gebhart/patrepeval huggingface dataset:
Guidance and Self‐Sorting of Active Swimmers: 3D Periodic Arrays Increase Persistence Length of Human Sperm Selecting for the Fittest (2017)

Male infertility is a reproductive disease, and existing clinical solutions for this condition often involve long and cumbersome sperm sorting methods, including preprocessing and centrifugation-based steps. These methods also fall short when sorting for sperm free of reactive oxygen species, DNA damage, and epigenetic aberrations. Although several microfluidic platforms exist, they suffer from structural complexities, i.e., pumps or chemoattractants, setting insurmountable barriers to clinical adoption. Inspired by the natural filter-like capabilities of the female reproductive tract for sperm selection, a model-driven design, featuring pillar arrays that efficiently and noninvasively isolate highly motile and morphologically normal sperm, with lower epigenetic global methylation, from raw semen, is presented. The <b>S</b>imple <b>P</b>eriodic <b>AR</b>ray for <b>T</b>rapping <b>A</b>nd isolatio<b>N</b> (SPARTAN) created here modulates the directional persistence of sperm, increasing the spatial separation between progressive and nonprogressive motile sperm populations within an unprecedentedly short 10 min assay time. With over 99% motility of sorted sperm, a 5-fold improvement in morphology, 3-fold increase in nuclear maturity, and 2-4-fold enhancement in DNA integrity, SPARTAN offers to standardize sperm selection while eliminating operator-to-operator variations, centrifugation, and flow. SPARTAN can also be applied in other areas, including conservation ecology, breeding of farm animals, and design of flagellar microrobots for diagnostics.
Plasminogen promotes cholesterol efflux by the ABCA1 pathway (2017)

Using genetic and biochemical approaches, we investigated proteins that regulate macrophage cholesterol efflux capacity (CEC) and ABCA1-specific CEC (ABCA1 CEC), 2 functional assays that predict cardiovascular disease (CVD). Macrophage CEC and the concentration of HDL particles were markedly reduced in mice deficient in apolipoprotein A-I (APOA1) or apolipoprotein E (APOE) but not apolipoprotein A-IV (APOA4). ABCA1 CEC was markedly reduced in APOA1-deficient mice but was barely affected in mice deficient in APOE or APOA4. High-resolution size-exclusion chromatography of plasma produced 2 major peaks of ABCA1 CEC activity. The early-eluting peak, which coeluted with HDL, was markedly reduced in APOA1- or APOE-deficient mice. The late-eluting peak was modestly reduced in APOA1-deficient mice but little affected in APOE- or APOA4-deficient mice. Ion-exchange chromatography and shotgun proteomics suggested that plasminogen (PLG) accounted for a substantial fraction of the ABCA1 CEC activity in the peak not associated with HDL. Human PLG promoted cholesterol efflux by the ABCA1 pathway, and PLG-dependent efflux was inhibited by lipoprotein(a) [Lp(a)]. Our observations identify APOA1, APOE, and PLG as key determinants of CEC. Because PLG and Lp(a) associate with human CVD risk, interplay among the proteins might affect atherosclerosis by regulating cholesterol efflux from macrophages.
Path Cover and Path Pack Inequalities for the Capacitated Fixed-Charge Network Flow Problem (2017)

Capacitated fixed-charge network flows are used to model a variety of problems in telecommunication, facility location, production planning, and supply chain management. In this paper, we investigate capacitated path substructures and derive strong and easy-to-compute path cover and path pack inequalities. These inequalities are based on an explicit characterization of the submodular inequalities through a fast computation of parametric minimum cuts on a path, and they generalize the well-known flow cover and flow pack inequalities for the single-node relaxations of fixed-charge flow models. We provide necessary and sufficient facet conditions. Computational results demonstrate the effectiveness of the inequalities when used as cuts in a branch-and-cut algorithm.
Mechanical and Elastic Properties of Sulfur Vulcanized EPDM as a Function of Third Monomer Content (2001)

