Miracle-dz/UniFAR-FTUs huggingface dataset:
Comprehensive analysis of CRP, CFH Y402H and environmental risk factors on risk of neovascular age-related macular degeneration

Purpose To examine if the gene encoding C-reactive protein (CRP), a biomarker of inflammation, confers risk for neovascular age-related macular degeneration (AMD) in the presence of other modifiers of inflammation, including body mass index (BMI), diabetes, smoking, and complement factor H (CFH) Y402 genotype. Additionally we examined the degree to which CRP common variation was in linkage disequilibrium (LD) within our cohort. Methods We ascertained 244 individuals from 104 families where at least one member had neovascular AMD, and a sibling had normal maculae and was past the age of the index patient’s diagnosis of neovascular AMD. We employed a direct sequencing approach to analyze the 5′-promoter region as well as the entire coding region and the 3′-untranslated region of the CRP gene. CFH Y402 genotype data was available for all participants. Lifestyle and medical factors were obtained via administration of a standardized questionnaire. The family-based association test, haplotype analysis, McNemar’s test, and conditional logistic regression were used to determine significant associations and interactions. Haploview was used to calculate the degree of LD (r2) between all CRP variants identified. Results Six single nucleotide polymorphisms (SNPs; rs3091244, rs1417938, rs1800947, rs1130864, rs1205, and rs3093068) comprised one haplotype block of which only rs1130864 and rs1417938 were in high LD (r2=0.94). SNP rs3093068 was in LD but less so with rs3093059 (r2=0.83), which is not part of the haplotype block. Six SNPs made up six different haplotypes with ≥ 5% frequency, none of which were significantly associated with AMD risk. No statistically significant association was detected between any of the nine common variants in CRP and neovascular AMD when considering disease status alone or when controlling for smoking exposure, BMI, diabetes, or CFH genotype. Significant interactions were not found between CRP genotypes and any of the risk factors studied. No novel CRP variation was identified. Conclusions We provide evidence that if elevated serum/plasma levels of CRP are associated with neovascular AMD, it is likely not due to genetic variation within CRP, but likely due to variations in some other genetic as well as epidemiological factors.
Bi-directional Attention with Agreement for Dependency Parsing

We develop a novel bi-directional attention model for dependency parsing, which learns to agree on headword predictions from the forward and backward parsing directions. The parsing procedure for each direction is formulated as sequentially querying the memory component that stores continuous headword embeddings. The proposed parser makes use of {\it soft} headword embeddings, allowing the model to implicitly capture high-order parsing history without dramatically increasing the computational complexity. We conduct experiments on English, Chinese, and 12 other languages from the CoNLL 2006 shared task, showing that the proposed model achieves state-of-the-art unlabeled attachment scores on 6 languages.
A Regional Reduction in Ito and IKACh in the Murine Posterior Left Atrial Myocardium Is Associated with Action Potential Prolongation and Increased Ectopic Activity

Background The left atrial posterior wall (LAPW) is potentially an important area for the development and maintenance of atrial fibrillation. We assessed whether there are regional electrical differences throughout the murine left atrial myocardium that could underlie regional differences in arrhythmia susceptibility. Methods We used high-resolution optical mapping and sharp microelectrode recordings to quantify regional differences in electrical activation and repolarisation within the intact, superfused murine left atrium and quantified regional ion channel mRNA expression by Taqman Low Density Array. We also performed selected cellular electrophysiology experiments to validate regional differences in ion channel function. Results Spontaneous ectopic activity was observed during sustained 1Hz pacing in 10/19 intact LA and this was abolished following resection of LAPW (0/19 resected LA, P<0.001). The source of the ectopic activity was the LAPW myocardium, distinct from the pulmonary vein sleeve and LAA, determined by optical mapping. Overall, LAPW action potentials (APs) were ca. 40% longer than the LAA and this region displayed more APD heterogeneity. mRNA expression of Kcna4, Kcnj3 and Kcnj5 was lower in the LAPW myocardium than in the LAA. Cardiomyocytes isolated from the LAPW had decreased Ito and a reduced IKACh current density at both positive and negative test potentials. Conclusions The murine LAPW myocardium has a different electrical phenotype and ion channel mRNA expression profile compared with other regions of the LA, and this is associated with increased ectopic activity. If similar regional electrical differences are present in the human LA, then the LAPW may be a potential future target for treatment of atrial fibrillation.
Detection of Moving Cast Shadows for Object Segmentation

