gebhart/patrepeval huggingface dataset:
Structural characterization of a protein adsorbed on aluminum hydroxide adjuvant in vaccine formulation (2019)

The heterogeneous composition of vaccine formulations and the relatively low concentration make the characterization of the protein antigens extremely challenging. Aluminum-containing adjuvants have been used to enhance the immune response of several antigens over the last 90 years and still remain the most commonly used. Here, we show that solid-state NMR and isotope labeling methods can be used to characterize the structural features of the protein antigen component of vaccines and to investigate the preservation of the folding state of proteins adsorbed on Alum hydroxide matrix, providing the way to identify the regions of the protein that are mainly affected by the presence of the inorganic matrix. l-Asparaginase from <i>E. coli</i> has been used as a pilot model of protein antigen. This methodology can find application in several steps of the vaccine development pipeline, from the antigen optimization, through the design of vaccine formulation, up to stability studies and manufacturing process.
Plasmon Modes and Hot Spots in Gold Nanostar–Satellite Clusters (2014)

Gold nanostars display strong electromagnetic field enhancement at their tips, and tip plasmon resonances can be tuned within the visible and near-infrared, which has been applied toward plasmonic molecular sensing. However, the sensitivity can be further increased by linking gold nanostars to other plasmonic nanoparticles and thereby inducing the creation of hot spots. We report the controlled formation of core–satellite assemblies comprising a central gold nanostar with gold spheres adsorbed to the tips via Raman active molecular linkers. Surface-enhanced Raman scattering (SERS) was recorded at the level of single gold nanostar–satellite clusters, and the experimental results were compared with detailed electromagnetic simulations.
Communication Smoothness Estimation Using F0 Information (2016)

The purpose of this study is to explore a system which provides a topic of discussion for carrying on lively and smooth human-to-human communication. When sensing there has been little progress during the conversation, the system attempts to provide a topic for leading a smoother discussion. To develop a process for estimating conversation smoothness, we confirmed the effectiveness of using fundamental frequency (F0). For each utterance, we calculated the F0’s average values and the F0’s standard deviation (SD) values, and compared these values between “smooth” utterances and “non-smooth” utterances. The differences are shown to be significant when using a t-test, where the confidence level is 95%. The linear discriminant analysis (LDA) were applied to the distribution between the Ave_F0 and the SD for classifying all utterances to “smooth” and “non-smooth”. The classification rates, which mean “% of correctly classified” are over 70% for four speakers. If laughter sounds are included in the utterances, the estimation performance decreased extremely. To keep high performance, it is necessary to except the laughter parts from utterances. We confirmed the Ave_F0 and the SD_F0 value are also effective to detect the laughter sounds. The t-test where the confidence level is 95% was applied on the distribution of the Ave_F0 and the SD_F0 for each speaker. As a result of t-test, the difference between the laughter parts and the speech parts are significant for all four speakers.
Transforming growth factor-β1, connective tissue growth factor et fibrose pulmonaire (2005)

During physiological pregnancy, changes in lung functions, ventilatory patterns and gas exchanges happen. Therefore, the dyspnea experienced by a majority of women is usually due to pregnancy itself and is very difficult to differentiate from a pathophysiological state. Anamnesis and clinical examination alone do not rule out dyspnea of ​​thromboembolic origin. Therefore, a structured approach, based on a thromboembolic risk assessment, the application of a specific management algorithm and the use of imaging exams is required for emergency management of dyspnea occurring during the pregnancy and in the postpartum.
Modeling and analysis of sulfur hexafluoride plasma etching for silicon microcavity resonators (2021)

Silicon microcavity resonators are an important component in modern photonics. In order to optimize their performance, it is fundamental to control their final shape, in particular with respect to the involved CMOS compatible, two-step sulfur hexafluoride plasma etching fabrication process. To that end, we use a ray-tracing based pseudo-particle model to enhance a level-set topography simulator enabling us to effectively capture the characteristics of sulfur hexafluoride plasma etching in the low-voltage-bias regime. By introducing a novel and robust calibration procedure and by applying it to experimental data of a reference two-step etching process, we are able to optimize the etch times and photoresist geometry without costly reactor-scale simulations and simultaneously explore beyond conventional statistical process modeling. Through defining objective design criteria by way of Gaussian beam analysis, we analyze the plasma etching process and provide new insights into alternative processing guidelines which impact shape measurements such as cavity opening and parabolic form. By means of scale analysis, we propose that the radius of curvature of the microcavity is optimized with a reduction of the photoresist opening diameter. After simulated fabrication runs, we surmise that the cavity quality parameters are improved by increasing the duration of the first etch step by a factor of 2 and by decreasing the second etch step duration by up to in comparison to the reference two-step etching process. This results in an overall reduction of etch time of at least , allowing to significantly optimize the overall fabrication process.
Myriad: Design and implementation of a federated database prototype (1995)

