bluuebunny/crossref_metadata_2025 huggingface dataset:
Caregivers’ experiences of accessing HIV Early Infant Diagnosis (EID) services and its barriers and facilitators, India
Authors: Nikhare Kalyani , Gawde Nilesh , Kamble Suchit , Goel Noopur , Kamble Sushmita , Pawar Swapna , More Pratik , Kapoor Neha , Verma Vinita , Kushwaha Bhawani Singh , Das Chinmoyee , Rajan Shobini
Published: January 2024

Background

India has rolled out Early Infant Diagnosis (EID) program for HIV infection in all states. EID program consists of testing of Infants exposed to HIV periodically over 18 months of age which is a multi-step complex testing cascade. Caregivers represent the primary beneficiary of EID program i.e., infants exposed to HIV and face multiple challenges to access EID services. As part of national EID program outcome assessment study, this study narrates caregivers’ perspectives on barriers and facilitators to access and utilize EID services.

Methods

The study was conducted in 31 integrated counselling and testing centres (ICTCs) located in 11 high burden HIV states. A total of 66 in-depth interviews were conducted with caregivers’ of infants enrolled in EID program. Thematic analysis was carried out to help identify themes underlying barriers and facilitators to access EID services and utilization from caregivers’ perspectives.

Results

The stigma and discrimination prevalent in society about HIV remains a key demand side (caregiver-level) barrier. Non-disclosure or selective disclosure of HIV status led to missed or delayed EID tests and delayed HIV diagnosis and initiation of Anti-Retroviral Therapy (ART) for infants exposed to HIV. On supply side (health system-level), accessibility of healthcare facility with EID services was reported as a key barrier. The distance, time and cost were key concerns. Many caregivers faced difficulties to remember the details of complex EID test schedule and relied on a phone call from ICTC counsellor for next due EID test. Delayed EID test results and lack of communication of test results to caregiver were reported as primary barriers for completing the EID test cascade.

Discussion

The study reports caregiver-level and health system-level barriers and facilitators for access to EID services from the caregivers’ perspectives. While, decentralisation and single window approaches can improve the access, timely communication of test results to the caregiver also need to be built in with appropriate use of technology. A holistic intervention including PLHIV support networks and the peer-led support mechanisms would be useful to address societal factors.

Conclusion

The study findings have high significance for developing program implementation strategies to improve access and to build right-based and patient-centred EID services.
Reliability and validity of the Patient Experiences Questionnaire for Interdisciplinary Treatment for Substance Dependence – Continuous Electronic Measurement (PEQ-ITSD – CEM)
Authors: Iversen Hilde Hestad , Haugum Mona , Ellingsen-Dalskau Lina Harvold , Bjertnaes Oyvind
Published: January 2024

Background

Inpatient experiences with interdisciplinary treatment for substance dependence and mental health care are measured using continuous electronic measurements in Norway. Major changes in data collection from cross-sectional surveys to continuous measurements necessitated the revalidation of the instrument. The main purpose of the present study was to determine the psychometric properties of the Patient Experiences Questionnaire for Interdisciplinary Treatment for Substance Dependence – Continuous Electronic Measurement (PEQ-ITSD – CEM). We also aimed to develop a short version of this tool, since completing the original version can be burdensome for some patients.

Methods

The study included adult inpatients (aged ≥ 16 years) who received substance-dependence treatment at 102 different sections in Norway during 2020–2022 (n = 2,850). Factor structure and item performance were assessed. A short version was developed based on the psychometric testing results that included item response theory analysis.

Results

The PEQ-ITSD – CEM comprised three empirically based scales with good internal consistency, reliability and validity, which covers treatment and personnel (14 items), milieu (6 items) and outcome (5 items). The results supported a seven-item short version, with three items selected for the treatment and personnel scale, two items for the milieu scale and two items for the outcome scale.

Conclusions

The PEQ-ITSD – CEM can be recommended for future assessments of patient experiences with interdisciplinary treatment for substance dependence in Norway and in other countries with similar healthcare systems. This short-form version can be applied when respondent burden is a crucial issue.
Lifting the curtain on the emergency department crisis: a multi-method reception study of Larry Saves the Canadian Healthcare System
Authors: Kreindler Sara A. , Hunter Mikayla , Lea Graham W. , Archibald Mandy , Rieger Kendra , West Christina , Hasan Shaikh Mehdi
Published: January 2024

Background

Despite growing evidence of the potential of arts-based modalities to translate knowledge and spark discussion on complex issues, applications to health policy are rare. This study explored the potential of a research-based theatrical video to increase public capacity and motivation to engage with the complex issues that make Emergency Department wait times such an intractable problem.

Methods

Larry Saves the Canadian Healthcare System is a digital musical micro-series developed from extensive research examining system-level causes of Emergency crowding and the ineffectiveness of prevailing approaches. We released individual episodes and a revised full-length version on YouTube, using organic promotion strategies and paid advertising. We used YouTube Analytics to track views, engagement and viewer demographics, and content-analyzed viewer comments. We also conducted five university-based screenings; 92 students completed questionnaires, rating Larry on 16 descriptors using a 7-point Likert scale.

