bluuebunny/crossref_metadata_2025_split huggingface dataset:
Der Verlauf der Diamorphinbehandlung unter den Bedingungen der gesundheitlichen Regelversorgung – eine 12-Monats-Analyse
Authors: Verthein Uwe , Kuhn Silke , Schäfer Ingo 
Published: February 2014

Hintergrund: Nachdem das bundesdeutsche Modellprojekt zur heroingestützten Behandlung 2007 auslief, wurde vom Zentrum für Interdisziplinäre Suchtforschung der Universität Hamburg (ZIS) ein Qualitätssicherungsprojekt aufgelegt, durch das die regelmäßige Dokumentation von Behandlungsstandards und Effekten weiterhin sicher gestellt werden konnte. Fragestellung: Im Mittelpunkt der Auswertung steht die Beschreibung von aktuellem Status und 1-Jahres-Behandlungsverlauf der nach der Studie neu in die Diamorphinbehandlung aufgenommenen Patienten. Der Behandlungsverlauf kann denen der Studienpatienten gegenüber gestellt werden. Methodik: Von den behandelnden Ärzten wurde zu Beginn und im 6-Monats-Abstand pro Patient anhand eines standardisierten Erhebungsbogens der Aufnahmestatus sowie der Behandlungsverlauf dokumentiert. Für die Beschreibung des aktuellen Zustands wurde die letzte Dokumentation in 2011 herangezogen, der Verlauf wurde anhand eines Vergleichs von Aufnahme- und 1-Jahres-Dokumentation analysiert. Ergebnisse: Über 341 Diamorphinpatienten liegen in 2011 Informationen zum aktuellen Zustand vor, davon sind 205 (60,1 %) nach dem Modellprojekt aufgenommen worden. Die Mehrheit kommt für 2 Vergaben am Tag. Die mittlere Tagesdosis Diamorphin der seit durchschnittlich mehr als 8 Jahre behandelten Modellprojektpatienten beträgt 358 mg, die der seit durchschnittlich eineinhalb Jahren behandelten Neuaufnahmen 432 mg. 3,6 % sind HIV-positiv, 75,0 % mit Hepatitis C infiziert. Bei einem Viertel wurden depressive Störungen diagnostiziert. Die Mehrheit lebt in stabilen Wohnverhältnissen, ein Viertel hat eine regelmäßige Arbeit oder Jobs. Justitielle Delikte werden von 6,7 % der Diamorphinpatienten berichtet. 5,1 % konsumierten innerhalb der letzten 30 Tage noch Straßenheroin, 22,4 % Kokain. Hinsichtlich der Veränderungen innerhalb des ersten Behandlungsjahres zeigen sich in den Bereichen Gesundheit, soziale Situation und Drogenkonsum deutliche und statistisch signifikante Verbesserungen. Schlussfolgerung: Die Diamorphinbehandlung in Deutschland wird auch unter den Bedingungen der Regelversorgung erfolgreich durchgeführt. Die aktuelle Situation der sich seit vielen Jahren in Behandlung befindlichen Modellprojektpatienten stellt sich stabiler dar, was darauf hindeutet, dass weitreichende Veränderungen viel Zeit benötigen. Die positiven Wirkungen nach einem Jahr Diamorphinbehandlung sind denen aus dem Bundesmodellprojekt vergleichbar.
Efficient terahertz devices based on III–V semiconductor photoconductors
Authors: Kostakis Ioannis , Saeedkia Daryoosh , Missous Mohamed 
Published: February 2014

A series of planar aperture and dipole antenna structures fabricated on low temperature grown GaAs and InP‐based photoconductors have been evaluated as terahertz (THz) emitters and detectors in a time‐domain spectroscopy system under pulsed excitation. The combination of large aperture antennas as emitters and short dipole antennas as detectors results in efficient THz devices operating at 800 nm, 1 μm and 1.55 μm excitation wavelengths. The system responses of these materials are among the best ever reported and allow high‐quality measurements to be made. Finally, characterisation of a structure able to be biased vertically and its evaluation as THz emitter is reported for the first time. The THz response of this material with a strong THz signal at low‐voltage bias makes the development of battery‐operated THz devices possible.
Electrically pumped continuous‐wave 1.3‐µm InAs/GaAs quantum dot lasers monolithically grown on Si substrates
Authors: Wu Jiang , Lee Andrew , Jiang Qi , Tang Mingchu , Seeds Alwyn J. , Liu Huiyun 
Published: February 2014

