bluuebunny/crossref_metadata_2025 huggingface dataset:
Explainable AI for Bioinformatics: Methods, Tools and Applications
Authors: Karim Md Rezaul , Islam Tanhim , Shajalal Md , Beyan Oya , Lange Christoph , Cochez Michael , Rebholz-Schuhmann Dietrich , Decker Stefan
Published: July 2023

Artificial intelligence (AI) systems utilizing deep neural networks and machine learning (ML) algorithms are widely used for solving critical problems in bioinformatics, biomedical informatics and precision medicine. However, complex ML models that are often perceived as opaque and black-box methods make it difficult to understand the reasoning behind their decisions. This lack of transparency can be a challenge for both end-users and decision-makers, as well as AI developers. In sensitive areas such as healthcare, explainability and accountability are not only desirable properties but also legally required for AI systems that can have a significant impact on human lives. Fairness is another growing concern, as algorithmic decisions should not show bias or discrimination towards certain groups or individuals based on sensitive attributes. Explainable AI (XAI) aims to overcome the opaqueness of black-box models and to provide transparency in how AI systems make decisions. Interpretable ML models can explain how they make predictions and identify factors that influence their outcomes. However, the majority of the state-of-the-art interpretable ML methods are domain-agnostic and have evolved from fields such as computer vision, automated reasoning or statistics, making direct application to bioinformatics problems challenging without customization and domain adaptation. In this paper, we discuss the importance of explainability and algorithmic transparency in the context of bioinformatics. We provide an overview of model-specific and model-agnostic interpretable ML methods and tools and outline their potential limitations. We discuss how existing interpretable ML methods can be customized and fit to bioinformatics research problems. Further, through case studies in bioimaging, cancer genomics and text mining, we demonstrate how XAI methods can improve transparency and decision fairness. Our review aims at providing valuable insights and serving as a starting point for researchers wanting to enhance explainability and decision transparency while solving bioinformatics problems. GitHub: https://github.com/rezacsedu/XAI-for-bioinformatics.
A machine learning based approach to identify carotid subclinical atherosclerosis endotypes
Authors: Chen Qiao Sen , Bergman Otto , Ziegler Louise , Baldassarre Damiano , Veglia Fabrizio , Tremoli Elena , Strawbridge Rona J , Gallo Antonio , Pirro Matteo , Smit Andries J , Kurl Sudhir , Savonen Kai , Lind Lars , Eriksson Per , Gigante Bruna
Published: July 2023

Aims

To define endotypes of carotid subclinical atherosclerosis.

Methods and results

We integrated demographic, clinical, and molecular data (n = 124) with ultrasonographic carotid measurements from study participants in the IMPROVE cohort (n = 3340). We applied a neural network algorithm and hierarchical clustering to identify carotid atherosclerosis endotypes. A measure of carotid subclinical atherosclerosis, the c-IMTmean-max, was used to extract atherosclerosis-related features and SHapley Additive exPlanations (SHAP) to reveal endotypes. The association of endotypes with carotid ultrasonographic measurements at baseline, after 30 months, and with the 3-year atherosclerotic cardiovascular disease (ASCVD) risk was estimated by linear (β, SE) and Cox [hazard ratio (HR), 95% confidence interval (CI)] regression models. Crude estimates were adjusted by common cardiovascular risk factors, and baseline ultrasonographic measures. Improvement in ASCVD risk prediction was evaluated by C-statistic and by net reclassification improvement with reference to SCORE2, c-IMTmean-max, and presence of carotid plaques. An ensemble stacking model was used to predict endotypes in an independent validation cohort, the PIVUS (n = 1061). We identified four endotypes able to differentiate carotid atherosclerosis risk profiles from mild (endotype 1) to severe (endotype 4). SHAP identified endotype-shared variables (age, biological sex, and systolic blood pressure) and endotype-specific biomarkers. In the IMPROVE, as compared to endotype 1, endotype 4 associated with the thickest c-IMT at baseline (β, SE) 0.36 (0.014), the highest number of plaques 1.65 (0.075), the fastest c-IMT progression 0.06 (0.013), and the highest ASCVD risk (HR, 95% CI) (1.95, 1.18–3.23). Baseline and progression measures of carotid subclinical atherosclerosis and ASCVD risk were associated with the predicted endotypes in the PIVUS. Endotypes consistently improved measures of ASCVD risk discrimination and reclassification in both study populations.

Conclusions

We report four replicable subclinical carotid atherosclerosis—endotypes associated with progression of atherosclerosis and ASCVD risk in two independent populations. Our approach based on endotypes can be applied for precision medicine in ASCVD prevention.
Nonsurgical hypoparathyroidism is associated with skeletal muscle dysfunction and restrictive lung disease
Authors: Babu Takasi Anush , Hashim Zia , Neyaz Zafar , Mani Vinita E , Jain Neeraj , Bhatia Eesh , Mishra Anjali , Sahoo Saroj Kumar
Published: July 2023

Context

Systematic assessment of skeletal muscle function is lacking in patients with nonsurgical hypoparathyroidism (HP). Whether muscle dysfunction involves respiratory muscles and results in restrictive lung disease (RLD) is not studied.

Objective

To assess skeletal muscle and pulmonary functions in patients with HP.

Design

Observational case–control study.

