gebhart/patrepeval huggingface dataset:
Sofosbuvir (Sovaldi) for the treatment of hepatitis C (2014)

Hepatitis C (HCV) remains an important cause of chronic liver disease worldwide. Historically, treatment included pegylated-interferon and ribavirin with low efficacy and numerous side effects contributing to poor adherence and impairment of patients' well-being. The next step in developing better treatment regimens for HCV led to the development of the first-generation direct acting antivirals (DAAs). Although these DAAs improved efficacy, they also added substantial side effects. The next generation of DAAs include Simeprevir and Sofosbuvir (SOF) which not only further enhanced the efficacy of the regimens but also improve their safety profile. This review summarizes the current clinical experience with SOF. SOF, an HCV-specific uridine nucleotide analog which inhibits the NS5B polymerase, is now available in the USA, Canada and Europe. Clinical trials of SOF-containing regimens have shown that these regimens are safe, efficacious, and well-tolerated in all genotypes. Additionally, SOF is associated with improved patient reported outcomes.
Recovery of Artemisinin from a Complex Reaction Mixture Using Continuous Chromatography and Crystallization (2015)

Artemisinin, a secondary metabolite of sweet wormwood, is the basis for the production of the most effective antimalarial drugs. Since the amount of artemisinin currently produced from plants is not sufficient to treat the worldwide malaria cases, an effective semisynthetic method was developed recently that is capable of producing artemisinin from dihydroartemisinic acid (DHAA). DHAA is a byproduct obtained during the extraction of artemisinin from plant leaves. The photocatalytic reaction to convert DHAA to artemisinin can be performed continuously in a tubular reactor using toluene as a solvent. The reactor effluent contains besides artemisinin the photocatalyst (dicyanoanthracene) and several compounds that are structurally similar to artemisinin, including unreacted DHAA starting material. To isolate artemisinin from the reaction mixture, two separation techniques were applied, crystallization and chromatography. The solid obtained by seeded cooling crystallization was highly enriched in artemisinin but contained also traces of the photocatalyst. In contrast, using a variant of continuously operated multicolumn simulated moving bed (SMB) chromatography, which splits the feed into three fractions, we were able to recover efficiently the photocatalyst in the raffinate stream. The extract stream provided already almost pure artemisinin, which could be finally further purified in a simple crystallization step.
The leucine zipper of c-Myc is required for full inhibition of erythroleukemia differentiation. (1990)

The leucine zipper motif has been observed in a number of proteins thought to function as eucaryotic transcription factors. Mutation of the leucine zipper interferes with protein dimerization and DNA binding. We examined the effect of point mutations in the leucine zipper of c-Myc on its ability to dimerize in vitro and to inhibit Friend murine erythroleukemia (F-MEL) differentiation. Glutaraldehyde cross-linking studies failed to provide evidence for homodimerization of in vitro-synthesized c-Myc protein, although it was readily demonstrated for c-Jun. Nevertheless, whereas transfected wild-type c-myc sequences strongly inhibited F-MEL differentiation, those with single or multiple mutations in the leucine zipper were only partially effective in this regard. Since the leucine zipper domain of c-Myc is essential for its cooperative effect in ras oncogene-mediated transformation, this study emphasizes the close relationship that exists between transformation and hematopoietic commitment and differentiation. c-Myc may produce its effects on F-MEL differentiation through leucine zipper-mediated heterodimeric associations rather than homodimeric ones.
Optical Integrated Circuits: A Personal Perspective (2008)

<para xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink"> The remarkable early success and current explosive growth of electronic integrated circuits have fascinated photonics researchers since 1969 with the prospect of similar success in optical integrated circuits. Alas, physical and economic factors have stymied their efforts. Two recent commercial optical integrated circuits may be the first points on a photonic Moore's law curve. The author presents his view of the progress of optical integrated circuits since S. E. Miller's proposal in the 1969 <emphasis emphasistype="boldital">Bell Systems Technical Journal</emphasis>. </para>
Highly multiplexed genotyping of coronary artery disease-associated SNPs using MALDI-TOF mass spectrometry (2002)

