Miracle-dz/UniFAR-FTUs huggingface dataset:
Genetic Variation in the Nucleotide Excision Repair Pathway and Bladder Cancer Risk

Nucleotide excision repair (NER) is critical for protecting against damage from carcinogens in tobacco smoke. We evaluated the influence of common genetic variation in the NER pathway on bladder cancer risk by analyzing 22 single nucleotide polymorphisms (SNP) in seven NER genes (XPC, RAD23B, ERCC1, ERCC2, ERCC4, ERCC5, and ERCC6). Our study population included 1,150 patients with transitional cell carcinoma of the urinary bladder and 1,149 control subjects from Spain. Odds ratios (OR) and 95% confidence intervals (95% CI) were adjusted for age, gender, region, and smoking status. Subjects with the variant genotypes for SNPs in four of the seven genes evaluated had small increases in bladder cancer risk compared to subjects with the homozygous wild-type genotypes: RAD23B IVS5-15A>G (OR, 1.3; 95% CI, 1.1-1.5; P = 0.01), ERCC2 R156R (OR, 1.3; 95% CI, 1.1-1.6; P = 0.006), ERCC1 IVS5+33A>C (OR, 1.2; 95% CI, 1.0-1.5; P = 0.06; Ptrend = 0.04), and ERCC5 M254V (OR, 1.4; 95% CI, 1.0-2.0; P = 0.04). A global test for pathway effects indicated that genetic variation in NER characterized by the 22 SNPs analyzed in this study significantly predicts bladder cancer risk (P = 0.04). Pairwise comparisons suggested that carrying variants in two genes could result in substantial increases in risk. Classification tree analyses suggested the presence of subgroups of individuals defined by smoking and NER genotypes that could have substantial increases in risk. In conclusion, these findings provide support for the influence of genetic variation in NER on bladder cancer risk. A detailed characterization of genetic variation in key NER genes is warranted and might ultimately help identify multiple susceptibility variants that could be responsible for substantial joint increases in risk. (Cancer Epidemiol Biomarkers Prev 2006;15(3):536–42)
Regulation of Eukaryotic Initiation Factor 4E Phosphorylation in the Nervous System of Aplysia californica

We have used an antibody that specifically recognizes eukaryotic initiation factor 4E (eIF4E) when it is phosphorylated at Ser207 to characterize eIF4E phosphorylation in the nervous system of Aplysia. The level of phosphorylated eIF4E, but not the level of total eIF4E, was significantly correlated with the basal rate of translation measured from different animals. Serotonin (5‐HT), a transmitter that regulates the rate of translation in Aplysia neurons, had mixed effects on eIF4E phosphorylation. 5‐HT decreased eIF4E phosphorylation in sensory cell clusters through activation of protein kinase C. 5‐HT increased eIF4E phosphorylation in the whole pleural ganglia. In the Aplysia nervous system, eIF4E phosphorylation correlated with phosphorylation of the p38 MAP kinase, but not the p42 MAP kinase (ERK). Furthermore, an inhibitor of the p38 MAP kinase significantly decreased basal eIF4E phosphorylation, but an inhibitor of the MAP or ERK kinase (MEK) did not. Despite the correlation of eIF4E phosphorylation with the basal rate of translation, inhibition of eIF4E phosphorylation by an inhibitor of the p38 MAP kinase did not significantly decrease the rate of translation.
A metabolic protective strategy could improve long-term survival in patients with LV-dysfunction undergoing CABG

