gebhart/patrepeval huggingface dataset:
Enhancing Enzyme Activity and Immobilization in Nanostructured Inorganic–Enzyme Complexes (2017)

Understanding the chemical and physical interactions at the interface of protein surfaces and inorganic crystals has important implications in the advancement of immobilized enzyme catalysis. Recently, enzyme-inorganic hybrid complexes have been demonstrated as effective materials for enzyme immobilization. The precipitation of phosphate nanocrystals in the presence of enzymes creates enzyme-Cu<sub>3</sub>(PO<sub>4</sub>)<sub>2</sub>·3H<sub>2</sub>O particles with high surface-to-volume ratios, enhanced activity, and increased stability. Here, we begin to develop a mechanistic understanding of enzyme loading in such complexes. Using a series of enzymes including horseradish peroxidase (HRP), a thermostable alcohol dehydrogenase (AdhD), diaphorase, catalase, glucose oxidase (GOx), and the protein bovine serum albumin (BSA), we identified a correlation between particle synthesis temperature, overall enzyme charge, and enzyme loading. The model enzyme HRP has a high predicted pI of ∼7.5 and maintains an overall positive charge under the synthesis conditions, phosphate buffer pH 7.4. HRP loading in HRP-Cu<sub>3</sub>(PO<sub>4</sub>)<sub>2</sub> complexes was enhanced by 4.2-fold when synthesis was carried out at 37 °C in comparison with synthesis at 4 °C. HRP loading was further enhanced with synthesis at pH 8.0, correlating with a decrease in overall enzyme charge. Proteins with lower predicted pI values and negative overall charge (AdhD, pI of 5.6; diaphorase, pI of 6.8; GOx, pI of 5.2; catalase, pI of 6.9; and, BSA, pI of 5.7) exhibited higher enzyme loadings with 4 °C synthesis, 2.7-, 2.6-, 2.5-, 1.8-, and 1.7-fold protein loading enhancements, respectively. Using HRP as a model system, we also demonstrate that activity increased concomitantly with enzyme loading, and that particle nanostructure was minimally affected by synthesis temperature. Combined, the results presented here demonstrate the control of enzyme loading in enzyme-inorganic particles opening up new possibilities in enzyme and multienzyme catalysis.
Architecture of the vir regulons of group A streptococci parallels opacity factor phenotype and M protein class (1992)

Group A streptococci have traditionally been categorized into two broad groups based on the presence or absence of serum opacity factor (OF). Recent studies show that these two groups vary in a number of properties in addition to the OF phenotype, including sequence variations in the constant region of the antiphagocytic M protein genes, the presence or absence of immunoglobulin G Fc receptor proteins, and the presence or absence of multiple M protein-like genes situated in a tandem array. The M protein genes (emm) in OF- streptococcal strains are known to be part of a regulon of virulence-related genes controlled by the trans-acting positive regulatory gene, virR, situated just upstream of emm. In OF+ strains, however, the region adjacent to virR is occupied by an M protein-related, type IIa immunoglobulin G Fc receptor gene (fcrA), and the relative position of emm has not been determined. To further define the vir regulon in OF+ streptococci, we used the polymerase chain reaction to show that fcrA49 is situated immediately upstream of emm49 in the OF+ type 49 strain CS101. This result shows for the first time the separate identity and genetic linkage of these two genes in the vir regulon of an OF+ group A streptococcal strain and confirms our previous hypothesis that emm49 exists as the central gene in a trio of emm-like genes. Additionally, using DNA hybridizations, we found considerable sequence divergence between OF- and OF+ group A streptococci in virR and in the noncoding sequences between virR and the emm or fcrA expression site. We found, however, a high degree of sequence conservation in this region within each of the two groups of strains.
Busulfan target exposure attainment in children undergoing allogeneic hematopoietic cell transplantation: a single day versus a multiday therapeutic drug monitoring regimen. (2023)

