gebhart/patrepeval huggingface dataset:
Mapping of phosphomonoester and apparent phosphodiester bonds of the oncogene product p53 from simian virus 40-transformed 3T3 cells. (1986)

The oncogene product p53, isolated from SV3T3 cells where it forms a complex with simian virus 40 large tumor antigen (T antigen) in the nucleus, has been found to be phosphorylated at at least four distinct sites on the 390 amino acid protein. Separation of tryptic phosphopeptides has permitted identification of two sites as Ser-312 and Ser-389, and permitted analysis of the types of phosphate bonds. The peptide containing Ser-312 separates electrophoretically into three charged forms; two are resistant to dephosphorylation by both alkaline phosphatase and alkaline hydrolysis, suggesting a phosphodiester. The carboxyl-terminal phosphopeptide containing Ser-389 was alkaline phosphatase-resistant and liberated four ribonucleoside monophosphates upon base or RNase hydrolysis, suggesting that Ser-389 may be covalently linked to RNA. Phosphorylation of Ser-389 decreased markedly at the nonpermissive temperature in simian virus 40 tsA58-transformed cells, indicating a dependence on native T antigen function and a possible role in transformation by T antigen. Two additional phosphorylation sites, one involving serine and one involving threonine, probably reside in the amino-terminal segment of p53 and appear to be peptide-phosphate monoesters.
Cerebral Infusion of AAV9 Vector-encoding Non-self Proteins Can Elicit Cell-mediated Immune Responses (2012)

There is considerable interest in the use of adeno-associated virus serotype 9 (AAV9) for neurological gene therapy partly because of its ability to cross the blood-brain barrier to transduce astrocytes and neurons. This raises the possibility that AAV9 might also transduce antigen-presenting cells (APC) in the brain and provoke an adaptive immune response. We tested this hypothesis by infusing AAV9 vectors encoding foreign antigens, namely human aromatic L-amino acid decarboxylase (hAADC) and green fluorescent protein (GFP), into rat brain parenchyma. Over ensuing weeks, both vectors elicited a prominent inflammation in transduced brain regions associated with upregulation of MHC II in glia and associated lymphocytic infiltration. Transduction of either thalamus or striatum with AAV9-hAADC evinced a significant loss of neurons and induction of anti-hAADC antibodies. We conclude that AAV9 transduces APC in the brain and, depending on the immunogenicity of the transgene, can provoke a full immune response that mediates significant brain pathology. We emphasize, however, that these observations do not preclude the use of AAV serotypes that can transduce APC. However, it does potentially complicate preclinical toxicology studies in which non-self proteins are expressed at a level sufficient to trigger cell-mediated and humoral immune responses.
Production and Titration of Lentiviral Vectors (2007)

Lentiviral vectors have emerged over the last decade as powerful, reliable and safe tools for stable gene transfer in a wide variety of mammalian cells. Unlike other vectors derived from oncoretroviruses, they allow for stable gene delivery into most nondividing primary cells. This is why LVs are becoming useful and promising tools for future gene and cell therapy approaches. Lentivectors (LVs) derived from HIV-1 have gradually evolved to display many desirable features aimed at increasing both their safety and their versatility. These latest designs are reviewed in this unit. This unit also describes protocols for production and titration of LVs that can be implemented in a research laboratory setting, with an emphasis on standardization to improve transposability of results between laboratories.
The Role of Chemokines and Chemokine Receptors in Mucosal Inflammation (2000)

Chemokines represent a large family of small cytokines, the main function of which is the attraction of leukocytes to different tissues. Several chemokines and their receptors have been shown to play a critical role in lymphoid development, mucosal immunity, and inflammation. In this article we review recent advances in chemokinc physiology and their potential role in the pathogenesis of mucosal inflammation. We also discuss the potential for the use of chemokine or chemokine receptor antagonists as novel therapies for inflammatory bowel disease.
Fluorescence microscopy with a coded aperture snapshot spectral imager (2009)

