gebhart/patrepeval huggingface dataset:
Cancer treatment and survivorship statistics, 2016 (2016)

The number of cancer survivors continues to increase because of both advances in early detection and treatment and the aging and growth of the population. For the public health community to better serve these survivors, the American Cancer Society and the National Cancer Institute collaborate to estimate the number of current and future cancer survivors using data from the Surveillance, Epidemiology, and End Results cancer registries. In addition, current treatment patterns for the most prevalent cancer types are presented based on information in the National Cancer Data Base and treatment-related side effects are briefly described. More than 15.5 million Americans with a history of cancer were alive on January 1, 2016, and this number is projected to reach more than 20 million by January 1, 2026. The 3 most prevalent cancers are prostate (3,306,760), colon and rectum (724,690), and melanoma (614,460) among males and breast (3,560,570), uterine corpus (757,190), and colon and rectum (727,350) among females. More than one-half (56%) of survivors were diagnosed within the past 10 years, and almost one-half (47%) are aged 70 years or older. People with a history of cancer have unique medical and psychosocial needs that require proactive assessment and management by primary care providers. Although there are a growing number of tools that can assist patients, caregivers, and clinicians in navigating the various phases of cancer survivorship, further evidence-based resources are needed to optimize care. CA Cancer J Clin 2016;66:271-289. © 2016 American Cancer Society.
Transgenic elite indica rice plants expressing CryIAc ∂-endotoxin of Bacillus thuringiensis are resistant against yellow stem borer ( Scirpophaga incertulas ) (1997)

Generation of insect-resistant, transgenic crop plants by expression of the insecticidal crystal protein (ICP) gene of Bacillus thuringiensis (Bt) is a standard crop improvement approach. In such cases, adequate expression of the most appropriate ICP against the target insect pest of the crop species is desirable. It is also considered advantageous to generate Bt-transgenics with multiple toxin systems to control rapid development of pest resistance to the ICP. Larvae of yellow stem borer (YSB), Scirpophaga incertulas, a major lepidopteran insect pest of rice, cause massive losses of rice yield. Studies on insect feeding and on the binding properties of ICP to brush border membrane receptors in the midgut of YSB larvae revealed that cryIAb and cryIAc are two individually suitable candidate genes for developing YSB-resistant rice. Programs were undertaken to develop Bt-transgenic rice with these ICP genes independently in a single cultivar. A cryIAc gene was reconstructed and placed under control of the maize ubiquitin 1 promoter, along with the first intron of the maize ubiquitin 1 gene, and the nos terminator. The gene construct was delivered to embryogenic calli of IR64, an elite indica rice cultivar, using the particle bombardment method. Six highly expressive independent transgenic ICP lines were identified. Molecular analyses and insect-feeding assays of two such lines revealed that the transferred synthetic cryIAc gene was expressed stably in the T2 generation of these lines and that the transgenic rice plants were highly toxic to YSB larvae and lessened the damage caused by their feeding.
Polyphasic taxonomy of Aspergillus section Fumigati and its teleomorph Neosartorya (2007)

The taxonomy of Aspergillus section Fumigati with its teleomorph genus Neosartorya is revised. The species concept is based on phenotypic (morphology and extrolite profiles) and molecular (beta-tubulin and calmodulin gene sequences) characters in a polyphasic approach. Four new taxa are proposed: N. australensis N. ferenczii, N. papuaensis and N. warcupii. All newly described and accepted species are illustrated. The section consists of 33 taxa: 10 strictly anamorphic Aspergillus species and 23 Neosartorya species. Four other Neosartorya species described previously were not available for this monograph, and consequently are relegated to the category of doubtful species.
Proteolysis of Specific Porcine Zona Pellucida Glycoproteins by Boar Acrosin1 (1985)

