bluuebunny/crossref_metadata_2025_split huggingface dataset:
The nutrient requirements of horses: historical perspectives
Authors: Lawrence Laurie 
Published: February 2022

Abstract
The National Research Council (NRC) published the Recommended Nutrient Allowances for Horses in 1949. The subsequent publication was renamed the Nutrient Requirements of Horses and the 6th revised edition was published in 2007. The document has increased in size and scope from the initial publication in 1949 that contained 29 pages to the most recent version with 341 pages. Several formats for expressing requirements (dietary concentrations or daily amounts) have been utilized. In addition, a variety of methods have been employed to determine the nutrient requirements of horses since 1949. Many of the requirement estimates are based on research studies with the target class of horse. However, some estimates have been derived from practical experience or extrapolated from other species and there is ample opportunity for future research related to many nutrients. Equine nutritionists may also explore additional methods to express the recommended daily nutrient intakes of horses.
Augmented Reality Spine Surgery Navigation
Authors: Felix Brent , Kalatar Seyed Babak , Moatz Bradley , Hofstetter Christoph , Karsy Michael , Parr Ryan , Gibby Wendell 
Published: February 2022

Study Design.
Collectively, seven cadavers were instrumented with 124 thoracolumbar pedicle screws using VisAR augmented reality/guidance. Sixty-five screws were inserted into four donors using open dissection spine surgery. Fifty-nine screws were positioned in three donors with a minimally invasive spine surgery (MISS) procedure. For both open and MISS, VisAR was used exclusively for pedicle screw navigation.

Objective.
The objective of this study was to determine the accuracy of pedicle screw placement using VisAR for open spine and MISS procedures.

Summary of Background Data.
Pedicle screw placement can be challenging depending on anatomical location and a surgeon's experience. AR may minimize fluoroscopy use and speed screw insertion.

Methods.
Prior to computed tomography (CT) a series of four image visible April Tag optical fiducials were attached to the backs’ of the donors. Resulting images were used preoperatively for planned virtual pedicle screw pathways including entry point, trajectory, and depth. The study link was encrypted on a quick response (QR) code, printed, and viewed in the operating room (OR) by the surgeon using VisAR (HoloLens 2 headset). Viewing the code wirelessly uploads and launches the study, converting the DICOM data to holographic images which register to the fiducials on the donor's back. The annotated pathways for each pedicle were called up by voice command and the surgeon positioned each screw by aligning with the virtual guidance hologram.

Results.
Overall, 124 pedicle screws were inserted with VisAR navigation with 96% accuracy (Gertzbein-Robbins grades A and B). The combined angle of error was 2.4° and the distance error was 1.9 mm.

Conclusion.
Augmented reality is a highly accurate, emerging technology for navigating both open and minimally invasive spine surgery techniques with off-the-shelf headset hardware.

Level of Evidence.
N/A
The Impact of Antimicrobial Stewardship in Children in Low- and Middle-income Countries
Authors: Abo Yara-Natalie , Freyne Bridget , Kululanga Diana , Bryant Penelope A. 
Published: February 2022

Background:
Antimicrobial stewardship (AMS) is central to the World Health Organisation Global Action Plan against antimicrobial resistance (AMR). If antibiotics are used without restraint, morbidity and mortality from AMR will continue to increase. In resource-rich settings, AMS can safely reduce antibiotic consumption. However, for children in low- and middle-income countries (LMIC), the impact of different AMS interventions is unknown.

Aim:
To determine the impact of different AMS interventions on antibiotic use and clinical and microbiologic outcomes in children in LMIC.

Methods:
MEDLINE, Embase and PubMed were searched for studies of AMS interventions in pediatric population in LMIC settings. Controlled trials, controlled before-and-after studies and interrupted time series studies were included. Outcomes assessed were antibiotic use, multidrug-resistant organism (MDRO) rates, clinical outcomes and cost.

