gebhart/patrepeval huggingface dataset:
Gene expression analysis in biomarker research and early drug development using function tested reverse transcription quantitative real-time PCR assays (2012)

The identification of new biomarkers is essential in the implementation of personalized health care strategies that offer new therapeutic approaches with optimized and individualized treatment. In support of hypothesis generation and testing in the course of our biomarker research an online portal and respective function-tested reverse transcription quantitative real-time PCR assays (RT-qPCR) facilitated the selection of relevant biomarker genes. We have established workflows applicable for convenient high throughput gene expression analysis in biomarker research with cell lines (in vitro studies) and xenograft mouse models (in vivo studies) as well as formalin-fixed paraffin-embedded tissue (FFPET) sections from various human research and clinical tumor samples. Out of 92 putative biomarker candidate genes selected in silico, 35 were shown to exhibit differential expression in various tumor cell lines. These were further analysed by in vivo xenograft mouse models, which identified 13 candidate genes including potential response prediction biomarkers and a potential pharmacodynamic biomarker. Six of these candidate genes were selected for further evaluation in FFPET samples, where optimized RNA isolation, reverse transcription and qPCR assays provided reliable determination of relative expression levels as precondition for differential gene expression analysis of FFPET samples derived from projected clinical studies. Thus, we successfully applied function tested RT-qPCR assays in our biomarker research for hypothesis generation with in vitro and in vivo models as well as for hypothesis testing with human FFPET samples. Hence, appropriate function-tested RT-qPCR assays are available in biomarker research accompanying the different stages of drug development, starting from target identification up to early clinical development. The workflow presented here supports the identification and validation of new biomarkers and may lead to advances in efforts to achieve the goal of personalized health care.
Automated and Autonomous Driving: Regulation under Uncertainty (2015)

Many cars sold today are already capable of some level of automated operation, and prototype cars capable of driving autonomously have been - and continue to be - tested on public roads in Europe, Japan and the United States. These technologies have arrived rapidly on the market and their future deployment is expected to accelerate. Autonomous driving promises many benefits: improved safety, reduced congestion and lower stress for car occupants, among others. Authorities will have to adapt existing rules and create new ones in order to ensure the full compatibility of these vehicles with the public’s expectations regarding safety, legal responsibility and privacy. This report explores the strategic issues that will have to be considered by authorities as more fully automated and ultimately autonomous vehicles arrive on our streets and roads.
Non-standard biological activities of lipopolysaccharide from Helicobacter pylori (2001)

As assessed by the lipopolysaccharide (LPS)-specific chromogenic Limulus amoebocyte lysate (LAL) assay, Helicobacter pylori LPS extracted by the phenol-water procedure showed full potency to coagulate LAL, as did LPS from Salmonella minnesota and Escherichia coli. However, pretreatment of H. pylori LPS with polymyxin B, which easily destroys the endotoxic activity of enterobacterial LPS/lipid A, had little effect on the LAL coagulation activity, although the same treatment of E. coli LPS markedly diminished its activity. The H. pylori LPS induced very weak production of nitric oxide (NO) or tumour necrosis factor (TNF) by murine macrophages and TNF by human peripheral whole blood in vitro in comparison with S. minnesota LPS. These findings indicate that H. pylori LPS has the unique endotoxic characteristic of retaining full LAL coagulation activity with polymyxin B resistance, despite losing its endotoxic potencies such as the ability to induce NO and TNF production.
[Identification and molecular cloning and sequence analysis of a novel coronavirus from patients with SARS by RT-PCR]. (2003)

The SARS patients in Shenzhen were infected with coronavirus and this novel coronavirus is associated with SARS. The sequence analysis indicated that the coronavirus from SARS patients in Shenzhen is the same as that identified from other areas such as Canada and Hong Kong. A specific diagnostic nested RT-PCR was developed to identify this novel coronavirus infection.
Predicting response to treatment for colorectal cancer: a review of relevant mechanisms and potential biomarkers (2015)

Neoadjuvant therapy for colorectal cancer offers potential oncological benefits but is associated with increased surgical risk. Predictive biomarkers would allow the personalization of this risk/benefit balance, with treatment stratified by likely response. Although current clinical application of predictive biomarkers is limited, a number of potential targets have been proposed. This review summarizes some of the approaches being used to develop predictive biomarkers for the personalization of colorectal cancer management.
STRUCTURE AND FUNCTION OF DIPHTHERIA TOXIN: FROM PATHOLOGY TO ENGINEERING (2002)

