gebhart/patrepeval huggingface dataset:
Synergistic effects of growth factor-based serum-free medium and tendon-like substrate topography on tenogenesis of mesenchymal stem cells (2023)

Addressing clinical challenges for tendon injuries requires a deeper understanding of the effects that biological and biophysical cues have on tenogenesis. Although prior studies have identified tenogenic growth factors (GFs) or elucidated the effects of substrate topography on tenocyte behavior, few have characterized their combined effect in the presence of a tendon-like substrate. In this study, we assessed the effect of biological (GFs) and biophysical (substrate topography) cues on tenogenic proliferation and differentiation under defined, serum-free conditions. Specifically, human bone marrow-derived mesenchymal stem cells (hMSCs) were cultured in a serum-free culture medium containing a GF cocktail comprised of fibroblast growth factor-2 (FGF-2), transforming growth factor-beta 3 (TGF-β3), and insulin-like growth factor-1 (IGF-1), either alone or in combination with tendon-like substrate topography produced by replica casting of tendon tissue sections. Our data demonstrated that the use of serum-free GF cocktail medium alone promoted hMSC proliferation, as shown via DNA staining as well as Ki67 protein levels and gene expression. In particular, gene expression of Ki67 was increased by 8.46-fold in all three donors relative to serum-free medium control. Also, serum-free GF cocktail promoted tenogenic differentiation, on the basis of expression of tendon-associated gene and protein markers, scleraxis (SCX), tenascin C (TNC), and collagen type I (COL1A1) including increased normalized collagen production by 1.4-fold in two donors relative to serum-free medium control. Interestingly, hMSCs cultured on a tendon-like substrate exhibited highly oriented cell morphology and extracellular matrix (ECM) alignment reminiscent of tendon. In particular, when this GF cocktail was combined with tendon-like topography, they showed a synergistically increased expression of tendon-related markers and anisotropic organization of ECM proteins with moderate-to-large effect sizes. Together, in addition to showing the utility of a GF cocktail for expansion and differentiation of tenocyte-like cells, our findings clearly demonstrate the synergistic relationship between GF-mediated and substrate topography-related effects on hMSC tenogenic differentiation. This information provides insights into the design of strategies that combine biological and biophysical cues for ex vivo tenocyte production and tendon tissue engineering.
Fungi.guru: comparative genomic and transcriptomic database for the Fungi kingdom (2020)

ABSTRACT The fungi kingdom is composed of eukaryotic heterotrophs, which are responsible for balancing the ecosystem and play a major role as decomposers. They also produce a vast diversity of secondary metabolites, which have antibiotic or pharmacological properties. However, our lack of knowledge of gene function in fungi precludes us from tailoring them to our needs and tapping into their metabolic diversity. To remedy this, we gathered genomic and gene expression data of 19 most widely-researched fungi to build a database, fungi.guru, which contains tools for cross-species identification of conserved pathways, functional gene modules, and gene families. We exemplify how our database can elucidate the molecular function, biological process and cellular component of genes involved in various biological processes, by identifying a secondary metabolite pathway producing gliotoxin in Aspergillus fumigatus , the catabolic pathway of cellulose in Coprinopsis cinerea and the conserved DNA replication pathway in Fusarium graminearum and Pyricularia oryzae . The database is available at www.fungi.guru .
Magnetic Brightening of Dark Excitons in Carbon Nanotubes (2006)

To gain insight into the internal energy structure and radiative properties of excitons in single-walled carbon nanotubes, we have studied photoluminescence from individualized HiPco and CoMoCAT samples as a function of magnetic field (B) and temperature (T). In pulsed-field experiments (<60 T), we used film samples and varied T from 4.2 K to room temperature; photoluminescence intensity increased, or brightened,with B and the amount of brightening decreased with T. In steady-field experiments (<45 T), we used micelle-suspended nanotubes at room temperature; photoluminescence peaks showed B-induced splitting with B-dependent relative intensities. These results are consistent with the existence of a dark state below the first bright state [1]. Magnetic flux removes K-K valley degeneracy, producing two equally-bright states at high B [2,3]. We calculate photoluminescence spectra through B-dependent effective masses, populations of finite-k states, and acoustic phonon scattering.
Enhancing Response in the Cardiac Resynchronization Therapy Patient (2017)

