gebhart/patrepeval huggingface dataset:
Modulation of hypoglossal motoneuron excitability by NK1 receptor activation in neonatal mice in vitro (2001)

1. The effects of substance P (SP), acting at NK1 receptors, on the excitability and inspiratory activity of hypoglossal (XII) motoneurons (MNs) were investigated using rhythmically active medullary-slice preparations from neonatal mice (postnatal day 0-3). 2. Local application of the NK1 agonist [SAR(9),Met (O(2))(11)]-SP (SP(NK1)) produced a dose-dependent, spantide- (a non-specific NK receptor antagonist) and GR82334-(an NK1 antagonist) sensitive increase in inspiratory burst amplitude recorded from XII nerves. 3. Under current clamp, SP(NK1) significantly depolarized XII MNs, potentiated repetitive firing responses to injected currents and produced a leftward shift in the firing frequency-current relationships without affecting slope. 4. Under voltage clamp, SP(NK1) evoked an inward current and increased input resistance, but had no effect on inspiratory synaptic currents. SP(NK1) currents persisted in the presence of TTX, were GR82334 sensitive, were reduced with hyperpolarization and reversed near the expected E(K). 5. Effects of the alpha(1)-noradrenergic receptor agonist phenylephrine (PE) on repetitive firing behaviour were virtually identical to those of SP(NK1). Moreover, SP(NK1) currents were completely occluded by PE, suggesting that common intracellular pathways mediate the actions of NK1 and alpha(1)-noradrenergic receptors. In spite of the similar actions of SP(NK1) and PE on XII MN responses to somally injected current, alpha(1)-noradrenergic receptor activation potentiated inspiratory synaptic currents and was more than twice as effective in potentiating XII nerve inspiratory burst amplitude. 6. GR82334 reduced XII nerve inspiratory burst amplitude and generated a small outward current in XII MNs. These observations, together with the first immunohistochemical evidence in the newborn for SP immunopositive terminals in the vicinity of SP(NK1)-sensitive inspiratory XII MNs, support the endogenous modulation of XII MN excitability by SP. 7. In contrast to phrenic MNs (Ptak et al. 2000), blocking NMDA receptors with AP5 had no effect on the modulation of XII nerve activity by SP(NK1). 8. In conclusion, SP(NK1) modulates XII motoneuron responses to inspiratory drive primarily through inhibition of a resting, postsynaptic K+ leak conductance. The results establish the functional significance of SP in controlling upper airway tone during early postnatal life and indicate differential modulation of motoneurons controlling airway and pump muscles by SP.
Molecular factors of 5-fluorouracil metabolism in colorectal cancer: Analysis of primary tumor and lymph node metastasis (2006)

Thymidylate synthase (TS), dihydropyrimidine dehydrogenase (DPD) and thymidine phosphorylase (TP) are predictive markers for tumor response to 5-fluorouracil-based therapies. To determine whether gene expression values measured in primary cancer tissue would be useful for prediction of response of lymph node metastases, the expressions of these genes were quantitatively analyzed in 35 pairs of primary colorectal cancer (CRC) and corresponding lymph node metastases using real-time PCR. DPD and TP mRNA levels were significantly lower in the primary colorectal tumor and lymph node metastases compared with the normal adjacent stroma tissue (p<0.01), whereas TS mRNA levels were significantly higher in the primary tumor and lymph node metastases than in the normal adjacent tissue (p<0.001). Median gene expression levels of TP and TS did not differ significantly between primary colorectal tumor and corresponding lymph node metastasis but median DPD gene expression levels in the lymph node metastases were significantly higher compared to matched primary colorectal tumors (p=0.015). There was a significant correlation for DPD, TP and TS gene expression levels between primary colorectal tumor specimens and the matched lymph node metastasis. These results suggest that biopsies of the tumor of origin may be valid for determining predictive markers for chemotherapy response in patients with metastatic CRC.
An Integrated Solution for Wafer-Level Packaging and Electrostatic Actuation of Out-of-Plane Devices (2009)

