gebhart/patrepeval huggingface dataset:
Alterations in dorsal horn neurones in a rat model of cancer-induced bone pain (2003)

Cancer-induced bone pain is a major clinical problem. A rat model based on intra-tibial injection of MRMT-1 mammary tumour cells was used to mimic progressive cancer-induced bone pain. At the time of stable behavioural changes (decreased thresholds to mechanical and cold stimuli) and bone destruction, in vivo electrophysiology was used to characterize natural (mechanical, thermal, and cold) and electrical-evoked responses of superficial and deep dorsal horn neurones in halothane-anaesthetized rats. Receptive field size was significantly enlarged for superficial neurones in the MRMT-1 animals. Superficial cells were characterised as either nociceptive specific (NS) or wide dynamic range (WDR). The ratio of WDR to NS cells was substantially different between sham operated (growth media alone) (26:74%) and MRMT-1 injected rats (47:53%). NS cells showed no significant difference in their neuronal responses in MRMT-1-injected compared to sham rats. However, superficial WDR neurones in MRMT-1-injected rats had significantly increased responses to mechanical, thermal and electrical (A beta-, C fibre-, and post-discharge evoked response) stimuli. Deep WDR neurones showed less pronounced changes to the superficial dorsal horn, however, the response to thermal and electrical stimuli, but not mechanical, were significantly increased in the MRMT-1-injected rats. In conclusion, the spinal cord is significantly hyperexcitable with previously superficial NS cells becoming responsive to wide-dynamic range stimuli possibly driving this plasticity via ascending and descending facilitatory pathways. The alterations in superficial dorsal horn neurones have not been reported in neuropathy or inflammation adding to the evidence for cancer-induced bone pain reflecting a unique pain state.
Interstitial chromosomal deletion within 4q11-q13 in a human hepatoma cell line. (1991)

Southern blot analysis revealed the presence of an aberrant albumin gene as well as a normal one in a human hepatoma cell line, HuH-7. A genomic sequence carrying this altered gene was isolated and characterized. This clone contains a 3-kbp 3' segment of the albumin gene linked to a non-albumin sequence at intron 11. The non-albumin sequence is assigned to chromosome 4q12-q13 by in situ hybridization. This indicates an interstitial deletion of a chromosomal segment within 4q11-q13 because the albumin gene is mapped there. The truncated albumin gene is detected in an early passage of HuH-7 cells and has been maintained stably in cell culture.
Conversion of Single-Stranded Oligonucleotides into Cloned Duplexes and its Consecutive Application to Short Artificial Genes. (1991)

A general method to convert single-stranded, chemically synthesized oligonucleotides into cloned duplexes is described. Oligonucleotides supplied with 3'-terminal extensions that are complementary to 3'-protruding ends obtained by certain restriction enzymes can be cloned either directly or with the help of an adapter molecule into double-stranded vectors. Two methods have also been developed for consecutive cloning applications. According to these methods, the synthetic oligonucleotides (and their enzymatically prepared complementary strands) are joined, one after the other, inside a cloning vector, each joining requiring one cloning step. Synthetic genes are thus built up from oligonucleotides corresponding to only one strand of the DNA. The sequential assembly of the cloned duplex takes place in the 5' to 3' direction. Each oligonucleotide is supplied with a four-nucleotide-long 3'-terminal extension, but this sequence is eliminated when the joining takes place, leaving no limiting sequence between the oligonucleotides. The two consecutive cloning methods, the adapter and the polycloning site methods, are illustrated by the assembly of short artificial genes.
Chemically Programmed Bispecific Antibodies That Recruit and Activate T Cells (2012)

Bispecific antibodies (biAbs) that mediate cytotoxicity by recruiting and activating endogenous immune cells are an emerging class of next-generation antibody therapeutics. Of particular interest are biAbs of relatively small size (∼50 kDa) that can redirect cytotoxic T cells through simultaneous binding of tumor cells. Here we describe a conceptually unique class of biAbs in which the tumor cell specificity of a humanized antibody fragment that recognizes CD3 on T cells is chemically programmed through a C-terminal selenocysteine (Sec) residue. We demonstrate that through chemically programmed specificity for integrin α(4)β(1) or folate receptor 1 (FOLR1), and common specificity for CD3, these hybrid molecules exert potent and specific in vitro and ex vivo cytotoxicity toward tumor cell lines and primary tumor cells in the presence of primary T cells. Importantly, the generic nature of chemical programming allows one to apply our approach to virtually any specificity, promising a broad utility of chemically programmed biAbs in cancer therapy.
Tnf-alpha negatively regulates Th2 differentiation in humans (2017)

