gebhart/patrepeval huggingface dataset:
Regulated Expression of ATF5 Is Required for the Progression of Neural Progenitor Cells to Neurons (2003)

An important milestone in brain development is the transition of neuroprogenitor cells to postmitotic neurons. We report that the bZIP transcription factor ATF5 plays a major regulatory role in this process. In developing brain ATF5 expression is high within ventricular zones containing neural stem and progenitor cells and is undetectable in postmitotic neurons. In attached clonal neurosphere cultures ATF5 is expressed by neural stem/progenitor cells and is undetectable in tau-positive neurons. In PC12 cell cultures nerve growth factor (NGF) dramatically downregulates endogenous ATF5 protein and transcripts, whereas exogenous ATF5 suppresses NGF-promoted neurite outgrowth. Such inhibition requires the repression of CRE sites. In contrast, loss of function conferred by dominant-negative ATF5 accelerates NGF-promoted neuritogenesis. Exogenous ATF5 also suppresses, and dominant-negative ATF5 and a small-interfering RNA targeted to ATF5 promote, neurogenesis by cultured nestin-positive telencephalic cells. These findings indicate that ATF5 blocks the differentiation of neuroprogenitor cells into neurons and must be downregulated to permit this process to occur.
Phase 1 study results of the type II glycoengineered humanized anti-CD20 monoclonal antibody obinutuzumab (GA101) in B-cell lymphoma patients (2012)

Whereas the chimeric type I anti-CD20 Ab rituximab has improved outcomes for patients with B-cell malignancies significantly, many patients with non-Hodgkin lymphoma (NHL) remain incurable. Obinutuzumab (GA101) is a glycoengineered, humanized anti-CD20 type II Ab that has demonstrated superior activity against type I Abs in vitro and in preclinical studies. In the present study, we evaluated the safety, efficacy, and pharmacokinetics of GA101 in a phase 1 study of 21 patients with heavily pretreated, relapsed, or refractory CD20(+) indolent NHL. Patients received GA101 in a dose-escalating fashion (3 per cohort, range 50/100-1200/2000 mg) for 8 × 21-day cycles. The majority of adverse events (AEs) were grades 1 and 2 (114 of 132 total AEs). Seven patients reported a total of 18 grade 3 or 4 AEs. Infusion-related reactions were the most common AE, with most occurring during the first infusion and resolving with appropriate management. Three patients experienced grade 3 or 4 drug-related infusion-related reactions. The best overall response was 43%, with 5 complete responses and 4 partial responses. Data from this study suggest that GA101 was well tolerated and demonstrated encouraging activity in patients with previously treated NHL up to doses of 2000 mg. This trial is registered at www.clinicaltrials.gov as NCT00517530.
IndustryNet: a model for commerce on the World Wide Web (1995)

In describing a Web-based on-line information gathering tool, the authors show how the system adapts to meet each user's needs and learns from user behaviour. One of the system that has begun to make good on the early predictions is the IndustryNet marketplace on the Web. IndustryNet provides several services for its users. It is a news service, an on-line trade journal that provides instant reader service information, a searchable archive of new product announcements, a searchable archive of design application cases, and a provider of interactive access to manufacturer and distributor information. We outline the IndustryNet approach to conducting commerce on the Internet. We examine how IndustryNet is enhancing the relationship between buyers/specifiers, manufacturers, and distributors.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
The Ring Opening Metathesis Polymerisation Toolbox (2004)

Abstract Summary: The success of metathesis chemistry techniques has sparked a tremendous interest in polymer and material chemistry. This contribution provides an overview of the state of the art in ring opening metathesis polymerisation (ROMP). It is intended to provide the reader with useful information on the interplay of initiators, monomers, and reaction conditions, thus aiding polymer chemists to utilise the ROMP toolbox. Prominent and illustrative examples from current research are given in the article. The “ROMP toolbox”. magnified image The “ROMP toolbox”.
Technique to improve the effective fill factor of digital mammographic imagers (1998)

