gebhart/patrepeval huggingface dataset:
The Vascular Endothelial Growth Factor Receptor Flt-1 Mediates Biological Activities (1996)

Two distinct receptors for vascular endothelial growth factor (VEGF), the tyrosine kinase receptors Flt-1 and Flk-1/KDR, have been described. In this study we show that monocytes, in contrast to endothelium, express only the VEGF receptor Flt-1, and that this receptor specifically binds also the VEGF homolog placenta growth factor (PlGF). Both VEGF and PlGF stimulate tissue factor production and chemotaxis in monocytes at equivalent doses. In contrast, endothelial cells expressing both the Flt-1 and the Flk-1/KDR receptors produce more tissue factor upon stimulation with VEGF than after stimulation with PlGF. Neutralizing antibodies to the KDR receptor reduce the VEGF-stimulated tissue factor induction in endothelial cells to levels obtained by stimulation with PlGF alone, but do not affect PlGF-induced tissue factor induction in endothelial cells nor the VEGF-dependent tissue factor production in monocytes. These findings strongly suggest Flt-1 as a functional receptor for VEGF and PlGF in monocytes and endothelial cells and identify this receptor as a mediator of monocyte recruitment and procoagulant activity.
B7-H1 (PD-L1, CD274) suppresses host immunity in T-cell lymphoproliferative disorders (2009)

Stromal elements present within the tumor microenvironment may suppress host immunity and promote the growth of malignant lymphocytes in B cell-derived non-Hodgkin lymphoma (NHL). In contrast, little is known about the microenvironment's role in T cell-derived NHL. B7-H1 (PD-L1, CD274), a member of the B7 family of costimulatory/co-inhibitory ligands expressed by both malignant cells and stromal cells within the tumor microenvironment, has emerged as an important immune modulator capable of suppressing host immunity. Therefore, B7-H1 expression and function were analyzed in cutaneous and peripheral T-cell NHL. B7-H1 was expressed by tumor cells, monocytes, and monocyte-derived cells within the tumor microenvironment in T-cell NHL and was found to inhibit T-cell proliferation and promote the induction of FoxP3(+) regulatory T cells. Collectively, the data presented provide the first evidence implicating B7-H1 in the suppression of host immunity in T-cell lymphoproliferative disorders and suggest that the targeting of B7-H1 may represent a novel therapeutic approach.
Cytokine-induced immune deviation as a therapy for inflammatory autoimmune disease. (1994)

The properties and outcome of an immune response are best predicted by the lymphokine phenotype of the responding T cells. Cytokines produced by CD4+ T helper type 1 (Th1) T cells mediate delayed type hypersensitivity (DTH) and inflammatory responses, whereas cytokines produced by Th2 T cells mediate helper T cell functions for antibody production. To determine whether induction of Th2-like cells would modulate an inflammatory response, interleukin 4 (IL-4) was administered to animals with experimental allergic encephalomyelitis (EAE), a prototypic autoimmune disease produced by Th1-like T cells specific for myelin basic protein (MBP). IL-4 treatment resulted in amelioration of clinical disease, the induction of MBP-specific Th2 cells, diminished demyelination, and inhibition of the synthesis of inflammatory cytokines in the central nervous system (CNS). Modulation of an immune response from one dominated by excessive activity of Th1-like T cells to one dominated by the protective cytokines produced by Th2-like T cells may have applicability to the therapy of certain human autoimmune diseases.
Enhanced adaptive modulation and coding schemes based on multiple channel reportings for wireless multicast systems (2006)

