bluuebunny/crossref_metadata_2025_split huggingface dataset:
Correlation between Preoperative Kimura Inching Studies and Intraoperative Findings during Endoscopic-Assisted Decompression of the Ulnar Nerve at the Elbow
Authors: Agnew Sonya Paisley , Minieka Michael M. , Patel Ronak M. , Nagle Daniel J. 
Published: October 2012

Background During the evolution of the senior author's technique of ulnar nerve transposition to in situ decompression for ulnar neuropathy at the elbow, nerve conduction studies (NCS) including the Kimura inching method were performed preoperatively in an effort to ensure that all potential sites of compression were investigated intraoperatively. The purpose of this study is to compare the results of the Kimura inching technique with the intraoperative findings noted during decompression of the ulnar nerve at the elbow. Methods The medical records of consecutive patients who underwent in situ decompression of their ulnar nerves combined with endoscopic examination between March and December of 2009 were retrospectively reviewed. The site of ulnar nerve compression noted using the Kimura inching technique was compared with the intraoperative findings. Results Twelve consecutive patients (four with bilateral symptoms) underwent endoscopic ulnar nerve compression in the study period for a total of 16 cases analyzed. In 12 cases, the Kimura method localized the site of compression to Osborne's bands and/or the aponeurosis of the flexor carpi ulnaris (FCU). Intraoperatively, compression was noted at Osborne's bands, the FCU aponeurosis, and/or the FCU) muscle proper in all 16 patients. There was partial or full correlation between the nerve conduction data and intraoperative findings in 13/16 cases. Conclusions There was good but not perfect agreement between the NCS and intraoperative findings, perhaps because transcutaneous NCS are less accurate when a nerve is surrounded by muscle. The information obtained in this study is valuable when planning surgery to address ulnar nerve compression.
Sorafenib-induced acute interstitial pneumonia in patients with advanced hepatocellular carcinoma: report of three cases
Authors: Takeda Haruhiko , Nishikawa Hiroki , Iguchi Eriko , Matsuda Fumihiro , Kita Ryuichi , Kimura Toru , Osaki Yukio 
Published: October 2012

AbstractLittle is known about acute interstitial pneumonia (AIP) induced by sorafenib therapy in patients with advanced hepatocellular carcinoma (HCC). Here, we present three patients with advanced HCC who developed AIP during sorafenib therapy, with fatal complications in two cases. Case 1 was a 76-year-old man who developed dyspnea. Chest CT showed interstitial pneumonia. Sorafenib was discontinued immediately, and prednisolone was started. His pneumonia resolved. A drug-induced lymphocyte stimulation test for sorafenib was positive. Case 2 was a 75-year-old man and case 3 was a 77-year-old man, both of whom developed high-grade fever and hypoxemia during sorafenib therapy, and were diagnosed with AIP. In spite of high-dose steroid therapy, their respiratory failure worsened and both patients died. In all three cases, serum KL-6 or surfactant protein D concentrations were elevated, and blood and sputum cultures did not grow pathogens. All three patients were smokers with restrictive lung disease on preoperative respiratory function testing, but did not have respiratory symptoms before sorafenib therapy. The clinical features of these three cases suggest that male gender, older age, smoking history, and lung disease are associated with acute sorafenib-induced AIP in patients with advanced HCC.
Predicting sRNAs and Their Targets in Bacteria
Authors: Li Wuju , Ying Xiaomin , Lu Qixuan , Chen Linxi 
Published: October 2012

Abstract
Bacterial small RNAs (sRNAs) are an emerging class of regulatory RNAs of about 40–500 nucleotides in length and, by binding to their target mRNAs or proteins, get involved in many biological processes such as sensing environmental changes and regulating gene expression. Thus, identification of bacterial sRNAs and their targets has become an important part of sRNA biology. Current strategies for discovery of sRNAs and their targets usually involve bioinformatics prediction followed by experimental validation, emphasizing a key role for bioinformatics prediction. Here, therefore, we provided an overview on prediction methods, focusing on the merits and limitations of each class of models. Finally, we will present our thinking on developing related bioinformatics models in future.
A model for improving the treatment and care of Alzheimer's disease patients through interdisciplinary research
Authors: Trojanowski John Q. , Arnold Steven E. , Karlawish Jason H. , Naylor Mary , Brunden Kurt R. , Lee Virginia M.‐Y. 
Published: October 2012