Cardiac resynchronization therapy (CRT) is an established nonpharmacological treatment for patients with heart failure (HF), reduced left ventricular (LV) ejection fraction, and a wide QRS complex. Although the therapy was developed 30 years ago and approved by the Food and Drug Administration in 2001, attempts to improve it have never stopped. Such improvements have been facilitated by combining knowledge from bench (basic science), bits (computer modeling), and bedside (clinical studies); these issues are addressed in the present review. Improvements include better patient selection, positioning of the LV lead, pacing from multiple sites, and optimization of atrioventricular and ventriculo-ventricular intervals. Overall, patterns of electrocardiographic and echocardiographic (strain) signals appear to be more useful for patient selection than timing intervals (QRS duration, time-to-peak shortening). Quadripolar leads have significantly improved CRT outcome due to increased electrical and mechanical lead performance (avoiding phrenic nerve stimulation and improving lead stability), but also thanks to the flexibility offered by the novel leads to avoid in-scar pacing. The benefit of multiple site stimulation over optimal conventional biventricular pacing seems small and is awaiting evidence from large trials. There is rapidly growing interest in merging imaging information to guide positioning of the LV lead in late activated regions without scar and in LV lead positions other than the epicardial coronary veins (LV endocardium, His bundle, LV septum). All these developments look promising but await further clinical validation. Finally, computer modeling is rapidly becoming important in understanding the substrate for CRT, in improving and assisting patient selection, as well as in guiding therapy planning.
Immersive experimentation in a wave propagation laboratory (2013)

A wave propagation laboratory is proposed which enables the study of the interaction of broadband signals with complex materials. A physical experiment is dynamically linked to a numerical simulation in real time through transmitting and recording transducer surfaces surrounding the target. The numerical simulation represents an arbitrarily larger domain, allowing experiments to be performed in a total environment much greater than the laboratory experiment itself. Specific applications include the study of non-linear effects or wave propagation in media where the physics of wave propagation is not well understood such as the effect of fine scale heterogeneity on broadband propagating waves.
Kinematic Representations of Pop-Up Paper Mechanisms (2007)

Pop-up paper mechanisms use techniques very similar to the well-studied paper folding techniques of origami. However, popups differ in both the manner of construction and the target uses, warranting further study. This paper outlines the use of planar and spherical kinematics to model commonly used pop-up paper mechanisms. A survey of common joint types is given, including folds, interlocking slots, bends, pivots, sliders and rotating sliders. Also included is an overview of common onepiece and layered mechanisms, including single-slit, double-slit, V-fold, tent, tube strap and arch mechanisms. Each mechanism or joint is described using a kinematic or compliant mechanism representation. In addition, it is shown that more complex mechanisms may be created by combining simple mechanisms in various ways. The principles presented are applied to the creation of new pop-up joints and mechanisms. The new mechanisms employ both spherical and spatial kinematic chains. Various other applications are also mentioned which could benefit from the use of pop-up mechanism principles. Possible applications include deployable structures, packaging and instruments for minimally invasive surgery.
Development and manufacture of reactive-transfer-printed CIGS photovoltaic modules (2010)

In recent years, thin-film photovoltaic (PV) companies started realizing their low manufacturing cost potential, and grabbing an increasingly larger market share from multicrystalline silicon companies. Copper Indium Gallium Selenide (CIGS) is the most promising thin-film PV material, having demonstrated the highest energy conversion efficiency in both cells and modules. However, most CIGS manufacturers still face the challenge of delivering a reliable and rapid manufacturing process that can scale effectively and deliver on the promise of this material system. HelioVolt has developed a reactive transfer process for CIGS absorber formation that has the benefits of good compositional control, high-quality CIGS grains, and a fast reaction. The reactive transfer process is a two stage CIGS fabrication method. Precursor films are deposited onto substrates and reusable print plates in the first stage, while in the second stage, the CIGS layer is formed by rapid heating with Se confinement. High quality CIGS films with large grains were produced on a full-scale manufacturing line, and resulted in high-efficiency large-form-factor modules. With 14% cell efficiency and 12% module efficiency, HelioVolt started to commercialize the process on its first production line with 20 MW nameplate capacity.
Molecular scale deformation mechanisms in cellulose crystals (I and II) by molecular dynamics - synergy between covalent and hydrogen bonds (2015)