Current clinical mammographic imaging has been limited to screen/film, but advances in photodetector and x-ray converter technology has opened up the possibility of significantly improving mammographic screening with digital imagers. One limitation of some recently developed in direct detection imagers is a limited optical fill factor in the photodetector. A small fill factor reduces the amount of light collected from individual x-ray interactions in the screen. It can also lead to an overall reduction in the number of x-ray quanta detected. In addition, the fill factor usually decreases with an increase in photodetector resolution. To reduce these effects, we propose a technique for improving the effective fill factor of any indirect detection imager by incorporating focusing microlens arrays between the phosphor screen and the photodetector. In this investigation, we evaluate the light collection efficiencies of our proposed imager/microlens combination using Monte Carlo simulation and optical ray tracing.
3-D RPET-NET: Development of a 3-D PET Imaging Convolutional Neural Network for Radiomics Analysis and Outcome Prediction (2019)

Radiomics is now widely used to improve the prediction of treatment response and patient prognosis in oncology. In this paper, we propose an end-to-end prediction model based on a 3-D convolutional neural network (CNN), called 3-D RPET-NET, that extracts 3-D image features through four layers. Our model was evaluated for its ability to predict the response to radio-chemotherapy in 97 patients with esophageal cancer from positron emission tomography (PET) images. The accuracy of the model was compared to five other methods proposed in the literature for PET images, based on 2-D CNN and random forest algorithms. The role of the volume of interest on the accuracy of 3-D RPET-NET was also evaluated using isotropic margins of 1-4 cm around the tumor volume. After segmentation of the lesion using a fixed threshold value of 40% of the maximum standard uptake value, the best accuracy of 3-D RPET-NET reached 72% and outperformed the other methods tested. We also showed that using an isotropic margin of 2 cm around the tumor volume improved the performances of 3-D RPET-NET to reach an accuracy of 75%.
The Influence of Charge Transport and Recombination on the Performance of Dye‐Sensitized Solar Cells (2008)

Electrochemical impedance spectroscopy (EIS) and transient voltage decay measurements are applied to compare the performance of dye sensitized solar cells (DSCs) using organic electrolytes, ionic liquids and organic-hole conductors as hole transport materials (HTM). Nano-crystalline titania films sensitized by the same heteroleptic ruthenium complex NaRu(4-carboxylic acid-4'-carboxylate) (4,4'-dinonyl-2,2'-bipyridyl)(NCS)(2) , coded Z-907Na are employed as working electrodes. The influence of the nature of the HTM on the photovoltaic figures of merit, that is, the open circuit voltage, short circuit photocurrent and fill factor is evaluated. In order to derive the electron lifetime, as well as the electron diffusion coefficient and charge collection efficiency, EIS measurements are performed in the dark and under illumination corresponding to realistic photovoltaic operating conditions of these mesoscopic solar cells. A theoretical model is established to interpret the frequency response off the impedance under open circuit conditions, which is conceptually similar to photovoltage transient decay measurements. Important information on factors that govern the dynamics of electron transport within the nanocrystalline TiO(2) film and charge recombination across the dye sensitized heterojunction is obtained.
FLIP: an internetwork protocol for supporting distributed systems (1993)

Most modern network protocols give adequate support for traditional applications such as file transfer and remote login. Distributed applications, however, have different requirements (e.g., efficient at-most-once remote procedure call even in the face of processor failures). Instead of using ad hoc protocols to meet each of the new requirements, we have designed a new protocol, called the Fast Local Internet Protocol (FLIP), that provides a clean and simple integrated approach to these new requirements. FLIP is an unreliable message protocol that provides both point-to-point communication and multicast communication, and requires almost no network management. Furthermore, by using FLIP we have simplified higher-level protocols such as remote procedure call and group communication, and enhanced support for process migration and security. A prototype implementation of FLIP has been built as part of the new kernel for the Amoeba distributed operating system, and is in daily use. Measurements of its performance are presented.
Glycosylation-dependent activity of baculovirus-expressed human liver carboxylesterases: cDNA cloning and characterization of two highly similar enzyme forms (1993)

