Miracle-dz/UniFAR-FTUs huggingface dataset:
Transgene regulation in plants by alternative splicing of a suicide exon

Compared to transcriptional activation, other mechanisms of gene regulation have not been widely exploited for the control of transgenes. One barrier to the general use and application of alternative splicing is that splicing‐regulated transgenes have not been shown to be reliably and simply designed. Here we demonstrate that a cassette bearing a suicide exon can be inserted into a variety of open reading frames (ORFs), generating transgenes whose expression is activated by exon skipping in response to a specific protein inducer. The surprisingly minimal sequence requirements for the maintenance of splicing fidelity and regulation indicate that this splicing cassette can be used to regulate any ORF containing one of the amino acids Glu, Gln, or Lys. Furthermore, a single copy of the splicing cassette was optimized by rational design to confer robust gene activation with no background expression in plants. Thus, conditional splicing has the potential to be generally useful for transgene regulation.
Total homocysteine in patients with angiographic coronary artery disease correlates with inflammation markers

Summary Moderate hyperhomocysteinaemia is considered as an independent risk marker for cardiovascular disease and stroke. Earlier, increased homocysteine production was detected in stimulated immunocompetent cells in vitro, and several markers of inflammation like neopterin or C-reactive protein (CRP) were demonstrated as significant indicators of cardiovascular risk. The relationship between coronary artery disease (CAD), homocysteine metabolism and markers of immune activation and inflammation was investigated in a population of 1717 patients undergoing coronary angiography, recruited as participants of the LUdwigshafen RIsk and Cardiovascular Health (LURIC) study. 1325 patients (77.2%) suffered from coronary artery disease (CAD), which was was defined as the occurrence of a visible luminal narrowing (≥20% stenosis) in at least 1 of 15 coronary segments according to the classification of the American Heart Association, the remaining 392 individuals of the study population served as controls. Significant differences regarding systolic blood pressure, homocysteine, neopterin and folic acid concentrations were observed between patients and controls. Older age, decreased creatinine-clearance and higher concentrations of homocysteine and CRP were indicative for CAD. Low B-vitamin availability, therapy and the extent of immune activation strongly influenced homocysteine concentrations. Homocysteine concentrations were correlated with neopterin levels (rs =0.325, p<0.001), and hyperhomocysteinaemic patients also presented with significantly higher CRP concentrations. Homocysteine accumulation coincided with impaired renal and heart function (as reflected by ProBNP[Brain natriuretic peptide]-concentrations). We conclude that homocysteine accumulation could result from B-vitamin deficiency which is related to chronic immune activation.
Platinum-based chemotherapy in triple-negative breast cancer.

BACKGROUND Experimental data suggest that triple-negative (TN) breast cancer may have increased sensitivity to platinum-based chemotherapy but clinical data are limited. We present our long-term results with platinum-based chemotherapy for TN breast cancer. PATIENTS AND METHODS In all, 94 (17 TN), 79 (11 TN) and 155 (34 TN) patients receiving platinum-based chemotherapy in neo-adjuvant/adjuvant and advanced setting were included. Response rates and outcome were compared for TN tumours versus others. RESULTS Neo-adjuvant complete response rates were significantly higher for TN tumours (88%) than others (51%; P = 0.005). The 5-year overall survival (OS) for TN tumours following adjuvant/neo-adjuvant chemotherapy was 64% [95% confidence interval (CI) 44% to 79%] compared with 85% (95% CI 79% to 90%) for others. Five-year disease-free survival for TN tumours was 57% (95% CI 37% to 73%) compared with 72% (95% CI 64% to 78%) for others. For patients with advanced breast cancer, overall response rates were 41% for TN tumours and 31% for others (P = 0.3). Patients with TN tumours had a significantly prolonged progression-free survival of 6 months compared with 4 months for others (P = 0.05), though the OS was not significantly different between the two groups (11 versus 7 months). CONCLUSION Platinum-based chemotherapy achieves increased response rates for TN tumours, with a trend towards worse survival in early breast cancer through an improved survival in advanced disease. Prospective randomised trials are warranted.
A translation system for enabling data mining applications on GPUs

