gebhart/patrepeval huggingface dataset:
A Tool for Scalable Profiling and Tracing of Java and Native Code Interactions (2011)

Java workloads have two different execution spaces: one in JVM and the other in the native environment. Understanding workload activity in native and non-native (Java) spaces and its impact on the overall resource consumption of Java workloads can be very useful. For example, this knowledge can be exploited in code optimization and for efficient process level scheduling especially in emerging hybrid systems. Existing Java run time tracing tools are quite heavyweight and/or offer limited useful information for understanding Java and native space interactions. We developed an extremely lightweight tracing tool for enterprise Java workloads. The tool captures detailed per-thread statistics related to resource usage and activity in JVM and native spheres. Efficient design based on innovative thread and memory management principles enables us to achieve scalable monitoring with our tool on multi-core systems running enterprise workloads. The information captured by the tool is used to build workload profiles which can then be used for predictive performance of Java workloads in emerging systems and architectures.
Avoidance of Facial Nerve Injury in Lateral Skull Base Surgery (2011)

ABSTRACT In the radiosurgery era, the treatment strategies for vestibular schwannoma have changed at most centers. This new paradigm holds that rational CPA tumor therapy requires balancing often competing goals of therapy, and the associated risks and benefits of different therapies or combination of therapies. The present review discusses this new paradigm and its specific implications for CPA tumor surgery. Inevitably, such a review will focus largely on minimizing facial nerve morbidity, as this is both the most modifiable risk, and the risk that is most reduced with the use of adjuvant therapies, such as stereotactic radiosurgery (like Gamma knife). The facts about facial nerve preservation in CPA tumor surgery will be reviewed, and methods for avoiding facial nerve morbidity will be discussed.
Best-First Minimax Search: First Results (1993)

We present a very simple selective minimax search algorithm for two-player gaines. It ahvays expands next the frontier node at the end of the principal variation, or current best line of play, which is the node that determines the minimax value of the root. The algorithm requires no information other than a static evaluation function, and its time overhead per node is similar to that of alpha-beta minimax. On random game trees, our algorithm outperforms an efficient implementation of alpha-beta, giving both the same amount of computation. In the game of Othello, using the evaluation function from Bill, the world’s best program, best-first minimax also outplays alpha-beta. We present an implementation of the algorithm that reduces its space complexity from exponential to linear in the search depth, at the cost of increased time complexity. Finally, we present a hybrid best-first extension algorithin that combines alpha-beta and best-first minimax, and performs significantly better than either pure algorithm in both domains. 1
Multi-curvature liquid meniscus in a nanochannel: Evidence of interplay between intermolecular and surface forces (2009)

We examined the formation of a multiply curved meniscus inside rectangular nanochannels, whose width ranges from 50 to 800 nm at a constant height of 200 nm. When the channel width is smaller than approximately 400 nm under partial wetting conditions, a distinct multi-curvature meniscus was observed at the advancing front with an edge disjoined from the wall. In contrast, a typical pre-wetting film was observed at the front regardless of the channel size for complete wetting conditions. Our theoretical analysis demonstrated that the multi-curvature meniscus is generated from the increased contribution of an extra pressure due to intermolecular interactions near the wall. In particular, a plug-like meniscus profile was observed at the advancing liquid front for the 50 nm wide channel owing to an overlap between convex curvatures at the channel walls. Finally, we showed that the filling velocity of liquid can be decreased by decreasing the channel size due to the reduced wettability.
Supplementary Table 1 from Resveratrol Induces Differentiation Markers Expression in Anaplastic Thyroid Carcinoma via Activation of Notch1 Signaling and Suppresses Cell Growth (2023)

&lt;p&gt;PDF file - 44K, Primer sequences for quantitative real-time PCR.&lt;/p&gt;
Detection and characterization of immunoconglutinins in patients with systemic lupus erythematosus (SLE): serial analysis in relation to disease course (1992)

