bluuebunny/crossref_metadata_2025_split huggingface dataset:
Meta-analysis of randomized controlled trials on the safety and effectiveness of early versus delayed laparoscopic cholecystectomy for acute cholecystitis
Authors: Gurusamy K , Samraj K , Gluud C , Wilson E , Davidson B R 
Published: December 2009

Abstract

Background
In many countries laparoscopic cholecystectomy for acute cholecystitis is mainly performed after the acute episode has settled because of the anticipated increased risk of morbidity and higher conversion rate from laparoscopic to open cholecystectomy.

Methods
A systematic review was performed with meta-analysis of randomized clinical trials of early laparoscopic cholecystectomy (ELC; performed within 1 week of onset of symptoms) versus delayed laparoscopic cholecystectomy (performed at least 6 weeks after symptoms settled) for acute cholecystitis. Trials were identified from The Cochrane Library trials register, Medline, Embase, Science Citation Index Expanded and reference lists. Risk ratio (RR) or mean difference was calculated with 95 per cent confidence intervals (c.i.) based on intention-to-treat analysis.

Results
Five trials with 451 patients were included. There was no significant difference between the two groups in terms of bile duct injury (RR 0·64 (95 per cent c.i. 0·15 to 2·65)) or conversion to open cholecystectomy (RR 0·88 (95 per cent c.i. 0·62 to 1·25)). The total hospital stay was shorter by 4 days for ELC (mean difference −4·12 (95 per cent c.i. −5·22 to −3·03) days).

Conclusion
ELC during acute cholecystitis appears safe and shortens the total hospital stay.
Anti‐TNF‐alpha drugs ‐ moving into the mainstream?
Authors: Ding Tina , Deighton Chris 
Published: December 2009

AbstractAnti‐TNF drugs are a major treatment advance in the management of inflammatory disorders such as rheumatoid arthritis, and are typically considered following unsuccessful treatment with conventional disease‐modifying antirheumatic drugs (DMARDs). Drs Chris Deighton and Tina Ding review the available anti‐TNF‐alpha drugs, and consider their future place in therapy. Copyright © 2009 John Wiley & Sons, Ltd.
Consolidation hyperthermic intraperitoneal chemotherapy using paclitaxel in patients with epithelial ovarian cancer
Authors: Kim Jin Hwi , Lee Joon Mo , Ryu Ki Sung , Lee Yong Seok , Park Yong Gyu , Hur Soo Young , Lee Keun Ho , Lee Sung Ha , Kim Seung Jo 
Published: December 2009

AbstractBackgroundWe evaluated the efficacy and feasibility of hyperthermic intraperitoneal chemotherapy (HIPEC) using paclitaxel as consolidation therapy in patients with epithelial ovarian cancer.MethodsBetween November 1999 and January 2004, 18 patients with a negative second‐look and 1 patient with positive peritoneal cytology only with stage Ic–IIIc epithelial ovarian cancer received consolidation intra‐operative HIPEC using paclitaxel. The HIPEC was performed with open‐abdomen technique, using 6 L of lactated Ringer's solution containing paclitaxel 175 mg/m2, for 90 min in hyperthermic phase (43–44°C). The survival rates were compared with 24 patients treated with conventional therapy (control group).ResultsThe 8‐year progression‐free survival rates were 63.16% in the HIPEC‐paclitaxel group and 29.17% in the control group (P = 0.027). The 8‐year overall survival rates were 84.21% in the HIPEC‐paclitaxel group and 25.00% in the control group (P = 0.0004). The time interval between initial treatment and HIPEC was statistically significant with respect to progression‐free and overall survival in the HIPEC‐paclitaxel group.ConclusionHIPEC with paclitaxel during 2nd‐look laparotomy is feasible and relatively safe and showed a good effect on survival. In patients with epithelial ovarian cancer who have a complete pathologic response, HIPEC with paclitaxel should be considered as a consolidation treatment option. J. Surg. Oncol. 2010;101:149–155. © 2009 Wiley‐Liss, Inc.
Factors associated with recurrence and survival following hepatectomy for large hepatocellular carcinoma: A multicenter analysis
Authors: Schiffman Suzanne C. , Woodall Charles E. , Kooby David A. , Martin Robert C.G. , Staley Charles A. , Egnatashvili Vasili , McMasters Kelly M. , Scoggins Charles R. 
Published: December 2009

