gebhart/patrepeval huggingface dataset:
Tensile Loading Modulates Bone Marrow Stromal Cell Differentiation and the Development of Engineered Fibrocartilage Constructs (2010)

Mesenchymal progenitors such as bone marrow stromal cells (BMSCs) are an attractive cell source for fibrocartilage tissue engineering, but the types or combinations of signals required to promote fibrochondrocyte-specific differentiation remain unclear. The present study investigated the influences of cyclic tensile loading on the chondrogenesis of BMSCs and the development of engineered fibrocartilage. Cyclic tensile displacements (10%, 1 Hz) were applied to BMSC-seeded fibrin constructs for short (24 h) or extended (1-2 weeks) periods using a custom loading system. At early stages of chondrogenesis, 24 h of cyclic tension stimulated both protein and proteoglycan synthesis, but at later stages, tension increased protein synthesis only. One week of intermittent cyclic tension significantly increased the total sulfated glycosaminoglycan and collagen contents in the constructs, but these differences were lost after 2 weeks of loading. Constraining the gels during the extended culture periods prevented contraction of the fibrin matrix, induced collagen fiber alignment, and increased sulfated glycosaminoglycan release to the media. Cyclic tension specifically stimulated collagen I mRNA expression and protein synthesis, but had no effect on collagen II, aggrecan, or osteocalcin mRNA levels. Overall, these studies suggest that the combination of chondrogenic stimuli and tensile loading promotes fibrochondrocyte-like differentiation of BMSCs and has the potential to direct fibrocartilage development in vitro.
Simulation of cyber physical models using SysML and numerical solvers (2013)

We demonstrate a modeling and simulation technique that allows integrating controller/plant behavior specified in numerical solvers, such as Simulink and Modelica, within the SysML model. This allows the mixing of discrete and continuous behaviors in a context of a system model that can be simulated as a complete system level specification. Our approach involves code generation, rather than semantic mappings or model transformation of behaviors, combined with the capability to transform the interface and type specification from one modeling language to the other. Using such complementary languages/tools allows the specification of a complete design model that can be simulated for various purposes such as verification and validation and trade studies.
Multi-Sectoral Partnerships and Patient-Engagement Strategies in Accountable Care Organizations (2016)

Background: Patient-engagement strategies are increasingly recognized for enriching traditional medical care and improving population health. Accountable Care Organizations (ACOs) may be well positioned to leverage multi-sector organizational partnerships to improve the reach of their patient-engagement strategies, particularly given incentives to meet cost, quality and population health goals. Little is currently known about the relation of multi-sector partnerships and patient engagement in ACOs. Purpose: To examine the relation of patient-engagement strategies and breadth of multi-sectoral organizational partnerships in 71 primary care practices affiliated with one of two ACOs. Methods: Clinical and administrative leaders from each practice were surveyed. Questions assessed practice use of 12 different partnership sectors and the adoption of 14 patient-engagement strategies. Bivariate tests examined associations between patient-engagement strategies and practice use of partnership sectors. Multivariate linear regression estimated the extent to which practices with a greater number of multi-sector organizational partnerships had greater adoption of patient-engagement strategies. Results: Practices reported partnering with a mean of 3.2 (standard deviation, SD= 2.1) out of 12 sectors and implementing a mean of 7.1 (SD=3.4) out of 14 patient-engagement strategies. Each additional type of multi-sector partnership was associated with greater adoption of patient-engagement strategies (β = 0.59, 95% CI = 0.23–0.95, for all partnerships and β = 0.92, 95% CI = 0.42–1.43, when restricted to nonmedical partnerships) Implications: Practices with a greater breadth of multi-sector partnerships, particularly nonmedical partnerships, use a wider range of strategies to engage patients in their own care.
Mutations in CECR1 associated with a neutrophil signature in peripheral blood (2014)

We hypothesise that ADA2 may act as a regulator of neutrophil activation, and that a reduction of ADA2 activity results in significant endothelial damage via a neutrophil-driven process.
Development of antibodies against the fluoroquinolone sarafloxacin and molecular modeling studies of cross‐reactive compounds (1997)

