gebhart/patrepeval huggingface dataset:
The Zinc Finger Domain of the Archaeal Minichromosome Maintenance Protein Is Required for Helicase Activity (2001)

The minichromosome maintenance (MCM) proteins, a family of six conserved polypeptides found in all eukaryotes, are essential for DNA replication. The archaeon Methanobacterium thermoautotrophicum Delta H contains a single homologue of MCM with biochemical properties similar to those of the eukaryotic enzyme. The amino acid sequence of the archaeal protein contains a putative zinc-binding domain of the CX(2)CX(n)CX(2)C (C(4)) type. In this study, the roles of the zinc finger domain in MCM function were examined using recombinant wild-type and mutant proteins expressed and purified from Escherichia coli. The protein with a mutation in the zinc motif forms a dodecameric complex similar to the wild-type enzyme. The mutant enzyme, however, is impaired in DNA-dependent ATPase activity and single-stranded DNA binding, and it does not possess helicase activity. These results illustrate the importance of the zinc-binding domain for archaeal MCM function and suggest a role for zinc binding in the eukaryotic MCM complex as well, since four out of the six eukaryotic MCM proteins contain a similar zinc-binding motif.
Drug Delivery Strategies for Combating Multiple Drug Resistance (2013)

Abstract Although cancer research has been steady for the past 40 years, only modest gains have been observed in reducing cancer mortality rates, most significantly from prevention campaigns and less from drug therapy. This chapter outlines major mechanisms of drug resistance in tumors, emphasizing the contribution of each mechanism to the whole classification called multiple drug resistance (MDR), which is the simultaneous resistance to a wide range of drugs unrelated in structure or mechanism of action. For patients who demonstrate MDR markers, clinical outcomes tend to be poor. The chapter then samples innovative strategies to circumvent or overcome these resistance mechanisms, including the use of nanoparticles and new treatments that overcome drug delivery barriers.
Quantitative imaging of cancer in the postgenomic era: Radio(geno)mics, deep learning, and habitats (2018)

Although cancer often is referred to as "a disease of the genes," it is indisputable that the (epi)genetic properties of individual cancer cells are highly variable, even within the same tumor. Hence, preexisting resistant clones will emerge and proliferate after therapeutic selection that targets sensitive clones. Herein, the authors propose that quantitative image analytics, known as "radiomics," can be used to quantify and characterize this heterogeneity. Virtually every patient with cancer is imaged radiologically. Radiomics is predicated on the beliefs that these images reflect underlying pathophysiologies, and that they can be converted into mineable data for improved diagnosis, prognosis, prediction, and therapy monitoring. In the last decade, the radiomics of cancer has grown from a few laboratories to a worldwide enterprise. During this growth, radiomics has established a convention, wherein a large set of annotated image features (1-2000 features) are extracted from segmented regions of interest and used to build classifier models to separate individual patients into their appropriate class (eg, indolent vs aggressive disease). An extension of this conventional radiomics is the application of "deep learning," wherein convolutional neural networks can be used to detect the most informative regions and features without human intervention. A further extension of radiomics involves automatically segmenting informative subregions ("habitats") within tumors, which can be linked to underlying tumor pathophysiology. The goal of the radiomics enterprise is to provide informed decision support for the practice of precision oncology.
Imidazolium- and Pyrrolidinium-Based Ionic Liquids as Cocatalysts for CO2 Electroreduction in Model Molecular Electrocatalysis (2020)

The structure effect on the role of different ionic liquids (ILs) as a simultaneous supporting electrolyte and cocatalyst for CO2 electroreduction in the presence of a model molecular catalyst [Re(bpy)(CO)3Cl] has not been addressed yet. In particular, we varied the nature of the cation, anion, and cation alkyl chain by a choice of five different ILs, including imidazolium and pyrrolidinium cations, and we compared their results to benchmark the supporting electrolyte. We report an overpotential diminution of 0.33 V for CO2 to CO conversion in the presence of ILs under CO2 catalytic conditions. We prove the IL cation-dependent overpotential diminution due to the electrostatic stabilization of the negatively charged active form of the catalyst, with the π–π stacking interaction provided by imidazolium cations responsible for their outstanding performance. Finally, a mechanistic explanation is provided to justify a weaker IL cocatalytic effect when CO2 electroreduction takes place in the presence of a proton source.
Bone Marrow‐Derived Mesenchymal Stromal Cells Enhanced by Platelet‐Rich Plasma Maintain Adhesion to Scaffolds in Arthroscopic Simulation (2017)

