Miracle-dz/UniFAR-FTUs huggingface dataset:
Three-dimensional contact of TITH cartilage layers, a closed-form solution

Inhomogeneity and anisotropy play a crucial role in attributing articular cartilage its properties. The frictionless contact model constructed here consists in two thin biphasic transversely isotropic transversely homogeneous (TITH) cartilage layers firmly attached onto rigid substrates and shaped as elliptic paraboloids of different radii. Using asymptotic techniques, a solution to the deformation problem of such material has been recently obtained extending previous ones referred to homogeneous materials. The layer itself is thin in comparison with the size of the contact area and the observed time is shorter than the hydrogel characteristic time. The emerging three-dimensional contact problem is solved in closed-form and numerical benchmarks for constant and oscillating loads are given. The results are shown in terms of contact pressure and approach of the bones. The latter is derived to be directly proportional to the contact area. Existing experimental data are reinterpreted in view of the current model formulation. Comparisons are made with existing solutions for homogeneous biphasic materials in order to underline the functional importance of inhomogeneity in spreading the contact pressure distribution across the contact area. Particular attention is paid to the applicability of the retrieved formulas for interpreting measurements of in vivo experiments. Future directions are also prospected.
Homologous and non‐homologous recombination differentially affect DNA damage repair in mice

Ionizing radiation and interstrand DNA crosslinking compounds provide important treatments against cancer due to their extreme genotoxicity for proliferating cells. Both the efficacies of such treatments and the mutagenic potential of these agents are modulated by the ability of cells to repair the inflicted DNA damage. Here we demonstrate that homologous recombination‐deficient mRAD54−/− mice are hypersensitive to ionizing radiation at the embryonic but, unexpectedly, not at the adult stage. However, at the adult stage mRAD54 deficiency dramatically aggravates the ionizing radiation sensitivity of severe combined immune deficiency (scid) mice that are impaired in DNA double‐strand break repair through DNA end‐joining. In contrast, regardless of developmental stage, mRAD54−/− mice are hypersensitive to the interstrand DNA crosslinking compound mitomycin C. These results demonstrate that the two major DNA double‐strand break repair pathways in mammals have overlapping as well as specialized roles, and that the relative contribution of these pathways towards repair of ionizing radiation‐induced DNA damage changes during development of the animal.
On the Fixation Process of a Beneficial Mutation in a Variable Environment

A population that adapts to gradual environmental change will typically experience temporal variation in its population size and the selection pressure. On the basis of the mathematical theory of inhomogeneous branching processes, we present a framework to describe the fixation process of a single beneficial allele under these conditions. The approach allows for arbitrary time-dependence of the selection coefficient s(t) and the population size N(t), as may result from an underlying ecological model. We derive compact analytical approximations for the fixation probability and the distribution of passage times for the beneficial allele to reach a given intermediate frequency. We apply the formalism to several biologically relevant scenarios, such as linear or cyclic changes in the selection coefficient, and logistic population growth. Comparison with computer simulations shows that the analytical results are accurate for a large parameter range, as long as selection is not very weak.
Exploring pathways across stories Conference Item

This paper describes a method for supporting the exploration of a collection of documents organized as a hypertext by investigating relations between documents along userspecified paths. The approach is demonstrated on a corpus of stories about the World War Two activities of the British Government Code and Cypher School at Bletchley Park. Each story is described by one or more events and annotated in terms of domain ontologies. A pathway in the document space is a sequence of events in which adjacent events share common binding concepts. The criteria for selecting the pathway include a measure of the adherence to the user-specified part of the document space and the mutual information between adjacent documents calculated from their annotations.
An Iterative Multiuser Detector for DS-CDMA

We propose an iterative multiuser detector for Turbo coded Direct Sequence CDMA (DS-CDMA) systems. The receiver is derived from the Maximum a-Posteriori (MAP) estimation of the single user’s transmitted data, conditioned on information about the estimate of the Multiple Access Interference (MAI) and the received signal from the channel. The complexity of the proposed receiver increases linearly with the number of users. Performances that are very close to the single user performance are obtained after few numbers of iterations. Keywords-Iterative decoding, Multiuser detection, Code-division multiple access (CDMA), Turbo codes.
Fast and Robust Semi-Automatic Registration of Photographs to 3D Geometry

