bluuebunny/crossref_metadata_2025_split huggingface dataset:
Integral field spectroscopy of luminous infrared main-sequence galaxies at cosmic noon
Authors: Hogan L , Rigopoulou D , Magdis G E , Pereira-Santaella M , García-Bernete I , Thatte N , Grisdale K , Huang J-S 
Published: February 2021

ABSTRACT
We present the results of an integral field spectroscopy survey of a sample of dusty (ultra) luminous infrared galaxies (U/LIRGs) at 2 &lt; z &lt; 2.5 using KMOS on the Very Large Telescope. The sample has been drawn from Herschel deep field surveys and benefits from ancillary multiwavelength data. Our goal is to investigate the physical characteristics, kinematics, and the drivers of star formation in the galaxies whose contribution dominates the peak of the cosmic star formation density. Two-thirds of the sample are main-sequence galaxies in contrast to the starburst nature of local U/LIRGs. Our kinematic study, unique in its focus on z ∼ 2 dusty star-forming galaxies, uses the H α emission line to find that ∼40 per cent appear to be isolated discs based on the ratio of rotational velocity to the velocity dispersion, suggesting steady-state mechanisms are sufficient to power the large star formation rates (SFRs). The ratio of obscured to unobscured star formation indicates the sample of galaxies experiences less dust obscuration compared to intermediate and local counterparts, while also hosting cooler dust than local U/LIRGs. In addition to H α we detect [N ii] 6583 Å in our targets and show the gas-phase metallicities do not exhibit the metal deficiency of local U/LIRGs. These results indicate that, despite their extreme IR luminosity, the underlying mechanisms driving the massive SFRs found at cosmic noon are due to scaled up disc galaxies as opposed to mergers.
TMSNP: a web server to predict pathogenesis of missense mutations in the transmembrane region of membrane proteins
Authors: Garcia-Recio Adrián , Gómez-Tamayo José Carlos , Reina Iker , Campillo Mercedes , Cordomí Arnau , Olivella Mireia 
Published: February 2021

Abstract
The massive amount of data generated from genome sequencing brings tons of newly identified mutations, whose pathogenic/non-pathogenic effects need to be evaluated. This has given rise to several mutation predictor tools that, in general, do not consider the specificities of the various protein groups. We aimed to develop a predictor tool dedicated to membrane proteins, under the premise that their specific structural features and environment would give different responses to mutations compared to globular proteins. For this purpose, we created TMSNP, a database that currently contains information from 2624 pathogenic and 196 705 non-pathogenic reported mutations located in the transmembrane region of membrane proteins. By computing various conservation parameters on these mutations in combination with annotations, we trained a machine-learning model able to classify mutations as pathogenic or not. TMSNP (freely available at http://lmc.uab.es/tmsnp/) improves considerably the prediction power of commonly used mutation predictors trained with globular proteins.
CRISPR-SE: a brute force search engine for CRISPR design
Authors: Li Bin , Chen Poshen B , Diao Yarui 
Published: February 2021

Abstract
CRISPR is a revolutionary genome-editing tool that has been broadly used and integrated within novel biotechnologies. A major component of existing CRISPR design tools is the search engines that find the off-targets up to a predefined number of mismatches. Many CRISPR design tools adapted sequence alignment tools as the search engines to speed up the process. These commonly used alignment tools include BLAST, BLAT, Bowtie, Bowtie2 and BWA. Alignment tools use heuristic algorithm to align large amount of sequences with high performance. However, due to the seed-and-extend algorithms implemented in the sequence alignment tools, these methods are likely to provide incomplete off-targets information for ultra-short sequences, such as 20-bp guide RNAs (gRNA). An incomplete list of off-targets sites may lead to erroneous CRISPR design. To address this problem, we derived four sets of gRNAs to evaluate the accuracy of existing search engines; further, we introduce a search engine, namely CRISPR-SE. CRISPR-SE is an accurate and fast search engine using a brute force approach. In CRISPR-SE, all gRNAs are virtually compared with query gRNA, therefore, the accuracies are guaranteed. We performed the accuracy benchmark with multiple search engines. The results show that as expected, alignment tools reported an incomplete and varied list of off-target sites. CRISPR-SE performs well in both accuracy and speed. CRISPR-SE will improve the quality of CRISPR design as an accurate high-performance search engine.
Paraneoplastic neurological syndrome: an evolving story
Authors: Jitprapaikulsan Jiraporn , Paul Pritikanta , Thakolwiboon Smathorn , Mittal Shivam Om , Pittock Sean J , Dubey Divyanshu 
Published: February 2021