A cDNA, designated hCE, encoding the entire sequence of a carboxylesterase, was isolated from a human liver lambda gt11 library. The hCE-deduced protein sequence contained 568 amino acids, including an 18 amino acid signal peptide sequence, and had a calculated molecular mass of the mature protein of 60,609 Da. A second cDNA, designated hCEv, was isolated from the same lambda gt11 library and contained a 3-bp deletion resulting in the loss of the final amino acid in the signal peptide sequence (Ala-1) and a second 3-bp deletion leading to an in-frame loss of Gln345. Expression of mRNA corresponding to both hCE and hCEv was detected in eight adult human liver samples, with individual levels varying 5-fold (hCE) and 12-fold (hCEv). A single immunoreactive protein was detected in 13 adult human liver samples when probed with antibody directed against a rat carboxylesterase. Based on allele-specific oligonucleotide hybridizations, we believe that the hCE and hCEv cDNAs represent two distinct members of the carboxylesterase family. The carboxylesterase genes were localized to human chromosome 16 using a somatic cell hybrid mapping strategy. Baculovirus expression of hCE in Sf9 cells produced a protein with an estimated molecular mass of 59,000 Da. This enzyme was able to hydrolyze aromatic and aliphatic esters but possessed no catalytic activity toward amides or a fatty acyl CoA ester. Baculovirus-mediated expression of the hCEv cDNA yielded a second protein of 56,000 Da resulting from inefficient N-glycosylation of the hCEv protein. Although the substrate specificity for the hCEv protein was identical to that of expressed hCE for any given substrate, the specific activity for the hCE protein was always higher than that for the hCEv protein. Tunicamycin inhibition studies provided the first evidence that N-glycosylation of these luminal enzymes is essential for maximal catalytic activity.
Effect of Systemic and Intrathecal Morphine in a Rat Model of Postoperative Pain (1997)

This is the first study to demonstrate that mechanical hyperalgesia to a nonpunctate stimulus occurs after a surgical incision in the rat. This rat model of postoperative has several similarities to postoperative patients: mechanical hyperalgesia to punctate and nonpunctate stimuli, nonevoked pain, and pain behaviors inhibited by SC and IT morphine. This model also may be useful for predicting analgesia by investigational agents for postoperative pain.
Electrospinning jets and nanofibrous structures (2011)

Electrospinning is a process that creates nanofibers through an electrically charged jet of polymer solution or melt. This technique is applicable to virtually every soluble or fusible polymer and is capable of spinning fibers in a variety of shapes and sizes with a wide range of properties to be used in a broad range of biomedical and industrial applications. Electrospinning requires a very simple and economical setup but is an intricate process that depends on several molecular, processing, and technical parameters. This article reviews information on the three stages of the electrospinning process (i.e., jet initiation, elongation, and solidification). Some of the unique properties of the electrospun structures have also been highlighted. This article also illustrates some recent innovations to modify the electrospinning process. The use of electrospun scaffolds in the field of tissue engineering and regenerative medicine has also been described.
Application of majority voting to pattern recognition: an analysis of its behavior and performance (1997)

It has been demonstrated that combining the decisions of several classifiers can lead to better recognition results. The combination can be implemented using a variety of strategies, among which majority vote is by far the simplest, and yet it has been found to be just as effective as more complicated schemes in improving the recognition results. This paper examines the mode of operation of the majority vote method in order to gain a deeper understanding of how and why it works, so that a more solid basis can be provided for its future applications to different data and/or domains. In the course of our research, we have analyzed this method from its foundations and obtained many new and original results regarding its behavior. Particular attention has been directed toward the changes in the correct and error rates when classifiers are added, and conditions are derived under which their addition/elimination would be valid for the specific objectives of the application. At the same time, our theoretical findings are compared against experimental results, and these results do reflect the trends predicted by the theoretical considerations.
Investigations into the Electrostatically Induced Aggregation of Au Nanoparticles (2000)