This paper describes the application of a coded aperture snapshot spectral imager (CASSI) to fluorescence microscopy. CASSI records an interleaved spatially varying, spectrally filtered map of an object on a 2D focal plane. Convex optimization techniques combining least squares QR factorization with a total variance constraint are used to reconstruct a 3D data cube from a spectrally encoded 2D scene. CASSI records a 3D dataset at video rate - making it suitable for dynamic cellular imaging. We report on the reconstruction of fluorescent microspheres used in fluorescence microscopy applications and compare the results with images from a multi-spectral confocal system.
Star Synthesis Using Macroinitiators via Electrochemically Mediated Atom Transfer Radical Polymerization (2013)

Electrochemically mediated atom transfer radical polymerization (eATRP) was investigated for synthesis of star polymers using macroinitiators (MIs), achieving high star yield with low Cu catalyst loading (∼100 ppm, w/w). The arm first method, using MIs, is one of the most robust procedures for star polymer synthesis. During the polymerization, MIs can react with cross-linkers (divinyl or multivinyl compounds) for initial chain extension followed by the cross-linking reaction. The MIs can be transformed to arms of the star, and the cross-linker can form the star core. In this study, poly(ethylene oxide) (PEO, Mn = 2000) based MIs (PEO MIs) were prepared, and the chain-end functionalities were confirmed by 1H NMR analysis. The ATRP functionalized PEO MIs were then used for the star synthesis by reacting with ethylene glycol diacrylate cross-linkers. Various experimental conditions were conducted for optimizing star formation, including MI concentration, MI to cross-linker molar ratio, and applied potential (Eapp).
Computational modeling of epidural cortical stimulation (2008)

Epidural cortical stimulation (ECS) is a developing therapy to treat neurological disorders. However, it is not clear how the cortical anatomy or the polarity and position of the electrode affects current flow and neural activation in the cortex. We developed a 3D computational model simulating ECS over the precentral gyrus. With the electrode placed directly above the gyrus, about half of the stimulus current flowed through the crown of the gyrus while current density was low along the banks deep in the sulci. Beneath the electrode, neurons oriented perpendicular to the cortical surface were depolarized by anodic stimulation, and neurons oriented parallel to the boundary were depolarized by cathodic stimulation. Activation was localized to the crown of the gyrus, and neurons on the banks deep in the sulci were not polarized. During regulated voltage stimulation, the magnitude of the activating function was inversely proportional to the thickness of the CSF and dura. During regulated current stimulation, the activating function was not sensitive to the thickness of the dura but was slightly more sensitive than during regulated voltage stimulation to the thickness of the CSF. Varying the width of the gyrus and the position of the electrode altered the distribution of the activating function due to changes in the orientation of the neurons beneath the electrode. Bipolar stimulation, although often used in clinical practice, reduced spatial selectivity as well as selectivity for neuron orientation.
The relationship between reduced testosterone, stimulated growth hormone secretion and increased carotid intima‐media thickness in obese men (2010)

These results demonstrate a strong relationship between FT and GH in obesity and suggest that this relationship is more a function of excess adiposity rather than a direct relationship. While reduced FT and GH are both related to increased cIMT, the relationship with reduced GH remains significant controlling for reduced FT and traditional cardiovascular disease risk markers.
The VEGF family in cancer and antibody-based strategies for their inhibition (2010)

Angiogenesis is required in normal physiological processes, but is also involved in tumor growth, progression and metastasis. Vascular endothelial growth factor (VEGF), a primary mediator of angiogenesis in normal physiology and in disease, and other VEGF family members and their receptors provide targets that have been explored extensively for cancer therapy. Small molecule inhibitors and antibody/protein-based strategies that target the VEGF pathway have been studied in multiple types of cancer. This review will focus on VEGF pathway targeting antibodies that are currently being evaluated in pre-clinical and clinical studies.
Understanding Lustre Internals (2009)

