Miracle-dz/UniFAR-FTUs huggingface dataset:
Methamphetamine induced regional-specific transcriptomic and epigenetic changes in the rat brain

Background Methamphetamine (METH) is a highly addictive central nervous system stimulant. Chronic use of METH is associated with multiple neurological and psychiatric disorders. An overdose of METH can cause brain damage and even death. Mounting evidence indicates that epigenetic changes and functional impairment in the brain occur due to addictive drug exposures. However, the responses of different brain regions to a METH overdose remain unclear. Results We investigated the transcriptomic and epigenetic responses to a METH overdose in four regions of the rat brain, including the nucleus accumbens, dentate gyrus, Ammon’s horn, and subventricular zone. We found that 24 hours after METH overdose, 15.6% of genes showed changes in expression and 27.6% of open chromatin regions exhibited altered chromatin accessibility in all four rat brain regions. Interestingly, only a few of those differentially expressed genes and differentially accessible regions were affected simultaneously. Among four rat brain regions analyzed, 149 transcription factors and 31 epigenetic factors were significantly affected by METH overdose. METH overdose also resulted in opposite-direction changes in regulation patterns of both gene and chromatin accessibility between the dentate gyrus and Ammon’s horn. Approximately 70% of chromatin-accessible regions with METH-induced alterations in the rat brain are conserved at the sequence level in the human genome, and they are highly enriched in neurological processes. Many of these conserved regions are active brain-specific enhancers and harbor SNPs associated with human neurological functions and diseases. Conclusion Our results indicate strong region-specific transcriptomic and epigenetic responses to a METH overdose in distinct rat brain regions. We describe the conservation of region-specific gene regulatory networks associated with METH overdose. Overall, our study provides clues toward a better understanding of the molecular responses to METH overdose in the human brain.
Analyzing influence of COVID-19 on crypto & financial markets and sentiment analysis using deep ensemble model

COVID-19 affected the world’s economy severely and increased the inflation rate in both developed and developing countries. COVID-19 also affected the financial markets and crypto markets significantly, however, some crypto markets flourished and touched their peak during the pandemic era. This study performs an analysis of the impact of COVID-19 on public opinion and sentiments regarding the financial markets and crypto markets. It conducts sentiment analysis on tweets related to financial markets and crypto markets posted during COVID-19 peak days. Using sentiment analysis, it investigates the people’s sentiments regarding investment in these markets during COVID-19. In addition, damage analysis in terms of market value is also carried out along with the worse time for financial and crypto markets. For analysis, the data is extracted from Twitter using the SNSscraper library. This study proposes a hybrid model called CNN-LSTM (convolutional neural network-long short-term memory model) for sentiment classification. CNN-LSTM outperforms with 0.89, and 0.92 F1 Scores for crypto and financial markets, respectively. Moreover, topic extraction from the tweets is also performed along with the sentiments related to each topic.
Multimorbidity patterns in the working age population with the top 10% medical cost from exhaustive insurance claims data of Japan Health Insurance Association

Although the economic burden of multimorbidity is a growing global challenge, the contribution of multimorbidity in patients with high medical expenses remains unclear. We aimed to clarify multimorbidity patterns that have a large impact on medical costs in the Japanese population. We conducted a cross-sectional study using health insurance claims data provided by the Japan Health Insurance Association. Latent class analysis (LCA) was used to identify multimorbidity patterns in 1,698,902 patients who had the top 10% of total medical costs in 2015. The present parameters of the LCA model included 68 disease labels that were frequent among this population. Moreover, subgroup analysis was performed using a generalized linear model (GLM) to assess the factors influencing annual medical cost and 5-year mortality. As a result of obtaining 30 latent classes, the kidney disease class required the most expensive cost per capita, while the highest portion (28.6%) of the total medical cost was spent on metabolic syndrome (MetS) classes, which were characterized by hypertension, dyslipidemia, and type 2 diabetes. GLM applied to patients with MetS classes showed that cardiovascular diseases or complex conditions, including malignancies, were powerful determinants of medical cost and mortality. MetS was classified into 7 classes based on real-world data and accounts for a large portion of the total medical costs. MetS classes with cardiovascular diseases or complex conditions, including malignancies, have a significant impact on medical costs and mortality.
UDP-glucose dehydrogenase (UGDH) in clinical oncology and cancer biology

