gebhart/patrepeval huggingface dataset:
Measurement of physical activity with accelerometers in children (2007)

The aim of this dissertation was to examine the use of accelerometers to measure physical activity (PA) in children with and without disabilities and address some of the current methodological issues involved with their use. Study I compared the activity level of children with Down syndrome (DS), children with intellectual disabilities without DS, and children without disability. Subjects wore ActiGraph accelerometers for seven days. There were no significant differences in PA level among the three groups of children as measured by mean ActiGraph counts per day. No difference was found between groups in the amount of time spent daily at different activity intensities. This study was the first to objectively assess PA in children with disabilities using accelerometers and demonstrated that accelerometers are feasible for PA measurement in children with cognitive impairments. Study II and Study III examined methodology issues with accelerometer data interpretation. Study II compared the accuracy of several count cut-point values used to define activity intensity ranges. Fifty-one children wore an ActiGraph at the hip while performing locomotor or free-play activities. Actual MET level, measured via indirect calorimetry, was compared to the predicted MET level from the different ActiGraph cut-points. Percent agreement between actual and estimated intensity level ranged from five to 100 percent between the different cut-point thresholds. These results quantified the differences in intensity classification seen with the different cut-points and demonstrated ActiGraph results extrapolated from different cut-points cannot be compared. Study III assessed the use of the count coefficient of variation (CV) to distinguish locomotor from non-locomotor activities in children. The accuracy of energy expenditure (EE) prediction using a dual-equation method based on count CV was compared to the accuracy of using a single prediction equation. The count CV distinguished between locomotor and non-locomotor activities quite well. Despite this, using the activity specific dual-equation method to predict EE did not improve accuracy compared to single prediction equations. No prediction equation tested adequately estimated EE from count values in this study. Due to the variable nature of movement and play in children, and metabolic and size differences, predicting EE from hip-mounted accelerometers is not ideal.
The Winners and Losers of War: Stock Market Effects of Armed Conflict, 1990-2000 (2004)

on Stock Markets ” that Schneider presented at the Centro de Estudios Avanzados en Ciencias Sociales on 28 November 2003. War opponents frequently assert that the economic interests of the defence industry and other sectors drive the warring parties into the use of force. This paper evaluates this claim indirectly and identifies with a refined version of “commercial liberalism ” the sectors that loose or gain during an intensification of the hostilities. Our time series analysis examines how the ups and downs in three conflicts (Iraq, Israel-Palestine, Ex-Yugoslavia) affected sub-indices of three major Western stock market indices (CAC, Dow Jones, FTSE) throughout the 1990s. GARCH (1, 1) models show in line with the distributional theory of war that the defence sector occasionally profits from an intensification of a conflict, while other sectors (aviation, hotels, leisure) lose under an escalation of the hostilities. Our model also accounts for the negative reactions of the “military-industrial complex ” to cooperative events that the analysis uncovers for some conflicts.
A review of the treatment options for Huntington?s disease (2004)

Huntington’s disease (HD) is an autosomal dominant, inherited, neuropsychiatric disease which gives rise to progressive motor, cognitive and behavioural symptoms. Its core pathology involves degeneration of the basal ganglia, in particular, the caudate and putamen, and is caused by a single autosomal gene coding for a mutated form of the protein, huntingtin. At the present time, the only treatment options available in HD are symptomatic. There are several substances available today for the treatment of chorea. Other neurological symptoms, such as dystonia, can be treated, but treatment is associated with a high risk of adverse events. Psychiatric symptoms, on the other hand, are often amenable to treatment and relief of these symptoms may provide significant improvement in quality of life.
Multiple Sclerosis (1982)

(First of Two Parts)The lesions of multiple sclerosis were probably described as early as 1838,1 but it was Charcot in 18682 who recognized the characteristic clinical and pathologic features of the disease. Since that time, the disorder has been studied extensively. Numerous distinguished, even renowned physicians and scientists have investigated various aspects of multiple sclerosis. Although much has been learned and many theories have emerged, the cause and pathogenesis of this disease remains unknown. No preventive measures or definitive therapies exist. The purpose of this article is to review the classic clinical and pathologic aspects of the disease and . . .
Dominant negative myostatin produces hypertrophy without hyperplasia in muscle (2000)

