gebhart/patrepeval huggingface dataset:
The REC2 gene encodes the homologous pairing protein of Ustilago maydis. (1994)

Amino acid sequence analysis has established that the homologous pairing protein of Ustilago maydis, known previously in the literature as rec1, is encoded by REC2, a gene essential for recombinational repair and meiosis with regional homology to Escherichia coli RecA. The 70-kDa rec1 protein is most likely a proteolytic degradation product of REC2, which has a predicted mass of 84 kDa but which runs anomalously during sodium dodecyl sulfate-gel electrophoresis with an apparent mass of 110 kDa. To facilitate purification of the protein product, the REC2 gene was overexpressed from a vector that fused a hexahistidine leader sequence onto the amino terminus, enabling isolation of the REC2 protein on an immobilized metal affinity column. The purified protein exhibits ATP-dependent DNA renaturation and DNA-dependent ATPase activities, which were reactions characteristic of the protein as purified from cell extracts of U. maydis. Homologous pairing activity was established in an assay that measures recognition via non-Watson-Crick bonds between identical DNA strands. A size threshold of about 50 bp was found to govern pairing between linear duplex molecules and homologous single-stranded circles. Joint molecule formation with duplex DNA well under the size threshold was efficiently catalyzed when one strand of the duplex was composed of RNA. Linear duplex molecules with hairpin caps also formed joint molecules when as few as three RNA residues were present.
Synthesis, characterization, and in vitro cell culture viability of degradable poly(N‐isopropylacrylamide‐co‐5,6‐benzo‐2‐methylene‐1,3‐dioxepane)‐based polymers and crosslinked gels (2008)

Poly(N-isopropylacrylamide-co-5,6-benzo-2-methylene-1,3-dioxepane) (poly(NIPAAm-co-BMDO)) was synthesized by atom transfer radical polymerization (ATRP) and reversible addition-fragmentation chain transfer (RAFT) polymerization. Using UV-vis spectroscopy, the lower critical solution temperature (LCST) of poly(NIPAAm) and poly(NIPAAm-co-BMDO) copolymers were measured, varying with respect to the amount of incorporated BMDO. This material is degradable and possesses a LCST above room temperature and below body temperature, making it a potential candidate for use as an injectable tissue engineering scaffold to enhance fracture repair. ATRP and RAFT enabled preparation of polymers with control over molecular weight up to M(n) = 50,000 g/mol and M(w)/M(n) < 1.2. Degradation studies were performed in basic solution and in complete Dulbecco's modified Eagle medium. The cytotoxicity of the material and its degradation products were analyzed by in vitro cell culture analyses, including cytotoxicity live/dead and CyQUANT cell proliferation assays. Crosslinked scaffolds with degradable units within the polymer backbone and at the crosslinking sites were prepared using an ester-containing diacrylate crosslinker. Furthermore, incorporation of a GRGDS peptide sequence improved cell attachment to the gels. Controlled/living radical polymerization techniques allow for precise control over macromolecular structure and are poised to become powerful tools for tissue engineering scaffold synthesis.
Lack of specificity of fibroblast-specific protein 1 in cardiac remodeling and fibrosis (2013)

Understanding the role of fibroblasts in pathologic conditions is hampered by the absence of specific markers. Fibroblast-specific protein (FSP)1 has been suggested as a fibroblast-specific marker in normal and fibrotic tissues; FSP1 reporter mice and FSP1-Cre-driven gene deletion are considered reliable strategies to investigate fibroblast biology. Because fibroblasts are abundant in normal and injured mammalian hearts, we studied the identity of FSP1(+) cells in the infarcted and remodeling myocardium using mice with green fluorescent protein (GFP) expression driven by the FSP1 promoter. Neonatal and adult mouse hearts had low numbers of FSP1(+) cells. Myocardial infarction induced marked infiltration with FSP1-expressing cells that peaked after 72 h of reperfusion. Using flow cytometry, we identified 50% of FSP1(+) cells as hematopoietic cells; many endothelial cells were also FSP1(+). Increased infiltration with FSP1(+) cells was also noted in the pressure-overloaded myocardium. Although some FSP1(+) cells had fibroblast morphology, >30% were identified as hematopoietic cells, endothelial cells, or vascular smooth muscle cells. In contrast, periostin did not stain leukocytes or vascular cells but labeled spindle-shaped interstitial cells and, as a typical matricellular protein, was deposited in the matrix. CD11b(+) myeloid cells sorted from the infarcted heart had higher FSP1 expression than corresponding CD11b-negative cells, highlighting the predominant expression by hematopoietic cells. FSP1 is not a specific marker for fibroblasts in cardiac remodeling and fibrosis.
Principles and Practice of the Biologic Therapy of Cancer (2000)

