Miracle-dz/UniFAR-FTUs huggingface dataset:
In Stallion Spermatozoa, Superoxide Dismutase (Cu–Zn) (SOD1) and the Aldo-Keto-Reductase Family 1 Member b (AKR1B1) Are the Proteins Most Significantly Reduced by Cryopreservation

Although cryopreservation is widely used in animal breeding, the technique is still suboptimal. The population of spermatozoa surviving the procedure experiences changes attributed to alteration in their redox regulation. In order to expand our knowledge regarding this particular aspect, the proteome in fresh and frozen thawed aliquots of equine spermatozoa was studied to identify the proteins most severely affected by the procedure. If alteration of redox regulation is a major factor explaining cryodamage, proteins participating in redox regulation should be principally affected. Using a split sample design, 30 ejaculates from 10 different stallions were analyzed as fresh spermatozoa, and another aliquot from the same ejaculate was analyzed as a frozen thawed sample. The proteome was studied under both conditions using UHPLC-MS/MS and bioinformatic analysis conducted to identify discriminant variables between both conditions. Data are available through the ProteomeXchange Consortium with identifier PXD022236. The proteins most significantly reduced were Aldo-keto reductase family 1 member B (p = 2.2 × 10–17) and Superoxide dismutase (Cu–Zn) (p = 4.7 × 10–14). This is the first time that SOD1 has been identified as a discriminating variable using bioinformatic analysis, where it was one of the most highly significantly different proteins seen between fresh and frozen thawed semen. This finding strongly supports the theory that alteration in redox regulation and oxidative stress is a major factor involved in cryodamage and suggests that control of redox regulation should be a major target to improve current cryopreservation procedures.
Efficacy of indoor residual spraying with broflanilide (TENEBENAL), a novel meta-diamide insecticide, against pyrethroid-resistant anopheline vectors in northern Tanzania: An experimental hut trial

Novel chemistry for vector control is urgently needed to counter insecticide resistance in mosquitoes. Here a new meta-diamide insecticide, broflanilide (TENEBENALTM), was evaluated in East African experimental huts in Moshi, northern Tanzania. Two consecutive experimental hut trials with broflanilide 50WP were conducted; the first evaluating the efficacy of three concentrations, 50 mg/m2, 100 mg/m2, and 200 mg/m2 using a prototype formulation, and the second trial evaluating an improved formulation. The IRS treatments were applied on both mud and concrete surfaces and efficacy was monitored over time. The mortality, blood-feeding inhibition and exiting behaviour of free-flying wild mosquitoes was compared between treatment arms. Additionally, cone assays with pyrethroid-susceptible and resistant mosquito strains were conducted in the huts to determine residual efficacy. The first trial showed a dosage-mortality response of the prototype formulation and 3–8 months of residual activity, with longer activity on concrete than mud. The second trial with an improved formulation showed prolonged residual efficacy of the 100 mg/m2 concentration to 5–6 months on mud, and mosquito mortality on the concrete surface ranged between 94–100% for the full duration of the trial. In both trials, results with free-flying, wild Anopheles arabiensis echoed the mortality trend shown in cone assays, with the highest dose inducing the highest mortality and the improved formulation showing increased mortality rates. No blood-feeding inhibition or insecticide-induced exiting effects were observed with broflanilide. Broflanilide 50WP was effective against both susceptible and pyrethroid-resistant mosquito strains, demonstrating an absence of cross resistance between broflanilide and pyrethroids. The improved formulation, which has now been branded VECTRONTM T500, resulted in a prolonged residual efficacy. These results indicate the potential of this insecticide as an addition to the arsenal of IRS products needed to maintain both control of malaria and resistance management of malaria-transmitting mosquitoes.
Climate change impacts on population growth across a species’ range differ due to nonlinear responses of populations to climate and variation in rates of climate change

