gebhart/patrepeval huggingface dataset:
SYNTHESIS OF COLLOIDAL PARTICLES IN MINIEMULSIONS (2006)

▪ Abstract Miniemulsions are specially formulated heterophase systems in which stable nanodroplets of one phase are dispersed in a second, continuous phase. Because each of the nanodroplets can be regarded as a nanoscopic, individual batch reactor, a whole variety of reactions and processes resulting in both organic and inorganic nanoparticles can be performed. This chapter reviews the wide range of possibilities of reactions in miniemulsions for the formation of structured nanoparticles. Different kinds of polymerizations, such as radical, anionic, and enzymatic polymerization, as well as polyaddition and polycondensation can be carried out in the nanodroplets, which permits the formulation of a variety of polymers, copolymers, or hybrid particles that previously have not been synthesized in other heterophase processes. Additionally, this review shows that miniemulsions are also highly suited for the encapsulation of various organic and inorganic, solid or liquid materials and for the functionalization of the particle surface.
Reflective systems design study for soft x-ray projection lithography (1990)

We have investigated several all-reflective designs which have potential application for soft x-ray projection lithography. The resolution goal for all designs was 0.1 μm or better. Different design aspects including usable field size, distortion, obscuration, number of mirrors, surface shape (spherical versus aspheric), and system packaging were explored. Trade-off studies were made between three types of systems: strip field scanning systems, and large field nonscanning systems with both curved and flat mask. Several candidate unobscured designs with 0.1 μm resolution are presented.
Lower serum vitamin D levels are associated with a higher relapse risk in multiple sclerosis (2012)

Our finding that higher vitamin D levels are associated with decreased exacerbation risk in relapsing-remitting MS suggests a beneficial effect of vitamin D on disease course in MS. However, the possibility of reverse causality cannot be ruled out completely. Randomized intervention studies are therefore needed to investigate the effect of vitamin D supplementation in MS.
Photoinduced Electron Transfer between Fluorescent Dyes and Guanosine Residues in DNA-Hairpins (2003)

Nucleobase-specific quenching interactions of fluorescent dyes can be used in singly labeled hairpin-shaped oligonucleotides to detect hybridization to specific target DNA sequences. In these DNA-hairpins, the dye is attached at the 5‘-end and quenched by guanosine residues in the complementary stem. Upon hybridization, a conformational reorganization occurs reflected in an increase in fluorescence intensity. To gain a better insight into the underlying quenching mechanism, we have performed intermolecular quenching experiments with different dyes (rhodamine and oxazine derivatives) and DNA nucleotides. The bimolecular dynamic quenching rate constants kq,dyn of ∼1.0−2.0 × 109 M-1 s-1 are relatively small for all dyes investigated though the measured decrease in fluorescence intensity indicates strong static fluorescence quenching. The data give evidence for the formation of weak or nonfluorescent (fluorescence lifetime, τ < 40 ps) ground-state complexes between the fluorophores and guanosine residues. Only within these complexes, that is, upon contact formation, efficient fluorescence quenching via electron transfer occurs. Using a model DNA-hairpin labeled at the 5‘-end with the oxazine derivative MR121, we varied the position of guanosine in the complementary stem sequence to reveal the distance dependence of fluorescence quenching. Qualitatively, it is apparent that the double-stranded stem of the DNA-hairpin facilitates efficient electron transfer from the guanosine residue to MR121 with a shallow distance dependence. This result strongly supports the idea that an end-capped conformation with stacking interactions and subsequent DNA mediated electron transfer is required for efficient fluorescence quenching. Our data show that the quenching efficiency can be increased substantially by the attachment of additional overhanging single-stranded nucleotides at the 3‘-end and the substitution of guanosine by stronger electron-donating nucleotides, such as 7-deazaguanosine residues. Consideration of the data obtained in this study enables the synthesis of DNA-hairpins solely quenched by guanosine residues and its analogous with a 20-fold increase in fluorescence intensity upon specific binding to the target sequence.
IL-7: a limited resource during thymopoiesis (2004)

Comment on Munitic et al, page [4165][1] 

The tight regulation of the interleukin-7 receptor (IL-7R) during T-cell development occurs so that developing pro- and pre-T cells are uniquely poised to use limited IL-7, especially after the initial wave of T-cell production. 

