gebhart/patrepeval huggingface dataset:
Nucleotide sequences of the mRNA's encoding the vesicular stomatitis virus G and M proteins determined from cDNA clones containing the complete coding regions (1981)

The complete nucleotide sequences of the vesicular stomatitis virus mRNA's encoding the glycoprotein (G) and the matrix protein (M) have been determined from cDNA clones that contain the complete coding sequences from each mRNA. The G protein mRNA is 1,665 nucleotides long, excluding polyadenylic acid, and encodes a protein of 511 amino acids including a signal peptide of 16 amino acids. G protein contains two large hydrophobic domains, one in the signal peptide and the other in the transmembrane segment near the COOH terminus. Two sites of glycosylation are predicted at amino acid residues 178 and 335. The close correspondence of the positions of these sites with the reported timing of the addition of the two oligosaccharides during synthesis of G suggests that glycosylation occurs as soon as the appropriate asparagine residues traverse the membrane of the rough endoplasmic reticulum. The mRNA encoding the vesicular stomatitis virus M protein is 831 nucleotides long, excluding polyadenylic acid, and encodes a protein of 229 amino acids. The predicted M protein sequence does not contain any long hydrophobic or nonpolar domains that might promote membrane association. The protein is rich in basic amino acids and contains a highly basic amino terminal domain. Details of construction of the nearly full-length cDNA clones are presented.
The Conserved G/F Motif of the DnaJ Chaperone Is Necessary for the Activation of the Substrate Binding Properties of the DnaK Chaperone (1995)

The universally conserved DnaK and DnaJ molecular chaperone proteins bind in a coordinate manner to protein substrates to prevent aggregation, to disaggregate proteins, or to regulate proper protein function. To further examine their synergistic mechanism of action, we constructed and characterized two DnaJ deletion proteins. One has an 11-amino-acid internal deletion that spans amino acid residues 77-87 (DnaJ delta 77-87) and the other amino acids 77-107 (DnaJ delta 77-107). The DnaJ delta 77-87 mutant protein, was normal in all respects analyzed. The DnaJ delta 77-107 mutant protein has its entire G/F (Gly/Phe) motif deleted. This motif is found in most, but not all DnaJ family members. In vivo, DnaJ delta 77-107 supported bacteriophage lambda growth, albeit at reduced levels, demonstrating that at least some protein function was retained. However, DnaJ delta 77-107 did not exhibit other wild type properties, such as proper down-regulation of the heat-shock response, and had an overall poisoning effect of cell growth. The purified DnaJ delta 77-107 protein was shown to physically interact and stimulate DnaK's ATPase activity at wild type levels, unlike the previously characterized DnaJ259 point mutant (DnaJH33Q). Moreover, both DnaJ delta 77-107 and DnaJ259 bound to substrate proteins, such as sigma 32, at similar affinities as DnaJ+. However, DnaJ delta 77-107 was found to be largely defective in activating the ATP-dependent substrate binding mode of DnaK. In vivo, the ability of the mutant DnaJ proteins to down-regulate the heat-shock response was correlated only with their in vitro ability to activate DnaK to bind sigma 32, in an ATP-dependent manner, and not with their ability to bind sigma 32. We conclude, that although the G/F motif of DnaJ does not directly participate in the stimulation of DnaK's ATPase activity, nevertheless, it is involved in an important manner in modulating DnaK's substrate binding activity.
Microtubule: A Common Target for Parkin and Parkinson’s Disease Toxins (2006)

Parkinson's disease (PD) is characterized by the selective loss of nigral dopaminergic (DA) neurons, which have long axons enriched with microtubules. Depolymerization of microtubules by PD toxins such as rotenone disrupts vesicular transport. The ensuing accumulation of vesicles in the cell body leads to increased cytosolic concentration of dopamine due to leakage of the vesicles. Elevated oxidative stress induced by dopamine oxidation may thus trigger the selective demise of DA neurons. Many strategies have been developed to protect DA neurons by stabilizing microtubules either directly or through intracellular signaling cascades. On the other hand, parkin, one of the most frequently mutated genes in PD, encodes for a protein-ubiquitin E3 ligase that strongly binds to microtubules. Parkin stabilizes microtubules through three domains that provide strong and independent interactions with tubulin and microtubules. These interactions anchor parkin on microtubules and may facilitate its E3 ligase activity on misfolded proteins transported along microtubules. Thus, parkin and rotenone, two prominent genetic and environmental factors linked to PD, act in an opposing manner on the same molecular target in the cell, microtubules, whose destruction underlies the selective vulnerability of dopaminergic neurons.
Oxalate Degradation by Microbes of the Large Bowel of Herbivores: The Effect of Dietary Oxalate (1981)