Results

From June 2022 through May 2023, Larry garnered over 100,000 views (76,752 of the full-length version, 35,535 of episodes), 1329 likes, 2780 shares, and 139 comments. Views and watch time were higher among women and positively associated with age. Among YouTube comments, the predominating themes were praise for the video and criticism of the healthcare system. Many commenters applauded the show’s accuracy, humor, and/or resonance with their experience; several shared healthcare horror stories. Students overwhelmingly agreed with all positive and disagreed with all negative descriptors, and nearly unanimously deemed the video informative, thought-provoking, and entertaining. Most also affirmed that it had increased their knowledge, interest, and confidence to participate in discussions about healthcare issues. Neither gender, primary language, nor employment in healthcare predicted ratings, but graduate students and those 25+ years old evaluated the video most positively.

Discussion

These findings highlight the promise of research-informed musical satire to inform and invigorate discourse on an urgent health policy problem. Larry has reached tens of thousands of viewers, garnered excellent feedback, and received high student ratings. Further research should directly assess educational and behavioural outcomes and explore what facilitative strategies could maximize this knowledge translation product’s potential to foster informed, impactful policy dialogue.
Identifying vital sign trajectories to predict 28-day mortality of critically ill elderly patients with acute respiratory distress syndrome
Authors: Li Mingzhuo , Liu Fen , Yang Yang , Lao Jiahui , Yin Chaonan , Wu Yafei , Yuan Zhongshang , Wei Yongyue , Tang Fang
Published: January 2024

Background

The mortality rate of acute respiratory distress syndrome (ARDS) increases with age (≥ 65 years old) in critically ill patients, and it is necessary to prevent mortality in elderly patients with ARDS in the intensive care unit (ICU). Among the potential risk factors, dynamic subphenotypes of respiratory rate (RR), heart rate (HR), and respiratory rate-oxygenation (ROX) and their associations with 28-day mortality have not been clearly explored.

Methods

Based on the eICU Collaborative Research Database (eICU-CRD), this study used a group-based trajectory model to identify longitudinal subphenotypes of RR, HR, and ROX during the first 72 h of ICU stays. A logistic model was used to evaluate the associations of trajectories with 28-day mortality considering the group with the lowest rate of mortality as a reference. Restricted cubic spline was used to quantify linear and nonlinear effects of static RR-related factors during the first 72 h of ICU stays on 28-day mortality. Receiver operating characteristic (ROC) curves were used to assess the prediction models with the Delong test.

Results

A total of 938 critically ill elderly patients with ARDS were involved with five and 5 trajectories of RR and HR, respectively. A total of 204 patients fit 4 ROX trajectories. In the subphenotypes of RR, when compared with group 4, the odds ratios (ORs) and 95% confidence intervals (CIs) of group 3 were 2.74 (1.48–5.07) (P = 0.001). Regarding the HR subphenotypes, in comparison to group 1, the ORs and 95% CIs were 2.20 (1.19–4.08) (P = 0.012) for group 2, 2.70 (1.40–5.23) (P = 0.003) for group 3, 2.16 (1.04–4.49) (P = 0.040) for group 5. Low last ROX had a higher mortality risk (P linear = 0.023, P nonlinear = 0.010). Trajectories of RR and HR improved the predictive ability for 28-day mortality (AUC increased by 2.5%, P = 0.020).

Conclusions

For RR and HR, longitudinal subphenotypes are risk factors for 28-day mortality and have additional predictive enrichment, whereas the last ROX during the first 72 h of ICU stays is associated with 28-day mortality. These findings indicate that maintaining the health dynamic subphenotypes of RR and HR in the ICU and elevating static ROX after initial critical care may have potentially beneficial effects on prognosis in critically ill elderly patients with ARDS.
Transcription factors-related molecular subtypes and risk prognostic model: exploring the immunogenicity landscape and potential drug targets in hepatocellular carcinoma
Authors: Wang Meixia , Guo Hanyao , Zhang Bo , Shang Yanan , Zhang Sidi , Liu Xiaoyu , Cao Pengxiu , Fan Yumei , Tan Ke
Published: January 2024

Background

Hepatocellular carcinoma (HCC) is the most prevalent form of liver cancer, with a high mortality rate and poor prognosis. Mutated or dysregulated transcription factors (TFs) are significantly associated with carcinogenesis. The aim of this study was to develop a TF-related prognostic risk model to predict the prognosis and guide the treatment of HCC patients.

Methods

RNA sequencing data were obtained from the TCGA database. The ICGC and GEO databases were used as validation datasets. The consensus clustering algorithm was used to classify the molecular subtypes of TFs. Kaplan‒Meier survival analysis and receiver operating characteristic (ROC) analysis were applied to evaluate the prognostic value of the model. The immunogenic landscape differences of molecular subtypes were evaluated by the TIMER and xCell algorithms. Autodock analysis was used to predict possible binding sites of trametinib to TFs. RT‒PCR was used to verify the effect of trametinib on the expression of core TFs.

