gebhart/patrepeval huggingface dataset:
BioAssay templates for the semantic web (2016)

Annotation of bioassay protocols using semantic web vocabulary is a way to make experiment descriptions machine-readable. Protocols are communicated using concise scientific English, which precludes most kinds of analysis by software algorithms. Given the availability of a sufficiently expressive ontology, some or all of the pertinent information can be captured by asserting a series of facts, expressed as semantic web triples (subject, predicate, object). With appropriate annotation, assays can be searched, clustered, tagged and evaluated in a multitude of ways, analogous to other segments of drug discovery informatics. The BioAssay Ontology (BAO) has been previously designed for this express purpose, and provides a layered hierarchy of meaningful terms which can be linked to. Currently the biggest challenge is the issue of content creation: scientists cannot be expected to use the BAO effectively without having access to software tools that make it straightforward to use the vocabulary in a canonical way. We have sought to remove this barrier by: (1) defining a bioassay template data model; (2) creating a software tool for experts to create or modify templates to suit their needs; and (3) designing a common assay template (CAT) to leverage the most value from the BAO terms. The CAT was carefully assembled by biologists in order to find a balance between the maximum amount of information captured vs. low degrees of freedom in order to keep the user experience as simple as possible. The data format that we use for describing templates and corresponding annotations is the native format of the semantic web (RDF triples), and we demonstrate some of the ways that generated content can be meaningfully queried using the SPARQL language. We have made all of these materials available as open source (http://github.com/cdd/bioassay-template), in order to encourage community input and use within diverse projects, including but not limited to our own commercial electronic lab notebook products.
Supplementary methods and legends from The Driver Mutational Landscape of Ovarian Squamous Cell Carcinomas Arising in Mature Cystic Teratoma (2023)

&lt;p&gt;Supplementary Methods and legends for Supplementary tables and figures&lt;/p&gt;
Three Mutations in the Paired Homeodomain of <i>PAX3That </i>Cause Waardenburg Syndrome Type 1 (1997)

Genomic DNA from probands of various Waardenburg syndrome (WS) families were PCR-amplified using primers flanking the 8 exons of PAX3. The PCR fragments were screened for sequence variants, and subsequently cycle sequenced. Mutations were detected in exon 6 for 3 probands of WS type 1 families. These mutations all occur in the paired homeodomain DNA-binding motif.
Introduction to Nonlinear Systems (2018)

Almost all physical dynamic systems are nonlinear. The superposition techniques the authors used are not applicable in cases in which the systems under investigation are nonlinear. It is known that most components found in physical systems have nonlinear characteristics. In practice, the authors found some devices that have moderate nonlinear characteristics, or the nonlinear properties of these devices may occur if the devices are driven into certain nonlinear regions. In these cases modeling these strongly nonlinear devices by linear systems can be valid only for a limited range of operation. The chapter discusses the four ways to analyze nonlinear systems: analytical solution to the nonlinear system can be found under consideration; software application tools can be used to compute numerical solutions for specific parameters in a nonlinear system; equations describing the nonlinear system can be numerically solved using computers; and the nonlinear system can be replaced by a linear system that behaves nearly the same as the nonlinear system.
In Chronic Lymphocytic Leukemia the JAK2/STAT3 Pathway Is Constitutively Activated and Its Inhibition Leads to CLL Cell Death Unaffected by the Protective Bone Marrow Microenvironment (2019)

