bluuebunny/crossref_metadata_2025 huggingface dataset:
Perturbations of the T-cell immune repertoire in kidney transplant rejection
Authors: Sigdel Tara K. , Fields Paul A. , Liberto Juliane , Damm Izabella , Kerwin Maggie , Hood Jill , Towfighi Parhom , Sirota Marina , Robins Harlan S. , Sarwal Minnie M.
Published: November 2022

In this cross-sectional and longitudinal analysis of mapping the T-cell repertoire in kidney transplant recipients, we have investigated and validated T-cell clonality, immune repertoire chronology at rejection, and contemporaneous allograft biopsy quantitative tissue injury, to better understand the pathobiology of acute T-cell fraction, T-cell repertoire and antibody-mediated kidney transplant rejection. To follow the dynamic evolution of T-cell repertoire changes before and after engraftment and during biopsy-confirmed acute rejection, we sequenced 323 peripheral blood samples from 200 unique kidney transplant recipients, with (n=100) and without (n=100) biopsy-confirmed acute rejection. We report that patients who develop acute allograft rejection, have lower (p=0.01) T-cell fraction even before transplantation, followed by its rise after transplantation and at the time of acute rejection accompanied by high TCR repertoire turnover (p=0.004). Acute rejection episodes occurring after the first 6 months post-transplantation, and those with a component of antibody-mediated rejection, had the highest turnover; p=0.0016) of their T-cell repertoire. In conclusion, we validated that detecting repertoire changes in kidney transplantation correlates with post-transplant rejection episodes suggesting that T-cell receptor sequencing may provide recipient pre-transplant and post-transplant predictors of rejection risk.
Tissue-resident memory T cells in the era of (Neo) adjuvant melanoma management
Authors: Plunkett Kai R. , Armitage Jesse D. , Inderjeeth Andrisha-Jade , McDonnell Alison M. , Waithman Jason , Lau Peter K. H.
Published: November 2022

Tissue-resident memory T (TRM) cells have emerged as key players in the immune control of melanoma. These specialized cells are identified by expression of tissue retention markers such as CD69, CD103 and CD49a with downregulation of egress molecules such as Sphingosine-1-Phosphate Receptor-1 (S1PR1) and the lymphoid homing receptor, CD62L. TRM have been shown to be integral in controlling infections such as herpes simplex virus (HSV), lymphocytic choriomeningitis virus (LCMV) and influenza. More recently, robust pre-clinical models have also demonstrated TRM are able to maintain melanoma in a dormant state without progression to macroscopic disease reminiscent of their ability to control viral infections. The discovery of the role these cells play in anti-melanoma immunity has coincided with the advent of immune checkpoint inhibitor (ICI) therapy which has revolutionized the treatment of cancers. ICIs that target programmed death protein-1 (PD-1) and cytotoxic T lymphocyte antigen-4 (CTLA-4) have led to substantial improvements in outcomes for patients with metastatic melanoma and have been rapidly employed to reduce recurrences in the resected stage III setting. While ICIs mediate anti-tumor activity via CD8+ T cells, the specific subsets that facilitate this response is unclear. TRM invariably exhibit high expression of immune checkpoints such as PD-1, CTLA-4 and lymphocyte activating gene-3 (LAG-3) which strongly implicates this CD8+ T cell subset as a crucial mediator of ICI activity. In this review, we present pre-clinical and translational studies that highlight the critical role of TRM in both immune control of primary melanoma and as a key CD8+ T cell subset that mediates anti-tumor activity of ICIs for the treatment of melanoma.
Pathophysiological mechanisms of thrombosis in acute and long COVID-19
Authors: Jing Haijiao , Wu Xiaoming , Xiang Mengqi , Liu Langjiao , Novakovic Valerie A. , Shi Jialan
Published: November 2022

COVID-19 patients have a high incidence of thrombosis, and thromboembolic complications are associated with severe COVID-19 and high mortality. COVID-19 disease is associated with a hyper-inflammatory response (cytokine storm) mediated by the immune system. However, the role of the inflammatory response in thrombosis remains incompletely understood. In this review, we investigate the crosstalk between inflammation and thrombosis in the context of COVID-19, focusing on the contributions of inflammation to the pathogenesis of thrombosis, and propose combined use of anti-inflammatory and anticoagulant therapeutics. Under inflammatory conditions, the interactions between neutrophils and platelets, platelet activation, monocyte tissue factor expression, microparticle release, and phosphatidylserine (PS) externalization as well as complement activation are collectively involved in immune-thrombosis. Inflammation results in the activation and apoptosis of blood cells, leading to microparticle release and PS externalization on blood cells and microparticles, which significantly enhances the catalytic efficiency of the tenase and prothrombinase complexes, and promotes thrombin-mediated fibrin generation and local blood clot formation. Given the risk of thrombosis in the COVID-19, the importance of antithrombotic therapies has been generally recognized, but certain deficiencies and treatment gaps in remain. Antiplatelet drugs are not in combination with anticoagulant treatments, thus fail to dampen platelet procoagulant activity. Current treatments also do not propose an optimal time for anticoagulation. The efficacy of anticoagulant treatments depends on the time of therapy initiation. The best time for antithrombotic therapy is as early as possible after diagnosis, ideally in the early stage of the disease. We also elaborate on the possible mechanisms of long COVID thromboembolic complications, including persistent inflammation, endothelial injury and dysfunction, and coagulation abnormalities. The above-mentioned contents provide therapeutic strategies for COVID-19 patients and further improve patient outcomes.
Holocene sedimentary of the Pearl River Delta in South China: OSL and radiocarbon dating of cores from Zhuhai
Authors: Lin Penghui , Xu Xiaolin , Yan Chaoyang , Luo Lan , Abbas Mahmoud , Lai Zhongping
Published: November 2022