S ignaling through the IL-
Pseudomonas aeruginosa gram-negative folliculitis (1979)

Three patients with sudden, unmanageable exacerbation of acne vulgaris were shown to have Gram-negative folliculitis due to Pseudomonas aeruginosa. In each patient, the source of the Pseudomonas proved to be an otitis externa infection. In contrast to previous cases of Gram-negative folliculitis due to Proteus, Escherichia coli, or Klebsiella, the anterior nares were not colonized. Treatment of the otitis externa and the Gram-negative folliculitis with acetic acid compresses and topical antibiotics led to prompt resolution without recurrence.
Engineered Human tmpk/AZT As a Novel Enzyme/Prodrug Axis for Suicide Gene Therapy (2007)

Gene therapy and stem cell transplantation safety could be enhanced by control over the fate of therapeutic cells. Suicide gene therapy uses enzymes that convert prodrugs to cytotoxic entities; however, heterologous moieties with poor kinetics are employed. We describe a novel enzyme/prodrug combination for selectively inducing apoptosis in lentiviral vector-transduced cells. Rationally designed variants of human thymidylate kinase (tmpk) that effectively phosphorylate 3'-azido-3'-deoxythymidine (AZT) were efficiently delivered. Transduced Jurkat cell lines were eliminated by AZT. We demonstrate that this schema targeted both dividing and non-dividing cells, with a novel killing mechanism involving apoptosis induction via disruption of the mitochondrial inner membrane potential and activation of caspase-3. Primary murine and human T cells were also transduced and responded to AZT. Furthermore, low-dose AZT administration to non-obese diabetic/severe combined immunodeficiency (NOD/SCID) mice injected with transduced K562 cells suppressed tumor growth. This novel suicide gene therapy approach can thus be integrated as a safety switch into therapeutic vectors.
Characterization of Low-Affinity Complexes between RNA and Small Molecules Using Electrospray Ionization Mass Spectrometry (2000)

Electrospray ionization mass spectrometry (ESI-MS) provides a sensitive method for the characterization of low-affinity (∼mM) complexes between nucleic acids and small molecules. Such complexes can be generated in solution and moved into the gas phase for detection using MS by reducing the energy imparted during the desolvation process. The affinity and binding stoichiometry of ligands can be determined directly from the observed masses and abundances of the complexes. These benefits are demonstrated for complexes between a 27-mer RNA model of the 16S rRNA, 2-deoxystreptamine (2-DOS), and a series of small organic ligands. We observe two types of 2-DOS−RNA complexes that undergo collisionally activated dissociation in a quadrupole ion trap mass spectrometer at different energies. Molecular modeling results are consistent with this observation. When multiple compounds are mixed with the RNA, the mode of binding can be determined from the abundances of the respective ternary complexes and from the activation energies required to effect gas-phase dissociation in the capillary−skimmer interface region of the instrument. ESI-MS should have considerable utility in studies of macromolecule−ligand complexes where the receptor has multiple binding sites for the ligand.
A humanized antibody that binds to the interleukin 2 receptor. (1989)

The anti-Tac monoclonal antibody is known to bind to the p55 chain of the human interleukin 2 receptor and to inhibit proliferation of T cells by blocking interleukin 2 binding. However, use of anti-Tac as an immunosuppressant drug would be impaired by the human immune response against this murine antibody. We have therefore constructed a "humanized" antibody by combining the complementarity-determining regions (CDRs) of the anti-Tac antibody with human framework and constant regions. The human framework regions were chosen to maximize homology with the anti-Tac antibody sequence. In addition, a computer model of murine anti-Tac was used to identify several amino acids which, while outside the CDRs, are likely to interact with the CDRs or antigen. These mouse amino acids were also retained in the humanized antibody. The humanized anti-Tac antibody has an affinity for p55 of 3 x 10(9) M-1, about 1/3 that of murine anti-Tac.
Enzymes of Sphingolipid Metabolism:  From Modular to Integrative Signaling (2001)

