Miracle-dz/UniFAR-FTUs huggingface dataset:
Visualizing thymocyte motility using 2‐photon microscopy

Summary: Our view of a thymocyte based on its behavior in tissue culture and appearance in fixed tissue sections was of a round sessile cell. Its travel through the thymus might occur slowly, perhaps even passively, leaving it in contact with the support cells that happened to be in its immediate environment. However, when we got our first look at the behavior of thymocytes in a 3D cellular stromal cell environment, that picture changed dramatically. Instead we found that thymocytes are actively crawling, allowing them to explore their environment over relatively long distances and interact with peptide‐major histocompatibility complex (pMHC)‐bearing thymic stromal cells in both dynamic and stable modes. In this review, we discuss the implications of thymocyte motility for T‐cell repertoire selection and for the mechanisms that determine the spatial organization of thymocyte subsets within the thymus.
A peer-to-peer environment to share medical images and diagnoses providing context-based searching

The enormous amount of radiological data obtained nowadays comprises a huge quantity of clinical knowledge that it is not efficiently exploited. Although many peer-reviewed radiological databases are available, the number of cases and the variety of pathologies are not enough for research. The most of the information remains locally in hospitals and clinics without being shared. Sharing medical studies is not trivial. The vast amount of data that image studies involve, the difficulty on indexing the information and the lack of adequate tools prevent radiologists from sharing information at a larger scale. This paper presents a peer-to-peer (P2P) environment that assists image diagnosis apprenticeship and research, enabling radiologists to share DICOM studies and its corresponding diagnoses. The P2P environment presented in the paper proposes a solution to ease searching and securely sharing medical data. Automatic anonymisation of data is done, including blurring of clinically relevant data. Searching is performed by context (based on the mutual information function or relative entropy) and using different filter expressions, based on DICOM metadata. Since the amount of clinical data is huge, storage and searching is performed distributed in a P2P manner. The system presented is a collaborative environment designed for sharing DICOM images and diagnoses that constitutes a distributed virtual database; accessible by the radiologists' community enabling distributed context-based searching on DICOM images.
Priming immunization against cholera toxin and E. coli heat‐labile toxin by a cholera toxin short peptide‐beta‐galactosidase hybrid synthesized in E. coli.

A synthetic oligodeoxynucleotide encoding for a small peptide was employed for the expression of this peptide in a form suitable for immunization. The encoded peptide, namely, the region 50‐64 of the B subunit of cholera toxin (CTP3), had previously been identified as a relevant epitope of cholera toxin. Thus, multiple immunizations with its conjugate to a protein carrier led to an efficient neutralizing response against native cholera toxin. Immunization with the resulting fusion protein of CTP3 and beta‐galactosidase, followed by a booster injection of a sub‐immunizing amount (1 microgram) of cholera toxin, led to a substantial level of neutralizing antibodies against both cholera toxin and the heat‐labile toxin of Escherichia coli.
A new outer loop power control algorithm based on fuzzy control in cdma2000

In this paper, a new outer loop power control algorithm based on continuous fuzzy control is proposed. The output value, controlled by the fuzzy rules and the two input values which are processed with fuzzy method, is adopted as the adjustment step-size of SIRtar in the inner loop power control. The algorithm can calculate the best adjustment step-size to overcome the robust phenomenon of traditional algorithms to a large extent. Experimental results indicate that the algorithm provides the optimal SIRtar suiting the transient wireless environment with the ensured QoS as precondition. As a result, it can achieve the best network performance by reducing the transmitter power and interference as much as possible.
Robust Recognition of Noisy Speech and its Hardware Design for Real Time Processing

In this paper, we propose a novel technique focusing on robust speech recognition and introduce a hardware based new speech recognition system. The realization of the proposed method is quite dicult in case of software processing since high computational cost is required for noise robust. In order to overcome the shortage, we adopt the scalable architecture focused on the word HMM structure. The proposed architecture can flexibly improve recognition performance and extend word vocabularies. In addition, the computation time is considerably decreasing. In the last part, this paper presents the verification platform for the proposed system to test various tasks on recognition systems. The developed FPGA platform enables real-time recognition experiments under various conditions.
Energy-Efficient Flow Time Scheduling: An Experimental Study