Among bacterial protein toxins with an intracellular target, diphtheria toxin is one of the most studied. Since the first publication of its crystal structure in 1992, tremendous progress has been made describing the molecular events involved in its toxicity. However, the precise mechanism of translocation is not fully understood yet. The diphtheria toxin contains three structural domains, each carrying a distinct biological function implicated in the intoxication of the cell. The receptor-binding domain mediates the recognition of a specific receptor on the surface of targeted cells. This binding event allows the internalization of the toxin by the cells and its routing towards acidic intracellular compartments. The translocation (or transmembrane) domain, reacting to the low pH, penetrates the membrane and assists the transport of the catalytic domain through this membrane into the cytoplasm. There, the catalytic domain transfers an ADP-ribose from cytosolic NAD to its substrate, the elongation factor 2. This activity blocks the synthesis of cellular proteins, leading to cell death. All three domains of the diphtheria toxin, isolated or combined with other proteins, are now exploited for their biological properties to design new biotechnological tools and new therapeutics.
Serum IgE and IgG reactivity to Aspergillus recombinant antigens in patients with cystic fibrosis (2019)

The use of multiple recombinant antigens may improve the diagnostic accuracy in CF complicated with ABPA or AB. Asp f1 reactivity may relate to the presence of actively growing Aspergillus spp., which might be a useful marker for guiding antifungal therapy in ABPA.
Green Technologies for Room Temperature Nucleic Acid Storage (2010)

Maintaining the long-term integrity of nucleic acids in the laboratory has traditionally required the use of freezers. However, novel nucleic acid stabilization technologies may allow for the storage of DNA and RNA at room temperature in a cost-effective, environmentally friendly manner. In this study, we evaluated two novel products for room temperature DNA storage: Biomatrica's DNA SampleMatrix technology and GenVault's GenTegra DNA technology. We compared the integrity and quality of DNA stored using these products against DNA stored in a -20 C freezer by performing downstream testing with short range PCR, long range PCR, DNA sequencing, and SNP microarrays. In addition, we tested Biomatrica's RNAstable product for its ability to preserve RNA at room temperature for use in a quantitative reverse transcription PCR assay.
Evaluation of contrast densities in the diagnosis of carotid stenosis by CT angiography. (1997)

The accuracy of CT angiography in measuring carotid stenosis depends on the luminal attenuation value. An optimum contrast density is 150 H for ionic contrast material; for nonionic contrast material, 150-200 H (at the window and level settings of 300 H and 40 H).
2A1-B05 Human-Friendly/Cooperative working support Robot -PaDY- for the Production Site : 7th Report: Quantitative Evaluation of Assembly Task Partner Robot(Cooperation between Human and Machine) (2011)

We have been developing a novel human-friendly/cooperative work support robot. This system named PaDY (in-time Parts/tools Delivery to You robot) supports worker by delivering parts and tools to worker based on statistical analysis of the worker's work in an automobile assembly line to reduce the worker's physical workload and improve work efficiency. In this paper, the quantitative evaluation of the effectiveness in this system is proposed.
Rh-Catalyzed Reductive Coupling Reaction of Aldehydes with Conjugated Dienes Promoted by Triethylborane (2009)

Rh(I) catalyzes the reductive coupling reaction of a wide variety of aldehydes with conjugated dienes in the presence of a stoichiometric amount of triethylborane to provide homoallyl alcohols in a single operation.
Comparative Assessment of Biological Activities of Mistletoes for Cosmetic Applications: Viscum Album Var. Coloratum (Kom.) Ohwi and Loranthus Tanakae Franch. & Sav. (2019)

Mistletoes, hemiparasites, contain many components with various biological activities and have been used in cosmetics industry. Loranthacease (1,000 species) and Viscaceae (550 species) have the most dominant species in mistletoes (nearly 1,600 species). It can be expected that the biological activities vary from species to species; therefore, we have tested <i>Viscum album var. coloratum (Kom.) Ohwi</i> (belonging to Santalaceae) and <i>Loranthus tanakae Franch. & Sav.</i> (belonging to Loranthacease) for a comparative study of their cosmetic properties, including antioxidant, antimelanogenic, and antiwrinkle activities. As results, the ethanol extract of <i>L. tanakae</i> had higher phenolic content and showed effective antioxidant activity and elastase inhibition. Meanwhile, the ethanol extract of <i>V. album</i> more effectively inhibited tyrosinase. Comparing with ethanol extracts, the water extracts of both mistletoes showed lower biological efficacy than the ethanol extracts or no significant effect. Thus, these results show that different extracts of mistletoe have different levels of biological activities, presumably because of the differences in their phytochemical profiles and because of the different extraction methods used.
Localization, Nonlinear σ Model and String Theory (1992)

