bluuebunny/crossref_metadata_2025_split huggingface dataset:
Elephant Genomes Reveal Accelerated Evolution in Mechanisms Underlying Disease Defenses
Authors: Tollis Marc , Ferris Elliott , Campbell Michael S , Harris Valerie K , Rupp Shawn M , Harrison Tara M , Kiso Wendy K , Schmitt Dennis L , Garner Michael M , Aktipis Christina Athena , Maley Carlo C , Boddy Amy M , Yandell Mark , Gregg Christopher , Schiffman Joshua D , Abegglen Lisa M 
Published: April 2021

Abstract
Disease susceptibility and resistance are important factors for the conservation of endangered species, including elephants. We analyzed pathology data from 26 zoos and report that Asian elephants have increased neoplasia and malignancy prevalence compared with African bush elephants. This is consistent with observed higher susceptibility to tuberculosis and elephant endotheliotropic herpesvirus (EEHV) in Asian elephants. To investigate genetic mechanisms underlying disease resistance, including differential responses between species, among other elephant traits, we sequenced multiple elephant genomes. We report a draft assembly for an Asian elephant, and defined 862 and 1,017 conserved potential regulatory elements in Asian and African bush elephants, respectively. In the genomes of both elephant species, conserved elements were significantly enriched with genes differentially expressed between the species. In Asian elephants, these putative regulatory regions were involved in immunity pathways including tumor-necrosis factor, which plays an important role in EEHV response. Genomic sequences of African bush, forest, and Asian elephant genomes revealed extensive sequence conservation at TP53 retrogene loci across three species, which may be related to TP53 functionality in elephant cancer resistance. Positive selection scans revealed outlier genes related to additional elephant traits. Our study suggests that gene regulation plays an important role in the differential inflammatory response of Asian and African elephants, leading to increased infectious disease and cancer susceptibility in Asian elephants. These genomic discoveries can inform future functional and translational studies aimed at identifying effective treatment approaches for ill elephants, which may improve conservation.
Amino Acid Interactions (INTAA) web server v2.0: a single service for computation of energetics and conservation in biomolecular 3D structures
Authors: Vymětal Jiří , Jakubec David , Galgonek Jakub , Vondrášek Jiří 
Published: April 2021

Abstract
Interactions among amino acid residues are the principal contributor to the stability of the three-dimensional structure of a protein. The Amino Acid Interactions (INTAA) web server (https://bioinfo.uochb.cas.cz/INTAA/) has established itself as a unique computational resource, which enables users to calculate the contribution of individual residues in a biomolecular structure to its total energy using a molecular mechanical scoring function. In this update, we describe major additions to the web server which help solidify its position as a robust, comprehensive resource for biomolecular structure analysis. Importantly, a new continuum solvation model was introduced, allowing more accurate representation of electrostatic interactions in aqueous media. In addition, a low-overhead pipeline for the estimation of evolutionary conservation in protein chains has been added. New visualization options were introduced as well, allowing users to easily switch between and interrelate the energetic and evolutionary views of the investigated structures.
Drones and deep learning produce accurate and efficient monitoring of large-scale seabird colonies
Authors: Hayes Madeline C , Gray Patrick C , Harris Guillermo , Sedgwick Wade C , Crawford Vivon D , Chazal Natalie , Crofts Sarah , Johnston David W 
Published: April 2021

AbstractPopulation monitoring of colonial seabirds is often complicated by the large size of colonies, remote locations, and close inter- and intra-species aggregation. While drones have been successfully used to monitor large inaccessible colonies, the vast amount of imagery collected introduces a data analysis bottleneck. Convolutional neural networks (CNN) are evolving as a prominent means for object detection and can be applied to drone imagery for population monitoring. In this study, we explored the use of these technologies to increase capabilities for seabird monitoring by using CNNs to detect and enumerate Black-browed Albatrosses (Thalassarche melanophris) and Southern Rockhopper Penguins (Eudyptes c. chrysocome) at one of their largest breeding colonies, the Falkland (Malvinas) Islands. Our results showed that these techniques have great potential for seabird monitoring at significant and spatially complex colonies, producing accuracies of correctly detecting and counting birds at 97.66% (Black-browed Albatrosses) and 87.16% (Southern Rockhopper Penguins), with 90% of automated counts being within 5% of manual counts from imagery. The results of this study indicate CNN methods are a viable population assessment tool, providing opportunities to reduce manual labor, cost, and human error.
Do metal mines and their runoff affect plumage color? Streak-backed Orioles in Mexico show unexpected patterns
Authors: Kiere Lynna Marie , Osorio-Beristain Marcela , Sorani Valentino , Prieto-Torres David A , Navarro-Sigüenza Adolfo G , Sánchez-González Luis Antonio 
Published: April 2021