AbstractThe emerging global epidemic of Alzheimer's disease (AD) demands novel paradigms to address the two unmet needs of the field: (a) cost‐effective health care delivery programs/services, and (b) clinical and basic research to accelerate therapy discovery/development. This report outlines a model demonstration project, the Marian S. Ware Alzheimer Program at the University of Pennsylvania, which was designed to achieve four specific aims: (1) improve the integration and continuity of AD care; (2) identify biomarkers that detect the earliest presence of AD and related neurodegenerative cognitive disorders; (3) enhance both the design and conduct of clinical trials as well as review their results to more effectively test new AD therapies and translate valuable therapies into clinical practice; and (4) discover and develop novel disease‐modifying small molecule treatments for AD.The “Ware‐UPenn” program has been presented in this report as a useful prototype for partnerships between private philanthropy and academia in planning and developing programs to address a major national public health problem.
Inter-institutional decision-making: The case of the Common Agricultural Policy
Authors: Greer Alan , Hind Thomas 
Published: October 2012

Abstract
The dominant portrayal of the policy process around the Common Agricultural Policy (CAP) emphasises a system of inter-governmental bargaining, close links between institutions and farming interests, and compartmentalised closed policy networks. This article considers how inter-institutional relationships might be reshaped by the extension of ‘co-decision’ powers to the European Parliament in the Lisbon Treaty. This raises the possibility that policy proposals and outcomes may increasingly reflect the participation of a broader range of actors and interests. Using four scenarios that reflect different institutional configurations, a preliminary analysis of the 2011 dairy regime proposals (the ‘Milk Package’) is used to draw some conclusions about whether the agricultural policy agenda is likely to be broadened through de-compartmentalisation, leading to a more fluid policy arena characterised by more actors with conflicting values.
The QuranicMushrikūnand the resurrection (Part I)
Authors: Crone Patricia 
Published: October 2012

AbstractThis article examines the attitudes of the Quranicmushrikūnto the resurrection and the afterlife, focusing on those who doubted or denied the reality of both. The first part of the article argues that the doubters and deniers had grown up in a monotheist environment familiar with both concepts and that it was from within the monotheist tradition that they rejected them. The second part (published in a forthcoming issue ofBSOAS) relates their thought to intellectual currents in Arabia and the Near East in general, arguing that the role of their pagan heritage in their denial is less direct than normally assumed. It is also noted thatmutakallims such as Abū ʿĪsā al-Warrāq and al-Māturīdī anticipated the main conclusions reached in this paper.
Genetic sensitivity to the environment, across lifetime
Authors: Homberg Judith R. 
Published: October 2012

AbstractThe target article by Charney convincingly argues that genomic plasticity perinatally induced by the environment creates a complication in determining which parts of behavior are attributed to nature and which to nurture. I argue that real life is even more complex because (1) genotype influences sensitivity to environmental stimuli, and (2) the genome continues to be modified throughout life.
From gene activity to behavior (and back again)
Authors: Lickliter Robert 
Published: October 2012

AbstractDocumenting the bidirectional traffic from gene action to the external environment and its effects on behavior remains a major conceptual, empirical, and analytical challenge for developmental science. Charney has provided an instructive snapshot of where we are in meeting this challenge and, in so doing, exposes the considerable shortcomings of the traditional genomic model employed by behavior genetics.
Clinicians learn less and less about more and more until they know nothing about everything; researchers learn more and more about less and less until they know everything about nothing: Discuss
Authors: Aitken Kenneth John 
Published: October 2012

AbstractA number of recent developments in our understanding of the biology of heritability question commonly held views on the immutability of genetic factors. These have numerous potential implications for improving understanding and practice in pre- and postconceptional care and for infant and child mental health, and they carry a cautionary message against overgeneralization.
Transitioning from active treatment: Colorectal cancer survivors’ health promotion goals
Authors: Palmer Nynikka R.A. , Bartholomew L. Kay , McCurdy Sheryl A. , Basen-Engquist Karen M. , Naik Aanand D. 
Published: October 2012

