bluuebunny/crossref_metadata_2025_split huggingface dataset:
MetaSpark: a spark-based distributed processing tool to recruit metagenomic reads to reference genomes
Authors: Zhou Wei , Li Ruilin , Yuan Shuo , Liu ChangChun , Yao Shaowen , Luo Jing , Niu Beifang 
Published: November 2016

Abstract

Summary
With the advent of next-generation sequencing, traditional bioinformatics tools are challenged by massive raw metagenomic datasets. One of the bottlenecks of metagenomic studies is lack of large-scale and cloud computing suitable data analysis tools. In this paper, we proposed a Spark-based tool, called MetaSpark, to recruit metagenomic reads to reference genomes. MetaSpark benefits from the distributed data set (RDD) of Spark, which makes it able to cache data set in memory across cluster nodes and scale well with the datasets. Compared with previous metagenomics recruitment tools, MetaSpark recruited significantly more reads than many programs such as SOAP2, BWA and LAST and increased recruited reads by ∼4% compared with FR-HIT when there were 1 million reads and 0.75 GB references. Different test cases demonstrate MetaSpark’s scalability and overall high performance.

Availability
https://github.com/zhouweiyg/metaspark

Supplementary information
Supplementary data are available at Bioinformatics online
PBIT: Pipeline Builder for Identification of drug Targets for infectious diseases
Authors: Shende Gauri , Haldankar Harshala , Barai Ram Shankar , Bharmal Mohammed Husain , Shetty Vinit , Idicula-Thomas Susan 
Published: November 2016

Abstract

Summary
PBIT (Pipeline Builder for Identification of drug Targets) is an online webserver that has been developed for screening of microbial proteomes for critical features of human drug targets such as being non-homologous to human proteome as well as the human gut microbiota, essential for the pathogen’s survival, participation in pathogen-specific pathways etc. The tool has been validated by analyzing 57 putative targets of Candida albicans documented in literature. PBIT integrates various in silico approaches known for drug target identification and will facilitate high-throughput prediction of drug targets for infectious diseases, including multi-pathogenic infections.

Availability and Implementation
PBIT is freely accessible at http://www.pbit.bicnirrh.res.in/.

Supplementary information
Supplementary data are available at Bioinformatics online.
Low-dose or low-dose-rate ionizing radiation–induced bioeffects in animal models
Authors: Tang Feng Ru , Loke Weng Keong , Khoo Boo Cheong 
Published: November 2016

AbstractAnimal experimental studies indicate that acute or chronic low-dose ionizing radiation (LDIR) (≤100 mSv) or low-dose-rate ionizing radiation (LDRIR) (&lt;6 mSv/h) exposures may be harmful. It induces genetic and epigenetic changes and is associated with a range of physiological disturbances that includes altered immune system, abnormal brain development with resultant cognitive impairment, cataractogenesis, abnormal embryonic development, circulatory diseases, weight gain, premature menopause in female animals, tumorigenesis and shortened lifespan. Paternal or prenatal LDIR/LDRIR exposure is associated with reduced fertility and number of live fetuses, and transgenerational genomic aberrations. On the other hand, in some experimental studies, LDIR/LDRIR exposure has also been reported to bring about beneficial effects such as reduction in tumorigenesis, prolonged lifespan and enhanced fertility. The differences in reported effects of LDIR/LDRIR exposure are dependent on animal genetic background (susceptibility), age (prenatal or postnatal days), sex, nature of radiation exposure (i.e. acute, fractionated or chronic radiation exposure), type of radiation, combination of radiation with other toxic agents (such as smoking, pesticides or other chemical toxins) or animal experimental designs. In this review paper, we aimed to update radiation researchers and radiologists on the current progress achieved in understanding the LDIR/LDRIR-induced bionegative and biopositive effects reported in the various animal models. The roles played by a variety of molecules that are implicated in LDIR/LDRIR-induced health effects will be elaborated. The review will help in future investigations of LDIR/LDRIR-induced health effects by providing clues for designing improved animal research models in order to clarify the current controversial/contradictory findings from existing studies.
In-room computed tomography–based brachytherapy for uterine cervical cancer:
results of a 5-year retrospective study
Authors: Ohno Tatsuya , Noda Shin-Ei , Okonogi Noriyuki , Murata Kazutoshi , Shibuya Kei , Kiyohara Hiroki , Tamaki Tomoaki , Ando Ken , Oike Takahiro , Ohkubo Yu , Wakatsuki Masaru , Saitoh Jun-Ichi , Nakano Takashi 
Published: November 2016

