gebhart/patrepeval huggingface dataset:
Human allograft acceptance is associated with immune regulation (2000)

The ultimate goal of transplantation is drug-free allograft acceptance, which is rarely encountered in transplant recipients. Using a novel human-to-mouse "trans vivo" delayed-type hypersensitivity assay, we assessed donor-reactive cell-mediated immune responses in kidney and liver transplant patients, four of whom discontinued all immunosuppression. One of these subjects (J.B.) rejected his graft after 7 years of stable function, while the others (D.S., R.D., M.L.) continue to have excellent graft function 5, 28, and 4 years after the cessation of immunosuppression. PBMCs from J.B. exhibited strong responses to both donor and recall antigens whereas PBMCs from patients D.S., R.D., and M.L. responded strongly to recall, but not donor, antigens. Furthermore, when donor and recall antigens were colocalized, the recall response in these three patients was inhibited. This donor antigen-linked nonresponsiveness was observed in four other patients who are still maintained on immunosuppression. The weakness of donor-reactive DTH responses in these patients is due to donor alloantigen-triggered regulation that relies on either TGF-beta or IL-10. In D.S., regulation is triggered by a single donor HLA Class I antigen, either in membrane-bound or soluble form. This demonstrates that allograft acceptance in humans is associated with an immune regulation pattern, which may be useful in the diagnosis and/or monitoring of transplant patients for allograft acceptance.
Introduction to Next Generation Sequencing Technologies (2017)

The skills required to apply computational analysis to target research on a wide range of applications that include identifying causes of cancer, vaccine design, new antibiotics, drug development, personalized medicine and higher crop ...
Intestinal Hyperplasia Induced by Simian Virus 40 Large Tumor Antigen Requires E2F2 (2007)

The simian virus 40 large T antigen contributes to neoplastic transformation, in part, by targeting the Rb family of tumor suppressors. There are three known Rb proteins, pRb, p130, and p107, all of which block the cell cycle by preventing the transcription of genes regulated by the E2F family of transcription factors. T antigen interacts directly with Rb proteins and disrupts Rb-E2F complexes both in vitro and in cultured cells. Consequently, T antigen is thought to inhibit transcriptional repression by the Rb family proteins by disrupting their interaction with E2F proteins, thus allowing E2F-dependent transcription and the expression of cellular genes needed for entry into S phase. This model predicts that active E2F-dependent transcription is required for T-antigen-induced transformation. To test this hypothesis, we have examined the status of Rb-E2F complexes in murine enterocytes. Previous studies have shown that T antigen drives enterocytes into S phase, resulting in intestinal hyperplasia, and that the induction of enterocyte proliferation requires T-antigen binding to Rb proteins. In this paper, we show that normal growth-arrested enterocytes contain p130-E2F4 complexes and that T-antigen expression destroys these complexes, most likely by stimulating p130 degradation. Furthermore, unlike their normal counterparts, enterocytes expressing T antigen contain abundant levels of E2F2 and E2F3a. Concomitantly, T-antigen-induced intestinal proliferation is reduced in mice lacking either E2F2 alone or both E2F2 and E2F3a, but not in mice lacking E2F1. These studies support a model in which T antigen eliminates Rb-E2F repressive complexes so that specific activator E2Fs can drive S-phase entry.
Novel high efficiency low ripple charge pump using variable frequency modulation (2010)

A novel charge pump with variable frequency modulation (VFM) is proposed in this paper. To provide base for its design and improvement, detailed models for VFM charge pump are derived. And it is successfully implemented for the charge pump to introduce a voltage controlled oscillator (VCO) to control the switching frequency, which results in its high efficiency and low ripple output both at high load and light load. The chip is designed and fabricated in TSMC 0.35um mixed signal process. The simulation and test results show that high efficiency (up to 75%) and very low ripple output ( around 10 mV) is realized as expected. Besides, the accuracy of the model's prediction is proved.
Role of calcium channel subtypes in calcium transients in hippocampal CA3 neurons (1995)

