Miracle-dz/UniFAR-FTUs huggingface dataset:
Measurement of ligand-induced activation in single viable T cells using the lacZ reporter gene.

We have used the bacterial beta-galactosidase gene (lacZ) as a reporter gene for the rapid measurement of T-cell antigen receptor (TCR)-mediated activation of individual T cells. The reporter construct contained the lacZ gene under the control of the nuclear factor of activated T cells (NF-AT) element of the human interleukin 2 enhancer [Fiering, S. , Northrop, J. P., Nolan, G. P., Matilla, P., Crabtree, G. R. & Herzenberg, L. A. (1990) Genes Dev. 4, 1823-1834]. The activity of the intracellular lacZ enzyme was analyzed by flow cytometric measurement of fluorescein accumulation in cells loaded with the fluorogenic beta-galactosidase substrate fluorescein di-beta-D-galactopyranoside. As a model system, the T-cell hybridoma BO4H9.1, which is specific for the lysozyme peptide (amino acids 74-88)/Ab complex, was transfected with the NF-AT-lacZ construct. lacZ activity was induced in 50-100% of the transfectant cells following exposure to pharmacological agents, to the physiological peptide/major histocompatibility complex ligand, or to other TCR-specific stimuli. Interestingly, increasing concentrations of the stimulus increased the fraction of lacZ+ cells, but not the level of lacZ activity per cell. Even under widely varying levels of stimulus, the level of lacZ activity in individual lacZ+ cells remained within a remarkably narrow range. These results demonstrate that TCR-mediated activation can be readily measured in single T cells and strongly suggest that, once committed to activation, the level of NF-AT transcriptional activity in individual T cells is independent of the form or concentration of stimulus. This assay is likely to prove useful for the study of early activation events in individual T cells and of TCR ligands.
Prognostic factors in oropharyngeal cancer – analysis of 627 cases receiving definitive radiotherapy

Introduction. The aim of this retrospective analysis was to analyze the results of conventional radical radiotherapy in the treatment of oropharyngeal cancer and to identify pre-treatment and treatment-related prognostic factors for outcome. Material and methods. The records of 627 patients with oropharyngeal cancer treated with radical radiotherapy with conventional techniques were analyzed. Results. The median age was 56 years. History of tobacco abuse was present in 80.5%. Eighty six percent had stage III or IV disease. Radical radiotherapy alone was the treatment modality for 71.2% and concomitant or neoadjuvant chemotherapy was used in 28.8%. The 3-year local control (LC), loco-regional control (LRC), disease-free survival (DFS) and overall survival (OS) was 49%, 40.6%, 38.9% and 36.1% respectively. The 3-year DFS rates were 80.3% for stage I, 65.8% for stage II, 46.1% for stage III and 25.2% for stage IV disease. Multivariate analysis was performed for prognostic factors. Prior history of tobacco abuse was an independent prognostic factor for both DFS and LRC. Karnofsky Performance Score (KPS) < 80, higher nodal stage, lower total radiotherapy dose (<66 Gy) in those receiving > 60 Gy, and overall treatment time > 50 days were other independent prognostic factors for inferior DFS and LRC. KPS < 80, higher T stage, higher nodal stage, RT dose < 66 Gy and longer overall treatment time (>50 days) were independent prognostic factors for poorer local control. Conclusions. Several patient-, disease- and treatment-related variables independently affect survival outcomes after radical radiotherapy for oropharyngeal cancer. Oropharyngeal cancers in those without a history of tobacco abuse may be biologically different and more amenable to cure with radiotherapy.
Oligomerization of Dopamine Transporters Visualized in Living Cells by Fluorescence Resonance Energy Transfer Microscopy*