The aggregation of Au nanoparticles in solution is induced and influenced by cationic and oligocationic species. This solution-state aggregation bears similarities to multilayer formation on surfaces but is more facile because of the nanoparticles' intrinsic instability in solution. Aggregation is followed by transmission electron microscopy (TEM) and the appearance of features at λ = 600−900 nm in the absorbance spectrum. It is found that these features are a function of factors such as the aggregant size, charge, and concentration, and the method of mixing the components, and they can be related to aggregate morphology. It seems that there are two mechanisms that can act to cause aggregation. Multiply charged aggregants can bind nanoparticles together into dense aggregates, displaying a defined absorbance at ca. λ = 700 nm, whereas singly charged aggregants cause a slower aggregation into string-like aggregates with a less defined absorbance. Whereas multiply charged aggregants can “cross-link” the layers in a multilayer structure on a surface, singly charged aggregants cannot.
Protein engineering to increase the potential of a therapeutic antibody Fab for long-acting delivery to the eye (2017)

To date, ocular antibody therapies for the treatment of retinal diseases rely on injection of the drug into the vitreous chamber of the eye. Given the burden for patients undergoing this procedure, less frequent dosing through the use of long-acting delivery (LAD) technologies is highly desirable. These technologies usually require a highly concentrated formulation and the antibody must be stable against extended exposure to physiological conditions. Here we have increased the potential of a therapeutic antibody antigen-binding fragment (Fab) for LAD by using protein engineering to enhance the chemical and physical stability of the molecule. Structure-guided amino acid substitutions in a negatively charged complementarity determining region (CDR-L1) of an anti-factor D (AFD) Fab resulted in increased chemical stability and solubility. A variant of AFD (AFD.v8), which combines light chain substitutions (VL-D28S:D30E:D31S) with a substitution (VH-D61E) to stabilize a heavy chain isomerization site, retained complement factor D binding and inhibition potency and has properties suitable for LAD. This variant was amenable to high protein concentration (>250 mg/mL), low ionic strength formulation suitable for intravitreal injection. AFD.v8 had acceptable pharmacokinetic (PK) properties upon intravitreal injection in rabbits, and improved stability under both formulation and physiological conditions. Simulations of expected human PK behavior indicated greater exposure with a 25-mg dose enabled by the increased solubility of AFD.v8.
Robust sound source localization using a microphone array on a mobile robot (2004)

The hearing sense on a mobile robot is important because it is omnidirectional and it does not require direct line-of-sight with the sound source. Such capabilities can nicely complement vision to help localize a person or an interesting event in the environment. To do so the robot auditory system must be able to work in noisy, unknown and diverse environmental conditions. In this paper, we present a robust sound source localization method in three-dimensional space using an array of 8 microphones. The method is based on time delay of arrival estimation. Results show that a mobile robot can localize in real time different types of sound sources over a range of 3 meters and with a precision of 3/spl deg/.
STAR: ultrafast universal RNA-seq aligner (2012)

STAR is implemented as a standalone C++ code. STAR is free open source software distributed under GPLv3 license and can be downloaded from http://code.google.com/p/rna-star/.
Proteolytic Conversion of STAT3α to STAT3γ in Human Neutrophils (2004)

Four isoforms (alpha, beta, gamma, and delta) have been identified for signal transducer and activator of transcription 3 (STAT3). It has been reported that STAT3gamma, which is derived from STAT3alpha by limited proteolysis during granulocytic differentiation, is a major STAT3 isoform expressed in human neutrophils. We confirmed that STAT3gamma was a major STAT3 isoform detected in human neutrophil lysates prepared with the conventional lysis buffer. The enzymes capable of converting STAT3alpha to STAT3gamma in vitro were localized in neutrophil granule fraction and were released into the medium upon ionomycin stimulation. The enzyme activity was strongly inhibited by phenylmethylsulfonyl fluoride, CuSO(4), and ONO-5046 (a specific inhibitor of neutrophil elastase), but not by aprotinin, leupeptin, benzamidine, and EDTA. STAT3gamma was effectively generated in vitro from STAT3alpha by limited proteolysis with human neutrophil elastase or proteinase 3 but not cathepsin G. The converting activity in neutrophil lysates was reduced by immunodepletion of elastase but not proteinase 3. Unexpectedly, STAT3gamma was undetected in the lysates of neutrophil-derived cytoplasts, which lack granules, and the cytosol fraction prepared by nitrogen cavitation. The STAT3 isoform detected in these preparations was primarily STAT3alpha. STAT3gamma was also undetected in the lysates of PMSF-pretreated neutrophils and was markedly decreased in the lysates of ionomycin-pretreated neutrophils. These findings indicate that, in contrast to the previous reports, STAT3alpha, but not STAT3gamma, is primarily expressed in human neutrophils, and STAT3gamma is rapidly generated from STAT3alpha by limited proteolysis with granule-derived serine proteases during preparation of neutrophil lysates with the conventional lysis buffer.
Electrophysiological Findings During Ablation of Persistent Atrial Fibrillation With Electroanatomic Mapping and Double Lasso Catheter Technique (2005)

