Miracle-dz/UniFAR-FTUs huggingface dataset:
Active transport of glucose across the jejunal epithelium decreases with age in broiler chickens.

Intestinal glucose absorption varies with growth; however, the dynamics of these variations has not been yet fully elucidated in broiler chickens. The present study aimed to compare jejunal glucose uptake and maltose digestion in broilers of 2 different ages, i.e., 1- vs. 5 wk old. Oral D-maltose gavage, everted sac, and Ussing chamber experiments were carried out to investigate intestinal glucose absorption and mRNA expression of glucose-transport-related genes as well as jejunal maltase activity. Upon gavage, glucose concentrations peaked at 10 min post-administration in 1-wk-old chicks, while they peaked at 40 min in 5-wk-old chickens. Glucose concentrations at 10 min were significantly higher in the 1-wk-old chicks (P = 0.010). Using the everted sacs experimental setup, 5 intestinal regions i.e., duodenum, proximal jejunum, distal jejunum, proximal ileum, and distal ileum, were targeted to examine D-maltose digestion and glucose transport across the intestinal mucosa. In the distal and proximal ileum, glucose concentrations were found to be significantly higher in the serosal compartment of the 1-wk-old chicks upon incubation with D-maltose (25 mM) (P < 0.05), while in the mucosal compartment the levels were significantly higher in the 5-wk-old chickens (P < 0.05). An Ussing chamber setup was employed to measure glucose-induced short-circuit current (ΔIsc) in the mucosal epithelium of the jejunum. In response to the addition of D-maltose (10 mM) into the mucosal compartment, ΔIsc was significantly higher in the 1-wk-old chicks (P = 0.018). Furthermore, no variations in jejunal maltase activity were observed between the 2 age groups. While jejunal glucose absorption was lower in the 5-wk-old chickens, the mRNA expression levels of jejunal SGLT1, GLUT2, and Na+/K+-ATPase did not show any significant differences between the 2 age groups. Our results suggest that the active transport of glucose across the jejunal epithelium decreases upon growth in broiler chickens but is not accompanied by any variations in maltase activity or in the expression of glucose-absorption-related genes.
Identification of caveolin-1 domain signatures via machine learning and graphlet analysis of single-molecule super-resolution data

Motivation Network analysis and unsupervised machine learning processing of single molecule localization microscopy (SMLM) of caveolin-1 (Cav1) antibody labeling of prostate cancer cells identified biosignatures and structures for caveolae and three distinct non-caveolar scaffolds (S1A, S1B and S2) (Khater et al., 2018). To obtain further insight into low-level molecular interactions within these different structural domains, we now introduce graphlet decomposition over a range of proximity thresholds and show that frequency of different subgraph (k = 4 nodes) patterns for machine learning approaches (classification, identification, automatic labeling, etc.) effectively distinguishes caveolae and scaffold blobs. Results Caveolae formation requires both Cav1 and the adaptor protein CAVIN1 (also called PTRF). As a supervised learning approach, we applied a wide-field CAVIN1/PTRF mask to CAVIN1/PTRF-transfected PC3 prostate cancer cells (PC3-PTRF cells) and used the random forest classifier to classify blobs based on graphlet frequency distribution (GFD). GFD of CAVIN1/PTRF-positive (PTRF+) and -negative (PTRF-) Cav1 clusters showed poor classification accuracy that was significantly improved by stratifying the PTRF+ clusters by either number of localizations or volume. Low classification accuracy (<50%) of large PTRF+ clusters and caveolae blobs identified by unsupervised learning suggests that their GFD is specific to caveolae. High classification accuracy for small PTRF+ clusters and caveolae blobs argues that CAVIN1/PTRF associates not only with caveolae but also non-caveolar scaffolds. At low proximity thresholds (PTs) (50-100 nm), the caveolae groups showed reduced frequency of highly connected graphlets and increased frequency of completely disconnected graphlets. GFD analysis of SMLM Cav1 clusters defines changes in structural organization in caveolae and scaffolds independent of association with CAVIN1/PTRF. Supplementary information Supplementary data are available at Bioinformatics online.
Reducing energy intake and energy density for a sustainable diet: a study based on self-selected diets in French adults.