Abstract A key problem in providing ‘enterprise‐wide’ information is the integration of databases that have been independently developed. An important requirement is to accommodate heterogeneity and maintain the autonomy of component databases. Myriad is a federated database prototype developed at the University of Minnesota, to provide a testbed for investigating alternatives in architecture and algorithms for database integration, query processing and optimization, and concurrency control and recovery. The system incorporates our group's research results in these areas. This paper describes our experiences in the design and implementation of Myriad, and in the project management. Special emphasis is given to discussing design alternatives and their impact on Myriad. This paper also presents the software engineering principles and the project management techniques we used in developing Myriad and the lessons we learned. We believe these lessons would be useful for practitioners who wish to develop a similar system. Handling heterogeneity and autonomy were prime objectives throughout the prototyping effort. We are convinced that a prototype federated database is an important infrastructural requirement for the overall goal of ‘enterprise‐integration’, and believe Myriad to be a significant contribution towards this.
S92 Genomic investigation unmasks evidence of transmission across mycobacterium abscessus cystic fibrosis patients (2017)

<h3>Background</h3> <i>Mycobacterium abscessus</i> (<i>Mabs</i>) is a critical respiratory pathogen in Cystic Fibrosis (CF), with significant challenges in diagnosis and treatment. Recent whole genome sequencing (WGS) studies have challenged the assumption that acquisition in CF is primarily from soil and water systems.<sup>1</sup> We sought to investigate potential transmission of <i>Mabs</i> within and between CF centres through WGS analysis of CF isolates from the Scottish Mycobacteria Reference Laboratory. <h3>Methods</h3> 64 isolates were recovered and sequenced from CF samples positive for <i>Mabs</i> between 2008 and 2016. Multilocus sequence typing (MLST), and phylogenetic analysis based on core genome Single Nucleotide Polymorphisms (SNPs) was used to identify dominant circulating clones. Probable transmission clusters were defined by &lt;20 SNPs between isolates, as suggested by previous studies. This work was carried out as part of a public health investigation. <h3>Results</h3> MLST analysis of the 64 confirmed <i>Mabs</i> isolates demonstrated the following: 8 strain types (ST) associated with <i>Mabs</i> subspecies <i>abscessus</i>, including ST9 (n=18), ST24 (12), ST5 (7), ST26 (4), ST21 (3), and ST10 (2); 11 identified as subspecies <i>massiliense associated with</i> ST4 (4), ST6 (3), ST7 (2) and ST3 (2); 4 identified as subspecies <i>bolletti</i>. Phylogenomic analysis provided higher resolution and identified significant relatedness between and within clonal complexes. The most prevalent subspecies <i>abscessus</i> clone was ST9, of which 16 isolates were distinguished by &lt;20 SNPs, 12 of which from one hospital region. Five of the ST9 isolates were indistinguishable at the SNP level, and yet originated from different Health Board regions and different hospitals. ST5, ST24 and ST26 also contained isolates distinguished by &lt;20 SNPs and originated from several geographically distinct regions. <h3>Conclusion</h3> WGS has provided strong evidence of the circulation of dominant clones between and within CF centres across geographically diverse settings over an 8 year period. The high genomic relatedness provides strong evidence of transmission between CF patients, even though the precise mechanisms of transmission remain uncertain. Further studies are underway to understand the mechanism of transmission in this clinical context. <h3>Reference</h3> Bryant JM, Grogono DM, Rodriguez-Rincon D, Everall I, Brown KP, Moreno P, Floto RA, <i>et al</i>. Emergence and spread of human-transmissible multidrug-resistant nontuberculous mycobacterium. <i>Science (New York)</i> 2016;354(6313):751–757. https://doi.org/10.1126/science.aaf8156
Simultaneous Detection of Multiple Transgenes for Genetically-Modified Mouse Strains (2009)