To examine the oligomeric state and trafficking of the dopamine transporter (DAT) in different compartments of living cells, human DAT was fused to yellow (YFP) or cyan fluorescent protein (CFP). YFP-DAT and CFP-DAT were transiently and stably expressed in porcine aortic endothelial (PAE) cells, human embryonic kidney (HEK) 293 cells, and an immortalized dopaminergic cell line 1RB3AN27. Fluorescence microscopic imaging of cells co-expressing YFP-DAT and CFP-DAT revealed fluorescence resonance energy transfer (FRET) between CFP and YFP, which is consistent with an intermolecular interaction of DAT fusion proteins. FRET signals were detected between CFP- and YFP-DAT located at the plasma membrane and in intracellular membrane compartments. Phorbol esters or amphetamine induced the endocytosis of YFP/CFP-DAT to early and recycling endosomes, identified by Rab5, Rab11, Hrs and EEA.1 proteins. Interestingly, however, DAT was mainly excluded from Rab5- and Hrs-containing microdomains within the endosomes. The strongest FRET signals were measured in endosomes, indicative of efficient oligomerization of internalized DAT. The intermolecular DAT interactions were confirmed by co-immunoprecipitation. A DAT mutant that was retained in the endoplasmic reticulum (ER) after biosynthesis was used to show that DAT is oligomeric in the ER. Moreover, co-expression of an ER-retained DAT mutant and wild-type DAT resulted in the retention of wild-type DAT in the ER. These data suggest that DAT oligomers are formed in the ER and then are constitutively maintained both at the cell surface and during trafficking between the plasma membrane and endosomes.
Dynamics of anti‐human leukocyte antigen antibodies after renal transplantation and their impact on graft outcome

The purpose of this study was to sequentially monitor anti‐HLA antibodies and correlate the results with antibody‐mediated rejection (AMR), graft survival (GS), and graft function (GF). We collected sera from 111 kidney transplant recipients on transplant days 0, 7, 14, 30, 60, 90, 180, and 360 and analyzed PRA levels by ELISA. DSAs were analyzed by single‐antigen beads in rejecting kidneys. At pre‐transplant, 79.3% of the patients were non‐sensitized (PRA = 0%) and 20.7% were sensitized (PRA > 1%). After transplant, patients were grouped by PRA profile: no anti‐HLA antibodies pre‐ or post‐transplant (group HLApre−/post−; n = 80); de novo anti‐HLA antibodies post‐transplant (group HLApre−/post+; n = 8); sensitized pre‐transplant/increased PRA post‐transplant (group HLApre+/post↑; n = 9); and sensitized pre‐transplant/decreased PRA post‐transplant (group HLApre+/post↓; n = 14). De novo anti‐HLA antibodies were detected at 7–180 d. In sensitized patients, PRA levels changed within the first 30 d post‐transplant. Incidence of AMR was higher in HLApre−/post+ and HLApre+/post↑ than in HLApre−/post−, and HLApre+/post↓ (p < 0.001) groups. One‐yr death‐censored GS was 36% in group HLApre+/post↑, compared with 98%, 88% and 100% in groups HLApre−/post−, HLApre−/post+, and HLApre+/post↓, respectively (p < 0.001). Excluding first‐year graft losses, GF and GS were similar among the groups. In conclusion, post‐transplant antibody monitoring can identify recipients at higher risk of AMR.
Accurate modeling for lossy conductors based on two-region surface integral equations

Accurate electromagnetic (EM) modeling for lossy conductors requires to consider their finite conductivity and the conducting loss is usually accounted for by an approximate surface impedance when the skin depth of current is small. However, such an approximation may not be valid for large skin depth caused by low frequencies or small conductivities. We propose a different approach to model the lossy conductors by treating them as penetrable objects and using a two-region electric field integral equations (EFIEs) to formulate their EM interaction. The EFIEs are solved with the method of moments (MoM) in which the Rao-Wilton-Glisson (RWG) and n×RWG basis functions are used to represent the electric and magnetic current densities, respectively, so that the resulting system matrix has a good conditioning. A typical numerical example is presented to demonstrate the approach and its robustness has been verified.
Non-invasive metabolomic analysis using a commercial NIR instrument for embryo selection

