gebhart/patrepeval huggingface dataset:
Transforming growth factor-beta-induced growth inhibition in a Smad4 mutant colon adenoma cell line. (2001)

Transforming growth factor-beta (TGF-beta) inhibits growth and induces apoptosis of colon epithelial cells. Binding of TGF-beta to its receptor induces phosphorylation of the Smad proteins Smad2 and Smad3, which then form heteromeric complexes with Smad4, translocate to the nucleus, and activate gene transcription. Smad4 function has been considered an obligate requirement for TGF-beta signaling, and Smad4 mutations present in some cancers have been considered sufficient to inactivate TGF-beta signaling. In this work, we describe studies with a nontransformed human colon epithelial cell line that is mutant for Smad4 but remains growth-inhibited by TGF-beta. The colon cell line VACO-235 has lost one of its Smad4 alleles via a chromosome 18q deletion. The remaining allele bears two missense point mutations located in regions important for Smad4 trimer formation, which is thought necessary for Smad4 function. As expected, pSBE4-BV/Luc, a Smad4-activated transcriptional reporter, was inactive in VACO-235. Nonetheless, VACO-235 demonstrated 80% growth inhibition in response to TGF-beta, as well as retention of some TGF-beta-mediated activation of the p3TP-Lux transcriptional reporter. Transient transfection of the VACO-235 Smad4 mutant allele into a Smad4-null cell line confirmed that this allele is functionally inactive as assayed by both the pSBE4-BV and p3TP-Lux reporters. The simplest explanation of these results is that there is a non-Smad4-dependent pathway for TGF-beta-mediated signaling and growth inhibition in VACO-235 cells.
[Gastrointestinal surgery and gastroenterology. XIII. Classification and diagnosis of perianal fistulas]. (2001)

Intersphincteric abscesses due to inflammation of an anal gland are the origin of most perianal fistulas. Perianal fistulas are classified into four types. Intersphincteric and transsphincteric fistulas are the most common. The appropriate surgical treatment of perianal fistulas is dependent upon their correct classification. Despite new imaging-techniques, physical examination of the perianal region remains of paramount importance for the preoperative classification of perianal fistulas. At present, endoanal ultrasound with the injection of hydrogen peroxide into the fistulous tract, is advocated as the most suitable method for the preoperative imaging of perianal fistulas.
Membrane Filtration in Animal Cell Culture (2007)

Membrane filtration is frequently used in animal cell culture for bioreactor harvesting, protein concentration, buffer exchange, virus filtration, and sterile filtration. A variety of membrane materials and pore sizes ranging from loose microfiltration membranes to tight ultrafiltration membranes, which reject small proteins, are frequently found in a purification train. While all of these operations make use of the same size-based separation principle, the actual methods of operation vary significantly. Microfiltration is often the first of the unit operations in the purification train. Microfiltration membranes have pores in the micrometer size range. Microfiltration is used to remove cells and cell debris. This chapter begins by describing tangential flow microfiltration. A typical method of operation is included. Concentration of the product and buffer exchange is often required toward the end of the purification train. Ultrafiltration membranes are used for both operations. The theory of tangential flow ultrafiltration is briefly described followed by a typical method of operation. Today, large-pore ultrafiltration membranes (molecular weight cutoff 100–500 kDa) are finding increasing applications for virus filtration. Validation of virus cleaner is a major concern in the biopharmaceutical industry. At the same time, purification of virus particles for viral vaccines and applications in gene therapy is a major separations challenge. Consequently, the second part of this chapter focuses on these membrane filtration applications.
Interpretational applications of spectral decomposition in reservoir characterization (1999)

Spectral decomposition provides a novel means of utilizing seismic data and the discrete Fourier transform (DFT) for imaging and mapping temporal bed thickness and geologic discontinuities over large 3-D seismic surveys. By transforming the seismic data into the frequency domain via the DFT, the amplitude spectra delineate temporal bed thickness variability while the phase spectra indicate lateral geologic discontinuities. This technology has delineated stratigraphic settings (such as channel sands and structural settings involving complex fault systems) in 3-D surveys.
Noggin is required for induction of the hair follicle growth phase in postnatal skin (2001)

