gebhart/patrepeval huggingface dataset:
Modelling as a tool for increasing the specific productivity of single-chain antibody fragments from Pichia pastoris (2013)

Pichia pastoris is a commonly used recombinant protein expression host, predominantly due to ease of genetic manipulation and its capacity for high cell densities in cheap culture media. While considerable yields can be achieved in this way, the specific productivity is relatively low. Consequently, the full impact of this host on industrial biotechnology has not yet been realised. This research aimed to develop a strategy to optimise production of single chain antibody fragments (scFvs), an industrially relevant protein, using an integrated modelling and experimental approach. Initially, a dynamic model was constructed from literature sources to reproduce the scFv production pathway in P. pastoris. It incorporated aspects of transcription, translation, folding and misfolding in the endoplasmic reticulum (ER). Moreover, the unfolded protein response (UPR) and ER-associated degradation (ERAD) were added as these two stress pathways are crucial to productivity. Simulations qualitatively reproduced phenomena including secretion saturation and the negative influence of high gene copy numbers on yield. The model was used to target evaluation of the experimental system: P. pastoris strains expressing the scFvs BC1 and MFE23. RT Q-PCR and LC-MS/MS results revealed some surprising correlations between certain factors, such as the concentration of Kar2 and PDI, and yield. Moreover, it showed that there was more than one route to high productivity. Finally, it suggested that there may be an internal regulation of Kar2 that would be crucial to strategies aiming to increase yield through overexpression of that chaperone. Together, the results revealed a more complex picture of productivity than previously understood. In order to develop a strategy for optimal scFv production in P. pastoris, a greater understanding of the underlying biology and biochemistry is required. This research has suggested targets for future work which should generate insight into the network of factors responsible.
Dual-component model of respiratory motion based on the periodic autoregressive moving average (periodic ARMA) method (2007)

A new approach to the problem of modelling and predicting respiration motion has been implemented. This is a dual-component model, which describes the respiration motion as a non-periodic time series superimposed onto a periodic waveform. A periodic autoregressive moving average algorithm has been used to define a mathematical model of the periodic and non-periodic components of the respiration motion. The periodic components of the motion were found by projecting multiple inhale-exhale cycles onto a common subspace. The component of the respiration signal that is left after removing this periodicity is a partially autocorrelated time series and was modelled as an autoregressive moving average (ARMA) process. The accuracy of the periodic ARMA model with respect to fluctuation in amplitude and variation in length of cycles has been assessed. A respiration phantom was developed to simulate the inter-cycle variations seen in free-breathing and coached respiration patterns. At +/-14% variability in cycle length and maximum amplitude of motion, the prediction errors were 4.8% of the total motion extent for a 0.5 s ahead prediction, and 9.4% at 1.0 s lag. The prediction errors increased to 11.6% at 0.5 s and 21.6% at 1.0 s when the respiration pattern had +/-34% variations in both these parameters. Our results have shown that the accuracy of the periodic ARMA model is more strongly dependent on the variations in cycle length than the amplitude of the respiration cycles.
High Prevalence of<i> Leptotrichia amnionii</i>,<i> Atopobium vaginae</i>,<i> Sneathia sanguinegens</i>, and Factor 1 Microbes and Association of Spontaneous Abortion among Korean Women (2017)

<i>Objective.</i> The purpose of this study was to (i) determine the cervical microbial composition in different abortion samples and to (ii) investigate the correlation between spontaneous abortion and cervical microbes in Korean women. <i>Methods.</i> We collected cervical swabs from women who had never undergone abortion (<i>N</i> = 36), had spontaneous abortion (<i>N</i> = 23), and had undergone induced abortion (<i>N</i> = 88) and subjected those samples to 16S rRNA pyrosequencing. Further, factor analysis and correlation between cervical microbiota and spontaneous abortion were evaluated by logistic regression analysis. <i>Results.</i> In spontaneous abortion women, 16 S rRNA gene sequences showed significant increases in <i>Atopobium vaginae</i>, <i>Megasphaera</i> spp., <i>Gardnerella vaginalis</i>, <i>Leptotrichia amnionii</i>, and <i>Sneathia sanguinegens</i> compared to women in nonabortion group. In multivariate logistic regression analysis, <i>A. vaginae</i> (OD = 11.27; 95% = 1.57-81)<i>, L. amnionii</i> (OD = 11.47; 95% = 1.22-107.94), <i>S. sanguinegens</i> (OD = 6.89; 95% = 1.07-44.33), and factor 1 microbes (OD = 16.4; 95% = 1.88-42.5) were strongly associated with spontaneous abortion. <i>Conclusions.</i> This study showed a high prevalence of <i>L. amnionii, A. vaginae, S. sanguinegens</i>, and factor 1 microbes in spontaneous abortion and association with spontaneous abortion in Korean women.
On the use of vertical superjunction collectors for enhanced breakdown performance in SiGe HBTs (2016)

