gebhart/patrepeval huggingface dataset:
Epithelial-to-mesenchymal transition in breast cancer: a role for insulin-like growth factor I and insulin-like growth factor&ndash;binding protein 3? (2015)

Evidence indicates that for most human cancers the problem is not that gene mutations occur but is more dependent upon how the body deals with damaged cells. It has been estimated that only about 1% of human cancers can be accounted for by unmistakable hereditary cancer syndromes, only up to 5% can be accounted for due to high-penetrance, single-gene mutations, and in total only 5%-15% of all cancers may have a major genetic component. The predominant contribution to the causation of most sporadic cancers is considered to be environmental factors contributing between 58% and 82% toward different cancers. A nutritionally poor lifestyle is associated with increased risk of many cancers, including those of the breast. As nutrition, energy balance, macronutrient composition of the diet, and physical activity levels are major determinants of insulin-like growth factor (IGF-I) bioactivity, it has been proposed that, at least in part, these increases in cancer risk and progression may be mediated by alterations in the IGF axis, related to nutritional lifestyle. Localized breast cancer is a manageable disease, and death from breast cancer predominantly occurs due to the development of metastatic disease as treatment becomes more complicated with poorer outcomes. In recent years, epithelial-to-mesenchymal transition has emerged as an important contributor to breast cancer progression and malignant transformation resulting in tumor cells with increased potential for migration and invasion. Furthermore, accumulating evidence suggests a strong link between components of the IGF pathway, epithelial-to-mesenchymal transition, and breast cancer mortality. Here, we highlight some recent studies highlighting the relationship between IGFs, IGF-binding protein 3, and epithelial-to-mesenchymal transition.
Ultrafast compound imaging for 2-D motion vector estimation: application to transient elastography (2002)

This paper describes a new technique for two-dimensional (2-D) imaging of the motion vector at a very high frame rate with ultrasound. Its potential is experimentally demonstrated for transient elastography. But, beyond this application, it also could be promising for color flow and reflectivity imaging. To date, only axial displacements induced in human tissues by low-frequency vibrators were measured during transient elastography. The proposed technique allows us to follow both axial and lateral displacements during the shear wave propagation and thus should improve Young's modulus image reconstruction. The process is a combination of several ideas well-known in ultrasonic imaging: ultra-fast imaging, multisynthetic aperture beamforming, 1-D speckle tracking, and compound imaging. Classical beamforming in the transmit mode is replaced here by a single plane wave insonification increasing the frame rate by at least a factor of 128. The beamforming is achieved only in the receive mode on two independent subapertures. Comparison of successive frames by a classical 1-D speckle tracking algorithm allows estimation of displacements along two different directions linked to the subapertures beams. The variance of the estimates is finally improved by tilting the emitting plane wave at each insonification, thus allowing reception of successive decorrelated speckle patterns.
An Aggregate-Inducing Peripherin Isoform Generated through Intron Retention Is Upregulated in Amyotrophic Lateral Sclerosis and Associated with Disease Pathology (2008)

The neuronal intermediate filament protein peripherin is a component of ubiquitinated inclusions and of axonal spheroids in amyotrophic lateral sclerosis (ALS). Overexpression of peripherin causes motor neuron degeneration in transgenic mice and variations within the peripherin gene have been identified in ALS cases. We have shown previously the abnormal expression of a neurotoxic peripherin splice variant in transgenic mice expressing mutant superoxide dismutase-1. These findings indicated that abnormalities of peripherin splicing may occur in ALS. In the current study, peripherin splice variants were identified by reverse transcription-PCR of human neuronal RNA and comparisons in expression made between control and ALS spinal cord using Western blot analysis and immunocytochemistry. Using this approach we have identified a novel peripherin transcript retaining introns 3 and 4 that results in a 28 kDa splice isoform, designated Per 28. Using an antibody specific to Per 28, we show that this isoform is expressed at low stoichiometric levels from the peripherin gene, however causes peripherin aggregation when its expression is upregulated. Importantly we show an upregulation of Per 28 expression in ALS compared with controls, at both the mRNA and protein levels, and that Per 28 is associated with disease pathology, specifically round inclusions. These findings are the first to establish that peripherin splicing abnormalities occur in ALS, generating aggregation-prone splice isoforms.
Association of the melatonin circadian rhythms with clock 3111T/C gene polymorphism in Caucasian and Asian menopausal women with insomnia (2018)

