gebhart/patrepeval huggingface dataset:
A new method for implementation of regularization in cortical potential imaging (2002)

It is of great importance to image cortical electrical activities from noninvasive scalp EEG measurements. The regularization method has been widely used to obtain the inverse solution in order to overcome the ill-posed nature of the inverse problem. In this paper, a new method is presented for implementation of regularization to reconstruct the cortical potential distribution from scalp potential measurements. The simulation study indicates that the newly developed method is an excellent alternative for cortical imaging study.
The Safety and Effect of Topically Applied Recombinant Basic Fibroblast Growth Factor on the Healing of Chronic Pressure Sores (1992)

The first randomized, blinded, placebo-controlled human trials of recombinant basic fibroblast growth factor (bFGF) for pressure sore treatment were performed. Three different concentrations of bFGF in five dosing schedules were tested for safety using hematology, serum chemistries, urinalysis, absorption, antibody formation, and signs of toxicity. Efficacy was evaluated by wound volumes, histology, and photography. No toxicity, significant serum absorption, or antibody formation occurred. In six of eight subgroups, there was a trend toward efficacy with bFGF treatment. When all subgroups were combined, comparison of the slopes of the regression curves of volume decrease over initial pressure sore volume demonstrated a greater healing effect for the bFGF-treated patients (p < 0.05). Histologically, bFGF-treated wound sections demonstrated increased fibroblasts and capillaries. More patients treated with bFGF achieved > 70% wound closure (p < 0.05). Blinded observers were able to distinguish differences in visual wound improvement between bFGF and placebo groups. These data suggest that bFGF may be effective in the treatment of chronic wounds.
Drill Cutting Transport in Full Scale Vertical Annuli (1974)

This paper was prepared for the 48th Annual Fall Meeting of theSociety of Petroleum Engineers of AIME, to be held in Las Vegas, Nev., Sept. 30-Oct. 3, 1973. Permission to copy is restricted toan abstract of not more than 300 words. Illustrations may not be copied.The abstract should contain conspicuous acknowledgement of where and bywhom the paper is presented. Publication elsewhere after publication inthe JOURNAL OF PETROLEUM TECHNOLOGY or the SOCIETY OF PETROLEUM ENGINEERSJOURNAL is usually granted upon request to the Editor of the appropriatejournal provided agreement to give proper credit is made. Discussion of this paper is invited. Three copies of any discussionshould be sent to the Society of Petroleum Engineers Office. Suchdiscussion may be presented at the above meeting and, with the paper, maybe considered for publication in one of the two SPE magazines. Abstract The absence of the basic data needed tofully evaluate present field practices andcurrent concepts on drill cutting transportprompted this full scale study. Several drill prompted this full scale study. Several drill pipe and casing sizes were used in a 140-ft pipe and casing sizes were used in a 140-ft vertical flow system to define the variablesaffecting drill cutting transport under steadystate conditions. Variables evaluated were annular velocity(4 to 200 ft/min), fluid rheologicalproperties (mud, water, oils), cutting size (3-6 properties (mud, water, oils), cutting size (3-6 mesh), fluid weight (12-15 ppg), rotary speed(0-200 rpm), drilling rate (cutting feedconcentration), drill pipe position(centered-eccentric), and annular size. Annularvelocity and fluid rheological properties werethe most significant variables. Annularvelocities well below the 120 ft/min used in mosthydraulic programs were found adequate toclean the hole. Increasing apparent viscositydramatically improved cutting transport. Theother variables showed 2nd and 3rd ordereffects. Terminal slip velocities were a goodindicator for the velocities required toinitiate transport, but observed transport was75 to 90% of the theoretical values.These findings should destroy many mythson drill cutting transport and provide afactual basis for improving drillinghydraulics. Introduction The drilling literature does not answeror else gives conflicting answers to many ofthe questions asked about drilling hydraulics.Some of these unresolved questions are: Should mud viscosity be raised or loweredto clean the hole? What velocity is requiredto prevent excessive cutting buildup in theannulus? Can the annular velocity be lowerin slow drilling areas? As mud weightincreases, can annular velocity be decreased?How does drill pipe rotation, position(centered or eccentric) and annular clearancesaffect cutting transport and pressure drops?Is an annular velocity of 100-120 ft/minneeded to keep the hole clean? If not, whatvelocity is required? What are the "ideal"mud properties? Are our current hydraulicprograms a technical and economic "overkill"? programs a technical and economic "overkill"?
Development of a Functional Backbone Cyclic Mimetic of the HIV-1 Tat Arginine-rich Motif (2000)

