gebhart/patrepeval huggingface dataset:
Adaptations to Environmental Stresses. (1995)

Environmental stresses come in many forms, yet the most prevalent stresses have in common their effect on plant water status. The availability of water for its biological roles as solvent and transport medium, as electron donor in the Hill reaction, and as evaporative coolant is often impaired by environmental conditions. Although plant species vary in their sensitivity and response to the decrease in water potential caused by drought, low temperature, or high salinity, it may be assumed that all plants have encoded capability for stress perception, signaling, and response. First, most cultivated species have wild relatives that exhibit excellent tolerance to abiotic stresses. Second, biochemical studies have revealed similarities in processes induced by stress that lead to accumulated metabolites in vascular and nonvascular plants, algae, fungi, and bacteria (Csonka, 1989; Galinski, 1993; Potts, 1994). These metabolites include nitrogen-containing compounds (proline, other amino acids, quaternary amino compounds, and polyamines) and hydroxyl compounds (sucrose, polyols, and oligosaccharides) (McCue and Hanson, 1990). Accumulation of any single metabolite is not restricted to taxonomic groupings, indicating that these are evolutionarily old traits. Third, molecular studies have revealed that a wide variety of species express a common set of genes and similar proteins (for example, Rab-related proteins and dehydrins) when stressed (Skriver and Mundy, 1990; Vilardell et al., 1994). Although functions for many of these genes have not yet been unequivocally assigned, it is likely, based on their characteristics, that these proteins play active roles in the response to stress. Learning about the biochemical and molecular mechanisms by which plants tolerate environmentat stresses is necessary for genetic engineering approaches to improving crop performance under stress. By investigating plants under stress, we can learn about the plasticity of metabolic pathways and the limits to their functioning. Also, questions of an ecological and evolutionary nature need investigation. Are the genes that confer salt tolerance on halophytes and/or drought tolerance on xerophytes evolutionarily ancient genes that have been selected against in saltand drought-sensitive plants (glycophytes) for the sake of productivity? Or have some species obtained nove1 genes in their evolutionary history that have enabled them to occupy stressful environments? How will the
Raman Spectrum of Semiconducting and Metallic VO2 (1971)

The Raman scattering spectrum of V${\mathrm{O}}_{2}$ is reported between 4.2 and 600\ifmmode^\circ\else\textdegree\fi{}K. In the semiconducting monoclinic phase only sharp phonon structure is observed. The metallic rutile phase exhibits a pronounced softening and damping in the observed phonon spectrum. This evidence supports a recently proposed phenomenological mechanism for the semiconductor-to-metal transition.
The Autogenous Tissue Heart Valve: Current Status (1991)

Residual antigenicity of xenograft tissue after glutaraldehyde tanning may be a factor that determines calcification and durability of bioprostheses. We have pursued the concept of a nonantigenic, noncalcifying, more durable bioprosthesis. We previously described a technique for rapid intraoperative fabrication of an autogenous tissue heart valve (ATHV). That technique has been modified to improve reliability and ease of learning. With the modified technique, a geometrically perfect trileaflet valve can be made in 5 minutes. Although any suitable tissue can be used, the pericardial ATHV is the subject of this report. Autogenous pericardium immersed for 5 minutes in glutaraldehyde has proven satisfactory for valve construction. In vitro testing in the pulse duplicator and accelerated life tester has shown that the stent assembly is capable of function beyond 800,000,000 cycles without failure. In vivo testing has been performed in the juvenile sheep model as described by the National Institutes of Health group. Five sheep were maintained for 5 months postimplant before sacrifice. Explanted valves showed no tissue thickening or shrinkage, problems seen with earlier valves made with untreated autogenous tissue, and the leaflets remained pliable, free of the degenerative changes usually seen in the sheep model.
Synthesis of 7-Substituted Tetracycline Derivatives (2000)

[formula: see text] The synthesis of 7-substituted tetracycline derivatives has been accomplished in high yield from 7-halotetracyclines by modified Suzuki and Stille coupling protocols. These novel derivatives may serve as a new class of tetracycline antibiotics effective against multi-antibiotic-resistant bacteria.
Meiotic chromosomes: it takes two to tango (1997)

