gebhart/patrepeval huggingface dataset:
Structure-Function Relationships of Human C5a and C5aR (2003)

Using peptides that represent linear regions of the powerful complement activation product, C5a, or loops that connect the four alpha helices of C5a, we have defined the ability of these peptides to reduce binding of (125)I-C5a to human neutrophils, inhibit chemotactic responses of neutrophils to C5a, and reduce H(2)O(2) production in neutrophils stimulated with PMA. The data have defined likely sites of interaction of C5a with C5aR. The peptides had no functional activity per se on neutrophils and did not interfere with neutrophil responses to the unrelated chemotactic peptide, N-formyl-Met-Leu-Phe. Although previous data have suggested that there are two separate sites on C5a reactive with C5aR, the current data suggest that C5a interacts with C5aR in a manner that engages three discontinuous regions of C5a.
Lower Plasma Levels and Accelerated Clearance of High Density Lipoprotein (HDL) and Non-HDL Cholesterol in Scavenger Receptor Class B Type I Transgenic Mice (1999)

Recent studies have indicated that the scavenger receptor class B type I (SR-BI) may play an important role in the uptake of high density lipoprotein (HDL) cholesteryl ester in liver and steroidogenic tissues. To investigate the in vivo effects of liver-specific SR-BI overexpression on lipid metabolism, we created several lines of SR-BI transgenic mice with an SR-BI genomic construct where the SR-BI promoter region had been replaced by the apolipoprotein (apo)A-I promoter. The effect of constitutively increased SR-BI expression on plasma HDL and non-HDL lipoproteins and apolipoproteins was characterized. There was an inverse correlation between SR-BI expression and apoA-I and HDL cholesterol levels in transgenic mice fed either mouse chow or a diet high in fat and cholesterol. An unexpected finding in the SR-BI transgenic mice was the dramatic impact of the SR-BI transgene on non-HDL cholesterol and apoB whose levels were also inversely correlated with SR-BI expression. Consistent with the decrease in plasma HDL and non-HDL cholesterol was an accelerated clearance of HDL, non-HDL, and their major associated apolipoproteins in the transgenics compared with control animals. These in vivo studies of the effect of SR-BI overexpression on plasma lipoproteins support the previously proposed hypothesis that SR-BI accelerates the metabolism of HDL and also highlight the capacity of this receptor to participate in the metabolism of non-HDL lipoproteins.
Delta-Sleep-Inducing Peptide: Solution Conformational Studies of a Membrane-Permeable Peptide (1994)

Peptides and peptide-like molecules as a class have very poor permeability through biological membranes, which severely compromises their potential effectiveness as therapeutic agents. In order to gain insight into the problem of delivering peptide and protein drugs and to establish a model in which the effects of systematic structural variations on transport can be explored, an investigation of the solution conformation of a membrane-permeable peptide was undertaken. Delta-sleep-inducing peptide (DSIP, MW 849) was used in this investigation. DSIP is a charged, hydrophilic peptide that possesses the unusual ability to diffuse passively across the blood-brain barrier (BBB) in vivo [Kastin, A. J., Banks, W. A., Castellanos, P. F., Nissen, C., & Coy, D. H. (1982) Pharmacol. Biochem. Behav. 17, 1187-1191] and across monolayers of brain microvessel endothelial cells in vitro, a model of the BBB [Raeissi, S., & Audus, K. L. (1989) J. Pharm. Pharmacol. 41, 848-852]. This nonapeptide was studied in solution using one- and two-dimensional nuclear magnetic resonance (NMR), circular dichroism (CD), Fourier transform infrared (FT-IR), and fluorescence spectroscopies in conjunction with molecular modeling. Our spectroscopic findings suggest that DSIP exists in a dynamic equilibrium between unordered and folded structures. Residues 2-5 and 6-9 tend to form type I beta-turns in aqueous solution and a similar, but more ordered, helix-like structure inducible in 40% trifluoroethanol (TFE). NMR, FT-IR, and CD studies in aqueous solution support the dynamic equilibrium hypothesis with the IR data, suggesting that the beta-turn population is approximately 40%.(ABSTRACT TRUNCATED AT 250 WORDS)
Ultrasound of the male genital tract in relation to male reproductive health (2014)

