bluuebunny/crossref_metadata_2025_split huggingface dataset:
Runs of homozygosity and analysis of inbreeding depression
Authors: Sumreddee Pattarapol , Toghiani Sajjad , Hay El Hamidi , Roberts Andrew , Aggrey Samuel E , Rekaya Romdhane 
Published: November 2020

Abstract
Pedigree information was traditionally used to assess inbreeding. The availability of high-density marker panels provides an alternative to assess inbreeding, particularly in the presence of incomplete and error-prone pedigrees. Assessment of autozygosity across chromosomal segments using runs of homozygosity (ROH) has emerged as a valuable tool to estimate inbreeding due to its general flexibility and ability to quantify the chromosomal contribution to genome-wide inbreeding. Unfortunately, the identification of ROH segments is sensitive to the parameters used during the search process. These parameters are heuristically set, leading to significant variation in the results. The minimum length required to identify an ROH segment has major effects on the estimation of inbreeding and inbreeding depression, yet it is arbitrarily set. To overcome this limitation, a search algorithm to approximate mutation enrichment was developed to determine the minimum length of ROH segments. It consists of finding genome segments with significant effect differences in trait means between animals with high and low burdens of autozygous intervals with a specific length. The minimum length could be determined heuristically as the smallest interval at which a significant signal is detected. The proposed method was tested in an inbred Hereford cattle population genotyped for 30,220 SNPs. Phenotypes recorded for six traits were used for the approximation of mutation loads. The estimated minimum length was around 1 Mb for yearling weight (YW) and average daily gain (ADG) and 4 Mb for birth weight and weaning weight. These trait-specific thresholds estimated using the proposed method could be attributed to a trait-dependent effect of homozygosity. The detection of significant inbreeding effects was well aligned with the estimated thresholds, especially for YW and ADG. Although highly deleterious alleles are expected to be more frequent in recent inbreeding (long ROH), short ROH segments (&lt;5 Mb) could contain a large number of less deleterious mutations with substantial joint effects on some traits (YW and ADG). Our results highlight the importance of accurate estimation of the ROH-based inbreeding and the necessity to consider a trait-specific minimum length threshold for the identification of ROH segments in inbreeding depression analyses. These thresholds could be determined using the proposed method provided the availability of phenotypic information.
Racial Disparities in Recurrence and Overall Survival in Patients With Locoregional Colorectal Cancer
Authors: Snyder Rebecca A , Hu Chung-Yuan , Zafar Syed Nabeel , Francescatti Amanda , Chang George J 
Published: November 2020

Abstract

Background
The purpose of this study was to determine the association between race and long-term cancer outcomes (recurrence and overall survival) within a population of US patients with locoregional colorectal cancer (CRC).

Methods
A cohort study of primary patient data merged with the National Cancer Database as part of a Commission on Cancer Special Study was performed. The study population was a random sample of patients undergoing surgery for stage I to III CRC between years 2006 and 2007 with 5 years of follow-up. Propensity-weighted multivariable Cox regression was performed with pooled results to yield statistical inferences. Prespecified sensitivity analysis was performed only for patients who received guideline concordant care (GCC) of primary CRC. All statistical tests were 2-sided.

Results
The study population included 8176 patients, 9.9% (n = 811) Black and 90.1% (n = 7365) White. Black patients were more likely to be uninsured or underinsured, have lower household income, and lower educational status (all P &lt; .001). Rates of GCC were higher among Black vs White patients with colon cancer (76.9% vs 72.6%, P = .02), and Black and White patients with rectal cancer were treated with radiation at similar rates (69.1% vs 66.6%, P = .64). Black race was independently associated with increased risk of recurrence (hazard ratio [HR] = 1.48, 95% confidence interval [CI] = 1.26 to 1.73) and mortality (HR = 1.37, 95% CI = 1.18 to 1.59). In sensitivity analysis of only patients who received GCC, observed effects for recurrence (HR = 1.51, 95% CI = 1.27 to 1.79) and overall survival (HR = 1.40, 95% CI = 1.18 to 1.66) persisted.

