Miracle-dz/UniFAR-FTUs huggingface dataset:
Cell surface Thomsen-Friedenreich proteome profiling of metastatic prostate cancer cells reveals potential link with cancer stem cell-like phenotype

The tumor-associated Thomsen-Friedenreich glycoantigen (TF-Ag) plays an important role in hematogenous metastasis of multiple cancers. The LTQ Orbitrap LC-MS/MS mass spectrometry analysis of cell surface TF-Ag proteome of metastatic prostate cancer cells reveals that several cell surface glycoproteins expressing this carbohydrate antigen in prostate cancer (CD44, α2 integrin, β1 integrin, CD49f, CD133, CD59, EphA2, CD138, transferrin receptor, profilin) are either known as stem cell markers or control important cancer stem-like cell functions. This outcome points to a potential link between TF-Ag expression and prostate cancer stem-like phenotype. Indeed, selecting prostate cancer cells for TF-Ag expression resulted in the enrichment of cells with stem-like properties such as enhanced clonogenic survival and growth, prostasphere formation under non-differentiating and differentiating conditions, and elevated expression of stem cell markers such as CD44 and CD133. Further, the analysis of the recent literature demonstrates that TF-Ag is a common denominator for multiple prostate cancer stem-like cell populations identified to date and otherwise characterized by distinct molecular signatures. The current paradigm suggests that dissemination of tumor cells with stem-like properties to bone marrow that occurred before surgery and/or radiation therapy is largely responsible for disease recurrence years after radical treatment causing a massive clinical problem in prostate cancer. Thus, developing means for destroying disseminated prostate cancer stem-like cells is an important goal of modern cancer research. The results presented in this study suggest that multiple subpopulation of putative prostate cancer stem-like cells characterized by distinct molecular signatures can be attacked using a single target commonly expressed on these cells, the TF-Ag.
Small-Signal and Large-Signal Analysis of the Two-Transformer Asymmetrical Half-Bridge Converter Operating in Continuous Conduction Mode

The asymmetrical half-bridge converter (AHBC) has many advantages over other PWM converters. The possibility of soft switching in primary switches and reduced switching losses in the secondary ones implies that the AHBC is a suitable topology for many high-performance applications. Besides, the lack of dead times, except those needed for achieving soft switching, is a very interesting feature to implement self-driven synchronous rectification. Moreover, the small size of its output filter is also a remarkable advantage in some fields (e.g., LED lighting). On the other hand, it also has some disadvantages. One of them is the short range of the duty cycle (lower than 0.5) and the other one is the difficult regulation due to a complex transfer function. The two-transformer AHBC (TTAHBC) solves the first problem as it enlarges the duty cycle range making its top limit higher than 0.5. Nevertheless, the regulation of this converter is still very complex and, besides, the transfer functions of the standard AHBC are not valid for the TTAHBC. As a consequence, the small- and large-signal models have yet to be studied. In this paper, the complete small-signal and large-signal analysis of the TTAHBC operating in continuous conduction mode is provided. The large-signal and small-signal models are developed taking into account the main parasitic components that affect the transient response of this converter. The validation of the resulting model is carried out by means of both, simulation and experimental results. The prototype is a 60-W TTAHBC designed for an input voltage of 400 V and an output voltage of 48 V.
Active contours for localizing polyps in colonoscopic NBI image data

Colon cancer is the third most common type of cancer in the United States of America. Every year about 140,000 people are newly diagnosed with colon cancer. Early detection is crucial for a successful therapy. The standard screening procedure is called colonoscopy. Using this endoscopic examination physicians can find colon polyps and remove them if necessary. Adenomatous colon polyps are deemed a preliminary stage of colon cancer. The removal of a polyp, though, can lead to complications like severe bleedings or colon perforation. Thus, only polyps diagnosed as adenomatous should be removed. To decide whether a polyp is adenomatous the polyp's surface structure including vascular patterns has to be inspected. Narrow-Band imaging (NBI) is a new tool to improve visibility of vascular patterns of the polyps. The first step for an automatic polyp classification system is the localization of the polyp. We investigate active contours for the localization of colon polyps in NBI image data. The shape of polyps, though roughly approximated by an elliptic form, is highly variable. Active contours offer the flexibility to adapt to polyp variation well. To avoid clustering of contour polygon points we propose the application of active rays. The quality of the results was evaluated based on manually segmented polyps as ground truth data. The results were compared to a template matching approach and to the Generalized Hough Transform. Active contours are superior to the Hough transform and perform equally well as the template matching approach.
Etude des algorithmes des moindres carres transversaux rapides et application a l'identification de reponses impulsionnelles acoustique