Power management has become a vital issue in the design of modern processors. A popular technology to reduce energy usage is dynamic speed scaling [5, 8] where a processor can vary its speed dynamically. This has been adopted in technologies like AMD’s Cool ‘n’ Quiet [1] and Intel’s Speedstep [6]. Running a job at a slower speed saves energy, yet it takes longer time and may affect the performance. The challenge arises from the conflicting objectives of providing good “quality of service” (QoS) and conserving energy. In the past few years, a lot of effort has been devoted to revisiting classical scheduling problems with energy in concern (e.g., [2, 4, 9]). One commonly used QoS measurement is the total flow time (or equivalently average response time). The flow time of a job is the time elapsed from its arrival to completion. When energy is not a concern, the objective is to minimize the total flow time of all jobs, and it is well known that SRPT (shortest remaining processing time first) produces a schedule with the smallest possible flow time. To understand the tradeoff between flow and energy, Albers and Fujiwara [3] initiated the study of minimizing a linear combination of total flow and energy. An algorithm called AJC (active job count) has been proposed [3, 7], in which the speed of the processor is determined by the number of active jobs that have arrived but not completed yet. We present an experimental study of scheduling to minimize flow time plus energy. We evaluate the performance of AJC along with two fixed speed heuristics of which one has prior knowledge of the job instance and the other does not. We study both single processor and multi-processor settings.
Identification of individual human immunodeficiency virus type 1 gp120 amino acids important for CD4 receptor binding

The binding of the CD4 receptor by the human immunodeficiency virus type 1 gp120 exterior envelope glycoprotein is important for virus entry and cytopathic effect. To investigate the CD4-binding region of the gp120 glycoprotein, we altered gp120 amino acids, excluding cysteines, that are conserved among the primate immunodeficiency viruses utilizing the CD4 receptor. Changes in two hydrophobic regions (Thr-257 in conserved region 2 and Trp-427 in conserved region 4) and two hydrophilic regions (Asp-368 and Glu-370 in conserved region 3 and Asp-457 in conserved region 4) resulted in significant reductions in CD4 binding. For most of the mutations affecting these residues, the observed effects on CD4 binding did not apparently result from global conformational disruption of the gp120 molecule, as assessed by measurements of precursor processing, subunit association, and monoclonal antibody recognition. The two hydrophilic regions exhibit a strong propensity for beta-turn formation, are predicted to act as efficient B-cell epitopes, and are located adjacent to hypervariable, glycosylated regions. This study defines a small number of gp120 residues important for CD4 binding, some of which might constitute attractive targets for immunologic intervention.
Weak keys of the Diffie Hellman key exchange II : Pairing based schemes on elliptic curves

This paper investigates the Diffie-Hellman key exchange scheme over the group F∗ p of nonzero elements of finite fields and shows that there exist exponents k, l satisfying certain conditions called the modulus conditions, for which the Diffie Hellman Problem (DHP) can be solved in polynomial number of operations in m without solving the discrete logarithm problem (DLP). These special private keys of the scheme are termed weak and depend also on the generator a of the cyclic group. More generally the triples (a, k, l) with generator a and one of private keys k, l weak, are called weak triples. A sample of weak keys is computed and it is observed that their number may not be insignificant to be ignored in general. Next, an extension of the analysis and weak triples is carried out for the Diffie Hellman scheme over the matrix group GLn and it is shown that for an analogous class of session triples, the DHP can be solved without solving the DLP in polynomial number of operations in the matrix size n. A revised Diffie Hellman assumption is stated, taking into account the above exceptions.
Von Willebrand Factor Gene Variants Associate with Herpes simplex Encephalitis

