bluuebunny/crossref_metadata_2025_split huggingface dataset:
Fabrication of Y2O3 microspheres by homogeneous precipitation method
Authors: Song Li , Li Junwei , Zhang Min , Zhang Baohang , Wang Jiaxin , Li Zhehui 
Published: December 2016

Y2O3 microspheres were obtained via homogeneous precipitation method. Y2O3 microspheres with different sizes and morphologies were prepared by adjusting the reaction temperature, the concentration of ytterbium nitrate and urea (H2NCONH2), and the amount and species of surfactants. The structure and morphology of the as‐obtained Y2O3 were analysed by using X‐ray diffraction, scanning electron microscopy and transmission electron microscopy, and the results showed that the sample showed the optimal microscopy when it was prepared at 80°C with the concentration of ytterbium nitrate, H2NCONH2 and betaine fixed at 0.01 M, 0.04 M and 4 g/l, respectively. Moreover, the as‐prepared samples were uniform and smooth‐surfaced.
HNTs‐templated preparation of carbon nanorods by nanocasting method
Authors: Liu Zan , Cheng Zhi‐Lin , Liu Ying‐Ying 
Published: December 2016

Carbon nanorods (CNRs) have been attracting increasing interest because of their potential applications in high‐performance nanoscale materials and electronic devices. Among the many preparation methods, the nanocasting method via inorganic template materials exhibited a controllable and facile feature. This work was to present a novel preparation of CNRs through the nanocasting method using halloysite nanotubes (HNTs) as the template and polyvinyl alcohol (PVA) as the nanocasting carbon source. For the sake of PVA nanocasted in the hollow structure of HNTs, we adopted the repeated soakage method. The forming process and structure of CNRs were revealed by XRD, FT‐IR, SEM, TEM, SAED XPS, Raman and Brunner–Emmet–Teller (BET) characterisation techniques. The results showed that the as‐obtained CNRs with the rod‐like structure had a high specific surface area of ca. 284 m2/g and exhibited typical mesoporous features.
The cleavage site preference of the porcine pepsin on the N-terminal α1 chain of bovine type I collagen: a focal analysis with mass spectrometry
Authors: Qian Jun , Ito Shinji , Satoh Junko , Geng Hongmin , Tanaka Keisuke , Hattori Shunji , Kojima Kenji , Takita Teisuke , Yasukawa Kiyoshi 
Published: December 2016

Abstract
Bovine type I collagen consists of two α1 and one α2 chains, containing the internal triple helical regions and the N- and C-terminal telopeptides. In industries, it is frequently digested with porcine pepsin to produce a triple helical collagen without the telopeptides. However, the digestion mechanism is not precisely understood. Here, we performed a mass spectrometric analysis of the pepsin digest of the N-terminal telopeptide pQLSYGYDEKSTGISVP (1–16) in the α1 chain. When purified collagen was digested, pQLSYGY (1–6) and pQLSYGYDEKSTG (1–12) were identified, while DEKSTG (7–12) was not. When the N-terminal telopeptide mimetic synthetic peptide pQLSK(MOCAc)GYDEKSTGISK(Dnp)P-NH2 was digested, pQLSK(MOCAc)GYDEKSTG (1–12) and ISK(Dnp)P-NH2 (13−16) were readily identified, pQLSK(MOCAc)GY (1−6) and DEKSTGISK(Dnp)P-NH2 (7−16) were weakly detected, and DEKSTG (7–12) was hardly identified. These results suggest that pepsin preferentially cleaves Tyr6–Asp7 and less preferentially Gly12–Ile13. They also suggest that the former cleavage requires native collagen structure, while the latter cleavage does not.
Algorithm sensitivity analysis and parameter tuning for tissue image segmentation pipelines
Authors: Teodoro George , Kurç Tahsin M , Taveira Luís F R , Melo Alba C M A , Gao Yi , Kong Jun , Saltz Joel H 
Published: December 2016

Abstract

Motivation
Sensitivity analysis and parameter tuning are important processes in large-scale image analysis. They are very costly because the image analysis workflows are required to be executed several times to systematically correlate output variations with parameter changes or to tune parameters. An integrated solution with minimum user interaction that uses effective methodologies and high performance computing is required to scale these studies to large imaging datasets and expensive analysis workflows.

