gebhart/patrepeval huggingface dataset:
Poly (ADP-Ribose) synthetase. Separation and identification of three proteolytic fragments as the substrate-binding domain, the DNA-binding domain, and the automodification domain. (1984)

Poly(ADP-ribose) synthetase of Mr = 120,000 is cleaved by limited proteolysis with alpha-chymotrypsin into two fragments of Mr = 54,000 (54K) and Mr = 66,000 (66K). When the native enzyme is modified with 3-(bromoacetyl)pyridine, both portions of the enzyme are alkylated; however, alkylation of the 54K portions of the enzyme is protected by the addition of the substrate, NAD, or its analog, nicotinamide, suggesting that the substrate-binding site is localized in the 54K fragment. When the enzyme previously automodified with a low concentration of [adenine-U-14C] NAD is digested with alpha-chymotrypsin, the radioactivity is detected exclusively in the 66K fragment. The 66K fragment thus labeled is further cleaved with papain into two fragments of Mr = 46,000 and Mr = 22,000. With these two fragments, the label is detected only in the 22K fragment, but not in the 46K fragment. The 46K fragment binds to a DNA-cellulose column with the same affinity as that of the native enzyme, while the 22K fragment and the 54K fragment have little affinity for the DNA ligand. These results indicate that poly (ADP-ribose) synthetase contains three separable domains, the first possessing the site for binding of the substrate, NAD, the second containing the site for binding of DNA, and the third acting as the site(s) for accepting poly(ADP-ribose).
SNMPv3: A security enhancement for SNMP (1998)

Simple network management protocol (SNMP) is the most widely-used network management protocol on TCP/IP-based networks. The functionality of SNMP was enhanced with the publication of SNMPv2. However, both these versions of SNMP lack security features, notably authentication and privacy, that are required to fully exploit SNMP. A recent set of RFCs, known collectively as SNMPv3, correct this deficiency. This article outlines the overall network management framework defined in SNMPv3, and then looks at the principal security facilities defined in SNMPv3: authentication, privacy, and access control.
Pro-apoptotic Mechanisms of Action of a Novel Vitamin E Analog (α-TEA) and a Naturally Occurring Form of Vitamin E (δ-Tocotrienol) in MDA-MB-435 Human Breast Cancer Cells (2004)

Vitamin E derivative, RRR-alpha-tocopheryl succinate (vitamin E succinate, VES), is a potent pro-apoptotic agent, inducing apoptosis by restoring both transforming growth factor-beta (TGF-beta) and Fas (CD95) apoptotic signaling pathways that contribute to the activation of c-Jun N-terminal kinase (JNK)-mediated apoptosis. Objectives of these studies were to characterize signaling events involved in the pro-apoptotic actions of a naturally occurring form of vitamin E, delta-tocotrienol, and a novel vitamin E analog, alpha-tocopherol ether acetic acid analog [alpha-TEA; 2,5,7,8-tetramethyl-2R-(4R,8R,12-trimethyltridecyl)chroman-6-yloxyacetic acid]. Like VES, alpha-TEA and delta-tocotrienol induced estrogen-nonresponsive MDA-MB-435 and estrogen-responsive MCF-7 human breast cancer cells to undergo high levels of apoptosis in a concentration- and time-dependent fashion. Like VES, the two compounds induced either no or lower levels of apoptosis in normal human mammary epithelial cells and immortalized but nontumorigenic human MCF-10A cells. The pro-apoptotic mechanisms triggered by the structurally distinct alpha-TEA and delta-tocotrienol were identical to those previously reported for VES, that is, alpha-TEA- and delta-tocotrienol-induced apoptosis involved up-regulation of TGF-beta receptor II expression and TGF-beta-, Fas- and JNK-signaling pathways. These data provide a better understanding of the anticancer actions of a dietary form of vitamin E (delta-tocotrienol) and a novel nonhydrolyzable vitamin E analog (alpha-TEA).
Poorly Differentiated Breast Carcinoma is Associated with Increased Expression of the Human Polycomb Group EZH2 Gene (2003)

