bluuebunny/crossref_metadata_2025_split huggingface dataset:
ARTS-DB: a database for antibiotic resistant targets
Authors: Mungan Mehmet Direnç , Blin Kai , Ziemert Nadine 
Published: October 2021

Abstract
As a result of the continuous evolution of drug resistant bacteria, new antibiotics are urgently needed. Encoded by biosynthetic gene clusters (BGCs), antibiotic compounds are mostly produced by bacteria. With the exponential increase in the number of publicly available, sequenced genomes and the advancements of BGC prediction tools, genome mining algorithms have uncovered millions of uncharacterized BGCs for further evaluation. Since compound identification and characterization remain bottlenecks, a major challenge is prioritizing promising BGCs. Recently, researchers adopted self-resistance based strategies allowing them to predict the biological activities of natural products encoded by uncharacterized BGCs. Since 2017, the Antibiotic Resistant Target Seeker (ARTS) facilitated this so-called target-directed genome mining (TDGM) approach for the prioritization of BGCs encoding potentially novel antibiotics. Here, we present the ARTS database, available at https://arts-db.ziemertlab.com/. The ARTS database provides pre-computed ARTS results for &gt;70,000 genomes and metagenome assembled genomes in total. Advanced search queries allow users to rapidly explore the fundamental criteria of TDGM such as BGC proximity, duplication and horizontal gene transfers of essential housekeeping genes. Furthermore, the ARTS database provides results interconnected throughout the bacterial kingdom as well as links to known databases in natural product research.
Invasive Pulmonary Aspergillosis Complicating Noninfluenza Respiratory Viral Infections in Solid Organ Transplant Recipients
Authors: Apostolopoulou Anna , Clancy Cornelius J , Skeel Abigail , Nguyen M Hong 
Published: October 2021

Abstract

Background
Invasive pulmonary aspergillosis (IPA) is increasingly recognized as a complication of severe influenza and coronavirus disease 2019. The extent to which other respiratory viral infections (RVIs) predispose to IPA is unclear.

Methods
We performed a retrospective review of IPA occurring within 90 days of respiratory syncytial virus (RSV), parainfluenza, or adenovirus infections (noninfluenza respiratory viral infections [NI-RVIs]) in patients who underwent solid organ transplant between 1/15/2011 and 12/19/2017.

Results
At a median post-transplant follow-up of 43.4 months, 221 of 2986 patients (7.4%) developed 255 RSV, parainfluenza, or adenovirus infections. IPA complicating these NI-RVIs was exclusively observed in lung and small bowel transplant recipients, in whom incidence was 5% and 33%, respectively. Cumulative prednisone doses &gt;140mg within 7 days and pneumonia at the time of NI-RVI were independent risk factors for IPA (odds ratio [OR], 22.6; 95% CI, 4.5–112; and OR, 7.2; 95% CI, 1.6–31.7; respectively). Mortality at 180 days following NI-RVI was 27% and 7% among patients with and without IPA, respectively (P = .04).

Conclusions
In conclusion, IPA can complicate RSV, parainfluenza, and adenovirus infection in lung and small bowel transplant recipients. Future research is needed on the epidemiology of IPA complicating various RVIs. In the interim, physicians should be aware of this complication.
Intranasal oxytocin treatment on the day of weaning does not decrease walking behavior or improve plasma metabolites in beef calves placed on pasture
Authors: Nickles Kirsten R , Relling Alejandro E , Parker Anthony J 
Published: October 2021

