gebhart/patrepeval huggingface dataset:
Cloning and expression of recombinant, functional ricin B chain. (1987)

The cDNA encoding the B chain of the plant toxin ricin has been cloned and expressed in monkey kidney COS-M6 cells. The recombinant B chain was detected by labeling the transfected cells with [35S]methionine and [35S]-cysteine and demonstrating the secretion of a protein with a Mr of 30,000-32,000 that was not present in the medium of mock-transfected COS-M6 cells. This protein was specifically immunoprecipitated by an anti-ricin or anti-B-chain antibody and the amount of recombinant B chain secreted by the COS-M6 cells was determined by a radioimmunoassay. Virtually all of the recombinant B chain formed active ricin when mixed with native A chain; it could also bind to the galactose-containing glycoprotein asialofetuin as effectively as native B chain. These results indicate that the vast majority of recombinant B chains secreted into the medium of the COS-M6 cells retain biological function.
Generation of Oxynitrenes and Confirmation of Their Triplet Ground States (2006)

New sulfoximine- and phenanthrene-based photochemical precursors to oxynitrenes have been developed. These precursors have been used to examine the chemistry and spectroscopy of oxynitrenes. The first EPR spectra of oxynitrenes are reported and are consistent with their triplet ground states. Additional support for the triplet ground state of oxynitrenes is provided by trapping and reactivity studies, nanosecond time-resolved IR investigations, and computational studies.
Ultra Lightweight Proppants: Their Use and Application in the Barnett Shale (2004)

Abstract One of the more active areas for drilling gas wells has been in the Fort Worth Basin in North Texas in a fractured shale formation called the Barnett Shale. Over 2000 wells have been drilled in this non-conventional gas reservoir over the past five years. Initial stimulation treatments in the Barnett Shale began in the early 1980&amp;#39;s and consisted of pumping moderate fracture stimulations of approximately 300,000 gals. of fluid and 300,000 lbs. of proppant, typically sand. These treatments quickly evolved to massive hydraulic fracture treatments that used extremely large volumes of conventional crosslinked fracture fluids utilizing over 750,000 gallons of fluid and over 1.0 million pounds of sand. These treatments continued to evolve through early 1997 based on the success in the East Texas area of the slickwater fracturing technique being applied to tight gas sands, in particular the Cotton Valley Sand. Since that time many operators have found success in these types of reservoirs utilizing large volumes of slickwater with low concentrations of proppant. A major concern in utilizing slickwater and fracture injection rate as the only means to transport proppant into the reservoir is the inefficiency of obtaining the most effective propped fracture. The next evolution to improving proppant transport and ultimately more effective fracture length is the use of Ultra Lightweight proppants. This paper will present the application and results of fracture treatments performed in the Barnett Shale using a new ultra lightweight propping agent. The paper will also discuss the applicable Newtonian solids transport theory and it&amp;#39;s relation to the density of the proppant and the fluid in which it is being pumped.
Integrating Customer Load and GIS Data for Improved Distribution Planning &amp; Operations (2006)

This paper describes the methodology, tools, and results for integrating customer metering and billing data with GIS and SCADA data to enhance distribution planning and operating processes, optimize capital spending, and reduce device overloading and failure. The paper features case studies of results and benefits achieved by two US utilities
Poor Clinical Sensitivity of Rapid Antigen Test for Influenza A Pandemic (H1N1) 2009 Virus (2009)

Influenza A pandemic (H1N1) 2009 virus RNA was detected by reverse transcription-PCR in 144 clinical samples from Bonn, Germany. A common rapid antigen-based test detected the virus in only 11.1% of these samples. The paramount feature of rapid test-positive samples was high virus concentration. Antigen-based rapid tests appear unsuitable for virologic diagnostics in the current pandemic.
Semiparametric Regression Functionals (1995)

