bluuebunny/crossref_metadata_2025 huggingface dataset:
bollito: a flexible pipeline for comprehensive single-cell RNA-seq analyses
Authors: García-Jimeno Luis , Fustero-Torre Coral , Jiménez-Santos María José , Gómez-López Gonzalo , Di Domenico Tomás , Al-Shahrour Fátima
Published: November 2021

bollito is an automated, flexible and parallelizable computational pipeline for the comprehensive analysis of single-cell RNA-seq data. Starting from FASTQ files or preprocessed expression matrices, bollito performs both basic and advanced tasks in single-cell analysis integrating >30 state-of-the-art tools. This includes quality control, read alignment, dimensionality reduction, clustering, cell-marker detection, differential expression, functional analysis, trajectory inference and RNA velocity. bollito is built using the Snakemake workflow management system, which easily connects each execution step and facilitates the reproducibility of results. bollito’s modular design makes it easy to incorporate other packages into the pipeline enabling its expansion with new functionalities.

Availability and implementation

Source code is freely available at https://gitlab.com/bu_cnio/bollito under the MIT license.

Supplementary information

Supplementary data are available at Bioinformatics online.
Limits and potential of combined folding and docking
Authors: Pozzati Gabriele , Zhu Wensi , Bassot Claudio , Lamb John , Kundrotas Petras , Elofsson Arne
Published: November 2021

Motivation

In the last decade, de novo protein structure prediction accuracy for individual proteins has improved significantly by utilising deep learning (DL) methods for harvesting the co-evolution information from large multiple sequence alignments (MSAs). The same approach can, in principle, also be used to extract information about evolutionary-based contacts across protein–protein interfaces. However, most earlier studies have not used the latest DL methods for inter-chain contact distance prediction. This article introduces a fold-and-dock method based on predicted residue-residue distances with trRosetta.

Results

The method can simultaneously predict the tertiary and quaternary structure of a protein pair, even when the structures of the monomers are not known. The straightforward application of this method to a standard dataset for protein–protein docking yielded limited success. However, using alternative methods for generating MSAs allowed us to dock accurately significantly more proteins. We also introduced a novel scoring function, PconsDock, that accurately separates 98% of correctly and incorrectly folded and docked proteins. The average performance of the method is comparable to the use of traditional, template-based or ab initio shape-complementarity-only docking methods. Moreover, the results of conventional and fold-and-dock approaches are complementary, and thus a combined docking pipeline could increase overall docking success significantly. This methodology contributed to the best model for one of the CASP14 oligomeric targets, H1065.

Availability and implementation

All scripts for predictions and analysis are available from https://github.com/ElofssonLab/bioinfo-toolbox/ and https://gitlab.com/ElofssonLab/benchmark5/. All models joined alignments, and evaluation results are available from the following figshare repository https://doi.org/10.6084/m9.figshare.14654886.v2.

Supplementary information

Supplementary data are available at Bioinformatics online.
ProSeqViewer: an interactive, responsive and efficient TypeScript library for visualization of sequences and alignments in web applications
Authors: Bevilacqua Martina , Paladin Lisanna , Tosatto Silvio C E , Piovesan Damiano
Published: November 2021

Biological data is ever-increasing in amount and complexity. The mapping of this data to biological entities such as nucleotide and amino acid sequences supports biological data analysis, classification and prediction. Sequence alignments and comparison allow the transfer of knowledge to evolutionary-related entities, the mapping of functional domains, the identification of binding and modification sites. To support these types of studies, we developed ProSeqViewer, a tool to visualize annotation on single sequences and multiple sequence alignments. This state-of-the-art multifunctional library was developed as a modular component to be integrated into static or dynamic web resources and support intuitive visualization of sequence features. ProseSeqViewer is extremely lightweight, fast, interactive, dynamic, responsive and works at any screen size. It generates pure HTML which is compatible with any browser and operating system. ProSeqViewer can exchange events with other visualization components and is already used by multiple biological databases.

Availability and implementation

ProSeqViewer is an open-source TypeScript library compatible with state-of-the-art website environments. The source code and an extensive documentation including use cases are available from the URL: https://github.com/BioComputingUP/ProSeqViewer.
Effect of primary tumour resection without curative intent in patients with metastatic neuroendocrine tumours of the small intestine and right colon: meta-analysis
Authors: Van Den Heede Klaas , Chidambaram Swathikan , Van Slycke Sam , Brusselaers Nele , Warfvinge Carl Fredrik , Ohlsson Håkan , Nordenström Erik , Almquist Martin
Published: November 2021

Background

Patients with small intestinal neuroendocrine tumours (siNETs) usually present with advanced disease. Primary tumour resection without curative intent is controversial in patients with metastatic siNETs. The aim of this meta-analysis was to investigate survival after primary tumour resection without curative intent compared with no resection in patients with metastatic siNETs.

Methods

A systematic literature search was performed, using MEDLINE® (PubMed), Embase®, Web of Science, and the Cochrane Library up to 25 February 2021. Studies were included if survival after primary tumour resection versus no resection in patients with metastatic siNETs was reported. Results were pooled in a random-effects meta-analysis, and are reported as hazard ratios (HRs) with 95 per cent confidence intervals. Sensitivity analyses were undertaken to enable comment on the impact of important confounders.

