gebhart/patrepeval huggingface dataset:
A Point Cluster Method for In Vivo Motion Analysis: Applied to a Study of Knee Kinematics (1998)

A new method for deriving limb segment motion from markers placed on the skin is described. The method provides a basis for determining the artifact associated with nonrigid body movement of points placed on the skin. The method is based on a cluster of points uniformly distributed on the limb segment. Each point is assigned an arbitrary mass. The center of mass and the inertia tensor of this cluster of points are calculated. The eigenvalues and eigenvectors of the inertia tensor are used to define a coordinate system in the cluster as well as to provide a basis for evaluating non-rigid body movement. The eigenvalues of the inertia tensor remain invariant if the segment is behaving as a rigid body, thereby providing a basis for determining variations for nonrigid body movement. The method was tested in a simulation model where systematic and random errors were introduced into a fixed cluster of points. The simulation demonstrated that the error due to nonrigid body movement could be substantially reduced. The method was also evaluated in a group of ten normal subjects during walking. The results for knee rotation and translation obtained from the point cluster method compared favorably to results previously obtained from normal subjects with intra-cortical pins placed into the femur and tibia. The resulting methodology described in this paper provides a unique approach to the measurement of in vivo motion using skin-based marker systems.
Design Considerations and Field Performance of an Advanced Automatic Driller (2003)

Abstract Automatic Drillers have been used for decades. Most of these systems did a poor job of controlling weight on bit, which resulted in equally poor performance. Thus prompting two questions: "What is required to achieve a much better level of control of drilling parameters like weight on bit?" and "What field performance results do we see from improved control?" This paper will address these questions by examining the development and field performance of an advanced automatic drilling system. It will show how the entire system, not just the mechanics or the software, needs to be designed from a control system point of view. It will present the results of field usage of the system, and demonstrating the performance benefits resulting from improved control. Finally, it will suggest future developments for this type of advanced product.
Still-Picture Broadcasting-A New Informational and Instructional Broadcasting System (1973)

Huge transmission capacity will be required for informational and instructional service in the near future. To satisfy the requirement, a new broadcasting system using still pictures with sound is proposed. This paper presents the basic idea including classification of program types and characteristics of the transmission signal, especially the means of handling effectively a large number of sound signals. A pilot system developed for studying multiple transmission of programs is also described.
Non-hydrogen Bond Interactions Involving the Methionine Sulfur Atom (2001)

Of all the nonbonded interactions, hydrogen bond, because of its geometry involving polar atoms, is the most easily recognizable. Here we characterize two interactions involving the divalent sulfur of methionine (Met) residues that do not need any participation of proton. In one an oxygen atom of the main-chain carbonyl group or a carboxylate side chain is used. In another an aromatic atom interacting along the face of the ring is utilized. In these, the divalent sulfur behaves as an electrophile and the other electron-rich atom, a nucleophile. The stereochemistry of the interaction is such that the nucleophile tends to approach approximately along the extension of one of the covalent bonds to S. The nitrogen atom of histidine side chain is extensively used in these nonbonded contacts. There is no particular geometric pattern in the interaction of S with the edge of an aromatic ring, except when an N-H group in involved, which is found within 40 degrees from the perpendicular to the sulfide plane, thus defining the geometry of hydrogen bond interaction involving the sulfur atom. As most of the Met residues which partake in such stereospecific interactions are buried, these would be important for the stability of the protein core, and their incorporation in the binding site would be useful for molecular recognition and optimization of the site's affinity for partners (especially containing aromatic and heteroaromatic groups). Mutational studies aimed at replacing Met by other residues would benefit from the delineation of these interactions.
Twist1-Mediated Adriamycin-Induced Epithelial-Mesenchymal Transition Relates to Multidrug Resistance and Invasive Potential in Breast Cancer Cells (2009)

Our studies show the diverse responses to Adriamycin treatment in cells at different phases, suggest an unrecognized role of EMT in regulating MDR and invasion, and show the efficacy of Twist1 RNA interference in Adriamycin-based chemotherapies for breast cancer.
Allogeneic adipose‐derived stem cells for the treatment of perianal fistula in Crohn's disease: a pilot clinical trial (2015)

