Miracle-dz/UniFAR-FTUs huggingface dataset:
Identification of genes involved in cell wall biogenesis in grasses by differential gene expression profiling of elongating and non-elongating maize internodes

Despite the economic importance of grasses as food, feed, and energy crops, little is known about the genes that control their cell wall synthesis, assembly, and remodelling. Here a detailed transcriptome analysis that allowed the identification of genes involved in grass cell wall biogenesis is provided. Differential gene expression profiling, using maize oligonucleotide arrays, was used to identify genes differentially expressed between an elongating internode, containing cells exhibiting primary cell wall synthesis, and an internode that had just ceased elongation and in which many cells were depositing secondary cell wall material. This is one of only a few studies specifically aimed at the identification of cell wall-related genes in grasses. Analysis identified new candidate genes for a role in primary and secondary cell wall biogenesis in grasses. The results suggest that many proteins involved in cell wall processes during normal development are also recruited during defence-related cell wall remodelling events. This work provides a platform for studies in which candidate genes will be functionally tested for involvement in cell wall-related processes, increasing our knowledge of cell wall biogenesis and its regulation in grasses. Since several grasses are currently being developed as lignocellulosic feedstocks for biofuel production, this improved understanding of grass cell wall biogenesis is timely, as it will facilitate the manipulation of traits favourable for sustainable food and biofuel production.
Stroke Assessment With Diffusional Kurtosis Imaging

Background and Purpose— Despite being the gold standard technique for stroke assessment, conventional diffusion MRI provides only partial information about tissue microstructure. Diffusional kurtosis imaging is an advanced diffusion MRI method that yields, in addition to conventional diffusion information, the diffusional kurtosis, which may help improve characterization of tissue microstructure. In particular, this additional information permits the description of white matter (WM) in terms of WM-specific diffusion metrics. The goal of this study is to elucidate possible biophysical mechanisms underlying ischemia using these new WM metrics. Methods— We performed a retrospective review of clinical and diffusional kurtosis imaging data of 44 patients with acute/subacute ischemic stroke. Patients with a history of brain neoplasm or intracranial hemorrhages were excluded from this study. Region of interest analysis was performed to measure percent change of diffusion metrics in ischemic WM lesions compared with the contralateral hemisphere. Results— Kurtosis maps exhibit distinct ischemic lesion heterogeneity that is not apparent on apparent diffusion coefficient maps. Kurtosis metrics also have significantly higher absolute percent change than complementary conventional diffusion metrics. Our WM metrics reveal an increase in axonal density and a larger decrease in the intra-axonal (Da) compared with extra-axonal diffusion microenvironment of the ischemic WM lesion. Conclusions— The well-known decrease in the apparent diffusion coefficient of WM after ischemia is found to be mainly driven by a significant drop in the intra-axonal diffusion microenvironment. Our results suggest that ischemia preferentially alters intra-axonal environment, consistent with a proposed mechanism of focal enlargement of axons known as axonal swelling or beading.
MOLECULAR AND CELLULAR BIOLOGY OF ADDICTION

Addiction to alcohol, tobacco, and illegal drugs represents a substantial burden to societies worldwide. In terms of health-related outcomes, addiction results in enormous direct medical costs, premature mortality (tobacco alone may be responsible for 450,000 deaths yearly in the United States), and disability. In terms of broader social costs, addiction results in crime, negative impacts on families, derailed lives, and personal suffering. The major categories of drugs most likely to produce addiction are psychostimulants (including cocaine and amphetamines), opiates, ethanol, nicotine, marijuana, and phencyclidine-like drugs. Understanding the molecular and cellular actions of addictive drugs is obligatory if we are to better understand pathophysiology and develop potent pharmacotherapies to treat addiction. Of course, the molecular and cellular information presented in this chapter cannot be applied directly to the behavioral expression of addiction without putting it into the context of systems level neuroscience described in other chapters. Acutely, addictive drugs are both rewarding (i.e., interpreted by the brain as intrinsically positive) and reinforcing (i.e., behaviors associated with drug use tend to be repeated). With repeated use, however, addictive drugs produce molecular changes that, within a vulnerable brain, promote continued drug-taking behavior in a manner that becomes increasingly difficult to control. The central feature of addiction is compulsive drug use—the loss of control over the apparently voluntary acts of drug seeking and drug taking. Once it has taken hold, addiction tends to follow a chronic course with periods of abstinence (that may or may not follow treatment), followed by relapse to active drug use. Even after extended periods of drug abstinence, the risk of relapse remains high. From the point of view of developing treatments, a central problem in addiction research in-
Comparison of HIV-, HBV-, HCV- and Co-Infection Prevalence between Chinese and Burmese Intravenous Drug Users of the China-Myanmar Border Region

