Miracle-dz/UniFAR-FTUs huggingface dataset:
VARIATION IN EXPRESSION OF ENDOTHELIAL ADHESION MOLECULES IN PRETRANSPLANT AND TRANSPLANTED KIDNEYS‐CORRELATION WITH INTRAGRAFT EVENTS

Endothelial adhesion molecules are directly involved in the localization and migration of leukocytes from the circulation into tissues at sites of inflammation. We have compared the expression of PECAM-1 (CD31), ELAM-1, ICAM-1 (CD54), and VCAM-1 in pretransplant (n=20) and needle-core biopsies from renal transplants obtained during different clinical circumstances (n=42). PECAM-1 was consistently expressed on all endothelium in both pretransplant and transplant biopsies. In contrast, there was variation in endothelial expression of ELAM-1 and in proximal tubular expression of ICAM-1 and VCAM-1 between pretransplant biopsies. After transplantation induced expression of endothelial ELAM-1 and VCAM-1 and tubular induction of ICAM- 1 and VCAM-1 was detected. Induced adhesion molecule expression was frequently associated with focal leukocyte infiltration, and there was a significantly higher level of CD45 and CD25 positive cell infiltration in biopsies with induced adhesion molecule expression. The induction of adhesion molecule expression is evidence of endothelial activation in these transplant biopsies. Comparison of adhesion molecule expression and HLA-class II antigen expression revealed that induced tubular class II antigens may be detected in the absence of induced adhesion molecule expression.
Optimizing the Design of a TIR Lens Using SVR, VIKOR, and the Artificial Bee Colony Algorithm

Abstract—Multi-response parameter design problems have become increasingly important and have received considerable attention from both researchers and practitioners since there are usually several quality characteristics that must be optimized simultaneously in most modern products/processes. This study applies support vector regression (SVR), VlseKriterijumska Optimizacija I Kompromisno Resenje (VIKOR), and the artificial bee colony (ABC) algorithm to resolve these common and complicated parameter design problems. The feasibility and effectiveness of the proposed approach are demonstrated via a case study in which the design of a total internal reflection (TIR) lens is optimized while fabricating an MR16 light-emitting diode (LED) lamp. Experimental results indicate that the proposed solution procedure can provide highly robust design parameter settings for TIR lenses that can be directly applied in real manufacturing processes. The comparison revealed that the ABC algorithm can search the solution spaces in continuous domains modeled via SVR instead of in the limited discrete experiment levels thus finding a more robust design.
Patient-perceived barriers to antiretroviral adherence: Associations with race

New antiretroviral (ARV) regimens require strict adherence if optimal suppression of HIV is to be maintained. This study is a theory-based examination of racial differences in patient-perceived barriers and reported ARV adherence. Participants (N=149) completed the Patient Medication Adherence Questionnaire (PMAQ), measuring adherence and perceived barriers to adherence. Adherence was defined as a self-report of 100% adherence in the past four weeks. Odds ratios were calculated to determine the relation of reported barriers to adherence for race and gender groups, and for the sample overall. For every ten-point increase in barrier score, there was an 86% increased risk of being non-adherent (OR=1.86; 95% CI: 1.19, 2.91). Adherence was not different between racial and gender groups, nor was total barrier score. However, individual barriers were differentially endorsed across groups. Rather than relying on demographic predictors, which may be only an indirect marker of adherence, evaluations of adherence should examine the psychological and social barriers to positive adherence outcomes in individual patients. Our findings support the use of theory-based behavioural interventions that address perceived barriers to adherence and other health promotion activities.
Sulphur chemistry and molecular shocks : The case of NGC 1333-IRAS 2

We present SO and SO2 observations in the region of the low mass protostar IRAS2/NGC1333. The East-West outflow originating from this source has been mapped in four transitions of both SO and SO2. In addition, CS observations published in the literature have been used. We compute the SO, SO2 and CS column densities and the physical conditions at several positions of the outflow using LTE and a non-LTE LVG approximations. The SO2/SO and CS/SO abundance ratios are compared with the theoretical predictions of a chemical model adapted to the physical conditions in the IRAS2 outflow. The SO2/SO abundance ratios are constant in the two lobes of the outflow whereas CS/SO is up to 6 times lower in the shocked gas of the East lobe than in the West one. The comparison with the chemical model allows us to constrain the age of the outflow produced by IRAS2 to >5e3yr. We find low densities and temperatures for the outflow of IRAS2 ( 70 K) from SO and SO2 emission probably because the two molecules trace the cooled entrained material. The East lobe of the outflow shows denser gas compared to the West lobe. We also discuss some constraints on the depleted form of sulphur.
Assessing the Blood Supply Status of the Focal Ground-Glass Opacity in Lungs Using Spectral Computed Tomography

