Miracle-dz/UniFAR-FTUs huggingface dataset:
Retinal Microvascular Abnormalities and Risk of Renal Failure in Asian Populations

Background Retinal microvascular signs may provide insights into the structure and function of small vessels that are associated with renal disease. We examined the relationship of retinal microvascular signs with both prevalent and incident end-stage renal disease (ESRD) in a multi-ethnic Asian population. Methods A total of 5763 subjects (aged ≥40 years) from two prospective population-based studies (the Singapore Malay Eye Study and the Singapore Prospective Study) were included for the current analysis. Retinopathy was graded using the modified Airlie House classification system. Retinal vascular parameters were measured using computer-assisted programs to quantify the retinal vessel widths (arteriolar and venular caliber) and retinal vascular network (fractal dimension). Data on ESRD was obtained by record linkage with the ESRD cases registered by National Registry of Diseases Office, Singapore. Multi-variable adjusted regression analyses were performed to assess the associations of baseline retinal vascular parameters and prevalent and incident ESRD. Results At baseline, 21(0.36%) persons had prevalent ESRD. During a median follow-up of 4.3 years, 33 (0.57%) subjects developed ESRD. In our analyses, retinopathy was associated with prevalent ESRD (multi-variable adjusted odds ratio [OR], 3.21, 95% confidence interval [CI]: 1.28–8.05) and incident ESRD (multi-variable adjusted hazard ratio [HR], 2.51, 95%CI: 1.14–5.54). This association was largely seen in person with diabetes (HR, 2.60, 95%CI: 1.01–6.66) and not present in persons without diabetes (HR, 1.65, 95%CI: 0.14–18.98). Retinal arteriolar caliber, retinal venular caliber and retinal vascular fractal dimension were not associated with ESRD. Conclusion Retinopathy signs in persons with diabetes are related to an increased risk of ESRD; however, other microvascular changes in the retina are not associated with ESRD.
A New Linear Programming Approach to Decoding Linear Block Codes

In this paper, we propose a new linear programming formulation for the decoding of general linear block codes. Different from the original formulation given by Feldman, the number of total variables to characterize a parity-check constraint in our formulation is less than twice the degree of the corresponding check node. The equivalence between our new formulation and the original formulation is proven. The new formulation facilitates to characterize the structure of linear block codes, and leads to new decoding algorithms. In particular, we show that any fundamental polytope is simply the intersection of a group of the so-called minimum polytopes, and this simplified formulation allows us to formulate the problem of calculating the minimum Hamming distance of any linear block code as a simple linear integer programming problem with much less auxiliary variables. We then propose a branch-and-bound method to compute a lower bound to the minimum distance of any linear code by solving a corresponding linear integer programming problem. In addition, we prove that, for the family of single parity-check (SPC) product codes, the fractional distance and the pseudodistance are both equal to the minimum distance. Finally, we propose an efficient algorithm for decoding SPC product codes with low complexity and maximum-likelihood (ML) decoding performance.
Promoter Hypermethylation-Related Reduced Somatostatin Production Promotes Uncontrolled Cell Proliferation in Colorectal Cancer

