Miracle-dz/UniFAR-FTUs huggingface dataset:
Sperm count and chromatin structure in men exposed to inorganic lead: lowest adverse effect levels

Objectives: To obtain knowledge on male reproductive toxicity of inorganic lead at current European exposure levels and to establish lowest adverse effect levels, if any. Methods: A cross sectional survey of the semen of 503 men employed by 10 companies was conducted in the United Kingdom, Italy, and Belgium. The mean blood lead concentration was 31.0 μg/dl (range 4.6–64.5) in 362 workers exposed to lead and 4.4 μg/dl (range below the detection limit of 19.8) in 141 reference workers. Semen volume and sperm concentration were determined in a fresh semen sample according to an agreed protocol subject to quality assurance. The sperm chromatin structure assay (SCSA) was performed at a centralised laboratory. Extraneous determinants including centre, period of sexual abstinence, and age were taken into account in the statistical analysis. If appropriate, possible thresholds were examined by iterative threshold slope linear regression. Results: The median sperm concentration was reduced by 49% in men with blood lead concentration above 50 μg/dl. There was no indication of a linear trend of lower sperm concentration with increasing blood lead values, but threshold slope least square regression identified a blood lead concentration of 44 μg/dl (β=−0.037, F=4.35, p=0.038) as a likely threshold. Abnormal sperm chromatin structure was not related to blood lead concentration, but some indications of deterioration of sperm chromatin was found in men with the highest concentrations of lead within spermatozoa. Biological monitoring data did not indicate long term effects of lead on semen quantity or sperm chromatin. Conclusion: Adverse effects of lead on sperm concentration and susceptibility to acid induced denaturation of sperm chromatin are unlikely at blood lead concentrations below 45 μg/dl. Effects of low level exposure to lead on other measures of testicular function cannot be ruled out.
Multilayered retinal microglial response to optic nerve transection in rats.

PURPOSE Microglia normally exist in several layers across the retinal thickness. When retinal ganglion cells undergo apoptosis after lesion to their axons, microglial cells proliferate and promptly clear the debris. We have previously reported on the phagocytic response following optic nerve axotomy. Here, we present how microglial cells of deeper retinal layers are affected by transection of the optic nerve. METHODS Normal and reactive microglia in the retina of adult rats whose optic nerves had been lesioned were labeled by using antibodies OX42 and ED1. Analysis of the time course (between 1 and 180 days post-axotomy) of appearance and distribution of microglial cells in the retinal layers was performed. RESULTS In normal retinas, microglia were found in the ganglion cell layer (GCL), the superficial inner nuclear layer (INL) and the outer plexiform layer (OPL). Increases in numbers of microglia occurred maximally in the GCL at day 12 post-axotomy. Increases were also detected in the superficial INL. The proliferation of these phagocytic cells led to their highest numbers in the more central eccentricities in the two most superficial layers. Microglia in the OPL remained undisturbed. Microglial normal histology is restored over a period of 6 months as dying ganglion cells disappear. CONCLUSIONS Histological characteristics of normal rat retinal microglia are uniform across different retinal eccentricities for each of the three laminae where they exist. Retinal microglia of various layers respond to optic nerve damage. Their increase in numbers and morphological transformation follow retinal ganglion cell death. Their morphology, density, and layered distribution slowly return to normal, confirming that retinal ganglion cells, or their densities, do not play any role in dictating microglial distribution within the different retinal layers.
cHCC‐CCA: Consensus terminology for primary liver carcinomas with both hepatocytic and cholangiocytic differentation

Primary liver carcinomas with both hepatocytic and cholangiocytic differentiation have been referred to as “combined (or mixed) hepatocellular‐cholangiocarcinoma. ” These tumors, although described over 100 years ago, have attracted greater attention recently because of interest in possible stem cell origin and perhaps because of greater frequency and clinical recognition. Currently, because of a lack of common terminology in the literature, effective treatment and predictable outcome data have been challenging to accrue. This article represents a consensus document from an international community of pathologists, radiologists, and clinicians who have studied and reported on these tumors and recommends a working terminology for diagnostic and research approaches for further study and evaluation. Conclusion: It is recommended that diagnosis is based on routine histopathology with hematoxylin and eosin (H&E); immunostains are supportive, but not essential for diagnosis. (Hepatology 2018;68:113‐126).
A parametric model for constitutive properties governing multiphase flow in porous media

