gebhart/patrepeval huggingface dataset:
The use of mutants and transgenic plants to study amino acid metabolism (1994)

ABSTRACT Mutants of higher plants with alterations in amino acid metabolism have now been available for 20 years. Following the realization that at least four distinct classes of herbicides (phosphinothricins, glyphosates, imidazolinones and sulphonylureas) act by the inhibition of amino acid biosynthesis, mutants resistant to the herbicides have also been obtained. More recently, transgenic plants containing altered levels of enzymes of amino acid biosynthesis have been constructed. In this article, we have attempted to review several areas of amino acid biosynthesis including ammonia assimilation, the aspartate pathway, branched chain amino acids, aromatic amino acids and proline.
Configuration and management of a real-time smart transducer network (2004)

Smart transducer technology supports the composability, configurability, and maintainability of sensor/actuator networks. The configuration and management of such networks, when carried out manually, is an expensive and error-prone task. Therefore, many existing fieldbus systems provide means of "plug-and-play" that assist the user in these tasks. In this paper we describe configuration and management aspects in the area of dependable real-time fieldbus systems. We propose a configuration and management framework for a low-cost real-time fieldbus network. The framework uses formal XML descriptions to describe node and network properties in order to enable a data representation that comes with low overhead on nodes and enables the easy integration with software tools. The framework builds on the infrastructure and interfaces defined in the OMG smart transducers interface standard. As a case study, we have implemented a TTP/A configuration tool operating on a basic framework using the described concepts and mechanisms.
Nitropeptin, a new dipeptide antibiotic possessing a nitro group. (1987)

During the course of our screening program for new antibiotics effective against blast of rice, we have recently isolated nitropeptin (1), a dipeptide antibiotic possessing a nitro group, from the culture broth of Streptomyces xanthochromogenus 6257-MQ. The producing strain was isolated from a soil sample collected at Matsushima-cho, Miyagi prefecture, Japan, and was classified as S. xanthochromogenus 6257-MQ by taxonomic studies and direct comparison with a type strain.
A dynamic wavelength allocation scheme with status information for fixed- and variable-length messages (2002)

We propose a new multiple access protocol to support both fixed- and variable-length messages, in a wavelength division multiple access (WDM) based local network using a passive star coupler. The proposed protocol is the dynamic wavelength allocation scheme based on a contention-based reservation protocol. In the proposed protocol, a whole message can be transmitted after the first reservation of the control channel is successfully completed. To reserve the subsequent slots, the status information is used, instead of the control channel. Moreover, the data channels are dynamically allocated to the nodes that win the reservation. Thus, the proposed protocol can reduce the probability of the control and data channel conflicts, and uses the same data channel while transmitting a whole message.
SAW Quadraphase Code Generator (1981)

Radar emissions are now subject to regulation that limits their spectral splatter. Quadraphase codes are used to make an MSK-like pulse that has a narrower spectrum than a biphase pulse, and furthermore, it is tolerant of filtering. The design of a SAW pattern is described which yields a device that is both an encoder and filter. When it is energized by an impulse a valuable, spectral limited radar pulse is generated. The performance of this pulse is shown to meet certain desirable criteria. The correlator for the pulse is simply derived from the code generator and its performance is shown. Comparison with non-SAW methods of performing the same functions is given.
Spin-torque oscillator with tilted fixed layer magnetization (2008)

A spin-torque oscillator with a fixed layer magnetization tilted out of the film plane is capable of strong microwave signal generation in zero magnetic field. Through numerical simulations, we study the microwave signal generation as a function of drive current for two realistic tilt angles. The tilted magnetization of the fixed layer can be achieved by using a material with high out-of-plane magnetocrystalline anisotropy, such as L10 FePt.
A physical map of the Chinese chestnut (Castanea mollissima) genome and its integration with the genetic map (2012)

