gebhart/patrepeval huggingface dataset:
Inhibition of T Cell Metabolism as a Novel Means of Preventing Graft Rejection and Promoting Long Term Tolerance. (2014)

Background: Upon antigen recognition and costimulation, T cells up-regulate the metabolic machinery necessary to sustain effector function and proliferation. A hallmark of this response is a switch to aerobic glycolysis and an increased necessity for glutamine. Based on these observations, we hypothesize that inhibition of glycolysis and glutamine metabolism might represent a novel means of preventing graft rejection. Method: OVA antigen-specific CD4+ or CD8+ Thy1.1+ cells were isolated from OT-I or OT-II transgenic mice and adoptively transferred into C57BL/6 Thy1.2+ host, which were then infected with OVA-expressing Vaccinia to stimulate and expand the antigen-specific cells. The mice were treated with vehicle or combinations of 2DG (an inhibitor of glycolysis) plus metformin (an AMP-kinase activator) and DON (an inhibitor of glutamine metabolism) for 3-5 days. Host splenocytes were harvested for analyzing the number and population of donor cells by flow cytometry and their capacity of cytokine production by ELISA. From these experiments we determined the most effective combinations of metabolic inhibitors and then applied them to a BALB/c à C57BL/6 full thickness skin graft model. Results: For CD8+ T cells responses to vaccinia we found the combination of 2DG+metformin resulted in a greater than 50% decrease in effector cells and IFN-g production. For CD4+ T cells we observed this decrease along with an increase in Foxp3+ regulatory T cells. When we applied this regimen to the mismatched skin graft model we were able to have an increase of 42% in graft median survival time(MST). Furthermore, the addition of rapamycin to this regimen led to a 2-fold increase in MST versus rapamycin alone. Inhibition of glutamine with DON resulted in a greater than 80% decrease in effector cells and IFN-g production in the vaccinia model and ongoing studies demonstrate even longer graft survival using DON as well. Conclusion: Our data suggest that anti-metabolic therapy represents a novel means of inhibiting T cell effector function while preserving mechanisms of immune regulation. Such a regimen can inhibit acute rejection and promote graft survival. Future studies will combine anti-metabolic therapy with costimulatory blockade in an effort to promote long term tolerance in the absence of long term immunosuppression.
Topic Field Selection and Smoothing for XML Retrieval (2003)

Information retrieval from XML documents offers an opportunity to go below the document level in search of relevant information, making any element of an XML document a retrievable unit. We consider two dimensions along which we compare this element retrieval task with the traditional document retrieval task. We investigate how different topic representations and language model smoothing approaches affect the performance of the two tasks. We evaluate our ideas against the INEX 2002 XML retrieval test-suite.
Choroid Plexus Segmentation Using Optimized 3D U-Net (2020)

The choroid plexus is the primary organ that secretes the cerebrospinal fluid. Its structure and function may be associated with the brain drainage pathway and the clearance of amyloid-beta in Alzheimer's Disease. However, choroid plexus segmentation methods have rarely been studied. Therefore, the purpose of this work is to fill the gap using a deep convolutional network. MR images of 10 healthy subjects ( 75.5±8.0 years) were retrospectively selected from the Alzheimer's Disease Neuroimaging Initiative database (ADNI). The benchmark of choroid plexus segmentation was provided by the FreeSurfer package and manual correction. A 3D U-Net was developed and optimized in the patch extraction, augmentation, and loss function. In leave-one-out cross-validations, the optimized U-Net provided superior performance compared to the FreeSurfer results (Dice score 0.732±0.046 vs 0.581±0.093, Jaccard coefficient 0.579±0.057 vs 0.416±0.091, 95% Hausdorff distance 1.871±0.549 vs 7.257±5.038, and sensitivity 0.761 ±0.078 vs 0.539±0.117).
High quality multi-rate CELP speech coding for wireless ATM networks (2002)

