bluuebunny/crossref_metadata_2025_split huggingface dataset:
Construction of an enzyme-constrained metabolic network model for Myceliophthora thermophila using machine learning-based kcat data
Authors: Wang Yutao , Mao Zhitao , Dong Jiacheng , Zhang Peiji , Gao Qiang , Liu Defei , Tian Chaoguang , Ma Hongwu 
Published: May 2024

Abstract
Background
Genome-scale metabolic models (GEMs) serve as effective tools for understanding cellular phenotypes and predicting engineering targets in the development of industrial strain. Enzyme-constrained genome-scale metabolic models (ecGEMs) have emerged as a valuable advancement, providing more accurate predictions and unveiling new engineering targets compared to models lacking enzyme constraints. In 2022, a stoichiometric GEM, iDL1450, was reconstructed for the industrially significant fungus Myceliophthora thermophila. To enhance the GEM’s performance, an ecGEM was developed for M. thermophila in this study.

Results
Initially, the model iDL1450 underwent refinement and updates, resulting in a new version named iYW1475. These updates included adjustments to biomass components, correction of gene-protein-reaction (GPR) rules, and a consensus on metabolites. Subsequently, the first ecGEM for M. thermophila was constructed using machine learning-based kcat data predicted by TurNuP within the ECMpy framework. During the construction, three versions of ecGEMs were developed based on three distinct kcat collection methods, namely AutoPACMEN, DLKcat and TurNuP. After comparison, the ecGEM constructed using TurNuP-predicted kcat values performed better in several aspects and was selected as the definitive version of ecGEM for M. thermophila (ecMTM). Comparing ecMTM to iYW1475, the solution space was reduced and the growth simulation results more closely resembled realistic cellular phenotypes. Metabolic adjustment simulated by ecMTM revealed a trade-off between biomass yield and enzyme usage efficiency at varying glucose uptake rates. Notably, hierarchical utilization of five carbon sources derived from plant biomass hydrolysis was accurately captured and explained by ecMTM. Furthermore, based on enzyme cost considerations, ecMTM successfully predicted reported targets for metabolic engineering modification and introduced some new potential targets for chemicals produced in M. thermophila.

Conclusions
In this study, the incorporation of enzyme constraint to iYW1475 not only improved prediction accuracy but also broadened the model’s applicability. This research demonstrates the effectiveness of integrating of machine learning-based kcat data in the construction of ecGEMs especially in situations where there is limited measured enzyme kinetic parameters for a specific organism.
Efficacy of Pirikool® 300 CS used for indoor residual spraying on three different substrates in semi-field experimental conditions
Authors: Fodjo Behi Kouadio , Tchicaya Emile , Yao Laurence Aya , Edi Constant , Ouattara Alassane Foungoye , Kouassi Loukou Bernard , Yokoly Firmain N’dri , Benjamin Koudou Guibéhi 
Published: May 2024

Abstract
Background
Vector control using insecticides is a key prevention strategy against malaria. Unfortunately, insecticide resistance in mosquitoes threatens all progress in malaria control. In the perspective of managing this resistance, new insecticide formulations are being tested to improve the effectiveness of vector control tools.

Methods
The efficacy and residual activity of Pirikool® 300 CS was evaluated in comparison with Actellic® 300 CS in experimental huts at the Tiassalé experimental station on three substrates including cement, wood and mud. The mortality, blood-feeding inhibition, exiting behaviour and deterrency of free-flying wild mosquitoes was evaluated. Cone bioassay tests with susceptible and resistant mosquito strains were conducted in the huts to determine residual efficacy.

Results
A total of 20,505 mosquitoes of which 10,979 (53%) wild female Anopheles gambiae were collected for 112 nights. Residual efficacy obtained from monthly cone bioassay was higher than 80% with the susceptible, laboratory-maintained An. gambiae Kisumu strain, from the first to the tenth study period on all three types of treated substrate for both Actellic® 300CS and Pirikool® 300CS. This residual efficacy on the wild Tiassalé strain was over 80% until the 4th month of study on Pirikool® 300CS S treated substrates. Overall 24-h mortalities of wild free-flying An. gambiae sensu lato which entered in the experimental huts over the 8-months trial on Pirikool® 300CS treatment was 50.5%, 75.9% and 52.7%, respectively, on cement wall, wood wall and mud wall. The positive reference product Actellic® 300CS treatment induced mortalities of 42.0%, 51.8% and 41.8% on cement wall, wood wall and mud wall.

