Miracle-dz/UniFAR-FTUs huggingface dataset:
Forecasting dengue and influenza incidences using a sparse representation of Google trends, electronic health records, and time series data

Dengue and influenza-like illness (ILI) are two of the leading causes of viral infection in the world and it is estimated that more than half the world’s population is at risk for developing these infections. It is therefore important to develop accurate methods for forecasting dengue and ILI incidences. Since data from multiple sources (such as dengue and ILI case counts, electronic health records and frequency of multiple internet search terms from Google Trends) can improve forecasts, standard time series analysis methods are inadequate to estimate all the parameter values from the limited amount of data available if we use multiple sources. In this paper, we use a computationally efficient implementation of the known variable selection method that we call the Autoregressive Likelihood Ratio (ARLR) method. This method combines sparse representation of time series data, electronic health records data (for ILI) and Google Trends data to forecast dengue and ILI incidences. This sparse representation method uses an algorithm that maximizes an appropriate likelihood ratio at every step. Using numerical experiments, we demonstrate that our method recovers the underlying sparse model much more accurately than the lasso method. We apply our method to dengue case count data from five countries/states: Brazil, Mexico, Singapore, Taiwan, and Thailand and to ILI case count data from the United States. Numerical experiments show that our method outperforms existing time series forecasting methods in forecasting the dengue and ILI case counts. In particular, our method gives a 18 percent forecast error reduction over a leading method that also uses data from multiple sources. It also performs better than other methods in predicting the peak value of the case count and the peak time.
Biomaterials for In Situ Tissue Regeneration: A Review

This review focuses on a somewhat unexplored strand of regenerative medicine, that is in situ tissue engineering. In this approach manufactured scaffolds are implanted in the injured region for regeneration within the patient. The scaffold is designed to attract cells to the required volume of regeneration to subsequently proliferate, differentiate, and as a consequence develop tissue within the scaffold which in time will degrade leaving just the regenerated tissue. This review highlights the wealth of information available from studies of ex-situ tissue engineering about the selection of materials for scaffolds. It is clear that there are great opportunities for the use of additive manufacturing to prepare complex personalized scaffolds and we speculate that by building on this knowledge and technology, the development of in situ tissue engineering could rapidly increase. Ex-situ tissue engineering is handicapped by the need to develop the tissue in a bioreactor where the conditions, however optimized, may not be optimum for accelerated growth and maintenance of the cell function. We identify that in both methodologies the prospect of tissue regeneration has created much promise but delivered little outside the scope of laboratory-based experiments. We propose that the design of the scaffolds and the materials selected remain at the heart of developments in this field and there is a clear need for predictive modelling which can be used in the design and optimization of materials and scaffolds.
HSF1Base: A Comprehensive Database of HSF1 (Heat Shock Factor 1) Target Genes

HSF1 (heat shock factor 1) is an evolutionarily conserved master transcriptional regulator of the heat shock response (HSR) in eukaryotic cells. In response to high temperatures, HSF1 upregulates genes encoding molecular chaperones, also called heat shock proteins, which assist the refolding or degradation of damaged intracellular proteins. Accumulating evidence reveals however that HSF1 participates in several other physiological and pathological processes such as differentiation, immune response, and multidrug resistance, as well as in ageing, neurodegenerative demise, and cancer. To address how HSF1 controls these processes one should systematically analyze its target genes. Here we present a novel database called HSF1Base (hsf1base.org) that contains a nearly comprehensive list of HSF1 target genes identified so far. The list was obtained by manually curating publications on individual HSF1 targets and analyzing relevant high throughput transcriptomic and chromatin immunoprecipitation data derived from the literature and the Yeastract database. To support the biological relevance of HSF1 targets identified by high throughput methods, we performed an enrichment analysis of (potential) HSF1 targets across different tissues/cell types and organisms. We found that general HSF1 functions (targets are expressed in all tissues/cell types) are mostly related to cellular proteostasis. Furthermore, HSF1 targets that are conserved across various animal taxa operate mostly in cellular stress pathways (e.g., autophagy), chromatin remodeling, ribosome biogenesis, and ageing. Together, these data highlight diverse roles for HSF1, expanding far beyond the HSR.
Is one nerve transfer enough? A systematic review and pooled analysis comparing ulnar fascicular nerve transfer and double ulnar and median fascicular nerve transfer for restoration of elbow flexion after traumatic brachial plexus injury