Continuous‐wave (CW) operation of InAs/GaAs quantum dot (QD) lasers monolithically grown on Si substrates by molecular beam epitaxy is presented. The peak lasing wavelength of 1278 nm is accompanied by a low threshold current density of 458 A/cm2 at 8°C using a GaAs buffer layer directly grown on the Si substrates. The improvement in laser performance is due to improved crystal quality of the GaAs buffer layer. The demonstration of a CW QD laser also benefits from using top–top contacts, which route the current through the laser active layer to avoid the high‐density defects near the Si/GaAs interface. These results demonstrate the growing potential of the monolithically integrated III–V QD lasers on the Si substrates.
Strong Meissner screening change in superconducting radio frequency cavities due to mild baking
Authors: Romanenko A. , Grassellino A. , Barkov F. , Suter A. , Salman Z. , Prokscha T. 
Published: February 2014

We investigate “hot” regions with anomalous high field dissipation in bulk niobium superconducting radio frequency cavities for particle accelerators by using low energy muon spin rotation (LE-μSR) on corresponding cavity cutouts. We demonstrate that superconducting properties at the hot region are well described by the non-local Pippard/BCS model for niobium in the clean limit with a London penetration depth λL=23±2 nm. In contrast, a cutout sample from the 120 ∘C baked cavity shows a much larger λ&gt;100 nm and a depth dependent mean free path, likely due to gradient in vacancy concentration. We suggest that these vacancies can efficiently trap hydrogen and hence prevent the formation of hydrides responsible for rf losses in hot regions.
Archaeological data provide alternative hypotheses on Pacific herring (Clupea pallasii) distribution, abundance, and variability
Authors: McKechnie Iain , Lepofsky Dana , Moss Madonna L. , Butler Virginia L. , Orchard Trevor J. , Coupland Gary , Foster Fredrick , Caldwell Megan , Lertzman Ken 
Published: February 2014

SignificanceOver the last century, Pacific herring, a forage fish of tremendous cultural, economic, and ecological importance, has declined in abundance over much of its range. We synthesize archaeological fisheries data spanning the past 10,000 y from Puget Sound in Washington to southeast Alaska to extend the ecological baseline for herring and contextualize the dynamics of modern industrial fisheries. While modern herring populations can be erratic and exhibit catastrophic declines, the archaeological record indicates a pattern of consistent abundance, providing an example of long-term sustainability and resilience in a fishery known for its modern variability. The most parsimonious explanation for the discrepancy between herring abundance in the ancient and more recent past is industrial harvesting over the last century.
Synergies between climate and management for Atlantic cod fisheries at high latitudes
Authors: Kjesbu Olav Sigurd , Bogstad Bjarte , Devine Jennifer A. , Gjøsæter Harald , Howell Daniel , Ingvaldsen Randi B. , Nash Richard D. M. , Skjæraasen Jon Egil 
Published: February 2014

Significance
Currently many exploited fish populations, including many of the Atlantic cod stocks, are at historically low levels with widespread concern about whether contemporary management is capable of facilitating population recovery. In contrast, the spawning stock biomass of Barents Sea cod is now at an historic high. Here we demonstrate that successful management actions interacting synergistically with prevailing climate caused this increase. Warming of water masses in the Barents Sea over the last decade positively reinforced management actions. A unique and possibly generic mechanism of climate affecting marine animals at high latitudes, especially when at the polar extreme of their distribution, is identified: adjustment of the suitable feeding area. This adjustment is linked closely to community dynamics and increased stock productivity.
Mechanosensitivity is mediated directly by the lipid membrane in TRAAK and TREK1 K
+
channels
Authors: Brohawn Stephen G. , Su Zhenwei , MacKinnon Roderick 
Published: February 2014

Significance
Mechanical force opens mechanosensitive ion channels in the cellular membrane to produce electrical signals that underlie sensation of touch, hearing, and other mechanical stimuli. An unanswered question is: How are mechanical forces transmitted to eukaryotic mechanosensitive channels in the membrane? We show that two mechanosensitive ion channels in eukaryotes, TRAAK (K2P4.1) and TREK1 (K2P2.1), are directly opened by mechanical force through the lipid membrane in the absence of all other cellular components. This finding extends the “force-from-lipid” paradigm established in bacterial channels to TRAAK and TREK1, eukaryotic mechanosensors.
Structures of the PutA peripheral membrane flavoenzyme reveal a dynamic substrate-channeling tunnel and the quinone-binding site
Authors: Singh Harkewal , Arentson Benjamin W. , Becker Donald F. , Tanner John J. 
Published: February 2014

