gebhart/patrepeval huggingface dataset:
The effect of interactions between a bacterial strain isolated from drinking water and a pathogen surrogate on biofilms formation diverged under static vs flow conditions (2017)

This study highlights the complexity of species interactions on biofilm formation and suggests that environmental conditions such as the flow regime can be taken into consideration for the management of microbial contamination in drinking water systems.
OS0907-170 Fatigue Crack Propagation Analysis of Cladded Plates by eXtended finite element method (2015)

In order to evaluate fatigue crack propagation behavior at J-welding portions of Bottom Mounted Instrumentation (BMI) in Reactor Pressure Vessel (RPV), crack propagation crossing dissimilar material interface between base metal and clad should be investigated. This paper shows crack propagation analyses of cladded plates under cyclic tension load by XFEM, which can model crack independently of finite elements, as a preliminary study for crack propagation analyses considering cladding interface.
Aggressiveness of human melanoma xenograft models is promoted by aneuploidy-driven gene expression deregulation (2012)

Melanoma is a devastating skin cancer characterized by distinct biological subtypes. Besides frequent mutations in growth- and survival-promoting genes like BRAF and NRAS, melanomas additionally harbor complex non-random genomic alterations. Using an integrative approach, we have analysed genomic and gene expression changes in human melanoma cell lines (N=32) derived from primary tumors and various metastatic sites and investigated the relation to local growth aggressiveness as xenografts in immuno-compromised mice (N=22). Although the vast majority >90% of melanoma models harbored mutations in either BRAF or NRAS, significant differences in subcutaneous growth aggressiveness became obvious. Unsupervised clustering revealed that genomic alterations rather than gene expression data reflected this aggressive phenotype, while no association with histology, stage or metastatic site of the original melanoma was found. Genomic clustering allowed separation of melanoma models into two subgroups with differing local growth aggressiveness in vivo. Regarding genes expressed at significantly altered levels between these subgroups, a surprising correlation with the respective gene doses (>85% accordance) was found. Genes deregulated at the DNA and mRNA level included well-known cancer genes partly already linked to melanoma (RAS genes, PTEN, AURKA, MAPK inhibitors Sprouty/Spred), but also novel candidates like SIPA1 (a Rap1GAP). Pathway mining further supported deregulation of Rap1 signaling in the aggressive subgroup e.g. by additional repression of two Rap1GEFs. Accordingly, siRNA-mediated down-regulation of SIPA1 exerted significant effects on clonogenicity, adherence and migration in aggressive melanoma models. Together our data suggest that an aneuploidy-driven gene expression deregulation drives local aggressiveness in human melanoma.
Structure of Rhoptry Neck Protein 2 is essential for the interaction in vitro with Apical Membrane Antigen 1 in Plasmodium vivax (2019)

The results show that the PvRON2 structure, particularly the S-S bond between C2051 and C2063, is determinant for the existence of the interaction between PvAMA1 and PvRON2.
17β-Oestradiol enhances the stimulatory effect of 1,25-dihydroxyvitamin D3 on alkaline phosphatase activity in human osteosarcoma SaOS-2 cells in a differentiation-dependent manner (1996)

