gebhart/patrepeval huggingface dataset:
Gene Discovery of Modular Diterpene Metabolism in Nonmodel Systems   (2013)

Plants produce over 10,000 different diterpenes of specialized (secondary) metabolism, and fewer diterpenes of general (primary) metabolism. Specialized diterpenes may have functions in ecological interactions of plants with other organisms and also benefit humanity as pharmaceuticals, fragrances, resins, and other industrial bioproducts. Examples of high-value diterpenes are taxol and forskolin pharmaceuticals or ambroxide fragrances. Yields and purity of diterpenes obtained from natural sources or by chemical synthesis are often insufficient for large-volume or high-end applications. Improvement of agricultural or biotechnological diterpene production requires knowledge of biosynthetic genes and enzymes. However, specialized diterpene pathways are extremely diverse across the plant kingdom, and most specialized diterpenes are taxonomically restricted to a few plant species, genera, or families. Consequently, there is no single reference system to guide gene discovery and rapid annotation of specialized diterpene pathways. Functional diversification of genes and plasticity of enzyme functions of these pathways further complicate correct annotation. To address this challenge, we used a set of 10 different plant species to develop a general strategy for diterpene gene discovery in nonmodel systems. The approach combines metabolite-guided transcriptome resources, custom diterpene synthase (diTPS) and cytochrome P450 reference gene databases, phylogenies, and, as shown for select diTPSs, single and coupled enzyme assays using microbial and plant expression systems. In the 10 species, we identified 46 new diTPS candidates and over 400 putatively terpenoid-related P450s in a resource of nearly 1 million predicted transcripts of diterpene-accumulating tissues. Phylogenetic patterns of lineage-specific blooms of genes guided functional characterization.
Classification of Obesity and Assessment of Obesity‐Related Health Risks (2002)

The barriers to the evaluation and treatment of obesity by health-care providers include a lack of awareness of obesity as an independent risk factor for morbidity and mortality and inadequate training in the medical management of obesity. However, the increased risk of medical disorders and emotional consequences associated with obesity make the disorder a priority for physicians to assess and treat. Obesity researchers have published and promoted the use of evidence-based, practical guidelines to educate physicians about how best to approach obesity as a medical disorder. The guidelines support classification and assessment of obesity as an important component of the patient's medical care. Assessment begins with classification by body mass index (BMI), with overweight and obesity defined as a BMI of 25 and 30 kg/m(2), respectively. Patients with high-risk combinations of BMI, waist circumference, and specific cardiovascular risk factors should begin a weight-loss program if no contraindications are present. Proper assessment also includes evaluation of complicating factors for obesity, such as sleep apnea and type 2 diabetes, psychosocial factors, and the use of medications that may contribute to obesity. Special attention should be paid to elements of the physical examination that often are performed incorrectly in obese patients, such as pelvic exams. Gathering this information will allow the clinician to tailor a weight-loss program to each patient individually. Although this represents the most challenging component of obesity care, resources are available to guide the clinician.
Validity of Acoustic Reflectometry in Detecting Middle Ear Effusion (1987)

Pneumootoscopy, tympanometry, and acoustic reflectometry were performed in 256 middle-class children seen in a surburban pediatric office. The results demonstrated that relectometry, when validated by otoscopic findings, detected middle ear effusion with 88% sensitivity and 83% specificity when a cut-off of 5 linear units was used. Corresponding values for tympanometry were 87% and 77.5%. These results are in keeping with those of earlier studies on acoustic reflectometry and demonstrate the usefulness of this simple technique in detecting chronic and acute otitis media with effusion.
Improved edge detection for EWOC depth upscaling (2012)

The need for accurate depth information in three-dimen-sional television (3DTV) encourages the use of range sensors,i.e. time-of-ﬂight (ToF) cameras. Since these sensors provideonly limited spatial resolution compared to modern high res-olution image sensors, upscaling methods are much needed.Typical depth upscaling algorithms fuse low resolution depthinformation with appropriate high resolution texture frames,taking advantage of the additional texture information in theupscaling process. We recently introduced a promising up-scaling method, utilizing edge information from the textureframe to upscale low resolution depthmaps. This paper exam-ines how a more thorough edge detection can be achieved byinvestigating different edge detection sources, such as inten-sity, color spaces and difference signals. Our ﬁndings showthat a combination of sources based on the perceptual quali-ties of the human visual system (HVS) leads to slightly im-proved results. On the other hand these improvements implya more complex edge detection.
High CD21 expression inhibits internalization of anti‐CD19 antibodies and cytotoxicity of an anti‐CD19‐drug conjugate (2007)

