Miracle-dz/UniFAR-FTUs huggingface dataset:
Characterization of Carbon Black Filled PDMS-Composite Membranes for Sensor Applications

This paper describes the characterization of conductive PDMS (CPDMS) composites. Composite have been achieved by filling the PDMS with CarbonBlack (CB). Two different methods were used to prepare the CPDMS composites: (A) direct mixing of CB with PDMS (CB-PDMS); (B) dissolving of CB in methanol before mixing with PDMS (CB-Methanol-PDMS). At a certain critical CB concentration, called percolation threshold, the membranes get conductive. Membranes of CPDMS (thickness ≈ 100µm) have been fabricated. CPDMS membranes of method (B) show a smoother surface profile as membranes of method (A). By means of a two–point resistivity measurement, the electrical resistance of CPDMS membranes was measured. With an increase of the CB concentration, the resistance decreases. Membranes of method (B) show a low percolation threshold and a low surface resistivity. Effects of pressure and temperature on the membrane resistance were investigated, too. Around the percolation threshold, the resistance shows the highest sensitivity on pressure and temperature variations. The Young’s modulus of CPDMS membranes exponentially increase with an increase of the CB concentration.
eg-VSSA: An extragradient variable sample-size stochastic approximation scheme: Error analysis and complexity trade-offs

Given a sampling budget M, stochastic approximation (SA) schemes for constrained stochastic convex programs generally utilize a single sample for each projection, requiring an effort of M projection operations, each of possibly significant complexity. We present an extragradient-based variable sample-size SA scheme (eg-VSSA) that uses N<inf>k</inf> samples at step k where Σ<inf>k</inf> N<inf>k</inf> ≤ M. We make the following contributions: (i) In strongly convex regimes, the expected error decays linearly in the number of projection steps; (ii) In convex settings, if the sample-size is increased at suitable rates and the steplength is optimally chosen, the error diminishes at O(1/K<sup>1−δ1</sup>) and O(1/√M), requiring O(M<sup>1</sup>/<sup>(2−δ2)</sup>) steps, where K denotes the number of steps and δ<inf>1</inf>,δ<inf>2</inf> > 0 can be made arbitrarily small. Preliminary numerics reveal that increasing sample-size schemes provide solutions of similar accuracy to SA schemes but with effort reduced by factors as high as 20.
An automated multi-satellite approach for soil moisture mapping using visible/infrared, passive microwave data and topographic attributes

This work presents a methodology for soil wetness mapping over a northern watershed. The approach is based on the use of a combination of passive microwave data from AMSR-E images, visible data provided by MODIS sensor and topographic attributes from a Digital Elevation Model. Classic topographical wetness indices, which are defined exclusively using topographic attributes, are static and unable to catch the temporal variability of soil moisture. In this work, we propose to overcome the static behavior of classic topographical wetness indices by assessing the temporal variability of the soil water content using passive microwave data and by introducing the vegetation effect into a wetness index. AMSR-E 37 GHz will be used to assess the wetness of the area. The proposed approach is an improvement in a dynamic sense over the classic topographic indices. The new topographic wetness index will downscale the global information about soil moisture provided by passive microwave data and take into account the variability of the surface conditions in the basin. The results obtained were compared to those derived from the classic index to assess the reliability of the dynamic index. The proposed index has provided a better estimation of the wetness over the basin. This implies that a combination of passive microwave data and topographic attributes has an interesting potential to improve the water balance closure over northern basins.
Construction and characterization of a fimA mutant of Porphyromonas gingivalis

