gebhart/patrepeval huggingface dataset:
Identification of the glycosaminoglycan-attachment site of mouse invariant-chain proteoglycan core protein by site-directed mutagenesis. (1988)

The invariant chain (Ii), a nonpolymorphic glycoprotein that associates with the immunoregulatory Ia proteins encoded by the major histocompatibility complex, has a proteoglycan form (Ii-CS) that bears a chondroitin sulfate glycosaminoglycan. In this proteoglycan form, Ii may remain associated with Ia at the cell surface. Inhibitors that prevent the addition of glycosaminoglycan to Ii have been found to depress antigen-presenting function. Ii does not have multiple candidate glycosaminoglycan-attachment sites, and we used site-directed mutagenesis to replace a candidate serine glycosaminoglycan-acceptor site with alanine at position 201 in the murine Ii protein. Transfection of the normal or altered gene into Ii-negative COS-7 cells showed that equivalent amounts of core Ii protein and its acidic, terminally glycosylated forms were synthesized, but the Ala-201 mutant Ii did not give rise to Ii-CS. The mutant protein had apparently normal transport through the Golgi compartment and associated stably with Ia molecules. Thus, this mutation directly identifies the site of glycosaminoglycan addition and shows that it can be eliminated without adversely affecting the overall biosynthesis of Ii.
IL-15 Amplifies the Pathogenic Properties of CD4+CD28− T Cells in Multiple Sclerosis (2015)

CD4(+)CD28(-) T cells arise through repeated antigenic stimulation and are present in diseased tissues of patients with various autoimmune disorders, including multiple sclerosis (MS). These cells are believed to have cytotoxic properties that contribute to the pathogenic damaging of the target organ. Endogenous cues that are increased in the diseased tissue may amplify the activity of CD4(+)CD28(-) T cells. In this study, we focused on IL-15, a cytotoxicity-promoting cytokine that is increased in the serum and cerebrospinal fluid of MS patients. Using immunohistochemistry, we demonstrate that IL-15 is mainly produced by astrocytes and infiltrating macrophages in inflammatory lesions of MS patients. Moreover, in vitro transmigration studies reveal that IL-15 selectively attracts CD4(+)CD28(-) T cells of MS patients, but not of healthy individuals. IL-15 further induces the expression of chemokine receptors and adhesion molecules on CD4(+)CD28(-) T cells, as investigated using flow cytometry, resulting in enhanced migration over a monolayer of human brain endothelial cells. Finally, flow cytometric analyses revealed that IL-15 increases the proliferation and production of GM-CSF, expression of cytotoxic molecules (NKG2D, perforin, and granzyme B), and degranulation capacity of CD4(+)CD28(-) T cells. Taken together, these findings indicate that increased peripheral and local levels of IL-15 amplify the pathogenic potential of CD4(+)CD28(-) T cells, thus contributing to tissue damage in MS brain lesions.
Classification of Lignin According to Chemical and Molecular Structure (1999)

The commercial trade in isolated lignins generated in conjunction with the fractionation of biomass into constitutive components, including pulp and paper and saccharification/fermentation processes, requires the adoption of standard analytical techniques by both suppliers and users of such products. Simple, reliable, quantitative, and widely accepted techniques include elemental analysis, functional group analysis, analytical degradations, various spectroscopic techniques, molecular weight analysis, and thermal analysis. These techniques are capable of elucidating the chemical composition of repeat units; the nature of intermonomer bonds; molecular weights and weight distributions; and the potential for inter- and intramolecular interactions. Several aspects of this classification methodology are reviewed.
Nine patients with anti‐neutrophil cytoplasmic antibody‐positive vasculitis successfully treated with rituximab (2005)

RIT seems promising and safe in ANCA-positive vasculitis, and controlled studies should be conducted.
Solution Structure of Methionine-Oxidized Amyloid β-Peptide (1−40). Does Oxidation Affect Conformational Switching?, (1998)

