gebhart/patrepeval huggingface dataset:
Long-Range Heterogeneous Electron Transfer Between Ferrocene and Gold Mediated By n-Alkane and N-Alkyl-Carboxamide Bridges (2000)

Electron-transfer rates between ferrocene and gold were measured for two series of ferrocene-based alkanethiolate monolayers on gold electrodes. In one series, the bridge linking the ferrocene group to gold consisted of a simple alkane chain, and in the other, the bridge was modified such that the two methylene linkages immediately adjacent to the ferrocene group were replaced by a carboxamide linkage. Monolayers in both series were studied using a novel ac voltammetry method to measure the standard electron-transfer rate constants for oxidation/reduction of the ferrocene groups. Rate constants were nearly the same for pairs of molecules in the two series when the number of bonds in the direct pathway linking ferrocene to gold was the same, regardless of whether the group immediately adjacent to ferrocene was a pair of methylene units or a carboxamide unit. This observation suggests that the contribution of the carboxamide group to the overall bridge-mediated electronic coupling is not greatly different from that of a pair of methylene groups. An unusual “even−odd effect” in the diminution of rate with chain length for both monolayer series was also noted. Several factors that could cause such an alternation in rate are proposed, including an unusual quantum interference effect in the bridge-mediated coupling that has been predicted theoretically.
Fit To Be Tied:  Conformation-Directed Macrocyclization of Peptoid Foldamers (2007)

Covalent macrocyclic constraints can be readily installed on N-substituted glycine "peptoid" oligomer substrates. Cu(I)-catalyzed [3+2] cycloaddition reactions were conducted on solid support to ligate peptoid side chain azide and alkyne functionalities. Intramolecular macrocycle formation is facilitated by preorganizing the reactive groups across one turn of the helical secondary structure. These results confirm that conformational ordering can be exploited to assist the macrocyclization of folded oligomers.
Clinical and preclinical studies presented at the Keystone Symposium on Arthritis, Related Diseases, and Cytokines. (1993)

Topics include treatment of multiple sclerosis (MS) with T cell receptor (TCR) peptides, rheumatoid arthritis (RA) with IL-1ra, IL-2 toxin conjugate, or antibodies to TNF, to CD4, or to ICAM-1, sepsis and five other diseases with IL-1ra, and treatment of experimental animal diseases with soluble receptors, IL-12, TGF-beta2, or small molecule antagonists of cytokines.
Synthetic antibodies from a four-amino-acid code: A dominant role for tyrosine in antigen recognition (2004)

Antigen-binding fragments (Fabs) with synthetic antigen-binding sites were isolated from phage-displayed libraries with restricted complementarity-determining region (CDR) diversity. Libraries were constructed such that solvent-accessible CDR positions were randomized with a degenerate codon that encoded for only four amino acids (tyrosine, alanine, aspartate, and serine). Nonetheless, high-affinity Fabs (K(d) = 2-10 nM) were isolated against human vascular endothelial growth factor (hVEGF), and the crystal structures were determined for two distinct Fab-hVEGF complexes. The structures revealed that antigen recognition was mediated primarily by tyrosine side chains, which accounted for 71% of the Fab surface area that became buried upon binding to hVEGF. In contrast, aspartate residues within the CDRs were almost entirely excluded from the binding interface. Alanine and serine residues did not make many direct contacts with antigen, but they allowed for space and conformational flexibility and thus played an auxiliary role in facilitating productive contacts between tyrosine and antigen. Tyrosine side chains were capable of mediating most of the contacts necessary for high-affinity antigen recognition, and, thus, it seems likely that the overabundance of tyrosine in natural antigen-binding sites is a consequence of the side chain being particularly well suited for making productive contacts with antigen. The findings shed light on the basic principles governing the evolution of natural immune repertoires and should also aid the development of improved synthetic antibody libraries.
Peptide-YY, a New Partner in the Negative Feedback Control of Pancreatic Secretion* (1991)

