Miracle-dz/UniFAR-FTUs huggingface dataset:
Emerging patterns and implications of HIV-1 integrase inhibitor resistance

Purpose of review This review highlights recent data on the pathways of resistance that impact the clinical activity of first-generation and second-generation integrase inhibitors. Recent findings Raltegravir (RAL) and elvitegravir (EVG) are highly efficacious in first-line antiretroviral therapy, with small numbers of virological failures observed in clinical trials. Durable activity in treatment-experienced patients requires a fully supportive background regimen. RAL and EVG show a low-to-moderate genetic barrier to resistance and extensive cross-resistance, which preclude their sequential use. Resistance to dolutegravir (DTG) is not selected as readily in vitro and has not emerged in studies of treatment-naïve patients to date. Both in vitro and in vivo, DTG retains activity against several RAL and EVG resistant strains, but susceptibility is variably impaired by multiple mutations within the G148 pathway, which are common after RAL or EVG failure. Cross-resistance can be partially overcome by doubling DTG dosing to twice daily, but durability of responses remains dependent on a supportive background regimen. There is variability in the integrase gene of circulating HIV strains, which does not appear to reduce drug activity, although it may influence the emergence and evolution of integrase resistance. Transmission of integrase resistance remains rare but surveillance is required. Summary Integrase inhibitors provide a potent option for the treatment of HIV infection. Drug resistance remains a challenge, which may be partially overcome by the introduction of second-generation compounds. Prompt management of RAL and EVG failure is required to prevent the accumulation of multiple resistance mutations that reduce DTG susceptibility.
Hessian eigenmaps: Locally linear embedding techniques for high-dimensional data

We describe a method for recovering the underlying parametrization of scattered data (mi) lying on a manifold M embedded in high-dimensional Euclidean space. The method, Hessian-based locally linear embedding, derives from a conceptual framework of local isometry in which the manifold M, viewed as a Riemannian submanifold of the ambient Euclidean space ℝn, is locally isometric to an open, connected subset Θ of Euclidean space ℝd. Because Θ does not have to be convex, this framework is able to handle a significantly wider class of situations than the original ISOMAP algorithm. The theoretical framework revolves around a quadratic form ℋ(f) = ∫M ∥Hf(m)∥\documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{mathrsfs} \setlength{\oddsidemargin}{-69pt} \begin{document} \begin{equation*}{\mathrm{_{{\mathit{F}}}^{2}}}\end{equation*}\end{document}dm defined on functions f : M ↦ ℝ. Here Hf denotes the Hessian of f, and ℋ(f) averages the Frobenius norm of the Hessian over M. To define the Hessian, we use orthogonal coordinates on the tangent planes of M. The key observation is that, if M truly is locally isometric to an open, connected subset of ℝd, then ℋ(f) has a (d + 1)-dimensional null space consisting of the constant functions and a d-dimensional space of functions spanned by the original isometric coordinates. Hence, the isometric coordinates can be recovered up to a linear isometry. Our method may be viewed as a modification of locally linear embedding and our theoretical framework as a modification of the Laplacian eigenmaps framework, where we substitute a quadratic form based on the Hessian in place of one based on the Laplacian.
Secret dither estimation in lattice-quantization data hiding: a set membership approach

In this paper, security of lattice-quantization data hiding is considered under a cryptanalytic point of view. Security in this family of methods is implemented by means of a pseudorandom dither signal which randomizes the codebook, preventing unauthorized embedding and/or decoding. However, the theoretical analysis shows that the observation of several watermarked signals can provide sufficient information for an attacker willing to estimate the dither signal, quantifying information leakages in different scenarios. The practical algorithms proposed in this paper show that such information leakage may be successfully exploited with manageable complexity, providing accurate estimates of the dither using a small number of observations. The aim of this work is to highlight the security weaknesses of lattice data hiding schemes whose security relies only on secret dithering.
Improving the Attractiveness of Faces in Images

Advertising images increasingly require attractive faces to attract the public's attention. Several studies have been conducted to enhance facial attractiveness in images. While some researchers suggest changes in geometrical shape, others advocate modifying the appearance of the facial skin, however, there have been few attempts to explore the possibility of combining both techniques. This paper sets out a novel method of doing this: facial geometry and skin texture modifications. Our method, which is based on supervised machine learning techniques, is able to improve the attractiveness of faces in images while preserving the original features of the picture. We also demonstrate the effectiveness of this combination by carrying out two different evaluations. Accordingly, we analyze the significance of each change that is designed to improve attractiveness by comparing the original image with a) the image in which only the facial geometry has been modified, b) the image in which only the texture skin has been modified and finally c) the image with both modifications. Our results reveal that the combination of geometric and skin texture modifications results in the most significant enhancement. It also demonstrates that modifications to the skin texture can be regarded as more important to obtain an attractive face than changes to the facial geometry. Additionally, evaluations are provided to quantify the gain in facial attractiveness and it should be pointed out that our method is the first to employ these, since there are no references to such tests in the literature.
Management of Tendinopathy

