gebhart/patrepeval huggingface dataset:
Carbonized starch microcellular foam-cellulose fiber composite structures (2008)

The production of microporous carbon foams from renewable starch microcellular foam-fiber (SMCF-Fiber) composites is described. Carbon foams are used in applications such as thermal insulation, battery electrodes, filters, fuel cells, and medical devices. SMCF-Fiber composites were created from an aquagel. The water in the aquagel was exchanged with ethanol and then dried and carbonized. Higher amylose content starches and fiber contents of up to 4% improved the processability of the foam. The SMCF structure revealed agglomerates of swollen starch granules connected by a web of starch with pores in the 50-200 nanometer range. Heating the SMCF-fiber in a nitrogen atmosphere to temperatures between 350-700˚C produced carbon foams with a three-dimensional closed cell foam structure with cell diameters around 50 microns and pore walls around 1-3 microns. The stress versus strain compression data for carbonized samples displayed a linear elastic region and a plateau indicative of brittle crushing, typical of an elastic-brittle foam. The carbon foam products from these renewable precursors are promising carbon structures with moderate strength and low density.
The α4‐containing form of protein phosphatase 2A in liver and hepatic cells (2008)

The Ser/Thr phosphatase PP2A is a set of multisubunit enzymes that regulate many cellular processes. In yeast, the PP2A regulatory subunit Tap42 forms part of the target of rapamycin (TOR) signaling pathway that links nutrient and energy availability to cell growth. The physiological intersection between the mammalian orthologs of Tap42 and TOR, alpha4 and mTOR, has not been fully characterized. We used two in vivo models of liver growth in the rat, late gestation fetal development and regeneration after partial hepatectomy, to explore the regulation of the alpha4-containing form of PP2A. The alpha4/PP2A catalytic subunit (alpha4/PP2A-C) complex was present in both fetal and adult liver extracts. There was a trend towards higher levels of alpha4 protein in fetal liver, but the complex was more abundant in adult liver. Fractionation of extracts by ion exchange chromatography and transient transfection of the AML12 mouse hepatic cell line indicated that alpha4 associates with PP2A-C but that these complexes have low catalytic activity with both peptide and protein substrates. alpha4 was able to associate with forms of PP2A-C that were both methylated and non-methylated at the carboxy-terminus. The mTOR inhibitor rapamycin did not block the formation of alpha4/PP2A-C in liver or hepatic cells, nor did it appear to modulate PP2A activity. Furthermore, sensitivity to the growth inhibitory effects of rapamycin among a panel of hepatic cell lines did not correlate with levels of alpha4 or alpha4/PP2A-C. Our results indicate that the yeast Tap42/TOR paradigm is not conserved in hepatic cells.
A differentiated service mechanism considering SLA for heterogeneous cluster Web systems (2006)

As the Web is becoming more widely used as the preferred method for critical information exchange, it is necessary to provide differentiated service mechanisms not only at the network level but also at the Web server level. In this paper, we study performance isolation and admission control concepts of heterogeneous cluster-based Web systems and study the availability of primary-backup Web switches. Due to the types of requests of clients, the SLA (service level agreement) between the clients and the service provider is considered.
Two-Dimensional Analytical Modeling of Fully Depleted DMG SOI MOSFET and Evidence for Diminished SCEs (2004)

A two-dimensional (2-D) analytical model for the surface potential variation along the channel in fully depleted dual-material gate silicon-on-insulator MOSFETs is developed to investigate the short-channel effects (SCEs). Our model includes the effects of the source/drain and body doping concentrations, the lengths of the gate metals and their work functions, applied drain and substrate biases, the thickness of the gate and buried oxide and also the silicon thin film. We demonstrate that the surface potential in the channel region exhibits a step function that ensures the screening of the drain potential variation by the gate near the drain resulting in suppressed SCEs like the hot-carrier effect and drain-induced barrier-lowering (DIBL). The model is extended to find an expression for the threshold voltage in the submicrometer regime, which predicts a desirable "rollup" in the threshold voltage with decreasing channel lengths. The accuracy of the results obtained using our analytical model is verified using 2-D numerical simulations.
Managing heterogeneous ecological data using Morpho (2003)

