bluuebunny/crossref_metadata_2025 huggingface dataset:
Idiosyncratic fixation patterns generalize across dynamic and static facial expression recognition
Authors: Paparelli Anita , Sokhn Nayla , Stacchi Lisa , Coutrot Antoine , Richoz Anne-Raphaëlle , Caldara Roberto
Published: July 2024

Facial expression recognition (FER) is crucial for understanding the emotional state of others during human social interactions. It has been assumed that humans share universal visual sampling strategies to achieve this task. However, recent studies in face identification have revealed striking idiosyncratic fixation patterns, questioning the universality of face processing. More importantly, very little is known about whether such idiosyncrasies extend to the biological relevant recognition of static and dynamic facial expressions of emotion (FEEs). To clarify this issue, we tracked observers’ eye movements categorizing static and ecologically valid dynamic faces displaying the six basic FEEs, all normalized for time presentation (1 s), contrast and global luminance across exposure time. We then used robust data-driven analyses combining statistical fixation maps with hidden Markov Models to explore eye-movements across FEEs and stimulus modalities. Our data revealed three spatially and temporally distinct equally occurring face scanning strategies during FER. Crucially, such visual sampling strategies were mostly comparably effective in FER and highly consistent across FEEs and modalities. Our findings show that spatiotemporal idiosyncratic gaze strategies also occur for the biologically relevant recognition of FEEs, further questioning the universality of FER and, more generally, face processing.
Examining the influence of technological self-efficacy, perceived trust, security, and electronic word of mouth on ICT usage in the education sector
Authors: Xu Shuo , Khan Kanwal Iqbal , Shahzad Muhammad Farrukh
Published: July 2024

The context of education has changed due to revolutionary developments in the information communication technology (ICT) industry in the post-COVID era. Innovative learning methods were introduced in the education sector to promote quality education. The students find it more convenient to use ICT tools to integrate their knowledge-seeking. China has recently paid more attention to developing and adopting electronic infrastructure. The study assesses the effect of technology self-efficacy (TSE) on ICT acceptance and implementation in China’s education sector. It also analyzed the role of perceived trust, perceived security, and electronic word of mouth (eWOM) in integrating digital information sharing and interaction tools. Data is collected from 382 business students at Chinese universities. The results revealed that perceived trust mediates the relationship between TSE and the actual use of ICT tools, intention to use ICT tools for information, and intention to use ICT tools for interaction. Further, perceived security and eWOM significantly moderate the relationship between TSE and perceived trust. The findings indicate that it is essential to offer assistance and instruction to students in the educational sector so they can use ICT technology more frequently. It is also crucial for organizations to establish a supportive culture and provide the necessary technological resources to facilitate the use of ICT.
Co-designing the integration of voice-based conversational AI and web augmentation to amplify web inclusivity
Authors: Pucci Emanuele , Piro Ludovica , Possaghi Isabella , Mulfari Davide , Matera Maristella
Published: July 2024

The Web has become an essential resource but is not yet accessible to everyone. Assistive technologies and innovative, intelligent frameworks, for example, those using conversational AI, help overcome some exclusions. However, some users still experience barriers. This paper shows how a human-centered approach can shed light on technology limitations and gaps. It reports on a three-step process (focus group, co-design, and preliminary validation) that we adopted to investigate how people with speech impairments, e.g., dysarthria, browse the Web and how barriers can be reduced. The methodology helped us identify challenges and create new solutions, i.e., patterns for Web browsing, by combining voice-based conversational AI, customized for impaired speech, with techniques for the visual augmentation of web pages. While current trends in AI research focus on more and more powerful large models, participants remarked how current conversational systems do not meet their needs, and how it is important to consider each one’s specificity for a technology to be called inclusive.
Energy efficient and sustainable design of a multi-story building based on embodied energy and cost
Authors: Qing Zhang Qing , Li Na Zhang
Published: July 2024

