Miracle-dz/UniFAR-FTUs huggingface dataset:
Viral Genetics Modulate Orolabial Herpes Simplex Virus Type 1 Shedding in Humans

BACKGROUND Orolabial herpes simplex virus type 1 (HSV-1) infection has a wide spectrum of severity in immunocompetent persons. To study the role of viral genotype and host immunity, we characterized oral HSV-1 shedding rates and host cellular response, and genotyped viral strains, in monozygotic (MZ) and dizygotic (DZ) twins. METHODS A total of 29 MZ and 22 DZ HSV-1-seropositive twin pairs were evaluated for oral HSV-1 shedding for 60 days. HSV-1 strains from twins were genotyped as identical or different. CD4+ T-cell responses to HSV-1 proteins were studied. RESULTS The median per person oral HSV shedding rate was 9% of days that a swab was obtained (mean, 10.2% of days). A positive correlation between shedding rates was observed within all twin pairs, and in the MZ and DZ twins. In twin subsets with sufficient HSV-1 DNA to genotype, 15 had the same strain and 14 had different strains. Viral shedding rates were correlated for those with the same but not different strains. The median number of HSV-1 open reading frames recognized per person was 16. The agreement in the CD4+ T-cell response to specific HSV-1 open reading frames was greater between MZ twins than between unrelated persons (P = .002). CONCLUSION Viral strain characteristics likely contribute to oral HSV-1 shedding rates.
A Metabolic Labeling Strategy for Relative Protein Quantification in Clostridioides difficile

Clostridioides difficile (formerly Clostridium difficile) is a Gram-positive, anaerobe, spore-forming pathogen, which causes drug-induced diseases in hospitals worldwide. A detailed analysis of the proteome may provide new targets for drug development or therapeutic strategies to combat this pathogen. The application of metabolic labeling (ML) would allow for accurate quantification of significant differences in protein abundance, even in the case of very small changes. Additionally, it would be possible to perform more accurate studies of the membrane or surface proteomes, which usually require elaborated sample preparation. Such studies are therefore prone to higher standard deviations during the quantification. The implementation of ML strategies for C. difficile is complicated due to the lack in arginine and lysine auxotrophy as well as the Stickland dominated metabolism of this anaerobic pathogen. Hence, quantitative proteome analyses could only be carried out by label free or chemical labeling methods so far. In this paper, a ML approach for C. difficile is described. A cultivation procedure with 15N-labeled media for strain 630Δerm was established achieving an incorporation rate higher than 97%. In a proof-of-principle experiment, the performance of the ML approach in C. difficile was tested. The proteome data of the cytosolic subproteome of C. difficile cells grown in complex medium as well as two minimal media in the late exponential and early stationary growth phase obtained via ML were compared with two label free relative quantification approaches (NSAF and LFQ). The numbers of identified proteins were comparable within the three approaches, whereas the number of quantified proteins were between 1,110 (ML) and 1,861 (LFQ) proteins. A hierarchical clustering showed clearly separated clusters for the different conditions and a small tree height with ML approach. Furthermore, it was shown that the quantification based on ML revealed significant altered proteins with small fold changes compared to the label free approaches. The quantification based on ML was accurate, reproducible, and even more sensitive compared to label free quantification strategies.
Linked Data for Building a Map of Researchers

Researchers Map is a simple mash-up application that provides a map of professors of the German database community, or more precisely, of the professors’ workplaces (cf. Figure 1). The list of professors represented in the map can be filtered by research interests such as query optimization or data warehousing. Selecting a professor opens a list of her/his publications. We developed Researchers Map to showcase the potential of Linked Data for mash-up applications. For this reason, Researchers Map is solely based on data that is published following the Linked Data principles [1].
Microstructure Formation of Functional Polymers by Evaporative Self-Assembly under Flexible Geometric Confinement