Highly multiplexed genotyping methods are needed to support a comprehensive analysis of single nucleotide polymorphisms (SNPs) in coronary artery disease (CAD)-related genes. In this study we evaluated chip-based MALDI-TOF mass spectrometry for multiplexed genotyping of SNPs associated with CAD. Our analysis included 14 healthy Japanese individuals and 19 Japanese patients with myocardial infarction whose first attack occurred before age 50. We selected 29 candidate genes involved in 1) the renin-angiotensin system, 2) lipid metabolism, 3) cytokines and adhesion molecules, 4) growth factors, and 5) the coagulation-fibrinolysis system. Genotyping of candidate SNPs was performed by MALDI-TOF MS using a MassARRAY system, and 4-plex analysis was achieved at a maximum. All 39 SNPs determined by the fluorescent dye-terminator cycle sequencing method from four randomly selected patients were found to be in complete agreement with the results obtained from MassARRAY system. Significant differences were observed in the -1965delG of PAI1 (SERPINE1) with respect to allelic frequency, the G>A in the promoter region SNP in SM22 (TAGLN) for dominant genotype, and in two other SNPs (C>T in intron 1 of HGF, and -1965delG of PAI1) for recessive genotype. Three SNPs (803T>C of AGT, 677CT of MTHFR, 190T>C of ADRB3) showed weak differences in allelic frequency. MALDI-TOF-MS provided high performance with a multiplex assay design for analysis of CAD-related SNPs by increasing the throughput while maintaining a high level of accuracy.
Chimeric Antigen Receptors T Cell Therapy in Solid Tumor: Challenges and Clinical Applications (2017)

Adoptive cellular immunotherapy (ACT) employing engineered T lymphocytes expressing chimeric antigen receptors (CARs) has demonstrated promising antitumor effects in advanced hematologic cancers, such as relapsed or refractory acute lymphoblastic leukemia, chronic lymphocytic leukemia, and non-Hodgkin lymphoma, supporting the translation of ACT to non-hematological malignancies. Although CAR T cell therapy has made remarkable strides in the treatment of patients with certain hematological cancers, in solid tumors success has been limited likely due to heterogeneous antigen expression, immunosuppressive networks in the tumor microenvironment limiting CAR T cell function and persistence, and suboptimal trafficking to solid tumors. Here, we outline specific approaches to overcome barriers to CAR T cell effectiveness in the context of the tumor microenvironment and offer our perspective on how expanding the use of CAR T cells in solid tumors may require modifications in CAR T cell design. We anticipate these modifications will further expand CAR T cell therapy in clinical practice.
Reversal of multidrug resistance in human breast cancer cell by psoralen (2004)

Objective To investigate the effect of reversing multidrug resistance (MDR) of psoralen in human breast cancer cell. Methods Psoralen, one kind of herd medicine, was selected and its reversal effect to MCF 7/ADR cell line was studied. MTT method used to determine the toxic effect and IC 50 and was used to examine the expression of P170 protein of multidrug resistance cell. Verapamil was used as positive control.Results Psoralen could reduce the value of IC 50 of adriamycin against MDR cells line MCF 7/ADR at non cytotoxic concentration and enhance the accumulation of adriamycin,but no marked change in expression of P 170 protein was observed. Conclusion Psoralen can reverse MDR of MCF 7/ADR cell of human breast cancer.
The association of hypotestosteronemia with coronary artery disease in men. (1994)

Hyperestrogenemia and hypotestosteronemia have been observed in association with myocardial infarction (MI) and its risk factors. To determine whether these abnormalities may be prospective for MI, estradiol and testosterone, as well as risk factors for MI, were measured in 55 men undergoing angiography who had not previously had an MI. Testosterone (r = -.36, P = .008) and free testosterone (r = -.49, P < .001) correlated negatively with the degree of coronary artery disease after controlling for age and body mass index. When the patient group was successively reduced to a final study group of 34 men by excluding the patients with other major disorders, the testosterone and free testosterone correlations persisted (r = -.43, P < .02 and r = -.62, P < .001, respectively). Neither estradiol nor the risk factors, except for high-density lipoprotein cholesterol, correlated with the degree of coronary artery disease in the final group. Testosterone correlated negatively with the risk factors fibrinogen, plasminogen activator inhibitor-1, and insulin and positively with high-density lipoprotein cholesterol. The correlations found in this study between testosterone and the degree of coronary artery disease and between testosterone and other risk factors for MI raise the possibility that in men hypotestosteronemia may be a risk factor for coronary atherosclerosis.
Homology-dependent Gene Silencing inParamecium (1998)