Polyclonal antibodies were prepared against the fluoroquinolone sarafloxacin. Sarafloxacin was conjugated directly to cationized bovine serum albumin (BSA) and ovalbumin. Balb/c mice were immunized with the sarafloxacin‐BSA conjugate (cBSA‐saraflox) and sarafloxacin‐reactive sera (1–5) were obtained from these mice. Serum from mouse 1 (Abl) exhibited the lowest IC50 for free sarafloxacin using an indirect competitive inhibition ELISA (ci‐ELISA). Other structurally related quinolones, including difloxacin, enrofloxacin, norfloxacin, trovafloxacin and nalidixic acid, demonstrated cross‐reactivity with the sarafloxacin antibodies as determined by ci‐ELISA. In an effort to correlate antibody binding with three‐dimensional properties of the cross‐reactive compounds, all of the fluoroquinolones as well as nalidixic acid were modeled, and global energy minima were determined using molecular mechanical and quantum mechanical methods. The results demonstrate that the three‐dimensional models can yield information that explains observed cross‐reactivity data. These models are particularly helpful when the chemical structure of an analog varies greatly from the immunogen yet the IC50 value for the compound is not vastly different. Furthermore, conformational and electronic data from this study can be used to predict whether other fluoroquinolones will exhibit good cross‐reactivity in this ELISA.
Fano antiresonances in the optical-absorption spectra of<mml:math xmlns:mml="http://www.w3.org/1998/Math/MathML" display="inline"><mml:mrow><mml:msup><mml:mrow><mml:mi mathvariant="normal">Cr</mml:mi></mml:mrow><mml:mrow><mml:mn>3</mml:mn><mml:mo>+</mml:mo></mml:mrow></mml:msup></mml:mrow></mml:math>-doped<mml:math xmlns:mml="http://www.w3.org/1998/Math/MathML" display="inline"><mml:mrow><mml:msub><mml:mrow><mml:mi mathvariant="normal">La</mml:mi></mml:mrow><mml:mrow><mml:mn>3</mml:mn></mml:mrow></mml:msub></mml:mrow></mml:math><mml:math xmlns:mml="http://www.w3.org/1998/Math/MathML" display="inline"><mml:mrow><mml:msub><mml:mrow><mml:mi mathvariant="normal">Ga</mml:mi></mml:mrow><mml:mrow><mml:mn>5.5</mml:mn></mml:mrow></mml:msub></mml:mrow></mml:math><mml:math xmlns:mml="http://www.w3.org/1998/Math/MathML" display="inline"><mml:mrow><mml:msub><mml:mrow><mml:mi mathvariant="normal">Nb</mml:mi></mml:mrow><mml:mrow><mml:mn>0.5</mml:mn></mml:mrow></mml:msub></mml:mrow></mml:math><mml:math xmlns:mml="http://www.w3.org/1998/Math/MathML" display="inline"><mml:mrow><mml:msub><mml:mrow><mml:mi mathvariant="normal">O</mml:mi></mml:mrow><mml:mrow><mml:mn>14</mml:mn></mml:mrow></mml:msub></mml:mrow></mml:math>and<mml:math xmlns:mml="http://www.w3.org/1998/Math/MathML" display="inline"><mml:mrow><mml:msub><mml:mrow><mml:mi mathvariant="normal">La</mml:mi></mml:mrow><mml:mrow><mml:mn>3</mml:mn></mml:mrow></mml:msub></mml:mrow></mml:math><mml:math xmlns:mml="http://www.w3.org/1998/Math/MathML" display="inline"><mml:mrow><mml:msub><mml:mrow><mml:mi mathvariant="normal">Ga</mml:mi></mml:mrow><mml:mrow><mml:mn>5.5</mml:mn></mml:mrow></mml:msub></mml:mrow></mml:math><mml:math xmlns:mml="http://www.w3.org/1998/Math/MathML" display="inline"><mml:mrow><mml:msub><mml:mrow><mml:mi mathvariant="normal">Ta</mml:mi></mml:mrow><mml:mrow><mml:mn>0.5</mml:mn></mml:mrow></mml:msub></mml:mrow></mml:math><mml:math xmlns:mml="http://www.w3.org/1998/Math/MathML" display="inline"><mml:mrow><mml:msub><mml:mrow><mml:mi mathvariant="normal">O</mml:mi></mml:mrow><mml:mrow><mml:mn>14</mml:mn></mml:mrow></mml:msub></mml:mrow></mml:math>crystals (1994)