Le travail concerne l'etude theorique et pratique des algorithmes des moindres carres transversaux rapides (mcr) en vue de les appliquer a certains nouveaux systemes de communication locale qui font intervenir une prise de son dans des conditions particulieres. Citons la teleconference et les postes telephoniques "mains libres" ou apparait le phenomene d'echo-acoustique
Interval type-2 fuzzy sets for enhanced learning in deep belief networks

Restricted Boltzmann Machine (RBM) is a generative, stochastic neural network with two separate layers of hidden and visible units. Training data samples in RBM are usually corrupted by noise. RBM is not robust enough to handle such noises, which leads to uncertainty. In the literature, Fuzzy RBM (FRBM) has already been proposed for enhancing deep learning. In FRBM, the parameters of RBM are modelled as type-1 fuzzy numbers. However, there can be multiple sources of uncertainties such as noises in the data measurements, variations in the environment where they are deployed, etc. Such uncertainties cannot be modelled by type-1 fuzzy sets (T1 FS), since their membership values are themselves crisp in nature. On the other side, IT2 FS can model higher order uncertainties with their fuzzy membership grades. So, we propose to use interval type-2 fuzzy sets (IT2 FS) to model uncertain parameters of RBMs in the learning stage. Since deep neural network (DNN) is pre-trained using stacked RBMs, modeling noises using IT2 FS would demonstrate high performance and low root mean square error (RMSE) while learning. Thus, we propose a new algorithm viz. Interval type-2 fuzzy set based approach for enhanced deep learning (IT2 FS-EDL) in which RBM parameters are modeled as type-2 fuzzy sets in the learning process. Numerical examples and experimentations have been demonstrated to present the suitability of our proposed approach.
Apical epithelial cap morphology and fibronectin gene expression in regenerating axolotl limbs

Urodele amphibians (salamanders) are unique among adult vertebrates in their ability to regenerate limbs. The regenerated structure is often indistinguishable from the developmentally produced original. Thus, the two processes by which the limb is produced — development and regeneration — are likely to use many conserved biochemical and developmental pathways. Some of these limb features are also likely to be conserved across vertebrate families. The apical ectodermal ridge (AER) of the developing amniote limb and the larger apical epithelial cap (AEC) of the regenerating urodele limb are both found at the limb's distal‐most tip and have been suggested to be functionally similar even though their morphology is quite different. Both structures are necessary for limb outgrowth. However, the AEC is uniformly smooth and thickly covers the entire limb‐tip, unlike the AER, which is a protruding ridge covering only the dorsoventral boundary. Previous data from our laboratory suggest the multilayered AEC may be subdivided into separate functional compartments. We used hematoxylin and eosin (H+E) staining as well as in situ hybridization to examine the basal layer of the AEC, the layer that lies immediately over the distal limb mesenchyme. In late‐stage regenerates, this basal layer expresses fibronectin (FN) message very strongly in a stripe of cells along the dorsoventral boundary. H+E staining also reveals the unique shape of basal cells in this area. The stripe of cells in the basal AEC also contains the notch/groove structure previously seen in avian and reptilian AERs. In addition, AEC expression of FN message in the cells around the groove correlates with previous amniote AER localization of FN protein inside the groove. The structural and biochemical analyses presented here suggest that there is a specialized ridge‐like compartment in the basal AEC in late‐stage regenerates. The data also suggest that this compartment may be homologous to the AER of the developing amniote limb. Thus, the external differences between amniote limb development and urodele limb regeneration may be outweighed by internal similarities, which enable both processes to produce morphologically complete limbs. In addition, we propose that this basal layer of the AEC is uniquely responsible for AEC functions in regeneration, such as secreting molecules to promote mesenchymal cell cycling and dictating the direction of limb outgrowth. Finally, we include here a clarification of existing nomenclature to facilitate further discussion of the AEC and its basal layer. Dev Dyn;217:216–224. © 2000 Wiley‐Liss, Inc.
Is There a Role for Assisted Reproductive Technology in Recurrent Miscarriage?