Abstract A regression method is developed for a general class of functionals. A semiparametric linear model is adopted, and the regression parameters are estimated by maximizing a profiled nonparametric or empirical likelihood based on a local estimate of the conditional distribution function. Simulated and real data examples are shown, including an application of quantile regression to censored survival data from a clinical trial for myeloma.
Anti-insulin Activity in IgG-fractions from Children with Newly-diagnosed Type 1 Diabetes and Negative for Insulin Autoantibodies (2003)

Insulin autoantibodies (IAA) are often detected as the first humoral sign of beta-cell autoimmunity in prospective studies in young children with increased genetic risk of type 1 diabetes. After the appearance of IAA their level typically rise but seems to decline in many cases before the clinical presentation of type 1 diabetes. We hypothesized that the reason for the sudden drops in the levels of IAA could be the formation of immune complexes caused by binding of antibodies to free insulin in plasma. We studied whether isolation of the IgG-fraction and dissociation of immune complexes by acid treatment using protein A column results in the appearance of detectable IAA in those children with newly-diagnosed type 1 diabetes whose plasma samples test negative for IAA. IAA assay was performed in IgG-fractions and corresponding plasma samples from 17 children with type 1 diabetes and 23 unaffected children all testing negative for plasma IAA. The levels of IAA measured from IgG-fractions of diabetic children were higher than the levels of IAA measured from IgG-fractions in the control children (p = 0.004 in Mann-Whitney U-test). Forty-seven percent (8 out of 17) of newly-diagnosed patients negative for plasma IAA before IgG separation had increased levels of IAA in IgG-fractions and only 13% (3 out of 23) of controls. The levels of glutamate decarboxylase autoantibodies (GADA) did not differ between patients (n = 14) and controls (n = 21) negative for plasma GADA when measured in IgG-fractions. Our results suggest that formation of immune complexes results in false negative results in tests for IAA but not for GADA.
Gastrulation in the mouse : Growth and regionalization of the epiblast (1977)

ABSTRACT Histological determination of cell numbers in the mouse embryo between and days post coitum show that growth during this period, in which gastrulation occurs, is not uniform. Prior to primitive streak formation mean cell generation time is about 9 h. Co-incidental with the appearance of the primitive streak the embryo enters a period of rapid growth, lasting about 24 h, during which the mean cell generation time must be about 5 h in order to account for the increase in cell numbers. A more detailed study, in which variations in mitotic activity in different regions of the embryo have been analysed, has identified a small region, the so-called ‘proliferative zone’, constituting about 10 % of the whole epiblast, in which cell generation time may average as little as 2·3 h over a 24 h period. The cell generation time for other epiblast regions is estimated at about 6·5 h. It is calculated that the proliferative zone, in the 24 h period commencing with primitive streak formation, could generate about half the cells in the -day embryo. The topographical consequences of such a rapidly expanding region in the embryo are discussed in the light of other, circumstantial evidence, and it is postulated that the cells generated in the PZ may constitute the ectoderm of later stage embryos.
Intranasal Boosting with an Adenovirus-Vectored Vaccine Markedly Enhances Protection by Parenteral <i>Mycobacterium bovis</i> BCG Immunization against Pulmonary Tuberculosis (2006)

Parenterally administered Mycobacterium bovis BCG vaccine confers only limited immune protection from pulmonary tuberculosis in humans. There is a need for developing effective boosting vaccination strategies. We examined a heterologous prime-boost regimen utilizing BCG as a prime vaccine and our recently described adenoviral vector expressing Ag85A (AdAg85A) as a boost vaccine. Since we recently demonstrated that a single intranasal but not intramuscular immunization with AdAg85A was able to induce potent protection from pulmonary Mycobacterium tuberculosis challenge in a mouse model, we compared the protective effects of parenteral and mucosal booster immunizations following subcutaneous BCG priming. Protection by BCG prime immunization was not effectively boosted by subcutaneous BCG or intramuscular AdAg85A. In contrast, protection by BCG priming was remarkably boosted by intranasal AdAg85A. Such enhanced protection by intranasal AdAg85A was correlated to the numbers of gamma interferon-positive CD4 and CD8 T cells residing in the airway lumen of the lung. Our study demonstrates that intranasal administration of AdAg85A represents an effective way to boost immune protection by parenteral BCG vaccination.
Ultrastructure of Outermost Layer of Cell Wall in &lt;italic&gt;Candida albicans&lt;/italic&gt; Observed by Rapid-freezing Technique (1986)