Although fimbriae of Porphyromonas gingivalis have been implicated as playing a major role in adherence to gingival tissue surfaces, no conclusive genetic evidence has yet been obtained. The fimA gene, the determinant for the major fimbrial subunit protein, was cloned and sequenced (D. P. Dickinson, M. A. Kubiniec, F. Yoshimura, and R. J. Genco, J. Bacteriol. 170:1658-1665, 1988). We undertook to inactivate the fimA gene by a homologous recombination technique and examined the fimA mutant for changes in surface properties, including production of fimbriae, adherence to human gingival fibroblasts and epithelial cells, hemagglutinating activity, and surface hydrophobicity. To inactivate the fimA gene, we disrupted a fimA clone by insertion of a DNA segment containing an erythromycin resistance (Emr) gene. This was then delivered into P. gingivalis ATCC 33277 from an Escherichia coli K-12 strain, SM10 lambda pir, by using a mobilizable suicide vector, pGP704; recombination at the fimA locus led to the isolation of a fimA mutant. Disruption of the fimA locus and disappearance of FimA production were confirmed by Southern hybridization with a fimA-specific DNA probe and Western immunoblotting with a monoclonal antibody against the FimA protein, respectively. The fimA mutant constructed failed to express long (0.5- to 1.0-micron) fimbriae from the bacterial surface and had a diminished adhesive capacity to tissue-cultured human gingival fibroblasts and epithelial cells. Observation of the bacteria adhering to human gingival fibroblasts by scanning electron microscopy revealed that the wild-type strain had dramatic local changes in the appearance of the microvilli at the point of contact with large bacterial clumps, whereas the fimA mutant did not. In contrast, neither the hemagglutinating activity nor the surface hydrophobicity was changed in the fimA mutant. These data thus constitute the first direct genetic evidence demonstrating that the FimA protein of P. gingivalis is essential for the interaction of the organism with human gingival tissue cells through a function(s) encoded by the fimA gene.
Reconstructing tree crowns from laser scanner data for feature extraction

The objective of this study was to carry out reconstruction of single tree crowns from laser scanner data to use the obtained vector model for feature extraction. The reconstruction was implemented in several stages. First, pulses which have reflected from each tree were marked off from the original point cloud. Ground points were then separated from all points using digital terrain model and analysing the histogram of terrain height values. In the next stage canopy was described with vector polygons, and the location of the trunk was estimated. With respect to the location of the trunk, tree points were transferred from (xyz)-co-ordinate system to the polarco-ordinate system (α,r,h), and features were estimated from the vector model. Evaluation of the reconstruction was performed choosing a test area and processing 50 single trees, and comparing results to the field measurements. In the study it was found that dense laser scanner data detail describes the upper canopy of forest and therefore is suitable for tree height information extraction. The lower crown was found less detail measured with laser scanner and parameters extracted from that part were less accurate, but trend setting. Obtained distance profile seemed to give tendency for the tree specie.
Large-scale genome-wide association analysis of bipolar disorder identifies a new susceptibility locus near ODZ 4 Psychiatric GWAS Consortium Bipolar Disorder

Bipolar disorder is a severe mood disorder affecting more than 1% of the population 1. Family, twin and adoption studies consistently have found relative risks to first-degree relatives of affected individuals of ~8 and a concordance of ~40–70% for a monozygotic co-twin of affected individuals 1,2. Bipolar disorder shares phenotypic similarities with other psychiatric diseases, and relatives of individuals with bipolar disorder are at an increased risk of schizophrenia, major depression and schizoaffective disorder, suggesting a partially shared genetic basis for these disorders 3,4. Despite robust evidence for heritability, causal mutations have not been identified through linkage or candidate gene association studies 1. GWAS for bipolar disorder have been performed with multiple partially overlapping samples 5–11. In a previous small study, researchers reported a genome-wide significant association to DGKH (encoding diacylglycerol kinase eta) 5. Subsequently, researchers in another study 8 identified the region of ANK3 (encoding ankyrin 3) and those from a third 12 recently reported an association to NCAN (encoding neurocan); other studies did not report genome-wide significant loci 5,9,10,13. The Psychiatric GWAS Consortium (PGC) was established to facilitate the combination of primary genotype data and to allow analyses both within and across psychiatric disorders 14,15. Here, the PGC Bipolar Disorder Working Group reports results from our association study of bipolar disorder from 16,731 samples and a replication sample of 46,918 individuals. We received primary genotype and phenotype data (Table 1, Supplementary Note and Supplementary Table 1). Results have been reported singly 6,7,9–11 and in combinations 8,9,12 in seven publications with case and control overlap. We divided the data into 11 case and control groupings and assigned each individual to only one group (Table 1). The final dataset comprised 7,481 unique cases and 9,250 unique controls. Cases had the following diagnoses: bipolar disorder type 1 (n = 6,289; 84%), bipolar disorder type 2 (n = 824; 11%) and schizoaffective disorder bipolar (n = 263; 4%), and there were 105 individuals with other bipolar diagnoses (1%). We directly genotyped 46,234 SNPs in all 11 groups and genotyped 1,016,924 SNPs in between 2 and 11 groups. Based on reference haplotypes from the HapMap phase 2 CEU sample, we imputed missing genotypes using BEAGLE 16. We analyzed imputed SNP dosages from 2,415,422 autosomal SNPs with a minor allele frequency ≥1% and imputation quality score r 2 > 0.3. We performed logistic regression of case status on imputed SNP dosage including as covariates …
Polarized transport of the polymeric immunoglobulin receptor in transfected rabbit mammary epithelial cells