Background Somatostatin (SST) has anti-proliferative and pro-apoptotic effects. Our aims were to analyze and compare the SST expression during normal aging and colorectal carcinogenesis at mRNA and protein levels. Furthermore, we tested the methylation status of SST in biopsy samples, and the cell growth inhibitory effect of the SST analogue octreotide in human colorectal adenocarcinoma cell line. Methods Colonic samples were collected from healthy children (n1 = 6), healthy adults (n2 = 41) and colorectal cancer patients (CRCs) (n3 = 34) for SST mRNA expression analysis, using HGU133 Plus2.0 microarrays. Results were validated both on original (n1 = 6; n2 = 6; n3 = 6) and independent samples ((n1 = 6; n2 = 6; n3 = 6) by real-time PCR. SST expressing cells were detected by immunohistochemistry on colonic biopsy samples (n1 = 14; n2 = 20; n3 = 23). The effect of octreotide on cell growth was tested on Caco-2 cell line. SST methylation percentage in biopsy samples (n1 = 5; n2 = 5; n3 = 9) was defined using methylation-sensitive restriction enzyme digestion. Results In case of normal aging SST mRNA expression did not alter, but decreased in cancer (p<0.05). The ratio of SST immunoreactive cells was significantly higher in children (0.70%±0.79%) compared to CRC (0%±0%) (p<0.05). Octreotide significantly increased the proportion of apoptotic Caco-2 cells. SST showed significantly higher methylation level in tumor samples (30.2%±11.6%) compared to healthy young individuals (3.5%±1.9%) (p<0.05). Conclusions In cancerous colonic mucosa the reduced SST production may contribute to the uncontrolled cell proliferation. Our observation that in colon cancer cells octreotide significantly enhanced cell death and attenuated cell proliferation suggests that SST may act as a regulator of epithelial cell kinetics. The inhibition of SST expression in CRC can be epigenetically regulated by promoter hypermethylation.
Modification of the Susceptibility of Gram-Negative Rods Producing ESβLS to β-Lactams by the Efflux Phenomenon

The production of β-lactamases is the most important mechanism of Gram-negative rod resistance to β-lactams. Resistance to ceftazidime and cefepime in clinical isolates of Enterobacteriaceae (especially ESβL-positive E. coli and K. pneumoniae) and P. aeruginosa is life-threatening. However, all strains of the above mentioned species possess chromosomally encoded RND efflux pump systems in addition to β-lactamase production. The main goal of this study was to assess the role of efflux pump systems in cefepime and/or ceftazidime resistant phenotypes of ESβL-positive clinical strains of Enterobacteriaceae and P. aeruginosa. The influence of the efflux pump inhibitor PAβN on the minimum inhibitory concentration (MIC) values of tested cephalosporins was species-dependent. Generally, a significant reduction (at least four-fold) of β-lactam MICs was observed in the presence of PAβN only in the case of P. aeruginosa clinical isolates as well as the ESβL-producing transformant PAO1161 ΔampC. The usage of this agent resulted in the restoration of susceptibility to cefepime and/or ceftazidime in the majority of the P. aeruginosa ESβL-positive strains with low and moderate resistance to the above cephalosporins. Moreover, an outer membrane permeabilizing effect in the presence of PAβN was identified. Strain-dependent β-lactamase leakage upon PAβN or β-lactam treatment was demonstrated. The most important observation was the restoration of susceptibility of P. aeruginosa WUM226 to cefepime (MIC decrease from 32 to 4 mg/L) and ceftazidime (MIC decrease from 128 to 4 mg/L) in the presence of PAβN, which occurred despite an almost complete lack of β-lactamase leakage from bacterial cells. In conclusion, these data indicate that RND efflux pumps can modify the susceptibility to β-lactams in Gram-negative rods producing ESβLs. However, this phenomenon occurs only in P. aeruginosa strains and was not observed among E. coli and K. pneumoniae strains, representing the Enterobacteriaceae family.
Black-Tailed Prairie Dogs, Cattle, and the Conservation of North America’s Arid Grasslands

Prairie dogs (Cynomys spp.) have been eliminated from over 95% of their historic range in large part from direct eradication campaigns to reduce their purported competition with cattle for forage. Despite the longstanding importance of this issue to grassland management and conservation, the ecological interactions between cattle and prairie dogs have not been well examined. We address this issue through two complementary experiments to determine if cattle and prairie dogs form a mutualistic grazing association similar to that between prairie dogs and American bison. Our experimental results show that cattle preferentially graze along prairie dog colony edges and use their colony centers for resting, resembling the mutualistic relationship prairie dogs have with American bison. Our results also show that prairie dog colonies are not only an important component of the grassland mosaic for maintaining biodiversity, but also provide benefits to cattle, thereby challenging the long-standing view of prairie dogs as an undesirable pest species in grasslands.
Inclusion of Bacillus amyloliquefaciens strain TOA5001 in the diet of broilers suppresses the symptoms of coccidiosis by modulating intestinal microbiota.

