gebhart/patrepeval huggingface dataset:
Extended bit-filling and LDPC code design (2002)

Campello, Modha and Rajagopalan (see Proc. Int. Conf. Communications (ICC), Helsinki, Finland, 2001) proposed a simple-to-implement heuristic, namely, bit-filling, for constructing high rate and high girth LDPC codes. In the present work, we extend bit-filling, and demonstrate that the extended algorithm produces better codes, that is, codes with higher rate/girth and good bit error rate performance. We demonstrate the positive effect of girth on bit error rate performance.
Two doses of sclerostin antibody in cynomolgus monkeys increases bone formation, bone mineral density, and bone strength (2010)

The development of bone-rebuilding anabolic agents for treating bone-related conditions has been a long-standing goal. Genetic studies in humans and mice have shown that the secreted protein sclerostin is a key negative regulator of bone formation. More recently, administration of sclerostin-neutralizing monoclonal antibodies in rodent studies has shown that pharmacologic inhibition of sclerostin results in increased bone formation, bone mass, and bone strength. To explore the effects of sclerostin inhibition in primates, we administered a humanized sclerostin-neutralizing monoclonal antibody (Scl-AbIV) to gonad-intact female cynomolgus monkeys. Two once-monthly subcutaneous injections of Scl-AbIV were administered at three dose levels (3, 10, and 30 mg/kg), with study termination at 2 months. Scl-AbIV treatment had clear anabolic effects, with marked dose-dependent increases in bone formation on trabecular, periosteal, endocortical, and intracortical surfaces. Bone densitometry showed that the increases in bone formation with Scl-AbIV treatment resulted in significant increases in bone mineral content (BMC) and/or bone mineral density (BMD) at several skeletal sites (ie, femoral neck, radial metaphysis, and tibial metaphysis). These increases, expressed as percent changes from baseline were 11 to 29 percentage points higher than those found in the vehicle-treated group. Additionally, significant increases in trabecular thickness and bone strength were found at the lumbar vertebrae in the highest-dose group. Taken together, the marked bone-building effects achieved in this short-term monkey study suggest that sclerostin inhibition represents a promising new therapeutic approach for medical conditions where increases in bone formation might be desirable, such as in fracture healing and osteoporosis.
LOCAL INJECTION TREATMENT OF TENNIS ELBOW—HYDROCORTISONE, TRIAMCINOLONE AND LIGNOCAINE COMPARED (1991)

Corticosteroid injections are the mainstay of treating tennis elbow even though their effectiveness has not been well established by controlled studies. A survey of consultant rheumatologists confirmed a widespread preference for this treatment but they varied in their choice of steroid dose and preparation. We examined the value of some practices by comparing local injections of 2 ml 1% lignocaine with either 10 mg triamcinolone or 25 mg hydrocortisone made up to 2 ml with 1% lignocaine (Study 1). The investigation was conducted double blind. Within the first 8 weeks, pain relief was greater for triamcinolone than hydrocortisone although the differences were not statistically significant. The response to both steroid preparations was significantly better than for lignocaine up to this point but at 24 weeks, the degrees of improvement were similar for all three groups and many patients still had pain. Relapse was common. In a separate but similarly designed study, triamcinolone 10 mg was compared with 20 mg of the same agent. Improvements of pain were similar and followed the same time scale. Post-injection worsening of pain occurred in approximately half of all steroid treated patients in both studies and this was sometimes severe and persistent. It was less frequent amongst those given lignocaine alone. Skin atrophy was reported in all groups but was more frequent amongst those given triamcinolone in Study 1. In conclusion, more rapid relief of symptoms was achieved with 10 mg triamcinolone than with 25 mg hydrocortisone or lignocaine alone and there was less needed to repeat injections. Results obtained with 20 mg triamcinolone were similar to those of the smaller dose.(ABSTRACT TRUNCATED AT 250 WORDS)
Binding of cobalamin and cobinamide to transcobalamin from bovine milk (1995)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTBinding of cobalamin and cobinamide to transcobalamin from bovine milkSergey N. Fedosov, Torben E. Petersen, and Ebba NexoCite this: Biochemistry 1995, 34, 49, 16082–16087Publication Date (Print):December 12, 1995Publication History Published online1 May 2002Published inissue 12 December 1995https://pubs.acs.org/doi/10.1021/bi00049a023https://doi.org/10.1021/bi00049a023research-articleACS PublicationsRequest reuse permissionsArticle Views147Altmetric-Citations18LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InRedditEmail Other access optionsGet e-Alertsclose Get e-Alerts
Curcumin-Induced Apoptosis in Scleroderma Lung Fibroblasts (2004)

