gebhart/patrepeval huggingface dataset:
Studies on human serum high density lipoproteins. Self-association of apolipoprotein A-I in aqueous solutions. (1976)

Human serum apolipoprotein A-I (apo-A-I), the major protein component of the human serum high density lipoproteins, was studied in aqueous solutions of differing ionic strength and pH by the techniques of sedimentation equilibrium ultracentrifugation and frontal analysis gel chromatography. The ultracentrifugal studies indicate the apo-A-I is a self-associating system that is dependent upon protein concentration, but relatively independent of the nature of the medium. The apparent weight average molecular weights obtained from solutions of initial apo-A-I concentration between 0.2 and 0.9 mg/ml were in the range of 3.0 to 16.7 x 10(4) (monomer molecular weight = 28,014). Of the several models of self-associated examined, that which gave the best theoretical fit was for the monomer-dimertetramer-octamer model. The self-association of apo-A-I in aqueous solutions was further documented by frontal analysis gel chromatography, which not only corroborated the ultracentrifugal results, but also indicated that the multiple species of apo-A-I in solution attain equilibrium rather rapidly. Besides having intrinsic importance, these results indicate that the solution properties of apo-A-I must be established before ligand binding studies are conducted and interpreted.
TimeTree: a public knowledge-base of divergence times among organisms (2006)

TimeTree is available at http://www.timetree.net
Docking and 3-D QSAR Studies on Indolyl Aryl Sulfones. Binding Mode Exploration at the HIV-1 Reverse Transcriptase Non-Nucleoside Binding Site and Design of Highly Active N-(2-Hydroxyethyl)carboxamide and N-(2-Hydroxyethyl)carbohydrazide Derivatives (2004)

Three-dimensional quantitative structure-activity relationship (3-D QSAR) studies and docking simulations were developed on indolyl aryl sulfones (IASs), a class of novel HIV-1 non-nucleoside reverse transcriptase (RT) inhibitors (Silvestri, et al. J. Med. Chem. 2003, 46, 2482-2493) highly active against wild type and some clinically relevant resistant strains (Y181C, the double mutant K103N-Y181C, and the K103R-V179D-P225H strain, highly resistant to efavirenz). Predictive 3-D QSAR models using the combination of GRID and GOLPE programs were obtained using a receptor-based alignment by means of docking IASs into the non-nucleoside binding site (NNBS) of RT. The derived 3-D QSAR models showed conventional correlation (r(2)) and cross-validated (q(2)) coefficients values ranging from 0.79 to 0.93 and from 0.59 to 0.84, respectively. All described models were validated by an external test set compiled from previously reported pyrryl aryl sulfones (Artico, et al. J. Med. Chem. 1996, 39, 522-530). The most predictive 3-D QSAR model was then used to predict the activity of novel untested IASs. The synthesis of six designed derivatives (prediction set) allowed disclosure of new IASs endowed with high anti-HIV-1 activities.
In vitro and in vivo correlation of clotting protease activity: Effect of heparin (1977)

The thrombogenicity of three highly purified proteases (thrombin, activated Factor X, and activated Factor IX) was determined quantitatively in an animal model. The minimal amounts required to produce a standard score 4 thrombus were 1.1 nmol for thrombin, 0.12 nmol for activated Factor X, and 0.018 nmol for activated Factor IX. After the administration of heparin at 5, 10, and 20 units/kg in rabbits, the thrombogenicity of each of these proteases decreased progressively. The heparin-induced inhibition of thrombosis decreased in the order, activated Factor IX > activated Factor X > thrombin at each heparin concentration. These differences were statistically significant. These in vivo data provide support for the following hypotheses originally developed from in vitro experiments: (i) activation of the blood coagulation system, which proceeds through a cascade mechanism, incorporates biochemical amplification; (ii) the inhibition of activated Factor IX by antithrombin III in the presence of heparin is an important reaction in the prevention of thrombosis; (iii) less heparin is required to inhibit thrombosis prior to thrombin generation than afterward; (iv) an increase in the reactivity of antithrombin III reflects a decreased tendency to thrombosis while a decrease in this reactivity reflects an increased tendency to thrombosis.
The Influence of a Eutectic Mixture of Lidocaine and Prilocaine on Minor Surgical Procedures (2009)

