bluuebunny/crossref_metadata_2025_split huggingface dataset:
Positive selection and compensatory adaptation interact to stabilize non-transmissible plasmids
Authors: Millan A. San , Peña-Miller R. , Toll-Riera M. , Halbert Z. V. , McLean A. R. , Cooper B. S. , MacLean R. C. 
Published: October 2014

AbstractPlasmids are important drivers of bacterial evolution, but it is challenging to understand how plasmids persist over the long term because plasmid carriage is costly. Classical models predict that horizontal transfer is necessary for plasmid persistence, but recent work shows that almost half of plasmids are non-transmissible. Here we use a combination of mathematical modelling and experimental evolution to investigate how a costly, non-transmissible plasmid, pNUK73, can be maintained in populations of Pseudomonas aeruginosa. Compensatory adaptation increases plasmid stability by eliminating the cost of plasmid carriage. However, positive selection for plasmid-encoded antibiotic resistance is required to maintain the plasmid by offsetting reductions in plasmid frequency due to segregational loss. Crucially, we show that compensatory adaptation and positive selection reinforce each other’s effects. Our study provides a new understanding of how plasmids persist in bacterial populations, and it helps to explain why resistance can be maintained after antibiotic use is stopped.
Collective Structural Changes in Vermiculite Clay Suspensions Induced by Cesium Ions
Authors: Motokawa Ryuhei , Endo Hitoshi , Yokoyama Shingo , Nishitsuji Shotaro , Kobayashi Tohru , Suzuki Shinichi , Yaita Tsuyoshi 
Published: October 2014

AbstractFollowing the Fukushima Daiichi nuclear disaster in 2011, Cs radioisotopes have been dispersed over a wide area. Most of the Cs has remained on the surface of the soil because Cs+ is strongly adsorbed in the interlayer spaces of soil clays, particularly vermiculite. We have investigated the microscopic structure of an aqueous suspension of vermiculite clay over a wide length scale (1–1000 Å) by small-angle X-ray scattering. We determined the effect of the adsorption behavior of Cs+ on the structural changes in the clay. It was found that the abruption of the clay sheets was induced by the localization of Cs+ at the interlayer. This work provides important information for predicting the environmental fate of radioactive Cs in polluted areas and for developing methods to extract Cs from the soil and reduce radioactivity.
Extracellular ATP, a danger signal, is recognized by DORN1 in Arabidopsis
Authors: Choi Jeongmin , Tanaka Kiwamu , Liang Yan , Cao Yangrong , Lee Sang Yeol , Stacey Gary 
Published: October 2014

ATP, the universal energy currency of all organisms, is released into the extracellular matrix and serves as a signal among cells, where it is referred to as an extracellular ATP. Although a signalling role for extracellular ATP has been well studied in mammals over the last 40 years, investigations of such a role in plants are at an early stage. Recently, the first plant receptor for extracellular ATP, DOes not Respond to Nucleotides (DORN1), was identified in Arabidopsis thaliana by mutant screening. DORN1 encodes a legume-type lectin receptor kinase that is structurally distinct from the mammalian extracellular ATP receptors. In the present review, we highlight the genetic and biochemical evidence for the role of DORN1 in extracellular ATP signalling, placing this within the wider context of extracellular ATP signalling during plant stress responses.
Molekulare Ansatzpunkte für systemische Therapien adenoidzystischer Karzinome im Kopf-Hals-Bereich
Authors: Büchsenschütz K. , Veit J. , Schuler P. , Thierauf J. , Laban S. , Fahimi F. , Bankfalvi A. , Lang S. , Sauerwein W. , Hoffmann T. 
Published: October 2014

