bluuebunny/crossref_metadata_2025_split huggingface dataset:
Comparative assessment of the capability of machine learning-based radiomic models for predicting omental metastasis in locally advanced gastric cancer
Authors: Wu Ahao , Luo Lianghua , Zeng Qingwen , Wu Changlei , Shu Xufeng , Huang Pang , Wang Zhonghao , Hu Tengcheng , Feng Zongfeng , Tu Yi , Zhu Yanyan , Cao Yi , Li Zhengrong 
Published: July 2024

AbstractThe study aims to investigate the predictive capability of machine learning algorithms for omental metastasis in locally advanced gastric cancer (LAGC) and to compare the performance metrics of various machine learning predictive models. A retrospective collection of 478 pathologically confirmed LAGC patients was undertaken, encompassing both clinical features and arterial phase computed tomography images. Radiomic features were extracted using 3D Slicer software. Clinical and radiomic features were further filtered through lasso regression. Selected clinical and radiomic features were used to construct omental metastasis predictive models using support vector machine (SVM), decision tree (DT), random forest (RF), K-nearest neighbors (KNN), and logistic regression (LR). The models’ performance metrics included accuracy, area under the curve (AUC) of the receiver operating characteristic curve, sensitivity, specificity, positive predictive value (PPV), and negative predictive value (NPV). In the training cohort, the RF predictive model surpassed LR, SVM, DT, and KNN in terms of accuracy, AUC, sensitivity, specificity, PPV, and NPV. Compared to the other four predictive models, the RF model significantly improved PPV. In the test cohort, all five machine learning predictive models exhibited lower PPVs. The DT model demonstrated the most significant variation in performance metrics relative to the other models, with a sensitivity of 0.231 and specificity of 0.990. The LR-based predictive model had the lowest PPV at 0.210, compared to the other four models. In the external validation cohort, the performance metrics of the predictive models were generally consistent with those in the test cohort. The LR-based model for predicting omental metastasis exhibited a lower PPV. Among the machine learning algorithms, the RF predictive model demonstrated higher accuracy and improved PPV relative to LR, SVM, KNN, and DT models.
Synergistic effect of Al2O3-decorated reduced graphene oxide on microstructure and mechanical properties of 6061 aluminium alloy
Authors: Wang Hongding , Zheng Haitao , Hu Mingshuai , Ma Zhonglei , Liu Hong 
Published: July 2024

AbstractIn this study, Al6061 alloy matrix composites reinforced Al2O3-decorated reduced graphene oxide (Al2O3/RGO) with 0.1, 0.3 and 0.5 weight present (wt%) were successfully fabricated using high energy ball milling and hot extrusion techniques. The microstructures of these Al2O3/RGO/Al6061 aluminum matrix composites (Al MMCs) were characterized. The results showed that Al2O3/RGO were uniformly distributed within the Al6061 matrix and tightly bonded to the matrix. Al2O3 encapsulation on RGO surface would prevent the formation of Al4C3 brittle phase in matrix, ensuring that there was no reaction between the reinforcement and the matrix Al6061. Tensile strength and Vickers hardness tests demonstrated that the mechanical properties of Al MMCs significantly increased with addition of Al2O3/RGOs. Remarkably, Al MMCs with 0.1 wt% reinforcement showed tensile yield and tensile strengths of 270 MPa and 286 MPa, respectively, which were 49% and 43% higher than those of pure Al6061 prepared using the same process. Furthermore, the 0.1 wt% Al2O3/RGO composite also showed the best plastic deformation capability in considering of the strength.
Southern marsh deer (Blastocerus dichotomus) populations assessed using Amplicon Sequencing on fecal samples
Authors: Wolfenson Laura I. , Pereira Javier A. , Ruzzante Daniel E. , Solé-Cava Antonio M. , McCracken Gregory R. , Gómez-Fernández María J. , Pereyra María D. , Mirol Patricia M. 
Published: July 2024

