gebhart/patrepeval huggingface dataset:
Expression of the Glucocorticoid Receptor from the 1A Promoter Correlates with T Lymphocyte Sensitivity to Glucocorticoid-Induced Cell Death (2004)

Abstract Glucocorticoid (GC) hormones cause pronounced T cell apoptosis, particularly in immature thymic T cells. This is possibly due to tissue-specific regulation of the glucocorticoid receptor (GR) gene. In mice the GR gene is transcribed from five separate promoters designated: 1A, 1B, 1C, 1D, and 1E. Nearly all cells express GR from promoters 1B–1E, but the activity of the 1A promoter has only been reported in the whole thymus or lymphocyte cell lines. To directly assess the role of GR promoter use in sensitivity to glucocorticoid-induced cell death, we have compared the activity of the GR 1A promoter with GC sensitivity in different mouse lymphocyte populations. We report that GR 1A promoter activity is restricted to thymocyte and peripheral lymphocyte populations and the cortex of the brain. The relative level of expression of the 1A promoter to the 1B–1E promoters within a lymphocyte population was found to directly correlate with susceptibility to GC-induced cell death, with the extremely GC-sensitive CD4+CD8+ thymocytes having the highest levels of GR 1A promoter activity, and the relatively GC-resistant αβTCR+CD24int/low thymocytes and peripheral T cells having the lowest levels. DNA sequencing of the mouse GR 1A promoter revealed a putative glucocorticoid-response element. Furthermore, GR 1A promoter use and GR protein levels were increased by GC treatment in thymocytes, but not in splenocytes. These data suggest that tissue-specific differences in GR promoter use determine T cell sensitivity to glucocorticoid-induced cell death.
VSEARCH: a versatile open source tool for metagenomics (2016)

Background. VSEARCH is an open source and free of charge multithreaded 64-bit tool for processing metagenomics nucleotide sequence data. It is designed as an alternative to the widely used USEARCH tool (Edgar 2010) for which the source code is not publicly available, algorithm details are only rudimentarily described, and only a memory-confined 32-bit version is freely available for academic use. Methods. When searching nucleotide sequences, VSEARCH uses a fast heuristic based on words shared by the query and target sequences in order to quickly identify similar sequences, a similar strategy is probably used in USEARCH. VSEARCH then performs optimal global sequence alignment of the query against potential target sequences, using full dynamic programming instead of the seed-and-extend heuristic used by USEARCH. Pairwise alignments are computed in parallel using vectorisation and multiple threads. Results. VSEARCH includes most commands for analysing nucleotide sequences available in USEARCH version 7 and several of those available in USEARCH version 8, including searching (exact or based on global alignment), clustering by similarity (using length pre-sorting, abundance pre-sorting or a user-defined order), chimera detection (reference-based or de novo ), dereplication (full length or prefix), pairwise alignment, reverse complementation, sorting, and subsampling. VSEARCH also includes commands for FASTQ file processing, i.e. format detection, filtering, read quality statistics, and merging of paired reads. Furthermore, VSEARCH extends functionality with several new commands and improvements, including shuffling, rereplication, masking of low-complexity sequences with the well-known DUST algorithm, a choice among different similarity definitions, and FASTQ file format conversion. VSEARCH is here shown to be more accurate than USEARCH when performing searching, clustering, chimera detection and subsampling, while on a par with USEARCH for paired-ends read merging. VSEARCH is slower than USEARCH when performing clustering and chimera detection, but significantly faster when performing paired-end reads merging and dereplication. VSEARCH is available at https://github.com/torognes/vsearch under either the BSD 2-clause license or the GNU General Public License version 3.0. Discussion. VSEARCH has been shown to be a fast, accurate and full-fledged alternative to USEARCH. A free and open-source versatile tool for sequence analysis is now available to the metagenomics community.
A defined mechanistic correlate of protection against Plasmodium falciparum malaria in non-human primates (2019)

