gebhart/patrepeval huggingface dataset:
Sef is synexpressed with FGFs during chick embryogenesis and its expression is differentially regulated by FGFs in the developing limb (2005)

The signaling pathways leading to growth and patterning of various organs are tightly controlled during the development of any organism. These control mechanisms usually involve the utilization of feedback- and pathway-specific antagonists where the pathway induces the expression of its own antagonist. Sef is a feedback antagonist of fibroblast growth factor (FGF) signaling, which has been identified recently in zebrafish and mammals. Here, we report the isolation of chicken Sef (cSef) and demonstrate the conserved nature of the regulatory relationship with FGF signaling. In chick embryos, Sef is expressed in a pattern that coincides with many known sites of FGF signaling. In the developing limb, cSef is expressed in the mesoderm underlying the apical ectodermal ridge (AER) in the region known as the progress zone. cSef message first appeared after limb budding and AER formation. Expression was intense at stages of rapid limb outgrowth, and gradually decreased to almost undetectable levels when differentiation was clearly apparent. Gain- and loss-of-function experiments showed that FGFs differentially regulate the expression of cSef in various tissues. Thus, removal of the AER down-regulated cSef expression, and FGF2 but not FGF4 or FGF8 beads substituted for the AER in maintaining cSef expression. At sites where cSef is not normally expressed, FGF4 and FGF2, but not FGF8 beads, induced cSef expression. Our results demonstrate the complexity of cSef regulation by FGFs and point to FGF2 as a prime candidate in regulating cSef expression during normal limb development. The spatiotemporal pattern of cSef expression during limb development suggests a role for cSef in regulating limb outgrowth but not limb initiation.
Probing Conformational Changes in the I-like Domain and the Cysteine-rich Repeat of Human β3 Integrins following Disulfide Bond Disruption by Cysteine Mutations (2001)

We have investigated receptor function and epitope expression of recombinant alpha(IIb)beta(3) mutated at Cys(177) or Cys(273) in the I-like domain as well as Cys(598), located in the fourth repeat of the membrane-proximal cysteine-rich region and mutated in a Glanzmann's thrombasthenia type II patient. The beta(3) mutants beta(3)C177A, beta(3)C273A, and beta(3)C598Y exhibited a decreased electrophoretic mobility in SDS-polyacrylamide gel electrophoresis under nonreducing conditions, confirming the disruption of the respective disulfide loops. Despite reduced surface expression, the alpha(IIb)beta(3)C177A, alpha(IIb)beta(3)C273A, and alpha(IIb)beta(3)C598Y receptors mediated cell adhesion to immobilized fibrinogen and translocated into focal adhesion plaques. The beta(3)C598Y mutation, but not the beta(3)C177A or beta(3)C273A mutations, induced spontaneous binding of the ligand mimetic monoclonal antibody PAC-1, while the beta(3)C177A and beta(3)C273A mutants exhibited reduced complex stability in the absence of Ca(2+). Epitope mapping of function-blocking monoclonal antibodies (mAbs) allowed the identification of two distinct subgroups; mAbs A2A9, pl2-46, 10E5, and P256 did not interact with alpha(IIb)beta(3)C273A and bound only weakly to alpha(IIb)beta(3)C177A, while mAbs AP2, LM609 and 7E3 bound normally to mutant alpha(IIb)beta(3)C273A, but interacted only weakly with mutant alpha(IIb)beta(3)C177A. Furthermore, a cryptic epitope recognized by mAb 4D10G3 and not exposed on wild type alpha(IIb)beta(3) became accessible only on mutant alpha(IIb)beta(3)C177A and was mapped to the 60-kDa chymotrypsin fragment of beta(3). Finally, the ligand-induced binding site (LIBS) epitopes AP5, D3, LIBS1, and LIBS2 were spontaneously expressed on all three mutants independent of RGDS or dithiothreitol treatment. Our results provide evidence that disruption of a single cysteine disulfide bond in the cysteine-rich repeat domain, but not in the I-like domain, activates integrin alpha(IIb)beta(3). In contrast, disruption of each of the disulfide bonds in the two long insertions of the I-like domain predicted to be in close contact with the alpha subunit beta-propeller domain affect the stability of the alpha(IIb)beta(3) heterodimer and inhibit complex-specific mAb binding without affecting the RGD binding capacity of the metal ion-dependent adhesion site-like domain.
Schottky diodes of Ni/Au on n-GaN grown on sapphire and SiC substrates (2001)

