gebhart/patrepeval huggingface dataset:
Use of carbohydrate derivatives for studies of phosphorus stereochemistry. Part I. Stereochemistry of 1,3,2-dioxaphosphorinan-2-ones and synthesis of optically active phosphine oxides (1974)

Pairs of 1,3,2-dioxaphosphorinan-2-ones, epimeric at phosphorus, have been prepared by treatment of methyl 2,3-di-O-methyl-α-D-glucopyranoside and -galactopyranoside with phosphonic or phosphoric dihalides. The configuration at phosphorus in these derivatives has been assigned on the basis of n.m.r. and i.r. data and of comparison of the rates of formation and relative stabilities of the epimers. For the formation of the 1,3,2-dioxaphosphorinan-2-ones it is suggested that the kinetic preference for the thermodynamically less stable isomers depends on steric interactions in twist-ring transition intermediates, and that the subsequent equilibration depends on the relative stabilities of the chair conformers. The conversions of methyl 2,3-di-O-methyl-α-D-glucopyranoside (R)- and (S)-4,6-methyl phosphonate into (S)- and (R)-ethylmethylphenylphosphine oxide, respectively, by sequential addition of phenylmagnesium bromide and ethylmagnesium bromide provide examples of the utility of carbohydrate 1,3,2-dioxaphosphorinan-2-ones for the stereospecific synthesis of optically active phosphine oxides.
Absolute mRNA quantification using the polymerase chain reaction (PCR). A novel approach by aPCR aidedtranscipttitration assay (PATTY) (1989)

The polymerase chain reaction (PCR) is used as part of a new approach to the absolute quantification of mRNA. We describe a PCR aided transcript titration assay (PATTY) which is based on the co-amplification of an in vitro generated transcript differing by a single base exchange from the target mRNA. Identical portions of a total RNA sample are "spiked" with different amounts of this mutated standard RNA, converted to cDNA and amplified by PCR. Because the base exchange creates a novel restriction endonuclease site, the ratio of co-amplified DNA derived from target mRNA to amplified DNA derived from standard RNA can be determined after restriction endonuclease digestion and separation by gel electrophoresis. This method gives accurate results within 24 hours and is useful especially for the quantification of either low-abundance mRNA or more abundant mRNA present in very small amounts of total RNA. The low-abundance mRNA encoding 4-coumarate:CoA ligase (4CL) in cultured potato cells (Solanum tuberosum L.) was measured in a case study. About 100 molecules per assay could be accurately detected by the new method.
Signature of balancing selection in Arabidopsis (2002)

Natural selection and genetic linkage cause DNA segments to have genealogical histories resembling those of the selected sites. When a polymorphism maintained by selection is old, it will have an island of enhanced sequence variability surrounding it, which represents a detectable "signature of selection." We investigate the structure of single-nucleotide polymorphisms (SNPs) in a 20-kb interval containing the Arabidopsis thaliana disease resistance gene RPS5, a locus containing common alleles for the presence/absence of the entire locus. The alleles are considerably diverged at surrounding sites, indicative of an old polymorphism maintained by selection. The island of "enhanced" variability extends several kilobases to either side of the RPS5 deletion junction, and these SNPs are in nearly complete linkage disequilibrium with the RPS5 insertion/deletion. At a distance of 10 kb to either side of the locus, however, we find low levels of polymorphism and the absence of linkage disequilibrium between individual SNPs and RPS5 alleles. Our results show that the interval of enhanced variability surrounding this balanced polymorphism in Arabidopsis is large enough to be readily detected, but small enough to span the focal gene and few others. For this species it should be possible to identify the complete set of genes with long-lived polymorphisms, a potentially important subset of genes segregating for functional variants.
Adding range restriction capability to dynamic data structures (1985)

A database is said to allow range restrictions if one may request that only records with some specified field in a specified range be considered when answering a given query. A transformation is presented that enables range restrictions to be added to an arbitrary dynamic data structure on n elements, provided that the problem satisfies a certain decomposability condition and that one is willing to allow increases by a factor of O (log n ) in the worst-case time for an operation and in the space used. This is a generalization of a known transformation that works for static structures. This transformation is then used to produce a data structure for range queries in k dimensions with worst-case times of O (log k n ) for each insertion, deletion, or query operation.
Unsupervised Learning of Video Representations using LSTMs (2015)

