gebhart/patrepeval huggingface dataset:
O2‐07‐04: Copy number polymorphism at chromosome 19 locus associated with late‐onset Alzheimer's disease (2010)

Late onset Alzheimer disease (LOAD) has a clear genetic risk component. However, known common variants explain less than half of the heritable component of LOAD. One alternate hypothesis that has received little attention is that copy number and structural variants such as gene duplication and deletion events could contribute to LOAD risk. To test this hypothesis we have performed copy number analysis on 1729 samples that have been genotyped using genome-wide platforms Genome-wide genotyping was performed on 882 Alzheimer cases and 847 cognitive controls using the Illumina 550k HumanHap beadchip and the Illumina 1M beadchip; data were processed using the BeadStudio software. Allelic intensities were exported from BeadStudio and CNVs were called using the PennCNV software package. Additionally, as confirmation the cnvPartition algorithm, as implemented in BeadStudio, was also used to call CNVs. Association was tested using logistic regression using covariates to account for potential population substructure. CNVs associated with disease and confirmed by both beadchips and calling algorithms are being tested using quantitative PCR to confirm their presence. There were seventeen CNV loci associated with LOAD on both platforms. P-values ranged from 0.05 to 0.0005. Of these, there were seven loci with the same type of copy variation (deletion or duplication) detected on both beadchips and detected with association using both PennCNV and cnvPartition. These seven loci are being genotyped using quantitative PCR; genotyping has already been completed for two of these loci. The qPCR has confirmed both the presence and association of loci on chromosomes 19q and 1p. The chromosome 19q locus (48 Mb) shows duplications with greater frequency among Alzheimer cases (p = 0.002). The analysis at the chromosome 1p locus (10.5Mb) also confirms duplications at the locus, and confirms their association with LOAD (p = 0.04). A complete analysis of all loci will be presented. These results confirm that copy number variations such as duplications likely contribute to LOAD risk. Allelic intensities generated from genotyping arrays are useful for copy-number but should be confirmed through other molecular methods such as quantitative PCR. More importantly, this analysis provides novel targets for functional assessment and additional genetic association studies.
New insights on the interaction mechanism of rhTNFα with its antagonists Adalimumab and Etanercept (2020)

Abstract TNFα is a pro-inflammatory cytokine that is a therapeutic target for inflammatory autoimmune disorders. Thus, TNFα antagonists are successfully used for the treatment of these disorders. Here, new association patterns of rhTNFα and its antagonists Adalimumab and Etanercept are disclosed. Active rhTNFα was purified by IMAC from the soluble fraction of transformed E. coli. Protein detection was assessed by SDS-PAGE and western blot. The K D values for rhTNFα interactions with their antagonists were obtained by non-competitive ELISA and by microscale thermophoresis. Molecular sizes of the complexes were characterized by SEC-HPLC. Surprisingly, both antagonists recognized the monomeric form of rhTNFα under reducing and non-reducing conditions, indicating unexpected bindings of the antagonists to lineal epitopes and to one protomer of rhTNFα. Binding curves of two phases with low and high K D values (&lt;10 −9 M and &gt;10 −8 M) were observed during thermophoresis experiments, suggesting the generation of complexes with different stoichiometry, which were confirmed by SEC-HPLC. This pioneer investigation revealed interactions of rhTNFα with Adalimumab and Etanercept never described before, which constitute valuable data for future approaches into the study of their interaction mechanism.
Bio-Regenerative Life Support System Development for Lunar/Mars Habitats (2012)

Bio-regenerative Life Support Systems (BLSS) uses biological processes to support an astronaut crew, and includes atmosphere revitalization, water recycling, food production, and organic waste recycling. The University of Arizona Controlled Environment Agriculture Center (UA-CEAC), Systems and Industrial Engineering Department, Sadler Machine Co. (USA) and Italian collaborators, Thales Alenia Space Italia (TAS-I), Aero-Sekur, SpA, and University of Naples Federico II are developing BLSS for future Lunar/Mars surface missions. Current efforts at UA-CEAC include operation of four BLSS Lunar Greenhouse (LGH) Prototype Units with the primary purpose of demonstrating poly-culture production of food crops in a semi-closed gaseous cycle, and preliminary efforts of waste DWEComposting, Solar Concentrating Plant Lighting/Power System, and System Monitoring/Telepresence Support. TAS-I, the University of Naples, and Aero-Sekur BLSS efforts in Italy include operation of Recyclab, the EDEN chamber, and the development of space plant growth chambers. UA-CEAC efforts are supported by NASA Ralph Steckler Phase II Space Grant while the Italian collaborators have been supported by ESA, ASI, and regional, and internal sources. Based on NASA crop production area estimates the LGH with its four modules will support a four person crew with 100% of their water/atmosphere
A Unique Genome-wide Association Study of a Psychiatric Disorder From India (2019)

