gebhart/patrepeval huggingface dataset:
Overview: Engineering Transgenic Constructs and Mice (2009)

Cell biology research encompasses everything from single cells to whole animals. Recent discoveries concerning particular gene functions can be applied to the whole animal for understanding genotype-phenotype relationships underlying disease mechanisms. For this reason, genetically manipulated mouse models are now considered essential to correctly understand disease processes in whole animals. This unit reviews the basic mouse technologies used to generate conventional transgenic mice, which represent a gain-of-function approach. First, an overview of transgenic construct design is presented. This unit then explains basic strategies for the identification and establishment of independent transgenic mouse lines, followed by comments on historical and emerging techniques. It then describes typical problems that are encountered when researchers start to generate transgenic mice.
Aryl Hydrocarbon Receptor-Null Allele Mice Have Hematopoietic Stem/Progenitor Cells with Abnormal Characteristics and Functions (2010)

The aryl hydrocarbon receptor (AhR) belongs to the basic helix-loop-helix family of DNA-binding proteins that play a role in the toxicity and carcinogenicity of certain chemicals. The most potent ligand of the AhR known is 2,3,7,8-tetracholorodibenzo-p-dioxin. We previously reported tetrachlorodibenzo-p-dioxin-induced alterations in numbers and function of hematopoietic stem cells (HSCs). To better understand a possible role of the AhR in hematopoiesis, studies were undertaken in young adult AhR null-allele (KO) mice. These mice have enlarged spleens with increased number of cells from different lineages. Altered expression of several chemokine, cytokine, and their receptor genes were observed in spleen. The KO mice have altered numbers of circulating red and white blood cells, as well as a circadian rhythm-associated 2-fold increase in the number of HSC-enriched Lin(-)Sca-1(+)c-Kit(+) (LSK) cells in bone marrow. Primary cultures of KO HSCs and in vivo bromodeoxyuridine incorporation studies demonstrated an approximate 2-fold increased proliferative ability of these cells. More LSK cells from KO mice were in G(1) and S phases of cell cycle. Competitive repopulation studies also indicated significant functional changes in KO HSCs. LSK cells showed increased expression of Cebpe and decreased expression of several hematopoiesis-associated genes. These data indicate that AhR has a physiological and functional role in hematopoiesis. The AhR appears to play a role in maintaining the normal quiescence of HSCs.
Cell interactions in the initial contact between cultured melanoma cells and syngeneic macrophages. (1979)

Thioglycolate-induces peritoneal macrophages from melanoma-bearing mice (immune macrophages) or from control mice (control macrophages) were cultured with syngeneic melanoma cells (P51) to determine the surface characteristics of the effector cells during interaction and destruction of the target cells. After a short culture period (3 hours), immune macrophages had extensive connections via filopodia and ruffled membranes to the surfaces of the melanoma cells; control macrophages did not exhibit the same behavior. A dense region in the cytoplasm immediately beneath the macrophage plasmalemma was observed at the point of contact with the target tumor cell. With longer periods of culture (24 hours), effector cells began phagocytosis of the target cells; immune macrophages, however, had more fine filopodial connections and were more cytostatic than were controls. These observations indicate that one of the initial mechanisms of tumor cell destruction was contact-induced lysis, with phagocytosis playing a minor part.
A Semi-Automated Methodology for Extracting Access Control Rules from the European Data Protection Directive (2016)

Handling personal data in a legally compliant way is an important factor for ensuring the trustworthiness of a service provider. The EU data protection directive (EU DPD) is built in such a way that the outcomes of rules are subject to explanations, contexts with dependencies, and human interpretation. Therefore, the process of obtaining deterministic and formal rules in policy languages from the EU DPD is difficult to fully automate. To tackle this problem, we demonstrate in this paper the use of a Controlled Natural Language (CNL) to encode the rules of the EU DPD, in a manner that can be automatically converted into the policy languages XACML and PERMIS. We also show that forming machine executable rules automatically from the controlled natural language grammar not only has the benefit of ensuring the correctness of those rules but also has potential of making the overall process more efficient.
Femtosecond pulse generation from a titanium-doped sapphire laser using nonlinear external cavity feedback (1989)

