Miracle-dz/UniFAR-FTUs huggingface dataset:
Novel Polyfermentor Intestinal Model (PolyFermS) for Controlled Ecological Studies: Validation and Effect of pH

In vitro gut fermentation modeling offers a useful platform for ecological studies of the intestinal microbiota. In this study we describe a novel Polyfermentor Intestinal Model (PolyFermS) designed to compare the effects of different treatments on the same complex gut microbiota. The model operated in conditions of the proximal colon is composed of a first reactor containing fecal microbiota immobilized in gel beads, and used to continuously inoculate a set of parallel second-stage reactors. The PolyFermS model was validated with three independent intestinal fermentations conducted for 38 days with immobilized human fecal microbiota obtained from three child donors. The microbial diversity of reactor effluents was compared to donor feces using the HITChip, a high-density phylogenetic microarray targeting small subunit rRNA sequences of over 1100 phylotypes of the human gastrointestinal tract. Furthermore, the metabolic response to a decrease of pH from 5.7 to 5.5, applied to balance the high fermentative activity in inoculum reactors, was studied. We observed a reproducible development of stable intestinal communities representing major taxonomic bacterial groups at ratios similar to these in feces of healthy donors, a high similarity of microbiota composition produced in second-stage reactors within a model, and a high time stability of microbiota composition and metabolic activity over 38 day culture. For all tested models, the pH-drop of 0.2 units in inoculum reactors enhanced butyrate production at the expense of acetate, but was accompanied by a donor-specific reorganization of the reactor community, suggesting a concerted metabolic adaptation and trigger of community-specific lactate or acetate cross-feeding pathways in response to varying pH. Our data showed that the PolyFermS model allows the stable cultivation of complex intestinal microbiota akin to the fecal donor and can be developed for the direct comparison of different experimental conditions in parallel reactors continuously inoculated with the exact same microbiota.
How teachers integrate a math computer game: Professional development use, teaching practices, and student achievement

As more attention is placed on designing digital educational games to align with schools 0 academic aims (e.g., Common Core), questions arise regarding how professional development (PD) may support teachers 0 using games for instruction and how such integration might impact students 0 achievement. This study seeks to (a) understand how teachers use PD resources (e.g., technology personnel and game ‐ use workshops) for integration; (b) determine how teachers integrate games into their instruction; and (c) examine how those teaching practices are associated with student achievement. This mixed method study used survey and interview responses from elementary school teachers ( n = 863) with access to PD resources for implementing a math game intervention and standardized math ‐ test scores from their second ‐ through sixth ‐ grade students ( n = 10,715). Findings showed few teachers sought PD assistance for integration, but many desired such support. Some reported using integrative practices (i.e., referencing game and using game ‐ generated progress reports) to identify struggling students, whereas several found integration challenging. Teachers 0 reordering of game objectives to align with lessons and viewing of game ‐ based PD videos were associated with increased student math achievement in our OLS ‐ analysis. However, this result was no longer statistically significant within a school fixed ‐ effects model, suggesting school differences may influence how strongly teachers 0 practices are associated with student achievement.
Peripheral and Alveolar Cell Transcriptional Programs Are Distinct in Acute Respiratory Distress Syndrome