Polycomb group (PcG) genes contribute to the maintenance of cell identity, cell cycle regulation, and oncogenesis. We describe the expression of five PcG genes (BMI-1, RING1, HPC1, HPC2, and EZH2) innormal breast tissues, invasive breast carcinomas, and their precursors. Members of the HPC-HPH/PRC1 PcG complex, including BMI-1, RING1, HPC1, and HPC2, were detected in normal resting and cycling breast cells. The EED-EZH/PRC2 PcG complex protein EZH2 was only found in rare cycling cells, whereas normal resting breast cells were negative for EZH2. PcG gene expression patterns in ductal hyperplasia (DH), well-differentiated ductal carcinoma in situ (DCIS), and well-differentiated invasive carcinomas closely resembled the pattern in healthy cells. However, poorly differentiated DCIS and invasive carcinomas frequently expressed EZH2 in combination with HPC-HPH/PRC1 proteins. Most BMI-1/EZH2 double-positive cells in poorly differentiated DCIS were resting. Poorly differentiated invasive carcinoma displayed an enhanced rate of cell division within BMI-1/EZH2 double-positive cells. We propose that the enhanced expression of EZH2 in BMI-1(+) cells contributes to the loss of cell identity in poorly differentiated breast carcinomas, and that increased EZH2 expression precedes high frequencies of proliferation. These observations suggest that deregulated expression of EZH2 is associated with loss of differentiation and development of poorly differentiated breast cancer in humans.
Human inhibitory receptors Ig-like transcript 2 (ILT2) and ILT4 compete with CD8 for MHC class I binding and bind preferentially to HLA-G (2003)

Ig-like transcript 4 (ILT4) (also known as leukocyte Ig-like receptor 2, CD85d, and LILRB2) is a cell surface receptor expressed mainly on myelomonocytic cells, whereas ILT2 (also known as leukocyte Ig-like receptor 1, CD85j, and LILRB1) is expressed on a wider range of immune cells including subsets of natural killer and T cells. Both ILTs contain immunoreceptor tyrosine-based inhibitory receptor motifs in their cytoplasmic tails that inhibit cellular responses by recruiting phosphatases such as SHP-1 (Src homology 2 domain containing tyrosine phosphatase 1). Although these ILTs have been shown to recognize a broad range of classical and nonclassical human MHC class I molecules (MHCIs), their precise binding properties remain controversial. We have used surface plasmon resonance to analyze the interaction of soluble forms of ILT4 and ILT2 with several MHCIs. Although the range of affinities measured was quite broad (Kd = 2-45 microM), some interesting differences were observed. ILT2 generally bound with a 2- to 3-fold higher affinity than ILT4 to the same MHCI. Furthermore, ILT2 and ILT4 bound to HLA-G with a 3- to 4-fold higher affinity than to classical MHCIs, suggesting that ILT/HLA-G recognition may play a dominant role in the regulation of natural killer, T, and myelomonocytic cell activation. Finally, we show that ILT2 and ILT4 effectively compete with CD8 for MHCI binding, raising the possibility that ILT2 modulates CD8+ T cell activation by blocking the CD8 binding as well as by recruiting inhibitory molecules through its immunoreceptor tyrosine-based inhibitory receptor motif.
Grain boundary and triple junction constraints during martensitic transformation in shape memory alloys (2013)

We investigate the role of grain constraint upon martensitic transformation through in situ scanning electron microscope tensile experiments on shape memory microwires with a small number of grains and grain junctions. The martensite transformation morphology becomes more complex with increasing grain constraint: In unconstrained monocrystalline regions, the transformation is simple, single variant, and complete; near grain boundaries, the transformation is only partial, containing regions of untransformed austenite; near a triple junction, the morphology is complex, the transformation is partial and also multi-variant. These observations speak of transformation-induced stress concentrations that are more severe around triple junctions than around grain boundaries. Finite element modeling also provides an estimate for constraint effects on martensitic transformation yielding higher stresses near triple junctions than near grain boundaries. Towards the goal of developing polycrystalline Cu-based shape memory alloys that avoid intergranular fracture, our results support three design objectives: (1) Removal of triple junctions, (2) reduction of the total grain boundary area, and (3) geometry design containing unconstrained regions where the transformation can be most easily accommodated.
Gene Transfer of Ig-Fusion Proteins Into B Cells Prevents and Treats Autoimmune Diseases (2002)

