gebhart/patrepeval huggingface dataset:
Expression in plants of two bacterial antibiotic resistance genes after protoplast transformation with a new plant expression vector (1986)

Two bacterial antibiotic resistance genes, one coding for the neomycin phosphotransferase (NPT I) from Tn903, and the other coding for the chloramphenicol acetyltransferase from Tn9 were used as plant selectable markers. Both genes were introduced into the Nicotiana tabacum genome in a new plant expression vector, using the direct gene transfer method. The vector pDH51, used in these experiments contains a plant expression unit as a movable cassette, consisting of the strong cauliflower mosaic virus (CaMV) 35S RNA promoter and transcription terminator separated by a polylinker containing several unique restriction sites.
Mouse Model of Mutated in Colorectal Cancer Gene Deletion Reveals Novel Pathways in Inflammation and Cancer (2019)

Loss of Mcc may promote cancer through a failure to repair inflammation-induced DNA damage. We provide a comprehensive transcriptome data set of early colorectal lesions and evidence for the in vivo significance of MCC silencing in colorectal cancer.
Effects of Vagal Stimulation on Experimentally Induced Seizures in Rats (1990)

Repetitive stimulation of the vagus nerve inhibits chemically induced seizures in dogs. We report here the results and conclusions from studies designed to answer some of the immediate questions raised by this finding. (1) Maximal stimulation of vagal C fibers at frequencies greater than 4 Hz prevents or reduces chemically and electrically induced seizures in young male rats. (2) Antiepileptic potency is directly related to the fraction of vagal C fibers stimulated. (3) Vagal stimulation shortens but does not shut down a chemical seizure once it has begun. (4) In rats, optimal stimulus frequency is approximately 10-20 Hz; duration of stimulus, 0.5-1 ms; and stimulus strength, 0.2-0.5 mA/mm2 of nerve cross-section. These results, when taken together with similar results obtained from dogs, monkeys, and humans, strongly suggest that periodic stimulation of the vagus nerve using appropriate stimulation parameters is a powerful method for preventing seizures. The data from the literature suggest that the antiepileptic actions of vagal stimulation are largely mediated by widespread release of GABA and glycine in the brainstem and cerebral cortex. The probable pathway is via projections from the nucleus of the solitary tract to the reticular formation and thence by diffuse projections to the cortex and other areas. Intermittent vagal stimulation has the potentiality of reducing the number and/or the intensity of seizures in patients with intractable epilepsy. These results indicate that feasibility studies in humans should be continued and expanded.
Heart Atria Granularity Effects of Changes in Water-Electrolyte Balance (1979)

SummaryAtrial granularity was measured using a new morphometric method in rats subjected to procedures known to alter water-electrolyte balance. It was found that water deprivation and sodium deficiency lead to atrial hypergranulation, whereas, the combined administration of desoxycorticosterone (2.5 mg/100 g body wt/day) and 2% NaCl in the drinking water leads to degranulation. A statistically significant correlation was found between atria granularity and hematocrit values in water deprivation; animals with higher hematocrit had more granules. The findings point to a relationship between atrial-specific granules and the regulation of water-electrolyte balance in these situations.
Phytocannabinoids: a unified critical inventory (2016)

Covering up to January 2016Cannabis sativa L. is a prolific, but not exclusive, producer of a diverse group of isoprenylated resorcinyl polyketides collectively known as phytocannabinoids. The modular nature of the pathways that merge into the phytocannabinoid chemotype translates in differences in the nature of the resorcinyl side-chain and the degree of oligomerization of the isoprenyl residue, making the definition of phytocannabinoid elusive from a structural standpoint. A biogenetic definition is therefore proposed, splitting the phytocannabinoid chemotype into an alkyl- and a β-aralklyl version, and discussing the relationships between phytocannabinoids from different sources (higher plants, liverworts, fungi). The startling diversity of cannabis phytocannabinoids might be, at least in part, the result of non-enzymatic transformations induced by heat, light, and atmospheric oxygen on a limited set of major constituents (CBG, CBD, Δ<sup>9</sup>-THC and CBC and their corresponding acidic versions), whose degradation is detailed to emphasize this possibility. The diversity of metabotropic (cannabinoid receptors), ionotropic (thermos-TRPs), and transcription factors (PPARs) targeted by phytocannabinoids is discussed. The integrated inventory of these compounds and their biological macromolecular end-points highlights the opportunities that phytocannabinoids offer to access desirable drug-like space beyond the one associated to the narcotic target CB<sub>1</sub>.
Immunogenetic and protective activity of an extract of Schistosoma mansoni (1982)

