Miracle-dz/UniFAR-FTUs huggingface dataset:
A Semi-Lagrangian Semi-Implicit Numerical Method for Models of the Urine Concentrating Mechanism

Mathematical models of the urine concentrating mechanism consist of large systems of coupled differential equations. The numerical methods that have usually been used to solve the steady-state formulation of these equations involve implicit Newton-type solvers that are limited by numerical instability attributed to transient flow reversal. Dynamic numerical methods, which solve the dynamic formulation of the equations by means of a direction-sensitive time integration until a steady state is reached, are stable in the presence of transient flow reversal. However, when an explicit, Eulerian-based dynamic method is used, prohibitively small time steps may be required owing to the CFL condition and the stiffness of the problem. In this report, we describe a semi-Lagrangian semi-implicit (SLSI) method for solving the system of hyperbolic partial differential equations that arises in the dynamic formulation. The semi-Lagrangian scheme advances the solution in time by integrating backward along flow trajectories, thus allowing large time steps while maintaining stability. The semi-implicit approach controls stiffness by averaging transtubular transport terms in time along flow trajectories. For sufficiently refined spatial grids, the SLSI method computes stable and accurate solutions with substantially reduced computation costs.
Inverse Volume Inequalities for Matrix Weights

For weights in the matricial Muckenhoupt classes we investigate a number of properties analogous to properties which hold in the scalar Muckenhoupt classes. In contrast to the scalar case we exhibit for eachp ,1 <p<1, a matrix weight W 2Ap;qn S p0<pAp0;q0. We also give a necessary and suYcient condition on W inAp;q, a "reverse inverse volume inequality", to ensure thatW is inAp0;q0 for somep 0 <p .
Pathology and prognosis of gastric carcinoma

The most important parameters predicting outcome of patients with gastric carcinoma are the depth of wall invasion and the status of lymph node metastasis, but the prognostic significance of histologic type is unclear. The aim of this study was to clarify the prognostic value of two major histologic types of gastric carcinoma, that is well and poorly differentiated types.
Creating and Analyzing Source Code Repository Models - A Model-based Approach to Mining Software Repositories

With mining software repositories (MSR), we analyze the rich data created during the whole evolution of one or more software projects. One major obstacle in MSR is the heterogeneity and complexity of source code as a data source. With model-based technology in general and reverse engineering in particular, we can use abstraction to overcome this obstacle. But, this raises a new question: can we apply existing reverse engineering frameworks that were designed to create models from a single revision of a software system to analyze all revisions of such a system at once? This paper presents a framework that uses a combination of EMF, the reverse engineering framework Modisco, a NoSQL-based model persistence framework, and OCL-like expressions to create and analyze fully resolved AST-level model representations of whole source code repositories. We evaluated the feasibility of this approach with a series of experiments on the Eclipse code-base.
An Attack-Tolerant Framework for Web Services

Web services which allow the interoperability and communication of heterogeneous systems in the Web through Internet protocols, are also subject to attacks a well as destructive as sophisticated. Contrariwise, very few solutions exist to ensure the availability of Web services in the presence of these attacks. In order to tackle these issues, we propose a comprehensive and complete attack-tolerance methodology whose characteristics are: i) upstream detection of attacks before their propagation, ii) a failover system to mitigate the effects of the attack and, iii) an active reconfiguration process to mitigate attacks that are not easy or impossible to detect by monitoring. Our approach will leverage and explore, in particular, monitoring, diversity and software engineering techniques for devising a fine-grained attack-tolerance system. We conducted preliminary experiments with an e-health Web service, which is a simplified version of a case study of the European project CLARUS.
Cross-polarization modulation effects in long semiconductor optical amplifiers

The aim of the present work is to present an analysis of the impact of Semiconductor Optical Amplifier length variation on the cross-polarization modulation (XPolM) effect in the structure. This nonlinear behavior, which is exploited to assure high speed devices and various applications for the high bit rate optical networks, is investigated referring to numerical simulations based on Stokes parameters measurement. Consequently, it is shown that the azimuth and the ellipticity parameters at the output undergo changes by varying the input polarization, bias current and obviously the SOA length which plays an important role in the gain dynamics of the structure.
The association of educational attainment, cognitive level of job, and leisure activities during the course of adulthood with cognitive performance in old age: the role of openness to experience

