bluuebunny/crossref_metadata_2025_split huggingface dataset:
GeneCodeq: quality score compression and improved genotyping using a Bayesian framework
Authors: Greenfield Daniel L. , Stegle Oliver , Rrustemi Alban 
Published: June 2016

Abstract
Motivation: The exponential reduction in cost of genome sequencing has resulted in a rapid growth of genomic data. Most of the entropy of short read data lies not in the sequence of read bases themselves but in their Quality Scores—the confidence measurement that each base has been sequenced correctly. Lossless compression methods are now close to their theoretical limits and hence there is a need for lossy methods that further reduce the complexity of these data without impacting downstream analyses.
Results: We here propose GeneCodeq, a Bayesian method inspired by coding theory for adjusting quality scores to improve the compressibility of quality scores without adversely impacting genotyping accuracy. Our model leverages a corpus of k-mers to reduce the entropy of the quality scores and thereby the compressibility of these data (in FASTQ or SAM/BAM/CRAM files), resulting in compression ratios that significantly exceeds those of other methods. Our approach can also be combined with existing lossy compression schemes to further reduce entropy and allows the user to specify a reference panel of expected sequence variations to improve the model accuracy. In addition to extensive empirical evaluation, we also derive novel theoretical insights that explain the empirical performance and pitfalls of corpus-based quality score compression schemes in general. Finally, we show that as a positive side effect of compression, the model can lead to improved genotyping accuracy.
Availability and implementation: GeneCodeq is available at: github.com/genecodeq/eval
Contact: dan@petagene.com
Supplementary information: Supplementary data are available at Bioinformatics online.
J-GEM follow-up observations to search for an optical counterpart of the first gravitational wave source GW150914
Authors: Morokuma Tomoki , Tanaka Masaomi , Asakura Yuichiro , Abe Fumio , Tristram Paul J. , Utsumi Yousuke , Doi Mamoru , Fujisawa Kenta , Itoh Ryosuke , Itoh Yoichi , Kawabata Koji S. , Kawai Nobuyuki , Kuroda Daisuke , Matsubayashi Kazuya , Motohara Kentaro , Murata Katsuhiro L. , Nagayama Takahiro , Ohta Kouji , Saito Yoshihiko , Tamura Yoichi , Tominaga Nozomu , Uemura Makoto , Yanagisawa Kenshi , Yatsu Yoichi , Yoshida Michitoshi 
Published: June 2016

AbstractWe present our optical follow-up observations to search for an electromagnetic counterpart of the first gravitational wave source GW150914 in the framework of the Japanese collaboration for Gravitational wave ElectroMagnetic follow-up (J-GEM), which is an observing group utilizing optical and radio telescopes in Japan, as well as in New Zealand, China, South Africa, Chile, and Hawaii. We carried out a wide-field imaging survey with the Kiso Wide Field Camera (KWFC) on the 1.05 m Kiso Schmidt telescope in Japan and a galaxy-targeted survey with Tripole5 on the B&C 61 cm telescope in New Zealand. Approximately 24 deg2 regions in total were surveyed in i-band with KWFC and 18 nearby galaxies were observed with Tripole5 in g-, r-, and i-bands 4–12 days after the gravitational wave detection. Median 5 σ depths are i ∼ 18.9 mag for the KWFC data and g ∼ 18.9 mag, r ∼ 18.7 mag, and i ∼ 18.3 mag for the Tripole5 data. The probability for a counterpart to be in the observed area is 1.2% in the initial skymap and 0.1% in the final skymap. We do not find any transient source associated to an external galaxy with spatial offset from its center, which is consistent with the local supernova rate.
Histone Deacetylase Inhibition Protects Mice Against Lethal Postinfluenza Pneumococcal Infection
Authors: Yagi Kazuma , Ishii Makoto , Namkoong Ho , Fujii Hideki , Asami Takahiro , Suzuki Shoji , Asakura Takanori , Mizoguchi Kosuke , Kamo Tetsuro , Tasaka Sadatomo , Iwata Satoshi , Kunkel Steven L. , Hasegawa Naoki , Betsuyaku Tomoko 
Published: June 2016

Objectives:
Secondary bacterial pneumonia following influenza virus infection is associated with high mortality, but the mechanism is largely unknown. Epigenetic gene regulation appears to play key roles in innate and adaptive immunity. We hypothesized that histone acetylation, a major epigenetic mechanism associated with transcriptionally active chromatin, might contribute to the poor outcome of postinfluenza pneumonia.