Abstract Objective. Adverse outcome after CABG is closely related to postoperative heart failure precipitated by ischemia and myocardial infarction. Restrictive use of inotropes is therefore desirable. Patients with preoperative left ventricular dysfunction are a high-risk group in this respect. To reduce myocardial oxygen expenditure we evolved a metabolic strategy for perioperative care. Design. Observational study on 104 consecutive patients with severe left ventricular dysfunction undergoing CABG. The metabolic strategy implied physiological measures to minimize myocardial oxygen expenditure including restrictive use of inotropes and specific measures such as extended CPB and metabolic support to facilitate myocardial recovery. Hemodynamic state was primarily assessed by mixed venous oxygen saturation (SvO2). Follow-up averaged 9.7±1.4 years. Results. LVEF was 0.30±0.05 (range 0.20–0.37) and 3.5±1.3 vessels were bypassed. Inotropes were used in 6.7% for weaning from CPB. Increase of s-creatinine by ≥50% compared to preoperative values was observed in 2.9%. Logistic EuroSCORE was 8.3% whereas observed 30-day mortality was 1.0%. Crude 5-year survival was 89.4%. Conclusions. The metabolic strategy allowed restrictive use of inotropes and was associated with encouraging long-term survival. Renal function was well preserved suggesting that SvO2 served as an adequate marker of circulation. Randomized trials with metabolic support are warranted.
Minimax Estimation of Bandable Precision Matrices

The inverse covariance matrix provides considerable insight for understanding statistical models in the multivariate setting. In particular, when the distribution over variables is assumed to be multivariate normal, the sparsity pattern in the inverse covariance matrix, commonly referred to as the precision matrix, corresponds to the adjacency matrix representation of the Gauss-Markov graph, which encodes conditional independence statements between variables. Minimax results under the spectral norm have previously been established for covariance matrices, both sparse and banded, and for sparse precision matrices. We establish minimax estimation bounds for estimating banded precision matrices under the spectral norm. Our results greatly improve upon the existing bounds; in particular, we find that the minimax rate for estimating banded precision matrices matches that of estimating banded covariance matrices. The key insight in our analysis is that we are able to obtain barely-noisy estimates of $k \times k$ subblocks of the precision matrix by inverting slightly wider blocks of the empirical covariance matrix along the diagonal. Our theoretical results are complemented by experiments demonstrating the sharpness of our bounds.
Ehrlichioses and anaplasmoses: (re)emerging tickborne zoonoses in humans and in animals.

One cannot but point out that the variety of topics related to zoonoses, and in particular zoonoses transmitted by ticks, is fascinating and ranges from environmental to clinical sciences, also in emergency situations, from veterinary sciences to human epidemiology, in a finely woven network of interactive ecological, social and health factors. Anthropic and cultural factors are correlated to the presence and distribution of zoonoses and, in most cases, become risk factors themselves. The epidemiology of zoonoses is, in fact, closely tied to the socio-economic conditions and the characteristics of the different rural areas, where complex interrelations and close living conditions exist between men and animals and are often unavoidable. In recent years the situation has become even worse, making zoonoses one of the most serious problems of Public Health. The list of zoonoses is extensive and the agents responsible for infection include bacteria, fungi, chlamydiae, rickettsiae, viruses and protozoa, transmitted by faeces, food, animal bites or inoculations by arthropods. The role of arthropods is significant and is in constant expansion. Human activities modify the ecological balance and facilitate an increase in arthropods and, consequently, the spread of pathogens they transmit with their relative pathologies [1-3]. Because of the vast range of hosts among pets and wild animals, it is very difficult to control arthropods and their respective pathologies. The same tick may have different specificities of hosts, the same host may be parasitized by various species of ticks. Mammals, birds, and reptiles can be hosts for ticks, which transmit more pathogens than any other vector and can guarantee the transmission and continuance in nature even by transtadial or transovarial means. In recent years, moreover, the epidemiology of arthropods has changed: new forms of transmission have been described and new pathogens have been isolated [4-8].
Physiological profile in relation to playing position of elite college Gaelic footballers

Objective: To examine the physiological profile, and its relation to playing position, of elite college Gaelic footballers. Method: The subjects were 28 elite Gaelic footballers (12 backs, 12 forwards, and four midfielders; mean (SD) age 21 (1.67) years), who won a major intervarsity tournament (Sigerson Cup) three times in succession. Results: There was general similarity among the members of the team, probably the result of a typical, common training programme. The team means for stature (1.81 (0.05) m), body mass index (81.6 (6.5)) and percentage body fat (14.5 (3.1)%), power output by Wingate test (absolute power 912 (152) W or 10.72 (1.6) W/kg) and sit and reach test (22.3 (5.5) cm) displayed no significant differences when analysed according to playing position. However, midfielders did have significantly larger body mass than backs (p<0.05) and greater maximal oxygen consumption (p<0.01) and greater vertical jumping ability than backs and forwards (vertical jump power output, p<0.01; vertical jump, p<0.01). Midfielders also had greater absolute handgrip strength (p<0.01). Conclusion: The differences exhibited by midfielders despite identical training suggests that they stem from physiological adaptation to competition rather than training.
Group Delay Investigation of Rat-Race Coupler Design With Tunable Power Dividing Ratio