The implementation of a “superjunction” collector design in a silicon-germanium heterojunction bipolar transistor is explored for enhancing breakdown performance. The superjunction collector is formed through the placement of a series of alternating pn-junction layers in the collector-base space charge region to modify the carrier energy profile and reduce avalanche generation. An overview of the physics underlying superjunction collector operation is presented with TCAD simulations, and practical superjunction design techniques are discussed. The first measured data on a superjunction collector is also presented and shows a 57% improvement in breakdown performance.
Eye tracking in virtual reality (2019)

The intent of this paper is to provide an introduction into the bourgeoning field of eye tracking in Virtual Reality (VR). VR itself is an emerging technology on the consumer market, which will create many new opportunities in research. It offers a lab environment with high immersion and close alignment with reality. An experiment which is using VR takes place in a highly controlled environment and allows for a more in-depth amount of information to be gathered about the actions of a subject. Techniques for eye tracking were introduced more than a century ago and are now an established technique in psychological experiments, yet recent development makes it versatile and affordable. In combination, these two techniques allow unprecedented monitoring and control of human behavior in semi-realistic conditions. This paper will explore the methods and tools which can be applied in the implementation of experiments using eye tracking in VR following the example of one case study. Accompanying the technical descriptions, we present research that displays the effectiveness of the technology and show what kind of results can be obtained when using eye tracking in VR. It is meant to guide the reader through the process of bringing VR in combination with eye tracking into the lab and to inspire ideas for new experiments.
Sequence analysis of photoaffinity‐labelled peptides derived by proteolysis of photosystem‐2 reaction centres from thylakoid membranes treated with [<sup>14</sup>C]azidoatrazine (1992)

Photosystem-2 reaction centres were prepared from pea thylakoid membranes that had been photoaffinity labelled with [14C]-azidoatrazine (2-azido-4-ethylamino-6-isopropylamino-s-triazine), a derivative of the herbicide atrazine which binds to the secondary plastoquinone electron-acceptor site of photosystem 2. SDS/PAGE of the 14C-labelled reaction centres followed by fluorography revealed photoaffinity-labelled proteins of apparent molecular masses 30 kDa and 55 kDa, which corresponded to the D1 polypeptide and to an SDS-stable heterodimer of the D1 and D2 polypeptides, respectively. To obtain sequence information on the site of photoaffinity labelling, an 8-kDa photoaffinity-labelled peptide, generated by proteolysis of the reaction-centre material with trypsin, was isolated and purified to apparent homogeneity using reverse-phase and size-exclusion HPLC techniques. The amino terminus of the photoaffinity-labelled peptide was determined to be Leu-Gly-Met-Arg-Pro-Xaa-Ile-Ala-Val-Ala-Tyr by Edman sequencing. This corresponds to the amino terminus of a predicted tryptic peptide of D1 and confirms that azidoatrazine photolabels the D1 polypeptide of photosystem 2 in the region Leu137-Arg225. Chymotrypsin/trypsin digestion of photoaffinity-labelled reaction centres followed by reverse-phase HPLC was used to isolate a smaller photoaffinity-labelled peptide. On Edman sequencing, Ser-Ala were identified as the first two residues and 14C was released on the third cycle, after which further degradation was blocked. The two potential peptide fragments with Ser-Ala at the amino terminus in the region Leu137-Arg225 are Ser148-Ala-Pro and Ser212-Ala-Met. Proline is an unlikely target for reaction with the nitrene of the photoactivated azidoatrazine, and the data are thus consistent with Met214 as the site of photoaffinity labelling on D1 when thylakoid membranes are illuminated with ultraviolet irradiation in the presence of [14C]azidoatrazine.
POWER7<sup>TM</sup> local clocking and clocked storage elements (2010)

