bluuebunny/crossref_metadata_2025_split huggingface dataset:
Detachment and successive re-attachment of multiple, reversibly-binding tethers result in irreversible bacterial adhesion to surfaces
Authors: Sjollema Jelmer , van der Mei Henny C. , Hall Connie L. , Peterson Brandon W. , de Vries Joop , Song Lei , Jong Ed D. de , Busscher Henk J. , Swartjes Jan J. T. M. 
Published: June 2017

AbstractBacterial adhesion to surfaces occurs ubiquitously and is initially reversible, though becoming more irreversible within minutes after first contact with a surface. We here demonstrate for eight bacterial strains comprising four species, that bacteria adhere irreversibly to surfaces through multiple, reversibly-binding tethers that detach and successively re-attach, but not collectively detach to cause detachment of an entire bacterium. Arguments build on combining analyses of confined Brownian-motion of bacteria adhering to glass and their AFM force-distance curves and include the following observations: (1) force-distance curves showed detachment events indicative of multiple binding tethers, (2) vibration amplitudes of adhering bacteria parallel to a surface decreased with increasing adhesion-forces acting perpendicular to the surface, (3) nanoscopic displacements of bacteria with relatively long autocorrelation times up to several seconds, in absence of microscopic displacement, (4) increases in Mean-Squared-Displacement over prolonged time periods according to tα with 0 < α ≪ 1, indicative of confined displacement. Analysis of simulated position-maps of adhering particles using a new, in silico model confirmed that adhesion to surfaces is irreversible through detachment and successive re-attachment of reversibly-binding tethers. This makes bacterial adhesion mechanistically comparable with the irreversible adsorption of high-molecular-weight proteins to surfaces, mediated by multiple, reversibly-binding molecular segments.
The common cuckoo is an effective indicator of high bird species richness in Asia and Europe
Authors: Morelli Federico , Møller Anders Pape , Nelson Emma , Benedetti Yanina , Liang Wei , Šímová Petra , Moretti Marco , Tryjanowski Piotr 
Published: June 2017

AbstractCommon cuckooCuculus canorusis a charismatic bird species with a dominant presence in human culture: from folklore legends to nowadays there is evidence of cuckoos being a prime candidate as a surrogate of bird diversity. Recent studies demonstrated that the cuckoo can predict hotspots of taxonomic diversity and functional diversity of bird communities in European countries. In this study, we demonstrated that the cuckoo is an excellent bioindicator at multi-spatial scale, extending cuckoo surrogacy from Europe to Asia. Even using three different survey methods (transect, square, point counts), comparing the new findings with results of our research in Europe, sites where the cuckoo is present were characterized by greater species richness, while the cuckoo was absent from sites with low species richness. The goodness of fit of models based on point counts ranged between 71 and 92%. Furthermore, the cuckoo population trend mirrors the average population trend and climate suitability of overall bird communities in Europe. The common cuckoo is therefore a suitable intercontinental bioindicator of hotspots of bird richness, even under climate change scenarios or in areas where the species co-occurs with other cuckoo species, opening a new avenue for standardized citizen science on bird biodiversity surveys worldwide.
Degradation of black phosphorus is contingent on UV–blue light exposure
Authors: Ahmed Taimur , Balendhran Sivacarendran , Karim Md Nurul , Mayes Edwin L. H. , Field Matthew R. , Ramanathan Rajesh , Singh Mandeep , Bansal Vipul , Sriram Sharath , Bhaskaran Madhu , Walia Sumeet 
Published: June 2017

AbstractLayered black phosphorous has recently emerged as a promising candidate for next generation nanoelectronic devices. However, the rapid ambient degradation of mechanically exfoliated black phosphorous poses challenges in its practical implementation in scalable devices. As photo-oxidation has been identified as the main cause of degradation, to-date, the strategies employed to protect black phosphorous have relied upon preventing its exposure to atmospheric oxygen. These strategies inhibit access to the material limiting its use. An understanding of the effect of individual wavelengths of the light spectrum can lead to alternatives that do not require the complete isolation of black phosphorous from ambient environment. Here, we determine the influence of discrete wavelengths ranging from ultraviolet to infrared on the degradation of black phosphorous. It is shown that the ultraviolet component of the spectrum is primarily responsible for the deterioration of black phosphorous in ambient conditions. Based on these results, new insights into the degradation mechanism have been generated which will enable the handling and operating of black phosphorous in standard fabrication laboratory environments.
Predicting outcomes of gastric endoscopic submucosal dissection using a Bayesian approach: a step for individualized risk assessment
Authors: Libânio Diogo , Dinis-Ribeiro Mário , Pimentel-Nunes Pedro , Dias Cláudia , Rodrigues Pedro 
Published: June 2017