Coccidiosis is an intestinal parasitic infection and one of the most prevalent and economically damaging diseases of chickens. Furthermore, coccidia-induced mucogenesis promotes secondary colonization by Clostridium perfringens, a major pathogen of chickens that causes necrotic enteritis. Our previous work found that supernatant of a culture of Bacillus amyloliquefaciens strain TOA5001 (BA) inhibited the growth of C. perfringens on Gifu anaerobic broth medium. Accordingly, we evaluated the effectiveness of dietary BA administration in inhibiting C. perfringens colonization of the intestine in broilers that were experimentally infected with coccidia. Ten healthy broilers from a BA-supplemented (2 × 105 colony-forming units/g of feed) broiler group and 10 from a non-treated group were challenged with Eimeria tenella and E. maxima (5000 oocysts of each species/chick) at 28 days old. At 36 days old, five chicks from each group were slaughtered, whereas the remaining five in each group were killed at 49 days old. Dietary BA administration into Eimeria-challenged birds reduced coccidial symptoms such as intestinal lesions. It also modified the cecal microbiota through suppressing C. perfringens and E. coli colonization, and inducing domination of Faecalibacterium prausnitzii, the Lactobacillus group and unknown Lachnospiraceae genera by bacterial DNA-based metagenome analyses. B. amyloliquefaciens TOA5001 supplementation suppressed the symptoms of coccidiosis by modulating cecal microbiota in Eimeria-challenged broilers.
Effects of Vendor and Genetic Background on the Composition of the Fecal Microbiota of Inbred Mice

The commensal gut microbiota has been implicated as a determinant in several human diseases and conditions. There is mounting evidence that the gut microbiota of laboratory mice (Mus musculus) similarly modulates the phenotype of mouse models used to study human disease and development. While differing model phenotypes have been reported using mice purchased from different vendors, the composition and uniformity of the fecal microbiota in mice of various genetic backgrounds from different vendors is unclear. Using culture-independent methods and robust statistical analysis, we demonstrate significant differences in the richness and diversity of fecal microbial populations in mice purchased from two large commercial vendors. Moreover, the abundance of many operational taxonomic units, often identified to the species level, as well as several higher taxa, differed in vendor- and strain-dependent manners. Such differences were evident in the fecal microbiota of weanling mice and persisted throughout the study, to twenty-four weeks of age. These data provide the first in-depth analysis of the developmental trajectory of the fecal microbiota in mice from different vendors, and a starting point from which researchers may be able to refine animal models affected by differences in the gut microbiota and thus possibly reduce the number of animals required to perform studies with sufficient statistical power.
Molecular and Biochemical Analysis of Chalcone Synthase from Freesia hybrid in Flavonoid Biosynthetic Pathway

Chalcone synthase (CHS) catalyzes the first committed step in the flavonoid biosynthetic pathway. In this study, the cDNA (FhCHS1) encoding CHS from Freesia hybrida was successfully isolated and analyzed. Multiple sequence alignments showed that both the conserved CHS active site residues and CHS signature sequence were found in the deduced amino acid sequence of FhCHS1. Meanwhile, crystallographic analysis revealed that protein structure of FhCHS1 is highly similar to that of alfalfa CHS2, and the biochemical analysis results indicated that it has an enzymatic role in naringenin biosynthesis. Moreover, quantitative real-time PCR was performed to detect the transcript levels of FhCHS1 in flowers and different tissues, and patterns of FhCHS1 expression in flowers showed significant correlation to the accumulation patterns of anthocyanin during flower development. To further characterize the functionality of FhCHS1, its ectopic expression in Arabidopsis thaliana tt4 mutants and Petunia hybrida was performed. The results showed that overexpression of FhCHS1 in tt4 mutants fully restored the pigmentation phenotype of the seed coats, cotyledons and hypocotyls, while transgenic petunia expressing FhCHS1 showed flower color alteration from white to pink. In summary, these results suggest that FhCHS1 plays an essential role in the biosynthesis of flavonoid in Freesia hybrida and may be used to modify the components of flavonoids in other plants.
Hybrid Group Decoding for Scalable Video over MIMO-OFDM Downlink Systems

