bluuebunny/crossref_metadata_2025_split huggingface dataset:
Swallowing Mechanics Associated With Artificial Airways, Bolus Properties, and Penetration–Aspiration Status in Trauma Patients
Authors: Dietsch Angela M. , Rowley Christopher B. , Solomon Nancy Pearl , Pearson, William G. 
Published: August 2017

Purpose
Artificial airway procedures such as intubation and tracheotomy are common in the treatment of traumatic injuries, and bolus modifications may be implemented to help manage swallowing disorders. This study assessed artificial airway status, bolus properties (volume and viscosity), and the occurrence of laryngeal penetration and/or aspiration in relation to mechanical features of swallowing.

Method
Coordinates of anatomical landmarks were extracted at minimum and maximum hyolaryngeal excursion from 228 videofluoroscopic swallowing studies representing 69 traumatically injured U.S. military service members with dysphagia. Morphometric canonical variate and regression analyses examined associations between swallowing mechanics and bolus properties based on artificial airway and penetration–aspiration status.

Results

Significant differences in swallowing mechanics were detected between extubated versus tracheotomized (
D
= 1.32,
p
< .0001), extubated versus decannulated (
D
= 1.74,
p
< .0001), and decannulated versus tracheotomized (
D
= 1.24,
p
< .0001) groups per post hoc discriminant function analysis. Tracheotomy-in-situ and decannulated subgroups exhibited increased head/neck extension and posterior relocation of the larynx. Swallowing mechanics associated with (a) penetration–aspiration status and (b) bolus properties were moderately related for extubated and decannulated subgroups, but not the tracheotomized subgroup, per morphometric regression analysis.

Conclusion
Specific differences in swallowing mechanics associated with artificial airway status and certain bolus properties may guide therapeutic intervention in trauma-based dysphagia.
Analysis and design of an unequal termination impedance power divider with bandpass filtering response
Authors: Kim P. , Chaudhary G. , Jeong Y. 
Published: August 2017

The design of an unequal termination power divider (PD) with a bandpass filtering response and wide out‐of‐band suppression characteristics is presented. The two‐cascaded coupled lines can be designed with a low impedance transforming ratio. For the validation, a 50‐to‐5 Ω termination impedance PD was implemented at a centre frequency (f0) of 2.6 GHz. The measured results are in good agreement with the simulations, showing input and output return losses that are better than 19 dB over a passband bandwidth of 190 MHz (2.51–2.7 GHz), and an out‐of‐band suppression that is better than 19.6 dB from DC to 2.25 and 2.9 to 7.2 GHz. The isolation between the output ports is 39.2 dB at f0, and it is better than 19 dB with a broadband frequency (DC to 7.2 GHz).
Outcomes of Patients with Behçet's Syndrome after Pulmonary Endarterectomy
Authors: Yıldızeli Şehnaz , Yanartaş Mehmed , Taş Serpil , Direskeneli Haner , Mutlu Bülent , Ceyhan Berrin , Yıldızeli Bedrettin 
Published: August 2017

Background Behçet's syndrome (BS) is a multisystem disorder and is not known as a risk factor for chronic thromboembolic pulmonary hypertension (CTEPH), for which the treatment of choice is pulmonary endarterectomy (PEA). The aim of this study was to review our experience in the surgical treatment of CTEPH in patients with BS.
Methods Data were collected prospectively for consecutive patients with BS who underwent PEA over a 6-year period.
Results We identified nine patients (seven males, two females, mean age: 34.7 ± 9.9 years) with BS. The mean disease duration before PEA was 88.0 ± 70.2 months. All patients but one received immunosuppressive therapy before the surgery. Exercise-induced dyspnea presented symptoms in six patients. One patient had associated intracardiac thrombosis. PEA was bilateral in five patients, unilateral in three, and lobar in one. No perioperative mortality was observed; however, one patient died four weeks after PEA due to massive hemoptysis. Morbidity was observed in two patients. The systolic pulmonary artery pressure fell significantly from 59.0 ± 22.7 mm Hg to 30.0 ± 6.5 mm Hg after surgery (p = 0.031). Pulmonary vascular resistance also improved significantly from 611.8 ± 300.2 to 234.7 ± 94.9 dyn/s/cm5 (p = 0.031). After a median follow-up of 29.4 months, all patients improved to the New York Heart Association (NYHA) functional class I and II.
Conclusion Patients with BS may suffer recurrent pulmonary embolism and develop CTEPH. In patients who do not respond to anticoagulation or immunosuppressive therapy, PEA may be a therapeutic option when thrombotic lesions are surgically accessible. Due to the high risk of perioperative mortality, the procedure should be undertaken in centers with experience.
Außerklinische Beatmung – Konzepte und Therapieempfehlungen
Authors: Schwarz Sarah , Magnet Friederike , Schönhofer Bernd , Windisch Wolfram 
Published: August 2017

