gebhart/patrepeval huggingface dataset:
Spinobulbar muscular atrophy: polyglutamine-expanded androgen receptor is proteolytically resistant in vitro and processed abnormally in transfected cells (1998)

The neuronotoxicity of genes with expanded CAG repeats is most likely mediated by their respective polyglutamine (Gln)-expanded gene products. Gln- expanded portions of these products may be sufficient, or necessary, for pathogenesis. We tested whether a Gln-expanded human androgen receptor (AR) is structurally altered, so that it allows for the proteolytic generation of a potentially pathogenic portion that may be resistant to further degradation. We found, in vitro , that a Gln-expanded AR is more proteolytically resistant than normal, and that it yields a distinct set of Gln-expanded fragments even after extended proteolysis in the presence of 2 M urea. Furthermore, COS cells transfected with CAG-expanded AR cDNA generate an aberrant, nuclear-associated 75 kDa derivative containing the Gln-expanded tract. They are also twice as likely to die by 24 h apoptotically than those transfected with normal AR cDNA. Our data support the notion that an unconventional derivative of the Gln- expanded AR is a component of the proximate motor neuronopathic agent in spinobulbar muscular atrophy. They also focus attention on two ways in which neuronotoxic derivatives may originate from various Gln-expanded proteins: (i) generation of an unusual derivative that is pathogenic de novo ; and (ii) the toxic accumulation of a normal derivative because of an inability to dispose of it.
Native cellulose I nanofibers allow flexible aerogels and hierarchically porous templates for functionalities (2009)

Native cellulose I nanofibers allow flexible aerogels and hierarchically porous templates for functionalities
EASE: EM-Assisted Source Extraction from calcium imaging data (2020)

Abstract Combining two-photon calcium imaging (2PCI) and electron microscopy (EM) provides arguably the most powerful current approach for connecting function to structure in neural circuits. Recent years have seen dramatic advances in obtaining and processing CI and EM data separately. In addition, several joint CI-EM datasets (with CI performed in vivo, followed by EM reconstruction of the same volume) have been collected. However, no automated analysis tools yet exist that can match each signal extracted from the CI data to a cell segment extracted from EM; previous efforts have been largely manual and focused on analyzing calcium activity in cell bodies, neglecting potentially rich functional information from axons and dendrites. There are two major roadblocks to solving this matching problem: first, dense EM reconstruction extracts orders of magnitude more segments than are visible in the corresponding CI field of view, and second, due to optical constraints and non-uniform brightness of the calcium indicator in each cell, direct matching of EM and CI spatial components is nontrivial. In this work we develop a pipeline for fusing CI and densely-reconstructed EM data. We model the observed CI data using a constrained nonnegative matrix factorization (CNMF) framework, in which segments extracted from the EM reconstruction serve to initialize and constrain the spatial components of the matrix factorization. We develop an efficient iterative procedure for solving the resulting combined matching and matrix factorization problem and apply this procedure to joint CI-EM data from mouse visual cortex. The method recovers hundreds of dendritic components from the CI data, visible across multiple functional scans at different depths, matched with densely-reconstructed three-dimensional neural segments recovered from the EM volume. We publicly release the output of this analysis as a new gold standard dataset that can be used to score algorithms for demixing signals from 2PCI data. Finally, we show that this database can be exploited to (1) learn a mapping from 3d EM segmentations to predict the corresponding 2d spatial components estimated from CI data, and (2) train a neural network to denoise these estimated spatial components. This neural network denoiser is a stand-alone module that can be dropped in to enhance any existing 2PCI analysis pipeline.
Panoptic-DeepLab: A Simple, Strong, and Fast Baseline for Bottom-Up Panoptic Segmentation (2020)

