Miracle-dz/UniFAR-FTUs huggingface dataset:
A C6/C5 co‐fermenting Saccharomyces cerevisiae strain with the alleviation of antagonism between xylose utilization and robustness

During second‐generation bioethanol production from lignocellulosic biomass, the desired traits for fermenting microorganisms, such as Saccharomyces cerevisiae, are high xylose utilization and high robustness to inhibitors in lignocellulosic hydrolysates. However, as observed previously, these two traits easily showed the antagonism, one rising and the other falling, in the C6/C5 co‐fermenting S. cerevisiae strain. In this study, LF1 obtained in our previous study is an engineered budding yeast strain with a superior co‐fermentation capacity of glucose and xylose, and was then mutated by atmospheric and room temperature plasma (ARTP) mutagenesis to improve its robustness. The ARTP‐treated cells were grown in 50% (v/v) leachate from lignocellulose pretreatment with high inhibitors content for adaptive evolution. After 30 days, the generated mutant LF1‐6 showed significantly enhanced tolerance, with a six‐fold increase in cell density in the above leachate. Unfortunately, its xylose utilization dropped markedly, indicating the recurrence of the negative correlation between xylose utilization and robustness. To alleviate this antagonism, LF1‐6 cells were iteratively mutated with ARTP mutagenesis and then anaerobically grown using xylose as the sole carbon source, and xylose utilization was restored in the resulting strain 6M‐15. 6M‐15 also exhibited increased co‐fermentation performance of xylose and glucose with the highest ethanol productivity reported to date (0.525 g g−1 h−1) in high‐level mixed sugars (80 g L−1 glucose and 40 g L−1 xylose) with no inhibitors. Meanwhile, its fermentation time was shortened by 8 h compared to that of LF1. During the fermentation of non‐detoxified lignocellulosic hydrolysate with high inhibitor concentrations at pH ~3.5, 6M‐15 can efficiently convert glucose and xylose with an ethanol yield of 0.43 g g−1. 6M‐15 is also regarded as a potential chassis cell for further design of a customized strain suitable for production of second‐generation bioethanol or other high value‐added products from lignocellulosic biomass.
Beyond TNBC: Repositioning of Clofazimine Against a Broad Range of Wnt-Dependent Cancers

Wnt signaling plays key roles in oncogenic transformation and progression in a number of cancer types, including tumors in the breast, colon, ovaries, liver, and other tissues. Despite this importance, no therapy targeting the Wnt pathway currently exists. We have previously shown that the anti-mycobacterium drug clofazimine is a specific inhibitor of Wnt signaling and cell proliferation in triple-negative breast cancer (TNBC). Here, we expand the applicability of clofazimine to a set of other Wnt-dependent cancers. Using a panel of cell lines from hepatocellular carcinoma, glioblastoma, as well as colorectal and ovarian cancer, we show that the efficacy of clofazimine against a given cancer type correlates with the basal levels of Wnt pathway activation and the ability of the drug to inhibit Wnt signaling in it, being further influenced by the cancer mutational spectrum. Our study establishes the basis for patient stratification in the future clinical trials of clofazimine and may ultimately contribute to the establishment of the Wnt pathway-targeted therapy against a diverse set of cancer types relying on the oncogenic Wnt signaling.
Electrochemical reduction of carbon dioxide on copper electrodes

