gebhart/patrepeval huggingface dataset:
Multi-well fungal co-culture for de novo metabolite-induction in time-series studies based on untargeted metabolomics (2014)

The induction of fungal metabolites by fungal co-cultures grown on solid media was explored using multi-well co-cultures in 2 cm diameter Petri dishes. Fungi were grown in 12-well plates to easily and rapidly obtain the large number of replicates necessary for employing metabolomic approaches. Fungal culture using such a format accelerated the production of metabolites by several weeks compared with using the large-format 9 cm Petri dishes. This strategy was applied to a co-culture of a Fusarium and an Aspergillus strain. The metabolite composition of the cultures was assessed using ultra-high pressure liquid chromatography coupled to electrospray ionisation and time-of-flight mass spectrometry, followed by automated data mining. The de novo production of metabolites was dramatically increased by nutriment reduction. A time-series study of the induction of the fungal metabolites of interest over nine days revealed that they exhibited various induction patterns. The concentrations of most of the de novo induced metabolites increased over time. However, interesting patterns were observed, such as with the presence of some compounds only at certain time points. This result indicates the complexity and dynamic nature of fungal metabolism. The large-scale production of the compounds of interest was verified by co-culture in 15 cm Petri dishes; most of the induced metabolites of interest (16/18) were found to be produced as effectively as on a small scale, although not in the same time frames. Large-scale production is a practical solution for the future production, identification and biological evaluation of these metabolites.
The Cloning of Mouse Globin and Surrounding Gene Sequences in Bacteriophage (1978)

We have developed a rather straightforward procedure that brings virtually any segment of the mammalian genome within cloning range of a very versatile EK2 bacteriophage λ vector. We illustrate the procedure in terms of cloning a segment of the mouse genome containing a β-like globin gene and its surrounding sequences. Surprisingly, the sequence cloned does not contain a continuous representation of the globin messenger RNA (mRNA) sequence, but instead is interrupted about two-thirds through by an approximately 550-base-long intervening sequence. The significance of this structure and its possible generality are discussed together with the notion that single polypeptide chains may be encoded by discrete and separate gene sequences.
Current and Foreseeable Applications of Supercritical Water for Energy and the Environment (2008)

It is crucial to develop economical and energy-efficient processes for the sustainable transformation of biomass into fuels and chemicals. In this context, supercritical water biomass valorization (SCBV) processes are an alternative way to produce biogas, biofuels, and valuable chemicals. Supercritical water technology has seen much progress over the last fifteen years and an industrial application has merged: the supercritical water oxidation of wastes. The evolution from lab-scale to pilot-scale facilities has provided data on reaction mechanisms, kinetics, modeling, and reactor technology as well as an important know-how, which can now be exploited to use the reactivity in supercritical water to transform biomass into gases (CO, H(2), CO(2), CH(4), and N(2)) or into liquids (liquid fuel and valuable chemicals) with the supercritical water biomass gasification and liquefaction processes, respectively. This Review highlights the potential of SCBV processes to transform biomass into gas and liquid energy sources and highlights the developments that are still necessary to push this technology onto the market.
Acoustic radiation force for vascular stem cell therapy: An in vitro validation (2011)

Coronary stent placement and angioplasty may lead to vascular injury such as postprocedural stent thrombosis and restenosis. Mesenchymal stem cells (MSCs) have been reported to participate in effective restoration of functional endothelium following vascular injury. Our group has recently investigated a new technique for the delivery of MSCs to a site of arterial injury which involved surface-coating MSCs with cationic lipid microbubbles (MB) and directing them to target areas using acoustic radiation force (ARF). The objective of this study was to characterize ultrasound parameters for effective MSC delivery through in vitro experiments in which MB-labeled MSCs flowing through a phantom vessel were radially displaced towards the vessel wall using ARF applied with an intravascular ultrasound catheter driven at varying acoustic pressures and duty cycles. Experimental data indicated that MSC radial velocity was linearly related to the time-averaged ultrasound intensity up to 0.83 W/cm <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sup> . Experimental data agreed with model predictions only up to this intensity level possibly due to MB destruction before the MB-MSC complexes reached the target area at high acoustic pressures. MSC adhesion to the phantom vessel wall increased with the time-averaged ultrasound intensity up to 1.65 W/cm <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sup> , after which further adhesion did not occur. Using higher time-averaged ultrasound intensities may not substantially benefit the adhesion of complexes to the target vessel wall, but could cause undesirable biological effects such as heating to the MB-MSC complexes and surrounding tissue.
Creating an Interactive Light Studio for the American Sign Language and English Lower School (2011)