ZusammenfassungDas adenoidzystische Karzinom (ACC) ist ein neurotroper Speicheldrüsentumor mit einer hohen hämatogenen Metastasierungstendenz. Die Therapie der Wahl ist bei lokal begrenztem Wachstum die vollständige chirurgische Resektion und in Abhängigkeit vom Resektionsstatus eine adjuvante Strahlentherapie. Aufgrund der verhältnismäßig hohen Rezidivrate mit eingeschränkter lokaler Interventionsmöglichkeit und der im weiteren langfristigen Krankheitsverlauf häufig vorzufindenden hämatogenen Fernmetas­tasen, wird man als Therapeut zwangsläufig mit der Frage nach einer adäquaten systemischen Therapie konfrontiert. Die Ansprechraten des Tumors sind bei einer Vielzahl der eingesetzten Chemotherapeutika als gering zu bezeichnen, anhaltende Komplettremissionen oder gar Heilungen sind äußerst selten. Neben der klassischen Chemotherapie kommen Immuntherapeutika und „Targetsubstanzen“ mit z. T. günstigem Nebenwirkungsprofil zum Einsatz, wobei aufgrund der geringen Patientenzahlen in den zur Verfügung stehenden Studien eine definitive Aussage zur Effektivität kaum gemacht werden kann. Hieraus ergibt sich die Notwendigkeit zu multizentrischen Studienbemühungen, die im prospektiven Design klare Handlungsempfehlungen zur Systemtherapie des Tumors erlauben. Die vorliegende Arbeit gibt eine Übersicht zu den subzellulären und genetischen Charakteristika des ACC, die einen Angriffspunkt für systemische Therapiebemühungen darstellen und teilweise in klinischen Studien bereits Berücksichtigung gefunden haben.
Differenzialdiagnostik der Hörstörungen
Authors: Schulze A. , Zahnert T. 
Published: October 2014

ZusammenfassungDie Beeinträchtigung des Hörvermögens ist die weltweit häufigste Funktionseinschränkung eines Sinnesorgans. WHO-Schätzungen zufolge waren 2012 weltweit 360 Mio Menschen von Hörstörungen betroffen, 91% davon sind Erwachsene, 9% Kinder.Hörstörungen können Folge lokal destruierender Prozesse (chronische Otitis media, Cholesteatom oder traumatisch bedingte Läsionen) oder systemischer Einflüsse wie infektiöse oder ototoxische Agenzien (Masern-, Mumpsviren, Meningokokkenmeningitis oder Medikamente und industrielle Substanzen) sein. Kongenitale Fehlbildungen, perinatale Komplikationen und genetisch bedingte Veränderungen können ebenso in Hördefiziten resultieren. Eine zunehmende ursächliche Bedeutung gewinnt die akute oder chronische übermäßig lange oder intensive Lärmbelastung, vor allem durch ein verändertes Freizeitverhalten in den Industrienationen. Um die jeweils individuell optimale Hörrehabilitation anstreben zu können, ist eine spezifische Differenzialdiagnostik unerlässlich.
Quality-of-Life Outcomes following Thoracolumbar and Lumbar Fusion with and without the Use of Recombinant Human Bone Morphogenetic Protein-2: Does Recombinant Human Bone Morphogenetic Protein-2 Make a Difference?
Authors: Lubelski Daniel , Alvin Matthew D. , Torre-Healy Andrew , Abdullah Kalil G. , Nowacki Amy S. , Whitmore Robert G. , Steinmetz Michael P. , Benzel Edward C. , Mroz Thomas E. 
Published: October 2014

Design Retrospective study. Objectives (1) To investigate the quality-of-life (QOL) outcomes in the population undergoing lumbar spine surgery with versus without recombinant human bone morphogenetic protein-2 (rhBMP-2); (2) to determine QOL outcomes for those patients who experience postoperative complications; and (3) to identify the effect of patient characteristics on postoperative QOL outcomes. Methods A retrospective review of QOL questionnaires, including the Patient Health Questionnaire-9, Patient Disability Questionnaire (PDQ), EuroQol-5D (EQ-5D), and quality of life-year (QALY), was performed for all patients who underwent thoracolumbar and lumbar fusion surgery with versus without rhBMP-2 between March 2008 and September 2010. Individual preoperative and postoperative QOL data were compared for each patient. Demographic factors and complications were reviewed. Results We identified 266 patients, including 60 with and 206 without rhBMP-2. Questionnaires were completed an average of 10.3 ± 5 months after surgery. For all measures, average scores improved postoperatively compared with preoperatively. No differences in postoperative QOL outcomes were identified between the rhBMP-2 and the control cohorts. Median annual household income was positively associated with EQ-5D and QALY. Compared with those without, patients with postoperative complications had fewer QOL improvements. Conclusions There was no difference in QOL outcomes in the rhBMP-2 compared with the control group. Socioeconomic status and postoperative complications affected QOL outcomes following surgery. The QOL questionnaires provide the clinician with information regarding the patients’ self-perceived well-being and can be helpful in the selection of surgical candidates and for understanding the effectiveness of a given surgical procedure.
Risk Factor Analysis of Hinge Fusion Failure after Plate-Only Open-Door Laminoplasty
Authors: Lee Sungjoon , Chung Chun Kee , Kim Chi Heon 
Published: October 2014