Objective To exploit material decomposition analysis in dual-energy spectral computed tomography (CT) to assess the blood supply status of the ground-glass opacity (GGO) in lungs. Materials and Methods This retrospective study included 48 patients with lung adenocarcinoma, who underwent a contrast-enhanced dual-energy spectral CT scan before treatment (53 GGOs in total). The iodine concentration (IC) and water content (WC) of the GGO, the contralateral and ipsilateral normal lung tissues were measured in the arterial phase (AP) and their differences were analyzed. IC, normalized IC (NIC), and WC values were compared between the pure ground-glass opacity (pGGO) and the mixed ground-glass opacity (mGGO), and between the group of preinvasive lesions and the minimally invasive adenocarcinoma (MIA) and invasive adenocarcinoma (IA) groups. Results The values of pGGO (IC = 20.9 ± 6.2 mg/mL and WC = 345.1 ± 87.1 mg/mL) and mGGO (IC = 23.8 ± 8.3 mg/mL and WC = 606.8 ± 124.5 mg/mL) in the AP were significantly higher than those of the contralateral normal lung tissues (IC = 15.0 ± 4.9 mg/mL and WC = 156.4 ± 36.8 mg/mL; IC = 16.2 ± 5.7 mg/mL and WC = 169.4 ± 41.0 mg/mL) and ipsilateral normal lung tissues (IC = 15.1 ± 6.2 mg/mL and WC = 156.3 ± 38.8 mg/mL; IC = 15.9 ± 6.0 mg/mL and WC = 174.7 ± 39.2 mg/mL; all p < 0.001). After normalizing the data according to the values of the artery, pGGO (NIC = 0.1 and WC = 345.1 ± 87.1 mg/mL) and mGGO (NIC = 0.2 and WC = 606.8 ± 124.5 mg/mL) were statistically different (p = 0.049 and p < 0.001, respectively), but not for the IC value (p = 0.161). The WC values of the group with preinvasive lesions and MIA (345.4 ± 96.1 mg/mL) and IA (550.1 ± 158.2 mg/mL) were statistically different (p < 0.001). Conclusion Using dual-energy spectral CT and material decomposition analysis, the IC in GGO can be quantitatively measured which can be an indicator of the blood supply status in the GGO.
QU-IR at SemEval 2016 Task 3: Learning to Rank on Arabic Community Question Answering Forums with Word Embedding

Resorting to community question answering (CQA) websites for finding answers has gained momentum in the past decade with the explosive rate at which social media has been proliferating. With many questions left unanswered on those websites, automatic and smart question answering systems have seen light. One of the main objectives of such systems is to harness the plethora of existing answered questions; hence transforming the problem to finding good answers to newly posed questions from similar previously-answered ones. As SemEval 2016 Task 3 “Community Question Answering” has focused on this problem, we have participated in the Arabic Subtask. Our system has adopted a supervised learning approach in which a learning-to-rank model is trained over data (questions and answers) extracted from Arabic CQA forums using word2vec features generated from that data. Our primary submission achieved a 29.7% improvement over the MAP score of the baseline. Post submission experiments were further conducted to integrate variations of the word2vec features to our system. Integrating covariance word embedding features has raised the the improvement over the baseline to 37.9%.
The coherence of speech in audio-visual integration : Commentary on auditory-visual spatial interaction (M. Radeau)

Since the expression ventriloquism effect originally referred to speech, the main question to ask speech scientists could be the following : How can an invisible speech production be attributed to a visible puppet and captured by its face movements, which are only roughly coherent with ventriloquist's speech sounds, creating a sound location illusion, in spite of the knowledge that the source of both signals is the illusionist's skill? The As. will only focus here on the perceptual side of the phenomenom, in spite of the fact that the observed preference for coherence of acoustics and optics in adults, children, and infants, is surely related to a deep link between speech perception and speech production
Mycotoxin occurrence in commodities, feeds and feed ingredients sourced in the Middle East and Africa