Conclusion
Pirikool® 300CS has performed really well against resistant strains of An. gambiae using indoor residual spraying method in experimental huts. It could be an alternative product for indoor residual spraying in response to the vectors' resistance to insecticides.
Cost-effectiveness of village health worker-led integrated community case management (iCCM) versus health facility based management for childhood illnesses in rural southwestern Uganda
Authors: Mulogo Edgar , Ntaro Moses , Wesuta Andrew , Namusisi Jane , Kawungezi Peter , Batwala Vincent , Matte Michael 
Published: May 2024

Abstract
Background
In Uganda, village health workers (VHWs) manage childhood illness under the integrated community case management (iCCM) strategy. Care is provided for malaria, pneumonia, and diarrhoea in a community setting. Currently, there is limited evidence on the cost-effectiveness of iCCM in comparison to health facility-based management for childhood illnesses. This study examined the cost-effectiveness of the management of childhood illness using the VHW-led iCCM against health facility-based services in rural south-western Uganda.

Methods
Data on the costs and effectiveness of VHW-led iCCM versus health facility-based services for the management of childhood illness was collected in one sub-county in rural southwestern Uganda. Costing was performed using the ingredients approach. Effectiveness was measured as the number of under-five children appropriately treated. The Incremental Cost-Effectiveness Ratio (ICER) was calculated from the provider perspective.

Results
Based on the decision model for this study, the cost for 100 children treated was US$628.27 under the VHW led iCCM and US$87.19 for the health facility based services, while the effectiveness was 77 and 71 children treated for VHW led iCCM and health facility-based services, respectively. An ICER of US$6.67 per under five-year child treated appropriately for malaria, pneumonia and diarrhoea was derived for the provider perspective.

Conclusion
The health facility based services are less costly when compared to the VHW led iCCM per child treated appropriately. The VHW led iCCM was however more effective with regard to the number of children treated appropriately for malaria, pneumonia and diarrhoea. Considering the public health expenditure per capita for Uganda as the willingness to pay threshold, VHW led iCCM is a cost-effective strategy. VHW led iCCM should, therefore, be enhanced and sustained as an option to complement the health facility-based services for treatment of childhood illness in rural contexts.
Causal relationship of interleukin-6 and its receptor on sarcopenia traits using mendelian randomization
Authors: Chen Baixing , Li Shaoshuo , Lin Shi , Dong Hang 
Published: May 2024

Abstract
Background
Previous research has extensively examined the role of interleukin 6 (IL-6) in sarcopenia. However, the presence of a causal relationship between IL-6, its receptor (IL-6R), and sarcopenia remains unclear.

Method
In this study, we utilized summary-level data from genome-wide association studies (GWAS) focused on appendicular lean mass (ALM), hand grip strength, and walking pace. Single nucleotide polymorphisms (SNPs) were employed as genetic instruments for IL-6 and IL-6R to estimate the causal effect of sarcopenia traits. We adopted the Mendelian randomization (MR) approach to investigate these associations using the inverse variance weighted (IVW) method as the primary analytical approach. Additionally, we performed sensitivity analyses to validate the reliability of the MR results.

Result
This study revealed a significant negative association between main IL-6R and eQTL IL-6R on the left grip strength were − 0.013 (SE = 0.004, p < 0.001) and -0.029 (SE = 0.007, p < 0.001), respectively. While for the right grip strength, the estimates were − 0.011 (SE = 0.001, p < 0.001) and − 0.021 (SE = 0.008, p = 0.005). However, no evidence of an association for IL-6R with ALM and walking pace. In addition, IL-6 did not affect sarcopenia traits.

Conclusion
Our study findings suggest a negative association between IL-6R and hand grip strength. Additionally, targeting IL-6R may hold potential value as a therapeutic approach for the treatment of hand grip-related issues.
iTRAQ-based proteomic study on monocyte cell model discovered an association of LAMP2 downregulation with HIV-1 latency
Authors: Yin Lin , Wang Qimin , Liu Siyuan , Chen Jun , Zhang Yujiao , Lu Lingqing , Lu Hongzhou , Song Zhigang , Zhang Lijun 
Published: May 2024

Abstract
Background
Patients with immunodeficiency virus-1 (HIV-1) infection are challenging to be cured completely due to the existence of HIV-1 latency reservoirs. However, the knowledge of the mechanisms and biomarkers associated with HIV-1 latency is limited. Therefore, identifying proteins related to HIV-1 latency could provide new insights into the underlying mechanisms of HIV-1 latency, and ultimately contribute to the eradication of HIV reservoirs.