AbstractBackgroundOptimal management of large (>5 cm) hepatocellular carcinoma (HCC) remains controversial. We sought to determine the factors associated with recurrence and survival for patients with large HCC following hepatectomy.MethodsAn analysis of a combined prospective database from two tertiary care centers was performed on consecutive patients who underwent hepatectomy for HCC > 5 cm. Univariate and multivariate analyses were performed to determine factors associated with recurrence, disease‐free (DFS) and overall survival (OS).ResultsSeventy‐eight patients were identified: 32 (41%) had hepatic fibrosis. Forty‐six patients (59%) underwent a major hepatectomy with a morbidity rate of 41% and a mortality rate of 13%. Fibrosis was associated with male gender (P = 0.045), hepatitis C (P = 0.003), higher Child‐Pugh (P < 0.0001) and Okuda score (P = 0.002), smaller tumors (6.25 cm vs. 10.5 cm; P < 0.001), positive‐margin resection (P = 0.01), and death (P = 0.047). Factors associated with recurrence include tumor multifocality (P = 0.03) and vascular invasion (P = 0.02). Predictors of OS include multifocal tumors (P = 0.05), margin status (P = 0.02), vascular invasion (P = 0.01), and treatment complications (P = 0.004). The median overall DFS and OS were 12 and 20 months, respectively. Fibrosis had no impact on DFS (P = 0.24) or OS (P = 0.20).ConclusionsFor patients with HCC larger than 5 cm, tumor‐related factors predict outcomes and survival. J. Surg. Oncol. 2010;101:105–110. © 2009 Wiley‐Liss, Inc.
Prescription refill records as a screening tool to identify antidepressant non‐adherence
Authors: Hansen Richard A. , Dusetzina Stacie B. , Dominik Rosalie C. , Gaynes Bradley N. 
Published: December 2009

AbstractPurposeNon‐adherence is a significant problem with antidepressants. Identifying patients at highest risk for discontinuing antidepressant treatment can be used to target clinical management. Accordingly, our purpose was to determine the shortest gap in medication supply that is predictive of discontinuation, while minimizing false positive results.MethodsA retrospective cohort study of medical and prescription claims from a national health plan affiliated with i3 Innovus. Sensitivities, specificities, and positive and negative predictive values were calculated for gap lengths to assess how well they predicted discontinuation. Continuously insured individuals aged 18–65 with newly diagnosed major depression and an antidepressant prescription within 45 days of diagnosis were included. Gap length was defined as the maximum number of continuous days without medication supply during acute phase treatment. Discontinuation was defined as a continuous gap of 30 or more days between an expected refill and actual refill.ResultsOf 4545 eligible patients, 73% discontinued antidepressant treatment during the study period. A maximum continuous gap of 14 days had a sensitivity of 87% and a specificity of 82% for predicting discontinuation. In analyses that varied the way gaps and discontinuation were defined, gap lengths between 8 and 19 days were highly predictive of discontinuation without exceeding a 20% false positive rate.ConclusionsBased on administrative pharmacy records, screening for gaps in medication supply of at least 14 days can accurately identify four of every five patients at risk for discontinuing. This early indicator can be used to target clinical interventions. Copyright © 2009 John Wiley & Sons, Ltd.
Collective plume tracing: A minimal information approach to collective control
Authors: Robinett Rush D. , Wilson David G. 
Published: December 2009

AbstractA team of simple robots are used to trace a chemical plume to its source in order to find buried landmines. The goal of this paper is to analyze and design ‘emergent’ behaviors to enable the team of simple robots to perform plume tracing with the assistance of information theory. The first step in the design process is to define a fundamental trade‐off for collective systems between processing, memory, and communications for each robot in order to execute the desired collective behaviors. The baseline problem is to determine the minimum values for processing, memory, and communications simultaneously. This will enable the designer to determine the required information flow and how effectively the information resources are being utilized in collective systems. The solution to this baseline problem is an 8‐bit processor, no memory, and three words to communicate. The details of this solution are described in this paper. The second step is to extend the previous kinematic solution to a more general Hamiltonian‐based solution to develop a Fisher Information Equivalency. The Fisher Information Equivalency leads directly to necessary and sufficient conditions for stability and control of nonlinear collective systems via physical and information exergy flows. In particular, the creation of a ‘virtual/information potential’ by the team of robots via the decentralized distributed networked sensors produces a direct relationship between proportional feedback control, stored exergy in the system, and Fisher Information. This nonlinear stability formulation through Fisher Information directly provides an optimization problem to ‘tune’ the performance of the team of robots as a function of required information resources. Copyright © 2009 John Wiley & Sons, Ltd.
Size‐specific growth patterns and estimated longevity of the unionid mussel (Pronodularia japanensis)
Authors: Negishi Junjiro N. , Kayaba Yuichi 
Published: December 2009

