bluuebunny/crossref_metadata_2025 huggingface dataset:
Prenatal Diagnosis of Craniosynostosis Using Ultrasound
Authors: DeFreitas Christopher A. , Carr Stephen R. , Merck Derek L. , Byrne Margaret M. , Linden Olivia E. , Stiles Emily A. , Sullivan Stephen R. , Taylor Helena O.
Published: August 2022

Background:

Craniosynostosis is rarely diagnosed in utero, but rather postnatally through clinical exam and radiographic findings. Prenatal diagnosis would allow for improved parental counseling and facilitate timely intervention. The authors’ purpose is to determine if prenatal ultrasound can be used to diagnose nonsyndromic craniosynostosis, by quantitatively comparing calvarial dimensions of fetuses with known craniosynostosis, to age-matched controls.

Methods:

The authors reviewed 22 prenatal ultrasounds of infants known to have nonsyndromic craniosynostosis and 22 age matched controls. Cross sectional images at the plane used to measure biparietal diameter (BPD) were selected, and cranial shape of each subject was parameterized with a radial spoke model. Cephalic indices were calculated from the cross-sectional ultrasound images for cases of sagittal synostosis and compared to age-matched controls without craniosynostosis. We used the radial parameterization to discriminate affected patients from controls. The results from quantitative shape analysis were compared to results from a blinded visual inspection of ultrasound images conducted by the two senior authors (SRS, HOT).

Results:

Among the 22 patients, the most common diagnosis was sagittal synostosis (11), followed by metopic synostosis (6). The average gestational age at time of ultrasound of both controls and synostotic patients was 26 weeks and 6.8 days, at the junction of the second and third trimesters. The controls and synostotic cases segregated into statistically different populations by their shape profiles (P<0.001). An automatic shape classifier using leave-one-out cross validation correctly classified the 44 images as normals vs. synostotic cases 85% of the time (sensitivity 82%, specificity 87%). Cephalic index was a poor indicator of sagittal synostosis (45% sensitivity). Visual inspection alone demonstrated only a fair level of accuracy (40-50% agreement) in identifying cases of synostosis (kappa 0.09-0.23).

Conclusions:

Cases of craniosynostosis can be identified on prenatal ultrasound with good sensitivity using formal shape analysis. Cephalic index and visual inspection alone performed poorly in identifying cases of craniosynostosis.

CLINICAL QUESTION/LEVEL OF EVIDENCE:

Diagnostic, II.
“How Low Should We Go? Safety and Craniometric Impact of the Low Occipital Osteotomy in Posterior Vault Remodeling”
Authors: Zapatero Zachary D. , Kosyk Mychajlo S. , Kalmar Christopher L. , Cheung Liana , Carlson Anna R. , Heuer Gregory G. , Bartlett Scott P. , Taylor Jesse A. , Lang Shih-Shan , Swanson Jordan W.
Published: August 2022

Background:

A larger volume cranial vault expansion is likely facilitated by a low posterior cranial osteotomy beneath the torcula; however, this may impart an increased risk of venous bleeding. This study compares the safety infra-torcular to supra-torcular osteotomy in patients undergoing posterior vault reconstruction (PVR) or posterior vault distraction osteogenesis (PVDO). We also analyzed volumetric changes.

Methods:

Patients undergoing initial PVR and PVDO between 2009-2021 at our institution were grouped by occipital osteotomy location, and retrospectively analyzed. Craniometric analysis was performed if patients had high-resolution CT scans available within 180 days pre-and post-operatively.

Results:

A total of 187 patients were included: 106 (57%) who underwent PVDO, and 81 (43%) PVR. Infra-torcular osteotomy was more common in PVR (n=65, 80%) than PVDO (n=61, 58%; p<0.002.). Blood transfused was similar between low and high osteotomy cohorts in PVDO (p=0.285) and PVR (p=0.342). However, median transfused blood volume per kilogram of patient weight was greater in the low- vs high-osteotomy PVDO (p=0.010) and PVR (p=0.041) cohorts. Intra-operative venous sinus injury was rare. In the PVDO cohort, there was increased median intracranial volumetric gain in the low (263 mL) compared to high-osteotomy cohort (127 mL; p=0.043); however, when controlled for distraction distance only a trend was observed (p=0.221). Patients undergoing PVDO showed a larger median intracranial volume increase (168 mL) compared to those undergoing PVR (73 mL; p<0.001).

