gebhart/patrepeval huggingface dataset:
Building a Data Warehouse for Decision Support (1995)

From the Publisher:
In Building a Data Warehouse for Decision Support, Second Edition, a team of the world's leading experts presents a start-to-finish, state-of-the-art guide to designing and implementing data warehouses. You'll find up-to-the-minute solutions-oriented recommendations for the entire data warehouse development lifecycle, including best practices for requirements gathering and identifying business objectives; critical success factors - why and how they affect the success of your project; planning, scoping, and managing your data warehouse project; and managing metadata for a production data warehouse.
Idiotype vaccination against murine B cell lymphoma. Humoral and cellular requirements for the full expression of antitumor immunity. (1990)

The roles of humoral and cellular antitumor immune responses induced by immunization with tumor-derived idiotypic IgM were studied in a syngeneic, transplantable B cell lymphoma (38C13) of C3H mice. Id vaccination with keyhole limpet hemocyanin-conjugated Id induced protection against a subsequent lethal tumor challenge. Such immunizations elicited anti-idiotypic antibodies that were cytotoxic in in vitro antibody-dependent cellular cytotoxicity assays as well as in vivo passive transfer experiments. L3T4+ T cells, which proliferated in vitro in response to the specific Id protein, were also induced. However, cells mediating direct cytotoxicity, either in vitro or in vivo, were not observed in the lymph nodes, spleens, or peritoneal cavity of immune mice or at the site of tumor regression as demonstrated by using a tumor sponge implantation model. In addition, in vitro sensitization of immune lymphocytes against 38C13 tumor cells failed to induce cytotoxicity. Immunization with lipid conjugated Id also elicited a T cell proliferative response but failed to induce anti-idiotypic antibodies and did not confer resistance to tumor growth. These results suggest that anti-idiotypic antibodies play the major role in the destruction of 38C13 tumor cells. However, in vivo depletion of L3T4+ or Lyt-2+ cells from 38C-Id-keyhole limpet hemocyanin-immunized mice resulted in diminished protection against a tumor challenge. Thus, although humoral responses appear to play the predominant part in tumor destruction, cellular responses are also required for the full expression of antitumor immunity in this system.
New CFSE-based assay to determine susceptibility to lysis by cytotoxic T cells of leukemic precursor cells within a heterogeneous target cell population (2003)

For the clinical evaluation of the efficacy of cellular immunotherapy it is necessary to analyze the effector functions of T cells against primary leukemic target cell populations which are usually considerably heterogeneous caused by differential maturation stages of the leukemic cells. An appropriate assay should not only allow the quantitative analysis of rapid cell death induction as measured by the conventional 51Cr release assay but also of the more slowly executing pathways of T-cell-induced apoptosis occurring within days instead of hours which cannot be measured using this method. Furthermore, it should dissect the differential susceptibility to T-cell-induced cell death of various target cell subpopulations and characterize the malignant precursor cells capable of producing malignant progeny. To fulfill these requirements we developed a new assay based on carboxyfluorescein diacetate succinimidyl ester (CFSE) labeling of the target cell population combined with antibody staining of specific cell populations and addition of fluorescent microbeads to quantitatively monitor target cell death occurring within a longer time frame up to at least 5 days. This new assay facilitates the analysis of differential recognition of distinct cell types within a heterogeneous target cell population and allows simultaneously evaluation of the proliferative status of surviving target cells in response to relevant cytokines.
Immunomodulatory activity ofLactobacillusstrains isolated from fermented vegetables and infant stool (2011)

Four Lactobacillus strains - Lactobacillus plantarum CJLP133, L. plantarum CJLP243, L. plantarum CJNR26, and Lactobacillus gasseri CJMF3 - were isolated from Korean fermented food or healthy infant feces, and their capacity to modulate cellular and humoral immune responses was studied. Feeding of the tested lactobacilli for 8 weeks did not alter the weight of and cell numbers in the spleen of mice. However, CJLP133 and CJLP243 strains increased the T lymphocyte population in the spleen of mice, while CJNR26 and CJMF3 increased the B lymphocyte population. In splenocytes treated with concanavalin A, ingestion of CJLP133 and CJLP243 promoted T lymphocyte proliferation and secretion of T cell cytokines, whereas feeding of the CJNR26 and CJMF3 strains enhanced B lymphocyte proliferation in splenocytes treated with lipopolysaccharide and plaque formation. These results suggest that CJLP133 and CJLP243 have immunostimulating activity through the enhancement of T cell activation, while CJNR26 and CJMF3 exhibit immunopotentiation through the increment of B cell activation.
Specificity versus stability in computational protein design (2005)