In this work, we introduce Panoptic-DeepLab, a simple, strong, and fast system for panoptic segmentation, aiming to establish a solid baseline for bottom-up methods that can achieve comparable performance of two-stage methods while yielding fast inference speed. In particular, Panoptic-DeepLab adopts the dual-ASPP and dual-decoder structures specific to semantic, and instance segmentation, respectively. The semantic segmentation branch is the same as the typical design of any semantic segmentation model (e.g., DeepLab), while the instance segmentation branch is class-agnostic, involving a simple instance center regression. As a result, our single Panoptic-DeepLab simultaneously ranks first at all three Cityscapes benchmarks, setting the new state-of-art of 84.2% mIoU, 39.0% AP, and 65.5% PQ on test set. Additionally, equipped with MobileNetV3, Panoptic-DeepLab runs nearly in real-time with a single 1025x2049 image (15.8 frames per second), while achieving a competitive performance on Cityscapes (54.1 PQ% on test set). On Mapillary Vistas test set, our ensemble of six models attains 42.7% PQ, outperforming the challenge winner in 2018 by a healthy margin of 1.5%. Finally, our Panoptic-DeepLab also performs on par with several top-down approaches on the challenging COCO dataset. For the first time, we demonstrate a bottom-up approach could deliver state-of-the-art results on panoptic segmentation.
A Hierarchical Particle–Shell Architecture for Long‐Term Cycle Stability of Li2S Cathodes (2015)

A hierarchical particle-shell architecture for long-term cycle stability of Li2S cathodes is described. Multiscale and multilevel protection prevents mechanical degradation and polysulfide dissolution in lithium-sulfur battery chemistries.
An oxygenation agent and radiation sensitizer, dodecafluoropentane, for the treatment of glioblastoma multiforme. (2015)

TPS2078 Background: Post-resected glioblastoma multiforme (GMB) patients were treated with dodecafluoropentane emulsion (DDFPe) to evaluate the pharmacokinetics (PK), safety and potential survival benefit in combination with the current standard of care: radiation therapy (RT) and temozolomide (TMZ). DDFPe is an oxygen transport agent, which carries more than 100x more oxygen than other tested fluorocarbons. Studies in tumor xenografts show that DDFPe increases tumor pO2 by up to 400% and mitigates radiation resistance (J Biomed Nanotechnology, Vol 11, No 2, Feb2015, pp. 274-281). Methods: DDFPe is being dosed using an accelerated escalation design with one patient per dose level. Eligible patients have previously-untreated GBM with residual enhancing tumor on an early post-operative MRI scan, ECOG score 0-2, satisfactory blood counts and adequate renal and hepatic function. Since an increase in the frequency and extent of radiation necrosis is a theoretical risk of increased oxygenation, the location and size of the radiation field must be assessed as having a manageable risk should radiation necrosis occur. NVX-108 is infused intravenously prior to each fraction of radiation (total 60 Gray in 30 fractions), with patients breathing carbogen gas (2% CO2 and 98% O2) concurrently. Blood samples are drawn to evaluate DDFP PK. Objective tumor responses are assessed with serial gadolinium-enhanced MRI scans using RANO criteria. In addition, molecular analysis of tumor biopsies and tissue oxygen level dependent (TOLD) MRI measurement of tumor oxygenation are being used as exploratory predictive and pharmacodynamic biomarkers. The dose escalation schedule will study NVX-108 doses between 0.05 and 0.35 mL/kg in 5 planned dose levels. Dose levels 1 and 2 have been treated without dose-limiting toxicity. Data will be presented summarizing current safety, PK and preliminary efficacy results, as well as our progress in qualifying TOLD MRI as a potential biomarker of tumor hypoxia and re-oxygenation by DDFPe. Clinical trial information: 2014/007283.
Flow-Through Atmospheric Pressure-Atomic Layer Deposition Reactor for Thin-Film Deposition in Capillary Columns (2022)

We demonstrate the development of a new atmospheric pressure-atomic layer deposition(AP-ALD) system to coat the inner walls of capillary columns for gas chromatography (GC). Unlike traditional ALD, this reactor operates at near-atmospheric pressure and addresses the challenges of depositing thin films inside capillaries, which include long pump down times, deposition in high-aspect-ratio materials, and temperature control. We show ALD of alumina in 5 and 12 m capillaries (0.53 mm ID) via sequential half reactions of trimethylaluminum and water. Our system yields pinhole-free, uniform thin films. It includes small witness chambers for witness silicon shards before and after the capillary. An engineering flow/transport analysis of the device is provided. Our ALD alumina thin films are characterized by spectroscopic ellipsometry (SE), X-ray photoelectron spectroscopy, transmission electron microscopy (TEM), and energy-dispersive X-ray spectroscopy. Alumina film growth achieved is 1.4-1.5 Å/cycle, which is consistent with previously reported results. Film thickness measurements by SE on witness shards of silicon and by TEM at both ends of the capillary are in good agreement. A capillary column coated with alumina is used to separate different gases by GC, although the retention times of gases are essentially the same as with an untreated fused silica capillary. This successful deposition of ALD alumina in long capillaries opens the door for other possible ALD coatings, including hybrid organic-inorganic coatings, using the 450+ ALD precursors available today.
Multi-tenant solution for IT service management: A quantitative study of benefits (2009)

