bluuebunny/crossref_metadata_2025_split huggingface dataset:
NAMS webserver: coding potential assessment and functional annotation of plant transcripts
Authors: Sun Kun , Wang Huating , Sun Hao 
Published: August 2020

Abstract
Recent advances in transcriptomics have uncovered lots of novel transcripts in plants. To annotate such transcripts, dissecting their coding potential is a critical step. Computational approaches have been proven fruitful in this task; however, most current tools are designed/optimized for mammals and only a few of them have been tested on a limited number of plant species. In this work, we present NAMS webserver, which contains a novel coding potential classifier, NAMS, specifically optimized for plants. We have evaluated the performance of NAMS using a comprehensive dataset containing more than 3 million transcripts from various plant species, where NAMS demonstrates high accuracy and remarkable performance improvements over state-of-the-art software. Moreover, our webserver also furnishes functional annotations, aiming to provide users informative clues to the functions of their transcripts. Considering that most plant species are poorly characterized, our NAMS webserver could serve as a valuable resource to facilitate the transcriptomic studies. The webserver with testing dataset is freely available at http://sunlab.cpy.cuhk.edu.hk/NAMS/.
mixtureS: a novel tool for bacterial strain genome reconstruction from reads
Authors: Li Xin , Hu Haiyan , Li Xiaoman 
Published: August 2020

Abstract

Motivation
It is essential to study bacterial strains in environmental samples. Existing methods and tools often depend on known strains or known variations, cannot work on individual samples, not reliable, or not easy to use, etc. It is thus important to develop more user-friendly tools that can identify bacterial strains more accurately.

Results
We developed a new tool called mixtureS that can de novo identify bacterial strains from shotgun reads of a clonal or metagenomic sample, without prior knowledge about the strains and their variations. Tested on 243 simulated datasets and 195 experimental datasets, mixtureS reliably identified the strains, their numbers and their abundance. Compared with three tools, mixtureS showed better performance in almost all simulated datasets and the vast majority of experimental datasets.

Availability and implementation
The source code and tool mixtureS is available at http://www.cs.ucf.edu/˜xiaoman/mixtureS/.

Supplementary information
Supplementary data are available at Bioinformatics online.
Exercise alters brain activation in Gulf War Illness and Myalgic Encephalomyelitis/Chronic Fatigue Syndrome
Authors: Washington Stuart D , Rayhan Rakib U , Garner Richard , Provenzano Destie , Zajur Kristina , Addiego Florencia Martinez , VanMeter John W , Baraniuk James N 
Published: August 2020

AbstractGulf War Illness affects 25–30% of American veterans deployed to the 1990–91 Persian Gulf War and is characterized by cognitive post-exertional malaise following physical effort. Gulf War Illness remains controversial since cognitive post-exertional malaise is also present in the more common Myalgic Encephalomyelitis/Chronic Fatigue Syndrome. An objective dissociation between neural substrates for cognitive post-exertional malaise in Gulf War Illness and Myalgic Encephalomyelitis/Chronic Fatigue Syndrome would represent a biological basis for diagnostically distinguishing these two illnesses. Here, we used functional magnetic resonance imaging to measure neural activity in healthy controls and patients with Gulf War Illness and Myalgic Encephalomyelitis/Chronic Fatigue Syndrome during an N-back working memory task both before and after exercise. Whole brain activation during working memory (2-Back &gt; 0-Back) was equal between groups prior to exercise. Exercise had no effect on neural activity in healthy controls yet caused deactivation within dorsal midbrain and cerebellar vermis in Gulf War Illness relative to Myalgic Encephalomyelitis/Chronic Fatigue Syndrome patients. Further, exercise caused increased activation among Myalgic Encephalomyelitis/Chronic Fatigue Syndrome patients within the dorsal midbrain, left operculo-insular cortex (Rolandic operculum) and right middle insula. These regions-of-interest underlie threat assessment, pain, interoception, negative emotion and vigilant attention. As they only emerge post-exercise, these regional differences likely represent neural substrates of cognitive post-exertional malaise useful for developing distinct diagnostic criteria for Gulf War Illness and Myalgic Encephalomyelitis/Chronic Fatigue Syndrome.
Diagnosing anastomotic leak post-esophagectomy: a systematic review
Authors: Barbaro Antonio , Eldredge Thomas A , Shenfine Jonathan 
Published: August 2020