This paper shows various schemes to change Mod- ulation and Coding Schemes(MCS) adaptively for multicasting. Applying Adaptive Modulation and Coding(AMC) scheme to multicasting will show better performance in view of spectrum efficiency aspect than fixing MCS level. Since there exist mul- tiple receivers for a data in multicasting, there is much more difficulty in determining the overall MCS level which satisfies all the receivers. Based on the channel quality information of the receivers, the source can determine the overall MCS level by three schemes; minimum MCS algorithm, average MCS algorithm, and weighted average MCS algorithm. Here, a tradeoff between spectrum efficiency and robustness exists: minimum MCS algorithm chooses robustness that guarantees low error rate to all the receivers, while average MCS algorithm chooses spectrum efficiency to improve throughput performance. A compromise between spectrum efficiency and robustness can be made by introducing weights to averaging MCS. Depending on the parameters related to the weights, more robustness or spec- trum efficiency can be achieved. This paper presents numerical analysis showing the performance of the proposed schemes and a conventional scheme. Also simulation is presented to verify the numerical analysis results and shows the performance of weighted MCS algorithm.
A New Efficient Synthesis of 3-Nitropyridine and Substituted Derivatives (1997)

Pyridine and pyridine derivatives have been nitrated in the β-position by reaction with N2O5 or NO2 ⋅ BF4 in MeNO2, THF or MeCN to form the N-nitropyridinium salt. This was then reacted with an aqueous solution of a nucleophile to give the β-nitro compound in moderate to good yield.
Wireless Implantable Electronic Platform for Chronic Fluorescent-Based Biosensors (2011)

The development of a long-term wireless implantable biosensor based on fluorescence intensity measurement poses a number of technical challenges, ranging from biocompatibility to sensor stability over time. One of these challenges is the design of a power efficient and miniaturized electronics, enabling the biosensor to move from bench testing to long term validation, up to its final application in human beings. In this spirit, we present a wireless programmable electronic platform for implantable chronic monitoring of fluorescent-based autonomous biosensors. This system is able to achieve extremely low power operation with bidirectional telemetry, based on the IEEE802.15.4-2003 protocol, thus enabling over three-year battery lifetime and wireless networking of multiple sensors. During the performance of single fluorescent-based sensor measurements, the circuit drives a laser diode, for sensor excitation, and acquires the amplified signals from four different photodetectors. In vitro functionality was preliminarily tested for both glucose and calcium monitoring, simply by changing the analyte-binding protein of the biosensor. Electronics performance was assessed in terms of timing, power consumption, tissue exposure to electromagnetic fields, and in vivo wireless connectivity. The final goal of the presented platform is to be integrated in a complete system for blood glucose level monitoring that may be implanted for at least one year under the skin of diabetic patients. Results reported in this paper may be applied to a wide variety of biosensors based on fluorescence intensity measurement.
Endoscopie treatment of gastrointestinal tumors: Indications and results of laser photocoagulation and photodynamic therapy (1995)

Both Nd:YAG laser and photodynamic therapy (PDT) have ideal indications in endoscopic treatment of gastrointestinal (GI) tumors. A retrospective analysis of 3,505 Nd:YAG laser treatments in 1,015 patients revealed that recanalization of inoperable tumors can be obtained in 93% and 97% of patients with upper and lower GI neoplasms, respectively. Subjective improvement of symptoms was achieved in 74% and 97%, respectively. The overall morbidity and mortality rates were 3% and 1%, respectively, for upper GI tumors and 3% and 0.5% for lower GI tumors. Colorectal adenomas were eradicated in 84% of cases, with a morbidity and mortality of 5% and 0%, respectively. Early stage esophageal and gastric carcinomas were treated with Nd:YAG laser when lesions had well-defined borders or protruded over the mucosal surface and with PDT (38 PDT cycles in 27 patients) in the case of undefined borders or ulcerated lesions. The cure rate was 73% for esophageal tumors and 85% for gastric tumors. Sunburns after photosensitization and local complications occurred in 7% and 6% of patients, respectively. No death was related to endoscopic treatment.
Rapid assessment of the effect of ciprofloxacin on chromosomal DNA from Escherichia coli using an in situ DNA fragmentation assay (2009)

This procedure for determining DNA fragmentation is a simple and rapid test for studying and evaluating the effect of quinolones.
Signaling Pathways in Cartilage Repair (2014)