UDP-glucose-6-dehydrogenase (UGDH) is a cytosolic, hexameric enzyme that converts UDP-glucose to UDP-glucuronic acid (UDP-GlcUA), a key reaction in hormone and xenobiotic metabolism and in the production of extracellular matrix precursors. In this review, we classify UGDH as a molecular indicator of tumor progression in multiple cancer types, describe its involvement in key canonical cancer signaling pathways, and identify methods to inhibit UGDH, its substrates, and its downstream products. As such, we position UGDH as an enzyme to be exploited as a potential prognostication marker in oncology and a therapeutic target in cancer biology.
PTR-MS measurements of concentrations and fluxes of biogenic VOCs in the humid tropics - rain forest vs. oil palm plantation

For the first time, concentrations and eddy covariance fluxes of several of the most abundant biogenic volatile organic compounds (VOCs) have been measured by PTR-MS in SE Asia (Malaysian Borneo) at two locations: at 75 m on a GAW tower over secondary rain forest and above an oil palm canopy. The operation of the instrument at both sites and the results are discussed in respect of the extremely high ambient humidity levels, which are not generally encountered outside of the humid tropics. Despite the challenging conditions, smooth operation could be achieved through instrument optimisation and anticondensation protection of the instrument set-up generally. The most abundant VOC was isoprene, with peak emissions of 4.7 mg m-2 h-1 above the rainforest and 30 mg m-2 h-1 above the oil palms. For most VOCs good sensitivities were obtained, but some of the strongly cluster-dependent OVOC species suffered a reduction in their detection limits. The results from both sites are presented, focussing on the effect of the different ambient humidity, which affected the normalised signal. At standard drift conditions the proton transfer reaction is known to dominate over the reaction with water clusters. However, at high humidities, water clusters appear to play a more significant role in the ultimate detection efficiencies. Nevertheless, PTR-MS has been proven to be capable of measuring various VOCs even in extreme tropical environments. In addition, some ideas for future instrument adjustments to facilitate tropical measurements are proposed.
The age of the oldest Scandinavian glaciations in mid-eastern Poland and southwestern Belarus

Analysis of type localities of Pleistocene deposits from mid-eastern Poland (Kozi Grzbiet, Łukow, Biala Podlaska and Wilczyn) and southwestern Belarus (Smolarka and Postolovo) has provided a new view on the age, limits and correlation of the oldest Scandinavian glaciations in the area. Integration of palaeontological data with determination of the Brunhes/Matuyama boundary (780 ka) at Kozi Grzbiet and Smolarka suggests that the first glaciation (Narevian) preceded this boundary and had a slightly smaller extent in SW Belarus than hitherto considered. The second glaciation (Nidanian) occurred slightly above or at this palaeomagnetic boundary. In Poland it is the first South Polish Glaciation, a till of which can be traced as far as the Holy Cross Mts. In SW Belarus it is represented by a till to the south of Brest and Bereza, and connected there with the oldest glaciation.
Simulation and Experimental Verification of Magnetic Field Diffusion at the Launch Load during Electromagnetic Launch

The unique magnetic field environment during electromagnetic launch imposes higher requirements on the design and protection of the internal electronic system within the launch load. This low-frequency, Tesla-level extreme magnetic field environment is fundamentally distinct from the Earth’s geomagnetic field. The excessive change rate of magnetic flux can readily induce voltage within the circuit, thus disrupting the normal operation of intelligent microchips. Existing simulation methods primarily focus on the physical environments of rails and armatures, making it challenging to precisely compute the magnetic field environment at the load’s location. In this paper, we propose a computational rail model based on the magneto–mechanical coupling model of a railgun. This model accounts for the dynamic current distribution during the launch process and simulates the magnetic flux density distribution at the load location. To validate the model’s accuracy, three-axis magnetic sensors were placed in front of the armature, and the dynamic magnetic field distribution during the launch process was obtained using the projectile-borne-storage testing method. The results indicate that compared to the previous literature methods, the approach proposed in this paper achieves higher accuracy and is closer to experimental results, providing valuable support for the design and optimization of the launch load.
Infant Outcomes Categorized by Birth Weight Percentile for Deliveries Between 28 and 41 Weeks of Gestation

