gebhart/patrepeval huggingface dataset:
Consequences of lack of beta 1 integrin gene expression in mice. (1995)

beta 1 integrins are cell-surface receptors that mediate cell-cell and cell-matrix interactions. We have generated a null mutation in the gene for the beta 1 integrin subunit in mice and embryonic stem (ES) cells. Heterozygous mice are indistinguishable from normal littermates. Homozygous null embryos develop normally to the blastocyst stage, implant, and invade the uterine basement membrane but die shortly thereafter. Using beta 1 integrin-deficient ES cells we have established chimeric embryos and adult mice. Analysis of the chimeric embryos demonstrated the presence of beta 1 integrin-deficient cells in all germ layers indicating that beta 1-null cells can differentiate and migrate in a context of normal tissue. When evaluated at embryonic day 9.5 (E9.5), embryos with a beta 1-null cell contribution below 25% were developing normally, whereas embryos with a contribution above this threshold were distorted and showed abnormal morphogenesis. In adult chimeric mice beta 1 integrin-deficient cells failed to colonize liver and spleen but were found in all other tissues analyzed at levels from 2%-25%. Immunostaining of chimeric mice showed that in cardiac muscle, there were small, scattered patches of myocytes that were beta 1-null. In contrast, many myotubes showed some beta 1-null contribution as a result of fusion between wild-type and mutant myoblasts to form mixed myotubes. The adult chimeric brain contained beta 1-null cells in all regions analyzed. Also, tissues derived from the neural crest contained beta 1 integrin-deficient cells indicating that migration of neuronal cells as well as neural crest cells can occur in the absence of beta 1 integrins.
Modeling and Control of Livestock Ventilation Systems and Indoor Environments (2005)

The hybrid ventilation systems have been widely used for livestock barns to provide optimum indoor climate by controlling the ventilation rate and air flow distribution within the ventilated building structure. The purpose of this paper is to develop models for livestock ventilation systems and indoor environments with a major emphasis on the prediction of indoor horizontal variation of temperature and concentration adapted to the design of appropriate controlling strategy and control systems. The Linear Quadratic (LQ) optimal control method taking into account of the effect of necessary constraints and random disturbances is designed through system linearization. The well designed control systems are able to determine the demand ventilation rate and airflow pattern, improve and optimize the indoor Thermal Comfort (TC), Indoor Air Quality (IAQ) and energy use.
DC and RF characterization of fully depleted strained SOI MOSFETs (2005)

The RF characteristics of strained SOI (SSOI) MOSFETs are reported for the first time. Fully depleted n- and p-MOSFETs were fabricated on SOI and SSOI wafers. Higher mobility was measured on the SSOI wafers and SSOI n- and p-MOSFETs showed higher transconductance as well as higher f/sub T/ and f/sub max/ than the SOI FETs for the entire gate length range studied. For n-MOSFETs with approximately 180 nm gate length, the best f/sub T/ and f/sub max/ is 75 GHz for SSOI and 60 and 69 GHz, respectively for SOI. The f/sub T/ for the p-MOSFET with 180-nm gate length is 36 GHz for SSOI and 30 GHz for SOI.
Plasmid complements of Streptococcus lactis NCDO 712 and other lactic streptococci after protoplast-induced curing (1983)

The production and regeneration of bacterial protoplasts promoted the loss of three different plasmid-specified traits in Streptococcus lactis subsp. diacetylactis strains. The loss of five different plasmids, including small multicopy molecules, was readily detected in Streptococcus lactis 712 by screening lysates of random protoplast regenerants on agarose gels. In this strain sequential rounds of protoplast regeneration were used to produce a plasmid-free strain and derivatives carrying only single molecules from the plasmid complement. During these experiments a 33-megadalton plasmid, pLP712, was found to encode genes for lactose and protein utilization. Only this plasmid was required for normal growth and acid production in milk; the remaining four plasmids appeared to be cryptic. Lactose-defective derivatives of a strain carrying only pLP712 were readily isolated. Although these derivatives included instances of plasmid loss, deletions of pLP712 were frequently found. Many different deleted derivatives of pLP712, including some in which the lactose or protein utilization determinant or both were lost, were isolated. The molecular instability of pLP712 largely accounted for previous observations of plasmid complements in S. lactis 712 after lactose determinant curing or transfer by conjugation and transduction. Curing of cryptic molecules from multiple plasmid complements by protoplast regeneration may prove to be generally valuable in lactic streptococci and other gram-positive species.
Fundamentals of protein interaction network mapping (2015)

