bluuebunny/crossref_metadata_2025_split huggingface dataset:
Collagen structure: new tricks from a very old dog
Authors: Bella Jordi 
Published: April 2016

The main features of the triple helical structure of collagen were deduced in the mid-1950s from fibre X-ray diffraction of tendons. Yet, the resulting models only could offer an average description of the molecular conformation. A critical advance came about 20 years later with the chemical synthesis of sufficiently long and homogeneous peptides with collagen-like sequences. The availability of these collagen model peptides resulted in a large number of biochemical, crystallographic and NMR studies that have revolutionized our understanding of collagen structure. High-resolution crystal structures from collagen model peptides have provided a wealth of data on collagen conformational variability, interaction with water, collagen stability or the effects of interruptions. Furthermore, a large increase in the number of structures of collagen model peptides in complex with domains from receptors or collagen-binding proteins has shed light on the mechanisms of collagen recognition. In recent years, collagen biochemistry has escaped the boundaries of natural collagen sequences. Detailed knowledge of collagen structure has opened the field for protein engineers who have used chemical biology approaches to produce hyperstable collagens with unnatural residues, rationally designed collagen heterotrimers, self-assembling collagen peptides, etc. This review summarizes our current understanding of the structure of the collagen triple helical domain (COL×3) and gives an overview of some of the new developments in collagen molecular engineering aiming to produce novel collagen-based materials with superior properties.
Sentence Repetition Accuracy in Adults With Developmental Language Impairment: Interactions of Participant Capacities and Sentence Structures
Authors: Poll Gerard H. , Miller Carol A. , van Hell Janet G. 
Published: April 2016

Purpose
We asked whether sentence repetition accuracy could be explained by interactions of participant processing limitations with the structures of the sentences. We also tested a prediction of the procedural deficit hypothesis (Ullman & Pierpont, 2005) that adjuncts are more difficult than arguments for individuals with developmental language impairment (DLI).

Method
Forty-four young adults participated, 21 with DLI. The sentence repetition task varied sentence length and the use of arguments and adjuncts. We also administered measures of working memory and processing speed. Our regression models focused on these interactions: group and argument status; processing speed, length, and argument status; and working memory capacity, length, and argument status.

Results
Language ability group was a significant predictor of sentence repetition accuracy but did not interact with argument status. Processing speed interacted with sentence length and argument status. Working memory capacity and its separate interactions with argument status and sentence length predicted sentence repetition accuracy.

Conclusions
Many adults with DLI may have difficulty with adjuncts as a result of their working memory limitations rather than their language ability. Cognitive limitations common to individuals with DLI are revealed more by particular sentence structures, suggesting ways to construct more diagnostically accurate sentence repetition tasks.

Supplemental Material

https://doi.org/10.23641/asha.14963784
Stärken und Schwächen der ICD-10 bei der Depressionsdiagnostik aus Sicht von HausärztInnen
Authors: Kammerer K. , Falk K. , Döpfmer S. , Heintze C. 
Published: April 2016

Zusammenfassung
Zielsetzung: HausärztInnen sind für die Versorgung depressiv erkrankter Menschen häufig wichtige AnsprechpartnerInnen. Einige Studien geben Hinweise auf eine Unterdiagnostizierung dieser PatientInnengruppe in der hausärztlichen Praxis. Umstritten ist, welche Bedeutung die ICD-10 für die Diagnostik hat. Die BMBF-geförderte Studie „PSYTIA – Psychotherapie im Alter“ beschäftigt sich u. a. mit der Versorgung älterer Menschen mit Depression in der Hausarztpraxis. Der vorliegende Beitrag präsentiert Ergebnisse zur hausärztlichen Sicht auf Stärken und Schwächen der ICD-10 bei der Depressionsdiagnostik.
Methodik: 402 hausärztliche LehrärztInnen wurden mit einem Fragebogen zur Versorgung älterer Menschen (60+) mit depressiver Erkrankung befragt. Der Rücklauf betrug 23,6%. In 2 offenen Fragen wurde die hausärztliche Sicht auf Stärken und Schwächen der ICD-10 in Hinblick auf die Depressionsdiagnostik erfragt. Die Antworten wurden induktiv entwickelten übergreifenden Kategorien zugeordnet.
Ergebnisse: Ca. drei Viertel der Teilnehmenden beantworteten die beiden Fragen. Während ein knappes Fünftel keine Meinung zur Tauglichkeit der ICD-10 als Diagnoseinstrument im Hinblick auf Depression hat oder keine äußern möchte, gaben 41% der Teilnehmenden Schwächen und ein Drittel der Befragten Stärken der ICD an. Diese beziehen sich überwiegend auf Differenziertheit des Instrumentes und Handhabbarkeit im Praxisalltag.
Schlussfolgerungen: Die Ergebnisse der Befragung zeigen, dass bei der Anwendung der ICD-10 in der hausärztlichen Praxis ein ganzheitliches, hermeneutisches Fallverständnis der HausärztInnen sowie die Notwendigkeit einer effizienten Praxisführung und Abrechnung aufeinander treffen und zu der ausgesprochen heterogenen und ambivalenten Einschätzung der Tauglichkeit der ICD-10 für die hausärztliche Diagnostik depressiver Erkrankungen führen.
Allgemeinmedizin in einer universitären Notaufnahme – Konzept, Umsetzung und Evaluation
Authors: Schleef T. , Schneider N. , Tecklenburg A. , Junius-Walker U. , Krause O. 
Published: April 2016

