gebhart/patrepeval huggingface dataset:
Privacy preserving mining of association rules (2002)

We present a framework for mining association rules from transactions consisting of categorical items where the data has been randomized to preserve privacy of individual transactions. While it is feasible to recover association rules and preserve privacy using a straightforward "uniform" randomization, the discovered rules can unfortunately be exploited to find privacy breaches. We analyze the nature of privacy breaches and propose a class of randomization operators that are much more effective than uniform randomization in limiting the breaches. We derive formulae for an unbiased support estimator and its variance, which allow us to recover itemset supports from randomized datasets, and show how to incorporate these formulae into mining algorithms. Finally, we present experimental results that validate the algorithm by applying it on real datasets.
PepNovo:  De Novo Peptide Sequencing via Probabilistic Network Modeling (2005)

We present a novel scoring method for de novo interpretation of peptides from tandem mass spectrometry data. Our scoring method uses a probabilistic network whose structure reflects the chemical and physical rules that govern the peptide fragmentation. We use a likelihood ratio hypothesis test to determine whether the peaks observed in the mass spectrum are more likely to have been produced under our fragmentation model than under a model that treats peaks as random events. We tested our de novo algorithm PepNovo on ion trap data and achieved results that are superior to popular de novo peptide sequencing algorithms. PepNovo can be accessed via the URL http://www-cse.ucsd.edu/groups/bioinformatics/software.html.
Characterization of cancer omics and drug perturbations in panels of lung cancer cells (2019)

To better understand the disruptions of transcriptional regulations and gene expression in lung cancers, we constructed a multi-omics catalogue of the responses of lung cancer cells to a series of chemical compounds. We generated and analyzed 3,240 RNA-seq and 3,393 ATAC-seq libraries obtained from 23 cell lines treated with 95 well-annotated compounds. To demonstrate the power of the created multi-omics resource, we attempted to identify drugs that could induce the designated changes alone or in combination. The basal multi-omics information was first integrated into co-expression modules. Among these modules, we identified a stress response module that may be a promising drug intervention target, as new combinations of compounds that could be used to regulate this module and the consequent phenotypic appearance of cancer cells have been identified. We believe that the multi-omics profiles generated in this study and the strategy used to stratify them will lead to more rational and efficient development of anticancer drugs.
Walker's pediatric gastrointestinal disease : phyisiology, diagnosis, management (2008)

The revision of this definitive reference work (in two volumes) is dedicated to the maintenance of a comprehensive approach to the practice of Pediatric Gastroenterology. The text of the fifth edition was extensively reviewed to assess the continuing relevance and, as a result, the size and content of various sections have been modified and new chapters have been added. Each author, selected because of particular expertise in the field, has provided an authoritative and comprehensive account of his/her topic. Chapters have been reorganized such that normal anatomy, physiology, biochemistry is followed by pathology and disease states with diagnosis and treatment. Added emphasis on the genetic and molecular biology that underpins pathological states. The book fully covers the syllabus necessary for pediatric gastroenterologists in training, not only in North America, but throughout the world. Regularly brought up to date, with assessment of the quality of the chapters on each new edition.
Storage conditions of intestinal microbiota matter in metagenomic analysis (2012)

Though this preliminary work explored a very limited number of parameters, the results suggest that storage conditions of fecal samples affect the integrity of DNA and RNA and the composition of their microbial community. For optimal preservation, stool samples should be kept at room temperature and brought at the laboratory within 24 h after collection or be stored immediately at -20°C in a home freezer and transported afterwards in a freezer pack to ensure that they do not defrost at any time. Mixing the samples with RNAse inhibitors outside the laboratory is not recommended since proper homogenization of the stool is difficult to monitor.
RACIAL DIFFERENCES IN COLOR VISION; DO THEY EXIST? (1975)