Methods

Thirty patients with HP (mean age 37.7 years, 60% males) and 40 age-, sex-, and body mass index (BMI)-matched healthy controls were assessed for skeletal muscle function by handgrip strength, the short physical performance battery (SPPB) test, dual-energy X-ray absorptiometry (DXA), and electromyography (EMG). Pulmonary function was assessed by spirometry, body plethysmography, diffusion lung capacity for carbon monoxide, and diaphragmatic ultrasound (DUS).

Results

Patients with HP had lower serum calcium (2.25 ± 0.15 vs 2.4 ± 0.12 mmol/L, P < .001), serum magnesium (median [interquartile range] 0.74 [0.69-0.82] vs 0.78 [0.69-0.90] mmol/L, P = .04), handgrip strength (18.08 ± 8.36 vs 22.90 ± 7.77 kg, P = .01), and composite SPPB scores (9.5 [7-10] vs 12 [12-12], P < .001) compared to healthy controls. Electromyographic evidence of myopathy was seen in 23% (5 of 22) of patients with HP but in none of the controls (P = .08). The prevalence of RLD was higher in the HP cohort compared to that in controls (24% vs 0%, P = .01). Diaphragmatic excursion (DE) (4.22 ± 1.38 vs 5.18 ± 1.53 cm, P = .01) and diaphragmatic thickness (DT) (3.79 ± 1.18 vs 4.28 ± 0.94 mm, P = .05) on deep inspiration were reduced in patients with HP.

Conclusion

Detailed testing of patients with HP without overt muscle and lung diseases revealed significant impairment in parameters of skeletal muscle function. Myopathy and RLD were observed in a considerable proportion of patients with HP.
A systematic review of how social connectedness influences associations between racism and discrimination on health outcomes
Authors: Ransome Yusuf , Valido Alberto D , Espelage Dorothy L , Clements Graceson L , Harrell Crystal , Eckel Caroline , Price Natalie , Nassau Rachel , Nyhan Kate , Taggart Tamara L
Published: July 2023

Racial discrimination is a well-known risk factor of racial disparities in health. Although progress has been made in identifying multiple levels through which racism and racial discrimination influences health, less is known about social factors that may buffer racism’s associations with health. We conducted a systematic review of the literature with a specific focus on social connectedness, racism, and health, retrieving studies conducted in the United States and published between January 1, 2012, and July 30, 2022, in peer-reviewed journals. Of the 787 articles screened, 32 were selected for full-text synthesis. Most studies (72%) were at the individual level, cross-sectional, and among community/neighborhood, school, or university samples. Studies had good methodological rigor and low risk of bias. Measures of racism and racial discrimination varied. Discrimination scales included unfair treatment because of race, schedule of racist events, experiences of lifetime discrimination, and everyday discrimination. Measures of social connectedness (or disconnectedness) varied. Social-connectedness constructs included social isolation, loneliness, and social support. Mental health was the most frequently examined outcome (75%). Effect modification was used in 56% of studies and mediation in 34% of studies. In 81% of studies, at least 1 aspect of social connectedness significantly buffered or mediated the associations between racism and health. Negative health associations were often weaker among people with higher social connectedness. Social connectedness is an important buffering mechanism to mitigate the associations between racial discrimination and health. In future studies, harmonizing metrics of social connectedness and racial discrimination can strengthen causal claims to inform interventions.
Sleep need, the key regulator of sleep homeostasis, is indicated and controlled by phosphorylation of threonine 221 in salt-inducible kinase 3
Authors: Li Yang , Li Chengang , Liu Yuxiang , Yu Jianjun , Yang Jingqun , Cui Yunfeng , Wang Tao V , Li Chaoyi , Jiang Lifen , Song Meilin , Rao Yi
Published: July 2023

Sleep need drives sleep and plays a key role in homeostatic regulation of sleep. So far sleep need can only be inferred by animal behaviors and indicated by electroencephalography (EEG). Here we report that phosphorylation of threonine (T) 221 of the salt-inducible kinase 3 (SIK3) increased the catalytic activity and stability of SIK3. T221 phosphorylation in the mouse brain indicates sleep need: more sleep resulting in less phosphorylation and less sleep more phosphorylation during daily sleep/wake cycle and after sleep deprivation (SD). Sleep need was reduced in SIK3 loss of function (LOF) mutants and by T221 mutation to alanine (T221A). Rebound after SD was also decreased in SIK3 LOF and T221A mutant mice. By contrast, SIK1 and SIK2 do not satisfy criteria to be both an indicator and a controller of sleep need. Our results reveal SIK3-T221 phosphorylation as a chemical modification which indicates and controls sleep need.
The questionable necessity of a new human right against being subject to automated decision-making
Authors: Abrusci Elena , Mackenzie-Gray Scott Richard
Published: July 2023