Abstract
Background and study aims Efficacy and adverse events probabilities influence decisions regarding the best options to manage patients with gastric superficial lesions. We aimed at developing a Bayesian model to individualize the prediction of outcomes after gastric endoscopic submucosal dissection (ESD).
Patients and methods Data from 245 gastric ESD were collected, including patient and lesion factors. The two endpoints were curative resection and post-procedural bleeding (PPB). Logistic regression and Bayesian networks were built for each outcome; their predictive value was evaluated in-sample and validated through leave-one-out and cross-validation. Clinical decision support was enhanced by the definition of risk matrices, direct use of Bayesian inference software and by a developed online platform.
Results ESD was curative in 85.3 % and PPB occurred in 7.7 % of patients. In univariate analysis, male sex, ASA status, carcinoma histology, polypoid or depressed morphology, and lesion size ≥ 20 mm were associated with non-curative resection, while ASA status, antithrombotics and lesion size ≥ 20 mm were associated with PPB. Naïve Bayesian models presented AUROCs of ~80 % in the derivation cohort and ≥ 74 % in cross-validation for both outcomes. Risk matrices were computed, showing that lesions with cancer at biopsies, ≥ 20 mm, proximal or in the middle third, and polypoid are more prone to non-curative resection. PPB risk was < 5 % in lesions < 20 mm in the absence of antithrombotics.
Conclusions The derived Bayesian model presented good discriminative power in the prediction of ESD outcomes and can be used to predict individualized probabilities, improving patient information and supporting clinical and management decisions.
Vordere Kreuzbandplastik mit der
Semitendinosussehne
Authors: Wagenhäuser Kirsten , Feustel Martin 
Published: June 2017

Zusammenfassung
OP-Ablauf In Deutschland treten jedes Jahr über 350 000 Knieverletzungen
mit Kreuzbandriss auf, das vordere Kreuzband reißt zehnmal häufiger als das
hintere. Ungefähr 90 000 Kreuzbandrisse werden operativ mit einer
Kreuzbandplastik (Kreuzbandrekonstruktion) versorgt. Im OP-Ablauf schildert das
Team des Leopoldina Krankenhauses in Schweinfurt, wie die vordere
Kreuzbandplastik (VKB) mithilfe der Semitendinosussehne in
ACL-TightRope®-Technik durchgeführt wird.
Surveillant landscapes
Authors: Jones Rodney H. 
Published: June 2017

Abstract
Most linguistic landscape research to date has focused on how people read and write language in the material world. Much less attention has been paid to the way linguistic landscapes sometimes read and write their inhabitants through technologies like CCTV cameras, intruder alarms, and other aspects of the built environment designed to make people ‘visible’ – what I call surveillant landscapes. This article puts forth a framework for analyzing the surveillant nature of linguistic landscapes based on tools from mediated discourse analysis. It sees surveillant landscapes in terms of the way they communicate practices of surveillance to the people who inhabit them (‘discourses in place’), the kinds of social relationships and social identities that they make possible (‘interaction orders’), and the ways architectures of surveillance come to be internalized by citizens, while at the same time aspects of their behaviors and identities come to be sedimented into their environments (‘historical bodies’). I argue that studies of linguistic landscapes should take more account of the agenitive nature of linguistic landscapes and their increasing ability to recognize and to entextualize what takes place within them, and the consequences of this both on situated social interactions and on broader political and economic realities.
Partitioned learning of deep Boltzmann machines for SNP data
Authors: Hess Moritz , Lenz Stefan , Blätte Tamara J , Bullinger Lars , Binder Harald 
Published: June 2017

Abstract

Motivation
Learning the joint distributions of measurements, and in particular identification of an appropriate low-dimensional manifold, has been found to be a powerful ingredient of deep leaning approaches. Yet, such approaches have hardly been applied to single nucleotide polymorphism (SNP) data, probably due to the high number of features typically exceeding the number of studied individuals.