EMLA effectively reduces the preprocedural needle-stick pain and procedural pain associated with minor surgical procedures.
Reduced Expression of Endothelial Nitric Oxide Synthase in the Lungs of Patients with Pulmonary Hypertension (1995)

Pulmonary hypertension is associated with diminished expression of endothelial nitric oxide synthase. It is possible that decreased expression of nitric oxide synthase may contribute to pulmonary vasoconstriction and to the excessive growth of the tunica media observed in this disease.
Multipoint analysis of human quantitative genetic variation. (1990)

A unique method of partitioning human quantitative genetic variation into effects due to specific chromosomal regions is presented. This method is based on estimating the proportion of genetic material, R, shared identical by descent (IBD) by sibling pairs in a specified chromosomal region, on the basis of their marker genotypes at a set of marker loci spanning the region. The mean and variance of the distribution of R conditional on IBD status and recombination pattern between two marker loci are derived as a function of the distance between the two loci. The distribution of the estimates of R is exemplified using data on 22 loci on chromosome 7. A method of using the estimated R values and observed values of a quantitative trait in a set of sibships to estimate the proportion of total genetic variance explained by loci in the region of interest is presented. Monte Carlo simulation techniques are used to show that this method is more powerful than existing methods of quantitative linkage analysis based on sib pairs. It is also shown through simulation studies that the proposed method is sensitive to genetic variation arising from both a single locus of large effect as well as from several loosely linked loci of moderate phenotypic effect.
Practical Genetic Algorithms (2003)

Introduction to Optimization The Binary Genetic Algorithm The Continuous Parameter Genetic Algorithm Applications An Added Level of Sophistication Advanced Applications Evolutionary Trends Appendix Glossary Index.
Pneumocystis cariniiDihydropteroate Synthase but Not Dihydrofolate Reductase Gene Mutations Correlate with Prior Trimethoprim‐Sulfamethoxazole or Dapsone Use (1999)

Recent studies of the human Pneumocystis carinii dihydropteroate synthase (DHPS) gene suggest that P. carinii is developing resistance to sulfamethoxazole (SMX) and dapsone. To explore whether P. carinii is also developing resistance to trimethoprim (TMP), the human P. carinii dihydrofolate reductase (DHFR) gene was cloned, DHFR and DHPS genes in 37 P. carinii isolates from 35 patients were sequenced, and the relationship between TMP-SMX or dapsone use and gene mutations was analyzed. The DHFR gene sequences were identical in all isolates except 1 with a synonymous substitution. In contrast, the DHPS gene sequences showed mutations in 16 of the 37 isolates; prior sulfa/sulfone prophylaxis was associated with the presence of these mutations (P<.001). In addition to suggesting that there is less selective pressure on DHFR than on DHPS, this study reinforces the hypothesis that mutations in the DHPS gene are likely involved in the development of sulfa resistance in P. carinii.
Local dimer exchange in surfactant-mediated epitaxial growth (1992)

While the effectiveness of surfactants in suppressing islanding in Si/Ge heteroepitaxial growth has been demonstrated in previous studies, the atomic scale growth processes have remained unknown. Here we present images of the growing Si(001)/Ge surface obtained with in situ low-energy electron microscopy. From our previous we conclude that surfactant-mediated growth of Ge on Si(001) proceeds by highly local Ge incorporation with minimum surface diffusion. We propose a new two-dimer correlated exchange mechanism to explain this unusual growth mode, as well as the absence of islanding at high Ge coverage.
Treatment of Muscle Injuries by Local Administration of Autologous Conditioned Serum: A Pilot Study on Sportsmen with Muscle Strains (2004)

