gebhart/patrepeval huggingface dataset:
Purification of a rat neurotensin receptor expressed in Escherichia coli (1996)

A truncated rat neurotensin receptor (NTR), expressed in Escherichia coli with the maltose-binding protein fused to its N-terminus and the 13 amino acid Bio tag fused to its C-terminus, was purified to apparent homogeneity in two steps by use of the monomeric avidin system followed by a novel neurotensin column. This purification protocol was developed by engineering a variety of affinity tags on to the C-terminus of NTR. Surprisingly, expression levels varied considerably depending on the C-terminal tag used. Functional expression of NTR was highest (800 receptors/cell) when thioredoxin was placed between the receptor C-terminus and the tag, indicating a stabilizing effect of the thioredoxin moiety. Several affinity chromatography methods were tested for purification. NTR with the in vivo-biotinylated Bio tag was purified with the highest efficiency compared with NTR with the Strep tag or a hexa-histidine tail. Co-expression of biotin ligase improved considerably the in vivo biotinylation of the Bio tag and, therefore, the overall purification yield. Proteolysis of the NTR fusion protein was prevented by removing a protease-sensitive site discovered at the N-terminus of NTR. The ligand binding properties of the purified receptor were similar to those of the membrane-bound protein and the native receptor. The scale-up of this purification scheme, to provide sufficient protein for biophysical studies, is in progress.
The transfer of current through skin and muscle during electrical stimulation with sine, square, Russian and interferential waveforms (2009)

Electrical stimulation is a commonly used modality for both athletic training and physical therapy. However, there are limited objective data available to determine the waveform which provides the maximum muscle strength as well as minimizing pain. In the present investigation, two groups of subjects were examined. Group 1 was composed of six males and four females and group 2 was composed of three male and three female subjects. The first series of experiments investigated muscle strength with stimulation at currents of 20, 40 and 60 milliamps using sine, square, Russian and interferential waveforms evaluating strength production and pain as outcomes. The second phase of experiments compared the effect of the different waveforms on current dispersion in surface versus deep muscle electrodes with these same waveforms. The results of the experiments showed that sine wave stimulation produced significantly greater muscle strength and significantly less pain than square wave, Russian or interferential stimulation at that same current. The most painful stimulation was square wave. Strength production was greatest with sine wave and least with Russian and interferential. An explanation of these findings may be the filtering effect of the fat layer separating skin from muscle. The highly conductive muscle and skin dermal layers would form the plates of a capacitor separated by the subcutaneous fat layer providing an RC filter. This filtering effect, while allowing sine wave stimulation to pass to the muscle, reduced power transfer in square wave, Russian and interferential stimulation is observed.
3D Polymer Microframes That Exploit Length‐Scale‐Dependent Mechanical Behavior (2006)

Holographic interference lithography is used to create a 3D polymer microframe with sub-micrometer periodicity, low density, and 200 nm feature size. These structures exhibit interesting deformational characteristics (see figure) with ultimate strains reaching ca. 300 %, much higher than the strains attainable in bulk films of either the fully crosslinked solid polymeric material or the uncrosslinked glassy monomer precursor.
Structural Study of the Blood Group A Active Glycolipids of Hog Gastric Mucosa (1974)

Abstract Two forms of blood group A active glycolipids (L and U) containing oligosaccharides of 7 sugar residues have been isolated from hog stomach mucosa lipid extract (Slomiany, A., and Horowitz, M. I. (1973) J. Biol. Chem. 248, 6232–6238. Partial acid hydrolysis, infrared spectroscopy, periodate oxidation, permethylation, and sequential enzymatic degradation were used to elucidate the glycolipid structures. The structures were shown to be: [see PDF for equation]
Protocol for the Use of a Bead Array for the Multiple Detection of Genotype of Chlamydia trachomatis (2012)

