Miracle-dz/UniFAR-FTUs huggingface dataset:
Elucidation of Operon Structures across Closely Related Bacterial Genomes

About half of the protein-coding genes in prokaryotic genomes are organized into operons to facilitate co-regulation during transcription. With the evolution of genomes, operon structures are undergoing changes which could coordinate diverse gene expression patterns in response to various stimuli during the life cycle of a bacterial cell. Here we developed a graph-based model to elucidate the diversity of operon structures across a set of closely related bacterial genomes. In the constructed graph, each node represents one orthologous gene group (OGG) and a pair of nodes will be connected if any two genes, from the corresponding two OGGs respectively, are located in the same operon as immediate neighbors in any of the considered genomes. Through identifying the connected components in the above graph, we found that genes in a connected component are likely to be functionally related and these identified components tend to form treelike topology, such as paths and stars, corresponding to different biological mechanisms in transcriptional regulation as follows. Specifically, (i) a path-structure component integrates genes encoding a protein complex, such as ribosome; and (ii) a star-structure component not only groups related genes together, but also reflects the key functional roles of the central node of this component, such as the ABC transporter with a transporter permease and substrate-binding proteins surrounding it. Most interestingly, the genes from organisms with highly diverse living environments, i.e., biomass degraders and animal pathogens of clostridia in our study, can be clearly classified into different topological groups on some connected components.
Minimum inhibitory concentration, pharmacokinetics/pharmacodynamics and therapeutic drug monitoring: An integrated approach for multidrug-resistant tuberculosis

Lung India • Vol 32 • Issue 4 • Jul Aug 2015 and high‐level isoniazid resistance the breakpoints were proposed to be 0.0312 mg/L and 0.125 mg/L, respectively. The susceptibility breakpoint for rifampin was proposed to be 0.0625 mg/L, for pyrazinamide 50 mg/L, for ethambutol 4.0 mg/L, and for moxifloxacin was projected as 1.0 mg/L. [7] This was followed by another study from South Africa projecting the susceptibility breakpoint for ofloxacin as 0.5 mg/L[8] using the same methods applied by Gumbo. [7] These PK/PD derived susceptibility breakpoints are now backed by clinical studies. In one such study Gene‐Xpert technology demonstrated that some rifampin resistance isolates with rpoB mutations had MICs below the standard 1.0 mg/L and these MIC values were as low as 0.125 mg/L. [9] Interestingly this observed lower MIC was very close to the one derived from PK/PD and simulation studies (0.0625 mg/L). [7] As predicted by simulation[7] these patients failed to improve on rifampin‐containing standard combination therapy. [9] Second supporting evidence comes from the study done in the Netherlands reporting isolates with a rifampin MIC of 0.25‐1.0 mg/L harboring mutation at Asp516Tyr of rpoB gene. [10]
All-directions through the wall radar imaging using a synthetic array formed by a finite number of Moving Robots

This paper introduces a new concept for all directional through the wall radar imaging using an ad hoc network of mobile transceivers. In the proposed method, instead of using a large array of transmitting and receiving antennas which usually limits the imaging of the buildings' interior from outside, a limited number of transceivers mounted on moving robots are used. As robots move, reflected signal is sampled at different positions. By applying an appropriate beam forming technique to the samples of the scattered signal, a 360o view of the building interior can be obtained with a high cross-range resolution and significantly reduce the ambiguity in the detection of the objects' positions. Applying this method enables imaging of buildings from inside which results in obtaining more accurate map of buildings' interiors.
Inhibition of endogenous TRP 1 decreases capacitative Ca 2 entry and attenuates pulmonary artery smooth muscle cell proliferation