Peptide YY (PYY), a newly discovered ileocolonic peptide, is released by nutrients in the proximal and distal intestine and inhibits pancreatic secretion. However, it is not clear whether PYY can be released in the absence of nutrients in the intestine or whether a physiological role exists for endogenous PYY in negative feedback regulation of pancreatic secretion by pancreatic proteases. In the present study we measured plasma PYY concentrations and determined the effects of anti-PYY serum during stimulation of pancreatic secretion by pancreatic juice diversion (PJD). The effect of SMS 201-995 (SMS; an analog of somatostatin), another inhibitor of pancreatic secretion, on regulation of PYY release induced by PJD was also investigated. Male Wistar rats equipped with pancreatic, biliary, duodenal, and jugular venous cannulas were studied 4-6 days postoperatively. After 90 min of basal collection, pancreatic juice was diverted for 4 h with or without infusion of SMS (2 micrograms/kg.h), given either iv or intraduodenally (ID). Plasma PYY concentrations were significantly increased from a basal level of 177 +/- 15 pg/ml to a peak level of 328 +/- 43 pg/ml 2 h after PJD. These increases in PYY concentration paralleled those in pancreatic protein and fluid outputs. Both iv and ID infusion of SMS during the first 2 h of PJD markedly decreased the plasma PYY concentration to 134 +/- 27 pg/ml and 156 +/- 19 pg/ml, respectively; the total incremental PYY release during 4 h of PJD was inhibited by 100% and 84% by iv and ID SMS, respectively. One milliliter of anti-PYY serum given iv significantly augmented the increment in protein and fluid output during PJD. These results suggest that endogenous PYY released by PJD may play a physiological role in negative feedback regulation of pancreatic secretion in rats.
An Open Software Environment to Optimize the Productivity of Robotized Laboratories (1994)

A robotic system for processing chemical and biological samples is composed of a hardware environment and a software environment. This article describes the features of a software tool for the design, simulation, optimization, and real-time management of robotic systems. The software has access to powerful scheduling algorithms based on heuristics that allow parallel processing of samples at various status levels. These features are explained via an application that prepares and analyzes fatty acid methyl esters derived from whole cells of bacteria. The software is based on the strategic concepts of global approach and open architecture. The application of these concepts simplify the implementation of any computer-driven device. They also provide the necessary flexibility and evolvability features that permit the robotic environment to be modified, extended, and upgraded to multi-application multirobot systems.
Mice expressing a humanized form of VEGF-A may provide insights into the safety and efficacy of anti-VEGF antibodies (2007)

VEGF-A is important in tumor angiogenesis, and a humanized anti-VEGF-A monoclonal antibody (bevacizumab) has been approved by the FDA as a treatment for metastatic colorectal and nonsquamous, non-small-cell lung cancer in combination with chemotherapy. However, contributions of both tumor- and stromal-cell derived VEGF-A to vascularization of human tumors grown in immunodeficient mice hindered direct comparison between the pharmacological effects of anti-VEGF antibodies with different abilities to block host VEGF. Therefore, by gene replacement technology, we engineered mice to express a humanized form of VEGF-A (hum-X VEGF) that is recognized by many anti-VEGF antibodies and has biochemical and biological properties comparable with WT mouse and human VEGF-A. The hum-X VEGF mouse model was then used to compare the activity and safety of a panel of VEGF Mabs with different affinities for VEGF-A. Although in vitro studies clearly showed a correlation between binding affinity and potency at blocking endothelial cell proliferation stimulated by VEGF, in vivo experiments failed to document any consistent correlation between antibody affinity and the ability to inhibit tumor growth and angiogenesis in most animal models. However, higher-affinity antibodies were more likely to result in glomerulosclerosis during long-term treatment.
A Stable Mixed Disulfide between Thioredoxin Reductase and Its Substrate, Thioredoxin:  Preparation and Characterization (1996)