Conclusion:

Infra-torcular osteotomy can be performed safely in most patients undergoing cranial vault remodeling, and does not appear associated with greater hemodynamic instability or sinus injury.
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.
Contrasting long-term dynamics of antimicrobial resistance and virulence plasmids in Salmonella Typhimurium from animals
Authors: Mellor Kate C. , Blackwell Grace A. , Cawthraw Shaun A. , Mensah Nana E. , Reid Stuart W. J. , Thomson Nicholas R. , Petrovska Liljana , Mather Alison E.
Published: August 2022

Plasmids are mobile elements that can carry genes encoding traits of clinical concern, including antimicrobial resistance (AMR) and virulence. Population-level studies of

Enterobacterales

, including Escherichia coli, Shigella and

Klebsiella

, indicate that plasmids are important drivers of lineage expansions and dissemination of AMR genes.

Salmonella

Typhimurium is the second most common cause of salmonellosis in humans and livestock in the UK and Europe. The long-term dynamics of plasmids between S. Typhimurium were investigated using isolates collected through national surveillance of animals in England and Wales over a 25-year period. The population structure of S. Typhimurium and its virulence plasmid (where present) were inferred through phylogenetic analyses using whole-genome sequence data for 496 isolates. Antimicrobial resistance genes and plasmid markers were detected in silico. Phenotypic plasmid characterization, using the Kado and Liu method, was used to confirm the number and size of plasmids. The differences in AMR and plasmids between clades were striking, with livestock clades more likely to carry one or more AMR plasmid and be multi-drug-resistant compared to clades associated with wildlife and companion animals. Multiple small non-AMR plasmids were distributed across clades. However, all hybrid AMR–virulence plasmids and most AMR plasmids were highly clade-associated and persisted over decades, with minimal evidence of horizontal transfer between clades. This contrasts with the role of plasmids in the short-term dissemination of AMR between diverse strains in other

Enterobacterales

in high-antimicrobial-use settings, with implications for predicting plasmid dissemination amongst S. Typhimurium.
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

A 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

We 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

Grignard 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.

Synopsis

Limited 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

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

During 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 STATEMENT

This 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

Objective

As 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).

Results

The 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

Enisamium (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

The 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.
Does regional tissue oxygenation vary in infants transported by road and air. A prospective observational within-subject analysis of regional oxygenation measured by near infrared spectroscopy in infants transported in Western Australia.
Authors: O'Dea Mary , Saito-Benz Maria , Tremblay Genevieve , Trawber Rory , Resnick Steven , Tan Jason , Davis Jonathan W
Published: August 2022

Objective
Infants in Western Australia who are unwell frequently require air retrieval for tertiary care. Travelling at altitude may worsen hypoxia.

Design, Setting and Patients
We examined tissue oxygenation using near infrared spectroscopy (NIRS) during retrieval by road and air. Study design was prospective and observational comparing cerebral/mesenteric oxygenation (crS02 and mS02) and fractional tissue extraction (cFTOE and mFTOE) in newborns transported by fixed-wing aircraft and road ambulance. Transport by fixed-wing aircraft was a combination of by road and by air. Transport by ambulance was by road only. Primary outcome measure was a within-subjects comparison of oxygenation and tissue oxygen extraction (flight vs. road transit). Measurements in those transported by road were made as control (first and third quarter of road transit).