Three Chinese chestnut bacterial artificial chromosome (BAC) libraries were developed and used for physical map construction. Specifically, high information content fingerprinting was used to assemble 126,445 BAC clones into 1,377 contigs and 12,919 singletons. Integration of the dense Chinese chestnut genetic map with the physical map was achieved via high-throughput hybridization using overgo probes derived from sequence-based genetic markers. A total of 1,026 probes were anchored to the physical map including 831 probes corresponding to 878 expressed sequence tag-based markers. Within the physical map, three BAC contigs were anchored to the three major fungal blight-resistant quantitative trait loci on chestnut linkage groups B, F, and G. A subset of probes corresponding to orthologous genes in poplar showed only a limited amount of conserved gene order between the poplar and chestnut genomes. The integrated genetic and physical map of Chinese chestnut is available at www.fagaceae.org/physical_maps .
Internal laser parameters and optical properties of laser with CdSe quantum dots in ZnSe matrix (2006)

Abstract Photoluminescence (PL), PL excitation (PLE) spectra as well as internal laser characteristics of CdSe quantum dots (QDs) in ZnSe matrix grown by molecular beam epitaxy (MBE) and multi‐cycle migration enhanced epitaxy (MEE) were investigated. The peak PL intensity of the CdSe QDs grown by MEE in an asymmetric waveguide is by one order of magnitude more than that of the CdSe QDs grown by MBE in a symmetric waveguide. As a result, the laser characteristics have been significantly improved. The internal laser parameters were estimated to be: ΓG 0 ∼ 66 cm –1 , η i ∼ 13–17%, α i ∼ 5–15 cm –1 for MBE CdSe QDs and ΓG 0 ∼ 69 cm –1 , η i ∼ 42%, α i ∼ 2–10 cm –1 for MEE CdSe QDs. (© 2006 WILEY‐VCH Verlag GmbH &amp; Co. KGaA, Weinheim)
Continuous Hot Electron Generation in Pt/TiO2, Pd/TiO2, and Pt/GaN Catalytic Nanodiodes from Oxidation of Carbon Monoxide (2005)

Thin films (<10 nm) of platinum or palladium were deposited on TiO2 or GaN to form Schottky diodes. We detected and monitored the continuous electron flow across the metal-oxide interfaces of Pt/TiO2, Pd/TiO2, and Pt/GaN during the catalytic oxidation of carbon monoxide. The electron excitation and flow in the metals were due to conversion of energy released by the oxidation of carbon monoxide into the kinetic energy of free electrons in platinum and palladium. The best conversion of three electrons per four CO2 molecules was observed from 5 nm Pt/TiO2.
PWM and PFM Hybrid Modulation Scheme for Dual-input LLC Resonant Converter (2020)

This paper proposes a pulse-width-modulation (PWM) and pulse-frequency-modulation (PFM) hybrid modulation scheme to minimize the light load switching loss of a dual-input LLC resonant converter for photovoltaic (PV) applications. The converter voltage gain is controlled by adjusting the duty cycle at light load and varying the operating frequency at heavy load. Zero-voltage-switching (ZVS) is realized in all primary switches and zero-current-switching (ZCS) is achieved in secondary diodes over the entire range of source voltages and load conditions. In addition, voltage stress across switches does not exceed the input PV voltage. The dual-input LLC converter with proposed control scheme was established in L Tspice+PSIM softwares to analyze the performance. A 500-W dual-input LLC prototype was built to experimentally demonstrate the performance of the proposed hybrid modulation scheme. The input voltage range was selected to be 25 V to 50 V with an output voltage regulated at 200 V DC. Experimental results are closely matching the simulation results. With the proposed modulation scheme, the converter light load efficiency can be improved by maximum 6% while maintaining the conversion efficiency above 90% for the entire power range.
A hierarchical public bicycle dispatching policy for dynamic demand (2016)

The dispatching policy of public bicycles during peak hours largely determines the sharing rate of bicycles and service level of public bicycle system. Firstly, a dynamic demand prediction model of public bicycle system is proposed considering reservation data and historical data. Secondly, a hierarchical dispatching policy and network partitioning method are discussed. Thirdly, an optimization model with time window to decide the number of bicycles that need to be dispatched is put forward considering the cost of dispatching and waiting time of passengers, and the method to decide the path of dispatching is also discussed. Finally, a case study in Guangzhou shows that the proposed policy could provide lower waiting time for passengers and better bicycle sharing rate of bicycles.
VirTex: Learning Visual Representations from Textual Annotations (2021)