A cDNA for the rabbit low Mr polymeric immunoglobulin (poly-Ig) receptor was expressed in an immortalized rabbit mammary cell line. The intracellular routing of the receptor and its cell surface expression was analyzed in stably transfected cells grown on permeable supports. Initially the cells formed a monolayer with no transmural electrical resistance. All monolayer cells expressed the poly-Ig receptor and cytokeratin 7 filaments characteristic of luminal mammary cells but absent in myoepithelial cells. Within 7 d in culture, the cells underwent cytodifferentiation and formed a bilayer with a transepithelial electrical resistance of approximately 500 omega x cm2. Upper layer cells formed tight junctions with adjacent cells and gap junctions with basal cells. Expression of the poly-Ig receptor and cytokeratin 7 was restricted to the cells from the upper layer. The kinetics of receptor biosynthesis and processing was similar to that reported for rabbit mammary gland and rat liver. The receptor was cleaved at the apical cell surface and release of secretory component into the apical medium occurred with a half-time of approximately 2 h. Selective cell surface trypsinization combined with pulse-chase experiments served to determine at which cell surface domain newly synthesized receptor appeared first. The receptor was digested with a half-time of approximately 60 min with trypsin present in the basolateral medium and 90 min with apical trypsin. These data are consistent with selective targeting of newly synthesized receptor to the basolateral surface. The results indicate that transcytosis of the receptor from basolateral to apical membrane in the presence or the absence of its ligand requires approximately 30 min. Cleavage of the receptor by endogenous protease is not concomitant with its appearance at the apical surface, but requires additional time, thus explaining the presence of intact receptor on the apical membrane.
Intercostal thoracotomy in 20 dogs: muscle-sparing versus traditional techniques

The levels of pain, duration of approaching and closure, and surgical exposure associated with intercostal thoracotomy were compared between muscle-sparing and traditional techniques in 20 dogs. Postoperative pain was assessed based on numerical pain scores using behavioral observation, heart rate, respiratory rate, and wound palpation. Time for approaching and closure were measured, and the extent of intrathoracic organ exposure for the surgical procedures was described for each technique. There were significant differences in numerical pain scores at 2 h as well as 1, 2, 3, 4, 5, 6, and 7 days after surgery between the two groups (p < 0.0001). There was no significant (p = 0.725) difference in times for approaching and closure between the two groups. Compared to the traditional method, the muscle-sparing technique also achieved the desired exposure without compromising exposure of the target organs. Our results suggest that the muscle-sparing technique is more effective than the traditional method for providing a less painful recovery during the first 7 days after intercostal thoracotomy. Additionally, the muscle-sparing technique is as effective as the traditional modality for providing an appropriate time for approaching and closure during intercostal thoracotomy as well as adequate organ exposure for the surgical procedures.
Analysis of Polyubiquitin Conjugates Reveals That the Rpn10 Substrate Receptor Contributes to the Turnover of Multiple Proteasome Targets*S