Recent advances in the genetic manipulation of mice have enabled us to generate transgenic and knockout mice. However, it is not easy to maintain these genetically-modified mice with the high-quality necessary to meet both scientific and legal requirements. RIKEN BRC has collected various transgenic, knockout, and conditional knockout mice. To examine the genetic modifications in these strains quickly and thoroughly, we established a simultaneous PCR test to detect multiple transgenes. We have called this, the "KO-survey". The PCR condition was optimized to detect neo, puro, pgk-neo, lacZ, and HSVtk-neo in set I, and hyg, IRES, cre, flp, and Gfp in set II. This "KO-survey" is useful for providing users with mouse strains of the highest genetic quality and accurate information on their genetic modifications.
Mechanistic Studies of Protein Tyrosine Phosphatases YopH and Cdc25A withm-Nitrobenzyl Phosphate (2004)

Protein tyrosine phosphatases (PTPs) constitute a large family of signaling enzymes that include both tyrosine specific and dual-specificity phosphatases that hydrolyze pSer/Thr in addition to pTyr. Previous mechanistic studies of PTPs have relied on the highly activated substrate p-nitrophenyl phosphate (pNPP), an aryl phosphate with a leaving group pK(a) of 7. In the study presented here, we employ m-nitrobenzyl phosphate (mNBP), an alkyl phosphate with a leaving group pK(a) of 14.9, which mimics the physiological substrates of the PTPs. We have carried out pH dependence and kinetic isotope effect measurements to characterize the mechanism of two important members of the PTP superfamily: Yersinia PTP (YopH) and Cdc25A. Both YopH and Cdc25A exhibit bell-shaped pH-rate profiles for the hydrolysis of mNBP, consistent with general acid catalysis. The slightly inverse (18)(V/K)(nonbridge) isotope effects (0.9999 for YopH and 0.9983 for Cdc25A) indicate a loose transition state with little nucleophilic participation for both enzymes. The smaller (18)(V/K)(bridge) primary isotope effects (0.9995 for YopH and 1.0012 for Cdc25A) relative to the corresponding isotope effects for pNPP hydrolysis suggest that protonation of the leaving group oxygen at the transition state by the general acid is ahead of P-O bond fission with the alkyl substrate, while general acid catalysis of pNPP by YopH is more synchronous with P-O bond fission. The isotope effect data also confirm findings from previous studies that Cdc25A utilizes general acid catalysis for substrates with a leaving group pK(a) of >8, but not for pNPP. Interestingly, the difference in the kinetic isotope effects for the reactions of aryl phosphate pNPP and alkyl phosphate mNBP by the PTPs parallels what is observed in the uncatalyzed reactions of their monoanions. In these reactions, the leaving group is protonated in the transition state, as is the case in PTP-catalyzed reactions. Also, the phosphoryl group in the transition states of the enzymatic reactions does not differ substantially from those of the uncatalyzed reactions. These results provide further evidence that these enzymes do not change the transition state but simply stabilize it.
코로나19에 대한 북한의 대응: 『로동신문』 보도를 중심으로 (2020)

이 연구는 코로나19에 대한 북한의 대응을 살펴보기 위해 노동당 중앙위원회 기관지 『로동신문』에 보도된 ‘코로나19’ 관련 기사의 양적 특징과 주요 내용을 분석하였다.
분석결과 북한은 첫째, 국제사회의 보건의료협력과 같은 보편적 대응과 달리 ‘봉쇄와 통제라는’ 고립된 방역체계를 고수하고 있지만, 둘째, 제한된 환경과 상황 속에서 필수적 방역물품의 중요성을 인식하고 자력 생산을 통한 공급을 시행하고 있으며, 셋째, 국제사회 동향에 대한 분석을 바탕으로 한 정책 결정 등 코로나19 지속에 따른 일상의 변화에도 비교적 유연하고 안정된 상황관리를 하고 있다고 평가된다. 그러나 이러한 북한 당국의 방역 강화 기조에도 네 번째 특징인 기강 해이가 발생하고 있는 것을 고려할 때 지도부의 관리·감독 등 통제에 대한 영향력이 일정 부분 감소한 것으로 추정할 수 있어, 이에 대한 지속적인 분석이 요구된다.
이 연구는 올 한해 전 세계를 휩쓴 코로나19가 여전히 진행 중인 상황에서 이에 대한 북한의 대응과 그 특징을 분석했다는 점에서 유의미한 정보를 제공하고 있으며, 나아가 향후 잠재적 전염병 발발에 대한 방역대책 수립 및 남북보건의료 협력 방향성에 기초자료가 될 수 있다는 점에 의미가 있다.
Saturated fatty Acid–Induced Insulin Resistance in Rat Adipocytes (1994)