Double fascicular transfer is argued to result in improved elbow flexion compared to the traditional ulnar fascicular transfer because it reinnervates both the biceps and the brachialis. This study seeks to determine if double fascicular transfer should be preferred over ulnar fascicular transfer to restore elbow flexion in patients with upper trunk brachial plexus injuries (BPI) by analyzing the current database of literature on the topic.
Rosiglitazone ameliorates tissue plasminogen activator‐induced brain hemorrhage after stroke

Delayed thrombolytic therapy with recombinant tissue plasminogen activator (tPA) may exacerbate blood‐brain barrier (BBB) breakdown after ischemic stroke and lead to catastrophic hemorrhagic transformation (HT). Rosiglitazone(RSG), a widely used antidiabetic drug that activates peroxisome proliferator‐activated receptor‐γ (PPAR‐γ), has been shown to protect against cerebral ischemia through promoting poststroke microglial polarization toward the beneficial anti‐inflammatory phenotype. However, whether RSG can alleviate HT after delayed tPA treatment remains unknown. In this study, we sort to examine the role of RSG on tPA‐induced HT after stroke.
Postoperative Pullthrough Obstruction in Hirschsprung Disease: Etiologies and Diagnosis

Some patients continue to have obstructive symptoms and/or incontinence after pullthrough surgery for Hirschsprung disease. Incontinence can be due to injury to the anal sphincter and/or dentate line, abnormal colonic motility (nonretentive), or a chronic large stool burden (retentive). A diagnostic algorithm based on clinical and pathological evaluations can be applied to distinguish potential etiologies for obstructive symptoms, which segregate into anatomic (mechanical or histopathological) or physiologic subgroups. Valuable clinical information may be obtained by anorectal examination under anesthesia, radiographic studies, and anorectal or colonic manometry. In addition, histopathological review of a patient’s original resection specimen(s) as well as postoperative biopsies of the neorectum usually are an important component of the diagnostic workup. Goals for the surgical pathologist are to exclude incomplete resection of the aganglionic segment or transition zone and to identify other neuromuscular pathology that might explain the patient’s dysmotility. Diagnoses established from a combination of clinical and pathological data dramatically alter management strategies. In rare instances, reoperative pullthrough surgery is required, in which case the pathologist must be aware of histopathological features specific to redo pullthrough resection specimens.
Molecular dynamics guided insight, binding free energy calculations and pharmacophore-based virtual screening for the identification of potential VEGFR2 inhibitors

Abstract Vascular endothelial growth factor-A (VEGF-A) is a crucial member of the Vascular endothelial growth factor (VEGF) family which mediates the metastasis of tumor by ‘angiogenic switch’. Therefore, targeting a VEGF-A mediated VEGFR2 signaling pathway is the most promising approach to repress the angiogenesis of tumor cells. VEGFR2 inhibitors are two types: Type I and Type II. Type II inhibitors have more chemical space to exploit and have better selectivity because of allosteric binding pocket over type I inhibitors. Hence, The present study encompasses identification of potential type II VEGFR2 inhibitors employing pharmacophore based virtual screnning. In this study, ten five featured pharmacophore model were generated from a dataset of 39 biaryl urea analogs.Out of all, ADDRR_1 pharmacophore model were used to screen the library of 5.2 million compounds retrieved from NCI, Maybridge, Asinex and Zinc databases. 7000 hits were filtered out from the pharmacophore-based virtual screening based on the phase fitness score. Among all best ten hits were identified employing extra precision mode of GLIDE module. ZINC00759038 and 211246 were chosen as top hits based on docking score, free binding energy, and ADME profile. They were subjected to molecular-dynamic studies to assess the hits-VEGFR2 binding stability. It suggests that ZINC00759038-VEGFR2 and 211246-VEGFR2 complexes are quite stable for the 20 ns simulation period. The strength of hit-protein complexes were further assessed by thermodynamic analysis of MD simulation studies by MMGBSA. Interestingly, these hits retains 90% similarity with standard VEGFR2 inhibitor (Sorafenib). Hence, these identified hits may led to new lead compounda as VEGFR2 inhibitors.
Recovery from tactile agnosia: a single case study