The identification of Chlamydia trachomatis genotypes is important for both molecular epidemiology and infection control such as contact tracing and identification of high-risk groups. Currently, at least 19 human serovars have been recognized by using polyclonal and monoclonal antibodies against the major outer membrane protein. In sexually transmitted diseases, multiple pathogens or genotype infections are not uncommon. Hence, detection of multiple gene targets in one reaction is becoming increasingly important. Here, we describe the multiplex detection of eight genotypes of C. trachomatis by a combination of a PCR amplification with a multiplex bead array detection. The bead array system comprises distinct bead sets, which are color coded by different fluorescent intensities and a dual-laser flow cytometer analyzer to identify the identity of the bead and the intensity of the reporter dye that binds to the target molecules. The DNA sequences of the variable segments (VS2 or VS1-VS2) in outer membrane protein (omp1) gene are PCR amplified and biotin labeled and used as a gene target for the genotyping of C. trachomatis. Genotype-specific probes coupled to beads are used for capturing the labeled target amplicons through specific hybridization. Thus, multiple genotypes are detected and differentiated simultaneously by yielding quantitative data.
Dopamine and μ-opioid receptor dysregulation in the brains of binge-eating female rats – possible relevance in the psychopathology and treatment of binge-eating disorder (2017)

Adult, female rats given irregular, limited access to chocolate develop binge-eating behaviour with normal bodyweight and compulsive/perseverative and impulsive behaviours similar to those in binge-eating disorder. We investigated whether (a) dysregulated central nervous system dopaminergic and opioidergic systems are part of the psychopathology of binge-eating and (b) these neurotransmitter systems may mediate the actions of drugs ameliorating binge-eating disorder psychopathology. Binge-eating produced a 39% reduction of striatal D<sub>1</sub> receptors with 22% and 23% reductions in medial and lateral caudate putamen and a 22% increase of striatal μ-opioid receptors. There was no change in D<sub>1</sub> receptor density in nucleus accumbens, medial prefrontal cortex or dorsolateral frontal cortex, striatal D<sub>2</sub> receptors and dopamine reuptake transporter sites, or μ-opioid receptors in frontal cortex. There were no changes in ligand affinities. The concentrations of monoamines, metabolites and estimates of dopamine (dopamine/dihydroxyphenylacetic acid ratio) and serotonin/5-hydroxyindolacetic acid ratio turnover rates were unchanged in striatum and frontal cortex. However, turnover of dopamine and serotonin in the hypothalamus was increased ~20% and ~15%, respectively. Striatal transmission via D<sub>1</sub> receptors is decreased in binge-eating rats while μ-opioid receptor signalling may be increased. These changes are consistent with the attenuation of binge-eating by lisdexamfetamine, which increases catecholaminergic neurotransmission, and nalmefene, a μ-opioid antagonist.
Impaired in vivo vasculogenic potential of endothelial progenitor cells in comparison to human umbilical vein endothelial cells in a spheroid‐based implantation model (2009)

Our results indicate that vascular-derived endothelial cells, such as HUVECs are superior to EPCs in terms of promoting in vivo vascularization of engineered tissues.
The role of segment polarity genes during Drosophila neurogenesis. (1989)

Segment polarity genes in Drosophila are required for the proper formation of epidermal pattern within each segment. Here we show that certain segment polarity genes are also critical for the determination of specific neuronal identities in the developing central nervous system (CNS) of the Drosophila embryo. For several mutants, however, the pattern defects do not simply parallel their cuticular phenotypes. In fused, armadillo, and cubitus interruptus Dominant mutants, much of the CNS appears relatively normal. In hedgehog mutants, the CNS is highly disorganized, but this disruption may occur secondary to the initial events of neurogenesis. The specific cellular defects in patched mutants suggests that this gene specifies a subset of neuroblasts and neural progeny underlying the region of epidermal pattern defect. gooseberry mutants display a complex series of alterations in neuronal identity both underlying and outside of the region of epidermal modification. Neuronal identities of a set of cells along the midline appear to be changed in Cell mutants. The phenotype of wingless mutants is the most restricted and may be due to improper communication between sibling neurons. Thus, in addition to their functions in epidermal pattern formation, at least four of the segment polarity genes (gooseberry, patched, Cell, and wingless) appear to have specific roles in the control of cell fates during neurogenesis.
Automatic Generation of Statistical Pose and Shape Models for Articulated Joints (2013)