Multiple subtypes of voltage-gated calcium channels are differentially localized in brain neurons suggesting that they serve distinct roles in neuronal excitation and signaling. In organotypic hippocampal slice cultures, class D (L-type) calcium channels are predominantly located in the cell bodies of CA3 neurons while class B (N-type) and class A (P or Q-type) are localized in dendrites and associated presynaptic terminals with relatively low somal expression. Using specific antagonists to inhibit calcium transients recorded in CA3 neuronal cell bodies, we found that L-type calcium channels have a predominant role in somal calcium transients elicited by trains of strong stimuli applied to either the soma or the distal apical dendrite while class A calcium channels make a smaller contribution. Presynaptic class B (N- type) and class A (P- and/or Q-type) calcium channels are critical for glutamate-mediated synaptic transmission onto the dendrites of CA3 neurons. Postsynaptic class A and B calcium channels detected on the dendritic shaft by immunocytochemistry were not found to contribute substantially to somal calcium transients during repetitive stimulation of distal dendrites, but sodium channels were required for calcium transients elicited by somatic or dendritic stimulation. Our results show that the different calcium channel subtypes serve distinct roles in cellular activation and transmission of signals in CA3 neurons, consistent with their differential subcellular localization.
Progress In Otdr Optical Fiber Sensor Networks (1987)

There is great interest for distributed or multiplexed fiber optic sensor networks for process control automation. Optical Time Domain Reflectometry (OTDR) is a potentially very useful method for monitoring several sensors distributed along a fiber, but its actual capabilities, using present concepts, are too restricted to allow competitive industrial performance. We present here a novel scheme of OTDR fiber sensor multiplexing which allows, ,the monitoring of up to 50 ON/OFF switches along a given fiber under practical and realistic conditions. Detection of reflected, rather than backscattered, light makes much better use of the in-line loss introduced by each sensor, yielding a larger dynamic range which explains this very significant improvement in the number of multiplexed sensors. Theoretical considerations about this novel scheme and its limits, taking into account present OTDR technology, are presented together with experimental results of a twenty ON/OFF sensor network feasibility prototype .
Generative modeling for continuous non-linearly embedded visual inference (2004)

Many difficult visual perception problems, like 3D human motion estimation, can be formulated in terms of inference using complex generative models, defined over high-dimensional state spaces. Despite progress, optimizing such models is difficult because prior knowledge cannot be flexibly integrated in order to reshape an initially designed representation space. Nonlinearities, inherent sparsity of high-dimensional training sets, and lack of global continuity makes dimensionality reduction challenging and low-dimensional search inefficient. To address these problems, we present a learning and inference algorithm that restricts visual tracking to automatically extracted, non-linearly embedded, low-dimensional spaces. This formulation produces a layered generative model with reduced state representation, that can be estimated using efficient continuous optimization methods. Our prior flattening method allows a simple analytic treatment of low-dimensional intrinsic curvature constraints, and allows consistent interpolation operations. We analyze reduced manifolds for human interaction activities, and demonstrate that the algorithm learns continuous generative models that are useful for tracking and for the reconstruction of 3D human motion in monocular video.
Kerberos: an authentication service for computer networks (1994)

When using authentication based on cryptography, an attacker listening to the network gains no information that would enable it to falsely claim another's identity. Kerberos is the most commonly used example of this type of authentication technology. The authors concentrate on authentication for real-time, interactive services that are offered on computer networks. They use the term real-time loosely to mean that a client process is waiting for a response to a query or command so that it can display the results to the user, or otherwise continue performing its intended function. This class of services includes remote login, file system reads and writes, and information retrieval for applications like Mosaic.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>
Design of an Advanced Programmable Current-Source Gate Driver for Dynamic Control of SiC Device (2019)