Results

According to the differential expression of TFs, HCC samples were divided into two clusters (C1 and C2). The survival time, signaling pathways, abundance of immune cell infiltration and responses to chemotherapy and immunotherapy were significantly different between C1 and C2. Nine TFs with potential prognostic value, including HMGB2, ESR1, HMGA1, MYBL2, TCF19, E2F1, FOXM1, CENPA and ZIC2, were identified by Cox regression analysis. HCC patients in the high-risk group had a poor prognosis compared with those in the low-risk group (p < 0.001). Moreover, the area under the ROC curve (AUC) values of the 1-year, 2-year and 3-year survival rates were 0.792, 0.71 and 0.695, respectively. The risk model was validated in the ICGC database. Notably, trametinib sensitivity was highly correlated with the expression of core TFs, and molecular docking predicted the possible binding sites of trametinib with these TFs. More importantly, the expression of core TFs was downregulated under trametinib treatment.

Conclusions

A prognostic signature with 9 TFs performed well in predicting the survival rate and chemotherapy/immunotherapy effect of HCC patients. Trimetinib has potential application value in HCC by targeting TFs.
Intragastric free cancer cells may be attached to automatic staplers during anastomosis in patients with gastric cancer
Authors: Ohki Atsuko , Takagi Taisuke , Kojima Yohei , Tsurumi Masanao , Hashimoto Yoshikazu , Takeuchi Hirohisa , Kamma Hiroshi , Sakamoto Yoshihiro , Sunami Eiji , Abe Nobutsugu
Published: January 2024

Background

Automatic staplers are often used to reconstruct the digestive tract during surgeries for gastric cancer. Intragastric free cancer cells adhering to automatic staplers may come in contact with the laparoscopic port area and progress to port site recurrence. This study aimed to investigate the presence/absence of cancer cells adhering to automatic staplers during gastric cancer surgery using cytological examinations. We further determined the positive predictive clinicopathological factors and clinical implications of free cancer cells attached to automatic staplers.

Methods

This study included 101 patients who underwent distal gastrectomy for gastric cancer. Automatic staplers used for anastomosis in gastric cancer surgeries were shaken in 150 ml of saline solution to collect the attached cells. Papanicolaou stains were performed. We tested the correlation between cancer-cell positivity and clinicopathological factors to identify risk factors arising from the presence of attached cancer cells to the staplers.

Results

Based on the cytology, cancer cells were detected in 7 of 101 (6.9%) stapler washing fluid samples. Univariate analysis revealed that circular staplers, type 1 tumors, and positive lymph nodes were significantly associated with higher detection of free cancer cells adhering to staplers. No significant differences in other factors were detected. Of the seven cases with positive cytology, one developed anastomotic recurrence.

Conclusions

Exfoliated cancer cells adhered to the automatic staplers used for anastomoses in 6.9% of the staplers used for distal gastrectomies in patients with gastric cancer. Staplers used for gastric cancer surgeries should be handled carefully.
Risk factors for peripherally inserted central catheter-related venous thrombosis in adult patients with cancer
Authors: Wang Pinghu , He Lianxiang , Yuan Qiong , Lu Juan , Ji Qingqiong , Peng An , Liu Wanli
Published: January 2024

Purpose

The purpose of this study was to understand and analyze the risk factors of peripherally inserted central catheter (PICC)-related venous thrombosis in adult patients with cancer.

Methods

This observational cohort study included adult patients with cancer who underwent color Doppler ultrasound at the Xiangya Hospital of Central South University, Hunan Provincial Maternal and Child Healthcare Hospital, and Xiangya Changde Hospital, Hunan Province, from January 1, 2017 to December 31, 2021. Univariate and multivariate logistic regression analyses were performed to determine the risk factors of PICC-related venous thrombosis.

Results

After risk adjustment, multivariate logistic regression analysis revealed statistically significant associations between PICC-related venous thrombosis and age > 65 years old (OR: 1.791, CI: 1.343–2.389), male sex (OR: 1.398, CI: 1.057–1.849), white blood cell count > 9.5 × 109 /L (OR: 1.422, CI: 1.041–1.942), APTT < 25 s (OR: 2.006, CI: 1.431–2.811), gastrointestinal tumor (OR: 2.191, CI: 1.406–3.414), infection (OR:7.619, CI: 5.783–10.037), the use of cisplatin (OR: 2.374, CI: 1.714–3.214), vincristine (OR: 2.329, CI: 1.447–3.749), the use of polyurethane (OR: 2.449, CI: 1.863–3.219) and open-ended catheters (OR:1.660, CI: 1.131–2.439), keeping time of the catheter (days) (OR: 1.003, CI: 1.001–1.005) were associated with PICC-related venous thrombosis.

Conclusion

We identified that the presence of age > 65 years old, male sex, white blood cell count > 9.5 × 109 /L, APTT < 25 s, gastrointestinal tumor, infection, the use of cisplatin and vincristine, the use of polyurethane, open-ended catheters and keeping time of the catheter (days), were associated with PICC-related venous thrombosis.
A primary pulmonary artery sarcoma masquerading pulmonary embolism: a case report and literature review
Authors: Liu Zhiyue , Fan Lili , Liang Shichu , Wu Zhong , Huang He
Published: January 2024

Background

Primary pulmonary artery sarcoma (PAS) is an extremely rare malignant tumor with a poor prognosis. The clinical manifestations of PAS are diverse, including dyspnea, chest pain, cough, and hemoptysis. The poor prognosis is often due to delayed diagnosis caused by similarity in imaging findings with pulmonary thromboembolism (PTE). These cues of diagnosis include the “wall eclipsing sign”, lobulated bulging margins, gadolinium enhancement during MRI imaging, and FDG uptake during PET/CT imaging. However, there are still many misdiagnoses.