Polymer microstructures are widely used in optics, flexible electronics, and so forth. We demonstrate a cost-effective bottom-up manner for patterning polymer microstructures by evaporative self-assembly under a flexible geometric confinement at a high temperature. Two-parallel-plates confinement would become curve-to-flat shape geometric confinement as the polydimethylsiloxane (PDMS) cover plate deformed during solvent swelling. We found that a flexible cover plate would be favorable for the formation of gradient microstructures, with various periodicities and widths obtained at varied heights of clearance. After thermal annealing, the edge of the PMMA (Poly-methylmethacrylate) microstructures would become smooth, while the RR-P3HT (regioregular-poly(3-hexylthiophene)) might generate nanocrystals. The morphologies of RR-P3HT structures included thick films, straight lines, hierarchical stripes, incomplete stripes, and regular dots. Finally, a simple field-effect transistor (FET) device was demonstrated with the RR-P3HT micropattern as an active layer.
Wall following Navigation Control for a Sonar based Mobile Robot

In this paper, an algorithm is proposed for mobile robot to follow walls. Firstly the wall shapes of the indoor environment are classified into different types for which wall following strategies are designed respectively. When the mobile robot moves, the wall following status changes, based on Finite State Machine (FSM), then the corresponding wall following strategy is chosen to control the mobile robot. Experiments on the Pioneer 2DX mobile robot are conducted to evaluate the performance of the algorithm, and good results are obtained.
Antisense oligonucleotides targeting mutant Ataxin-7 restore visual function in a mouse model of spinocerebellar ataxia type 7

Intravitreal injection of antisense oligonucleotides targeting mutated Ataxin-7 improves visual function in a mouse model of spinocerebellar ataxia type 7. Improving vision in spinocerebellar ataxia Spinocerebellar ataxia type 7 (SCA7) is a genetic disorder caused by mutations in the ATAXIN-7 gene. SCA7 is characterized by impairments in coordination, balance, and speech and by retinal degeneration that results in complete blindness. Here, Niu et al. developed a strategy for treating visual impairments in SCA7 by inhibiting the mutated Ataxin-7 in the retina using antisense oligonucleotides (ASOs). Intravitreal injection of ASOs specifically targeting the mutated Ataxin-7 reduced protein expression in the retina and ameliorated pathology and vision loss in a SCA7 mouse model. The results suggest that ASOs targeting ATAXIN-7 might be effective in treating retinal degeneration in patients with SCA7. Spinocerebellar ataxia type 7 (SCA7) is an autosomal dominant neurodegenerative disorder characterized by cerebellar and retinal degeneration, and is caused by a CAG-polyglutamine repeat expansion in the ATAXIN-7 gene. Patients with SCA7 develop progressive cone-rod dystrophy, typically resulting in blindness. Antisense oligonucleotides (ASOs) are single-stranded chemically modified nucleic acids designed to mediate the destruction, prevent the translation, or modify the processing of targeted RNAs. Here, we evaluated ASOs as treatments for SCA7 retinal degeneration in representative mouse models of the disease after injection into the vitreous humor of the eye. Using Ataxin-7 aggregation, visual function, retinal histopathology, gene expression, and epigenetic dysregulation as outcome measures, we found that ASO-mediated Ataxin-7 knockdown yielded improvements in treated SCA7 mice. In SCA7 mice with retinal disease, intravitreal injection of Ataxin-7 ASOs also improved visual function despite initiating treatment after symptom onset. Using color fundus photography and autofluorescence imaging, we also determined the nature of retinal degeneration in human SCA7 patients. We observed variable disease severity and cataloged rapidly progressive retinal degeneration. Given the accessibility of neural retina, availability of objective, quantitative readouts for monitoring therapeutic response, and the rapid disease progression in SCA7, ASOs targeting ATAXIN-7 might represent a viable treatment for SCA7 retinal degeneration.
Preferential Default Reasoning on the Semantic Web

The world of the Semantic Web includes many inconsistent knowledge bases, whose axioms are often unreliable and can therefore be naturally interpreted as defaults. In this article we introduce an extension of Sengupta et. al.'s semantics [12] with a preference order on the defaults with respect to satisfaction. In particular, the semantics we propose is an improved version of Heymans et. al.'s semantics [8] for a defeasible ontology language. One crucial difference we adopt is that the preference relation between interpretations is not only defined with respect to the same individuals, but any. We provide an algorithm to translate the entailment problem with respect to ordered default knowledge bases to the one for classical knowledge bases, and show its soundness and completeness. As a practical application scenario, we test our algorithm on various subsets of LOD Cloud, and report on our result.
Human sperm competition: ejaculate adjustment by males and the function of masturbation

