Miracle-dz/UniFAR-FTUs huggingface dataset:
Regulation of megakaryocyte phenotype in human erythroleukemia cells.

Induction of human erythroleukemia (HEL) cells with nanomolar tumor-promoting phorbol myristate acetate (PMA) diesters results in the synchronous acquisition of multiple markers of the megakaryocyte phenotype. Induced cells markedly increase their content of cytoplasm and show features of morphological maturation. At the ultrastructural level, PMA-treated cells show increases in cytoplasm, nuclear lobulation and nucleolar content, and free ribosomes. Limited numbers of cells also express alpha-granules and nascent demarcation membrane systems. Functionally, PMA-stimulated HEL cells express increased amounts of the megakaryocyte/platelet proteins: glycoprotein IIb/IIIa, platelet factor 4, von Willebrand factor, glycoprotein Ib, and thrombospondin. No changes are observed in antigenic markers of the erythroid (glycophorin A) or macrophage lineages (MO-1 or MO-2). The increases in antigenic expression are rapid, reaching maximum levels within 3-4 d under serum-free conditions. Treatment with PMA also abruptly (within 1-2 d) inhibits cellular division in these cells. Washout studies indicate that phorbols exert their effect within 18-24 h, the approximate cell cycle time for these cells. Consistent with proliferative arrest, c-myc proto-oncogene transcripts begin to decline within 8 h of PMA treatment, although transcripts of c-myb are unaffected. Importantly, megakaryocyte differentiation is associated with endomitotic DNA synthesis (i.e., continued DNA synthesis in the absence of mitosis and cytokinesis), with HEL cells reaching a DNA content of 3-12 times that of unstimulated cells. Endomitosis is coordinately regulated with changes in antigenic expression and cell size such that those cells having the highest DNA content are the largest and also express the greatest levels of antigen.
Transmission et plasticité activité-dépendante au niveau des synapses cortico-striatales

Le striatum a pour role de selectionner et d’integrer les informations provenant du cortex et ainsi construire et transmettre une reponse adaptee aux stimuli environnementaux. Nous avons caracterise les proprietes electrophysiologiques des differents neurones du striatum (neurones de sortie, NETM, et interneurones) dans des conditions normales, et lors d’une depletion de dopamine striatale. Grâce a un modele de tranche de cerveau de rat dans laquelle les afferences cortico-striatales sont conservees intactes, nous avons mis en evidence une plasticite synaptique bidirectionnelle dans les NETM ainsi qu’une homeostasie puissante au niveau des synapses cortico-striatales. Nous avons ensuite observe que, outre les NETM, le cortex contacte egalement les interneurones striataux, avec une sequence d’activation particuliere et qu’il existe une specificite cellulaire de la « spike-timing dependent plasticity » (STDP) dans le striatum. Enfin, nous avons mis en evidence que, au niveau des NETM, des signaux sous-liminaires, en coincidence avec une activite corticale, sont capables d’induire des phenomenes de plasticite synaptique a long-terme.
A Novel Discriminative Feature Extraction for Acoustic Scene Classification Using RNN Based Source Separation

Various types of classifiers and feature extraction methods for acoustic scene classification have been recently proposed in the IEEE Detection and Classification of Acoustic Scenes and Events (DCASE) 2016 Challenge Task 1. The results of the final evaluation, however, have shown that even top 10 ranked teams, showed extremely low accuracy performance in particular class pairs with similar sounds. Due to such sound classes being difficult to distinguish even by human ears, the conventional deep learning based feature extraction methods, as used by most DCASE participating teams, are considered facing performance limitations. To address the low performance problem in similar class pair cases, this letter proposes to employ a recurrent neural network (RNN) based source separation for each class prior to the classification step. Based on the fact that the system can effectively extract trained sound components using the RNN structure, the mid-layer of the RNN can be considered to capture discriminative information of the trained class. Therefore, this letter proposes to use this mid-layer information as novel discriminative features. The proposed feature shows an average classification rate improvement of 2.3% compared to the conventional method, which uses additional classifiers for the similar class pair issue. key words: acoustic scene classification, transfer learning, recurrent neural network, bottleneck feature
Skew convolution semigroups and affine Markov processes

