gebhart/patrepeval huggingface dataset:
Simultaneous reconstruction of scatter and unscattered PET coincidences using TOF and energy information (2011)

In positron emission tomography (PET), a typical iterative reconstruction algorithm relies on a method to estimate and subtract the scatter from the net trues coincidences: the remaining unscattered coincidences are then used to reconstruct an image of the original activity distribution. The introduction of time-of-flight (TOF) PET opens the possibility to change this scheme, and use the spatial information carried by the scattered events for the reconstruction. The combined knowledge of TOF difference and detected photon energy provide spatial information on the position of the source even after single scattering, and can be used for reconstruction of scattered photons, using a “scatter back projector” in addition to the conventional “trues back projector”. In the scatter back projector, the scattering angle is derived from the energy of the scattered photon through the Compton kinematics, and this identifies a set of possible scattering trajectories, or “broken” line-of-response (LOR). The TOF information localizes the position of the source along the set of broken LOR. The advantages of this proposed method are twofold: including the spatial information about the origin of the scattered pairs could improve the image quality particularly in low counts data set; the lower threshold of energy window can be lowered to include more scatter, increasing sensitivity.
Polarization management to mitigate misalignment-induced fringe fading in fiber-based optical coherence tomography (2017)

In fiber-based optical coherence tomography (OCT), the interference fringes suffer from the fading effect due to misalignment of the light polarization states between the reference and sample arms, resulting in sensitivity degradation and image intensity variation. We theoretically and experimentally analyzed the relation between the misalignment and the fading coefficient. Assuming that the variation of the light polarization in single-mode fiber (SMF) was a random process, we statistically quantified the fading effect. Furthermore, in OCT configuration based on the Michelson interferometer, we reported an interesting observation that the polarization states of light traveling a round-trip in SMF are not evenly distributed on the Poincare sphere. Based on this observation, we demonstrated the existence of an optimal output polarization state of the reference arm to mitigate the fading effect. We demonstrated that in an optimal setup, the statistical average signal-to-noise ratio could be 3.5 dB higher than a setup without proper polarization management.
Searching in one billion vectors: Re-rank with source coding (2011)

Recent indexing techniques inspired by source coding have been shown successful to index billions of high-dimensional vectors in memory. In this paper, we propose an approach that re-ranks the neighbor hypotheses obtained by these compressed-domain indexing methods. In contrast to the usual post-verification scheme, which performs exact distance calculation on the short-list of hypotheses, the estimated distances are refined based on short quantization codes, to avoid reading the full vectors from disk. We have released a new public dataset of one billion 128 dimensional vectors and proposed an experimental setup to evaluate high dimensional indexing algorithms on a realistic scale. Experiments show that our method accurately and efficiently re-ranks the neighbor hypotheses using little memory compared to the full vectors representation.
Transcriptional response of <i>Prochlorococcus</i> to co-culture with a marine <i>Alteromonas</i>: differences between strains and the involvement of putative infochemicals (2016)

Interactions between marine microorganisms may determine the dynamics of microbial communities. Here, we show that two strains of the globally abundant marine cyanobacterium Prochlorococcus, MED4 and MIT9313, which belong to two different ecotypes, differ markedly in their response to co-culture with a marine heterotrophic bacterium, Alteromonas macleodii strain HOT1A3. HOT1A3 enhanced the growth of MIT9313 at low cell densities, yet inhibited it at a higher concentration, whereas it had no effect on MED4 growth. The early transcriptomic responses of Prochlorococcus cells after 20 h in co-culture showed no evidence of nutrient starvation, whereas the expression of genes involved in photosynthesis, protein synthesis and stress responses typically decreased in MED4 and increased in MIT313. Differential expression of genes involved in outer membrane modification, efflux transporters and, in MIT9313, lanthipeptides (prochlorosins) suggests that Prochlorococcus mount a specific response to the presence of the heterotroph in the cultures. Intriguingly, many of the differentially-expressed genes encoded short proteins, including two new families of co-culture responsive genes: CCRG-1, which is found across the Prochlorococcus lineage and CCRG-2, which contains a sequence motif involved in the export of prochlorosins and other bacteriocin-like peptides, and are indeed released from the cells into the media.
Lymphotropic Virions Affect Chemokine Receptor-Mediated Neural Signaling and Apoptosis: Implications for Human Immunodeficiency Virus Type 1-Associated Dementia (1999)

