Miracle-dz/UniFAR-FTUs huggingface dataset:
Serum Soluble Interleukin-2 Receptor is Increased in Malnourished and Immunosuppressed Patients With Gastric and Colorectal Cancer: Possible Influence of Myeloid-Derived Suppressor Cells

Background Soluble IL-2 receptor (sIL-2R) is the circulating form of a membrane receptor localized on lymphoid and some tumor cells; its biological function is not completely understood. Methods Serum levels of sIL-2R in blood samples taken from 51 cancer patients (21 gastric and 30 colorectal) and 18 healthy volunteers were measured and found to be significantly higher in the patients. Results Concentrations were significantly inversely correlated to nutritional parameters, including total protein and short turnover proteins such as prealbumin, retinol binding protein and transferrin, as well as to the stimulation index, which is a classical parameter of cell-mediated immunity. Concentrations were significantly positively correlated to neutrophil count and inversely to lymphocyte count. Significantly elevated levels of circulating myeloid-derived suppressor cells (MDSCs) were found in patients; this was significantly correlated to sIL-2R levels. Conclusions Increased production of sIL-2R correlated with systemic inflammation, nutritional impairment and inhibition of cell-mediated immunity, and thus may be involved in immunological mechanisms inducing cancer cachexia. The same factors also appear to relate closely to induction of MDSCs.
Environmental influences on maize-Aspergillus flavus interactions and aflatoxin production

Since the early 1960s, the fungal pathogen Aspergillus flavus (Link ex Fr.) has been the focus of intensive research due to the production of carcinogenic and highly toxic secondary metabolites collectively known as aflatoxins following pre-harvest colonization of crops. Given this recurrent problem and the occurrence of a severe aflatoxin outbreak in maize (Zea mays L.), particularly in the Southeast U.S. in the 1977 growing season, a significant research effort has been put forth to determine the nature of the interaction occurring between aflatoxin production, A. flavus, environment and its various hosts before harvest. Many studies have investigated this interaction at the genetic, transcript, and protein levels, and in terms of fungal biology at either pre- or post-harvest time points. Later experiments have indicated that the interaction and overall resistance phenotype of the host is a quantitative trait with a relatively low heritability. In addition, a high degree of environmental interaction has been noted, particularly with sources of abiotic stress for either the host or the fungus such as drought or heat stresses. Here, we review the history of research into this complex interaction and propose future directions for elucidating the relationship between resistance and susceptibility to A. flavus colonization, abiotic stress, and its relationship to oxidative stress in which aflatoxin production may function as a form of antioxidant protection to the producing fungus.
The Preparation and Properties of Bioactive Composites Based on Modification Bioactive Glass and Poly(Lactide-Co-Glycolide)

PLGA/bioactive glass composites were prepared as promising bone-repairing materials. The bioactive glass was fabricated by Sol-gel method. Surface Modification was done to improve the phase compatibility between polymer and the inorganic phase. PLGA/bioactive glass composites were successfully prepared via solution dispersion method. Composites films with different content of bioactive glass were obtained. The mechanical properties of composites were characterized by the three-point-bending test and composites films were investigated by in vitro bioactive test. These results indicate that the fractions of bioactive glass in composites produce no significant influence on mechanical properties. Compared to pure PLGA film the PLGA/bioactive glass composites demonstrate greater capability to induce the formation of apatite particles on the film surface.
Role of endothelial lipase in plasma HDL levels in a murine model of hypertriglyceridemia.

