gebhart/patrepeval huggingface dataset:
A unified sample preparation protocol for proteomic and genomic profiling of cervical swabs to identify biomarkers for cervical cancer screening (2008)

Cervical cancer screening is ideally suited for the development of biomarkers due to the ease of tissue acquisition and the well-established histological transitions. Furthermore, cell and biologic fluid obtained from cervix samples undergo specific molecular changes that can be profiled. However, the ideal manner and techniques for preparing cervical samples remains to be determined. To address this critical issue a patient screening protein and nucleic acid collection protocol was established. RNAlater was used to collect the samples followed by proteomic methods to identify proteins that were differentially expressed in normal cervical epithelial versus cervical cancer cells. Three hundred ninety spots were identified via 2-D DIGE that were expressed at either higher or lower levels (>three-fold) in cervical cancer samples. These proteomic results were compared to genes in a cDNA microarray analysis of microdissected neoplastic cervical specimens to identify overlapping patterns of expression. The most frequent pathways represented by the combined dataset were: cell cycle: G2/M DNA damage checkpoint regulation; aryl hydrocarbon receptor signaling; p53 signaling; cell cycle: G1/S checkpoint regulation; and the ER stress pathway. HNRPA2B1 was identified as a biomarker candidate with increased expression in cancer compared to normal cervix and validated by Western blot.
The Middle-Aged Patient With Hip Arthritis (2002)

Younger patients with a long life expectancy and higher activity levels who require total hip arthroplasty present a unique challenge to the reconstructive surgeon. To improve the longevity of total hip arthroplasty, particularly in younger, more active patients, femoral components inserted without cement have been used in an attempt to create a more durable reconstruction. Extensively-coated implants are an attractive option because they are associated with excellent initial implant stability and contact a large area of strong cortical bone in the femoral diaphysis where bony ingrowth reliably occurs. In a cohort of 304 patients (348 hips) who were between 45 and 65 years at the time of surgery and who were followed up for a mean of 14.2 years, 99.4% of the femoral reconstructions were stable with no cases of late failure secondary to loosening and a 96% rate of good to excellent clinical results. Although stress shielding, thigh pain, and difficulty of removal have been cited as problems with the use of these devices, in the current authors' experience they have not proved to be clinically relevant issues that limit the successfulness of total hip arthroplasty in this patient population.
Effects of 1,8-diiodooctane on domain nanostructure and charge separation dynamics in PC71BM-based bulk heterojunction solar cells (2018)

Transient absorption and X-ray scattering demonstrate 1,8-diiodooctane impact on morphology and charge generation in mixed phases in bulk heterojunction solar cells.
Role of Prostaglandin D<sub>2</sub> for delayed wound healing in Streptozotocin-induced diabetic mice (2020)

Delayed wound healing is a major problem in patients with diabetes, which significantly impairs their quality of life. Prostaglandin (PG) D 2 is a major inflammatory lipid mediator synthesized by hematopoietic PGD 2 synthase (H-PGDS) from PGH 2 , a common precursor of all of PGs. In the present study, we investigated the role of PGD 2 in cutaneous wound healing in streptozotocin (STZ)-induced diabetic mice. C57BL/6 mice were injected with 50 mg/kg of STZ intraperitoneally daily for 5 days. Four weeks after the injection of STZ, a full thickness wound was created with an 8-mm diameter biopsy punch on the dorsal of mice. Wound healing was significantly decelerated and cutaneous H-PGDS mRNA was significantly increased in diabetic mice compared with non-diabetic mice. Daily administration of H-PGDS inhibitor for 14 days was significantly promoted wound healing in diabetic mice. These results suggest that PGD 2 involved in delayed wound healing in STZ-induced diabetic mice.
Evaluating Downlink MU-MIMO: Laboratory Experimentation and Results (2012)

