Miracle-dz/UniFAR-FTUs huggingface dataset:
Development of an HIV-1 Microbicide Based on Caulobacter crescentus: Blocking Infection by High-Density Display of Virus Entry Inhibitors

The HIV/AIDS pandemic remains an enormous global health concern. Despite effective prevention options, 2.6 million new infections occur annually, with women in developing countries accounting for more than half of these infections. New prevention strategies that can be used by women are urgently needed. Topical microbicides specific for HIV-1 represent a promising prevention strategy. Conceptually, using harmless bacteria to display peptides or proteins capable of blocking entry provides an inexpensive approach to microbicide development. To avoid the potential pitfalls of engineering commensal bacteria, our strategy is to genetically display infection inhibitors on a non-native bacterium and rely on topical application of stabilized bacteria before potential virus exposure. Due to the high density cell-surface display capabilities and the inherent low toxicity of the bacterium, the S-layer mediated protein display capabilities of the non-pathogenic bacterium Caulobacter crescentus has been exploited for this approach. We have demonstrated that C. crescentus displaying MIP1α or CD4 interfered with the virus entry pathway and provided significant protection from HIV-1 pseudovirus representing clade B in a standard single cycle infection assay. Here we have expanded our C. crescentus based microbicide approach with additional and diverse classes of natural and synthetic inhibitors of the HIV-1 entry pathway. All display constructs provided variable but significant protection from HIV-1 infection; some with protection as high as 70%. Further, we describe protection from infection with additional viral clades. These findings indicate the significant potential for engineering C. crescentus to be an effective and readily adaptable HIV-1 microbicide platform.
A WordNet-based Algorithm for Word Sense Disambiguation

We present an algorithm for automatic word sense disambiguation based on lexical knowledge contained in WordNet and on the results of surface-syntactic analysis The algorithm is part of a system that analyzes texts in order to acquire knowledge in the presence of as little pre-coded semantic knowledge as possible On the other hand, we want to make the besl use of public-domain information sources such as WordNet Rather than depend on large amounts of hand-crafted knowledge or statistical data from large corpora, we use syntactic information and information in WordNet and minimize the need for other knowledge sources in the word sense disambiguation process We propose to guide disambiguation by semantic similarity between words and heuristic rules based on this similarity The algorithm has been applied to the Canadian Income Tax Guide Test results indicate that even on a relatively small text the proposed method produces correct noun meaning more than 72% of the time.
Genome of Multidrug-Resistant Uropathogenic Escherichia coli Strain NA114 from India

ABSTRACT Uropathogenic Escherichia coli (UPEC) causes serious infections in people at risk and has a significant environmental prevalence due to contamination by human and animal excreta. In developing countries, UPEC assumes importance in certain dwellings because of poor community/personal hygiene and exposure to contaminated water or soil. We report the complete genome sequence of E. coli strain NA114 from India, a UPEC strain with a multidrug resistance phenotype and the capacity to produce extended-spectrum beta-lactamase. The genome sequence and comparative genomics emanating from it will be significant in under-standing the genetic makeup of diverse UPEC strains and in boosting the development of new diagnostics/vaccines.
Multi-Resolution K-Means Clustering of Time Series and Application to Images

Clustering is vital in the process of condensing and outlining information, since it can provide a synopsis of the stored data. However, the high dimensionality of multimedia data today presents an insurmountable challenge for clustering algorithms. Based on the well known fact that time series and image histograms can both be represented accurately in a lower resolution using orthonormal decompositions, we present an anytime version of the k-Means algorithm. The algorithm works by leveraging the multi-resolution property of wavelets. The dilemma of choosing the initial centers for k-Means is mitigated by assigning the final centers at each approximation level as the initial centers for the subsequent, finer approximation. This process is repeated until the clustering results stabilize or until the finest “approximation” level is reached. In addition to casting kMeans as an anytime algorithm, our approach has two other very desirable properties. We observe that even by working at coarser approximations, the achieved quality is better than the batch algorithm, and even if the algorithm is run to completion, the running time is significantly reduced. We show how this algorithm can be suitably extended to chromatic and textural features extracted from images. Finally, we demonstrate the applicability of this approach on the online image search engine scenario.
Intraepithelial and invasive squamous cell carcinoma of the conjunctiva: analysis of 60 cases