The polyubiquitin receptor Rpn10 targets ubiquitylated Sic1 to the 26S proteasome for degradation. In contrast, turnover of at least one ubiquitin-proteasome system (UPS) substrate, CPY*, is impervious to deletion of RPN10. To distinguish whether RPN10 is involved in the turnover of only a small set of cell cycle regulators that includes Sic1 or plays a more general role in the UPS, we sought to develop a general method that would allow us to survey the spectrum of ubiquitylated proteins that selectively accumulate in rpn10Δ cells. Polyubiquitin conjugates from yeast cells that express hexahistidine-tagged ubiquitin (H6-ubiquitin) were first enriched on a polyubiquitin binding protein affinity resin. This material was then denatured and subjected to IMAC to retrieve H6-ubiquitin and proteins to which it may be covalently linked. Using this approach, we identified 127 proteins that are candidate substrates for the 26S proteasome. We then sequenced ubiquitin conjugates from cells lacking Rpn10 (rpn10Δ) and identified 54 proteins that were uniquely recovered from rpn10Δ cells. These include two known targets of the UPS, the cell cycle regulator Sic1 and the transcriptional activator Gcn4. Our approach of comparing the ubiquitin conjugate proteome in wild-type and mutant cells has the resolving power to identify even an extremely inabundant transcriptional regulatory protein and should be generally applicable to mapping enzyme substrate networks in the UPS.
High frequency of copy‐neutral LOH in MUTYH‐associated polyposis carcinomas

Genetic instability is known to drive colorectal carcinogenesis. Generally, a distinction is made between two types of genetic instability: chromosomal instability (CIN) and microsatellite instability (MIN or MSI). Most CIN tumours are aneuploid, whereas MSI tumours are considered near‐diploid. However, for MUTYH‐associated polyposis (MAP) the genetic instability involved in the carcinogenesis remains unclear, as near‐diploid adenomas, aneuploid adenomas and near‐diploid carcinomas have been reported. Remarkably, our analysis of 26 MAP carcinomas, using SNP arrays and flow sorting, showed that these tumours are often near‐diploid (52%) and mainly contain chromosomal regions of copy‐neutral loss of heterozygosity (LOH) (71%). This is in contrast to sporadic colon cancer, where physical loss is the main characteristic. The percentage of chromosomal gains (24%) is comparable to sporadic colorectal cancers with CIN. Furthermore, we verified our scoring of copy‐neutral LOH versus physical loss in MAP carcinomas by two methods: fluorescence in situ hybridization, and LOH analysis using polymorphic markers on carcinoma fractions purified by flow sorting. The results presented in this study suggest that copy‐neutral LOH is an important mechanism in the tumorigenesis of MAP. Copyright © 2008 Pathological Society of Great Britain and Ireland. Published by John Wiley & Sons, Ltd.
The Physical Church–Turing Thesis: Modest or Bold?

This article defends a modest version of the Physical Church-Turing thesis (CT). Following an established recent trend, I distinguish between what I call Mathematical CT—the thesis supported by the original arguments for CT— and Physical CT. I then distinguish between bold formulations of Physical CT, according to which any physical process—anything doable by a physical system—is computable by a Turing machine, and modest formulations, according to which any function that is computable by a physical system is computable by a Turing machine. I argue that Bold Physical CT is not relevant to the epistemological concerns that motivate CT and hence not suitable as a physical analog of Mathematical CT. The correct physical analog of Mathematical CT is Modest Physical CT. I propose to explicate the notion of physical computability in terms of a usability constraint, according to which for a process to count as relevant to Physical CT, it must be usable by a finite observer to obtain the desired values of a function. Finally, I suggest that proposed counterexamples to Physical CT are still far from falsifying it because they have not been shown to satisfy the usability constraint. 1 The Mathematical Church–Turing Thesis 2 A Usability Constraint on Physical Computation 3 The Bold Physical Church–Turing Thesis 3.1 Lack of confluence 3.2 Unconstrained appeals to real-valued quantities 3.3 Falsification by irrelevant counterexamples 4 The Modest Physical Church–Turing Thesis 4.1 Hypercomputation: genuine and spurious 4.2 Relativistic hypercomputers 4.3 Other challenges to Modest Physical CT 5 Conclusion 1 The Mathematical Church–Turing Thesis 2 A Usability Constraint on Physical Computation 3 The Bold Physical Church–Turing Thesis 3.1 Lack of confluence 3.2 Unconstrained appeals to real-valued quantities 3.3 Falsification by irrelevant counterexamples 3.1 Lack of confluence 3.2 Unconstrained appeals to real-valued quantities 3.3 Falsification by irrelevant counterexamples 4 The Modest Physical Church–Turing Thesis 4.1 Hypercomputation: genuine and spurious 4.2 Relativistic hypercomputers 4.3 Other challenges to Modest Physical CT 4.1 Hypercomputation: genuine and spurious 4.2 Relativistic hypercomputers 4.3 Other challenges to Modest Physical CT 5 Conclusion
Rules in database systems