The levels of IgA, IgG and IgM immunoconglutinins (IK) were assessed in sera from 20 patients with SLE which were followed for 8-month periods. At the time of the exacerbation, IgG IKs were significantly increased to 226 +/- 90 arbitrary units (mean +/- s.e.m.) compared with both the minimum value of 75 +/- 28 in the SLE patients and with 31 +/- 2 in healthy controls (P < 0.05). There was no difference between SLE patients and controls in the levels of IgM and IgA IKs. Most of the SLE patients in this material showed maximal IgG IK levels before exacerbation, but there was no correlation between the clinical disease index and the levels of IgG IK. The specificity of IgG IKs showed a broad diversity for microtitre-fixed C3b, iC3b, C3c and C3dg. The antibodies were of IgG1, IgG3 and in two patients, IgG4 subclass. IgG IKs were correlated to the C3d/C3 ratio which suggested that the IK responses were secondary to C3 activation. In summary, unlike other conditions associated with complement activation where elevated IgM IKs are common, an increase in IgG IK levels was observed. It is possible that this diverging IK response contributes to the pathophysiology of the disease.
Genome of a Low-Salinity Ammonia-Oxidizing Archaeon Determined by Single-Cell and Metagenomic Analysis (2011)

Ammonia-oxidizing archaea (AOA) are thought to be among the most abundant microorganisms on Earth and may significantly impact the global nitrogen and carbon cycles. We sequenced the genome of AOA in an enrichment culture from low-salinity sediments in San Francisco Bay using single-cell and metagenomic genome sequence data. Five single cells were isolated inside an integrated microfluidic device using laser tweezers, the cells' genomic DNA was amplified by multiple displacement amplification (MDA) in 50 nL volumes and then sequenced by high-throughput DNA pyrosequencing. This microscopy-based approach to single-cell genomics minimizes contamination and allows correlation of high-resolution cell images with genomic sequences. Statistical properties of coverage across the five single cells, in combination with the contrasting properties of the metagenomic dataset allowed the assembly of a high-quality draft genome. The genome of this AOA, which we designate Candidatus Nitrosoarchaeum limnia SFB1, is ∼1.77 Mb with >2100 genes and a G+C content of 32%. Across the entire genome, the average nucleotide identity to Nitrosopumilus maritimus, the only AOA in pure culture, is ∼70%, suggesting this AOA represents a new genus of Crenarchaeota. Phylogenetically, the 16S rRNA and ammonia monooxygenase subunit A (amoA) genes of this AOA are most closely related to sequences reported from a wide variety of freshwater ecosystems. Like N. maritimus, the low-salinity AOA genome appears to have an ammonia oxidation pathway distinct from ammonia oxidizing bacteria (AOB). In contrast to other described AOA, these low-salinity AOA appear to be motile, based on the presence of numerous motility- and chemotaxis-associated genes in the genome. This genome data will be used to inform targeted physiological and metabolic studies of this novel group of AOA, which may ultimately advance our understanding of AOA metabolism and their impacts on the global carbon and nitrogen cycles.
Familial cortical myoclonus with a mutation in NOL3 (2012)

We propose that familial cortical myoclonus is a novel movement disorder that may be caused by mutation in NOL3. Further investigation of the role of NOL3 in neuronal physiology may shed light on neuronal membrane hyperexcitability and pathophysiology of myoclonus and related disorders.
Metal–organic frameworks based membranes for liquid separation (2017)

Metal-organic frameworks (MOFs) represent a fascinating class of solid crystalline materials which can be self-assembled in a straightforward manner by the coordination of metal ions or clusters with organic ligands. Owing to their intrinsic porous characteristics, unique chemical versatility and abundant functionalities, MOFs have received substantial attention for diverse industrial applications, including membrane separation. Exciting research activities ranging from fabrication strategies to separation applications of MOF-based membranes have appeared. Inspired by the marvelous achievements of MOF-based membranes in gas separations, liquid separations are also being explored for the purpose of constructing continuous MOFs membranes or MOF-based mixed matrix membranes. Although these are in an emerging stage of vigorous development, most efforts are directed towards improving the liquid separation efficiency with well-designed MOF-based membranes. Therefore, as an increasing trend in membrane separation, the field of MOF-based membranes for liquid separation is highlighted in this review. The criteria for judicious selection of MOFs in fabricating MOF-based membranes are given. Special attention is paid to rational design strategies for MOF-based membranes, along with the latest application progress in the area of liquid separations, such as pervaporation, water treatment, and organic solvent nanofiltration. Moreover, some attractive dual-function applications of MOF-based membranes in the removal of micropollutants, degradation, and antibacterial activity are also reviewed. Finally, we define the remaining challenges and future opportunities in this field. This Tutorial Review provides an overview and outlook for MOF-based membranes for liquid separations. Further development of MOF-based membranes for liquid separation must consider the demands of strict separation standards and environmental safety for industrial application.
Novel berbamine derivatives block Jak2/Stat3 signaling, associated with induction of apoptosis on human melanoma cells (2012)