The present experiment investigated the possibility that variation in fundus pigmentation among individuals may be related to differential color sensitivity. Fifty black and white observers representing a wide range of skin (and fundus) pigmentation made direct heterochromatic brightness matches for a white standard field against each of five chromatic comparison fields. Results indicated that pigment (i.e., racial) differences in color vision do not exist, as measured by the two psychophysical methods used. The data showed that the heterochromatic matches were less reliable for the more saturated colors, violet and red, and also that the psychophysical methods used to obtain the matching data differentially influenced the results for the more saturated colors.
Microfabrication by microcontact printing of self‐assembled monolayers (1994)

Microcontact printing , is described. It offers extreme experimental simplicity and flexibility, relying on the ability of self‐assembled monolayers (SAMs) of longchain alkanethiolates on gold and other metals to act as nanometer resists. The Figure is an electron micrograph of a silicon microstructure resulting from chemical etching of a patterned SAM. magnified image
A Mouse Model for Breast Cancer Induced by Amplification and Overexpression of the neu Promoter and Transgene (2000)

Evidently minor perturbations in amplified neu expression are sufficient to alter mammary development and induce malignant transformation.
Noise-Shaping Sense Amplifier for MRAM Cross-Point Arrays (2006)

A sensing technique using a voltage-mode architecture, noise-shaping modulator, and digital filter (a counter) is presented for use with cross-point MRAM arrays and magnetic tunnel junction memory cells. The presented technique eliminates the need for precision components, the use of calibrations, and reduces the effects of power supply noise. To obviate the effects of cell-to-cell variations in the array, a digital self-referencing scheme using the counter is presented. Measured experimental results in a 180-nm CMOS process indicate an RMS sensing noise of 20 /spl mu/V for a 5-/spl mu/s sense time. Further increases in sense time are shown to increase the signal-to-noise ratio. The current used by the sense amplifier and counter was measured as 10 /spl mu/A when running at 100 MHz or 10 mA when 1000 sense amplifiers are used with a memory subarray having 1000 bitlines.
Comparison Of Three Data Acquisition Techniques For 3-D Tooth Surface Mapping (2005)

Three techniques to obtain a high resolution (under 20 micron), complete, 3D surface map of an entire tooth surface are compared. Stereophotogrammetric techniques can provide the required resolution but lens configurations that provide adequate spot size and MTF performance have depth of field substantially less than the length of tooth. Triangulation digitizing can provide adequate resolution but time for data acquisition is excessive. Miniature mechanical linkages can provide a complete surface map in under 1 minute to a resolution of under 20 microns.
INCREASED EXPRESSION OF THE NOVEL MOLECULE OX-2 IS INVOLVED IN PROLONGATION OF MURINE RENAL ALLOGRAFT SURVIVAL1 (1998)

Our data suggest that OX-2 is functionally important in the increased graft survival seen in p.v.-immunized mice receiving renal allografts.
Combination immunotherapy with prostatic acid phosphatase pulsed antigen‐presenting cells (provenge) plus bevacizumab in patients with serologic progression of prostate cancer after definitive local therapy (2006)

The combination of APC8015 and bevacizumab induces an immune response and modulates PSA in patients with biochemically recurrent prostate cancer.
Plant Growth-Promoting Rhizobacteria-Mediated Acquired Systemic Resistance in Plants Against Pests and Diseases (2016)

Plant growth-promoting rhizobacteria (PGPR) are indispensable part of rhizosphere microbiota that grow in association with the host plants and stimulate the plant growth. PGPR microcosm establishes in soil ecosystem because of its adaptability in varied environments with faster growth rate and biochemical versatility. In recent years researches have emphasised the key role of PGPR in improving nutrition and productivity of important crops with therapeutic and industrial significance. Hence, therefore, the present chapter highlights PGPR-mediated acquired systemic resistance against phytopathogens and insect pests involving mechanisms of action. Field applications of PGPR-mediated results reflect their substantial role in inducing systemic resistance in crop plants.
Relationship Between Obesity and Depression (2013)

BMI was related to clinical presentation and prevalence of comorbidities, but not antidepressant outcomes. Lower BMI classes had more psychiatric comorbidities, potentially obscuring the relationship between BMI and antidepressant effects. Trial Registration ClinicalTrials.gov identifier: NCT00590863.
Identification of a novel Arg→Cys mutation in the LDL receptor that contributes to spontaneous hypercholesterolemia in pigs (1999)