Ultrastructures of the surface layer of unfixed and frozen-hydrated Candida albicans were observed using a low temperature technique for scanning electron microscopy (cryo-SEM), and, as a comparison, freeze-substitution and fixation for transmission electron microscopy (FSF TEM). The C. albicans showed a brush-like fibrous structure densely arranged perpendicularly to the outermost layer of the cell wall; this was confirmed and further revealed as a fibrillar layer In thin-sections by FSF TEM. The Interconnection was formed with fibrils between one cell and the next, and between the cell and its surrounding materials. It is suggested that the adherence of C. albicans cells to the host cell was mediated by the fibrillar networks or free extracellular materials secreted from the Candida cell. A similar fibrillar layer on the cell wall has also been recognized in germ tube cells and chlamydospores of C. albicans, and in other Candida species, and in Saccharomyces cerevisiae. The findings in this study, and our previous results obtained with the cell surface antigens of C. albicans by immuno-ferritin test, support us in suggesting that brush-like fibrillar structure is an intrinsic part of the cell wall in some fungi, and it may be a part of the wall mannan-protein complex In the yeast phase of C. albicans.
An encoding method for multifield sorting and indexing (1977)

Sequences of character strings with an order relation imposed between sequences are considered. An encoding scheme is described which produces a single, order-preserving string from a sequence of strings. The original sequence can be recovered from the encoded string, and one sequence of strings precedes another if and only if the encoding of the first precedes the encoding of the second. The strings may be variable length, without a maximum length restriction, and no symbols need be reserved for control purposes. Hence any symbol may occur in any string. The scheme is useful for multifield sorting, multifield indexing, and other applications where ordering on more than one field is important.
Principles of Data Mining (2001)

The growing interest in data mining is motivated by a common problem across disciplines: how does one store, access, model, and ultimately describe and understand very large data sets? Historically, different aspects of data mining have been addressed independently by different disciplines. This is the first truly interdisciplinary text on data mining, blending the contributions of information science, computer science, and statistics. The book consists of three sections. The first, foundations, provides a tutorial overview of the principles underlying data mining algorithms and their application. The presentation emphasizes intuition rather than rigor. The second section, data mining algorithms, shows how algorithms are constructed to solve specific problems in a principled manner. The algorithms covered include trees and rules for classification and regression, association rules, belief networks, classical statistical models, nonlinear models such as neural networks, and local "memory-based" models. The third section shows how all of the preceding analysis fits together when applied to real-world data mining problems. Topics include the role of metadata, how to handle missing data, and data preprocessing.
Effective Synthesis of Tamoxifen Using Nickel-Catalyzed Arylative Carboxylation (2006)

Tamoxifen was synthesized using a nickel-catalyzed arylative carboxylation developed by our group. The key compound, tetrasubstituted alkene, was synthesized from disubstituted alkyne using a catalytic amount of Ni(0) and DBU in the presence of Ph2Zn under an atmosphere of carbon dioxide. The reaction proceeded smoothly in a regio- and stereoselective manner, and the resultant tetrasubstituted alkene was converted into tamoxifen.
Identification of a Gliadin T‐Cell Epitope in Coeliac Disease: General Importance of Gliadin Deamidation for Intestinal T‐Cell Recognition (1998)

