Miracle-dz/UniFAR-FTUs huggingface dataset:
Multiomics Analyses With Stool-Type Stratification in Patient Cohorts and Blautia Identification as a Potential Bacterial Modulator in Type 2 Diabetes Mellitus

Heterogeneity in host and gut microbiota hampers microbial precision intervention of type 2 diabetes mellitus (T2DM). Here, we investigated novel features for patient stratification and bacterial modulators for intervention, using cross-sectional patient cohorts and animal experiments. We collected stool, blood, and urine samples from 103 patients with recent-onset T2DM and 25 healthy control subjects (HCs), performed gut microbial composition and metabolite profiling, and combined it with host transcriptome, metabolome, cytokine, and clinical data. Stool type (dry or loose stool), a feature of the stool microenvironment recently explored in microbiome studies, was used for stratification of patients with T2DM as it explained most of the variation in the multiomics data set among all clinical parameters in our covariate analysis. T2DM with dry stool (DM-DS) and loose stool (DM-LS) were clearly differentiated from HC and each other by LightGBM models, optimal among multiple machine learning models. Compared with DM-DS, DM-LS exhibited discordant gut microbial taxonomic and functional profiles, severe host metabolic disorder, and excessive insulin secretion. Further cross-measurement association analysis linked the differential microbial profiles, in particular Blautia abundances, to T2DM phenotypes in our stratified multiomics data set. Notably, oral supplementation of Blautia to T2DM mice induced inhibitory effects on lipid accumulation, weight gain, and blood glucose elevation with simultaneous modulation of gut bacterial composition, revealing the therapeutic potential of Blautia. Our study highlights the clinical implications of stool microenvironment stratification and Blautia supplementation in T2DM, offering promising prospects for microbial precision treatment of metabolic diseases. Article Highlights Heterogeneity in host and gut microbiota hampers microbial precision intervention of type 2 diabetes mellitus (T2DM), requiring novel features for patient stratification and bacterial modulators for intervention. Stool type outperformed other clinical parameters in stratifying the T2DM population based on multiomics profiles of T2DM. In-depth analyses of stool-type–stratified multiomics data sets revealed a more favorable T2DM profile in patients with dry stools than those with loose stools. Blautia, differentially behaving in our stratified patient cohorts with regard to its abundance and links to T2DM, inhibited obesity and glucolipid metabolic disorder and modified microbial compositions in T2DM mouse models. Our study highlights clinical implications of stool-type–based stratification and Blautia supplementation in T2DM.
Advances in new targets for immunotherapy of small cell lung cancer

Small cell lung cancer (SCLC) is one of the highly aggressive malignancies characterized by rapid growth and early metastasis, but treatment options are limited. For SCLC, carboplatin or cisplatin in combination with etoposide chemotherapy has been considered the only standard of care, but the standard first‐line treatment only results in 10‐month survival. The majority of patients relapse within a few weeks to months after treatment, despite the relatively sensitive response to chemotherapy. Over the past decade, immunotherapy has made significant progress in the treatment of SCLC patients. However, there have been limited improvements in survival rates for SCLC patients with the current immune checkpoint inhibitors PD‐1/PD‐L1 and CTLA‐4. In the face of high recurrence rates, small beneficiary populations, and low survival benefits, the exploration of new targets for key molecules and signals in SCLC and the development of drugs with novel mechanisms may provide fresh hope for immunotherapy in SCLC. Therefore, the aim of this review was to explore four new targets, DLL3, TIGIT, LAG‐3, and GD2, which may play a role in the immunotherapy of SCLC to find useful clues and strategies to improve the outcome for SCLC patients.
Data‐Driven Compound Identification in Atmospheric Mass Spectrometry

