bluuebunny/crossref_metadata_2025_split huggingface dataset:
Impact of different antithrombotics on the microcirculation and viability of perforator-based ischaemic skin flaps in a small animal model
Authors: Fichter Andreas M. , Ritschl Lucas M. , Robitzky Luisa K. , Wagenpfeil Stefan , Mitchell David A. , Wolff Klaus-Dietrich , Mücke Thomas 
Published: October 2016

AbstractThe effects of antithrombotic drugs on random and free flap survival have been investigated in the past, but the experimental and clinical results are not in agreement. A perforator-based critical ischaemia model was used to evaluate the effects of different perioperatively administered pharmaceutical agents on tissue ischaemia and to assess the potential additional haemorheological or vasodilative effects of antithrombotics on flap microcirculation. Combined laser Doppler flowmetry and remission spectroscopy revealed an increase in certain microcirculation parameters in most groups in comparison with saline controls, and these changes correlated with flap survival. Clopidogrel and hirudin significantly improved the amount of viable flap tissue in comparison with controls, while unfractioned heparin had a negative effect on flap survival. Low molecular weight heparin, aspirin, pentoxifylline, and hydroxyethyl starch had no impact on the amount of viable flap tissue. A higher complication rate was observed in all experimental groups, but only clopidogrel had a negative impact on the flap viability. Our results add to the body of evidence supporting the conclusion that perioperative antithrombotic treatment improves flap survival. Clopidogrel and hirudin are effective pharmacological agents that significantly increased the viability of perforator-based skin flaps in rats, but at a higher risk of postoperative bleeding.
A dual-targeting approach to inhibit Brucella abortus replication in human cells
Authors: Czyż Daniel M. , Jain-Gupta Neeta , Shuman Howard A. , Crosson Sean 
Published: October 2016

AbstractBrucella abortus is an intracellular bacterial pathogen and an etiological agent of the zoonotic disease known as brucellosis. Brucellosis can be challenging to treat with conventional antibiotic therapies and, in some cases, may develop into a debilitating and life-threatening chronic illness. We used multiple independent assays of in vitro metabolism and intracellular replication to screen a library of 480 known bioactive compounds for novel B. abortus anti-infectives. Eighteen non-cytotoxic compounds specifically inhibited B. abortus replication in the intracellular niche, which suggests these molecules function by targeting host cell processes. Twenty-six compounds inhibited B. abortus metabolism in axenic culture, thirteen of which are non-cytotoxic to human host cells and attenuate B. abortus replication in the intracellular niche. The most potent non-cytotoxic inhibitors of intracellular replication reduce B. abortus metabolism in axenic culture and perturb features of mammalian cellular biology including mitochondrial function and receptor tyrosine kinase signaling. The efficacy of these molecules as inhibitors of B. abortus replication in the intracellular niche suggests “dual-target” compounds that coordinately perturb host and pathogen are promising candidates for development of improved therapeutics for intracellular infections.
Targeting erythrocyte carbonic anhydrase and 18O-isotope of breath CO2 for sorting out type 1 and type 2 diabetes
Authors: Ghosh Chiranjit , Mandal Santanu , Banik Gourab D. , Maity Abhijit , Mukhopadhyay Prabuddha , Ghosh Shibendu , Pradhan Manik 
Published: October 2016

AbstractThe inability to envisage the acute onset and progression of type 1 diabetes (T1D) has been a major clinical stumbling block and an important area of biomedical research over the last few decades. Therefore there is a pressing need to develop a new and an effective strategy for early detection of T1D and to precisely distinguish T1D from type 2 diabetes (T2D). Here we describe the precise role of the enzymatic activity of carbonic anhydrase (CA) in erythrocytes in the pathogenesis of T1D and T2D. We show that CA activities are markedly altered during metabolism of T1D and T2D and this facilitates to the oxygen-18 (18O) isotopic fractionations of breath CO2. In our observations, T1D exhibited considerable depletions of 18O-isotopes of CO2, whereas T2D manifested isotopic enrichments of 18O in breath CO2, thus unveiling a missing link of breath18O-isotopic fractionations in T1D and T2D. Our findings suggest that the alterations in erythrocytes CA activities may be the initial step of altered metabolism of T1D and T2D, and breath 18O-isotope regulated by the CA activity is a potential diagnostic biomarker that can selectively and precisely distinguish T1D from T2D and thus may open a potential unifying strategy for treating these diseases.
Management of fluoroscopy-induced radiation ulcer: One-stage radical excision and immediate reconstruction
Authors: Wei Kai-Che , Yang Kuo-Chung , Chen Lee-Wei , Liu Wen-Chung , Chen Wen-Chieh , Chiou Wen-Yen , Lai Ping-Chin 
Published: October 2016