AbstractMetal mining causes serious ecological disturbance, due partly to heavy metal (HM) pollution that can accumulate at mining sites themselves and be dispersed downstream as runoff. Plumage coloration is important in birds’ social and ecological interactions and sensitive to environmental stressors, and several local-scale studies have found decreased carotenoid-based plumage and/or increased melanin-based plumage in wild birds exposed to HM pollution. We investigated regional-scale effects of proximity to mines and their downstream rivers as a proxy of exposure to HM-contaminated mining waste on plumage coloration in Streak-backed Orioles (Icterus pustulatus) in south-central Mexico. We measured the plumage color of museum skins using reflectance spectrometry and digital photography, then used geographic information systems to estimate each specimen’s distance from the nearest mining concession and river and determine whether that river’s watershed contained mines. Proximity to mines and their downstream rivers was related to ventral (but not dorsal) carotenoid-based coloration; birds collected farther from mines had more vivid yellow-orange breast plumage, and belly plumage was more vivid and redder with increasing distance from rivers with upstream mines. Breast background reflectance unexpectedly decreased with mine distance and was higher among birds whose nearest river had mines upstream. The area (but not reflectance) of melanin-based plumage was also related to mines. The area of dark back streaks decreased with mine distance, while the bib patch was smaller among birds presumably more exposed to mining waste. While some of these results are consistent with predicted effects of HM pollution on plumage, most were not straightforward, and effects differed among plumage patches and variables. Further investigation is needed to understand the direct (e.g., toxicity, oxidative stress) and/or indirect (e.g., decreased availability of carotenoid-rich food) mechanisms responsible and their individual-, population-, and community-level implications.
Science, religion and state: a multidimensional perspective
Authors: Corpuz Jeff Clyde G 
Published: April 2021

Abstract
The SARS-CoV-2 (COVID-19) does not discriminate; it affects everyone regardless of beliefs, gender, nationality, skin color, and social class. A recent correspondence published in the Journal of Public Health proposed the ‘collaboration of science and religion in COVID-19 vaccine promotion.’ The said article was in response to a previously published correspondence, which proposed a multi-sectoral approach on coronavirus disease 2019 (COVID-19) vaccination hesitancy. This article further adds that science, religion and state are not mutually exclusive with each other. What this article, therefore, proposes is a multidimensional relationship of science, religion and state to promote the COVID-19 vaccine and other science-based findings to combat the public fear of the public on vaccine and virus.
The last rites in a time of pandemic
Authors: Brazal Dr Agnes M 
Published: April 2021

Abstract
This correspondence argues that it is not only rituals after the death of a loved one that are important for grieving and eventual healing but also rituals at the point of death, such as the Last Rites in the Catholic Church. Because of the raging pandemic, however, the Last Rites have been done virtually for a number of Covid 19 patients. Cybertechnologies have provided an alternative space for the Last Rites to enable the dying, the family, and friends, to experience the gracious presence of God, the support of the Christian community, and to find meaning in their suffering.
Immunosuppressive therapy withdrawal after remission achievement in patients with lupus nephritis
Authors: Zen Margherita , Fuzzi Enrico , Loredo Martinez Marta , Depascale Roberto , Fredi Micaela , Gatto Mariele , Larosa Maddalena , Saccon Francesca , Iaccarino Luca , Doria Andrea 
Published: April 2021

Abstract

Objectives
Whether immunosuppressive therapy may be safely withdrawn in lupus nephritis (LN) is still unclear. We assessed rate and predictors of flare after IS withdrawal in patients with LN in remission.