A parametric model is developed to describe relative permeability-saturation-fluid pressure functional relationships in two- or three-fluid phase porous media systems subject to monotonic saturation paths. All functions are obtained as simple closed-form expressions convenient for implementation in numerical multiphase flow models. Model calibration requires only relatively simple determinations of saturation-pressure relations in two-phase systems. A scaling procedure is employed to simplify the description of two-phase saturation-capillary head relations for arbitrary fluid pairs and experimental results for two porous media are presented to demonstrate its applicability. Extension of two-phase relations to three- phase systems is obtained under the assumption that fluid wettability follows the sequence water > nonaqueous phase liquid > air. Expressions for fluid relative permeabilities are derived from the scaled saturation-capillary head function using a flow channel distribution model to estimate effective mean fluid-conducting pore dimensions. Constraints on model application are discussed.
Bending and vibration of monolayer MoS2 beams by molecular dynamics simulations

Molecular dynamics simulations based on reactive empirical bond-order potentials were conducted to investigate the bending and vibration of defect-free and defective monolayer MoS2. The effects of constrained boundary conditions and single sulfur point vacancies were concerned. Three types of boundary conditions were discussed in our work, including the simply supported boundary, the pinned-pinned boundary, and the clamped-clamped boundary. For the simply supported beam, typical linear and nonlinear elasticity responses to the lateral loading were observed, distinct from the other beams. The lower concentrations of VS defect were found to have insignificant effects on the bending and vibrational responses of the defective MoS2, despite a slight frequency drift appeared. However, higher order resonant frequencies were arisen in some monolayer MoS2 with randomly distributed VS defects.
Haptic, Auditory, or Visual?: Towards Optimal Error Feedback at Manual Assembly Workplaces

We are observing a trend that more and more manual assembly workplaces are equipped with sensor technology to assist workers during complex work tasks. These assistive systems mostly use visual feedback for providing assembly instructions or hinting at errors. However, a red light indicating an error might not always be the best solution for communicating that an error was made, or might be overlooked in stressful situations. Therefore, we extended an assitsive system to compare haptic, auditory, and visual error feedback at the manual assembly workplace. Through two user studies, we first determine suitable variants for each error feedback modality and second compare the error feedback modalities against each other. The results show that haptic feedback is appropriate for retaining the worker's privacy, and auditory feedback is perceived as most distracting. The subjective feedback reveals interesting insights for future research in communicating errors as a combination of haptic and visual feedback might lead to noticing an error faster.
Output Convergence between Western Balkans and EU-15

This paper analyses the relative position of the Western Balkan countries (ex-Yugoslavia countries and Albania) in comparison to more advanced European economies in the context of possible further EU enlargement. First, the question of convergence between Western Balkan countries and the EU-15 is empirically estimated. The paper also discusses the evolution of the gap and the possible determinants that could act in the direction of its decrease. The main findings are that Western Balkan countries show no sign of convergence. Furthermore, the factors that should contribute to closing the gap are not widely featured in the analysed countries.
Reconstruction and Interpretation of 3 D Whole Body Surface Images

In this talk we will present recent developments in techniques for the reconstruction and interpretation of 3D human, whole-body surface images. The data captured by whole-body image capture systems is typically noisy, and has areas of occlusion, such as at the branch points of the body. This causes a number of problems in the reconstruction of the whole body surface, extracting useful anthropometric information, rendering or animating body models. The use of model-based approaches, which include knowledge about human body topology, leads to improved results over general-purpose techniques. Once the body surface has been constructed, landmark features and anthropometric information can be extracted. Approaches to feature detection will be described, and recent results for 3D anthropometry presented and discussed. Reconstruction et interprétation d'images 3D de la surface du corps entier Nous présentons ici les développements récents des techniques de reconstruction et d'interprétation d'images de la surface du corps humain tout entier. Les données acquises par un système d'acquisition corps entier sont généralement bruitées, et ont des zones d'occlusion, par exemple aux points de jonction du corps. Ceci amène un certain nombre de problèmes lors de la reconstruction du corps, pour extraire des données anthropométriques pertinentes, obtenir un rendu et animer des modèles du corps. L'utilisation d'approches à base de modèles, qui incluent des connaissances sur la topologie du corps humain, améliorent les résultats quelque-soit l'objectif. Une fois la surface du corps construite, des points de repère ainsi que des données anthropométriques peuvent être extraits. Nous décrirons des approches pour la détection d'éléments caractéristiques, et nous présenterons et discuterons des résultats récents d'anthropométrie 3D.
Composition of supra- and subgingival biofilm of subjects with healthy and diseased implants.

