Miracle-dz/UniFAR-FTUs huggingface dataset:
Orca: a modular query optimizer architecture for big data

The performance of analytical query processing in data management systems depends primarily on the capabilities of the system's query optimizer. Increased data volumes and heightened interest in processing complex analytical queries have prompted Pivotal to build a new query optimizer. In this paper we present the architecture of Orca, the new query optimizer for all Pivotal data management products, including Pivotal Greenplum Database and Pivotal HAWQ. Orca is a comprehensive development uniting state-of-the-art query optimization technology with own original research resulting in a modular and portable optimizer architecture. In addition to describing the overall architecture, we highlight several unique features and present performance comparisons against other systems.
Adiponectin Gene Polymorphisms are Associated with Increased Risk of Colorectal Cancer

Background This meta-analysis investigates the associations of adiponectin (ADIPOQ) genetic polymorphisms with the susceptibility to colorectal cancer (CRC). Material/Methods 2 reviewers independently searched 6 databases – PubMed, Cochrane Library, Ovid, Embase, China National Knowledge Infrastructure (CNKI) and Wanfang databases – to identify published studies relevant to adiponectin gene polymorphisms and CRC. Studies retrieved from database searches were screened using our stringent inclusion and exclusion criteria. Full texts of the selected studies were accessed and related data was extracted using a standardized data extraction form. Comprehensive Meta-analysis 2.0 software was used for statistical analyses. Results A total of 188 studies were initially retrieved from database search, and 6 studies were eventually selected, through a rigorous screening process, for inclusion in this meta-analysis. The 6 studies contained a total of 1897 patients (Asians: 1190; white: 707) with CRC in case group and 2475 healthy controls (Asians: 1325; white: 1150) in the control group. Results of the current meta-analysis revealed that the rs2241766 T>G single-nucleotide polymorphisms (SNP) increase the risk of CRC; rs1501299 G>T under dominant model was associated with increased risk of CRC; and rs266729 C>G SNP under allele model conferred an increased risk of CRC. Conclusions Our meta-analysis strongly suggests that the ADIPOQ rs2241766 T>G, rs1501299 G>T, and rs266729 C>G SNPs correlate with an increased risk of CRC.
Apoptotic U1-70 kd is antigenically distinct from the intact form of the U1-70-kd molecule.

OBJECTIVE To determine whether immune responses to an apoptotically modified form of a human lupus autoantigen can be distinguished from immune responses to the intact form of the same antigen. METHODS Immunoblot and enzyme-linked immunosorbent assay techniques were used to test human autoimmune sera for the presence of antibodies to apoptotic forms of the U1- 70-kd small nuclear RNP antigen, while antibody recognition of intact U1-70 kd was blocked. RESULTS poptosis-specific U1-70-kd antibodies were identified by immunoblot in 15 of 29 sera with antibodies to intact U1-70 kd and in 2 of 25 sera without measurable antibodies to intact U1-70 kd. Bacterially produced, purified, caspase-cleaved U1-70 kd without additional posttranslational modifications was a target of apoptosis-specific antibodies in 3 of 9 U1-70-kd-positive sera tested. CONCLUSION The apoptotic form of U1-70 kd displays B cell epitopes that are not displayed on the intact form of U1-70 kd. Caspase cleavage in the absence of additional posttranslational modifications is sufficient to induce the display of some of these epitopes. Immunity to apoptotically modified proteins can develop against caspase-cleaved forms or against forms that undergo additional posttranslational modification.
An optimal adaptive mixed finite element method

Various applications in fluid dynamics and computational continuum mechanics motivate the development of reliable and efficient adaptive algorithms for mixed finite element methods. In order to save degrees of freedom, not all but just some selected set of finite element domains are refined. Hence the fundamental question of convergence as well as the question of optimality require new mathematical arguments. The presented adaptive algorithm for Raviart-Thomas mixed finite element methods solves the Poisson model problem, with optimal convergence rate. Chen, Holst, and Xu presented "convergence and optimality of adaptive mixed finite element methods" (2008) following arguments of Rob Stevenson for the conforming finite element method. Their algorithm reduces oscillations separately, before approximating the solution by some adaptive algorithm in the spirit of W. Dorfler (1996). The algorithm proposed here appears more natural in switching to either reduction of the edge-error estimator or of the oscillations.
Perceptual Learning of Phonetic Information That Indicates Morphological Structure