The solution structure of Abeta(1-40)Met(O), the methionine-oxidized form of amyloid beta-peptide Abeta(1-40), has been investigated by CD and NMR spectroscopy. Oxidation of Met35 may have implications in the aetiology of Alzheimer's disease. Circular dichroism experiments showed that whereas Abeta(1-40) and Abeta(1-40)Met(O) both adopt essentially random coil structures in water (pH 4) at micromolar concentrations, the former aggregates within several days while the latter is stable for at least 7 days under these conditions. This remarkable difference led us to determine the solution structure of Abeta(1-40)Met(O) using 1H NMR spectroscopy. In a water-SDS micelle medium needed to solubilize both peptides at the millimolar concentrations required to measure NMR spectra, chemical shift and NOE data for Abeta(1-40)Met(O) strongly suggest the presence of a helical region between residues 16 and 24. This is supported by slow H-D exchange of amide protons in this region and by structure calculations using simulated annealing with the program XPLOR. The remainder of the structure is relatively disordered. Our previously reported NMR data for Abeta(1-40) in the same solvent shows that helices are present over residues 15-24 (helix 1) and 28-36 (helix 2). Oxidation of Met35 thus causes a local and selective disruption of helix 2. In addition to this helix-coil rearrangement in aqueous micelles, the CD data show that oxidation inhibits a coil-to-beta-sheet transition in water. These significant structural rearrangements in the C-terminal region of Abeta may be important clues to the chemistry and biology of Abeta(1-40) and Abeta(1-42).
On the realization of AnSpeechCollector, system for creating transcribed speech database (2014)

In this paper we present system which is used for creating transcribed speech database in a fast and efficient manner. The system consists of a client application running on Android based mobile phones and a dedicated server. We also present a database of approximately 55 hours of speech created with this system.
Synthesis and localization of fibronectin during collagenous matrix-mesenchymal cell interaction and differentiation of cartilage and bone in vivo. (1980)

The biosynthesis of fibronectin during the in vivo development of matrix-induced endochondral bone was investigated by using [35S]methionine in rats. The dmineralized bone matrix that was implanted subcutaneously to induce local bone formation bound circulating fibronectin. This may be an important initial requirement for cell attachment to the matrix. Fibronectin was present throughout the development of bone but accounted for the largest percentage of total protein synthesized during mesenchymal cell proliferation and hematopoiesis. Fibronectin was identified in tissue extracts by its (i) comigration on electrophoretic NaDodSO4/polyacrylamide gels with human and rat plasma fibronectin, (ii) affinity for denatured collagen, (iii) crossreactivity with purified antibody of rat plasma fibronectin, and (iv) insensitivity to collagenase digestion. Fibronectin was localized by immunofluorescence in the extracellular matrix during the period of mesenchymal cell proliferation. During chondrogenesis, fibronectin was demonstrated in the differentiating chondrocytes. Fibronectin was detectable in the cartilage matrix only after hyaluronidase treatment. During vascular invasion, prior to osteogenesis, fibronectin was localized in association with endothelial cells. These observations demonstrate a possible role of fibronectin in collagenous matrix-mesenchymal cell interaction in vivo.
Efficient laboratory evolution of computationally designed enzymes with low starting activities using fluorescence-activated droplet sorting (2016)

De novo biocatalysts with non-natural functionality are accessible by computational enzyme design. The catalytic activities obtained for the initial designs are usually low, but can be optimized significantly by directed evolution. Nevertheless, rate accelerations approaching the level of natural enzymes can only be achieved over many rounds of tedious and time-consuming laboratory evolution. In this work, we show that microfluidic-based screening using fluorescence-activated droplet sorting (FADS) is ideally suited for efficient optimization of designed enzymes with low starting activity, essentially straight out of the computer. We chose the designed retro-aldolase RA95.0, which had been previously evolved by conventional microtiter plate screening, as an example and reoptimized it using the microfluidic-based assay. Our results show that FADS is sufficiently sensitive to detect enzyme activities as low as kcat/Km = 0.5 M−1s−1. The ultra-high throughput of this system makes screening of large mutant libraries possible in which clusters of up to five residues are randomized simultaneously. Thus, combinations of beneficial mutations can be identified directly, leading to large jumps in catalytic activity of up to 80-fold within a single round of evolution. By exploring several evolutionary trajectories in parallel, we identify alternative active site arrangements that exhibit comparably enhanced efficiency but opposite enantioselectivity.
Parvovirus B19 transmission by heat‐treated clotting factor concentrates (2002)

B19 transmissions can be confirmed by nucleic acid sequencing. However, due to the low variability of the B19 genome, a large part of the B19 genome must be analyzed. The transmissions show that the applied heat treatment procedures were not sufficient to inactivate B19 completely.
Three dimensional micro integrated fluid systems (MIFS) fabricated by stereo lithography (2002)