The Anderson localization problem is studied by the renormalization group analysis of the string theory. The renormalization group functions of the Anderson localization are obtained from the scattering amplitudes of the string background fields. The higher derivative terms and the higher moments of the fields, which are relevant to the higher moments of the conductance fluctuation, are investigated in terms of the dilaton and the massive fields of the string theory. Nonperturbative effects are discussed based upon the string theory.
Transport model for shale gas well leakage through the surrounding fractured zones of a longwall mine (2020)

The environmental risks associated with casing deformation in unconventional (shale) gas wells positioned in abutment pillars of longwall mines is a concern to many in the mining and gas well industry. With the recent interest in shale exploration and the proximity to longwall mining in Southwestern Pennsylvania, the risk to mine workers could be catastrophic as fractures in surrounding strata create pathways for transport of leaked gases. Hence, this research by the National Institute for Occupational Safety and Health (NIOSH) presents an analytical model of the gas transport through fractures in a low permeable stratum. The derived equations are used to conduct parametric studies of specific transport conditions to understand the influence of stratum geology, fracture lengths, and the leaked gas properties on subsurface transport. The results indicated that the prediction that the subsurface gas flux decreases with an increase in fracture length is specifically for a non-gassy stratum. The sub-transport trend could be significantly impacted by the stratum gas generation rate within specific fracture lengths, which emphasized the importance of the stratum geology. These findings provide new insights for improved understanding of subsurface gas transport to ensure mine safety.
Position estimation of leg inertial sensors to improve accuracy of stride length estimation (2022)

Human gait analysis generally needs acceleration at the center of joints where inertial measurement units (IMU) cannot be attached. The joint acceleration estimation requires the position vectors from the IMU to the center of the joint in the sensor coordinate system. Past studies have proposed a method to estimate the position vector of the joint center from two IMUs attached to two rigid bodies, respectively. The idea is based on the equality of a joint center acceleration estimated from two IMUs. However, the estimation accuracy of the position vector depends on the calibration movement. The purpose of this study is to verify the accuracy of the position vector from a lower leg IMU to the ankle joint with calibration movements. We determined the movements as a squat movement and a unidirectional knee rotating movement and compared their accuracy. We assumed that the ankle joint keeps resting throughout the calibration movements. The result demonstrated that the accuracy was better for the unidirectional knee rotation movement and dependent on the quality of the calibration movement.
Chemistry of Amino Acids and Proteins (1941)

The Hippo pathway was initially discovered in Drosophila melanogaster as a key regulator of tissue growth. It is an evolutionarily conserved signaling cascade regulating numerous biological processes, including cell growth and fate decision, organ size ...Read More
Long-Term Clinical Results of 2 Different Ablation Strategies in Patients With Paroxysmal and Persistent Atrial Fibrillation (2008)

A long-term follow-up of AF ablation shows that short-term results cannot be considered permanent because AF recurrences are still present after the first year especially in patients who have had "PVI" strategy. PVI isolation plus LL is superior to the PVI strategy in maintaining SR without antiarrhythmic drugs after procedures 1 and 2 both in paroxysmal and persistent AF.
Supplementary Table S1 from Manipulation of Cell-Type Selective Antibody Internalization by a Guide-Effector Bispecific Design (2023)

&lt;p&gt;Summary of antigen density and EphA2/ALCAM ratio in various tumor cell lines studied.&lt;/p&gt;
Physical Audio Digital Filters (2017)

We propose an approach to insert physical objects in audio digital signal processing chains, filtering the sound with the acoustic impulse response of any solid measured in real-time. We model physical objects as a linear time-invariant system, which is used as an audio filter. By interacting with the object or with the measuring hardware we can dynamically modify the characteristics of the filter. The impulse response is obtained correlating a noise signal injected in the object through an acoustic actuator with the signal received from an acoustic sensor placed on the object. We also present an efficient multichannel implementation of the system, which enables further creative applications beyond audio filtering, including tangible signal patching and sound spatialization.
N-terminus conservation in the anchor polypeptide of a prokaryotic and eukaryotic alga. [Nostoc; Porphydium cruentum] (1987)

