Miracle-dz/UniFAR-FTUs huggingface dataset:
Improved cryopreservation of in vitro produced bovine embryos using FGF2, LIF, and IGF1

In vitro embryo production systems are limited by their inability to consistently produce embryos with the competency to develop to the blastocyst stage, survive cryopreservation, and establish a pregnancy. Previous work identified a combination of three cytokines [fibroblast growth factor 2 (FGF2), leukemia inhibitory factor (LIF), and insulin-like growth factor 1 (IGF1)], called FLI, that we hypothesize improve preimplantation development of bovine embryos in vitro. To test this hypothesis, FLI was supplemented into oocyte maturation or embryo culture medium. Embryos were produced in vitro using abattoir-derived oocytes and fertilized with sperm from a single bull known to have high fertility. After an 18–20 h fertilization period, putative zygotes were cultured in synthetic oviductal fluid (SOF) for 8 days. The addition of FLI to the oocyte maturation medium increased (P < 0.05) the dissociation of transzonal projections at 12, 18, and 24 h of maturation, as well as, the proportion of oocytes that reached the metaphase II stage of meiosis. Additionally, lipid content was decreased (P < 0.05) in the blastocyst stage embryo. The addition of FLI during the culture period increased development to the blastocyst stage, cytoskeleton integrity, and survival following slow freezing, as well as, decreased post thaw cell apoptosis (P < 0.05). In conclusion, the supplementation of these cytokines in vitro has the potential to alleviate some of the challenges associated with the cryo-survival of in vitro produced bovine embryos through improving embryo development and embryo quality.
Microbial Diversity Dynamics in a Methanogenic-Sulfidogenic UASB Reactor

In this study, the long-term performance and microbial dynamics of an Upflow Anaerobic Sludge Blanket (UASB) reactor targeting sulfate reduction in a SOx emissions treatment system were assessed using crude glycerol as organic carbon source and electron donor under constant S and C loading rates. The reactor was inoculated with granular sludge obtained from a pulp and paper industry and fed at a constant inlet sulfate concentration of 250 mg S-SO42−L−1 and a constant C/S ratio of 1.5 ± 0.3 g Cg−1 S for over 500 days. Apart from the regular analysis of chemical species, Illumina analyses of the 16S rRNA gene were used to study the dynamics of the bacterial community along with the whole operation. The reactor was sampled along the operation to monitor its diversity and the changes in targeted species to gain insight into the performance of the sulfidogenic UASB. Moreover, studies on the stratification of the sludge bed were performed by sampling at different reactor heights. Shifts in the UASB performance correlated well with the main shifts in microbial communities of interest. A progressive loss of the methanogenic capacity towards a fully sulfidogenic UASB was explained by a progressive wash-out of methanogenic Archaea, which were outcompeted by sulfate-reducing bacteria. Desulfovibrio was found as the main sulfate-reducing genus in the reactor along time. A progressive reduction in the sulfidogenic capacity of the UASB was found in the long run due to the accumulation of a slime-like substance in the UASB.
Two-Step Formation of Methane-Propane Mixed Gas Hydrates in A Batch-Type Reactor

Vapor compositions of methane and propane mixed gas in a batch-type reactor were measured by gas chromatography during hydrate crystallization at 274 K with molar ratios of propane below 10 vol %. The volume ratio of propane in the vapor decreased as the hydrate crystallization progressed. When the initial propane concentration was between 4 and 8 vol %, rapid gas consumption occurred for about 1 h, causing an initial pressure drop, and after a temporary stabilization of the pressure, a second pressure drop occurred; that is, hydrate crystallization occurred in two steps. X-Ray diffraction and Raman spectroscopic analyses on samples taken from the reactor during each step revealed that the structure II methane–propane mixed gas hydrates crystallized in the first step, and structure I methane hydrates in the second step. This process was observed only when the partial pressure of methane was above the equilibrium pressure of methane hydrate at the end of the first step. © 2004 American Institute of Chemical Engineers AIChE J, 50: 518–523, 2004
Optogenetic brain‐stimulation reward: A new procedure to re‐evaluate the rewarding versus aversive effects of cannabinoids in dopamine transporter‐Cre mice

