bluuebunny/crossref_metadata_2025 huggingface dataset:
Radiomics based on HRCT can predict RP-ILD and mortality in anti-MDA5 + dermatomyositis patients: a multi-center retrospective study
Authors: He Wenzhang , Cui Beibei , Chu Zhigang , Chen Xiaoyi , Liu Jing , Pang Xueting , Huang Xuan , Yin Hongkun , Lin Hui , Peng Liqing
Published: June 2024

Objectives

To assess the effectiveness of HRCT-based radiomics in predicting rapidly progressive interstitial lung disease (RP-ILD) and mortality in anti-MDA5 positive dermatomyositis-related interstitial lung disease (anti-MDA5 + DM-ILD).

Methods

From August 2014 to March 2022, 160 patients from Institution 1 were retrospectively and consecutively enrolled and were randomly divided into the training dataset (n = 119) and internal validation dataset (n = 41), while 29 patients from Institution 2 were retrospectively and consecutively enrolled as external validation dataset. We generated four Risk-scores based on radiomics features extracted from four areas of HRCT. A nomogram was established by integrating the selected clinico-radiologic variables and the Risk-score of the most discriminative radiomics model. The RP-ILD prediction performance of the models was evaluated by using the area under the receiver operating characteristic curves, calibration curves, and decision curves. Survival analysis was conducted with Kaplan-Meier curves, Mantel-Haenszel test, and Cox regression.

Results

Over a median follow-up time of 31.6 months (interquartile range: 12.9–49.1 months), 24 patients lost to follow-up and 46 patients lost their lives (27.9%, 46/165). The Risk-score based on bilateral lungs performed best, attaining AUCs of 0.869 and 0.905 in the internal and external validation datasets. The nomogram outperformed clinico-radiologic model and Risk-score with AUCs of 0.882 and 0.916 in the internal and external validation datasets. Patients were classified into low- and high-risk groups with 50:50 based on nomogram. High-risk group patients demonstrated a significantly higher risk of mortality than low-risk group patients in institution 1 (HR = 4.117) and institution 2 cohorts (HR = 7.515).

Conclusion

For anti-MDA5 + DM-ILD, the nomogram, mainly based on radiomics, can predict RP-ILD and is an independent predictor of mortality.
Chronic obstructive pulmonary disease affects outcome in surgical patients with perioperative organ injury: a retrospective cohort study in Germany
Authors: Hochhausen Nadine , Mechelinck Mare , Kroh Andreas , Rossaint Rolf , Kork Felix
Published: June 2024

Background

The impact of chronic obstructive pulmonary disease (COPD) on outcome in perioperative organ injury (POI) has not yet been investigated sufficiently.

Methods

This retrospective cohort study analysed data of surgical patients with POI, namely delirium, stroke, acute myocardial infarction, acute respiratory distress syndrome, acute liver injury (ALI), or acute kidney injury (AKI), in Germany between 2015 and 2019. We compared in-hospital mortality, hospital length of stay (HLOS) and perioperative ventilation time (VT) in patients with and without COPD.

Results

We analysed the data of 1,642,377 surgical cases with POI of which 10.8% suffered from COPD. In-hospital mortality was higher (20.6% vs. 15.8%, p < 0.001) and HLOS (21 days (IQR, 12–34) vs. 16 days (IQR, 10–28), p < 0.001) and VT (199 h (IQR, 43–547) vs. 125 h (IQR, 32–379), p < 0.001) were longer in COPD patients. Within the POI examined, AKI was the most common POI (57.8%), whereas ALI was associated with the highest mortality (54.2%). Regression analysis revealed that COPD was associated with a slightly higher risk of in-hospital mortality (OR, 1.19; 95% CI:1.18–1.21) in patients with any POI.

Conclusions

COPD in patients with POI is associated with higher mortality, longer HLOS and longer VT. Especially patients suffering from ALI are susceptible to the detrimental effects of COPD on adverse outcome.
EfficientNet-based machine learning architecture for sleep apnea identification in clinical single-lead ECG signal data sets
Authors: Liu Meng-Hsuan , Chien Shang-Yu , Wu Ya-Lun , Sun Ting-Hsuan , Huang Chun-Sen , Hsu Kai-Cheng , Hang Liang-Wen
Published: June 2024

Objective

Our objective was to create a machine learning architecture capable of identifying obstructive sleep apnea (OSA) patterns in single-lead electrocardiography (ECG) signals, exhibiting exceptional performance when utilized in clinical data sets.

Methods

We conducted our research using a data set consisting of 1656 patients, representing a diverse demographic, from the sleep center of China Medical University Hospital. To detect apnea ECG segments and extract apnea features, we utilized the EfficientNet and some of its layers, respectively. Furthermore, we compared various training and data preprocessing techniques to enhance the model’s prediction, such as setting class and sample weights or employing overlapping and regular slicing. Finally, we tested our approach against other literature on the Apnea-ECG database.

Results

Our research found that the EfficientNet model achieved the best apnea segment detection using overlapping slicing and sample-weight settings, with an AUC of 0.917 and an accuracy of 0.855. For patient screening with AHI > 30, we combined the trained model with XGBoost, leading to an AUC of 0.975 and an accuracy of 0.928. Additional tests using PhysioNet data showed that our model is comparable in performance to existing models regarding its ability to screen OSA levels.