Sustainable multi-story building designs are gaining increasing attention in light of the green development of the building industry. Recently, many studies have been conducted to determine the optimized embodied energy considering size of structural members and materials strength using a single objective function. In this context, the current study adopted a multi-objective function based on cost and Embodied Energy (EE) for the sustainable design of the entire multi-story building. A BuildingEnergy computer program is used to assess the energy consumption performance of a multi-story reinforcement cement concrete building. Based on the proposed method, an analysis is carried out to compare the optimal solutions for multi-story building. Furthermore, a detailed parametric study was conducted to explore the main factors for energy-efficient column and beam design. The results revealed that with a comparison of the most “carbon-friendly” and “cost-friendly” solutions, an added cost of 6–7% can contribute up to a 13% emission reduction. The sectional dimensions, steel rebar, concrete strengths, cost ratio, building height, and eccentricity remarkably influence sustainable design, cost optimization, and minimum carbon emission. Overall, this study could help to define cost-effective and energy-efficient structural members. Eventually, the EE is confirmed to be a feasible parameter for designing more sustainable multi-story RCC buildings.
Fingerphoto morphing attack generation using texture descriptors based landmarks
Authors: Li Hailin , Ramachandra Raghavendra
Published: July 2024

Smartphone-based biometric authentication has been widely used in various applications. Among several biometric characteristics, fingerphoto biometrics captured from smartphones are gaining popularity owing to their usability, scalability across different smartphones, and reliable verification. However, fingerphoto verification systems are vulnerable to both direct and indirect attacks. In this work, we propose a novel method to generate morphing attacks on fingerphoto biometrics captured using smartphones. We introduce three different image-level fingerphoto morphing attack generation algorithms that can generate high-quality fingerphoto morphing images with minimum distortions. Extensive experiments were conducted on two datasets captured using different smartphones under various environmental conditions. The results demonstrate that the proposed morphing algorithms are highly vulnerable to commercial off-the-shelf and block-directional fingerprint verification systems. To effectively detect morphing attacks on fingerphoto biometrics, we propose the use of fingerphoto morphing attack detection algorithms that utilize both handcrafted and deep features. However, our detection results showed a high error rate in accurately detecting these types of attacks.
Quantitative evaluation of 67Ga-citrate scintigraphy in the management of nephritis
Authors: Matsuda Noritake , Otsuka Hideki , Kasai Ryosuke , Otani Tamaki , Bollos Leah Anne Christine Locsin , Azane Shota , Kunikane Yamato , Otomi Yoichi , Ueki Yuya , Okabe Mana , Amano Masafumi , Tamaki Masanori , Wakino Shu , Takao Shoichiro , Harada Masafumi
Published: July 2024

In 67Ga-citrate scintigraphy (Ga-S), visual assessment is used by evaluating renal-uptake comparison with liver and spine and is simple and objective. We adopted the standardized uptake value (SUV) for 67Ga-citrate and proposed two quantitative indices, active nephritis volume (ANV) and total nephritis uptake (TNU). This study clarified the utility of new Ga-S-based quantitative indices in nephritis management. Before SUV measurement, the Becquerel calibration factor of 67Ga-citrate was obtained using a phantom experiment. Seventy patients who underwent SPECT/CT imaging were studied. SUV, ANV, and TNU were calculated using a quantitative analysis software for bone SPECT. SUVmean, ANV, and TNU were analyzed using the (1) threshold method (set 40%) and constant-value method for (2) vertebral SUVmax, and (3) vertebral SUVmean. ROC analysis was used to evaluate SUV, ANV, and TNU diagnostic abilities to distinguish nephritis presence and absence as well as interstitial nephritis (IN) and non-IN. The area under the curve (AUC) for nephritis presence or absence had a good value (0.80) for SUVmean (1), ANV (3), and TNU (3). The AUC for differentiation between IN and non-IN groups had a good value (0.80) for SUVmean (1). Thus, the new Ga-S-based quantitative indices were useful to evaluate nephritis and distinguish IN and non-IN.
Acute effects of cannabigerol on anxiety, stress, and mood: a double-blind, placebo-controlled, crossover, field trial
Authors: Cuttler Carrie , Stueber Amanda , Cooper Ziva D. , Russo Ethan
Published: July 2024

