gebhart/patrepeval huggingface dataset:
Comprehensive analysis on SCM specifications for high-performance SCM/NAND flash hybrid SSD with through-silicon via (2017)

By adding SCM to NAND flash-based SSD, SCM/NAND flash hybrid SSDs have been proposed for performance improvement. This paper analyzes effects of SCM specifications such as read/write latency, capacity and I/O frequency on performance of the hybrid SSD with through-silicon via (TSV). From the evaluation results, TSV reduces energy consumption by 38% when the SCM capacity is 1% of the NAND flash capacity. In addition, the hybrid SSD achieves 2.1-times Input/Output per Second (IOPS) performance improvement compared with NAND flash-only SSD. The power consumption dependency of the SCM read/write latency and I/O frequency is also analyzed. Only SCM capacity affects the power consumption reduction by TSV. When the SCM capacity is 1% in the hybrid SSD, TSV reduces power consumption by up to 38%. In contrast to the result of power consumption, SCM capacity, read/write latency, and I/O frequency have a large effect on the IOPS performance. Up to 81-times IOPS performance is achieved when SCM capacity, latency, and I/O frequency are 10%, 100 ns, 4266 MHz, respectively.
Crystallization Retardation of Ultrathin Films of Poly[(R)-3-hydroxybutyrate] and a Random Copolymer Poly[(R)-3-hydroxybutyrate-co-(R)-3-hydroxyhexanoate] on an Aluminum Oxide Surface (2019)

Ultrathin films of biodegradable poly[(R)-3-hydroxybutyrate] (PHB) and its random copolymer poly[(R)-3-hydroxybutyrate-co-(R)-3-hydroxyhexanoate] (PHBHx) were prepared by spin-coating onto aluminum substrates with a naturally oxidized aluminum oxide (AO) surface layer or, alternatively, on gold substrates. The opposite surface of the film was in contact with ambient air. Isothermal crystallization kinetics of these films at room temperature were studied using infrared reflection absorption spectroscopy. The overall crystallization rate for all the polymers when crystallizing on AO is significantly retarded compared with the same polymer crystallizing on gold. It was found that the retardation effect was not due to a confinement effect. The crystallization retardation effect was especially enhanced for PHBHx with a higher (R)-3-hydroxyhexanoate content. Avrami analysis showed that the crystallization rate constant k (min–1) for all of the polymers on AO is approximately 3 to 4 orders of magnitude less than that found for the same polymer on gold. Grazing incident wide-angle X-ray diffraction showed that polymers on gold have both flat-on and edge-on crystallite orientations, whereas polymers on AO have a dominating edge-on crystallite orientation. Infrared studies on a quasi-monolayer film revealed no detectable H-bonding between PHB/PHBHx and the AO surface. The crystallization retardation mechanism was explained as being a sum of the dipole–dipole interactions of −C═O of PHB or PHBHx and the −O–Al–O– groups of AO coupled with the rigid disordered amorphous nature of the AO surface.
Figure S5 from LKB1-Dependent Regulation of TPI1 Creates a Divergent Metabolic Liability between Human and Mouse Lung Adenocarcinoma (2023)

&lt;p&gt;Figure S5. LKB1 regulates the multimeric state of hTPI1 but not mTpi1 and substitution of Cys in hTPI1 causes formation of a covalent TPI1 dimer.&lt;/p&gt;
Characterization of a Benzyl Alcohol Dehydrogenase from Lactobacillus plantarum WCFS1 (2008)