AIM To evaluate the clinical features, treatment results, and recurrence rates in patients with either intraepithelial or invasive squamous cell carcinoma of the conjunctiva. METHODS Retrospective analysis of 60 cases (22 conjunctival intraepithelial and 38 invasive squamous cell carcinomas) to determine patterns of clinical presentation, aetiological factors, and treatment results. The mean patient age was 64 years old. 70% of the patients were male. Patients were treated with a variety of therapies, depending on the degree of tumour involvement; most cases were treated with frozen section controlled excision and adjunctive cryotherapy. Modified eye wall resection or enucleation was done for intraocular invasion and exenteration was done for orbital involvement. RESULTS Red eye (68%) and ocular irritation (57%) were the most common presenting symptoms. 44% of the patients had other eye findings consistent with extensive solar exposure. 20% of the patients had a history of malignant skin tumours. Visceral malignancies developed in 8%. Scleral involvement was present in 14 (37%), intraocular involvement in five (13%), and orbital invasion in four (11%) cases with invasive squamous cell carcinoma. After a mean follow up of 56 months (18–226 months) the rate of new or recurrent tumours was 4.5% for intraepithelial squamous carcinoma and 5.3% for invasive squamous cell carcinoma. No patient developed metastases or tumour related deaths. CONCLUSION Excision with intraoperative control of the surgical margins and adjunctive cryotherapy results in good tumour control rates.
“A magical little pill that will relieve you of your womanly issues”: What young women say about menstrual suppression

Perceptions of menstruation by media discourses portray this bodily function to be messy, inconvenient, and as an unnecessary phenomenon to be controlled or possibly eliminated. Commercials shown on YouTube targeted toward young women suggest that having a monthly period is not healthy and a lifestyle that is menses free is both pharmacologically available and recommended in order to live a fuller life. We explored the meanings attached to online menstrual suppression commercials with 10 women aged between 18 and 25. In-depth open-ended interviews were conducted over a 10-month period in 2014 after each participant viewed three menstrual suppression online advertisements. Feminist critical discourse was used for analysis with both authors coding for inter-rater reliability recognizing how our age difference and relationship as mother and daughter informed our interpretation. An overarching theme of tension emerged from the interviews with participants feeling detached due to the gendered stereotypes the commercials used to frame menstruation as compared to their own lived experience. Meanings associated with the menstrual suppression commercials were contrary to the participants’ lived experience of menstruation as a healthy process not a detrimental one to their well-being as suggested by the commercials. Subliminal messages within the advertisements were identified as reinforcing gender bias and prejudices, including those associated with femininity. Despite attempting to emulate popular culture, the menstrual suppression advertisements were largely dismissed by this group of participants as undermining their intelligence and of intentionally creating divisive binaries between groups of women. This study suggests that historical bias and stereotypical prejudices were identified by this group of young women within the marketing of menstrual suppression products and, as such, were dismissed as inauthentic to the menstruation experience reflecting a form of menstrual activism.
An Integrated Statistical Approach to Compare Transcriptomics Data Across Experiments: A Case Study on the Identification of Candidate Target Genes of the Transcription Factor PPARα

An effective strategy to elucidate the signal transduction cascades activated by a transcription factor is to compare the transcriptional profiles of wild type and transcription factor knockout models. Many statistical tests have been proposed for analyzing gene expression data, but most tests are based on pair-wise comparisons. Since the analysis of microarrays involves the testing of multiple hypotheses within one study, it is generally accepted that one should control for false positives by the false discovery rate (FDR). However, it has been reported that this may be an inappropriate metric for comparing data across different experiments. Here we propose an approach that addresses the above mentioned problem by the simultaneous testing and integration of the three hypotheses (contrasts) using the cell means ANOVA model. These three contrasts test for the effect of a treatment in wild type, gene knockout, and globally over all experimental groups. We illustrate our approach on microarray experiments that focused on the identification of candidate target genes and biological processes governed by the fatty acid sensing transcription factor PPARα in liver. Compared to the often applied FDR based across experiment comparison, our approach identified a conservative but less noisy set of candidate genes with same sensitivity and specificity. However, our method had the advantage of properly adjusting for multiple testing while integrating data from two experiments, and was driven by biological inference. Taken together, in this study we present a simple, yet efficient strategy to compare differential expression of genes across experiments while controlling for multiple hypothesis testing.
Influence of Estradiol and Androstenedione on ACTH and Cortisol Secretion in the Ovine Fetus

Objective: To test the hypothesis that physiologic increases in fetal plasma 17β-estradiol and androstenedione modulate the activity of the fetal hypothalamic-pituitary-adrenal (HPA) axis. Methods: Seventeen pregnant ewes and their fetuses were chronically catherized. At the time of surgery, the fetuses received implants that released 17β-estradiol (n = 5) alone or 17β-estradiol and androstenedione (n = 6), each at a rate of approximately 250 μg/day for each steroid. The control group (n = 6) received either no pellet (n = 2) or a “placebo” pellet, which contained no steroid (n = 4). Fetal blood samples were drawn for hormone and blood gas analysis at 1-3-day intervals until the time of spontaneous parturition. Fetal plasma ACTH and cortisol concentrations were fit to semilogarithmic equations and analyzed by stepwise multiple linear regression analysis for statistically significant effects of 17β-estradiol and androstenedione. Results: Estradiol significantly increased and androstenedione significantly decreased the ACTH and cortisol concentrations. Treatment with both 17β-estradiol and androstenedione resulted in parturition approximately 4 days earlier than in the other groups (P < .05). Conclusions: Physiologic increases in fetal plasma estradiol and androstenedione modify the activity of the HPA axis.
Hardware-in-the-Loop Overhead Line Emulator for Active Pantograph Testing