The paper presents a multi-rate CELP speech coder which meets the requirements of high perceptive quality, robustness to noisy environments and flexibility required by speech communications in the wireless ATM scenario. The codec, exploiting new robust algorithms for multilevel phonetic classification and efficient activity/inactivity speech coding models, presents an average bit rate of 4 kbit/s with an algorithmic delay of 15 ms and a perceptive quality better than that of the GSM full-rate 13 kbit/s codec and similar to that of the 8 kbit/s ITU-T 0.729 standard, both in the discontinuous transmission mode. In addition, the paper demonstrates that the multi-rate speech coder proposed is a promising coding approach for future wireless ATM-based networks in that it exploits the bit rate variability within talkspurts, thus guaranteeing, with the same average bit rate as an on-off speech coder, greater robustness to packet loss and therefore a better quality of service (QoS).
The Distribution of Cells Containing Estrogen Receptor-α (ERα) and ERβ Messenger Ribonucleic Acid in the Preoptic Area and Hypothalamus of the Sheep: Comparison of Males and Females (2000)

We have used in situ hybridization to compare the distributions of estrogen receptor alpha (ERalpha) and ERbeta messenger RNA (mRNA)-containing cells in the preoptic area and hypothalamus of ewes and rams. Perfusion-fixed brain tissue was collected from luteal phase ewes and intact rams (n = 4) during the breeding season. Matched pairs of sections were hybridized with sheep-specific, 35S-labeled riboprobes, and semiquantitative image analysis was performed on emulsion-dipped slides. A number of sex differences were observed, with females having a greater density of labeled cells than males (P < 0.001) and a greater number of silver grains per cell (P < 0.01) in the ventromedial nucleus for both ER subtypes. In addition, in the retrochiasmatic area, males had a greater (P < 0.05) cell density for ERalpha mRNA-containing cells than females, whereas in the paraventricular nucleus, females had a greater density (P < 0.05) of ERalpha mRNA-containing cells than males. There was a trend (P = 0.068) in the arcuate nucleus for males to have a greater number of silver grains per cell labeled for ERalpha mRNA. In both sexes, there was considerable overlap in the distributions of ERalpha and ERbeta mRNA-containing cells, but the density of labeled cells within each nucleus differed in a number of instances. Nuclei that contained a higher (P < 0.001) density of ERalpha than ERbeta mRNA-containing cells included the preoptic area, bed nucleus of the stria terminalis, and ventromedial nucleus, whereas the subfornical organ (P < 0.001), paraventricular nucleus (males only, P < 0.05), and retrochiasmatic nucleus (females only, P < 0.05) had a greater density of ERalpha than ERbeta mRNA-containing cells. The anterior hypothalamic area and supraoptic nucleus had similar densities of cells containing both ER subtypes. The lateral septum and arcuate nucleus contained only ERalpha, whereas only ERbeta mRNA-containing cells were seen in the zona incerta. The sex differences in the populations of ER mRNA-containing cells in the ventromedial and arcuate nuclei may explain in part the sex differences in the neuroendocrine and behavioral responses to localized estrogen treatment in these nuclei. Within sexes, the differences between the distributions of ERalpha and ERbeta mRNA-containing cells may reflect differential regulation of the actions of estrogen in the sheep hypothalamus. Low levels of ERbeta mRNA in the preoptic area and ventromedial and arcuate nuclei, regions known to be important for the regulation of reproduction, suggest that ERbeta may not be involved in these functions.
On the Design of Variable-Length Error-Correcting Codes (2013)

A joint source-channel coding problem that combines the efficient compression of discrete memoryless sources with their reliable communication over memoryless channels via binary prefix-free variable-length error-correcting codes (VLECs) is considered. Under a fixed free distance constraint, a priority-first search algorithm is devised for finding an optimal VLEC with minimal average codeword length. Two variations of the priority-first-search-based code construction algorithm are also provided. The first one improves the resilience of the developed codes against channel noise by additionally considering a performance parameter B <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">dfree</sub> without sacrificing optimality in average codeword length. In the second variation, to accommodate a large free distance constraint as well as a large source alphabet such as the 26-symbol English data source, the VLEC construction algorithm is modified with the objective of significantly reducing its search complexity while still yielding near-optimal codes. A low-complexity sequence maximum a posteriori (MAP) decoder for all VLECs (including our constructed optimal code) is then proposed under the premise that the receiver knows the number of codewords being transmitted. Simulations show that the realized optimal and suboptimal VLECs compare favorably with existing codes in the literature in terms of coding efficiency, search complexity and error rate performance.
ChemInform Abstract: A New Stereoselective Approach to the Manzamine Alkaloids. (1999)