Molecular scale deformation mechanisms in cellulose crystals (I and II) by molecular dynamics - synergy between covalent and hydrogen bonds
The Challenge of Regulatory Compliance and Multiple Facility Upgrades - A Progressive System Approach (2012)

The Challenge of Regulatory Compliance and Multiple Facility Upgrades - A Progressive System ApproachThis paper describes the Business Case Evaluation (BCE) performed by Hampton Roads Sanitation District (HRSD) in the course of its Biosolids Resource and Recovery Master Plan Project. Given the numerous challenges, uncertainties, and risks affecting HRSD's biosolids management program, a progressive systems approach was taken to evaluate alternatives. Guiding principles ensured the final...Author(s)Jay BernasCharles BottRhonda BowenMark FeltnerJeff LayneMike ElenbaasJason De StigterLori StonePatricia ScanlanHari SanthaSourceProceedings of the Water Environment FederationDocument typeConference PaperPublisherWater Environment FederationPrint publication date Sep, 2012ISSN1938-6478DOI10.2175/193864712811703865Volume / Issue2012 / 7Content sourceWEFTECCopyright2012Word count158
Simultaneous Enhancement of Free Isoflavone Content and Antioxidant Potential of Soybean by Fermentation with Aspergillus oryzae (2011)

In order to determine the fungal strain and fermentation period which produce the highest antioxidant activity of fermented soy product, soybean was fermented with Aspergillus oryzae NL 5 isolated from Korean traditional meju produced in Sunchang Yeastopia Land in Korea, and was subjected to analyzing isoflavone profiles and assaying antioxidant activity. Antioxidant potential of the samples was evaluated by ferric reducing antioxidant power assay, 2,2'-azinobis (2-ethylbenzthiazoline-6-sulfonic acid) radical scavenging activity and total phenolic contents. In addition, antioxidant assay using fluorescent probes, 2',7'-dichlorofluorescin diacetate and dihydroethidium, in HepG2 cells was conducted for the samples. The results showed that both high isoflavone variety Aga 3 and medium isoflavone variety Daewon of soybean fermented with Asp oryzae NL5 for 4 to 5 d showed the highest increase in free isoflavone contents, together with the highest antioxidant activity. In conclusion, the antioxidant activity of fermented soy was proportional to the concentration of free isoflavones, and was significantly influenced by total isoflavone content of soybean variety and fermentation period. Practical Application: Isoflavone profile and antioxidant capacity of soybean were widely variable during fermentation with Asp oryzae, and thereby it is recommended that meju (or koji) preparation condition, in particular, fermentation time is carefully optimized to maximize the antioxidant capacity of soy products fermented by Asp oryzae.
Optimization criteria for checkpoint placement (1984)

Mean response time and availability as optimization criteria for checkpoint placement are better replaced by workable formulas that calculate the ratio between the marginal gain accrued to users who experience system failure and the (presumably slight) loss suffered on average by all users.
CONTROL OF A HELICOPTER MAIN GEARBOX ACTIVE SUSPENSION SYSTEM (2014)

International audience
Two Novel Resveratrol Trimers from Dipterocarpus grandiflorus (2009)

Abstract magnified image Two new resveratrol (=5‐[( E )‐2‐(4‐hydroxyphenyl)ethenyl]benzene‐1,3‐diol) trimers, grandiphenols C ( 1 ) and D ( 2 ), were isolated from the stem of Dipterocarpus grandiflorus (Dipterocarpaceae). The structures of 1 and 2 were elucidated by spectral analysis including 1D‐ and 2D‐NMR experiments and by computer‐aided molecular modeling. The NMR characteristics caused by the steric hindrance and the biogenetic relationship of the isolates are also discussed in this work.
Polygonization of remote sensing classification maps by mesh approximation (2017)