The very competitive business climate dictates efficient and cost effective delivery and support of IT services. Compounded by complexity of IT environments and criticality of IT to business success, IT service providers seek multi-tenant solutions to reduce operational cost and improve service quality. In this paper we consider a multi-tenant solution for IT service management and examine its critical aspects for realizing business benefits. We conduct a quantitative study of its benefits using a complexity based value assessment methodology. By regarding complexity as a substitute for potential labor cost, we estimate the business value of the multi-tenant solution before its actual deployment.
High-temperature depletion-mode metal-oxide-semiconductor field-effect transistors in beta-SiC thin films (1987)

Depletion-mode n-channel metal-oxide-semiconductor field-effect transistors were fabricated on n-type β-SiC (111) thin films epitaxially grown by chemical vapor deposition on the Si (0001) face of 6H α-SiC single crystals. The gate oxide was thermally grown on the SiC; the source and drain were doped n+ by N+ ion implantation at 823 K. Stable saturation and low subthreshold current were achieved at drain voltages exceeding 25 V. Transconductances as high as 11.9 mS/mm were achieved. Stable transistor action was observed at temperatures as high as 923 K, the highest temperature reported to date for a transistor in any material.
Effects of different head groups and functionalised side chains on the cytotoxicity of ionic liquids (2007)

To enlarge the restricted knowledge about the hazard potentials of ionic liquids to men and the environment we have concentrated on systematically analysing the effects of 7 head groups, 10 side chains (mainly containing functional groups) and 4 anions on cytotoxicity. For our investigations, we used the promyelotic leukemia rat cell line IPC-81 as test system, with the reduction of the WST-1 dye as an indicator of cell viability. Our results show that most of the tested 100 ionic liquids generally exhibit a low cytotoxicity compared to previously investigated ionic liquids in consequence of their polar ether, hydroxyl and nitrile functional groups within the side chains. Those functional groups hamper cellular uptake by membrane diffusion and reduce lipophilicity based interactions with the cell membrane.
Abstract 4534: Label free molecular imaging of tumor sections for two and three dimensional tissue classification and pathway mapping (2019)

Mass spectrometry imaging allows for the presence and abundance of a wide range of bio-molecules to be measured directly from tissue sections without the use of labels or tags. This results in the ability to compare the spatial distribution of hundreds of metabolites, lipids, peptides, and proteins within the same section in a single experiment. Desorption electrospray ionization (DESI) mass spectrometry imaging can differentiate and classify tissue types, and associated disease states, by measuring the unique characteristic molecular fingerprints of the tissues1,2. Furthermore, using histologically annotated databases of molecular profiles, unknown tissues can be classified using the mass spectrometry output coupled to machine learning approaches. A major benefit of DESI is that the analyzed sections are left largely unchanged by the process; the sections can subsequently be stained and the results validated by immunohistochemistry or conventional H&E approaches. During DESI fingerprinting analyses, a full mass spectrum on a cell by cell resolution of 20-50µm pixel size is collected. Chemical changes on very small scales can be distinguished and explored, allowing the chemistry of tumor margins and interface zones to be understood through mapping results onto metabolic pathways. As the data in a DESI experiment is collected and stored, multiple interrogations of the data are possible; as new discoveries are made, previously collected data can be retrospectively mined for additional insights. In this study, the three-dimensional chemical heterogeneity of drug dosed spheroids and tumor xenografts was measured with DESI and compared with MRI and PET imaging modalities and with FT-IR spectroscopic techniques. We demonstrate the power of this multi-analytical approach in glioma models and in colorectal and prostrate tumor samples to uncover metabolic and lipidomic changes during disease progression and to reveal the inherent heterogeneity within a tumor. 1. 1. Calligaris, D.Caragacianu, D.Liu, et al; PNAS, 2014, 111, 15185-151892. Guenther, S., Muirhead, L.J., et al, Cancer Res, 2015, 75, 1828-1837Citation Format: Emrys A. Jones, Dipa Gurung, Fiona Henderson, Matthew Gentry, Danielle McDougall, Yasmin Shanneik, James Langridge, Adam McMahon, Zoltan Takats. Label free molecular imaging of tumor sections for two and three dimensional tissue classification and pathway mapping [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2019; 2019 Mar 29-Apr 3; Atlanta, GA. Philadelphia (PA): AACR; Cancer Res 2019;79(13 Suppl):Abstract nr 4534.
DSTBC based DF cooperative networks in the presence of timing and frequency offsets (2013)

