bluuebunny/crossref_metadata_2025_split huggingface dataset:
Climate influence the human leptospirosis cases in Brazil, 2007–2019: a time series analysis
Authors: Costa Anna Cecília Trolesi Reis Borges , Pereira Carine Rodrigues , Sáfadi Thelma , Heinemann Marcos Bryan , Dorneles Elaine Maria Seles 
Published: June 2021

Abstract

Background
Human leptospirosis is responsible for great losses and deaths, especially in developing countries, which can be mitigated by knowing the correct health indicators and climate influence on the disease.

Methods
Leptospirosis cases and deaths, population and precipitation were recovered from different databases (2007–2019). Annual incidence, mortality and case fatality rates (CFRs) of human leptospirosis and average precipitation were calculated for Brazil and its regions. Time series analysis using an moving average with external variable (ARMAX) model was used to analyse the monthly contribution and precipitation influence over leptospirosis cases for each Brazilian region and for the whole country. A forecast model to predict cases for 2020 was created for Brazil.

Results
Human leptospirosis exhibited heterogeneous distribution among Brazilian regions, with most cases occurring during the rainy season and precipitation influenced the disease occurrence in all regions but the South. The forecast model predicted 3276.99 cases for 2020 (mean absolute percentage error 14.680 and root mean square error 53.013). Considering the annual average for the period, the leptospirosis incidence was 1913 cases per 100 000 inhabitants, mortality was 0.168 deaths per 100 000 inhabitants and the CFR was 8.83%.

Conclusions
The models built can be useful for planning leptospirosis surveillance and control actions for the whole country and its regions and, together with the health indicators, revealed no uniform epidemiological situation of leptospirosis in Brazil.
Molecular phylogenetics and evolutionary analysis of a highly recombinant begomovirus, Cotton leaf curl Multan virus, and associated satellites
Authors: Farooq Tahir , Umar Muhammad , She Xiaoman , Tang Yafei , He Zifu 
Published: June 2021

Abstract
Cotton leaf curl Multan virus (CLCuMuV) and its associated satellites are a major part of the cotton leaf curl disease (CLCuD) caused by the begomovirus species complex. Despite the implementation of potential disease management strategies, the incessant resurgence of resistance-breaking variants of CLCuMuV imposes a continuous threat to cotton production. Here, we present a focused effort to map the geographical prevalence, genomic diversity, and molecular evolutionary endpoints that enhance disease complexity by facilitating the successful adaptation of CLCuMuV populations to the diversified ecosystems. Our results demonstrate that CLCuMuV populations are predominantly distributed in China, while the majority of alphasatellites and betasatellites exist in Pakistan. We demonstrate that together with frequent recombination, an uneven genetic variation mainly drives CLCuMuV and its satellite’s virulence and evolvability. However, the pattern and distribution of recombination breakpoints greatly vary among viral and satellite sequences. The CLCuMuV, Cotton leaf curl Multan alphasatellite, and Cotton leaf curl Multan betasatellite populations arising from distinct regions exhibit high mutation rates. Although evolutionarily linked, these populations are independently evolving under strong purifying selection. These findings will facilitate to comprehensively understand the standing genetic variability and evolutionary patterns existing among CLCuMuV populations across major cotton-producing regions of the world.
A Problem of Classification: 2 Cases of Epstein–Barr Virus + Primary Cutaneous Plasmacytoma Arising in Immunocompetent Elderly Patients
Authors: Robson Alistair , Kempf Werner , Kolm Isabel , Kutzner Heinz , Willsmore Zena , Moonim Mufaddal 
Published: June 2021

Abstract:
Primary extramedullary plasmacytoma is rare monoclonal proliferation of plasma cells, which arise in various nonosseous anatomic locations without detectable underlying systemic disease. Historically, cutaneous infiltrates rich in mature neoplastic plasma cells have fallen into one of the following categories, plasmacytoma, lymphoplasmacytic lymphoma, and marginal zone lymphoma, which included immunocytoma. Since 2005, each of these was subsumed under the marginal zone lymphoma umbrella, largely on the basis of acknowledged diagnostic difficulties in some of these cases. We describe 2 cases in which the cutaneous infiltrates consisted of a pure population of light chain–restricted mature plasma cells in the absence of any other evidence for a marginal zone proliferation, or evidence of extracutaneous involvement, including a paraprotein. We propose that primary cutaneous plasmacytoma is the accurate diagnosis and is consistent with wider nomenclature. The unusual observation of widespread Epstein–Barr virus expression in both tumors is also discussed.
Scurvy and Tinea Corporis Simulating Leukocytoclastic Vasculitis
Authors: Heibel Haley D. , Ibad Sidra , Chao Yusuf , Patel Komal K. , Hutto Jake , Redd Lucas E. , Nussenzveig Daniel R. , Laborde Kimberly H. , Cockerell Clay J. , Shwin Kyawt 
Published: June 2021