Background Co-infection with HIV and HCV and/or HBV is highly prevalent in intravenous drug users (IDUs). Because of the proximity to the “Golden Triangle”, HIV prevalence among the IDUs is very high in the China-Myanmar border region. However, there are few studies about co-infection with HIV and HCV and/or HBV, especially in the region that belongs to Myanmar. Methods 721 IDUs, including 403 Chinese and 318 Burmese, were investigated for their HIV, hepatitis B virus (HBV), and hepatitis C virus (HCV) serological status. Statistical analysis was performed to evaluate the differences of the epidemic situation between the Chinese IDUs and the Burmese IDUs. Results Among the Chinese IDUs and the Burmese IDUs, HCV infection was the most prevalent (69.0% vs 48.1%, P<0.001), followed by HBV (51.6% vs 43.1%, P<0.05) and HIV (33.7% vs 27.0%, P>0.05). Besides, there were more HIV-HBV co-infected IDUs (20.1% vs 11.3%, P<0.005), and HIV-HCV co-infected IDUs (31.8% vs 23.9%, P<0.05) in China than in Myanmar, as well as HIV-HBV-HCV triple infection (19.1% vs 10.4%, P<0.005). Conclusion Co-infection with HIV and HCV and/or HBV is highly prevalent among the IDUs in the China-Myanmar border region. The HIV epidemic appears to be in a downward trend, compared with previous reports. However, all infections were more prevalent among the Chinese IDUs than among the Burmese.
PHYSICAL ACTIVITY OF CHILDREN WITH DEVELOPMENTAL COORDINATION DISORDER IN THE PRESENCE OF ATTENTION DEFICIT HYPERACTIVITY DISORDER: DOES GENDER MATTER?

Baerg, S. , Cairney, J., Hay, J., Rempel, L. and Faught, B.E. (2009). Physical Activity of Children with Developmental Coordination Disorder in the Presence of Attention Deficit Hyperactivity Disorder: Does Gender Matter? Brock University, St. Catharines, Ontario, CANADA. Children with Developmental Coordination Disorder (DCD) have difficulties in motor coordination. Attention-deficit hyperactive disorder (ADHD) is considered the condition most co-morbid with DCD at approximately 50%. Children with DCD are generally less physically active (PA) than their peers, while children with ADHD are often considered more physically active. It is not known if the physical activity patterns of children with DCD-ADHD resemble those of children with primarily DCD or that of their healthy peers. The primary objective of this research was to contrast physical activity patterns between children with DCD, DCD-ADHD, and healthy controls. Since boys are generally reported as more physically active than girls, a secondary objective was to determine if gender moderated the association between groups and physical activity. A sample of males (n=66) and females (n=44) were recruited from the Physical Health Activity Study Team (PHAST) longitudinal study. The Movement Assessment Battery for Children (2 Ed.) was used to identify probable cases of DCD, and Connor's Revised Parent Rating ScaleShort Version to identify ADHD. Subjects (mean age=12.8±.4 yrs) were allocated to three groups; DCD (n=32), DCD-ADHD (n=30) and control (n=48). Physical activity was monitored for seven days with the Actical® accelerometer (activity count, step count and energy expenditure). Children completed the Participation Questionnaire (PQ) during the in-school session of data collection for the PHAST study. Height, weight and body mass index (BMI) were also determined. Analysis of variance showed significant group differences for activity count (F(2,56)=5.36, p=. 007) and PQ (F(2,44 )=6. 71, p=. 003) in males, while a significant group difference for step count (F(2,37)=3.55, p=. 04) was found in females. Post hoc comparison tests (Tukey) identified significantly lower PQ and activity count between males with OCD and controls (p=.004) and males with DCD-ADHD and controls (p=.003). Conversely, females with DCD-ADHD had significantly more step counts than their controls (p=.01). Analysis of covariance demonstrated a gender by DCD groups negative interaction for males (activity count) (F(2,92):;:3.11, p=. 049) and a positive interaction for females (step count) (F(1,92)=4.92, p=. 009). Hyperactivity in females with DCD-ADHD appears to contribute to more physical activity, whereas DCD may contribute to decreased activity in males with DCD and DCDADHD. Further research is needed to examine gender differences in physical activity within the context of DCD and ADHD.
Effect of modifiers on structural and optical properties of Titania (TiO2) nanoparticles