AbstractDespite the dwindling populations and an urgent need for conservation of unionid freshwater mussels in Japan, there are gaps in our understating of their fundamental ecology. This study examined size‐dependent annual growth rates, elucidated size‐specific intra‐annual growth patterns, and estimated age and longevity of P. japanensis individuals for two locally isolated populations in agricultural drainage channels. Annual growth rates of P. japanensis were strongly size‐dependent, with growth rates being exponentially decelerated with increasing shell length. Irrespective of sizes, individuals ceased to grow in winter when water temperature fell below 10°C. Intra‐annual growth patterns were weakly explained by the changes in water temperature and differed among size classes; juveniles (<25 mm) maximized growth rate in May whereas the growth rates were the highest in June or July for larger individuals. Only adult individuals exhibited growth cessation in the July–August period, suggesting that energy investment was directed towards reproductive activities. Adults also showed negative growth rates (shrinkage of individuals) in winter, suggesting possible dissolution of shell margins. Age estimation based on two 1‐year periods suggests that large numbers of P. japanensis individuals were >10 years old, and the oldest individuals were >20 years old for both study populations. Our findings suggest that anthropogenic activities conducted in spring may have strong influences on juveniles and population dynamics of P. japanensis and underscore the need for accurately determining age and longevity of remaining populations of unionid mussels.
Influence of seed size on feeding preferences and diet composition of three sympatric harvester ants in the central Monte Desert, Argentina
Authors: Pirk Gabriela Inés , Lopez de Casenave Javier 
Published: December 2009

AbstractSelective seed consumption by harvester ants may affect seed abundance and composition and, ultimately, plant communities. We evaluated the influence of seed size on preferences and diet of Pogonomyrmex mendozanus, P. rastratus, and P. inermis in the central Monte Desert, Argentina. In choice experiments with Pappophorum spp. seeds of different sizes, P. mendozanus and P. rastratus preferred large seeds, maximizing energy reward. P. inermis showed a less‐marked preference for large seeds, which was probably due to morphological constraints imposed by its small body size. Under natural conditions, none of the three species selected larger Pappophorum spp. seeds probably because of high travel and handling costs. Seeds of intermediate size predominated in the diet of the three species but a slight size match was detected as P. mendozanus carried larger seeds than P. rastratus and this than P. inermis, matching body‐size differences. Thus, ants probably maximize energy reward but face morphological restrictions and higher costs when carrying and holding large seeds. While seeds of intermediate size are the most vulnerable ones to ant predation, small seeds are favored, as they are abundant in the soil seed bank and lowly predated.
Impact of adopting a vegan diet or an olestra supplementation on plasma organochlorine concentrations: results from two pilot studies
Authors: Arguin Hélène , Sánchez Marina , Bray George A. , Lovejoy Jennifer C. , Peters John C. , Jandacek Ronald J. , Chaput Jean-Philippe , Tremblay Angelo 
Published: December 2009

