gebhart/patrepeval huggingface dataset:
Campylobacter enteritis: a "new" disease. (1977)

By selective culture campylobacters (C jejuni and C coli) were isolated from the faeces of 57 (7-1%) out of 803 unselected patients with diarrhoea; none were isolated from 194 people who had not got diarrhoea. Specific agglutinins were found in the sera of 31 out of 38 patients with campylobacter enteritis and 10 of them had a rising titre. Half the patients were aged 15 to 44 years, but the incidence was highest in young children. All the patients with campylobacters had a distinctive clinical illness with severe abdominal pain. Campylobacters are a relatively unrecognised cause of acute enteritis, but these findings suggest that they may be a common cause. Spread of infection was observed within 12 out of 29 households, and in these cases children were usually implicated. Several patients were apparently infected from chickens, both live and dressed, and poultry may be the primary source of the organism. In two cases dogs with diarrhoea were found to be infected with strains indistinguishable from their human contacts. Ten patients acquired their infections while travelling abroad.
Folate Deficiency Induces Neurodegeneration and Brain Dysfunction in Mice Lacking Uracil DNA Glycosylase (2008)

Folate deficiency and resultant increased homocysteine levels have been linked experimentally and epidemiologically with neurodegenerative conditions like stroke and dementia. Moreover, folate deficiency has been implicated in the pathogenesis of psychiatric disorders, most notably depression. We hypothesized that the pathogenic mechanisms include uracil misincorporation and, therefore, analyzed the effects of folate deficiency in mice lacking uracil DNA glycosylase (Ung-/-) versus wild-type controls. Folate depletion increased nuclear mutation rates in Ung-/- embryonic fibroblasts, and conferred death of cultured Ung-/- hippocampal neurons. Feeding animals a folate-deficient diet (FD) for 3 months induced degeneration of CA3 pyramidal neurons in Ung-/- but not Ung+/+ mice along with decreased hippocampal expression of brain-derived neurotrophic factor protein and decreased brain levels of antioxidant glutathione. Furthermore, FD induced cognitive deficits and mood alterations such as anxious and despair-like behaviors that were aggravated in Ung-/- mice. Independent of Ung genotype, FD increased plasma homocysteine levels, altered brain monoamine metabolism, and inhibited adult hippocampal neurogenesis. These results indicate that impaired uracil repair is involved in neurodegeneration and neuropsychiatric dysfunction induced by experimental folate deficiency.
Treatment of leukemia antigen-loss relapses occurring after CD19-targeted immunotherapies by combination of anti-CD123 and anti-CD19 chimeric antigen receptor T cells (2015)

Meeting abstracts Anti-CD19 chimeric antigen receptor T cells (CART19) and bi-specific anti-CD19/CD3 antibodies (blinatumomab) are generating unprecedented complete responses in relapsing/refractory B-cell acute lymphoblastic leukemia (r/r B-ALL). However, a subset of patients still relapse and
Parahydrogen‐induced polarization in imaging: Subsecond 13C angiography (2001)

High nuclear spin polarization of (13)C was reached in organic molecules. Enhancements of up to 10(4), compared to thermal polarization at 1.5 T, were achieved using the parahydrogen-induced polarization technique in combination with a field cycling method. While parahydrogen has no net polarization, it has a high spin order, which is retained when hydrogen is incorporated into another molecule by a chemical reaction. By subjecting this molecule to a sudden change of the external magnetic field, the spin order is transferred into net polarization. A (13)C angiogram of an animal was generated in less than a second. Magn Reson Med 46:1-5, 2001.
Maintenance therapy of cyclical mastalgia using low-dose danazol. (1989)

In an open study, low-dose danazol (mean total dose 700 mg/month) was given during the luteal phase to 20 women with severe relapsing cyclical mastalgia. All subjects had previously obtained a useful clinical response on conventional dosage of danazol, but side effects occurred in 13 (65%). On the low-dose regimen, complete relief of symptoms was attained by 11 women (55%) and the remainder achieved a substantial clinical improvement; no side effects were reported. A low-dose regimen may be suitable for women with chronic relapsing cyclical mastalgia or those who develop side effects on conventional dosage.
Characterization of nuclei in in vitro collagen fibril formation (1977)