Analysis of the product selectivity and potential of Cu cathodes during galvanostatic CO2 reduction is reported. Initially, it is found that clean Cu cathodes are more selective for hydrogen evolution, but as the Cu is slowly poisoned by CO2 reduction products (most likely carbon) the cathode potential becomes more negative, which in turn drives the formation of CH4, C2H4 and CO. As the accumulation of surface poisons continues, the selectivity towards CH4 and C2H4 begins to decrease due to the loss in neighbouring reaction sites that support the hydrogenation of COads by Hads. In an attempt to avoid these changes in product selectivity, periodic cyclic voltammetry and potentiostatic steps were used throughout extended periods of galvanostatic CO2 reduction. Contrary to previous literature, it is demonstrated that temporarily interrupting galvanostatic CO2 reduction with short periods at potentials between −0.5 and −0.1 V vs Ag|AgCl suppresses the formation of CH4, CO and C2H4. It is proposed that this is due to the partial removal or oxidation of adsorbed CO2 reduction intermediates and that this “clean” cathode surface is more active for the hydrogen evolution reaction. However, when brief potentiostatic steps (84 and 200 s) were conducted at more negative potentials (−1.2 V vs Ag|AgCl), the CO2 reduction selectivity could be switched from CH4 to CO, and maintained for at least 2 hours. This change in selectivity is proposed to be caused by an increase in the surface coverage of COads (at the expense of Hads) during the brief −1.2 V steps, which then enables the Cu cathode to switch between multiple steady-state surface coverages when the cathodic current is re-applied.
Disrupted Amygdala Connectivity Is Associated With Elevated Anxiety in Sensorineural Hearing Loss

Background and Purpose: Hearing loss is associated with rising risks of emotional impairments, suggesting emotional processing networks might be involved in the neural plasticity after hearing loss. This study was conducted to explore how functional connectivity of the amygdala reconfigures in the auditory deprived brain and better understand the neural mechanisms underlying hearing loss-related emotional disturbances. Methods: In total, 38 chronic sensorineural hearing loss (SNHL) patients and 37 healthy controls were recruited for multimodal magnetic resonance imaging scanning and neuropsychological assessments. Voxel-wise functional connectivity (FC) maps of both the left and right amygdala were conducted and compared between the SNHL patients and healthy controls. The uncinate fasciculus (UF), an association fiber pathway, was reconstructed in both groups. The track number, mean track length, fractional anisotropy (FA) and mean diffusion values of the left and right UF were further quantified, respectively. Besides, Pearson's correlation analyses were conducted to investigate the relationship between the functional/structural abnormalities and the negative emotional states in SNHL patients. Results: The SNHL patients presented higher depressive and anxious levels compared to the healthy controls. Decreased FCs were detected between the amygdala and the auditory cortex, striatum, multimodal processing areas, and frontoparietal control areas in the SNHL patients. The amygdala was found to be structurally connected with several FC decreased regions through the UF. Moreover, the hypo-synchronization and the white matter impairment were both found to be associated with patients' elevated anxious status. Conclusions: These functional and structural findings depicted the reconfiguration of the amygdala in SNHL, which provided a new perspective toward the functional circuit mechanisms targeting the emotional impairments related to hearing loss.
Autism Screening in Early Childhood: Discriminating Autism From Other Developmental Concerns

Early identification of autism, followed by appropriate intervention, has the potential to improve outcomes for autistic individuals. Numerous screening instruments have been developed for children under 3 years of age. Level 1 screeners are used in large-scale screening to detect at-risk children in the general population; Level 2 screeners are concerned with distinguishing children with signs of autism from those with other developmental problems. The focus here is evaluation of Level 2 screeners. However, given the contributions of Level 1 screeners and the necessity to understand how they might interface with Level 2 screeners, we briefly review Level 1 screeners and consider instrument characteristics and system variables that may constrain their effectiveness. The examination of Level 2 screeners focuses on five instruments associated with published evaluations in peer-reviewed journals. Key criteria encompass the traditional indices of test integrity such as test reliability (inter-rater, test-retest) and construct validity, including concurrent and predictive validity, sensitivity (SE), and specificity (SP). These evaluations reveal limitations, including inadequate sample sizes, reliability issues, and limited involvement of independent researchers. Also lacking are comparative test evaluations under standardized conditions, hindering interpretation of differences in discriminative performance across instruments. Practical considerations constraining the use of such instruments—such as the requirements for training in test administration and test administration time—are canvassed. Published Level 2 screener short forms are reviewed and, as a consequence of that evaluation, future directions for assessing the discriminative capacity of items and measures are suggested. Suggested priorities for future research include targeting large and diverse samples to permit robust appraisals of Level 2 items and scales across the 12–36 month age range, a greater focus on precise operationalization of items and response coding to enhance reliability, ongoing exploration of potentially discriminating items at the younger end of the targeted age range, and trying to unravel the complexities of developmental trajectories in autistic infants. Finally, we emphasize the importance of understanding how screening efficacy is dependent on clinicians' and researchers' ability not only to develop screening tests but also to negotiate the complex organizational systems within which screening procedures must be implemented.
Information Theory Can Help Quantify the Potential of New Phenotypes to Originate as Exaptations