Meiosis is a special type of cell division that produces haploid gametes from diploid parental cells. Chromosome number is reduced during meiosis because a single round of DNA replication is followed by two rounds of chromosome segregation (Fig. 1). Fusion of two gametes during sexual reproduction restores the diploid chromosome complement. The second division of meiosis (the equational division) resembles mitosis: Sister chromatids separate and segregate. The first division, however, is unique. Reductional chromosome segregation at meiosis I differs from mitosis and meiosis II in a number of respects. First, sister chromatids remain associated with each other. Second, the two copies of the same chromosome (called homologous chromosomes or homologs) behave in a coordinate fashion, such that one chromosome moves to one pole of the spindle apparatus and its homolog moves to the opposite pole. This coordination in chromosome behavior depends on complex processes and elaborate structures that bring homologs together during meiotic prophase and hold them together until the transition between metaphase I and anaphase I. In most organisms, the relevant processes include alignment of homologs, assembly of the synaptonemal complex (SC, described below), genetic recombination, and the formation of chiasmata (stable connections between homologs formed at the sites of crossovers). These events occur during a very lengthy prophase that is divided into a series of substages based on changes in chromosome morphology (Table 1). This article reviews our current knowledge of the processes and structures that promote and maintain interactions between homologs and thereby ensure proper reductional chromosome segregation. Emphasis is placed on observations made in recent years, particularly those that have enhanced our understanding of the molecular mechanisms underlying meiotic chromosome behavior.
13C nuclear magnetic resonance studies on the conformation of substituted hydantoins (1980)

A number of hydantoins were synthesized and their 13C n.m.r. spectra were studied using special solvents and shift reagents. Some interesting features of their conformation were deduced. In the case of hydantoins derived from phenylalanine evidence was found for non-bonded attraction between the hydantoin ring and the phenyl group in the side chain.
D2 dopamine receptor gene is associated but not linked with alcoholism (1991)

There has been intense interest in replicating the 1990 report in<i>JAMA</i>that the minor allele of<i>DRD2</i>(the D<sub>2</sub>dopamine receptor gene on human chromosome 11 at q22-q23) may increase susceptibility to severe alcoholism in some cases. In May 1990 Blum et al<sup>1</sup>reported that 24 (69%) of 35 alcoholics carried the Al allele of<i>DRD2</i>compared with only seven (20%) of 35 nonalcoholics. Their analysis was based on brain tissue of deceased subjects, and the alcoholics were described as having experienced repeated treatment failures in their alcoholism rehabilitation, with their deaths attributable primarily to the chronic damaging effects of alcohol. It was surprising that a single gene could be so strongly associated with a common disorder that is known to be developmentally complex and genetically heterogeneous.<sup>2</sup>Accordingly, there was caution and skepticism about the report because of its small sample size and the surprising strength
Infusion of dendritic cells pulsed with HLA-A2-specific prostate-specific membrane antigen peptides: A phase II prostate cancer vaccine trial involving patients with hormone-refractory metastatic disease (1999)

Over 30% of study participants in this group showed a positive response at the conclusion of the trial. This study suggested that DC-based cancer vaccines may provide an alternative therapy for prostate cancer patients whose disease no longer responds to hormone therapy.
Imaging of the optic disc and retinal nerve fiber layer: the effects of age, optic disc area, refractive error, and gender (2002)

We cross-sectionally examined the relationship between age, optic disc area, refraction, and gender and optic disc topography and retinal nerve fiber layer (RNFL) measurements, using optical imaging techniques. One eye from each of 155 Caucasian subjects (age range 23.0-80.8 y) without ocular pathology was included. Measurements were obtained by using the Heidelberg Retina Tomography (HRT), the GDx Nerve Fiber Analyzer, and the Optical Coherence Tomograph (OCT). The effects of age were small (R2 < 17%) and were limited to specific HRT, GDx, and OCT parameters. Disc area was significantly associated with most HRT parameters and isolated GDx and OCT parameters. Refraction and gender were not significantly associated with any optic disc or RNFL parameters. Although effects of age on the optic disc and RNFL are small, they should be considered in monitoring ocular disease. Optic disc area should be considered when cross-sectionally evaluating disc topography and, to a lesser extent, RNFL thickness.
FLT4 receptor tyrosine kinase contains seven immunoglobulin-like loops and is expressed in multiple human tissues and cell lines. (1992)