SUMMARY
Esophagectomy is the gold-standard treatment for esophageal cancer; however, postoperative anastomotic leakage remains the primary concern for surgeons. No consensus exists on the optimal investigations to predict an anastomotic leak. This systematic review aims to identify a single test or combination of tests with acceptable sensitivity and specificity to identify anastomotic leak after esophagectomy and to formulate a diagnostic algorithm to facilitate surgical decision-making. A systematic review of PubMed and EMBASE databases was undertaken to evaluate diagnostic investigations for anastomotic leak post-esophagectomy. Each study was reviewed and where possible, the sensitivity, specificity, positive predictive value, and negative predictive value were extracted. The review identified 3,204 articles, of which 49 met the inclusion criteria. Investigations most commonly used for diagnosis of anastomotic leak were: C-reactive protein (CRP), oral contrast imaging, computed tomography (CT), pleural drain amylase concentration, and the ‘NUn score’. The sensitivity of CRP for detecting anastomotic leak varied from 69.2% to 100%. Oral contrast studies sensitivities varied between 16% and 87.5% and specificity varied from 20% to 100%. Pleural drain amylase sensitivities ranged between 75% and 100% and specificity ranged from 52% to 95.5%. The NUn score sensitivities ranged from 0% to 95% and specificity from 49% to 94.4%. No single investigation was identified to rule out anastomotic leak in asymptomatic patients. However, the authors propose a diagnostic algorithm incorporating CRP, pleural drain amylase concentration, and CT with oral contrast to aid clinicians in predicting anastomotic leak to facilitate safe, timely discharge post-esophagectomy.
Incremental benefit of a novel signal recording system during mapping and ablation
Authors: Padmanabhan Deepak , Sugrue Alan , Vaidya Vaibhav , Witt Chance , Yasin Omar , Naksuk Niyada , Killu Ammar , Foxall Thomas , Drakulic Budimir S , Venkatachalam Kalapathi Lakshminarayana , Asirvatham Samuel J 
Published: August 2020

Abstract

Aims
Current electrophysiology signal recording and mapping systems have limited dynamic range (DR) and bandwidth, which causes loss of valuable information during acquisition of cardiac signals. We evaluated a novel advanced signal processing platform with the objective to obtain and assess additional information of clinical importance.

Methods and results
Over 10 canines, we compared intracardiac recordings within all cardiac chambers, in various rhythms, in pacing and during radiofrequency (RF) ablation across two platforms; a conventional system and the PURE EP™ [(PEP); Bio Sig Technologies, Inc., Los Angeles, CA, USA]. Recording cardiac signals with varying amplitudes were consistently and reproducibly observed, without loss of detail or introduction of artefact. Further the amplitude of current of injury (COI) on the unipolar signals correlated with the instantaneous contact force (CF) recorded on the sensing catheter in all the animals (r2 = 0.94 in ventricle). The maximum change in the unipolar COI correlated with the change in local electrogram amplitude during non-irrigated RF ablation (r2 = 0.61 in atrium). Reduction in artefact attributable to pacing (20 sites) and noise during ablation (48 sites) was present on the PEP system. Within the PEP system, simultaneous display of identical signals, filtered differently, aided the visualization of discrete conduction tissue signals.

Conclusion
Compared to current system, the PEP system provided incremental information including identifying conduction tissue signals, estimates of CF and a surrogate for lesion formation. This novel signal processing platform with increased DR and minimal front-end filtering may be useful in clinical practice.
Social Support, Everyday Discrimination, and Depressive Symptoms Among Older African Americans: A Longitudinal Study
Authors: Qin Weidi , Nguyen Ann W , Mouzon Dawne M , Hamler Tyrone C , Wang Fei 
Published: August 2020

Abstract

Background and Objectives
The purpose of the study was to explore the long-term effects of everyday discrimination on depressive symptoms among older African Americans, as well as the moderating role of social support in this association.

Research Design and Methods
Mixed-effects negative binomial regression analyses were performed on data selected from 6 waves of the Health and Retirement Study (2006–2016; baseline N = 1,144). The number of depressive symptoms was calculated based on an 8-item Center for Epidemiologic Studies Depression measure. Everyday discrimination was measured using a 6-item scale. Contact with and perceived support from extended family and friends were assessed.