Activated Jak/Stat3 signaling has been validated as a promising molecular target for cancer therapeutics discovery and development. Berbamine (BBM), a natural bis-benzylisoquinoline alkaloid, was identified from the traditional Chinese herbal medicine Berberis amurensis used for treatment of cancer patients. Here, we determine the antitumor activities of thirteen synthetic berbamine derivatives (BBMDs) against human solid tumor cells. BBMD3, which is the most potent in this series of novel BBMDs, exhibits over 6-fold increase in biological activity compared to natural BBM. Moreover, BBMD3, directly inhibits Jak2 autophosphorylation kinase activity in vitro with IC50 =0.69µM. Autophosphorylation of Jak2 kinase at Tyr1007/1008 sites also was strongly inhibited by BBMD3 in human melanoma cells. Following inhibition of autophosphorylation of Jak2, BBMD3 blocked constitutive activation of downstream Stat3 signaling in melanoma cells, associated with induction of apoptosis. In sum, our findings demonstrate that the novel BBMD3 is an inhibitor of the Jak2/Stat3 signaling pathway, suggesting evidence for a molecular mechanism whereby BBMD3 exerts at least part of apoptosis of human melanoma cells. In addition, BBMD3 represents a promising lead compound for development of new therapeutics for cancer treatment.
Overexpression of REDUCED WALL ACETYLATION C increases xylan acetylation and biomass recalcitrance in Populus (2023)

Plant lignocellulosic biomass, i.e. secondary cell walls of plants, is a vital alternative source for bioenergy. However, the acetylation of xylan in secondary cell walls impedes the conversion of biomass to biofuels. Previous studies have shown that REDUCED WALL ACETYLATION (RWA) proteins are directly involved in the acetylation of xylan but the regulatory mechanism of RWAs is not fully understood. In this study, we demonstrate that overexpression of a Populus trichocarpa PtRWA-C gene increases the level of xylan acetylation and increases the lignin content and S/G ratio, ultimately yielding poplar woody biomass with reduced saccharification efficiency. Furthermore, through gene coexpression network and expression quantitative trait loci (eQTL) analysis, we found that PtRWA-C was regulated not only by the secondary cell wall hierarchical regulatory network but also by an AP2 family transcription factor HARDY (HRD). Specifically, HRD activates PtRWA-C expression by directly binding to the PtRWA-C promoter, which is also the cis-eQTL for PtRWA-C. Taken together, our findings provide insights into the functional roles of PtRWA-C in xylan acetylation and consequently saccharification and shed light on synthetic biology approaches to manipulate this gene and alter cell wall properties. These findings have substantial implications for genetic engineering of woody species, which could be used as a sustainable source of biofuels, valuable biochemicals, and biomaterials.
Effect of Nb on the Proof Strength of Ferritic Stainless Steels at Elevated Temperatures. (2002)

The effect of Nb on the high temperature proof strength of 0.46% Nb-added ferritic stainless steel was studied from the viewpoints of solid solution strengthening, precipitation strengthening, and precipitation strengthening during tensile test and/or preceding hold time. The results obtained were as follows.(1) The increase in high temperature proof strength in Nb-added ferritic stainless steel is particularly remarkable at around 700°C in comparison with that in Ti-added steels.(2) After aging treatment for 2 h at 700°C, in addition to the approximately 0.14 % content of coarse Nb carbides and nitrides which had precipitated before this aging treatment, fine Fe2Nb Laves phase particles with a size of 0.02 μm precipitated out in an amount of approximately 0.3%, and virtually no solid solution Nb existed in the steel. The 700°C proof strength in this condition showed a value near the 700°C proof strength before the aging treatment, that is, when approximately 0.3% solid solution Nb was present.(3) When aging treatment is performed at 700°C for 2 h or more, virtually all the added Nb precipitates out. The coarsening of the Fe2Nb laves phase particles within the range of 0.02-0.05 μm during aging at 700°C greatly decreases the high temperature proof strength at 700°C.(4) Cold rolled steel sheets of Nb-added ferritic stainless steel are normally manufactured by annealing at a temperature of 900°C or higher in order to cause recrystallization. Accordingly, before measurement of the proof strength at 700°C, the steel contains a large quantity of solid solution Nb. The phenomenon of particularly high strength at 700°C is considered to be attributable to the precipitation of this solid solution Nb as a fine Fe2Nb Laves phase during the tensile test and/or preceding hold time.
Green energy driven user association in cellular networks with dual battery system (2016)