Abstract
The purpose of this study was to evaluate the effect of intranasal oxytocin administered at abrupt weaning on weaning behaviors such as walking distance and time devoted to walking, calf body weight, and plasma non-esterified fatty acids (NEFAs), β-hydroxybutyrate (β-HB), and cortisol. Twenty Simmental × Angus heifer calves were randomly assigned to one of two treatments: intranasal oxytocin (OXT; n = 10) or intranasal saline (CON; n = 10). All calves were given the respective intranasal treatment on the day of weaning (day 0) and then placed on pasture together. Calves were weighed and a blood sample was obtained on days 0, 1, 7, and 14 postweaning. Blood samples were subsequently used to quantify plasma NEFA, β-HB, and cortisol concentrations. All calves in both treatment groups were fitted with an individual global positioning system that recorded calf location every 10 s for a 16-h period on days 0, 7, and 14 to quantify and evaluate walking behaviors. There was no treatment × day effect for distance walked (P = 0.82), walking time (P = 0.80), non-walking time (P = 0.88), area utilization index (P = 0.84), calf body weight (P = 0.82), average daily gain (P = 0.54), NEFA (P = 0.22), or cortisol concentrations (P = 0.32). There was a tendency for a treatment × day effect observed for average walking speed (P = 0.09) and β-HB (P = 0.10), such that calves in the CON treatment tended to have lesser average walking speeds on day 14 and tended to have greater β-HB concentration after weaning. There was a treatment effect (P = 0.02) for NEFA concentrations, with the CON calves having a greater plasma NEFA concentration throughout the study compared with OXT calves. These data imply that OXT calves may have had differing metabolic responses immediately after weaning that could have altered the mobilization of NEFA, but this change was not substantial enough to impact body weights or walking behaviors.
Immune Memory Response After a Booster Injection of mRNA-1273 for Severe Acute Respiratory Syndrome Coronavirus-2 (SARS-CoV-2)
Authors: Chu Laurence , Montefiori David , Huang Wenmei , Nestorova Biliana , Chang Ying , Carfi Andrea , Edwards Darin K. , Oestreicher Judy , Legault Holly , Girard Bethany , Pajon Rolando , Miller Jacqueline M. , Das Rituparna , Leav Brett , McPhee Roderick 
Published: October 2021

AbstractRising breakthrough infections of coronavirus-2 (SARS-CoV-2) in previously immunized individuals has raised concerns for a booster to combat suspected waning immunity and new variants. Participants immunized 6-8 months earlier with a primary series of two doses of 50 or 100 µg of mRNA-1273 were administered a booster injection of 50 µg of mRNA-1273. Neutralizing antibody levels against wild-type virus and the Delta variant at one month after the booster were 1.7-fold and 2.1-fold higher, respectively, than those 28 days post primary series second injection indicating an immune memory response. The reactogenicity after the booster dose was similar to that after the second dose in the primary series of two doses of mRNA-1273 (50 or 100 µg) with no serious adverse events reported in the one-month follow-up period. These results demonstrate that a booster injection of mRNA-1273 in previously immunized individuals stimulated an immune response greater than the primary vaccination series.
Pruning Digital Contact Networks for Meso-scale Epidemic Surveillance Using Foursquare Data
Authors: Hurtado Sofia , Marculescu Radu , Drake Justin A. , Srinivasan Ravi 
Published: October 2021

AbstractWith the recent boom in human sensing, the push to incorporate human mobility tracking with epidemic modeling highlights the lack of groundwork at the meso-scale (e.g., city-level) for both contact tracing and transmission dynamics. Although GPS data has been used to study city-level outbreaks, current approaches fail to capture the path of infection at the individual level. Consequently, in this paper, we extend the usefulness of epidemics prediction from estimating the size of an outbreak at the population level to estimating the individuals who may likely get infected within a finite period of time. To this end, we propose a network-based method to first build and then prune the dynamic contact networks for recurring interactions; these networks can serve as the backbone topology for mechanistic epidemics modeling. We test our method using Foursquare’s Points of Interest (POI) smart-phone geolocation data from over 1.3 million devices and show that we can recreate the COVID-19 infection curves for two major (yet very different) US cities (i.e., Austin and New York City) while maintaining the granularity of individual transmissions and reducing model uncertainty. Our method provides a foundation for building a disease prediction framework at the meso-scale that can help both policy makers and individuals of their estimated state of health and help with pandemic planning.
Effectiveness of mRNA-1273 against Delta, Mu, and other emerging variants
Authors: Bruxvoort Katia J. , Sy Lina S. , Qian Lei , Ackerson Bradley K. , Luo Yi , Lee Gina S. , Tian Yun , Florea Ana , Aragones Michael , Tubert Julia E. , Takhar Harpreet S. , Ku Jennifer H. , Paila Yamuna D. , Talarico Carla A. , Tseng Hung Fu 
Published: October 2021