BACKGROUND Studies on theoretical diets are not sufficient to implement sustainable diets in practice because of unknown cultural acceptability. In contrast, self-selected diets can be considered culturally acceptable. OBJECTIVE The objective was to identify the most sustainable diets consumed by people in everyday life. DESIGN The diet-related greenhouse gas emissions (GHGE) for self-selected diets of 1918 adults participating in the cross-sectional French national dietary survey Individual and National Survey on Food Consumption (INCA2) were estimated. "Lower-Carbon," "Higher-Quality," and "More Sustainable" diets were defined as having GHGE lower than the overall median value, a probability of adequate nutrition intake (PANDiet) score (a measure of the overall nutritional adequacy of a diet) higher than the overall median value, and a combination of both criteria, respectively. Diet cost, as a proxy for affordability, and energy density were also assessed. RESULTS More Sustainable diets were consumed by 23% of men and 20% of women, and their GHGE values were 19% and 17% lower than the population average (mean) value, respectively. In comparison with the average value, Lower-Carbon diets achieved a 20% GHGE reduction and lower cost, but they were not sustainable because they had a lower PANDiet score. Higher-Quality diets were not sustainable because of their above-average GHGE and cost. More Sustainable diets had an above-average PANDiet score and a below-average energy density, cost, GHGE, and energy content; the energy share of plant-based products was increased by 20% and 15% compared with the average for men and women, respectively. CONCLUSIONS A strength of this study was that most of the dimensions for "sustainable diets" were considered, ie, not only nutritional quality and GHGE but also affordability and cultural acceptability. A reduction in diet-related GHGE by 20% while maintaining high nutritional quality seems realistic. This goal could be achieved at no extra cost by reducing energy intake and energy density and increasing the share of plant-based products.
Transplantation of pancreatic islets into the kidney capsule of diabetic mice.

UNLABELLED Our protocol was developed to cleanly and easily deliver islets or cells under the kidney capsule of diabetic or normal mice. We found that it was easier to concentrate the islets or cells into pellets in the final delivery tubing (PE50) used to transplant the cells under the kidney capsule. This technique provides both speed and ease while reducing any undue stress to the cells or to the mouse. LOADING: Settled, hand picked, islets or pelleted cells are carefully aspirated off the bottom of a 1.5 mL microcentrifuge tube using a p200 pipetteman and a straight, thin-wall pipette tip. A length of PE50 tubing is attached to the pipette tip using a small silicone adapter tubing. Cells are allowed to settle, in the tip, and then are transferred to the PE50 tubing by slowly dialing the pipetteman. Once the cells are near the end of the PE50 tubing, a kink is made and the silicone adaptor tubing is placed over the kink. The PE50 tubing is transferred to a 15 mL conical containing a cut 5 mL pipet, and the PE50 tubing is taped over the side of the 5 mL pipet to prevent curling during centrifuging. Cells are allowed to reach 1,000 rpm and stopped. TRANSPLANTATION Recipient mice are anesthetized, shaved, and cleaned. A small incision is made on the left flank of the mouse and the kidney is exposed. The kidney, fat, and tissue are kept moist with normal saline swab. The distal end of the PE50 is attached to a Hamilton screw drive syringe, containing a pipette tip, using the silicone adaptor tubing. A small nick is made on the right flank side of the kidney, not too large nor too deep. The beveled end of the PE50 tubing, nearest the cells, is carefully placed under the capsule, the tubing is moved around gently to make space while swabbing normal saline; a dry capsule can tear easily. A small air bubble is delivered under the capsule by slowly dialing the syringe screw drive. Islets are then slowly delivered behind the air bubble. Once the islets have been delivered kidney homeostasis is maintained and the knick is cauterized with low heat. The kidney is placed back into the cavity and the peritoneum and skin are sutured and stapled. Mice are immediately treated with Flunixin and Buprenorphine s.q. and placed in a cage on a heating pad.
SeismoWatch

