bluuebunny/crossref_metadata_2025_split huggingface dataset:
A Ten-Year Retrospective Review of the Nonsurgical Treatment of Infant Ear Anomalies
Authors: Charipova Karina , Rogers Ashley , Barra Christina , Baker Stephen B. 
Published: August 2022

Background:
A review of a single surgeon’s ten-year experience treating congenital ear anomalies using nonsurgical ear molding is presented. This study assesses the efficacy of treating a variety of anomalies in infants age less than 1 week to 22 weeks and identifies potential barriers to care.

Methods:
A retrospective chart and photographic review of 246 consecutive infants treated with ear molding between 2010 and 2019 was undertaken. Data regarding patient demographics, anomaly classification, device selection, treatment duration, adverse events, and satisfaction with outcomes were collected.

Results:
This study included 385 infant ear anomalies in 246 patients. Median age at initiation of treatment was 16 days and median treatment duration was 29.5 days. A median of 3 devices was needed to complete bilateral treatment. Treated anomalies included mixed deformity, helical rim, prominent, lidding/lop, Stahl’s ear, conchal crus, cupping, and cryptotia. Complications occurred in 47 patients with skin breakdown being the most common (26 patients, 55.3%). Satisfaction rate was 92% in 137 surveyed parents. Median patient household income was approximately $112,911, and treatment was covered by insurance for 244 of 246 patients.

Conclusions:
Our outcomes demonstrate that ear molding can be effective in patients as old as 22 weeks without compromising treatment duration or complexity. Additionally, in the authors’ experience, molding is an effective treatment for the majority of infant ear deformities. Despite a steady increase in patient volume over the past 10 years and consistent coverage of treatment by insurance, our catchment area continues to be largely limited to affluent households.
Preoperative Multiparametric Prostate Magnetic Resonance Imaging Structured Report Informs Risk for Positive Apical Surgical Margins During Radical Prostatectomy
Authors: Costa Daniel N. , Meng Xiaosong , Tverye Aaron , Bagrodia Aditya , Recchimuzzi Debora Z. , Xi Yin , Arraj Patrick , Shah Rajal B. , Subramanian Naveen , de Leon Alberto Diaz , Roehrborn Claus G. , Rofsky Neil M. , Chen Heng , Pedrosa Ivan 
Published: August 2022

Background
The prostatic apex is the most frequent location of positive surgical margin (PSM) after surgery. Data regarding the ability of multiparametric magnetic resonance imaging (mpMRI) to prospectively identify men at risk for apical PSMs (aPSMs) using a structured report are lacking.

Objectives
The aims of the study are to determine and to compare the rate of aPSM in men with versus without prospectively flagged at-risk prostate lesions during clinical mpMRI interpretation using whole-mount histopathology as the reference standard.

Methods
This single-center, retrospective study of prospectively collected data included treatment-naive men with abnormal 3T mpMRI (PI-RADS v2 score ≥3) between January 2016 and December 2018 followed by surgery. During routine clinical interpretation, radiologists flagged prostate lesions abutting the apical most gland and/or encircling the distal most prostatic urethra using standardized language available as a “pick list” option in the structured report. Logistic regression was used to compare the rate of PSM in 2 groups (flagged vs nonflagged men). Propensity score covariate adjustment corrected for potential selection bias according to age, prostate-specific antigen (PSA), PSA density, grade group, and pT stage. The estimate was further adjusted by including surgeon as a covariate.

Results
A total of 428 men were included. A statistically significant higher proportion of aPSMs was noted in flagged (56% [51/91]) compared with nonflagged apical lesions (31% [105/337]; adjusted odds ratio, 2.5; 95% confidence interval, 1.6–4.1; P < 0.01). The difference in aPSM between both groups also varied according to the surgeon performing the RP. Prostate-specific antigen, PSA density, lesion size, apical location, Prostate Imaging Reporting & Data System score, grade group, pT stage, and surgeon's experience were associated with higher PSM rate. Biochemical recurrence, defined as PSA greater than 0.2 ng/mL on 2 measurements after RP, was significantly associated with PSM status (propensity score adjusted odds ratio, 3.1; 95% confidence interval, 1.8–5.3; P < 0.0001); however, patients flagged by radiologists did not have a significant difference in biochemical recurrence rates as compared with nonflagged patients (P = 0.11).