Sweeney, Michele, Ying Yu, Oleksandr Platoshyn, Shen Zhang, Sharon S. McDaniel, and Jason X. -J. Yuan. Inhibition of endogenous TRP1 decreases capacitative Ca2 entry and attenuates pulmonary artery smooth muscle cell proliferation. Am J Physiol Lung Cell Mol Physiol 283: L144–L155, 2002. First published February 8, 2002; 10.1152/ ajplung.00412. 2001. —Pulmonary vascular medial hypertrophy due to proliferation of pulmonary artery smooth muscle cells (PASMC) greatly contributes to the increased pulmonary vascular resistance in pulmonary hypertension patients. A rise in cytosolic free Ca2 concentration ([Ca2 ]cyt) is an important stimulus for cell growth in PASMC. Resting [Ca2 ]cyt, intracellularly stored [Ca2 ], capacitative Ca2 entry (CCE), and store-operated Ca2 currents (ISOC) are greater in proliferating human PASMC than in growth-arrested cells. Expression of TRP1, a transient receptor potential gene proposed to encode the channels responsible for CCE and ISOC, was also upregulated in proliferating PASMC. Our aim was to determine if inhibition of endogenous TRP1 gene expression affects ISOC and CCE and regulates cell proliferation in human PASMC. Cells were treated with an antisense oligonucleotide (AS, for 24 h) specifically designed to cleave TRP1 mRNA and then returned to normal growth medium for 40 h before the experiments. Then, mRNA and protein expression of TRP1 was downregulated, and amplitudes of ISOC and CCE elicited by passive depletion of Ca2 from the sarcoplasmic reticulum using cyclopiazonic acid were significantly reduced in the AS-treated PASMC compared with control. Furthermore, the rate of cell growth was decreased by 50% in AS-treated PASMC. These results indicate that TRP1 may encode a store-operated Ca2 channel that plays a critical role in PASMC proliferation by regulating CCE and intracellular [Ca2 ]cyt.
The Effect of Social Support on Functional Recovery and Well‐Being in Older Adults Following Joint Arthroplasty

&NA; Projections by the U.S. Census Bureau indicate a continual rise in the population of older adults. Along with increased dependency among older adults, chronic illness and aging may have attendant social and personal concerns in the areas of health care, community health services, and quality of life. Direct and indirect costs of osteoarthritis are $120 billion per year in medical treatment and lost wages. Every year more than 300,000 knee replacements and 120,000 hip replacements are performed in the United States (Sapountzi‐Krepia et al., 2007). A large percentage of joint replacement patients have now assumed responsibility for their recovery process. This exploratory study assessed and measured social support and evaluated its impact on functional recovery and well‐being in older adults after joint arthroplasty. Although social support, associated with the covariates of “living arrangements” and “age,” demonstrated a positive relationship with perceived well‐being, no relationship was demonstrated with high or low levels of social support and functional recovery.
the effectiveness of giving pursed lips breathing therapy towards kids' oxygenation status with pneumonia

Background Pneumonia is the second most common disease that brings about death in children under five years of age in the world. It seems, Symptoms that appear in the case of Pneumonia are acute respiratory problems that need to be overcome appropriately. Objectives the aim of this research is to identify the effect of pursed lips breathing therapy through tongue blowing activity on the oxygenation status of preschoolers with Pneumonia. Method this research used quasi experimental with pre-post test group design. The sampling technique is purposive random sampling with 36 people consisting of 18 intervention groups and 18 control groups. Data were analyzed using univariate and bivariate tests (t-test) Result The results showed a significant difference between oxygenation status before and after intervention with tongue blowing therapy (PLB), namely p value= 0.045 on respiratory frequency (RR), p value = 0.037 to saturation oxygen (Sa02) and p value=0.036 on heart rate (HR). Recommendation The results of this study can add alternatives to independent nurse interventions in dealing with pediatric patients who have pneumonia or with oxygenation disorders.
Age-Related Cataract, Cataract Surgery and Subsequent Mortality: A Systematic Review and Meta-Analysis

