bluuebunny/crossref_metadata_2025 huggingface dataset:
Double-stranded RNA sequencing reveals distinct riboviruses associated with thermoacidophilic bacteria from hot springs in Japan
Authors: Urayama Syun-ichi , Fukudome Akihito , Hirai Miho , Okumura Tomoyo , Nishimura Yosuke , Takaki Yoshihiro , Kurosawa Norio , Koonin Eugene V. , Krupovic Mart , Nunoura Takuro
Published: January 2024

Metatranscriptome sequencing expanded the known diversity of the bacterial RNA virome, suggesting that additional riboviruses infecting bacterial hosts remain to be discovered. Here we employed double-stranded RNA sequencing to recover complete genome sequences of two ribovirus groups from acidic hot springs in Japan. One group, denoted hot spring riboviruses (HsRV), consists of viruses with distinct RNA-directed RNA polymerases (RdRPs) that seem to be intermediates between typical ribovirus RdRPs and viral reverse transcriptases. This group forms a distinct phylum, Artimaviricota, or even kingdom within the realm Riboviria. We identified viruses encoding HsRV-like RdRPs in marine water, river sediments and salt marshes, indicating that this group is widespread beyond extreme ecosystems. The second group, denoted hot spring partiti-like viruses (HsPV), forms a distinct branch within the family Partitiviridae. The genome architectures of HsRV and HsPV and their identification in bacteria-dominated habitats suggest that these viruses infect thermoacidophilic bacteria.
Solving olympiad geometry without human demonstrations
Authors: Trinh Trieu H. , Wu Yuhuai , Le Quoc V. , He He , Luong Thang
Published: January 2024

Proving mathematical theorems at the olympiad level represents a notable milestone in human-level automated reasoning1–4, owing to their reputed difficulty among the world’s best talents in pre-university mathematics. Current machine-learning approaches, however, are not applicable to most mathematical domains owing to the high cost of translating human proofs into machine-verifiable format. The problem is even worse for geometry because of its unique translation challenges1,5, resulting in severe scarcity of training data. We propose AlphaGeometry, a theorem prover for Euclidean plane geometry that sidesteps the need for human demonstrations by synthesizing millions of theorems and proofs across different levels of complexity. AlphaGeometry is a neuro-symbolic system that uses a neural language model, trained from scratch on our large-scale synthetic data, to guide a symbolic deduction engine through infinite branching points in challenging problems. On a test set of 30 latest olympiad-level problems, AlphaGeometry solves 25, outperforming the previous best method that only solves ten problems and approaching the performance of an average International Mathematical Olympiad (IMO) gold medallist. Notably, AlphaGeometry produces human-readable proofs, solves all geometry problems in the IMO 2000 and 2015 under human expert evaluation and discovers a generalized version of a translated IMO theorem in 2004.
Inherited polygenic effects on common hematological traits influence clonal selection on JAK2V617F and the development of myeloproliferative neoplasms
Authors: Guo Jing , Walter Klaudia , Quiros Pedro M. , Gu Muxin , Baxter E. Joanna , Danesh John , Di Angelantonio Emanuele , Roberts David , Guglielmelli Paola , Harrison Claire N. , Godfrey Anna L. , Green Anthony R. , Vassiliou George S. , Vuckovic Dragana , Nangalia Jyoti , Soranzo Nicole
Published: January 2024

Myeloproliferative neoplasms (MPNs) are chronic cancers characterized by overproduction of mature blood cells. Their causative somatic mutations, for example, JAK2V617F, are common in the population, yet only a minority of carriers develop MPN. Here we show that the inherited polygenic loci that underlie common hematological traits influence JAK2V617F clonal expansion. We identify polygenic risk scores (PGSs) for monocyte count and plateletcrit as new risk factors for JAK2V617F positivity. PGSs for several hematological traits influenced the risk of different MPN subtypes, with low PGSs for two platelet traits also showing protective effects in JAK2V617F carriers, making them two to three times less likely to have essential thrombocythemia than carriers with high PGSs. We observed that extreme hematological PGSs may contribute to an MPN diagnosis in the absence of somatic driver mutations. Our study showcases how polygenic backgrounds underlying common hematological traits influence both clonal selection on somatic mutations and the subsequent phenotype of cancer.
Profiling the interactome of oligonucleotide drugs by proximity biotinylation
Authors: Hanswillemenke Alfred , Hofacker Daniel Tobias , Sorgenfrei Michèle , Fruhner Carolin , Franz-Wachtel Mirita , Schwarzer Dirk , Maček Boris , Stafforst Thorsten
Published: January 2024

Drug-ID is a novel method applying proximity biotinylation to identify drug–protein interactions inside living cells. The covalent conjugation of a drug with a biotin ligase enables targeted biotinylation and identification of the drug-bound proteome. We established Drug-ID for two small-molecule drugs, JQ1 and SAHA, and applied it for RNaseH-recruiting antisense oligonucleotides (ASOs). Drug-ID profiles the drug–protein interactome de novo under native conditions, directly inside living cells and at pharmacologically effective drug concentrations. It requires minimal amounts of cell material and might even become applicable in vivo. We studied the dose-dependent aggregation of ASOs and the effect of different wing chemistries (locked nucleic acid, 2′-methoxyethyl and 2′-Fluoro) and ASO lengths on the interactome. Finally, we demonstrate the detection of stress-induced, intracellular interactome changes (actinomycin D treatment) with an in situ variant of the approach, which uses a recombinant biotin ligase and does not require genetic manipulation of the target cell.
The developmental timing of spinal touch processing alterations predicts behavioral changes in genetic mouse models of autism spectrum disorders
Authors: Tasnim Aniqa , Alkislar Ilayda , Hakim Richard , Turecek Josef , Abdelaziz Amira , Orefice Lauren L. , Ginty David D.
Published: January 2024