Abstract Aerosol particles found in the atmosphere affect the climate and worsen air quality. To mitigate these adverse impacts, aerosol particle formation and aerosol chemistry in the atmosphere need to be better mapped out and understood. Currently, mass spectrometry is the single most important analytical technique in atmospheric chemistry and is used to track and identify compounds and processes. Large amounts of data are collected in each measurement of current time‐of‐flight and orbitrap mass spectrometers using modern rapid data acquisition practices. However, compound identification remains a major bottleneck during data analysis due to lacking reference libraries and analysis tools. Data‐driven compound identification approaches could alleviate the problem, yet remain rare to non‐existent in atmospheric science. In this perspective, the authors review the current state of data‐driven compound identification with mass spectrometry in atmospheric science and discuss current challenges and possible future steps toward a digital era for atmospheric mass spectrometry.
IGF‐I protects porcine granulosa cells from hypoxia‐induced apoptosis by promoting homologous recombination repair through the PI3K/AKT/E2F8/RAD51 pathway

Severe hypoxia induced by vascular compromise (ovarian torsion, surgery), obliteration of vessels (aging, chemotherapy, particularly platinum drugs) can cause massive follicle atresia. On the other hand, hypoxia increases the occurrence of DNA double‐strand breaks (DSBs) and triggers cellular damage repair mechanisms; however, if the damage is not promptly repaired, it can also induce the apoptosis program. Insulin‐like growth factor‐I (IGF‐I) is a polypeptide hormone that plays essential roles in stimulating mammalian follicular development. Here, we report a novel role for IGF‐I in protecting hypoxic GCs from apoptosis by promoting DNA repair through the homologous recombination (HR) process. Indeed, the hypoxic environment within follicles significantly inhibited the efficiency of HR‐directed DNA repair. The presence of IGF‐I‐induced HR pathway to alleviate hypoxia‐induced DNA damage and apoptosis primarily through upregulating the expression of the RAD51 recombinase. Importantly, we identified a new transcriptional regulator of RAD51, namely E2F8, which mediates the protective effects of IGF‐I on hypoxic GCs by facilitating the transcriptional activation of RAD51. Furthermore, we demonstrated that the PI3K/AKT pathway is crucial for IGF‐I‐induced E2F8 expression, resulting in increased RAD51 expression and enhanced HR activity, which mitigates hypoxia‐induced DNA damage and thereby protects against GCs apoptosis. Together, these findings define a novel mechanism of IGF‐I‐mediated GCs protection by activating the HR repair through the PI3K/AKT/E2F8/RAD51 pathway under hypoxia.
Research on Interpretable Fake News Detection Technology Based on Co-Attention Mechanism

The wide dissemination of false news is increasingly threatening both individuals and society. Aiming at the problem of insufficient interpretability in false news detection task, the model TCIN based on collaborative attention mechanism is proposed. The model integrates the advantages of the existing dEFEND model and GCAN model. It captures more detailed semantic features through three attention layers (sentence-level cooperative attention layer, word-level cooperative attention layer and sentence-comment cooperative attention layer). The experimental results show that, compared with the model before combination, the accuracy of this model is 9.7% higher on the data set of Weibo-20 and on Twitter15 data set the accuracy is increased by 7.43%.
EasyCircR: Detection and reconstruction of circular RNAs post-transcriptional regulatory interaction networks

Circular RNAs (circRNAs) are regulatory RNAs that play a crucial role in various biological activities and have been identified as potential biomarkers for the development of neurological disorders and cancer. CircRNAs have emerged as significant regulators of gene expression through different mechanisms, including regulation of transcription and splicing, modulation of translation, and post-translational modification. Additionally, some circRNAs function as microRNA (miRNA) sponges in the cytoplasm, enhancing the expression of target genes by suppressing miRNA activity. Although existing pipelines reconstruct circRNAs, identify miRNAs sponged by them, retrieve cascade-regulated mRNAs, and represent the regulatory interactions as complex circRNA-miRNA-mRNA networks, none of the state-of-the-art approaches can discriminate the biological level at which the mRNAs involved in the interactions are regulated. EasyCircR is a novel R package that combines circRNA detection and reconstruction with post-transcriptional gene expression analysis (exon-intron split analysis) and miRNA response element prediction. The package enables estimation and visualization of circRNA-miRNA-mRNA interactions through an intuitive Shiny application, taking advantage of the post-transcriptional regulatory nature of circRNAs and excluding unrealistic regulatory outcomes. EasyCircR source code, Docker container and user guide are available at: https://github.com/InfOmics/EasyCircR
Review and Trends of Thermoelectric Generator Heat Recovery in Automotive Applications