Coeliac disease probably results from a T‐cell response to wheat gliadin and is associated to HLA‐DQ2. No gliadin epitopes recognized by intestinal T cells have yet been identified, limiting our understanding of the pathogenesis. Gut‐lesion‐derived DQ2‐restricted T cells from coeliac disease patients were used to identify an epitope within a purified γ‐type gliadin. The structure of the epitope was characterized by mass spectrometry and verified by synthesis. The epitope (QPQQSFPEQQ) results from deamidation of a distinct glutamine in the native structure. This deamidation is important for binding to DQ2 and T‐cell recognition. Other gut‐derived T cells fail to recognize the epitope, although deamidation of unfractionated gliadin enhances the response of all gut‐derived DQ2‐restricted T cells isolated from several patients. Several DQ2‐restricted T‐cell epitopes exist, but for all of them deamidation of glutamine residues appears to be critical for creation of active epitopes. Native gliadin has few negatively charged residues but is very rich in glutamine. After deamidation gliadin becomes a rich source of DQ2 epitopes thus providing a link between DQ2, gliadin and coeliac disease. The necessity for modification may have general immunological relevance.
[Genes related with male gonadal morphogenesis in mammals]. (2008)

Gene expressions are sex-specific in the sex development of mammals. Different genes express in different phases and tend to change with the time. The functions of some genes, such as SRY, SOX9, SOX8, DAX1, and FGF9, have already been defined in male gonadal morphogenesis. This paper presents a review of the genes involved in the formation of the male gonad in mammals.
Synthesis and applications of oligoribonucleotides with selected 2′-O-methylation using the 2′-O-[1-(2-fluorophenyl)-4-methoxypiperidin-4-yl] protecting group (1990)

The synthesis of base protected 5'-O-dimethoxytrityl-2'-O-[1-(2- fluorophenyl)-4-methoxypiperidin-4-yl]-3'-O-(2-cyanoethyl N,N-diisopropylphosphoramidites) is described, using phenoxyacetyl protection for the exocyclic amino groups of guanosine and adenosine and acetyl protection of the amino group of cytidine. High yield assembly of these building blocks into oligoribonucleotides on aminopropyl controlled pore glass was achieved using 5-(4-nitrophenyl)-1H-tetrazole as activator. Mixed sequences containing selected 2'-O-methylation were also synthesised and their significance for the study of RNA biochemistry is discussed.
A promoterless retroviral vector indicates that there are sequences in U3 required for 3' RNA processing. (1987)

We constructed a retrovirus vector in which all viral transcriptional signals are deleted during provirus formation. This vector would be safer and more useful in gene-transfer experiments. Construction of this vector involved the deletion of all of the U3 sequence except for 10 base pairs, required for integration, from the right-side long terminal repeat. We found that this deletion resulted in an inability to propagate virus efficiently. When we inserted sequences containing all of the signals for polyadenylylation of simian virus 40 late mRNA at the end of our vector, we were able to propagate virus efficiently. This result indicates that there are sequences in U3 upstream from AAUAAA that are essential for 3' processing of viral RNA.
Synthesis of 3-Pyridinols. II. Reaction of 4-Methyloxzaole with Dienophiles (1965)

Condensation of I with several dienophiles caused three types of reaction, i.e. reaction A, B, and C; reaction B and C afforded 3-pyridinol derivatives. A likely mechanism of these reactions are considered as Diels-Alder's condensation of I with dienophiles and subsequent aromatization to pyridine nuclei.
Enhancing the Take of Injected Adipose Tissue by a Simple Method for Concentrating Fat Cells (2005)

Injection of aspirated fat for the correction of tissue defects is a common procedure in plastic surgery. The reported rates of fat cell survival vary greatly in the medical literature, and different techniques of harvesting, processing, and reinjecting the fat cells are claimed to be responsible for these differences. However, there is no agreement concerning the best way to process the harvested fat before reinjection. The present study was initiated to examine and evaluate the effect of a simple method of isolating the fat particles on the outcome of fat graft survival. In this study, the nude mouse model was used to examine the survival and take of the fat graft concentrated before injection by the cumbersome recommended closed centrifugation technique in comparison with the authors' recommended open method, using an operating room cotton towel as a platform for concentrating the fat cells and separating them from fluids, oil, and debris. One milliliter of concentrated human fat cells preprocessed by towel separation was injected into the nuchal subcutis of 11 nude mice in the study group, and the same amount of fat that was preprocessed by centrifugation was injected into 11 control mice. Injected fat survived in both groups. No significant differences were found regarding fat graft weight and volume, although a tendency for better survival was noticed in the experimental group. Histologic evaluation of the grafts revealed significantly less fibrosis within the study group, meaning that the quality of the fat grafts was better. The authors found this method to be simple, cheap, and friendly to the surgeon in comparison with traditional processing using the centrifuge.
Network Neutrality: Verizon v. FCC (2012)