ABSTRACT Background: The relevance of mental health for everyday life functioning and well-being is crucial. In this context, higher educational attainment, higher cognitive level of one's occupation, and more engaging in stimulating leisure activities have been found to be associated with better cognitive functioning in old age. Yet, the detailed pattern of the potential interplay of such a cognitively engaged lifestyle with personality dimensions, such as openness to experience, in their relations to cognitive functioning remains unclear. Methods: Two thousand eight hundred and twelve older adults served as sample for the present study. Psychometric tests on verbal abilities and processing speed were administered. In addition, individuals were retrospectively interviewed on their educational attainment, occupation, and regarding 18 leisure activities that had been carried out in mid-life. Moreover, openness to experience was assessed. Results: We found that the effect of openness to experience on cognitive functioning was mediated by educational attainment, cognitive level of job, and engaging in different leisure activities. Data were not better described by alternative moderation models testing for interactive (i.e. dependent) effects of openness to experience and cognitively stimulating engagement. Conclusions: To explain interindividual differences in cognitive functioning in old age, present data are in line with a mechanism in which individuals with high openness to experience may have been more engaged in stimulating activities in early and mid-life. Possibly by increasing their cognitive reserve throughout adulthood, this may finally enhance their cognitive performance level later in old age.
Cell division in cocci: localization and properties of the Streptococcus pneumoniae FtsA protein

We studied the cytological and biochemical properties of the FtsA protein of Streptococcus pneumoniae. FtsA is a widespread bacterial cell division protein that belongs to the actin superfamily. In Escherichia coli and Bacillus subtilis, FtsA localizes to the septal ring after FtsZ, but its exact role in septation is not known. In S. pneumoniae, we found that, during exponential growth, the protein localizes to the nascent septa, at the equatorial zones of the dividing cells, where an average of 2200 FtsA molecules per cell are present. Likewise, FtsZ was found to localize with the same pattern and to be present at an average of 3000 molecules per cell. Consistent with the colocalization, FtsA was found to interact with FtsZ and with itself. Purified FtsA is able to bind several nucleotides, the affinity being highest for adenosine triphosphate (ATP), and lower for other triphosphates and diphosphates. The protein polymerizes in vitro, in a nucleotide‐dependent manner, forming long corkscrew‐like helixes, composed of 2 + 2 paired protofilaments. No nucleotide hydrolytic activity was detected. Consistent with the absence of an ATPase activity, the polymers are highly stable and not dynamic. These results suggest that the FtsA protein could also polymerize in vivo and the polymers participate in septation.
COMPUTING CREDIT VALUATION ADJUSTMENT FOR BERMUDAN OPTIONS WITH WRONG WAY RISK

We study the impact of wrong way risk (WWR) on credit valuation adjustment (CVA) for Bermudan options. WWR is modeled by a dependency between the underlying asset and the intensity of the counterparty’s default. Two WWR models are proposed, based on a deterministic function and a CIR-jump (CIRJ) model, respectively. We present a nonnested Monte Carlo approach for computing CVA–VaR and CVA–expected shortfall (ES) for Bermudan options. By varying correlation coefficients, we study the impact of credit quality and WWR on the optimal exercise boundaries and CVA values of Bermudan products. Stress testing is performed.
Reactive Polymer Coatings: A Platform for Patterning Proteins and Mammalian Cells onto a Broad Range of Materials

We report a procedure for surface modification based on chemical vapor deposition polymerization of functionalized [2.2]paracyclophanes that is essentially substrate-independent. Poly(p-xylylene-2,3-dicarboxylic anhydride) and poly[p-xylylene carboxylic acid pentafluorophenolester-co-p-xylylene] are examined as templates for cell patterning. Both reactive coatings are deposited on poly(tetrafluoroethylene), polyethylene, silicon, gold, stainless steel, and glass and show excellent adhesion when deposited in thin films (ca. 100 nm) under optimized polymerization conditions. X-ray photoelectron spectroscopy and grazing angle infrared spectroscopy have been used to confirm chemical homogeneity in both cases. Reactive coatings are subsequently patterned by microcontact printing of an amino-terminated biotin ligand and serve as templates for layer-by-layer self-assembly. Streptavidin selectively binds to the biotin-exposing surface regions and allows surface confinement of a biotin-tethered antibody against α5.
The Care Home Activity Project: Does introducing an occupational therapy programme reduce depression in care homes?