The development and interest in decision-making that is or can be automated have opened the doors of debate regarding the form and substance of related means of regulating its application. Part of this discourse involves proposals advocating for the creation of a new human right not to be subject to an automated decision. This article questions whether such a right is necessary in light of existing substantive rules under legal frameworks already applicable to automated decision-making, specifically data protection, non-discrimination and human rights. There are also procedural challenges requiring treatment if automated decision-making is to be adequately addressed by application of the law. Exploring these challenges helps appreciate the significance of ensuring that existing substantive law is better implemented for the purpose of protecting human beings in settings where automated decision-making poses risks to individuals and groups.
Short communication: evaluation of an endotoxin challenge and intraruminal bacterial inoculation model to induce liver abscesses in Holstein steers
Authors: McDaniel Zach S , Hales Kristin E , Nagaraja T G , Lawrence Ty E , Amachawadi Raghavendra G , Carroll Jeff A , Burdick Sanchez Nicole C , Galyean Michael L , Smock Taylor M , Ballou Michael A , Machado Vinicius S , Broadway Paul R
Published: July 2023

Holstein steers (n = 40; initial body weight [BW] = 96.0 ± 10.5 kg) were individually housed in a climate-controlled barn to evaluate potential models for the genesis of liver abscesses (LA). In this 2 × 2 factorial, steers were balanced by BW and randomly assigned to one of two treatments: 1) intravenous saline injection followed by intraruminal bacterial inoculation with Fusobacterium necrophorum subsp. necrophorum (1 × 109 colony forming unit [CFU]/mL) and Salmonella enterica serovar Lubbock (1 × 106 CFU/mL; CON; n = 20 steers); or 2) intravenous injection with 0.25 µg/kg BW of lipopolysaccharide (LPS; Escherichia coli O111:B4) followed by intraruminal bacterial inoculation of F. necrophorum subsp. necrophorum (1 × 109 CFU/mL) and S. enterica serovar Lubbock (1 × 106 CFU/mL; LBI; n = 20 steers) and 1 of 2 harvest dates (3 or 10 d post LPS infusion). Body weights were recorded on days −4, −1, 3, and 10, and blood was collected for hematology on days −4, 3, and 10, relative to LPS infusion on day 0. Intraruminal bacterial inoculation occurred on day 1. Steers from each treatment group were harvested at two different time points on day 3 or 10 to perform gross pathological examination of the lung, rumen, liver, LA (if present), and colon. Feed disappearance was less for LBI than CON (P < 0.01); however, BW did not differ (P = 0.33) between treatments. Neither treatment nor time differed for hematology (P ≥ 0.13), and no gross pathological differences were noted in the lung, liver, LA, or colon (P ≥ 0.25). A treatment × harvest date interaction was noted for ruminal pathology in which LBI had an increased percentage of abnormal rumen scores on day 3 (P < 0.01). These results suggest that an LPS challenge in combination with intraruminal bacterial inoculation of pathogens commonly isolated from LA was not sufficient to induce LA in steers within 3 or 10 d (P = 0.95) when compared to CON. Further evaluation is needed to produce a viable model to investigate the genesis and prevention of LA in cattle.
Inhibition of Sirt2 Decreases ApoE Secretion in Astrocytes and Microglial Cells
Authors: Chen Yuxin , Zhou Chunyu , Abdelhamid Mona , Jung Cha-Gyun , Michikawa Makoto
Published: July 2023

Amyloid-β (Aβ) accumulation caused by an imbalance of the production and clearance of Aβ in the brain is associated with the development of Alzheimer's disease (ad). Apolipoprotein E (ApoE) (the strongest genetic risk factor) enhances Aβ clearance, preventing Aβ deposition. Sirtuin 2 (Sirt2) is an NAD+-dependent histone deacetylase and its inhibition has been reported to ameliorate memory impairment in ad-like model mice. However, the role of Sirt2 in ApoE secretion is unknown. Here, we found that inhibition of Sirt2 activity in primary cultured astrocytes and BV2 cells decreased ApoE secretion, resulting in the accumulation of intracellular ApoE and inhibiting extracellular Aβ degradation. However, the reduction of Sirt2 protein level by Sirt2 siRNA decreased ApoE protein level, which ultimately reduces ApoE secretion. In addition, the knockdown of Sirt2 in the HEK293-APP cells also decreased levels of intracellular ApoE leading to reduction of its secretion, which is accompanied by increased Aβ levels without altering APP and APP processing enzymes. Our findings provide a novel role of Sirt2 in ApoE secretion.
A note on the worship of the Ācārya’s pādukās among the Śrīvaiṣṇavas
Authors: Anandakichenin Suganya
Published: July 2023

Worshipping the feet, footprints, and sandals (pādukā) of deities and revered people is a widespread practice across South Asia (and throughout the world) that cuts across belief systems. And the Śrīvaiṣṇavas are no exception: on the one hand, they receive the benediction of the Lord’s feet upon their heads in the form of the śaṭhāri, on a visit to a temple or a maṭha. And on the other hand, they worship the feet of their own Ācārya(s) and/or their pādukās, as well as those who belonged to their Ācārya lineage. In this article, I shall deal with the second practice, with a special focus on the manifold ways in which the Ācāryas’ pādukās are honoured institutionally in some of the Śrīvaiṣṇava maṭhas in South India, and on how the disciples of those religious institutions replicate some of the customs at home for their private worship. Given that there are many branches and families of Śrīvaiṣṇavas, differences in the worshipping practices have inevitably crept in, and in this article, I shall seek to understand those differences based on a few examples.
Nutritional approaches targeting mitochondria for the prevention of sarcopenia
Authors: Hahm Jeong-Hoon , Nirmala Farida S , Ha Tae Youl , Ahn Jiyun
Published: July 2023