Based on the tolerogenic properties of IgG carriers and B cell Ag presentation, we developed a retrovirally mediated gene expression approach for treatment of autoimmune conditions. In this study, we show that the IgG-Ag retroviral constructs, expressing myelin basic protein (MBP) or glutamic acid decarboxylase in B cells, can be used for the treatment of murine models for multiple sclerosis and diabetes. Transduction of syngeneic B cells with MBP-IgG leads to the amelioration of ongoing experimental allergic encephalomyelitis induced by the transfer of primed cells from PLxSJL F(1) mice with ongoing disease and could be effective even after symptoms appeared. This effect is specific and does not involve bystander suppression because treatment with MBP-IgG does not affect disease induced after immunization with proteolipid protein immunodominant peptide plus MBP. Interestingly, if donor B cells are derived from gld mice (Fas ligand-negative), then tolerance is not induced with a model Ag although there was no evidence for Fas ligand-mediated deletion of target T cells. In spontaneous diabetes in nonobese diabetic mice, we were able to stop the ongoing autoimmune process by treatment at 7-10 wk with glutamic acid decarboxylase-IgG retrovirally transduced B cells, or attenuate it with B cells transduced with an insulin B chain (B9-23) epitope IgG fusion protein. Furthermore, IgG fusion protein gene therapy can also protect primed recipients from Ag-induced anaphylactic shock, and thus does not cause immune deviation. These results demonstrate proof of principle for future efforts to develop this approach in a clinical setting.
Antisense oligonucleotides for the treatment of cardiomyopathy in Duchenne muscular dystrophy. (2019)

Duchenne muscular dystrophy (DMD) is an X-linked recessive fatal neuromuscular disorder characterized by progressive muscle degeneration which affects one in 3500-5000 males born worldwide. DMD is caused by loss-of-function mutations in the <i>dystrophin</i> (<i>DMD</i>) gene encoding for dystrophin, a cytoskeletal protein that supports the structural integrity of myofibers during cycles of muscle contraction and relaxation. DMD patients do not only experience skeletal muscle deterioration but also severe cardiomyopathy, which is recognized as the current leading cause of death for the disease. Among the therapies being developed, exon skipping using antisense oligonucleotides (AOs) is one of the most promising approaches. AOs effectively restore dystrophin expression in skeletal muscles; however, they are highly inefficient in the heart due to endosomal entrapment. Improving skeletal muscle function without restoring dystrophin expression in cardiac tissue may exacerbate cardiomyopathy due to increased voluntary activity. This review consolidates the preclinical antisense approaches to improve dystrophin restoration, with a special focus on the heart.
Avoiding the Rush Hours: WiFi Energy Management via Traffic Isolation (2011)

WiFi continues to be a prime source of energy consumption in mobile devices. This paper observes that, despite a rich body of research in WiFi energy management, there is room for improvement. Our key finding is that WiFi energy optimizations have conventionally been designed with a single AP in mind. However, network contention among different APs can dramatically increase a client's energy consumption. Each client may have to keep awake for long durations before its own AP gets a chance to send it packets to it. As AP density increases, the waiting time inflates, resulting in a proportional decrease in battery life. We design SleepWell, a system that achieves energy efficiency by evading network contention. The APs regulate the sleeping window of their clients in a way that different APs are active/inactive during nonoverlapping time windows. The solution is analogous to the common wisdom of going late to office and coming back late, thereby avoiding the rush hours. We implement SleepWell on a testbed of eight Laptops and nine Android phones, and evaluate it over a wide variety of scenarios and traffic patterns. Results show a median gain of up to 2x when WiFi links are strong; when links are weak and the network density is high, the gains can be even more.
A Highly Enantio-Selective Hexitol Nucleic Acid Template for Nonenzymatic Oligoguanylate Synthesis (1999)

The authors compare the enantiomeric cross-inhibition of D- and L-guanosine 5'-phosphoro-2-methyl-imidazole (I) polymn. on C10 (RNA), dC10 (DNA), or hC10 (hexitol nucleic acid) (II). RNA or DNA templates catalyze efficient oligomerization of D-I, with a strong enantiomeric cross-inhibition by L-I, but II shows efficient oligomerization of D-I with a less sever cross-inhibition, resulting in G6-9 polymers, thus showing that efficient selection of one optical isomer from a racemic mixt. of nucleotides during nonenzymic oligo-nucleotide synthesis on an analog of a nucleic acid template is possible, which may be of relevance to prebiotic conditions. [on SciFinder (R)]
Positive-Type Photopolyimide Based on Vinyl Ether Crosslinking and De-Crosslinking. (2000)

