gebhart/patrepeval huggingface dataset:
Nonparametric Estimation of Nonstationary Spatial Covariance Structure (1992)

Abstract Estimation of the covariance structure of spatial processes is a fundamental prerequisite for problems of spatial interpolation and the design of monitoring networks. We introduce a nonparametric approach to global estimation of the spatial covariance structure of a random function Z(x, t) observed repeatedly at times ti (i = 1, …, T) at a finite number of sampling stations xi (i = 1, 2, …, N) in the plane. Our analyses assume temporal stationarity but do not assume spatial stationarity (or isotropy). We analyze the spatial dispersions var(Z(xi, t) − Z(xj, t)) as a natural metric for the spatial covariance structure and model these as a general smooth function of the geographic coordinates of station pairs (xi, xj ). The model is constructed in two steps. First, using nonmetric multidimensional scaling (MDS) we compute a two-dimensional representation of the sampling stations for which a monotone function of interpoint distances δij approximates the spatial dispersions. MDS transforms the problem into one for which the covariance structure, expressed in terms of spatial dispersions, is stationary and isotropic. Second, we compute thin-plate splines to provide smooth mappings of the geographic representation of the sampling stations into their MDS representation. The composition of this mapping f and a monotone function g derived from MDS yields a nonparametric estimator of var(Z(xa, t) − Z(xb, t)) for any two geographic locations xa and xb (monitored or not) of the form g(|f(xa ) − f(xb )|). By restricting the monotone function g to a class of conditionally nonpositive definite variogram functions, we ensure that the resulting nonparametric model corresponds to a nonnegative definite covariance model. We use biorthogonal grids, introduced by Bookstein in the field of morphometrics, to depict the thin-plate spline mappings that embody the nature of the anisotropy and nonstationarity in the sample covariance matrix. An analysis of mesoscale variability in solar radiation monitored in southwestern British Columbia demonstrates this methodology.
Partitioned successive-cancellation list decoding of polar codes (2016)

Successive-cancellation list (SCL) decoding is an algorithm that provides very good error-correction performance for polar codes. However, its hardware implementation requires a large amount of memory, mainly to store intermediate results. In this paper, a partitioned SCL algorithm is proposed to reduce the large memory requirements of the conventional SCL algorithm. The decoder tree is broken into partitions that are decoded separately. We show that with careful selection of list sizes and number of partitions, the proposed algorithm can outperform conventional SCL while requiring less memory.
Prediction Markets (2004)

We analyze the extent to which simple markets can be used to aggregate disperse information into efficient forecasts of uncertain future events. Drawing together data from a range of prediction contexts, we show that market-generated forecasts are typically fairly accurate, and that they outperform most moderately sophisticated benchmarks. Carefully designed contracts can yield insight into the market's expectations about probabilities, means and medians, and also uncertainty about these parameters. Moreover, conditional markets can effectively reveal the market's beliefs about regression coefficients, although we still have the usual problem of disentangling correlation from causation. We discuss a number of market design issues and highlight domains in which prediction markets are most likely to be useful.
An investigation on the operational improvement in robotic palletisation (2010)

A Pallet Loading Problem (PLP) occurs when identical rectangular boxes are to be stacked and packed on a rectangular pallet. The problem has many practical applications in distribution and logistics in packaging industries. An increase in the number of boxes that can be shipped on a pallet directly reduces the cost. In automated manufacturing palletising operations, the Pallet Loading Problem (PLP) usually deals with generating optimal pallet patterns of boxes on a pallet but a purely mathematical solution does not consider the physical aspects and restrictions encountered when using the robot and the gripper to implement these patterns. Therefore, merely getting an optimal pallet pattern does not guarantee an optimal pattern placement strategy. Very few published literature is available to address this problem, there is a need to develop a methodology that considers the palletisers physical characteristics and limitations in robotic palletising systems. This paper presents the development of a pallet pattern placement strategy with practical implementations for five-block patterns with the aim of improving the operational efficiency in robotic palletisation.
Genome-Wide Association Analysis Identifies Loci for Type 2 Diabetes and Triglyceride Levels (2007)

