bluuebunny/crossref_metadata_2025_split huggingface dataset:
The Dual BKR Inequality and Rudich's Conjecture
Authors: KAHN JEFF , SAKS MICHAEL , SMYTH CLIFFORD 
Published: December 2010

Let be a set of terms over an arbitrary (but finite) number of Boolean variables. Let U() be the set of truth assignments that satisfy exactly one term in . Motivated by questions in computational complexity, Rudich conjectured that there exist ∊, δ > 0 such that, if is any set of terms for which U() contains at least a (1−∊)-fraction of all truth assignments, then there exists a term t ∈ such that at least a δ-fraction of assignments satisfy some term of sharing a variable with t [8].We prove a stronger version: for any independent assignment of the variables (not necessarily the uniform one), if the measure of U() is at least 1 − ∊, there exists a t ∈ such that the measure of the set of assignments satisfying either t or some term incompatible with t (i.e., having no satisfying assignments in common with t) is at least $\Gd = 1- \Ge - \frac{4\Ge}{1-\Ge}$. (A key part of the proof is a correlation-like inequality on events in a finite product probability space that is in some sense dual to Reimer's inequality [11], a.k.a. the BKR inequality [5], or the van den Berg–Kesten conjecture [3].)
Criterion Validity of the Delis-Kaplan Executive Function System (D-KEFS) Fluency Subtests After Traumatic Brain Injury
Authors: Strong Carrie-Ann H. , Tiesma David , Donders Jacobus 
Published: December 2010

AbstractThe performance of 65 patients with complicated mild–severe traumatic brain injury was evaluated on the Verbal and Design Fluency subtests of the Delis-Kaplan Executive Function System (D-KEFS), and compared with that of 65 demographically matched healthy controls. There were statistically significant group differences on Letter Fluency and Category Switching but not on any of the Design Fluency tasks. Combined, these two Verbal Fluency subtests had a classification accuracy of 65.39%, associated with a likelihood ratio of 1.87. The impact of length of coma on Letter Fluency performance but not Category Switching was mediated at least in part by processing speed. The findings suggest modest criterion validity of some of the D–KEFS Verbal Fluency subtests in the assessment of patients with complicated mild–severe traumatic brain injury. (JINS, 2011, 17, 230–237)
Preferred providers and the credible commitment problem in health insurance: first experiences with the implementation of managed competition in the Dutch health care system
Authors: Boonen Lieke H. H. M. , Schut Frederik T. 
Published: December 2010

AbstractWe investigate the impact of the transition towards managed competition in the Dutch health care system on health insurers’ contracting behaviour. Specifically, we examine whether insurers have been able to take up their role as prudent buyers of care and examine consumers’ attitudes towards insurers’ new role. Health insurers’ contracting behaviour is investigated by an extensive analysis of available information on purchasing practices by health insurers and by interviews with directors of health care purchasing of the four major health insurers, accounting for 90% of the market. Consumer attitudes towards insurers’ new role are investigated by surveys among a representative sample of enrollees over the period 2005–2009. During the first four years of the reform, health insurers were very reluctant to engage in selective contracting and preferred to use ‘soft’ positive incentives to encourage preferred provider choice rather than engaging in restrictive managed care activities. Consumer attitudes towards channelling vary considerably by type of provider but generally became more negative in the first two years after the reform. Insurers’ reluctance to use selective contracting can be at least partly explained by the presence of a credible-commitment problem. Consumers do not trust that insurers with restrictive networks are committed to provide good quality care. The credible-commitment problem seems to be particularly relevant to the Netherlands, since Dutch enrollees are not used to restrictions on provider choice. Since consumers are quite sensitive to differences in provider quality, more reliable information about provider quality is required to reduce the credible-commitment problem.
Physiological and evolutionary studies of NAP systems in Shewanella piezotolerans WP3
Authors: Chen Ying , Wang Fengping , Xu Jun , Mehmood Muhammad Aamer , Xiao Xiang 
Published: December 2010