Results
There were 24 infants transported by air and 31 by road. The median (interquartile range) gestations and weights were similar [39+1(31 to 41+3) vs. 40+1(35+3 to 43) wk; 3.3 (1.8 to 4.95) vs. 3.2 (2.2 to 4.2) Kg]. Most were treated for respiratory disease. There was no difference in SpO2, respiratory support or haemoglobin between groups. During transport by fixed-wing aircraft, infants had lower crS02 (75.3 (6.2) vs 77.9 (6.2); p=<0.0001) and mS02 (69.3 (16.6) vs. 74.2 (11.6); p=<0.01) and increased cFTOE (0.18 (0.07) vs. 0.21 (0.07), p<0.001) and mFTOE (0.22 (0.12) vs. 0.28 (0.17); P=0.006) than when travelling by road. There was no difference in the control group.

Conclusion
Newborn infants who travelled by air had lower cerebral saturations and greater oxygen tissue extraction when travelling by air. The pathogenesis and impact of these findings need further exploration.
“Look straight ahead” – A new test to diagnose spatial neglect by computed tomography
Authors: Marques Joel Coelho , Hanke Jens , Schell Caroline , Andres Frank , Karnath Hans-Otto
Published: August 2022

Spatial neglect is the dominant behavioral disorder after right hemisphere brain lesions. Reliable diagnosis by formal neuropsychological testing is often achieved only later during hospitalization, leading to delays in targeted therapies. We propose a way to diagnose spatial neglect right at admission. We measured the conjugated eye deviation (CED) on the initial computed tomography (CT) scans, in combination with the verbal instruction “Please look straight ahead” during the scan. The command was implemented in the scanner program and automatically played before a cranial CT started. This prospective study included a total 46 consecutive subjects (16 patients with first ever right brain damage and no spatial neglect, 12 patients with first ever right brain damage and spatial neglect, and 18 healthy controls). The right brain damaged groups were submitted to paper pencil tests to access the diagnosis of a spatial neglect after radiological confirmation of the brain damage during the initial phase of their hospitalisation. This procedure allowed us to define a cut-off value of 14.1 degrees of CED to the ipsilesional side to differentiate right hemispheric stroke patients with versus without spatial neglect with a confidence interval of 99%. This simple addition to a radiological routine procedure provides a new tool to help diagnose spatial neglect at the earliest stage possible and thus offers the possibility of providing patients with optimized rehabilitative therapy from a very early stage on.
Integration of biomarker polygenic risk score improves prediction of coronary heart disease in UK Biobank and FinnGen
Authors: Lin Jake , Mars Nina , Fu Yu , Ripatti Pietari , Kiiskinen Tuomo , FinnGen  , Tukiainen Taru , Ripatti Samuli , Pirinen Matti
Published: August 2022

Background

In addition to age and sex, also smoking history and levels of blood pressure, cholesterol, lipoproteins and inflammation are established biomarkers for coronary heart disease (CHD). As standard polygenic risk scores (PRS) have recently proven successful for CHD prediction, it remains of high interest to determine how a combined PRS of biomarkers (BioPRS) constructed from statistically relevant biomarkers can further improve genetic prediction of CHD.

Methods

We developed CHDBioPRS, which combines BioPRS with PRS of CHD, via regularized regression in UK Biobank (UKB) training data (n = 208,010). The resulting CHDBioPRS was tested on an independent UK Biobank subset (n = 25,765) and on the FinnGen study (n = 306,287).

Results

We observed a consistent pattern across all data sets where BioPRS was clearly predictive of CHD and improved standard PRS for CHD when the two were combined. In UKB test data, CHDPRS had a hazard ratio (HR) of 1.78 (95% confidence interval 1.67-1.91, area under the curve (AUC) 0.808) and CHDBioPRS had a HR of 1.88 (1.75-2.01, AUC 0.811) per one standard deviation of PRS. In FinnGen data, HR of CHDPRS was 1.57 (1.55-1.60, AUC 0.752) and HR of CHDBioPRS was 1.60 (1.58-1.62, AUC 0.755). We observed larger effects of CHDBioPRS in subsets of early onset cases with HR of 2.07 (1.85-2.32, AUC 0.790) in UKB test data and of 2.10 (2.04-2.16, AUC 0.791) in FinnGen. Results were similar when stratified by sex.