Many enzymes of sphingolipid metabolism are regulated in response to extra- and intracellular stimuli and in turn serve as regulators of levels of bioactive lipids (such as sphingosine, ceramide, sphingosine 1-phosphate, and diacylglycerol), and as such, they serve a prototypical modular function in cell regulation. However, lipid metabolism is also closely interconnected in that a product of one enzyme serves as a substrate for another. Moreover, many cell stimuli regulate more than one of these enzymes, thus adding to the complexity of regulation of lipid metabolism. In this paper, we review the status of enzymes of sphingolipid metabolism in cell regulation and propose a role for these enzymes in integration of cell responses, a role that builds on the modular organization while also taking advantage of the complexity and interconnectedness of lipid metabolism, thus providing for a combinatorial mechanism of generating diversity in cell responses. This may be a general prototype for the involvement of metabolic pathways in cell regulation.
Expression of human immunoglobulin E ε chain cDNA inE.coli (1983)

Using the cDNA of human epsilon chain, three expression plasmids that code directly the constant portion of the epsilon chain (C epsilon 1-C epsilon 4, C epsilon 2-C epsilon 4 and C epsilon 3-C epsilon 4 domains) were constructed. These epsilon chain peptides were synthesized in E. coli under the control of the trp promoter-operator. The bacterially produced peptides have the antigenicity of human epsilon chain and gave the molecular weights equal to the values calculated from the amino acid sequence of the constructed plasmids.
Effects of Growth Hormone in Osteoporosis (1976)

The effect of chronic administration of growth hormone (GH) to osteoporotic patients was studied using the techniques of total body neutron activation analysis, whole body counting, calcium tracer kinetics, photon absorptiometry, quantitative microradiography, and urinary hydroxyproline. Two dosage schedules were utilized for six months each: 2 units daily and 0.2 w3/4 units of GH daily (where W represents body weight expressed in kg). The lower dosage (2 units) did not produce any appreciable change in the indices studied. Following the higher dose, no evidence of any anabolic effect was apparent in most patients (i.e., no increase in total body levels of Ca, Na, K, P, or Cl). Increases were noted in the urinary calcium excretion rate and in the urinary hydroxyproline excretion. Bone mineral content decreased. The bone biopsies displayed an increase in bone formation and resorption surfaces in response to treatment, but these changes were not statistically significant. It may be concluded that under the conditions of this study, GH administration did not result in an increment in skeletal mass. Several side effects that are characteristic of acromegaly were observed, including hyperglycemia, hypertension, arthralgia, and the carpal tunnel syndrome. Because of the lack of demonstrated benefit and the associated complications of therapy, GH administration does not appear to be of value in the treatment of osteoporosis.
A simple method of duct cannulation and localization for galactography before excision in patients with nipple discharge. (1995)

A monofilament polypropylene guiding suture was inserted into a secreting duct in 72 female patients (aged 15-78 years) with nipple discharge. Cannulation and injection of contrast material was successful in all patients before galactography and of methylene blue dye before excision. Patients did not report discomfort, no injuries ensued, and no duct was perforated. This technique should expedite excision of a discharging duct and any lobules.
Abstract 2156: Left Atrial Fibrosis Impacts Left Ventricular Ejection Fraction in Patients with Atrial Fibrillation (2008)

Background. The extent of left atrial (LA) wall fibrosis detected by delayed enhancement MRI (DE-MRI) appears to be correlated with advanced atrial fibrillation (AF). However, the effect of LA fibrosis on left ventricular function (LVEF) is not well understood. We report the relationship between left atrial fibrosis and LVEF in patients with AF. Methods. Sixty-seven patients underwent DE-MRI and 2-dimensional trans-thoracic echocardiography prior to ablation for AF. Three dimensional segmentation of the LA was performed and the extent of fibrosis was quantified using a semi-automated algorithm. Patients were assigned to one of three groups based on the degree of LA fibrosis; 1) mild enhancement where the fibrosis &lt; 15% of the LA wall, 2) moderate enhancement where fibrosis &gt; 15% and &lt; 35%, and extensive where fibrosis &gt; 35% of the LA wall. LVEF was determined both prior to and 3 months following pulmonary vein antrum isolation with posterior wall and septal debulking. Results. The average pre-ablation LVEF among patients with mild fibrosis was 53.2% ± 9.9% (n = 41), 52.3% ± 7.4% (n = 19) among patients with moderate fibrosis and 42.1% ± 9.9% (n = 7) among those with extensive enhancement (p = 0.01,one way ANOVA). The difference remains significant after controlling for patient age, gender, hypertension, MI, AF type, mitral valve regurgitation, CAD and the presence of non-AF related CHF. Following ablation, all groups had an increase in the LVEF. The greatest increase occurred among patients in the extensive group. On average, this group experienced an overall improvement of 10.8% ± 14.1%. Patients in the mild enhancement group had an average improvement of 3.3% ± 11.1% and those in the moderate group had an average improvement of 3.8% ± 5.6%. The post-ablation LVEF among patients with mild fibrosis was 56.6% ± 8.3%, 56.2% ± 6.4% among patients with moderate fibrosis and 53.0% ± 15.4% among patients with extensive fibrosis. Conclusion. From our preliminary experience with DE-MRI fibrosis detection, patients with extensive LA fibrosis appear to have depressed LV function pre-ablation. This group of patients seems to experience a large improvement (~11%) in LV function post-ablation compared to patients with less LA fibrosis.
Antigen Density Presented By Dendritic Cells In Vivo Differentially Affects the Number and Avidity of Primary, Memory, and Recall CD8+ T Cells (2003)

