gebhart/patrepeval huggingface dataset:
Bioengineering a Unique Deimmunized Bispecific Targeted Toxin That Simultaneously Recognizes Human CD22 and CD19 Receptors in a Mouse Model of B-Cell Metastases (2010)

A drug of high potency and reduced immunogenicity is needed to develop a targeted biological drug that when injected systemically can penetrate to malignant B cells. Therefore, a novel deimmunized bispecific ligand-directed toxin targeted by dual high-affinity single-chain Fvs (scFv) spliced to PE38 with a KDEL COOH-terminus was genetically engineered. The aims were to reduce toxin immunogenicity using mutagenesis, measure the ability of mutated drug to elicit antitoxin antibody responses, and show that mutated drug was effective against systemic B-cell lymphoma in vivo. Both human anti-CD22 scFv and anti-CD19 scFv were cloned onto the same single-chain molecule with truncated pseudomonas exotoxin (PE38) to create the drug. Site-specific mutagenesis was used to mutate amino acids in seven key epitopic toxin regions that dictate B-cell generation of neutralizing antitoxin antibodies. Bioassays were used to determine whether mutation reduced potency, and ELISAs were done to determine whether antitoxin antibodies were reduced. Finally, a powerful genetically altered luciferase xenograft model was used that could be imaged in real time to determine the effect on systemic malignant human B-cell lymphoma, Raji-luc. Patient B-lineage acute lymphoblastic leukemia, B-cell chronic lymphocytic leukemia, and B lymphoma were high in CD22 and CD19 expression. 2219KDEL7mut was significantly effective against systemic Raji-luc in mice and prevented metastatic spread. Mutagenesis reduced neutralizing antitoxin antibodies by approximately 80% with no apparent loss in in vitro or in vivo activity. Because 2219KDEL7mut immunogenicity was significantly reduced and the drug was highly effective in vivo, we can now give multiple drug treatments with targeted toxins in future clinical trials.
Association of Prostate Cancer Risk Variants with Clinicopathologic Characteristics of the Disease (2008)

Prostate cancer risk variants recently discovered from genome-wide case-control association studies are not associated with clinicopathologic variables in this population. Case-case studies are urgently needed to discover genetic variants that predict tumor aggressiveness.
Temperature dependence of the surface plasmon resonance of Au/SiO2 nanocomposite films (2000)

The optical response of Au/SiO2 nanocomposite films at temperatures spanning the transition to the liquid state has been measured. The change in the optical constants of gold from those corresponding to the crystalline material to those of the liquid occurs gradually and at temperatures below the bulk melting point. The similarity of the temperature-induced changes in the Au interband absorption edge to that observed with decreasing particle size suggests that a gradual transition to the liquid phase also occurs in small particles.
Primary and secondary structures of rRNA spacer regions in enterococci (1997)

The 16S-23S and 23S-5S rRNA spacer DNA regions (spacer regions 1 and 2, respectively) from Enterococcus faecalis, Enterococcus faecium, Enterococcus hirae, Enterococcus durans and Enterococcus mundtii were amplified by PCR. Their nucleotide sequences were established and a secondary structure model showing the interaction between the two spacer regions was built. Whereas lactococci and Streptococcus sensu stricto are characterized by a single type of spacer region 1, the enterococci show a high degree of variability in this region; thus the spacer regions 1 with and without tRNA(Ala) were characterized. However, as shown for lactococci and Streptococcus sensu stricto, the tRNA(Ala) gene does not encode the 3'-terminal CCA trinucleotide. A putative antitermination signal is found downstream from the tRNA(Ala) gene. Based on comparison with Lactococcus lactis and Streptococcus thermophilus, a double-stranded processing stem is proposed. In E, hirae, one of the three different types of spacer region 1 contains no tRNA(Ala), but displays a 107 nt insertion that forms a long stem-loop structure. A similar insertion (115 nt in length) was found in E. faecium and base compensatory mutations preserve the ability to form the long stem-loop structure. Such insertions may correspond to mobile intervening sequences, as found in the 23S rRNA coding sequences of some Gram-negative bacteria. The spacer regions 1 and 2 from the three subgroups of streptococci were compared, and except for the tRNA(Ala) gene and the double-stranded processing sites, little similarity was found, which opens large possibilities for future development of DNA-based typing methods.
Cloning and expression of rat histidase. Homology to two bacterial histidases and four phenylalanine ammonia-lyases. (1990)