Conclusions
Standard language built into structured reports for mpMRI of the prostate helps identify preoperatively patients at risk for aPSM.

Clinical Impact
Multiparametric MRI is able to identify patients at increased risk for aPSM, and this information can be conveyed in a structured report to urologists, facilitating patient counseling and treatment decisions.
Surgical Management of Necrotizing Fasciitis of the Head and Neck
Authors: Acharya Pankti P. , Cohn Jason E. , Shokri Tom , Bundrick Paige , Ducic Yadranko 
Published: August 2022

Objective:
The purpose of this study was to highlight risk factors and surgeries for necrotizing fasciitis (NF) of the head and neck in the literature. NF is rare but can rapidly progress.

Materials and Methods:
A literature search was done using PubMed and SCOPUS. Articles that discussed NF of the head and neck and a specific surgical technique were included. A bivariate Pearson correlation was conducted using an α level of 0.05.

Results:
The study included 31 articles encompassing 77 patients who presented with head and neck NF. Diabetes mellitus (23.4%) was the most common comorbidity observed. Surgical techniques, such as debridement (96.10%) and incision/exploration (97.40%), were common.

Conclusion:
Immediate surgical intervention should be performed when treating patients presenting with NF of the head and neck.
Review Paper on Penetrating Brain Injury
Authors: Zakrison Tanya L. , Essig Rachael , Polcari Ann , McKinley William , Arnold Damon , Beyene Robel , Wilson Kenneth , Rogers Selwyn , Matthews Jeffrey B. , Millis J. Michael , Angelos Peter , O’Connor Michael , Mansour Ali , Goldenberg Fernando , Spiegel Thomas , Horowitz Peleg , Das Paramita , Slidell Mark , Chokshi Nikunj , Okeke Iheoma , Barth Rolf , Wilkins Harry E. , Kass-Hout Tareq , Lazaridis Christos 
Published: August 2022

Objective:
The aim of this review was to review the ethical and multidisciplinary clinical challenges facing trauma surgeons when resuscitating patients presenting with penetrating brain injury (PBI) and multicavitary trauma.

Background:
While there is a significant gap in the literature on managing PBI in patients presenting with multisystem trauma, recent data demonstrate that resuscitation and prognostic features for such patients remains poorly described, with trauma guidelines out of date in this field.

Methods:
We reviewed a combination of recent multidisciplinary evidence-informed guidelines for PBI and coupled this with expert opinion from trauma, neurosurgery, neurocritical care, pediatric and transplant surgery, surgical ethics and importantly our community partners.

Results:
Traditional prognostic signs utilized in traumatic brain injury may not be applicable to PBI with a multidisciplinary team approach suggested on a case-by-case basis. Even with no role for neurosurgical intervention, neurocritical care, and neurointerventional support may be warranted, in parallel to multicavitary operative intervention. Special considerations should be afforded for pediatric PBI. Ethical considerations center on providing the patient with the best chance of survival. Consideration of organ donation should be considered as part of the continuum of patient, proxy and family-centric support and care. Community input is crucial in guiding decision making or protocol establishment on an institutional level.

Conclusions:
Support of the patient after multicavitary PBI can be complex and is best addressed in a multidisciplinary fashion with extensive community involvement.
Trade-off between grain yield and protein concentration is modulated by canopy photosynthesis in Japanese wheat cultivars
Authors: Murakami Keach , Ikawa Hiroki 
Published: August 2022

AbstractA negative correlation between grain yield and protein concentration hinders an efficient nutrient supply. To analyze the causation of this inverse relationship, we compared the leaf and canopy photosynthesis of two Japanese wheat cultivars. Gas exchange measurements of leaves revealed that ‘Kitahonami’ (a high-yielding and low-protein cultivar) maintained high stomatal conductance from pre-anthesis to late grain-filling stage while stomata of ‘Yumechikara’ (a low-yielding and high-protein cultivar) were closed during the daytime, leading to decreased photosynthesis. We simulated canopy photosynthesis using a model and quantified the contribution of distinct stomatal behavior to canopy carbon gain. Although daily canopy photosynthetic gain was comparable or slightly low in ‘Yumechikara’ when model parameters obtained in the morning were used, the gain was substantially lower in ‘Yumechikara’ than in ‘Kitahonami’ when midday parameters were used. Canopy respiratory loss in ‘Yumechikara’ was greater than that in ‘Kitahonami’ during the middle of the grain-filling period because of its high canopy nitrogen content, leading to a considerable difference in net canopy carbon gain between the cultivars. Our study suggests one of the pathways for a lower carbon gain of a high protein cultivar and the greater nitrogen content does not necessarily result in a greater carbon gain.
A pilot study of 0.4% povidone-iodine nasal spray to eradicate SARS-CoV-2 in the nasopharynx
Authors: Sirijatuphat Rujipas , Leelarasamee Amorn , Puangpet Thanapat , Thitithanyanont Arunee 
Published: August 2022