Chemokine receptors pivotal for human immunodeficiency virus type 1 (HIV-1) infection in lymphocytes and macrophages (CCR3, CCR5, and CXCR4) are expressed on neural cells (microglia, astrocytes, and/or neurons). It is these cells which are damaged during progressive HIV-1 infection of the central nervous system. We theorize that viral coreceptors could effect neural cell damage during HIV-1-associated dementia (HAD) without simultaneously affecting viral replication. To these ends, we studied the ability of diverse viral strains to affect intracellular signaling and apoptosis of neurons, astrocytes, and monocyte-derived macrophages. Inhibition of cyclic AMP, activation of inositol 1,4,5-trisphosphate, and apoptosis were induced by diverse HIV-1 strains, principally in neurons. Virions from T-cell-tropic (T-tropic) strains (MN, IIIB, and Lai) produced the most significant alterations in signaling of neurons and astrocytes. The HIV-1 envelope glycoprotein, gp120, induced markedly less neural damage than purified virions. Macrophage-tropic (M-tropic) strains (ADA, JR-FL, Bal, MS-CSF, and DJV) produced the least neural damage, while 89.6, a dual-tropic HIV-1 strain, elicited intermediate neural cell damage. All T-tropic strain-mediated neuronal impairments were blocked by the CXCR4 antibody, 12G5. In contrast, the M-tropic strains were only partially blocked by 12G5. CXCR4-mediated neuronal apoptosis was confirmed in pure populations of rat cerebellar granule neurons and was blocked by HA1004, an inhibitor of calcium/calmodulin-dependent protein kinase II, protein kinase A, and protein kinase C. Taken together, these results suggest that progeny HIV-1 virions can influence neuronal signal transduction and apoptosis. This process occurs, in part, through CXCR4 and is independent of CD4 binding. T-tropic viruses that traffic in and out of the brain during progressive HIV-1 disease may play an important role in HAD neuropathogenesis.
Establishment and characterization of continuous cell line MTC-SK derived from a human medullary thyroid carcinoma. (1990)

Tumor cells of a human medullary thyroid carcinoma were isolated and propagated in tissue culture. Several cell lines with different morphology developed from the primary culture, among others a fibroblast-like growing cell line (MTC-F) and a cell line growing as a suspension of single cells and spherical cell clusters (MTC-SK). The MTC-SK cell line was serially propagated for 90 passages, over 3 years. When examined at different times throughout the in vitro period, MTC-SK exhibited properties characteristic of medullary thyroid carcinomas: the cells maintained their epithelioid morphology; endocrine granules were demonstrated in the cytoplasm by electron microscopy; in situ hybridization confirmed the production of calcitonin- and bombesin-mRNA (gastrin releasing peptide); the cells revealed positive immunoreactivity with antibodies to calcitonin, calcitonin gene-related peptide, and bombesin. The in vitro properties of the MTC-SK cells corresponded to the results obtained from the tissue of origin. Cytogenetic studies of the MTC-F cell line revealed a supernumerary metacentric chromosome (20?). In the MTC-SK cell line the predominant findings were terminal chromosomal rearrangements most frequently concerning chromosome 11p, i.e., the locus of the calcitonin and calcitonin gene-related peptide genes and the H-ras oncogene, and a characteristic instability of the centromeric region of chromosome 16 and somatic pairing of the homologous chromosomes 16.
Desorption properties of amine species during atomic layer epitaxy of GaAs using amino-As (1992)

