gebhart/patrepeval huggingface dataset:
Engineering a minimal SilkCatcher/Tag pair compatible with SpyCatcher/Tag pair for the production of native-sized spider silk (2022)

Abstract Protein/peptide pairs, called Catcher/Tag pairs, are applied for biological isopeptide-bond mediated Click-reactions. Covalent protein ligation using Catcher/Tag pairs has turned out to be a valuable tool in biotechnology and biomedicines. It is essential to increase the current toolbox of Catcher/Tag pairs to expand the range of applications further, e.g., for multiple-fragment ligation that requires several orthogonal ligases. We report here engineering of novel Catcher/Tag pairs for protein ligation, aided by a new crystal structure of a minimal CnaB domain from Lactobacillus plantarum . We engineer several split variants, characterize in detail one of them, named SilkCatcher/Tag pair, and show that the newly engineered SilkCatcher/Tag pair is orthogonal and compatible with the widely used SpyCatcher/Tag pair. Finally, we demonstrate the use of the new SilkCatcher/Tag pair in the production of native-sized highly repetitive spider-silk-like proteins with &gt;90% purity, which is not possible with the traditional recombinant production.
A Genetic Study of Signaling Processes for Repression of PHO5 Transcription in Saccharomyces cerevisiae (1998)

In the yeast Saccharomyces cerevisiae, transcription of a secreted acid phosphatase, PHO5, is repressed in response to high concentrations of extracellular inorganic phosphate. To investigate the signal transduction pathway leading to transcriptional regulation of PHO5, we carried out a genetic selection for mutants that express PHO5 constitutively. We then screened for mutants whose phenotypes are also dependent on the function of PHO81, which encodes an inhibitor of the Pho80p-Pho85p cyclin/cyclin-dependent kinase complex. These mutations are therefore likely to impair upstream functions in the signaling pathway, and they define five complementation groups. Mutations were found in a gene encoding a plasma membrane ATPase (PMA1), in genes required for the in vivo function of the phosphate transport system (PHO84 and PHO86), in a gene involved in the fatty acid synthesis pathway (ACC1), and in a novel, nonessential gene (PHO23). These mutants can be classified into two groups: pho84, pho86, and pma1 are defective in high-affinity phosphate uptake, whereas acc1 and pho23 are not, indicating that the two groups of mutations cause constitutive expression of PHO5 by distinct mechanisms. Our observations suggest that these gene products affect different aspects of the signal transduction pathway for PHO5 repression.
Correction: A Novel Candidate Vaccine for Cytauxzoonosis Inferred from Comparative Apicomplexan Genomics (2013)

Cytauxzoonosis is an emerging infectious disease of domestic cats (Felis catus) caused by the apicomplexan protozoan parasite Cytauxzoon felis. The growing epidemic, with its high morbidity and mortality points to the need for a protective vaccine against cytauxzoonosis. Unfortunately, the causative agent has yet to be cultured continuously in vitro, rendering traditional vaccine development approaches beyond reach. Here we report the use of comparative genomics to computationally and experimentally interpret the C. felis genome to identify a novel candidate vaccine antigen for cytauxzoonosis. As a starting point we sequenced, assembled, and annotated the C. felis genome and the proteins it encodes. Whole genome alignment revealed considerable conserved synteny with other apicomplexans. In particular, alignments with the bovine parasite Theileria parva revealed that a C. felis gene, cf76, is syntenic to p67 (the leading vaccine candidate for bovine theileriosis), despite a lack of significant sequence similarity. Recombinant subdomains of cf76 were challenged with survivor-cat antiserum and found to be highly seroreactive. Comparison of eleven geographically diverse samples from the south-central and southeastern USA demonstrated 91-100% amino acid sequence identity across cf76, including a high level of conservation in an immunogenic 226 amino acid (24 kDa) carboxyl terminal domain. Using in situ hybridization, transcription of cf76 was documented in the schizogenous stage of parasite replication, the life stage that is believed to be the most important for development of a protective immune response. Collectively, these data point to identification of the first potential vaccine candidate antigen for cytauxzoonosis. Further, our bioinformatic approach emphasizes the use of comparative genomics as an accelerated path to developing vaccines against experimentally intractable pathogens.
Average wavelet coefficient-based detection of chaos in oscillatory circuits (2017)