Design:
Prospective experimental study.

Setting:
University research laboratory.

Subjects:
C57BL/6 male mice.

Interventions:
Mice were infected intranasally with 1.0 × 104 colony-forming units of Streptococcus pneumoniae, 7 days after intranasal inoculation with five plaque-forming units of influenza virus A/H1N1/PR8/34. The mice were intraperitoneally injected with the histone deacetylase inhibitor trichostatin A (1 mg/kg) or vehicle once a day from 1 hour after pneumococcal infection throughout the course of the experiment. The primary outcome was survival rate.

Measurements and Main Results:
Trichostatin A significantly suppressed histone deacetylase activity and significantly improved the survival rate of mice (56.3%) after postinfluenza pneumococcal infection when compared with vehicle-treated mice (20.0%), which was associated with a significant decrease in the total cell count of the bronchoalveolar lavage fluid. The interleukin-1β level in the serum and the number of natural killer cells in the lungs were significantly lower in the trichostatin A-treated group.

Conclusions:
The histone deacetylase inhibitor trichostatin A protects mice against postinfluenza pneumonia possibly through multiple factors, including decreasing local cell recruitment into the lungs and suppressing systemic inflammation.
A Model of Consultation in Prostate Cancer Care
Authors: Paterson Catherine , Nabi Ghulam 
Published: June 2016

Background:
There has been an evolution of various consultation models in the literature. Men affected by prostate cancer can experience a range of unmet supportive care needs. Thus, effective consultations are paramount in the delivery of supportive care to optimize tailored self-management plans at the individual level of need.

Objective:
The aim of this study is to critically appraise existing models of consultation and make recommendations for a model of consultation within the scope of clinical practice for prostate cancer care.

Methods:
A systematic review was conducted according to the Preferred Reporting Items for Systematic Reviews and Meta-Analyses Statement Guidelines. Electronic databases were searched using a wide range of keywords and free text items to increase the sensitivity and inclusiveness of the searches. Findings were integrated in a narrative synthesis.

Results:
A total of 1829 articles were retrieved and 17 papers were included. Beneficial features ranged across a number of models that included a person-centered consultation, shared management plans, and safety netting. None of the reviewed models of consultation are suitable for use in prostate cancer care because of a range of limitations and the clinical context in which models were developed. A Cancer Care Consultation Model was informed from critical appraisal of the evidence and expert clinical and service user comment.

Conclusion:
Further research is needed to empirically test consultation models in routine clinical practice, specifically for advanced cancer specialist nurses.

Implications for Practice:
The Prostate Cancer Model of Consultation can be used to structure clinical consultations to target self-management care plans at the individual level of need over the cancer care continuum.
A Pilot Study of Proinflammatory Cytokines and Fatigue in Women With Breast Cancer During Chemotherapy
Authors: Raudonis Barbara M. , Kelley Ingrid H. , Rowe Nancy , Ellis Jenny 
Published: June 2016

Background:
Fatigue remains a prevalent, persistent, and debilitating side effect of chemotherapy for stage I and II breast cancer patients. Severity of fatigue varies among patients. Evidence suggests that proinflammatory cytokines contribute to the development of fatigue.

Objective:
The aim of this study is to investigate predictors of fatigue and cytokine levels in women undergoing chemotherapy for stage I or II breast cancer.

Methods:
Piper Fatigue Scales and blood samples for interleukin-6 (IL-6) and tumor necrosis factor-α (TNF-α) levels were collected at baseline and days 7, 14, and 21 for each chemotherapy cycle. Descriptive statistics, general linear mixed models, and graphic analysis were used to analyze the data.

Results:
The predominantly white convenience sample was composed of 11 women with stage I or II breast cancer who were 37 to 72 years old (mean, 52 years). Predictors of fatigue were type of chemotherapy drugs, time, and IL-6 levels. A predictor of IL-6 and TNF-α levels was whether chemotherapy was administered at the visit. Type of chemotherapy significantly predicted TNF-α levels. Fatigue patterns were characterized by chaotic pattern of peaks and troughs unique to each woman.

Conclusions:
Women with stage I and II breast cancer experienced variability in the severity of fatigue and levels of IL-6 and TNF-α throughout their treatment trajectories. The presence and role of genetic variants related to cancer-related fatigue may explain the individual variation and warrant further research.

