gebhart/patrepeval huggingface dataset:
Role of Sucrose Synthase and Other Related Enzymes in Sucrose Accumulation in Peach Fruit. (1991)

Four peach cultivars differing in their maturation time and sugar composition were analyzed for the detection of seasonal changes in the content of sugars in the flesh and peduncle, and in the activity of sucrose-metabolizing enzymes. Besides the accumulation of sucrose as a major sugar at the mature stage in all the cultivars, the fructose content was similar to glucose content in 'Akatsuki' and 'Yuzora'. While in 'Naganoyaseito-early' and 'Hokimomo' the fructose content was low. Of the enzymes assayed, there were no clear differences in the activity among the peach cultivars. In all the cultivars, the sucrose synthase (SS) activity increased with sucrose accumulation, suggesting the importance of its role in sucrose accumulation in peach fruit. On the contrary, the sucrose-phosphate synthase (SPS) activity did not increase with sucrose accumulation. The acid invertase activity decreased with fruit development. The decrease in the acid invertase activity appeared to reflect fruit maturation, during which sucrose accumulated. The UDPglucose pyrophosphorylase activity was also assayed in these peaches throughout the development of fruit. However, typical seasonal fluctuations of the activity were not observed among the four cultivars. Kinetic parameters of SS from immature and mature peach fruit suggested that SS tended to be involved in sucrose synthesis in the mature peach fruit compared with the immature one. The differences in sucrose synthesis between peach and other fruits were also discussed, based on the activities and properties of these enzymes.
1-mJ energy, 1-MW peak-power, 10-W average-power, spectrally narrow, diffraction-limited pulses from a photonic-crystal fiber amplifier (2005)

We report on a diode-pumped master-oscillator/fiber-amplifier (MOFA) system consisting of a passively Q-switched, single-frequency Nd:LSB microchip laser that seeds a dual-stage Yb-doped fiber amplifier. A large-core, single-mode photonic crystal fiber was used for the final amplifier. The MOFA generated 1062nm wavelength, 1-ns long, ~10kHz repetition-rate, diffraction-limited pulses of energy >1mJ, peak power >1MW, average power >10W, and spectral linewidth ~9 GHz.
Rules for Identifying Ancient Life (1996)

J. William Schopf (University of California, Los Angeles) has spent many years examining ancient rocks on Earth to identify the oldest fossils. This work is painstaking and frought with difficulty and potential errors. The worse mistake is to identify an ancient fossil, only to find out later that you were fooled by a nonbiologic mineral grain that looked like a fossil, but was not. This work has led to a set of criteria, or rules, that must be met for establishing credible evidence for past life in geologic samples.
Human kallikrein 14: a new potential biomarker for ovarian and breast cancer. (2003)

Human kallikrein gene 14 (KLK14) is a recently discovered member of the tissue kallikrein family of secreted serine proteases, which includes hK3/prostate-specific antigen, the best cancer biomarker to date. Given that KLK14 is hormonally regulated, differentially expressed in endocrine-related cancers, and a prognostic marker for breast and ovarian cancer at the mRNA level, we hypothesize that its encoded protein, hK14, like hK3/prostate-specific antigen, may constitute a new biomarker for endocrine-related malignancies. The objective of this study was to generate immunological reagents for hK14, to develop an ELISA and immunohistochemical techniques to study its expression in normal and cancerous tissues and biological fluids. Recombinant hK14 was produced in Pichia pastoris, purified by affinity chromatography, and injected into mice and rabbits for polyclonal antibody generation. Using the mouse and rabbit antisera, a sandwich-type immunofluorometric ELISA and immunohistochemical methodologies were developed for hK14. The ELISA was sensitive (detection limit of 0.1 micro g/liter), specific for hK14, linear from 0 to 20 micro g/liter with between-run and within-run coefficients of variation of <10%. hK14 was quantified in human tissue extracts and biological fluids. Highest levels were observed in the breast, skin, prostate, seminal plasma, and amniotic fluid, with almost undetectable levels in normal serum. hK14 concentration was higher in 40% of ovarian cancer tissues compared with normal ovarian tissues. Serum hK14 levels were elevated in a proportion of patients with ovarian (65%) and breast (40%) cancers. Immunohistochemical analyses indicated strong cytoplasmic staining of hK14 by the epithelial cells of normal and malignant skin, ovary, breast, and testis. In conclusion, we report the first ELISA and immunohistochemical assays for hK14 and describe its distribution in tissues and biological fluids. Our preliminary data indicate that hK14 is a potential biomarker for breast and ovarian cancers.
Mel Frequency Cepstral Coefficients: An Evaluation Of Robustness Of Mp3 Encoded Music. (2006)