Purpose Changes in lens may reflect the status of systemic health of human beings but the supporting evidences are not well summarized yet. We aimed to determine the relationship of age-related cataract, cataract surgery and long-term mortality by pooling the results of published population-based studies. Methods We searched PubMed and Embase from their inception till March, 2014 for population-based studies reporting the associations of any subtypes of age-related cataract, cataract surgery with all-cause mortality. We pooled the effect estimates (hazards ratios [HRs]) under a random effects model. Results Totally, we identified 10 unique population-based studies including 39,659 individuals at baseline reporting the associations of any subtypes of cataract with all-cause mortality from 6 countries. The presence of any cataract including cataract surgery was significantly associated with a higher risk of death (pooled HR: 1.43, 95% CI, 1.21, 2.02; P<0.001; I2 = 64.2%). In the meta-analysis of 9 study findings, adults with nuclear cataract were at higher risks of mortality (pooled HR: 1.55, 95% CI, 1.17, 2.05; P = 0.002; I2 = 89.2%). In the meta-analysis of 8 study findings, cortical cataract was associated with higher risks of mortality (pooled HR: 1.26, 95% CI, 1.12, 1.42; P<0.001, I2 = 29.7%). In the meta-analysis of 6 study findings, PSC cataract was associated with higher risks of mortality (pooled HR: 1.37, 95% CI, 1.04, 1.80; P = 0.03; I2 = 67.3%). The association between cataract surgery and mortality was marginally non-significant by pooling 8 study findings (pooled HR: 1.27, 95% CI, 0.97, 1.66; P = 0.08; I2 = 76.6%). Conclusions All subtypes of age-related cataract were associated with an increased mortality with nuclear cataract having the strongest association among the 3 cataract subtypes. However, cataract surgery was not significantly related to mortality. These findings indicated that changes in lens may serve as markers for ageing and systemic health in general population.
The inhibitory receptor toll interleukin-1R 8 (TIR8/IL-1R8/SIGIRR) is downregulated in chronic lymphocytic leukemia

Abstract Toll interleukin-1 receptor 8 (also known as TIR8, SIGIRR, or IL1R8) is a transmembrane receptor that inhibits inflammation. Accordingly, genetic inactivation of this protein exacerbates chronic inflammation and inflammation-associated tumors in mice. In particular, lack of TIR8 triggers leukemia progression in a mouse model of chronic lymphocytic leukemia (CLL), supporting its role as a novel tumor restrainer. The aim of this study was to measure the amount of TIR8 mRNA and protein in CLL cells, and to analyze its regulation of expression. Circulating leukemic cells expressed lower levels of TIR8 compared to normal B-lymphocytes. Treatment of CLL cells with Azacytidine restored higher levels of TIR8 suggesting that DNA methylation may be involved in modulating TIR8 expression, with implications for novel therapeutic strategies.
Dependency Parsing with Structure Knowledge

A new probability-based parsing model DPSK (Dependency Parsing with Structure Knowledge) is presented for dependency parsing. Similar to a bottom-up chart parsing algorithm, DPSK select the best dependency arc between two words in a sentence according to the probability. The arc probability depends on two kinds of information: (1) Features extracting from two words of the arc. (2) Features extracting according to arc child word and those children words of arc parent. The first kind feature information is relevant to the case grammar theory, while the second kind feature information is relevant to Context-free grammars. A Maximum Entropy model is used to train and calculate single arc probabilities. DPSK is evaluated experimentally using the dataset distributed in CoNLL 2008 share-task. An unlabelled arc score of 90.2 % is reported. This work will contribute to and stimulate other researches in the field of parsing.
A Data-Driven Clustering Approach for Fault Diagnosis

Clustering is an important approach in fault diagnosis. The dominant sets algorithm is a graph-based clustering algorithm, which defines the dominant set as a concept of a cluster. In this paper, we make an in-depth investigation of the dominant sets algorithm. As a result, we find that this algorithm is dependent on the similarity parameter in constructing the pairwise similarity matrix, and has the tendency to generate spherical clusters only. Based on the merits and drawbacks of this algorithm, we apply the histogram equalization transformation to the similarity matrices for the purpose of removing the influence of similarity parameters, and then use a density-based cluster expansion process to improve the clustering results. In experimental validation of the proposed algorithm, we use two criterions to evaluate the clustering results in order to arrive at convincing conclusions. Data clustering experiments on ten data sets and fault detection experiments on the Tennessee Eastman process demonstrate the effectiveness of the proposed algorithm.
In vitro probiotic potential of Lactobacillus spp . isolated from fermented milks