We present a simple, fast and robust technique for semi-automatic 2D-3D registration capable to align a large set of unordered images to a massive point cloud with minimal human effort. Our method converts the hard to solve image-to-geometry registration problem in a Structure-from-Motion (SfM) plus a 3D-3D registration problem. We exploit a SfM framework that, starting just from the unordered image collection, computes an estimate of camera parameters and a sparse 3D geometry deriving from matched image features. We then coarsely register this model to the given 3D geometry by estimating a global scale and absolute orientation using minimal manual intervention. A specialized sparse bundle adjustment (SBA) step, exploiting the correspondence between the model deriving from image features and the fine input 3D geometry, is then used to refine intrinsic and extrinsic parameters of each camera. Output data is suitable for photo blending frameworks to produce seamless colored models. The effectiveness of the method is demonstrated on a series of real-world 3D/2D Cultural Heritage datasets.
Effects of non‐sedative anxiolytic drugs on responses to GABA and on diazepam‐induced enhancement of these responses on mouse neurones in cell culture

1 Intracellular microelectrode recording techniques were performed on mouse spinal cord and cerebral hemisphere neurones grown in primary dissociated cell culture. The effects of several anxiolytics applied by local pressure ejection on responses to γ‐aminobutyric acid (GABA) evoked by iontophoresis were investigated. Responses to GABA were depolarizing since intracellular chloride ion concentration was increased by injection from potassium chloride (3 M)‐filled recording micropipettes and neurones were held at large negative membrane potentials (—70 to —90 mV). The agents studied were six ‘non‐sedative anxiolytics’, CL 218,872 (3‐methyl‐6‐(3‐trifluoromethyl‐phenyl) 1, 2,4‐triazolo(4,3‐b) pyridazine), PK 8165 (2‐phenyl‐4‐(2‐(4‐piperidinyl)ethyl)‐quinoline), PK 9084 (2‐phenyl‐4‐(2‐(3‐piperidinyl)ethyl)‐quinoline), CGS 9896 (2‐(4‐chlorophenyl)‐2,5‐dihydropyrazolo(4,3‐c)quinoline‐3(3H)‐one), ZK 91296 (ethyl 5‐benzyloxy‐4‐methoxymethyl‐β‐carboline‐3‐β‐carboxylate), buspirone (8‐4‐[4‐(2‐pyrimidinyl)‐1‐piperazinyl]butyl‐8‐azaspiro[4.5]decane‐7,9‐dione), and two sedative anxiolytics, diazepam and zopiclone ([6‐(5‐chloro‐2‐pyridyl)‐6,7‐dihydro‐7‐oxo‐5 H‐pyrrolo [3,4‐b] pyrazin‐5‐yl] 4‐methyl‐1‐piperazinecarboxylate). 2 Direct effects on responses to GABA were studied for all drugs applied in varying concentrations. For the drugs which significantly altered responses to GABA, the effects of the benzodiazepine receptor antagonists Ro 15–1788 (ethyl‐8‐fluoro‐5,6‐dihydro‐5‐methyl‐6‐oxo‐4H‐imidazo(1,5a)‐(1,4)benzodiazepine‐3‐carboxylate) and CGS 8216 (2‐phenylpyrazolo(4,3‐c)‐quinolin‐3(5H)‐one) were evaluated. For the drugs devoid of significant direct effect on responses to GABA, the influence on diazepam‐induced enhancement of responses to GABA was evaluated. 3 Diazepam, zopiclone and CL 218,872 concentration‐dependently and reversibly enhanced responses to GABA. Maximal enhancement was 82% for diazepam (500 nM), 64% for zopiclone (10 μM) and 20% for CL 218,872 (10 μM). PK 8165 effects varied with concentration, enhancing responses to GABA (up to 18%) at nM concentrations and reducing responses to GABA (up to 90%) at μM concentrations. CGS 9896, ZK 91296, PK 9084 and buspirone, in concentrations ranging from 1 nM to 10 μM, lacked significant direct effects on responses to GABA. 4 The enhancing effects of diazepam, zopiclone, CL 218,872 and PK 8165 were antagonized by Ro 15–1788. However, the reducing effect on responses to GABA of PK 8165 at μM concentrations was not antagonized by CGS 8216. CGS 9896 and ZK 91296 concentration‐dependently blocked the diazepam‐induced enhancement of responses to GABA. However, PK 9084 and buspirone did not antagonize the diazepam‐induced enhancement of responses to GABA. 5 These results indicate that diazepam and zopiclone may be full agonists, CL 218,872 and PK 8165 are partial agonists, and CGS 9896 and ZK 91296 are pure antagonists at benzodiazepine receptors. On the other hand, PK 9084 and buspirone do not interact with benzodiazepine receptors.
Neuromechanical response of musculo-skeletal structures in cockroaches during rapid running on rough terrain