Sperm competition theory argues that the number of sperm inseminated into a female by a male is a trade-off between two opposing pressures. On the one hand, the risk that sperm may find themselves in competition with the sperm from another male favours the male inseminating more sperm. On the other hand, ejaculates are costly to produce and males are favoured who economize over the number of sperm inseminated. This paper analyses: (1) sperm numbers and other ejaculation data for 35 human couples; and (2) data relating to the most recent copulation reported by 3587 women. Three sets of predictions based on sperm competition theory are tested. These are that the number of sperm inseminated should be a function of: (1) risk of sperm competition; (2) female reproductive value; and (3) optimum partitioning of ejaculates between successive in-pair copulations. During in-pair copulation the male used successive inseminations to 'top-up' the population of sperm in his female partner. In accordance with sperm competition theory: (1) individual males inseminated more sperm when the pair had spent a smaller proportion of their time together and hence risk of sperm competition was greater; and (2) larger females wore inseminated with more sperm than smaller females. In apparent contradiction to sperm competition theory, the number of sperm inseminated did not vary according to female orgasm pattern or the probability of conception. This apparent failure of the theory may instead be due to the male's lack of necessary information. Paradoxically, male mammals seem to waste huge numbers of sperm through spontaneous emission and self-masturbation. Such shedding of sperm could be adaptive if it led to more competitive and/or more fertile inseminates at the next copulation. The data showed that a recent male masturbation reduced the number of sperm inseminated at the next copulation but not the number retained by the female. It is concluded that masturbation is a male strategy to increase sperm fitness without increasing sperm numbers in the female tract. The possibility that, in the absence of sperm competition, the probability of fertilization decreases if too many sperm are inseminated is discussed. This latter factor may be more important than ejaculate cost in favouring male restraint over the number of sperm inseminated.
Inhibition of Advanced Glycation End Products Formation Attenuates Cardiac Electrical and Mechanical Remodeling and Vulnerability to Tachyarrhythmias in Diabetic Rats

Diabetic patients with cardiomyopathy show a higher incidence of arrhythmias and sudden death. Chronic hyperglycemia induces the formation of advanced glycation end products (AGEs), which contribute to the pathogenesis of diabetic cardiomyopathy. This study investigated whether inhibition of AGEs formation by aminoguanidine (AG) could prevent cardiac electromechanical and arrhythmogenic remodeling in diabetes mellitus. Streptozotocin-induced diabetic rats received AG (100 mg/kg daily, i.p.) or vehicle (normal saline, i.p.) for 5 weeks. The rats underwent hemodynamic recording to evaluate cardiac function, and heart preparations were used to determine the electrical, mechanical, and biochemical functions. In vitro high glucose-induced AGEs formation, reactive oxygen species (ROS) generation, and action potential changes were examined in HL-1 atrial cells. AG treatment improved the diabetes-induced depression in left ventricular pressure and the relaxation rate, and normalized the prolongation of QTc intervals in anesthetized rats. AG reduced the vulnerabilities to atrial and ventricular tachyarrhythmias in perfused diabetic hearts. AG normalized the prolonged action potential duration in diabetic atrial and ventricular muscles, which was correlated with the restoration of both transient outward (Ito) and steady-state outward (ISS) K+ current densities in cardiomyocytes. The abnormal kinetics of Ca2+ transients and contraction were reversed in cardiomyocytes from AG-treated diabetic rats, along with parallel preservation of sarco(endo)plasmic reticulum Ca2+-ATPase (SERCA2a) expression. Furthermore, ex vivo and in vitro studies showed AG attenuated AGEs and ROS formation. Thus, long-term administration of AG ameliorated cardiac electromechanical remodeling and arrhythmogenicity in diabetic rats and may present an effective strategy for the prevention of diabetes-associated arrhythmias.
CSF1R Inhibition Reduces Microglia Proliferation, Promotes Tissue Preservation and Improves Motor Recovery After Spinal Cord Injury