Extending database systems with deductive and active rules is one of the major steps in the recent evolution of database technology. By means of rules, database designers express both declarative and procedural knowledge about their applications; rules introduce a significant increase of the expressive power of database languages, resulting in the enhancement of processing capabilities within database servers. Deductive rules were influenced by work in logic programming and offer a rich query language that extends SQL in many important directions (including support for aggregation, negation, and recursion). Deductive rules express declarative knowledge: they represent queries in a style that reflects the meaning of the query itself and does not depend on the query evaluation strategy. Thus they have a pure declarative semantics. In addition, rules may be interpreted as integrity constraints. Computationally, the goal of deductive databases is to deal with a superset of relational algebra that includes support for recursion in a way that permits efficient handling of disk data. Evaluation strategies should retain Prolog’s goal-directed flavor, but be more set-ata-time. There are two aspects to setorientation:
13C Metabolic Flux Analysis Identifies an Unusual Route for Pyruvate Dissimilation in Mycobacteria which Requires Isocitrate Lyase and Carbon Dioxide Fixation

Mycobacterium tuberculosis requires the enzyme isocitrate lyase (ICL) for growth and virulence in vivo. The demonstration that M. tuberculosis also requires ICL for survival during nutrient starvation and has a role during steady state growth in a glycerol limited chemostat indicates a function for this enzyme which extends beyond fat metabolism. As isocitrate lyase is a potential drug target elucidating the role of this enzyme is of importance; however, the role of isocitrate lyase has never been investigated at the level of in vivo fluxes. Here we show that deletion of one of the two icl genes impairs the replication of Mycobacterium bovis BCG at slow growth rate in a carbon limited chemostat. In order to further understand the role of isocitrate lyase in the central metabolism of mycobacteria the effect of growth rate on the in vivo fluxes was studied for the first time using 13C-metabolic flux analysis (MFA). Tracer experiments were performed with steady state chemostat cultures of BCG or M. tuberculosis supplied with 13C labeled glycerol or sodium bicarbonate. Through measurements of the 13C isotopomer labeling patterns in protein-derived amino acids and enzymatic activity assays we have identified the activity of a novel pathway for pyruvate dissimilation. We named this the GAS pathway because it utilizes the Glyoxylate shunt and Anapleurotic reactions for oxidation of pyruvate, and Succinyl CoA synthetase for the generation of succinyl CoA combined with a very low flux through the succinate – oxaloacetate segment of the tricarboxylic acid cycle. We confirm that M. tuberculosis can fix carbon from CO2 into biomass. As the human host is abundant in CO2 this finding requires further investigation in vivo as CO2 fixation may provide a point of vulnerability that could be targeted with novel drugs. This study also provides a platform for further studies into the metabolism of M. tuberculosis using 13C-MFA.
Androgen receptor polymorphisms and the incidence of prostate cancer.

The human androgen receptor gene contains polymorphic CAG and GGC repeats in exon 1. We investigated whether the number of CAG and/or GGC repeats is related to prostate cancer risk in a case-control study nested within the beta Carotene and Retinol Efficacy Trial. Among 300 cases and 300 controls, we did not observe any increase in risk associated with fewer CAG or GGC repeats. We observed a nonsignificant decrease in risk associated with each unit of decrease in CAG length [odds ratio (OR), 0.98; 95% confidence interval (CI), 0.93-1.03). Men with CAG <22 had a relative risk of prostate cancer of 0.89 (95% CI, 0.65-1.23) compared with men with CAG > or =22. There was no appreciable difference in the mean number of GGC repeats between cases and controls; the estimated change in the risk of prostate cancer associated with one fewer GGC repeat was 0.97 (95% CI, 0.88-1.06). The risk in men at or below the mean number of GGC repeats (17) was 0.80 (95% CI, 0.57-1.12). In contrast to prior reports, men with both short CAG (<22) and short GGC (< or =17) repeats were not at increased risk of prostate cancer (OR, 0.56; 95% CI, 0.32-0.98), compared with men with > or =22 CAG repeats and >17 GGC repeats. Our results do not support the hypothesis that a small number of CAG or GGC repeats in the androgen receptor gene increases a man's risk of prostate cancer.