Miracle-dz/UniFAR-FTUs huggingface dataset:
Performance evaluation with different mobility models for dynamic probabilistic flooding in MANETs

Broadcasting is an essential and effective data propagation mechanism, with several of important applications such as route discovery, address resolution, as well as many other network services. As data broadcasting has many advantages, also causing a lot of contention, collision, and congestion, which induces what is known as "broadcast storm problems". Broadcasting has traditionally been based on the flooding protocol, which simply overflows the network with high number of rebroadcast messages until the messages reach to all network nodes. A good probabilistic broadcasting protocol can achieve higher saved rebroadcast, low collisions and less number of relays. In this paper, we propose a dynamic probabilistic approach that dynamically fine-tunes the rebroadcasting probability according to the number of neighbour's nodes distributed in the ad hoc network for routing request packets (RREQs). The performance of the proposed approach is investigated and compared with the simple AODVand fixed probabilistic schemes using the GloMoSim network simulator under different mobility models. The performance results reveal that the improved approach is able to achieve higher saved rebroadcast and low collision as well as low number of relays than the fixed probabilistic scheme and simple AODV.
Implementation of a self-adaptive real time recommendation system using spark machine learning libraries

Real time recommendation systems have become an essential component of e-commerce web applications. With increasing volume and velocity of data handled by these applications, known as the bigdata problem, traditional recommendation systems that analyze data and update models at regular time intervals would not be able to satisfy this requirement. With the evolution of technologies for processing bigdata in real time, it has become fairly easy to implement real time recommendation systems. Stream-computing is a new computing paradigm for handling the velocity attribute of bigdata which makes it possible to develop real time bigdata applications. This paper gives the details of implementation of a real time recommendation system using Apache Spark, a widely used platform for stream computing. This system is implemented for recommending TV channels to viewers in real time. This becomes a challenging task due to continuous changes in the set of available channels and the context dependent preference of viewers. In channel recommendation scenario, characterized by its dynamic nature, volume of data, and tight time constraints, traditional approaches cannot be used. We have implemented a highly scalable TV channel recommendation system optimized for the processing of real-time data streams originating from set-top boxes. The proposed system implements a self-adaptive approach for model building. The system effectively uses distributed processing power of Apache Spark to make recommendations in real time with scalability to meet the real time constraints with increasing load. The Spark Machine Learning Libraries (Spark MLLib) provide several algorithms which were used for developing the proposed recommendation system. The large amount of data in the system is efficiently managed by the data processing method of Lambda Architecture.
Gastroesophageal reflux disease in patients with rheumatoid arthritis

Abstract Objective. Patients with rheumatoid arthritis (RA) are frequently complicated with gastric mucosal injury; however, there are few reports investigating gastroesophageal reflux disease (GERD) among patients with RA. We investigated the frequency of GERD and the correlation between GERD and the clinical characteristics of RA including patient's global assessment (PGA). Methods. Patients with RA were investigated for GERD using self-administered frequency scale for the symptoms of GERD (FSSG). The correlation between GERD and the clinical characteristics of RA was analyzed statistically. Results. Two hundred and eleven patients in Japan were investigated. The prevalence of GERD among patients with RA (24.6%) was significantly higher than that in the Japanese population (11.5%) (p < 0.001). FSSG was positively correlated with modified health assessment questionnaire (mHAQ), PGA, evaluator's global assessment (EGA) (p < 0.001), disease activity score (DAS)28-erythrocyte sedimentation rate (ESR) (p < 0.05), DAS28-C-reactive protein (CRP), simplified disease activity index (SDAI) and clinical disease activity index (CDAI) (p < 0.001). The patients with GERD showed significantly higher scores in mHAQ, PGA, EGA, tenderness joint count, DAS28-ESR, DAS28-CRP, SDAI and CDAI (p < 0.001). Furthermore, the patients with GERD showed lower remission rates based on DAS28-ESR (p < 0.05), DAS28-CRP, SDAI and CDAI (p < 0.001). Conclusion. GERD complicated with RA increases PGA and the indices of disease activity. GERD symptoms analyzed using FSSG may be desirable to avoid the overestimation as part of the total management of patients with RA.
Structure–activity relationships of fowlicidin‐1, a cathelicidin antimicrobial peptide in chicken