The Federal Communications Commission (“FCC”) is once again locking horns with the broadband behemoth, Verizon, over the issue of network neutrality. Although this conflict between the government and corporate giants is far from new, recent events have forced courts to give it close scrutiny. Given the explosive pace at which technology has expanded and permeated citizens’ daily lives, the judgments rendered have greater significance now than ever before.
Laser Ray Tracing versus Hartmann–Shack sensor for measuring optical aberrations in the human eye (2000)

A comparison and validation study of Laser Ray Tracing (LRT) and Hartmann-Shack wave-front-sensor (to be referred to as H-S) methods was carried out on both artificial and human eyes. The aim of this work was double. First, we wanted to verify experimentally the equivalence of single- and double-pass measurements for both H-S and LRT. This interest is due to the impossibility of making single-pass measurements in human eyes. In addition, we wanted to validate the LRT technique by comparing it with the H-S wave-front sensor, currently used in many physiological optics laboratories. Comparison of the different methods and configurations carried out in the artificial eye yielded basically the same results in all cases, which means a reciprocal validation of both LRT and H-S, in either single- or double-pass configurations. Other aspects, such as robustness against speckle noise or the influence of the size of the entrance (H-S) or exit (LRT) pupil were studied as well. As a global reference, the point-spread function (PSF) of the artificial eye was recorded directly on a CCD camera and compared with simulated PSF's computed from the experimental aberration data. We also applied these two methods to real eyes (double pass), finding again a close match between the resulting aberration coefficients and also between the standard errors for two normal subjects. However, for one myopic eye with an especially low optical quality (RMS wave-front error >2 microm) and asymmetric aberrations, the array of spots recorded with the H-S sensor was highly distorted and too difficult to analyze.
A Murine Model in Which Protection Correlates with Pertussis Vaccine Efficacy in Children Reveals Complementary Roles for Humoral and Cell-Mediated Immunity in Protection against<i>Bordetella pertussis</i> (1998)

The results of phase 3 efficacy trials have shown that acellular and whole-cell pertussis vaccines can confer protection against whooping cough. However, despite the advances in vaccine development, clinical trials have not provided significant new information on the mechanism of protective immunity against Bordetella pertussis. Classical approaches based on measurement of antibody responses to individual antigens failed to define an immunological correlate of protection. A reliable animal model, predictive of acellular and whole-cell pertussis vaccine potency in children, would facilitate an elucidation of the mechanism of immune protection against B. pertussis and would assist in the regulatory control and future development of pertussis vaccines. In this study, we have shown that the rate of B. pertussis clearance following respiratory challenge of immunized mice correlated with vaccine efficacy in children. Using this model together with mice with targeted disruptions of the gamma interferon (IFN-gamma) receptor, interleukin-4 or immunoglobulin heavy-chain genes, we have demonstrated an absolute requirement for B cells or their products in bacterial clearance and a role for IFN-gamma in immunity generated by previous infection or immunization with the whole-cell pertussis vaccine. The results of passive immunization experiments suggested that protection early after immunization with acellular pertussis vaccines is mediated by antibody against multiple protective antigens. In contrast, more complete protection conferred by previous infection or immunization with whole-cell pertussis vaccines reflected the induction of Th1 cells. Our findings suggest that the mechanism of immunity against B. pertussis involves humoral and cellular immune responses which are not directed against a single protective antigen and thus provide an explanation for previous failures to define an immunological correlate of protection.