ABSTRACT In a patient suffering from tactile agnosia a comparison was made (using the ABABAB paradigm) between three blocks of neuropsychological rehabilitation sessions involving off-line anodal transcranial direct current stimulation (anodal-tDCS) and three blocks of rehabilitation sessions without tDCS. During the blocks with anodal-tDCS, the stimulation was administered in counterbalanced order to two sites: i) the perilesional parietal area (specific stimulation) and ii) an occipital area far from the lesion (nonspecific stimulation). Rehabilitation associated with anodal-tDCS (in particular in the perilesional areas) is more efficacious than without stimulation.
Validation of stroke-specific protocols for the 10-meter walk test and 6-minute walk test conducted using 15-meter and 30-meter walkways

ABSTRACT Background: Stroke-specific protocols for the 10-meter and 6-minute walk tests that include instructions for people with aphasia, accessible walkway lengths, and allow provision of assistance to walk are needed to facilitate uptake in hospital settings. Objectives: To estimate the test-retest reliability, measurement error, and construct validity of stroke-specific protocols for the 10-meter walk test (10mWT), and 6-minute walk test conducted using a 15-meter walkway (6MWT15m) and 30-meter walkway (6MWT30m), in people post-stroke. Methods: A quantitative, cross-sectional study involving ambulatory people post-stroke was conducted. Results: Data were collected from 21 and 20 participants at baseline and retest, respectively, 1–3 days apart. Mean age was 61 years, median time post-stroke was 134 days, and 90% had experienced an ischemic stroke. Performance on the 10mWT, 6MWT15m, and 6MWT30m across sessions yielded intraclass correlation coefficient (ICC2, 1) estimates of test-retest reliability of 0.83, 0.97, 0.95, respectively, and minimal detectable change values at the 95% confidence level of 0.40m/s, 44.0m, and 67.5m, respectively. Pearson correlation coefficients were 0.80–0.95 (p < .001) between results on all three walk tests and 0.27–0.48 (p < .25) between walk test results and strength subscale scores on the Stroke Impact Scale. Conclusions: Findings showed excellent test-retest reliability; measurement error values similar to current literature; and support for construct validity of the 10mWT, 6MWT15m, and 6MWT30m. Due to the shorter walkway, the 6MWT15m may be more feasible to implement than the 6MWT30m in hospital settings. A larger sample with more severe deficits is required to improve generalizability.
The Bis(ferrocenyl)phosphenium Ion Revisited

Abstract The bis(ferrocenyl)phosphenium ion, [Fc2P]+, reported by Cowley et al. (J. Am. Chem. Soc. 1981, 103, 714–715), was the only claimed donor‐free divalent phosphenium ion. Our examination of the molecular and electronic structure reveals that [Fc2P]+ possesses significant intramolecular Fe⋅⋅⋅P contacts, which are predominantly electrostatic and moderate the Lewis acidity. Nonetheless, [Fc2P]+ undergoes complex formation with the Lewis bases PPh3 and IPr to give the donor–acceptor complexes [Fc2P(PPh3)]+ and [Fc2P(IPr)]+ (IPr=1,3‐bis(2,6‐diisopropylphenyl)imidazole‐2‐ylidene).
Integrated paper-based flexible Li-ion batteries made by rod coating method.