In adult healthy cartilage, chondrocytes are in a quiescent phase characterized by a fine balance between anabolic and catabolic activities. In ageing, degenerative joint diseases and traumatic injuries of cartilage, a loss of homeostatic conditions and an up-regulation of catabolic pathways occur. Since cartilage differentiation and maintenance of homeostasis are finely tuned by a complex network of signaling molecules and biophysical factors, shedding light on these mechanisms appears to be extremely relevant for both the identification of pathogenic key factors, as specific therapeutic targets, and the development of biological approaches for cartilage regeneration. This review will focus on the main signaling pathways that can activate cellular and molecular processes, regulating the functional behavior of cartilage in both physiological and pathological conditions. These networks may be relevant in the crosstalk among joint compartments and increased knowledge in this field may lead to the development of more effective strategies for inducing cartilage repair.
Blockchain for Vehicular Internet of Things: Recent Advances and Open Issues (2020)

The vehicular Internet of Things (IoT) comprises enabling technologies for a large number of important applications including collaborative autonomous driving and advanced transportation systems. Due to the mobility of vehicles, strict application requirements, and limited communication resources, the conventional centralized control fails to provide sufficient quality of service for connected vehicles, so a decentralized approach is required in the vicinity to satisfy the requirements of delay-sensitive and mission-critical applications. A decentralized system is also more resistant to the single point of failure problem and malicious attacks. Blockchain technology has been attracting great interest due to its capability of achieving a decentralized, transparent, and tamper-resistant system. There are many studies focusing on the use of blockchain in managing data and transactions in vehicular environments. However, the application of blockchain in vehicular environments also faces some technical challenges. In this paper, we first explain the fundamentals of blockchain and vehicular IoT. Then, we conduct a literature review on the existing research efforts of the blockchain for vehicular IoT by discussing the research problems and technical issues. After that, we point out some future research issues considering the characteristics of both blockchain and vehicular IoT.
Peroxisomal alanine : glyoxylate aminotransferase (AGT1) is a photorespiratory enzyme with multiple substrates in Arabidopsis thaliana (2001)

At least two glyoxylate aminotransferases are hypothesized to participate in the steps of photorespiration located in peroxisomes. Until recently, however, genes encoding these enzymes had not been identified. We describe the isolation and characterization of an alanine : glyoxylate aminotransferase (AGT1, formerly AGT) cDNA from Arabidopsis thaliana. Southern blot analysis confirmed that Arabidopsis AGT1 is encoded by a single gene. Homologs of this class IV aminotransferase are also known in other plants, animals, and methylotrophic bacteria, suggesting an ancient evolutionary origin of this enzyme. AGT1 transcripts were present in all tissues of Arabidopsis, but were most abundant in green, leafy tissues. Purified, recombinant Arabidopsis AGT1 expressed in Escherichia coli catalyzed three transamination reactions using the following amino donor : acceptor combinations: alanine : glyoxylate, serine : glyoxylate, and serine : pyruvate. AGT1 had the highest specific activity with the serine : glyoxylate transamination, and apparent Km measurements indicate that this is the preferred in vivo reaction. In vitro import experiments and subcellular fractionations localized AGT1 to peroxisomes. Sequence analysis of the photorespiratory sat mutants revealed a single nucleotide substitution in the AGT1 gene from these plants. This transition mutation is predicted to result in a proline-to-leucine substitution at residue 251 of AGT1. When this mutation was engineered into the recombinant AGT1 protein, enzymatic activity using all three donor : acceptor pairs was abolished. We conclude that Arabidopsis AGT1 is a peroxisomal photorespiratory enzyme that catalyzes transamination reactions with multiple substrates.
Preconditioning of Low-Frequency Repetitive Transcranial Magnetic Stimulation with Transcranial Direct Current Stimulation: Evidence for Homeostatic Plasticity in the Human Motor Cortex (2004)