A decline in function and loss of mass, a condition known as sarcopenia, is observed in the skeletal muscles with aging. Sarcopenia has a negative effect on the quality of life of elderly. Individuals with sarcopenia are at particular risk for adverse outcomes, such as reduced mobility, fall-related injuries, and type 2 diabetes mellitus. Although the pathogenesis of sarcopenia is multifaceted, mitochondrial dysfunction is regarded as a major contributor for muscle aging. Hence, the development of preventive and therapeutic strategies to improve mitochondrial function during aging is imperative for sarcopenia treatment. However, effective and specific drugs that can be used for the treatment are not yet approved. Instead studies on the relationship between food intake and muscle aging have suggested that nutritional intake or dietary control could be an alternative approach for the amelioration of muscle aging. This narrative review approaches various nutritional components and diets as a treatment for sarcopenia by modulating mitochondrial homeostasis and improving mitochondria. Age-related changes in mitochondrial function and the molecular mechanisms that help improve mitochondrial homeostasis are discussed, and the nutritional components and diet that modulate these molecular mechanisms are addressed.
Considerations for fitting occupancy models to data from eBird and similar volunteer-collected data
Authors: Hochachka Wesley M , Ruiz-Gutierrez Viviana , Johnston Alison
Published: July 2023

An occupancy model makes use of data that are structured as sets of repeated visits to each of many sites, in order to estimate the actual probability of occupancy (i.e. proportion of occupied sites) after correcting for imperfect detection using the information contained in the sets of repeated observations. We explore the conditions under which preexisting, volunteer-collected data from the citizen science project eBird can be used for fitting occupancy models. Because the majority of eBird’s data are not collected in the form of repeated observations at individual locations, we explore 2 ways in which the single-visit records could be used in occupancy models. First, we assess the potential for space-for-time substitution: aggregating single-visit records from different locations within a region into pseudo-repeat visits. On average, eBird’s observers did not make their observations at locations that were representative of the habitat in the surrounding area, which would lead to biased estimates of occupancy probabilities when using space-for-time substitution. Thus, the use of space-for-time substitution is not always appropriate. Second, we explored the utility of including data from single-visit records to supplement sets of repeated-visit data. In a simulation study we found that inclusion of single-visit records increased the precision of occupancy estimates, but only when detection probabilities are high. When detection probability was low, the addition of single-visit records exacerbated biases in estimates of occupancy probability. We conclude that subsets of data from eBird, and likely from similar projects, can be used for occupancy modeling either using space-for-time substitution or supplementing repeated-visit data with data from single-visit records. The appropriateness of either alternative will depend on the goals of a study and on the probabilities of detection and occupancy of the species of interest.
One health system’s morbidity and mortality conference survey: a step on the journey to organizational high reliability
Authors: Raper Steven E. , Sullivan Patricia G. , Levin Lawrence S.
Published: July 2023

Background:

The goal of this study was to understand the state of morbidity and mortality conferences held throughout our health system. Assessment of current approaches is necessary for a journey toward organizational high reliability and an opportunity to reduce unnecessary variation in patient and process outcomes.

Study Design:

Forty-two anonymous surveys were distributed through the Health System’s Vice-chairs of Quality to those in the best position to answer questions. Answers from all departments and—where semi-autonomous—divisions were solicited. Categories, among others, included written guidelines, who presented, what events were chosen for presentation, and what was done with the data.

Results:

Forty-one surveys were returned. Seventeen departments or divisions have written guidelines as to which events should be reported. Twenty-two of the departmental or divisional conferences present selected cases, only 13 present all mortalities. Decisions on how events are classified are made most often by the director of Quality with 13 responses. There was no consensus on how best to enhance the clinical learning environment for residents and fellows.

Conclusion:

Opportunities identified by our survey to reduce practice variation include best practices for written guidelines and standardized classification formats for morbidity and mortality events. A mortality committee charged with event review and classification should be considered. Lastly, more effort should be made to enhance the clinical learning environment of trainees in event review and presentation.
Study on the mechanism of Shujin Tongluo granules in treating cervical spondylosis based on network pharmacology and molecular docking
Authors: Wang Yixuan , Tao Xiaoyu , Gao Yifei , Jin Zhengsen , Guo Siyu , Li Zhenjiang , Wang Mengmeng , Zhao Ruoqi , Zhou Wei , Wu Jiarui
Published: July 2023

Background:

To investigate the potential active ingredients and possible mechanisms of Shujin Tongluo granules (SJTLG) in the treatment of cervical spondylosis (CS) by network pharmacology and molecular docking.

Methods:

The active ingredients and potential targets of SJTLG were obtained through databases such as traditional Chinese medicine system (TCMSP) and BATMAN-traditional Chinese medicine (TCM), and the relevant human targets of CS were identified through databases such as OMIM, GeneCards, and DisGeNET. The intersection targets were imported into STRING for protein-protein interaction (PPI) analysis. The obtained data were imported into Cytoscape 3.9.0 software for visualization, and module analysis was performed using the MCODE plug-in. The representative targets were screened through the Metascape website for pathway enrichment analysis in Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG). Cytoscape software was used to build networks such as “drug-compound-target” and “drug-compound-target-pathway.” Finally, the key targets were selected for molecular docking with the corresponding compounds by Autodock Tools 1.5.7 and visualized by PyMol.