Our website uses cookies to enhance your experience. By continuing to use our site, or clicking "Continue," you are agreeing to our Cookie Policy | Continue JAMA Psychiatry HomeNew OnlineCurrent IssueFor Authors Podcast Publications JAMA JAMA Network Open JAMA Cardiology JAMA Dermatology JAMA Health Forum JAMA Internal Medicine JAMA Neurology JAMA Oncology JAMA Ophthalmology JAMA Otolaryngology–Head & Neck Surgery JAMA Pediatrics JAMA Psychiatry JAMA Surgery Archives of Neurology & Psychiatry (1919-1959) JN Learning / CMESubscribeJobsInstitutions / LibrariansReprints & Permissions Terms of Use | Privacy Policy | Accessibility Statement 2023 American Medical Association. All Rights Reserved Search All JAMA JAMA Network Open JAMA Cardiology JAMA Dermatology JAMA Forum Archive JAMA Health Forum JAMA Internal Medicine JAMA Neurology JAMA Oncology JAMA Ophthalmology JAMA Otolaryngology–Head & Neck Surgery JAMA Pediatrics JAMA Psychiatry JAMA Surgery Archives of Neurology & Psychiatry Input Search Term Sign In Individual Sign In Sign inCreate an Account Access through your institution Sign In Purchase Options: Buy this article Rent this article Subscribe to the JAMA Psychiatry journal
Multiple-dose pharmacokinetics of ciprofloxacin administered intravenously to normal volunteers (1985)

We administered multiple doses of ciprofloxacin intravenously over 30 min every 12 h for 1 week to nine healthy volunteers. Three volunteers received a placebo (vehicle) intravenously. Doses of 100, 150, and 200 mg were evaluated with a 1-week wash-out period intervening between each dose level. Terminal excretion half-lives averaged 3.67 +/- 0.65, 3.60 +/- 0.26, and 4.00 +/- 0.69 h for the 100-, 150-, and 200-mg doses, respectively. Serum clearances were 30.1 +/- 3.4, 29.8 +/- 4.0, and 26.9 +/- 4.1 liters/h per 1.73 m2 for these doses. Urine concentrations remained in excess of the MIC for 90% of the relevant urinary tract pathogens for the full 12-h dosing interval at each dose. Renal clearance accounted for 56 to 71% of the serum clearance. However, because a microbiologic assay was used and biologically active, renally excreted metabolites were identified, the renal clearance determinations are likely to be in excess of the true values. The doses of ciprofloxacin administered intravenously were well tolerated, and the drug concentrations appeared adequate for the treatment of the vast majority of cases of nosocomially acquired sepsis and urinary tract infections. For patients with serious Pseudomonas infections and perhaps staphylococcal infections, either an 8-h dosing schedule or larger doses on a 12-h schedule should be considered.
[Cost-benefit analysis in setting up limitation standards of aflatoxins in foods]. (2011)

The following limiting standards is advisable: 20 microg/kg for total aflatoxins and 15 microg/kg for Aflatoxin B1 in peanut and its products, 20 microg/kg for total aflatoxins and 15 microg/kg for aflatoxin B1 in corn, 10 microg/kg for total aflatoxins and 5 microg/kg or 10 microg/kg for aflatoxin B1 in rice.
Decreased IL‐10 production by psoriatic peripheral blood mononuclear cells stimulated with streptococcal superantigen (2002)