Implications for Practice:
These findings highlight the importance of symptom assessments including fatigue at each clinic visit and individualized interventions throughout the cancer trajectory.
Arnica Ointment 10% Does Not Improve Upper Blepharoplasty Outcome: A Randomized, Placebo-Controlled Trial
Authors: van Exsel Denise C. E. , Pool Shariselle M. W. , van Uchelen Jeroen H. , Edens Mireille A. , van der Lei Berend , Melenhorst Wynand B. W. H. 
Published: June 2016

Background:
It has been suggested that arnica can reduce postoperative edema and ecchymosis associated with cosmetic surgical procedures and improve outcome. Despite a high incidence of arnica use among upper blepharoplasty patients, evidence to support its treatment effect is lacking. The authors performed a randomized, double-blind, placebo-controlled trial to investigate the efficacy of arnica ointment after upper blepharoplasty.

Methods:
One hundred thirty-six bilateral upper blepharoplasty patients were randomized between arnica ointment 10% and placebo ointment. In both study arms, one periorbital area was designated as the treatment side (either arnica or placebo ointment), and the contralateral side served as an untreated (no ointment) internal control. As the primary endpoint, the overall periorbital appearance as based on light photography and judged by a medical and nonmedical panel, was assessed after 3 days, 7 days, and 6 weeks. Secondary endpoints were swelling, ecchymosis, erythema, pain, and patient satisfaction with recovery and outcome.

Results:
There was no significant difference between arnica and placebo in overall judgment of periorbital appearance 3 days, 7 days, and 6 weeks after surgery. Furthermore, swelling, ecchymosis, erythema, pain, and patient satisfaction with recovery and outcome did not differ between arnica and placebo. Postoperative outcome in untreated eyelids was not different from eyelids treated with either arnica or placebo on any of the studied outcome measures.

Conclusion:
The authors’ study demonstrates that topical arnica ointment after upper blepharoplasty does not improve postoperative outcome.

CLINICAL QUESTION/LEVEL OF EVIDENCE:
Therapeutic, II.
Multisite Lymphaticovenular Bypass Using Supermicrosurgery Technique for Lymphedema Management in Lower Lymphedema Cases
Authors: Mihara Makoto , Hara Hisako , Tange Shuichi , Zhou Han Peng , Kawahara Mari , Shimizu Yohei , Murai Noriyuki 
Published: June 2016

Background:The impact of lymphaticovenous anastomosis on lymphedema has yet to be defined. The authors investigated the clinical evidence regarding the effectiveness of lymphaticovenous anastomosis in lower limb lymphedema.Methods:Eighty-four patients (162 limbs; 73 female and 11 male patients) with lower limb lymphedema who underwent multisite lymphaticovenous anastomosis in the authors’ clinic between August of 2010 and May of 2014 were included in this retrospective study. Lymphedema was diagnosed using lymphoscintigraphy and indocyanine green lymphography. All lymphaticovenous anastomoses were performed under local anesthesia. The lymphatic vessels that were identified were classified using the normal, ectasis, contraction, and sclerosis type (NECST) classification. Limb circumference, subjective symptoms, and frequency of cellulitis were evaluated.Results:The average patient age was 60 years (range, 24 to 94 years); mean postoperative follow-up period was 18.3 months (range, 6 to 51 months). The postoperative change rate in limb circumference indicated that 67 limbs (47.7 percent) were classified as improved, 35 (27.3 percent) were classified as stable, and 32 (25 percent) were classified as worse. Postoperative interview revealed improvement in subjective symptoms in 67 limbs (61.5 percent), no change in 38 (34.9 percent), and exacerbation in four (3.7 percent). The postoperative mean occurrence of cellulitis was decreased to 0.13 times per year compared with 0.89 preoperatively, which was statistically significant (p= 0.00084). Multiple regression analysis using the postanastomosis limb circumference and NECST classification confirmed the following results: change rate (percent) = −0.40 + (0.30 × N) + (−0.84 × E) + (0.22 × C) + (−0.61 × S).Conclusion:Lymphaticovenous anastomosis is effective for lower limb lymphedema, in point of limb circumference, subjective symptoms, and the frequency of cellulitis.CLINCAL QUESTION/LEVEL OF EVIDENCE:Therapeutic, IV.
Remote Ischemic Preconditioning Recipient Tissues Improves the Viability of Murine Fat Transfer
Authors: Gassman Andrew A. , Lewis Michael S. , Lee Justine C. 
Published: June 2016

Background:
Local ischemia before the development of recipient circulation may contribute to the highly variable long-term results of fat grafting. Remote ischemic preconditioning before adipose procurement augments the retention of fat grafts and limits subsequent liposclerosis. However, there is no literature examining what role remote ischemic preconditioning has on the fat graft recipient site.