Results:

A total of 132 active compounds and 996 targets from SJTLG and 678 targets from CS were screened with 116 intersection targets. The key targets were AKT1, GAPDH, ALB, IL-6, TP53, TNF, VEGFA, IL-1β, EGFR, HSP90AA1, ESR1, and JUN. The results of GO and KEGG enrichment analysis showed that the treatment of CS was mainly related to biological processes such as cellular response to nitrogen compound, cellular response to organonitrogen compound, and positive regulation of locomotion, and the targets were mainly focused on pathways in cancer, Kaposi sarcoma-associated herpesvirus infection, PI3K-Akt signaling pathway, lipid, and atherosclerosis. Molecular docking results showed that the minimum binding energy between the core targets and the corresponding compound was <−5.0 kcal·mol−1.

Conclusion:

This study preliminarily elucidates the potential active ingredients and mechanism of anti-inflammatory, analgesic, microcirculation improvement, vasodilation, osteoporosis inhibition and nerve nutrition effects of SJTLG in the treatment of CS and provides a reference for its clinical application.
Comparison of serodiagnosis methods for community-acquired Mycoplasma pneumoniae respiratory tract infections in children
Authors: Liu Mengyang , Meng Ke , Jiang Jun , Zhang Li , Sun Shiying
Published: July 2023

This study aimed to evaluate the diagnostic value of chemiluminescence immunoassay (CLIA), passive particle agglutination (PPA), and indirect immunofluorescence assay (IFA) in detecting Mycoplasma pneumoniae infection in children. Serum samples from 165 children with acute community-acquired respiratory tract infections were examined using CLIA, PPA, and IFA, and consistency coefficient, specificity, and sensitivity were analyzed. Compared with the PPA (titer ≥ 1:160), the consistency coefficients of the immunoglobulin(Ig)M-CLIA, immunoglobulin(Ig)G-CLIA and IgM-IFA methods were 93.94%, 75.76%, and 83.64%, respectively. The positive likelihood ratio (PLR) and specificity of IgM-CLIA was 19.40 and 95.49%, respectively. The consistency coefficient of (IgM+IgG)-CLIA and PPA (titer ≥ 1:160) was 89.1%, and the sensitivity and negative predictive value of (IgM+IgG)-CLIA were 96.88% and 98.94%, respectively. CLIA MP-IgM has high concordance with PPA, and its specificity and sensitivity are higher than those of CLIA MP-IgG and IFA MP-IgM, suggesting its better diagnosis of early MP infection. The sensitivity and negative predictive value of CLIA MP (IgM+IgG) were higher than those of PPA or IFA, indicating that it should be considered as a priority in the diagnosis of MP infection.
Axillary lymphadenopathy as the initial manifestation in ANCA-associated systemic vasculitis: A case report
Authors: Du Jie , Wang Hongyue , Zhang Lili , Li Hongyu , Li Shuang , Zhang Chao , Sun Fangfang , Zhao Lirong
Published: July 2023

Background:

The anti-neutrophil cytoplasmic antibody (ANCA) associated vasculitides are a collection of relatively rare autoimmune diseases characterized by the presence of ANCAs, predominantly against myeloperoxidase and proteinase 3. Multiple organs and systems are involved, but superficial lymph node involvement is rarely reported.

Case presentation:

A 31-year-old woman initially presented with bilateral axillary lymphadenopathy and that the hilums were not clear. We report the rare case of a patient who presented with an ANCA-associated systemic vasculitis whose initial manifestation was axillary lymphadenopathy. The axillary lymph node needle biopsy specimens had reactive hyperplasia. One year later, the bilateral inguinal lymph nodes had similar morphological and structural changes, and laboratory test results showed renal insufficiency. A renal biopsy revealed the presence of sclerotic glomeruli, crescentic glomeruli, and fibrous crescentic glomeruli, but no deposition of immunocomplex or complement. Finally, the patient was treated with prednisone and mycophenolate mofetil. As the laboratory indicators normalized, so did the sizes of the axillary lymph nodes. A subsequent laboratory examination showed that in addition to urine protein all indicators had normalized, ultrasonography showed slight enlargement of unilateral axillary lymph nodes and normal hilum structure.

Conclusions:

Superficial lymphadenopathy is very rare in ANCA-associated systemic vasculitis. Studying this case improves our understanding of the initial manifestations of ANCA-associated vasculitis and may help provide accurate early diagnosis, thus allowing timely treatment and improved patient prognosis.
Differences in gross appearance and histopathology of the outer membrane of the subdural hematoma envelope over time: A respective case series and literature review
Authors: Ryu Han Seung , Kim Sung Sun , Hong Woo Jun , Kim Tae-Sun , Joo Sung-Pil
Published: July 2023

Rationale:

Chronic subdural hematoma (CSDH) is a common disorder among elderly males. The most common theory of its cause is a minor brain injury resulting in the rupture of a bridging vein. The outer membrane of subdural hematoma (SDH) evolves like cutaneous wound healing with different phases. This report aims to use a surgical microscope and an electron microscope to show the pathophysiological differences in the temporal flow of the outer membrane of SDH.

Patient concerns:

This study retrospectively reviewed the cases of 6 patients who underwent craniotomy from 2016 to 2021 at the single center of Chonnam National University Hospital.