Lustre was initiated and funded, almost a decade ago, by the U.S. Department of Energy (DoE) Office of Science and National Nuclear Security Administration laboratories to address the need for an open source, highly-scalable, high-performance parallel filesystem on by then present and future supercomputing platforms. Throughout the last decade, it was deployed over numerous medium-to-large-scale supercomputing platforms and clusters, and it performed and met the expectations of the Lustre user community. As it stands at the time of writing this document, according to the Top500 list, 15 of the top 30 supercomputers in the world use Lustre filesystem. This report aims to present a streamlined overview on how Lustre works internally at reasonable details including relevant data structures, APIs, protocols and algorithms involved for Lustre version 1.6 source code base. More importantly, it tries to explain how various components interconnect with each other and function as a system. Portions of this report are based on discussions with Oak Ridge National Laboratory Lustre Center of Excellence team members and portions of it are based on our own understanding of how the code works. We, as the authors team bare all responsibilities for all errors and omissions in this document. We can only hope it helps current and future Lustre users and Lustre code developers as much as it helped us understanding the Lustre source code and its internal workings.
Development of New Chiral P,N Ligands and Their Application in the Cu-Catalyzed Enantioselective Conjugate Addition of Diethylzinc to Enones (1999)

High enantioselectivity (up to 98 % ee) has been achieved for the conjugate addition of diethylzinc to acyclic enones utilizing Cu(I) complexes of the novel chiral P,N ligands 1. The high enantioselectivities are best achieved using [Cu(OTf)](2) small middle dotC(6)H(6) as the copper catalyst precursor in nonpolar solvents such as toluene or Cl(CH(2))(2)Cl. R=H, CH(3); Tf=F(3)CSO(2).
Automated Formation of Lipid-Bilayer Membranes in a Microfluidic Device (2006)

Although membrane channel proteins are important to drug discovery and hold great promise as engineered nanopore sensing elements, their widespread application to these areas has been limited by difficulties in fabricating planar lipid-bilayer membranes. We present a method for forming these sub-5-nm-thick free-standing structures based on a self-assembly process driven by solvent extraction in a microfluidic channel. This facile automatable process forms high-quality membranes able to host channel proteins measurable at single-molecule conductance resolution.
Regulation of fungal gene expression via short open reading frames in the mRNA 5′untranslated region (2003)

We review how the expression of fungal mRNAs can be controlled by ribosome interactions with short upstream open reading frames (uORFs) within the 5'untranslated region. The efficiency of uAUG recognition modulates the impact of a uORF but steps during and after translation of the uORF also influence uORF function. The post-termination behaviour of ribosomes, therefore, plays a major role in determining the expression level of these main ORFs. Translation of a uORF can produce a cis-acting peptide that causes effector molecule-dependent stalling of the ribosomes at the end of the uORF. In other cases it is the length or position, or other features of the uORF, rather than the peptide it encodes, that determine the efficiency with which ribosomes reinitiate translation downstream of it. Whether the form of the ribosome that resumes scanning after termination is the 40S subunit alone or the entire 80S ribosome is not known. Translation of the uORF can also control gene expression by affecting the stability of the mRNA. Finally, trans-acting factors may participate in the regulatory mechanisms. Future work will need not only to provide more information on the mechanisms underlying the known cases of uORF-mediated control but also to define the full complement of uORF-containing mRNAs in at least one fungal organism.
Measurement of hydration in the stratum corneum with the MoistureMeter and comparison with the Corneometer (2004)

The capacitive measuring principle of the MoistureMeter was demonstrated in an experimental arrangement. Although both instruments yielded equivalent data with the base formulation, the MoistureMeter was a more sensitive device than the Corneometer CM 820 and independent of added salt in the formulations.
Does Depression Reduce the Effectiveness of Behavioral Weight Loss Treatment? (2009)

Limited evidence suggests that depression is associated with poorer outcomes in behavioral weight loss programs; however, people with major depression are typically excluded from weight loss intervention trials. This study examined the effect of depression on women's participation and weight loss in behavioral treatment. Non-treatment seeking obese women over 40 years of age with major depressive disorder (MDD, n = 65) and without MDD (n = 125) were recruited into a 26-session group intervention. Primary analyses compared participants' mean weight change from baseline to 6 and 12 months; at 6 months, women with MDD lost a mean of 3.8 kg vs 4.3 kg for women without MDD (t = 0.54, p = .59). At 12 months, women with MDD lost 3.0 kg and women without MDD lost 3.6 kg (t = 0.44, p =.66). Women who attended at least 12 treatment sessions lost more weight than women who attended fewer sessions, regardless of depression status (ie, there was no significant interaction between depression and session attendance). Results suggest that depression should not be an exclusion criterion for weight loss intervention programs.
Ratiometric Displacement Approach to Cu(II) Sensing by Fluorescence (2005)

