gebhart/patrepeval huggingface dataset:
Preliminary results: exploring the interactions of quantum dots with whole blood components (2005)

Biocompatible ZnS capped CdSe fluorescent semiconductor nanocrystals (quantum dots, QDs) exhibit great potential as imaging agents with biomedical and clinical relevance. However, little is known about the fate of the quantum dots <i>in vivo</i>, and the importance of chemical and physical composition that may influence their behavior <i>in vivo</i>. When the QDs are introduced <i>in vivo</i>, the first interactions with blood components will dictate their kinetic behavior <i>in vivo</i>. We present some preliminary results that demonstrate the interactions of the quantum dots with plasma proteins and that quantum dots can be trapped in fibrous networks.
Cardiovascular Burden and Adverse Events in Patients With Esophageal Cancer Treated With Chemoradiation for Curative Intent (2021)

A systematic cardiac evaluation prior to chemoradiation in patients with EC revealed a high prevalence of undetected CVD, inadequately treated pre-existing CVD, and a high incidence of CV events after chemoradiation. These findings highlight the need for a systematic baseline cardiac examination in patients with EC to optimize CVD treatment. (Impact of Cancer Therapy on Myocardial Function in Patients With Esophagus Cancer [Heartcheck]; NCT03619317).
Intrinsic Selectivity and Structure Sensitivity of Rhodium Catalysts for C2+ Oxygenate Production (2016)

Synthesis gas (CO + H2) conversion is a promising route to converting coal, natural gas, or biomass into synthetic liquid fuels. Rhodium has long been studied as it is the only elemental catalyst that has demonstrated selectivity to ethanol and other C2+ oxygenates. However, the fundamentals of syngas conversion over rhodium are still debated. In this work a microkinetic model is developed for conversion of CO and H2 into methane, ethanol, and acetaldehyde on the Rh (211) and (111) surfaces, chosen to describe steps and close-packed facets on catalyst particles. The model is based on DFT calculations using the BEEF-vdW functional. The mean-field kinetic model includes lateral adsorbate-adsorbate interactions, and the BEEF-vdW error estimation ensemble is used to propagate error from the DFT calculations to the predicted rates. The model shows the Rh(211) surface to be ∼6 orders of magnitude more active than the Rh(111) surface, but highly selective toward methane, while the Rh(111) surface is intrinsically selective toward acetaldehyde. A variety of Rh/SiO2 catalysts are synthesized, tested for catalytic oxygenate production, and characterized using TEM. The experimental results indicate that the Rh(111) surface is intrinsically selective toward acetaldehyde, and a strong inverse correlation between catalytic activity and oxygenate selectivity is observed. Furthermore, iron impurities are shown to play a key role in modulating the selectivity of Rh/SiO2 catalysts toward ethanol. The experimental observations are consistent with the structure-sensitivity predicted from theory. This work provides an improved atomic-scale understanding and new insight into the mechanism, active site, and intrinsic selectivity of syngas conversion over rhodium catalysts and may also guide rational design of alloy catalysts made from more abundant elements.
Scaling challenges of NAND flash memory and hybrid memory system with storage class memory &amp; NAND flash memory (2013)

This paper summarizes the scaling challenges of the conventional 2D floating-gate cell NAND flash memories [1, 2]. The scaling trends and limits of the bulk and SOI NAND flash memories are investigated in terms of short channel effects and channel boosting leakage from 20nm to below 10nm generation using 3D-device simulation. In the bulk NAND cell, 13nm generation is the scaling limit for realizing both channel boosting during program-inhibit and SCE suppression. The SOI NAND cell scaling limit is decreased to 8nm generation. Then, scaling problems and device design for 3D-stackable NAND flash memory are investigated [3]. Control gate length (L <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">g</sub> ) and spacing (L <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">space</sub> ) are paid attention since they can be separately varied in 3D NAND and significantly affect the cell area of the 3D NAND as well as the electrical characteristics. L <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">g</sub> and L <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">space</sub> should be the same to cope with the tradeoff between memory window and disturbance. If the number of stacked layers is 18 with the layer pitch of 40nm, the effective cell size of the 3D NAND corresponds to that of 15nm planar NAND technology. Then, this paper discusses an error prediction (EP) low density parity check (LDPC) error correcting code (ECC) which realizes an over 10-times extended lifetime [4, 5]. As the design rule shrinks, the floating gate (FG)-FG capacitive coupling among neighboring memory cells seriously degrades the memory cell reliability. The EP-LDPC ECC calibrates the inter-cell coupling without access time penalty. Finally, this paper overviews a state-of-the-art hybrid memory solution with storage class memory (SCM) and NAND flash memory for the big data solid-state storage system [5, 6]. Data fragmentation of MLC NAND flash memory is suppressed and efficient MLC NAND flash usage is realized by storing small hot data to SCM. The 3D TSV hybrid SSD realizes 11 times performance increase, 6.9 times endurance enhancement and 93% write energy reduction.
Dual-tracer PET of viable tumor volume and hypoxia for identification of necrosis-containing radio-resistant Sub-volumes (2019)