Herpes simplex encephalitis (HSE) is a rare complication of Herpes simplex virus type-1 infection. It results in severe parenchymal damage in the brain. Although viral latency in neurons is very common in the population, it remains unclear why certain individuals develop HSE. Here we explore potential host genetic variants predisposing to HSE. In order to investigate this we used a rat HSE model comparing the HSE susceptible SHR (Spontaneously Hypertensive Rats) with the asymptomatic infection of BN (Brown Norway). Notably, both strains have HSV-1 spread to the CNS at four days after infection. A genome wide linkage analysis of 29 infected HXB/BXH RILs (recombinant inbred lines—generated from the prior two strains), displayed variable susceptibility to HSE enabling the definition of a significant QTL (quantitative trait locus) named Hse6 towards the end of chromosome 4 (160.89–174Mb) containing the Vwf (von Willebrand factor) gene. This was the only gene in the QTL with both cis-regulation in the brain and included several non-synonymous SNPs (single nucleotide polymorphism). Intriguingly, in human chromosome 12 several SNPs within the intronic region between exon 43 and 44 of the VWF gene were associated with human HSE pathogenesis. In particular, rs917859 is nominally associated with an odds ratio of 1.5 (95% CI 1.11–2.02; p-value = 0.008) after genotyping in 115 HSE cases and 428 controls. Although there are possibly several genetic and environmental factors involved in development of HSE, our study identifies variants of the VWF gene as candidates for susceptibility in experimental and human HSE.
Towards Context-adaptive Natural Language Processing Systems

In this paper we will discuss several issues and requirements for enabling natural language processing systems to become context-adaptive. Given the fact that emerging systems feature speaker independent continuous speech recognition restricted to individual domains and are equipped with syntactic and semantic parsers for understanding input from these domains, we should begin to envision open multi-domain natural language processing systems. We will address the following issues arising in such open systems: How to divide natural language processing modules in context-variant and context-invariant components and how to enable the ensuing systems to detect contextual changes for processing the context-variant phenomena.
Insulin-like growth factor-I stimulates differentiation of ATII cells to ATI-like cells through activation of Wnt 5 a

Manik C. Ghosh, Vijay Gorantla, Patrudu S. Makena, Charlean Luellen, Scott E. Sinclair, Andreas Schwingshackl, and Christopher M. Waters Department of Physiology, University of Tennessee Health Science Center, Memphis, Tennessee; Department of Medicine, University of Tennessee Health Science Center, Memphis, Tennessee; and Department of Pediatrics, University of Tennessee Health Science Center, Memphis, Tennessee
Computer-aided classification of liver tumors in 3D ultrasound images with combined deformable model segmentation and support vector machine

In this study, we propose a computer-aided classification scheme of liver tumor in 3D ultrasound by using a combination of deformable model segmentation and support vector machine. For segmentation of tumors in 3D ultrasound images, a novel segmentation model was used which combined edge, region, and contour smoothness energies. Then four features were extracted from the segmented tumor including tumor edge, roundness, contrast, and internal texture. We used a support vector machine for the classification of features. The performance of the developed method was evaluated with a dataset of 79 cases including 20 cysts, 20 hemangiomas, and 39 hepatocellular carcinomas, as determined by the radiologist's visual scoring. Evaluation of the results showed that our proposed method produced tumor boundaries that were equal to or better than acceptable in 89.8% of cases, and achieved 93.7% accuracy in classification of cyst and hemangioma.
Tacrolimus Analysis: A Comparison of Different Methods and Matrices

