Miracle-dz/UniFAR-FTUs huggingface dataset:
Improvement in Aphasia Scores After Stroke Is Well Predicted by Initial Severity

Background and Purpose— Most improvement from poststroke aphasia occurs within the first 3 months, but there remains unexplained variability in recovery. Recently, we reported a strong correlation between initial impairment and change scores in motor recovery at 90 days. We wanted to determine whether aphasia recovery (defined as a change from baseline to 90 days) shows a comparably strong correlation and whether the relation was similar to that in motor recovery. Methods— Twenty-one stroke patients had aphasia scores on the Western Aphasia Battery (WAB) obtained on stroke admission (WABinitial) and at 90 days (WAB3 mo). The relation between actual change (&Dgr;) scores (defined as WAB3 mo− WABinitial) and WABinitial was calculated in multiple-regression analysis. Results— Regression analysis demonstrated that WABinitial was highly correlated with &Dgr;WAB (R2=0.81, P<0.001) and that, in addition, the relation between WABinitial and &Dgr;WAB was proportional, such that patients recovered 0.73 of maximal potential recovery (WABmaximum−WABinitial). Conclusions— We show that, like motor recovery, there is a highly predictable relation between aphasia recovery and initial impairment, which is also proportional in nature. The comparability of recovery from motor and language impairment suggests that common mechanisms may govern reduction of poststroke neurologic impairment across different functional domains and that they could be the focus of therapeutic intervention.
Comprehensive population-based genome sequencing provides insight into hematopoietic regulatory mechanisms

Significance Human blood cell production is coordinated to ensure balanced levels of all lineages. The basis of this regulation remains poorly understood. Identification of genetic differences in human populations associated with blood cell measurements can shed light on such regulatory mechanisms. Here, we used whole-genome sequencing data to perform a genetic association study in a population-based biobank from Estonia. We identified a number of potential causal variants and underlying mechanisms. For example, we identified a regulatory element that is necessary for basophil production, which acts specifically during this process to regulate expression of the transcription factor CEBPA. We demonstrate how genome sequencing, genetic fine-mapping, and functional data can be integrated to gain important insight into blood cell production. Genetic variants affecting hematopoiesis can influence commonly measured blood cell traits. To identify factors that affect hematopoiesis, we performed association studies for blood cell traits in the population-based Estonian Biobank using high-coverage whole-genome sequencing (WGS) in 2,284 samples and SNP genotyping in an additional 14,904 samples. Using up to 7,134 samples with available phenotype data, our analyses identified 17 associations across 14 blood cell traits. Integration of WGS-based fine-mapping and complementary epigenomic datasets provided evidence for causal mechanisms at several loci, including at a previously undiscovered basophil count-associated locus near the master hematopoietic transcription factor CEBPA. The fine-mapped variant at this basophil count association near CEBPA overlapped an enhancer active in common myeloid progenitors and influenced its activity. In situ perturbation of this enhancer by CRISPR/Cas9 mutagenesis in hematopoietic stem and progenitor cells demonstrated that it is necessary for and specifically regulates CEBPA expression during basophil differentiation. We additionally identified basophil count-associated variation at another more pleiotropic myeloid enhancer near GATA2, highlighting regulatory mechanisms for ordered expression of master hematopoietic regulators during lineage specification. Our study illustrates how population-based genetic studies can provide key insights into poorly understood cell differentiation processes of considerable physiologic relevance.
Angiotensinogen M235T and chymase gene CMA/B polymorphisms are not associated with nephropathy in type II diabetes.

