gebhart/patrepeval huggingface dataset:
A Quantitative Comparison of Human HT-1080 Fibrosarcoma Cells and Primary Human Dermal Fibroblasts Identifies a 3D Migration Mechanism with Properties Unique to the Transformed Phenotype (2013)

Here, we describe an engineering approach to quantitatively compare migration, morphologies, and adhesion for tumorigenic human fibrosarcoma cells (HT-1080s) and primary human dermal fibroblasts (hDFs) with the aim of identifying distinguishing properties of the transformed phenotype. Relative adhesiveness was quantified using self-assembled monolayer (SAM) arrays and proteolytic 3-dimensional (3D) migration was investigated using matrix metalloproteinase (MMP)-degradable poly(ethylene glycol) (PEG) hydrogels ("synthetic extracellular matrix" or "synthetic ECM"). In synthetic ECM, hDFs were characterized by vinculin-containing features on the tips of protrusions, multipolar morphologies, and organized actomyosin filaments. In contrast, HT-1080s were characterized by diffuse vinculin expression, pronounced β1-integrin on the tips of protrusions, a cortically-organized F-actin cytoskeleton, and quantitatively more rounded morphologies, decreased adhesiveness, and increased directional motility compared to hDFs. Further, HT-1080s were characterized by contractility-dependent motility, pronounced blebbing, and cortical contraction waves or constriction rings, while quantified 3D motility was similar in matrices with a wide range of biochemical and biophysical properties (including collagen) despite substantial morphological changes. While HT-1080s were distinct from hDFs for each of the 2D and 3D properties investigated, several features were similar to WM239a melanoma cells, including rounded, proteolytic migration modes, cortical F-actin organization, and prominent uropod-like structures enriched with β1-integrin, F-actin, and melanoma cell adhesion molecule (MCAM/CD146/MUC18). Importantly, many of the features observed for HT-1080s were analogous to cellular changes induced by transformation, including cell rounding, a disorganized F-actin cytoskeleton, altered organization of focal adhesion proteins, and a weakly adherent phenotype. Based on our results, we propose that HT-1080s migrate in synthetic ECM with functional properties that are a direct consequence of their transformed phenotype.
Online Case Study: The Clinical and Pathological Differential Diagnosis of Encephalopathy (“The Mysterious Case of ‘John Doe’”) (2013)

Abstract Introduction This online clinical case was designed to complement and reinforce material covered in the module on Nutritional/Metabolic disturbances in a second-year brain and behavior course. The goal of this exercise was to have the student apply important concepts previously presented in class to a realistic patient. It could also be utilized during the clinical years for a review of the basic science underlying encephalopathy. Methods The module was created to be an enjoyable, interactive, multimedia experience that guides the student through clinical decision making in a patient presenting with confusion. A brief discussion of this disorder concludes the exercise. Case efficacy was evaluated through a posttest and a student survey. Results The case was available to half of the class of 143 students (Group 1) for a period of 6 days following completion of the Nutritional/Metabolic Disturbances module. The remaining 72 students (Group 2) did not initially have access to the case. After the case was closed, an elective seven multiple-choice question online quiz was opened to all 143 students. The average total score (out of max of 7) for Group 1 was 5.58, while the score of Group 2 was 4.57 (p = .0004). For the survey, feedback was incorporated into an anonymous postcourse evaluation. Seven questions about the exercise were evaluated on a Likert scale from 1–5. In addition, free-text comments were solicited. Fifty-three students completed the survey. The quiz and survey results indicate that the case is both well-received and effective for short-term learning. Discussion The significance of the work is the integration of basic science/pathology and clinical medicine in the format of an engaging case review of encephalopathy. The case is appropriate both for preclinical students learning about clinical workup, as well as for students in the clerkship and post-clerkship years reviewing the underpinnings of basic science in clinical medicine.
Correlation model for 3D texture (1999)