Malaria vaccine design and prioritization has been hindered by the lack of a mechanistic correlate of protection. We previously demonstrated a strong association between protection and merozoite-neutralizing antibody responses following vaccination of non-human primates against Plasmodium falciparum reticulocyte binding protein homolog 5 (PfRH5). Here, we test the mechanism of protection. Using mutant human IgG1 Fc regions engineered not to engage complement or FcR-dependent effector mechanisms, we produce merozoite-neutralizing and non-neutralizing anti-PfRH5 chimeric monoclonal antibodies (mAbs) and perform a passive transfer-P. falciparum challenge study in Aotus nancymaae monkeys. At the highest dose tested, 6/6 animals given the neutralizing PfRH5-binding mAb c2AC7 survive the challenge without treatment, compared to 0/6 animals given non-neutralizing PfRH5-binding mAb c4BA7 and 0/6 animals given an isotype control mAb. Our results address the controversy regarding whether merozoite-neutralizing antibody can cause protection against P. falciparum blood-stage infections, and highlight the quantitative challenge of achieving such protection.
Deep Centers in Semiconductors (2013)

Abstract The sections in this article are Introduction Shallow and Deep Impurities: Technological and Physical Relevance The Identification Problem and the Localization‐Delocalization Puzzle Deep Centers: Electronic Transitions and Concepts Ionization at Thermal Equilibrium Franck‐Condon Transitions and Relaxation Phenomenological Models and Electronic Structure The Point‐Ion Crystal Field Model The Defect Molecule Picture Example: Nitrogen in Gallium Phosphide Transition Metals Transition Metals: Results of Quantitative Calculations Gap Levels and High Spin–Low Spin Ordering Coulomb Induced Nonlinear Screening and Self‐Regulating Response Ionization Energies and Trends Transition Metals in Silicon Compound Semiconductors and Bulk References Excited States Internal Transitions Rydberg‐Like States Properties of Selected Systems Chalcogens in Silicon Sulfur, Selenium, and Tellurium in Silicon Oxygen and Nitrogen in Silicon DX Centers in Al x Ga 1− x As Large Lattice Relaxation and Metastability Microscopic Models for DX Centers Deep Transition Metal Donor–Shallow Acceptor Pairs in Silicon Electronic Structure and Trends Charge State Controlled Metastability Thermal Donors in Silicon Hydrogen Passivation Appendix: Ionization Energies and Level Positions of Isolated Transition Metal Impurities in Silicon
Survey of the Speech Recognition Techniques for Mobile Devices (2011)

This paper presents an overview of different approaches for providing automatic speech recognition (ASR) technology to mobile users. Three principal system architectures in terms of employing wireless communication link are analyzed: Embedded Speech Recognition Systems, Network Speech Recognition (NSR) and Distributed Speech Recognition (DSR). Overview of the solutions which became standards by now as well as some critical analysis of the latest developments in the field of the speech recognition in mobile environments is given. Open issues, pros and cons of the different methodologies and techniques are highlighted. Special emphasis is made on the constraints and limitations the ASR applications encounter under the different architectures. 1.
Peningkatan Kemandirian Belajar Peserta Didik pada Materi Teori Kinetik Gas Melalui Penerapan Media Pembelajaran Interaktif Berbasis iSpring Suite 8 (2019)

Penelitian ini bertujuan untuk meningkatkan kemandirian belajar peserta didik pada materi teori kinetik gas dengan menerapkan media pembelajaran interaktif berbasis  iSpring Suite 8 . Subjek penelitian terdiri dari 27 peserta didik kelas XI IPA 6 SMA Negeri Karangpandan tahun 2017. Penelitian tindakan kelas ini dilakukan dengan model Kemmis dan McTaggart yang dilaksanakan dalam dua siklus. Masing-masing siklus dilakukan dengan tahap perencanaan, pelaksanaan, observasi, dan refleksi. Data diperoleh melalui observasi, wawancara, dan angket. Data tersebut dianalisis secara kualitatif dan didukung dengan data kuantitatif. Penelitian ini menghasilkan kesimpulan yaitu peningkatan kemandirian belajar peserta didik pada materi teori kinetik gas dengan menerapkan media pembelajaran interaktif berbasis  iSpring Suite 8  tercapai dalam dua siklus hingga sebagian besar peserta didik memiliki kemandirian belajar pada kategori Baik dan Sangat Baik.
Prospective heart tracking for whole‐heart magnetic resonance angiography (2016)

Compared with a conventional diaphragm-NAV, Heart-NAV achieves similar image quality in a slightly shorter scan time and eliminates inflow artifact. Magn Reson Med 77:759-765, 2017. © 2016 International Society for Magnetic Resonance in Medicine.
Practical Aspects of CO2 Flooding (2002)