Study Design Retrospective study. Objectives To analyze lamina hinge fusion failure after plate-only open-door laminoplasty. Methods Thirty-one patients who underwent plate-only open-door laminoplasty (110 levels) for cervical myelopathy and who had serial computed tomography (CT) scans at 6 and 12 months were analyzed. Risk factors for fusion failure at 12 months were analyzed, including age, sex, smoking, presence of diabetes mellitus and ossification of posterior longitudinal ligament, bone mineral density (T-score), preoperative cervical curvature, operated levels, presence of a ventral cortical bony continuity, and reflection angle of the lamina hinge. Clinical outcomes were assessed with neck pain score using visual analog scale, neck disability index, and Japanese Orthopedic Association score. Results Hinge fusion occurred in 84% (26/31) of patients at 12 months. A significant risk factor for fusion failure was the absence of a ventral cortical bony continuity at 6 months ( p < 0.01; 100 versus 48%). No lamina with ventral cortical bony continuity at 6 months showed depression at 12 months, but two lamina without continuity showed depression of 2.5 and 2.1 mm, respectively, at 12 months. Clinical outcomes were not different between patients with and without hinge fusion. Conclusion Absence of a ventral cortical bony continuity at 6 months is a risk factor for fusion failure at 12 months. However, bicortically defective laminae usually heal with minimal displacement, although it may take longer than 12 months.
The Importance of Juvenile Migration Tactics to Adult Recruitment in Stream‐Type Chinook Salmon Populations
Authors: Copeland Timothy , Venditti David A. , Barnett Bruce R. 
Published: October 2014

AbstractThe existence of multiple migration tactics within a population has been observed for several fish species, and they may contribute differentially to adult recruitment. Relative contribution by juveniles using the same habitats on different schedules is variable; therefore, understanding and conserving this diversity should be important to fisheries managers. We investigated adult recruitment by two distinct juvenile migration tactics in several spawning populations of stream‐type Chinook Salmon Oncorhynchus tshawytscha in Idaho: those leaving the spawning grounds as subyearlings during June through November (downstream rearing, or DSR, type) and those emigrating from natal areas 1 year after emergence (natal reach rearing, or NRR, type). The DSR type had greater juvenile abundance in all populations, although the NRR type exhibited better survival from the natal reach to the migratory corridor. The DSR type had greater survival from smoltification to adult return to freshwater compared with the NRR type. More DSR emigrants than NRR emigrants returned to freshwater as adults, although the difference was influenced by cohort and population. Adult recruits to stream‐type Chinook Salmon populations in Idaho are comprised mostly of DSR emigrants, i.e., fish that dispersed from their natal habitats and reared in reaches downstream. This finding is ubiquitous, although the size of the effect depends on cohort and population. We demonstrated that juvenile Chinook Salmon in Idaho do indeed use downstream rearing habitats effectively, thereby increasing recruitment of adults back to the spawning gravels in these populations. This study illustrates how dispersive life histories are essential to achieve the full productive potential of migratory stream fish populations.Received March 31, 2014; accepted July 16, 2014
Using Spatial Resampling to Assess Redd Count Survey Length Requirements for Pacific Lamprey
Authors: Mayfield M. P. , Schultz L. D. , Wyss L. A. , Colvin M. E. , Schreck C. B. 
Published: October 2014