A simple process is presented for the preparation of TiO2 nanoparticles by Co-precipitation method. This process is relatively cheaper and by using different variation we can control particle size and shape. TiCl4 was used as primary precursor along with Na2CO3 for synthesis of Rutile nanoparticles. Synthesis was done with and without modifier. Structural characterizations of samples were performed by using X-ray diffraction (XRD) and scanning electron microscopy (SEM). Results from these techniques confirmed the formation of single phase rutile nanoparticles. For compositional analysis EDX was employed. We observed the reduction in Band gap, in case of sample modified and then compare with other sample. This reduction in band Gap was very important to enhance the photocatalytic and electrical properties.
Inferring Chord Sequence Meanings via Lyrics: Process and Evaluation

We improve upon our simple approach for learning the “associational meaning” of chord sequences from lyrics based on contingency statistics induced over a set of lyrics with chord annotations. Specifically, we refine this process by using word alignment tools developed for statistical machine translation, and we also use a much larger set of chord annotations. In addition, objective evaluation measures are included. Thus, this work validates a novel application of lexicon induction techniques over parallel corpora to a domain outside of natural language learning. To confirm the associations commonly attributed to major versus minor chords (i.e., happy and sad, respectively), we compare the inferred word associations against synonyms reflecting this dichotomy. To evaluate meanings associated with chord sequences, we check how often tagged chords occur in songs labeled with the same overall meaning.
Multivariable analysis of predictive factors related to outcome at 6 months after intra-arterial thrombolysis for acute ischemic stroke.

BACKGROUND AND PURPOSE Recent reports have suggested that a rapid assessment of pretreatment residual cerebral blood flow (CBF) could be used to optimize selection criteria for thrombolysis in patients with acute ischemic stroke to improve clinical outcome. We investigated retrospectively residual CBF and other clinical factors related to outcome at 6 months after intra-arterial thrombolysis by using multivariable analysis. METHODS Seventy-six patients received intra-arterial thrombolysis within 6 hours of symptom onset. The multiple regression method was used to analyze associations between the modified Rankin scale (MRS) at 6 months after treatment and clinical factors including age, infarction type, duration of ischemia, dose of urokinase, degree of recanalization, hemorrhage, National Institutes of Health Stroke Scale score (NIHSSS), and residual CBF evaluated by pretreatment single-photon emission-computed tomography; these values were assessed with the use of the regional-to-cerebellar activity (R/CE) ratio of ischemic region to cerebellum and asymmetry index. RESULTS MRS at 6 months was good (0 to 3) in 65% and poor (4 to 6) in 35%. Factors significantly related to MRS at 6 months were R/CE ratio (P<0.0001), NIHSSS at baseline and the following day (P<0.0001), cardioembolic infarction (P=0.0014), age (P=0.0074), and recanalization grade (P=0. 007). NIHSSS of >20, R/CE ratio of <0.35, cardioembolic infarction, incomplete recanalization (grade <3), and older age (>75 years) were determined to be significant independent predictors of poor outcome. CONCLUSIONS The residual CBF, neurological score at baseline and the following day, age, and recanalization grade correlated significantly with long-term outcome. The NIHSSS of >20 and R/CE ratio of <0.35 were determined to be significant independent predictors of poor outcome by multivariable analysis.
Realizing a fault-tolerant embedded controller on distributed real-time systems

Advances in real-time, embedded and distributed systems along with control and communication theory have catalyzed the rapid emergence of cyber-physical systems such as a self-driving car. The importance of fault-tolerance support on a cyber-physical system (CPS) has been greatly emphasized by recent research due to the nature of CPS that senses its surroundings, processes sensor data, and reacts using its actuators. In order to tackle this challenge, we proposed SAFER (System-level Architecture for Failure Evasion in Real-time Applications) in our previous work. SAFER is able to tolerate fail-stop processor and/or task failures for distributed embedded real-time systems. One of its limitations, however, is that SAFER is not capable of tolerating a failure of a processor with a dedicated connection to an actuator. This paper provides a method that relaxes this limitation by (1) deploying a small piece of hardware to avoid a dedicated connection between a processor and an actuator, (2) adding a software module that monitors and controls the hardware, and (3) enhancing the failure detection and recovery mechanisms of SAFER to support these changes. The detailed implementation and evaluation of the SAFER extension is on-going work.
TOR-dependent post-transcriptional regulation of autophagy