[TODO] Add abstract here.
The Binding Properties and Biological Activities of Bcl-2 and Bax in Cells Exposed to Apoptotic Stimuli (1998)

The oncogene product Bcl-2 protects cells from apoptosis whereas its homolog Bax functions to kill cells. Several binding partners of Bcl-2 and Bax have been isolated, but none of them has yet provided clues as to exactly how Bcl-2 and Bax work. According to one view, Bcl-2 and Bax interact with survival and death effector molecules, respectively, and neutralize each other through heterodimerization. Alternatively, Bcl-2 requires Bax for death protection, and additional proteins bind to the heterodimer to regulate its activity. Here we used a co-immunoprecipitation strategy to distinguish between these two possibilities. We show that the Bcl-2-Bax heterodimer is maintained, and no other protein associates stably in detectable amounts with Bcl-2, Bax, or the heterodimer in anti-Bcl-2 and anti-Bax immunoprecipitates from normal cells and cells exposed to apoptotic stimuli. Analysis of cells expressing various levels of Bcl-2 and Bax, however, revealed that the degree of protection against apoptosis does not correlate with the number of Bcl-2-Bax heterodimers but the amount of Bcl-2 that is free of Bax. In addition, the survival activity of Bcl-2 is unaffected when Bax expression is ablated by an antisense strategy. Our findings suggest that the Bcl-2-Bax heterodimer is a negative regulator of death protection, and that Bcl-2 requires neither Bax nor major, stable interactions with other cellular proteins to exert its survival function. We therefore propose that Bcl-2 acts as an enzyme (capturing substrates in a transient way), as a homodi- or multimer, or through the interaction with non-proteaceous targets (lipids, ions).
Purified envelope glycoproteins from human immunodeficiency virus type 1 variants induce individual, type-specific neutralizing antibodies (1988)

Repeated immunizations of goats, horses, or chimpanzees with envelope glycoprotein gp120 isolated from human immunodeficiency virus type 1 (HIV-1) resulted in type-specific neutralizing-antibody responses, which began to decay approximately 20 days following the administration of antigen. This was true repeatedly for serum samples from animals hyperimmunized with gp120s from either the HTLV-IIIB (IIIB) or the envelope-divergent HTLV-IIIRF (RF) HIV-1 isolates. Animals previously immunized with the IIIB gp120 were then inoculated with purified RF gp120. The first response in these animals was an anamnestic resurgence of neutralizing antibody to IIIB without detectable neutralizing antibody for RF. However, with later RF gp120 boosts, the IIIB neutralizing-antibody titers fell and an RF type-specific neutralizing-antibody response developed. When assessed with other HIV-1 variants, no group-specific neutralizing antibody was seen in any of the vaccination protocols evaluated. These results will pose real obstacles in the development of an effective vaccine for HIV.
IL-15 has stimulatory activity for the induction of B cell proliferation and differentiation. (1995)

The identification and cloning of the novel cytokine IL-15 were recently described. IL-15 is produced by a wide range of cell types, with the highest levels of IL-15 mRNA being detected in epithelial lines, monocytes, muscle, and placenta. Although it has no sequence identity with IL-2, IL-15 shares many of the T cell-stimulatory activities described for IL-2. We have examined IL-15 for its ability to stimulate B cells and have compared its activity with that of IL-2. IL-15 costimulates proliferation of B cells activated with immobilized anti-human IgM or phorbol ester, but has no stimulatory effect on resting B cells. In combination with recombinant CD40L, IL-15 is a potent inducer of polyclonal IgM, IgG1, and IgA secretion, but does not cause production of IgG4 or IgE. The activity of IL-15 in B cell proliferation and differentiation assays is comparable with that of IL-2. Studies that used neutralizing Abs have demonstrated that, for signal transduction in B cells, IL-15 uses the beta-chain of the IL-2R complex but, unlike IL-2, does not require the alpha-chain. IL-2 is required for the generation of a human primary Ag-specific in vitro response using sheep erythrocytes as Ag. Of all cytokines examined, only IL-15 has the capacity to replace IL-2 in this system, although only partially. In summary, IL-15 has comparable activity with IL-2 for the induction of B cell proliferation and differentiation and uses at least some of the components of the IL-2R complex to mediate its effects.
The T-box Repressors TBX2 and TBX3Specifically Regulate the Tumor Suppressor Genep14 via a Variant T-site in the Initiator (2002)