Methods
Patients with biopsy-proven LN treated with immunosuppressants (IS) between 1980 and 2020 were considered. Remission was defined as normal serum creatinine, proteinuria &lt;0.5 g/24 h, inactive urine sediment, and no extra-renal SLE activity on stable immunosuppressive and/or antimalarial therapy and/or prednisone ≤5mg/day. IS discontinuation was defined as the complete withdrawal of immunosuppressive therapy, flares according to SLEDAI Flare Index. Predictors of flare were analysed by multivariate logistic regression analysis.

Results
Among 513 SLE patients included in our database, 270 had LN. Of them, 238 underwent renal biopsy and were treated with IS. Eighty-three patients (34.8%) discontinued IS, 46 (30) months after remission achievement. During a mean (s.d.) follow-up of 116.5 (78) months, 19 patients (22.9%) developed a flare (8/19 renal) and were re-treated; 14/19 (73.7%) re-achieved remission after restarting therapy. Patients treated with IS therapy for at least 3 years after remission achievement had the lowest risk of relapse (OR 0.284, 95% CI: 0.093, 0.867; P = 0.023). At multivariate analysis, antimalarial maintenance therapy (OR 0.194, 95% CI: 0.038, 0.978; P = 0.047), age at IS discontinuation (OR 0.93, 95% CI: 0.868, 0.997; P = 0.040), remission duration &gt;3 years before IS discontinuation (OR 0.231, 95% CI: 0.058, 0.920; P = 0.038) were protective against disease flares.

Conclusions
Withdrawal of IS is feasible in LN patients in remission for at least 3 years and on antimalarial therapy. Patients who experience flares can re-achieve remission with an appropriate treatment.
MEASUREMENT AND ANALYSIS OF ELECTRIC AND MAGNETIC FIELD STRENGTH IN GRID-TIED PHOTOVOLTAIC POWER SYSTEM COMPONENTS
Authors: Bedeloğlu Merve , İl Niyazi , Ateş Kayhan , Özen Şükrü 
Published: April 2021

Abstract
In this study, electric field and magnetic field strengths at 50 Hz are measured in a solar power plant located far from residential areas, and the measurement results near various sources of the electric and magnetic fields in the power plant are presented. Although the measured values for the electric field caused by the solar panel range between 0.07 and 1.33 V/m, the measured values for the magnetic field by the solar panel range between 0.037 and 0.19 μT. In front of the inverter, the measured value of the electric field reaches 0.7 V/m, whereas the measured value of the magnetic field reaches 2.2 μT. The results are presented and evaluated in light of the exposure limits to electromagnetic fields published by international organisations.
Abnormal bone marrow microenvironment: the “harbor” of acute lymphoblastic leukemia cells
Authors: Chen Zehui , Zheng Yaxin , Yang Yaling , Kang Junnan , You M. James , Tian Chen 
Published: April 2021

Abstract
Bone marrow (BM) microenvironment regulates and supports the production of blood cells which are necessary to maintain homeostasis. In analogy to normal hematopoiesis, leukemogenesis is originated from leukemic stem cells (LSCs) which gives rise to more differentiated malignant cells. Leukemia cells occupy BM niches and reconstruct them to support leukemogenesis. The abnormal BM niches are the main sanctuary of LSCs where they can evade chemotherapy-induced death and acquire drug resistance. In this review, we focus on the protective effects of BM niche cells on acute lymphoblastic leukemia cells.
SIEVE: identifying robust single cell variable genes for single-cell RNA sequencing data
Authors: Zhang Yinan , Xie Xiaowei , Wu Peng , Zhu Ping 
Published: April 2021

Abstract
Single-cell RNA-seq data analysis generally requires quality control, normalization, highly variable genes screening, dimensionality reduction and clustering. Among these processes, downstream analysis including dimensionality reduction and clustering are sensitive to the selection of highly variable genes. Though increasing number of tools for selecting the highly variable genes have been developed, an evaluation of their performances and a general strategy are lack. Here, we compare the performance of nine commonly used methods for screening variable genes by using single-cell RNA-seq data from hematopoietic stem/progenitor cells and mature blood cells, and find that SCHS outperforms other methods regarding to reproducibility and accuracy. However, this method prefers the selection of highly expressed genes. We further propose a new strategy SIEVE (SIngle-cEll Variable gEnes) by multiple rounds of random sampling, therefore minimizing the stochastic noise and identifying a robust set of variable genes. Moreover, SIEVE recovers lowly expressed genes as variable genes and substantially improves the accuracy of single cell classification, especially for the methods with lower reproducibility. The SIEVE software is freely available at https://github.com/YinanZhang522/SIEVE.
The Kappa Line as a Regional Modification of the K-line
Authors: Lee Dong-Ho , Park Sehan , Kim Hyoungmin , Hwang Chang Ju , Cho Jae Hwan , Yang Jae Jun , Lee Choon Sung 
Published: April 2021