Conclusions
Despite higher rates of GCC for CRC, Black patients experience a higher risk of recurrence and mortality compared with White patients.
A systemic approach to the quantification of the phenotypic plasticity of plant physiological traits: the multivariate plasticity index
Authors: Pennacchi João Paulo , Lira Jean Marcel Sousa , Rodrigues Marcelo , Garcia Fernando Henrique Silva , Mendonça Ane Marcela das Chagas , Barbosa João Paulo Rodrigues Alves Delfino 
Published: November 2020

Abstract
The phenotype of an individual emerges from the interaction of its genotype with the environment in which it is located. Phenotypic plasticity (PP) is the ability of a specific genotype to present multiple phenotypes in response to the environment. Past and current methods for quantification of PP present limitations, mainly in what constitutes a systemic analysis of multiple traits. This research proposes an integrative index for quantifying and evaluating PP. The multivariate plasticity index (MVPi) was calculated based on the Euclidian distance between scores of a canonical variate analysis. It was evaluated for leaf physiological traits in two cases using Brazilian Cerrado species and sugarcane varieties, grown under diverse environmental conditions. The MVPi was sensitive to plant behaviour from simple to complex genotype–environment interactions and was able to inform coarse and fine changes in PP. It was correlated to biomass allocation, showing agreement between plant organizational levels. The new method proved to be elucidative of plant metabolic changes, mainly by explaining PP as an integrated process and emergent property. We recommend the MVPi method as a tool for analysis of phenotypic plasticity in the context of a systemic evaluation of plant phenotypic traits.
Excluding possible sites of high-energy emission in 3C 84
Authors: Linhoff Lena , Sandrock Alexander , Kadler Matthias , Elsässer Dominik , Rhode Wolfgang 
Published: November 2020

ABSTRACT
The FR-I galaxy 3C 84, that is identified with the misaligned blazar NGC 1275, is well known as one of the very few radio galaxies emitting gamma-rays in the TeV range. Yet, the gamma-ray emission region cannot be pinpointed and the responsible mechanisms are still unclear. We calculate the optical absorption depth of high-energy photons in the broad-line region of 3C 84 depending on their energy and distance to the central black hole. Based on these calculations, a lower limit on the distance of the emission region from the central black hole can be derived. These lower limits are estimated for two broad-line region geometries (shell and ring) and two states of the source, the low state in 2016 October–December and a flare state in 2017 January. For the shell geometry, we can place the emission region outside the Ly α radius. For the ring geometry and the low flux activity, the minimal distance between the black hole, and the gamma-ray emission region is close to the Ly α radius. In the case of the flaring state (ring geometry), the results are not conclusive. Our results exclude the region near the central black hole as the origin of the gamma-rays detected by Fermi–LAT and Major Atmospheric Gamma-Ray Imaging Cherenkov. With these findings, we can constrain the theoretical models of acceleration mechanisms and compare the possible emission region to the source’s morphology resolved by radio images from the Very Long Baseline Array.
Indigenous Peoples
Authors: Plotkin Mark J. 
Published: November 2020

When did the first humans arrive in Amazonia?

Deciphering the prehistory of ancient Amazonia presents a multitude of challenges. Bodies do not readily mummify in the ubiquitous heat, humidity, and constant precipitation. There exist no written records of pre-​Columbian Amazonia that can be deciphered Champollion-​like with some...
How Authoritarian Regimes Gain Power
Authors: Frantz Erica 
Published: November 2020

How Do Authoritarian Regimes Gain Power?

From 1946 to 2010, 250 new authoritarian regimes came to power. About half of the time (46 percent), these regimes toppled pre-​existing authoritarian regimes; just over a quarter of the time (29 percent), they toppled democracies; and the rest of...
What Are the Treatments for PTSD?
Authors: Rothbaum Barbara O. , Rauch Sheila A. M. 
Published: November 2020

In
Chapter 3 of this book, we described what it’s like to live with PTSD. The bad news is it stinks to have PTSD, as it disrupts people’s lives, health, and relationships. And as hard as it is to live with PTSD, it...
Original Research: Assessing Organizational Focus on Health Literacy in North Texas Hospitals
Authors: Howe Carol J. , Adame Tracine , Lewis Brennan , Wagner Teresa 
Published: November 2020

ABSTRACT

Overview:
In 2012, the Institute of Medicine Roundtable on Health Literacy established 10 attributes of a health literate health care organization that, if instated, would improve health information and empower patients to make more informed health decisions. Few studies have assessed how well organizations meet these attributes.