While an exact definition of texture is somewhat elusive, texture can be qualitatively described as a distribution of color, albedo or local normal on a surface. In the literature, the word texture is often used to describe a color or albedo variation on a smooth surface. We refer to such texture as 2D texture. In real world scenes, texture is often due to surface height variations and can be termed 3D texture. Because of local foreshortening and masking, oblique views of 3D texture are not simple transformations of the frontal view. Consequently, texture representations such as the correlation function or power spectrum are also affected by local foreshortening and masking. This work presents a correlation model for a particular class of 3D textures. The model characterizes the spatial relationship among neighboring pixels in an image of 3D texture and the change of this spatial relationship with viewing direction.
Supplemental Figure 5 from The Genomic Landscape of Intrinsic and Acquired Resistance to Cyclin-Dependent Kinase 4/6 Inhibitors in Patients with Hormone Receptor–Positive Metastatic Breast Cancer (2023)

&lt;p&gt;Figure S5&lt;/p&gt;
Characterization of absorption losses in rear side n-type polycrystalline silicon passivating contacts (2019)

Passivating contacts consisting of polycrystalline silicon (poly-Si) and thin silicon-oxide (SiOx) layers facilitate a significant reduction of recombination losses in silicon solar cells. Nevertheless, these gains come with short circuit current density (Jsc) losses due to parasitic absorption by the poly-Si. Even if the passivating contacts are employed at the rear side only, absorption, particularly due to free carriers (FCA) in the heavily doped poly-Si, may still lead to significant Jsc losses. In this work, these losses are characterized as a function of the poly-Si thickness (tpoly) by the analysis of front reflectance spectra in the infrared (IR). For this study, two sets of samples with different n-type full-area poly-Si passivating contacts at the rear are compared to references with a phosphorus(P)-diffused back surface field (BSF) instead. For the two sets, Jsc losses with respect to the references (ΔJsc) are 0.10 mA/cm2 and 0.42 mA/cm2 per 100 nm thick poly-Si, respectively. The difference between the two values is studied by Hall measurements and interpreted to be due to the over three times as high free carrier concentration (ND,act) in the poly-Si layers of the second set of samples as the first set. On the other hand, lifetime measurements showed an excellent passivation yielding an implied open circuit voltage (iVoc) up to 736 mV only for the samples with the more heavily doped poly-Si, whereas iVoc of 683 mV was measured for the first set, which indicates a trade-off between absorption losses and passivation quality.
Use of word level side information to improve speech recognition (2002)

Word level information obtained from the output of a speech recognizer has been used in the past to extract confidence features for the hypothesized words. This work describes a post-recognition process which treats these word-level features as independent knowledge sources and combines them in one log linear model for the posterior probability of a word sequence. This model is used for rescoring the hypotheses. The parameters of the model are optimized using a discriminative model combination approach, where a simplex optimization method, known as amoeba search, is used to minimize the non-smooth function of empirical error rate on training data. The method is evaluated on the SWITCHBOARD database. After training 20 new parameters, we obtain a significant word error rate reduction over the baseline system. A correlation measure between features and word accuracy is defined to help analyze and explain the results.
Business Case and Technology Analysis for 5G Low Latency Applications (2017)

A large number of new consumer and industrial applications are likely to change the classic operator’s business models and provide a wide range of new markets to enter. This paper analyzes the most relevant 5G use cases that require ultra-low latency, from both technical and business perspectives. Low latency services pose challenging requirements to the network, and to fulfill them, operators need to invest in costly changes in their network. In this sense, it is not clear whether such investments are going to be amortized with these new business models. In light of this, specific applications and requirements are described and the potential market benefits for operators are analyzed. Conclusions show that the operators have clear opportunities to add value and position themselves strongly with the increasing number of services to be provided by 5G.
Orientationally Registered Crystals in Thin Film Crystalline/Amorphous Block Copolymers (2001)