Results:
Of 1462 studies, 34 met inclusion criteria including a total population of >5,000,000 in 17 countries. Twenty were in inpatients, 2 in ED, 10 in OPD and 2 in both. Seven studies were randomized controlled trials. All types of interventions reported a positive impact on antibiotic prescribing. AMS bundles with education, and clinical decision tools appeared more effective than guidelines alone. AMS interventions resulted in significantly decreased clinical infections (4/4 studies) and clinical failure (2/2) and reduced MDRO colonization rate (4/4). There was no concomitant increase in mortality (4/4 studies) or length of stay (2/2).

Conclusion:
Multiple effective strategies exist to reduce antibiotic consumption in LMIC. However, marked heterogeneity limit conclusions regarding the most effective approach, particularly regarding clinical outcomes. Overall, AMS strategies are important tools in the reduction of MDRO-related morbidity in children in LMIC.
Proteome remodeling and organelle clearance in mammalian terminal erythropoiesis
Authors: Ren Kehan , Li Ermin , Ji Peng 
Published: February 2022

Purpose of review
The differentiation from colony forming unit-erythroid (CFU-E) cells to mature enucleated red blood cells is named terminal erythropoiesis in mammals. Apart from enucleation, several unique features during these developmental stages include proteome remodeling and organelle clearance that are important to achieve hemoglobin enrichment. Here, we review the recent advances in the understanding of novel regulatory mechanisms in these processes, focusing on the master regulators that link these major events during terminal erythropoiesis.

Recent findings
Comprehensive proteomic studies revealed a mismatch of protein abundance to their corresponding transcript abundance, which indicates that the proteome remodeling is regulated in a complex way from transcriptional control to posttranslational modifications. Key regulators in organelle clearance were also found to play critical roles in proteome remodeling.

Summary
These studies demonstrate that the complexity of terminal erythropoiesis is beyond the conventional transcriptomic centric perspective. Posttranslational modifications such as ubiquitination are critical in terminal erythroid proteome remodeling that is also closely coupled with organelle clearance.
Ambient air pollution is associated with vascular disease in Ugandan HIV-positive adolescents
Authors: Toe Sophia , Nagy Matthew , Albar Zainab , Yu Jiao , Sattar Abdus , Nazzinda Rashida , Musiime Victor , Etajak Samuel , Walyawula Felix , McComsey Grace A. , Atuyambe Lynn M. , Dirajlal-Fargo Sahera 
Published: February 2022

Objective:
In this study, we aim to investigate the relationship between particulate matter, a common proxy indicator for air pollution, and markers of inflammation, monocyte activation, and subclinical vascular disease.

Design:
A cross-sectional study.

Methods:
Adolescents with perinatally acquired HIV (PHIV) and HIV-uninfected adolescents between 10 and 18years living near Kampala, Uganda were included. Daily ambient concentrations of particulate matter (PM2.5) were measured from the Eastern Arica GEOHealth Hub. Outcome variables measured were carotid intima-media thickness (IMT), as well as plasma markers of systemic inflammation, oxidized lipids, and gut integrity. Multivariable quantile regression models were used to explore the relationship between PM2.5 and IMT.

Results:
One hundred and nineteen participants (69 PHIV, 50 HIV-uninfected) were included. The median (Q1, Q3) age was 12.7 (11.4,14.2) years, 55% were girls. Median daily PM2.5 exposure was 29.08 μg/m3 (23.40, 41.70). There was no significant difference in exposure of PM2.5 between groups (P
= 0.073). PM2.5 significantly correlated with intestinal permeability (zonulin; r = 0.43, P < 0.001), monocyte activation (soluble CD163: r
= 0.25, P = 0.053), and IMT (r
= 0.35, P = 0.004) in PHIV but not in HIV-uninfected (P ≥ 0.05). In multivariable quantile regression, after adjusting for age, sex, poverty level, soluble CD163, and zonulin, daily PM2.5 concentrations remained associated with IMT [β
= 0.005, 95% CI (0.0003–0.010), P = 0.037] in adolescents with PHIV.

