bluuebunny/crossref_metadata_2025_split huggingface dataset:
Brief Report: The Impact of Disease Stage on Early Gaps in ART in the “Treatment for All” Era—A Multisite Cohort Study
Authors: Katz Ingrid T. , Musinguzi Nicholas , Bell Kathleen , Cross Anna , Bwana Mwebesa B. , Amanyire Gideon , Asiimwe Stephen , Orrell Catherine , Bangsberg David R. , Haberer Jessica E. ,   On Behalf of the META (Measuring Early Treatment Adherence) Team Investigators
Published: December 2020

Background:
Adoption of “Treat All” policies has increased antiretroviral therapy (ART) initiation in sub-Saharan Africa; however, unexplained early losses continue to occur. More information is needed to understand why treatment discontinuation continues at this vulnerable stage in care.

Methods:
The Monitoring Early Treatment Adherence Study involved a prospective observational cohort of individuals initiating ART at early-stage versus late-stage disease in South Africa and Uganda. Surveys and HIV-1 RNA levels were performed at baseline, 6, and 12 months, with adherence monitored electronically. This analysis included nonpregnant participants in the first 6 months of follow-up; demographic and clinical factors were compared across groups with χ2, univariable, and multivariable models.

Results:
Of 669 eligible participants, 91 (14%) showed early gaps of ≥30 days in ART use (22% in South Africa and 6% in Uganda) with the median time to gap of 77 days (interquartile range: 43–101) and 87 days (74, 105), respectively. Although 71 (78%) ultimately resumed care, having an early gap was still significantly associated with detectable viremia at 6 months (P ≤ 0.01). Multivariable modeling, restricted to South Africa, found secondary education and higher physical health score protected against early gaps [adjusted odds ratio (aOR) 0.4, 95% confidence interval (CI): 0.2 to 0.8 and (aOR 0.93, 95% CI: 0.9 to 1.0), respectively]. Participants reporting clinics as “too far” had double the odds of early gaps (aOR 2.2: 95% CI: 1.2 to 4.1).

Discussion:
Early gaps in ART persist, resulting in higher odds of detectable viremia, particularly in South Africa. Interventions targeting health management and access to care are critical to reducing early gaps.
Clinical and Economic Outcomes of Enhanced Recovery Dissemination in Michigan Hospitals
Authors: Regenbogen Scott E. , Cain-Nielsen Anne H. , Syrjamaki John D. , Norton Edward C. 
Published: December 2020

Objective:
To evaluate real-world effects of enhanced recovery protocol (ERP) dissemination on clinical and economic outcomes after colectomy.

Summary Background Data:
Hospitals aiming to accelerate discharge and reduce spending after surgery are increasingly adopting perioperative ERPs. Despite their efficacy in specialty institutions, most studies have lacked adequate control groups and diverse hospital settings and have considered only in-hospital costs. There remain concerns that accelerated discharge might incur unintended consequences.

Methods:
Retrospective, population-based cohort including patients in 72 hospitals in the Michigan Surgical Quality Collaborative clinical registry (N = 13,611) and/or Michigan Value Collaborative claims registry (N = 14,800) who underwent elective colectomy, 2012 to 2018. Marginal effects of ERP on clinical outcomes and risk-adjusted, price-standardized 90-day episode payments were evaluated using mixed-effects models to account for secular trends and hospital performance unrelated to ERP.

Results:
In 24 ERP hospitals, patients Post-ERP had significantly shorter length of stay than those Pre-ERP (5.1 vs 6.5 days, P < 0.001), lower incidence of complications (14.6% vs 16.9%, P < 0.001) and readmissions (10.4% vs 11.3%, P = 0.02), and lower episode payments ($28,550 vs $31,192, P < 0.001) and postacute care ($3,384 vs $3,909, P < 0.001). In mixed-effects adjusted analyses, these effects were significantly attenuated—ERP was associated with a marginal length of stay reduction of 0.4 days (95% confidence interval 0.2–0.6 days, P = 0.001), and no significant difference in complications, readmissions, or overall spending.