Results
After a brief overview of how deep Boltzmann machines (DBMs), a deep learning approach, can be adapted to SNP data in principle, we specifically present a way to alleviate the dimensionality problem by partitioned learning. We propose a sparse regression approach to coarsely screen the joint distribution of SNPs, followed by training several DBMs on SNP partitions that were identified by the screening. Aggregate features representing SNP patterns and the corresponding SNPs are extracted from the DBMs by a combination of statistical tests and sparse regression. In simulated case–control data, we show how this can uncover complex SNP patterns and augment results from univariate approaches, while maintaining type 1 error control. Time-to-event endpoints are considered in an application with acute myeloid leukemia patients, where SNP patterns are modeled after a pre-screening based on gene expression data. The proposed approach identified three SNPs that seem to jointly influence survival in a validation dataset. This indicates the added value of jointly investigating SNPs compared to standard univariate analyses and makes partitioned learning of DBMs an interesting complementary approach when analyzing SNP data.

Availability and implementation
A Julia package is provided at ‘http://github.com/binderh/BoltzmannMachines.jl’.

Supplementary information
Supplementary data are available at Bioinformatics online.
pqsfinder: an exhaustive and imperfection-tolerant search tool for potential quadruplex-forming sequences in R
Authors: Hon Jiří , Martínek Tomáš , Zendulka Jaroslav , Lexa Matej 
Published: June 2017

Abstract

Motivation
G-quadruplexes (G4s) are one of the non-B DNA structures easily observed in vitro and assumed to form in vivo. The latest experiments with G4-specific antibodies and G4-unwinding helicase mutants confirm this conjecture. These four-stranded structures have also been shown to influence a range of molecular processes in cells. As G4s are intensively studied, it is often desirable to screen DNA sequences and pinpoint the precise locations where they might form.

Results
We describe and have tested a newly developed Bioconductor package for identifying potential quadruplex-forming sequences (PQS). The package is easy-to-use, flexible and customizable. It allows for sequence searches that accommodate possible divergences from the optimal G4 base composition. A novel aspect of our research was the creation and training (parametrization) of an advanced scoring model which resulted in increased precision compared to similar tools. We demonstrate that the algorithm behind the searches has a 96% accuracy on 392 currently known and experimentally observed G4 structures. We also carried out searches against the recent G4-seq data to verify how well we can identify the structures detected by that technology. The correlation with pqsfinder predictions was 0.622, higher than the correlation 0.491 obtained with the second best G4Hunter.

Availability and implementation
http://bioconductor.org/packages/pqsfinder/ This paper is based on pqsfinder-1.4.1.

Supplementary information
Supplementary data are available at Bioinformatics online.
Hemodynamic Changes after Unilateral Revascularization for Moyamoya Disease: Serial Assessment by Quantitative Magnetic Resonance Angiography
Authors: Kim Tackeun , Bang Jae Seung , Kwon O-Ki , Hwang Gyojun , Kim Jeong Eun , Kang Hyun-Seung , Cho Won-Sang , Jung Cheolkyu , Oh Chang Wan 
Published: June 2017

Abstract

BACKGROUND: Ultrasonic flow meters and quantitative magnetic resonance angiography quantitatively assess flow during hemodynamic evaluation of cerebral ischemia. Although their reliability and reproducibility have been verified, their clinical impact in moyamoya disease has rarely been reported.

OBJECTIVE: To investigate flow measurement outcomes in moyamoya disease patients pre- and postoperatively through a retrospective observational study.

METHODS: We evaluated 41 patients undergoing their first revascularization surgery who were followed ≥6 mo. Hemodynamic parameters were recorded preoperatively, at 1 and 6 mo postoperatively, and at the last follow-up. Demographic factors, Suzuki stage, and stroke development were also analyzed.

RESULTS: Patients’ median age was 37 yr (interquartile range [IQR], 27-43), and 16 (39.0%) patients were men. During follow-up, 9 (22.0%) patients experienced postoperative stroke (4 major strokes). Hemodynamic status was improved in 34 (82.9%) patients at the 6-mo follow-up. Median intraoperative flow was 41 mL/min (IQR, 25-59). Bypass flow peaked at 6 mo (median, 67 mL/min; IQR, 35-99). At the 1- and 6-mo follow-ups, ipsilateral hemispheric flow was significantly increased. The median proportion of posterior circulation at 6 mo was 44.4%, significantly lower than the preoperative proportion (50.1%). Abundant intraoperative bypass flow was associated with hemodynamic improvement, while low contralateral hemispheric flow was related with immediate postoperative ischemic stroke.