The Third Generation Partnership Project (3GPP) finalized the radio interface specifications for the next generation mobile communication system, Long Term Evolution (LTE), as Release 8 [1], [2]. LTE provides full IP packet-based radio access with low latency and adopts orthogonal frequency division multiple access (OFDMA) and single-carrier frequency division multiple access (SC-FDMA) as multiple access schemes in the downlink and uplink, respectively. In Japan, the NTT DOCOMO launched a commercial LTE service in December 2010 under the new service brand Xi (crossy) [3]. Meanwhile, in 3GPP standardization, there have been efforts toward establishing an enhanced LTE radio interface, LTEAdvanced (LTE Release 10 and beyond), and specifications for LTE Release 10 were finalized [4], [5]. In LTE-Advanced, it is necessary to support a wider bandwidth than that in LTE Release 8, i.e., 20 MHz, to satisfy the high level requirements corresponding to the target peak data rate of greater than 1 Gb/s. To this end, LTEAdvanced supports carrier aggregation (CA) up to 100 MHz by aggregating multiple component carriers (CCs) with backward compatibility to LTE Release 8. In addition, to satisfy the requirements for further improvement in terms of spectrum efficiency, enhanced multiple-input multiple-output (MIMO) techniques such as higher-order MIMO multiplexing and multiuser (MU)-MIMO are supported.
The effect of β-hydroxy-β-methylbutyrate (HMB) on the proliferative response of blood lymphocytes and the phagocytic activity of blood monocytes and granulocytes in calves (2013)

The objective of this study was to evaluate the effect of HMB on selected indicators of immunity in calves. The experiment was performed on 14 calves aged 30 +/- 2 days, divided into two equal groups of control (group I) and experimental (group II) animals. The feed administered to experimental group calves was supplemented with HMB at 40 mg/kg BW, whereas control calves were administered standard farm-made feed without supplementation. Blood was sampled from the jugular vein immediately before the experiment (day 0) and on experimental days 15, 30 and 60 to determine the following parameters of immunity: proliferative response of LPS- and ConA-stimulated lymphocytes (MTT), respiratory burst activity (RBA) and potential killing activity (PKA) of phagocytes. The results revealed a significant increase in RBA and MTT values in calves administered HMB in comparison with the control group throughout the experiment. In the group of animals receiving HMB, an increase in PKA values was noted only on day 30.
Vitamin B12 Uptake by the Gut Commensal Bacteria Bacteroides thetaiotaomicron Limits the Production of Shiga Toxin by Enterohemorrhagic Escherichia coli (2016)

Enterohemorrhagic Escherichia coli (EHEC) are foodborne pathogens responsible for the development of bloody diarrhea and renal failure in humans. Many environmental factors have been shown to regulate the production of Shiga toxin 2 (Stx2), the main virulence factor of EHEC. Among them, soluble factors produced by human gut microbiota and in particular, by the predominant species Bacteroides thetaiotaomicron (B. thetaiotaomicron), inhibit Stx2 gene expression. In this study, we investigated the molecular mechanisms underlying the B. thetaiotaomicron-dependent inhibition of Stx2 production by EHEC. We determined that Stx2-regulating molecules are resistant to heat treatment but do not correspond to propionate and acetate, two short-chain fatty acids produced by B. thetaiotaomicron. Moreover, screening of a B. thetaiotaomicron mutant library identified seven mutants that do not inhibit Stx2 synthesis by EHEC. One mutant has impaired production of BtuB, an outer membrane receptor for vitamin B12. Together with restoration of Stx2 level after vitamin B12 supplementation, these data highlight vitamin B12 as a molecule produced by gut microbiota that modulates production of a key virulence factor of EHEC and consequently may affect the outcome of an infection.
Parallel computing patterns for Grid workflows (2006)