Altered somatosensory reactivity is frequently observed among individuals with autism spectrum disorders (ASDs). Here, we report that although multiple mouse models of ASD exhibit aberrant somatosensory behaviors in adulthood, some models exhibit altered tactile reactivity as early as embryonic development, whereas in others, altered reactivity emerges later in life. Additionally, tactile overreactivity during neonatal development is associated with anxiety-like behaviors and social behavior deficits in adulthood, whereas tactile overreactivity that emerges later in life is not. The locus of circuit disruption dictates the timing of aberrant tactile behaviors, as altered feedback or presynaptic inhibition of peripheral mechanosensory neurons leads to abnormal tactile reactivity during neonatal development, whereas disruptions in feedforward inhibition in the spinal cord lead to touch reactivity alterations that manifest later in life. Thus, the developmental timing of aberrant touch processing can predict the manifestation of ASD-associated behaviors in mouse models, and differential timing of sensory disturbance onset may contribute to phenotypic diversity across individuals with ASD.
A database of thermally activated delayed fluorescent molecules auto-generated from scientific literature with ChemDataExtractor
Authors: Huang Dingyun , Cole Jacqueline M.
Published: January 2024

A database of thermally activated delayed fluorescent (TADF) molecules was automatically generated from the scientific literature. It consists of 25,482 data records with an overall precision of 82%. Among these, 5,349 records have chemical names in the form of SMILES strings which are represented with 91% accuracy; these are grouped in a subsidiary database. Each data record contains one of the following four properties: maximum emission wavelength (λEM), photoluminescence quantum yield (PLQY), singlet-triplet energy splitting (ΔEST), and delayed lifetime (τD). The databases were created through text mining using ChemDataExtractor, a chemistry-aware natural-language-processing toolkit, which has been adapted for TADF research. The text-mined corpus consisted of 2,733 papers from the Royal Society of Chemistry and Elsevier. To the best of our knowledge, these databases are the first databases that have been auto-generated for TADF molecules from existing publications. The databases have been publicly released for experimental and computational applications in the TADF research field.
Climate influences scrub typhus occurrence in Vellore, Tamil Nadu, India: analysis of a 15-year dataset
Authors: D’Cruz Solomon , Sreedevi Kotamreddy , Lynette Cheryl , Gunasekaran Karthik , Prakash John Antony Jude
Published: January 2024

Climate is one of the major factors determining the prevalence and seasonality of vector borne diseases like scrub typhus (ST). We analyzed, the association of the meteorological factors like temperature, rainfall and humidity with scrub typhus using the 15 years scrub typhus data from a tertiary care hospital in Vellore, South India. Demographic data of permanent residents of Vellore, who had IgM ELISA results for scrub typhus for the time period of May 2005 to April 2020 were included. Meteorological data was correlated with the monthly scrub typhus cases; negative binomial regression model was used to predict the relation between scrub typhus occurrence and climate factors. Maximum number of ST cases were reported between the months August and February with October recording the highest number of cases. Elderly people, farmers, agricultural workers and housewives were at higher risk for scrub typhus. For an increase of 1 °C in mean temperature, the monthly ST cases reduced by 18.8% (95% CI − 24.1, − 13.2%). On the contrary, for 1 percent increase in mean relative humidity (RH), there is an increase of 7.6% (95% CI 5.4, 9.9%) of monthly ST cases. Similarly, an increase of 1 mm of rainfall contributed to 0.5 to 0.7% of monthly ST cases (after 2 months) depending on the variables included in the analysis. This study provides information that meteorological factors influence ST occurrence in Vellore. The rise of scrub typhus cases is maximal 2 months post rainfall. Whereas a rise in relative humidity, causes a rise in scrub typhus cases in same month, while rise in temperature has a negative impact on scrub typhus during the same month. These findings based on a retrospective analysis need validation by prospective studies.
First application of data assimilation-based control to fusion plasma
Authors: Morishita Yuya , Murakami Sadayoshi , Kenmochi Naoki , Funaba Hisamichi , Yamada Ichihiro , Mizuno Yoshinori , Nagahara Kazuki , Nuga Hideo , Seki Ryosuke , Yokoyama Masayuki , Ueno Genta , Osakabe Masaki
Published: January 2024

Magnetic fusion plasmas, which are complex systems comprising numerous interacting elements, have large uncertainties. Therefore, future fusion reactors require prediction-based advanced control systems with an adaptive system model and control estimation robust to uncertainties in the model and observations. To address this challenge, we introduced a control approach based on data assimilation (DA), which describes the system model adaptation and control estimation based on the state probability distribution. The first implementation of a DA-based control system was achieved at the Large Helical Device to control the high temperature plasma. The experimental results indicate that the control system enhanced the predictive capability using real-time observations and adjusted the electron cyclotron heating power for a target temperature. The DA-based control system provides a flexible platform for advanced control in future fusion reactors.
Insights into vehicle conflicts based on traffic flow dynamics
Authors: Ding Shengxuan , Abdel-Aty Mohamed , Wang Zijin , Wang Dongdong
Published: January 2024