Muscle injuries represent a major part of sports injuries and are a challenging problem in traumatology. Strain injuries are the most common muscle injuries after contusions. These injuries can lead to significant pain and disability causing time to be lost to training and competition. Despite the frequency of strain injuries the treatment available is limited and is generally not sufficient to enhance muscle regeneration efficiently when fast resumption of sport activity is a primary target. A number of growth factors play a specific role in regeneration and it has been proven that a previously described method of physically and chemically stimulating whole blood (to produce autologous conditioned serum) induces concentration increases in FGF-2, HGF, and TGF-beta1. A preliminary study was conducted on muscle strain injuries in professional sportsmen receiving either: 1. autologous conditioned serum (ACS) or 2. Actovegin/Traumeel treatment as control. Assessment of recovery from injury was done by: 1. sport professional's ability to participate to 100 % under competition conditions in their respective sport and 2. MRI analysis. A significant difference in the recovery time from injury was demonstrated: 16.6 +/- 0.9 in the ACS treated instead of 22.3 +/- 1.2 (mean +/- SEM) days in the Actovegin/Traumeel control group (p = 0.001). MRI analysis supported the observed acceleration of the lesion recovery time. We conclude that ACS injection is a promising approach to reduce the time to recovery from muscle injury.
Mišljenje pacijenata o našem radu element u procjeni kvalitete (Pacient Opinion about Ours Work Part of Quality Evaulation) (2007)

Misljenje pacijenta o nasem radu važan je element pri određivanju kvalitete tog rada. U suradnji sa clanovima Upravnog odbora Hrvatskog drustva lijecnika obiteljskih doktora, autor je proveo anonimnu anketu na razlicitim podrucjima sa slicnom organizacijom službe. Obuhvacena su podrucja sjeverozapadne i istocne Hrvatske, izvan najvecih gradova. Cilj istraživanja je bio istražiti stavove pacijenata o nasem radu i o problemima koje bi trebalo otkloniti. Koristen je modificirani Europep upitnik (koji se koristi u Europi kod slicnih anketa). Podijeljeno je 10.000 anketnih listica u 100 ordinacija obiteljske medicine (po 100 u svakoj ordinaciji). Anketa je provedena na podrucju Rovinja, Poreca, Umaga, Labina, Opatije, cakovca, cakova i Vinkovaca. Kako je anketa rađena na relativno velikom broju uzoraka, podaci su statisticki znacajni za anketirana podrucja. Sve podatke iznad 10% negativnih odgovora smatrali smo znacajnim. Postotak negativnih odgovora varirao je od 15-45%, pa se vecina pacijenata ipak izrazila pozitivno o nasem radu. Na svim ispitanim podrucjima pacijenti su se požalili na cetiri ista problema: 	»Nedovoljno zanimanje lijecnika za njihove probleme, ne pozivanje na sistematske preglede i potrebna cijepljenja, ne pripremanje za specijalisticki pregled ili bolnicu i na dugo cekanje u cekaonici	». Na nekim se podrucjima i kod nekih lijecnika javljao i mnogo siri spektar negativnih odgovora, sto ukazuje i na određene razlike u kvaliteti zdravstvene zastite, sto je bila potvrda nase postavke, da anketa primarno mora poslužiti nama samima, da bi otklonili nedostatke i poboljsali vlastiti rad.
The use of cluster hierarchies in hypertext information retrieval (1989)

The graph-traversal approach to hypertext information retrieval is a conceptualization of hypertext in which the structural aspects of the nodes are emphasized. A user navigates through such hypertext systems by evaluating the semantics associated with links between nodes as well as the information contained in nodes. [Fris88] In this paper we describe an hierarchical structure which effectively supports the graphical traversal of a document collection in a hypertext system. We provide an overview of an interactive browser based on cluster hierarchies. Initial results obtained from the use of the browser in an experimental hypertext retrieval system are presented.
Compositionally and functionally distinct sinus microbiota in chronic rhinosinusitis patients have immunological and clinically divergent consequences (2017)

A large proportion of CRS patient heterogeneity may be explained by the composition of their sinus bacterial microbiota and related host immune response-features which may inform strategies for tailored therapy in this patient population.
The Geometry of Diarthrodial Joints, its Physiologic Maintenance, and the Possible Significance of Age-Related Changes in Geometry-to-Load Distribution and the Development of Osteoarthritis (1981)

Diarthrodial joints are governed by physiologic mechanisms that maintain stability and an equitable distribution of load. Modeling continues throughout life to maintain the necessary physiologic incongruity. However, in old age the system seems to go awry, and the result is an increasing congruity yielding possibly increased stability but interfering with cartilage nutrition and altering the distribution of load. The increasing maldistribution of load, with age, it is proposed, mechanically overtaxes the previously underloaded and, presumably, atrophic cartilage. Overtaxing the cartilage in turn leads to further depletion of proteoglycans, collagen fraying and eventually osteoarthritis. Thus arthritis, at least in one of its forms, appears to be inevitable because of the maldistribution of load that results from the age-related changes in joint shape possibly dictated by the joint's requirement for stability.
A hierarchical bayesian model of invariant pattern recognition in the visual cortex (2006)