Abstract Busulfan exposure has previously been linked to clinical outcomes, hence the need for therapeutic drug monitoring (TDM). Study objective was to evaluate the effect of day 1 TDM-guided dosing (regimen d1) versus days 1 + 2 TDM-guided dosing (regimen d1 + 2) on attaining adequate busulfan exposure. In this observational study, we included all children receiving busulfan based allogeneic hematopoietic cell transplantation. Primary outcome was the percentage of patients achieving busulfan target attainment in both TDM regimens. Secondary outcomes were the variance in busulfan exposure and day-4 clearance (Clday4) estimates between both TDM regimens and dosing day 1 and 2. In regimen d1, 84.3% (n = 91/108) attained a therapeutic busulfan exposure, while in regimen d1 + 2 a proportion of 90.9% was found (n = 30/33, not-significant). Variance of Clday4 estimate based on busulfan day 2 concentrations was significantly smaller than the variance of Clday4 estimates based on day 1 concentrations (p &lt; 0.001). Therefore, day 1-guided TDM (pharmacometric-model based) of busulfan may be sufficient for attaining optimal target exposure, provided that subsequent TDM is carried out if required. However, performing TDM on subsequent days may be beneficial, as measurements on day 2 seemed to reduce the variance in the estimated clearance as compared to day 1 sampling.
A focus group interview with health professionals: establishing efficient transition care plan for older adult patients in Korea (2022)

Through the interview, physicians in the field recognized barriers to a smooth transition care process from tertiary level hospitals to community care, especially for older adults. Participants emphasized both the patients and hospital sides of adjustment on behaviors, communication, and greater attention for the individuals during the transition period.
Mobile radio network management supported by a planning tool (2002)

The rapid development of mobile radio networks confronts the operators with serious problems in the planning and management of their networks. Due to the nature of the medium a number of new tasks appears if compared with fixed networks. Especially for a GSM network a large number of parameters related to the radio interface have to be planned and optimized. The effect of parameter settings is not limited to single or connected network elements but may extend over the whole area of radio coverage. This is strongly influencing the quality of the network.
Quorum-sensing regulation in staphylococci—an overview (2015)

Staphylococci are frequent human commensals and some species can cause disease. Staphylococcus aureus in particular is a dangerous human pathogen. In staphylococci, the ability to sense the bacterial cell density, or quorum, and to respond with genetic adaptations is due to one main system, which is called accessory gene regulator (Agr). The extracellular signal of Agr is a post-translationally modified peptide containing a thiolactone structure. Under conditions of high cell density, Agr is responsible for the increased expression of many toxins and degradative exoenzymes, and decreased expression of several colonization factors. This regulation is important for the timing of virulence factor expression during infection and the development of acute disease, while low activity of Agr is associated with chronic staphylococcal infections, such as those involving biofilm formation. Accordingly, drugs inhibiting Agr are being evaluated for their capacity to control acute forms of S. aureus infection.
Design of Compact Infrared Zoom Lens System (2012)

Infrared zoom lens system with cooled focal plane array (FPA) detector is widely used in military application. Relevant information about optical design can be got easily, but research on infrared zoom lens system with low cost and high image quality for commercial application is less. This paper design a Compact infrared zoom lens system with only four lenses, using an uncooled focal plane array (FPA) with 384×288 pixels with zoom ratio 3:1. Because of large F number and less lenses, transmission of the whole zoom system is greatly improved. NETD and MRTD of infrared system will be satisfying by this compact design. There is no special surface such as diffractive surface, HOE in zoom lens system, and only Ge and Znse infrared materials are chosen which result in lower production cost of infrared zoom lens system for commercial applications.
MRI of the Breast for the Detection and Assessment of the Size of Ductal Carcinoma in Situ (2007)

MRI was more accurate for the detection and assessment of the size of DCIS than mammography.
Development of the real-time visualization system on network (2005)

