Miracle-dz/UniFAR-FTUs huggingface dataset:
Long Non-Coding RNA H19 Positively Associates With Aspirin Resistance in the Patients of Cerebral Ischemic Stroke

Background and purpose Aspirin is a novel anti-platelet drug that is intensively recommended for the prevention and treatment of cerebral ischemic stroke. However, the existence of aspirin resistance weakens the effects of aspirin and usually induces the recurrence of ischemic stroke. While the mechanism underlying aspirin resistance is still unclear. Long non-coding RNA H19 (H19) is closely associated with the onset and prognosis of cerebral ischemic stroke. Since the relationship between H19 and aspirin resistance have never been reported, herein, we aimed to evaluate the H19 expression in aspirin-resistant ischemic stroke patients and subsequently, ascertain the ability of H19 to diagnose aspirin resistance. Methods We included 150 patients with acute cerebral ischemic stroke who were followed up for one year to determine stroke recurrence. Levels of 11-dehydro thromboxane B2 (11dhTXB2) in urine were tested to evaluate the status of aspirin resistance, and those of H19 and 8-iso-prostaglandin-2α in plasma were assessed. The relationship between 11dhTXB2 or and 8-iso-prostaglandin-2α and H19, and the receiver operating characteristic curve of H19, the association of H19 and aspirin resistance with the recurrence of stoke were statistically analyzed. Results Plasma H19 was significantly up-regulated in patients with aspirin resistance (p=0.0203), and the H19 levels were positively associated with urine 11dhTXB2/creatinine (R=0.04364, p=0.0106) and positively associated with the level of 8-iso-PGF2α (R=0.04561, p=0.0089). The ROC curves indicated that H19 can sensitively and specifically diagnose aspirin resistance (area under the curve, 0.8005; 95% CI, 0.7301–0.8710; p < 0.0001; specificity, 75.86207%; sensitivity, 73.84615%.). H19 is an independent risk factor for aspirin resistance (OR=1.129, p=0.0321), and aspirin resistance and H19 are closely related with ischemic stroke recurrence. Conclusions H19 is closely associated with aspirin resistance, and H19 probably induces aspirin resistance through increasing the production of 8-iso-prostaglandin-2α. Besides which, H19 may serve as a serological marker for diagnosing aspirin resistance with high specificity and sensitivity, and the test of H19 could give clues to the recurrence of ischemic stroke.
Combination of Trace Metal to Improve Solventogenesis of Clostridium carboxidivorans P7 in Syngas Fermentation

Higher alcohols such as butanol (C4 alcohol) and hexanol (C6 alcohol) are superior biofuels compared to ethanol. Clostridium carboxidivorans P7 is a typical acetogen capable of producing C4 and C6 alcohols natively. In this study, the composition of trace metals in culture medium was adjusted, and the effects of these adjustments on artificial syngas fermentation by C. carboxidivorans P7 were investigated. Nickel and ferrous ions were essential for growth and metabolite synthesis during syngas fermentation by P7. However, a decreased dose of molybdate improved alcohol fermentation performance by stimulating carbon fixation and solventogenesis. In response to the modified trace metal composition, cells grew to a maximum OD600nm of 1.6 and accumulated ethanol and butanol to maximum concentrations of 2.0 and 1.0 g/L, respectively, in serum bottles. These yields were ten-fold higher than the yields generated using the original composition of trace metals. Furthermore, 0.5 g/L of hexanol was detected at the end of fermentation. The results from gene expression experiments examining genes related to carbon fixation and organic acid and solvent synthesis pathways revealed a dramatic up-regulation of the Wood–Ljungdahl pathway (WLP) gene cluster, the bcs gene cluster, and a putative CoA transferase and butanol dehydrogenase, thereby indicating that both de novo synthesis and acid re-assimilation contributed to the significantly elevated accumulation of higher alcohols. The bdh35 gene was speculated to be the key target for butanol synthesis during solventogenesis.
The Thermal Dependence of Locomotion, Tongue Flicking, Digestion, and Oxygen Consumption in the Wandering Garter Snake