Abstract
Most of the Shewanella species contain two periplasmic nitrate reductases (NAP-α and NAP-β), which is a unique feature of this genus. In the present study, the physiological function and evolutionary relationship of the two NAP systems were studied in the deep-sea bacterium Shewanella piezotolerans WP3. Both of the WP3 nap gene clusters: nap-α (napD1A1B1C) and nap-β (napD2A2B2) were shown to be involved in nitrate respiration. Phylogenetic analyses suggest that NAP-β originated earlier than NAP-α. Tetraheme cytochromes NapC and CymA were found to be the major electron deliver proteins, and CymA also served as a sole electron transporter towards nitrite reductase. Interestingly, a ΔnapA2 mutant with the single functional NAP-α system showed better growth than the wild-type strain, when grown in nitrate medium, and it had a selective advantage to the wild-type strain. On the basis of these results, we proposed the evolution direction of nitrate respiration system in Shewanella: from a single NAP-β to NAP-β and NAP-α both, followed by the evolution to a single NAP-α. Moreover, the data presented here will be very useful for the designed engineering of Shewanella for more efficient respiring capabilities for environmental bioremediation.
Quantification of virus genes provides evidence for seed-bank populations of phycodnaviruses in Lake Ontario, Canada
Authors: Short Cindy M , Rusanova Oksana , Short Steven M 
Published: December 2010

Abstract
Using quantitative PCR, the abundances of six phytoplankton viruses DNA polymerase (polB) gene fragments were estimated in water samples collected from Lake Ontario, Canada over 26 months. Four of the polB fragments were most related to marine prasinoviruses, while the other two were most closely related to cultivated chloroviruses. Two Prasinovirus-related genes reached peak abundances of &gt;1000 copies ml−1 and were considered ‘high abundance’, whereas the other two Prasinovirus-related genes peaked at abundances &lt;1000 copies ml−1 and were considered ‘low abundance’. Of the genes related to chloroviruses, one peaked at ca 1600 copies ml−1, whereas the other reached only ca 300 copies ml−1. Despite these differences in peak abundance, the abundances of all genes monitored were lowest during the late fall, winter and early spring; during these months the high abundance genes persisted at 100–1000 copies ml−1 while the low abundance Prasinovirus- and Chlorovirus-related genes persisted at fewer than ca 100 copies ml−1. Clone libraries of psbA genes from Lake Ontario revealed numerous Chlorella-like algae and two prasinophytes demonstrating the presence of candidate hosts for all types of viruses monitored. Our results corroborate recent metagenomic analyses that suggest that aquatic virus communities are composed of only a few abundant populations and many low abundance populations. Thus, we speculate that an ecologically important characteristic of phycodnavirus communities is seed-bank populations with members that can become numerically dominant when their host abundances reach appropriate levels.
An integrative study of a meromictic lake ecosystem in Antarctica
Authors: Lauro Federico M , DeMaere Matthew Z , Yau Sheree , Brown Mark V , Ng Charmaine , Wilkins David , Raftery Mark J , Gibson John A E , Andrews-Pfannkoch Cynthia , Lewis Matthew , Hoffman Jeffrey M , Thomas Torsten , Cavicchioli Ricardo 
Published: December 2010

Abstract
In nature, the complexity and structure of microbial communities varies widely, ranging from a few species to thousands of species, and from highly structured to highly unstructured communities. Here, we describe the identity and functional capacity of microbial populations within distinct layers of a pristine, marine-derived, meromictic (stratified) lake (Ace Lake) in Antarctica. Nine million open reading frames were analyzed, representing microbial samples taken from six depths of the lake size fractionated on sequential 3.0, 0.8 and 0.1 μm filters, and including metaproteome data from matching 0.1 μm filters. We determine how the interactions of members of this highly structured and moderately complex community define the biogeochemical fluxes throughout the entire lake. Our view is that the health of this delicate ecosystem is dictated by the effects of the polar light cycle on the dominant role of green sulfur bacteria in primary production and nutrient cycling, and the influence of viruses/phage and phage resistance on the cooperation between members of the microbial community right throughout the lake. To test our assertions, and develop a framework applicable to other microbially driven ecosystems, we developed a mathematical model that describes how cooperation within a microbial system is impacted by periodic fluctuations in environmental parameters on key populations of microorganisms. Our study reveals a mutualistic structure within the microbial community throughout the lake that has arisen as the result of mechanistic interactions between the physico-chemical parameters and the selection of individual members of the community. By exhaustively describing and modelling interactions in Ace Lake, we have developed an approach that may be applicable to learning how environmental perturbations affect the microbial dynamics in more complex aquatic systems.
Diversity and distribution of single-stranded DNA phages in the North Atlantic Ocean
Authors: Tucker Kimberly P , Parsons Rachel , Symonds Erin M , Breitbart Mya 
Published: December 2010