MGT-CDUS is a useful tool in detecting abnormalities related to impaired male reproductive health. However, it suffers from a lack of standardization and often produces subjective/vague diagnoses. To fill this gap, the European Academy of Andrology has promoted an ongoing multicenter study aimed at defining the MGT-CDUS characteristics of healthy, fertile men.
Green tea catechins such as (−)‐epicatechin and (−)‐epigallocatechin accelerate Cu2+‐induced low density lipoprotein oxidation in propagation phase (1997)

Effects of (-)-epicatechin (EC) and (-)-epigallocatechin (EGC) on Cu2+-induced low density lipoprotein (LDL) oxidation were studied in initiation and propagation phases. When 1.5 microM EC or EGC was added to the mixture of isolated human LDL and Cu2+ in the initiation phase, the oxidation of LDL was inhibited in agreement with previous findings. In contrast, in the propagation phase, 1.5 microM of EC or EGC worked as an accelerator of the oxidation, and acceleration ratios (maximum about 6 times) were modified depending on the concentrations of catechin used and the oxidation process in the propagation phase. The evidence was obtained from formation of thiobarbituric acid reactive substances (TBARS), detecting conjugated diene measured by absorbance at 234 nm and investigating fragmentation of apoprotein B (apo B) in LDL. Even in the propagation phase of LDL oxidation, the elevated concentrations of EC or EGC worked as inhibitors: after 40 min incubation of LDL with Cu2+, 10.0 microM EC or 2.0 microM EGC inhibited LDL oxidation. Yet, nitric oxide (NO) released from 5 microM zwitterionic polyamine/NO adducts had an inhibitory in all phases of LDL oxidation. These results indicate that catechins such as EC and EGC can act as free radical terminators (reducing agents) or accelerators (oxidizing agents) under oxidation circumstances, which is a different character from NO. From the above evidence, further investigations are needed on many natural flavonoids, the most potent antioxidative compounds in foods.
Biochemical modulation of skin reactions : transdermals, topicals, cosmetics (2000)

SECTION I: INTRODUCTION AND GENERAL CONSIDERATIONS Fundamental Concepts in Transdermal Delivery of Drugs-Agis F. Kydonieus, John J. Wille, and George F. Murphy The Skin as a Barrier: Structure and Function-Thomas J. Franz and Paul A. Lehman Epidermal Lipid Metabolism and Barrier Function of Stratum Corneum-Philip W. Wertz and Bozena B. Michniak Methods for Testing the Irritation and Sensitization Potential of Drugs and Enhancers-Saqib J. Bashir and Howard I. Maibach Quantitative Structure Analysis Relationships in the Prediction of Skin Sensitization Potential-Saqib J. Bashir and Howard I. Maibach Methods for Testing the Phototoxicity and Photosensitization of Drugs-Norbert J. Neumann, B. Homey, H.W. Vohr, and P. Lehmann SECTION II: CELLULAR AND HUMORAL REGULATION AND PATHOGENESIS Mechanisms of Allergic and Irritant Contact Dermatitis-Paul Wakem and Anthony A. Gaspari The Langerhans Cell: Antigen Processing/Antigen Presentation-Ralf W. Denfeld and Jan C. Simon The Keratinocyte in Cutaneous Irritation and Sensitization-Alain Coquette, Nancy Berna, Yves Poumay, and Mark R. Pittelkow Pathogenesis of Allergic Contact Dermatitis: Role of T-Cells-Richard S. Kalish The Keratinocyte In Cutaneous Irritation and Sensitization- Mast Cells Regulate Endothelial Cell Function in Inflammation and Repair-Marcia R. Monteiro and George F. Murphy Interleukin-1 Receptors and Signal Transduction-Charles A. Dinarello Proinflammatory Mediators of the Arachidonic Acid Cascade-Kouichi Kiai SECTION III: BIOCHEMICAL MODULATORS AND MODES OF ACTION Modulation of Skin Reactions: A General Overview-Agis F. Kydonieus and John J. Wille Glucocorticoids-Michel Cormier, James Matriano, and Alfred Amkraut Ion Channel Modulation of Contact Dermatitis-John J. Wille, Agis F. Kydonieus, and Richard S. Kalish Mast Cell Degranulating Agents Modulate Skin Immune Responses-John J. Wille, Agis F. Kydonieus, and George F. Murphy Modulation of Neurogenic Inflammation by Strontium-Gary S. Hahn Skin Tolerability of Iontophoresis Treatment-Bret Berner and Donald R. Wilson The Effects of Ultraviolet Radiation on the Immune Response-Stephen E. Ullrich Immune Tolerance and Its Potential to Control Skin Reactions-Richard S. Kalish Future Prospects and Areas of Promising Research-J. Wayne Streifeiy and Sharmila Masli Index
Flexibility of dna binding domain of trp repressor required for recognition of different operator sequences (1996)