We tested the effect of osteoblastic differentiation on the interactive effects of 17 beta-oestradiol (E2) and 1,25-dihydroxyvitamin D3 (1,25(OH)2D3) on alkaline phosphatase activity. As cell models we utilized the more differentiated human osteosarcoma (SaOS) cells that had been cultured for 6 days in medium containing 10 nM dexamethasone (Dex) (SaOS+Dex cells) and the less differentiated cells cultured in the absence of Dex (SaOS-Dex cells). The cells were challenged with 1,25(OH)2D3 in the presence or absence of Dex for 24 h and then with E2 for an additional 24 h. In SaOS-Dex cells, alkaline phosphatase activity remained constant over the 48-h period and was not significantly affected by E2, 1,25(OH)2D3 or 1,25(OH)2D3+E2 treatment. On the other hand, in SaOS+Dex cells, 1,25(OH)2D3 and E2+1,25(OH)2D3 stimulated alkaline phosphatase activity (ANOVA, F = 154.2, P < 0.0001) with the maximal response at 48 h (P < 0.01). In SaOS+Dex cells, 1,25(OH)2D3 had dose-dependent stimulatory effects which were strongly enhanced by 10 nM E2 (ANOVA, F = 46.0, P < 0.001). Studies on dose-dependent effects of E2, in the presence or absence of 100 nM 1,25(OH)2D3, revealed that in the presence of 1,25(OH)2D3, the E2 dose-response curve was biphasic in SaOS+Dex cells (ANOVA, F = 3.40, P < 0.005), with maximum stimulation at 10 nM E2 (P < 0.01). The specificity of E2 was verified using the inactive 17 alpha-oestradiol and the oestrogen antagonist, tamoxifen. These data indicate that E2 and 1,25(OH)2D3 have positive interactive effects on alkaline phosphatase activity in human osteoblasts, and suggest that the expression of this interaction is dependent on the stage of differentiation of the cells.
Correction: Resolving the degradation pathways of the O3-type layered oxide cathode surface through the nano-scale aluminum oxide coating for high-energy density sodium-ion batteries (2018)

Correction for ‘Resolving the degradation pathways of the O3-type layered oxide cathode surface through the nano-scale aluminum oxide coating for high-energy density sodium-ion batteries’ by Jang-Yeon Hwang <italic>et al.</italic>, <italic>J. Mater. Chem. A</italic>, 2017, <bold>5</bold>, 23671–23680.
The psychopharmacogenetic–neurodevelopmental interface in serotonergic gene pathways (2002)

This chapter appraises prototypical genomic variation with impact on gene expression, and complementary studies of gene and environmental effects on brain development and synaptic plasticity in the mouse model. Special emphasis is given to molecular mechanisms of neurodevelopmental genetics. Relevant conceptual and methodological issues pertinent to the dissection of the psychopharmacogenetic-neurodevelopmental interface are also considered. Many genes that influence complex traits and psychopharmacological drug responses are likely to be distributed continuously. Such genes are referred to as quantitative trait loci. Connecting drug response with relevant functional DNA variants in the brain and with differences in gene expression in brain regions represents the ultimate goal for pharmacogenetic research. The serotonergic gene pathways is a rewarding area of investigation because of numerous and essential functions of the central serotonin (5-HT) system, the wealth of drug targets within this system, and the range of serotonergic compounds available in the clinical setting.
Improved Ruggedness for Membrane-Based Amperometric Sensors Using a Pulsed Amperometric Method (1997)

This paper introduces a new approach to the use of membrane-based amperometric sensors which is expected to improve the ruggedness of these sensors significantly relative to the steady-state method in common use. In this new method, the fixed-voltage source used with the conventional steady-state method is replaced by a pulsed-voltage source. Unlike the fixed-source approach, which yields steady-state currents corresponding to large differences between analyte concentrations inside and outside the isolating membrane, the pulsed-source approach permits measurement of currents corresponding to near-equilibrium conditions between solutions inside and outside the membrane. Because the measured currents correspond to near-equilibrium conditions, results are expected to be virtually independent of variables that affect rates of mass transport to and across the membrane. The new approach is evaluated using the "oxygen electrode" as a model system. Results obtained using the new method are compared with results obtained using the conventional steady-state option as well as a coulometric approach described recently. The reproducibility of the pulsed amperometric approach and the scatter of data about least-squares calibration lines are an order of magnitude or more better than for the conventional steady-state option. As expected, the pulsed amperometric method is 40-100-fold less dependent on changes in membrane thickness, stirring rate, and temperature than the conventional steady-state option.
Viewing angle enhancement of an integral imaging display using Bragg mismatched reconstruction of holographic optical elements (2015)

Holographic-optical-element (HOE)-based integral imaging display can be applied to augmented reality. However, a narrow viewing angle is a bottleneck for commercialization. Here, we propose a method to enhance the viewing angle of the integral imaging display using Bragg mismatched reconstruction of HOEs. The viewing angle of the integral imaging display can be enlarged with two probe waves, which form two different viewing zones. The effect of Bragg mismatched reconstruction is analyzed with simulation and experiment. In order to show feasibility of the proposed method, a display experiment is demonstrated.
Fritz Heitmann: Hunter, dentist, hardware baron, and Houston leader. (2011)