Case presentation

This article reports a woman of reproductive age presenting with a pulmonary artery mass. The computed tomographic pulmonary angiography and positron emission tomography/computed tomography did not show obvious signs of pulmonary artery sarcoma, however, contrast-enhanced echocardiography showed moderate perfusion, which helped differentiate between pulmonary artery sarcoma and pulmonary artery thrombosis, leading to timely surgical treatment.

Conclusions

PAS is a rare form of cancer that can occasionally be visually similar to PTE on radiographic images. Early diagnosis of PAS is of vital importance to the prognosis of the patients. There are several visual cues that can help differentiate between the two conditions. Additionally, contrast-enhanced echocardiography provides additional information on tumor perfusion, offering another effective approach for a prompt and accurate diagnosis.
Risk factors for carotid plaque formation in type 2 diabetes mellitus
Authors: Chen Jin , Li Wenwen , Cao Jingzhu , Lu Yuhan , Wang Chaoqun , Lu Jin
Published: January 2024

Object

Patients with type 2 diabetes mellitus (T2DM) are at higher risk of developing atherosclerosis. Previous studies have analyzed the factors associated with diabetic macrovascular disease, although whether these factors are applicable to T2DM patients with carotid atherosclerosis remains unclear. Therefore, the aim of this study was to investigate the risk factors for the formation of carotid atherosclerotic plaque in hospitalized T2DM patients and to provide a theoretical basis for early prevention and treatment of carotid atherosclerosis in these patients.

Methods

A total of 949 patients with T2DM were included in the study. Carotid ultrasound identified 531 patients with carotid atherosclerotic plaque. The waist-to-hip ratio (WHR), blood glucose, liver and kidney function, blood lipid profile, islet function, and other indicators were measured at the same time to identify the risk factors and predictive significance of T2DM carotid plaque.

Results

The proportions of men, diabetes nephropathy (DN) and hypertension in T2DM patients with carotid plaque are higher than those without carotid plaque(P < 0.05). Age, duration of diabetes, WHR, Postprandial glucose (PPG), lipoprotein (a) [Lip (a)], carcinoembryonic antigen(CEA) and estimated glomerular filtration rate (eGFR) in T2DM patients with carotid plaque were higher than those without plaque (P < 0.05). Age, WHR, duration of diabetes, hypertension, males, and Lip (a) were independent risk factors for T2DM patients with carotid plaque. Age, WHR, duration of diabetes, and Lip (a) had a higher AUC to predict T2DM with carotid artery plaque (AUC: 0.750, 0.640, 0.678, 0.552 respectively; P all < 0.001). After constructing the logit (P) value of the above risk factors, the area under the ROC curve was 0.816 (0.789–0.842, P < 0.001).

Conclusion

Age, WHR, duration of diabetes, hypertension, males, and Lip (a) levels are the main risk factors for the formation of carotid plaque in T2DM patients. Combining the above risk factors provides a better prediction of carotid plaque formation in T2DM.
Identification of female-enriched and disease-associated microglia (FDAMic) contributes to sexual dimorphism in late-onset Alzheimer’s disease
Authors: Wu Deng , Bi Xiaoman , Chow Kim Hei-Man
Published: January 2024

Background

Late-onset Alzheimer’s disease (LOAD) is the most common form of dementia; it disproportionally affects women in terms of both incidence rates and severity of progression. The cellular and molecular mechanisms underlying this clinical phenomenon remain elusive and ill-defined.

Methods

In-depth analyses were performed with multiple human LOAD single-nucleus transcriptome datasets to thoroughly characterize cell populations in the cerebral cortex. ROSMAP bulk human brain tissue transcriptome and DNA methylome datasets were also included for validation. Detailed assessments of microglial cell subpopulations and their relevance to sex-biased changes at the tissue level were performed. Clinical trait associations, cell evolutionary trajectories, and transcription regulon analyses were conducted.

Results

The relative numbers of functionally defective microglia were aberrantly increased uniquely among affected females. Substratification of the microglia into different subtypes according to their transcriptomic signatures identified a group of female-enriched and disease-associated microglia (FDAMic), the numbers of which were positively associated with disease severity. Phenotypically, these cells exhibit transcriptomic signatures that support active proliferation, MHC class II autoantigen presentation and amyloid-β binding, but they are also likely defective in phagocytosis. FDAMic are likely evolved from female activated response microglia (ARMic) with anAPOE4background and compromised estrogen receptor (ER) signaling that is deemed to be active among most subtypes of microglia.