Deltaic sediments provide a window for investigating delta development processes and the effects of human activities. Despite the fact that numerous studies have been conducted in the Pearl River Delta (PRD), the chronological data are still very limited, which hinder the detailed interpretation of the sedimentary records. The current study aims to establish high-resolution chronology on two cores from Zhuhai using quartz optically stimulated luminescence (OSL) and radiocarbon (14C) dating and, further, to reconstruct the Holocene sedimentary history of the PRD. Core P1-1 has a depth of 79 m and core P3-2 a depth of 60 m. Thirteen quartz OSL samples from P1-1 produced ages between 10.4 and 0.16 ka. Eight OSL and eight 14C ages from P3-2 span from 10.7 to 0.3 ka. The OSL and 14C dates show a good agreement above the depth of 26 m (1.4–0.3 ka), but with discrepancies at depths of 26–54 m. 14C ages (10.7–8.1 ka) are generally older (up to c. 2 ka) than quartz OSL ages, and the discrepancy decreases with depth. The age model shows three phases of the sedimentation process: (1) rapid accumulation rates of 7.48 (P1-1) and 7.52 (P3-2) m/ka between c. 10.7 and 7.5 ka in response to high sea level, (2) followed by a significantly reduced rate of 2.24 m/ka (P1-1) and a depositional hiatus (P3-2) from 7.5 to 2.5 ka as a result of reduced sediment supply and strong scouring by tidal processes, and (3) high sedimentation rates of 8.86 (P1-1) and 9.07 (P3-2) m/ka since 2.5 ka associated with intensive human activities and weakening tidal hydrodynamics. This sedimentary pattern is also evident in many other Asian deltas.
Polyethylene microplastics increases the tissue damage caused by 4-nonylphenol in the common carp (Cyprinus carpio) juvenile
Authors: Ammar Esraa , Mohamed Mahmoud S. , Sayed Alaa El-Din H.
Published: November 2022

Plastic particles have the ability to transfer harmful chemical pollutants due to their high adsorption capacity. Therefore, this study aimed to investigate the effects of combined exposure to polyethylene microplastics (PE-MPs) and 4-nonylphenol (4-NP) on juvenile common carp (Cyprinus carpio) using histopathological and histochemical biomarkers. Fish were separated into a control group and three treatment groups (10 mg/L PE-MPs; 10 mg/L PE-MPs + 200 µg/L 4-NP; 200 µg/L 4-NP) for a two-week continuous exposure experiment followed by two weeks of recovery. The three treatment groups showed histopathological changes compared to the control. These alterations included severe edema, lifting of the outer epithelium, interlamellar fusion and vacuolation, secondary lamellar shortening and complete fusion, increased mucous cell numbers in the gill tissue, enlargement of inner layer stratum periventricular, cell degeneration with pyknotic nuclei, increased blood capillaries, spongiosis in the brain tissue (optic tectum), central vein hemorrhage, shrunken and fatty degeneration of hepatocytes, rosette shapes around small congested blood sinusoids, vacuoles, necrosis, and severe glycogen reduction in the liver tissue. Some tissue changes improved during the two-week recovery period but did not return to normal. In conclusion, the mixture exposure of the PE-MPs and 4-NP on fish carp induced some histological alterations in most studied tissues and post-exposure made improvement in cellular and tissue structure.
A review of reproduction in the seaweed genus Fucus (Ochrophyta, Fucales): Background for renewed consideration as a model organism
Authors: Hatchett William J. , Coyer James A. , Sjøtun Kjersti , Jueterbock Alexander , Hoarau Galice
Published: November 2022

The genusFucusdominates the intertidal and shallow subtidal rocky reefs of the North Atlantic and also is commonly found in the intertidal of the North Pacific. It likely diversified 12.2-2.7 mya into two genetically distinct lineages: Lineage 1 with one species in the North Pacific and two in the North Atlantic; and Lineage 2 found only in the North Atlantic (one species recently introduced into the North Pacific). With 10 accepted species,Fucusspp. (and the Fucales) are unique among algae in having a diplontic life cycle, whereby the only haploid stage is the single-celled gamete. Further,Fucusspp. produce eight eggs in each oogonium; have hermaphroditic and dioecious species in each lineage; display sperm:egg ratios differing by more than one order of magnitude; have synchronized and predictable release of gametes; are capable of self- and/or cross- fertilization and asexual (fragmentationviaadventitious branching) reproduction; readily hybridize in culture, as well as the field; and form ecads (free-living individuals with morphological variability linked to habitat) by hybridization or polyploidy. Consequently, the genus is an excellent model for a variety of studies in reproductive biology, employing laboratory and field manipulations as well as detailed genetic studies using the molecular ‘omics’. We review here the relevant literature in order to fully understand and appreciate the unique opportunities thatFucusspp. provide as model organisms for future studies of reproduction.
Nutrient turnover by large sulfur bacteria on the Namibian mud belt during the low productivity season
Authors: Chuang Pei-Chuan , Anderson Chloe H. , Kossack Michael , Fabian Jenny , Su Chih-Chieh , Vosteen Paul , Zabel Matthias , Scholz Florian , Schulz-Vogt Heide N. , Sommer Stefan , Dale Andrew W.
Published: November 2022