To prevent moving shadows being misclassified as moving objects or parts of moving objects, this paper presents an explicit method for detection of moving cast shadows on a dominating scene background. Those shadows are generated by objects moving between a light source and the background. Moving cast shadows cause a frame difference between two succeeding images of a monocular video image sequence. For shadow detection, these frame differences are detected and classified into regions covered and regions uncovered by a moving shadow. The detection and classification assume plane background and a nonnegligible size and intensity of the light sources. A cast shadow is detected by temporal integration of the covered background regions while subtracting the uncovered background regions. The shadow detection method is integrated into an algorithm for two-dimensional (2-D) shape estimation of moving objects from the informative part of the description of the international standard ISO/MPEG-4. The extended segmentation algorithm compensates first apparent camera motion. Then, a spatially adaptive relaxation scheme estimates a change detection mask for two consecutive images. An object mask is derived from the change detection mask by elimination of changes due to background uncovered by moving objects and by elimination of changes due to background covered or uncovered by moving cast shadows. Results obtained with MPEG-4 test sequences and additional sequences show that the accuracy of object segmentation is substantially improved in presence of moving cast shadows. Objects and shadows are detected and tracked separately.
Impact of Interventions Targeting Unhealthy Alcohol Use in Kenya on HIV Transmission and AIDS-Related Deaths

Background HIV remains a major cause of preventable morbidity and mortality in Kenya. The effects of behaviors that accompany unhealthy alcohol consumption are a pervasive risk factor for HIV transmission and progression. Our objective was to estimate the portion of HIV infections attributable to unhealthy alcohol use and to evaluate the impact of hypothetical interventions directed at unhealthy alcohol use on HIV infections and deaths. Methods We estimated outcomes over a time horizon of 20 years using a computer simulation of the Kenyan population. This computer simulation integrates a compartmental model of HIV transmission with a mechanistic model of HIV progression that was previously validated in sub-Saharan Africa. Integration of the transmission and progression models allows simultaneous consideration of alcohol's effects on HIV transmission and progression (e.g., lowering antiretroviral adherence may increase transmission risk by elevating viral load, and may simultaneously increase progression by increasing the likelihood of AIDS). The simulation considers important aspects of heterogeneous sexual mixing patterns, including assortativeness of partners by age and activity level, age-discordant relationships, and high activity subgroups. Outcomes included number of new HIV infections, number of AIDS deaths, and infectivity (number of new infections per infected person per year). Results Our model estimated that the effects of behaviors accompanying unhealthy alcohol consumption are responsible for 13.0% of new HIV infections in Kenya. An alcohol intervention with effectiveness similar to that observed in a published randomized controlled trial of a cognitive-behavioral therapy-based intervention in Kenya (45% reduction in unhealthy alcohol consumption) could prevent nearly half of these infections, reducing their number by 69,858 and reducing AIDS deaths by 17,824 over 20 years. Estimates were sensitive to assumptions with respect to the magnitude of alcohol's underlying effects on condom use, antiretroviral therapy adherence, and sexually transmitted infection prevalence. Conclusions A substantial number of new HIV infections in Kenya are attributable to unhealthy alcohol use. An alcohol intervention with the effectiveness observed in a published randomized controlled trial has the potential to reduce infections over 20 years by nearly 5% and avert nearly 18,000 deaths related to HIV.
The Saddlepoint Approximation: A Unification of Exponents, Dispersions and Moderate Deviations