Results
The experiments with two segmentation workflows show that the proposed approach can (i) quickly identify and prune parameters that are non-influential; (ii) search a small fraction (about 100 points) of the parameter search space with billions to trillions of points and improve the quality of segmentation results (Dice and Jaccard metrics) by as much as 1.42× compared to the results from the default parameters; (iii) attain good scalability on a high performance cluster with several effective optimizations.

Conclusions
Our work demonstrates the feasibility of performing sensitivity analyses, parameter studies and auto-tuning with large datasets. The proposed framework can enable the quantification of error estimations and output variations in image segmentation pipelines.

Availability and Implementation
Source code: https://github.com/SBU-BMI/region-templates/.

Supplementary information
Supplementary data are available at Bioinformatics online.
dAPE: a web server to detect homorepeats and follow their evolution
Authors: Mier Pablo , Andrade-Navarro Miguel A 
Published: December 2016

Abstract

Summary
Homorepeats are low complexity regions consisting of repetitions of a single amino acid residue. There is no current consensus on the minimum number of residues needed to define a functional homorepeat, nor even if mismatches are allowed. Here we present dAPE, a web server that helps following the evolution of homorepeats based on orthology information, using a sensitive but tunable cutoff to help in the identification of emerging homorepeats.

Availability and Implementation
dAPE can be accessed from http://cbdm-01.zdv.uni-mainz.de/∼munoz/polyx.

Supplementary information
Supplementary data are available at Bioinformatics online.
Improving Tuberculosis (TB) and Human Immunodeficiency Virus (HIV) Treatment Monitoring in South Africa: Evaluation of an Advanced TB/HIV Course for Healthcare Workers
Authors: Galagan Sean , Jed Suzanne , Sumitani Jeri , Gilvydis Jennifer M. , Bakor Albert , Cooke Richard , Naidoo Evasen , Winters Debra , Weaver Marcia R. 
Published: December 2016

Abstract

Background
South Africa has dual epidemics of human immunodeficiency virus (HIV) and tuberculosis (TB). Nurse-focused training was combined with onsite mentoring for nurses to improve HIV and TB care. A pre-/postevaluation was conducted in 3 districts in South Africa to assess the effects of the course on clinical patient monitoring and integration of TB and HIV care.

Methods
Two cross-sectional, unmatched samples of patient charts at 76 primary healthcare facilities were collected retrospectively in 2014 to evaluate the impact of training on treatment monitoring. Proportions of HIV patients receiving a viral load test 6 months after initiating antiretroviral therapy (ART) and TB patients receiving end of intensive phase sputum testing were compared pre- and posttraining. Analysis of creatinine clearance testing and integration of TB and HIV care were also performed.

Results
Data were analyzed from 1074 pretraining and 1048 posttraining records among patients initiating ART and from 1063 pretraining and 1008 posttraining among patients initiating TB treatment. Documentation of a 6-month viral load test was 36.3%, and a TB test at end of intensive phase was 70.7%, and neither increased after training. Among patients with a viral load test, the percentage with viral load less than 50 copies/mL increased from 48.6% pretraining compared with 64.2% posttraining (P = .001). Integration of TB and HIV care such as isoniazid preventive therapy increased significantly.

Conclusions
The primary outcome measures did not change after training. However, the evaluation documented many other improvements in TB and HIV care that may have been supported by the course.
Isoflurane Sedation on the ICU in Cardiac Arrest Patients Treated With Targeted Temperature Management: An Observational Propensity-Matched Study
Authors: Krannich Alexander , Leithner Christoph , Engels Martin , Nee Jens , Petzinka Victor , Schröder Tim , Jörres Achim , Kruse Jan , Storm Christian 
Published: December 2016

Objective:
Targeted temperature management after cardiac arrest requires deep sedation to prevent shivering and discomfort. Compared to IV sedation, volatile sedation has a shorter half-life and thus may allow more rapid extubation and neurologic assessment.

Design:
Observational analysis of clinical data.

Setting:
University hospital, medical ICU.

Patients:
Four hundred thirty-two cardiac arrest survivors underwent targeted temperature management; of those, 110 were treated with volatile sedation using an anesthetic conserving device and isoflurane, and 322 received standard IV sedation.