BACKGROUND Several studies have suggested that the same genetic factors may be involved in the predisposition to both essential hypertension and diabetic nephropathy, but the molecular mechanism underlying this predisposition still remains unclear. In particular, the role of genes involved in blood-pressure regulation and angiotensin II action is still controversial. This study examines a possible association between angiotensinogen M235T and chymase gene CMA/B polymorphisms with the presence of nephropathy in type II diabetic Caucasians. METHODS For the purposes of the study, 323 microalbuminuric and 127 overt proteinuric cases, together with 243 normoalbuminuric controls with long-duration diabetes were selected from a group of 941 type II diabetic patients with established renal status. RESULTS No differences in the genotype distributions or allele frequencies of the examined polymorphisms between the study groups were observed. The study groups were also stratified by gender, diabetes duration, level of glycaemic control, body mass index, hypertension, and retinopathy status, but still no distortion in the distributions of genotypes of any of the examined polymorphisms in any of the strata was shown. CONCLUSIONS Our study provided evidence against an association between angiotensinogen M235T or chymase gene CMA/B polymorphisms and the presence of incipient or overt nephropathy in Caucasian patients with type II diabetes.
Modeling Seasonal Influenza Outbreak in a Closed College Campus: Impact of Pre-Season Vaccination, In-Season Vaccination and Holidays/Breaks

Background College and university students experience substantial morbidity from influenza and influenza-like illness, and they can benefit substantially from vaccination. Public health authorities encourage vaccination not only before the influenza season but also into and even throughout the influenza season. We conducted the present study to assess the impact of various vaccination strategies including delayed (i.e., in-season) vaccination on influenza outbreaks on a college campus. Methods/Findings We used a Susceptible → Infected → Recovered (SIR) framework for our mathematical models to simulate influenza epidemics in a closed, college campus. We included both students and faculty/staff in the model and derived values for the model parameters from the published literature. The values for key model parameters were varied to assess the impact on the outbreak of various pre-season and delayed vaccination rates; one-way sensitivity analyses were conducted to test the sensitivity of the model outputs to changes in selected parameter values. In the base case, with a pre-season vaccination rate of 20%, no delayed vaccination, and 1 student index case, the total attack rate (total percent infected, TAR) was 45%. With higher pre-season vaccination rates TARs were lower. Even if vaccinations were given 30 days after outbreak onset, TARs were still lower than the TAR of 69% in the absence of vaccination. Varying the proportions of vaccinations given pre-season versus delayed until after the onset of the outbreak gave intermediate TAR values. Base case outputs were sensitive to changes in infectious contact rates and infectious periods and a holiday/break schedule. Conclusion Delayed vaccination and holidays/breaks can be important adjunctive measures to complement traditional pre-season influenza vaccination for controlling and preventing influenza in a closed college campus.
Liaison and Castelnuovo-Mumford regularity

In this article we establish bounds for the Castelnuovo-Mumford regularity of projective schemes in terms of the degrees of their defining equations. The main new ingredient in our proofs is to show that generic residual intersections of complete intersection rational singularities again have rational singularities. When applied to the theory of residual intersections this circle of ideas also sheds new light on some known classes of free resolutions of residual ideals.
Hierarchical Fault Diagnosis: Application to an Ozone Plant

A framework for diagnosis in hierarchical finite-state machines is presented and applied to an ozone plant. In this approach, the model of the system is broken into simpler substructures called D-holons. At any instant, instead of the complete system model, only the D-holons associated with the ongoing phase of operation are used for diagnosis, which reduces memory requirement. Furthermore, within the above setup, a semimodular diagnosis method is presented and used to reduce design computations. Following the proposed framework, a diagnosis system is designed for the ozone plant. It is shown that the proposed approach significantly reduces the complexity of constructing and storing the diagnosis system.
Effects of Two-Year Vitamin B12 and Folic Acid Supplementation on Depressive Symptoms and Quality of Life in Older Adults with Elevated Homocysteine Concentrations: Additional Results from the B-PROOF Study, an RCT