Modern GPUs offer much computing power at a very modest cost. Even though CUDA and other related recent developments are accelerating the use of GPUs for general purpose applications, several challenges still remain in programming the GPUs. Thus, it is clearly desirable to be able to program GPUs using a higher-level interface. In this paper, we offer a solution that targets a specific class of applications, which are the data mining and scientific data analysis applications. Our work is driven by the observation that a common processing structure, that of generalized reductions, fits a large number of popular data mining algorithms. In our solution, the programmers simply need to specify the sequential reduction loop(s) with some additional information about the parameters. We use program analysis and code generation to map the applications to a GPU. Several additional optimizations are also performed by the system. We have evaluated our system using three popular data mining applications, k-means clustering, EM clustering, and Principal Component Analysis (PCA). The main observations from our experiments are as follows. The speedup that each of these applications achieve over a sequential CPU version ranges between 20 and 50. The automatically generated version did not have any noticeable overheads compared to hand written codes. Finally, the optimizations performed in the system resulted in significant performance improvements.
Optical gain and spontaneous emission of strain-compensated InGaN-AlGaN quantum wells including carrier screening effect

Strain-compensated InGaN quantum well (QW) active region employing tensile AlGaN barriers was analyzed as improved gain media for laser diodes emitting at 430-440 nm by taking into account the carrier screening effect. The use of strain-compensated InGaN-AlGaN structure is advantageous because the tensile barriers compensate the compressive strain in the InGaN QW and the larger band offset allows high temperature operation. The band structure is calculated by using a 6-band k times p formalism, taking into account valence band mixing, strain effect, spontaneous and piezoelectric polarizations. The carrier screening effect is incorporated in the calculation, which is solved self-consistently. The spontaneous emission spectra show a significant improvement of the radiative emission for strain-compensated structure. The optical gain analysis shows enhancement in the peak optical gain for the strain-compensated QW structures. Threshold analysis of both the conventional InGaN-GaN QW and strain-compensated InGaN-AlGaN QW active regions indicate a reduction in the threshold carrier density and threshold current density for diode laser employing the strain-compensated QW as its active region.
Predominant Expression of Hybrid N-Glycans Has Distinct Cellular Roles Relative to Complex and Oligomannose N-Glycans

Glycosylation modulates growth, maintenance, and stress signaling processes. Consequently, altered N-glycosylation is associated with reduced fitness and disease. Therefore, expanding our understanding of N-glycans in altering biological processes is of utmost interest. Herein, clustered regularly interspaced short palindromic repeats/caspase9 (CRISPR/Cas9) technology was employed to engineer a glycosylation mutant Chinese Hamster Ovary (CHO) cell line, K16, which expresses predominantly hybrid type N-glycans. This newly engineered cell line enabled us to compare N-glycan effects on cellular properties of hybrid type N-glycans, to the well-established Pro−5 and Lec1 cell lines, which express complex and oligomannose types of N-glycans, respectively. Lectin binding studies revealed the predominant N-glycan expressed in K16 is hybrid type. Cell dissociation and migration assays demonstrated the greatest strength of cell–cell adhesion and fastest migratory rates for oligomannose N-glycans, and these properties decreased as oligomannose type were converted to hybrid type, and further decreased upon conversion to complex type. Next, we examined the roles of three general types of N-glycans on ectopic expression of E-cadherin, a cell–cell adhesion protein. Microscopy revealed more functional E-cadherin at the cell–cell border when N-glycans were oligomannose and these levels decreased as the oligomannose N-glycans were processed to hybrid and then to complex. Thus, we provide evidence that all three general types of N-glycans impact plasma membrane architecture and cellular properties.
Relatedness in trait group models of social evolution.