We have used the backbone cyclic proteinomimetics approach to develop peptides that functionally mimic the arginine-rich motif (ARM) of the HIV-1 Tat protein. This consensus sequence serves both as a nuclear localization signal (NLS) and as an RNA binding domain. Based on the NMR structure of Tat, we have designed and synthesized a backbone cyclic ARM mimetic peptide library. The peptides were screened for their ability to mediate nuclear import of the corresponding BSA conjugates in permeabilized cells. One peptide, designated "Tat11," displayed active NLS properties. Nuclear import of Tat11-BSA was found to proceed by the same distinct pathway used by the Tat-NLS and not by the common importin alpha pathway, which is used by the SV40-NLS. Most of the Tat-derived backbone cyclic peptides display selective inhibitory activity as demonstrated by the inhibition of the nuclear import mediated by the Tat-NLS and not by the SV40-NLS. The Tat-ARM-derived peptides, including Tat-11, also inhibited binding of the HIV-1 Rev-ARM to its corresponding RNA element (Rev response element) with inhibition constants of 5 nm. Here we have shown for the first time (a) a functional mimetic of a protein sequence, which activates a nuclear import receptor and (b) a mimetic of a protein sequence with a dual functionality. Tat11 is a lead compound which can potentially inhibit the HIV-1 life cycle by a dual mechanism: inhibition of nuclear import and of RNA binding.
Diffusion‐tensor MRI: theory, experimental design and data analysis – a technical review (2002)

This article treats the theoretical underpinnings of diffusion-tensor magnetic resonance imaging (DT-MRI), as well as experimental design and data analysis issues. We review the mathematical model underlying DT-MRI, discuss the quantitative parameters that are derived from the measured effective diffusion tensor, and describe artifacts that arise in typical DT-MRI acquisitions. We also discuss difficulties in identifying appropriate models to describe water diffusion in heterogeneous tissues, as well as in interpreting experimental data obtained in such issues. Finally, we describe new statistical methods that have been developed to analyse DT-MRI data, and their potential uses in clinical and multi-site studies.
The DEXH Protein Product of the DHX36 Gene Is the Major Source of Tetramolecular Quadruplex G4-DNA Resolving Activity in HeLa Cell Lysates (2005)

G4-DNA is a highly stable alternative DNA structure that can form spontaneously in guanine-rich regions of single-stranded DNA under physiological conditions. Since a number of biological processes create such single-stranded regions, G4-DNA occurrence must be regulated. To date, resolution of tetramolecular G4-DNA into single strands (G4-resolvase activity) has been observed only in recombinant RecQ DNA helicases. We previously reported that human cell lysates possess tetramolecular G4-DNA resolving activity (Harrington, C., Lan, Y., and Akman, S. (1997) J. Biol Chem. 272, 24631-24636). Here we report the first complete purification of a major non-RecQ, NTP-dependent G4-DNA resolving enzyme from human cell lysates. This enzyme is identified as the DEXH helicase product of gene DHX36 (also known as RHAU). G4-DNA resolving activity was captured from HeLa cell lysates on G4-DNA affinity beads and further purified by gel filtration chromatography. The DHX36 gene product was identified by mass spectrometric sequencing of a tryptic digest from the protein band on SDS-PAGE associated with activity. DHX36 was cloned within a His(6)-tagging vector, expressed, and purified from Escherichia coli. Inhibition and substrate resolution assays showed that recombinant DHX36 protein displayed robust, highly specific G4-DNA resolving activity. Immunodepletion of HeLa lysates by a monoclonal antibody to the DHX36 product removed ca. 77% of the enzyme from lysates and reduced G4-DNA resolving activity to 46.0 +/- 0.4% of control, demonstrating that DHX36 protein is responsible for the majority of tetramolecular G4-DNA resolvase activity.
De novo production of resveratrol from glucose or ethanol by engineered Saccharomyces cerevisiae (2015)