Conclusions

Integration of biomarker based BioPRS improved on the standard PRS for CHD and the gain was largest with early onset CHD cases. These findings highlight the benefit of enriching polygenic risk prediction of CHD with the genetics of associated biomarkers.
Helicobacter pylori vacuolating cytotoxin A exploits human endosomes for intracellular activation
Authors: Palframan Samuel L , Mahmud Md. Toslim , Tan Kher Shing , Grinter Rhys , Xin Vicky , Dunstan Rhys A , Micati Diana , Kerr Genevieve , McMurrick Paul J , Smith Andrew , Abud Helen , Nguyen Thanh Ngoc , Lazarou Michael , Kleifeld Oded , Lithgow Trevor , Cover Timothy L , Gabriel Kipros , Gorrell Rebecca J , Kwok Terry
Published: August 2022

Helicobacter pylori infection is the main cause of gastric cancer. Vacuolating cytotoxin A (VacA) is a H. pylori pore-forming toxin and a key determinant of gastric cancer risk. VacA is secreted as an 88-kDa polypeptide (p88) that upon interaction with host cells induces cytotoxic effects, including cell vacuolation and mitochondrial dysfunction. These effects are currently believed to be due to VacA p88 accumulating inside host cells and forming oligomeric anion-specific channels in membranes of intracellular compartments. However, the molecular nature of intracellular VacA channels in host cells remains undefined. Here we show that VacA p88 does not accumulate inside human epithelial cells, but instead is rapidly processed in endosomes into smaller p31/p28 and p37 products in a manner that precedes VacA-induced vacuolation. VacA processing requires endosomal acidification and concerted cleavage by multiple endo-lysosomal proteases including cathepsins. In situ structural mapping reveals that upon processing, the toxin’s central hydrophilic linker and globular C-terminus are excised, whereas oligomerization determinants are retained. Congruently, the processed products are constituents of a high-molecular-weight complex inside the host cell ─ which we propose is the intracellular, mature and active VacA pore. These findings suggest that VacA exploits human endosomes for proteolytic processing and intracellular activation.

Significance Statement

Helicobacter pylori is a cancer-causing bacterium that infects the stomach of billions of people worldwide. Vacuolating cytotoxin A (VacA) is an important H. pylori virulence factor and its activity directly correlates with gastric carcinogenesis. Yet despite decades of intense research, the mechanisms underlying VacA activity in human cells remain incompletely understood. Here, we present evidence suggesting that VacA is activated inside human cells by multi-step proteolytic processing involving endo-lysosomal proteases including cathepsins. We also track and identify the functional processed VacA isoforms in host cells. These results revolutionize our understanding of the mechanism of VacA activation in human cells, whilst expanding our knowledge of the diversity of microbial virulence factors that exploit human endo-lysosomes for pathogenesis.
Integrating carbon stocks and wildlife connectivity for nature-based climate solutions
Authors: O’Brien Paul , Gunn John S. , Clark Alison , Gleeson Jenny , Pither Richard , Bowman Jeff
Published: August 2022

Actions to protect against biodiversity loss and climate change will require a framework that addresses synergies between these interrelated issues. In this study we present methods for identifying areas important for the implementation of nature-based climate solutions and biodiversity conservation by intersecting high resolution spatial data for carbon storage and terrestrial connectivity. We explored the spatial congruence of carbon and connectivity in Ontario, Canada and examined effectiveness of current protected areas coverage. We found a weak positive relationship between carbon stocks and terrestrial connectivity; however, our maps revealed large hotspots, with high values of both indices, throughout the boreal forest and northern peatlands and smaller, isolated hotspots in the settled landscapes of the south. Location of hotspots varied depending on whether we considered forest or soil carbon. Further, our results show that current protected and conserved areas in Ontario only cover 13% of landscapes with the highest values for both carbon storage and connectivity. Protection or restoration of areas that maximize the co-benefits of carbon storage and connectivity would make significant contributions towards ambitious national targets to reduce greenhouse gas emissions and conserve biodiversity.
CIPK-B is essential for salt stress signalling in Marchantia polymorpha
Authors: Tansley Connor , Houghton James , Rose Althea M. E. , Witek Bartosz , Payet Rocky D. , Wu Taoyang , Miller J. Benjamin
Published: August 2022

Calcium signalling is central to many plant processes, with families of calcium decoder proteins having expanded across the green lineage and redundancy existing between decoders. The liverwort Marchantia polymorpha has fast become a new model plant, but it is unclear what calcium decoders exist in this species.

