bluuebunny/crossref_metadata_2025_split huggingface dataset:
araGWAB: Network-based boosting of genome-wide association studies in Arabidopsis thaliana
Authors: Lee Tak , Lee Insuk 
Published: February 2018

AbstractGenome-wide association studies (GWAS) have been applied for the genetic dissection of complex phenotypes in Arabidopsis thaliana. However, the significantly associated single-nucleotide polymorphisms (SNPs) could not explain all the phenotypic variations. A major reason for missing true phenotype-associated loci is the strict P-value threshold after adjustment for multiple hypothesis tests to reduce false positives. This statistical limitation can be partly overcome by increasing the sample size, but at a much higher cost. Alternatively, weak phenotype-association signals can be boosted by integrating other types of data. Here, we present a web application for network-based Arabidopsisgenome-wide association boosting—araGWAB—which augments the likelihood of association with the given phenotype by integrating GWAS summary statistics (SNP P-values) and co-functional gene network information. The integration utilized the inherent values of SNPs with subthreshold significance, thus substantially increasing the information usage of GWAS data. We found that araGWAB could more effectively retrieve genes known to be associated with various phenotypes relevant to defense against bacterial pathogens, flowering time regulation, and organ development in A. thaliana. We also found that many of the network-boosted candidate genes for the phenotypes were supported by previous publications. The araGWAB is freely available at http://www.inetbio.org/aragwab/.
Structure of prothrombin in the closed form reveals new details on the mechanism of activation
Authors: Chinnaraj Mathivanan , Chen Zhiwei , Pelc Leslie A. , Grese Zachary , Bystranowska Dominika , Di Cera Enrico , Pozzi Nicola 
Published: February 2018

AbstractThe clotting factor prothrombin exists in equilibrium between closed and open conformations, but the physiological role of these forms remains unclear. As for other allosteric proteins, elucidation of the linkage between molecular transitions and function is facilitated by reagents stabilized in each of the alternative conformations. The open form of prothrombin has been characterized structurally, but little is known about the architecture of the closed form that predominates in solution under physiological conditions. Using X-ray crystallography and single-molecule FRET, we characterize a prothrombin construct locked in the closed conformation through an engineered disulfide bond. The construct: (i) provides structural validation of the intramolecular collapse of kringle-1 onto the protease domain reported recently; (ii) documents the critical role of the linker connecting kringle-1 to kringle-2 in stabilizing the closed form; and (iii) reveals novel mechanisms to shift the equilibrium toward the open conformation. Together with functional studies, our findings define the role of closed and open conformations in the conversion of prothrombin to thrombin and establish a molecular framework for prothrombin activation that rationalizes existing phenotypes associated with prothrombin mutations and points to new strategies for therapeutic intervention.
Quantitative analysis of the methane gas emissions from municipal solid waste in India
Authors: Singh Chander Kumar , Kumar Anand , Roy Soumendu Shekhar 
Published: February 2018

AbstractIncreased emissions of greenhouse gases have altered the global ambient temperature and adversely affected global climatic conditions. The municipal solid waste (MSW) generated by households is considered the third largest anthropogenic source of methane (CH4) emissions, constituting 11% of all global CH4 emissions. The current study derived total MSW CH4 emission estimates using the IPCC default method (DM), modified triangular method (MTM) and first order decay method (FOD). The estimated CH4 emission was higher for the DM than the other methods, and was comparable to estimates from other studies. This study observed that the net annual emission of CH4 from landfills in India increased from 404 Gg in 1999–2000 to 990 Gg and 1084 Gg in 2011 and 2015, respectively. We also found that CH4 emissions were highly correlated (R2 = 0.8) with the gross state domestic product (GSDP) of states and the gross domestic product (GDP) of the country, which is an indicator of human well-being. The MSW management policy of India needs to be reviewed in a current policy context, as the management and efficient utilization of MSW technologies might help increase the use of CH4 as an energy source and thereby improve its sustainable and cost-effective management.
A heading date QTL, qHD7.2, from wild rice (Oryza rufipogon) delays flowering and shortens panicle length under long-day conditions
Authors: Jing Li , Rui Xu , Chunchao Wang , Lan Qi , Xiaoming Zheng , Wensheng Wang , Yingbin Ding , Lizhen Zhang , Yanyan Wang , Yunlian Cheng , Lifang Zhang , Weihua Qiao , Qingwen Yang 
Published: February 2018