AbstractWe studied the virucidal efficacy of 0.4% povidone-iodine (PVP-I) nasal spray against SARS-CoV-2 in the patients’ nasopharynx at 3 minutes and 4 hours after PVP-I exposure. We used an open-label, before and after design, single arm pilot study of adult patients with RT-PCR-confirmed COVID-19 within 24 hours. All patients received three puffs of 0.4% PVP-I nasal spray in each nostril. Nasopharyngeal (NP) swabs were collected before the PVP-I spray (baseline, left NP samples), and at 3 minutes (left and right NP samples) and 4 hours post-PVP-I spray (right NP samples). All swabs were coded to blind assessors and transported to diagnostic laboratory and tested by RT-PCR and cultured to measure the viable SARS-CoV-2 within 24 hours after collection. Fourteen patients were enrolled but viable SARS-CoV-2 was cultured from 12 patients (85.7%). The median viral titer at baseline was 3.5 log TCID50/mL (IQR 2.8-4.0 log TCID50/mL). At 3 minutes post-PVP-I spray via the left nostril, viral titers were reduced in 8 patients (66.7%). At 3 minutes post-PVP-I, the median viral titer was 3.4 log TCID50/mL (IQR 1.8-4.4 log TCID50/mL) (P=0.162). At 4 hours post-PVP-I spray via the right nostril, 6 of 11 patients (54.5%) had either the same or minimal change in viral titers. The median viral titer 3 minutes post-PVP-I spray was 2.7 log TCID50/mL (IQR 2.0-3.9 log TCID50/mL). Four hours post-PVP-I spray the median titer was 2.8 log TCID50/mL (IQR 2.2-3.9 log TCID50/mL) (P=0.704). No adverse effects of 0.4% PVP-I nasal spray were detected. We concluded that 0.4% PVP-I nasal spray demonstrated minimal virucidal efficacy at 3 minutes post-exposure. At 4 hours post-exposure, the viral titer was considerably unchanged from baseline in 10 cases. The 0.4% PVP-I nasal spray showed poor virucidal activity and is unlikely to reduce transmission of SARS-CoV-2 in prophylaxis use.
The efficiency of Grignard Pure™ to inactivate airborne SARS-CoV-2 surrogate
Authors: Desai Grishma , Ramachandran Gurumurthy , Goldman Emanuel , Galione Antony , Lal Altaf , Choueiri Toni K. , Fay Andre , Jordan William , Schaffner Donald W. , Caravanos Jack , Grignard Etienne , Mainelis Gediminas 
Published: August 2022

AbstractGrignard Pure™ (GP) is a unique and proprietary blend of Triethylene Glycol (TEG) and inert ingredients designed for continuous antimicrobial treatment of air. GP received approval from the US EPA under its Section 18 Public Health Emergency Exemption program for use in seven states. This study characterizes the efficacy of GP for inactivating MS2 bacteriophage – a non-enveloped virus widely used as a surrogate for SARs-CoV-2. Experiments measured the decrease in the airborne viable MS2 concentration in the presence of different concentrations of GP from 60 to 90 minutes, accounting for both natural die-off and settling of MS2. Experiments were conducted both by introducing GP aerosol into air containing MS2 and by introducing airborne MS2 into air containing GP aerosol. GP is consistently able to rapidly reduce viable MS2 bacteriophage concentration by 2-3 logs at GP concentrations of 0.02 mg/m3 to 0.5 mg/m3 (corresponding to TEG concentrations of 0.012 mg/m3 to 0.287 mg/m3). Related GP efficacy experiments by the US EPA, as well as GP (TEG) safety and toxicology, are also discussed.SynopsisLimited research on the germicidal properties of triethylene glycol against airborne pathogens was conducted during the 1940s and 50s. This paper investigates the inactivation rate of airborne bacteriophage MS2 by Grignard Pure™ product, containing a unique and proprietary blend of Triethylene Glycol (TEG) and inert ingredients.
Cryo-EM structures and binding of mouse ACE2 to SARS-CoV-2 variants of
concern
Authors: Ni Dongchun , Turelli Priscilla , Beckert Bertrand , Nazarov Sergey , Uchikawa Emiko , Myasnikov Alexander , Pojer Florence , Trono Didier , Stahlberg Henning , Lau Kelvin 
Published: August 2022