Energy flow between the extrinsic phycobilisomes and the photosystems within thylakoids, is probably mediated by a blue anchor polypeptide. Polypeptides in the 94 kD range, purified by LiDS-PAGE from phycobilisomes of Nostoc and Porphyrdium cruentum, crossreacted with anti-Nostoc-94 (although weakly with the latter). Though rich in ASP and GLU, the polypeptides were very hydrophobic, and low in MET, CYS, and HIS. Partial sequence of the N-terminus shows considerable homology 1 - 5 - 10 - 15 - 20 N: (S)-V-K-A-S-G-G-S-S-V-A-(R)-P-Q-L-Y-Q-(G)-L-(A)-V- P: V-()-K-A-S-G-G-S-P-V-V-K-P-Q-L-Y-(K)-()-A-(S)- between the species. There is a lack of homology when compared with ..cap alpha.. and ..beta.. polypeptides of allophycocyanin with rod linkers of phycobilisomes and other phycobiliproteins. Polypeptides of 94 and 92 kD from thylakoids of Nostoc, also immunoreactive with anti-94, were blocked at the N-terminus.
Lipopolysaccharide-binding proteins of Limulus amebocyte lysate (1993)

Limulus amebocyte lysate, obtained from horseshoe crab (Limulus polyphemus) blood cells, contains a coagulation system which is activated by bacterial lipopolysaccharide (LPS). A chromatographic fraction of Limulus lysate, containing the endotoxin-sensitive factor(s) which initiates the coagulation cascade, was studied. We utilized a photoreactive, cleavable, radiolabeled derivative of Salmonella minnesota LPS, LPS-(p-azidosalicylamido)-1,3'-dithiopropionamide (LPS-ASD), to identify LPS-binding proteins. The lysate fraction was incubated with LPS-ASD, and LPS-binding proteins were identified by autoradiography of sodium dodecyl sulfate-polyacrylamide gels. An 82-kDa protein, a major protein component of this fraction from Limulus lysate, was identified as a LPS-binding protein in a majority of lysates. Incubation of whole Limulus lysate with antiserum to this protein resulted in enhanced sensitivity of the lysate to LPS, suggesting that this 82-kDa protein is a negative regulator of coagulation. A minor 50-kDa protein component of lysate also was identified as a LPS-binding protein and is a candidate for the LPS-sensitive coagulation protein in L. polyphemus.
Orange-red emitting praseodymium doped yttrium-molybdate nanophosphors for multifunctional applications (2021)

Orange-red emitting praseodymium (Pr3+) activated yttrium molybdenum oxide (Y2MoO6) nanophosphors (NPs) were synthesized via low-temperature solution combustion method using Aloe vera gel as a surfactant and fuel. The synthesized NPs were subjected to structural, morphological, optical, and electrical studies. The powder X-ray diffraction (PXRD) study reveals that the Y2MoO6 composite consists of a monoclinic crystal phase. Peak shift to the left side was observed with increase in the doping concentration of Pr3+ ions into the crystal system, which is attributed to the strain. Foamy type morphology was revealed from scanning electron microscope studies, whereas the nanostructural features of the samples were confirmed by both transmission electron microscope and PXRD. From the diffused reflectance spectroscopy study, the optical band gap was estimated to be in the range of 3.36–3.48 eV. Fourier transforms infrared spectroscopy was used to identify the metal oxygen bonds along with the other types of bonds if any. The AC conductivity and dielectric properties were measured in the frequency range of 100 Hz–5 MHz. The photoluminescence (PL) studies revealed the characteristic of emission peaks of Pr3+ ions. The Commission International de l'Eclairage (CIE) coordinates were located in orange-red color. The average correlated color temperature analysis indicates that the Y2MoO6:Pr3+ NPs can be useful for use in warm light sources. The Y2MoO6: Pr3+ (5 mol%) NPs were used for the design of anti-counterfeiting ink in security applications. The tunable properties of the prepared Y2MoO6:Pr3+ NPs make them suitable for multifunctional applications.
Oxides Studied Through XANES and XEOL Structure and Luminescence of Rare Earth-doped Silicon (2013)

