Miracle-dz/UniFAR-FTUs huggingface dataset:
The effects of age at mating on female life-history traits in a seed beetle

Age at first reproduction is an important component of life history across taxa and can ultimately affect fitness. Because genetic interests of males and females over reproductive decisions commonly differ, theory predicts that conflict may arise over the temporal distribution of matings. To determine the potential for such sexual conflict, we studied the direct costs and benefits associated with mating at different times for females, using seed beetles (Acanthoscelides obtectus) as a model system. Virgin females were resistant to male mating attempts at a very early age but subsequently reduced their resistance. Although we found no difference in life span or mortality rates between females mated early in life and those mated later, females that mated early in life suffered a 12% reduction in lifetime fecundity. Thus, there are direct costs associated with mating early in life for females. Yet, males mate even with newly hatched females. We suggest that these data indicate a potential for sexual conflict over the timing of first mating and that female resistance to mating, at least in part, may represent a female strategy aimed at delaying mating to a later time in life. Copyright 2007, Oxford University Press.
The social epidemiology of human immunodeficiency virus/acquired immunodeficiency syndrome.

Social epidemiology is defined as the study of the distribution of health outcomes and their social determinants (1). It builds on the classic epidemiologic triangle of host, agent, and environment to focus explicitly on the role of social determinants in infectious disease transmission and progression. These determinants are the “features of and pathways by which societal conditions affect health” (2, p. 697). Early studies of human immunodeficiency virus (HIV)/acquired immunodeficiency syndrome (AIDS) focused on individual characteristics and behaviors in determining HIV risk, an approach that Fee and Krieger (3) refer to as “biomedical individualism. ” Biomedical individualism is the basis of risk factor epidemiology; by contrast, the social epidemiology perspective emphasizes social conditions as fundamental causes of disease (4) (table 1). Social epidemiologists examine how persons become exposed to risk or protective factors and under what social conditions individual risk factors are related to disease. Social factors are thus the focus of analysis and are not simply adjusted for as potentially confounding factors or used as proxies for unavailable individual-level data. Social factors are indeed critical to understanding nonuniform infectious disease patterns that emerge as a result of the dependent nature of disease transmission or the idea that an outcome in one person is dependent upon outcomes and exposures in others (5, 6).
Modelling three‐dimensional trajectories by using Bézier curves with application to hand motion

Summary. A modelling approach for three‐dimensional trajectories with particular application to hand reaching motions is described. Bézier curves are defined by control points which have a convenient geometrical interpretation. A fitting method for the control points to trajectory data is described. These fitted control points are then linked to covariates of interest by using a regression model. This allows the prediction of new trajectories and the ability to model the variability in trajectories. The methodology is illustrated with an application to hand trajectory modelling for ergonomics. Motion capture was used to collect a total of about 2000 hand trajectories performed by 20 subjects to a variety of targets. A simple model with strong predictive performance and interpretablility is developed. The use of hand trajectory models in the digital human models for virtual manufacturing applications is discussed.
Semen Extenders and Artificial Insemination in Ruminants

1 Abstract Artificial insemination is one of the important tools for genetic improvement in modern dairy breeding practices and it is only possible with efficient extender. Extender has a vital role in the preservation of sperm cell and its quality parameters such as viability, motility, acrosome and membrane integrity etc. Semen extenders contain buffering system to maintain pH of the medium (Tris, sodium phosphate, citric acid), cryoshock preservatives (glycerin, egg yolk, soy-lecithin, milk), provide energy (fructose) and guarantee the microbial free environment i.e. antibiotics (streptomycin, penicillin, polymyxin B). Here, in this review we will focus on the effects of different extender ingredients used for dilution of semen in ruminants to achieve Artificial insemination (AI).
Structural Simplification of Hybrid Neuro-Logistic Regression Models in Multispectral Analysis of Remote Sensed Data