Methods:
Subcutaneous adipose tissue from transgenic mice expressing green fluorescent protein/luciferase was injected into skin folds of wild-type mice. Donors and recipients experienced intermittent temporary hindlimb tourniquet application before harvest and transfer, respectively. The viability of the transferred tissue was examined over 28 days by luciferin bioluminescence and subsequent histologic analysis.

Results:
There was a difference in bioluminescence at days 0, 14, and 28. The remote ischemic preconditioning donor or recipient mouse–alone groups demonstrated an approximately 2- to 3-fold increase in bioluminescence. Donor and recipient remote ischemic preconditioning had a 9-fold increase in bioluminescence. Histologic analysis at 28 days confirmed the presence of donor adipocytes, and they were gradually replaced by recipient inflammation and scar tissue. However, the amount of interstitial fibrosis was substantially less in the remote ischemic preconditioning groups. These findings were more pronounced when remote ischemic preconditioning was used for both donor and recipient mice.

Conclusions:
Remote ischemic preconditioning has the ability to increase the viability of donor adipocytes and limit interstitial fibrosis. More specifically, remote ischemic preconditioning treatment of both donated adipose tissue and recipient wound beds demonstrates the greatest overall adipose cellular viability and native architecture.
Modified Great Toe Wraparound Flap with Preservation of Plantar Triangular Flap for Reconstruction of Degloving Injuries of the Thumb and Fingers: Long-Term Follow-Up
Authors: Shen Xiao Fang , Mi Jing Yi , Xue Ming Yu , Zhao Gang , Qiang Li , Zhou Xiao , Rui Yong Jun , Chim Harvey 
Published: June 2016

Background:
The purpose of this article is to report the authors’ experience with the use of the modified great toe wraparound flap with preservation of a plantar triangular flap for reconstructing degloving injuries of the thumb and fingers.

Methods:
Between 2007 and 2012, 31 patients underwent reconstruction with 37 flaps. Twenty-seven patients underwent reconstruction with 31 flaps for a degloved thumb and fingers, and four patients underwent reconstruction with six flaps for degloved fingers only. A modified great toe wraparound flap with second toe medial toe hemipulp flap on a common pedicle was used for reconstruction of degloved fingers in four patients. Twelve patients had long-term follow-up, with a mean duration of 5 years (range, 2 to 8 years).

Results:
All flaps survived. The contour of the reconstructed digits was similar to the contralateral one. In patients with long-term follow-up, mean two-point discrimination of reconstructed digits was 6.2 mm (range, 3 to 8 mm). Mean Disabilities of the Arm, Shoulder and Hand questionnaire score was 0.8 ± 1.0. Mean Michigan Hand Outcomes Questionnaire score was 87.3 ± 3.7. Mean Foot and Ankle Disability Index score was 95.5 ± 2.7. The width of the preserved plantar triangular flap expanded from 35 percent to 67 percent of the width of the great toe and completely covered the weight-bearing area.

Conclusions:
Reconstruction of degloved thumb and fingers with a modified great toe wraparound flap, preserving a plantar triangular flap, results in excellent contour and functional outcome. Donor-site morbidity in the foot was minimal.

CLINICAL QUESTION/LEVEL OF EVIDENCE:
Therapeutic, IV.
Google Glass in the Operating Room: The Plastic Surgeon’s Perspective
Authors: Sinkin Jeremy C. , Rahman Omar F. , Nahabedian Maurice Y. 
Published: June 2016

Summary:
New technologies and innovations are common in the delivery of modern health care. Google Glass is one such device gaining increased attention in medical specialties. The authors surveyed residents and attending physicians in the Department of Plastic Surgery, MedStar Georgetown University Hospital, on their experience using Google Glass in the operating room. Ease of use, quality of images, gaze disruption, and distraction during surgery were measured. Overall, subjects found the device to be comfortable and satisfying to wear and use during surgery to capture images of good quality. Despite some identified weaknesses, Google Glass is a unique technology with a promising plastic surgical application in the operating room.
Modified Lipoabdominoplasty: Updating Concepts
Authors: Ribeiro Ricardo Cavalcanti , Matos Wilson Novaes , Cruz Pedro Felipe Suárez 
Published: June 2016