A general affine Markov semigroup is formulated as the convolution of a homogeneous one with a skew convolution semigroup. We provide some sufficient conditions for the regularities of the homogeneous affine semigroup and the skew convolution semigroup. The corresponding affine Markov process is constructed as the strong solution of a system of stochastic equations with non-Lipschitz coefficients and Poisson-type integrals over some random sets. Based on this characterization, it is proved that the affine process arises naturally in a limit theorem for the difference of a pair of reactant processes in a catalytic branching system with immigration.
Sinu-atrial Node of Mature Dromedary Camel Heart (Camelus dromedarius)with special Emphasis on the Atrial Purkinje like Cardiomyocytes

The sinu-atrial node (SAN) is one of the impulse conducting system of the camel heart. Anatomically, it lies beneath the epicardium, at the cranial end of the terminal sulcus, near the junction between the superior vena cava to the lateral wall of the right atrium and the right auricle. Histologically, SAN is located in the subepicardial layer of the terminal crest and can be identified as a mass of specialized and modified cardiac myocytes. Moreover, it appeared elongated in shape and bent oblong. SAN appears strongly similar to the general structure of the glands where, it is formed of two parts; the stroma and the parenchyma. The stroma is consisted of a fibrous connective tissue capsule that is completely investing the SAN from all sides. From the capsule, thin connective tissue septa or trabeculae are extending to inside the node, dividing the later into lobes. These lobes form the SAN head or the SAN body. From this body, the SAN arms processes take their way out. These arms are considered the internodal and interatrial pathways to the different sites in the right and left atria. So, the SAN head with arms giving the octopus likeappearance for the node. The parenchyma is consisted of three different types of specialized and modified cardiac myocytes; the perinuclear clear zone cells (“P” cells), the transitional cells (“T” cells) and the atrial Purkinje like cells or Purkinje like conducting cells.
Auditory stream segregation relying on timbre involves left auditory cortex

An important aspect of auditory scene analysis is sequential grouping of sounds that are similar to one another in preference to sounds that follow one another. This grouping problem is captured by stream segregation tasks with alternating distinct sounds. We examined human auditory cortex activity with low noise fMRI in a stream segregation experiment relying on timbre differences of alternating harmonic tones (organ-like and trumpet-like). We found that stream segregation performance in comparison to monitoring a non-separable control stream increased activation exclusively in left auditory cortex and particularly in posterior areas. Our results suggest that left auditory cortex is selectively involved in this complex sequential task although the available cue for sequential grouping was timbre, usually attributed to right hemisphere analysis.
Regression Testing of GPU/MIC Systems for HPCC

Multicore GPU, Intel MIC, and FPGA supplemental parallel processors have become widely implemented in High Performance Computing Clusters (HPCCs). In HPCCs, Computing nodes are assembled with these supplemental processors for specific research applications, images are applied to do the research. Since HPCC computing nodes require completely different design configuration from one day to the next, System Administrators are being challenged to verify that each of these computing images work correctly, in all needed applications. Due to the large cost in man-hours that are expended with manual testing of each computing node and the entire HPCC system for defects, there is a need for automated regression testing on parallel, distributed, and heterogeneous computing nodes. Existing approaches at automated regression testing deals only with simple homogeneous HPCC topologies. What is needed is a regression testing technique to include heterogeneous HPCC topologies that deal with computing nodes containing supplemental GPUs, Intel MIC cards, FPGAs, etc. This paper presents a case-study to perform regression testing using Equivalence Class Partitioning (ECP) and Boundary Value testing techniques. The method has been employed to test HPCCs configured of heterogeneous computing nodes. More specifically, the computing nodes configured for this experiment include NVidia GPU and Intel MIC Xeon Phi cards deployed in HPCC clusters.
Cell migration and chimerism--a unifying concept in transplantation--with particular reference to HLA matching and tolerance induction.