Abstract:
Leukocytoclastic vasculitis (LCV) is a small vessel inflammatory condition considered to be caused by circulating immune complexes and often occurs after an acute infection or exposure to a new medication, although it may be associated with an underlying systemic disease or be idiopathic in nature. It is important to determine the etiology, identify the extent of the disease for early intervention and appropriate management, and treat and/or eliminate the underlying cause. Here, we report cases of scurvy and tinea corporis that presented with histopathologic features of LCV and had significant clinical improvement with treatment of the underlying etiologies. These cases emphasize that histopathologic features of early evolving LCV may be seen in other settings including scurvy and tinea corporis. Appropriate treatment of the underlying condition is important for optimized patient management.
Doubly Misdiagnosed: Exophiala Masquerading as Squamous Cell Carcinoma and Chromoblastomycosis
Authors: Guerra Ricardo , Guffey Darren , Russell Mark 
Published: June 2021

Abstract:
Deep cutaneous fungal infections (DCFI) can arise in the setting of skin trauma and immunosuppression. DCFI may be secondary to chromoblastomycosis, which is typically characterized by pseudoepitheliomatous hyperplasia histologically and can be mistaken for squamous cell carcinoma. In addition, “copper penny” spore–like pigmented yeast forms on Grocott's methenamine silver stain can suggest chromoblastomycosis, but this finding is not specific. By contrast, phaeohyphomycosis characteristically exhibits circumscribed pseudocyst or abscess on histopathology, and both yeast and hyphae can be seen. Our case reports a DCFI with pseudoepitheliomatous hyperplasia and “copper penny” yeast forms, ultimately diagnosed as phaeohyphomycosis after isolating Exophiala spinifera on fungal culture.
Onclarity Performance in Human Papillomavirus DNA Detection in Formalin-Fixed Paraffin-Embedded Cervical Samples
Authors: Bottari Fabio , Passerini Rita , Renne Giuseppe , Guerrieri Maria Elena , Sandri Maria Teresa , Li Aojun , Orlandini Anna , Iacobone Anna Daniela 
Published: June 2021

Objectives
Diagnosis of HPV infection is usually performed from cervical liquid-based cytology specimens (LBC), but these often contain a large amount of human papillomavirus (HPV) genotypes, most of which might cause transient infections. The aim of the study was to evaluate the performance of BD Onclarity HPV test genotyping method on formalin-fixed, paraffin-embedded (FFPE) cervical specimens compared with genotyping results from LBC.

Materials and Methods
Formalin-fixed, paraffin-embedded specimens from women surgically treated for cervical intraepithelial lesions (CINs) at the European Institute of Oncology, Milan, from September 2012 to June 2013 were retrieved from the archives of the Department of Pathology of the European Institute of Oncology. The FFPE and LBC specimens were genotyped using the same extended genotyping Onclarity assay.

Results
We collected 99 samples (26 CIN 1, 30 CIN 2, and 43 CIN 3+), but 15 were excluded from the analysis: these 84 samples show an overall agreement of 89% for HPV status between FFPE Onclarity samples versus LBC samples. The FFPE and LBC samples showed identical genotype in 75% samples, compatible genotype (at least 1 of the genotypes detected in LBC sample was found in the tissue sample) in 14% specimens, and discrepant genotype in 11% samples.

Conclusions
Our data demonstrate a very good concordance between HPV genotypes found in cytological and tissue samples, suggesting that the Onclarity method could also be used to detect HPV in tissue samples and that the HPV genotype detected in FFPE samples is one of the HPV detected in cytological samples, supporting the thesis that one lesion is caused by one HPV genotype.
Predictors and outcomes of acute recoil after ultrathin bioresorbable polymer sirolimus-eluting stents implantation: an intravascular ultrasound in native coronary arteries
Authors: Sato Takao , Goto Sonoka , Yuasa Sho , Akazawa Kohei , Aizawa Yoshifusa 
Published: June 2021

Background
Ultrathin bioresorbable polymer sirolimus-eluting stents (BP-SESs) may easily lead to acute recoil. This study investigated acute recoil after BP-SES implantation on the basis of intravascular ultrasound (IVUS).