This letter presents, for the first time, the theoretical and experimental investigation of the group delay characteristics of a rat-race coupler with variable power dividing ratio. By analytically study, the group delays associated with different transmission paths are found to be identical and can be made independent of the power dividing ratio by the proper design of the embedded networks. For validation, both simulated and measured results of a 1 GHz variable rat-race coupler implemented on microstrip are shown.
Lexical Transfer Ambiguity Resolution Using Automatically-Extracted Concept Co-occurrence Information

This paper describes a method for lexical transfer ambiguity resolution using corpus and concept information. Previous research has restricted the use of linguistic knowledge to the lexical level. Since the extracted knowledge is stored in words themselves, these methods require a large amount of space with a low recall rate. On the contrary, we resolve word sense ambiguity by using concept co-occurrence information extracted from an automatically sense-tagged corpus. The tested accuracy of our method exceeds 82.4% for nominal words, and 83% for verbal words.
Enhancing Pre-service Teacher's Self-efficacy and Technological Pedagogical Content Knowledge in Designing Digital Media with Self-Regulated Learning Instructional Support in Online Project-Based Learning

This study investigated pre-service teachers’ self-efficacy in designing digital media and their technological pedagogical content knowledge (TPCK) for designing digital media using different forms of self- regulated learning instructional support for online project-based learning. The study used a 2x2 factorial research design. The sample consisted of 232 pre-service teachers from an institution situated in Bangkok, Thailand. The four different forms of self-regulated learning instructional support for online project-based learning were PB+SQ+PA, PB+SQonly, PB+PAonly, and PBonly. Two-way Multivariate Analysis of Variance (MANOVA) was used for data analysis. The results showed significant differences in pre-service teachers’ self-efficacy and TPCK posttest scores. No main effect was found between two different self-regulated learning strategies (SQ and PA) upon the means of self-efficacy in designing digital media scores and TPCK scores. The self-regulated learning strategies (SQ and PA) had a statistically significant interaction upon the means of self-efficacy in designing digital media scores while the self-regulated learning strategies (SQ and PA) had no interaction upon the means of the TPCK scores.
Tight folding of a passenger protein can interfere with the targeting function of a mitochondrial presequence.

The first seven residues of the yeast cytochrome oxidase subunit IV presequence are insufficient to target attached mouse dihydrofolate reductase into isolated yeast mitochondria. However, the targeting function of this truncated presequence can be restored by presenting the fusion protein to isolated mitochondria either as nascent, unfolded chains, or as full‐length chains whose dihydrofolate reductase moiety had been destabilized either by urea treatment or by point mutations. The targeting efficiency of a mitochondrial presequence can thus be strongly influenced by the conformation of the attached ‘passenger protein’. These results also underscore the difficulty of defining a ‘minimal’ mitochondrial targeting signal.
MARKERS OF OXIDATIVE STRESS IN ANGIOGRAPHICALLY PROVED CORONARY ARTERY DISEASE PATIENTS

Background & Objective: Growing evidence indicates that overproduction of reactive oxygen species (ROS) under pathophysiologic conditions is integral in the development of cardiovascular diseases. ROS mediates various signaling pathways that underlie vascular inflammation in atherogenesis from the initiation of fatty streak development through lesion progression to ultimate plaque rupture. Hence this pilot study was conducted to evaluate the level of oxidative stress markers like malondialdehyde (MDA), superoxide dismutase (SOD) and ascorbic acid in angiographically proved coronary artery disease (CAD ) patient compared with healthy individuals along with routine plasma glucose & lipid parameters
Closing the Circle: An Analysis of Emil Post's Early Work