Genetic relatedness is a central concept in the study of social evolution. Though originally defined in terms of genealogy, the modern version of relatedness accommodates genetic similarity of any origin. This paper examines relatedness in group structured modes, in which a trait affects the fitness of all group members. Such traits can be divided into two types, based on whether their group fitness effects encompass all group members including the actor ("whole-group traits"), or only group members other than the actor ("other-only traits"). Both trait types are common in nature as well as in theoretical models, but they have rarely been distinguished clearly. The average relatedness of recipients to actors differs for the two trait types within the same population and even the same individual, leading to different selection pressures and evolutionary outcomes. Total relatedness in group-structured models can be partitioned into two components: structural relatedness due to the size and number of groups in the population, and assortative relatedness due to the distribution of genotypes among groups. Each component differs for whole-group vs. other-only traits, both in terms of their values and the factors that influence them. Some key differences include: positive relatedness requires positive assortment for other-only but not for whole-group traits; negative relatedness is possible for other-only but not whole-group traits; relatedness depends on average group size for whole-group but not other-only traits, and non-random assortment into groups affects relatedness more strongly for other-only than whole-group traits. Recognizing the distinction between these trait types resolves some apparent contradictions in the literature, and clarifies the limits of some previous results.
Relation of serum valproate concentration to response in mania.

OBJECTIVE This study was designed to determine the relation of valproate serum levels to clinical improvement and development of adverse effects in hospitalized patients with acute mania. The initial fixed-dose escalation design, the monotherapy with divalproex, and the control of variables that is possible only with hospitalized patients reduced the confounding factors present in most outpatient studies of serum level-response relationships. METHOD Sixty-five hospitalized patients who met the Research Diagnostic Criteria for bipolar disorder with mania were treated with divalproex, 750 mg/day for 2 days and then 1,000 mg/day on days 3-5; the dosage was subsequently adjusted as clinically indicated for the remainder of the 21-day study. Manic symptoms were assessed with the Mania Rating Scale, which is derived from the Schedule for Affective Disorders and Schizophrenia. RESULTS At day 5, patients with serum valproate levels > or = 45 micrograms/ml were two to seven times as likely as patients with levels < 45 micrograms/ml to show 20% or greater improvement in scores on the manic syndrome subscale, the behavior and ideation subscale, elevated mood, increased activity, motor hyperactivity, and psychosis. Endpoint analyses yielded similar results. Adverse experiences characteristic of divalproex treatment were disproportionately associated with serum levels > or = 125 micrograms/ml. CONCLUSIONS Acutely manic patients treated with divalproex who have valproate serum levels between 45 and 100-125 micrograms/ml are much more likely to have efficacious and well-tolerated responses than patients with lower or higher levels of valproate.
A mixed nodal-mesh formulation for efficient extraction and passive reduced-order modeling of 3D interconnects

As VLSI circuit speeds have increased, reliable chip and system design can no longer be performed without accurate three-dimensional interconnect models. In this paper, we describe an integral equation approach to modeling the impedance of interconnect structures accounting for both the charge accumulation on the surface of conductors and the current traveling in their interior. Our formulation, based on a combination of nodal and mesh analysis, has the required properties to be combined with Model Order Reduction techniques to generate accurate and guaranteed passive low order interconnect models for efficient inclusion in standard circuit simulators. Furthermore, the formulation is shown to be more flexible and efficient than previously reported methods.
Facial Features in Perceived Intensity of Schematic Facial Expressions

Facial expressions may be perceived continuously or categorically, i.e., perception of facial expressions may be explained by feature-based models or holistic models. A linear additive model is proposed, with weightings for facial features to reflect configural spatial relationships or distances of features from each other. Predictions from the model regarding the perception of affect intensities (e.g., of anger and sadness) were tested using schematic faces, with three facial features, eyebrows, eyes, and mouth as predictors. Model predictions, based on multiple regression analyses, corresponded well with rating judgments of anger and sadness in three experiments. The results suggest not only the limit of feature–configural models of facial expression perception but the feature-selective configuration of facial features and continuous perception of facial expressions. Findings also indicate that the salience or weight of each feature varies with the emotion perceived by observers.
Starch consolidation of M3/2 high speed steel powder – influence of process parameters on resulting microstructure