GaN films were grown on sapphire and SiC substrates. The crystal qualities of GaN films were investigated by photoluminescence, atomic force microscopy, and electron-beam-induced current measurements, etc. It was found that the crystal quality of GaN on SiC is better than the one on sapphire. Ni/Au Schottky contacts were formed on the both samples. The electronic characteristics were obtained by current–voltage and capacitance–voltage measurements. Schottky diodes on sapphire substrate show breakdown voltage of −80 V. While for SiC substrate, the strong breakdown was not observed even at −100 V. The reverse leakage current of diodes based on SiC is over three orders of magnitude lower than that of sapphire substrate when the reverse voltage is above 50 V, which is due to the presence of low dislocation density and high thermal conductivity.
Methyl-β-Cyclodextrin Impairs the Monocyte-Adhering Ability of Endothelial Cells by Down-Regulating Adhesion Molecules and Caveolae and Reorganizing the Actin Cytoskeleton (2016)

Due to its powerful ability to deplete cholesterol from the plasma membrane of cells, methyl-β-cyclodextrin (MβCD) has been widely used as a putative research tool in cell biology. Recently, recruiting MβCD as an effective drug (e.g., antitumor drugs) has been developed. However, it remains unclear whether MβCD, when it enters the blood circulation as a drug, influences the functions of the endothelium, e.g., the adhesion of leukocytes to the endothelium. In this study, we found that MβCD can impair the adhesion of monocytes to the monolayer of endothelial cells by lowering the cell-surface adhesive force and expression of adhesion molecules and caveolae-related molecules on/in endothelial cells, and reorganizing the actin cytoskeleton of endothelial cells. The data imply that MβCD, when recruited as a drug, potentially helps to inhibit inflammation or initiation/progression of atherosclerosis since its important early step is the adhesion of circulating leukocytes (e.g., monocytes) to the endothelium.
A Portable Wireless Particulate Sensor System for Continuous Real-Time Environmental Monitoring (2012)

Airborne particulate matter has been shown to be associated with morbidity and mortality, and may interfere with certain sensitive experiment. Understanding the levels and movements of particulate matter in an enclosed space can lead to a reduction in the impact of this material on health and experimental results. A system of environmental sensors including particulate matter, selected gasses, humidity, temperature, and pressure can be used to assist in tracking air movement, providing real-time mapping of potential contaminants as they move through a space. In this paper we present a system that is capable of sensing these environmental factors, collecting data from multiple dispersed nodes and presenting the aggregated information in real-time. The highly modular system is based on a flexible and scalable framework developed for use in aircraft cabin environments. Use of this framework enables the deployment of a custom suite of sensors with minimal development effort. Individual nodes communicate using a self-organizing mesh network and can be powered from a variety of sources, bringing a high level of flexibility in the arrangement and distribution of the sensor array. Sensor data is transmitted to a coordinator node, which then passes the time-correlated information to a server-hosted database through a choice of wired or wireless networks. Presentation software is used to either monitor the real-time data stream, or to extract records of interest from the database. A reference implementation has been created for the National Institutes of Health consisting of a custom optical particle counter and off-the-shelf sensors for CO2, CO, temperature, humidity, pressure, and acoustic noise. The total environmental sensing system provides continuous, real-time data in a readable format that can be used to analyze ambient air for events of interest.
ASPO Distinguished Achievement Award Lecture. Studies on the epidemiology and natural history of benign breast disease and breast cancer using nipple aspirate fluid. (1993)