Despite extensive research, the rewarding effects of cannabinoids are still debated. Here, we used a newly established animal procedure called optogenetic intracranial self‐stimulation (ICSS) (oICSS) to re‐examine the abuse potential of cannabinoids in mice. A specific adeno‐associated viral vector carrying a channelrhodopsin gene was microinjected into the ventral tegmental area (VTA) to express light‐sensitive channelrhodopsin in dopamine (DA) neurons of transgenic dopamine transporter (DAT)‐Cre mice. Optogenetic stimulation of VTA DA neurons was highly reinforcing and produced a classical “sigmoidal”‐shaped stimulation–response curve dependent upon the laser pulse frequency. Systemic administration of cocaine dose‐dependently enhanced oICSS and shifted stimulation–response curves upward, in a way similar to previously observed effects of cocaine on electrical ICSS. In contrast, Δ9‐tetrahydrocannabinol (Δ9‐THC), but not cannabidiol, dose‐dependently decreased oICSS responding and shifted oICSS curves downward. WIN55,212‐2 and ACEA, two synthetic cannabinoids often used in laboratory settings, also produced dose‐dependent reductions in oICSS. We then examined several new synthetic cannabinoids, which are used recreationally. XLR‐11 produced a cocaine‐like increase, AM‐2201 produced a Δ9‐THC‐like reduction, while 5F‐AMB had no effect on oICSS responding. Immunohistochemistry and RNAscope in situ hybridization assays indicated that CB1Rs are expressed mainly in VTA GABA and glutamate neurons, while CB2Rs are expressed mainly in VTA DA neurons. Together, these findings suggest that most cannabinoids are not reward enhancing, but rather reward attenuating or aversive in mice. Activation of CB1R and/or CB2R in different populations of neurons in the brain may underlie the observed actions.
Mesenchymal Stem Cell-Derived Exosomes as New Remedy for the Treatment of Neurocognitive Disorders

Mesenchymal stem cell (MSC)-derived exosomes (MSC-Exo) are nano-sized extracellular vesicles enriched with MSC-sourced neuroprotective and immunomodulatory microRNAs, neural growth factors, and anti-inflammatory cytokines, which attenuate neuro-inflammation, promote neo-vascularization, induce neurogenesis, and reduce apoptotic loss of neural cells. Accordingly, a large number of experimental studies demonstrated MSC-Exo-dependent improvement of cognitive impairment in experimental animals. In this review article, we summarized current knowledge about molecular and cellular mechanisms that were responsible for MSC-Exo-based restoration of cognitive function, emphasizing therapeutic potential of MSC-Exos in the treatment of neurocognitive disorders.
Exploration of Attendance, Active Participation, and Behavior Change in a Group-Based Responsive Stimulation, Maternal and Child Health, and Nutrition Intervention

ABSTRACT Delivery of interventions through group sessions allows for in-depth discussions and creates opportunities for group members to work together to identify and solve common problems. However, low attendance may limit impact. We explored factors affecting attendance, active participation, and behavior change in an integrated group-based child development and maternal and child health intervention in Bangladesh. Community health workers (CHWs) facilitated two sessions a month including material on child stimulation; water, sanitation, and hygiene; nutrition, maternal depression, and lead exposure prevention. Sessions were conducted with 320 pregnant women and mothers with children younger than 24 months, in 16 villages in Kishoreganj district. After 4 and 9 months of intervention, we conducted focus group discussions and in-depth interviews with mothers (n = 55 and n = 48) to identify determinants of attendance and behavior change, and to examine potential for intervention scale-up. Recruiting family members to assist with childcare resulted in improved attention during sessions. Adopting a storytelling format for presentation of session materials resulted in more engaged participation during courtyard sessions. Session attendance and behavior change, especially purchasing decisions, were difficult for participants without the support of male heads of the household. Selecting a rotating leader from among the group members to remind group members to attend sessions and support CHWs in organizing the sessions was not successful. Facilitating self-appraisals and planning for water and sanitation allowed participants to identify areas for improvement and track their progress. Key determinants of a participant’s attendance were identified, and the resulting intervention shows promise for future implementation at scale.
Quantitative intravital imaging in zebrafish reveals in vivo dynamics of physiological-stress-induced mitophagy