The immunogenic and protective activity of an extract of S. mansoni, obtained by incubation of viable adult worms in buffered saline, was evaluated in rabbits and mice. Animal immunization with this extract resulted in the development of both humoral and cellular immune response. All immunized rabbits developed high levels (91 to 100%) of cytotoxic antibodies as determined by in vitro assays of cytotoxic activity of their sera against viable schistosomules. Immunized animals challenged with S. mansoni cercariae showed a lower parasite load than that of normal controls. Protective activity was 88.6% and 54.0% in immunized rabbits and mice, respectively.
Lungs are a major organ site of cytomegalovirus latency and recurrence (1993)

Recurrence of infectious virus from the latent viral genomes is the initiating event in the pathogenesis of cytomegalovirus (CMV) disease during states of immunodeficiency. Interstitial pneumonia is a frequent manifestation of posttransplantation CMV disease, in particular after bone marrow transplantation and heart and lung transplantations. Recurrence can occur within the transplant derived from a latent infected donor as well as within latently infected organs of the transplant recipient. The reason for a predilection of the lungs as a site of CMV pathology is so far unknown. In a murine model of CMV latency, the lungs were identified as an authentic site of latent infection, since the viral genome remained detectable in lung tissue even after it was cleared to an undetectable level in blood and bone marrow. A comparison between the lungs and the spleen, the previously most thoroughly investigated site of murine CMV latency, revealed a 10-fold-higher burden of latent viral genome for the lungs. Most important, the organ-specific risk of in vivo recurrence was found to correlate with the organ-specific viral genomic load. This new finding thus characterizes the lungs as a high-risk organ for CMV recurrence, and this fact may explain in part why interstitial pneumonia is a frequent manifestation of recurrent CMV infection.
Analysis of Electromagnetic Field Polarizations in Multiantenna Systems (2004)

This paper provides an analytical framework useful for assessing the use of all six electric and magnetic electromagnetic field polarizations for multiantenna communications systems. The approach uses a mapping between the induced signal currents and the received electromagnetic field in order to formulate a diversity interpretation of the six-polarization problem. Application of the framework to a simple, yet representative, channel model demonstrates that for full multipath elevation and azimuthal angle spread, six communication modes are theoretically possible. However, to implement the system requires more antenna design work since a straightforward implementation is found to reduce the potential number of modes to three.
LC-MS/MS Quantification of Sulforaphane and Indole-3-carbinol Metabolites in Human Plasma and Urine after Dietary Intake of Selenium-Fortified Broccoli (2011)

This study aimed at developing a sensitive LC-MS/MS method for the quantification of sulforaphane (SFN) and indole-3-carbinol metabolites in plasma and urine after dietary intake of regular and selenium-fertilized broccoli using stable isotope dilution analysis. In a three-armed, placebo-controlled, randomized human intervention study with 76 healthy volunteers, 200 g of regular (485 μg of total glucosinolates and <0.01 μg of selenium per gram fresh weight) or selenium-fertilized broccoli (589 μg of total glucosinolates and 0.25 μg of selenium per gram fresh weight) was administered daily for 4 weeks. Glucoraphanin and glucobrassicin metabolites quantified in plasma and urine were SFN-glutathione, SFN-cysteine, SFN-cysteinylglycine, SFN-acetylcysteine, and indole-3-carboxaldehyde, indole-3-carboxylic acid, and ascorbigen, respectively. Dietary intake of selenium-fertilized broccoli increased serum selenium concentration analyzed by means of atomic absorption spectroscopy by up to 25% (p < 0.001), but affected neither glucosinolate concentrations in broccoli nor their metabolite concentrations in plasma and urine compared to regular broccoli.
The Effects of Low Levels of Dystrophin on Mouse Muscle Function and Pathology (2012)