Results

After screening 3659 abstracts, 16 studies, published between 1992 and 2021, met the inclusion criteria, with a total of 9428 patients. Thirteen studies reported HRs adjusted for important confounders and were included in the meta-analysis. Median overall survival was 112 (i.q.r. 82–134) months in the primary tumour resection group compared with 60 (74–88) months in the group without resection. Five-year overall survival rates were 74 (i.q.r. 67–77) and 44 (34–45) per cent respectively. Primary tumour resection was associated with improved survival compared with no resection (HR 0.55, 95 per cent c.i. 0.47 to 0.66). This effect remained in sensitivity analyses.

Conclusion

Primary tumour resection is associated with increased survival in patients with advanced, metastatic siNETs, even after adjusting for important confounders.
Cognitive Evolution and China’s International Development Cooperation
Authors: Yu Bowen
Published: November 2021

China’s approach to International Development Cooperation (IDC) has been one of continuous evolution. The 2000s version of Chinese IDC applied a request-/project-centrism methodology, focused on the infrastructure sector, and mixed aid with business. Since the launch of the Belt and Road Initiative (BRI), the methodological dimension of the existing IDC model has changed by virtue of a growing emphasis on top-level design, sectoral programmes, and high standards for project implementation. How to explain these changes? Different from the conventional material-functionalist approaches, this article attributes the development of China’s IDC to cognitive evolution—an intra-community collective learning mechanism that drives changes in norms and practices. Cognitive evolution consists of the following three interconnected processes: uncertainty build-up; experimentation; and selection. Three factors that may shape the trajectories of cognitive evolution are as follows: the legacy of orthodox norms; the availability of transferable local ideas; and the communal interpretation of candidate ideas’ performance. The IDC model of the 2000s was constructed based on critical reflections on the internationalist foreign aid model of the Mao era and on the IDC policy community’s interpretation and transplantation of China’s development experience. The methodology of this IDC model—request-/project-centrism—has come under new pressure for change due to the BRI’s ambition to engender more substantial and sustainable developmental impact.
Playing together, laughing together: rapid facial mimicry and social sensitivity in lowland gorillas
Authors: Bresciani Chiara , Cordoni Giada , Palagi Elisabetta
Published: November 2021

In nonhuman animals, the phenomenon of rapid facial mimicry (RFM)—the automatic, involuntary, and rapid (<1 s) replication of others’ facial expressions—has been mainly investigated in the playful domain. In immature lowland gorillas Gorilla gorilla gorilla both play face (PF) and full PF (FPF) are rapidly mimicked between the players. This makes the species suitable to test hypotheses on the factors influencing RFM during play. The observations on 3 captive groups of lowland gorillas (N = 27) revealed that contrary to expectations, the closeness of social bond negatively influenced the occurrence of RFM but it did not affect either RFM latency or its overlapping index (OVERLAP). RFM was affected by the degree of symmetry of play fighting: the more balanced the session, the higher the occurrence of RFM. Players of the same sex class responded faster than players of different sex. These findings suggest that RFM may help synchronizing behaviors of playmates matching in size (same-sex) and promote symmetric playful interactions. “Laughing together” (measured by the RFM OVERLAP) lasted longer when the responder perfectly mirrored the partner expression (PF→PF; FPF→FPF). If PF and FPF convey information on the different play roughness degree, through “laughing together” the players could coordinate their actions and share positive moods and playful intensity. If the perfect congruency in the motor resonance, also known as social sensitivity, can foster a possible emotional dialogue between gorillas remains to be investigated.
Characteristics of Psychologists Assessing Deaf and Hard of Hearing Clients
Authors: Wilkins Alexander M , Morere Donna A , Pick Lawrence H , Day Lori A , Anderson Melissa L
Published: November 2021

Psychological assessment plays a large part in the practice of psychology. Over the years, steps have been taken towards ensuring ethical and culturally sensitive psychological assessment for underserved populations, but little is known about the current state of the field of assessment of deaf and hard-of-hearing (DHH) individuals. An exploratory survey of school and clinical psychologists who work with DHH clients (n = 30) was conducted to obtain a snapshot of the state of the field. The current article focuses on sociodemographic characteristics, clinical training, clinical experiences, and language abilities of clinical psychologists who work with DHH clients. Participants averaged 15 years of assessment experience and almost all participants had some type of specialized training in assessing DHH clients. More than half of participants reported their ability to use multiple languages and communication approaches as either excellent or good. Current findings were compared with a similar survey from nearly 50 years ago (Levine, E. S. (1974). Psychological tests and practices with the deaf: A survey of the state of the art. Volta Review, 76, 298–319), and significant differences were found in participants’ self-reported experience with DHH clients, training, and methods of communication.
Intravascular ultrasound-guided drug-coated balloon venoplasty for in-stent restenosis in pulmonary veins stenosis: a case report
Authors: Portero-Portaz Juan J , Córdoba-Soriano Juan G , Gallardo-López Arsenio , Jiménez-Mazuecos Jesús M
Published: November 2021

Background

Pulmonary veins stenosis (PVS) after atrial fibrillation radiofrequency ablation is an uncommon complication. When it occurs, percutaneous treatment is the preferred approach. There is a lack of standardized procedures, and when stenting restenosis is relatively common.