Impacts of climate change can differ substantially across species’ geographic ranges, and impacts on a given population can be difficult to predict accurately. A commonly used approximation for the impacts of climate change on the population growth rate is the product of local changes in each climate variable (which may differ among populations) and the sensitivity (the derivative of the population growth rate with respect to that climate variable), summed across climate variables. However, this approximation may not be accurate for predicting changes in population growth rate across geographic ranges, because the sensitivities to climate variables or the rate of climate change may differ among populations. In addition, while this approximation assumes a linear response of population growth rate to climate, population growth rate is typically a nonlinear function of climate variables. Here, we use climate-driven integral projection models combined with projections of future climate to predict changes in population growth rate from 2008 to 2099 for an uncommon alpine plant species, Douglasia alaskana, in a rapidly warming location, southcentral Alaska USA. We dissect the causes of among-population variation in climate change impacts, including magnitude of climate change in each population and nonlinearities in population response to climate change. We show that much of the variation in climate change impacts across D. alaskana’s range arises from nonlinearities in population response to climate. Our results highlight the critical role of nonlinear responses to climate change impacts, suggesting that current responses to increases in temperature or changes in precipitation may not continue indefinitely under continued changes in climate. Further, our results suggest the degree of nonlinearity in climate responses and the shape of responses (e.g., convex or concave) can differ substantially across populations, such that populations may differ dramatically in responses to future climate even when their current responses are quite similar.
Use and accuracy of the filter‐paper technique for measurement of soil matric potential

Summary A filter–paper technique that can be used to measure the matric potential of field soil is described in detail. When a calibrated batch of filter papers is used, the precision is limited by the variability between individual papers and the limitation of weighing to the nearest mg. The absolute accuracy is also limited by the instruments used for calibration. There was reasonable agreement between batches of the same type of paper, suggesting that our generalized calibration curves can be used for Whatman No. 42 filter papers where accuracy is not paramount. For potentials ≥−2.5 MPa, papers need to be equilibrated with the soil for 6 d. To achieve the same accuracy at lower potentials longer equilibration periods are required. Results suggest that the technique should be effective down to at least −100 MPa if soils are allowed to equilibrate fully with the papers. Coefficients of determination (r2) for the calibration lines were all ≥0.92. A regression of log(-matric potential) measured by the filter paper technique against measurements made using tensiometers and a psychrometer over a range of potentials between −1 kPa and −10 MPa gave an r2 value of 0.995.
The Microbicidal Effect of Low‐Temperature Plasma Generated by Corona Discharge: Comparison of Various Microorganisms on an Agar Surface or in Aqueous Suspension

The sensitivity of various microbes to the low temperature plasma generated by negative corona discharge in the point-to-plane mode was tested. On the surface of agar semisolid cultivation media, the inhibition zones in microbial cultures were obtained and their areas were compared as a measure of microbicidal effect for nine microbial species including bacterial spores and a yeast species. This experimental arrangement resembles the testing of antibiotic sensitivity by the well-known disc diffusion technique. The effect of comparable magnitude was found for all vegetative forms, but Candida albicans and Deinococcus radiodurans appeared to be the most and Geobacillus stearothermophilus the least susceptible. The effect on spores was in order of magnitude lesser than on vegetative forms. Following the action of the same plasma on bacteria in aqueous suspensions, the complete sterilization of Escherichia coli was achieved within 120 s and Staphylococcus epidermidis within 4–5min. On the other hand, the yeast Candida albicans in water appeared to be less susceptible requiring 30min for its complete inactivation.
Electron Transfer through a Monolayer of Hexadecylquinolinium Tricyanoquinodimethanide