Conclusions:
ERPs are associated with small reduction in postoperative length of hospitalization after colectomy, without unwanted increases in readmission or postacute care spending. The real-world effects across a variety of hospitals may be smaller than observed in early-adopting specialty centers.
Interim evaluation of Google AI forecasting for COVID-19 compared with statistical forecasting by human intelligence in the first week
Authors: Kurita Junko , Sugawara Tamie , Ohkusa Yasushi 
Published: December 2020

AbstractBackgroundSince June, Google (Alphabet Inc.) has provided forecasting for COVID-19 outbreak by artificial intelligence (AI) in the USA. In Japan, they provided similar services from November, 2020.ObjectWe compared Google AI forecasting with a statistical model by human intelligence.MethodWe regressed the number of patients whose onset date was day t on the number of patients whose past onset date was 14 days prior, with information about traditional surveillance data for common pediatric infectious diseases including influenza, and prescription surveillance 7 days prior. We predicted the number of onset patients for 7 days, prospectively. Finally, we compared the result with Googles AI-produced forecast. We used the discrepancy rate to evaluate the precision of prediction: the sum of absolute differences between data and prediction divided by the aggregate of data.ResultsWe found Google prediction significantly negative correlated with the actual observed data, but our model slightly correlated but not significant. Moreover, discrepancy rate of Google prediction was 27.7% for the first week. The discrepancy rate of our model was only 3.47%.Discussion and ConclusionResults show Googles prediction has negatively correlated and greater difference with the data than our results. Nevertheless, it is noteworthy that this result is tentative: the epidemic curve showing newly onset patients was not fixed.
Soil Chemistry and Microbiome Determine N2O Emission Potential in Soils
Authors: Highton Matthew P. , Bakken Lars R. , Dörsch Peter , Tobias-Hunefeldt Sven , Molstad Lars , Morales Sergio E. 
Published: December 2020

AbstractMicrobial nitrogen (N) transformations in soil, notably denitrification, result in the production of the potent greenhouse and ozone depleting gas nitrous oxide (N2O). Soil chemistry and microbiome composition impact N2O emission potential but the relative importance of these factors as determinants of N2O emission in denitrifying systems is rarely tested. In addition, previous linkages between microbiome composition and N2O emission potential rarely demonstrate causality. Here, we determined the relative impact of microbiome composition (i.e. soil extracted cells) and chemistry (i.e. water extractable chemicals) on N2O emission potential utilizing an anoxic cell based assay system. Cells and chemistry for assays were sourced from soils with contrasting N2O/N2O+N2ratios, combined in various combinations and denitrification gas production was measured in response to nitrate addition. Average directionless effects of cell and chemical extract on N2O/N2O+N2(Cell: Δ0.16, Chemical extract: Δ0.22) and total N2O hypothetically emitted (Cell: Δ2.62 μmol-N, Chemical extract: Δ4.14 μmol-N) indicated chemistry is the most important determinant of N2O emissions. Independent pH differences of just 0.6 points impacted N2O/N2O+N2on par with independent chemical extract differences, supporting the dominance of this variable in previous studies. However, impacts on overall N2O hypothetically emitted were smaller suggesting that soil pH manipulation may not necessarily be a successful approach to mitigate emissions over a fixed time period. In addition, we observed increased N2O accumulation and emission potential at the end of incubations concomitant with predicted decreases in carbon availability suggesting that carbon limitation increases N2O emission transiently with the magnitude of emission dependent on the both chemical and microbiome controls.
Oxygen saturation instability in suspected covid-19 patients; contrasting effects of reduced VA/Q and shunt
Authors: Jones J.Gareth 
Published: December 2020