There are different patterns in the association between birth weight percentile and infant mortality across deliveries at 28–41 weeks of gestation. OBJECTIVE: To examine the association between birth weight percentile and severe infant outcomes according to gestational age category. METHODS: We conducted a population-based retrospective cohort study using publicly available U.S. birth certificate data linked to infant death data from 2017 to 2019. Maternal–neonate pairs of singleton live births between 28 0/7 and 41 6/7 weeks of gestation (vaginal or cesarean delivery) were evaluated. We excluded infants with major fetal anomalies, chromosomal disorders, missing data, and birth weight outliers. The primary outcome was infant mortality within 1 year of life. Neonates were divided into eight sex-specific birth weight percentile categories: less than the 3rd, 3rd–less than the 10th, 10th–less than the 25th, 25th–to less than the 49th, 50th–less than the 75th, 75th–to less than the 90th, 90th–less than the 97th, and 97th or higher. RESULTS: There were 10,459,388 births between 28 and 41 weeks of gestation: 69,793 (0.7%) at 28–31 weeks, 88,673 (0.8%) at 32–33 weeks, 635,904 (6.1%) at 34–36 weeks, 2,763,110 (26.4%) at 37–38 weeks, 6,269,894 (59.9%) at 39–40 weeks, and 632,014 (6.0%) at 41 weeks. Infant mortality during the first year of life significantly increased at higher and lower birth weight percentiles at 28–36 weeks of gestation, with the lowest risk observed at the 50th–less than the 75th percentile. The highest mortality rates were 13.6% at less than the 3rd percentile and 8.4% at the 97th percentile or higher at 28–31 weeks of gestation; the second-highest mortality rates were 7.7% at less than the 3rd percentile and 3.1% at the 97th percentile or higher at 32–33 weeks of gestation. At 34–36 weeks of gestation, the highest and second-highest mortality rates were 3.4% at less than the 3rd percentile and 1.4% at the 3rd–10th percentile. At 37–41 weeks of gestation, infant mortality was associated with lower birth weight percentile, but higher birth weight percentiles were not significantly associated with increased mortality. CONCLUSION: We found different patterns in the association between birth weight percentile and infant mortality depending on gestational age category.
Household food insecurity in South Africa from 1999 to 2021: a metrics perspective

Abstract Objective: To review and synthesize studies on household food security in South Africa. Design: Systematic mapping review of metrics (methodological review). Setting: Electronic databases, including EBSCOHost, Scopus and Web of Science, were searched for studies and reports on household food security in South Africa, reporting household food security published between 1999 and 2021. Searching, selecting and reporting were performed according to the PRISMA (Preferred Reporting Items for Systematic reviews and Meta-Analyses) statement. Participants: South African households Results: Forty-eight articles reporting on six national surveys (one repeated annually since 2002) and forty sub-national studies meeting the inclusion criteria were selected. Various metrics, with different recall periods and ways of categorizing food security levels, were identified. Surveys that used similar metrics showed that the percentage of South African households that have experienced food insecurity and hunger has decreased over the review period yet remains concerning. However, the multitude of metrics used to assess the different components and levels of food security limits the comparability of the results to evaluate the scope and scale of the problem. Conclusions: There is growing support for developing multi-variable approaches for food security research in sub-Saharan Africa. Future research should focus on finding the most appropriate combination of complementary metrics that would allow comparable data while holistically capturing food security and providing insight into the causes and consequences.
A double-negative feedback loop between miR319c and JAW-TCPs establishes growth pattern in incipient leaf primordia in Arabidopsis thaliana