Frederick (Fritz) A. Heitmann was a Houston business and civic leader in the late 1800's and early 1900's. He succeeded his father in the family hardware business, was hugely successful, and was known for helping establish the Houston Ship Channel among other large projects. His great success obscured his earlier contribution to the frontier as a dentist in the gold fields of Colorado. His father insisted he learn a skill independent of fluctuations in the business world. He apprenticed himself to a dentist and used those abilities, along with others, to gain a large stake to build the business. Also, he had strong opinions, and liked to talk. He told his story to his grandson, and his grandson's buddy, the co-author of this article.
Learning Optical Flow, Depth, and Scene Flow Without Real-World Labels (2022)

Self-supervised monocular depth estimation enables robots to learn 3D perception from raw video streams. This scalable approach leverages projective geometry and ego-motion to learn via view synthesis, assuming the world is mostly static. Dynamic scenes, which are common in autonomous driving and human-robot interaction, violate this assumption. Therefore, they require modeling dynamic objects explicitly, for instance via estimating pixel-wise 3D motion, i.e. scene flow. However, the simultaneous self-supervised learning of depth and scene flow is ill-posed, as there are infinitely many combinations that result in the same 3D point. In this letter we propose DRAFT, a new method capable of jointly learning depth, optical flow, and scene flow by combining synthetic data with geometric self-supervision. Building upon the RAFT architecture, we learn optical flow as an intermediate task to bootstrap depth and scene flow learning via triangulation. Our algorithm also leverages temporal and geometric consistency losses across tasks to improve multi-task learning. Our DRAFT architecture simultaneously establishes a new state of the art in all three tasks in the self-supervised monocular setting on the standard KITTI benchmark.
Description of FORMAT, a text-processing program (1969)

FORMAT is a production program which facilitates the editing and printing of “finished” documents directly on the printer of a relatively small (64k) computer system. It features good performance, totally free-form input, very flexible formatting capabilities including up to eight columns per page, automatic capitalization, aids for index construction, and a minimum of nontext items. It is written entirely in FORTRAN IV.
Attachment and growth of cultured fibroblast cells on silk protein matrices (1995)

Abstract The attachment and growth of L‐929 cells on films made of Bombyx mori silk proteins—fibroin and sericin and their mixtures—was studied by a cell culture method. Both cell attachment and growth were dependent on a minimum of around 90% sericin in the mixture. The results from electron micrography as well as from the DSC measurements supported the notion that the mixture of the two proteins fibroin and sericin has a phase‐separated structure in the solid state. The observed minimum of sericin in the cell attachment and growth is thought to be a result of this phase‐separated structure. Films of pure component proteins (i.e., 100% fibroin or sericin) exhibited as high a cell attachment and growth as collagen, a widely used mammalian cell culture substrate. However, a morphological study of the attached cells revealed that the cells attached to silk fibroin were extended and had a spindle shape, just like the cells attached to collagen, while the cells attached to the silk sericin had a different shape. It is concluded, therefore, that the attachment condition on silk fibroin is ideal for the viability, growth and function of the cells. © 1995 John Wiley &amp; Sons, Inc.
BAROMETERS AND BLADDERS: A PRIMER ON PRESSURES (2000)

Despite a broad range of units, systems and applications, a consilient view of pressure in medicine can be approached. This perspective is fundamental to understanding the significance of pressures in the expanding clinimetric arena and should mitigate against misplaced concreteness that is tempting in modern medical practice, whereby laboratory tests become virtual realities and are mistaken for patients.
Test Results Report and Technology Development Report, HLH/ATC Drive System Aft Rotor Shaft Bearing Test (1974)

Abstract : The report presents the results of a program to define criteria and to design, fabricate, and test simulated HLH aft rotor shaft tapered roller bearings. Tests were performed in a back-to-back test rig which simulated the expected loading, lubrication, housing stiffness, and preload of the HLH aft rotor shaft application. Technical test inspection and evaluation were used to determine bearing performance and adequacy of bearing fatigue life under predicted operating conditions. Trade studies conducted of the HLH aft rotor shaft support bearing show that large-pitch-diameter and high-contact-angle duplex tapered roller bearings provide the most effective method of reacting the HLH rotor loads. This bearing configuration resulted in the lightest weight and most compact bearing system for the HLH aft rotor shaft bearing application.
Random image motion analysis with Ivory 2.0 FE models (2007)