Abstract
Herein, we investigate the long-term clinical outcomes for cervical cancer patients treated with in-room computed tomography–based brachytherapy. Eighty patients with Stage IB1–IVA cervical cancer, who had undergone treatment with combined 3D high-dose rate brachytherapy and conformal radiotherapy between October 2008 and May 2011, were retrospectively analyzed. External beam radiotherapy (50 Gy) with central shielding after 20–40 Gy was performed for each patient. Cisplatin-based chemotherapy was administered concurrently to advanced-stage patients aged ≤75 years. Brachytherapy was delivered in four fractions of 6 Gy per week. In-room computed tomography imaging with applicator insertion was performed for treatment planning. Information from physical examinations at diagnosis, and brachytherapy and magnetic resonance imaging at diagnosis and just before the first brachytherapy session, were referred to for contouring of the high-risk clinical target volume. The median follow-up duration was 60 months. The 5-year local control, pelvic progression-free survival and overall survival rates were 94%, 90% and 86%, respectively. No significant differences in 5-year local control rates were observed between Stage I, Stage II and Stage III–IVA patients. Conversely, a significant difference in the 5-year overall survival rate was observed between Stage II and III–IVA patients (97% vs 72%; P = 0.006). One patient developed Grade 3 late bladder toxicity. No other Grade 3 or higher late toxicities were reported in the rectum or bladder. In conclusion, excellent local control rates were achieved with minimal late toxicities in the rectum or bladder, irrespective of clinical stage.
Frequency of E-cigarette Use, Health Status, and Risk and Protective Health Behaviors in Adolescents
Authors: Dunbar Michael S. , Tucker Joan S. , Ewing Brett A. , Pedersen Eric R. , Miles Jeremy N.V. , Shih Regina A. , D’Amico Elizabeth J. 
Published: November 2016

Objectives:
E-cigarettes (ECs) are increasingly popular among adolescents, who perceive them as “safer” than cigarettes. Although research has examined risk factors for adolescent EC use, little is known about how EC use correlates with health status and protective health behaviors.

Methods:
In all, 2488 adolescents (mean age = 17.31 years, SD = 0.67; 46% male) completed a survey on EC and cigarette use, physical and mental health, physical activity, diet, sleep, and alcohol and other drug (AOD) use. Logistic regression compared EC-only users to dual EC/cigarette users, cigarette-only users, and nonusers on these health factors. Among EC-only users, separate ordinary least-squares regression models assessed the effects of health status/behavior variables on frequency of past-year EC use, controlling for demographics and smokeless tobacco use.

Results:
User groups were similar on physical health and engagement in protective health behaviors (physical activity, sleep duration/quality, healthy diet), but EC-only users reported fewer mental health symptoms and less AOD use than dual or cigarette-only users. Among EC-only users, AOD use (all P < 0.0001) predicted more frequent EC use; healthy diet predicted less frequent use (P < 0.01).

Conclusions:
EC-only use is associated with lower engagement in risky behaviors, but not better health status or higher engagement in protective health behaviors, compared with cigarette smoking. Dual EC/cigarette users may represent a particularly high-risk group due to their greater AOD use and cigarette consumption. Among “intermediate-risk” EC-only users, AOD use and unhealthy diet correlated with heavier use, and may be important targets for preventing escalation to more harmful tobacco use.
Characterization of the Adverse Effects Induced by Acetaminophen and Nonsteroidal Anti-Inflammatory Drugs Based on the Analysis of the Japanese Adverse Drug Event Report Database
Authors: Nagai Junko , Uesawa Yoshihiro , Shimamura Ryotaro , Kagaya Hajime 
Published: November 2016

Objectives:
Acetaminophen and nonsteroidal anti-inflammatory drugs (NSAIDs) are antipyretic analgesics with established adverse effects (AEs); however, only a few studies have compared their AEs simultaneously. We aimed to compare the AEs of these medications to confirm the respective frequencies of both rare and major AEs.