CD19 and CD21 (CR2) are co-receptors found on B-cells and various B-cell lymphomas, including non-Hodgkin lymphoma. To evaluate their suitability as targets for therapy of such lymphomas using internalization-dependent antibody-drug conjugates [such as antibody-4-(N-maleimidomethyl)cyclohexane-1-carboxylate, (N2'-deacetyl-N2'-(3-mercapto-1-oxopropyl)-maytansine) (MCC-DM1) conjugates, which require lysosomal degradation of the antibody moiety for efficacy], we examined uptake of antibodies to CD19 and CD21 in a panel of B-cell lines. Anti-CD21 antibodies were not sufficiently internalized even in the highest CD21-expressing Raji cells, resulting in lack of efficacy with anti-CD21-MCC-DM1 conjugates. Anti-CD19 antibody uptake was variable, and was unexpectedly negatively correlated with CD21 expression. Thus, high CD21-expressing Raji, ARH77 and primary B-cells only very slowly internalized anti-CD19 antibodies, while CD21-negative or low expressing cells, including Ramos and Daudi, rapidly internalized these antibodies in clathrin-coated vesicles followed by lysosomal delivery. Anti-CD19-MCC-DM1 caused greater cytotoxicity in the faster anti-CD19-internalizing cell lines, implying that the rate of lysosomal delivery and subsequent drug release is important. Furthermore, transfection of Ramos cells with CD21 impeded anti-CD19 uptake and decreased anti-CD19-MCC-DM1 efficacy, suggesting that CD21-negative tumours should respond better to such anti-CD19 conjugates. This may have possible clinical implications, as anti-CD21 immunohistochemistry revealed only approximately 30% of 54 diffuse large B-cell lymphoma patients lack CD21 expression.
Resonant antenna-source system for generation of high-power wideband pulses (2002)

High-power electromagnetic pulse sources are of interest for a variety of applications such as transient radar and for investigations concerning radio-frequency effects on electronic systems. For such work, a simple, mobile, and robust source system has been developed at the Defence Science and Technology Organization, Edinburgh, Australia. It is comprised of a pulsed-resonant transformer, a spark-gap switch, and a modified biconical antenna. The antenna is charged to a high voltage, in the order of hundreds of kV, by the transformer and then is shorted at the bicone center by the spark-gap switch. The charge energy stored in the antenna then oscillates at the resonant frequency of the system and produces high-power electromagnetic pulses. In this paper, we describe the system design, present results of numerical simulations and measurements, and discuss areas for further improvements in energy-transfer efficiency, and power output.
Promoter Escape by RNA Polymerase II (1997)

Shortly after initiating promoter-specific transcription in vitro, mammalian RNA polymerase II becomes highly susceptible to arrest in a promoter-proximal region 9-13 base pairs downstream of the transcriptional start site (Dvir, A., Conaway, R. C., and Conaway, J. W. (1996) J. Biol. Chem. 271, 23352-23356). Arrest by polymerase in this region is suppressed by TFIIH in an ATP-dependent reaction (Dvir, A., Conaway, R. C., and Conaway, J. W. (1997) Proc. Natl. Acad. Sci. U. S. A. 94, 9006-9010). In this report, we present evidence that, in addition to TFIIH and an ATP cofactor, efficient transcription by RNA polymerase II through this promoter-proximal region requires formation of an "escape-competent" transcriptional intermediate. Formation of this intermediate requires template DNA 40-50 base pairs downstream of the transcriptional start site. This requirement for downstream DNA is transient, since template DNA downstream of +40 is dispensable for assembly of the preinitiation complex, for initiation and synthesis of the first 10-12 phosphodiester bonds of nascent transcripts and for further extension of transcripts longer than approximately 14 nucleotides. Thus, promoter escape requires that the RNA polymerase II transcription complex undergoes a critical structural transition, likely driven by interaction of one or more components of the transcriptional machinery with template DNA 40-50 base pairs downstream of the transcriptional start site.
Spin Rings in Semiconductor Microcavities (2008)