A continuous-wave, argon-ion-pumped, titanium-doped sapphire laser has been constructed. Pulses of 80-psec duration obtained through active mode locking have been compressed to less than 800 fsec using nonlinear external cavity feedback.
Vaccination with Purified Dr Fimbriae Reduces Mortality Associated with Chronic Urinary Tract Infection Due toEscherichia coliBearing Dr Adhesin (2004)

The vaccination of C3H/HeJ mice with Escherichia coli Dr fimbrial antigen reduced mortality associated with an experimental urinary tract infection due to a homologous strain bearing Dr adhesin. Immune sera with high titers of anti-Dr antibody inhibited bacterial binding to bladders and kidneys but did not affect the rate of renal colonization.
Factors Associated with Esophageal Candidiasis and Its Endoscopic Severity in the Era of Antiretroviral Therapy (2013)

Low CD4+ counts and high HIV VL were found to be factors associated with CE, and advanced immunosuppression was associated with the development of severity. Endoscopy is useful as it can detect CE, even severe CE, in patients without GI symptoms, those with high CD4 counts, and those without oral candidiasis.
Sclerosing Cholangitis in Ulcerative Colitis (1982)

In the 5-year period 1974-78, 48 (14%) of 336 patients with ulcerative colitis were found to have hepatobiliary disease. Endoscopic retrograde cholangiography (ERC) was successfully performed in 39 of these 48 patients, and sclerosing cholangitis was demonstrated in 19. One is excluded from this series because Crohn's disease was diagnosed at reclassification of the bowel disease. Two of the 18 patients with ulcerative colitis and sclerosing cholangitis have died, one of cholangiocarcinoma and one of an unrelated cause. The remaining 16 patients have been observed for a median period of 6 years (3-13 years) since the diagnosis of hepatobiliary disease. Ten have remained symptom-free, four have had intermittent or non-progressive symptoms, and two have developed symptoms of advanced chronic liver disease. The bilirubin level, which was initially raised in one of the patients, was elevated in four at the follow-up examination. Otherwise the laboratory values have remained stationary. Evidence of a progression of the hepatobiliary disease was found in most patients by repeated liver biopsy and particularly ERC. It is concluded that sclerosing cholangitis may remain asymptomatic for several years. Since progressive cholangiographic changes were often seen without concomitant worsening of symptoms, laboratory data, and liver biopsy findings, it is concluded that these criteria are of limited use in evaluating the progression of this disease.
The digital compression facility-a solution to today's compression needs (2002)

Compression of motion video and hi-fidelity audio for real-time playback targeted at a number of different playback platforms has entered the domain of big business. The choice of architectures for this compression is varied. The most versatile solution for compression uses a general-purpose supercomputer-class computer. This choice allows for the highest quality moving pictures expert group (MPEG) compression by providing the mechanisms for processing of video and audio to follow any number of tunable, user-definable, customizable and computationally expensive operations.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
An Italian family with autosomal recessive inclusion-body myopathy and mutations in the GNE gene (2002)

The term hereditary inclusion-body myopathies (h-IBM) refers to several syndromes with autosomal recessive (AR) or dominant inheritance.1 Although clinical presentation may vary among different forms, they all lead to severe disability and share common findings at muscle biopsy. The most common form of AR h-IBM, originally described in Persian-Jewish (PJ) patients, is characterized by onset in the second to third decade of life with weakness and atrophy of distal lower limb muscles, progressing proximally with relative sparing of the quadriceps.1

AR h-IBM is associated with mutations in the UDP-N-acetylglucosamine 2-epimerase/N-acetylmannosamine kinase ( GNE ) gene on chromosome 9p12–13.2 A homozygous T→C mutation at nucleotide position (np) 2186 in the GNE gene, converting methionine to threonine, was found in all PJ patients, whereas patients of other ethnic origins were compound heterozygotes for other mutations.2 GNE mutations have been found in patients with AR Nonaka myopathy, another form of h-IBM.1,3⇓ GNE is a bifunctional enzyme with epimerase and kinase activities, which has a critical role in sialic acid biosynthesis.4