Abstract
Pacific Lamprey Entosphenus tridentatus has declined across its range along the West Coast of North America, and an understanding of all life history phases is needed to address population recovery. Spawning surveys (redd counts) are common tools currently used to monitor returning adult salmonids, but such methodologies are in their infancy for Pacific Lamprey. Our objective was to assess the minimum spawning survey distance required to detect the presence of Pacific Lamprey redds and obtain precise redd density estimates from these data. To do this, we statistically resampled existing spawning locations of Pacific Lamprey collected during spawning surveys in four streams of the Willamette River Basin, Oregon, during spring of 2013. We found that the minimum survey distance for Pacific Lamprey redd detection was inversely related to the observed redd density and was always less than 1.2 km. Survey distance requirements to obtain precise redd counts (±20% of observed redd densities) were also inversely related to redd density and habitat availability, and varied between 1.3 km and 13.7 km. Our results suggest that spawning surveys are a potential tool for monitoring adult Pacific Lamprey abundance, but the specific objectives of the monitoring programs and acknowledgment of unknowns must be considered prior to implementation into recovery plans.
Received January 2, 2014; accepted May 19, 2014
Dyck’s surfaces, systoles, and capacities
Authors: Katz Mikhail , Sabourau Stéphane 
Published: October 2014

We prove an optimal systolic inequality for nonpositively curved Dyck’s surfaces. The extremal surface is flat with eight conical singularities, six of angle

ϑ
\vartheta

and two of angle

9
π
−
3
ϑ

9 \pi -3 \vartheta

for a suitable

ϑ
\vartheta

with

cos
⁡
(
ϑ
)
∈

Q

(

19

)

\cos (\vartheta )\in \mathbb {Q}(\sqrt {19})

. Relying on some delicate capacity estimates, we also show that the extremal surface is not conformally equivalent to the hyperbolic Dyck’s surface with maximal systole, yielding a first example of systolic extremality with this behavior.
NOVA: a software to analyze complexome profiling data
Authors: Giese Heiko , Ackermann Jörg , Heide Heinrich , Bleier Lea , Dröse Stefan , Wittig Ilka , Brandt Ulrich , Koch Ina 
Published: October 2014

Abstract
Summary: We introduce nova , a software for the analysis of complexome profiling data. nova supports the investigation of the composition of complexes, cluster analysis of the experimental data, visual inspection and comparison of experiments and many other features.
Availability and implementation: nova is licensed under the Artistic License 2.0. It is freely available at http://www.bioinformatik.uni-frankfurt.de . nova requires at least Java 7 and runs under Linux, Microsoft Windows and Mac OS.
Contact: ina.koch@bioinformatik.uni-frankfurt.de
PDB-wide collection of binding data: current status of the PDBbind database
Authors: Liu Zhihai , Li Yan , Han Li , Li Jie , Liu Jie , Zhao Zhixiong , Nie Wei , Liu Yuchen , Wang Renxiao 
Published: October 2014

AbstractMotivation: Molecular recognition between biological macromolecules and organic small molecules plays an important role in various life processes. Both structural information and binding data of biomolecular complexes are indispensable for depicting the underlying mechanism in such an event. The PDBbind database was created to collect experimentally measured binding data for the biomolecular complexes throughout the Protein Data Bank (PDB). It thus provides the linkage between structural information and energetic properties of biomolecular complexes, which is especially desirable for computational studies or statistical analyses.Results: Since its first public release in 2004, the PDBbind database has been updated on an annual basis. The latest release (version 2013) provides experimental binding affinity data for 10 776 biomolecular complexes in PDB, including 8302 protein–ligand complexes and 2474 other types of complexes. In this article, we will describe the current methods used for compiling PDBbind and the updated status of this database. We will also review some typical applications of PDBbind published in the scientific literature.Availability and implementation: All contents of this database are freely accessible at the PDBbind-CN Web server at http://www.pdbbind-cn.org/ .Contact: wangrx@mail.sioc.ac.cn .Supplementary information: Supplementary data are available at Bioinformatics online.
A depth camera based approach for automatic control of video cameras in lecture halls
Authors: Winkler Michael , Michael Höver Kai , Mühlhäuser Max 
Published: October 2014

Purpose
– The purpose of this study is to present a depth information-based solution for automatic camera control, depending on the presenter’s moving positions. Talks, presentations and lectures are often captured on video to give a broad audience the possibility to (re-)access the content. As presenters are often moving around during a talk, it is necessary to steer recording cameras.