Results
Older African Americans who experienced more frequent perceived discrimination had more depressive symptoms over time. Significant interactions between discrimination and perceived support from extended family and friends were found, indicating that among older African Americans who reported higher support from extended family and friends, perceived discrimination was positively associated with depressive symptoms over time. However, perceived discrimination and depressive symptoms were not longitudinally related among those who reported lower levels of perceived support.

Discussion and Implications
This is one of the few studies to examine the effects of discrimination on depressive symptoms over time and the first longitudinal study to test the role of social support in coping with discrimination in older African Americans. This study extends cross-sectional works on discrimination and mental health, indicating that experiences of discrimination can result in worse mental health over time. The significant interactions are consistent with the resource mobilization framework, which suggests that individuals who are more negatively affected by discrimination (more depressive symptoms) are more likely to reach out to friends and family to cope with discrimination.
Obstacle Negotiation in Older Adults: Prefrontal Activation Interpreted Through Conceptual Models of Brain Aging
Authors: Chatterjee Sudeshna A , Seidler Rachael D , Skinner Jared W , Lysne Paige E , Sumonthee Chanoan , Wu Samuel S , Cohen Ronald A , Rose Dorian K , Woods Adam J , Clark David J 
Published: August 2020

AbstractBackground and ObjectivesThe influence of interindividual differences on brain activation during obstacle negotiation and the implications for walking performance are poorly understood in older adults. This study investigated the extent to which prefrontal recruitment during obstacle negotiation is explained by differences in age, executive function, and sex. These data were interpreted according to the Compensation-Related Utilization of Neural Circuits Hypothesis (CRUNCH) framework of brain aging. We also tested the association between prefrontal recruitment and walking performance.Research Design and MethodsPrefrontal oxygenated hemoglobin concentration (O2Hb) was measured during typical walking (Typical) and obstacle negotiation (Obstacles) tasks in 50 adults aged 65 years and older using functional near-infrared spectroscopy. The primary outcome was the change in prefrontal recruitment (∆PFR), measured as Obstacles ∆O2Hb minus Typical ∆O2Hb. Multiple regression was used to test the relationship between ∆PFR and age, executive function measured by the Trail Making Test, and sex. Pearson’s correlation coefficient was used to investigate the association between ∆PFR and the cost of Obstacles walking speed relative to Typical walking.ResultsAge, executive function, and their interaction significantly predicted greater ∆PFR (R2 = 0.34, p = .01). Participants were subgrouped according to age and executive function to examine the interaction effects. Adults of lower age and with lower executive function exhibited greater ∆PFR during Obstacles compared to their peers with higher executive function (p = .03). Adults of advanced age exhibited a ceiling of prefrontal recruitment during obstacle negotiation, regardless of executive function level (p = .87). Greater ∆PFR was significantly associated with a smaller cost of Obstacles (r = 0.3, p = .03).Discussion and ImplicationsThese findings are consistent with the CRUNCH framework: neural inefficiency where a greater amount of brain activation is needed for task performance at a similar level, compensatory overactivation to prevent a steeper decline in task performance, and capacity limitation with a recruitment ceiling effect.
Associations between health-related skills and young adults’ work ability within a structural health literacy model
Authors: Stassen Gerrit , Grieben Christopher , Hottenrott Nina , Rudolf Kevin , Froböse Ingo , Schaller Andrea 
Published: August 2020