In this current study an Italian family with AR quadriceps-sparing h-IBM, previously shown to be linked to …
Peptide- and Aptamer-Functionalized Nanovectors for Targeted Delivery of Therapeutics (2009)

Targeted delivery of therapeutics is an area of vigorous research, and peptide- and aptamer-functionalized nanovectors are a promising class of targeted delivery vehicles. Both peptide- and aptamer-targeting ligands can be readily designed to bind a target selectively with high affinity, and more importantly are molecules accessible by chemical synthesis and relatively compact compared with antibodies and full proteins. The multitude of peptide ligands that have been used for targeted delivery are covered in this review, with discussion of binding selectivity and targeting performance for these peptide sequences where possible. Aptamers are RNA or DNA strands evolutionarily engineered to specifically bind a chosen target. Although use of aptamers in targeted delivery is a relatively new avenue of research, the current state of the field is covered and promises of future advances in this area are highlighted. Liposomes, the classic drug delivery vector, and polymeric nanovectors functionalized with peptide or aptamer binding ligands will be discussed in this review, with the exclusion of other drug delivery vehicles. Targeted delivery of therapeutics, from DNA to classic small molecule drugs to protein therapeutics, by these targeted nanovectors is reviewed with coverage of both in vitro and in vivo deliveries. This is an exciting and dynamic area of research and this review seeks to discuss its broad scope.
Assessment of the beta-adrenergic receptor pathway in the intact failing human heart: progressive receptor down-regulation and subsensitivity to agonist response. (1986)

We developed methods for identifying beta-adrenergic receptors in human right ventricular endomyocardial biopsy tissue with the radioligand (-)[125I]iodocyanopindolol (ICYP). Specific ICYP binding in a crude, high-yield membrane preparation derived from endomyocardial biopsy tissue was high (specificity greater than 90%), of high affinity (KD around 20 pM), saturable and stereospecific for the (-) vs the (+) isomer of isoproterenol. Subjects with mild-moderate and severe biventricular dysfunction had respective decreases in beta-adrenergic receptor density of 38.2% and 57.7% when normalization methods were averaged, with no significant differences in ICYP dissociation constant. A subgroup of subjects was subdivided by left ventricular ejection fraction (LVEF) into those with mild cardiac dysfunction (LVEF less than 0.50 greater than 0.40) and severe heart failure (LVEF less than 0.20) and given graded sequential infusions of dobutamine and calcium gluconate. Those with severe cardiac dysfunction had marked impairment of the dobutamine dP/dt and stroke work index response, whereas these responses to calcium did not differ in the two groups. These data indicate that in the intact human heart endomyocardial biopsy may be used for direct analysis of beta-adrenergic receptors, heart failure-associated myocardial beta-adrenergic down-regulation begins with mild-moderate ventricular dysfunction, reduction in myocardial beta-receptor density is related to degree of heart failure, and beta-receptor down-regulation is associated with pharmacologically specific impairment of the beta-agonist-mediated contractile response.
Effects of Ginsenoside Rbi on Central Cholinergic Metabolism (1991)

Ginsenosides, the saponins of ginseng, are bioactive ingredients which exert many beneficial effects. One ginsenoside, Rb1, extracted from North American ginseng (Panax quinquefolium L.), partially prevents the memory deficits induced by a cholinergic agent (scopolamine) in rats. In vitro studies show that Rb1 has no effect on quinuclidinyl benzylate binding or on acetylcholinesterase activity, but facilitates the release of acetylcholine (ACh) from hippocampal slices. The increase in ACh release is associated with an increased uptake of choline into nerve endings; however, calcium influx is unaltered. The ability of Rb1 to prevent memory deficits may be related to facilitation of ACh metabolism in the central nervous system.
Cardiovascular Disease Risk in Adult Women with Congenital Adrenal Hyperplasia Due to 21-Hydroxylase Deficiency (2009)