Case summary

We present a young patient with recurrence of PVS after first percutaneous treatment. The recurrence of haemoptysis and dyspnoea after treatment in PVS allowed the diagnosis of significant stenosis again in our patient. In the Heart Team, we opted for a new percutaneous treatment, using intravascular ultrasound (IVUS) to optimize the final result.

Discussion

Nowadays, percutaneous approach is preferred and among percutaneous treatments for PVS, stenting has shown better results than balloon angioplasty (BA). Despite this, experience in in-stent restenosis is limited, and there is a lack of adequate and specific material for its approach. In this case, we present the possible role of the IVUS and the drug-coated BA in this entity.
Long-term outcomes following rheumatic heart disease diagnosis in Australia
Authors: Stacey Ingrid , Hung Joseph , Cannon Jeff , Seth Rebecca J , Remenyi Bo , Bond-Smith Daniela , Griffiths Kalinda , Sanfilippo Frank , Carapetis Jonathan , Murray Kevin , Katzenellenbogen Judith M
Published: November 2021

Aims 

Rheumatic heart disease (RHD) is a major contributor to cardiac morbidity and mortality globally. This study aims to estimate the probability and predictors of progressing to non-fatal cardiovascular complications and death in young Australians after their first RHD diagnosis.

Methods and results 

This retrospective cohort study used linked RHD register, hospital, and death data from five Australian states and territories (covering 70% of the whole population and 86% of the Indigenous population). Progression from uncomplicated RHD to all-cause death and non-fatal cardiovascular complications (surgical intervention, heart failure, atrial fibrillation, infective endocarditis, and stroke) was estimated for people aged <35 years with first-ever RHD diagnosis between 2010 and 2018, identified from register and hospital data. The study cohort comprised 1718 initially uncomplicated RHD cases (84.6% Indigenous; 10.9% migrant; 63.2% women; 40.3% aged 5–14 years; 76.4% non-metropolitan). The composite outcome of death/cardiovascular complication was experienced by 23.3% (95% confidence interval: 19.5–26.9) within 8 years. Older age and metropolitan residence were independent positive predictors of the composite outcome; history of acute rheumatic fever was a negative predictor. Population group (Indigenous/migrant/other Australian) and sex were not predictive of outcome after multivariable adjustment.

Conclusion 

This study provides the most definitive and contemporary estimates of progression to major cardiovascular complication or death in young Australians with RHD. Despite access to the publically funded universal Australian healthcare system, one-fifth of initially uncomplicated RHD cases will experience one of the major complications of RHD within 8 years supporting the need for programmes to eradicate RHD.
What Is Acting?
Authors: Guo Yuchen
Published: November 2021

We can portray or take on the role of someone whom we are not. For example, a professional actor can play the role of a fictional character who does not exist in the real world, although she believes she is not that person. This behavior is named “acting.” My aim here is to locate the necessary and sufficient conditions of acting. In my view, acting is a process of communication between actors and audiences. One of its necessary components is that actors use their own features to represent those features that their characters have; another is that actors intend to make their audiences imagine that they are themselves identical to their characters. In this article, I specify these two components, critique other views of the definition of acting and distinguish acting from other similar processes.
Immunodeficiency and Autoantibodies to Cytokines
Authors: Knight Vijaya
Published: November 2021

Background

Anti-cytokine autoantibodies (AAbs) associated with an infectious phenotype are now included along with anti-complement AAbs and somatic pathogenic gene variants as a distinct category termed ‘phenocopies of primary immunodeficiencies’ in the classification of inborn errors of immunity. Anti-cytokine AAbs target specific cytokine pathways, leading to inordinate susceptibility to specific organisms, generally in the setting of immunocompetence.

Content

Anti-cytokine AAbs are detected in the majority of healthy individuals and may play a regulatory role in limiting exaggerated responses to cytokines. While it is not well understood why some individuals with anti-cytokine AAbs develop increased susceptibility to organisms of low pathogenicity and others do not, it is likely that genetics and environment play a role. To date, AAbs to interferon gamma (IFNγ), interferon alpha (IFNα), interleukins-17 and 22 (IL-17/IL-22), interleukin-6 and granulocyte macrophage colony stimulating factor (GM-CSF) and their association with increased susceptibility to nontuberculous mycobacteria and other intracellular organisms, viral infections, Candida albicans, Staphylococcus aureus and other pyogenic organisms, and fungal infections respectively, have been described. The clinical phenotype of these patients is very similar to that of individuals with pathogenic gene variants in the specific cytokine pathway that the autoantibody targets, hence the term ‘phenocopy.’ Recognition of anti-cytokine AAbs as a distinct cause of immunodeficiency or immune dysregulation is important for appropriate management of such patients.