AbstractParaneoplastic neurological syndrome (PNS) comprises a group of neurological disorders that result from a misguided immune response to the nervous system triggered by a distant tumor. These disorders frequently manifest before the diagnosis of the underlying neoplasm. Since the first reported case in 1888 by Oppenheim, the knowledge in this area has evolved rapidly. Several classic PNS have been described, such as limbic encephalitis, paraneoplastic cerebellar degeneration, encephalomyelitis, opsoclonus-myoclonus, sensory neuronopathy, Lambert-Eaton Myasthenic syndrome, and chronic gastrointestinal dysmotility. It is now recognized that PNS can have varied nonclassical manifestations that extend beyond the traditional syndromic descriptions. Multiple onconeural antibodies with high specificity for certain tumor types and neurological phenotypes have been discovered over the past 3 decades. Increasing use of immune checkpoint inhibitors (ICIs) has led to increased recognition of neurologic ICI-related adverse events. Some of these resemble PNS. In this article, we review the clinical, oncologic, and immunopathogenic associations of PNS.
Associations of dietary vitamin B1, vitamin B2, vitamin B6, and vitamin B12 with the risk of depression: a systematic review and meta-analysis
Authors: Wu Yanjun , Zhang Liming , Li Suyun , Zhang Dongfeng 
Published: February 2021

Abstract

Context
The results from epidemiologic studies on the intake of dietary vitamin B1, B2, B6, and B12 and association with risk of developing depression have been inconsistent.

Objective
The purpose of this systematic review and meta-analysis was to summarize the existing evidence and synthesize the results.

Data Sources
The databases of Web of Science and PubMed were searched for relevant articles published in English until September 2020.

Study Selection
Observational studies that evaluated the associations between depression and dietary vitamin B1, B2, B6, and B12 were included in this study.

Data Extraction
The job of data extraction was undertaken by 2 authors, and the pooled relative risks (RRs) and 95% confidence intervals (CIs) were calculated using a fixed-effects model.

Results
Thirteen articles related to 18 studies were eligible for inclusion in this systematic review and meta-analysis. The pooled RR (95% CI) of depression for the highest vs the lowest category of dietary vitamin B1, B2, B6, and B12 was 0.69 (0.55–0.87), 0.77 (0.67–0.89), 0.81 (0.71–0.93), and 0.86 (0.75–0.99), respectively. The pooled RR (95% CI) of depression for the highest vs the lowest category of dietary vitamin B2 was 0.80 (0.64–0.99) in females and 0.83 (0.67–1.02) in males, for dietary vitamin B6 was 0.71 (0.59–0.86) in females and 0.92 (0.76–1.12) in males, and for dietary vitamin B12 was 0.79 (0.65–0.97) in females and 0.94 (0.77–1.15) in males.

Conclusion
This study suggested that the intake of dietary vitamin B1, B2, B6, and B12 may be inversely associated with the risk of depression; the inverse associations observed between depression and intake of dietary vitamin B2, B6, and B12 were significant in females, but not in males. Further studies are needed to confirm these results.
Digital Intra-Party Democracy: An Exploratory Analysis of Podemos and the Labour Party
Authors: García Lupato Fabio , Meloni Marco 
Published: February 2021

Abstract
The role of technology is growing in intra-party democracy (IPD) processes. This article presents a proposal for analysing digital IPD, by applying empirical democratic theory dimensions. To test our methodology, we analyse two different types of parties, a new digital one, Pos, and a traditional one undergoing reform, the Labour Party. Our analysis shows, first, that the application of technology is not neutral, with a differential impact depending on the specific democratic dimension considered and, secondly, that—due to convergent developments—new and established parties are closer in their digital IPD than expected. These results point out the relevance, for the ongoing debate on the quality of IPD, of considering the impact of digital on different democratic dimensions and its evolution over time.
An epigenetic pathway in rice connects genetic variation to anaerobic germination and seedling establishment
Authors: Castano-Duque Lina , Ghosal Sharmistha , Quilloy Fergie A , Mitchell-Olds Thomas , Dixit Shalabh 
Published: February 2021

