gebhart/patrepeval huggingface dataset:
Discovering Differences in Acoustic Emission Between Healthy and Osteoarthritic Knees Using a Four-Phase Model of Sit-Stand-Sit Movements (2010)

By performing repeated sit-stand-sit movements to create stress on knee joints, short transient bursts of high frequency acoustic emission (AE) released by the knee joints were acquired from two age matched groups consisting of healthy and osteoarthritic (OA) knees, and significant differences between these two groups were discovered from the signal analysis performed. The analysis is based on a four-phase model of sit-stand-sit movements and a two-feature descriptor of AE bursts. The four phases are derived from joint angle measurement during movement, and they consist of the ascending-acceleration and ascending-deceleration phases in the sit-to-stand movement, followed by the descending-acceleration and descending-deceleration phases in the stand-to-sit movement. The two features are extracted from AE measurement during movement, and they consist of the peak magnitude value and average signal level of each AE burst. The proposed analysis method is shown to provide a high sensitivity for differentiation of the two age matched healthy and OA groups, with the most significant difference found to come from the peak magnitude value in the ascending-deceleration phase, clear quantity and strength differences in the image based visual display of their AE feature profiles due to substantially more AE bursts from OA knee joints with higher peak magnitude values and higher average signal levels, and two well separated clusters in the space formed by the principal components. These results provide ample support for further development of AE as a novel tool to facilitate dynamic integrity assessment of knee joints in clinic and home settings.
Does Hypogonadism Contribute to the Occurrence of a Minimal Trauma Hip Fracture in Elderly Men? (1991)

The risk of MTHF in hypogonadal elderly men was investigated with a case-control model. Cases and controls were selected from males age 65 years and older residing in the 120-bed McGuire Veterans Affairs Medical Center Nursing Home Care Unit over a 5-day interval. Historical data and serum free testosterone (fTe) were available on 17 subjects with MTHF and 61 controls. When groups were compared for differences in age, race, alcohol abuse, cigarette abuse, and diseases or drugs that may be associated with MTHF, only race was significantly different. Although 25.6% of residents were black, 100% of MTHF subjects were white (P = 0.004). Hypogonadism was defined as a random fTe less than 9 pg/mL (normal 9 to 46 pg/mL) and was found in 21 subjects (26.9%). Of cases with a MTHF, 58.8% were hypogonadal compared with only 18.0% of controls. Utilizing logistic regression, a highly significant association was found between hypogonadism and MTHF (P = 0.008), and using the odds ratio, subjects with hypogonadism were 6.5 times more likely to have a MTHF (95% CI 2.0 to 20.6). To adjust for race, the odds ratio was repeated excluding black subjects, and the results remained highly significant (4.6, 95% CI 1.3 to 16.2). We conclude that hypogonadal elderly white men may be at increased risk for MTHF.
A human antibody directed to the factor VIII C1 domain inhibits factor VIII cofactor activity and binding to von Willebrand factor (2000)

The occurrence of factor VIII (fVIII) inhibitory antibodies is a rare complication of fVIII substitution therapy in mild/moderate hemophilia A patients. fVIII mutations in certain regions such as the C1 domain are, however, more frequently associated with inhibitor, for reasons which remain unclear. To determine whether inhibitors could map to the mutation site, we analyzed at the clonal level the immune response of such a patient with an inhibitor to wild-type but not self-fVIII and an Arg2150His substitution in the C1 domain. Immortalization of the patient B lymphocytes provided a cell line producing an anti-fVIII IgG4κ antibody, LE2E9, that inhibited fVIII cofactor activity, following type 2 kinetics and prevented fVIII binding to von Willebrand factor. Epitope mapping with recombinant fVIII fragments indicated that LE2E9 recognized the fVIII C1 domain, but not the Arg2150His-substituted C1 domain. Accordingly, LE2E9 did not inhibit Arg2150His fVIII activity. These observations identify C1 as a novel target for fVIII inhibitors and demonstrate that Arg2150His substitution alters a B-cell epitope in the C1 domain, which may contribute to the higher inhibitor incidence in patients carrying such substitution. (Blood. 2000; 95:156-163)
Substrate recognition by ADAR1 and ADAR2 (2001)