The fms-like tyrosine kinase 4 (FLT4) complementary DNA was cloned from a human HEL erythroleukemia cell library by polymerase chain reaction-amplification. We previously reported a partial sequence of FLT4 and showed that the FLT4 gene maps to chromosomal region 5q33-qter (O. Aprelikova, K. Pajusola, J. Partanen, E. Armstrong, R. Alitalo, S. Bailey, J. McMahon, J. Wasmuth, K. Huebner, and K. Alitalo, Cancer Res., 52: 746-748, 1992). Here we present the full-length sequence of the predicted FLT4 protein. The extracellular domain of FLT4 consists of 7 immunoglobulin-like loops, including 12 potential glycosylation sites. On the basis of structural similarities FLT4 and the previously known FLT1 and kinase insert domain-containing receptor tyrosine kinase/fetal liver kinase 1 (KDR/FLK1) receptors constitute a subfamily of class III tyrosine kinases. FLT4 was expressed as 5.8- and 4.5-kilobase mRNAs which were found to differ in their 3' sequences and to be differentially expressed in the HEL and DAMI leukemia cells. Interestingly, a Wilms' tumor cell line, a retinoblastoma cell line, and a nondifferentiated teratocarcinoma cell line expressed FLT4, whereas differentiated teratocarcinoma cells were negative. Most fetal tissues also expressed the FLT4 mRNA, with spleen, brain intermediate zone, and lung showing the highest levels. In in situ hybridization the FLT4 autoradiographic grains decorated bronchial epithelial cells of fetal lung. No evidence was obtained for the expression of FLT4 in the endothelial cells of blood vessels.
Potent Family-18 Chitinase Inhibitors (2011)

Six novel inhibitors of Vibrio harveyi chitinase A (VhChiA), a family-18 chitinase homolog, were identified by in vitro screening of a library of pharmacologically active compounds. Unlike the previously identified inhibitors that mimicked the reaction intermediates, crystallographic evidence from 14 VhChiA-inhibitor complexes showed that all of the inhibitor molecules occupied the outer part of the substrate-binding cleft at two hydrophobic areas. The interactions at the aglycone location are well defined and tightly associated with Trp-397 and Trp-275, whereas the interactions at the glycone location are patchy, indicating lower affinity and a loose interaction with two consensus residues, Trp-168 and Val-205. When Trp-275 was substituted with glycine (W275G), the binding affinity toward all of the inhibitors dramatically decreased, and in most structures two inhibitor molecules were found to stack against Trp-397 at the aglycone site. Such results indicate that hydrophobic interactions are important for binding of the newly identified inhibitors by the chitinase. X-ray data and isothermal microcalorimetry showed that the inhibitors occupied the active site of VhChiA in three different binding modes, including single-site binding, independent two-site binding, and sequential two-site binding. The inhibitory effect of dequalinium in the low nanomolar range makes this compound an extremely attractive lead compound for plausible development of therapeutics against human diseases involving chitinase-mediated pathologies.
ChemInform Abstract: Silicon Nanoparticles: Preparation, Properties, and Applications (2015)

Abstract Review: 128 refs.
Protein Tyrosine Phosphatase 1B Antagonizes Signalling by Oncoprotein Tyrosine Kinase p210 bcr-abl In Vivo (1998)