Background:
Abdominoplasty is a commonly performed aesthetic surgical procedure worldwide, and one of the most frequently performed cosmetic surgical procedures in the United States. Classic abdominoplasty was merged with liposuction in the past decade to create a new technique—lipoabdominoplasty—that was proven to be safe and effective and that improves body contour. The authors have been using lipoabdominoplasty since 2003 with excellent outcomes; however, some details have been added to improve significant shortcomings, including the lack of treatment of the pubic area and flanks, the presence of a high-position scar and, sometimes, a bulging inferior abdomen.

Methods:
The authors retrospectively studied 348 patients who underwent lipoabdominoplasty with these related surgical improvements between January of 2010 and February of 2015. Improvements to the original surgical technique included deep liposuction in the lower abdomen, pubic liposuction, and liposuction of the flanks or dorsum with power-assisted liposuction, Scarpa fascia removal in the inferior abdomen, lipoplasty and mons lipolifting, and pubic fixation.

Results:
Following these key points, superior flap slides to the pubic region by elongation of the vessels and nerves, preserving those structures, avoiding creation of a dead space, and reducing the number of the most common complications. Scarpa fascia removal in the infraumbilical region avoided bulging without increasing the seroma rate. Pubic lifting and its fixation promote rejuvenation of the entire region and avoid elevation of the remnant scar.

Conclusion:
These surgical modifications are safe and avoid common complications related to lipoabdominoplasty, with improved outcomes.

CLINICAL QUESTION/LEVEL OF EVIDENCE:
Therapeutic, IV.
A High Density Map for Navigating the Human Polycomb Complexome
Authors: Hauri Simon , Comoglio Federico , Seimiya Makiko , Gerstung Moritz , Glatter Timo , Hansen Klaus , Aebersold Ruedi , Paro Renato , Gstaiger Matthias , Beisel Christian 
Published: June 2016

AbstractPolycomb group (PcG) proteins are major determinants of gene silencing and epigenetic memory in higher eukaryotes. Here, we used a robust affinity purification mass spectrometry (AP-MS) approach to systematically map the human PcG protein interactome, uncovering an unprecedented breadth of PcG complexes. The obtained high density protein interaction data identified new modes of combinatorial PcG complex formation with proteins previously not associated with the PcG system, thus providing new insights into their molecular function and recruitment mechanisms to target genes. Importantly, we identified two human PR-DUB de-ubiquitination complexes, which comprise the O-linked N-acetylglucosamine transferase OGT1 and a number of transcription factors. By further mapping chromatin binding of PR-DUB components genome-wide, we conclude that the human PR-DUB and PRC1 complexes bind distinct sets of target genes and impact on different cellular processes in mammals.
Virtual screening of inhibitors for the Zika virus proteins
Authors: Feranchuk S. , Potapova U. , Belikov S. 
Published: June 2016

AbstractThe NS3 protease and NS5 polymerase structures of the Zika virus were constructed and processed using a virtual screening pipeline. MM-PBSA calculations show that some of the ligands found by the pipeline demonstrate a good affinity to vulnerable sites in both proteins. The anti-hypertension drug eprosartan is among the selected ligands; and inhibition of the tick-borne encephalitis virus has already been confirmed in vivo by a previous study. In the present study phytochemicals bisabolol and andrographolide are suggested as the candidates for antiviral therapy.
Comparative distribution of antisense-RNA regulated toxin-antitoxin systems
Authors: Coray Dorien S , Wheeler Nicole , Heinemann Jack A , Gardner Paul P 
Published: June 2016

AbstractToxin-antitoxin (TA) systems are gene modules that appear to be widely horizontally mobile. It has been proposed that type I TA systems, with an antisense RNA-antitoxin, are less mobile than other TAs but no direct comparisons have been made. We searched for type I, II and III toxin families on chromosomes, plasmids and phages across bacterial phyla.The distribution of type I TA systems were more narrow than most type II and III system families, though this was less true of more recently discovered families.We discuss how the function and phenotypes of type I TA systems as well as biases in our databases and discovery of these modules may account for differences in their distribution.