Conclusion

This study offered important insights at both the cellular and molecular levels into how ER signaling affects microglial heterogeneity and function. FDAMic are associated with more advanced pathologies and severe trends of cognitive decline. Their emergence could, at least in part, explain the phenomenon of greater penetrance of theAPOE4genotype found in females. The biases of FDAMic emergence toward female sex andAPOE4 status may also explain why hormone replacement therapy is more effective inAPOE4carriers. The pathologic nature of FDAMic suggests that selective modulations of these cells may help to regain brain neuroimmune homeostasis, serving as a new target for future drug development.
Gut microbiota, circulating cytokines and dementia: a Mendelian randomization study
Authors: Ji Dong , Chen Wen-Zhu , Zhang Lei , Zhang Zhi-Hua , Chen Li-Jian
Published: January 2024

Background

Some studies have shown that gut microbiota may be associated with dementia. However, the causal effects between gut microbiota and different types of dementia and whether cytokines act as a mediator remain unclear.

Methods

Gut microbiota, cytokines, and five dementia types, including Alzheimer’s disease (AD), frontotemporal dementia (FTD), dementia with Lewy body (DLB), vascular dementia (VD), and Parkinson’s disease dementia (PDD) were identified from large-scale genome-wide association studies (GWAS) summary data. We used Mendelian randomization (MR) to investigate the causal relationships between gut microbiota, cytokines, and five types of dementia. Inverse variance weighting (IVW) was used as the main statistical method. In addition, we explored whether cytokines act as a mediating factor in the pathway from gut microbiota to dementia.

Results

There were 20 positive and 16 negative causal effects between genetic liability in the gut microbiota and dementia. Also, there were five positive and four negative causal effects between cytokines and dementias. Cytokines did not act as mediating factors.

Conclusions

Gut microbiota and cytokines were causally associated with five types of dementia, and cytokines seemed not to be the mediating factors in the pathway from gut microbiota to dementia.
Peripheral blood amyloid-β involved in the pathogenesis of Alzheimer’s disease via impacting on peripheral innate immune cells
Authors: Shi Mingchao , Chu Fengna , Zhu Feiqi , Zhu Jie
Published: January 2024

A key pathological factor of Alzheimer’s disease (AD), the most prevalent form of age-related dementia in the world, is excessive β-amyloid protein (Aβ) in extracellular aggregation in the brain. And in the peripheral blood, a large amount of Aβ is derived from platelets. So far, the causality between the levels of peripheral blood Aβ and its aggregation in the brain, particularly the role of the peripheral blood Aβ in the pathology of AD, is still unclear. And the relation between the peripheral blood Aβ and tau tangles of brain, another crucial pathologic factor contributing to the pathogenesis of AD, is also ambiguous. More recently, the anti-Aβ monoclonal antibodies are approved for treatment of AD patients through declining the peripheral blood Aβ mechanism of action to enhance plasma and central nervous system (CNS) Aβ clearance, leading to a decrease Aβ burden in brain and improving cognitive function, which clearly indicates that the levels of the peripheral blood Aβ impacted on the Aβ burden in brain and involved in the pathogenesis of AD. In addition, the role of peripheral innate immune cells in AD remains mostly unknown and the results obtained were controversial. In the present review, we summarize recent studies on the roles of peripheral blood Aβ and the peripheral innate immune cells in the pathogenesis of AD. Finally, based on the published data and our own work, we believe that peripheral blood Aβ plays an important role in the development and progression of AD by impacting on the peripheral innate immune cells.
Characterization of an imported HIV-1 A1/A7/G recombinant in China
Authors: Li Qing-Hai , Zhang Yun-Qi , Li En-Long , Guo Qi , Chen Xiao-Hong , Wang Fu-Xiang , Wang Jia-Ye
Published: January 2024

Background

International migration has accelerated the HIV-1 spread across national borders, gradually reducing the restrictions on the geographical distribution of HIV-1 subtypes. Subtypes A and G are globally recognized as the third and sixth most dominant HIV-1 genotypes, mainly prevalent in Africa, but rarely detected in China. Here we reported an imported HIV-1 recombinant which was composed of sub-subtypes A1 and A7 of subtype A and subtype G genes in a Chinese female. This virus was the first HIV-1 recombinant including A7 genes reported in the world.

Case presentation

The near full-length genome (NFLG) was obtained from the plasma sample of the female in an HIV-1 molecular epidemiological survey with 853 participants in China. Phylogenetic analyses showed that this NFLG sequence contains three A7 segments, four G segments and one A1 segment with seven breakpoints, and all these segments were closely related to HIV-1 references circulating in Africa. The evidence from epidemiological investigation indicated that this female participant had a more-than-two-years heterosexual contact history with a fixed partner from Nigeria, a country in west Africa, which further supported the results of phylogenetic analyses. By the Bayesian phylogenetic analyses, the times of most recent common ancestors (tMRCA) of the partialpolgene (nt2308-3284, A7 region) and full-lengthvpr-vpuplus partialenvgene (nt5534-6858, G region) were estimated around 1989 and 1984, respectively.