The flavoenzyme thioredoxin reductase (TrR) catalyzes the reduction of the small redox protein thioredoxin (Tr) by NADPH. It has been proposed that a large conformational change is required in catalysis by TrT in order to visualize a complete pathway for reduction of equivalents. The proposal is based on the comparison of the crystal structures of TrR and glutathione reductase, the latter being a well-understood member of the enzyme family [Waksman, G., et al. (1994) J. Mol. Biol. 236, 800-816]. Bound NADPH is perfectly positioned for electron transfer to the FAD in glutathione reductase, but in TrR, these two components are 17 angstroms apart. In order to provide evidence for the proposed conformational change, a complex between TrR and its substrate Tr involving a mixed disulfide between TrR and Tr was prepared. The redox active disulfide of TrR is composed of Cys135 and Cys138, and the redox active disulfide of Tr is made up of Cys32 and Cys35. The complex C135S-C32S is prepared from forms of TrR and Tr altered by site-directed mutagenesis where Cys138 and Cys35 are remaining in TrR and Tr, respectively. The purified C135S-C32S presents a band on a nonreducing sodium dodecyl sulfate-polyacrylamide gel electrophoresis responding to a molecular weight sum of one subunit of TrR and one of Tr. Several observations indicate that C135S-C32S can adopt only one conformation. It was reported previously that TrR C135S can form a charge transfer complex in the presence of ammonium cation in which the donor is the remaining thiolate of Cys138 [Prongay, A.J., et al., (1989) J. Biol. Chem. 264, 2656-2664], while titration of C135S-C32S with NH4Cl does not induce charge transfer, presumably because Cys138 is participating in the mixed dissulfide. Reduction of C135S-C32S with dithiothreitol (DTT) results in a decrease of epsilon454 to a value similar to that of TrR C135S, and subsequent NH4Cl titration leads to charge transfer complex formation in the nascent TrR C135S. Reductive titrations show that approximately 1 equiv of sodium dithionite or NADPH is required to fully reduce C135S-C32S, and treatment with NH4Cl and DTT demonstrates that the mixed disulfide between Cys138 of TrR C135S and Cys35 of TrC32S that locks the structure in a conformation where FAD can be reduced by NADPH, but electrons cannot flow from FADH2 to the mixed disulfide bond.
"Destemming" Cancer Stem Cells (2007)

Cancer stem cells have been variously defined as cells within a cancer that have the exclusive ability to self-renew and to differentiate into the heterogeneous lineages of cancer cells that comprise the tumor. Interest in cancer stem cells is currently high, arising from recent reports identifying cell surface markers that can be used to sort such cells from primary human tumors. However, use of the term cancer stem cell may be misleading. A better term might be cancer-initiating cells because it remains to be demonstrated that cancer stem cells have the properties that define normal stem cells, including multipotency and the ability to undergo asymmetric and symmetric divisions. Many properties of cancer stem cells remain unclear, particularly the stability of their phenotype. These uncertainties must be considered in the development and testing of compounds targeted against putative cancer stem cells. Tumors apparently contain very few cancer stem cells, so that when tests of compounds targeted to such cells are designed, short-term response trials may not be informative and long-term trials must be planned, particularly if the drugs could also kill normal stem cells.
Point to Set Similarity Based Deep Feature Learning for Person Re-Identification (2017)

Person re-identification (Re-ID) remains a challenging problem due to significant appearance changes caused by variations in view angle, background clutter, illumination condition and mutual occlusion. To address these issues, conventional methods usually focus on proposing robust feature representation or learning metric transformation based on pairwise similarity, using Fisher-type criterion. The recent development in deep learning based approaches address the two processes in a joint fashion and have achieved promising progress. One of the key issues for deep learning based person Re-ID is the selection of proper similarity comparison criteria, and the performance of learned features using existing criterion based on pairwise similarity is still limited, because only P2P distances are mostly considered. In this paper, we present a novel person Re-ID method based on P2S similarity comparison. The P2S metric can jointly minimize the intra-class distance and maximize the inter-class distance, while back-propagating the gradient to optimize parameters of the deep model. By utilizing our proposed P2S metric, the learned deep model can effectively distinguish different persons by learning discriminative and stable feature representations. Comprehensive experimental evaluations on 3DPeS, CUHK01, PRID2011 and Market1501 datasets demonstrate the advantages of our method over the state-of-the-art approaches.
Immunoregulatory functions of VISTA (2017)