The morphologic and biochemical effects on the structure and constituent glycoproteins of the zona pellucida (ZP) by a specific sperm enzyme, acrosin, and a nonsperm enzyme, trypsin, have been evaluated. Intact porcine ZP matricies, exposed to either acrosin or trypsin, were analyzed microscopically. Changes in specific glycoproteins were monitored by high-resolution two-dimensional polyacrylamide gel electrophoresis (2D-PAGE) and the silver-based color stain, GELCODE. Although these enzymes did not alter the macroscopic properties of the ZP matrix, the 2D-PAGE ZP protein patterns were markedly altered. The high molecular weight glycoprotein families (II and III) were sensitive to proteolytic digestion, whereas the major glycoprotein family (I) of the porcine zona was only partially proteolyzed by acrosin and trypsin. Furthermore, it was demonstrated that acrosin had unique substrate specificity compared to that of trypsin, since the ZP peptide patterns were found to be different. These studies are the first to demonstrate which integral glycoproteins of the native porcine ZP matrix are specifically proteolyzed by acrosin from the homologous species and that this proteolysis occurs without the dissolution of the native porcine matrix.
Experimental study of atmospheric pressure surface discharge in helium (2001)

The surface discharge generated at atmospheric pressure in helium was examined by monitoring the current and voltage atthe discharge electrode. The discharge generated in helium behaves differently when compared to that generated in other gases (e.g. air). The single discharge duration and the time between consecutive discharges are longer because there is a different mechanism of discharge evolution. The metastable helium atoms play the most important role for discharge generation. Streamer-like and glow types of discharge were observed. The decay of helium metastables concentration determines the discharge regime. Hence, operation conditions have strong influence on the discharge regime. The introduction of gas flow removes metastable quenchers /gaseous products from dielectric and electrode surfaces) and transition to glow discharge is observed. Also covering the discharge electrode with thin dielectric foil to suppress Auger de-excitation of metastables at metal surface leads to generation of atmospheric pressure glow surface discharge. Properties of this discharge are comparable with properties of glow discharge at low pressure (e.g. the electron concentration).
Spoken and Written Textual Dimensions in English: Resolving the Contradictory Findings (1986)

Although similarities and differences between speech and writing have often been studied, contradictory claims concerning the linguistic relationship between the two modes are still common. These contradictions can arise from basing global conclusions on restricted methodologies—such as assigning undue weight to individual linguistic features, or to choice of particular text samples and text types. The present study uses a ‘multi-feature/multi-dimension’ approach, which includes a broad range of linguistic features and text types in a single quantitative analysis, to provide a global description of similarities and differences among spoken/written text types in English. The distribution of 41 linguistic features in 545 text samples of approximately 2000 words each is subjected to factor analysis (a multivariate statistical technique). Three underlying textual dimensions are identified: Interactive vs. Edited Text, Abstract vs. Situated Content, and Reported vs. Immediate Style. To demonstrate the value of the multi-feature/multi-dimension approach, the specific findings of earlier studies are reconciled within the model proposed here.
Assembly of the mitochondrial membrane system. CBP6, a yeast nuclear gene necessary for synthesis of cytochrome b. (1985)

A new gene function involved in the expression of mitochondrial cytochrome b is described. E158 is a respiratory deficient strain of Saccharomyces cerevisiae with a recessive mutation in nuclear DNA. The block in mitochondrial respiration is a consequence of the mutant's inability to synthesize cytochrome b. This has been confirmed by analysis of the mitochondrial translation products in E158. Since the mutant has wild-type concentrations of mature cytochrome b mRNA, the absence of the cytochrome b protein cannot be due to a transcriptional or RNA-processing defect. The wild-type gene (CBP6) responsible for the observed phenotype has been cloned by transformation of E158 with a genomic library of yeast nuclear DNA. The cloned gene has been sequenced and shown to code for a basic protein with a molecular weight of 18,657. Both deletion and disruption of the CBP6 coding sequence in chromosomal DNA of wild-type yeast lead to respiratory deficiency with a concomitant loss of cytochrome b. Part of the CBP6 gene has been fused to the trpE gene on a high expression Escherichia coli vector. The hybrid protein encoded by the trpE/CBP6 fusion has been purified from E. coli and used as an antigen for antibody production. Antibodies to the hybrid protein cross-react with an 18-kDa protein present in yeast mitochondria.
Treatment of Unicameral Calcaneal Bone Cysts in Children (2004)