ABSTRACTPatients in the UK at risk of Covid-19 pneumonia, but not needing immediate hospital attention, are to be given pulse oximeters to identify a fall in oxygen saturation (SaO2 or SpO2) at home. A recent finding in Covid-19 pneumonia is a dominant reduction in ventilation to perfused alveoli (VA/Q). A mathematical model of gas exchange was used to predict the effect of shunt or reduced VA/Q on SaO2 stability inferred from the slope of the PIO2 vs SaO2 curve as it intersected the line representing ambient PIO2. A ±1 kPa variation in PIO2 predicted a 1.5% and 8% change in SpO2 with 15% shunt and 0.4 VA/Q respectively. As a consistency check, two patients with pre-existing lung disease and 12 hour continuous SpO2 monitoring breathing air had gas exchange impairment analysed in terms of shunt and reduced VA/Q. The patient with 16% shunt and normal VA/Q had a stable but reduced SpO2 (circa 93±1%) throughout the 12 hr period. The patient with a VA/Q reduced to 0.48 had SpO2 ranging from 75-95% during the same period. SpO2 monitoring in suspected covid-19 patients should focus on SpO2 varying >5% in 30 minutes. Such instability in at risk patients is not diagnostic of Covid-19 pneumonia but this may be suspected from a dominant reduction in VA/Q if episodic hypoxaemia has progressed from a stable SpO2.
Tuberculosis alters immune-metabolic pathways resulting in perturbed IL-1 responses
Authors: Llibre Alba , Smith Nikaïa , Rouilly Vincent , Musvosvi Munyaradzi , Nemes Elisa , Posseme Céline , Mabwe Simba , Charbit Bruno , Mbandi Stanley Kimbung , Filander Elizabeth , Africa Hadn , Saint-André Violaine , Bondet Vincent , Bost Pierre , Mulenga Humphrey , Bilek Nicole , Albert Matthew L , Scriba Thomas J , Duffy Darragh 
Published: December 2020

SUMMARYTuberculosis (TB) remains a major public health problem with host-directed therapeutics offering potential as novel treatment strategies. However, their successful development still requires a comprehensive understanding of howMycobacterium tuberculosis(M.tb) infection impacts immune responses. To address this challenge, we applied standardised immunomonitoring tools to compare TB antigen, BCG and IL-1β induced immune responses between individuals with latentM.tbinfection (LTBI) and active TB disease, at diagnosis and after cure. This revealed distinct responses between TB and LTBI groups at transcriptomic, proteomic and metabolomic levels. At baseline, we identified pregnane steroids and the PPARγ pathway as new immune-metabolic drivers of elevated plasma IL-1ra in TB. We also observed dysregulated induced IL-1 responses after BCG stimulation in TB patients. Elevated IL-1 antagonist responses were explained by upstream differences in TNF responses, while for IL-1 agonists it was due to downstream differences in granzyme mediated cleavage. Finally, the immune response to IL-1β driven signalling was also dramatically perturbed in TB disease but was completely restored after successful antibiotic treatment. This systems immunology approach improves our knowledge of how immune responses are altered during TB disease, and may support design of improved diagnostic, prophylactic and therapeutic tools.
KwARG: Parsimonious Reconstruction of Ancestral Recombination Graphs with Recurrent Mutation
Authors: Ignatieva Anastasia , Lyngsø Rune B. , Jenkins Paul A. , Hein Jotun 
Published: December 2020

AbstractThe reconstruction of possible histories given a sample of genetic data in the presence of recombination and recurrent mutation is a challenging problem, but can provide key insights into the evolution of a population. We present KwARG, which implements a parsimony-based greedy heuristic algorithm for finding plausible genealogical histories (ancestral recombination graphs) that are minimal or near-minimal in the number of posited recombination and mutation events. Given an input dataset of aligned sequences, KwARG outputs a list of possible candidate solutions, each comprising a list of mutation and recombination events that could have generated the dataset; the relative proportion of recombinations and recurrent mutations in a solution can be controlled via specifying a set of ‘cost’ parameters. We demonstrate that the algorithm performs well when compared against existing methods. The software is made available on GitHub.
Activation of the type 3 secretion system of enteropathogenicE. colileads to remodeling of its membrane composition and function
Authors: Zacharia Anish , Pal Ritesh Ranjan , Katsowich Naama , Mannully Chanchal Thomas , ibrahim Aida , Alfandary Sivan , Serruya Raphael , Baidya Amit K , Ben-Yehuda Sigal , Rosenshine Ilan , Moussaieff Arieh 
Published: December 2020