Utilization of negative checkpoint regulators (NCRs) for cancer immunotherapy has garnered significant interest with the completion of clinical trials demonstrating efficacy. While the results of monotherapy treatments are compelling, there is increasing emphasis on combination treatments in an effort to increase response rates to treatment. One of the most recently discovered NCRs is VISTA (V-domain Ig-containing Suppressor of T cell Activation). In this review, we describe the functions of this molecule in the context of cancer immunotherapy. We also discuss factors that may influence the use of anti-VISTA antibody in combination therapy and how genomic analysis may assist in providing indications for treatment.
Effects of fiber length on the tensile strength of epoxy/glass fiber and polyester/glass fiber composites (1980)

Abstract In discontinuous fiber‐reinforced composites, the shear strength at the fiber–matrix interface plays an important role in determining the reinforcing effect. In this paper, a method was devised to accurately determine this shear strength, taking the strength distribution of glass fiber into consideration. Calculated strength values based on the shear strenght obtained by the method were in better agreement with the experimental observations than those calculated by employing the shear strength obtained on the assumption that the fiber strength was uniform. The tensile strength of composites increases with increasing aspect ratio of the reinforcing fibers. This trend is almost the same regardless of the kind of matrix, the nature of interfacial treatment, and the environmental temperature. When composites are reinforced with random‐planar orientation of short glass fibers of 1.5 times the mean critical fiber length, the tensile strength of composite reaches about 90% of the theoretical strength of composites reinforced with continuous glass fiber. Reinforcing with glass fibers 5 times the critical length, the tensile strength reaches about 97% of theoretical. However, from a practical point of view, it is adequate to reinforce with short fibers of 1.5–2.0 times the mean critical fiber lenght.
MiR-124 Inhibits Growth and Enhances Radiation-Induced Apoptosis in Non-Small Cell Lung Cancer by Inhibiting STAT3 (2017)

Taking these observations into consideration, we illustrated that miR-124 is a potential target for enhancing the radiosensitivity of NSCLC cells by targeting STAT3.
Solar simulator for concentrator photovoltaic systems (2008)

A solar simulator for measuring performance of large area concentrator photovoltaic (CPV) modules is presented. Its illumination system is based on a Xenon flash light and a large area collimator mirror, which simulates natural sun light. Quality requirements imposed by the CPV systems have been characterized: irradiance level and uniformity at the receiver, light collimation and spectral distribution. The simulator allows indoor fast and cost-effective performance characterization and classification of CPV systems at the production line as well as module rating carried out by laboratories.
BCL-2 Overexpression Attenuates Cortical Cell Loss after Traumatic Brain Injury in Transgenic Mice (1998)

The proto-oncogene, BCL-2, has been suggested to participate in cell survival during development of, and after injury to, the CNS. Transgenic (TG) mice overexpressing human Bcl-2 (n = 21) and their wild-type (WT) littermates (n = 18) were subjected to lateral controlled cortical impact brain injury. Lateral controlled cortical impact brain injury resulted in the formation of a contusion in the injured cortex at 2 days, which developed into a well-defined cavity by 7 days in both WT and TG mice. At 7 days after injury, brain-injured TG mice had a significantly reduced cortical lesion (volume = 1.99 mm3) compared with that of the injured WT mice (volume = 5.1 mm3, P < 0.01). In contrast, overexpression of BCL-2 did not affect the extent of hippocampal cell death after lateral controlled cortical impact brain injury. Analysis of motor function revealed that both brain-injured WT and TG mice exhibited significant right-sided deficits at 2 and 7 days after injury (P < 0.05 compared with the uninjured controls). Although composite neuroscores (sum of scores from forelimb and hind limb flexion, lateral pulsion, and inclined plane tests) were not different between WT and TG brain-injured mice, TG mice had a slightly but significantly reduced deficit in the inclined plane test (P < 0.05 compared to the WT mice). These data suggest that the cell death regulatory gene, BCL-2, may play a protective role in the pathophysiology of traumatic brain injury.
Comparison of Topoisomerase I Inhibition, DNA Damage, and Cytotoxicity of Camptothecin Derivatives Presently in Clinical Trials (1994)