Understanding the roles that anti-cytokine AAbs play in health and disease continues to be a fascinating area of research. Evaluating generally immunocompetent individuals who present with chronic, treatment refractory, or unusual infections for anti-cytokine AAbs is critical as it may direct therapy and disease management.
Needle in a haystack: a case report of splenic foreign body-associated sepsis
Authors: Turner Benedict R H , Barnacle James , Sheth Hemant
Published: November 2021

Instances of foreign bodies impacted in solid organs are rare, and rarer still are reports of objects in the spleen. A 42-year-old presented septic with abdominal pain, high inflammatory markers and haemodynamic instability. She was found to have a splenic haematoma and a 4-cm hyperdense foreign body within the spleen. Ultrasound-guided drainage of the haematoma isolated Streptococcus anginosus and conservative management with intravenous antibiotics avoided the need for emergency splenectomy. The bacterium isolated was the same cultured 9 months previously from the patient’s empyema fluid. The origin of the foreign body was not identified, though is made of metal and pre-dates any hospital admissions. The case raised the question of how an object might penetrate the spleen without knowledge of the patient and highlighted the risks of foreign body-associated sepsis, the risks and benefits of emergency splenectomy and management of complex cases with paucity of evidence.
Patient Experience in Obstetrics in a Military Patient Satisfaction Survey: Findings and Recommendations for Improvement
Authors: Marshall-Aiyelawo Kimberley , Gliner Melissa , Pedraza Omar , Beekman Janine , Messinger Seth , Roshwalb Alan
Published: November 2021

Introduction

This study examines the care experience of obstetric patients within the Military Health System and compares them to those of medical and surgical care patients. Specifically, the study seeks to (1) examine how obstetric inpatient experience ratings differ from medical and surgical inpatient experience ratings, (2) understand specific aspects of care that drive overall experience ratings within this population, (3) test whether adherence to nursing practices such as hourly rounding and nurse leader visits affect experience ratings, and (4) describe ways that patient experience information can be presented to healthcare providers to improve performance.

Materials and Methods

Data for this study include Military Health System patient experience survey data (based on the Hospital Consumer Assessment of Healthcare Providers and Systems) collected from 2011 through 2019. Analysis includes data collected from 338,124 patients aged 18 years and older. Our analysis involved z-test comparisons of patient experience measure scores, trend analysis, logistic regression-based driver analysis, and correlations.

Results

Obstetric ratings are generally lower than those of medical and surgical patients; however, they have been improving at a slightly faster rate year over year. Effective nurse communications with patients are a particularly strong driver for improving their overall care experiences, and practices like hourly nurse rounding, nurse leader visits, and nurse–patient shift change conversations are positively correlated with obstetric patient experience ratings.

Conclusions

This study contextualizes how obstetric inpatient experience ratings differ from those of medical and surgical care patients. Healthcare administrators and policymakers should be aware that obstetric patients may have unique needs and expectations that lead to patient experience ratings differing from those of medical and surgical patients. Effective nurse–patient communications, hourly rounding, nurse leader visits, and nurse–patient shift change conversations could be strategies used to improve obstetric experience ratings.
A Descriptive Analysis of Supermassive Transfusion Recipients Among US and Coalition Forces During Combat Operations in Afghanistan and Iraq
Authors: Fisher Andrew D , Lavender Jason S , April Michael D , Hill Ronnie , Bynum James , Schauer Steven G
Published: November 2021

Introduction

Hemorrhage is the leading cause of potentially preventable death on the battlefield. Resuscitation with blood products is essential to restore circulating volume, repay the oxygen debt, and prevent coagulopathy. Massive transfusion (MT) occurs frequently after major trauma; a subset of casualties requires a supermassive transfusion (SMT), and thus, mobilization of additional resources remains unclear.

Materials and Methods

This is a secondary analysis of a previously described dataset from the Department of Defense Trauma Registry. In this analysis, we isolated U.S. and Coalition casualties that received at least 1 unit of packed red blood cells (PRBCs) or whole blood (WB). Given a lack of consensus on the definition of SMT recipients, we included those patients receiving the top quartile of PRBC and WB administered within the first 24 hours following arrival to a military treatment facility.

Results

We identified 25,897 adult casualties from January 1, 2007 to March 17, 2020. Within this dataset, 2,608 (9.0%) met inclusion for this analysis. The median number of total products administered within the first 24 hours was 8 units of PRBC or WB. The upper quartile was 18 units (n = 666). Compared to all other blood product recipients, patients in the SMT cohort had a higher median injury severity score (27 vs 18, P < 0.001), were most frequently injured by explosives (84.9% vs 68.6%, P < 0.001), had a higher mean emergency department (ED) pulse (128 vs 111, P < 0.001), a lower mean systolic blood pressure (122 vs 132 mm Hg, P < 0.001), and a higher mean international normalized ratio (1.68 vs 1.38, P < 0.001). SMT patients experienced lower survival to hospital discharge (85.8% vs 93.3%, P < 0.001).

Conclusions

Compared to all other PRBC and WB recipients, SMT patients experienced more injury by explosives, severe injury patterns, ED vital sign derangements, and mortality. These findings may help identify those casualties who may require earlier aggressive resuscitation. However, more data is needed to define this population early in their clinical course for early identification to facilitate rapid resource mobilization. Identifying casualties who are likely to die within 24 hours compared to those who are likely to survive, may assist in determining a threshold for a SMT.
The Impact of Nosocomial Bloodstream Infections on Mortality: A Retrospective Propensity-Matched Cohort Study
Authors: Petersiel Neta , Sherman Assa , Paul Mical
Published: November 2021

Background

The mortality toll of nosocomial infections drives infection control efforts. We aimed to assess the contemporary mortality associated with nosocomial bloodstream infections (BSIs).