The Cooper Union for the Advancement of Science and Art created an Interactive Light Studio for pre-kindergarten students at The American Sign Language and English Lower School (P.S. 347) in New York City. Specific goals included designing a space for science exploration and creating ways for both deaf and hearing students to explore light and sound. Deaf and hearing impaired students, in particular, benefit from the design of a sound-to-light installation that uses microphones to provide visual feedback. Another installation includes a network of circuits, which imitate the interaction of fireflies when placed in various configurations by the children. The Interactive Light Studio promotes science to young children and engages a diverse student population in science and engineering. The project offers undergraduate engineering students an opportunity to improve their technical and professional skills and develop a broader appreciation of the role of engineers in bettering society.
Online high-efficiency haemodiafiltration achieves higher serum free light chain removal than high-flux haemodialysis in multiple myeloma patients: preliminary quantitative study (2011)

This preliminary quantitative study demonstrates the superiority of high-efficiency HDF over high-flux HD for serum FLC removal in multiple myeloma patients on RRT. No negative impact on total plasma proteins was noted.
Achieving balanced execution through runtime detection of performance variation (2023)

Systems, apparatuses, and methods for achieving balanced execution in a multi-node cluster through runtime detection of performance variation are described. During a training phase, performance counters and an amount of time spent waiting for synchronization is monitored for a plurality of tasks for each node of the multi-node cluster. These values are utilized to generate a model which correlates the values of the performance counters to the amount of time spent waiting for synchronization. Once the model is built, the values of the performance counters are monitored for a period of time at the start of each task, and these values are input into the model. The model generates a prediction of whether a given node is on the critical path. If the given node is predicted to be on the critical path, the power allocation of the given node is increased.
Pharmacotherapy for stress urinary incontinence. (2003)

The purpose of this review article is to highlight new pharmacotherapies on the horizon for the treatment of stress urinary incontinence. Although behavioral and surgical therapies are currently the mainstay of treatment for this condition, we are hopeful that pharmacotherapy will one day take center stage of the various treatment options. Currently, there are no medications approved by the US Food and Drug Administration for the treatment of stress urinary incontinence. However, exciting clinical data are becoming available about an oral medication for the treatment of stress urinary incontinence that appears to be clinically safe and efficacious. In addition to discussing medications currently under development, this article also discusses pharmacologic targets that could be suitable future targets to treat stress urinary incontinence.
ChemInform Abstract: C—H Bond Functionalizations with Palladium(II): Intramolecular Oxidative Annulations of Arenes. (2008)

Abstract ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 200 leading journals. To access a ChemInform Abstract of an article which was published elsewhere, please select a “Full Text” option. The original article is trackable via the “References” option.
Protein-Based Nanoparticle Preparation via Nanoprecipitation Method (2018)

Nanoparticles are nowadays largely investigated in the field of drug delivery. Among nanoparticles, protein-based particles are of paramount importance since they are natural, biodegradable, biocompatible, and nontoxic. There are several methods to prepare proteins containing nanoparticles, but only a few studies have been dedicated to the preparation of protein- based nanoparticles. Then, the aim of this work was to report on the preparation of bovine serum albumin (BSA)-based nanoparticles using a well-defined nanoprecipitation process. Special attention has been dedicated to a systematic study in order to understand separately the effect of each operating parameter of the method (such as protein concentration, solvent/non-solvent volume ratio, non-solvent injection rate, ionic strength of the buffer solution, pH, and cross-linking) on the colloidal properties of the obtained nanoparticles. In addition, the mixing processes (batch or drop-wise) were also investigated. Using a well-defined formulation, submicron protein-based nanoparticles have been obtained. All prepared particles have been characterized in terms of size, size distribution, morphology, and electrokinetic properties. In addition, the stability of nanoparticles was investigated using Ultraviolet (UV) scan and electrophoresis, and the optimal conditions for preparing BSA nanoparticles by the nanoprecipitation method were concluded.
Requirement Considerations for Ubiquitous Integration of Cooperating Objects (2011)