Purpose:
This study sought to describe the extent to which health care systems in North Texas were adopting policies and practices that address the 10 attributes of a health literate health care organization. More specifically, we sought to describe key organizational leaders' and clinicians' perceptions in this regard.

Study design and methods:
This was a mixed-methods study, conducted with a convenience sample of 74 key informants from 13 hospitals across five health care systems. Informants provided demographic data, and their perceptions of the extent to which their hospital met the 10 attributes were measured via the Health Literate Health Care Organization 10-item questionnaire (HLHO-10) and semistructured interviews.

Results:
Mean scores for HLHO-10 items ranged from 3.74 to 5.39, with 7 as a maximum score. Qualitative data provided richer content, elaborating on the survey results. Workforce training in health literacy, patient inclusion in health information development and evaluation, and communication about health care costs were rated the lowest and were described as issues of concern.

Conclusion:
Study findings indicated limited leadership and little systemic promotion of efforts to ensure health literate health care organizations, although individual health literacy champions sometimes stepped up with creative initiatives.
DEA Disconnect Leads to Buprenorphine Bottlenecks
Authors: Ostrach Bayla , Carpenter Delesha , Cote Larry P. 
Published: November 2020

Objectives:
To describe a buprenorphine dispensing bottleneck resulting from a pharmacist-perceived Drug Enforcement Administration “cap” on the amount of buprenorphine that can be ordered or stocked.

Methods:
Expert review and preliminary fieldwork.

Results:
We find no such cap exists, though medication distributors struggle to accurately understand and interpret regulatory guidelines, with implications for medication availability.
In states where opioid overdose rates remain higher and efforts to increase the number of eligible health care providers prescribing medications to treat opioid use disorder are underway, patients prescribed buprenorphine products report difficult filling prescriptions and pharmacists perceive limits on how much medication they can order and stock.

Conclusions:
We recommend Drug Enforcement Administration policy clarifications or changes to facilitate distributor interpretation; pharmacist workflow; and patient access to medication. We also advise continuing education with pharmacists and buprenorphine prescribers. These steps would facilitate greater access to lifesaving treatment for opioid use disorder.
Influence of Depressive Symptoms on the Outcome of Lumbar Spine Fusion—A 5-year Follow-up Study
Authors: Toivonen Leevi , Häkkinen Arja , Pekkanen Liisa , Salonen Anne , Kautiainen Hannu , Neva Marko H. 
Published: November 2020

Study Design.
Prospective follow-up study.

Objective.
The aim of this study was to assess whether depressive symptoms change the outcome of lumbar spine fusion (LSF) surgery at a 5-year follow-up.

Summary of Background Data.
Previous reports of the influence of depressive symptoms on the results of spine surgery are controversial, but the patient characteristics and indications for surgery varied widely between the studies. The influence of depressive symptoms on the 5-year outcome of LSF has not been studied.

Methods.
The study was based on data from a local LSF database from two hospitals comprising 392 consecutive patients (mean age 61 years, 277 women) who underwent an instrumented LSF and fulfilled the 5-year follow-up. At the 5-year follow-up, the patients were compared with a control group from the general population (n = 477, age-, sex-, and residential area-matched) extracted from Official Statistics of Finland. The prevalence of depressive symptoms was evaluated using the Depression Scale (DEPS; 0–30) and disability was evaluated by the Oswestry Disability Index (ODI; 0–100%). A DEPS score ≥12 was considered to indicate depressive symptoms.

Results.
Before surgery, 35% of the patients had depressive symptoms. The proportion diminished to 13% at 3 months postoperatively and increased to 24% at 5 years. In the population, the prevalence was 11% at baseline and 10% at the 5-year follow-up. The preoperative ODI was 54 in the patients with depressive symptoms, and it was 41 in the patients with no depressive symptoms. The changes at 5-year follow-up were −20 and −18, correspondingly. The same congruence was preserved when analyzing short and long fusions separately. These changes were statistically and clinically significant. In the control population, the ODI remained around 24 in depressive people and 10 in nondepressive people.

