gebhart/patrepeval huggingface dataset:
APOE-ε2 allele associated with higher prevalence of sporadic Parkinson disease (2004)

Unlike Alzheimer disease, for which the APOE-epsilon4 allele increases the prevalence and the APOE-epsilon2 allele is protective, the authors' analysis shows the APOE-epsilon2 allele, but not the APOE-epsilon4 allele, to be positively associated with sporadic Parkinson disease.
De Novo Expression of Transfected Human Class 1 Aldehyde Dehydrogenase (ALDH) Causes Resistance to Oxazaphosphorine Anti-cancer Alkylating Agents in Hamster V79 Cell Lines (1996)

Human class 1 aldehyde dehydrogenase (hALDH-1) can oxidize aldophosphamide, a key aldehyde intermediate in the activation pathway of cyclophosphamide and other oxazaphosphorine (OAP) anti-cancer alkylating agents. Overexpression of class 1 ALDH (ALDH-1) has been observed in cells selected for survival in the presence of OAPs. We used transfection to induce de novo expression of human ALDH-1 in V79/SD1 Chinese hamster cells to clearly quantitate the role of hALDH-1 expression in OAP resistance. Messenger RNA levels correlated well with hALDH-1 protein levels and enzyme activities (1.5-13.6 milliunits/mg with propionaldehyde/NAD+ substrate, compared to < 1 milliunit/mg in controls) in individual clonal transfectant lines, and slot blot analysis confirmed the presence of the transfected cDNA. Expressed ALDH activity was closely correlated (r = 0.99) with resistance to mafosfamide, up to 21-fold relative to controls. Transfectants were cross-resistant to other OAPs but not to phosphoramide mustard, ifosfamide mustard, melphalan, or acrolein. Resistance was completely reversed by pretreatment with 25 microM diethylaminobenzaldehyde, a potent ALDH inhibitor. Alkaline elution studies showed that expression of ALDH-1 reduced the number of DNA cross-links commensurate with mafosfamide resistance, and this reduction in cross-links was fully reversed by the inhibitor. Thus, overexpression of human class 1 ALDH alone is sufficient to confer OAP-specific drug resistance.
Effect of age on functional P-glycoprotein in the blood-brain barrier measured by use of (R)-[11C]verapamil and positron emission tomography (2006)

This study showed decreased P-gp activity during aging. Consequently, the brain may be exposed to higher drug and toxin levels in elderly subjects.
Best-case results for nearest-neighbor learning (1995)

Proposes a theoretical model for analysis of classification methods, in which the teacher knows the classification algorithm and chooses examples in the best way possible. The authors apply this model using the nearest-neighbor learning algorithm, and develop upper and lower bounds on sample complexity for several different concept classes. For some concept classes, the sample complexity turns out to be exponential even using this best-case model, which implies that the concept class is inherently difficult for the NN algorithm. The authors identify several geometric properties that make learning certain concepts relatively easy. Finally the authors discuss the relation of their work to helpful teacher models, its application to decision tree learning algorithms, and some of its implications for experimental work.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Drought-adaptive traits derived from wheat wild relatives and landraces (2006)

Exotic parents are being used to increase allelic diversity in bread wheat breeding through (i) interspecific hybridization of the ancestral genomes to produce so-called synthetic derived (SYN-DER) wheat, and (ii) crossing with landrace accessions, originating in abiotically stressed environments, that have become isolated from mainstream gene pools. Evaluation of the inherent genetic diversity encompassed by drought-adapted landraces compared with checks using DNA fingerprinting confirmed that some landraces were not only distant from checks but also showed significant diversity among each other. Improvement in performance of SYN-DER lines compared with recurrent parents was not associated with a larger overall investment in root dry weight, but rather an increased partitioning of root mass to deeper soil profiles (between 60 cm and 120 cm) and increased ability to extract moisture from those depths. The best Mexican landraces showed superior ability in terms of water extraction from soil depth, as well as increased concentration of soluble carbohydrates in the stem shortly after anthesis. Although it can be argued that inferring theoretical yield gains from the over-expression of any of these traits is questionable, since compensatory mechanisms may be at work, the fact remains that mechanistic or genetic linkages among physiological traits remain largely un-established. In the meantime, trait information is being used to make strategic crosses based on the theoretical combination of useful stress-adaptive traits with the possibility of realizing additive gene action in selected progeny. Candidates for crossing with elite check cultivars include landraces identified that showed relatively high biomass under drought combined with favourable expression of physiological traits such as stem carbohydrates, water extraction characteristics, and transpiration efficiency.
Genetic analysis of adeno-associated virus: properties of deletion mutants constructed in vitro and evidence for an adeno-associated virus replication function (1984)