Cannabigerol (CBG) is a phytocannabinoid increasing in popularity, with preclinical research indicating it has anxiolytic and antidepressant effects. However, there are no published clinical trials to corroborate these findings in humans. The primary objective of this study was to examine acute effects of CBG on anxiety, stress, and mood. Secondary objectives were to examine whether CBG produces subjective drug effects or motor and cognitive impairments. A double-blind, placebo-controlled cross-over field trial was conducted with 34 healthy adult participants. Participants completed two sessions (with a one-week washout period) via Zoom. In each, they provided ratings of anxiety, stress, mood, and subjective drug effects prior to double-blind administration of 20 mg hemp-derived CBG or placebo tincture (T0). These ratings were collected again after participants ingested the product and completed an online survey (T1), the Trier Social Stress Test (T2), a verbal memory test and the DRUID impairment app (T3). Relative to placebo, there was a significant main effect of CBG on overall reductions in anxiety as well as reductions in stress at T1. CBG also enhanced verbal memory relative to placebo. There was no evidence of subjective drug effects or impairment. CBG may represent a novel option to reduce stress and anxiety in healthy adults.
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

The 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

In 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

Populations 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

The 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

The 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

Government 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

Immunoinflammation 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

In 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

In 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

To 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

Serum 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

Pancreatic 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.
Comparative metagenomic analysis from Sundarbans ecosystems advances our understanding of microbial communities and their functional roles
Authors: Das Basanta Kumar , Chakraborty Hirak Jyoti , Kumar Vikash , Rout Ajaya Kumar , Patra Biswanath , Das Sanjoy Kumar , Behera Bijay Kumar
Published: July 2024

The Sundarbans mangrove, located at the mouth of the Ganges and Brahmaputra Rivers, is the world’s largest tidal mangrove forest. These mangroves are also one of the most striking sources of microbial diversity, essential in productivity, conservation, nutrient cycling, and rehabilitation. Hence, the main objective of this study was to use metagenome analysis and provide detailed insight into microbial communities and their functional roles in the Sundarbans mangrove ecosystem. A comparative analysis was also done with a non-mangrove region of the Sundarbans ecosystem to assess the capability of the environmental parameters to explain the variation in microbial community composition. The study found several dominant bacteria, viz., Alphaproteobacteria, Actinomycetota, Bacilli, Clostridia, Desulfobacterota, Gammaproteobacteria, and Nitrospira, from the mangrove region. The mangrove sampling site reports several salt-tolerant bacteria like Alkalibacillus haloalkaliphilus, Halomonas anticariensis, and Salinivibrio socompensis. We found some probiotic species, viz., Bacillus clausii, Lactobacillus curvatus, Vibrio mediterranei and Vibrio fluvialis, from the Sundarbans mangrove. Nitrifying bacteria in Sundarbans soils were Nitrococcus mobilis, Nitrosococcus oceani, Nitrosomonas halophila, Nitrospirade fluvii, and others. Methanogenic archaea, viz., Methanoculleus marisnigri, Methanobrevibacter gottschalkii, and Methanolacinia petrolearia, were highly abundant in the mangroves as compared to the non-mangrove soils. The identified methanotrophic bacterial species, viz., Methylobacter tundripaludum, Methylococcus capsulatus, Methylophaga thiooxydans, and Methylosarcina lacus are expected to play a significant role in the degradation of methane in mangrove soil. Among the bioremediation bacterial species identified, Pseudomonas alcaligenes, Pseudomonas mendocina, Paracoccus denitrificans, and Shewanella putrefaciens play a significant role in the remediation of environmental pollution. Overall, our study shows for the first time that the Sundarbans, the largest mangrove ecosystem in the world, has a wide range of methanogenic archaea, methanotrophs, pathogenic, salt-tolerant, probiotic, nitrifying, and bioremediation bacteria.
Model based on the automated AI-driven CT quantification is effective for the diagnosis of refractory Mycoplasma pneumoniae pneumonia
Authors: Qian Yali , Tao Yunxi , Wu Lihui , Zhou Changsheng , Liu Feng , Xu Shenglong , Miao Hongjun , Gao Xiucheng , Ge Xuhua
Published: July 2024