Logistic Regression (LR) has become a widely used and accepted method to analyze binary or multiclass outcome variables, since it is a flexible tool that can predict the probability for the state of a dichotomous variable. A recently proposed LR method is based on the hybridization of a linear model and Evolutionary Product-Unit Neural Network (EPUNN) models for binary classification. This produces a high number of coefficients, so two different methods for simplifying the structure of the final model by reducing the number of initial or PU covariates are presented in this paper, both being based on the Wald test. The first method is a Backtracking Backward Search (BBS) method and the second is similar but based on the standard Simulated Annealing process for the decision steps (SABBS). In this study, we used aerial imagery taken in mid-May to evaluate the potential of two different combinations of LR and EPUNN (LR using PUs (LRPU), as well as LR using Initial covariates and PUs (LRIPU)) and the two presented methods for structural simplification of the final models (BBS and SABBS) for discriminating Ridolfia segetum patches (one of the most dominant, competitive and persistent weed in sunflower crops) in one naturally infested field of southern Spain. Then, we compared the performance of these methods to six commonly used classification algorithms, our proposals obtaining a competitive performance and a lower number of coefficients.
Toward quantitative digital histopathology for prostate cancer: comparison of inter-slide interpolation methods for tumour measurement

Accurate pathology assessment of post-prostatectomy specimens is important to determine the need for and to guide potentially life-saving adjuvant therapy. Digital pathology imaging is enabling a transition to a more objective quantification of some surgical pathology assessments, such as tumour volume, that are currently visually estimated by pathologists and subject to inter-observer variability. One challenge for tumour volume quantification is the traditional 3–5 mm spacing of images acquired from sections of radical prostatectomy specimens. Tumour volume estimates may benefit from a well-motivated approach to inter-slide tumour boundary interpolation. We implemented and tested a level set-based interpolation method and found that it produced 3D tumour surfaces that may be more biologically plausible than those produced via a simpler nearest-slide interpolation. We found that the simpler method produced larger tumour volumes, compared to the level set method, by a median factor of 2.3. For contexts where only tumour volume is of interest, we determined that the volumes produced via the simpler method can be linearly adjusted to the level setproduced volumes. The smoother surfaces from level set interpolation yielded measurable differences in tumour boundary location; this may be important in several clinical/research contexts (e.g. pathology-based imaging validation for focal therapy planning).
A model of a CA3 hippocampal pyramidal neuron incorporating voltage-clamp data on intrinsic conductances.

1. We have developed a 19-compartment cable model of a guinea pig CA3 pyramidal neuron. Each compartment is allowed to contain six active ionic conductances: gNa, gCa, gK(DR) (where DR stands for delayed rectifier), gK(A), gK(AHP), and gK(C). THe conductance gCa is of the high-voltage activated type. The model kinetics for the first five of these conductances incorporate voltage-clamp data obtained from isolated hippocampal pyramidal neurons. The kinetics of gK(C) are based on data from bullfrog sympathetic neurons. The time constant for decay of submembrane calcium derives from optical imaging of Ca signals in Purkinje cell dendrites. 2. To construct the model from available voltage-clamp data, we first reproduced current-clamp records from a model isolated neuron (soma plus proximal dendrites). We next assumed that ionic channel kinetics in the dendrites were the same as in the soma. In accord with dendritic recordings and calcium-imaging data, we also assumed that significant gCa occurs in dendrites. We then attached sections of basilar and apical dendritic cable. By trial and error, we found a distribution (not necessarily unique) of ionic conductance densities that was consistent with current-clamp records from the soma and dendrites of whole neurons and from isolated apical dendrites. 3. The resulting model reproduces the Ca(2+)-dependent spike depolarizing afterpotential (DAP) recorded after a stimulus subthreshold for burst elicitation. 4. The model also reproduces the behavior of CA3 pyramidal neurons injected with increasing somatic depolarizing currents: low-frequency (0.3-1.0 Hz) rhythmic bursting for small currents, with burst frequency increasing with current magnitude; then more irregular bursts followed by afterhyperpolarizations (AHPs) interspersed with brief bursts without AHPs; and finally, rhythmic action potentials without bursts. 5. The model predicts the existence of still another firing pattern during tonic depolarizing dendritic stimulation: brief bursts at less than 1 to approximately 12 Hz, a pattern not observed during somatic stimulation. These bursts correspond to rhythmic dendritic calcium spikes. 6. The model CA3 pyramidal neuron can be made to resemble functionally a CA1 pyramidal neuron by increasing gK(DR) and decreasing dendritic gCa and gK(C). Specifically, after these alterations, tonic depolarization of the soma leads to adapting repetitive firing, whereas stimulation of the distal dendrites leads to bursting. 7. A critical set of parameters concerns the regulation of the pool of intracellular [Ca2+] that interacts with membrane channels (gK(C) and gK(AHP)), particularly in the dendrites. (ABSTRACT TRUNCATED AT 400 WORDS)
DUTIR at the BioCreative VI Precision Medicine Track : Document Triage for Identifying PPIs Affected by Genetic Mutations

