bluuebunny/crossref_metadata_2025_split huggingface dataset:
Multiplex PCR: Aid to more-timely and directed therapeutic intervention for patients with infectious gastroenteritis
Authors: Montasser Karim , Osman Heba Ahmed , Abozaid Hanan , Khalil Haidy S. , Hatem Amer Wesam , Sabry Abeer M. M. 
Published: October 2022

Background:
Multiplex PCR is a sensitive and rapid method compared with conventional methods. Therefore, we use multiplex PCR for the rapid detection of the four major intestinal pathogens causing gastroenteritis (Shigella spp., Campylobacter spp., Aeromonas spp. and Enterohemorrhagic Escherichia coli [EHEC]) in stool specimens.

Materials and methods:
A prospective randomized study using 200 stool samples obtained from patients presented with acute gastroenteritis during the study period (between February 2019 and December 2021). Bacteria in stool samples were identified using conventional culture methods and multiplex PCR for stool samples

Results:
The identified organisms using conventional cultures; were Shigella (27%), Aeromonas species (10%) and EHEC (O157) (8%). Using multiplex PCR. Shigella spp. was the most commonly identified pathogen (detected in 40.5% of positive samples), followed by Aeromonas spp. (30%), EHEC (20%) and Campylobacter species was only detected in (1%) of positive samples. The diagnostic evaluation of multiplex PCR in relation to conventional method in diagnosis of Shigella, EHEC and Aeromonas showed, sensitivity of 100% (for each), specificity of 88.5%, 92.4%, 77.8% respectively. However, the diagnostic evaluation of multiplex PCR in relation to conventional method in diagnosis of Campylobacter showed specificity of 99% and NPV of 100%.

Conclusions:
Multiplex PCR is an accurate and rapid method for detection of common intestinal pathogens causing severe gastroenteritis. a rapid method that could be used in outbreaks for diagnosis of the common enteric pathogens causing fatal gastroenteritis.
Graves’ hyperthyroidism induced pancytopenia, epilepsia and muscle weakness: A case report
Authors: Fu Bao , He Dinghong , Geng Zhengguang , Fu Xiaoyun 
Published: October 2022

Rationale:
Pancytopenia and epilepsia are rare complications of Graves’ disease (GD). Muscle weakness is a physical sign of GD. It is extremely rare for GD patients to present 3 symptoms at the same time.

Patient concerns:
A 35-year-old female was admitted to hospital for dizziness for 1 day. The results of laboratory examination on admission showed pancytopenia and hypothyroidism. Her clinical manifestations include pancytopenia, epilepsy, and muscle weakness.

Diagnosis:
Graves’ hyperthyroidism.

Interventions:
She received endotracheal intubation, ventilator, antithyroid drugs, and hormone therapy.

Outcome:
The patient was discharged after treatment.

Lesson:
Severe complications caused by GD are rare and require antithyroid therapy. Although glucocorticoid is not recommended by the guidelines, it can effectively improve thrombocytopenia.
Silent progressive bilateral papillitis after COVID-19 vaccination: A case report
Authors: Lee Geun Woo , Park Hyeong Seok , Lee Donghun 
Published: October 2022

Rationale:
We report the case of a patient who developed asymptomatic bilateral papillitis after coronavirus disease 2019 (COVID-19) vaccination.

Patient concerns:
A 61-year-old man presented to our tertiary clinic with bilateral optic disc edema, which was incidentally detected during his visit to a primary ophthalmology clinic. He had received an adenovirus-vectored COVID-19 vaccine 2 weeks before the optic disc edema was detected and had experienced no ocular discomfort, except for a floater in his right eye. Although his visual acuity was normal and he had no color vision deficiencies or marked visual field defects, the optic disc edema worsened over several days. Orbital magnetic resonance imaging showed no optic tract enhancement, and lumbar puncture revealed normal cerebrospinal fluid pressure. The patient tested negative for aquaporin-4 and myelin oligodendrocyte glycoprotein antibodies and Leber hereditary optic neuropathy-associated gene mutations.

Diagnosis:
The patient was diagnosed with bilateral papillitis, possibly induced by the COVID-19 vaccination.

Interventions:
The patient received steroid pulse therapy with methylprednisolone (500 mg/day) for 3 days followed by an oral prednisolone taper for 3 weeks.