The strong association of acute guttate psoriasis and streptococcal throat infection has suggested a role for streptococcal antigens in the pathogenesis of psoriasis. We have reported that psoriatic peripheral blood mononuclear cells (PBMCs) showed significantly lower responses to cytoplasmic membrane-associated protein (CAP) isolated from group A beta-hemolytic streptococci, a kind of streptococcal superantigen. The objectives were to evaluate the abnormal cytokine production by psoriatic PBMCs to streptococcal superantigen, CAP. We compared the production of four different cytokines, i.e. IL-4, IL-5, IL-10, and IFN-gamma, by PBMCs between psoriatic patients and healthy controls after stimulation with CAP or two different staphylococcal superantigens, staphylococcal enterotoxin A (SEA) or E (SEE). When PBMCs were stimulated with CAP, the production of IL-10 was significantly lower by psoriatic PBMCs than by those from healthy controls, whereas those of IL-4, IL-5, or IFN-gamma were not different between the two groups. Such a significant decrease in IL-10 production by psoriatic PBMCs was not observed when they were stimulated with staphylococcal superantigens. Flow cytometric analysis of intracytoplasmic IL-10 demonstrated defective IL-10 production by psoriatic PBMCs in both CD3+ T cells and CD14+ monocytes. There was a significant positive correlation between IFN-gamma production by PBMCs and the proliferation of Vbeta8+ T cells preferentially stimulated by CAP. These data demonstrating the defective IL-10 production by psoriatic PBMCs stimulated with streptococcal superantigen seem to explain why only psoriatic patients evolve sustained and Th-1 deviated skin lesions after streptococcal upper respiratory infection.
Tagging Funding Agencies and Grants in Scientific Articles using Sequential Learning Models (2017)

In this paper we present a solution for tagging funding bodies and grants in scientific articles using a combination of trained sequential learning models, namely conditional random fields (CRF), hidden markov models (HMM) and maximum entropy models (MaxEnt), on a benchmark set created in-house. We apply the trained models to address the BioASQ challenge 5c, which is a newly introduced task that aims to solve the problem of funding information extraction from scientific articles. Results in the dry-run data set of BioASQ task 5c show that the suggested approach can achieve a micro-recall of more than 85% in tagging both funding bodies and grants.
Effects of ibrutinib treatment on murine platelet function during inflammation and in primary hemostasis (2016)

Ibrutinib is an irreversible inhibitor of Bruton’s tyrosine kinase (BTK), which has emerged as a potent molecular therapy in the treatment of B-cell malignancies, and continues to be investigated for treatment in a variety of blood cancers. Despite an excellent safety profile and high tolerability
Primary Structure of Stallion Seminal Plasma Protein HSP‐7, a Zona‐Pellucida‐Binding Protein of the Spermadhesin Family (1996)

The primary-structure of HSP-7, a 14-kDa protein isolated from stallion seminal plasma, has been determined, HSP-7 belongs to the spermadhesin protein family, shares 98% sequence identity with the boar seminal plasma protein AWN, and, like its boar homolog, displays zona-pellucida-binding activity. Despite these conserved structural and functional features, the equine and porcine spermadhesins differ in their topography on spermatozoa.
Construction of Semiconductor Nanoparticle Layers on Gold by Self-Assembly Technique (1997)

Cadmium sulfide (CdS) nanoparticles were prepared using the Aerosol-OT (AOT)/heptane inverse-micelle method. The particle size was controlled by changing the [H 2 O]/[AOT] ratio in the preparation process to be ca. 3 nm, which was estimated from their absorption maximum ( ca. 385 nm) and absorption edge ( ca. 450 nm) in heptane solutions. Self-assembled monolayers (SAMs) of α,ω-dithiols were prepared on (111)-oriented gold substrates. They were highly stable in aqueous solutions and showed a blocking effect toward electron exchange between the gold substrate and the electroactive species in the solution. Mono- and multi-layers of CdS nanoparticles were prepared by immersing the SAM-covered gold substrates in a heptane solution containing CdS particles. Infrared reflection-absorption spectra revealed that CdS particles on SAMs were surrounded by AOT and that a sequential immersion procedure led to the alternately layered structure of CdS particles and dithiol molecules.
Bone Mineral Density In Male Runners And Climbers (2005)