Congenital adrenal hyperplasia (CAH) due to 21-hydroxylase deficiency is a common autosomal recessive disorder characterized by impaired cortisol biosynthesis, with or without aldosterone deficiency, and androgen excess. Patients with the classic (severe) form also have epinephrine deficiency. Patients with CAH have an increased prevalence of risk factors for cardiovascular disease including obesity, hypertension, and insulin resistance. Androgen excess in women appears to be an additional risk factor for cardiovascular disease. Carotid intima-media thickness, a measure of subclinical atherosclerosis, also has been found to be increased in adults with CAH. The multiple hormonal imbalances present in the adult woman with CAH, in combination with chronic glucocorticoid therapy, contribute to cardiovascular disease risk. Further investigation of the predisposition to cardiovascular disease in women with CAH is warranted. Longitudinal studies are needed, and interventions targeting obesity, insulin resistance, hypertension, and hyperandrogenism may offer improved outcome.
"GrabCut" (2004)

The problem of efficient, interactive foreground/background segmentation in still images is of great practical importance in image editing. Classical image segmentation tools use either texture (colour) information, e.g. Magic Wand, or edge (contrast) information, e.g. Intelligent Scissors. Recently, an approach based on optimization by graph-cut has been developed which successfully combines both types of information. In this paper we extend the graph-cut approach in three respects. First, we have developed a more powerful, iterative version of the optimisation. Secondly, the power of the iterative algorithm is used to simplify substantially the user interaction needed for a given quality of result. Thirdly, a robust algorithm for "border matting" has been developed to estimate simultaneously the alpha-matte around an object boundary and the colours of foreground pixels. We show that for moderately difficult examples the proposed method outperforms competitive tools.
Identification of β-Adrenoceptor Subtypes in Lower Urinary Tract of the Female Pig (2002)

Apparently beta3-adrenoceptors are the predominant beta-adrenoceptor subtype present in the lower urinary tract of the pig.
Proteomic Analysis of Human Cervico-Vaginal Fluid (2007)

Human cervico-vaginal fluid (CVF) is a mixture of fluids originating from the vagina, cervix, endometrium, and oviduct. CVF has been shown to play an important role in protecting the vagina from infection. We used "bottom-up" proteomic approaches to characterize the protein repertoire of human CVF. We applied two different sample prefractionation methods, one-dimensional-SDS-PAGE (1D-SDS-PAGE) and strong cation-exchange chromatography, followed by LC-MS/MS and bioinformatic analysis. We identified a total of 685 proteins. Strong cation-exchange chromatography prefractionation resulted in a larger number of proteins identified when compared with 1D-SDS-PAGE. Extracellular or membrane proteins made up 30% of the proteins identified, according to Genome Ontology (GO) classifications. We confirmed the presence of defense-related proteins, such as haptoglobin, defensins, and lactoferrin; and identified new ones such as azurocidin and dermcidin. We also identified many serine and cysteine proteases, including 6 members of the kallikrein family (KLKs 6, 7, 10, 11, 12, and 13). The same KLKs were also confirmed quantitatively by ELISA assays. Knowledge of the CVF proteome will aid in the discovery of potential biomarkers for gynecological malignancies and infections and provide additional clues for its physiological functions.
Endosomal Translocation of CpG-Oligodeoxynucleotides Inhibits DNA-PKcs-Dependent IL-10 Production in Macrophages (2008)

Synthetic oligodeoxynucleotides containing unmethylated CpG motifs (CpG-ODNs) function as powerful immune adjuvants by activating macrophages, dendritic cells, and B cells. However, the molecular recognition mechanism that initiates signaling in response to CpG-ODN has not fully been identified. We show in this study that peritoneal macrophages from SCID mice having mutations in the catalytic subunit of DNA-protein kinase (DNA-PKcs) were almost completely defective in the production of IL-10 and in ERK activation when treated with CpG-ODN. In contrast, IL-12 p70 production significantly increased. Furthermore, small interfering RNA (siRNA)-mediated knockdown of DNA-PKcs expression in the mouse monocyte/macrophage cell line RAW264.7 led to reduced IL-10 production and ERK activation by CpG-ODN. IL-10 and IL-12 p70 production, but not ERK activation, are blocked by chloroquine, an inhibitor of endosomal acidification. Endosomal translocation of CpG-ODN in a complex with cationic liposomes consisting of 1,2-dioleoyl-3-trimethylammonium-propane (DOTAP) (CpG-DOTAP-liposomes) decreased IL-10 production and ERK activation, whereas the endosomal escape of CpG-ODN in a complex with cationic liposomes consisting of DOTAP and dioleyl-phosphatidylethanolamine (DOPE) (CpG-DOTAP/DOPE-liposomes) increased. In contrast, IL-12 p70 production was increased by CpG-DOTAP-liposomes and decreased by CpG-DOTAP/DOPE-liposomes. IL-10 production induced by CpG-DOTAP/DOPE-liposomes was not observed in macrophages from SCID mice. Thus, our findings suggest that DNA-PKcs in the cytoplasm play an important role in CpG-ODN-induced production of IL-10 in macrophages. In addition, DNA-PKcs-mediated production of IL-10 and IL-12 p70 can be regulated by manipulating the intracellular trafficking of CpG-ODN in macrophages.
The development of articular cartilage: I. The spatial and temporal patterns of collagen types. (1996)