Abstract ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 100 leading journals. To access a ChemInform Abstract of an article which was published elsewhere, please select a “Full Text” option. The original article is trackable via the “References” option.
Philosophy of the Body (2011)

To say I enjoyed the Santorini Voice would be a lie. It also would be a ridiculous understatement. I was terrified on my way to Greece. I was also exhausted--having just finished teaching in Italy and Turkey--and certainly not feeling physically or mentally sharp. On top of this, I felt ill-prepared for what lay ahead. My ideal self had prepared for the ominously titled Symposium by studying all the philosophical texts that had been recommended, in addition to researching appropriate texts on the teaching of voice. Unfortunately, my true self landed in Santorini with nothing ready: shaky hands, empty head, and a barely memorized sonnet. Here's the thing, the truth: I have always felt, deep within, unintelligent. I think I pretend. What I mean is that, while I'm sure I come across as reasonably smart, beneath this layer I have a real fear about questioning another human being too deeply, fighting for a point of view, or speaking my mind, always assuming that the other person is smarter than I am, and that, if my pretence layer gets stripped away, the truth of my unintelligence will be outed. The horrible reality, however, is that I am a voice teacher. It is my professional responsibility to create the circumstances in a studio or classroom for actors to question, to fight for a point of view, and to exclaim it with passion! Somehow I had not given myself permission to do the same. And so, entering the land of PhDs, experts, and academics, I was bone-chillingly terrified. The jig was up. These people had written things! Books! Conference papers! My mind swam. What could I talk about? What could I possibly offer? Why was I here? [ILLUSTRATION OMITTED] What I discovered in the Santorini landscape of startling white and deepest blue, with that special group of human beings, was that I am a philosopher. And that I am smart. And that I am a researcher. I cannot express how meaningful this realization was to me. I was respected as a researcher and as an equal. Advice was sought. Ideas were exchanged. Questions were asked. This may seem silly, but I always believed that being intelligent meant reading something once and understanding it. When I heard the philosophers talk about researching the same texts for twenty years, I was stunned. And relieved. And stunned again: it suddenly occurred to me that that's what I do. I am a philosopher of the body! I have been on a research expedition for sixteen years. …
New Insight on the Unusually High Ionic Mobility in Chevrel Phases (2009)

Chevrel Phases (CPs), MxMo6T8 (M = metal, T = S, Se) are unique materials, which allow for a fast and reversible insertion of various cations at RT. Earlier, CPs were divided into two major types: type I with large immobile cations, which block any ionic transport in the diffusion channels, and type II with small mobile cations. Our analysis of available experimental data shows that the transport behavior in CPs cannot be understood in the framework of the blocking concept; it is much more complex and includes: (i) apparent immobility of the large M cations like Pb2+, Sn2+, Ag+ in the ternary phases, MMo6T8; (ii) coupled M + M′ diffusion in the quaternary phases, MxM′yMo6T8, where both large and small cations can assist; (iii) cation trapping in the Mg−Mo6S8, Cd−Mo6S8, and Na−Mo6T8 systems; (iv) a combination of low and high rate diffusion kinetics at the first and last intercalation stages, respectively, for the Cu−Mo6S8, Mn−Mo6S8, and Cd−Mo6Se8 systems; and (v) a fast ionic transport for small cations like Ni2+, Zn2+, and Li+. A general structural approach (analysis of the polyhedral linkage in the diffusion channels of CPs and mapping of all the cation sites combined with their bond valence sum values and the distances from the adjacent Mo atoms) used for the first time for a variety of CPs shows two competing diffusion pathways of inserted ions for most of CPs: circular motion within the same cavity between the Mo6T8 blocks with activation energy Ec, and progressive diffusion from one cavity to the adjacent one with activation energy Ed. The character of the ionic transport depends mostly on the distribution of the repulsive forces for the inserted cations, as well as on the Ed/Ec ratio, affected in turn by the cation position, its size, cation−Mo interactions, and the anion nature.
Multiagent Meta-level Control for a Network of Weather Radars. (2010)