AbstractWith increasing use of cardiac fluoroscopic intervention, the incidence of fluoroscopy-induced radiation ulcer is increasing. Radiation ulcer is difficult to manage and currently there are no treatment guidelines. To identify the optimal treatment approaches for managing cardiac fluoroscopy-induced radiation ulcers, we retrospectively reviewed medical records of 13 patients with fluoroscopy-induced radiation ulcers receiving surgical interventions and following up in our hospital from 2012 to 2015. Conventional wound care and hyperbaric oxygen therapy were of little therapeutic benefit. Twelve patients received reconstruction with advancement flap or split thick skin graft. One-stage radical excision of radiation damaged area in eight cases with immediate reconstruction led to better outcomes than conservative excisions in four cases. Radical surgical excision to remove all the radiation damaged tissues in combination with immediate reconstruction appears to offer the optimal treatment results for cardiac fluoroscopy-induced radiation ulcers. Adequate excision of the damaged areas in both vertical (to the muscular fascia) and horizontal (beyond the sclerotic areas) dimension is pivotal to achieve good treatment outcomes.
Reduction of sidelobe radiations of the standard pyramidal horn using a thin metamaterial lens
Authors: Chen Xuxiang , Ge Yuehe , Bird Trevor S. 
Published: October 2016

A method is reported to suppress the sidelobe radiation of a standard pyramidal horn using a thin single‐layer metamaterial lens. The metamaterial lens is composed of two identical metallic dipole arrays printed on both sides of a single dielectric layer. By placing the metamaterial lens inside a standard pyramidal horn, the electromagnetic fields over the horn aperture can be modified, resulting in low‐sidelobe radiation in both the E‐ and H‐planes of the horn. The measurement of a prototype lens gave a 10 dB reduction of the first sidelobe level in the E‐plane, compared with that of the original air‐filled pyramidal horn. Other design possibilities with a compensating lens are suggested.
The African middle class(es) – in the middle of what?
Authors: Melber Henning 
Published: October 2016

SUMMARY
This Briefing/Debate article critically engages with the middle class phenomenon, which emerged as a prominent focus in Development Studies a decade ago and has more recently also become the subject of more informed African Studies, adding necessary and more nuanced analysis.
1
It critically examines the background and assumptions of the debate, pointing out the lack of class analysis, and suggests that the current focus still partly distracts from the underlying issues.
Effect of the European design of TBMs on ITER wall loads due to fast ions in the baseline (15 MA), hybrid (12.5 MA), steady-state (9 MA) and half-field (7.5 MA) scenarios
Authors: Kurki-Suonio T. , Äkäslompolo S. , Särkimäki K. , Varje J. , Asunta O. , Cavinato M. , Gagliardi M. , Hirvijoki E. , Parail V. , Saibene G. , Sipilä S. , Snicker A. 
Published: October 2016