Transfection of a pBR322-based, recombinant plasmid, pAV2, containing the entire adeno-associated virus (AAV) type 2 genome into human 293 cells in the presence of helper adenovirus resulted in rescue and replication of AAV to yield infectious particles. We constructed mutants of pAV2 containing deletions within the AAV sequence. We describe here the phenotypes of these AAV deletion mutants. The results can be summarized as follows. Mutants (cap-) with deletions between map positions 53 and 85 did not synthesize capsid antigen or progeny single-stranded DNA but accumulated normal levels of duplex replicating form DNA. Mutants (rep-) with deletions between map positions 17 and 36 failed to rescue or replicate any AAV DNA. The rep- mutants could be complemented for replicating form DNA synthesis by a cap- mutant. This clearly demonstrates an AAV-coded replication function which is different from the capsid antigen. Other mutants (inf-) with deletions in the region between map positions 40 and 52 synthesized abundant amounts of replicating form DNA and capsid antigen but gave a low yield of infectious particles. This suggests that there may be an additional region of AAV, perhaps within the intron, which is required for efficient particle assembly. This work shows that AAV is genetically complex and expresses at least three clearly different functions.
The autoimmune nature of chronic urticaria (2008)

The association between chronic urticaria (CU) and autoimmune disease has been recognized for some time, especially with autoimmune thyroid disease. More recently, functional IgG autoantibodies against FcepsilonRIalpha and less commonly against IgE have been reported in a subset of patients with CU. These patients have been described as having more severe and difficult-to-control urticaria. The autologous serum skin test has been proposed as a surrogate test to define presence of these autoantibodies, although it identifies presence of histamine releasing factor, not necessarily antibody. Basophil histamine release and basophil activation assays using flow cytometry to measure CD63 and, more recently, CD203c expression have been used to identify patients with autoimmune urticaria. New research suggests that in some patients with CU, the activation of the extrinsic coagulation pathway with thrombin generation might play an important role in their CU.
Biomimetic Mineralization of Collagen by Combined Fibril Assembly and Calcium Phosphate Formation (1999)

To find new ways for the synthesis of improved bone implant materials, we studied the mineralization of collagen in vitro. Collagen was mineralized by combining the collagen fibril assembly and the formation of calcium phosphate in one process step. Both reactions were initiated simultaneously by mixing an acid, calcium-containing collagen solution with a phosphate-containing neutralization buffer. Under suitable conditions first fibril assembly occurred along with the precipitation of an amorphous calcium phosphate phase. Subsequently, the amorphous calcium phosphate transformed into a crystalline, apatite-like phase, as revealed by IR spectroscopy and X-ray diffraction. In this way, a homogeneously mineralized collagen gel was obtained, consisting of a three-dimensional network of collagen fibrils covered with calcium phosphate. The attachment between the collagen fibrils and the calcium phosphate crystals could be further improved by the addition of polyaspartate to the reaction mixture. In the absence of polyaspartate the calcium phosphate crystals formed clusters loosely bound to the fibrils, while in its presence separate crystals were located on or inside the collagen fibrils. The applied method is useful for studying the mineralization of collagen and offers a promising approach for the development of new bone implant materials.
Mitochondrial uncoupling protein from mouse brown fat. Molecular cloning, genetic mapping, and mRNA expression. (1985)

We have identified cDNAs clones for several cold-inducible mRNAs from the brown adipose tissue of mice. pCIN-1, a plasmid with a 900-base pair insert, encoded the mitochondrial uncoupling protein (UCP) as determined by the ability of the cDNA insert to select, by hybridization, an mRNA that could be translated into a 32,000-Da protein immunoprecipitable with anti-UCP antibodies. Nine tissues were analyzed; however, UCP cDNA hybridized to an mRNA species of 1.6 and 2.0 kilobase pairs only in brown adipose tissue. A maximum induction of 10-fold occurred within 6 h of exposure to cold (5 degrees C). A BamHI restriction fragment polymorphism detected by Southern blot analysis of genomic DNA in recombinant inbred mouse strains allowed us to map the UCP gene to Chromosome 8. The analysis of the UCP gene expression in diabetic (db) and obese (ob) mice maintained at 27 degrees C for 3 days followed by cold exposure for 4 h at 5 degrees C indicated that UCP mRNA levels in mutant mice were unaffected at 27 degrees C and only slightly reduced at 5 degrees C. Accordingly, the inability of diabetic and obese mice to thermoregulate is not associated with a lack of UCP mRNA induction.
Nucleotide sequence of the feline retroviral oncogene v-fms shows unexpected homology with oncogenes encoding tyrosine-specific protein kinases. (1984)