Significance
Bifunctional enzymes catalyze two sequential reactions of a metabolic pathway using spatially separated and covalently connected active sites. Combining two enzymes into one protein chain creates efficiency because the product of the first reaction can be shuttled directly to the active site, catalyzing the second reaction in a process called substrate channeling. Here, we use X-ray crystallography to elucidate the three-dimensional structural basis of substrate channeling in the proline catabolic pathway. Structures of the bifunctional enzyme proline utilization A (PutA) reveal an elaborate and dynamic tunnel system featuring a 75-Å-long substrate-channeling path that links the two active sites. Furthermore, we have identified the elusive quinone-binding site of PutA, which provides insight into how PutAs interact with the membrane.
Gating of steering signals through phasic modulation of reticulospinal neurons during locomotion
Authors: Kozlov Alexander K. , Kardamakis Andreas A. , Hellgren Kotaleski Jeanette , Grillner Sten 
Published: February 2014

Significance
In many vertebrate and invertebrate species descending motor commands are phasically modulated in synchrony with rhythmic movements. The physiological role of this modulation has remained enigmatic. We report here, from the lamprey locomotor system, that steering signals from for instance tectum can be gated by a downstream locomotor-related modulation of the reticulospinal command neurons. Such gating will ascertain that the steering commands will be transmitted in the appropriate phase of a swimming cycle and be suppressed out-of-phase. Another consequence of this mechanism is the relative independence of the motor response on the timing of the steering signal.
Condition-specific target prediction from motifs and expression
Authors: Meng Guofeng , Vingron Martin 
Published: February 2014

Abstract
Motivation: It is commonplace to predict targets of transcription factors (TFs) by sequence matching with their binding motifs. However, this ignores the particular condition of the cells. Gene expression data can provide condition-specific information, as is, e.g. exploited in Motif Enrichment Analysis.
Results: Here, we introduce a novel tool named condition-specific target prediction (CSTP) to predict condition-specific targets for TFs from expression data measured by either microarray or RNA-seq. Based on the philosophy of guilt by association, CSTP infers the regulators of each studied gene by recovering the regulators of its co-expressed genes. In contrast to the currently used methods, CSTP does not insist on binding sites of TFs in the promoter of the target genes. CSTP was applied to three independent biological processes for evaluation purposes. By analyzing the predictions for the same TF in three biological processes, we confirm that predictions with CSTP are condition-specific. Predictions were further compared with true TF binding sites as determined by ChIP-seq/chip. We find that CSTP predictions overlap with true binding sites to a degree comparable with motif-based predictions, although the two target sets do not coincide.
Availability and implementation: CSTP is available via a web-based interface at http://cstp.molgen.mpg.de.
Contact: meng@molgen.mpg.de
Supplementary information: Supplementary data are available at Bioinformatics online.
LPmerge: an R package for merging genetic maps by linear programming
Authors: Endelman Jeffrey B. , Plomion Christophe 
Published: February 2014

Abstract
Summary: Consensus genetic maps constructed from multiple populations are an important resource for both basic and applied research, including genome-wide association analysis, genome sequence assembly and studies of evolution. The LPmerge software uses linear programming to efficiently minimize the mean absolute error between the consensus map and the linkage maps from each population. This minimization is performed subject to linear inequality constraints that ensure the ordering of the markers in the linkage maps is preserved. When marker order is inconsistent between linkage maps, a minimum set of ordinal constraints is deleted to resolve the conflicts.
Availability and implementation: LPmerge is on CRAN at http://cran.r-project.org/web/packages/LPmerge.
Contact: endelman@wisc.edu
Supplementary information: Supplementary data are available at Bioinformatics online.
EXTREME: an online EM algorithm for motif discovery
Authors: Quang Daniel , Xie Xiaohui 
Published: February 2014