AbstractPopulations in isolated and small fragments lose genetic variability very fast and are usually of conservation concern because they are at greater risk of local extinction. The largest native deer in South America, Blastocerus dichotomus (Illiger, 1815), is a Vulnerable species according to the IUCN categorization, which inhabits tropical and subtropical swampy areas. In Argentina, its presence has been restricted to four isolated fragments. Here we examine the genetic diversity and differentiation among three of them, including the three different patches that form the southernmost population, using 18 microsatellite markers genotyped by Amplicon Sequencing of DNA extracted from fecal samples. Genetic diversity was low (HE < 0.45) in all three populations studied. We found three genetic clusters compatible with the geographic location of the samples. We also found a metapopulation dynamics that involves the patches that make up the southernmost population, with evidence of a barrier to gene flow between two of them. Our results point to the creation of a corridor as a necessary and urgent management action. This is the first study, at the population level, employing microsatellite genotyping by Amplicon Sequencing with non-invasive samples in an endangered species.
Assessing the impact of MSH3 and MSH6 polymorphisms on lung cancer risk in North Indian patients undergoing platinum chemotherapy through molecular dynamics simulation
Authors: Singh Sidhartha , Singh Navneet , Gupta Parth Sarthi Sen , Panda Saroj Kumar , Dhamija Isha , Nathiya Deepak , Kumar Sandeep , Sharma Siddharth 
Published: July 2024

AbstractThe present study investigated the relationship between MSH3 and MSH6 genes in lung cancer patients. Genotyping of lung cancer patients and healthy controls was performed. Odds ratio values were calculated and survival analysis performed. Patients with mutant genotype (TT) for MSH6 polymorphism have 1.5-fold risk for the development of lung cancer (p = 0.03). For non-smokers, the mutant-type genotype had a threefold increased risk of lung cancer (p = 0.01). Patients administered with docetaxel and carbo/cisplatin and carrying GT genotype for MSH6 polymorphism, patients reported a decrease in median survival time (4.9 vs 9.13 months). MSH3 and MSH6 polymorphisms are involved in modulating the risk towards lung cancer. MSH6 polymorphism is associated with high mortality rate for patients undergoing cisplatin and docetaxel chemotherapy.
Apple polysaccharide improves age-matched cognitive impairment and intestinal aging through microbiota-gut-brain axis
Authors: Zhang Wenming , Zhong Yuchun , Wang Zhuoya , Tang Furui , Zheng Cihua 
Published: July 2024

AbstractThe Apple polysaccharides (AP), extracted from the fruit of apple, has been used to treat multiple pathological diseases. In this study, we evaluated the effects of AP on cognitive impairment and intestinal aging in naturally aging mice. As a result, it was found that AP could improve spatial learning and memory impairment in aging mice through the Morris water maze experiment. Additionally, AP intervention can upregulate the expression of nerve growth factor (BDNF), postsynaptic marker (PSD95), and presynaptic marker (SYP) proteins. Moreover, AP can enhance total antioxidant capacity, reduce the level of pro-inflammatory cytokine, and inhibit the activation of the NF-κB signaling pathway, exerting anti-inflammatory and antioxidant functions. And the administration of AP restored intestinal mucosal barrier function, reduced the expression of aging and apoptosis related proteins. The administration of AP also altered the gut microbiota of mice. At the genus level, AP decreased the abundance of Helicobacter and Bilophila, while increased the abundance of Lactobacillus and Bacteroides. In summary, these data demonstrate that AP treatment can alleviate cognitive impairment, oxidative stress, and inflammatory reactions, repair the intestinal mucosal barrier, reduce intestinal aging, and alter specific microbial characteristics, ultimately improving the health of the elderly.
Absence of effects of widespread badger culling on tuberculosis in cattle
Authors: Torgerson Paul R. , Hartnack Sonja , Rasmussen Philip , Lewis Fraser , Langton Thomas E. S. 
Published: July 2024