TNF- is a pleotropic cytokine with multiple physiological functions and is mainly produced from monocytes, macrophages, DCs and T-cells. Along with its physiological functions TNF- is also a therapeutic target in rheumatoid arthritis, cerebral malaria, sepsis, IBD and psoriasis. However its role in T helper cell differentiation and homeostasis in the above diseases is unclear. In this study we show that TNF- selectively inhibits the differentiation of human Th2 cells without affecting Th1 and Th17. TNF- decreased the ROS generation there by lowered the Erk1/2 phosphorylation in differentiating nave Tells there by down modulated the IL4 synthesis. Whereas cells treated with Anti TNF- has shown completely opposite effect. Consequently increased TNF- in T2DM and RA may account for the lowered Th2 differentiation and their increased AICD sensitivity thus exacerbating pre-existing inflammation.
Visible-spectrum (λ=650 nm) photopumped (pulsed, 300 K) laser operation of a vertical-cavity AlAs–AlGaAs/InAlP–InGaP quantum well heterostructure utilizing native oxide mirrors (1995)

Data are presented on the 300 K photopumped (pulsed) laser operation of a visible-spectrum (λ=650 nm) AlAs–AlGaAs/InAlP–InGaP quantum-well heterostructure (QWH) crystal that utilizes high-index-contrast AlAs-native-oxide/Al0.6Ga0.4As distributed Bragg reflector mirrors. The mirrors are formed by the lateral oxidation (H2O+N2, 425 °C) of two sets of four ‘‘buried’’ AlAs layers that are separated by Al0.6Ga0.4As. These mirrors, which create a high-Q cavity in the vertical direction, ‘‘sandwich’’ a one-wavelength InAlP–InGaP QW active region, thus forming a compact microcavity that ‘‘tunes’’ the carrier scattering and recombination into a narrow spectrum (∼25 Å) and supports laser operation in the vertical direction.
Scalable Active Learning by Approximated Error Reduction (2018)

We study the problem of active learning for multi-class classification on large-scale datasets. In this setting, the existing active learning approaches built upon uncertainty measures are ineffective for discovering unknown regions, and those based on expected error reduction are inefficient owing to their huge time costs. To overcome the above issues, this paper proposes a novel query selection criterion called approximated error reduction (AER). In AER, the error reduction of each candidate is estimated based on an expected impact over all datapoints and an approximated ratio between the error reduction and the impact over its nearby datapoints. In particular, we utilize hierarchical anchor graphs to construct the candidate set as well as the nearby datapoint sets of these candidates. The benefit of this strategy is that it enables a hierarchical expansion of candidates with the increase of labels, and allows us to further accelerate the AER estimation. We finally introduce AER into an efficient semi-supervised classifier for scalable active learning. Experiments on publicly available datasets with the sizes varying from thousands to millions demonstrate the effectiveness of our approach.
Antimicrobial proteins and peptides of blood: templates for novel antimicrobial agents (2000)

The innate immune system provides rapid and effective host defense against microbial invasion in a manner that is independent of prior exposure to a given pathogen.1 It has long been appreciated that the blood contains important elements that mediate rapid responses to infection. Thus, anatomic compartments with ample blood supply are less frequently infected and recover more readily once infected, whereas regions with poor perfusion are prone to severe infection and may require surgical débridement. Blood-borne innate immune mediators are either carried in circulating blood cells (ie, leukocytes and platelets) or in plasma after release from blood cells or on secretion by the liver.
Protection of Humans against Malaria by Immunization with Radiation‐AttenuatedPlasmodium falciparumSporozoites (2002)

During 1989-1999, 11 volunteers were immunized by the bites of 1001-2927 irradiated mosquitoes harboring infectious sporozoites of Plasmodium falciparum (Pf) strain NF54 or clone 3D7/NF54. Ten volunteers were first challenged by the bites of Pf-infected mosquitoes 2-9 weeks after the last immunization, and all were protected. A volunteer challenged 10 weeks after the last immunization was not protected. Five previously protected volunteers were rechallenged 23-42 weeks after a secondary immunization, and 4 were protected. Two volunteers were protected when rechallenged with a heterologous Pf strain (7G8). In total, there was protection in 24 of 26 challenges. These results expand published findings demonstrating that immunization by exposure to thousands of mosquitoes carrying radiation-attenuated Pf sporozoites is safe and well tolerated and elicits strain-transcendent protective immunity that persists for at least 42 weeks.
Research and Design of Smart Home System Based on ZigBee Technology (2013)