New strategies for prevention and treatment of type 2 diabetes (T2D) require improved insight into disease etiology. We analyzed 386,731 common single-nucleotide polymorphisms (SNPs) in 1464 patients with T2D and 1467 matched controls, each characterized for measures of glucose metabolism, lipids, obesity, and blood pressure. With collaborators (FUSION and WTCCC/UKT2D), we identified and confirmed three loci associated with T2D-in a noncoding region near CDKN2A and CDKN2B, in an intron of IGF2BP2, and an intron of CDKAL1-and replicated associations near HHEX and in SLC30A8 found by a recent whole-genome association study. We identified and confirmed association of a SNP in an intron of glucokinase regulatory protein (GCKR) with serum triglycerides. The discovery of associated variants in unsuspected genes and outside coding regions illustrates the ability of genome-wide association studies to provide potentially important clues to the pathogenesis of common diseases.
Diagnosis of luteal phase inadequacy. (1980)

Plasma progesterone concentrations drawn at the time of endometrial biopsy in 26 infertility patients with histologically documented luteal phase inadequacy were compared with those of 26 infertility patients with normal biopsies. Although as a group the former patients had lower progesterone values and shorter cycles, there was considerable overlap. Therefore, although plasma progesterone determinations and temperature charts are useful in the detection of ovulation and in the interpretation of the biopsy results, a properly obtained endometrial biopsy is essential for the diagnosis of luteal phase inadequacy.
Preparation of Small‐Molecule Microarrays by trans‐Cyclooctene Tetrazine Ligation and Their Application in the High‐Throughput Screening of Protein–Protein Interaction Inhibitors of Bromodomains (2013)

Fast and efficient: A library of trans-cyclooctene (TCO)-modified small molecules were immobilized on tetrazine-functionalized glass slides by using the fastest bioorthogonal reaction known. The resulting small-molecule microarray was screened against a variety of human bromodomains to identify protein–protein interaction inhibitors. As a service to our authors and readers, this journal provides supporting information supplied by the authors. Such materials are peer reviewed and may be re-organized for online delivery, but are not copy-edited or typeset. Technical support issues arising from supporting information (other than missing files) should be addressed to the authors. Please note: The publisher is not responsible for the content or functionality of any supporting information supplied by the authors. Any queries (other than missing content) should be directed to the corresponding author for the article.
Liver regeneration and hepatocarcinogenesis in transforming growth factor-α-targeted mice (1996)

Transforming growth factor-alpha (TGF alpha), a member of the epidermal growth factor receptor ligand family, has been implicated in the regeneration and transformation of liver. Our recent development of mice that are homozygous for a disrupted TGF alpha gene allowed us to assess the requirement for this growth factor in these complex processes. We report here that although a 70% hepatectomy produced a significant increase in hepatic TGF alpha protein levels in wild-type mice, liver regeneration nevertheless proceeded normally in the absence of the growth factor. The hepatocyte labeling indices determined for homozygous targeted and wild-type mice at 36 and 48 h after hepatectomy were comparable, and the total liver DNA to body weight ratios 8 d after hepatectomy were essentially identical for the two genotypes. These results indicate that TGF alpha, is not necessary for liver regeneration. To test its requirement in liver carcinogenesis, young mice were administered single doses of diethylnitrosamine (DEN) with or without subsequent chronic treatment with the promoting agent phenobarbital (PB). Both wild-type and homozygous mutant male mice treated with DEN or DEN plus PB developed multiple preneoplastic foci or tumors by 9 mo of age with relatively high incidence. However, while five of 88 tumors in wild-type mice attained a diameter greater than 5 mm and were classified as hepatocellular carcinomas, none of 132 tumors in livers of targeted mice reached this size. Furthermore, three of these large wild-type tumors expressed significantly elevated levels of TGF alpha protein compared with normal liver. These results indicate that TGF alpha is not required for early events in chemically induced hepatocarcinogenesis but suggest that it could be important in the progression from small preneoplastic foci to large tumors.
Tumor necrosis factor enhances eosinophil toxicity to Schistosoma mansoni larvae. (1986)