Overuse disorders of tendons, or tendinopathies, present a challenge to sports physicians, surgeons, and other health care professionals dealing with athletes. The Achilles, patellar, and supraspinatus tendons are particularly vulnerable to injury and often difficult to manage successfully. Inflammation was believed central to the pathologic process, but histopathologic evidence has confirmed the failed healing response nature of these conditions. Excessive or inappropriate loading of the musculotendinous unit is believed to be central to the disease process, although the exact mechanism by which this occurs remains uncertain. Additionally, the location of the lesion (for example, the midtendon or osteotendinous junction) has become increasingly recognized as influencing both the pathologic process and subsequent management. The mechanical, vascular, neural, and other theories that seek to explain the pathologic process are explored in this article. Recent developments in the nonoperative management of chronic tendon disorders are reviewed, as is the rationale for surgical intervention. Recent surgical advances, including minimally invasive tendon surgery, are reviewed. Potential future management strategies, such as stem cell therapy, growth factor treatment, and gene transfer, are also discussed.
Psychosocial aspect of quality of life of Polish women with breast cancer.

INTRODUCTION AND OBJECTIVE Breast cancer is one of the most frequently occurring malignant tumours among women in Poland. The highest incidence of the disease is registered among women aged 50 and more. Cancer imposes a considerable psychological strain on a woman. It causes a sense of uncertainty about one's health and further life, as well as frequent problems with accepting the image of one's own body. It often results in low self-esteem and a feeling of embarrassment, accompanied by symptoms of apathy and detachment. The aim of the study was to determine mental and social life quality of Polish women treated for breast cancer. MATERIALS AND METHODS The research encompassed 107 women aged between 45 and 65 (SD=6.11) undergoing treatment for breast cancer. The WHOQOL-Bref scale was applied in the research. RESULTS The social field was better evaluated in comparison with the mental sphere. There was a statistical correlation between place of residence and social sphere of quality of life (p=,036), with higher ratings assigned by respondents residing in rural areas (M=15.36) compared with residents of towns (M=14.15). CONCLUSIONS Given the fact that respondents were coping with cancer or its consequences, paradoxically, perception of the overall quality of life and examined areas was generally good, especially among women with higher education, those who were single and those living in rural areas. Along with age, there decreases at the respondents the experienced quality of life, however a rise of evaluations of the mental sphere is accompanying the rise in the education level.
WT1 Peptide Cancer Vaccine for Patients with Hematopoietic Malignancies and Solid Cancers

Wild-type Wilms' tumor gene WT1 is expressed at a high level in hematopoietic malignancies including acute leukemia, chronic myelogenous leukemia, and myelodysplastic syndromes, as well as in various kinds of solid cancers. Human cytotoxic T lymphocytes (CTLs), which could specifically lyse WT1-expressing tumor cells with HLA class I restriction, were generated in vitro. It was also demonstrated that mice immunized with the WT1 peptide rejected challenges by WT1-expressing cancer cells and survived with no signs of autoaggression to normal organs that physiologically expressed WT1. Furthermore, we and others detected IgM and IgG WT1 antibodies in patients with hematopoietic malignancies, indicating that the WT1 protein was highly immunogenic, and that immunoglobulin class-switch-inducing, WT1-specific, cellular immune responses were elicited in these patients. CD8+ WT1-specific CTLs were also detected in peripheral blood or tumor-draining lymph nodes of cancer patients. These results provided us with the rationale for elicitation of CTL responses targeting the WT1 product for cancer immunotherapy. On the basis of these findings, we performed a phase I clinical trial of a WT1 peptide cancer vaccine for the patients with malignant neoplasms. These results strongly suggested that the WT1 peptide cancer vaccine had efficacy in the clinical setting because clinical responses, including reduction of leukemic blast cells or regression of tumor masses, were observed after the WT1 vaccination in patients with hematopoietic malignancies or solid cancers. The power of a tumor-associated-antigen (TAA)-derived cancer vaccine may be enhanced in combination with stronger adjuvants, helper peptide, molecular-target-based drugs, or some chemotherapy drugs, such as gemcitabine, which has been revealed to suppress regulartory T-cell function. In contrast, reduction of WT1 peptide dose may be needed for the treatment of patients with hematological stem cell diseases, because rapid and strong destruction of malignant cell-sustained hematopoiesis before recovery of normal hematopoiesis may lead to pancytopenia in these patients.
Gravitational Lensing from a Spacetime Perspective