Methods

Retrospective propensity-matched cohort study conducted in 1 hospital in Israel between January 2010–December 2020. Adults >18 years old with nosocomial BSI were matched to controls using nearest neighbor matching of the propensity score for nosocomial BSI. We assessed all-cause mortality at 30 days, 90 days, and survival up to 1 year starting on the BSI day or matched hospital-day among controls; and the functional and cognitive change between admission and discharge using the Norton score among patients discharged alive. Residual differences between matched groups were addressed through Cox regression for 1-year survival.

Results

A total of 1361 patients with nosocomial BSI were matched to 1361 patients without BSI. Matching achieved similar patient groups, with small differences remaining in the Charlson score and albumin and hemoglobin levels. At 90 days, mortality was higher among patients with BSI (odds ratio [OR], 3.36 [95% confidence interval {CI}, 2.77–4.07]). ORs were higher when the BSI was caused by multidrug-resistant bacteria (OR, 5.22 [95% CI, 3.3–8.26]) and with inappropriate empirical antibiotics in the first 24 hours (OR, 3.85 [95% CI, 2.99–4.94]). Following full adjustment, the hazard ratio for 1-year mortality with nosocomial BSI was 2.28 (95% CI, 1.98–2.62). The Norton score declined more frequently among patients with BSI (OR, 2.27 [95% CI, 1.81–2.86]).

Conclusions

Nosocomial BSIs incur a highly significant mortality toll, particularly when caused by multidrug-resistant bacteria. Among hospital survivors, BSIs are associated with functional decline.
In-depth Characterization of Vaccine Breakthrough Infections With SARS-CoV-2 Among Health Care Workers in a Dutch Academic Medical Center
Authors: Rümke Lidewij W , Groenveld Femke C , van Os Yvonne M G , Praest Patrique , Tanja Anniek A N , de Jong Dorien T C M , Symons Jori , Schuurman Rob , Reinders Tessa , Hofstra L Marije , Nierkens Stefan , Thijsen Steven F T , Heron Michiel , Lebbink Robert-Jan , Beekman Jeffrey M , Nijhuis Monique , Wensing Annemarie M J
Published: November 2021

Severe acute respiratory syndrome coronavirus 2 infection after coronavirus disease 2019 vaccination raises concerns about the emergence of vaccine escape variants. Here we characterize 14 breakthrough infections among 5860 fully vaccinated Dutch health care workers ≥14 days after the final dose of vaccination with either BNT162b2, mRNA-1273, or Ad26.COV2.S. These breakthrough infections presented with regular B.1.1.7 (Alpha) and B.1.617.2 (Delta) variants and high viral loads, despite normal vaccine-induced B- and T-cell immune responses detected by live virus neutralization assays and ELISpot. High-risk exposure settings, such as in households, indicate a potential risk of viral transmission despite full vaccination.
Social Cognition Impairments in 22q11.2DS Individuals With and Without Psychosis: A Comparison Study With a Large Population of Patients With Schizophrenia
Authors: Accinni Tommaso , Buzzanca Antonino , Frascarelli Marianna , Carlone Luca , Ghezzi Francesco , Kotzalidis Georgios D , Bucci Paola , Giordano Giulia Maria , Girardi Nicoletta , Panzera Alessia , Montaldo Simone , Fanella Martina , Di Bonaventura Carlo , Putotto Carolina , Versacci Paolo , Marino Bruno , Pasquini Massimo , Biondi Massimo , Di Fabio Fabio
Published: November 2021

Background

22q11.2 Deletion Syndrome (22q11DS) represents one of the most important genetic risk factors for schizophrenia (SCZ) and a reliable biological model to study endophenotypic characters of SCZ. The aim of the study was to investigate Social Cognition impairments in subjects with 22q11.2DS compared to a considerable sample of schizophrenic patients.

Methods

Forty-four individuals with 22q11.2DS (DEL) and 18 patients with 22q11.2DS and psychosis (DEL_SCZ) were enrolled; these groups were compared to 887 patients with schizophrenia (SCZ) and 780 healthy controls (HCs); the latter groups were recruited by the Italian Network for Research on Psychoses (NIRP) to which our Centre took part. Social cognition was evaluated through The Awareness of Social Inference Test (TASIT). A resampling procedure was employed to balance differences in samples size.

Results

All clinical groups (DEL; DEL_SCZ; and SCZ) showed worse performance on TASIT than HCs, except in Sincere scale. No differences between-clinical groups were found, except for Simple Sarcasm, Paradoxical Sarcasm and Enriched Sarcasm scales.