Surface sediments of the coastal mud belt in the Benguela Upwelling System (BUS) off Namibia host extensive communities of chemotrophic large sulfur bacteria (LSB) of the family Beggiatoaceae such as Thiomargarita spp. and Candidatus Maribeggiatoa spp. In order to understand the role of these bacteria in N and P cycling, biogeochemical data from three sites in the mud belt were simulated with a biogeochemical model including LSB catabolic pathways. Organic carbon remineralization was dominated by the reduction of sulfate to hydrogen sulfide (5.0–7.7 mmol C m−2 d−1). At the two stations where LSB were observed, produced hydrogen sulfide was almost completely oxidized by LSB using nitrate as the electron acceptor. Modeled rates of nitrate reduction to N2 by LSB were over two times higher than nitrate reduction to ammonium. This points toward a potential negative feedback by LSB on primary production. Furthermore, loss of fixed N strongly enriched the benthic fluxes in P relative to N. Although the model included intracellular polyphosphate accumulation by LSB and subsequent breakdown to phosphate, a clear link between polyphosphate dynamics and hydroxyapatite precipitation and burial could not be clearly substantiated. This is partly due to simplifying assumptions in the model and analytical uncertainties in distinguishing between authigenic hydroxyapatite and allochthonous hydroxyapatite (e.g., fish bones), both of which are major components of particulate P in the BUS. Our modeling suggests a significant control of LSB on benthic N and P fluxes to the water column. Given the extensive coverage of LSB on the shelf (>30,000 km2), more accurate forecasts of nutrient cycling and primary production in the BUS necessitate a closer inspection of benthic P sources and sinks in the mud belt and a clearer understanding of the controls on the end product of nitrate reduction by LSB.
Novel injectable calcium phosphate scaffold with human periodontal ligament stem cell encapsulation in microbeads for bone regeneration
Authors: Qiu Gengtao , Huang Mingguang , Ke Difeng , Liu Jin , Weir Michael D. , Ma Tao , Wang Ping , Oates Thomas W. , Schneider Abraham , Xia Yang , Xu Hockin H. K. , Zhao Liang
Published: November 2022

Objectives: 1) Develop a novel construct of human periodontal ligament stem cells (hPDLSCs) encapsulated in degradable alginate microbeads (DAMB) with human platelet lysate (hPL) and injectable calcium phosphate cement (ICPC); 2) Investigate the proliferation and osteogenic differentiation of hPDLSCs in ICPC with hPL as a xeno-free supplement and animal serum replacement for bone tissue engineering applications.

Methods: hPDLSCs were encapsulated in alginate-fibrin microbeads (DAMB + fibrin), alginate-hPL degradable microbeads (DAMB + hPL), or alginate-fibrin-hPL microbeads (DAMB + fibrin + hPL). The proliferation and osteogenic differentiation of hPDLSCs were investigated in culturing with the ICPC scaffold.

Results: Flexural strength of ICPC was 8.4 ± 0.91 MPa, and elastic modulus was 1.56 ± 0.1 GPa, exceeding those of cancellous bone. hPDLSCs had higher viability in DAMB + fibrin + hPL group than in DAMB + fibrin. ALP was 69.97 ± 16.96 mU/mg for ICPC + DAMB + fibrin + hPL group, higher than 30.68 ± 2.86 mU/mg of ICPC + DAMB + fibrin (p < 0.05) and 4.12 ± 1.65 mU/mg of control (p < 0.01). At 7 days, osteogenic gene expressions (ALP, RUNX2, COL1, and OPN) in ICPC + DAMB + fibrin + hPL and ICPC + DAMB + fibrin were 4–11 folds that of control. At 21 days, the hPDLSC-synthesized bone mineral amounts in ICPC + DAMB + fibrin + hPL and ICPC + DAMB + fibrin were 13.2 folds and 11.1 folds that of control group, respectively.

Conclusion: The novel injectable CPC scaffold encapsulating hPDLSCs and hPL is promising to protect and deliver hPDLSCs. The hPL-based medium significantly enhanced the osteogenic differentiation of hPDLSCs in ICPC + DAMB + fibrin + hPL construct, suggesting a promising xeno-free approach for bone tissue regeneration applications.
Follicular dendritic cell differentiation is associated with distinct synovial pathotype signatures in rheumatoid arthritis
Authors: El Shikh Mohey Eldin M. , El Sayed Riham , Aly Nesreen Amer Ramadan , Prediletto Edoardo , Hands Rebecca , Fossati-Jimack Liliane , Bombardieri Michele , Lewis Myles J. , Pitzalis Costantino
Published: November 2022