Design and fabrication of flexible Li-ion batteries (FLIBs) with excellent electrochemical and structural stability via scalable fabrication techniques are important for their practical applications. A wide range of FLIBs with excellent flexibility have been reported. However, sophisticated designs and complex fabrication techniques are often used in fabricating FLIBS, making them difficult to be realized in industrial production. Here, we fabricate FLIBs with an integrated structure by assembling LiFePO4 cathode, Li4Ti5O12 anode, graphene current collectors and poly(vinylidene fluoride) (PVDF) electrolyte all together on commercial printing paper via conventional and scalable Meyer rod coating. In the design, the commercial paper serves as flexible substrate to enable good flexibility of the device, and the paper is coated twice with PVDF to avoid the short circuit problem and create a strong binding to integrate the device. The resultant integrated FLIBs exhibit excellent internal structural stability and good electrochemical performance under cycling bending for 100 times.
The Impact of a Workplace Wellness Program on Provider Health in Early Childhood Education Settings

Background: Early childhood education (ECE) working environments often contribute to poor health outcomes. The purpose of this study was to describe healthy eating–related and physical activity–related awareness and adoption of behavior change of ECE providers after participating in a workplace wellness (WW) program and to explore facilitators and barriers to ECE provider participation in WW program. Methods: The WW program offered healthy eating and physical activity challenges to promote ECE provider health and well-being. Approximately 1,000 ECE providers in Colorado from 35 ECE settings were invited to participate. After the intervention, ECE providers completed two surveys: (a) a provider postsurvey and (b) a WW challenge survey. Multivariable logistic regression modeling was used to examine factors associated with percent agreement that participation in the WW program increased awareness and adoption of health behaviors. Findings: A total of 250 (25%) ECE providers participated in WW program from 2015 to 2017. After participation, approximately 84% of respondents agreed they were more aware of the importance of eating fruits and vegetables and of being physically active, while 81% reported eating more fruits and vegetables, and 80% reported being more physically active in the workplace. Logistic regression models found that the length of time teaching in ECE settings was positively and significantly associated (odds ratio [OR] = 1.10, 95% confidence interval [CI] = [1.00, 1.21]) with the odds of providers agreeing that participation in the WW program increased their awareness of health behaviors. Conclusion/Application to Practice: The design and implementation of WW programs that emphasize facilitators, such as intrinsic and extrinsic motivation, as well as reduce barriers, such as time constraints and unachievable goal setting, may increase the awareness and adoptions of healthy eating–related and physical activity–related behaviors among ECE work settings.
Morphological assessment of embryo quality during assisted reproduction: A systematic review

Background: Various parameters of embryo morphology have been routinely used to select the embryo/s with maximum implantation potential during in vitro fertilization (IVF). Hence, there is a dilemma in clinical practice as to which morphological scoring system/test to use. We performed a systemic review to determine the predictive power as well as the clinical and cost-effectiveness of existing morphological tests of embryo quality described in an IVF setting. Materials and Methods: The preferred reporting items for systematic reviews and meta-analyses (PRISMA) guidelines for systematic review were followed. A mixed-method analysis was performed. Qualitative and quantitative techniques were used to synthesize the final results. A narrative summary approach was used for initial data exploration and description, followed by the pooling of data, where appropriate, using Meta-DiSc software. Receiver operating characteristic (ROC) curves were plotted wherever appropriate, and the area under the curve (AUROC) was determined. Results: Day 3, day 5, and early cleavage (EC) all had similar discriminatory value for predicting implantation (AUC 0.66, 067, and 0.63 respectively). There was no evidence of improvement in pregnancy rates due to routinely doing EC. No studies were identified that determined the cost-effectiveness of any of the tests. Conclusions: All tests have low accuracy. They lack the discriminatory power to identify an embryo that will/will not lead to implantation. Appropriately designed studies are required to assess the predictive value and the clinical and cost-effectiveness of novel embryo scoring technologies.
The role of intestinal bacteria in the ammonia detoxification ability of teleost fish