CONTEXT: Metabolomics was introduced in human in vitro fertilization (IVF) for noninvasive identification of viable embryos with the highest developmental competence. AIMS: To determine whether embryo selection using a commercial version of metabolomic analysis leads to increased implantation rates (IRs) with fetal cardiac activity (FCA) compared with morphology evaluation alone. SETTING AND DESIGN: Randomized controlled trial from April to December 2010 at a private IVF unit. The study was terminated prematurely due to the market withdrawal of the instrument. MATERIALS AND METHODS: IVF patients ≥18 and ≤43 years with ≥4 × 2PN were randomly allocated to metabolomic analysis combined with embryo morphology (ViaMetrics-E; metabolomics + morphology group) or embryo morphology alone (morphology group). Cycles with frozen embryos, oocyte donations, or testicular biopsy were excluded. STATISTICAL ANALYSIS: Categorical and continuous data were analyzed for statistical significance using 2-tailed Fisher's exact test and t-test, respectively. Statistical significance was accepted when P > 0.05. RESULTS: A total of 125 patients were included in the study; 39 patients were allocated to metabolomics + morphology group and 86 patients to morphology group. Patients were stratified according to the day of embryo transfer (Days 2, 3, or 5). IRs with FCA were similar for Days 2 and 3 transfers in both groups. For Day 5 transfers, IRs with FCA were significantly higher in the metabolomics + morphology group (46.8% vs. 28.9%; P = 0.041; 95% confidence intervalp [CI]: 1.09-34.18). Pregnancy and live births rates were similar for Days 2, 3, and 5 in both groups. The study was terminated early following the voluntary market withdrawal of ViaMetrics-E in December 2010. CONCLUSIONS: Metabolomic analysis using the commercial near-infrared (NIR) instrument does not appear to have a beneficial effect on pregnancy and live births, with improvement in IR with FCA for Day 5 transfers. However, no solid conclusions can be reached due to the lack of adequate study power.ClinicalTrials. gov Identifier: NCT01490515
Treatment of impulsive aggression in correctional settings.

PURPOSE This article reports the implementation of Dialectical Behavioral Therapy-Corrections Modified (DBT-CM) for difficult to manage, impulsive and/or aggressive correctional populations. METHODS Participants were English-speaking women (n = 18) and men (n = 45) of diverse cultural backgrounds between the ages of 16 and 59 years old retained in state-run prisons in Connecticut. Following consent, and a psychological assessment battery, twice-weekly DBT-CM groups were held over 16 weeks followed by random assignment to DBT coaching or case management condition, with sessions taking place individually for eight weeks. Data analysis. A mixed effects regression model was used to test the hypotheses: participants will show decreased aggression, impulsivity, and psychopathology, as well as improved coping, after completing the DBT-CM groups; and will show greater reduction in targeted behaviors than those receiving case management at the six month and 12 month follow-up assessment periods. RESULTS Significant reduction in targeted behavior was found from baseline to following the 16 week DBT-CM skills treatment groups. Both case management and DBT coaching were significant at 12 month follow-up. A significant difference was found for adult men and women. CONCLUSIONS The study supports the value of DBT-CM for management of aggressive behaviors in prison settings.
Recursive estimation of vehicle position by using navigation sensor fusion

In this paper, a sensor fusion scheme is employed to reduce positioning error of a vehicle since the GPS signal is fail. The vehicular information, such as position, heading direction, and velocity, can be obtained through GPS signal. Generally, the positioning accuracy of commercial GPS module is within the 3 meters, however, the GPS module may disconnect the signals from satellites since the vehicle is maneuvered under shelters, e.g. parking garage, tunnel, high dense urban, etc. Therefore, our proposed methodology is able to improve the estimation accuracy of vehicle position based on dead reckoning method. The first step, the Kalman filter is utilized to reject the noise of velocity measurement which is captured from gearbox and wheel speed sensor and also predict the velocity and displacement of vehicle in next sample time. The second step is to construct the displacement model of the vehicle by adopting ARMA model, which is able to estimate the state of vehicle. Digital map information which is applied to correct the positioning result of ARMA model is addressed in the last step. A real time experiment result of GPS signal lost in a tunnel is carried out to demonstrate the performance of our proposed method.
MEASURING BANK EFFICIENCY IN DEVELOPING COUNTRIES: THE CASE OF WAEMU (WEST AFRICAN ECONOMIC MONETARY UNION)

This paper offers to measure WAEMU banks efficiency and its determining factors, after the banking system reforms from 1993 to 1996. At this purpose, we use Data Envelopment Analysis method (DEA) for assessing technical efficiency and Stochastic Frontier Analysis (SFA) for cost efficiency. Our results suggest similar evolutions for the two types of efficiency for every WAEMU countries apart from Ivory Coast and Burkina Faso. A detailed analysis per banking shareholder’s equity group reveals that local private banks are the most efficient ones, followed by foreign and then state owned banks. Despite technological changes that occurred in the banking system, Malmquist index shows that the increase of technical efficiency is much more the fact of scale efficiency change than that of the incorporation of technological innovations. Lastly, we found that WAEMU banks efficiency is sensitive to variables like financial soundness, the ratio of bad loans per country, the banking concentration and the GDP per capita.
The Relative Impact of Market Orientation and Entrepreneurship on Export Performance: Do We Really Know Enough?