Outcomes:
The patient’s papillitis started to subside 3 weeks after he received systemic steroid therapy and completely resolved without any sequelae 2 months later. A year after the diagnosis, the fundus remained stable without disease recurrence or optic disc atrophy.

Lessons:
Healthy individuals receiving COVID-19 vaccines may present with various manifestations of optic neuritis. In the present case, the patient presented with asymptomatic progressive bilateral optic disc edema and had a favorable long-term course after receiving steroid therapy.
Prescription of Steroids in General Pediatric Intensive Care Patients—A Two-Center Retrospective Observational Study
Authors: Mitting Rebecca , Fitchett Elizabeth J. A. , Peters Mark J. , Ray Samiran 
Published: October 2022

OBJECTIVES:
Designing randomized trials to determine utility, dose, and timing of steroid administration in the management of critically unwell children may be difficult owing to a high proportion of patients who receive steroid as part of current care. We aimed to describe steroid use among all patients on two general PICUs.

DESIGN:
Retrospective observational study using a multilevel logistic regression model.

SETTING:
Two tertiary, general mixed medical and surgical PICUs.

PATIENTS:
All admissions between 2016 and 2019. All parenteral or enteral steroid prescriptions were identified, and steroid type, frequency, timing, and peak daily doses were recorded. The outcome measure was mortality prior to PICU discharge.

INTERVENTIONS:
None.

MEASUREMENTS AND MAIN RESULTS:
There were 5,483 admissions during the study period, and 1,804 (33%) of these involved prescription of at least one steroid. Among patients prescribed steroids, the median peak daily dose when steroids were prescribed was 2.4 mg/kg/d prednisolone equivalent (interquartile range, 1.6–3.6), and the median time to peak steroid doses was 2 days (1–5 d). Administration of steroid was associated with increased risk-adjusted mortality odds ratio (OR) of 1.37 (95% CI, 1.04–1.79). Steroids were prescribed in 42.3% of admissions, in which the child did not survive to PICU discharge. Among children who were prescribed steroids, use of hydrocortisone (OR, 6.75; 95% CI, 3.79–12.27) and methylprednisolone (OR, 7.85; 95% CI, 4.21–14.56), or starting steroids later than 2 days after PICU admission were associated with an increased mortality (OR, 1.93; 95% CI, 1.15–3.25).

CONCLUSIONS:
Steroids are widely used in pediatric critical illness and nonsurvival associated with increased frequency of use. This association appears to be related to steroid class and timing of dose, both likely to reflect indication for steroid prescription. Prospective trials are required to estimate these complex risks and benefits, and study design will need to consider these patterns.
Sporadic Cerebellar Hemangioblastoma With Strong SSTR Expression on 68Ga-DOTANOC PET/CT
Authors: Dev Indraja D. , Rangarajan Venkatesh , Puranik Ameya D. , Agrawal Archi , Shah Sneha , Sahay Ayushi , Purandare Nilendu C. 
Published: October 2022

Abstract
Sporadic cerebellar hemangioblastomas are rare with majority of these tumors presenting as a part of von Hippel–Lindau syndrome. We demonstrate an unusual case of a symptomatic sporadic cerebellar hemangioblastoma mimicking a meningioma on MRI and 68Ga-DOTANOC PET imaging.
The Role of Dynamic DNA Methylation in Liver Transplant Rejection in Children
Authors: Ningappa Mylarappa , Shao Xiaojian , Ashokkumar Chethan , Xu Qingyong , Zeevi Adriana , Grundberg Elin , Pastinen Tomi , Sindhi Rakesh 
Published: October 2022

Background.
Transcriptional regulation of liver transplant (LT) rejection may reveal novel predictive and therapeutic targets. The purpose of this article is to test the role of differential DNA methylation in children with biopsy-proven acute cellular rejection after LT.

Methods.
Paired peripheral blood DNA samples were obtained before and after LT from 17 children, including 4 rejectors (Rs) and 13 nonrejectors (NRs), and assayed with MethylC capture sequencing approach covering 5 million CpGs in immune-cell–specific regulatory elements. Differentially methylated CpGs (DMCs) were identified using generalized linear regression models adjusting for sex and age and merged into differentially methylated regions (DMRs) comprising 3 or more DMCs.