This paper presents an innovative way to integrate electrodes into our hermetic wafer-level epi-polysilicon encapsulation for out-of-plane actuated devices. The epitaxial-grown silicon encapsulation process was modified to integrate electrodes in the out-of-plane direction and realize ultra-compact packaging. The integration allows reduction of parasitic resistance by more than 180X relative to other conventional interconnects to out-of-plane electrodes. A 200 KHz "see-saw" mode resonator is demonstrated with parasitic resistance of approximately 1 Omega.
B-cell restricted saporin immunotoxins: activity against B-cell lines and chronic lymphocytic leukemia cells (1989)

B cell-restricted immunotoxins were constructed by conjugating anti-B monoclonal antibodies to saporin, the major ribosome inactivating protein from the seeds of the plant Saponaria officinalis. HD37-SAP is directed against CD19, the broadest B cell-specific determinant. HD39- SAP and HD6-SAP recognize two different epitopes on the CD22 molecule, an antigen present on the cell surface of B cells at late stages of differentiation. All three immunotoxins inhibited DNA synthesis and protein synthesis in target B lymphoma cells with a dose-related effect, in short incubation times and in the absence of potentiators. A clonogenic assay demonstrated that all immunotoxins could eliminate more than two logs of clonogenic malignant B cells with a two-hour incubation at concentrations not toxic to cells not bearing target antigens. The immunotoxin activity was evaluated by DNA synthesis inhibition in fresh B-chronic lymphocytic leukemia cells (B-CLL) stimulated to proliferate by incubation with an antibody specific for the receptor of C3b complement component (CR1) plus B cell growth factor. B-CLL cell DNA synthesis was actively inhibited by treatment at low immunotoxin concentration without need of potentiators. Immunotoxins exerted their effect also in whole blood of CLL patients under conditions achievable in vivo. We conclude that B cell-restricted immunotoxins HD37-SAP, HD39-SAP, and HD6-SAP are good candidates for in vivo therapy of B-cell malignancies.
The Amyloid Peptide and Its Precursor in Alzheimer's Disease (1995)

Alzheimer's disease, the most frequent cause of dementia, is characterized by the formation in the brain of neurofibrillary tangles and senile plaques. Neurofibrillary tangles are composed of bundles of paired helical filaments containing the microtubule-associated protein tau. In autopsy-derived brain samples from patients with Alzheimer's disease, tau is hyperphosphorylated and constitutes a promising disease marker. Senile plaques contain a small amyloid peptide derived from the amyloid precursor protein. Mutations of the amyloid precursor protein gene have been identified in rare cases of familial Alzheimer's disease, suggesting a causal role for amyloid peptide deposition in the disease. However, Alzheimer's disease has been demonstrated to be characterized by an important genetic heterogeneity. The identification of pathogenic DNA mutations, different from those of the amyloid precursor protein gene, will reveal whether the corresponding genes are involved in either an increased production of the amyloid peptide or a decrease of its removal, or in the fibrillogenic properties of the peptide, which seem to be related to its toxicity. Several mammalian cells are able to produce the amyloid peptide from its precursor. Understanding the cellular mechanisms that determine how cleavages occur in cells could help to identify new strategies for modulating amyloid peptide production. In attempts to produce animal models of Alzheimer's disease, investigators have used transgenic strategies. To date, these efforts have not been very successful. However, the expression in transgenic mice of both mutated amyloid peptide precursor and amyloid associated proteins should prove useful for examining the importance of putative etiological factors, and for testing novel therapies including anti-amyloidogenic strategies.
Continuous Flow Microfluidic Device for Rapid Erythrocyte Lysis (2004)