Conclusion.
Our data suggest that patients with and without depressive symptoms may benefit equally well from LSF.

Level of Evidence:
3
Comparison of Morphometric Measurements of Traditional Posterior Cervical Screw and Paravertebral Foramen Screw in Chinese Population
Authors: Chen Xi , Yang Qing , Kalisi Kupu Uluakimata Mei Muli , Yuan Suomao , Tian Yonghao , Liu Xinyu 
Published: November 2020

Study Design.
A morphometric measurement study.

Objective.
To measure the length and angle parameters of the screw paths of pedicle screws (PS), lateral mass screws (LMS), and paravertebral foramen screws (PVFS) of subaxial cervical spine in Chinese population.

Summary of Background Data.
Aramomi proposed a novel internal fixation technology, named PVFS, as an alternative to LMS and PS for subaxial cervical vertebrae (C3-C7).

Methods.
This study measured the length and medial angles of screw paths on the three-dimensional reconstruction model of cervical computerized tomography data of 50 patients (25 men and 25 women) in our hospital from January 2018 to June 2018.

Results.
In general, the optimum length and medial angle of the PVFS in Chinese population were 10.65 mm and 21.12° at C3; 10.12 mm, 22.62° at C4; 9.82 mm, 23.66° at C5; 9.19 mm, 24.13° at C6; and 9.10 mm, 27.54° at C7. The optimum axial length and medial angle of PS in Chinese population were 30.94 mm, 33.92° at C3; 30.50 mm, 34.95° at C4; 31.92 mm, 33.42° at C5; 30.50 mm, 31.94° at C6; and 29.87 mm, 31.01° at C7. The optimum lengths of LMS paths in Chinese population were C3, 14.84 mm; C4, 15.33 mm; C5, 15.44 mm; C6, 14.74 mm; and C7, 14.06 mm.

Conclusion.
Although the length of PVFS is limited, it still can be used as an effective substitute for LMS and PS. The PVFS does not have the risk of directly injuring the vertebral artery, its safety angle of insertion is larger than that in PS, and it has higher surgical safety.

Level of Evidence: 3
Greater Socioeconomic Disadvantage Is Associated with Worse Symptom Severity at Initial Presentation in Patients Seeking Care for Lumbar Disc Herniation
Authors: Bernstein David N. , Merchan Nelson , Fear Kathleen , Rubery Paul T. , Mesfin Addisu 
Published: November 2020

Study Design.
Retrospective, observational study.

Objective.
To determine the association of patient socioeconomic disadvantage, insurance type, and other characteristics on presenting symptom severity in patients with isolated lumbar disc herniation.

Summary of Background Data.
Little is known of the impact of socioeconomic disadvantage and other patient characteristics on the level of self-reported symptom severity when patients first seek care for lumbar disc herniation.

Methods.
Between April 2015 and December 2018, 734 patients newly presenting for isolated lumbar disc herniation who completed the Patient-Reported Outcomes Measurement Information System Physical Function (PF), Pain Interference (PI), and Depression Computer Adaptive Tests (CATs) were identified. Socioeconomic disadvantage was determined using the Area Deprivation Index, a validated measure of socioeconomic disadvantage at the census block group level (0–100, 100 = highest socioeconomic disadvantage). Bivariate analyses were used. Multivariable linear regression was used to determine if there was an association between socioeconomic disadvantage, insurance type, and other patient factors and presenting patient-reported health status.

Results.
Significant differences in age, insurance type, self-reported race, marital status, and county of residence were appreciated when comparing patient characteristics by socioeconomic disadvantage levels (all comparisons, P < 0.01). In addition, significant differences in age, insurance type, marital status, and county of residence were appreciated when comparing patient characteristics by self-reported race (all comparisons, P < 0.01). Being in the most socioeconomically disadvantaged cohort was associated with worse presenting Patient-Reported Outcomes Measurement Information System scores (Physical Function: β = -3.27 (95% confidence interval [CI]: -4.89 to -1.45), P < 0.001; Pain Interference: β = 3.20 (95% CI: 1.58–4.83), P < 0.001; Depression: β = 3.31 (95% CI: 1.08–5.55), P = 0.004.