I: Principles and Practice of Cytokine Therapy II: Principles and Practice of Cell Transfer Therapy III: Principles and Practice of Monoclonal Antibody Therapy IV: Priciples and Practice of Cancer Vaccines V: Principles and Practice of Gene Therapy VI: Principles and Practice of Antiangiogenic Therapy VII: Evolving Approaches to Biologic Therapy Index
Structures, Sensory Activity, and Dose/Response Functions of 2,5-Diketopiperazines in Roasted Cocoa Nibs (Theobroma cacao) (2005)

The taste compounds inducing the blood-like, metallic bitter taste sensation reported recently for a dichloromethane extract prepared from roasted cocoa nibs were identified as a series of 25 diketopiperazines by means of HPLC degustation, LC-MS/MS, and independent synthesis. Among these 25 compounds, 13 cis-configured diketopiperazines, namely, cyclo(L-IIe-L-Phe), cyclo(L-Val-L-Leu), cyclo(L-Pro-L-Pro), cyclo(L-IIe-L-Pro), cyclo(L-Val-L-Tyr), cyclo(L-Ala-L-Tyr), cyclo(L-Phe-L-Ser), cyclo(L-Ala-L-IIe), cyclo(L-Leu-L-Phe), cyclo(L-Pro-L-Val), cyclo(L-Pro-L-Thr), cyclo(L-Pro-L-Tyr), and cyclo(L-Val-L-Val) were identified for the first time in cocoa. In addition, the taste recognition thresholds for the metallic as well as the bitter taste of the diketopiperazines were determined, and after quantitative analysis by using two diastereomeric diketopiperazines as the internal standards, the sensory impact of the diketopiperazines was evaluated on the basis of their dose-over-threshold (DoT) factors calculated as the ratio of the concentration and the threshold concentration of a compound. These data revealed DoT factors above 1.0 exclusively for cis-cyclo(L-Pro-L-Val), cis-cyclo(L-Val-L-Leu), cis-cyclo(L-Ala-L-Ile), cis-cyclo(L-Ala-L-Leu), and cis-cyclo(L-Ile-L-Pro), whereas all of the other diketopiperazines were present below their individual bitter taste threshold concentrations and should therefore not contribute to the cocoa taste. Because the DoT factors do not consider the nonlinear relationship between the concentration and gustatory response of an individual compound, we, for the first time, report on the recording of dose/response functions describing the human bitter taste perception of diketopiperazines more precisely.
Carbon diffusion in silicon (1998)

Carbon diffusion in silicon has been investigated by using a superlattice structure of carbon spikes (10 nm-wide, carbon concentration &amp;gt;1019 cm−3, spikes spaced 100 nm apart) grown epitaxially by Si molecular beam epitaxy. Samples were annealed in the range between 680 and 850 °C. The diffusive behavior of carbon was monitored by secondary ion mass spectrometry. Carbon diffusion profiles observed at temperatures above 800 °C show highly nonregular behavior. The diffusion results are interpreted in terms of the kick-out mechanism.
Adipose-derived Stem Cells Attenuates Diabetic Osteoarthritis via Inhibition of Glycation-mediated Inflammatory Cascade (2018)

Diabetes mellitus (DM) is well-known to exert complications such as retinopathy, cardiomyopathy and neuropathy. However, in recent years, an elevated osteoarthritis (OA) complaints among diabetics have been observed, portending the risk of diabetic OA. Since formation of advanced glycation end products (AGE) is believed to be the etiology of various diseases under hyperglycemic conditions, we firstly established that streptozotocin-induced DM could potentiate the development of OA in C57BL/6J mouse model, and further explored the intra-articularly administered adipose-derived stem cell (ADSC) therapy focusing on underlying AGE-associated mechanism. Our results demonstrated that hyperglycemic mice exhibited OA-like structural impairments including a proteoglycan loss and articular cartilage fibrillations in knee joint. Highly expressed levels of carboxymethyl lysine (CML), an AGE and their receptors (RAGE), which are hallmarks of hyperglycemic microenvironment were manifested. The elevated oxidative stress in diabetic OA knee-joint was revealed through increased levels of malondialdehyde (MDA). Further, oxidative stress-activated nuclear factor kappa B (NF-κB), the marker of proinflammatory signalling pathway was also accrued; and levels of matrix metalloproteinase-1 and 13 were upregulated. However, ADSC treatment attenuated all OA-like changes by 4 weeks, and dampened levels of CML, RAGE, MDA, NF-κB, MMP-1 and 13. These results suggest that during repair and regeneration, ADSCs inhibited glycation-mediated inflammatory cascade and rejuvenated cartilaginous tissue, thereby promoting knee-joint integrity in diabetic milieu.
MetaNet: a metadata term thesaurus to enable semantic interoperability between metadata domains (2001)