Billions of devices are expected to be online by 2020. These will not only provide information by monitoring the real-world, but create complex collaborations in order to provide sophisticated value-added services. Slowly, we are witnessing the emergence of Cooperating Objects in the Internet of Things, which will rapidly change the way we design, develop and realize cyber-physical dependent applications. We investigate which requirements this poses, and evaluate several middleware systems which we have used in the past. Finally we prioritize the requirements, and discuss on future directions that could be followed.
Ultracapacitor Performance of Reduced Graphene Oxide - Silica Composite (2011)

Graphene's unique properties show great promise for ultracapacitor applications. However, increasing the surface area available to electrolyte to increase the specific capacitance remains a challenge. In this paper we report on a method to synthesize a reduced graphene oxide-silica nanoparticle composite followed by etching with hydrofluoric acid. The composite and the etched samples were characterized using scanning electron microscopy, transmission electron microscopy and X-ray photoelectron spectroscopy. Nitrogen adsorption and capacitance measurements indicated an increase in the specific surface area and the specific capacitance in the post-etched samples suggesting that the silica nanoparticles act as a sacrificial jamming agent.
Distributed effects model for cascaded traveling-wave electroabsorption modulator (2001)

A distributed model based on the large-signal electrooptic conversion is proposed to analyze cascaded traveling-wave electroabsorption modulators (TWEAMs) for high-speed optical switching applications. The microwave propagation loss, velocity mismatch, as well as frequency chirping are included. The model predicts that a cascaded TWEAM structure has the advantage of a high design tolerance to various distributed effects and an improved extinction ratio and optical loss in comparison to a single device of same total length. The agreement between experimental and calculated results indicates that the cascaded structures can be implemented for efficient TWEAM design.
Recent developments in high-moment electroplated materials for recording heads (2005)

The continuous and rapid increase of areal density in magnetic data storage systems required a continuous increase of the coercivity of the storage media. In order to be able to record on these ever-higher-coercivity media, new soft magnetic materials for pole tips with increased magnetic moment had to be developed. Significant progress has been made during the last few years in electroplating alloys with high saturation magnetic flux density for use in writing heads. We review recent progress made in this area, with particular emphasis on the work done at IBM since the review paper on the subject was published in this journal in 1998 by Andricacos and Robertson. Reviewed here are the high-moment alloys of NiFe, particularly in the very high iron range [an extension of permalloy (Ni <inf xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">80</inf> Fe <inf xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">20</inf> ) and Ni <inf xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">45</inf> Fe <inf xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">55</inf> ]; very-high-cobalt CoFeCu alloys; ternary CoNiFe; and binary iron-rich CoFe alloys. With the latter binary alloy films, we have demonstrated that it is possible to reach by electroplating the saturation flux density limit of 2.4—2.5 T reported for cast alloys. Since the electroplating of good-magnetic-quality iron-rich CoFe alloys posed a considerable challenge, the behavior of the CoFe plating system was studied in detail, using in situ surface pH measurements and a rotating-cylinder Hull cell.
25.3 A 128b AES Engine with Higher Resistance to Power and Electromagnetic Side-Channel Attacks Enabled by a Security-Aware Integrated All-Digital Low-Dropout Regulator (2019)