Silicon carbide (SiC) power devices outperform Silicon-based devices in operational voltage levels, power densities, operational temperatures and switching frequencies. However, the gate oxide of SiC-based device is more fragile compared with its Si counterpart. The vulnerability of the gate oxide in SiC power devices requires the development of a gate driver that is able to have more control during the turn-on and turn-off process. This paper proposes an innovative current-source gate driver where the gate current can be fully programmed. The novelty of the gate driver is that the dynamic switching transients and the static on/off-state can be controlled independently. In order to achieve this approach, a signal decomposition and reconstruction technique is proposed to apply the separate control over the dynamic switching transient and the static on/off-state gate voltage respectively. The fundamental principle of the proposed circuit is verified in simulation. In addition, a prototype of the active gate driver has been built and tested to validate the effectiveness of the flexible control over the gate voltage.
Unsupervised Transcription of Historical Documents (2013)

We present a generative probabilistic model, inspired by historical printing processes, for transcribing images of documents from the printing press era. By jointly modeling the text of the document and the noisy (but regular) process of rendering glyphs, our unsupervised system is able to decipher font structure and more accurately transcribe images into text. Overall, our system substantially outperforms state-of-the-art solutions for this task, achieving a 31 % relative reduction in word error rate over the leading commercial system for historical transcription, and a 47 % relative reduction over Tesseract, Google’s open source OCR system. 1
Aberrant promoter methylation of the transcription factor genes PAX5 alpha and beta in human cancers. (2003)

Aberrant methylation of 5'CpG islands is a key epigenetic event in many human cancers. A PCR-based technique of methylated CpG island amplification followed by representational difference analysis was used to identify genes methylated in cancer. Two of the CpG islands identified mapped to the 5' untranslated region of the PAX5 alpha and beta genes. These genes, located on chromosome 9p13, are transcribed from two distinct promoters and form two alternative first exons that are subsequently spliced to the common exons 2-10. The resulting splice variants encode two distinct transcription factors important in cell differentiation and embryonic development. Examination of the methylation status of each gene using methylation-specific PCR revealed that both genes are methylated in approximately 65% of breast and lung tumors. Bisulfite sequencing revealed dense methylation patterns within each 5'CpG island, strongly correlating with transcriptional silencing. Expression in cell lines with dense methylation of either the PAX5 alpha or beta promoter region was restored after treatment with the demethylating agent 5-Aza-2'-deoxycytidine. The PAX5 beta gene encodes for the transcription factor B cell-specific activating protein that, in turn, directly regulates CD19, a gene shown to negatively control cell growth. A strong association was observed between PAX5 beta methylation and loss of expression of the CD19 gene demonstrating that inactivation of the PAX5 beta gene likely contributes to neoplastic development by inhibiting growth regulation through effects on CD19 gene expression. Recent studies have demonstrated the importance of PAX5 gene alterations in human cancer. Our results are the first to identify aberrant promoter methylation as a common mechanism for dysregulation of these genes in solid tumors.
GeneMANIA Cytoscape plugin: fast gene function predictions on the desktop (2010)

The GeneMANIA Cytoscape plugin is implemented in Java and is freely available at http://www.genemania.org/plugin/.
Metacognition in 3-6 Years Old:Evidence from a Kindergarten in Hong Kong (2013)

The study explores metacognition in young children of 3-6 years old. It presents finding from a study
exploring the development of self-regulatory and metacognitive abilities in young children. The study
takes the form of a descriptive, interpretative investigation using both quantitative and qualitative
research methods. It involved 60 children in a local kindergarten in Hong Kong to participate in three
different activities. Children participated in the activities were either done without any helped or with
some forms of support. The first two activities were conducted two times, children needed to finish the
task on their own the first time and with help the second time. For the third activity, the children were
divided into a control and an experimental group while the control group needed to finish the task on
their own and support was provided to the experimental group. In the first two activities quantitative data
was collected according to the correct amount of items children were able to remember and in the third
activity, a score was given to each child based on their metacognitive ability using the rubrics from
Project Spectrum as reference. Qualitative data was collected in all three activities based on their
behavioural performance in each activity that was video-taped. The findings showed children in age 3-6
years old have a certain sense of metacognition and the older the children the more traits of
metacognitive ability can be seen during the tasks. Furthermore, in a meaningful task with different
external factors provided, children were able to perform better.
<i>In vitro</i>measurements of absolute blood oxygen saturation using pulsed near-infrared photoacoustic spectroscopy: accuracy and resolution (2005)