Conclusions

In this study, by using the NFLG sequencing, we identified an imported HIV-1 A1/A7/G recombinant which was estimated to originate around 1980s in Africa and introduced into China with international migration. This study highlighted the complexity of the global HIV-1 epidemic, the necessity of using genome sequences to determine HIV-1 genotypes and the importance of real-time monitoring of HIV-1 infection among international migrants and travelers.
From beer to breadboards: yeast as a force for biological innovation
Authors: Gaikani Hamid Kian , Stolar Monika , Kriti Divya , Nislow Corey , Giaever Guri
Published: January 2024

The history of yeast Saccharomyces cerevisiae, aka brewer’s or baker’s yeast, is intertwined with our own. Initially domesticated 8,000 years ago to provide sustenance to our ancestors, for the past 150 years, yeast has served as a model research subject and a platform for technology. In this review, we highlight many ways in which yeast has served to catalyze the fields of functional genomics, genome editing, gene–environment interaction investigation, proteomics, and bioinformatics—emphasizing how yeast has served as a catalyst for innovation. Several possible futures for this model organism in synthetic biology, drug personalization, and multi-omics research are also presented.
Comparison of T-cell receptor diversity of people with myalgic encephalomyelitis versus controls
Authors: Dibble Joshua J , Ferneyhough Ben , Roddis Matthew , Millington Sam , Fischer Michael D , Parkinson Nick J , Ponting Chris P
Published: January 2024

Objective

Myalgic Encephalomyelitis (ME; sometimes referred to as Chronic Fatigue Syndrome) is a chronic disease without laboratory test, detailed aetiological understanding or effective therapy. Its symptoms are diverse, but it is distinguished from other fatiguing illnesses by the experience of post-exertional malaise, the worsening of symptoms even after minor physical or mental exertion. Its frequent onset after infection suggests autoimmune involvement or that it arises from abnormal T-cell activation.

Results

To test this hypothesis, we sequenced the genomic loci of α/δ, β and γ T-cell receptors (TCR) from 40 human blood samples from each of four groups: severely affected people with ME; mildly or moderately affected people with ME; people diagnosed with Multiple Sclerosis, as disease controls; and, healthy controls. Seeking to automatically classify these individuals’ samples by their TCR repertoires, we applied P-SVM, a machine learning method. However, despite working well on a simulated data set, this approach did not allow statistically significant partitioning of samples into the four subgroups. Our findings do not support the hypothesis that blood samples from people with ME frequently contain altered T-cell receptor diversity.
The impact of SLC10A3 on prognosis and immune microenvironment in colorectal adenocarcinoma
Authors: Wang Bangting , Fan Wentao , Tao Yuwen , Zhang Shijie , Wang Jiankun , Fan Zhining , Liu Li , Wang Yan
Published: January 2024

Background

SLC10A3, a gene upregulated in pan-cancer, lacks full understanding regarding its prognostic implications and association with immune infiltration in colorectal cancer (CRC). This study comprehensively analyzed SLC10A3 in CRC, evaluating its prognostic significance and influence on the tumor's immune microenvironment.

Methods

Transcriptomic data from TCGA were obtained to compare SLC10A3 expression in both colorectal cancer (CRC) and normal tissues. Prognostic value was assessed for overall survival (OS), disease-specific survival (DSS), and progression-free interval (PFI). DNA methylation patterns of SLC10A3 and correlation with DNA mismatch repair (MMR) were explored. Genetic alterations in SLC10A3 were scrutinized. The study also delved into the influence of SLC10A3 on the immune microenvironment of CRC, including immune cell infiltration and chemokines. Involvement of cancer-associated fibroblasts (CAFs) was explored. Methylation status of specific CpG islands in the SLC10A3 gene correlated with CRC patient prognosis. CRC tissue microarray was performed to verify the expression of SLC10A3 and its relationship with prognosis.

Results

The research revealed that SLC10A3 is significantly upregulated in CRC and holds promise as a potential diagnostic marker. Elevated SLC10A3 expression was linked to poorer OS, DSS, and PFI. Methylation patterns of SLC10A3 displayed prognostic relevance, and genetic alterations in the gene were identified. SLC10A3 was shown to impact the immune microenvironment, with significant correlations observed between its expression and various immune cell types, chemokines, and markers associated with CAFs. Furthermore, an inverse relationship between SLC10A3 and MMR molecules was established. Methylation status of specific CpG islands within the SLC10A3 gene was associated with CRC patient prognosis. Tissue microarray showed that SLC10A3 was highly expressed in CRC and significantly correlated with poor prognosis.

Conclusion

The study underscores the importance of elevated SLC10A3 in CRC, associating it with decreased survival and immune infiltration, proposing it as a diagnostic biomarker and appealing immunotherapy target, given its significant overexpression and influence on the immune microenvironment and prognosis through methylation patterns.

Graphical Abstract
Grammar enhancement in EFL instruction: a reflection on the effects of self-evaluation, teacher support, and L2 grit
Authors: Wang Kelu
Published: January 2024

Advancement in learning grammar and using it practically is one of the challenges of English as foreign learners (EFL) learners. Its progression may be expedited or slowed down by a variety of causes. Among the crucial factors, the possible effects of self-evaluation, teacher support, and L2 grit were still untouched which is the target of the current research. In so doing, 86 EFL students at the intermediate level were divided into two groups (i.e., experimental group and control group). The students in the control group (CG) are exposed to normal education, whereas learners in experimental group (EG) get extra instruction to practice self-evaluation and L2 Grit. Moreover, the emphasis on the teacher’s position as a facilitator and supporter was more prominent in the EG. Based on data screening which was completed via one-way ANCOVA, learners in EG were more successful in grammar assessment due to the treatment. Further research avenues and educational implications were elaborated upon.
Angle-dependent 4D seismic time-strain inversion for estimating subsurface thickness and velocity changes
Authors: Taweesintananon Kittinat , Landrø Martin , Narongsirikul Sirikarn , Folstad Per Gunnar
Published: January 2024