Conclusions

Our suggested architecture, coupled with training and preprocessing techniques, showed admirable performance with a diverse demographic dataset, bringing us closer to practical implementation in OSA diagnosis.

Trial registration The data for this study were collected retrospectively from the China Medical University Hospital in Taiwan with approval from the institutional review board CMUH109-REC3-018.
Diurnal variation of heart rate variability in individuals with spinal cord injury
Authors: Saengsuwan Jittima , Ruangsuphaphichat Arphatsorn , Brockmann Lars , Sirasaporn Patpiya , Manimmanakorn Nuttaset , Hunt Kenneth J.
Published: June 2024

Background

Heart rate variability (HRV) may provide objective information about cardiogenic autonomic balance in individuals with spinal cord injury (SCI). The aim of this study was to characterize the diurnal variation of HRV in individuals with SCI at lesion level T6 and above and lesion level below T6.

Methods

This was a retrospective analysis of a prior cross-sectional study. Individuals with chronic SCI underwent 24 h recording of the time between consecutive R waves (RR interval) to derive parameters of HRV as follows: standard deviation of all normal-to-normal R–R intervals (SDNN) and square root of the mean of the squared differences between successive R–R intervals (RMSSD) (time domain); and high frequency power (HF), low-frequency power (LF), very low frequency power (VLF), ultra-low frequency power (ULF) and total power (TP) (frequency domain). Changes in the magnitude of HRV outcomes over the 24 h period were investigated using a novel multi-component cosinor model constrained to the form of a three-harmonic Fourier series.

Results

Participants were grouped as lesion level T6 and above (n = 22) or below T6 (n = 36). Most of them were male (n = 40, 69%) and the median age (interquartile range) was 50.5 (28) years. Both groups exhibited similar diurnal patterns in most HRV metrics. The lowest values occurred in the late afternoon (4–6 pm) and gradually increased, peaking around midnight to early morning (1–6 am). Exceptions included RMSSD, which peaked before midnight, and ULF, which showed a double peak pattern that peaked from 11 am to 1 pm and 4–6 am in participants with lesion level at T6 and above. The HRV values in participants with lesion level T6 and above were generally lower than participants with lesion level below T6, except for peak values of RMSSD, HF and LF.

Conclusion

This study demonstrated substantial diurnal variation of HRV in participants with SCI in both groups of participants. In clinical and research settings, diurnal variations in HRV must be taken into consideration.
Successful management of chromoblastomycosis utilizing conventional antifungal agents and imiquimod therapy
Authors: Zheng Jinjin , Liu Shougang , Xie Zhenmou , Chen Yangxia , Xi Liyan , Liu Hongfang , Liu Yinghui
Published: June 2024

Chromoblastomycosis (CBM), a chronic fungal infection affecting the skin and subcutaneous tissues, is predominantly caused by dematiaceous fungi in tropical and subtropical areas. Characteristically, CBM presents as plaques and nodules, often leading to scarring post-healing. Besides traditional diagnostic methods such as fungal microscopy, culture, and histopathology, dermatoscopy and reflectance confocal microscopy can aid in diagnosis. The treatment of CBM is an extended and protracted process. Imiquimod, acting as an immune response modifier, boosts the host’s immune response against CBM, and controls scar hyperplasia, thereby reducing the treatment duration. We present a case of CBM in Guangdong with characteristic reflectance confocal microscopy manifestations, effectively managed through a combination of itraconazole, terbinafine, and imiquimod, shedding light on novel strategies for managing this challenging condition.
A novel role for KIFC1-MYH9 interaction in triple-negative breast cancer aggressiveness and racial disparity
Authors: Garlapati Chakravarthy , Joshi Shriya , Yang Chunhua , Chandrashekar Darshan Shimoga , Rida Padmashree , Aneja Ritu
Published: June 2024

African American (AA) women are twice as likely to develop triple-negative breast cancer (TNBC) as women of European descent. Additionally, AA women with TNBC present a much more aggressive disease course than their European American (EA) counterparts. Thus, there is an unmet clinical need to identify race-specific biomarkers and improve survival outcomes in AA patients with TNBC. The minus-end directed microtubule motor protein kinesin family member C1 (KIFC1) promotes centrosome clustering and chromosomal instability and is often overexpressed in TNBC. Previous findings suggest that KIFC1 plays a role in cell proliferation and migration in TNBC cells from AAs and that the levels of nuclear KIFC1 (nKIFC1) are particularly high in AA patients with TNBC. The nuclear localization of KIFC1 in interphase may underlie its previously unrecognized race-specific association. In this study, we found that in TNBC cells derived from AAs, nKIFC1 interacted with the tumor suppressor myosin heavy chain 9 (MYH9) over EA cells. Treatment of AA TNBC cells with commercial inhibitors of KIFC1 and MYH9 disrupted the interaction between KIFC1 and MYH9. To characterize the racial differences in the KIFC1-MYH9-MYC axis in TNBC, we established homozygous KIFC1 knockout (KO) TNBC cell lines. KIFC1 KO significantly inhibited proliferation, migration, and invasion in AA TNBC cells but not in EA TNBC cells. RNA sequencing analysis showed significant downregulation of genes involved in cell migration, invasion, and metastasis upon KIFC1 KO in TNBC cell lines from AAs compared to those from EAs. These data indicate that mechanistically, the role of nKIFC1 in driving TNBC progression and metastasis is stronger in AA patients than in EA patients, and that KIFC1 may be a critical therapeutic target for AA patients with TNBC.

