimer’s disease brain gene expression signatures in humans and mouse models
Authors: Wan Ying-Wooi , Al-Ouran Rami , Mangleburg Carl Grant , Lee Tom V. , Allison Katherine , Neuner Sarah , Kaczorowski Catherine , Phillip Vivek , Howell Gareth , Martini-Stoica Heidi , Zheng Hui , Kim Jungwoo Wren , Dawson Valina , Dawson Ted , Pao Ping-Chieh , Tsai Li-Huei , Haure-Mirande Jean-Vianney , Wang Minghui , Ehrlich Michelle E. , Mei Hongkang , Zhong Xiaoyan , Chakrabarty Paramita , Levites Yona , Golde Todd E. , Levey Allan I. ,   Accelerating Medicines Partnership-Alzheimer’s Disease Consortium, Logsdon Benjamin , Mangravite Lara , Liu Zhandong , Shulman Joshua M. 
Published: January 2019

SUMMARYHuman brain transcriptomes can highlight biological pathways associated with Alzheimer’s disease (AD); however, challenges remain to link expression changes with causal triggers. We have examined 30 AD-associated, gene coexpression modules from human brains for overlap with 251 differentially-expressed gene sets from mouse brain RNA-sequencing experiments, including from models of AD and other neurodegenerative disorders. Human-mouse overlaps highlight responses to amyloid versus neurofibrillary tangle pathology and further reveal age- and sex-dependent expression signatures for AD progression. Human coexpression modules enriched for neuronal and/or microglial genes overlap broadly with signatures from mouse models of AD, Huntington’s disease, Amyotrophic Lateral Sclerosis, and also aging. Several human AD coexpression modules, including those implicated in the unfolded protein response and oxidative phosphorylation, were not activated in AD models, but instead were detected following other, unexpected mouse genetic manipulations. Our results comprise a powerful, cross-species resource and pinpoint experimental models for diverse features of AD pathophysiology from human brain transcriptomes.
ENVIRONMENTAL PERTURBATIONS AND TRANSITIONS BETWEEN ECOLOGICAL AND EVOLUTIONARY EQUILIBRIA: AN ECO-EVOLUTIONARY FEEDBACK FRAMEWORK
Authors: Coulson Tim 
Published: January 2019

AbstractI provide a general framework for linking ecology and evolution. I start from the fact that individuals require energy, trace molecules, water, and mates to survive and reproduce, and that phenotypic resource accrual traits determine an individual’s ability to detect and acquire these resources. Optimum resource accrual traits, and their values, are determined by the dynamics of resources, aspects of the environment that hinder resource detection and acquisition by imposing risks of mortality and reproductive failure, and the energetic costs of developing and maintaining the traits – part of an individual’s energy budget. These budgets also describe how individuals utilize energy by partitioning it into maintenance, development and/or reproduction at each age and size, age and size at sexual maturity, and the size and number of offspring produced at each reproductive event. The optimum energy budget is consequently determined by the optimum life history strategy that describes how resources are utilized to maximize fitness by trading off investments in maintenance, development, and reproductive output at each age and size. The optimum life history in turn determines body size. An eco-evolutionary feedback loop occurs when resource accrual traits evolve to impact the quality and quantity of resources that individuals accrue, resulting in a new optimum life history strategy and energy budget required to deliver it, a change in body size, and altered population dynamics that, in turn, impact the resource base. These feedback loops can be complex, but can be studied by examining the eco-evolutionary journey of communities from one equilibrium state to another following a perturbation to the environment.
Contrasting paternal and maternal genetic histories of Thai and Lao populations
Authors: Kutanan Wibhu , Kampuansai Jatupol , Srikummool Metawee , Brunelli Andrea , Ghirotto Silvia , Arias Leonardo , Macholdt Enrico , Hübner Alexander , Schröder Roland , Stoneking Mark 
Published: January 2019

AbstractThe human demographic history of Mainland Southeast Asia (MSEA) has not been well-studied; in particular there have been very few sequence-based studies of variation in the male-specific portions of the Y chromosome (MSY). Here, we report new MSY sequences of ∼2.3 mB from 914 males, and combine these with previous data for a total of 928 MSY sequences belonging to 59 populations from Thailand and Laos who speak languages belonging to three major MSEA families: Austroasiatic (AA), Tai-Kadai (TK) and Sino-Tibetan (ST). Among the 92 MSY haplogroups, two main MSY lineages (O1b1a1a* (O-M95*) and O2a* (O-M324*)) contribute substantially to the paternal genetic makeup of Thailand and Laos. We also analyse complete mtDNA genome sequences published previously from the same groups, and find contrasting pattern of male and female genetic variation and demographic expansions, especially for the hill tribes, Mon, and some major Thai groups. In particular, we detect an effect of post-marital residence pattern on genetic diversity in patrilocal vs. matrilocal groups. Additionally, both male and female demographic expansions were observed during the early Mesolithic (∼10 kya), with two later major male-specific expansions during the Neolithic period (∼4-5 kya) and the Bronze/Iron Age (∼2.0-2.5 kya). These two later expansions are characteristic of the modern AA and TK groups, respectively, consistent with recent ancient DNA studies. We simulate MSY data based on three demographic models (continuous migration, demic diffusion and cultural diffusion) of major Thai groups and find different results from mtDNA simulations, supporting contrasting male and female genetic histories.