Lowering elevated plasma homocysteine (Hcy) concentrations by supplementing vitamin B12 and folic acid may reduce depressive symptoms and improve health-related quality of life (HR-QoL) in older adults. This study aimed to test this hypothesis in a randomized controlled trial. Participants (N = 2919, ≥65 years, Hcy concentrations ≥12 µmol/L) received either 500 µg vitamin B12 and 400 µg folic acid daily or placebo for two years. Both tablets contained 15 µg vitamin D3. Depressive symptoms were measured with the Geriatric Depression Scale-15 (GDS-15). HR-QoL was assessed with the SF-12 Mental and Physical component summary scores and the EQ-5D Index score and Visual Analogue Scale. Differences in two-year change scores were analyzed with Analysis of Covariance (ANCOVA). Hcy concentrations decreased more in the intervention group, but two-year change scores of the GDS-15 and three of four HR-QoL measures did not differ between groups. The EQ-5D Index score declined less in the intervention group than in the placebo group (mean change 0.00 vs. −0.02, p = 0.004). In conclusion, two-year supplementation with vitamin B12 and folic acid in older adults with hyperhomocysteinemia showed that lowering Hcy concentrations does not reduce depressive symptoms, but it may have a small positive effect on HR-QoL.
Fluoride Release and Recharge Ability of a Novel Fluoride Release Composite Resin

Objective: To evaluate the fluoride release rates and fluoride recharge capability of a experimental resin composite, a compomer, a giomer and a resin-modified glass ionomer cement. Methods: Ten disc specimens of each material were prepare and polished with abrasive paper, followed by clearing with oil-free compressed air jet. The specimens were placed in a plastic vessel containing 5ml deionized water immediately after fabrication. Each specimen was removed and put to a new a vessel containing deionized water each day, and the sample solution was test for fluoride concentration each day using a compound fluoride ion selective electrode and a conductivity meter. All specimens were removed from container after 28 days and were recharged by immersing in a fluoride foam solution for four minutes. Then fluoride release from these recharged samples was measured daily for 7 days. Recharge was repeated three times. Result: Fuji II LC demonstrated the highest fluoride release ( p <0.01), followed by experimental resin and Compoglass. Both Beautufil and Charisma presented the lowest fluoride release ( p <0.01) during the first two weeks. All materials except Charisma demonstrated a sharp decline of fluoride release, followed by a comparatively stable stage of fluoride release for about twenty days. All materials presented fluoride release increase substantially one day after recharge but declines rapidly almost to the baseline level after 2 days except for Fuji II LC that showed a continual fluoride release for 5 days. Conclusion: The experimental composite resin has a capability of fluoride release and recharge that are comparable to compomers.
Using Thermal Shock to Inhibit Biofilm Formation in the Treated Sewage Source Heat Pump Systems

Treated sewage source heat pump systems can reuse the waste energy in the treated sewage. However, biofilms in the heat exchangers decrease the system efficiency. This work investigates the feasibility of thermal shock at accessible temperatures in heat exchangers for biofilm inhibition. Bacillus subtilis biofilms were formed on coupons and in a miniaturized plate heat exchanger. Thermal shocks at different temperatures (50–80 °C) for different exposure times (1–60 min) were used to treat the biofilms. The results showed that thermal shock had a significant bactericidal and biofilm inhibition effect, and the effect was enhanced as the temperature and the exposure time increased. Data fitting of the biomass showed that temperature had a more significant influence on the biofilm inhibition effect than exposure time. The results of the heat exchanging experiments showed that high temperature thermal shock could significantly mitigate the heat transfer deterioration caused by the biofilms, indicating that thermal shock could be used as a viable biofilm inhibition approach for heat exchangers.
Inductive expression of the NOD1 signalling pathway in chickens infected with Salmonella pullorum