Abstract
We assess the effect of the European design of the pebble-bed helium-cooled test blanket modules (TBM) on fast ion power loads on ITER material surfaces. For this purpose, the effect of not only the TBMs but also the ferritic inserts (FI), used for mitigating the toroidal field ripple, were included in unprecedented detail in the reconstruction of the 3-dimensional magnetic field. This is important because, due to their low collisionality, fast ions follow the magnetic geometry much more faithfully than the thermal plasma. The Monte Carlo orbit-following code ASCOT was used to simulate all the foreseen operating scenarios of ITER: the baseline 15 MA standard H-mode operation, the 12.5 MA hybrid scenario, the 9 MA advanced scenario, and the half-field scenario with helium plasma that will be ITER’s initial operating scenario. The effect of TBMs was assessed by carrying out the simulations in pairs: one including only the effect of ferritic inserts, and the other including also the perturbation due to TBMs. Both thermonuclear fusion alphas and NBI ions from ITER heating beams were addressed. The TBMs are found to increase the power loads, but the absolute values remain small. Neither do they produce any additional hot spots.
Isomorphic semantic mapping of variant call format (VCF2RDF)
Authors: Penha Emanuel Diego S , Iriabho Egiebade , Dussaq Alex , de Oliveira Diana Magalhães , Almeida Jonas S 
Published: October 2016

Abstract

Summary
The move of computational genomics workflows to Cloud Computing platforms is associated with a new level of integration and interoperability that challenges existing data representation formats. The Variant Calling Format (VCF) is in a particularly sensitive position in that regard, with both clinical and consumer-facing analysis tools relying on this self-contained description of genomic variation in Next Generation Sequencing (NGS) results. In this report we identify an isomorphic map between VCF and the reference Resource Description Framework. RDF is advanced by the World Wide Web Consortium (W3C) to enable representations of linked data that are both distributed and discoverable. The resulting ability to decompose VCF reports of genomic variation without loss of context addresses the need to modularize and govern NGS pipelines for Precision Medicine. Specifically, it provides the flexibility (i.e. the indexing) needed to support the wide variety of clinical scenarios and patient-facing governance where only part of the VCF data is fitting.

Availability and Implementation
Software libraries with a claim to be both domain-facing and consumer-facing have to pass the test of portability across the variety of devices that those consumers in fact adopt. That is, ideally the implementation should itself take place within the space defined by web technologies. Consequently, the isomorphic mapping function was implemented in JavaScript, and was tested in a variety of environments and devices, client and server side alike. These range from web browsers in mobile phones to the most popular micro service platform, NodeJS. The code is publicly available at https://github.com/ibl/VCFr, with a live deployment at: http://ibl.github.io/VCFr/.
gargammel: a sequence simulator for ancient DNA
Authors: Renaud Gabriel , Hanghøj Kristian , Willerslev Eske , Orlando Ludovic 
Published: October 2016

Abstract

Summary
Ancient DNA has emerged as a remarkable tool to infer the history of extinct species and past populations. However, many of its characteristics, such as extensive fragmentation, damage and contamination, can influence downstream analyses. To help investigators measure how these could impact their analyses in silico, we have developed gargammel, a package that simulates ancient DNA fragments given a set of known reference genomes. Our package simulates the entire molecular process from post-mortem DNA fragmentation and DNA damage to experimental sequencing errors, and reproduces most common bias observed in ancient DNA datasets.

Availability and Implementation
The package is publicly available on github: https://grenaud.github.io/gargammel/ and released under the GPL.

Supplementary information
Supplementary data are available at Bioinformatics online.
PhenoCurve: capturing dynamic phenotype-environment relationships using phenomics data
Authors: Yang Yifan , Xu Lei , Feng Zheyun , Cruz Jeffrey A , Savage Linda J , Kramer David M , Chen Jin 
Published: October 2016

AbstractMotivationPhenomics is essential for understanding the mechanisms that regulate or influence growth, fitness, and development. Techniques have been developed to conduct high-throughput large-scale phenotyping on animals, plants and humans, aiming to bridge the gap between genomics, gene functions and traits. Although new developments in phenotyping techniques are exciting, we are limited by the tools to analyze fully the massive phenotype data, especially the dynamic relationships between phenotypes and environments.ResultsWe present a new algorithm called PhenoCurve, a knowledge-based curve fitting algorithm, aiming to identify the complex relationships between phenotypes and environments, thus studying both values and trends of phenomics data. The results on both real and simulated data showed that PhenoCurve has the best performance among all the six tested methods. Its application to photosynthesis hysteresis pattern identification reveals new functions of core genes that control photosynthetic efficiency in response to varying environmental conditions, which are critical for understanding plant energy storage and improving crop productivity.Availability and ImplementationSoftware is available at phenomics.uky.edu/PhenoCurveSupplementary informationSupplementary data are available at Bioinformatics online.
BP Piscium: its flaring disc imaged with SPHERE/ZIMPOL
Authors: de Boer J. , Girard J. H. , Canovas H. , Min M. , Sitko M. , Ginski C. , Jeffers S. V. , Mawet D. , Milli J. , Rodenhuis M. , Snik F. , Keller C. U. 
Published: October 2016