The bone marrow microenvironment promotes proliferation and drug resistance in chronic lymphocytic leukemia (CLL). Although ibrutinib is active in CLL, it is rarely able to clear leukemic cells protected by bone marrow mesenchymal stromal cells (BMSCs) within the marrow niche. We investigated the modulation of JAK2/STAT3 pathway in CLL by BMSCs and its targeting with AG490 (JAK2 inhibitor) or Stattic (STAT3 inhibitor). B cells collected from controls and CLL patients, were treated with medium alone, ibrutinib, JAK/Signal Transducer and Activator of Transcription (STAT) inhibitors, or both drugs, in the presence of absence of BMSCs. JAK2/STAT3 axis was evaluated by western blotting, flow cytometry, and confocal microscopy. We demonstrated that STAT3 was phosphorylated in Tyr705 in the majority of CLL patients at basal condition, and increased following co-cultures with BMSCs or IL-6. Treatment with AG490, but not Stattic, caused STAT3 and Lyn dephosphorylation, through re-activation of SHP-1, and triggered CLL apoptosis even when leukemic cells were cultured on BMSC layers. Moreover, while BMSCs hamper ibrutinib activity, the combination of ibrutinib+JAK/STAT inhibitors increase ibrutinib-mediated leukemic cell death, bypassing the pro-survival stimuli derived from BMSCs. We herein provide evidence that JAK2/STAT3 signaling might play a key role in the regulation of CLL-BMSC interactions and its inhibition enhances ibrutinib, counteracting the bone marrow niche.
Risk of dislocation using large- vs. small-diameter femoral heads in total hip arthroplasty (2012)

Large-diameter femoral head articulations may reduce dislocation rates in patients who have a high pre-operative risk for dislocation while providing the same functional improvements and safety as small-diameter bearings.
Joule heating and its effects on electroosmotic flow in microfluidic channels (2006)

Joule heating is resulted from inevitable volumetric heating when an electric field is applied across conducting media and it would impose limitations to the performance of electrokinetic microfluidic devices. In this paper, the Joule heating and its effects on electroosmotic flow (EOF) in PDMS microfluidic channels are reported. 3D numerical simulation of the Joule heating induced temperature field and its effects on the EOF and electrophoretic transport of solutes in microchannels was performed. Experiments were carried out to verify the proposed models and the developed numerical code. A Rhodamine B based thermometry technique was used to measure the solution temperature distributions in PDMS microfluidic channels. The micro particle image velocimetry (micro-PIV) technique was used to characterize the velocity profiles of the EOF under the influence of Joule heating. The numerical simulations were compared with the experimental results, and reasonable agreement is found. Both the numerical simulations and the experimental results show that the presence of the Joule heating causes the EOF velocity to deviate from its normal ''plug-like'' profile; the EOF velocity exhibits a concaved shape in the hydrodynamically developing region and a convex (parabolic) pattern in the fully developed region.
General Patterns in the Photochemistry of Pregna-1,4-dien-3,20-diones (2003)

The photochemistry of six pregna-1,4-dien-3,20-diones has been compared and found to involve both the cyclohexadienone moiety in ring A and the isolated ketone at C-20. The two reactions take place proportionally to the fraction of light absorbed by each chromophore. The cross-conjugated ketone absorbs predominantly or exclusively at both 254 and 366 nm and undergoes the "lumi" rearrangement to bicyclo[3.1.0]hex-3-en-2-one. The quantum yield of the reaction diminished somewhat with increasing lambda(exc), e.g., for prednisolone Phi(254) (nm) = 0.42, Phi(366) (nm) = 0.3. A much stronger lowering is caused by halogen substitution in position 9 (by a factor of 3 for F, >50 for Cl), apparently due to a shortened triplet lifetime caused by heavy atom effect. At 310 nm, both chromophores absorb to a comparable degree and both may react. The reaction at C(20) ketone involves either quite efficient alpha-cleavage (C(17)-C(20)) for compounds bearing an acetal or hydroxyl function at C(17) or less effective (by a factor of ca. 10) hydrogen abstraction from the 18-methyl group in the other cases (finally resulting in Norrish II fragmentation or Yang cyclization). The results allow generalizing how the substitution pattern surrounding each chromophore affects the photoreactivity at that site and the competition between the two modes, allowing predicting the photochemistry of this family of antiinflammatory drugs.
Reaction pathways for the enzymatic degradation of poly(ethylene terephthalate): What characterizes an efficient PET-hydrolase? (2022)