The polarized optical absorption spectra of ${\mathrm{Cr}}^{3+}$ ions have been systematically investigated in two acentric crystals with Ca-gallogermanate structure: ${\mathrm{La}}_{3}$${\mathrm{Ga}}_{5.5}$${\mathrm{Nb}}_{0.5}$${\mathrm{O}}_{14}$ and ${\mathrm{La}}_{3}$${\mathrm{Ga}}_{5.5}$${\mathrm{Ta}}_{0.5}$${\mathrm{O}}_{14}$. Crystal-field parameters have been determined for both ${\mathrm{Cr}}^{3+}$-doped crystals. Features observed in the long-wavelength $^{4}$${\mathit{A}}_{2}$${\ensuremath{\rightarrow}}^{4}$${\mathit{T}}_{2}$ absorption band of ${\mathrm{Cr}}^{3+}$ have been associated with Fano antiresonances, due to interaction between the $^{2}$E and $^{2}$${\mathit{T}}_{1}$ sharp levels and the vibrationally broadened $^{4}$${\mathit{T}}_{2}$ quasicontinuum. The line shapes have been analyzed in terms of the four-parameter theory of Fano, so that the interaction has been evaluated for both crystals and compared with other ${\mathit{d}}^{3}$ ion-doped systems.
Sparse regularized regression identifies behaviorally-relevant stimulus features from psychophysical data (2012)

As a prerequisite to quantitative psychophysical models of sensory processing it is necessary to learn to what extent decisions in behavioral tasks depend on specific stimulus features, the perceptual cues. Based on relative linear combination weights, this study demonstrates how stimulus-response data can be analyzed in this regard relying on an L(1)-regularized multiple logistic regression, a modern statistical procedure developed in machine learning. This method prevents complex models from over-fitting to noisy data. In addition, it enforces "sparse" solutions, a computational approximation to the postulate that a good model should contain the minimal set of predictors necessary to explain the data. In simulations, behavioral data from a classical auditory tone-in-noise detection task were generated. The proposed method is shown to precisely identify observer cues from a large set of covarying, interdependent stimulus features--a setting where standard correlational and regression methods fail. The proposed method succeeds for a wide range of signal-to-noise ratios and for deterministic as well as probabilistic observers. Furthermore, the detailed decision rules of the simulated observers were reconstructed from the estimated linear model weights allowing predictions of responses on the basis of individual stimuli.
Advanced timing analysis based on post-OPC extraction of critical dimensions (2005)

While performance specifications are verified before sign-off for a modern nanometer scale design, extensive application of optical proximity correction substantially alters the layout introducing systematic variations to the simulated and verified performance. As a result, actual on-silicon chip performance is quite different from sign-off expectations. This paper presents a new methodology to provide better estimates of on-silicon performance. The technique relies on the extraction of residual OPC errors from placed and routed full chip layouts to derive actual (i.e., calibrated to silicon) CD values that are then used in timing analysis and speed path characterization. This approach is applied to a state-of-the-art microprocessor and contrasted with traditional design flow practices where ideal (i.e., drawn) Lgate values are employed, leading to a subsequent lack of predictive power. We present a platform for diagnosing and improving OPC quality on gates with specific functionality such as critical gates or matching transistors. Furthermore, with more accurate timing analysis we highlight the necessity of a post-OPC verification embedded design flow, by showing substantial differences in the Si-based timing simulations in terms of significant reordering of speed path criticality and a 36.4% increase in worst-case slack. Extensions of this methodology to multi-layer extraction and timing characterization are also proposed.
Impact of Defect Distribution on Resistive Switching Characteristics of Sr<sub>2</sub>TiO<sub>4</sub> Thin Films (2009)

The resistive switching properties of Sr2TiO4 thin films with specific defect distribution have been studied. Junctions of Sr2TiO4 thin films containing a high density of defects show well-pronounced resistive switching properties while those with well-ordered microstructure exhibited insignificant hysteresis windows. This work clearly demonstrates the crucial role of defects for the microscopic switching mechanisms in oxide thin films. Detailed facts of importance to specialist readers are published as ”Supporting Information”. Such documents are peer-reviewed, but not copy-edited or typeset. They are made available as submitted by the authors. Please note: The publisher is not responsible for the content or functionality of any supporting information supplied by the authors. Any queries (other than missing content) should be directed to the corresponding author for the article.
Matrix Metalloproteinase 13 (MMP13) and Tissue Inhibitor of Matrix Metalloproteinase 1 (TIMP1), Regulated by the MAPK Pathway, Are Both Necessary for Madin-Darby Canine Kidney Tubulogenesis (2007)