RNA editing catalyzed by ADAR1 and ADAR2 involves the site-specific conversion of adenosine to inosine within imperfectly duplexed RNA. ADAR1- and ADAR2-mediated editing occurs within transcripts of glutamate receptors (GluR) in the brain and in hepatitis delta virus (HDV) RNA in the liver. Although the Q/R site within the GluR-B premessage is edited more efficiently by ADAR2 than it is by ADAR1, the converse is true for the +60 site within this same transcript. ADAR1 and ADAR2 are homologs having two common functional regions, an N-terminal double-stranded RNA-binding domain and a C-terminal deaminase domain. It is neither understood why only certain adenosines within a substrate molecule serve as targets for ADARs, nor is it known which domain of an ADAR confers its specificity for particular editing sites. To assess the importance of several aspects of RNA sequence and structure on editing, we evaluated 20 different mutated substrates, derived from four editing sites, for their ability to be edited by either ADAR1 or ADAR2. We found that when these derivatives contained an A:C mismatch at the editing site, editing by both ADARs was enhanced compared to when A:A or A:G mismatches or A:U base pairs occurred at the same site. Hence substrate recognition and/or catalysis by ADARs could involve the base that opposes the edited adenosine. In addition, by using protein chimeras in which the deaminase domains were exchanged between ADAR1 and ADAR2, we found that this domain played a dominant role in defining the substrate specificity of the resulting enzyme.
Formation of gutingimycin: analytical investigation of trioxacarcin A-mediated alkylation of dsDNA (2008)

Formation and fragmentation of recognition complexes between trioxacarcin A and various DNA sequences were examined by temperature-dependent UV and CD spectroscopy, HPLC analysis, and ESI mass spectrometry with regard to reaction conditions, intermediates, products, mechanism, and sequence specificity. Cleavage of the trioxacarcin–DNA complexes provided the natural product gutingimycin by guanine abstraction. The resulting DNA with an abasic site was further cleaved into a DNA fragment with a furanyl unit at the 3′-end and an oligonucleotide with a phosphorylated 5′-end.
The recombinant proregion of transforming growth factor beta1 (latency-associated peptide) inhibits active transforming growth factor beta1 in transgenic mice. (1996)

All three isoforms of transforming growth factors beta (TGF-betal, TGF-beta2, and TGF-beta3) are secreted as latent complexes and activated extracellularly, leading to the release of the mature cytokines from their noncovalently associated proregions, also known as latency-associated peptides (LAPs). The LAP region of TGF-beta1 was expressed in a baculovirus expression system and purified to homogeneity. In vitro assays of growth inhibition and gene induction mediated by TGF-beta3 demonstrate that recombinant TGF-beta1 LAP is a potent inhibitor of the activities of TGF-betal, -beta2, and -beta3. Effective dosages of LAP for 50% neutralization of TGF-beta activities range from 4.7- to 80-fold molar excess depending on the TGF-beta isoform and activity examined. Using 125I-labeled LAP, we show that the intraperitoneal application route is effective for systemic administration of LAP. Comparison of concentrations of LAP in tissues shows a homogenous pattern in most organs with the exception of heart and muscle, in which levels of LAP are 4- to 8-fold lower. In transgenic mice with elevated hepatic levels of bioactive TGF-betal, treatment with recombinant LAP completely reverses suppression of the early proliferative response induced by TGF-beta1 in remnant livers after partial hepatectomy. The results suggest that recombinant LAP is a potent inhibitor of bioactive TGF-beta both in vitro and in vivo, after intraperitoneal administration. Recombinant LAP should be a useful tool for novel approaches to study and therapeutically modulate pathophysiological processes mediated by TGF-beta3.
Cloning and characterization of canadine synthase involved in noscapine biosynthesis in opium poppy (2013)

Noscapine biosynthesis in opium poppy is thought to occur via N-methylcanadine, which would be produced through 9-O-methylation of (S)-scoulerine, methylenedioxy bridge formation on (S)-tetrahydrocolumbamine, and N-methylation of (S)-canadine. Only scoulerine 9-O-methyltransferase has been functionally characterized. We report the isolation and characterization of a cytochrome P450 (CYP719A21) from opium poppy that converts (S)-tetrahydrocolumbamine to (S)-canadine. Recombinant CYP719A21 displayed strict substrate specificity and high affinity (Km=4.63±0.71 μM) for (S)-tetrahydrocolumbamine. Virus-induced gene silencing of CYP719A21 caused a significant increase in (S)-tetrahydrocolumbamine accumulation and a corresponding decrease in the levels of putative downstream intermediates and noscapine in opium poppy plants.
Shell crosslinked polymer assemblies: Nanoscale constructs inspired from biological systems (2000)