Intervention:
No intervention.

Measurement and Main Results:
A matched pairs analysis revealed that time on ventilator (difference of median, 98.5 hr; p = 0.003) and length of ICU stay (difference of median, 4.5 d; p = 0.006) were significantly shorter in patients sedated with isoflurane when compared with IV sedation although no differences in neurologic outcome (45% of patients with cerebral performance category 1–2 in both groups) were observed. Significant hypercapnia occurred more frequently during anesthetic conserving device use (6.4% vs 0%; p = 0.021).

Conclusions:
Volatile sedation is feasible in cardiac arrest survivors. Prospective controlled studies are necessary to confirm the beneficial effects on duration of ventilation and length of ICU stay observed in our study. Our data argue against a major effect on neurologic outcome. Close monitoring of Paco
2 is necessary during sedation via anesthetic conserving device.
Food and Drug Administration Efforts to Mitigate Contact Lens Discomfort
Authors: Hampton Denise , Green Joffre Angelo , Robboy Marc , Eydelman Malvina 
Published: December 2016

Abstract:
The premarket review of contact lenses and accessories by the FDA involves the assessment of nonclinical and clinical information in support of clearance or approval of marketing applications. The review process for these medical devices, including attributes, which may contribute to comfort for lens wearers, is summarized, as are mechanisms by which FDA continues to assess and improve recommendations through the review process and through collaboration with external entities.
Characterization of the Corneal Subbasal Nerve Plexus in Limbal Stem Cell Deficiency
Authors: Chuephanich Pichaya , Supiyaphun Chantaka , Aravena Carolina , Bozkurt Tahir Kansu , Yu Fei , Deng Sophie X. 
Published: December 2016

Purpose:
To quantify the changes in the subbasal nerve plexus in patients with limbal stem cell deficiency (LSCD) using in vivo laser scanning confocal microscopy.

Methods:
In this retrospective cross-sectional comparative study, confocal images of 51 eyes of 37 patients with LSCD collected between 2010 and 2015 by the Heidelberg Retina Tomograph III Rostock Corneal Module Confocal Microscope were analyzed. Two independent observers evaluated the scans of the central cornea. Seventeen normal eyes of 13 subjects served as controls. Total subbasal nerve density (SND), density of long nerves (ie, nerves 200 μm or longer), and the degree of tortuosity were quantified.

Results:
The mean (±SD) total SND and long nerve density were 48.0 ± 34.2 and 9.7 ± 10.9 nerves/mm2, respectively, in all eyes with LSCD and 97.3 ± 29.9 and 35.3 ± 25.3 nerves/mm2, respectively, in eyes of the control group (P < 0.001 for both comparisons). Compared with SND in control subjects, SND was reduced by 34.9% in the early stage, 54.0% in the intermediate stage, and 73.5% in the late stage of LSCD. The degrees of nerve tortuosity were significantly greater in patients with LSCD than in control subjects and differed among the early, intermediate, and late stages of LSCD. Reductions in total SND and long nerve density were positively correlated with the severity of LSCD.

Conclusions:
Reductions in total SND and long nerve density were accompanied by increases in nerve tortuosity in eyes with LSCD. These parameters could be used as quantifiable measures of LSCD severity.
Russian Keratoprosthesis in Stevens–Johnson Syndrome
Authors: Ma Xiao , Xiang Ran , Meng Xiaoli , Qin Limin , Wu Ying , Tain Lei , Jiang Yanming , Huang Yifei , Wang Liqing 
Published: December 2016

Purpose:
To evaluate the efficacy and safety of Moscow Eye Microsurgery Complex in Russia (MICOF) keratoprosthesis (KPro) implantation in patients with Stevens–Johnson syndrome (SJS).

Methods:
This was a retrospective case series. Fourteen eyes of 13 patients with SJS underwent KPro implantation at the Chinese People's Liberation Army General Hospital between April 1, 2000, and December 24, 2014. The visual outcome, KPro retention rate, and incidence of postoperative complications and their management were recorded and investigated.