AIM Hypertriglyceridemia is the most common cause of low plasma high-density lipoprotein cholesterol (HDL-C) levels; however, the correlation between high triglyceride (TG) and low HDL-C remains unclear. Endothelial lipase (EL) is a determinant of plasma HDL levels. We investigated the role of EL in HDL metabolism in a murine model of acute hypertriglyceridemia. METHODS AND RESULTS To establish TG-dominant hyperlipidemia, EL-/- and wild-type (WT) mice were injected with Poloxamer-407 (P-407, 0.5 g/kg, i.p.). A single injection of P-407 resulted in a marked increase in plasma TG and cholesterol levels together with a decrease in HDL-C levels. Although plasma TG levels were similar in EL-/- and WT mice after P-407 injection, HDL-C levels were 80% higher and the HDL particle size was significantly larger in EL-/- mice than in WT mice. P-407 treatment inhibited plasma lipoprotein lipase activity and EL phospholipase activity, without decreasing their expressions. Adenovirus-mediated overexpression of EL in the liver reduced plasma HDL-C levels in both normo- and hyperlipidemic mice, while overexpression of catalytically inactive EL reduced HDL-C levels in hyperlipidemic mice. Cell culture experiments revealed that both catalytically active and inactive EL promoted cellular HDL uptake to the same extent. CONCLUSION EL regulates plasma HDL levels in mice in the normolipidemic as well as the acute hypertriglyceridemic state. EL can modulate plasma HDL-CHOL levels through both its lipolytic and ligand-binding functions in hypertriglyceridemic mice, while lipolytic activity appears to be the main determinant for its effects on HDL metabolism in normolipidemic mice.
A Multivariate Approach for Interpreting Treadmill Exercise Tests in Coronary Artery Disease

SUMMARY To determine the value of a multivariate approach for the analysis of the treadmill exercise tolerance test (ETT), 237 patients referred for evaluation of chest pain who underwent a standard Bruce protocol ETT and coronary arteriography were studied. Predictive value of a positive ETT was 0.78 (43/55) using 1.0-1.9 mm ST segment depression criterion, 0.97 (59/61) using > 2.0 mm ST segment depression. When the 1.0-1.9 mm ST criterion was combined with peak systolic blood pressure-heart rate product (double product) < 23,000, exercise duration less than 6 minutes, and ST depression for greater than 3 minutes into recovery, predictive value improved to 0.89 in 18 patients with any two of the above. Predictive value for multivessel disease was also improved using non-ST criteria. Predictive value of a negative ETT for absence of coronary artery disease was 0.60 (29/48), and was 0.86 (12/14) if double product was > 30,000. Presence of chest pain during ETT did not improve predictive value of any type of test. Digitalis ingestion in 33 patients was not associated with decreased predictive value of a positive test. These data suggest that the predictive value of both positive and negative ETT in a symptomatic population can be improved with a multivariate approach.
An RNA-Seq Transcriptome Analysis of Histone Modifiers and RNA Silencing Genes in Soybean during Floral Initiation Process

Epigenetics has been recognised to play vital roles in many plant developmental processes, including floral initiation through the epigenetic regulation of gene expression. The histone modifying proteins that mediate these modifications involve the SET domain-containing histone methyltransferases, JmjC domain-containing demethylase, acetylases and deacetylases. In addition, RNA interference (RNAi)-associated genes are also involved in epigenetic regulation via RNA-directed DNA methylation and post-transcriptional gene silencing. Soybean, a major crop legume, requires a short day to induce flowering. How histone modifications regulate the plant response to external cues that initiate flowering is still largely unknown. Here, we used RNA-seq to address the dynamics of transcripts that are potentially involved in the epigenetic programming and RNAi mediated gene silencing during the floral initiation of soybean. Soybean is a paleopolyploid that has been subjected to at least two rounds of whole genome duplication events. We report that the expanded genomic repertoire of histone modifiers and RNA silencing genes in soybean includes 14 histone acetyltransferases, 24 histone deacetylases, 47 histone methyltransferases, 15 protein arginine methyltransferases, 24 JmjC domain-containing demethylases and 47 RNAi-associated genes. To investigate the role of these histone modifiers and RNA silencing genes during floral initiation, we compared the transcriptional dynamics of the leaf and shoot apical meristem at different time points after a short-day treatment. Our data reveal that the extensive activation of genes that are usually involved in the epigenetic programming and RNAi gene silencing in the soybean shoot apical meristem are reprogrammed for floral development following an exposure to inductive conditions.
Comparisons of Properties of Tandem Repeats Associated with Beteen Diabetes Genes and Non-Diabetes Disease Genes