Abstract In 1931 Kurt Gödel published his incompleteness results, and some years later Church and Turing showed that the decision problem for certain systems of symbolic logic has a negative solution. However, already in 1921 the young logician Emil Post worked on similar problems which resulted in what he called an “anticipation” of these results. For several reasons though he did not submit these results to a journal until 1941. This failure ‘to be the first’, did not discourage him: his contributions to mathematical logic and its foundations should not be underestimated. It is the purpose of this article to show that an interest in the early work of Emil Post should be motivated not only by this historical fact, but also by the fact that Post's approach and method differs substantially from those offered by Gödel, Turing and Church. In this paper it will be shown how this method evolved in his early work and how it finally led him to his results.
The poor accuracy of indirect measurements of cadaveric donor kidney weights

Reports that examined the issue of whether transplantation of inadequate nephron mass may be a risk factor for long‐term allograft failure yielded conflicting results. One of the more accurate methods of estimating glomerular mass is kidney weight. Most of the clinical studies used body surface area (BSA) or kidney length as estimates of kidney weight. To test the hypothesis that indirect measures of kidney weight are accurate estimates of kidney weight, we compared the kidney weight of 41 consecutive cadaveric kidneys to donor BSA, dimensions measured with calipers at the time of transplantation, and dimensions supplied by the Organ Procurement Agency (OPA). Linear regression analysis was used with kidney weight as the dependent variable and BSA, kidney length, or kidney volume as the independent variable. Kidney length measured with calipers was also compared to kidney length supplied by the OPA. Kidney weight had the best correlation with kidney volume and kidney length determined by caliper measurements (r=0.640 and 0.646, respectively). The regression analysis showed that the correlation of kidney weight with BSA was 0.487. The correlation of OPA‐provided kidney length with kidney weights was poor (r=0.410). The linear regression of caliper‐measured kidney length versus OPA length yielded a slope of 0.360, instead of an ideal slope of 1.The assumption has been made that kidney weight or a surrogate of kidney weight has an excellent correlation with nephron mass. Some of the variability in studies that attempted to examine the effect of transplanted nephron mass on allograft outcome may be due to inaccurate estimates used for kidney weight. Our data suggest that surrogate measurements of kidney weight may not be accurate. We recommend that measured kidney weight should be used in studies examining the effect of donor renal mass on allograft outcomes.
Radioselenium in Duodenal Aspirate as an Assessment of Pancreatic Exocrine Function*

A new test of pancreatic exocrine function is described in which radioselenium is measured in duodenal aspirate after an intravenous injection of 75Se-selenomethionine and administration of a Lundh test meal. Duodenal 75Se activity gave good separation between normals and subjects with disease of the exocrine pancreas and correlated well with trypsin levels in the aspirate.
The complete plastid genome sequence of Panax notoginseng, a famous traditional Chinese medicinal plant of the family Araliaceae

Abstract We report complete nucleotide sequence of the Panax notoginseng chloroplast genome using next-generation sequencing technology. The genome consists of 156 324 bp containing a pair of inverted repeats (IRs) of 26 105 bp, which was separated by a large single-copy region and a small single-copy region of 86 082 bp and 18 032 bp, respectively. The P. notoginseng cp genome encodes 114 unigenes (80 protein-coding genes, 4 rRNA genes, and 30 tRNA genes), in which 18 are duplicated in the IR regions. The genic regions account for 51.1% of whole cp genome, and the GC content of the plastome was 38.1%. A phylogenomic analysis of the 10 complete chloroplast genomes from Araliaceae using Hydrocotyle verticillata outgroup showed that P. notoginseng is closely related to P. ginseng that belongs to the genus Panax.
Assessing Genetic Structure in Common but Ecologically Distinct Carnivores: The Stone Marten and Red Fox