Conclusion:
Adolescents in urban Uganda are exposed to high levels of air pollution. Both PM2.5 and HIV have independently been observed to contribute to atherosclerotic disease, and our findings suggest the combined effects of HIV and air pollution may amplify the development of cardiovascular disease.
Influence of Experimental Skull Defects on Brain
Authors: Bin Peng , Run-Ming Qu , Guo-Hua Wang , Li-Hua Xu , Zheng-Lin Jiang 
Published: February 2022

Abstract:
This study was aimed to observe the effects of skull defects on the brain in rats and further to investigate its underlying pathophysiological. Three different sizes of skull were removed in rats to produce models of skull defect, and then the behavioral changes were detected using a grip strength meter and neurobehavioral severity scale scores. The authors further examined the levels of cell apoptosis and autophagy, the cerebral blood flow with immunoblotting, and immunofluorescence micro-ultrasound system, respectively. The authors found that the sensory function but not the grip was impaired on the 6th day after a 5 × 10 mm defect while the motor function was on the 2nd day. In addition, the authors found an increment in B-cell lymphoma-2/BCL2-Associated X (Bcl2/Bax) and LC3 II/I expression, a maker of apoptosis and autophagy, respectively, in the defective hemisphere especially at the edge of the defective area. Importantly, the blood flow of internal carotid artery began to decline at 2 hours, and reached minimum on the 4th day, but began to recover on the 6th day in the hemi-defect group. In conclusion, a larger skull defect could impair the cognitive function but not the motor function and its underlying pathophysiology were mainly related to a decrease in cerebral flow.
Comparative analysis of cell-cell communication at single-cell resolution
Authors: Wilk Aaron J. , Shalek Alex K. , Holmes Susan , Blish Catherine A. 
Published: February 2022

ABSTRACTInference of cell-cell communication (CCC) from single-cell RNA-sequencing data is a powerful technique to uncover putative axes of multicellular coordination, yet existing methods perform this analysis at the level of the cell type or cluster, discarding single-cell level information. Here we present Scriabin – a flexible and scalable framework for comparative analysis of CCC at single-cell resolution. We leverage multiple published datasets to show that Scriabin recovers expected CCC edges and use spatial transcriptomic data, genetic perturbation screens, and direct experimental manipulation of receptor-ligand interactions to validate that the recovered edges are biologically meaningful. We then apply Scriabin to uncover co-expressed programs of CCC from atlas-scale datasets, validating known communication pathways required for maintaining the intestinal stem cell niche and revealing species-specific communication pathways. Finally, we utilize single-cell communication networks calculated using Scriabin to follow communication pathways that operate between timepoints in longitudinal datasets, highlighting bystander cells as important initiators of inflammatory reactions in acute SARS-CoV-2 infection. Our approach represents a broadly applicable strategy to leverage single-cell resolution data maximally toward uncovering CCC circuitry and rich niche-phenotype relationships in health and disease.
EMoMiS: A Pipeline for Epitope-based Molecular Mimicry Search in Protein Structures with Applications to SARS-CoV-2
Authors: Stebliankin Vitalii , Baral Prabin , Balbin Christian , Nunez-Castilla Janelle , Sobhan Masrur , Cickovski Trevor , Mondal Ananda Mohan , Siltberg-Liberles Jessica , Chapagain Prem , Mathee Kalai , Narasimhan Giri 
Published: February 2022