A new type of real three dimensional micro fabrication using micro stereo lithography and electro plating named the "IH process" has been proposed and demonstrated by the authors. This process is applicable to both polymer and metal microstructures. In the first part of this paper, a new type of micro integrated fluid system (MIFS) whose concept is a hybrid system combined with the conventional silicon process and the new IH process are discussed. A three dimensional MIFS is prototyped successfully. Secondly, a special conductive UV solidified polymer is developed by the authors, together with an electrostatic microactuator made of it by using the IH process. The thirdly, the micro solidification process is carefully observed and a theoretical model of this process is proposed. The simulation results based on this model show good agreement with the experimental results.
Peptidoglycan Signaling in Innate Immunity and Inflammatory Disease (2005)

The ability to detect harmful pathogens and eradicate them is essential for the survival of an organism. One of the first lines of defense is the innate immune system, a broad specificity inflammatory response characterized by the recruitment and activation of phagocytes. This type of immune response is well conserved from invertebrates through higher mammals and is stimulated by the recognition of conserved components of microorganisms called pathogen-associated molecular patterns (PAMPs).1 These PAMPs consist of molecules not found in the host, including bacterial cell wall components such as peptidoglycan (PGN).
Murine Model of Immune-Mediated Rejection of the Acute Lymphoblastic Leukemia 70Z/3 (2006)

70Z/3 is a murine pre-B cell leukemia line derived from BDF(1) mice and has been used in the study of signaling pathways in B cells. 70Z/3 cells were initially found to cause widespread disease upon injections in animals. We have isolated 70Z/3 variants divergent in their capacity to lead to morbidity after injections. One variant, 70Z/3-NL, elicits an immune response protecting the animal from tumor growth. Another variant, 70Z/3-L, does not induce an effective immune response and causes morbidity. We demonstrated that both CD4(+) and CD8(+) T cells are required for the rejection of 70Z/3-NL cells. Interestingly, the immune response generated against 70Z/3-NL cells was found to protect against a challenge with the lethal variant, 70Z/3-L. This indicates that although both lines can be recognized and killed by the immune system, only 70Z/3-NL is capable of inducing a protective response. Further observations, using subclones isolated from 70Z/3-NL, demonstrated that immune recognition of a portion of the cells was sufficient for protection. Depletion of CD4(+) and CD8(+) T cells in animals injected previously with 70Z/3-NL cells showed that T cells, and not Abs, were required for the maintenance of the protection initiated by 70Z/3-NL. We tested the capacity of 70Z/3-NL cells to treat mice challenged with 70Z/3-L. We can delay injections of 70Z/3-NL and still provide protection for the animals. We have a model of immune-mediated rejection which will allow us to dissect the requirements for the initiation of immune responses against an ALL tumor cell line.
von Willebrand Factor Type C Domain-containing Proteins Regulate Bone Morphogenetic Protein Signaling through Different Recognition Mechanisms (2007)

Bone morphogenetic protein (BMP) function is regulated in the extracellular space by many modulator proteins, including those containing a von Willebrand factor type C (VWC) domain. The function of the VWC domain-containing proteins in development and diseases has been extensively studied. The structural basis, however, for the mechanism by which BMP is regulated by these proteins is still poorly understood. By analyzing chordin, CHL2 (chordin-like 2), and CV2 (crossveinless 2) as well as their individual VWC domains, we show that the VWC domain is a versatile binding module that in its multiple forms and environments can expose a variety of binding specificities. Three of four, two of three, and one of five VWCs from chordin, CHL2, and CV2, respectively, can bind BMPs. Using an array of BMP-2 mutant proteins, it can be demonstrated that the binding-competent VWC domains all use a specific subset of BMP-2 binding determinants that overlap with the binding site for the type II receptors (knuckle epitope) or for the type I receptors (wrist epitope). This explains the competition between modulator proteins and receptors for BMP binding and therefore the inhibition of BMP signaling. A subset of VWC domains from CHL2 binds to the Tsg (twisted gastrulation) protein similar to chordin. A stable ternary complex consisting of BMP-2, CHL2, and Tsg can be formed, thus making CHL2 a more efficient BMP-2 inhibitor. The VWCs of CV2, however, do not interact with Tsg. The present results show that chordin, CHL2, and CV2 regulate BMP-2 signaling by different recognition mechanisms.
Oxidation rate of conjugated linoleic acid and conjugated linolenic acid is slowed by triacylglycerol esterification and α‐tocopherol (2004)