The nucleotide sequence encoding the transforming polyprotein of the McDonough strain of feline sarcoma virus was determined. This sequence includes 231 nucleotides specifying a leader peptide, 1,377 nucleotides encoding most of the feline leukemia virus-derived gag gene, and 2,969 nucleotides representing the viral transforming gene v-fms. A single open reading frame was predicted to encode a fusion polyprotein of 160,000 daltons (P160gag-fms). Fourteen potential sites for glycosylation were predicted within the v-fms-encoded portion of the protein, consistent with previous observations that the primary translation product is rapidly glycosylated. The presence of hydrophobic signal peptides within the amino-terminal leader sequence and in the middle of the v-fms-encoded moiety suggests that the transforming glycoprotein becomes oriented with its amino terminus within the lumen of the rough endoplasmic reticulum and its carboxyl terminus protruding across the membrane of the rough endoplasmic reticulum into the cytoplasm. The latter portion of the protein shows unexpected homology to tyrosine-specific protein kinases encoded by several of the known retroviral oncogenes.
Antibody Responses of Man to Three Types of Antityphoid Immunizing Agents: Heat-Phenol Fluid Vaccine, Acetone-Dehydrated Vaccine, and Isolated Vi and 0 Antigens (1954)

Antibody Responses of Man to Three Types of Antityphoid Immunizing Agents: Heat-Phenol Fluid Vaccine, Acetone-Dehydrated Vaccine, and Isolated Vi and 0 Antigens Affiliation Maurice Landy, Sidney Gaines, John R. Seal, and James E. Whiteside CopyRight https://doi.org/10.2105/AJPH.44.12.1572 Published Online: August 29, 2011
DMSO cryopreservation is the method of choice to preserve cells for droplet-based single-cell RNA sequencing (2019)

Combining single-cell RNA sequencing (scRNA-seq) with upstream cell preservation procedures such as cryopreservation or methanol fixation has recently become more common. By separating cell handling and preparation, from downstream library generation, scRNA-seq workflows are more flexible and manageable. However, the inherent transcriptomic changes associated with cell preservation and how they may bias further downstream analysis remain unknown. Here, we present a side-by-side droplet-based scRNA-seq analysis, comparing the gold standard - fresh cells - to three different cell preservation workflows: dimethyl sulfoxide based cryopreservation, methanol fixation and CellCover reagent. Cryopreservation proved to be the most robust protocol, maximizing both cell integrity and low background ambient RNA. Importantly, gene expression profiles from fresh cells correlated most with those of cryopreserved cells. Such similarities were consistently observed across the tested cell lines (R ≥ 0.97), monocyte-derived macrophages (R = 0.97) and immune cells (R = 0.99). In contrast, both methanol fixation and CellCover preservation showed an increased ambient RNA background and an overall lower gene expression correlation to fresh cells. Thus, our results demonstrate the superiority of cryopreservation over other cell preservation methods. We expect our comparative study to provide single-cell omics researchers invaluable support when integrating cell preservation into their scRNA-seq studies.
Novel oestrogen sulfamates: a new approach to oral hormone therapy (1998)