Rates of oxalate degradation by microbes in gastrointestinal contents from rabbits, guinea pigs, swine and a horse increased after additional of oxalate to diets. A similar response was previously observed with ruminal microbes from cattle and sheep. Bacterial that utilize oxalate for growth appear to be selected by increased levels of dietary oxalate.
Mechanisms of the biofungicide Serenade (Bacillus subtilisQST713) in suppressing clubroot (2011)

Abstract Clubroot is a serious threat to canola production in western Canada. The biofungicide Serenade® (Bacillus subtilis QST713) reduced the disease substantially in controlled environment, but showed variable efficacy in field trials. To better understand how this biofungicide works, two of the product components, i.e., B. subtilis and its metabolites (product filtrate), were assessed under controlled conditions for their relative contribution to clubroot control. The information may be used to optimize the product formulation. The bacterium or product filtrate alone was only partially effective against clubroot, reducing disease severity by about 60% relative to untreated controls. In contrast, Serenade controlled the disease by over 90%. This pattern of response was mirrored in quantitative PCR assessment on P. brassicae DNA within canola roots; the lowest and highest amounts of pathogen DNA were found in roots of Serenade treatment (0.02 and 0.01 ng/g) and controls (0.52 and 13.35 ng/g), respectively, at 2 and 3 weeks after treatment. During this period, the amount of DNA changed little in Serenade-treated roots but increased by almost 30-fold in the control. The product filtrate or B. subtilis also reduced the pathogen DNA substantially (0.03–1.16 ng/g). Serenade decreased the germination and viability of P. brassicae resting spores only marginally. It is suggested that biofungicide Serenade controls clubroot largely via suppressing root-hair and cortical infection by P. brassicae zoospores. The bacterial metabolites in the product formulation possibly assist B. subtilis in rhizosphere colonization and clubroot control by minimizing the competition from other soil microbes.
EPI-001 is a selective peroxisome proliferator-activated receptor-gamma modulator with inhibitory effects on androgen receptor expression and activity in prostate cancer (2015)

The androgen receptor (AR) is a driver of prostate cancer (PCa) cell growth and disease progression. Therapies for advanced PCa exploit AR dependence by blocking the production or action of androgens, but these interventions inevitably fail via multiple mechanisms including mutation or deletion of the AR ligand binding domain (LBD). Thus, the development of new inhibitors which act through non-LBD interfaces is an unmet clinical need. EPI-001 is a bisphenol A-derived compound shown to bind covalently and inhibit the AR NH2-terminal domain (NTD). Here, we demonstrate that EPI-001 has general thiol alkylating activity, resulting in multilevel inhibitory effects on AR in PCa cell lines and tissues. At least one secondary mechanism of action associated with AR inhibition was found to be selective modulation of peroxisome proliferator activated receptor-gamma (PPARγ). These multi-level effects of EPI-001 resulted in inhibition of transcriptional activation units (TAUs) 1 and 5 of the AR NTD, and reduced AR expression. EPI-001 inhibited growth of AR-positive and AR-negative PCa cell lines, with the highest sensitivity observed in LNCaP cells. Overall, this study provides new mechanistic insights to the chemical biology of EPI-001, and raises key issues regarding the use of covalent inhibitors of the intrinsically unstructured AR NTD.
Scavenger receptor Bl and cholesterol trafficking (1999)

Scavenger receptor BI (SR-BI) mediates the selective uptake of HDL cholesteryl ester into steroidogenic cells and the liver and is a major determinant of the plasma HDL concentration in the mouse. Recent studies indicate that SR-BI also alters the metabolism of apolipoprotein B-containing particles and influences the development of atherosclerosis in several animal models. These results and the similar pattern of SR-BI expression in humans emphasize that it is important to learn how this receptor influences lipoprotein metabolism and atherosclerosis in people.
Genome-wide Detection of Allelic Imbalance Using Human SNPs and High-density DNA Arrays (2000)