Duchenne muscular dystrophy (DMD) is a severe progressive muscular disorder caused by reading frame disrupting mutations in the DMD gene, preventing the synthesis of functional dystrophin. As dystrophin provides muscle fiber stability during contractions, dystrophin negative fibers are prone to exercise-induced damage. Upon exhaustion of the regenerative capacity, fibers will be replaced by fibrotic and fat tissue resulting in a progressive loss of function eventually leading to death in the early thirties. With several promising approaches for the treatment of DMD aiming at dystrophin restoration in clinical trials, there is an increasing need to determine more precisely which dystrophin levels are sufficient to restore muscle fiber integrity, protect against muscle damage and improve muscle function.To address this we generated a new mouse model (mdx-Xist(Δhs)) with varying, low dystrophin levels (3-47%, mean 22.7%, stdev 12.1, n = 24) due to skewed X-inactivation. Longitudinal sections revealed that within individual fibers, some nuclei did and some did not express dystrophin, resulting in a random, mosaic pattern of dystrophin expression within fibers.Mdx-Xist(Δhs), mdx and wild type females underwent a 12 week functional test regime consisting of different tests to assess muscle function at base line, or after chronic treadmill running exercise. Overall, mdx-Xist(Δhs) mice with 3-14% dystrophin outperformed mdx mice in the functional tests. Improved histopathology was observed in mice with 15-29% dystrophin and these levels also resulted in normalized expression of pro-inflammatory biomarker genes, while for other parameters >30% of dystrophin was needed. Chronic exercise clearly worsened pathology, which needed dystrophin levels >20% for protection. Based on these findings, we conclude that while even dystrophin levels below 15% can improve pathology and performance, levels of >20% are needed to fully protect muscle fibers from exercise-induced damage.
Error analysis of an optical current transducer operating with a digital signal processing system (2000)

This paper analyzes errors associated with the analog-to-digital (A/D) conversion process of a digital signal processing unit (DSP) within the operation of an optical current transducer (OCT). Quantization of the analog current measurement signal leads to measurement errors which are a direct consequence of the uncertainty with which an N-bit resolution A/D assigns a binary word for a given analog input value. This paper presents comprehensive simulations of the performance of different current sensors monitored by the DSP unit and discusses aspects of compatibility between the sensor dynamic range and the resolution of an A/D conversion process. Recommendations are given on how to match the OCT to the given A/D parameters, and vice versa, in order to meet specified accuracy requirements.
Molecular and flow cytometric analysis of the Vβ repertoire for clonality assessment in mature TCRαβ T-cell proliferations (2001)

Clonality assessment through Southern blot (SB) analysis of TCRB genes or polymerase chain reaction (PCR) analysis of TCRG genes is important for diagnosing suspect mature T-cell proliferations. Clonality assessment through reverse transcription (RT)-PCR analysis of Vbeta-Cbeta transcripts and flow cytometry with a Vbeta antibody panel covering more than 65% of Vbeta domains was validated using 28 SB-defined clonal T-cell receptor (TCR)alphabeta(+) T-ALL samples and T-cell lines. Next, the diagnostic applicability of the V(beta) RT-PCR and flow cytometric clonality assays was studied in 47 mature T-cell proliferations. Clonal Vbeta-Cbeta RT-PCR products were detected in all 47 samples, whereas single Vbeta domain usage was found in 31 (66%) of 47 patients. The suspect leukemic cell populations in the other 16 patients showed a complete lack of Vbeta monoclonal antibody reactivity that was confirmed by molecular data showing the usage of Vbeta gene segments not covered by the applied Vbeta monoclonal antibodies. Nevertheless, this could be considered indirect evidence for the "clonal" character of these cells. Remarkably, RT-PCR revealed an oligoclonal pattern in addition to dominant Vbeta-Cbeta products and single Vbeta domain expression in many T-LGL proliferations, providing further evidence for the hypothesis raised earlier that T-LGL derive from polyclonal and oligoclonal proliferations of antigen-activated cytotoxic T cells. It is concluded that molecular Vbeta analysis serves to assess clonality in suspect T-cell proliferations. However, the faster and cheaper Vbeta antibody studies can be used as a powerful screening method for the detection of single Vbeta domain expression, followed by molecular studies in patients with more than 20% single Vbeta domain expression or large suspect T-cell populations (more than 50%-60%) without Vbeta reactivity.
Protofoil (1994)