Myostatin, a TGF-beta family member, is a negative regulator of muscle growth. Here, we generated transgenic mice that expressed myostatin mutated at its cleavage site under the control of a muscle specific promoter creating a dominant negative myostatin. These mice exhibited a significant (20-35%) increase in muscle mass that resulted from myofiber hypertrophy and not from myofiber hyperplasia. We also evaluated the role of myostatin in muscle degenerative states, such as muscular dystrophy, and found significant downregulation of myostatin. Thus, further inhibition of myostatin may permit increased muscle growth in muscle degenerative disorders.
Development of an Fc-Enhanced Anti–B7-H3 Monoclonal Antibody with Potent Antitumor Activity (2012)

This data supports evaluation of MGA271 clinical utility in B7-H3-expressing cancer, while validating a combination of a nontarget biased approach of intact cell immunizations and immunohistochemistry to identify novel cancer antigens with Fc-based mAb engineering to enable potent antitumor activity.
Inhibition of LPS‐induced nitric oxide and TNF‐α production by α‐lipoic acid in rat Kupffer cells and in RAW 264.7 murine macrophages (2002)

The activation of Kupffer cells represents a central mechanism of inflammatory liver injury involving the production of two important inflammatory mediators, nitric oxide and TNF-alpha. The aim of this study was to investigate the effect of the hepatoprotective compound alpha-lipoic acid (thioctic acid) on the production of nitric oxide and TNF-alpha in isolated rat Kupffer cells and RAW 264.7 macrophages. Isolated rat Kupffer cells or RAW 264.7 were either untreated, treated with alpha-lipoic acid (500 micro g/mL), or activated with 1 micro g/mL of lipopolysaccharide in the presence or absence of alpha-lipoic acid (0.2-500 micro g/mL). After 20 h the accumulation of nitrite was measured by the Griess assay. Tumour necrosis factor-alpha secretion was quantified after 4 h by L929 bioassay. Cell viability was determined by mitochondrial reduction of 3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyl tetrazolium bromide (MTT) test, nuclear factor-kappaB (NF-kappaB) and activator protein-1 (AP-1) DNA binding activity by gelshift assays. Treatment of Kupffer cells and RAW 264.7 with alpha-lipoic acid alone had no effect on basal nitric oxide production. However, alpha-lipoic acid significantly inhibited lipopolysaccharide-induced nitrite accumulation. alpha-Lipoic acid did not alter basal TNF-alpha secretion in Kupffer cells, whereas it significantly inhibited lipopolysaccharide-induced TNF-alpha production. alpha-Lipoic acid attenuated the activation of nuclear factor-kappaB and AP-1, two transcription factors pivotal in induction of inducible nitric oxide synthase and TNF-alpha. alpha-Lipoic acid significantly inhibits lipopolysaccharide-induced macrophage production of nitric oxide and TNF-alpha via an attenuated activation of NF-kappaB and activator protein-1. The reduced production of nitric oxide and TNF-alpha in Kupffer cells may be involved in the hepatoprotective action conveyed by alpha-lipoic acid.
Intestinal Subepithelial Myofibroblasts Support in vitro and in vivo Growth of Human Small Intestinal Epithelium (2011)

