gebhart/patrepeval huggingface dataset:
Nonlinear Dynamics of Electrokinetic Instabilities (2005)

Electrokinetic instabilities are generated by a coupling of electric fields and ionic conductivity gradients. This coupling results in an electric body force in the bulk liquid that can generate temporal, convective, and absolute flow instabilities. In this work, we perform a parametric experimental study of convective instabilities in cross-shaped microchannels using epifluorescence microscopy and high speed digital imaging. We report temporal power spectra and spatiotemporal maps as a function of the applied field. The spectral analyses reveal that disturbances induced by electrokinetic instability are purely sinuous at the onset of instability and exhibit higher-order harmonics, frequency bifurcations, and continuous power spectra with increasing electric Rayleigh number. Electrokinetic instabilities (EKI) in cross-shaped channels are relevant to injections for field amplified sample stacking, electrokinetic flows at the intersections in multi-dimensional assay devices, and systems with indeterminate sample chemistry.
Supplementary Figure 4 from A Chimeric Switch-Receptor Targeting PD1 Augments the Efficacy of Second-Generation CAR T Cells in Advanced Solid Tumors (2023)

&lt;p&gt;Ex-vivo killing of and cytokine secretion in response to tumor targets by TILs isolated from EMMESO flank tumors.&lt;/p&gt;
Crowdsourced mapping of unexplored target space of kinase inhibitors (2021)

Despite decades of intensive search for compounds that modulate the activity of particular protein targets, a large proportion of the human kinome remains as yet undrugged. Effective approaches are therefore required to map the massive space of unexplored compound-kinase interactions for novel and potent activities. Here, we carry out a crowdsourced benchmarking of predictive algorithms for kinase inhibitor potencies across multiple kinase families tested on unpublished bioactivity data. We find the top-performing predictions are based on various models, including kernel learning, gradient boosting and deep learning, and their ensemble leads to a predictive accuracy exceeding that of single-dose kinase activity assays. We design experiments based on the model predictions and identify unexpected activities even for under-studied kinases, thereby accelerating experimental mapping efforts. The open-source prediction algorithms together with the bioactivities between 95 compounds and 295 kinases provide a resource for benchmarking prediction algorithms and for extending the druggable kinome.
In-depth genetic analysis ofClostridiumdifficilePCR-ribotype 027 strains reveals high genome fluidity including point mutations and inversions (2010)

Previously, we demonstrated that the recently evolved PCR-ribotype 027 hypervirulent Clostridium difficile strain (R20291) has acquired five genetic regions compared to the historic 027 counterpart strain (CD196), that may in part explain phenotypic traits relating to survival, antimicrobial resistance and virulence. Closer scrutiny of the three genome sequences reveals that, in addition to gene gain/loss, point mutations and inversions appear to have accumulated. Inversions are located upstream of potential coding sequences and could affect expression of these. C. difficile has a highly fluid genome with multiple mechanisms to modify its genetic content and is continuing to evolve in our hospitals influenced by environmental changes and human activity.
Functional specialization of hippocampal somatostatin-expressing interneurons (2023)

Hippocampal somatostatin-expressing (<i>Sst</i>) GABAergic interneurons (INs) exhibit considerable anatomical and functional heterogeneity. Recent single cell transcriptome analyses have provided a comprehensive <i>Sst</i>-IN subtype census, a plausible molecular ground truth of neuronal identity whose links to specific functionality remain incomplete. Here, we designed an approach to identify and access subpopulations of <i>Sst</i>-INs based on transcriptomic features. Four mouse models based on single or combinatorial Cre- and Flp- expression differentiated functionally distinct subpopulations of CA1 hippocampal <i>Sst</i>-INs that largely tiled the morpho-functional parameter space of the <i>Sst</i>-INs superfamily. Notably, the <i>Sst;;Tac1</i> intersection revealed a population of bistratified INs that preferentially synapsed onto fast-spiking interneurons (FS-INs) and were both necessary and sufficient to interrupt their firing. In contrast, the <i>Ndnf;;Nkx2-1</i> intersection identified a population of oriens lacunosum-moleculare (OLM) INs that predominantly targeted CA1 pyramidal neurons, avoiding FS-INs. Overall, our results provide a framework to translate neuronal transcriptomic identity into discrete functional subtypes that capture the diverse specializations of hippocampal <i>Sst</i>-INs.
Smart battery concept: A battery that can breathe (2022)