Graphical abstract
Integrating DNA/RNA microbe detection and host response for accurate diagnosis, treatment and prognosis of childhood infectious meningitis and encephalitis
Authors: Xing Zhihao , Jiang Hanfang , Liu Xiaorong , Chai Qiang , Xin Zefeng , Zhu Chunqing , Bao Yanmin , Chen Hongyu , Gao Hongdan , Ma Dongli
Published: June 2024

Background

Infectious meningitis/encephalitis (IM) is a severe neurological disease that can be caused by bacterial, viral, and fungal pathogens. IM suffers high morbidity, mortality, and sequelae in childhood. Metagenomic next-generation sequencing (mNGS) can potentially improve IM outcomes by sequencing both pathogen and host responses and increasing the diagnosis accuracy.

Methods

Here we developed an optimized mNGS pipeline named comprehensive mNGS (c-mNGS) to monitor DNA/RNA pathogens and host responses simultaneously and applied it to 142 cerebrospinal fluid samples. According to retrospective diagnosis, these samples were classified into three categories: confirmed infectious meningitis/encephalitis (CIM), suspected infectious meningitis/encephalitis (SIM), and noninfectious controls (CTRL).

Results

Our pipeline outperformed conventional methods and identified RNA viruses such as Echovirus E30 and etiologic pathogens such as HHV-7, which would not be clinically identified via conventional methods. Based on the results of the c-mNGS pipeline, we successfully detected antibiotic resistance genes related to common antibiotics for treating Escherichia coli, Acinetobacter baumannii, and Group B Streptococcus. Further, we identified differentially expressed genes in hosts of bacterial meningitis (BM) and viral meningitis/encephalitis (VM). We used these genes to build a machine-learning model to pinpoint sample contaminations. Similarly, we also built a model to predict poor prognosis in BM.

Conclusions

This study developed an mNGS-based pipeline for IM which measures both DNA/RNA pathogens and host gene expression in a single assay. The pipeline allows detecting more viruses, predicting antibiotic resistance, pinpointing contaminations, and evaluating prognosis. Given the comparable cost to conventional mNGS, our pipeline can become a routine test for IM.
De novo assembly of transcriptomes and differential gene expression analysis using short-read data from emerging model organisms – a brief guide
Authors: Jackson Daniel J. , Cerveau Nicolas , Posnien Nico
Published: June 2024

Many questions in biology benefit greatly from the use of a variety of model systems. High-throughput sequencing methods have been a triumph in the democratization of diverse model systems. They allow for the economical sequencing of an entire genome or transcriptome of interest, and with technical variations can even provide insight into genome organization and the expression and regulation of genes. The analysis and biological interpretation of such large datasets can present significant challenges that depend on the ‘scientific status’ of the model system. While high-quality genome and transcriptome references are readily available for well-established model systems, the establishment of such references for an emerging model system often requires extensive resources such as finances, expertise and computation capabilities. The de novo assembly of a transcriptome represents an excellent entry point for genetic and molecular studies in emerging model systems as it can efficiently assess gene content while also serving as a reference for differential gene expression studies. However, the process of de novo transcriptome assembly is non-trivial, and as a rule must be empirically optimized for every dataset. For the researcher working with an emerging model system, and with little to no experience with assembling and quantifying short-read data from the Illumina platform, these processes can be daunting. In this guide we outline the major challenges faced when establishing a reference transcriptome de novo and we provide advice on how to approach such an endeavor. We describe the major experimental and bioinformatic steps, provide some broad recommendations and cautions for the newcomer to de novo transcriptome assembly and differential gene expression analyses. Moreover, we provide an initial selection of tools that can assist in the journey from raw short-read data to assembled transcriptome and lists of differentially expressed genes.
Molecular surveillance for dengue serotypes among the population living in Moyen-Ogooué province, Gabon; evidence of the presence of dengue serotype 1
Authors: Bikangui Rodrigue , Parkouda Soulemane , More Ayong , Magossou Mbadinga Marien Veraldy , Boussoukou Ismael Piérrick Mikelet , Ondo Georgelin Nguema , Nkoma Anne Marie Mouina , Adamou Rafiou , Honkpehedji Yabo Josiane , Rossatanga Elie Gide , Ushijima Yuri , Abe Haruka , Lell Bertrand , Dejon-Agobé Jean Claude , Yasuda Jiro , Adegnika Ayola Akim
Published: June 2024

Background

Despite dengue virus (DENV) outbreak in Gabon a decade ago, less is known on the potential circulation of DENV serotypes in the country. Previous studies conducted in some areas of the country, are limited to hospital-based surveys which reported the presence of some cases of serotype 2 and 3 seven years ago and more recently the serotype 1. As further investigation, we extend the survey to the community of Moyen Ogooué region with the aim to assess the presence of the dengue virus serotypes, additionally to characterize chikungunya (CHIKV) infection and describe the symptomatology associated with infections.