ABSTRACT Mitophagy, the selective recycling of mitochondria through autophagy, is a crucial metabolic process induced by cellular stress, and defects are linked to aging, sarcopenia and neurodegenerative diseases. To therapeutically target mitophagy, the fundamental in vivo dynamics and molecular mechanisms must be fully understood. Here, we generated mitophagy biosensor zebrafish lines expressing mitochondrially targeted, pH-sensitive fluorescent probes, mito-Keima and mito-EGFP–mCherry, and used quantitative intravital imaging to illuminate mitophagy during physiological stresses, namely, embryonic development, fasting and hypoxia. In fasted muscle, volumetric mitolysosome size analyses documented organelle stress response dynamics, and time-lapse imaging revealed that mitochondrial filaments undergo piecemeal fragmentation and recycling rather than the wholesale turnover observed in cultured cells. Hypoxia-inducible factor (Hif) pathway activation through physiological hypoxia or chemical or genetic modulation also provoked mitophagy. Intriguingly, mutation of a single mitophagy receptor (bnip3) prevented this effect, whereas disruption of other putative hypoxia-associated mitophagy genes [bnip3la (nix), fundc1, pink1 or prkn (Parkin)] had no effect. This in vivo imaging study establishes fundamental dynamics of fasting-induced mitophagy and identifies bnip3 as the master regulator of Hif-induced mitophagy in vertebrate muscle. Highlighted Article: Live imaging of mitophagy reporter zebrafish shows mitophagy occurs via a piece-by-piece mechanism in vivo. Hypoxia induces mitophagy in muscle in a bnip3-dependent but pink1-independent manner.
Mycobacterium tuberculosis Rv0580c Impedes the Intracellular Survival of Recombinant Mycobacteria, Manipulates the Cytokines, and Induces ER Stress and Apoptosis in Host Macrophages via NF-κB and p38/JNK Signaling

The Mycobacterium tuberculosis (M. tb) genome encodes a large number of hypothetical proteins, which need to investigate their role in physiology, virulence, pathogenesis, and host interaction. To explore the role of hypothetical protein Rv0580c, we constructed the recombinant Mycobacterium smegmatis (M. smegmatis) strain, which expressed the Rv0580c protein heterologously. We observed that Rv0580c expressing M. smegmatis strain (Ms_Rv0580c) altered the colony morphology and increased the cell wall permeability, leading to this recombinant strain becoming susceptible to acidic stress, oxidative stress, cell wall-perturbing stress, and multiple antibiotics. The intracellular survival of Ms_Rv0580c was reduced in THP-1 macrophages. Ms_Rv0580c up-regulated the IFN-γ expression via NF-κB and JNK signaling, and down-regulated IL-10 expression via NF-κB signaling in THP-1 macrophages as compared to control. Moreover, Ms_Rv0580c up-regulated the expression of HIF-1α and ER stress marker genes via the NF-κB/JNK axis and JNK/p38 axis, respectively, and boosted the mitochondria-independent apoptosis in macrophages, which might be lead to eliminate the intracellular bacilli. This study explores the crucial role of Rv0580c protein in the physiology and novel host-pathogen interactions of mycobacteria.
Identification of a Depolymerase Specific for K64-Serotype Klebsiella pneumoniae: Potential Applications in Capsular Typing and Treatment

Carbapenem-resistant Klebsiella pneumoniae (CRKP), one of the major nosocomial pathogens, is increasingly becoming a serious threat to global public health. There is an urgent need to develop effective therapeutic and preventive approaches to combat the pathogen. Here, we identified and characterized a novel capsule depolymerase (K64-ORF41) derived from Klebsiella phage SH-KP152410, which showed specific activities for K. pneumoniae K64-serotype. We showed that this depolymerase could be used in the identification of K64 serotypes based on the capsular typing, and the results agreed well with those from the conventional serotyping method using antisera. From this study, we also identified K64 mutant strains, which showed typing discrepancy between wzi-sequencing based genotyping and depolymerase-based or antiserum-based typing methods. Further investigation indicated that the mutant strain has an insertion sequence (IS) in wcaJ, which led to the alteration of the capsular serotype structure. We further demonstrated that K64-ORF41 depolymerase could sensitize the bacteria to serum or neutrophil killing by degrading the capsular polysaccharide. In summary, the identified K64 depolymerase proves to be an accurate and reliable tool for capsular typing, which will facilitate the preventive intervention such as vaccine development. In addition, the polymerase may represent a potential and promising therapeutic biologics against CRKP-K64 infections.
Leach Models for Contaminants Immobilized by pH-Dependent Mechanisms