AbstractThe cell envelope of gram-negative bacteria is a complex structure, essential for bacterial survival and for resistance to many antibiotics. Channels that cross the bacterial envelope and the host cell membrane form secretion systems that are activated upon attachment to host, enabling bacteria to inject effector molecules into the host cell, required for bacterial-host interaction. The type III secretion system (T3SS) is critical for the virulence of several pathogenic bacteria, including enteropathogenicE. coli(EPEC). The EPEC T3SS activation is associated with repression of carbon storage regulator (CsrA), resulting in gene expression remodeling, which is known to affect EPEC central carbon metabolism and contributes to the adaptation to a cell-adherent lifestyle in a poorly understood manner. We reasoned that the changes in bacterial envelope upon attachment to host and the activation of a secretion system may involve a modification of the lipid composition of bacterial envelope. Accordingly, we performed a lipidomics analysis on mutant strains that simulate T3SS activation. We saw a shift in glycerophospholipid metabolism towards the formation of lysophospholipids, attributed to corresponding upregulation of the phospholipasepldAand the acyltransferaseygiHupon T3SS activation in EPEC. We also detected a shift from menaquinones and ubiquinones to undecaprenyl lipids, concomitant to abnormal synthesis of O-antigen. The remodeling of lipid metabolism is mediated by CsrA and associated with increased bacteria cell size and Zeta potential, and a corresponding alteration in EPEC permeability to vancomycin, increasing the sensitivity of T3SS-activated strains and of adherent wild type EPEC to the antibiotic.ImportanceThe characterization of EPEC membrane lipid metabolism upon attachment to host is an important step towards a better understanding the shift of EPEC, a notable human pathogen, from a planktonic to adherent life style. It may also apply to other pathogenic bacteria that use this secretion system. We predict that upon attachment to host cells the lipid remodeling upon T3SS activation contributes to bacterial fitness and promotes host colonization, and show that it is associated with increased cell permeability and higher sensitivity to vancomycin.To the best of our knowledge, this is the first demonstration of a bacterial lipid remodeling due to activation of a secretion system.
Gastrointestinal ulceration in calves presented to a central Iowa veterinary referral facility: An underappreciated morbidity?
Authors: Mosichuk Allison , Smith Joe , Tatarniuk Dane , Kreuder Amanda 
Published: December 2020

Summary and ImplicationsThe objective of this retrospective investigation is to identify the incidence of gastrointestinal ulceration as a co-morbidity in calves presenting to a referral veterinary hospital. Approximately 24% of calves presented to the hospital that died or were euthanized had evidence of gastrointestinal ulceration. Previous administration of an NSAID was significantly associated with the presence of ulcers, whereas antibiotic administration, age at presentation, gender, or breed were not. Clinicians and producers should consider the risk of ulceration in calves treated with NSAIDs, in light of antiulcer therapies.
Public adherence to governmental recommendations regarding quarantine and testing for COVID-19 in two Norwegian cohorts
Authors: Carlsen Ellen Ø , Caspersen Ida Henriette , Trogstad Lill , Gjessing Håkon K , Magnus Per 
Published: December 2020

AbstractBackgroundCombatting the COVID-19 pandemic relies at present on non-pharmacological interventions. Governments are using various approaches from general advice to full lockdown. There is a need to describe and understand adherence to public health actions.MethodsParticipants from two ongoing cohorts, the Norwegian Mother, Father and Child Cohort Study (MoBa) and The Norwegian Influenza Pregnancy Cohort (NorFlu), answered questionnaires every 14 days since March 2020. From the summer of 2020, testing for presence of SARS-CoV-2 became easily available. Recommendations were that respiratory symptoms should lead to testing, and that confirmed or suspected COVID-19 should be followed by quarantine. We estimated the adherence to these guidelines in responses from cohort participants in the period August to October 2020.ResultsLess than 40% of men who were ill and less than 45% of women who were ill, tested themselves for SARS-CoV-2 during the same 14-day periods. Among subjects tested for COVID-19, about 53% of men and 59% of women reported quarantine. For subjects with a confirmed or suspected COVID-19 diagnosis, the proportions quarantined were 65% for men and 72% for women.ConclusionsPublic adherence to governmental recommendations regarding testing and quarantine were lower than expected in a country with high trust in government. This leaves considerable room for improvement in adherence, possibly reducing the need for more restrictive interventions.
The Easter Egg Weevil (Pachyrhynchus) genome reveals synteny in Coleoptera across 200 million years of evolution
Authors: Van Dam Matthew H. , Cabras Analyn Anzano , Henderson James B. , Pérez Estrada Cynthia , Omer Arina D. , Dudchenko Olga , Aiden Erez Lieberman , Lam Athena W. 
Published: December 2020