Conclusions

SC was impaired in individuals with 22q11.2DS regardless of psychotic symptomatology, similarly to people with SCZ. Therefore, SC deficits may represent potential endophenotypes of SCZ contributing to the vulnerability to psychosis.
Time-sequential detection of quantitative trait loci and candidate genes underlying the dynamic growth of Salix suchowensis
Authors: Wei Suyun , Yang Guo , Yang Yonghua , Yin Tongming
Published: November 2021

Elucidating the genetic factors underlying long-term biological processes remains challenging since the relevant genes and their effects may vary across different developmental stages. In this study, we carried out a large-scale field trial of the progeny of an F1 full-sib pedigree of Salix suchowensis and measured plant height and ground diameter periodically over a time course of 240 days. With the obtained data, we characterized plant growth rhythms and performed time-sequential analyses of quantitative trait loci underlying the dynamic growth of the plants. The dynamic mapping of quantitative trait loci revealed that stem height and ground diameter were under the control of four quantitative trait loci, and the effects of these quantitative trait loci varied greatly throughout the growth process, in which two quantitative trait loci were found to exert a pleiotropic effect determining the correlation between stem height and ground diameter. The analysis of candidate genes in the target genetic intervals showed that the pleiotropic effect of the two quantitative trait loci arises from the colocalization of genes with independent effects on stem height and ground diameter. Further examination of the expression patterns of the candidate genes indicated that height and circumference growth involve different activities of leaf and cambium tissues. This study provides unprecedented information to help us understand the dynamic growth of plants and presents an applicable strategy for elucidating the genetic mechanism underlying a long-term biological process by using plant growth as an example.
Is osteoarthritis a mitochondrial disease? What is the evidence
Authors: Fernández-Moreno Mercedes , Rego-Pérez Ignacio , Blanco Francisco J.
Published: November 2021

Propose of review

To summarize the evidence that suggests that osteoarthritis (OA) is a mitochondrial disease.

Recent findings

Mitochondrial dysfunction together with mtDNA damage could contribute to cartilage degradation via several processes such as: (1) increased apoptosis; (2) decreased autophagy; (3) enhanced inflammatory response; (4) telomere shortening and increased senescence chondrocytes; (5) decreased mitochondrial biogenesis and mitophagy; (6) increased cartilage catabolism; (7) increased mitochondrial fusion leading to further reactive oxygen species production; and (8) impaired metabolic flexibility

Mitochondria play an important role in some events involved in the pathogenesis of OA, such as energy production, the generation of reactive oxygen and nitrogen species, apoptosis, authophagy, senescence and inflammation. The regulation of these processes in the cartilage is at least partially controlled by retrograde regulation from mitochondria and mitochondrial genetic variation. Retrograde regulation through mitochondrial haplogroups exerts a signaling control over the nuclear epigenome, which leads to the modulation of nuclear genes, cellular functions and development of OA. All these data suggest that OA could be considered a mitochondrial disease as well as other complex chronic disease as cancer, cardiovascular and neurologic diseases.
Diesel exhaust exposure and risk of non-Hodgkin lymphoma: a meta-analysis
Authors: Vilardi Valeria , Boffetta Paolo
Published: November 2021

Objective

We aimed at carrying out a systematic review and meta-analysis of epidemiological studies on the association between occupational and non-occupational exposures to diesel exhaust and risk of non-Hodgkin lymphoma.

Methods

We conducted a systematic search of the literature and identified 16 cohort studies and 7 case-control studies that analyzed non-Hodgkin lymphoma alone or combined with Hodgkin lymphoma or multiple myeloma, from which we extracted 29 independent risk estimates. We performed random-effects meta-analyses for ever-exposure to diesel exhaust, overall and after stratification for outcome and study design.

Results

The meta-relative risk of non-Hodgkin lymphoma was 0.97 (95% confidence interval, 0.93–1.01; P-heterogeneity = 0.43). The meta-relative risk of results of cohort studies was 0.97 (95% confidence interval, 0.94–1.01) that of case-control studies was 1.00 (95% confidence interval, 0.84–1.17). Similar results were obtained when the meta-analysis was restricted to studies that analyzed only non-Hodgkin lymphoma. There was no indication of publication bias.

Conclusion

Our meta-analysis provided no overall evidence of an increased risk of non-Hodgkin lymphoma in subjects exposed to diesel exhausted.
Comparison of First and Second Wave Cohorts of Multisystem Inflammatory Disease Syndrome IN Children
Authors: Harahsheh Ashraf S. , Sharron Matthew P. , Bost James E. , Ansusinha Emily , Wessel David , DeBiasi Roberta L.
Published: November 2021

Comparing first and second wave MIS-C cohorts at our quaternary pediatric institution, second wave were older, presented more frequently with shortness of breath, higher maximum troponin and N-terminal BNP, and more frequently required advanced respiratory and inotropic support. Despite increased severity in the second cohort, both cohorts had similar rates of coronary artery abnormalities, systolic dysfunction, and length of stay.
Sutureless Transconjunctival Insertion of Eyelid Weights: A Novel Technique
Authors: Elahi Ebby , Afshin Evan E. , Guthrie Ashley J. , Lo Christopher
Published: November 2021

Purpose:

To describe a novel surgical technique for implanting eyelid weights via a sutureless transconjunctival approach. In comparison to the traditional supratarsal crease approach, this technique does not involve any external incisions or suture placement. The procedure can reduce surgical time and complications associated with the traditional external approach.

Methods:

 This case series includes 13 patients who underwent eyelid weight placement via the transconjunctival approach for paralytic lagophthalmos secondary to facial nerve paralysis (12 patients had unilateral paralysis and 1 patient had bilateral) with a total of 14 eyelid weights placed. The procedures were performed at an outpatient office-based surgical center. All procedures were performed or supervised by the same surgeon. Patients were followed for an average 6-month postoperative period for postoperative complications.