Method

A cross-sectional survey was conducted from April 2020 to March 2021. The study included participants of both sexes and any age one year and above, with fever or history of fever in the past seven days until blood collection. Eligible volunteers were clinically examined, and blood sample was collected for the detection of DENV and CHIKV using RT-qPCR. Positive samples were selected for the target sequencing.

Results

A total of 579 volunteers were included. Their mean age (SD) was 20 (20) years with 55% of them being female. Four cases of DENV infection were diagnosed giving a prevalence of 0.7% (95%CI: 0.2–1.8) in our cohort while no case of CHIKV was detected. The common symptoms and signs presented by the DENV cases included fatigue, arthralgia myalgia, cough, and loss of appetite. DENV-1was the only virus detected by RT-qPCR.

Conclusion

Our results confirm the presence of active dengue infection in the region, particularly DENV-1, and could suggest the decline of DENV-2 and DENV-3. Continuous surveillance remains paramount to comprehensively describe the extent of dengue serotypes distribution in the Moyen-Ogooué region of Gabon.
Graph analysis uncovers an opposing impact of methylphenidate on connectivity patterns within default mode network sub-divisions
Authors: Daood Maryana , Magal Noa , Peled-Avron Leehe , Nevat Michael , Ben-Hayun Rachel , Aharon-Peretz Judith , Tomer Rachel , Admon Roee
Published: June 2024

Background

The Default Mode Network (DMN) is a central neural network, with recent evidence indicating that it is composed of functionally distinct sub-networks. Methylphenidate (MPH) administration has been shown before to modulate impulsive behavior, though it is not yet clear whether these effects relate to MPH-induced changes in DMN connectivity. To address this gap, we assessed the impact of MPH administration on functional connectivity patterns within and between distinct DMN sub-networks and tested putative relations to variability in sub-scales of impulsivity.

Methods

Fifty-five right-handed healthy adults underwent two resting-state functional MRI (rs-fMRI) scans, following acute administration of either MPH (20 mg) or placebo, via a randomized double-blind placebo-controlled design. Graph modularity analysis was implemented to fractionate the DMN into distinct sub-networks based on the impact of MPH (vs. placebo) on DMN connectivity patterns with other neural networks.

Results

MPH administration led to an overall decreased DMN connectivity, particularly with the auditory, cinguloopercular, and somatomotor networks, and increased connectivity with the parietomedial network. Graph analysis revealed that the DMN could be fractionated into two distinct sub-networks, with one exhibiting MPH-induced increased connectivity and the other decreased connectivity. Decreased connectivity of the DMN sub-network with the cinguloopercular network following MPH administration was associated with elevated impulsivity and non-planning impulsiveness.

Conclusion

Current findings highlight the intricate effects of MPH administration on DMN rs-fMRI connectivity, uncovering its opposing impact on distinct DMN sub-divisions. MPH-induced dynamics in DMN connectivity patterns with other neural networks may account for some of the effects of MPH administration on impulsive behavior.
Mis-localization of endogenous TDP-43 leads to ALS-like early-stage metabolic dysfunction and progressive motor deficits
Authors: Hu Yiying , Hruscha Alexander , Pan Chenchen , Schifferer Martina , Schmidt Michael K. , Nuscher Brigitte , Giera Martin , Kostidis Sarantos , Burhan Özge , van Bebber Frauke , Edbauer Dieter , Arzberger Thomas , Haass Christian , Schmid Bettina
Published: June 2024

Background

The key pathological signature of ALS/ FTLD is the mis-localization of endogenous TDP-43 from the nucleus to the cytoplasm. However, TDP-43 gain of function in the cytoplasm is still poorly understood since TDP-43 animal models recapitulating mis-localization of endogenous TDP-43 from the nucleus to the cytoplasm are missing.

Methods

CRISPR/Cas9 technology was used to generate a zebrafish line (called CytoTDP), that mis-locates endogenous TDP-43 from the nucleus to the cytoplasm. Phenotypic characterization of motor neurons and the neuromuscular junction was performed by immunostaining, microglia were immunohistochemically localized by whole-mount tissue clearing and muscle ultrastructure was analyzed by scanning electron microscopy. Behavior was investigated by video tracking and quantitative analysis of swimming parameters. RNA sequencing was used to identify mis-regulated pathways with validation by molecular analysis.

Results

CytoTDP fish have early larval phenotypes resembling clinical features of ALS such as progressive motor defects, neurodegeneration and muscle atrophy. Taking advantage of zebrafish’s embryonic development that solely relys on yolk usage until 5 days post fertilization, we demonstrated that microglia proliferation and activation in the hypothalamus is independent from food intake. By comparing CytoTDP to a previously generated TDP-43 knockout line, transcriptomic analyses revealed that mis-localization of endogenous TDP-43, rather than TDP-43 nuclear loss of function, leads to early onset metabolic dysfunction.