Methods
We enrolled 40 consecutive stents. Absolute acute recoil by quantitative coronary angiography was defined as the difference between the mean diameter of the last inflated balloon (X) and mean lumen diameter of the BP-SES immediately after balloon deflation (Y). Percent (%) acute recoil was defined as (X−Y)×100/X. IVUS was performed within the culprit lesion. Plaque eccentricity, % plaque burden and calcification grade score were assessed using IVUS. Calcification grade was scored on the basis of quadrants. On the basis of the median acute recoil value of 5.0%, the stents were divided into two groups: low (LAR, n = 20) and high % acute recoil (HAR, n = 20).

Results
Mean % acute recoil was 5.8 ± 5.3%. Plaque eccentricity, % plaque burden and stent/artery ratio were significantly higher in the HAR group than in the LAR group. Significant differences in % acute recoil were not observed regarding the types of stent diameter. In multivariate logistic regression and multiple linear regression analysis, plaque eccentricity and % plaque burden in the culprit plaque were significant positive predictors for the occurrence of % acute recoil. No significant differences, including clinical outcomes, were found between both groups at follow-up.

Conclusion
Acute recoil of BP-SESs may be influenced by an eccentric plaque with a large burden, which did not affect long-term outcomes. However, the present study might suggest the proper strategy (e.g. a more exhaustive plaque preparation) before BP-SES implantation in a case with these IVUS characteristics.
Considering Domain-Specific Experiential Learning: Self-Efficacy in Pediatric Physical Therapy Education
Authors: Scott Kimberley , Wissinger Jennifer , Hand Brittany , Heathcock Jill 
Published: June 2021

Background:
Variability exists in pediatric training in physical therapy programs. Little is known about educator implementation of curriculum recommendations. Few options exist for evaluating student outcomes following pediatric instruction.

Purpose:
The purposes of this study are to describe the pediatric curriculum of a physical therapy program, quantify changes in self-efficacy following pediatric instruction, and define relationships between self-efficacy, prior experience, and interest in future pediatric practice.

Methods:
A prospective cohort study included 48 students. Measures were pediatric content hours, the Pediatric Communication and Handling Self-Efficacy Scale, prior experience, and self-reported interest in future pediatric practice.

Results:
Pediatric content hours followed published recommendations. There was a significant increase in self-efficacy after pediatric instruction. Prior experience and interest in future pediatric practice were significantly related to self-efficacy.

Conclusions:
Our results indicate that physical therapy programs reaching the recommended content hours for pediatric instruction support growth in student communication and handling self-efficacy.
Experiential Learning in Pediatric Physical Therapist Education: Faculty and Student Perceptions
Authors: Fiss Alyssa LaForme , Rapport Mary Jane , Gagnon Kendra , Wynarczuk Kimberly , Kendall Eydie , Schreiber Joseph 
Published: June 2021

This study aimed to describe use of experiential learning (EL) with children in entry-level doctor of physical therapy programs. Experiential learning is a recommended educational strategy for building physical therapy knowledge and skills.

Subjects:
Faculty teaching pediatric content in accredited doctor of physical therapy programs was recruited; 106 responded. Students representing 20 participating programs were also invited to participate; 23 responded.

Methods:
Participants received an online questionnaire including closed- and open-ended questions regarding EL with children. Descriptive statistics were used to describe responses. Responses to open-ended questions were compiled and reviewed.

Results:
Respondents reported an average of 12.4 hours of EL with children in required courses. Satisfaction with quality was stronger than with amount of EL. Several perceived barriers and facilitators were reported.

Conclusions:
Use of and satisfaction with EL with children in physical therapists' education vary. Continued research on this variation and potential effects to educational outcomes is needed.
Pediatric Physical Therapy Telehealth and COVID-19: Factors, Facilitators, and Barriers Influencing Effectiveness—a Survey Study
Authors: Hall Jamie B. , Woods Morgan L. , Luechtefeld Jessica T. 
Published: June 2021

Purpose:
The purpose of this study was to identify the important factors, facilitators, and barriers for telehealth effectiveness as described by pediatric physical therapists, transitioning from in-person to telehealth during the COVID-19 pandemic.