AbstractThe prognosis of patients receiving home mechanical ventilation is very heterogeneous and depends on the underlying disease, the degree of respiratory dependency and the comorbidities. Due to the severe chronic diseases, the initiation of a long-term NIV must be done during an inpatient treatment. Two recently published randomized controlled trials using more aggressive forms of NPPV targeted at normalizing hypercapnic PaCO2 values, showed improved long term survival also in patients with an underlying diagnosis of COPD. Consequently, the number of patients receiving home mechanical ventilation has dramatically increased in recent years and more and more outpatient settings has been established without scientific evidence. Nevertheless, beside reliable care structures, ethical aspects and health related quality of life are of great importance in the context of home mechanical ventilation.
Duale antithrombozytäre Therapie – Perioperativ absetzen oder weiterführen?
Authors: Koscielny Jürgen , von Heymann Christian , Zeymer Uwe , Cremer Jochen , Spannagl Michael , Labenz Joachim , Giannitsis Evangelos , Goss Franz 
Published: August 2017

Zusammenfassung
Hintergrund Bei Patienten nach akutem Koronarsyndrom wird die duale antithrombozytäre Therapie (DAPT) mit Acetylsalicylsäure und einem P2Y12-Adenosindiphosphat-Rezeptorblocker wie Clopidogrel, Prasugrel und Ticagrelor für eine Dauer von 12 Monaten in den Leitlinien empfohlen. Wenn diese Hochrisikopatienten sich einem chirurgischen Eingriff unterziehen müssen, herrscht oft Unsicherheit bezüglich der DAPT: Kann die Therapie ohne Unterbrechung fortgeführt werden? Wenn nein, welches Therapie-Karenzkonzept wird empfohlen? Was muss beim perioperativen Management beachtet werden?
Methoden Eine interdisziplinäre Gruppe erfahrener Experten aus den Bereichen Kardiologie, Kardiochirurgie, Gastroenterologie, Anästhesiologie, Intensivmedizin und Hämostaseologie hat auf Basis der aktuellen wissenschaftlichen Datenlage praxisrelevante Informationen und Empfehlungen erarbeitet.
Ergebnisse Die Empfehlungen schließen Hinweise für die Einschätzung des Patienten- und Operations-spezifischen Blutungs- und Ischämierisikos, generelle Hinweise bezüglich des Karenzkonzeptes der DAPT und konkrete Empfehlungen hinsichtlich Thrombozytenfunktionshemmung bei häufigen chirurgischen Eingriffen ein.
Diskussion Diese Zusammenstellung soll allen beteiligten medizinischen Disziplinen den Umgang mit Patienten unter DAPT erleichtern und damit eine optimale perioperative Versorgung der Patienten gewährleisten.
Fahreignung bei Morbus Parkinson
Authors: Buhmann Carsten , Vesper Jan , Oelsner Henriette 
Published: August 2017

ZusammenfassungEtwa 60 % aller Parkinson-Patienten und 50 % der Parkinson-Patienten mit Tiefer Hirnstimulation (THS) und Führerschein fahren aktiv Auto.
Parkinsonerkrankte weisen jedoch häufig körperliche und/oder psychische Einschränkungen mit potentiellem Verlust der Fahreignung (syn.
Fahrtauglichkeit) auf. Die Fahrfähigkeit (syn. Fahrtüchtigkeit) kann auch durch Parkinson-Medikamente eingeschränkt sein. Vom behandelnden
Arzt wird verlangt, seine Patienten hinsichtlich ihrer Fähigkeit, ein Kraftfahrzeug zu führen, zu beraten. Dies ist jedoch in der Praxis
schwierig. Zum einen gibt es keine standardisierte, prädiktive Testbatterie zur Beurteilung der Fahreignung, zum anderen korreliert die
Ausprägung der motorischen Einschränkung nur unzureichend mit der Fahreignung. Dieser Artikel gibt einen Überblick, welche motorischen und
nicht-motorischen Symptome die generelle Fahreignung und/oder die situativ-geprägte Fahrfähigkeit bei M. Parkinson beeinträchtigen können,
welche Kriterien eine relative oder absolute Fahruntauglichkeit anzeigen, welche neuropsychologischen Untersuchungen sinnvoll sind und wie
Patienten mit THS hinsichtlich der Fahreignung zu bewerten und zu beraten sind.
The Personal Antipsychotic Choice Index
Authors: van Dijk Floor , de Wit Iris , Blankers Matthijs , Sommer Iris , de Haan Lieuwe 
Published: August 2017