In time-lapse (also called 4D) seismic analysis, the time shift of a certain seismic reflection event is caused by changes in the seismic velocity and the depth of the event. An interpretation of 4D time shifts is normally simplified by neglecting displacement changes (strains) or assuming linear relations between thickness and velocity strains. Here, we go beyond these assumptions and propose a least-squares optimization method to simultaneously estimate the thickness and velocity strains in vertical transverse isotropic media from angle-dependent 4D seismic time strains. Through examples from synthetic and field data, we show that 4D thickness strains, velocity strains, and anisotropic parameter changes can be estimated simultaneously without prior knowledge about the geomechanics of the survey area. Our time-strain inversion method can be applied to any other 4D seismic data set in which angle-stack images are available. We see that our method has high potential in many other applications, because thickness and velocity strains are the fundamental components of most physical properties used in 4D seismic and geomechanics applications.
Updates on Systemic Therapy for Hepatocellular Carcinoma
Authors: Ntellas Panagiotis , Chau Ian
Published: January 2024

This review explores the dynamic landscape of hepatocellular carcinoma (HCC) treatment, emphasizing on recent developments across various stages and therapeutic approaches. Although curative strategies such as hepatectomy and thermal ablation are standard for early-stage cases, high relapse rates drive investigations into adjuvant and perioperative treatment. Adjuvant therapies face hurdles, but noteworthy advances include IMbrave050 setting a new standard with atezolizumab/bevacizumab. Locoregional treatments gain significance, especially for multifocal HCC, with the integration of innovative combinations with systemic therapies, showing improved outcomes. In the advanced setting, the evolution from sorafenib as the primary first-line option to new standards, such as atezolizumab/bevacizumab and tremelimumab/durvalumab, to other emerging therapies such as tislelizumab and pembrolizumab with lenvatinib, is explored. Additionally, second-line treatments and insights into the interplay between immunotherapies and antiangiogenic agents, as well as novel combination strategies that add complexity to treatment decisions, are discussed.
Organogenetic transcriptomes of the Drosophila embryo at single cell resolution
Authors: Peng Da , Jackson Dorian , Palicha Bianca , Kernfeld Eric , Laughner Nathaniel , Shoemaker Ashleigh , Celniker Susan E. , Loganathan Rajprasad , Cahan Patrick , Andrew Deborah J.
Published: January 2024

To gain insight into the transcription programs activated during the formation of Drosophila larval structures, we carried out single cell RNA sequencing during two periods of Drosophila embryogenesis: stages 10-12, when most organs are first specified and initiate morphological and physiological specialization; and stages 13-16, when organs achieve their final mature architectures and begin to function. Our data confirm previous findings with regards to functional specialization of some organs – the salivary gland and trachea – and clarify the embryonic functions of another – the plasmatocytes. We also identify two early developmental trajectories in germ cells and uncover a potential role for proteolysis during germline stem cell specialization. We identify the likely cell type of origin for key components of the Drosophila matrisome and several commonly used Drosophila embryonic cell culture lines. Finally, we compare our findings with other recent related studies and with other modalities for identifying tissue-specific gene expression patterns. These data provide a useful community resource for identifying many new players in tissue-specific morphogenesis and functional specialization of developing organs.
Social influence and external feedback control in humans
Authors: Weiß Martin , Gollwitzer Mario , Hewig Johannes
Published: January 2024

This article aims to unravel the dynamics of social influence by examining the processes that occur when one person is the target of another’s influence. We hypothesized that these processes are part of a feedback loop system in an individual. This loop involves the situation (input), a goal state (reference), a comparator, a selection mechanism, a feedback predictor, and an action (output). Each element can become the target of social influence, and different types of social influence can be classified and explained by how these elements are targeted. For instance, attempting to persuade another person with strong arguments targets the goal state of the affected individual, while obedience targets the selection mechanism, and violence targets the action. In summary, this article aims to categorize, order, and explain phenomena in social influence research using a feedback loop framework focusing on the influenced individual.
Pesticide exposure and lung cancer risk: A case-control study in Nakhon Sawan, Thailand
Authors: Kangkhetkron Teera , Juntarawijit Chudchawal
Published: January 2024