ABSTRACT
Investigation of potential hosts of the severe acute respiratory syndrome
coronavirus-2 (SARS-CoV-2) is crucial to understanding future risks of spillover
and spillback. SARS-CoV-2 has been reported to be transmitted from humans to
various animals after requiring relatively few mutations.1
Mice are well adapted to human environments, frequently come in contact with
humans, are used widely as infection models, and may act as reservoirs for
SARS-CoV-2.2 Structural and binding data of the mouse
ACE2 receptor with the Spike protein of newly identified SARS-CoV-2 variants are
needed to better understand the impact of variants of concern (VOC). Previous
studies have developed mouse-adapted variants and have identified some
determinants of binding.3,4 Here we report the cryo-EM
structures of mouse ACE2 bound to Spike ectodomains of four different VOC: Beta,
Omicron BA.1, Omicron BA.2.12.1 and Omicron BA.4/5. These variants represent the
oldest to the newest variants that are able to bind the mouse ACE2 receptor. Our
high-resolution structural data complemented with bio-layer interferometry (BLI)
binding assays reveal a requirement for a combination of mutations in the Spike
protein to enable the binding to mouse ACE2.
A Trypanosoma cruzi Antigen and Epitope Atlas: deep characterization of antibody specificities in Chagas Disease patients across the Americas
Authors: Ricci Alejandro D. , Bracco Leonel , Ramsey Janine M. , Nolan Melissa S. , Lynn M. Katie , Altcheh Jaime , Ballering Griselda , Torrico Faustino , Kesper Norival , Villar Juan C. , Marco Jorge D. , Agüero Fernán 
Published: August 2022

ABSTRACTDuring an infection, the immune system produces pathogen-specific antibodies. With time, these antibody repertoires become specific to the history of infections and represent a rich source of diagnostic markers. However, the specificities of these antibodies are mostly unknown. Here, using high-density peptide arrays we examined the specificities of human antibody repertoires of Chagas disease patients. Chagas disease is a neglected disease caused by Trypanosoma cruzi, a protozoan parasite that evades immune mediated elimination and mounts long-lasting chronic infections. We describe here the first proteome-wide search for antigens and epitopes and their seroprevalence at the individual level and across human populations. In a first discovery screening of 2.84 million short peptides spanning two T. cruzi proteomes we found 3,868 distinct antigenic protein regions. Further analysis of repertoires from 71 individuals provided information on their seroprevalence and showed a large fraction of private epitopes of low seroprevalence (<20%), and novel high seroprevalence antigens. Using single-residue mutagenesis we found the core epitopes required for antibody binding for 232 of these epitopes. These datasets enable the study of the Chagas antibody repertoire at an unprecedented depth and granularity, while also providing a rich source of novel serological biomarkers.IMPACT STATEMENTThis work reveals the diversity and extent of antibody specificities in Chagas Disease and provides a wealth of well-defined antigenic markers for diagnosis and development of serological applications for this neglected infectious disease.
Comparison ofde novoand reference genome-based transcriptome assembly pipelines for differential expression analysis of RNA sequencing data
Authors: Oomen Rebekah A. , Knutsen Halvor , Olsen Esben M. , Jentoft Sissel , Stenseth Nils Chr. , Hutchings Jeffrey A. 
Published: August 2022