Practical Aspects of CO2 Flooding serves as a logical guide to the practicing engineer focused on the “how to” and “why” of miscible and immiscible CO2 flooding. The book outlines the entire project development sequence from conception and justification through field design and operation. Discussion centers on current and practical CO2 flooding technologies and industry experiences, and it targets those involved in planning, designing, and implementing CO2 floods. The book has five appendices including a compendium of practical, field-specific publications.
Rab22 controls NGF signaling and neurite outgrowth in PC12 cells (2011)

Rab22 is a small GTPase that is localized on early endosomes and regulates early endosomal sorting. This study reports that Rab22 promotes nerve growth factor (NGF) signaling-dependent neurite outgrowth and gene expression in PC12 cells by sorting NGF and the activated/phosphorylated receptor (pTrkA) into signaling endosomes to sustain signal transduction in the cell. NGF binding induces the endocytosis of pTrkA into Rab22-containing endosomes. Knockdown of Rab22 via small hairpin RNA (shRNA) blocks NGF-induced pTrkA endocytosis into the endosomes and gene expression (VGF) and neurite outgrowth. Overexpression of human Rab22 can rescue the inhibitory effects of the Rab22 shRNA, suggesting a specific Rab22 function in NGF signal transduction, rather than off-target effects. Furthermore, the Rab22 effector, Rabex-5, is necessary for NGF-induced neurite outgrowth and gene expression, as evidenced by the inhibitory effect of shRNA-mediated knockdown of Rabex-5. Disruption of the Rab22-Rabex-5 interaction via overexpression of the Rab22-binding domain of Rabex-5 in the cell also blocks NGF-induced neurite outgrowth, suggesting a critical role of Rab22-Rabex-5 interaction in the biogenesis of NGF-signaling endosomes to sustain the signal for neurite outgrowth. These data provide the first evidence for an early endosomal Rab GTPase as a positive regulator of NGF signal transduction and cell differentiation.
Covariances for smoothed estimates in state space models (1988)

Journal Article Covariances for smoothed estimates in state space models Get access PIET DE JONG, PIET DE JONG Faculty of Commerce and Business Administration, University of British ColumbiaVancouver, British Columbia V6T1Y8, Canada Search for other works by this author on: Oxford Academic Google Scholar MURRAY J. MACKINNON MURRAY J. MACKINNON Faculty of Commerce and Business Administration, University of British ColumbiaVancouver, British Columbia V6T1Y8, Canada Search for other works by this author on: Oxford Academic Google Scholar Biometrika, Volume 75, Issue 3, September 1988, Pages 601–602, https://doi.org/10.1093/biomet/75.3.601 Published: 01 September 1988 Article history Received: 01 July 1987 Revision received: 01 December 1987 Published: 01 September 1988
Compounding of Fillers (1974)

The several methods available to produce glass-reinforced thermoplastic materials vary greatly in their methods and results. Data obtained on pre-compounded glass-reinforced polypropylene show that physical properties vary significantly with vanous compounding techniques. Proper selection of compounding equipment and optimizing equipment parameters can substantially increase mechanical properties of the final product. Methods of selecting the most efficient equipment for a given compounding operation must take into consideration degree of shear required, temperature sensitivity, residence time distribution, and volume to be produced. When dealing with glass fibers, abrasion or corrosion of the compounding equipment plays a substantial role in economics. The simplicity and accuracy of the compounding process are also important.
Microstructural Features of 'Quenching and Partitioning': A New Martensitic Steel Heat Treatment (2007)

The microstructure following a new martensite heat treatment has been examined, principally by high-resolution microanalytical transmission electron microscopy and by atom probe tomography. The new process involves quenching to a temperature between the martensite-start (Ms) and martensite-finish (Mf) temperatures, followed by ageing either at or above, the initial quench temperature, whereupon carbon can partition from the supersaturated martensite phase to the untransformed austenite phase. Thus the treatment has been termed ‘Quenching and Partitioning’ (Q&P). The carbon must be protected from competing reactions, primarily carbide precipitation, during the first quench and partitioning steps, thus enabling the untransformed austenite to be enriched in carbon and largely stabilised against further decomposition to martensite upon final quenching to room temperature. This microstructural objective is almost directly opposed to conventional quenching and tempering of martensite, which seeks to eliminate retained austenite and where carbon supersaturation is relieved by carbide precipitation. This study focuses upon a steel composition representative of a TRIP-assisted sheet steel. The Q&P microstructure is characterised, paying particular attention to the prospect for controlling or suppressing carbide precipitation by alloying, through examination of the carbide precipitation that occurs.
The Rac activator Tiam1 controls tight junction biogenesis in keratinocytes through binding to and activation of the Par polarity complex (2005)