Conclusions

The new TDP-43 model mimics the ALS/FTLD hallmark of progressive motor dysfunction. Our results suggest that functional deficits of the hypothalamus, the metabolic regulatory center, might be the primary cause of weight loss in ALS patients. Cytoplasmic gain of function of endogenous TDP-43 leads to metabolic dysfunction in vivo that are reminiscent of early ALS clinical non-motor metabolic alterations. Thus, the CytoTDP zebrafish model offers a unique opportunity to identify mis-regulated targets for therapeutic intervention early in disease progression.
The role of big data management, data registries, and machine learning algorithms for optimizing safe definitive surgery in trauma: a review
Authors: Pape Hans-Christoph , Starr Adam J. , Gueorguiev Boyko , Wanner Guido A.
Published: June 2024

Digital data processing has revolutionized medical documentation and enabled the aggregation of patient data across hospitals. Initiatives such as those from the AO Foundation about fracture treatment (AO Sammelstudie, 1986), the Major Trauma Outcome Study (MTOS) about survival, and the Trauma Audit and Research Network (TARN) pioneered multi-hospital data collection. Large trauma registries, like the German Trauma Registry (TR-DGU) helped improve evidence levels but were still constrained by predefined data sets and limited physiological parameters. The improvement in the understanding of pathophysiological reactions substantiated that decision making about fracture care led to development of patient’s tailored dynamic approaches like the Safe Definitive Surgery algorithm. In the future, artificial intelligence (AI) may provide further steps by potentially transforming fracture recognition and/or outcome prediction. The evolution towards flexible decision making and AI-driven innovations may be of further help. The current manuscript summarizes the development of big data from local databases and subsequent trauma registries to AI-based algorithms, such as Parkland Trauma Mortality Index and the IBM Watson Pathway Explorer.
The clock gene BHLHE40 and atypical CCNG2 control androgen-induced cellular senescence as a novel tumor suppressive pathway in prostate cancer
Authors: Heidari Horestani Mehdi , Atri Roozbahani Golnaz , Baniahmad Aria
Published: June 2024

Background

The androgen receptor (AR) is a drug target used to inhibit AR and prostate cancer (PCa) growth. Surprisingly, treatment with supraphysiological androgen level (SAL), used in bipolar androgen therapy, inhibits growth of PCa suggesting a tumor-suppressive activity by SAL. SAL was shown to induce cellular senescence in PCa.

Methods

RNA-seq and transcriptome analysis, ChIP-seq, human 3D PCa spheroids, mouse xenografted castration-resistant PCa, knockdown and overexpression, Co-immunoprecipitation (Co-IP), translocation analysis, immune detection, qRT-PCR, protein–protein interaction modelling.

Results

Here, mice xenografts with castration-resistant PCa tumors show that SAL inhibits cancer growth in vivo suggesting that SAL activates a tumor-suppressive mechanism. RNA-seq and ChIP-seq revealed the clock gene BHLHE40 is a novel direct AR target. Compared to adjacent human prostate tissues, the expression of BHLHE40 is reduced in PCa tumors and associated with reduced survival. Knockdown suggests that BHLHE40 mediates SAL-induced cellular senescence including tumor spheroids. Interestingly, a large overlap of differentially expressed gene sets was identified between BHLHE40 and SAL leading to the identification of four classes of SAL-BHLHE40 transcriptome landscapes. Co-IP and modelling suggest binding of BHLHE40 to AR and their co-translocation into nucleus by SAL treatment. Further, RNA-seq and ChIP-seq analysis indicate that the atypical tumor suppressive cyclin G2 emerged as a novel downstream target of BHLHE40 and a mediator of SAL-induced cellular senescence.

Conclusions

The data provide evidence of the tumor suppressive activity of SAL and a novel signaling by the AR-BHLHE40-CCNG2 axis for androgen-induced cellular senescence, linking circadian rhythm factor to androgen signaling as a novel tumor suppressive pathway.
Evaluation of somatic copy number variation detection by NGS technologies and bioinformatics tools on a hyper-diploid cancer genome
Authors: Masood Daniall , Ren Luyao , Nguyen Cu , Brundu Francesco G. , Zheng Lily , Zhao Yongmei , Jaeger Erich , Li Yong , Cha Seong Won , Halpern Aaron , Truong Sean , Virata Michael , Yan Chunhua , Chen Qingrong , Pang Andy , Alberto Reyes , Xiao Chunlin , Yang Zhaowei , Chen Wanqiu , Wang Charles , Cross Frank , Catreux Severine , Shi Leming , Beaver Julia A. , Xiao Wenming , Meerzaman Daoud M.
Published: June 2024

Background

Copy number variation (CNV) is a key genetic characteristic for cancer diagnostics and can be used as a biomarker for the selection of therapeutic treatments. Using data sets established in our previous study, we benchmark the performance of cancer CNV calling by six most recent and commonly used software tools on their detection accuracy, sensitivity, and reproducibility. In comparison to other orthogonal methods, such as microarray and Bionano, we also explore the consistency of CNV calling across different technologies on a challenging genome.

Results

While consistent results are observed for copy gain, loss, and loss of heterozygosity (LOH) calls across sequencing centers, CNV callers, and different technologies, variation of CNV calls are mostly affected by the determination of genome ploidy. Using consensus results from six CNV callers and confirmation from three orthogonal methods, we establish a high confident CNV call set for the reference cancer cell line (HCC1395).