Exaptations are adaptive traits that do not originate de novo but from other adaptive traits. They include complex macroscopic traits, such as the middle ear bones of mammals, which originated from reptile jaw bones, but also molecular traits, such as new binding sites of transcriptional regulators. What determines whether a trait originates de novo or as an exaptation is unknown. I here use simple information theoretic concepts to quantify a molecular phenotype’s potential to give rise to new phenotypes. These quantities rely on the amount of genetic information needed to encode a phenotype. I use these quantities to estimate the propensity of new transcription factor binding phenotypes to emerge de novo or exaptively, and do so for 187 mouse transcription factors. I also use them to quantify whether an organism’s viability in one of 10 different chemical environment is likely to arise exaptively. I show that informationally expensive traits are more likely to originate exaptively. Exaptive evolution is only sometimes favored for new transcription factor binding, but it is always favored for the informationally complex metabolic phenotypes I consider. As our ability to genotype evolving populations increases, so will our ability to understand how phenotypes of ever-increasing informational complexity originate in evolution.
Virtual Reality Analgesia for Children With Large Severe Burn Wounds During Burn Wound Debridement

The objective of this study was to compare the effect of adjunctive virtual reality vs. standard analgesic pain medications during burn wound cleaning/debridement. Participants were predominantly Hispanic children aged 6–17 years of age, with large severe burn injuries (TBSA = 44%) reporting moderate or higher baseline pain during burn wound care. Using a randomized between-groups design, participants were randomly assigned to one of two groups, (a) the Control Group = pain medications only or (b) the VR Group = pain medications + virtual reality. A total of 50 children (88% Hispanic) with large severe burns (mean TBSA > 10%) received severe burn wound cleaning sessions. For the primary outcome measure of worst pain (intensity) on Study Day 1, using a between groups ANOVA, burn injured children in the group that received virtual reality during wound care showed significantly less pain intensity than the No VR control group, [mean worst pain ratings for the No VR group = 7.46 (SD = 2.93) vs. 5.54 (SD = 3.56), F(1,48) = 4.29, < 0.05, MSE = 46.00]. Similarly, one of the secondary pain measures, “lowest pain during wound care” was significantly lower in the VR group, No VR = 4.29 (SD = 3.75) vs. 1.68 (2.04) for the VR group, F(1,47) = 9.29, <0.005, MSE = 83.52 for Study Day 1. The other secondary pain measures showed the predicted pattern on Study Day 1, but were non-significant. Regarding whether VR reduced pain beyond Study Day 1, absolute change in pain intensity (analgesia = baseline pain minus the mean of the worst pain scores on Study days 1–10) was significantly greater for the VR group, F(1,48) = 4.88, p < 0.05, MSE = 34.26, partial eta squared = 0.09, but contrary to predictions, absolute change scores were non-significant for all secondary measures.
Zoonotic Tick-Borne Pathogens in Temperate and Cold Regions of Europe—A Review on the Prevalence in Domestic Animals