Zusammenfassung
Hintergrund: Die Notaufnahmen der Krankenhäuser sehen sich mit steigenden Patientenzahlen konfrontiert. Während die stationären Aufnahmequoten weitgehend konstant geblieben sind, betreffen die Zuwächse insbesondere den Anteil ambulanter Fälle. Die Medizinische Hochschule Hannover (MHH) hat auf diese Entwicklung reagiert, indem angestellte Allgemeinärzte zusätzlich zu den anderen Fachdisziplinen in der Zentralen Notaufnahme (ZNA) eingesetzt werden. Erste Ergebnisse der Begleitevaluation liegen vor.
Methode: Im Jahr 2014 wurden alle Patientenkontakte der Allgemeinärzte in der ZNA über die Routinedaten des Krankenhausinformationssystems und einem eigens entwickeltem Dokumentationsbogen ausgewertet. Der Bogen umfasste unter anderem Fragen zur Besuchsart, vorgenommene Untersuchungen und zum Verbleib des Patienten.
Ergebnisse: 2014 wurden in der ZNA der MHH 1 646 Patienten von Allgemeinärzten versorgt, es entfielen 76% auf Selbstzuweisungen und 23% auf eingewiesene Patienten. Als Behandlungsgründe dominierten Rückenschmerzen, gefolgt von Gastroenteritis und arterieller Hypertonie. Technische Untersuchungen und Konsile waren selten erforderlich. 81% der Patienten konnten ambulant verbleiben und erhielten meistens eine Empfehlung für eine haus- und/oder fachärztliche Weiterbehandlung. Mehrfachbesucher waren mit 58 Patienten kaum vorhanden.
Schlussfolgerung: Die Versorgung ambulanter Patienten in der ZNA durch Allgemeinmediziner stellt ein vielversprechendes Konzept dar, um das steigende Patientenaufkommen zu bewältigen. Weitere Untersuchungen, z. B. zur Diagnosesicherheit und Patientenzufriedenheit, sind erforderlich.
Finanzierung regionaler Demenznetzwerke: Determinanten einer nachhaltigen Finanzierung am Beispiel spezialisierter Gesundheitsnetzwerke
Authors: Michalowsky B. , Wübbeler M. , Thyrian J. , Holle B. , Gräske J. , Schäfer-Walkmann S. , Fleßa S. , Hoffmann W. 
Published: April 2016

