gebhart/patrepeval huggingface dataset:
A Generalization of Band Joins and the Merge-Purge Problem (1995)

The problem of merging multiple databases of information about common entities is frequently encountered in large commercial and government organizations. The problem we study is often called the Merge/Purge problem and is difficult to solve both in scale and accuracy. Large repositories of data always have numerous duplicate information entries about the same entities that are difficult to cull together without an intelligent "equational theory" that identifies equivalent items by a complex, domain dependent matching process. We have developed a system for accomplishing this task for lists of names of potential customers in a direct marketing-type application. Our results for statistically generated data are shown to be accurate and effective when processing the data multiple times using different keys for sorting. The system provides a rule programming module that is easy to program and quite good at finding duplicates especially in an environment with massive amounts of data.
Genomic localization of novel candidate tumor suppressor gene loci in human parathyroid adenomas. (1996)

Only one oncogene, cyclin D1/PRAD1, has an established role in parathyroid tumorigenesis, and parathyroid tumor suppressor genes on chromosome arms 1p and 11q, which still have not been identified, have also been implicated by loss of heterozygosity analysis. To investigate whether other putative tumor suppressor genes are involved in the pathogenesis of parathyroid adenomas, we performed a more comprehensive analysis of allelic losses in these tumors. Using 39 polymorphic markers, we examined each chromosome arm, excluding the short arms of the acrocentric chromosomes. In 25 parathyroid adenomas, frequent loss of heterozygosity, in > 25% of the informative cases, was observed on chromosome arms 6q (30%), 11p (27%), and 15q (35%), in addition to previously reported 1p (30%) and 11q (38%) allelic losses. To more specifically localize the smallest shared regions of molecular genetic deletion, we examined the following chromosomes in greater detail: chromosome 6 (9 additional markers), chromosome 11 (8 additional markers), and chromosome 15 (15 additional markers). The regions most commonly deleted in these tumors were 6q22-23, 6q26-27, 11q13, 15q11-21, and 15q26-qter. All tumors with 11p loss had patterns consistent with monosomy for chromosome 11. These findings provide novel evidence for the existence of tumor suppressor genes on chromosome arms 6q and 15q that contribute commonly to the pathogenesis of parathyroid adenomas.
High-temperature superconducting conductors and cables (1996)

This is the final report of a 3-year LDRD project at LANL. High-temperature superconductivity (HTS) promises more efficient and powerful electrical devices such as motors, generators, and power transmission cables; however this depends on developing HTS conductors that sustain high current densities J{sub c} in high magnetic fields at temperatures near liq. N2`s bp. Our early work concentrated on Cu oxides but at present, long wire and tape conductors can be best made from BSCCO compounds with high J{sub c} at low temperatures, but which are degraded severely at temperatures of interest. This problem is associated with thermally activated motion of magnetic flux lines in BSCCO. Reducing these dc losses at higher temperatures will require a high density of microscopic defects that will pin flux lines and inhibit their motion. Recently it was shown that optimum defects can be produced by small tracks formed by passage of energetic heavy ions. Such defects result when Bi is bombarded with high energy protons. The longer range of protons in matter suggests the possibility of application to tape conductors. AC losses are a major limitation in many applications of superconductivity such as power transmission. The improved pinning of flux lines reduces ac losses, but optimization also involves other factors. Measuring and characterizing these losses with respect to material parameters and conductor design is essential to successful development of ac devices.
Quantitative Chemical Analysis at the Nanoscale Using the Photothermal Induced Resonance Technique (2017)