The current norm for measuring blood pressure (BP) at home is using an automated BP cuff based on oscillometry. Despite providing a viable and familiar method of tracking BP at home, oscillometric devices can be both cumbersome and inaccurate with the inconvenience of the hardware typically limiting measurements to once or twice per day. To address these limitations, a wrist-watch BP monitor was developed to measure BP through a simple maneuver: holding the watch against the sternum to detect micro-vibrations of the chest wall associated with the heartbeat. As a pulse wave propagates from the heart to the wrist, an accelerometer and optical sensor on the watch measure the travel time -- pulse transit time (PTT) -- to estimate BP. In this paper, we conducted a study to test the accuracy and repeatability of our device. After calibration, the diastolic pressure estimations reached a root-mean-square error of 2.9 mmHg. The watch-based system significantly outperformed (p<0.05) conventional pulse arrival time (PAT) based wearable blood pressure estimations -- the most commonly used method for wearable BP sensing in the existing literature and commercial devices. Our device can be a convenient means for wearable BP monitoring outside of clinical settings in both health-conscious and hypertensive populations.
Association of Functional Screening Tests and Noncontact Injuries in Division I Women Student-Athletes.

Warren, M, Lininger, M, Smith, CA, Copp, A, and Chimera, NJ. Association of functional screening tests and noncontact injuries in Division I women student-athletes. J Strength Cond Res XX(X): 000-000, 2018-To determine the association between functional screening tests and lower-body, noncontact injuries in Division I women basketball, soccer, and volleyball student-athletes (SA). Sixty-eight injury-free women SA (age: 19.1 ± 1.1 years, height: 171.3 ± 8.7 cm, and mass: 68.4 ± 9.5 kg) were tested preseason with single hop (SH), triple hop (TH), and crossover hop (XH) for distance, and isometric hip strength (abduction, extension, and external rotation) in randomized order. The first lower-body (spine and lower extremity), noncontact injury requiring intervention by the athletic trainer was abstracted from the electronic medical record. Receiver operating characteristic and area under the curve (AUC) were calculated to determine cut-points for each hopping test from the absolute value of between-limb difference. Body mass-adjusted strength was categorized into tertiles. Logistic regression determined the odds of injury with each functional screening test using the hopping tests cut-points and strength categories, adjusting for previous injury. Fifty-two SA were injured during the sport season. The cut-point for SH was 4 cm (sensitivity = 0.77, specificity = 0.43, and AUC = 0.53), and for TH and XH was 12 cm (sensitivity = 0.75 and 0.67, specificity = 0.71 and 0.57, AUC = 0.59 and 0.41, respectively). A statistically significant association with TH and injuries (adjusted odds ratio = 6.50 [95% confidence interval: 1.69-25.04]) was found. No significant overall association was found with SH or XH, nor with the strength tests. Using a clinically relevant injury definition, the TH showed the strongest predictive ability for noncontact injuries. This hopping test may be a clinically useful tool to help identify increased risk of injury in women SA participating in high-risk sports.
A mouse model of seizures in anti–N‐methyl‐d‐aspartate receptor encephalitis

Seizures develop in 80% of patients with anti–N‐methyl‐d‐aspartate receptor (NMDAR) encephalitis, and these represent a major cause of morbidity and mortality. Anti‐NMDAR antibodies have been linked to memory loss in encephalitis; however, their role in seizures has not been established. We determined whether anti‐NMDAR antibodies from autoimmune encephalitis patients are pathogenic for seizures.
Metabolic Reprogramming of the Host Cell by Human Adenovirus Infection

Viruses are obligate intracellular parasites that alter many cellular processes to create an environment optimal for viral replication. Reprogramming of cellular metabolism is an important, yet underappreciated feature of many viral infections, as this ensures that the energy and substrates required for viral replication are available in abundance. Human adenovirus (HAdV), which is the focus of this review, is a small DNA tumor virus that reprograms cellular metabolism in a variety of ways. It is well known that HAdV infection increases glucose uptake and fermentation to lactate in a manner resembling the Warburg effect observed in many cancer cells. However, HAdV infection induces many other metabolic changes. In this review, we integrate the findings from a variety of proteomic and transcriptomic studies to understand the subtleties of metabolite and metabolic pathway control during HAdV infection. We review how the E4ORF1 protein of HAdV enacts some of these changes and summarize evidence for reprogramming of cellular metabolism by the viral E1A protein. Therapies targeting altered metabolism are emerging as cancer treatments, and similar targeting of aberrant components of virally reprogrammed metabolism could have clinical antiviral applications.
Working with parents to counteract bullying: A randomized controlled trial of an intervention to improve parent‐school cooperation