Spinal cord injury (SCI) induces a pronounced neuroinflammation driven by activation and proliferation of resident microglia as well as infiltrating peripheral monocyte-derived macrophages. Depending on the time post-lesion, positive and detrimental influences of microglia/macrophages on axonal regeneration had been reported after SCI, raising the issue whether their modulation may represent an attractive therapeutic strategy. Colony-stimulating factor 1 (CSF1) regulates microglia/macrophages proliferation, differentiation and survival thus, pharmacological treatments using CSF1 receptor (CSF1R) inhibitors had been used to ablate microglia. We analyzed the effect of chronic (10 weeks) food diet containing GW2580 (a CSF1R inhibitor) in mice that underwent lateral spinal cord hemisection (HS) at vertebral thoracic level 9. Treatment started 4 weeks prior to SCI and continued until 6 weeks post-lesion. We first demonstrate that GW2580 treatment did not modify microglial response in non-injured spinal cords. Conversely, a strong decrease in proliferating microglia was observed following SCI. Second, we showed that GW2580 treatment improved some parameters of motor recovery in injured animals through better paw placement. Using in and ex vivo magnetic resonance imaging (MRI), we then established that GW2580 treatment had no effect on lesion extension and volume. However, histological analyses revealed that GW2580-treated animals had reduced gliosis and microcavity formation following SCI. In conclusion, CSF1R blockade using GW2580 specifically inhibits SCI-induced microglia/macrophages proliferation, reduces gliosis and microcavity formations and improves fine motor recovery after incomplete SCI. Preventing microglial proliferation may offer therapeutic approach to limit neuroinflammation, promote tissue preservation and motor recovery following SCI.
Anti-inflammatory Effects of Homotaurine in Patients With Amnestic Mild Cognitive Impairment

Alzheimer’s disease (AD) is a fatal dementing neurodegenerative disease, currently lacking an efficacious disease-modifying therapy. In the last years, there has been some interest in the use of homotaurine as a potential therapeutic compound for AD, but more work is still needed to prove its efficacy as disease modifier in dementia. Since inflammation is believed to play a key role in AD development, we sought to investigate here the in vivo homotaurine effect on inflammatory response in patients at the earliest stages of AD, i.e., suffering from amnestic mild cognitive impairment (aMCI). Thus, the present study aims to evaluate the effects of homotaurine supplementation on cytokine serum levels and memory performances in MCI patients. Neuropsychological, clinical and cytokine assessment was performed at baseline (T0) and after 1 year (T12) of homotaurine supplementation in 20 patients categorized as carriers (n = 9) or no carriers (n = 11) of the ε4 allele of the apolipoprotein E (APOE) gene, the strongest genetic risk factor for AD. The serum levels of the pro-inflammatory mediators Interleukin (IL) 1β, Tumor necrosis factor-alpha (TNFα), IL-6 and IL-18, contextually with the anti-inflammatory molecules IL-18 binding protein (IL-18BP) and Transforming growth factor-beta (TGFβ), were analyzed to explore significant differences in the inflammatory status between T0 and T12 in the two APOE variant carrier groups. No significant differences over time were observed in patients as for most cytokines, except for IL-18. Following homotaurine supplementation, patients carrying the APOEε4 allele showed a significant decrease in IL-18 (both in its total and IL-18BP unbound forms), in turn associated with improved short-term episodic memory performance as measured by the recency effect of the Rey 15-word list learning test immediate recall. Thus, homotaurine supplementation in individuals with aMCI may have a positive consequence on episodic memory loss due, at least in part, to homotaurine anti-inflammatory effects. This study strongly suggests that future research should focus on exploring the mechanisms by which homotaurine controls brain inflammation during AD progression.
Survey of Image Processing Techniques for Brain Pathology Diagnosis: Challenges and Opportunities