Abstract Bioprocessing of polyester waste has emerged as a promising tool in the quest for a cyclic plastic economy. One key step is the enzymatic breakdown of the polymer, and this entails a complicated pathway with substrates, intermediates, and products of variable size and solubility. We have elucidated this pathway for poly(ethylene terephthalate) (PET) and four enzymes. Specifically, we combined different kinetic measurements and a novel stochastic model, and found that the ability to hydrolyze internal bonds in the polymer (endo-lytic activity) was a key parameter for overall enzyme performance. Endo-lytic activity promoted the release of soluble PET fragments with two or three aromatic rings, which, in turn, were broken down with remarkable efficiency (k cat /K M -values of about 10 5 M -1 s -1 ) in the aqueous bulk. This meant that about 70% of the final, monoaromatic products was formed via soluble di-or tri-aromatic intermediates.
On the Nature of Resistive Transition in Disordered Superconducting Nanowires (2007)

Hot-electron single-photon counters based on long superconducting nanowires are starting to become popular in optical and infrared technologies due to their ultimately high sensitivity and very high response speed. We investigate intrinsic fluctuations in long NbN nanowires in the temperature range of 4.2 K-20 K, i.e. above and below the superconducting transition. These fluctuations are responsible for fluctuation resistivity and also determine the noise in practical devices. Measurements of the fluctuation resistivity were performed at low current densities and also in external magnetic fields up to 5 T. Above the BCS critical temperature T <i xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink"><sub>co</sub></i> the resistivity is well described by the Aslamazov-Larkin (AL) theory for two-dimensional samples. Below T <i xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink"><sub>co</sub></i> the measured resistivity is in excellent agreement with the Langer-Ambegaokar-McCumber-Halperin (LAMH) theory developed for one-dimensional superconductors. Despite that our nanowires of 100 nm width are two-dimensional with respect to the coherence length, our analysis shows that at relatively low current densities the one-dimensional LAMH mechanism based on thermally induced phase slip centers dominates over the two-dimensional mechanism related to unbinding of vortex-antivortex pairs below the Berezinskii-Kosterlitz-Thouless transition.
The swimming of a deforming helix (2018)

Many microorganisms and artificial microswimmers use helical appendages in order to generate locomotion. Though often rotated so as to produce thrust, some species of bacteria such Spiroplasma, Rhodobacter sphaeroides and Spirochetes induce movement by deforming a helical-shaped body. Recently, artificial devices have been created which also generate motion by deforming their helical body in a non-reciprocal way (A. Mourran et al. Adv. Mater. 29, 1604825, 2017). Inspired by these systems, we investigate the transport of a deforming helix within a viscous fluid. Specifically, we consider a swimmer that maintains a helical centreline and a single handedness while changing its helix radius, pitch and wavelength uniformly across the body. We first discuss how a deforming helix can create a non-reciprocal translational and rotational swimming stroke and identify its principle direction of motion. We then determine the leading-order physics for helices with small helix radius before considering the general behaviour for different configuration parameters and how these swimmers can be optimised. Finally, we explore how the presence of walls, gravity, and defects in the centreline allow the helical device to break symmetries, increase its speed, and generate transport in directions not available to helices in bulk fluids.
Energy and environmental characterization of operational modes of plug-in vehicles (2013)

This paper presents an energy and environmental characterization of the two most relevant Plug-in Hybrid Electric Vehicles available in the market (Opel Ampera and Toyota Prius Plug-in), in order to provide an estimate of fuel and electricity consumption, tailpipe emissions and charge depleting mode mileage for any drive cycle studied, based on vehicle specific power methodology. These vehicles were monitored under real-world operation with a portable laboratory that collects data from vehicle sensors (via on-board diagnosis port), exhaust gas composition and GPS in a second-by-second basis. An indirect method to measure battery energy fluxes and consequently estimating electric range was developed, providing maximum errors for the Charge Depleting driving range of 4.2% for the Toyota Prius Plug-in and -0.2% for the Opel, when comparing with measured data. Regarding fuel consumption, the maximum error verified was of -4.1%. Using two driving profiles measured in Portugal and the USA, the performance of the two vehicles under charge depleting (CD) and charge sustaining (CS) conditions was compared. Major findings indicate that Opel Ampera is more efficient in CD mode, while the Prius Plug-In is more efficient under CS conditions, but highly dependent on driving behavior when in CD mode.
Modelos culturales y retratos de identidad. Un estudio empírico con jóvenes de distintos contextos sociodemográficos (2010)