Smart home system is the inevitable trend of home network in the future. In this article, it built one interior network of smart home system based on ZigBee technology, designed one Home gateway, and configured one embedded Web server Boa on the gateway to realize one interactive network inside and outside the smart home, to provide one solution forwidely adaptation and energy saving smart home system.
Wavelength multiplexing DH AlGaAs injection laser source with a graded composition along the active layer (1981)

The use of DH (AlGa)As wafers with graded composition along the active layer for creation of multiwavelength laser source for a wavelength-division-multiplexing systems is proposed. The possibility of obtaining such structures by the LPE method under the condition of isothermal mixing is investigated. Electroluminescence measurements show that significant variation of emission wavelength along the structure does not cause the increase in threshold current density above a common level. The source fabricated is a set of monolithically integrated DBR lasers. Similarity of experimental dispersion of the effective guide indexes and that of refractive indexes of guide material facilitates the choice of DBR grating periods.
Epidermal Growth Factor Receptor as a Genetic Therapy Target for Carcinoma Cell Radiosensitization (2001)

Transduction of MDA-MB-231 xenograft tumors with Ad-EGFR-CD533 conferred a dominant-negative EGFR phenotype and induced tumor radiosensitization. Therefore, disruption of EGFR function through overexpression of EGFR-CD533 may hold promise as a gene therapeutic approach to enhance the sensitivity of tumor cells to ionizing radiation.
Application of the single radial diffusion test for assay of antibody to influenza type A viruses (1975)

Single radial diffusion (SRD) tests for antibodies to influenza type A hemagglutinin, neuraminidase, nucleoprotein, and matrix protein antigens were compared with conventional hemagglutination inhibition, neuraminidase inhibition, and complement fixation tests. Sera used in this study were obtained in 1968-1969 from volunteers before and after vaccination and before and after an ensuing epidemic of Hong Kong influenza. The SRD test compared favorably with conventional tests for assessment of vaccine- or infection-induced rises in antibody titers to influenza type A viruses. Little linear relationshiip was seen between zone areas with SRD and titers with conventional tests, suggesting that the SRD test may detect antibody of different quality or specificity. The SRD seemed equal to the hemagglutination inhibition test for predicting susceptibility to influenza. SRD is a simple test for the recognition of antibody to various antigenic components of the influenza virus and could prove to be a valuable epidemiological tool.
The cost of ethanol production from lignocellulosic biomass -- A comparison of selected alternative processes. Final report (1993)

The purpose of this report is to compare the cost of selected alternative processes for the conversion of lignocellulosic biomass to ethanol. In turn, this information will be used by the ARS/USDA to guide the management of research and development programs in biomass conversion. The report will identify where the cost leverages are for the selected alternatives and what performance parameters need to be achieved to improve the economics. The process alternatives considered here are not exhaustive, but are selected on the basis of having a reasonable potential in improving the economics of producing ethanol from biomass. When other alternatives come under consideration, they should be evaluated by the same methodology used in this report to give fair comparisons of opportunities. A generic plant design is developed for an annual production of 25 million gallons of anhydrous ethanol using corn stover as the model substrate at $30/dry ton. Standard chemical engineering techniques are used to give first order estimates of the capital and operating costs. Following the format of the corn to ethanol plant, there are nine sections to the plant; feed preparation, pretreatment, hydrolysis, fermentation, distillation and dehydration, stillage evaporation, storage and denaturation, utilities, and enzyme production. There are three pretreatment alternatives considered: the AFEX process, the modified AFEX process (which is abbreviated as MAFEX), and the STAKETECH process. These all use enzymatic hydrolysis and so an enzyme production section is included in the plant. The STAKETECH is the only commercially available process among the alternative processes.
Selective Decoration of a Phase-Separated Diblock Copolymer with Thiol-Passivated Gold Nanocrystals (1998)