Results.
Contrasting Rs versus NRs, we identified 2238 DMCs in post-LT and 2620 DMCs in pre-LT samples, which clustered in 216 and 282 DMRs, respectively. DMCs associated with R were enriched in enhancers and depleted in promoters. Among DMRs, the proportion of hypomethylated DMRs increased from 61/282 (22%) in pre-LT to 103/216 (48%, P < 0.0001) in post-LT samples. The highest-ranked biological processes enriched in post-LT DMCs were antigen processing and presentation via major histocompatibility complex (MHC) class I, MHC class I complex, and peptide binding (P < 7.92 × 10−17), respectively. Top-ranked DMRs mapped to genes that mediate B-cell receptor signaling (ADAP1) or regulate several immune cells (ARRB2) (P < 3.75 × 10−08). DMRs in MHC class I genes were enriched for single nucleotide polymorphisms (SNPs), which bind transcription factors, affect gene expression and splicing, or alter peptide-binding amino acid sequences.

Conclusions.
Dynamic methylation in distal regulatory regions reveals known transplant-relevant MHC-dependent rejection pathways and identifies novel loci for future mechanistic evaluations in pediatric transplant subcohorts.
The big six: key principles for effective use of Behavior substitution in interventions to de-implement low-value care
Authors: Patey Andrea M. , Grimshaw Jeremy M. , Francis Jill J. 
Published: October 2022

ABSTRACT
Healthcare professionals provide care to help patients; however, sometimes that care is of low value – at best ineffective and at worst harmful. To address this, recent frameworks provide guidance for developing and investigating de-implementation interventions; yet little attention has been devoted to identifying what strategies are most effective for de-implementation. In this paper, we discuss Behavior substitution, a strategy whereby an unwanted behavior is replaced with a wanted behavior, thereby making it hypothetically easier to reduce or stop the unwanted behavior. We discuss why Behavior substitution may be a useful de-implementation strategy, and why it may not be suitable for all circumstances. On the basis of the body of knowledge in behavioral science, we propose a list of principles to consider when selecting a substitute behavior for a de-implementation intervention. Applying these principles should increase the likelihood that this technique will be effective in reducing low-value care.
Improving HIV Pre Exposure Prophylaxis (PrEP) uptake and initiation: process evaluation and recommendation development from a national PrEP programme
Authors: Estcourt Claudia S , MacDonald Jen , Saunders John , Nandwani Rak , Young Ingrid , Frankis Jamie , Clutterbuck Dan , Steedman Nicola , McDaid Lisa , Dalrymple Jenny , Flowers Paul 
Published: October 2022

AbstractBackgroundHIV pre-exposure prophylaxis (PrEP) is key to HIV transmission elimination but implementation is challenging and under-researched. We undertook a process evaluation of the first two years of a national PrEP programme to explore barriers and facilitators to implementation and to develop recommendations to improve implementation, focussing on PrEP uptake and initiation.MethodsStage 1 involved semi-structured telephone interviews and focus groups (09/2018-07/2019) with geographically and demographically diverse patients seeking/using/declining/stopping PrEP (n=39), sexual healthcare professionals (n= 54), community-based organisation service users (n=9) and staff (n=15) across Scotland. We used deductive thematic analysis, to derive and then map key barriers and facilitators to priority areas that experts agreed would enhance initiation and uptake. In Stage 2 we used analytic tools from implementation science to systematically generate evidence-based, theoretically-informed recommendations to enhance uptake and initiation of PrEP.ResultsBarriers and facilitators were multi-levelled and interdependent. Barriers included the rapid pace of implementation without additional resource, and a lack of familiarity with PrEP prescribing. Facilitators included opportunities for acquisition of practice-based knowledge and normalisation of initiation activities. We refined our 68 “long-list” recommendations to 41 using expert input and the APEASE criteria. Examples include: provision of PrEP in diverse settings to reach all in need; co-produced, culturally sensitive training resources for healthcare professionals, with focused content on non-daily dosing; meaningful collaborative working across all stakeholders.ConclusionsThese evidence-based, theory informed recommendations provide a robust framework for optimising PrEP uptake and initiation in diverse settings to ensure PrEP reaches all who may benefit.Summary for table of contentsZero new HIV infections could become a reality if HIV pre-exposure prophylaxis (PrEP) programmes are successfully implemented but the World Health Organisation recognizes that large scale roll out is challenging.We used implementation science research tools in novel ways to evaluate one of the world’s first national PrEP programmes, to develop evidence-based recommendations for use across a range of settings to improve PrEP uptake and initiation.Adopting these recommendations could enable governments and societies to better address HIV prevention goals.
Understanding mental health trends during COVID-19 pandemic in the United States using network analysis
Authors: Kobayashi Hiroko , Saenz-Escarcega Raul , Fulk Alexander , Agusto Folashade B. 
Published: October 2022