Between February and October 2009, 324 grain, feed and feed commodity samples were sourced directly at animal farms or feed production sites in Middle East and Africa and tested for the presence of A- and B-trichothecenes, zearalenone, fumonisins, aflatoxins and ochratoxin A, or for selected groups of mycotoxins only. Samples were analyzed after clean-up by immunoaffinity or solid-phase extraction followed by HPLC with derivatization where appropriate and fluorescence, UV or mass spectrometric detection. The percentage of positive samples of B-trichothecenes ranged from 0 to 87% of tested samples. The prevalence of fumonisins in the different countries was >50% in most cases. Zearalenone was present in tested commodities from all countries except three. The presence of aflatoxin in analyzed samples varied from 0 to 94%. Ochratoxin A was present in 67% of samples in Sudan and in 100% of Nigerian samples. No A-trichothecenes were found in this survey.
Somatosensation in the superior colliculus of the star‐nosed mole

The superior colliculus (or optic tectum in nonmammals) plays a critical role in the visual system and is essential for integrating sensory inputs to guide eye and head movements. However, what is the role of the superior colliculus (SC) in species that depend almost exclusively on touch? In this study we examined the SC of the star‐nosed mole, a subterranean mammal that, instead of using vision, explores its environment using its tactile star. The star acts like a mechanosensory eye with a central tactile fovea that is constantly shifted in a saccadic manner. Multiunit microelectrode recordings were used to determine the topography and receptive field organization of somatosensory inputs to the SC and to test for visual and auditory responses. Here we report an SC dominated by somatosensory inputs in which neurons in all layers responded to mechanosensory stimulation, forming a topographic representation of contralateral body dominated by the mechanosensory star. Receptive fields were large, and appendage representations overlapped, suggesting that the SC may use a distributed, population code to guide the saccadic movements of the mole's touch fovea. No auditory or visual responses were recorded from the SC, although neurons in the neighboring inferior colliculus responded to auditory stimuli. Layers IVb–VII were identified, and a layer superficial to IVb contained neurons that responded to somatosensory stimulation, suggesting that there are unique patterns of afferents in the star‐nosed mole's SC. J. Comp. Neurol. 464:415–425, 2003. © 2003 Wiley‐Liss, Inc.
Vesiculation and sorting from PC12-derived endosomes in vitro.

Formation of small vesicles resembling synaptic vesicles can be reconstituted in vitro by incubating labeled homogenates of PC12 cells with ATP and two cytoplasmic proteins, AP3 and ARF1 [Faúndez, V. , Horng, J.-T. & Kelly, R. B. (1998) Cell 93, 423-432]. To determine whether AP3 was mediating budding from plasma membranes or endosomes the organelle that generated the synaptic vesicles was characterized. The budding activity was enriched in organelles that labeled at 15 degrees C, but not at 4 degrees C, that excluded a marker of plasma membranes and that contained internalized transferrin, indicating that the precursor was an endosome. Vesicles formed from the endosomal precursor in vitro excluded transferrin. We conclude that ARF-mediated vesiculation into synaptic vesicle-sized organelles uses an endosomal precursor and occurs simultaneously in vitro with sorting of synaptic vesicle proteins from other membrane protein constituents of the endosome.
The function of photosystem I. Quantum chemical insight into the role of tryptophan-quinone interactions.