The utilization of traffic conflict indicators is crucial for assessing traffic safety, especially when the crash data is unavailable. To identify traffic conflicts based on traffic flow characteristics across various traffic states, we propose a framework that utilizes unsupervised learning to automatically establish surrogate safety measures (SSM) thresholds. Different traffic states and corresponding transitions are identified with the three-phase traffic theory using high-resolution trajectory data. Meanwhile, the SSMs are mapped to the corresponding traffic states from the perspectives of time, space, and deceleration. Three models, including k-means, GMM, and Mclust, are investigated and compared to optimize the identification of traffic conflicts. It is observed that Mclust outperforms the others based on the evaluation metrics. According to the results, there is a variation in the distribution of traffic conflicts among different traffic states, wide moving jam (phase J) has the highest conflict risk, followed by synchronous flow (phase S), and free flow (phase F). Meanwhile, the thresholds of traffic conflicts cannot be fully represented by the same value through different traffic states. It reveals that the heterogeneity of thresholds is exhibited across traffic state transitions, which justifies the necessity of dynamic thresholds for traffic conflict analysis.
Global characterization of biosynthetic gene clusters in non-model eukaryotes using domain architectures
Authors: Kwon Taehyung , Hovde Blake T.
Published: January 2024

The majority of pharmaceuticals are derived from natural products, bioactive compounds naturally synthesized by organisms to provide evolutionary advantages. Although the rich evolutionary history of eukaryotic algal species implicates a high potential for natural product-based drug discovery, it remains largely untouched. This study investigates 2762 putative biosynthetic gene clusters (BGCs) from 212 eukaryotic algal genomes. To analyze a vast set of structurally diverse BGCs, we employed comparative analysis based on the vectorization of biosynthetic domains, referred to as biosynthetic domain architecture (BDA). By characterizing core biosynthetic machineries through BDA, we identified key BDAs of modular BGCs in diverse eukaryotes and introduced 16 candidate modular BGCs with similar BDAs to previously validated BGCs. This study provides a global characterization of eukaryotic algal BGCs, offering an alternative to laborious manual curation for BGC prioritization.
Modulating the difficulty of a visual oddball-like task and P3m amplitude
Authors: Boetzel Cindy , Stecher Heiko I. , Kasten Florian H. , Herrmann Christoph S.
Published: January 2024

It is often necessary to modulate the difficulty of an experimental task without changing physical stimulus characteristics that are known to modulate event-related potentials. Here, we developed a new, oddball-like visual discrimination task with varying levels of difficulty despite using almost identical visual stimuli. Gabor patches of one orientation served as frequent standard stimuli with 75% probability. Gabor patches with a slightly different orientation served as infrequent target stimuli (25% probability). Analyzing the behavioral outcomes revealed a successful modulation of task difficulty, i.e. the hard condition revealed decreased d' values and longer reaction times for standard stimuli. In addition, we recorded MEG and computed event-related fields in response to the stimuli. In line with our expectation, the amplitude of the P3m was reduced in the hard condition. We localized the sources of the P3m with a focus on those that are modulated by changes in task difficulty. The sources of P3m modulation by difficulty were found primarily in the centro-parietal regions of both hemispheres. Additionally, we found significant differences in source activity between the easy and hard conditions in parts of the pre and post-central gyrus and inferior parietal lobe. Our findings are in line with previous research suggesting that the brain areas responsible for the conventional P3m generators also contribute to a modulation by task difficulty.
Exploring the presence of oral bacteria in non-oral sites of patients with cardiovascular diseases using whole metagenomic data
Authors: Chopra Aditi , Franco-Duarte Ricardo , Rajagopal Anjale , Choowong Phannaphat , Soares Pedro , Rito Teresa , Eberhard Joerg , Jayasinghe Thilini N.
Published: January 2024

Cardiovascular diseases (CVDs) encompass various conditions affecting the heart and its blood vessels and are often linked with oral microbes. Our data analysis aimed to identify oral bacteria from other non-oral sites (i.e., gut, arterial plaque and cultured blood) that could be linked with CVDs. Taxonomic profiling identified bacteria to the species level and compared with the Human Oral Microbiome Database (HOMD). The oral bacteria in the gut, cultured blood and arterial plaque samples were catalogued, with their average frequency calculated for each sample. Additionally, data were filtered by comparison with the Human Microbiome Project (HMP) database. We identified 17,243 microbial species, of which 410 were present in the HOMD database and further denominated as “oral”, and were found in at least one gut sample, but only 221 and 169 species were identified in the cultured blood and plaque samples, respectively. Of the 410 species, 153 were present solely in oral-associated environments after comparison with the HMP database, irrespective of their presence in other body sites. Our results suggest a potential connection between the presence of specific species of oral bacterial and occurrence of CVDs. Detecting these oral bacterial species in non-oral sites of patients with CVDs could help uncover the link between oral health and general health, including cardiovascular conditions via bacterial translocation.
Structural validity of the Pittsburgh Sleep Quality Index among medical students in Iran
Authors: Shadzi Mohammad Reza , Rahmanian Mahdi , Heydari Aigin , Salehi Alireza
Published: January 2024