This paper presents a saddlepoint approximation of the the random-coding union bound of Polyanskiy et al. for i.i. d. random coding over discrete memoryless channels. The approximation can be computed efficiently, and is shown to be asymptotically tight and recover several known asymptotic results at both fixed and varying rates, unifying the regimes of error exponents, second-order coding rates, and moderate deviations. For fixed rates, novel exact-asymptotics expressions are specified to within a multiplicative 1+o(1) term. A numerical example is provided for which the saddlepoint approximation is remarkably accurate even at short block lengths.
Adhesion to and invasion of HeLa cells by pathogenic Escherichia coli carrying the afa-3 gene cluster are mediated by the AfaE and AfaD proteins, respectively

The afa-3 gene cluster, expressed by uropathogenic and diarrhea-associated Escherichia coli strains, determines the formation of an afimbrial adhesive sheath composed of the AfaD and AfaE-III adhesins. The adherence to HeLa cells by recombinant HB101 strains producing both or only one of these two adhesins was investigated. Ultrastructural analyses of the interaction and gentamicin protection assays showed adherence to HeLa cells by HB101 producing both the AfaD and AfaE-III proteins and internalization of a subpopulation of the bacteria into the cells. The interactions of HeLa cells either with HB101 mutants producing AfaD or AfaE-III or with polystyrene beads coated with purified His6-tagged AfaD or His6-tagged AfaE-III proteins were studied. These experiments demonstrated that AfaE-III allows binding to HeLa cells and that AfaD mediates the internalization of the adherent bacteria. Ultrastructural analyses of the interaction of His6-AfaD-gold complexes with HeLa cells confirmed that AfaD is able to bind to the HeLa cell surface and indicated that it penetrates the cells via clathrin vesicles. These data demonstrate that the afa gene cluster is unique among bacteria, as alone it encodes both adhesion to and invasion of epithelial cells.
Synchronous replication initiation in novel Mycobacterium tuberculosis dnaA cold‐sensitive mutants

The genetic aspects of oriC replication initiation in Mycobacterium tuberculosis are largely unknown. A two‐step genetic screen was utilized for isolating M. tuberculosis dnaA cold‐sensitive (cos) mutants. First, a resident plasmid expressing functional dnaA integrated at the attB locus in dnaA null background was exchanged with an incoming plasmid bearing a mutagenized dnaA gene. Next, the mutants that were defective for growth at 30°C, a non‐permissive temperature, but resumed growth and DNA synthesis when shifted to 37°C, a permissive temperature, were subsequently selected. Nucleotide sequencing analysis located mutations to different regions of the dnaA gene. Modulation of the growth temperatures led to synchronized DNA synthesis. The dnaA expression under synchronized DNA replication conditions continued to increase during the replication period, but decreased thereafter reflecting autoregulation. The dnaAcos mutants at 30°C were elongated suggesting that they may possibly be blocked during the cell division. The DnaA115 protein is defective in its ability to interact with ATP at 30°C, but not at 37°C. Our results suggest that the optimal cell cycle progression and replication initiation in M. tuberculosis requires that the dnaA promoter remains active during the replication period and that the DnaA protein is able to interact with ATP.
Masticatory Deficiency as a Risk Factor for Cognitive Dysfunction

Several studies have demonstrated that chewing helps to maintain cognitive functions in brain regions including the hippocampus, a central nervous system (CNS) region vital for memory and learning. Epidemiological studies suggest that masticatory deficiency is associated with development of dementia, which is related to spatial memory deficits especially in older animals. The purpose of this paper is to review recent work on the effects of masticatory impairment on cognitive functions both in experimental animals and humans. We show that several mechanisms may be involved in the cognitive deficits associated with masticatory deficiency. The epidemiological data suggest a positive correlation between masticatory deficit and Alzheimer's disease. It may be concluded that chewing has important implications for the mechanisms underlying certain cognitive abilities.
THE HESSIAN OF THE DISTANCE FROM A SURFACE IN THE HEISENBERG GROUP