Protein-protein interactions can be designed computationally by using positive strategies that maximize the stability of the desired structure and/or by negative strategies that seek to destabilize competing states. Here, we compare the efficacy of these methods in reengineering a protein homodimer into a heterodimer. The stability-design protein (positive design only) was experimentally more stable than the specificity-design heterodimer (positive and negative design). By contrast, only the specificity-design protein assembled as a homogenous heterodimer in solution, whereas the stability-design protein formed a mixture of homodimer and heterodimer species. The experimental stabilities of the engineered proteins correlated roughly with their calculated stabilities, and the crystal structure of the specificity-design heterodimer showed most of the predicted side-chain packing interactions and a main-chain conformation indistinguishable from the wild-type structure. These results indicate that the design simulations capture important features of both stability and structure and demonstrate that negative design can be critical for attaining specificity when competing states are close in structure space.
Simple Constructions of Almost k‐wise Independent Random Variables (1992)

Abstract We present three alternative simple constructions of small probability spaces on n bits for which any k bits are almost independent. The number of bits used to specify a point in the sample space is (2 + o (1)) (log log n + k /2 + log k + log 1/ϵ), where ϵ is the statistical difference between the distribution induced on any k bit locations and the uniform distribution. This is asymptotically comparable to the construction recently presented by Naor and Naor (our size bound is better as long as ϵ &lt; 1/( k log n )). An additional advantage of our constructions is their simplicity.
Compartmental and noncompartmental pharmacokinetic analyses of minocycline hydrochloride in the dog (1985)

Six adult dogs were given 5 mg of minocycline hydrochloride/kg of body weight IV. Pharmacokinetic evaluation of the serum drug concentration versus time data was performed, using the 2-compartment open model, the 3-compartment open model, and a noncompartmental model involving use of the statistical moment theory. All pharmacokinetic values except clearance were model independent. Minocycline half-life ranged between 6.48 and 7.24 hours; volume of distribution at steady state, between 1.859 +/- 0.368 and 2.001 +/- 0.468 L/kg; and clearance, between 3.195 +/- 0.618 and 3.424 +/- 0.684 ml/min/kg. These data are similar to those reported for oxytetracycline and indicate that the frequency of administration of the 2 tetracyclines should be the same. Three of the 6 dogs developed an adverse response to the IV injection of minocycline. Dog 1 developed urticaria and had initial serum drug concentrations of approximately 2 times the mean concentrations for the other dogs; values were not included in the pharmacokinetic analysis. Two other dogs had transient signs indicating cardiovascular depression or hypotension; their data were included. Due to the frequency of the unexpected reactions found in this study, it was concluded that dogs should not be given minocycline rapidly IV.
Elevated synovial fluid levels of interleukin‐6 and tumor necrosis factor associated with early experimental canine osteoarthritis (1993)

This is the first study of SF levels of cytokines in early experimental OA. Our results show surprisingly high levels of IL-6 in operated joints, where the cytokine could act directly on the chondrocytes, and thus play a role in mediating their responses to cartilage injury.
High specific activity chemiluminescent and fluorescent markers: Their potential application to high sensitivity and ‘multi‐analyte’ immunoassays (1989)