The substantial expansion of the temperature range for atomic layer epitaxy (ALE) was reported using triethyl-gallium by K. Fujii, I. Suemune, T. Koui, and M. Yamanishi [Appl. Phys. Lett. 60, 1498 (1992)]. This was observed by replacing arsine with an amino-As, tris-dimethylamino-arsenic {As[N(CH3)2]3}. The self-limiting mechanism was attributed to the adsorption of amine species on the Ga as well as As surfaces. The time constants and the activation energies for the desorption of the amine species were measured using transient quadrupole mass spectrometry. It is shown that the adsorption properties of the amine species on the Ga surfaces are intermediate between those of methyl and ethyl species.
PTSD Elderly War Veterans: A Clinical Controlled Pilot Study (2010)

Around 25,000 war veterans in Portugal suffer posttraumatic stress disorder (PTSD). This clinically controlled study evaluates virtual reality exposure therapy (VRET) as an alternative procedure to reduce PTSD symptoms. Ten patients were assigned to three groups: VRET, exposure in imagination (EI), and waiting list (WL). The patients were Portuguese veterans from a series of wars fought in former African colonies more than 30 years ago. While the EI group participated in traditional imagination therapy, the VRET group was exposed to a virtual reality (VR) war scenario. Cues such as ambush, mortar blasting, and waiting for rescue were used in the VR. Patients enrolled in the VRET group showed statistical reduction of PTSD-associated disorders like depression and anxiety. Far from being conclusive, this pilot study nonetheless presents some promising data on the use of VRET on old war veteran populations.
Commercial Property Tokenizing With Smart Contracts (2018)

Trading commercial property currently involves several middlemen who are extra time-consuming and cost-consuming elements in a transaction. With recent blockchain-based smart contract innovations, it is possible to use distributed applications (Dapps) for disintermediating third parties and enabling direct peer-to-peer (P2P) transactions. The blockchain serves as an immutable, event-recording ledger that facilitates trust-less P2P transactions. The Evareium system is a distributed application for enabling blockchain-based commercial-property trades that make middlemen superfluous and consequently, investors benefit from cost reductions, faster transaction times, greater transparency and reduced regulatory burdens. As a consequence of the Evareium system, investors and other stake-holders are able to avail a direct interface with the creation and dissemination of optimal financial gains from such investments without interdiction. The corresponding Evareium token is structured for governing platform-related incentives. The Evareium token is also intended for Internet-of-Things (IoT) based hotelmanagement services such as controlling hotel-room blindfolds, A/C, smart keys, checkin, spa, restaurant, room service, and so on.
Comparison of CO2 Photoreduction Systems: A Review (2014)

Carbon dioxide (CO2) emissions are a major contributor to the climate change equation, and thus strategies need to be developed in order to reduce increases in CO2 levels in the atmosphere. One of the most promising approaches is to convert CO2 into useful products in engineered processes. The photocatalytic reduction of CO2 into hydrocarbon fuels is a promising way to recycle CO2 as a fuel feedstock by taking advantage of the readily available solar energy. This article reviews the basics of CO2 photoreduction mechanisms, limiting steps, possible strategies to enhance photoreduction efficiency, and the state-of-the-art photocatalytic systems for CO2 reduction. In particular, a comparison between different catalytic systems, including biological (plants and algae), inorganics (semiconductors), organics (molecular complexes), and hybrid (enzyme/semiconductors) systems is provided.
Computation and Formal Verification of SRT Quotient and Square Root Digit Selection Tables (2012)

We present a comprehensive, self-contained, and mechanically verified proof of correctness of a maximally redundant SRT design for floating-point division and square root extraction, supported by verified procedures that 1) test the admissibility of a proposed digit selection table, 2) determine the minimal dimensions of an admissible table for a given arbitrary radix, and 3) generate these tables. For square root extraction, we also provide a verified procedure for generating an initial approximation that meets the accuracy requirement of the algorithm and ensures that the digit selection index derived from successive partial roots remains static throughout the computation. A radix-8 instantiation of these algorithms has been implemented in the floating-point unit of the AMD processor code-named Steamroller. To ensure their correctness, all of our results and procedures have been formalized and mechanically checked by the ACL2 prover. We present evidence of the value of this approach by comparing it to that of a more conventional published paper that reports similar results, which are shown to be fatally flawed.
Formation of silver nanoshells on latex spheres (2004)