Methods:
Pediatric physical therapists' responses to 3 open-ended questions and 1 multipart Likert Scale question from an anonymous survey were collected and analyzed using thematic analysis and descriptive statistics.

Results:
Three overarching themes (Caregiver Engagement, Technology, and Resilience) were identified and accompanied by 3 subthemes (Personal Attributes, Equity, and COVID-Specific Considerations). Themes were supported by the Likert Scale question with Child/Caregiver Interaction, Internet Connection, and Family Factors identified as the most important factors related to telehealth effectiveness.

Conclusions:
High caregiver engagement and access to stable technology were most important for telehealth effectiveness. The telehealth service model met a need during the pandemic; however, emerging evidence suggests that it could be considered as an effective service delivery mode postpandemic.
Parental Satisfaction With Autonomous Pediatric Ambulatory Surgery Units
Authors: Poves-Álvarez Rodrigo , Gómez-Sánchez Esther , Martínez-Rafael Beatriz , Bartolomé Cecilia , Alvarez-Fuente Elisa , Muñoz-Moreno María Fe , Eiros José María , Tamayo Eduardo , Gómez-Pesquera Estefanía 
Published: June 2021

Background and Objectives:
Ambulatory surgery is much favored in children, as they are usually healthy with no major comorbidities. Obvious benefits are minimization of health costs, optimal utilization of resources, decreased exposure to infections, and psychological and emotional advantages of avoiding admission of the patient, especially for the family. Parental satisfaction is a challenge in pediatric surgery processes. The objective of this study was to compare satisfaction in parents whose children underwent surgery without overnight stays with parents whose children were operated on in an autonomous major ambulatory surgery unit (hospital isolated).

Methods:
This was a prospective observational study of 200 children who received surgery on an outpatient basis (133 were included in an outpatient unit and 67 in a hospital setting). Different variables were collected, including sex, age, type of surgery, and length of stay in the hospital and location, and a telephone perception survey was conducted (questionnaire of satisfaction of 14 questions with possible answers from 1 to 4 on a Likert scale and a 15th question on global satisfaction, with an answer from 0 to 10).

Results:
Overall satisfaction during the hospital stay was higher in the group operated on in the autonomous major surgery unit (3.54 ± 0.57 vs 3.28 ± 0.64, P = .004). Whether parents respond as being very satisfied with the hospital stay is influenced by several factors, among which are: being treated at major ambulatory surgery units (odds ratio [OR] = 2.16), good or very good information received prior to surgery (OR = 2.03), and good or very good information received at discharge (OR = 2.48).

Conclusions:
Parents of children who received surgery on an outpatient basis were more satisfied if the procedure was performed in an autonomous major ambulatory surgery unit compared with hospitalization, even if it was not overnight. The information received during the care process influenced the parents' satisfaction. These findings suggest that efforts should be devoted to the creation of autonomous units for ambulatory surgery and to the improvement of perioperative information.
High throughput SARS-CoV-2 variant analysis using molecular barcodes coupled with Next Generation Sequencing
Authors: Cohen-Aharonov Lyora A. , Rebibo-Sabbah Annie , Yaacov Adar , Granit Roy Z. , Strauss Merav , Colodner Raul , Cheshin Ori , Rosenberg Shai , Eavri Ronen 
Published: June 2021

AbstractThe identification of SARS-CoV-2 variants across the globe and their implications on the outspread of the pandemic, infection potential and resistance to vaccination, requires modification of the current diagnostic methods to map out viral mutations rapidly and reliably. Here, we demonstrate that integrating DNA barcoding technology, sample pooling and Next Generation Sequencing (NGS) provide an applicable solution for large-population viral screening combined with specific variant analysis.Our solution allows high throughput testing by barcoding each sample, followed by pooling of test samples using a multi-step procedure. First, patient-specific barcodes are added to the primers used in a one-step RT-PCR reaction, amplifying three different viral genes and one human housekeeping gene (as internal control). Then, samples are pooled, purified and finally, the generated sequences are read using an Illumina NGS system to identify the positive samples with a sensitivity of 82.5% and a specificity of 97.3%. Using this solution, we were able to identify six known and one unknown SARS-CoV-2 variants in a screen of 960 samples out of which 258 (27%) were positive for the virus.Thus, our diagnostic solution integrates the benefits of large population and epidemiological screening together with sensitive and specific identification of positive samples including variant analysis at a single nucleotide resolution.
Chronic SARS-CoV-2 infection and viral evolution in a hypogammaglobulinaemic individual
Authors: Williamson Maia Kavanagh , Hamilton Fergus , Hutchings Stephanie , Pymont Hannah M. , Hackett Mark , Arnold David , Maskell Nick A , MacGowan Alasdair , Albur Mahableshwar , Jenkins Megan , Heys Izak , Knapper Francesca , Elsayed Mustafa , Milligan Rachel ,   The COVID-19 Genomics UK (COG-UK) Consortium, Muir Peter , Vipond Barry , Matthews David A , Moran Ed , Davidson Andrew D. 
Published: June 2021