The theory of gravitational lensing is reviewed from a spacetime perspective, without quasi-Newtonian approximations. More precisely, the review covers all aspects of gravitational lensing where light propagation is described in terms of lightlike geodesics of a metric of Lorentzian signature. It includes the basic equations and the relevant techniques for calculating the position, the shape, and the brightness of images in an arbitrary general-relativistic spacetime. It also includes general theorems on the classification of caustics, on criteria for multiple imaging, and on the possible number of images. The general results are illustrated with examples of spacetimes where the lensing features can be explicitly calculated, including the Schwarzschild spacetime, the Kerr spacetime, the spacetime of a straight string, plane gravitational waves, and others.
A Framework for

Glaucoma is an optic neuropathy affecting the entire visual system. The understanding of the glaucoma mechanism and causes remains unresolved. Diffusion tensor imaging (DTI) has been used to analyze the optic nerve and optic radiation showing global fiber abnormalities associated with glaucoma. Nevertheless, the complex structure of the optic radiation and the limitations of DTI make the localization of the glaucoma effect a difficult task. The aim of this work is to establish a framework for the determination of the local changes of the optic radiation due to glaucoma using DTI. The proposed system utilizes a semi-automated algorithm to produce an efficient identification of the optic radiation. Segmented optic radiations are transformed to a unified space using shape-based non-rigid registration. Using the deformation fields that resulted from the registration, the maps of the diffusion tensorderived parameters are transformed to the unified space. This allows for statistical voxel-wise analysis to produce significant abnormality maps. The proposed system is applied to a group of 13 glaucoma patients and a normal control group of 10 subjects. The groups are age matched to eliminate the age effect on the analysis. Diffusion related parameters (axial, radial, and mean diffusivities) and an anisotropy index (fractional anisotropy) are studied. The anisotropy analysis indicates that the majority of the significant voxels show decreased fractional anisotropy in the glaucoma patients compared to the control group. Additionally, the significant regions are mainly distributed in the middle (in reference to anterior-posterior orientation) of the optic radiation. Glaucoma subjects have increased radial diffusivity and mean diffusivity significant voxels with a main concentration in the proximal part of the right optic radiation. The proposed analysis provides a framework to capture the significant local changes of the optic radiation due to glaucoma. The preliminary analysis suggests that the glaucomatous optic radiation may suffer from localized white matter degeneration. The framework facilitates further studies and understanding of the pathophysiology of glaucoma.
Musically Informed Sonification for Chronic Pain Rehabilitation: Facilitating Progress & Avoiding Over-Doing

In self-directed chronic pain physical rehabilitation it is important that the individual can progress as physical capabilities and confidence grow. However, people with chronic pain often struggle to pass what they have identified as safe boundaries. At the same time, over-activity due to the desire to progress fast or function more normally, may lead to setbacks. We investigate how musically-informed movement sonification can be used as an implicit mechanism to both avoid overdoing and facilitate progress during stretching exercises. We sonify an end target-point in a stretch exercise, using a stable sound (i.e., where the sonification is musically resolved) to encourage movements ending and an unstable sound (i.e., musically unresolved) to encourage continuation. Results on healthy participants show that instability leads to progression further beyond the target-point while stability leads to a smoother stop beyond this point. We conclude discussing how these findings should generalize to the CP population.
Heterogeneous Models Place the Root of the Placental Mammal Phylogeny

Heterogeneity among life traits in mammals has resulted in considerable phylogenetic conflict, particularly concerning the position of the placental root. Layered upon this are gene- and lineage-specific variation in amino acid substitution rates and compositional biases. Life trait variations that may impact upon mutational rates are longevity, metabolic rate, body size, and germ line generation time. Over the past 12 years, three main conflicting hypotheses have emerged for the placement of the placental root. These hypotheses place the Atlantogenata (common ancestor of Xenarthra plus Afrotheria), the Afrotheria, or the Xenarthra as the sister group to all other placental mammals. Model adequacy is critical for accurate tree reconstruction and by failing to account for these compositional and character exchange heterogeneities across the tree and data set, previous studies have not provided a strongly supported hypothesis for the placental root. For the first time, models that accommodate both tree and data set heterogeneity have been applied to mammal data. Here, we show the impact of accurate model assignment and the importance of data sets in accommodating model parameters while maintaining the power to reject competing hypotheses. Through these sophisticated methods, we demonstrate the importance of model adequacy, data set power and provide strong support for the Atlantogenata over other competing hypotheses for the position of the placental root.
Non-Metastatic Pelvic Ewing's Sarcoma : oncologic outcomes and evaluation of prognostic factors.