The prediction of refractory Mycoplasma pneumoniae pneumonia (RMPP) remains a clinically significant challenge. This study aimed to develop an early predictive model utilizing artificial intelligence (AI)-derived quantitative assessment of lung lesion extent on initial computed tomography (CT) scans and clinical indicators for RMPP in pediatric inpatients. A retrospective cohort study was conducted on patients with M. pneumoniae pneumonia (MP) admitted to the Children’s Hospital of Nanjing Medical University, China from January 2019 to December 2020. An early prediction model was developed by stratifying the patients with Mycoplasma pneumoniae pneumonia (MPP) into two cohorts according to the presence or absence of refractory pneumonia. A retrospective cohort of 126 children diagnosed with Mycoplasma pneumoniae pneumonia (MPP) was utilized as a training set, with 85 cases classified as RMPP. Subsequently, a prospective cohort comprising 54 MPP cases, including 37 instances of RMPP, was assembled as a validation set to assess the performance of the predictive model for RMPP from January to December 2021. We defined a constant Φ which can combine the volume and CT value of pulmonary lesions and be further used to calculate the logarithm of Φ to the base of 2 (Log2Φ). A clinical-imaging prediction model was then constructed utilizing Log2Φ and clinical characteristics. Performance was evaluated by the area under the receiver operating characteristic curve (AUC). The clinical model demonstrated AUC values of 0.810 and 0.782, while the imaging model showed AUC values of 0.764 and 0.769 in the training and test sets, respectively. The clinical-imaging model, incorporating Log2Φ, temperature(T), aspartate aminotransferase (AST), preadmission fever duration (PFD), and preadmission macrolides therapy duration (PMTD), achieved the highest AUC values of 0.897 and 0.895 in the training and test sets, respectively. A prognostic model developed through automated quantification of lung disease on CT scans, in conjunction with clinical data in MPP may be utilized for the early identification of RMPP.
A trajectory similarity computation method based on GAT-based transformer and CNN model
Authors: Dongjiang Liu , Leixiao Li , Jie Li
Published: July 2024

Trajectory similarity computation is very important for trajectory data mining. It is applied into many trajectory mining tasks, including trajectory clustering, trajectory classification and trajectory search etc. So efficient trajectory similarity computation method is very useful for improving trajectory mining result. Nowadays many trajectory similarity computation methods have been proposed. But most of them can not be applied into long trajectories similarity calculation efficiently. So a new algorithm called TrajGAT is proposed. This algorithm can calculate similarity for long trajectories. It treats long trajectory as a long sequence. By doing so, long-term dependency of long trajectory is considered by this algorithm while computing similarity value. But, the spatial feature of long trajectories is not considered. As long trajectory can be presented in many different shapes, if two long trajectories are judged as similar trajectories, the outline shape of these two trajectories should be similar as well. To solve this problem, a new trajectory similarity computation method is proposed in this paper. This method not only takes the long-term dependence feature into consideration, but also considers the outline feature of long trajectory. The proposed method employs GAT-based transformer to extract long-term dependence feature from long trajectory. And it applies Convolutional Neural Network to extract outline feature.
The shared mechanism and potential diagnostic markers for premature ovarian failure and dry eye disease
Authors: Long Xi , Wu Zixuan , Jiang Pengfei , Tan Kang , Liu Pei , Peng Qinghua
Published: July 2024