CONCLUSION: Ipsilateral hemispheric flow was increased during 6-mo follow-up, and posterior circulation flow burden was diminished. Abundant intraoperative bypass flow was associated with postoperative hemodynamic improvement. Low preoperative contralateral hemispheric flow was related with immediate postoperative ischemic stroke.
The Effect of Aging and Priming on Same/Different Judgments Between Text and Partially Masked Speech
Authors: Freyman Richard L. , Terpening Jenna , Costanzi Angela C. , Helfer Karen S. 
Published: June 2017

Objectives:
It is well known from previous research that when listeners are told what they are about to hear before a degraded or partially masked auditory signal is presented, the speech signal “pops out” of the background and becomes considerably more intelligible. The goal of this research was to explore whether this priming effect is as strong in older adults as in younger adults.

Design:
Fifty-six adults—28 older and 28 younger—listened to “nonsense” sentences spoken by a female talker in the presence of a 2-talker speech masker (also female) or a fluctuating speech-like noise masker at 5 signal-to-noise ratios. Just before, or just after, the auditory signal was presented, a typed caption was displayed on a computer screen. The caption sentence was either identical to the auditory sentence or differed by one key word. The subjects’ task was to decide whether the caption and auditory messages were the same or different. Discrimination performance was reported in d'. The strength of the pop-out perception was inferred from the improvement in performance that was expected from the caption-before order of presentation. A subset of 12 subjects from each group made confidence judgments as they gave their responses, and also completed several cognitive tests.

Results:
Data showed a clear order effect for both subject groups and both maskers, with better same-different discrimination performance for the caption-before condition than the caption-after condition. However, for the two-talker masker, the younger adults obtained a larger and more consistent benefit from the caption-before order than the older adults across signal-to-noise ratios. Especially at the poorer signal-to-noise ratios, older subjects showed little evidence that they experienced the pop-out effect that is presumed to make the discrimination task easier. On average, older subjects also appeared to approach the task differently, being more reluctant than younger subjects to report that the captions and auditory sentences were the same. Correlation analyses indicated a significant negative association between age and priming benefit in the two-talker masker and nonsignificant associations between priming benefit in this masker and either high-frequency hearing loss or performance on the cognitive tasks.

Conclusions:
Previous studies have shown that older adults are at least as good, if not better, at exploiting context in speech recognition, as compared with younger adults. The current results are not in disagreement with those findings but suggest that, under some conditions, the automatic priming process that may contribute to benefits from context is not as strong in older as in younger adults.
Remodeling after arthroscopic reduction of glenohumeral joint in adduction internal rotation shoulder deformity in obstetric brachial plexus palsy
Authors: Ghaly Nabil , Elabd Mostafa , Samir Shady , Samy Maged , Kotb Ahmed , Fayyad Tamer 
Published: June 2017

Background:
Lesions of the upper trunk in obstetric brachial plexus palsy (OBPP) commonly leads to long-term shoulder dysfunction. The constant internal rotation lead to early glenohumeral (GH) joint deformity by 6 mo of age and to advanced deformity by 2 yr. Halting or reversing GH deformity and the percentage of the humeral head anterior to the midscapular line is an important surgical goal to restore shoulder function. The purpose of this study was to assess the ability of arthroscopic anterior release (with or without tendon transfers) to correct GH deformity.

Methods:
Twenty-one patients were included in this study. The average age was 26 mo (17 to 50 mo). Sixteen patients (76.2%) had C5 or 6 lesion, while five (23.8%) had C5, 6 or 7 lesion. Seven patients had grade II GH deformity (33.3%), ten had grade III (47.6%), and four had grade IV (19.1%). Ten children underwent isolated release and 11 underwent concomitant tendon transfers. Functional and radiographic assessments were used to assess outcome after at least 1-year follow-up. The average follow-up period was 19±7 mo (range 12-41 mo).