The sensitivities of immunoassays relying on conventional radioisotopic labels (i.e. radioimmunoassay (RIA) and immunoradiometric assay (IRMA) permit the measurement of analyte concentrations above ca 10(7) molecules/ml. This limitation primarily derives, in the case of 'competitive' or 'limited reagent' assays, from the 'manipulation errors arising in the system combined with the physicochemical characteristics of the particular antibody used; however, in the case of 'non-competitive' systems, the specific activity of the label may play a more important constraining role. It is theoretically demonstrable that the development of assay techniques yielding detection limits significantly lower than 10(7) molecules/ml depends on: (1) the adoption of 'non-competitive' assays designs; (2) the use of labels of higher specific activity than radioisotopes; (3) highly efficient discrimination between the products of the immunological reactions involved. Chemiluminescent and fluorescent substances are capable of yielding higher specific activities than commonly used radioisotopes when used as direct reagent labels in this context, and both thus provide a basis for the development of 'ultra-sensitive', non-competitive, immunoassay methodologies. Enzymes catalysing chemiluminescent reactions or yielding fluorescent reaction products can likewise be used as labels yielding high effective specific activities and hence enhanced assay sensitivities. A particular advantage of fluorescent labels (albeit one not necessarily confined to them) lies in the possibility they offer of revealing immunological reactions localized in 'microspots' distributed on an inert solid support. This opens the way to the development of an entirely new generation of 'ambient analyte' microspot immunoassays permitting the simultaneous measurement of tens or even hundreds of different analytes in the same small sample, using (for example) laser scanning techniques. Early experience suggests that microspot assays with sensitivities surpassing that of isotopically based methodologies can readily be developed.
Cellular variability in the development of tight junctions after activation of protein kinase C (1992)

Phorbol 12-myristate 13-acetate (PMA) decreases the tight junction conductance (TJC) during the reorganization of LLC-PK1A monolayers, but has the opposite effect in LLC-PK1B4, MDCK, and MDCK4 cells. Because no protein synthesis was required for the effects of PMA on the TJC of LLC-PK1A monolayers, we conclude that the regulation of the tight junction by protein kinase C (PKC) is a posttranslational event. In LLC-PK1A monolayers with existing tight junctions, PMA produced an initial increase in the TJC that reverted later to control values despite the continuous presence of PMA and cycloheximide. The inhibitory effect of PMA on the other cell lines was not revertible. A downregulation of total PKC activity and phorbol ester receptors was only observed during the reorganization of LLC-PK1A monolayers. PMA further increases this downregulation. This indicates that the peculiar response to PMA observed in LLC-PK1A monolayers is the result of two concurrent events: 1) the early activation of the enzyme just before the reorganization of the tight junctions begin, and 2) its late downregulation induced after prolonged exposure to phorbol esters. We conclude that PKC regulates the development of the occluding junctions, but through different mechanisms dependent on the characteristics of the cells.
Fast Calculation of Molecular Polar Surface Area as a Sum of Fragment-Based Contributions and Its Application to the Prediction of Drug Transport Properties (2000)

Molecular polar surface area (PSA), i.e., surface belonging to polar atoms, is a descriptor that was shown to correlate well with passive molecular transport through membranes and, therefore, allows prediction of transport properties of drugs. The calculation of PSA, however, is rather time-consuming because of the necessity to generate a reasonable 3D molecular geometry and the calculation of the surface itself. A new approach for the calculation of the PSA is presented here, based on the summation of tabulated surface contributions of polar fragments. The method, termed topological PSA (TPSA), provides results which are practically identical with the 3D PSA (the correlation coefficient between 3D PSA and fragment-based TPSA for 34 810 molecules from the World Drug Index is 0.99), while the computation speed is 2-3 orders of magnitude faster. The new methodology may, therefore, be used for fast bioavailability screening of virtual libraries having millions of molecules. This article describes the new methodology and shows the results of validation studies based on sets of published absorption data, including intestinal absorption, Caco-2 monolayer penetration, and blood-brain barrier penetration.
Combination of Serine Protease Inhibitor FUT-175 and Thromboxane Synthetase Inhibitor OKY-046 Decreases Cerebral Vasospasm in Patients with Subarachnoid Hemorrhage. (1998)