Trp repressor (25 kDa) is a regulatory protein that controls transcription initiation in the tryptophan biosynthetic operon and at least four other operons in Escherichia coli. An alanine to valine mutation (AV77) in the DNA binding domain is known to increase repressor activity at the trp operator in vivo, but not in vitro. We report here the amide proton exchange rates for the DNA-binding domains of both the wild-type and AV77 proteins. We find that the alanine to valine change stabilizes the flexible DNA-binding domain of the repressor. We present in vivo data showing that, although the AV77 repressor is more inhibitory at the trp operator than the wild-type repressor, it does not have increased activity at the aroH or trpR operator; repression at the aroH operator is, in fact, reduced. Our results suggest that the flexibility exhibited by the wild-type repressor allows a broader range of repressor/DNA interactions, whereas the increased rigidity resulting from the AV77 change limits the repressor's effectiveness at some operators.
Clustering and conservation patterns of human microRNAs (2005)

MicroRNAs (miRNAs) are approximately 22 nt-long non-coding RNA molecules, believed to play important roles in gene regulation. We present a comprehensive analysis of the conservation and clustering patterns of known miRNAs in human. We show that human miRNA gene clustering is significantly higher than expected at random. A total of 37% of the known human miRNA genes analyzed in this study appear in clusters of two or more with pairwise chromosomal distances of at most 3000 nt. Comparison of the miRNA sequences with their homologs in four other organisms reveals a typical conservation pattern, persistent throughout the clusters. Furthermore, we show enrichment in the typical conservation patterns and other miRNA-like properties in the vicinity of known miRNA genes, compared with random genomic regions. This may imply that additional, yet unknown, miRNAs reside in these regions, consistent with the current recognition that there are overlooked miRNAs. Indeed, by comparing our predictions with cloning results and with identified miRNA genes in other mammals, we corroborate the predictions of 18 additional human miRNA genes in the vicinity of the previously known ones. Our study raises the proportion of clustered human miRNAs that are <3000 nt apart to 42%. This suggests that the clustering of miRNA genes is higher than currently acknowledged, alluding to its evolutionary and functional implications.
Improvement of Metal–Insulator–Semiconductor-Type Organic Light-Emitting Transistors (2008)

We developed metal–insulator–semiconductor-type organic light-emitting transistors (MIS-OLETs), and improved their properties by optimizing the device structure. MIS-OLETs showed a maximum drain current of ID = -149 µA, maximum luminance of 1034 cd/m2 (VD = -20 V, VG = -50 V) and on/off ratio of over 104. Moreover an active-matrix display using MIS-OLETs on a plastic substrate was fabricated. The developed 16×16 active-matrix-drive organic light-emitting transistors (AMOLET) showed excellent properties by optimizing device structure.
Back to the future: Ribonuclease A (2007)

Pancreatic ribonuclease A (EC 3.1.27.5, RNase) is, perhaps, the best-studied enzyme of the 20th century. It was isolated by René Dubos, crystallized by Moses Kunitz, sequenced by Stanford Moore and William Stein, and synthesized in the laboratory of Bruce Merrifield, all at the Rockefeller Institute/University. It has proven to be an excellent model system for many different types of experiments, both as an enzyme and as a well-characterized protein for biophysical studies. Of major significance was the demonstration by Chris Anfinsen at NIH that the primary sequence of RNase encoded the three-dimensional structure of the enzyme. Many other prominent protein chemists/enzymologists have utilized RNase as a dominant theme in their research. In this review, the history of RNase and its offspring, RNase S (S-protein/S-peptide), will be considered, especially the work in the Merrifield group, as a preface to preliminary data and proposed experiments addressing topics of current interest. These include entropy-enthalpy compensation, entropy of ligand binding, the impact of protein modification on thermal stability, and the role of protein dynamics in enzyme action. In continuing to use RNase as a prototypical enzyme, we stand on the shoulders of the giants of protein chemistry to survey the future.
Superparamagnetic Photonic Crystals (2001)

Photonic crystals consisting of monodisperse superparamagnetic colloidal particles have been synthesized. The particles (see Figure) are obtained by emulsion polymerization of styrene in the presence of freshly precipitated surface-modified iron oxide nanoparticles. A magnetic field self-assembles the particles and controls the diffraction wavelength and crystal parameters of the array.
Metal-organic frameworks—New materials for hydrogen storage (2007)