AbstractThe emergence of COVID-19 in the United States resulted in a series of federal and state-level lock-downs and COVID-19 related health mandates to manage the spread of the virus. These policies may negatively impact the mental health state of the population. This study focused on the trends in mental health indicators following the COVID-19 pandemic amongst four United States geographical regions, and political party preferences. Indicators of interest included feeling anxious, feeling depressed, and worried about finances. Survey data from Delphi Group in Carnegie Mellon University were analyzed using clustering algorithms and dynamic connectome obtained from sliding window analysis. United States maps were generated to observe spatial trends and identify communities with similar mental health and COVID-19 trends. Between March 3rd, 2021 and January 10th, 2022, states in the south geographic region showed similar trends for reported values of feeling anxious and worried about finances. There were no identifiable communities resembling geographical regions or political party affiliation for the feeling depressed indicator. We observed a high degree of correlation among southern states as well as within republican states, where the highest correlation values from the dynamic connectome analysis for feeling anxious and feeling depressed variables seemingly overlapped with an increase in COVID-19 related cases, deaths, hospitalizations, and rapid spread of the COVID-19 Delta variant.
A neural mechanism underlying predictive visual motion processing in patients with schizophrenia
Authors: Scheliga Sebastian , Schwank Rosalie , Scholle Ruben , Habel Ute , Kellermann Thilo 
Published: October 2022

AbstractPsychotic symptoms may be traced back to sensory sensitivity. Thereby, visual motion (VM) processing particularly has been suggested to be impaired in schizophrenia (SCZ). In healthy brains, VM underlies predictive processing within hierarchically structured systems. However, less is known about predictive VM processing in SCZ. Therefore, we performed fMRI during a VM paradigm with three conditions of varying predictability, i.e., predictable-, random-, and arbitrary motion. The study sample comprised 17 SCZ patients and 23 healthy controls. We calculated general linear model (GLM) analysis to assess group differences in VM processing across motion conditions. Here, we identified significantly lower activity in right temporoparietal junction (TPJ) for SCZ patients. Therefore, right TPJ was set as seed for connectivity analyses. For patients, across conditions we identified increased connections to higher regions, namely medial prefrontal cortex, or paracingulate gyrus. Healthy subjects activated sensory regions as area V5, or superior parietal lobule. Since TPJ operates as hub modulating network shifts, aberrant functional connectivity with higher structures may thus reflect a compensatory mechanism co-occurring to impaired TPJ activity in SCZ. In sum, these altered neural patterns provide a framework for future studies focusing on predictive VM processing to identify potential biomarkers of psychosis.
Effect of behavioral conditions on silk characteristics in the Indian meal moth (Plodia interpunctella)
Authors: Barve Toshita V. , Godfrey R. Keating , Storer Caroline G. , Kawahara Akito Y. 
Published: October 2022

ABSTRACTLepidopteran silks are produced during the larval stage and are used for mobility and protection from predators, parasitoids, and pathogens. Our knowledge of silk structure and production in Lepidoptera is based largely on the biology of the domestic silk moth (Bombyx mori), but recent comparative evidence suggests that silk production and structure vary widely across moth taxa. Some species like the Indian meal moth (Plodia interpunctella) are becoming important biological models to study silk for its potential application to materials science and medicine, but many aspects of silk production in this species remain unknown. Here we characterize the silk ofP. interpunctellaby measuring the width of wandering and pupal silk strands and find that pupal silk is significantly thicker than the latter. We then report individual variation in pupal silk production in our lab-reared colony with a very small number of individuals forgoing pupal silk (< 4%) and find that overcrowding had no effect on this, whereas exposure to elevated temperatures reduced rates of pupal silk production.
Data Descriptor: Human whole exome genotype data for Alzheimer’s Disease
Authors: Leung Yuk Yee , Naj Adam C , Chou Yi-Fan , Valladares Otto , Wheeler Nicholas , Lin Honghuang , Gangadharan Prabhakaran , Qu Liming , Clark Kaylyn , Cantwell Laura , Issen Heather ,   the Alzheimer’s Disease Sequencing Project, Seshadri Sudha , Brkanac Zoran , Cruchaga Carlos , Pericak-Vance Margaret , Mayeux Richard P. , Kuzma Amanda B , Lee Wan-Ping , Bush William S. , Destefano Anita , Martin Eden , Schellenberg Gerard D. , Wang Li-San 
Published: October 2022