Green communications has received much attention in recent years. In cellular networks, base stations (BSs) account for more than 50 percent of the energy consumption. Reducing energy consumption of BSs is essential to realizing green cellular networks. Utilizing green energy to power BSs is a promising way to reduce the on-grid energy consumption. Maximizing the utilization of green energy has thus been proposed to furthest save the on-grid energy. In this paper, we propose a green energy driven user-BS association with dual battery system to maximize the utilization of green energy at BSs. The BSs of cellular networks are powered by both on-grid energy and green energy. The optimal usage of green energy is achieved by balancing the mobile users among BSs according to the amount of residual green energy in their batteries. This green energy driven user association optimization problem is NP-hard. Hence, we propose some heuristics to maximize the green energy utilization and approximate the optimal user association with low computational complexity. Finally, we validate the performance of the proposed algorithm through extensive simulations.
Replacement Rules for Water Mains (1987)

Decisions about whether to replace water mains are usually based on engineering judgment. Some quantitative rules for water main replacement have been developed based on a comparison of replacement costs with the costs of breaks. The formulas presented in this article represent an improvement in that they include the costs caused by leakage and inoperative valves.
Engineering high-speed allosteric hammerhead ribozymes (2007)

Full-length hammerhead ribozymes were subjected to in vitro selection to identify variants that are allosterically regulated by theophylline in the presence of a physiologically relevant concentration of Mg(2+). The population of allosteric ribozymes resulting from 15 rounds of in vitro selection yielded variants with observed rate constants (k (obs)) as high as 8 min(-1) in the presence of theophylline and maximal k (obs) increases of up to 285-fold compared to rate constants measured in the absence of effector. The selected ribozymes have kinetic characteristics that are predicted to be sufficient for cellular gene control applications, but do not exhibit any activity in reporter gene assays. The inability of the engineered RNAs to control gene expression suggests that the in vitro and in vivo folding pathways of the RNAs are different. These results provide several key pieces of information that will aid in future efforts to engineer allosteric ribozymes for gene control applications.
Brief Report: Dclk1 Deletion in Tuft Cells Results in Impaired Epithelial Repair After Radiation Injury (2013)

The role of Dclk1(+) tuft cells in the replacement of intestinal epithelia and reestablishing the epithelial barrier after severe genotoxic insult is completely unknown. Successful restoration requires precise coordination between the cells within each crypt subunit. While the mechanisms that control this response remain largely uncertain, the radiation model remains an exceptional surrogate for stem cell-associated crypt loss. Following the creation of Dclk1-intestinal-epithelial-deficient Villin-Cre;Dclk1(flox/flox) mice, widespread gene expression changes were detected in isolated intestinal epithelia during homeostasis. While the number of surviving crypts was unaffected, Villin-Cre;Dclk1(flox/flox) mice failed to maintain tight junctions and died at approximately 5 days, where Dclk1(flox/flox) mice lived until day 10 following radiation injury. These findings suggest that Dclk1 plays a functional role critical in the epithelial restorative response.
The molecular basis of homocystinuria due to cystathionine beta-synthase deficiency in Italian families, and report of four novel mutations. (1995)