Follicular dendritic cells (FDCs) fundamentally contribute to the formation of synovial ectopic lymphoid-like structures in rheumatoid arthritis (RA) which is associated with poor clinical prognosis. Despite this critical role, regulation of FDC development in the RA synovium and its correlation with synovial pathotype differentiation remained largely unknown. Here, we demonstrate that CNA.42+FDCs distinctively express the pericyte/fibroblast-associated markers PDGFR-β, NG2, and Thy-1 in the synovial perivascular space but not in established follicles. In addition, synovial RNA-Seq analysis revealed that expression of the perivascular FDC markers was strongly correlated with PDGF-BB and fibroid synovitis, whereas TNF-α/LT-β was significantly associated with lymphoid synovitis and expression of CR1, CR2, and FcγRIIB characteristic of mature FDCs in lymphoid follicles. Moreover, PDGF-BB induced CNA.42+FDC differentiation and CXCL13 secretion from NG2+synovial pericytes, and together with TNF-α/LT-β conversely regulated early and late FDC differentiation genes in unsorted RA synovial fibroblasts (RASF) and this was confirmed in flow sorted stromal cell subsets. Furthermore, RASF TNF-αR expression was upregulated by TNF-α/LT-β and PDGF-BB; and TNF-α/LT-β-activated RASF retained ICs and induced B cell activation inin vitrogerminal center reactions typical of FDCs. Additionally, FDCs trapped peptidyl citrulline, and strongly correlated with IL-6 expression, and plasma cell, B cell, and T cell infiltration of the RA synovium. Moreover, synovial FDCs were significantly associated with RA disease activity and radiographic features of tissue damage. To the best of our knowledge, this is the first report describing the reciprocal interaction between PDGF-BB and TNF-α/LT-β in synovial FDC development and evolution of RA histological pathotypes. Selective targeting of this interplay could inhibit FDC differentiation and potentially ameliorate RA in clinically severe and drug-resistant patients.
MP-VHPPI: Meta predictor for viral host protein-protein interaction prediction in multiple hosts and viruses
Authors: Asim Muhammad Nabeel , Fazeel Ahtisham , Ibrahim Muhammad Ali , Dengel Andreas , Ahmed Sheraz
Published: November 2022

Viral-host protein-protein interaction (VHPPI) prediction is essential to decoding molecular mechanisms of viral pathogens and host immunity processes that eventually help to control the propagation of viral diseases and to design optimized therapeutics. Multiple AI-based predictors have been developed to predict diverse VHPPIs across a wide range of viruses and hosts, however, these predictors produce better performance only for specific types of hosts and viruses. The prime objective of this research is to develop a robust meta predictor (MP-VHPPI) capable of more accurately predicting VHPPI across multiple hosts and viruses. The proposed meta predictor makes use of two well-known encoding methods Amphiphilic Pseudo-Amino Acid Composition (APAAC) and Quasi-sequence (QS) Order that capture amino acids sequence order and distributional information to most effectively generate the numerical representation of complete viral-host raw protein sequences. Feature agglomeration method is utilized to transform the original feature space into a more informative feature space. Random forest (RF) and Extra tree (ET) classifiers are trained on optimized feature space of both APAAC and QS order separate encoders and by combining both encodings. Further predictions of both classifiers are utilized to feed the Support Vector Machine (SVM) classifier that makes final predictions. The proposed meta predictor is evaluated over 7 different benchmark datasets, where it outperforms existing VHPPI predictors with an average performance of 3.07, 6.07, 2.95, and 2.85% in terms of accuracy, Mathews correlation coefficient, precision, and sensitivity, respectively. To facilitate the scientific community, the MP-VHPPI web server is available at https://sds_genetic_analysis.opendfki.de/MP-VHPPI/.
Pleural involvements in pulmonary sarcoidosis: A case report and review of the literature
Authors: Ji Xiaoqing , Lu Jiameng , Zuo Anli , Sun Fei , Peng Haiying , Lu Degan
Published: November 2022

As a chronic and multisystemic granulomatosis of unknown origin, sarcoidosis can affect multiple organs throughout the body with variable progression and prognosis. Sarcoidosis may present with a battery of symptoms and signs, such as dyspnea, non-productive cough, uveitis, and erythema nodosum. Although the lungs and mediastinal lymph nodes are almost affected in sarcoidosis, involvements of the pleurae remain uncommon. Herein, we report a case of sarcoidosis with both pleural effusions and pleural nodules as confirmed by thoracoscopic pleural biopsy.
Sleep deprivation and immunoglobulin E level
Authors: Yang Shih-Wei , Yang Hui-Fang , Chen Yuan-Yuei , Chen Wei-Liang
Published: November 2022

Objectives

Sleep deprivation is a common issue for modern people and leads to many morbidities and mortality. Some papers also suspected the relationship between Immunoglobulin E (IgE) level and sleep deprivation. The purpose of this article is to make the vicious circle between serum IgE level and sleep deprivation clear.

Materials and methods

In this study, we included 4,460 population aged around 48 years old respective 2,145 males and 2,315 females enrolled in the National Health and Nutrition Examination Survey (NHANES). Sleep durations were recorded, in hours, in whole numbers by the participants. The levels of total IgE were measured by anti-IgE. All procedures were analyzed using SPSS version 18 (SPSS, Inc., Chicago, IL, USA).

Result

The statistical significance between higher IgE level and≤5 h sleep duration was noted (Beta coefficients: 64.04, 95% confidence interval (CI): 2.35, 125.72,P= 0.042). In sex difference, the correlation between short sleep duration and high serum IgE levels was noted in male [Beta coefficients: 120.225 (P= 0.008)] but not in female. There were no positive findings in the ethnicity-based correlation between serum IgE levels and sleep duration.

