bluuebunny/crossref_metadata_2025_split huggingface dataset:
The status of Streptococcus pneumoniae in Iran compared to the world: a systematic review
Authors: Asadollahi Parisa , Darbandi Atieh , Lohrasbi Vahid , Hasannejad-Bibalan Meysam , Talebi Malihe 
Published: September 2021

Introduction:

Streptococcus pneumoniae is a leading cause of vaccine-preventable deaths worldwide. Sero-epidemiological data on S. pneumoniae is needed in each country to monitor the burden of this important pathogen in each population. The aim of this study was to evaluate the prevalence, antibiotic resistance, prevalent serotypes and virulence factors of S. pneumoniae in Iran, compared to other parts of the world.

Methods:
A search via Google Scholar, Scopus, PubMed, ISI, Iranmedex, Magiran, SID and ISC was conducted for original articles investigating S. pneumoniae in Iran. The search terms were ‘Streptococcus pneumoniae’, ‘S. pneumoniae’, ‘prevalence’, ‘antibiotic resistance’, ‘antimicrobial resistance’, ‘typing’, ‘serotyping’, ‘virulence factors’, ‘Iran’.

Results:
The overall prevalence of invasive pneumococcal disease had an increasing trend in Iran. The most common serotypes amongst Iranian population were 1, 19A, 6A/ 6B, 23F, 14,18C, 20, 19, 3, 6, 9 V, 11A and 19F. Resistance to penicillin and co-trimoxazole had significant decreasing trends whilst resistance to erythromycin was increasing although insignificantly. The most prevalent pneumococcal virulence genes were lytA and pspC.

Conclusion:
Since pneumococcal serotypes differ in invasiveness, virulence, and antibiotic resistance it is important to closely monitor the changes on evolving serotypes, antibiotic resistance and virulence factors of this pathogen to be able to implement suitable prevention and therapeutic strategies.
Many but small HIV-1 non-B transmission chains in the Netherlands
Authors: Bezemer Daniela , Blenkinsop Alexandra , Hall Matthew , van Sighem Ard , Cornelissen Marion , Wessels Els , van Kampen Jeroen , van de Laar Thijs , Reiss Peter , Fraser Christophe , Ratmann Oliver 
Published: September 2021

Objective:
The aim of this study was to investigate introductions and spread of different HIV-1 subtypes in the Netherlands.

Design:
We identified distinct HIV-1 transmission chains in the Netherlands within the global epidemic context through viral phylogenetic analysis of partial HIV-1 polymerase sequences from individuals enrolled in the ATHENA national HIV cohort of all persons in care since 1996, and publicly available international background sequences.

Methods:
Viral lineages circulating in the Netherlands were identified through maximum parsimony phylogeographic analysis. The proportion of HIV-1 infections acquired in-country among heterosexuals and MSM was estimated from phylogenetically observed, national transmission chains using a branching process model that accounts for incomplete sampling.

Results:
As of 1 January 2019, 2589 (24%) of 10 971 (41%) HIV-1 sequenced individuals in ATHENA had non-B subtypes (A1, C, D, F, G) or circulating recombinant forms (CRF01AE, CRF02AG, CRF06-cpx). The 1588 heterosexuals were in 1224, and 536 MSM in 270 phylogenetically observed transmission chains. After adjustments for incomplete sampling, most heterosexual (75%) and MSM (76%) transmission chains were estimated to include only the individual introducing the virus (size = 1). Onward transmission occurred mostly in chains size 2–5 amongst heterosexuals (62%) and in chains size at least 10 amongst MSM (64%). Considering some chains originated in-country from other risk-groups, 40% (95% confidence interval: 36–44) of non-B-infected heterosexuals and 62% (95% confidence interval: 49–73) of MSM-acquired infection in-country.

Conclusion:
Although most HIV-1 non-B introductions showed no or very little onward transmission, a considerable proportion of non-B infections amongst both heterosexuals and MSM in the Netherlands have been acquired in-country.
TMS Bursts Can Modulate Local and Networks Oscillations During Lower-Limb Movement
Authors: Espinoza Arturo I. , Scholl Jamie L. , Singh Arun 
Published: September 2021

Purpose:
Lower-limb motor functions involve processing information via both motor and cognitive control networks. Measuring oscillations is a key element in communication within and between cortical networks during high-order motor functions. Increased midfrontal theta oscillations are related to improved lower-limb motor performances in patients with movement disorders. Noninvasive neuromodulation approaches have not been explored extensively to understand the oscillatory mechanism of lower-limb motor functions. This study aims to examine the effects of repetitive transcranial magnetic stimulation on local and network EEG oscillations in healthy elderly subjects.