Four new mutations in the cystathionine beta-synthase (CBS) gene have been identified in Italian patients with homocystinuria. The first mutation is a G-to-A transition at base 374 in exon 3, causing an arginine-to-glutamic acid substitution at position 125 of the protein (R125Q). This mutation has been found in homozygosity in a patient partially responsive to pyridoxine treatment. The second mutation is a C-to-T transition at base 770 in exon 7, causing a threonine-to-methionine substitution at amino acid 257 of the protein (T257M). This mutation has been observed in homozygosity in a patient nonresponsive to the cofactor treatment. The third mutation, found in heterozygosity in a patient responsive to pyridoxine treatment, is an insertion of 68 bp in exon 8 at base 844, which introduces a premature termination codon. The fourth mutation is C-to-T transition in exon 2 at base 262, causing a proline-to-serine substitution at position 88 of the protein (P88S). This mutation is carried on a single allele in three affected sisters responsive to the cofactor treatment. In addition, six previously reported mutations (A114V, E131D, P145L, I278T, G307S, and A1224-2C) have been tested in 14 independent Italian families. Mutations A114V and I278T are carried by three and by seven independent alleles, respectively. The other four mutations--including G307S and A1224-2C, common among northern European patients--have not been detected.
Immediate provisional restoration of Osseotite implants: a clinical report of 18-month results. (2004)

The results of this study suggest that immediate restoration of Osseotite implants can be accomplished with results that are similar to the results obtained with the traditional 1- or 2-stage surgical, unloaded healing protocols.
Phosphorus: An Alternative for High Capacity Li-Ion Battery Anodes (2014)

Greater gravimetric and volumetric electrode capacities could result in battery technologies finding greater use in transportation, industrial equipment, electronics, and electric grid applications. Currently, the volumetric capacities of graphite electrodes used in commercial Li-ion cells approach 500 mAh/cm 3 , while the volumetric capacities of commercial cathodes approach 700 mAh/cm 3 . Thus, there is a pressing need to develop high capacity anodes to match or exceed the volumetric capacities of cathodes. Tin (Sn) and silicon (Si) – based anodes have been heavily investigated in recent years, while many other materials have received significantly less attention (1). Phosphorus (P) had attracted very little interest until recent years, perhaps due to its difficulty in handling, but has since been shown to offer high gravimetric capacity and rate capability (2). Furthermore, the theoretical volumetric capacity of P is higher than that of Si (2266 mAh/cm 3 for Li 3 P vs. 2190 mAh/cm 3 for Li 15 Si 4 ) (3,4), and Li 3 P is known to have high Li + conductivity (5). Here we report on our early investigations of P-based anodes produced using various polymeric binders. The choice of binder material is key to the development of well performing electrodes (6,7). A broad range of binders were tested and analyzed for their impact on the stability and rate performance of phosphorous-carbon composites. Scanning electron microscopy (SEM), transmission electron microscopy (TEM), energy dispersive spectroscopy (EDS) and X-ray photoelectron spectroscopy (XPS) were used to analyze both the structure and chemistry of the anode materials before and after cycling. Atomic force microscopy (AFM) was used to test mechanical properties of polymer binders (such as swelling and stiffness) in electrolyte solvent solution. Cyclic voltammetry (CV) at different rates was used to test both the electrochemical stability of the polymers and performance of P-based anodes, while electrochemical impedance spectroscopy (EIS) and galvanostatic charge-discharge cycling at different current densities were additionally used to test the electrochemical performance of the final electrodes in half cells. Our results indicate significant promise for P-based anodes in select applications. REFERENCES N. Nitta and G. Yushin, Part. Part. Syst. Char. , (2013). J. Qian, D. Qiao, X. Ai, Y. Cao, and H. Yang, Chem. Commun. , 48 , 8931 (2012). A. Jain, S.P. Ong, G. Hautier, W. Chen, W.D. Richards, S. Dacek, S. Cholia, D. Gunter, D. Skinner, G. Ceder, K.A. Persson, APL Materials , 1 , 01002 (2013). F. Zhou, M. Cococcioni, C. Marianetti, D. Morgan, G. Ceder, Phys. Rev. B , 70 , 235121 (2004). G. Nazri, Solid State Ionics , 34 , 97 (1989). A. Magasinski, B. Zdyrko, I. Kovalenko, B. Hertzberg, R. Burtovyy, C. F. Huebner, T. F. Fuller, I. Luzinov, and G. Yushin, ACS Appl. Mater. Interfaces , 2 , 3004 (2010). I. Kovalenko, B. Zdyrko, A. Magasinski, B. Hertzberg, Z. Milicev, R. Burtovyy, I. Luzinov, and G. Yushin, Science , 334 , 75 (2011).