Tandem repeats (TRs) are associated with disease genes, play an important role in evolution and are important in genomic organization and function. Much research has been done on descriptions of properties of tandem repeats, such as copy-number, period, etc, and correlation between mutations within tandem repeats and disease. This project aims to detect some differences which may exist within the features of different tandem repeats as-associated with disease in human whole-genome. The features of tandem repeats associated with diabetes genes were compared to the counterparts of non- diabetes disease genes by comparisons of chromosome properties; chromosome 12 was detected as a representative of all human 24 chromosomes. A database, TRbase, to study the associations between disease genes and previously uncharacterized tandem repeats was ex-tended to whole human genomes. It was found that the percentage match and indels (insets and deletions) of TRs of diabetes genes were significantly different to the non-diabetes disease genes.
Identifying the Age Cohort Responsible for Transmission in a Natural Outbreak of Bordetella bronchiseptica

Identifying the major routes of disease transmission and reservoirs of infection are needed to increase our understanding of disease dynamics and improve disease control. Despite this, transmission events are rarely observed directly. Here we had the unique opportunity to study natural transmission of Bordetella bronchiseptica – a directly transmitted respiratory pathogen with a wide mammalian host range, including sporadic infection of humans – within a commercial rabbitry to evaluate the relative effects of sex and age on the transmission dynamics therein. We did this by developing an a priori set of hypotheses outlining how natural B. bronchiseptica infections may be transmitted between rabbits. We discriminated between these hypotheses by using force-of-infection estimates coupled with random effects binomial regression analysis of B. bronchiseptica age-prevalence data from within our rabbit population. Force-of-infection analysis allowed us to quantify the apparent prevalence of B. bronchiseptica while correcting for age structure. To determine whether transmission is largely within social groups (in this case litter), or from an external group, we used random-effect binomial regression to evaluate the importance of social mixing in disease spread. Between these two approaches our results support young weanlings – as opposed to, for example, breeder or maternal cohorts – as the age cohort primarily responsible for B. bronchiseptica transmission. Thus age-prevalence data, which is relatively easy to gather in clinical or agricultural settings, can be used to evaluate contact patterns and infer the likely age-cohort responsible for transmission of directly transmitted infections. These insights shed light on the dynamics of disease spread and allow an assessment to be made of the best methods for effective long-term disease control.
Engineering Transcriptional Regulator Effector Specificity using Computational Design and In Vitro Rapid Prototyping: Developing a Vanillin Sensor

The pursuit of circuits and metabolic pathways of increasing complexity and ro-bustness in synthetic biology will require engineering new regulatory tools. Feedback control based on relevant molecules, including toxic intermediates and environmental signals, would enable genetic circuits to react appropriately to changing conditions. In this work, variants of qacR, a tetR family repressor, were generated by computational protein design and screened in a cell-free transcription-translation (TX-TL) system for responsiveness to a new targeted effector. The modified repressors target vanillin, a growth-inhibiting small molecule found in lignocellulosic hydrolysates and other industrial processes. Promising candidates from the in vitro screen were further characterized in vitro and in vivo in a gene circuit. The screen yielded two qacR mutants that respond to vanillin both in vitro and in vivo. We believe this process, a combination of the generation of variants coupled with in vitro screening, can serve as a framework for designing new sensors for other target compounds.
Assessment of CBC Changes in Breast Cancer Patients Following Treatment with 5-Flourouracil, Adriamycin and Cyclophosphamide (FAC-Protocol) and Adriamycin and Cyclophosphamide (AC-Protocol)