Unexplained recurrent miscarriage (RM) is a significant health problem for which no effective treatment is available yet. In only 50% of couples with RM a cause can be found. In clinical practice, a frequently asked question is whether assisted reproductive technology (ART) is a treatment option. The scientific rationale and the chances of success for ART in couples with unexplained RM are still controversial. Presently, there is not enough evidence to justify IVF or intrauterine insemination (IUI) as a treatment option. Research on oocyte donation has been reported in one article. It is questionable whether couples with unexplained RM would undergo the potential risks and emotional aspects of ART. There is insufficient data on whether preimplantation genetic diagnosis improves the live birthrate in carriers of a structural chromosome rearrangement with a history of RM. No randomized controlled trials are available for preimplantation genetic screening (PGS) for unexplained RM. A recently published review concluded that the live birthrate for IVF/PGS and natural conception groups appears to be quite similar. Because evidence is lacking, we recommend refraining from ART in couples with recurrent miscarriage.
Using Simpler Algorithm for Cavity Flow Problem

Selecting compute nodes and solution grid generation are the first steps of numerical solutions. The most distinct manner is storing the values of dependent variables in the same set of nodes and using the identical control volumes for all variables. Such a grid is called Collocated. Collocated grid arrangement has many positive results in problems with complex solving range, especially with discontinuous boundary conditions. But this arrangement was not used for a long time for incompressible flow due to pressure and velocity isolation problems and creation of fluctuations in pressure. So the researchers in the mid-60s, have developed a new arrangement to reduce this isolation and increase the coupling between pressure and velocity. This new arrangement called staggered grid, provided the field of a new method for solving fluid flow problems called SIMPLE (Semi-Implicit Method for Pressure-Linked Equation) algorithm [1]. This report presents the solution to the continuity, Navier-Stokes equations. Standard fundamental methods like SIMPLER and primary variable formulation have been utilized. The results were analyzed for standard CFD test case- cavity flow. Different Reynold number (1000, 3000) and grid sizes with the finest meshes ie (100×100), (1000×1000) have been studied.
Simulated patients in medical teaching.

]%/|"OCK warfare, mock trials and aircraft . *-*-¦trainers are but a few examples of simula¬ tion used to teach, evaluate and provide practi¬ cal experience for the student before he is ready to assume full responsibility. Simulated teaching is controlled, the student's experience is free of unexpected or unknown variables, and his responses or actions can be recorded and evaluated relative to performances by other students and the goals of the teacher. Over the past three years we have developed patient simulation in many areas of medical education to teach and evaluate clinical performance by the student. To teach patient care is the stated goal of our medical school and certainly a goal implied in the M.D. degree. Despite this, it is amazing how few means are available in medi¬ cal education to appraise accurately the per¬ formance of a physician-to-be at the bedside and to teach clinical medicine in a simulated or con¬ trolled situation that provides experience dictated by the teacher. For patient simulation we use persons who have been specially trained and oriented to per¬ form as patients. In many instances this requires that they should give a history and simulate the clinical findings of a patient with a particular disease entity.
Structured higher-order algorithmic differentiation in the forward and reverse mode with application in optimum experimental design

This thesis provides a framework for the evaluation of first and higher-order derivatives and Taylor series expansions through large computer programs that contain numerical linear algebra (NLA) functions. It is a generalization of traditional algorithmic differentiation (AD) techniques in that NLA functions are regarded as black boxes where the inputs and outputs are related by defining equations. Based on the defining equations, structure-exploiting algorithms are derived. More precisely, novel algorithms for the propagation of Taylor polynomials through the QR, Cholesky,and real-symmetric eigenvalue decomposition are shown. Recurrences for the reverse mode of AD, which require essentially only the returned factors of the decomposition, are also derived. Compared to the traditional approach where all intermediates of an algorithm are stored, this is a reduction from O(N3) to O(N2) for algorithms with O(N3) complexity. N denotes the matrix size. The derived algorithms make it possible to use existing high-performance implementations. A runtime comparison shows that the treatment of NLA functions as atomic can be more than one order of magnitude faster than an automatic differentiation of the underlying algorithm. Furthermore, the computational graph is orders of magnitudes smaller. This reduces the additional memory requirements, as well as the overhead, of operator overloading techniques to a fraction. It is then demonstrated that the novel algorithms can be used to compute the gradient of the optimum experimental design (OED) objective function in the reverse mode of AD. Since the evaluation of the objective function already requires the evaluation of nested derivatives, this is a nonstandard situation. One can show that the computation of the gradient is only about three times as expensive as the function evaluation itself and hence is in very good agreement with the theoretical bound. The proposed method is a combination of the reverse mode, univariate Taylor polynomial arithmetic and interpolation/polarization techniques. This is a significant improvement over previous work and makes it possibly to apply OED to a larger class of problems. Furthermore, this study discusses how the necessary higherorder derivatives can be computed using Taylor polynomial arithmetic. This is also an improvement over the previously used finite difference schemes. Numerical examples from chemical engineering are used to verify the algorithms.
Southern East Asian origin and coexpansion of Mycobacterium tuberculosis Beijing family with Han Chinese