We use multilayer Long Short Term Memory (LSTM) networks to learn representations of video sequences. Our model uses an encoder LSTM to map an input sequence into a fixed length representation. This representation is decoded using single or multiple decoder LSTMs to perform different tasks, such as reconstructing the input sequence, or predicting the future sequence. We experiment with two kinds of input sequences - patches of image pixels and high-level representations ("percepts") of video frames extracted using a pretrained convolutional net. We explore different design choices such as whether the decoder LSTMs should condition on the generated output. We analyze the outputs of the model qualitatively to see how well the model can extrapolate the learned video representation into the future and into the past. We try to visualize and interpret the learned features. We stress test the model by running it on longer time scales and on out-of-domain data. We further evaluate the representations by finetuning them for a supervised learning problem - human action recognition on the UCF-101 and HMDB-51 datasets. We show that the representations help improve classification accuracy, especially when there are only a few training examples. Even models pretrained on unrelated datasets (300 hours of YouTube videos) can help action recognition performance.
Low intercellular adhesion molecule 1 and high 5T4 expression on tumor cells correlate with reduced disease-free survival in colorectal carcinoma patients. (1997)

The purpose of this study was to investigate the prognostic value of the expression of intercellular adhesion molecule 1 (ICAM-1), leukocyte function antigen 3 (LFA-3), human leukocyte differentiation antigen (HLA)-ABC, HLA-DR, and 5T4 with regard to disease-free survival in Dukes' B and C colorectal carcinoma patients. Forty-one patients (28 Dukes' B and 13 Dukes' C) were entered into this study. Immunocytochemistry was performed on cytospin preparations of enzymatically digested colorectal carcinoma cell suspensions. The frequency of metastases and the duration of disease-free survival were compared between the 25% lowest expressers and the 75% remaining patients for ICAM-1, LFA-3, HLA-ABC, and HLA-DR, and between the 25% highest expressers and the 75% remaining patients for 5T4. Low numbers of ICAM-1-expressing tumor cells were associated with a shorter disease-free survival (P < 0. 001), independent of Dukes' stage. High numbers of 5T4-expressing tumor cells were associated with shorter disease-free survival in Dukes' B patients (P = 0.04). Cox proportional hazard analysis indicated that low numbers of ICAM-1(+) and high numbers of 5T4(+) cells were independent prognostic factors with relative risks of 13. 0 (P = 0.0002) and 4.7 (P = 0.02), respectively. The combination of 5T4 and ICAM-1 marker information identified subgroups of patients with a good (high ICAM-1) or poor (low ICAM-1/high 5T4) prognosis. Neither a lack of HLA-ABC and LFA-3 expression nor the presence of HLA-DR on the tumor cells gave additional prognostic information. These findings demonstrate that low ICAM-1 and high 5T4 expression on tumor cells are prognostic markers, additional to Dukes' stage, for reduced disease-free survival in Dukes' B and C colorectal carcinoma patients.
Effect of valproate derivatives on human brain myo-inositol-1-phosphate (MIP) synthase activity and amphetamine-induced rearing. (2008)

We have recently shown that valproate (VPA) decreases intracellular concentrations of inositol, like lithium but via a different mechanism, namely by inhibiting myo-inositol-1-phosphate (MIP) synthase. Valnoctamide (VCD) and valrocemide (VGD) are VPA derivatives which are anticonvulsants and have been shown in animal models to be significantly less teratogenic than VPA. We now show that 1 mM of either VCD or VGD drastically inhibits human brain crude homogenate MIP synthase activity. We studied the mechanism of the effect of VCD and found that it reduced the enzyme activity by an apparent competitive mode of inhibition at concentrations within the therapeutic range of VPA(Ki = 0.18 mM). We studied the behavioral effect of VGD and found that both lithium and VGD attenuated amphetamine-induced increase in rearing. These data support clinical study of these VPA-derivatives in bipolar disorder.
Forensic DNA typing : biology & technology behind STR markers (2001)