We determined the trough blood and plasma concentrations of tacrolimus from the day of transplantation through 30 days posttransplantation in four liver and four kidney transplant patients by three different methods. The first method involved a solid phase extraction of the blood or plasma using Sep-Pak columns (SPs) followed by quantitation of tacrolimus using an enzyme-linked immunosorbent assay (ELISA); the second method involved a liquid-liquid extraction using methylene chloride (MC) followed by quantitation of tacrolimus using the ELISA, and the third method involved a high-performance liquid chromatography (HPLC) fractionation of the extract obtained from the solid-phase extraction and quantitation of tacrolimus in the fractions by ELISA. The trough plasma tacrolimus concentrations ranged from 0.1 to 5.2 ng/ml. While the trough plasma concentrations of tacrolimus were similar and independent of the method of analysis in kidney transplant patients and in liver transplant patients with normal biochemical profile, in patients with liver dysfunction, tacrolimus plasma concentrations were higher when measured by SP-ELISA and MC-ELISA methods as compared to the HPLC-ELISA method. In plasma samples obtained from liver transplant patients with liver dysfunction, the presence of some metabolites that cross-reacted with the antibody used in the ELISA could be documented in the HPLC fraction corresponding to the metabolites. This indicates that while tacrolimus metabolites that cross-react significantly with the antibody used in the ELISA do not accumulate in kidney transplant patients, they can appear in the plasma of patients with liver dysfunction. The trough blood tacrolimus concentrations in patients were significantly higher than the corresponding plasma concentrations and ranged from 1.4 to 107 ng/ml. The trough blood tacrolimus concentrations were similar and independent of the method of analysis in kidney and liver transplant patients, suggesting unchanged tacrolimus to be the major component in the blood. The HPLC fractions corresponding to the metabolites of tacrolimus did not contain any components that cross-reacted with the antibody used. This study documents that the methods used in this study for the analysis of blood concentrations of tacrolimus appear to be specific for the parent tacrolimus and can be used in future pharmacokinetic and clinical studies.
Relation between the upper ocean heat content in the equatorial Atlantic during boreal spring and the Indian monsoon rainfall during June–September

Earlier studies have identified a teleconnection between the Atlantic zonal mode (AZM) and Indian summer monsoon rainfall (ISMR), both of which are active during the boreal summer (AZM: June–August; ISMR: June–September). It is known that El Niño‐Southern Oscillation (ENSO)‐like coupled dynamics are operational in the tropical Atlantic during the AZM events. Our goal here is to extend this process understanding to seek a predictive relation between the tropical Atlantic and the ISMR based on these known teleconnections. Monthly composite analysis of the zonal surface winds, heat content, and sea surface temperature (SST) in the equatorial Atlantic tells us that signatures of a warm or cold AZM event begin to emerge as early as January of that year. We found significant correlations between the ISMR and the low level zonal winds in the western equatorial Atlantic and heat content in the eastern equatorial Atlantic in the boreal spring season. Tracking coherent changes in these winds and the evolution of the heat content in the deep tropical Atlantic in the boreal spring may offer the potential for skillful predictions of the ensuing summer monsoon anomalies, especially during non‐ENSO years when the predictability of ISMR tends to be low.
3D SAR imaging of the snowpack in presence of propagation velocity changes: Results from the AlpSAR campaign

In this paper we present results relative to the 3D GBSAR surveys acquired in february 2013 on the Austrian Alps as a part of the ESA campaign AlpSAR. The GBSAR was operated at X- and Ku-Band with a bandwidth of 4 GHz and employing a 2D synthetic aperture, resulting in 3D resolution capabilities at a resolution of few centimeters. Images produced at two different sites reveal the presence of multiple layers within the snowpack. The strongest backscatter contributions have been observed to correspond to bottom layers, that dominate the ones from the snow/air interface and the near subsurface. GBSAR data are observed to provide sensitivity to the propagation velocity into the snowpack, as revealed by the apparent depth variation with respect to the incidence angle.
Mutagenesis of Legionella pneumophila using Jn903 dllIacZ: identification of a growth‐phase‐regulated pigmentation gene