In decode-and-forward (DF) relaying networks, the received signal at the destination may be affected by multiple impairments such as multiple channel gains, multiple timing offsets (MTOs), and multiple carrier frequency offsets (MCFOs). This paper proposes novel optimal and sub-optimal minimum mean-square error (MMSE) receiver designs at the destination node to detect the signal in the presence of these impairments. Distributed space-time block codes (DSTBCs) are used at the relays to achieve spatial diversity. The proposed sub-optimal receiver uses the estimated values of multiple channel gains, MTOs, and MCFOs, while the optimal receiver assumes perfect knowledge of these impairments at the destination and serves as a benchmark performance measure. To achieve robustness to estimation errors, the estimates statistical properties are exploited at the destination. Simulation results show that the proposed optimal and sub-optimal MMSE compensation receivers achieve full diversity gain in the presence of channel and synchronization impairments in DSTBC based DF cooperative networks.
An Experimental Investigation of the Use of Combined Resistivity and Temperature Logs for Scale Monitoring In Carbonate Formations During CO2 Sequestration (2014)

This study investigates the prospect of using permanent downhole resistivity and temperature sensors for scale monitoring during CO2 sequestration in saline carbonate aquifer. Current industry practice involves continuous geochemical analysis of produced formation water and petrographic analysis of cuttings at the surface. A major limitation of such methods is that formation scale dynamics is not captured in situ and in real time. Moreover, high cost and compositional change of produced fluid caused by evolution of dissolved gases are other setbacks. In this study, resistivity and temperature measurements were logged continuously for several months at 30 min interval during CO2 storage in brine saturated core samples. Carbonate samples were acquired from Indiana outcrops in the United States and cut into cylindrical cores. Samples were saturated with synthetic formation brine and CO2 was injected and stored at a temperature of 45 °C, pore pressure of 2000 psig, and an overburden pressure of 2500 psig. The pressure, temperature and resistivity of samples were collected and transmitted to a PC computer at an interval of 30 min for the period of storage. A base line log recorded after CO2 injection but prior to CO2/brine/rock interaction (CBRI) allowed us to track onset of dissolution and precipitation. Deflection away from the baseline either inward or outward during the period of storage marks two distinct reaction phenomenon-dissolution and precipitation. Our hypothesis was justified by results of geochemical analysis of prestorage brine and poststorage brine, and also by petrographic study of the cores. Several other tests were also run to ensure consistency. This study is new compared to previous works in the following ways: Many previous works focused on the applicability of electrical resistivity measurements to track CO2 migration by way of resistivity change as a function of CO2 saturation changes during CO2 sequestration. Many others also studied the effect of CO2 injection on the petrophysical and electrical properties of rocks. Previous works of these types used continuous flow of fluid in and out of the sample and such flow experiments lasted only few hours. The fate of formation resistivity under static condition and at longer storage period was not considered.
A Heated Water Humidifier with a Rotating Wick (1979)

Amirdivani, Mahnoosh MD; Siegel, David BS; Chalon, Jack MD; Ramanathan, Sivam MD; Turndorf, Herman MD Author Information
DPN-Generated Combinatorial Libraries (2012)