AbstractGovernment policy in England aims for the elimination of bovine tuberculosis (bTB). This policy includes culling of European badger (Meles meles) to reduce cattle TB incidence. The rationale is based on a field trial, the Randomised Badger Culling Trial (RBCT) 1998–2005, which reported a substantial decrease in bTB herd incidence where badger culling had been implemented, in comparison to untreated control areas. The RBCT was undertaken because previous studies of reductions in badgers by culling, reported a possible association between bTB in badger and cattle, but none could directly show causation. The effect of intensive widespread (proactive) culling in the RBCT was reported in 2006 in the journal Nature. Analysis of an extensive badger removal programme in England since 2013 has raised concerns that culling has not reduced bTB herd incidence. The present study re-examined RBCT data using a range of statistical models. Most analytical options showed no evidence to support an effect of badger culling on bTB herd incidence ‘confirmed’ by visible lesions and/or bacterial culture post mortem following a comparative intradermal skin test (SICCT). However, the statistical model chosen by the RBCT study was one of the few models that showed an effect. Various criteria suggest that this was not an optimal model, compared to other analytical options available. The most likely explanation is that the RBCT proactive cull analysis over-fitted the data with a non-standard method to control for exposure giving it a poor predictive value. Fresh appraisal shows that there was insufficient evidence to conclude RBCT proactive badger culling affected bTB breakdown incidence. The RBCT found no evidence of an effect of culling on ‘total’ herd incidence rates. Total herd incidences include those confirmed as bTB at necropsy and those herds where there was at least one animal animal positive to the comparative intradermal skin test, the standard diagnostic test used for routine surveillance, but not confirmed at necropsy. This was also the case using the more suitable statistical models. Use only of ‘confirmed’ herd incidence data, together with a more recent (2013) published perception that RBCT data presented ‘a strong evidence base….with appropriate detailed statistical or other quantitative analysis’ should be reconsidered. The results of the present report are consistent with other analyses that were unable to detect any disease control benefits from badger culling in England (2013–2019). This study demonstrates one form of potential driver to the reproducibility crisis, in this case with disease control management in an increasingly intensified livestock industry.
Peripheral immunity is associated with cognitive impairment after acute minor ischemic stroke and transient ischemic attack
Authors: Zhao PanPan , Zhang GuiMei , Wang YongChun , Wei ChunXiao , Wang ZiCheng , Zhai WeiJie , Shen YanXin , Shi Lin , Sun Li 
Published: July 2024

AbstractImmunoinflammation is associated with the development of post-stroke cognitive impairment (PSCI), however, peripheral immunity has not been fully explored. We aimed to investigate the association between PSCI and peripheral immune indicators, including neutrophil, lymphocyte, and mononuclear percentages and counts; the systemic immune inflammation index; platelet-to-lymphocyte ratio; neutrophil-to-lymphocyte ratio (NLR); and lymphocyte-to-monocyte ratio. A total of 224 patients with acute minor ischemic stroke or transient ischemic attack with 6–12 months of follow-up were included. PSCI was defined as a Montreal Cognitive Assessment score < 22 during the follow-up period. We performed logistic regression, subgroup analyses based on age and sex, and further established predictive models. We found that increased innate immunity indicators (neutrophils, neutrophil percentage) increased the risk of PSCI, whereas increased adaptive immunity indicator (lymphocytes) were protective against PSCI, especially in patients aged 50–65 years. Neutrophil percentage and NLR improved the predictive efficacy of the models that included demographic, clinical, and imaging information, with the area under the curve increased from 0.765 to 0.804 and 0.803 (P = 0.042 and 0.049, respectively). We conducted a comprehensive analysis of peripheral immunity in PSCI, providing a novel perspective on the early detection, etiology, and treatment of PSCI.
Efficient synthesis of CRISPR-Cas13a-antimicrobial capsids against MRSA facilitated by silent mutation incorporation
Authors: Shimamori Yuzuki , Tan Xin-Ee , Li Feng-Yu , Nishikawa Yutaro , Watanabe Shinya , Sasahara Teppei , Miyanaga Kazuhiko , Aiba Yoshifumi , Veeranarayanan Srivani , Thitiananpakorn Kanate , Nguyen Huong Minh , Batbold Anujin , Nayanjin Tergel , Lian Adeline Yeo Syin , Hossain Sarah , Kawaguchi Tomofumi , Alessa Ola , Kumwenda Geofrey , Sarangi Jayathilake , Revilleza Jastin Edrian C. , Baranwal Priyanka , Arbaah Mahmoud , Maniruzzaman  , Yi Liu , Duyen Ho Thi My , Sugano Takashi , Sultana Sharmin , Faruk Mohammad Omar , Hidaka Yuya , Thu Myat , Shimojyo Takayuki , Kiga Kotaro , Cui Longzhu 
Published: July 2024