SUMMARY A musculo-skeletal structure can stabilize rapid locomotion using neural and/or mechanical feedback. Neural feedback results in an altered feedforward activation pattern, whereas mechanical feedback using visco-elastic structures does not require a change in the neural motor code. We selected musculo-skeletal structures in the cockroach (Blaberus discoidalis) because their single motor neuron innervation allows the simplest possible characterization of activation. We ran cockroaches over a track with randomized blocks of heights up to three times the animal's `hip' (1.5 cm), while recording muscle action potentials (MAPs) from a set of putative control musculo-skeletal structures (femoral extensors 178 and 179). Animals experienced significant perturbations in body pitch, roll and yaw, but reduced speed by less than 20%. Surprisingly, we discovered no significant difference in the distribution of the number of MAPs, the interspike interval, burst phase or interburst period between flat and rough terrain trials. During a few very large perturbations or when a single leg failed to make contact throughout stance, neural feedback was detectable as a phase shift of the central rhythm and alteration of MAP number. System level responses of appendages were consistent with a dominant role of mechanical feedback. Duty factors and gait phases did not change for cockroaches running on flat versus rough terrain. Cockroaches did not use a follow-the-leader gait requiring compensatory corrections on a step-by-step basis. Arthropods appear to simplify control on rough terrain by rapid running that uses kinetic energy to bridge gaps between footholds and distributed mechanical feedback to stabilize the body.
Evidence that methylation of hepatitis B virus covalently closed circular DNA in liver tissues of patients with chronic hepatitis B modulates HBV replication

Epigenetic factors may modulate chronic Hepatitis B viral infection by affecting virion gene transcription. The aim of this study was to compare the methylation status of the intrahepatic covalently closed circular DNA (cccDNA) CpG island 2 and HBV replication capability. HBV cccDNA was extracted from liver biopsies of 55 HBsAg‐positive patients with chronic hepatitis B (32 HBeAg‐positive and 23 HBeAg‐negative), and was analyzed for methylation status and quantity. The two Hpa II recognition sequences CCpGG in the CpG island 2 were methylated in infected liver tissues from 24 (43.6%) of 55 patients. Positive ratios of cccDNA methylation were significantly higher in HBeAg‐negative patients (15/23, 65.2%) than HBeAg‐positive patients (9/32, 28.1%) (P < 0.05). The percentage of methylated‐cccDNA/total‐cccDNA of HBeAg‐negative samples (a median of 48%, ranging from 5% to 83%) was significantly higher (P < 0.001) than HBeAg‐positive samples (a median of 14%, ranging from 0.26% to 35%). Ratios of relaxed circular DNA (rcDNA) to cccDNA molecules revealed that cccDNA methylation correlated with impaired virion productivity in HBeAg‐positive individuals (P < 0.05). The bisulfite DNA sequencing showed that methylation density was significantly higher in HBeAg‐negative than in HBeAg‐positive patients (P < 0.05). The methylation level of the CpG island 2 of the cccDNA in HBeAg‐negative patients was higher than that in HBeAg‐positive patients, suggesting that HBV cccDNA methylation may be relevant to replication capability of HBV. J. Med. Virol. 81:1177–1183, 2009. © 2009 Wiley‐Liss, Inc.
Population Pharmacokinetic Model of Carbamazepine Derived from Routine Therapeutic Drug Monitoring Data