The body temperature (Tb) of garter snakes (Thamnophis elegans) can vary considerably in the course of a day (e.g., 4-33 C), and information on how Tb affects physiological and behavioral processes is required to evaluate the significance of that variation. We measured crawling speed, swimming speed, tongue-flicking rate, digestive rate, and oxygen consumption at Tb's of 5-35 C in snakes collected in eastern Washington and acclimated to September field photoperiod and temperature cycles. All functions were strongly dependent on Tb. The maximum speed of crawling (X̄ = 0.74 m s−1) occurred at Tb = 34.5 C; that of swimming (X̄ = 0.69 m s−1) occurred at Tb = 28.5. At < 30 C, the snakes crawled more slowly than they swam, but the reverse was true at higher Tb. At Tb = 30 C, the snakes moved their tongues up and down at a maximum rate of 22 Hz. Digestion rate increased sharply above 20 C, to a maximum of 0.45 mice/day within the Tb range of 25-35 C. All snakes regurgitated their meal at 10 C. The Q10 values for mass-specific oxygen consumption over the 5-15, 15-25, and 25-35 C Tb ranges were 2.4, 1.3, and 5.0, respectively. Among the performances studied, swimming speed was the least sensitive, and digestion rate the most sensitive, to Tb. FieldTb data indicate that all functions would be near maximum levels during the day but would be significantly reduced at night. We conclude that no single Tb is best for the ecological tasks of prey capture, predator avoidance, and energy conservation.
CVB3 VP1 interacts with MAT1 to inhibit cell proliferation by interfering with Cdk-activating kinase complex activity in CVB3-induced acute pancreatitis

Coxsackievirus B3 (CVB3) belongs to the genus Enterovirus of the family Picornaviridae and can cause acute acinar pancreatitis in adults. However, the molecular mechanisms of pathogenesis underlying CVB3-induced acute pancreatitis have remained unclear. In this study, we discovered that CVB3 capsid protein VP1 inhibited pancreatic cell proliferation and exerted strong cytopathic effects on HPAC cells. Through yeast two-hybrid, co-immunoprecipitation, and confocal microscopy, we show that Menage a trois 1 (MAT1), a subunit of the Cdk-Activating Kinase (CAK) complex involved in cell proliferation and transcription, is a novel interaction protein with CVB3 VP1. Moreover, CVB3 VP1 inhibited MAT1 accumulation and localization, thus interfering with its interaction with CDK7. Furthermore, CVB3 VP1 could suppress CAK complex enzymic phosphorylation activity towards RNA Pol II and CDK4/6, direct substrates of CAK. VP1 also suppresses phosphorylation of retinoblastoma protein (pRb), an indirect CAK substrate, especially at phospho-pRb Ser780 and phospho-pRb Ser807/811 residues, which are associated with cell proliferation. Finally, we present evidence using deletion mutants that the C-terminal domain (VP1-D8, 768-859aa) is the minimal VP1 region required for its interaction with MAT1, and furthermore, VP1-D8 alone was sufficient to arrest cells in G1/S phase as observed during CVB3 infection. Taken together, we demonstrate that CVB3 VP1 can inhibit CAK complex assembly and activity through direct interaction with MAT1, to block MAT1-mediated CAK-CDK4/6-Rb signaling, and ultimately suppress cell proliferation in pancreatic cells. These findings substantially extend our basic understanding of CVB3-mediated pancreatitis, providing strong candidates for strategic therapeutic targeting.
Is a Long Essay Always a Good Essay? The Effect of Text Length on Writing Assessment

The assessment of text quality is a transdisciplinary issue concerning the research areas of educational assessment, language technology, and classroom instruction. Text length has been found to strongly influence human judgment of text quality. The question of whether text length is a construct-relevant aspect of writing competence or a source of judgment bias has been discussed controversially. This paper used both a correlational and an experimental approach to investigate this question. Secondary analyses were performed on a large-scale dataset with highly trained raters, showing an effect of text length beyond language proficiency. Furthermore, an experimental study found that pre-service teachers tended to undervalue text length when compared to professional ratings. The findings are discussed with respect to the role of training and context in writing assessment.
Parent and Teacher Depictions of Gender Gaps in Secondary Student Appraisals of Their Academic Competences