Nanocrystalline gold particles passivated with alkane- and arenethiols were deposited on microphase-separated ultrathin films of poly(styrene-block-methyl methacrylate). The nanocrystals preferentially adsorbed to the polystyrene phases over areas of the substrate as large as 10 μm2, as seen by transmission electron microscopy. The basis for the separation is postulated to be the difference in interaction energies between the thiol passivants and the two polymers. The resulting patterns of nanocrystals are more than an order of magnitude smaller than features which can be produced by optical lithography.
Oxidation of Methionine in Proteins: Roles in Antioxidant Defense and Cellular Regulation (2000)

The roles of methionine residues in proteins have not been well defined, but a review of available studies leads to the conclusion that methionine, like cysteine, functions as an antioxidant and as a key component of a system for regulation of cellular metabolism. Methionine is readily oxidized to methionine sulfoxide by many reactive species. The oxidation of surface exposed methionines thus serves to protect other functionally essential residues from oxidative damage. Methionine sulfoxide reductases have the potential to reduce the residue back to methionine, increasing the scavenging efficiency of the system. Reversible covalent modification of amino acids in proteins provides the mechanistic basis for most systems of cellular regulation. Interconversion of methionine and methionine sulfoxide can function to regulate the biological activity of proteins, through alteration in catalytic efficiency and through modulation of the surface hydrophobicity of the protein.
Ret inhibition decreases growth and metastatic potential of estrogen receptor positive breast cancer cells (2013)

We show that elevated levels of Ret receptor are found in different sub-types of human breast cancers and that high Ret correlates with decreased metastasis-free survival. The role of Ret in ER+ breast cancer models was explored combining in vitro and in vivo approaches. Our analyses revealed that ligand-induced Ret activation: (i) stimulates migration of breast cancer cells; (ii) rescues cells from anti-proliferative effects of endocrine treatment and (iii) stimulates expression of cytokines in the presence of endocrine agents. Indeed, we uncovered a positive feed-forward loop between the inflammatory cytokine IL6 and Ret that links them at the expression and the functional level. In vivo inhibition of Ret in a metastatic breast cancer model inhibits tumour outgrowth and metastatic potential. Ret inhibition blocks the feed-forward loop by down-regulating Ret levels, as well as decreasing activity of Fak, an integrator of IL6-Ret signalling. Our results suggest that Ret kinase should be considered as a novel therapeutic target in subsets of breast cancer.
Identification of Selective, Nonpeptidic Nitrile Inhibitors of Cathepsin S Using the Substrate Activity Screening Method (2006)

The substrate activity screening method, a substrate-based fragment identification and optimization method for the development of enzyme inhibitors, was previously applied to cathepsin S to obtain low nanomolar 1,4-disubstituted-1,2,3-triazole-based aldehyde inhibitors (Wood, W. J. L.; Patterson, A. W.; Tsuruoka, H.; Jain, R. K.; Ellman, J. A. J. Am. Chem. Soc. 2005, 127, 15521-15527). Replacement of the metabolically labile aldehyde pharmacophore with the nitrile pharmacophore provided inhibitors with moderate potency for cathepsin S. The inhibitors showed good selectivity over cathepsins B and L but no selectivity over cathepsin K. X-ray structures of two crystal forms (1.5 and 1.9 A) of a complex between cathepsin S and a triazole inhibitor incorporating a chloromethyl ketone pharmacophore guided the design of triazole substrates with increased cleavage efficiency and selectivity for cathepsin S over cathepsins B, L, and K. Conversion of select substrates to nitrile inhibitors yielded a low molecular weight (414 Da) and potent (15 nM) cathepsin S inhibitor that showed >1000-fold selectivity over cathepsins B, L, and K.
The Prolactin Receptor and Severely Truncated Erythropoietin Receptors Support Differentiation of Erythroid Progenitors (1997)