Ecological and environmental data cover a wide range of topics, from biodiversity surveys to measurements of trace gas fluxes, and are modeled using a tremendous variety of schemas. We have developed Morpho, a data management application designed to assist researchers in managing this heterogeneous collection of ecological data. Our goal in developing Morpho was to ease the burden of data management on scientists while improving access to and documentation for ecological data. Morpho allows ecological researchers to describe their data using a comprehensive and flexible metadata specification, and to share their data publicly or to specific collaborators over the Knowledge Network for Biocomplexity (KNB). Morpho's main features include: (1) flexible metadata creation and editing using an XML syntax for metadata exchange; (2) a 'wizard' interface for collecting metadata; (3) automated metadata extraction while importing data; (4) an XML editor that is configurable using multiple XML DTDs; (5) compliance with the Ecological Metadata Language; (6) powerful metadata search on the network or locally; and, (7) comprehensive revision control for data and metadata.
Projection image enhancement for explosive detection systems (2008)

Automated Explosive Detection Systems (EDS) utilizing Computed Tomography (CT) generate a series of 2-D projections from a series of X-ray scans OF luggage under inspection. 3-D volumetric images can also be generated from the collected data set. Extensive data manipulation of the 2-D and 3-D image sets for detecting the presence of explosives is done automatically by EDS. The results are then forwarded to human screeners for final review. The final determination as to whether the luggage contains an explosive and needs to be searched manually is performed by trained TSA (Transportation Security Administration) screeners following an approved TSA protocol. The TSA protocol has the screeners visually inspect the resulting images and the renderings from the EDS to determine if the luggage is suspicious and consequently should be searched manually. Enhancing those projection images delivers a higher quality screening, reduces screening time and also reduces the amount of luggage that needs to be manually searched otherwise. This paper presents a novel edge detection algorithm that is geared towards, though not exclusive to, automated explosive detection systems. The goal of these enhancements is to provide a higher quality screening process while reducing the overall screening time and luggage search rates. Accurately determining the location of edge pixels within 2-D signals, often the first step in segmentation and recognition systems indicates the boundary between overlapping objects in a luggage. Most of the edge detection algorithms such as Canny, Prewitt, Roberts, Sobel, and Laplacian methods are based on the first and second derivatives/difference operators. These operators detect the discontinuities in the differences of pixels. These approaches are sensitive to the presence of noise and could produce false edges in noisy images. Including large scale filters, may avoid errors generated by noise, but often simultaneously eliminating the finer edge details as well. This paper proposes a novel pixels ratio based edge detection algorithm which is immune to noise. The new method compares ratios of pixels in multiple directions to an adaptive threshold to determine edges in different directions.
Identification of programmed cell death 1 and its ligand in the testicular tissue of mice (2018)

PD-1 and PD-L1 were present in the testicular tissue of adult mice. The expression and localization of PD-1 fluctuated with age, and PD-1 was mainly localized to advanced germ cells, suggesting that it may play a role in spermiogenesis. PD-L1 was constitutively expressed in the nucleus of Sertoli cells, which could secrete sPD-L1 into the testicular interstitial space and thus may be involved in testicular immune privilege.
Analysis of Algorithms Generalizing B-Spline Subdivision (1998)

A new set of tools for verifying smoothness of surfaces generated by stationary subdivision algorithms is presented. The main challenge here is the verification of injectivity of the characteristic map. The tools are sufficiently versatile and easy to wield to allow, as an application, a full analysis of algorithms generalizing biquadratic and bicubic B-spline subdivision. In the case of generalized biquadratic subdivision the analysis yields a hitherto unknown sharp bound strictly less than 1 on the second largest eigenvalue of any smoothly converging subdivision.
Quantification of the length and diameter of root segments with public domain software (1995)