Kinetics of the reversal of drug-induced SSB in isolated nuclei suggest that dissociation of SN-38 from cleavable complexes is much slower than that of CPT. Cleavage patterns of CPT and 9-AC were similar but differed from those of TPT and SN-38. Although in vitro analyses do not necessarily reflect chemotherapeutic efficacy, this study found that SN-38 is the most potent compound and that 9-AC and TPT are less active than CPT in this system. The effect of CPT-11 is minimal. Therefore, the clinical activity of CPT-11 may strongly depend on its hydrolysis to SN-38. Differences in DNA sequence selectivity and the stability of cleavable complexes induced by the drugs may also contribute to differences among CPT derivatives.
Cytokine patterns in adults with aids (1997)

The character of cytokine response in AIDS patients may be directly related to the stimulus employed in test systems. There is no evidence for Th1/Th2 dysregulation. Cytokine elevations in AIDS patients generally are reflective of chronic infection (the virus). Lymphocytes from AIDS patients do not respond as well to stimulation as do those from normal healthy volunteers. The stimulated lymphocyte response in AIDS patients suggests there is underlying low-grade host versus virus reaction in these patients (exaggerated responses of IL-3, IL-4, IL-8, TGF-B).
Mutational Landscape of the Essential Autophagy Gene BECN1 in Human Cancers (2014)

Contrary to previous reports, BECN1 is not significantly mutated in human cancer and not a tumor-suppressor gene, as originally thought. VISUAL OVERVIEW: http://mcr.aacrjournals.org/content/early/2014/04/01/1541-7786.MCR-13-0614/F1.large.jpg.
Troponin elevation in coronary vs. non-coronary disease (2010)

Acute myocardial infarction is defined as myocardial cell death due to prolonged myocardial ischaemia. Cardiac troponins (cTn) are the most sensitive and specific biochemical markers of myocardial injury and with the new high-sensitivity troponin methods very minor damages on the heart muscle can be detected. However, elevated cTn levels indicate cardiac injury, but do not define the cause of the injury. Thus, cTn elevations are common in many disease states and do not necessarily indicate the presence of a thrombotic acute coronary syndrome (ACS). In the clinical work it may be difficult to interpret dynamic changes of troponin in conditions such as stroke, pulmonary embolism, sepsis, acute perimyocarditis, Tako-tsubo, acute heart failure, and tachycardia. There are no guidelines to treat patients with elevated cTn levels and no coronary disease. The current strategy of treatment of patients with elevated troponin and non-acute coronary syndrome involves treating the underlying causes. The aim of this paper is to review data from studies of non-ACS patients with acutely elevated troponin who in clinical practice may be difficult to discriminate from ACS patients.
Bioseparation of proteins : unfolding/folding and validations (1998)

Introduction. Steps in Bioseparation Processes. High Resolution Fractionation Processes. Protein Inactivation during Bioseparation. Adsorption Influence on Bioseparation and Inactivation. Process Monitoring and Validation. Applications and Economics of Bioseparation. Protein Inactivation Avoidance and Refolding during Bioseparation. Subject Index.
Jointly Optimized Multiuser Beamforming for the MIMO Broadcast Channel with Limited Feedback (2007)

This paper considers the joint optimization of the transmitter beamforming filters and receiver combining filters for the multiple-input multiple-output (MIMO) broadcast channel. A low-complexity iterative algorithm to compute the filters is proposed and then a closed-form expression of the filters for the downlink with two transmit antennas is derived, avoiding the need for iterative computation in this case. To enable practical implementation, a new limited feedback algorithm is proposed that exploits the channel structure in the closed form solution, and is independent of the number of receive antennas. Performance is evaluated by Monte Carlo simulations as a function of the amount of feedback. With two receive antennas, the proposed method performs close to the sum capacity of the MIMO broadcast channel, without the need for multiuser diversity and with only limited feedback.