Whereas a consensus has been reached on defining the set of workflow patterns for business process modeling languages, no such patterns exists for workflows applied to scientific computing on the Grid. By looking at different kinds of parallelism, in this paper we identify a set of workflow patterns related to parallel and pipelined execution. The paper presents how these patterns can be represented in different Grid workflow languages and discusses their implications for the design of the underlying workflow management and execution infrastructure. A preliminary classification of these patterns is introduced by surveying how they are supported by several existing advanced scientific and Grid workflow languages.
Kinetic measurements for the reaction of amidogen + nitric oxide over the temperature range 294-1215 K (1982)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTKinetic measurements for the reaction of amidogen + nitric oxide over the temperature range 294-1215 KJoel A. Silver and Charles E. KolbCite this: J. Phys. Chem. 1982, 86, 16, 3240–3246Publication Date (Print):August 1, 1982Publication History Published online1 May 2002Published inissue 1 August 1982https://pubs.acs.org/doi/10.1021/j100213a033https://doi.org/10.1021/j100213a033research-articleACS PublicationsRequest reuse permissionsArticle Views87Altmetric-Citations72LEARN 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 options Get e-Alerts
Functional amplification and preservation of human gut microbiota (2017)

<b>Background</b>: The availability of fresh stool samples is a prerequisite in most gut microbiota functional studies. <b>Objective</b>: Strategies for amplification and long-term gut microbiota preservation from fecal samples would favor sample sharing, help comparisons and reproducibility over time and between laboratories, and improve the safety and ethical issues surrounding fecal microbiota transplantations. <b>Design</b>: Taking advantage of <i>in vitro</i> gut-simulating systems, we amplified the microbial repertoire of a fresh fecal sample and assessed the viability and resuscitation of microbes after preservation with some common intracellular and extracellular acting cryoprotective agents (CPAs), alone and in different combinations. Preservation efficiencies were determined after 3 and 6 months and compared with the fresh initial microbiota diversity and metabolic activity, using the chemostat-based Environmental Control System for Intestinal Microbiota (ECSIM) <i>in vitro</i> model of the gut environment. Microbial populations were tested for fermentation gas, short-chain fatty acids, and composition of amplified and resuscitated microbiota, encompassing methanogenic archaea. <b>Results</b>: Amplification of the microbial repertoire from a fresh fecal sample was achieved with high fidelity. Dimethylsulfoxide, alone or mixed with other CPAs, showed the best efficiency for functional preservation, and the duration of preservation had little effect. <b>Conclusions</b>: The amplification and resuscitation of fecal microbiota can be performed using specialized <i>in vitro</i> gut models. Correct amplification of the initial microbes should ease the sharing of clinical samples and improve the safety of fecal microbiota transplantation. <b>Abbreviations</b>: CDI, <i>Clostridium difficile</i> infection; CPA, cryoprotective agent; D, DMSO, dimethylsulfoxide; FMT, fecal microbiota transplantation; G, glycerol; IBD, inflammatory bowel disease; P, PEG-4000, polyethylene glycol 4000 g.mol<sup>-1</sup>; SCFA, short-chain fatty acid; SNR, signal-to-noise ratio.
Scrum + Engineering Practices: Experiences of Three Microsoft Teams (2011)

The Scrum methodology is an agile software development process that works as a project management wrapper around existing engineering practices to iteratively and incrementally develop software. With Scrum, for a developer to receive credit for his or her work, he or she must demonstrate the new functionality provided by a feature at the end of each short iteration during an iteration review session. Such a short-term focus without the checks and balances of sound engineering practices may lead a team to neglect quality. In this paper we present the experiences of three teams at Microsoft using Scrum with an additional nine sound engineering practices. Our results indicate that these teams were able to improve quality, productivity, and estimation accuracy through the combination of Scrum and nine engineering practices.
A Computational and Experimental Investigation of the Human Thermal Plume (2006)

The behavior of the buoyant plume of air shed by a human being in an indoor environment is important to room ventilation requirements, airborne disease spread, air pollution control, indoor air quality, and the thermal comfort of building occupants. It also becomes a critical factor in special environments like surgery rooms and clean-rooms. Of the previous human thermal plume studies, few have used actual human volunteers, made quantitative plume velocity measurements, or considered thermal stratification of the environment. Here, a study of the human thermal plume in a standard room environment, including moderate thermal stratification, is presented. We characterize the velocity field around a human volunteer in a temperature-stratified room using particle image velocimetry (PIV). These results are then compared to those obtained from a steady three-dimensional computational fluid dynamics (CFD) solution of the Reynolds-averaged Navier-Stokes equations (RANS) using the RNG k‐ε two-equation turbulence model. Although the CFD simulation employs a highly simplified model of the human form, it nonetheless compares quite well with the PIV data in terms of the plume centerline velocity distribution, velocity profiles, and flow rates. The effect of thermal room stratification on the human plume is examined by comparing the stratified results with those of an additional CFD plume simulation in a uniform-temperature room. The resulting centerline velocity distribution and plume flow rates are presented. The reduction in plume buoyancy produced by room temperature stratification has a significant effect on plume behavior.
Direct Transfection of Dendritic Cells in the Epidermis After Plasmid Delivery Enhanced by Surface Electroporation (2014)