Aroma is an important sensory parameter of food products. Lactic acid bacteria have enzymatic activities that could be important in the modification of food aroma. The complete genome sequence from Lactobacillus plantarum WCFS1 shows a gene (lp_3054) putatively encoding a protein with benzyl alcohol dehydrogenase activity. To confirm its enzymatic activity lp_3054 from this strain has been overexpressed and purified. Protein alignment indicated that lp_3054 is a member of the family of NAD(P)-dependent long-chain zinc-dependent alcohol dehydrogenases. In lp_3054 all of the residues involved in zinc and cofactor binding are conserved. It is also conserved the residue that determines the specificity of the dehydrogenase toward NAD (+) rather than NADP (+) and, therefore, L. plantarum benzyl alcohol dehydrogenase is less active in the presence of NADP (+) than in the presence of NAD (+). The purified enzyme exhibits optimal activity at pH 5.0 and 30 degrees C. The kinetic parameters K m and V max on benzyl alcohol as a substrate were, respectively, 0.23 mM and 204 mumol h (-1) mg (-1). Besides its activity toward benzyl alcohol, it showed activity against nerol, geraniol, phenethyl alcohol, cinnamyl alcohol, and coniferyl alcohol, all of which are volatile compounds involved in determining food aroma. The biochemical demonstration of a functional benzyl alcohol dehydrogenase activity in this lactic acid bacteria species should be considered when the influence of bacterial metabolism in the aroma of food products is determined.
Error-budget paradigms and laser mask pattern generator evolution (2009)

The evolution of the ALTA<sup>(R)</sup> series of laser mask pattern generators has increased the relative contribution of intensity errors on critical-dimension (CD) control to those from placement errors. This paradigm shift has driven a change in rasterization strategy wherein aerial image sharpness is improved at the cost of a slight decrease in the averaging of column-to-column placement errors. Print performance evaluation using small-area CD test patterns show improvements in stripe-axis local CD uniformity (CDU) 3&sigma; values of 15-25% using the new strategy, and systematic brush-error contributions were reduced by 50%. The increased importance of intensity errors, coupled with the improvement of ALTA system performance, has also made the mask-blank and process-induced errors a more significant part of the overall error budget. A simple model based on two components, a pattern-invariant footprint and one related to the exposure density &rho;<i>(x, y),</i> is shown to describe adequately the errors induced by these sources. The first component is modeled by a fourth-order, two-dimensional polynomial, whereas the second is modeled as a convolution of &rho;<i>(x, y)</i> with one or more Gaussian kernels. Implementation of this model on the ALTA 4700 system shows improvements in global CDU of 50%.
Buckling instabilities in periodic composite polymeric materials (2010)

Although buckling instabilities in elastic solids have been known for a long time, high interest in this phenomenon is relatively recent. The current and prospective applications in flexible electronics, materials with tunable surface properties (adhesion and wettability), responsive photonic and phononic structures, and reinforced nanocomposites led to a surge in the interest in buckling instabilities. In fact, some of the applications, such as flexible electronics and metrology, have advanced at a tremendous pace only within the past few years. In this review, we discuss some of the most recent progress in the fundamental understanding of buckling instabilities in periodic multi-component polymer materials and porous polymer structures. We also discuss how the buckling can be localized to predetermined regions and hence form periodic instability patterns. Finally, we present several recent examples where buckling instabilities have been employed as a patterning tool to realize complex surface arrays of various materials.
Phytepsin, a barley vacuolar aspartic proteinase, is highly expressed during autolysis of developing tracheary elements and sieve cells (1998)

Vacuolarisation, formation of autophagocytotic vacuoles and tonoplast disruption have been reported in plant cells undergoing developmentally regulated programmed cell death (PCD), but little is known about the vacuolar proteins involved. In HeLa cells, cathepsin D, a lysosomal aspartic proteinase has been shown to mediate PCD. Based on immunohistochemical staining of barley roots, we show here that the previously well characterised barley vacuolar aspartic proteinase (phytepsin), a plant homologue to cathepsin D, is highly expressed both during formation of tracheary elements and during partial autolysis of sieve cells. In serial transverse sections of the vascular cylinder, starting from the root tip, phytepsin is expressed in root cap cells, in the tracheary elements of early and late metaxylem, and in the sieve cells of the protophloem and metaphloem. Aleurain, a barley vacuolar cysteine proteinase, is expressed similarly in root cap cells but differently in the tracheary elements of protoxylem and early metaxylem. This is the first evidence that a vacuolar aspartic proteinase, in analogy to cathepsin D in animals, may play a role in the active autolysis of plant cells.
Dissemination of Flow Specification Rules for IPv6 Implementation Report (2015)