Metadata interoperability is a fundamental requirement for access to information within networked knowledge organization systems. The Harmony International Digital Library Project [1] has developed a common underlying data model (the ABC model) to enable the scalable mapping of metadata descriptions across domains and media types. The ABC model, described in [2], provides a set of basic building blocks for metadata modeling and recognizes the importance of 'events' to unambiguously describe metadata for objects with a complex history. In order to test and evaluate the interoperability capabilities of this model, we applied it to some real multimedia examples and analysed the results of mapping from the ABC model to various different metadata domains using XSLT [3]. This work revealed serious limitations in XSLT's ability to support flexible dynamic semantic mapping. In order to overcome this, we developed MetaNet [4], a metadata term thesaurus which provides the additional semantic knowledge which is non-existent within declarative XML-encoded metadata descriptions. This paper describes MetaNet, its RDF Schema [5] representation and a hybrid mapping approach which combines the structural and syntactic mapping capabilities of XSLT with the semantic knowledge of MetaNet, to enable flexible and dynamic mapping among metadata standards.
Prediction of spontaneous preterm delivery from maternal factors, obstetric history and placental perfusion and function at 11–13 weeks (2011)

Patient-specific risk of preterm delivery is provided by maternal factors and obstetric history. Placental perfusion and function at 11-13 weeks are not altered in pregnancies resulting in spontaneous early delivery.
Construction, Expression, and Purification of Chimeric Protein Reagents Based on Immunoglobulin Fc Regions (2011)

Recombinant fusion proteins incorporating experimental protein domains fused to immunoglobulin Fc regions have become widely utilized in studies of protein-ligand interactions. The advantages of these systems include an inherent increase in avidity provided by the multimerization of Fc regions, combined with robust detection methods based on numerous commercially available secondary reagents directed against the Fc tag. We describe a set of methods for subcloning, expression, and purification of chimeric protein reagents containing a protein domain (or domains) of interest fused to a C-terminal moiety derived from the Fc region of either IgG or IgM.
GS28, a 28-Kilodalton Golgi SNARE That Participates in ER-Golgi Transport (1996)

Little is known about the integral membrane proteins that participate in the early secretory pathway of mammalian cells. The complementary DNA encoding a 28-kilodalton protein (p28) of the cis-Golgi was cloned and sequenced. The protein was predicted to contain a central coiled-coil domain with a carboxyl-terminal membrane anchor. An in vitro assay for endoplasmic reticulum-Golgi transport was used to show that p28 participates in the docking and fusion stage of this transport event. Biochemical studies established that p28 is a core component of the Golgi SNAP receptor (SNARE) complex.
Pharmacological studies on 3-[gamma-(p-fluorobenzoyl)propyl]-2,3,4,4a,5,6-hexahydro-1-(H)-pyrazino(1,2-a)quinoline hydrochloride (compound 69/183). Part IV: other CNS effects and acute toxicity. (1978)

3-[gamma-(p-Fluorobenzoyl)propyl]-2,3,4,4a,5,6-hexahydro-1-(H)-pyrazino(1,2-a)quinoline hydrochloride (centpyraquin), a potent antihypertensive and tranquillising agent, was tested for anticonvulsant, analgesic and anti-inflammatory activities in mice and for anti-emetic activity in dogs. It did not modify supramaximal electroshock seizures and failed to protect the animals against pentylenetetrazole and strychnine induced convulsions. It, however, produced some elevation in the threshold dose of strychnine. Tremorine induced tremors and salivation were not antagonised. The compound had weak analgesic activity as detected by antagonism to phenylquinone writhing and the hot plate test. It had no anti-inflammatory activity. Centpyraquin had strong anti-emetic activity against apomorphine as well as morphine. At high doses it produced fall out in the rota-rod test. The LD50 of centpyraquin in mice was 296 mg/kg i.p. and more than 1000 mg/kg p.o. and in rats it was 161 mg/kg i.p. and more than 800 mg/kg p.o. The observed CNS effects resemble those of other neuroleptics.
Automated Fluorescent DNA Sequencing (2003)