The intestinal crypt-niche interaction is thought to be essential to the function, maintenance, and proliferation of progenitor stem cells found at the bases of intestinal crypts. These stem cells are constantly renewing the intestinal epithelium by sending differentiated cells from the base of the crypts of Lieberkühn to the villus tips where they slough off into the intestinal lumen. The intestinal niche consists of various cell types, extracellular matrix, and growth factors and surrounds the intestinal progenitor cells. There have recently been advances in the understanding of the interactions that regulate the behavior of the intestinal epithelium and there is great interest in methods for isolating and expanding viable intestinal epithelium. However, there is no method to maintain primary human small intestinal epithelium in culture over a prolonged period of time. Similarly no method has been published that describes isolation and support of human intestinal epithelium in an in vivo model. We describe a technique to isolate and maintain human small intestinal epithelium in vitro from surgical specimens. We also describe a novel method to maintain human intestinal epithelium subcutaneously in a mouse model for a prolonged period of time. Our methods require various growth factors and the intimate interaction between intestinal sub-epithelial myofibroblasts (ISEMFs) and the intestinal epithelial cells to support the epithelial in vitro and in vivo growth. Absence of these myofibroblasts precluded successful maintenance of epithelial cell formation and proliferation beyond just a few days, even in the presence of supportive growth factors. We believe that the methods described here can be used to explore the molecular basis of human intestinal stem cell support, maintenance, and growth.
Message from the CE : Water Institute of Southern Africa : CE's comment (2006)

This promotional issue of the new WISA magazine called Water&Sanitation Africa has been made possible by the generosity of the WISA patron members who have sponsored the printing costs of the magazine and the publisher, 3S Media, which is bearing the editorial costs of the magazine. It is testimony to the speed and efficiency of the WISA structures, such as the executive board and 3S Media, that this publishing arrangement has been concluded and a promotional issue of Water&Sanitation Africa has been created and printed within three months of the decision to publish WISA's own magazine.
Compounds Contributing to the Odor of Aqueous Slurries of Soy Protein Concentrate (2001)

ABSTRACT: Gas chromatography olfactometry/mass spectrometry (GCO/MS) studies on static and concentrated headspace of the aqueous slurries from soy protein concentrate (SPC) revealed acetaldehyde, methanethiol, hexanal, dimethyl trisulfide (DMTS), and 2‐pentyl furan as the most odorous volatiles. Further aroma extract dilution analysis (AEDA) of the volatile extracts identified the following as the odorous substances: hexanal, 2‐heptanone, octanal, 2‐octanone, 1‐octen‐3‐one, DMTS, 3‐octen‐2‐one, 2‐decanone, benzaldehyde, 2‐pentyl pyridine and trans, trans ‐2,4‐ nonadienal, along with several unidentified odorants. Methanethiol and acetaldehyde, which have low boiling points, were not detected by AEDA, however. This is the first time that acetaldehyde, methanethiol, and dimethyl trisulfide have been identified as primary odorants in SPC.
The synchronous data flow programming language LUSTRE (1991)

The authors describe LUSTRE, a data flow synchronous language designed for programming reactive systems-such as automatic control and monitoring systems-as well as for describing hardware. The data flow aspect of LUSTRE makes it very close to usual description tools in these domains (block-diagrams, networks of operators, dynamical sample-systems, etc.), and its synchronous interpretation makes it well suited for handling time in programs. Moreover, this synchronous interpretation allows it to be compiled into an efficient sequential program. The LUSTRE formalism is very similar to temporal logics. This allows the language to be used for both writing programs and expressing program properties, which results in an original program verification methodology.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Expression profile reveals novel prognostic biomarkers in hepatocellular carcinoma (2010)

The purpose of this study was to identify and validate novel prognostic biomarkers in human hepatocellular carcinoma (HCC). We analyzed gene expression profiles not only between 33 HCCs and their corresponding noncancerous liver tissues, but also between 25 HCCs and pooled normal liver tissues using cDNA microarrays containing 12800 genes. Functional analysis of differentially expressed genes involved in HCC carcinogenesis and tumor progression revealed that up-regulated and down-regulated genes are mainly associated with cell cycle and immune response, respectively. We detected two regions of cytogenetic changes only in poorly-differentiated HCCs using the expression data. We identified a 9-gene expression signature, which was able to predict differentiation degree and survival of HCC samples. Among the 9 most discriminatory genes, minichromosome maintenance protein 2 (MCM2), a significantly up-regulated gene involved in cell cycle pathway, was selected for further analysis. Overexpression of MCM2 protein related to poor-differentiation in HCC was validated using tissue microarray-based immunohistochemistry containing 96 HCCs. Our studies show that the 9-gene expression signature may serve as promising prognostic biomarkers involved in hepatocarcinogenesis and tumor progression.
Infectious Bronchitis Virus as a Vector for the Expression of Heterologous Genes (2013)