Pulsed photoacoustic spectroscopy was used to measure blood oxygen saturation in vitro. An optical parametric oscillator laser system provided nanosecond excitation pulses over the wavelength range 740-1040 nm which were used to generate photoacoustic signals in a cuvette through which a saline suspension of red blood cells was circulated. The signal amplitude and the effective attenuation coefficient were extracted from the photoacoustic signals as a function of wavelength to provide photoacoustic spectra of the blood. From these, the relative concentrations of oxy- and deoxyhaemoglobin, and therefore blood oxygen saturation (SO2), were determined using forward models of the absorbed energy distribution based on diffusion theory. A standard linear model of the dependence of absorbance on the concentration of chromophores was also used to calculate the blood oxygen saturation from the signal amplitude spectra. The diffusion approximation model was shown to produce the highest accuracy in blood SO2. The photoacoustically determined oxygen saturation was found to have an accuracy of +/-4% SO2 for signal amplitude data and +/-2.5% SO2 for effective attenuation spectra. The smallest change in oxygen saturation that can be measured using this technique was +/-1% SO2.
Diagnosis of pregnancy (2011)

This issue of eMedRef provides information to clinicians on the pathophysiology, diagnosis, and therapeutics of pregnancy.
The assessment of the antibacterial and antifungal activities of aspirin, EDTA and aspirin-EDTA combination and their effectiveness as antibiofilm agents (2009)

There is a continuous need for the discovery of new antimicrobial agents. Aspirin and EDTA are 'nonantibiotic drugs', the combination of which can be used successfully to treat and eradicate biofilms established on abiotic surfaces.
Dramatic inhibition of osteoclast sealing ring formation and bone resorption in vitro by a WASP-peptide containing pTyr294 amino acid (2008)

Wiskott Aldrich Syndrome protein (WASP) has a unique regulatory role in sealing ring formation and bone resorption in osteoclasts. Here, using the TAT-transduction method, we show the possible role of WASP domain(s) in sealing ring formation and bone resorption. Transduction of TAT-fused full-length WASP peptide induced Arp2/3 complex formation, F-actin content, sealing ring formation and bone resorption. Transduction of WASP peptides containing basic, verpolin-central, pTyr294, and proline-rich regions inhibited the processes listed above at various levels. The ability to resorb bone by WASP peptides containing basic, verpolin-central, and proline-rich regions was reduced and the resorbed area matched the size of the sealing ring. However, osteoclasts transduced with WASP peptide containing pTyr294aa demonstrated the following: a) a considerable decrease in the interaction and phosphorylation of c-Src with endogenous WASP; b) total loss of sealing ring-like structures; c) formation of actin-rich patches at the peripheral edge that contains filopodia-like projections; d) reduced capacity for bone resorption in vitro. These findings suggest that modulation of phosphorylation state of pTyr294aa assists in integrating multiple signaling molecule and pathways that partake in the assembly of sealing ring.
Analysis of Transmission Lines on Integrated-Circuit Chips (1967)

The availability of very fast semiconductor switching devices and the possibilities of large scale integration have increased the importance of the interconnection problem for the design of high-speed computers. The interconnection delay represents a fundamental boundary which limits the ultimate speed of logic circuits. The transmission-line behavior of interconnections on integrated-circuit chips, especially for subnanosecond applications, is the prime concern of this paper. A lumped circuit model is proposed and justified on physical and experimental grounds. It is shown that interconnections behave like RC transmission lines at low frequencies, with the effect of inductance showing up at midrange and high frequencies. Some simple formulas are included for design use.
A 93-to-113GHz BiCMOS 9-element imaging array receiver utilizing spatial-overlapping pixels with wideband phase and amplitude control (2013)