Leukocyte isolation from whole blood to study inflammation requires the removal of contaminating erythrocytes. Leukocytes, however, are sensitive to prolonged exposure to hyper/hypoosmotic solutions, temperature changes, mechanical manipulation, and gradient centrifugation. Even though care is taken to minimize leukocyte activation and cell loss during erythrocyte lysis, it is often not possible to completely avoid it. Most procedures for removal of contaminating erythrocytes from leukocyte preparations are designed for bulk processing of blood, where the sample is manipulated for longer periods of time than necessary at the single-cell level. Ammonium chloride-mediated lysis is the most commonly used method to obtain enriched leukocyte populations but has been shown to cause some activation and selective loss of certain cell types. The leukocyte yield and subsequent activation status of residual leukocytes after NH(4)Cl-mediated lysis have been shown to depend on the time of exposure to the lysis buffer. We have developed a microfluidic lysis device that deals with erythrocyte removal at nearly the single-cell level. We can achieve complete lysis of erythrocytes and approximately 100% recovery of leukocytes where the cells are exposed to an isotonic lysis buffer for less than 40 s, after which the leukocytes are immediately returned to physiological conditions. Theoretically, this process can be made massively parallel to process several milliliterss of whole blood to obtain a pure leukocyte population in less than 15 min.
Staphylococcus epidermidis Extracted Slime Inhibits the Antimicrobial Action of Glycopeptide Antibiotics (1990)

Certain strains of Staphylococcus epidermidis produce a mucoid slime that appears to be an important virulence factor. After crude slime was isolated from selected strains of S. epidermidis, phenol and chloroform were used to remove proteins and lipids. The remaining extract contained a polysaccharide that was seen on SDS gels stained with Stains-all. This extract was an inhibitor of the antimicrobial action of vancomycin, raising the minimum inhibitory concentration (MIC) to vancomycin in all 18 isolates of S. epidermidis. A dose-response curve was seen between the amount of extract added and the degree of resistance, as measured by both MIC and growth curves. A similar effect was noted with MICs of organisms to teicoplanin. Addition of the extract did not change the MIC to LY146032, although a modest effect on growth rate was observed. The extract did not raise the MIC to clindamycin, rifampin, and cefazolin. The extract reversed the synergism seen between vancomycin and gentamicin in the 5 strains tested in time-kill studies. The interference by slime of the antimicrobial effect of vancomycin and teicoplanin may explain why these antibiotics are sometimes ineffective in eradicating foreign body infections due to slime-producing coagulase-negative staphylococci.
Mind the Gap (2011)

This chapter considers Thomas Nagel's approach to political philosophy and argues that his various statements about reasonable rejection generate an inconsistency at a politically sensitive point. Nagel is aware that his endorsement of rich people's opposition to radical redistribution “may seem to authorize pure selfishness,” but, he says, “that is too harsh a word for resistance to a radical drop in the standard of living of oneself and one's family.” That word might be too harsh, but Nagel's verdict that the rich need accept only a moderate (that is, nonradical) drop in their wealth is too soft. Officially, and, in Cohen's view, rightly, he depreciates the moral weight of the status quo, but the status quo seems, in the end, to preponderate in his judgment.
Using Encyclopedic Knowledge for Named Entity Disambiguation (2006)

We present a new method for detecting and disambiguating named entities in open domain text. A disambiguation SVM kernel is trained to exploit the high coverage and rich structure of the knowledge encoded in an online encyclopedia. The resulting model significantly outperforms a less informed baseline.
Vpr Is Required for Efficient Replication of Human Immunodeficiency Virus Type-1 in Mononuclear Phagocytes (1995)

HIV-1 vpr encodes a 96-amino acid, nuclear protein whose function is not well understood. Unlike the other lentivirus regulatory proteins, Vpr is present in virions at relatively high copy number. In cells, Vpr is localized to the nucleus. Possible functions for vpr consistent with these findings include the nuclear import of preintegration complexes, transactivation of cellular genes, or induction of cellular differentiation. We show here, using both replication competent, macrophage-tropic virus and a sensitive, single-cycle luciferase HIV-1 reporter vector, that vpr is important for efficient viral replication in primary monocyte/macrophages, but appears to play no role in activated or resting T cell infection. The block to infection in monocytes was localized by PCR analysis of newly synthesized viral DNA and with the luciferase reporter vector to a stage in the viral life cycle after entry and reverse transcription, yet prior to, or at the time of, proviral transcription. In addition, infection of mononuclear phagocytes with virions that had been loaded with Vpr molecules in the producer cells by trans-complementation still showed a vpr-phenotype. These data suggest a role for vpr molecules produced in newly infected cells, in addition to its presumed function in the virion.
Preparation of uniform calcium alginate gel beads by membrane emulsification coupled with internal gelation (2002)