Pantograph active control is considered as a means to improve the current collection quality in high-speed railways. Different studies have focused on the assessment of pantograph control systems, addressing actuator configurations and control strategies, mainly by means of numerical experiments. In the last few years, it has become possible to transfer the knowledge gained from numerical experiments to real operating conditions. Due to the high cost of on-track tests, which are necessary for the final assessment of active pantograph performances, it is desirable to perform these tests on a system that has already demonstrated its capabilities with less expensive laboratory tests, in which at least the basic features of the real operating conditions are reproduced. This paper deals with the development of a hardware-in-the-loop (HIL) test rig, which allows the reproduction of the dynamical interaction between the overhead lines and the pantograph in high-speed railways. The HIL test rig makes it possible to verify the control strategies, the electrical drive configurations for active control, and the contact force estimation procedures on a real pantograph under conditions that are similar to those encountered on the real line. Some examples of test bench applications for pantograph active control and contact force estimation are also presented.
Myosin isozymes in normal and cross-reinnervated cat skeletal muscle fibers

Immunocytochemical characteristics of myosin have been demonstrated directly in normal and cross-reinnervated skeletal muscle fibers whose physiological properties have been defined. Fibers belonging to individual motor units were identified by the glycogen-depletion method, which permits correlation of cytochemical and physiological data on the same fibers. The normal flexor digitorum longus (FDL) of the cat is composed primarily of fast-twitch motor units having muscle fibers with high myosin ATPase activity. These fibers reacted with antibodies specific for the two light chains characteristic of fast myosin, but not with antibodies against slow myosin. Two categories of fast fibers, corresponding to two physiological motor unit types (FF and FR), differed in their immunochemical response, from which it can be concluded that their myosins are distinctive. The soleus (SOL) consists almost entirely of slow-twitch motor units having muscle fibers with low myosin ATPase activity. These fibers reacted with antibodies against slow myosin, but not with antibodies specific for fast myosin. When the FDL muscle was cross-reinnervated by the SOL nerve, twitch contraction times were slowed about twofold, and motor units resembled SOL units in a number of physiological properties. The corresponding muscle fibers had low ATPase activity, and they reacted with antibodies against slow myosin only. The myosin of individual cross-reinnervated FDL muscle units was therefore transformed, apparently completely, to a slow type. In contrast, cross-reinnervation of the SOL muscle by FDL motoneurons did not effect a complete converse transformation. Although cross-reinnervated SOL motor units had faster than normal twitch contraction times (about twofold), other physiological properties characteristic of type S motor units were unchanged. Despite the change in contraction times, cross-reinnervated SOL muscle fibers exhibited no change in ATPase activity. They also continued to react with antibodies against slow myosin, but in contrast to the normal SOL, they now showed a positive response to an antibody specific for one of the light chains of fast myosin. The myosins of both fast and slow muscles were thus converted by cross-reinnervation, but in the SOL, the newly synthesized myosin was not equivalent to that normally present in either the FDL or SOL. This suggests that, in the SOL, alteration of the nerve supply and the associated dynamic activity pattern are not sufficient to completely respecify the type of myosin expressed.
Dynamic network selection in HetNets: A social-behavioral (SoBe) approach

In this paper, we propose a two-layer game-theoretic framework to solve the network selection problem in heterogeneous wireless networks (HetNets). At the intra-network layer, a hierarchical game among the SP and its admitted users is employed, and the closed-form equilibrium solutions for the pricing and transmission rate are provided. Meanwhile, at the inter-network layer, all service providers (SP) and the active users are engaged in a dynamic hedonic game and finally self-organized into a Nash-stable coalition structure. The key feature of our proposed approach is the inclusion of social-behavioral (SoBe) constraints capturing the real-world user and SP preferences, hierarchy and membership. Not only that SoBe more accurately models practical scenarios, it also leads to markedly reduced unnecessary handovers, and well maintained call blocking rate. Simulations confirm the superior performance of SoBe in comparison with the widely adopted user-driven alternative in terms of nearly all critical performance criteria.
The merger of populations, the incidence of marriages, and aggregate unhappiness