A comparative analysis of melatonin circadian rhythms in Caucasian (incoming population) and Asian (indigenous population) menopausal women with/without sleep disorders depending on the genotype of Clock 3111T/C gene polymorphism was realized.The melatonin level in the saliva was determined four times a day (6:00-7:00, 12:00-13:00, 18:00-19:00, 23:00-00:00 h). The Caucasian women-carriers of the TT-genotype with insomnia as compared to control group-had a higher morning melatonin level and a lower night melatonin level. The Asian women with TT-genotype and insomnia had a lower levels of melatonin as compared to control at daytime, evening and night. A significantly higher melatonin level in the early morning hours was detected in the Caucasian women-carriers of the TT-genotype with insomnia as compared to group womencarriers of the minor 3111C-allele. There were no statistically significant differences in the circadian rhythms of melatonin in the Asian women depending on the genotype of the Clock 3111T/C polymorphism. An assumption with respect to the protective role of the minor allele 3111C in the development of insomnia associated with the displacement of melatonin circadian rhythms in the representatives of the incoming population was made.
Disruption of Pheromone Communication through the Use of Puffers for Control of Beet Armyworm (Lepidoptera: Noctuidae) in Tomatoes (1996)

Journal Article Disruption of Pheromone Communication through the Use of Puffers for Control of Beet Armyworm (Lepidoptera: Noctuidae) in Tomatoes Get access Harry H. Shorey, Harry H. Shorey 1 Department of Entomology, University of California, Riverside, CA 92521 1Affiliated with University of California, Kearney Agricultural Center, 9240 South Riverbend Avenue, Parlier, CA 93648. Search for other works by this author on: Oxford Academic PubMed Google Scholar Roland G. Gerber Roland G. Gerber 1 Department of Entomology, University of California, Riverside, CA 92521 1Affiliated with University of California, Kearney Agricultural Center, 9240 South Riverbend Avenue, Parlier, CA 93648. Search for other works by this author on: Oxford Academic PubMed Google Scholar Environmental Entomology, Volume 25, Issue 6, 1 December 1996, Pages 1401–1405, https://doi.org/10.1093/ee/25.6.1401 Published: 01 December 1996 Article history Received: 25 March 1996 Accepted: 19 August 1996 Published: 01 December 1996
[Effects of potent analgesic 3-(beta-phenylethyl)-9 beta-methoxy-9 alpha-(m-hydroxyphenyl)-3-azabicyclo [3,3,1]-nonane (p-5721) on electroencephalography in rabbits]. (1988)

P-7521 is a potent analgesic derived from 3-azabicyclo [3,3,1]-nonanes. The investigation was carried out on the unanesthetized. non-curarized rabbits. After iv 0.8, 4.0 0r 450 Vg/kg. a predominatly synchronized EEG which was characterized by the appearance of high voltage 1-3 Hz waves was seen both in the cortical and deep leads. The integration value of 6 activity increased from about 29% to higher than 50% while that of e activity decreased. In the sensorimotor cortex the spindle waves were poorly organized and slowed down. The EEG activated reaction produced by phonic stimulus was abolished. In all EEG records of P-7521 the spikes or the electrographic seizure were not seen. All of these EEG changes were associated with behavioral tranquillization. stupor and immobility. After icv P-7521 4.0 or 45.0 vg/kg the EEG changes were similar to those after iv. The EEG and behavioral effects of P-7521 could be antagonized by naloxone. The EEG changes were accompanied by the respiratory depression and the heart rate descent.
Characterization of intracellular inclusions formed by Pseudomonas oleovorans during growth on octane (1983)

The growth of Pseudomonas oleovorans on n-octane was characterized by the formation of intracellular structures. These inclusions were isolated and characterized. Morphologically, they resembled the poly-beta-hydroxybutyrate granules found in Bacillus cereus, as shown by freeze-fracture electron microscopy. The elemental analysis of isolated granules showed, however, that they do not contain poly-beta-hydroxybutyric acid. Instead, the analysis was consistent with a C8 polyester, which interpretation was supported by the fatty acid analysis of hydrolyzed granules. From the evidence presented here, we conclude that P. oleovorans forms poly-beta-hydroxyoctanoate granules when grown on n-octane.
Adoptive immunotherapy for indolent non-Hodgkin lymphoma and mantle cell lymphoma using genetically modified autologous CD20-specific T cells (2008)