ABSTRACT The impact of international corporate entrepreneurship and market orientation on firm performance is well acknowledged in the literature, but their relative influence on the performance of exporting firms remains inconclusive. This study seeks to help clarify the influence of these organizational resources by introducing a third complementary resource, namely commitment to learning. The results, based on data obtained from a survey of exporters in China, show that commitment to learning mediates the relationship between market orientation and entrepreneurship. It was also found that market orientation could be a double-edged sword for exporters in that it can enhance export satisfaction through entrepreneurship, but it can also have negative impact on profit.
Tactics to Directly Map CNN Graphs on Embedded FPGAs

Deep convolutional neural networks (CNNs) are the state-of-the-art in image classification. Since CNN feed forward propagation involves highly regular parallel computation, it benefits from a significant speed-up when running on fine grain parallel programmable logic devices. As a consequence, several studies have proposed field-programmable gate array (FPGA)-based accelerators for CNNs. However, because of the large computational power required by CNNs, none of the previous studies has proposed a direct mapping of the CNN onto the physical resources of an FPGA, allocating each processing actor to its own hardware instance. In this letter, we demonstrate the feasibility of the so called direct hardware mapping (DHM) and discuss several tactics we explore to make DHM usable in practice. As a proof of concept, we introduce the HADDOC2 open source tool, that automatically transforms a CNN description into a synthesizable hardware description with platform-independent DHM.
Tomato Spotted Wilt Virus Glycoproteins Exhibit Trafficking and Localization Signals That Are Functional in Mammalian Cells

ABSTRACT The glycoprotein precursor (G1/G2) gene of tomato spotted wilt virus (TSWV) was expressed in BHK cells using the Semliki Forest virus expression system. The results reveal that in this cell system, the precursor is efficiently cleaved and the resulting G1 and G2 glycoproteins are transported from the endoplasmic reticulum (ER) to the Golgi complex, where they are retained, a process that could be blocked by tunicamycin. Expression of G2 alone resulted in transport to and retention in the Golgi complex, albeit less efficient, suggesting that G2 contains a Golgi retention signal. G1 alone was retained in the ER, irrespective of whether it contained the precursor's signal sequence or its own N-terminal hydrophobic sequence. Coexpression of G1 and G2 from separate gene constructs resulted in rescue of efficient G1 transport, as the proteins coaccumulated in the Golgi complex, indicating that their interaction is essential for proper targeting to this organelle. The results demonstrate that transport and targeting of the plant TSWV glycoproteins in mammalian BHK cells are strikingly similar to those of animal-infecting bunyavirus glycoproteins in mammalian cells. The observations are likely to reflect the dual tropism of TSWV, which replicates both in its plant host and in its animal (thrips) vector.
Polymeric nanogels containing the triphosphate form of cytotoxic nucleoside analogues show antitumor activity against breast and colorectal cancer cell lines