The Pittsburgh Sleep Quality Index (PSQI) is a self-reported questionnaire evaluating sleep quality based on seven domains of sleep disorders. However, the factor structure of PSQI needs to be well-established among medical students. This study was conducted to establish the factor structure of PSQI among medical students. Four-hundred and four medical students completed the PSQI. Considering each PSQI component as an "observed variable," exploratory factor analysis was conducted. Six models explaining the factor structure of PSQI were compared by confirmatory factor analysis to achieve the best model. All PSQI components were loaded on three factors. The first factor included sleep duration and habitual sleep efficiency, the second was subjective sleep quality and sleep latency, and the third was sleep disturbances, sleeping medications, and daytime dysfunction (root mean square error of approximation =  < 0.01, goodness of fit index = 0.99). The differences in Bayesian information criteria and root mean square error of approximation between our best-fit model and each of the other resulted in rejection of all other Models. Besides confirming the structural validity among medical students, our findings indicated the adequacy of the 3-factor structure of PSQI, including sleep efficiency, perceived sleep quality, and daily disturbances in this population.
Inhibition of mucus secretion by niclosamide and benzbromarone in airways and intestine
Authors: Ousingsawat Jiraporn , Centeio Raquel , Reyne Nicole , McCarron Alexandra , Cmielewski Patricia , Schreiber Rainer , diStefano Gabriella , Römermann Dorothee , Seidler Ursula , Donnelley Martin , Kunzelmann Karl
Published: January 2024

The Ca2+ activated Cl− channel TMEM16A (anoctamin 1; ANO1) is expressed in secretory epithelial cells of airways and intestine. Previous studies provided evidence for a role of ANO1 in mucus secretion. In the present study we investigated the effects of the two ANO1-inhibitors niclosamide (Niclo) and benzbromarone (Benz) in vitro and in vivo in mouse models for cystic fibrosis (CF) and asthma. In human CF airway epithelial cells (CFBE), Ca2+ increase and activation of ANO1 by adenosine triphosphate (ATP) or ionomycin was strongly inhibited by 200 nM Niclo and 1 µM Benz. In asthmatic mice airway mucus secretion was inhibited by intratracheal instillation of Niclo or Benz. In homozygous F508del-cftr mice, intestinal mucus secretion and infiltration by CD45-positive cells was inhibited by intraperitoneal injection of Niclo (13 mg/kg/day for 7 days). In homozygous F508del-cftr rats intestinal mucus secretion was inhibited by oral application of Benz (5 mg/kg/day for 60 days). Taken together, well tolerated therapeutic concentrations of niclosamide and benzbromarone corresponding to plasma levels of treated patients, inhibit ANO1 and intracellular Ca2+ signals and may therefore be useful in inhibiting mucus hypersecretion and mucus obstruction in airways and intestine of patients suffering from asthma and CF, respectively.
Detection of sub-nmol amounts of the antiviral drug favipiravir in 19F MRI using photo-chemically induced dynamic nuclear polarization
Authors: Bernarding J. , Bruns C. , Prediger I. , Mützel M. , Plaumann M.
Published: January 2024

In biological tissues, 19F magnetic resonance (MR) enables the non-invasive, background-free detection of 19F-containing biomarkers. However, the signal-to-noise ratio (SNR) is usually low because biomarkers are typically present at low concentrations. Measurements at low magnetic fields further reduce the SNR. In a proof-of-principal study we applied LED-based photo-chemically induced dynamic nuclear polarization (photo-CIDNP) to amplify the 19F signal at 0.6 T. For the first time, 19F MR imaging (MRI) and spectroscopy (MRS) of a fully biocompatible model system containing the antiviral drug favipiravir has been successfully performed. This fluorinated drug has been used to treat Ebola and COVID-19. Since the partially cyclic reaction scheme for photo-CIDNP allows for multiple data acquisitions, averaging further improved the SNR. The mean signal gain factor for 19F has been estimated to be in the order of 103. An in-plane resolution of 0.39 × 0.39 mm2 enabled the analysis of spatially varying degrees of hyperpolarization. The minimal detectable amount of favipiravir per voxel was estimated to about 500 pmol. The results show that 19F photo-CIDNP is a promising method for the non-invasive detection of suitable 19F-containing drugs and other compounds with very low levels of the substance.
Data-driven models for the prediction of coronary atherosclerotic plaque progression/regression
Authors: Bulant Carlos A. , Boroni Gustavo A. , Bass Ronald , Räber Lorenz , Lemos Pedro A. , García-García Héctor M. , Blanco Pablo J.
Published: January 2024