ResumenEl artículo examina la naturaleza cultural de la identidad humana a partir de un estudio que tenía el objetivo de analizar empíricamente las relaciones entre ciertos contextos de actividad, con estructuras sociodemo- gráficas determinadas (rural-tradicional, urbano-occidental y urbano-rural), con ciertos relatos y retratos de identidad. Participaron en el estudio seis indígenas de una comunidad rural de Chiapas (Zinacantán), seis estudiantes universitarios de una ciudad occidental (Girona, España), y seis estudiantes universitarios que provenían de contextos rurales pero vivían en una ciudad (San Cristóbal de las Casas, Chiapas). Según el análisis efectuado se observan diferencias en las categorías utilizadas para autodefinirse. Se interpretan y examinan estas diferencias en base a la teoría ecocultural de Keller, quién sintetiza aspectos de la tradición cross- cultural con aspectos de la tradición sociocultural
Cyclic AMP Activation of the Extracellular Signal-regulated Kinases 1 and 2 (2004)

The proliferative compartment of the intestinal crypt is critical in the process of intestinal epithelial cell homeostasis. The ability of these progenitor crypt cells to resist apoptosis and ensure restitution during a potentially lethal insult, but retain the ability to remove damaged or altered cells afterward, is necessary for preservation of the crypt-villus unit. We have examined the ability of cAMP to transiently inhibit apoptosis via the extracellular signal-regulated kinases 1 and 2 (ERK1/2), in T84 cells, an intestinal crypt-like cell line. Using the cAMP analog 8-bromo-cAMP and cholera toxin (CT), cAMP-mediated ERK1/2 activation was first measured by Western blot analysis of the phosphorylated (activated) and total (activated and inactivated) forms of ERK1/2. Cyclic AMP activated ERK1/2 in a time- and dose-dependent manner, and the effect was inhibited by PD098059, an inhibitor of the ERK1/2 signaling pathway. However, inhibition of protein kinase A (PKA) did not alter the activation of ERK1/2. CT transiently inhibited both staurosporine and Fas antibody mediated apoptosis as measured by a caspase-3 activation assay and the detection of nucleosomes in an apoptosis based enzyme-linked immunosorbent assay. This inhibitory effect was reversed by the simultaneous addition of PD098059. Our data suggest that in the T84 cell line, cAMP activates ERK1/2 in a PKA independent fashion and a physiological consequence of this activated pathway is the transient inhibition of apoptosis. These findings suggest a novel pathway that intestinal cells use to protect against injury while maintaining the overall ability to remove damaged cells and preserve intestinal homeostasis.
Contactless Transport and Mixing of Liquids on Self-Sustained Sublimating Coatings (2017)

Controlled handling of liquids and colloidal suspensions as they interact with surfaces, targeting a broad palette of related functionalities, is of great importance in science, technology, and nature. When small liquid volumes (drops on the order of microliters or nanoliters) need to be processed in microfluidic devices, contamination on the solid/liquid interface and loss of liquid due to adhesion on the transport channels are two very common problems that can significantly alter the process outcome, for example, the chemical reaction efficiency or the purity and the final concentration of a suspension. It is, therefore, no surprise that both levitation and minimal contact transport methods-including nonwetting surfaces-have been developed to minimize the interactions between liquids and surfaces. Here, we demonstrate contactless surface levitation and transport of liquid drops, realized by harnessing and sustaining the natural sublimation of a solid-carbon-dioxide-coated substrate to generate a continuous supporting vapor layer. The capability and limitations of this technique in handling liquids of extreme surface tension and kinematic viscosity values are investigated both experimentally and theoretically. The sublimating coating is capable of repelling many viscous and low-surface-tension liquids, colloidal suspensions, and non-Newtonian fluids as well, displaying outstanding omniphobic properties. Finally, we demonstrate how sublimation can be used for liquid transport, mixing, and drop coalescence, with a sublimating layer coated on an underlying substrate with prefabricated channels, conferring omniphobicity using a simple physical approach (i.e., phase change) rather than a chemical one. The independence of the surface levitation principle from material properties, such as electromagnetic, thermal or optical, surface energy, adhesion, or mechanical properties, renders this method attractive for a wide range of potential applications.
A methodology for evaluation of boundary detection algorithms on medical images (1997)