We previously carried out genetic and metabolic studies in a partially inbred herd of pigs carrying cholesterol-elevating mutations. Quantitative pedigree analysis indicated that apolipoprotein (apo)B and a second major gene were responsible for the hypercholesterolemia in these animals. In this study, we assessed LDL receptor function by three different methods: ligand blots of liver membranes using beta-very low density lipoprotein (VLDL) as a ligand; low density lipoprotein (LDL)-dependent proliferation of T-lymphocytes; and direct binding of 125I-labeled LDL to cultured skin fibroblasts. All three methods demonstrated that LDL receptor ligands bound with decreased affinity to the LDL receptor in these animals. In skin fibroblasts from the hypercholesterolemic pigs, the Kd of binding was about 4-fold higher than in cells from normal pigs. The cDNA of the pig LDL receptor from normal and hypercholesterolemic pigs was isolated and sequenced. We identified a missense mutation that results in an Arg'Cys substitution at the position corresponding to Arg94 of the human LDL receptor. The mutation is in the third repeat of the ligand binding domain of the receptor. By single-stranded conformational polymorphism (SSCP) analysis, we studied the relationship between LDL receptor genotype and plasma cholesterol phenotype. In contrast to humans, the hypercholesterolemia associated with the LDL receptor mutation in pigs was expressed as a recessive trait. The LDL receptor mutation made a far more significant contribution to hypercholesterolemia than did the apoB mutation, consistent with observations made in human subjects with apoB mutations. Within each genotypic group (mutated apoB or mutated receptor), there was a wide range in plasma cholesterol. As the animals were on a well-controlled low-fat diet, this suggests that there are additional genetic factors that influence the penetrance of cholesterol-elevating mutations.
The inhibition of monocarboxylate transporter 2 (MCT2) by AR-C155858 is modulated by the associated ancillary protein (2010)

In mammalian cells, MCTs (monocarboxylate transporters) require association with an ancillary protein to enable plasma membrane expression of the active transporter. Basigin is the preferred binding partner for MCT1, MCT3 and MCT4, and embigin for MCT2. In rat and rabbit erythrocytes, MCT1 is associated with embigin and basigin respectively, but its sensitivity to inhibition by AR-C155858 was found to be identical. Using RT (reverse transcription)-PCR, we have shown that Xenopus laevis oocytes contain endogenous basigin, but not embigin. Co-expression of exogenous embigin was without effect on either the expression of MCT1 or its inhibition by AR-C155858. In contrast, expression of active MCT2 at the plasma membrane of oocytes was significantly enhanced by co-expression of exogenous embigin. This additional transport activity was insensitive to inhibition by AR-C155858 unlike that by MCT2 expressed with endogenous basigin that was potently inhibited by AR-C155858. Chimaeras and C-terminal truncations of MCT1 and MCT2 were also expressed in oocytes in the presence and absence of exogenous embigin. L-Lactate Km values for these constructs were determined and revealed that the TM (transmembrane) domains of an MCT, most probably TM7-TM12, but not the C-terminus, are the major determinants of L-lactate affinity, whereas the associated ancillary protein has little or no effect. Inhibitor titrations of lactate transport by these constructs indicated that embigin modulates MCT2 sensitivity to AR-C155858 through interactions with both the intracellular C-terminus and TMs 3 and 6 of MCT2. The C-terminus of MCT2 was found to be essential for its expression with endogenous basigin.
Action of Light on Frog Pigment Cells in Culture (1990)

Solar radiation induces numerous biologic effects in skin but the mechanism underlying these responses is poorly understood. To study the etiology of these phenomena, we investigated the effect of light on cultured Xenopus laevis melanophores. Visible light stimulated a marked increase in intracellular cAMP levels within the first minute of irradiation. This light-induced elevation in cAMP was blocked by melatonin and was not seen in fibroblasts irradiated in a similar manner. These data show that the photoresponse of pigment cells from amphibian skin can be mediated by a cAMP-dependent mechanisms and suggest that a unique member of the rhodopsin family is involved in this process.
Abstract Meaning Representation for Sembanking (2013)