Let a society’s unhappiness be measured by the aggregate of the levels of relative deprivation of its members. When two societies of equal size, F and M, merge, unhappiness in the merged society is shown to be higher than the sum of the levels of unhappiness in the constituent societies when apart; merger alone increases unhappiness. But when societies F and M merge and marriages are formed such that the number of households in the merged society is equal to the number of individuals in one of the constituent societies, unhappiness in the merged society is shown to be lower than the aggregate unhappiness in the two constituent societies when apart. This result obtains regardless of which individuals from one society form households with which individuals from the other, and even when the marriages have not (or not yet) led to income gains to the married couples from increased efficiency, scale economies, and the like. While there are various psychological reasons for people to become happier when they get married as opposed to staying single, the very formation of households reduces social distress even before any other happiness-generating factors kick in.
Moderate Asphericity of the SN 2002ic Circumstellar Envelope

The polarization of the supernova SN 2002ic interacting with a dense circumstellar envelope is calculated in the context of the asymmetric version of a previously proposed spherical interaction model. The circumstellar envelope is taken to be oblate. The observed polarization can be reproduced for an aspect ratio of 0.65-0.7, assuming inclination angles of >60°. This model predicts a weak sensitivity of the line profiles to the orientation, which is in agreement with the absence of significant variations of the line profiles among SN 2002ic-like supernovae. We propose a test for distinguishing between the binary and single-star progenitor scenarios on the basis of the polarization distribution function for the growing sample of these events.
Approximation Schemes for Steiner Forest on Planar Graphs and Graphs of Bounded Treewidth

We give the first polynomial-time approximation scheme (PTAS) for the Steiner forest problem on planar graphs and, more generally, on graphs of bounded genus. As a first step, we show how to build a Steiner forest spanner for such graphs. The crux of the process is a clustering procedure called prize-collecting clustering that breaks down the input instance into separate subinstances which are easier to handle; moreover, the terminals in different subinstances are far from each other. Each subinstance has a relatively inexpensive Steiner tree connecting all its terminals, and the subinstances can be solved (almost) separately. Another building block is a PTAS for Steiner forest on graphs of bounded treewidth. Surprisingly, Steiner forest is NP-hard even on graphs of treewidth 3. Therefore, our PTAS for bounded-treewidth graphs needs a nontrivial combination of approximation arguments and dynamic programming on the tree decomposition. We further show that Steiner forest can be solved in polynomial time for series-parallel graphs (graphs of treewidth at most two) by a novel combination of dynamic programming and minimum cut computations, completing our thorough complexity study of Steiner forest in the range of bounded-treewidth graphs, planar graphs, and bounded-genus graphs.
Presenilin 1 mediates the turnover of telencephalin in hippocampal neurons via an autophagic degradative pathway

Presenilin 1 (PS1) interacts with telencephalin (TLN) and the amyloid precursor protein via their transmembrane domain (Annaert, W.G., C. Esselens, V. Baert, C. Boeve, G. Snellings, P. Cupers, K. Craessaerts, and B. De Strooper. 2001. Neuron. 32:579–589). Here, we demonstrate that TLN is not a substrate for γ-secretase cleavage, but displays a prolonged half-life in PS1−/− hippocampal neurons. TLN accumulates in intracellular structures bearing characteristics of autophagic vacuoles including the presence of Apg12p and LC3. Importantly, the TLN accumulations are suppressed by adenoviral expression of wild-type, FAD-linked and D257A mutant PS1, indicating that this phenotype is independent from γ-secretase activity. Cathepsin D deficiency also results in the localization of TLN to autophagic vacuoles. TLN mediates the uptake of microbeads concomitant with actin and PIP2 recruitment, indicating a phagocytic origin of TLN accumulations. Absence of endosomal/lysosomal proteins suggests that the TLN-positive vacuoles fail to fuse with endosomes/lysosomes, preventing their acidification and further degradation. Collectively, PS1 deficiency affects in a γ-secretase–independent fashion the turnover of TLN through autophagic vacuoles, most likely by an impaired capability to fuse with lysosomes.
Quantitative Evaluation of BIPV Visual Impact in Building Retrofits Using Saliency Models

BIPV (Building Integrated Photovoltaics) integration in urban spaces requires, not only careful technical, but also aesthetic considerations as its visual impact is seen as a kind of environmental effect. To manage this effect, different methods were developed to measure it; however, most existing evaluation methods are either based on subjective speculations and have no continuous criteria standards, or they do not show much relevance to neuropsychological findings. This paper presents an alternative and complementary method for evaluating the BIPV visual impact using the saliency method with an objective, quantitative and neuropsychological-based approach. The application of the method was tested and is discussed in the context of an example case study in Switzerland. Several different BIPV designs were developed for the case study, purposely in ways that made it difficult to rank their visual impacts with one’s subjective instinct. Using the proposed saliency method; however, the differences in BIPV visual impact across all designs could be identified, demonstrated and calculated sensitively. Potential applications of this proposed method include being a helping tool in deciding which BIPV design causes the least or most visual impact among others. Additionally, when combined with solar cadaster, the method enables a comprehensive estimation of BIPV potential in urban areas from both technical and societal aspects.