The p210 bcr-abl protein tyrosine kinase (PTK) appears to be directly responsible for the initial manifestations of chronic myelogenous leukemia (CML). In contrast to the extensive characterization of the PTK and its effects on cell function, relatively little is known about the nature of the protein tyrosine phosphatases (PTPs) that may modulate p210 bcr-abl-induced signalling. In this study, we have demonstrated that expression of PTP1B is enhanced specifically in various cells expressing p210 bcr-abl, including a cell line derived from a patient with CML. This effect on expression of PTP1B required the kinase activity of p210 bcr-abl and occurred rapidly, concomitant with maximal activation of a temperature-sensitive mutant of the PTK. The effect is apparently specific for PTP1B since, among several PTPs tested, we detected no change in the levels of TCPTP, the closest relative of PTP1B. We have developed a strategy for identification of physiological substrates of individual PTPs which utilizes substrate-trapping mutant forms of the enzymes that retain the ability to bind to substrate but fail to catalyze efficient dephosphorylation. We have observed association between a substrate-trapping mutant of PTP1B (PTP1B-D181A) and p210 bcr-abl, but not v-Abl, in a cellular context. Consistent with the trapping data, we observed dephosphorylation of p210 bcr-abl, but not v-Abl, by PTP1B in vivo. We have demonstrated that PTP1B inhibited binding of the adapter protein Grb2 to p210 bcr-abl and suppressed p210 bcr-abl-induced transcriptional activation that is dependent on Ras. These results illustrate selectivity in the effects of PTPs in a cellular context and suggest that PTP1B may function as a specific, negative regulator of p210 bcr-abl signalling in vivo.
Udenafil Improves Exercise Capacity in Patients with Chronic Obstructive Pulmonary Disease: A Prospective Study (2012)

Pulmonary hypertension (PH) is a serious complication of chronic obstructive pulmonary disease (COPD), and there is no effective pharmacological treatment for COPD-associated PH. We evaluated the effect of udenafil, a phosphodiesterase-5 (PDE-5) inhibitor, on the exercise capacity of patients with severe COPD. Patients with severe and very severe COPD (forced expiratory volume in one second (FEV(1)) <50% of predicted) received udenafil (50 mg daily) for 8 weeks. A 6-min walk test (6MWT), lung function test, Doppler echocardiography, and Saint George's Respiratory Questionnaire (SGRQ) were completed before and after therapy. The primary outcome was a change in the 6-min walk distance (6MWD). Thirty-eight patients were screened for eligibility, and 23 completed the study. After 8 weeks of udenafil treatment, the mean 6MWD increased from 315 to 348 m (p = 0.02), and median PASP decreased from 36 to 30 mmHg (p = 0.02). There were no changes in the SGRQ score, Borg dyspnea score, or pulmonary function parameters. The PDE-5 inhibitor udenafil improved exercise capacity and decreased pulmonary artery pressure in patients with severe COPD. However, due to the small sample size, uncontrolled design and high dropout rate, the efficacy of udenafil in severe COPD needs to be confirmed in a large-scale randomized controlled study. This study was registered at ClinicalTrials.gov (number: NCT01364181).
Electroactive polymers: an emerging technology for MEMS (2004)

Electroactive polymer (EAP) transducers are an emerging technology with many features that are desirable for MEMS devices. These advantages include simple fabrication in a variety of size scales, and ruggedness due to their inherent flexibility. Dielectric elastomer, a type of EAP transducer that couples the deformation of a rubbery polymer film to an applied electric field, shows particular promise because it can produce high strain and energy density, high efficiency and fast speed of response, and inherent environmental tolerance. A variety of proof-of-principle dielectric elastomer actuator configurations have been demonstrated at the small size scales needed for MEMS devices, including rolled "artificial muscle" actuators for insect-inspired microrobots, framed and bending beam actuators for efficient opto-mechanical switches, diaphragm and enhanced-thickness-mode actuators for microfluidic pumps, and valves and arrays of diaphragms for haptic displays. Several challenges remain for EAPs, including integration with driving electronics, and operational lifetime.
Selective Expression of the Insulin I Gene in Rat Insulinoma-Derived Cell Lines (1990)

Four rat insulinoma-derived cell lines were found to express only the rat insulin I gene, although an apparently normal insulin II gene was present in each cell line. This finding was reflected by the absence of insulin II and the presence of insulin I gene transcripts in the products of run-on transcription assays, the absence of insulin II and the presence of insulin I unprocessed (pre-) mRNA, and the absence of mature insulin II and the presence of insulin I mRNA. Analysis of insulin II genes in cell lines by gene amplification indicated that the lack of insulin II gene transcription is not explained by the absence of or gross alterations in the insulin II genes per se. These studies indicate that the two nonallelic insulin genes do not function equivalently in pancreas-derived cells.
Milk cytokines and subclinical breast inflammation in Tanzanian women: effects of dietary red palm oil or sunflower oil supplementation (1999)