Adoptive immunotherapy with T cells expressing a tumor-specific chimeric T-cell receptor is a promising approach to cancer therapy that has not previously been explored for the treatment of lymphoma in human subjects. We report the results of a proof-of-concept clinical trial in which patients with relapsed or refractory indolent B-cell lymphoma or mantle cell lymphoma were treated with autologous T cells genetically modified by electroporation with a vector plasmid encoding a CD20-specific chimeric T-cell receptor and neomycin resistance gene. Transfected cells were immunophenotypically similar to CD8(+) effector cells and showed CD20-specific cytotoxicity in vitro. Seven patients received a total of 20 T-cell infusions, with minimal toxicities. Modified T cells persisted in vivo 1 to 3 weeks in the first 3 patients, who received T cells produced by limiting dilution methods, but persisted 5 to 9 weeks in the next 4 patients who received T cells produced in bulk cultures followed by 14 days of low-dose subcutaneous interleukin-2 (IL-2) injections. Of the 7 treated patients, 2 maintained a previous complete response, 1 achieved a partial response, and 4 had stable disease. These results show the safety, feasibility, and potential antitumor activity of adoptive T-cell therapy using this approach. This trial was registered at www.clinicaltrials.gov as #NCT00012207.
Multilocus Sequence Typing (MLST) for Characterization of Enterobacter cloacae (2013)

Enterobacter cloacae is an important emerging pathogen, which sometime causes respiratory infection, surgical site infection, urinary infection, sepsis, and outbreaks at neonatal units. We have developed a multilocus sequence typing (MLST) scheme utilizing seven housekeeping genes and evaluated the performance in 101 clinical isolates. The MLST scheme yielded 83 sequence types (ST) including 78 novel STs found in the clinical isolates. These findings supported the robustness of the MLST scheme developed in this study.
Developments In Pressure-Sensitive Products (2005)

Since the first groundbreaking edition of Developments in Pressure-Sensitive Products was introduced in 1998, heavy research has resulted in substantial progress in the field. Fully updated and expanded to reflect this activity, Developments in Pressure-Sensitive Products, Second Edition provides a detailed overview of the entire range of pressure-
P-Element-Induced Male Recombination and Gene Conversion in Drosophila (1996)

A P-element insertion flanked by 13 restriction fragment length polymorphism (RFLP) marker sites was used to examine male recombination and gene conversion at an autosomal site. The great majority of crossovers on chromosome arm 2R occurred within the 4-kb region containing the P element and RFLP sites. Of the 128 recombinants analyzed, approximately two-thirds carried duplications or deletions flanking the P element. These rearrangements are described in more detail in the accompanying report. In a parallel experiment, we examined 91 gene conversion tracts resulting from excision of the same autosomal P element. We found the average tract length was 1463 bp, which is essentially the same as found previously at the white locus. The distribution of conversion tract endpoints was indistinguishable from the distribution of crossover points among the nonrearranged male recombinants. Most recombination events can be explained by the "hybrid element insertion" model, but, for those lacking a duplication or deletion, a second step involving double-strand gap repair must be postulated to explain the distribution of crossover points.
Cloning, sequencing, and expression of the Escherichia coli peptide methionine sulfoxide reductase gene. (1992)

The gene encoding peptide methionine sulfoxide reductase was cloned from an Escherichia coli genomic library using an oligonucleotide probe based on the amino-terminal sequence of the protein. The nucleotide sequence revealed that the gene codes for a polypeptide of 212 amino acid residues with a calculated molecular weight of 23,314. The protein has been overexpressed in E. coli and is present as a soluble active species.
Protein Tyrosine Phosphatases: Structure and Function, Substrate Specificity, and Inhibitor Development (2002)