Conclusion

This study indicated that short sleep duration (≤5 h) is associated with higher serum IgE levels, especially in men. Further longitudinal investigations concerning the effect of sleep deprivation on serum IgE might provide a better explanation for the pathophysiology underlying autoimmune disease and sleep deprivation.
Tuberculosis and COVID-19 co-infection in Serbia: Pandemic challenge in a low-burden country
Authors: Adzic-Vukicevic Tatjana , Stosic Maja , Antonijevic Gordana , Jevtic Miroslav , Radovanovic-Spurnic Aleksandra , Velickovic Jelena
Published: November 2022

Introduction

COVID-19 and tuberculosis (TB) represent global threats to the public health system. The impact of COVID-19 on TB results in a reduction in the number of notified TB cases, delayed diagnosis and treatment, and increased case fatality and mortality rates. The aim of the study was to analyze the TB/COVID-19 co-infected cohort in Serbia as a low-burden country and compare it to the global TB/COVID-19 cohort.

Methods

A retrospective analysis was done on 53 TB and COVID-19 co-infected patients treated in COVID hospital “Batajnica” in Belgrade and Special Hospital for Pulmonary Diseases “Ozren” Sokobanja in the period from 6 March 2020 to 1 April 2022. A comparative analysis with the global cohort published recently was also performed.

Results

TB/COVID-19 cohort in Serbia included significantly fewer migrants and diabetes cases, but more cases with chronic respiratory diseases compared to the global. Descriptive analysis of TB cases in the Serbian TB/COVID-19 cohort showed fewer cases diagnosed with sputum smear and Gene Xpert/HAIN, fewer EPTB and mono-resistant cases, and more cases diagnosed with solid culture, unilateral pulmonary infiltrate (with bilateral cavity lesions), and bilateral pulmonary infiltrate (no cavities) compared to TB/COVID-19 cases worldwide. Nasal congestion and fever were more common COVID-19 symptoms in the global cohort. Radiology was more commonly used for the diagnosis of COVID-19 in Serbia. Typical bilateral ground opacities were less common among Serbian patients. Serbian patients spent fewer days in the hospital and achieved a higher PCR conversion rate and TB treatment success rate.

Conclusion

The Serbian TB/COVID-19 cohort achieved a higher treatment success rate compared to the global cohort. Encouraging vaccination against SARS-CoV-2 for people with a current or past TB disease, as well as rapid diagnosis and targeted treatment of TB in highly specialized pulmonology institutions, presents key points to avoid excessive morbidity and mortality.
The impact of “To Err Is Human” on patient safety in anesthesiology. A bibliometric analysis of 20 years of research
Authors: Neuhaus Christopher , Grawe Petra , Bergström Johan , St.Pierre Michael
Published: November 2022

Background

Patient safety gained public notoriety following the 1999 report of the Institute of Medicine: To Err is Human – Building a Safer Health System which summarized a culminated decades' worth of research that had so far been largely ignored. The aim of this study was to analyze the report's impact on patient safety research in anesthesiology.

Methods

A bibliometric analysis was performed on all anesthesiologic publications from 2000 to 2019 that referenced To Err Is Human. In bibliometric literature, references are understood to represent an author's conscious decision to express a relationship between his own manuscript and the cited document.

Results

The anesthesiologic data base contained 1.036 publications. The journal with the most references to the IOM report is Anesthesia & Analgesia. By analyzing author keywords and patterns of collaboration, changes in the patient safety debate and its core themes in anesthesiology over time could be visualized. The generic notion of “error,” while initially a central topic in the scientific discourse, was subsequently replaced by terms representing a more granular, team-oriented, and educational approach. Patient safety research in anesthesia, while profiting from a certain intellectual and conceptual head start, showed a discursive shift toward more managerial, quality-management related topics as observed in the health care system as a whole.

Conclusions

Over the last 20 years, the research context expanded from the initial focus set forth by the IOM report, which ultimately led to an underrepresentation of research on critical incident reporting and systemic approaches to safety. Important collaborations with safety researchers from outside of health care dating back to the 1990's were gradually reduced, while previous research within anesthesiology was aligned with a broader, more managerial patient safety agenda.
Nocardiosis: A two-center analysis of clinical characteristics
Authors: Wang Lumin , Xu Yijiao , Chen Zhisheng , Jiang Weiwen , Xiao Xiong , Shen Yun , Ye Yanrong
Published: November 2022

Objective

The objective of the present study was to describe and analyze the clinical characteristics of nocardiosis.

Materials and methods

We described and analyzed the clinical characteristics of nocardiosis cases from two centers over the past 5 years from the following aspects: age and sex, Nocardia species, sites of Nocardia infection, test specimens, detection methods, concurrent pathogens, symptoms, imaging features, co-conditions, drug susceptibility tests, antibiotic therapy/duration, outcomes, and follow-up.

Results

The median age of the 19 cases was 64 years, with an interquartile range (IQR) of 56–68 years. Eight cases (42.1%) were immunocompromised [those who had been on corticosteroid use (62.5%), those who had used immunosuppressants (50.0%), or those who had suffered from chronic nephrosis (37.5%) or diabetes mellitus (DM) (25.0%)]. The plethora of comorbidities of these cases included diabetes (10.5%), chronic kidney disease (CDK) (15.8%), chronic lung disease (36.8%), and rheumatic diseases (10.5%). Cough and expectoration (73.7%) was the most common symptom of nocardiosis. The respiratory tract (89.5%) was the most common site of the clinical disease. Nearly half (9 cases, 47.3%) of these patients had concurrent infections. The most common Nocardia isolation site was the respiratory tract (73.7%). All patients were given antibiotic therapies, out of whom as many as 63.6% of patients were treated with two concurrent antimicrobial agents, 15.8% of patients were treated under monotherapy and 21.1% of patients were treated with three or more concurrent antimicrobial agents.