Abstract
Introduction We present an online decision aid to involve patients with a psychotic disorder in shared decision-making concerning the selection of antipsychotic medication.
Method Patients selected effectiveness and adverse effects criteria from the Subject’s Response to Antipsychotics-34 questionnaire. Numerical data from meta-analyses, clinical trial data, receptor affinities and expert opinions were used to rank antipsychotics on each criterion. When using the the tool, patients indicate on a 5-point Likert scale how they value each (adverse) effect. The Likert scale values are combined in an algorithm with the rank orders of antipsychotics to create a personalized ranking.
Results Criteria used were: effectiveness concerning psychotic, depressive and cognitive symptoms, weight gain, sexual dysfunction, drowsiness, hypersomnia, extrapyramidal symptoms, anticholinergic adverse effects, hypersalivation, nausea, dizziness, energy loss, blunted affect/less need for companionship. High-level evidence was available for ranking weight gain, sexual dysfunction, menstrual disorders, extrapyramidal symptoms and effectiveness on psychotic symptoms. We used lower level evidence ranking the remaining criteria.
Discussion A transparent procedure has resulted in an updateable tool to produce individual ranking of antipsychotics based on the patients’ input.
Unique, but still best practice? The Research Excellence Framework (REF) from an international perspective
Authors: Sivertsen Gunnar 
Published: August 2017

AbstractInspired by The Metric Tide report (2015) on the role of metrics in research assessment and management, and Lord Nicholas Stern’s report Building on Success and Learning from Experience (2016), which deals with criticisms of REF2014 and gives advice for a redesign of REF2021, this article discusses the possible implications for other countries. It also contributes to the discussion of the future of the REF by taking an international perspective. The article offers a framework for understanding differences in the motivations and designs of performance-based research funding systems (PRFS) across countries. It also shows that a basis for mutual learning among countries is more needed than a formulation of best practice, thereby both contributing to and correcting the international outlook in The Metric Tide report and its supplementary Literature Review.
Genomic evidence reveals a radiation of placental mammals uninterrupted by the KPg boundary
Authors: Liu Liang , Zhang Jin , Rheindt Frank E. , Lei Fumin , Qu Yanhua , Wang Yu , Zhang Yu , Sullivan Corwin , Nie Wenhui , Wang Jinhuan , Yang Fengtang , Chen Jinping , Edwards Scott V. , Meng Jin , Wu Shaoyuan 
Published: August 2017

SignificanceWe produced a genome-scale dataset from representatives of all placental mammal orders to infer diversification timing relative to the Cretaceous–Paleogene (KPg) boundary. Our sensitivity analyses show that divergence time estimates within placentals are considerably biased by the specific way in which a given dataset is processed. We examined the performance of various dating approaches using a comprehensive scheme of likelihood analyses and computational simulations, allowing us to identify the optimal molecular clock parameters, gene sets, and gene partitioning schemes for reliable dating. Based on the optimal methodology, we present a hypothesis of mammalian divergence timing that is more consistent with the fossil record than previous molecular clock reconstructions, suggesting that placental mammals underwent a continuous radiation across the KPg boundary.
Early photosynthetic eukaryotes inhabited low-salinity habitats
Authors: Sánchez-Baracaldo Patricia , Raven John A. , Pisani Davide , Knoll Andrew H. 
Published: August 2017

SignificanceAlthough it is widely accepted that the chrloroplasts in photosynthetic eukaryotes can be traced back to a single cyanobacterial ancestor, the nature of that ancestor remains debated. Chloroplasts have been proposed to derive from either early- or late-branching cyanobacterial lineages, and similarly, the timing and ecological setting of this event remain uncertain. Phylogenomic and Bayesian relaxed molecular clock analyses show that the chloroplast lineage branched deep within the cyanobacterial tree of life ∼2.1 billion y ago, and ancestral trait reconstruction places this event in low-salinity environments. The chloroplast took another 200 My to become established, with most extant groups originating much later. Our analyses help to illuminate the little known evolutionary history of early life on land.
Behavioral responses to annual temperature variation alter the dominant energy pathway, growth, and condition of a cold-water predator
Authors: Guzzo Matthew M. , Blanchfield Paul J. , Rennie Michael D. 
Published: August 2017