The GTPases Rac and Cdc42 play a pivotal role in the establishment of cell polarity by stimulating biogenesis of tight junctions (TJs). In this study, we show that the Rac-specific guanine nucleotide exchange factor Tiam1 (T-lymphoma invasion and metastasis) controls the cell polarity of epidermal keratinocytes. Similar to wild-type (WT) keratinocytes, Tiam1-deficient cells establish primordial E-cadherin-based adhesions, but subsequent junction maturation and membrane sealing are severely impaired. Tiam1 and V12Rac1 can rescue the TJ maturation defect in Tiam1-deficient cells, indicating that this defect is the result of impaired Tiam1-Rac signaling. Tiam1 interacts with Par3 and aPKCzeta, which are two components of the conserved Par3-Par6-aPKC polarity complex, and triggers biogenesis of the TJ through the activation of Rac and aPKCzeta, which is independent of Cdc42. Rac is activated upon the formation of primordial adhesions (PAs) in WT but not in Tiam1-deficient cells. Our data indicate that Tiam1-mediated activation of Rac in PAs controls TJ biogenesis and polarity in epithelial cells by association with and activation of the Par3-Par6-aPKC polarity complex.
Method for Rapid Purification of Class IIa Bacteriocins and Comparison of Their Activities (2000)

A three-step method was developed for the purification of mesentericin Y105 (60% yield) from the culture supernatant of Leuconostoc mesenteroides Y105. The same procedure was successfully applied to the purification of five other anti-Listeria bacteriocins identified by mass spectrometry. Specific activities of the purified bacteriocins were compared.
Actuated bivalve robot study of the burrowing locomotion in sediment (2010)

This paper presents the design and control of an actuated bivalve robot, which has been developed to study the burrowing locomotion of bivalves in sediment. The setup consists of a tank filled with sand and water, plastic models of bivalve shells capable of expelling water and an external actuation mechanism simulating the rocking burrowing motion typically used by these animals. The realistic shell shapes have been realized using three-dimensional plotting techniques allowing testing influences of different shell shapes and surface structures (sculptures) on the burrowing efficiency. Based on the experimental setup, the burrowing process has been reproduced. The results show that this setup can be used to identify correlations in the burrowing process. Further experimental work will investigate the influence of factors such as shell shape and sculpture or the motion sequence on the burrowing performance.
Pre-emptive gabapentin significantly reduces postoperative pain and morphine demand following lower extremity orthopaedic surgery. (2007)

Pre-emptive use of gabapentin 300 mg orally significantly decreases postoperative pain and rescue analgesic requirements in patients who undergo lower extremity orthopaedic surgery.
Biologically inspired rosette nanotubes and nanocrystalline hydroxyapatite hydrogel nanocomposites as improved bone substitutes (2009)

Today, bone diseases such as bone fractures, osteoporosis and bone cancer represent a common and significant public health problem. The design of biomimetic bone tissue engineering materials that could restore and improve damaged bone tissues provides exciting opportunities to solve the numerous problems associated with traditional orthopedic implants. Therefore, the objective of this in vitro study was to create a biomimetic orthopedic hydrogel nanocomposite based on the self-assembly properties of helical rosette nanotubes (HRNs), the osteoconductive properties of nanocrystalline hydroxyapatite (HA), and the biocompatible properties of hydrogels (specifically, poly(2-hydroxyethyl methacrylate), pHEMA). HRNs are self-assembled nanomaterials that are formed from synthetic DNA base analogs in water to mimic the helical nanostructure of collagen in bone. In this study, different geometries of nanocrystalline HA were controlled by either hydrothermal or sintering methods. 2 and 10 wt% nanocrystalline HA particles were well dispersed into HRN hydrogels using ultrasonication. The nanocrystalline HA and nanocrystalline HA/HRN hydrogels were characterized by x-ray diffraction, transmission electron microscopy, and scanning electron microscopy. Mechanical testing studies revealed that the well dispersed nanocrystalline HA in HRN hydrogels possessed improved mechanical properties compared to hydrogel controls. In addition, the results of this study provided the first evidence that the combination of either 2 or 10 wt% nanocrystalline HA and 0.01 mg ml(-1) HRNs in hydrogels greatly increased osteoblast (bone-forming cell) adhesion up to 236% compared to hydrogel controls. Moreover, this study showed that HRNs stimulated HA nucleation and mineralization along their main axis in a way that is very reminiscent of the HA/collagen assembly pattern in natural bone. In summary, the presently observed excellent properties of the biomimetic nanocrystalline HA/HRN hydrogel composites make them promising candidates for further study for bone tissue engineering applications.
Expression of a mutation affecting F incompatibility in the integrated but not the autonomous state of F (1976)