The primary aim of the study was to test the hypothesis that depression severity in care homes for older people would be reduced by an occupational therapy programme. This was a feasibility study for a cluster randomised controlled trial and involved four intervention and four control homes in northern England. In each intervention home a registered occupational therapist worked full-time for one year delivering an individualised programme to participants. Pre- and post-intervention data for the Geriatric Mental State–Depression Scale (primary outcome measure) were obtained for 143 participants. Secondary outcomes included dependency and quality of life. No significant intervention effects were found in any of the quantitative outcome measures, though qualitative interviews showed the intervention was valued by many participants, staff and relatives. Therapist ratings and qualitative interviews suggested that the intervention was beneficial to some participants but no distinctive characteristics were found that might enable prediction of likely benefit on initial assessment. This exploratory study provides no evidence that this intervention produced benefits in terms of depression, dependency or quality of life. Lack of prior power calculations means these are not definitive findings; but numbers were sufficient to perform the required analyses and data did not suggest effects that would have reached statistical significance with a larger sample. This study highlights issues for consideration in providing such services in care homes.
Association of Specific Genetic Polymorphisms with Age-related Macular Degeneration in a Northern Chinese Population

Abstract Purpose: The associations between genetic variants located in CFH, CFB, ARMS2 and HTRA1 and the risk of age-related macular degeneration (AMD) in a northern Chinese population were investigated. Methods: A case-control association study of 150 AMD patients and 145 ethnicity- and gender-matched controls were recruited. Genomic DNA was prepared from peripheral blood after the participants underwent comprehensive eye examinations. All individuals were genotyped for eight single nucleotide polymorphisms (SNPs) in four specific genes. Genotypic distribution was tested for Hardy-Weinberg equilibrium. Statistical analysis was performed for genotype, allele and haplotype frequencies along with their p values and corresponding odds ratios (OR), 95% confidence intervals (95% CI) and measures of linkage disequilibrium (LD). Bonferroni corrections for multiple comparisons were performed. Results: Among the SNPs genotyped, p values of seven SNPs were less than 0.05 in the genotypic distributions and allele frequencies between AMD and control subjects. However, after Bonferroni correction, the genotype and allele distributions of two SNPs in CFH (rs10737680, rs1410996), one SNP (rs10490924) in ARMS2 and one SNP (rs11200638) in HTRA1 differed significantly between the controls and AMD patients. Two SNPs were significantly associated with AMD in the allele distributions. They were rs800292 (pallele = 0.006, OR [CI] = 1.643[1.155–2.336]) in CFH and rs641153 (pallele = 0.002, OR [CI] = 0.273[0.120–0.620]) in CFB. Five haplotypes in CFH significantly predisposed patients to AMD after 50,000 permutations (p = 0.0099, p = 0.0099, p = 0.0013, p = 0.0414 and p = 0.0327). Conclusions: Gene variants in CFH, ARMS2 and HTRA1 are related to an increased risk of AMD in a northern Chinese population.
Optimisation of an enzymatic method for beta-galactosidase.

BACKGROUND The enzyme beta-galactosidase present in the Kupffer cells of the liver has potential as a marker of liver dysfunction prior to transplantation. Spectrophotometric methods have insufficient sensitivity. METHODS Fluorimetric methods have the required sensitivity and we have optimised such a method in a microtitre plate format to improve its utility. beta-galactosidase acts on the substrate 4-methylumbelliferyl-galactoside (MUG) to produce 4-methylumbelliferone (4-MU), detected fluorimetrically with excitation wavelength 355 nm and emission wavelength 460 nm. RESULTS Reaction conditions in a citrate-phosphate buffer were optimised to give maximal enzyme activity: pH was optimal at 4.4 (range investigated 3.6-5.0) and substrate concentration at 3.33 mmol/l. A small specimen volume (10 microl) in 80 microl of substrate solution produced adequate fluorescent yield after an incubation period of 30 to 60 min at 37 degrees C. Reaction was terminated by addition of 200 microl of glycine-NaOH, pH 12.8. The assay is linear to 3,000 U/ml. The intra-assay coefficient of variation (CV%) at 50, 502, and 2,012 U/ml was 4.7, 3.1, and 3.4, respectively (n=10). Inter-assay CV% at 51, 496, and 1,986 U/ml was 7.0, 4.0, and 3.9, respectively (n=10). CONCLUSIONS The assay has greater practical utility and demonstrated significant differences in the perfusate beta-galactosidase between cold-stored and warm-perfused livers in a porcine model of transplantation.
Control and guidance of a hovering AUV pitching up or down