These data suggest that allogeneic adipose-derived stem cells may be a feasible treatment option for perianal fistula in Crohn's disease.
Safety and Pharmacokinetics of an Intramuscular Monoclonal Antibody (SB 209763) against Respiratory Syncytial Virus (RSV) in Infants and Young Children at Risk for Severe RSV Disease (1999)

We conducted a multicenter, double-blind, placebo-controlled, randomized trial of a humanized monoclonal antibody against a respiratory syncytial virus (RSV) fusion protein (SB 209763) to evaluate its safety, pharmacokinetics, and fusion inhibition and neutralization titers. Forty-three infants who were either delivered prematurely (</=35 weeks' gestation) or exhibited bronchopulmonary dysplasia were administered either single or repeat (two doses, 8 weeks apart) intramuscular injections of SB 209763 at a concentration of 0.25, 1.25, 5.0, or 10.0 mg/kg or of a placebo. Four of 229 adverse events were considered related to the study drug, including purpura (n = 3) and thrombocytosis (n = 1). No subject developed a detectable level of anti-SB 209763 antibody. Approximately 1 week after administration of the second dose of SB 209763 at 10 mg/kg, the mean plasma concentration (n = 9) was 68.5 micrograms/ml. The terminal half-life (T1/2) determined by noncompartmental analysis ranged from 22 to 50 days. The population pharmacokinetics for SB 209763 following intramuscular administration was appropriately described by a one-compartment model with first-order input and elimination. Higher values for clearance and volume of distribution at steady state were observed for younger patients, with values decreasing to 0.143 (ml/h)/kg and 161 mL/kg, respectively, by a mean age of 298 days (approximately 10 months). The mean T1/2 of SB 209763 for the study population was 32.5 days. No other factor (dose, weight, gender, race, premature birth, or bronchopulmonary dysplasia) was observed to alter the population pharmacokinetics of SB 209763 in this study of infants and young children. The mean neutralization titer on day 6 was 286, and the mean fusion inhibition titer was 36. At least 57% of subjects dosed at 1.25 to 10.0 mg of SB 209763 per kg of body weight who were seronegative at baseline experienced a fourfold or greater increase in fusion inhibition titer. Nine RSV infections were documented during the 16-week course of the study; the numbers of RSV infections were similar for the different regimens, including the placebo. The doses of SB 209763 studied may have been insufficient to confer protection against RSV lower respiratory tract disease; these results suggest that additional trials using higher doses of monoclonal antibody for immunoprophylaxis should be considered.
Commercial applications on the AP3000 parallel computer (2002)

Recently, commercial parallel applications became important in parallel computing with the increase of parallel computer users. In this study, we parallelize two commercial applications, a fulltext search system and a data mining system. In this paper, the implementation of each application and its performance evaluation on the AP3000 parallel computer are shown. A parallel framework, a novel parallelizing approach applied to those applications, is also described.
Phospshoinositide 3-Kinase (PI3K)/Mammalian Target of Rapamycin (mTOR) Dual Inhibitors: Discovery and Structure–Activity Relationships of a Series of Quinoline and Quinoxaline Derivatives (2011)

The phosphoinositide 3-kinase (PI3K) family catalyzes the ATP-dependent phosphorylation of the 3'-hydroxyl group of phosphatidylinositols and plays an important role in cell growth and survival. There is abundant evidence demonstrating that PI3K signaling is dysregulated in many human cancers, suggesting that therapeutics targeting the PI3K pathway may have utility for the treatment of cancer. Our efforts to identify potent, efficacious, and orally available PI3K/mammalian target of rapamycin (mTOR) dual inhibitors resulted in the discovery of a series of substituted quinolines and quinoxalines derivatives. In this report, we describe the structure-activity relationships, selectivity, and pharmacokinetic data of this series and illustrate the in vivo pharmacodynamic and efficacy data for a representative compound.
Effects of Prostaglandins on the Ovine Corpus Luteum: Blood Flow, Secretion of Progesterone and Morphology1 (1976)