Abstract A comparison is made of the vulcanization kinetics as studied with rheometry and of the mechanical and elastic properties for 65 ethylene—propylene—diene rubbers (EPDMs) vulcanized with an activated sulfur system according to the ISO 4097 recipe. The selected 50 commercial EPDMs and 15 development grades provide a broad range of chemical and physical structures, including different third monomer (TM) structures and contents ([TM]). At low [TM] (up to 40 mmol TM/100 g EPDM: for example ∼4.5 wt % 5-ethylidene-2-norbornene, ENB) the mechanical and elastic properties of EPDM are strongly affected by [TM], but at higher [TM] they are more or less unaffected. For fully-cured EPDMs this transition at ∼40 mmol TM/100 g is independent of the TM type (ENB, dicyclopentadiene, DCPD, 1,4-hexadiene, HD, etc.). In previous Fourier transform Raman (FT-Raman) spectroscopy and 1 H NMR relaxation time studies it was established that for the ISO 4097 vulcanization system the average length of the sulfur crosslinks is ∼3 S-atoms/crosslink. From this it can be calculated that at ∼35 mmol TM/100 g EPDM a stoichiometric point is reached, where all sulfur is used for crosslinking. As a result, the properties of ISO 4097 EPDM vulcanizates level off when [TM] is increased beyond the stoichiometric point. The scatter in data at high [TM] is due to both experimental errors and differences in ethene/propene ratio, molecular weight (distribution) and/or degree of branching. It should be noted that the maximum cure rate (RH), being a kinetic parameter, remains dependent on [TM] over the whole chemical composition range although it also levels off at very high [TM]. In contrast to other studies it was found that RH is first order in both [TM] and [sulfur] at low [TM].
Table S2 from Medium-throughput Drug Screening of Patient-derived Organoids from Colorectal Peritoneal Metastases to Direct Personalized Therapy (2023)

&lt;p&gt;Patient characteristics &amp; analyses.&lt;/p&gt;
Establishing an Artificial Pathway for De Novo Biosynthesis of Vanillyl Alcohol in Escherichia coli (2017)

Vanillyl alcohol is a phenolic alcohol and is used as a flavoring agent in foods and beverages. In this paper, we propose a novel artificial pathway for microbial production of vanillyl alcohol from simple carbon sources. The pathway extends from 4-hydroxybenzoic acid (4-HBA), and needs only three heterologous enzymes, p-hydroxybenzoate hydroxylase (PobA), carboxylic acid reductase (CAR) and caffeate O-methyltransferase (COMT). First, we examined the promiscuous activity of COMT toward 3,4-dihydroxybenzyl alcohol and found a k<sub>cat</sub> value of 0.097 s<sup>-1</sup>. Meanwhile, 499.36 mg/L vanillyl alcohol was produced by COMT in vivo catalysis when fed with 1000 mg/L 3,4-dihydroxybenzyl alcohol. In the following experiment, de novo biosynthesis of vanillyl alcohol was carried out and 240.69 mg/L vanillyl alcohol was produced via modular optimization of pathway genes. This work was to date the first achievement for microbial production of vanillyl alcohol. Additionally, the present study demonstrates the application of enzyme promiscuity of COMT in the design of an artificial pathway for the production of high-value methylated aromatic compounds.
Combustion Characteristics of Natural Gas Fueled, Premixed Turbulent Jet Flame Arrays Confined in a Hexagonal Combustor (2019)

Abstract In order to extend the operation regime of existing gas turbine combustion systems to lower the minimum loads, the applicability of matrix burners (arrays of jet flames) as an alternative to conventional swirl stabilized burners has been considered. In comparison to well-studied single jet flame systems, the effects of geometry and thermodynamic parameters on characteristics of matrix burner systems have not been studied in detail. Information, which is essential for design processes e.g. scaling of matrix burners, is not yet available in public domain. This work involves a systematic investigation of a matrix burner system operating at highly turbulent flow conditions (Reynolds Number ≈ 20000) prevailing in gas turbine combustion systems. In order to understand the effects of geometrical scaling, three variants of jet diameter have been investigated. A detailed test campaign including lean blow out limits detection, velocity field measurement and hydroxyl radical (OH*) chemiluminescence recording has been conducted. Influence of variation in stoichiometry and exit velocity of fuel-air mixture has been captured. The results show that it is possible to generalize the scaling of the matrix burner using the well-known Peclet criterion.
Urine Stone Risk Factors in Nephrolithiasis Patients With and Without Bowel Disease (2005)