The possibility to produce near net shape high speed steel components with an adequate microstructure by the combination of starch consolidation (SC) and super solidus liquid phase sintering (SLPS) has been evaluated using a gas atomised M3/2 high speed steel (HSS) powder. Characterisation of the green body and as sintered microstructures using light optical microscopy (LOM), scanning electron microscopy (SEM), and energy dispersive X-ray spectroscopy (EDX) reveals that both the SC and SLPS processes strongly influence the resulting microstructure and thus the properties of the high speed steel material. The results obtained show that the morphology and distribution of starch to a high extent affect the green body surface strength and that the large pores remaining after sintering originates from entrapped air introduced in the fabrication process of the green body. The results illuminate the possibility to combine SC and SLPS to produce HSS components with fully dense microstructures and retained green body geometry from a powder with particle size distribution 50–150 μm.
Moisture-Depend some Postharvest Properties of Two Varieties of Safflower(Darab and Goldasht)

The moisture-dependent physical properties are important to investigate for designing the post harvest equipments of the product . This study was carried out to determine the effect of moisture content on some physical properties. Four levels of moisture content ranging from 4-22% d.b (wet basis) and 4-22% d.b. for Darab and Goldasht, respectively was used. The average length, width, thickness, geometric mean diameter, equivalent diameter, arithmetic diameter, sphericity, thousand grain mass, angle of repose, grain volume, surface area and aspect ratio ranged from 7.52 to 7.89 mm, 3.95 to4.48 mm, 3.36 to 3.70 mm, 4.51 to 4.99 mm and 4.52 to5.00 mm, 4.89 to 5.36 mm, 60% to 63%, 32.2 to40.7 gr, 43o to 51o, 34.83 to 47.43 mm3, 57.28 to 70.38 mm2, 52.57% to 56.74% as the moisture content increased from 4 to 22% d.b. for Darab and from 7.41 to 7.67 mm, 4.59 to 4.74 mm, 3.57 to 3.84 mm, 4.93 to 5.18 mm, 4.88 to 5.12 mm, 5.17 to 5.41 mm, 66.37% to 68.56%, 50.50 to 59.2 gr, 47° to 56°, 40.76 to 53.12 mm3, 62.27 to 72.38 mm2, 64.22% to 62.95% with increase in moisture content from 4 to 22% d.b. for Goldasht. Goldasht has higher static angle of repose than Darab in all moisture content levels. As the moisture content increased, the bulk density was found to decrease from 547 to 520 kgm-3 and from 640 to 601 kgm-3 for Goldasht and Darab, respectively whereas true density and porosity were found to decrease from 1070 to 1010 kgm-3 and 48.87% to 48.51% for Goldasht and from 940 to 850 kgm-3, 31.91% to 29.29% for Darab. The static coefficients of friction on various surfaces, namely, galvanized metal, plywood and plastic also increased linearly with an increase in moisture content. For galvanized metal and plastic Darab was higher correlated with moisture content than Goldasht.
Circuit class therapy for improving mobility after stroke: a systematic review.

OBJECTIVE To examine the effectiveness of group circuit class therapy for improving the mobility of adults after stroke. DESIGN Cochrane systematic review. METHODS A comprehensive search strategy was used to find randomized and quasi-randomized controlled trials of adults post-stroke receiving circuit class therapy. Two authors independently selected trials for inclusion, assessed the methodological rigor and extracted data. RESULTS Six trials were included, involving 292 participants; most were community-dwelling survivors who were able to walk independently. Circuit class therapy was effective in improving walking ability (6-minute walk test mean difference, 76.6 m, 95% confidence interval 38.4-114.7, walking speed mean difference 0.12 m/s, 95% confidence interval 0-0.24) and balance (step test mean difference 3.0 steps, 95% confidence interval 0.08-5.9, activities specific balance confidence mean difference 7.76 points, 95% confidence interval 0.66-14.9). Other balance measures did not show a difference in effect. Results from two studies suggest that circuit class therapy can reduce length of hospital stay (mean difference -19.7 days, 95% confidence interval -35.4 to -4.0). Two studies measured adverse events (falls); all were minor. CONCLUSION Circuit class therapy is safe and effective in improving mobility in people after stroke and, when provided as part of hospital-based rehabilitation, may reduce length of stay.
Nucleotide diversity in Silene latifolia autosomal and sex-linked genes