AbstractMotivationEpitope-based molecular mimicry occurs when an antibody cross-reacts with two different antigens due to structural and chemical similarities. Molecular mimicry between proteins from two viruses can lead to beneficial cross-protection when the antibodies produced by exposure to one also react with the other. On the other hand, mimicry between a protein from a pathogen and a human protein can lead to auto-immune disorders if the antibodies resulting from exposure to the virus end up interacting with host proteins. While cross-protection can suggest the possible reuse of vaccines developed for other pathogens, cross-reaction with host proteins may explain side effects. There are no computational tools available to date for a large-scale search of antibody cross-reactivity.ResultsWe present a comprehensive Epitope-based Molecular Mimicry Search (EMoMiS) pipeline for computational molecular mimicry searches. EMoMiS, when applied to the SARS-CoV-2 Spike protein, identified eight examples of molecular mimicry with viral and human proteins. These findings provide possible explanations for (a) differential severity of COVID-19 caused by cross-protection due to prior vaccinations and/or exposure to other viruses, and (b) commonly seen COVID-19 side effects such as thrombocytopenia and thrombophilia. Our findings are supported by previously reported research but need validation with laboratory experiments. The developed pipeline is generic and can be applied to find mimicry for novel pathogens. It has applications in improving vaccine design.AvailabilityThe developed Epitope-based Molecular Mimicry Search Pipeline (EMoMiS) is available from https://biorg.cs.fiu.edu/emomis/.Contactgiri@cs.fiu.edu
Food insecurity disparities and mental health impacts among cancer survivors during the COVID-19 pandemic
Authors: Camacho-Rivera Marlene , Islam Jessica Yasmine , Rodriguez Diane R. , Vidot Denise C. , Bailey Zinzi 
Published: February 2022

Food insecurity can negatively impact adherence and receipt of high-quality cancer care. The purpose of the study was to (1) compare the prevalence of COVID-19 associated food insecurity by cancer history and (2) examine determinants associated with COVID-19 related food insecurity among cancer survivors.We used nationally-representative data from the COVID-19 Household Impact Survey (n = 10,760), collected at three time points: April 20-26, May 4-10, and May 30th -June 8th of 2020. Our primary exposure was cancer survivor status, based on participant’s self-report of a cancer diagnosis (n=854, 7.1%). Primary outcomes of food insecurity were categorized on how often participants reported the following: “We worried our food would run out before we got money to buy more” or “The food that we bought just didn’t last, and we didn’t have money to get more”; Respondents were categorized as food insecure if they chose often true or sometimes true. Multivariable Poisson regression was used to identify demographic determinants of food insecurity among cancer survivors.Thirty-two percent of cancer survivors were food insecure. Cancer survivors aged 30-44 years and those aged ≥60 were more likely to report being food insecure compared to respondents without a history of cancer in the same age categories (30-44 years, 59.9% versus 41.2% p = 0.01, ≥60 years 27.2% versus 20.2%, p = 0.01). Cancer survivors without a high school diploma were more likely to report food insecurity compared to adults with no history of cancer (87.0% versus 64.1%, p = 0.001). In multivariable models, uninsured cancer survivors (adjusted Prevalence Ratio (aPR) aPR: 2.39, 95% CI: 1.46-3.92) and those on Medicaid (aPR: 2.10, 95% CI: 1.40-3.17) were also more likely to report being food insecure.Food insecurity during the COVID-19 pandemic is vast but disparities persist. Among cancer survivors, differences in food insecurity were observed by age and SES.
Statistical learning and uncommon soil microbiota explain biogeochemical responses after wildfire
Authors: Honeyman Alexander S. , Fegel Timothy S. , Peel Henry F. , Masters Nicole A. , Vuono David C. , Kleiber William , Rhoades Charles C. , Spear John R. 
Published: February 2022