Articular cartilage is both morphologically and biochemically heterogeneous. Its susceptibility to degenerative diseases such as arthritis and its limited repair capacity have made cartilage the focus of intense study; surprisingly, little is known of its development. Using a panel of specific antibodies, we have documented the temporal and spatial patterns of collagen types I, II, III, VI and X in the developing knee cartilage of the marsupial Monodelphis domestica from parturition to adulthood. Type I collagen was initially detected in the presumptive articular cartilage of the epiphyses in addition to the perichondrium. By 14 d postparturition, type I collagen was not detectable in the epiphyseal cartilage apart from insertion sites of ligaments and tendons of the joint. Similarly, type III collagen was detected at insertion sites of the major ligaments and tendons and within the perichondrium/periosteum but was never detected in the cartilage per se. Type II collagen was predictably distributed throughout the cartilage matrix and was also detected in the perichondrium. Type VI collagen was widely distributed throughout the cartilage matrix at parturition, but during development became restricted to a pericellular location particularly towards the presumptive articular cartilage, i.e. the epiphysis. Interestingly, generalised matrix immunopositivity was only retained in the hypertrophic cartilage of the secondary centre of ossification. After the formation of the secondary centre, type VI collagen became localised pericellularly in the deeper regions of the articular cartilage but was absent in the cartilage of the growth plate. Type X collagen showed a novel distribution pattern. In addition to being synthesised by hypertrophic chondrocytes, this collagen type was also expressed transiently by some cells at the presumptive articular surface. Furthermore, these surface chondrocytes also stained histochemically for alkaline phosphatase, suggesting that they were terminally differentiated. The fate of these terminally differentiated cells is unknown.
Identification and characterization of cellular receptors for the growth regulator, oncostatin M (1989)

Oncostatin M is a polypeptide growth regulator produced by activated T cells and phorbol ester-treated U937 cells. To identify specific cellular receptors for this factor, we have characterized the binding of 125I-labeled oncostatin M to a variety of normal and malignant mammalian cells. Recombinant oncostatin M was labeled with 125I with full retention of growth inhibitory activity on A375 melanoma cells. 125I-Oncostatin M bound to sensitive cells in a time- and temperature-dependent fashion. Binding was specifically inhibited by unlabeled native or recombinant oncostatin M, but not by other polypeptide growth factors tested. Binding to human leukemic and normal blood cells was generally less than to nonhematopoietic cells. With four different cell lines, maximal growth inhibition by oncostatin M was achieved at less than maximal binding site occupancy. Scatchard graphs of direct binding data were curvilinear and indicated that 125I-oncostatin M bound with higher apparent affinity at lower 125I-oncostatin M concentrations. Using a two binding site model, affinity constants of Kd1 = 11 +/- 11 pM and Kd2 = 1000 +/- 380 pM were extrapolated from binding data with A375 cells, and values of Kd1 = 3 +/- 2 pM and Kd2 = 400 +/- 44 pM from A549 cells. The major 125I-oncostatin M binding species in a number of mammalian cell lines was identified by chemical cross-linking as a specific protein(s) of Mr = 150,000-160,000. 125I-Oncostatin M was internalized (t1/2 = 30 min) and degraded subsequent to binding to a responsive cell line.(ABSTRACT TRUNCATED AT 250 WORDS)