<b>Introduction:</b> Positron emission tomography (PET) using hypoxia-selective tracers like FAZA may guide radiation dose-escalation approaches. However, poor resolution combined with slow tracer retention in relatively inaccessible target cells and slow clearance of unbound tracer results in low-contrast images, and areas where viable hypoxic tracer retaining cells and necrosis (no tracer) are intermixed may pass unnoticed during image thresholding. Here we hypothesized that a clinical feasible one-day dual tracer approach that combines a short-lived (e.g., <sup>11</sup>C labeled) metabolic tracer that provides voxel-wise information on viable tissue volume (preferably independently of tumor microenvironment) and a hypoxia marker, may limit threshold-based errors. <b>Material and methods:</b> <sup>11</sup>C-acetate and <sup>11</sup>C-methionine uptake was quantified in tumor cell lines under tumor microenvironment-mimicking conditions of high/low O<sub>2</sub> (21%/0%) and pH (7.4/6.7). Next, tumor-bearing mice were administered FAZA and sacrificed 1 h (mimics a clinical low-contrast image scenario) or 4 h (high contrast) later. In addition, all mice were administered pimonidazole (hypoxia) and <sup>14</sup>C-methionine 1 h prior to sacrifice. Tumor tissue sections were analyzed using dual-tracer autoradiography. Finally, FAZA, or FAZA normalized to <sup>14</sup>C-methionine retention (to adjust for differences in viable tissue volume) was compared to hypoxic fraction (deduced from immune-histological analysis of pimonidazole; ground truth) in PET-mimicking macroscopic pixels with variable extent of necrosis/hypoxia. <b>Results/conclusions:</b> Low pH stimulated <sup>11</sup>C-acetate retention in many cell lines, and uptake was further modified by anoxia, compromising its usefulness as a universal marker of viable tumor volume. In contrast, <sup>11</sup>C-methionine was largely unaffected by the <i>in vitro</i> microenvironment and was further tested in mice. Necrosis increased the risk of missing hypoxia-containing pixels during thresholding and hypoxic fraction and FAZA signal correlated poorly in the low contrast-scenario. Voxel-based normalization to <sup>14</sup>C-methionine increased the likelihood of detecting voxels harboring hypoxic cells profoundly, but did not consistently improve the correlation between the density of hypoxic cells and tracer signal.
Parallel and Distributed Algorithms (1995)

In this chapter we discuss the solution of problems by a number of processors working in concert. In specifying an algorithm for such a setting, we must specify not only the sequence of actions of individual processors, but also the actions they take in response to the actions of other processors. The organization and use of multiple processors has come to be divided into two categories: parallel processing and distributed processing. In the former, a number of processors are coupled together fairly tightly: they are similar processors running at roughly the same speeds and they frequently exchange information with relatively small delays in the propagation of such information. For such a system, we wish to assert that at the end of a certain time period, all the processors will have terminated and will collectively hold the solution to the problem. In distributed processing, on the other hand, less is assumed about the speeds of the processors or the delays in propagating information between them. Thus, the focus is on establishing that algorithms terminate at all, on guaranteeing the correctness of the results, and on counting the number of messages that are sent between processors in solving a problem. We begin by studying a model for parallel computation. We then describe several parallel algorithms in this model: sorting, finding maximal independent sets in graphs, and finding maximum matchings in graphs. We also describe the randomized solution of two problems in distributed computation: the choice coordination problem and the Byzantine agreement problem.
Sequencing of allotetraploid cotton (Gossypium hirsutum L. acc. TM-1) provides a resource for fiber improvement (2015)