The design of the clocked storage elements (CSEs) and associated local clocking circuitry is a critical consideration for modern microprocessor projects[1], and the POWER7 <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">™</sup> chip[2], designed in a 45nm silicon-on-insulator (SOI) technology, was no exception. The digital logic contained over 2M CSEs, and the design of these elements had a major impact not only on the area, power, and performance of the chip, but also on the reliability, testability, and the ability to debug and optimize the hardware. This paper will focus on the special features added to the CSE design with these considerations in mind.
Computation of Q3D Viscous Flows in Various AnnularTurbine Stages with Heat Transfer (1997)

A better understanding of the flow inside the multi‐stage turbomachines will be very useful to both the designer and operator. The numerical calculation for single blade row has been well established with the time marching computation of the Navier‐Stokes equations. But there will exist much more difficulties for the multi‐blade rows due to the rotor‐stator interaction. The major problems are related to the unsteady flow which will inevitably exist in the blade passages due to the different rotating speed and possible the different in blade number. A method is presented for simulating various turbine blade rows in single‐stage environment. A solver has been developed for studying the complex flow analysis of ‘proposed high pressure turbine’ (HPT) using quasi‐3‐D Reynolds‐averaged Navier‐Stokes (Q3D RNS) equations. The code achieves good quality solutions quickly even with relatively coarse mesh sizes. The work is first validated both with UTRC′s and Zeschky and Gallus′ subsonic turbine test cases covering inlet boundary conditions and Reynolds‐averaged values. A H‐type grid is adopted as it is easy to generate and can readily extend to 3D application. When rows are closely spaced, there can be a strong interaction which will impact the aerodynamic, thermal and structural performance of the blade.
Identification of a novel nuclear localization signal in Tbx1 that is deleted in DiGeorge syndrome patients harboring the 1223delC mutation (2005)

DiGeorge syndrome (DGS) is the most common human chromosomal deletion syndrome and is frequently associated with deletions on chromosome 22q11. Approximately 17% of patients with the phenotypic features of this syndrome have no detectable genomic deletion. Animal studies using mouse models have implicated Tbx1 as a critical gene within the commonly deleted region, and several mutations in TBX1 have been identified recently in non-deleted patients, including missense and frameshift mutations. The mechanisms by which these mutations cause disease have remained unclear. We have identified a previously unrecognized and novel nuclear localization signal (NLS) at the C-terminus of Tbx1 that is deleted by the 1223delC mutation, thus explaining the mechanism of disease in these patients. This NLS is conserved across species, among a subfamily of T-box proteins including Brachyury and Tbx10, and among additional nuclear proteins. By providing functional data to indicate loss-of-function produced by the 1223delC TBX1 mutation, our results provide strong support for the conclusion that TBX1 mutations can cause DGS in humans.
A qualitative study on stress, coping strategies and feasibility of music intervention among women with cancer receiving chemotherapy during COVID-19 pandemic in Vietnam (2023)

Breast and gynaecological cancer (BGC) patients receiving chemotherapy may experience high levels of stress during the COVID-19 pandemic. Music interventions may be effective in lowering their stress levels. This study explored stressors, coping strategies, and the feasibility of music interventions among BGC patients in Vietnam. An exploratory qualitative study with individual face-to-face semi-structured interviews was conducted. A convenience sample of BGC patients receiving chemotherapy was recruited from the oncology centre of a public hospital in Vietnam. Twenty patients were interviewed with open-ended questions developed based on the transactional model of stress and coping to explore stress-causing factors and coping strategies and based on guidelines for music therapy practice to explore their music preferences and perceptions. Field notes and interview transcripts were analysed following the qualitative content analysis approach. Two stressor themes were identified: undesirable experiences during treatment and patients' inability to fulfil their own roles and responsibilities. Our findings revealed a new coping strategy-self-realisation of responsibilities towards the family-that is not listed in the transactional model of stress and coping. Future psychological interventions for stress management among BGC patients should focus on raising the patients' awareness of their values and responsibilities towards their families. Three categories of preferred music genres for stress reduction were identified: religious, softly melodic, and revolutionary music. The patients were aware of the positive effects of music and had different musical preferences. This study also explored the acceptance of music interventions and facilitators and barriers to implementing them among BGC patients in Vietnam. The findings suggest that before implementing music interventions, the musical preferences, religions, and beliefs of each individual should be considered to achieve desirable results. Music interventions for BGC patients receiving chemotherapy in Vietnam are feasible. Further intervention studies are needed to evaluate their effectiveness.
Non-Covalent Functionalization of Multi-Walled Carbon Nanotubes with Organic Aromatic Compounds (2007)

