gebhart/patrepeval huggingface dataset:
Synthesis of Nonspherical Colloidal Particles with Anisotropic Properties (2006)

We describe a promising and flexible technique for fabricating uniform nonspherical particles with anisotropic phase and surface properties. Our approach is based on the seeded polymerization technique in which monomer-swollen particles are polymerized. The polymerization causes a phase separation to occur, giving rise to two-phase nonspherical particles. We show that the elastic contraction of the swollen polymer particles induced by elevated polymerization temperatures plays an important role in the phase separation. Moreover, chemical anisotropy of nonspherical particles can be obtained by using immiscible polymer pairs and by employing surface treatments. Furthermore, we are able to produce amphiphilic dumbbell particles consisting of two different bulbs: hydrophilic poly (ethylene imine)-coated polystyrene and hydrophobic polystyrene. Controlled geometries of these amphiphilic nonspherical particles will allow a wide range of potential applications, such as engineered colloid surfactants.
Recipient-type specific CD4+CD25+ regulatory T cells favor immune reconstitution and control graft-versus-host disease while maintaining graft-versus-leukemia (2003)

CD4+CD25+ regulatory T cells (Treg's) play a pivotal role in preventing organ-specific autoimmune diseases and in inducing tolerance to allogeneic organ transplants. We and others recently demonstrated that high numbers of Treg's can also modulate graft-versus-host disease (GVHD) if administered in conjunction with allogeneic hematopoietic stem cell transplantation in mice. In a clinical setting, it would be impossible to obtain enough freshly purified Treg's from a single donor to have a therapeutic effect. Thus, we performed regulatory T cell expansion ex vivo by stimulation with allogeneic APCs, which has the additional effect of producing alloantigen-specific regulatory T cells. Here we show that regulatory T cells specific for recipient-type alloantigens control GVHD while favoring immune reconstitution. Irrelevant regulatory T cells only mediate a partial protection from GVHD. Preferential survival of specific regulatory T cells, but not of irrelevant regulatory T cells, was observed in grafted animals. Additionally, the use of specific regulatory T cells was compatible with some form of graft-versus-tumor activity. These data suggest that recipient-type specific Treg's could be preferentially used in the control of GVHD in future clinical trials.
Keratin gene expression in mouse epidermis and cultured epidermal cells. (1983)

The major differentiation products of mouse epidermis are keratins of 40-70 kilodaltons (kDal). We have prepared a library of cDNA clones from total poly(A)+ RNA from newborn mouse epidermis. Clones corresponding to the major in vivo keratins of 55, 59, and 67 kDal have been isolated and characterized. By RNA blot analysis of poly(A)+ RNA from newborn mouse epidermis, we have identified RNA species that are approximately 1,600, 2,000, and 2,400 nucleotides in length and are complementary to the cDNAs for the 55-, 59-, and 67-kDal keratins, respectively. Analysis of RNA from primary cultures of newborn mouse epidermis by this same technique shows greatly reduced levels of these RNAs. Transcripts complementary to all three cloned cDNAs are abundant in 14- to 16-day embryonic and adult mouse skin. Thus, altered expression in culture does not appear to be due to induction of a developmentally programmed switch by placing the cells in culture but instead is due to factors modulating expression within the culture system. Because the 55-, 59-, and 67-kDal keratins are the major proteins in epidermis they probably represent keratin associated with terminal differentiation. The expression data suggest that cultured cells are blocked in expression of differentiation keratins but instead synthesize other keratin family members probably related to cytoskeletal functions.
TREM2 is upregulated in amyloid plaque‐associated microglia in aged APP23 transgenic mice (2008)