Foreword Introduction Acknowledgements Overview and History of DNA Typing Biology DNA Biology Review Sample Collection and Preparation (DNA Extraction and Quantification) The Polymerase Chain Reaction (DNA Amplification) Commonly Used Short Tandem Repeat Markers Biology of STRs: Stutter Products, Non-Template Addition, Microvariants, Null Alleles, and Mutation Rates Forensic Issues: Degraded DNA, PCR Inhibition, Contamination, and Mixed Samples Additional DNA Markers: Amelogenin, Y-Chromosome STRs, mtDNA, SNPs, Alu Repeats Technology DNA Separation Methods: Slab-Gel and Capillary Electrophoresis DNA Detection Methods: Fluorescent Dyes and Silver Staining The ABI Prism 310 Genetic Analyzer The Hitachi FMBIO II Fluorescence Imaging System STR Genotyping Issues Laboratory Validation New Technologies and Automation Combined DNA Index System (CODIS) and the Use of DNA Database Biology, Technology and Genetics DNA Testing in High-Profile Cases Appendix I: Reported STR Alleles: Sizes and Sequences Appendix II: CEPH Family Study Appendix III: DNA Advisory Board Quality Assurance Standards Appendix IV: Suppliers of DNA Analysis Equipment, Products, or Services Index
Spatiotemporal segmentation and tracking of objects in color image sequences (2002)

In this paper a procedure is described for the segmentation and tracking of objects in color image sequences. For this purpose, we propose the novel procedure of K-Means with a connectivity constraint algorithm as a general segmentation algorithm combining several types of information including color, motion and compactness. In this algorithm, the use of spatiotemporal regions is introduced since a number of frames is analyzed simultaneously and as a result the same region is present in consequent frames. Experimental results in real image sequences evaluate the performance of the algorithm.
Thalamocortical dysrhythmia syndrome: MEG imaging of neuropathic pain (2005)

Abnormal thalamocortical dynamics have been proposed as the underlying mechanism for a subset of neurological and psychiatric disorders that include centrally generated pain. Spectral analysis and independent component-based localization of neuromagnetic signals reveal ongoing theta-range activity localized to physiologically significant cortical regions in a group of subjects with well-characterized central and peripheral lesions. In addition, recordings from subjects who failed to obtain relief from spinal cord stimulation (SCS) and from those in whom SCS was successful further delineate thalamocortical dysrhythmias as a mechanism that underlies chronic pain.
Getting Ready (2018)

This book defines a philosophy, but it is also intended to illuminate the practical aspects of that philosophy with experiments that you can perform. Because we SysAdmins are a hands-on group of individuals, this book provides a number of simple experiments that you can perform in order to more fully appreciate and understand the tenets of the philosophy. Most experiments usually consist of a one-line bash shell command or program. Some of the experiments do use more than one line.
Dilute‐solution properties of ring polystyrenes (1985)

Abstract The temperature Θ A2 at which the second virial coefficient A 2 is zero for ring polystyrenes is 28.5°C in cyclohexane, independent of molecular weight in the range 2 × 10 4 to 4.5 × 10 5 . This cannot be explained solely by the Candau–Rempp–Benoit theory, which takes into account the effect of segment density on Θ A2 The radius of gyration of a ring is found to be approximately one‐half that of a linear polymer with the same molecular weight. The intrinsic viscosities [η] and intrinsic translational friction coefficients [ f ] of ring polystyrenes with molecular weights ranging from 7 × 10 3 to 4.5 × 10 5 have been measured in cyclohexane at 34.5°C (Θ, the Flory theta temperature for linear polystyrenes) and in toluene (a good solvent). The results are compared with those for linear polystyrene. It is found that the Mark–Houwink exponent is less than one‐half in cyclohexane at Θ. In toluene it is 0.67 compared to 0.73 for linear polystyrene. The hydrodynamic measurements suggest that large rings are less expanded than the linear polymers with the same molecular weight, contrary to many predictions.
Sequence Diversity, Predicted Two-Dimensional Protein Structure, and Epitope Mapping of Neisserial Opa Proteins (1998)