Histidase (histidine ammonia-lyase, EC 4.3.1.3) catalyzes the deamination of histidine to urocanic acid. Apart from phenylalanine ammonia-lyase, which is not expressed in animals, histidase is the only enzyme known to have a dehydroalanine residue in its active site. The amino site precursor and the mechanism of formation of dehydroalanine are not known. As an initial step to determining the precursor of dehydroalanine in histidase, we have isolated a functional cDNA clone for histidase from a rat liver cDNA library using an affinity-purified antiserum. The 2.2-kilobase cDNA has a 1,971-base pair open reading frame coding for a 657-amino acid polypeptide with a predicted molecular mass of 72,165 Da. The cDNA has a rare polyadenylation signal (AAUACA) that appears to inefficiently direct polyadenylation in transfected COS monkey kidney cells. Conversion of this sequence to the consensus polyadenylation signal (AAUAAA) resulted in increased levels of stable mRNA. COS cells transfected with a histidase expression vector produce active histidase. The formation of active histidase in cells that have no endogenous histidase activity suggests either that the requisite modifying enzyme is present in these cells or that the dehydroalanine residue forms by an autocatalytic mechanism. Rat histidase was found to have 41 and 43% amino acid identity to Pseudomonas putida and Bacillus subtilis histidases, respectively. Phenylalanine ammonia-lyases from parsley, kidney bean, and two yeast strains were also found to have approximately 20% amino acid identity to rat histidase. On the basis of the similarity of function of histidase and phenylalanine ammonia-lyase, dehydroalanine at the active sites, and the sequence conservation over a large evolutionary distance (mammals, bacteria, yeast, and plants), we propose that the genes for histidase and phenylalanine ammonia-lyase have diverged from a common ancestral gene, of which the most conserved regions are likely to be involved in catalysis or dehydroalanine formation.
Conversion Reaction Mechanisms in Lithium Ion Batteries: Study of the Binary Metal Fluoride Electrodes (2011)

Materials that undergo a conversion reaction with lithium (e.g., metal fluorides MF(2): M = Fe, Cu, ...) often accommodate more than one Li atom per transition-metal cation, and are promising candidates for high-capacity cathodes for lithium ion batteries. However, little is known about the mechanisms involved in the conversion process, the origins of the large polarization during electrochemical cycling, and why some materials are reversible (e.g., FeF(2)) while others are not (e.g., CuF(2)). In this study, we investigated the conversion reaction of binary metal fluorides, FeF(2) and CuF(2), using a series of local and bulk probes to better understand the mechanisms underlying their contrasting electrochemical behavior. X-ray pair-distribution-function and magnetization measurements were used to determine changes in short-range ordering, particle size and microstructure, while high-resolution transmission electron microscopy (TEM) and electron energy-loss spectroscopy (EELS) were used to measure the atomic-level structure of individual particles and map the phase distribution in the initial and fully lithiated electrodes. Both FeF(2) and CuF(2) react with lithium via a direct conversion process with no intercalation step, but there are differences in the conversion process and final phase distribution. During the reaction of Li(+) with FeF(2), small metallic iron nanoparticles (<5 nm in diameter) nucleate in close proximity to the converted LiF phase, as a result of the low diffusivity of iron. The iron nanoparticles are interconnected and form a bicontinuous network, which provides a pathway for local electron transport through the insulating LiF phase. In addition, the massive interface formed between nanoscale solid phases provides a pathway for ionic transport during the conversion process. These results offer the first experimental evidence explaining the origins of the high lithium reversibility in FeF(2). In contrast to FeF(2), no continuous Cu network was observed in the lithiated CuF(2); rather, the converted Cu segregates to large particles (5-12 nm in diameter) during the first discharge, which may be partially responsible for the lack of reversibility in the CuF(2) electrode.
Cloning Human DNA Repair Genes (1994)

Many human genes involved in the repair of UV damage have been cloned using different procedures and they have been of great value in assisting the understanding of the mechanism of nucleotide excision—repair. Genes involved in repair of ionizing radiation damage have proved more difficult to isolate. Positional cloning has localized the XRCC5 gene to a small region of chromosome 2q33–35, and a series of yeast artificial chromosomes covering this region have been isolated. Very recent work has shown that the XRCC5 gene encodes the 80 kDa subunit of the Ku DNA-binding protein. The Ku80 gene also maps to this region. Studies with fission yeast have shown that radiation sensitivity can result not only from defective DNA repair but also from abnormal cell cycle control following DNA damage. Several genes involved in this ‘checkpoint’ control in fission yeast have been isolated and characterized in detail. It is likely that a similar checkpoint control mechanism exists in human cells.
Synthesis and evaluation of 1,2,2-tris(sulfonyl)hydrazines as antineoplastic and trypanocidal agents (1990)