Silver nanoshells on styrene–acrylic acid copolymer latex spheres (PSA) were deposited by an in situ chemical reduction method, ageing a colloid solution at 85 °C containing PSA latex, AgNO3, urotropine, and poly-(vinylpyrrolidone). SEM and TEM observations showed that the silver nanoshells were made of closely packed silver nanoparticles of different sizes and morphologies. UV–visible absorption spectra were recorded to investigate their optical properties.
Decreased Sigmoidal ABCB1 (P-Glycoprotein) Expression in Ulcerative Colitis is Associated with Disease Activity (2009)

Cytokine-mediated downregulation of the major human efflux transporter ABCB1 in inflamed intestine of UC patients is presumably dependent on disease activity, with a possible contribution from IL8.
Oxidative Stress and the JNK Pathway are Involved in the Development of Type 1 and Type 2 Diabetes (2007)

Failure of pancreatic beta-cells is the common characteristic of type 1 and type 2 diabetes. Type 1 diabetes mellitus is induced by destruction of pancreatic beta-cells which is mediated by an autoimmune mechanism and consequent inflammatory process. Various inflammatory cytokines and oxidative stress are produced during this process, which has been proposed to play an important role in mediating beta-cell destruction. The JNK pathway is also activated by such cytokines and oxidative stress, and is involved in beta-cell destruction. Type 2 diabetes is the most prevalent and serious metabolic disease, and beta-cell dysfunction and insulin resistance are the hallmark of type 2 diabetes. Under diabetic conditions, chronic hyperglycemia gradually deteriorates beta-cell function and aggravates insulin resistance. This process is called "glucose toxicity". Under such conditions, oxidative stress is provoked and the JNK pathway is activated, which is likely involved in pancreatic beta-cells dysfunction and insulin resistance. In addition, oxidative stress and activation of the JNK pathway are also involved in the progression of atherosclerosis which is often observed under diabetic conditions. Taken together, it is likely that oxidative stress and subsequent activation of the JNK pathway are involved in the pathogenesis of type 1 and type 2 diabetes.
Understanding spatial configuration of robot's environment from stereo motion images (2002)

When a robot moves around, it obtains a large number of input images of its environment taken at different viewpoints. The mobile robot considered has binocular vision and it obtains a sequence of stereo images from the environment. This paper proposes a method to build the 3D model of the robot's environment and to understand its spatial configuration from these input images, which is one of the central problems for the study of an intelligent mobile robot.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>
HIV interactions with monocytes and dendritic cells: viral latency and reservoirs (2009)

HIV is a devastating human pathogen that causes serious immunological diseases in humans around the world. The virus is able to remain latent in an infected host for many years, allowing for the long-term survival of the virus and inevitably prolonging the infection process. The location and mechanisms of HIV latency are under investigation and remain important topics in the study of viral pathogenesis. Given that HIV is a blood-borne pathogen, a number of cell types have been proposed to be the sites of latency, including resting memory CD4+ T cells, peripheral blood monocytes, dendritic cells and macrophages in the lymph nodes, and haematopoietic stem cells in the bone marrow. This review updates the latest advances in the study of HIV interactions with monocytes and dendritic cells, and highlights the potential role of these cells as viral reservoirs and the effects of the HIV-host-cell interactions on viral pathogenesis.
Acquisition of biologically relevant gene expression data by Affymetrix microarray analysis of archival formalin-fixed paraffin-embedded tumours (2008)

Robust protocols for microarray gene expression profiling of archival formalin-fixed paraffin-embedded tissue (FFPET) are needed to facilitate research when availability of fresh-frozen tissue is limited. Recent reports attest to the feasibility of this approach, but the clinical value of these data is poorly understood. We employed state-of-the-art RNA extraction and Affymetrix microarray technology to examine 34 archival FFPET primary extremity soft tissue sarcomas. Nineteen arrays met stringent QC criteria and were used to model prognostic signatures for metastatic recurrence. Arrays from two paired frozen and FFPET samples were compared: although FFPET sensitivity was low ( approximately 50%), high specificity (95%) and positive predictive value (92%) suggest that transcript detection is reliable. Good agreement between arrays and real time (RT)-PCR was confirmed, especially for abundant transcripts, and RT-PCR validated the regulation pattern for 19 of 24 candidate genes (overall R(2)=0.4662). RT-PCR and immunohistochemistry on independent cases validated prognostic significance for several genes including RECQL4, FRRS1, CFH and MET - whose combined expression carried greater prognostic value than tumour grade - and cmet and TRKB proteins. These molecules warrant further evaluation in larger series. Reliable clinically relevant data can be obtained from archival FFPET, but protocol amendments are needed to improve the sensitivity and broad application of this approach.
Antiviral Effects of Atropine and Caffeine (1980)