In this paper, we present an approach to control an autonomous underwater vehicle in the vertical and the horizontal planes while pitching down or up (θ = ±π/2). Such a capability is explored in MARES, a small-sized, torpedo-shaped hovering AUV with four degrees of freedom. Despite the fact that roll angle is not controllable, we find a guidance law that makes the vehicle reach any point in the horizontal plane while maintaining the vehicle in the vertical position.
Targeting of Yersinia Yop proteins into the cytosol of HeLa cells: one‐step translocation of YopE across bacterial and eukaryotic membranes is dependent on SycE chaperone

Pathogenic Yersiniae adhere to and kill macrophages by targeting some of their Yop proteins into the eukaryotic cytosol. There is debate about whether YopE targeting proceeds as a direct translocation of polypeptide between cells or in two distinct steps, each requiring specific signals for YopE secretion across the bacterial envelope and for translocation into the eukaryotic cytosol. Here, we used the selective solubilization of the eukaryotic plasma membrane with digitonin to measure Yop targeting during Yersinia infections of HeLa cells. YopE, YopH, YopM and YopN were found in the eukaryotic cytosol but not in the extracellular medium. When bound to SycE chaperone in the Yersinia cytoplasm, YopE residues 1–100 are necessary and sufficient for the targeting of hybrid neomycin phosphotransferase. Electron microscopic analysis failed to detect an extracellular intermediate of YopE targeting, suggesting a one‐step translocation mechanism.
The Link between Fundamentals and Proximate Factors in Development

The paper introduces a framework for studying the hierarchy of growth factors, from deep to more immediate. The specific setting we examine is 18th and 19th century Germany, when institutional changes introduced by reforms and transportation improvements converged to create city growth. We assess the impact of institutions on growth by allowing two ways for institutions to affect growth. Institutions can directly affect growth, or it can impact on trade, which in turn affects growth. Once we separately quantify the link from institutions to trade, and trade to growth, the independent effect of institutions on growth is small. This suggests that part of what is often understood as trade's effect on growth can be attributed to institutional change. It is straightforward to apply this framework to other settings.
The NMR solution structure of the pheromone Er‐2 from the ciliated protozoan Euplotes raikovi

The NMR structure of the pheromone Er‐2 from the ciliated protozoan Euplotes raikovi has been determined in aqueous solution. The structure of this 40‐residue protein was calculated with the distance geometry program DIANA from 621 distance constraints and 89 dihedral angle constraints; the program OPAL was employed for the energy minimization. For a group of 20 conformers used to characterize the solution structure, the average pairwise RMS deviation from the mean structure calculated for the backbone heavy atoms N, Cα, and C′ of residues 3–37 was 0.31 Å. The molecular architecture is dominated by an up‐down‐up bundle of 3 short helices of residues 5–11, 14–20, and 23–33, which is similar to the structures of the homologous pheromones Er‐1 and Er‐10. Novel structural features include a well‐defined N‐cap on the first helix, a 1‐residue deletion in the second helix resulting in the formation of a 310‐helix rather than an α‐helix as found in Er‐1 and Er‐10, and the simultaneous presence of 2 different conformations for the C‐terminal tetrapeptide segment, i.e., a major conformation with the Leu 39‐Pro 40 peptide bond in the trans form and a minor conformation with this peptide bond in the cis form.
Jasmonate Biochemical Pathway