Abstract
Rice production is shifting from transplanting seedlings to direct sowing of seeds. Following heavy rains, directly sown seeds may need to germinate under anaerobic environments, but most rice (Oryza sativa) genotypes cannot survive these conditions. To identify the genetic architecture of complex traits, we quantified percentage anaerobic germination (AG) in 2,700 (wet-season) and 1,500 (dry-season) sequenced rice genotypes and performed genome-wide association studies (GWAS) using 693,502 single nucleotide polymorphisms. This was followed by post-GWAS analysis with a generalized SNP-to-gene set analysis, meta-analysis, and network analysis. We determined that percentage AG is intermediate-to-high among indica subpopulations, and AG is a polygenic trait associated with transcription factors linked to ethylene responses or genes involved in metabolic processes that are known to be associated with AG. Our post-GWAS analysis identified several genes involved in a wide variety of metabolic processes. We subsequently performed functional analysis focused on the small RNA and methylation pathways. We selected CLASSY 1 (CLSY1), a gene involved in the RNA-directed DNA methylation (RdDm) pathway, for further analyses under AG and found several lines of evidence that CLSY1 influences AG. We propose that the RdDm pathway plays a role in rice responses to water status during germination and seedling establishment developmental stages.
A year of COVID-19 and the spiritual well-being of the people
Authors: Rosales Renniel Jayson Jacinto 
Published: February 2021

Abstract
The global impact of the coronavirus disease 2019 pandemic has caused innumerable damages to the total well-being of the people. In previous studies, spirituality has shown positive effect to the well-being of the people. As the Catholic Church continuously provide religious and spiritual nourishment through online or virtual celebration of the liturgy, the ideal and lived experience of the select Catholic faithful shows no dissonance. The online and virtual celebrations give hope and to the people post-pandemic, as we enter to the new normal.
COVID-19: vaccination in a developing country
Authors: Gutiérrez-Zevallos Juan Diego , Espíritu-Martínez Libertad Beatriz 
Published: February 2021

Abstract
The common good and public service are important to gain public trust especially in the midst of a pandemic of misinformation about vaccines and miracle therapies being spread on social media. Controversies in the government of a developing country do not help to control the SARS-COV-2 pandemic. Is it only the government’s responsibility or can doctors and medical students promote the truth with appropriate communication strategies to decrease COVID-19 vaccine hesitancy?
Embedding Learning in a Learning Health Care System to Improve Clinical Practice
Authors: McEvoy Matthew D. , Dear Mary Lynn , Buie Reagan , Fowler Leslie C. , Miller Bonnie , Fleming Geoffrey M. , Moore Don , Rice Todd W. , Bernard Gordon R. , Lindsell Christopher J. ,   for the Vanderbilt Learning Healthcare System Investigators
Published: February 2021

Problem
In an ideal learning health care system (LHS), clinicians learn from what they do and do what they learn, closing the evidence-to-practice gap. In operationalizing an LHS, great strides have been made in knowledge generation. Yet, considerable challenges remain to the broad uptake of identified best practices. To bridge the gap from generating actionable knowledge to applying that knowledge in clinical practice, and ultimately to improving outcomes, new information must be disseminated to and implemented by frontline clinicians. To date, the dissemination of this knowledge through traditional avenues has not achieved meaningful practice change quickly.

Approach
Vanderbilt University Medical Center (VUMC) developed QuizTime, a smartphone application learning platform, to provide a mechanism for embedding workplace-based clinician learning in the LHS. QuizTime leverages spaced education and retrieval-based practice to facilitate practice change. Beginning in January 2020, clinician–researchers and educators at VUMC designed a randomized, controlled trial to test whether the QuizTime learning system influenced clinician behavior in the context of recent evidence supporting the use of balanced crystalloids rather than saline for intravenous fluid management and new regulations around opioid prescribing.

Outcomes
Whether spaced education and retrieval-based practice influence clinician behavior and patient outcomes at the VUMC system level will be tested using the data currently being collected.