A chelation-enhanced fluorescence method for the detection of paramagnetic copper(II) ions is developed. Two dyes with unequal metal ion binding constants are used, each giving strong fluorescence enhancement in the presence of a diamagnetic reporter ion such as cadmium(II). Upon presentation of copper(II) to a 1:1:1 mixture of the two dyes and cadmium(II), the Cd(II) is displaced from one dye to the other, resulting in quenching of one dye by the Cu(II) and enhancement of the weaker binding dye by complexation of the Cd(II). Although several criteria must be met, this method holds promise for analysis of a wide range of analytes.
Optical fiber transmission systems using stimulated Raman scattering: Theory (1985)

Forward and backward stimulated Raman scattering is theoretically discussed. For forward stimulated Raman scattering, the discussion is made taking account of the pump depletion due to the stimulated Raman scattering process. On the basis of the results, the optical transmission systems using stimulated Raman scattering are discussed and the possibility of repeater spacing more than 400 km is presented.
Immunoreactivity of a 70 kD protein purified from Mycobacterium bovis Bacillus Calmette-Guerin by monoclonal antibody affinity chromatography. (1986)

The protein antigens from Mycobacterium bovis (BCG), M. tuberculosis, and M. leprae share a number of common determinants. We have used a murine mAb (L7) recognizing such a determinant on a protein of Mr 70,000 to purify this antigen from M. bovis sonicate by affinity chromatography. Enrichment of the protein in column eluates was confirmed by immunoblotting and in antigen inhibition assays. After radiolabelling with 125I, the protein could be immunoprecipitated with human lepromatous leprosy sera. Stimulation of peripheral blood mononuclear cells from BCG-vaccinated and naturally mantoux-positive individuals induced proliferation and IFN-gamma secretion, while intradermal injection of purified antigen into the same subjects resulted in a delayed-type hypersensitivity reaction. Thus, the 70,000 molecule carried epitopes capable of reacting with B cells, and eliciting a potentially protective T cell response. The first 15 N-terminal residues were sequenced using a gas-phase sequenator.
Pathology Correlations with Optical Biopsy Techniquesa (1998)

Traditional surgical pathology predicts the future course of a patient's disease based on subjective comparison of the biopsy with the outcome of similar biopsies that have been seen previously. Optical techniques are being designed to aid the clinician in evaluating the patients' tissue in vivo. These technologies assess the disease process itself, associated structural alterations or do not have a known physical basis. These techniques will have an almost immediate application in directing the location to biopsy. The true optical biopsy where a definitive diagnosis is made by in vivo optical technology is a laudable goal, but only a few such applications are likely to become available in the near future. In addition to these approaches, the movement towards telemedicine is going to increase the demand for this type of technology for remote monitoring at home as well as in hospital settings.
Human response against NP-4, a mouse antibody to carcinoembryonic antigen: human anti-idiotype antibodies mimic an epitope on the tumor antigen. (1991)

Anti-idiotype antibodies (Ab2) were purified from a cancer patient treated with NP-4, a murine monoclonal antibody to carcinoembryonic antigen (CEA). These Ab2 were specific for NP-4 and inhibited the binding between NP-4 and CEA. BALB/c mice immunized with these human Ab2 produced anti-Ab2 antibodies that were also reactive with the CEA epitope recognized by NP-4. These results indicate that human Ab2 to NP-4 can antigenically mimic the CEA epitope recognized by NP-4.
Origin and evolution of human and simian T-cell lymphotropic viruses (1999)