We describe Abstract Meaning Representation (AMR), a semantic representation language in which we are writing down the meanings of thousands of English sentences. We hope that a sembank of simple, whole-sentence semantic structures will spur new work in statistical natural language understanding and generation, like the Penn Treebank encouraged work on statistical parsing. This paper gives an overview of AMR and tools associated with it.
GEViTRec: Data Reconnaissance Through Recommendation Using a Domain-Specific Visualization Prevalence Design Space (2021)

Genomic Epidemiology (genEpi) is a branch of public health that uses many different data types including tabular, network, genomic, and geographic, to identify and contain outbreaks of deadly diseases. Due to the volume and variety of data, it is challenging for genEpi domain experts to conduct data reconnaissance; that is, have an overview of the data they have and make assessments toward its quality, completeness, and suitability. We present an algorithm for data reconnaissance through automatic visualization recommendation, GEViTRec. Our approach handles a broad variety of dataset types and automatically generates visually coherent combinations of charts, in contrast to existing systems that primarily focus on singleton visual encodings of tabular datasets. We automatically detect linkages across multiple input datasets by analyzing non-numeric attribute fields, creating a data source graph within which we analyze and rank paths. For each high-ranking path, we specify chart combinations with positional and color alignments between shared fields, using a gradual binding approach to transform initial partial specifications of singleton charts to complete specifications that are aligned and oriented consistently. A novel aspect of our approach is its combination of domain-agnostic elements with domain-specific information that is captured through a domain-specific visualization prevalence design space. Our implementation is applied to both synthetic data and real Ebola outbreak data. We compare GEViTRec's output to what previous visualization recommendation systems would generate, and to manually crafted visualizations used by practitioners. We conducted formative evaluations with ten genEpi experts to assess the relevance and interpretability of our results. Code, Data, and Study Materials Availability: https://github.com/amcrisan/GEVitRec.
Genetic and enzymatic basis for the differential expression of GM2 and GD2 gangliosides in human cancer cell lines. (1993)

Using beta 1,4-N-acetylgalactosaminyltransferase (EC 2.4.1.92) complementary DNA, the correlation of gene expression, enzyme activity, and expression of ganglioside antigens was analyzed in 20 human tumor cell lines. In many lines, GM2 and/or GD2 were the most complex structures examined. Northern blot analysis revealed 5.2- and 3.0-kilobase mRNAs in almost all cell lines expressing GD2 and/or GM2. Some melanoma lines, however, showed no bands although they expressed fairly high levels of GD2. These cell lines expressed very high levels of alpha 2,8-sialyltransferase and the resulting product, GD3. Semiquantitative RT-PCR demonstrated that even cell lines with no bands in Northern blot contained 0.4-2.5% of mRNA level in the highest expressing cell line. These results indicate that GD2 expression on individual cell lines is regulated not only by the expression level of the N-acetylgalactosaminyl transferase but also by the amount of its precursor structure (GD3) and alpha 2,8-sialyltransferase present in the cells. beta 1,4-N-acetylgalactosaminyltransferase activities and mRNA levels generally correlated quite closely. A few lines, however, showed lower enzyme activities than expected from their mRNA levels, indicating the possibility that the enzyme is being regulated by translational or posttranslational modification such as phosphorylation and glycosylation as well as by transcriptional regulation. Depending on their patterns of ganglioside synthesis and expression, the lines examined were classified into 6 groups which were characteristic of different tumor cell types.
Phase I trial of interleukin 2 in combination with the soluble tumor necrosis factor receptor p75 IgG chimera. (1996)