The ultimate goal of land mapping from remote sensing image classification is to produce polygonal representations of Earth's objects, to be included in geographic information systems. This is most commonly performed by running a pixelwise image classifier and then polygonizing the connected components in the classification map. We here propose a novel polygonization algorithm, which uses a labeled triangular mesh to approximate the input classification maps. The mesh is optimized in terms of an l <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">1</sub> norm with respect to the classifiers's output. We use a rich set of optimization operators, which includes a vertex relocator, and add a topology preservation strategy. The method outperforms current approaches, yielding better accuracy with fewer vertices.
Large-cell and immunoblastic lymphoma of the mediastinum: prognostic features and treatment outcome in 57 patients. (1993)

Patients with primary mediastinal large-cell and immunoblastic lymphoma have an approximate 50% chance of surviving disease-free after initial therapy. The presence of pleural effusion at presentation was associated with an extremely poor outcome. Bulk disease per se was a negative predictive factor only in patients without pleural effusions when compared with patients who did not have bulk disease. In addition, all patients with involvement of two or more extranodal sites relapsed when treated with standard chemotherapy.
1-Substituted (Dibenzo[b,d]thiophen-4-yl)-2-morpholino-4H-chromen-4-ones Endowed with Dual DNA-PK/PI3-K Inhibitory Activity (2013)

Analogues of (dibenzo[b,d]thiophen-4-yl)-2-morpholino-4H-chromen-4-one (NU7441), a potent inhibitor of DNA-dependent protein kinase (DNA-PK; IC50 = 42 ± 2 nM), have been synthesized in which water-solubilizing groups [NHCO(CH₂)nNR¹R², where n = 1 or 2 and the moiety R¹R²N was derived from a library of primary and secondary amines, e.g., morpholine] were placed at the 1-position. Several of the newly synthesized compounds exhibited high potency against DNA-PK and potentiated the cytotoxicity of ionizing radiation (IR) in vitro 10-fold or more (e.g., 2-(4-ethylpiperazin-1-yl)-N-(4-(2-morpholino-4-oxo-4H-chromen-8-yl)dibenzo[b,d]thio-phen-1-yl)acetamide, 39; DNA-PK IC₅₀ = 5.0 ± 1 nM, IR dose modification ratio = 13). Furthermore, 39 was shown to potentiate not only IR in vitro but also DNA-inducing cytotoxic anticancer agents, both in vitro and in vivo. Counter-screening against other members of the phosphatidylinositol 3-kinase (PI-3K) related kinase (PIKK) family unexpectedly revealed that some of the compounds were potent mixed DNA-PK and PI-3K inhibitors.
SPIRO: Turning elephants into mice with efficient RF transport (2015)

Cloud-RANs (Radio Access Networks) assume the existence of a high-capacity, low-delay/latency fronthaul to support cooperative transmission schemes such as CoMP (Coordinated Multi-Point) and coordinated beamforming. However, building such hierarchical wired fronthauls is challenging as the typical I/Q data stream is non-elastic - I/Q data over the wired fronthaul has little tolerance for delay jitters and zero tolerance for losses. Any distortion to the I/Q data stream will make the resulting wireless transmission completely unintelligible. We propose Spiro, a mechanism that efficiently transports RF signals over a wired fronthaul network. The primary goal of Spiro is to make I/Q data streams elastic and resilient to unexpected network condition changes. This is accomplished through a novel combination of compression and data prioritization of I/Q data on the wired fronthaul. For a given wireless throughput, Spiro can reduce the bandwidth demand of the fronthaul data stream by up to 50% without any noticeable degradation in the wireless reception quality. Further bandwidth reduction via compression and frame losses only have a limited impact on the wireless throughput.
Droplet deformation and alignment for high-efficiency polarization-dependent holographic polymer-dispersed liquid-crystal reflection gratings (2008)

Droplet deformation and alignment are achieved in holographic polymer-dispersed liquid-crystal reflection gratings by applying an in situ shear during recording. High diffraction efficiency (99%) is obtained for light polarized parallel to the shear, with nearly zero efficiency for perpendicular polarization, and no increase of incoherent scattering. Permanent polarization dependence is related to stress-induced morphology changes of liquid-crystal droplets that are frozen by polymerization. The system is studied by electron microscopy and modeled by anisotropic coupled-wave and scattering theory. The morphology is consistent with the theory of small deformations of liquid droplets in fluid flow. Diffraction efficiency measurements are in agreement with theory incorporating this morphology as well as concomitant orientation and alignment of liquid-crystal molecules.
Understanding Mid-Air Hand Gestures: A Study of Human Preferences in Usage of Gesture Types for HCI (2012)