A series of different acid value polyimides with carboxyl groups in the ends of main chain was synthesized and used for the three-component photopolymers, consisting of the polyimide, a vinyl ether monomer, and a photo-acid generator (PAG). This polyimide acts as a positive-type resist with the process of prebaking (PB), exposure to light, and post-exposure baking (PEB). The effect of the acid value correspond to molecular weight on the characteristics of the photopolyimide, such as sensitivity and contrast, was investigated. An increase in the acid value and a decrease in the molecular weight enhance the increment of sensitivity based on solubilization rate by cleavage reaction. This positive-type photopolyimide showed a sensitivity of 137mJ/cm2 and a gamma value of 2.9.
Evidence for the presence of two tumor suppressor genes on chromosome 8p for colorectal carcinoma. (1993)

We have examined loss of heterozygosity on the short arm of chromosome 8 in 133 colorectal carcinomas, using 20 restriction fragment length polymorphism markers. Loss of heterozygosity was observed in 58 (44%) of 131 tumors that were informative with at least one locus. Among these 58, 32 revealed a partial or interstitial deletion of chromosome 8p. Detailed deletion mapping of chromosome 8p in these tumors identified two distinct, commonly deleted regions. One was located between markers C18-266 and pSVL-LPL at 8p23.2-8p22, and the other between CI8-319 and CI8-494 at 8p21.3-8p11.22. The genetic lengths of these two intervals were estimated to be 28 and 18 cM, respectively. The results suggest that at least two tumor suppressor genes associated with colorectal carcinomas are present on chromosome 8p. Correlation of loss of heterozygosity on 8p to the clinicopathological stage was also detected, suggesting that inactivation of a tumor suppressor gene(s) on 8p plays a role in progression of colorectal carcinomas.
Measuring colorfulness in natural images (2003)

We want to integrate colourfulness in an image quality evaluation framework. This quality framework is meant to evaluate the perceptual impact of a compression algorithm or an error prone communication channel on the quality of an image. The image might go through various enhancement or compression algorithms, resulting in a different -- but not necessarily worse -- image. In other words, we will measure quality but not fidelity to the original picture. While modern colour appearance models are able to predict the perception of colourfulness of simple patches on uniform backgrounds, there is no agreement on how to measure the overall colourfulness of a picture of a natural scene. We try to quantify the colourfulness in natural images to perceptually qualify the effect that processing or coding has on colour. We set up a psychophysical category scaling experiment, and ask people to rate images using 7 categories of colourfulness. We then fit a metric to the results, and obtain a correlation of over 90% with the experimental data. The metric is meant to be used real time on video streams. We ignored any issues related to hue in this paper.
PHARMACOLOGY AND FUNCTIONS OF METABOTROPIC GLUTAMATE RECEPTORS (1997)

In the mid to late 1980s, studies were published that provided the first evidence for the existence of glutamate receptors that are not ligand-gated cation channels but are coupled to effector systems through GTP-binding proteins. Since those initial reports, tremendous progress has been made in characterizing these metabotropic glutamate receptors (mGluRs), including cloning and characterization of cDNA that encodes a family of eight mGluR subtypes, several of which have multiple splice variants. Also, tremendous progress has been made in developing new highly selective mGluR agonists and antagonists and toward determining the physiologic roles of the mGluRs in mammalian brain. These findings have exciting implications for drug development and suggest that the mGluRs provide a novel target for development of therepeutic agents that could have a significant impact on neuropharmacology.
Approximation Algorithms for Reducing the Spectral Radius to Control Epidemic Spread (2015)

The largest eigenvalue of the adjacency matrix of a network (referred to as the spectral radius) is an important metric in its own right. Further, for several models of epidemic spread on networks (e.g., the ‘flu-like’ SIS model), it has been shown that an epidemic dies out quickly if the spectral radius of the graph is below a certain threshold that depends on the model parameters. This motivates a strategy to control epidemic spread by reducing the spectral radius of the underlying network. In this paper, we develop a suite of provable approximation algorithms for reducing the spectral radius by removing the minimum cost set of edges (modeling quarantining) or nodes (modeling vaccinations), with different time and quality tradeoffs. Our main algorithm, GREEDYWALK, is based on the idea of hitting closed walks of a given length, and gives an O(log2 n)-approximation, where n denotes the number of nodes; it also performs much better in practice compared to all prior heuristics proposed for this problem. We further present a novel sparsification method to improve its running time. In addition, we give a new primal-dual based algorithm with an even better approximation guarantee (O(log n)), albeit with slower running time. We also give lower bounds on the worst-case performance of some of the popular heuristics. Finally we demonstrate the applicability of our algorithms and the properties of our solutions via extensive experiments on multiple synthetic and real networks.
Polymer Solar Cells Based on a Low‐Bandgap Fluorene Copolymer and a Fullerene Derivative with Photocurrent Extended to 850 nm (2005)