A MWIR FLIR has been designed as the principal pointing and tracking system for a turret full of other sensors and systems in its payload. The payload is stabilized and vibration isolated but some vehicle disturbances get through these systems to excite the optical bench of the payload. These residual disturbances cause boresight shift and image blur of the IR image on the FLIR's cooled detector. Ivory was used to prepare a thermal and structural dynamic NASTRAN model of the FLIR image's response to the residual disturbances. The physical prescription for the FLIR optics was put into Ivory and it calculated all the influence coefficients between the image on the detector and all the lens design variables and all the lens motions. Ivory then prepared the portion of the NASTRAN model that relates the optical element displacements to the image motions. The Ivory optical model was then attached to an elastic model of the FLIR and payload and the effects on the image of temperature changes, gravitational vector changes and residual random vibrations were analyzed in NASTRAN. This paper discusses the Ivory modeling process, the error budgets associated with the analysis, the debugging of the models and the final analytical results.
Introducing a simplified approach to insulin therapy in type 2 diabetes: a comparison of two single‐dose regimens of insulin glulisine plus insulin glargine and oral antidiabetic drugs (2008)

A single bolus of glulisine, added to glargine and OADs, resulted in significantly improved HbA(1c) levels, irrespective of whether glulisine was administered at breakfast or at main mealtime. These results may represent a simplified and effective approach to treatment intensification in type 2 diabetes patients.
HIV-1 Non-Nucleoside Reverse Transcriptase Inhibitors: SAR and Lead Optimization Using CoMFA and CoMSIA Studies (1995-2016) (2017)

Overall, this review enlightens the protein-ligand interactions with a detailed SAR discussion for chemotypes. Such discussion will help medicinal chemist to gain a better understanding for the design of novel and promising NNRTI candidates.
Clusters of Nucleotide Substitutions and Insertion/Deletion Mutations Are Associated with Repeat Sequences (2011)

The genome-sequencing gold rush has facilitated the use of comparative genomics to uncover patterns of genome evolution, although their causal mechanisms remain elusive. One such trend, ubiquitous to prokarya and eukarya, is the association of insertion/deletion mutations (indels) with increases in the nucleotide substitution rate extending over hundreds of base pairs. The prevailing hypothesis is that indels are themselves mutagenic agents. Here, we employ population genomics data from Escherichia coli, Saccharomyces paradoxus, and Drosophila to provide evidence suggesting that it is not the indels per se but the sequence in which indels occur that causes the accumulation of nucleotide substitutions. We found that about two-thirds of indels are closely associated with repeat sequences and that repeat sequence abundance could be used to identify regions of elevated sequence diversity, independently of indels. Moreover, the mutational signature of indel-proximal nucleotide substitutions matches that of error-prone DNA polymerases. We propose that repeat sequences promote an increased probability of replication fork arrest, causing the persistent recruitment of error-prone DNA polymerases to specific sequence regions over evolutionary time scales. Experimental measures of the mutation rates of engineered DNA sequences and analyses of experimentally obtained collections of spontaneous mutations provide molecular evidence supporting our hypothesis. This study uncovers a new role for repeat sequences in genome evolution and provides an explanation of how fine-scale sequence contextual effects influence mutation rates and thereby evolution.
Proceedings of the 2014 SIAM International Conference on Data Mining (2014)

Data mining is an important tool in science, engineering, industrial processes, healthcare, business, and medicine. The datasets in these fields are large, complex, and often noisy. Extracting knowledge requires the use of sophisticated, high performance and principled analysis techniques and algorithms, based on sound theoretical and statistical foundations. These techniques in turn require implementations that are carefully tuned for performance; powerful visualization technologies; interface systems that are usable by scientists, engineers, and physicians as well as researchers; and infrastructures that support them. This conference provides a venue for researchers who are addressing these problems to present their work in a peer-reviewed forum. It also provides an ideal setting for graduate students and others new to the field to learn about cutting-edge research by hearing outstanding invited speakers and attending presentations and tutorials (included with conference registration). A set of focused workshops are also held on the last day of the conference. The proceedings of the conference arepublished in archival form, and are also made available on the SIAM web site
512 Development of a linear-motor-driven table with hydrostatic water bearings : Basic design and static stiffness (2006)