Zusammenfassung
Ziele: Darstellung unterschiedlicher Finanzierungskonzepte, Bestimmung nachhaltiger Finanzierungsstrukturen und deren Determinanten in regionalen Demenznetzwerken (DN).
Methode: In einer vergleichenden qualitativen Analyse wurden Experteninterviews mit Verantwortlichen von 13 DN geführt. Der angewandte halbstrukturierte Interviewleitfaden fokussierte die finanzrelevante Organisation, die Kostenstruktur, die Finanzierungsquellen und die Nachhaltigkeit der DN.
Ergebnisse: Mitgliedsbeiträge, Einnahmen aus Angeboten, öffentlichen Fördergeldern sowie Geld- und Sachleistungen einer Gebietskörperschaft oder von Trägern waren hauptsächliche Finanzierungsquellen der DN. 62% der DN bezeichneten sich als finanziell nachhaltig. Geldleistungen zur Stärkung des personellen Netzwerkaufbaus, ein Mix aus Innen- und Außenfinanzierung und eine kommunale Beteiligung waren Determinanten einer nachhaltigen Finanzierung. DN in ländlichen Regionen schienen strukturell benachteiligt.
Schlussfolgerung: DN verfügen insbesondere in leistungsanbieterreichen Regionen über nachhaltige Finanzierungsstrukturen. Ein Finanzierungsvolumen von mindestens 50.000 €/Jahr zur Anstellung hauptamtlicher Mitarbeiter fördert eine nachhaltige Netzwerktätigkeit.
Effects of Bosentan on Peripheral Endothelial Function in Patients with Pulmonary Arterial Hypertension or Chronic Thromboembolic Pulmonary Hypertension
Authors: Hirashiki Akihiro , Adachi Shiro , Nakano Yoshihisa , Kamimura Yoshihiro , Shimokata Shigetake , Takeshita Kyosuke , Murohara Toyoaki , Kondo Takahisa 
Published: April 2016

Endothelin receptor antagonists (ERAs) have been shown to improve the prognosis of patients with pulmonary arterial hypertension (PAH). However, the effect of the oral dual ERA bosentan on peripheral endothelial dysfunction (PED), as assessed by flow‐mediated vasodilation (FMD), in patients with pulmonary hypertension is not well characterized. We investigated the effect of bosentan on PED in patients with PAH or inoperable chronic thromboembolic pulmonary hypertension (CTEPH). A total of 18 patients with PAH and 8 with CTEPH were treated with bosentan. All patients underwent FMD assessment before and after 3 months of bosentan treatment. Whereas FMD increased from 6.01% ± 2.42% at baseline to 8.07% ± 3.18% after 3 months (P < 0.0001) in patients with PAH, those with CTEPH showed no change in FMD after bosentan therapy. In addition, FMD at baseline showed no correlation with pulmonary vascular resistance (r = 0.09) or plasma brain natriuretic peptide levels (r = −0.23) in patients with PAH. Bosentan treatment ameliorated PED in patients with PAH but not in those with inoperable CTEPH. In addition, FMD did not correlate with PAH severity.
ProtAnnot: an App for Integrated Genome Browser to display how alternative splicing and transcription affect proteins
Authors: Mall Tarun , Eckstein John , Norris David , Vora Hiral , Freese Nowlan H. , Loraine Ann E. 
Published: April 2016

Abstract
Summary: One gene can produce multiple transcript variants encoding proteins with different functions. To facilitate visual analysis of transcript variants, we developed ProtAnnot, which shows protein annotations in the context of genomic sequence. ProtAnnot searches InterPro and displays profile matches (protein annotations) alongside gene models, exposing how alternative promoters, splicing and 3′ end processing add, remove, or remodel functional motifs. To draw attention to these effects, ProtAnnot color-codes exons by frame and displays a cityscape graphic summarizing exonic sequence at each position. These techniques make visual analysis of alternative transcripts faster and more convenient for biologists.
Availability and implementation: ProtAnnot is a plug-in App for Integrated Genome Browser, an open source desktop genome browser available from http://www.bioviz.org.
Contact: aloraine@uncc.edu
mDCC_tools: characterizing multi-modal atomic motions in molecular dynamics trajectories
Authors: Kasahara Kota , Mohan Neetha , Fukuda Ikuo , Nakamura Haruki 
Published: April 2016

Abstract
Summary: We previously reported the multi-modal Dynamic Cross Correlation (mDCC) method for analyzing molecular dynamics trajectories. This method quantifies the correlation coefficients of atomic motions with complex multi-modal behaviors by using a Bayesian-based pattern recognition technique that can effectively capture transiently formed, unstable interactions. Here, we present an open source toolkit for performing the mDCC analysis, including pattern recognitions, complex network analyses and visualizations. We include a tutorial document that thoroughly explains how to apply this toolkit for an analysis, using the example trajectory of the 100 ns simulation of an engineered endothelin-1 peptide dimer.
Availability and implementation: The source code is available for free at http://www.protein.osaka-u.ac.jp/rcsfp/pi/mdcctools/, implemented in C ++ and Python, and supported on Linux.
Contact: kota.kasahara@protein.osaka-u.ac.jp
Supplementary information: Supplementary data are available at Bioinformatics online.
gEVAL — a web-based browser for evaluating genome assemblies
Authors: Chow William , Brugger Kim , Caccamo Mario , Sealy Ian , Torrance James , Howe Kerstin 
Published: April 2016