During postnatal development, the hair follicle (HF) shows cyclic activity with periods of relative resting, active growth (anagen), and regression. We demonstrate that similar to the HF induction in embryonic skin, initiation of a new hair growth phase in postnatal skin requires neutralization of the inhibitory activity of bone morphogenetic protein 4 (BMP4) by the BMP antagonist noggin. In the resting HF, BMP4 mRNA predominates over noggin in the epithelium and mesenchyme, and the BMP receptor IA is prominently expressed in the follicular germ. Anagen development is accompanied by down-regulation of the BMP4 and increased noggin mRNA in the HF. Furthermore, administration of noggin protein induces new hair growth phase in postnatal telogen skin in vivo. In contrast, BMP4 induces selective arrest of anagen development in the non-tylotrich (secondary) HF. As a hair growth inducer, noggin increases Shh mRNA in the HF whereas BMP4 down-regulates Shh. This suggests that modulation of BMP4 signaling by noggin is essential for hair growth phase induction in postnatal skin and that the hair growth-inducing effect of noggin is mediated, at least in part, by Shh.
An Upside Down View of Cholesterol’s Condensing Effect: Does Surface Occupancy Play a Role? (2010)

The condensing action of cholesterol has been compared with that of a structural isomer having its hydroxyl group located at the C-25 position (i.e., 25-OH'), that is, an isomer favoring an "upside down" orientation in lipid membranes. Surface pressure-area isotherms of mixed monolayers made from 1,2-dimyristoyl-sn-glycero-3-phosphocholine (DMPC)/cholesterol and DMPC/25-OH' have established that 25-OH' has a weaker condensing effect than cholesterol. Nearest-neighbor recognition measurements in liposomes made from 1,2-dipalmitoyl-sn-glycero-3-phosphocholine (DPPC) have also shown that 25-OH' has a weaker condensing effect in the physiologically relevant fluid bilayer state. These findings provide support for surface occupancy playing a role in the condensing action of cholesterol.
A novel thick-layer electrochemical cell for in situ x-ray diffraction (1998)

In this article we describe an electrochemical cell allowing x-ray diffraction from the working electrode in situ. The key feature of our novel design is a hemispherical fused silica dome serving as the x-ray window. The electrode is covered with a thick layer of electrolyte during the x-ray measurement, avoiding mass transport limitations inherent to common setups, where the thickness of the electrolyte layer is strongly reduced for the diffraction experiment. This allows in particular the monitoring of electrode processes which are associated with the consumption of species from solution and/or generation of a significant amount of reaction products. All solid angles in the hemisphere above the sample surface are accessible for the incoming and outgoing x-ray beam at a constant path length in the electrolyte. Thus, our cell is perfectly suitable for in situ surface x-ray diffraction, truncation rod scattering, and specular reflectivity measurements. We demonstrate the performance of the new cell by monitoring the electrochemical stripping of a 50 nm thick amorphous As layer on GaAs(001) in 0.5 M H2SO4 in situ with x rays.
Changes in the cell surface properties of Treponema pallidum that occur during in vitro incubation of freshly extracted organisms (1987)

We previously reported that a number of Treponema pallidum membrane proteins appear to reside on the cell surface, since intact treponemes radiolabeled by overnight incubation in medium containing [35S]methionine bind immunoglobulin G (IgG) antibodies directed against these proteins. In the present study, it was found that freshly extracted organisms radiolabeled in vitro for only 2 h inefficiently bound IgG antibodies directed against just two proteins of molecular weights 40,000 and 34,000. An in vitro incubation period of greater than 8 h was required before IgG antibodies present in rabbit syphilitic serum could recognize additional protein antigens on the cell surface. Treatment of aged treponemes, but not freshly extracted organisms, with 0.04% sodium dodecyl sulfate selectively removed a membranous layer from the treponemal surface. Only three treponemal proteins were found associated with this structure, including the same 40,000- and 34,000-molecular-weight proteins mentioned above. These two proteins most likely represent endoflagellar subunits, since they were precipitated with rabbit antisera prepared against purified endoflagellar subunits of the cultivable treponemal strain Treponema phagedenis. Further evidence also was obtained that cells of T. pallidum actively secrete into their extracellular environment a unique class of low-molecular-weight proteins.
Protective Regulatory T Cell Generation in Autoimmune Diabetes by DNA Covaccination with Islet Antigens and a Selective CTLA-4 Ligand (2006)