Abstract Roots control the uptake of water and nutrients by plants, and hence their dry matter production. One of the greatest constraints to our understanding of root dynamics has been the laborious tedium associated with accurate measurements of various root parameters. A technique is presented for the fast and accurate measurement of the length and diameter of all fragments of corn (Zea mays L.) roots contained in most 0.04 by 0.15 m soil cores by analyzing a single NIH‐Image of those roots. These parameters are determined by measuring the perimeter and area of each root fragment utilizing NIH‐Image analyses contained in a public domain software (NIH‐Image). When length and diameter are coupled with nutrient uptake data, we will have a better understanding of where plants extract nutrients and water in space and time.
Anion diffusivity in highly conductive nanocrystalline BaF2:CaF2 composites prepared by high-energy ball milling (2008)

We report on the fluorine diffusivity in nanocrystalline BaF2 and CaF2 as well as in BaF2:CaF2 composites prepared by high-energy ball milling. Mechanical treatment of polycrystalline BaF2 together with CaF2 results in a nanocrystalline composite with an unexpectedly high dc conductivity of about 0.1 mS cm−1 at 450 K. X-ray diffraction and 19F magic angle spinning NMR measurements at extraordinary high spinning speeds reveal that this can be explained inter alia by the interplay of structural disorder and the formation of a mixed (Ba,Ca)F2 phase.
CHAPTER V (2010)

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ViaComplex: software for landscape analysis of gene expression networks in genomic context (2009)

(http://lief.if.ufrgs.br/pub/biosoftwares/viacomplex).
The Peptide That Binds (2010)

Oxytocin is a neuropeptide involved in a wide variety of social behaviors in diverse species. Recent research on its effects in humans has generated an arresting picture of its role in the dynamic function of the social brain. This review presents a broad overview of this uniquely social peptide, with a particular focus on extant studies of its effects in humans. After a short discussion of the evolutionary history of the oxytocin system, critical aspects of its peripheral and central physiology, and several salient technical issues surrounding human oxytocin research, a systematic review of studies of the effects of intranasal oxytocin in humans is presented. These effects include alterations in social decision making, processing of social stimuli, certain uniquely social behaviors (e.g., eye contact), and social memory. Oxytocin's prosocial influence is then framed by an evolutionary perspective on its role in mammalian social bonding and attachment. Finally, limitations in current human oxytocin research and oxytocin's potential therapeutic applications are discussed. Key conclusions are (1) human research with intranasal oxytocin has uniquely enhanced our understanding of the microstructure and function of the human social brain, and (2) the oxytocin system is a promising target for therapeutic interventions in a variety of conditions, especially those characterized by anxiety and aberrations in social function.
Phenylalanine Dehydrogenase Catalyzed Reductive Amination of 6-(1′,3′-Dioxolan-2′-YL)-2-Keto-Hexanoic Acid to 6-(1′,3′-Dioxolan-2′-YL)-2S-Aminohexanoic Acid with Nadh Regeneration and Enzyme and Cofactor Retention (2000)

Two systems were analyzed that make it possible to reuse enzymes and cofactors in the reductive amination of the lithium salt of 6-(1′,3′-dioxolan-2′-yl)-2-keto-hexanoic acid (compound 1) to 6-(1′,3′-dioxolan-2′-yl)-2S-aminohexanoic acid, lithium salt (compound 2) catalyzed by phenylalanine dehydrogenase (PDH) with in situ NADH regeneration catalyzed by formate dehydrogenase (FDH). First, both enzymes and PEG-NADH, a mass-enlarged cofactor, were encapsulated within semipermeable microcapsules. These microcapsules catalyzed the biotransformation in the absence of external NAD. About 20 mg of compound 2 was formed per mL microcapsule per day. Substrate diffusion into the microcapsules was not rate-limiting. PEG(35,000)—NADH, but not PEG(20,000)—NADH, was retained within the microcapsules. The activity of the encapsulated enzyme was about 15–25% of the activity of the free enzyme. If saturating free NAD was added to microcapsules, the activity increased about threefold. The microcapsules could be reused, and lost about half of their activity after eight days of continuous use at 40°C. The stability of FDH limited the reusability of microcapsules. As an alternative system, enzymes and PEG-NADH were used in a membrane reactor. Preliminary results showed the production of about 1 g of product per day in a 10 mL reactor over a period of ten days at ambient temperature without loss of activity.
Stabalized Estimation of Primaries by Sparse Inversion (2010)