The aim of the present study was to develop a population pharmacokinetic model of carbamazepine from routine therapeutic drug monitoring data. Steady-state carbamazepine plasma concentrations determined by homogenous enzyme immunoassay technique, dosing history including cotherapy, schedule of blood sampling, and patients' demographic characteristics were collected retrospectively from patients' chart histories. A one-compartment model was fitted to the data using nonlinear mixed effects modeling. The influence of weight, age, gender, smoking, allergy, carbamazepine daily dose, and cotherapy on clearance (CL/F) was evaluated. Additionally, bioavailability of controlled-release relative to immediate-release tablets was assessed. Two hundred sixty-five patients (423 concentrations) were used to develop a population pharmacokinetic model. The population estimate of CL/F from the base model was 5.14 L/h with interindividual variability of 50.20%. Patients' gender, age, smoking, allergy, cotherapy with lamotrigine and benzodiazepines had no effect on CL/F. Patient weight (WT), daily carbamazepine dose (DCBZ), daily dose of phenobarbitone (DPB) and valproic acid (VPA), when its daily dose exceeded 750 mg, significantly influenced CL/F and were included in the final model: where VPA is 1 if dose is greater than 750 mg or 0 otherwise. No difference in bioavailability of carbamazepine between controlled- and immediate-release tablets was detected. The model predictions in the validation set had no bias and satisfactory precision. The model can be used for estimation of carbamazepine CL/F in individual patients in the postautoinduction phase and for selection of optimum dosing regimen in routine patient care.
Probiotics as beneficial agents in the management of diabetes mellitus: a systematic review

Probiotics have been suggested to play an important role in the management of diabetes. We conducted a systematic review on the role of probiotics in modulating parameters related to diabetes in animal and human experiments. We searched Pubmed, Scopus and Cochrane central until June 2014, concerning the effects of probiotics on hyperglycemia, hyperinsulinemia and their anti‐diabetic efficacies by modulating the activities of proinflammatory and antioxidant factors. Our initial search retrieved 1120 reports. After screening titles and abstracts, 72 full‐text articles were reviewed for eligibility. Ultimately, 33 articles met our inclusion criteria consisting of five human and twenty eight animal reports. Lactobacillus strains were, in particular, used in all studies with or without other strains. We found that probiotics have beneficial effects on glycemic controls, as all human studies showed significant reductions in at least one of the primary outcome endpoints which were the levels of fasting plasma glucose, postprandial blood glucose, glycated haemoglobin, insulin, insulin resistance and onset of diabetes; similarly, all the animal reports, except for two, documented significant changes in these parameters. Regarding secondary outcome measures, that is, lipid profiles, pro‐inflammatory and anti‐oxidant factors, only one human and one animal study failed to show any significant changes in any of these parameters. This systematic review generally demonstrated beneficial effects of the probiotic administration, especially Lactobacillus sub‐strains, on the management of diabetes‐related blood parameters, although, more evidence, especially from human trials, is needed to confirm these effects and also to conduct a meta‐analysis. Copyright © 2015 John Wiley & Sons, Ltd.
Exploring ANN back-ends for i-vector based speaker age estimation

We address the problem of speaker age estimation using ivectors. We first compare different i-vector extraction setups and then focus on (shallow) artificial neural net (ANN) backends. We explore ANN architecture, training algorithm and ANN ensembles. The results on NIST 2008 and 2010 SRE data indicate that, after extensive parameter optimization, ANN back-end in combination with i-vectors reaches mean absolute errors (MAEs) of 5.49 (females) and 6.35 (males), which are 4.5% relative improvement in comparison to our support-vector regression (SVR) baseline. Hence, the choice of back-end did not affect the accuracy much; a suggested future direction is therefore focusing more on front-end processing. Index Terms: age estimation, i-vector, multilayer perceptron
COMPRESSIVE, FLEXURAL AND SPLITTING TENSILE STRENGTHS OF LIGHTWEIGHT FOAMED CONCRETE WITH INCLUSION OF STEEL FIBRE

Lightweight foamed concrete (LFC) application in building construction is rather limited due to its low strength and brittleness. This study has been undertaken to investigate the effects of steel fibers lightweight foamed concrete at a relatively low volume fraction (0.2 % and 0.4 %) on the mechanical properties such as compressive strength, flexural strength and splitting tensile strength. Steel fibres were used as additives. The foamed concrete was designed to achieve the result of effect from volume fraction of steel fibres used with different density of 700 and 1200 kg/m 3 at the age of 7, 28 and 60 days. Detail experiments were setup to study the behavior and reaction of additives which is expected to give different results on mechanical properties of lightweight foamed concrete. The result showed, addition steel fibres have greater contributions in terms of mechanical properties in LFC.
Human RNase H1 Uses One Tryptophan and Two Lysines to Position the Enzyme at the 3′-DNA/5′-RNA Terminus of the Heteroduplex Substrate*