AbstractHeading date (HD) and panicle length (PL) are important traits that affect rice breeding and are controlled by pleiotropic genes. Some alleles associated with HD and PL from wild relatives might differ from those in cultivated rice. In this study, a main effect HD quantitative trait locus from wild rice, qHD7.2, was identified using a chromosomal segment substitution line (CSSL) population. First, qHD7.2 was determined to be located near RM172 on chromosome 7 based on association analysis of phenotype data from six environments and 181 polymorphic molecular markers. CSSL39, which has the latest flowering of all CSSLs and carries qHD7.2, was selected for further study, and qHD7.2 was narrowed to a 101.1-kb interval using a CSSL39/9311 F2 population. An OsPRR37-homologous gene was found within this region. The wild type allele delayed flowering and shortened PL under long-day conditions. The HD7.2, which was identified as a candidate gene for qHD7.2, transcript level was substantially higher than that in 9311. Our data showed that HD7.2 is likely a novel OsPRR37 allele. Sequence analysis revealed that OsPRR37 in cultivated rice had multiple origins, and natural variation in the coding domain sequence and promoter region contribute to flowering time diversity in cultivated rice.
A chemoenzymatic process for amide bond formation by an adenylating enzyme-mediated mechanism
Authors: Hara Ryotaro , Hirai Kengo , Suzuki Shin , Kino Kuniki 
Published: February 2018

AbstractAmide bond formation serves as a fundamental reaction in chemistry, and is practically useful for the synthesis of peptides, food additives, and polymers. However, current methods for amide bond formation essentially generate wastes and suffer from poor atom economy under harsh conditions. To solve these issues, we demonstrated an alternative synthesis method for diverse tryptophyl-N-alkylamides by the combination of the first adenylation domain of tyrocidine synthetase 1 with primary or secondary amines as nucleophiles. Moreover, the physiological role of this domain is l-phenylalanine adenylation; however, we revealed that it displayed broad substrate flexibility from mono-substituted tryptophan analogues to even d-tryptophan. To the best of our knowledge, this is the first evidence for an adenylating enzyme-mediated direct amide bond formation via a sequential enzymatic activation of amino acids followed by nucleophilic substitution by general amines. These findings facilitate the design of a promising tool for biocatalytic straightforward amide bond formation with less side products.
Performance Feedback to Increase Use of Counseling Skills
Authors: Muñoz Karen , Ong Clarissa , Butcher Grayson , Nelson Lauri , Twohig Michael , Finai Jalin 
Published: February 2018

AbstractCounseling is a critical component of audiological care and when implemented purposefully can yield multiple benefits for patients. Professional guidelines indicate that counseling is within the scope of practice for audiologists, yet research has shown that audiologists feel unprepared and are not comfortable providing adjustment counseling. This may be due to inadequate counseling training in audiology graduate programs. To identify ways to address this counseling training gap, this study examined the use of performance feedback to increase counseling skills among audiology graduate students. In this study, participants (n = 5) were recorded during clinical session encounters, and recordings were coded for time spent counseling. A licensed clinical psychologist reviewed the recordings and provided individual performance feedback to participants over the course of the study. Time spent counseling increased by the end of the study, although improvement varied across participants. Results suggest that performance feedback can be used as a method to increase counseling skills in audiology students. However, factors, such as participant motivation, feedback timing, and prerequisite counseling skills, may influence response to feedback. More research is needed on ways to maximize gains from feedback, as well as other methods to improve counseling skills in audiology students.
Teaching Counseling Microskills to Audiology Students: Recommendations from Professional Counseling Educators
Authors: Kulzer Jamie , Beck Kelly 
Published: February 2018