Although the document imaging industry has taken off in the last few years, document image filing for the individual information worker is still not widespread or effective. In this paper, we focus on building an electronic tiling system for paper documents that supports the ad hoc, multifarious work of information workers. Motivated by interviews with researchers and a survey of descriptive studies of paper document filing, we have focussed on minimizing or delaying costs of document filing and supporting a rich variety of methods for accessing and using stored documents. We have implemented a prototype system called Protofoil for storing, retrieving, and manipulating paper documents as electronic images that integrates many user interface-paper and workstation—and information retrieval technologies. Protofoil has been tested through use in our laboratory. and has been deployed in a field study at a lawyer’s office.
Biorefining: Heterogeneously Catalyzed Reactions of Carbohydrates for the Production of Furfural and Hydroxymethylfurfural (2011)

Furfurals are important intermediates in the chemical industry. They are typically produced by homogeneous catalysis in aqueous solutions. However, heterogeneously catalyzed processes would be beneficial in view of the principles of green chemistry: the elimination of homogeneous mineral acids makes the reaction mixtures less corrosive, produces less waste, and facilitates easy separation and recovery of the catalyst. Finding an active and stable water-tolerant solid acid catalyst still poses a challenge for the production of furfural (furan-2-carbaldehyde) and 5-(hydroxymethyl)-2-furaldehyde (HMF). Furfural is produced in the dehydration of xylose, and HMF is formed from glucose and fructose in the presence of an acidic catalyst. Bases are not active in dehydration reaction but do catalyze the isomerization of monosaccharides, which is favorable when using glucose as a raw material. In addition to the desired dehydration of monosaccharides, many undesired side reactions take place, reducing the selectivity and deactivating the catalyst. In addition, the catalyst properties play an important role in the selectivity. In this Review, catalytic conversion approaches are summarized, focusing on the heterogeneously catalyzed formation of furfural. The attractiveness of catalytic concepts is evaluated, keeping in mind productivity, sustainability, and environmental footprint.
HLA class I supertypes: a revised and updated classification (2008)

As a result of this updated analysis, HLA supertype associations have been defined for over 750 different HLA-A and -B alleles. This information is expected to facilitate epitope identification and vaccine design studies, as well as investigations into disease association and correlates of immunity. In addition, the approach utilized has been made more transparent, allowing others to utilize the classification approach going forward.
Circulating antibodies to Saccharomyces cerevisiae (bakers'/brewers' yeast) in gastrointestinal disease. (1999)

Raised antibodies to yeast, although not completely specific for Crohn's disease, may have a future role in diagnosis. The assays described here could be used to address this question in the context of a prospective study.
Collateral Nervous Damages After Cryoballoon Pulmonary Vein Isolation (2011)

Gastroparesis and PNP could be observed in a significant number of cases after cryoballoon ablation of AF. These complications are likely due to cryo-induced damages to nervous structures surrounding the heart.
Gain limiting processes in Er-doped Si nanocrystal waveguides in SiO2 (2002)

Erbium-doped Si nanocrystal based optical waveguides were formed by Er and Si ion implantation into SiO2. Optical images of the waveguide output facet show a single, well-confined optical mode. Transmission measurements reveal a clear Er related absorption of 2.7 dB/cm at 1.532 μm, corresponding to a cross section of 8×10−20 cm2. The Si nanocrystals act as sensitizers for Er but under high doping conditions (∼50 Er ions per nanocrystals) no pump-induced change in the Er related absorption is observed under optical pumping (λ=458 nm), which is ascribed to an Auger quenching effect. For very high pump powers, a broad absorption feature is observed, attributed to free carrier absorption.
A study on the transmission characteristics of the human body towards broadband intra-body communications (2005)