Design/methodology/approach
– We use depth information from Kinect to implement a prototypical application to automatically steer multiple cameras for recording a talk.

Findings
– We present our experiences with the system during actual lectures at a university. We found out that Kinect is applicable for tracking a presenter during a talk robustly. Nevertheless, our prototypical solution reveals potential for improvements, which we discuss in our future work section.

Originality/value
– Tracking a presenter is based on a skeleton model extracted from depth information instead of using two-dimensional (2D) motion- or brightness-based image processing techniques. The solution uses a scalable networking architecture based on publish/subscribe messaging for controlling multiple video cameras.
Potential of virtual-social-physical convergence for project manufacturing
Authors: Fox Stephen 
Published: October 2014

Purpose– The purpose of this paper is to provide an analysis of how virtual-social-physical (VSP) convergence can affect different types of project manufacturing. In particular, VSP convergence that involves combining the read-write functionality of Web 2.0 and related social media together with digital tools for virtual design and for physical manufacturing.Design/methodology/approach– Literature review and interviews with experts in technologies covering VSP convergence: digital data capture, photogrammetry, generative computation, Web 2.0 and social media, digitally driven manufacturing.Findings– VSP convergence can enable the replacement of slow and expensive traditional project manufacturing practices with much faster and less expensive digitally driven technologies.Practical implications– There are new opportunities for expansion of some types of project manufacturing. Notably, there are opportunities in non-industrial developing countries because VSP convergence reduces reliance on industrial infrastructure for the manufacturing of goods. By contrast, opportunities may be limited for expansion of established project manufacturing companies with exclusive brands.Originality/value– The originality is that VSP convergence is related to different types of project manufacturing. Based on VSP convergence, traditional types and new types of project manufacturing are categorized together for the first time. The value of this paper is that it is explained how VSP convergence can address barriers to expansion of different types of project manufacturing.
External technology acquisition of SMEs in the engineering industry of Bangalore
Authors: Bala Subrahmanya M.H. 
Published: October 2014

Purpose
– The purpose of this paper is to ascertain: first, India's public policy support for small and medium enterprises (SMEs) for external technology acquisition (ETA); second, objectives of SMEs for ETA; and third, factors which induced them to obtain their first ETA.

Design/methodology/approach
– Public policy is examined through survey of literature, whereas objectives and factors influencing first ETAs by SMEs are analyzed based on primary data collected from 64 SMEs in Bangalore. Objectives of ETAs are analyzed descriptively whereas factors which facilitated/hindered early ETAs are examined through Cox regression analysis.

Findings
– Public policy for ETAs by SMEs includes technology information, assistance and fiscal incentives. The technology focus of these SMEs has been shifting from conventional lathes to computer numerical control (CNC) machines. Most of the SMEs have gone for technology up-gradation with the objective of improving product quality, scale expansion, and meeting customer demand. Majority of these SMEs have obtained their first ETA within six years of their inception. Firm level factors have significantly influenced the time taken by these SMEs for their first ETAs. Overall, when technology is well developed and easily accessible, SMEs would hardly look for external support for ETAs.

Research limitations/implications
– The shifting technology focus from conventional lathes to CNC machines is a welcome development, which is driven by the need for “competitiveness enhancement”. Since there is no major obstacle for ETAs, policy makers may focus more on providing SMEs with market information and market developments.

Practical implications
– The shifting technology focus from conventional lathes to CNC machines in Indian SMEs is a welcome development, which is largely driven by the need for better product quality, scale expansion and customer demand, and internal factors played a crucial role in the time taken by these SMEs in accomplishing their first ETA. As such there is no major obstacle for these SMEs in going for ETAs since technology suppliers are available at the door-step and finance is available from the banks. Therefore, policy makers may focus more on providing SMEs with market information and market developments in the domestic as well as international market.

Originality/value
– This is a first attempt to examine public policy, objectives and factors influencing SMEs for ETAs in India, after 1991.