Microinjection at high copy number of plasmids containing only the coding region of a gene into the Paramecium somatic macronucleus led to a marked reduction in the expression of the corresponding endogenous gene(s). The silencing effect, which is stably maintained throughout vegetative growth, has been observed for all Paramecium genes examined so far: a single-copy gene (ND7), as well as members of multigene families (centrin genes and trichocyst matrix protein genes) in which all closely related paralogous genes appeared to be affected. This phenomenon may be related to posttranscriptional gene silencing in transgenic plants and quelling in Neurospora and allows the efficient creation of specific mutant phenotypes thus providing a potentially powerful tool to study gene function in Paramecium. For the two multigene families that encode proteins that coassemble to build up complex subcellular structures the analysis presented herein provides the first experimental evidence that the members of these gene families are not functionally redundant.
Persistence of Abdominal Symptoms After Successful Surgery for Idiopathic Slow Transit Constipation (2002)

To achieve predictable success in managing constipated patients, it is important that underlying pathophysiologic conditions be identified objectively, so that patients amenable to aggressive medical or surgical intervention can be identified. This review considers possible causes of persistence of abdominal symptoms after surgical relief of constipation.
Self-Assembly of Phosphate Fluorosurfactants in Carbon Dioxide (2004)

Anionic phosphodiester surfactants, possessing either two fluorinated chains (F/F) or one hydrocarbon chain and one fluorinated chain (H/F), were synthesized and evaluated for solubility and self-assembly in liquid and supercritical carbon dioxide. Several surfactants, of both F/F and H/F types and having varied counterions, were found to be capable of solubilizing water-in-CO2 (W/C), via the formation of microemulsions, expanding upon the family of phosphate fluorosurfactants already found to stabilize W/C microemulsions. Small-angle neutron scatteringwas used to directly characterize the microemulsion particles at varied temperatures, pressures, and water loadings, revealing behavior consistent with previous results on W/C microemulsions.
Orthodontic Rare Earth Magnets—In Vitro Assessment of Cytotoxicity (1994)

The aim of this study was to assess and compare in vitro the cytotoxic effects of uncoated and parylene-coated rare earth magnets, used in orthodontics. Cytotoxicity of samarium-cobalt magnets (SmCo5 and Sm2Co17) and neodymium-iron-boron magnets (Nd2Fe14B) was assessed by two in vitro methods, the millipore filter method and an extraction method. Orthodontic stainless steel brackets served as controls. Uncoated SmCo5-magnets showed high cytotoxicity while uncoated Sm2Co17-magnets demonstrated moderate cytotoxicity. Uncoated neodymium-iron-boron magnets, as well as parylene coated Sm2Co17-magnets and parylene-coated neodymium-iron-boron magnets, showed negligible cytotoxicity. Short-term exposure to a static magnetic field did not cause any cytotoxic effect on the cells.
Protocol Independent Multicast-Sparse Mode (PIM-SM): Protocol Specification (1998)

This document specifies Protocol Independent Multicast - Sparse Mode
(PIM-SM). PIM-SM is a multicast routing protocol that can use the
underlying unicast routing information base or a separate multicast-
capable routing information base. It builds unidirectional shared
trees rooted at a Rendezvous Point (RP) per group, and optionally
creates shortest-path trees per source. This document obsoletes RFC
2362, an Experimental version of PIM-SM. [STANDARDS-TRACK]
Monoclonal Antibody to a Highly Glycosylated Protein Reacts in Fixed Tissue With Melanoma and Other Tumors (1985)

A highly glycosylated protein with a molecular weight of 30,000 to 60,000 and a protein core of 20,000 daltons has been identified by antimelanoma monoclonal antibodies. The antigenicity of this melanoma-associated glycoprotein (MAG) was not destroyed in fixed paraffin-embedded melanoma tissue, and was present in malignant cells of cutaneous superficial spreading melanomas in skin (31/33) and in half of all metastatic melanomas examined (5/10). The antigen was not expressed by normal melanocytes. The strong reactivity of dysplastic nevi with the anti-MAG antibodies was comparable to that seen in radial growth phase melanoma. Antigen expression was much weaker in compound nevi where reactivity ranged from moderate in the junctional component and the upper dermis to absent at the base of the nevus.
The HA2 subunit of influenza hemagglutinin inserts into the target membrane prior to fusion. (1991)