Plants possess an interrelated family of potent fatty acid-derived regulators—the jasmonates. These compounds, which play roles in both defense and development, are derived from tri-unsaturated fatty acids [α-linolenic acid (18:3) or 7Z,10Z,13Z-hexadecatrienoic acid (16:3)]. The lipoxygenase-catalyzed addition of molecular oxygen to α-linolenic acid initiates jasmonate synthesis by providing a 13-hydroperoxide substrate for the formation of an unstable allene oxide that is then subject to enzyme-guided cyclization to produce 12-oxo-phytodienoic acid (OPDA). OPDA has several fates, including esterification into plastid lipids or transformation into the 12-carbon co-regulator jasmonic acid (JA). JA, the best-characterized member of the family, regulates both male and female fertility (depending on the plant species) and is an important mediator of defense gene expression. JA is itself a substrate for further diverse modifications. Genetic dissection of the pathway is revealing how the different jasmonates modulate different physiological processes. Each new family member that is discovered provides another key to understanding the fine control of gene expression in immune responses, in the initiation and maintenance of long-distance signal transfer in response to wounding, in the regulation of fertility, and in the turnover, inactivation, and sequestration of jasmonates, among other processes. The Jasmonate Biochemical Pathway provides an overview of the growing jasmonate family, and new members will be included in future versions of the Connections Map.
Optimal Design of an SPM Motor Using Genetic Algorithms and Taguchi Method

This paper presents the use of genetic algorithms (GAs) and the Taguchi method in optimizing an surface-mounted permanent magnet (SPM) motor for use as a fan motor in air-conditioners. GAs were used to optimize the efficiency of the motor, and the Taguchi optimization method was used and the finite-element method (FEM) analysis was conducted to compute the performance of the motor design generated by the Taguchi design of experiments.
Preoperative identification of patients at risk for delirium after major head and neck cancer surgery

This study was performed to determine preoperative criteria for identifying patients at risk for delirium after major head and neck cancer surgery. The authors prospectively evaluated 138 consecutive patients undergoing head and neck cancer surgery lasting more than 2 hours at the Arthur G. James Cancer Hospital and Research Institute, Ohio State University, Columbus, from July 1993 through May 1994.
A novel synthesis of graphene nanoscrolls with tunable dimension at a large scale

Graphene nanoscrolls which could overcome the chirality dependence of metallic or semiconducting behavior in carbon nanotubes have been recently investigated and proposed for a wide variety of applications. In order to further improve their practical applications, a variety of synthetic approaches have been widely explored but with various limitations. For instance, it remains challenging to produce graphene nanoscrolls with tunable dimensions and high quantity, which greatly hinders their potential applications. Herein, we report a new and general approach to synthesize graphene nanoscrolls with accurately tunable widths and lengths at a large scale. The resulting high-quality graphene nanoscrolls show promising applications in a wide variety of electronic devices.
Cancer-Related Fatigue in Patients Attending Oncological Rehabilitation Programs: Prevalence, Patterns and Predictors

Background: Fatigue is one of the most frequent symptoms in cancer patients. It is the aim of medical and psychosocial rehabilitation programs to reduce physical impairments and psychosocial distress. There are no reliable data on the prevalence or the pattern of fatigue in patients attending such rehabilitation programs. We therefore initiated a cross-sectional study to evaluate this phenomenon. Patients and Methods: Using the EORTC QLQ-C30, HADS and MFI questionnaires in 144 patients with different malignant diseases the incidence, patterns and necessity of treatment of fatigue were evaluated. Results: One third of the patients were diagnosed with breast cancer, 27% with gastrointestinal cancers and 20% suffered from haematologic/lymphatic diseases. There was a good correlation between fatigue levels in the 3 instruments used. 22% of all patients showed significant symptoms of fatigue. The univariate analysis did not reflect any significant differences in severity of fatigue with respect to diagnosis, haemoglobin levels, medical and therapeutic history or sociodemographic data. However, using cluster analysis we could identify 3 groups of patients that differ significantly in fatigue and quality-of-life measurements. Conclusion: We conclude from our data that fatigue is an important phenomenon in cancer patients who attend medical and psychosocial rehabilitation programs. This has an impact on the ability and degree to reintegrate these patients into everyday life.