While in running the weight-bearing bones are stressed predominantly by high-impact ground-reaction forces, in climbing bones of the total skeleton are stressed by vigorous muscle contractions. Purpose To determine the influence of two disciplines of sport which are characterised by different loading patterns and a different anatomical distribution of the loads on bone mineral density (BMD) of male athletes. Methods We compared the BMD of age-, weight-, and height matched competitive male runners, competitive climbers, and controls. Total body (TB) and regional (upper extremity, lower extremity) BMD were measured by dual-energy X-ray absorptiometry (DXA). Quantitative computed tomographic (QCT) scans were made from the femoral neck (FN) and the lumbar spine (LS). Quantitative ultrasound (QUS) measurements were performed at the calcaneus. ResultsTableRunners and climbers had about the same TB BMD value which was significantly higher than in the control group. The regional analysis showed significant differences between runners and climbers in favour to the mechanically loaded sites. At the FN the runners had a significantly higher trabecular BMD than the climbers and the controls, while the climbers had a significantly higher cortical BMD than the runners and the controls. At the LS the runners and the climbers had similar values for trabecular BMD, which differed significantly from the controls. As expected, runners had the highest QUI value at the calcaneus. Conclusion The results indicate that both, sports producing impact loading as well as sports producing forces by vigorous muscle contraction have beneficial effects on BMD. The bone adaptation is site specific. The inhomogeneous results at the FN (QCT) might be due to the different loading pattern. We suggest that bones that are loaded by compression due to ground reaction forces preliminary adapt by increasing the trabecular BMD while bones loaded by bending resulting from muscle contraction, adapt by increasing the cortical BMD.
Hyperhomocysteinemia as an independent risk factor for silent brain infarction (2003)

This study demonstrates that hyperhomocysteinemia is an independent risk factor for SBI, and provides the possibility of reducing the risk for SBI in the MTHFR 677TT genotype by folate supplementation.
Novel Hydrogel-Based Preparation-Free EEG Electrode (2010)

The largest obstacles to signal transduction for electroencephalography (EEG) recording are the hair and the epidermal stratum corneum of the skin. In typical clinical situations, hair is parted or removed, and the stratum corneum is either abraded or punctured using invasive penetration devices. These steps increase preparation time, discomfort, and the risk of infection. Cross-linked sodium polyacrylate gel swelled with electrolyte was explored as a possible skin contact element for a prototype preparation-free EEG electrode. As a superabsorbent hydrogel, polyacrylate can swell with electrolyte solution to a degree far beyond typical contemporary electrode materials, delivering a strong hydrating effect to the skin surface. This hydrating power allows the material to increase the effective skin contact surface area through wetting, and noninvasively decrease or bypass the highly resistive barrier of the stratum corneum, allowing for reduced impedance and improved electrode performance. For the purposes of the tests performed in this study, the polyacrylate was prepared both as a solid elastic gel and as a flowable paste designed to penetrate dense scalp hair. The gel can hold 99.2% DI water or 91% electrolyte solution, and the water content remains high after 29 h of air exposure. The electrical impedance of the gel electrode on unprepared human forearm is significantly lower than a number of commercial ECG and EEG electrodes. This low impedance was maintained for at least 8 h (the longest time period measured). When a paste form of the electrode was applied directly onto scalp hair, the impedance was found to be lower than that measured with commercially available EEG paste applied in the same manner. Time-frequency transformation analysis of frontal lobe EEG recordings indicated comparable frequency response between the polyacrylate-based electrode on unprepared skin and the commercial EEG electrode on abraded skin. Evoked potential recordings demonstrated signal-to-noise ratios of the experimental and commercial electrodes to be effectively equivalent. These results suggest that the polyacrylate-based electrode offers a powerful option for EEG recording without scalp preparation.
Recording Mouse Ultrasonic Vocalizations to Evaluate Social Communication (2016)

Mice emit ultrasonic vocalizations in different contexts throughout development and in adulthood. These vocal signals are now currently used as proxies for modeling the genetic bases of vocal communication deficits. Characterizing the vocal behavior of mouse models carrying mutations in genes associated with neuropsychiatric disorders such as autism spectrum disorders will help to understand the mechanisms leading to social communication deficits. We provide here protocols to reliably elicit ultrasonic vocalizations in pups and in adult mice. This standardization will help reduce inter-study variability due to the experimental settings. Pup isolation calls are recorded throughout development from individual pups isolated from dam and littermates. In adulthood, vocalizations are recorded during same-sex interactions (without a sexual component) by exposing socially motivated males or females to an unknown same-sex conspecific. We also provide a protocol to record vocalizations from adult males exposed to an estrus female. In this context, there is a sexual component in the interaction. These protocols are established to elicit a large amount of ultrasonic vocalizations in laboratory mice. However, we point out the important inter-individual variability in the vocal behavior of mice, which should be taken into account by recording a minimal number of individuals (at least 12 in each condition). These recordings of ultrasonic vocalizations are used to evaluate the call rate, the vocal repertoire and the acoustic structure of the calls. Data are combined with the analysis of synchronous video recordings to provide a more complete view on social communication in mice. These protocols are used to characterize the vocal communication deficits in mice lacking ProSAP1/Shank2, a gene associated with autism spectrum disorders. More ultrasonic vocalizations recordings can also be found on the mouseTube database, developed to favor the exchange of such data.
Blind Symbol Rate Estimation and Testbed Implementation for Linearly Modulated Signals (2013)