Abstract : Here, we summarize the accomplishments relating to generating combinatorial libraries using dip-pen nanolithography (DPN) that we achieved during this AFOSR grant. Through powerful technological advances, we were able to meet the aims laid out in the proposal. Our first objective was to universally control the transport of matter at the nanoscale to improve the capabilities of DPN. To this end, we performed a systematic study to understand the dynamics of ink transport while developing agarose- and matrix-assisted DPN for the deposition of arbitrary materials. We achieved our next goal -- individually inking pens in order to write patterns with multiple inks at once -- by directly depositing ink in a self-correcting manner onto individual pens via ink-jet printing. Our final objective was to synthesize combinatorial arrays on a surface for biological screening, and we have made great progress towards this by developing massively parallel cantilever-free scanning probe lithography techniques (polymer pen lithography, hard-tip soft-spring lithography) that enabled the creation of combinatorial arrays of biomolecules with defined feature size and demonstrated their utility in studying cell differentiation. Furthermore, we developed a method to generate combinatorial arrays of sub-5 nm single crystal nanoparticles that act as binding sites for single proteins or as catalysts.
Annealing-induced optical-bandgap widening of Cu2ZnSnS4thin films with observation of simultaneous increase in local-structure ordering (2014)

We achieved annealing-induced optical-bandgap widening in Cu2ZnSnS4 (CZTS), which is a promising material for use in high-efficiency thin-film solar cells, and we performed synchrotron-radiation X-ray absorption fine structure (XAFS) measurements to study the reasons underlying the widening. CZTS thin-film samples were fabricated at a low temperature of 230 °C via sputtering with a CZTS ceramic target followed by annealing at up to 550 °C. Optical absorption spectroscopy revealed optical bandgap widening when the annealing temperature was ≥350 °C. Compositional changes, phase separations, and lattice strains were excluded as possible reasons. XAFS measurements revealed that the radial distribution functions (RDFs) around the Zn K-absorption edge almost completely corresponded to those of a kesterite structure. In addition, the RDFs indicated that the disorder of atomic positions within 1 nm from zinc atoms tended to decrease with increasing annealing temperature, which we conclude is the primary reason for the optical-bandgap widening.
Technical Note: scuda: A software platform for cumulative dose assessment (2016)

The authors developed a unified software platform that provides accurate and efficient monitoring of anatomical changes and computation of actually delivered dose to the patient, thus realizing an efficient cumulative dose computation workflow. Evaluation on HN cases demonstrated the utility of our platform for monitoring the treatment quality and detecting significant dosimetric variations that are keys to successful ART.
CoVE (2023)

Multi-tenant computing platforms are typically comprised of several software and hardware components including platform firmware, operating system, virtualization monitor, and tenant workloads (typically in a virtual machine, container, or application). This model is well established in large scale commercial deployments, but the downside is that all platform components and operators are in the Trusted Computing Base (TCB) of the tenant. This aspect is ill-suited for privacy-oriented workloads that aim to minimize the TCB. Confidential computing [1] presents a good stepping-stone towards providing a quantifiable TCB for computing. Confidential computing requires the use of a HW-attested Trusted Execution Environment for data-in-use protection. The RISC-V architecture presents a strong foundation for meeting the requirements for Confidential Computing in a clean slate manner. This paper describes a reference architecture and discusses ISA, non-ISA and System-on-Chip (SoC) requirements for confidential computing on RISC-V Platforms. It discusses proposed RISC-V ISA and non-ISA for Confidential Virtual-machine Extension, referred to as CoVE.
Genetic architecture distinguishes systemic juvenile idiopathic arthritis from other forms of juvenile idiopathic arthritis: clinical and therapeutic implications (2016)

The lack of shared genetic risk factors between sJIA and other JIA subtypes supports the hypothesis that sJIA is a unique disease process and argues for a different classification framework. Research to improve sJIA therapy should target its unique genetics and specific pathophysiological pathways.
Neuroendocrine ACTH-Producing Tumor of the Thymus—Experience with 12 Patients over 25 Years (2012)

Thymic ACTH-producing NET is an aggressive disease that should be considered in CS with ectopic ACTH secretion, particularly in younger patients.