Regulation of autophagy is required to maintain cellular equilibrium and prevent disease. While extensive study of post-translational mechanisms has yielded important insights into autophagy induction, less is known about post-transcriptional mechanisms that could potentiate homeostatic control. In our study, we showed that the RNA-binding protein, Dhh1 in Saccharomyces cerevisiae and Vad1 in the pathogenic yeast Cryptococcus neoformans is involved in recruitment and degradation of key autophagy mRNAs. In addition, phosphorylation of the decapping protein Dcp2 by the target of rapamycin (TOR), facilitates decapping and degradation of autophagy-related mRNAs, resulting in repression of autophagy under nutrient-replete conditions. The post-transcriptional regulatory process is conserved in both mouse and human cells and plays a role in autophagy-related modulation of the inflammasome product IL1B. These results were then applied to provide mechanistic insight into autoimmunity of a patient with a PIK3CD/p110δ gain-of-function mutation. These results thus identify an important new post-transcriptional mechanism of autophagy regulation that is highly conserved between yeast and mammals.
Stability conditions and phase transition for Kalman filtering over Markovian channels

This paper investigates the stability of Kalman filtering over Gilbert-Elliott channels where the random packet drop follows a time-homogeneous two-state Markov chain whose state transition is determined by a pair of failure and recovery rates. First, we establish a relaxed condition guaranteeing peak-covariance stability described by an inequality in terms of the spectral radius of the system matrix and transition probabilities of the Markov chain. We show that this condition can be rewritten as a linear matrix inequality feasibility problem. Next, we prove that the peak-covariance stability implies mean-square stability, if the system matrix has no defective eigenvalues on the unit circle. This implication holds for any random packet drop process, and is thus not restricted to Gilbert-Elliott channels. We prove that there exists a critical curve in the failure-recovery rate plane, below which the Kalman filter is mean-square stable and above is unstable for some initial values. Finally, a lower bound for this critical failure rate is obtained making use of the relationship we establish between the two stability criteria, based on an approximate relaxation of the system matrix.
Lag Analysis of Genetic Networks in the Cell Cycle of Budding Yeast

The recent emergence of whole-genome expression data requires a novel computational method to efficiently extract biological information from the large-scale data. The typical method for extracting information about genetic networks is cluster analysis and Fourier analysis of gene-expression patterns [2, 3, 4]. These analyses have uncovered some of the genetic networks. However, in order to comprehend all of the genetic networks in a variety of biological processes, it is necessary to develop computational methods from various viewpoints. Here we propose a computational time-series analysis to infer gene-regulatory networks from whole-genome expression data.
Potential pitfalls of healthcare performance indicators

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Sex-differential and non-specific effects of routine vaccinations in a rural area with low vaccination coverage: an observational study from Senegal.

BACKGROUND We examined the potential sex-differential and non-specific effects of bacille Calmette-Guérin (BCG), diphtheria-tetanus-pertussis (DTP) and measles vaccine (MV) in a rural area of Senegal. METHODS The 4133 children born in the area between 1996 and 1999 were included in the study. Vaccinations were provided at three health centres. Vaccine information was collected through 3-monthly home visits. The survival analysis compared the effects of BCG and DTP according to the following sequence of vaccinations: BCG-first, BCG+DTP1-first, or DTP1-first. We compared DTP and MV between 9 and 24 months of age, as 9 months is the minimum age for MV. RESULTS At 12 months the vaccination coverage was 44%, 46% and 9%, respectively, for BCG, DTP1 and MV. Most children received BCG+DTP1-first and this combination was associated with a significantly lower mortality rate ratio (MRR) of 0.69 (0.53-0.89) compared with unvaccinated children. There was no benefit for children receiving BCG-first or DTP1-first. The female-male MRR was 0.79 (0.64-0.96) among unvaccinated children, but was significantly inversed with 1.45 (1.00-2.10) for children receiving DTP vaccination (test of homogeneity, p=0.006). Children who had received DTP simultaneously with MV or DTP after MV had significantly higher mortality (MRR=2.59 [1.32-5.07]) compared with children having MV-only as their most recent vaccination. After 9 months, the female-male MRR was 0.61 (0.31-1.19) for measles-vaccinated children but remained 1.54 (1.03-2.31) for DTP-vaccinated children who had not received MV (p=0.01). CONCLUSIONS The sequence of routine vaccinations is important for the overall impact on child survival and these vaccines are associated with sex-differential effects.