Improved healing after tendon repair can lead to better clinical outcomes. BMSCs are attractive for enhancing healing given their accessibility and regenerative potential. Application of bMSCs using scaffolds as cell carriers relies on arthroscopic feasibility.
Correlated expression of adhesive properties for both white and red blood cells during inflammation (2000)

The state of leukocyte and erythrocyte adhesiveness/aggregation was determined in the peripheral blood of 382 patients with infection/inflammation as well as in 72 controls by using a simple slide test and image analysis. A highly significant correlation (r = 0.4, n = 455, p < 0.001) was found between the state of leukocyte and erythrocyte adhesiveness/aggregation. The extent of both leukocyte and erythrocyte aggregation correlated with the concentration of fibrinogen. Significant aggregation of leukocytes with erythrocytes was noted as well. We conclude that both leukocyte and erythrocyte aggregation occur in the peripheral blood of patients with infection/inflammation. Such cell aggregation, which might have detrimental rheological consequences, can be detected by using our novel technique.
Supplementary Figures 1-3 from Proteolytic Activation of Pro-Macrophage-Stimulating Protein by Hepsin (2023)

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The administration route is decisive for the ability of the vaccine adjuvant CAF09 to induce antigen-specific CD8 + T-cell responses: The immunological consequences of the biodistribution profile (2016)

cell responses: The immunological consequences of the biodistribution profile
Comparison of phenotypic expression with genotypic transformation by using cloned, selectable markers. (1982)

The frequency of phenotypic expression of the herpes simplex virus type 1 tk and Escherichia coli gpt genes was compared with the frequency of genotypic transformation after calcium phosphate-mediated DNA transfection of a number of tk- and hprt- cell lines. In three of the five lines tested, the frequency of phenotypic expression was at most 10-fold higher than that of genotypic transformation as indicated by frequency of HAT resistance. The remaining two lines showed phenotypic responses which were 50- to 100-fold greater than the genotypic responses. The data indicate that the efficiency of DNA-mediated transformation with some cell lines can be limited by events after the uptake and expression of transfected DNA.
Photochemical Regulation of Restriction Endonuclease Activity (2009)

Removal by the light: The photochemical regulation of restriction endonucleases, which are important enzymes in molecular biology, has been investigated. Photolabile protecting groups have been installed on DNA substrates and have been demonstrated to inhibit restriction endonuclease activity until removed by UV light irradiation. Interestingly, these groups do not appear to dramatically affect initial binding of the enzyme to the DNA substrate, but rather prevent recognition of the specific cleavage site.
Renal Effects of an Angiotensin II Antagonist in Stroke-Prone Spontaneously Hypertensive Rat (1997)

We evaluated the renal effects of the new angiotensin II type 1 (AT ) receptor antagonist, HR 720, in the stroke-prone spontaneously hypertensive rat. Rats were treated with either vehicle, HR 720, MK-954 (a selective AT1 receptor antagonist) or enalapril for 6 weeks. Blood pressure was decreased to a similar extent by HR 720, MK-954 and enalapril (203 +/- 4, 202 +/- 5 and 190 +/- 4 vs. 247 +/- 4 mm Hg for control). Urinary protein secretion was also decreased (5.2 +/- 0.3, 5.3 +/- 0.2 and 5.5 +/- 0.6 vs. 25.2 +/- 4.6 mg/100g/24h). The glomerular hypertensive change was improved in each drug-treated group (2.0 +/- 0.2, 3.3 +/- 0.3 and 1.6 +/- 0.1 vs. 17.6 +/- 1.5%; p < 0.0001). These results show that, in addition to its antihypertensive effect, HR 720 has a beneficial effect on renal function.
Delivery and efficacy of synthetic oligonucleotide vectors to an ARDS model by vibrating mesh nebulisation (2020)