The present study examines a group of secondary teachers’ and parents’ appraisals of gender gaps in secondary students’ self-assessment of competence in Science, Technology, Engineering, and Mathematics (STEM) and non-STEM domains. Eight focus groups with 39 parents and 34 secondary teachers were conducted for this purpose. In light of the observed gender gaps in students’ performance and self-perception of ability in the different subject areas, the participants were particularly surprised by girls’ underestimation of their abilities in STEM subjects, compared with boys’ tendency to overestimate their abilities in STEM. Most participants agreed on the need for measures to combat these inaccuracies and discussed possible causes. Some participants associated these gender disparities in students’ self-assessment of ability with gender gaps in their choices of subject areas and occupations. The role played by school, teachers, families, and other socialization agents in reinforcing gender stereotypes about academic competence was also discussed in most of the focus groups. Interestingly, some teachers questioned why gender attainments obtained in schools do not serve as an example when it comes to neutralizing the sexism and gender inequality messages offered by the media and society. Likewise, technology teachers proposed changes in school practices to close gender gaps in certain areas (i.e., boys’ appropriation of the playground, or the reproduction of gender roles in the classroom). Few parents acknowledged their unconscious reproduction of gender roles and stereotypes in raising their children.
Non-Cell-Autonomous Mechanisms in Radial Projection Neuron Migration in the Developing Cerebral Cortex

Concerted radial migration of newly born cortical projection neurons, from their birthplace to their final target lamina, is a key step in the assembly of the cerebral cortex. The cellular and molecular mechanisms regulating the specific sequential steps of radial neuronal migration in vivo are however still unclear, let alone the effects and interactions with the extracellular environment. In any in vivo context, cells will always be exposed to a complex extracellular environment consisting of (1) secreted factors acting as potential signaling cues, (2) the extracellular matrix, and (3) other cells providing cell–cell interaction through receptors and/or direct physical stimuli. Most studies so far have described and focused mainly on intrinsic cell-autonomous gene functions in neuronal migration but there is accumulating evidence that non-cell-autonomous-, local-, systemic-, and/or whole tissue-wide effects substantially contribute to the regulation of radial neuronal migration. These non-cell-autonomous effects may differentially affect cortical neuron migration in distinct cellular environments. However, the cellular and molecular natures of such non-cell-autonomous mechanisms are mostly unknown. Furthermore, physical forces due to collective migration and/or community effects (i.e., interactions with surrounding cells) may play important roles in neocortical projection neuron migration. In this concise review, we first outline distinct models of non-cell-autonomous interactions of cortical projection neurons along their radial migration trajectory during development. We then summarize experimental assays and platforms that can be utilized to visualize and potentially probe non-cell-autonomous mechanisms. Lastly, we define key questions to address in the future.
High-Resolution Imaging of Tumor Spheroids and Organoids Enabled by Expansion Microscopy

Three-dimensional cell cultures are able to better mimic the physiology and cellular environments found in tissues in vivo compared to cells grown in two dimensions. In order to study the structure and function of cells in 3-D cultures, light microscopy is frequently used. The preparation of 3-D cell cultures for light microscopy is often destructive, including physical sectioning of the samples, which can result in the loss of 3-D information. In order to probe the structure of 3-D cell cultures at high resolution, we have explored the use of expansion microscopy and compared it to a simple immersion clearing protocol. We provide a practical method for the study of spheroids, organoids and tumor-infiltrating immune cells at high resolution without the loss of spatial organization. Expanded samples are highly transparent, enabling high-resolution imaging over extended volumes by significantly reducing light scatter and absorption. In addition, the hydrogel-like nature of expanded samples enables homogenous antibody labeling of dense epitopes throughout the sample volume. The improved labeling and image quality achieved in expanded samples revealed details in the center of the organoid which were previously only observable following serial sectioning. In comparison to chemically cleared spheroids, the improved signal-to-background ratio of expanded samples greatly improved subsequent methods for image segmentation and analysis.
Formal Elements of Art Products Indicate Aspects of Mental Health