Studying protein interaction networks of all proteins in an organism ("interactomes") remains one of the major challenges in modern biomedicine. Such information is crucial to understanding cellular pathways and developing effective therapies for the treatment of human diseases. Over the past two decades, diverse biochemical, genetic, and cell biological methods have been developed to map interactomes. In this review, we highlight basic principles of interactome mapping. Specifically, we discuss the strengths and weaknesses of individual assays, how to select a method appropriate for the problem being studied, and provide general guidelines for carrying out the necessary follow-up analyses. In addition, we discuss computational methods to predict, map, and visualize interactomes, and provide a summary of some of the most important interactome resources. We hope that this review serves as both a useful overview of the field and a guide to help more scientists actively employ these powerful approaches in their research.
Simple and Effective Gap-Repair Cloning Using Short Tracts of Flanking Homology in Fission Yeast (2010)

Gap-repair cloning for plasmid construction in budding yeast is very effective and often used. In contrast, the same method is not widely used in fission yeast, because of a shortage of information on it. Here we describe simple and effective gap-repair cloning for plasmid construction using short tracts of flanking homology. By this method, we combined concentrated DNA fragments with short (20 bp) tracts of flanking homology with the marker gene or the pre-existing gene module. In addition, we found that this method can be applied to one-step cloning of multiple DNA fragments to construct a fusion gene.
Spatial management of information (1978)

Methods of spatially managing data are currently under study at the Architecture Machine Group. Management concepts are drawn from everyday examples of paper and document handling. However, the work elaborates data types to include: animation, movies, and sound-sync computer graphics. Beyond the application of management information systems, the paper portrays a sophisticated surround of keyboardless, interactive, and large scale graphics. Computer graphics, image processing, and broadcast are viewed as one. The system includes three frame buffers, four minicomputers, two touch sensitive displays, an octophonic sound system, and an MCA Optical Videodisc.
Ultrasonic Technique for Residual Stress Measurement in Ductile Iron Continuous Cast Round Bars (1992)

Abstract An ultrasonic technique using critically refracted longitudinal (LOR) waves was used to determine the residual stresses in ductile iron bars in the as-cast, annealed, normalized as well as quenched and tempered states. The results conform to expected trends based on differential cooling rate and phase transformation effects.
Interactions between Integrase and Excisionase in the Phage Lambda Excisive Nucleoprotein Complex (2002)

Bacteriophage lambda site-specific recombination comprises two overall reactions, integration into and excision from the host chromosome. Lambda integrase (Int) carries out both reactions. During excision, excisionase (Xis) helps Int to bind DNA and introduces a bend in the DNA that facilitates formation of the proper excisive nucleoprotein complex. The carboxyl-terminal alpha-helix of Xis is thought to interact with Int through direct protein-protein interactions. In this study, we used gel mobility shift assays to show that the amino-terminal domain of Int maintained cooperative interactions with Xis. This finding indicates that the amino-terminal arm-type DNA binding domain of Int interacts with Xis.
THE CLINICAL USEFULNESS OF THE RENAL ALLOGRAFT BIOPSY IN THE CYCLOSPORINE ERA (1999)

Renal allograft biopsy findings alter patient management recommendations in approximately 40% of patients in whom a presumptive diagnosis had been made on the basis of clinical and laboratory findings. Patients who had a change in patient management because of biopsy findings demonstrated a response to therapy and allograft survival similar to those of patients who had no alteration in management plan after the biopsy.
CD28-mediated signaling in vivo prevents activation-induced apoptosis in the thymus and alters peripheral lymphocyte homeostasis (1995)