Abstract
Knowledge of marine phages is highly biased toward double-stranded DNA (dsDNA) phages; however, recent metagenomic surveys have also identified single-stranded DNA (ssDNA) phages in the oceans. Here, we describe two complete ssDNA phage genomes that were reconstructed from a viral metagenome from 80 m depth at the Bermuda Atlantic Time-series Study (BATS) site in the northwestern Sargasso Sea and examine their spatial and temporal distributions. Both genomes (SARssφ1 and SARssφ2) exhibited similarity to known phages of the Microviridae family in terms of size, GC content, genome organization and protein sequence. PCR amplification of the replication initiation protein (Rep) gene revealed narrow and distinct depth distributions for the newly described ssDNA phages within the upper 200 m of the water column at the BATS site. Comparison of Rep gene sequences obtained from the BATS site over time revealed changes in the diversity of ssDNA phages over monthly time scales, although some nearly identical sequences were recovered from samples collected 4 years apart. Examination of ssDNA phage diversity along transects through the North Atlantic Ocean revealed a positive correlation between genetic distance and geographic distance between sampling sites. Together, the data suggest fundamental differences between the distribution of these ssDNA phages and the distribution of known marine dsDNA phages, possibly because of differences in host range, host distribution, virion stability, or viral evolution mechanisms and rates. Future work needs to elucidate the host ranges for oceanic ssDNA phages and determine their ecological roles in the marine ecosystem.
A Selective Annotated Bibliography for Clinical Audiology (1989–2009): Books
Authors: Ferrer-Vinent Susan T. , Ferrer-Vinent Ignacio J. 
Published: December 2010

Purpose
This is the 2nd in a series of 3 planned companion articles that present a selected, annotated, and indexed bibliography of clinical audiology publications from 1989 through 2009.

Method
Research and preparation of the bibliography were based on published guidelines, professional audiology experience, and professional librarian experience.

Results
The first article in the series covered reference works. This article focuses on other books. The planned third companion article will present periodicals and online resources.

Conclusions
Audiologists and librarians can use this bibliography to help them identify relevant clinical audiology literature.
Speech and Language of Children Using Hearing Aids With Adaptive Directional and Noise Reduction Features
Authors: Auriemmo Jane , Stenger Patti 
Published: December 2010

AbstractThis paper reviews longitudinal speech-language outcomes of a group of school age children using hearing aid noise reduction and adaptive directional features. These results, obtained through collaboration between school audiologist and speech-language pathologist, reveal that receptive and expressive language scores are stable or improved over a three-year period of use.
Word Order and Tense Choice in Standard Written French
Authors: Engel Dulcie M. 
Published: November 2010

SUMMARY
In modern French, the use of simple and composed tenses varies with respect to word order in two specific cases: firstly with subject inversion, and secondly with insertion of material between the auxiliary and the past participle. With the 'passé simple' (past historic) and the 'passé composé' (perfect), both of which can express past punctual actions, this difference in	word order may influence tense choice. If a particular effect (contrast, emphasis...) is desired in the phrase, either the 'passé simple' or the 'passé composé' can be used to express the punctual past, the choice being dependent on their respective influence on word order.
RESUME
L'emploi des temps simples et des temps composés en français moderne diffère du point de vue de l'ordre de mots, en deux cas spécifiques: premièrement, avec l'inversion du sujet; et deuxièmement avec la possibilité de l'insertion de mots entre l'auxiliaire et le participe passé. Pour le passé simple et le passé composé, qui expriment tous les deux des actions passées et ponctuelles, cette différence d'ordre peut influencer le choix du temps: si l'on désire creer un effet particulier dans la phrase (contraste, emphase...), on pourrait employer soit le passé simple, soit le passé composé pour exprimer le passé ponctuel, selon leur influence sur l'ordre des mots.
Fluctuations in out-of-equilibrium systems: from theory to experiment
Authors: Ciliberto S , Joubaud S , Petrosyan A 
Published: December 2010