Quantum chemical calculations have provided evidence for the role of tryptophan residues in the electron transfer process of photosystem I (PS-I). The interaction of Trp with quinone acceptors and their radical anions in the A(1) site of PS-I has been modeled by various indole-quinone and indole-semiquinone complexes. MP2 optimizations show that, while neutral quinones and an indole molecule prefer a pi-stacked arrangement, semiquinone radical anions prefer a T-stacked conformation with significant N-H.pi hydrogen bonding interactions. Comparison of density functional calculations of electronic g-tensors with electron paramagnetic resonance data strongly suggests that hydrogen-bonded T-shaped arrangements occur upon reduction of quinone acceptors without an extended side chain (e.g., duroquinone or naphthoquinone), when reconstituted into the phylloquinone-depleted A(1) site of PS-I. In contrast, for the native phylloquinone (vitamin K(1), Q(K)), reorientation of the semiquinone radical anion is prevented by side chain-protein interactions. For a fixed pi-stacked arrangement, the extent of the intermolecular interaction is reduced upon one-electron reduction. This corresponds to a lowering of the redox potential of the P(700)(+)*Q(K)(-)* radical pair, due to interactions of Q(K) with a tryptophan. Together with the comparably weak hydrogen bonding in PS-I, the proposed model explains the very negative redox potential of the A(1) site, needed for forward electron transfer. T-stacking hydrogen bonds to semiquinones may also have to be considered in many other electron transfer processes in living organisms.
Improved Performance of Wind-driven Isolated Induction Generators by Six-phase Operation

paper describes a new, generalized and efficient steady- state model for the performance analysis of isolated six-phase induction generators. The mathematical model is formed directly from the equivalent circuit of six-phase induction generator by nodal admittance method. The proposed model is very simple which completely avoids lengthy derivations of non linear equations. The model results in matrix form so that inclusion or elimination of any equivalent circuit elements can be easily achieved. Also, this model is flexible to find any combination of unknown quantities of the equivalent circuit. The matrix equation is solved by genetic algorithm to determine the steady-state performance of isolated six-phase induction generator (ISPIG). To validate the improvement of performance by six-phase operation, the experimental and theoretical results were compared with three-phase operation. In addition, the winding diagram of the six-phase / three- phase induction generator which is used as a prototype model for the experimental study is also presented. Keywords-phase induction generator, Steady-state analysis, Genetic
Notch ligand‐bearing thymic epithelial cells initiate and sustain Notch signaling in thymocytes independently of T cell receptor signaling

Thymic epithelial cells are specialized to play essential roles at multiple stages of T cell development in the thymus, yet the molecular basis of this specialization is largely unknown. Recently, the Notch family of transmembrane proteins has been implicated in thymocyte development. Such proteins interact with cell surface proteins of the Delta‐like and Jagged families. It is known that Notch ligands are expressed intrathymically, and that Notch signaling is regulated by Notch ligands expressed on either the same or third‐party cells. However, functional analysis of Notch ligand expression, and elucidation of the mechanism of Notch ligand signaling in thymocyte development, are unclear. Here, we find that Notch ligand expression in the thymus is compartmentalized, with MHC class II+ thymic epithelium, but not thymocytes nor dendritic cells, expressing Jagged‐1, Jagged‐2 and Delta‐like‐1. We also provide evidence that contact with Notch ligands on thymic epithelium is necessary to activate and sustain Notch signaling in thymocytes, and that this can occur independently of positive selection induction. Our data suggest that Notch ligand expression by thymic epithelium may partly explain the specialization of these cells in supporting thymocyte development, by regulating Notch activation via an inductive signaling mechanism independently of signaling leading to positive selection.
A new approach to studying the impact of intermittent renewable resources

This paper presents results of a study that combines the use of two standard industry tools - ABB GridView and GE-PSLF - and an in-house tool developed by KEMA called KERMIT. The paper proposes using system frequency to select worst-case conditions rather than the commonly used system load and contingencies. The approach redefines contingencies as continuous events. Using actual utility data, the results demonstrate the proposed approach's effectiveness in answering critical questions related to system reliability and stability following various renewable contingency events. Characterizing the inherent risks of integrating renewable generating resources into the power system, this paper examines and validates a range of mitigating solutions including energy storage as a means to provide “synthetic” inertia, in addition to demand response, capacitor placement and other T&D upgrades. Contingency results are interpreted in terms of the industry standard Low Voltage Ride Through criteria.
Synaptotagmins I and IX function redundantly in regulated exocytosis but not endocytosis in PC12 cells