Nine unicameral bone cysts of the calcaneus in children were managed surgically using the technique of continuous decompression with titanium cannulated cancellous screws. The average age of the patients at surgery was 12.8 years. At follow-up a minimum of 2 years after surgery, eight cysts showed complete healing; one patient showed healing with residuals. Irritation at the screw insertion site necessitated early removal of the screw in one patient; implant-related problems were not observed in the other patients. Patients were allowed to bear weight after surgery. Implant extraction was performed after full consolidation of the cyst and was uneventful in all patients. A review of the literature and the different treatment modalities used for managing calcaneal cysts is also presented.
Cell Confluence-induced Activation of Signal Transducer and Activator of Transcription-3 (Stat3) Triggers Epithelial Dome Formation via Augmentation of Sodium Hydrogen Exchanger-3 (NHE3) Expression (2007)

Cell confluence induces the activation of signal transducer and activator of transcription-3 (Stat3) in various cancer and epithelial cells, yet the biological implications and the associated regulatory mechanisms remain unclear. Because confluent polarized epithelia demonstrate dome formation and sodium influx that mimic the onset of differentiation, we sought to elucidate the role of Stat3 in association with the regulation of selective epithelial transporters in this biological phenomenon. This study established the correlation between Stat3 activation and cell confluence-induced dome formation in Madin-Darby canine kidney cells (MDCK) by following Stat3 activation events in dome-forming cells. Epifluorescent and confocal microscopy provided evidence showing specific localization of phosphorylated Stat3 Tyr(705) in the nuclei of dome-forming cells at initial stages. The relationship was further elucidated by the establishment of tetracycline-inducible expression of constitutive Stat3 mutant (Stat3-C) in MDCK cells or expression of dominant negative Stat3 (Stat3-D) stable cell lines (MDCK and NMuMG). Dome formation was promoted by the expression of Stat3-C but inhibited by Stat3-D. Two trans-epithelial transporters, NHE3 and ENaC alpha-subunit, were found to be increased during cell confluence. Interestingly, NHE3 expression could be specifically up-regulated by Stat3-C but inhibited by Stat3-D through promoter regulation, whereas NHE1 and ENaC alpha-subunit were not affected by Stat3 expression. Application of NHE3 shRNA, NHE3 inhibitors (EIPA and S3226) suppressed confluence-induced dome formation in MDCK or NMuMG cells. These results demonstrate a cell confluence-induced Stat3 signaling pathway in epithelial cells in triggering dome formation through NHE3 augmentation.
Inorganic Nanoparticles for Predictive Oncology of Breast Cancer (2008)

Nanoparticles (NPs) and nanosized objects are being incorporated rapidly into clinical medicine and particularly into the field of medical oncology, including breast cancer. A number of novel methods for breast cancer diagnosis and treatment, which are based on NPs and other nanodevices, are now available for translation into clinical practice. Computer tomography and MRI with iron-based magnetic NPs are promising methods for radiological detection of cancers. Semiconductor fluorescent NPs (quantum dots) are being developed for simultaneous detection and localization of multiple breast cancer biomarkers, enabling the personalization of therapeutic regimens for each patient. Additionally, inorganic NPs can be conjugated with tumor-specific ligands and used for tumor-selective delivery of chemotherapeutic or hormonal agents. NPs bearing tumor-targeted antibodies and oligonucleotides for anticancer gene therapy are a novel and rapidly developing therapeutic approach in oncology. Nab-paclitaxel and liposomal anthracyclines are US FDA-approved NP-based drug-delivery systems that have demonstrated at least equivalent efficacy and decreased toxicity compared with conventional chemotherapeutic agents used in the treatment of breast cancer. This review focuses on recent applications of NPs into predictive oncology of breast cancer with an emphasis placed on the role of inorganic nanosized objects in the diagnosis and treatment of this malignancy.
Whole body distribution of deuterated linoleic and α-linolenic acids and their metabolites in the rat (2007)