Abstract Heat precipitation fibril formation in collagen solutions depends upon the prior thermal history of the solution. Collagen solutions were heat precipitated to various extents at 30°C, cooled, and then brought to a second precipitation. Kinetic analysis of the secondary precipitation demonstrated that only the nucleation phase of the precipitation was affected, not the fibril growth phase. Thermal history, or memory, is thus related to the formation of low‐temperature‐stable nuclei. A range of nuclei sizes is evident, supporting the concept of a homogeneous nucleation process. Schiffs base formation and establishment of cross‐linkages play no role in the in vitro nucleation: thiosemicarbazide treated collagen behaves identically to untreated collagen in kinetics of assembly to fibrils. Low‐temperature‐stable nuclei formed at neutral pH are dissociated in the cold in acetic acid at pH 4. Pronase and pepsin susceptible molecular end regions are important in establishing the low‐temperature‐stable nuclei. Pronase treatment completely abolishes the acquisition of memory of prior thermal history in collagen solutions. We speculate that biological control mechanisms for fibril formation in vivo relate to specific interactions between non‐helical, enzyme susceptible regions on collagen molecules.
CfAdmin: A User Interface for cfengine (2001)

CfAdmin provides a relatively easy-to-use web interface for system administrators to package and deploy software using GNU Cfengine. It conceals the intricacies of cfengine configuration and reduces potential errors by storing all configuration data in a relational database.The interface is divided into administration, inventory, package and deployment sections to follow an administrator's work-flow. In addition to implementing most of the features of cfengine, CfAdmin provides a configuration file template system to allow customization of packages per deployment. This allows an administrator to readily leverage a single package, such as Apache, across multiple installations by modifying templated areas of the configuration file (i.e., httpd.conf ServerRoot).CfAdmin was created to streamline the deployment of software for a managed service provider, but could be equally at home in other environments with large numbers of applications and servers. It is an update to an existing cfengine installation supporting over 200 servers in various colocation facilities and has the side-benefit of being a self-documenting system.
The accumulation of five quinolone antibacterial agents by Escherichia coli (1990)

The accumulation of five radiolabelled quinolone antibacterial agents by Escherichia coli KL16 was examined using a vacuum filtration method. Preliminary experiments were performed to determine the optimum quinolone concentration, inoculum of cells, filter washing regimen and filter type. All five quinolones showed a similar biphasic pattern of accumulation with high radioactive counts cell-associated during the first ten seconds of the assay, followed by steadily increasing accumulation over 30 min. Analysis of the mean accumulation after 30 min for each quinolone showed that there was no direct relationship between quinolone accumulation and antibacterial activity (as quantified by the MIC or bactericidal activity). Mechanistic investigations showed that accumulation was decreased by low reaction temperatures, acid pH and the presence of the metabolic inhibitors 2,4-dinitrophenol, potassium cyanide and sodium azide. These results suggest that quinolone accumulation by E. coli KL16 is partly dependent on cell metabolism and may proceed by an active transport mechanism. Treatment of cells with EDTA was found not to increase quinolone accumulation, suggesting that the outer membrane of E. coli KL16 does not act as a permeability barrier to these quinolones. The implication of these results in terms of possible mechanisms of bacterial resistance to quinolones is discussed.
Binding and transcytosis of glycoalbumin by the microvascular endothelium of the murine myocardium: evidence that glycoalbumin behaves as a bifunctional ligand. (1988)