No AccessJournal of UrologyAdult Urology: Urological Survey: Urolithiasis, Endourology And Laparoscopy1 Mar 2005Urine Stone Risk Factors in Nephrolithiasis Patients With and Without Bowel Disease Ralph V. ClaymanM.D. Ralph V. ClaymanRalph V. Clayman More articles by this author View All Author Informationhttps://doi.org/10.1097/01.ju.0000152202.47215.1bAboutFull TextPDF ToolsAdd to favoritesDownload CitationsTrack CitationsPermissionsReprints ShareFacebookLinked InTwitterEmail "Urine Stone Risk Factors in Nephrolithiasis Patients With and Without Bowel Disease." The Journal of Urology, 173(3), p. 866 © 2005 by American Urological Association, Inc.FiguresReferencesRelatedDetailsCited ByAssimos D (2018) Re: Characterization of Urolithiasis in Patients following Lower Urinary Tract Reconstruction with Intestinal SegmentsJournal of Urology, VOL. 198, NO. 3, (479-479), Online publication date: 1-Sep-2017. Volume 173Issue 3March 2005Page: 866 Advertisement Copyright & Permissions© 2005 by American Urological Association, Inc.MetricsAuthor Information Ralph V. Clayman More articles by this author Expand All Advertisement PDF DownloadLoading ...
Effect of mutations on the binding and translocation functions of a chloroplast transit peptide. (1989)

We studied transport and binding to intact chloroplasts of 10 mutants in three regions of the transit peptide of a precursor to the small subunit of ribulose 1,5-bisphosphate carboxylase/oxygenase [3-phospho-D-glycerate carboxy-lyase (transphosphorylating), E.C.4.1.1.39]. Transport was assayed in a reconstituted system using isolated pea chloroplasts and radioactively labeled precursor. Binding to the chloroplast envelope was assayed in a similar manner using chloroplasts pretreated with nigericin. Most mutants showed a dramatically decreased capacity of binding, although some of them transported relatively well. The accumulation of the mutant proteins inside the chloroplast as a function of time was examined. Although the authentic small subunit precursor was imported rapidly, uptake of most mutant precursors was considerably slower and continued until the last time point examined. In terms of assigning functions to individual regions, we found that at least the middle region and parts of the amino and the carboxyl termini of the transit peptide are more important for receptor binding than for translocation. A two-step processing mechanism has been postulated for the maturation of the small subunit precursor. This model predicts the occurrence of processing intermediates. When precursors carrying carboxyl-terminal deletions were presented to the chloroplast, no defined intermediates could be detected. Instead, a number of proteins, probably resulting from aberrant processing, accumulated simultaneously inside the chloroplasts.
A High Concentration of Epidermal Growth Factor Increases the Growth and Survival of Neurogenic Radial Glial Cells Within Human Neurosphere Cultures (2007)

Human neural progenitor cells (hNPC) isolated from the fetal cortex can be expanded as aggregates of cells termed neurospheres. Traditional methods have used 20 ng/ml epidermal growth factor (EGF) to drive the proliferation of these cells. Here, we show that 100 ng/ml EGF can significantly increase growth rates of hNPC at later passages. This was through increased survival of dividing cells rather than increased proliferation and associated with prolonged activation of ErbB2 and phosphorylated Akt. High EGF also resulted in a larger proportion of elongated "radial glial"-like cells within the growing neurospheres and increased expression of the radial glial markers. The number of new neurons generated from cultures maintained in 100 ng/ml EGF was significantly higher than from 20 ng/ml EGF. Thus, high concentrations of EGF increase the survival of a highly neurogenic human radial glial cell.
Digital Imaging Technology in Trauma Education: A Quantum Leap Forward (1999)

Assistant ProfessorDepartments of Critical Care and AnesthesiologyUniversity of Texas/M.D. Anderson Cancer Center, andDepartment of AnesthesiologyBaylor College of MedicineHouston, TexasE-mail: [email protected]
VIGraph – A Framework for Verifiable Information (2017)