Cationic antimicrobial peptides are naturally occurring antibiotics that are actively being explored as a new class of anti‐infective agents. We recently identified three cathelicidin antimicrobial peptides from chicken, which have potent and broad‐spectrum antibacterial activities in vitro (Xiao Y, Cai Y, Bommineni YR, Fernando SC, Prakash O, Gilliland SE & Zhang G (2006) J Biol Chem281, 2858–2867). Here we report that fowlicidin‐1 mainly adopts an α‐helical conformation with a slight kink induced by glycine close to the center, in addition to a short flexible unstructured region near the N terminus. To gain further insight into the structural requirements for function, a series of truncation and substitution mutants of fowlicidin‐1 were synthesized and tested separately for their antibacterial, cytolytic and lipopolysaccharide (LPS)‐binding activities. The short C‐terminal helical segment after the kink, consisting of a stretch of eight amino acids (residues 16–23), was shown to be critically involved in all three functions, suggesting that this region may be required for the peptide to interact with LPS and lipid membranes and to permeabilize both prokaryotic and eukaryotic cells. We also identified a second segment, comprising three amino acids (residues 5–7) in the N‐terminal flexible region, that participates in LPS binding and cytotoxicity but is less important in bacterial killing. The fowlicidin‐1 analog, with deletion of the second N‐terminal segment (residues 5–7), was found to retain substantial antibacterial potency with a significant reduction in cytotoxicity. Such a peptide analog may have considerable potential for development as an anti‐infective agent.
Insight to the Interaction of the Dihydrolipoamide Acetyltransferase (E2) Core with the Peripheral Components in the Escherichia coli Pyruvate Dehydrogenase Complex via Multifaceted Structural Approaches*

Background: The pyruvate dehydrogenase complex produces acetyl-CoA and NADH, utilizing three protein components whose structural interactions need elucidation. Results: The E3 structure and interaction loci between E2 and E3 were determined. Conclusion: The peripheral subunit-binding domain of E2 establishes key interactions with E1 and E3. Significance: The multifaceted approach used could help delineate interaction surfaces in other 2-oxoacid dehydrogenase complexes. Multifaceted structural approaches were undertaken to investigate interaction of the E2 component with E3 and E1 components from the Escherichia coli pyruvate dehydrogenase multienzyme complex (PDHc), as a representative of the PDHc from Gram-negative bacteria. The crystal structure of E3 at 2.5 Å resolution reveals similarity to other E3 structures and was an important starting point for understanding interaction surfaces between E3 and E2. Biochemical studies revealed that R129E-E2 and R150E-E2 substitutions in the peripheral subunit-binding domain (PSBD) of E2 greatly diminished PDHc activity, affected interactions with E3 and E1 components, and affected reductive acetylation of E2. Because crystal structures are unavailable for any complete E2-containing complexes, peptide-specific hydrogen/deuterium exchange mass spectrometry was used to identify loci of interactions between 3-lipoyl E2 and E3. Two peptides from the PSBD, including Arg-129, and three peptides from E3 displayed statistically significant reductions in deuterium uptake resulting from interaction between E3 and E2. Of the peptides identified on E3, two were from the catalytic site, and the third was from the interface domain, which for all known E3 structures is believed to interact with the PSBD. NMR clearly demonstrates that there is no change in the lipoyl domain structure on complexation with E3. This is the first instance where the entire wild-type E2 component was employed to understand interactions with E3. A model for PSBD-E3 binding was independently constructed and found to be consistent with the importance of Arg-129, as well as revealing other electrostatic interactions likely stabilizing this complex.
Clinical significance of different types of p53 gene alteration in surgically treated prostate cancer