The precision medicine initiative promises to identify individualized treatment depending on a patients’ genetic profile and their related responses. In order to help health professionals and researchers in the precision medicine endeavor, the BioCreative VI Precision Medicine Track focuses on mining protein-protein interactions (PPIs) affected by genetic mutations from the scientific published literature. This paper describes our method used to create our submissions to the document triage subtask. In our method, several deep learning models for document triage are used, and the ensemble of them performs better than any individual model. Our best submission achieves an F-score of 0.6909 on the test set. Keywords—Document Triage; Precision Medicine; Deep Learning; Ensemble
Feedback insensitive integrated semiconductor ring laser concept using weak intracavity isolation

External optical feedback can influence semi-conductor laser performance to a great extent. Strong optical isolators with reasonable insertion loss are not available in a photonic integrated circuit due to material incompatibilities, preventing the use of an isolator external to the laser cavity to suppress any feedback effects. In this work the feedback sensitivity of a semiconductor ring laser with an intra-cavity isolation of less than 10 dB is studied using a rate equation analysis. It is found that the relative intensity noise and linewidth are insensitive to feedback strengths over −10 dB.
LREC 2018 Workshop AREA Annotation , Recognition and Evaluation of Actions PROCEEDINGS

Modeling action as an important topic in robotics and human-computer communication assumes by default examining a large set of actions as described by natural language. We offer a procedure for how to extract actions from WordNet. It is based on the analysis of the whole set of verbs and includes 5 steps for implementation. The result is not just a set of extracted actions but a hierarchical structure. In the second part of the article, we describe how an action hierarchy can give an additional benefit in a representation of actions, in particular how it can improve an action representation through semantic roles.
Vascular differentiation from pluripotent stem cells in 3‐D auxetic scaffolds

Auxetic scaffolds, that is, scaffolds that can display negative Poisson's ratio, have unique physical properties and can expand transversally when axially strained or contract under compression. Auxetic materials have been used for bioprostheses and artery stents due to the enhanced compressive strength and shear stiffness. In vascular tissue engineering, auxetic scaffolds allow the widening of blood vessels when blood flows through (creating compressive stress) to prevent the blockage. However, the influence of auxetic materials on the cellular fate decision in local environment is unclear. In this study, auxetic polyurethane foams were used to support vascular differentiation from pluripotent stem cells. The expression of alkaline phosphatase, Oct‐4, and Nanog was lower after 4 days of differentiation for the cells grown in auxetic scaffolds. Higher expression of vascular markers CD31 and VE‐cadherin was observed for the cells from auxetic scaffolds compared with those from the scaffolds before auxetic conversion. Little influence on the expression of cardiac marker α‐actinin was observed. The vascular cells secreted extracellular matrix proteins vitronectin and laminin and expressed membrane‐bound matrix metalloproteinase 9. The examination of Yes‐associated protein expression indicated more cytoplasmic retention in the cells from auxetic scaffolds compared with those from regular scaffolds, suggesting that the auxetic scaffolds may affect cellular contraction. This study demonstrates a novel 3‐D culture based on auxetic scaffolds for vascular differentiation and provides a platform to study the influence of biophysical microenvironments on differentiation of pluripotent stem cells. The outcome of this study has implications for regenerative medicine and drug discovery.
Chronic Granulomatous Disease: Epidemiology, Pathophysiology, and Genetic Basis of Disease