Sulfamate substitution at the C-3 position of the steroid skeleton leads to orally active prodrugs of ethinyloestradiol, oestradiol, oestrone, oestriol and probably many other natural or synthetic steroidal oestrogens. These compounds have higher systemic, but reduced hepatic, oestrogenic activity than their parent steroids. The release of the parent oestrogen results from the passage of the sulfamates in the erythrocyte compartment through the liver and the systemic hydrolysis of the sulfamate ester. Sulfamates may be used to generate natural oestrogens, oestradiol and other oestrogens for different types of oral oestrogen therapy, e.g., as oestriol for hindered oestrogen or as 17-alpha oestradiol for 'non-feminising' oestrogen. Oestradiol sulfamate J995 is currently in the initial stages of clinical testing. It has per se no oestrogen receptor affinity or oestrogenic activity in vitro, i.e., is inactive without hydrolysis. Its oral uterotropic activity in rats is approximately 100-times higher than that of oestradiol, its hepatotropic activity, however, is only 2- to 3-fold higher than oestradiol. Oral oestradiol sulfamate treatment should, therefore, reduce the hepatic side-effects seen with conventional oral hormone therapy, while at the same time lead to full stimulation of the uterus and the vagina, and suppression of gonadotropin. In the rat, orally administered oestradiol is effectively extracted from the portal vein and excreted via the bile. In contrast, oestradiol sulfamate is present in the circulation at high concentrations, up to 30% of the dose. Initially, 98% of this is found in the erythrocyte compartment and only 2% in the plasma. Significant oestradiol levels in the blood are recorded during the depletion of this pool. Pharmacokinetic and toxicological studies reveal complete excretion of the compound and its metabolites. No toxic effects have been seen in rats and cynomolgus monkeys at any dose, in spite of the compound's distinct oestrogenicity. The evaluation of genotoxicity also yielded negative results.
Direct Determination of MCPD Fatty Acid Esters and Glycidyl Fatty Acid Esters in Vegetable Oils by LC–TOFMS (2010)

Analysis of MCPD esters and glycidyl esters in vegetable oils using the indirect method proposed by the DGF gave inconsistent results when salting out conditions were varied. Subsequent investigation showed that the method was destroying and reforming MCPD during the analysis. An LC time of flight MS method was developed for direct analysis of both MCPD esters and glycidyl esters in vegetable oils. The results of the LC-TOFMS method were compared with the DGF method. The DGF method consistently gave results that were greater than the LC-TOFMS method. The levels of MCPD esters and glycidyl esters found in a variety of vegetable oils are reported. MCPD monoesters were not found in any oil samples. MCPD diesters were found only in samples containing palm oil, and were not present in all palm oil samples. Glycidyl esters were found in a wide variety of oils. Some processing conditions that influence the concentration of MCPD esters and glycidyl esters are discussed.
Intracellular precursors and secretion of alkaline extracellular protease of Yarrowia lipolytica. (1988)

Processing and secretion of the alkaline extracellular protease (AEP) from the yeast Yarrowia lipolytica was studied by pulse-chase and immunoprecipitation experiments. Over half of newly synthesized AEP was secreted by 6 min. Over 99% of AEP activity which was external to the cytoplasmic membrane was located in the supernatant medium. Polypeptides of 55, 52, 44, 36, and 32 kilodaltons (55K, 52K, 44K, 36K, and 32K polypeptides) were immunoprecipitated from [3H]leucine-labeled cell extracts by rabbit antibodies raised against mature, secreted AEP (32K polypeptide). Experiments with tunicamycin and endoglycosidase H indicated that the 55K, 52K, and 44K polypeptides contained about 2 kilodaltons of N-linked oligosaccharide and that the 36K and 32K polypeptides contained none. Results of pulse-chase experiments did not fit a simple precursor-product relationship of 55K----52K----44K----36K----32K. In fact, maximum labeling intensity of the 52K polypeptide occurred later than for the 44K and 36K polypeptides. Secretion of polypeptides of 19 and 20 kilodaltons derived from the proregion of AEP indicated that one major processing pathway was 55K----52K----32K. The gene coding for AEP (XPR2) was cloned and sequenced. The sequence and the immunoprecipitation results suggest that AEP is originally synthesized with an additional preproI-proII-proIII amino-terminal region. Processing definitely involves cleavage(s) after pairs of basic amino acids and the addition of one N-linked oligosaccharide. Signal peptidase cleavage, dipeptidyl aminopeptidase cleavages, and at least one additional proteolytic cleavage may also be involved.
Anaerobic Respiration in EngineeredEscherichia coliwith an Internal Electron Acceptor to Produce Fuel Ethanol (2008)