Formal elements are often used in art therapy assessment. The assumption is that formal elements are observable aspects of the art product that allow reliable and valid assessment of clients’ mental health. Most of the existing art therapy assessment instruments are based on clinical expertise. Therefore, it is not clear to what degree these instruments are restricted to formal elements. Other aspects might also be included, such as clinical expertise of the therapist. This raises the question of whether and how formal elements as observable aspects of the art product are related to clients’ mental health. To answer this question, four studies are presented that look at: (1) a meta-theoretical description of formal elements; (2) operationalization of these formal elements so they can be analyzed reliably in clients’ art products; (3) establishment of reliable and clinically relevant formal elements; (4) the relationship between formal elements and adult clients’ mental health. Results show that the combination of the formal elements “movement,” “dynamic,” and “contour” are significantly interrelated and related to clients’ mental health, i.e., psychopathology, psychological flexibility, experiential avoidance, and adaptability. These findings give insight in the diagnostic value of art products and how they may add to clients’ verbal expression and indicate their potential to benefit from therapy.
Two Rationally Identified Novel Glitazones Reversed the Behavioral Dysfunctions and Exhibited Neuroprotection Through Ameliorating Brain Cytokines and Oxy-Radicals in ICV-LPS Neuroinflammatory Rat Model

The present study has planned to evaluate the neuroprotective activity of two novel glitazones in a neuroinflammatory rat model. Two novel glitazones were selected from an in-house virtual library of glitazones based on their docking scores against peroxisome proliferator-activated receptor-gamma (PPAR-γ) protein and other parameters studied in in silico computational studies. Initially, an acute oral toxicity study was carried out for glitazones in rats to assess the toxicity profile and to determine the therapeutic range for neuroprotective evaluation. Prior to induction of neuroinflammation, the treatments with glitazones (G1 and G2) and standard pioglitazone were made for four consecutive days to respective groups. On the fifth day, the neuroinflammation was induced by intracerebroventricular (ICV) administration of lipopolysaccharides (LPS) (2 μg/μl) using stereotaxic apparatus. After 7 days, the rats were subjected to behavioral assessment followed by neurobiochemical evaluation and histopathological studies. The pre-treatment with glitazones at two dose levels (15 and 30 mg/kg) has significantly reversed behavioral dysfunctions. Glitazones have shown significant reduction in the levels of LPO, NO, TNF-α, and IL-1β and also increased the levels of antioxidant enzymes such as SOD, CAT, and GSH in the brain of LPS-administered rats. The neuroprotection exhibited by two novel glitazones is comparable with standard pioglitazone. The PPAR-γ-dependent amelioration of cytokines and oxy-radicals released by novel glitazones during neuroinflammatory conditions may be attributed to the reversal of behavioral dysfunctions through preventing the degeneration of neurons in major regions of the brain.
Extending Crop Type Reference Data Using a Phenology-Based Approach

The combination of high spatial resolution and multi-date satellite imagery offers new opportunities for mapping and monitoring crop types of different agricultural field sizes. However, mapping of crop types at high spatial resolution requires high-quality crop type reference data typically collected from the ground-based surveys to create the maps and/or to assess the map accuracy. The availability of sufficient crop type reference data is limited over large geographic regions because of the time, effort, cost, and accessibility in different parts of the world. To generate large area crop type maps, any existing, but limited reference data must be spatially extended to other regions using appropriate and available non-ground-based sources. There is the potential to classify High Resolution Imagery (HRI) using a phenology-based approach as demonstrated in this paper to generate additional reference data within similar agriculture ecological zones (AEZs) based on the crop characteristics, their types, and their growing season. Therefore, the objective of this study was to evaluate if existing, limited crop type reference data could be extended using this approach. Multi-date, high spatial resolution satellite images were used to spatially extend the limited crop type reference data from one region [called the training region (TR)] to another region [called the test region (TE)] within the same AEZ using a phenology-based Decision Tree (DT) classifier for three different field sizes. The results demonstrate that this phenology-based classification approach can efficiently and effectively extend the limited crop type reference data to other regions in same AEZ for different field sizes.
Restricted constrictors: Space use and habitat selection of native Burmese pythons in Northeast Thailand