Activation of the erythropoietin receptor is essential for the survival, proliferation, and differentiation of erythroid progenitors. To understand the role of erythropoietin receptor (EpoR) activation in erythroid differentiation, we infected primary erythroid progenitors with high-titer retrovirus encoding the non-hematopoietic prolactin receptor. The infected progenitors responded to prolactin in the absence of Epo by generating fully differentiated erythroid colonies. Therefore, differentiation of erythroid progenitors does not require an intracellular signal generated uniquely by the EpoR; the EpoR does not have an instructive role in erythroid differentiation. We also infected primary erythroid progenitors with retrovirus encoding chimeric receptors containing the extracellular domain of PrlR and the intracellular domain of either the wild-type or truncated EpoRs. A chimeric receptor containing only the membrane-proximal 136 amino acids of the EpoR cytoplasmic domain efficiently supported prolactin-dependent differentiation of erythroid progenitors. Substitution of the single cytoplasmic domain tyrosine in this receptor with phenylalanine (Y343F) eliminated its ability to support differentiation. The minimal EpoR cytoplasmic domain required for erythroid differentiation is therefore the same as that previously reported to be sufficient to support cell proliferation (D'Andrea, A. D., Yoshimura, A., Youssoufian, H., Zon, L. I., Koo, J. W., and Lodish, H. F. (1991) Mol. Cell. Biol. 11, 1980-1987; Miura, O., D'Andrea, A. D., Kabat, D., and Ihle, J. N. (1991) Mol. Cell. Biol. 11, 4895-4902; He, T.-C., Jiang, N., Zhuang, H., Quelle, D. E., and Wojchowski, D. M. (1994) J. Biol. Chem. 269, 18291-18294).
DNA methylation studies on imprinted loci in a male monozygotic twin pair discordant for Beckwith-Wiedemann syndrome (2010)

Beckwith–Wiedemann syndrome (BWS) is one of the most prevalent congenital disorders predominantly caused by epigenetic alterations. Here we present an extensive case study of a monozygotic monochorionic male twin pair discordant for BWS. Our analysis allows to correlate BWS symptoms, like a protruding tongue, indented ears and transient neonatal hypoglycaemia, to an abnormal methylation at the KvDMR1. DNAs extracted from peripheral blood, skin fibroblasts, saliva and buccal swab of both twins, their sister and parents were analysed at 11 differentially methylated regions (DMRs) including all four relevant DMRs of the BWS region. The KvDMR1 was exclusively found to be hypomethylated in all cell types of the affected BWS twin, while the unaffected twin and the relatives showed normal methylation in fibroblasts, buccal swab and saliva DNA. Interestingly, the twins share a common blood-specific hypomethylation phenotype most probably caused by a feto-fetal transfusion between both twins. Because microsatellite analysis furthermore revealed a normal biparental karyotype for chromosome 11, our results point to an exclusive correlation of the observed BWS symptoms to locally restricted epimutations at the KvDMR1 of the maternal chromosome.
Hierarchical CAD Tools for Radiation Hardened Mixed Signal Electronic Circuits (2005)

Abstract : This report covers the final report of our phase I effort to develop a mixed signal simulator with radiation modeling capability. Silvaco's Harmony-AMS(Analog/Mixed Signal) simulator was modified to enable the simulation of single events, total ionizing dose, and dose rate in a commercial hierarchical design flow.
COMPARISON OF FATTY ACID AND SENSORY PROFILES OF BEEF FROM FORAGE‐FED CATTLE WITH RETAIL UNITED STATES DEPARTMENT OF AGRICULTURE CHOICE AND SELECT BEEF (2006)

ABSTRACT Over two consecutive years, steaks from cattle ( n = 107) grazing three cool‐season grazing systems consisting of either orchard grass pasture or fescue pasture, each with soyhull (SH) supplementation or fescue pasture with no supplementation, were compared with retail United States Department of Agriculture (USDA) Choice and Select steaks obtained from area supermarkets for fatty acid and sensory characteristics. Steaks from all three forage treatments had greater ( P &lt; 0.05) proportions of longissimus conjugated linoleic acid (CLA; cis‐9, trans‐11) and lower ( P &lt; 0.05) n‐6–n‐3 fatty acid ratios than USDA Choice or Select steaks. Sensory evaluation revealed that steaks from the SH‐supplemented treatments had similar ( P &gt; 0.05) beef/brothy and grassy flavor intensities than retail USDA Choice and Select steaks, whereas steaks from unsupplemented forage‐fed cattle had decreased ( P &lt; 0.05) beef/brothy and increased ( P &lt; 0.05) grassy flavor intensities than USDA Choice and Select steaks. These results suggest that supplementing SHs to cattle on forage can enhance beef flavor and reduce grassy flavor characteristics similar to retail USDA Choice and Select steaks while maintaining heightened CLA proportions and a lower n‐6–n‐3 ratio.