gebhart/patrepeval huggingface dataset:
Analysis of T-cell immune response in renal cell carcinoma: Polarization to type 1-like differentiation pattern, clonal T-cell expansion and tumor-specific cytotoxicity (1997)

We assessed the naturally occurring T-cell immune response in primary renal cell carcinoma (RCC) tumors from 12 unselected patients. A predominance of CD3+ T-cell receptor (TCR)alpha/beta+ T cells was observed in tumor-infiltrating lymphocytes (TILs), in contrast with peripheral blood lymphopenia found in some patients. Activation antigen expression on TILs revealed an imbalance in the activation status, with a significant percentage of CD69+ and HLA-DR+ and a low percentage of CD25+ and CD71+ TILs. The lymphocyte activation gene-3 (LAG-3) was detected in some TIL subpopulations and especially in one patient in whom TILs were predominantly TCR alpha/beta+CD8+DR+LAG-3+. In addition, we found that RCC TILs are polarized to a global type 1-like (Th1/Tc1) differentiation pattern (strong secretion of interferon-gamma and interleukin-2 (IL-2) following CD3/TCR crosslinking) but are under the influence of the down-modulatory cytokines IL-6 (secreted by tumor cells) and IL-10, within the tumor microenvironment. In 3 of 5 patients, clonal T-cell expansion at the tumor site was found for several Vbeta specificities, suggesting that in situ stimulation of specific clonotypes in response to potential tumor antigens is a frequent event in RCC. Furthermore, in one patient, selective intratumor amplification of a Vbeta1 subpopulation (5% of TCR alpha/beta+ cells) corresponding to 2 distinct Vbeta1-Jbeta1.6 and Vbeta1-Jbeta2.3 tumor-specific MHC class I-restricted cytotoxic T lymphocytes supports the view that discrete T-cell subsets contribute readily to in situ immunosurveillance.
Concise Review: Role of Mesenchymal Stem Cells in Wound Repair (2012)

Wound healing requires a coordinated interplay among cells, growth factors, and extracellular matrix proteins. Central to this process is the endogenous mesenchymal stem cell (MSC), which coordinates the repair response by recruiting other host cells and secreting growth factors and matrix proteins. MSCs are self-renewing multipotent stem cells that can differentiate into various lineages of mesenchymal origin such as bone, cartilage, tendon, and fat. In addition to multilineage differentiation capacity, MSCs regulate immune response and inflammation and possess powerful tissue protective and reparative mechanisms, making these cells attractive for treatment of different diseases. The beneficial effect of exogenous MSCs on wound healing was observed in a variety of animal models and in reported clinical cases. Specifically, they have been successfully used to treat chronic wounds and stimulate stalled healing processes. Recent studies revealed that human placental membranes are a rich source of MSCs for tissue regeneration and repair. This review provides a concise summary of current knowledge of biological properties of MSCs and describes the use of MSCs for wound healing. In particular, the scope of this review focuses on the role MSCs have in each phase of the wound-healing process. In addition, characterization of MSCs containing skin substitutes is described, demonstrating the presence of key growth factors and cytokines uniquely suited to aid in wound repair.
Synthesis and Rheological Behavior of New Hydrophobically Modified Hydrogels with Tunable Properties (2006)

