Miracle-dz/UniFAR-FTUs huggingface dataset:
A memory element imposes epigenetic behavior on intrinsically labile RNAi-induced heterochromatin spread

The heterochromatin spreading reaction is a central contributor to the formation of gene-repressive structures, which are re-established with high fidelity following replication. The high fidelity of this process is not obviously encoded in the primary spreading reaction. To resolve origins of stable inheritance of repression, we probed the intrinsic fidelity of spreading events in fission yeast using a system that quantitatively describes the spreading reaction in live single cells. We show that spreading from RNAi-nucleated elements is stochastic, multimodal, and fluctuates dynamically across time. In contrast, a second form of spreading, nucleated by the cis-acting element REIII, is deterministic, has high memory capacity and acts as the source of locus fidelity. REIII enables fidelity in part by endowing the locus with resistance to perturbations. Together, our results suggest that epigenetic capacity may not be intrinsically encoded in the spreading reaction, but rather requires collaboration with specialized memory elements.
Bioavailability and tissue distribution of dietary phytoestrogens in rats

The fate of isoflavones in rats after oral and intravenous injection (IV) of soy was investigated. A liquid chromatography-mass spectrometry method to determine isoflavones in rat plasma was developed with a short run time of 16 minutes. Serum samples from a multigeneration reproductive study conducted to examine the effects of diets containing alcohol-washed soy protein supplemented with increasing amounts of NovasoyTM, in male and female Sprague Dawley (SD) rats, were analyzed for isoflavones. Gender and age differences were observed and warranted additional investigations into the effects of gender, source of isoflavones and the role of glycosidation of isoflavones on the biovailability and pharmacokinetics of soy isoflavones. The bioavailability of isoflavones from NovasoyTM, a mixture of synthetic glucosides, and a mixture of synthetic aglyconees was examined in female and male (3-month-old) SD rats, and male Fisher 344 (20-month-old) rats. For the synthetic aglycone and synthetic glucoside sources, bioavailability was independent of gender. However, for NovasoyTM, a gender difference was observed for daidzein, with higher plasma concentrations found in male rats. Bioavailability values for daidzein, genistein and glycitein were significantly (p < 0.05) higher (up to sevenfold) from NovasoyTM and the synthetic glucosides compared with the synthetic aglyconees. Therefore, the source of isoflavones had significant effects on isoflavone bioavailability.
Galectin-13, a different prototype galectin, does not bind beta-galacto-sides and forms dimers via intermolecular disulfide bridges between Cys-136 and Cys-138

During pregnancy, placental protein-13 (galectin-13) is highly expressed in the placenta and fetal tissue, and less so in maternal serum that is related to pre-eclampsia. To understand galectin-13 function at the molecular level, we solved its crystal structure and discovered that its dimer is stabilized by two disulfide bridges between Cys136 and Cys138 and six hydrogen bonds involving Val135, Val137, and Gln139. Native PAGE and gel filtration demonstrate that this is not a crystallization artifact because dimers also form in solution. Our biochemical studies indicate that galectin-13 ligand binding specificity is different from that of other galectins in that it does not bind β-galactosides. This is partly explained by the presence of Arg53 rather than His53 at the bottom of the carbohydrate binding site in a position that is crucial for interactions with β-galactosides. Mutating Arg53 to histidine does not re-establish normal β-galactoside binding, but rather traps cryoprotectant glycerol molecules within the ligand binding site in crystals of the R53H mutant. Moreover, unlike most other galectins, we also found that GFP-tagged galectin-13 is localized within the nucleus of HeLa and 293 T cells. Overall, galectin-13 appears to be a new type of prototype galectin with distinct properties.
Prevalence of Antibiotic-Resistant Pulmonary Tuberculosis in Bangladesh: A Systematic Review and Meta-Analysis