AbstractObjective:The purpose of this study is to describe the post-treatment goals of colorectal cancer (CRC) survivors. We sought to determine whether goals were a salient concept during the period immediately following treatment, and whether a goal-setting intervention might be feasible and acceptable to these patients.Method:Semi-structured qualitative interviews were administered to a convenience sample of 41 CRC patients who were 0–24 months post-treatment. Topics discussed included expectations and goals for future health, cancer prevention awareness, health-promoting behavior-change goals, and post-treatment cancer issues. Content analysis was used to explore emergent themes.Results:Overall, participants’ health-related goals were: being healthy, getting back to normal, and not having a cancer recurrence. Most of the CRC survivors reported being proactive with their health by maintaining healthy behaviors or making healthy behavior changes, or had goals to change their behavior. All respondents had plans to maintain follow-up care and regular screening appointments. Some patients were managing treatment side effects or non-cancer issues that limited their functional abilities. Many respondents were satisfied with the care they received, and felt it was now their responsibility to do their part in taking care of themselves.Significance of results:CRC survivors talk about goals, and many of them are either making or have an interest in making health behavior changes. Self-management support could be an appropriate strategy to assist patients with achieving their health goals post-treatment. Patients may need help addressing lingering treatment side effects or non-cancer issues. Healthcare providers should consider assessing patients’ goals to help patients resolve post-treatment issues and promote healthy behaviors.
Work culture among healthcare personnel in a palliative medicine unit
Authors: André Beate , Sjøvold Endre , Rannestad Toril , Holmemo Marte , Ringdal Gerd I. 
Published: October 2012

AbstractObjective:Understanding and assessing health care personnel's work culture in palliative care is important, as a conflict between “high tech” and “high touch” is present. Implementing necessary changes in behavior and procedures may imply a profound challenge, because of this conflict. The aim of this study was to explore the work culture at a palliative medicine unit (PMU).Method:Healthcare personnel (N = 26) at a PMU in Norway comprising physicians, nurses, physiotherapists, and others filled in a questionnaire about their perception of the work culture at the unit. The Systematizing Person-Group Relations (SPGR) method was used for gathering data and for the analyses. This method applies six different dimensions representing different aspects of a work culture (Synergy, Withdrawal, Opposition, Dependence, Control, and Nurture) and each dimension has two vectors applied. The method seeks to explore which aspects dominate the particular work culture, identifying challenges, limitations, and opportunities. The findings were compared with a reference group of 347 ratings of well-functioning Norwegian organizations, named the “Norwegian Norm.”Results:The healthcare personnel working at the PMU had significantly higher scores than the “Norwegian Norm” in both vectors in the “Withdrawal” dimension and significant lower scores in both vectors in the “Synergy,” “Control,” and “Dependence” dimensions.Significance of results:Healthcare personnel at the PMU have a significantly different perception of their work culture than do staff in “well-functioning organizations” in several dimensions. The low score in the “Synergy” and “Control” dimensions indicate lack of engagement and constructive goal orientation behavior, and not being in a position to change their behavior. The conflict between “high tech” and “high touch” at a PMU seems to be an obstacle when implementing new procedures and alternative courses of action.
Device-Associated Infections among Neonatal Intensive Care Unit Patients: Incidence and Associated Pathogens Reported to the National Healthcare Safety Network, 2006–2008
Authors: Hocevar Susan N. , Edwards Jonathan R. , Horan Teresa C. , Morrell Gloria C. , Iwamoto Martha , Lessa Fernanda C. 
Published: October 2012