Estimation of Primaries by Sparse Inversion (EPSI) is a recent method for surface-related multiple removal using a direct estimation method closely related to Amundsen inversion, where under a sparsity assumption the primary impulse response is determined directly from a data-driven wavefield inversion process. One of the major difficulties in its practical adoption is that one must have precise knowledge of a time-window that contains multiple-free primaries during each update. Moreover, due to the nuances involved in regularizing the model impulse response in the inverse problem, the EPSI approach has an additional number of inversion parameters where it may be difficult to choose a reasonable value. We show that the specific sparsity constraint on the EPSI updates lead to an inherently intractable problem, and that the time-window and other inversion variables arise in the context of additional regularizations that attempts to drive towards a meaningful solution. We furthermore suggest a way to remove almost all of these parameters via convexification, which stabilizes the inversion while preserving the crucial sparsity assumption in the primary impulse response model.
Melatonin decreases delirium in elderly patients: A randomized, placebo‐controlled trial (2010)

Exogenous low dose melatonin administered nightly to elderly patients admitted to acute care may represent a potential protective agent against delirium.
GHz-Band Monolithic Modem IC's (1987)

GHz-band monolithic modem IC's, such as a double balanced mixer IC, a 90° phase shifter IC, and a carrier switch IC, for high-speed QPSK modems have been developed using monolithic lumped constant circuit techniques and advanced silicon bipolar process technology and are discussed in this paper. A double balanced mixer with unbalance-balance converters and a common-mode feedback circuit has achieved an amplitude error of less than 0.2 dB/sub p-p/ and a phase error of Iew than 1.7° p-p at 1 GHz local oscillator frequency. A precise monolithic 90° phase shifter for the 1-GHz band was constructed by using variable RC phase stiifters. An ON/OFF ratio of more than 65 dB for frequencies below 1 GHz has been achieved by employing a carrier switch consisting of a differential stage with a cascode circuit configuration. These IC's are applicable to QPSK modems transmitting baseband signals to the extent of 400 Mb/s at 1 GHz local oscillator frequency.
A Transfer-Less, Multi-Well Liquid Culture Feeding System for Screening Small Molecules that Affect the Longevity of <i>Caenorhabditis Elegans</i> (2009)

Agricultural sciences rely almost entirely on chemical assays to screen the thousands of crop cultivars generated in a crop improvement program for potential human health benefits. This situation exists in part because most animal models are expensive to implement, utilize large amounts of plant material, and require specialized facilities and technical training. A cost-effective, high-throughput animal model to screen crop extracts for small molecules with biological activity related to human health benefits would provide a much-needed resource. Here we introduce a new, relatively high-throughput method incorporating the microscopic Caenorhabditis elegans nematode, which is suitable for screening chemical extracts for bioactivity without the need for robotics. This system was chosen because longevity extension in C. elegans has been previously associated with human health benefits. Through the use of cell culture inserts, C. elegans can be exposed to fresh crop extracts daily throughout their lifespan without mechanical manipulation of the worm, thus minimizing stress and creating an environment suitable for experiments measuring longevity. Additionally, the duration of longevity experiments can be reduced by using type II right censoring in experimental design and survival analyses.
Sequences in the rev‐responsive element responible for premature translational arrest in the human‐immunodeficiency‐virus‐type‐1 envelope (1993)