Resistance to anti-tuberculosis (anti-TB) antibiotics is a major public health concern for many high-TB burden countries in Asia, including Bangladesh. Therefore, to represent the overall drug-resistance pattern against TB in Bangladesh, a systematic review and meta-analysis was conducted. Databases such as PubMed, Scopus, and Google Scholar were searched to identify studies related to antibiotic-resistant TB. A total of 24 studies covering 13,336 patients with TB were secured and included. The random-effects model was used to calculate the summary estimates. The pooled prevalence of any, mono, multi, poly, and extensive anti-TB antibiotic-resistances were 45.3% [95% CI: 33.5–57.1], 14.3% [95% CI: 11.4–17.2], 22.2% [95% CI: 18.8–25.7], 7.7% [95% CI: 5.6–9.7], and 0.3% [95% CI: 0.0–1.0], respectively. Among any first and second-line anti-TB drugs, isoniazid (35.0%) and cycloserine (44.6%) resistances were the highest, followed by ethambutol (16.2%) and gatifloxacin (0.2%). Any, multi, and poly drug-resistances were higher in retreatment cases compared to the newly diagnosed cases, although mono drug-resistance tended to be higher in newly diagnosed cases (15.7%) than that in retreatment cases (12.5%). The majority (82.6%) of the included studies were of high quality, with most not exhibiting publication bias. Sensitivity analyses confirmed that all outcomes are robust and reliable. It is concluded that resistance to anti-TB drugs in Bangladesh is rampant and fast growing. Therefore, the implementation of a nationwide surveillance system to detect suspected and drug-resistant TB cases, as well as to ensure a more encompassing treatment management by national TB control program, is highly recommended.
Adaptive Neural Digital Control of Hysteretic Systems With Implicit Inverse Compensator and Its Application on Magnetostrictive Actuator

Hysteresis is a complex nonlinear effect in smart materials-based actuators, which degrades the positioning performance of the actuator, especially when the hysteresis shows asymmetric characteristics. In order to mitigate the asymmetric hysteresis effect, an adaptive neural digital dynamic surface control (DSC) scheme with the implicit inverse compensator is developed in this article. The implicit inverse compensator for the purpose of compensating for the hysteresis effect is applied to find the compensation signal by searching the optimal control laws from the hysteresis output, which avoids the construction of the inverse hysteresis model. The adaptive neural digital controller is achieved by using a discrete-time neural network controller to realize the discretization of time and quantizing the control signal to realize the discretization of the amplitude. The adaptive neural digital controller ensures the semiglobally uniformly ultimately bounded (SUUB) of all signals in the closed-loop control system. The effectiveness of the proposed approach is validated via the magnetostrictive-actuated system.
The Landscape of Glycogen Synthase Kinase-3 Beta Genomic Alterations in Cancer

Glycogen synthase kinase-3β (GSK-3β), a serine/threonine kinase, has been implicated in the pathogenesis of many cancers, with involvement in cell-cycle regulation, apoptosis, and immune response. Small-molecule GSK-3β inhibitors are currently undergoing clinical investigation. Tumor sequencing has revealed genomic alterations in GSK-3β, yet an assessment of the genomic landscape in malignancies is lacking. This study assessed >100,000 tumors from two databases to analyze GSK-3β alterations. GSK-3β expression and immune cell infiltrate data were analyzed across cancer types, and programmed death-ligand 1 (PD-L1) expression was compared between GSK-3β–mutated and wild-type tumors. GSK-3β was mutated at a rate of 1%. The majority of mutated residues were in the kinase domain, with frequent mutations occurring in a GSK-3β substrate binding pocket. Uterine endometrioid carcinoma was the most commonly mutated (4%) tumor, and copy-number variations were most commonly observed in squamous histologies. Significant differences across cancer types for GSK-3β–mutated tumors were observed for B cells (P = 0.018), monocytes (P = 0.002), dendritic cells (P = 0.005), neutrophils (P = 0.0003), and endothelial cells (P = 0.014). GSK-3β mRNA expression was highest in melanoma. The frequency of PD-L1 expression was higher among GSK-3β–mutated tumors compared with wild type in colorectal cancer (P = 0.03), endometrial cancer (P = 0.05), melanoma (P = 0.02), ovarian carcinoma (P = 0.0001), and uterine sarcoma (P = 0.002). Overall, GSK-3β molecular alterations were detected in approximately 1% of solid tumors, tumors with GSK-3β mutations displayed a microenvironment with increased infiltration of B cells, and GSK-3β mutations were associated with increased PD-L1 expression in selected histologies. These results advance the understanding of GSK-3β complex signaling network interfacing with key pathways involved in carcinogenesis and immune response.
Serum kynurenine levels are a novel biomarker to predict the prognosis of patients with hepatocellular carcinoma