AbstractPatterns of genomic architecture across insects remain largely undocumented or decoupled from a broader phylogenetic context. For instance, it is unknown whether translocation rates differ between insect orders? We address broad scale patterns of genome architecture across Insecta by examining synteny in a phylogenetic framework from open source insect genomes. To accomplish this, we add a chromosome level genome to a crucial lineage, Coleoptera. Our assembly of thePachyrhynchus sulphureomaculatusgenome is the first chromosome scale genome for the hyperdiverse Phytophaga lineage and currently the largest insect genome assembled to this scale. The genome is significantly larger than those of other weevils, and this increase in size is caused by repetitive elements. Our results also indicate that, among beetles, there are instances of long-lasting (>200 Ma) localization of genes to a particular chromosome with few translocation events. While some chromosomes have a paucity of translocations, intra-chromosomal synteny was almost absent, with gene order thoroughly shuffled along a chromosome. To place our findings in an evolutionary context, we compared syntenic patterns across Insecta. We find that synteny largely scales with clade age, with younger clades, such as Lepidoptera, having especially high synteny. However, we do find subtle differences in the maintenance of synteny and its rate of decay among the insect orders.
FBW7 couples structural integrity with functional output of primary cilia
Authors: Petsouki Eleni , Gerakopoulos Vasileios , Szeto Nicholas , Chang Wenhan , Humphrey Mary Beth , Tsiokas Leonidas 
Published: December 2020

AbstractStructural defects in cilia have robust effects in diverse tissues and systems. However, how ciliary length changes influence signaling output are unknown. Here, we examined the functional role of a ciliary length control mechanism whereby FBW7-mediated destruction of NDE1 positively regulated ciliary length, in mesenchymal stem cell differentiation. We show that FBW7 functions as a master regulator of both negative (NDE1) and positive (TALPID3) regulators of ciliogenesis, with an overall positive net effect on cilia formation, MSC differentiation, and bone architecture. Deletion ofFbxw7suppresses ciliation, Hedgehog activity, and differentiation, which are rescued inFbxw7/Nde1-null cells. However, despite formation of abnormally long cilia inNde1-null cells, MSC differentiation is suppressed. NDE1 promotes MSC differentiation by increasing the activity of the Hedgehog pathway by direct binding and enhancing GLI2 activity in a cilia-independent manner. We propose that ciliary structure-function coupling is determined by intricate interactions of structural and functional proteins.
Increased functional connectivity of the intraparietal sulcus underlies the attenuation of numerosity estimations for self-generated words
Authors: Stripeikyte Giedre , Pereira Michael , Rognini Giulio , Potheegadoo Jevita , Blanke Olaf , Faivre Nathan 
Published: December 2020

ABSTRACTPrevious studies have shown that self-generated stimuli in auditory, visual, and somatosensory domains are attenuated, producing decreased behavioral and neural responses compared to the same stimuli that are externally generated. Yet, whether such attenuation also occurs for higher-level cognitive functions beyond sensorimotor processing remains unknown. In this study, we assessed whether cognitive functions such as numerosity estimations are subject to attenuation. We designed a task allowing the controlled comparison of numerosity estimations for self (active condition) and externally (passive condition) generated words. Our behavioral results showed a larger underestimation of self-compared to externally-generated words, suggesting that numerosity estimations for self-generated words are attenuated. Moreover, the linear relationship between the reported and actual number of words was stronger for self-generated words, although the ability to track errors about numerosity estimations was similar across conditions. Neuroimaging results revealed that numerosity underestimation involved increased functional connectivity between the right intraparietal sulcus and an extended network (bilateral supplementary motor area, left inferior parietal lobule and left superior temporal gyrus) when estimating the number of self vs. externally generated words. We interpret our results in light of two models of attenuation and discuss their perceptual versus cognitive origins.