AbstractTo provide the highest quality services, audiologists incorporate counseling into their professional practice. This article, written by professional counselors, highlights the distinction between services provided by professional counselors (i.e., psychotherapy) and counseling microskills used by all health and rehabilitation professionals. Effective application of counseling microskills facilitates a strong therapeutic alliance, which research shows contributes to positive therapeutic outcomes. Counseling microskills should be taught early in graduate programs, because they serve as the foundation for the therapeutic alliance and allow for more effective application of other therapeutic interventions. The four most critical counseling microskills for audiologists are active listening, nonverbal communication, silence, and empathy. These skills should be taught using experiential learning activities (i.e., classroom role-play and use of simulated patients) that incorporate practice, repetition, and feedback. Students should be evaluated on their ability to perform counseling microskills using a detailed grading rubric. Instructors should deliver feedback on these skills with care to reduce potential negative reactions. Ultimately, effectively teaching counseling microskills in graduate programs can improve students' ability to facilitate the therapeutic alliance and facilitate better health outcomes for patients.
Clinical Information Systems Integration in New York City's First Mobile Stroke Unit
Authors: Kummer Benjamin , Lerario Michael , Navi Babak , Ganzman Adam , Ribaudo Daniel , Mir Saad , Pishanidar Sammy , Lekic Tim , Williams Olajide , Kamel Hooman , Marshall Randolph , Hripcsak George , Elkind Mitchell , Fink Matthew 
Published: February 2018

Background Mobile stroke units (MSUs) reduce time to thrombolytic therapy in acute ischemic stroke. These units are widely used, but the clinical information systems underlying MSU operations are understudied.
Objective The first MSU on the East Coast of the United States was established at New York Presbyterian Hospital (NYP) in October 2016. We describe our program's 7-month pilot, focusing on the integration of our hospital's clinical information systems into our MSU to support patient care and research efforts.
Methods NYP's MSU was staffed by two paramedics, one radiology technologist, and a vascular neurologist. The unit was equipped with four laptop computers and networking infrastructure enabling all staff to access the hospital intranet and clinical applications during operating hours. A telephone-based registration procedure registered patients from the field into our admit/discharge/transfer system, which interfaced with the institutional electronic health record (EHR). We developed and implemented a computerized physician order entry set in our EHR with prefilled values to permit quick ordering of medications, imaging, and laboratory testing. We also developed and implemented a structured clinician note to facilitate care documentation and clinical data extraction.
Results Our MSU began operating on October 3, 2016. As of April 27, 2017, the MSU transported 49 patients, of whom 16 received tissue plasminogen activator (t-PA). Zero technical problems impacting patient care were reported around registration, order entry, or intranet access. Two onboard network failures occurred, resulting in computed tomography scanner malfunctions, although no patients became ineligible for time-sensitive treatment as a result. Thirteen (26.5%) clinical notes contained at least one incomplete time field.
Conclusion The main technical challenges encountered during the integration of our hospital's clinical information systems into our MSU were onboard network failures and incomplete clinical documentation. Future studies are necessary to determine whether such integrative efforts improve MSU care quality, and which enhancements to information systems will optimize clinical care and research efforts.
Endoscopic Endonasal Approach to a Suprasellar Craniopharyngioma
Authors: Todeschini Alexandre , Montaser Alaa , Shahein Mostafa , Revuelta Juan , Otto Bradley , Carrau Ricardo , Prevedello Daniel 
Published: February 2018