Upland cotton is a model for polyploid crop domestication and transgenic improvement. Here we sequenced the allotetraploid Gossypium hirsutum L. acc. TM-1 genome by integrating whole-genome shotgun reads, bacterial artificial chromosome (BAC)-end sequences and genotype-by-sequencing genetic maps. We assembled and annotated 32,032 A-subgenome genes and 34,402 D-subgenome genes. Structural rearrangements, gene loss, disrupted genes and sequence divergence were more common in the A subgenome than in the D subgenome, suggesting asymmetric evolution. However, no genome-wide expression dominance was found between the subgenomes. Genomic signatures of selection and domestication are associated with positively selected genes (PSGs) for fiber improvement in the A subgenome and for stress tolerance in the D subgenome. This draft genome sequence provides a resource for engineering superior cotton lines.
Active sites in char gasification. Quarterly technical progress report, 1 October-31 December 1984 (1985)

This project is concerned with the study of the nature and behavior of active sites in the gasification of chars produced from synthesized model compounds, primarily those of the phenol-formaldehyde family of resins. One of the tasks defined for this project is to conduct transient kinetic studies on the gasification of these model compound chars. A new jet-stirred, pyro-gasifier reactor had to be developed for this purpose. Preliminary design considerations and calculations for this reactor were presented in a previous quarterly report (DOE/PC60800-2). Since that report, the reactor has been constructed and has undergone some preliminary testing. The current quarterly technical progress report summarizes the work to date on this reactor. 8 refs., 2 figs., 1 tab.
Number Systems for Deep Neural Network Architectures: A Survey (2023)

Deep neural networks (DNNs) have become an enabling component for a myriad of artificial intelligence applications. DNNs have shown sometimes superior performance, even compared to humans, in cases such as self-driving, health applications, etc. Because of their computational complexity, deploying DNNs in resource-constrained devices still faces many challenges related to computing complexity, energy efficiency, latency, and cost. To this end, several research directions are being pursued by both academia and industry to accelerate and efficiently implement DNNs. One important direction is determining the appropriate data representation for the massive amount of data involved in DNN processing. Using conventional number systems has been found to be sub-optimal for DNNs. Alternatively, a great body of research focuses on exploring suitable number systems. This article aims to provide a comprehensive survey and discussion about alternative number systems for more efficient representations of DNN data. Various number systems (conventional/unconventional) exploited for DNNs are discussed. The impact of these number systems on the performance and hardware design of DNNs is considered. In addition, this paper highlights the challenges associated with each number system and various solutions that are proposed for addressing them. The reader will be able to understand the importance of an efficient number system for DNN, learn about the widely used number systems for DNN, understand the trade-offs between various number systems, and consider various design aspects that affect the impact of number systems on DNN performance. In addition, the recent trends and related research opportunities will be highlighted
A CMOS image sensor using high-speed lock-in pixels for stimulated Raman scattering (2016)

A CMOS image sensor using high-speed lock-in pixels for stimulated Raman scattering (SRS) spectroscopy is presented in this paper. The effective SRS signal from the stimulated emission of SRS mechanism is very small in contrast to the offset of a probing laser source, which is in the ratio of 10<sup>-4</sup> to 10<sup>-5</sup>. In order to extract this signal, the common offset component is removed, and the small difference component is sampled using switched-capacitor integrator with a fully differential amplifier. The sampling is performed over many integration cycles to achieve appropriate amplification. The lock-in pixels utilizes high-speed lateral electric field charge modulator (LEFM) to demodulate the SRS signal which is modulated at high-frequency of 20MHz. A prototype chip is implemented using 0.11&mu;m CMOS image sensor technology.
Identification of cytoskeletal proteins as binding partners of Bri2 BRICHOS domain (2023)