Alzheimer's disease (AD) is characterized by extracellular deposits of amyloid-beta protein which attract dense clusters of microglial cells. Here, we analyzed amyloid plaque-associated areas in aged APP23 transgenic mice, an animal model of AD, by combining laser microdissection with microarray analysis and quantitative RT-PCR (qPCR). By comparing gene expression profiles, we found that 538 genes (1.3% of a total of 41,234 analyzed genes) were differentially expressed in plaque-associated versus plaque-free tissue of aged APP23 transgenic mice. One of these genes is the microglia-associated triggering receptor expressed on myeloid cells (TREM2) which enhances phagocytosis, but abrogates cytokine production as well as TLR and Fc receptor-mediated induction of TNF secretion. Western Blot analysis demonstrated an upregulation of TREM2 protein in APP23 transgenic compared with nontransgenic mice. Confocal imaging studies, furthermore, confirmed colocalization of TREM2 protein with microglia. Thus, when TREM2 is induced on microglia in plaque-loaded brain areas the respective signaling may prevent inflammation-induced bystander damage of neurons. At the same time, TREM2 signaling may also account for the failure to sufficiently eliminate extracellular amyloid with the help of a systemic immune response.
Genome sequence and comparative microarray analysis of serotype M18 group A Streptococcus strains associated with acute rheumatic fever outbreaks (2002)

Acute rheumatic fever (ARF), a sequelae of group A Streptococcus (GAS) infection, is the most common cause of preventable childhood heart disease worldwide. The molecular basis of ARF and the subsequent rheumatic heart disease are poorly understood. Serotype M18 GAS strains have been associated for decades with ARF outbreaks in the U.S. As a first step toward gaining new insight into ARF pathogenesis, we sequenced the genome of strain MGAS8232, a serotype M18 organism isolated from a patient with ARF. The genome is a circular chromosome of 1,895,017 bp, and it shares 1.7 Mb of closely related genetic material with strain SF370 (a sequenced serotype M1 strain). Strain MGAS8232 has 178 ORFs absent in SF370. Phages, phage-like elements, and insertion sequences are the major sources of variation between the genomes. The genomes of strain MGAS8232 and SF370 encode many of the same proven or putative virulence factors. Importantly, strain MGAS8232 has genes encoding many additional secreted proteins involved in human-GAS interactions, including streptococcal pyrogenic exotoxin A (scarlet fever toxin) and two uncharacterized pyrogenic exotoxin homologues, all phage-associated. DNA microarray analysis of 36 serotype M18 strains from diverse localities showed that most regions of variation were phages or phage-like elements. Two epidemics of ARF occurring 12 years apart in Salt Lake City, UT, were caused by serotype M18 strains that were genetically identical, or nearly so. Our analysis provides a critical foundation for accelerated research into ARF pathogenesis and a molecular framework to study the plasticity of GAS genomes.
Fosfomycin in Treatment of Respiratory Bacterial Infections (1977)

A study was made of 40 patients suffering from clinically and bacteriologically demonstrated bacterial respiratory infections which were all treated with fosfomycin as the only antibiotic. Studies were made of the sensitivity of the isolated organisms and control of the eradicated and selected organisms. Analytical controls were performed on all patients before, during and after treatment. The average dose employed was 60 mg/kg/day, divided into four doses and administered parenterally. The duration of the treatment fluctuated between 6 and 11 days in 87% of the cases. A clinical and bacteriological evaluation was made of the results. The clinical response was satisfactory in 75% of the cases, partial in 7.5% and poor in 17.5%. The bacteriological evolution was satisfactory in 62.5%, partial in 12.5% and poor in 20%. It was not possible to control the evolution in 15% of the patients. The concentrations of the antibiotic were determined in the sputum of 6 patients and fluctuated between 0.6 and 12.9 mug/ml. In no case could any significant disorders be attributed to the antibiotic.
Proppant and Fluid Selection To Optimize Performance of Horizontal Shale Fracs (2012)

Abstract The productivity and economics of horizontal wells are governed by the ability of the transverse fractures to communicate efficiently with the wellbore, which is strongly controlled by the conductivity of the proppant bed and the effectiveness of the fluid additives. These impact the relative permeability, the capillary pressure and the effective conductivity in the proppant bed. When time at temperature, stress cycling, embedment, multi-phase flow and non-Darcy effects are considered, the effective conductivity can be reduced 100-fold. Another investigated parameter is the impact of the wellbore location relative to the propagated fracture. If the wellbore is high in the fracture, gravity segregation will cause liquid removal from the lower portion of the fracture to be very difficult. In low conductivity proppant beds, capillary pressure will tend to retain high water saturations, thus lower conductivity even for the portions of the fracture above the wellbore. Laboratory experiments have addressed these issues for proppants with a range of permeabilities from 10 to 100 Darcies; 100 mesh to 20/40 mesh and ceramics. The relative permeability to gas can be as low as 0.01, with as much as a 70-fold improvement when suitable proppants and additives are employed. Evaluation of the production performance of 240 wells, 98 with effective additives and 142 without, and covering a similar range of proppant types and sizes, shows a similar benefit to the wells’ normalized 30 day recovery and gross value. These results clearly demonstrate that economic expediency can be detrimental to a well’s ultimate value and hydrocarbon recovery.
Wavelet transform as a processing tool in white-light interferometry (1997)