Tumor necrosis factor (TNF) is a monocyte product that kills or inhibits the growth of certain tumor cells. Its cell source and physical characteristics suggest that it is similar to a monokine, eosinophil-cytotoxicity-enhancing factor (M-ECEF), that activates human eosinophil toxicity to Schistosoma mansoni larvae. The availability of recombinant human TNF allowed us to test this possibility. The data show that TNF has no direct effect on the parasites but enhances eosinophil toxicity to the parasites in a dose-dependent fashion. This effect is specific for eosinophils and not neutrophils. TNF and the eosinophil-specific activity of TNF are coeluted with M-ECEF in reversed-phase HPLC. Further, M-ECEF activity in HPLC fractions is reduced by treatment with rabbit anti-TNF antibody and protein A-Sepharose. This demonstrates physical similarity and at least partial immunological identity of TNF and a fraction of M-ECEF. Thus, TNF can enhance eosinophil function and may constitute an important immunological regulatory mechanism. This effect should be considered when TNF is applied clinically.
Evaluating a visualisation of image similarity as a tool for image browsing (2003)

A similarity metric based on the low-level content of images can be used to create a visualisation in which visually similar images are displayed close to each other. We are carrying out a series of experiments to evaluate the usefulness of this type of visualisation as an image browsing aid. The initial experiment, described, considered whether people would find a given photograph more quickly in a visualisation than in a randomly arranged grid of images. The results show that the subjects were faster with the visualisation, although in post-experiment interviews many of them said that they preferred the clarity and regularity of the grid. We describe an algorithm with which the best aspects of the two layout types can be combined.
A study of highly scalable DG-FinDRAM (2005)

This letter reports the scalability of a capacitor-less 1T-DRAM, and proposes a new concept about extending the use of 1T-DRAM to gate lengths of less than 50 nm. Superior characteristics such as long retention time and large sense margin even for gate lengths around 50 nm can be obtained with a double-gate fully depleted FinFET DRAM. Considering capacity, speed, power, and structural complexity of embedded memory, the capacitor-less 1T-DRAM has the possibility of playing the leading role among other memories.
Extracellular vesicle-mediated transfer of processed and functional RNY5 RNA (2015)

Extracellular vesicles (EVs) have been proposed as a means to promote intercellular communication. We show that when human primary cells are exposed to cancer cell EVs, rapid cell death of the primary cells is observed, while cancer cells treated with primary or cancer cell EVs do not display this response. The active agents that trigger cell death are 29- to 31-nucleotide (nt) or 22- to 23-nt processed fragments of an 83-nt primary transcript of the human RNY5 gene that are highly likely to be formed within the EVs. Primary cells treated with either cancer cell EVs, deproteinized total RNA from either primary or cancer cell EVs, or synthetic versions of 31- and 23-nt fragments trigger rapid cell death in a dose-dependent manner. The transfer of processed RNY5 fragments through EVs may reflect a novel strategy used by cancer cells toward the establishment of a favorable microenvironment for their proliferation and invasion.
Design and dynamic modeling of a rotary wing aircraft with morphing capabilities (2014)

The aim of this paper is to introduce a multi-rotorcraft with morphing capabilities. Unlike conventional multi-copters whose body fly in a horizontal configuration, the proposed platform is be able to rotate its body into a vertical flying mode configuration. The research presented considers an 8-engine vehicle that is able to fly with 4-engines in case of rotor failure. The vertical flight mode is also intended for enabling navigation through narrow areas where conventional helicopter are too big to operate properly. Also, the convertible flight functionality allows saving battery if necessary. The dynamic model of the vehicle while performing in horizontal and vertical configurations is presented. An animated model shows the functionality of the vehicle while performing the transition maneuver.
Expression of an antisense hla fragment in Staphylococcus aureus reduces alpha-toxin production in vitro and attenuates lethal activity in a murine model (1997)