The general approach involving the organization of polymers into micellar assemblies followed by stabilization through covalent intramicellar crosslinking of the assemblies has emerged as a powerful method for the production of well-defined nanostructured materials, having an amphiphilic core-shell morphology. When the covalent crosslinks are limited to the chain segments that compose the polymer micelle shell, then shell crosslinked knedel-like (SCK) nanostructures result. The shell composition dictates the interactions of the SCKs with external agents, forms a barrier layer over the core domain, and provides robust character to the nanoparticle. Because of the stability that the crosslinked shell provides, the core domain can be of dramatically different compositions and properties—glassy, fluidlike, and crystalline polymer chains have been employed for the core material and the effects that each contributes to the overall nanostructure properties have been examined. Most notably, the shell crosslinks allow for complete removal of the core to generate hollow (solvent-filled) nanoscale cagelike structures. © 2000 John Wiley & Sons, Inc. J Polym Sci A: Polym Chem 38: 1397–1407, 2000
Utilization of the Pleiotropy of a Peptidic Aptamer To Fabricate Heterogeneous Nanodot-Containing Multilayer Nanostructures (2006)

Peptide aptamers (=binders) against inorganic materials often show a capacity for mineralization of their target atoms; thus they are able to function both as binding molecules and as mediators for mineralization. Although the mechanisms underlying these two properties of peptide aptamers are not yet fully understood, they have been used separately to fabricate various nanostructures. Here, we present a novel method of nanofabrication, in which binding and mineralization by a peptide aptamer are alternately utilized to assemble multilayered nanostructures comprised of metal loaded cage proteins ornamented with Ti-binding peptides.
Tunable PDL of twisted-tilted fiber gratings (2003)

We fabricated highly tilted fiber gratings and demonstrated that the broad-band polarization-dependent loss (PDL) of the gratings may be tuned by twisting the fiber along the length of the grating. We show that the PDL for a given twist angle can be determined from a simple Jones matrix calculation which can also take into account birefringence on the PDL axis. We combine the twisted-tilted grating with a polarization controller to form a PDL compensator and use it to minimize the polarization-dependent responsivity of a nonlinear silicon avalanche photodiode.
Salivary binding antibodies induced by human immunodeficiency virus type 1 recombinant gp120 vaccine. The NIAID AIDS Vaccine Evaluation Group (1996)

Salivary binding antibodies induced by candidate human immunodeficiency virus type 1 (HIV-1) vaccines in healthy, HIV-1 uninfected volunteers were assessed in a clinical trial evaluating intramuscularly injected HIV-1MN recombinant gp120 (rgp120) vaccine alone or with HIV-1IIIB rgp120 vaccine. The two rgp120 vaccines induced envelope glycoprotein-specific immunoglobulin G (IgG) and IgA antibodies in whole saliva and serum.
c-jun and Egr-1 Participate in DNA Synthesis and Cell Survival in Response to Ionizing Radiation Exposure (1995)

Exposure of mammalian cells to ionizing radiation results in the induction of the immediate early genes, c-jun and Egr-1, which encode transcription factors implicated in cell growth as well as the cellular response to oxidative stress. We studied the role of these immediate early genes in cell cycle kinetics and cell survival following x-irradiation of clones containing inducible dominant negatives to c-jun and Egr-1. The dominant negative constructs to c-jun (delta 9) and Egr-1 (WT/Egr) prevented x-ray induction of transcription through the AP-1 and Egr binding sites, respectively. Twenty percent of confluent, serum-deprived SQ20B human tumor cells, normal fibroblasts, and fibroblasts from patients with ataxia telangiectasia entered S phase within 5 h of irradiation. Clones containing inducible delta 9 and WT/Egr dominant negative constructs demonstrated attenuation of the percentage of cells exiting G1 phase and reduced survival following irradiation. These data indicate that the dominant negatives to the stress-inducible immediate early genes Egr-1 and c-jun prevent the onset of S phase and reduce the survival of human cells exposed to ionizing radiation.
Basic fibroblast growth factor in human prostate cancer cells. (1992)