New effects of self-organization and polarization pattern formation in semiconductor microcavities, operating in the nonlinear regime, are predicted and theoretically analyzed. We show that a spatially inhomogeneous elliptically polarized optical cw pump leads to the formation of a strongly circularly polarized ring in real space. This effect is due to the polarization multistability of cavity polaritons which was recently predicted. The possible switching between different stable configurations allows the realization of a localized spin memory element, suitable for an optical data storage device.
Chronic Central Administration of Apelin‐13 Over 10 Days Increases Food Intake, Body Weight, Locomotor Activity and Body Temperature in C57BL/6 Mice (2007)

The peptide apelin has been located in a wide range of tissues, including the gastrointestinal tract, stomach and adipose tissue. Apelin and its receptor has also been detected in the arcuate and paraventricular nuclei of the hypothalamus, which are involved in the control of feeding behaviour and energy expenditure. This distribution suggests apelin may play a role in energy homeostasis, but previous attempts to discern the effects of apelin by acute injection into the brain have yielded conflicting results. We examined the effect of a chronic 10-day intracerebroventricular (i.c.v.) infusion of apelin-13 into the third ventricle on food intake, body temperature and locomotor activity in C57BL/6 mice. Apelin-13 (1 microg/day) increased food intake significantly on days 3-7 of infusion; thereafter, food intake of treated and control individuals converged. This convergence was potentially because of progressive conversion of apelin-13 to [Pyr(1)]apelin-13 which has a four-fold lower receptor binding affinity at the orphan G protein-coupled receptor, APJ. Locomotor activity was also higher in the apelin-treated mice, especially during the nocturnal peak, when most feeding occurs, and the first hours of the light phase. Body temperature was also elevated during this increased period of activity, but was otherwise unaffected. Apelin-13-infused animals gained more weight than the saline-infused controls, suggesting the elevated locomotor activity did not offset the increased food intake. Elevated locomotion and the consequent increases in body temperature were probably secondary effects to the increased food intake. These results suggest that apelin-13 may play a central role in the control of feeding behaviour and is one of only two peripheral ligands known to stimulate rather than inhibit intake. As apelin production is elevated during obesity, this may provide an important feed-forward mechanism exacerbating the problem. Antagonists of the apelin receptor may therefore be useful pharmaceuticals in the treatment of obesity.
An h <i>Per2</i> Phosphorylation Site Mutation in Familial Advanced Sleep Phase Syndrome (2001)

Familial advanced sleep phase syndrome (FASPS) is an autosomal dominant circadian rhythm variant; affected individuals are "morning larks" with a 4-hour advance of the sleep, temperature, and melatonin rhythms. Here we report localization of the FASPS gene near the telomere of chromosome 2q. A strong candidate gene (hPer2), a human homolog of the period gene in Drosophila, maps to the same locus. Affected individuals have a serine to glycine mutation within the casein kinase Iepsilon (CKIepsilon) binding region of hPER2, which causes hypophosphorylation by CKIepsilon in vitro. Thus, a variant in human sleep behavior can be attributed to a missense mutation in a clock component, hPER2, which alters the circadian period.
Biochemical aspects of dementias (2003)

Alzheimer's disease, frontotemporal dementia, dementia with Lewy bodies, and prion diseases are age-related neurodegenerative disorders associated with a progressive decline of cognitive brain functions. Due to the increase in prevalence rates, and the rising costs associated with clinical and social care, treatments designed to prevent or reverse these diseases are urgently needed. The most common major biochemical characteristic of these neurodegenerative diseases is the deposition of abnormal protein aggregates in brain. The decryption of the mechanisms of aggregation and associated neurotoxicity may reveal new therapeutic targets, which will enable treatment for these devastating conditions.
Novel, robust and cost-effective authentication techniques for online services (2009)