The de-facto approach to many vision tasks is to start from pretrained visual representations, typically learned via supervised training on ImageNet. Recent methods have explored unsupervised pretraining to scale to vast quantities of unlabeled images. In contrast, we aim to learn high-quality visual representations from fewer images. To this end we revisit supervised pretraining, and seek data-efficient alternatives to classification-based pretraining. We propose VirTex – a pretraining approach using semantically dense captions to learn visual representations. We train convolutional networks from scratch on COCO Captions, and transfer them to downstream recognition tasks including image classification, object detection, and instance segmentation. On all tasks, VirTex yields features that match or exceed those learned on ImageNet – supervised or unsupervised – despite using up to ten times fewer images.
A Computational and Experimental Analysis of Higher Order Modes in a Strongly Focusing Optical Cavity (2022)

Optical cavities operating in the near-concentric regime are the fundamental tools to perform high precision experiments like cavity QED applications. A strong focusing regime unfortunately is prone to excite higher-order modes. Higher-order mode excitation is challenging to avoid for the realistic strong focusing cavities, and if these modes are closely spaced, overall cavity linewidth gets significantly broadened. In this study, a computational method alongside the experiment is provided for the optical mode decomposition into cavity eigenmodes with justified approximations. It is shown that it is possible to recreate the intensity and spectral profile of the cavity transmission, with the provided model. As a result, a more complete treatment of the realistic near-concentric cavities can be done.
An Unusual Foreign Body in the Hand: Delayed Presentation of an Intact Human Tooth (1995)

A 44 year old man presented with a painful, swollen right hand 10 days after a brawl. A radiography showed an intact human tooth embedded in the soft tissue between the metacarpals of the middle and index fingers. The tooth was removed, and the wound debrided and left to heal by second intention. He made a complete recovery. This case emphasizes the importance of a plain radiography, particularly when skin has been breached, and of removal and adequate debridement. Our patient was lucky to have had a successful outcome after so long a delay in treatment.
Elucidating the Drug Repurposing Spectra of COVID-19 with itsAnalogues SARS and MERS (2021)

Corona Virus Disease-2019 (COVID-19), caused by the SARS CoV-2 virus, has been announced as a pandemic by the World Health Organization. COVID-19 has affected people globally, infecting more than 39.8 million people and claiming up to 1.11 million lives, yet there is no effective treatment strategy to cure this disease. As vaccine development is a time-consuming process, currently, efforts are being made to develop alternative plans for the timely and effective management of this disease. Drug repurposing always fascinated researchers and can be utilized as the most acceptable alternative to develop the therapeutics for COVID-19 using the pre-approved drugs. Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) has shown resemblance with distinctive enzyme targets, such as 3CLpro/Mpro, RdRp, Cathepsin L, and TMPRSS2 present in SARS CoV and MERS CoV. Therefore, the drugs that have shown efficacy in these viruses can also be used for the treatment of COVID-19. This review focuses on why repurposing could provide a better alternative in COVID- 19 treatment. The similarity in the structure and progression of infection of SARS CoV and MERS viruses offers a direction and validation to evaluate the drugs approved for SARS and MERS against COVID-19. It has been indicated that multiple therapeutic options that demonstrate efficacy against SARS CoV 2 are available to mitigate the potential emergence of COVID-19 infection.
Identification of novel small RNAs using comparative genomics and microarrays (2001)

A burgeoning list of small RNAs with a variety of regulatory functions has been identified in both prokaryotic and eukaryotic cells. However, it remains difficult to identify small RNAs by sequence inspection. We used the high conservation of small RNAs among closely related bacterial species, as well as analysis of transcripts detected by high-density oligonucleotide probe arrays, to predict the presence of novel small RNA genes in the intergenic regions of the Escherichia coli genome. The existence of 23 distinct new RNA species was confirmed by Northern analysis. Of these, six are predicted to encode short ORFs, whereas 17 are likely to be novel functional small RNAs. We discovered that many of these small RNAs interact with the RNA-binding protein Hfq, pointing to a global role of the Hfq protein in facilitating small RNA function. The approaches used here should allow identification of small RNAs in other organisms.
Suspended Load Path Tracking Control Using a Tilt-rotor UAV Based on Zonotopic State Estimation (2018)