Photothermal induced resonance (PTIR), also known as AFM-IR, is a scanning probe technique that provides sample composition information with a lateral resolution down to 20 nm. Interest in PTIR stems from its ability to identify unknown samples at the nanoscale thanks, in first approximation, to the direct comparability of PTIR spectra with far-field infrared databases. The development of rapidly tuning quantum cascade lasers has increased the PTIR throughput considerably, making nanoscale hyperspectral imaging within a reasonable time frame possible. Consequently, a better understanding of PTIR signal generation and of the fine details of PTIR analysis has become of paramount importance for extending complex IR analysis methods developed in the far-field, e.g., for classification and hyperspectral imaging, to nanoscale PTIR spectra. Here we calculate PTIR spectra via thin-film optics, to identify subtle changes (band shifts, deviation from linear approximation, etc.) for common sample parameters in the case of PTIR with total internal reflection illumination. Results show signal intensity linearity and small band shifts as long as the sample is prepared correctly, with band shifts typically smaller than macroscale attenuated total reflection (ATR) spectroscopy. Finally, a generally applicable algorithm to retrieve the pure imaginary component of the refractive index (i.e., the chemically specific information) is provided to overcome the PTIR spectra nonlinearity.
Sequential Dose-Dense Doxorubicin, Paclitaxel, and Cyclophosphamide for Resectable High-Risk Breast Cancer: Feasibility and Efficacy (1999)

Dose-dense sequential adjuvant chemotherapy with doxorubicin, paclitaxel, and cyclophosphamide (A-->T-->C) is feasible and promising. Several ongoing phase III trials are evaluating this approach.
Low Dose Ketoconazole With Replacement Doses of Hydrocortisone in Patients With Progressive Androgen Independent Prostate Cancer (2002)

The regimen of low dose ketoconazole with replacement doses of hydrocortisone is well tolerated and has moderate activity in patients with progressive androgen independent prostate cancer.
Phenotypic and Functional Characterization of Human Mammary Stem/Progenitor Cells in Long Term Culture (2009)

Thus, the self-renewal potential of human breast stem cells is exhausted within five in vitro passages of mammospheres, suggesting the need for further improvisation in culture conditions for their long-term maintenance.
Spinal Micturition Reflex Mediated by Afferents in the Deep Perineal Nerve (2004)

Reflexes mediated by urethral sensory pathways are integral to urinary function. This study investigated the changes in bladder pressure and urethral sphincter activity resulting from electrical stimulation of afferents in the deep perineal nerve (DP), which innervates the urethra and surrounding muscles, before and after acute spinal cord transection (SCT) in cats anesthetized with alpha-chloralose monitored by blood pressure and heart rate. DP stimulation elicited bladder contractions before and after SCT but only if the bladder contained a sufficient volume of fluid (78% of the volume needed to cause distention-evoked reflex contractions). The volume dependency was mediated by a neuronal mechanism in the lumbosacral spinal cord and was not attributable to length-tension properties of the detrusor muscle. Stimulation at 2-40 Hz initiated bladder contractions, but 20-40 Hz was more effective than lower frequencies in evoking and sustaining bladder contractions for the duration of the stimulus train. Decreases in urethral sphincter activity occurred during sustained bladder contractions evoked by 20- to 40-Hz stimulation before and within 16 h after SCT. After SCT, average bladder pressure increases evoked by DP stimulation were smaller than those evoked before SCT, but in some animals, bladder pressures elicited by DP stimulation continued to increase as time after SCT increased and reached pretransection amplitudes at 8-16 h posttransection. These data confirm the presence of a spinal circuit that can mediate coordinated bladder-sphincter responses and show that afferents from the DP can activate this circuit under appropriate conditions.
Unstructured surface and volume decimation of tessellated domains (1995)

A general algorithm for decimating unstructured discretized data sets is presented. The discretized space may be a planar triangulation, a general 3D surface triangulation, or a 3D tetrahedrization. The decimation algorithm enforces Dirichlet boundary conditions, uses only existing vertices, and assumes manifold geometry. Local dynamic vertex removal is performed without history information while preserving the initial topology and boundary geometry. The tessellation at each step of the algorithm is preserved and, in the pathological case, every interior vertex is a candidate for removal. The research focuses on how to remove a vertex from an existing unstructured n-dimensional tessellation, not on the formulation of decimation criteria. Criteria for removing a candidate vertex may be based on geometric properties or any scalar governing function specific to the application. Use of scalar functions to adaptively control or optimize tessellation resolution is particularly applicable to the computer graphics, computational fluids, and structural analysis disciplines. Potential applications in the geologic exploration and medical or industrial imaging fields are promising.
PCR-Based Detection of Bacillus anthracis in Formalin-Fixed Tissue from a Patient Receiving Ciprofloxacin (2002)