AbstractWe present the case of a 57-year-old male who presented with progressive right side vision loss whose workup revealed a large suprasellar lesion with invasion of the third ventricle. The pituitary stalk was not visible.Hormonal panel showed no hormonal deficits. The initial diagnosis was of a type II transinfundibular craniopharyngioma (as classified by Kassam et al).An endoscopic endonasal transplanum transtuberculum approach was done using a standard binostril four-hand technique, with the patient positioned supine with the head turned to the right side and tilted to the left, fixed in a three-pin head clamp, under imaging guidance. The tumor was carefully dissected away from the optic apparatus while preserving the vessels, mainly the superior hypophyseal artery. The stalk was identified around the tumor and preserved. The third ventricle was entered and inspected at the end of the procedure and a near-total resection (a small residual in the right hypothalamus) with decompression of the optic apparatus was achieved. Reconstruction was done in a multilayered fashion, using collagen matrix and a nasoseptal flap. Patient had an uneventful postoperative stay and was discharged on POD 4, neurologically stable with no hormonal deficits. Pathology confirmed an adamantinomatous craniopharyngioma. Due to a small growth of the residual, patient underwent fractionated stereotactic radiation (50.4Gy in 28 sessions). He presented with panhypopituitarism 2 years after radiation therapy. At 3-month follow-up, his vision was back to normal and 6-year postoperative magnetic resonance imaging showed no signs of recurrence.The link to the video can be found at: https://youtu.be/chG7XIz7a_A.
Macrophage Density Predicts Facial Nerve Outcome and Tumor Growth after Subtotal Resection of Vestibular Schwannoma
Authors: Graffeo Christopher , Perry Avital , Raghunathan Aditya , Kroneman Trynda , Jentoft Mark , Driscoll Colin , Neff Brian , Carlson Matthew , Jacob Jeffrey , Link Michael , Van Gompel Jamie 
Published: February 2018

Introduction Vestibular schwannoma (VS) behavior following subtotal resection (STR) is highly variable. Overall progression rates have been reported as high as 44%, and optimal treatment is controversial. Correspondingly, identification of a reliable clinical or pathologic marker associated with progression after STR would help guide decision-making.
Methods A prospectively maintained institutional VS registry from 1999 to 2014 was retrospectively reviewed for sporadic VS patients who underwent primary STR without preceding stereotactic radiosurgery (SRS) by a single neurosurgery-neurotology team. Primary endpoints included tumor progression and postoperative facial nerve function. Pathologic specimens were stained for Ki67, CD68, S100, and SOX10 and were quantitated by digital imaging analysis. Macrophage density was defined as the ratio of CD68+ macrophages to S100+ macrophages and Schwannian tumor cells. Clinical outcomes were correlated with pathologic markers.
Results Forty-six patients met the study inclusion criteria. Thirteen (28%) progressed during a mean 57 months of follow-up (range 15–149). Favorable postoperative facial nerve function (House–Brackmann I–II) was achieved in 37 (80%). CD68+ cells were present at significantly higher concentrations in tumors that progressed (p = 0.03). Higher macrophage density was significantly associated with both tumor progression (p = 0.02) and unfavorable facial nerve function (p = 0.02). Ki67 percent positivity was not significantly associated with either primary endpoint (p = 0.83; p = 0.58).
Conclusions Macrophage density may provide an important marker for individuals at the highest risk for progression of VS after STR, potentially prompting closer surveillance or consideration for upfront SRS following STR. This finding supports preceding conclusions that an intratumoral macrophage-predominant inflammatory response may be a marker for tumor growth and a potential therapeutic target.
Complications and outcomes of routine endoscopy in the very elderly
Authors: Miyanaga Ryoichi , Hosoe Naoki , Naganuma Makoto , Hirata Kenro , Fukuhara Seiichiro , Nakazato Yoshihiro , Ojiro Keisuke , Iwasaki Eisuke , Yahagi Naohisa , Ogata Haruhiko , Kanai Takanori 
Published: February 2018