Recent experimental work in animals has emphasized the importance of homeostatic plasticity as a means of stabilizing the properties of neuronal circuits. Here, we report a phenomenon that indicates a homeostatic pattern of cortical plasticity in healthy human subjects. The experiments combined two techniques that can produce long-term effects on the excitability of corticospinal output neurons: transcranial direct current stimulation (TDCS) and repetitive transcranial magnetic stimulation (rTMS) of the left primary motor cortex. "Facilitatory preconditioning" with anodal TDCS caused a subsequent period of 1 Hz rTMS to reduce corticospinal excitability to below baseline levels for >20 min. Conversely, "inhibitory preconditioning" with cathodal TDCS resulted in 1 Hz rTMS increasing corticospinal excitability for at least 20 min. No changes in excitability occurred when 1 Hz rTMS was preceded by sham TDCS. Thus, changing the initial state of the motor cortex by a period of DC polarization reversed the conditioning effects of 1 Hz rTMS. These preconditioning effects of TDCS suggest the existence of a homeostatic mechanism in the human motor cortex that stabilizes corticospinal excitability within a physiologically useful range.
An Iterative Algorithm for Background Removal in Spectroscopy by Wavelet Transforms (2009)

Wavelet transforms are an extremely powerful tool when it comes to processing signals that have very "low frequency" components or non-periodic events. Our particular interest here is in the ability of wavelet transforms to remove backgrounds of spectroscopic signals. We will discuss the case of surface-enhanced Raman spectroscopy (SERS) for illustration, but the situation it depicts is widespread throughout a myriad of different types of spectroscopies (IR, NMR, etc.). We outline a purpose-built algorithm that we have developed to perform an iterative wavelet transform. In this algorithm, the effect of the signal peaks above the background is reduced after each iteration until the fit converges close to the real background. Experimental examples of two different SERS applications are given: one involving broad backgrounds (that do not vary much among spectra), and another that involves single molecule SERS (SM-SERS) measurements with narrower (and varying) backgrounds. In both cases, we will show that wavelet transforms can be used to fit the background with a great deal of accuracy, thus providing the framework for automatic background removal of large sets of data (typically obtained in time-series or spatial mappings). A MATLAB((R)) based application that utilizes the iterative algorithm developed here is freely available to download from http://www.victoria.ac.nz/raman/publis/codes/cobra.aspx.
Timing Recovery in Digital Synchronous Data Receivers (1976)

A new class of fast-converging timing recovery methods for synchronous digital data receivers is investigated. Starting with a worst-case timing offset, convergence with random binary data will typically occur within 10-20 symbols. The input signal is sampled at the baud rate; these samples are then processed to derive a suitable control signal to adjust the timing phase. A general method is outlined to obtain near-minimum-variance estimates of the timing offset with respect to a given steady-state sampling criterion. Although we make certain independence assumptions between successive samples and postulate ideal decisions to obtain convenient analytical results, our simulations with a decision-directed reference and baud-to-baud adjustments yield very similar results. Convergence is exponential, and for small loop gains the residual jitter is proportional and convergence time is inversely proportional to the loop gain. The proposed algorithms are simple and economic to implement. They apply to binary or multilevel PAM signals as well as to partial response signals.
Rapid and robust spatiotemporal dynamics of the first-order phase transition in crystals of the organic-inorganic perovskite (C12H25NH3)2PbI4 (2015)

The dynamics of the thermally induced first-order structural phase transition in a high-quality single crystal of the organic-inorganic perovskite (C12H25NH3)2PbI4 was investigated by optical microscopy. The propagation of the straight phase front (habit plane) during the phase transition along the cooling and heating pathways of the thermal hysteresis was observed. The thermochromic character of the transition allowed monitoring of the thermal dependence of average optical density and aided the visualization of the interface propagation. The thermal hysteresis loop is 10 K wide, and the interface velocity is constant at V ≈ 1.6 mm s(-1). The transition is accompanied with sizeable change in crystal size, with elongation of ~6% along the b axis and compression of ~ -2% along the a axis, in excellent agreement with previously reported X-ray diffraction data. The progression of the habit plane is at least 160 times faster than in spin-crossover materials, and opens new prospects for organic-inorganic perovskites as solid switching materials. Moreover, the crystals of (C12H25NH3)2PbI4 are unusually mechanically robust and present excellent resilience to thermal cycling. These hitherto unrecognized properties turn this and possibly similar hybrid perovskites into perspective candidates as active medium for microscopic actuation.
Processing of seismic data from an automatic digital recorder (1963)