Intra-uterine administration of prostaglandin F2α-tham salt (PGF2α) to ewes on Days 9 or 10 of the estrous cycle was followed by reduced flow of blood to the ovary containing the corpus luteum and reduced levels of progesterone in the systemic circulation. These parameters were highly correlated (P<0.01). In an attempt to separate a direct effect of PG on the luteal cell from the effects on ovarian blood flow, analogs of PGF2α, ICI-79939 and ICI-81008, having 10 times more and 50 times less smooth muscle stimulating activity than PGF2α, respectively, were administered intramuscularly to ewes on Day 10 of the estrous cycle. Levels of progesterone in the systemic circulation and blood flow to the ovary with a corpus luteum decreased to basal levels within 12 h after treatment in both groups of ewes. Ovarian blood flow and systemic progesterone levels were also correlated in ewes receiving ICI-79939 (r = 0.87, P<0.01) and ICI-81008 (r = 0.50, P<0.05) In corpora lutea removed from ewes 0, 6, 12, 24 and 48 h after administration of PGF2α there was a decrease in percentage of the total volume of the corpus luteum occupied by endothelial cells (P<0.001), red blood cells (P<0.01) and lumens of capillaries (P<0.05) with time. There was an increase in cellular debris in the extra-cellular space (P<0.01) and within capillaries (P<0.05) after injection of PGF2α. Percent volume of the corpus luteum occupied by theca-lutein cells, fibroblasts, eosinophils, connective tissue and white blood cells was not affected by this treatment. Ultrastructurally, corpora lutea removed from ewes 6 h after injection of PGF2α were similar to corpora lutea removed from control ewes. By 12 h, a proliferation of coated vesicles, dense bodies and lipid droplets was observed in granulosa-lutein cells and local areas of cytoplasmic degeneration were visible. By 24 h after treatment with PGF2α many of the capillaries which were present contained cellular debris, nucleoli in granulosa-lutein cells were rare and granules within the matrix of the mitochondria were numerous. By 48 h, granulosa-lutein cells were extremely shrunken, contained irregular nuclei with condensed chromatin, abundant lipid droplets and swollen mitochondria. Morphological changes occurring in the theca-lutein cells after administration of PGF2α to ewes were similar to the changes described for granulosa-lutein cells. The data obtained from these experiments indicate that administration of PGF2α to ewes reduced blood flow to the ovary with a corpus luteum and reduced secretion of progesterone. Morphological studies suggested that PGF2α affected the vascular component of the corpus luteum.
Environmental Contributions to the Obesity Epidemic (1998)

The current epidemic of obesity is caused largely by an environment that promotes excessive food intake and discourages physical activity. Although humans have evolved excellent physiological mechanisms to defend against body weight loss, they have only weak physiological mechanisms to defend against body weight gain when food is abundant. Control of portion size, consumption of a diet low in fat and energy density, and regular physical activity are behaviors that protect against obesity, but it is becoming difficult to adopt and maintain these behaviors in the current environment. Because obesity is difficult to treat, public health efforts need to be directed toward prevention.
Nucleotide sequence and expression of a novel pectate lyase gene (pel-3) and a closely linked endopolygalacturonase gene (peh-1) of Erwinia carotovora subsp. carotovora 71 (1994)

Our previous genetic analysis (J. W. Willis, J. K. Engwall, and A. K. Chatterjee, Phytopathology 77:1199-1205, 1987) had revealed a tight linkage between pel-3 (pel, pectate lyase gene) and peh-1 (peh, polygalacturonase gene) within the chromosome of Erwinia carotovora subsp. carotovora 71. Nucleotide sequencing, transcript assays, and expression of enzymatic activities in Escherichia coli have now confirmed that a 3,500-bp segment contains the open reading frames (ORFs) for Pel-3 and Peh-1. The 1,041-bp pel-3 ORF and the 1,206-bp peh-1 ORF are separated by a 579-bp sequence. The genes are transcribed divergently from their own promoters. In E. coli and E. carotovora subsp. carotovora 71, peh-1 is better expressed than pel-3. However, plant signals activate the expression of both the genes in E. carotovora subsp. carotovora. A consensus integration host factor (IHF)-binding sequence upstream of pel-3 appears physiologically significant, since pel-3 promoter activity is higher in an E. coli IHF+ strain than in an IHF- strain. While peh-1 has extensive homology with plant and bacterial peh genes, pel-3 appears not to have significant homology with the pel genes belonging to the pelBC, pelADE, or periplasmic pel families. Pel-3 also is unusual in that it is predicted to contain an ATP- and GTP-binding site motif A (P-loop) not found in the other Pels.
A JSW-based cooperative transmission scheme for underwater acoustic networks (2012)