Ticks transmit a variety of pathogens affecting both human and animal health. In temperate and cold regions of Europe (Western, Central, Eastern, and Northern Europe), the most relevant zoonotic tick-borne pathogens are tick-borne encephalitis virus (TBEV), Borrelia spp. and Anaplasma phagocytophilum. More rarely, Rickettsia spp. , Neoehrlichia mikurensis, and zoonotic Babesia spp. are identified as a cause of human disease. Domestic animals may also be clinically affected by these pathogens, and, furthermore, can be regarded as sentinel hosts for their occurrence in a certain area, or even play a role as reservoirs or amplifying hosts. For example, viraemic ruminants may transmit TBEV to humans via raw milk products. This review summarizes the role of domestic animals, including ruminants, horses, dogs, and cats, in the ecology of TBEV, Borrelia spp. , A. phagocytophilum, Rickettsia spp. , N. mikurensis, and zoonotic Babesia species. It gives an overview on the (sero-)prevalence of these infectious agents in domestic animals in temperate/cold regions of Europe, based on 148 individual prevalence studies. Meta-analyses of seroprevalence in asymptomatic animals estimated an overall seroprevalence of 2.7% for TBEV, 12.9% for Borrelia burgdorferi sensu lato (s.l.), 16.2% for A. phagocytophilum and 7.4% for Babesia divergens, with a high level of heterogeneity. Subgroup analyses with regard to animal species, diagnostic test, geographical region and decade of sampling were mostly non-significant, with the exception of significantly lower B. burgdorferi s.l. seroprevalences in dogs than in horses and cattle. More surveillance studies employing highly sensitive and specific test methods and including hitherto non-investigated regions are needed to determine if and how global changes in terms of climate, land use, agricultural practices and human behavior impact the frequency of zoonotic tick-borne pathogens in domestic animals.
Assessed by Machines: Development of a TAM-Based Tool to Measure AI-based Assessment Acceptance Among Students

In recent years, the use of more and more technology in education has been a trend. The shift of traditional learning procedures into more online and tech-ish approaches has contributed to a context that can favor integrating Artificial-Intelligence-based or algorithm-based assessment of learning. Even more, with the current acceleration because of the COVID-19 pandemic, more and more learning processes are becoming online and are incorporating technologies related to automatize assessment or help instructors in the process. While we are in an initial stage of that integration, it is the moment to reflect on the students' perceptions of being assessed by a non-conscious software entity like a machine learning model or any other artificial intelligence application. As a result of the paper, we present a TAM-based model and a ready-to-use instrument based on five aspects concerning understanding technology adoption like the AI-based assessment on education. These aspects are perceived usefulness, perceived ease of use, attitude towards use, behavioral intention, and actual use. The paper's outcomes can be relevant to the research community since there is a lack of this kind of proposal in the literature.
A Hematological-Related Prognostic Scoring System for Patients With Newly Diagnosed Glioblastoma

Background Glioblastoma is the most common primary malignant brain tumor. Recent studies have shown that hematological biomarkers have become a powerful tool for predicting the prognosis of patients with cancer. However, most studies have only investigated the prognostic value of unilateral hematological markers. Therefore, we aimed to establish a comprehensive prognostic scoring system containing hematological markers to improve the prognostic prediction in patients with glioblastoma. Patients and Methods A total of 326 patients with glioblastoma were randomly divided into a training set and external validation set to develop and validate a hematological-related prognostic scoring system (HRPSS). The least absolute shrinkage and selection operator Cox proportional hazards regression analysis was used to determine the optimal covariates that constructed the scoring system. Furthermore, a quantitative survival-predicting nomogram was constructed based on the hematological risk score (HRS) derived from the HRPSS. The results of the nomogram were validated using bootstrap resampling and the external validation set. Finally, we further explored the relationship between the HRS and clinical prognostic factors. Results The optimal cutoff value for the HRS was 0.839. The patients were successfully classified into different prognostic groups based on their HRSs (P < 0.001). The areas under the curve (AUCs) of the HRS were 0.67, 0.73, and 0.78 at 0.5, 1, and 2 years, respectively. Additionally, the 0.5-, 1-y, and 2-y AUCs of the HRS were 0.51, 0.70, and 0.79, respectively, which validated the robust prognostic performance of the HRS in the external validation set. Based on both univariate and multivariate analyses, the HRS possessed a strong ability to predict overall survival in both the training set and validation set. The nomogram based on the HRS displayed good discrimination with a C-index of 0.81 and good calibration. In the validation cohort, a high C-index value of 0.82 could still be achieved. In all the data, the HRS showed specific correlations with age, first presenting symptoms, isocitrate dehydrogenase mutation status and tumor location, and successfully stratified them into different risk subgroups. Conclusions The HRPSS is a powerful tool for accurate prognostic prediction in patients with newly diagnosed glioblastoma.
Insights Into Plant Surgery: An Overview of the Multiple Grafting Techniques for Arabidopsis thaliana