Study Design:
This is a retrospective cohort study

Objective:
The aim was to introduce Kappa line (modification of K-line) for the prediction of postoperative neurological recovery after selective cervical laminoplasty (LMP) and use in determining the decompression level.

Summary of Background Data:
The K-line is a radiographic marker that can predict prognosis and aid in surgical planning for patients undergoing LMP through C3 to C7. However, its efficacy in LMP involving limited segments is unclear. Furthermore, no specific radiographic marker to predict the prognosis of selective LMP has been reported.

Materials and Methods:
Fifty-one consecutive patients with a minimum 2-year follow-up after selective LMP for cervical myelopathy caused by ossification of posterior longitudinal ligament were retrospectively reviewed. The Kappa line was defined as a straight line connecting the midpoints of the spinal canal made by remaining bony structure after decompression procedures on a plain lateral radiograph in the neutral position. Patients were classified as K-line (+) or (−) and Kappa line (+) or (−) based on whether the ossified mass crossed the indicator line.

Results:
The Kappa line (+) group demonstrated significantly higher Japanese Orthopaedic Association (JOA) recovery rate (P=0.01), final JOA score (P<0.01), and dural sac diameter (P<0.01) postoperatively than the Kappa line (−) group. Cord compression grade was significantly lesser in the Kappa line (+) group. However, the K-line-based classification did not demonstrate significant difference in JOA recovery rate, final JOA score, and cord compression grade between the (+) and (−) groups; the dural sac diameter was significantly higher in the K-line (+) group (P<0.01).

Conclusions:
The Kappa line showed better correlation with ossification of posterior longitudinal ligament size and cervical alignment, providing better prediction of neurological recovery and remaining cord compression following selective LMP. Therefore, the Kappa line can aid in determining the level of decompression in selective LMP.
Checklists Improve Team Performance During Simulated Extracorporeal Membrane Oxygenation Emergencies: A Randomized Trial
Authors: Stentz Michael J. , Wiepking Matthew D. , Hodge Kiley A. , Ramonell Richard P. , Jabaley Craig S. 
Published: April 2021

Objectives:
Extracorporeal membrane oxygenation–related complications are potentially catastrophic if not addressed quickly. Because complications are rare, high-fidelity simulation is recommended as part of the training regimen for extracorporeal membrane oxygenation specialists. We hypothesized that the use of standardized checklists would improve team performance during simulated extracorporeal membrane oxygenation emergencies.

Design:
Randomized simulation-based trial.

Setting:
A quaternary-care academic hospital with a regional extracorporeal membrane oxygenation referral program.

Subjects:
Extracorporeal membrane oxygenation specialists and other healthcare providers.

Interventions:
We designed six read-do checklists for use during extracorporeal membrane oxygenation emergencies using a modified Delphi process. Teams of two to three providers were randomized to receive the checklists or not. All teams then completed four simulated extracorporeal membrane oxygenation emergencies.

Measurements and Main Results:
Simulation sessions were video-recorded, and the number of critical tasks performed and time-to-completion were compared between groups. A survey instrument was administered before and after simulations to assess participants’ attitudes toward the simulations and checklists. We recruited 36 subjects from a single institution, randomly assigned to 15 groups. The groups with checklists completed more critical tasks than participants in the control groups (90% vs 75%; p < 0.001). The groups with checklists performed a higher proportion of both nontechnical tasks (71% vs 44%; p < 0.001) and extracorporeal membrane oxygenation–specific technical tasks (94% vs 86%; p < 0.001). Both groups reported an increase in reported self-efficacy after the simulations (p = 0.003). After adjusting for multiple comparisons, none of the time-to-completion measures achieved statistical significance.