We introduce from an experimental point of view the main concepts of fluctuation
theorems for work, heat and entropy production in out-of-equilibrium systems. We will
discuss the important difference between the applications of these concepts to
stochastic systems and to a second class of systems (chaotic systems) where the
fluctuations are induced either by chaotic flows or by fluctuating driving forces. We
will mainly analyze the stochastic systems using the measurements performed
in two experiments: (a) a harmonic oscillator driven out of equilibrium by an
external force; (b) a colloidal particle trapped in a time-dependent double-well
potential. We will rapidly describe some consequences of fluctuation theorems and
some useful applications to the analysis of experimental data. As an example,
the case of a molecular motor will be analyzed in some detail. Finally we will
discuss the problems related to the applications of fluctuation theorems to chaotic
systems.
maxAlike: maximum likelihood-based sequence reconstruction with application to improved primer design for unknown sequences
Authors: Menzel Peter , Stadler Peter F. , Gorodkin Jan 
Published: December 2010

Abstract
Motivation: The task of reconstructing a genomic sequence from a particular species is gaining more and more importance in the light of the rapid development of high-throughput sequencing technologies and their limitations. Applications include not only compensation for missing data in unsequenced genomic regions and the design of oligonucleotide primers for target genes in species with lacking sequence information but also the preparation of customized queries for homology searches.
Results: We introduce the maxAlike algorithm, which reconstructs a genomic sequence for a specific taxon based on sequence homologs in other species. The input is a multiple sequence alignment and a phylogenetic tree that also contains the target species. For this target species, the algorithm computes nucleotide probabilities at each sequence position. Consensus sequences are then reconstructed based on a certain confidence level. For 37 out of 44 target species in a test dataset, we obtain a significant increase of the reconstruction accuracy compared to both the consensus sequence from the alignment and the sequence of the nearest phylogenetic neighbor. When considering only nucleotides above a confidence limit, maxAlike is significantly better (up to 10%) in all 44 species. The improved sequence reconstruction also leads to an increase of the quality of PCR primer design for yet unsequenced genes: the differences between the expected Tm and real Tm of the primer-template duplex can be reduced by ~26% compared with other reconstruction approaches. We also show that the prediction accuracy is robust to common distortions of the input trees. The prediction accuracy drops by only 1% on average across all species for 77% of trees derived from random genomic loci in a test dataset.
Availability: maxAlike is available for download and web server at: http://rth.dk/resources/maxAlike.
Contact: gorodkin@rth.dk
Supplementary information: Supplementary data are available at Bioinformatics online.
Open source platform for the execution and analysis of mechanical refolding experiments
Authors: Aioanei Daniel , Brucale Marco , Samorí Bruno 
Published: December 2010

Abstract
Motivation: Single-molecule force spectroscopy has facilitated the experimental investigation of biomolecular force-coupled kinetics, from which the kinetics at zero force can be extrapolated via explicit theoretical models. The atomic force microscope (AFM) in particular is routinely used to study protein unfolding kinetics, but only rarely protein folding kinetics. The discrepancy arises because mechanical protein refolding studies are more technically challenging.
Results: We developed software that can drive and analyse mechanical refolding experiments when used with the commercial AFM setup ‘Picoforce AFM’, Bruker (previously Digital Instruments). We expect the software to be easily adaptable to other AFM setups. We also developed an improved method for the statistical characterization of protein folding kinetics, and implemented it into an AFM-independent software module.
Availability: Software and documentation are available at http://code.google.com/p/refolding under Apache License 2.0.
Contact: aioaneid@gmail.com
Supplementary information: Supplementary data are available at Bioinformatics online.
Randomized controlled trial of a brief intervention for unhealthy alcohol use in hospitalized Taiwanese men
Authors: Liu Shen‐Ing , Wu Shu‐I , Chen Su‐Chiu , Huang Hui‐Chun , Sun Fang‐Ju , Fang Chun‐Kai , Hsu Chien‐Chi , Huang Chiu‐Ron , Yeh Hsiao‐Mei , Shih Shou‐Chuan 
Published: December 2010