Methods:
We used a high-quality database for spontaneous adverse drug event reporting in Japan. Data were extracted regarding the AEs of acetaminophen and NSAIDs to compare the tendency of the appearance of those AEs between the drugs. We also performed a principal component analysis using the AE data to assess the characteristics of major AEs.

Results:
Cutaneous disorders and hepatic disorders were the most common AEs induced by acetaminophen and NSAIDs, with gastrointestinal tract disorders also common with NSAID use. Principal component analysis quantitatively showed the tendencies of specific AEs, and it helped demonstrate the characteristics of AEs. Acetaminophen and NSAIDs showed different tendencies in the occurrence of AEs. Each NSAID was plotted based on the tendency of the appearance of major AEs, and AEs were classified by their likelihood of being pharmacological or idiosyncratic.

Conclusions:
These findings may help clinicians select an appropriate drug for patients considering their backgrounds, instead of choosing merely based on the class of the drug, for example, cyclooxygenase selectivity. This selection, based on the characteristic information on AEs occurring in clinical settings, might be more suitable for patients.
Formulating Clinical Trials in Prosthetics and Orthotics and Allied Health Fields
Authors: Wininger Michael 
Published: November 2016

ABSTRACT

Introduction
Clinical trials (CTs) are an essential component of modern health care, and a prerequisite to policy making. Clinical trials are the foundation of evidence-based practice and are the final legitimizer of any clinical discipline. Today, the allied health fields in general, and prosthetics and orthotics (P&O) in particular, are at an especially opportune position to launch CT initiatives: There are many “big questions” needing answers and a critical mass of field professionals capable of executing a CT operation.

Materials and Methods
None.

Results
None.

Conclusion
Here, we formalize the call for active engagement in CTs within P&O and provide a framework for CT design, with guidance that generalizes across the allied health fields.
Long-term Symptom-specific Outcomes for Patients With Petrous Apex Cholesterol Granulomas: Surgery Versus Observation
Authors: Stevens Shawn M. , Manning Amy , Pensak Myles L. , Samy Ravi N. 
Published: November 2016

Objective:
Review long-term symptom-specific outcomes for petrous apex cholesterol granulomas (PACG).

Study Design:
Retrospective review.

Setting:
Tertiary center.

Patients:
Adults with PACG were assessed from 1998 to 2015.

Intervention(s):
Symptomatic patients were stratified into surgical and observation subgroups.

Main Outcome Measure(s):
Resolution rates of individual symptoms and chief complaints were assessed as was the impact of surgical approach and stent usage on symptom-specific outcomes. Symptom recurrence rates were tabulated.

Results:
Twenty-seven patients were included whose mean age was 44.8 ± 3.3 years. Fourteen and 13 patients stratified into the surgical and observation subgroups respectively. The surgical subgroup trended toward a longer follow-up period (mean 68.5 vs. 33.8 mo; p = 0.06). Overall, the most frequent symptoms encountered were headache (52%), aural fullness, tinnitus, and vestibular complaints (41% each). Visual complaints, retro-orbital pain, and cranial neuropathies were less common (18%, 15%, 11%). The overall symptom resolution rate was significantly higher in the surgical subgroup (48% vs. 26%, p = 0.03). In both subgroups, headache, retro-orbital pain, and visual complaints had the highest resolution rates. Vestibular complaints and tinnitus were very unlikely to resolve. Significantly more patients in the surgical group resolved their chief complaints (70% vs. 25%, p = 0.02). While approach type and stent usage did not significantly influence symptom outcomes, all patients with symptom recurrence (11%) were initially managed without stents.

Conclusion:
Symptom-specific outcomes were better in patients managed surgically for PACG. Individual symptom resolution rates were highly variable. Some symptoms were refractory regardless of management strategy. Surgical approach and stent usage did not significantly influence symptom outcomes.
Initial Results of a Safety and Feasibility Study of Auditory Brainstem Implantation in Congenitally Deaf Children
Authors: Wilkinson Eric P. , Eisenberg Laurie S. , Krieger Mark D. , Schwartz Marc S. , Winter Margaret , Glater Jamie L. , Martinez Amy S. , Fisher Laurel M. , Shannon Robert V. 
Published: November 2016

Objective:
To determine the safety and feasibility of the auditory brainstem implant (ABI) in congenitally deaf children with cochlear aplasia and/or cochlear nerve deficiency.