ADVERTISEMENT RETURN TO ISSUEPREVCommunication to the...Communication to the EditorNEXTOrientationally Registered Crystals in Thin Film Crystalline/Amorphous Block CopolymersSheng Hong, William J. MacKnight, Thomas P. Russell, and Samuel P. GidoView Author Information Polymer Science and Engineering Department, Materials Research Science and Engineering Center, W. M. Keck Electron Microscopy Laboratory, University of Massachusetts, Amherst, Massachusetts 01003 Cite this: Macromolecules 2001, 34, 8, 2398–2399Publication Date (Web):March 15, 2001Publication History Received20 December 2000Revised19 February 2001Published online15 March 2001Published inissue 1 April 2001https://doi.org/10.1021/ma002167iCopyright © 2001 American Chemical SocietyRIGHTS & PERMISSIONSArticle Views364Altmetric-Citations38LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InReddit Read OnlinePDF (279 KB) Get e-AlertsSUBJECTS:Copolymers,Crystal structure,Crystallization,Layers,Thin films Get e-Alerts
The Receptor Interaction Region of Tyk2 Contains a Motif Required for Its Nuclear Localization (2001)

Janus kinases have so far been viewed as enzymatic intermediates that couple a variety of cell surface receptors to downstream substrates with diverse effector functions. Tyk2 is a member of this family that is involved in the interferon-alpha/beta and interleukin-12 signaling pathways via its specific interaction with the IFNAR1 and the beta1 receptor subunits. Here, we have analyzed the subcellular distribution of the wild-type Tyk2 protein and of several mutants expressed in Tyk2-deficient human cells. Direct GFP-associated fluorescence and immunostaining showed a diffuse localization of Tyk2 throughout the cell, including the nuclear compartment. The nuclear localization of Tyk2 requires a nuclear localization signal-like motif rich in arginine residues that maps within the region mediating interaction with cytokine receptors. To address the question of the role of the Tyk2 nuclear pool in interferon-alpha/beta-induced biological effects, cells expressing a membrane-targeted form of Tyk2-green fluorescent protein were analyzed for their interferon-alpha responses. Our studies demonstrate that Tyk2 can reside in the nucleus independently of receptor binding and that the nuclear pool is dispensable for the transcriptional and anti-vesicular stomatitis virus responses induced by interferon-alpha.
Sulfonated Poly(arylene sulfide sulfone nitrile) Multiblock Copolymers with Ordered Morphology for Proton Exchange Membranes (2013)

Ordered morphologies in disulfonated poly(arylene sulfide sulfone nitrile) (SPSN) copolymers were generated via thermal annealing followed by multiblock copolymer synthesis. While SPSN random copolymers (R-SPSN) showed featureless morphologies, the SPSN multiblock copolymers (B-SPSN) exhibited cocontinuous lamellar morphologies with a center-to-center interdomain size of up to 40 nm. In spite of the well-ordered, interconnected hydrophilic domains, the water self-diffusion coefficient (e.g., D = (0.7–2.0) × 10–10 m2 s–1) and proton conductivity (e.g., σ = 0.16–0.20 S cm–1 in deionized water at 30 °C) through B-SPSN were lower than those of the corresponding R-SPSN (e.g., D = (3.5–3.9) × 10–10 m2 s–1 and σ = 0.21 S cm–1) due to the relatively lower water uptake of the B-SPSN after thermal annealing. The reduced water uptake of B-SPSN was beneficial to reduction of peroxide degradation rate. Thermal annealing produced significant gains in morphological ordering and finer control over desired membrane properties for proton conduction applications.
Drug release from poly(ortho esters)-poly(ethylene glycol) polyblend (1999)

A polyblend of poly(ortho esters)–poly(ethylene glycol) (POE–PEG) was prepared. The release behavior of the acetanilide-loaded film of the POE–PEG polyblend was studied. Blending POE with water-soluble PEG can promote the release of drug in pH 7.4 PBS buffer at 37°C, while POE has plasticizing effect on PEG. Infrared and X-ray diffraction studies reveal that there is some interaction between POE and acetanilide. The SEM micrographs disclose that the porosity of the drug-loaded film enhances with an increase immersing time. © 1999 John Wiley & Sons, Inc. J Appl Polym Sci 71: 303–309, 1999
Suppl. Figures legends from Dual NAMPT and BTK Targeting Leads to Synergistic Killing of Waldenström Macroglobulinemia Cells Regardless of MYD88 and CXCR4 Somatic Mutation Status (2023)