Purpose The purpose of this paper is to propose a new algorithm for detection of chaos in oscillatory circuits. The algorithm is based on the wavelet transform. Design/methodology/approach The proposed detection is developed by using a specific measure obtained by averaging wavelet coefficients. This measure exhibits various values for chaotic and periodic states. Findings The proposed algorithm is applied to signals from autonomous systems such as the Chua’s oscillatory circuit, the Lorenz chaotic system and non-autonomous systems such as the Duffing oscillator. In addition, the detection is applied to sequences obtained from the logistic map. The results are compared to those obtained with a detrended fluctuation analysis and a time-frequency signal analysis based on detectors of chaotic states. Originality/value In this paper, a new algorithm is proposed for the detection of chaos from a single time series. The proposed technique is robust to the noise influence, having smaller calculation complexity with respect to the state-of-the-art techniques. It is suitable for real-time detection with delay that is about half of the window width.
Six-Fold Acceleration of High-Spatial Resolution 3D SPACE MRI of the Knee Through Incoherent k-Space Undersampling and Iterative Reconstruction—First Experience (2015)

We demonstrate the successful clinical implementation of 3D TSE MRI with incoherent k-space undersampling and iterative reconstruction for 6-fold accelerated high spatial resolution isotropic 3D MRI data acquisition. Our preliminary assessments suggest similar image quality and diagnostic performance of a comprehensive 10-minute 3D TSE MRI prototype protocol and 20-minute TSE MRI standard protocol.
EVALUATION OF HEALTH INFORMATION REQUIREMENT IN MANAGEMENT INFORMATION SYSTEM (2011)

: Introduction: Considering the importance of information, providing the management with 
a reliable information system, can facilitate decision making regarding planning, organizing 
and controlling. This study aimed to analyze and evaluate information needs of managers at 
vice - chancellorship for treatment in Iranian medical science universities. 
Methods: This cross-sectional study was carried out during 2009. The study population 
consisted all managers of vice-chancellor for treatment of 39 medical universities. Data 
collection was based on a predesigned questionnaire. In this study two methods of business 
system planning (BSP) and critical system factors (CSF). Data were analysed by SPSS 
software. 
Results: Of 669 identified information needs, 45% were initial information needs of 
managers. 12% of the needs were not priorities and thus excluded. 14% of information 
needs were obtained through the forms, 4% through the database, 21% through both the 
form and database, 5% through the web site and 56% were without any sources. 
Conclusion: It was shown that 56% of information needs of managers were without 
sources, So, designing management information system based on critical success factors and 
other scientific methods is necessary.
All-optical bistable transistor in photonic crystals (2004)

We demonstrate all-optical switching in a nonlinear photonic crystal cross-waveguide geometry with instantaneous Kerr nonlinearity, in which the transmission of a signal is reversibly switched on and off by a low power control input.
Abstract 11910: Contemporary In-Hospital Outcomes of Bifurcation Percutaneous Coronary Interventions: Update From the Prospective Global Registry for the Study of Bifurcation Lesion Interventions (PROGRESS-BIFURCATION) (2022)

Introduction: Bifurcation percutaneous coronary intervention (PCI) techniques are rapidly evolving and can be challenging to perform. Methods: We examined the angiographic, procedural characteristics, and outcomes of 472 bifurcation PCIs in Prospective Global Registry for the Study of Bifurcation Lesion Interventions (PROGRESS-BIFURCATION, NCT05100992). Results: A total of 472 bifurcation PCIs were included. Mean age was 67±12 years, 74% were men with a high prevalence of comorbidities: hypertension (81%), diabetes mellitus (36%), dyslipidemia (90%). Overall technical success was 95%. The incidence of in-hospital major adverse cardiovascular events (MACE) was 5.1%. The most common stenting strategy was provisional (71%), double-kissing (DK) crush (12%), mini-crush wish 2 stents (3%), culotte (3%), T-and protrusion (4%), and T-stenting (1.5%). Patients treated with the DK-crush had more severe stenosis of the left main (35%±38 vs. 19%±30, p&lt;0.001), proximal left anterior descending (68%±29, vs. 52%±35, p=0.001), and side branch lesion (82%±15, 51%±36, p&lt;0.001). Medina classification was more often 1,1,1 (79% vs. 39%, p&lt;0.001), with higher use of intravascular ultrasound/optical coherence tomography (57% vs. 31%, p&lt;0.001) compared to non-DK crush. The DK-crush required use of more contrast and took longer to perform (Table). Conclusions: Despite high patient comorbidity, bifurcation PCI can be performed with high technical success and low in-hospital MACE rates. DK-crush technique was more commonly preferred in bifurcation lesions with more severe/proximal vessel involvement.
Modeling Capacitive Low-Power Voltage Transformer Behavior over Temperature and Frequency (2021)