The therapeutic efficiency of anticancer nucleoside analogues (NA) strongly depends on their intracellular accumulation and conversion into 5′-triphosphates. Because active NATP cannot be directly administrated due to instability, we present here a strategy of nanoencapsulation of these active drugs for efficient delivery to tumors. Stable lyophilized formulations of 5′-triphosphates of cytarabine (araCTP), gemcitabine (dFdCTP), and floxuridine (FdUTP) encapsulated in biodegradable PEG-cl-PEI or F127-cl-PEI nanogel networks (NGC and NGM, respectively) were prepared by a self-assembly procedure. Cellular penetration, in vitro cytotoxicity, and drug-induced cell cycle perturbations of these nanoformulations were analyzed in breast and colorectal cancer cell lines. Cellular accumulation and NATP release from nanogel was studied by confocal microscopy and direct high-performance liquid chromatography analysis of cellular lysates. Antiproliferative effect of dFdCTP nanoformulations was evaluated in human breast carcinoma MCF7 xenograft animal model. Nanoencapsulated araCTP, dFdCTP, and FdUTP showed similar to NA cytotoxicity and cell cycle perturbations. Nanogels without drugs showed very low cytotoxicity, although NGM was more toxic than NGC. Treatment by NATP nanoformulations induced fast increase of free intracellular drug concentration. In human breast carcinoma MCF7 xenograft animal model, i.v. dFdCTP-nanogel was equally effective in inhibiting tumor growth at four times lower administered drug dose compared with free gemcitabine. Active triphosphates of NA encapsulated in nanogels exhibit similar cytotoxicity and cell cycle perturbations in vitro and faster cell accumulation and equal tumor growth-inhibitory activity in vivo at much lower dose compared with parental drugs, illustrating their therapeutic potential for cancer chemotherapy. [Mol Cancer Ther 2008;7(10):3373–80]
Genetic structure, diversity, and inbreeding of eastern white pine under different management conditions

Resource sustainability requires a thorough understanding of the influence of forest management programs on the conservation of genetic diversity in tree populations. To observe how differences in forest structure affect the genetic structure of eastern white pine (Pinus strobus L.), we evaluated six eastern white pine sites across the 234 000 acre (1 acre = 0.4046856 ha) Menominee Indian Reservation in northeastern Wisconsin (45°00′N, 88°45′W). The six sites sampled for nuclear and chloroplast DNA microsatellite markers were of contrasting densities and managed by different management systems: shelterwood, pine release, plantation, and old growth. Three of the sites had natural regeneration, which was also sampled. Mean values of spatial genetic autocorrelation were positive in all mature populations and variable; the strongest spatial structuring of genes occurred in the least disturbed old-growth site (I – E(I) = 0.031). Genetic structuring at the historical old-growth site fit the isolation-by-distanc.
Beyond poverty and criminalization: Splintering youth groups and ‘conflict of governmentalities’ in urban Ghana

Youth violence is a universal phenomenon and can take many shapes and forms. In Ghana the upsurge, scale and scope of such violence in major cities are becoming worrying, making it imperative to examine the nexus between poverty, splintering youth groups, and crime. Typically, youth criminal and antisocial behaviour raise questions as to whether city authorities lack effective structures to cope with increasing urbanization or are being overly accommodating to varying crime responses, some of which are above and beyond legal policing measures. Using content analysis of media reports, archival records, scholarly literature, 50 key informant interviews (KIIs), and 15 focus group discussions (FGDs), we examine the multiple fields of youth ‘governmentalities’ and their preoccupation with security issues—issues that are of great significance to formal state institutions. Borrowing from the philosophy of methodological individualism embedded in rational choice theory, our study reveals the emergence of a number of local youth groups whose activities, predicated mainly on the quest for better livelihood, incorporate varied rationalities, techniques, and practices, some of which are negatively impacting on the urban fabric. We contend that some of these activities not only challenge the legitimacy of the state but also call into question the ability of the official institutions responsible for maintaining law and order to guarantee protection and secure justice for all. Keywords : urbanization; youth groups; organized crime; governmentalities; Ghana
Optimum torque control algorithm for wide speed range and four quadrant operation of stator flux oriented induction machine drive without regenerative unit

In general, low power induction motor drive systems are equipped with PWM inverter using a diode rectifier frond-end (has not a regenerative unit) to supply the ac power from the mains to the dc link. The main features of the proposed algorithm are the capability to generate the optimum torque, for four quadrant operation of drive system, over the wide speed range that is fed by PWM inverter equipped with diode rectifier front-end. The algorithm offers the optimum torque capability for the induction motor drive despite significant changes in dc link voltage and machine parameters. The algorithm identifies when the machine enters in the flux weakening region and also adjust the stator flux reference and q-axis current limit according to the dc link voltage and the operating mode. In the motor mode a PI voltage controller generates the stator flux reference and the q-axis current limit, while in the generator mode the power is dissipated in the machine and a PI overvoltage controller increases the stator flux reference limit and limits the q-axis current.