gebhart/patrepeval huggingface dataset:
Efficient genome editing in hematopoietic stem cells with helper-dependent Ad5/35 vectors expressing site-specific endonucleases under microRNA regulation (2015)

Genome editing with site-specific endonucleases has implications for basic biomedical research as well as for gene therapy. We generated helper-dependent, capsid-modified adenovirus (HD-Ad5/35) vectors for zinc-finger nuclease (ZFN)- or transcription activator-like effector nuclease (TALEN)-mediated genome editing in human CD34+ hematopoietic stem cells (HSCs) from mobilized adult donors. The production of these vectors required that ZFN and TALEN expression in HD-Ad5/35 producer 293-Cre cells was suppressed. To do this, we developed a microRNA (miRNA)-based system for regulation of gene expression based on miRNA expression profiling of 293-Cre and CD34+ cells. Using miR-183-5p and miR-218-5p based regulation of transgene gene expression, we first produced an HD-Ad5/35 vector expressing a ZFN specific to the HIV coreceptor gene ccr5. We demonstrated that HD-Ad5/35.ZFNmiR vector conferred ccr5 knock out in primitive HSC (i.e., long-term culture initiating cells and NOD/SCID repopulating cells). The ccr5 gene disruption frequency achieved in engrafted HSCs found in the bone marrow of transplanted mice is clinically relevant for HIV therapy considering that these cells can give rise to multiple lineages, including all the lineages that represent targets and reservoirs for HIV. We produced a second HD-Ad5/35 vector expressing a TALEN targeting the DNase hypersensitivity region 2 (HS2) within the globin locus control region. This vector has potential for targeted gene correction in hemoglobinopathies. The miRNA regulated HD-Ad5/35 vector platform for expression of site-specific endonucleases has numerous advantages over currently used vectors as a tool for genome engineering of HSCs for therapeutic purposes.
An in-cache address translation mechanism (1986)

In the design of SPUR, a high-performance multiprocessor workstation, the use of large caches and hardware-supported cache consistency suggests a new approach to virtual address translation. By performing translation in each processor's virtually-tagged cache, the need for separate translation lookaside buffers (TLBs) is eliminated. Eliminating the TLB substantially reduces the hardware cost and complexity of the translation mechanism and eliminates the translation consistency problem. Trace-driven simulations show that normal cache behavior is only minimally affected by caching page table entries, and that in many cases, using a separate device would actually reduce system performance.
Convenient Model To Describe the Combined Effects of Temperature and pH on Microbial Growth (1995)

A new model in which the maximum microbial specific growth rate ((mu)(infmax)) is described as a function of pH and temperature is presented. The seven parameters of this model are the three cardinal pH parameters (the pH below which no growth occurs, the pH above which no growth occurs, and the pH at which the (mu)(infmax) is optimal), the three cardinal temperature parameters (the temperature below which no growth occurs, the temperature above which no growth occurs, and the temperature at which the (mu)(infmax) is optimal), and the specific growth rate at the optimum temperature and optimum pH. The model is a combination of the cardinal temperature model with inflection and the cardinal pH model (CPM). The CPM was compared with the models of Wijtzes et al. and Zwietering et al. by using previously published data sets. The models were compared on the basis of the usual criteria (simplicity, biological significance and minimum number of parameters, applicability, quality of fit, minimum structural correlations, and ease of initial parameter estimation), and our results justified the choice of the CPM. Our combined model was constructed by using the hypothesis that the temperature and pH effects on the (mu)(infmax) are independent. An analysis of this new model with an Escherichia coli O157:H7 data set showed that there was a good correspondence between observed and calculated (mu)(infmax) values. The potential and convenience of the model are discussed.
Cargo-selective endosomal sorting for retrieval to the Golgi requires retromer (2004)