ABSTRACT 1. The aim of this study was to describe the role of Nucleotide-binding oligomerization domain-containing protein 1 (NOD1) receptor signalling in chicken. 2. Tissue-specific expression analysis of NOD1, receptor-interacting serine-threonine kinase 2 (RIPK2), nuclear factor kappa B (NF-κB) and mitogen-activated protein kinase 11 (MAPK11 or p38) by quantitative real-time PCR (qRT-PCR) revealed their wide distribution in various organs and tissues. 3. Salmonella pullorum infection activated NOD1 receptor signalling in vivo and in vitro, resulting in significant induction of downstream signalling molecules RIPK2, NF-κB/p65, MAPK11/p38 and the effector molecules IL-1b and IL-8. 4. Activation of NOD1 by its agonist bacterial γ-D-glutamyl-meso-diaminopimelic acid (iE-DAP) in HD11 cells induced the adapter molecular RIPK2 and activated the NF-κB/p65 and MAPK11/p38 pathways, resulting in an increase in IL-8 but not IL-1β. Additionally, inhibition of NOD1 using NOD1-shRNA resulted in downregulation of RIPK2, MAPK11 and IL-8, while NF-κB/p65 and IL-1β were unaltered. 5. These results highlight the important role of NOD1 receptors in eliciting the innate immune response following pathogenic invasion in chicken.
Recurrent neural network based language model personalization by social network crowdsourcing

Speech recognition has become an important feature in smartphones in recent years. Different from traditional automatic speech recognition, the speech recognition on smartphones can take advantage of personalized language models to model the linguistic patterns and wording habits of a particular smartphone owner better. Owing to the popularity of social networks in recent years, personal texts and messages are no longer inaccessible. However, data sparseness is still an unsolved problem. In this paper, we propose a three-step adaptation approach to personalize recurrent neural network language models (RNNLMs). We believe that its capability to model word histories as distributed representations of arbitrary length can help mitigate the data sparseness problem. Furthermore, we also propose additional user-oriented features to empower the RNNLMs with stronger capabilities for personalization. The experiments on a Facebook dataset showed that the proposed method not only drastically reduced the model perplexity in preliminary experiments, but also moderately reduced the word error rate in n-best rescoring tests. Index Terms: Recurrent Neural Network, Personalized Language Modeling, Social Network, LM adaptation
Widespread FRA1-Dependent Control of Mesenchymal Transdifferentiation Programs in Colorectal Cancer Cells

Tumor invasion and metastasis involves complex remodeling of gene expression programs governing epithelial homeostasis. Mutational activation of the RAS-ERK is a frequent occurrence in many cancers and has been shown to drive overexpression of the AP-1 family transcription factor FRA1, a potent regulator of migration and invasion in a variety of tumor cell types. However, the nature of FRA1 transcriptional targets and the molecular pathways through which they promote tumor progression remain poorly understood. We found that FRA1 was strongly expressed in tumor cells at the invasive front of human colorectal cancers (CRCs), and that its depletion suppressed mesenchymal-like features in CRC cells in vitro. Genome-wide analysis of FRA1 chromatin occupancy and transcriptional regulation identified epithelial-mesenchymal transition (EMT)-related genes as a major class of direct FRA1 targets in CRC cells. Expression of the pro-mesenchymal subset of these genes predicted adverse outcomes in CRC patients, and involved FRA-1-dependent regulation and cooperation with TGFβ signaling pathway. Our findings reveal an unexpectedly widespread and direct role for FRA1 in control of epithelial-mesenchymal plasticity in CRC cells, and suggest that FRA1 plays an important role in mediating cross talk between oncogenic RAS-ERK and TGFβ signaling networks during tumor progression.
Single Deranged Physiologic Parameters Are Associated With Mortality in a Low-Income Country