AbstractBigger sample size can help to identify new genetic variants contributing to an increased risk of developing Alzheimer’s disease. However, the heterogeneity of the whole-exome sequencing (WES) data generation methods presents a challenge to a joint analysis. Here we present a bioinformatics strategy for joint calling 20,504 WES samples collected across nine studies and sequenced using ten different capture kits in fourteen sequencing centers in the Alzheimer’s Disease Sequencing Project. gVCFs of samples were joint-called by the Genome Center for Alzheimer’s Disease into a single VCF, containing only positions within the union of capture kits. The VCF was then processed using specific strategies to account for the batch effects arising from the use of different capture kits from different studies.We identified 8.2 million autosomal variants. 96.82% of the variants are high-quality, and are located in 28,579 Ensembl transcripts. 41% of the variants are intronic and 15% are missense variants. 1.8% of the variants are with CADD>30.Our new strategy for processing these diversely generated WES samples has shown to generate high-quality data. The improved ability to combine data sequenced in different batches benefits the whole genomics research community. The WES data are accessible to the scientific community viahttps://dss.niagads.org/.
Fully Automated Point Spread Function Analysis Using Pycalibrate
Authors: Metz J , Gintoli M , Corbett AD 
Published: October 2022

AbstractReproducibility is severely limited if instrument performance is assumed rather than measured. Within optical microscopy, instrument performance is typically measured using sub-resolution fluorescent beads. However, the process is performed infrequently as it is requires time and suitably trained staff to acquire and then process the bead images. Analysis software still requires the manual entry of imaging parameters. Human error from repeatedly typing these parameters can significantly affect the outcome of the analysis, rendering the results less reproducibile. To avoid this issue, PyCalibrate has been developed to fully automate the analysis of bead images. PyCalibrate can be accessed either by executing the Python code locally or via a user-friendly web portal to further improve accessibility when moving between locations and machines. PyCalibrate interfaces with the BioFormats library to make it compatible with a wide range of proprietary image formats. In this study, PyCalibrate analysis performance is directly compared with alternative free-access analysis software PSFj, MetroloJ QC and DayBook3 and is demonstrated to have equivalent performance but without the need for user supervision.
Immune-modulatory effects of low dose γ-radiation on wax moth (Galleria mellonella) larvae
Authors: Copplestone David , Coates Christopher J , Lim Jenson 
Published: October 2022

ABSTRACTLarvae of the greater wax mothGalleria mellonellaare common pests of beehives and commercial apiaries, and in more applied settings, these insects act as alternativein vivobioassays to rodents for studying microbial virulence, antibiotic development, and toxicology. In the current study, our overall aim was to assess the putative adverse effects of background gamma radiation levels onG. mellonella. To achieve this, we exposed larvae to low (0.014 mGy/h), medium (0.056 mGy/h), and high (1.33 mGy/h) doses of caesium-137 and measured larval pupation events, weight, faecal discharge, susceptibility to bacterial and fungal challenges, immune cell counts, activity, and viability (i.e., haemocyte encapsulation) and melanisation levels. The effects of low and medium levels of radiation were distinguishable from the highest dose rates used – the latter insects weighed the least and pupated earlier. In general, radiation exposure modulated cellular and humoral immunity over time, with larvae showing heighted encapsulation/melanisation levels at the higher dose rates but were more susceptible to bacterial (Photorhabdus luminescens) infection. There were few signs of radiation impacts after 7 days exposure, whereas marked changes were recorded between 14 and 28 days. Our data suggest thatG. mellonellademonstrates plasticity at the whole organism and cellular levels when irradiated and offers insight into how such animals may cope in radiologically contaminated environments.