The interaction between influenza virus and target membrane lipids during membrane fusion was studied with hydrophobic photoactivatable probes. Two probes, the newly synthesized bisphospholipid diphosphatidylethanolamine trifluoromethyl [3H]phenyl diazirine and the phospholipid analogue 1-palmitoyl-2(11-[4-[3-(trifluoromethyl)diazirinyl]phenyl]-[2-3H]- undecanoyl]-sn-glycero-3-phosphocholine (Harter, C., Bächi, T., Semenza, G., and Brunner , J. (1988) Biochemistry 27, 1856-1864), were used. Both labeled the HA2 subunit of the virus at low pH. By measuring virus-liposome interactions at 0 degrees C, it could be demonstrated that HA2 was inserted into the target membrane prior to fusion. As we have recently demonstrated, at this temperature, exposure of the fusion peptide of HA2 takes place within 15 s after acidification, but fusion does not start for 4 min (Stegmann, T., White, J. M., and Helenius, A. (1990) EMBO J. 9, 4231-4241). HA2 was labeled at least 2 min before fusion. No labeling of the HA1 subunit was seen. These data indicate that fusion is triggered by a direct interaction of the HA2 subunit of a kinetic intermediate form of HA with the lipids of the target membrane. Most likely, it is the fusion peptide of HA2 that is inserted into the target membrane. Just before fusion, HA is thus an integral membrane protein in both membranes. In contrast, the bromelain-derived ectodomain of HA was labeled by 1-palmitoyl-2(11-[4-[3-(trifluoromethyl)diazirinyl]phenyl]- [2-3H]undecanoyl)-sn-glycerol-3-phosphocholine at low pH but not by diphosphatidylethanolamine trifluoromethyl [3H]phenyl diazirine. This indicates that insertion of the fusion peptide of the bromelain-derived ectodomain of HA into a membrane differs from that of viral HA during fusion.
Clinical Management of Hospitalized Coronavirus Disease 2019 Patients in the United States (2021)

Clinical management of COVID-19 is rapidly evolving. This large observational study found that use of evidence-based treatments increased from May to December 2020, whereas improvement in outcomes occurred over this time-period.
Combination of Digital Mammography with Semi-automated 3D Breast Ultrasound (2004)

This paper describes work aimed at combining 3D ultrasound with full-field digital mammography via a semi-automatic prototype ultrasound scanning mechanism attached to the digital mammography system gantry. Initial efforts to obtain high x-ray and ultrasound image quality through a compression paddle are proving successful. Registration between the x-ray mammogram and ultrasound image volumes is quite promising when the breast is stably compressed. This prototype system takes advantage of many synergies between the co-registered digital mammography and pulse-echo ultrasound image data used for breast cancer detection and diagnosis. In addition, innovative combinations of advanced US and X-ray applications are being implemented and tested along with the basic modes. The basic and advanced applications are those that should provide relatively independent information about the breast tissues. Advanced applications include x-ray tomosynthesis, for 3D delineation of mammographic structures, and non-linear elasticity and 3D color flow imaging by ultrasound, for mechanical and physiological information unavailable from conventional, non-contrast x-ray and ultrasound imaging.
Functional validation of new pathways in lipoprotein metabolism identified by human genetics (2011)

This review summarizes recent developments in the use of human genetics to validate candidate genes in lipoprotein metabolism as well as in the functional validation of novel GWAS loci associated with plasma lipid traits.
Evolution of current state of assays for measuring parathyroid hormone (2010)

tcomin gs led to the de ve lop me nt of the newer im mu no met ric as says (IMA) that al lowed for bet ter cha rac te ri za tion and un der stan di ng of the PTH mole cu le sec re tion, ac tion and me ta bo li sm. Newer as says al so al lowed for re liab le diag no sis of pri ma ry hyper pa rat hyroi di sm and hypo pa rat hyroi di sm in the ma jo ri ty of the pa tien ts. Howe ver, des pi te ap pa re nt im pro ve men ts in the as say's cha rac te ris ti cs, con si de rab le di cul ties re main in as ses sment of the bo ne me ta bo li sm in the pa tien ts wi th end sta ge re nal di sea se. Com bi ni ng the re sul ts of se co nd ge ne ra
Biochemical and Genetic Defects in the DNA-Dependent Protein Kinase in Murine scid Lymphocytes (1996)