Coronary artery disease is defined by the existence of atherosclerotic plaque on the arterial wall, which can cause blood flow impairment, or plaque rupture, and ultimately lead to myocardial ischemia. Intravascular ultrasound (IVUS) imaging can provide a detailed characterization of lumen and vessel features, and so plaque burden, in coronary vessels. Prediction of the regions in a vascular segment where plaque burden can either increase (progression) or decrease (regression) following a certain therapy, has remained an elusive major milestone in cardiology. Studies like IBIS-4 showed an association between plaque burden regression and high-intensity rosuvastatin therapy over 13 months. Nevertheless, it has not been possible to predict if a patient would respond in a favorable/adverse fashion to such a treatment. This work aims to (i) Develop a framework that processes lumen and vessel cross-sectional contours and extracts geometric descriptors from baseline and follow-up IVUS pullbacks; and to (ii) Develop, train, and validate a machine learning model based on baseline/follow-up IVUS datasets that predicts future percent of atheroma volume changes in coronary vascular segments using only baseline information, i.e. geometric features and clinical data. This is a post hoc analysis, revisiting the IBIS-4 study. We employed 140 arteries, from 81 patients, for which expert delineation of lumen and vessel contours were available at baseline and 13-month follow-up. Contour data from baseline and follow-up pullbacks were co-registered and then processed to extract several frame-wise features, e.g. areas, plaque burden, eccentricity, etc. Each pullback was divided into regions of interest (ROIs), following different criteria. Frame-wise features were condensed into region-wise markers using tools from statistics, signal processing, and information theory. Finally, a stratified 5-fold cross-validation strategy (20 repetitions) was used to train/validate an XGBoost regression models. A feature selection method before the model training was also applied. When the models were trained/validated on ROI defined by the difference between follow-up and baseline plaque burden, the average accuracy and Mathews correlation coefficient were 0.70 and 0.41 respectively. Using a ROI partition criterion based only on the baseline’s plaque burden resulted in averages of 0.60 accuracy and 0.23 Mathews correlation coefficient. An XGBoost model was capable of predicting plaque progression/regression changes in coronary vascular segments of patients treated with rosuvastatin therapy in 13 months. The proposed method, first of its kind, successfully managed to address the problem of stratification of patients at risk of coronary plaque progression, using IVUS images and standard patient clinical data.
Management of acute diverticulitis in Stage 0-IIb: indications and risk factors for failure of conservative treatment in a series of 187 patients
Authors: Agnes Amedea L. , Agnes Annamaria , Di Grezia Marta , Giambusso Mauro , Savia Eleonora , Grieco Michele , Cozza Valerio , Magalini Sabina , Sganga Gabriele
Published: January 2024

Left-sided acute diverticulitis in WSES Stage 0-IIb preferentially undergoes conservative management. However, there is limited understanding of the risk factors for failure of this approach. The aim of this study was to investigate the factors associated with the decision to perform conservative treatment as well as the predictors of its failure. We included patients with a diagnosis of WSES diverticulitis CT-driven classification Stage 0-IIb treated in the Emergency Surgery Unit of the Agostino Gemelli University Hospital Foundation between 2014 and 2020. The endpoints were the comparison between the characteristics and clinical outcomes of acute diverticulitis patients undergoing conservative versus operative treatment. We also identified predictors of conservative treatment failure. A set of multivariable backward logistic analyses were conducted for this purpose. The study included 187 patients. The choice for operative versus conservative treatment was associated with clinical presentation, older age, higher WSES grade, and previous conservative treatment. There were 21% who failed conservative treatment. Of those, major morbidity and mortality rates were 17.9% and 7.1%, respectively. A previously failed conservative treatment as well as a greater WSES grade and a lower hemoglobin value were significantly associated with failure of conservative treatment. WSES classification and hemoglobin value at admission were the best predictors of failure of conservative treatment. Patients failing conservative treatment had non-negligible morbidity and mortality. These results promote the consideration of a combined approach including baseline patients’ characteristics, radiologic features, and laboratory biomarkers to predict conservative treatment failure and therefore optimize treatment of acute diverticulitis.
Availability of ChatGPT to provide medical information for patients with kidney cancer
Authors: Choi Joongwon , Kim Jin Wook , Lee Yong Seong , Tae Jong Hyun , Choi Se Young , Chang In Ho , Kim Jung Hoon
Published: January 2024

ChatGPT is an advanced natural language processing technology that closely resembles human language. We evaluated whether ChatGPT could help patients understand kidney cancer and replace consultations with urologists. Two urologists developed ten questions commonly asked by patients with kidney cancer. The answers to these questions were produced using ChatGPT. The five-dimension SERVQUAL model was used to assess the service quality of ChatGPT. The survey was distributed to 103 urologists via email, and twenty-four urological oncologists specializing in kidney cancer were included as experts with more than 20 kidney cancer cases in clinic per month. All respondents were physicians. We received 24 responses to the email survey (response rate: 23.3%). The appropriateness rate for all ten answers exceeded 60%. The answer to Q2 received the highest agreement (91.7%, etiology of kidney cancer), whereas the answer to Q8 had the lowest (62.5%, comparison with other cancers). The experts gave low assessment ratings (44.4% vs. 93.3%, p = 0.028) in the SERVQUAL assurance (certainty of total answers) dimension. Positive scores for the overall understandability of ChatGPT answers were assigned by 54.2% of responders, and 70.8% said that ChatGPT could not replace explanations provided by urologists. Our findings affirm that although ChatGPT answers to kidney cancer questions are generally accessible, they should not supplant the counseling of a urologist.
Optimizing classification of diseases through language model analysis of symptoms
Authors: Hassan Esraa , Abd El-Hafeez Tarek , Shams Mahmoud Y.
Published: January 2024