Background We examined serum kynurenine levels in patients with chronic hepatitis C virus infection, and the relationship between serum kynurenine and prognosis in patients with hepatocellular carcinoma (HCC) and chronic hepatitis C. Methods We retrospectively analyzed 604 patients with HCC diagnosed between January 1999 and December 2015, and 288 patients without HCC who were seen at the National Hospital Organization Nagasaki Medical Center between October 2014 and November 2017. The association between serum kynurenine and prognosis was evaluated using the Cox’s proportional hazards regression analysis. Results Patients with HCC had significantly higher values of serum kynurenine than patients without HCC (median: 557.1 vs. 464.2 ng/mL, p<0.001). Five-year survival rates of HCC patients with serum kynurenine ≥900 (n = 65), 600–899 (n = 194), and <600 ng/mL (n = 345) were 30.6%, 47.4%, and 61.4%, respectively (p = 0.001, log-rank test). Multivariate analysis identified serum kynurenine as an independent predictor for prognosis of HCC patients. The hazard ratio of serum kynurenine ≥900, and 600–899 compared with serum kynurenine <600 ng/mL were 1.91 (p<0.001) and 1.37 (p = 0.015), respectively. Conclusions A high level of serum kynurenine correlated with poor prognosis of HCC. Serum kynurenine levels may be a novel biomarker to predict the prognosis of patients with HCC. The development of drugs that inhibit kynurenine production is expected to help improve the prognosis of patients with HCC.
Unconsciously Implanted Visuoauditory Memory in the Presence of Cholecystokinin Retrieved in Behavioral Contexts

We investigated whether visuoauditory association can be artificially implanted in rodents and then retrieved in a behaviorally relevant context. Rats were trained to approach the left or right hole of a behavioral apparatus to retrieve a reward depending on the side of electrical stimulation of the auditory cortex (EAC) they received and mice were fear-conditioned to EAC. Next, an irrelevant visual stimulus (VS) was repeatedly paired with EAC in the presence of cholecystokinin (CCK) or with activation of terminals of entorhinal CCK neurons in the auditory cortex. In subsequent behavioral testing with VS, rats approached the hole associated with reward availability and mice showed a freezing response to the VS. A CCK antagonist blocked the establishment of visuoauditory association, whereas a CCK agonist rescued the deficit of association. Our findings provide a scientific foundation for “memory implantation” and indicate that CCK is the switching chemical for formation of visuoauditory association.
Breeding Wheat for Resistance to Bacterial Leaf Streak Caused by Xanthomonas Campestris Pv. Translucens.

Bacterial leaf streak or black chaff caused by Xanthomonas campestris pv. translucens (Xct) can cause yield loss in wheat, especially in warm, high rainfall environments. Bactericidal chemicals have not been effective in controlling the disease, however, host resistance to leaf streak may be an effective control measure. Studies were conducted in the field and greenhouse to determine the relationship between the black chaff and leaf streak symptoms caused by Xct, to quantify yield loss, to calculate the heritability of leaf streak reaction and to evaluate germplasm for resistance to leaf streak. The results showed that ’Florida 304’ is very susceptible to leaf streak but is resistant to black chaff. All other cultivars tested are susceptible to both black chaff and leaf streak. In the field, average leaf streak severity on individual flag leaves ranged from 2% on ’Terral 101’ to 11% on Florida 304 at Feekes’ growth stage 10.5. 4. Yield losses estimated from these levels of leaf streak were 3% and 9% in Terral 101 and Florida 304, respectively. There was no relationship between black chaff severity and yield. Estimates of the narrow sense heritability of reaction to leaf streak range from 0.12 to 0.70 and averaged 0.31. Entry mean heritability increased to 0.47 with testing over three replications at one location. Lastly, 64 bread wheat lines were identified that were resistant to leaf streak in two years of field testing. These studies show that some cultivars may be resistant to black chaff but susceptible to leaf streak and that yield loss is related to leaf streak and not black chaff. Yield loss caused by leaf streak was estimated at 9% in Florida 304, the most susceptible cultivar tested. This is not a severe yield reduction, given
Network Structure of Affective Communication and Shared Emotion in Teams