Animal movement and resource use are tightly linked. Investigating these links to understand how animals utilize space and select habitats is especially relevant in areas that have been affected by habitat fragmentation and agricultural conversion. We set out to explore the space use and habitat selection of Burmese pythons (Python bivittatus) in a patchy land use matrix dominated by agricultural crops and human settlements. We used radio telemetry to record daily locations of seven Burmese pythons over the course of our study period of approximately 22 months. We created dynamic Brownian Bridge Movement Models (dBBMMs) for all individuals, using occurrence distributions to estimate extent of movements and motion variance to reveal temporal patterns. Then we used integrated step selection functions to determine whether individual movements were associated with particular landscape features (aquatic agriculture, forest, roads, settlements, terrestrial agriculture, water), and whether there were consistent associations at the population level. Our dBBMM estimates suggested that Burmese pythons made use of small areas (98.97 ± 35.42 ha), with low mean individual motion variance characterized by infrequent moves and long periods at a single location. At both the individual and population level, Burmese pythons in the agricultural matrix were associated with aquatic environments. Only one individual showed a strong avoidance for human settlements which is troublesome from a human-wildlife conflict angle, especially as Burmese pythons have been observed entering human settlements and consuming livestock in our study site. Our study is one of the first to contribute to the knowledge of Burmese python ecology in their native range as the majority of studies have focused on invasive populations.
Common genetic variation in humans impacts in vitro susceptibility to SARS-CoV-2 infection

The host response to SARS-CoV-2, the etiologic agent of the COVID-19 pandemic, demonstrates significant inter-individual variability. In addition to showing more disease in males, the elderly, and individuals with underlying co-morbidities, SARS-CoV-2 can seemingly render healthy individuals with profound clinical complications. We hypothesize that, in addition to viral load and host antibody repertoire, host genetic variants also impact vulnerability to infection. Here we apply human induced pluripotent stem cell (hiPSC)-based models and CRISPR-engineering to explore the host genetics of SARS-CoV-2. We demonstrate that a single nucleotide polymorphism (rs4702), common in the population at large, and located in the 3’UTR of the protease FURIN, impacts alveolar and neuron infection by SARS-CoV-2 in vitro. Thus, we provide a proof-of-principle finding that common genetic variation can impact viral infection, and thus contribute to clinical heterogeneity in SARS-CoV-2. Ongoing genetic studies will help to better identify high-risk individuals, predict clinical complications, and facilitate the discovery of drugs that might treat disease.
Routes to roots: direct evidence of water transport by arbuscular mycorrhizal fungi to host plants

Arbuscular mycorrhizal fungi (AMF) form symbiotic associations with 80% of surveyed land plant species and are well-recognized for accessing and transferring nutrients to plants1. Yet AMF also perform other essential functions, notably improving plant-water relations2. Some research attributes the role of AMF in plant-water relations solely to enhancing plant nutrition and osmoregulation for plants partnered with AMF3,4,5, while indirect evidence suggests AMF may transport water to plants1,6,7. Here, we used isotopically-labeled water and a fluorescent dye to directly track and quantify water transport by AMF to plants in a greenhouse experiment. We specifically assessed whether AMF can access water in soil unavailable to plants and transport it across an air gap to host plants. Plants grown with AMF that had access to a physically separated 18O-labeled water source transpired twice as much, and this transpired water contained three times as much label compared to plants with AMF with no access to the separated labeled water source. We estimated that water transported by AMF could explain 46.2% of the water transpired. In addition, a fluorescent dye indicated that water was transported via an extracytoplasmic hyphal pathway.