Abstract Chronic Granulomatous Disease is one of the classic primary immunodeficiencies of childhood. While the incidence and severity of bacterial and fungal infections have been greatly reduced in this patient population, much remains to be learned about the pathophysiology of the disease, particularly for autoinflammatory manifestations. In this review, we examine the epidemiology, pathophysiology, and genetic basis for CGD.
Play Worth Remembering: Are Playgrounds Too Safe?

Abstract:Are playgrounds too safe? The Play Worth Remembering project involved an online survey that asked adults this very question. Research on children's outdoor play environments has found that safety has become the key driver of play space design, and that children's free play with natural elements has decreased with time. Adults reflecting upon their own childhood frequently recall playing on their own and in natural settings. In order to better understand the types of landscapes that people considered memorable for play and if these landscapes offered beneficial challenges, we asked participants to recall their favorite outdoor play spaces and the elements contained in these spaces, to describe the benefits they received by playing in these places and to consider if they were safe play spaces. Of the 592 respondents, 69 percent found today's playgrounds too safe. When recollecting their own childhood, 59 percent of participants preferred natural play spaces, compared to 14 percent who preferred spaces designed specifically for play (like a traditional playground). The results suggest public support for rethinking the design of children's outdoor play spaces to include more challenging play opportunities, natural elements, and access to unstructured play areas.
Humidity-regulated CLCA2 protects the epidermis from hyperosmotic stress

High environmental humidity rescues atopic dermatitis-like signs in mice, and CLCA2 protects the epidermis from hyperosmotic stress. Humidity—Harbinger of health? Low environmental humidity can aggravate symptoms of atopic dermatitis (AD), an inflammatory skin disease. Seltmann et al. investigated the link between humidity and epidermal barrier function. Using a mouse model that exhibits AD-like symptoms, they found that high humidity reduced epidermal thickness and skin inflammation. Chloride channel accessory 2 protein was highly expressed in keratinocytes in response to hyperosmotic stress, and it increased cell-cell adhesions and protected cells from apoptosis. This osmoregulated protein was up-regulated in skin samples from patients with AD, which suggests a compensatory mechanism to maintain epidermal barrier function. Low environmental humidity aggravates symptoms of the inflammatory skin disease atopic dermatitis (AD). Using mice that develop AD-like signs, we show that an increase in environmental humidity rescues their cutaneous inflammation and associated epidermal abnormalities. Quantitative proteomics analysis of epidermal lysates of mice kept at low or high humidity identified humidity-regulated proteins, including chloride channel accessory 3A2 (CLCA3A2), a protein with previously unknown function in the skin. The epidermis of patients with AD, organotypic skin cultures under dry conditions, and cultured keratinocytes exposed to hyperosmotic stress showed up-regulation of the nonorthologous human homolog CLCA2. Hyperosmolarity-induced CLCA2 expression occurred via p38/c-Jun N-terminal kinase–activating transcription factor 2 signaling. CLCA2 knockdown promoted keratinocyte apoptosis induced by hyperosmotic stress through impairment of cell-cell adhesion. These findings provide a mechanistic explanation for the beneficial effect of high environmental humidity for AD patients and identify CLCA3A2/CLCA2 up-regulation as a mechanism to protect keratinocytes from damage induced by low humidity.
Visual metrics for the evaluation of sensor data quality in outdoor perception