Results:
The mean age and follow-up duration were 61.5 ± 17.3 years (range: 27–87 yrs) and 62 ± 39.1 months (range: 13–144 mo). Thirteen eyes (92.9%) achieved a best-corrected visual acuity of 20/200 or better, and 8 eyes (57.1%) achieved a best-corrected visual acuity of 20/40 or better after surgery. However, 71.4% (10/14) experienced visual decline because of different postoperative complications. Common complications included corneal melting, glaucoma, vitritis, superficial tissue overgrowth, and retroprosthetic membrane, and the incidence of these complications was 71.4%, 28.6%, 35.7%, 14.3%, and 28.6%, respectively. After repair and autoauricular cartilage reinforcement, all cases had stable anatomical retention at the last visit.

Conclusions:
The MICOF KPro improved vision of patients with SJS, but lifelong surveillance is necessitated because of a high rate of postoperative complications. Corneal melting was the main reason for KPro failure. Infectious endophthalmitis and glaucoma were the main risk factors for visual loss.
Clinical Findings of Anterior Segment Spectral Domain Optical Coherence Tomography Images in Cytomegalovirus Corneal Endotheliitis
Authors: Kobayashi Reiko , Hashida Noriyasu , Soma Takeshi , Koh Shizuka , Miki Atsuya , Usui Shinichi , Maeda Naoyuki , Nishida Kohji 
Published: December 2016

Purpose:
To evaluate the morphological characteristics of posterior corneal regions including keratic precipitates in eyes with cytomegalovirus (CMV) corneal endotheliitis using anterior segment spectral domain optical coherence tomography (SD-OCT).

Methods:
Thirteen eyes of 13 patients with polymerase chain reaction–proven CMV corneal endotheliitis were included in this study. Slit-lamp images and anterior segment SD-OCT images of the posterior cornea were obtained to analyze the clinical characteristics of corneal structures and keratic precipitates. Morphological changes in the posterior cornea throughout the course of an antiviral treatment were also investigated.

Results:
Anterior SD-OCT images showed protruding structures at the posterior cornea. These protruding structures exhibited dendritic, dome-shaped, quadrangular, or saw-tooth appearance, and reflectivity of these structures was high. Reflectivity of posterior corneal images including the endothelium and deep stromal corneal regions were also high (76.9%). Because corneal inflammation and corneal edema improved, the protruding structures and high-intensity regions of posterior corneal images were resolved after a course of antiviral treatment.

Conclusions:
The anterior segment SD-OCT examination represents a useful noninvasive alternative to diagnose and monitor CMV corneal endotheliitis.
The “Facemask Blinder”
Authors: Tsze Daniel S. , Woodward Hilary A. 
Published: December 2016

Abstract
We present the case of a 7-year-old boy with a forehead laceration that required suture repair. The child was anxious and uncooperative, and the initial plan was to administer intranasal midazolam to facilitate the repair. However, a facemask blinder was first implemented as a visual barrier to block the child’s view of any anxiety-provoking stimuli and appeared to improve the child’s cooperation with the procedure. Intranasal midazolam was not administered, and the laceration was cleaned and repaired successfully. In conjunction with adequate local anesthesia and distraction techniques, the facemask blinder helped to facilitate the completion of the laceration repair without the need for any physical restraint or pharmacologic anxiolysis or sedation.
PathogenicASXL1somatic variants in reference databases complicate germline variant interpretation for Bohring-Opitz Syndrome
Authors: Carlston Colleen M. , O’Donnell-Luria Anne H. , Underhill Hunter R. , Cummings Beryl B. , Weisburd Ben , Minikel Eric V. , Birnbaum Daniel P. ,   Exome Aggregation Consortium, Tvrdik Tatiana , MacArthur Daniel G. , Mao Rong 
Published: December 2016

ABSTRACTThe interpretation of genetic variants identified during clinical sequencing has come to rely heavily on reference population databases such as the Exome Aggregation Consortium (ExAC). Genuinely pathogenic variants, particularly in genes associated with severe autosomal dominant conditions, are assumed to be absent or extremely rare in these databases. Clinical exome sequencing of a six-year-old female patient with seizures, global developmental delay, dysmorphic features and failure to thrive identified anASXL1variant that was previously reported as causative of Bohring-Opitz syndrome (BOS). Surprisingly, the variant was observed seven times in the ExAC database, presumably in individuals without BOS. Although the BOS phenotype matched the presentation of the patient, the presence of the variant in reference population databases introduced ambiguity in result interpretation. Interrogation of the literature revealed that acquired somatic mosaicism ofASXL1variants (including known pathogenic variants) during hematopoietic clonal expansion may be concomitant with aging in healthy individuals. We examined all high qualityASXL1predicted truncating variant calls in the ExAC database and determined the majority could be attributed to this phenomenon. Failure to consider somatic mosaicism may lead to the inaccurate assumption that conditions like Bohring-Opitz syndrome have reduced penetrance, or the misclassification of potentially pathogenic variants.
Recent evolution of extreme cestode growth suppression by a vertebrate host
Authors: Weber Jesse N. , Steinel Natalie C. , Chuan Shim Kum , Bolnick Daniel I. 
Published: December 2016