Several 1,2,2-tris(sulfonyl)hydrazines, conceived as prodrugs of 1,2-bis(sulfonyl)hydrazines, were synthesized and evaluated for antineoplastic and trypanocidal activities in mice. 1-Methyl-1,2,2-tris(methylsulfonyl)hydrazine emerged as an extremely efficacious antitrypanosomal agent, whereas 1-(2-chloroethyl)-1,2,2-tris(methylsulfonyl)hydrazine was inactive. In contrast, 1-(2-chloroethyl)-1,2,2-tris(methylsulfonyl)hydrazine displayed potent antineoplastic activity, producing several 60-day "cures" of mice bearing leukemia L1210, leukemia P388, or Sarcoma 180. Furthermore, the fact that the tris(sulfonyl) derivatives will not generate isocyanates, which contribute to the host toxicity of nitrosoureas like 1,3-bis(2-chloroethyl)-1-nitrosourea (BCNU), makes them agents of significant promise in trypanosomal and cancer chemotherapy.
Drastic Enhancement of Catalytic Activity via Post‐oxidation of a Porous MnII Triazolate Framework (2014)

Mn(III) is a powerful active site for catalytic oxidation of alkyl aromatics, but it can be only stabilized by macrocyclic chelating ligands such porphyrinates. Herein, by using benzobistriazolate as a rigid bridging ligand, a porous Mn(II) azolate framework with a nitrogen-rich coordinated environment similar to that of metalloporphyrins was synthesized, in which the Mn(II) ions can be post-oxidized to Mn(III) to achieve drastic increase of catalytic (aerobic) oxidation performance.
Role of Coagulation Inhibitors in Inflammation (2001)

It is becoming increasingly clear that coagulation augments inflammation and that anticoagulants, particularly natural anticoagulants, can limit the coagulation induced increases in the inflammatory response. The latter control mechanisms appear to involve not only the inhibition of the coagulation proteases, but interactions with the cells that either generate anti-inflammatory substances, such as prostacyclin, or limit cell activation. Recent studies have demonstrated a variety of mechanisms by which coagulation, particularly the generation of thrombin, factor Xa and the tissue factor-factor VIIa complex, can augment acute inflammatory responses. Many of these responses are due to the activation of one or more of the protease activated receptors. Activation of these receptors on endothelium can lead to the expression of adhesion molecules and platelet activating factor, thereby facilitating leukocyte activation. Therefore, anticoagulants that inhibit any of these factors would be expected to dampen the inflammatory response. The three major natural anticoagulant mechanisms seem to exert a further inhibition of these processes by impacting cellular responses. Antithrombin has been shown in vitro to increase prostacyclin responses and activated protein C has been shown to inhibit a variety of cellular responses including endotoxin induced calcium fluxes in monocytes and the nuclear translocation of NFKB, a key step in the generation of the inflammatory response. In some, but not all, in vivo models, these natural anticoagulants have been able to inhibit endotoxin/E. coli-mediated leukocyte activation and to diminish cytokine elaboration (TNF, IL-6 and IL-8). Phase III clinical studies for treatment of patients with severe sepsis have been completed for APC, which was successful (1), and for antithrombin, which was not (2). A phase III trial with tissue factor pathway inhibitor is in progress. In this review, the mechanisms by which the different natural anticoagulants are thought to function will be reviewed.
Induction and Isolation of a Minicell-Producing Strain of Salmonella typhimurium (1974)

A mutant of S. typhimurium which produces small spherical anucleate bodies (minicells) was induced and isolated after treatment of a normal strain of S. typhimurium with increasing amounts of triethylenemelamine (TEM).
Enterotoxigenic Escherichia coli infection in pigs and its diagnosis (2002)