Cell-free translation in the presence of pancreatic microsomal membranes of the full-length envelope transcript of the human immunodeficiency virus type 1 (HIV-1) yielded the expected extensively glycosylated and immunologically reactive gp160 envelope-protein precursor. In addition to this gp160, a shorter glycoprotein, which we designated gp120*, was produced due to a premature translation arrest. Utilizing kinetic experiments, pulse-chase analyses and various gp160 envelope RNA mutants, we demonstrated that the in-vitro-produced gp120* was not formed by cleavage of the gp160 precursor or by internal initiation of translation. A gp120 produced before gp160 synthesis was completed, and, independent of the gp160 proteolytic processing, has been shown to be produced and sequestered in the endoplasmic reticulum of HIV-1-infected cells [Willey, R. L., Klimkait, T., Frucht, D. M., Bonifacino, J. S. & Martin, M. A. (1991) Virology 184, 319-329]. The specific translational arrest shown to occur in vitro was found to be dependent on the Rev-responsive element, since deletion of this highly structured sequence abolished the production of gp120*. We found that the combination of two contiguous putative stem loops of the Rev-responsive element, located at nucleotides 7494-7522 and 7525-7550 of the HIV-1 Rev-responsive-element sequence, was responsible for the production of this truncated protein. To our knowledge, these stem-loop structures, distinct from that known to bind the Rev protein, represent the first example responsible for the production of alternative products by premature translational arrest in higher eukaryotes.
CD30 expression in acute lymphoblastic leukemia as assessed by flow cytometry analysis (2013)

We assessed CD30 expression in patients with acute lymphoblastic leukemia (ALL) of either T-cell or B-cell lineage to examine the potential benefit of anti-CD30-targeted therapy in this group of patients. Bone marrow specimens of 34 patients with T- and 44 with B-ALL were assessed for CD30 expression by multicolor flow cytometry immunophenotyping analysis. Of these 78 patients, 75 (96%) were adults; and 63 (81%) had refractory/relapsed disease. Using an arbitrary 20% cut-off, 13/34 (38%) cases of T-ALL and 6/44 (13%) cases of B-ALL were considered to express CD30. In five patients with T-ALL with sequential bone marrow tested, increased CD30 expression was observed during the course of high-dose chemotherapy (p = 0.025). Philadelphia chromosome/BCR-ABL1 fusion was positive in 14/44 cases of B-ALL and 2/32 cases of T-ALL, which showed no significant correlation with CD30 expression. In summary, we detected CD30 expression in approximately one-third of patients with T-ALL, and less frequently in B-ALL (p = 0.017). In T-ALL, CD30 expression is up-regulated during high-dose chemotherapy. These data indicate that anti-CD30-targeted therapy may be a potential option for patients with T-ALL with refractory/relapsed disease.
HaRP: Rapid Packet Classification via Hashing Round-Down Prefixes (2010)

Packet classification is central to a wide array of Internet applications and services, with its approaches mostly involving either hardware support or optimization steps needed by software-oriented techniques (to add precomputed markers and insert rules in the search data structures). Unfortunately, an approach with hardware support is expensive and has limited scalability, whereas one with optimization fails to handle incremental rule updates effectively. This work deals with rapid packet classification, realized by hashing round-down prefixes (HaRP) in a way that the source and the destination IP prefixes specified in a rule are rounded down to “designated prefix lengths” (DPL) for indexing into hash sets. HaRP exhibits superb hash storage utilization, able to not only outperform those earlier software-oriented classification techniques but also well accommodate dynamic creation and deletion of rules. HaRP makes it possible to hold all its search data structures in the local cache of each core within a contemporary processor, dramatically elevating its classification performance. Empirical results measured on an AMD 4-way 2.8 GHz Opteron system (with 1 MB cache for each core) under six filter data sets (each with up to 30 K rules) obtained from a public source unveil that HaRP enjoys up to some 3.6× throughput level achievable by the best known decision tree-based counterpart, HyperCuts (HC).
Plant Food Allergens (2006)

This chapter contains sections titled: Allergenicity-What is It? Known Plant Food Allergens Identifying Potential Allergens in Foods Application of GM Technology to Plant Allergens Conclusions Acknowledgment References