This paper investigated the use of language models and deep learning techniques for automating disease prediction from symptoms. Specifically, we explored the use of two Medical Concept Normalization—Bidirectional Encoder Representations from Transformers (MCN-BERT) models and a Bidirectional Long Short-Term Memory (BiLSTM) model, each optimized with a different hyperparameter optimization method, to predict diseases from symptom descriptions. In this paper, we utilized two distinct dataset called Dataset-1, and Dataset-2. Dataset-1 consists of 1,200 data points, with each point representing a unique combination of disease labels and symptom descriptions. While, Dataset-2 is designed to identify Adverse Drug Reactions (ADRs) from Twitter data, comprising 23,516 rows categorized as ADR (1) or Non-ADR (0) tweets. The results indicate that the MCN-BERT model optimized with AdamP achieved 99.58% accuracy for Dataset-1 and 96.15% accuracy for Dataset-2. The MCN-BERT model optimized with AdamW performed well with 98.33% accuracy for Dataset-1 and 95.15% for Dataset-2, while the BiLSTM model optimized with Hyperopt achieved 97.08% accuracy for Dataset-1 and 94.15% for Dataset-2. Our findings suggest that language models and deep learning techniques have promise for supporting earlier detection and more prompt treatment of diseases, as well as expanding remote diagnostic capabilities. The MCN-BERT and BiLSTM models demonstrated robust performance in accurately predicting diseases from symptoms, indicating the potential for further related research.
Analysis of two layered peristaltic-ciliary transport of Jeffrey fluid and in vitro preimplantation embryo development
Authors: Ashraf Hameed , Siddique Imran , Siddiqa Ayesha , Tawfiq Ferdous M. O. , Tchier Fairouz , Zulqarnain Rana Muhammad , Rehman Hamood Ur , Bhatti Shahzad , Rehman Abida
Published: January 2024

The analysis of peristaltic-ciliary transport in the human female fallopian tube, specifically in relation to the growing embryo, is a matter of considerable physiological importance. This paper proposes a biomechanical model that incorporates a finite permeable tube consisting of two layers, where the Jeffrey fluid model characterizes the viscoelastic properties of the growing embryo and continuously secreting fluid. Jeffrey fluid entering with some negative pressure gradient forms the core fluid layer while continuously secreting Jeffrey fluid forms the peripheral fluid layer. The resulting partial differential equations are solved for closed-form solutions after employing the assumption of long wavelength. The analysis delineated that increasing the constant secretion velocity, Darcy number, and Reynolds number leads to a decrease in the appropriate residue time of the core fluid layer and a reduction in the size of the secreting fluid bolus in the peripheral fluid layer. Eventually, the boluses completely disappear when the constant secretion velocity exceeds 3.0 Progesterone ($$P_4$$

P
4

) and estradiol ($$E_2$$

E
2

) directly regulate the transportation of the growing embryo, while luteinizing hormone (LH) and follicle-stimulating hormone (FSH), prolactin, anti-mullerian hormone (AMH), and thyroid-stimulating hormone (TSH) have an indirect effects. Based on the number and size of blastomeres, the percentage of fragmentation, and the presence of multinucleated blastomeres two groups were formed in an in vitro experiment. Out of 50 patients, 26 (76.5%) were pregnant in a group of the good quality embryos, and only 8 (23.5%) were in a group of the bad quality embryos. The transport of growing embryo in the human fallopian tube and preimplantation development of human embryos in in vitro are constraint by baseline hormones FSH, LH, prolactin, $$E_{2}$$

E
2

, AMH, and TSH.
New colonisers drive the increase of the emerging loggerhead turtle nesting in Western Mediterranean
Authors: Luna-Ortiz Astrid , Marín-Capuz Gisela , Abella Elena , Crespo-Picazo José Luis , Escribano Fernando , Félix Guillem , Giralt Silvia , Tomás Jesús , Pegueroles Cinta , Pascual Marta , Carreras Carlos
Published: January 2024

The loggerhead sea turtle (Caretta caretta) is sensitive to climate change and is responding by colonising the Western Mediterranean. To understand the rapid nesting increase in recent years in Spain, we sampled 45 hatchlings from 8 nests between 2016 and 2019. We sequenced a mtDNA D‐loop region, genotyped 2291 SNPs using 2bRAD and collected data on clutch size, hatching success, and incubation duration. We confirmed that the colonisation has a Mediterranean and Atlantic mixed origin and we detected that these nests were laid by different females, except for two nests within the same season. Our results suggest that the recent increase in nesting is due to an increase in the number of colonising individuals rather than females born in the same area returning to breed. We hypothesize that this increase in the number of colonisers results from successful conservation efforts, feminisation of the populations of origin and earlier sexual maturation. However, the percentage of offspring females produced in Spain suggests that future returning individuals will aid to the settlement of the new population. These results allow defining the current status of this colonisation although future efforts are needed to detect remigrants to confirm the establishment of a resident population.
Longitudinal analysis of influenza vaccination implicates regulation of RIG-I signaling by DNA methylation
Authors: Fu Hongxiang , Pickering Harry , Rubbi Liudmilla , Ross Ted M. , Reed Elaine F. , Pellegrini Matteo
Published: January 2024

Influenza virus infection alters the promoter DNA methylation of key immune response-related genes, including type-1 interferons and proinflammatory cytokines. However, less is known about the effect of the influenza vaccine on the epigenome. We utilized a targeted DNA methylation approach to study the longitudinal effects (day 0 pre-vaccination and day 28 post-vaccination) on influenza vaccination responses in peripheral blood mononuclear cells. We found that baseline, pre-vaccination methylation profiles are associated with pre-existing, protective serological immunity. Additionally, we identified 481 sites that were differentially methylated between baseline and day 28 post-vaccination. These were enriched for genes involved in the regulation of the RIG-I signaling pathway, an important regulator of viral responses. Our results suggest that DNA methylation changes to components of the RIG-I pathway are associated with vaccine effectiveness. Therefore, immunization strategies that target this pathway may improve serological responses to influenza vaccination.
Analysis of optimal control strategies on the fungal Tinea capitis infection fractional order model with cost-effective analysis
Authors: Teklu Shewafera Wondimagegnhu , Meshesha Abebe Addise , Ullah Saif
Published: January 2024