Several aromatic compounds derived from benzene by its annelation (naphthalene, anthracene, phenanthrene, pyrene) and exocyclic substitution (e.g., nitrobenzene, dinitrobenzenes, trinitrobenzene, chlorobenzene, N,N-dimethylaniline, and others) and endocyclic substitution (pyridine, quinoline, isoquinoline) efficiently sorbed on multi-walled carbon nanotubes (MWCNTs). Equilibrium constants for the sorption process have been determined. Computations of the energy of formation were performed for surface complexes of those arenes on single-walled carbon nanotubes (SWCNTs). Formation energies of those complexes were correlated against the experimental equilibrium constants. The latter were also correlated against calculated LUMO energy of the arenes. Solely, limited tendencies to the linearity could be observed. The analysis of the results of the correlations indicated that the arenes acting as the charge acceptors formed stronger complexes than arenes with a high electron density in the molecular orbital, for instance, N, N-dimethylaniline. The area of the arene--SWCNT contact was very essential for the complexation. The proximity of the HOMO orbital of SWCNT and LUMO of the arene was another essential factor. Bulky substituents in the arene molecules obscured their efficient contact with SWCNT.
Atomistic simulation of structure and dynamics of columnar phases of hexabenzocoronene derivatives (2006)

Using atomistic molecular dynamics simulations we study solid and liquid crystalline columnar discotic phases formed by alkyl-substituted hexabenzocoronene mesogens. Correlations between the molecular structure, packing, and dynamical properties of these materials are established.
Varying Tolerance to Glyphosate in a Population of Palmer Amaranth with Low EPSPS Gene Copy Number (2013)

A Palmer amaranth population (seeds collected in the year 2000; Washington Co., MS) suspected to be susceptible to glyphosate was examined as a population and as individual plants and found to exhibit varying tolerance or resistance to glyphosate. Whole plant spraying of glyphosate (0.84 kg·ha?1) to the population revealed that approximately 40% of this population were resistant to glyphosate and an LD50 of 0.75 kg·ha?1 was determined. Spray application of glyphosate indicated that some plants displayed varying degrees of resistance 14 days after treatment. Initial tests using leaf disc bioassays on 10 individual plants selected randomly from the population, allowed characterization of glyphosate resistance using both visual ratings of injury and quantitative measurement via chlorophyll content analysis. After initial bioassays and spray application, five plants with a range of tolerance to glyphosate were selected for cloning so that further studies could be accomplished on these individuals. Q-PCR analysis of these clones showed that resistance was not due to elevated EPSPS gene copy number. Shikimate levels were lower in the resistant and higher in the susceptible clones which correlated with varying degrees of resistance demonstrated in bioassays and spray application of glyphosate of these clones. Results demonstrate that individuals in a population can vary widely with respect to herbicide resistance and suggest that uptake, translocation, sequestration, metabolism or altered target site may contribute to the resistance in some individuals of this population.
Photosynthetic stimulation under long‐term CO<sub>2</sub> enrichment and fertilization is sustained across a closed <i>Populus</i> canopy profile (EUROFACE) (2006)