Blind symbol or baud rate estimation is one of the most important parts of the blind signal detection process. Most of the blind symbol rate estimation algorithms provided in the literature either estimate symbol rate from the baseband signal or require prior knowledge of transmitted signal parameters. Moreover, these algorithms had been mostly limited to theoretical studies. In this paper, a cyclic correlation based blind symbol rate estimation is considered for linearly modulated signals. The estimation is performed directly from an intermediate frequency (IF) signal and without having prior knowledge of transmitted signal parameters. The algorithm is implemented on a National Instruments (NI) hardware to measure its performance in a realistic environment. Theoretical and experimental results are provided and compared with existing methods.
Lipopolysaccharide Inhibits TNF-Induced Apoptosis: Role of Nuclear Factor-κB Activation and Reactive Oxygen Intermediates (1999)

Abstract LPS, a component of the cell wall in Gram-negative bacteria, induces inflammation and septic shock syndrome by stimulating various inflammatory cytokines including TNF. How LPS affects the TNF-mediated cellular responses, however, is not understood. In this study, the effect of LPS on TNF-mediated apoptosis in human histiocytic lymphoma U-937 cells was investigated. We found that treatment of cells with LPS completely abolished TNF-mediated cytotoxicity and activation of caspase-3. LPS-chelating antibiotic, polymyxin B, suppressed the antiapoptotic activity, indicating the specificity of the effect. Within minutes, LPS through CD14 induced the activation of NF-κB, degradation of IκBα (inhibitory subunit of NF-κB) and IκBβ, and nuclear translocation of p65. An antioxidant, pyrrolidine dithiocarbamate, which blocked LPS-induced NF-κB activation, also abolished the antiapoptotic effects of LPS at the same time. Besides TNF, the apoptosis induced by taxol and okadaic acid was also sensitive to LPS-induced NF-κB activation, whereas that induced by H2O2, doxorubicin, daunomycin, vincristine, and vinblastine was NF-κB insensitive. Tumor cells that constitutively expressed NF-κB also showed resistance to the apoptotic effects of TNF, taxol, and okadaic acid, but sensitivity to all other agents, indicating the critical role of NF-κB in blocking apoptosis induced by certain agents. Overall, these results indicate that LPS induces resistance to the apoptotic effects of TNF and other agents, and that NF-κB activation, whether induced or constitutive, inhibits this apoptosis.
Fabrication and Characterization of Graphitic Carbon Nanostructures with Controllable Size, Shape, and Position (2009)

The incorporation of carbon materials in micro- and nanoscale devices is being widely investigated due to the promise of enhanced functionality. Challenges in the positioning and addressability of carbon nanotubes provide the motivation for the development of new processes to produce nanoscale carbon materials. Here, the fabrication of conducting, nanometer-sized carbon structures using a combination of electron beam lithography (EBL) and carbonisation is reported. EBL is used to directly write predefined nanometer-sized patterns in a thin layer of negative resist in controllable locations. Careful heat treatment results in carbon nanostructures with the size, shape, and location originally defined by EBL. The pyrolysis process results in significant shrinkage of the structures in the vertical direction and minimal loss in the horizontal direction. Characterization of the carbonized material indicates a structure consisting of both amorphous and graphitized carbon with low levels of oxygen. The resistivity of the material is similar to other disordered carbon materials and the resistivity is maintained from the bulk to the nanoscale. This is demonstrated by fabricating a nanoscale structure with predictable resistance. The ability to fabricate these conductive structures with known dimensions and in predefined locations can be exploited for a number of applications. Their use as nanoband electrodes is also demonstrated.