ABSTRACTAims  To evaluate the effectiveness of a brief intervention in hospitalized Taiwanese men to reduce unhealthy alcohol consumption.Design  Randomized controlled trial.Setting  Medical/surgical wards of a medical centre in Taipei, Taiwan.Participants  Of 3669 consecutive adult male in‐patients, 616 were identified as unhealthy alcohol users (>14 drinks/week) and assigned randomly to either usual care (n = 308) or a brief intervention (n = 308).Measurements  Primary outcomes were changes in alcohol consumption at 4, 9 and 12 months, including self‐reported weekly alcohol consumption, drinking days and heavy drinking episodes assessed by 7‐day time‐line follow‐back. Secondary outcomes were (i) self‐reported alcohol problems, (ii) health‐care utilization (hospital days and emergency department visits), (iii) self‐reported seeking of speciality treatment for alcohol problems and (iv) 3‐month Quick Drinking Screen.Findings  Based on intention‐to‐treat analyses, the intervention group consumed significantly less alcohol than the control group among both unhealthy drinkers and the subgroup of alcohol‐dependent participants over 12 months, on both 7‐day and 3‐month assessments. Adjunctive analyses of only those who completed all assessments found that total drinks consumed did not remain significant. Significantly more participants with alcohol use disorders in the intervention than in the control group (8.3%, 19 of 230 versus 2.1%, four of 189) consulted specialists by 12 months (P = 0.01). However, alcohol‐related problems and health‐care utilization did not differ significantly in the two groups during follow‐up.Conclusions  Data from Taiwan confirm that brief in‐hospital intervention can result in a reduction in alcohol intake by men who drink heavily or are diagnosed with an alcohol use disorder.
Albendazole‐praziquantel interaction in healthy volunteers: kinetic disposition, metabolism and enantioselectivity
Authors: Lima Renata Monteiro , Ferreira Maria Augusta Drago , de Jesus Ponte Carvalho Teresa Maria , Dumêt Fernandes Bruno José , Takayanagui Osvaldo Massaiti , Garcia Hector Hugo , Coelho Eduardo Barbosa , Lanchote Vera Lucia 
Published: December 2010

WHAT IS ALREADY KNOWN ABOUT THIS SUBJECT • Pharmacokinetic interactions between albendazole and praziquantel are based on plasma concentrations of the enantiomeric mixture of both drugs with contradictory data, although the antiparasitic activity arises from (−)‐(R)‐praziquantel and (+)‐albendazole sulfoxide. WHAT THIS STUDY ADDS • The pharmacokinetic interaction between albendazole and praziquantel is enantioselective. Praziquantel increased the plasma concentrations of (+)‐albendazole sulfoxide more than those of (−)‐albendazole sulfoxide and the administration of albendazole did not change the kinetic disposition of (+)‐(S)‐praziquantel, but increased the plasma concentration of (−)‐(R)‐praziquantel.AIM This study investigated the kinetic disposition, metabolism and enantioselectivity of albendazole (ABZ) and praziquantel (PZQ) administered alone and in combination to healthy volunteers.METHODS A randomized crossover study was carried out in three phases (n= 9), in which some volunteers started in phase 1 (400 mg ABZ), others in phase 2 (1500 mg PZQ), and the remaining volunteers in phase 3 (400 mg ABZ + 1500 mg PZQ). Serial blood samples were collected from 0–48 h after drug administration. Pharmacokinetic parameters were calculated using a monocompartmental model with lag time and were analyzed using the Wilcoxon test; P≤ 0.05.RESULTS The administration of PZQ increased the plasma concentrations of (+)‐ASOX (albendazole sulphoxide) by 264% (AUC 0.99 vs. 2.59 µg ml−1 h), (−)‐ASOX by 358% (0.14 vs. 0.50 µg ml−1 h) and albendazole sulfone (ASON) by 187% (0.17 vs. 0.32 µg ml−1 h). The administration of ABZ did not change the kinetic disposition of (+)‐(S)‐PZQ (–)‐(R)‐4‐OHPZQ or (+)‐(S)‐4‐OHPZQ, but increased the plasma concentration of (–)‐(R)‐PZQ by 64.77% (AUC 0.52 vs. 0.86 µg ml−1 h).CONCLUSIONS The pharmacokinetic interaction between ABZ and PZQ in healthy volunteers was demonstrated by the observation of increased plasma concentrations of ASON, both ASOX enantiomers and (–)‐(R)‐PZQ. Clinically, the combination of ABZ and PZQ may improve the therapeutic efficacy as a consequence of higher concentration of both active drugs. On the other hand, the magnitude of this elevation may represent an increased risk of side effects, requiring, certainly, reduction of the dosage. However, further studies are necessary to evaluate the efficacy and safety of this combination.