We developed a real-time network-based visualization system, using Jini technology and UNICORE. Jini technology provides an environment for creating dynamically networked components. UNICORE is grid middleware, that effectively uses computer resources. With this system a user can easily check the results of a CFD calculation in the middle of the calculation.
Novel Multiprotein Complexes Identified in the Hyperthermophilic Archaeon Pyrococcus furiosus by Non-denaturing Fractionation of the Native Proteome (2008)

Virtually all cellular processes are carried out by dynamic molecular assemblies or multiprotein complexes, the compositions of which are largely undefined. They cannot be predicted solely from bioinformatics analyses nor are there well defined techniques currently available to unequivocally identify protein complexes (PCs). To address this issue, we attempted to directly determine the identity of PCs from native microbial biomass using Pyrococcus furiosus, a hyperthermophilic archaeon that grows optimally at 100 degrees C, as the model organism. Novel PCs were identified by large scale fractionation of the native proteome using non-denaturing, sequential column chromatography under anaerobic, reducing conditions. A total of 967 distinct P. furiosus proteins were identified by mass spectrometry (nano LC-ESI-MS/MS), representing approximately 80% of the cytoplasmic proteins. Based on the co-fractionation of proteins that are encoded by adjacent genes on the chromosome, 106 potential heteromeric PCs containing 243 proteins were identified, only 20 of which were known or expected. In addition to those of unknown function, novel and uncharacterized PCs were identified that are proposed to be involved in the metabolism of amino acids (10), carbohydrates (four), lipids (two), vitamins and metals (three), and DNA and RNA (nine). A further 30 potential PCs were classified as tentative, and the remaining potential PCs (13) were classified as weakly interacting. Some major advantages of native biomass fractionation for PC identification are that it provides a road map for the (partial) purification of native forms of novel and uncharacterized PCs, and the results can be utilized for the recombinant production of low abundance PCs to provide enough material for detailed structural and biochemical analyses.
Azide–alkyne cycloaddition for universal post-synthetic modifications of nucleic acids and effective synthesis of bioactive nucleic acid conjugates (2014)

The regioselective post-synthetic modifications of nucleic acids are essential to studies of these molecules for science and applications. Here we report a facile universal approach by harnessing versatile phosphoramidation reactions to regioselectively incorporate alkynyl/azido groups into post-synthetic nucleic acids primed with phosphate at the 5' termini. With and without the presence of copper, the modified nucleic acids were subjected to azide-alkyne cycloaddition to afford various nucleic acid conjugates including a peptide-oligonucleotide conjugate (POC) with high yield. The POC was inoculated with human A549 cells and demonstrated excellent cell-penetrating ability despite cell deformation caused by a small amount of residual copper chelated to the POC. The combination of phosphoramidation and azide-alkyne cycloaddition reactions thus provides a universal regioselective strategy to post-synthetically modify nucleic acids. This study also explicated the toxicity of residual copper in synthesized bioconjugates destined for biological systems.
A Proposed NFC Payment Application (2013)

Near Field Communication (NFC) technology is based on a short range radio communication channel which enables users to exchange data between devices. With NFC technology, mobile services establish a contactless transaction system to make the payment methods easier for people. Although NFC mobile services have great potential for growth, they have raised several issues which have concerned the researches and prevented the adoption of this technology within societies. Reorganizing and describing what is required for the success of this technology have motivated us to extend the current NFC ecosystem models to accelerate the development of this business area. In this paper, we introduce a new NFC payment application, which is based on our previous “NFC Cloud Wallet” model [1] to demonstrate a reliable structure of NFC ecosystem. We also describe the step by step execution of the proposed protocol in order to carefully analyse the payment application and our main focus will be on the Mobile Network Operator (MNO) as the main player within the ecosystem.
Ultrafast imaging of free carriers: controlled excitation with chirped ultrafast laser Bessel beams (2014)