Nicholas L. Petrakis, M.D., was presented the American Society of Preventive Oncology's Distinguished Achievement Award at the Society's annual meeting on March 15, 1992, in Bethesda, Maryland. The basis for choosing Dr. Petrakis was his distinguished achievements for over 20 years in research and education concerning the etiology and prevention of cancer, with substantial emphasis on breast cancer. Dr. Petrakis obtained a Bachelor of Arts degree from Augustana College, Sioux Falls, South Dakota, and his Doctor of Medicine degree from Washington University, St. Louis, Missouri. He has held numerous principal positions at the University of California, beginning with a position with the U.S. Public Health Service, National Cancer Institute Laboratory of Experimental Oncology, and then the Cancer Research Institute, both at the University of California, San Francisco. Dr. Petrakis has held continuing appointments in the Department of Preventive Medicine and Department of Epidemiology and International Health, beginning as an Assistant Professor. He was subsequently promoted to Associate Professor and Professor of Preventive Medicine. During the years from 1978 to 1989, Dr. Petrakis was chair of the Department of Epidemiology and International Health. Since 1981 he has been Professor of Epidemiology, University of California, Berkeley, School of Public Health. In 1989 he became Professor Emeritus of Preventive Medicine and Epidemiology.(ABSTRACT TRUNCATED AT 250 WORDS)
An oligopeptide transporter is expressed at high levels in the pancreatic carcinoma cell lines AsPc-1 and Capan-2. (1998)

Carcinomas of the exocrine pancreas are poorly understood and have a poor prognosis because of their highly malignant nature. Using two human pancreatic cancer cell lines, AsPc-1 and Capan-2, we have investigated avenues that might be useful in targeting the delivery of antineoplastic agents to such cancers. Qualitative RNA PCRs established the presence of the oligopeptide transporter PEPT 1 in these pancreatic cell lines. Northern analysis confirmed the presence of a 3.3-kb transcript. The transporter is normally expressed primarily in small intestinal epithelial cells for nutrient absorption. It is also expressed in a human intestinal cell line, Caco-2. High levels of PEPT 1 protein expression in AsPc-1 and Capan-2, as multiple glycosylated forms (Mr approximately 90,000-120,000), were confirmed by Western immunoblotting, when compared with Caco-2 cell cultures. Absorption of the model dipeptide glycyl-L-sarcosine by AsPc-1 and Capan-2 cells was similar to glycyl-L-sarcosine absorption by Caco-2 cells and a Chinese hamster ovary cell line expressing human PEPT 1 (CHO-PEPT 1). Uptake was pH dependent and inhibited by several di/tripeptides and bestatin, but it remained unaffected by glycine and tetraglycine. Peptide solute transport by AsPc-1 and Capan-2 cells exhibited binding affinities (Kms) similar to those previously reported for PEPT 1, whereas the transport maximal velocity (Vmax) of the AsPc-1 cells was much greater than those of the Capan-2 and Caco-2 cells. Immunomicroscopy demonstrated PEPT 1 protein localized at the plasma membrane and in intracellular vesicular structures, similar to that observed for Caco-2 and CHO-PEPT 1 cells. These data suggest that the pancreatic cancer cells AsPc-1 and Capan-2 express surprisingly high levels of a solute transporter that was previously thought to be restricted in function to the absorption of nutrients from the small intestine.
Protein‐free fed‐batch culture of non‐GS NS0 cell lines for production of recombinant antibodies (2006)

Presented is a novel antibody production platform based on the fed-batch culture of recombinant, NS0-derived cell lines. A standardized fed-batch cell culture process was developed for five non-GS NS0 cell lines using enriched and optimized protein-free, cholesterol-free, and chemically defined basal and feed media. The process performed reproducibly and scaled faithfully from the 2-L to the 100-L bioreactor scale achieving a volumetric productivity of > 120 mg/L per day. Fed-batch cultures for all five cell lines exhibited significant lactate consumption when the cells entered the stationary or death phase. Peak and final lactate concentrations were low relative to a previously developed fed-batch process (FBP). Such low lactate production and high lactate consumption rates were unanticipated considering the fed-batch culture basal medium has an unconventionally high initial glucose concentration of 15 g/L, and an overall glucose consumption in excess of 17 g/L. The potential of this process platform was further demonstrated through additional media optimization, which has resulted in a final antibody concentration of 2.64 +/- 0.19 g/L and volumetric productivity of > 200 mg/L per day in a 13-day FBP for one of the five production cell lines. Use of this standardized protein-free, cholesterol-free NS0 FBP platform enables consistency in development time and cost effectiveness for manufacturing of therapeutic antibodies.
Molecular characterization of immunoglobulin D in mammals: immunoglobulin heavy constant delta genes in dogs, chimpanzees and four old world monkey species (2006)