Premature ovarian failure (POF), which is often comorbid with dry eye disease (DED) is a key issue affecting female health. Here, we explored the mechanism underlying comorbid POF and DED to further elucidate disease mechanisms and improve treatment. Datasets related to POF (GSE39501) and DED (GSE44101) were identified from the Gene Expression Omnibus (GEO) database and subjected to weighted gene coexpression network (WGCNA) and differentially expressed genes (DEGs) analyses, respectively, with the intersection used to obtain 158 genes comorbid in POF and DED. Kyoto Encyclopedia of Genes and Genomes (KEGG) and Gene Ontology (GO) analyses of comorbid genes revealed that identified genes were primarily related to DNA replication and Cell cycle, respectively. Protein–Protein interaction (PPI) network analysis of comorbid genes obtained the 15 hub genes: CDC20, BIRC5, PLK1, TOP2A, MCM5, MCM6, MCM7, MCM2, CENPA, FOXM1, GINS1, TIPIN, MAD2L1, and CDCA3. To validate the analysis results, additional POF- and DED-related datasets (GSE48873 and GSE171043, respectively) were selected. miRNAs-lncRNAs-genes network and machine learning methods were used to further analysis comorbid genes. The DGIdb database identified valdecoxib, amorfrutin A, and kaempferitrin as potential drugs. Herein, the comorbid genes of POF and DED were identified from a bioinformatics perspective, providing a new strategy to explore the comorbidity mechanism, opening up a new direction for the diagnosis and treatment of comorbid POF and DED.
Integrating apaQTL and eQTL analysis identifies a potential causal variant associated with lung adenocarcinoma risk in the Chinese population
Authors: Xu Huiwen , Wu Yutong , Chen Qiong , Yu Yuhui , Meng Qianyao , Qin Na , Zhang Wendi , Tao Xiaobo , Li Siqi , Tian Tian , Zhang Lei , Ma Hongxia , Cui Jiahua , Chu Minjie
Published: July 2024

Alternative polyadenylation (APA) plays a crucial role in cancer biology. Here, we used data from the 3′aQTL-atlas, GTEx, and the China Nanjing Lung Cancer GWAS database to explore the association between apaQTL/eQTL-SNPs and the risk of lung adenocarcinoma (LUAD). The variant T allele of rs277646 in NIT2 is associated with an increased risk of LUAD (OR = 1.12, P = 0.015), lower PDUI values, and higher NIT2 expression. The 3′RACE experiment showed multiple poly (A) sites in NIT2, with the rs277646-T allele causing preferential use of the proximal poly (A) site, resulting in a shorter 3′UTR transcript. This leads to the loss of the hsa-miR-650 binding site, thereby affecting LUAD malignant phenotypes by regulating the expression level of NIT2. Our findings may provide new insights into understanding and exploring APA events in LUAD carcinogenesis.
Repurposing Type I-A CRISPR-Cas3 for a robust diagnosis of human papillomavirus (HPV)
Authors: Hu Tao , Ji Quanquan , Ke Xinxin , Zhou Hufeng , Zhang Senfeng , Ma Shengsheng , Yu Chenlin , Ju Wenjun , Lu Meiling , Lin Yu , Ou Yangjing , Zhou Yingsi , Xiao Yibei , Xu Chunlong , Hu Chunyi
Published: July 2024