Acute respiratory distress syndrome (ARDS) continues to have a high mortality with no effective specific therapy. Anti-inflammatory and anti-oxidant therapeutic proteins have previously shown promise in in vivo ARDS models. Similarly, targeting cell permeability (‘leakiness’) associated with ARDS has shown potential. A synthetic mRNA vector for rapid production of protein, coupled with direct delivery to the injured lung via nebulisation, could overcome these limitations. mRNA complexed with a novel transfection reagent (Factor Bioscience Ltd.) encoding green fluorescent protein (GFP), anti-inflammatory and anti-oxidant therapeutic proteins was administered to aseptic or septic rat lungs through a vibrating mesh nebuliser (Aerogen), via the flexiVent (SCIREQ). Animals were harvested and physiological and histological parameters were assessed. An in vitro model of cell permeability employing Calu-3 epithelial cells was also examined using TIE2 and ANGPT1 mRNA targets. A system incorporating Ussing chambers facilitating the measurement of specific ionic transport mechanisms, and by extension fluid dynamics across cell monolayers, was enrolled. GFP mRNA expressed rapidly in lung epithelial cells (&lt; 4hrs) and expression can be detected up to 14 days post administration in rat lungs. Transfection efficacy was not reduced by nebulisation. Anti-inflammatory and anti-oxidant mRNA demonstrated therapeutic effects in septic rat lungs. In summary, synthetic mRNA can be delivered to rat lung, expressing transgenes rapidly and efficiently using a novel transfection reagent. Further studies will continue to investigate efficacy of the therapeutic molecules in vitro and in vivo.
A profit-based unit commitment GA for the competitive environment (2000)

As the electrical industry restructures, many of the traditional algorithms for controlling generating units need modification or replacement, previously utilized to schedule generation units in a manner that minimizes costs while meeting all demand, the unit commitment (UC) algorithm must be updated. A UC algorithm that maximizes profit will play an essential role in developing successful bidding strategies for the competitive generator. Simply bidding to win contracts is insufficient; bidding strategies must result in contracts that, on average, cover the total generation costs. No longer guaranteed to be the only electricity supplier, a generation company's share of the demand will be more difficult to predict than in the past. Removing the obligation to serve softens the demand constraint. In this paper the authors provide a price/profit-based UC formulation which considers the softer demand constraint and allocates fixed and transitional costs to the scheduled hours. The authors describe a genetic algorithm solution to this new UC problem and present results for an illustrative example.
Differences in the commonly used genotype imputation algorithms and their imputation accuracy estimates (2018)

Genotype imputation is a computational method where probable genotypes are inferred to a lower-density dataset (target) based on a higher-density reference panel and it is considered to be a cost-effective approach to prepare data for various purposes, including genome-wide association studies (GWAS). In order for the final outcomes of any downstream analysis to be trustworthy, it is important to choose the most optimal method available for the imputation step. The main focus of this study is to compare and evaluate different available genotype imputation algorithms and their overall performance together with their respective quality metrics using the data obtained through SISu and FinMetSeq projects. Of special interest is the accuracy of low-frequency and rare variants.
Distributed multi-layered workload synthesis for testing stream processing systems (2008)

Testing and benchmarking of stream processing systems requires workload representative of real world scenarios with myriad of users, interacting through different applications over different modalities with different underlying protocols. The workload should have realistic volumetric and contextual statistics at different levels: user level, application level, packet level etc. Further realistic workload is inherently distributed in nature. We present a scalable framework for synthesis of distributed workload based on identifying different layers of workload corresponding to different time-scales. The architecture is extensible and modular, promotes reuse of libraries at different layers and offers the flexibility to add additional plug-ins at different layers without sacrificing the efficiency.
DIRECT NUMERICAL SIMULATION OF TURBULENT CONCENTRIC ANNULAR PIPE FLOW (2001)

A direct numerical simulation is performed for a turbulent concentric annular pipe flow at ReDh = 8900 for two radius ratios (R1/R2 =0.1 and 0.5). The main emphasis is placed on the transverse curvature effect on near-wall turbulent structures. Near-wall turbulent structures close to the inner and outer walls are scrutinized by computing various turbulent statistics.
Rare, convergent antibodies targeting the stem helix broadly neutralize diverse betacoronaviruses (2023)