The murine tumor suppressor p19(ARF) (p14(ARF) in humans) is thought to fulfill an important protective role in preventing primary cells from oncogenic transformation via its action in the p53 pathway. Several disease-implicated regulators of p19(ARF) are known to date, among which are the T-box genes TBX2, which resides on an amplicon in primary breast tumors, and TBX3, which is mutated in the human developmental disorder Ulnar-Mammary syndrome. Here we identify a variant T-site, matching 13 of 20 nucleotides of a consensus T-site, as the essential TBX2/TBX3-binding element in the human p14(ARF) promoter. Mutant analysis indicates that both the consensus T-box and a C-terminal conserved repression domain are essential for p14(ARF) repression. Whereas the core nucleotides required for interaction of the archetypal T-box protein Brachyury with a consensus T-site are conserved in the variant site, additional flanking nucleotides contribute to the specificity of TBX2 binding. This is illustrated by the inability of TBX1A or Xbra to activate via the variant p14(ARF) T-site. Importantly, this suggests a hitherto unsuspected level of specificity associated with T-box factors and corresponding recognition sites in regulating their target genes in vivo.
Reducing implant-related infections: active release strategies (2006)

Despite sterilization and aseptic procedures, bacterial infection remains a major impediment to the utility of medical implants including catheters, artificial prosthetics, and subcutaneous sensors. Indwelling devices are responsible for over half of all nosocomial infections, with an estimate of 1 million cases per year (2004) in the United States alone. Device-associated infections are the result of bacterial adhesion and subsequent biofilm formation at the implantation site. Although useful for relieving associated systemic infections, conventional antibiotic therapies remain ineffective against biofilms. Unfortunately, the lack of a suitable treatment often leaves extraction of the contaminated device as the only viable option for eliminating the biofilm. Much research has focused on developing polymers that resist bacterial adhesion for use as medical device coatings. This tutorial review focuses on coatings that release antimicrobial agents (i.e., active release strategies) for reducing the incidence of implant-associated infection. Following a brief introduction to bacteria, biofilms, and infection, the development and study of coatings that slowly release antimicrobial agents such as antibiotics, silver ions, antibodies, and nitric oxide are covered. The success and limitations of these strategies are highlighted.
A Chemical Genetics Approach for the Functional Assessment of Novel Cancer Genes (2015)

Assessing the functional significance of novel putative oncogenes remains a significant challenge given the limitations of current loss-of-function tools. Here, we describe a method that employs TALEN or CRISPR/Cas9-mediated knock-in of inducible degron tags (Degron-KI) that provides a versatile approach for the functional characterization of novel cancer genes and addresses many of the shortcomings of current tools. The Degron-KI system allows for highly specific, inducible, and allele-targeted inhibition of endogenous protein function, and the ability to titrate protein depletion with this system is able to better mimic pharmacologic inhibition compared with RNAi or genetic knockout approaches. The Degron-KI system was able to faithfully recapitulate the effects of pharmacologic EZH2 and PI3Kα inhibitors in cancer cell lines. The application of this system to the study of a poorly understood putative oncogene, SF3B1, provided the first causal link between SF3B1 hotspot mutations and splicing alterations. Surprisingly, we found that SF3B1-mutant cells are not dependent upon the mutated allele for in vitro growth, but instead depend upon the function of the remaining wild-type alleles. Collectively, these results demonstrate the broad utility of the Degron-KI system for the functional characterization of cancer genes.
Cohort Study of Somatostatin-Based Radiopeptide Therapy With [90Y-DOTA]-TOC Versus [90Y-DOTA]-TOC Plus [177Lu-DOTA]-TOC in Neuroendocrine Cancers (2012)