Image segmentation is the partition of an image into a set of nonoverlapping regions whose union is the entire image. The image is decomposed into meaningful parts which are uniform with respect to certain characteristics, such as gray level or texture. In this paper, we propose a methodology for evaluating medical image segmentation algorithms wherein the only information available is boundaries outlined by multiple expert observers. In this case, the results of the segmentation algorithm can be evaluated against the multiple observers' outlines. We have derived statistics to enable us to find whether the computer-generated boundaries agree with the observers' hand-outlined boundaries as much as the different observers agree with each other. We illustrate the use of this methodology by evaluating image segmentation algorithms on two different applications in ultrasound imaging. In the first application, we attempt to find the epicardial and endocardial boundaries from cardiac ultrasound images, and in the second application, our goal is to find the fetal skull and abdomen boundaries from prenatal ultrasound images.
Liver-Assist Device With a Microfluidics-Based Vascular Bed in an Animal Model (2010)

This device is the first to incorporate a microfluidics network in the systemic circulatory system. The microvascular network supported viability and function of liver cells in a short-term ex vivo model. Parenchymal chamber pressure generated in an arteriovenous shunt model is a critical parameter that affects viability and must be considered in future designs. The microfluidics-based vascular network is a promising platform for generating a large-scale medical device capable of augmenting liver function in a clinical setting.
Analysis of the temporal response of computed tomography fluoroscopy (1997)

Computed tomography fluoroscopy (CTF) has found many applications in interventional procedures. The advantage of CTF is its ability to remove overlapping structures in the human anatomy and, thereby, provide accurate spatial information. Another advantage is its ability to reconstruct images in a short period of time so that "real-time" information can be provided. In this paper, we perform theoretical analysis and computer simulations to evaluate the temporal response of the CTF. We investigate the impact of various reconstruction algorithms on CTF and demonstrate the inherent limitations of the CTF in terms of the time lag and delay. The analysis provides a useful guidance to the CTF operators to avoid potential pitfalls.
Hyperprogressive Disease in Anorectal Melanoma Treated by PD-1 Inhibitors (2018)

The 5-year survival rate of primary anorectal malignant melanoma is less than 20%. Optimal treatment of this condition remains controversial regarding locally disease, and whether any preferential survival benefit arises from either abdominoperineal resection or wide local excision remains unknown. The majority of patients progress to metastatic disease, and for decades, the use of chemotherapies, such as platines or dacarbazine, has been advocated to improve overall survival. The therapeutic use of new checkpoint inhibitors in a variety of trials has provided evidence for an antitumoral effect of PD-1 and/or CTL4 inhibitors in mucosal melanomas, but these treatments must still be further evaluated. Some anecdotal occurrences of rapid progression [i.e., hyperprogressive disease (HPD)] while using these immune agents have been described, suggesting potentially deleterious effects of these drugs for some patients. We report a 77-year-old male metastatic anorectal melanoma patient presenting with HPD over 2 months of a PD1 inhibitor treatment course and document this HPD blood phenotype.
ANATOMICAL STUDIES OF IN VITRO ORGANOGENESIS INDUCED IN LEAF-DERIVED EXPLANTS OF PASSIONFRUIT (1999)

With the aim of studying the organogenesis in vitro in Passiflora edulis Sims f. flavicarpa Deg., the passionfruit, leaf-derived explants were cultured on media containing NAA or BAP and incubated either in continuous darkness or in light. The histological events leading to de novo organ formation were evaluated. Darkness induces rhizogenesis in the presence of NAA, whereas direct shoot regeneration is stimulated by light and BAP. This latter condition is recommended for passionfruit micropropagation as several adventitious shoot buds were formed from meristemoids of parenchymal origin.