In order to avail of some service, a user may need to share with a service provider her personal chronological information, e.g., identity, financial record, health information and so on. In the context of financial organisations, a process often referred to as the know your customer (KYC) is carried out by financial organisations to collect information about their customers. Sharing this information with multiple service providers duplicates the data making it difficult to keep it up-to-date as well as verify. Furthermore, the user has limited to no control over the, mostly sensitive, data that is released to such organisations. In this preliminary work, we propose an efficient framework – Verifiable Information Graph or VIGraph – based on generalised hash trees, which can be used for verification of data with selective release of sensitive information. Throughout the paper, we use personal profile information as the running example to which our proposed framework is applied.
Faculty Opinions recommendation of Structural identification of a bacterial quorum-sensing signal containing boron. (2002)

Cell-cell communication in bacteria is accomplished through the exchange of extracellular signalling molecules called autoinducers. This process, termed quorum sensing, allows bacterial populations to coordinate gene expression. Community cooperation probably enhances the effectiveness of processes such as bioluminescence, virulence factor expression, antibiotic production and biofilm development. Unlike other autoinducers, which are specific to a particular species of bacteria, a recently discovered autoinducer (AI-2) is produced by a large number of bacterial species. AI-2 has been proposed to serve as a 'universal' signal for inter-species communication. The chemical identity of AI-2 has, however, proved elusive. Here we present the crystal structure of an AI-2 sensor protein, LuxP, in a complex with autoinducer. The bound ligand is a furanosyl borate diester that bears no resemblance to previously characterized autoinducers. Our findings suggest that addition of naturally occurring borate to an AI-2 precursor generates active AI-2. Furthermore, they indicate a potential biological role for boron, an element required by a number of organisms but for unknown reasons. PMID: 11823863
In vitroandin vivopharmacological profile of UFP‐512, a novel selective δ‐opioid receptor agonist; correlations between desensitization and tolerance (2007)

There was a correlation between weak desensitization, significant internalization and recycling of the human DOP receptors and lack of tolerance to UFP-512. This suggests that this compound would be a promising drug prototype for exploring innovative treatments for mood disorders.
Three dimensional conformal postoperative radiotherapy for unilateral parotid gland cancer: A comparison of three different parotid gland irradiation techniques (2013)

IntroductionPostoperative radiotherapy of the parotid gland could be achieved with various radiotherapy techniques. However they irradiate differently the surrounding organs at risk (OARs) in particular the cochlea, oral cavity & contralateral parotid causing significant increase in the risk of oral mucositis, xerostomia, and hearing deficits on the irradiated side.ObjectivesThe aim of this study was to compare radiation doses received by target volume and different surrounding OARs using three different parotid irradiation techniques aiming to achieve the optimum technique which shows adequate target coverage and sparing of surrounding OARs during postoperative 3DCRT treatment of parotid gland cancer patients.MethodologyTen patients diagnosed as having parotid cancer were included in this study. They were subjected to CT simulation and scans were transferred to the treatment planning system. Target volumes and contralateral parotid, oral cavity, cochlea, spinal cord, brain stem, eyes, lenses and optic nerves were contoured. Three plans were done using (a) ipsilateral oblique wedged photon pair, (b) oblique wedged photon pair and direct lateral field, and (c) ipsilateral mixed photon electron beams.For three plans, the dose volume parameters (DVPs) for target volume and surrounding OARs were compared and analyzed statistically.ResultsTarget dose coverage was adequate and comparable for techniques 1 and 2. Technique 2 showed the best dose homogeneity and conformity and lowest max dose to PTV and to the whole body and although the dose to OARs was higher compared to technique 1 it was far lower than OARs tolerance. On the other hand, technique 3 showed unaccepted underdose & dose inhomogeneity within the PTV, the highest doses to OARs and the highest PTV max and body max dose.ConclusionThe ipsilateral oblique wedged photon pair and direct lateral photon field technique is an optimal treatment technique for parotid cancer patients in comparison to other plans.
An integrated quantum network node in diamond (2019)

We present quantum network nodes that leverage integration of nanophotonic, electromechanical, and microwave technology to control the optical and spin properties of silicon-vacancy (SiV) color-centers in diamond. We demonstrate strain induced quantum interference between SiV color centers coupled to nanophotonic devices.
Adenovirus Transduction and Culture Conditions Affect the Immunogenicity of Murine Dendritic Cells (2005)