Background Pesticide exposure might increase risk of lung cancer. The purpose of this study was to investigate the association between the historical use of pesticides and lung cancer using a case-control design. Methods This case-control study compared a lifetime pesticide exposure of 233 lung cancer cases, and 447 healthy neighbours matched for gender, and age (±5 years). Data on demographic, pesticide exposure and other related factors were collected using a face-to-face interview questionnaire. Associations between lung cancer and types of pesticides as well as individual pesticides were analysed using logistic regression adjusted for gender, age, cigarette smoking, occupation, cooking fumes exposure, and exposure to air pollution. Results It was found that lung cancer was positively associated with the lifetime use of herbicides and insecticides. Compared to people in the non-exposed groups, those in Q3-Q4 days of using herbicides and insecticides had an elevated risk of lung cancer, with odds ratio (OR) between 2.20 (95% confidence interval (CI) 1.24-3.89), and 3.99 (95% CI 1.62-7.11) (p < 0.001). For individual pesticides, those presenting a significant association with lung cancer were dieldrin (OR = 2.56; 95% CI 1.36-4.81), chlorpyrifos (OR = 3.29; 95 % CI 1.93-5.61), and carbofuran (OR = 2.10; 95% CI 1.28-3.42). It was also found, for the first time, carbofuran, glyphosate, and paraquat to be significantly associated with lung cancer. Conclusions The study confirmed dieldrin, and chlorpyrifos as risk factors and suggested carbofuran, glyphosate, and paraquat as potential risk factors for the disease. The paper stands as a noteworthy contribution to literature, particularly because the majority of publications on the topic originate from developed Western countries. However, further studies are imperative to validate the results and pinpoint additional individual pesticides that may be associated with lung cancer.
Convolution Neural Networks for Disease Prediction: Applications and Challenges
Authors: Mushtaq Snowber , Singh Omkar
Published: January 2024

More people are using Deep Learning techniques in the healthcare field as a result of the quick development in domains like Computer Vision, Graphics Processing Technology, and the accessibility of medical imaging datasets. Convolutional Neural Networks (CNNs), in particular, have quickly emerged as the preferred technique for processing clinical data. CNN-based designs have been embraced by the diagnostic imaging group to assist physicians with disease identification. Since AlexNet's enormous success in 2012, CNNs have indeed been employed more and more in the analysis of medical images to boost the effectiveness of physicians. This article summarises various CNN architectures for predicting medical diseases and their challenges. We examine the utilization of Deep Learning for the prediction of various diseases, including Brain diseases, Diabetic Retinopathy, and Lung cancer. This research also provides a survey of datasets available for analysis.
Network Security with Virtual Reality based Antivirus Protection and Reduced Detection Delays
Authors: Song Chunna , Cheng Jinfang , Zhang Guoqiu
Published: January 2024

Addressing the persistent delay problem in traditional network security antivirus protection systems, this paper introduces an innovative approach utilizing virtual reality (VR) technology. The primary objective is to significantly reduce detection delays and enhance the efficiency of network security measures. An enhanced decision-making algorithm is proposed to identify relevant features associated with network security. These features are then weighted and optimized to improve the overall detection process. An injection list is generated through web crawling techniques to strengthen security measures. A virtual protection block is also developed to serve as a barrier against potential threats. The proposed method claims a detection delay of only 75.33 milliseconds, significantly outperforming two traditional methods that recorded 290.11 milliseconds and 337.30 milliseconds, respectively. This substantial decrease in detection delay emphasizes the effectiveness of automatic detection within the context of VR technology. Practical implementation and empirical evidence further validate the success of this approach. The automatic detection of network security vulnerabilities within the VR technology framework is efficient and exhibits considerable progress. As such, this research offers a promising solution to the delay problem in network security antivirus protection. Embracing VR technology achieves shorter detection delays, ultimately improving the security posture of network systems.
Computer Network Virus Defense with Data Mining-based Active Protection
Authors: Li Xiaohong , Li Yang , He Hong
Published: January 2024

A novel approach is presented in this paper to address the limitations of virtual machine technology, active kernel technology, heuristic killing technology, and behaviour killing technology in computer network virus defence. The proposed method provides data mining technology, specifically Object-Oriented Analysis (OOA) mining, to detect deformed and unknown viruses by analyzing the sequence of Win API calls in PE files. Experimental results showcase the Data Mining-based Antivirus (DMAV) system's superiority over existing virus scanning software in multiple aspects: higher accuracy in deformed virus detection, enhanced active defence capabilities against unknown viruses (with a recognition rate of 92%), improved efficiency, and a reduced false alarm rate for non-virus file detection. Furthermore, the paper introduces an OOA rule generator to optimize feature extraction, enhancing the system's intelligence and robustness. This research provides a promising solution to support virus detection accuracy, active defence mechanisms, and overall efficiency while minimizing false positives in virus scanning, thus contributing significantly to the advancement of computer network security.
Application of Nonlinear Big Data Analysis Techniques in Computer Software Reliability Prediction
Authors: Gao Li , Wang Hai
Published: January 2024

This research addresses the difficulties of underfitting, overfitting, and convergence to local minima in artificial neural networks for software dependability prediction. The work specifically focuses on enhancing the performance of the conventional PSO-SVM model for software reliability prediction. The analysis of the conventional PSO-SVM model and the special features of software reliability prediction serve as the foundation. An improved PSO-SVM software reliability prediction model is developed and the PSO-SVM model and a Backpropagation (BP) prediction model are compared experimentally. The critical metrics assessed include training error, and efficiency. The experimental results reveal that the training error of the enhanced PSO-LSSVM prediction model diminishes rapidly, levelling off after approximately 200 training generations. The BP prediction model requires 1,733 generations to meet training requirements. Furthermore, the improved PSO-LSSVM prediction model demonstrates significantly higher training efficiency than the BP prediction model. The optimized prediction model exhibits superior adaptability to small sample sizes, swift training, and high prediction accuracy, making it a more suitable choice for software reliability prediction applications.