Methods:
Eleven healthy elderly subjects (67–73 years) were recruited via advertisements, and they underwent both active and sham stimulation procedures in a random, counterbalanced design. Transcranial magnetic stimulation bursts (θ-transcranial magnetic stimulation; 4 pulses/second) were applied over the midfrontal lead (vertex) before a GO-Cue pedaling task, and signals were analyzed using time–frequency methods.

Results:
Transcranial magnetic stimulation bursts increase the theta activity in the local (p = 0.02) and the associated network during the lower-limb pedaling task (p = 0.02). Furthermore, after task-related transcranial magnetic stimulation burst sessions, increased resting-state alpha activity was observed in the midfrontal region (p = 0.01).

Conclusions:
This study suggests the ability of midfrontal transcranial magnetic stimulation bursts to directly modulate local and network oscillations in a frequency manner during lower-limb motor task. Transcranial magnetic stimulation burst–induced modulation may provide insights into the functional roles of oscillatory activity during lower-limb movement in normal and disease conditions.
Readmissions in Patients with Cerebral Cavernous Malformations (CCMs): A National Readmission Database (NRD) Study
Authors: Padarti Akhil , Amritphale Amod , Eliyas Javed Khader , Rigamonti Daniele , Zhang Jun 
Published: September 2021

AbstractBACKGROUNDCerebral cavernous malformations (CCMs) are microvascular CNS lesions prone to hemorrhage leading to neurological sequela such as stroke and seizure. A subset of CCM patients have aggressive disease leading to multiple bleeding events, likely resulting multiple hospitalizations. Hospital admission rates are an important metric that has direct financial impact on hospitals and an indicator of overall disease burden. Furthermore, analysis of hospital readmissions can lead to early identification of high-risk patients and provides insight into the pathogenesis of CCM lesions. The purpose of this study is to identify high risk CCM patients with increased all cause readmission and comorbidities associated with increased readmissions.METHODSAll US hospital admissions due to CCMs were searched using the 2017 National Readmission Database (NRD). Patients with readmissions within 30 days of discharge from index hospitalization were identified and analyzed, relative to the remaining population.RESULTSAmong all patients hospitalized for CCM, 14.9% (13.7-16.2%) required all cause readmission within 30 days. Multivariate logistical regression analysis showed that substance abuse (p=0.003), diabetes (p=0.018), gastrointestinal bleed (p=0.002), renal failure (p=0.027), and coronary artery disease (p=0.010) were predictive of all cause readmissions, while age group 65-74 (p=0.042), private insurance (p<0.001), and treatment at a metropolitan teaching institution (p=0.039) were protective. Approximately half of all readmissions are caused by neurological (33.9%) and infectious (14.6%) etiologies. The 30-day lesion bleeding rate after index hospitalization is 0.8% (0.5-1.2%).CONCLUSIONSAll identified comorbidities associated with increased risks of readmission contribute to vascular stress, suggesting its role in lesion pathogenesis. This is the first and only study to analyze readmission metrics for CCMs in order to identify high risk patient factors to date.
Cardiovascular Risk Factors and Outcomes in COVID-19: Hospital-Based Prospective Study in India
Authors: Sharma Arvind , Baig Vaseem Naheed , Sharma Sonali , Dalela Gaurav , Panwar Raja Babu , Katoch Vishwa Mohan , Gupta Rajeev 
Published: September 2021