Proteins must fold into three-dimensional structures to execute their biological functions. Therefore, maintenance of protein homeostasis, proteostasis, including prevention of protein misfolding is essential for cellular activity and health. Molecular chaperones are key actors in proteostasis. BRICHOS domain is an intramolecular chaperone that also interferes with several aggregation-prone proteins including amyloid β (Aβ), involved in Alzheimer's disease (AD). To extend the knowledge about Bri2 BRICHOS interactome we here used recombinant human (rh) Bri2 BRICHOS-mCherry fusion protein to probe for potential binding partners. Firstly, exogenously added Bri2 BRICHOS-mCherry was used to stain brain sections of wildtype and amyloid precursor protein (App) knock-in AD mice exhibiting robust Aβ pathology. Unexpectedly, we found that rh Bri2 BRICHOS-mCherry stained the cytoplasm of neurons which are devoid of Aβ deposits. To identify these intraneuronal proteins that bind to the rh Bri2 BRICHOS domain, we performed co-immunoprecipitation (co-IP) of mouse brain hippocampi homogenates using the Bri2 BRICHOS-mCherry probe and analyzed co-IP proteins by LC-MS/MS. This identified several cytoskeletal proteins including spectrin alpha and beta chain, drebrin, tubulin β3, and β-actin as binding partners. The interactions were confirmed by a second round of pulldown experiments using rh Bri2 BRICHOS linked to magnetic beads. The interaction of rh Bri2 BRICHOS and tubulin β3 was further investigated by staining both mouse brain sections and SH-SY5Y neuroblastoma cells with rh Bri2 BRICHOS-mCherry and tubulin β3 immunostaining, which revealed partial co-localization. These data suggest a possible interplay of extracellular chaperone Bri2 BRICHOS domain in the intracellular space including the cytoskeleton.
Timetal® 407: A Titanium Alloy to Enable Cost Reduction (2016)

TIMETAL®407 [Ti-407] is a new alpha/beta titanium alloy developed by TIMET’ s Henderson Technical laboratory (HTL) in collaboration with TIMET UK. It was designed, primarily, for improved ductility allowing it to excel for components requiring improved manufacturability, including low temperature forming and increased machining speeds. It can be used as a direct replacement to Ti-6Al-4V or Ti-3Al-2.5V alloy, particularly in applications where energy absorption during fracture and HCF endurance limit are the key design criteria. These stated benefits are achieved through a combination of high ductility and medium strength, i.e. an optimum strength/ductility balance for certain applications. Full scale production tests and the evaluation of materials for a number of applications are currently in progress. Technical details of Ti-407 properties and processing, as well as a metallurgical background of the alloy design, are to be discussed herein. TIMETAL® 407 is US patent pending.
Functional Differentiation of Multiple Perilesional Zones after Focal Cerebral Ischemia (2000)

Transient and permanent focal cerebral ischemia results in a series of typical pathophysiologic events. These consequences evolve in time and space and are not limited to the lesion itself, but they can be observed in perilesional (penumbra) and widespread ipsi- and sometimes contralateral remote areas (diaschisis). The extent of these areas is variable depending on factors such as the type of ischemia, the model, and the functional modality investigated. This review describes some typical alterations attributable to focal cerebral ischemia using the following classification scheme to separate different lesioned and perilesional areas: (1) The lesion core is the brain area with irreversible ischemic damage. (2) The penumbra is a brain region that suffers from ischemia, but in which the ischemic damage is potentially, or at least partially, reversible. (3) Remote brain areas are brain areas that are not directly affected by ischemia. With respect to the etiology, several broad categories of remote changes may be differentiated: (3a) remote changes caused by brain edema; (3b) remote changes caused by waves of spreading depression; (3c) remote changes in projection areas; and (3d) remote changes because of reactive plasticity and systemic effects. The various perilesional areas are not necessarily homogeneous; but a broad differentiation of separate topographic perilesional areas according to their functional state and sequelae allows segregation into several signaling cascades, and may help to understand the functional consequences and adaptive processes after focal brain ischemia.
Association Between Proposed Definitions of Clinical Remission/Response and Well-Being in Patients With Crohn’s Disease (2021)