OBJECTIVES The purpose of this study was to compare the microbial composition of supra- and subgingival biofilm in subjects with and without peri-implantitis. MATERIAL AND METHODS Forty-four subjects (mean age 48.9 +/- 13.51 years) with at least one implant restored and functional for at least 2 years were assigned to two groups: a peri-implantitis group (n=22), consisting of subjects presenting peri-implant sites with radiographic defects >3 mm, bleeding on probing and/or suppuration; and a control group (n=22), consisting of subjects with healthy implants. The clinical parameters evaluated were plaque index, gingival bleeding, bleeding on probing, suppuration, probing depth and clinical attachment level. Supra- and subgingival biofilm samples were taken from the deepest sites of each implant and analyzed for the presence of 36 microorganisms by checkerboard DNA-DNA hybridization. RESULTS Higher mean counts of Porphyromonas gingivalis, Treponema denticola and Tannerella forsythia were observed in the peri-implantitis group, both supra- and subgingivally (P<0.05). The proportions of the pathogens from the red complex were elevated, while host-compatible beneficial microbial complexes were reduced in diseased compared with healthy implants. The microbiological profiles of supra- and subgingival environments did not differ substantially within each group. CONCLUSION Marked differences were observed in the composition of supra- and subgingival biofilm between healthy and diseased implants. The microbiota associated with peri-implantitis was comprised of more periodontal pathogenic bacterial species, including the supragingival biofilm.
A Content Independent Model for Context Adaptation and Individualization in Information Retrieval

The consideration of context in information retrieval is expected to improve retrieval effectiveness. Most current approaches rely on the similarity of content which can only partly capture the complexity of the task. In this paper, we present a model for context adaptation which can be realized independently from content. The model is built in the framework of the MIMOR model (Multiple Indexing and Method-Object Relations) for the long-term learning of user preferences in information retrieval. MIMOR integrates a fusion method and a relevance feedback processor into a learning model.
Optimal Superconducting Coil Integrated Into DFIG Wind Turbine for Fault Ride Through Capability Enhancement and Output Power Fluctuation Suppression

The vital problems of the grid-connected doubly fed induction generator (DFIG) wind turbine are the fault ride through (FRT) capability and the output power fluctuation. To tackle these problems, this paper focuses on the optimization of the superconducting coil (SC) integrated into a dc link of the DFIG wind turbine for an enhancement of the FRT capability and a suppression of the output power fluctuation. The dcdc converter, which is used to control the exchanged energy between the SC and the system, is additionally connected between the grid side converter (GSC) and the rotor side converter. During normal operation, the SC acts as an energy storage device to exchange energy with the system so that the power fluctuation of the DFIG wind turbine can be alleviated. On the other hand, when severe faults occur in the system, the SC is used as the current limiting inductor to suppress both overcurrent in the rotor and stator, and overvoltage in the dc link of the DFIG. In the optimization, the inductance of the SC, the initial necessary stored energy in the SC, and the proportional integral (PI) parameters of the dcdc converter are tuned simultaneously so that both objectives can be achieved. Simulation study elucidates the control effect of the DFIG wind turbine with the optimal SC.
Provenance-based Indexing Support in Micro-blog Platforms

Recently, lots of micro-blog message sharing applications have emerged on the web. Users can publish short messages freely and get notified by the subscriptions instantly. Prominent examples include Twitter, Facebook's statuses, and Sina Weibo in China. The Micro-blog platform becomes a useful service for real time information creation and propagation. However, these messages' short length and dynamic characters have posed great challenges for effective content understanding. Additionally, the noise and fragments make it difficult to discover the temporal propagation trail to explore development of micro-blog messages. In this paper, we propose a provenance model to capture connections between micro-blog messages. Provenance refers to data origin identification and transformation logging, demonstrating of great value in recent database and workflow systems. To cope with the real time micro-message deluge, we utilize a novel message grouping approach to encode and maintain the provenance information. Furthermore, we adopt a summary index and several adaptive pruning strategies to implement efficient provenance updating. Based on the index, our provenance solution can support rich query retrieval and intuitive message tracking for effective message organization. Experiments conducted on a real dataset verify the effectiveness and efficiency of our approach. Provenance refers to data origin identification and transformation monitoring, which has been demonstrated of great value in database and workflow systems. In this paper, we propose a provenance model in micro-blog platforms, and design an indexing scheme to support provenance-based message discovery and maintenance, which can capture the interactions of messages for effective message organization. To cope with the real time micro-message tornadoes, we introduce a novel virtual annotation grouping approach to encode and maintain the provenance information. Furthermore, we design a summary index and adaptive pruning strategies to facilitate efficient message update. Based on this provenance index, our approach can support query and message tracking in micro-blog systems. Experiments conducted on real datasets verify the effectiveness and efficiency of our approach.
Spatiotemporal Neural Integration for Bistable Perception in a Response-Time Structure-From-Motion Task