Study Design:
Phase I feasibility clinical trial of surgery in 10 children, ages 2 to 5 years, over a 3-year period.

Setting:
Tertiary children's hospital and university-based pediatric speech/language/hearing center.

Intervention(s):
ABI implantation and postsurgical programming.

Main Outcome Measure(s):
The primary outcome measure is the number and type of adverse events during ABI surgery and postsurgical follow-up, including behavioral mapping of the device. The secondary outcome measure is access to and early integration of sound.

Results:
To date, nine children are enrolled. Five children have successfully undergone ABI surgery and postoperative behavioral programming. Three children were screen failures, and one child is currently undergoing candidacy evaluation. Expected adverse events have been documented in three of the five children who received the ABI. One child experienced a cerebral spinal fluid leak, which resolved with lumbar drainage. One child demonstrated vestibular side effects during device programming, which resolved by deactivating one electrode. One child experienced postoperative vomiting resulting in an abdominal radiograph. Four children have completed their 1-year follow-up and have speech detection thresholds of 30 to 35 dB HL. Scores on the IT-MAIS/MAIS range from 8 to 31 (out of a total of 40), and the children are demonstrating some ability to discriminate between closed-sets words that differ by number of syllables (pattern perception).

Conclusion:
ABI surgery and device activation seem to be safe and feasible in this preliminary cohort.
Effect of Spatial Orientation of the Horizontal Semicircular Canal on the Vestibulo-Ocular Reflex
Authors: Maxwell Rebecca , von Kirschbaum Constantin , Jerin Claudia , Lehnen Nadine , Krause Eike , Gürkov Robert 
Published: November 2016

Objective:
To determine if an alignment of the horizontal semi-circular canal (hSCC) with the plane of rotation would enhance the vestibular-ocular reflex (VOR) gain result as it has been previously suggested.

Study Design:
Comparative study of a physiological vestibular function test in healthy subjects.

Setting:
Tertiary referral center for otology and neurotology.

Patients:
Twenty two healthy volunteers were recruited for this study. Their mean age was 25.6 years and the sex distribution was 14:8 (M:F). None of the subjects had a history of audiovestibular disorders.

Intervention:
The video Head Impulse Test (v-HIT) was performed with the hSCC in the conventional position (head upright, horizontal gaze) and also with the hSCC in-line with the earth horizontal.

Main Outcome Measures:

1. the VOR gain at 60 ms,2. the regression slope VOR gain,

depending on the alignment of the hSCC with the plane of head rotation.

Results:
There was no significant difference between the results, either for the VOR gain at 60 ms, or the regression slope gain, when the two alternative head positions were compared.

Conclusions:
The data acquired in this study show that the VOR as measured by the v-HIT is not enhanced by aligning the plane of the hSCC with the plane of rotation during the testing procedure. Hence, we recommend that the positioning of the patient, with the head upright and a horizontal gaze direction should be routinely used in the clinical evaluation of the angular VOR by v-HIT.
Rescue therapies for acute respiratory distress syndrome: what to try first?
Authors: Moerer Onnen , Tonetti Tommaso , Quintel Michael 
Published: November 2016

Purpose of review
Severe respiratory failure due to the acute respiratory distress syndrome (ARDS) might require rescue therapy measures beyond even extended standard care to ensure adequate oxygenation and survival. This review provides a summary and assessment of treatment options that can be beneficial when the standard approach fails.

Recent findings
‘Life-threatening’ conditions or refractory hypoxemia during mechanical ventilation are more a matter of personal rating than an objective diagnosis based on defined and/or unanimously agreed thresholds that would mandate the use of rescue therapies. Although the outcome might vary with different rescue procedures, most of them will improve oxygenation. Prone positioning maintains a predominant role as rescue therapy in severe hypoxemia and does not only improve oxygenation in but also survival of ARDS patients. Recruitment maneuvers can have temporary positive effects. Inhaled nitric oxide, as well as high-frequency oscillatory ventilation might acutely improve oxygenation and can be used as a ‘bridge’ to alternative rescue therapies, but neither provides any survival advantage by itself and might even be detrimental. Although increasingly employed in other than the rescue indication, extracorporeal membrane oxygenation should still primarily be used in patients who do not respond to differentiated mechanical ventilation, which includes a careful evaluation of nonextracorporeal membrane oxygenation rescue therapies that might be combined in order to overcome the life-threatening situation. Early involvement of an ARDS or extracorporeal membrane oxygenation center should be considered to ensure optimal care.