The avian coronavirus infectious bronchitis virus (IBV) is the causative agent of the respiratory disease infectious bronchitis of domestic fowl, and is controlled by routine vaccination. To explore the potential use of IBV as a vaccine vector a reverse genetics system was utilised to generate infectious recombinant IBVs (rIBVs) expressing the reporter genes enhanced green fluorescent protein (eGFP) or humanised Renilla luciferase (hRluc). Infectious rIBVs were obtained following the replacement of Gene 5 or the intergenic region (IR) with eGFP or hRluc, or the replacement of ORFs 3a and 3b with hRluc. The replacement of Gene 5 with an IBV codon-optimised version of the hRluc gene also resulted in successful rescue of infectious rIBV. Reporter gene expression was confirmed by fluorescence microscopy, or luciferase activity assays, for all successfully rescued rIBVs following infection of primary chick kidney (CK) cells. The genetic stability of rIBVs was analysed by serial passage on CK cells. Recombinant IBV stability varied depending on the genome region being replaced, with the reporter genes maintained up to at least passage 8 (P8) following replacement of Gene 5, P7 for replacement of the IR and P5 for replacement of ORFs 3a and 3b. Codon-optimisation of the hRluc gene, when replacing Gene 5, resulted in an increase in genome stability, with hRluc expression stable up to P10 compared to P8 for standard hRluc. Repeated passaging of rIBVs expressing hRluc at an MOI of 0.01 demonstrated an increase in stability, with hRluc expression stable up to at least P12 following the replacement of Gene 5. This study has demonstrated that heterologous genes can be incorporated into, and expressed from a range of IBV genome locations and that replacement of accessory Gene 5 offers a promising target for realising the potential of IBV as a vaccine vector for other avian pathogens.
Mechanistic Analysis of a Suicide Inactivator of Histone Demethylase LSD1 (2007)

Lysine-specific demethylase 1 (LSD1) is a transcriptional repressor and a flavin-dependent amine oxidase that is responsible for the removal of methyl from lysine 4 of histone H3. In this study, we characterize the mechanism and scope of LSD1 inhibition by a propargylamine-derivatized histone H3 substrate (1). Unlike aziridinyl and cyclopropylamine-derivatized histone H3 peptide substrate analogues, compound 1 appears to covalently modify and irreversibly inactivate LSD1 with high potency. Accompanying this inactivation is a spectroscopic change, which shifts the absorbance maximum to 392 nm. Spectral changes associated with the 1-LSD1 complex and reactivity to decreased pH and sodium borohydride treatment were suggestive of a structure involving a flavin-linked inhibitor conjugate between N5 of the flavin and the terminal carbon of the inhibitor. Using a 13C-labeled inhibitor, NMR analysis of the 1-flavin conjugate was consistent with this structural assignment. Kinetic analysis of the spectroscopic shift induced by 1 showed that the flavin adduct formed in a reaction with kinetic constants similar to those of the LSD1 inactivation process. Taken together, these data support a mechanism of LSD1 inactivation by 1 involving amine oxidation followed by Michael addition to the propargylic imine. We further examined the potential for a biotinylated analogue of 1 (1-Btn) to be used as a tool in affinity pulldown experiments. Using 1-Btn, it was feasible to selectively pull down spiked and endogenous LSD1 from HeLa cell nuclear extracts, setting the stage for activity-based demethylase proteomics.
ASC Speck Formation as a Readout for Inflammasome Activation (2013)