We have recently shown that alpha-eleostearic acid (alpha-ESA), a conjugated linolenic acid, has a stronger antitumor effect than conjugated linoleic acid (CLA), both in vitro and in vivo. In this study, the oxidative stability of alpha-ESA was examined compared with linoleic acid (LA), alpha-linolenic acid (LnA), and CLA. Thin layers of the FA (LA, 9Z,11 E-CLA, 10E,12Z-CLA, LnA, and alpha-ESA) were auto-oxidized at 37 degrees C, and the FA remaining, the absorbed oxygen volume, the lipid hydroperoxide content, and the TBARS content were determined. The oxidation rate of alpha-ESA was faster than that of the unconjugated FA and CLA (9Z, 11 E-CLA and 10E, 12Z-CLA). However, the lipid hydroperoxide and TBARS contents following alpha-ESA oxidation were low, suggesting production of only small amounts of rapid-reacting secondary oxidation products. Furthermore, the oxidative stability of conjugated FA (CLA and CLnA) in which the carboxylic acid group was esterified with triacylglycerol was greater than that of the FFA. Addition of an antioxidant (alpha-tocopherol) also increased the stability of the conjugated FA to a level similar to that of the unconjugated FA.
Purification and characterization of two enone reductases from Saccharomyces cerevisiae (1998)

Two enone reductases catalyzing irreversibly the enantioselective reduction of alpha,beta-unsaturated carbonyls have been purified 165-fold and 257-fold, respectively, from the cytosolic fraction of Saccharomyces cerevisiae by means of streptomycin sulfate treatment, Sephadex G-25 filtration, DEAE-Sepharose CL-6B chromatography, blue Sepharose CL-6B chromatography and Superdex 200 preparation-grade filtration. One enzyme (E I) was NADPH-dependent, showed a molecular mass of 75 kDa and decomposed under denaturing electrophoretic conditions into two subunits of 34 kDa and 37 kDa. The other enzyme (E II) was NADH linked and the molecular mass estimated by means of Superdex 200 preparation-grade filtration, was 130 kDa. The enzyme decomposed into subunits of 56 kDa and 64 kDa on SDS/PAGE. Both enzymes were most active at pH 4.8 and accepted 1-octen-3-one, 1-hexen-3-one, 3-alken-2-ones, 4-alken-3-ones, 2-cyclohexen-1-ones, 2-alkenals, 2,4-alkadienals, 2-phenyl-2-alkenals, and 2-alkyl-2-alkenals as substrates. Both enzymes showed their highest activities with 1-hexen-3-one and 1-octen-3-one, respectively. The Km values for 1-octen-3-one were estimated as 0.54 mM (E I) and 0.20 mM (E II), respectively. Both enzymes catalyzed the enantioselective reduction of cis- and trans-2-phenyl-2-butenal into (R)-2-phenylbutanal.
Osseous healing with a composite of allograft and demineralized bone matrix: adverse effects of smoking. (2007)

We report on our use of a composite graft of lyophilized cancellous allogenic chips and demineralized bone matrix (DBM; Grafton; Osteotech, Eatontown, NJ) to manage traumatic osseous defects and nonunions. Data were prospectively collected from all patients who received this composite bone graft between 1996 and 2000. Only acute fractures with bone loss resulting in a uncontained defect and atrophic non-unions were included in the present study. Demographic data and complications related to composite use, tobacco use, and other comorbidities that could affect healing were evaluated. One hundred seven patients (112 bone graft sites) were followed up for a mean of 32 months (range, 12-60 months). Graft sites included the forearm, femur and tibia. Of the 112 patients, there were 56 smokers (25 non-unions and 31 fractures) and 56 non-smokers (28 fractures and 28 non-unions). Healing occured in 38/56 smokers compared with 49/56 non-smokers. In failed cases, smoking was characteristic in 7/9 non-unions and 11/16 fractures. There were 26 acute uncontained injuries, 29 acute contained defects, and 67 nonunions. Grafting sites were radius/ulna (13 cases), humerus (17), femur (31), and tibia/fibula (51). Significant comorbidities were diabetes mellitus (4 cases), fungal osteomyelitis (1), and pulmonary alveolar proteinosis (1). Eight (73%) of the 11 patients with graft failure had a significant smoking history. This composite graft is an option for managing osseous defects and nonunions traditionally treated with autologous bone grafting but should be used with caution when treating patients who are smokers.
PNA-Mediated Purification of PCR Amplifiable Human Genomic DNA from Whole Blood (1997)