Results of the application of wavelet transform for signal processing in white-light interferometry are reported. The mother wavelet frequency is chosen to be the light-source correlogram 1's, and accurate phase measurements are obtained from simple correlation computations. The fringe envelope is also addressed and permits a complete analysis of coherence-limited fringe patterns. Miscalibrations of phase shift and mean wavelength are also considered.
Prediction of the Coding Sequences of Unidentified Human Genes. VII. The Complete Sequences of 100 New cDNA Clones from Brain Which Can Code for Large Proteins in vitro (1997)

In this series of projects of sequencing human cDNA clones which correspond to relatively long transcripts, we newly determined the entire sequences of 100 cDNA clones which were screened on the basis of the potentiality of coding for large proteins in vitro. The cDNA libraries used were the fractions with average insert sizes from 5.3 to 7.0 kb of the size-fractionated cDNA libraries from human brain. The randomly sampled clones were single-pass sequenced from both the ends to select clones that are not registered in the public database. Then their protein-coding potentialities were examined by an in vitro transcription/translation system, and the clones that generated proteins larger than 60 kDa were entirely sequenced. Each clone gave a distinct open reading frame (ORF), and the length of the ORF was roughly coincident with the approximate molecular mass of the in vitro product estimated from its mobility on SDS-polyacrylamide gel electrophoresis. The average size of the cDNA clones sequenced was 6.1 kb, and that of the ORFs corresponded to 1200 amino acid residues. By computer-assisted analysis of the sequences with DNA and protein-motif databases (GenBank and PROSITE databases), the functions of at least 73% of the gene products could be anticipated, and 88% of them (the products of 64 clones) were assigned to the functional categories of proteins relating to cell signaling/communication, nucleic acid managing, and cell structure/motility. The expression profiles in a variety of tissues and chromosomal locations of the sequenced clones have been determined. According to the expression spectra, approximately 11 genes appeared to be predominantly expressed in brain. Most of the remaining genes were categorized into one of the following classes: either the expression occurs in a limited number of tissues (31 genes) or the expression occurs ubiquitously in all but a few tissues (47 genes).
Characterization of glucagon‐like peptide‐I(7–36)amide receptors of rat lung membranes by covalent cross‐linking (1991)

125I-labelled GLP-I(7-36)amide was cross-liked to a specific binding protein in rat lung membranes using disuccinimidyl suberate. A single radio-labelled band at Mr 66,000 was identified by SDS-PAGE after solubilization of the ligand-binding protein complex which is consistent with the presence of a single class of binding sites on rat lung membranes. The band was undetectable when 1 mumol/l GLP-I(7-36)amide was included in the binding assay. No change in the mobility of the band was observed under reducing conditions suggesting that the binding protein in the receptor is not part of a larger disulphide-linked protein. The intensity of the radiolabelled protein band was reduced when the incubation with 125I-labelled GLP-I(7-36)amide was carried out in the presence of guanine nucleotides suggesting that the GLP-I(7-36)amide receptor is coupled to the adenylate cyclase system.
Assuring Distributed Trusted Mach (2002)

Distributed Trusted Mach (DTMach) is an operating system designed by Secure Computing Corporation. The goal of the project is to use the Mach 3.0 kernel as the base for a secure, distributed system. As a first step in developing the DTMach security policy, a categorization of general security concerns was constructed. Concerns that were not adequately addressed by the Mach 3.0 kernel indicated potential security vulnerabilities. The authors describe these general security concerns, the manner in which the Mach 3.0 kernel addresses each concern, and the manner in which DTMach addresses each concern. The focus is on the DTMach security policy and security mechanisms. It is first necessary to identify the general threats against which DTMach must protect. The next step is to identify control mechanisms that are sufficient to protect against each of the threats. The DTMach design makes extensive use of type enforcement in addressing the threats. The general threats and the countermeasures provided by DTMach are described, which provide more evidence of the usefulness of type enforcement in general and the high assurance provided by the DTMach type of enforcement policy.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Clinical experience on hydrocephalus after surgery of traumatic brain injury (2018)

Objective
To analyze and summarize the high risk factors of hydrocephalus after surgery of traumatic brain injury (TBI) and therapeutic experiences, and to provide theoretical basis for the prevention of postoperative hydrocephalus.