(Cell Host & Microbe 31, 97–111.e1–e12; January 11, 2023) In Figure 6A, the authors discovered after publication that the neutralization NT50 values of two similar IGHV1-46/IGKV3-20 mAbs (COV30-14 and COV72-37) for several SARS-CoV-2 variants were switched due to a copying error. This correction does not impact the conclusions of the original paper. The affected NT50 values of the two mAbs only differed <2 fold. The authors regret the inconvenience caused by this error, which has been corrected in the original article online. Rare, convergent antibodies targeting the stem helix broadly neutralize diverse betacoronavirusesDacon et al.Cell Host & MicrobeNovember 7, 2022In BriefThe characteristics of antibodies that broadly neutralize coronaviruses are poorly understood. Here, Dacon et al. identify a class of stem helix-specific monoclonal antibodies from COVID-19 convalescent donors that neutralize diverse betacoronaviruses, use an IGHV1-46/IGKV3-20 gene signature, and bind in a conserved manner to the spike protein. Full-Text PDF Open Access
VR-SMART: A Virtual Reality System for Smart Home Environments (2011)

Virtual reality (VR) technologies and systems have the potential to play a key role in assisting disabled inhabitants of smart home environments with instrumental activities of daily living (IADLs). While immersive environments have useful applications in the fields of gaming, simulation, and manufacturing, their capabilities have been largely untapped in smart home environments. We have developed an integrated CAD and virtual reality system which assists a smart home resident in locating and navigating to objects in the home. Using the methods presented in this paper, a room modeled in a CAD system is imported into a virtual environment, which is linked to an audio query-response interface. The user’s head and room objects are fitted with the sensors which are part of a six DOF motion tracking system. Methods have been created to allow the inhabitant to move objects around in the room and then later issue an audio query for the location of the object. The system generates an audio response with the object’s position relative to the person’s current position and orientation. As he approaches the object, information is derived from the virtual models of both the room and the objects within the room to provide better guidance. The ability of the VR-SMART system to guide a resident to an object was tested by mounting a head mounted display (HMD) on a user located in a room. This allowed the user to navigate through the virtual world that simulated the room he occupied, thereby providing a way to test the positional accuracy of the virtual system. Results of the testing in the immersive environment showed that although the overall system shows promise at a 30% success rate, the success of the system depends on the accuracy and calibration of the tracking system. In order to improve the success of the system, we explored the precision of a second motion capture system, with more accurate results. Results confirmed that the VR-SMART system could significantly improve the assistance of disabled people in finding objects easily in the room when implemented only as an assistive system without the head-mounted display.
Tribological Profile of Binderless Niobium Carbide (2013)

This chapter contains sections titled: Introduction Experimental Procedure Tribological Results Conclusions
ChemInform Abstract: α‐Olefins as Alkenylmetal Equivalents in Catalytic Conjugate Addition Reactions. (2008)

Abstract ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 200 leading journals. To access a ChemInform Abstract of an article which was published elsewhere, please select a “Full Text” option. The original article is trackable via the “References” option.
Hydrophone Spatial Averaging Correction for High-Frequency Arrays (2022)

A hydrophone spatial averaging correction algorithm, previously validated in the 5–8 MHz range [1, 2], was tested at higher frequencies using two high-frequency linear arrays: L12-5 (9 MHz; F/1.6) and L22-14 (15 MHz; F/3). Seven hydrophones (with capsule, needle, and membrane designs and sensitive element diameters ( <tex xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">$d_{g}$</tex> ) ranging from 85 to 1000 µm) were used, one at a time, to measure the beams at the focal point. Spatial averaging errors were characterized by percent change in parameter (peak compressional pressure <tex xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">$p_{c}$</tex> , peak rarefactional pressure <tex xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">$P_{r}$</tex> , pulse intensity integral pii, and spatial-peak temporal average intensity Ispta) measurement for every 100 µm of hydrophone sensitive element diameter. The spatial averaging correction algorithm reduced errors in measurements of <tex xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">$p_{c}$</tex> from 11%±2 % to 3 %±2 % per 100 µm, measurements of <tex xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">$P_{r}$</tex> from 7%±1% to 0%±4% per 100 µm and measurements of intensities from 12%±1% to 0%±2% per 100 µm. The spatial averaging correction was effective up to at least 15 MHz and resulted in significant reduction in errors of measurements for acoustic pressures and intensities from clinical high-frequency linear arrays.
A Visualizable Chain‐Terminating Inhibitor of Glycosaminoglycan Biosynthesis in Developing Zebrafish (2014)