ABSTRACTBackground & ObjectivesPresence of cardiovascular (CV) risk factors enhance adverse outcomes in COVID-19. To determine association of risk factors with clinical outcomes in India we performed a study.MethodsSuccessive virologically confirmed patients of COVID-19 at a government hospital were recruited at admission and in-hospital outcome and other details obtained. The cohort was classified according to age, sex, hypertension, diabetes and tobacco use. To compare intergroup outcomes we performed univariate and multivariate logistic regression.ResultsFrom March-September 2020 we recruited 4645 (men 3386, women 1259) out of 5103 COVID-19 patients (91.0%). Mean age was 46±18y, hypertension was in 17.8%, diabetes in 16.6% and tobacco-use in 29.5%. Duration of hospital stay was 6.8±3.7 days, supplemental oxygen was in 18.4%, non-invasive ventilation in 7.1%, mechanical ventilation in 3.6% and 7.3% died. Unadjusted and age-sex adjusted odds ratio and 95% confidence intervals, respectively were, age ≥50y (4.16, 3.22-5.37 and 4.15,3.21-5.35), men (1.88,1.41-2.51 and 1.26,0.91-1.48); hypertension (2.22,1.74-2.83 and 1.32,1.02-1.70), diabetes (1.88,1.46-2.43 and 1.16,0.89-1.52) and tobacco (1.29,1.02-1.63 and 1.28,1.00-1.63). Need for invasive ventilation was greater in age >50y (3.06,2.18-4.28 and 3.06,2.18-4.29) and diabetes (1.64,1.14-2.35 and 1.12,0.77-1.62). Non-invasive ventilation was more in age ≥50y (2.27,1.80-2.86 and 2.26,1.79-2.85) and hypertension (1.82,1.41-2.35 and 1.29,0.99-1.69). Multivariate adjustment for presenting factors attenuated the significance.ConclusionCardiovascular risk factors-age, male sex, hypertension, diabetes and tobacco-are associated with greater risk of death and adverse outcomes in COVID-19 patients in India.
Identification and quantification of chimeric sequencing reads in a highly multiplexed RAD-seq protocol
Authors: Martin Cerezo Maria Luisa , Raval Rohan , de Haro Reyes Bernardo , Kucka Marek , Chan Frank Yingguang , Bryk Jarosław 
Published: September 2021

AbstractHighly multiplexed approaches have become a common practice in genomic studies. They have improved the cost-effectiveness of genotyping hundreds of individuals by using combinatorially-barcoded adapters. These strategies, however, can potentially misassign reads to incorrect samples. Here we used a modified quaddRAD protocol to analyse the occurrence of index hopping and PCR chimeras in a series of experiments with up to a 100 multiplexed samples per sequencing lane (total n = 639). We created two types of sequencing libraries: four libraries of Type A, where PCR reactions were run on individual samples before multiplexing, and three libraries of Type B, where PCRs were run on pooled samples. We used fixed pairs of inner barcodes to identify chimeric reads. Type B libraries show a higher percentage of misassigned reads (1.15%) compared to Type A libraries (0.65%). We also quantify the commonly undetectable chimeric sequences that occur whenever multiplexed groups of samples with different outer barcodes are sequenced together on a single flow cell. Our results suggest that these types of chimeric sequences represent up to 1.56% and 1.29% of reads in Type A and B libraries, respectively. We review the source of such errors, provide recommendations for developing highly-multiplexed RAD-seq protocols and analysing the resulting data to minimise the generation of chimeric sequences, allow their quantification, and provide finer control over the number of PCR cycles necessary to generate enough input DNA for library preparation.
Elevated alpha diversity in disturbed sites obscures regional decline and homogenization of amphibian diversity
Authors: Dehling D. Matthias , Dehling J. Maximilian 
Published: September 2021

AbstractLoss of natural habitat is one of the major threats for biodiversity worldwide. Habitat conversion not only changes diversity and species composition locally (alpha diversity) but might also lead to large-scale homogenization of species communities and decrease in regional species richness (gamma diversity). We investigated the effect of farmland conversion on amphibian communities in Rwanda and compared local and regional (country-wide) taxonomic, functional and phylogenetic diversity between natural and farmland sites (agricultural marais). Alpha diversity was higher in the disturbed farmland than in natural sites. However, species turnover among farmland sites was much lower than among natural sites, resulting in highly homogenized amphibian communities and much lower country-wide taxonomic, functional and phylogenetic gamma diversity in farmland compared to natural sites. The few frog species found in farmland were mostly disturbance-tolerant species that are widespread in Eastern Africa and beyond. In contrast, most of the regionally endemic frog species that make this region a continent-scale hotspot of amphibian diversity were found only in the natural habitats. Ongoing farmland conversion might lead to a loss of regional endemism and a widespread homogenization of species communities across sub-Saharan Africa.
Optimised multiplex amplicon sequencing for mutation identification using the MinION nanopore sequencer
Authors: Whitford Whitney , Hawkins Victoria , Moodley Kriebashne , Grant Matthew J. , Lehnert Klaus , Snell Russell G. , Jacobsen Jessie C. 
Published: September 2021