The antiviral activities of atropine and caffeine were investigated. Atropine inhibited the multiplication of enveloped viruses and caffeine suppressed th growth of polio, influenza, herpes simplex and vaccinia viruses but not Japanese encephalitis virus, Newcastle disease virus and type 2 adenovirus.
Ligand-independent Activation of Transforming Growth Factor (TGF) β Signaling Pathways by Heteromeric Cytoplasmic Domains of TGF-β Receptors (1996)

Transforming growth factor beta (TGF-beta) transduces signals through two related serine/threonine kinase receptors, the type I and type II receptors, which have the ability to interact with each other. In the heteromeric complex, the type II receptor is the primary determinant of ligand binding and phosphorylates the cytoplasmic domain of the type I receptor. Using a chimeric receptor strategy, we and others have shown previously that a functional TGF-beta receptor complex requires heteromerization of both extracellular and intracellular domains of type I and type II receptors. In the current study, we show that overexpression of two receptors carrying a heteromeric combination of cytoplasmic domains resulted in ligand-independent responses, further supporting the functional requirement of the two heterologous cytoplasmic domains in TGF-beta signaling. Furthermore, coexpression of only the cytoplasmic domains of both the type I and II receptors or tethering the type II to the type I cytoplasmic domain activated TGF-beta responses in a ligand-independent manner. In cotransfected COS-1 cells, both cytoplasmic domains are associated with each other. Our results indicate that the cytoplasmic domains of the type I and type II TGF-beta receptors physically and functionally interact with each other in the heteromeric complex.
Low crosstalk and low loss 1 × 8 digitaloptical switch using silicone resin waveguides (1999)

A high-performance 1 × 8 digital thermo-optic (TO) switch that uses silicone resin waveguides has been developed. The compact 40 mm long switch uses short Y-branching switches with a large branching angle. It has a low insertion loss of < 3 dB and a low crosstalk of < –40 dB at 1550 nm.
Anti‐inflammatory effect of ibuprofen‐loaded embolization beads in sheep uterus (2007)

Embolization of blood vessels may result in a variety of side effects which can include pain and inflammation. The objective of this study was to assess the release and effect of ibuprofen (IBU) from Bead Block microspheres (BB) loaded with IBU (IBU-BB) on the foreign body inflammatory reaction in a sheep uterine artery model. Both uterine arteries of 12 hormonally cycled ewes were embolized with 0.5 mL of 500-700 microm BB (n = 6) or IBU-BB (n = 6). Animals were sacrificed at 1 week (1W) or 3 weeks (3W) (n = 3 each group). The gross examination of the organs was performed and distribution of the beads in the tissue was assessed. Inflammation was estimated histologically by quantitative and semiquantitative classification of inflammatory cells on HES and MGG stains and use of videoanalysis after immunohistolabeling with CD-antibodies to a variety of inflammatory cells. At 1W, a significant decrease of inflammatory response was observed for IBU-BB relative to BB in terms of number of lymphocytes and of immunohistochemical staining for CD172a, MHC-II, CD3, and CD4. At 3W, the inflammatory response for IBU-BB was similar to that for BB at 1W in terms of cell populations and moderate intensity. There was no or low amounts of staining for CD8 and CD45RA and none for CD21 in all four groups. Immunohistochemical detection of IBU showed that some drug was still present in the beads at 1W but none was detectable at 3W suggesting it had all eluted. These results signify that the inflammatory response is dampened by the action of IBU eluted from the beads and that IBU-BB can delay postembolization inflammatory reaction.