It is crucial for embedded systems to adapt to the dynamics of open environments. This adaptation process becomes especially challenging in the context of multiagent systems. In this paper, we argue that multiagent meta-level control is an effective way to determine when this adaptation process should be done and how much effort should be invested in adaptation as opposed to continuing with the current action plan. We develop a reinforcement learning based mechanism for multiagent meta-level control that facilitates the metalevel control component of each agent to learn policies in a decentralized fashion that (a) it can efficiently support agent interactions with other agents and (b) reorganize the underlying network when needed. We evaluate this mechanism in the context of a multiagent tornado tracking application called NetRads. Empirical results show that adaptive multiagent meta-level control significantly improves the performance of the tornado tracking network for a variety of weather scenarios.
Double atom interferometer (1998)

A double atom interferometer based upon the Stern-Gerlach method in which the first interferometer acts as a ``nonordinary'' source for the second one is described. Experiments have been carried out with a wide-velocity-distribution beam of metastable hydrogen atoms, using two different operating modes: (i) continuous mode in which the magnitude of the magnetic field in the first interferometer is fixed whereas that of the second one is scanned; (ii) time-of-flight mode in which both magnetic fields are fixed. In the former case lateral interference patterns appear, in the latter one an overmodulation of the time-of-flight distribution is observed. It is predicted that this overmodulation becomes more and more marked as the number of interferometers is increased, leading to a limiting behavior characteristic of a quantum Zeno effect.
Characterization of a Congenitally LPS-Resistant, Athymic Mouse Strain (1979)

C57BL/10ScN (nu/nu) mice have B cells and macrophages unresponsive to a phenol-water extracted preparation of Escherichia coli K 235 LPS. This unresponsiveness was demonstrated in vitro by the inability of spleen cells to incorporate 3H-thymidine after a 48 hr incubation with LPS (Ph) and by the inability of LPS (Ph) to inhibit macrophage phagocytosis of 51 Cr-labeled, opsonized sheep erythrocytes. Furthermore, macrophage cultures stimulated with LPS (Ph) produced low levels of LAF and PGE2 when compared with macrophages from the LPS-sensitive C3H/HeN and C3H/HeN (nu/nu) strains. Therefore, the C57BL/10ScN (nu/nu) strain is similar in its LPS unresponsiveness to the well-characterized C3H/HeJ and C57BL/10ScCR strains. The combination of endotoxin unresponsiveness and the athymic nature of this mouse strain may provide a powerful new tool for studying the cellular events mediating endotoxicity.
Leupaxin Is a Novel LIM Domain Protein That Forms a Complex with PYK2 (1998)

We have identified a novel cytoplasmic protein, leupaxin, that is preferentially expressed in hematopoietic cells and is most homologous to the focal adhesion protein, paxillin. Leupaxin possesses two types of protein interaction domains. There are four carboxyl-terminal LIM domains in leupaxin that share 70% amino acid identity and 80% similarity with those in paxillin. Paxillin LIM domains mediate localization to focal contacts. In the amino-terminal region of leupaxin there are three short stretches of approximately 13 amino acids that share 70-90% similarity with paxillin LD motifs. Paxillin LD motifs have been implicated in focal adhesion kinase (FAK) and vinculin binding resulting in the localization of FAK to focal adhesions. Leupaxin is expressed in cell types, such as macrophage, that lack FAK. We demonstrate here that leupaxin associates with a second FAK family member, PYK2. As leupaxin and PYK2 are both preferentially expressed in leukocytes they may therefore form a cell type-specific signaling complex. We also demonstrate that leupaxin is a substrate for a tyrosine kinase in lymphoid cells and thus may function in and be regulated by tyrosine kinase activity. Leupaxin is thus a phosphotyrosine protein with LD and LIM binding motifs most homologous to paxillin that may assemble and regulate PYK2 signaling complexes in leukocytes.
Isolation of a new HIV-2 group in the US (2008)