A classic model of tubulogenesis utilizes Madin-Darby canine kidney (MDCK) cells. MDCK cells form monoclonal cysts in three-dimensional collagen and tubulate in response to hepatocyte growth factor, which activates multiple signaling pathways, including the mitogen-activated protein kinase (MAPK) pathway. It was shown previously that MAPK activation is necessary and sufficient to induce the first stage of tubulogenesis, the partial epithelial to mesenchymal transition (p-EMT), whereas matrix metalloproteinases (MMPs) are necessary for the second redifferentiation stage. To identify specific MMP genes, their regulators, tissue inhibitors of matrix metalloproteinases (TIMPs), and the molecular pathways by which they are activated, we used two distinct MAPK inhibitors and a technique we have termed subtraction pathway microarray analysis. Of the 19 MMPs and 3 TIMPs present on the Canine Genome 2.0 Array, MMP13 and TIMP1 were up-regulated 198- and 169-fold, respectively, via the MAPK pathway. This was confirmed by two-dimensional and three-dimensional real time PCR, as well as in MDCK cells inducible for the MAPK gene Raf. Knockdown of MMP13 using short hairpin RNA prevented progression past the initial phase of p-EMT. Knockdown of TIMP1 prevented normal cystogenesis, although the initial phase of p-EMT did occasionally occur. The MMP13 knockdown phenotype is likely because of decreased collagenase activity, whereas the TIMP1 knockdown phenotype appears due to increased apoptosis. These data suggest a model, which may also be important for development of other branched organs, whereby the MAPK pathway controls both MDCK p-EMT and redifferentiation, in part by activating MMP13 and TIMP1.
Usefulness of Near-Infrared Reflectance (NIR) Spectroscopy and Chemometrics To Discriminate Fishmeal Batches Made with Different Fish Species (2005)

Near-infrared reflectance (NIR) spectroscopy combined with chemometrics was used to identify and authenticate fishmeal batches made with different fish species. Samples from a commercial fishmeal factory (n = 60) were scanned in the NIR region (1100-2500 nm) in a monochromator instrument in reflectance. Principal component analysis (PCA), dummy partial least-squares regression (DPLS), and linear discriminant analysis (LDA) based on PCA scores were used to identify the origin of fishmeal produced using different fish species. Cross-validation was used as validation method when classification models were developed. DPLS correctly classified 80 and 82% of the fishmeal samples. LDA calibration models correctly classified >80% of fishmeal samples according to fish species The results demonstrated the usefulness of NIR spectra combined with chemometrics as an objective and rapid method for the authentication and identification of fish species used to manufacture the fishmeal.
High-transconductance <i>p</i> -type SiGe modulation-dopedfield-effect transistor (1995)

High-transconductance 1.5 µm-gate-length p-type modulation-doped field-effect transistors (MODFETs) have been fabricated using standard optical lithography on a high hole-mobility SiGe heterostructure grown by ultrahigh vacuum chemical vapour deposition (UHV-CVD). A maximum DC extrinsic (intrinsic) transconductance of 95 mS/mm (138 mS/mm) at room temperature has been achieved, which to our knowledge is the highest for p-type field-effect transistors at this gate length. A unity current-gain frequency ft of 2.1 GHz has been measured. The gate leakage current was quite low and was of the order of a few µA/mm. These enhancement-mode devices exhibit reasonable pinch-off characteristics.
Instructional Support for Teachers and Guided Feedback for Students in an Adaptive eLearning Environment (2011)

Adaptive Tutorials are Intelligent Tutoring Systems (ITS) in which students typically interact with a simulation towards a task-goal while being guided and remediated. Adaptive Tutorials can exhibit different kinds of feedback: students are given guidance based on their interaction, and teachers can also receive feedback on their own authoring choices to drive reflection and content adaptation. This paper will discuss different types of feedback which students are given within Adaptive Tutorials and their pedagogical utility. It will then look at providing teachers with timely support and feedback as well as post-hoc solution traces, to improve student learning. We suggest a refined ITS design and development lifecycle to better support teachers in the design of good pedagogy. We provide this in the form of the Adaptive eLearning Platform, which is a tool to support teachers in the adaptation of tutorials and the creation of customized student feedback. This in turn can result in an improved student experience, with more guidance and better learning.
Small Phenolic Compounds Production from Kraft Black Liquor by Lignin Depolymerization with Different Catalytic Agents (2017)