We demonstrate that Bacillus anthracis may be detected from a formalin-fixed, paraffin-embedded biopsy specimen, even after the patient has received antibiotic treatment. Although traditional PCR methods may not be sufficiently sensitive for anthrax detection in such patients, cycle numbers can be increased or PCR can be repeated by using an aliquot from a previous PCR as the template.
Administration of a Soluble Activin Type IIB Receptor Promotes the Transplantation of Human Myoblasts in Dystrophic Mice (2012)

Duchenne muscular dystrophy (DMD) is a recessive disease caused by a dystrophin gene mutation. Myoblast transplantation permits the introduction of the dystrophin gene into dystrophic muscle fibers. However, this strategy has so far produced limited results. Modulation of transforming growth factor-β (TGF-β) superfamily signaling promotes skeletal muscle differentiation and growth and myogenic regeneration. We investigated the possibility that the combination of TGF-β superfamily signaling inhibition with myoblast transplantation might be an effective therapeutic approach in dystrophin-deficient patients. In vitro, blocking myostatin and other ligands with a soluble form of the extracellular domain of the activin IIB receptor (ActRIIB/Fc) upregulated the expression of myogenic differentiation factors and increased human myoblast fusion. In vivo, systemic inhibition of activin IIB receptor signaling by delivery of ActRIIB/Fc increased the success of the myoblast transplantation. This effect was further increased by forcing the mice to swim weekly to induce cycles of muscle degeneration and regeneration. Treatment of dystrophic mice with ActRIIB/Fc led to increased body weight, increased skeletal muscle mass, and improved myoblast transplantation. Thus, ActRIIB/Fc represents an effective therapeutic strategy for muscular dystrophies, and its effects are enhanced when combined with muscle exercise.
Human beta-globin messenger RNA. III. Nucleotide sequences derived from complementary DNA. (1977)

Sequence analysis studies were carried out on human beta-globin mRNA (beta-mRNA) prepared from alpha-thalassemic, sickle cell, and Hb A reticulocytes. Highly purified beta-mRNA served as substrate for the preparation of cDNA by RNA-dependent DNA polymerase. The cDNA was transcribed by Escherichia coli RNA polymerase and the resulting cRNA was analyzed. Over 300 nucleotides were assigned to the beta-mRNA coding region and 37 nucleotides were assigned to the 3'-terminal noncoding region. The normal termination codon is UAA which is separated by 28 nucleotides from an out of phase UAA triplet. The origin of each of the abnormally long beta-globin variants Tak and Cranston is consistent with reduplication of dinucleotides prior to the normal termination codon, and both globin variants can terminate at the out of phase UAA.
Gluten Protein Adhesives for Wood Panels (2010)

Adhesives for wood particleboards based on hydroxymethylated or glyoxalated hydrolysed gluten protein with addition of an equal proportion of tannin/hexamine resin or without any addition of synthetic resins are shown to yield results satisfying the relevant standard specifications for interior wood boards. Even better are resins based on hydroxymethylated or glyoxalated hydrolysed gluten protein to which has been added a small proportion of an isocyanate (pMDI). Adhesive resins formulations based on the latter in which the total content of natural material was either 70% or 80% of the total resin solids content gave good results. Resins based on the former in which the natural material content was approximately 90–95% also gave good results. The 30/70 pMDI/hydroxymethylated lignin adhesive formulation was tried at progressively shorter pressing times yielding internal bond strength results acceptable for relevant interior grade standards at industrially significant pressing times.
Solubilities of amino acids (1978)

Abstract The Mettler/Paar precision density meter DMA‐02D has been used to determine the concentration of saturated solutions of amino acids at 20.0, 25.0, and 29.8 °C. The technique has proven itself an elegant and precise method. The solubilities of all of the amino acids with the exceptions of proline, lysine, and cystine have been measured. The Gibbs free energies of transfer from saturated water solution to 1 M Na 2 SO 4 and to 1 M Gu·HCL along with the van't Hoff heats and entropies have been calculated. The van't Hoff heats have been compared with the calorimetrically determined heats for some of the amino acids. The Lumry‐Rajender relation between the entropy and heats has been observed. The process of transfer of the amino acids from water to the solvents is primarily enthalpic rather than entropic.
InParanoid 8: orthology analysis between 273 proteomes, mostly eukaryotic (2014)