AbstractObjectiveRapid, cost-effective identification of genetic variants in small candiate genomic regions remains a challenge, particularly for less well equipped or lower throughput laboratories. Application of Oxford Nanopore Technologies’ MinION sequencer has the potential to fulfil this requirement. We have developed a multiplexing assay which pools PCR amplicons for MinION sequencing to enable sequencing of multiple templates from multiple individuals which could be applied to gene-targeted diagnostics.MethodsA combined strategy of barcoding and sample pooling was developed for simultaneous multiplex MinION sequencing of 100 PCR amplicons, spanning 30 loci in DNA isolated from 82 neurodevelopmental cases and family members. The target regions were chosen for further interegation because a potentially disease-causative variants had been identified in affected individuals by Illumina exome sequencing. The pooled MinION sequences were deconvoluted by aligning to custom references using the guppy aligner software.ResultsOur multiplexing approach produced interpretable and expected sequence from 29 of the 30 targeted genetic loci. The sequence variant which was not correctly resolved in the MinION sequence was adjacent to a five nucleotide homopolymer. It is already known that homopolymers present a resolution problem with the MinION approach. Interstingly despite equimolar quantities of PCR amplicon pooled for sequencing, significant variation in the depth of coverage (139x – 21,499x; mean = 9,050, std err = 538.21) was observed. We observed independent relationships between depth of coverage and target length, and depth of coverage and GC content. These relationships demonstrate biases of the MinION sequencer for longer templates and those with lower GC content.ConclusionWe demonstrate an efficient approach for variant discovery or confirmation from short DNA templates using the MinION sequencing device. With less than 140x depth of coverage required for accurate genotyping, the methodology described here allows for rapid highly multiplexed targeted sequencing of large numbers of samples in a minimally equipped laboratory.
Risk factors associated with development and persistence of long COVID
Authors: Miyazato Yusuke , Tsuzuki Shinya , Morioka Shinichiro , Terda Mari , Kutsuna Satoshi , Saito Sho , Shimanishi Yumiko , Takahashi Kozue , Sanada Mio , Akashi Masako , Kuge Chika , Osanai Yasuyo , Tanaka Keiko , Suzuki Michiyo , Hayakawa Kayoko , Ohmagari Norio 
Published: September 2021

AbstractBackgroundLong COVID has been a social concern. Though patient characteristics associated with developing long COVID are partially known, those associated with persisting it have not been identified.MethodsWe conducted a cross-sectional questionnaire survey of patients after COVID-19 recovery who visited the National Center for Global Health and Medicine between February 2020 and March 2021. Demographic and clinical data, and the presence and duration of long COVID were obtained. We identified factors associated with development and persistence of long COVID using multivariate logistic and linear regression analysis, respectively.ResultsWe analyzed 457 of 526 responses (response rate, 86.9%). The median age was 47 years, and 378 patients (84.4%) had mild disease in acute phase. The number of patients with any symptoms after 6 and 12 months after onset or diagnosis were 120 (26.3%) and 40 (8.8%), respectively. Women were at risk for development of fatigue (OR 2.03, 95% CI 1.31-3.14), dysosmia (OR 1.91, 95% CI 1.24-2.93), dysgeusia (OR 1.56, 95% CI 1.02-2.39), and hair loss (OR 3.00, 95% CI 1.77-5.09), and were at risk for persistence of any symptoms (coefficient 38.0, 95% CI 13.3-62.8). Younger age and low body mass index were risk factors for developing dysosmia (OR 0.96, 95% CI 0.94-0.98, and OR 0.94, 95% CI 0.89-0.99, respectively) and dysgeusia (OR 0.98, 95% CI 0.96-1.00, and OR 0.93, 95% CI 0.88-0.98, respectively).ConclusionWe identified risk factors for the persistence as well as development of long COVID. Many patients suffer from long-term residual symptoms, even in mild cases.SummaryOur cross-sectional questionnaire survey of patients recovering from COVID-19 revealed that women, young age, and low body mass index were risk factors for the development of multiple symptoms, and that even mild cases of COVID-19 suffered from long-term residual symptoms.
How Our Cells Become Our Selves: The Cellular Phylodynamic Biology of Growth and Development
Authors: Chodrow Philip , Su Jessica , Lee Daniel , Ahmed Tahmid , He Neil , Ruben De Man , Tiwari Ankur , Mannherz William , Citi Luca , DiCorpo Daniel , Michaelson James Selib 
Published: September 2021