We propose a scalable video broadcasting scheme over MIMO-OFDM systems. The scalable video source layers are channel encoded and modulated into independent signal streams, which are then transmitted from the allocated antennas in certain time-frequency blocks. Each receiver employs the successive group decoder to decode the signal streams of interest by treating other signal streams as interference. The transmitter performs adaptive coding and modulation, and transmission antenna and subcarrier allocation, based on the rate feedback from the receivers. We also propose a hybrid receiver that switches between the successive group decoder and the MMSE decoder depending on the rate. Extensive simulations are provided to demonstrate the performance gain of the proposed group-decoding-based scalable video broadcasting scheme over the one based on the conventional MMSE decoding.
Tropical Forest Fragmentation Affects Floral Visitors but Not the Structure of Individual-Based Palm-Pollinator Networks

Despite increasing knowledge about the effects of habitat loss on pollinators in natural landscapes, information is very limited regarding the underlying mechanisms of forest fragmentation affecting plant-pollinator interactions in such landscapes. Here, we used a network approach to describe the effects of forest fragmentation on the patterns of interactions involving the understory dominant palm Astrocaryum mexicanum (Arecaceae) and its floral visitors (including both effective and non-effective pollinators) at the individual level in a Mexican tropical rainforest landscape. Specifically, we asked: (i) Does fragment size affect the structure of individual-based plant-pollinator networks? (ii) Does the core of highly interacting visitor species change along the fragmentation size gradient? (iii) Does forest fragment size influence the abundance of effective pollinators of A. mexicanum? We found that fragment size did not affect the topological structure of the individual-based palm-pollinator network. Furthermore, while the composition of peripheral non-effective pollinators changed depending on fragment size, effective core generalist species of pollinators remained stable. We also observed that both abundance and variance of effective pollinators of male and female flowers of A. mexicanum increased with forest fragment size. These findings indicate that the presence of effective pollinators in the core of all forest fragments could keep the network structure stable along the gradient of forest fragmentation. In addition, pollination of A. mexicanum could be more effective in larger fragments, since the greater abundance of pollinators in these fragments may increase the amount of pollen and diversity of pollen donors between flowers of individual plants. Given the prevalence of fragmentation in tropical ecosystems, our results indicate that the current patterns of land use will have consequences on the underlying mechanisms of pollination in remnant forests.
Using Data-Driven Model-Brain Mappings to Constrain Formal Models of Cognition

In this paper we propose a method to create data-driven mappings from components of cognitive models to brain regions. Cognitive models are notoriously hard to evaluate, especially based on behavioral measures alone. Neuroimaging data can provide additional constraints, but this requires a mapping from model components to brain regions. Although such mappings can be based on the experience of the modeler or on a reading of the literature, a formal method is preferred to prevent researcher-based biases. In this paper we used model-based fMRI analysis to create a data-driven model-brain mapping for five modules of the ACT-R cognitive architecture. We then validated this mapping by applying it to two new datasets with associated models. The new mapping was at least as powerful as an existing mapping that was based on the literature, and indicated where the models were supported by the data and where they have to be improved. We conclude that data-driven model-brain mappings can provide strong constraints on cognitive models, and that model-based fMRI is a suitable way to create such mappings.
Evaluation of reinforced concrete structural durability in the post-occupation phase - A case study in Novo Hamburgo/RS