The scid gene product has been identified as the 460-kDa catalytic subunit of the DNA-dependent protein kinase (DNA-PKcs p460), a member of the phosphatidylinositol 3-kinase family. DNA-PK activity is undetectable in scid cells, but the molecular basis for this defect has not been identified. Here we report that expression of p460 in scid lymphocyte precursors is detectable but is reduced at least 10-fold relative to that in wild-type lymphocytes. In addition, we show that the scid mutation disturbs p460 nuclear association, presumably affecting its role in DNA repair pathways. To examine the molecular basis for our observations, we used a degenerate PCR strategy to clone the C-terminal p460 kinase domain from wild-type and scid thymocytes. Northern (RNA) analysis with these probes revealed normal steady-state p460 mRNA levels in scid cells, suggesting that the reduced abundance of p460 protein is due to a posttranscriptional defect. Sequence comparisons identified a single-base-pair alteration in the scid C-terminal p460 kinase domain, resulting in a premature stop codon. This mutation is predicted to truncate p460 by approximately 8 kDa, but it preserves the conserved motifs required for kinase activity in members of the phosphoinositidyl 3-kinase family. Despite a computed molecular weight alteration of less than 2%, we were able to visualize this difference by Western blot (immunoblot) analysis of wild-type and scid p460. These data demonstrate that the scid DNA-PKes mutation is not a null allele and suggest a molecular rationale for the well-described leakiness of the scid phenotype.
Sortilin Controls Intracellular Sorting of Brain-Derived Neurotrophic Factor to the Regulated Secretory Pathway (2005)

Brain-derived neurotrophic factor (BDNF), after activity-dependent secretion from neurons, modulates critical nervous system functions. Recently, a variant in the human bdnf gene, resulting in a valine to methionine substitution in the prodomain, has been shown to lead to defective regulated secretion from neurons and memory impairment. Here, we report a novel function for a Vps10p domain protein, sortilin, in controlling BDNF sorting to the regulated secretory pathway. Sortilin interacts specifically with BDNF in a region encompassing the methionine substitution and colocalizes with BDNF in secretory granules in neurons. A truncated form of sortilin causes BDNF missorting to the constitutive secretory pathway without affecting neurotrophin-4 (NT-4) secretion. In addition, sortilin small interfering RNA introduced into primary neurons also led to BDNF missorting from the regulated to the constitutive secretory pathway. Together, these data suggest a mechanism to understand the defect associated with variant BDNF and provide a framework, based on divergent presynaptic regulation of sorting to secretory pathways, to explain how two ligands for tropomyosin-related kinase B, BDNF and NT-4, can mediate diverse biological responses.
Communication between Switch II and Switch III of the Transducin α Subunit Is Essential for Target Activation (1997)

Comparisons of the tertiary structures of the GDP-bound and guanosine 5'-O-(thiotriphosphate) (GTPgammaS)-bound forms of the alpha subunit of transducin (alphaT) indicate that there are three regions that undergo changes in conformation upon alphaT activation. Two of these regions, Switch I and Switch II, were originally identified in Ras, while Switch III appears to be unique to trimeric GTP-binding proteins (G proteins). We find that replacement of the Switch III region (aspartic acid 227 through asparagine 237) with a single alanine residue yields an alphaT subunit that fully binds and hydrolyzes GTP but no longer stimulates the activity of the cyclic GMP phosphodiesterase (PDE), the physiological target for transducin. We also show that changing glutamic acid 232 of alphaT to a leucine (E232L) had no effect on rhodopsin-stimulated GTP-GDP exchange nor on the GTP hydrolytic activity of alphaT. However, the GTPgammaS-bound form of the alphaTE232L mutant was unable to stimulate the activity of the cyclic GMP PDE. The lack of stimulation was not due to an inability of the alphaTE232L mutant to bind to the target. Taken together, these results indicate that glutamic acid 232 mediates a conformational coupling between Switch II and Switch III, which is essential for converting GTP-dependent G protein-target interactions into a stimulation of target/effector activity.