In recent years, a number of new products introduced to the global market combine intelligent robotics, artificial intelligence and smart interfaces to provide powerful tools to support professional decision making. However, while brain disease diagnosis from the brain scan images is supported by imaging robotics, the data analysis to form a medical diagnosis is performed solely by highly trained medical professionals. Recent advances in medical imaging techniques, artificial intelligence, machine learning and computer vision present new opportunities to build intelligent decision support tools to aid the diagnostic process, increase the disease detection accuracy, reduce error, automate the monitoring of patient's recovery, and discover new knowledge about the disease cause and its treatment. This article introduces the topic of medical diagnosis of brain diseases from the MRI based images. We describe existing, multi-modal imaging techniques of the brain's soft tissue and describe in detail how are the resulting images are analyzed by a radiologist to form a diagnosis. Several comparisons between the best results of classifying natural scenes and medical image analysis illustrate the challenges of applying existing image processing techniques to the medical image analysis domain. The survey of medical image processing methods also identified several knowledge gaps, the need for automation of image processing analysis, and the identification of the brain structures in the medical images that differentiate healthy tissue from a pathology. This survey is grounded in the cases of brain tumor analysis and the traumatic brain injury diagnoses, as these two case studies illustrate the vastly different approaches needed to define, extract, and synthesize meaningful information from multiple MRI image sets for a diagnosis. Finally, the article summarizes artificial intelligence frameworks that are built as multi-stage, hybrid, hierarchical information processing work-flows and the benefits of applying these models for medical diagnosis to build intelligent physician's aids with knowledge transparency, expert knowledge embedding, and increased analytical quality.
Timing and probability of ovulation in relation to sex skin swelling in wild West African chimpanzees, Pan troglodytes verus


Females of many catharrine primates show a periodic and often pronounced swelling of the perineum, the functional significance of which is unclear. Several hypotheses that exist to explain the function of this conspicuous trait are based on assumptions about the temporal relation between the period of maximum swelling and ovulation, and remain largely untested. We examined this relation in free-living chimpanzees of the Tao ¨ National Park, Cote d'Ivoire, and assessed the reliability of perineal swelling as an indicator of ovulation in this species. We used noninvasive urinary progestogen analysis of female reproductive status, together with observational data on swelling characteristics, to determine the variability of timing of ovulation within the maximum swelling phase in 36 cycles from 12 females. The period of maximum swelling was highly variable, lasting from 6 to 18 days. Although ovulation was virtually restricted to the second half of the period of maximum tumescence, its timing varied considerably in relation to both the onset and the end of the maximum tumescence phase. Probability of ovulation, however, was not random, but peaked on day 7 after the onset of the maximum swelling phase, and was almost 60% between days 7 and 9. Thus, in wild chimpanzees perineal swelling indicates the probability of ovulation, but does not provide sufficient information to deduce its exact timing. Given the temporal variability of ovulation relative to the last day of maximum tumescence, field workers should try to include hormonal analysis if information on timing of ovulation is required for interpretation of observational data.  2003 Published by Elsevier Ltd on behalf of The Association for the Study of Animal Behaviour.
Pyrethrum flowers: production, chemistry, toxicology, and uses

Pyrethrum is the most important natural botanical pesticide. Pyrethrins are effective against virtually all insect pests, yet are of very low toxicity to mammals, and break down quickly on exposure to light and air. This study of the place of pyrethrum in ecology and pest management includes discussion of the new synthetic pyrethroids that have been developed, in addition to continuing work on natural product pyrethrins.
Dial2Desc: End-to-end Dialogue Description Generation

We first propose a new task named Dialogue Description (Dial2Desc). Unlike other existing dialogue summarization tasks such as meeting summarization, we do not maintain the natural flow of a conversation but describe an object or an action of what people are talking about. The Dial2Desc system takes a dialogue text as input, then outputs a concise description of the object or the action involved in this conversation. After reading this short description, one can quickly extract the main topic of a conversation and build a clear picture in his mind, without reading or listening to the whole conversation. Based on the existing dialogue dataset, we build a new dataset, which has more than one hundred thousand dialogue-description pairs. As a step forward, we demonstrate that one can get more accurate and descriptive results using a new neural attentive model that exploits the interaction between utterances from different speakers, compared with other baselines.