Published data on the physical sorption of hydrogen by new materials with a large specific surface area, crystalline microporous metal-organic frameworks (MOFs), are systematized and analyzed. The hydrogen-accumulating properties of MOFs are compared with those of traditional materials (charcoals and zeolites) and nanocarbon systems. The role of secondary hydrogen spillover in the development of new approaches to increase the adsorption capacity of hydrogen storage materials is separately considered.
Ado-trastuzumab Emtansine (2014)

Ado-trastuzumab emtansine is a novel ADC effective for HER2-positive MBC in patients previously treated with trastuzumab, lapatinib, and a taxane. Further studies will determine its use in the adjuvant and neoadjuvant setting and in combination with pertuzumab.
CD69-triggered ERK activation and functions are negatively regulated by CD94 / NKG2-A inhibitory receptor (2000)

CD69 represents a functional triggering molecule on activated NK and T cells, capable of inducing cytotoxic activity and costimulating cytokine production. It belongs to the C-lectin type superfamily, and its gene maps in the NK gene complex, close to other genes coding for NK receptors. CD94 / NKG2-A complex is the inhibitory receptor for the non classical MHC class I molecule HLA-E on human NK cells. To investigate CD69-initiated signal transduction pathways, and to evaluate CD94 / NKG2-A interference on CD69 triggering ability, we have generated transfectants expressing both receptors in the RBL cell line. Here we report that CD69 engagement leads to the activation of extracellular signal-regulated kinase (ERK) enzymes belonging to the MAPK family, and that this event is required for CD69-mediated cell degranulation. Moreover, we show that the co-engagement of CD94 / NKG2-A inhibitory receptor effectively suppresses both CD69-triggered cell degranulation in RBL transfectants, through the inhibition of ERK activation, and CD69-induced cytotoxicity in human NK cells. Thus, here we provide new information on the molecular mechanisms initiated by CD69 activation receptor, and show that CD69-initiated signaling pathways and functional activity are negatively regulated by CD94 / NKG2-A inhibitory complex.
Domain Shapes and Patterns: The Phenomenology of Modulated Phases (1995)

A wide variety of two- and three-dimensional physical-chemical systems display domain patterns in equilibrium. The phenomenology of these patterns, and of the shapes of their constituent domains, is reviewed here from a point of view that interprets these patterns as a manifestation of modulated phases. These phases are stabilized by competing interactions and are characterized by periodic spatial variations of the pertinent order parameter, the corresponding modulation period generally displaying a dependence on temperature and other external fields. This simple picture provides a unifying framework to account for striking and substantial similarities revealed in the prevalent "stripe" and "bubble" morphologies as well as in commonly observed, characteristic domain-shape instabilities. Several areas of particular current interest are discussed.
EEG sleep changes as predictors in depression (1976)

The authors conducted a study of 18 depressed patients to see whether EEG sleep measurements might provide a predictive tool for response to antidepressant medication. They found that although the sedative characteristics of amitriptyline did not differentiate good responders from poor responders until the third week of drug treatment, the good responders showed significant increases in REM latency, decreases in REM sleep time, decreases in REM sleep percent, and decreases in REM activity after only 2 nights of drug treatment.
Kyphoplasty and Vertebroplasty for the Treatment of Painful Osteoporotic Compression Fractures (2001)

Study Design: Literature review Objectives: To describe new treatments for painful osteoporotic compression fractures in light of available scientific literature and clinical experience. Summary of Background Data. Painful vertebral osteoporotic compression fractures lead to significant morbidity and mortality. This relates to pulmonary dysfunction, eating disorders (nutritional deficits), pain, loss of independence, and mental status change (related to pain and medications). Medications to treat osteoporosis (primarily antiresorptive) do not effectively treat the pain or the fracture, and require over 1 year to reduce the degree of osteoporosis. Kyphoplasty and vertebroplasty are new techniques that help decrease the pain and improve function in fractured vertebrae. Methods. This is a descriptive review of the background leading to vertebroplasty and kyphoplasty, a description of the techniques, a review of the literature, as well as current ongoing studies evaluating kyphoplasty. Results: Both techniques have had a very high acceptance and use rate. There is 95% improvement in pain and significant improvement in function following treatment by either of these percutaneous techniques. Kyphoplasty improves height of the fractured vertebra, and improves kyphosis by over 50%, if performed within 3 months from the onset of the fracture (onset of pain). There is some height improvement, though not as marked, along with 95% clinical improvement, if the procedure is performed after 3 months. Complications occur with both and relate to cement leakage in both, and cement emboli with vertebroplasty. Conclusion: Kyphoplasty and vertebroplasty are safe and effective, and have a useful role in the treatment of painful osteoporotic vertebral compression fractures that do not respond to conventional treatments. Kyphoplasty offers the additional advantage of realigning the spinal column and regaining height of the fractured vertebra, which may help decrease the pulmonary, GI, and early morbidity consequences related to these fractures. Both procedures are technically demanding. [
Hydroxyurea for the Treatment of Sickle Cell Anemia (2008)