Objective: FAC (5 fluorouracil, Adriamycin and cyclophosphamide) and AC (Adriamycin and cyclophosphamide) protocols have significant anti-tumor activity in patients with breast cancer. Our objective was to evaluate the CBC changes in patients undergoing FAC and AC protocols. Methodology: A comparative retrospective study was performed to determine CBC changes in breast cancer patients following 5-Flourouracil, Adriamycin and Cyclophosphamide (FAC-Protocol) and Adriamycin and cyclophosphamide (ACProtocol) among 150 breast cancer patients following 4 cycles of respective protocols. Marital status, surgical history, stages, diagnosis and receptor status were also determined. The parameters under observation were hemoglobin, platelets, MCV, MCHC, RBC’s, WBC’s, monocytes, lymphocytes, eosinophils and neutrophils. Data was analyzed using SPSS. Results: FAC and AC protocol influenced the values of CBC in breast cancer patients in different patterns. A mild decrease in the Hemoglobin level and a significant decrease in the value of RBC’s and significant increase in the level of MCV was observed in the study population after 4 cycles of both FAC and AC protocols of chemotherapy where most of the parameters such as platelets, MCV, Monocytes, Neutrophils, Eosinophils, Lymphocytes and WBCs remained in the normal range except hemoglobin, MCHC and RBCs by the end of 4th cycle of the therapy. Conclusion: No significant difference was observed with the CBC changes in both protocols. A frequent investigation of CBC parameters and careful selection of chemotherapy protocol should be done in patients who are prone to CBC
Selection and characterization of fluoroquinolone-resistant mutants of Campylobacter jejuni using enrofloxacin.

Significant levels of fluoroquinolone resistance were obtained in Campylobacterjejuni isolates after an unique step of selection using enrofloxacin. An Asp90-to-Asn and a Thr86-to-Ile change in the gyrase subunit GyrA were found associated with a low (MIC < or = 8 /microg/ml) or a high (MIC > or = 16 microg/ml) level of resistance to ciprofloxacin, respectively. An association of both mutations conferred a higher level of resistance (MIC > or = 128 microg/ml). Further steps of selection increased the MICs of fluoroquinolones but did not result in a multiple antibiotic resistance phenotype. The Thr86-to-Ile change was found to confer different levels of resistance, pointing out other mechanisms of resistance. However, sequencing revealed no mutation in gyrB, and several attempts did not enable any amplification of the parC gene coding for topoisomerase IV, suggesting an absence of this secondary target in C. jejuni. In addition, no difference in the major outer membrane protein expression was found among the isolates. Furthermore, the use of the recently identified efflux pump inhibitor Phe-Arg-beta-naphthylamide did not result in a significant decrease of fluoroquinolone MICs or change in the frequency of isolation of enrofloxacin-resistant mutants, and thus appears ineffective against fluoroquinolone-resistant C. jejuni isolates. Results obtained during ciprofloxacin accumulation studies confirmed that efflux probably plays a minor role in fluoroquinolone resistance of C. jejuni.
A supramolecular assembly formed by influenza A virus genomic RNA segments

The influenza A virus genome consists of eight viral RNAs (vRNAs) that form viral ribonucleoproteins (vRNPs). Even though evidence supporting segment-specific packaging of vRNAs is accumulating, the mechanism ensuring selective packaging of one copy of each vRNA into the viral particles remains largely unknown. We used electron tomography to show that the eight vRNPs emerge from a common ‘transition zone’ located underneath the matrix layer at the budding tip of the virions, where they appear to be interconnected and often form a star-like structure. This zone appears as a platform in 3D surface rendering and is thick enough to contain all known packaging signals. In vitro, all vRNA segments are involved in a single network of intermolecular interactions. The regions involved in the strongest interactions were identified and correspond to known packaging signals. A limited set of nucleotides in the 5′ region of vRNA 7 was shown to interact with vRNA 6 and to be crucial for packaging of the former vRNA. Collectively, our findings support a model in which the eight genomic RNA segments are selected and packaged as an organized supramolecular complex held together by direct base pairing of the packaging signals.
Effects of a robot-mediated locomotor training on EMG activation in healthy and SCI subjects