ABSTRACTBackgroundReal-world studies have found high vaccine effectiveness (VE) of mRNA-based COVID-19 vaccines, but reduced VE against the Delta variant and waning protection have been reported, with few studies examining mRNA-1273 variant-specific VE.MethodsWe conducted a test-negative case-control study at Kaiser Permanente Southern California. Whole genome sequencing was conducted for SARS-CoV-2 positive specimens collected from 3/1/2021 to 7/27/2021. Test-positive cases were matched 1:5 to test-negative controls on age, sex, race/ethnicity, and specimen collection date. Outcomes included SARS-CoV-2 infection and hospitalization. Exposures were 2 doses or 1 dose of mRNA-1273 ≥14 days prior to specimen collection versus no COVID-19 vaccination. Conditional logistic regression was used to compare odds of vaccination among cases versus controls, adjusting for confounders. VE was calculated as (1-odds ratio)x100%.ResultsThe study included 8,153 cases and their matched controls. Two-dose VE (95% confidence interval) was 86.7% (84.3-88.7%) against Delta infection, 98.4% (96.9-99.1%) against Alpha, 90.4% (73.9-96.5%) against Mu, 96-98% against other identified variants, and 79.9% (76.9-82.5%) against unidentified variants. VE against Delta declined from 94.1% (90.5-96.3%) 14-60 days after vaccination to 80.0% (70.2-86.6%) 151-180 days after vaccination. Waning was less pronounced for non-Delta variants. VE against Delta was lower among individuals aged ≥65 years (75.2% [59.6-84.8%]) than those aged 18-64 years (87.9% [85.5-89.9%]). VE against Delta hospitalization was 97.6% (92.8-99.2%). One-dose VE was 77.0% (60.7-86.5%) against Delta infection.ConclusionsTwo doses of mRNA-1273 were highly effective against all SARS-CoV-2 variants. However, VE against Delta moderately declined with increasing time since vaccination.Trial Registration NumberNot applicableFundingModerna Inc.
A HOME-TREATMENT ALGORITHM BASED ON ANTI-INFLAMMATORY DRUGS TO PREVENT HOSPITALIZATION OF PATIENTS WITH EARLY COVID-19: A MATCHED-COHORT STUDY (COVER 2)
Authors: Consolaro Elena , Suter Fredy , Rubis Nadia , Pedroni Stefania , Moroni Chiara , Pastò Elena , Paganini Maria Vittoria , Pravettoni Grazia , Cantarelli Umberto , Perico Norberto , Perna Annalisa , Peracchi Tobia , Ruggenenti Piero , Remuzzi Giuseppe 
Published: October 2021

AbstractBackground and AimWhile considerable success has been achieved in the management of patients hospitalized with severe coronavirus disease 2019 (COVID-19), far less progress has been made with early outpatient treatment. We assessed whether the implementation of a home treatment algorithm – designed based upon on a pathophysiologic and pharmacologic rationale - during the initial, mild phase of COVID-19, could effectively reduce hospital admissions.MethodsThis fully academic, matched-cohort study evaluated outcomes in 108 consecutive consenting patients with mild COVID-19 managed at home by their family doctors from January 2021 to May 2021, according to the proposed treatment algorithm and in 108 age-, sex-, and comorbidities-matched patients who were given other therapeutic schedules (ClinicalTrials.gov: NCT04854824). The primary outcome was COVID-19-related hospitalization. Analyses were by intention-to-treat.ResultsOne (0.9%) patient in the ‘recommended’ cohort and 12 (11.1%) in the ‘control’ cohort were admitted to hospital (P=0.0136). The proposed algorithm reduced, by 85%, the cumulative length of hospital stays (from 141 to 19 days) and related costs (from € 60.316 to € 9.058). Only 9.8 patients needed to be treated with the recommended algorithm to prevent one hospitalization event. The rate of resolution of major symptoms was numerically, but not significantly, higher in the ‘recommended’ compared to the ‘control’ cohort (97.2% versus 93.5%, respectively; P=0.322). Other symptoms lingered in a lower proportion of patients in the ‘recommended’ than in the‘control’ cohort (20.4% versus 63.9%, respectively; P<0.001), and for a shorter period.ConclusionThe adoption of the proposed outpatient treatment algorithm during the early, mild phase of COVID-19 reduced the incidence of subsequent hospitalization and related costs.
Anti-neuronal IgG4 autoimmune diseases and IgG4-related diseases may not be part of the same spectrum: a comparative study
Authors: Endmayr Verena , Tunc Cansu , Ergin Lara , de Rosa Anna , Weng Rosa , Wagner Lukas , Yu Thin-Yau , Fichtenbaum Andreas , Perkmann Thomas , Haslacher Helmuth , Kozakowski Nicolas , Schwaiger Carmen , Ricken Gerda , Hametner Simon , Dutra Lívia Almeida , Lechner Christian , de Simoni Désirée , Poppert Kai-Nicolas , Müller Georg Johannes , Pirker Susanne , Pirker Walter , Angelovski Aleksandra , Valach Matus , Maestri Michelangelo , Guida Melania , Ricciardi Roberta , Frommlet Florian , Sieghart Daniela , Pinter Miklos , Höftberger Romana , Koneczny Inga 
Published: October 2021