Scleroderma, a disease involving excessive collagen deposition, can be studied using fibroblasts cultured from affected tissues. We find that curcumin, the active component of the spice turmeric, causes apoptosis in scleroderma lung fibroblasts (SLF), but not in normal lung fibroblasts (NLF). This effect is likely to be linked to the fact that although curcumin induces the expression of the phase 2 detoxification enzymes heme oxygenase 1 and glutathione S-transferase P1 (GST P1) in NLF, SLF are deficient in these enzymes, particularly after curcumin treatment. The sensitivity of cells to curcumin-induced apoptosis and the expression of GST P1 (but not heme oxygenase 1) are regulated by the epsilon isoform of protein kinase C (PKCepsilon). SLF, which contain less PKCepsilon and less GST P1 than NLF, become less sensitive to curcumin-induced apoptosis and express higher levels of GST P1 when transfected with wild-type PKCepsilon, but not with dominant-negative PKCepsilon. Conversely, NLF become sensitive to curcumin-induced apoptosis and express lower levels of GST P1 when PKCepsilon expression or function is inhibited. The subcellular distribution of PKCepsilon also differs in NLF and SLF. PKCepsilon is predominantly nuclear or perinuclear in NLF but is associated with stress fibers in SLF. Just as PKCepsilon levels are lower in SLF than in NLF in vitro, PKCepsilon expression is decreased in fibrotic lung tissue in vivo. In summary, our results suggest that a signaling pathway involving PKCepsilon and phase 2 detoxification enzymes provides protection against curcumin-induced apoptosis in NLF and is defective in SLF. These observations suggest that curcumin may have therapeutic value in treating scleroderma, just as it has already been shown to protect rats from lung fibrosis induced by a variety of agents.
Point-of-care quantification of blood-borne filarial parasites with a mobile phone microscope (2015)

Parasitic helminths cause debilitating diseases that affect millions of people in primarily low-resource settings. Efforts to eliminate onchocerciasis and lymphatic filariasis in Central Africa through mass drug administration have been suspended because of ivermectin-associated serious adverse events, including death, in patients infected with the filarial parasite Loa loa. To safely administer ivermectin for onchocerciasis or lymphatic filariasis in regions co-endemic with L. loa, a strategy termed "test and (not) treat" has been proposed whereby those with high levels of L. loa microfilariae (>30,000/ml) that put them at risk for life-threatening serious adverse events are identified and excluded from mass drug administration. To enable this, we developed a mobile phone-based video microscope that automatically quantifies L. loa microfilariae in whole blood loaded directly into a small glass capillary from a fingerprick without the need for conventional sample preparation or staining. This point-of-care device automatically captures and analyzes videos of microfilarial motion in whole blood using motorized sample scanning and onboard motion detection, minimizing input from health care workers and providing a quantification of microfilariae per milliliter of whole blood in under 2 min. To validate performance and usability of the mobile phone microscope, we tested 33 potentially Loa-infected patients in Cameroon and confirmed that automated counts correlated with manual thick smear counts (94% specificity; 100% sensitivity). Use of this technology to exclude patients from ivermectin-based treatment at the point of care in Loa-endemic regions would allow resumption/expansion of mass drug administration programs for onchocerciasis and lymphatic filariasis in Central Africa.
Interaction of Substrate Analogues with Escherichia coli DNA-Dependent RNA Polymerase (1976)

The inhibition of RNA polymerase with ATP and UTP analogues modified in the phosphate and ribose moieties has been investigated. 1. Modification of the terminal phosphate with a loss of the negative charge [adenosine 5'-(3-O-methyl)triphosphate, Ki = 1.75 mM] substantially weakens the binding ability of these analogues to the enzyme whereas modification with retention of the charge is not so detrimental [adenosine tetraphosphate, Ki = 0.17 mM]. 2. 2'-Modified analogues are only weak competitive inhibitors [2'-amino-2'-deoxyadenosine 5'-triphosphate, Ki = 2.3 mM] of their corresponding substrates [ATP, Km = 0.07 mM] whereas 3'-modified analogues are extremely potent in their inhibition [3'-amino-3'-deoxyadenosine 5'-triphosphate, Ki = 2.3 muM]. 3. A difference was observed in the inhibition of the elongation step of RNA polymerase by ATP and UTP analogues. Thus ATP analogues showed a strong binding to the CT form of the poly[d(A-T)] ternary complex and only a weak binding to the CA form. UTP analogues, on the other hand, showed a similar binding to both forms of the complex.
A cell epigenotype specific model for the correction of brain cellular heterogeneity bias and its application to age, brain region and major depression (2013)