The robot-mediated locomotor training in paraplegic subjects was recently introduced for gait recovery. The objectives of the present work were 1) to study the changes in the muscular recruitment after locomotion rehabilitation using a robotic system in SCI subjects and 2) to compare muscular recruitment in two different conditions of subject-robot cooperation.
A fast layout algorithm for visual video summaries

We created an improved layout algorithm for automatically generating visual video summaries reminiscent of comic book pages. The summaries are comprised of images from the video that are sized according to their importance. The algorithm performs a global optimization with respect to a layout cost function that encompasses features such as the number of resized images and the amount of whitespace in the presentation. The algorithm creates summaries that: always fit exactly into the requested area, are varied by containing few rows with images of the same size, and have little whitespace at the end of the last row. The layout algorithm is fast enough to allow the interactive resizing of the summaries and the subsequent generation of a new layout.
Image-Based Environmental Monitoring Sensor Application Using an Embedded Wireless Sensor Network

This article discusses the experiences from the development and deployment of two image-based environmental monitoring sensor applications using an embedded wireless sensor network. Our system uses low-power image sensors and the Tenet general purpose sensing system for tiered embedded wireless sensor networks. It leverages Tenet's built-in support for reliable delivery of high rate sensing data, scalability and its flexible scripting language, which enables mote-side image compression and the ease of deployment. Our first deployment of a pitfall trap monitoring application at the James San Jacinto Mountain Reserve provided us with insights and lessons learned into the deployment of and compression schemes for these embedded wireless imaging systems. Our three month-long deployment of a bird nest monitoring application resulted in over 100,000 images collected from a 19-camera node network deployed over an area of 0.05 square miles, despite highly variable environmental conditions. Our biologists found the on-line, near-real-time access to images to be useful for obtaining data on answering their biological questions.
Anisotropic Elastography for Local Passive Properties and Active Contractility of Myocardium from Dynamic Heart Imaging Sequence

Major heart diseases such as ischemia and hypertrophic myocardiopathy are accompanied with significant changes in the passive mechanical properties and active contractility of myocardium. Identification of these changes helps diagnose heart diseases, monitor therapy, and design surgery. A dynamic cardiac elastography (DCE) framework is developed to assess the anisotropic viscoelastic passive properties and active contractility of myocardial tissues, based on the chamber pressure and dynamic displacement measured with cardiac imaging techniques. A dynamic adjoint method is derived to enhance the numerical efficiency and stability of DCE. Model-based simulations are conducted using a numerical left ventricle (LV) phantom with an ischemic region. The passive material parameters of normal and ischemic tissues are identified during LV rapid/reduced filling and artery contraction, and those of active contractility are quantified during isovolumetric contraction and rapid/reduced ejection. It is found that quasistatic simplification in the previous cardiac elastography studies may yield inaccurate material parameters.
Online stereo calibration using FPGAs

Online stereo calibration is useful in many situations where the cameras are moving relative to each other. The motion can either be intentional, as in an active stereo head, or due to vibrations, heat etc. which is commonly found in automotive applications. However, most approaches for finding the essential matrix relating the two cameras are computationally very expensive and, hence, this problem must be addressed. In this paper, we suggest deferring a large portion of the image processing onto a field programmable gate array (FPGA) since most operations can be heavily parallelized. The specific algorithm chosen to find point correspondences between the left and the right images is SIFT, which has the advantage of producing a very small number of outliers. Having few outliers is important as computing the essential matrix from point correspondences is an inherently unstable problem, particularly in the case where the cameras are nearly parallel. We present a system, which computes the computationally intensive parts of SIFT (Gaussian pyramid, Sobel etc) using an FPGA. The host computer then uses the resulting point correspondences to estimate the essential matrix with the help of a reduced model of the camera setup. On-line stereo calibration at frame rate (60Hz) is then possible without excessively loading the host computer.