Results:
Significant improvement was noted in both the glenohumeral retroversion angle (GRV) angle and percentage of humeral head anterior to the midscapular line at 1-year follow-up The mean preoperative GRV angle was −27.8 degrees and postoperatively −11.8 degrees. The mean percentage of humeral head anterior to the midscapular line was 25% preoperatively and 43% postoperatively. Aggregate Mallet score also demonstrated statistically significant improvement.

Conclusions:
Arthroscopic release and reduction of GH joint with or without tendon transfer for the sequela of OBPP was associated with GH remodeling. The current study confirmed that the improvement was achieved after nearly 1-year follow-up. The clinical improvements paralleled the radiographic ones.

Level of evidence:
IV.
Neurobiologic Correlates of Attention and Memory Deficits Following Critical Illness in Early Life*
Authors: Schiller Raisa M. , IJsselstijn Hanneke , Madderom Marlous J. , Rietman André B. , Smits Marion , van Heijst Arno F. J. , Tibboel Dick , White Tonya , Muetzel Ryan L. 
Published: June 2017

Objectives:Survivors of critical illness in early life are at risk of long-term–memory and attention impairments. However, their neurobiologic substrates remain largely unknown.Design:A prospective follow-up study.Setting:Erasmus MC-Sophia Children’s Hospital, Rotterdam, the Netherlands.Patients:Thirty-eight school-age (8–12 yr) survivors of neonatal extracorporeal membrane oxygenation and/or congenital diaphragmatic hernia with an intelligence quotient greater than or equal to 80 and a below average score (zscore ≤ –1.5) on one or more memory tests.Interventions:None.Measurements and Main Results:Intelligence, attention, memory, executive functioning, and visuospatial processing were assessed and compared with reference data. White matter microstructure and hippocampal volume were assessed using diffusion tensor imaging and structural MRI, respectively. Global fractional anisotropy was positively associated with selective attention (β= 0.53;p= 0.030) and sustained attention (β= 0.48;p= 0.018). Mean diffusivity in the left parahippocampal region of the cingulum was negatively associated with visuospatial memory, both immediate (β= –0.48;p= 0.030) and delayed recall (β= –0.47;p= 0.030). Mean diffusivity in the parahippocampal region of the cingulum was negatively associated with verbal memory delayed recall (left:β= –0.52,p= 0.021; right:β= –0.52,p= 0.021). Hippocampal volume was positively associated with verbal memory delayed recall (left:β= 0.44,p= 0.037; right:β= 0.67,p= 0.012). Extracorporeal membrane oxygenation treatment or extracorporeal membrane oxygenation type did not influence the structure-function relationships.Conclusions:Our findings indicate specific neurobiologic correlates of attention and memory deficits in school-age survivors of neonatal extracorporeal membrane oxygenation and congenital diaphragmatic hernia. A better understanding of the neurobiology following critical illness, both in early and in adult life, may lead to earlier identification of patients at risk for impaired neuropsychological outcome with the use of neurobiologic markers.
Using the Venous Pectoral Branch from the Thoracoacromial System as a Lifeboat in Autologous Breast Reconstruction
Authors: Tarakji Michael , Bartow Matthew J. , Dupin Charles , Tessler Oren 
Published: June 2017

Summary:
The most common recipient vessels for autologous free flap breast reconstruction are the internal mammary vessels. At times, there are problems with the exposed internal mammary vein (IMV) that require other options such as using the contralateral IMV, superior rib resection to access proximal IMV, retrograde IMV use, and thoracodorsal vein access with or without a vein graft. This case demonstrates using the pectoral branch of the thoracoacromial venous system without a vein graft as a lifeboat option when the IMV is not suitable for anastomosis. C.W. was a 65-year-old female who underwent right-sided mastectomy with placement of a tissue expander. After adjuvant radiation therapy, C.W. underwent deep inferior epigastric perforator free flap breast reconstruction. During exposure of the internal mammary artery and IMV, an iatrogenic venotomy occurred that precluded the use of this vessel as a reliable recipient. The deep inferior epigastric perforator flap pedicle was then dissected proximal to isolate the artery and vein, and the vein was successfully anastomosed to the venous pectoral branch of the thoracoacromial system. The postoperative course was uneventful and patient was discharged home on postoperative day 4. Using the venous pectoral branch of the thoracoacromial is a safe and valuable option that can be considered in difficult situations when the IMV is not a suitable option.