1. Center for International Blood and Marrow Transplant Research (CIBMTR), National Marrow Donor Program (NMDP), European Blood and Marrow Transplant Group (EBMT), American Society of Blood and Marrow Transplantation (ASBMT), Canadian Blood and Marrow Transplant Group (CBMTG), Infectious Disease Society of America (IDSA), Society for Healthcare Epidemiology of America (SHEA), Association of Medical Microbiology and Infectious Diseases Canada (AMMI), Centers for Disease Control and Prevention (CDC). Guidelines for preventing infectious complications among hematopoietic cell transplant recipients: a global perspective. Bone Marrow Transplant 2009;44:453–558. 2. Wilson MR, Naccache SN, Samayoa E, Biagtan M, Bashir H, Yu G, et al. Actionable diagnosis of neuroleptospirosis by next-generation sequencing. N Engl J Med 2014;370:2408–2417. 3. Doan T, Wilson MR, Crawford ED, Chow ED, Khan LM, Knopp KA, et al. Illuminating uveitis: metagenomic deep sequencing identifies common and rare pathogens. Genome Med 2016;8:90. 4. Langelier C, Zinter MS, Kalantar KK, Yanik GA, Christenson S, O’Donovan B, et al. Data from: Metagenomic sequencing detects respiratory pathogens in hematopoietic cellular transplant patients. Dryad Digital Repository. 2017. Available from: https://doi.org/10.5061/ dryad.800tj. 5. Jain S, Self WH, Wunderink RG, Fakhran S, Balk R, Bramley AM, et al. CDC EPIC Study Team. Community-acquired pneumonia requiring hospitalization among U.S. adults. N Engl J Med 2015;373:415–427. 6. Tunkel AR, Sepkowitz KA. Infections caused by viridans streptococci in patients with neutropenia. Clin Infect Dis 2002;34:1524–1529. 7. Dı́ez-Aguilar M, Ruiz-Garbajosa P, Fernández-Olmos A, Guisado P, Del Campo R, Quereda C, et al. Non-diphtheriae Corynebacterium species: an emerging respiratory pathogen. Eur J Clin Microbiol Infect Dis 2013;32:769–772. 8. Heinonen S, Jartti T, Garcia C, Oliva S, Smitherman C, Anguiano E, et al. Rhinovirus detection in symptomatic and asymptomatic children: value of host transcriptome analysis. Am J Respir Crit Care Med 2016; 193:772–782. 9. Abreu NA, Nagalingam NA, Song Y, Roediger FC, Pletcher SD, Goldberg AN, et al. Sinus microbiome diversity depletion and Corynebacterium tuberculostearicum enrichment mediates rhinosinusitis. Sci Transl Med 2012;4:151ra124. 10. Liberzon A, Birger C, Thorvaldsdóttir H, Ghandi M, Mesirov JP, Tamayo P. The Molecular Signatures Database (MSigDB) hallmark gene set collection. Cell Syst 2015;1:417–425.
International Journal of Behavioral Nutrition and Physical Activity the Multimedia Activity Recall for Children and Adolescents (marca): Development and Evaluation

Background: Self-report recall questionnaires are commonly used to measure physical activity, energy expenditure and time use in children and adolescents. However, self-report questionnaires show low to moderate validity, mainly due to inaccuracies in recalling activity in terms of duration and intensity. Aside from recall errors, inaccuracies in estimating energy expenditure from self-report questionnaires are compounded by a lack of data on the energy cost of everyday activities in children and adolescents. This article describes the development of the Multimedia Activity Recall for Children and Adolescents (MARCA), a computer-delivered use-of-time instrument designed to address both the limitations of self-report recall questionnaires in children, and the lack of energy cost data in children.
Comparison of Carotid Plaque Score and Coronary Artery Calcium Score for Predicting Cardiovascular Disease Events: The Multi‐Ethnic Study of Atherosclerosis

Background Coronary artery calcium (CAC) predicts coronary heart disease (CHD) events better than carotid wall plaque presence; however, differences in the utility of CAC burden and carotid plaque burden across the spectrum of cardiovascular disease (CVD) events is unknown. Methods and Results CVD, CHD and stroke/transient ischemic attack (TIA) events were evaluated prospectively in a multiethnic cohort without CVD at baseline. Carotid plaque score was determined by the number of ultrasound‐detected plaques in the common, bifurcation, and internal carotid artery segments. CAC was detected by computed tomography. Predictive values were compared using Cox proportional hazards models, C‐statistics, and net reclassification, adjusting for traditional CVD risk factors. At baseline, the 4955 participants were mean (SD) 61.6 (10.1) years old and 52.8% female; 48.9% had CAC >0 and 50.8% had at least 1 carotid plaque. After 11.3 (3.0) years of follow‐up, 709 CVD, 498 CHD, and 262 stroke/TIA events occurred. CAC score compared to carotid plaque score was a stronger predictor of CVD (hazard ratio [HR], 1.78; 95% CI, 1.16–1.98; P<0.001 vs HR, 1.27; 95% CI, 1.16–1.40; P<0.001) and CHD events (HR, 2.09; 95% CI, 1.84–2.38; P<0.001 vs HR, 1.35; 95% CI, 1.21–1.51; P<0.001). CAC score and carotid plaque score were weak predictors of stroke/TIA. CAC score had better reclassification statistics than carotid plaque score, except for stroke/TIA, which had similar predictive values. Conclusions CAC score improved prediction, discrimination, and reclassification of CVD and CHD better than carotid ultrasound measures, although prediction and discrimination were similar for stroke/TIA.
Handgrip strength and its prognostic value for mortality in Moscow, Denmark, and England