The identification of populations and spatial genetic patterns is important for ecological and conservation research, and spatially explicit individual-based methods have been recognised as powerful tools in this context. Mammalian carnivores are intrinsically vulnerable to habitat fragmentation but not much is known about the genetic consequences of fragmentation in common species. Stone martens (Martes foina) and red foxes (Vulpes vulpes) share a widespread Palearctic distribution and are considered habitat generalists, but in the Iberian Peninsula stone martens tend to occur in higher quality habitats. We compared their genetic structure in Portugal to see if they are consistent with their differences in ecological plasticity, and also to illustrate an approach to explicitly delineate the spatial boundaries of consistently identified genetic units. We analysed microsatellite data using spatial Bayesian clustering methods (implemented in the software BAPS, GENELAND and TESS), a progressive partitioning approach and a multivariate technique (Spatial Principal Components Analysis-sPCA). Three consensus Bayesian clusters were identified for the stone marten. No consensus was achieved for the red fox, but one cluster was the most probable clustering solution. Progressive partitioning and sPCA suggested additional clusters in the stone marten but they were not consistent among methods and were geographically incoherent. The contrasting results between the two species are consistent with the literature reporting stricter ecological requirements of the stone marten in the Iberian Peninsula. The observed genetic structure in the stone marten may have been influenced by landscape features, particularly rivers, and fragmentation. We suggest that an approach based on a consensus clustering solution of multiple different algorithms may provide an objective and effective means to delineate potential boundaries of inferred subpopulations. sPCA and progressive partitioning offer further verification of possible population structure and may be useful for revealing cryptic spatial genetic patterns worth further investigation.
Architecture and method for optimization of cloud resources used in software testing

Nowadays systems can evolve quickly, and to this growth is associated, for example, the production of new features, or even the change of system perspective, required by the stakeholders. These conditions require the development of software testing in order to validate the systems. Run a large battery of tests sequentially can take hours. However, tests can run faster in a distributed environment with rapid availability of pre-configured systems, such as cloud computing. There is increasing demand for automation of the entire process, including integration, build, running tests and management of cloud resources.This paper aims to demonstrate the applicability of the practice continuous integration (CI) in Information Systems, for automating the build and software testing performed in a distributed environment of cloud computing, in order to achieve optimization and elasticity of the resources provided by the cloud.
simba: the average properties of the circumgalactic medium of 2 ≤ z ≤ 3 quasars are determined primarily by stellar feedback

We use the simba cosmological hydrodynamic simulation suite to explore the impact of feedback on the circumgalactic medium (CGM) and intergalactic medium (IGM) around 2 ≤ z ≤ 3 quasars. We identify quasars in simba as the most rapidly accreting black holes, and show that they are well matched in bolometric luminosity and correlation strength to real quasars. We extract Lyα absorption in spectra passing at different transverse distances ($10 \, \mathrm{kpc} \lesssim b \lesssim 10 \, \rm Mpc$) around those quasars, and compare to observations of the mean Lyα absorption profile. The observations are well reproduced, except within $100 \, \, \rm kpc$ from the foreground quasar, where simba overproduces absorption; this could potentially be mitigated by including ionization from the quasar itself. By comparing runs with different feedback modules activated, we find that (mechanical) AGN feedback has little impact on the surrounding CGM even around these most highly luminous black holes, while stellar feedback has a significant impact. By further investigating thermodynamic and kinematic properties of CGM gas, we find that stellar feedback, and not AGN feedback, is the primary physical driver in determining the average properties of the CGM around z ∼ 2–3 quasars. We also compare our results with previous works, and find that simba predicts much more absorption within $100 \, \rm kpc$ than the nyx and illustris simulations, showing that the Lyα absorption profile can be a powerful constraint on simulations. Instruments such as VLT-MUSE and upcoming surveys (e.g. WEAVE and DESI) promise to further improve such constraints.
Free Charge Carriers Trapping Properties in Neutron-Irradiated DOFZ Silicon Pad Detectors

Silicon pad-detectors fabricated from diffused oxygenated silicon were irradiated with reactor neutrons with fluences between 1 times 10<sup>14</sup> n<sub>eq</sub>/cm<sup>2</sup> and 1 times 10<sup>15</sup> n<sub>eq</sub>/cm<sup>2</sup>. The transient current technique was used to measure the trapping probability for holes and electrons. The results obtained support the model of a linear increase with fluence. Also the temperature dependence of the trapping time constant for electrons is investigated. This temperature dependence was found independent on the irradiated fluence.