Study of the molecular basis for Legionella pneumophila pathogenicity would be facilitated with an efficient mutagen that can not only mark genomic mutations, but can also be used to reflect gene expression during macrophage infection. A derivative of Jn903, Tn903dlllacZ, is shown to transpose with high efficiency in L. pneumophila. Tn903dlllacZ encodes resistance to kanamycin (KmR) and carries a 5’truncated lacZ gene that can form translational fusions to L. pneumophila genes upon transposition. The cls‐acting Tn903 transposase is supplied outside Tn903dlllacZ, and hence chromosomally integrated copies are stable. KmR LacZ+ insertion mutants of L. pneumophila were isolated and shown by DNA hybridization to carry a single Tn903dlllacZ inserted within their chromosomes at various locations. One particular KmR LacZ+ mutant, AB1156, does not produce the brown pigment (Pig) characteristic of Legionella species. Tn903dlllacZ is responsible for this phenotype since reintroduction of the transposonlinked mutation into a wild‐type background results in a Pig phenotype. L. pneumophila pigment production is normally observed in stationary‐phase growth of cells in culture, and β‐galactosidase activity measured from the pig::lacZ fusion increased during the logarithmic‐phase growth and peaked at the onset of stationary phase. Interestingly, pig::lacZ expression also increased during macrophage infection. The pigment itself, however, does not appear to be required for L. pneumophila to grow within or kill host macrophages.
Analyses of Flood-Flow Frequency for Selected Gaging Stations in South Dakota

The South Dakota Department of Tranportation has a continuing need for data pertaining to flood-flow frequency for use in the design of highway structures. Flood-flow frequency analyses were made for 111 continuous-record gaging stations in South Dakota using the log-Pearson Type III procedure as recommended by the U.S. Water Resources Council. The publication is chiefly tables.
The NICE recommendation for drug-coated balloons and its global impact

Objectives: The clinical efficacy and safety of drug-coated balloon (DCB) angioplasty in patients with coronary in-stent restenosis (ISR) has been demonstrated. The objective of this article is to provide comparative cost efficacy data for DCB angioplasty in various countries based on the original methodology of the Medical Technologies Evaluation Programme (MTEP) at the National Institute for Health and Clinical Excellence (NICE) in 2010. Study design: Published and unpublished Health Technology Assessment (HTA) reports were evaluated for comparison in selected countries. Furthermore, a systematic review of economic evaluations of DCB angioplasty versus standard treatments (uncoated balloon angioplasty or drug-eluting stent implantations) was conducted. Methods: National cost efficacy data were evaluated using Markov state transition models which were adapted to fit each country’s device and procedure related costs. The clinical input for adverse events was defined with two relevant trials for in-stent restenosis of bare metal stents (BMS-ISR) and of drug-eluting stents (DES-ISR). Results: In the UK, Germany, Switzerland, South Africa, Japan and Brazil, DCB angioplasty is cost-effective when compared with drug-eluting stents to treat either BMS-ISR or DES-ISR. Conclusions: DCB angioplasty ought to be the preferred treatment option for patients with BMS-ISR and DES-ISR from the payers’ point of view.
Rivastigmine is associated with restoration of left frontal brain activity in Parkinson's disease

The objective of this study was to investigate how acetylcholinesterase inhibitor (ChEI) treatment affects brain function in Parkinson's disease (PD). Twelve patients with PD and either dementia or mild cognitive impairment underwent task‐free functional magnetic resonance imaging before and after 3 months of ChEI treatment and were compared with 15 age‐ and sex‐matched neurologically healthy controls. Regional spontaneous brain activity was measured using the fractional amplitude of low‐frequency fluctuations. At baseline, patients showed reduced spontaneous brain activity in regions important for motor control (eg, caudate, supplementary motor area, precentral gyrus, thalamus), attention and executive functions (eg, lateral prefrontal cortex), and episodic memory (eg, precuneus, angular gyrus, hippocampus). After treatment, the patients showed a similar but less extensive pattern of reduced spontaneous brain activity relative to controls. Spontaneous brain activity deficits in the left premotor cortex, inferior frontal gyrus, and supplementary motor area were restored such that the activity was increased posttreatment compared with baseline and was no longer different from controls. Treatment‐related increases in left premotor and inferior frontal cortex spontaneous brain activity correlated with parallel reaction time improvement on a test of controlled attention. PD patients with cognitive impairment show numerous regions of decreased spontaneous brain function compared with controls, and rivastigmine is associated with performance‐related normalization in the left frontal cortex function. © 2013 International Parkinson and Movement Disorder Society