Conclusions

An uncommon life-threatening infection, nocardiosis, affects those patients with structural lung disease or immunosuppression. Although nocardiosis is capable of progressing into a serious and metastatic disease, early recognition and prompt treatment usually result in successful outcomes benefitting the patient.
Cow’s microbiome from antepartum to postpartum: A long-term study covering two physiological challenges
Authors: Tröscher-Mußotter Johanna , Deusch Simon , Borda-Molina Daniel , Frahm Jana , Dänicke Sven , Camarinha-Silva Amélia , Huber Korinna , Seifert Jana
Published: November 2022

Little is known about the interplay between the ruminant microbiome and the host during challenging events. This long-term study investigated the ruminal and duodenal microbiome and metabolites during calving as an individual challenge and a lipopolysaccharide-induced systemic inflammation as a standardized challenge. Strong inter- and intra-individual microbiome changes were noted during the entire trial period of 168 days and between the 12 sampling time points.Bifidobacteriumincreased significantly at 3 days after calving. Both challenges increased the intestinal abundance of fiber-associated taxa, e.g.,Butyrivibrioand unclassifiedRuminococcaceae. NMR analyses of rumen and duodenum samples identified up to 60 metabolites out of which fatty and amino acids, amines, and urea varied in concentrations triggered by the two challenges. Correlation analyses between these parameters indicated a close connection and dependency of the microbiome with its host. It turns out that the combination of phylogenetic with metabolite information supports the understanding of the true scenario in the forestomach system. The individual stages of the production cycle in dairy cows reveal specific criteria for the interaction pattern between microbial functions and host responses.
An optimized approach and inflation media for obtaining complimentary mass spectrometry-based omics data from human lung tissue
Authors: Lukowski Jessica K. , Olson Heather , Velickovic Marija , Wang Juan , Kyle Jennifer E. , Kim Young-Mo , Williams Sarah M. , Zhu Ying , Huyck Heidi L. , McGraw Matthew D. , Poole Cory , Rogers Lisa , Misra Ravi , Alexandrov Theodore , Ansong Charles , Pryhuber Gloria S. , Clair Geremy , Adkins Joshua N. , Carson James P. , Anderton Christopher R.
Published: November 2022

Human disease states are biomolecularly multifaceted and can span across phenotypic states, therefore it is important to understand diseases on all levels, across cell types, and within and across microanatomical tissue compartments. To obtain an accurate and representative view of the molecular landscape within human lungs, this fragile tissue must be inflated and embedded to maintain spatial fidelity of the location of molecules and minimize molecular degradation for molecular imaging experiments. Here, we evaluated agarose inflation and carboxymethyl cellulose embedding media and determined effective tissue preparation protocols for performing bulk and spatial mass spectrometry-based omics measurements. Mass spectrometry imaging methods were optimized to boost the number of annotatable molecules in agarose inflated lung samples. This optimized protocol permitted the observation of unique lipid distributions within several airway regions in the lung tissue block. Laser capture microdissection of these airway regions followed by high-resolution proteomic analysis allowed us to begin linking the lipidome with the proteome in a spatially resolved manner, where we observed proteins with high abundance specifically localized to the airway regions. We also compared our mass spectrometry results to lung tissue samples preserved using two other inflation/embedding media, but we identified several pitfalls with the sample preparation steps using this preservation method. Overall, we demonstrated the versatility of the inflation method, and we can start to reveal how the metabolome, lipidome, and proteome are connected spatially in human lungs and across disease states through a variety of different experiments.
Wall-free droplet microfluidics for probing biological processes by high-brilliance X-ray scattering techniques
Authors: Marinaro G. , Graceffa R. , Riekel C.
Published: November 2022

Here we review probing biological processes initiated by the deposition of droplets on surfaces by micro- and nanobeam X-ray scattering techniques using synchrotron radiation and X-ray free-electron laser sources. We review probing droplet evaporation on superhydrophobic surfaces and reactions with substrates, basics of droplets deposition and flow simulations, droplet deposition techniques and practical experience at a synchrotron beamline. Selected applications with biological relevance will be reviewed and perspectives for the latest generation of high-brilliance X-ray sources discussed.
Tetrazine bioorthogonal chemistry derived in vivo imaging
Authors: Zhao Gaoxiang , Li Zhutie , Zhang Renshuai , Zhou Liman , Zhao Haibo , Jiang Hongfei
Published: November 2022

Bioorthogonal chemistry represents plenty of highly efficient and biocompatible reactions that proceed selectively and rapidly in biological situations without unexpected side reactions towards miscellaneous endogenous functional groups. Arise from the strict demands of physiological reactions, bioorthogonal chemical reactions are natively selective transformations that are rarely found in biological environments. Bioorthogonal chemistry has long been applied to tracking and real-time imaging of biomolecules in their physiological environments. Thereinto, tetrazine bioorthogonal reactions are particularly important and have increasing applications in these fields owing to their unique properties of easily controlled fluorescence or radiation off-on mechanism, which greatly facilitate the tracking of real signals without been disturbed by background. In this mini review, tetrazine bioorthogonal chemistry for in vivo imaging applications will be attentively appraised to raise some guidelines for prior tetrazine bioorthogonal chemical studies.
A morphometric analysis of the circumolivary fiber bundle of the human brainstem
Authors: Brendel Victor A. , Schmeisser Michael J. , Schumann Sven
Published: November 2022