The sequence diversity of 45 Opa outer membrane proteins from Neisseria meningitidis, Neisseria gonorrhoeae, Neisseria sicca, and Neisseria flava indicates that horizontal genetic exchange of opa alleles has been rare between these species. A two-dimensional structural model containing four surface-exposed loops was constructed based on rules derived from porin crystal structure and on conservation of sequence homology within transmembrane beta-strands. The minimal continuous epitopes recognized by 23 monoclonal antibodies were mapped to loops 2 and 3. Some of these epitopes are localized on the bacterial cell surface, in support of the model.
The non-Watson-Crick base pairs and their associated isostericity matrices (2002)

RNA molecules exhibit complex structures in which a large fraction of the bases engage in non-Watson-Crick base pairing, forming motifs that mediate long-range RNA-RNA interactions and create binding sites for proteins and small molecule ligands. The rapidly growing number of three-dimensional RNA structures at atomic resolution requires that databases contain the annotation of such base pairs. An unambiguous and descriptive nomenclature was proposed recently in which RNA base pairs were classified by the base edges participating in the interaction (Watson-Crick, Hoogsteen/CH or sugar edge) and the orientation of the glycosidic bonds relative to the hydrogen bonds (cis or trans). Twelve basic geometric families were identified and all 12 have been observed in crystal structures. For each base pairing family, we present here the 4 x 4 'isostericity matrices' summarizing the geometric relationships between the 16 pairwise combinations of the four standard bases, A, C, G and U. Whenever available, a representative example of each observed base pair from X-ray crystal structures (3.0 A resolution or better) is provided or, otherwise, theoretically plausible models. This format makes apparent the recurrent geometric patterns that are observed and helps identify isosteric pairs that co-vary or interchange in sequences of homologous molecules while maintaining conserved three-dimensional motifs.
Recent Advances in Chemokines and Chemokine Receptors (1999)

Chemokines are a superfamily of small cytokine-like molecules which have been described primarily on the basis of their ability to mediate the migration of verious cell types, particularly those of lymphoid origin. The receptors for these molecules are all seven-transmembrane domain G protein-coupled receptors that have historically been excellent targets for small-molecule drugs. This fact, coupled with the advent of large-scale DNA database mining and the recognition that chemokine receptors are also coreceptors for HIV, has driven discovery in this field at a tremendous rate. This process has included not just an expansion of the number of known chemokines and chemokine receptors, but also a greater appreciation for the variety of functions that chemokines are involved in. We review here the molecules that have come from the most recent years of chemokine research as well as many of the new functions that have been ascribed to them.
Phase-dispersion optical tomography (2001)

We report on phase-dispersion optical tomography, a new imaging technique based on phase measurements using low-coherence interferometry. The technique simultaneously probes the target with fundamental and second-harmonic light and interferometrically measures the relative phase shift of the backscattered light fields. This phase change can arise either from reflection at an interface within a sample or from bulk refraction. We show that this highly sensitive (~5 degrees ) phase technique can complement optical coherence tomography, which measures electric field amplitude, by revealing otherwise undetectable dispersive variations in the sample.
Reduced Evoked Gamma Oscillations in the Frontal Cortex in Schizophrenia Patients: A TMS/EEG Study (2008)

Schizophrenia patients showed a decrease in EEG-evoked responses in the gamma band when TMS was applied to directly stimulate the frontal cortex while these responses were recorded. Since EEG responses to direct cortical stimulation are not affected by an individual's motivation, attention, or cognitive capacity and are not relayed through peripheral afferent pathways, these findings suggest that there might be an intrinsic dysfunction in frontal thalamocortical circuits in individuals with schizophrenia.
Daily cytokine fluctuations, driven by leptin, are associated with fatigue severity in chronic fatigue syndrome: evidence of inflammatory pathology (2013)

Our results support the role of cytokines in the pathophysiology of CFS.
Anaphylaxis following intranasal challenge of mice sensitized with ovalbumin. (1984)