An association between improvements in patient-reported general well-being and clinical remission/response was observed using outcomes of SF and AP, supporting the clinical remission/response endpoint definitions used in clinical studies of CD. Clinical Trial Registrations [ClinicalTrials.gov]: NCT00077779 [CHARM]; NCT00348283 [EXTEND]; NCT02365649 [CELEST].
Chicken egg white: Hatching of a new old biomaterial (2020)

Chicken egg white is an abundant, inexpensive and natural source of important proteins such as ovalbumin and lysozyme. Thanks to its bioactivity, easy handling, anti-bacterial activity and biodegradability, egg white is being used since centuries as excipient of poultices for the treatment of various disorders. Owing to unique thermal and electrical features, egg white is currently used in bioplastic development and in fabrication of field-effect transistors, but it could also contribute to various biomedical applications in the future. Indeed, egg white and some of its byproducts were shown to improve tissue engraftment and to stimulate angiogenesis, making it particularly attractive in wound healing and tissue engineering applications. Moreover, egg white can be manipulated to obtain versatile platforms for tridimensional in vitro tissue models or drug delivery systems. This review describes the structure and physicochemical properties of egg white as well as its biological features. It also summarizes fabrication methods from egg white for the generation of functional platforms, and provides a comprehensive overview of the role and performance of egg white in various biomedical applications. Finally, new perspectives for future studies in health with this ancient material are critically discussed.
Bloating in Gastroparesis: Prevalence, Impact and Associated Factors (2009)

Purpose: Patients with gastroparesis usually present with nausea and vomiting, but may also report bloating. The prevalence, impact, and factors associated with bloating in gastroparesis are uninvestigated. The aims of this study were: (i) quantify prevalence of bloating in gastroparesis, (ii) relate bloating to clinical factors and quality of life, (iii) characterize associated factors (obesity, gastric retention, medications). Methods: 353 gastroparesis patients were enrolled from 6 centers of the NIH Gastroparesis Clinical Research Consortium from Jan 2007 to Apr 2009. Validated survey, exam, and scintigraphy data were compared in those with bloating as the predominant symptom on initial query, bloating as a symptom but a non-predominant one, and without bloating. Results: Bloating was predominant in 27 patients (8%) and non-predominant in 171 (48%). 155 (44%) had no bloating. Those with predominant bloating were older (48±12 yr) vs. 40±14 with no bloating and 44±13 yr with non-predominant bloating (P=0.006). No differences in gender (80% female) or etiology (1/3 diabetic) were noted in the 3 groups. Investigator-defined gastric failure (ER visits, supplemental feeding, IV therapy) trended lower with predominant bloating (7.4%) vs. non-predominant and no bloating (both 31%) (P=0.08). Gastroparesis Cardinal Symptom Index nausea/vomiting subscale scores were lowest with predominant bloating (0.7) and highest with no bloating (3.0) (P<0.0001). Visible distention was higher with predominant (82%) and non-predominant bloating (73%) vs. no bloating (43%) (P<0.0001). SF-36 and Patient Assessment of GI Quality of Life scores were no higher with predominant bloating vs. no bloating. BMI, waist, and hip circumference were similar in all groups as was 4 hr gastric retention (median 19%). Antidepressant use related to bloating with an odds ratio of 1.64 (95% CI 1.06-2.54) (P=0.03). Tricyclic use decreased with increasing bloating (no bloating 60%, non-predominant bloating 39%, predominant bloating 12%), while SSRIs increased (no bloating 20%, non-predominant bloating 22%, predominant bloating 62%) (P=0.05). Conclusion: Bloating is prevalent in gastroparesis, relating to age but not gender or etiology, and is predominant in a minority of patients. Bloating predominant patients experience less nausea and vomiting, but note increased visible distention. Bloating does not lead to gastric failure or impair quality of life nor does it correlate with obesity or gastric retention. Increased predominant bloating on SSRIs and reductions on tricyclics warrant study into potential symptom modulation by antidepressants. This study provides insight into this underappreciated symptom of gastroparesis. Supported by NIH U01 DK073975.