DNA vaccination of autoimmune diabetes-prone NOD mice with unmodified target islet antigens, i.e., preproinsulin (PPIns) or glutamic acid decarboxylase 65 (GAD65), is poorly protective. However, in this study, we demonstrate protection against disease by covaccination with a mutant B7-1 molecule (B7-1wa) that binds the negative T cell regulator CTLA-4 (CD152), but not CD28. Codelivery of plasmids encoding a PPIns-GAD65 fusion construct and B7-1wa protected against both insulitis and diabetes. In vitro, the T cells of covaccinated mice had negative responses to both insulin and GAD65, and this was restored by adding blocking antibodies to transforming growth factor beta1 (TGF-beta1), suggesting a role for this cytokine. Adoptive transfer experiments revealed that DNA vaccination generated protective CD4(+) regulatory T cells (Tr) of either CD25(+) or CD25(-) phenotype. Furthermore, vaccinated mice had increased numbers of T cells with Tr-associated markers, such as CTLA-4, Foxp3, and membrane-bound TGF-beta1. Tr cells inhibited the responses of diabetogenic T cells to islet antigens, and depletion of T cells expressing membrane-bound TGF-beta1 abolished the suppressive effect. Thus, selective engagement of CTLA-4 during islet-antigen DNA vaccination induces Tr cells that protect against this autoimmune disease.
Characterization of a UDP-GalNAc:Polypeptide N-Acetylgalactosaminyltransferase That Displays Glycopeptide N-Acetylgalactosaminyltransferase Activity (1999)

We report the cloning, expression, and characterization of a novel member of the mammalian UDP-GalNAc:polypeptide N-acetylgalactosaminyltransferase (ppGaNTase) family that transfers GalNAc to a GalNAc-containing glycopeptide. Northern blot analysis revealed that the gene encoding this enzyme, termed ppGaNTase-T6, is expressed in a highly tissue-specific manner. Significant levels of transcript were found in rat and mouse sublingual gland, stomach, small intestine, and colon; trace amounts were seen in the ovary, cervix, and uterus. Recombinant constructs were expressed transiently in COS7 cells but demonstrated no transferase activity in vitro against a panel of unmodified peptides, including GTTPSPVPTTSTTSAP (MUC5AC). However, when incubated with the total glycosylated products obtained by action of ppGaNTase-T1 on MUC5AC (mainly GTT(GalNAc)PSPVPTTSTT(GalNAc)SAP), additional incorporation of GalNAc was achieved, resulting in new hydroxyamino acids being modified. The MUC5AC glycopeptide failed to serve as a substrate for ppGaNTase-T6 after modification of the GalNAc residues by periodate oxidation and sodium borohydride reduction, indicating a requirement for the presence of intact GalNAc. This suggests that O-glycosylation of multisite substrates may proceed in a specific hierarchical manner and underscores the potential complexity of the processes that regulate O-glycosylation.
Gain-of-function mutations in interleukin-7 receptor-α ( IL7R ) in childhood acute lymphoblastic leukemias (2011)

Interleukin-7 receptor α (IL7R) is required for normal lymphoid development. Loss-of-function mutations in this gene cause autosomal recessive severe combined immune deficiency. Here, we describe somatic gain-of-function mutations in IL7R in pediatric B and T acute lymphoblastic leukemias. The mutations cause either a serine-to-cysteine substitution at amino acid 185 in the extracellular domain (4 patients) or in-frame insertions and deletions in the transmembrane domain (35 patients). In B cell precursor leukemias, the mutations were associated with the aberrant expression of cytokine receptor-like factor 2 (CRLF2), and the mutant IL-7R proteins formed a functional receptor with CRLF2 for thymic stromal lymphopoietin (TSLP). Biochemical and functional assays reveal that these IL7R mutations are activating mutations conferring cytokine-independent growth of progenitor lymphoid cells. A cysteine, included in all but three of the mutated IL-7R alleles, is essential for the constitutive activation of the receptor. This is the first demonstration of gain-of-function mutations of IL7R. Our current and recent observations of mutations in IL7R and CRLF2, respectively suggest that the addition of cysteine to the juxtamembranous domains is a general mechanism for mutational activation of type I cytokine receptors in leukemia.
Prevalence, Age Distribution, and Gender of Patients With Atrial Fibrillation (1995)