The InParanoid database (http://InParanoid.sbc.su.se) provides a user interface to orthologs inferred by the InParanoid algorithm. As there are now international efforts to curate and standardize complete proteomes, we have switched to using these resources rather than gathering and curating the proteomes ourselves. InParanoid release 8 is based on the 66 reference proteomes that the 'Quest for Orthologs' community has agreed on using, plus 207 additional proteomes from the UniProt complete proteomes--in total 273 species. These represent 246 eukaryotes, 20 bacteria and seven archaea. Compared to the previous release, this increases the number of species by 173% and the number of pairwise species comparisons by 650%. In turn, the number of ortholog groups has increased by 423%. We present the contents and usages of InParanoid 8, and a detailed analysis of how the proteome content has changed since the previous release.
Gait asymmetry in patients with limb length discrepancy (2003)

Foot loading patterns and neuromuscular function of both limbs during walking were investigated on 25 patients with limb length discrepancy. Plantar pressures and 2-D ground reaction forces were recorded simultaneously with electromyographic activities at two different walking speeds. Bilateral comparison indicated that moderate limb length discrepancies resulted in asymmetrical gait patterns. The duration of the stance phase was reduced in the short limb in both walking speeds. The vertical ground reaction force (F) in the push-off phase was greater in the long limb both at normal (1.33 (SO, 0.05 BW) vs. 1.29 (SD, 0.09 BW)) (P=0.0027) and fast walking speed (1.55 (SD, 0.11) vs. 1.48 (SD, 0.15 BW)) (P=0.001). Peak plantar pressures were higher under the big toe in the long leg and the heel-off occurred faster. The push-off phase was initiated earlier in the short leg. The maximum isometric torque of the long limb was considerably greater (673 Nm vs. 239 Nm) (P=0.026). The results imply that the loading of the long limb is greater and the foot loading patterns shifted more to the forefoot in the long, limb to compensate walking disturbances caused by limb length discrepancies.
Enhanced Mucosal Delivery of Antigen with Cell Wall Mutants of Lactic Acid Bacteria (2004)

The potential of recombinant lactic acid bacteria (LAB) to deliver heterologous antigens to the immune system and to induce protective immunity has been best demonstrated by using the C subunit of tetanus toxin (TTFC) as a model antigen. Two types of LAB carriers have mainly been used, Lactobacillus plantarum and Lactococcus lactis, which differ substantially in their abilities to resist passage through the stomach and to persist in the mouse gastrointestinal tract. Here we analyzed the effect of a deficiency in alanine racemase, an enzyme that participates in cell wall synthesis, in each of these bacterial carriers. Recombinant wild-type and mutant strains of L. plantarum NCIMB8826 and L. lactis MG1363 producing TTFC intracellularly were constructed and used in mouse immunization experiments. Remarkably, we observed that the two cell wall mutant strains were far more immunogenic than their wild-type counterparts when the intragastric route was used. However, intestinal TTFC-specific immunoglobulin A was induced only after immunization with the recombinant L. plantarum mutant strain. Moreover, the alanine racemase mutant of either LAB strain allowed induction of a much stronger serum TTFC-specific immune response after immunization via the vagina, which is a quite different ecosystem than the gastrointestinal tract. The design and use of these mutants thus resulted in a major improvement in the mucosal delivery of antigens exhibiting vaccine properties.
Identification of Residues in the Human Respiratory Syncytial Virus Fusion Protein That Modulate Fusion Activity and Pathogenesis (2014)

Human respiratory syncytial virus (RSV) is the most important lower respiratory tract pathogen of infants for which there is no vaccine. Elucidating mechanisms of RSV pathogenesis is important for rational vaccine and drug design. We defined specific amino acids in the fusion (F) protein of RSV strain line 19 critical for fusion activity and elucidated a correlation between fusion activity and viral load in mice. Further, we identified two distinct amino acids in F as contributing to the mucogenic phenotype of the A2-line19F virus. Taken together, these results illustrate a role for RSV F in virulence.
Multiverse recommendation (2010)