Lithium-ion batteries are used in a wide range of applications such as electric vehicles and energy storage systems. However, the aging of the battery cell is inevitable. Especially for battery packs with hundreds of battery cells connected in series/parallel, the aging process will be aggravated due to the difference between battery cells, leading to a limited lifetime and reliability issues. This paper introduces the concept of Smart Battery that combines advanced power electronics and artificial intelligence (AI) intending to develop a new generation of battery solutions for transportation and grid storage. The key feature for controlling the lifetime is the bypass device, a half-bridge that can control individual cell-level load management without affecting the load. An advanced AI-based lifetime controller is trained to recognize the signs of stressed battery cells and decide to insert rest time, resulting in a pulsed current operation. Finally, the following features are expected to be achieved: increased safety and reliability by fault-tolerant operation, user-controlled lifetime, and software reconfiguration for 2nd life applications. The early experimental results are promising, showing cycle lifetime extension over 50%.
ChemInform Abstract: Covalent C=N Bond Hydration in Heteroaromatic Compounds — Chemical and Biological Aspects (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.
ETV6 Deficiency and Microsatellite Enhancers Drive Transcriptional Dysregulation in B-Lymphoblastic Leukemia (2022)

Abstract Distal enhancers play critical roles in sustaining oncogenic gene expression programs. We identify aberrant enhancer-like activation of GGAA tandem repeats as a characteristic feature of B-cell acute lymphoblastic leukemia (B-ALL) with genetic defects of the ETV6 transcriptional repressor, including ETV6-RUNX1 + and ETV6 -null B-ALL. We show that GGAA repeat enhancers are direct activators of previously identified ETV6-RUNX1 + B-ALL “signature” genes, including likely oncogenic drivers. When restored to ETV6-deficient B-ALL cells, ETV6 directly binds to GGAA repeat enhancers, represses their acetylation, downregulates adjacent genes, and inhibits B-ALL growth. In ETV6-deficient B-ALL cells, we find that the ETS transcription factor ERG directly binds to GGAA microsatellite enhancers and is required for sustained activation of many repeat enhancer-activated genes. Together, our findings reveal a novel epigenetic gatekeeper function of the ETV6 tumor suppressor gene and establish microsatellite enhancers as a key mechanism underlying the unique gene expression program of ETV6-RUNX1 + B-ALL. Significance We show that the oncogenic gene expression program of a common pediatric leukemia relies on repetitive noncoding elements that are not conserved between humans and rodents, placing important limitations on animal models for this disease. Our findings may present new opportunities for targeting cancer-specific chromatin dysregulation in leukemia.
Capillary Electrophoresis Frontal Analysis for Characterization of αvβ3 Integrin Binding Interactions (2008)

The specific binding characteristics of alphavbeta3 integrins with an arginine-glycine-aspartic-acid (RGD) containing fluorescently labeled cyclic peptide is investigated with capillary electrophoresis-frontal analysis method. The new algorithm used to calculate the binding constants and binding stoichiometry was derived without the assumptions made in the commonly used Scatchard Plot method, thus enabling the determination of specific binding parameters in the presence of nonspecific binding. The alphavbeta3 integrin, a membrane protein, was studied in solution, without the need of immobilization or any other kind of modification. An RGD containing fluorescently labeled cyclic pentapeptide is used as the ligand with both specific and nonspecific binding characteristics, and an arginine-alanine-aspartic-acid (RAD) containing peptide is used as the control for nonspecific binding. While a typical specific binding isotherm has a shape of a rectangular hyperbola, a nonspecific binding isotherm is linear in the same ligand concentration region. A 1:2 specific binding stoichiometry was revealed with the second binding having a similar affinity compared to the first binding event.
Figure S11 from A Phase II Trial of Guadecitabine plus Atezolizumab in Metastatic Urothelial Carcinoma Progressing after Initial Immune Checkpoint Inhibitor Therapy (2023)