The design of the MAC protocols for underwater acoustic sensor networks (UASNs) poses significant challenges due to the characteristics of underwater acoustic channels such as limited bandwidth, high bit error rate and long propagation delay. While cooperative transmission renders diversity gain through relay nodes. In this paper, we investigate cooperative transmission techniques for UASNs by integrating the juggling-like stop-and-wait (JSW) transmission scheme into data transmission based on traditional reservation-based MAC protocols. Specifically, upon completion of channel reservation between a pair of nodes, the data transmission between the transmitter and the receiver is operated in the JSW manner; the receiver forwards the just correctly received packets to its own intended receiver immediately, which can be treated as an implicit ACK by the transmitter. By doing so, the transmitter can know whether a data packet has been correctly received while the receiver's intended receiver, which is one of the transmitter's hidden terminals and is required to keep silent in traditional reservation modes, can piggyback receive most of the data from the two-hop node, which remarkably enhances the UASN's transmission efficiency. Simulation results validate the superior performance of data transmission with our proposed cooperative transmission scheme compared to the classic one with non-cooperative transmission scheme.
Method To Compare Collision-Induced Dissociation Spectra of Peptides:  Potential for Library Searching and Subtractive Analysis (1998)

We report the development of a method to compare collision-induced dissociation (CID) spectra of peptides. This method employs a cross-correlation analysis of a CID spectrum to a reference spectrum and normalizes the cross-correlation score to the autocorrelation of the CID spectra. The query spectrum is compared by using both mass information and fragmentation patterns. Fragmentation patterns are compared to each other using a correlation function. To evaluate the specificity of the approach, a set of 2180 tandem mass spectra obtained from both triple-quadrupole tandem mass spectrometers (TSQ) and quadrupole ion trap mass spectrometers (LCQ) was created. Comparisons are performed between tandem mass spectra obtained on the same instrument type as well as between different instrument types. Accurate and reliable comparisons are demonstrated in both types of analyses. The scores obtained in the cross-comparison of TSQ and LCQ tandem mass spectra of the same peptide are found to be slightly lower than comparisons performed with spectra obtained on the same instrument type. The method appears insensitive to variations in day-to-day performance of the instrument, minor variations in fragment ion abundance, and instrumental differences inherent in the same instrument model. The use of this method of comparison is demonstrated for library searching and subtractive analysis of tandem mass spectra obtained during LC/MS/MS experiments.
Non-canonical Transit Peptide for Import into the Chloroplast (2002)

The large majority of plastid proteins are nuclear-encoded and, thus, must be imported within these organelles. Unlike most of the outer envelope proteins, targeting of proteins to all other plastid compartments (inner envelope membrane, stroma, and thylakoid) is strictly dependent on the presence of a cleavable transit sequence in the precursor N-terminal region. In this paper, we describe the identification of a new envelope protein component (ceQORH) and demonstrate that its subcellular localization is limited to the inner membrane of the chloroplast envelope. Immunopurification, microsequencing of the natural envelope protein and cloning of the corresponding full-length cDNA demonstrated that this protein is not processed in the N-terminal region during its targeting to the inner envelope membrane. Transient expression experiments in plant cells were performed with truncated forms of the ceQORH protein fused to the green fluorescent protein. These experiments suggest that neither the N-terminal nor the C-terminal are essential for chloroplastic localization of the ceQORH protein. These observations are discussed in the frame of the endosymbiotic theory of chloroplast evolution and suggest that a domain of the ceQORH bacterial ancestor may have evolved so as to exclude the general requirement of an N-terminal plastid transit sequence.
Interferon γ (IFNγ) and Tumor Necrosis Factor α Synergism in ME-180 Cervical Cancer Cell Apoptosis and Necrosis (2001)