Statistical analysis of motion patterns of body joints is potentially useful for detecting and quantifying pathologies. However, building a statistical motion model across different subjects remains a challenging task, especially for a complex joint like the wrist. We present a novel framework for simultaneous registration and segmentation of multiple 3-D (CT or MR) volumes of different subjects at various articulated positions. The framework starts with a pose model generated from 3-D volumes captured at different articulated positions of a single subject (template). This initial pose model is used to register the template volume to image volumes from new subjects. During this process, the Grow-Cut algorithm is used in an iterative refinement of the segmentation of the bone along with the pose parameters. As each new subject is registered and segmented, the pose model is updated, improving the accuracy of successive registrations. We applied the algorithm to CT images of the wrist from 25 subjects, each at five different wrist positions and demonstrated that it performed robustly and accurately. More importantly, the resulting segmentations allowed a statistical pose model of the carpal bones to be generated automatically without interaction. The evaluation results show that our proposed framework achieved accurate registration with an average mean target registration error of 0.34 ±0.27 mm. The automatic segmentation results also show high consistency with the ground truth obtained semi-automatically. Furthermore, we demonstrated the capability of the resulting statistical pose and shape models by using them to generate a measurement tool for scaphoid-lunate dissociation diagnosis, which achieved 90% sensitivity and specificity.
Angiopoietin-2 TIEs Up Macrophages in Tumor Angiogenesis (2011)

Angiopoietin-2 (ANG2), a ligand of the TIE2 receptor, modulates endothelial cell biology and destabilizes blood vessels to facilitate angiogenesis. Recent reports have shown that ANG2 inhibition, for example, by monoclonal antibodies, peptibodies, or CovX-Bodies, may achieve substantial antiangiogenic and antitumor responses in a variety of mouse tumor models, including spontaneous MMTV-PyMT mammary and RIP1-Tag2 pancreatic islet adenocarcinomas. There is also evidence that targeting the ANG2/TIE2 signaling pathway may inhibit the functions of TIE2-expressing macrophages (TEM), a tumor-associated macrophage subset endowed with proangiogenic activity in mouse tumor models. The clinical opportunities afforded by simultaneously targeting the effects of ANG2 on tumor angiogenesis and the proangiogenic activity of TEMs are discussed.
Infinite-Horizon Model Predictive Control for Periodic Tasks with Contacts (2011)

We present a method that combines offline trajectory optimization and online Model Predictive Control (MPC), generating robust controllers for complex periodic behavior in domains with unilateral constraints (e.g., contact with the environment). MPC offers robust and adaptive control even in high-dimensional domains; however, the online optimization gets stuck in local minima when the domains has discontinuous dynamics. Some methods of trajectory optimization that are immune to such problems, but these are often too slow to be applied online.
Optimal multi-step k-nearest neighbor search (1998)

For an increasing number of modern database applications, efficient support of similarity search becomes an important task. Along with the complexity of the objects such as images, molecules and mechanical parts, also the complexity of the similarity models increases more and more. Whereas algorithms that are directly based on indexes work well for simple medium-dimensional similarity distance functions, they do not meet the efficiency requirements of complex high-dimensional and adaptable distance functions. The use of a multi-step query processing strategy is recommended in these cases, and our investigations substantiate that the number of candidates which are produced in the filter step and exactly evaluated in the refinement step is a fundamental efficiency parameter. After revealing the strong performance shortcomings of the state-of-the-art algorithm for k-nearest neighbor search [Korn et al. 1996], we present a novel multi-step algorithm which is guaranteed to produce the minimum number of candidates. Experimental evaluations demonstrate the significant performance gain over the previous solution, and we observed average improvement factors of up to 120 for the number of candidates and up to 48 for the total runtime.
Alignment of the Apolipophorin-III α-Helices in Complex with Dimyristoylphosphatidylcholine. (1995)