Summary
A well timed, multimodal approach is required for patients with ARDS suffering from life-threatening hypoxemia. Understanding the limits of each type of rescue measure is of vital importance.
How best to set the ventilator on extracorporeal membrane lung oxygenation
Authors: Gattinoni Luciano , Tonetti Tommaso , Quintel Michael 
Published: November 2016

Purpose of review
Extracorporeal respiratory support in patients with acute respiratory distress syndrome is applied either as rescue maneuver for life-threatening hypoxemia or as a tool to reduce the harm of mechanical ventilation. Depending on the blood and gas flow, extracorporeal support may completely substitute the natural lung as a gas exchanger (high-flow venovenous bypass) or reduce the need for mechanical ventilation, enabling the removal of a fraction of the metabolically produced CO2.

Recent findings
Recent studies provide a description on how mechanical ventilation is normally applied in combination with extracorporeal support in acute respiratory distress syndrome. The data show a general trend: a variable decrease of fraction of inspired oxygen (0.9 to 0.7 or 0.4), a consistent decrease in tidal volume (by 2 ml/kg), no change in positive end-expiratory pressure (maintained around 12–13 cmH2O) and a moderate decrease in the respiratory rate (22 to 15 bpm). These ventilatory settings are applied in whatever extracorporeal membrane lung oxygenation modality (venovenous versus venoarterial) and independent from the extent of extracorporeal support (partial or total substitution of gas exchange).

Summary
Mechanical ventilation and extracorporeal support are marginally integrated. The best environment for lung healing – complete lung collapse or protective ventilation strategy or fully open and immobile lung (all three conditions feasible with extracorporeal support) – remains to be defined.
Maternal epigenetics and fetal and neonatal growth
Authors: Kitsiou-Tzeli Sofia , Tzetis Maria 
Published: November 2016

Purpose of review
The article provides an update on new insights of factors altering inherited maternal epigenome that ultimately affect fetal and neonatal growth.

Recent findings
A number of new publications have identified mechanisms through which maternal nutrition, environmental exposures such as stress and toxic substances altering expression of imprinted genes during pregnancy can influence fetal and neonatal phenotype and susceptibility to disease development later in life. The possible causes of metabolic syndrome by in-utero epigenetic alterations of genes involved in energy metabolism (PPARγ and PPARα), microRNAs, arginine methyltransferases, lysine demethylases, and histone deacetylaces have been elucidated. Moreover associations between methylation of key genes (NRC31, HSD11β1/2, GFI1) involved in the hypothalamic-pituitary-adrenal axis have been identified. Alcohol exposure during pregnancy was found to alter methylation patterns of several imprinted genes (H19, SLC22A18, SLC6A3, DRD4). Finally alterations in vulnerable epigenetic marks of imprinted genes such as H19/IGF2, during early stages of embryonic development result in intrauterine growth restriction.

Summary
All these investigations continue to provide new insights for improved clinical management of in-utero development.
Cognitive behavioral therapy for cancer-related cognitive dysfunction
Authors: Kucherer Shelly , Ferguson Robert J. 
Published: November 2016

Purpose of review
To provide the reader with an overview of the cognitive-behavioral conceptualization of cancer-related cognitive dysfunction (CRCD) and how cognitive behavioral therapy (CBT) can play an important role in treatment.

Recent findings
Recent findings show that Memory and Attention Adaptation Training (MAAT), a CBT developed to help cancer survivors develop adaptive skills to improve daily cognitive performance and emotional coping, may be an efficacious treatment of CRCD and can be delivered through videoconference technology to improve survivor access to care.

Summary
The etiology of CRCD remains largely undetermined and likely is produced by multiple mechanisms. This can include neuronal death, microvascular damage, inflammatory processes, and psychological factors of perceptions of inadequate cognitive capacity to meet performance demands and related emotional distress. As a result, there are a variety of treatments currently being researched. More research with larger sample sizes, multiple clinicians and multiple sites are needed to confirm efficacy, but CBT approaches such as Memory and Attention Adaptation Training that address multiple psychological factors involved may offer a flexible nonpharmacological approach to CRCD that optimizes quality of life outcomes.