Resveratrol is a natural antioxidant compound, used as food supplement and cosmetic ingredient. Microbial production of resveratrol has until now been achieved by supplementation of expensive substrates, p-coumaric acid or aromatic amino acids. Here we engineered the yeast Saccharomyces cerevisiae to produce resveratrol directly from glucose or ethanol via tyrosine intermediate. First we introduced the biosynthetic pathway, consisting of tyrosine ammonia-lyase from Herpetosiphon aurantiacus, 4-coumaryl-CoA ligase from Arabidopsis thaliana and resveratrol synthase from Vitis vinifera, and obtained 2.73 ± 0.05 mg L(-1) resveratrol from glucose. Then we over-expressed feedback-insensitive alleles of ARO4 encoding 3-deoxy-D-arabino-heptulosonate-7-phosphate and ARO7 encoding chorismate mutase, resulting in production of 4.85 ± 0.31 mg L(-1) resveratrol from glucose as the sole carbon source. Next we improved the supply of the precursor malonyl-CoA by over-expressing a post-translational de-regulated version of the acetyl-CoA carboxylase encoding gene ACC1; this strategy further increased resveratrol production to 6.39 ± 0.03 mg L(-1). Subsequently, we improved the strain by performing multiple-integration of pathway genes resulting in resveratrol production of 235.57 ± 7.00 mg L(-1). Finally, fed-batch fermentation of the final strain with glucose or ethanol as carbon source resulted in a resveratrol titer of 415.65 and 531.41 mg L(-1), respectively.
Changes in Soluble Carbohydrates during Seed Storage (1992)

The soluble sugars present in the maize (Zea mays L.) embryo may serve as important components of protection or may contribute to the deteriorative changes occurring during seed storage. Examination of the changes in sugars during accelerated aging of maize seeds indicates that the decline in vigor is associated with a marked decline in monosaccharides and in raffinose. Sucrose content remains relatively stable. The depletion of raffinose may have special relevance to the decline in seed vigor.
Retrovirus Packaging Cells (1990)

Retroviral vectors promote the efficient transfer of genes into a variety of cell types from many animal species. An important contribution to their utility was the development of retrovirus packaging cells, which allow the production of retroviral vectors in the absence of replication-competent virus. Because of their ability to transfer genes efficiently into cells that are difficult to transfect by other methods, retroviral vectors are prime candidates for gene transfer into human somatic cells. Indeed, a retroviral vector recently has been used to mark tumor infiltrating lymphocytes in patients with melanoma to follow the persistence and distribution of these cells following infusion into patients. Hopefully these vectors will soon be used for the treatment of disease by transfer of functional genes, or gene therapy. Here I will review the available packaging cell lines and their properties with a focus on their ultimate application to human gene therapy.
Developmental and tissue-specific regulation of mouse telomerase and telomere length. (1995)

Telomere shortening and telomerase activation in human somatic cells have been implicated in cell immortalization and cellular senescence. To further study the role of telomerase in immortalization, we assayed telomere length and telomerase activity in primary mouse fibroblasts, in spontaneously immortalized cell clones, and in mouse tissues. In the primary cell cultures, telomere length decreased with increased cell doublings and telomerase activity was not detected. In contrast, in spontaneously immortalized clones, telomeres were maintained at a stable length and telomerase activity was present. To determine if telomere shortening occurs in vivo, we assayed for telomerase and telomere length in tissues from mice of different ages. Telomere length was similar among different tissues within a newborn mouse, whereas telomere length differed between tissues in an adult mouse. These findings suggest that there is tissue-specific regulation of mouse telomerase during development and aging in vivo. In contrast to human tissues, most mouse tissues had active telomerase. The presence of telomerase in these tissues may reflect the ease of immortalization of primary mouse cells relative to human cells in culture.
Transcript levels of aquaporin 1 and carbonic anhydrase IV as predictive indicators for prognosis of renal cell carcinoma patients after nephrectomy (1998)