Antibodies are adaptor molecules that neutralize pathogens and link humoral and cellular defence mechanisms. Immunoglobulin D (IgD), one of the five antibody classes present in mammals, is expressed as an antigen receptor on naïve B cells. The functional role that IgD plays in the immune response is still poorly understood, but the recent characterization of immunoglobulin heavy constant delta genes (IGHD) in a variety of species challenges the view that IgD is of minor importance and is not present in many animals. On the basis of serological studies, IgD appears to be expressed in the majority of mammalian species examined. To confirm, at the molecular level, that IgD is present in different species, we cloned and sequenced IGHD cDNA from dogs and five non-human primate species (chimpanzee, rhesus macaque, cynomolgus macaque, baboon and sooty mangabey). Our results show that in all six species, IgD heavy chains possess three immunoglobulin domains and a long hinge region encoded by two exons. Only the hinge region of non-human primates is similar to the human hinge region, with conservation of O-glycosylation sites and multiple charged residues at opposing ends. The preservation of IgD in primates, dogs and previously characterized species suggests an important functional role for IgD, possibly involving binding to a receptor. The high degree of similarity existing between the structural features of human and non-human primate IgD suggests that non-human primates are suitable for in vivo studies designed to define the role that IgD plays in the immune response.
Redesign of extensive protein–DNA interfaces of meganucleases using iterative cycles of in vitro compartmentalization (2014)

LAGLIDADG homing endonucleases (meganucleases) are sequence-specific DNA cleavage enzymes used for genome engineering. Recently, meganucleases fused to transcription activator-like effectors have been demonstrated to efficiently introduce targeted genome modifications. However, retargeting meganucleases to genomic sequences of interest remains challenging because it usually requires extensive alteration of a large number of amino acid residues that are situated in and near the DNA interface. Here we describe an effective strategy to extensively redesign such an extensive biomolecular interface. Well-characterized meganucleases are computationally screened to identify the best candidate enzyme to target a genomic region; that protein is then redesigned using iterative rounds of in vitro selections within compartmentalized aqueous droplets, which enable screening of extremely large numbers of protein variants at each step. The utility of this approach is illustrated by engineering three different meganucleases to cleave three human genomic sites (found in two exons and one flanking intron in two clinically relevant genes) and a fourth endonuclease that discriminates between single-nucleotide polymorphism variants of one of those targets. Fusion with transcription activator-like effector DNA binding domains significantly enhances targeted modification induced by meganucleases engineered in this study. Simultaneous expression of two such fusion endonucleases results in efficient excision of a defined genomic region.
Etanercept treatment of psoriatic arthritis: Safety, efficacy, and effect on disease progression (2004)

Etanercept reduced joint symptoms, improved psoriatic lesions, inhibited radiographic progression, and was well tolerated in patients with PsA.
Biphasic Currents Evoked by Chemical or Thermal Activation of the Heat-gated Ion Channel, TRPV3 (2005)