We describe a hierarchical model of invariant visual pattern recognition in the visual cortex. In this model, the knowledge of how patterns change when objects move is learned and encapsulated in terms of high probability sequences at each level of the hierarchy. Configuration of object parts is captured by the patterns of coincident high probability sequences. This knowledge is then encoded in a highly efficient Bayesian network structure. The learning algorithm uses a temporal stability criterion to discover object concepts and movement patterns. We show that the architecture and algorithms are biologically plausible. The large scale architecture of the system matches the large scale organization of the cortex and the micro-circuits derived from the local computations match the anatomical data on cortical circuits. The system exhibits invariance across a wide variety of transformations and is robust in the presence of noise. Moreover, the model also offers alternative explanations for various known cortical phenomena.
CD40/CD40 Ligand Interactions Are Critical for Elicitation of Autoimmune-Mediated Fibrosis in the Lung (2001)

Pulmonary interstitial fibrosis (PIF), associated with persistent inflammation and increased collagen deposition in the interstitium, is often considered an autoimmune disease. Hapten immune PIF (HIPIF), a model for PIF, is elicited in the lung by a single intratracheal (i.t.) challenge in mice sensitized with hapten (2,4,6-trinitrobenzene sulfonic acid, TNBS). In this study, we characterized the role of CD40/CD40 ligand (CD40L) interactions in the elicitation of secondary cell-mediated immune responses that lead to development of fibrosis in the lung using an adoptive transfer model of HIPIF. The expression of CD40 was detected on bronchoalveolar lavage (BAL) cells 1-3 days after i.t. challenge with hapten in the HIPIF lung, but not lungs from the control mice. The CD40(bright) BAL cells morphologically resembled infiltrating monocytes. Furthermore, blocking CD40/CD40L interactions with blocking Ab decreased BAL production of Th1-mediators (IL-12 and TNF-alpha). Moreover, either blocking CD40/CD40L interactions with the Ab or using IL-12 knockout recipient mice prevented the increased collagen deposition (accumulation of hydroxyproline) in the lungs during HIPIF induction. We conclude that second signals (CD40/CD40L interactions) are required for elicitation of secondary immune responses that lead to PIF in vivo. The results support the notion that CD40/CD40L interactions are involved in the pathogenesis of an ongoing autoimmune disease.
GATA-1 Transactivates the WT1 Hematopoietic Specific Enhancer (1995)

The Wilms' tumor gene, WT1, is believed to play a role in hematopoiesis as it is expressed in the spleen and in immature leukemias in addition to the developing genitourinary system. WT1 is down-regulated in differentiated leukemia cells both in vivo and in vitro and is up-regulated in fetal spleen and immature leukemia cells. The modulation of WT1 expression was examined in many cell types, and a hematopoietic-specific enhancer element has been identified. Here we describe the transcriptional response of this enhancer to hematopoietic-specific transcription factors. We found co-expression of WT1 and GATA-1 mRNA in K562 cells and in mouse spleen, suggesting potential interactions between these two transcription factors. We find that the activity of the 3' WT1 enhancer is positively correlated with the expression of GATA-1. Gel shift competition experiments and transactivation studies revealed that this functional activity is mediated via binding at a GATA-binding site in the WT1 enhancer. The transactivation of the WT1 enhancer by GATA-1 implies that GATA-1 plays a role in the regulation of WT1 during hematopoiesis.
Generation of nitric oxide by enzymatic oxidation of N-hydroxy-N-nitrosamines. (1985)