Abstract Data from a three-component, long-period seismometer system is recorded in digital form on magnetic tape by a device which has been described by Miller. Preliminary editing and processing is performed to select events of interest from the 24-hour tapes and place them on a library tape that is compatible with a computer. Emphasis is placed on location, correction, and flagging of errors that occur during the recording and editing process. Processing routines developed include: correction for seismometer response, orbital motion functions, energy computation, band pass filtering for mode separation, etc. The dynamic range of the system is 86 db and the response is adequate over the range .02 to 2.0 cps. For the purpose of detailed analysis, digital records from this system are superior to paper records from any of the existing seismographs in use at this laboratory. The main disadvantage of data in this form is the difficulty of inspecting signals by eye in order to make preliminary interpretations.
MT1‐MMP: A potent modifier of pericellular microenvironment (2005)

Cells are regulated by many different means, and there is more and more evidence emerging that changes in the microenvironment greatly affect cell function. MT1-MMP is a type I transmembrane proteinase which participates in pericellular proteolysis of extracellular matrix (ECM) macromolecules. The enzyme is cellular collagenase essential for skeletal development, cancer invasion, growth, and angiogenesis. MT1-MMP promotes cell invasion and motility by pericellular ECM degradation, shedding of CD44 and syndecan1, and by activating ERK. Thus MT1-MMP is one of the factors that influence the cellular microenvironment and thereby affect cell-signaling pathways and eventually alters cellular behavior. As a proteinase, MT1-MMP is regulated by inhibitors, but it also requires formation of a homo-oligomer complex, localization to migration front of the cells, and internalization to become a "functionally active" cell function modifier. Developing new means to inhibit "functional activity" of MT1-MMP may be a new direction to establish treatments for the diseases that MT1-MMP mediates such as cancer and rheumatoid arthritis.
An engineered pathway for the biosynthesis of renewable propane (2014)

The deployment of next-generation renewable biofuels can be enhanced by improving their compatibility with the current infrastructure for transportation, storage and utilization. Propane, the bulk component of liquid petroleum gas, is an appealing target as it already has a global market. In addition, it is a gas under standard conditions, but can easily be liquefied. This allows the fuel to immediately separate from the biocatalytic process after synthesis, yet does not preclude energy-dense storage as a liquid. Here we report, for the first time, a synthetic metabolic pathway for producing renewable propane. The pathway is based on a thioesterase specific for butyryl-acyl carrier protein (ACP), which allows native fatty acid biosynthesis of the Escherichia coli host to be redirected towards a synthetic alkane pathway. Propane biosynthesis is markedly stimulated by the introduction of an electron-donating module, optimizing the balance of O2 supply and removal of native aldehyde reductases.
The Double Bromodomain-containing Chromatin Adaptor Brd4 and Transcriptional Regulation (2007)

Brd4 is a double bromodomain-containing protein that binds preferentially to acetylated chromatin. It belongs to the BET (bromodomains and extraterminal) family that includes mammalian Brd2, Brd3, Brd4, Brdt, Drosophila Fsh, yeast Bdf1, Bdf2, and corresponding homologues in other species. Brd4 is essential for cellular growth and has been implicated in cell cycle control, DNA replication, and gene rearrangement found in t(15;19)-associated carcinomas. Recently, Brd4 has been found in several transcription complexes, including the general cofactor Mediator and the P-TEFb elongation factor, and is capable of stimulating HIV-1 transcription in a Tat-independent manner. In addition, Brd4 is used as a cellular adaptor by some animal and human papillomaviruses (HPV) for anchoring viral genomes to mitotic chromosomes. This tethering, mediated by Brd4 interaction with virus-encoded E2 protein, facilitates viral genome segregation during mitosis. Interestingly, Brd4 is also identified in a transcriptional silencing complex assembled by HPV E2 and turns out to be the long sought cellular corepressor that inhibits the expression of HPV-encoded E6 and E7 oncoproteins that antagonize p53 and pRB tumor suppressor activity, respectively. The dual role of Brd4 in gene activation and repression illustrates how a dynamic chromatin-binding adaptor is able to recruit distinct transcriptional regulators to modulate promoter activity through cell cycle progression.