New hydrophobically modified hydrogels have been designed in order to obtain a series of gels with identical elastic moduli but variable dissipative properties. The synthesis of these systems has been realized following a three-step procedure: (1) introduction of double bonds onto a poly(acrylic acid) backbone [PAA], (2) hydrophobic modification of the PAA with dodecylamine, and (3) cross-linking of double bonds using dithiol. The characterization of gel precursors shows that hydrophobically modified polymers self-assemble in semidilute solution forming physical gels with temporary hydrophobic clusters. The gelation mechanism induced by reacting pendant double bonds with dithiol was studied by DSC, specific titrations, and rheology. The gelation process was not perturbed by the presence of the hydrophobic groups, and the kinetics follows a first-order dependence on thiol. In the entangled regime, the thiol conversion reaches around 80%, but only about 10% of the thiols effectively promote the formation of chemical cross-links while the other 90% are incorporated into the gel as loops or dangling chains. Once the gels are formed, NMR and SANS clearly demonstrate that hydrophobic side chains continue to form micelles within the network and that these micelles display a much better long-range order than their un-cross-linked precursors in aqueous solutions. All gels, both hydrophilic and hydrophobically modified, display a storage modulus G‘ which only depends on total polymer concentration and can be described on the basis of the percolation theory (G‘ ∼ ε2.6) with ε, the reduced concentration defined from a fixed concentration at the gel point Cg = 2%. On the other hand, the loss modulus G‘ ‘ increases dramatically relative to the corresponding hydrophilic gel, when hydrophobic groups which formed reversible associations are introduced.
Configuration prefetch for single context reconfigurable coprocessors (1998)

Current reconfigurable systems suffer from a significant overhead due to the time it takes to reconfigure their hardware. In order to deal with this overhead, and increase the power of reconfigurable systems, it is important to develop hardware and software systems to reduce or eliminate this delay. In this paper we propose one technique for significantly reducing the reconfiguration latency: the prefetching of configurations. By loading a configuration into the reconfigurable logic in advance of when it is needed, we can overlap the reconfiguration with useful computation. We demonstrate the power of this technique, and propose an algorithm for automatically adding prefetch operations into reconfigurable applications. This results in a significant decrease in the reconfiguration overhead for these applications.
Intravital Microscopy on a Closed Cranial Window in Mice: A Model to Study Trigeminovascular Mechanisms Involved in Migraine (2006)

The purpose of the study was to develop a mouse model to study trigeminovascular mechanisms using intravital microscopy on a closed cranial window. In addition, we studied exogenous and endogenous calcitonin gene-related peptide (CGRP)-mediated vasodilation in dural arteries. Arteries in C57BL/6Jico mice were constricted with endothelin-1, which reduced the baseline diameter by 65-75%. Subsequently, vasodilation was induced by alpha-CGRP, capsaicin or transcranial electrical stimulation of perivascular trigeminal nerves in the absence or presence of different concentrations of BIBN4096BS or sumatriptan. Both alpha-CGRP and capsaicin induced vasodilation in preconstricted arteries. Transcranial electrical stimulation also induced current-dependent relaxation of dural arteries with 100 microA producing maximal dilation in the control group. BIBN4096BS blocked the responses evoked by alpha-CGRP and capsaicin, as well as electrical stimulation, whereas sumatriptan attenuated only vasodilation induced by electrical stimulation. This model is likely to prove useful in dissecting elements of the trigeminovascular system and for exploring pathophysiological aspects of migraine, especially in future studies using transgenic mice with mutations relevant to those observed in patients with migraine.
Nanoparticle conjugation of CpG enhances adjuvancy for cellular immunity and memory recall at low dose (2013)

In subunit vaccines, strong CD8(+) T-cell responses are desired, yet they are elusive at reasonable adjuvant doses. We show that targeting adjuvant to the lymph node (LN) via ultrasmall polymeric nanoparticles (NPs), which rapidly drain to the LN after intradermal injection, greatly enhances adjuvant efficacy at low doses. Coupling CpG-B or CpG-C oligonucleotides to NPs led to better dual-targeting of adjuvant and antigen (codelivered on separate NPs) in cross-presenting dendritic cells compared with free adjuvant. This led to enhanced dendritic cell maturation and T helper 1 (Th1)-cytokine secretion, in turn driving stronger effector CD8(+) T-cell activation with enhanced cytolytic profiles and, importantly, more powerful memory recall. With only 4 μg CpG, NP-CpG-B could substantially protect mice from syngeneic tumor challenge, even after 4 mo of vaccination, compared with free CpG-B. Together, these results show that nanocarriers can enhance vaccine efficacy at a low adjuvant dose for inducing potent and long-lived cellular immunity.
Linear FMCW radar techniques (1992)