Abstract
Background and study aims In Japan, the elderly population has been increasing annually. The number of elderly patients for whom esophagogastroduodenoscopy (EGD) and colonoscopy (CS) is indicated also has been rising. The aim of this study was to evaluate the safety and efficacy of routine endoscopy in a cohort of octogenarians aged 85 years and older – defined by the World Health Organization as the very elderly.
Patients and methods A total of 5,586 patients underwent EGDs, and 2,484 patients underwent CSs performed at the Keio University Hospital from January to September 2014. One hundred eighty-five EGDs and 70 of the CS were performed in the very elderly. Six hundred nine EGDs and 262 CS were performed on younger patients (aged forties). Statistical analysis was performed by univariate and multivariate analyses.
Results On univariate analysis, the rate of adverse events (AEs) in the very elderly was significantly higher compared to the younger group (6.3 % vs. 1.1 %; P < 0.01). Moreover, the very elderly cohort received substantial therapeutic intervention as compared to the younger (16.9 % vs. 6.9 %; P < 0.01). On multivariate analysis, independent risk factors of AEs included: very elderly patients (odds ratio (OR) 3.30, 95 % confidence interval (CI) 1.05 – 10.35), inpatients (OR 3.22, 95 % CI 1.34 – 7.74), and use of pethidine hydrochloride prescription (OR 3.44, 95 % CI 1.51 – 7.81).
Conclusions Routine endoscopy in the very elderly incurs a significant risk of AEs, particularly when combined with pethidine hydrochloride prescription.
The Impact of Mild Heat Stress During Prolonged Running On Gastrointestinal Integrity, Gastrointestinal Symptoms, Systemic Endotoxin and Cytokine Profiles
Authors: Snipe Rhiannon , Khoo Anthony , Kitic Cecilia , Gibson Peter , Costa Ricardo 
Published: February 2018

AbstractThe study aimed to determine the effects of mild exertional heat stress on intestinal injury, permeability, gastrointestinal symptoms, and systemic endotoxin and cytokine responses. Ten endurance runners completed 2 h of running at 60% V̇O2max in warm (WARM: 30°C) and temperate (TEMP: 22°C) ambient conditions. Rectal temperature (Tre) and gastrointestinal symptoms were recorded every 10 min during exercise. Blood samples were collected pre- and post-exercise, and during recovery to determine plasma intestinal fatty acid-binding protein (I-FABP) and cortisol concentrations, and systemic endotoxin and inflammatory cytokine profiles. Urinary lactulose:L-rhamnose ratio (L/R) was used to measure small intestine permeability. Compared with TEMP, WARM significantly increased Tre from 50 min onwards (38.1±0.3°C vs. 38.4±0.5°C, respectively; p<0.01), gastrointestinal symptoms (p=0.017), post-exercise plasma cortisol (26% vs. 59%, respectively; p<0.001) and I-FABP (127% vs. 184%, respectively; p<0.001) concentrations. Circulatory anti-endotoxin antibodies increased post-exercise (p<0.001) on WARM (20%) and TEMP (28%). No differences were observed for plasma endotoxin concentration (6% vs. 5% increase, respectively) or small intestine permeability (L/R 0.026±0.010 and 0.025±0.015, respectively). Both pro- and anti-inflammatory cytokines increased post-exercise, with inflammatory response cytokines TNF-α (p=0.015) and IL-8 (p=0.044), and compensatory anti-inflammatory cytokines IL-10 (p=0.065), and IL-1ra higher on WARM than TEMP. Findings suggest that exposure to warm ambient conditions during prolonged submaximal running induces transient intestinal epithelial injury, increases gastrointestinal symptoms, and promotes greater perturbations to the systemic cytokine profile compared to running in temperate conditions.
Externally Acquired Radiological Data for the Clinical Routine – A Review of the Reimbursement Situation in Germany
Authors: Schreyer Andreas , Steinhäuser René , Rosenberg Britta 
Published: February 2018

Background Interdisciplinary radiological conferences and boards can improve therapeutic pathways. Because of the reinterpretation and presentation of external image data, which already was read, an additional workload is created which is currently not considered by health care providers. In this review we discuss the ongoing basics and possibilities in health economy for a radiological second opinion for the outpatient and inpatient sector in Germany.
Method Based on up-to-date literature and jurisdiction, we discuss the most important questions for the reimbursement for second opinions and conference presentations of external image data in an FAQ format. Additionally, we focus on the recently introduced E-Health law accordingly.
Results Radiological services considering second opinion or board presentation of externally acquired image data are currently not adequately covered by health care providers. In particular, there is no reimbursement possibility for the inpatient sector. Only patients with private insurance or privately paid second opinions can be charged when these patients visit the radiologist directly.
Conclusion Currently there is no adequate reimbursement possibility for a radiological second opinion or image demonstrations in clinical conferences. It will be essential to integrate adequate reimbursement by health care providers in the near future because of the importance of radiology as an essential diagnostic and therapeutic medical partner.
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