The circumolivary fiber bundle (CFB) is considered to be an anatomical variation, which can be found on the surface of the human medulla oblongata. The macroscopical fiber bundle runs downwards from either the anterior median fissure, the pyramid, or both, around the inferior pole of the olive and turns upwards to reach the restiform body of the inferior cerebellar peduncle. Multiple fiber systems feed the constitution of the CFB (collateral corticospinal fibers, fibers connecting to the reticular formation, anterior external arcuate fibers). With this examination we provide a systematic analysis of the frequency of occurrence (6.14%), size, and laterality of the CFB. Including all three fiber bundle parts (descending part, genu, and ascending part), the left-sided sizes were increased. Likewise, the appearance of an unilateral left-sided CFB could be detected in more than 60% of our cases. Our morphometrical analysis currently covers the largest sample of investigated brainstem sides (n = 489) so far. This investigation should widen the perspective on how anatomists, neuroradiologists, and neurosurgeons expect the anterolateral surface of the human medulla oblongata.
The comparison of electroencephalography power and event related potential in success and failure during multitask game
Authors: Sanuki Fumiya , Nakphu Nonthaporn , Tahara Ayumi , Iramina Keiji
Published: November 2022

The first game-based treatment for children with attention-deficit hyperactivity disorder (ADHD) was approved by the United States Food and Drug Administration (FDA) in 2020. This game was developed for use at home as part of everyday training and can be used along with one’s usual training plan. In this game, two tasks are performed in parallel: (1) a perceptual discrimination targeting task (response and not response and avoiding responding to sudden pop-up targets) and (2) a sensory-motor navigation task (players continuously adjust their location to interact with or avoid positional targets). However, the brain activity of people playing this game was not examined, and the immersive environment (3D virtual world) was not considered. Therefore, we aimed to develop a system to investigate brain activity using electroencephalography (EEG) during multitask gameplay in virtual reality (VR). In this experiment, we focused on the difference between the success and failure of the Go/No-Go task in a multitask game. We created a color discrimination task and a target tracking task in VR. The content of this game task was designed using previous multitask training. EEG and event data were recorded. Using event data, we can analyze the data in detail. We divided the trial types (Go and No-Go) and results (success and failure). We then compared the success and failure of each task. In the Go trial, the relative theta power in success at Fz was significantly higher than that of failure. However, no difference in power was observed in the No-Go trial. On the other hand, theta power was no different between success and failure in the other task. These results of the Go trial suggest that the participants were attentive to processing both tasks. Thus, it is possible that theta power in the frontal area 1 s before stimulation could predict the success or failure of the Go trial. On the other hand, the results of the No-Go trial may be due to the low number of No-Go failure trials and the fact that stimulus oversight is one of the factors for success.
A detection method of the rescue targets in the marine casualty based on improved YOLOv5s
Authors: Bai Jing , Dai Jiacheng , Wang Zhongchao , Yang Shujie
Published: November 2022

In recent years, with the deep exploitation of marine resources and the development of maritime transportation, ship collision accidents occur frequently, which leads to the increasingly heavy task of maritime Search and Rescue (SAR). Unmanned Aerial Vehicles (UAVs) have the advantages of flexible maneuvering, robust adaptability and extensive monitoring, which have become an essential means and tool for emergency rescue of maritime accidents. However, the current UAVs-based drowning people detection technology has insufficient detection ability and low precision for small targets in high-altitude images. Moreover, limited by the load capacity, UAVs do not have enough computing power and storage space, resulting in the existing object detection algorithms based on deep learning cannot be directly deployed on UAVs. To solve the two issues mentioned above, this paper proposes a lightweight deep learning detection model based on YOLOv5s, which is used in the SAR task of drowning people of UAVs at sea. First, an extended small object detection layer is added to improve the detection effect of small objects, including the extraction of shallow features, a new feature fusion layer and one more prediction head. Then, the Ghost module and the C3Ghost module are used to replace the Conv module and the C3 module in YOLOv5s, which enable lightweight network improvements that make the model more suitable for deployment on UAVs. The experimental results indicate that the improved model can effectively identify the rescue targets in the marine casualty. Specifically, compared with the original YOLOv5s, the improved model mAP@0.5 value increased by 2.3% and the mAP@0.5:0.95 value increased by 1.1%. Meanwhile, the improved model meets the needs of the lightweight model. Specifically, compared with the original YOLOv5s, the parameters decreased by 44.9%, the model weight size compressed by 39.4%, and Floating Point Operations (FLOPs) reduced by 22.8%.
A theoretical model reveals specialized synaptic depressions and temporal frequency tuning in retinal parallel channels
Authors: He Liuyuan , He Yutao , Ma Lei , Huang Tiejun
Published: November 2022