Apolipophorin-III (apoLp-III) from Manduca sexta can exist in two alternate states: as a globular, lipid-free helix bundle or a lipid surface-associated apolipoprotein. Previous papers (Ryan R.O., Oikawa K., and Kay C. M. (1993) J. Biol. Chem. 268, 1525-1530; Wientzek M., Kay C.M., Oikawa K., and Ryan R.O. (1994) J. Biol. Chem. 269, 4605-4612) have investigated the structures and properties of apolipophorin-III from M. sexta in the lipid-free state and associated to lipids. Association of apoLp-III with dimyristoylphosphatidylcholine vesicles leads to the formation of uniform lipid discs with an average diameter and thickness of 18.5 +/- 2.0 and 4.8 +/- 0.8 nm, respectively. These discs contain six molecules of apoLp-III. Geometrical calculations based on these data, together with x-ray crystallographic data from the homologous L. migratoria apoLp-III (Breiter D. R., Kanost M.R., Benning M.M., Wesenberg G., Law J.H., Wells M.A., Rayment I., and Holden H.M. (1991) Biochemistry 30, 603-608), have allowed the presentation of a model of lipid-protein interaction, in which the alpha-helices of the apoLp-III orient perpendicular to the phospholipid chains and surround the lipid disc. Here, using polarized Fourier transform-attenuated total reflection infrared spectroscopy, we provide the first experimental evidence of a unique perpendicular orientation of the alpha-helices with respect to the fatty acyl chains of the phospholipids in the disc.
A chloride-inducible gene expression cassette and its use in induced lysis of Lactococcus lactis (1997)

A chloride-inducible promoter previously isolated from the chromosome of Lactococcus lactis (J. W. Sanders, G. Venema, J. Kok, and K. Leenhouts, Mol. Gen. Genet., in press) was exploited for the inducible expression of homologous and heterologous genes. An expression cassette consisting of the positive-regulator gene gadR, the chloride-inducible promoter Pgad, and the translation initiation signals of gadC was amplified by PCR. The cassette was cloned upstream of Escherichia coli lacZ, the holin-lysin cassette (lytPR) of the lactococcal bacteriophage r1t, and the autolysin gene of L. lactis, acmA. Basal activity of Pgad resulted in a low level of expression of all three proteins. Growth in the presence of 0.5 M NaCl of a strain containing the gadC::lacZ fusion resulted in a 1,500-fold increase of beta-galactosidase activity. The background activity levels of LytPR and AcmA had no deleterious effects on cell growth, but induction of lysin expression by addition of 0.5 M NaCl resulted in inhibition of growth. Lysis was monitored by following the release of the cytoplasmic marker enzyme PepX. Released PepX activity was maximal at 1 day after induction of lytPR expression with 0.1 M NaCl. Induction of acmA expression resulted in slower release of PepX from the cells. The presence of the inducing agent NaCl resulted in the stabilization of osmotically fragile cells.
Fabrication of one-dimensional nanowire structures utilizing crystallographic orientation in silicon and their conductance characteristics (1997)

We propose a process for fabricating one-dimensional Si nanowires with a point contact. The nanowire structure can be easily obtained through two steps: KOH etching of a {110} Si layer of a silicon on insulator substrate and sufficient oxidation of the Si patterns formed by etching. In the etching process, vertical sidewalls comprised of {111} planes are formed into a wire. In addition, other {111} planes, projecting obliquely along the vertical sidewalls, spontaneously appear in the etched substrate. This is due to the fact that the etching proceeds as {111} planes appear because the etch rate of the {111} plane is the lowest of all planes. The bottom-corner region of two inclined {111} planes becomes a point-contact structure by making the distance between two inclined planes appropriate. The oxidation process converts the two-dimensional wire into one-dimensional nanowire by the stress-dependent oxidation phenomena of the Si wire. Consequently, a Si nanowire with a point contact can be formed in the bottom region. The Si nanowires fabricated through this process show clear conductance steps with little fluctuation on plateaus at 45 K. In addition, we discuss the conductance step characteristics in connection with a calculated energy level for a nanowire in (110) Si.
A health education campaign to prevent osteomalacia in Asian women in Glasgow: 1984–86 (1989)

Vitamin D deficiency is common in Asian women in Britain. Self‐supplementation with vitamin D provides effective prophylaxis. Between 1984‐86 a Health Education campaign promoted vitamin D supplementation by Asian women in Glasgow. Vitamin D supplements were provided at cost‐price in Health Board clinics and a co‐ordinator and four Asian link‐workers promoted the aims of the campaign. Despite the campaign few Asian women presently purchase vitamin D supplements. Serum 25‐OHD and calcium concentrations were significantly lower in a post‐campaing survey (1986) of Asian women than in a pre‐campaign survey (1982‐83). In contrast, the majority of Asian children in the city receive a vitamin D supplement which their mothers perceive as important for their welfare. The failure of the present campaign suggests that early detection and treatment of symptomatic osteomalacia constitutes the only means of reducing the morbidity caused by this disease.
[Chromosomal aberration analyzed by comparative genomic hybridization in nasopharyngeal carcinoma]. (2001)