The microRNA miR319 and its target JAW-TCP transcription factors regulate the proliferation-to-differentiation transition of leaf pavement cells in diverse plant species. In young Arabidopsis leaf primordia, JAW-TCPs are detected towards the distal region whereas the major mRNA319-encoding gene MIR319C, is expressed at the base. Little is known about how this complementary expression pattern of MIR319C and JAW-TCPs is generated. Here, we show that MIR319C is initially expressed uniformly throughout the incipient primordia and is later abruptly down-regulated at the distal region, with concomitant distal appearance of JAW-TCPs, when leaves grow to ~100 μm long. Loss of JAW-TCPs causes distal extension of the MIR319C expression domain, whereas ectopic TCP activity restricts MIR319C more proximally. JAW-TCPs are recruited to and are capable of depositing histone H3K27me3 repressive marks on the MIR319C chromatin. JAW-TCPs fail to repress MIR319C in transgenic seedlings where the TCP-binding cis-elements on MIR319C are mutated, causing miR319 gain-of-function-like phenotype in the embryonic leaves. Based on these results, we propose a model for growth patterning in leaf primordia wherein MIR319C and JAW-TCPs repress each other and divide the uniformly growing primordia into distal differentiation zone and proximal proliferation domain.
Automated and Efficient Test-Generation for Grid-Based Multiagent Systems

Automatic generation of random test inputs is an approach that can alleviate the challenges of manual test case design. However, random test cases may be ineffective in fault detection and increase testing cost, especially in systems where test execution is resource- and time-consuming. To remedy this, the domain knowledge of test engineers can be exploited to select potentially effective test cases. To this end, test selection constraints suggested by domain experts can be utilized either for filtering randomly generated test inputs or for direct generation of inputs using constraint solvers. In this paper, we propose a domain specific language (DSL) for formalizing locality-based test selection constraints of autonomous agents and discuss the impact of test selection filters, specified in our DSL, on randomly generated test cases. We study and compare the performance of filtering and constraint solving approaches in generating selective test cases for different test scenario parameters and discuss the role of these parameters in test generation performance. Through our study, we provide criteria for suitability of the random data filtering approach versus the constraint solving one under the varying size and complexity of our testing problem. We formulate the corresponding research questions and answer them by designing and conducting experiments using QuickCheck for random test data generation with filtering and Z3 for constraint solving. Our observations and statistical analysis indicate that applying filters can significantly improve test efficiency of randomly generated test cases. Furthermore, we observe that test scenario parameters affect the performance of the filtering and constraint solving approaches differently. In particular, our results indicate that the two approaches have complementary strengths: random generation and filtering works best for large agent numbers and long paths, while its performance degrades in the larger grid sizes and more strict constraints. On the contrary, constraint solving has a robust performance for large grid sizes and strict constraints, while its performance degrades with more agents and long paths.
MUSKRATS (ONDATRA ZIBETHICUS) ARE COMPETENT INTERMEDIATE HOSTS OF ECHINOCOCCUS MULTILOCULARIS IN NORTH AMERICA

Abstract: The tapeworm Echinococcus multilocularis is an emerging pathogen of significance to human and animal health in Canada, yet little is known about key rodent intermediate hosts in local urban ecosystems. In Europe, invasive muskrats (Ondatra zibethicus) are an important indicator intermediate host species; however, the role of this semiaquatic rodent in the ecology of E. multilocularis is undetermined in the North American context. We examined 93 muskrats that were livetrapped in the spring of 2017 within Calgary, Alberta, Canada, for the presence of E. multilocularis infection. The objectives of this study were to 1) diagnose alveolar echinococcosis using macroscopic assessment, histopathology, and molecular analyses; 2) quantify infection severity; and 3) assess host demographic risk factors for infection. Macroscopic cysts consistent with alveolar echinococcosis were present in 24% of muskrats (22/93). Most individuals had hepatic cysts; however, cysts were also occasionally detected in the mesentery, reproductive organs, omentum, peritoneum, spleen, diaphragm, lung, or kidney. The mean number of cysts per liver was 2.1 (range, 1–4). We examined hepatic cysts from 18 individuals using histology; all had lesions compatible with alveolar echinococcosis. Protoscoleces, indicative of patent infections, were present in 14/18 (78%). No demographic risk factors (sex, body condition, body mass) were significantly associated with infection. Muskrats in the North American context are competent intermediate hosts with high infection prevalence and may play an important role in the ecology of this emerging parasite.
Impact of stroke history on procedural cerebrovascular insult probability and long‐term outcome after TAVI