Methods
An Isobaric Tags for Relative and Absolute Quantification (iTRAQ)-labeled subcellular proteomic study was performed on an HIV-1 latently infected cell model (U1, a HIV-1-integrated U937 cell line) and its control (U937). Differentially expressed proteins (DEPs) were analyzed using STRING-DB. Selected DEPs were further evaluated by western blotting and multiple reaction monitoring technology in both cell model and patient-derived cluster of differentiation 4 (CD4)+ T cells. Finally, we investigated the relationship between a specific DEP lysosome-associated membrane glycoprotein 2 (LAMP2) and HIV-1 reactivation by panobinostat or lysosome regulation by a lysosomotropic agent hydroxychloroquine in U1 and U937 cells.

Results
In total, 110 DEPs were identified in U1 cells comparing to U937 control cells. Bioinformatics analysis suggested associations of the altered proteins with the immune response and endosomal/lysosomal pathway. LAMP2, leukocyte surface antigen CD47, CD55, and ITGA6 were downregulated in HIV-1 latent cells. Downregulated LAMP2 was further confirmed in resting CD4+ T cells from patients with latent HIV-1 infection. Furthermore, both HIV-1 reactivation by panobinostat and stimulation with hydroxychloroquine upregulated LAMP2 expression.

Conclusions
Our results indicated the involvement of the endosomal/lysosomal pathway in HIV-1 latency in macrophage cell model. The down-modulation of LAMP2 was associated with HIV latency, and the restoration of LAMP2 expression accompanied the transition of viral latency to active infection. This study provides new insights into the mechanism of HIV-1 latency and potential strategies for eradicating HIV-1 reservoirs by targeting LAMP2 expression.
Knockdown of trem2 promotes proinflammatory microglia and inhibits glioma progression via the JAK2/STAT3 and NF-κB pathways
Authors: Yan Yunji , Bai Shengwei , Han Hongxi , Dai Junqiang , Niu Liang , Wang Hongyu , Dong Qiang , Yin Hang , Yuan Guoqiang , Pan Yawen 
Published: May 2024

Abstract
Background
In the tumor immune microenvironment (TIME), triggering receptor expressed on myeloid cells 2 (trem2) is widely considered to be a crucial molecule on tumor-associated macrophages(TAMs). Multiple studies have shown that trem2 may function as an immune checkpoint in various malignant tumors, mediating tumor immune evasion. However, its specific molecular mechanisms, especially in glioma, remain elusive.

Methods
Lentivirus was transfected to establish cells with stable knockdown of trem2. A Transwell system was used for segregated coculture of glioma cells and microglia. Western blotting, quantitative real-time polymerase chain reaction (qRT‒PCR), and immunofluorescence (IF) were used to measure the expression levels of target proteins. The proliferation, invasion, and migration of cells were detected by colony formation, cell counting kit-8 (CCK8), 5-ethynyl-2’-deoxyuridine (EdU) and transwell assays. The cell cycle, apoptosis rate and reactive oxygen species (ROS) level of cells were assessed using flow cytometry assays. The comet assay and tube formation assay were used to detect DNA damage in glioma cells and angiogenesis activity, respectively. Gl261 cell lines and C57BL/6 mice were used to construct the glioma orthotopic transplantation tumor model.

Results
Trem2 was highly overexpressed in glioma TAMs. Knocking down trem2 in microglia suppressed the growth and angiogenesis activity of glioma cells in vivo and in vitro. Mechanistically, knockdown of trem2 in microglia promoted proinflammatory microglia and inhibited anti-inflammatory microglia by activating jak2/stat1 and inhibiting the NF-κB p50 signaling pathway. The proinflammatory microglia produced high concentrations of nitric oxide (NO) and high levels of the proinflammatory cytokines TNF-α, IL-6, and IL-1β, and caused further DNA damage and promoted the apoptosis rate of tumor cells.