Automotive vehicles with internal combustion engines, such as conventional gasoline and electric hybrid vehicles, exhibit inherent irreversibilities that hinder them from achieving high efficiencies. These irreversibilities manifest themselves in the form of thermal losses in the engine and contribute to the total energy consumption in the transportation sector. Waste heat recovery is a method to increase the overall fuel efficiency of vehicles by recovering thermal energy that would be lost from the engine to the environment and converting it to useful energy for the vehicle. In the past years, thermoelectric generators have been intensively investigated for waste heat recovery in vehicles because they are solid-state devices that convert heat directly into electricity and hence have no moving parts, operate quietly, are relatively small, and require low maintenance. This paper presents a review of the literature on waste heat recovery in vehicles through the implementation of thermoelectric generators. First, potential sources or locations in a vehicle for waste heat recovery are presented. Second, the available thermoelectric technology for vehicle applications is reviewed. Then, the components required to create a waste heat recovery system are discussed. The approach for modeling thermoelectric generators to predict the power output is then considered. Finally, experimental investigations by researchers are presented as well as the future trends observed for waste recovery via thermoelectrics.
TABAQUISMO EN COSTA RICA. IMPLICACIONES DEL FUMADO ACTIVO Y PASIVO EN LA POBLACION GENERAL 1 SMOKING IN COSTA RICA. IMPLICATIONS OF ACTIVE AND PASSIVE SMOKING IN THE GENERAL POPULATION

This article presents the results of a study, which aimed to compile information on tobacco consumption in a national sample of 4645 subjects within 12 thru 70 years of age. Specific questions were designed to explore the level of exposition to nicotine, as much in active smokers as in passive ones. This survey used the technique of house
Evaluating TF-IDF and Transformers-based models for Detecting COVID-19 related Conspiracies

The proliferation of misinformation and conspiracy theories on online social media platforms has become a significant concern for public health and safety. To effectively combat this issue, a new generation of data mining and analysis algorithms is essential for early detection and tracking of these information cascades. In this paper, we employed a multifaceted approach for detecting and identifying conspiracy theories and misinformation spreaders related to the Coronavirus pandemic. Specifically, we utilized Text-Based Detection (Task 1) through a combination of TF-IDF-based and Transformers-based methods, Graph-Based Detection (Task 2) through a graph convolutional network, and alternative Transformers-based methods to improve the results of Task 1. Our efforts have yielded promising results, with our best models achieving an impressive MCC score of 0.705 for Task 1, 0.041 for Task 2, and 0.698 for Task 3.
Dysregulated iron homeostasis in dystrophin-deficient cardiomyocytes: correction by gene editing and pharmacological treatment

Abstract Aims Duchenne muscular dystrophy (DMD)-associated cardiomyopathy is a serious life-threatening complication, the mechanisms of which have not been fully established, and therefore no effective treatment is currently available. The purpose of the study was to identify new molecular signatures of the cardiomyopathy development in DMD. Methods and results For modelling of DMD-associated cardiomyopathy, we prepared three pairs of isogenic control and dystrophin-deficient human induced pluripotent stem cell (hiPSC) lines. Two isogenic hiPSC lines were obtained by CRISPR/Cas9-mediated deletion of DMD exon 50 in unaffected cells generated from healthy donor and then differentiated into cardiomyocytes (hiPSC-CM). The latter were subjected to global transcriptomic and proteomic analyses followed by more in-depth investigation of selected pathway and pharmacological modulation of observed defects. Proteomic analysis indicated a decrease in the level of mitoNEET protein in dystrophin-deficient hiPSC-CM, suggesting alteration in iron metabolism. Further experiments demonstrated increased labile iron pool both in the cytoplasm and mitochondria, a decrease in ferroportin level and an increase in both ferritin and transferrin receptor in DMD hiPSC-CM. Importantly, CRISPR/Cas9-mediated correction of the mutation in the patient-derived hiPSC reversed the observed changes in iron metabolism and restored normal iron levels in cardiomyocytes. Moreover, treatment of DMD hiPSC-CM with deferoxamine (DFO, iron chelator) or pioglitazone (mitoNEET stabilizing compound) decreased the level of reactive oxygen species in DMD hiPSC-CM. Conclusion To our knowledge, this study demonstrated for the first time impaired iron metabolism in human DMD cardiomyocytes, and potential reversal of this effect by correction of DMD mutation or pharmacological treatment. This implies that iron overload-regulating compounds may serve as novel therapeutic agents in DMD-associated cardiomyopathy.
Mixed-Type Data Augmentations for Environmental Sound Classification