Frequency modulated continuous wave (FMCW) radar uses a very low probability of intercept waveform, which is also well suited to make good use of simple solid-state transmitters. FMCW is finding applications in such diverse fields as naval tactical navigation radars, smart ammunition sensors and automotive radars. The paper discusses some features of FMCW radar which are not dealt with in much detail in the generally available literature. In particular, it discusses the effects of noise reflected back from the transmitter to the receiver and the application of moving target indication to FMCW radars. Some of the strengths and weaknesses of FMCW radar are considered. The paper describes how the strengths are utilised in some systems and how the weaknesses can be mitigated. It also discusses a modern implementation of a reflected power canceller, which can be used to suppress the leakage between the transmitter and the receiver, a well known problem with continous wave radars.
Decoding Substitution Ciphers by Means of Word Matching with Application to OCR (1987)

A substitution cipher consists of a block of natural language text where each letter of the alphabet has been replaced by a distinct symbol. As a problem in cryptography, the substitution cipher is of limited interest, but it has an important application in optical character recognition. Recent advances render it quite feasible to scan documents with a fairly complex layout and to classify (cluster) the printed characters into distinct groups according to their shape. However, given the immense variety of type styles and forms in current use, it is not possible to assign alphabetical identities to characters of arbitrary size and typeface. This gap can be bridged by solving the equivalent of a substitution cipher problem, thereby opening up the possibility of automatic translation of a scanned document into a standard character code, such as ASCII. Earlier methods relying on letter n-gram frequencies require a substantial amount of ciphertext for accurate n-gram estimates. A dictionary-based approach solves the problem using relatively small ciphertext samples and a dictionary of fewer than 500 words. Our heuristic backtrack algorithm typically visits only a few hundred among the 26! possible nodes on sample texts ranging from 100 to 600 words.
ChemInform Abstract: Enantioselective Synthesis of Fused Cycloheptadienes by a Tandem Intramolecular Cyclopropanation/Cope Rearrangement Sequence. (2000)

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.
Quantifying Vinyl Monomer Coordination to CuI in Solution and the Effect of Coordination on Monomer Reactivity in Radical Copolymerization (2005)

The association/dissociation equilibrium between vinyl monomers (M) and the complex [CuI(PMDETA)]BPh4 (where PMDETA = N,N,N‘,N‘ ‘,N‘ ‘-pentamethyldiethylenetriamine) to form [CuI(PMDETA)(π-M)]BPh4 was studied by variable temperature 1H NMR. The enthalpy and entropy of coordination and the relative binding constants of methyl acrylate (MA), 1-octene (Oct), styrene (Sty), and methyl methacrylate (MMA) were determined. The affinity of the monomers to the CuI center decreased in the order MA > Oct > Sty > MMA with formation constants (at room temperature) equal to 760, 320, 250, and 6 M-1, respectively. Quantification of this equilibrium process allowed the study of the effect that coordination has on the reactivity of the monomer in free radical polymerization. During these studies, an additional side reaction between free radical azo-initiators (AIBN and V-70) and the CuI complex was identified and analyzed. Additionally, the consequence of monomer coordination to CuI in atom transfer radical polymerization (ATRP) was examined. The reactivity of the monomers in conventional free and ATRP was not significantly affected by the coordination.
Health-related quality of life outcomes in chronic kidney disease (2010)

Certain determinants of HRQOL in CKD, namely anemia and depression, are treatable. Early identification and correction may improve overall well being of patients. Clinical trials are required to demonstrate whether treatment interventions benefit HRQOL in this high-risk population. Furthermore, whether integration of HRQOL assessment into routine clinical practice will improve HRQOL outcomes remains to be determined.
Coupled hidden Markov models for complex action recognition (2002)