High precision, low production-cost, and environment-friendly table systems are required from machine tool builders. A linear-motor-driven table with hydrostatic water bearings is newly developed and its performance is investigated. The table supported by constant-flow water bearings is preloaded by magnetic force of the linear motor. A magnet plate of the linear motor is mounted on an inclined base of the table system so as to preload the table in horizontal and vertical directions. Static stiffness of the table system is affected by bearing clearance and water-flow volume. Load carrying capacity and static stiffness of the developed table under 6μm bearing clearance were estimated at 17.6kN and 1.95kN/μm respectively.
Substituted 2-Azabicyclo[2.1.1]hexanes as Constrained Proline Analogues:  Implications for Collagen Stability. (2006)

Among the proteinogenic amino acids, only proline is a secondary amine and only proline has a\nsaturated ring. Electronegative substituents on C-4 (that is, C&lt;sup&gt;γ&lt;/sup&gt;) have a substantial effect on the\ntrans/cis ratio of the prolyl peptide bond and the pucker of the pyrrolidine ring. 2-Azabicyclo[2.1.1]hexane is, in essence, a proline analogue with two C&lt;sup&gt;γ&lt;/sup&gt; atoms, one in each of the two prevalent ring\npuckers of proline. Here, 2-azabicyclo[2.1.1]hexane analogues of 2&lt;i&gt;S-&lt;/i&gt;proline, (2&lt;i&gt;S&lt;/i&gt;,4&lt;i&gt;S&lt;/i&gt;)-4-hydroxyproline, and (2&lt;i&gt;S&lt;/i&gt;,4&lt;i&gt;S&lt;/i&gt;)-4-fluoroproline residues were synthesized, and their trans/cis ratios were shown\nto be invariant in a particular solvent. Thus, the substitution of a proline residue on C-4 affects\nthe trans/cis ratio by altering the pucker of its pyrrolidine ring. This finding has implications for\nthe conformation of collagen, which has an abundance of 2&lt;i&gt;S-&lt;/i&gt;proline and (2&lt;i&gt;S&lt;/i&gt;,4&lt;i&gt;R&lt;/i&gt;)-4-hydroxyproline\nresidues, and can be stabilized by (2&lt;i&gt;S&lt;/i&gt;,4&lt;i&gt;R&lt;/i&gt;)-4-fluoroproline and (2&lt;i&gt;S&lt;/i&gt;,4&lt;i&gt;S&lt;/i&gt;)-4-fluoroproline residues.
Supplementary Figure 2 from Deletion of the Endothelial Bmx Tyrosine Kinase Decreases Tumor Angiogenesis and Growth (2023)

&lt;p&gt;PDF file - 93K, No effect on tumor growth in the Bmx-deleted male mice in the chemically induced skin carcinogenesis model or RIP1-Tag2 pancreatic insulinomas&lt;/p&gt;
R-ALOHA with priority (PR-ALOHA) in non ideal channel with capture effects (2010)

The performance of reservation ALOHA (R-ALOHA) with priority is analyzed using computer simulation. Priority is introduced to the R-ALOHA protocol by reserving specific time slots in the frame exclusively for high priority traffic. Traffic is produced and divided into either low or high priority. We considered non ideal channel with communication errors and capture effects. Performance is measured in terms of packet throughput and message transfer delay for each priority level. The analysis gives results for varying numbers of reserved high priority slots and varying levels of high priority traffic ultimately leading to a dynamic high priority slot reservation scheme. Multipriority protocols are important in such applications as intervehicle communication, where high priority may represent safety related messages, and multimedia communication, where high priority is given to streaming audio or video. In both applications low delay and high throughput are absolutely necessary for standard performance. The simulation results indicate that as the number of slots reserved for high priority traffic increases the delay of the high priority messages decreases. However, low priority throughput decreases and its delay increases.