Abstract
Motivation: For most research approaches, genome analyses are dependent on the existence of a high quality genome reference assembly. However, the local accuracy of an assembly remains difficult to assess and improve. The gEVAL browser allows the user to interrogate an assembly in any region of the genome by comparing it to different datasets and evaluating the concordance. These analyses include: a wide variety of sequence alignments, comparative analyses of multiple genome assemblies, and consistency with optical and other physical maps. gEVAL highlights allelic variations, regions of low complexity, abnormal coverage, and potential sequence and assembly errors, and offers strategies for improvement. Although gEVAL focuses primarily on sequence integrity, it can also display arbitrary annotation including from Ensembl or TrackHub sources. We provide gEVAL web sites for many human, mouse, zebrafish and chicken assemblies to support the Genome Reference Consortium, and gEVAL is also downloadable to enable its use for any organism and assembly.
Availability and Implementation: Web Browser: http://geval.sanger.ac.uk, Plugin: http://wchow.github.io/wtsi-geval-plugin.
Contact: kj2@sanger.ac.uk
Supplementary information: Supplementary data are available at Bioinformatics online.
DiscoMark: Nuclear marker discovery from orthologous sequences using draft genome data
Authors: Rutschmann Sereina , Detering Harald , Simon Sabrina , Fredslund Jakob , Monaghan Michael T. 
Published: April 2016

AbstractHigh-throughput sequencing has laid the foundation for fast and cost-effective development of phylogenetic markers. Here we present the program DISCOMARK, which streamlines the development of nuclear DNA (nDNA) markers from whole-genome (or whole-transcriptome) sequencing data, combining local alignment, alignment trimming, reference mapping and primer design based on multiple sequence alignments in order to design primer pairs from input orthologous sequences. In order to demonstrate the suitability of DISCOMARKwe designed markers for two groups of species, one consisting of closely related species and one group of distantly related species. For the closely related members of the species complex ofCloeon dipterums.l. (Insecta, Ephemeroptera), the program discovered a total of 78 markers. Among these, we selected eight markers for amplification and Sanger sequencing. The exon sequence alignments (2,526 base pairs (bp)) were used to reconstruct a well supported phylogeny and to infer clearly structured haplotype networks. For the distantly related species we designed primers for several families in the insect order Ephemeroptera, using available genomic data from four sequenced species. We developed primer pairs for 23 markers that are designed to amplify across several families. The DISCOMARKprogram will enhance the development of new nDNA markersby providing a streamlined, automated approach to perform genome-scale scans for phylogenetic markers. The program is written in Python, released under a public license (GNU GPL v2), and together with a manual and example data set available at:https://github.com/hdetering/discomark.
Magnetite biomineralization in Magnetospirillum magneticum is regulated by a switch-like behavior in the HtrA protease MamE
Authors: Hershey David M. , Browne Patrick J. , Iavarone Anthony T. , Teyra Joan , Lee Eun H. , Sidhu Sachdev S. , Komeili Arash 
Published: April 2016

AbstractMagnetotactic bacteria are aquatic organisms that produce subcellular magnetic particles in order to orient in the earth’s geomagnetic field. MamE, a predicted HtrA protease required to produce magnetite crystals in the magnetotactic bacteriumMagnetospirillum magneticumAMB-1, was recently shown to promote the proteolytic processing of itself and two other biomineralization factorsin vivo. Here, we have analyzed thein vivoprocessing patterns of three proteolytic targets and used this information to reconstitute proteolysis with a purified form of MamEin vitro. MamE cleaves a custom peptide substrate with positive cooperativity, and its auto-proteolysis can be stimulated with exogenous substrates or peptides that bind to either of its PDZ domains. A misregulated form of the protease that circumvents specific genetic requirements for proteolysis causes biomineralization defects, showing that proper regulation of its activity is required during magnetite biosynthesisin vivo. Our results represent the first reconstitution of MamE’s proteolytic activity and show that its behavior is consistent with the previously proposed checkpoint model for biomineralization.
State capitalism and clusters: the case of Brazilian shipbuilding
Authors: DuBois Frank L. , Primo Marcos Andre Mendes 
Published: April 2016