The preventive effect of the serine protease inhibitor FUT-175 (nafamostat mesilate), a potent inhibitor of the complement system, against vasospasm was evaluated in 34 high risk patients with thick and diffuse subarachnoid hemorrhage (SAH) demonstrated by computed tomography corresponding to Fisher group 3. All patients underwent surgery within 96 hours following SAH and received the thromboxane A2 synthetase inhibitor, OKY-046, as part of standard care. FUT-175 (40-160 mg/day) was administered during the initial 4 days following surgery. 455 patients treated without FUT-175 in the Nagasaki SAH Data Bank (non-FUT group) formed the control group. FUT-175 significantly decreased the incidence of symptomatic vasospasm in patients with severe neurological grade (Hunt and Hess grade 3, p < 0.02; Hunt and Hess grade 4, p < 0.02). The incidence of favorable outcome was 76.5% in the FUT group and 60.4% in the non-FUT group, but not statistically different. However, when patients of Hunt and Hess grade 5 were excluded, the FUT group had a significantly improved outcome (p < 0.05). This study suggests that FUT-175 has an additive effect to OKY-046 in preventing vasospasm in high risk patients with severe SAH.
The virus neutralizing activity of antibodies specific to the envelope and nucleocapsid of equine herpesvirus type 1. (1979)

Antibodies specific to the envelope or nucleocapsid of the Kentucky-D strain of equine herpesvirus type 1 were isolated from convalescent horse serum by immunoadsorption on cyanogen bromide-activated Sepharose conjugated with equine herpesvirus type 1 envelopes or nucleocapsids, with subsequent elution by glycine buffer. In double immunodiffusion and immunolectrophoresis reactions, the eluted proteins appeared to belong to the IgG fraction of horse serum. Antibodies directed against the viral envelope neutralized equine herpesvirus type 1 in a plaque neutralization test, while antibodies against the nucleocapsid showed no virus neutralizing activity.
A 0.13[mu]m CMOS 78dB SNDR 87mW 20MHz BW CT [Delta Sigma] ADC with VCO-based integrator and quantizer (2009)

In this paper we demonstrate a new technique that eliminates the impact of K[subscript v] nonlinearity by preserving the integral relationship of the VCO output phase to the input signal. Leveraging the VCO output phase directly precludes the need to span the entire nonlinear K[subscript v] characteristic since small perturbations (in the range of 10s of mV) at the tuning node are sufficient to shift the VCO phase by a substantial amount. Since an open-loop VCO is sensitive to frequency offsets and drift, and easily saturates its phase detector for large input signals, some form of negative feedback is necessary. Here, a multibit DAC subtracts the previously quantized phase value from the VCO input, creating a residue that is integrated during the next clock cycle. This feedback loop not only allows large signals to drive the VCO without incurring distortion from K[subscript v] nonlinearity, but also it is a 1s,-order CT DeltaSigma ADC loop, and it therefore 1s,-order shapes quantization noise.
Synthesis of sugar-containing polymers by self-condensation with diboronic acid (1995)

Self-condensation of 3,3′-bis(N,N-di-n-butylaminomethyl)biphenyl-4,4′-diboronic acid and saccharides yields polymers containing saccharides in the main chain: they show unique CD spectroscopic properties which reflect the chirality of saccharides.
Estimating Vessel Travel Time Statistics for Inland Waterways with Automatic Identification System Data (2015)

A constrained fiscal environment has pushed the U.S. Army Corps of Engineers (USACE) in recent years towards an asset management paradigm that seeks objective and consistent performance measures for assessing navigation project performance, identifying risks to waterway system functionality, and gaining a better understanding of how operations and maintenance decisions translate into levels of service provided to the national marine transportation system. One emerging technology that is supporting these efforts is the Automatic Identification System (AIS), required for most commercial vessels operating in U.S. coastal waters and widely used voluntarily by vessels operating on the inland waterway system as well. Archived AIS vessel position reports can be mined to obtain robust statistical representations of waterway performance through time, as measured via quantities such as origin-destination travel times, average vessel speeds, and dwell times within congested port areas. In this paper, a methodology is presented for establishing baseline travel time statistics from archived AIS position reports for waterway segments within the inland river system. Established methods from traditional traffic engineering approaches to freeway performance monitoring are applied to marine vessels traveling through segments along the Lower Mississippi River. Specifically, link-based travel time statistics for individual segments of waterway are compared to the full origin-destination, path-based statistics. Though marine traffic along the inland river system lends itself in part to analysis via traditional traffic engineering methods, the operational logistics of inland river shipping (e.g. stopovers for staging barges, loading and unloading cargo, etc.) also create some fundamental differences in traffic patterns that require additional analysis and new metrics to accurately capture waterway level of service to marine transportation stakeholders. The methods presented here will help the USACE and vessel operators determine baseline travel times for inland shipping, provide valuable voyage planning information that can be broadcast to mariners through the River Information Services (RIS) and e-Navigation programs, and when coupled with a rolling archive of AIS position reports, provide a robust capability for monitoring and quantifying waterway performance going forward.
Axonal Morphometric Correlates of Evoked Potentials in Experimental Spinal Cord Injury (1990)