Electron transfer through a Langmuir-Blodgett monolayer of hexadecylquinolinium tricyanoquinodimethanide (C 16 H 33 Q-3CNQ) sandwiched between metal electrodes is studied carefully. Either current rectification (rectification ratio as high as ∼20) for positive bias applied on the metal overlayer or symmetric current voltage curves were observed for samples with the highest resistivity. More leaky devices (resistivity of about a decade lower) show rectification (with a smaller ratio ≤5) for a negative bias on the top electrode. These results are analyzed regarding various mechanisms: (1) Aviram and Ratner proposal for a molecular diode, (2) geometrical asymmetry of the metal/Langmuir-Blodgett monolayer/metal structure, and (3) a polarization charge density effect. This study leads us to confirm that the observed electron-transfer properties through the C 16 H 33 Q-3CNQ LB monolayers are not only due to possible geometrical asymmetry in the metal/LB monolayer/metal structure but are also related to the strong asymmetry of the donor-π-bridge-acceptor C 16 H 33 Q-3CNQ molecules.
Integrating cognitive processing therapy for posttraumatic stress disorder with cognitive behavioral therapy for eating disorders in PROJECT RECOVER

ABSTRACT Posttraumatic stress disorder (PTSD) frequently co-occurs with eating disorders (ED) and is likely to be a powerful ED maintaining factor for a significant subgroup of individuals. The goal of PROJECT RECOVER is to develop and evaluate concurrent integrated treatment approaches for ED-PTSD to enable these individuals to recover from both their ED and PTSD. To date, we have trialed two approaches to concurrent/integrated treatment in PROJECT RECOVER: (1) concurrent delivery of Cognitive Processing Therapy (CPT) for PTSD to individuals receiving intensive ED treatment, and (2) delivery of a manualized individual cognitive-behavioral therapy (CBT) addressing both ED and PTSD (Integrated CBT for ED-PTSD) following a period of initial ED treatment. Interventions from both CBT for ED, and CPT for PTSD can be utilized and adapted to address the functional relationship between ED and PTSD, and promote full recovery from both disorders. Examples include integrating PTSD symptoms into the cognitive-behavioral individualized formulation of ED maintenance; integrating the ED into psychoeducation about PTSD maintenance; and identifying maladaptive beliefs that connect the ED to the trauma and/or PTSD. Emerging evidence suggests that CPT can be successfully integrated with CBT for ED.
Screening of MicroRNA Biomarkers Related to the Progression of Bladder Cancer.

Objective: This study aimed to identify the novel microRNAs (miRNAs) for early diagnosis of bladder cancer. Materials and Methods: Differentially expressed miRNAs between early and advanced bladder cancer were identified by differential expression analysis, using miRNA-seq data from The Cancer Genome Atlas (TCGA). The optimal subset of feature miRNAs for pathologic stage prediction was acquired by Random Forest algorithm and was used to construct a support vector machine (SVM) classifier. The performance of the SVM classifier in predicting the progression of bladder cancer samples was validated using an independent validating dataset. An miRNA-regulated target gene network was finally constructed and functional annotation were performed for the target genes. Results: A total of 52 significantly differentially expressed miRNAs were identified between early and advanced bladder cancer samples and 17 of these miRNAs were identified to be feature miRNAs. The 17 feature miRNAs were used to construct an SVM classifier, which showed a high performance in pathologic stage prediction for both training and validating dataset. Besides, our functional annotation analysis showed that the feature miRNAs were significantly involved in biological processes and pathways related to extracellular matrix process and PI3K/Akt signaling. Conclusions: The optimal subset of miRNAs may act as potential therapeutic targets and diagnostic markers of bladder cancer.
Studies on physical properties and structure of silk. Glass transition and crystallization of silk fibroin

Amorphous silk fibroin with random coil conformation shows endothermic and exothermic peaks and endothermic shift on the DSC (differential scanning calorimetry) curve. The endothermic shift observed at 175°C was due to the glass transition. The exothermic peak at 212°C is recognized to be the crystallization, which later was confirmed by x-ray diffraction pattern. The endothermic peak at 280°C is shown to be the degradation.
Brain derived neurotrophic factor (BDNF) polymorphism rs 10767664 affects metabolic parameters after weight loss secondary to high fat hypocaloric diet with Mediterranean pattern.