AbstractMotivation: Identifying regulatory elements is a fundamental problem in the field of gene transcription. Motif discovery—the task of identifying the sequence preference of transcription factor proteins, which bind to these elements—is an important step in this challenge. MEME is a popular motif discovery algorithm. Unfortunately, MEME’s running time scales poorly with the size of the dataset. Experiments such as ChIP-Seq and DNase-Seq are providing a rich amount of information on the binding preference of transcription factors. MEME cannot discover motifs in data from these experiments in a practical amount of time without a compromising strategy such as discarding a majority of the sequences.Results: We present EXTREME, a motif discovery algorithm designed to find DNA-binding motifs in ChIP-Seq and DNase-Seq data. Unlike MEME, which uses the expectation-maximization algorithm for motif discovery, EXTREME uses the online expectation-maximization algorithm to discover motifs. EXTREME can discover motifs in large datasets in a practical amount of time without discarding any sequences. Using EXTREME on ChIP-Seq and DNase-Seq data, we discover many motifs, including some novel and infrequent motifs that can only be discovered by using the entire dataset. Conservation analysis of one of these novel infrequent motifs confirms that it is evolutionarily conserved and possibly functional.Availability and implementation: All source code is available at the Github repository http://github.com/uci-cbcl/EXTREME.Contact: xhx@ics.uci.eduSupplementary information: Supplementary data are available at Bioinformatics online.
ZDOCK server: interactive docking prediction of protein–protein complexes and symmetric multimers
Authors: Pierce Brian G. , Wiehe Kevin , Hwang Howook , Kim Bong-Hyun , Vreven Thom , Weng Zhiping 
Published: February 2014

Abstract
Summary: Protein–protein interactions are essential to cellular and immune function, and in many cases, because of the absence of an experimentally determined structure of the complex, these interactions must be modeled to obtain an understanding of their molecular basis. We present a user-friendly protein docking server, based on the rigid-body docking programs ZDOCK and M-ZDOCK, to predict structures of protein–protein complexes and symmetric multimers. With a goal of providing an accessible and intuitive interface, we provide options for users to guide the scoring and the selection of output models, in addition to dynamic visualization of input structures and output docking models. This server enables the research community to easily and quickly produce structural models of protein–protein complexes and symmetric multimers for their own analysis.
Availability: The ZDOCK server is freely available to all academic and non-profit users at: http://zdock.umassmed.edu. No registration is required.
Contact: brian.pierce@umassmed.edu or zhiping.weng@umassmed.edu
How we all kill whales
Authors: Moore Michael J. 
Published: February 2014

AbstractToday there is enormous popular interest in marine mammals. Western media tend to dwell on the ongoing debate about commercial whaling by Japan, Norway and Iceland. There is, however, relative silence as to how the shipping and fishing industries of many if not all maritime countries are also catching and sometimes killing whales, albeit unintentionally. Thus, western countries have, through the development and increase in fishing and shipping in continental shelf waters, essentially resumed whaling as vessel speeds and fishing gear strength have increased in recent decades. The ways in which these animals die, especially in fixed fishing gear that they become entangled in and swim off with, would raise substantial concern with consumers of seafood were they to be aware of what they were enabling.
Considering the Impact of the ‘Right to Bargain’ Legislation in Ireland: A Review
Authors: Cullinane Niall , Dobbins Anthony 
Published: February 2014

Abstract
Ireland is rare among advanced economies in not having statutory trade union recognition legislation for collective bargaining purposes. The matter has been a source of policy contention over the years with attempts to resolve it encapsulated in the so-called ‘Right to Bargain’ legislation, introduced in 2001. This legislation has sought to circumvent statutory recognition in Ireland by putting in place an alternative mechanism for unions to represent members in non-union firms where collective bargaining is not practiced. This review, based on a mixture of empirical and documentary evidence, demonstrates that this legislation was moderately successful for a short period in generating pay rises, improved employment conditions and better access to procedures for union members in non-unionised firms. Indeed, in some respects, it was a superior institutional mechanism to a statutory recognition regime.
X-ray luminous binaries, metallicity, and the early Universe
Authors: Kaaret Philip 
Published: February 2014