Despite a multitude of p53 immunohistochemistry (IHC) studies, data on the combined effect of nuclear p53 protein accumulation and TP53 genomic inactivation are lacking for prostate cancer. A tissue microarray including 11,152 prostate cancer samples was analyzed by p53 IHC and fluorescence in situ hybridization. Nuclear p53 accumulation was found in 10.1% of patients including 1.4% with high‐level and 8.7% with low‐level immunostaining. TP53 sequencing revealed that 17 of 22 (77%) cases with high‐level p53 immunostaining, but only 3% (1 of 31) low‐level p53 cases carried putative dominant‐negative mutations. TP53 deletions occurred in 14.8% of cancers. Both deletions and protein accumulation were linked to unfavorable tumor phenotype and prostate specific antigen (PSA) recurrence (p < 0.0001 each). The combination of both methods revealed subgroups with remarkable differences in their clinical course. Tumors with either TP53 deletion (14%) or low‐level p53 positivity (8.7%) had identical risks of PSA recurrence, which were markedly higher than in cancers without p53 alterations (p < 0.0001). Tumors with both p53 deletion and low‐level p53 positivity (1.5%) had a worse prognosis than patients with only one of these alterations (p < 0.0001). Tumors with strong p53 immunostaining or homozygous inactivation through deletion of one allele and disrupting translocation involving the second allele had the worst outcome, independent from clinical and pathological parameters. These data demonstrate a differential clinical impact of various TP53 alterations in prostate cancer. Strong p53 immunostaining—most likely accompanying dominant negative or oncogenic p53 mutation—has independent prognostic relevance and may thus represent a clinical useful molecular feature of prostate cancer.
A population-based study of hemoglobin, race, and mortality in elderly persons.

BACKGROUND Anemia is associated with increased mortality risk. The impact of mildly low hemoglobin concentration (Hb) on risk for mortality remains unclear, especially among blacks. We examined the racial differences between Hb and mortality. METHODS This was a population-based study conducted from 1993 through 2006, in a geographically defined community of Chicago, Illinois. A stratified, random sample of 1806 participants 65 years old or older and 50% black, who were participating in the Chicago Health Aging Project and underwent clinical evaluation. Mortality was ascertained using the National Death Index. Cox proportional hazard models were used to assess the independent relation of Hb to mortality risk. RESULTS The proportion of participants with anemia by World Health Organization (WHO) criteria (Hb < 13.0 g/dL for men and < 12.0 g/dL for women) was 39% among blacks, and 17% among whites. Blacks had lower mean Hb (12.6 +/- 1.5 g/dL) than did whites (13.5 +/- 1.5 g/dL). In multivariable analysis, anemia was associated with increased mortality risk in blacks (hazard ratio [HR], 1.90; 95% confidence interval [CI], 1.43-2.53) and in whites (HR, 1.85; 95% CI, 1.32-2.59). Among blacks, Hb 0-0.9 g/dL below the anemia threshold is associated with increased mortality risk compared to Hb 0-0.9 g/dL above the anemia cutoff (HR, 1.84; 95% CI, 1.21-2.79), Hb 1.1-2.0 g/dL above the anemia cutoff (HR, 1.35; 95% CI, 0.88-2.05) and Hb 2.1-3.0 g/dL above the anemia cutoff (HR, 2.24; 95% CI, 1.12-4.47). The terms for interaction between black ethnicity/race and anemia suggested that blacks did not have a statistically significant difference in mortality risk compared to whites. Subgroup analyses of interaction terms suggested that Hb 0.1-1.0 g/dL above anemia cutoff group, blacks may have lower mortality risk compared to whites in the mildly low normal ranges of Hb (p =.02). CONCLUSION Both anemia by WHO criteria and mild reductions in Hb were related to increased risk of mortality in older blacks and whites.
Ultrabithorax protein is necessary but not sufficient for full activation of decapentaplegic expression in the visceral mesoderm.

To elucidate the mechanisms by which homeotic selector (HOM) genes specify the unique features of Drosophila segments, we have analyzed the regulation of decapentaplegic (dpp), a transforming growth factor (TGF)‐beta superfamily member, and have found that the Ultrabithorax (Ubx) HOM protein directly activates dpp expression in parasegment 7 (PS7) of the embryonic visceral mesoderm. Other factors are also required, including one that appears to act through homeodomain protein binding sites and may be encoded by extradenticle (exd). The exd protein binds in a highly co‐operative manner to regulatory sequences mediating PS7‐specific dpp expression, consistent with a genetic requirement for exd function in normal visceral mesoderm expression of dpp. A second mechanism contributing to PS7 expression of dpp appears not to require Ubx protein directly, and involves a general visceral mesoderm enhancer coupled to a spatially specific repression element. Thus, even in an apparently simple case where visceral mesoderm expression of the dpp target gene mirrors that of the Ubx HOM protein, full activation by Ubx protein requires at least one additional factor. In addition, a distinct regulatory mode not directly involving Ubx protein also appears to contribute to PS7‐specific expression.
Exercise hyperventilation in patients with McArdle's disease.