Benefiting from aggressive feature size scaling, silicon technologies have recently shown the capability of implementing W-band imaging receivers with an image resolution of 1.5mm and temperature resolutions of less than 0.5K [1-4]. This paper extends the capability of an imaging array receiver by improving image resolution using the novel concept of spatial-overlapping sub-arrays and enhancing image capture time using a phased-array within an imaging array receiver (RX). Specifically, the design and implementation of a BiCMOS 9-element array RX consisting of four 2×2 overlapping sub-arrays is presented. The RF-path-sharing between neighboring sub-arrays leads to a reduction in the chip area by 40% as compared to a conventional imaging array consisting of four 2×2 non-overlapping sub-arrays, while improving the RX's spatial resolution due to the higher sub-array density. Each 2×2 sub-array in this imaging array RX forms a pixel (Fig. 8.5.1).
Structure, stereochemistry, and thermal isomerization of the male sex pheromone of the longhorn beetle Anaglyptus subfasciatus. (1995)

Male-released sex pheromone constituents of the longhorn beetle Anaglyptus subfasciatus (Coleoptera: Cerambycidae) are identified by GC-MS and GC-Fourier transform infrared as a 7:1 molar mixture of 3-hydroxy-2-hexanone and 3-hydroxy-2-octanone. These two compounds undergo thermal isomerization during GC analyses to give the corresponding 2-hydroxy-3-alkanones. Comparison of GC retention times of the natural products with those of synthesized enantiomerically pure compounds revealed that both semiochemicals have (R)-stereochemistry. These absolute configurations were confirmed by comparisons of the (R)-methoxy(trifluoromethyl)phenylacetic acid esters of insect-derived and synthetic samples.
Soluble silk‐like organic matrix in the nacreous layer of the bivalve <i>Pinctada maxima</i> (2002)

Nacre organic matrix has been conventionally classified as both 'water-soluble' and 'water-insoluble', based on its solubility in aqueous solutions after decalcification with acid or EDTA. Some characteristics (aspartic acid-rich, silk-fibroin-like content) were specifically attributed to either one or the other. The comparative study on the technique of extraction (extraction with water alone vs. demineralization with EDTA) presented here, seems to reveal that this generally accepted classification may need to be reconsidered. Actually, the nondecalcified soluble organic matrix, extracted in ultra-pure water, displays many of the characteristics of what until now has been called 'insoluble matrix'. We present the results obtained on this extract and on a conventional EDTA-soluble matrix, with various characterization methods: fractionation by size-exclusion and anion-exchange HPLC, amino acid analysis, glycosaminoglycan and calcium quantification, SDS/PAGE and FTIR spectroscopy. We propose that the model for the interlamellar matrix sheets of nacre given by Nakahara [In: Biomineralization and Biological Metal Accumulation, Westbroek, P. & deJong, E.W., eds, (1983) pp. 225-230. Reidel, Dordrecht, Holland] and Weiner and Traub [Phil. Trans. R. Soc. Lond. B (1984) 304, 425-434] may no longer be valid. The most recent model, proposed by Levi-Kalisman et al. [J. Struct. Biol. (2001) 135, 8-17], seemed to be more in accordance with our findings.
Transcriptional regulation of the human factor IX promoter by the orphan receptor superfamily factors, HNF4, ARP1 and COUP/Ear3 (1996)

A study of the human clotting factor IX promoter by DNase I footprinting and gel shifts in vitro, and by functional analysis of HepG2 cells in vivo, suggests that the liver-enriched transcription factor, HNF4, is involved in transactivating two cis-acting elements, i.e. X (nucleotides -15 to +3) and Y (nucleotides +15 to +36), in addition to the well-known element centred around nucleotide -20. Other members of the orphan receptor superfamily, e.g. ARP1 and COUP/Ear3, repress the factor IX promoter possibly by competition with HNF4 binding sites in the X and Y elements, but probably not at the -20 element. Mutations at -6 in the promoter, similar to those found in patients with haemophilia B, hinder HNF4 binding and transactivation of the X element, suggesting that impaired HNF4 binding contributes to the down-regulation of the factor IX expression in these patients, but is unlikely to be the only factor involved.