&lt;p&gt;Supplementary Figure 11: Peripheral immune cells are activated mid-treatment cycle.&lt;/p&gt;
Illumination sources based on multiple light-emitting diodes (2004)

Luminous efficacies and color rendering capabilities of illumination sources based on tri- and tetra-chromatic light-emitting diodes (LEDs) are investigated. Tri-chromatic sources with a CRI of 84 and a luminous efficiency of 32 Im/W are demonstrated.
Mid-infrared optical properties of thin films of aluminum oxide, titanium dioxide, silicon dioxide, aluminum nitride, and silicon nitride (2012)

The complex refractive index components, n and k, have been studied for thin films of several common dielectric materials with a low to medium refractive index as functions of wavelength and stoichiometry for mid-infrared (MIR) wavelengths within the range 1.54-14.29 μm (700-6500 cm(-1)). The materials silicon oxide, silicon nitride, aluminum oxide, aluminum nitride, and titanium oxide are prepared using room temperature reactive sputter deposition and are characterized using MIR variable angle spectroscopic ellipsometry. The investigation shows how sensitive the refractive index functions are to the O2 and N2 flow rates, and for which growth conditions the materials deposit homogeneously. It also allows conclusions to be drawn on the degree of amorphousness and roughness. To facilitate comparison of the materials deposited in this work with others, the index of refraction was also determined and provided for the near-IR and visible ranges of the spectrum. The results presented here should serve as a useful information base for designing optical coatings for the MIR part of the electromagnetic spectrum. The results are parameterized to allow them to be easily used for coating design.
Targeting surface nucleolin with multivalent HB-19 and related Nucant pseudopeptides results in distinct inhibitory mechanisms depending on the malignant tumor cell type (2011)

Our results suggest that targeting surface nucleolin could change the organization of the 500-kDa complex to interfere with the proper functioning of surface nucleolin and the associated proteins, and thus lead to distinct inhibitory mechanisms. Consequently, HB-19 and related Nucant pseudopeptides provide novel therapeutic opportunities in treatment of a wide variety of cancers and related malignancies.
Supplementary Figure Legends from Leukemia Cell-Rhabdovirus Vaccine: Personalized Immunotherapy for Acute Lymphoblastic Leukemia (2023)

&lt;p&gt;Supplementary Figure Legends - PDF file 75K, Legends for Supplemental Figures S1 - S7&lt;/p&gt;
Adaptive Coefficient Scanning Based on the Intra Prediction Mode (2007)

ABSTRACTThis letter presents an adaptive coefficient scanning method for intra mode coding in H.264. The proposed adaptive scanning uses six alternative scanning orders based on the intra prediction mode. Experimental results show that the proposed method improves the coding efficiency up to 3% compared to conventional scanning methods without additional computations. Keywords H.264, intra prediction, alternate scan.
Design and performance analysis of HomePNA 2.0 transceiver chip circuit (2006)

In this paper, we present the architecture of Home Phoneline Networking Alliance (HomePNA) 2.0 transceiver chip circuit which can establish a home network using existing in-home phone line, and it provides a data rate of 4-32 Mbps. We evaluate the performance of HomePNA 2.0 transceiver chip by running a simulation to study mean squared error (MSE), eye diagram and constellation. By analyzing the results of each simulation, we also analyze the performance of HomePNA 2.0 transceiver chip in a comprehensive manner
Database Self-Management: Taming the Monster. (2011)

We describe our experience in the development of self-managing technologies in Sybase SQL Anywhere, a full-featured relational database system that is commonly embedded with applications developed by Independent Software Vendors (ISVs). We illustrate how SQL Anywhere’s embeddability features work in concert to provide a robust data management solution in zero-administration environments.
New amorphous semiconductor: 2CdO⋅PbOx (1996)