Activation of T lymphocytes can result in a functional immune response, anergy or apoptosis. Functional T cell activation requires the interaction of the TCR with Ag presented by MHC molecules on APC concurrent with appropriate interactions between cell surface accessory molecules. Interestingly, the level of CD28 expression is regulated during T cell development as well as during T cell activation and proliferation, suggesting that CD28 could play a role in determining the outcome of activation of TCR during T cell ontogeny. We identify, herein, a novel function of murine CD28 in the regulation of activation-induced apoptosis in thymocytes. In vivo, or combined in vivo and in vitro treatment with mAbs to CD28 prevents apoptosis of CD4+CD8+ thymocytes induced by Abs to the TCR complex. Prolonged administration of anti-CD28 Abs increased the number of both CD4+CD8- and CD4-CD8+ T cells in the thymus, while the number of CD4+CD8+ T cells is relatively unchanged. Furthermore, this treatment leads to a dramatic enlargement of peripheral lymphoid organs characterized primarily by the expansion of B cells. The number of CD4+CD8- T cells in the spleen of anti-CD28-treated mice is also moderately increased, while the number of CD4-CD8+ cells is relatively unchanged.
A Metric Scale for 'Abstractness' of the Word Meaning (2012)

Web personalization involves automated content analysis of text, and modern technologies of semantic analysis of text rely on a number of scales. Among them is the of meaning, which is not captured by more traditional measures of sentiment, such as valence, arousal and dominance. The present work introduces a physics-inspired approach to constructing the scale based on databases of hypernym-hyponym relations, e.g., WordNet 3.0. The idea is to define an energy as a function of word coordinates that are distributed in one dimension, and then to find a global minimum of this energy function by relocating words in this dimension. The result is a one-dimensional distribution that assigns abstractness values to words. While positions of individual words on this scale are subject to noise, the entire distribution globally defines the universal semantic dimension associated with the notion of hypernym-hyponym relations, called here abstractness.
The Network of Glucokinase-Expressing Cells in Glucose Homeostasis and the Potential of Glucokinase Activators for Diabetes Therapy (2006)

The glucose-phosphorylating enzyme glucokinase has structural, kinetic, and molecular genetic features that are ideal for its primary role as glucose sensor in a network of neuro/endocrine sentinel cells that maintain glucose homeostasis in many vertebrates including humans. The glucokinase-containing, insulin-producing beta-cells of the pancreas take the prominent lead in this network, functioning in the aggregate as the master gland. The beta-cells are also conceptualized as the prototype for all other glucose sensor cells, which determines our current understanding of many extrapancreatic glucose sensors. About 99% of the enzyme resides, however, in the hepato-parenchymal cells and serves its second role in a high-capacity process of blood glucose clearance. Two examples strikingly illustrate how pivotal a position glucokinase has in the regulation of glucose metabolism: 1) activating and inactivating mutations of the enzyme cause hypo- and hyperglycemia syndromes in humans described collectively as "glucokinase disease" and fully explained by the glucose sensor paradigm, and 2) glucokinase activator drugs (GKAs) have been discovered that bind to an allosteric site and increase the kcat and lower the glucose S(0.5) of the enzyme. GKAs enhance glucose-stimulated insulin release from pancreatic islets and glucose disposition by the liver. They are now intensively explored to develop a novel treatment for diabetes. Future biophysical, molecular, genetic, and pharmacological studies hold much promise to unravel the evolving complexity of the glucokinase glucose sensor system.
Diet‐Induced Changes in Membrane Gangliosides in Rat Intestinal Mucosa, Plasma and Brain (2005)

: The authors conclude that dietary ganglioside is absorbed in the small intestine and transported to different membrane sites, altering ganglioside levels in the intestinal mucosa, plasma and brain and thus possibly having the potential to change developing enterocyte function (and possibly that of other cell lines).
A Robust Approach for Local Interest Point Detection in Line-Drawing Images (2012)

In this paper, we propose a new method to detect local interest points as junctions in line-drawing images. Our approach takes advantages of different aspects. Firstly, we extract skeleton of image and then construct a Skeleton Connective Graph with the expectation that it provides a first level of junction detection from shapes. Secondly, instead of employing low-level operators to detect junctions as described in many traditional techniques, our method works at path level taking different skeleton branches into account to gain robustness. Thirdly, we exploit the benefits of wavelet transform (e.g. multi-resolution analysis, discontinuity detection, fast computation, less sensitive to noises) to efficiently detect the dominant points from 1D representations of the paths. Finally, a post-process of pruning and connecting the skeleton segments is performed to discard false detected points and to refine the skeleton. We present in experiments interesting results compared to different methods.
Detection and identification of fungal pathogens in blood by using molecular probes (1997)