Background This study compares handgrip strength and its association with mortality across studies conducted in Moscow, Denmark, and England. Materials The data collected by the Study of Stress, Aging, and Health in Russia, the Study of Middle-Aged Danish Twins and the Longitudinal Study of Aging Danish Twins, and the English Longitudinal Study of Ageing was utilized. Results Among the male participants, the age-standardized grip strength was 2 kg and 1 kg lower in Russia than in Denmark and in England, respectively. The age-standardized grip strength among the female participants was 1.9 kg and 1.6 kg lower in Russia than in Denmark and in England, respectively. In Moscow, a one-kilogram increase in grip strength was associated with a 4% (hazard ratio [HR] = 0.96, 95% confidence interval [CI]: 0.94, 0.99) reduction in mortality among men and a 10% (HR = 0.90, 95%CI: 0.86, 0.94) among women. Meanwhile, a one-kilogram increase in grip strength was associated with a 6% (HR = 0.94, 95%CI: 0.93, 0.95) and an 8% (HR = 0.92, 95%CI: 0.90, 0.94) decrease in mortality among Danish men and women, respectively, and with a 2% (HR = 0.98, 95%CI: 0.97, 0.99) and a 3% (HR = 0.97, 95%CI: 0.95, 0.98) reduction in mortality among the English men and women, respectively. Conclusion The study suggests that, although absolute grip strength values appear to vary across the Muscovite, Danish, and English samples, the degree to which grip strength is predictive of mortality is comparable across national populations with diverse socioeconomic and health profiles and life expectancy levels.
IGFBP3 deposited in the human umbilical cord mesenchymal stem cell‐secreted extracellular matrix promotes bone formation

The extracellular matrix (ECM) contains rich biological cues for cell recruitment, proliferationm, and even differentiation. The osteoinductive potential of scaffolds could be enhanced through human bone marrow mesenchymal stem cell (hBMSC) directly depositing ECM on surface of scaffolds. However, the role and mechanism of human umbilical cord mesenchymal stem cells (hUCMSC)‐secreted ECM in bone formation remain unknown. We tested the osteoinductive properties of a hUCMSC‐secreted ECM construct (hUCMSC‐ECM) in a large femur defect of a severe combined immunodeficiency (SCID) mouse model. The hUCMSC‐ECM improved the colonization of endogenous MSCs and bone regeneration, similar to the hUCMSC‐seeded scaffold and superior to the scaffold substrate. Besides, the hUCMSC‐ECM enhanced the promigratory molecular expressions of the homing cells, including CCR2 and TβRI. Furthermore, the hUCMSC‐ECM increased the number of migrated MSCs by nearly 3.3 ± 0.1‐fold, relative to the scaffold substrate. As the most abundant cytokine deposited in the hUCMSC‐ECM, insulin‐like growth factor binding protein 3 (IGFBP3) promoted hBMSC migration in the TβRI/II‐ and CCR2‐dependent mechanisms. The hUCMSC‐ECM integrating shRNA‐mediated silencing of Igfbp3 that down‐regulated IGFBP3 expression by approximately 60%, reduced the number of migrated hBMSCs by 47%. In vivo, the hUCMSC‐ECM recruited 10‐fold more endogenous MSCs to initiate bone formation compared to the scaffold substrate. The knock‐down of Igfbp3 in the hUCMSC‐ECM inhibited nearly 60% of MSC homing and bone regeneration capacity. This research demonstrates that IGFBP3 is an important MSC homing molecule and the therapeutic potential of hUCMSC‐ECM in bone regeneration is enhanced by improving MSC homing in an IGFBP3‐dependent mechanism.
G-Cimp Status Prediction Of Glioblastoma Samples Using mRNA Expression Data