Isogeneic bacterial strains that differ only in the production of a single microbial factor have been invaluable in studying the pathogenesis of bacterial infections. The targeted, intentional inactivation of a gene encoding a potential virulence determinant generally requires homologous recombination to replace the gene with an inactivated allele. To determine whether the insertion and expression of a fragment of a bacterial gene in an antisense orientation could be used as a rapid alternative to allelic inactivation for producing paired isogeneic isolates, we inverted a 600-bp fragment of the Staphylococcus aureus gene encoding alpha-toxin, hla, behind its native promoter on an Escherichia coli-S. aureus shuttle vector. A transformant of an S. aureus strain carrying the antisense hla fragment produced antisense hla RNA and made 16-fold less alpha-toxin than either its parent or an isogeneic transformant containing vector DNA without hla. Also, intraperitoneal injection of 1.5 x 10(9) CFU of the antisense hla-containing transformant was significantly less lethal in a murine model than that of the parent (1 of 10 versus 7 of 10 mice expired [P < 0.02]) or the transformant without hla (1 of 10 versus 7 of 7 mice expired [P < 0.001]). We conclude that the expression of a fragment of hla in an antisense orientation in S. aureus on a plasmid vector reduces alpha-toxin production and the lethal activity of the strain in a murine model. The antisense strategy for creating isogeneic strains of bacteria may facilitate molecular investigations into the pathogenesis of infection. It also may be useful in creating novel live-attenuated strains of bacteria for use as vaccine candidates.
Immunogenicity of novel recombinant human activated factor VII analogues on factor VII neonatally-tolerized rats (2007)

Recombinant activated factor VII (rFVIIa; NovoSeven) has been widely used to treat bleeding in patients with haemophilia with inhibitors. To increase the intrinsic activity, analogues of rFVIIa (rFVIIa Q, rFVIIa DVQ, and rFVIIa DVQA) with altered amino acid sequence at or near the active centre have been developed. The immunogenicity of these analogues was tested in a rat immune tolerance model. Neonatal rats received rFVIIa intraperitoneally on post-natal Day 1 and were subsequently challenged with rFVIIa in Freunds Incomplete Adjuvant subcutaneously on Days 10 and 24. Rats were tested for tolerance on Day 32; the tolerant cohort and a parallel cohort of untreated control rats were challenged with rFVIIa, rFVIIa Q, rFVIIa DVQ, or rFVIIa DVQA on Days 46 and 76. Immune responses determined by enzymelinked immunosorbent assay (ELISA) on Day 84 showed no statistically significant difference between the responses in the four control cohorts. Immune responses were higher in the control than in the tolerant cohort. Compared with rFVIIa (4/16), there was no difference in the proportion of rats that broke tolerance following challenge with rFVIIa DVQ (3/16) and rFVIIa DVQA (7/16), whereas a statistically significant greater proportion broke tolerance after challenge with rFVIIa Q (11/16). Therefore, in this model rFVIIa DVQ or rFVIIa DVQA were not more immunogenic than rFVIIa.
Multivalent Binding in the Design of Bioactive Compounds (2001)

Over the past several years, much research has centered on the development of small molecules that, through multivalent binding interactions, enhance the regulation of fundamental biological functions. The design of a wide range of potential therapeutics focuses on mimicking natural systems that control the biological effect of protein-ligand interactions through multivalency. In this review, the various approaches to achieving multivalency are discussed. Recent advances in the design of multivalent ligands are also presented.
Rapid Determination of Epstein-Barr Virus–Specific CD8+T-Cell Frequencies by Flow Cytometry (1999)

We have developed an efficient and rapid method for detection of Epstein-Barr virus (EBV)-specific CD8+ T-cell frequencies both in freshly isolated peripheral blood mononuclear cells (PBMCs) and in vitro established cytotoxic T lymphocyte (CTL) lines. Responder cells are thereby stimulated with an autologous lymphoblastoid cell line for 5 hours and intracellular accumulation of interferon γ (IFNγ) is detected by multiparameter flow cytometric analysis. EBV-specific CD8+ T-cell frequencies ranged between 0.63% and 1.29% in PBMCs of 5 healthy long-term EBV carriers. Using EBV-specific T-cell lines, it was shown that flow cytometric analysis is more sensitive than limiting dilution analysis for CTL precursors and enzyme-linked immunospot assay detecting IFNγ-producing T cells. The class I restriction of IFNγ production was confirmed using an anti-class I monoclonal antibody (MoAb). Information on other cytokine production of EBV-specific CTLs could be obtained using combinations of anti-cytokine MoAbs. The sensitive and rapid nature of the flow cytometric assay for EBV-specific CD8+ T-cell frequency has significant advantages for evaluation of EBV-specific CD8+ T-cell responses in PBMCs of patients with EBV-related diseases.
A Formal Synthesis of (-)-Cephalotaxine (2008)