AbstractBackgroundIgG4 is associated with two emerging groups of rare diseases: 1) IgG4 autoimmune diseases (IgG4-AID) and 2) IgG4-related diseases (IgG4-RLD). Anti-neuronal IgG4-AID include MuSK myasthenia gravis, LGI1- and Caspr2-encephalitis and autoimmune nodo-/paranodopathies (CNTN1 or NF155 antibodies). IgG4-RLD is a multiorgan disease hallmarked by tissue-destructive fibrotic lesions with lymphocyte and IgG4 plasma cell infiltrates and increased serum IgG4 concentrations. It is unclear, whether IgG4-AID and IgG4-RLD share relevant clinical and immunopathological features.MethodsWe collected and analysed serological, clinical, and histopathological data in 50 patients with anti-neuronal IgG4-AID and 16 patients with IgG4-RLD.ResultsA significantly higher proportion of IgG4-RLD patients had serum IgG4 elevation when compared to IgG4-AID patients (50% vs. 16%, p = .015). Moreover, those IgG4-AID patients with elevated IgG4 did not meet the diagnostic criteria of IgG4-RLD, and their autoantibody titres did not correlate with their serum IgG4 concentrations. In addition, patients with IgG4-RLD were negative for anti-neuronal/neuromuscular autoantibodies and among these patients, men showed a significantly higher propensity for IgG4 elevation, when compared to women (p = .041). Last, a kidney biopsy from a patient with autoimmune paranodopathy due to CNTN1/Caspr1-complex IgG4 autoantibodies and concomitant nephrotic syndrome did not show fibrosis or IgG4+ plasma cells, which are diagnostic hallmarks of IgG4-RLD.ConclusionOur observations suggest that anti-neuronal IgG4-AID and IgG4-RLD are most likely distinct disease entities.
Development and validation of a length- and habitus-based method of total body weight estimation for critically ill adults requiring urgent weight-based medical intervention
Authors: Wells Mike , Goldstein Lara Nicole , Cattermole Giles 
Published: October 2021

ABSTRACTBackgroundErroneous weight estimation during the management of emergency presentations in adults may contribute to patient harm and poor outcomes. Patients can often not be weighed during emergencies and a weight estimation is required to facilitate weight-based therapies. Many existing methods of weight estimation are either unacceptably inaccurate or very difficult to use during the provision of emergency care.MethodsThe weight estimation system developed in this study was based on and modified from the PAWPER XL-MAC method, a paediatric weight estimation system that uses recumbent length and mid-arm circumference (MAC) to predict total body weight. This model was validated in the 2015 – 2018 National Health and Nutrition Examination Survey (NHANES) datasets. The primary outcome measure was to achieve >95% of estimations within 20% of measured weight (P20>95%).ResultsThe modified PAWPER XL-MAC model achieved a P20 of 96.0% and a P10 of 71.3% in the validation dataset (N=11520). This accuracy (P20>95%) was maintained in both sexes, all ages, all ethnic groups, all lengths and in all habitus-types, except for the subgroup of severely obese individuals.ConclusionsThe modified PAWPER XL-MAC model proved to be a very accurate method of weight estimation. It is more accurate than most other published reports of existing methods of weight estimation, except for patients’ own estimations. It therefore could have a role in facilitating emergency drug dose calculations, if prospective studies bear out the accuracy found in this study.
Dynamical modeling of the H3K27 epigenetic landscape in mouse embryonic stem cells
Authors: Newar Kapil , Abdulla Amith Z. , Salari Hossein , Fanchon Eric , Jost Daniel 
Published: October 2021