Previously we have described a mutant Hfr strain in which incompatibility between the integrated F factor and an autonomous F-prime (F') factor was abolished. The mutation (inc) was located in the integrated F factor. F-prime factors isolated from the mutant Hfr strain have the same incompatibility behavior as those isolated from normal Hfr strains. Reintegration of these F' factors into the chromosome restores the Inc- phenotype characteristic of the mutant Hfr. The inc mutation thus affects incompatibility between integrated F and autonomous F(Fi-Fa incompatibility) but not incompatibility between two autonomous F factors (Fa-Fa incompatibility). The implications of this finding for the mechanism of plasmid incompatibility are discussed.
KRAB-Zinc Finger Proteins: A Repressor Family Displaying Multiple Biological Functions (2013)

Zinc finger proteins containing the Kruppel associated box (KRAB-ZFPs) constitute the largest individual family of transcriptional repressors encoded by the genomes of higher organisms. KRAB domain, positioned at the NH2 terminus of the KRAB-ZFPs, interacts with a scaffold protein, KAP-1, which is able to recruit various transcriptional factors causing repression of genes to which KRAB ZFPs bind. The relevance of such repression is reflected in the large number of the KRAB zinc finger protein genes in the human genome. However, in spite of their numerical abundance little is currently known about the gene targets and the physiological functions of KRAB- ZFPs. However, emerging evidence links the transcriptional repression mediated by the KRAB-ZFPs to cell proliferation, differentiation, apoptosis and cancer. Moreover, the fact that KRAB containing proteins are vertebrate-specific suggests that they have evolved recently, and that their key roles lie in some aspects of vertebrate development. In this review, we will briefly discuss some regulatory functions of the KRAB-ZFPs in different physiological and pathological states, thus contributing to better understand their biological roles.
Status of the Advanced Dish Development System Project (2003)

The Advanced Dish Development System (ADDS) project is a system-level dish/engine development activity aimed at the extensive but challenging remote power market. The ADDS project involves integration and test of advanced dish/Stirling systems. The ADDS designs utilize the WGAssociates solar concentrator and controls, and the SOLO 161 Stirling Power Conversion Unit. Development has focused on extending the application of dish/Stirling systems to water pumping, and reliability and performance improvement. Testing includes unattended, automatic operation of stand-alone dish/Stirling solar power generation systems in both on and off-grid modes at the National Solar Thermal Test Facility (NSTTF) in Albuquerque, NM. In 1999, a first generation (Mod 1) system was fielded at the NSTTF and routine unattended operation initiated. In 2000, a system reliability tracking system was implemented on the Mod 1 system and an upgraded, second-generation (Mod 2) system, including a stand-alone water-pumping capability was developed. In 2001 and 2002 system performance and reliability were improved. Overall, the ADDS project has been successful with most of the original system specifications and objectives having been met or exceeded. The ADDS designs are efficient and maintainable and have proven the ability to operate autonomously in a remote environment. The Mod 1 system net power rating was increased from 9 to 10 kWe even while the concentrator mirror area was reduced by over 14%. The Mod 2 design is the first modern dish/engine system to operate independent of the utility grid and is capable of interfacing with standard three-phase, 480-volt, water-pump or other single motor applications. In this paper, the ADDS project plan and history, technical approach, and the major system components and features are briefly described. Project milestones and status along with test results are also presented.