The potential of in vitro probiotic Lactobacillus spp. was evaluated in fermented milks marketed in Belo Horizonte, MG, Brazil. Of the samples analyzed, 86.7% had at least 10 6 CFU/mL of Lactobacillus spp. , complying with the Brazilian quality standards for fermented milks. Furthermore, 56.7% had minimum count ranging from 10 8 to 10 9 CFU/mL, which is in accordance with legal parameters. The remaining 43.3% would not be able to satisfactorily guarantee benefits to consumers. The amount of Lactobacillus spp. varied between batches of products, which may indicate failures in monitoring during manufacture, transport or storage. All strains of Lactobacillus spp. showed some inhibitory activity against the indicator microorganisms, being more pronounced against pathogenic microorganisms than against non-pathogenic (P<0.05). Samples of Lactobacillus spp. showed different profiles of antimicrobial susceptibility, with an occurrence of cases of multidrug resistance. All strains tested showed sensitivity to bile salts (0.3%) and resistance to gastric pH (2.0). Lactobacillus spp. of commercial fermented milks should be present in higher amounts in some brands, be resistant to bile salts and have no multiple resistance to antimicrobials.
Ginsenosides protect striatal neurons in a cellular model of Huntington's disease

Ginseng, the root of Panax ginseng C.A. Meyer (Araliaceae), is a widely used herbal medicine. Ginsenosides, the active ingredients of ginseng, are the main components responsible for many beneficial actions of ginseng. In the present study, we tested 10 different ginsenosides in the previously developed in vitro Huntington's disease (HD) assay with primary medium spiny striatal neuronal cultures (MSN) from the YAC128 HD mouse model. We found that nanomolar concentrations of ginsenoside Rb1 and Rc effectively protected YAC128 medium spiny neurons from glutamate‐induced apoptosis and that Rg5 was protective at micromolar concentration. The other seven ginsenosides tested were not effective or exerted toxic effects in MSN cultures. From further experiments, we suggested that neuroprotective effects of ginsenosides Rb1, Rc, and Rg5 could correlate with their ability to inhibit glutamate‐induced Ca2+ responses in cultured MSN. From these results we concluded that ginsenosides Rb1, Rc, and Rg5 offer a potential therapeutic choice for the treatment of HD and possibly other neurodegenerative disorders. © 2009 Wiley‐Liss, Inc.
Corticospinal Motor Neurons Are Susceptible to Increased ER Stress and Display Profound Degeneration in the Absence of UCHL1 Function

Corticospinal motor neurons (CSMN) receive, integrate, and relay cerebral cortex's input toward spinal targets to initiate and modulate voluntary movement. CSMN degeneration is central for numerous motor neuron disorders and neurodegenerative diseases. Previously, 5 patients with mutations in the ubiquitin carboxy-terminal hydrolase-L1 (UCHL1) gene were reported to have neurodegeneration and motor neuron dysfunction with upper motor neuron involvement. To investigate the role of UCHL1 on CSMN health and stability, we used both in vivo and in vitro approaches, and took advantage of the Uchl1nm3419 (UCHL1−/−) mice, which lack all UCHL1 function. We report a unique role of UCHL1 in maintaining CSMN viability and cellular integrity. CSMN show early, selective, progressive, and profound cell loss in the absence of UCHL1. CSMN degeneration, evident even at pre-symptomatic stages by disintegration of the apical dendrite and spine loss, is mediated via increased ER stress. These findings bring a novel understanding to the basis of CSMN vulnerability, and suggest UCHL1−/− mice as a tool to study CSMN pathology.
What Is Meant by “TICI”?