AbstractParasites can be a major cause of natural selection on hosts, which consequently evolve a variety of strategies to avoid, eliminate, or tolerate infection. When ecologically similar host populations present disparate infection loads, this natural variation can reveal immunological strategies underlying adaptation to infection and population divergence. For instance, the tapewormSchistocephalus soliduspersistently infects between 0% to 80% of threespine stickleback (Gasterosteus aculeatus) in lakes on Vancouver Island. To test whether these heterogeneous infection rates are due to evolved differences in immunity, we experimentally exposed lab-reared fish from high-and low-infection populations, which are not known to differ in natural exposure risk, to controlled doses ofSchistocephalus.We observed heritable between-population differences in several immune traits: fish from the naturally uninfected population initiated a stronger granulocyte response toSchistocephalusinfection, and their granulocytes constitutively generated threefold more reactive oxygen species (ROS). Despite these immunological differences,Schistocephaluswas equally successful at establishing initial infections in both host populations. However, the low-infection fish dramatically suppressed tapeworm growth relative to high-infection fish, and parasite size was intermediate in F1 hybrid hosts. Our results show that stickleback recently evolved heritable variation in their capacity to suppress helminth growth. Comparative data from many from natural populations indicate that growth suppression is widespread but not universal and, when present, is associated with reduced infection prevalence. Host suppression of helminth somatic growth may be an important immune strategy that aids in parasite clearance, or in mitigating the fitness costs of persistent infection.SignificanceLarge parasites remain a persistent source of morbidity and mortality in humans, domesticated animals, and wildlife. Hosts are subject to strong natural selection to eliminate or tolerate these parasite infections. Here, we document the recent evolution of a striking form of resistance by a vertebrate host (threespine stickleback) against its cestode parasite (Schistocephalus solidus).After Pleistocene glacial retreat, marine stickleback colonized freshwater lakes, encounteredSchistocephalus, and evolved varying levels of resistance to it. We show that a heavily-and a rarely-infected population of stickleback have similar resistance toSchistocephaluscolonization, but rarely-infected fish suppress parasite growth by orders of magnitude. These populations represent ends of a natural continuum of cestode growth suppression, which is associated with reduced infection prevalence.
Lysine methyltransferase SETD6 modifies histones and non-histone proteins
Authors: Binda Olivier 
Published: December 2016

ABSTRACTAlthough central to regulating the access to genetic information, most lysine methyltransferases remain poorly characterised relative to other family of enzymes. Herein, we report new substrates for the lysine methyltransferase SETD6. Based on the SETD6- catalysed site on the histone variant H2AZ, we identified similar sequences in the canonical histones H2A, H3, and H4 that are modified by SETD6in vitro, and putative non-histone substrates. We herein expend the repertoire of substrates for methylation by SETD6.
C. elegansdiscriminate colors without eyes or opsins
Authors: Ghosh D. Dipon , Jin Xin , Nitabach Michael 
Published: December 2016

AbstractHere we establish that, contrary to expectations,Caenorhabditis elegansnematode worms possess a color discrimination system despite lacking any opsin or other known visible light photoreceptor genes. We found that white light guidesC. elegansforaging decisions away from harmful bacteria that secrete a blue pigment toxin. Absorption of amber light by this blue pigment toxin alters the color of light sensed by the worm, and thereby triggers an increase in avoidance. By combining narrow-band blue and amber light sources, we demonstrated that detection of the specific blue:amber ratio by the worm guides its foraging decision. These behavioral and psychophysical studies thus establish the existence of a color detection system that is distinct from those of other animals.