This study was undertaken to determine if patients who lack muscle phosphorylase (i.e., McArdle's disease), and therefore the ability to produce lactic acid during exercise, demonstrate a normal hyperventilatory response during progressive incremental exercise. As expected these patients did not increase their blood lactate above resting levels, whereas the blood lactate levels of normal subjects increased 8- to 10-fold during maximal exercise. The venous pH of the normal subjects decreased markedly during exercise that resulted in hyperventilation. The patients demonstrated a distinct increase in ventilation with respect to O2 consumption similar to that seen in normal individuals during submaximal exercise. However their hyperventilation resulted in an increase in pH because there was no underlying metabolic acidosis. End-tidal partial pressures of O2 and CO2 also reflected a distinct hyperventilation in both groups at approximately 70-85% maximal O2 consumption. These data show that hyperventilation occurs during intense exercise, even when there is no increase in plasma [H+]. Since arterial CO2 levels were decreasing and O2 levels were increasing during the hyperventilation, it is possible that nonhumoral stimuli originating in the active muscles or in the brain elicit the hyperventilation observed during intense exercise.
Surfacing contextual hate speech words within social media

Social media platforms have recently seen an increase in the occurrence of hate speech discourse which has led to calls for improved detection methods. Most of these rely on annotated data, keywords, and a classification technique. While this approach provides good coverage, it can fall short when dealing with new terms produced by online extremist communities which act as original sources of words which have alternate hate speech meanings. These code words (which can be both created and adopted words) are designed to evade automatic detection and often have benign meanings in regular discourse. As an example, "skypes", "googles", and "yahoos" are all instances of words which have an alternate meaning that can be used for hate speech. This overlap introduces additional challenges when relying on keywords for both the collection of data that is specific to hate speech, and downstream classification. In this work, we develop a community detection approach for finding extremist hate speech communities and collecting data from their members. We also develop a word embedding model that learns the alternate hate speech meaning of words and demonstrate the candidacy of our code words with several annotation experiments, designed to determine if it is possible to recognize a word as being used for hate speech without knowing its alternate meaning. We report an inter-annotator agreement rate of K=0.871, and K=0.676 for data drawn from our extremist community and the keyword approach respectively, supporting our claim that hate speech detection is a contextual task and does not depend on a fixed list of keywords. Our goal is to advance the domain by providing a high quality hate speech dataset in addition to learned code words that can be fed into existing classification approaches, thus improving the accuracy of automated detection.
A Novel Approach to Decrease Sialic Acid Expression in Cells by a C-3-modified N-Acetylmannosamine*

Background: Inhibitors of cellular sialic acid expression offer substantial therapeutic promise for diseases associated with oversialylation. Results: 2-Acetylamino-2-deoxy-3-O-methyl-d-mannose reduces the sialic acid concentration in cells and inhibits the UDP-GlcNAc-2-epimerase/ManNAc kinase. Conclusion: Inhibition of the key enzyme of sialic acid biosynthesis by a ManNAc analog decreases cellular sialic acid expression. Significance: ManNAc analogs represent a new class of sialic acid inhibitors. Due to its position at the outermost of glycans, sialic acid is involved in a myriad of physiological and pathophysiological cell functions such as host-pathogen interactions, immune regulation, and tumor evasion. Inhibitors of cell surface sialylation could be a useful tool in cancer, immune, antibiotic, or antiviral therapy. In this work, four different C-3 modified N-acetylmannosamine analogs were tested as potential inhibitors of cell surface sialylation. Peracetylated 2-acetylamino-2-deoxy-3-O-methyl-d-mannose decreases cell surface sialylation in Jurkat cells in a dose-dependent manner up to 80%, quantified by flow cytometry and enzyme-linked lectin assays. High-performance liquid chromatography experiments revealed that not only the concentration of membrane bound but also of cytosolic sialic acid is reduced in treated cells. We have strong evidence that the observed reduction of sialic acid expression in cells is caused by the inhibition of the bifunctional enzyme UDP-GlcNAc-2-epimerase/ManNAc kinase. 2-Acetylamino-2-deoxy-3-O-methyl-d-mannose inhibits the human ManNAc kinase domain of the UDP-GlcNAc-2-epimerase/ManNAc kinase. Binding kinetics of the inhibitor and human N-acetylmannosamine kinase were evaluated using surface plasmon resonance. Specificity studies with human N-acetylglucosamine kinase and hexokinase IV indicated a high specificity of 2-acetylamino-2-deoxy-3-O-methyl-d-mannose for MNK. This substance represents a novel class of inhibitors of sialic acid expression in cells, targeting the key enzyme of sialic acid de novo biosynthesis.
Albumin‐binding of diclofenac and the effect of a site II inhibitor in the aqueous humor of cataract patients with the instillation of diclofenac