We have performed phylogenetic analyses to identify the Calcineurin B-Like (CBL) and CBL-Interacting Protein Kinase (CIPK) network of M. polymorpha. We analysed CBL-CIPK expression during salt stress, and determined protein-protein interactions using yeast two-hybrid and bimolecular fluorescence complementation. We also created genetic knockouts using CRISPR/Cas9.

We confirm that M. polymorpha has two CIPKs and three CBLs. Both CIPKs and only one CBL show salt-responsive transcriptional changes. All M. polymorpha CBL-CIPKs interact with each other in planta. Knocking out CIPK-B causes increased sensitivity to salt suggesting that this CIPK is involved in salt signalling.

We have identified CBL-CIPKs that form part of a salt tolerance pathway in M. polymorpha. Phylogeny and interaction studies imply that these CBL-CIPKs form an evolutionarily conserved Salt Overly Sensitive (SOS) pathway. Hence, salt responses may be some of the early functions of CBL-CIPK networks and increased abiotic stress tolerance required for land plant emergence.
Structural and functional insights into the type III-E CRISPR-Cas immunity
Authors: Liu Xi , Zhang Laixing , Wang Hao , Xiu Yu , Huang Ling , Gao Zhengyu , Li Ningning , Li Feixue , Xiong Weijia , Gao Teng , Zhang Yi , Yang Maojun , Feng Yue
Published: August 2022

The type III-E CRISPR-Cas system comprises a Cas effector (gRAMP), a TPR-CHAT and several ancillary proteins. However, both the structural features of gRAMP and the immunity mechanism remain unknown for this system. Here, we report a series of structures of gRAMP-crRNA, either its alone or in complex with target RNA or TPR-CHAT (called Craspase), and Craspase complexed with cognate (CTR) or non-cognate target RNA (NTR). Importantly, the 3’ anti-tag region of NTR and CTR bind at two distinct channels in the Craspase, and CTR with a non-complementary 3’ anti-tag induces a marked conformational change of the TPR-CHAT, which allosterically activates its protease activity to cleave an ancillary protein Csx30. This cleavage then triggers an abortive infection as the antiviral strategy of the type III-E system. Together, our study provides crucial insights into both the catalytic mechanism of the gRAMP and the immunity mechanism of the type III-E CRISPR-Cas system.
Characterizing control of memory CD8 T cell differentiation by BTB-ZF transcription factor Zbtb20
Authors: Preiss Nicholas K. , Kamal Yasmin , Williams Owen M. , Li Chenyang , Kolling Fred W. , Trask Heidi W. , Usherwood Young-Kwang , Cheng Chao , Frost Hildreth R. , Usherwood Edward J.
Published: August 2022

Members of the BTB-ZF transcription factor family regulate the immune system. Our lab identified that family member Zbtb20 contributes to the differentiation, recall responses and metabolism of CD8 T cells. Here, we report a characterization of the transcriptional and epigenetic signatures controlled by Zbtb20 at single-cell resolution during the effector and memory phases of the CD8 T cell response. Without Zbtb20, transcriptional programs associated with memory CD8 T cell formation were upregulated throughout the CD8 T response. A signature of open chromatin was associated with genes controlling T cell activation, consistent with the known impact on differentiation. Additionally, memory CD8 T cells lacking Zbtb20 were characterized by open chromatin regions with overrepresentation of AP-1 transcription factor motifs and elevated RNA- and protein-level expression of the corresponding AP-1 components. Finally, we describe motifs and genomic annotations from the DNA targets of Zbtb20 in CD8 T cells identified by CUT&RUN. Together, these data establish the transcriptional and epigenetic networks contributing to the control of CD8 T cell responses by Zbtb20.
resevol: an R package for spatially explicit models of pesticide resistance given evolving pest genomes
Authors: Duthie A. Bradley , Mangan Rosie , McKeon C. Rose , Tinsley Matthew C. , Bussière Luc F.
Published: August 2022