In this study, we have formulated and analyzed the Tinea capitis infection Caputo fractional order model by implementing three time-dependent control measures. In the qualitative analysis part, we investigated the following: by using the well-known Picard–Lindelöf criteria we have proved the model solutions' existence and uniqueness, using the next generation matrix approach we calculated the model basic reproduction number, we computed the model equilibrium points and investigated their stabilities, using the three time-dependent control variables (prevention measure, non-inflammatory infection treatment measure, and inflammatory infection treatment measure) and from the formulated fractional order model we re-formulated the fractional order optimal control problem. The necessary optimality conditions for the Tinea capitis fractional order optimal control problem and the existence of optimal control strategies are derived and presented by using Pontryagin’s Maximum Principle. Also, the study carried out the sensitivity and numerical analysis to investigate the most sensitive parameters and to verify the qualitative analysis results. Finally, we performed the cost-effective analysis to investigate the most cost-effective measures from the possible proposed control measures, and from the findings we can suggest that implementing prevention measures only is the most cost-effective control measure that stakeholders should consider.
Tracking the carbon flows in municipal waste management in China
Authors: Zhang Jing , Du Huanzheng , Wang Tao , Xiao Peiyuan , Lu Sha , Zhao Gang , Zhao Jianfu , Li Guangming
Published: January 2024

Municipal solid waste (MSW), a carbon-intensive waste stream, may create both instant and indirect impacts onto environmental and climate management. Despite multiple studies made for greenhouse gases (GHGs) emissions of municipal waste, this research aims to achieve a comprehensive assessment for the carbon cycle by exploring evolution of waste composition and temporal-spatial disparities in waste management. Carbon flows embodied in MSW have been estimated across 31 provinces in Mainland China in the period 2000–2018. This improved estimation could be 15–40% smaller than the conventional estimation employing a constant waste composition. Aggregately some 578 ± 117 megatonnes carbon (MtC) were contained in MSW, including 239 ± 60 Mt of fossil carbon and 339 ± 58 Mt of degradable organic carbon. After treatment, 299 ± 66 MtC were possibly deposited in landfills and dumps. 279 ± 51 MtC were released to the atmosphere, creating net GHGs emissions equivalent to1870 ± 334 megatonnes of CO2 (MtCO2e). MSW generation in China nearly doubled during the period, net GHGs emissions increased by 1.8×, whereas fossil carbon grew by a factor of 3.5, mainly propelled by an increasing content of waste plastic in MSW. More rapid growth was witnessed in provinces in southern China than in northern. Distinct spatial–temporal evolution of waste and carbon metabolism was driven by increment, composition, and management effects. In the long run, the increment and composition effects may drop off. Enhanced practices of waste management integrating the circular economy are needed to fully recycle carbon flows, minimize emissions, and manage carbon deposits in aging landfills and dumps.
Highly efficient emerging Ag2BaTiSe4 solar cells using a new class of alkaline earth metal-based chalcogenide buffers alternative to CdS
Authors: Arockiya Dass Kaviya Tracy , Hossain M. Khalid , Marasamy Latha
Published: January 2024

Cu2ZnSn(S,Se)4 is a non-toxic, earth-abundant photovoltaic absorber. However, its efficiency is limited by a large open circuit voltage (VOC) deficit occurring due to its antisite defects and improper band alignment with toxic CdS buffer. Therefore, finding an absorber and non-toxic buffers that reduce VOC deficit is crucial. Herein, for the first time, Ag2BaTiSe4 is proposed as an alternative absorber using SCAPS-1D wherein a new class of alkaline earth metal chalcogenide such as MgS, CaS, SrS, and BaS is applied as buffers, and their characteristics are compared with CdS to identify their potential and suitability. The buffer and absorber properties are elucidated by tuning their thickness, carrier concentration, and defect density. Interestingly, optimization of the buffer’s carrier concentration suppressed the barrier height and accumulation of charge carriers at the absorber/buffer interface, leading to efficiencies of 18.81%, 17.17%, 20.6%, 20.85%, 20.08% in MgS, CaS, SrS, BaS, and CdS-based solar cells respectively. Upon optimizing Ag2BaTiSe4, MoSe2, and interface defects maximum efficiency of > 28% is achieved with less VOC loss (~ 0.3 V) in all solar cells at absorber’s thickness, carrier concentration, and defect density of 1 µm, 1018 cm−3, 1015 cm−3 respectively, underscoring the promising nature of Ag2BaTiSe4 absorber and new alkaline earth metal chalcogenide buffers in photovoltaics.
Cardiac vein retroinjections provide an efficient approach for global left ventricular gene transfer with adenovirus and adeno-associated virus
Authors: Lampela Jaakko , Pajula Juho , Järveläinen Niko , Siimes Satu , Laham-Karam Nihay , Kivelä Antti , Mushimiyimana Isidore , Nurro Jussi , Hartikainen Juha , Ylä-Herttuala Seppo
Published: January 2024