Summary
Young adults have a high societal relevance but are still an under-represented target group in health promotion. Health literacy is widely acknowledged as one of the strongest predictors and key determinant of health, so its influence on work ability is of great interest. The purpose of the study was to examine the associations between health-related skills and work ability within the structural model of health literacy of Lenartz, Soellner and colleagues, which explains health behaviour and health through the indirect and direct influence of six ‘advanced skills’ (‘self-perception’, ‘proactive approach to health’, ‘dealing with health information’, ‘self-control’, ‘self-regulation’ and ‘communication and cooperation’). The cross-sectional study was based on baseline data of a health literacy promotion intervention (495 vocational school students, 59.0% female, age span 18–25 years). Structural equation modelling with partial least squares was used to examine the associations between the six constructs of the model and the Work Ability Index (WAI). Mean WAI score was 39.7 ± 4.5 (51.1% categorized ‘moderate’/‘poor’). Five out of six constructs of the model showed a statistically significant indirect or direct effect, respectively, on work ability. The model explained 24.8% of the WAI score variance. Our findings show associations between the health literacy model and the work ability among young employees. In view of demographic change, it is crucial to develop and analyse target group-specific health literacy interventions. The model offers new facets in the modelling of health literacy.
Energy analysis of cyclic parameters of organic Rankine cycle system
Authors: Yan Jinglu , Jia Wenguang , Li Kunling , Yu Hang , Guo Xianpei 
Published: August 2020

Abstract
Geothermal energy is a kind of green and non-polluting renewable energy. Medium and low-temperature geothermal energy below 150 °C is usually used directly for heating, industrial and agricultural heating, bathing, etc., and the utilization rate is low. Organic Rankine cycle (ORC) system can be used in a low-temperature geothermal power generation systems. Thermodynamic analysis of the thermal cycle system is carried out in this paper. Based on the principle of exergy analysis, the cycle parameters such as evaporation temperature, condensation temperature, superheating temperature, and supercooling temperature are analyzed. The results show that the exergy efficiency and system output power can improve by increasing evaporation temperature and the exergy loss can decrease in the evaporator. Increasing superheating temperature enhances the output power of the expander and the exergy loss in the condenser, decreases the exergy efficiency simultaneously. Increasing condensation temperature decreases the exergy efficiency of the system and the output power of the expander, and increases the exergy loss of the system. Although the output power of the expander will not be affected by supercooling temperature, the rise of supercooling temperature will reduce the exergy efficiency of the system and increase the exergy loss of the evaporator.
Corporate Governance, Employee Voice and the Interests of Employees: The Broken Promise of a ‘World Leading Package of Corporate Reforms’
Authors: Villiers Charlotte 
Published: August 2020

Abstract
Following a series of corporate governance scandals which involved exploitative treatment of workers, reforms were introduced to the UK’s corporate governance system in 2018, presented both as an attempt to rebuild trust and to afford a stronger voice for workers in that system. This paper explores the new landscape from a workers’ voice and protection perspective. It highlights that, while corporate governance has a role in ensuring workers’ needs are met, there is a tension between the goals of any reforms in this territory: board-level employee representation could be seen as a way of democratising the economy and valuing the part played by labour in that process, but it could also be seen as a way of increasing corporate value, economic performance or employee motivation, and disregarding the implications for labour. It is argued in this paper that worker protection requires a more genuine workplace democracy with full involvement of trade union representation. This would also help to broaden the corporate governance framework’s horizon towards a more genuine stakeholder vision beyond the existing tokenistic legal and regulatory nods in that direction.
Identification of Functional HLA-A*01:01–Restricted Epstein-Barr Latent Membrane Protein 2–Specific T-Cell Receptors
Authors: Huisman Wesley , Gille Ilse , van der Maarel Lieve E , Hageman Lois , Morton Laura T , de Jong Rob C M , Heemskerk Mirjam H M , Amsen Derk , Falkenburg J H Frederik , Jedema Inge 
Published: August 2020

Abstract

Background
Adoptive transfer of genetically engineered T cells expressing antigen-specific T-cell receptors (TCRs) is an appealing therapeutic approach for Epstein-Barr virus (EBV)–associated malignancies of latency type II/III that express EBV antigens (LMP1/2). Patients who are HLA-A*01:01 positive could benefit from such products, since no T cells recognizing any EBV-derived peptide in this common HLA allele have been found thus far.

Methods
HLA-A*01:01–restricted EBV-LMP2–specific T cells were isolated using peptide major histocompatibility complex (pMHC) tetramers. Functionality was assessed by production of interferon gamma (IFN-γ) and cytotoxicity when stimulated with EBV-LMP2–expressing cell lines. Functionality of primary T cells transduced with HLA-A*01:01–restricted EBV-LMP2–specific TCRs was optimized by knocking out the endogenous TCRs of primary T cells (∆TCR) using CRISPR-Cas9 technology.