The aim of these studies was to evaluate the potential of some nutritional approaches to prevent or reduce the body load of organochlorines (OC) in humans. Study 1 compared plasma OC concentrations between vegans and omnivores while study 2 verified if the dietary fat substitute olestra could prevent the increase in OC concentrations that is generally observed in response to a weight-reducing programme. In study 1, nine vegans and fifteen omnivores were recruited and the concentrations of twenty-six OC (β-hexachlorocyclohexane (β-HCH),p,p′-dichlorodiphenyldichloroethane (p,p′-DDE),p,p′-dichlorodiphenyltrichloroethane (p,p′-DDT), hexachlorobenzene, mirex, aldrin, α-chlordane, γ-chlordane, oxychlordane,cis-nonachlor,trans-nonachlor, polychlorinated biphenyl (PCB) nos. 28, 52, 99, 101, 105, 118, 128, 138, 153, 156, 170, 180, 183 and 187, and aroclor 1260) were determined. In study 2, the concentrations of these twenty-six OC were measured before and after weight loss over 3 months in thirty-seven obese men assigned to one of the following treatments: standard group (33 % fat diet;n13), fat-reduced group (25 % fat diet;n14) or fat-substituted group (1/3 of dietary lipids substituted by olestra;n10). In study 1, plasma concentrations of five OC compounds (aroclor 1260 and PCB 99, PCB 138, PCB 153 and PCB 180) were significantly lower in vegans compared with omnivores. In study 2, β-HCH was the only OC which decreased in the fat-substituted group while increasing in the other two groups (P = 0·045). In conclusion, there was a trend toward lesser contamination in vegans than in omnivores, and olestra had a favourable influence on β-HCH but did not prevent plasma hyperconcentration of the other OC during ongoing weight loss.
Effect of postprandial modulation of glucose availability: short- and long-term analysis
Authors: Nazare Julie-Anne , de Rougemont Alexis , Normand Sylvie , Sauvinet Valérie , Sothier Monique , Vinoy Sophie , Désage Michel , Laville Martine 
Published: December 2009

Low glycaemic index (LGI) foods have been proposed as potential means to decrease postprandial glucose excursions and thus to improve diabetes management. We modulated glucose availability of cereal products and thus their glycaemic index to study the metabolic effect of LGI foods on daylong glucose control acutely and in the long term following a 5-week GI intervention diet in free-living subjects. In this randomised, parallel trial, two groups of nineteen overweight subjects followed an ad libitum 5-week intervention diet in which usual starch was replaced by either LGI or high GI (HGI) starch. During the exploration days (days 1 and 36), subjects ate their assigned 13C-labelled test breakfast (LGI or HGI), and total and exogenous glucose kinetics (using stable isotopes), postprandial concentrations of glucose, insulin, lipid profile and nutrient oxidation were assessed after the test breakfast and a standardised lunch. At day 1, LGI breakfast significantly decreased post-breakfast glycaemic response with a parallel decrease in exogenous and total glucose appearance (P < 0·05). Post-lunch and post-breakfast glycaemic responses were positively correlated (r 0·79, P < 0·0001). Following the 5-week diet, difference between the groups in terms of glucose kinetics and response was maintained (no significant interaction group × time) but tended to decrease over time for the post-breakfast glycaemic response. Post-lunch and post-breakfast glycaemic responses remained positively correlated (r 0·47, P = 0·004). Modulation of postprandial glucose availability at breakfast decreased plasma exogenous glucose appearance and improved glucose control at the subsequent lunch. After 5 weeks, these effects were maintained in healthy subjects but remained to be confirmed in the longer term.
Manifold Grace in John Cassian and Prosper of Aquitaine
Authors: Hwang Alexander Y. 
Published: December 2009

AbstractThis article is about John Cassian and Prosper of Aquitaine's understanding of grace and free will as put forward during the initial phase of the Western Church's struggle to define the doctrine of grace in the wake of the Pelagian controversy. Although both figured prominently in this struggle, both Cassian and Prosper's later understandings of grace and free will, which appreciated the diverse expressions of grace, failed to have any influence on the terms of the debate set forth in the Pelagian controversy. The history of the debate on grace and free will followed the mutually exclusive model in which salvation was the result of either grace or free will. Cassian and Prosper, who both offered an alternative to the mutually exclusive model, have not been fully recognised for their innovative views.
DCDB: Drug combination database
Authors: Liu Yanbin , Hu Bin , Fu Chengxin , Chen Xin 
Published: December 2009