Significance
Climate warming is having wide-ranging effects on aquatic ecosystems. Fish are believed to adapt their feeding behavior as temperatures change, but empirical evidence of this behavior in nature and its impacts on individual fitness are lacking. We monitored the feeding behavior and growth of a temperature-sensitive fish population in a pristine lake for 11 y. Fish adjusted their feeding behavior annually in response to differences in temperature. In cooler years, fish ate more large prey from shallow nearshore regions, resulting in higher growth and condition than in warmer years, when fish ate more small prey from deep offshore regions. This suggests that the impacts of warming on aquatic ecosystems can scale from the individual to the food web level.
Kinetic and high-throughput profiling of epigenetic interactions by 3D-carbene chip-based surface plasmon resonance imaging technology
Authors: Zhao Shuai , Yang Mo , Zhou Wenfei , Zhang Baichao , Cheng Zhiqiang , Huang Jiaxin , Zhang Min , Wang Zhiyou , Wang Rui , Chen Zhonglei , Zhu Jinsong , Li Haitao 
Published: August 2017

Significance
In the era of functional proteomics, a myriad of new interactions, notably those modification-dependent ones, are widely suggested by advanced proteomic approaches and bioinformatic analysis. Therefore, there exists an urgent need to develop a technology for high-throughput mapping and quantitative characterization of biomolecular binding events. This study achieved the immobilization and kinetic detection of various biomacromolecules (including modified peptides and modified nucleic acids) in high throughput through the 3D-carbene chip-based surface plasmon resonance imaging (SPRi) technology. Modified histone peptides and nucleic acids, which are key epigenetic marks, could be efficiently probed by this platform. We envision that the 3D-carbene SPRi technology described here will have wide appeal in profiling and discovering biological recognitions in and beyond epigenetics.
Immune evasion by a staphylococcal inhibitor of myeloperoxidase
Authors: de Jong Nienke W. M. , Ramyar Kasra X. , Guerra Fermin E. , Nijland Reindert , Fevre Cindy , Voyich Jovanka M. , McCarthy Alex J. , Garcia Brandon L. , van Kessel Kok P. M. , van Strijp Jos A. G. , Geisbrecht Brian V. , Haas Pieter-Jan A. 
Published: August 2017

SignificanceStaphylococcus aureussecretes numerous proteins to evade our innate immune system, for example to evade opsonization and phagocytosis by neutrophils. Here we describe the discovery thatS. aureushas evolved a protein, called SPIN, that specifically binds and inhibits the human myeloperoxidase enzyme (MPO). MPO is located inside the granules of neutrophils and is important in the oxidative burst against pathogens. We identify the molecular mode of action of SPIN inhibiting MPO, illustrate this with the cocrystal structure, and show that SPIN is important for bacterial survival by MPO-dependent killing. Our study shows thatS. aureusfights back after it is engulfed by neutrophils, which will help our understanding of the complex nature ofS. aureusinfections.
Mechanical constraint from growing jaw facilitates mammalian dental diversity
Authors: Renvoisé Elodie , Kavanagh Kathryn D. , Lazzari Vincent , Häkkinen Teemu J. , Rice Ritva , Pantalacci Sophie , Salazar-Ciudad Isaac , Jernvall Jukka 
Published: August 2017

Significance
Good examples of the relative autonomy of organ development are teeth, and for decades researchers have cultured isolated mouse teeth on a petri dish by starting from the earliest recognizable stage. We have cultured cheek teeth of voles, another species of rodent, and show how the cultured vole teeth lack their species-specific morphology. Based on computational modeling, 3D imaging, and experiments in which we culture mouse and vole teeth between microscopic braces, we suggest that the development of vole tooth shape requires the lateral support of the jaw. Because mice lack the vole-specific morphology, the requirement of the jaw for tooth shape has not been possible to uncover previously. Comparative studies are required for the understanding of organogenesis.
Next step in the ongoing arms race between myxoma virus and wild rabbits in Australia is a novel disease phenotype
Authors: Kerr Peter J. , Cattadori Isabella M. , Liu June , Sim Derek G. , Dodds Jeff W. , Brooks Jason W. , Kennett Mary J. , Holmes Edward C. , Read Andrew F. 
Published: August 2017