The binding and transport of glycoalbumin (gA) by the endothelium of murine myocardial microvessels were studied by perfusing in situ 125I-gA or gA-gold complexes (gA-Au) and examining the specimens by radioassays and EM, respectively. After a 3-min perfusion, the uptake of radioiodinated gA is 2.2-fold higher than that of native albumin; it is partially (approximately 55%) competed by either albumin or D-glucose, and almost completely abolished by the concomitant administration of both competitors or by gA. D-mannose and D-galactose are not effective competitors. Unlike albumin-gold complexes that bind restrictively to plasmalemmal vesicles, gA-Au labels the plasma-lemma proper, plasmalemmal vesicles open on the lumen, and most coated pits. Competing albumin prevents gA-Au binding to the membrane of plasmalemmal vesicles, while glucose significantly reduces the ligand binding to plasmalemma proper. Competition with albumin and glucose gives additive effects. Transcytosis of gA-Au, already detected at 3 min, becomes substantial by 30 min. No tracer exit via intercellular junctions was detected. gA-Au progressively accumulates in multivesicular bodies. The results of the binding and competition experiments indicate that the gA behaves as a bifunctional ligand which is recognized by two distinct binding sites: one, located on the plasma membrane, binds as a lectin the glucose residues of gA; whereas the other, confined to plasmalemmal vesicles, recognizes presumably specific domains of the albumin molecule.
Vitamin D: its role and uses in immunology 1 (2001)

In recent years there has been an effort to understand possible noncalcemic roles of vitamin D, including its role in the immune system and, in particular, on T cell-medicated immunity. Vitamin D receptor is found in significant concentrations in the T lymphocyte and macrophage populations. However, its highest concentration is in the immature immune cells of the thymus and the mature CD-8 T lymphocytes. The significant role of vitamin D compounds as selective immunosuppressants is illustrated by their ability to either prevent or markedly suppress animal models of autoimmune disease. Results show that 1,25-dihydroxyvitamin D3 can either prevent or markedly suppress experimental autoimmune encephalomyelitis, rheumatoid arthritis, systemic lupus erythematosus, type I diabetes, and inflammatory bowel disease. In almost every case, the action of the vitamin D hormone requires that the animals be maintained on a normal or high calcium diet. Possible mechanisms of suppression of these autoimmune disorders by the vitamin D hormone have been presented. The vitamin D hormone stimulates transforming growth factor TGFbeta-1 and interleukin 4 (IL-4) production, which in turn may suppress inflammatory T cell activity. In support of this, the vitamin D hormone is unable to suppress a murine model of the human disease multiple sclerosis in IL-4-deficient mice. The results suggest an important role for vitamin D in autoimmune disorders and provide a fertile and interesting area of research that may yield important new therapies.
Recognition of multi-agent interaction in video surveillance (1999)

This paper describes a probabilistic syntactic approach to the detection and recognition of temporally extended activities and interactions between multiple agents. A complete system consisting of an adaptive tracker, an event generator and the parser performs segmentation and labelling of a surveillance video of a parking lot; the system correctly identifies activities such as pick-up and drop-off, which involve person-vehicle interactions. The main contributions of this paper are extending the parsing algorithm to handle multi-agent interactions within a single parser, providing a general mechanism for consistency-based pruning, and developing an efficient incremental parsing algorithm.
Indication that the Nitrogen Source Influences Both Amount and Size of Exopolysaccharides Produced by Streptococcus thermophilus LY03 and Modelling of the Bacterial Growth and Exopolysaccharide Production in a Complex Medium (1999)

Streptococcus thermophilus LY03 is a yogurt strain producing the same exopolysaccharide material in both milk and MRS broth. Actually, two types of exopolysaccharides are produced simultaneously. The two exopolysaccharides are identical in monomer composition (galactose and glucose in a 4:1 ratio) but differ in molecular size. Gel permeation chromatography revealed a high-molecular-mass exopolysaccharide (1.8 x 10(6)) and a low-molecular-mass exopolysaccharide (4.1 x 10(5)). Both exopolysaccharides can be isolated from the fermentation broth separately. The proportion in which they are produced is strongly dependent on the carbon/nitrogen ratio of the fermentation broth. A shift from a high-molecular-mass exopolysaccharide to a low-molecular-mass exopolysaccharide was observed with increasing initial complex nitrogen concentrations. All necessary biokinetic parameters to study the kinetics of S. thermophilus LY03 fermentations were obtained from a mathematical model which describes both S. thermophilus LY03 growth and exopolysaccharide production and degradation. The model is valid with various initial complex nitrogen concentrations and can be applied to simulate exopolysaccharide production in a milk medium.
Semantic Video Segmentation by Gated Recurrent Flow Propagation (2018)