1AbstractWildfires are a perennial event globally and the biogeochemical underpinnings of soil responses at relevant spatial and temporal scales are unclear. Soil biogeochemical processes regulate plant growth and nutrient losses that affect water quality, yet the response of soil after variable intensity fire is difficult to explain and predict. To address this issue, we examined two wildfires in Colorado, USA across the first and second post-fire years and leveraged Statistical Learning (SL) to predict and explain biogeochemical responses. We found that SL predicts biogeochemical responses in soil after wildfire with surprising accuracy. Of the 13 biogeochemical analytes analyzed in this study, 9 are best explained with a hybrid microbiome + biogeochemical SL model. Biogeochemical-only models best explain 3 features, and 1 feature is explained equally well with hybrid or biogeochemical-only models. In some cases, microbiome-only SL models are also effective (such as predicting NH4+). Whenever a microbiome component is employed, selected features always involve uncommon soil microbiota (i.e., the ‘rare biosphere’, existing at<1% relative abundance). Here, we demonstrate that SL paired with DNA sequence and biogeochemical data predict environmental features in post-fire soils, though this approach could likely be applied to any biogeochemical system.
Discovery of integrons in Archaea: platforms for cross-domain gene transfer
Authors: Ghaly Timothy M. , Tetu Sasha G. , Penesyan Anahit , Qi Qin , Rajabal Vaheesan , Gillings Michael R. 
Published: February 2022

SummaryHorizontal gene transfer between different domains of life is increasingly being recognised as an important driver of evolution, with the potential to provide the recipient with new gene functionality and assist niche adaptation1-3. However, the molecular mechanisms underlying the integration of exogenous genes from foreign domains are mostly unknown. Integrons are a family of genetic elements that facilitate this process within Bacteria via site-specific DNA recombination4-7. Integrons, however, have not been reported outside Bacteria, and thus their potential role in cross-domain gene transfer has not been investigated. Here we show that integrons are also present among diverse phyla within the domain Archaea. Further, we provide experimental evidence that integron-mediated recombination can facilitate the recruitment of archaeal genes by bacteria. Our findings establish a new mechanism that can facilitate horizontal gene transfer between the two domains of prokaryotes, which has important implications for prokaryotic evolution in both clinical and environmental contexts.
Feasibility, usability and acceptability of a novel digital hybrid-system for reporting of routine health information in Southern Tanzania: A mixed-methods study
Authors: Unkels Regine , Manzi Fatuma , Kapologwe Ntuli A. , Baker Ulrika , Ahmad Aziz , Nabiev Rustam , Berndtsson Maria , Baraka Jitihada , Hanson Claudia , Hirose Atsumi 
Published: February 2022

AbstractBackgroundHealth information systems are important for health planning and monitoring of progress. Still, data from health facilities are often of limited quality in Low-and-Middle-Income Countries. Quality deficits are partially rooted in the fact that paper-based documentation is still the norm at facility level, leading to mistakes in summarizing and manual copying. Digitalization of data at facility level would allow automatization of these procedural steps. Here we aimed to evaluate the feasibility, usability and acceptability of a scanning innovation called Smart Paper Technology for digital data processing.MethodsWe used a mixed-methods design to understand users’ engagement with Smart Paper Technology and to identify potential positive and negative effects of this innovation in three health facilities in Southern Tanzania. Eight focus group discussions and 11 in-depth interviews with users were conducted. We quantified time used by health care providers for documentation and patient care using time-motion methods. Thematic analysis was used to analyze qualitative data. Descriptive statistics and multivariable linear models were generated to compare the difference before and after introduction and adjust for confounders.ResultsHealth care providers and health care managers appreciated the forms’ simple design features and perceived Smart Paper Technology as time-saving and easy to use. The time-motion study with 273.3 and 224.0 hours of observations before and after introduction of Smart Paper Technology, respectively, confirmed that working time spent on documentation did not increase (27.0% at baseline and 26.4% post-introduction; adjusted p=0.763). Time spent on patient care was not negatively impacted (26.9% at baseline and 37.1% at post-intervention; adjusted p=0.001). Health care providers described positive effects on their accountability for data and service provision relating to the fact that individually signed forms were filled.DiscussionHealth care providers perceived Smart Paper Technology as feasible, easy to integrate and acceptable in their setting, particularly as it did not add time to documentation.