AbstractThe Polycomb system via the methylation of the lysine 27 of histone H3 (H3K27) plays central roles in the silencing of many lineage-specific genes during development. Recent experimental evidence suggested that the recruitment of histone modifying enzymes like the Polycomb repressive complex 2 (PRC2) at specific sites and their spreading capacities from these sites are key to the establishment and maintenance of a proper epigenomic landscape around Polycomb-target genes. Here, to test whether such mechanisms, as a minimal set of qualitative rules, are quantitatively compatible with data, we developed a mathematical model that can predict the locus-specific distributions of H3K27 modifications based on previous biochemical knowledge. Within the biological context of mouse embryonic stem cells, our model showed quantitative agreement with experimental profiles of H3K27 acetylation and methylation around Polycomb-target genes in wild-type and mutants. In particular, we demonstrated the key role of the reader-writer module of PRC2 and of the competition between the binding of activating and repressing enzymes in shaping the H3K27 landscape around transcriptional start sites. The predicted dynamics of establishment and maintenance of the repressive trimethylated H3K27 state suggest a slow accumulation, in perfect agreement with experiments. Our approach represents a first step towards a quantitative description of PcG regulation in various cellular contexts and provides a generic framework to better characterize epigenetic regulation in normal or disease situations.
Representation of motion concepts in occipitotemporal cortex: fMRI activation, decoding and connectivity analyses
Authors: Zhang Yueyang , Lemarchand Rafael , Asyraff Aliff , Hoffman Paul 
Published: October 2021

AbstractEmbodied theories of semantic cognition predict that brain regions involved in motion perception are engaged when people comprehend motion concepts expressed in language. Left lateral occipitotemporal cortex (LOTC) is implicated in both motion perception and motion concept processing but prior studies have produced mixed findings on which parts of this region are engaged by motion language. We scanned participants performing semantic judgements about sentences describing motion events and static events. We performed univariate analyses, multivariate pattern analyses (MVPA) and psychophysiological interaction (PPI) analyses to investigate the effect of motion on activity and connectivity in different parts of LOTC. In multivariate analyses that decoded whether a sentence described motion or not, the middle and posterior parts of LOTC showed above-chance level performance, with performance exceeding that of other brain regions. Univariate ROI analyses found the middle part of LOTC was more active for motion events than static ones. Finally, PPI analyses found that when processing motion events, the middle and posterior parts of LOTC (overlapping with motion perception regions), increased their connectivity with cognitive control regions. Taken together, these results indicate that the more posterior parts of LOTC, including motion perception cortex, respond differently to motion vs. static events. These findings are consistent with embodiment accounts of semantic processing, and suggest that understanding verbal descriptions of motion engages areas of the occipitotemporal cortex involved in perceiving motion.
A morphometric double dissociation: cortical thickness is more related to aging; surface area is more related to cognition
Authors: Borgeest G. Sophia , Henson Richard N. , Kietzmann Tim C. , Madan Christopher R. , Fox Theresa , Malpetti Maura , Fuhrmann Delia , Knights Ethan , Carlin Johan D. ,   Cam-CAN, Kievit Rogier A. 
Published: October 2021

AbstractThe thickness and surface area of cortex are genetically distinct aspects of brain structure, and may be affected differently by age. However, their potential to differentially predict age and cognitive abilities has been largely overlooked, likely because they are typically aggregated into the commonly used measure of volume. In a large sample of healthy adults (N=647, aged 18-88), we investigated the brain-age and brain-cognition relationships of thickness, surface area, and volume, plus five additional morphological shape metrics. Cortical thickness was the metric most strongly associated with age cross-sectionally, as well as exhibiting the steepest longitudinal change over time (subsample N=261, aged 25-84). In contrast, surface area was the best single predictor of age-residualized cognitive abilities (fluid intelligence), and changes in surface area were most strongly associated with cognitive change over time. These findings were replicated in an independent dataset (N=1345, aged 18-93). Our results suggest that cortical thickness and surface area make complementary contributions the age-brain-cognition triangle, and highlight the importance of considering these volumetric components separately.