fEndosome-to-Golgi retrieval of the mannose 6-phosphate receptor (MPR) is required for lysosome biogenesis. Currently, this pathway is poorly understood. Analyses in yeast identified a complex of proteins called "retromer" that is essential for endosome-to-Golgi retrieval of the carboxypeptidase Y receptor Vps10p. Retromer comprises five distinct proteins: Vps35p, 29p, 26p, 17p, and 5p, which are conserved in mammals. Here, we show that retromer is required for the efficient retrieval of the cation-independent MPR (CI-MPR). Cells lacking mammalian VPS26 fail to retrieve the CI-MPR, resulting in either rapid degradation of or mislocalization to the plasma membrane. We have localized mVPS26 to multivesicular body endosomes by electron microscopy, and through the use of CD8 reporter protein constructs have examined the effect of loss of mVPS26 upon the trafficking of membrane proteins that cycle between the endosome and the Golgi. The data presented here support the hypothesis that retromer performs a selective function in endosome-to-Golgi transport, mediating retrieval of the CI-MPR, but not furin.
Solution Structure of the SH3 Domain from Bruton's Tyrosine Kinase<sup>,</sup> (1998)

X-linked agammaglobulinemia (XLA) is a heritable immunodeficiency caused by mutations in the gene coding for Bruton's tyrosine kinase (Btk). Btk belongs to the Tec family of tyrosine kinases. Each member of the family contains five regions and mutations causing XLA have been isolated in all five regions. We have determined the solution structure of the Src homology 3 (SH3) domain of Btk using two- and three-dimensional nuclear magnetic resonance (NMR) spectroscopy on natural abundance and 15N-labeled protein material. The structure determination is complemented by investigation of backbone dynamics based on 15N NMR relaxation. The Btk SH3 forms a well-defined structure and shows the typical SH3 topology of two short antiparallel beta-sheets packed almost perpendicular to each other in a sandwich-like fold. The N- and C-termini are more flexible as are peptide fragments in the RT and n-Src loops. The studied Btk SH3 fragment adopts two slowly interconverting conformations with a relative concentration ratio of 7:1. The overall fold of the minor form is similar to that of the major form, as judged on the basis of observed NOE connectivities and small chemical shift differences. A tryptophan (W251) ring flip is the favored mechanism for interconversion, although other possibilities cannot be excluded. The side chain of Y223, which becomes autophosphorylated upon activation of Btk, is exposed within the potential SH3 ligand binding site. Finally, we compare the present Btk SH3 structure with other SH3 structures.
Role of collocations and case-markers in word sense disambiguation: a clustering-based approach (2005)

In this paper we present a new unsupervised approach for Word Sense Disambiguation (WSD) based on clustering. We also explore the applicability of case markers in WSD for inflectional languages such as Tamil. All the occurrences of an ambiguous word are grouped into as many unique clusters as the number of senses of the ambiguous word in such a way that each cluster contains occurrences in a single sense. After clustering the occurrences, highly reliable collocation words indicating strongly one particular sense of the ambiguous word are automatically selected from each cluster. Then for each set of collocations obtained, senses are assigned manually. This approach when compared to Decision tree approach (Yarowsky 1995) requires less manual labour. In our approach, collocations are induced automatically, and manual efforts are needed only in assigning the senses to different set of collocations, which is much easier task compared to Yarowsky’s method. The hypothesis for case-marker based disambiguation is that Each sense of the ambiguous word takes different case markers in its neighbourhood. Our preliminary analysis proves the worthiness of this property and this method combined with the clustering based approach performs well in disambiguating the senses. Though the tested accuracy is around 84% now, we are hopeful of approaching the accuracy levels of (Yarowsky 1995).
Transepithelial chemotaxis of rat peritoneal exudate cells. (1983)