Since failure of differentiation has been suggested to be involved in the neoplastic process and progression of tumors, we evaluated whether the transcript levels of differentiation markers of proximal renal tubular cells, from which renal cell carcinoma (RCC) arises, could be used as prognostic markers. We used Northern blot analysis to study the expression of aquaporin 1 (aqp1) and carbonic anhydrase IV (ca4) genes in 66 paired samples of primary RCC and non-tumorous kidney tissues. Poor differentiation of tumor cells and non-clear cell-subtype RCC were significantly associated with low levels of aqp1 transcripts. When patients were divided into 2 groups according to level of aqpI transcript in RCC, a low level of aqp1 was significantly associated with unfavorable outcome. Among 18 patients with metastatic RCC and 40 patients with moderately differentiated RCC, those with RCC expressing low levels of aqpl mRNA demonstrated poorer survival than those with RCC expressing relatively high levels of aqp1. Similarly, decreased expression of ca4 mRNA in RCC was associated with poor survival. On multivariate analysis, transcript levels of aqpI and stage of the tumor were the independent factors predicting disease-specific survival. Transcript levels of aqp1 may serve as a new molecular prognostic marker in patients with RCC following nephrectomy.
Heat-stable Enterotoxin (STh) of Human Enterotoxigenic Escherichia coli (Strain SK-1). Structure-activity Relationship (1984)

Abstract For examination of the structure-activity relationship of STh, five shorter analogs of STh lacking one to five N-terminal amino acid residues of STh were synthesized. The synthetic peptides were confirmed to have the same intramolecular disulfide linkages as those in native STh. These peptides caused fluid accumulation in the intestine of suckling mice at almost the same molar levels as that of native STh. The toxicities of these peptides were also neutralized by antisera raised against native STh. These results indicated that the toxic and antigenic sites of STh are both located in the amino acid sequence between the Cys residue at the 5th position from the N-terminus and the C-terminal Tyr residue.
Irritable Bowel Syndrome (2005)

Purpose: Although IBS greatly affects quality-of-life, the patients' perspective is not well understood. This study evaluated the attitudes, fears, and concerns of IBS patients (Pts). Methods: 736 Pts diagnosed with IBS using the Rome II criteria at an academic medical center over a 3 year period were eligible for inclusion. Each Pt was mailed a questionnaire. The first part requested demographic information (age, sex, race, marital status, education, income). The second part evaluated patients' beliefs, attitudes, and concerns regarding IBS. Results: Of 682 deliverable questionnaires, 261 Pts responded (38.3%); 84% were women. The mean age was 53.7 years; the mean duration of symptoms was 14.2 years. With regards to the etiology of IBS, half (49.2%) believed that IBS symptoms develop due to a food allergy or intolerance while an even larger percentage (82%) reported that a change in their daily routine caused IBS. Significant misconceptions were identified regarding the natural history of IBS as one-third (31.8%) of respondents believed that once IBS develops it will never resolve, while 16.7% believed that IBS will turn into cancer. Nearly all respondents (87%) stated that IBS affects their life, with daily activities (40.1%), work life (19.3%), and social life (11.2%) being most frequently affected. In regards to health care, 57.1% believed that their primary care physician adequately addressed their concerns, and 72.4% believed that their complaints were taken seriously. The majority (70.9%) stated that a gastroenterologist was best qualified to treat their IBS. Conclusions: Our survey demonstrates that IBS Pts have significant misconceptions regarding the etiology and natural history of their disorder. Pts report that IBS markedly impacts their daily life and interferes with relationships both at home and work. A substantial proportion of patients (27.6%) noted that their complaints were not taken seriously, and nearly half stated that their concerns were not addressed. These results indicate that patient reassurance and education need to be more effectively integrated into our current treatment plans.
CONTROLLED TRIALS OF HYPERBARIC OXYGEN AND TRACHEAL INTUBATION IN ASPHYXIA NEONATORUM (1967)

University Department of Child Health, the Queen Mother's Hospital, and the Royal Maternity Hospital, Glasgow, Scotland
Lasers in dermatology (1993)

Lasers have many applications in dermatology. Recent developments in laser technology have produced significant therapeutic advances in several areas. The introduction of pulsed tunable dye lasers has considerably improved the treatment of vascular lesions, particularly port wine stain malformations in children. A wider range of continuous-wave and quasi-continuous-wave lasers have also become available for treating vascular lesions, and their use in conjunction with automated delivery systems has improved results whilst reducing adverse effects. Increasing interest in treatment of pigmented lesions and tattoos has led to investigation of a range of high-power short-pulse lasers, and early results look very promising. However, further work is needed in all these areas to determine which lesions respond best to each laser system, and which treatment techniques are optimal.
Microglia and cytokines in neurological disease, with special reference to AIDS and Alzheimer's disease (1993)