ABSTRACT Protein catabolism during digestion generates appreciable levels of ammonia in the gastrointestinal tract (GIT) lumen. Amelioration by the enterocyte, via enzymes such as glutamine synthetase (GS), glutamate dehydrogenase (GDH), and alanine and aspartate aminotransferases (ALT; AST), is found in teleost fish. Conservation of these enzymes across bacterial phyla suggests that the GIT microbiome could also contribute to ammonia detoxification by providing supplemental activity. Hence, the GIT microbiome, enzyme activities and ammonia detoxification were investigated in two fish occupying dissimilar niches: the carnivorous rainbow darter and the algivorous central stoneroller. There was a strong effect of fish species on the activity levels of GS, GDH, AST and ALT, as well as GIT lumen ammonia concentration, and bacterial composition of the GIT microbiome. Furthermore, removal of the intestinal bacteria impacted intestinal activities of GS and ALT in the herbivorous fish but not in the carnivore. The repeatability and robustness of this relationship was tested across field locations and years. Within an individual waterbody, there was no impact of sampling location on any of these factors. However, different waterbodies affected enzyme activities and luminal ammonia concentrations in both fish, while only the central stoneroller intestinal bacteria populations varied. Overall, a relationship between GIT bacteria, enzyme activity and ammonia detoxification was observed in herbivorous fish while the carnivorous fish displayed a correlation between enzyme activity and ammonia detoxification alone that was independent of the GIT microbiome. This could suggest that carnivorous fish are less dependent on non-host mechanisms for ammonia regulation in the GIT. Highlighted Article: Variable reliance on enzymatic pathways to ameliorate toxic levels of ammonia found within the intestinal lumen of fish during digestion is possibly due to the inconstant contribution of bacterial inhabitants.
The JAK-Inhibitor Tofacitinib Rescues Human Intestinal Epithelial Cells and Colonoids from Cytokine-Induced Barrier Dysfunction.

BACKGROUND Alterations to epithelial tight junctions can compromise the ability of the epithelium to act as a barrier between luminal contents and the underlying tissues, thereby increasing intestinal permeability, an early critical event in inflammatory bowel disease (IBD). Tofacitinib (Xeljanz), an orally administered pan-Janus kinase (JAK) inhibitor, was recently approved for the treatment of moderate to severe ulcerative colitis. Nevertheless, the effects of tofacitinib on intestinal epithelial cell functions are largely unknown. The aim of this study was to determine if JAK inhibition by tofacitinib can rescue cytokine-induced barrier dysfunction in intestinal epithelial cells (IECs). METHODS T84 IECs were used to evaluate the effects of tofacitinib on JAK-signal transducer and activator of transcription (STAT) activation, barrier permeability, and expression and localization of tight junction proteins. The impact of tofacitinib on claudin-2 promoter activity was assessed in HT-29 IECs. Tofacitinib rescue of barrier function was also tested in human colonic stem cell-derived organoids. RESULTS Pretreatment with tofacitinib prevented IFN-γ-induced decreases in transepithelial electrical resistance (TER) and increases in 4 kDa FITC-dextran permeability (FD4), partly due to claudin-2 transcriptional regulation and restriction of ZO-1 rearrangement at tight junctions. Although tofacitinib administered after IFN-γ challenge only partially normalized TER and claudin-2 levels, FD4 permeability and ZO-1 localization were fully recovered. The IFN-γ-induced FD4 permeability in primary human colonoids was fully rescued by tofacitinib. CONCLUSIONS These data suggest differential therapeutic efficacy of tofacitinib in the rescue of pore vs leak-tight junction barrier defects and indicate a potential contribution of improved epithelial barrier function to the beneficial effects of tofacitinib in IBD patients.
Using Statistical Measures and Machine Learning for Graph Reduction to Solve Maximum Weight Clique Problems

In this article, we investigate problem reduction techniques using stochastic sampling and machine learning to tackle large-scale optimization problems. These techniques heuristically remove decision variables from the problem instance, that are not expected to be part of an optimal solution. First we investigate the use of statistical measures computed from stochastic sampling of feasible solutions compared with features computed directly from the instance data. Two measures are particularly useful for this: 1) a ranking-based measure, favoring decision variables that frequently appear in high-quality solutions; and 2) a correlation-based measure, favoring decision variables that are highly correlated with the objective values. To take this further we develop a machine learning approach, called Machine Learning for Problem Reduction (MLPR), that trains a supervised learning model on easy problem instances for which the optimal solution is known. This gives us a combination of features enabling us to better predict the decision variables that belong to the optimal solution for a given hard problem. We evaluate our approaches using a typical optimization problem on graphs—the maximum weight clique problem. The experimental results show our problem reduction techniques are very effective and can be used to boost the performance of existing solution methods.