Diagnoses:

These patients had a history of intracranial hematoma (ICH) at the surgical site on brain computed tomography (CT) before craniotomy. This study aimed to observe the morphological changes over time in the outer membrane of SDH and analyzed them through macroscopic and pathological findings.

Interventions and Outcomes:

The outer membrane of SDH was confirmed in all six patients who underwent surgery, and macroscopic analysis was performed using an operating microscope. Three patients underwent pathological analysis through histological examination, and through this, the difference according to ICH occurrence and detection time was analyzed.

Lessons:

This study suggests that the outer membrane of SDH contains inflammatory and collagen cells in the early stages and thickens over time. This healing response is similar to cutaneous wound healing.
Treatment of Tourette syndrome by acupuncture combined with Chinese medicine based on syndrome differentiation: A review
Authors: Lin Kexin , Wang Yijie , Wang Jiaqi , Zhang Chuanyu , Feng Qiuju
Published: July 2023

Tourette syndrome (TS) is a chronic neurodevelopmental disorder characterized by involuntary motor and speech tics, which can greatly reduce the quality of life of patients. The pathophysiology of TS involves both genetic and environmental factors. Assessing TS pathogenesis is complex, and its underlying pathophysiology is not fully understood. It is gratifying that the research in the past 5 years has brought new research progress on the genetic, neurophysiological and brain network changes of TS. However, despite the progress of research, the treatment methods and drugs of modern medicine are still unsatisfactory, and it is difficult to achieve satisfactory results. Traditional Chinese medicine, as a part of complementary and alternative medicine, has unique efficacy in the treatment of TS, and the safety of its treatment is also worthy of attention. Based on the latest achievements in the pathophysiology of TS, this article will discuss the treatment of TS by acupuncture combined with medicine.
A novel PIBF1-RET gene fusion identified from a stage IA lung adenocarcinoma: A case report
Authors: Zhao Weidi , Sun Jia’en , Zhu Huangkai , Zhao Guofang
Published: July 2023

Introduction:

Rearranged during transfection (RET) gene fusions occur in 0.7% to 2% in lung cancer and 1% to 2% in non-small cell lung cancer. Systemic therapies for RET fusion-positive non-small cell lung cancer consist mostly of targeted therapy with RET inhibitors such as selpercatinib and pralsetinib. To date, approximately 40 fusion partners have been reported. Herein, we report a novel progesterone immunomodulatory binding factor 1 (PIBF1)-RET gene fusion identified from a stage IA lung adenocarcinoma and was further validated by RNA sequencing analysis.

Patient concerns:

A 55-year-old male smoker was found by chest computed tomography to have a solid nodule in the right lower lobe of the lung and enlarged mediastinal lymph nodes.

Diagnoses:

The patient was then diagnosed with stage IA lung adenocarcinoma (T1N0M0).

Intervention:

The patient then underwent thoracoscopic lobectomy of the right lower lobe and mediastinal lymph node dissection. Molecular testing with a targeted panel of 8 lung cancer-associated driver genes detected a novel PIBF1-RET (P16:R12) fusion, which putatively encodes a gene in which the first 16 exons of PIBF1 was concatenated to RET exon 13 and its downstream sequence, retaining the RET kinase domain. The genomic translocation was further validated by RNA sequencing with a panel of 115 cancer-associated genes, which found no other aberrations.

Outcomes:

The patient was discharged 3 days after surgery.

Conclusion:

We report a novel PIBF1-RET fusion in early-stage lung adenocarcinoma. This finding expands the spectrum of RET fusion partners and warrants further studies in characterizing the oncogenic role of this genomic aberration and response to RET-targeted therapies.
Application effect of gastrointestinal bundle nursing on the protection of gastrointestinal function in patients with gastric cancer
Authors: Wei Xiao-Ning , Cai Wen-Yan , Wu Kai-Ling , Zeng Fei-Ge
Published: July 2023

Evidence-based nursing practice was used to formulate the enhanced recovery surgery bundle nursing strategy and apply it to patients with gastric cancer, to explore its safety, effectiveness and feasibility in perioperative gastrointestinal function protection in patients with gastric cancer. Selected the clinical medical records of 100 gastric cancer patients treated in our hospital from June 2019 to June 2021 as the research objects, and divided them into the control group and the observation group with 50 cases in each group according to the random number table. Among them, the control group was given routine nursing measures for nursing intervention, and the observation group was given gastrointestinal enhanced recovery surgery cluster nursing on the basis of the control group. The differences in stress response, gastrointestinal function protection, negative emotions and pain scores of gastric cancer patients before and after nursing were compared between the 2 groups. The postoperative bowel sounds recovery time, first anal exhaust, and first defecation time in the observation group were lower than those in the control group, and the differences were statistically significant (P < .05). Before nursing, there was no significant difference in the scores of stress response changes between the 2 groups (P > .05). After nursing, heart rate (HR), mean arterial pressure (MAP), norepinephrine (NE), and epinephrine (E2) in the observation group were lower than those in the control group, and the difference was statistically significant (P < .05). The pain scores of the 2 groups were significantly improved at different time points, and the observation group was significantly less than the control group, and the difference was statistically significant (P < .05). Gastrointestinal enhanced recovery surgery bundle nursing can effectively improve the gastrointestinal function of patients with gastric cancer, improve the emotional response and stress response of patients, and has certain reference value for the nursing of patients with gastric cancer.
Meta-analysis of liver injury in patients with COVID-19
Authors: Li Xinghai , Fan Caiping , Tang Jin , Zhang Ning
Published: July 2023

Background:

The coronavirus disease 2019 (COVID-19) is a major public health problem threatening human health. It can lead to multiple system complications, among which liver damage is also a common complication of COVID-19. The pathogenesis of liver injury is complex and involves the interaction of multiple factors. This study aims to investigate the incidence and risk factors of liver injury in COVID-19 patients and analyze the impact of liver injury on clinical prognosis of patients, so as to provide corresponding basis for clinical diagnosis and treatment.