Previously, we have found that subclinical breast inflammation, as indicated by raised breastmilk concentrations of sodium and the inflammatory cytokine, interleukin-8 (IL-8), was highly prevalent in Bangladesh and associated with poor infant growth. In order to investigate further the prevalence of subclinical breast inflammation and to assess the impact of dietary intervention, we studied rural Tanzanian women taking part in a study of dietary sunflower or red palm oil supplementation during late pregnancy and lactation. We measured breastmilk concentrations of IL-8, the anti-inflammatory cytokine, transforming growth factor-beta2 (TGF-beta) and the ratio of sodium to potassium. We also estimated systemic inflammation by plasma concentrations of the acute phase proteins, alpha1-acid glycoprotein and C-reactive protein. There were highly significant intercorrelations among milk Na/K ratio and concentrations of IL-8 and TGF-beta, the last only after treatment with bile salts which also improved TGF-beta recovery in the enzyme-linked immunosorbent assay (ELISA). Plasma acute phase protein concentrations tended to correlate with milk Na/K ratio and IL-8, suggesting that subclinical breast inflammation was related to systemic inflammation. Dietary supplementation with vitamin E-rich sunflower oil but not provitamin A-containing red palm oil decreased milk Na/K, IL-8 and TGF-beta at 3 months postpartum; however, the effect was significant only for Na/K ratio. The results suggest that milk Na/K ratio, IL-8, and TGF-beta all measure the same phenomenon of subclinical breast inflammation but that Na/K ratio, having the lowest assay variability, is the most useful. Subclinical breast inflammation may result in part from systemic inflammation and may be improved by increased dietary intake of vitamin E-rich sunflower oil.
Biliverdin Reductase-Induced Phytochrome Chromophore Deficiency in Transgenic Tobacco (2001)

Targeted expression of mammalian biliverdin IXalpha reductase (BVR), an enzyme that metabolically inactivates linear tetrapyrrole precursors of the phytochrome chromophore, was used to examine the physiological functions of phytochromes in the qualitative short-day tobacco (Nicotiana tabacum cv Maryland Mammoth) plant. Comparative phenotypic and photobiological analyses of plastid- and cytosol-targeted BVR lines showed that multiple phytochrome-regulated processes, such as hypocotyl and internode elongation, anthocyanin synthesis, and photoperiodic regulation of flowering, were altered in all lines examined. The phytochrome-mediated processes of carotenoid and chlorophyll accumulation were strongly impaired in plastid-targeted lines, but were relatively unaffected in cytosol-targeted lines. Under certain growth conditions, plastid-targeted BVR expression was found to nearly abolish the qualitative inhibition of flowering by long-day photoperiods. The distinct phenotypes of the plastid-targeted BVR lines implicate a regulatory role for bilins in plastid development or, alternatively, reflect the consequence of altered tetrapyrrole metabolism in plastids due to bilin depletion.
Systemic Modulation of Gene Expression in Tomato by Trichoderma hamatum 382 (2007)

ABSTRACT A light sphagnum peat mix inoculated with Trichoderma hamatum 382 consistently provided a significant (P = 0.05) degree of protection against bacterial spot of tomato and its pathogen Xanthomonas euvesicatoria 110c compared with the control peat mix, even though this biocontrol agent did not colonize aboveground plant parts. To gain insight into the mechanism by which T. hamatum 382 induced resistance in tomato, high-density oligonucleotide microarrays were used to determine its effect on the expression pattern of 15,925 genes in leaves just before they were inoculated with the pathogen. T. hamatum 382 consistently modulated the expression of genes in tomato leaves. We identified 45 genes to be differentially expressed across the replicated treatments, and 41 of these genes could be assigned to at least one of seven functional categories. T. hamatum 382-induced genes have functions associated with biotic or abiotic stress, as well as RNA, DNA, and protein metabolism. Four extensin and extensin-like proteins were induced. However, besides pathogenesis-related protein 5, the main markers of systemic acquired resistance were not significantly induced. This work showed that T. hamatum 382 actively induces systemic changes in plant physiology and disease resistance through systemic modulation of the expression of stress and metabolism genes.