In TAVI procedural stroke is one of the most feared complications and for this reason also extensively studied. But there is a lack of data concerning the impact of previous stroke on procedural stroke and on long‐term survival. The aim of this registry‐based cohort study is to evaluate the prevalence of previous stroke in TAVI patients and its impact on procedural stroke risk as well as long‐term outcome.
Swine influenza A virus isolates containing the pandemic H1N1 origin matrix gene elicit greater disease in the murine model

Since the 1990’s, endemic North American swine influenza A viruses (swFLUAV) contained an internal gene segment constellation referred to as the triple reassortment internal gene (TRIG) cassette. In 2009, the H1N1 pandemic (pdmH1N1) virus spilled back into swine, but did not become endemic. However, the pdmH1N1 did contribute the matrix gene segment (pdmM) to the swFLUAVs circulating in the pig population; which replaced the classical swine matrix gene (swM) found in the TRIG cassette, suggesting that the pdmM has a fitness benefit. Others have shown that swFLUAV containing the pdmM have greater neuraminidase activity and transmission efficiency compared to viruses containing the swM gene segment. We hypothesized that the matrix gene could also affect disease and utilized two infection models, resistant BALB/c and susceptible DBA/2 mice, to assess swFLUAV pathogenicity. We infected BALB/c and DBA/2 mice with a panel of H1 and H3 swFLUAVs containing the swM or pdmM gene and measured lung virus titers, morbidity, mortality, and lung histopathology. H1 influenza strains containing the pdmM gene caused greater morbidity and mortality in both resistant and susceptible murine strains, while H3 swFLUAVs caused no clinical disease. However, both H1 and H3 swFLUAVs containing the pdmM replicated to higher viral titers in the lungs and pdmM containing H1 viruses induced greater histological changes compared to swM H1 viruses. While the surface glycoproteins contribute to swFLUAV pathogenicity, and other genes also influence disease, these data suggest that the origin of the matrix gene also contributes to pathogenicity of swFLUAV viruses in mice.
Design Strengths for an Offshore Clay

Stability analyses for stage construction of a breakwater located offshore New Jersey required a detailed evaluation of the undrained stress‐strain‐strength properties of a plastic marine clay. One set of analyses, representing “conventional” practice, used UU triaxial compression tests to obtain the initial undrained strength (cu) and CIU triaxial compression tests to predict strength increases with consolidation. The second approach employed the Stress History And Normalized Soil Engineering Properties (SHANSEP) design procedure. This involved extensive consolidation testing to measure the in‐situ preconsolidation pressure and a comprehensive program of CKoU tests sheared in compression, extension and direct simple shear modes of failure at varying overconsolidation ratios. A strain compatibility technique was applied to the SHANSEP data to account for the effects of anisotropy and progressive failure in circular arc‐ and wedge‐type stability analyses. The SHANSEP approach yielded design strengths signi.
Human-like scene interpretation by a guided counterstream processing

Significance Understanding a visual scene is an unsolved and daunting task, since scenes can contain a large number of objects, their properties, and interrelations. Extracting the full scene structure is therefore infeasible, but often unnecessary, since it will be sufficient to extract a partial scene structure, which depends on the observer’s goal and interest. The presented model has a human-like ability to perform such a partial interpretation, focusing on scene structures of interest, evolving sequentially, in a goal-directed manner. The model uses a cortex-like combination of bottom–up and top–down networks, where the goal is achieved by automatically providing a sequence of top–down instructions that guide the process in an efficient manner, which generalizes broadly across different scene structures.