Given a smooth surface S in the Heisenberg group, we compute the Hessian of the function measuring the Carnot Charatheodory distance from S in terms of the mean curvature of S and of an "imaginary curvature" which was introduced in [2] in order to find the geodesies which are metrically normal to S. Explicit formulae arc given when S is a plane or the metric sphere.
Grading of vegetative cuttings using computer vision

This paper reports on recent progress in the development of system to group populations of vegetative cuttings. The system is required to assign a classification to cuttings such that they appear uniform after a growing period using single two-dimensional monochrome images. We have developed a fast segmentation technique that is able to measure plant features and a supervised learning scheme that learns a mapping from the features to a scalar classification. We report results based on segmentation of over 2000 geranium cuttings. The system is able to process images at 2 Hz and has an accuracy of over 90%. Both metrics exceed human performance.
FASER: fast analysis of soft error susceptibility for cell-based designs

This paper is concerned with statically analyzing the susceptibility of arbitrary combinational circuits to single event upsets that are becoming a significant concern for reliability of commercial electronics. For the first time, a fast and accurate methodology FASER based on static, vector-less analysis of error rates due to single event upsets in general combinational circuits is proposed. Accurate models are based on STA-like pre-characterization methods, and logical masking is computed via binary decision diagrams with circuit partitioning. Experimental results indicate that FASER achieves good accuracy compared to the SPICE-based simulation method. The average error across the benchmark circuits is 12% at over 90,000X speed-up. The accuracy can be further improved by more accurate cell library characterization. The run-time for ISCAS '85 benchmark circuits ranges from 10 to 120 minutes. The estimated bit error rate (BER) for the ISCAS'85 benchmark circuits implemented in the 100nm CMOS technology is about 10-5 FIT
Early diagnosis of typhoid fever by nested PCR for flagellin gene of Salmonella enterica serotype Typhi

Background & objectives: Typhoid fever caused by Salmonella Typhi continues to be a major health problem in spite of the use of antibiotics and the development of newer antibacterial drugs. Inability to make an early laboratory diagnosis and resort to empirical therapy, often lead to increased morbidity and mortality in cases of typhoid fever. This study was aimed to optimize a nested PCR for early diagnosis of typhoid fever and using it as a diagnostic tool in culture negative cases of suspected typhoid fever. Methods: Eighty patients with clinical diagnosis of typhoid fever and 40 controls were included in the study. The blood samples collected were subjected to culture, Widal and nested PCR targeting the flagellin gene of S. Typhi. Results: The sensitivity of PCR on blood was found to be 100 per cent whereas the specificity was 76.9 per cent. The positive predictive value (PPV) of PCR was calculated to be 76.9 per cent with an accuracy of 86 per cent. None of the 40 control samples gave a positive PCR. Interpretation & conclusions: Due to its high sensitivity and specificity nested PCR can be used as a useful tool to diagnose clinically suspected, culture negative cases of typhoid fever.
Investigations into Audiovestibular Manifestations in Patients with Psoriatic Arthritis