This paper proposes an experimental study of quality metrics that can be applied to visual and infrared images acquired from cameras onboard an unmanned ground vehicle (UGV). The relevance of existing metrics in this context is discussed and a novel metric is introduced. Selected metrics are evaluated on data collected by a UGV in clear and challenging environmental conditions, represented in this paper by the presence of airborne dust or smoke.
Use of Living Strategies among Adults Aging with HIV in Canada: Comparison by Age-Group Using Data from the HIV, Health and Rehabilitation Survey

Objective: To examine the type and frequency of living strategies used by adults living with HIV. Methods: We conducted a cross-sectional web-based survey that included 51 living strategies: maintaining sense of control, attitudes and beliefs, blocking HIV out of the mind, and social interaction. We examined the frequency of use and compared the proportion of respondents who engaged in strategies across 3 age-groups (<40 years, 40-49 years, and ≥50 years). Results: Of the 935 participants, the majority were men (79%) and most (≥60%) engaged “most” or “all of the time” in healthy lifestyle strategies and maintained a positive outlook living with HIV. Compared to younger participants, a higher proportion of older adults (≥50 years) engaged “most” or “all the time” in strategies that involved maintaining control over health and adopting positive attitudes and outlook living with HIV. Conclusions: Findings can help to inform the role of self-management to enhance successful aging with HIV.
Investigating the Dynamic Aspects of Drug-Protein Recognition through a Combination of MD and NMR Analyses: Implications for the Development of Protein-Protein Interaction Inhibitors

In this paper, we investigate the dynamic aspects of the molecular recognition between a small molecule ligand and a flat, exposed protein surface, representing a typical target in the development of protein-protein interaction inhibitors. Specifically, we analyze the complex between the protein Fibroblast Growth Factor 2 (FGF2) and a recently discovered small molecule inhibitor, labeled sm27 for which the binding site and the residues mainly involved in small molecule recognition have been previously characterized. We have approached this problem using microsecond MD simulations and NMR-based characterizations of the dynamics of the apo and holo states of the system. Using direct combination and cross-validation of the results of the two techniques, we select the set of conformational states that best recapitulate the principal dynamic and structural properties of the complex. We then use this information to generate a multi-structure representation of the sm27-FGF2 interaction. We propose this kind of representation and approach as a useful tool in particular for the characterization of systems where the mutual dynamic influence between the interacting partners is expected to play an important role. The results presented can also be used to generate new rules for the rational expansion of the chemical diversity space of FGF2 inhibitors.
Depletion of mRNA export regulator DBP5/DDX19, GLE1 or IPPK that is a key enzyme for the production of IP6, resulting in differentially altered cytoplasmic mRNA expression and specific cell defect

DBP5, also known as DDX19, GLE1 and inositol hexakisphosphate (IP6) function in messenger RNA (mRNA) export at the cytoplasmic surface of the nuclear pore complex in eukaryotic cells. DBP5 is a DEAD-box RNA helicase, and its activity is stimulated by interactions with GLE1 and IP6. In addition, these three factors also have unique role(s). To investigate how these factors influenced the cytoplasmic mRNA expression and cell phenotype change, we performed RNA microarray analysis to detect the effect and function of DBP5, GLE1 and IP6 on the cytoplasmic mRNA expression. The expression of some cytoplasmic mRNA subsets (e.g. cell cycle, DNA replication) was commonly suppressed by the knock-down of DBP5, GLE1 and IPPK (IP6 synthetic enzyme). The GLE1 knock-down selectively reduced the cytoplasmic mRNA expression required for mitotic progression, results in an abnormal spindle phenotype and caused the delay of mitotic process. Meanwhile, G1/S cell cycle arrest was observed in DBP5 and IPPK knock-down cells. Several factors that function in immune response were also down-regulated in DBP5 or IPPK knock-down cells. Thereby, IFNβ-1 mRNA transcription evoked by poly(I:C) treatment was suppressed. These results imply that DBP5, GLE1 and IP6 have a conserved and individual function in the cytoplasmic mRNA expression. Variations in phenotype are due to the difference in each function of DBP5, GLE1 and IPPK in intracellular mRNA metabolism.