This document is an implementation report for the BGP Flow
Specification Rules for IPv6 as defined in [I-D.ietf-idr-flow-
spec-v6]. The respondents are experts with the implementations they
reported on, and their responses are considered authoritative for the
implementations for which their responses represent.
Swapping Variables for High-Dimensional Sparse Regression with\n Correlated Measurements (2013)

We consider the high-dimensional sparse linear regression problem of\naccurately estimating a sparse vector using a small number of linear\nmeasurements that are contaminated by noise. It is well known that the standard\ncadre of computationally tractable sparse regression algorithms---such as the\nLasso, Orthogonal Matching Pursuit (OMP), and their extensions---perform poorly\nwhen the measurement matrix contains highly correlated columns. To address this\nshortcoming, we develop a simple greedy algorithm, called SWAP, that\niteratively swaps variables until convergence. SWAP is surprisingly effective\nin handling measurement matrices with high correlations. In fact, we prove that\nSWAP outputs the true support, the locations of the non-zero entries in the\nsparse vector, under a relatively mild condition on the measurement matrix.\nFurthermore, we show that SWAP can be used to boost the performance of any\nsparse regression algorithm. We empirically demonstrate the advantages of SWAP\nby comparing it with several state-of-the-art sparse regression algorithms.\n
Abstract 5680: Quantitative cellular and molecular imaging of the intact tumor microenvironment (2018)

Abstract The causes underlying the extent and character of tumor-associated immune responses in cancer are not well defined and are likely multifactorial, including cancer cell heterogeneity, host genotype, and the immune status of individual patients. Tumors are organized tissues with numerous reciprocal local and systemic connections with immune cell populations of both the myeloid and lymphoid lineages. Understanding the cellular and molecular composition of tumors could help uncover the variation in immune response to cancer in patients and to delineate interpatient patterns that could help elucidate causes of disease progression. Multiparameter flow cytometry and single-cell transcriptomics technologies have provided an unprecedented level of cell typing and annotation of cells present in tumors. However, these methods require tissue dissociation into single-cell suspensions. This is routinely linked with cell loss and artifacts due to enzymatic treatment, and cell sorting en route to transcriptomic analysis as well as cell contamination. Furthermore, tissue dissociation and single-cell analysis do not enable the determination of cellular context in which the cells find themselves at the time of analysis. Given this, we have established a comprehensive approach to cellular and molecular analysis of intact non-dissociated tissues. To this end, we have developed polychromatic (10+) immunofluorescence staining protocols for frozen tissue sections that are analyzed by confocal microscopy and whole-tissue scanning. Post-acquisition quantitation is based on adapted and improved histocytometry method based on Gerner et al. (Immunity 2012 Aug 24;37(2):364-76) with dynamic cell segmentation using Imaris software and a flow cytometry-like analysis conducted with Flowjo, allowing us to gate on different immune populations and subpopulations based on their phenotype while preserving each cell's original location within the tissue. In the next step, specific cells of interest are harvested based on their location with laser capture microdissection and profiled with RNA-seq. Transcripts derived by this computational pipeline are further analyzed using in situ hybridization with ViewRNA to confirm cell expression and establish the cellular context. We are also implementing light-sheet microscopy for 3D assessment of tissue architecture and organization by a given molecule. Thus, we are generating extensive quantitative and qualitative “maps” of cancer, stromal and immune infiltrate, allowing us to study its dynamic within the tissue. Citation Format: Jan Martinek, Hannah M. Brookes, Te-chia Wu, Lili Sun, Philipp Henrich, Kyung In Kim, Joshy George, Paul Robson, Jacques Banchereau, Karolina Palucka. Quantitative cellular and molecular imaging of the intact tumor microenvironment [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2018; 2018 Apr 14-18; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2018;78(13 Suppl):Abstract nr 5680.
Transformation of organic micropollutants during river bank filtration: laboratory versus field data (2012)