AbstractThere is widespread interest in the capacity for SARS-CoV-2 evolution in the face of selective pressures from host immunity, either naturally acquired post-exposure or from vaccine acquired immunity. Allied to this is the potential for long perm persistent infections within immune compromised individuals to allow a broader range of viral evolution in the face of sub-optimal immune driven selective pressure. Here we report on an immunocompromised individual who is hypogammaglobulinaemic and was persistently infected with SARS-CoV-2 for over 290 days, the longest persistent infection recorded in the literature to date. During this time, nine samples of viral nucleic acid were obtained and analysed by next-generation sequencing. Initially only a single mutation (L179I) was detected in the spike protein relative to the prototypic SARS-CoV-2 Wuhan-Hu-1 isolate, with no further changes identified at day 58. However, by day 155 the spike protein had acquired a further four amino acid changes, namely S255F, S477N, H655Y and D1620A and a two amino acid deletion (ΔH69/ΔV70). Infectious virus was cultured from a nasopharyngeal sample taken on day 155 and next-generation sequencing confirmed that the mutations in the virus mirrored those identified by sequencing of the corresponding swab sample. The isolated virus was susceptible to remdesivirin vitro, however a 17-day course of remdesivir started on day 213 had no effect on the viral RT-PCR cycle threshold (Ct) value. On day 265 the patient was treated with the combination of casirivimab and imdevimab. The patient experienced progressive resolution of all symptoms over the next 8 weeks and by day 311 the virus was no longer detectable by RT-PCR. The ΔH69/ΔV70 deletion in the N-terminus of the spike protein which arose in our patient is also present in the B.1.1.7 variant of concern and has been associated with viral escape mutagenesis after treatment of another immunocompromised patient with convalescent plasma. Our data confirms the significance of this deletion in immunocompromised patients but illustrates it can arise independently of passive antibody transfer, suggesting the deletion may be an enabling mutation that compensates for distant changes in the spike protein that arise under selective pressure.
CHST6-related macular corneal dystrophy: a matter of endothelium
Authors: Zhang Bi Ning , Qi Benxiang , Wang Xin , Dong Chunxiao , Cheng Jun , Li Dewei , Li Suxia , Chen Min , Zhang Bin , Zhou Qingjun , Xie Lixin 
Published: June 2021

AbstractMacular corneal dystrophy (MCD) is classified as corneal stromal dystrophy. In this study, we retrospectively reviewed the surgical outcomes of 118 MCD patients receiving surgical treatment in the past 30 years and found patients receiving penetrating keratoplasty had the lowest recurrence rate 13.75%, compared with 40.91% patients receiving deep anterior lamellar keratoplasty and 25% receiving phototherapeutic keratectomy. Transcriptomic analysis in human corneal single-cell sequencing atlas found the MCD pathogenic gene CHST6 was abundant in corneal endothelium rather than other cell types. CHST6 protein showed a similar expression pattern to its mRNA. The mouse homologous gene Chst5 was 120-fold higher in corneal endothelium than in the epithelial and stromal layers. Mice with specifically Chst5 knockdown in the endothelial layer by microinjection of the adeno-associated virus serotype 9 - shRNA plasmids into the anterior chamber, rather than Chst5 knockdown into the stroma, showed MCD-like phenotypes. Corneal opacification and abnormally larger collagen fibrils were observed in the endothelial Chst5 knockdown mice. The same corneal characteristics were observed after overexpressing human CHST6 mutant R50H in the mouse endothelium. These observations indicating the pathogenesis of MCD is more related to the corneal endothelium rather than the stroma.Significance StatementOur study gave evidence that corneal endothelium contributing more to the macular corneal dystrophy (MCD) development, rather than other cell types in the cornea. We proposed penetrating keratoplasty might serve as a more proper surgical treatment for MCD according to the recurrence rate analysis. We also provided a novel method to construct MCD mouse model.