Adenovirus vectors encoding carcinoembryonic antigen (Ad-CEA) or costimulatory molecules CD80, intercellular adhesion molecule-1 (ICAM-1) and leucocyte function-associated antigen-3 (LFA-3) (Ad-STIM) were used to transduce murine bone marrow-derived dendritic cells (BMDC). BMDC were characterized for expression of activation markers and for their ability to elicit protective immunity against MC38-CEA tumours in wildtype and CEA-transgenic (CEA-tg) mice. To determine optimal culture conditions, studies were conducted using BMDC cultured in heterologous bovine serum or autologous mouse serum. Transduction of cells grown in presence of heterologous serum increased the expression of costimulatory molecules, major histocompatibility complex class II, of IL-6 and IL-12. Upon vaccination, tumour protection was not specific and was observed also with untransduced cells. Transduced BMDC cultured in the presence of autologous serum showed low expression of the activation markers, did not express IL-6 and had reduced ability to stimulate T-cell proliferation. Nonetheless, CEA-specific CD8+ T-cell response was enhanced upon coinfection of Ad-STIM and Ad-CEA in both mouse strains, although this immune response was not sufficient to protect CEA-tg mice from tumour challenge. These studies support the use of BMDC transduced with Ad vectors encoding tumour antigens for cancer immunotherapy and demonstrate that culture conditions greatly affect the immunological properties of these cells.
Cost effective 300mm large scale eWLB (embedded Wafer Level BGA) technology (2011)

This paper will highlight some of the recent advancements in 300mm eWLB wafer development. Compared to 200mm case, 300mm eWLB wafer has more warpage and process issues due to its area increase. Thermo-mechanical simulation shows 100~150% more warpage with 300mm eWLB wafer compared to 200mm. So various design parameters were studied to optimized warpage, such as dielectric materials and thickness, molding compound thickness etc. This paper also presents study of process optimization for 300mm eWLB and on overall warpage behavior in different process steps. Finally 300mm eWLB test vehicles are fabricated and tested in JEDEC standard test conditions. It also describes mechanical characterization, reliability data including component/board level, challenges encountered and overcome, and future steps.
Use of genetically modified lactic acid bacteria and bifidobacteria as live delivery vectors for human and animal health (2022)

There is now strong evidence to support the interest in using lactic acid bacteria (LAB)in particular, strains of lactococci and lactobacilli, as well as bifidobacteria, for the development of new live vectors for human and animal health purposes. LAB are Gram-positive bacteria that have been used for millennia in the production of fermented foods. In addition, numerous studies have shown that genetically modified LAB and bifodobacteria can induce a systemic and mucosal immune response against certain antigens when administered mucosally. They are therefore good candidates for the development of new mucosal delivery strategies and are attractive alternatives to vaccines based on attenuated pathogenic bacteria whose use presents health risks. This article reviews the most recent research and advances in the use of LAB and bifidobacteria as live delivery vectors for human and animal health.
Thermo-Optic Switching Effect Based on Fluid-Filled Photonic Crystal Fiber (2009)

<para xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink"> We report a thermo-optic switching effect with a high extinction ratio of 30 dB by means of filling a fluid into air holes of a solid-core photonic crystal fiber (PCF). Such an effect can perform a turn <emphasis emphasistype="smcaps">on–off</emphasis> operation of the transmitted light via a small temperature adjustment of <formula formulatype="inline"> <tex Notation="TeX">$\pm$</tex></formula>10 <formula formulatype="inline"> <tex Notation="TeX">$^{\circ}\hbox{C}$</tex></formula>. The switching function attributes to the absorption of the filled fluid in combination with the interaction between the core mode and the excited “fluid rod” modes, resulting from the thermo-optic effect of the filled fluid. </para>
Evaluation of the communication latency over real-time channel in HARTS (2002)

In this paper, the end-to-end communication latency in HARTS (Hexagonal Architecture for Real-Time Systems) is evaluated, which depends on the intra-node delay as well as the inter-node delay. While the inter-node delay is bounded due to the point-to-point real-time channel, the intra-node delay is variable according to the message traffic and the internal structure of a HARTS node. The intra-node delay is evaluated analytically and by computer simulation for the various implementational models, and an arbitration algorithm is proposed to provide real-time scheduling for VMEbus-based HARTS node.