Protein tyrosine phosphatases (PTPs) are signaling enzymes that control a diverse array of cellular processes. Malfunction of PTP activity is associated with a number of human disorders. Recent genetic and biochemical studies indicate that PTPs represent a novel platform for drug discovery. Detailed knowledge of PTP substrate specificity and the wealth of structural data on PTPs provide a solid foundation for rational PTP inhibitor design. This review summarizes a correlation of PTP structure and function from mutagenesis experiments. The molecular basis for PTP1B and MKP3 substrate recognition is discussed. A powerful strategy is presented for creating specific and high-affinity bidentate PTP inhibitors that simultaneously bind both the active site and a unique adjacent site. Finally, recent advances in the development of potent and selective inhibitors for PTP1B and Cdc25 are described.
Protection against atherosclerosis by estrogen is independent of plasma cholesterol levels in LDL receptor-deficient mice (1999)

Low density lipoprotein (LDL) receptor-deficient (LDLR-/-) mice consuming a high fat diet were used to assess the effect of endogenous and exogenous estradiol (E2) on atherosclerosis. Sexually mature female mice were ovariectomized (OVX) and implanted with subcutaneous, slow-release pellets designed to release 6 microg/day of exogenous 17beta-estradiol (17beta-E2 ), 17alpha-estradiol (17alpha-E2 ), or placebo (E2- deficient). Sham-operated control female (endogenous E2 ) and male mice were studied as controls. Aortic atherosclerotic lesion area was reduced by physiologic amounts of both endogenous and exogenous E2 compared to E2-deficient female mice. Although plasma cholesterol levels were reduced by exogenous E2 despite the absence of the LDL receptor, endogenous E2 was not associated with any cholesterol changes. In contrast, only 17alpha-E2 was associated with decreased fasting triglyceride. In subgroup analyses matched for time-averaged plasma total cholesterol, aortic lesion area was reduced by the presence of estradiol (E2 ). E2 protected LDLR-/- female mice from atherosclerosis and this protection was independent of changes in plasma cholesterol levels.
Sepsis: rethinking the approach to clinical research (2008)

The clinical syndrome of sepsis encompasses a highly heterogeneous group of clinical disorders, varying with respect to the site, bacteriology, and even presence of infection and with the clinical syndrome evolving in the host. Clinical trials of strategies to modulate the host response that mediates sepsis were first initiated 25 years ago. A continuing record of disappointment has characterized subsequent work, and only a single new therapy has been licensed for clinical use. Yet, these commercial disappointments obscure a vibrant body of new knowledge that has clarified the biology of the innate immune response whose deranged expression is responsible for sepsis and that has provided important new insights into the failings of the traditional model of clinical research in sepsis. This review highlights advances in basic biology and underlines insights from clinical research that may point to new and more effective ways of translating an understanding of innate immunity into effective treatments for a leading cause of global morbidity and mortality.
A Mutation in the Cone-Specific pde6 Gene Causes Rapid Cone Photoreceptor Degeneration in Zebrafish (2007)

Photoreceptor degeneration is a common cause of inherited blindness worldwide. We have identified a blind zebrafish mutant with rapid degeneration of cone photoreceptors caused by a mutation in the cone phosphodiesterase c (pde6c) gene, a key regulatory component in cone phototransduction. Some rods also degenerate, primarily in areas with a low density of rods. Rod photoreceptors in areas of the retina that always have a high density of rods are protected from degeneration. Our findings demonstrate that, analogous to what happens to rod photoreceptors in the rd1 mouse model, loss of cone phosphodiesterase leads to rapid degeneration of cone photoreceptors. Furthermore, we propose that cell density plays a key role in determining whether rod photoreceptors degenerate as a secondary consequence to cone degeneration. Our zebrafish mutant serves as a model for developing therapeutic treatments for photoreceptor degeneration in humans.
Detection of Legionella pneumophila by Real-Time PCR for the mip Gene (2003)

A real-time PCR assay for the mip gene of Legionella pneumophila was tested with 27 isolates of L. pneumophila, 20 isolates of 14 other Legionella species, and 103 non-Legionella bacteria. Eight culture-positive and 40 culture-negative clinical specimens were tested. This assay was 100% sensitive and 100% specific for L. pneumophila.
Inflammation and Cancer: An Epidemiological Perspective (2004)