We investigated the molecular mechanism of the synergism between interferon gamma (IFNgamma) and tumor necrosis factor alpha (TNFalpha) documented in a variety of biological occasions such as tumor cell death and inflammatory responses. IFNgamma/TNFalpha synergistically induced apoptosis of ME-180 cervical cancer cells. IFNgamma induced STAT1 phosphorylation and interferon regulatory factor 1 (IRF-1) expression. Transfection of phosphorylation-defective STAT1 inhibited IFNgamma/TNFalpha-induced apoptosis, whereas IRF-1 transfection induced susceptibility to TNFalpha. Dominant-negative IkappaBalpha transfection sensitized ME-180 cells to TNFalpha. IFNgamma pretreatment attenuated TNFalpha- or p65-induced NF-kappaB reporter activity, whereas it did not inhibit p65 translocation or DNA binding of NF-kappaB. IRF-1 transfection alone inhibited TNFalpha-induced NF-kappaB activity, which was reversed by coactivator p300 overexpression. Caspases were activated by IFNgamma/TNFalpha combination; however, caspase inhibition did not abrogate IFNgamma/TNFalpha-induced cell death. Instead, caspase inhibitors directed IFNgamma/TNFalpha-treated ME-180 cells to undergo necrosis, as demonstrated by Hoechst 33258/propidium iodide staining and electron microscopy. Taken together, our results indicate that IFNgamma and TNFalpha synergistically act to destroy ME-180 tumor cells by either apoptosis or necrosis, depending on caspase activation, and STAT1/IRF-1 pathways initiated by IFNgamma play a critical role in IFNgamma/TNFalpha synergism by inhibiting cytoprotective NF-kappaB. IFNgamma/TNFalpha synergism appears to activate cell death machinery independently of caspase activation, and caspase activation seems to merely determine the mode of cell death.
Tumor cell heterogeneity: divided-colony assay for measuring drug response. (1987)

In vitro tests for predicting the response of tumors to chemotherapeutic agents might be improved if they were modified to take into account tumor-cell heterogeneity. We have studied the heterogeneity of cellular growth rate and drug response in mouse fibroblast NIH 3T3 cells and in NIH 3T3 cells transformed with the human HRAS gene (homologue of the Harvey sarcoma virus oncogene v-Ha-ras) from the EJ human bladder carcinoma cell line. Growth-rate heterogeneity was detected as a broad distribution of numbers of cells per colony. In spite of this heterogeneity, secondary colonies have numbers of cells per colony that resemble that of the primary colony from which they were derived. The variance between unrelated secondary colonies is increased by HRASEJ. Colony-size measurements are reliable because primary colonies divided in half formed two groups of secondary colonies (on two separate plates) that had indistinguishable mean colony sizes. Based on these observations, a divided-colony procedure was devised to detect the drug response of heterogeneous cell populations. Primary colonies are divided into two groups of cells, one of which is treated with a drug and the other is left untreated as a control. The size distribution of treated secondary colonies is then compared to that of the untreated control and to that of the primary colony from which it was derived. The divided-colony procedure is proposed as a modification of the human-tumor-cloning system to increase the sensitivity and reliability of in vitro procedures used to determine the drug response of heterogeneous tumor-cell populations.
Biocatalytic reduction of short‐chain carboxylic acids into their corresponding alcohols with syngas fermentation (2012)

Short-chain carboxylic acids generated by various mixed- or pure-culture fermentation processes have been considered valuable precursors for production of bioalcohols. While conversion of carboxylic acids into alcohols is routinely performed with catalytic hydrogenation or with strong chemical reducing agents, here, a biological conversion route was explored. The potential of carboxydotrophic bacteria, such as Clostridium ljungdahlii and Clostridium ragsdalei, as biocatalysts for conversion of short-chain carboxylic acids into alcohols, using syngas as a source of electrons and energy is demonstrated. Acetic acid, propionic acid, n-butyric acid, isobutyric acid, n-valeric acid, and n-caproic acid were converted into their corresponding alcohols. Furthermore, biomass yields and fermentation stoichiometry from the experimental data were modeled to determine how much metabolic energy C. ljungdahlii generated during syngas fermentation. An ATP yield of 0.4-0.5 mol of ATP per mol CO consumed was calculated in the presence of hydrogen. The ratio of protons pumped across the cell membrane versus electrons transferred from ferredoxin to NAD(+) via the Rnf complex is suggested to be 1.0. Based on these results, we provide suggestions how n-butyric acid to n-butanol conversion via syngas fermentation can be further improved.