This work is aimed to produce small phenolic compounds from Kraft black liquor. For this purpose, depolymerization reaction is directly carried out over the liquor, without a previous isolation of lignin. In this sense, the intensification of lignin valorization is carried out by the reduction of the total stages of the whole process. Due to the alkali degree of Kraft liquors, base catalyzed depolymerization is proposed for the lignin cleaved reaction. In addition, two facilitating agents (phenol and hydrogen peroxide) were used to reduce the amount of undesirable reaction products, such as residual lignin and coke. High yield of phenolic oil was recovered after treatment of the Kraft liquor in blank reaction (~30 %). However, high amount of undesirable products (residual lignin and coke) was also obtained (~65 % between both). The addition of phenol as capping agent reduced coke formation (almost to the half); and monomer phenolic compounds in oil were increased four times. The use of hydrogen peroxide reduces the phenolic oil yield (lower than 20 %). Catechol derivatives were the most plentiful products in the phenolic oil (92.44 % of total phenolic monomers) and a decreased of coke formation was similar to that in phenol. As summary it can be established that the intensification of the lignin depolymerization can be accomplished with high yields of phenolic oil production by avoiding the isolation of lignin and its further solubilization.
Australian Involvement in South-west Pacific Disaster Management (1995)

The impact of natural hazards on South-West Pacific countries with less concentration of population compared to Bangladesh and China is discussed. During disaster, the restricted links in these remote islands are frequently disrupted and hence survey teams might not be able to reach particular islands for some days of even weeks.
Supersymmetric laser arrays (2019)

Scaling up the radiance of coupled laser arrays has been a long-standing challenge in photonics. In this study, we demonstrate that notions from supersymmetry-a theoretical framework developed in high-energy physics-can be strategically used in optics to address this problem. In this regard, a supersymmetric laser array is realized that is capable of emitting exclusively in its fundamental transverse mode in a stable manner. Our results not only pave the way toward devising new schemes for scaling up radiance in integrated lasers, but also, on a more fundamental level, could shed light on the intriguing synergy between non-Hermiticity and supersymmetry.
Radiation-Induced Coloration of Photochromic Dithienylethene Derivatives in Polymer Matrices (2000)

Abstract The high-energy radiation-induced coloration of photochromic dithienylethenes was studied in various polymer matrices with the aim of developing a reusable color plastic dosimeter. Upon γ-irradiation, polystyrene films containing 1,2-bis(2,5-dimethyl-3-thienyl)perfluorocyclopentene 1a and 1,2-bis(2-methyl-5-phenyl-3-thienyl)perfluorocyclopentene 2a turned red and blue, respectively. The red and blue colors disappeared upon irradiation with visible light, and the films could be reused. In both films the absorption intensities of the colors increased linearly with the absorbed dose. Although radiation-induced coloration was clearly detected in polystyrene films, a color change was scarcely observed in poly(methyl methacrylate) (PMMA) and poly(N-vinyl carbazole) containing 1a and 2a. Excitation energy transfer from polymers to dithienylethenes is considered to play a role in the coloration process in polymer films.
Complete Genome Sequence of Human Respiratory Syncytial Virus Genotype A with a 72-Nucleotide Duplication in the Attachment Protein G Gene (2012)

The complete genome sequence of human respiratory syncytial virus genotype A (HRSV-A) with a 72-nucleotide duplication in the C-terminal part of the attachment protein G gene was determined and analyzed. The genome was 15,277 bp in length, and 0.46 to 6.03% variations were identified at the nucleotide level compared with the previously reported complete genome of HRSV-A. Characterization of the genome will improve understanding of the diversity of the HRSV-A major antigens and enable an in-depth analysis of its genetics.
The <i>piggyBac</i> Transposon Displays Local and Distant Reintegration Preferences and Can Cause Mutations at Noncanonical Integration Sites (2013)

The DNA transposon piggyBac is widely used as a tool in mammalian experimental systems for transgenesis, mutagenesis, and genome engineering. We have characterized genome-wide insertion site preferences of piggyBac by sequencing a large set of integration sites arising from transposition from two separate genomic loci and a plasmid donor in mouse embryonic stem cells. We found that piggyBac preferentially integrates locally to the excision site when mobilized from a chromosomal location and identified other nonlocal regions of the genome with elevated insertion frequencies. piggyBac insertions were associated with expressed genes and markers of open chromatin structure and were excluded from heterochromatin. At the nucleotide level, piggyBac prefers to insert into TA-rich regions within a broader GC-rich context. We also found that piggyBac can insert into sites other than its known TTAA insertion site at a low frequency (2%). Such insertions introduce mismatches that are repaired with signatures of host cell repair pathways. Transposons could be mobilized from plasmids with the observed noncanonical flanking regions, indicating that piggyBac could generate point mutations in the genome.