There are multiple regions of chromosomes with copy number changes in NPC. The tumor suppressor genes and oncogenes on these regions may be involved in the development and progress of nasopharyngeal carcinoma.
Activin-A Inhibits Proopiomelanocortin Messenger RNA Accumulation and Adrenocorticotropin Secretion of AtT20 Cells (1991)

The complexity of corticotropic cell regulation by multiple central and peripheral factors is well recognized. The present study provides evidence for the participation of an additional factor in the regulation of this cell type of the anterior pituitary. Using the clonal AtT20 cell line as a model for corticotropes, homodimeric activin-A was observed to suppress basal ACTH secretion and POMC mRNA accumulation by approximately 50%. These effects required prolonged treatment with activin-A and were concentration dependent; the half-maximum concentration was in the range of 30-50 pM. Consistently, AtT20 cells were found to express specific high affinity binding sites for [125I]activin-A. The simultaneous addition of inhibin-A along with increasing concentrations of activin-A did not alter the characteristics of the inhibition of ACTH secretion by activin-A alone. This is in contrast to observations with gonadotropes of the anterior pituitary as well as a number of other cell types in which inhibin-A can partially antagonize the biological actions of activin-A. The results may suggest the participation of a subclass of activin receptors that mediate effects on ACTH secretion and POMC mRNA accumulation. As previously shown, the incubation of AtT20 cells with a synthetic glucocorticoid, dexamethasone, attenuated basal ACTH secretion and POMC expression in a concentration-dependent manner. The inhibition of both of these parameters by activin-A, however, was independent of glucocorticoids, because the two agents were additive in their actions. In addition to effects on secretion and mRNA levels, treatment with activin-A also inhibited the rate of proliferation of AtT20 cells.(ABSTRACT TRUNCATED AT 250 WORDS)
Kras in metastatic colorectal cancer (2010)

Kras, a small intracellular GTPase, is a central intermediary of the epidermal growth factor receptor (EGFR) and other tyrosine kinase receptor pathways. Increased EGFR and Kras signalling is involved in colorectal carcinogenesis and tumour progression. Mutations of Kras result in the loss of its GTPase activity and thus in a constitutive activation of Kras signalling. Kras mutations are found in 30-60% of colorectal cancers. The concordance between Kras mutations in the primary tumour and related metastatic sites is high. Since mutation of Kras confers resistance to anti-EGFR-antibody therapy, it is critical to assess Kras mutational status in colorectal cancer patients. Anti-EGFR-antibody therapy improves survival in patients with metastatic colorectal cancer and wild-type Kras.
Glomectomy in the Treatment of Chronic Bronchial Asthma (1965)

THE proper management of the patient with chronic recurring bronchial asthma taxes the patience, ingenuity and integrity of the physician. Too often, as with many chronic diseases, the hope of "surgical cures" is brought up. Benefit has been described after a wide variety of surgical procedures, and, indeed, their proponents have "suggested" that these measures are specific.1 Occasionally, brilliant (temporary) results in patients with chronic bronchial asthma have been reported after procedures attacking the sympathetic or parasympathetic (vagal) system or both. This is a functional type of surgery that does not aim at the root of the disorder being treated. . . .
Structure–activity studies on a library of potent calix[4]arene-based PDGF antagonists that inhibit PDGF-stimulated PDGFR tyrosine phosphorylation (2006)

Platelet-derived growth factor (PDGF) and its receptor PDGFR are required for tumor growth and angiogenesis, so disruption of the PDGF-PDGFR interaction should lead to starvation of tumors and reduction of tumor growth. Potent PDGF antagonists have been discovered through the synthesis of a series of calix[4]arene-based compounds that are designed to bind to the three-loop region of PDGF. The effect of lower-rim alkylation, linker and number of interacting head groups on the calix[4]arene scaffold on PDGF affinity and cellular activity has been investigated.