Results
EBV-LMP2–specific T cells were successfully isolated and their TCRs were characterized. TCR gene transfer in primary T cells resulted in specific pMHC tetramer binding and reactivity against EBV-LMP2–expressing cell lines. The mean fluorescence intensity of pMHC-tetramer binding was increased 1.5–2 fold when the endogenous TCRs of CD8+ T cells was knocked out. CD8+/∆TCR T cells modified to express EBV-LMP2–specific TCRs showed IFN-γ secretion and cytotoxicity toward EBV-LMP2–expressing malignant cell lines.

Conclusions
We isolated the first functional HLA-A*01:01–restricted EBV-LMP2–specific T-cell populations and TCRs, which can potentially be used in future TCR gene therapy to treat EBV-associated latency type II/III malignancies.
A huge hepatic angiomyolipoma with growth during 5 years of follow-up
Authors: Machida Michio , Sugo Hiroyuki , Watanobe Ikuo 
Published: August 2020

Abstract
A 45-year-old woman was referred to our hospital with a huge liver tumor that had been diagnosed as a hepatic angiomyolipoma (HAML) 5 years previously. At the time of referral, it had enlarged from 12 to 20 cm within the previous 5 years and become symptomatic. Enhanced computed tomography revealed a very large, well-defined, low-density mass occupying the entire right lobe of the liver. The patient underwent right hemi-hepatectomy. The resected specimen weighed 1620 g and measured 20 × 14 × 8 cm. The pathological diagnosis was confirmed as benign HAML. The estimated growth rate of this tumor was 44% per year with a doubling time of 826 days. Although the majority of HAMLs are stable lesions, resection should perhaps be considered when the tumor is known to be growing and exceeds 6 cm in diameter, even if it has been diagnosed as benign.
Successful eradication of a large orbital hydatid cyst without rupture using fronto-orbitozygomatic approach, the first case reported from Syria
Authors: Abouassi Majd , Aloulou Mohammad , Hawa Nouran , Toutounji Tayf , Alyousef Safwan 
Published: August 2020

Abstract
Hydatid disease is a parasitic infection resulted by Echinococcus granulosus in the larval stage and is most prevalent in the Middle East, India, Africa, South America, New Zealand, Australia, Turkey and Southern Europe. However, orbital hydatid cysts are rare and represent a challenge to the surgeon to eradicate the cyst without rupture. Here, we report a case of a relatively large primary intraconal orbital cyst in a 21-year-old woman. We managed to eradicate the cyst without any complication using fronto-orbitozygomatic approach, and the patient remained disease free after the 3 months of follow-up.
The Usability of the Plan Quality Index to Support Evaluation of Community Health Action Plans
Authors: Courie Anna F , Tate Judith 
Published: August 2020

ABSTRACTIntroductionThe U.S. Army requires community health coalitions to develop targeted action plans in order to more effectively address top public health priorities. Reviews of community action plans indicate that they are often poorly developed and not fully implemented. To date, the U.S. Army has not implemented a standardized tool or process to evaluate action plans and provide recommendations for improvement to local installations. The Plan Quality Index (PQI) is an evidence-based, standardized tool that has been used successfully by technical experts to review and improve community action plans related to the prevention of obesity, injury and violence, and cancer.Materials and MethodsThe objective of this project was to determine the usability of the PQI and to provide recommendations for improving community health action plans focused on injury prevention for the U.S. Army. Five Health Promotion Project Officers and one Health Promotion Project Assistant at Army Public Health Center were trained on the PQI and reviewed injury prevention action plans for 17 installations. After using the PQI to assess injury prevention action plans, the individuals were given a System Usability Scale (SUS) survey to assess the usability of the PQI.ResultsResults of the SUS survey can range from 0 to 100, but do not represent percentages. A score of 65 indicates “greater than average” usability. Participant scores on the SUS demonstrated that the PQI has a high degree of usability. Mean usability was calculated at 83.3 (range 72.5–97.5, median 85, sd +/− 9.3).ConclusionThe PQI demonstrated a high level of usability by technical experts for providing feedback and recommendations regarding community health action plans for injury prevention in the U.S. Army. As a result, the PQI may be beneficial as a standard tool for community health improvement planning and consultation throughout the Army Public Health Center.