In a previous study, we showed that the RNA-binding domain of human RNase H1 is responsible for the positional preference for cleavage exhibited by the enzyme (Wu, H., Lima, W. F., and Crooke, S. T. (2001) J. Biol. Chem. 276, 23547–23553). Here, we identify the substituents on the heteroduplex substrate and the amino acid residues within the RNA-binding domain of human RNase H1 involved in positioning of the enzyme. The human RNase H1 cleavage patterns observed for heteroduplexes with various 3′-DNA/5′-RNA and 5′-DNA/3′-RNA termini indicate that the 5′-most cleavage site on the oligoribonucleotide is positioned 7 bp from the first 3′-DNA/5′-RNA base pair. The presence or absence of phosphate or hydroxyl groups at either the 3′-DNA or 5′-RNA terminus had no effect on the human RNase H1 cleavage pattern. Substitution of the 3′-deoxynucleotide with a ribonucleotide, 2′-methoxyethyl nucleotide, or mismatched deoxyribonucleotide resulted in the ablation of the 5′-most cleavage site on the oligoribonucleotide. Mutants in which Trp43 and Lys59-Lys60 of the RNA-binding domain were substituted with alanine showed a loss of the positional preference for cleavage. Comparison of the kcat, Km, and Kd for the alanine-substituted mutants with those for human RNase H1 suggests that Lys59 and Lys60 are involved in binding to the heteroduplex and that Trp43 is responsible for properly positioning the enzyme on the substrate for catalysis. These data suggest that Trp43, Lys59, and Lys60 constitute an extended nucleic binding surface for the RNA-binding domain of human RNase H1, with the entire interaction taking place at the 3′-DNA/5′-RNA pole of the heteroduplex. These results offer further insights into the interaction between human RNase H1 and the heteroduplex substrate as well as approaches to enhance the design of effective antisense oligonucleotides.
Effect of fuel film deposition on combustion process in PFI SI engine

The present paper discusses the experimental investigations on the flame induced by fuel film deposition ignition in a single cylinder, ported fuel injection, four-stroke, over-boosted spark-ignition engine with a four-valve production head. The engine was optically accessible and equipped with a transparent quartz window in the bottom of the combustion chamber. 2D-digital imaging and UV-visible natural emission spectroscopy were used to follow the flame propagation in the combustion chamber. Two colour pyrometers were applied to evaluate flame temperature and soot concentration. Particulate matter and soot primary particles diameters were measured and correlated with the soot amount produced in the combustion chamber. The effect of the intake air pressure and injection phasing was investigated. Optical setup for spectroscopic measurements and visible digital imaging, visible flame emission detected in the chamber for the selected operating conditions, visible emission spectra measured at 60 CAD ASOS in the chamber, soot concentration measured at the selected operating conditions, integral soot concentration measured at the selected operating conditions, particulate mass concentration measured by the Opacimeter and particles number concentration measured by LII at the engine exhaust are presented in the paper.
Evaluation of Endometrial Jet Wash Technic (Gravlee) in 303 Patients in a Community Hospital

Gravlee jet wash was performed on 303 patients under anesthesia, and the results correlated with histologic findings in all instances. The results were fully reliable in advanced endometrial cancer, although there were several failures in the diagnosis of focal cancer occurring in hyperplasia and in the diagnosis of hyperplasia of various types. Possible reasons for these failures are discussed in extenso. It Is suggested that the finding of hyperplastic endometrium in the jet wash cell block should trigger a search for endometrial carcinoma. It Is also suggested that a negative jet wash in a symptomatic patient is not sufficient indication for withholding a diagnostic curettage. The major advantage of the jet wash is to provide the pathologist with diagnostic material with which he has greater familiarity than with the cytologic sample. Failures with the jet wash technic arc in keeping with those incurred with other diagnostic procedures and should not detract from its use.