This paper identifies the relative effectiveness of two mechanisms of emotional contagion on shared emotion in teams: explicit mechanism (active spreading of one’s emotion) and implicit mechanism (passive mimicry of others’ emotion). Using social network analysis, this paper analyzes affective communication networks involving or excluding a focal person in the process of emotional contagion by disaggregating team emotional contagion into individual acts of sending or receiving emotion-laden responses. Through an experiment with 38 pre-existing work teams, including undergraduate or MBA project teams and teams of student club or co-op officers, we found that the explicit emotional contagion mechanism was a more stable channel for emotional contagion than the implicit emotional contagion mechanism. Active participation in affective communication, measured by outdegree centrality in affective communication networks, was positively and significantly associated with emotional contagion with other members. In contrast, a team member’s passive observation of humor, measured by ego network density, led to emotional divergence when all other members engaged in humor communication. Our study sheds light on the micro-level process of emotional contagion. The individual-level process of emotional convergence varies with the relational pattern of affective networks, and emotion contagion in teams depends on the interplay of the active expresser and the passive spectator in affective networks.
Using body measurements to estimate body weight in gilts

The absence of a scale on pig farms has led to indirect body weight (BW) estimation using regression models based on body measurements. The objectives of the present study were to (1) develop prediction equations for weight estimation in gilts using body measurements (FF: flank-to-flank distance; L: length; HG: heart girth; BF2: ultrasound backfat measurement; LD: loin depth; and BCS: body condition score) and (2) validate the use of an existing prediction equation for BW in gilts (HG2 × L × 69.3 = HGLW), only used for finishing pigs. Data set A (derivation, Large White × Landrace) included 42 gilts at first insemination, 45 gilts at the end of first gestation, and 58 gilts at weaning. Data set B (validation, Large White × Landrace) comprised of 14 gilts at first insemination, 15 gilts at the end of first gestation, and 19 gilts at weaning. Models were developed for each physiological state but a better BW prediction was obtained from an overall model, including an adjustment for physiological state (S1 a.
DNA insecticides: the lethal potency of LdMNPV IAP-2 gene antisense oligonucleotides in pre-infected gypsy moth (Lymantria dispar L.) larvae

ABSTRACT In this study, we designed and analysed the insecticidal effectiveness of two short single-stranded DNA fragments from LdMNPV (Lymantria dispar multicapsid nuclear polyhedrosis virus) IAP-2 gene. Our results show that the ssDNA fragments from the antisense region is selectively lethal, and rapidly decreases the population of second instar gypsy moth (Lymantria dispar L.) larvae one day post-treatment (Control-H2O group vs oligoAn group, χ2 = 5; p < 0.05) when infected with LdMNPV as a trigger, before treatment through feeding with 75 pmol/µl of synthesized fragments from LdMNPV IAP-2 gene. Data analysis on larvae biomass did not show significant influence in all groups of the experiment when compared with the Control-H2O group. Relatively, our preliminary evaluation of biochemical parameters (total glucose and total protein concentrations) did not show significant response to the applied ssDNA oligonucleotides. Our conclusive remarks based on mortality data support the concept that antisense oligonucleotides from LdMNPV IAP-2 gene can act as an insecticide against pre-infected gypsy moth larvae.
Characterization of a Candida albicans Mutant Defective in All MAPKs Highlights the Major Role of Hog1 in the MAPK Signaling Network

The success of Candida albicans as a pathogen relies on its ability to adapt and proliferate in different environmental niches. Pathways regulated by mitogen-activated protein kinases (MAPKs) are involved in sensing environmental conditions and developing an accurate adaptive response. Given the frequent cooperative roles of these routes in cellular functions, we have generated mutants defective in all combinations of the four described MAPKs in C. albicans and characterized its phenotype regarding sensitiveness to specific drugs, morphogenesis and interaction with host immune cells. We demonstrate that all MAPKs are dispensable in this yeast as a mutant defective in Cek1, Cek2, Mkc1 and Hog1 is viable although highly sensitive to oxidative and osmotic stress, displaying a specific pattern of sensitivity to antifungals. By comparing its phenotype with single, double and triple combinations of MAPK-deletion mutants we were able to unveil a Cek1-independent mechanism for Hog1 resistance to Congo red, and confirm the predominant effect of Hog1 on oxidative and osmotic adaptation. The quadruple mutant produces filaments under non-inducing conditions, but is unable to develop chlamydospores. Furthermore, cek1 cek2 mkc1 hog1 cells switch to the opaque state at high frequency, which is blocked by the ectopic expression of HOG1 suggesting a role of this kinase for phenotypic switching.
Incorporating GPS and Mobile Radio Frequency Identification to Detect PIT-Tagged Fish and Evaluate Habitat Utilization in Streams