Glioblastoma Multiforme (GBM) is a tumor with high mortality and no known cure. The dramatic molecular and clinical heterogeneity seen in this tumor has led to attempts to define genetically similar subgroups of GBM with the hope of developing tumor specific therapies targeted to the unique biology within each of these subgroups. Recently, a subset of relatively favorable prognosis GBMs has been identified. These glioma CpG island methylator phenotype, or G-CIMP tumors, have distinct genomic copy number aberrations, DNA methylation patterns, and (mRNA) expression profiles compared to other GBMs. While the standard method for identifying G-CIMP tumors is based on genome-wide DNA methylation data, such data is often not available compared to the more widely available gene expression data. In this study, we have developed and evaluated a method to predict the G-CIMP status of GBM samples based solely on gene expression data.
Co-occurrence of mycotoxins in commercial formula milk and cereal-based baby food on the Qatar market

ABSTRACT The present study was conducted to explore the occurrence of mycotoxins in commercial baby foods in Doha-Qatar. LCMS/MS- and HPLC-based analysis of baby food (n = 67) for 12 mycotoxins confirmed the presence of aflatoxin M1 (AFM1, 33%), ochratoxin A (OTA, 31%), deoxynivalenol (DON, 27%), aflatoxin B1 (AFB1, 22%), fumonisin B2 (FB2, 10%), zearalenone (ZEN, 4%) and T-2 toxin (2%). Noodles exhibited the maximum contamination percentage, with 33% of the samples being contaminated above the EU maximum limits, for at least one mycotoxin. Among the multi-grain flake samples, up to 28% and for the milk and milk-based-cereal samples, 14% contained at least one mycotoxin above the EU maximum limits. From all cereal-based food samples, 22%, 5%, 2% and 2% were concurrently contaminated with 2, 3, 4 and 5 mycotoxins, respectively. The occurrence of toxicological important mycotoxins in Qatari market warrants the implementation of strict regulatory limits to protect human health.
On the Asymptotic Capacity of Multi-Hop MIMO Ad Hoc Networks

Multi-input multi-output (MIMO) is a key technology to increase the capacity of wireless networks. Although there has been extensive work on MIMO at the physical and link layers, there is limited work on MIMO at the network layer (i.e., multi-hop MIMO network), particularly results on capacity scaling laws. In this paper, we investigate capacity scaling laws for MIMO ad hoc networks. Our goal is to find the achievable throughput of each node as the number of nodes in the network increases. We employ a MIMO network model that captures spatial multiplexing and interference cancellation. We show that for a MIMO network with n randomly located nodes, each equipped with α antennas and a rate of W on each data stream, the achievable throughput of each node is Θ(αW/√(n ln n)).
Climate-associated phenological advances in bee pollinators and bee-pollinated plants

The phenology of many ecological processes is modulated by temperature, making them potentially sensitive to climate change. Mutualistic interactions may be especially vulnerable because of the potential for phenological mismatching if the species involved do not respond similarly to changes in temperature. Here we present an analysis of climate-associated shifts in the phenology of wild bees, the most important pollinators worldwide, and compare these shifts to published studies of bee-pollinated plants over the same time period. We report that over the past 130 y, the phenology of 10 bee species from northeastern North America has advanced by a mean of 10.4 ± 1.3 d. Most of this advance has taken place since 1970, paralleling global temperature increases. When the best available data are used to estimate analogous rates of advance for plants, these rates are not distinguishable from those of bees, suggesting that bee emergence is keeping pace with shifts in host-plant flowering, at least among the generalist species that we investigated.
Crossmodal Connections of Primary Sensory Cortices Largely Vanish During Normal Aging

During aging, human response times (RTs) to unisensory and crossmodal stimuli decrease. However, the elderly benefit more from crossmodal stimulus representations than younger people. The underlying short-latency multisensory integration process is mediated by direct crossmodal connections at the level of primary sensory cortices. We investigate the age-related changes of these connections using a rodent model (Mongolian gerbil), retrograde tracer injections into the primary auditory (A1), somatosensory (S1), and visual cortex (V1), and immunohistochemistry for markers of apoptosis (Caspase-3), axonal plasticity (Growth associated protein 43, GAP 43), and a calcium-binding protein (Parvalbumin, PV). In adult animals, primary sensory cortices receive a substantial number of direct thalamic inputs from nuclei of their matched, but also from nuclei of non-matched sensory modalities. There are also direct intracortical connections among primary sensory cortices and connections with secondary sensory cortices of other modalities. In very old animals, the crossmodal connections strongly decrease in number or vanish entirely. This is likely due to a retraction of the projection neuron axonal branches rather than ongoing programmed cell death. The loss of crossmodal connections is also accompanied by changes in anatomical correlates of inhibition and excitation in the sensory thalamus and cortex. Together, the loss and restructuring of crossmodal connections during aging suggest a shift of multisensory processing from primary cortices towards other sensory brain areas in elderly individuals.
Association between lymph node yield and survival among patients undergoing radical nephroureterectomy for urothelial carcinoma of the upper tract