Abstract With the objective of making calcium alginate gel beads with small and uniform size, membrane emulsification coupled with internal gelation was proposed. Spherical gel beads with mean size of about 50 μm, and even smaller ones in water, and with narrow size distribution were successfully obtained. Experimental studies focusing mainly on the effect of process parameters on bead properties were performed. The size of the beads was mainly dependent on the diameter of the membrane pores. High transmembrane pressure made for large gel beads with wide size distribution. Low sodium alginate concentration produced nonspherical beads, whereas a high concentration was unsuitable for the production of small beads with narrow distribution. Thus 1.5% w/v was enough. A high surfactant concentration favored the formation of small beads, but the adverse effect on mass transfer should be considered in this novel process. © 2002 Wiley Periodicals, Inc. J Appl Polym Sci 87: 848–852, 2003
Rethinking Auxin Biosynthesis and Metabolism (1995)

Charles Darwin cited the 1871 Ph.D. thesis of Theophil Ciesielski when he postulated in 1880 that a transmitted present in the tip of plant shoots was responsible for gravitropism. Both Darwin and Ciesielski had realized that the influence was affecting growth differentially. This influence was given the name auxin more than 50 years later and subsequently any compound that promoted growth in specific bioassays was defined as an auxin. The chemical structure of the primary plant auxin, IAA (Fig. 1), has been known since the 1930s to be a 3-substituted indole like Trp. Since that time, the prevailing theory has been that IAA is derived from Trp. However, due to lack of convincing evidence, the biosynthetic pathway for IAA in plants is still undefined. Within the last 10 years, development of precise quantitative methods, good model systems for in vivo analysis, and mutants altered in IAA metabolism have resulted in substantial progress in our understanding of IAA biosynthesis. This review focuses on the new and more complex picture of IAA biosynthesis that has emerged as a result of recent experiments.
Mouse Model for Central Nervous System Neospora caninum Infections (1995)

Neospora caninum is a protozoan parasite that causes severe disease in transplacentally infected dogs and abortions in domestic ruminants. Rodent models of neosporosis rely on treatment of hosts with methylprednisolone acetate (MPA) to enhance infections. The present study reports the development of an inbred BALB/c mouse model that results in central nervous system neosporosis in the absence of MPA treatment. Seven of 12 BALB/c mice died 26-70 days after subcutaneous (s.c.) inoculation with tachyzoites of the NC-1 strain of N. caninum, and none of 12 BALB/c mice died after s.c. inoculation with tachyzoites of the NC-3 strain. None of 8 HSD:ICR mice (4 mice, NC-1 strain; 4 mice, NC-3 strain) developed clinical neosporosis or died after s.c. inoculation with tachyzoites. Control BALB/c (2) and HSD:ICR (2) mice s.c. inoculated with Hanks' balanced salt solution did not develop clinical signs of disease. Some mice in all N. caninum-inoculated groups had brain lesions, but significantly (P < 0.05) more BALB/c mice inoculated with the NC-1 strain had brain lesions.
Multi‐transient electromagnetic repeatability experiment over the North Sea Harding field‡ (2010)

ABSTRACT We present results of synthetic time‐lapse and real repeatability multi‐transient electromagnetic surveys over the North Sea Harding field. Using Archie's law to convert porosity and fluid saturation to resistivity we created 3D isotropic models of the reservoir resistivity at different stages of production from the initial state in 1996 through to complete hydrocarbon production by 2016 and, for each stage, we simulated an east‐west transient electromagnetic survey line across Harding. Unconstrained 1D full‐waveform Occam inversions of these synthetic data show that Harding should be detectable and its lateral extent reasonably well‐defined. Resistivity changes caused by hydrocarbon production from initial pre‐production state to production of the oil rim in 2011 are discernible as are significant changes from 2011–2016 during the modelled gas blowdown phase. The 2D repeatability surveys of 2007 and 2008 tied two wells: one on and the other off the structure. Between the two surveys the segment of the field under investigation produced 3.9 million barrels of oil – not enough to generate an observable time‐lapse electromagnetic anomaly with a signal‐to‐noise ratio of 40 dB. Processing of the 2007 and 2008 data included deconvolution for the measured source current and removal of spatially‐correlated noise, which increased the signal‐to‐noise ratio of the recovered impulse responses by about 20 dB and resulted in a normalized root‐mean‐square difference of 3.9% between the data sets. 1D full‐waveform Occam inversions of the real data showed that Harding was detectable and its lateral extent was also reasonably well‐defined. The results indicate that the multi‐transient electromagnetic method is suitable for exploration, appraisal and monitoring hydrocarbon production.
SOX9 expression is a general marker of basal cell carcinoma and adnexal‐related neoplasms (2008)