A component-based leach model for describing leaching of hazardous contaminants that are immobilized by pH-dependent reactions is presented, and applications to environmental problems are described. The model describes simple chemical systems in which a solid phase provides acid-neutralizing capacity, and the contaminants are immobilized by precipitation or sorption reactions that are dependent on pH. Results of model simulations are related to predictions based on simple analytical leach models. Internal concentration gradients within the solid are predicted by the model, and their forms are used to explain how contaminants are immobilized and re-immobilization within the solid and how the concentration of acid in the leaching solution affects leaching of contaminants. Simulations show that the concentration of acid in the leaching solution affects leaching of contaminants in a complex manner that cannot be simply related to leaching of acid-neutralizing capacity. Even with these complex chemical interac.
Seroprevalence of SARS-CoV-2 Antibodies in Children and Adults in St. Louis, Missouri, USA

This study determined the percentages of both children and adult samples from the greater St. Louis metropolitan area who had antibodies to SARS-CoV-2 in late April to early May 2020. ABSTRACT Reported coronavirus disease 2019 (COVID-19) case counts likely underestimate the true prevalence because mild or asymptomatic cases often go untested. Here, we use a sero-survey to estimate the seroprevalence of IgG antibodies against severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in the St. Louis, MO, metropolitan area in a symptom-independent manner. Five hundred three adult and 555 pediatric serum/plasma samples were collected from patients presenting to Barnes-Jewish Hospital or St. Louis Children’s Hospital between 14 April 2020 and 12 May 2020. We developed protocols for in-house enzyme-linked immunosorbent assays (ELISAs) using spike and nucleoprotein and used the assays to estimate a seroprevalence rate based on our samples. Overall IgG seropositivity was estimated to be 1.71% (95% credible interval [CI], 0.04% to 3.38%) in pediatric samples and 3.11% (95% CI, 0.92% to 5.32%) in adult samples. Seropositivity was significantly lower in children under 5 years of age than in adults, but rates between adults and children aged 5 or older were similar. Of the 176 samples tested from children under 4 years of age, none were positive. IMPORTANCE This study determined the percentages of both children and adult samples from the greater St. Louis metropolitan area who had antibodies to SARS-CoV-2 in late April to early May 2020. Approximately 1.7 to 3.1% of the tested individuals had antibodies, indicating that they had previously been infected by SARS-CoV-2. These results demonstrate that the extent of infection was about 10 times greater than the number of confirmed cases at that time. Furthermore, it demonstrated that by 5 years of age, children were infected to an extent similar to that of adults.
Predicting Kidney Discard Using Machine Learning

Background. Despite the kidney supply shortage, 18%–20% of deceased donor kidneys are discarded annually in the United States. In 2018, 3569 kidneys were discarded. Methods. We compared machine learning (ML) techniques to identify kidneys at risk of discard at the time of match run and after biopsy and machine perfusion results become available. The cohort consisted of adult deceased donor kidneys donated between December 4, 2014, and July 1, 2019. The studied ML models included Random Forests (RF), Adaptive Boosting (AdaBoost), Neural Networks (NNet), Support Vector Machines (SVM), and K-nearest Neighbors (KNN). In addition, a Logistic Regression (LR) model was fitted and used for comparison with the ML models’ performance. Results. RF outperformed other ML models. Of 8036 discarded kidneys in the test dataset, LR correctly classified 3422 kidneys, whereas RF correctly classified 4762 kidneys (area under the receiver operative curve [AUC]: 0.85 versus 0.888, and balanced accuracy: 0.681 versus 0.759). For the kidneys with kidney donor profile index of >85% (6079 total), RF significantly outperformed LR in classifying discard and transplant prediction (AUC: 0.814 versus 0.717, and balanced accuracy: 0.732 versus 0.657). More than 388 kidneys were correctly classified using RF. Including biopsy and machine perfusion variables improved the performance of LR and RF (LR’s AUC: 0.888 and balanced accuracy: 0.74 versus RF’s AUC: 0.904 and balanced accuracy: 0.775). Conclusions. Kidneys that are at risk of discard can be more accurately identified using ML techniques such as RF.
Addiction Problems, Aggression, and Quality of Life in People with Different Occupations in South Korea