AbstractIn response to the escalating global threat of antimicrobial resistance, our laboratory has established a phagemid packaging system for the generation of CRISPR-Cas13a-antimicrobial capsids targeting methicillin-resistant Staphylococcus aureus (MRSA). However, a significant challenge arose during the packaging process: the unintentional production of wild-type phages alongside the antimicrobial capsids. To address this issue, the phagemid packaging system was optimized by strategically incorporated silent mutations. This approach effectively minimized contamination risks without compromising packaging efficiency. The study identified the indispensable role of phage packaging genes, particularly terL-terS, in efficient phagemid packaging. Additionally, the elimination of homologous sequences between the phagemid and wild-type phage genome was crucial in preventing wild-type phage contamination. The optimized phagemid-LSAB(mosaic) demonstrated sequence-specific killing, efficiently eliminating MRSA strains carrying target antibiotic-resistant genes. While acknowledging the need for further exploration across bacterial species and in vivo validation, this refined phagemid packaging system offers a valuable advancement in the development of CRISPR-Cas13a-based antimicrobials, shedding light on potential solutions in the ongoing battle against bacterial infections.
Assessment of domestic pig–bushpig (Potamochoerus larvatus) interactions through local knowledge in rural areas of Madagascar
Authors: Rakotoarivony Rianja , Kassie Daouda , Andriamahefa Alpha , Andria-Mananjara Diana , Rakotoarinoro Mihaja , Ramaroson Herilantonirina Solotiana , Raliniaina Modestine , Rasamoelina Miatrana , Gomez-Vazquez Jose Pablo , Jori Ferran 
Published: July 2024

AbstractIn many parts of the world, domestic and wild animal populations interact at the interface between natural and agricultural ecosystems. Introduced with the first inhabitants arriving from eastern Africa, the bushpig (Potamochoerus larvatus) is the largest living terrestrial mammal in Madagascar. Bushpigs are regularly reported close to human settlements where they damage crops and gardens. As domestic pigs are often raised in free-ranging conditions around the villages, bushpigs and domestic pigs can interact leading to the transmission and circulation of shared swine pathogens that impact both animal and human health. In this study, we characterized the socio-ecological context of bushpig–domestic pig interactions in two different regions of western Madagascar. We conducted participatory mapping sessions and focus group interviews with 65 hunters, 80 pig farmers and 96 crop farmers in 20 fokontany, the smallest administrative unit in Madagascar. After discussing with participants, we gathered information about the spatialization of interactions and their potential geographical drivers. We explored data by performing multiple correspondence analysis and hierarchical clustering on principal components. Based on the reported occurrence or absence of bushpig-domestic pig interactions we were able to classify areas with high or intermediate levels of interactions or no interactions at all. Interactions between the two pig species were reported in only 25% of the fokontany assessed. Even though both suid species were attracted to fruit trees, crops, and water sources, only indirect interactions in those spots were reported. Direct interactions were reported in 10% of cases and referred to interspecific sexual and/or agonistic behavior. The participatory methods used to acquire local knowledge about natural events were confirmed as valuable, low-cost exploratory methods to characterize areas with wild-domestic animal interactions. The results of this study will help plan future studies to characterize the interface between the two species from an ecological or epidemiological perspective using more sensitive and sophisticated ecological approaches.
Predictive value of MRI-based deep learning model for lymphovascular invasion status in node-negative invasive breast cancer
Authors: Liang Rong , Li Fangfang , Yao Jingyuan , Tong Fang , Hua Minghui , Liu Junjun , Shi Chenlei , Sui Lewen , Lu Hong 
Published: July 2024