Brain cellular heterogeneity may bias cell type specific DNA methylation patterns, influencing findings in psychiatric epigenetic studies. We performed fluorescence activated cell sorting (FACS) of neuronal nuclei and Illumina HM450 DNA methylation profiling in post mortem frontal cortex of 29 major depression and 29 matched controls. We identify genomic features and ontologies enriched for cell type specific epigenetic variation. Using the top cell epigenotype specific (CETS) marks, we generated a publically available R package, "CETS," capable of quantifying neuronal proportions and generating in silico neuronal profiles from DNA methylation data. We demonstrate a significant overlap in major depression DNA methylation associations between FACS separated and CETS model generated neuronal profiles relative to bulk profiles. CETS derived neuronal proportions correlated significantly with age in the frontal cortex and cerebellum and accounted for epigenetic variation between brain regions. CETS based control of cellular heterogeneity will enable more robust hypothesis testing in the brain.
Coated Glass and Vicryl Microfibers as Artificial Axons (2006)

The complex interactions that occur between oligodendrocytes and axons during the process of central nervous system myelination and remyelination remain unclear. Elucidation of the cell-biological and -biochemical mechanisms supporting myelin production and elaboration requires a robust in vitro system that recapitulates the relationship between axons and oligodendrocytes in a manner that is open to molecular dissection. We provide evidence for an artificial axon culture system in which we observed oligodendrocytes extending large plasma membrane projections that frequently completely ensheathed fibers coated with a variety of extracellular matrix molecules. These membrane projections varied in extent and thickness depending upon the substrate and upon the diameter of the coated fiber. Matrigel-coated glass microfibers were found to support the development of thick membrane sheaths that extended for hundreds of microns and exhibited many features suggestive of the potential for true myelin deposition. Likewise, Matrigel-coated Vicryl fibers supported plasma membrane extensions that covered extremely large surface areas and occasionally wrapped the coated Vicryl fibers in more than one membrane layer. Our findings suggest that the deposition of molecular cues onto glass or polymer fibers either via adsorption or chemical modification may be a useful tool for the discovery or validation of axonal factors critical for myelination and remyelination. Herein, we provide evidence that polyglactin 910 and glass microfibers coated with adhesion factors may provide a reasonable system for the in vitro analysis of myelination, and may eventually serve a role in engineering artificial systems for neural repair.
Orchestrated Transcription of Key Pathways in Arabidopsis by the Circadian Clock (2000)

Like most organisms, plants have endogenous biological clocks that coordinate internal events with the external environment. We used high-density oligonucleotide microarrays to examine gene expression in Arabidopsis and found that 6% of the more than 8000 genes on the array exhibited circadian changes in steady-state messenger RNA levels. Clusters of circadian-regulated genes were found in pathways involved in plant responses to light and other key metabolic pathways. Computational analysis of cycling genes allowed the identification of a highly conserved promoter motif that we found to be required for circadian control of gene expression. Our study presents a comprehensive view of the temporal compartmentalization of physiological pathways by the circadian clock in a eukaryote.
ChemInform Abstract: Comprehensive Survey of Combinatorial Library Synthesis: 1999 (2001)

Abstract ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 100 leading journals. To access a ChemInform Abstract of an article which was published elsewhere, please select a “Full Text” option. The original article is trackable via the “References” option.
A local Wnt-3a signal is required for development of the mammalian hippocampus (2000)

The mechanisms that regulate patterning and growth of the developing cerebral cortex remain unclear. Suggesting a role for Wnt signaling in these processes, multiple Wnt genes are expressed in selective patterns in the embryonic cortex. We have examined the role of Wnt-3a signaling at the caudomedial margin of the developing cerebral cortex, the site of hippocampal development. We show that Wnt-3a acts locally to regulate the expansion of the caudomedial cortex, from which the hippocampus develops. In mice lacking Wnt-3a, caudomedial cortical progenitor cells appear to be specified normally, but then underproliferate. By mid-gestation, the hippocampus is missing or represented by tiny populations of residual hippocampal cells. Thus, Wnt-3a signaling is crucial for the normal growth of the hippocampus. We suggest that the coordination of growth with patterning may be a general role for Wnts during vertebrate development.
Efficient transfer of genetic material into mammalian cells using Starburst polyamidoamine dendrimers. (1996)

Starburst polyamidoamine dendrimers are a new class of synthetic polymers with unique structural and physical characteristics. These polymers were investigated for the ability to bind DNA and enhance DNA transfer and expression in a variety of mammalian cell lines. Twenty different types of polyamidoamine dendrimers were synthesized, and the polymer structure was confirmed using well-defined analytical techniques. The efficiency of plasmid DNA transfection using dendrimers was examined using two reporter gene systems: firefly luciferase and bacterial beta-galactosidase. The transfections were performed using various dendrimers, and levels of expression of the reporter protein were determined. Highly efficient transfection of a broad range of eukaryotic cells and cell lines was achieved with minimal cytotoxicity using the DNA/dendrimer complexes. However, the ability to transfect cells was restricted to certain types of dendrimers and in some situations required the presence of additional compounds, such as DEAE-dextran, that appeared to alter the nature of the complex. A few cell lines demonstrated enhanced transfection with the addition of chloroquine, indicating endosomal localization of the complexes. The capability of a dendrimer to transfect cells appeared to depend on the size, shape, and number of primary amino groups on the surface of the polymer. However, the specific dendrimer most efficient in achieving transfection varied between different types of cells. These studies demonstrate that Starburst dendrimers can transfect a wide variety of cell types in vitro and offer an efficient method for producing permanently transfected cell lines.
Effects of current limitation through the dielectric in atmospheric pressure glows in helium (2004)