In this paper we present the results of a study of human preferences in using mid-air gestures for directing other humans. Rather than contributing a specific set of gestures, we contribute a set of gesture types, which together make a set of the core actions needed to complete any of our six chosen tasks in the domain of human-to-human gestural communication without the speech channel. We observed 12 participants, cooperating to accomplish different tasks only using hand gestures to communicate. We analyzed 5,500 gestures in terms of hand usage and gesture type, using a novel classification scheme which combines three existing taxonomies in order to better capture this interaction space. Our findings indicate that, depending on the meaning of the gesture, there is preference in the usage of gesture types, such as pointing, pantomimic acting, direct manipulation, semaphoric, or iconic gestures. These results can be used as guidelines to design purely gesture driven interfaces for interactive environments and surfaces.
Evidence against insulin-stimulated phosphorylation of calmodulin in 3T3-L1 adipocytes (1989)

To examine the possibility that insulin might stimulate calmodulin phosphorylation in intact cells, we compared autoradiographs of two-dimensional gels of [35S]methionine- and 32P-labeled proteins from 3T3-L1 adipocytes, before and after immunoprecipitation with anti-calmodulin antiserum. Insulin stimulated the phosphorylation of one or two proteins of approximately 22 kDa and pI 4.6; this increased phosphorylation was accompanied by an apparent shift in the position of the analogous [35S]methionine-labeled proteins towards the anode. In contrast, insulin had no effect on the phosphorylation state of another protein of 18-22 kDa and pI 4.6. This protein was very heavily labeled with [35S]methionine, co-migrated exactly with purified calmodulin, reacted specifically with two anti-calmodulin antibodies by Western blotting, and was specifically immunoprecipitated with the anti-calmodulin antiserum. Similar amounts of [35S]methionine-labeled calmodulin were immunoprecipitated from control and insulin-stimulated cells, arguing against the possibility that insulin-stimulated phosphorylation of calmodulin changed its affinity for the antibody. We conclude that calmodulin is phosphorylated to a negligible extent in serum-deprived 3T3-L1 adipocytes and that insulin does not stimulate its phosphorylation under conditions in which it stimulates the phosphorylation of one or more neighboring proteins.
Causes of impaired biventricular pacing in cardiac resynchronization devices with left ventricular sensing (2020)

Inadequate programming (active LV sensing with T-wave protection) is the main cause of impaired resynchronization in devices with LV sensing. In general, we recommend the deactivation of the LV T-wave protection function.
Generative models for molecular discovery: Recent advances and challenges (2022)

Abstract Development of new products often relies on the discovery of novel molecules. While conventional molecular design involves using human expertise to propose, synthesize, and test new molecules, this process can be cost and time intensive, limiting the number of molecules that can be reasonably tested. Generative modeling provides an alternative approach to molecular discovery by reformulating molecular design as an inverse design problem. Here, we review the recent advances in the state‐of‐the‐art of generative molecular design and discusses the considerations for integrating these models into real molecular discovery campaigns. We first review the model design choices required to develop and train a generative model including common 1D, 2D, and 3D representations of molecules and typical generative modeling neural network architectures. We then describe different problem statements for molecular discovery applications and explore the benchmarks used to evaluate models based on those problem statements. Finally, we discuss the important factors that play a role in integrating generative models into experimental workflows. Our aim is that this review will equip the reader with the information and context necessary to utilize generative modeling within their domain. This article is categorized under: Data Science &gt; Artificial Intelligence/Machine Learning
Supplemental Figure 5 from Short- and Long-Term Effects of CDK4/6 Inhibition on Early-Stage Breast Cancer (2023)

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5-Octave Laser Source Based on Cr: ZnS-GaSe Tandem (2019)

We report laser architecture that enables generation of coherent femtosecond continua that span from visible to long-wave IR (0.5-18 μm), and features: high power (4W), high repetition rate (80 MHz), and intrinsic nonlinear interferometry. © 2019 The Author(s)