A simple and rapid procedure whereby human genomic DNA can be purified in a PCR amplifiable form from whole blood is described. In a first step, human genomic DNA is hybridized in solution to a biotinylated peptide nucleic acid (PNA), which forms a high-affinity triplex with A7 sequence motifs in the target DNA. The complex is then captured onto paramagnetic streptavidin-coated particles, which are subsequently transferred directly into the PCR. The purification method effectively removes inhibitors of the PCR from as much as 500 microL of whole blood.
Cerebellar precursors transplanted to the neonatal dentate gyrus express features characteristic of hippocampal neurons (1995)

During the development of the CNS, a salient issue is whether neuronal phenotype is defined by the lineage or by the environment of precursor cells. Transplants permit these two possibilities to be tested, as cell fate can be examined in a new location. Dissociated cerebellar cells from newborn rats treated with tritiated thymidine or from NSE-lacZ transgenic mice were grafted into the dentate gyrus of the developing hippocampus. Implanted cells integrated into the granule cell layer, which contains the cell bodies of host granule neurons. Immunohistochemistry showed that grafted cells in the granule cell layer, like the host hippocampal granule neurons, were calbindin positive and upregulated FOS in a seizure paradigm. Electron microscopic analysis also showed that cells grafted to the dentate gyrus share features with host dentate neurons. These assays indicate that transplanted cerebellar cells acquired morphological and antigenic features characteristic of hippocampal neurons. These results show that metencephalic precursors are capable of differentiating in response to signals in the telencephalon, suggesting that the environment controls the regional fate of neuronal precursor cells during neurogenesis.
Optimization of period and thickness of the corrugated Ag cathode for efficient cross coupling between SPP and microcavity modes in top-emitting OLEDs (2017)

The efficient cross coupling between the surface plasmon–polariton (SPP) and microcavity modes was employed in the top-emitting organic light-emitting devices (TOLEDs) to release the trade-off between efficiency and stability by using a periodic corrugated Ag cathode. As the main factors affecting the cross coupling, the thickness and period of the corrugated Ag cathode were optimized to excite the SPP at the two interfaces of the Ag cathode and achieve a matched resonance wavelength between the SPP and the microcavity mode. At the optimal values of the thickness and period, the cross coupling between the SPP and microcavity modes enhanced the light extraction efficiency, and the efficiency of the corrugated TOLEDs was enhanced by 38.6% at the current density of 100 mA cm−2.
Crystal structure of the human PRMT5:MEP50 complex (2012)

Protein arginine methyltransferases (PRMTs) play important roles in several cellular processes, including signaling, gene regulation, and transport of proteins and nucleic acids, to impact growth, differentiation, proliferation, and development. PRMT5 symmetrically di-methylates the two-terminal ω-guanidino nitrogens of arginine residues on substrate proteins. PRMT5 acts as part of a multimeric complex in concert with a variety of partner proteins that regulate its function and specificity. A core component of these complexes is the WD40 protein MEP50/WDR77/p44, which mediates interactions with binding partners and substrates. We have determined the crystal structure of human PRMT5 in complex with MEP50 (methylosome protein 50), bound to an S-adenosylmethionine analog and a peptide substrate derived from histone H4. The structure of the surprising hetero-octameric complex reveals the close interaction between the seven-bladed β-propeller MEP50 and the N-terminal domain of PRMT5, and delineates the structural elements of substrate recognition.
New Photochemically Labile Protecting Group for Phosphates (1993)

Abstract New photochemically labile phosphate protecting group was developed. These phosphate esters have high molar extinction coefficient (ε340 = 34500 dm3 mol−1 cm−1) and rapidly release parent phosphates upon irradiation ( &amp;gt;300 nm) with high quantum efficiency for disappearance (φdis = 0.22 at 340 nm).