OBJECTIVE We evaluated the effect of the genetic variant rs10767664 of BDNF gene on anthropometric and biochemical changes after weight loss secondary to a high-fat hypocaloric diet with a Mediterranean dietary pattern. PATIENTS AND METHODS A sample of 277 obese subjects was recruited. After subjects met the inclusion criteria, they received a nutritional intervention with a high-fat hypocaloric diet [36% of carbohydrates, 40% of fats (60.0% of monounsaturated fats, 25.0% of saturated fats and 15.0% of polyunsaturated fats) and 24% of proteins]. Biochemical and anthropometric parameters were measured at basal and 3 months. RESULTS One hundred and seventy-nine subjects (64.6%) had the genotype AA (wild group) and 98 (35.4%) subjects had the next genotypes; AT (81 patients, 29.2%) or TT (17 patients, 6.2%) (Mutant group). The improvement of BMI, weight, fat mass, waist circumference, systolic blood pressure, leptin, total cholesterol and LDL cholesterol was similar in both genotypes after dietary intervention. Secondary to weight loss and only in non-T allele, insulin levels (AA vs. At+TT) (-5.2+0.2 UI/L vs. -2.9+0.3 UI/L: p=0.02) and HOMA-IR (-2.1+0.2 units vs. -1.1+0.1 units: p=0.02) decreased significantly. CONCLUSIONS T allele carriers of the BDNF variant rs10767664 may be an independent predictor of the lack of improvement induced by weight loss on insulin levels and insulin resistance after a high-fat hypocaloric diet with a Mediterranean dietary pattern.
Plasma edge and its application to infrared measurement and detection

A steep plasma edge in infrared reflectivity spectra of Hg1−xCdxTe and HgSe:Fe has been observed. It is predicted that the edge is sensitive to the variation of carrier concentration, which indicates the possibility of developing a fast light‐controlled switch for infrared radiation as well as a new approach of infrared modulation and detection. The modulation gain in power and detectivity limited by the generation‐recombination process has been calculated and compared with the photoconductive counterpart.
High-Throughput Screen for Inhibitors of the Type IV Pilus Assembly ATPase PilB

Many bacterial pathogens use their type IV pili (T4P) to facilitate and maintain infection of a human host. Small chemical compounds that inhibit the production or assembly of T4P have promise in the treatment and prevention of infections, especially in the era of increasing threats from antibiotic-resistant bacteria. ABSTRACT The bacterial type IV pilus (T4P) is a prominent virulence factor in many significant human pathogens, some of which have become increasingly antibiotic resistant. Antivirulence chemotherapeutics are considered a promising alternative to antibiotics because they target the disease process instead of bacterial viability. However, a roadblock to the discovery of anti-T4P compounds is the lack of a high-throughput screen (HTS) that can be implemented relatively easily and economically. Here, we describe the first HTS for the identification of inhibitors specifically against the T4P assembly ATPase PilB in vitro. Chloracidobacterium thermophilum PilB (CtPilB) had been demonstrated to have robust ATPase activity and the ability to bind its expected ligands in vitro. We utilized CtPilB and MANT-ATP, a fluorescent ATP analog, to develop a binding assay and adapted it for an HTS. As a proof of principle, we performed a pilot screen with a small compound library of kinase inhibitors and identified quercetin as a PilB inhibitor in vitro. Using Myxococcus xanthus as a model bacterium, we found quercetin to reduce its T4P-dependent motility and T4P assembly in vivo. These results validated our HTS as effective in identifying PilB inhibitors. This assay may prove valuable in seeking leads for the development of antivirulence chemotherapeutics against PilB, an essential and universal component of all bacterial T4P systems. IMPORTANCE Many bacterial pathogens use their type IV pili (T4P) to facilitate and maintain infection of a human host. Small chemical compounds that inhibit the production or assembly of T4P hold promise in the treatment and prevention of infections, especially in the era of increasing threats from antibiotic-resistant bacteria. However, few chemicals are known to have inhibitory or anti-T4P activity. Their identification has not been easy due to the lack of a method for the screening of compound collections or libraries on a large scale. Here, we report the development of an assay that can be scaled up to screen compound libraries for inhibitors of a critical T4P assembly protein. We further demonstrate that it is feasible to use whole cells to examine potential inhibitors for their activity against T4P assembly in a bacterium.
Long-term effect of parental selenium supplementation on the one-carbon metabolism in rainbow trout (Oncorhynchus mykiss) fry exposed to hypoxic stress