The nitric oxide (N = O) free radical exhibits potent cytocidal, mutagenic and vasodilatory properties. We have examined the hypothesis that the hydroxynitrosamino functionality (see sequence in text), which occurs naturally in antineoplastic and antihypertensive agents, will directly generate N = O following peroxidatic 1-electron oxidation. Cupferron (see sequence in text) is indeed an excellent (k greater than 10(7) m-1 s-1) substrate for horseradish peroxidase. The products are N = O and nitrosobenzene (phi - N = O) which are generated and consumed as follows. First, cupferron is oxidized by the classical peroxidatic mechanism to form an unstable nitroxide free radical (see sequence in text) which then forms N = O and phi - N = O spontaneously (see sequence in text). The N = O then reacts with phi - N = O to reform cupferron (see sequence in text) or with the enzyme to generate the characteristic peroxidase--N = O chromophore. Simultaneously, in a competitive reaction with O2, the N = O is converted to NO-2 (4N = O + O2 + 2H2O------------4NO-2 + 4H+). The reactivity of hydroxynitrosamino compounds with horseradish peroxidase is in the order cupferron greater than hydroxynitrosaminomethane greater than alanosine. These model reactions, involving direct oxidation of the hydroxynitrosamino moiety, comprise a novel pathway for the biological production of N = O.
Designing nanosecond high voltage pulse generatorsusing power MOSFETs (1994)

Power MOSFETs in series are used for generating high voltage, &gt;1 kV, pulses with nanosecond rise and fall times. The design procedures for series operation and driving power MOSFETs to attain nanosecond switching times are given. A –1500 V pulse generator is designed with a 3 ns falltime and a 15 ns risetime into a 50 Ω load.
Pichia pastoris fermentation with mixed-feeds of glycerol and methanol: growth kinetics and production improvement (2003)

Fed-batch fermentation of a methanol utilization plus (Mut(+)) Pichia pastoris strain typically has a growth phase followed by a production phase (induction phase). In the growth phase glycerol is usually used as carbon for cell growth while in the production phase methanol serves as both inducer and carbon source for recombinant protein expression. Some researchers employed a mixed glycerol-methanol feeding strategy during the induction phase to improve production, but growth kinetics on glycerol and methanol and the interaction between them were not reported. The objective of this paper is to optimize the mixed feeding strategy based on growth kinetic studies using a Mut(+) Pichia strain, which expresses the heavy-chain fragment C of botulinum neurotoxin serotype C [BoNT/C(Hc)] intracellularly, as a model system. Growth models on glycerol and methanol that describe the relationship between specific growth rate ( micro ) and specific glycerol/methanol consumption rate ( nu(gly), nu(MeOH)) were established. A mixed feeding strategy with desired micro (gly)/ micro (MeOH) =1, 2, 3, 4 (desired micro (MeOH) set at 0.015 h(-1)) was employed to study growth interactions and their effect on production. The results show that the optimal desired micro (gly)/ micro (MeOH) is around 2 for obtaining the highest BoNT/C(Hc) protein content in cells: about 3 mg/g wet cells.
Statistical relational databases: normal forms (1991)

Problems associated with defining normal forms of relational tables relevant to statistical processing are discussed. The concepts of derived identifier, class identifier, derived class-counts, count domains, compact domains, and uniform domains for statistical relational tables are introduced. The structures of the first and the second statistical-normal forms and the relational decompositions needed to achieve them are also discussed. It is shown that the statistical-normal form can be an important method to determine whether the usual statistical analysis techniques are valid. Some suggestions are presented for extending the structured query language (SQL) statements to achieve these operations on statistical relational tables. Some results linking Codd's normal forms with statistical normal forms are discussed. Relational statistical abnormalities, called outlyers, are also discussed.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
The human touch (2012)

Traditional PD research offers a range of methods for participant engagement. Yet little is shared of the microdynamics of participation at its most intense, when the designer as facilitator is challenged by a range of social contingencies. Engaging people in change can be a messy process, especially when emotions run high. This paper explores two situations where communities were asked to collaborate on disaster mitigation plans and looks at how facilitation took place to engage with these concerns. It considers the relationship between method and its enactment, between the participatory practitioner and participant group, and between intention and outcome. In doing so, it questions the prevalent research culture that anonymises facilitation and its agency. Instead, we offer a more synthesised reading of practice, by focusing on aspects that compound the designers' task, such as the dynamics of the group and emotions manifested by participants. We argue that we need to orientate towards understanding the designers' participatory practice, rather than reporting participatory methods alone. The act of engaging others involves an embodied knowing, with moment-by-moment shifts in position, focus and delivery. Acknowledging this involves a rethink of our frameworks for reflecting and reporting on design.