Conclusions

NGS technologies and current bioinformatics tools can offer reliable results for detection of copy gain, loss, and LOH. However, when working with a hyper-diploid genome, some software tools can call excessive copy gain or loss due to inaccurate assessment of genome ploidy. With performance matrices on various experimental conditions, this study raises awareness within the cancer research community for the selection of sequencing platforms, sample preparation, sequencing coverage, and the choice of CNV detection tools.
Longitudinal tracking of hemocyte populations in vivo indicates lineage relationships and supports neural progenitor identity in adult neurogenesis
Authors: Edwards Alex J. , Beltz Barbara S.
Published: June 2024

Adult neurogenesis, which takes place in both vertebrate and invertebrate species, is the process by which new neurons are born and integrated into existing functional neural circuits, long after embryonic development. Most studies in mammals suggest that self-renewing stem cells are the source of the new neurons, although the extent of self-renewal is a matter of debate. In contrast, research in the crayfish Procambarus clarkii has demonstrated that the neural progenitors producing adult-born neurons are capable of both self-renewing and consuming (non-self-renewing) divisions. However, self-renewing divisions are relatively rare, and therefore the production of adult-born neurons depends heavily on progenitors that are not replenishing themselves. Because the small pool of neural progenitors in the neurogenic niche is never exhausted throughout the long lives of these animals, we hypothesized that there must also be an extrinsic source of these cells. It was subsequently demonstrated that the neural progenitors originate in hemocytes (blood cells) produced by the immune system that travel in the circulation before ultimately integrating into niches where the neural lineage begins. The current study examines the developmental lineage of the three hemocyte types — hyaline (HC), semigranular (SGC) and granular (GC) cells — with the goal of understanding the origins of the progenitor cells that produce adult-born neurons. Longstanding qualitative metrics for hemocyte classification were validated quantitatively. Then, in a longitudinal study, proliferation markers were used to label the hemocytes in vivo, followed by sampling the circulating hemocyte population over the course of two months. Hemolymph samples were taken at intervals to track the frequencies of the different hemocyte types. These data reveal sequential peaks in the relative frequencies of HCs, SGCs and GCs, which were identified using qualitative and quantitative measures. These findings suggest that the three hemocyte types comprise a single cellular lineage that occurs in the circulation, with each type as a sequential progressive stage in hemocyte maturation beginning with HCs and ending with GCs. When combined with previously published data, this timeline provides additional evidence that HCs serve as the primary neural progenitor during adult neurogenesis in P. clarkii.
Magnitude and associated factors of occupational hazard exposures among sanitary workers: Propose RASM model for risk mitigation for the public hospitals, eastern Ethiopia
Authors: Tolera Sina Temesgen , Assefa Nega , Geremew Abraham , Toseva Elka , Gobena Tesfaye
Published: June 2024

Background

Hospital sanitation workers (SWs) are exposed to numerous occupational hazards due to workplace conditions such as unsafe and unhygienic working environment in the hospitals. Therefore, knowing magnitude, types and source of occupational hazard exposures with their determinants are very significant for further mitigations.

Methods

Hospital based cross-sectional study design was conducted in public hospitals, eastern Ethiopia from 1st May to August 30th, 2023. 809 SWs participated. Data was entered into Epi Data Version 3.1 and Stata 17MP version used for analysis. Descriptive analysis was applied to describe the data. While, multilevel logistic regression was explored to determine the association between outcome and independents among at individual level (model 1), at hospitals (model 2) and combination of the two (model 3). The crude odds ratio (COR) and adjusted odds ratio (AOR) for models 2 and 3 were reported. Variables with an AOR with a 95% confidence interval (CI) at a p-value < 0.05 were reported.

Result

Out of 809 SWs, 729 (90.11%) responded. The overall magnitude of self-reported occupational hazard exposures among SWs was 63.65% (95% CI 0.60–0.67). Of this, biological, chemical, and ergonomic hazards accounted for 82.44%, 74.76%, and 70.92%, respectively. The multilevel logistic regression shows that having social recognition (AOR: 0.37, 95% CI 0.14, 0.91), neutral attitude (AOR: 0.48, 95% CI 0.17, 1.41) as compared to negative attitude. The model also found that SWs those supervised could reduce the likelihood of occupational hazard exposures by 50% times (AOR: 0.50, 95% CI 0.18, 1.38) as compared to non-supervised SWs. The final model predicted the variation of occupational hazard exposures among sanitary workers from the hospitals to hospitals was 26.59%.

Conclusions

The concluded that hospital sanitary workers are facing biological, chemical, ergonomic, physical, psychological, mechanical, and electrical hazards. This study’s findings predicted that dissatisfied with their environment, working more than 8 hr per a day,  a negative attitude towards workplace risks and inadequate supervision may serve as contributing factors for the likelihood of occupational hazard exposures among these groups. Thus, the study suggested that hospitals could reduce these hazard risks if they implement the Risk Assessment and Safety Management (RASM) model, which includes multi-modal strategies, indicators and tripartite philosophy.
The association of social networks and depression in community-dwelling older adults: a systematic review
Authors: Reiner Amelie , Steinhoff Paula
Published: June 2024

Background and objective

Depression is a globally prevalent mental condition, particularly among older adults. Previous research has identified that social networks have a buffering effect on depression. Existing systematic reviews have either limited their research to specific geographic areas or provided evidence from over a decade ago. The vast body of recent literature particularly from the last decade emphasizes the need for a comprehensive review. This systematic review aims to analyze the association of structural aspects of social networks and depression in older adults.