Most human cancers are characterized by genomic instability, the accumulation of multiple genetic alterations and allelic imbalance throughout the genome. Loss of heterozygosity (LOH) is a common form of allelic imbalance and the detection of LOH has been used to identify genomic regions that harbor tumor suppressor genes and to characterize tumor stages and progression. Here we describe the use of high-density oligonucleotide arrays for genome-wide scans for LOH and allelic imbalance in human tumors. The arrays contain redundant sets of probes for 600 genetic loci that are distributed across all human chromosomes. The arrays were used to detect allelic imbalance in two types of human tumors, and a subset of the results was confirmed using conventional gel-based methods. We also tested the ability to study heterogeneous cell populations and found that allelic imbalance can be detected in the presence of a substantial background of normal cells. The detection of LOH and other chromosomal changes using large numbers of single nucleotide polymorphism (SNP) markers should enable identification of patterns of allelic imbalance with potential prognostic and diagnostic utility.
High efficiency solar cells for concentrator systems: silicon or multi-junction? (2005)

Amonix has become the first company to begin production of high concentration silicon solar cells where volumes are over 10 MW/year. Higher volumes are available due to the method of manufacture; Amonix solely uses semiconductor foundries for solar cell production. In the previous years of system and cell field testing, this method of manufacturing enabled Amonix to maintain a very low overhead while incurring a high cost for the solar cell. However, recent simplifications to the solar cell processing sequence resulted in cost reduction and increased yield. This new process has been tested by producing small qualities in very short time periods, enabling a simulation of high volume production. Results have included over 90% wafer yield, up to 100% die yield and world record performance (&#951; =27.3%). This reduction in silicon solar cell cost has increased the required efficiency for multi-junction concentrator solar cells to be competitive / advantageous. Concentrator systems are emerging as a low-cost, high volume option for solar-generated electricity due to the very high utilization of the solar cell, leading to a much lower $/Watt cost of a photovoltaic system. Parallel to this is the onset of alternative solar cell technologies, such as the very high efficiency multi-junction solar cells developed at NREL over the last two decades. The relatively high cost of these type of solar cells has relegated their use to non-terrestrial applications. However, recent advancements in both multi-junction concentrator cell efficiency and their stability under high flux densities has made their large-scale terrestrial deployment significantly more viable. This paper presents Amonix's experience and testing results of both high-efficiency silicon rear-junction solar cells and multi-junction solar cells made for concentrated light operation.
Solution Structure of an RNA·DNA Hybrid Duplex Containing a 3‘-Thioformacetal Linker and an RNA A-Tract (1997)

Neutral and achiral backbone linkers are promising replacements for the phosphodiester linkages of antisense oligonucleotides that target mRNA sequences. Results are presented here for the solution structure elucidation by NMR of an RNA x DNA hybrid duplex, r(GCGCAAAACGCG) x d(CGCGTT-SCH2O-TTGCGC) (designated RIII), containing a 3'-thioformacetal (3'-TFMA) backbone substitution in the DNA strand. The 3'-thioformacetal linker can be accommodated in the hybrid duplex in a conformation that is drastically different from its form in a DNA x DNA duplex but close to that of the canonical A-form helix, reflecting the sequence requirement for hybridization. While the global features of RIII are similar to what are described in the literature, the 3'-TFMA modification drives sugar puckers of the adjacent residues to more C3'-endo-like conformations and causes distortions in related twist angles and helical rises. The helical conformation analyses of each of the two strands and the hybrid duplex enable a clear account of the conformational variability of both the DNA and RNA strands. The A-tract in the RNA strand features an overall straight helix and a more prominent bend at the 3'-end CG step. The structure of RIII provides a structural basis for the improved thermal stability of RIII compared to the corresponding DNA x DNA duplex and insights into the factors that are important concerns for the design of new, effective antisense oligonucleotides.
Protective Efficacy of Recombinant Modified Vaccinia Virus Ankara Delivering Middle East Respiratory Syndrome Coronavirus Spike Glycoprotein (2015)