The goal of environmental sound classification is to accurately identify and classify sounds in order to provide valuable insights about the environment. The classification task can be solved by training machine learning models, such as convolutional neural networks, on a dataset of labeled sound samples. Due to the small size of available datasets in this field, time-consuming and expensive labeling process, data augmentations have become a popular practice to artificially generate additional data. The purpose of this study is to analyze whether using Mixed-Type data augmentations improves the classification performance compared to results with no augmentations. Mixed-Type data augmentation methods were evaluated on ESC-50 and UrbanSound8K datasets for the pretrained ResNet-18 model with extracted mel-frequency cepstral coefﬁcients as feature inputs. Results for both datasets show that data augmentations can improve model performance with certain mixup probabilities and coefficients but specific methods and parameters used may vary for each dataset and task.
Nucleic Quasi-Primes: Identification of the Shortest Unique Oligonucleotide Sequences in a Species

Despite the exponential increase in sequencing information driven by massively parallel DNA sequencing technologies, universal and succinct genomic fingerprints for each organism are still missing. Identifying the shortest species-specific nucleic sequences offers insights into species evolution and holds potential practical applications in agriculture, wildlife conservation, and healthcare. We propose a new method for sequence analysis termed nucleic “quasi-primes”, the shortest occurring sequences in each of 45,785 organismal reference genomes, present in one genome and absent from every other examined genome. In the human genome, we find that the genomic loci of nucleic quasi-primes are most enriched for genes associated with brain development and cognitive function. In a single-cell case study focusing on the human primary motor cortex, nucleic quasi-prime genes account for a significantly larger proportion of the variation based on average gene expression. Non-neuronal cell-types, including astrocytes, endothelial cells, microglia perivascular-macrophages, oligodendrocytes, and vascular and leptomeningeal cells, exhibited significant activation of quasi-prime containing gene associations related to cancer, while simultaneously suppressing quasi-prime containing genes were associated with cognitive, mental, and developmental disorders. We also show that human disease-causing variants, eQTLs, mQTLs and sQTLs are 4.43-fold, 4.34-fold, 4.29-fold and 4.21-fold enriched at human quasi-prime loci, respectively. These findings indicate that nucleic quasi-primes are genomic loci linked to the evolution of species-specific traits and in humans they provide insights in the development of cognitive traits and human diseases, including neurodevelopmental disorders.
Deposition of the Morrison Formation (Jurassic), Northern Tobacco Root Mountains, Montana with Evidence against Recurrent Movement along the Willow Creek Fault Zone

Comparative sedimentologic and petrologic analysis of well-exposed sections of the Morrison Formation on opposite sides of the Willow Creek fault zone, a Proterozoic basement structure that was periodically reactivated throughout the Phanerozoic, indicates that the structure was inactive and had little or no influence on deposition of the Morrison Formation during the lat-est Jurassic. Results of our study, coupled with conclusions of previous work that the Willow Creek fault zone formed the southern boundary of the Belt Island during deposition of the underlying marine Ellis Group, indicate that the duration of Willow Creek fault movement during the Jurassic was at least 20-26 m.y. The most compelling evidence against movement along the fault is the identical fluvial facies architecture of the Morrison in outcrops north and south of the fault; limited petrographic and paleoflow data indicate similar provenance and paleoflow on both sides of the fault, and thus no structural control as well. Three stratigraphic intervals, defined by diagnostic facies elements, constitute the Morrison in both sets of outcrops. The lower interval, which is conformable with the underlying Swift Formation, consists dominantly of greenish to tan, fine-grained deposits with subordinate, less than 3 ft (lm) thick, lenticular limestone beds and isolated sheet sandstone complexes. In contrast, the middle interval contains approximately equal proportions of broadly channelized, sheet sandstone bodies (average widthlthickness ratio = 6011) and fine-grained deposits that are mostly red and purple in color. The upper interval contains multiple ribbon sand bodies (average WfI' ratio = 1011) encased within a slightly higher percentage of multi-colored, fine-grained deposits. In both the middle and upper intervals, carbonate nodules occur throughout the fine- grained deposits but discrete limestone horizons are relatively rare. The Morrison Formation in the study area
mRNA nuclear export: how mRNA identity features distinguish functional RNAs from junk transcripts