Environmental concerns and unease with U.S. dependence on foreign oil have renewed interest in converting biomass into fuel ethanol. The volume of plant matter available makes lignocellulose conversion to ethanol desirable, although no one isolated organism has been shown to break bonds in lignocellulose and efficiently metabolize resulting sugars into one product. This work reviews directed engineering coupled with metabolic evolution resulting in microbial biocatalysts that produce up to 45 g L(-1) ethanol in 48 hours in a simple mineral salts medium and that convert various compounds of lignocellulosic materials to ethanol. Mutations contributing to ethanologenesis are discussed along with adding enzymatic capabilities to existing biocatalysts in order to decrease the commercial enzymes required to reduce plant matter into fermentable sugars.
Cetuximab in metastatic or recurrent head and neck cancer: the EXTREME trial (2009)

Expression of EGF receptor (EGFR) is frequently elevated in squamous cell carcinoma of the head and neck (SCCHN). Cetuximab is an anti-EGFR monoclonal antibody that has been shown to improve overall survival in patients with locally advanced SCCHN when combined with radiotherapy. Data from Phase II trials suggest an interesting activity of cetuximab in patients with recurrent or metastatic SCCHN who are refractory to cisplatin. The Erbitux in First-Line Treatment of Recurrent or Metastatic Head and Neck Cancer (EXTREME) Phase III trial compared platin-5-fluorouracil alone versus combined with cetuximab as first-line treatment in recurrent or metastatic SCCHN. In the cetuximab arm of this study, a significant improvement in the overall survival (the main objective), progression-free survival and response rate were observed. The quality of life analyses (QLQ-C30 and QLQ-H&N35) showed no significant differences in most of the studied scores between the two treatment arms. Nevertheless, patients in the cetuximab arm displayed significant improvements in pain, swallowing problems and scores for speech and social eating problems. The results of the EXTREME study (and other studies evaluating cetuximab for the treatment of SCCHN) suggest a lack of a predictive value for the expression of EGFR (determined by immunohistochemistry) by the tumor and other biomarkers need to be investigated. The role of other targeted drugs and of possible combinations of these new drugs with cetuximab should be investigated in properly designed preclinical studies and clinical trials.
Partial gene duplication as a cause of human disease (1992)

Tandem duplication of large regions of DNA, including duplication of whole genes, provides a substrate for genetic evolution. Tandem duplication of smaller regions involving parts of genes is now recognized as a contributor to the mutation spectrum that results in genetic disease. In this review, more than 30 unrelated partial gene duplications that have been implicated in the genesis of human genetic disease are presented and the pathogenic effects and frequency of such duplications are summarized. The mechanisms of duplication formation are analyzed with special emphasis on the molecular details of the nucleotide sequences at the duplication junctions. Evidence to date suggests that duplication may arise from either homologous (Alu-Alu) recombination or nonhomologous recombination, the latter possibly mediated by topoisomerases. For the dystrophin gene, in which most duplications have been identified, these recombination events are intrachromosomal, suggesting that unequal sister chromatid exchange is the major mechanism.
A Novel Role for Vascular Endothelial Growth Factor as an Autocrine Survival Factor for Embryonic Stem Cells during Hypoxia (2004)

Vascular endothelial growth factor (VEGF) is best known for its angiogenic activity on endothelial cells, but it also affects neurons, pneumocytes, and other mature cell types as well as endothelial, neural, and hematopoietic progenitors. Here, we examined its effect on pluripotential embryonic stem (ES) cells under hypoxic stress. ES cells were found to produce VEGF and to express VEGF receptor-2 and neuropilin-1 (Nrp-1), a VEGF165 isoform-specific receptor. During hypoxia, expression levels of VEGF, Flk-1, and Nrp-1 were elevated. Inhibition or targeted gene inactivation of VEGF increased ES cell apoptosis during prolonged hypoxia (48 h) by about 10-fold. The survival activity of VEGF was specific since inhibition of other growth factors (including basic fibroblast growth factor, epidermal growth factor, insulin-like growth factor, platelet-derived growth factor, and placental growth factor) had no effect. Neuropilin-1 was involved in the VEGF-survival activity since overexpression of Nrp-1 decreased hypoxia-induced apoptosis about 3-fold. The hypoxia-response element, via which hypoxia-inducible transcription factors up-regulate VEGF expression under hypoxic conditions, was critical since targeted deletion of this element in the VEGF promoter enhanced hypoxia-induced ES cell apoptosis to the same extent as VEGF inhibition or gene inactivation. Thus, VEGF plays a critical role in survival of ES cells during prolonged hypoxia.