An enantioselective formal synthesis of the alkaloid (-)-cephalotaxine has been completed, using an alkylidene carbene 1,5-CH insertion reaction as a key step to construct the spiro[4.4]azanonane core D/E-ring system. A Heck-type cyclization was used to close the tetrahydroazepine C-ring and a selective epoxidation-rearrangement sequence was used to elaborate the E-ring.
Histologic evaluation of the pulsed Nd:YAG laser for laser lipolysis (2005)

Our study showed that the SmartLipo appeared to be histologically effective for destruction of human fat tissue.
Genetic Incorporation of Unnatural Amino Acids into Proteins in Mycobacterium tuberculosis (2010)

New tools are needed to study the intracellular pathogen Mycobacterium tuberculosis (Mtb), the causative agent of tuberculosis (TB), to facilitate new drug discovery and vaccine development. We have developed methodology to genetically incorporate unnatural amino acids into proteins in Mycobacterium smegmatis, BCG and Mtb, grown both extracellularly in culture and inside host cells. Orthogonal mutant tRNATyr/tyrosyl-tRNA synthetase pairs derived from Methanococcus jannaschii and evolved in Escherichia coli incorporate a variety of unnatural amino acids (including photocrosslinking, chemically reactive, heavy atom containing, and immunogenic amino acids) into proteins in response to the amber nonsense codon. By taking advantage of the fidelity and suppression efficiency of the MjtRNA/pIpaRS pair in mycobacteria, we are also able to use p-iodophenylalanine to induce the expression of proteins in mycobacteria both extracellularly in culture and inside of mammalian host cells. This provides a new approach to regulate the expression of reporter genes or mycobacteria endogenous genes of interest. The establishment of the unnatural amino acid expression system in Mtb, an intracellular pathogen, should facilitate studies of TB biology and vaccine development.
Complexity of the immediate early response of myeloid cells to terminal differentiation and growth arrest includes ICAM-1, Jun-B and histone variants. (1990)

Differentiation inducible leukemic as well as normal myeloid precursors treated with physiological myeloid differentiation inducer have been used to explore the immediate early genetic response of cells to terminal differentiation and growth arrest stimuli. cDNA clones of 12 distinct genes, referred to as MyD genes, which are activated in the absence of protein synthesis following induction of myeloid differentiation and growth arrest have been isolated. Sequence analysis of both ends of MyD cDNA clones, and analysis of MyD gene expression following induced differentiation of M1D+ and normal myeloid precursors, has shown that the immediate early genetic response of myeloid cells to the induction of terminal differentiation is complex. This complex response involves a variety of genes, some of which are known and others unknown, including: transient induction of ICAM-1, a gene encoding for a ligand to a cell surface adhesion receptor; stable induction of Jun-B, a gene encoding for a nuclear transcription factor; and increased expression of histone genes which encode for terminal differentiation histone variants. These findings demonstrate that terminal differentiation and growth arrest immediate early response genes encode for at least three distinct types of gene products, which may play a role to reprogram the transcriptional activity of proliferating and non-differentiated cells towards their conversion into terminally differentiated nonproliferating cells.
An interactive database end user facility for the definition and manipulation of forms (1984)

A system is presented which makes possible the definition and manipulation of views by users who are not familiar with the overall organization of the database. The method used is interactive conversation and the user's view of data is an abstract represented by a set of hierarchically related dataitems. A view is specified only in terms of a set of dataitems and the mappings required to materialize the data are automatically generated as the result of this conversation. The form becomes then the basis for accessing the database. Queries are submmited by specifying selection conditions on the fields of a form. Selected occurrences are retrieved from the database and may be scanned as conventional paper forms.