Next Steps
These findings will inform future directions for developing and deploying learning approaches at scale in an LHS, with the goal of closing the evidence-to-practice gap.
We Burn Out, We Break, We Die: Medical Schools Must Change Their Culture to Preserve Medical Student Mental Health
Authors: Veal Christopher Thomas 
Published: February 2021

The author explores medical student depression and suicide through the lens of the author’s personal struggle during the first 2 years of medical school. While the author’s story is unique, other medical students have also faced challenges that have led them to consider a permanent solution to a temporary problem. Although resources are available, stigma represents a significant barrier for students as they decide whether to seek help. Students fear that showing the slightest hint of vulnerability or imperfection will be used against them in an advancement committee, a course evaluation, or the dean’s letter for residency applications. This difficulty asking for help and the subsequent suppression of feelings can lead to burnout and ultimately to increased risk of suicide.
The author calls for medical schools to make changes to their culture to preserve medical student mental health. These include committing to helping students who are struggling academically or psychologically, implementing an institution-wide program to screen for individuals at risk for suicide, educating members of the institution’s community about depression to destigmatize seeking help for mental health, and ensuring confidential mental health services are readily available to those who need them. But, most importantly, medical schools must create a culture that normalizes the need for self-care and includes vulnerability as part of training in professionalism.
Association Between Medicaid Status, Social Determinants of Health, and Bariatric Surgery Outcomes
Authors: Liu Natalie , Venkatesh Manasa , Hanlon Bret M. , Muraveva Anna , Johnson Morgan K. , Hanrahan Lawrence P. , Funk Luke M. 
Published: February 2021

Objective:
To compare outcomes after bariatric surgery between Medicaid and non-Medicaid patients and assess whether differences in social determinants of health were associated with postoperative weight loss.

Background:
The literature remains mixed on weight loss outcomes and healthcare utilization for Medicaid patients after bariatric surgery. It is unclear if social determinants of health geocoded at the neighborhood level are associated with outcomes.

Methods:
Patients who underwent laparoscopic sleeve gastrectomy (SG) or Roux-en-Y gastric bypass (RYGB) from 2008 to 2017 and had ≥1 year of follow-up within a large health system were included. Baseline characteristics, 90-day and 1-year outcomes, and weight loss were compared between Medicaid and non-Medicaid patients. Area deprivation index (ADI), urbanicity, and walkability were analyzed at the neighborhood level. Median regression with percent total body weight (TBW) loss as the outcome was used to assess predictors of weight loss after surgery.

Results:
Six hundred forty-seven patients met study criteria (191 Medicaid and 456 non-Medicaid). Medicaid patients had a higher 90-day readmission rate compared to non-Medicaid patients (19.9% vs 12.3%, P < 0.016). Weight loss was similar between Medicaid and non-Medicaid patients (23.1% vs 21.9% TBW loss, respectively; P = 0.266) at a median follow-up of 3.1 years. In adjusted analyses, Medicaid status, ADI, urbanicity, and walkability were not associated with weight loss outcomes.

Conclusions:
Medicaid status and social determinants of health at the neighborhood level were not associated with weight loss outcomes after bariatric surgery. These findings suggest that if Medicaid patients are appropriately selected for bariatric surgery, they can achieve equivalent outcomes as non-Medicaid patients.
Oncological Impact of Gross Proximal Margin Length in Distal Gastrectomy for Gastric Cancer: Is the Japanese Recommendation Valid?
Authors: Hayami Masaru , Ohashi Manabu , Ishizuka Naoki , Hiki Naoki , Kumagai Koshi , Ida Satoshi , Sano Takeshi , Nunobe Souya 
Published: February 2021

Objective:
To identify an oncological impact of gross proximal margin (PM) length in distal gastrectomy for cancer.

Summary background data:
In Japan, to obtain pathologically negative PMs in gastrectomy for cancer, the Gastric Cancer Treatment Guidelines (GCTGs) recommend maintaining the PM length to at least 2 cm for cT1, 3 cm for the expansive growth type (Exp), and 5 cm for the infiltrative growth type (Inf) of cT2–4. The GCTGs also recommend confirming pathologically negative PMs by intraoperative frozen section analyses when the gross PMs are shorter than the recommendations. However, whether they are valid is unknown.