All inflammasomes require the adapter protein apoptosis associated speck-like protein containing a CARD (ASC) for the activation of caspase-1. After inflammasome activation, ASC assembles into a large protein complex, which is termed "speck". ASC specks can be observed as they reach a size of around 1 μm and in most cells only one speck forms upon inflammasome activation. Hence, ASC speck formation can be used as a simple upstream readout for inflammasome activation. Here, we describe a method for analyzing inflammasome activation by ASC speck visualization. First, we describe the generation of a clonal inflammasome reporter macrophage cell line overexpressing fluorescently tagged ASC. We then discuss stimulation conditions and the microscopic evaluation of ASC speck formation.
Interferon alfa, infectious virus, and virus antigen secretion in respiratory syncytial virus infections of graded severity. (1989)

Interferon alfa was measured by an immunoradiometric assay in the nasopharyngeal secretions of a group of infants admitted to hospital with respiratory syncytial virus infection. Virus replication in the upper respiratory tract was assessed by infectivity assay and by an enzyme linked immunoadsorbent assay for the viral fusion protein on the same nasopharyngeal secretions. All infants were examined daily while in hospital and allocated a score based upon a subjective assessment of the severity of their illness. There was no significant correlation between interferon, virus, or fusion (F) protein secretion and severity of illness or age of infant. It is concluded that poor interferon alfa secretion does not underly the susceptibility of infants to severe infections with this virus.
Robot-Aided Assessment of Wrist Proprioception (2015)

We currently lack established norm data on the proprioceptive acuity of the wrist to establish direct validity. However, the magnitude of our reported thresholds is physiological, plausible, and well in line with available threshold data obtained at the elbow joint. Moreover, system has high resolution and is sensitive enough to detect small differences in acuity. Finally, the system produces reliable data over repeated testing.
Poly(vinyl alcohol) hydrogels for synthetic articular cartilage material (1973)

Abstract As part of a program to develop a synthetic articular cartilage material for use in reconstructive joint surgery, this paper is concerned with the desiderata for such a material and with the properties of poly (vinyl alcohol) hydrogels reinforced by crystallinity as developed for this purpose. Reference is further made to the ultimate preparation of cationic PVA hydrogels to provide the low‐friction lubrication necessary in a cartilage prosthesis when in contact with natural synovial fluid.
Structure-Based Design of Macrocyclic Factor XIa Inhibitors: Discovery of the Macrocyclic Amide Linker (2017)

A novel series of macrocyclic FXIa inhibitors was designed based on our lead acyclic phenyl imidazole chemotype. Our initial macrocycles, which were double-digit nanomolar FXIa inhibitors, were further optimized with assistance from utilization of structure-based drug design and ligand bound X-ray crystal structures. This effort resulted in the discovery of a macrocyclic amide linker which was found to form a key hydrogen bond with the carbonyl of Leu41 in the FXIa active site, resulting in potent FXIa inhibitors. The macrocyclic FXIa series, exemplified by compound 16, had a FXIa K<sub>i</sub> = 0.16 nM with potent anticoagulant activity in an in vitro clotting assay (aPTT EC<sub>1.5x</sub> = 0.27 μM) and excellent selectivity against the relevant blood coagulation enzymes.
Selective Enrichment of Thiophosphorylated Polypeptides as a Tool for the Analysis of Protein Phosphorylation (2003)

A chemoselective alkylation method is described for the isolation and subsequent identification of thiophosphorylated peptides/proteins. The method involves thiophosphorylation of proteins using adenosine 5'-O-(thiotriphosphate) (ATPgammaS) followed by selective in situ alkylation of the newly thiophosphorylated proteins resulting in a stable covalent bond. The chemoselective alkylation exploits the relatively high nucleophilicity at low pH of the sulfur in thiophosphate residues, whereas the nucleophilicities of phosphates, amines, and other functionality of amino acids are negligible or significantly suppressed. Modified alkylation reagents linked to biotin or solid supports (e.g. glass or Sepharose beads) with or without a photocleavable linker facilitate the isolation of the thiophosphorylated peptide/proteins. This approach is demonstrated through the localization of phosphorylation sites on myosin regulatory light chain. We anticipate that this technique will be useful for isolation and subsequent identification of newly thiophosphorylated proteins, produced either in vivo or in vitro, thus facilitating the dissection of protein phosphorylation networks.