We studied the size and avidity of primary and recall CD8(+) T cell responses in vivo in mice immunized with dendritic cells presenting different densities of a MHC class I-restricted peptide. Increasing the epitope density on a fixed number of dendritic cells increased the size of the primary response, yet had no influence on the avidity of the effector cells. However, epitope density-based selection of cells with different avidities was evident in the subsequent memory population, and in recall responses. Additionally, mice primed with different peptide densities had similarly sized quiescent memory and recall responses. Our findings provide evidence for an important role for epitope density in the selection of T cells in vivo.
A Method for Discriminating Between Failure Density Functions Used In Reliability Predictions (1965)

Unless sufficient evidence to the contrary exists, the exponential distribution is often assumed as a model for the failure density function in reliability predictions. The generalized gamma distribution, with known location parameter, is a three parameter distribution which encompasses the exponential, Weibull, gamma and many others. In this paper, (i) maximum likelihood estimation for the three parameters is indicated, (ii) it is noted that these estimators are asymptotically multivariate normally distributed, and (iii) using the distribution of the estimators, probability regions for the estimators of the parameters of the generalized gamma distribution are established for large sample situations. In situations where the generalized gamma can be assumed as the correct density function, the exponential and the Weibull are special cases. A method is presented using experimental or life data for rejecting (with a known probability of false rejection) the Weibull and (or) the exponential functions when they do not appear to describe the failure density function of a unit.
Binding of the B cell activation antigen B7 to CD28 costimulates T cell proliferation and interleukin 2 mRNA accumulation. (1991)

A successful immune response requires intercellular contact between T and B lymphocytes. We recently showed that CD28, a T cell surface protein that regulates an activation pathway, could mediate intercellular adhesion with activated B cells by interaction with the B7 antigen. Here we show that CD28 is the primary receptor for B7 on activated peripheral blood T cells, that CD28 binds to B7 in the absence of other accessory molecules, and that interaction between CD28 and B7 is costimulatory for T cell activation. To characterize the binding of CD28 to B7, we have produced genetic fusions of the extracellular portions of B7 and CD28, and immunoglobulin (Ig) C gamma 1 chains. 125I-labeled B7 Ig bound to CD28-transfected Chinese hamster ovary (CHO) cells, and to immobilized CD28 Ig with a Kd approximately 200 nM. B7 Ig also inhibited CD28-mediated cellular adhesion. The function of CD28-B7 interactions during T cell activation was investigated with soluble fusion proteins and with B7-transfected CHO cells. Immobilized B7 Ig and B7+ CHO cells costimulated T cell proliferation. Stimulation of T cells with B7+ CHO cells also specifically increased levels of interleukin 2 transcripts. These results demonstrate that the CD28 signaling pathway could be activated by B7, resulting in increased T cell cytokine production and T cell proliferation. Cellular interactions mediated by B7 and CD28 may represent an important component of the functional interactions between T and B lymphoid cells.
A new faster algorithm for iterative placement improvement (2002)