The use of capacitive dividers (CDs) in medium-voltage (MV) networks started as simple voltage detectors and as rough voltage measurement instruments for protective purposes. Now, with the spread of intelligent electronic devices and renewable energy sources at the distribution level, capacitive dividers are designed and installed to perform accurate voltage measurements. Such a requirement is mandatory when the power quality has to be assessed. Therefore, CDs are currently being used either for power frequency or for high-frequency (supraharmonic- or partial-discharge-level) measurements. In this paper, typical off-the-shelf CDs are studied and modeled to understand how they behave in a wide range of frequencies and when the temperature varies. To this purpose, specific setups and tests have been developed and performed. From the results, it is clear that with proper modeling of CDs, it is possible to exploit them for measuring phenomena in a wide range of frequencies, including the effects due to temperature variations and self-resonances.
Study on protective effect of bFGF on hearing loss of guinea pigs following noise exposure (2002)

Objective To study the protective effects of bFGF on noise exposure hearing loss and effects on heat shock protein 70 of cochlea.Methods Preparing the animal model of noise induced hearing loss, and using ABC immunohistochemistry method for heat shock protein 70 analysis and ABR threshold. Results bFGF decreased the enhancing of ABR threshold by exposed to noise.Conclusion bFGF could resist the injure of cochlea by noise exposure,and decreased the express of the heat shock protein 70.
Seed lot, nursery, and bud dormancy effects on root electrolyte leakage of Douglas-fir (<i>Pseudotsuga menziesii</i>) seedlings (1999)

The effects of seed lot, nursery culture, and seedling bud dormancy status on root electrolyte leakage (REL) of Douglas-fir (Pseudotsuga menziesii (Mirb.) Franco) seedlings were assessed to determine if these factors should be considered when interpreting REL for seedling quality. The relationships of REL to survival, net photosynthesis (Pn), stomatal conductance (gwv), mid-day shoot water potential (Ψmid), root growth capacity (RGC), and relative height growth were determined for each factor. Nursery culture had no effect on the relationship between REL and all other measured attributes. Seed lot affected the relationship between REL and Pn, Ψmid, and survival. However, critical REL (i.e., lowest value associated with detectable root damage) and PS80 REL (i.e., level associated with an 80% probability for survival) were similar between seed lots. Bud dormancy status affected the relationship between REL and survival, RGC, and relative height growth. Control levels of REL, critical REL, and PS80 REL decreased as the number of days required for 50% terminal bud break declined. Thus, terminal bud dormancy status must be known before REL can be used to assess seedling quality. If the bud dormancy status of Douglas-fir populations is known, then critical and PS80 REL levels may be useful as indices of root damage.
Evaluation of absorption kinetics of oxygen scavenger sachets using response surface methodology (2010)

Abstract The performance of oxygen scavengers can be influenced by several conditions, such as temperature (T) and relative humidity (RH), which are considered to be the two major factors. Therefore, the development of new scavengers requires the study of their performance, with these conditions varied. In this paper, the response surface methodology (RSM) was used to study the performance of a newly developed oxygen scavenger sachet and to model the influences of T and RH and their interaction on the absorption capacity and rate constant of the developed sachet. Commercial oxygen scavenger sachets were used for comparison purposes. The oxygen absorption capacity and rate constant were evaluated with a 2 2 factorial design with a central point. The results showed that each absorber sachet presented a different behaviour and there were significant interactions between T and RH; so, the RSM was the most appropriate for these studies. The developed sachet presented a better performance compared with the commercial ones at 23°C and 53% RH, which represents the condition for commercialization at room temperature of foods of intermediary water activity, while in the extreme conditions (100% RH and 37°C) all sachets present a similar absorption capacity. Copyright © 2010 John Wiley &amp; Sons, Ltd.
3D Integration Using Self-Assembly at Air-Water-Solid Interface (2014)

This paper presents the first proof-of-concept 3D integration using fluidic self-assembly of chip-scale parts (2000 × 2000 ×100 μm <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">3</sup> ) at an air-water-solid interface. Four-layer 3D integration is achieved by assembling new parts over previously assembled parts. Assembly proceeds as an assembly substrate is pulled up through an air-water interface and electrical and mechanical bonding are achieved by solder reflow. Magnetic fields and temporary Faraday waves are introduced for one-to-one part-to-site registration in proper orientation. The alignment accuracy degrades with increasing number of layers due to weaker magnetic force. The maximum number of layers that can be achieved is simulated and analyzed. Via resistance including the effect of degradation of solder over repeated reflow process is measured.
Implanted neonatal human dermal fibroblasts influence the recruitment of endothelial cells in mice (2012)