WE recently reported that the acceptance of wholeorgan transplants connotes (and requires) a special kind of mixed chimerism involving an exchange between organ and recipient oflymphodendritic leukocytes (Fig 1 ). 1 The consequence in five of five patients studied 27 to 29V2 years after kidney transplantation from HLA-mismatched donors was the diffuse presence of donor dendritic cells in the lymph nodes and skin of the recipient. 2 Chronically surviving liver recipients have even more prominent evidence of systemic and graft chimerism,I.3 which can be shown with immunocytochemical techniques and confirmed with polymerase chain reaction (PCR) technology. Chimerism has been particularly easy to study after intestinal transplantation.4. 5 With the thesis that this cell migration, repopulation, and consequent chimerism is the basis of graft acceptance, no matter what the organ transplanted, I we are able to reexamine some controversies in transplantation immunology, including why HLA tissue matching to govern the distribution of cadaveric organs has been so nonpredictive of outcome. To understand these controversies, we must turn back the pages 50 years, when Peter Medawar planted the seed of our specialty.
Demonstration of Paneth cell granules using Naphthalene Black.

It is not uncommon for the Foundation Lecturer to gather material from personal archives and this has, to some extent, been the custom of previous lecturers of whom I name but two: our illustrious founder, Dr. Sydney Dyke, and one of my teachers, Dr. J. G. Greenfield. This I shall do relating my findings in some diseases due to trace metals to published work by other investigators. My interest in heavy metals in the brain began just before the last war but it was not until about 1947 or almost exactly 20 years ago that my first useful results were obtained. At that time I was estimating copper, iron, and manganese in normal and diseased cerebral tissues and I was fortunate enough to examine material from three cases of Wilson's disease, now universally agreed to be a condition in which there is an accumulation of copper in many tissues. Although that great authority, Thudichum, reported in 1884 his findings concerning brain biochemistry it is only in the last 25 years that exact knowledge has been obtained concerning some heavy metals, present in trace amounts in the brain. Consideration will be given here to only two, namely, iron and copper, but it is hoped to report upon other trace metals later.
Synaptic organization of the tectorecipient zone of the rat lateral posterior nucleus

Dorsal thalamic nuclei have been categorized as either “first‐order” nuclei that gate the transfer of relatively unaltered signals from the periphery to the cortex or “higher order” nuclei that transfer signals from one cortical area to another. To classify the tectorecipient lateral posterior (LPN), we examined the synaptic organization of tracer‐labeled cortical and tectal terminals and terminals labeled with antibodies against the type 1 and type 2 vesicular glutamate transporters (vGLUT1 and vGLUT2) within the caudal/lateral LPN of the rat. For this zone, we found that all tracer‐labeled cortical terminals, as well as vGLUT1 antibody‐labeled terminals, are small profiles with round vesicles (RS profiles) that innervate small‐caliber dendrites. Tracer‐labeled tecto‐LPN terminals, as well as vGLUT2 antibody‐labeled terminals, were medium‐sized profiles with round vesicles (RM profiles). Tecto‐LPN terminals were significantly larger than cortico‐LPN terminals and contacted significantly larger dendrites. These results indicate that, within the tectorecipient zone of the rat LPN, cortical terminals are located distal to tectal terminals and that vGLUT1 and vGLUT2 antibodies may be used as markers for cortical and tectal terminals, respectively. Finally, comparisons of the synaptic patterns formed by tracer‐labeled terminals with those of vGLUT antibody‐labeled terminals suggest that individual LPN neurons receive input from multiple cortical and tectal axons. We suggest that the tectorecipient LPN constitutes a third category of thalamic nucleus (“second‐order”) that integrates convergent tectal and cortical inputs. This organization may function to signal the movement of novel or threatening objects moving across the visual field. J. Comp. Neurol. 515:647–663, 2009. © 2009 Wiley‐Liss, Inc.
The mammalian proton-coupled peptide cotransporter PepT1: sitting on the transporter–channel fence?