Palmitate has been shown to stimulate glucose transport, translocation of GLUT4 and insulin receptor autophosphorylation in isolated rat adipocytes (Biochem Biophys Res Commun 177:343-49, 1991). Here we further characterize the ability of short-term treatment with free fatty acids to stimulate glucose transport in isolated rat adipocytes and demonstrate that prolonged treatment induces insulin resistance. Treatment of adipocytes for 15 min with 1 mM myristate (14:0), palmitate (16:0), or stearate (18:0) stimulates glucose transport by 119 +/- 33, 89 +/- 29, and 114 +/- 30%, respectively. In contrast, oleate (cis 18:1), 1), elaidate (trans 18:1), and linoleate (cis 18:2) do not stimulate glucose transport. Palmitate stimulates glucose transport in a concentration-dependent manner, demonstrating saturation at 1 mM and half-maximal stimulation at 0.25-0.5 mM. Prolonged treatment (4 h) of rat adipocytes with 1 mM palmitate induces insulin resistance. After a 4-h preincubation with palmitate (1 mM), insulin stimulates glucose transport in rat adipocytes by 4.4-fold +/- 0.8, vs. 8.8-fold +/- 0.8 in controls (n = 3). Palmitate-induced resistant cells demonstrated a 40% inhibition in maximal insulin responsiveness with little change in insulin sensitivity. Insulin binding is only slightly decreased (8%) in palmitate-pretreated cells. These studies indicate that saturated fatty acids stimulate glucose transport acutely and on prolonged exposure induce insulin resistance via a post-insulin binding defect. The underlying molecular mechanisms of insulin resistance induced by prolonged treatment with saturated fatty acids may now be investigated using this unique cellular model.
Effects of Land Use Change on Sediment and Water Yields in Yang Ming Shan National Park, Taiwan (2015)

The Soil and Water Assessment Tool (SWAT) is a watershed-based, semi-distributed hydrologic model for simulating hydrological processes at different spatial scales. The SWAT hydrology and erosion/sediment components are first validated after the hydrologic components calibration. The SWAT model also utilizes geographic information system (GIS) and digital elevation model (DEM) to delineate watersheds and extract the stream network. This study applies SWAT model to assess the impacts of land use change on soil and water losses from Yang Ming Shan National Park Watershed in northern Taiwan. Although the government has formulated regulations to limit the development, however, intense human activities, such as farming and building construction, still continue to exist. This study utilized two land-use data periods, one in 1996 and another in 2007, along with the SWAT model to simulate soil and water losses in Yang Ming Shan National Park. Based on the baseline scenario, the SWAT model was also successful in simulating the future scenario. Study results for scenario 2007, as compared to 1996 baseline period indicate that land use change shows forest land decreases about 6.9%, agricultural land increases about 9.5%, and causes sediment yield increase of 0.25 t/ha. Human activities deserve more attention when assessing soil and water losses because of their inevitable impacts. Government needs to modify land development policies and plans for land use change detection using satellite imagery to avoid illegal development activities.
Protein determination by microchip capillary electrophoresis using an asymmetric squarylium dye: Noncovalent labeling and nonequilibrium measurement of association constants (2008)

In response to a growing interest in the use of smaller, faster microchip (mu-chip) methods for the separation of proteins, advancements are proposed that employ the asymmetric squarylium dye Red-1c as a noncovalent label in mu-chip CE separations. This work compares on-column and precolumn labeling methods for the proteins BSA, beta-lactoglobulin B (beta-LB), and alpha-lactalbumin (alpha-LA). Nonequilibrium CE of equilibrium mixtures (NECEEM) represents an efficient method to determine equilibrium parameters associated with the formation of intermolecular complexes, such as those formed between the dye and proteins in this work, and it allows for the use of weak affinity probes in protein quantitation. In particular, nonequilibrium methods employing both mu-chip and conventional CE systems were implemented to determine association constants governing the formation of noncovalent complexes of the red luminescent squarylium dye Red-1c with BSA and beta-LB. By our mu-chip NECEEM method, the association constants K(assoc) for beta-LB and BSA complexes with Red-1c were found to be 3.53 x 10(3) and 1.65 x 10(5) M(-1), respectively, whereas association constants found by our conventional CE-LIF NECEEM method for these same protein-dye systems were some ten times higher. Despite discrepancies between the two methods, both confirmed the preferential interaction of Red-1c with BSA. In addition, the effect of protein concentration on measured association constant was assessed by conventional CE methods. Although a small decrease in K(assoc) was observed with the increase in protein concentration, our studies indicate that absolute protein concentration may affect the equilibrium determination less than the relative concentration of protein-to-dye.
&#x2211;&#x0394; ADC based current mode power supply controller with digital voltage loop (2008)