Intra-body communications is becoming a promising solution for body area networks with a lot of interesting potential applications towards a ubiquitous communication world. Our research is based on the near-field radio, wherein electromagnetic radio signals are transmitted through the human body from a transmitter to a receiver. In contrast with current studies, we aim to study the transmission characteristics of the human body as a conductor of radio signals with higher frequency carriers (up to 1400 MHz) in order to find an optimal frequency range for implementing, at last, broadband intra-body communications with high data rates. To achieve our first goal, we carry out experiments where we investigate the delay time profile and the attenuation of the received signal.
Management of Hyperglycemia in Type 2 Diabetes: A Consensus Algorithm for the Initiation and Adjustment of Therapy (2006)

The epidemic of type 2 diabetes in the latter part of the 20th and in the early 21st century, and the recognition that achieving specific glycemic goals can substantially reduce morbidity, have made the effective treatment of hyperglycemia a top priority (1–3). While the management of hyperglycemia, the hallmark metabolic abnormality associated with type 2 diabetes, has historically had center stage in the treatment of diabetes, therapies directed at other coincident features, such as dyslipidemia, hypertension, hypercoagulability, obesity, and insulin resistance, have also been a major focus of research and therapy. Maintaining glycemic levels as close to the nondiabetic range as possible has been demonstrated to have a powerful beneficial impact on diabetes-specific complications, including retinopathy, nephropathy, and neuropathy in the setting of type 1 diabetes (4,5); in type 2 diabetes, more intensive treatment strategies have likewise been demonstrated to reduce complications (6–8). Intensive glycemic management resulting in lower HbA1c (A1C) levels has also been shown to have a beneficial effect on cardiovascular disease (CVD) complications in type 1 diabetes (9,10); however, the role of intensive diabetes therapy on CVD in type 2 diabetes remains under active investigation (11,12). Some therapies directed at lowering glucose levels have additional benefits with regard to CVD risk factors, while others lower glucose without additional benefits.

The development of new classes of blood glucose–lowering medications to supplement the older therapies, such as lifestyle-directed interventions, insulin, sulfonylureas, and metformin, has increased the treatment options for type 2 diabetes. Whether used alone or in combination with other blood glucose–lowering interventions, the availability of the newer agents has provided an increased number of choices for practitioners and patients and heightened uncertainty regarding the most appropriate means of treating this widespread disease. Although numerous reviews on the …
Disease Ontology: a backbone for disease semantic integration (2011)

The Disease Ontology (DO) database (http://disease-ontology.org) represents a comprehensive knowledge base of 8043 inherited, developmental and acquired human diseases (DO version 3, revision 2510). The DO web browser has been designed for speed, efficiency and robustness through the use of a graph database. Full-text contextual searching functionality using Lucene allows the querying of name, synonym, definition, DOID and cross-reference (xrefs) with complex Boolean search strings. The DO semantically integrates disease and medical vocabularies through extensive cross mapping and integration of MeSH, ICD, NCI's thesaurus, SNOMED CT and OMIM disease-specific terms and identifiers. The DO is utilized for disease annotation by major biomedical databases (e.g. Array Express, NIF, IEDB), as a standard representation of human disease in biomedical ontologies (e.g. IDO, Cell line ontology, NIFSTD ontology, Experimental Factor Ontology, Influenza Ontology), and as an ontological cross mappings resource between DO, MeSH and OMIM (e.g. GeneWiki). The DO project (http://diseaseontology.sf.net) has been incorporated into open source tools (e.g. Gene Answers, FunDO) to connect gene and disease biomedical data through the lens of human disease. The next iteration of the DO web browser will integrate DO's extended relations and logical definition representation along with these biomedical resource cross-mappings.
Brca1 breast tumors contain distinct CD44+/CD24- and CD133+cells with cancer stem cell characteristics (2008)

Brca1-deficient mouse mammary tumors harbor heterogeneous cancer stem cell populations, and CD44+/CD24- cells represent a population that correlates with human breast cancer stem cells.