SignificanceWhen a pathogen emerges in a host population, will it evolve to do more or less harm to its host? A single strain of myxoma virus was released as a biocontrol agent against Australian rabbit populations in 1950. The subsequent coevolution has become a textbook classic, although there has been little experimental work on this topic since the early 1980s. Here, we show that the host–pathogen arms race continued with the evolution of highly lethal viruses that cause immune collapse. The possibility that pathogens can become highly immunosuppressive in response to increases in host resistance needs to be considered where genetic and immunologic manipulations are used to enhance host resistance, as, for instance, in agriculture.
Vibrio cholerae
type 6 secretion system effector trafficking in target bacterial cells
Authors: Ho Brian T. , Fu Yang , Dong Tao G. , Mekalanos John J. 
Published: August 2017

Significance
This work demonstrates that it is possible to alter the prey target range of the antibacterial activity of the type 6 secretion system (T6SS). Being able to change the T6SS target specificity is the first step toward using the T6SS as an antipathogen or commensal therapeutic, prophylactic, or probiotic. This work also uncovers a cryptic secretion mechanism(s) for delivering protein substrates from the bacterial cytosol to the periplasm. This mechanism is exploited by some T6SS effectors as an alternative pathway for reaching periplasmic targets when they are by chance delivered into the cytosol of target cells.
Charge mobility modification of semiconducting carbon nanotubes by intrinsic defects
Authors: Bai Hongcun , Ma Yujia , Ma Jinsuo , Mei Jingnan , Tong Yan , Ji Yongqiang 
Published: August 2017

Abstract
Charge carrier mobility is a central transport property in nanoscale electronics. Carbon nanotubes (CNTs) are supposed to have high carrier mobility. The preparation methods of CNTs have been greatly improved, but the defects always exist. This work presented first-principle investigations on the charge carrier mobility of carbon nanotubes containing several intrinsic defects. The charge carrier mobilities of zigzag (10, 0) tubes with Stone–Wales, mono vacant and 5/8/5 defects were studied as an example to explore the role of defects. Most carrier mobilities were decreased, but several values of mobility are unexpectedly increased upon the appearance of the defects. This interesting result is discussed based on the changes of the stretching modulus, the effective mass of the carrier and deformation potential constant induced by the defects.
Genome-wide association studies using a penalized moving-window regression
Authors: Bao Minli , Wang Kai 
Published: August 2017

AbstractMotivationGenome-wide association studies (GWAS) have played an important role in identifying genetic variants underlying human complex traits. However, its success is hindered by weak effect at causal variants and presence of noise at non-causal variants. In an effort to overcome these difficulties, a previous study proposed a regularized regression method that penalizes on the difference of signal strength between two consecutive single-nucleotide polymorphisms (SNPs).ResultsWe provide a generalization to the afore-mentioned method so that more adjacent SNPs can be incorporated. The choice of optimal number of SNPs is studied. Simulation studies indicate that when consecutive SNPs have similar absolute coefficients our method performs better than using LASSO penalty. In other situations, our method is still comparable to using LASSO penalty. The practical utility of the proposed method is demonstrated by applying it to Genetic Analysis Workshop 16 rheumatoid arthritis GWAS data.Availability and implementationAn implementation of the proposed method is provided in R package MWLasso.
ReMILO: reference assisted misassembly detection algorithm using short and long reads
Authors: Bao Ergude , Song Changjin , Lan Lingxiao 
Published: August 2017

Abstract

Motivation
Contigs assembled from the second generation sequencing short reads may contain misassemblies, and thus complicate downstream analysis or even lead to incorrect analysis results. Fortunately, with more and more sequenced species available, it becomes possible to use the reference genome of a closely related species to detect misassemblies. In addition, long reads of the third generation sequencing technology have been more and more widely used, and can also help detect misassemblies.

Results
Here, we introduce ReMILO, a reference assisted misassembly detection algorithm that uses both short reads and PacBio SMRT long reads. ReMILO aligns the initial short reads to both the contigs and reference genome, and then constructs a novel data structure called red-black multipositional de Bruijn graph to detect misassemblies. In addition, ReMILO also aligns the contigs to long reads and find their differences from the long reads to detect more misassemblies. In our performance test on short read assemblies of human chromosome 14 data, ReMILO can detect 41.8–77.9% extensive misassemblies and 33.6–54.5% local misassemblies. On hybrid short and long read assemblies of S.pastorianus data, ReMILO can also detect 60.6–70.9% extensive misassemblies and 28.6–54.0% local misassemblies.

Availability and implementation
The ReMILO software can be downloaded for free under Artistic License 2.0 from this site: https://github.com/songc001/remilo.

Supplementary information
Supplementary data are available at Bioinformatics online.