This work addresses the problem of path tracking control of a suspended load using a tilt-rotor UAV. The main challenge in controlling this kind of system arises from the dynamic behavior imposed by the load, which is usually coupled to the UAV by means of a rope, adding unactuated degrees of freedom to the whole system. Furthermore, to perform the load transportation it is often needed the knowledge of the load position to accomplish the task. Since available sensors are commonly embedded in the mobile platform, information on the load position may not be directly available. To solve this problem in this work, initially, the kinematics of the multi-body mechanical system are formulated from the load's perspective, from which a detailed dynamic model is derived using the Euler-Lagrange approach, yielding a highly coupled, nonlinear state-space representation of the system, affine in the inputs, with the load's position and orientation directly represented by state variables. A zonotopic state estimator is proposed to solve the problem of estimating the load position and orientation, which is formulated based on sensors located at the aircraft, with different sampling times, and unknown-but-bounded measurement noise. To solve the path tracking problem, a discrete-time mixed $\mathcal{H}_2/\mathcal{H}_\infty$ controller with pole-placement constraints is designed with guaranteed time-response properties and robust to unmodeled dynamics, parametric uncertainties, and external disturbances. Results from numerical experiments, performed in a platform based on the Gazebo simulator and on a Computer Aided Design (CAD) model of the system, are presented to corroborate the performance of the zonotopic state estimator along with the designed controller.
The human gene fro apurinic/apyrimidinic endonuclease (HAP1): sequence and localization to chromosome 14 band q12 (1992)

Journal Article The human gene fro apurinic/apyrimidinic endonuclease (HAP1): sequence and localization to chromosome 14 band q12 Get access Bimei Zhao, Bimei Zhao Search for other works by this author on: Oxford Academic PubMed Google Scholar David K. Grandy, David K. Grandy 1Division of Hematology and Medical Oncology Vollum Institute for Advanced Biomedical Research and the Department of Cell Biology and AnatomyPortland, OR 97201, USA Search for other works by this author on: Oxford Academic PubMed Google Scholar Jennifer M. Hagerup, Jennifer M. Hagerup Search for other works by this author on: Oxford Academic PubMed Google Scholar R. Ellen Magenis, R. Ellen Magenis 2Department of Molecular and Medical Genetics and Child Development anr Rehabilitation Center, Oregon Health Sciences UniverstiyPortalnd, OR 97201,USA Search for other works by this author on: Oxford Academic PubMed Google Scholar Leslie Smith, Leslie Smith 2Department of Molecular and Medical Genetics and Child Development anr Rehabilitation Center, Oregon Health Sciences UniverstiyPortalnd, OR 97201,USA Search for other works by this author on: Oxford Academic PubMed Google Scholar Balwant C. Chauhan, Balwant C. Chauhan Search for other works by this author on: Oxford Academic PubMed Google Scholar W. David Hennee W. David Hennee * * To whom correspondence should be addressed Search for other works by this author on: Oxford Academic PubMed Google Scholar Nucleic Acids Research, Volume 20, Issue 15, 11 August 1992, Pages 4097–4098, https://doi.org/10.1093/nar/20.15.4097 Published: 11 August 1992 Article history Received: 22 June 1992 Published: 11 August 1992
SLC25A34 regulates bioenergetic metabolism in the murine liver (2020)