Diclofenac instillation has been used widely in cataract surgery to prevent postoperative inflammation. Since diclofenac binds strongly to albumin in the circulation, it does not have a sufficient effect on patients in whom diclofenac binds strongly to albumin in the aqueous humor. A decrease in diclofenac binding and an increase in free diclofenac levels are necessary in these patients. The binding of diclofenac to albumin was investigated in the aqueous humor. In a diclofenac binding assay with albumin in the aqueous humor of individual patients, diclofenac was extracted from aliquots of the aqueous humor, and its total levels were measured using ultra high performance liquid chromatography (UHPLC). Free diclofenac levels were measured using ultrafiltration and UHPLC. The albumin‐binding fraction of diclofenac was 0.8 or higher in the aqueous humor of some patients. Ibuprofen significantly inhibited diclofenac binding to site II of albumin in mimic aqueous humor, but not in pooled aqueous humor. This difference may have been due to the weak binding of diclofenac to site II in the pooled aqueous humor. Flurbiprofen was used instead of diclofenac. Flurbiprofen has been shown to bind more strongly than diclofenac to the same site of albumin. Thus, the inhibitory effect of ibuprofen on the binding of flurbiprofen to albumin was investigated in pooled aqueous humor. The results indicated that ibuprofen significantly inhibited the flurbiprofen binding. An effective diclofenac administration method may be established for clinical application by the instillation of an appropriate inhibitor of binding to the albumin site II. Copyright © 2014 John Wiley & Sons, Ltd.
Effects of mosapride on esophageal functions and gastroesophageal reflux

Background and Aim: A substantial number of patients with gastroesophageal reflux disease show symptomatic resistance to high‐dose proton pump inhibitors. In those cases, prokinetics are possible candidates for treatment. The aim of the present study was to determine whether mosapride, a prokinetic agent, stimulates esophageal functions, and prevents acidic and non‐acidic gastroesophageal reflux.
Effect of 3 Weeks Use of Compression Garments on Stride and Impact Shock during a Fatiguing Run

Abstract Excessive and prolonged exposure to impact acceleration during running is associated with increased injury rate. Acute use of compressive garments has been speculated to improve attenuation. However, it is unknown how longer interventions of compressive garments influence attenuation in running. 40 runners trained with compressive and placebo stockings for 3 weeks. Perception of comfort, stride parameters (rate, length) and impact acceleration (head and tibial peak acceleration, magnitude, acceleration rate and attenuation) were measured every 5 min during a fatigue run (30 min at 80% of the individual’s maximal aerobic speed). Compressive stockings reduced tibial peak acceleration and magnitude compared to placebo stockings at every minute (p<0.05) except for the initial measurement (p>0.05). Moreover, compressive stockings led to a lower rate of increase in tibial peak acceleration (14%, p<0.005) and magnitude (16%, p<0.001) as a result of the development of fatigue compared to placebo stockings (24% and 26% increase, p=0.014 and p=0.003, respectively). Similar perception of comfort was reported for both garments. Training with compressive stockings for 3 weeks reduced impact acceleration and the rate of increase in acceleration compared to placebo stockings. These findings suggest that compressive stockings may play a protective role by reducing impact accelerations during running.