The evolution of pesticide resistance is a widespread problem with potentially severe consequences for global food security. We introduce the resevol R package, which simulates individual-based models of pests with evolving genomes that produce complex, polygenic, and covarying traits affecting pest life history and pesticide resistance. Simulations are modelled on a spatially-explicit and highly customisable landscape in which crop and pesticide application and rotation can vary, making the package a highly flexible tool for both general and tactical models of pest management and resistance evolution. We present the key features of the resevol package and demonstrate its use for a simple example simulating pests with two covarying traits. The resevol R package is open source under GNU Public License. All source code and documentation are available on GitHub.
Fast4DReg: Fast registration of 4D microscopy datasets
Authors: Pylvänäinen Joanna W , Laine Romain F , Saraiva Bruno M.S. , Ghimire Sujan , Follain Gautier , Henriques Ricardo , Jacquemet Guillaume
Published: August 2022

Unwanted sample drift is a common issue that plagues microscopy experiments, preventing accurate temporal quantification of biological processes. While multiple methods and tools exist to correct images post-acquisition, performing drift correction of large 3D videos using open-source solutions remains challenging and time-consuming. Here we present a new tool developed for ImageJ/Fiji called Fast4DReg that can quickly correct axial and lateral drift in 3D video microscopy datasets. Fast4DReg works by creating intensity projections along multiple axes and estimating the drift between frames using 2D cross-correlations. Using synthetic and acquired datasets, we demonstrate that Fast4DReg performs better than other state-of-the-art open-source drift correction tools and significantly outperforms them in speed (5x to 60x). We also demonstrate that Fast4DReg can be used to register misaligned channels in 3D using either calibration slides or misaligned images directly. Altogether Fast4DReg provides a quick and easy-to-use method to correct 3D imaging data before further visualization and analysis. Fast4DReg is available onGitHub.
Focal exocytosis of Syntaxin 3 and TRPML1 at pseudopodia of nascent phagosomes
Authors: Dabral Deepti , van Bogaart Geert
Published: August 2022

Macrophages clear invading pathogens by phagocytosis. Phagocytosis is a complex mechanism involving the local expansion of the membrane, cytoskeletal remodeling, and the delivery of phagosomal proteins to the nascent phagosomes. However, the organelle trafficking events underlying this are largely unclear. Here, we show in human blood monocyte-derived macrophages that TRPML1, a calcium channel involved in the phagocytic process, is delivered to phagosomes in Syntaxin 3-positive vesicles. Syntaxin 3 is a SNARE protein previously shown to mediate the secretion of IL-6 by macrophages. Total Internal Reflection Microscopy (TIRF) revealed that Syntaxin 3 positive compartments carry TRPML1 to pseudopodia for focal exocytosis at the nascent phagosomes during E. coli uptake. Using siRNA knockdown, we show that both Syntaxin 3 and TRPML1 are required for E. coli uptake. Moreover, using TRPML1 agonists we show that increased TRPML1 activity leads to increased E. coli uptake, whereas calcium chelation decreased intracellular E. coli load. Understanding the membrane trafficking pathways is critical for understanding how macrophages clear invading pathogens.

Key findings

Syntaxin 3 positive vesicles are delivered at the plasma membrane site of phagocytosis.

Syntaxin 3-positive vesicles carry TRPML1 to pseudopodia.

Bacterial phagocytosis correlates with Syntaxin 3 and TRPML1 expression levels.

Bacterial phagocytosis depends on calcium flux through TRPML1.

Syntaxin-3 vesicles carry the cytokine interleukin-6.