The skin is rich in antigen-presenting cells and as such is an excellent target tissue for vaccination strategies. Electroporation is a physical delivery method that potentiates the uptake of DNA vaccines into target cells. Intradermal electroporation offers a minimally invasive solution to DNA delivery in the clinic. Here we describe the direct transfection of dendritic cells in the epidermis, using a surface dermal electroporation device, and specifically show a dendritic cell transfected with plasmid expressing green fluorescent protein. The dendritic cell has used its motile capabilities after transfection to move from the epidermis into the dermis, making its way to the lymphatic system.
Perspectives of Homo sapiens lifespan extension: focus on external or internal resources? (2020)

<i>Homo sapiens</i> and naked mole rats (<i>Heterocephalus glaber</i>) are vivid examples of social mammals that differ from their relatives in particular by an increased lifespan and a large number of neotenic features. An important fact for biogerontology is that the mortality rate of <i>H. glaber</i> (a maximal lifespan of more than 32 years, which is very large for such a small rodent) negligibly grows with age. The same is true for modern people in developed countries below the age of 60. It is important that the juvenilization of traits that separate humans from chimpanzees evolved over thousands of generations and millions of years. Rapid advances in technology resulted in a sharp increase in the life expectancy of human beings during the past 100 years. Currently, the human life expectancy has exceeded 80 years in developed countries. It cannot be excluded that the potential for increasing life expectancy by an improvement in living conditions will be exhausted after a certain period of time. New types of geroprotectors should be developed that protect not only from chronic phenoptosis gradual poisoning of the body with reactive oxygen species (ROS) but also from acute phenoptosis, where strong increase in the level of ROS immediately kills an already aged individual. Geroprotectors might be another anti-aging strategy along with neoteny (a natural physiological phenomenon) and technical progress.
Production of light nuclei and anti-nuclei in pp and Pb-Pb collisions at energies available at the CERN Large Hadron Collider (2016)

The production of (anti-)deuteron and (anti-)He3 nuclei in Pb-Pb collisions at sNN=2.76 TeV has been studied using the ALICE detector at the LHC. The spectra exhibit a significant hardening with increasing centrality. Combined blast-wave fits of several particles support the interpretation that this behavior is caused by an increase of radial flow. The integrated particle yields are discussed in the context of coalescence and thermal-statistical model expectations. The particle ratios, He3/d and He3/p, in Pb-Pb collisions are found to be in agreement with a common chemical freeze-out temperature of Tchem≈156 MeV. These ratios do not vary with centrality which is in agreement with the thermal-statistical model. In a coalescence approach, it excludes models in which nucleus production is proportional to the particle multiplicity and favors those in which it is proportional to the particle density instead. In addition, the observation of 31 anti-tritons in Pb-Pb collisions is reported. For comparison, the deuteron spectrum in pp collisions at s=7 TeV is also presented. While the p/π ratio is similar in pp and Pb-Pb collisions, the d/p ratio in pp collisions is found to be lower by a factor of 2.2 than in Pb-Pb collisions.
Clavicular‐Sided Tears Were the Most Frequent Mode of Failure During Biomechanical Analysis of Acromioclavicular Ligament Complex Failure During Adduction of the Scapula (2021)

This biomechanical study simulates a potential mechanism of AC ligament injury. Additional knowledge about the mode of failure provides a better understanding of the ACLC, allowing for new information for the purpose of AC ligament reconstruction.
3-D Tumor Model forIn VitroEvaluation of Anticancer Drugs (2008)