A new amorphous semiconductor, 2CdO⋅PbOx (band gap: 1.58 eV), was found. Thin films of this material were prepared by rf sputtering of a Cd2PbO4 target in O2–Ar. The dc conductivity of the resulting amorphous thin films was ∼180 S cm−1 at 300 K and remained almost constant down to ∼4 K. The concentration of carrier electrons and the Hall mobility in the as-deposited state were 1×1020 cm−3 and 9 cm2 V−1 s−1, respectively. When the as-deposited specimens were heated to 250 °C, which is far below the crystallization (to Cd2PbO4) temperature (460 °C), the conductivity and the carrier concentration at 300 K became approximately twice as high. The thermal O2-desorption measurements demonstrated that carrier electrons are generated via the formation of oxygen vacancies at the initial stage (&amp;lt;250 °C) of thermal desorption of O2 from the amorphous structure. The effective mass of carrier electrons was estimated as 0.57m0.
Role of the p55-gamma subunit of PI3K in ALK-induced cell migration: RNAi-based selection of cell migration regulators (2016)

Recently, unbiased functional genetic selection identified novel cell migration-regulating genes. This RNAi-based functional selection was performed using 63,996 pooled lentiviral shRNAs targeting 21,332 mouse genes. After five rounds of selection using cells with accelerated or impaired migration, shRNAs were retrieved and identified by half-hairpin barcode sequencing using cells with the selected phenotypes. This selection process led to the identification of 29 novel cell migration regulators. One of these candidates, anaplastic lymphoma kinase (ALK), was further investigated. Subsequent studies revealed that ALK promoted cell migration through the PI3K-AKT pathway via the p55γ regulatory subunit of PI3K, rather than more commonly used p85 subunit. Western blot and immunohistochemistry studies using mouse brain tissues revealed similar temporal expression patterns of ALK, phospho-p55γ, and phospho-AKT during different stages of development. These data support an important role for the p55γ subunit of PI3K in ALK-induced cell migration during brain development.
Conformational locking for band gap control in 3,4-propylenedioxythiophene based electrochromic polymers (2006)

We report a tethered poly(3,4-propylenedioxythiophene) derivative with a built-in polymer conformation restriction which locks the conjugated chain at a specific dihedral angle, thus providing a handle in which to tune the optical and electronic properties of the material.
Up-to-date thromboprophylaxis in elective spinal surgery. A systematic review (2014)

Deep vein thrombosis (DVT) and pulmonary embolism (PE) present a high incidence after surgery, posing a high risk in surgical practice. Although a consensus does exist on thromboprophylaxis in orthopedic surgery, this topic remains controversial in regard to spinal surgery. In this current paper, we review and discuss the different forms of prophyilaxis presented in literature, in order to develop guidelines on prophylactic measures in spinal surgery, improving patient´s outcomes and reducing any medical/legal problems that could arise from a thrombotic complication.
Wearable feedback systems for rehabilitation (2005)

In this paper we describe LiveNet, a flexible wearable platform intended for long-term ambulatory health monitoring with real-time data streaming and context classification. Based on the MIT Wearable Computing Group's distributed mobile system architecture, LiveNet is a stable, accessible system that combines inexpensive, commodity hardware; a flexible sensor/peripheral interconnection bus; and a powerful, light-weight distributed sensing, classification, and inter-process communications software architecture to facilitate the development of distributed real-time multi-modal and context-aware applications. LiveNet is able to continuously monitor a wide range of physiological signals together with the user's activity and context, to develop a personalized, data-rich health profile of a user over time. We demonstrate the power and functionality of this platform by describing a number of health monitoring applications using the LiveNet system in a variety of clinical studies that are underway. Initial evaluations of these pilot experiments demonstrate the potential of using the LiveNet system for real-world applications in rehabilitation medicine.
CCDC 600135: Experimental Crystal Structure Determination (2006)

An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
Photothermally Triggered Shape‐Adaptable 3D Flexible Electronics (2017)