AbstractOur lives begin with 1 cell, then 2, then 4, then the trillion cell adult, comprised of cell lineages, tissues, organs. How does this occur? Examination in numbers of cells, N, Cellular Phylodynamics, revealed two previously unappreciated processes: UNI-GROWTH, the slowing of growth that occurs as we become larger, caused by fewer cells dividing, captured by the Universal Mitotic Fraction and Universal Growth Equations, with accuracy confirmed for 13 species, including nematodes, mollusks, and vertebrates; and ALLO-GROWTH, the creation of body parts from Founder Cells, captured by the Cellular Allometric Growth Equation, which describes mitotic expansion by Cell-Heritable change in the Cell Cycle Time. These equations can generate cell lineage approximations, bringing the power of coalescent theory to developmental biology.
Assessing the relationships between neurological and psychiatric diseases with astrocyte subtypes and psychotropic medications
Authors: Zhang Xiaolu , Wolfinger Alyssa , Shukla Rammohan , Lundh Anna , Wu Xiaojun , Abel Mackenzie , McCullumsmith Robert E. , O’Donovan Sinead M. 
Published: September 2021

AbstractAstrocytes have many important functions in the brain, but their roles in CNS disorders and their responses to psychotropic medications are still being elucidated. In this study, we used gene enrichment analysis to assess the relationships between different astrocyte subtypes, neurological and psychiatric diseases, and psychotropic medications. We also carried out qPCR analyses and “look-up” studies to further assess the chronic effects of these drugs on astrocyte marker gene expression. Our bioinformatic analysis identified differential gene enrichment of different astrocyte subtypes in CNS disorders. The “common” astrocyte subtype was the most frequently enriched across disorders, but the highest level of enrichment was found in depression, supporting a role for astrocytes in this disorder. We also identified common enrichment of metabolic and signal transduction-related biological processes in astrocyte subtypes and CNS disorders. However, enrichment of different psychotropic medications, including antipsychotics, antidepressants, and mood stabilizers, was limited in astrocyte subtypes. These results were confirmed by “look-up” studies and qPCR analysis, which also reported little effect of common psychotropic medications on astrocyte marker gene expression, suggesting that astrocytes are not a primary target of these medications. Overall, this study provides a unique view of astrocyte subtypes and the effect of medications on astrocytes in disease, which will contribute to our understanding of their role in CNS disorders and offers insights into targeting astrocytes therapeutically.
Live Monitoring of Inflammation Reveals Tissue and Sex-specific Responses to Western Diet and Butyrate treatment
Authors: Bonomo Raiza , Talley Sarah , Hatahet Jomana , Gavini Chaitanya , Cook Tyler , Chun Ben , Kekenes-Huskey Pete , Aubert Gregory , Campbell Edward , Mansuy-Aubert Virginie 
Published: September 2021

AbstractObesity is a current epidemic, affecting millions of individuals worldwide. Chronic obesity is characterized by a low-grade systemic inflammation besides not being a classic inflammatory disease. Many studies have tried to identify inflammatory insults dysregulated by a Westernized diet – consisted of high fat, high sucrose, and high cholesterol –mainly focusing on production and secretion of inflammatory cytokines. The gut microbiome and derived metabolites, including the short-chain fatty acid butyrate, have received increased attention as underlying some of the obesogenic features. In the present work, we utilized a novel biosensor mouse model capable of monitoring in vivo inflammation. We observed tissue- and sex- specific caspase-1 activation patterns in obese mice and treated with butyrate. Our work utilizing a caspase-1 biosensor mouse model, flow cytometry and computational analyses and offers new mechanistic insights underlying the effect of butyrate in obesity and its complications.