We present algorithms for coupling and training hidden Markov models (HMMs) to model interacting processes, and demonstrate their superiority to conventional HMMs in a vision task classifying two-handed actions. HMMs are perhaps the most successful framework in perceptual computing for modeling and classifying dynamic behaviors, popular because they offer dynamic time warping, a training algorithm and a clear Bayesian semantics. However the Markovian framework makes strong restrictive assumptions about the system generating the signal-that it is a single process having a small number of states and an extremely limited state memory. The single-process model is often inappropriate for vision (and speech) applications, resulting in low ceilings on model performance. Coupled HMMs provide an efficient way to resolve many of these problems, and offer superior training speeds, model likelihoods, and robustness to initial conditions.
Hypoxia Inhibits Myogenic Differentiation through Accelerated MyoD Degradation (2004)

Cells undergo a variety of biological responses when placed in hypoxic conditions, including alterations in metabolic state and growth rate. Here we investigated the effect of hypoxia on the ability of myogenic cells to differentiate in culture. Exposure of myoblasts to hypoxia strongly inhibited multinucleated myotube formation and the expression of differentiation markers. We showed that hypoxia reversibly inhibited MyoD, Myf5, and myogenin expression. One key step in skeletal muscle differentiation involves the up-regulation of the cell cycle-dependent kinase inhibitors p21 and p27 as well as the product of the retinoblastoma gene (pRb). Myoblasts cultured under hypoxic conditions in differentiation medium failed to up-regulate both p21 and pRb despite the G1 cell cycle arrest, as evidenced by p27 accumulation and pRb hypophosphorylation. Hypoxia-dependent inhibition of differentiation was associated with MyoD degradation by the ubiquitin-proteasome pathway. MyoD overexpression in C2C12 myoblasts overrode the differentiation block imposed by hypoxic conditions. Thus, hypoxia by inducing MyoD degradation blocked accumulation of early myogenic differentiation markers such as myogenin and p21 and pRb, preventing both permanent cell cycle withdraw and terminal differentiation. Our study revealed a novel anti-differentiation effect exerted by hypoxia in myogenic cells and identified MyoD degradation as a relevant target of hypoxia.
Regioselective Fluoroalkoxylation and Polyfluoroalkoxylation of Activated Polyhalobenzenes (1984)

Abstract A series of activated polyhalobenzenes have been reacted with various amounts of sodium 2,2,2-trifluoroethoxide in DMF or HMPA. The nature of these monosubstitution and polysubstitution reactions are described.
The In Vitro Synthesis of Fats in Cottonseed1 (1959)

Synopsis Acetate is used for the synthesis of lipides, and the incorporation of acetate into lipides increases with increasing concentration of acetate. Both biotin and light stimulate the synthesis of lipides in cottonseed.
A High Input Impedance Low Noise Integrated Front-End Amplifier for Neural Monitoring (2016)

Within neural monitoring systems, the front-end amplifier forms the critical element for signal detection and pre-processing, which determines not only the fidelity of the biosignal, but also impacts power consumption and detector size. In this paper, a novel combined feedback loop-controlled approach is proposed to compensate for input leakage currents generated by low noise amplifiers when in integrated circuit form alongside signal leakage into the input bias network. This loop topology ensures the Front-End Amplifier (FEA) maintains a high input impedance across all manufacturing and operational variations. Measured results from a prototype manufactured on the AMS 0.35 [Formula: see text] CMOS technology is provided. This FEA consumes 3.1 [Formula: see text] in 0.042 [Formula: see text], achieves input impedance of 42 [Formula: see text], and 18.2 [Formula: see text] input-referred noise.
Wavelet-Based Pavement Distress Classification (2005)

A two-step method–-wavelet transform followed by Radon transform–- is proposed for pavement distress classification. First, a pavement image is decomposed into different frequency subbands by wavelet transform. Distress is transformed into the high-amplitude wavelet coefficients, which are referred to as the details, in the high-frequency subbands. The wavelet modulus is calculated by combining the horizontal, vertical, and diagonal details. Since distress, especially crack, has dominant orientations in both the space domain and the wavelet domain, Radon transform is then applied to the wavelet modulus to transform cracks into peaks in the Radon domain. The patterns and parameters of the peaks are finally used for distress classification. Both simulated and experimental results demonstrate that the proposed two-step method is an effective method for pavement distress classification.
Connexin45 directly binds to ZO‐1 and localizes to the tight junction region in epithelial MDCK cells (2001)