The prevalence of atrial fibrillation (AF) is related to age. Anticoagulation is highly effective in preventing stroke in patients with AF, but the risk of hemorrhage may be increased in older patients. We reviewed the available epidemiologic data to define the age and sex distribution of people with AF. From four large recent population-based surveys, we estimated the overall age- and gender-specific prevalence of AF. These estimates were applied to the recent US census data to calculate the number of men and women with AF in each age group. There are an estimated 2.2 million people in the United States with AF, with a median age of about 75 years. The prevalence of AF is 2.3% in people older than 40 years and 5.9% in those older than 65 years. Approximately 70% of individuals with AF are between 65 and 85 years of age. The absolute number of men and women with AF is about equal. After age 75 years, about 60% of the people with AF are women. In contrast to people with AF in the general population, patients with AF in recent anticoagulation trials had a mean age of 69 years, and only 20% were older than 75 years. The risks and benefits of antithrombotic therapy in older individuals are important considerations in stroke prevention in AF.
Activation of casein kinase II in response to insulin and to epidermal growth factor. (1987)

Insulin treatment enhances casein kinase II (CKII) activity in 3T3-L1 mouse adipocytes and H4-IIE rat hepatoma cells, the magnitude of the activation varying from 30% to 150%. Activation of CKII was apparent after 5 min of exposure of 3T3-L1 cells to insulin, was maximal by 10 min, and persisted through 90 min. The insulin-stimulated activity was inhibited by low concentrations of heparin and was stimulated by spermine. Activation of CKII was effected by physiological concentrations of insulin (EC50 = 0.15 nM), suggesting that the effect is a true insulin response and not one mediated through insulin-like growth factor receptors. Epidermal growth factor (100 ng/ml for 10 min) also activated CKII in A431 human carcinoma cells, which is consistent with other observations that insulin and epidermal growth factor may have some common effects. Insulin stimulation of CKII activity was due to an increase in the maximal velocity of the kinase; the apparent Km for peptide substrate was not altered. Enhanced activity did not appear to result from increased synthesis of CKII protein, because cycloheximide did not block the effect and because an immunoblot developed with antiserum to CKII showed no effect of insulin on the cytosolic concentration of CKII. Because insulin-stimulated CKII activity was maintained after chromatography of cell extracts on Sephadex G-25, it is unlikely that the effect is mediated by a low-molecular-weight activator of the kinase. Rather, the results are consistent with the possibility that insulin activates CKII by promoting a covalent modification of the kinase.
Insecticidal Action of the Phytohemagglutinin in Black Beans on a Bruchid Beetle (1976)

Black bean (Phaseolus vulgaris) phytohemagglutinin added to the normal diet of a bruchid beetle (Callosobruchus maculatus) that can eat phytohemagglutinin-free cowpeas (Vigna unguiculata) but not P. vulgaris seeds kills the bruchid larvae. Trypsin inhibitors, found in both P. vulgaris and V. unguiculata seeds, have virtually no effect on the bruchid larvae. The conclusion is that a major part of the adaptive significance of phytohemagglutinins in black bean and other legume seeds is to protect them from attack by insect seed predators.
Cyanobacteriochrome TePixJ of Thermosynechococcus elongatus Harbors Phycoviolobilin as a Chromophore (2007)

Cyanobacteria have several putative photoreceptors (designated cyanobacteriochromes) that are related to but distinct from the established phytochromes. The GAF domain of the phototaxis regulator, PixJ, from a thermophilic cyanobacterium Thermosynechococcus elongatus BP-1 (TePixJ_GAF) is a cyanobacteriochrome which exhibits reversible photoconversion between a blue light-absorbing form (max = 433 nm) and a green light-absorbing form (max = 531 nm). To study the chromophore, we prepared TePixJ_GAF chromoprotein from heterologously expressed Synechocystis and performed spectral analysis after denaturation by comparing it with the cyanobacterial phytochrome Cph1 which harbors phycocyanobilin (PCB) as a chromophore. The results indicated that the chromophore of TePixJ is not PCB, but its isomer, phycoviolobilin (PVB). It is suggested that the GAF domain of TePixJ has auto-lyase and auto-isomerase activities.
On secondary transforms for scalable video coding (2013)