7 5 1 O c a 8 1 F b T S , a T S ± e 2 x t S + o N s e Y Table 1: Characteristics of enterotoxigenic Escherichia coli (ETEC) strains associated with infections in pigs of various ages1 Enterotoxigenic Escherichia coli (ETEC) is a major cause of illness and death in neonatal and recently weaned pigs. However, pigs older than approximately 8 weeks appear to be resistant to infection. Strains of ETEC that cause diarrhea in pigs possess two types of virulence factors, adhesins and enterotoxins, both of which are essential for disease to occur.
Experimental NIDDM: Development of a New Model in Adult Rats Administered Streptozotocin and Nicotinamide (1998)

We took advantage of the partial protection exerted by suitable dosages of nicotinamide against the beta-cytotoxic effect of streptozotocin (STZ) to create a new experimental diabetic syndrome in adult rats that appears closer to NIDDM than other available animal models with regard to insulin responsiveness to glucose and sulfonylureas. Among the various dosages of nicotinamide tested in 3-month-old Wistar rats (100-350 mg/kg body wt), the dosage of 230 mg/kg, given intraperitoneally 15 min before STZ administration (65 mg/kg i.v.) yielded a maximum of animals with moderate and stable nonfasting hyperglycemia (155 +/- 3 vs. 121 +/- 3 mg/dl in controls; P < 0.05) and 40% preservation of pancreatic insulin stores. We also evaluated beta-cell function both in vitro and in vivo 4-9 weeks after inducing diabetes. In the isolated perfused pancreas, insulin response to glucose elevation (5-11 mmol/l) was clearly present, although significantly reduced with respect to controls (P < 0.01). Moreover, the insulin response to tolbutamide (0.19 mmol/l) was similar to that observed in normal pancreases. Perfused pancreases from diabetic animals also exhibited a striking hypersensitivity to arginine infusion (7 mmol/l). In rats administered STZ plus nicotinamide, intravenous glucose tolerance tests revealed clear abnormalities in glucose tolerance and insulin responsiveness, which were interestingly reversed by tolbutamide administration (40 mg/kg i.v.). In conclusion, this novel NIDDM syndrome with reduced pancreatic insulin stores, which is similar to human NIDDM in that it has a significant response to glucose (although abnormal in kinetics) and preserved sensitivity to tolbutamide, may provide a particularly advantageous tool for pharmacological investigations of new insulinotropic agents.
Straining puborectalis reflex: Description and significance of a “new” reflex (1991)

The present communication studies the technique and clinical significance of a new reflex, termed straining puborectalis reflex. Nineteen healthy volunteers with an average age of 38.2 years were studied, including ten males and nine females. The intravesical pressure, representative of intra-abdominal pressure, was measured by means of a balloon-tipped catheter introduced into the urinary bladder and connected to a pressure transducer. The electromyographic (EMG) activity of the puborectalis muscle was recorded using a concentric needle electrode inserted into the muscle. The EMG response of the puborectalis muscle to straining at different pressures was recorded. The response to two types of straining--sudden momentary and slow, sustained--was observed. The procedure was repeated in ten subjects after puborectalis infiltration with xylocaine or saline. Sudden straining evoked puborectalis contraction, whereas slow, sustained straining did not. Puborectalis contraction increased with the increase in straining intensity. These results were reproducible. The anesthetized puborectalis did not respond to straining, whereas the saline-infiltrated muscle did. The latency of the reflex was studied. Besides its role as a voluntary continent sphincter, the puborectalis seems to have a role also in the involuntary continence of the pelvic organs through the straining-puborectalis reflex. The muscle contracts on sudden straining, sealing the rectal and vesical necks and thereby preventing fecal or urinary leak. However, it is only on sudden straining that the puborectalis contracts. Slow, sustained straining as occurs during defecation and micturition does not evoke the reflex action. The straining puborectalis reflex is informative and may be incorporated as an investigative tool in patients with fecal and urinary control disorders.
Non-Randomness of Google's Quantum Supremacy Benchmark (2021)

The first achievement of quantum supremacy has been claimed recently by Google for the random quantum circuit benchmark with 53 superconducting qubits. Here, we analyze the randomness of Google's quantum random-bit sampling. The heat maps of Google's random bit-strings show stripe patterns at specific qubits in contrast to the Haar-measure or classical random-bit strings. Google's data contains more bit 0 than bit 1, i.e., about 2.8\% difference, and fail to pass the NIST random number tests, while the Haar-measure or classical random-bit samples pass. Their difference is also illustrated by the Marchenko-Pastur distribution and the Girko circular law of random matrices of random bit-strings. The calculation of the Wasserstein distances shows that Google's random bit-strings are farther away from the Haar-measure random bit-strings than the classical random bit-strings. Our results imply that random matrices and the Wasserstein distance could be new tools for analyzing the performance of quantum computers.
An Immunohistochemical Study of Na+/I−Symporter in Human Thyroid Tissues and Salivary Gland Tissues (1998)