Methods:
Patients who intended to undergo curative distal gastrectomy were included. They were divided into groups A (adherence to the GCTGs) and NA (nonadherence) according to the PM length. The incidence of pathologically positive PMs and survival outcomes were compared between the groups. Propensity scores (PSs) were used in comparisons of survival outcomes to eliminate potential confounders.

Results:
A total of 1036 patients were eligible. Pathologically positive PMs were identified in group NA with cT1 and Inf, and the incidence was 1.6% and 3.1%, respectively. Adjusted analysis using the PSs showed comparable survival outcomes between the groups. However, the hazard ratios according to the PSs presented a possible survival advantage in maintaining the recommended gross PM lengths except for cT1 and Exp located in the lower stomach.

Conclusion:
Surgeons should maintain the gross PM lengths recommended in the GCTGs to both obtain pathologically negative PMs and avoid survival disadvantages.
Surgical Patients’ Hospital Experience Scores: Neighborhood Context Conceptual Framework
Authors: Kranjac Ashley Wendell , Kranjac Dinko , Fortier Michelle A. , Patton Pat , Giafaglione Brad , Kain Zeev N. 
Published: February 2021

Objective:
Through geocoding the physical residential address included in the electronic medical record to the census tract level, we present a novel model for concomitant examination of individual patient-related and residential context-related factors that are associated with patient-reported experience scores.

Summary Background Data:
When assessing patient experience in the surgical setting, researchers need to examine the potential influence of neighborhood-level characteristics on patient experience-of-care ratings.

Methods:
We geocoded the residential address included in the electronic medical record (EMR) from a tertiary care facility to the census tract level of Orange County, CA. We then linked each individual record to the matching census tract and use hierarchical regression analyses to test the impact of distinct neighborhood conditions on patient experience. This approach allows us to estimate how each neighborhood characteristic uniquely influences Hospital Consumer Assessment of Healthcare Providers and Systems (HCAHPS) scores.

Results:
Individuals residing in communities characterized by high levels of socioeconomic disadvantage have the highest experience ratings. Accounting for individual patient’s characteristics such as age, gender, race/ethnicity, primary language spoken at home, length of stay, and average pain levels during their hospital stay, neighborhood-level characteristics such as proportions of people receiving public assistance influence the ratings of hospital experience (0.01, P < 0.05) independent of, and beyond, these individual-level factors.

Conclusions:
This manuscript is an example of how geocoding could be used to analyze surgical patient experience scores. In this analysis, we have shown that neighborhood-level characteristics influence the ratings of hospital experience independent of, and beyond, individual-level factors
Adoption and Usage of Video Telehealth in a Large, Academic Department of Surgery
Authors: Lazar Andrew N. , Nemeth Samantha K. , Kurlansky Paul A. , Patel Virendra I. , Homma Shunichi , Morrissey Nicholas J. 
Published: February 2021

Objectives:
To understand the impact that video telehealth has on outpatient visit volume and reimbursement as a method of maintaining care.

Background:
As the coronavirus disease 2019 (COVID-19) spread across the United States starting in 2020, it caused numerous areas of medicine and healthcare to reexamine how we provide care to patients across all disciplines. One method clinicians used to rapidly adapt to these transformed settings was video telehealth, which was previously rarely used.

Methods:
This retrospective review examined outpatient volume and reimbursement data of a large, academic department of surgery. The study reviewed data during 2 time periods: pre-COVID-19 (February 1, 2020, to March 15, 2020) and COVID-19 (March 16, 2020, to April 30, 2020).

Results:
During the period of February 1 to April 30, 13,193 outpatient visits were analyzed. The pre-COVID-19 group contained 9041 (68.5%) visits, whereas the COVID-19 group contained 4152 (31.4%) visits. All divisions noted a drop in visit volume from pre-COVID-19 compared with COVID-19. There was rapid adoption of video telehealth during COVID-19, which made up most patient visits during that time (61.3%). We also found that video telehealth led to significant reimbursements while also allowing patients in numerous states to receive care.

Conclusions:
Previously, video telehealth was used by clinicians in a small portion of outpatient visits. However, safety concerns surrounding COVID-19 forced multiple changes to the way care is provided. Although outpatient volume at our center was less than that before the pandemic, video telehealth was rapidly adopted by providers and allowed for safe and effective outpatient care to patients in a high number of states while still being reimbursed at a high rate.