[(90)Y-DOTA]-TOC + [(177)Lu-DOTA]-TOC was associated with improved overall survival compared with [(90)Y-DOTA]-TOC alone in patients completing three or more cycles of treatment. Contrary to the current practice in radiopeptide therapy, our results suggest an advantage of using a combination of radioisotopes.
Thyroxine analogs. 23. Quantitative structure-activity correlation studies of in vivo and in vitro thyromimetic activities (1977)

Quantitative structure-activity correlation studies of thyroid hormone analogues have been utilized to examine (1) in vivo rat antigoiter activities; (2) in vitro binding affinities to intact rat hepatic nuclei, solubilized rat hepatic nuclear protein receptors, and the plasma protein thyroxine binding globulin; and (3) correlations between in vivo antigoiter activities and in vitro binding to nuclear receptors. These studies provide a more precise elucidation of the relative importance of the physiochemical factors which influence thyromimetic activities. In particular, they (1) provide the first systematic QSAR examination of drug-receptor interactions and of the dependence of in vivo activity on such interactions; (2) demonstrate the importance of the interactive effects of the 3' and 5' substituents and of the 4'-OH with each other as well as with nuclear receptors in influencing binding affinity; (3) support the hypothesis that binding to nuclear receptors is the first step in initiating the events which lead to subsequent hormonal expression; (4) show that the free energy of binding to nuclear receptors can be factored into the contributing physicochemical properties of the substituents; and (5) suggest factors that need to be considered in designing new analogues.
Weathering the Cytokine Storm in COVID-19: Therapeutic Implications (2020)

The pathophysiology of COVID-19 is far from being completely understood, and the lack of effective treatments leads to a sense of urgency to develop new therapeutic strategies based on pathophysiological assumptions. The exaggerated cytokine release in response to viral infection, a condition known as cytokine release syndrome (CRS) or cytokine storm, is emerging as the mechanism leading to ARDS and MOF in COVID-19, thus endorsing the hypothesis that properly timed anti-inflammatory therapeutic strategies could improve patients' clinical outcomes and prognosis. Key Messages: The objective of this article is to explore and comment on the potential role of the promising immunomodulatory therapies using pharmacological and nonpharmacological approaches to overcome the dysregulated proinflammatory response in COVID-19.
A reference model for firewall technology (2002)

The paper concentrates on one particular technological aspect of providing communications security, firewall technology. Currently firewall technology is a specialized engineering solution rather than a scientifically based solution. The paper introduces a reference model that captures existing firewall technology and allows for an extension to networking technologies to which it was not applied previously. It can serve as a framework in which firewall systems can be designed and validated. The essential components of the reference model are authentication, integrity assurance, access control, audit, and their enforcement. All components are governed by a centralized security policy, and they can be deployed in a distributed fashion to achieve scaling.
Quantifying Estimation Bias in Residential Appraisal (1988)

The purpose of this study was to empirically test the ability of residential appraisers to estimate market value of houses. Using a sample of over 500 appraisals made for corporate relocation firms, the appraisal estimates of market value were compared with the actual price that the houses sold for subsequently. The results indicate that current appraisal methods produce unbiased estimates of market value. Additional empirical results are presented that show that seasonal factors and regional economic conditions significantly explain variation in appraisal error.
Evidence that the vasodilator angiotensin-(1–7)-Mas axis plays an important role in erectile function (2007)