AbstractTo retrospectively assess the effectiveness of deep learning (DL) model, based on breast magnetic resonance imaging (MRI), in predicting preoperative lymphovascular invasion (LVI) status in patients diagnosed with invasive breast cancer who have negative axillary lymph nodes (LNs). Data was gathered from 280 patients, including 148 with LVI-positive and 141 with LVI-negative lesions. These patients had undergone preoperative breast MRI and were histopathologically confirmed to have invasive breast cancer without axillary LN metastasis. The cohort was randomly split into training and validation groups in a 7:3 ratio. Radiomics features for each lesion were extracted from the first post-contrast dynamic contrast-enhanced (DCE)-MRI. The Least Absolute Shrinkage and Selection Operator (LASSO) regression method and logistic regression analyses were employed to identify significant radiomic features and clinicoradiological variables. These models were established using four machine learning (ML) algorithms and one DL algorithm. The predictive performance of the models (radiomics, clinicoradiological, and combination) was assessed through discrimination and compared using the DeLong test. Four clinicoradiological parameters and 10 radiomic features were selected by LASSO for model development. The Multilayer Perceptron (MLP) model, constructed using both radiomic and clinicoradiological features, demonstrated excellent performance in predicting LVI, achieving a high area under the curve (AUC) of 0.835 for validation. The DL model (MLP-radiomic) achieved the highest accuracy (AUC = 0.896), followed by DL model (MLP-combination) with an AUC of 0.835. Both DL models were significantly superior to the ML model (RF-clinical) with an AUC of 0.720. The DL model (MLP), which integrates radiomic features with clinicoradiological information, effectively aids in the preoperative determination of LVI status in patients with invasive breast cancer and negative axillary LNs. This is beneficial for making informed clinical decisions.
Circulating levels of neurofilament light chain as a biomarker of infarct and white matter hyperintensity volumes after ischemic stroke
Authors: Holmegaard Lukas , Jensen Christer , Pedersen Annie , Blomstrand Christian , Blennow Kaj , Zetterberg Henrik , Jood Katarina , Jern Christina 
Published: July 2024

AbstractSerum neurofilament light chain protein (sNfL) shows promise as a biomarker for infarct size in acute ischemic stroke and for monitoring cerebral small vessel disease (cSVD). However, distinguishing the cSVD contribution after stroke may not be possible due to post-stroke sNfL increase. Additionally, it remains unclear if etiologic subtype differences exist. We measured infarct and white matter hyperintensity (WMH) volumes using MRI at the index stroke in ischemic stroke patients (n = 316, mean age 53 years, 65% males) and at 7-year follow-up (n = 187). Serum NfL concentration was measured in the acute phase (n = 235), at 3-months (n = 288), and 7-years (n = 190) post stroke. In multivariable regression, acute and 3-month sNfL concentrations were associated with infarct volume and time since stroke, but not with stroke etiology or infarct location. Seven years post-stroke, sNfL was associated with WMHs and age, but not with stroke etiology. Nonlinear regression estimated that sNfL peaks around 1 month, and declines by 50% at 3 months, and 99% at 9 months. We conclude that sNfL can indicate infarct volume and time since brain injury in the acute and subacute phases after stroke. Due to the significant post-stroke sNfL increase, several months are needed for reliable assessment of cSVD activity.
Building on the clinical applicability of ctDNA analysis in non-metastatic pancreatic ductal adenocarcinoma
Authors: Labiano Ibone , Huerta Ana E. , Alsina Maria , Arasanz Hugo , Castro Natalia , Mendaza Saioa , Lecumberri Arturo , Gonzalez-Borja Iranzu , Guerrero-Setas David , Patiño-Garcia Ana , Alkorta-Aranburu Gorka , Hernández-Garcia Irene , Arrazubi Virginia , Mata Elena , Gomez David , Viudez Antonio , Vera Ruth 
Published: July 2024

AbstractPancreatic ductal adenocarcinoma represents one of the solid tumors showing the worst prognosis worldwide, with a high recurrence rate after adjuvant or neoadjuvant therapy. Circulating tumor DNA analysis raised as a promising non-invasive tool to characterize tumor genomics and to assess treatment response. In this study, surgical tumor tissue and sequential blood samples were analyzed by next-generation sequencing and were correlated with clinical and pathological characteristics. Thirty resectable/borderline pancreatic ductal adenocarcinoma patients treated at the Hospital Universitario de Navarra were included. Circulating tumoral DNA sequencing identified pathogenic variants in KRAS and TP53, and in other cancer-associated genes. Pathogenic variants at diagnosis were detected in patients with a poorer outcome, and were correlated with response to neoadjuvant therapy in borderline pancreatic ductal adneocarcinoma patients. Higher variant allele frequency at diagnosis was associated with worse prognosis, and thesum of variant allele frequency was greater in samples at progression. Our results build on the potential value of circulating tumor DNA for non-metastatic pancreatic ductal adenocarcinoma patients, by complementing tissue genetic information and as a non-invasive tool for treatment decision. Confirmatory studies are needed to corroborate these findings.