Sigma-delta (SigmaDelta) modulators offer cost advantages in digitally controlled power supplies. Due to its noise shaping, high resolution, high speed ADCs and DACs are not necessary for digital control. This paper presents a low cost current-mode controller. The outer voltage loop is digital with SigmaDelta modulator and low resolution DAC. The inner current loop is kept analog with analog comparator and SR latch. An experimental circuit includes a SigmaDelta modulator test chip, a controller implemented on an FPGA, and a 30 V-to 3.3 V 10 W fly-back converter operating at 100 kHz. Experimental results demonstrate this mixed structure is a suitable solution for digital power supplies.
Enhanced expression of transforming growth factor‐β and its type‐I and type‐II receptors in human glioblastoma (1995)

Abstract Immunohistochemical studies of transforming growth factor‐p (TGF‐P) and its receptors have been carried out on 16 glioma tissues and compared with 5 cases of gliosis. Significantly higher expressions of TGF‐βI, as well as type‐I and type‐II TGF‐β receptors (TβR‐I and TβR‐II, respectively), were observed in advanced‐malignant‐glioma tissues when compared with non‐tumorous gliosis. Immunoreactivities of TGF‐β and TβR‐I were localized in the cytoplasm of spindle‐shaped tumor cells surrounding proliferating vessels or around areas of necrosis. The advancing edge of the tumor clusters frequently stained positive. Similar expression patterns were found for TGF‐β2 and TGF‐β3, whereas only weak or no expression was found for endoglin. In low‐grade astrocytomas and in gliosis cases, the expression was moderate for TβR‐I and weak for TGF‐β and TβR‐II. In 3 examined human malignant glioma cell lines, clear immunostainings were detected for TGF‐β and its receptors. Ligand‐induced heteromeric complexes of the receptors were formed in these cell lines, but the amount of the receptors was less than that of mink lung epithelial cells, which are sensitive target cells for TGF‐β. TGF‐β I showed no growth‐inhibitory activity on any of these glioma cell lines. These results suggest that malignant gliomas produce TGF‐β and receptors, but are refractory to TGF‐β, implying dysregulation in the signalling pathway in the tumor cells. It is possible that the released TGF‐β acts on neighboring cells and affects stromal growth, angiogenesis, metastasis or immune surveillance in human glioma. © 1995 Wiley‐Liss, Inc.
Atomic Oxygen and Hydroxyl Radical Generation in Round Helium-Based Atmospheric-Pressure Plasma Jets by Various Electrode Arrangements and Its Application in Sterilizing Streptococcus mutans (2014)

The reactive chemical species generated in an atmospheric-pressure plasma jet (APPJ), such as hydroxyl radical and atomic oxygen, are generally regarded as the major sources for several biomedical applications. In this paper, we propose an APPJ with a 25-kHz high-voltage powered stainless steel tube fixed inside a quartz tube and an aluminum grounded electrode that is wrapped around the quartz tube. The results show that the radical intensities of atomic oxygen and hydroxyl radical, gas temperature, and power absorption increase with increasing distance of discharge gap distance under the same applied voltage. Increasing the width of grounded electrode increases gas temperature and causes higher power absorption but only slight change of radical generation. We have applied the APPJ with the conditions of highest radical generation (grounded electrode width $=$ discharge gap distance $= 15$ mm) for effectively sterilizing Streptococcus mutans within 15 s, which shows a highly potential application for root canal disinfection.
Pontin is essential for murine hematopoietic stem cell survival (2012)

Pontin is a highly conserved DNA helicase/ATPase which is a component of several macromolecular complexes with functions that include DNA repair, telomere maintenance and tumor suppression. While Pontin is known to be essential in yeast, fruit flies and frogs, its physiological role in mammalian organisms remains to be determined. We here find that Pontin is highly expressed in embryonic stem cells and hematopoietic tissues. Through germline inactivation of Ruvbl1, the gene encoding Pontin, we found it to be essential for early embryogenesis, as Ruvbl1 null embryos could not be recovered beyond the blastocyst stage where proliferation of the pluripotent inner cell mass was impaired. Conditional ablation of Ruvbl1 in hematopoietic tissues led to bone marrow failure. Competitive repopulation experiments showed that this included the loss of hematopoietic stem cells through apopotosis. Pontin is, therefore, essential for the function of both embryonic pluripotent cells and adult hematopoietic stem cells.