A PCR assay was developed for the detection and identification of Candida and Aspergillus species. The design of the oligonucleotide primer pair as well as the species-specific probes used for species identification was derived from a comparison of the sequences of the 18S rRNA genes of various fungal pathogens. The primers targeted a consensus sequence for a variety of fungal pathogens. The assay was tested for sensitivity and specificity with 134 fungal and 85 nonfungal isolates. To assess clinical applicability, 601 blood samples from four defined groups were tested: group A (n = 35), controls; groups B to D (n = 86), patients with febrile neutropenia, without fungal colonization (group B; n = 29) and with fungal colonization (group C; n = 36); and patients with documented invasive fungal infection (IFI) (group D; n = 21). The assay detected and, by species-specific hybridization, identified most of the clinically relevant Candida and Aspergillus species at 1 CFU/ml of blood. Amplification was 100% sensitive for all molds and yeasts tested, with Histoplasma capsulatum being the only non-Aspergillus species hybridizing with the Aspergillus spp. probe. None of 35 group A patients and only 3 of 65 group B and C patients were PCR positive. The sensitivity of the assay for specimens from patients with IFI (21 patients in group D) was 100% if two specimens were tested. For specificity, 3 of 189 specimens from patients at risk but with negative cultures were positive by the assay, for a specificity of 98%. PCR preceded radiological signs by a median of 4 days (range, 4 to 7 days) for 12 of 17 patients with hepatosplenic candidiasis or pulmonary aspergillosis. For the 10 patients with IFI responding to antifungal therapy, PCR assays became persistently negative after 14 days of treatment, in contrast to the case for 11 patients, who remained PCR positive while not responding to antifungal therapy. Thus, the described PCR assay allows for the highly sensitive and specific detection and identification of fungal pathogens in vitro and in vivo. Preliminary data from the screening of a selected group of patients revealed some value in the early diagnosis and monitoring of antifungal therapy.
Bovine lactoferrin induces both mucosal and systemic immune response in mice (1998)

Lactoferrin (Lf) is a milk iron-binding glycoprotein that plays a role in iron transport and acts as both a bacteriostatic and a growth modulating agent. The aim of this study was to investigate the nature of immune responses induced by repeated oral administration of bovine milk Lf in mice. Groups of ten female BALB/c mice were fed daily for 4 weeks with two doses of protein antigen: a low (0.05 mg/g body weight per d) or high (1 mg/g body weight per d) dose of Lf, or water as a control. A fourth group was immunized intramuscularly with 0.01 mg Lf in complete Freund's adjuvant. Anti-Lf IgA and IgG were detected in the intestinal fluid and serum of mice given Lf. Total immunoglobulins were higher in the intestinal fluid in Lf groups than in the control group. No difference could be detected in the serum. IgA and IgG secretion was enhanced in Peyer's patches and spleen from Lf-fed mice, in comparison with controls. [3H]thymidine uptake into Peyer's patch and spleen cells from both control and Lf-fed mice was enhanced by 75 micrograms Lf/ml in vitro, but Lf groups had a greater proliferation rate than the control group. These findings suggested that Lf could act as an immunostimulating factor on the mucosal immune system and that activation of the mucosal immune system is dependent on the ability of Lf to bind to the intestinal mucosa.
Species- or isozyme-specific enzyme inhibitors. 9. Selective effects in inhibitions of rat pyruvate kinase isozymes by adenosine 5'-diphosphate derivatives (1982)