Abstract Heparan sulfate (HS) and chondroitin sulfate (CS) glycosaminoglycans (GAG) are proteoglycan‐associated polysaccharides with essential functions in animals. They have been studied extensively by genetic manipulation of biosynthetic enzymes, but chemical tools for probing GAG function are limited. HS and CS possess a conserved xylose residue that links the polysaccharide chain to a protein backbone. Here we report that, in zebrafish embryos, the peptide‐proximal xylose residue can be metabolically replaced with a chain‐terminating 4‐azido‐4‐deoxyxylose (4‐XylAz) residue by administration of UDP‐4‐azido‐4‐deoxyxylose (UDP‐4‐XylAz). UDP‐4‐XylAz disrupted both HS and CS biosynthesis and caused developmental abnormalities reminiscent of GAG biosynthesis and laminin mutants. The azide substituent of protein‐bound 4‐XylAz allowed for rapid visualization of the organismal sites of chain termination in vivo through bioorthogonal reaction with fluorescent cyclooctyne probes. UDP‐4‐XylAz therefore complements genetic tools for studies of GAG function in zebrafish embryogenesis.
Stability of airborne microbes in the Louvre Museum over time (2013)

The microbial content of air has as yet been little described, despite its public health implications, and there remains a lack of environmental microbial data on airborne microflora in enclosed spaces. In this context, the aim of this study was to characterize the diversity and dynamics of airborne microorganisms in the Louvre Museum using high-throughput molecular tools and to underline the microbial signature of indoor air in this human-occupied environment. This microbial community was monitored for 6 month during occupied time. The quantitative results revealed variations in the concentrations of less than one logarithm, with average values of 10(3) and 10(4) Escherichia coli/Aspergillus fumigatus genome equivalent per m(3) for bacteria and fungi, respectively. Our observations highlight the stability of the indoor airborne bacterial diversity over time, while the corresponding eukaryote community was less stable. Bacterial diversity characterized by pyrosequencing 454 showed high diversity dominated by the Proteobacteria which represented 51.1%, 46.9%, and 38.4% of sequences, for each of the three air samples sequenced. A common bacterial diversity was underlined, corresponding to 58.4% of the sequences. The core species were belonging mostly to the Proteobacteria and Actinobacteria, and to the genus Paracoccus spp., Acinetobacter sp., Pseudomonas sp., Enhydrobacter sp., Sphingomonas sp., Staphylococcus sp., and Streptococcus sp.
Instrumented Laparoscopic Spinal Fusion (1995)

Although this procedure is associated with a long learning curve, the technique, once mastered, is effective and advantageous over current approaches to lumbar fusion. Operative time and hospital stay are expected to decrease with future instrumentation development and surgeon experience.
STED Analysis of Droplet Deformation during Emulsion Electrospinning (2017)

The shape and size distribution of polystyrene (PS) compartments formed during emulsion electrospinning in a poly(vinyl alcohol) fiber is investigated. Stimulated emission depletion microscopy is employed to image the compartments with subdiffraction (super) resolution. The size distribution of the emulsion droplets in the spinning solution emulsions is found to be the key factor for fiber and compartment morphology. By varying the emulsification method, it is demonstrated that fibers spun from miniemulsions are characterized by a homogeneous distribution of PS compartments with no indication for coalescence or breakup of PS droplets. Coarse emulsions are prone to develop fiber instabilities associated with large PS domains. The domains are irregularly distributed in the fiber. Above a critical size of domains, breakup of these domains in two daughter domains is observed. The size dependence of the emulsion droplet breakup is explained by fluid dynamics.