Objective.To describe rates and pathogen distribution of device-associated infections (DAIs) in neonatal intensive care unit (NICU) patients and compare differences in infection rates by hospital type (children's vs general hospitals).Patients and Setting.Neonates in NICUs participating in the National Healthcare Safety Network from 2006 through 2008.Methods.We analyzed central line–associated bloodstream infections (CLABSIs), umbilical catheter–associated bloodstream infections (UCABs), and ventilator-associated pneumonia (VAP) among 304 NICUs. Differences in pooled mean incidence rates were examined using Poisson regression; nonparametric tests for comparing medians and rate distributions were used.Results.Pooled mean incidence rates by birth weight category (750 g or less, 751–1,000 g, 1,001–1,500 g, 1,501–2,500 g, and more than 2,500 g, respectively) were 3.94, 3.09, 2.25, 1.90, and 1.60 for CLABSI; 4.52, 2.77, 1.70, 0.91, and 0.92 for UCAB; and 2.36, 2.08, 1.28, 0.86, and 0.72 for VAP. When rates of infection between hospital types were compared, only pooled mean VAP rates were significantly lower in children's hospitals than in general hospitals among neonates weighing 1,000 g or less; no significant differences in medians or rate distributions were noted. Pathogen frequencies were coagulase-negative staphylococci (28%),Staphylococcus aureus(19%), andCandidaspecies (13%) for bloodstream infections andPseudomonasspecies (16%),S. aureus(15%), andKlebsiellaspecies (14%) for VAP. Of 673S. aureusisolates with susceptibility results, 33% were methicillin resistant.Conclusions.Neonates weighing 750 g or less had the highest DAI incidence. With the exception of VAP, pooled mean NICU incidence rates did not differ between children's and general hospitals. Pathogens associated with these infections can pose treatment challenges; continued efforts at prevention need to be applied to all NICU settings.
Ion-beam modifications of mechanical and dimensional properties of silicon carbide
Authors: Costantini Jean-Marc , Kerbiriou Xavier , Sauzay Maxime , Thomé Lionel 
Published: October 2012

Abstract
3C-SiC single crystal epitaxial layers, 6H-SiC single crystal plates and α-SiC Hexoloy sinters were irradiated with 4.0 MeV Xe or 4.0 MeV Au ions at room temperature. Mechanical and dimensional evolutions of silicon carbide are studied by means of nano-indentation and step-height measurements which are correlated with Rutherford backscattering spectrometry and channelling (RBS/C) data in single crystals. Irradiation with Xe ions induces a total lattice disorder related to amorphization for a fluence of 1 × 1015 cm−2 in both polytypes. When complete amorphization is reached, around the same values of Young's modulus (∼350 GPa) and Berkovich hardness (∼27 GPa) are found in both polytypes. The out-of-plane expansion increases with irradiation dose and the saturation value measured in the amorphous layer (normalized to the projected range of the ions) is close to 20–25%. Modifications of macroscopic properties are mainly governed by the disordered fraction of the material in a two-step damage process. A similar behaviour of material evolution is found for the cubic and hexagonal polytypes, either in single crystals or sintered polycrystalline samples. Calculations of Young's modulus and volume swelling are carried out using the analytical (Reuss and Voigt) models of homogenization.
Fast protein structure alignment using Gaussian overlap scoring of backbone peptide fragment similarity
Authors: Ritchie David W. , Ghoorah Anisah W. , Mavridis Lazaros , Venkatraman Vishwesh 
Published: October 2012

Abstract
Motivation: Aligning and comparing protein structures is important for understanding their evolutionary and functional relationships. With the rapid growth of protein structure databases in recent years, the need to align, superpose and compare protein structures rapidly and accurately has never been greater. Many structural alignment algorithms have been described in the past 20 years. However, achieving an algorithm that is both accurate and fast remains a considerable challenge.
Results: We have developed a novel protein structure alignment algorithm called ‘Kpax’, which exploits the highly predictable covalent geometry of Cα atoms to define multiple local coordinate frames in which backbone peptide fragments may be oriented and compared using sensitive Gaussian overlap scoring functions. A global alignment and hence a structural superposition may then be found rapidly using dynamic programming with secondary structure-specific gap penalties. When superposing pairs of structures, Kpax tends to give tighter secondary structure overlays than several popular structure alignment algorithms. When searching the CATH database, Kpax is faster and more accurate than the very efficient Yakusa algorithm, and it gives almost the same high level of fold recognition as TM-Align while being more than 100 times faster.
Availability and implementation: http://kpax.loria.fr/.
Contact: Dave.Ritchie@inria.fr.
Supplementary information: Supplementary data are available at Bioinformatics online.
A distorted wave Born approximation target strength model for Bering Sea euphausiids
Authors: Smith Joy N. , Ressler Patrick H. , Warren Joseph D. 
Published: October 2012