Prior studies examining the value of lymph node (LN) dissection (LND) in patients with urothelial carcinoma of the upper urinary tract (UTUC) have produced conflicting results. The objective of the current study was to assess the relationship between LN yield and survival among patients undergoing radical nephroureterectomy (RNU).
Polyspecific antibodies without persisting antigen in multiple sclerosis, neurolupus and Guillain-Barré syndrome: immune network connectivity in chronic diseases

ABSTRACT The polyspecific antibody synthesis in multiple sclerosis (MS) gained diagnostic relevance with the frequent combination of measles-, rubella- and varicella zoster antibodies (MRZ-antibody reaction) but their pathophysiological role remains unknown. This review connects the data for intrathecal polyspecific antibody synthesis in MS and neurolupus with observations in the blood of patients with Guillain-Barré syndrome (GBS). Simultaneously increased antibody and autoantibody titers in GBS blood samples indicate that the polyspecific antibodies are based on a general property of an immune network, supported by the deterministic day-to-day concentration variation of antibodies in normal blood. Strongly correlated measles- and rubella- antibody variations point to a particular connectivity between the MRZ antibodies. The immune network, which provides serological memory in the absence of an antigen, implements the continuous change of the MRZ pattern in blood, not followed by the earlier immigrated B cells without corresponding connectivity in the brain. This may explain the different antibody patterns in cerebrospinal fluid, aqueous humor and blood of the individual MS patient. A complexity approach must implement a different view on causation in chronic diseases and causal therapies.
Flexoelectricity in Bones

Bones generate electricity under pressure, and this electromechanical behavior is thought to be essential for bone's self‐repair and remodeling properties. The origin of this response is attributed to the piezoelectricity of collagen, which is the main structural protein of bones. In theory, however, any material can also generate voltages in response to strain gradients, thanks to the property known as flexoelectricity. In this work, the flexoelectricity of bone and pure bone mineral (hydroxyapatite) are measured and found to be of the same order of magnitude; the quantitative similarity suggests that hydroxyapatite flexoelectricity is the main source of bending‐induced polarization in cortical bone. In addition, the measured flexoelectric coefficients are used to calculate the (flexo)electric fields generated by cracks in bone mineral. The results indicate that crack‐generated flexoelectricity is theoretically large enough to induce osteocyte apoptosis and thus initiate the crack‐healing process, suggesting a central role of flexoelectricity in bone repair and remodeling.
Neuromotor Noise Is Malleable by Amplifying Perceived Errors

Variability in motor performance results from the interplay of error correction and neuromotor noise. This study examined whether visual amplification of error, previously shown to improve performance, affects not only error correction, but also neuromotor noise, typically regarded as inaccessible to intervention. Seven groups of healthy individuals, with six participants in each group, practiced a virtual throwing task for three days until reaching a performance plateau. Over three more days of practice, six of the groups received different magnitudes of visual error amplification; three of these groups also had noise added. An additional control group was not subjected to any manipulations for all six practice days. The results showed that the control group did not improve further after the first three practice days, but the error amplification groups continued to decrease their error under the manipulations. Analysis of the temporal structure of participants’ corrective actions based on stochastic learning models revealed that these performance gains were attained by reducing neuromotor noise and, to a considerably lesser degree, by increasing the size of corrective actions. Based on these results, error amplification presents a promising intervention to improve motor function by decreasing neuromotor noise after performance has reached an asymptote. These results are relevant for patients with neurological disorders and the elderly. More fundamentally, these results suggest that neuromotor noise may be accessible to practice interventions.