Methods

The electronic databases APA PsycINFO, ProQuest, PSYINDEX, PubMed, Scopus, SocINDEX, and Web of Science were searched from date of data base inception until 11 July 2023. Studies were eligible for inclusion if they reported on community-dwelling older adults (defined as a mean age of at least 60 years old), had an acceptable definition for depression, referred to the term social network in the abstract, and were published in English. Quality was appraised using the Newcastle Ottawa Scale for cross-sectional and longitudinal studies. Outcome data were extracted independently from each study and analyzed by direction of the relationship, social network domain and cross-sectional or longitudinal study design.

Results

In total, 127 studies were included. The study categorizes structural network aspects into seven domains and finds that larger and more diverse networks, along with closer social ties, help mitigate depression. The literature on the relationships between depression and network density, homogeneity, and geographical proximity is scarce and inconclusive.

Discussion and implications

Despite inconsistent findings, this review highlights the importance of quantifying complex social relations of older adults. Limitations of this review include publication and language bias as well as the exclusion of qualitative research. Further research should use longitudinal approaches to further investigate the reciprocal relationship between social networks and depression. Following this review, interventions should promote the integration of older adults in larger and more diverse social settings.

Other: This work was supported by the Deutsche Forschungsgemeinschaft (DFG, German Research Foundation) under Grant [454899704]. This systematic review was pre-registered. The review-protocol can be accessed at https://doi.org/10.17605/OSF.IO/6QDPK.
Biochar supplementation altered the expression of antioxidant proteins in rice leaf chloroplasts under high-temperature stress
Authors: Huang Min , Yin Xiaohong , Chen Jiana , Cao Fangbo
Published: June 2024

In order to identify the key antioxidant defense systems used to cope with high-temperature stress in rice leaf chloroplasts following biochar supplementation, the present study compared the expression levels of chloroplast proteins related to antioxidant defense in high-temperature stressed rice leaves between without (C0) and with biochar supplementation (C40; 40 g biochar kg–1 soil). A total of sixteen differentially expressed antioxidant chloroplastic proteins were identified. Among them, three antioxidant enzyme proteins and eight thioredoxin proteins were 62–123% and 37–225% higher under the C40 treatment compared to C0, respectively. These results suggest that both antioxidant enzymes and the thioredoxin system are central to the biochar-mediated protection of rice leaves exposed to high-temperature stress.
Recanalization of port-superior mesenteric vein thrombosis with long-term anticoagulant therapy after failed early anticoagulant therapy
Authors: Okada Ichiro , Hagiwara Masahiro , Yoneyama Hisashi , Kohara Saeko , Shoji Yokobori
Published: June 2024

Background

Anticoagulant therapy with heparin is the first-line treatment for acute mesenteric vein thrombosis and is effective in improving outcomes. Conversely, patients with failed early anticoagulant therapy occasionally develop bowel infarction requiring surgery. The efficacy of long-term anticoagulant therapy on recanalizing mesenteric vein thrombosis in patients with failed early anticoagulant therapy remains unclear. Herein, we report a patient who achieved recanalization of port-superior mesenteric vein thrombosis treated with anticoagulant therapy for 10 years after failed early anticoagulant therapy, followed by bowel resection.

Case presentation

A 38-year-old male patient visited an outpatient clinic due to acute exacerbation of abdominal pain that had persisted for a month. He was diagnosed with port-superior mesenteric vein thrombosis on contrast-enhanced computed tomography (CT) scan and was transferred to our institution. Although he presented with abdominal pain, his respiration and circulation were stable upon hospital arrival. Anticoagulant therapy with heparin was started, and the patient was admitted to the intensive care unit. However, the patient’s abdominal pain worsened, and he began to develop signs of peritonitis. Repeat CT scan revealed bowel infarction. Thus, the patient underwent bowel resection 6 h after admission. The initial surgery was completed with open abdomen management. Bowel anastomosis was performed on the second-look surgery on the first postoperative day. Finally, the abdomen was closed on the third postoperative day after confirming the absence of bowel ischemia progression. The patient had prolonged impaired bowel function with paralytic ileus, but was discharged on the 60th postoperative day. He was then diagnosed with protein C and S deficiency based on the tests performed. Anticoagulant therapy with warfarin was initiated. He also received anticoagulant therapy in the outpatient setting. The patient’s port-superior mesenteric vein thrombosis had improved gradually with warfarin during the follow-up period. At 10 years after surgery, total occlusion of the port-superior mesenteric vein was recanalized with improvement of the portal collateral vessels. In addition, no gastric or esophageal varices were observed.

Conclusions

Long-term anticoagulation therapy could affect the recanalization of extensive thrombus in multiple segments in patients with mesenteric venous thrombosis.
Genome streamlining in Parcubacteria transitioning from soil to groundwater
Authors: Chaudhari Narendrakumar M. , Pérez-Carrascal Olga M. , Overholt Will A. , Totsche Kai U. , Küsel Kirsten
Published: June 2024

Background

To better understand the influence of habitat on the genetic content of bacteria, with a focus on members of Candidate Phyla Radiation (CPR) bacteria, we studied the effects of transitioning from soil via seepage waters to groundwater on genomic composition of ultra-small Parcubacteria, the dominating CPR class in seepage waters, using genome resolved metagenomics.