Objective:To investigate whether deranged physiologic parameters at admission to an ICU in Tanzania are associated with in-hospital mortality and compare single deranged physiologic parameters to a more complex scoring system. Design:Prospective, observational cohort study of patient notes and admission records. Data were collected on vital signs at admission to the ICU, patient characteristics, and outcomes. Cutoffs for deranged physiologic parameters were defined a priori and their association with in-hospital mortality was analyzed using multivariable logistic regression. Setting:ICU at Muhimbili National Hospital, Dar es Salaam, Tanzania. Patients:All adults admitted to the ICU in a 15-month period. Measurements and Main Results:Two hundred sixty-nine patients were included: 54% female, median age 35 years. In-hospital mortality was 50%. At admission, 69% of patients had one or more deranged physiologic parameter. Sixty-four percent of the patients with a deranged physiologic parameter died in hospital compared with 18% without (p < 0.001). The presence of a deranged physiologic parameter was associated with mortality (adjusted odds ratio, 4.64; 95% CI, 1.95–11.09). Mortality increased with increasing number of deranged physiologic parameters (odds ratio per deranged physiologic parameter, 2.24 [1.53–3.26]). Every individual deranged physiologic parameter was associated with mortality with unadjusted odds ratios between 1.92 and 16.16. A National Early Warning Score of greater than or equal to 7 had an association with mortality (odds ratio, 2.51 [1.23–5.14]). Conclusion:Single deranged physiologic parameters at admission are associated with mortality in a critically ill population in a low-income country. As a measure of illness severity, single deranged physiologic parameters are as useful as a compound scoring system in this setting and could be termed “danger signs. ” Danger signs may be suitable for the basis of routines to identify and treat critically ill patients.
Moving shape dynamics: A signal processing perspective

This paper provides a new perspective on human motion analysis, namely regarding human motions in video as general discrete time signals. While this seems an intuitive idea, research on human motion analysis has attracted little attention from the signal processing community. Sophisticated signal processing techniques create important opportunities for new solutions to the problem of human motion analysis. This paper investigates how the deformations of human silhouettes (or shapes) during articulated motion can be used as discriminating features to implicitly capture motion dynamics. In particular, we demonstrate the applicability of two widely used signal transform methods, namely the discrete Fourier transform (DFT) and discrete wavelet transform (DWT), for characterization and recognition of human motion sequences. Experimental results show the effectiveness of the proposed method on two state-of-the-art data sets.
Case-Control Approach to Identify Plasmodium falciparum Polymorphisms Associated with Severe Malaria

Background Studies to identify phenotypically-associated polymorphisms in the Plasmodium falciparum 23 Mb genome will require a dense array of marker loci. It was considered promising to undertake initial allelic association studies to prospect for virulence polymorphisms in Thailand, as the low endemicity would allow higher levels of linkage disequilibrium (LD) than would exist in more highly endemic areas. Methodology/Principal Findings Assessment of LD was first made with 11 microsatellite loci widely dispersed in the parasite genome, and 16 microsatellite loci covering a ∼140 kb region of chromosome 2 (an arbitrarily representative non-telomeric part of the genome), in a sample of 100 P. falciparum isolates. The dispersed loci showed minimal LD (Index of Association, ISA = 0.013, P = 0.10), while those on chromosome 2 showed significant LD values mostly between loci <5 kb apart. A disease association study was then performed comparing parasites in 113 severe malaria cases and 245 mild malaria controls. Genotyping was performed on almost all polymorphisms in the binding domains of three erythrocyte binding antigens (eba175, eba140 and eba181), and repeat sequence polymorphisms ∼2 kb apart in each of three reticulocyte binding homologues (Rh1, Rh2a/b, and Rh4). Differences between cases and controls were seen for (i) codons 388-90 in eba175, and (ii) a repeat sequence centred on Rh1 codon 667. Conclusions/Significance Allelic association studies on P. falciparum require dense genotypic markers, even in a population of only moderate endemicity that has more extensive LD than highly endemic populations. Disease-associated polymorphisms in the eba175 and Rh1 genes encode differences in the middle of previously characterised erythrocyte binding domains, marking these for further investigation.
Partial Privatization and Firm Performance

Most privatization programs begin with a period of partial privatization in which only non-controlling shares of firms are sold on the stock market. Since management control is not transferred to private owners it is widely contended that partial privatization has little impact on firm behavior. This perspective ignores the role that the stock market can play in monitoring and rewarding managerial performance even when the government remains the controlling owner. Using data on the population of Indian state-owned enterprises we find that partial privatization has a positive and highly significant impact on firm sales, profits, and labor productivity.