The vascularization of new tissue within a reasonable time is a crucial prerequisite for the success of different cell- and material-based strategies. Considering that angiogenesis is a multi-step process involving humoral and cellular regulatory components, only in vivo assays provide the adequate information about vessel formation and the recruitment of endothelial cells. The present study aimed to investigate if neonatal human dermal fibroblasts could influence in vivo neovascularization. Results obtained showed that fibroblasts were able to recruit endothelial cells to vascularize the implanted matrix, which was further colonized by murine functional blood vessels after one week. The vessels exhibited higher levels of hemoglobin, compared with the control matrix, implanted without fibroblasts, in which no vessel formation could be observed. No significant differences were detected in systemic inflammation. The presence of vessels originated from the host vasculature suggested that host vascular response was involved, which constitutes a fundamental aspect in the process of neovascularization. Fibroblasts implanted within matrigel increased the presence of endothelial cells with positive staining for CD31 and for CD34 and the production of collagen influencing the angiogenic process and promoting the formation of microvessels. New strategies in tissue engineering could be delineated with improved angiogenesis using neonatal fibroblasts.
Liquid Biopsy in the Diagnosis of HPV DNA in Breast Lesions (2017)

Our data supports the use of liquid biopsy to detect HPV DNA in breast pathology.
Effect of thermal denaturation on vanillin binding to some food proteins (1998)

Interactions of food proteins--beta-lactoglobulin (BLG), bovine serum albumin (BSA) und ovalbumin (OA)--with vanillin and effect of thermal denaturation of the proteins on vanillin binding were studies by US-VIS spectrophotometry. This method has its origin in characteristic changes in the vanillin absorption spectrum at vanillin-protein complex formation and allows to calculate concentrations of the bound and free ligand in aqueous solutions. Thermodynamic parameters, the intrinsic association constants and the number of binding sites of the vanillin binding to the native and thermodenaturated proteins (monomers and clusters) were determined. It is shown that the vanillin affinity for the native proteins is decreased in the following order: BSA > BLG > OA. This sequence is reversed for the protein thermoclusters. The stepwise annealing allowing to derive complex protein mixtures composed of different types of the native and denatured protein mixtures composed of different types of the native and denatured protein particles was applied to thermodenaturation of BSA. The vanillin affinity for BSA is decreased in the order: native protein > denaturated monomer > denaturated clusters. Vanillin interaction with the proteins is mainly electrostatic in nature.
Evidence for a new extracellular peroxidase Manganese‐inhibited peroxidase from the white‐rot fungus Bjerkandera sp. BOS 55 (1992)

A novel enzyme activity was detected in the extracellular fluid of Bjerkandera sp, BOS 55. The purified enzyme could oxidize several compounds, such as Phenol red, 2,6‐dimethoxyphenol (DMP), Poly R‐478, ABTS and guaiacol, with H 2 O 2 as an electron acceptor. In contrast, veratryl alcohol was not a substrate. This enzyme also had the capacity to oxidize DMP in the absence of H 2 O 2 . With some substrates, a strong inhibition of the peroxidative activity by Mn 2+ was observed. Phenol red oxidation was inhibited by 84% with only 1 mM of this metal ion. Because DMP oxidation by this enzyme is only slightly inhibited by Mn 2+ , this substrate should not be used in assays to detect manganese peroxidase. The enzyme is tentatively named ‘Manganese‐Inhibited Peroxidase’.
Patients' perspectives of fluid management: A multicentre comparative study of home and incentre haemodialysis (2022)

Greater patient knowledge and its practice in HHD may contribute to improved fluid balance and outcomes. Whilst patient selection may contribute towards these differences, the training patients receive when opting for HHD and subsequent experience are likely to be key contributing factors. Integrating aspects of education on fluid management from HHD training programmes should be considered in IHD, and further targeted, robust education remains an unmet need.
The photochemical [3 + 2]cycloaddition reaction of 2,2,3,3-tetra-arylthiiranes and tetracyanoethylene through electron donor–acceptor complexes (1989)

Upon irradiation of the electron donor–acceptor complexes of 2,2,3,3-tetra-arylthiiranes and tetracyanoethylene (TCNE), the [3 + 2]cycloadditions occurred efficiently without the desulphurisation of thiiranes.
Effects of Endothelin-1 on Epithelial Ion Transport in Human Airways (2003)