Purpose– State capitalism is an economic model that relies on the role of a strong central government to support chosen firms and industries with subsidies, tax benefits and other advantages to which non-favored firms or industries do not have access (Bremmer, 2010). From an economic development perspective state capitalism is often used to redirect economic activity to underdeveloped regions (Wickham, 2009; Chobanyan and Leigh, 2006; Porter, 2008). The purpose of this paper is to examine the case of the Brazilian shipbuilding to illustrate the use of state capitalism to direct economic activity.Design/methodology/approach– Using Porter’s diamond factor model the authors analyze the development of an economic cluster focussed on the shipbuilding industry in northeastern Brazil. Using interviews with company executives and archival information, the authors profile the investments and incentives that the government has made in this region with particular attention to the mechanisms and policy directives designed to support local involvement in cluster activity.Findings– The authors find that the Brazilian shipbuilding industry offers a unique perspective on the role that governments play in the inducement of economic activity. The authors document the challenges that confront the local enterprise in meeting the requirements of the state controlled buyer and the difficulties associated with developing a local supplier base and finding a qualified workforce. The authors conclude with comments with regard to the applicability of this model to economic development activity in other country contexts.Research limitations/implications– This research adds to the body of literature on the role of governments in the creation of economic clusters.Practical implications– Economic development in emerging markets is often associated with strong government intervention. The authors use the Brazilian shipbuilding industry to illustrate the role of a state owned enterprise in facilitation of economic development.Social implications– Some countries may suffer from what has been known as the “resource curse,” that is, the misallocation of resource wealth into non-productive activities. In this paper, the authors illustrate and attempt by the Brazilian government to use this wealth to create employment opportunities in an underdeveloped region of the country.Originality/value– Emerging markets are challenged in developing viable enterprises that are competitive in global markets. Most research on the development of industrial clusters is focussed on developed markets. These markets do not have to confront the same challenges found in emerging markets. The research illustrates these challenges and the efforts that may be made to surmount them.
Competitiveness of clusters
Authors: Sarturi Greici , Vargas Carlos Augusto França , Boaventura João Maurício Gama , Santos Silvio Aparecido dos 
Published: April 2016

Purpose
– The purpose of this paper is to deepen the discussion regarding the competitiveness of clusters based on a theoretical and empirical study that compares the level of competitiveness of the Brazilian wine cluster located in Serra Gaúcha with the competitiveness of the Chilean cluster located in Valle del Maule.

Design/methodology/approach
– A qualitative-descriptive approach was applied to the study, and data collection was conducted through secondary sources.

Findings
– The analysis employed a competitiveness analysis model consisting of 11 competitiveness factors. The Chilean cluster presented a higher level of competitiveness in four competitiveness factors (“scope of viable and relevant business,” “introduction of new technologies,” “balance with no privileged positions” and “oriented strategy”), while the Brazilian cluster presented a higher level of competitiveness in three competitiveness factors (“concentration,” “cooperation” and “replacement”). For four of the competitiveness factors of the model, both clusters presented similar levels of competitiveness.

Practical implications
– By comparing the two wine clusters, it was possible to identify aspects that can be improved to increase competitiveness, especially in the Brazilian cluster. These aspects include, first, the need for bottle manufacturers in Serra Gaúcha, which would have a positive impact on production costs; second, the expansion of the geographical indication registration for the entire Serra Gaúcha region, resulting in an enhanced image of Brazilian wine abroad; and third, greater incentives for exports, which would result in an increase in market share.

Originality/value
– The paper proposes an explanation for the superior level of competitiveness of the Chilean cluster regarding the “scope of viable and relevant business,” “balance with no privileged positions,” “introduction of new technologies” and “strategy focussed on cluster development.” In terms of its contribution, the study developed additional metrics for the model adopted, which can be used for the competitive analysis of other agribusiness clusters.