Side channel attacks (SCA) exploit data-dependent information leakage through power consumption and electromagnetic (EM) emissions from cryptographic engines to uncover secret keys. Integrated inductive voltage regulators (IVR) with a randomized control loop [1] or switching frequency [2], and random voltage dithering [3] have demonstrated improved power side-channel analysis (PSCA) resistance. Simulation studies have shown PSCA resistance via shunt linear regulators [4]. This paper demonstrates improved power and EM SCA resistance of standard (unprotected) 128b AES engines with parallel (P-AES, 128b) and serial (S-AES, 8b) datapaths via an on-die security-aware all-digital series low-dropout (DLDO) regulator, commonly used for fine-grain SoC power management. The security-aware DLDO improves SCA resistance using control-loop induced perturbations in a baseline DLDO, enhanced by a random switching noise injector (SNI) via power stage control and a randomized reference voltage (R-VREF) generator coupled with all-digital clock modulation (ADCM).
A Robust and Fast Algorithm for Quantifying Spinal Cord Cross-sectional Area in Myelitis (P6.136) (2014)

OBJECTIVE: Develop a new MRI based method for quantifying the cross-sectional area of the spinal cord along the length of the entire cord. BACKGROUND: Several neurodegenerative diseases, such as multiple sclerosis (MS) and human T-cell lymphotropic virus-1 associated myelopathy/tropical spastic paraparesis (HAM/TSP), are associated with a progressive myelitis. MRI of the spinal cord often shows spinal cord thinning in such diseases. Here we present a robust and fast algorithm to quantify spinal cord cross-sectional area (SCCSA) along the length of the cord to better characterize myelitis. DESIGN/METHODS: MRI was performed on 18 HAM/TSP, 9 MS, and 10 healthy volunteers (HV) on a Siemens 3T Skyra system equipped with head-neck and spine array coils. On 3D T1-weighted images (GRE, TR/TE= 7.8/3ms, FA=16deg), SCCSA was measured perpendicular to the cord edge along multiple points from C1 to T10 and was normalized to the cord length. Clinical scores of disability, including Scripps Neurologic Rating Scale (SNRS), Extended Disability Status Scale (EDSS), Hauser Ambulation Index (AI), were measured in patients. SCCSA patterns were compared between groups (ANOVA) and correlated with disability scores in patients. RESULTS: SCCSA from MS patients were significantly smaller in the T-spine when compared to HV (p<0.001). SCCSA in the cervical cord in MS tended to be lower, but did not reach significance in the small group studied herein. In HAM/TSP patients, SCCSA was significantly lower than HV in both the C- and T-spine (p<0.0001). SCCSA in MS patients was significantly correlated with SNRS (C1-C5, T1-T7) and EDSS (C1-C3, T1-T6), whereas the SCCSA in HAM/TSP patients was correlated with disease duration (C1-C3, C6, T1-T2), EDSS (T2), and AI (T2, T6). CONCLUSIONS: These results suggest that the pattern of spinal cord tissue damage is specific to the underlying inflammatory disease. Our method could be used not only to develop an imaging marker for disease, but also to serve as a surrogate end point in clinical trials. Study Supported by: Intramural NIH
ChemInform Abstract: A Short Synthesis of (‐)‐Dendrobine. Some Observations on the Nickel‐Mediated Radical Cyclization and on the Pauson—Khand Reaction. (2001)

Abstract ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 100 leading journals. To access a ChemInform Abstract of an article which was published elsewhere, please select a “Full Text” option. The original article is trackable via the “References” option.
Free-Standing Hierarchically Sandwich-Type Tungsten Disulfide Nanotubes/Graphene Anode for Lithium-Ion Batteries (2014)

Transition metal dichalcogenides (TMD), analogue of graphene, could form various dimensionalities. Similar to carbon, one-dimensional (1D) nanotube of TMD materials has wide application in hydrogen storage, Li-ion batteries, and supercapacitors due to their unique structure and properties. Here we demonstrate the feasibility of tungsten disulfide nanotubes (WS2-NTs)/graphene (GS) sandwich-type architecture as anode for lithium-ion batteries for the first time. The graphene-based hierarchical architecture plays vital roles in achieving fast electron/ion transfer, thus leading to good electrochemical performance. When evaluated as anode, WS2-NTs/GS hybrid could maintain a capacity of 318.6 mA/g over 500 cycles at a current density of 1A/g. Besides, the hybrid anode does not require any additional polymetric binder, conductive additives, or a separate metal current-collector. The relatively high density of this hybrid is beneficial for high capacity per unit volume. Those characteristics make it a potential anode material for light and high-performance lithium-ion batteries.
Abstract 462: A novel and potent Cblb inhibitor demonstrates robust immunological profile and anti-tumor efficacy (2023)