&lt;p&gt;Suppl. figure legends&lt;/p&gt;
Frequency Response of Flag-Shaped Single Degree-of-Freedom Hysteretic Systems (2004)

Recognizing the importance of limiting residual deformations that are usually associated with the response of full hysteretic systems under seismic loading, a number of energy dissipating devices and innovative structural systems exhibiting a full recentering response have recently been developed. Although these systems encompass the highly desirable self-centering characteristic, they inherently have less energy dissipation capacity when compared to more traditional fuller hysteretic systems. Little information is available on the nonlinear dynamics of systems exhibiting this flag-shaped hysteresis. In this paper, the frequency response of single degree of freedom (SDOF) systems exhibiting the flag-shaped hysteresis is computed in a closed form using the method of slowly varying parameters. The solution is derived for two independent variables representing the postyielding stiffness and energy dissipation capacity that define all self-centering hysteretic systems. The hysteretic systems covered by this formulation range from bilinear elastic systems (with no energy dissipation) to full bilinear elastoplastic. The frequency response exhibits a softening branch with multiple solution regions. A relationship between the system properties and bounded response at resonance for a given amplitude of excitation is also derived. Further analysis is carried out to assess the stability of these multiple solution regions. It is found that both stable solution branches can be achieved depending on the nature of the excitation. An amplitude jump phenomenon is also present both in increasing frequency and decreasing frequency sweeps. The concept of theoretical versus likely response curve is discussed for less idealized excitation functions.
Use of Non-Gaussian Distribution for Analysis of Shaft Components (2006)

The drive train of a helicopter is a flight critical system in which the transmission of power results in both lift and thrust via a complex set of gears and shafts. Maintenance cost of this aircraft system is typically high due to the large damaging forces directed through these components. Consequently, monitoring the health of the drive train can potentially enhance flight safety and reduce operating costs. Health and usage management systems (HUMS) monitor the drive train by using accelerometers to measure component vibration. Algorithms process the time domain vibration data into various condition indicators (CI), which are used to determine component health via thresholding. For the rotating machinery, a standard set of CI are shaft order one, two and three (i.e. 1, 2 or 3 times the shaft RPM). Shaft order one (SOI) is indicative of an unbalance, where as higher shaft order can be used to detect a bent shaft or misalignment condition. The magnitude of the shaft orders sometimes have maximum allowable values set by the manufacture. At other times, some method is used to set thresholds, and maintenance is recommended when that vibration exceeds that threshold. In this paper, we present evidence that the distribution of the magnitude vibration is Rayleigh for nominal (health components) and the Rice for components that are damaged. A model for shaft magnitude is used which describes the Rayleigh distribution. It is shown that the Rice distribution is the general case of the Rayleigh distribution when the component has nonzero centrality (e.g. an imbalance). Threshold setting procedures for the Rayleigh distribution are given for anomaly detection (e.g. component is no longer normal) and for failure detection (component is damaged) and compared to Gaussian model. Finally, examples are given against real world conditions. The Rayleigh and Rice distribution are beneficial for diagnostics and prognostics as it measures non-centrality (imbalance) and variance (stiffness) in shaft vibration better than Gaussian models. We feel that use of this class of non-Gaussian distributions may allow accurate calculation of useful life remaining because it is sensitive to changes in shaft stiffness that is a precursor to component failure
Aphaeresis in New England (1973)