Middle East respiratory syndrome coronavirus (MERS-CoV) causes severe respiratory disease in humans. We tested a recombinant modified vaccinia virus Ankara (MVA) vaccine expressing full-length MERS-CoV spike (S) glycoprotein by immunizing BALB/c mice with either intramuscular or subcutaneous regimens. In all cases, MVA-MERS-S induced MERS-CoV-specific CD8(+) T cells and virus-neutralizing antibodies. Vaccinated mice were protected against MERS-CoV challenge infection after transduction with the human dipeptidyl peptidase 4 receptor. This MERS-CoV infection model demonstrates the safety and efficacy of the candidate vaccine.
The Synthesis of Aminoalcohols from Epoxides and Ammonia (1973)

Abstract In connection with another problem we had need for some simple aminoalcohols which were not commercially available. While textbooks make the reaction of ammonia and amines with epoxides appear inviting for the preparation of aminoalcohols, an examination of the literature yielded surprisingly few clearly written examples of the reactions of ammonia with epoxides and many of the good examples had undesirable features. For instance, one of the aminoalcohols desired was threo-3-amino-2-butanol. Lucas et al2. reported an improved synthesis of this compound in 76% yield by reacting the meso-epoxide with an excess of concentrated aqueous ammonia. The drawbacks to their synthesis were the long recommended reaction time (10 days) and the large volume of water to be removed by distillation (about 2 liters per mole of product obtained). While the yield is reasonably good, all other examples of the reaction that we have found report lower yields (18–70%). Malinovski3 has reviewed the general reaction and treats the side reaction products obtained. Our procedure does not totally avoid side reactions, but the time involved and the good yields make this method more attractive than former procedures for the derivatives that we have prepared.
Synthesis of Carbohydrates through Biotechnology (2004)

Polysaccharides are the least appreciated class of macromolecules though they constitute the largest part of the planet's bio-mass. This large bulk has perpetuated a compelling reason for their neglect: carbohydrates were thought to be biochemically uninteresting serving as structural and energy storage molecules. The second more insidious and perhaps contradictory reason for the relative slowness in carbohydrate research is that biochemically important carbohydrates are difficult to study. They seem haphazardly put together, without a template, creating enormous complexity that, at first, did not suggest specific functions. The past three decades have seen enormous strides in the understanding of the importance of carbohydrates feeding the quickly expanding and vibrant field of enzymatic carbohydrate synthesis. The clear goal of the research in this field is to supplant Nature as the supreme oligosaccharide maker to generate desired saccharides, be it natural or unnatural, in high yields, large quantities and at low cost.
Structural Basis of Agonist-induced Desensitization and Sequestration of the P2Y2 Nucleotide Receptor (1998)

Molecular determinants of P2Y2 receptor desensitization and sequestration have been investigated. Wild-type P2Y2 receptors and a series of five C-terminal truncation mutants of the receptor were epitope-tagged and stably expressed in 1321N1 cells. These constructs were used to assess the importance of the intracellular C terminus on 1) UTP-stimulated increases in intracellular calcium concentration, 2) homologous desensitization of the receptor, and 3) agonist-induced decreases in cell-surface density (receptor sequestration) of epitope-tagged receptors using fluorescence-activated cell sorting. The potency and efficacy of UTP were similar for the wild-type and all mutant P2Y2 receptors. Truncation of 18 or more amino acids from the C terminus increased by approximately 30-fold the concentration of UTP necessary to desensitize the receptor. Both the rate and magnitude of UTP-induced receptor sequestration were decreased with progressively larger truncations of the C terminus. Furthermore, the recovery from sequestration was slower for the most extensively truncated receptor. Complete desensitization was obtained with >50% of the original receptor complement remaining on the cell surface. Protein kinase C activation, which desensitizes the P2Y2 receptor, had no effect on sequestration, consistent with the ideas that desensitization and sequestration are discrete events and that agonist occupancy is required for receptor sequestration.
Copolymerization of Ethylene with Polar Monomers by Anionic Substitution. Theoretical Study Based on Acrylonitrile and the Brookhart Diimine Catalyst (2005)