Mice sensitized with two intraperitoneal injections of ovalbumin and challenged intranasally with the same antigen developed a non-fatal anaphylactic shock peaking in severity 30 min after challenge. Increases in haematocrit were noted which corresponded to the severity of signs of shock displayed by mice. Severity of shock also correlated with IgE and IgG levels. Sensitization by the nasal route, and use of B. pertussis vaccine as adjuvant had no qualitative effect upon the response. Cobra venom factor depletion of C3 in vivo did not alter the response of mice, which suggests anaphylaxis did not involve complement activation. Sensitivity was not transferrable to non-immune mice with serum. Passive sensitization with polyclonal and monoclonal antibodies produced inconsistent results. Possible mechanisms of anaphylaxis are discussed.
Design and control of motion compensation cardiac catheters (2010)

Robotic cardiac catheters have the potential to revolutionize heart surgery by extending minimally invasive techniques to complex surgical repairs inside the heart. However, catheter technologies are currently unable to track fast tissue motion, which is required to perform delicate procedures inside a beating heart. This paper proposes an actuated catheter tool that compensates for the motion of heart structures like the mitral valve apparatus by servoing a catheter guidewire inside a flexible sheath. We examine design and operation parameters that affect performance and establish that friction and backlash limit the tracking performance of the catheter system. Based on the results of these experiments and a model of the backlash behavior, we propose and implement compensation methods to improve trajectory tracking performance. The catheter system is evaluated with 3D ultrasound guidance in simulate <i>in vivo</i> conditions. The results demonstrate that with mechanical and control system design improvements, a robotic catheter system can accurately track the fast motion of the human mitral valve.
Groundwave Attenuation Function for Propagation Over A Highly Inductive Earth (1967)

Propagation of an electromagnetic groundwave over a plane surface in which the argument of the surface impedance is greater than π/4 but less than π/2 is considered in some detail. The numerical distance, p , over such a surface is characterized by 0 ≤ arg p ≤ π/2. The groundwave behaves in a peculiar manner, and this is attributed to the interaction of two phasor components representing a trapped wave and a Norton surface wave. Approximate expressions are derived which determine the magnitude and phase of the groundwave attenuation function when these two waves are inphase and antiphase. A method is also given for estimating the asymptotic phase for large | p | which was previously not possible except through detailed calculations. Finally, detailed curves are presented which show the amplitude and phase of the groundwave attenuation function versus p .
11 Ribonucleases H (1993)

I. INTRODUCTION Ribonuclease H (RNase H) (Ribonucleate [in RNA:DNA hybrids] 5′-oligonucleotidohydrolase, E.C.3.1.26.4) specifically cleaves the RNA strand in an RNA:DNA hybrid duplex. The designation H (for hybrid) was introduced by Hausen and Stein (1970) to describe a new ribonuclease activity discovered in extracts from calf thymus (Stein and Hausen 1969). All known nucleases with RNase H activity require divalent metal cations for hydrolysis of the RNA phosphodiester bond producing 5′-phosphate and 3′-hydroxyl termini. The presence of the free 3′-hydroxyl terminus makes the resulting RNA fragment suitable as a primer for DNA polymerase. RNases H comprise a family of ubiquitous enzymes, detected in multiple forms in all organisms from bacteria to mammals. However, with the exception of their well-understood function in the life cycle of retroviruses, the biological roles of other cellular RNases H are much less clear. In addition to their presumed involvement in DNA replication (and the practical usefulness of the isolated enzyme as a reagent for in vitro manipulations with nucleic acids), two other factors with possible therapeutic implications have contributed to the recent increased interest in RNases H: (1) the presumed role of endogenous RNase H activity in the mechanism of action of antisense oligonucleotides and (2) the potential importance of the enzyme as an antiviral target, especially in connection with human immunodeficiency virus (HIV) infection and acquired immunodeficiency syndrome (AIDS). Since the first comprehensive overview of RNases H by Crouch and Dirksen (1982), two more recent reviews have appeared (Crouch 1990; Wintersberger 1990) that deal with...