The proton-coupled di- and tripeptide transporter PepT1 (SLC15a1) is the major route by which dietary nitrogen is taken up from the small intestine, as well as being the route of entry for important therapeutic (pro)drugs such as the β-lactam antibiotics, angiotensin-converting enzyme inhibitors and antiviral and anti-cancer agents. PepT1 is a member of the major facilitator superfamily of 12 transmembrane domain transporter proteins. Expression studies in Xenopus laevis on rabbit PepT1 that had undergone site-directed mutagenesis of a conserved arginine residue (arginine282 in transmembrane domain 7) to a glutamate revealed that this residue played a role in the coupling of proton and peptide transport and prevented the movement of non-coupled ions during the transporter cycle. Mutations of arginine282 to other non-positive residues did not uncouple proton–peptide cotransport, but did allow additional ion movements when substrate was added. By contrast, mutations to positive residues appeared to function the same as wild-type. These findings are discussed in relation to the functional role that arginine282 may play in the way PepT1 operates, together with structural information from the homology model of PepT1 based on the Escherichia coli lactose permease crystal structure.
Technological Change and the Gender Unemployment Gap

In the United States, the female unemployment rate had been considerably higher than the male unemployment rate since World War II. However, this gap disappeared after 1980. This article argues that the sudden and sustained decrease in gender unemployment gap was due to technological changes that a¤ected skill demands and wages in certain male dominated occupations. To analyze this conjecture, we build a life-cycle search and matching model with endogenous job separation and heterogeneous experience levels. We nd that the model can account for the observed decrease in gender unemployment gap, both at the aggregate level and by age. Keywords: gender unemployment gap, technological change, wage growth, productivity growth, experience. JEL classi cation: E24, J6. We would like to thank Andrew Atkeson, David Autor, Eva Carceles-Poveda, Tiago Cavalcanti, Giancarlo Corsetti, Chryssi Giannitsarou, Giammario Impullitti and Jesus Fernandez-Villaverde for useful comments and suggestions.
The minimum latency problem

We are given a set of points p1, . , pn and a symmetric distance matrix (dij) giving the distance between pi and pj . We wish to construct a tour that minimizes ∑n i=1 `(i), where `(i) is the latency of pi, defined to be the distance traveled before first visiting pi. This problem is also known in the literature as the deliveryman problem or the traveling repairman problem. It arises in a number of applications including diskhead scheduling, and turns out to be surprisingly different from the traveling salesman problem in character. We give exact and approximate solutions to a number of cases, including a constant-factor approximation algorithm whenever the distance matrix satisfies the triangle inequality. ∗School of Computer Science, CMU. Supported in part by NSF National Young Investigator grant CCR9357793. †School of Computer Science, CMU. ‡IBM T.J. Watson Research Center.
Technical Brief: Using Implicit Information to Identify Smoking Status in Smoke-blind Medical Discharge Summaries

As part of the 2006 i2b2 NLP Shared Task, we explored two methods for determining the smoking status of patients from their hospital discharge summaries when explicit smoking terms were present and when those same terms were removed. We developed a simple keyword-based classifier to determine smoking status from de-identified hospital discharge summaries. We then developed a Naïve Bayes classifier to determine smoking status from the same records after all smoking-related words had been manually removed (the smoke-blind dataset). The performance of the Naïve Bayes classifier was compared with the performance of three human annotators on a subset of the same training dataset (n = 54) and against the evaluation dataset (n = 104 records). The rule-based classifier was able to accurately extract smoking status from hospital discharge summaries when they contained explicit smoking words. On the smoke-blind dataset, where explicit smoking cues are not available, two Naïve Bayes systems performed less well than the rule-based classifier, but similarly to three expert human annotators.
Smoking Use and Cessation Among People with Serious Mental Illness

Smoking rates in people with serious mental illness (SMI) are disproportionately high compared to the general population. It is a leading contributor to the early mortality in this population. Smoking cessation rates are low in this group, though patients are motivated to quit. Unfortunately, health care providers do not always prioritize smoking cessation for this population. This review provides an overview of prevalence rates, biological effects that maintain smoking, and evidence-based treatments for smoking cessation in SMI. In addition, objective and qualitative data from a chart review of 78 patients with SMI prescribed smoking cessation treatment at one community mental health center are described. Of these, 30 (38.5 percent) were found to either quit (16/78) or reduce (14/78) smoking. Varenicline appeared to be particularly effective. Review of the literature and results of this study suggest that smoking cessation pharmacotherapies are effective for SMI patients and should be offered to those who smoke.
Mask assignment and synthesis of DSA-MP hybrid lithography for sub-7nm contacts/vias