The migration of peritoneal exudate (PE) cells into plain Millipore filters mounted in Boyden chambers occurs under random, chemokinetic and chemotactic conditions. Significant migration of such cells in vivo, however, involves both transendothelial and transepithelial penetration and occurs predominantly under pathological conditions where chemotactic agents are presumed to be present in gradient form. When Madin-Darby canine kidney (MDCK) epithelial cells are grown as a confluent monolayer on the Millipore filter of a Boyden chamber, transepithelial migration is seen only under chemotactic conditions thus modelling in vivo behaviour more effectively. The MDCK cell line exists as 2 variant strains which model different regions of the mammalian nephron. Strain I MDCK cells share features of the distal and collecting tubules and have relatively high junctional resistance (greater than 1k omega cm2). Strain II MDCK cells model the proximal segment of the nephron and have relatively low junctional resistance (c. 70 omega cm2). We have found that PE cells penetrate the less resistant strain II MDCK monolayer at a faster rate (as assessed by leading front migration) than they penetrate the tighter strain I monolayer. We have also utilized the electrophysiological features of MDCK monolayers to monitor transepithelial penetration. Our electrophysiological data indicate that rat PE cells penetrate MDCK monolayers of either strain by a transjunctional route with consequent reversible dissolution of the junctional complex. This extracellular path of PE cell migration was confirmed by ultrastructural observations. The extent of junctional dissolution and the delay in re-establishment of monolayer integrity (as assessed by electrophysiological means) are related to the concentration of PE cells added to the MDCK monolayer. Brief treatment (10 min) of the MDCK monolayer with the cation chelating agent EDTA also disrupts monolayer integrity, although its re-establishment is significantly faster than when disruption occurs by PE cell transmigration. Our results show a clear parallel between PE cell migration across an MDCK monolayer and changes in its electrophysiological parameters and thus suggest that transepithelial chemotaxis may be directly assessed by electrophysiological means. The use of Boyden chambers modified by the incorporation of epithelial monolayers may prove useful in in vitro studies of inflammation and could be adapted for studies of other pathological processes, such as metastasis, where considerable cell invasion is involved.
Design of the Operating System Virtualization on L4 Microkernel (2008)

The importance of the virtualization in embedded computing area is currently emerging. The virtualization can enhance system flexibility by enabling the concurrent execution of an application OS and a real-time OS (RTOS) on the same processor. L4 microkernel can be used as an efficient hypervisor which provides environment for operating systems virtualization. In order to run the application OSes on L4 microkernel, the application OSes should be adapted. The source code of Linux kernel can be readily accessed and modified. Hence, the Linux kernel is chosen as virtualized operating systems. In this paper, the architecture for virtualization of Linux kernel which is based on L4 microkernel is proposed.
A High Rated Solar Water Distillation Unit for Solar Homes (2016)

India is presently focusing on complete utilization of solar energy and saving fossil fuels, which are limited. Various solar energy systems like solar cookers, solar water heaters, solar lanterns, solar PV lights, and solar lamps are continuously availing by the people of India at a low cost and on good subsidies. Apart from this, India is a solar energy promising country with a good number of solar homes (carrying solar energy systems) in its various locations. The present paper focuses on a unique combination of solar dish cooker (SDC) and solar water heater (SWH) to produce distilled water with a high distillate and a high daily productivity. The procedure has been discussed on the basis of experimental testing to produce distilled water by combining an evacuated type SWH and a SDC. Experimentation has been carried out in MIT, Moradabad (longitude, 28.83°N, and latitude, 78.78°E) by developing the same experimental setup on behalf of solar homes. The daily productivity of distilled water was found around 3.66 litres per day in full sunshine hours for an approximated pH value of 7.7 and a ppm value of 21. The payback period (PBP) has been estimated around 1.16 years of the present system.
Controlled trial of high-concentration capsaicin patch for treatment of painful HIV neuropathy (2008)

A single NGX-4010 application was safe and provided at least 12 weeks of pain reduction in patients with HIV-associated distal sensory polyneuropathy. These results suggest that NGX-4010 could provide a promising new treatment for painful HIV neuropathy.
DNA-friendly Cu(<scp>ii</scp>)/TEMPO-catalyzed 5-hydroxymethylcytosine-specific oxidation (2017)