Zonula occludens protein 1 (ZO-1) is a cytosolic tight junction protein that tethers transmembrane proteins such as occludin, claudin and junctional adhesion molecule to the actin cytoskeleton. The interaction between ZO-1 and claudin or junctional adhesion molecule occurs via the amino-terminal PSD95/Dlg/ZO-1 (PDZ) domains in ZO-1. A yeast two-hybrid screen to search for proteins that interact with the PDZ domains of ZO-1 identified connexin (Cx) 45. Cx45 interacts with the PDZ domains of ZO-1 and ZO-3, but not ZO-2, via a short C-terminal PDZ binding motif (SVWI). In transfected epithelial Madin-Darby canine kidney cells, Cx45 co-localizes with endogenous ZO-1 at or near tight junctions and co-precipitation experiments show that Cx45 and ZO-1 directly interact. Inactivating the C-terminal PDZ-binding motif in Cx45 affects its co-precipitation and co-localization with ZO-1. The growing number of connexins (i.e. Cx43 and Cx45) that can associate with ZO proteins indicate that ZO proteins may play a more general role in organizing gap junctions and/or in recruiting signaling molecules that regulate intercellular communication.
A central role for chromosome breakage in gene amplification, deletion formation, and amplicon integration. (1991)

A CHO cell line with a single copy of the DHFR locus on chromosome Z2 was used to analyze the structure of the amplification target and products subsequent to the initial amplification event. Dramatic diversity in the number and cytogenetic characteristics of DHFR amplicons was observed as soon as eight to nine cell doublings following the initial event. Two amplicon classes were noted at this early time: Small extrachromosomal elements and closely spaced chromosomal amplicons were detected in 30-40% of metaphases in six of nine clones, whereas three of nine clones contained huge amplicons spanning greater than 50 megabases. In contrast, the incidence of metaphases containing extrachromosomal amplicons fell to 1-2% in cells analyzed at 30-35 cell doublings, and most amplicons localized to rearranged or broken derivatives of chromosome Z2 at this time. Breakage of the Z2 chromosome near the DHFR gene, and deletion of the DHFR gene and flanking DNA was also observed in cells that had undergone the amplification process. To account for these diverse cytogenetic and molecular consequences of gene amplification, we propose that chromosome breakage plays a central role in the amplification process by (1) generating intermediates that are initially acentric and lead to copy number increase primarily by unequal segregation, (2) creating atelomeric ends that are either incompletely replicated or resected by exonucleases to generate deletions, and (3) producing recombinogenic ends that provide preferred sites for amplicon relocalization.
Ion Drag Pumping. I. Theory (1963)

The ion-drag pumping problem is re-examined. New theoretical results are presented for both the static and dynamic cases: in particular, the phenomena of ``cut-in'' voltage and hydrodynamic instability are shown to behave in a fashion different from that previously believed. The predictions of the theory are evaluated in the light of the published experimental evidence.
Diagnostic significance of urinary long non-coding PCA3 RNA in prostate cancer (2017)

Prostate cancer antigen 3(PCA3) is a long non-coding RNA, which was found increased expression in CaP patients than healthy individual. In this study, the individual nucleic acid of PCA3 and PSA was recombinant expressed as a reference reagent, and a quantitative RT-PCR with TaqMan assay was developed to examine the copies of PCA3 and PSA gene in urine. The results showed that the area under the receiver operating characteristic curve (AUROC) was 0.717, 0.444 and 0.916 for the number of PCA3 copy, PSA copy and for the score of PCA3/PSA RNA, respectively. Additionally, the AUROC for serum tPSA was 0.674 with a low specificity of 12.07%. Finally, the algorithm of PCA3 RNA <i>versus</i> PSA RNA was evaluated and corroborated as CaP biomarker by conducting a multicentric clinical trial. This study not only validated the developed technique of qRT-PCR with TaqMan assay for examination of urinary PCA3 and PSA RNA, it also demonstrated that the score of the PCA/PSA RNA was a reliable signature for CaP diagnosis.