The influence of the dielectric barrier on the discharge regime of a uniform atmospheric pressure glow discharge is studied through fast, time-resolved imaging of the discharge optical emission and by a one-dimensional fluid model. The experiments show that the discharge regime can be adjusted over a wide range from a glow-like regime with a pronounced Faraday dark space and positive column to a Townsend-like discharge regime in which those features are absent. The determining factor for the discharge regime is the current limitation through the dielectric. Results of the one-dimensional fluid model confirm this observation. The fluid model also indicates that metastable helium atoms generated during a discharge pulse contribute significantly to the pre-ionization of the gas before the next breakdown through Penning ionization of nitrogen impurities.
Purification of the migration stimulating factor produced by fetal and breast cancer patient fibroblasts. (1989)

We have previously shown that (i) human skin fibroblasts of fetal and adult origin display distinctive migratory phenotypes, (ii) this difference in cell behavior results from the production of a soluble "migration stimulating factor" (MSF) by fetal cells, and (iii) skin fibroblasts from breast cancer patients commonly resemble fetal fibroblasts both in migratory phenotype and in production of MSF. Data are now presented indicating that MSF present in the conditioned medium of fetal and cancer patient fibroblasts is precipitated at 10% saturation ammonium sulfate and binds to heparin and cation-exchange resins. Based on this information, we have devised a scheme for the purification of MSF involving the sequential application of ammonium sulfate precipitation, heparin affinity, gel filtration, and reverse-phase chromatography. Purified MSF has an estimated molecular mass of 70 kDa; amino acid analysis reveals a relatively high level of proline (13.34 residues per 100). Our results further suggest that skin fibroblasts from breast cancer patients produce an additional factor with migration stimulating activity; this factor is precipitated at higher concentrations of ammonium sulfate and binds to anion-exchange resins. We have previously discussed the possible direct involvement of fetal-like fibroblasts in cancer pathogenesis. The availability of MSF obtained from cancer patient fibroblasts provides a potential means with which to examine the complex cellular interactions contributing to this process as well as develop a screening regime for identifying individuals at elevated risk of developing cancer.
[Cardiovascular risk in patients with chronic renal failure. Patients in renal replacement therapy]. (2002)

Dialysis patients constitute a high-risk subset of patients for developing cardiovascular disease, which accounts for nearly 50% of deaths. After stratification for age, race and gender, cardiovascular mortality is 10-20 times higher in dialysis patients than in the general population. Cardiovascular disease in this population cannot be fully explained by the high prevalence of classical cardiovascular risk factors (age, hypertension, diabetes, hyperlipidemia, smoking, etc.). Thus, the involvement of "new" cardiovascular risk factors (hyperhomocysteinemia, hyperfibrinogenemia, high lipoprotein (a) levels, oxidative stress, inflammation, etc.), and uremia-related factors (anemia, impaired calcium-phosphorus metabolism, hyperparathyroidism, accumulation of endogenous inhibitors of nitric oxide synthesis, etc.) has been also invoked to play a role in the increased cardiovascular risk in these patients. Endothelial dysfunction is the initial event in the development of atherosclerosis. Uremic patients exhibit an endothelial dysfunction, even before starting dialysis, which persists o is even aggravated under dialysis treatment. Uremic patients must be considered at high risk of developing cardiovascular disease. Thus cardiovascular risk factors in these patients should be managed early, aggressive and multifactorially in order to reduce their high cardiovascular morbidity and mortality.
Enantioselective Synthesis of Protease Inhibitors and AntiHIV Agents (2001)

Part 1: A highly enantio-and diastereoselective Ireland-Claisen rearrangement of chiral C3(acyloxy)-vinyl silanes for the synthesis of anti-disubstituted succinic acid, an important intermediate for matrix metalloprotease inhibitors, has been developed (enantio-and anti/syn selectivities up to 95% and 38/1). The diastereoselectivity of this reaction was found to be sensitive to remote hydroxyl protecting groups, for example, with-OMOM group, the anti/syn ratio was 19/1, while with-OTBDMS, the ratio was 38/1. The resultant Ireland-Claisen rearrangement product was applied to the synthesis of macrocyclic MMP inhibitors, such as SL 422.