Methods:

PubMed and Cochrane Library were searched in computer to collect original studies on liver injury cases, laboratory indicators and clinical outcomes in COVID-19 patients. Articles were screened according to inclusion and exclusion criteria, and data were meta-analyzed using Stata12.0 software.

Results:

A total of 49 studies, including 23,611 patients with COVID-19, had a prevalence of liver injury of 39.63%. Subgroup analysis found that patients in the Americas had the highest incidence of liver injury at 43.7% and lowest in Africa (25.99%). The vast majority of liver injury is manifested by aminotransferase or bilirubin levels greater than 1 times the upper limit of normal (49.16%). The older the age, the male, the associated chronic liver disease, and the higher the levels of white blood cells, neutrophils, and C-reactive protein, the higher the risk of liver injury. The use of hormones, hydroxychloroquine, and tocilizumab increases the risk of liver injury. Patients with concurrent liver injury have longer hospital stays, are more likely to progress to severe cases, and have a higher risk of death than patients without liver injury.

Conclusion:

The incidence of liver injury in COVID-19 patients was high, affected by age, gender, chronic liver disease, inflammatory state and medication, and patients with liver injury were hospitalized longer and were more likely to have a poor prognosis. Therefore, clinical attention should be paid to early intervention.
The practices of intravenous sodium bicarbonate therapy in neonatal intensive care units: A multi-country survey
Authors: Al-Shehri Hassan , Alqahtani Renad , Alromih Aroob M. , Altamimi Amal , Alshehri Khloud , Almehaideb Latifah , Jabari Mosleh , Alzayed Abdullah
Published: July 2023

A common occurrence in the neonatal intensive care unit (NICU) is metabolic acidosis. Sodium bicarbonate (SB) has been widely used, but there is insufficient evidence on how SB affects neonates in NICUs with metabolic acidosis. The worsening of intracellular acidosis, the impairment of myocardial function, fluctuations in cerebral blood flow, and intracranial hemorrhage are some of the unfavorable effects of SB treatment in neonates that have been documented in the literature. This study aimed to explore neonatologists’ practices for using intravenous SB (ISB) in NICUs. A multi-country survey was carried out in 2022 using an online questionnaire sent to neonatologists in various countries in order to gather information about the use of ISB in NICUs. A previously validated questionnaire was adapted and used in this study. The response rate was 67%. The findings show that 91.2% of neonatologists were using SB to correct metabolic acidosis in the NICU; 71.4% did not have written guidelines for using sodium bicarbonate. The majority of them (78.9%) reported that dosage is included in their guidelines for the use of ISB. The findings of this study emphasize the critical importance of providing guidelines in using ISB for managing metabolic acidosis in NICU to standardize procedures and reduce the use of potentially unsuitable and unsafe treatments, as it has been shown that 71.4% of neonatologists worldwide use sodium bicarbonate without guidelines.
Application of orthodontics combined with porcelain laminate veneers in the aesthetic restoration and flora regulation of anterior teeth
Authors: Na Lu , Hai Bai , Quan Yuan , Qiang Zhang
Published: July 2023

To evaluate the effectiveness of orthodontics in combination with porcelain laminate veneers (PLV) in the aesthetic restoration and flora regulation of anterior teeth. A retrospective analysis of 336 patients who underwent aesthetic restoration of anterior teeth in our hospital from April 2019 to September 2022 was performed and divided into a control group (n = 168) and an observation group (n = 168) according to the restorative modality. The restorative modality in the control group was conventional restorative remediation, while the restorative modality in the observation group was orthodontic combined with PLV treatment. To evaluate the excellent rate of aesthetic restoration of anterior teeth in the 2 groups, and compare the color, shape, degree of translucency, edge aesthetic score, complications and satisfaction rate of restoration of anterior teeth in the 2 groups before and after restoration. The observation group had a significantly higher rate of excellent aesthetic restorations (95.23%) compared to the control group (80.95%) (P < .001). The scores of anterior tooth color, morphology, degree of translucency and marginal aesthetics were improved in both groups after restoration compared to before restoration, and the scores were significantly higher in the observation group (P < .05). After restoration, the subgingival Digestive streptococcus, Campylobacter and Propionibacterium increased in both groups, but the number of bacterial strains was significantly less in the observation group (P < .05). Compared with the total complication rate in the control group (16.66%), the total complication rate in the observation group (2.38%) was significantly lower (P < .001). Compared with the control group (85.71%), the observation group had a significantly higher restoration satisfaction rate of 97.61%, with a statistically significant difference (P < .001). The application of orthodontics combined with PLV in the aesthetic restoration of anterior teeth has a significant clinical effect, which is conducive to improving the aesthetic restoration and satisfaction rate of anterior teeth, reducing the subgingival microbial imbalance and decreasing the incidence of complications.
The relationship between walking ability, self-rated health, and depressive symptoms in middle-aged and elderly people after controlling demographic, health status, and lifestyle variables
Authors: Zhang Yaqun , Jiang Xin
Published: July 2023