Synaptotagmin I is considered to be a Ca2+ sensor for fast vesicle exocytosis. Because Ca2+-dependent vesicle exocytosis persists in synaptotagmin I mutants, there must be additional Ca2+ sensors. Multiple synaptotagmin isoforms co-reside on vesicles, which suggests that other isoforms complement synaptotagmin I function. We found that full downregulation of synaptotagmins I and IX, which co-reside on vesicles in PC12 cells, completely abolished Ca2+-dependent vesicle exocytosis. By contrast, Ca2+-dependent exocytosis persisted in cells expressing only synaptotagmin I or only synaptotagmin IX, which indicated a redundancy in function for these isoforms. Although either isoform was sufficient to confer Ca2+ regulation on vesicle exocytosis, synaptotagmins I and IX conferred faster and slower release rates, respectively, indicating that individual isoforms impart distinct kinetic properties to vesicle exocytosis. The downregulation of synaptotagmin I but not synaptotagmin IX impaired compensatory vesicle endocytosis, which revealed a lack of isoform redundancy and functional specialization of synaptotagmin I for endocytic retrieval.
Compact Dielectric Resonator Antennas With Ultrawide 60%–110% Bandwidth

The design of rectangular dielectric resonator antennas (DRA) with ultrawide bandwidths, in the range of 60-110%, is described. The DRA exploits multiple low-Q modes with overlapping bandwidths to achieve a wide contiguous bandwidth. This is achieved using a full-length, low-permittivity inset between a higher permittivity dielectric volume and a ground plane. With the proposed dielectric arrangement and a feed inside DR, it is possible to efficiently couple a sufficient number of such overlapping modes to a 50 Ω feedline. The volume of such DRAs is also reduced by means of a finite planar conducting wall. These advantages led to an example design with a bandwidth that is significantly wide and at the same time has a smaller DR volume than conventional DRAs. A prototype antenna designed to operate in the FCC UWB band from 3.1 to 10.6 GHz has a dielectric volume of 12 × 8 × 15.2 mm3 (or 1.7 × 10-3 λo3 at 3.1 GHz), and an average measured gain of 5 dB over the band.
Condom availability programs in Massachusetts high schools: relationships with condom use and sexual behavior.

OBJECTIVES This study assessed relationships between condom availability programs accompanied by community discussion and involvement and adolescent sexual practices. METHODS Sexual practice and condom use differences were assessed in a representative sample of 4166 adolescents enrolled in high schools with and without condom availability programs. RESULTS Adolescents in schools where condoms were available were more likely to receive condom use instruction and less likely to report lifetime or recent sexual intercourse. Sexually active adolescents in those schools were twice as likely to use condoms, but less likely to use other contraceptive methods, during their most recent sexual encounter. CONCLUSIONS The strategy of making condoms available, an indication of socioenvironmental support for condom use, may improve HIV prevention practices.
Suboptimal Porcine Endogenous Retrovirus Infection in Non-Human Primate Cells: Implication for Preclinical Xenotransplantation

Background Porcine endogenous retrovirus (PERV) poses a potential risk of zoonotic infection in xenotransplantation. Preclinical transplantation trials using non-human primates (NHP) as recipients of porcine xenografts present the opportunity to assess the zoonosis risk in vivo. However, PERV poorly infects NHP cells for unclear reasons and therefore NHP may represent a suboptimal animal model to assess the risk of PERV zoonoses. We investigated the mechanism responsible for the low efficiency of PERV-A infection in NHP cells. Principal Findings Two steps, cell entry and exit, were inefficient for the replication of high-titer, human-tropic A/C recombinant PERV. A restriction factor, tetherin, is likely to be responsible for the block to matured virion release, supported by the correlation between the levels of inhibition and tetherin expression. In rhesus macaque, cynomolgus macaque and baboon the main receptor for PERV entry, PERV-A receptor 1 (PAR-1), was found to be genetically deficient: PAR-1 genes in these species encode serine at amino acid 109 in place of the leucine in human PAR-1. This genetic defect inevitably impacts in vivo sensitivity to PERV infection of these species. In contrast, African green monkey (AGM) PAR-1 is functional, but PERV infection is still poor. Although the mechanism is unclear, tunicamycin treatment, which removes N-glycosylated sugar chains, increases PERV infection, suggesting a possible role for the glycosylation of the receptors. Conclusions Since cynomolgus macaque and baboon, species often used in pig-to-NHP xenotransplantation experiments, have a defective PAR-1, they hardly represent an ideal animal model to assess the risk of PERV transmission in xenotransplantation. Alternatively, NHP species, like AGM, whose both PARs are functional may represent a better model than baboon and cynomolgus macaque for PERV zoonosis in vivo studies.