Semantic video segmentation is challenging due to the sheer amount of data that needs to be processed and labeled in order to construct accurate models. In this paper we present a deep, end-to-end trainable methodology for video segmentation that is capable of leveraging the information present in unlabeled data, besides sparsely labeled frames, in order to improve semantic estimates. Our model combines a convolutional architecture and a spatiotemporal transformer recurrent layer that is able to temporally propagate labeling information by means of optical flow, adaptively gated based on its locally estimated uncertainty. The flow, the recognition and the gated temporal propagation modules can be trained jointly, end-to-end. The temporal, gated recurrent flow propagation component of our model can be plugged into any static semantic segmentation architecture and turn it into a weakly supervised video processing one. Our experiments in the challenging CityScapes and Camvid datasets, and for multiple deep architectures, indicate that the resulting model can leverage unlabeled temporal frames, next to a labeled one, in order to improve both the video segmentation accuracy and the consistency of its temporal labeling, at no additional annotation cost and with little extra computation.
Organ specific cytokine therapy. Local activation of mononuclear phagocytes by delivery of an aerosol of recombinant interferon-gamma to the human lung. (1991)

In the context of the central role of the alveolar macrophage in host defense of the respiratory epithelial surface, and the ability of IFN-gamma to activate mononuclear phagocytes, we have evaluated strategies to use rIFN-gamma to activate human alveolar macrophages in vivo. To accomplish this, rIFN-gamma was administered to nonsmoking normals, the amounts of IFN-gamma quantified in serum and respiratory epithelial lining fluid (ELF) and the status of IFN-gamma related activation of blood monocytes and alveolar macrophages was evaluated by quantifying the expression of mRNA transcripts of IP-10, a gene induced specifically by IFN-gamma. Systemic administration (subcutaneous) of maximally tolerated amounts of rIFN-gamma (250 micrograms) was followed by detectable levels of IFN-gamma in serum but not ELF, the expression of IP-10 transcripts in blood monocytes but not alveolar macrophages, and multiple systemic adverse effects. To circumvent the inability of systemic administration to reach respiratory ELF and activate alveolar macrophages, rIFN-gamma (250-1,000 micrograms) was inhaled as an aerosol once daily for 3 d. Strikingly, while IFN-gamma was not detected in serum it was detectable in respiratory ELF in a dose-dependent fashion. Further, alveolar macrophages, but not blood monocytes, expressed IP-10 mRNA transcripts and, importantly, inhalation of aerosolized rIFN-gamma was not associated with local or systemic adverse effects. Thus, it is feasible to use rIFN-gamma to activate alveolar macrophages by targeting the cytokine directly to the lung. These data suggest a potential strategy for targeted cytokine therapy, without systemic side effects, to augment respiratory tract defenses in individuals at risk for or with lung infection.
Non-moving scanner design for OCT systems (2016)

In this work, a novel beam scanner design based on non-moving parts is introduced which will eliminate the phase and inaccuracy problems of the mechanical scanners while providing two times imaging speed improvement for optical coherence tomography systems. The design is comprised of electro-optically activated switches that are placed on the sample arm. For the example considered here, lateral resolution of 20 µm, and lateral scanning range of 1 mm are aimed at which resulted in a scanner size of 1 mm × 9 mm. Due to its compact size, proposed design can also be implemented in forward-looking endoscopic probes.
Adaptation of a Retrovirus as a Eucaryotic Vector Transmitting the Herpes Simplex Virus Thymidine Kinase Gene (1982)