We present a new faster design-style independent iterative placement improvement algorithm. Randomized simulated annealing based algorithms produce good result. But on very large designs, the inherently long run-time makes it prohibitive to use randomized algorithm. On the other hand deterministic improvement methods do not produce as good a result as the simulated annealing based algorithms. Moreover, none of the existing placement improvement techniques addresses the non row-based design style. In this paper, we combine the advantages of both the random and deterministic approach to develop a new faster placement improvement algorithm. Experimental results show that our algorithm performs much better than existing placement improvement algorithm. On some benchmarks, our algorithm is as much as 8/spl times/ faster than that on Domino with a significant reduction in total net length.
Development and Prospective Validation of a Clinical Index to Predict Survival in Ambulatory Patients Referred for Cardiac Transplant Evaluation (1997)

Selection of candidates for cardiac transplantation may be improved by use of this noninvasive risk-stratification model.
Mice Heterozygous for Germ-line Mutations in Methylthioadenosine Phosphorylase ( MTAP ) Die Prematurely of T-Cell Lymphoma (2009)

Large homozygous deletions of 9p21 that inactivate CDKN2A, ARF, and MTAP are common in a wide variety of human cancers. The role for CDKN2A and ARF in tumorigenesis is well established, but whether MTAP loss directly affects tumorigenesis is unclear. MTAP encodes the enzyme methylthioadenosine phosphorylase, a key enzyme in the methionine salvage pathway. To determine if loss of MTAP plays a functional role in tumorigenesis, we have created an MTAP-knockout mouse. Mice homozygous for a MTAP null allele (Mtap(lacZ)) have an embryonic lethal phenotype dying around day 8 postconception. Mtap/Mtap(lacZ) heterozygotes are born at Mendelian frequencies and appear indistinguishable from wild-type mice during the first year of life, but they tend to die prematurely with a median survival of 585 days. Autopsies on these animals reveal that they have greatly enlarged spleens, altered thymic histology, and lymphocytic infiltration of their livers, consistent with lymphoma. Immunohistochemical staining and fluorescence-activated cell sorting analysis indicate that these lymphomas are primarily T-cell in origin. Lymphoma-infiltrated tissues tend to have reduced levels of Mtap mRNA and MTAP protein in addition to unaltered levels of methyldeoxycytidine. These studies show that Mtap is a tumor suppressor gene independent of CDKN2A and ARF.
A novel method for accurate operon predictions in all sequenced prokaryotes (2005)

We combine comparative genomic measures and the distance separating adjacent genes to predict operons in 124 completely sequenced prokaryotic genomes. Our method automatically tailors itself to each genome using sequence information alone, and thus can be applied to any prokaryote. For Escherichia coli K12 and Bacillus subtilis, our method is 85 and 83% accurate, respectively, which is similar to the accuracy of methods that use the same features but are trained on experimentally characterized transcripts. In Halobacterium NRC-1 and in Helicobacter pylori, our method correctly infers that genes in operons are separated by shorter distances than they are in E.coli, and its predictions using distance alone are more accurate than distance-only predictions trained on a database of E.coli transcripts. We use microarray data from six phylogenetically diverse prokaryotes to show that combining intergenic distance with comparative genomic measures further improves accuracy and that our method is broadly effective. Finally, we survey operon structure across 124 genomes, and find several surprises: H.pylori has many operons, contrary to previous reports; Bacillus anthracis has an unusual number of pseudogenes within conserved operons; and Synechocystis PCC 6803 has many operons even though it has unusually wide spacings between conserved adjacent genes.
Purification and partial characterization of a K99-antigen associated adhesin in Escherichia coli (637 strain). (1983)

The K99-antigen associated adhesin in Escherichia coli (637 Strain) has been purified to homogeneity by using conventional chromatographic procedures. Sodium deoxycholate was used in the precipitation steps to avoid hydrophobic interactions between the fimbriae and other membrane-associated components. Homogeneity of the purified adhesin was assessed by electrophoresis, isoelectrofocusing, analytical gel filtration and immunoprecipitation against K99 specific antiserum, being homogeneous in all cases. The purified adhesin is composed of protein sub-units with a molecular weight of 18,900 +/- 950 daltons. No sugars were detected in the molecule. The molecular weight of the adhesin was higher than 2 X 10(6) daltons, and its isoelectric point was estimated to be about 9.45.