Conclusions:
The use of checklists resulted in better team performance during simulated extracorporeal membrane oxygenation emergencies. As extracorporeal membrane oxygenation use continues to expand, checklists may be an attractive low-cost intervention for centers looking to reduce errors and improve response to crisis situations.
Hemodynamic Effects of an Increased Midodrine Dosing Frequency
Authors: Macielak Shea A. , Vollmer Nicholas J. , Haddad Natalie A. , Nabzdyk Christoph G. S. , Nei Scott D. 
Published: April 2021

Objectives:
In practice, midodrine has been used to reduce IV vasopressor requirements and decrease ICU length of stay. However, recent publications have failed to show clinical success when midodrine was administered every 8 hours. One possible reason for the lack of clinical efficacy at this dosing interval may be the pharmacokinetic properties of midodrine that support a more frequent dosing interval. Here, we report our institutional experience with midodrine at a dosing frequency of every 6 hours.

Design:
Single, quaternary academic medical center, retrospective, descriptive study.

Setting:
Floor and ICU patients admitted to Mayo Clinic, Rochester, from May 7, 2018, to September 30, 2020.

Patients:
Adult patients with an order for midodrine with a dosing frequency of “every 6 hours” or “four times daily” were eligible for inclusion.

Interventions:
No intervention performed. All data were abstracted retrospectively from the electronic medical record.

Measurements and Main Results:
Forty-four unique patients were identified that met inclusion criteria. Patients were an average of 65 years and 63.6% were male. The individual doses of midodrine ranged from 5 to 20 mg. Twenty-three patients (52.3%) were receiving IV vasopressors at the time midodrine was ordered every 6 hours. Vasopressor requirements decreased from an average of 0.10 norepinephrine equivalents 24 hours prior to the every 6-hour order to 0.05 norepinephrine equivalents 24 hours after an order for midodrine every 6 hour was placed.

Conclusions:
Increasing the dosing frequency of midodrine to every 6 hours may optimize its pharmacokinetic profile without compromising safety. This midodrine dosing frequency should be prospectively evaluated as a primary strategy for accelerated IV vasopressor wean.
Posttraumatic Stress Disorder Symptom Trajectories in ICU Family Caregivers
Authors: Wendlandt Blair , Chen Yi Tang , Lin Feng-Chang , Toles Mark , Gaynes Bradley , Hanson Laura , Carson Shannon 
Published: April 2021

Objectives:
To use latent class growth analysis to identify posttraumatic stress disorder symptom trajectories in ICU family caregivers.

Design:
Prospective cohort study.

Setting:
The medical ICU at a tertiary-care center in the United States.

Participants:
Adult patients experiencing acute cardiorespiratory failure (defined as requiring at least one of the following: 1) vasopressors, 2) noninvasive positive pressure ventilation, 3) high-flow nasal cannula, or 4) mechanical ventilation) were enrolled in a pair with their primary family caregivers.

Measurements and Main Results:
Participants were enrolled within the first 48 hours of ICU admission. Family caregiver posttraumatic stress disorder symptoms were measured using the Impact of Events Scale-Revised at four time points: at enrollment, shortly after ICU discharge, and at 3 and 6 months after ICU discharge. The data were examined using latent class growth analysis to identify posttraumatic stress disorder symptom trajectories. Two distinct symptom trajectories were identified: a persistently high trajectory, characterized by high posttraumatic stress disorder symptoms at initial assessment, which remained elevated over time, and a persistently low trajectory, characterized by low posttraumatic stress disorder symptoms at initial assessment, which remained low over time. Approximately two-thirds of caregivers belonged to the persistently high trajectory, and one-third of caregivers belonged to the persistently low trajectory.

Conclusions:
Using latent class growth analysis to measure 6-month ICU family caregiver posttraumatic stress disorder symptom trajectories, we identified two distinct trajectories (persistently low and persistently high). A larger cohort study is warranted to further delineate posttraumatic stress disorder trajectories in this population, with the ultimate goal of targeting high-risk caregivers for interventions to reduce psychologic distress and improve long-term caregiver outcomes.