This study examined the effectiveness of an intervention aimed at improving parent‐school cooperation in counteracting bullying. Using a randomized controlled trial, data of teachers, parents of non‐victimized children, and children themselves were collected at 13 intervention and 14 control schools (grades 3–6, N at post‐assessment: teachers = 83, parents = 153, children = 2,510) at two time points (time lag about 6 months). Results showed positive effects of the intervention for some aspects of the primary outcomes: parents’ and teachers’ attitudes and efforts, whereas no effects were found of teachers’ or parents’ competences in counteracting bullying. No intervention effects were found for secondary outcomes: children's self‐reported bullying, victimization, well‐being, and self‐esteem. The findings indicate that, due to the intervention, teachers and parents were more aligned and able to cooperate, even within the short time of the intervention: one school year. This is the first essential step to systematically addressing parents’ role in tackling bullying; future research is needed to examine the long‐term effects of parent and school interventions in enhancing the effectiveness of anti‐bullying programs.
Deficiency of Fhl2 leads to delayed neuronal cell migration and premature astrocyte differentiation

ABSTRACT The four and a half LIM domains protein 2 (Fhl2) is an adaptor protein capable of mediating protein–protein interactions. Here, we report for the first time phenotypic changes in the brain of Fhl2-deficient mice. We showed that Fhl2 is expressed in neural stem cells, precursors and mature cells of neuronal lineage. Moreover, Fhl2 deficiency leads to delayed neuroblast migration in vivo, premature astroglial differentiation of neural stem cells (NSCs) in vitro, and a gliosis-like accumulation of glial fibrillary acidic protein (GFAP)-positive astrocytes in vivo that substantially increases with age. Collectively, Fhl2-deficiency in the brain interrupts the maintenance and the balanced differentiation of adult NSCs, resulting in preferentially glial differentiation and early exhaustion of the NSC pool required for adult neurogenesis. Highlighted Article: Fhl2-deficiency in the brain interrupts maintenance and balanced differentiation of adult NSCs, resulting in preferentially glial differentiation and early exhaustion of the NSC pool required for adult neurogenesis.
Dynamics of Hydrology and Anaerobic Hydrocarbon Degrader Communities in A Tar-Oil Contaminated Aquifer

Aquifers are typically perceived as rather stable habitats, characterized by low biogeochemical and microbial community dynamics. Upon contamination, aquifers shift to a perturbed ecological status, in which specialized populations of contaminant degraders establish and mediate aquifer restoration. However, the ecological controls of such degrader populations, and possible feedbacks between hydraulic and microbial habitat components, remain poorly understood. Here, we provide evidence of such couplings, via 4 years of annual sampling of groundwater and sediments across a high-resolution depth-transect of a hydrocarbon plume. Specialized anaerobic degrader populations are known to be established at the reactive fringes of the plume. Here, we show that fluctuations of the groundwater table were paralleled by pronounced dynamics of biogeochemical processes, pollutant degradation, and plume microbiota. Importantly, a switching in maximal relative abundance between dominant degrader populations within the Desulfobulbaceae and Desulfosporosinus spp. was observed after hydraulic dynamics. Thus, functional redundancy amongst anaerobic hydrocarbon degraders could have been relevant in sustaining biodegradation processes after hydraulic fluctuations. These findings contribute to an improved ecological perspective of contaminant plumes as a dynamic microbial habitat, with implications for both monitoring and remediation strategies in situ.
Echinococcosis: Advances in the 21st Century

Echinococcosis is a zoonosis caused by cestodes of the genus Echinococcus (family Taeniidae). This serious and near-cosmopolitan disease continues to be a significant public health issue, with western China being the area of highest endemicity for both the cystic (CE) and alveolar (AE) forms of echinococcosis. SUMMARY Echinococcosis is a zoonosis caused by cestodes of the genus Echinococcus (family Taeniidae). This serious and near-cosmopolitan disease continues to be a significant public health issue, with western China being the area of highest endemicity for both the cystic (CE) and alveolar (AE) forms of echinococcosis. Considerable advances have been made in the 21st century on the genetics, genomics, and molecular epidemiology of the causative parasites, on diagnostic tools, and on treatment techniques and control strategies, including the development and deployment of vaccines. In terms of surgery, new procedures have superseded traditional techniques, and total cystectomy in CE, ex vivo resection with autotransplantation in AE, and percutaneous and perendoscopic procedures in both diseases have improved treatment efficacy and the quality of life of patients. In this review, we summarize recent progress on the biology, epidemiology, diagnosis, management, control, and prevention of CE and AE. Currently there is no alternative drug to albendazole to treat echinococcosis, and new compounds are required urgently. Recently acquired genomic and proteomic information can provide a platform for improving diagnosis and for finding new drug and vaccine targets, with direct impact in the future on the control of echinococcosis, which continues to be a global challenge.
Bioenergetic deficits in Huntington’s disease iPSC-derived neural cells and rescue with glycolytic metabolites