This paper investigates the degradation behavior of 14 organic micropollutants (OMPs), selected for their different physico-chemical properties (e.g., molecular weight, hydrophobicity and charge), in soil columns simulating the conditions prevailing in the first meter of river bank filtration (RBF) media. The results from the column system are compared to RBF field data obtained from the Vitens drinking water company in The Netherlands. The study explores the role of sorption media (sand filled columns and polyethylene tubes) as carrier material for the biomass. Polyethylene tubes with the same specific surface area as sand in the columns, were operated under similar conditions to compare OMP removal in the two systems. Both the column and field data indicate that negatively charged OMPs with Log D ranging from 0.65 to 1.95, positively charged OMPs with Log D ranging from −0.59 to 0.21 and neutral OMPs with Log D (−1.9 to 1.12) were more susceptible to biodegradation. The compounds that persisted (carbamazepine, atrazine, phenytoin, lincomycin) were positively charged with lower Log D (−1.33) or neutral with higher Log D (1.56 to 2.64). Hydrochlorothiazide showed poor biodegradability despite being neutral and having a lower log D (−0.71); it is an exception to the above behavior for reasons that have not yet been identified. A comparison of OMP removal in a biologically active polyethylene tube with a biologically active column showed that the biomass established in either systems removed the same OMPs and to similar extent for a majority of the OMPs. This finding supports the use of polyethylene tubes as a simple, cheap and quick method for investigating the trends in OMP removal in RBF.
Hydrodynamics of Superfluid Helium below 0.6°K. II. Velocity and Attenuation of Ultrasonic Waves (1973)

The attenuation and velocity of an ultrasonic wave in superfluid helium-4 have been calculated for temperatures below 0.6\ifmmode^\circ\else\textdegree\fi{}K. The calculation is based on the kinetic equations given by Khalatnikov. The phonon Boltzmann equation is solved numerically without making simplifying approximations about the form of the collision integral. The theory predicts that the velocity of sound increases with frequency for very low frequencies, passes through a maximum, decreases to a minimum, and finally increases towards a constant value at high frequencies. A simple explanation for this peculiar behavior is given. The theory is in good agreement with the experimental results of Abrahams et al., and Waters et al.
Highly Efficient Transgenesis in Ferrets Using CRISPR/Cas9-Mediated Homology-Independent Insertion at the ROSA26 Locus (2019)

The domestic ferret (Mustela putorius furo) has proven to be a useful species for modeling human genetic and infectious diseases of the lung and brain. However, biomedical research in ferrets has been hindered by the lack of rapid and cost-effective methods for genome engineering. Here, we utilized CRISPR/Cas9-mediated, homology-independent insertion at the ROSA26 "safe harbor" locus in ferret zygotes and created transgenic animals expressing a dual-fluorescent Cre-reporter system flanked by PhiC31 and Bxb1 integrase attP sites. Out of 151 zygotes injected with circular transgene-containing plasmid and Cas9 protein loaded with the ROSA26 intron-1 sgRNA, there were 23 births of which 5 had targeted integration events (22% efficiency). The encoded tdTomato transgene was highly expressed in all tissues evaluated. Targeted integration was verified by PCR analyses, Southern blot, and germ-line transmission. Function of the ROSA26-CAG-<sup>LoxP</sup>tdTomato<sup>StopLoxP</sup>EGFP (ROSA-TG) Cre-reporter was confirmed in primary cells following Cre expression. The Phi31 and Bxb1 integrase attP sites flanking the transgene will also enable rapid directional insertion of any transgene without a size limitation at the ROSA26 locus. These methods and the model generated will greatly enhance biomedical research involving lineage tracing, the evaluation of stem cell therapy, and transgenesis in ferret models of human disease.
Quantum networks based on cavity QED (2001)

We review an ongoing program of interdisciplinary research aimed at developing hardware and protocols for quantum communication networks. Our primary experimental goals are to demonstrate quantum state mapping from storage/processing media (internal states of trapped atoms) to transmission media (optical photons), and to investigate a nanotechnology paradigm for cavity QED that would involve the integration of magnetic microtraps with photonic bandgap structures.
High Affinity Binding of an Engineered, Modular Peptide to Bone Tissue (2013)