Integrating Directed Self Assembly (DSA) and Multiple Patterning (MP) is an attractive option for printing contact and via layers for sub-7nm process nodes. In the DSA-MP hybrid process, an optimized decomposition algorithm is required to perform the MP mask assignment while considering the DSA advantages and limitations. In this paper, we present an optimal Integer Linear Programming (ILP) formulation for the simultaneous DSA grouping and MP decomposition problem for contacts and vias. Then we propose a heuristic and develop an efficient algorithm for solving the same problem. In comparison to the optimal ILP results, the proposed algorithm is 197x faster and results in 16.3% more violations. The proposed algorithm produces 56% fewer violations than the sequential approaches which perform DSA grouping followed by MP decomposition and vice versa.
GPU Acceleration of a High-Order Discontinuous Galerkin Incompressible Flow Solver

We present a GPU-accelerated version of a high-order discontinuous Galerkin discretization of the unsteady incompressible Navier-Stokes equations. The equations are discretized in time using a semi-implicit scheme with explicit treatment of the nonlinear term and implicit treatment of the split Stokes operators. The pressure system is solved with a conjugate gradient method together with a fully GPU-accelerated multigrid preconditioner which is designed to minimize memory requirements and to increase overall performance. A semi-Lagrangian subcycling advection algorithm is used to shift the computational load per timestep away from the pressure Poisson solve by allowing larger timestep sizes in exchange for an increased number of advection steps. Numerical results confirm we achieve the design order accuracy in time and space. We optimize the performance of the most time-consuming kernels by tuning the fine-grain parallelism, memory utilization, and maximizing bandwidth. To assess overall performance we present an empirically calibrated roofline performance model for a target GPU to explain the achieved efficiency. We demonstrate that, in the most cases, the kernels used in the solver are close to their empirically predicted roofline performance.
Preferential V beta gene usage and lack of junctional sequence conservation among human T cell receptors specific for a tetanus toxin- derived peptide: evidence for a dominant role of a germline-encoded V region in antigen/major histocompatibility complex recognition

To investigate the structural and genetic basis of the T cell response to defined peptide/major histocompatibility (MHC) class II complexes in humans, we established a large panel of T cell clones (61) from donors of different HLA-DR haplotypes and reactive with a tetanus toxin- derived peptide (tt830-844) recognized in association with most DR molecules (universal peptide). By using a bacterial enterotoxin-based proliferation assay and cDNA sequencing, we found preferential use of a particular V beta region gene segment, V beta 2.1, in three of the individuals studied (64%, n = 58), irrespective of whether the peptide was presented by the DR6wcI, DR4w4, or DRw11.1 and DRw11.2 alleles, demonstrating that shared MHC class II antigens are not required for shared V beta gene use by T cell receptors (TCRs) specific for this peptide. V alpha gene use was more heterogeneous, with at least seven different V alpha segments derived from five distinct families encoding alpha chains able to pair with V beta 2.1 chains to form a tt830-844/DR- specific binding site. Several cases were found of clones restricted to different DR alleles that expressed identical V beta and (or very closely related) V alpha gene segments and that differed only in their junctional sequences. Thus, changes in the putative complementary determining region 3 (CDR3) of the TCR may, in certain cases, alter MHC specificity and maintain peptide reactivity. Finally, in contrast to what has been observed in other defined peptide/MHC systems, a striking heterogeneity was found in the junctional regions of both alpha and beta chains, even for TCRs with identical V alpha and/or V beta gene segments and the same restriction. Among 14 anti-tt830-844 clones using the V beta 2.1 gene segment, 14 unique V beta-D-J beta junctions were found, with no evident conservation in length and/or amino acid composition. One interpretation for this apparent lack of coselection of specific junctional sequences in the context of a common V element, V beta 2.1, is that this V region plays a dominant role in the recognition of the tt830-844/DR complex.