Abstract
Summary: Rapid advances in pharmaceutical sciences have brought ever-increasing interests in combined therapies for better clinical efficacy and safety, especially in cases of complicated and refractory diseases. Innovative experimental technologies and theoretical frameworks are being actively developed for multicomponent drug research. In this work, we present the Drug Combination Database, with aims to facilitate analyses of known drug combinations, to summarize patterns of beneficial drug interactions, and to provide a basis for theoretical modeling and simulation of such drug interactions. Its current version (1.0) collected 499 approved or investigational drug combinations, including 40 unsuccessful drug combinations, involving 485 individual drugs, from &gt;6000 references.
Availability: http://www.cls.zju.edu.cn/dcdb/.
Contact: xinchen@zju.edu.cn
Supplementary information: Supplementary data are available at the database website and Bioinformatics online.
BRAT: bisulfite-treated reads analysis tool
Authors: Harris Elena Y. , Ponts Nadia , Levchuk Aleksandr , Roch Karine Le , Lonardi Stefano 
Published: December 2009

Abstract
Summary: We present a new, accurate and efficient tool for mapping short reads obtained from the Illumina Genome Analyzer following sodium bisulfite conversion. Our tool, BRAT, supports single and paired-end reads and handles input files containing reads and mates of different lengths. BRAT is faster, maps more unique paired-end reads and has higher accuracy than existing programs. The software package includes tools to end-trim low-quality bases of the reads and to report nucleotide counts for mapped reads on the reference genome.
Availability: The source code is freely available for download at http://compbio.cs.ucr.edu/brat/ and is distributed as Open Source software under the GPLv3.0.
Contact: elenah@cs.ucr.edu
Expression Quantitative Trait Loci Analysis of Two Genes Encoding Rubisco Activase in Soybean
Authors: Yin Zhitong , Meng Fanfan , Song Haina , Wang Xiaolin , Xu Xiaoming , Yu Deyue 
Published: December 2009

Abstract
Rubisco activase (RCA) catalyzes the activation of Rubisco in vivo and plays a crucial role in photosynthesis. However, until now, little was known about the molecular genetics of RCA in soybean (Glycine max), one of the most important legume crops. Here, we cloned and characterized two genes encoding the longer α -isoform and the shorter β -isoform of soybean RCA (GmRCA α and GmRCA β, respectively). The two corresponding cDNAs are divergent in both the translated and 3 ′ untranslated regions. Analysis of genomic DNA sequences suggested that the corresponding mRNAs are transcripts of two different genes and not the products of a single alternatively splicing pre-mRNA. Two additional possible α -form RCA-encoding genes, GmRCA03 and GmRCA14, and one additional β -form RCA-encoding gene, GmRCA11, were also isolated. To examine the function and modulation of RCA genes in soybean, we determined the expression levels of GmRCA α and GmRCA β, Rubisco initial activity, photosynthetic rate, and seed yield in 184 soybean recombinant inbred lines. Correlation of gene expression levels with three other traits indicates that RCA genes could play an important role in regulating soybean photosynthetic capacity and seed yield. Expression quantitative trait loci mapping revealed four trans-expression quantitative trait loci for GmRCA α and GmRCA β. These results could provide a new approach for the modulation of RCA genes to improve photosynthetic rate and plant growth in soybean and other plants.
Variation in gene expression ofAndropogon gerardiiin response to altered environmental conditions associated with climate change
Authors: Travers Steven E. , Tang Zhongwen , Caragea Doina , Garrett Karen A. , Hulbert Scott H. , Leach Jan E. , Bai Jianfa , Saleh Amgad , Knapp Alan K. , Fay Philip A. , Nippert Jesse , Schnable Patrick S. , Smith Melinda D. 
Published: December 2009

Summary1. If we are to understand the mechanisms underlying species responses to climate change in natural systems, studies are needed that focus on responses of non‐model species under field conditions. We measured transcriptional profiles of individuals ofAndropogon gerardii, a C4grass native to North American grasslands, in a field experiment in which both temperature and precipitation were manipulated to simulate key aspects of forecasted climate change.2. By using microarrays developed for a closely related model species,Zea mays, we were able to compare the relative influence of warming versus altered soil moisture availability on expression levels of over 7000 genes, identify responsive functional groups of genes and correlate changes in gene transcription with physiological responses.3. We observed more statistically significant shifts in transcription levels of genes in response to thermal stress than in response to water stress. We also identified candidate genes that demonstrated transcription levels closely associated with physiological variables, in particular chlorophyll fluorescence.4.Synthesis. These results suggest that an ecologically important species responds differently to different environmental aspects of forecast climate change. These translational changes have the potential to influence phenotypic characters and ultimately adaptive responses.