Our purpose was to determine the effective biological dose and/or maximum tolerated dose of recombinant human tumor necrosis factor receptor:IgG chimera (rhuTNFR:Fc; Immunex, Seattle, WA) in combination with interleukin 2 (IL-2) with regard to reduction in IL-2 toxicity and modulation of biological effects of high-dose IL-2 administration. Twenty-four patients with metastatic cancer were treated with escalating doses of rhuTNFR:Fc at 1, 1, 5, 10, and 20 mg/m2 i.v. on days 1 and 15 (dose levels 1-5) or 10, 20, and 30 mg/m2 days 1 and 15 plus 50% dose on days 3, 5, 17, and 19 (dose levels 6-8) prior to IL-2 at doses of 300,000 IU/kg (dose level 1) and 600,000 IU/kg (dose levels 2-8) i.v. every 8 h on days 1-5 and 15-19. The t1/2 of rhuTNFR in patients receiving IL-2 was 72 h. The median number of IL-2 doses was 24, and central nervous system, skin, and cardiac arrhythmias were the major dose-limiting toxicities. TNF bioactivity was inhibited, and the polymorphonuclear leukocyte chemotactic defect normally seen with IL-2 was not observed. Increases in C-reactive protein, IL-6, IL-8, and IL-1 receptor antagonist levels were partially suppressed relative to historical controls, whereas peripheral blood mononuclear cell phenotypes, urinary nitrate, endothelial adhesion molecule expression in skin biopsies, and cellular infiltrates in tumor biopsies were consistent with findings in patients treated with IL-2 alone. Four patients developed thyroid dysfunction. There were five responses: two complete responses (both melanoma) and three partial responses (response rate, 21%). rhuTNFR:Fc may modulate the toxicity and some of the biological effects of IL-2 while preserving antitumor activity. Dose level 6 (10 mg/m2 on days 1 and 15, and 5 mg/m2 on days 3, 5, 17, and 19) has been chosen for a randomized, double-blind, placebo-controlled trial of IL-2 with and without rhuTNFR:Fc.
Infection in bone allografts. Incidence, nature, and treatment. (1988)

Of 283 patients who had a massive allograft of bone, an infection developed in thirty-three (11.7 per cent). To assess the frequency and identify the co-morbid and predisposing factors of this devastating complication, we compared demographic data for the infected and non-infected patients. Comparison of mean age, type of graft, anatomical site of the procedure, and stage of the tumor yielded no significant differences. Multiple-regression analysis of a subgroup of eighty-two patients who had a distal femoral graft showed a correlation between infection and factors that are associated with more extensive surgery (more loss of bone, soft tissue, or skin) or with multiple operations. Approximately 30 per cent of the patients who had an infected allograft had no co-morbid or predisposing factors that could be statistically correlated with an increased risk for infection. Gram-positive organisms were the most common cause of infection, with twelve infections (36 per cent) being due to Staphylococcus epidermidis. Six patients had a single gram-negative organism and nine had mixed flora. The final result in the thirty-three patients who had an infected allograft was poor compared with that of the over-all series and of the uninfected patients. Twenty-seven infected allografts (82 per cent) were considered to be failures of treatment because amputation of the limb or resection of the graft was required to control the infection.(ABSTRACT TRUNCATED AT 250 WORDS)
SERUM PROTEOMIC PROFILING CAN DISCRIMINATE PROSTATE CANCER FROM BENIGN PROSTATES IN MEN WITH TOTAL PROSTATE SPECIFIC ANTIGEN LEVELS BETWEEN 2.5 AND 15.0 NG/ML (2004)

Our data demonstrate that high resolution mass spectroscopy can generate serum proteomic patterns that discriminate men with elevated PSA due to benign processes from men with CaP even when PSA is within the diagnostic gray zone. We are currently expanding the testing set to determine the reliability of this new technology to decrease unnecessary prostate biopsies without compromising the detection of curable CaP.
Identification of conserved and divergent domains within the envelope gene of the acquired immunodeficiency syndrome retrovirus. (1986)

The nucleotide sequences of the envelope genes of an African and a North American acquired immunodeficiency syndrome (AIDS) viral isolate have been determined. When their deduced amino acid sequences were aligned with the envelopes of the lymphoadenopathy and AIDS-associated retrovirus isolates, conserved and divergent regions were readily identified. Hypervariable stretches of 28-74 amino acids, exhibiting 20-30% amino acid identity at each position and characterized by reciprocal insertions and deletions, were confined to the gp120 external envelope protein. The origin and clinical implications of the AIDS viral env gene diversity are discussed.