Nonlinear propagation of intense ultrafast laser pulses inside transparent materials has a strong influence on the fabrication quality and accuracy for 3D laser-material processing. Due to their ability to maintain near-constant fluence profiles over an appreciable distance along the propagation direction in linear and nonlinear media, ultrafast Bessel beams are ideal sources for high aspect ratio sub-micron structuring applications. We report here on the interaction of transparent materials, especially fused silica, with ultrafast non-diffractive beams of moderate cone angle at various laser energies and pulse durations and define their impact on photoinscription regimes, i.e. formation of isotropic and non-isotropic (positive and negative) refractive index structures. The laser pulse duration was observed to be key in deciding the type of the structures via excitation efficiency. To understand the significant mechanisms for forming these different structures, the free carrier behavior as a function of laser pulse duration and energy was studied by capturing instantaneous excitation profiles using time-resolved microscopy. Time-resolved imaging and simulation studies reveal that low carrier densities are generated for ultrashort pulses leading to soft positive index alterations via presumably non-thermally induced structural transitions via defects. On the other hand, the high free carrier density generation in the case of longer pulse durations leads to a hydrodynamic expansion resulting in high aspect ratio sub-micron size wide voids. Delayed ionization, carrier defocusing and lower nonlinear effects are responsible for the confinement of energy, resulting in efficient energy deposition on-axis.
Building a spring-transport package for spinning rotor gauges (2015)

Spinning rotor gauges (SRGs) are widely used as transfer standards in interlaboratory comparisons and as secondary standards by calibration laboratories. In both of these applications, it is necessary to ship the SRG for calibration, often internationally over long distances. A spring-transport mechanism is a device used to immobilize the SRG and keep it under vacuum during transport. To assure that the SRG will not be damaged during shipment, it is also important to have packaging that protects the SRG and spring-transport mechanism. This shop-note describes the design and mechanical testing of a robust spring-transport mechanism and shipping container built by National Institute of Standards and Technology.
Nano/Micro‐Structured Si/C Anodes with High Initial Coulombic Efficiency in Li‐Ion Batteries (2016)

One of the major challenges for designing high-capacity anode materials is to combine both Coulombic efficiency and cycling stability. Herein, nano/micro-structured Si/C composites are designed and synthesized to address this challenge by decreasing the specific surface area and improving the tap density of Si/C materials. An ultrahigh initial Coulombic efficiency of 91.2 % could be achieved due to a proper particle size, low specific surface area, and optimized structure. The nano/micro-structured Si/C anodes exhibit excellent cycling stability with 96.5 % capacity retention after 100 cycles under a current density of 0.2 A g(-1) .
Image based prognosis in head and neck cancer using convolutional neural networks: a case study in reproducibility and optimization (2023)

Abstract In the past decade, there has been a sharp increase in publications describing applications of convolutional neural networks (CNNs) in medical image analysis. However, recent reviews have warned of the lack of reproducibility of most such studies, which has impeded closer examination of the models and, in turn, their implementation in healthcare. On the other hand, the performance of these models is highly dependent on decisions on architecture and image pre-processing. In this work, we assess the reproducibility of three studies that use CNNs for head and neck cancer (HNC) outcome prediction by attempting to reproduce the published results. In addition, we propose a new network structure and assess the impact of image pre-processing and model selection criteria on performance. We used two publicly available datasets: one with 298 patients for training and validation and another with 137 patients from a different institute for testing. All three studies failed to report elements required to reproduce their results thoroughly, mainly the image pre-processing steps and the random seed. Our model either outperforms or achieves similar performance to the existing models with considerably fewer parameters. We also observed that the pre-processing efforts significantly impact the model's performance and that some model selection criteria may lead to suboptimal models. Although there have been improvements in the reproducibility of deep learning models, our work suggests that wider implementation of reporting standards is required to avoid a reproducibility crisis.
Data used in 2021 (2021)