Calculations have been carried out on the complexation energy of acrylonitrile and ethylene using derivatives of the cationic N∧N Ni(II)−diimine Brookhart complex. For acrylonitrile (CH2CHCN) considerations were given to both π binding through the olefinic CC functionality and σ binding through the NC group. The diimine ring system N∧N = −NR‘ ‘CR1CR2NR‘ ‘ with R‘ ‘ = 2,6-C6H3(i-Pr)2 and R1, R2 = CH3 was functionalized by substituting a carbon in the diimine ring by B- and R1 or R2 (or both) by anionic groups (BF3-, OBF3-, etc.). Substitutions were also carried out at the aryl rings by replacing H or i-Pr with anionic groups. The objective has been to find substitutions that would reduce or eliminate the preference for σ complexation of acrylonitrile, a prerequisite for ethylene/acrylonitrile copolymerization.
How Do Phenolic Compounds React toward Superoxide Ion? A Simple Electrochemical Method for Evaluating Antioxidant Capacity (2010)

The reactivities of different phenols and polyphenols versus superoxide ion (O₂(•-)) were investigated as an easy-to-handle electrochemical method for evaluating antioxidant capacities. In view of this application, the O₂/O₂(•-) couple and associated reactions between O₂(•-) and polyphenols (or phenols) were examined in an aprotic solvent [dimethylformamide (DMF)] by cyclic voltammetry. Comparisons based on simple criteria (reversibility of the O₂ reduction in the presence of the phenolic compound, electron stoichiometry, or apparent kinetic constants) allow discriminations between the possible mechanistic pathways (acid-base or radical reaction type). The results highlight that the proton-transfer and radical-transfer pathways are both present for monophenols and polyphenols, with the relative contributions of the two pathways depending on the phenol structure. In agreement with the literature, polyphenols containing an o-diphenol ring (as in flavonoids) were found to present the highest reactivities.
Artificial Leaf Turns Sunlight Into a Cheap Energy Source (2011)

For the first time, researchers have created a potentially cheap, practical artificial leaf that uses sunlight to knit chemical bonds.
Comparison of subjective and objective analgesic effects of intravenous and intrathecal morphine in chronic pain patients by heat beam dolorimetry (1989)

The pain tolerance latencies of 10 chronic pain patients were evaluated by heat beam dolorimetry (stimulus intensity 15.33 mW.cm-2.sec-1) prior to and following administration of morphine by intrathecal (n = 5) or intravenous (n = 5) routes. Patients not undergoing opiate withdrawal evinced increased baseline pain tolerance latencies prior to drug administration compared with normal volunteers. Two patients undergoing the opiate withdrawal syndrome at the time of test experienced reduced pain tolerance latencies compared with normal volunteers, most probably corresponding to the hyperesthesia symptom of the syndrome. Intravenous morphine infusion (30 mg) induced a time-dependent increase in cutaneous pain tolerance with peak effect occurring 1-2 h after administration. This persisted for up to 4 h and thereafter declined. The time course of subjective pain self-report by visual pain analog scale (VPAS) measurements corresponded to the time course of increasing cutaneous pain tolerance latency assessed by dolorimetry. Pain self-reports following intrathecal morphine infusion (2.25 or 1 mg) followed a similar though slower onset to that reported by patients receiving intravenous morphine and was of lesser degree. In contrast, heat beam dolorimetric evidence of increased cutaneous pain tolerance (which was of lesser degree than following i.v. morphine) did not reach its maximum during the 4 h measuring period. A dissociation was noted therefore between the self-reported relief of endogenous pain and dolorimetrically measured cutaneous analgesia following intrathecal morphine administration. Linear regression correlation analysis characterized this phenomenon as a positive correlation between cutaneous pain tolerance and pain relief self-report following intravenous morphine infusion and a negative correlation following intrathecal administration. We propose that the phenomenon may be due to intrathecal morphine acting via two separate compartments: one spinal and one supraspinal.(ABSTRACT TRUNCATED AT 250 WORDS)
Improved Survival in Patients with Locally Advanced Prostate Cancer Treated with Radiotherapy and Goserelin (1997)

Adjuvant treatment with goserelin, when started simultaneously with external irradiation, improves local control and survival in patients with locally advanced prostate cancer.