Abstract Altered cellular metabolism is believed to be an important contributor to pathogenesis of the neurodegenerative disorder Huntington’s disease (HD). Research has primarily focused on mitochondrial toxicity, which can cause death of the vulnerable striatal neurons, but other aspects of metabolism have also been implicated. Most previous studies have been carried out using postmortem human brain or non-human cells. Here, we studied bioenergetics in an induced pluripotent stem cell-based model of the disease. We found decreased adenosine triphosphate (ATP) levels in HD cells compared to controls across differentiation stages and protocols. Proteomics data and multiomics network analysis revealed normal or increased levels of mitochondrial messages and proteins, but lowered expression of glycolytic enzymes. Metabolic experiments showed decreased spare glycolytic capacity in HD neurons, while maximal and spare respiratory capacities driven by oxidative phosphorylation were largely unchanged. ATP levels in HD neurons could be rescued with addition of pyruvate or late glycolytic metabolites, but not earlier glycolytic metabolites, suggesting a role for glycolytic deficits as part of the metabolic disturbance in HD neurons. Pyruvate or other related metabolic supplements could have therapeutic benefit in HD.
ChIAPoP: a new tool for ChIA-PET data analysis

Abstract Chromatin Interaction Analysis by Paired-End Tag Sequencing (ChIA-PET) is a popular assay method for studying genome-wide chromatin interactions mediated by a protein of interest. The main goal of ChIA-PET data analysis is to detect interactions between DNA regions. Here, we propose a new method and the associated data analysis pipeline, ChIAPoP, to detect chromatin interactions from ChIA-PET data. We compared ChIAPoP with other popular methods, including a hypergeometric model (used in ChIA-PET tool), MICC (used in ChIA-PET2), ChiaSig and mango. The results showed that ChIA-PoP performed better than or at least as well as these top existing methods in detecting true chromatin interactions. ChIAPoP is freely available to the public at https://github.com/wh90999/ChIAPoP.
Dairy products and metabolic effects in overweight men and women: results from a 6-mo intervention study.

BACKGROUND Some epidemiologic studies have suggested inverse relations between intake of dairy products and components of the metabolic syndrome. OBJECTIVE The objective was to investigate the effects of an increased intake of dairy products in persons with a habitually low intake on body composition and factors related to the metabolic syndrome. DESIGN Middle-aged overweight subjects (n = 121) with traits of the metabolic syndrome were recruited in Finland, Norway, and Sweden and randomly assigned into milk or control groups. The milk group was instructed to consume 3-5 portions of dairy products daily. The control group maintained their habitual diet. Clinical investigations were conducted on admission and after 6 mo. RESULTS There were no significant differences between changes in body weight or body composition, blood pressure, markers of inflammation, endothelial function, adiponectin, or oxidative stress in the milk and the control groups. There was a modest unfavorable increase in serum cholesterol concentrations in the milk group (P = 0.043). Among participants with a low calcium intake at baseline (<700 mg/d), there was a significant treatment effect for waist circumference (P = 0.003) and sagittal abdominal diameter (P = 0.034). When the sexes were analyzed separately, leptin increased (P = 0.045) and vascular cell adhesion molecule-1 decreased (P = 0.001) in women in the milk group. CONCLUSIONS This study gives no clear support to the hypothesis that a moderately increased intake of dairy products beneficially affects aspects of the metabolic syndrome. The apparently positive effects on waist circumference and sagittal abdominal diameter in subjects with a low calcium intake suggest a possible threshold in relation to effects on body composition.