Significance Mycobacterium tuberculosis Beijing family is a group of globally emerging bacterial strains that are responsible for more than a quarter of the global tuberculosis epidemic. Here, we combine whole-genome sequencing and large-scale genotyping to map the temporal and spatial changes of the genetic diversity within this strain family. We reveal a southern East Asia origin and a parallel evolution of this bacterial genotype with modern humans in East Asia during the last 30,000 years. The recently globally emerged Beijing strains mainly belong to a hypervirulent subtype that most likely has initially been selected for adaption to increased population densities during the agricultural transition in northern China. The Beijing family is the most successful genotype of Mycobacterium tuberculosis and responsible for more than a quarter of the global tuberculosis epidemic. As the predominant genotype in East Asia, the Beijing family has been emerging in various areas of the world and is often associated with disease outbreaks and antibiotic resistance. Revealing the origin and historical dissemination of this strain family is important for understanding its current global success. Here we characterized the global diversity of this family based on whole-genome sequences of 358 Beijing strains. We show that the Beijing strains endemic in East Asia are genetically diverse, whereas the globally emerging strains mostly belong to a more homogenous subtype known as “modern” Beijing. Phylogeographic and coalescent analyses indicate that the Beijing family most likely emerged around 30,000 y ago in southern East Asia, and accompanied the early colonization by modern humans in this area. By combining the genomic data and genotyping result of 1,793 strains from across China, we found the “modern” Beijing sublineage experienced massive expansions in northern China during the Neolithic era and subsequently spread to other regions following the migration of Han Chinese. Our results support a parallel evolution of the Beijing family and modern humans in East Asia. The dominance of the “modern” Beijing sublineage in East Asia and its recent global emergence are most likely driven by its hypervirulence, which might reflect adaption to increased human population densities linked to the agricultural transition in northern China.
Glomerular filtration rate as a putative ‘surrogate end‐point’ for renal transplant clinical trials in children

Abstract: Only with prospective randomized controlled trials is it possible to evaluate the several immunosuppressive regimens available to renal allograft recipients. Commonly used surrogate markers of clinical outcome, such as patient and graft survival, are constantly improving. Current immunosuppressive protocols have improved 1‐yr graft survival to over 90%. The small differences in graft survival among the various immunosuppressive regimes require large patient cohorts in order to establish statistical significance. Such studies are often difficult to conduct in a timely manner, particularly in children. This necessitates the search for better surrogate markers sensitive enough to detect differences in smaller cohorts and in a shorter period of time. While the degree of fibrosis in transplant biopsies might well predict long‐term graft survival, protocol biopsies are expensive, invasive, and unpopular among clinicians. In native kidneys, glomerular filtration rate (GFR) closely correlates with disease progression and interstitial fibrosis and appears to be well positioned as a less invasive surrogate marker for long‐term outcome. Nonetheless, the ideal marker for GFR remains obscure. Serum creatinine has several major drawbacks, making it a poor predictor of GFR. This review discusses the several methods used to estimate or measure GFR with emphasis on 125I‐iothalamate clearance and serum cystatin C (cys‐C). Of all the serum markers, cys‐C is the most reliable and the most promising. However, cys‐C and other endogenous markers cannot replace the diagnostic sensitivity and reliability of radiolabeled markers of GFR such as 125I‐iothalamate in renal transplant clinical trials. Unfortunately, clearance of most radiolabeled markers of GFR including 125I‐iothalamate remain costly and time consuming.
Towards Refactoring-Aware Regression Test Selection

Regression testing checks that recent project changes do not break previously working functionality. Although important, regression testing is costly when changes are frequent. Regression test selection (RTS) optimizes regression testing by running only tests whose results might be affected by a change. Traditionally, RTS collects dependencies (e.g., on files) for each test and skips the tests, at a new project revision, whose dependencies did not change. Existing RTS techniques do not differentiate behavior-preserving transformations (i.e., refactorings) from other code changes. As a result, tests are run more frequently than necessary. We present the first step towards a refactoring-aware RTS technique, dubbed Reks, which skips tests affected only by behavior-preserving changes. Reks defines rules to update the test dependencies without running the tests. To ensure that Reks does not hide any bug introduced by the refactoring engines, we integrate Reks only in the pre-submit testing phase, which happens on the developers' machines. We evaluate Reks by measuring the savings in the testing effort. Specifically, we reproduce 100 refactoring tasks performed by developers of 37 projects on GitHub. Our results show that Reks would not run, on average, 33% of available tests (that would be run by a refactoring-unaware RTS technique). Additionally, we systematically run 27 refactoring types on ten projects. The results, based on 74,160 refactoring tasks, show that Reks would not run, on average, 16% of tests (max: 97% and SD: 24%). Finally, our results show that the Reks update rules are efficient.