ABSTRACT The division of the cellular space into nucleoplasm and cytoplasm promotes quality control mechanisms that prevent misprocessed mRNAs and junk RNAs from gaining access to the translational machinery. Here, we explore how properly processed mRNAs are distinguished from both misprocessed mRNAs and junk RNAs by the presence or absence of various ‘identity features’.
Quantum Material-Based Self-Propelled Microrobots for the Optical “On-the-Fly” Monitoring of DNA

Quantum dot-based materials have been found to be excellent platforms for biosensing and bioimaging applications. Herein, self-propelled microrobots made of graphene quantum dots (GQD–MRs) have been synthesized and explored as unconventional dynamic biocarriers toward the optical “on-the-fly” monitoring of DNA. As a first demonstration of applicability, GQD–MRs have been first biofunctionalized with a DNA biomarker (i.e., fluorescein amidite-labeled, FAM-L) via hydrophobic π-stacking interactions and subsequently exposed toward different concentrations of a DNA target. The biomarker–target hybridization process leads to a biomarker release from the GQD–MR surface, resulting in a linear alteration in the fluorescence intensity of the dynamic biocarrier at the nM range (1–100 nM, R2 = 0.99), also demonstrating excellent selectivity and sensitivity, with a detection limit as low as 0.05 nM. Consequently, the developed dynamic biocarriers, which combine the appealing features of GQDs (e.g., water solubility, fluorescent activity, and supramolecular π-stacking interactions) with the autonomous mobility of MRs, present themselves as potential autonomous micromachines to be exploited as highly efficient and sensitive “on-the-fly” biosensing systems. This method is general and can be simply customized by tailoring the biomarker anchored to the GQD–MR’s surface.
The practice investigation of the information technology efficiency for automated definition of terms in the semantic content of educational materials

Запропоновано інформаційну технологію, що ґрунтується на дисперсійній оцінці важливості слів, яка дозволяє з достатньо високою ефективністю визначати семантичні терміни в контенті навчальних матеріалів. Розглянуто фактори, що ускладнюють ефективне визначення семантичних термінів у навчальних матеріалах. Встановлена ефективність запропонованої технології сприяє її використанню для вирішення ряду актуальних задач, таких як оцінка відповідності навчальних матеріалів змістовим вимогам, оцінка відповідності наборів тестових завдань навчальним матеріалам, семантична допомога при створенні тестів, автоматизована генерація множин ключових слів та створення анотацій. Ключові слова: інформаційна технологія, семантичні терміни, навчальні матеріали, анотація.
Left ventricular assist device-associated driveline infections as a specific form of complicated skin and soft tissue infection/acute bacterial skin and skin structure infection – issues and therapeutic options

Purpose of review This review comments on the current guidelines for the treatment of wound infections under definition of acute bacterial skin and skin structure infections (ABSSSI). However, wound infections around a catheter, such as driveline infections of a left ventricular assist device (LVAD) are not specifically listed under this definition in any of the existing guidelines. Recent findings Definitions and classification of LVAD infections may vary across countries, and the existing guidelines and recommendations may not be equally interpreted among physicians, making it unclear if these infections can be considered as ABSSSI. Consequently, the use of certain antibiotics that are approved for ABSSSI may be considered as ‘off-label’ for LVAD infections, leading to rejection of reimbursement applications in some countries, affecting treatment strategies, and hence, patients’ outcomes. However, we believe driveline exit site infections related to LVAD can be included within the ABSSSI definition. Summary We argue that driveline infections meet the criteria for ABSSSI which would enlarge the ‘on-label’ antibiotic armamentarium for treating these severe infections, thereby improving the patients’ quality of life.