To increase our understanding of the potential role of basic fibroblast growth factor (bFGF) in malignant progression of prostate cancer, we determined the production of bFGF, the expression of FGF receptor (flg), and the response to exogenous bFGF in LNCaP, DU 145, and PC 3 cells. We observed that these three prostate cancer cell lines, which differed in their dependence on androgens for growth in vitro and in their in vivo behavior in nude mice, could be distinguished as follows: (a) androgen-sensitive LNCaP cells, which do not metastasize in nude mice, did not produce measurable amounts of bFGF, expressed small but measurable amounts of FGF receptor mRNA, and did respond to exogeneous bFGF; (b) androgen-insensitive, moderately metastatic DU 145 cells did produce measurable amounts of biologically active bFGF, expressed large amounts of FGF receptor mRNA, and responded to exogeneous bFGF and the heparin-binding fractions from DU 145 cell extracts; (c) androgen-insensitive and highly metastatic PC3 cells also produced measurable amounts of bFGF but did not demonstrate a growth response to either the heparin-binding fractions from PC3 cell extracts or exogenous bFGF, even though large amounts of FGF receptor mRNA were expressed in PC 3 cells. These results suggest the possibility that differences in production of, and response to, bFGF may be associated with different biological behavior.
A rigid and accurate piezo-stepper based on smooth learning hybrid force-position controlled clamping (2002)

Two new processes, ELID-grinding and high speed chipping, can combine high removal rates with high surface quality through a mechanism of sub-micron chip removal. For the successful application of these processes, ultra-precision positioning systems are needed. Classical solutions, based on traditional guideway technology, cannot meet the requirements of these new machining processes. The piezostepper solution presented in this paper can provide accurate motion, combined with high stiffness, through the use of piezoelectric actuators with high resolution. High passive stiffness is provided by integrating the driving, bearing and transmission functions. The same actuators can provide infinite active stiffness by referring the position of the positioning stage with respect to an absolute reference frame. In contrast with existing (position-controlled) piezo-steppers, this paper presents a way to provide smooth stepping by avoiding hammering through hybrid force-position controlled clamping and by rolling traction.
A comparison of dynamic fitness schedules for evolutionary design of amplifiers (2003)

High-level analog circuit design is a complex problem domain in which evolutionary search has recently produced encouraging results. However, little is known about how to best structure evolution far these tasks. The choices of circuit representation, fitness evaluation technique, and genetic operators clearly have a profound effect on the search process. In this paper, we examine fitness evaluation by comparing the effectiveness of four fitness schedules. Three fitness schedules are dynamic-the evaluation function changes over the course of the run, and one is static. Coevolutionary search is included, and we present a method of evaluating the problem population that is conducive to multiobjective optimization. Twenty-five runs of an analog amplifier design task using each fitness schedule are presented. The results indicate that solution quality is highest with static and coevolving fitness schedules as compared to the other two dynamic schedules. We discuss these results and offer two possible explanations for the observed behavior: retention of useful information, and alignment of problem difficulty with circuit proficiency.
Group Key Management Protocol (GKMP) Specification (1997)

This specification proposes a protocol to create grouped symmetric keys and distribute them amongst communicating peers. This protocol has the following advantages: 1) virtually invisible to operator, 2) no central key distribution site is needed, 3) only group members have the key, 4) sender or receiver oriented operation, 5) can make use of multicast communications protocols.
Mutans Streptococci Dose Response to Xylitol Chewing Gum (2006)

Xylitol is promoted in caries-preventive strategies, yet its effective dose range is unclear. This study determined the dose-response of mutans streptococci in plaque and unstimulated saliva to xylitol gum. Participants (n = 132) were randomized: controls (G1) (sorbitol/maltitol), or combinations giving xylitol 3.44 g/day (G2), 6.88 g/day (G3), or 10.32 g/day (G4). Groups chewed 3 pellets/4 times/d. Samples were taken at baseline, 5 wks, and 6 mos, and were cultured on modified Mitis Salivarius agar for mutans streptococci and on blood agar for total culturable flora. At 5 wks, mutans streptococci levels in plaque were 10x lower than baseline in G3 and G4 (P = 0.007/0.003). There were no differences in saliva. At 6 mos, mutans streptococci in plaque for G3 and G4 remained 10x lower than baseline (P = 0.007/0.04). Saliva for G3 and G4 was lower than baseline by 8 to 9x (P = 0.011/0.038). Xylitol at 6.44 g/day and 10.32 g/day reduces mutans streptococci in plaque at 5 wks, and in plaque and unstimulated saliva at 6 mos. A plateau effect is suggested between 6.44 g and 10.32 g xylitol/day.
Nitric oxide in plants: the history is just beginning (2001)