Methods
To enroll 126 cases of TBI patients with standard decompressive craniectomy and follow up at least with 6 months about the complication rate of hydrocephalus. The related clinical characteristics were compared and the therapeutic results were observed after ventriculo-peritoneal shunt (VPS).


Results
Age, time of coma, lower GCS and high APACHEⅡscore when admission, location of hematoma, subarachnoid hemorrhage, intraventricular hemorrhage, lumbar puncture, intra-operative dura suture and midline shift more than 10 mm were the high risk factors of hydrocephalus after standard decompressive craniectomy of TBI patients. There were significant differences in these factors between hydrocephalus group and control group. After VPS was applied to treat the hydrocephalus patients, the patients recovered well in 30 d with normal temperature and without language dysfunction.


Conclusion
The high risk factors should be evaluated before the surgery of patients with TBI to prevent the complication of hydrocephalus. If there were, VPS is a suitable choice for the treatment.


Key words: 
Traumatic brain injury; Hydrocephalus; High risk factor; Ventriculo peritoneal shunt
The isoprenoid biosynthetic pathway inSaccharomyces cerevisiaeis affected in amaf1-1mutant with altered tRNA synthesis (2002)

tRNA isopentenylation is a branch of an isoprenoid pathway in yeast. There is a competition for a substrate between isoprenoid biosynthetic enzyme Erg20p and tRNA isopentenyltransferase. Here we studied the direct effect of elevated tRNA biosynthesis on ERG20 expression. The maf1-1 mutant of Saccharomyces cerevisiae that has enhanced cellular tRNA levels was used. We show that both ERG20 transcript and Erg20 protein levels are increased in maf1-1. Additionally, maf1-1 leads to decreased ergosterol content in the cells. These effects of maf1-1 are dependent on functional tRNA isopentenyltransferase. Our results indicate that a complex regulation of the isoprenoid pathway involves also an effect of changes in tRNA biosynthesis.
Licorice and Cancer (2001)

Licorice root is one of the oldest and most frequently employed botanicals in Chinese medicine. In the United States, licorice products are most often used as flavoring and sweetening agents in food products. Constituents of licorice include triterpenoids, such as glycyrrhizin and its aglycone glycyrrhizic acid, various polyphenols, and polysaccharides. A number of pharmaceutical effects of licorice are known or suspected (anti-inflammatory, antivirus, antiulcer, anticarcinogenesis, and others). Licorice and its derivatives may protect against carcinogen-induced DNA damage and may be suppressive agents as well. Glycyrrhizic acid is an inhibitor of lipoxygenase and cyclooxygenase, inhibits protein kinase C, and downregulates the epidermal growth factor receptor. Licorice polyphenols induce apoptosis in cancer cells. These and other activities of licorice are reviewed, and a rationale is suggested for combinations of agents in preventive clinical trials.
Expression of the CXCL12/SDF-1 Chemokine Receptor CXCR7 in Human Brain Tumours (2012)

The results suggest that the CXCR7 may play a role in progression, metastasis and angiogenesis of brain tumours.
High Affinity Interactions of Nucleolin with G-G-paired rDNA (1999)