A thesis submitted to the University of Bedfordshire, in partial fulfilment of the requirements for the degree of Ph.D.
Fibronectin augments binding of fibrin to macrophages. (1989)

Because of the demonstrated ability of fibronectin to mediate particle uptake by macrophages and the demonstrated affinity of plasma fibronectin for fibrin, we investigated the ability of plasma fibronectin to augment macrophage binding of fibrin. Fibronectin significantly increased fibrin binding by elicited peritoneal macrophages and isolated hepatic Kupffer cells. The binding of fibrinogen was not augmented in the presence of fibronectin. The small amount of macrophage-associated fibrin observed in the absence of fibronectin was primarily internalized, whereas the increment in fibrin binding in the presence of fibronectin remained primarily surface bound, as indicated by susceptibility to removal by trypsin. An amino terminal fibrin-binding fragment of plasma fibronectin could similarly support binding of fibrin by peritoneal macrophages. Greater quantities of fibrin were associated with the macrophages in the presence of protease inhibitors, which inhibited elastase activity, but not in the presence of those that inhibited cathepsin activity, suggesting that an elastase-like protease may degrade surface-bound fibrin. Uptake of both fibrin and fibronectin was inhibited by prior treatment of cells with trypsin. Competitive binding studies suggested the presence of a high-affinity fibronectin receptor on peritoneal macrophages. Data from the current study thus support the conclusion that fibronectin augments binding of fibrin to the surface of mononuclear phagocytes.
A Ka-Band Cylindrical Paneled Reflectarray Antenna (2019)

Cylindrical parabolic reflectors have been widely used in those applications requiring high gain antennas. Their design is dictated by the geometric relation of the parabola, which relate the feed location, f, to the radiating aperture, D. In this work, the use of reflectarrays is proposed to increase D without changing the feed location. In the proposed approach, the reflecting surface is loaded with dielectric panels where the phase of the reflected field is controlled using continuous metal strips of variable widths. This solution is enabled by the cylindrical symmetry and, with respect to rectangular patches or to other discrete antennas, it provides increased gain. The proposed concept has been evaluated by designing a Ka-band antenna operating in the Rx SatCom band (19–21 GHz). A prototype has been designed and the results compared with the ones of a parabolic cylindrical reflector using the same feed architecture. Simulated results have shown how this type of antenna can provide higher gain in comparison to the parabolic counterpart, reaching a radiation efficiency of 65%.
Beta-adrenoceptor-blocking drugs and blood sugar control in diabetes mellitus. (1979)

The effects on diabetic control of the relative cardioselective beta-blocker metoprolol and the non-selective drug propranolol were compared in 20 hypertensive diabetic patients receiving diet alone or diet and oral hypoglycaemic agents. Each drug was given for one month in a double-blind, cross-over study. Fasting, noon, and mid-afternoon blood sugar concentrations rose by 1.0-1.5 mmol/l (18-27 mg/100 ml). The rise with propranolol was not significantly greater than with metoprolol. In a few patients the rise was clinically important. The small overall change observed in diabetic control should not deter the use of beta-blockers in non-insulin-dependent diabetics, provided control is carefully monitored at the onset of treatment.
pryB mutations as suppressors of arginine auxotrophy in Salmonella typhimurium (1980)

Salmonella typhimurium strains which produce high constitutive levels of aspartate transcarbamoylase due to the pyrH700 mutation were found to grow more slowly in minimal medium than pyrH+ controls. The addition of arginine or citrulline but not ornithine restored normal growth rates. This requirement for arginine was completely suppressed by pyrB mutations and partially suppressed by pyrC and pyrD mutations. No suppression was observed with mutants at the pyrF locus. Introduction of leaky mutation argI2002 resulted in a more extreme arginine requirement and accentuated suppression by pyrB mutations. Suppression by the pyrC and pyrD mutations was reduced as a result of the incorporation of the leaky argI2002 allele. These results indicate that in pyrH700 strains carbamoyl phosphate is preferentially directed toward the formation of intermediates in the pyrimidine biosynthetic pathway. Arginine auxotrophy results from the reduced availability of carbamoyl phosphate for the biosynthesis of arginine. Suppression of this arginine dependence for growth is used as a convenient positive selection technique for pyrB mutations.
A distributed graphics system for large tiled displays (2003)