Results

Bacterial metagenome-assembled genomes (MAGs), (318 total, 32 of Parcubacteria) were generated from seepage waters and compared directly to groundwater counterparts. The estimated average genome sizes of members of major phyla Proteobacteria, Bacteroidota and Cand. Patescibacteria (Candidate Phyla Radiation – CPR bacteria) were significantly higher in soil-seepage water as compared to their groundwater counterparts. Seepage water Parcubacteria (Paceibacteria) exhibited 1.18-fold greater mean genome size and 2-fold lower mean proportion of pseudogenes than those in groundwater. Bacteroidota and Proteobacteria also showed a similar trend of reduced genomes in groundwater compared to seepage. While exploring gene loss and adaptive gains in closely related CPR lineages in groundwater, we identified a membrane protein, and a lipoglycopeptide resistance gene unique to a seepage Parcubacterium genome. A nitrite reductase gene was also identified and was unique to the groundwater Parcubacteria genomes, likely acquired from other planktonic microbes via horizontal gene transfer.

Conclusions

Overall, our data suggest that bacteria in seepage waters, including ultra-small Parcubacteria, have significantly larger genomes and higher metabolic enrichment than their groundwater counterparts, highlighting possible genome streamlining of the latter in response to habitat selection in an oligotrophic environment.
Modified frontal horn index: a novel risk predictor for sunken flap syndrome in the patients undergoing shunt procedures for post-decompressive craniectomy hydrocephalus
Authors: Yadav Vikrant , Sahu Anurag , Prasad Ravi Shankar , Pandey Nityanand , Mishra Manish Kumar , Pradhan Ravi Shekhar
Published: June 2024

Background

Decompressive craniectomy (DC) is a neurosurgical procedure, frequently used in lowering the refractory intracranial pressure (ICP) following traumatic brain injuries. Post-traumatic hydrocephalus (PTH), a debilitating complication in the patients with traumatic brain injuries, occurs in 11.9–36% patients undergoing DCs. Sunken flap syndrome (SFS) is a rare entity, following DCs or cerebrospinal fluid (CSF) diversion procedures for PTH after DCs and leads to neurological deterioration of the patients. Literature regarding risk factors associated with SFS in the patients undergoing ventriculoperitoneal shunt procedures for hydrocephalus following DCs is scarce. The aim of this study is to determine the incidence of SFS and to establish a relationship between several clinico-radiological features and SFS in patients undergoing shunt procedures for PTH.

Results

This retrospective study was conducted in a tertiary care trauma centre upon 60 patients who underwent shunt procedures for PTH. Intraventricular haemorrhage (P < 0.0001), communicating-type hydrocephalus (P = 0.0006), and modified frontal horn index (P < 0.0001) were significantly associated with development of SFS. MFHI > 43 was a significant risk factor in development of SFS.

Conclusions

SFS is the common complication following shunt procedures for PTH after DCs. MFHI is significant risk predictor for SFS. MFHI > 43 is associated with higher chances of developing SFS following shunt insertion in PTH. Early cranioplasty following DCs might prevent development of SFS.
Utility of transmanubrial osteomuscular sparing approach and its modification in vascular surgery: a case series study of surgeries related to subclavian artery
Authors: Itagaki Kota , Katahira Shintaro , Hosoyama Katsuhiro , Suzuki Yusuke , Niikawa Hiromichi , Otani Masayuki , Taketomi Ryuichi , Ito Koki , Takahashi Goro , Kumagai Kiichiro , Okada Yoshinori , Saiki Yoshikatsu
Published: June 2024

Background

The operative field in subclavian vessel surgery is limited by thoracic inlet and outlet structures. Although endovascular therapy for the subclavian artery could be an option, open repair management is occasionally required in cases of large aneurysms, infectious vasculopathy, and trauma. The transmanubrial osteomuscular sparing approach, commonly used in thoracic surgery area to resect superior sulcus tumors, is a simple and safe procedure providing an excellent view of the operative field. Herein, we present three cases that underwent open repair of the subclavian artery using the transmanubrial osteomuscular sparing approach, and we also highlight the utility of the technique along with the procedural details.

Case presentation

Case 1: A 54-year-old man presented with a true aneurysm of the proximal portion of the right subclavian artery. The aneurysm measured 50 × 80 mm and compressed the right lung and trachea. We performed an aneurysm resection and a right subclavian artery reconstruction via the transmanubrial osteomuscular sparing approach under cardiopulmonary bypass support.

Case 2: A 72-year-old man who presented with an abscess that formed around the left subclavian artery due to an unremoved guidewire during thoracic endovascular aortic repair for an aortic arch aneurysm in another hospital. After the antibiotics administration, debridement and axillary-axillary bypass were performed, and the guidewire was removed via a transmanubrial osteomuscular sparing approach with a use of cardiopulmonary bypass.

Case 3: A 60-year-old man presented with misplacement of an indwelling dialysis catheter inserted for acute renal failure and hyperkalemia. The catheter was placed through the right neck, but had penetrated the right internal jugular vein and was misplaced from the right subclavian artery into the proximal aortic arch. Emergently, we removed the catheter using the transmanubrial osteomuscular sparing approach.

Conclusions

The transmanubrial osteomuscular sparing approach to the subclavian artery provides an excellent view and a wide surgical field, even in different pathological situations. This is a simple, safe, and highly useful procedure and could be the standard approach for subclavian artery surgeries.