ARECENT ARTICLE appearing in this journall discusses the occurrence and form of APHAERESIS in ordinary American-English conversation. Although Kypriotaki's claims appear to be substantially correct,2 they are unsupported by systematic data. This paper reports evidence of aphaeresis in New England, as documented in the Linguistic Atlas of New England.3 The authors take this opportunity to demonstrate the potential of the Atlas, and other resources of its kind, to provide facts of usage amenable to sociolinguistic theory. It is unfortunate that sociolinguists have typically failed to consult these valuable linguistic materials.4 The case argued in a sociolinguistic article could only be strengthened by an examination of all pertinent materials.
Technical Overview of Diagnostic Methods for Breast Cancer Detection (2012)

Article Technical Overview of Diagnostic Methods for Breast Cancer Detection was published on August 24, 2012 in the journal Biomedical Engineering / Biomedizinische Technik (volume 57, issue SI-1-Track-B).
Complete replacement set of amino acids at the C-terminus of thymidylate synthase: quantitative structure-activity relationship of mutants of an enzyme (1992)

The C-terminal residue of thymidylate synthase (TS) is highly conserved and has been implicated in cofactor binding, catalysis, and a conformational change. The codon for the C-terminal valine of Lactobacillus casei TS has been replaced with those for 19 other amino acids and the amber stop codon. Fourteen of the resulting mutant proteins were active by genetic complementation using a Thy- strain of Escherichia coli, and 18 mutants were active by in vitro assay. Only the aspartate and amber mutations had undetectable activity. All of the mutants were expressed at high levels (5-30% of soluble protein) and were purified by phosphocellulose chromatography. In general, the alterations at position 316 led to little effect on the Km for dUMP, an increase in Km for the folate cofactor, and a decrease in kcat. The observations show that TS can tolerate the substitution of most amino acids for valine at the C-terminus without a complete loss of activity, that hydrophobic substitutions are preferred, and that the C-terminal side chain is involved in both cofactor binding and catalysis. There was an excellent correlation between log kcat and hydrophobicity of the side chain at position 316 and an inverse correlation between log Km and the hydrophobicity of this residue. Kinetic parameters of the cofactor-independent TS-catalyzed dehalogenation of BrdUMP showed no variation with the side chain at position 316. In context of the structure of TS, it is proposed that binding of the cofactor triggers a conformational change in which the C-terminal side chain undergoes hydrophobic interactions that stabilize a rate-limiting transition state of the TS reaction.
Response to Comment on “CD226 Is Specifically Expressed on the Surface of Th1 Cells and Regulates Their Expansion and Effector Functions” (2006)

We recently described that CD226 is specifically expressed on differentiated Th1 T cells ([1][1]). Using a novel rat 10E5 mAb, we find that ∼40% of CD4+T cells purified from the spleen of C57BL/6 express CD226. Upon activation, CD226 is up-regulated on all CD4+ T cells, independent of their Th
Femtosekunden-Spektroskopie zur Protontransfer-Dynamik im elektronisch angeregten Zustand von 1.8-Dihydroxy-9.10-Anthrachinon (2003)

This thesis investigates the connection between the non-radiative relaxation dynamics of 1.8-dihydroxy-9.10-anthraquinone (1.8-DHAQ) and the intramolecular proton-transfer in the first electronically excited state. For this purpose pump-probe-measurements in benzyl alcohol as well as fluorescence-up-conversion measurements in benzyl alcohol, propylenecarbonate and tetrachloromethane were carried out. In addition the influence of the deuteration of the hydroxylgroups of 1.8-DHAQ in tetrachloromethane was tested. Analysis of the data shows, that the proton-transfer of 1.8-DHAQ in the first excited state can neither be described by a separate shift of the proton in the quasi-aromatic ring nor merely by a deformation of the molecular skeleton. The rearrangement of the molecular structure in the excited state has to comprise several degrees of vibrational freedom of the molecule. Therefore the interpretation of the results of the measurements have to be based on a Lippincott-Schroeder double-minimum potential along the proton-transfer coordinate taking account of the coupling between the (OH)-vibrational mode and other low frequency modes of the molecule.