Nucleolin is a very abundant eukaryotic protein that localizes to the nucleolus, where the rDNA undergoes transcription, replication, and recombination and where rRNA processing occurs. The top (non-template) strand of the rDNA is very guanine-rich and has considerable potential to form structures stabilized by G-G pairing. We have assayed binding of endogenous and recombinant nucleolin to synthetic oligonucleotides in which G-rich regions have formed intermolecular G-G pairs to produce either two-stranded G2 or four-stranded G4 DNA. We report that nucleolin binds G-G-paired DNA with very high affinity; the dissociation constant for interaction with G4 DNA is KD = 1 nM. Two separate domains of nucleolin can interact with G-G-paired DNA, the four RNA binding domains and the C-terminal Arg-Gly-Gly repeats. Both domains bind G4 DNA with high specificity and recognize G4 DNA structure independent of sequence context. The high affinity of the nucleolin/G4 DNA interaction identifies G-G-paired structures as natural binding targets of nucleolin in the nucleolus. The ability of two independent domains of nucleolin to bind G-G-paired structures suggests that nucleolin can function as an architectural factor in rDNA transcription, replication, or recombination.
Reduced genomic 5-methylcytosine content in human colonic neoplasia. (1988)

DNA methylation appears to play an important role in both physiological and experimentally modified gene expression, and alterations in DNA methylation have been described in animal tumor models and in transformed cells and tumor cell lines. However, there have been comparatively few reports on DNA methylation in primary human malignancies, and these reports are somewhat contradictory. While individual genes have shown hypomethylation in colon cancer and premalignant adenomas as well as in lung cancer, other genes have shown increased methylation, and absolute measures of 5-methylcytosine content have shown decreases in malignancies but not in premalignant adenomas. We have used a sensitive quantitative measurement of 5-methylcytosine content by high performance liquid chromatography revealing an unequivocal hypomethylation of tumor DNA. An average of 8 and 10% reduction in genomic 5-methylcytosine content was seen in apparently all colon adenomas and adenocarcinomas, respectively, and there was no significant difference between benign and malignant tumors. This is a substantial quantitative alteration and suggests a pervasive abnormality in the control of DNA methylation. Surprisingly, three patients with the highest 5-methylcytosine content in their normal colon appear to have a germline predisposition to cancer (Lynch syndrome).
Natural Structural Variants of the Nuclear Receptor Farnesoid X Receptor Affect Transcriptional Activation (2002)

The Farnesoid X receptor (FXR) is a member of the nuclear hormone receptor superfamily that has been shown to play an important role in bile acid and cholesterol homeostasis. Here we identify four murine FXR transcripts, derived from a single gene, that encode four isoforms, FXRalpha1, FXRalpha2, FXRbeta1, and FXRbeta2. FXRalpha and FXRbeta differ at their amino terminus, and FXRalpha1 and FXRbeta1 have a four-amino acid residue insertion in the hinge region immediately adjacent to the DNA binding domain. Real time PCR and 5'-rapid amplification of cDNA ends followed by Southern blotting reveal that these four transcripts are expressed differentially in liver, intestine, kidney, adrenals, stomach, fat, and heart. Electrophoretic mobility shift assays demonstrate that FXRalpha2 and FXRbeta2 bind to FXR response elements with a higher affinity as compared with FXRalpha1 and FXRbeta1, suggesting that the four-amino acid insert may affect FXR function. Consistent with this idea, the results of transient transfection experiments demonstrate that the four FXR isoforms differentially transactivated a number of promoter-reporter genes; activation of an ileal bile acid-binding protein promoter-reporter gene varied 20-fold depending on the FXR isoform; the rank order of activation was FXRbeta2 > FXRalpha2 FXRalpha1 = FXRbeta1. In contrast, SHP reporter or BSEP reporter genes were activated to similar degrees by each of the FXR isoforms. Finally, NIH3T3 cells were stably infected with individual murine FXR isoforms, and the cells were treated with FXR ligands. The endogenous ileal bile acid-binding protein gene was activated by the four FXR isoforms with the same rank order as seen in transfections. This effect was gene-specific, since induction of bile salt export pump mRNA was independent of the FXR isoform. These observations suggest that there are four distinct murine FXR isoforms that differentially regulate gene expression in numerous tissues in vivo.
Reactive haemophagocytic syndrome in children with inflammatory disorders. A retrospective study of 24 patients (2001)

RHS may be a more common complication of systemic disease in childhood than previously thought. This life-threatening complication should be diagnosed promptly, as it calls for the immediate withdrawal of potentially triggering medications, anti-infective therapy when relevant, and urgent immunosuppressive treatment, measures that are very often effective. Cyclosporin A may be the drug of choice.