Context has been recognized as an important factor to consider in personalized Recommender Systems. However, most model-based Collaborative Filtering approaches such as Matrix Factorization do not provide a straightforward way of integrating context information into the model. In this work, we introduce a Collaborative Filtering method based on Tensor Factorization, a generalization of Matrix Factorization that allows for a flexible and generic integration of contextual information by modeling the data as a User-Item-Context N-dimensional tensor instead of the traditional 2D User-Item matrix. In the proposed model, called Multiverse Recommendation, different types of context are considered as additional dimensions in the representation of the data as a tensor. The factorization of this tensor leads to a compact model of the data which can be used to provide context-aware recommendations.
Chemistry, properties and applications of PNA (Peptide Nucleic Acid) (1997)

Biokemi
Ultrasonic attenuation and propagation speed in normal human brain (1981)

Attenuation and propagation speed in the 1- to 5-MHz frequency range were measured in vitro in 22 tissue samples from six anatomic sites in five normal human brains obtained unfixed at autopsy. Two methods were used to measure attenuation: (1) received amplitude reduction resulting from insertion of tissue sample between a pair of transducers, and (2) radiation force reduction resulting from insertion of tissue sample between a transducer and a reflector. The piezoelectric transducer method gave attenuation values −10% to +90% higher than the radiation force method. Attenuation (by transducer method) was a function of frequency to the 1.08 power with a value of 0.87 dB ⋅ cm−1 at 1 MHz. Propagation speed was measured by observing signal arrival time change resulting from insertion of the tissue sample between the transducer pair. Propagation speed was 1562 m ⋅ s−1 at 1 MHz with a dispersion of 1.2 m ⋅ s−1 ⋅ MHz−1 over the 1- to 5-MHz frequency range. Ages at death were 3 days, 20, 21, 42, and 72 years. Results were similar in the 20- to 72-year range but attenuation for the 3-day case was about one-third that for adult. Formalin fixing decreased propagation speed by 10 m ⋅ s−1. One-day aging of unfixed tissue resulted in up to a 21% decrease in attenuation and up to a 10 m ⋅ s−1 decrease in propagation speed. White matter (corna radiata, medulla, pons) had attenuation 1.5 times that for gray (Island of Riel, cerebellum) with mixed (basal ganglia) having an intermediate value. Attenuation decreased with increasing temperature. Propagation speed as a function of temperature exhibited a minimum at about 15 °C.
Monovalent Cations Partially Repair a Conformational Defect in a Mutant Tryptophan Synthase α2β2 Complex (β-E109A) (1995)

We are using the tryptophan synthase alpha 2 beta 2 complex as a model system to investigate how ligands, protein-protein interaction, and mutations regulate enzyme activity, reaction specificity, and substrate specificity. The rate of conversion of L-serine and indole to L-tryptophan by the beta 2 subunit alone is quite low, but is activated by certain monovalent cations or by association with alpha subunit to form an alpha 2 beta 2 complex. Since monovalent cations and alpha subunit appear to stabilize an active conformation of the beta 2 subunit, we have investigated the effects of monovalent cations on the activities and spectroscopic properties of a mutant form of alpha 2 beta 2 complex having beta 2 subunit glutamic acid 109 replaced by alanine (E109A). The E109A alpha 2 beta 2 complex is inactive in reactions with L-serine but active in reactions with beta-chloro-L-alanine. Parallel experiments show effects of monovalent cations on the properties of wild type beta 2 subunit and alpha 2 beta 2 complex. We find that CsCl stimulates the activity of the E109A alpha 2 beta 2 complex and of wild type beta 2 subunit with L-serine and indole and alters the equilibrium distribution of L-serine reaction intermediates. The results indicate that CsCl partially repairs the deleterious effects of the E109A mutation on the activity of the alpha 2 beta 2 complex by stabilizing a conformation with catalytic properties more similar to those of the wild type alpha 2 beta 2 complex. This conclusion is consistent with observations that monovalent cations alter the catalytic and spectroscopic properties of several pyridoxal phosphate-dependent enzymes by stabilizing alternative conformations.