Recent interest in large displays has led to renewed development of tiled displays, which are comprised of several individual displays arranged in an array and used as one large logical display. Stanford's "Interactive Mural" is an example of such a display, using an overlapping four by two array of projectors that back-project onto a diffuse screen to form a 6' by 2' display area with a resolution of over 60 dpi. Writing software to make effective use of the large display space is a challenge because normal window system interaction metaphors break down. One promising approach is to switch to immersive applications; another approach, the one we are investigating, is to emulate office, conference room or studio environments which use the space to display a collection of visual material to support group activities. We describe a virtual graphics system that is designed to support multiple simultaneous rendering streams from both local and remote sites. The system abstracts the physical number of computers, graphics subsystems and projectors used to create the display. We provide performance measurements to show that the system scales well and thus supports a variety of different hardware configurations. The system is also interesting because it uses transparent "layers", instead of windows, to manage the screen.
Overexpression of COX-2 but not indoleamine 2,3-dioxygenase-1 enhances the immunosuppressive ability of human umbilical cord-derived mesenchymal stem cells (2015)

Owing to their immunosuppressive properties mesenchymal stem cells (MSCs) are widely applicable in the treatment of autoimmune disease. The aim of this study was to investigate whether the indoleamine 2,3-dioxygenase-1 (IDO-1) and cyclooxygenase-2 (COX-2) genes enhanced the immunosuppressive functional ability of MSCs following stable transfection. To strengthen the immunomodulatory ability of MSCs, IDO-1 and COX-2 were overexpressed in umbilical cord progenitor cell-derived MSCs using recombinant plasmids and electroporation. RT-qPCR analysis and western blotting confirmed the expression of IDO-1 and COX-2 in transfected MSCs. Further functional assays in co-culture experiments, including lymphocyte proliferation and cyto-toxicity assays showed that COX-2-transfected MSCs possessed more potent immunomodulatory cells than the untreated MSCs, or MSCs transfected with IDO-1. Additionally, synthesis of interferon-γ and tumor necrosis factor-α (TNF-α) was significantly inhibited in lymphocytes co-cultured with COX-2-transfected MSCs, which was consistent with changes in immune-related genes in MSCs. An enhanced expression of IDO-1, COX-2, heme-oxygenase-1, inducible nitric-oxide synthase, TNF-α-stimulated gene/protein-6, transforming growth factor-β (TGF-β), human leukocyte antigen molecule 5 (HLA-G5) and interleukin-10 (IL-10) was identified following COX-2 transfection. We showed that the overexpression of COX-2 enhanced the immunosuppressive function of MSCs. COX-2-modified MSCs more potently inhibited the activation and proliferation of peripheral blood mononuclear cells.
Incidence, characterization and prognostic significance of chromosomal abnormalities in 640 patients with primary myelodysplastic syndromes (2000)

Recently, a consensus International Prognostic Scoring System (IPSS) for predicting outcome and planning therapy in the myelodysplastic syndromes (MDS) has been developed. However, the intermediate-risk cytogenetic subgroup defined by the IPSS includes a miscellaneous number of different single abnormalities for which real prognosis at present is uncertain. The main aims of this study were to evaluate in an independent series the prognostic value of the IPSS and to identify chromosomal abnormalities with a previously unrecognized good or poor prognosis in 640 patients. In univariate analyses, cases with single 1q abnormalities experienced poor survival, whereas those with trisomy 8 had a higher risk of acute leukaemic transformation than the remaining patients (P = 0.004 and P = 0.009 respectively). Patients with single del(12p) had a similar survival to patients with a normal karyotype and showed some trend for a better survival than other cases belonging to the IPSS intermediate-risk cytogenetic subgroup (P = 0.045). Multivariate analyses demonstrated that IPSS cytogenetic prognostic subgroup, proportion of bone marrow blasts and haemoglobin level were the main prognostic factors for survival, and the first two characteristics and platelet count were the best predictors of acute leukaemic transformation risk. A large international co-operative study should be carried out to clarify these findings.