Derivatives of adenosine 5'-diphosphate (ADP) with a substituent of 1-4 atoms at any of eight positions have been synthesized and evaluated as substrates and inhibitors of the liver (L), muscle (M), and kidney (K) isozymes of rat pyruvate kinase (PK). Inhibitory potencies of the compounds were expressed as KM (ADP)/Ki or as KM (ADP)/KM when no Ki value was available. Nine of 14 ADP derivatives exhibited differential inhibitions. The M and K isozymes, which cross-react immunologically with each other but not with the L form, were inhibited differentially by 5 of the 14 derivatives. PK-K was preferentially inhibited by two derivatives, PK-L by three derivatives, and PK-M by two derivatives. Among the most selective and/or effective inhibitors were 3'-OMe-ADP [KM (ADP)/Ki = 0.07 with PK-K; inhibitory potency, K/M/L, 7.6:6.0:1], N6-Me,N6-(CH2)4N(Me)COMe-ADP (prepared previously) [KM (ADP)/KM = 0.43 with PK-L; inhibitory potency, L/K/M, 3:2:1], and 8-NHEt-ADP [KM (ADP)/Ki = 1.0 with PK-M; inhibitory potency, M/K/L, 7.1:1.2:1]. These and previous studies with two other enzymes indicate that monosubstituted substrate derivatives that bear short substituents (usually 1-4 atoms) at various positions are potentially useful probes in early stages of the attempted design of isozyme-selective inhibitors.
Psychometric characteristics of the aberrant behavior checklist. (1985)

Information was presented on the psychometric characteristics of the Aberrant Behavior Checklist. The internal consistency and test-retest reliability of the Checklist appeared to be very good. Interrater reliability tended to vary across raters and subscales and ranged from mediocre to good but was generally in the moderate range and acceptable for research purposes. Validity was assessed by comparing Checklist scores for residents presenting with attributes thought to reflect varying degrees of social adaptation. Validity was also evaluated by comparing Aberrant Behavior Checklist scores with ratings on adaptive behavior scales and with objective observations of behavior. In general, validity was established for most Aberrant Behavior Checklist subscales. Preliminary data from drug investigations suggested that the Checklist may provide a useful adjunct for the assessment of psychotropic drug effects.
Measurement of free and complexed soluble vascular endothelial growth factor receptor, Flt-1, in fluid samples: development and application of two new immunoassays (2001)

Vascular endothelial growth factor (VEGF) mediates endothelial cell mitogenesis and enhances vascular permeability. VEGF interacts with the endothelium via two membrane-spanning receptors, fms-like tyrosine kinase (Flt)-1 and kinase domain receptor. A soluble form of Flt-1 (sFlt-1) was isolated from endothelial cell media; however, its biological significance is still unknown, with limited data on plasma sFlt-1 levels in disease states. We have developed two new ELISAs for detecting free and VEGF-complexed sFlt-1, which were tested in accordance with standard validation and assessment methodologies employed in commercial settings. The intra-and inter-assay coefficients of variation are <5% and 10% respectively, and results are highly reproducible. Applying these ELISAs in a clinical setting, we measured levels of VEGF, free and complexed sFlt-1 in citrated plasma from 40 patients with cardiovascular disease and 40 healthy controls. Median (interquartile range) plasma levels of VEGF in patients were significantly greater than controls [403 pg/ml (158--925 pg/ml) versus 113 pg/ml (33--231 pg/ml), P< or =0.05]. Free sFlt-1 was significantly lower in patients compared with controls [8 ng/ml (2--22 ng/ml) versus 21 ng/ml (10--73 ng/ml), P< or =0.05]. There was no significant difference in the levels of complexed sFlt-1 between the two groups. Plasma levels of VEGF-complexed sFlt-1 are minimal, despite the presence of excess free sFlt-1. Thus unbound plasma VEGF detected by ELISA may represent the majority of circulating VEGF, and justifies the measurement of plasma VEGF as an indicator of circulating VEGF levels. Furthermore, these results suggest that circulating sFlt-1 may serve as a selective inhibitor of VEGF activity, and that this regulatory mechanism may be altered by pathological conditions.
Estimating Genomic Distance from DNA Sequence Location in Cell Nuclei by a Random Walk Model (1992)

The folding of chromatin in interphase cell nuclei was studied by fluorescent in situ sequences chromatin according to a random walk model. This model provides the basis for calculating the spacing of sequences along the linear DNA molecule from interphase distance measurements. An interphase mapping strategy based on this model was tested with 13 probes from a 4-megabase pair (Mbp) region of chromosome 4 containing the Huntington disease locus. The results confirmed the locations of the probes and showed that the remaining gap in the published maps of this region is negligible in size. Interphase distance measurements should facilitate construction of chromosome maps with an average marker density of one per 100 kbp, approximately ten times greater than that achieved by hybridization to metaphase chromosome. achieved by hybridization to metaphase chromosomes.