AbstractThe use of mobile radio frequency identification (RFID) systems to detect PIT tags has increased in support of research on fish movement, population dynamics, and habitat use. We describe the development and application of a mobile RFID system that incorporates GPS to detect PIT-tagged fish and evaluate habitat utilization in streams. The study was conducted in two distinct phases. First, development and testing of the RFID–GPS system were conducted using georeferenced, PIT-tagged rocks to evaluate detection probability and GPS accuracy. Second, the system was field deployed to estimate the abundance of PIT-tagged fish and evaluate habitat utilization. Detection probability was negatively influenced by stream width, distance from the stream center, and water depth, whereas detection probability increased with the number of passes. The GPS error between detected and surveyed positions averaged 4.5 m, with greater error observed in longitude than in latitude. Because of high capture and recapture pr.
Rotavirus A, C, and H in Brazilian pigs: potential for zoonotic transmission of RVA

Rotaviruses (RVs) have been identified as one of the main infectious causes of diarrhea in young pigs. We determined the prevalence of rotavirus A (RVA), C (RVC), and H (RVH) in pigs on a Brazilian farm. Samples were screened by reverse-transcription (RT)-PCR, and samples positive for RVA were genotyped by PCR amplification and sequencing analysis. Of the 329 fecal samples analyzed, 102 (30.9%) were positive for RV, 25 (7.6%) contained RVA only, 32 (9.7%) contained RVC only, and 31 (9.4%) contained RVH only. Co-circulation, the presence of ≥ 2 RVs in a sample, was detected in 14 (4.2%) samples. Of the 15 animals with diarrhea, 6 (40%) were positive for RV, and of the 314 asymptomatic animals, 96 (30.6%) were positive for RV; there was no statistically significant difference between the 2 groups (p = 0.441). Genotyping of RVA strains showed co-circulation of genotypes G1, G3, G9-P[8]-I1, and I2-E1. Phylogenetic analysis showed that some of the RVA genotypes found in pigs had high percentages of identity when compared with reference strains from humans, which suggests interspecies transmission. Because RVs may be zoonotic, excretion of RVs into the environment can result in transmission to agricultural workers causing interspecies infections and allowing the emergence of new reassorted viruses.
High‐throughput droplet microfluidics screening platform for selecting fast‐growing and high lipid‐producing microalgae from a mutant library

Abstract Biofuels derived from microalgal lipids have demonstrated a promising potential as future renewable bioenergy. However, the production costs for microalgae‐based biofuels are not economically competitive, and one strategy to overcome this limitation is to develop better‐performing microalgal strains that have faster growth and higher lipid content through genetic screening and metabolic engineering. In this work, we present a high‐throughput droplet microfluidics‐based screening platform capable of analyzing growth and lipid content in populations derived from single cells of a randomly mutated microalgal library to identify and sort variants that exhibit the desired traits such as higher growth rate and increased lipid content. By encapsulating single cells into water‐in‐oil emulsion droplets, each variant was separately cultured inside an individual droplet that functioned as an independent bioreactor. In conjunction with an on‐chip fluorescent lipid staining process within droplets, microalgal growth and lipid content were characterized by measuring chlorophyll and BODIPY fluorescence intensities through an integrated optical detection system in a flow‐through manner. Droplets containing cells with higher growth and lipid content were selectively retrieved and further analyzed off‐chip. The growth and lipid content screening capabilities of the developed platform were successfully demonstrated by first carrying out proof‐of‐concept screening using known Chlamydomonas reinhardtii mutants. The platform was then utilized to screen an ethyl methanesulfonate (EMS)‐mutated C. reinhardtii population, where eight potential mutants showing faster growth and higher lipid content were selected from 200,000 examined samples, demonstrating the capability of the platform as a high‐throughput screening tool for microalgal biofuel development.