Little is known about the uptake or metabolism of essential fatty acids (EFAs) in various mammalian organs. Thus, the distribution of deuterated alpha-linolenic acid (18:3n-3) and linoleic acid (18:2n-6) and their metabolites was studied using a stable isotope tracer technique. Rats were orally administered a single dose of a mixture (20 mg each) of ethyl D5-18:3n-3 and D5-18:2n-6, and 25 tissues per animal were analyzed for D5-labeled PUFAs at 4, 8, 24, 96, 168, 240, 360, and 600 h after dosing. Plasma, stomach, and spleen contained the highest concentrations of labeled precursors at the earliest time points, whereas other internal organs and red blood cells reached their maximal concentrations at 8 h. The time-course data were consistent with liver metabolism of EFAs, but local metabolism in other tissues could not be ruled out. Brain, spinal cord, heart, testis, and eye accumulated docosahexaenoic acid with time, whereas skin accumulated mainly 20:4n-6. On average, approximately 16-18% of the D5-18:3n-3 and D5-18:2n-6 initial dosage was eventually accumulated in tissues, principally in adipose, skin, and muscle. Approximately 6.0% of D5-18:3n-3 and 2.6% of D5-18:2n-6 were elongated/desaturated and stored, mainly in muscle, adipose, and the carcass. The remaining 78% of both precursors was apparently catabolized or excreted.
Treatment of acute agitation in psychotic disorders. (2005)

Several psychotic disorders, including schizophrenia, may be associated with symptoms of acute agitation and aggression. While drug treatment of agitation is often essential, non-pharmacological interventions, both environmental and behavioral, also play important roles in the complex management of agitated patients. The most extensively used psychotropic drugs are parenteral formulas of conventional antipsychotics and benzodiazepines. Recently, injection forms of two second generation antipsychotics, olanzapine and ziprasidone, have become available. Both drugs have shown adequate efficacy and tolerability in several double-blind trials of intramuscular administration in acutely agitated psychotic patients. Compared to conventional medication, injection forms of the new antipsychotics may have a faster onset of action and more favorable profile of adverse events. Alternative approaches to injection administration include liquid drug formula, orally disintegrating tablets and wafers, treatment initiation with high doses, or rapid dose escalation. Evidence suggests that second-generation antipsychotics should be among the first-line choices in the treatment of agitation in acute psychosis.
Persistence with dimethyl fumarate in relapsing-remitting multiple sclerosis: a population-based cohort study (2017)

DMF had a rapid market uptake likely due to high expectations held by both patients and clinicians. However, persistence with DMF in routine clinical practice was found to be low.
Ray Tracing for the Movie `Cars' (2006)

This paper describes how we extended Pixar's RenderMan renderer with ray tracing abilities. In order to ray trace highly complex scenes we use multiresolution geometry and texture caches, and use ray differentials to determine the appropriate resolution. With this method we are able to efficiently ray trace scenes with much more geometry and texture data than there is main memory. Movie-quality rendering of scenes of such complexity had only previously been possible with pure scanline rendering algorithms. Adding ray tracing to the renderer enables many additional effects such as accurate reflections, detailed shadows, and ambient occlusion. The ray tracing functionality has been used in many recent movies, including Pixar's latest movie `Cars'. This paper also describes some of the practical ray tracing issues from the production of `Cars'
Transforming single DNA molecules into fluorescent magnetic particles for detection and enumeration of genetic variations (2003)

Many areas of biomedical research depend on the analysis of uncommon variations in individual genes or transcripts. Here we describe a method that can quantify such variation at a scale and ease heretofore unattainable. Each DNA molecule in a collection of such molecules is converted into a single magnetic particle to which thousands of copies of DNA identical in sequence to the original are bound. This population of beads then corresponds to a one-to-one representation of the starting DNA molecules. Variation within the original population of DNA molecules can then be simply assessed by counting fluorescently labeled particles via flow cytometry. This approach is called BEAMing on the basis of four of its principal components (beads, emulsion, amplification, and magnetics). Millions of individual DNA molecules can be assessed in this fashion with standard laboratory equipment. Moreover, specific variants can be isolated by flow sorting and used for further experimentation. BEAMing can be used for the identification and quantification of rare mutations as well as to study variations in gene sequences or transcripts in specific populations or tissues.
Comparison of thermosensitive alleles of the CDC25 gene involved in the cAMP metabolism of Saccharomyces cerevisiae. (1990)