BACKGROUND: In 2003, Higashida et al proposed the Thrombolysis In Cerebral Infarction scale to evaluate angiographic intracranial flow. Our aim is to review how subsequently published studies define TICI. MATERIALS AND METHODS: We used the ISI Web of Knowledge and SciVerse Scopus databases to search for “TICI” and “thrombolysis in cerebral infarction” and for articles that cited the original TICI paper from January 2004 through May 2012. Articles were categorized according to their definition of the TICI categories, typically grades 0–4, with grade 2 (partial reperfusion) subdivided into 2a and 2b, and rate of contrast entry to the perfused area. In addition, we catalogued the type of redefinitions of TICI subcategory 2 and additions of new categories. RESULTS: Of 236 articles screened, 74 were included. Eight (11%) explicitly followed the TICI scale as originally defined. Thirty-seven (50%) cited Higashida but did not define their scale. Fifteen (21%) used and explained modified scales. Thirteen (18%) used the term TICI, but did not define the scale and did not cite Higashida. Eighteen (24%) specified a 2a subcategory. Nine defined grade 2a as <67% filling, 6 defined it as <50%, and 3 did not offer a percentage. Two studies added a 2c subcategory. Fifty-two (70%) used a cutoff level to define “successful reperfusion. ” Of these, 65% used TICI ≥2, 33% used TICI ≥2b, and 2% used TICI = 3. CONCLUSIONS: There is substantial variability in the definition and/or application of the TICI scale in the literature. This variability could considerably impact our understanding of results of revascularization studies.
Modelling the Texture of Paint

We present an extension to the WET & STICKY model. A method of modelling textured and shiny paint is described using bump mapping and standard illumination models. The qualities of the paint are used to supply input to the texture and lighting models. We demonstrate that a dynamic model of textured paint provides the user with valuable visual cluesfor the production of realistic painted images. We also propose further extensions which would allow the use of different lighting models for different paints, allowing for paint attributes which are unachievable either with traditional painting or with earlier forms of electronic painting.
Parameter-free subsequences time series clustering with various-width clusters

In time series mining, one of the interesting tasks that attract many researchers is time series clustering which is classified into two main categories. Whole time series clustering considers how to cluster multiple time series, and the other one is Subsequence Time Series (STS) clustering, a clustering of subparts or subsequences within a single time series. Deplorably, STS clustering is not preferable even though it had widely been used as a subroutine in various mining tasks, e.g., rule discovery, anomaly detection, or classification, due to the recent finding a decade ago that STS clustering problem can produce meaningless results. There have been numerous attempts to resolve this problem but seemed to be unsuccessful. Until the two most recent attempts, they seem to accomplish in producing meaningful results; however, their approaches do need some predefined constraint values, such as the width of the subsequences that are in fact quite subjective and sensitive. Thus, we propose a novel parameter-free clustering technique to eliminate this problem by utilizing a motif discovery algorithm and some statistical principles to properly determine these parameters. Our experimental results from well-known datasets demonstrate the effectiveness of the proposed algorithm in selecting the proper subsequence width, and in turn leading to meaningful and highly accurate results.
We Did the Right Thing: An Intervention Analysis Approach to Modeling Intervened SARS Propagation in Singapore

In this paper, we adopt the Intervention Analysis approach to model an intervened natural process, i.e., propagation of the severe acute respiratory syndrome (SARS) in Singapore, which is affected not only by its own evolutionary history but also by the control measures taken. Using this model, the propagation trend of the epidemic and the effects of different control measures on the outcomes of this epidemic can be simulated and quantitatively analyzed. Based on the model, we have performed an evaluation and sensitivity analysis of the Singapore government's responses to this epidemic. Preliminary results have shown that the control measures taken are effective in controlling the outbreak.
Pilot allocation and receive antenna selection: A Markov decision theoretic approach

This paper considers antenna selection (AS) for packet reception at a receiver equipped with multiple antenna elements but only a single radio frequency chain. The receiver makes its AS decisions based on noisy channel estimates obtained from the training symbols (pilots). The time-correlation of the wireless channel and the results of the link-layer error checks upon data packet reception provide additional information that can be exploited for AS. This information can also be used to optimally distribute pilots among the antenna elements, so that packet loss due to selection errors is minimized. The task of the receiver, then, is to sequentially select (a) the pilot symbol allocation for channel estimation on each of the receive antennas and (b) the antenna to be used for data packet reception. The goal is to maximize the expected throughput, based on the history of allocation and selection decisions, and the corresponding noisy channel estimates and error check observations. This joint problem of pilot allocation and AS is solved as a partially observed Markov decision problem (POMDP) and the solutions yield the optimal policies that maximize the long-term expected throughput. The performance of the POMDP solution is compared with several other schemes for a 2-state Markov channel model, and it is illustrated that it outperforms the others.