The vasodilator/antiproliferative peptide angiotensin-(1-7) [ANG-(1-7)] is released into the corpus cavernosum sinuses, but its role in erectile function has yet to be defined. In this study, we sought to determine whether ANG-(1-7) and its receptor Mas play a role in erectile function. The ANG-(1-7) receptor Mas was immunolocalized in rat corpus cavernosum by confocal microscopy. Infusion of ANG-(1-7) into corpus cavernosum at a rate of 15.5 pmol x kg(-1) x min(-1) potentiated the elevation of the corpus cavernosum pressure induced by electrical stimulation of the major pelvic ganglion (MPG) in rats. The facilitatory effect of ANG-(1-7) was completely blunted by the specific ANG-(1-7) receptor blocker A-779 and N(omega)-nitro-L-arginine methyl ester. Nitric oxide (NO) release in the corpus cavernosum was evaluated with the fluorescent dye 4-amino-5 methylamino-2',7'-difluorofluorescein diacetate. Electrical stimulated-release of NO in rat corpus cavernosum was potentiated by ANG-(1-7). Furthermore, incubation of rat and mouse corpus cavernosum strips with ANG-(1-7) at 10 nmol/l resulted in an increase of NO release. This effect was completely abolished in mas-deficient mice. More importantly, genetic deletion of Mas resulted in compromised erectile function as demonstrated by penile fibrosis and severely depressed response to electrical stimulation of the MPG. Furthermore, the attenuated erectile function of DOCA-salt hypertensive rats was fully restored by ANG-(1-7) administration. Together these data provide strong evidence for a key role of the ANG-(1-7)-Mas axis in erectile function.
The Ubiquitin Code (2012)

The posttranslational modification with ubiquitin, a process referred to as ubiquitylation, controls almost every process in cells. Ubiquitin can be attached to substrate proteins as a single moiety or in the form of polymeric chains in which successive ubiquitin molecules are connected through specific isopeptide bonds. Reminiscent of a code, the various ubiquitin modifications adopt distinct conformations and lead to different outcomes in cells. Here, we discuss the structure, assembly, and function of this ubiquitin code.
Monoclonal Antibodies to Three Widely Distributed Human Cell Surface Antigens (1983)

Four mouse monoclonal antibodies to widely distributed human cell surface antigens are described. The AJ2 antigen is one of the immunodominant antigens in mice immunized with human cells, as demonstrated by testing conventional mouse antisera. This antigen has four subunits having molecular weights (MW) of 170 kD, 140 kD, 140 kD, and 28 kD when immunoprecipitated from the immunizing cell line, an astrocytoma. With other cell lines the molecular weights and subunit composition varies, but the major component is always of MW 125-140 kD. The antigen was detected on all human tissue culture cells and on sections of all normal human tissues tested. Antibody MA99 detects the same antigenic complex but shows a slightly different pattern of reactivity with cell lines and tissues. The MA103 antigen has a similar ubiquitous distribution. It is a glycoprotein of MW 50-55 kD and the determinant detected is not denatured by treatment at 100 degrees C. MH99, the third common antigen detected, has two glycosylated subunits with MW of 29 kD and 38 kD. It is present on a subpopulation of tumor cell lines of most histologic types except that it is absent or weakly expressed on melanomas and astrocytomas. MH99 is present on some T lymphomas and leukemias and myeloid leukemias but was not detected on B lymphomas, null cell lymphomas and myelomas. It was detected preferentially on epithelial cells in tissue sections.
THE TREATMENT OF GLASSHOUSE SOILS WITH CHLOROPICRIN FOR THE CONTROL OF HETERODERA MARIONI (CORNU) GOODEY, AND OTHER SOIL PATHOGENS (1937)

Chloropicrin in 1 cc. doses is lethal to bulb nematodes at six inches from the point of injection or within a soil volume of one cubic foot. It is also lethal to fungi. The vegetative stages are destroyed at 1:195,000, and certain sclerotia at 1:90,000.The injection of chloropicrin into greenhouse soils lowered the incidence and pathogenicity of a root-knot infection on both a summer and winter crop of tomatoes and greatly increased the yields of fruit. The chloropicrin costs $1.65 per pound or $8.50 to treat 2000 sq. ft. of soil.
Under Microscopes the Poly(styrene/butadiene) Nanoparticles (2007)

There has been considerable interest, both academic and industrial, in developing synthesis processes for making polymeric nanoparticles. Our effort relied on the nanoassembly concepts of block macromolecules in solutions to prepare particles with a hard core made of crosslinked plastics and a soft shell made of low T(g) elastomer. By a suitable variation of the composition, polymer molecular weight and solute concentration, we were able to produce spherical, ellipsoidal, cylindrical, and chain-like nanoparticles. Under microscopes, the chain-like nanoparticles displayed very rich conformational features in diluted and dense states. Our observation on the conformation characters of the nanochains in 3D diluted state agreed well with the proposition of the self-avoid coil model. However, in 2D dense state, our observation on the nanochains appeared to be in contradiction with the segregated globule model proposed by de Gennes.