Abstract Background: Casitas B-lineage lymphoma b (Cbl-b), a RING finger E3 ligase, is a negative regulator of immune cell activation1. Genetic deletion or pharmacological inhibition of Cbl-b resulted in hyper-reactive and co-stimulation independent T cell activation and cytokine production1. In syngeneic tumor models, CD8 T-cell and NK-cell mediated rejection of tumours were observed1. These findings point to Cbl-b as a therapeutic target in cancer immunotherapy. Inhibition of Cbl-b also demonstrated the potential to enhance the efficacy of check-point blockers like anti-PD-1 antibody, an unmet need in the clinic. Methods: Using intuitive medicinal chemistry design supported by computational approaches, we identified a lead Cbl-b inhibitor. SAR was developed using a battery of biochemical assays, functional read-outs and primary human in vitro T-cell activation and exhaustion assays. In vivo efficacy was demonstrated in syngeneic mouse colon tumor model. Results: Our lead Cbl-b inhibitor demonstrated potent binding to Cbl-b, robust anti-tumor cytokine secretion in human and mouse T cells, whole blood and potent reversal of T cell exhaustion. A strong tumor growth inhibition was demonstrated by the lead compound in a mouse colon tumor model. Compared to single agent, a combination of the lead compound with anti-PD-1 antibody induced enhanced complete tumor rejections. Conclusions: We have identified a novel, potent and orally bioavailable Cbl-b inhibitor that demonstrated robust in vitro and in vivo anti-tumor profiles. Acknowledgements: We thank Sanjib Das, Ajit Patil, Gauri Gawas, Savita Pandita, Priya Yadav, Sneha Pusadkar, Mayura Behere, Subhadip Das, Shravankumar Kolli and Radheshyam Yadav for their contributions to the project References: 1. Clinical and Experimental Immunology, 204: 14-31, 2020 Citation Format: Murugan Chinnapattu, Sandeep Shelke, Prashant Ingale, Nayan Waghmare, Nanasaheb Kadlag, Manoj Pawar, Akshay Kangane, Sachin S. Chaudhari, Jagmohan Saini, Vidya Kattige, Arti Joshi, Colina Dutta, Debjyoti Boral, Sheetal Kadam, Varada Potdar, Jiju Mani, Pooja Sawant, Megha Marathe, Madhavi Mulay, Akshata Virdikar, Sravan Mandadi, Atul Akarte, Anuj Singh, Chandrasekhar Misra, Pandurang Lambade, Chaitanya Tirumalasetty, Raju Patole, Vikas Karande, Dayanidhi Behera, Pankaj Jain, Vishwanath Kurawattimath, Nagaraj Gowda, Pravin S. Iyer. A novel and potent Cblb inhibitor demonstrates robust immunological profile and anti-tumor efficacy [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 462.
Faculty Opinions recommendation of Solution structure of an intramolecular (3 + 1) human telomeric G-quadruplex bound to a telomestatin derivative. (2013)

Guanine-rich human telomeric DNA can adopt secondary structures known as G-quadruplexes, which can be targeted by small molecules to achieve anticancer effects. So far, the structural information on complexes between human telomeric DNA and ligands is limited to the parallel G-quadruplex conformation, despite the high structural polymorphism of human telomeric G-quadruplexes. No structure has been yet resolved for the complex with telomestatin, one of the most promising G-quadruplex-targeting anticancer drug candidates. Here we present the first high-resolution structure of the complex between an intramolecular (3 + 1) human telomeric G-quadruplex and a telomestatin derivative, the macrocyclic hexaoxazole L2H2-6M(2)OTD. This compound is observed to interact with the G-quadruplex through π-stacking and electrostatic interactions. This structural information provides a platform for the design of topology-specific G-quadruplex-targeting compounds and is valuable for the development of new potent anticancer drugs. PMID: 23909929