Abstract Effective contact between flexible electronics and soft biological tissues, which may have different surface curvatures, for medical applications has long been a challenge. Here, this study reports a strategy for preparing shape‐adaptable 3D flexible electronics by combining photothermally responsive poly( N ‐isopropylacrylamide)/gold nanorods (PNIPAM@AuNRs) composite hydrogels with conventional flexible microelectrode arrays (fMEAs). The fMEAs‐functionalized composite hydrogels are shape‐adaptable and can accommodate different surface geometries. Triggered remotely in seconds by near‐infrared (NIR) light at a wavelength of 808 nm, the composite hydrogel layer is grafted on the back side of the fMEAs shrinks to induce a desirable shape transformation in the fMEAs. By patterning the responsive hydrogel layer, the fMEAs can exhibit planar‐to‐twisted structural transformations in response to an external stimulus as a result of differential shrinkage and their elastic moduli. This strategy not only enables fMEAs to modify their shape to remotely accommodate unpredictable shapes of different surfaces by irradiation with NIR but also provides multiple architectures of 3D fMEAs upon stimulation. These photothermally responsive composite‐hydrogel‐based fMEAs may provide new methods for achieving wearable and implantable devices and facilitate deeper investigations into biological systems.
Refractive concentrator optics architectures, tracker precision, and cumulative energy harvest (2015)

Effective cost-reduction of tracked concentrator photovoltaic (CPV) solar power systems must optimize engineering of tracker precision against the angular acceptance of the concentrator optics. Wider CPV module angular acceptance allows cost reduction through relaxed tracker pointing precision. We assess field performance of a two-dimensional CPV tracker, and study several refractive concentrator optics architectures using triple-junction solar cells, including on-sun measurements of angular response compared to ray-tracing models, and cumulative energy harvest yield as a function of tracker pointing precision.
TOR kinase controls Arabidopsis shoot development by translational repression of cytokinin catabolic enzymes (2021)

Plants continuously adjust their developmental program including organ initiation and growth in accordance with endogenous and environmental signals. This plasticity requires that a diversity of signaling pathways acts in concert to modulate stem cell activity. We have shown previously that the TOR kinase network integrates metabolic- and light signals and controls expression of WUSCHEL, a transcriptional master regulator of stem cells in the shoot apical meristem. However, the mechanism linking TOR activity with the WUSCHEL promoter remained unresolved. Here we demonstrate that TOR regulates the accumulation of trans-zeatin, the cytokinin species mainly responsible for shoot development. Importantly, we identify translational repression of RNAs encoding cytokinin degrading CYTOKININ OXIDASES/DEHYDROGENASE enzymes by TOR as an underlying mechanism. Employing this system, plants can quickly adjust stem cell activity and developmental programs in response to changes in their environment.
Development of a preliminary in vitro drug screening assay based on a newly established culturing system for pre-adult fifth-stage Onchocerca volvulus worms (2019)

The culture system we have established for O. volvulus young adult worms offers a promising new platform to advance drug discovery against the human filarial parasite, O. volvulus and thus supports the continuous pursuit for effective macrofilaricidal drugs. However, this in vitro culturing system will have to be further validated for reproducibility before it can be rolled out as a drug screen for decision making in macrofilaricide drug development programs.
Measuring Spatially Resolved Collective Ionic Transport on Lithium Battery Cathodes Using Atomic Force Microscopy (2017)

One of the main challenges in improving fast charging lithium-ion batteries is the development of suitable active materials for cathodes and anodes. Many materials suffer from unacceptable structural changes under high currents and/or low intrinsic conductivities. Experimental measurements are required to optimize these properties, but few techniques are able to spatially resolve ionic transport properties at small length scales. Here we demonstrate an atomic force microscope (AFM)-based technique to measure local ionic transport on LiFePO<sub>4</sub> to correlate with the structural and compositional analysis of the same region. By comparing the measured values with density functional theory (DFT) calculations, we demonstrate that Coulomb interactions between ions give rise to a collective activation energy for ionic transport that is dominated by large phase boundary hopping barriers. We successfully measure both the collective activation energy and the smaller single-ion bulk hopping barrier and obtain excellent agreement with values obtained from our DFT calculations.