Abstract
Whether BP Piscium (BP Psc) is either a pre-main sequence T Tauri star at d ≈ 80 pc, or a post-main sequence G giant at d ≈ 300 pc is still not clear. As a first-ascent giant, it is the first to be observed with a molecular and dust disc. Alternatively, BP Psc would be among the nearest T Tauri stars with a protoplanetary disc (PPD). We investigate whether the disc geometry resembles typical PPDs, by comparing polarimetric images with radiative transfer models. Our Very Large Telescope/Spectro-Polarimetric High-contrast Exoplanet REsearch (SPHERE)/Zurich IMaging Polarimeter (ZIMPOL) observations allow us to perform polarimetric differential imaging, reference star differential imaging, and Richardson–Lucy deconvolution. We present the first visible light polarization and intensity images of the disc of BP Psc. Our deconvolution confirms the disc shape as detected before, mainly showing the southern side of the disc. In polarized intensity the disc is imaged at larger detail and also shows the northern side, giving it the typical shape of high-inclination flared discs. We explain the observed disc features by retrieving the large-scale geometry with mcmax radiative transfer modelling, which yields a strongly flared model, atypical for discs of T Tauri stars.
Spectral Ripple Discrimination in Normal-Hearing Infants
Authors: Horn David L. , Won Jong Ho , Rubinstein Jay T. , Werner Lynne A. 
Published: October 2016

Objectives:
Spectral resolution is a correlate of open-set speech understanding in postlingually deaf adults and prelingually deaf children who use cochlear implants (CIs). To apply measures of spectral resolution to assess device efficacy in younger CI users, it is necessary to understand how spectral resolution develops in normal-hearing children. In this study, spectral ripple discrimination (SRD) was used to measure listeners’ sensitivity to a shift in phase of the spectral envelope of a broadband noise. Both resolution of peak to peak location (frequency resolution) and peak to trough intensity (across-channel intensity resolution) are required for SRD.

Design:
SRD was measured as the highest ripple density (in ripples per octave) for which a listener could discriminate a 90° shift in phase of the sinusoidally-modulated amplitude spectrum. A 2 × 3 between-subjects design was used to assess the effects of age (7-month-old infants versus adults) and ripple peak/trough “depth” (10, 13, and 20 dB) on SRD in normal-hearing listeners (experiment 1). In experiment 2, SRD thresholds in the same age groups were compared using a task in which ripple starting phases were randomized across trials to obscure within-channel intensity cues. In experiment 3, the randomized starting phase method was used to measure SRD as a function of age (3-month-old infants, 7-month-old infants, and young adults) and ripple depth (10 and 20 dB in repeated measures design).

Results:
In experiment 1, there was a significant interaction between age and ripple depth. The infant SRDs were significantly poorer than the adult SRDs at 10 and 13 dB ripple depths but adult-like at 20 dB depth. This result is consistent with immature across-channel intensity resolution. In contrast, the trajectory of SRD as a function of depth was steeper for infants than adults suggesting that frequency resolution was better in infants than adults. However, in experiment 2 infant performance was significantly poorer than adults at 20 dB depth suggesting that variability of infants’ use of within-channel intensity cues, rather than better frequency resolution, explained the results of experiment 1. In experiment 3, age effects were seen with both groups of infants showing poorer SRD than adults but, unlike experiment 1, no significant interaction between age and depth was seen.