Abstract This study evaluated how different forms of selenium (Se) supplementation into rainbow trout broodstock diets modified the one-carbon metabolism of the progeny after the beginning of exogenous feeding and followed by hypoxia challenge. The progeny of three groups of rainbow trout broodstock fed either a control diet (Se level: 0·3 µg/g) or a diet supplemented with inorganic sodium selenite (Se level: 0·6 µg/g) or organic hydroxy-selenomethionine (Se level: 0·6 µg/g) was cross-fed with diets of similar Se composition for 11 weeks. Offspring were sampled either before or after being subjected to an acute hypoxic stress (1·7 mg/l dissolved oxygen) for 30 min. In normoxic fry, parental Se supplementation allowed higher glutathione levels compared with fry originating from parents fed the control diet. Parental hydroxy-selenomethionine treatment also increased cysteine and cysteinyl–glycine concentrations in fry. Dietary Se supplementation decreased glutamate–cysteine ligase (cgl) mRNA levels. Hydroxy-selenomethionine feeding also lowered the levels of some essential free amino acids in muscle tissue. Supplementation of organic Se to parents and fry reduced betaine-homocysteine S-methyltransferase (bhmt) expression in fry. The hypoxic stress decreased whole-body homocysteine, cysteine, cysteinyl-glycine and glutathione levels. Together with the higher mRNA levels of cystathionine beta-synthase (cbs), a transsulphuration enzyme, this suggests that under hypoxia, glutathione synthesis through transsulphuration might have been impaired by depletion of a glutathione precursor. In stressed fry, S-adenosylmethionine levels were significantly decreased, but S-adenosylhomocysteine remained stable. Decreased bhmt and adenosylmethionine decarboxylase 1a (amd1a) mRNA levels in stressed fry suggest a nutritional programming by parental Se also on methionine metabolism of rainbow trout.
Integration and transfer learning of single-cell transcriptomes via cFIT

Significance Overcorrection has been one of the main concerns in employing various data integration methods, which risk removing the biological distinction and are harmful for cell-type identification. Here, we present a simple yet surprisingly effective model named common factor integration and transfer learning for capturing various batch effects across experiments, technologies, subjects, and even species. The method generates robust results when batch effects are confounded with the variability of cell-type compositions and when the population exhibits continuous developing patterns. The successful integration and transfer uncover the transcriptional resemblance described by the proposed location-scale shift model across systems. In addition, the model enables transferring via low-rank matrix from more informative data to allow for precise identification in data of lower quality. Large, comprehensive collections of single-cell RNA sequencing (scRNA-seq) datasets have been generated that allow for the full transcriptional characterization of cell types across a wide variety of biological and clinical conditions. As new methods arise to measure distinct cellular modalities, a key analytical challenge is to integrate these datasets or transfer knowledge from one to the other to better understand cellular identity and functions. Here, we present a simple yet surprisingly effective method named common factor integration and transfer learning (cFIT) for capturing various batch effects across experiments, technologies, subjects, and even species. The proposed method models the shared information between various datasets by a common factor space while allowing for unique distortions and shifts in genewise expression in each batch. The model parameters are learned under an iterative nonnegative matrix factorization (NMF) framework and then used for synchronized integration from across-domain assays. In addition, the model enables transferring via low-rank matrix from more informative data to allow for precise identification in data of lower quality. Compared with existing approaches, our method imposes weaker assumptions on the cell composition of each individual dataset; however, it is shown to be more reliable in preserving biological variations. We apply cFIT to multiple scRNA-seq datasets of developing brain from human and mouse, varying by technologies and developmental stages. The successful integration and transfer uncover the transcriptional resemblance across systems. The study helps establish a comprehensive landscape of brain cell-type diversity and provides insights into brain development.