AbstractObjectiveAs sequencing technologies become more accessible and bioinformatic tools improve, genomic resources are increasingly available for non-model species. Using a draft genome to guide transcriptome assembly from RNA sequencing data, rather than performing assemblyde novo, affects downstream analyses. Yet, direct comparisons of these approaches are rare. Here, we compare the results of the standardde novoassembly pipeline (‘Trinity’) and two reference genome-based pipelines (‘Tuxedo’ and the ‘new Tuxedo’) for differential expression and gene ontology enrichment analysis of a companion study on Atlantic cod (Gadus morhua).ResultsThe new Tuxedo pipeline produced a higher quality assembly than the Tuxedo suite. However, greater enrichment of Trinity-identified differentially expressed genes suggests that a higher proportion of them represent biologically meaningful differences in transcription, as opposed to transcriptional noise or false positives. Coupled with the ability to annotate novel loci, the increased sensitivity of the Trinity pipeline might make it preferable over the reference genome-based approaches for studies aimed at broadly characterizing variation in the magnitude of expression differences and biological processes. However, the ‘new Tuxedo’ pipeline might be appropriate when a more conservative approach is warranted, such as for the identification of candidate genes.
RNA polymerase inhibitor enisamium for treatment of moderate COVID-19 patients: a randomized, placebo-controlled, multicenter, double-blind phase 3 clinical trial
Authors: Holubovska O. , Babich P. , Mironenko A. , Milde J. , Lebed Y. , Stammer H. , Mueller L. , te Velthuis A.J.W. , Margitich V. , Goy A. 
Published: August 2022

ABSTRACTEnisamium (trade name Amizon®MAX) is an orally available therapeutic that inhibits influenza A virus and SARS-CoV-2 replicationin vitroand improves influenza patient recovery. We evaluated the clinical efficacy of enisamium treatment combined with standard care compared to standard care plus treatment with a placebo control in adult, hospitalized patients with moderate COVID-19 requiring external oxygen. Hospitalized patients with laboratory-confirmed SARS-CoV-2 infection were randomly assigned to receive either enisamium (500 mg per dose, 4 times a day) or a placebo. All patients received standard of care as deemed necessary by the investigator and the health status of each patient. The primary outcome was an improvement of at least two points on an 8-point, modified WHO severity rating (SR) scale within 29 days of randomization. A total of 592 patients were enrolled and randomized between May 2020 and March 2021. Patients with a baseline SR of 4 were divided into two groups: 142 (49.8%) were assigned to the enisamium group and 143 (50.2%) to the placebo group. No differences were observed between the safety or patient tolerability profiles of the enisamium and placebo treatment. Analysis of the population showed that if patients were treated within 4 days of the onset of COVID-19 symptoms (n = 33), the median time to improvement was 8 days for the enisamium group and 13 days for the placebo group (p = 0.0051). For patients treated within 10 days of the onset of COVID-19 symptoms (n = 154), the median time to improvement was 10 days for the enisamium group and 12 days for the placebo group (p = 0.002). Comparison of groups using a stratified one-sided Logrank criterion (adjustment using stratification by age categories: “<40 years”, “40-<65 years” and “≥65 years”) showed statistically significant differences between the groups (p = 0.00945, one-sided). Our findings suggest that enisamium is safe to use in COVID-19 patients, and that enisamium treatment offers a clinical benefit when given to patients with moderate COVID-19 requiring supplementary oxygen, if enisamium is given within 10 days of the onset of symptoms. This trial was registered with ClinicalTrials.gov underNCT04682873.
Epithelial antigen presentation controls commensal-specific intraepithelial T-cells in the gut
Authors: Brabec Tomas , Schwarzer Martin , Kováčová Katarína , Dobešová Martina , Schierová Dagmar , Březina Jiří , Pacáková Iva , Šrůtková Dagmar , Ben-Nun Osher , Goldfarb Yael , Šplíchalová Iva , Kolář Michal , Abramson Jakub , Filipp Dominik , Dobeš Jan 
Published: August 2022

SummaryThe expression of MHCII by intestinal epithelial cells (IEC) determines the severity of intestinal immunopathological reactions. However, the function of MHCII on IEC under homeostatic conditions remains elusive. Here we report that MHCII expression on IECs is a hallmark of an adaptive wave of homeostatic intestinal immune responses to commensal segmented filamentous bacteria (SFB). Focusing on SFB-driven responses, we describe the expression pattern of MHCII and the associated antigen processing machinery among IEC subpopulations along with the cellular network that regulates MHCII induction. Furthermore, we show that SFB induce the accumulation of SFB-specific intraepithelial lymphocytes (IELs) that originate from conventional CD4+T-cells. Importantly, induced IELs are dependent on the epithelial MHCII. Finally, we demonstrate that both epithelial MHCII and the IEL functionality regulate the epithelial turnover. This study describes the organization of a commensal-targeted, IEL-driven immune response that is controlled by IEC antigen presentation and ultimately regulates IEC turnover.