The question of how perception arises from neuronal activity in the visual cortex is of fundamental importance to many issues in cognitive neuroscience. To address this question, we adopt a unique experimental paradigm in which bistable stimuli, namely structure from motion (SFM), are employed to dissociate the visual input from perception while monitoring cortical neural activity. In this paper, we analyze the dynamic responses of the multiunit activity, simultaneously collected from multiple channels in the middle temporal visual cortex of awake behaving macaque monkeys, for decoding the bistable percepts of SFM in a response-time (RT) perceptual discrimination task. Our goal is to understand how the perceptual discriminative information of neuronal population activity evolves and accumulates over time to mediate behaviors. Here, we used a discriminative classifier called the logistic regression and contrasted it with two generative classifiers, namely the quadratic discriminant analysis (QDA) and linear discriminant analysis (LDA), to achieve the spatiotemporal integration of neural activity and dynamically decode the perceptual reports on a single-trial basis. We found that the logistic regression outperforms both QDA and LDA in terms of decoding accuracy for both single-channel and multichannel decoding of bistable percepts. Subsequent analysis of the temporal profile of neural population decoding in relation to RT revealed that the amplitude and latency of the decoding accuracy are highly correlated with the RT, thus indicating that the monkeys respond faster when the decoding accuracy is higher and has shorter latency. These findings suggest that enhanced neuronal discrimination ability and shortened neuronal discrimination latency may impact monkeys' behaviors.
Identification of Unannotated Small Genes in Salmonella

Increasing evidence indicates that many, if not all, small genes encoding proteins ≤100 aa are missing in annotations of bacterial genomes currently available. To uncover unannotated small genes in the model bacterium Salmonella enterica Typhimurium 14028s, we used the genomic technique ribosome profiling, which provides a snapshot of all mRNAs being translated (translatome) in a given growth condition. For comprehensive identification of unannotated small genes, we obtained Salmonella translatomes from four different growth conditions: LB, MOPS rich defined medium, and two infection-relevant conditions low Mg2+ (10 µM) and low pH (5.8). To facilitate the identification of small genes, ribosome profiling data were analyzed in combination with in silico predicted putative open reading frames and transcriptome profiles. As a result, we uncovered 130 unannotated ORFs. Of them, 98% were small ORFs putatively encoding peptides/proteins ≤100 aa, and some of them were only expressed in the infection-relevant low Mg2+ and/or low pH condition. We validated the expression of 25 of these ORFs by western blot, including the smallest, which encodes a peptide of 7 aa residues. Our results suggest that many sequenced bacterial genomes are underannotated with regard to small genes and their gene annotations need to be revised.
Convexity of Fisher information with respect to Gaussian perturbation

Let X be an arbitrary continuous random variable and Z be an independent Gaussian random variable with zero mean and unit variance. In this paper, we show that the third order derivative of h(X + √tZ) is nonnegative, which implies that the Fisher information J(X+ √tZ) is convex in t. Following this result, we make two conjectures on h(X + √tZ): the first is that ∂<sup>n</sup>/∂t<sup>n</sup> h(X + √tZ) is nonnegative in t if n is odd, and negative otherwise; the second is that log J(X + √tZ) is convex in t.
ASADAL/SIM: An Incremental Multi-Level Simulation and Analysis Tool for Real-Time Software Specifications

Despite considerable advancement in software engineering methods during the past three decades, requirements engineering of large and complex software systems still remains a difficult and active research problem. One such difficulty lies in developing correct and useful methods for the validation and verification of real-time software specifications. One way of analyzing and validating/verifying software specifications is to mathematically derive or prove desired system properties based on formal specification languages. A full scale system analysis using such formal methods is limited in practice because of the required mathematical skills and computational costs. Formal methods are often used to check only a few very critical real-time properties. Simulation is a complementary approach to testing various system characteristics and validating user requirements. It is especially good for providing a rough picture of final system behavior. This paper presents ASADAL/SIM, a tool for multi-level simulation and analysis of real-time software specifications. It is a subsystem of a larger computer-aided real-time software development environment called ASADAL, and complements ASADAL/PROVER, another subsystem of ASADAL which is a formal verification module.1. With ASADAL/SIM, simulation primitives can be added to evolving specifications in order to assign stochastic behaviors to external entities and internal processes, and to build a simulation model. ASADAL/SIM can execute the model and, at the same time, demonstrate the final system behavior by graphically showing internal workings of the system; catch undesirable system behaviors with breakpoints; and present various analytical results and system statistics ASADAL/SIM, following ASADAL's philosophies of hierarchical system modeling and early system validation, allows users to simulate ‘evolving’ specifications at different, mixed, and wide levels of detail. In particular, algorithmic details may be specified for low level behavioral blocks, and simulated with abstract entities yet to be refined to such a level. This facilitates the tracking of critical data values at the specification level, and eases the next transformation into code level implementation. With ASADAL/SIM, ASADAL becomes an effective and comprehensive supporting tool for various existing software engineering approaches, particularly top-down refinement and incremental development practices. © 1998 John Wiley & Sons, Ltd.