Conclusion.
The most socioeconomically disadvantaged patients with symptomatic lumbar disc herniations present with worse functional limitations, pain levels, and depressive symptoms as compared to patients from the least socioeconomically disadvantaged cohort when accounting for other key patient factors.

Level of Evidence: 3
Growth of the Digital Footprint of the Society of Critical Care Medicine Annual Congress: 2014–2020
Authors: Carroll Christopher L. , Szakmany Tamas , Dangayach Neha S. , DePriest Ashley , Duprey Matthew S. , Kaul Viren , Kleinpell Ruth , Tegtmeyer Ken , Kudchadkar Sapna R. 
Published: November 2020

Objectives:
Since 2014, the Society of Critical Care Medicine has encouraged “live-tweeting” through the use of specific hashtags at each annual Critical Care Congress. We describe how the digital footprint of the Society of Critical Care Medicine Congress on Twitter has evolved at a time when social media use at conferences is becoming increasingly popular.

Design:
We used Symplur Signals (Symplur LLC, Pasadena, CA) to track all tweets containing the Society of Critical Care Medicine Congress hashtag for each annual meeting between 2014 and 2020. We collected data on the number of tweets, tweet characteristics, and impressions (i.e., potential views) for each year and data on the characteristics of the top 100 most actively tweeting users of that Congress.

Setting:
Twitter.

Subjects:
Users tweeting with the Critical Care Congress hashtag.

Interventions:
Not applicable.

Measurements and Main Results:
The Critical Care Congress digital footprint grew substantially from 2014 to 2020. The 2014 Critical Care Congress included 1,629 tweets by 266 users, compared with 29,657 tweets by 3,551 participants in 2020; average hourly tweets increased from 9.7 to 177. The percentage of tweets with mentions of other users and tweets with visual media increased. Users attending the conference were significantly more likely to compose original tweets, whereas those tweeting from afar were more likely to retweet Critical Care Congress content. There was a yearly increase in content-specific hashtags used in conjunction with Critical Care Congress hashtags (n = 429 in 2014 to n = 22,272 in 2020), most commonly related to pediatrics (18% of all hashtags), mobility/rehab (9%), sepsis (7%) social media (6%), and ICU burnout (1%).

Conclusions:
There has been significant growth in live-tweeting at the Critical Care Congress, along with the increased use of content-specific hashtags and visual media. This digital footprint is largely driven by a proportion of highly engaged users. As medical conferences transition to completely or partially online platforms, understanding of the digital footprint is crucial for success.
Postural Orthostatic Tachycardia Syndrome and Disordered Eating: Clarifying the Overlap
Authors: Benjamin Julia , Sim Leslie , Owens Michele Tsai , Schwichtenberg Andrea , Harrison Tracy , Harbeck-Weber Cindy 
Published: November 2020

ABSTRACT:

Objective:
Postural orthostatic tachycardia syndrome (POTS) is estimated to occur in up to 1% of adolescents, with symptoms of dizziness, fatigue, and pain impacting daily functioning. However, many risk factors and symptoms for POTS overlap with those of youth with disordered eating, and adolescents with POTS may be at increased risk for developing eating disorders. Therefore, the present study sought to better understand this overlap. We hypothesized that patients with POTS would have higher than expected rates of weight change, restrictive eating patterns, and food sensitivities.

Methods:
We conducted a retrospective chart review of 96 adolescents and young adults diagnosed with POTS who were participating in a 3-week intensive interdisciplinary pain rehabilitation program. We conducted descriptive and correlational statistical analyses on data from self-report measures, biomarkers of nutritional status, and abstracted information about eating and weight concerns from medical notes.

Results:
Nearly 3 quarters of participants described engaging in restrictive eating, and more than half of them described experiencing weight loss. They also endorsed experiencing food allergies, celiac disease, and eating disorder at higher rates than would be expected in the general population. One-fifth of the sample had experienced invasive interventions to correct for nutritional imbalances, such as having a feeding tube.

Conclusion:
Weight and eating are clear areas of risk for patients with orthostatic intolerance. It is essential that treatment team members thoroughly screen for eating disturbances and make recommendations that support regular and balanced eating habits.