The global aging problem is very serious. With the increase of age, the risk of depression in the elderly is also increasing. It is necessary to find effective strategies to reduce the depressive symptoms of the elderly. This study investigated the relationship between depressive symptoms, walking ability, and self-evaluation health of middle-aged and elderly Chinese after controlling demographic variables, health status, and lifestyle. The data is from the China health and retirement longitudinal study database in 2018. Six thousand eight hundred thirty-five people over the age of 50 have complete information on walking ability, self-assessed health status, and depressive symptoms. SPSS 27.0 software was used to conduct Z-test, logistic regression and linear hierarchical regression analysis on the collected data. The results showed that poor walking ability and poor self-evaluation health status of middle-aged and elderly people were significantly related to depression. The study concluded that middle-aged and elderly people with good walking ability and self-rated health status had a lower risk of depression. This study can provide reference for formulating specific and effective intervention measures for senile depression.
Correlation between trait emotional intelligence and prefrontal activation during a verbal fluency task: A functional near-infrared spectroscopy study
Authors: Fukumoto Takamasa , Amitani Haruka , Nishi Ryusei , Wada Midori , Oishi Naoya , Asakawa Akihiro
Published: July 2023

Stress is inevitable in humans and stress changes our physical and mental states. Stress has been studied epidemiologically, biologically, and psychologically. First defined in 1990, emotional intelligence (EI) affects psychological stress management. In contrast, the prefrontal cortex (PFC) is suggested to play a vital role in stress management. Human PFC activity can be inferred from the balance of oxygenated and deoxygenated hemoglobin in cerebral blood flow, which can be measured and calculated using functional near-infrared spectroscopy (fNIRS). An important cognitive activation task to activate the PFC is the verbal fluency task (VFT). Therefore, if the PFC is activated by the VFT and monitored by fNIRS, and the activity correlates with EI, fNIRS can be used to measure EI. In this study, Psychological tests using the self-rating depression scale, state-trait anxiety inventory (STAI), and trait emotional intelligence questionnaire-short form (TEIQue-SF) were conducted to evaluate the correlation with VFT performance. Relative oxygenated and deoxygenated hemoglobin concentrations were measured using an fNIRS device, and their correlation with VFT performance was tested. Spearman correlation coefficient was used to determine correlations. Results were as follows. Although VFT performance did not correlate with the oxygenated hemoglobin concentration ([Oxy-Hb]) changes, [Oxy-Hb] was elevated in all channels. VFT performance was significantly negatively correlated with the Zung self-rating depression scale (ρ = 0.063, P = .759), trait anxiety or anxiety level as a personal characteristic of STAI (ρ = 0.243, P = .232), and state anxiety or anxiety about an event of STAI (ρ = −0.138, P = .500), whereas no correlation was found with the TEIQue-SF (ρ = 0.303, P = .132). Healthy individuals PFC activity is not severely affected by their mental state and cognitive activation successfully activates the PFC, supporting the hypothesis that EI is correlated with frontal cortical activation during the VFT in a nonclinical population. EI may play a vital role in reducing stress associated with depression and anxiety in our social lives. Although we failed to show a statistical correlation between TEIQue-SF and [Oxy-Hb] due to a sample size shortage, our preliminary study was the first to attempt to show the PFC activity of EI through a hemodynamic response. Future research may elucidate the role of EI in reducing psychological stress in social life.
Mega-Enhancer Bodies Organize Neuronal Long Genes in the Cerebellum
Authors: Zhao Ziyu , Parra Omar Payán , Musella Francesco , Scrutton-Alvarado Nicolas , Fujita Shin-ichiro , Alber Frank , Yang Yue , Yamada Tomoko
Published: July 2023

Dynamic regulation of gene expression plays a key role in establishing the diverse neuronal cell types in the brain. Recent findings in genome biology suggest that three-dimensional (3D) genome organization has important, but mechanistically poorly understood functions in gene transcription. Beyond local genomic interactions between promoters and enhancers, we find that cerebellar granule neurons undergoing differentiationin vivoexhibit striking increases in long-distance genomic interactions between transcriptionally active genomic loci, which are separated by tens of megabases within a chromosome or located on different chromosomes. Among these interactions, we identify a nuclear subcompartment enriched for near-megabase long enhancers and their associated neuronal long genes encoding synaptic or signaling proteins. Neuronal long genes are differentially recruited to this enhancer-dense subcompartment to help shape the transcriptional identities of granule neuron subtypes in the cerebellum. SPRITE analyses of higher-order genomic interactions, together with IGM-based 3D genome modeling and imaging approaches, reveal that the enhancer-dense subcompartment forms prominent nuclear structures, which we term mega-enhancer bodies. These novel nuclear bodies reside in the nuclear periphery, away from other transcriptionally active structures, including nuclear speckles located in the nuclear interior. Together, our findings define additional layers of higher-order 3D genome organization closely linked to neuronal maturation and identity in the brain.