Objective. Although psoriatic arthritis (PsA) is a common chronic inflammatory rheumatic disease, little is known about audiovestibular impairment in this condition. We aimed to establish whether audiovestibular manifestations were present in patients with PsA. Methods. A set of 60 consecutive patients who fulfilled the Moll and Wright criteria for PsA and 60 matched controls were studied. During the period of recruitment, individuals were excluded who had a history of cardiovascular disease, cerebrovascular complications, peripheral artery disease, renal insufficiency, syphilis, Meniere disease and other vestibular syndromes, infections involving the inner ear, barotrauma, or were in treatment with ototoxic drugs. Results. Most patients with PsA were men (63%). The mean age at the time of our study was 52.9 years and the mean age at the onset of symptoms was 33 years. Thirty-six (60%) of the 60 patients showed abnormal hearing loss in the audiogram compared to only 5 (8.3%) of the 60 controls (p < 0.001). Values of audiometric tests (pure-tone average and speech reception threshold) yielded significant differences between patients and controls (p < 0.001). The audiogram disclosed a bilateral and symmetrical sensorineural hearing loss (SNHL) in PsA with predominant pattern of high frequency SNHL in patients with PsA (46.7%) compared to controls (8.3%, p < 0.001). Patients with PsA exhibited abnormal vestibular tests more commonly than controls. A significantly increased frequency of abnormal computerized dynamic posturography with a predominant vestibular loss pattern was also observed in patients (23.3%) compared to controls (0%, p < 0.001). Conclusion. Our current study demonstrates strong evidence for inner ear damage in patients with PsA.
Gender gap in computer science programs from Costa Rican Public universities

There is evidence that women tend to be underrepresented in computer science programs (CS) in many countries. Based on this fact, we analyzed the gender situation in Costa Rica finding that this situation also applies to the four public universities in the country. Furthermore, similar to the case of the U.S., the percentage of women graduating from CS programs from such universities is decreasing. Based on previous studies, we attempt to explain the gender gap in Costa Rican public universities, and present recommendations to reduce it.
Experimental study of starvation and flow behavior in grease-lubricated EHD contact

This paper describes an experimental study of starvation and flow behavior in grease-lubricated elastohydrodynamic contact. Rolling tests were conducted with four grease samples with different thickeners and base oils in a conventional ball-on-disk test rig. The EHL central film thickness was determined with SLIM, the Spacer Layer Imaging Method, and grease flow around the conjunction and the flow pattern on the track of the disk specimen were observed with CCD cameras. The grease track included some thickener deposited on the track and a corrugated fingerlike flow pattern outward from the center of the track. It was found that the flow pattern varied with grease type and test conditions, and that the average interval between fingers decreased with the entrainment speed. At higher speeds, inlet starvation occurred and the finger pattern was deformed and gradually ruptured. The speed of the finger-loss was higher than the speed at which starvation started. It was also found that the starvation speed was greater with greases having lower apparent viscosity at lower shear rate and higher apparent viscosity at high shear rate. This implied that the replenishment and entrainment of the greases depended on the viscosity characteristics of the greases.
Minor sounds of major importance-prosodic manipulation of synthetic backchannels in Swedish Åsa Wallers

Prosody plays a big role in the human speech and is used for expressing emotions and attitudes in addition to the lexical words. This study looks at the possibility to use prosody in expressing attitudes with backchannels, such as /oh/, /m/, /uhu/ etc. In the study, two monosyllabic backchannels, /a/ and /m/, were chosen, created synthetically and manipulated systematically with regards to the prosodic properties pitch, peak position, and duration. Each stimulus was put in a context, and the task was for the participants to choose among five answer alternatives a suitable interpretation of the backchannel. The results show that the meaning of a backchannel mainly changes with the peak position property, but interaction effects of the combination with pitch and duration could also be seen. Some stimuli have received fairly unambiguous results, which is an indication that they sound natural and are easy to interpret. This is a positive result for the continuous research of usage of backchannels in spoken dialogue systems.
An analysis of the block error probability performance of iterative decoding

Asymptotic iterative decoding performance is analyzed for several classes of iteratively decodable codes when the block length of the codes N and the number of iterations I go to infinity. Three classes of codes are considered. These are Gallager's regular low-density parity-check (LDPC) codes, Tanner's generalized LDPC (GLDPC) codes, and the turbo codes due to Berrou et al. It is proved that there exist codes in these classes and iterative decoding algorithms for these codes for which not only the bit error probability P/sub b/, but also the block (frame) error probability P/sub B/, goes to zero as N and I go to infinity.