Cortical somatosensory-evoked potentials recorded at a succession of intervals after contusion injury of the cat spinal cord were compared with the numbers of axons surviving in transverse sections of the lesion at 3 months postinjury. In a sample of 25 animals, with injuries varying from ca.87% to 99% loss of myelinated axons in the white matter, there was a significant correlation between chronic axonal survival and the amplitude of the SEP recorded from 30 min to 1 day postinjury. There was little or no correlation between axon numbers and SEPs recorded at 3 months, within this narrow but crucial range of injury intensity. Robust, relatively normal waveforms could be obtained from animals with as few as 2% of the original axon population surviving at the lesion site, and from animals in which all the surviving axons in the dorsal columns were restricted to the outer 100–200 um of tissue. In other cases, repeatable SEPs could not be recorded from animals with >5% survival of axons. SEPs were lost immediately after contusion injury, but partially recovered within the first 4 hours in ca.30% of cases. There was a secondary severe reduction of SEP amplitude within the first day in most examples of early recovery. Most of the final recovery of chronic SEP amplitude occurred within 2–4 weeks. SEPs from chronic injuries are useful indicators of conduction in spinal cord sensory tracts, though their amplitude cannot be interpreted as a measurement of axonal survival. Acute recovery of the SEP is predictive of chronic functional improvement and indicative of significant axonal survival. Reduction of SEP amplitude is a much more sensitive indicator of acute axonal distress than of chronic axonal loss.
Region-specific differentiation of neural tube-derived neuronal restricted progenitor cells after heterotopic transplantation (2000)

Spinal cord neuronal restricted progenitor (NRP) cells, when transplanted into the neonatal anterior forebrain subventricular zone, migrate to distinct regions throughout the forebrain including the olfactory bulb, frontal cortex, and occipital cortex but not to the hippocampus. Their migration pattern and differentiation potential is distinct from anterior forebrain subventricular zone NRPs. Irrespective of their final destination, NRP cells do not differentiate into glia. Rather they synthesize neurotransmitters, acquire region-specific phenotypes, and receive synapses from host neurons after transplantation. Spinal cord NRPs express choline acetyl transferase even in regions where host neurons do not express this marker. The restricted distribution of transplanted spinal cord NRP cells and their acquisition of varied region-specific phenotypes suggest that their ultimate fate and phenotype is dictated by a combination of intrinsic properties and extrinsic cues from the host.
Myeloid-Derived Suppressor Cells: Linking Inflammation and Cancer (2009)

Many cancer immunotherapies developed in experimental animals have been tested in clinical trials. Although some have shown modest clinical effects, most have not been effective. Recent studies have identified myeloid-origin cells that are potent suppressors of tumor immunity and therefore a significant impediment to cancer immunotherapy. "Myeloid-derived suppressor cells" (MDSC) accumulate in the blood, lymph nodes, and bone marrow and at tumor sites in most patients and experimental animals with cancer and inhibit both adaptive and innate immunity. MDSC are induced by tumor-secreted and host-secreted factors, many of which are proinflammatory molecules. The induction of MDSC by proinflammatory mediators led to the hypothesis that inflammation promotes the accumulation of MDSC that down-regulate immune surveillance and antitumor immunity, thereby facilitating tumor growth. This article reviews the characterization and suppressive mechanisms used by MDSC to block tumor immunity and describes the mechanisms by which inflammation promotes tumor progression through the induction of MDSC.