In this paper, we present a secondary transform scheme for inter-layer prediction residue in scalable video coding (SVC). Efficient prediction of the co-located blocks from the base layer (BL) can significantly improve the enhancement layer (EL) coding in SVC, especially when the temporal information from previous EL frames is less correlated than the co-located BL information. However, Guo et al. showed that because of the peculiar frequency characteristics of EL residuals, the conventional DCT Type-2 transform is suboptimal and is often outperformed by either the DCT Type-3, or DST Type-3 when these transforms are applied to the EL residuals. However, their proposed technique requires upto 8 additional transform cores, two of which are of size 32×32. Here, in this work, we propose a secondary transform scheme, where the proposed transform is applied only to the lower 8x8 frequency coefficients after DCT, for block sizes 8×8 to 32×32. Our proposed transform scheme requires at most only 2 additional cores. We also propose a low-complexity 8x8 Rotational Transform as a special case of secondary transforms in this paper. Simulation results show that the proposed transform scheme provides significant BD-Rate improvement over the conventional DCT-based coding scheme for video sequences in the ongoing scalable extensions of HEVC standardization.
Estimation of metabolite concentrations from localized in vivo proton NMR spectra (1993)

The LCModel method analyzes an in vivo spectrum as a Linear Combination of Model spectra of metabolite solutions in vitro. By using complete model spectra, rather than just individual resonances, maximum information and uniqueness are incorporated into the analysis. A constrained regularization method accounts for differences in phase, baseline, and lineshapes between the in vitro and in vivo spectra, and estimates the metabolite concentrations and their uncertainties. LCModel is fully automatic in that the only input is the time-domain in vivo data. The lack of subjective interaction should help the exchange and comparison of results. More than 3000 human brain STEAM spectra from patients and healthy volunteers have been analyzed with LCModel. N-acetylaspartate, cholines, creatines, myo-inositol, and glutamate can be reliably determined, and abnormal levels of these or elevated levels of lactate, alanine, scyllo-inositol, glutamine, or glucose clearly indicate numerous pathologies. A computer program will be available.
Isolation and Characterization of Pleurocidin, an Antimicrobial Peptide in the Skin Secretions of Winter Flounder (1997)

Antimicrobial peptides are found in both myeloid cells and mucosal tissues of many vertebrates and invertebrates. These peptides are predicted to operate as a first-line host defense mechanism exerting broad-spectrum activity against pathogenic bacteria, fungi, parasites, and enveloped viruses. We report the characterization of a novel 25-residue linear antimicrobial peptide found in the skin mucous secretions of the winter flounder (Pleuronectes americanus). This peptide was purified through multiple chromatographic methods to obtain a single peak by reversed-phase high performance liquid chromatography. This purified peptide, which we named pleurocidin, exhibited antimicrobial activity against Escherichia coli in a bacterial cell lysis plate assay. Mass spectrometry and amino acid sequence analysis indicated that it is 25 amino acids in length. Pleurocidin is predicted to assume an amphipathic alpha-helical conformation similar to many other linear antimicrobial peptides. There is a high degree of homology between pleurocidin and two antimicrobial peptides, ceratotoxin from the Mediterranean fruit fly and dermaseptin from the skin of a hylid frog. The minimal inhibitory concentration and minimal bactericidal concentration of pleurocidin were determined against 11 different Gram-negative and Gram-positive bacteria. Immunohistochemistry locates pleurocidin in the epithelial mucous cells of flounder skin. Pleurocidin represents a novel antimicrobial peptide found in fish and may play a role in innate host defense.
Dengue virus infection of the central nervous system (CNS): a case report from Brazil. (2002)

Dengue infection that is accompanied by unusual complications has been described in Brazil. We report on the presence of dengue virus in the central nervous system (CNS) of a patient who died in 1998 in Rio Grande do Norte, northeast Brazil. DEN-2 viruses were isolated from the brain liver, and lymphnode tissue of a 67-year-old man whose signs and symptoms were those of dengue infection and a secondary immune response. A postmortem revealed nose bleeds a liver that was brownish with yellow areas, and pulmonary and cerebrae congestion. Immunoperoxidase staining showed a dengue antigen-specific positive reaction in the gray matter cells of the cerebrall cortex; a granular citoplasmatic reaction was seen in the neurons. Dengue infection should always be considered as a cause encephalitis in tropical countries, especially in those where the disease is endemic.
Light-triggered polymerase chain reaction (2007)

Photochemical control of the polymerase chain reaction has been achieved through the incorporation of light-triggered nucleotides into DNA.