The plant Silene latifolia has separate sexes and sex chromosomes, and is of interest for studying the early stages of sex chromosome evolution, especially the evolution of non-recombining regions on the Y chromosome. Hitch-hiking processes associated with ongoing genetic degeneration of the non-recombining Y chromosome are predicted to reduce Y-linked genes' effective population sizes, and S. latifolia Y-linked genes indeed have lower diversity than X-linked ones. We tested whether this represents a true diversity reduction on the Y, versus the alternative possibility, elevated diversity at X-linked genes, by collecting new data on nucleotide diversity for autosomal genes, which had previously been little studied. We find clear evidence that Y-linked genes have reduced diversity. However, another alternative explanation for a low Y effective size is a high variance in male reproductive success. Autosomal genes should then also have lower diversity than expected, relative to the X, but this is not found in our loci. Taking into account the higher mutation rate of Y-linked genes, their low sequence diversity indicates a strong effect of within-population hitch-hiking on the Y chromosome.
Feasibility of Development of a Cohort in a Rural Area of Sub-Himalayan Region of India to Assess the Emergence of Cardiovascular Diseases Risk Factors

Introduction. Rural area of India is facing epidemiological transitions due to growth and development, warranting a longitudinal study to assess the development of CVDs risk factors. Objective. Feasibility of setting up a rural cohort for the assessment and development of biochemical risk factors for CVDs. Methodology. In Himachal Pradesh, house-to-house surveys were carried out in six villages for anthropometry and assessment of lipid profile. All the information was stored in specifically designed web-based software, which can be retrieved at any time. Results. A total of 2749 individuals of more than 20 years of age were recruited with a 14.3% refusal rate. According to Asian criteria, measured overweight and obesity (BMI > 27.5 kg/m2) were 44.9% and 10.5%, respectively. Obesity was significantly more (P = 0.01) among females (11.7%) as compared to males (8.4%). The prevalence of prehypertension and hypertension was observed to be 16.3% and 37.4%, respectively. Eighty percent of individuals had borderline (46.5%) to high (35.4%) level of triglycerides (TGs). Elevated total cholesterol (TC) and low density lipoprotein (LDL) level were observed among 30.0% and 11.0% individuals only. Conclusion. A high prevalence of biochemical risk factors for CVDs in a rural area urges establishment of an effective surveillance system.
Pharmacoeconomic Impact of Different Regimens to Prevent Cytomegalovirus Infection in Renal Transplant Recipients

Background: The aim of this study was to determine the cost impact of four different strategies for prevention of cytomegalovirus (CMV) disease after renal transplantation. Methods: Hospitalization data and medical resource utilization data were prospectively collected alongside two randomized trials. In the first trial, the patients were randomized to 3-month prophylaxis with either oral ganciclovir (1 g t.i.d., n = 36) or valacyclovir (2 g q.i.d., n = 35), and to the control group (n = 12) managed by deferred therapy. In the second trial, the patients were randomly assigned to 3-month valacyclovir prophylaxis (n = 34) or preemptive therapy with valganciclovir (900 mg b.i.d. for a minimum of 14 days, n = 36) for significant CMV DNAemia. The cost analysis involved all real costs directly related to CMV during the first year after renal transplantation. Results: The mean CMV-associated costs per patient were EUR 4,581, 2,577, 4,968, and 8,050 in patients in the ganciclovir, valacyclovir, preemptive, and deferred therapy groups, respectively (p < 0.001). Valacyclovir prophylaxis was significantly less expensive than any other regimen. The cost of one episode of CMV disease was EUR 7,510 per patient. Due to excessive incidence of CMV disease, deferred therapy was the most expensive strategy (p < 0.001). Conclusions: Valacyclovir prophylaxis is less expensive strategy compared with any other regimen.