Endothelin-1 (ET-1) exerts many biological effects in airways, including bronchoconstriction, airway mucus secretion, cell proliferation, and inflammation. We investigated the effect of ET-1 on Na absorption and Cl secretion in human bronchial epithelial cells. Addition of 10(-7) M ET-1 had no effect on the inhibition of the short circuit current (Isc) induced by amiloride, a Na channel blocker. Addition of 10(-7) M ET-1 to the apical bath in the presence of amiloride increased Isc in cultured human bronchial epithelial cells studied in Ussing chambers. No effect was observed when ET-1 was added to basolateral bath, indicating that the involved ET-1 receptors are likely present only in the apical membrane of the cells. Use of Cl-free solutions and bumetanide reduced the ET-1-induced increases in Isc, indicating that ET-1 stimulates Cl secretion. The ET-1-induced increase in Isc was prevented by exposure to the ETB receptor antagonist BQ-788 but not to the ETA receptor antagonist BQ-123. ET-1 did not raise intracellular Ca levels, but increased the intracellular concentration of cAMP. These findings indicate that ET-1 is a Cl secretagogue in human airways and acts presumably through apically located ETB receptors and activation of the cAMP pathway.
Adsorption of inorganic electrolytes on activated carbons from aqueous solution. (1986)

市販の活性炭ならびにそれらを表面改質処理した活性炭の合計12種類について代表的な無機電解質イオンの吸着挙動を調べるとともに,その吸着機構について考察した.無機電解質イオンの吸着実験は種々のpHに調整したそれぞれのイオンの水溶液について行なった. 水素イオンおよびハロゲン化物イオンは中性から酸性領域においていずれの場合にもほぼ同量が活性炭に吸着され, 吸着量は水素イオン濃度の増加とともに高くなった. 水素イオンおよびハロゲン化物イオンの吸着量はハロゲン化物イオンの種類によっていちじるしく異なり, 吸着量はヨウ化物イオン＞臭化物イオン＞塩化物イオンの順序であった. 水素イオンおよびハロゲン化物イオンの吸着量は塩化亜鉛賦活炭にくらべて水蒸気賦活炭の方が高く,また空気酸化処理した活性炭にくらべて高温で排気処理または水素還元処理した活性炭の方が高かった. 酸の吸着に関しては灰分による影響は見られなかった. 水酸化物イオンおよびナトリウムイオンは中性からアルカリ性領域において吸着され, 水酸化物イオンはナトリウムイオンにくらべてより多く活性炭に吸着された. これらのイオンの吸着量は水素イオンおよびハロゲン化物イオンの場合とは反対に塩化亜鉛賦活炭ならびに空気酸化処理した活性炭の方が高い傾向を示した. これらのイオンの吸着結果は塩基性表面酸化物機構またはイオン交換機溝により説明された.
Complete Genome Sequence of Bacillus velezensis LABIM40, an Effective Antagonist of Fungal Plant Pathogens (2018)

<i>Bacillus velezensis</i> strain LABIM40 holds high potential for biological control of plant pathogens. Its complete genome contains one chromosome of 3,972,310 bp with 3,777 DNA coding sequences and displays 33 gene clusters potentially involved in the suppression of fungal pathogens.
Mechanical Properties and Friction Dynamics of Organogels Solidified with Rice Paraffin (2023)

Raw materials suitable for a sustainable society have attracted interest in the cosmetics industry. We focused on rice bran as a sustainable material and evaluated the gelation behavior of paraffin extracted from rice bran (rice paraffin) against liquid paraffin, squalane, jojoba oil, and silicone oil. In addition, the frictional properties of the prepared organogel on an artificial skin surface were evaluated using a sinusoidal motion friction evaluation system. Rice paraffin solidified all oils even at the lowest wax concentration of 5 wt%. The hardness and kinetic friction coefficient μ <sub>k</sub> increased with an increase in the wax composition. The hardness and μ <sub>k</sub> of organogels solidified with rice paraffin were smaller than those of gels solidified with petroleum-derived paraffin. These differences are caused by the smaller carbon amount of rice paraffin. The friction parameters depended on the type of oil: the μ <sub>k</sub> of RLG composed of rice and liquid paraffin was greater than that of the other three oils (R, L, and G denote rice paraffin, liquid paraffin, and gel, respectively). These findings promote the development of lipsticks and cleansing gels consisting of sustainable development goal-responsive raw materials.