The CDC25 gene from Saccharomyces cerevisiae is an essential component of the RAS-adenylate cyclase pathway. Genetic and biochemical evidence has led to the proposal that the gene product may act upstream of RAS, possibly as a guanine nucleotide exchange factor. We report here the cloning, sequencing and characterization of four mutations in the CDC25 gene. All four are missense mutations which reside within the carboxy-terminal quarter of the single open reading frame found within the gene. Three of the four are missense mutations in the same amino acid codon. A search of protein data bases reveals that the carboxy terminus of the putative CDC25 gene product is similar to that of LTE1, a gene required for growth at low temperature and SCD25, a suppressor of cdc25. Taken together these data indicate that the carboxy terminus of CDC25 plays a critical role in the function of the CDC25 gene product and that other proteins, such as LTE1 or SCD25, may have related activities.
Evidence that free polyunsaturated fatty acids modify Na+ channels by directly binding to the channel proteins. (1996)

The effects of free polyunsaturated fatty acids (PUFA) on the binding of ligands to receptors on voltage-sensitive Na+ channels of neonatal rat cardiac myocytes were assessed. The radioligand was [benzoyl-2,5-(3)H] batrachotoxinin A 20alpha-benzoate ([(3)H]BTXB), a toxin that binds to the Na+ channel. The PUFA that have been shown to be antiarrhythmic, including eicosapentaenoic acid (EPA; C20:5n-3), docosahexaenoic acid (DHA; C22:6n-3), eicosatetraynoic acid (ETYA), linolenic acid (C18:3n-3), and linoleic acid (C18:2n-6), inhibited [(3)H]BTXB binding in a dose-dependent fashion with IC50 values of 28-35 microM, whereas those fatty acids that have no antiarrhythmic effects including saturated fatty acid (stearic acid, C18:0), monounsaturated fatty acid (oleic acid; C18:1n-9), and EPA methyl ester did not have a significant effect on [(3)H]BTXB binding. Enrichment of the myocyte membrane with cholesterol neither affected [(3)H]BTXB binding when compared with control cells nor altered the inhibitory effects of PUFA on [(3)H]BTXB binding. Scatchard analysis of [(3)H]BTXB binding showed that EPA reduced the maximal binding without altering the Kd for [(3)H]BTXB binding, indicating allosteric inhibition. The inhibition by EPA of [(3)H]BTXB binding was reversible (within 30 min) when delipidated bovine serum albumin was added. The binding of the PUFA to this site on the Na+ channel is reversible and structure-specific and occurs at concentrations close to those required for apparent antiarrhythmic effects and a blocking effect on the Na+ current, suggesting that binding of the PUFA at this site relates to their antiarrhythmic action.
A Comprehensive, Ethnically Diverse Library of Sickle Cell Disease-Specific Induced Pluripotent Stem Cells (2017)

Sickle cell anemia affects millions of people worldwide and is an emerging global health burden. As part of a large NIH-funded NextGen Consortium, we generated a diverse, comprehensive, and fully characterized library of sickle-cell-disease-specific induced pluripotent stem cells (iPSCs) from patients of different ethnicities, β-globin gene (HBB) haplotypes, and fetal hemoglobin (HbF) levels. iPSCs stand to revolutionize the way we study human development, model disease, and perhaps eventually, treat patients. Here, we describe this unique resource for the study of sickle cell disease, including novel haplotype-specific polymorphisms that affect disease severity, as well as for the development of patient-specific therapeutics for this phenotypically diverse disorder. As a complement to this library, and as proof of principle for future cell- and gene-based therapies, we also designed and employed CRISPR/Cas gene editing tools to correct the sickle hemoglobin (HbS) mutation.