We investigated the feasibility of using retroviruses as vectors for transferring DNA sequences into animal cells. The thymidine kinase (tk) gene of herpes simplex virus was chosen as a convenient model. The internal BamHI fragments of a DNA clone of Moloney leukemia virus (MLV) were replaced with a purified BamHI DNA segment containing the tk gene. Chimeric genomes were created carrying the tk insert in both orientations relative to the MLV sequence. Each was transfected into TK- cells along with MLV helper virus, and TK+ colonies were obtained by selection in the presence of hypoxanthine, aminopterin, and thymidine (HAT). Virus collected from TK+-transformed, MLV producer cells passed the TK+ phenotype to TK- cells. Nonproducer cells were isolated, and TK+ transducing virus was subsequently rescued from them. The chimeric virus showed single-hit kinetics in infections. Virion and cellular RNA and cellular DNA from infected cells were all shown to contain sequences which hybridized to both MLV- and tk-specific probes. The sizes of these sequences were consistent with those predicted for the chimeric virus. In all respects studied, the chimeric MLV-tk virus behaved like known replication-defective retroviruses. These experiments suggest great general applicability of retroviruses as eucaryotic vectors.
A Rapid and General Assay for Monitoring Endogenous Gene Modification (2010)

The development of zinc finger nucleases for targeted gene modification can benefit from rapid functional assays that directly quantify activity at the endogenous target. Here we describe a simple procedure for quantifying mutations that result from DNA double-strand break repair via non-homologous end joining. The assay is based on the ability of the Surveyor nuclease to selectively cleave distorted duplex DNA formed via cross-annealing of mutated and wild-type sequence.
Effects of nicotine in the dopaminergic system of mice lacking the alpha4 subunit of neuronal nicotinic acetylcholine receptors (2003)

The mesostriatal dopaminergic system influences locomotor activity and the reinforcing properties of many drugs of abuse including nicotine. Here we investigate the role of the alpha4 nicotinic acetylcholine receptor (nAChR) subunit in mediating the effects of nicotine in the mesolimbic dopamine system in mice lacking the alpha4 subunit. We show that there are two distinct populations of receptors in the substantia nigra and striatum by using autoradiographic labelling with 125I alpha-conotoxin MII. These receptors are comprised of the alpha4, beta2 and alpha6 nAChR subunits and non-alpha4, beta2, and alpha6 nAChR subunits. Non-alpha4 subunit-containing nAChRs are located on dopaminergic neurons, are functional and respond to nicotine as demonstrated by patch clamp recordings. In vivo microdialysis performed in awake, freely moving mice reveal that mutant mice have basal striatal dopamine levels which are twice as high as those observed in wild-type mice. Despite the fact that both wild-type and alpha4 null mutant mice show a similar increase in dopamine release in response to intrastriatal KCl perfusion, a nicotine-elicited increase in dopamine levels is not observed in mutant mice. Locomotor activity experiments show that there is no difference between wild-type and mutant mice in basal activity in both habituated and non-habituated environments. Interestingly, mutant mice sustain an increase in cocaine-elicited locomotor activity longer than wild-type mice. In addition, mutant mice recover from depressant locomotor activity in response to nicotine at a faster rate. Our results indicate that alpha4-containing nAChRs exert a tonic control on striatal basal dopamine release, which is mediated by a heterogeneous population of nAChRs.
Mutations in the organic cation/carnitine transporter OCTN2 in primary carnitine deficiency (1999)

Primary carnitine deficiency is an autosomal recessive disorder of fatty acid oxidation caused by defective carnitine transport. This disease presents early in life with hypoketotic hypoglycemia or later in life with skeletal myopathy or cardiomyopathy. The gene for this condition maps to 5q31.2-32 and OCTN2, an organic cation/carnitine transporter, also maps to the same chromosomal region. Here we test the causative role of OCTN2 in primary carnitine deficiency by searching for mutations in this gene in affected patients. Fibroblasts from patients with primary carnitine deficiency lacked mediated carnitine transport. Transfection of patient's fibroblasts with the OCTN2 cDNA partially restored carnitine transport. Sequencing of the OCTN2 gene revealed different mutations in two unrelated patients. The first patient was homozygous (and both parents heterozygous) for a single base pair substitution converting the codon for Arg-282 to a STOP codon (R282X). The second patient was a compound heterozygote for a paternal 1-bp insertion producing a STOP codon (Y401X) and a maternal 1-bp deletion that produced a frameshift creating a subsequent STOP codon (458X). These mutations decreased the levels of mature OCTN2 mRNA and resulted in nonfunctional transporters, confirming that defects in the organic cation/carnitine transporter OCTN2 are responsible for primary carnitine deficiency.