The mixture of copper(ii) perchlorate and 2,2,6,6-tetramethylpiperidine-1-oxyl (TEMPO) mildly and specifically oxidized 5-hydroxymethylcytosine to yield 5-formylcytosine because of its allyl alcohol specificity. The genomic DNA oxidized at 5-hydroxymethylcytosine by the copper(ii)/TEMPO oxidation was efficiently analyzed using various practical methods: DNA cleavage by piperidine, specific functionalization by hydrazone formation, and genome-wide high-resolution microarray.
The Influence of Solvent Properties and Functionality on the Electrospinnability of Polystyrene Nanofibers (2006)

Abstract Summary: In order to produce nanometer‐sized fibers at an industrial scale, not only the morphology but also the production rate of fibers is important. The effect of solvent properties and functionality on the production rate of electrospun PS nanofibers was investigated using eighteen different solvents. The solution concentration was varied between 10 and 30% w/v. Electrospinning of PS solutions was carried out at various applied voltages and tip‐to‐collector distances The production rate of the obtained PS nanofibers was quantified in terms of electrospinnability. We found that the chance for the resulting PS solution to be spinnable is greater for solvents with high dipole moment and low viscosity. The solvent that provided the highest electrospinnability for polystyrene was DMF and the functionalities that promoted high dipole moment and thus high spinnability were the carbonyl group and the nitrogen group with free electrons. General guidelines for choosing suitable solvents for successful production of electrospun nanofibers have also been proposed. SEM image of PS 685D at 200× magnification and the %‐coverage of the fibers obtained by using DMF, chloroform, and 1,4‐dioxane. magnified image SEM image of PS 685D at 200× magnification and the %‐coverage of the fibers obtained by using DMF, chloroform, and 1,4‐dioxane.
Multilength Scale Studies of the Confined Crystallization in Poly(<scp>l</scp>-lactide)-<i>block</i>-Poly(ethylene glycol) Copolymer (2012)

In this work, we investigated the structure and morphology formation in crystalline–crystalline diblock copolymer of poly(l-lactide)-block-poly(ethylene glycol) (PLLA-b-PEG) on different length scales with optical microscopy (OM), atomic force microscopy (AFM), synchrotron time-resolved small-angle X-ray scattering (TR-SAXS) and wide-angle X-ray scattering (WAXS) methods. The PLLA-b-PEG copolymer with 5000 of number-average of molecular weight of PLLA and PEG blocks was used in this work. The structure and morphology of PLLA-b-PEG copolymers were formatted by a two-step crystallization process: i.e., the PLLA block crystallized fully at 110 °C in the first step, and then the PEG block crystallized fully at 30 °C in the second step. The OM, AFM, and SAXS results indicated that the PEG block crystallized in the multilength scales amorphous regions confined by PLLA crystals. The PEG block crystallized not only in the interlamellar regions of PLLA crystals, but also in the interfibrillar regions of PLLA. However, the subsequent crystallization of PEG block did not alter the foregoing spherulitic morphology of PLLA on the micrometer scale.
임상병리(학)과 실험 실습기자재 표준화에 대한 설문조사 분석 (2019)

The purpose of this study was to create a standardized list of equipment necessary to set up a biomedical laboratory science department. A survey of professors that worked in university biomedical laboratory science departments was conducted between May 10, 2019 and August 31, 2019. Their responses were then applied to the Likert scale. The equipment with a score of 4.5 or higher was identified as equipment that was highly necessity for a biomedical laboratory science department. In this study, we seperated the necessary equipment by clinical and urinary chemistry, hematology, transfusion, microbiology, clinical physiology, histopathology and cytology, immunoserology and molecular biology laboratories and common materials. This study is expected to be used as data for the standardization of equipment in biomedical laboratory science departments, which is an important step towards the standardization of curriculum of said departments.
Research on Audit Supervision of Internet Finance (2020)