We are reporting our experience on patients with -pelvic Ewing's Sarcoma treated in our unit. We retrospectively reviewed a series of patients with non-metastatic pelvic Ewing's sarcoma treated between 1977 and 2009. Patients were classified into three groups according to the local treatment received : Group 1. radiotherapy-chemo ; Group 2. surgery-chemo and Group 3. radiotherapy-surgery-chemo. Recurrence free and overall survival rates were calculated using the Kaplan-Meier method. Influence of various factors (age at diagnosis, gender, tumour site and size, chemotherapy response, surgical margins and type of treatment) on survival was assessed with a logistic regression model. A total of 85 patients were treated with a mean follow-up of 65.8 months and mean -tumour volume of 435ml. The 5-year survival for all patients was 40.7% decreased to 36.2% at 10 years. A significant prognostic factor identified was chemotherapy response only. There was a trend for improved survival and local control rates for patients who had chemotherapy and surgery and the results were apparent for all tumours irrespective of size but not statistically significant. Currently, the optimal management of pelvic Ewing's sarcoma is contro-versial but our study shows a trend for improved -survival for patients treated with chemotherapy and surgery.
Linking and Cutting Spanning Trees

We consider the problem of uniformly generating a spanning tree, of a connected undirected graph. This process is useful to compute statistics, namely for phylogenetic trees. We describe a Markov chain for producing these trees. For cycle graphs we prove that this approach significantly outperforms existing algorithms. For general graphs we obtain no analytical bounds, but experimental results show that the chain still converges quickly. This yields an efficient algorithm, also due to the use of proper fast data structures. To bound the mixing time of the chain we describe a coupling, which we analyse for cycle graphs and simulate for other graphs.
In Situ Spatial Organization of Potato Virus A Coat Protein Subunits as Assessed by Tritium Bombardment

ABSTRACT Potato virus A (PVA) particles were bombarded with thermally activated tritium atoms, and the intramolecular distribution of the label in the amino acids of the coat protein was determined to assess their in situ steric accessibility. This method revealed that the N-terminal 15 amino acids of the PVA coat protein and a region comprising amino acids 27 to 50 are the most accessible at the particle surface to labeling with tritium atoms. A model of the spatial arrangement of the PVA coat protein polypeptide chain within the virus particle was derived from the experimental data obtained by tritium bombardment combined with predictions of secondary-structure elements and the principles of packing α-helices and β-structures in proteins. The model predicts three regions of tertiary structure: (i) the surface-exposed N-terminal region, comprising an unstructured N terminus of 8 amino acids and two β-strands, (ii) a C-terminal region including two α-helices, as well as three β-strands that form a two-layer structure called an abCd unit, and (iii) a central region comprising a bundle of four α-helices in a fold similar to that found in tobacco mosaic virus coat protein. This is the first model of the three-dimensional structure of a potyvirus coat protein.
“You know Because I Know”: A multidimensional network approach to human resources problem

Finding talents, often among the people already hired, is an endemic challenge for organizations. The social networking revolution, with online tools like Linkedin, made possible to make explicit and accessible what we perceived, but not used, for thousands of years: the exact position and ranking of a person in a network of professional and personal connections. To search and mine where and how an employee is positioned on a global skill network will enable organizations to find unpredictable sources of knowledge, innovation and know-how. This data richness and hidden knowledge demands for a multidimensional and multiskill approach to the network ranking problem. Multidimensional networks are networks with multiple kinds of relations. To the best of our knowledge, no network-based ranking algorithm is able to handle multidimensional networks and multiple rankings over multiple attributes at the same time. In this paper we propose such an algorithm, whose aim is to address the node multi-ranking problem in multidimensional networks.We test our algorithm over several real world networks, extracted from DBLP and the Enron email corpus, and we show its usefulness in providing less trivial and more flexible rankings than the current state of the art algorithms.
Evidence That Calls-Based and Mobility Networks Are Isomorphic

Social relations involve both face-to-face interaction as well as telecommunications. We can observe the geography of phone calls and of the mobility of cell phones in space. These two phenomena can be described as networks of connections between different points in space. We use a dataset that includes billions of phone calls made in Colombia during a six-month period. We draw the two networks and find that the call-based network resembles a higher order aggregation of the mobility network and that both are isomorphic except for a higher spatial decay coefficient of the mobility network relative to the call-based network: when we discount distance effects on the call connections with the same decay observed for mobility connections, the two networks are virtually indistinguishable.