Results:

The sutureless transconjunctival approach to eyelid weight insertion was successful in achieving the desired functional and aesthetic outcomes. Patients undergoing this technique avoided the discomfort of postoperative suture removal. All patients achieved comparable outcomes postoperatively. There were no complications reported across the 13 patients throughout the 6-month postoperative period.

Conclusions:

This case series demonstrates that the transconjunctival approach for metal eyelid weight insertion is practical, relatively easy to perform, and associated with functional outcomes that are comparable to those achieved with the traditional approach, however, without external incision or placement of sutures.
Diagnosis of invasive fungal disease in coronavirus disease 2019: approaches and pitfalls
Authors: White P. Lewis
Published: November 2021

Purpose of review

This review will comment on the current knowledge for the diagnosis of the main causes of COVID-19-associated invasive fungal disease (IFD); it will discuss the optimal strategies and limitations and wherever available, will describe international recommendations.

Recent findings

A range of secondary IFDs complicating COVID-19 infection have been described and while COVID-19-associated pulmonary aspergillosis was predicted, the presentation of significant numbers of COVID-19-associated candidosis and COVID-19-associated mucormycosis was somewhat unexpected. Given the range of IFDs and prolonged duration of risk, diagnostic strategies need to involve multiple tests for detecting and differentiating various causes of IFD. Although performance data for a range of tests to diagnose COVID-19-associated pulmonary aspergillosis is emerging, the performance of tests to diagnose other IFD is unknown or based on pre-COVID performance data.

Because of the vast numbers of COVID-19 infections, IFD in COVID-19 critical-care patients represents a significant burden of disease, even if incidences are less than 5%. Optimal diagnosis of COVID-19-associated IFD requires a strategic approach. The pandemic has highlighted the potential impact of IFD outside of the typical high-risk clinical cohorts, given the ever-increasing population at risk of IFD and enhanced surveillance of fungal infections is required.
Beyond antivirals: virus-specific T-cell immunotherapy for BK virus haemorrhagic cystitis and JC virus progressive multifocal leukoencephalopathy
Authors: Nelson Adam S. , Yalamarthi Niveditha , Yong Michelle K. , Blyth Emily
Published: November 2021

Purpose of review

The clinical manifestations of the polyomaviruses BK and JC in immunocompromised patients include BK virus (BKV) induced haemorrhagic cystitis and nephropathy, and JC virus (JCV) associated progressive multifocal leukoencephalopathy (PML) and are typically a consequence of impaired adaptive immunity in the host. To date, little clinical success has been achieved with antiviral agents or other drug therapies to treat these conditions. Here we review the methods and outcomes of the most recent clinical studies utilising adoptive immunotherapy with BK and/or JC virus-specific T-cells (VST) as either prophylaxis or treatment alternatives.

Recent findings

In the last 12–18 months, several clinical trials have been published in the post-haemopoietic stem cell transplant (HSCT) setting showing good clinical success with the use of VST for treatment of BK viremia ± haemorrhagic cystitis. Between 82 and 100% clinical response has been observed in haemorrhagic cystitis using either third-party or donor-derived VST. The therapy was well tolerated with few cases of graft versus host disease in HSCT recipients, but immune mediated renal allograft loss was observed in one renal transplant recipient. Studies using BKV/JCV VST to treat PML are hindered by few patients who are sufficiently stable to receive VST. In a condition that otherwise carries such poor prognosis, VST were associated with clearance of JC virus, clinical and radiological improvement in some patients. Immune reconstitution inflammatory syndrome was a noted adverse event.

Restoration of BK and JC virus immunity using VST immunotherapy has shown good clinical outcomes in BKV associated infections. Further evaluation with the administration of VST earlier in the course of disease is warranted for the treatment of BKV associated nephropathy in renal allograft and in JCV PML. In both indications, larger cohorts and standardisation of dosing and outcome measures would be of benefit.
Comparison of quality characteristics of ‘Makgeolli’ made using brown and white rice of ‘Mirchal’
Authors: Seong Gi-Un , Kang Ju-Won , Cho Soo-Min , Lee Sais-Beul , Cho Jun-Hyeon , Park Dong-Soo , Kwon Young-Ho , Lee So-Myeong , Lee Ji-Yoon
Published: November 2021

In this study, we fermented ‘Makgeolli’ prepared using brown or white rice from ‘Mirchal’ for seven days to investigate the differences in their quality characteristics. Moreover, the physicochemical characteristics and antioxidant activities of ‘Makgeolli’ were assessed using principal component analysis (PCA). From the second day of fermentation, brown rice ‘Makgeolli’ exhibited a higher alcohol content (7.00%) than that of white rice ‘Makgeolli’ (3.60%). Additionally, the total polyphenol contents and antioxidant activities increased with the duration of fermentation (p<0.05) and were higher in brown rice ‘Makgeolli’ than those in white rice ‘Makgeolli’. Moreover, the proportion of glucose in the total free sugar content in brown rice ‘Makgeolli’ was 0.88, which was higher than that in the total free sugar content in white rice ‘Makgeolli’ (0.60). However, the levels of soluble solids, sugars, reducing sugars, and free sugars were higher in white rice ‘Makgeolli’ than those in brown rice ‘Makgeolli’. The PCA revealed that the quality characteristics of ‘Makgeolli’ prepared using brown or white rice were very distinct. Furthermore, the main contributing factor to these differences was the free sugar content. Moreover, the quality characteristics during fermentation were affected by the total acidity, polyphenol content, and alcohol content. This study provides useful data for processing ‘Makgeolli’ prepared using brown or white rice from ‘Mirchal’.
Comparison of quality characteristics and antioxidant activity of
‘Kochujang’ comprising ‘Nuruk’ made from
pigmented or white rice flour
Authors: Lee Hee-Won , Shim Ki-Hoon , Huh Chang-Ki
Published: November 2021