Three fundamental technologies have emerged in genetic analysis that have widespread and immediate benefits. DNA synthesis, fluorescence-based DNA analysis, and the polymerase chain reaction (PCR) are being integrated for a range of applications, from forensics to the understanding and treatment of genetic disease. By combining the use of PCR and DNA sequencing, we now have a clear understanding of the molecular basis for many disease states (1). The technologies used to map and sequence the human genome are also being used in leading research establishments to detect DNA mutations leading to genetic diseases such as muscular dystrophy, cystic fibrosis, HIV, and cancer susceptibility (1–3). The detection of mutations within many disease-related genes can be automated using fluorescent labeled fragments generated by PCR or cycle sequencing. One of Applied Biosystem’s main goals is to develop genetic analysis technologies to meet the needs of the clinical and research settings of the future.
Impulsive Noise Mitigation in Powerline Communications Using Sparse Bayesian Learning (2013)

Asynchronous impulsive noise and periodic impulsive noises limit communication performance in OFDM powerline communication systems. Conventional OFDM receivers that assume additive white Gaussian noise experience degradation in communication performance in impulsive noise. Alternate designs assume a statistical noise model and use the model parameters in mitigating impulsive noise. These receivers require training overhead for parameter estimation, and degrade due to model and parameter mismatch. To mitigate asynchronous impulsive noise, we exploit its sparsity in the time domain, and apply sparse Bayesian learning methods to estimate and subtract the noise impulses. We propose three iterative algorithms with different complexity vs. performance trade-offs: (1) we utilize the noise projection onto null and pilot tones; (2) we add the information in the date tones to perform joint noise estimation and symbol detection; (3) we use decision feedback from the decoder to further enhance the accuracy of noise estimation. These algorithms are also embedded in a time-domain block interleaving OFDM system to mitigate periodic impulsive noise. Compared to conventional OFDM receivers, the proposed methods achieve SNR gains of up to 9 dB in coded and 10 dB in uncoded systems in asynchronous impulsive noise, and up to 6 dB in coded systems in periodic impulsive noise.
Enabling fast failure recovery in OpenFlow networks (2011)

OpenFlow is a novel technology designed at Stanford University which aims at decoupling the controller software from the forwarding hardware of a router or switch. The OpenFlow concept is based on the approach that the forwarding information base (FIB) of a switch can be programmed via a controller which resides at a separate hardware. The goal is to provide a standardized open management interface to the forwarding hardware of a router or switch. The aim of a project SPARC “SPlit ARchitecture Carrier grade networks” is to deploy OpenFlow in carrier grade networks. Reliability is a major issue to deploy OpenFlow in this networks. This work proposes the addition of a fast restoration mechanism in OpenFlow and evaluates the performance by comparing the switchover time and packet loss to existing restoration options in a current OpenFlow implementation.
Mechanisms of Bacterial Opsonization by Immune Globulin Intravenous: Correlation of Complement Consumption with Opsonic Activity and Protective Efficacy (1989)

To study the mechanism of bacterial opsonization by immune globulin intravenous (IGIV) complement consumption and polymorphonuclear leukocyte (PMNL) membrane receptor (FcRlo, CR1, and CR3)-mediated phagocytosis of Staphylococcus epidermidis, Klebsiella pneumoniae, and groups A and B streptococci were examined. IGIV alone did not consume complement and showed no opsonic activity by itself for these organisms. When these bacteria were preopsonized in IGIV, significant amounts of complement were consumed (44%-94%) and the uptake and killing of bacteria occurred. The in vitro opsonic activity of IGIV for these organisms was significantly correlated with the amount of complement consumed by the IGIV-opsonized bacteria (r = .85, P less than .05). The in vivo protective efficacy of IGIV also appeared to be directly associated with its ability to activate and consume complement (r = 1.0, P less than .001). Antibodies to FcRlo (Leu 11) markedly inhibited phagocytosis of bacteria opsonized in IGIV but not that of bacteria opsonized in specific IgM. Both CR1 and CR3 receptors on PMNLs were involved in uptake, but the contribution of each is different with different organisms.
JAK2 V617F-Dependent Upregulation of PU.1 Expression in the Peripheral Blood of Myeloproliferative Neoplasm Patients (2011)