An 18-year-old woman with sickle cell anemia presents with recurrent painful crises, and treatment with hydroxyurea is recommended. Hydroxyurea causes a shift toward the production of red cells containing fetal hemoglobin. A possible increase in the risk of acute leukemia due to hydroxyurea therapy remains the subject of debate.
Guaranteed global optimization of thin-film optical systems (2019)

Abstract A parallel deterministic global optimization algorithm for thin-film multilayer optical coatings is developed. This algorithm enables locating a global solution to an optimization problem in this class to within a user-specified tolerance. More specifically, the algorithm is a parallel branch-and-bound method with applicable bounds on the merit function computed using Taylor models. This study is the first one, to the best of our knowledge, to attempt guaranteed global optimization of this important class of problems, thereby providing an overview and an assessment of the current state of such techniques in this domain. As a proof of concept on a small scale, the method is illustrated numerically and experimentally in the context of antireflection coatings for silicon solar cells—we design and fabricate a three-layer dielectric stack on silicon that exhibits an average reflectance of (2.53 ± 0.10)%, weighted over a broad range of incident angles and the solar spectrum. The practicality of our approach is assessed by comparing its computational cost relative to traditional stochastic global optimization techniques which provide no guarantees on their solutions. While our method is observed to be significantly more computationally expensive, we demonstrate via our proof of concept that it is already feasible to optimize sufficiently simple practical problems at a reasonable cost, given the current accessibility of cloud computing resources. Ongoing advances in distributed computing are likely to bring more design problems within the reach of deterministic global optimization methods, yielding rigorous guaranteed solutions in the presence of practical manufacturing constraints.
The Human PICD Gene Encodes a Cytoplasmic and Peroxisomal NADP+-dependent Isocitrate Dehydrogenase (1999)

Human PICD was identified by homology probing the data base of expressed sequence tags with the protein sequence of Saccharomyces cerevisiae Idp3p, a peroxisomal NADP(+)-dependent isocitrate dehydrogenase. The human PICD cDNA contains a 1242-base pair open reading frame, and its deduced protein sequence is 59% identical to yeast Idp3p. Expression of PICD partially rescued the fatty acid growth defect of the yeast idp3 deletion mutant suggesting that PICD is functionally homologous to Idp3p. Kinetic studies on bacterially expressed PICD demonstrated that this enzyme catalyzed the oxidative decarboxylation of isocitrate to 2-oxoglutarate with a specific activity of 22.5 units/mg and that PICD displayed K(M) values of 76 microM for isocitrate and 112 microM for NADP(+). In subcellular fractionation experiments, we found PICD in both peroxisomes and cytoplasm of human and rat liver cells, with approximately 27% of total PICD protein associated with peroxisomes. The presence of PICD in mammalian peroxisomes suggests roles in the regeneration of NADPH for intraperoxisomal reductions, such as the conversion of 2, 4-dienoyl-CoAs to 3-enoyl-CoAs, as well as in peroxisomal reactions that consume 2-oxoglutarate, namely the alpha-hydroxylation of phytanic acid. As for cytoplasmic PICD, the phenotypes of patients with glucose-6-phosphate dehydrogenase deficiency (Luzzatto, L., and Mehta, A. (1995) in The Metabolic and Molecular Bases of Inherited Disease (Scriver, C. R., Beaudet, A. L., Sly, W. S., and Valle, D., eds) Vol. 3, 7th Ed., pp. 3367-3398, McGraw-Hill Inc., New York) suggest that PICD serves a significant role in cytoplasmic NADPH production, particularly under conditions that do not favor the use of the hexose monophosphate shunt (Luzzatto et al.).