Many chronic inflammatory conditions increase the risk of cancer in affected tissues. Clinical conditions that involve both inflammation and increased cancer risk include a broad range of immunological disorders, infections (bacterial, helminthic, viral), and chronic chemical and mechanical irritation. For example, the inflammatory bowel diseases, ulcerative colitis and Crohn's disease, predispose to the development of cancers of the large bowel and/or terminal ileum; chronic infection with the bacterium Helicobacter pylori causes atrophic gastritis, dysplasia, adenocarcinoma and an unusual form of gastric lymphoma; and parasitic infection with schistosomes and other trematodes cause cancers of the urinary bladder and the intrahepatic and extrahepatic biliary tract. Chronic reflux of gastric acid and bile into the distal oesophagus causes chemical injury, Barrett's oesophagus and oesophageal adenocarcinoma. Chronic cholecystitis and gallstones predispose to cancer of the gallbladder. Besides these clinical syndromes, subclinical inflammation may promote the development of certain tumours. The expression of COX-2 and lipid mediators of inflammation increases during the multistage progression of these tumours. Non-steroidal anti-inflammatory drugs (NSAIDs), which inhibit COX-2 activity and tumour development in many experimental and clinical settings, are inversely associated with certain cancers in epidemiological studies. Despite their promise, however, anti-inflammatory drugs are not yet recommended for the prevention or treatment of any cancers. Numerous questions must be resolved concerning their molecular and cellular targets of action, efficacy, safety, treatment regimen, indications, and the balance of risks and benefits from treatment in designated patient populations.
Estimation of conduction velocity vector fields from epicardial mapping data (1998)

An automated method to estimate vector fields of propagation velocity from observed epicardial extracellular potentials is introduced. The method relies on fitting polynomial surfaces T(x, y) to the space-time (x, y, t) coordinates of activity. Both speed and direction of propagation are computed from the gradient of the local polynomial surface. The components of velocity, which are total derivatives, are expressed in terms of the partial derivatives which comprise the gradient of T. The method was validated on two-dimensional (2-D) simulations of propagation and then applied to cardiac mapping data. Conduction velocity was estimated at multiple epicardial locations during sinus rhythm, pacing, and ventricular fibrillation (VF) in pigs. Data were obtained via a 528-channel mapping system from 23 x 22 and 24 x 21 arrays of unipolar electrodes sutured to the right ventricular epicardium. Velocity estimates are displayed as vector fields and are used to characterize propagation qualitatively and quantitatively during both simple and complex rhythms.
Location of a 1A g state in bithiophene (1992)

The 0–0 excitation energy of a 1Ag state of 2,2′-bithiophene has been determined by measuring the two-photon fluorescence excitation spectrum of a dilute solution of this molecule in crystalline n-hexane at 77 K. Because the 0–0 energy is what would have been predicted by extrapolating previously measured α,ω-dithienylpolyene 2 1Ag 0–0 energies to zero polyene chain length, it is assigned to the 2 1Ag state. The 0–0 band is centered at 36 173 cm−1, approximately 6570 cm−1 above the 0–0 of the 1 1Ag to 1 1Bu transition. This order of bithiophene excited singlet states is opposite to that of the linear polyene with the same number of double bond but may reverse for chains longer than six repeat units.
Induction of cellulolytic enzymes in Trichoderma reesei by sophorose (1979)

Sophorose (2-O-beta-glucopyranosyl-D-glucose) induces carboxymethyl cellulase in Trichoderma reesei QM6a mycelium with 1.5 to 2 h. The induction response to sophorose concentration, although complicated by the metabolism of sophorose, shows saturation kinetics. Most of the cellulase appears after most of the sophorose has been taken up, but the presence of an inducer is required to maintain cellulase synthesis because enzyme production ceases after separation of the mycelium from the induction medium. Cellulase appears simultaneously in the medium and in the mycelium, and no appreciable levels accumulate in the mycelium. Response to pH suggest either that synthesis and secretion of the enzyme are closely associated or concurrent events affected by surface interactions with the medium. Effects of temperature and pH on cellulase induction by sophorose are similar to those reported for induction by cellulose. The kinetics of absorption by mycelium differs from that of other beta-linked saccharides and glucose, the uptake of sophorose being much slower. Under our cultural conditions, sophorose appears to induce an incomplete array of cellulase enzymes, as indicated by enzymatic and electrophoretic studies.