Myeloproliferative neoplasms (MPN) are multiple disease entities characterized by clonal expansion of one or more of the myeloid lineages (i.e. granulocytic, erythroid, megakaryocytic and mast cell). JAK2 mutations, such as the common V617F substitution and the less common exon 12 mutations, are frequently detected in such tumor cells and have been incorporated into the diagnostic criteria published by the World Health Organization since 2008. However, the mechanism by which these mutations contribute to MPN development is poorly understood. We examined gene expression profiles of MPN patients focusing on genes in the JAK-STAT signaling pathway using low-density real-time PCR arrays. We identified the following 2 upregulated genes in MPN patients: a known target of the JAK-STAT axis, SOCS3, and a potentially novel target, SPI1, encoding PU.1. Induction of PU.1 expression by JAK2 V617F in JAK2-wildtype K562 cells and its downregulation by JAK2 siRNA transfection in JAK2 V617F-positive HEL cells supported this possibility. We also found that the ABL1 kinase inhibitor imatinib was very effective in suppressing PU.1 expression in BCR-ABL1-positive K562 cells but not in HEL cells. This suggests that PU.1 expression is regulated by both JAK2 and ABL1. The contribution of the two kinases in driving PU.1 expression was dominant for JAK2 and ABL1 in HEL and K562 cells, respectively. Therefore, PU.1 may be a common transcription factor upregulated in MPN. PU.1 is a transcription factor required for myeloid differentiation and is implicated in erythroid leukemia. Therefore, expression of PU.1 downstream of activated JAK2 may explain why JAK2 mutations are frequently observed in MPN patients.
Nutritional and biochemical aspects of the hypolipidemic action of rice bran oil: a review. (1991)

In this paper, we review the effects of rice bran oil (RBO), an unconventional oil recently introduced onto the Indian market for human use. RBO contains oleic acid (38.4%), linoleic acid (34.4%), and linolenic acid (2.2%) as unsaturated fatty acids, and palmitic (21.5%) and stearic (2.9%) acids as saturated fatty acids. The unsaponifiable fraction (4.2%) has total tocopherols (81.3 mg%), gamma-oryzanol (1.6%), and squalene (320 mg%). Oryzanol is a mixture of ferulic acid esters of triterpene alcohols such as cycloartenol (CA) (106 mg%) and 24-methylene cycloartanol (494 mg%). Studies on experimental rats demonstrated a hypolipidemic effect of RBO. The unsaponifiable fraction of RBO lowers cholesterol levels. Feeding phytosterols, CA, and 24-methylene cycloartanol in amounts present in RBO to hypercholesterolemic rats for 8 weeks indicates that CA alone reduces cholesterol and triglyceride levels significantly. Endogenous sterol excretion increases in animals given CA. The accumulation of CA in the liver inhibits cholesterol esterase activity, which in turn leads to reduction in circulating cholesterol levels. CA is structurally similar to cholesterol and may compete with the binding sites of cholesterol and sequestrate cholesterol, which is metabolized to its derivatives. RBO, which is rich in tocopherols and tocotrienols, may improve oxidative stability. Tocotrienols inhibit HMG CoA reductase, resulting in hypocholesterolemia. The hypolipidemic effect of RBO has also been established in human subjects. Thus, RBO could be a suitable edible oil for patients with hyperlipidemia.
Personalized vaccines for cancer immunotherapy (2018)

Cancer is characterized by an accumulation of genetic alterations. Somatic mutations can generate cancer-specific neoepitopes that are recognized by autologous T cells as foreign and constitute ideal cancer vaccine targets. Every tumor has its own unique composition of mutations, with only a small fraction shared between patients. Technological advances in genomics, data science, and cancer immunotherapy now enable the rapid mapping of the mutations within a genome, rational selection of vaccine targets, and on-demand production of a therapy customized to a patient's individual tumor. First-in-human clinical trials of personalized cancer vaccines have shown the feasibility, safety, and immunotherapeutic activity of targeting individual tumor mutation signatures. With vaccination development being promoted by emerging innovations of the digital age, vaccinating a patient with individual tumor mutations may become the first truly personalized treatment for cancer.
AMOLED Production: Entering a New Era? (2013)

Active‐matrix organic light‐emitting‐diode (AMOLED) displays have many attractive features that have led companies to attempt to manufacture them, but one country – Korea – currently accounts for the vast majority of AMOLED‐display manufacturing capacity. Ambitious investment plans in China, Japan, and Taiwan could change this balance over the next several years.