The present study compared the amino nitrogen content and the antioxidant
activity of ‘Kochujang’ (K1) comprising white rice
‘Nuruk’ with those of five types of ‘Kochujang’
(K2-K6) comprising pigmented rice ‘Nuruk’ made by various strains
of fungi. After 90 days of ripening, the amino nitrogen content was higher in
the K2-K6 samples than in the K1 sample. The total polyphenol content was high
in K5, which comprised pigmented rice ‘Nuruk’ made by
Aspergillus niger (10.57 mg/g), and in K2, which comprised
pigmented rice ‘Nuruk’ made by Aspergillus oryzae
(9.19 mg/g). The total flavonoid content was the highest in the K2 sample (0.84
mg/g). The 2,2-diphenyl-1-picrylhydrazyl (DPPH) radical-scavenging activities of
the samples in the K2-K6 groups were 71.31%-79.63%, which were approximately 20%
higher than that of the K1 group. Overall, the
2,2'-azino-bis(3-ethylbenzothiazoline-6-sulfonic acid) (ABTS) radical-scavenging
activity was also higher in the ‘Kochujang’ samples comprising
pigmented rice ‘Nuruk’ than in that comprising white rice
‘Nuruk’. The K2 sample had the highest superoxide dismutase
(SOD)-like activity (68.07%), and the K1 sample had the lowest SOD-like activity
(59.03%). However, there was no significant difference between K3, which
comprised pigmented rice ‘Nuruk’ made by Aspergillus
kawachii, and sample K5.
Effects of powder mixtures containing ark shell on IgE-mediated
allergic response in RBL-2H3 cells
Authors: Chung Mi Ja , Goh Eun , Bae So Hui , Lee Sanghyun , Hur Jong Moon , Yoo Goo Sang , Kim Deok Soon
Published: November 2021

The purpose of this study was to investigate the anti-allergic effects of a
powder mixture containing ark shells (MP) on rat basophilic leukemia (RBL)-2H3
mast cells. When RBL-2H3 cells were sensitized with anti-dinitrophenyl
(anti-DNP) IgE and subsequently stimulated with DNP-human serum albumin (HSA),
β-hexosaminidase was released from the cells following degranulation of
the activated mast cells. However, pretreatment with MP extract (MPCAS) before
stimulation with DNP-HSA attenuated the release of β-hexosaminidase in
IgE–antigen complex-stimulated RBL-2H3 cells. The levels of interleukin-4
(IL-4), IL-13, and TNF-α in the IgE-antigen complex-stimulated RBL-2H3
cells were measured using ELISA. Activated RBL-2H3 cells induced the expression
of the abovementioned inflammatory cytokines that are critical for the
pathogenesis of allergic diseases. MPCAS inhibited IL-4, IL-13, and TNF-α
secretion from activated RBL-2H3 cells. In addition, the present study
investigated the effects of MPCAS as an antigen on IgE-mediated activation of
RBL-2H3 cells. When RBL-2H3 cells were sensitized with IgE and subsequently
stimulated with MPCAS, β-hexosaminidase, IL-4, IL-13, and TNF-α
levels did not change compared with those in the control. Thus, MPCAS does not
act as an allergen in IgE-stimulated RBL-2H3 cells. These results indicate that
MPCAS can be developed as an allergy-reducing food material by suppressing
degranulation and inflammatory cytokine expression.
Physical Profile and Epidemiological Analysis of Injuries in a College Athletics Team: A Retrospective Analysis
Authors: Tenorio Pedro Rocha , de Oliveira Santos Jean Kleber , de Melo Mariana Emanuela Higa , Mariano Thaoan Bruno
Published: November 2021

Introduction

Athletics is a sport based on natural patterns and activities. As a sport, presents an array of benefices such as the improvement of physical condition and personal interaction, however, is not free of risks such as injuries related to training and competition.

Objectives

Analyze the physical profile and associated sports injuries in an athletics college team.

Methods

Subjects enrolled in a medicine college athletics team from Jan to Oct of 2021 of both genders had their characteristics collected and answered to a survey modified from the “NCAA Injury Surveillance System”.

Results

31 subjects answer the survey. 65% of the subjects present at least 1 injury, 73.9% of injuries were classified as severe, 0.27 injuries were reported per 1000 hours of exposure. Injured athletes had a practice time 2-fold greater than uninjured athletes. Quadriceps and shin injuries represent 52.17% of the injuries.

Conclusion

College athletics seems to present a high risk of severe sports injuries in the lower body, and the greater risk factor seems to be the practice time.