The long-term response of leaf photosynthesis to rising CO2 concentrations [CO2] depends on biochemical and morphological feedbacks. Additionally, responses to elevated [CO2] might depend on the nutrient availability and the light environment, affecting the net carbon uptake of a forest stand. After 6 yr of exposure to free-air CO2 enrichment (EUROFACE) during two rotation cycles (with fertilization during the second cycle), profiles of light, leaf characteristics and photosynthetic parameters were measured in the closed canopy of a poplar (Populus) short-rotation coppice. Net photosynthetic rate (A(growth)) was 49% higher in poplars grown in elevated [CO2], independently of the canopy position. Jmax significantly increased (15%), whereas leaf carboxylation capacity (Vcmax), leaf nitrogen (N(a)) and chlorophyll (Chl(a)) were unaffected in elevated [CO2]. Leaf mass per unit area (LMA) increased in the upper canopy. Fertilization created more leaves in the top of the crown. These results suggest that the photosynthetic stimulation by elevated [CO2] in a closed-canopy poplar coppice might be sustained in the long term. The absence of any down-regulation, given a sufficient sink capacity and nutrient availability, provides more carbon for growth and storage in this bioenergy plantation.
A pilot study to determine the effect of tazarotene gel 0.1% on steroid‐induced epidermal atrophy (2001)

Tazarotene gel 0.1% significantly reduces epidermal atrophy induced by diflorasone diacetate 0.05% ointment.
IL-16 Promotes Leukotriene C4 and IL-4 Release from Human Eosinophils via CD4- and Autocrine CCR3-Chemokine-Mediated Signaling (2002)

Human eosinophils are potential sources of inflammatory and immunomodulatory mediators, including cysteinyl leukotrienes, chemokines, and cytokines, which are pertinent to allergic inflammation. We evaluated the means by which IL-16, a recognized eosinophil chemoattractant, might act on eosinophils to affect their capacity to release leukotriene C(4) (LTC(4)) or their preformed stores of chemokines (eotaxin, RANTES) or Th1 (IL-12) or Th2 (IL-4) cytokines. IL-16 dose dependently (0.01-100 nM) elicited new lipid body formation, intracellular LTC(4) formation at lipid bodies, and priming for enhanced calcium ionophore-activated LTC(4) release. IL-16 also elicited brefeldin A-inhibitable, vesicular transport-mediated release of preformed IL-4, but not IL-12, from eosinophils. CD4 is a recognized IL-16R, and accordingly anti-CD4 Fab, soluble CD4, and a CD4 domain 4-based IL-16 blocking peptide inhibited the actions of IL-16 on eosinophils. Although CD4 is not G-protein coupled, pertussis toxin inhibited IL-16-induced eosinophil activation. IL-16 actions were found to be mediated by the autocrine activity, not of platelet-activating factor, but rather of endogenous CCR3-acting chemokines. IL-16 induced the rapid vesicular transport-mediated release of RANTES. The effects of IL-16 were blocked by CCR3 inhibitors (met-RANTES, anti-CCR3 mAb) and by neutralizing anti-eotaxin and anti-RANTES mAbs, but not by platelet-activating factor receptor antagonists (CV6209, BN52021). RANTES and eotaxin each enhanced LTC(4) and IL-4 (but not IL-12) release. Therefore, IL-16 activation of eosinophils is CD4-mediated to elicit the extracellular release of preformed RANTES and eotaxin, which then in an autocrine fashion act on plasma membrane CCR3 receptors to stimulate both enhanced LTC(4) production and the preferential release of IL-4, but not IL-12, from within eosinophils.
Precise location of two promoters for the beta-lactamase gene of pBR322. S1 mapping of ribonucleic acid isolated from Escherichia coli or synthesized in vitro. (1982)

We identified two promoters for the beta-lactamase gene of plasmid pBR322. RNA isolated from bacteria containing pBR322 or RNA transcribed in vitro on pBR322 templates was hybridized to 5' end-labeled single-stranded plasmid probes (Berk, A. J., and Sharp, P. A. (1977) Cell 12, 721-732). Electrophoretic analysis of the nuclease S1 digestion products next to Maxam-Gilbert sequencing ladders closely defines the transcriptional initiation points. The natural promoter lies near the coding sequence of the beta-lactamase gene, initiating transcription at -35 bases before the ATG initiation codon, while a second promoter initiates at positions -244 and/or -245 (on the opposite side of the Eco RI site). This promoter overlaps the promoter transcribing in the opposite direction toward the tetracycline gene(s) and starts in the -10 region of that promoter. S1 mapping of procaryotic mRNA, transcribed in vivo, allows both an accurate identification of promoters and the analysis of their transcriptional regulation.