Bone grafting procedures have become common due in part to a global trend of population aging. Native bone graft is a popular choice when compared to various synthetic bone graft substitutes, owing to superior biological activity. Nonetheless, the insufficient ability of bone allograft to induce new bone formation and the insufficient remodeling of native bone grafts call for osteoinductive factors during bone repair, exemplified by recombinant human bone morphogenetic protein 2 (rhBMP2). We previously developed a modular bone morphogenetic peptide (mBMP) to address complications associated with the clinical use of rhBMP2 as a bone graft substitute. The mBMP is designed to strongly bind to hydroxyapatite, the main inorganic component of bone and teeth, and to provide pro-osteogenic properties analogous to rhBMP2. Our previous in vivo animal studies showed that mBMP bound to hydroxyapatite-coated orthopedic implants with high affinity and stimulated new bone formation. In this study, we demonstrate specific binding of mBMP to native bone grafts. The results show that mBMP binds with high affinity to both cortical and trabecular bones, and that the binding is dependent on the mBMP concentration and incubation time. Importantly, efficient mBMP binding is also achieved in an ex vivo bone bioreactor where bone tissue is maintained viable for several weeks. In addition, mBMP binding can be localized with spatial control on native bone tissue via simple methods, such as dip-coating, spotting, and direct writing. Taken together with the pro-osteogenic activity of mBMP established in previous bone repair models, these results suggest that mBMP may promote bone healing when coated on native bone grafts in a clinically compatible manner.
Learning to share visual appearance for multiclass object detection (2011)

We present a hierarchical classification model that allows rare objects to borrow statistical strength from related objects that have many training examples. Unlike many of the existing object detection and recognition systems that treat different classes as unrelated entities, our model learns both a hierarchy for sharing visual appearance across 200 object categories and hierarchical parameters. Our experimental results on the challenging object localization and detection task demonstrate that the proposed model substantially improves the accuracy of the standard single object detectors that ignore hierarchical structure altogether.
High levels of circulating IL-10 in human malaria (1994)

IL-10 is a monocyte/lymphocyte derived cytokine which has been shown to inhibit certain cellular immune responses such as delayed hypersensitivity. In particular, the production of tumour necrosis factor (TNF), IL-1 and IL-6, which are involved in malaria pathology, are strongly inhibited by IL-10. Accordingly, we examined whether IL-10 could be involved in a human acute parasitic infection such as Plasmodium falciparum malaria. Human IL-10 levels in plasma were determined by two-site ELISA method, taking care to avoid non-specific reactions due to autoantibodies. Fourteen cerebral, 11 severe, and 20 mild malaria cases had mean IL-10 levels of 2812, 2882 and 913 pg/ml, respectively, while 98% of healthy individuals had undetectable (less than 100 pg/ml) circulating IL-10. Thirteen of the 25 cerebral/severe cases had > 2000 pg/ml. In 11 hospitalized patients, circulating IL-10 levels were found to return to virtually normal levels 7 days after antimalarial chemotherapy when biological and clinical malaria features had disappeared (mean levels fell from 3880 to 333 pg/ml). Further studies are required to determine whether these elevated levels of IL-10 play a beneficial role by reducing the parasite-induced inflammatory response, or a detrimental one by decreasing the cellular immune responses.
Transglutaminase 2 Undergoes a Large Conformational Change upon Activation (2007)

Human transglutaminase 2 (TG2), a member of a large family of enzymes that catalyze protein crosslinking, plays an important role in the extracellular matrix biology of many tissues and is implicated in the gluten-induced pathogenesis of celiac sprue. Although vertebrate transglutaminases have been studied extensively, thus far all structurally characterized members of this family have been crystallized in conformations with inaccessible active sites. We have trapped human TG2 in complex with an inhibitor that mimics inflammatory gluten peptide substrates and have solved, at 2-A resolution, its x-ray crystal structure. The inhibitor stabilizes TG2 in an extended conformation that is dramatically different from earlier transglutaminase structures. The active site is exposed, revealing that catalysis takes place in a tunnel, bridged by two tryptophan residues that separate acyl-donor from acyl-acceptor and stabilize the tetrahedral reaction intermediates. Site-directed mutagenesis was used to investigate the acyl-acceptor side of the tunnel, yielding mutants with a marked increase in preference for hydrolysis over transamidation. By providing the ability to visualize this activated conformer, our results create a foundation for understanding the catalytic as well as the non-catalytic roles of TG2 in biology, and for dissecting the process by which the autoantibody response to TG2 is induced in celiac sprue patients.