2-Aminoethyl diphenylborinate was recently identified as a chemical activator of TRPV1, TRPV2, and TRPV3, three heat-gated members of the transient receptor potential vanilloid (TRPV) ion channel subfamily. Here we demonstrated that two structurally related compounds, diphenylboronic anhydride (DPBA) and diphenyltetrahydrofuran (DPTHF), can also modulate the activity of these channels. DPBA acted as a TRPV3 agonist, whereas DPTHF exhibited prominent antagonistic activity. However, all three diphenyl-containing compounds promoted some degree of channel activation or potentiation, followed by channel block. Strong TRPV3 activation by DPBA often leads to the appearance of a secondary, enhanced, current phase. A similar biphasic response was observed during TRPV3 heat stimulation; an initial, gradually sensitizing phase (I(1)) was followed by an abrupt transition to a secondary phase (I(2)). I(2) was characterized by larger current amplitude, loss of outward rectification, and alterations in the following properties: permeability among cations; ruthenium red and DPTHF sensitivity; temperature dependence; and voltage-dependent gating. The I(1) to I(2) transition depended strongly on TRPV3 current density. Removal of extracellular divalent cations resulted in heat-evoked currents resembling I(2), whereas mutation of a putative Ca(2+)-binding residue in the pore loop domain, aspartate 641, facilitated detection of the I(1) to I(2) transition, suggesting that the conversion to I(2) resulted from the agonist- and time-dependent loss of divalent cationic inhibition. Primary keratinocytes overexpressing exogenous TRPV3 also exhibited biphasic agonist-evoked currents. Thus, strong activation by either chemical or thermal stimuli led to biphasic TRPV3 signaling behavior that may be associated with changes in the channel pore.
Protein Enhancement of Hammerhead Ribozyme Catalysis (1993)

When the recognition sequence of a ribozyme is extended beyond a certain length, turnover is slowed and specificity is decreased. Here, it is shown that a protein can help a ribozyme overcome these general limitations on ribozyme activity. Cleavage of an RNA oligonucleotide by a hammerhead ribozyme is enhanced 10- to 20-fold upon addition of a protein derived from the p7 nucleocapsid (NC) protein of human immunodeficiency virus-type 1. The NC protein also enhances the ability of the ribozyme to discriminate between cleavage of RNA oligonucleotides with differing sequences. These catalytic improvements can be attributed to the strand exchange activity of this RNA binding protein. It is conceivable that endogenous or added proteins may provide analogous increases in ribozyme activity and specificity in vivo.
Biodegradation of a poly‐(α‐amino acid) hydrogel. II. In vitro (1981)

Proteolytic enzymes have been employed in an in vitro model to simulate the in vivo degradation of a synthetic poly(amino acid) hydrogel. Trypsin and collagenase had no effect on crosslinked poly(2-hydroxyethyl-L-glutamine) but pronase and papain dissolved the hydrogel. The initial effect of papain was to decrease the effective crosslink density without producing soluble material. This effect was similar to that observed previously in vivo. Analysis of the papain digestion products showed that oligomers of degree of polymerization 4-9 were the chief products. The rate at which oligomers were formed increased with increasing crosslink density. This phenomenon was attributed to hydrophobic effects.
Dependence receptor TrkC is a putative colon cancer tumor suppressor (2013)

The TrkC neurotrophin receptor belongs to the functional dependence receptor family, members of which share the ability to induce apoptosis in the absence of their ligands. Such a trait has been hypothesized to confer tumor-suppressor activity. Indeed, cells that express these receptors are thought to be dependent on ligand availability for their survival, a mechanism that inhibits uncontrolled tumor cell proliferation and migration. TrkC is a classic tyrosine kinase receptor and therefore generally considered to be a proto-oncogene. We show here that TrkC expression is down-regulated in a large fraction of human colorectal cancers, mainly through promoter methylation. Moreover, we show that TrkC silencing by promoter methylation is a selective advantage for colorectal cell lines to limit tumor cell death. Furthermore, reestablished TrkC expression in colorectal cancer cell lines is associated with tumor cell death and inhibition of in vitro characteristics of cell transformation, as well as in vivo tumor growth. Finally, we provide evidence that a mutation of TrkC detected in a sporadic cancer is a loss-of-proapoptotic function mutation. Together, these data support the conclusion that TrkC is a colorectal cancer tumor suppressor.
Pharmacokinetics and pharmacodynamics of voxelotor (GBT440) in healthy adults and patients with sickle cell disease (2019)

This first-in-human study demonstrates voxelotor was well tolerated in SCD patients and healthy volunteers and established proof of mechanism on increasing Hb-oxygen affinity.