The data cover the period between 1 January 2020 and 17 September 2021. Time variant variables include total deaths per million population, total tests per million population, the share of tests that are positive, and the stringency index. Time-invariant variables include press freedom index (2020), the score of government cohesion (2019), domestic private health expenditure (% of current expenditure) (2017), domestic private health expenditure per capita, PPP (current international $) (2017), and GDP per capita (2010 US$) (2017), and Human Development index (2019).
Tuning the Selectivity of Photocatalytic Synthetic Reactions Using Modified TiO2 Nanotubes (2014)

Differently modified TiO2 nanotubes were used to achieve a drastic change in the selectivity of a photocatalytic reaction. For the photocatalytic oxidation of toluene, depending on the electronic properties of TiO2 (anatase, rutile, Ru-doped), a strong change in the main reaction product (namely benzoic acid versus benzaldehyde) can be achieved, and certain undesired reaction pathways can be completely shut down.
Multi-Fidelity Multi-Objective Bayesian Optimization: An Output Space Entropy Search Approach (2020)

We study the novel problem of blackbox optimization of multiple objectives via multi-fidelity function evaluations that vary in the amount of resources consumed and their accuracy. The overall goal is to appromixate the true Pareto set of solutions by minimizing the resources consumed for function evaluations. For example, in power system design optimization, we need to find designs that trade-off cost, size, efficiency, and thermal tolerance using multi-fidelity simulators for design evaluations. In this paper, we propose a novel approach referred as Multi-Fidelity Output Space Entropy Search for Multi-objective Optimization (MF-OSEMO) to solve this problem. The key idea is to select the sequence of candidate input and fidelity-vector pairs that maximize the information gained about the true Pareto front per unit resource cost. Our experiments on several synthetic and real-world benchmark problems show that MF-OSEMO, with both approximations, significantly improves over the state-of-the-art single-fidelity algorithms for multi-objective optimization. Please note: A corrigendum was submitted for this paper on 24 September 2020.
A Sequence-Based Variation Map of Zebrafish (2013)

Zebrafish (Danio rerio) is a popular vertebrate model organism largely deployed using outbred laboratory animals. The nonisogenic nature of the zebrafish as a model system offers the opportunity to understand natural variations and their effect in modulating phenotype. In an effort to better characterize the range of natural variation in this model system and to complement the zebrafish reference genome project, the whole genome sequence of a wild zebrafish at 39-fold genome coverage was determined. Comparative analysis with the zebrafish reference genome revealed approximately 5.2 million single nucleotide variations and over 1.6 million insertion-deletion variations. This dataset thus represents a new catalog of genetic variations in the zebrafish genome. Further analysis revealed selective enrichment for variations in genes involved in immune function and response to the environment, suggesting genome-level adaptations to environmental niches. We also show that human disease gene orthologs in the sequenced wild zebrafish genome show a lower ratio of nonsynonymous to synonymous single nucleotide variations.
To Promote the Reformation and Development of Vocational Education From Scientific Developmental Perspective (2005)

The vocational education must take man as the End . It should recognize and research cultivational quality of talent through complete harmonious continual scientific development view in order to make scientific system of talent's quality education come into being.
The Cable and Telecommunications Professionals' Reference, Volume 2, Third Edition: Transport Networks (2008)

Volume 2 of TERB 3ed covers the convergence of telephony and data transport, including wireless networks. Now that data is becoming the predominant source of traffic more efficient multiplexing schemes and more flexible control methods are needed in the transport network, such as giving the customer the ability to call for bandwidth on demand. With the development of control methods for switched data services it is now recognised that improved ways to control the transport network are possible and standards initiatives are taking place to establish and improve the network control layer. Detailed explanation of propagation in wireless and optical fibre systems requires a substantial amount of mathematics, also covered in this volume. For each of the math chapters there is an explanation of why the mathematics is important, where it is applied and references to other chapters.* AUTHORITATIVE: All contributors are recognized experts in their field and come from leading institutions.* INTERNATIONAL: In this age of globalization and standardization, special attention has been paidboth topically and authorially--to ensure the broad applicability and relevance of this material. * EXHAUSTIVE: A thorough reference describing the convergence of telephony and data transport, including wireless networks.