ABSTRACT Nitric oxide (NO) is a bioactive molecule that exerts a number of diverse activities in phylogenetically distant species, as well as opposing effects in related biological systems. It was firstly described in mammals as a major messenger in the cardiovascular, immune and nervous system, in which it plays regulatory, signalling, cytoprotective and cytotoxic effects ( Ignarro , Annual Review of Pharmacology and Toxicology 30, 535–560, 1990; Anbar , Experientia 51, 545–550, 1995). This versatility is mainly achieved through interactions with targets via either a redox or an additive chemistry (Stamler, Cell 78, 931–936, 1994). For this reason, metal‐ and thiol‐containing proteins serve as major target sites for NO: these include signalling proteins, receptors, enzymes, transcription factors and DNA, among others. Furthermore, NO is a small, highly diffusible molecule. It rapidly crosses biological membranes and triggers various different processes in a short period of time. In this context, NO can co‐ordinate and regulate cellular functions of microsomes and organelles such as mitochondria. The ubiquity of NO reactions, as well as the finding that the biochemical and molecular mechanisms underlying many physiological processes are well conserved between diverse species, have opened the exploration of NO chemistry in different organisms. Among these, plants were not the exception. The research in plants has been focused on three main fields: (i) the search for NO or any source of NO generation; (ii) the examination of the effects of NO upon exogenous treatments; and (iii) the search for the same molecules involved in NO‐sensitive transduction pathways as in animals (e.g. cGMP, Ca 2+ , calmodulin). As it is evident from this review, recent progress on NO functionality in plants has been impressive. With the use of biochemistry, molecular genetics and structural biology, together with classical physiological approaches, an explosion of new discoveries will surely begin. It is certainly a good time for plant biologists.
Effects of Thyroid Hormone on the Cardiovascular System (2004)

Increased or reduced action of thyroid hormone on certain molecular pathways in the heart and vasculature causes relevant cardiovascular derangements. It is well established that overt hyperthyroidism induces a hyperdynamic cardiovascular state (high cardiac output with low systemic vascular resistance), which is associated with a faster heart rate, enhanced left ventricular (LV) systolic and diastolic function, and increased prevalence of supraventricular tachyarrhythmias - namely, atrial fibrillation - whereas overt hypothyroidism is characterized by the opposite changes. However, whether changes in cardiac performance associated with overt thyroid dysfunction are due mainly to alterations of myocardial contractility or to loading conditions remains unclear. Extensive evidence indicates that the cardiovascular system responds to the minimal but persistent changes in circulating thyroid hormone levels, which are typical of individuals with subclinical thyroid dysfunction. Subclinical hyperthyroidism is associated with increased heart rate, atrial arrhythmias, increased LV mass, impaired ventricular relaxation, reduced exercise performance, and increased risk of cardiovascular mortality. Subclinical hypothyroidism is associated with impaired LV diastolic function and subtle systolic dysfunction and an enhanced risk for atherosclerosis and myocardial infarction. Because all cardiovascular abnormalities are reversed by restoration of euthyroidism ("subclinical hypothyroidism") or blunted by beta-blockade and L-thyroxine (L-T4) dose tailoring ("subclinical hyperthyroidism"), timely treatment is advisable in an attempt to avoid adverse cardiovascular effects. Interestingly, some data indicate that patients with acute and chronic cardiovascular disorders and those undergoing cardiac surgery may have altered peripheral thyroid hormone metabolism that, in turn, may contribute to altered cardiac function. Preliminary clinical investigations suggest that administration of thyroid hormone or its analogue 3,5-diiodothyropropionic acid greatly benefits these patients, highlighting the potential role of thyroid hormone treatment in patients with acute and chronic cardiovascular disease.