Surrey Ion Beam Centre, University of Surrey, Guildford GU2 7XH, United Kingdom Luminescent Si-based materials are of significant interest due to their potential applications in the fields of photonics and solid state lighting. The use of rare earth dopants incorporated into Si-based materials allows the attainment of specific wavelengths of emission for color tunability. Details of the RE luminescence and even the ability to obtain luminescence are strongly dependent on the composition and structure of the Si-based host material. Through the use of X-ray absorption spectroscopy details of the atomic bonding environment of the films has been obtained. X-ray excited optical luminescence, measured after excitation at the absorption edges of the constituent atoms within these materials, reveals that excitation of the rare earth ions occurs primarily at energies related to oxygen states.
L-Type Calcium Channel Blockers Exert an Antiinflammatory Effect by Suppressing Expression of Plasminogen Receptors on Macrophages (2009)

L-type Ca(2+) channel (LTCC) blockers, represented by amlodipine and verapamil, are widely used antihypertensive drugs that also have antiinflammatory activities. Plasminogen (Plg) is an important mediator of macrophage recruitment, and this role depends on its interaction with Plg receptors (Plg-Rs). Plg-Rs include histone 2B, alpha-enolase, annexin 2, and p11, all proteins which lack signal sequences for cell surface export. When human or murine monocytoid cells were induced to differentiate into macrophages, their Plg binding and Plg-R expression increased by 4-fold. These changes were suppressed by pretreatment with verapamil and amlodipine. Expression of the Ca(v)1.2 LTCC pore subunit was induced in differentiated macrophages, and siRNA against this subunit suppressed the upregulation of Plg binding and Plg-Rs. In vivo, amlodipine and verapamil suppressed peritoneal macrophage recruitment in response to thioglycollate by >60% at doses that did not affect blood pressure. In drug-treated animals, macrophages migrated into but not through the peritoneal membrane tissue and showed reduced surface expression of Plg-Rs. These findings demonstrate that Plg-R expression on macrophages is dependent on Ca(v)1.2 LTCC subunit expression. Suppression of Plg-Rs may contribute to the antiinflammatory effects of the widely used LTCC blockers.
In Vitro Selection of State-Specific Peptide Modulators of G Protein Signaling Using mRNA Display (2004)

The G protein regulatory (GPR) motif is a approximately 20-residue conserved domain that acts as a guanine dissociation inhibitor (GDI) for G(i/o)(alpha) subunits. Here, we describe the isolation of peptides derived from a GPR consensus sequence using mRNA display selection libraries. Biotinylated G(i)(alpha)(1), modified at either the N or C terminus, serves as a high-affinity binding target for mRNA-displayed GPR peptides. In vitro selection using mRNA display libraries based on the C terminus of the GPR motif revealed novel peptide sequences with conserved residues. Surprisingly, selected peptides contain mutations to a highly conserved Arg in the GPR motif, previously shown to be crucial for binding and inhibition activities. The dominant peptide from the selection, R6A, and a minimal 9-mer peptide, R6A-1, do not contain Arg residues yet retain high affinity (K(D) = 60 and 200 nM, respectively) and specificity for the GDP-bound state of G(i)(alpha)(1), as measured by surface plasmon resonance. The selected peptides also maintain GDI activity for G(i)(alpha)(1), inhibiting both the exchange of GDP in GTPgammaS binding assays and the AlF(4)(-)-stimulated enhancement of intrinsic tryptophan fluorescence. The kinetics of GDI activity, however, are different for the selected peptides and demonstrate biphasic kinetics, suggesting a complex mechanism for inhibition. Like the GPR motif, the R6A and R6A-1 peptides compete with G(betagamma) subunits for binding to G(i)(alpha)(1), suggesting their use as activators of G(betagamma) signaling.
二阶流体通过径向延伸平面时滑移、黏性耗散、焦耳热对MHD流动的影响 (2010)

研究了二阶导电的非Newton流体，在一个可径向放射状延伸，并伴有部分滑动表面上的流动及其热交换．部分滑移用一个无量纲的滑移因子控制，其取值范围从0（全黏着）到无穷大（全滑移）．使用适当的相似变换，把待求的非线性偏微分方程转化为常微分方程．讨论了边界条件的不足，在无需增加任何边界条件下，使用有效的数值格式，求解所得到的微分方程．部分滑移、磁场交互参数以及二阶流体的参数对速度场和温度场的综合分析发现，滑移量的增加，流体的动力边界层和热边界层增厚．因为当滑移量的增加，允许更多的流体通过该平面，表面摩擦因数的数值下降，并在更高的滑移参数下，摩擦因数趋于0，即流体无黏性地通过．还研究了磁场对速度场和温度场的重要影响．