Human immunodeficiency virus type 2 (HIV-2) emerged following cross-species transmission of simian immunodeficiency virus (SIV) from sooty mangabeys to humans several decades ago. The epidemic groups of HIV-2 have been established in the human population for at least 50 years. However, it is likely that new divergent SIVs can infect humans and lead to new outbreaks. We report the isolation of a new strain of HIV-2, HIV2-NWK08F, from an immunodeficient Sierra Leone immigrant. Health care providers in Sierra Leone and elsewhere need to be alerted that a subtype of HIV-2, which is not detected by PCR for epidemic HIV-2 strains, exists and can lead to immunosuppression.
ChemInform Abstract: Regioselective Synthesis of 6‐Halomethyl‐5,6‐dihydro‐4H‐1,2‐oxazines Based on Cyclizations of Arylalkenyl‐Oximes. (2008)

Abstract ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 200 leading journals. To access a ChemInform Abstract of an article which was published elsewhere, please select a “Full Text” option. The original article is trackable via the “References” option.
An editor's worst nightmare (2009)

Well, it must be a magazine editor's worst nightmareâ?¦The latest issue of Q magazine dropped through my door today. It had a full page front cover of Michael Jackson. Well, at first I didnâ??t give it a second glance because Jackson's picture has been everywhere. But then it occurred to me that it was impossible that the magazine could have been printed and posted so quickly. Then the horrible truth dawned on me as I ripped oven the plastic cover..
SYNCHRONOUS FLYBACK CONVERTER WITH SYNCHRONOUS BUCK POST REGULATOR (2014)

In general, conventional converter is used for converting the power level from one stage to another. But conventional type of converter has slightly more power losses & voltage drop, so efficiency is very sensitive for the low voltage specification and also cooling of dissipative elements floating at higher voltages is a difficult task. So high efficient scheme of synchronous flyback converter with synchronous buck post regulator was approached and low voltage drop, less power losses & very high efficiency was achieved.
JDI-T: Jointly trained Duration Informed Transformer for Text-To-Speech without Explicit Alignment (2020)

We propose Jointly trained Duration Informed Transformer (JDI-T), a feed-forward Transformer with a duration predictor jointly trained without explicit alignments in order to generate an acoustic feature sequence from an input text. In this work, inspired by the recent success of the duration informed networks such as FastSpeech and DurIAN, we further simplify its sequential, two-stage training pipeline to a single-stage training. Specifically, we extract the phoneme duration from the autoregressive Transformer on the fly during the joint training instead of pretraining the autoregressive model and using it as a phoneme duration extractor. To our best knowledge, it is the first implementation to jointly train the feed-forward Transformer without relying on a pre-trained phoneme duration extractor in a single training pipeline. We evaluate the effectiveness of the proposed model on the publicly available Korean Single speaker Speech (KSS) dataset compared to the baseline text-to-speech (TTS) models trained by ESPnet-TTS.
The Small Molecule IMR-1 Inhibits the Notch Transcriptional Activation Complex to Suppress Tumorigenesis (2016)

In many cancers, aberrant Notch activity has been demonstrated to play a role in the initiation and maintenance of the neoplastic phenotype and in cancer stem cells, which may allude to its additional involvement in metastasis and resistance to therapy. Therefore, Notch is an exceedingly attractive therapeutic target in cancer, but the full range of potential targets within the pathway has been underexplored. To date, there are no small-molecule inhibitors that directly target the intracellular Notch pathway or the assembly of the transcriptional activation complex. Here, we describe an in vitro assay that quantitatively measures the assembly of the Notch transcriptional complex on DNA. Integrating this approach with computer-aided drug design, we explored potential ligand-binding sites and screened for compounds that could disrupt the assembly of the Notch transcriptional activation complex. We identified a small-molecule inhibitor, termed Inhibitor of Mastermind Recruitment-1 (IMR-1), that disrupted the recruitment of Mastermind-like 1 to the Notch transcriptional activation complex on chromatin, thereby attenuating Notch target gene transcription. Furthermore, IMR-1 inhibited the growth of Notch-dependent cell lines and significantly abrogated the growth of patient-derived tumor xenografts. Taken together, our findings suggest that a novel class of Notch inhibitors targeting the transcriptional activation complex may represent a new paradigm for Notch-based anticancer therapeutics, warranting further preclinical characterization. Cancer Res; 76(12); 3593-603. ©2016 AACR.