The human Na+/I- symporter (hNIS) is the plasma membrane protein that mediates active iodide uptake into several tissues, such as the thyroid and salivary glands. To study the distribution and cellular localization of the hNIS protein, we have generated a polyclonal antibody that could detect the hNIS protein by immunohistochemical staining on tissue sections. In normal thyroids, hNIS expression is heterogeneous, and it is only detected in sporadic thyrocytes of a given follicle. The hNIS protein was not detected in thyroid carcinomas, yet it was detected in the majority of thyrocytes in Graves' thyroids. In salivary glands, hNIS protein was not detected in acinar cells, but it was detected in ductal cells. The hNIS proteins are clustered in the basal and lateral membranes in cells stained positive for hNIS.
Crystal and co-crystal (2003)

The first page of this article is displayed as the abstract.
Solid-State Light Sources Getting Smart (2005)

More than a century after the introduction of incandescent lighting and half a century after the introduction of fluorescent lighting, solid-state light sources are revolutionizing an increasing number of applications. Whereas the efficiency of conventional incandescent and fluorescent lights is limited by fundamental factors that cannot be overcome, the efficiency of solid-state sources is limited only by human creativity and imagination. The high efficiency of solid-state sources already provides energy savings and environmental benefits in a number of applications. However, solid-state sources also offer controllability of their spectral power distribution, spatial distribution, color temperature, temporal modulation, and polarization properties. Such "smart" light sources can adjust to specific environments and requirements, a property that could result in tremendous benefits in lighting, automobiles, transportation, communication, imaging, agriculture, and medicine.
Conformations of the Nucleotide and Polypeptide Binding Domains of a Cytosolic Hsp70 Molecular Chaperone Are Coupled (1996)

70-kDa heat shock protein (Hsp70) molecular chaperones are ATPases that participate in protein folding by regulating protein-protein interactions. ATP binds to the highly conserved amino-terminal domain, whereas polypeptides bind to the less conserved carboxyl-terminal domain. These domains are functionally coupled. Polypeptides were previously shown to dissociate from Hsp70s upon ATP binding and to stimulate ATPase activity. We probed the structure of the yeast cytosolic Hsp70 Ssa1p using limited proteolysis to determine whether the conformations of its nucleotide and polypeptide binding domains are also coupled. Ssa1p adopted three distinct conformations, nucleotide-free, ADP-dependent, and ATP-dependent. Complete conformational changes required K+ and Mg2+. Using amino-terminal sequencing, ATP-agarose chromatography, and a carboxyl-terminal-specific antibody, we mapped the locations of the major proteolytic fragments. Nucleotides altered the conformations of both the nucleotide and polypeptide binding domains. Similarly, a polypeptide altered the conformations of both domains. These results indicate that the conformations of the nucleotide and polypeptide binding domains are coupled.
Recommender systems (1997)

article Free Access Share on Recommender systems Authors: Paul Resnick AT&T, Labs-Research, Murray Hill, N.J. AT&T, Labs-Research, Murray Hill, N.J.View Profile , Hal R. Varian Dean of the School of Information Management and Systems, University of California, Berkeley Dean of the School of Information Management and Systems, University of California, BerkeleyView Profile Authors Info & Claims Communications of the ACMVolume 40Issue 3March 1997pp 56–58https://doi.org/10.1145/245108.245121Published:01 March 1997Publication History 2,605citation33,485DownloadsMetricsTotal Citations2,605Total Downloads33,485Last 12 Months5,625Last 6 weeks661 Get Citation AlertsNew Citation Alert added!This alert has been successfully added and will be sent to:You will be notified whenever a record that you have chosen has been cited.To manage your alert preferences, click on the button below.Manage my AlertsNew Citation Alert!Please log in to your account Save to BinderSave to BinderCreate a New BinderNameCancelCreateExport CitationPublisher SiteeReaderPDF
Kerckhoffs-Based Embedding Security Classes for WOA Data Hiding (2008)

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