Heart failure (HF) is a major burden worldwide, and new therapies are urgently needed. Gene therapy is a promising new approach to treat myocardial diseases. However, current cardiac gene delivery methods for producing global myocardial effects have been inefficient. The aim of this study was to develop an endovascular, reproducible, and clinically applicable gene transfer method for global left ventricular (LV) transduction. Domestic pigs (n = 52) were used for the experiments. Global LV myocardium coverage was achieved by three retrograde injections into the three main LV vein branches. The distribution outcome was significantly improved by simultaneous transient occlusions of the corresponding coronary arteries and the main anastomotic veins of the retroinjected veins. The achieved cardiac distribution was visualized first by administering Indian Ink solution. Secondly, AdLacZ (2 × 1012vp) and AAV2-GFP (2 × 1013vg) gene transfers were performed to study gene transduction efficacy of the method. By retrograde injections with simultaneous coronary arterial occlusions, both adenovirus (Ad) and adeno-associated virus (AAV) vectors were shown to deliver an efficient transduction of the LV. We conclude that retrograde injections into the three main LV veins is a potential new approach for a global LV gene transfer.
Outcomes of two-stage type II hybrid aortic arch repair in elderly patients with acute type A aortic dissection
Authors: Xiang Jun , He Ling , Pen Tailuan , Li Donglin , Wei Shuliang
Published: January 2024

Acute type A aortic dissection (a-TAAD) is a severe disease characterized by high mortality, which can be fatal in elderly patients. The objective of this study was to investigate the safety and efficacy of two-stage type II hybrid aortic arch repair (HAR) in elderly patients with acute type A aortic dissection (a-TAAD). This was a single-center, retrospective study involving 119 patients with a-TAAD, including 82 males and 37 females, aged 22–81 years old. Eighty-eight patients underwent total aortic arch replacement (TAR) with frozen elephant trunk (FET) implantation (TAR with FET group) and 31 patients underwent two-stage type II HAR (HAR group). Propensity score matching was applied to adjust for preoperative data, and match 25 pairs. The preoperative, perioperative, postoperative and follow-up data were recorded. Fifteen patients died during the perioperative period; 13 cases were in the TAR with FET group and 2 cases were in the HAR group. The age, body mass index, cerebral infarction, renal insufficiency were significantly higher, and the 24-h fluid drainage, the incidence of acute liver injury, acute kidney injury and pulmonary infection were lower in the HAR group (all P < 0.05). Moreover, the mechanical ventilation time, intensive care unit time, hospital stay time were shorter in the HAR group (all P < 0.05). The follow-up period ranged from 12 to 54 months, with 7 deaths (9.3%) in the TAR with FET group and 2 deaths (6.9%) in the HAR group. The true lumen of the aortic arch and the middle descending thoracic aorta were larger and the false lumen thrombosis rates of the middle descending thoracic aorta and renal artery level were higher in the HAR group (all P < 0.05). Two-stage type II HAR is a safe and effective method for the treatment of elderly patients with a-TAAD. It may be a good choice for elderly patients with a-TAAD and comorbidities.
Fusion and classification algorithm of octacalcium phosphate production based on XRD and FTIR data
Authors: Nascimben Mauro , Kovrlija Ilijana , Locs Janis , Loca Dagnija , Rimondini Lia
Published: January 2024

The present manuscript tested an automated analysis sequence to provide a decision support system to track the OCP synthesis from $$\alpha$$
α
-TCP over time. Initially, the XRD and FTIR signals from a hundredfold scaled-up hydrolysis of OCP from $$\alpha$$
α
-TCP were fused and modeled by the curve fitting based on the significantly established maxima from the literature and nine features extracted from the fitted shapes. Afterward, the analysis sequence enclosed the machine learning techniques for feature ranking, spatial filtering, and dimensionality reduction to support the automatic recognition of the synthesis stages. The proposed analysis pipeline for OCP identification might be the foundation for a decision support system explicitly targeting OCP synthesis. Future projects will exploit the suggested methodology for pinpointing the OCP production over time (including the intermediary phases present in the OCP formation) and for evaluating whether biological variables might be merged with biomaterial properties to build a unified model of tissue response to the implant.
Association between environmental mercury exposure and allergic disorders in Korean children: Korean National Environmental Health Survey (KoNEHS) cycles 3–4 (2015–2020)
Authors: Lee Ji-youn , Choi Yun-Hee , Choi Hyeon-il , Moon Kyong Whan
Published: January 2024

Although previous studies have suggested potential adverse effects of mercury on a child’s immune system, the associations have been inconsistent. We aimed to determine the association between urinary mercury levels and allergic diseases in Korean children with high mercury exposure. Data from 853 and 710 children aged 6–11 years in the Korean National Environmental Health Survey (KoNEHS) cycle 3 (2015–2017) and cycle 4 (2018–2020) were analyzed. We examined the association between mercury exposure and the prevalence of atopic dermatitis (AD), asthma, allergic rhinitis (AR), and allergic multimorbidity. After adjusting for all covariates, the urinary mercury level was positively associated with AD in the 2015–2017 study (OR = 1.34, 95% CI = 1.01, 1.79) and AR in 2018–2020 study (OR = 1.46, 95% CI = 1.01, 2.10). Pooled effects showed OR of 1.34 (95% CI = 1.01, 1.79) for AD and 1.47 (95% CI = 1.01, 2.12) for allergic multimorbidity. The association with allergic multimorbidity was greater in boys (OR = 1.88, 95% CI = 1.01, 3.49) than in girls (OR = 1.25, 95% CI = 0.73, 2.14). These results suggest that environmental mercury exposure may exacerbate symptoms of atopic dermatitis and allergic multimorbidity in children.