Plant grafting, the ancient practice of cutting and joining different plants, is gaining popularity as an elegant way to generate chimeras that combine desirable traits. Grafting was originally developed in woody species, but the technique has evolved over the past century to now encompass a large number of herbaceous species. The use of plant grafting in science is accelerating in part due to the innovative techniques developed for the model plant Arabidopsis thaliana. Here, we review these developments and discuss the advantages and limitations associated with grafting various Arabidopsis tissues at diverse developmental stages.
Phosphatase and Tensin Homolog Mutation in Immune Cell Infiltration and Clinicopathological Features of Low-Grade Gliomas

The mutation of phosphatase and tensin homolog (PTEN) genes frequently occur in low-grade gliomas (LGGs) and are deeply associated with a poor prognosis and survival rate. In order to identify the crucial signaling pathways and genes associated with the PTEN mutation, we performed bioinformatics analysis on the RNA sequencing results, which were obtained from The Cancer Genome Atlas database. A total of 352 genes were identified as differentially expressed genes (DEGs). The gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis suggested that the DEGs were significantly enriched in categories associated with cell division and multiple metabolic progressions. The histological stage was significantly associated with PTEN expression levels. In addition, the PTEN mutation was associated with an abundance of B cells, neutrophils, macrophages, dendritic cells, and CD8+ T cells during tumor infiltration. The results showed that patients with LGGs harboring the PTEN mutation had a poor prognosis and more serious immune cell infiltration occurred depending on the mRNA expression level. These results demonstrated that multiple genes and signaling pathways play a key role in LGG from low grade to high grade, and are associated with PTEN mutations. In this study, we outlined an approach to assess the influence of PTEN mutations on prognosis, overall survival, and messenger RNA (mRNA) expression. Our results provided alternative strategies for the personalized treatment of patients with LGGs harboring the PTEN mutation.
Phosphoglucoisomerase Is an Important Regulatory Enzyme in Partitioning Carbon out of the Calvin-Benson Cycle

Phosphoglucoisomerase (PGI) isomerizes fructose 6-phosphate (F6P) and glucose 6-phosphate (G6P) in starch and sucrose biosynthesis. Both plastidic and cytosolic isoforms are found in plant leaves. Using recombinant enzymes and isolated chloroplasts, we have characterized the plastidic and cytosolic isoforms of PGI. We have found that the Arabidopsis plastidic PGI Km for G6P is three-fold greater compared to that for F6P and that erythrose 4-phosphate is a key regulator of PGI activity. Additionally, the Km of spinach plastidic PGI can be dynamically regulated in the dark compared to the light and increases by 200% in the dark. We also found that targeting Arabidopsis cytosolic PGI into plastids of Nicotiana tabacum disrupts starch accumulation and degradation. Our results, in combination with the observation that plastidic PGI is not in equilibrium, indicates that PGI is an important regulatory enzyme that restricts flow and acts as a one-way valve preventing backflow of G6P into the Calvin-Benson cycle. We propose the PGI may be manipulated to improve flow of carbon to desired targets of biotechnology.