Conclusions
Our findings revealed that trem2 in microglia plays a significant role in the TIME of gliomas. Knockdown of trem2 in microglia might help to improve the efficiency of inhibiting glioma growth and delaying tumor progression and provide new ideas for further treatment of glioma.
Learning from the Active Hospital-Based Cancer Registry in India: An Ethnography Study
Authors: Jena Shubharanjan , Epari Venkatarao , Sahoo Krushna Chandra , Pradhan Smruti Priyambada , Agrawala Sunil , Padhi Sanjukta 
Published: May 2024

Abstract
Purpose
The increasing incidence of cancer in low- and middle-income countries highlights the need for better cancer data management. Hospital-based cancer registries (HBCRs) enhance patient outcomes by managing cancer data, reviewing clinical performance and allocating resources. However, sustainability remains a challenge despite government initiatives. Therefore, this study documented the functionalities, core processes, and team involvement of active HBCRs in India, aiming to identify factors that facilitate their sustainability.

Methods
An ethnographic study was conducted in two Indian hospitals, one specializing in cancer care and the other offering multispecialty services, focusing on their HBCRs. The study involved process observations, interviews, and record reviews, with thematic analysis guided by ethnographic investigations. The staff managing the HBCRs were key participants.

Results
The findings are categorized into three themes: (1) existing management strategies and infrastructure, (2) the implementation process, and (3) the sustainability and scalability of the registry model. This study highlights the key factors necessary for a sustainable HBCR, including human resources, training, and a well-structured management system. The involvement of oncologists and physicians, funding, qualified staff, adequate space, and digitalization are crucial for success. Data management errors can be minimized through training, while interdepartmental coordination and data quality play essential roles.

Conclusion
This study offers critical insights into enhancing cancer surveillance systems, thereby improving cancer care and public health interventions in India and similar contexts worldwide. Policymakers and healthcare practitioners can leverage these findings to strengthen existing systems and address the growing burden of cancer effectively.
Development of an interpretable machine learning model associated with genetic indicators to identify Yin-deficiency constitution
Authors: Li Jing , Zhai Yingying , Cao Yanqi , Xia Yifan , Yu Ruoxi 
Published: May 2024

Abstract
Background
Traditional Chinese Medicine (TCM) defines constitutions which are relevant to corresponding diseases among people. As one of the common constitutions, Yin-deficiency constitution influences a number of Chinese population in the disease onset. Therefore, accurate Yin-deficiency constitution identification is significant for disease prevention and treatment.

Methods
In this study, we collected participants with Yin-deficiency constitution and balanced constitution, separately. The least absolute shrinkage and selection operator (LASSO) and logistic regression were used to analyze genetic predictors. Four machine learning models for Yin-deficiency constitution classification with multiple combined genetic indicators were integrated to analyze and identify the optimal model and features. The Shapley Additive exPlanations (SHAP) interpretation was developed for model explanation.

Results
The results showed that, NFKBIA, BCL2A1 and CCL4 were the most associated genetic indicators with Yin-deficiency constitution. Random forest with three genetic predictors including NFKBIA, BCL2A1 and CCL4 was the optimal model, area under curve (AUC): 0.937 (95% CI 0.844–1.000), sensitivity: 0.870, specificity: 0.900. The SHAP method provided an intuitive explanation of risk leading to individual predictions.

Conclusion
We constructed a Yin-deficiency constitution classification model based on machine learning and explained it with the SHAP method, providing an objective Yin-deficiency constitution identification system in TCM and the guidance for clinicians.
Fusogenic vesicular stomatitis virus combined with natural killer T cell immunotherapy controls metastatic breast cancer
Authors: Nelson Adam , McMullen Nichole , Gebremeskel Simon , De Antueno Roberto , Mackenzie Duncan , Duncan Roy , Johnston Brent 
Published: May 2024

Abstract
Background
Metastatic breast cancer is a leading cause of cancer death in woman. Current treatment options are often associated with adverse side effects and poor outcomes, demonstrating the need for effective new treatments. Immunotherapies can provide durable outcomes in many cancers; however, limited success has been achieved in metastatic triple negative breast cancer. We tested whether combining different immunotherapies can target metastatic triple negative breast cancer in pre-clinical models.

Methods
Using primary and metastatic 4T1 triple negative mammary carcinoma models, we examined the therapeutic effects of oncolytic vesicular stomatitis virus (VSVΔM51) engineered to express reovirus-derived fusion associated small transmembrane proteins p14 (VSV-p14) or p15 (VSV-p15). These viruses were delivered alone or in combination with natural killer T (NKT) cell activation therapy mediated by adoptive transfer of α-galactosylceramide-loaded dendritic cells.