Background— Pulmonary veins (PVs) can be completely isolated with continuous circular lesions (CCLs) around the ipsilateral PVs. However, electrophysiological findings have not been described in detail during ablation of persistent atrial fibrillation (AF). Methods and Results— Forty patients with symptomatic persistent AF underwent complete isolation of the right-sided and left-sided ipsilateral PVs guided by 3D mapping and double Lasso technique during AF. Irrigated ablation was initially performed in the right-sided CCLs and subsequently in the left-sided CCLs. After complete isolation of both lateral PVs, stable sinus rhythm was achieved after AF termination in 12 patients; AF persisted and required cardioversion in 18 patients. In the remaining 10 patients, AF changed to left macroreentrant atrial tachycardia in 6 and common-type atrial flutter in 4 patients. All atrial tachycardias were successfully terminated during the procedure. Atrial tachyarrhythmias recurred in 15 of 40 patients at a median of 4 days after the initial ablation. A repeat ablation was performed at a median of 35 days after the initial procedure in 14 patients. During the repeat study, recovered PV conduction was found in 13 patients and successfully abolished by focal ablation of the conduction gap of the previous CCLs. After a mean of 8±2 months of follow-up, 38 (95%) of the 40 patients were free of AF. Conclusions— In patients with persistent AF, CCLs can result in either AF termination or conversion to macroreentrant atrial tachycardia in 55% of the patients. In addition, recovered PV conduction after the initial procedure is a dominant finding in recurrent atrial tachyarrhythmias and can be successfully abolished.
Localized, non-viral delivery of nucleic acids: Opportunities, challenges and current strategies (2014)

Localized delivery of drugs is an emerging field both with regards to drug delivery during disease as well as in tissue engineering. Despite significant achievements made in the last decades, the efficient delivery of proteins and peptides remains challenging, especially in cases requiring long-term release of proteins after application. The localized delivery of nucleic acids (NA) represents an interesting alternative due to higher physicochemical stability of NA, increased efficiency by harnessing cells as bioreactors for the production of required proteins and improved versatility with regards to expression of specific proteins through plasmid DNA or repression of gene products through siRNA. However, unlike most proteins and peptides, NA must be delivered to the cytoplasm or nucleus to be efficacious, resulting in significant delivery challenges. We herein describe frequently used non-viral vectors for the delivery of NA including polyplexes, lipoplexes and lipopolyplexes and summarize recent developments in the field of nucleic acid delivery systems for local application based on hydrogels, solid scaffolds and physical delivery methods. The challenges associated with the different approaches are identified and options to address these challenges are discussed.
Characterization of rpoB Mutations in Rifampin-Resistant Clinical Isolates of Mycobacterium tuberculosis from Turkey by DNA Sequencing and Line Probe Assay (2002)

Mutations in an 81-bp region of the rpoB gene associated with rifampin resistance were studied in 41 rifampin-resistant clinical strains of Mycobacterium tuberculosis isolated in Turkey. Fourteen different rpoB alleles, three of which had not been reported before, were found. A reverse hybridization-based line probe assay (the Inno-LiPA Rif.TB test) for rapid detection of the mutations was evaluated with these isolates. Rifampin resistance was correctly identified in 23 of 41 isolates (56.1%) with the kit's R probes specific for these mutations. Seventeen of 41 isolates (41.5%) yielded hybridization patterns, with at least one negative signal obtained with the S probes for the wild type. One isolate was identified as rifampin sensitive by the line probe assay. The rate of concordance of the results of the line probe assay with the results of the in vitro susceptibility test was high (97.6%). These results demonstrate that the line probe assay kit may be useful for the rapid diagnosis of rifampin-resistant tuberculosis.