Abstract
Smith, J. N., Ressler, P. H., and Warren, J. D. 2013. A distorted wave Born approximation target strength model for Bering Sea euphausiids. – ICES Journal of Marine Science, 70:204–214. Acoustic surveys monitor euphausiid populations in the Bering Sea because of their importance as prey for walleye pollock and other organisms. Various scattering models exist to convert acoustic backscatter data to estimates of euphausiid numerical density or biomass, but a target strength (TS) model specific to Bering Sea euphausiids has not been available. This study parameterized a distorted wave Born approximation (DWBA) scattering model using physical (length and body shape) and material (density contrast, g, and sound speed contrast, h) properties measured from live euphausiids. All model parameters (length, shape, material properties, orientation) were evaluated for their effect on predicted TS. A polynomial function was used to describe animal shape and produced smaller TS estimates compared to a taper function, as is traditionally used in DWBA scattering models of euphausiids. Animal length was positively correlated with TS, but variations in other parameters (including material properties and orientation) also produced large changes in TS. Large differences in TS between estimates calculated using measured versus literature material property values caused large variations in acoustic estimates of euphausiid numerical densities (animals m−3) which emphasizes the importance of collecting site-specific g and h measurements when possible.
Fish avoidance of research vessels and the efficacy of noise-reduced vessels: a review
Authors: De Robertis Alex , Handegard Nils Olav 
Published: October 2012

Abstract
De Robertis, A. and Handegard, N. O. 2013. Fish avoidance of research vessels and the efficacy of noise-reduced vessels: a review. – ICES Journal of Marine Science, 70:34–45. It has long been recognized that fish can avoid approaching vessels and that these behaviours can bias fishery surveys. Underwater noise is considered the primary stimulus, and standards for research vessel noise have been established to minimize fish reactions. We review the literature on fish reactions to vessels appearing since these recommendations were made, focusing on acoustic surveys, and compare how fish react to noise-reduced and conventional vessels. Reactions to approaching vessels are variable and difficult to predict. However, the behaviour can bias acoustic abundance measurements, and should be considered when performing acoustic surveys. The few comparisons of acoustic abundance measurements from noise-reduced and conventional vessels are contradictory, but demonstrate that the sound pressure level, on which the noise-reduction criterion is based, is insufficient to explain how fish react to survey vessels. Further research is needed to identify the stimuli fish perceive from approaching vessels and the factors affecting whether fish perceiving these stimuli will react before further recommendations to reduce vessel-avoidance reactions can be made. In the interim, measurement of the biases introduced by fish avoidance reactions during surveys, and timing of surveys when fish are in a less reactive state, may reduce errors introduced by vessel avoidance.
Bone marrow-induced Mef2c deficiency delays B-cell development and alters the expression of key B-cell regulatory proteins
Authors: Debnath Irina , Roundy Kirstin M. , Pioli Peter D. , Weis Janis J. , Weis John H. 
Published: October 2012

AbstractThe Mef2 family transcriptional regulator Mef2c (myocyte enhancer factor 2c) is highly expressed in maturing bone marrow and peripheral mature B-cells. To evaluate the role of this transcription factor in B-cell development, we generated a B-cell-specific conditional deletion of Mef2c using the Mb-1-Cre transgene that is expressed during the early stages of immunoglobulin rearrangement. Young mice possessing this defect demonstrated a significant impairment in B-cell numbers in bone marrow and spleen. This phenotype was evident in all B-cell subsets; however, as the animals mature, the deficit in the peripheral mature B-cell compartments was overcome. The absence of Mef2c in mature B-cells led to unique CD23+ and CD23− subsets that were evident in Mef2c knockout primary samples as well as Mef2c-deficient cultured, differentiated B-cells. Genome-wide expression analysis of immature and mature B-cells lacking Mef2c indicated altered expression for a number of key regulatory proteins for B-cell function including Ciita, CD23, Cr1/Cr2 and Tnfsf4. Chromatin immunoprecipitation analysis confirmed Mef2c binding to the promoters of these genes indicating a direct link between the presence (or absence) of Mef2c and altered transcriptional control in mature B-cells.