Conclusions:
Measurement of SRD thresholds in individual 3 to 7-month-old infants is feasible. Performance of normal-hearing infants on SRD may be limited by across-channel intensity resolution despite mature frequency resolution. These findings have significant implications for design and stimulus choice for applying SRD for testing infants with CIs. The high degree of variability in infant SRD can be somewhat reduced by obscuring within-channel cues.
Which Models Can I Use to Predict Adult ICU Length of Stay? A Systematic Review*
Authors: Verburg Ilona Willempje Maria , Atashi Alireza , Eslami Saeid , Holman Rebecca , Abu-Hanna Ameen , de Jonge Everet , Peek Niels , de Keizer Nicolette Fransisca 
Published: October 2016

Objective:
We systematically reviewed models to predict adult ICU length of stay.

Data Sources:
We searched the Ovid EMBASE and MEDLINE databases for studies on the development or validation of ICU length of stay prediction models.

Study Selection:
We identified 11 studies describing the development of 31 prediction models and three describing external validation of one of these models.

Data Extraction:
Clinicians use ICU length of stay predictions for planning ICU capacity, identifying unexpectedly long ICU length of stay, and benchmarking ICUs. We required the model variables to have been published and for the models to be free of organizational characteristics and to produce accurate predictions, as assessed by R2 across patients for planning and identifying unexpectedly long ICU length of stay and across ICUs for benchmarking, with low calibration bias. We assessed the reporting quality using the Checklist for Critical Appraisal and Data Extraction for Systematic Reviews of Prediction Modelling Studies.

Data Synthesis:
The number of admissions ranged from 253 to 178,503. Median ICU length of stay was between 2 and 6.9 days. Two studies had not published model variables and three included organizational characteristics. None of the models produced predictions with low bias. The R2 was 0.05–0.28 across patients and 0.01–0.64 across ICUs. The reporting scores ranged from 49 of 78 to 60 of 78 and the methodologic scores from 12 of 22 to 16 of 22.

Conclusion:
No models completely satisfy our requirements for planning, identifying unexpectedly long ICU length of stay, or for benchmarking purposes. Physicians using these models to predict ICU length of stay should interpret them with reservation.
INTRAVITREAL DEXAMETHASONE IMPLANT AS ADJUVANT TREATMENT FOR BEVACIZUMAB- AND RANIBIZUMAB-RESISTANT NEOVASCULAR AGE-RELATED MACULAR DEGENERATION
Authors: Barikian Anita , Salti Haytham , Safar Ammar , Mahfoud Ziyad R. , Bashshur Ziad F. 
Published: October 2016

Purpose:
To study the benefit of intravitreal dexamethasone implant in the management of neovascular age-related macular degeneration resistant to bevacizumab and ranibizumab.

Methods:
Patients with persistent macular fluid on optical coherence tomography despite monthly treatment with at least three consecutive bevacizumab injections followed by at least three ranibizumab injections were prospectively enrolled. A single dexamethasone implant was administered followed by intravitreal ranibizumab 1 week later. Ranibizumab was continued afterward on an as-needed basis. Main outcomes were improvement in central retinal thickness and best-corrected visual acuity.

Results:
Nineteen patients (19 eyes) were enrolled. There was no significant change in best-corrected visual acuity over 6 months. Greatest reduction in mean central retinal thickness, from 295.2 μm to 236.2 μm, occurred 1 month after dexamethasone implant (P < 0.0001). By Month 6, mean central retinal thickness was 287.3 μm (P = 0.16). Eyes with only intraretinal fluid (13 eyes) achieved a fluid-free macula. Eyes with predominantly subretinal fluid (6 eyes) did not improve central retinal thickness and continued monthly ranibizumab. Mean baseline intraocular pressure was 13.2 mmHg, which peaked at 15.6 mmHg by Month 2 (P = 0.004).

Conclusion:
Intravitreal dexamethasone implant improved only macular intraretinal fluid in eyes with neovascular age-related macular degeneration resistant to bevacizumab and ranibizumab. However, this treatment had a limited duration.