Internet finance is a new form of finance that applies capacities found on the Internet to the traditional financial industry. However, at the present stage, internet finance is faced with many problems, such as overly rapid development and non-standard operation. This paper adopted the evolutionary game theory as the analysis tool to design an evolutionary game model of government audit supervision of Internet finance, and analyzed the evolutionary stability of the strategies used by Internet financial institutions and government financial audit supervision departments. A simulation calculation was carried out by placing the calculation experimental method “Scenario–Coping”, which simulated the initial probability of different strategies adopted by both parties of the game and evaluated the influence of changing the penalty intensity of Internet financial institutions’ violation on the outcome of the evolutionary game. Based on the simulation analysis, the paper provided policy suggestions on strengthening audit supervision and promoting its sustainable development from three aspects: strengthening the construction of the Internet financial credit information system, improving Internet financial laws and regulations, and improving the early warning level of Internet financial credit risk.
Reverse Osmosis Biofilm Dispersal by Osmotic Back-Flushing: Cleaning via Substratum Perforation (2014)

We have demonstrated the application of osmotic back-flushing (OBF) for the removal of biofilms from reverse osmosis (RO) membranes and proposed a new biofilm dispersal mechanism. OBF was conducted in a laboratory-scale RO test cell by introducing a sequence of hypersaline solution (1.5 M NaCl) flushes into the feedwater, while still maintaining the applied hydraulic pressure (13.8 bar). OBF resulted in significant biofilm detachment, leaving a thin, perforated bacterial film (24 μm thickness) with vertical cavities ranging from 15 to 50 μm in diameter. Application of OBF led to significant reductionin the biovolume (70–79%) and substantial removal of total organic carbon and proteins (78 and 66%, respectively), resulting in 63% permeate water flux recovery. Our findings demonstrate the potential of this chemical-free RO membrane cleaning method while highlighting the possible challenges of the technique.
Reverse circulation air drilling can reduce well bore damage (1993)

Reverse circulation air drilling coupled with an air dryer at the surface helped eliminate formation damage in several gas wells. During reverse circulation drilling, the air flows down the annulus and up the drill pipe. The following were the three primary objectives of damage-free drilling (DFD): Reducing damage so the initial open flows would more accurately reflect natural permeability. Reducing damage for diagnostic tools (temperature logs, noise logs, mud [gas composition] logs, and borehole television) to better detect liquid and gas entry points. Improving sampling by returning larger cuttings with shorter and more precise lag times. The secondary objectives were to reduce drilling costs through the following: Lowering required circulating air volumes when cuttings are reversed up the drillstring. Reducing water influx from shallow water zones because of annular back pressure during circulation. Improving penetration rates for larger holes. This describes tests while drilling; the borehole television used in investigating air-drilled well bores; permeability tests; cuttings sample; drilling parameters; and operations and results from two field tests.
Effect of inulin on growth and bacteriocin production by <i>Lactobacillus plantarum</i> in stationary and shaken cultures (2015)

Summary The prebiotic effect of inulin added to MRS medium on growth and bacteriocin production by L. plantarum ST16 Pa was investigated in stationary cultures in anaerobic jars with medium containing 0.025% sodium thioglycolate or in flasks shaken at 100 rpm. In the presence of 1% inulin in anaerobic stationary cultures, this strain produced lactic acid at a level that was 36.5% higher than in the absence of the polysaccharide. In shaken cultures without inulin, cell count was 54% higher than in the stationary ones. Under stationary conditions in anaerobic jars, the addition of inulin increased the maximum specific growth rate from 0.37 to 0.49 h −1 and reduced the generation time from 1.85 h to 1.40 h. Consequently, the exponential phase was shortened from 12 to 9 h when the cells were grown in stationary cultures with the oxygen scavenger. Despite this effect of inulin on growth rate, stationary cultures without inulin displayed higher antimicrobial activity against Listeria monocytogenes L104 (3200 AU/mL) than cultures with inulin (1600 AU/mL); therefore, inulin behaved as a compound able to accelerate growth rather than to stimulate bacteriocin production. The results presented in this study are very promising, as L. monocytogenes is a well‐known foodborne pathogenic microorganism. Moreover , L. plantarum ST16 Pa has proven to be a potential producer of a natural food preservative at an industrial level.