Researches on building performance have been developed over time. The Brazilian Performance Standard - NBR 15575 - deals with the issues of durability applied to residential buildings, establishing criteria and parameters to classify the systems into minimum, intermediate and higher performance levels. In relation to the service life, studies are also associated with the building’s structural durability, in which the technical specifications and quality of materials, construction systems, building process, use and maintenance of the building are important factors for better performance. In order to evaluate the structural durability over the years, a case study was conducted in a building designed to meet the higher level established in the Brazilian Performance Standard, with service life of 75 years in the structural project, through the non-de-structive surface hardness of concrete test by using a Schmidt hammer and semi-de-structive carbonation tests. The superficial hardness test was conducted on a concrete column following the procedures of NBR 7584, while the carbonation samples were collected in 3 concrete columns in which a phenolphthalein solution was sprayed to ob-serve the alkalinity of the samples. For all tests, three different heights were considered. The concrete testing hammer indicated an average surface hardness of approximately 50 MPa, and for carbonation tests, it was noted that the concrete was not carbonated at a depth of 5mm. So, the criteria of service life could be considered attended.
Performance analysis of path rerouting algorithms for handoff control in mobile ATM networks

This paper studies the effects of user mobility and handoff path rerouting on the traffic distributions in a mobile network environment. In mobile ATM networks, extra traffic load may be added to network links due to user mobility and handoff path rerouting. This requires higher network link capacity and possible topology reengineering in order to support the same quality of service (QoS) for mobile services. To capture the dynamic variations in mobile ATM networks, we propose to use a flow model. The model represents the mobile-generated traffic as a set of stochastic flows over a set of origin-destination (OD) pairs. The user mobility is defined by transfer probabilities of the flows and the handoff path rerouting algorithm is modeled by a transformation between the routing functions for traffic flows. The analysis shows that user mobility may cause temporal variations as well as smoothing effects on the network traffic. Using the flow network model, typical handoff path rerouting algorithms are evaluated through both analytical and experimental approaches. The evaluation methodology can be used for either redesigning the network topology for a given path rerouting algorithm or selecting a path rerouting algorithm for a given network topology under a specific mobile service scenario.
Where Do the Poorest Go to Seek Outpatient Care in Bangladesh: Hospitals Run by Government or Microfinance Institutions?

Introduction Health programs implemented by microfinance institutions (MFIs) aim to benefit the poor, but whether these services reach the poorest remains uncertain. This study intended to investigate the socioeconomic distribution of patients in hospitals operated by microfinance institutions (i.e. MFI hospitals) in Bangladesh and compare the differences with public hospitals to determine if the programs were consistent with their pro-poor mandate. Methods In this cross-sectional study, we used the convenience sampling method to conduct an interviewer-assisted questionnaire survey among 347 female outpatients, with 170 in public hospitals and 177 in MFI hospitals. Independent variables were patient characteristics categorized into predisposing factors (age, education, marital status, family size), enabling factors (microcredit membership, household income) and need factors (self-rated health, perceived needs for care). We employed Generalized Estimating Equations (GEE) to evaluate how these factors contributed to MFI hospital use. Results Use of MFI hospitals was associated with microcredit membership over 5 years (OR=2.9, p<.01), moderately poor household (OR=4.09, p<.001), non-poor household (OR=7.34, p<.01) and need for preventive care (OR=3.4, p<.01), compared with public hospitals. Combining membership and income, we found microcredit members had a higher tendency towards utilization but membership effect pertained to the non- and moderately-poor. Compared with the group who were non-members and the poorest, microcredit members who were non-poor had the highest likelihood (OR=7.46, p<.001) to visit MFI hospitals, followed by members with moderate income (OR=6.91, p<.001) and then non-members in non-poor households (OR=4.48, p<.01). Those who were members but the poorest had a negative association (OR=0.42), though not significant. Despite a higher utilization of preventive services in MFI hospitals, expenditure there was significantly higher. Conclusion Inequity was more pronounced in MFI hospitals than public ones. MFI hospitals appeared to miss their target population. We suggest that MFIs reorganize health programs toward primary health care to make care equitable and universally accessible. This study holds practical implications for governments, development agencies and microfinance practitioners working at the grassroots level.