Addiction is related to aggression and quality of life. This study examined the relationship between these three factors according to occupation group in a mixed urban/rural area to better understand adult addiction problems. This study was a secondary data analysis of cross-sectional data collected by a 2017 regional survey of adults living in Gunsan City, South Korea. The survey included 500 people split into the unemployed (Group1), full-time homemakers (Group2), and primary (Group3), secondary (Group4), and tertiary (Group5) industry workers. Addiction problems and aggression were positively correlated (p < 0.01). Aggression and alcohol use disorder were correlated in Group3 (r = 0.31), Group4 (r = 0.34), and Group5 (r = 0.32), and aggression and smartphone addiction were correlated in Group2 (r = 0.39) and Group4 (r = 0.31). Problem gambling was correlated with aggression in Group5 (r = 0.39). A negative relationship between quality of life and alcohol use disorder occurred in Group1 (r = −0.36). According to the occupation group, the relationships between addiction problems, aggression, and quality of life were different. These findings suggest that addiction management for adults should be implemented in consideration of occupation groups.
Regulation of Fibroblast Cell Polarity by Src Tyrosine Kinase

Src protein tyrosine kinases (SFKs) are a family of nonreceptor tyrosine kinases that are localized beneath the plasma membrane and are activated during cell adhesion, migration, and elongation. Due to their involvement in the activation of signal transduction cascades, SFKs have been suggested to play important roles in the determination of cell polarity during cell extension and elongation. However, the mechanism underlying Src-mediated polarity formation remains unclear. The present study was performed to investigate the mechanisms underlying Src-induced cell polarity formation and cell elongation using Src knockout fibroblasts (SYFs) together with an inhibitor of Src. Normal and Src knockout fibroblasts were also transfected with a wild-type c-Src, dominant negative c-Src, or constitutively active c-Src gene to analyze the changes in cell morphology. SYF cells cultured on a glass substrate elongated symmetrically into spindle-shaped cells, with the formation of focal adhesions at both ends of the cells. When normal fibroblasts were treated with Src Inhibitor No. 5, a selective inhibitor of Src tyrosine kinases, they elongated into symmetrical spindle-shaped cells, similar to SYF cells. These results suggest that cell polarity during extension and elongation may be regulated by SFKs and that the expression and regulation of Src are important for the formation of polarity during cell elongation.
Clinical Evaluation of a Real-Time PCR Assay for Simultaneous Detection of Helicobacter pylori and Genotypic Markers of Clarithromycin Resistance Directly from Stool

Helicobacter pylori infection is mainly diagnosed noninvasively, with susceptibility testing traditionally requiring endoscopy. Treatment is empirical, with clarithromycin-based triple therapy recommended where resistance rates are below 15%. Rising rates of clarithromycin resistance, resulting in high therapy failure rates, are seen worldwide, but U.S. data are limited. ABSTRACT Helicobacter pylori infection is mainly diagnosed noninvasively, with susceptibility testing traditionally requiring endoscopy. Treatment is empirical, with clarithromycin-based triple therapy recommended where resistance rates are below 15%. Rising rates of clarithromycin resistance, resulting in high clarithromycin-based therapy failure rates, are seen worldwide, but U.S. data are limited. We developed a real-time PCR assay for simultaneous detection of H. pylori and genotypic markers of clarithromycin resistance directly from stool specimens. The assay was validated by testing 524 stool samples using an H. pylori stool antigen test as the reference method for detection accuracy and Sanger sequencing to confirm genotypic susceptibility results. A separate set of 223 antigen-positive stool samples was tested and retrospective medical record review conducted to define clinical utility. PCR resulted in 88.6% and 92.8% sensitivity in the validation and clinical study sets, respectively. Sequencing confirmed correct detection of clarithromycin resistance-associated mutations in all positive validation samples. The PCR-predicted clarithromycin resistance rate was 39% in the clinical data set overall and 31% in treatment-naive patients; the clarithromycin-based triple therapy eradication rate in treatment-naive patients was 62%. The clarithromycin-based triple therapy success was lower when resistance was predicted by PCR (41%) than when no resistance was predicted (70%; P = 0.03). PCR results were positive in 98% of antigen-positive stools from patients tested for eradication. The described PCR assay can accurately and noninvasively diagnose H. pylori, provide genotypic susceptibility, and test for eradication. Our findings support the need for susceptibility-guided therapy in our region if a clarithromycin-based regimen is considered.