R-loop-triggered collateral single-stranded DNA (ssDNA) nuclease activity within Class 1 Type I CRISPR-Cas systems holds immense potential for nucleic acid detection. However, the hyperactive ssDNase activity of Cas3 introduces unwanted noise and false-positive results. In this study, we identified a novel Type I-A Cas3 variant derived from Thermococcus siculi, which remains in an auto-inhibited state until it is triggered by Cascade complex and R-loop formation. This Type I-A CRISPR-Cas3 system not only exhibits an expanded protospacer adjacent motif (PAM) recognition capability but also demonstrates remarkable intolerance towards mismatched sequences. Furthermore, it exhibits dual activation modes—responding to both DNA and RNA targets. The culmination of our research efforts has led to the development of the Hyper-Active-Verification Establishment (HAVE, 惠父). This innovation enables swift and precise human papillomavirus (HPV) diagnosis in clinical samples, providing a robust molecular diagnostic tool based on the Type I-A CRISPR-Cas3 system. Our findings contribute to understanding type I-A CRISPR-Cas3 system regulation and facilitate the creation of advanced diagnostic solutions with broad clinical applicability.
CRISPR screens in 3D tumourspheres identified miR-4787-3p as a transcriptional start site miRNA essential for breast tumour-initiating cell growth
Authors: Stiff Tom , Bayraktar Salih , Dama Paola , Stebbing Justin , Castellano Leandro
Published: July 2024

Our study employs pooled CRISPR screens, integrating 2D and 3D culture models, to identify miRNAs critical in Breast Cancer (BC) tumoursphere formation. These screens combine with RNA-seq experiments allowing identification of miRNA signatures and targets essential for tumoursphere growth. miR-4787-3p exhibits significant up-regulation in BC, particularly in basal-like BCs, suggesting its association with aggressive disease. Surprisingly, despite its location within the 5’UTR of a protein coding gene, which defines DROSHA-independent transcription start site (TSS)-miRNAs, we find it dependant on both DROSHA and DICER1 for maturation. Inhibition of miR-4787-3p hinders tumoursphere formation, highlighting its potential as a therapeutic target in BC. Our study proposes elevated miR-4787-3p expression as a potential prognostic biomarker for adverse outcomes in BC. We find that protein-coding genes positively selected in the CRISPR screens are enriched of miR-4787-3p targets. Of these targets, we select ARHGAP17, FOXO3A, and PDCD4 as known tumour suppressors in cancer and experimentally validate the interaction of miR-4787-3p with their 3’UTRs. Our work illuminates the molecular mechanisms underpinning miR-4787-3p’s oncogenic role in BC. These findings advocate for clinical investigations targeting miR-4787-3p and underscore its prognostic significance, offering promising avenues for tailored therapeutic interventions and prognostic assessments in BC.
Exploring bat-inspired cyclic tryptophan diketopiperazines as ABCB1 Inhibitors
Authors: Koh Javier Yu Peng , Itahana Yoko , Krah Alexander , Mostafa Habib , Ong Mingmin , Iwamura Sahana , Vincent Dona Mariya , Radha Krishnan Sabhashina , Ye Weiying , Yim Pierre Wing Chi , Khopade Tushar M. , Chen Kunihiko , Kong Pui San , Wang Lin-Fa , Bates Roderick W. , Kimura Yasuhisa , Viswanathan Rajesh , Bond Peter J. , Itahana Koji
Published: July 2024

Chemotherapy-induced drug resistance remains a major cause of cancer recurrence and patient mortality. ATP binding cassette subfamily B member 1 (ABCB1) transporter overexpression in tumors contributes to resistance, yet current ABCB1 inhibitors have been unsuccessful in clinical trials. To address this challenge, we propose a new strategy using tryptophan as a lead molecule for developing ABCB1 inhibitors. Our idea stems from our studies on bat cells, as bats have low cancer incidences and high ABCB1 expression. We hypothesized that potential ABCB1 substrates in bats could act as competitive inhibitors in humans. By molecular simulations of ABCB1-substrate interactions, we generated a benzylated Cyclo-tryptophan (C3N-Dbn-Trp2) that inhibits ABCB1 activity with efficacy comparable to or better than the classical inhibitor, verapamil. C3N-Dbn-Trp2 restored chemotherapy sensitivity in drug-resistant human cancer cells with no adverse effect on cell proliferation. Our unique approach presents a promising lead toward developing effective ABCB1 inhibitors to treat drug-resistant cancers.