AbstractThree HTLV/STLV (together PTLV) types have been characterized: PTLV-I found inhumans and most old world simian species, PTLV-II found in humans and pygmychimpanzees and STLV-L only found in baboons. STLV-I clades and HTLV-I cladesdo not cluster according to species of origin, but rather according to geographicorigin of the host.Within PTLV-I, the oldest phylogenetic lineages are found inAsian macaques, and the African HTLV-I subtypes Ib, Id, Ie and If have closelyrelated simian relatives.The Melanesian/Australian HTLV-Ic and cosmopolitan Iasubtypes are also separated from the other subtypes by simian clades.Therefore,the different HTLV-I subtypes most probably each have a separate simian origin.HTLV-Ic most probably originated through interspecies transmission fromIndonesian macaques to humans migrating to Melanesia and Australia around 50000 years ago.The African human and simian T-cell lymphotropic lineages aroselater as a consequence of host migrations from Asia to Africa.The transmission ofAsian PTLV-I to African simians and humans, resulted in an explosive spread ofthis virus in Africa.The cosmopolitan HTLV-Ia, originating in Africa, was spreadover the world due to post-Columbian human migrations.Within PTLV-II, human andsimian viruses are phylogenetically well separated and it is not clear yet ifinterspecies transmissions took place within this PTLV type. Both clades have anAfrican origin.Three HTLV-II subtypes exist, HTLV-IId is found in Efe pygmies fromCongo and HTLV-IIa and IIb are found in Amerindian tribes, drug users and a fewAfricans. Most probably HTLV-IIa and IIb were brought from Africa to America as aresult of the migrations of the human host over the Bering strait, 10 000 to 35 000years ago, and were only recently introduced into injecting drug users. STLV-L alsohas an African origin, but whether PTLV originated in Africa or in Asia can not beconcluded form the available information.What is clear now is that this T-celllymphotropic virus repeatedly jumped from simians to humans, raising concernsabout xenotransplantation.Key wordsHTLV. Phylogeny. STLV. Interspecies transmission.
Design of a Reconfigurable Robot Arm for Assembly Operations inside an Aircraft Wing-Box (2006)

We present a design concept and two initial prototypes of a robot arm for assembly operations inside an aircraft wing-box. The wing-box has a large span, but is only accessible through multiple small portholes along its length. The arm is compact enough to enter the wing-box through the small portholes and is capable of subsequent reconfiguration so as to access a number of assembly points inside the wing-box. Traditional electromechanical actuators are unsuitable for our purpose, because of limited space and large payload requirements. We use an actuator module comprising Shape Memory Alloy (SMA) wires, which are known for their high stress to volume ratio. Our design also addresses the issue of limited strain of SMA wires through a displacement amplification mechanism. Our compact, high displacement actuator module can be readily integrated into the structure of the robot arm. We also discuss a deployment scheme for the robot arm, which eliminates gravity loading during the reconfiguration phase, and also helps to position the end effecter at the various assembly points inside the wing-box.
Proteolysis of insulin-like growth factor binding protein-3 during rat pregnancy: a role for matrix metalloproteinases. (1994)

Insulin-like growth factor binding protein-3 (IGFBP-3) is degraded by a cation-dependent protease(s) present in the serum of late gestation rats. Proteolysis of IGFBP-3 results in an increase in IGF-I clearance and possibly in IGF bioavailability. Based on our previous findings that matrix metalloproteinases (MMPs) degrade IGFBP-3 in fibroblast conditioned media, we hypothesized that MMPs might be involved in the degradation of IGFBP-3 by rat pregnancy serum. In the present study, we demonstrate that tissue inhibitor of metalloproteinases (TIMP-1), a specific inhibitor of all MMPs, inhibited significantly the degradation of 125I-rhIGFBP-3 by both rat pregnancy serum and rat placental extracts. Purified human MMPs (principally MMP-1 and MMP-3) degraded IGFBP-3 in solution; MMP-3 produced a pattern of IGFBP-3 degradation products identical in size to the fragments produced by pregnancy serum. Furthermore, the combined addition of antihuman MMP-1 IgG and anti-human MMP-3 IgG to rat pregnancy serum blocked almost completely the degradation of 125I-rhIGFBP-3, suggesting that these two MMPs are the principal MMPs involved in IGFBP-3 degradation in rat pregnancy serum. Together, these data suggest that MMPs function as IGFBP-3-degrading proteases in the serum of late gestational pregnant rats.