Abstract
High-mass X-ray binaries (HMXBs) may have had a significant impact on the heating of the intergalactic medium in the early Universe. Study of HMXBs in nearby, low-metallicity galaxies that are local analogues to early galaxies can help us understand early HMXBs. The total luminosity of HMXB populations is dominated by sources at high luminosities. These sources exhibit X-ray spectra that show curvature above 2 keV and the same is likely true of HMXB populations at high redshifts. The spectral curvature changes the K-correction for X-rays from HMXBs in a manner that weakens the constraints on X-ray emission of early HMXBs obtained from the soft X-ray background. Applied to deep X-ray surveys of star-forming galaxies, the modified K-correction suggests a moderate increase in the ratio of X-ray luminosity to star formation rate at intermediate redshifts, z = 3–5, and is consistent with a large enhancement at high redshifts, z = 6–7.
A Pilot Study Evaluating Presurgery Neuroanatomical Biomarkers for Postoperative Cognitive Decline after Total Knee Arthroplasty in Older Adults
Authors: Price Catherine C. , Tanner Jared J. , Schmalfuss Ilona , Garvan Cynthia Wilson , Gearen Peter , Dickey David , Heilman Kenneth , McDonagh David L. , Libon David J. , Leonard Christiana , Bowers Dawn , Monk Terri G. 
Published: February 2014

Abstract

Background:
Total knee arthroplasty improves quality of life but is associated with postoperative cognitive dysfunction in older adults. This prospective longitudinal pilot study with a parallel control group tested the hypotheses that (1) nondemented adults would exhibit primary memory and executive difficulties after total knee arthroplasty, and (2) reduced preoperative hippocampus/entorhinal volume would predict postoperative memory change, whereas preoperative leukoaraiosis and lacunae volumes would predict postoperative executive dysfunction.

Methods:
Surgery (n = 40) and age–education-matched controls with osteoarthritis (n = 15) completed pre- and postoperative (3 weeks, 3 months, and 1 yr) memory and cognitive testing. Hypothesized brain regions of interest were measured in patients completing preoperative magnetic resonance scans (surgery, n = 31; control, n = 12). Analyses used reliable change methods to identify the frequency of cognitive change at each time point.

Results:
The incidence of postoperative memory difficulties was shown with delay test indices (i.e., story memory test: 3 weeks = 17%, 3 months = 25%, 1 yr = 9%). Postoperative executive difficulty with measures of inhibitory function (i.e., Stroop Color Word: 3 weeks = 21%, 3 months = 22%, 1 yr = 9%). Hierarchical regression analysis assessing the predictive interaction of group (surgery, control) and preoperative neuroanatomical structures on decline showed that greater preoperative volumes of leukoaraiosis/lacunae were significantly contributed to postoperative executive (inhibitory) declines.

Conclusions:
This pilot study suggests that executive and memory declines occur in nondemented adults undergoing orthopedic surgery. Severity of preoperative cerebrovascular disease may be relevant for understanding executive decline, in particular.
Comparing Robotic Lung Resection with Thoracotomy and Video-Assisted Thoracoscopic Surgery Cases Entered into the Society of Thoracic Surgeons Database
Authors: Farivar Alexander S. , Cerfolio Robert J. , Vallières Eric , Knight Ariel W. , Bryant Ayesha , Lingala Vijaya , Aye Ralph W. , Louie Brian E. 
Published: February 2014

Objective The use of robotic lung surgery has increased dramatically despite being a new, costly technology with undefined benefits over standard of care. There is a paucity of published comparative articles justifying its use or cost. Furthermore, outcomes regarding robotic lung resection are either from single institutions with in-house historical comparisons or based on limited numbers. We compared consecutive robotic anatomic lung resections performed at two institutions with matched data from The Society of Thoracic Surgeons (STS) National Database for all open and video-assisted thoracoscopic surgery (VATS) resections. We sought to define any benefits to a robotic approach versus national outcomes after thoracotomy and VATS. Methods Data from all consecutive robotic anatomic lung resections were collected from two institutions (n = 181) from January 2010 until January 2012 and matched against the same variables for anatomic resections via thoracotomy (n = 5913) and VATS (n = 4612) from the STS National Database. Patients with clinical N2, N3, and M1 disease were excluded. Results There was a significant decrease in 30-day mortality and postoperative blood transfusion after robotic lung resection relative to VATS and thoracotomy. The patients stayed in the hospital 2 days less after robotic surgery than VATS and 4 days less than after thoracotomy. Robotic surgery led to fewer air leaks, intraoperative blood transfusions, need for perioperative bronchoscopy or reintubation, pneumonias, and atrial arrhythmias compared with thoracotomy. Conclusions This is the first comparative analysis using national STS data. It suggests potential benefits of robotic surgery relative to VATS and thoracotomy, particularly in reducing length of stay, 30-day mortality, and postoperative blood transfusion.