Results
Treatment of primary 4T1 tumors with VSV-p14 or VSV-p15 alone increased immunogenic tumor cell death, attenuated tumor growth, and enhanced immune cell infiltration and activation compared to control oncolytic virus (VSV-GFP) treatments and untreated mice. When combined with NKT cell activation therapy, oncolytic VSV-p14 and VSV-p15 reduced metastatic lung burden to undetectable levels in all mice and generated immune memory as evidenced by enhanced in vitro recall responses (tumor killing and cytokine production) and impaired tumor growth upon rechallenge.

Conclusion
Combining NKT cell immunotherapy with enhanced oncolytic virotherapy increased anti-tumor immune targeting of lung metastasis and presents a promising treatment strategy for metastatic breast cancer.
Association of area- and volumetric-mammographic density and breast cancer risk in women of Asian descent: a case control study
Authors: Mariapun Shivaani , Ho Weang-Kee , Eriksson Mikael , Mohd Taib Nur Aishah , Yip Cheng-Har , Rahmat Kartini , Hall Per , Teo Soo-Hwang 
Published: May 2024

Abstract
Background
Mammographic density (MD) has been shown to be a strong and independent risk factor for breast cancer in women of European and Asian descent. However, the majority of Asian studies to date have used BI-RADS as the scoring method and none have evaluated area and volumetric densities in the same cohort of women. This study aims to compare the association of MD measured by two automated methods with the risk of breast cancer in Asian women, and to investigate if the association is different for premenopausal and postmenopausal women.

Methods
In this case–control study of 531 cases and 2297 controls, we evaluated the association of area-based MD measures and volumetric-based MD measures with breast cancer risk in Asian women using conditional logistic regression analysis, adjusting for relevant confounders. The corresponding association by menopausal status were assessed using unconditional logistic regression.

Results
We found that both area and volume-based MD measures were associated with breast cancer risk. Strongest associations were observed for percent densities (OR (95% CI) was 2.06 (1.42–2.99) for percent dense area and 2.21 (1.44–3.39) for percent dense volume, comparing women in highest density quartile with those in the lowest quartile). The corresponding associations were significant in postmenopausal but not premenopausal women (premenopausal versus postmenopausal were 1.59 (0.95–2.67) and 1.89 (1.22–2.96) for percent dense area and 1.24 (0.70–2.22) and 1.96 (1.19–3.27) for percent dense volume). However, the odds ratios were not statistically different by menopausal status [p difference = 0.782 for percent dense area and 0.486 for percent dense volume].

Conclusions
This study confirms the associations of mammographic density measured by both area and volumetric methods and breast cancer risk in Asian women. Stronger associations were observed for percent dense area and percent dense volume, and strongest effects were seen in postmenopausal individuals.
High-definition transcranial direct current stimulation (HD-tDCS) in major depressive disorder with anxious distress—a study protocol for a double-blinded randomized sham-controlled trial
Authors: Zhang Danwei , Zhao Bei , Sun Xue , Ding Kaimo , Sun Jingjing , Tao Sheng 
Published: May 2024

Abstract
Background
Comorbid anxiety disorders and anxious distress are highly prevalent among individuals with major depressive disorder (MDD). The presence of the DSM-5 anxious distress specifier (ADS) has been associated with worse treatment outcomes and chronic disease course. Few studies have evaluated the therapeutic effects of High-definition transcranial direct current stimulation (HD-tDCS) on depressive and anxiety symptoms among MDD patients with ADS. The current randomized controlled trial aims to assess the efficacy of HD-tDCS as an augmentation therapy with antidepressants compared to sham-control in subjects of MDD with ADS.

Methods
MDD patients with ADS will be recruited and randomly assigned to the active HD-tDCS or sham HD-tDCS group. In both groups, patients will receive the active or sham intervention in addition to their pre-existing antidepressant therapy, for 2 weeks with 5 sessions per week, each lasting 30 min. The primary outcome measures will be the change of depressive symptoms, clinical response, and the remission rate as measured with the 17-item Hamilton Depression Rating Scale (HDRS-17) before and after the intervention and at the 2nd and 6th week after the completed intervention. Secondary outcome measures include anxiety symptoms, cognitive symptoms, disability assessment, and adverse effects.

Discussion
The HD-tDCS applied in this trial may have treatment effects on MDD with ADS and have minimal side effects.

Trial registration
The trial protocol is registered with www.chictr.org.cn under protocol registration number ChiCTR2300071726. Registered 23 May 2023.