The efficacy of potential anticancer drugs during preclinical development is generally tested in vitro using cancer cells grown in monolayer; however, a significant discrepancy in their efficacy is observed when these drugs are evaluated in vivo. This discrepancy, in part, could be due to the three-dimensional (3-D) nature of tumors as compared to the two-dimensional (2-D) nature of monolayer cultures. Therefore, there is a need for an in vitro model that would mimic the 3-D nature of tumors. With this objective, we have developed surface-engineered, large and porous biodegradable polymeric microparticles as a scaffold for 3-D growth of cancer cells. Using the MCF-7 cell line as model breast cancer cells, we evaluated the antiproliferative effect of three anticancer drugs: doxorubicin, paclitaxel and tamoxifen in 3-D model vs in 2-D monolayer. With optimized composition of microparticles and cell culture conditions, a density of 4.5 x 10 (6) MCF-7 cells/mg of microparticles, which is an 18-fold increase from the seeding density, was achieved in six days of culture. Cells were observed to have grown in clumps on the microparticle surface as well as in their interior matrix structure. The antiproliferative effect of the drugs in 3-D model was significantly lower than in 2-D monolayer, which was evident from the 12- to 23-fold differences in their IC 50 values. Using doxorubicin, the flow cytometry data demonstrated approximately 2.6-fold lower drug accumulation in the cells grown in 3-D model than in the cells grown as 2-D monolayer. Further, only 26% of the cells in 3-D model had the same concentration of drug as the cells in monolayer, thus explaining the reduced activity of the drugs in 3-D model. The collagen content of the cells grown in 3-D model was 2-fold greater than that of the cells grown in 2-D, suggesting greater synthesis of extracellular matrix in 3-D model, which acted as a barrier to drug diffusion. The microarray analysis showed changes in several genes in cells grown in 3-D, which could also influence the drug effect. In conclusion, the cells grown in 3-D are more resistant to chemotherapy than those grown in 2-D culture, suggesting the significant roles of cellular architecture, phenotypic variations, and extracellular matrix barrier to drug transport in drug efficacy. We propose that our model provides a better assessment of drug efficacy than the currently used 2-D monolayer as many of its characteristic features are similar to an actual tumor. A well-characterized 3-D model can particularly be useful for rapid screening of a large number of therapeutics for their efficacy during the drug discovery phase.
Measurement of spin correlations in tt‾ production using the matrix element method in the muon+jets final state in pp collisions at s=8 TeV (2016)

The consistency of the spin correlation strength in top quark pair production with the standard model (SM) prediction is tested in the muon+jets final state. The events are selected from pp collisions, collected by the CMS detector, at a centre-of-mass energy of 8 TeV, corresponding to an integrated luminosity of 19.7 fb -1 . The data are compared with the expectation for the spin correlation predicted by the SM and with the expectation of no correlation. Using a template fit method, the fraction of events that show SM spin correlations is measured to be 0.72 0.08 (stat) +0.15 -0.13 (syst), representing the most precise measurement of this quantity in the muon+jets final state to date.
Nitrenes (2004)

Abstract For Abstract see ChemInform Abstract in Full Text.
Electrical excitation of waveguided surface plasmons by a light-emitting tunneling optical gap antenna (2016)

We introduce a new type of electroplasmonic interfacing component to electrically generate surface plasmons. Specifically, an electron-fed optical tunneling gap antenna is integrated on a plasmonic waveguiding platform. When electrical charges are injected in the tunneling barrier of the gap antenna, a broad-band radiation is emitted from the feed area by a process identified as a thermal emission of hot electrons. Part of the emitted photons couples to surface plasmon modes sustained by the waveguide geometry. The transducing optical antenna is thus acting as a localized electrical source of surface plasmon polaritons. The integration of electrically-activated optical antennas into a plasmonic architecture mitigates the need for complex coupling scheme and proposes a solution for realizing nanoscale units at the interface between nano-electronics and photonics.