Background and Rationale Liver regeneration and diseases associated with altered mitochondrial metabolism, including NAFLD, are associated with alterations in ploidy. Many genes that regulate mitochondrial metabolism are also reported to alter hepatic polyploidy. SLC25A34 encodes an uncharacterized inner mitochondrial membrane protein, with a novel role in liver polyploidy. Interestingly, dysregulated Slc25a34 expression has been reported in numerous studies, which are all characterized by metabolic dysfunction, particularly altered glucose metabolism and fatty acid metabolism. We now hypothesize that SLC25A34 regulates various aspects of liver metabolism. Results In the current study, SLC25A34 was over expressed or knocked down in primary hepatocytes harvested from adult C57BL/6 mice and subsequent effects on different metabolic phenotypes were studied. Downregulation of SLC25A34 significantly increased the lipid droplets with a concurrent increase in expression of key players of fatty acid metabolism ( Cpt1A, Srebf1, Acly ). Maximal mitochondrial respiration and spare respiratory capacity were significantly elevated, possibly attributing to the increased levels of lipid droplets. Also, basal mitochondrial respiration and ATP‐linked mitochondrial respiration were significantly increased, accompanied by increased expression of regulators of mitochondrial biogenesis ( PGC‐1 alpha, PGC‐1 beta, Prc and Tfam ). In contrast, overexpression of SLC25A34 decreased expression of Cpt1A, Srebf1, Acly , but had no effect on lipid droplets. Unexpectedly, SLC25A34 overexpression also increased maximal mitochondrial respiration and spare respiratory capacity, as well as non‐mitochondrial respiration. Further, effect on energy intermediates (ADP, ATP and their ratio) and hepatocyte proliferation were studied. SLC25A34 depletion raised the ADP/ATP ratio and decreased hepatocyte proliferation, whereas overexpression of SLC25A34 decreased the ADP/ATP ratio and increased proliferation. Furthermore, SLC25A34 manipulation altered fatty acid oxidation and glycolysis functionally in primary hepatocytes as determined using the seahorse extracellular flux analyzer. Preliminary in‐vivo studies utilizing both whole‐body and liver‐specific SLC25A34 knockout mice indicate similar bioenergetic changes upon SLC25A34 deletion. Conclusion The data suggest that SLC25A34 is a key regulator of bioenergetic metabolism where it is involved in metabolic homeostasis and that modulation of SLC25A34 creates distinct metabolic phenotypes in the primary hepatocytes. Support or Funding Information This study is supported by NIDDKR01DK103645 and UPP Academic Foundation awarded to Dr. Andrew Wayne Duncan.
Human iPSC model reveals a central role for NOX4 and oxidative stress in Duchenne cardiomyopathy (2022)

Duchenne muscular dystrophy (DMD) is a progressive muscle disorder caused by mutations in the Dystrophin gene. Cardiomyopathy is a major cause of early death. We used DMD-patient-specific human induced pluripotent stem cells (hiPSCs) to model cardiomyopathic features and unravel novel pathologic insights. Cardiomyocytes (CMs) differentiated from DMD hiPSCs showed enhanced premature cell death due to significantly elevated intracellular reactive oxygen species (ROS) resulting from depolarized mitochondria and increased NADPH oxidase 4 (NOX4). CRISPR-Cas9 correction of Dystrophin restored normal ROS levels. ROS reduction by N-acetyl-L-cysteine (NAC), ataluren (PTC124), and idebenone improved hiPSC-CM survival. We show that oxidative stress in DMD hiPSC-CMs was counteracted by stimulating adenosine triphosphate (ATP) production. ATP can bind to NOX4 and partially inhibit the ROS production. Considering the complexity and the early cellular stress responses in DMD cardiomyopathy, we propose targeting ROS production and preventing detrimental effects of NOX4 on DMD CMs as promising therapeutic strategy.
Biotechnology, biodiversity, and the environment (2017)

This chapter addresses the potential for genetically modified organisms to become a potent form of invasive species. Biotechnology presents a complementary approach to traditional plant breeding. As with traditional breeding, new discoveries and technologies offer greater precision for genetic engineering. Recent advances in genome editing have the potential for developing an entirely new generation of genetically engineered (GE) crops. Since the introduction of GE crops in the early 1990s, the use of agricultural biotechnology expanded worldwide, from 1.7 million hectares in six countries to 185.1 million hectares in 26 countries, between 1996 and 2016. Currently, the most widely used varieties of GE crops carry introduced genes either for insect resistance or for herbicide resistance. Insect resistance comes from a natural insecticide gene found in the soil bacterium Bacillus thuringiensis. The use of GE plant and animal varieties for the developing world presents challenges for assessing environmental impact.
Data And Code For PhD Thesis Hybrid Solar Cells and Hybrid LEDs utilising Photonic Quasi Crystals and Colloidal Quantum Dots (2021)

Data And Code For University of Southampton PhD Thesis "Hybrid Solar Cells and Hybrid LEDs utilising Photonic Quasi Crystals and Colloidal Quantum Dots" The data is sorted by the figure to which it relates. The code is sorted in a folder structure by language and purpose.