Abstract Polymer solar cells have been fabricated from a recently synthesized low band‐gap alternating polyfluorene copolymer, APFO‐Green2, combined with [6,6]‐phenyl‐C 61 ‐butyric acid methyl ester (PCBM) from organic solutions. External quantum efficiencies (EQEs) of the solar cells show an onset at 850 nm and a peak of &gt; 10 % located at 650 nm, which corresponds to the extended absorption spectrum of the polymer. Photocurrent of 3.0 mA cm –2 , photovoltage of 0.78 V, and power conversion efficiency of 0.9 % have been achieved in solar cells based on this new low‐bandgap polymer under the illumination of air mass 1.5 (AM 1.5) (1000 W m –2 ) from a solar simulator.
The Heavy Chain Variable Segment Gene Repertoire in Chronic Chagas′ Heart Disease (2009)

Patients chronically infected with Trypanosoma cruzi develop chronic Chagas' heart disease (cChHD). Their Ab response is suspected to be involved in the cardiac pathogenesis. Reactivity of serum Abs from these patients has been extensively studied but little is known about the diversity of the in vivo IgG repertoire. We analyzed 125 variable H chain (VH) genes and compared it to repertoires from healthy individuals, and patients with autoimmune processes and other infections. VH were from plasma cells isolated from heart tissue of three cChHD patients and from a Fab combinatorial library derived from bone marrow of another cChHD patient. The role of the parasite in shaping the Ab repertoire was assessed analyzing VH genes before and after panning against T. cruzi Ag. Among recovered VH genes, a significantly increased representation of VH4 was observed. Plasma cells at the site of cardiac infiltration showed an increased VH1 usage. CDR3 lengths were similar to the ones found in the healthy repertoire and significantly shorter than in other infections. VH derived from anti-T. cruzi Fab and plasma cells showed a higher proportion of hypermutated genes, 46.9% and 43.75%, respectively, vs 30.9% of the cChHD patient repertoire, pointing to the role of parasite Ags in the shaping of the humoral response in Chagas' disease. No histological evidence of germinal center-like structures was observed in heart tissue. In accordance, VH analysis of heart plasmocytes revealed no evidence of clonal B cell expansion, suggesting that they migrated into heart tissue from secondary lymphoid organs.
Analysis of mutation in human cells by using an Epstein-Barr virus shuttle system. (1987)

We developed highly sensitive shuttle vector systems for detection of mutations formed in human cells using autonomously replicating derivatives of Epstein-Barr virus (EBV). EBV vectors carrying the bacterial lacI gene as the target for mutation were established in human cells and later returned to Escherichia coli for rapid detection and analysis of lacI mutations. The majority of the clonal cell lines created by establishment of the lacI-EBV vector show spontaneous LacI- frequencies of less than 10(-5) and are suitable for studies of induced mutation. The ability to isolate clonal lines represents a major advantage of the EBV vectors over transiently replicating shuttle vectors (such as those derived from simian virus 40) for the study of mutation. The DNA sequence changes were determined for 61 lacI mutations induced by exposure of one of the cell lines to N-nitroso-N-methylurea. A total of 33 of 34 lacI nonsense mutations and 26 of 27 missense mutations involve G X C to A X T transitions. These data provide support for the mutational theory of cancer.
Induced Pluripotent Stem Cells: Emerging Techniques for Nuclear Reprogramming (2011)

Introduction of four transcription factors, Oct3/4, Sox2, Klf4, and c-Myc, can successfully reprogram somatic cells into embryonic stem (ES)-like cells. These cells, which are referred to as induced pluripotent stem (iPS) cells, closely resemble embryonic stem cells in genomic, cell biologic, and phenotypic characteristics, and the creation of these special cells was a major triumph in cell biology. In contrast to pluripotent stem cells generated by somatic cell nuclear-transfer (SCNT) or ES cells derived from the inner cell mass (ICM) of the blastocyst, direct reprogramming provides a convenient and reliable means of generating pluripotent stem cells. iPS cells have already shown incredible potential for research and for therapeutic applications in regenerative medicine within just a few years of their discovery. In this review, current techniques of generating iPS cells and mechanisms of nuclear reprogramming are reviewed, and the potential for therapeutic applications is discussed.