Microglia are associated with central nervous system (CNS) pathology of both Alzheimer's disease (AD) and the acquired immunodeficiency syndrome (AIDS). In AD, microglia, especially those associated with amyloid deposits, have a phenotype that is consistent with a state of activation, including immunoreactivity with antibodies to class II major histocompatibility antigens and to inflammatory cytokines (interleukin-1-beta and tumor necrosis factor-alpha). Evidence from other studies in rodents indicate that microglia can be activated by neuronal degeneration. These results suggest that microglial activation in AD may be secondary to neurodegeneration and that, once activated, microglia may participate in a local inflammatory cascade that promotes tissue damage and contributes to amyloid formation. In AIDS, microglia are the primary target of retroviral infection. Both ramified and ameboid microglia, in addition to multinucleated giant cells, are infected by the human immunodeficiency virus (HIV-1). The mechanism of microglial infection is not known since microglia lack CD4, the HIV-1 receptor. Microglia display high affinity receptors for immunoglobulins, which makes antibody-mediated viral uptake a possible mechanism of infection. In AIDS, the extent of active viral infection and cytokine production may be critically dependent upon other factors, such as the presence of coinfecting agents. In the latter circumstance, very severe CNS pathology may emerge, including necrotizing lesions. In other circumstances, HIV infection of microglia probably leads to CNS pathology by indirect mechanisms, including release of viral proteins (gp120) and toxic cytokines. Such a mechanism is the best hypothesis for the pathogenesis of vacuolar myelopathy in adults and the diffuse gliosis that characterizes pediatric AIDS, in which very little viral antigen can be detected.
Yeast-specific DNA probes and their application for the detection of Candida albicans (1992)

Two DNA fragments cloned from the genome of Candida albicans ATCC 10261 may be useful in the rapid diagnosis of disseminated candidosis. One sequence (probe EOB1) was specific for C. albicans (positive hybridisation with 45 strains tested). The second sequence (probe EOB2) detected C. albicans, as well as five other pathogenic Candida spp. and Saccharomyces cerevisiae, but did not react with human or bacterial DNA. Both probes were repetitive sequences in the genome of C. albicans. Probe EOB1 was used to detect, without DNA amplification, 500 C. albicans yeast cells in 1 ml of human blood.
Free and Hemophore-Bound Heme Acquisitions through the Outer Membrane Receptor HasR Have Different Requirements for the TonB-ExbB-ExbD Complex (2004)

Many gram-negative bacteria have specific outer membrane receptors for free heme, hemoproteins, and hemophores. Heme is a major iron source and is taken up intact, whereas hemoproteins and hemophores are not transported: the iron-containing molecule has to be stripped off at the cell surface, with only the heme moiety being taken up. The Serratia marcescens hemophore-specific outer membrane receptor HasR can transport either heme itself or heme bound to the hemophore HasA. This second mechanism is much more efficient and requires a higher TonB-ExbB-ExbD (TonB complex) concentration than does free or hemoglobin-bound heme uptake. This requirement for more of the TonB complex is associated with a higher energy requirement. Indeed, the sensitivity of heme-hemophore uptake to the protonophore carbonyl cyanide m-chlorophenyl hydrazone is higher than that of heme uptake from hemoglobin. We show that a higher TonB complex concentration is required for hemophore dissociation from the receptor. This dissociation is concomitant with heme uptake. We propose that increasing the TonB complex concentration drives more energy to the outer membrane receptor and speeds up the release of empty hemophores, which, if they remained on receptors, would inhibit heme transport.
Cutting Edge: STAT6 Serves as a Positive and Negative Regulator of Gene Expression in IL-4-Stimulated B Lymphocytes (2002)

STAT6 plays an important role in IL-4-mediated B cell activation and differentiation. To identify primary and secondary target genes of STAT6, gene expression profiles of IL-4-stimulated B cells from STAT6+/+ vs STAT6-/- mice were compared. Statistical analysis revealed that 106 distinct probe sets including 70 known genes were differentially expressed between the 2 genotypes. These genes include transcription factors, kinases, and other enzymes, cell surface receptors, and Ig H chains. Surprisingly, although 31 genes were expressed at higher levels in STAT6+/+ B cells, 39 genes were expressed at higher abundance in STAT6-/- B cells. This result implies both positive and negative regulatory functions of STAT6 in IL-4-mediated gene expression. Furthermore, IL-4 induces expression of the transcription factor Krox20, which is required for maximal IL-4-induced transcription.