In the Outer Plexiform Layer of a retina, a cone pedicle provides synaptic inputs for multiple cone bipolar cell (CBC) subtypes so that each subtype formats a parallelized processing channel to filter visual features from the environment. Due to the diversity of short-term depressions among cone-CBC contacts, these channels have different temporal frequency tunings. Here, we propose a theoretical model based on the hierarchy Linear-Nonlinear-Synapse framework to link the synaptic depression and the neural activities of the cone-CBC circuit. The model successfully captures various frequency tunings of subtype-specialized channels and infers synaptic depression recovery time constants inside circuits. Furthermore, the model can predict frequency-tuning behaviors based on synaptic activities. With the prediction of region-specialized UV cone parallel channels, we suggest the acute zone in the zebrafish retina supports detecting light-off events at high temporal frequencies.
Use of person-centered goals to direct interdisciplinary care for military service members and Veterans with chronic mTBI and co-occurring psychological conditions
Authors: Wallace Tracey D. , McCauley Katherine L. , Hodge April T. , Moran Tim P. , Porter Stephen T. , Whaley Maya C. , Gore Russell K.
Published: November 2022

Objective

To explore the use of person-centered goals (PCGs) to direct interdisciplinary care to support PCG attainment in military service members and Veterans (SM/Vs) with chronic mild traumatic brain injury (mTBI) and co-occurring psychological conditions.

Methods

A retrospective chart review was completed for 146 United States military SM/Vs reporting chronic symptoms following mTBI and co-occurring psychological conditions who received care in the SHARE Military Initiative intensive outpatient program, a donor-funded program administered by a not-for-profit hospital, between April 1, 2015 and March 31, 2019. PCGs were used to direct care consisting of individual and group-based interventions and therapies delivered by an interdisciplinary, co-located team including behavioral health, case management, neurology or physiatry, nursing, occupational therapy, physical therapy, recreation therapy, speech-language pathology, and transition support. The primary outcome measure was PCG attainment measured via goal attainment scaling.

Results

Increased PCG attainment was demonstrated at program discharge and throughout the first year following program discharge. Predictors of goal attainment at discharge included longer participation in treatment, greater reduction in depressive symptoms and greater improvement in adjustment at discharge, male gender, and higher cognitive and physical abilities on admission.

Conclusions

This sample of military SM/Vs with mTBI and co-occurring psychological conditions who received intensive, interdisciplinary, PCG directed care demonstrated increased PCG attainment at program discharge which further increased with transition support over the year post-discharge. Results suggest PGC goal directed care is a feasible, promising methodology of individualizing treatment in this population. This exploratory study lays a foundation for future prospective, controlled, comparative effectiveness research that will further understanding of the effectiveness of intensive, interdisciplinary, PCG directed care.
The impact of early aging on visual perception of space and time
Authors: Incao Sara , Mazzola Carlo , Sciutti Alessandra
Published: November 2022

Visual perception of space and time has been shown to rely on context dependency, an inferential process by which the average magnitude of a series of stimuli previously experienced acts as a prior during perception. This article aims to investigate the presence and evolution of this phenomenon in early aging. Two groups of participants belonging to two different age ranges (Young Adults: average age 28.8 years old; Older Adults: average age 62.8 years old) participated in the study performing a discrimination and a reproduction task, both in a spatial and temporal conditions. In particular, they were asked to evaluate lengths in the spatial domain and interval durations in the temporal one. Early aging resulted to be associated to a general decline of the perceptual acuity, which is particularly evident in the temporal condition. The context dependency phenomenon was preserved also during aging, maintaining similar levels as those exhibited by the younger group in both space and time perception. However, the older group showed a greater variability in context dependency among participants, perhaps due to different strategies used to face a higher uncertainty in the perceptual process.
The inhibition of NCS-1 binding to Ric8a rescues fragile X syndrome mice model phenotypes
Authors: Cogram Patricia , Fernández-Beltrán Luis C. , Casarejos María José , Sánchez-Yepes Sonia , Rodríguez-Martín Eulalia , García-Rubia Alfonso , Sánchez-Barrena María José , Gil Carmen , Martínez Ana , Mansilla Alicia
Published: November 2022

Fragile X syndrome (FXS) is caused by the loss of function of Fragile X mental retardation protein (FMRP). FXS is one of the leading monogenic causes of intellectual disability (ID) and autism. Although it is caused by the failure of a single gene, FMRP that functions as an RNA binding protein affects a large number of genes secondarily. All these genes represent hundreds of potential targets and different mechanisms that account for multiple pathological features, thereby hampering the search for effective treatments. In this scenario, it seems desirable to reorient therapies toward more general approaches. Neuronal calcium sensor 1 (NCS-1), through its interaction with the guanine-exchange factor Ric8a, regulates the number of synapses and the probability of the release of a neurotransmitter, the two neuronal features that are altered in FXS and other neurodevelopmental disorders. Inhibitors of the NCS-1/Ric8a complex have been shown to be effective in restoring abnormally high synapse numbers as well as improving associative learning in FMRP mutant flies. Here, we demonstrate that phenothiazine FD44, an NCS-1/Ric8a inhibitor, has strong inhibition ability in situ and sufficient bioavailability in the mouse brain. More importantly, administration of FD44 to two different FXS mouse models restores well-known FXS phenotypes, such as hyperactivity, associative learning, aggressive behavior, stereotype, or impaired social approach. It has been suggested that dopamine (DA) may play a relevant role in the behavior and in neurodevelopmental disorders in general. We have measured DA and its metabolites in different brain regions, finding a higher metabolic rate in the limbic area, which is also restored with FD44 treatment. Therefore, in addition to confirming that the NCS-1/Ric8a complex is an excellent therapeutic target, we demonstrate the rescue effect of its inhibitor on the behavior of cognitive and autistic FXS mice and show DA metabolism as a FXS biochemical disease marker.