SOX9 expression is a general feature of BCC and adnexal skin neoplasms, suggesting a contribution of SOX9 to the pathogenesis of these tumors.
Characterization of hepatitis C virus replication in cloned cells obtained from a human T-cell leukemia virus type 1-infected cell line, MT-2 (1996)

We recently found that a human T-cell leukemia virus type 1-infected cell line, MT-2, could support the replication of hepatitis C virus (HCV) (N. Kato, T. Nakazawa, T. Mizutani, and K. Shimotohno, Biochem. Biophys. Res. Commun. 206:863-869, 1995). In order to develop a culture system in which HCV replicates more efficiently, we examined the efficiency of HCV replication in cloned MT-2 cell lines by the limiting dilution method. Consequently, we obtained five clones in which intracellular positive-stranded HCV RNA could be detected until at least 21 days postinoculation (p.i.), as opposed to 15 days p.i. in uncloned MT-2 cells. MT-2C, one of the five clones which supported HCV replication up to 30 days p.i., was used for further characterization of HCV replication. Semiquantitative analysis of HCV by PCR revealed that RNA synthesis in infected cells increased after inoculation, reached a maximum level at 4 days p.i., and maintained this level until at least 11 days p.i. The 5' untranslated region of negative-stranded HCV RNA was also detected in the infected cells by two different methods with strand specificity. These results suggest that HCV replicated and multiplied in the MT-2C cells. HCV-infected MT-2C cells that were treated with antibiotics, such as G418 and hygromycin B, sustained HCV RNA for a longer period than did untreated cells. We demonstrated inhibitory effects on HCV replication by an antisense oligonucleotide complementary to the HCV core encoding region and by interferon-alpha. Furthermore, cell-free viral transmission was demonstrated by this culture system. These results suggest that our cell culture system will be useful for studying the mechanism of HCV replication, for screening antiviral agents, and for developing HCV vaccines.
From range scans to 3D models (1999)

Each year, we see a growing number of 3D range scanning products on the SIGGRAPH exhibition floor. You may find yourself asking "how do these technologies work?" and "how can I make use of the shape data they produce?" In this article, I will describe a few of the more common range scanning technologies. Then, I will step through a pipeline that takes the range data into a single geometric model and will conclude with a discussion of the future of range scanning.
Mixed Sequence Reader: A Program for Analyzing DNA Sequences with Heterozygous Base Calling (2012)

The direct sequencing of PCR products generates heterozygous base-calling fluorescence chromatograms that are useful for identifying single-nucleotide polymorphisms (SNPs), insertion-deletions (indels), short tandem repeats (STRs), and paralogous genes. Indels and STRs can be easily detected using the currently available Indelligent or ShiftDetector programs, which do not search reference sequences. However, the detection of other genomic variants remains a challenge due to the lack of appropriate tools for heterozygous base-calling fluorescence chromatogram data analysis. In this study, we developed a free web-based program, Mixed Sequence Reader (MSR), which can directly analyze heterozygous base-calling fluorescence chromatogram data in .abi file format using comparisons with reference sequences. The heterozygous sequences are identified as two distinct sequences and aligned with reference sequences. Our results showed that MSR may be used to (i) physically locate indel and STR sequences and determine STR copy number by searching NCBI reference sequences; (ii) predict combinations of microsatellite patterns using the Federal Bureau of Investigation Combined DNA Index System (CODIS); (iii) determine human papilloma virus (HPV) genotypes by searching current viral databases in cases of double infections; (iv) estimate the copy number of paralogous genes, such as β-defensin 4 (DEFB4) and its paralog HSPDP3.
Revised NMR assignments for rapamycin. (1991)

Assignments7 major carbon c=o