Abstract Familiarity with a talker or accent can facilitate speech perception, but little is known about the acoustic-phonetic knowledge that is acquired during exposure to an unfamiliar talker, particularly with respect to how a talker realises grammatical and prosodic distinctions. The present experiment used relatively natural stimuli and tasks to investigate listeners' adaptation to a phonetic variant that is systematically associated with a morphological context, specifically the English /ri:/ prefix. Results showed that listeners who had previously been exposed to the atypical variant in /ri:/ prefixes in stories scored higher than control listeners in an intelligibility-in-noise task that included instances of the atypical variant. Perceptual learning was partly specific to the /ri:/ prefix, though there was weak generalisation of learning to word-initial /ri:/ syllables that were not prefixes. These results emphasise the value of developing context-sensitive, probabilistic models of speech perception which include multiple, parallel levels of representation.
Envelope tracking GaN power supply for 4G cell phone base stations

This paper introduces an envelope tracking (ET) power supply for 4G cell phone base stations using EPC eGaN® FETs. An analytical loss model is developed for design optimization and verified by a single phase synchronous buck converter using the zero-voltage switching (ZVS) technique. The model is then extended to four phases and is used to design a 60 W ET power supply with 20 MHz large signal bandwidth (BW). At 25 MHz per-phase switching frequency, measured static power stage efficiency peaks at 96.5% with 68 W output power delivered from 30 V. Experimental results demonstrate accurate tracking of 20 MHz 7 dB Peak-to-Average Power Ratio (PAPR) LTE envelope with 92.3% total efficiency, delivering 67 W average power from 30 V.
Finding Functional Features in Saccharomyces Genomes by Phylogenetic Footprinting

The sifting and winnowing of DNA sequence that occur during evolution cause nonfunctional sequences to diverge, leaving phylogenetic footprints of functional sequence elements in comparisons of genome sequences. We searched for such footprints among the genome sequences of six Saccharomyces species and identified potentially functional sequences. Comparison of these sequences allowed us to revise the catalog of yeast genes and identify sequence motifs that may be targets of transcriptional regulatory proteins. Some of these conserved sequence motifs reside upstream of genes with similar functional annotations or similar expression patterns or those bound by the same transcription factor and are thus good candidates for functional regulatory sequences.
A divide-and-conquer approach to test generation for large synchronous sequential circuits

A method for generating tests for synchronous sequential circuits that does not use the complete circuit description is proposed, to allow true divide-and-conquer to be applied to test generation. The method is based on the generation of primary input sequences such that for as many sequences generated by the adjacent subcircuits as possible, a test sequence for the subcircuit under consideration would result. Repeated application of test sequences is proposed as a means of increasing the probability of fault detection. Experimental results are presented to show that the method is applicable to subcircuits of large sequential circuits. <<ETX>>
Mast Cells Limit Systemic Bacterial Dissemination but Not Colitis in Response to Citrobacter rodentium

ABSTRACT Enteropathogenic Escherichia coli and enterohemorrhagic E. coli cause an inflammatory colitis in human patients characterized by neutrophil infiltration, proinflammatory cytokine expression, and crypt hyperplasia. Citrobacter rodentium causes a similar colitis in mice and serves as a model for enteropathogenic E. coli infection in humans. C. rodentium induces systemic T-cell-dependent antibody production that facilitates clearance of the bacteria and protects the host from reinfection. The role of innate immune cells in infectious colitis, however, is less well understood. In this study, we have determined the role of mast cells in the inflammatory response and disease induced by C. rodentium. Mice deficient in mast cells exhibit more severe colonic histopathology and have a higher mortality rate following infection with C. rodentium than do wild-type animals. Despite unimpaired neutrophil recruitment and lymphocyte activation, mast cell-deficient mice have a disseminated infection evident in crucial organ systems that contributes to sepsis. Importantly, mast cells also have the capacity to directly kill C. rodentium. Together, these results suggest that mast cells protect the host from systemic infection by reducing the bacterial load and preventing dissemination of the bacterium from the colon.
Firewall design: consistency, completeness, and compactness

A firewall is often placed at the entrance of each private network in the Internet. The function of a firewall is to examine each packet that passes through the entrance and decide whether to accept the packet and allow it to proceed or to discard the packet. A firewall is usually designed as a sequence of rules. To make a decision concerning some packets, the firewall rules are compared, one by one, with the packet until one rule is found to be satisfied by the packet: this rule determines the fate of the packet. We present the first ever method for designing the sequence of rules in a firewall to be consistent, complete, and compact. Consistency means that the rules are ordered correctly, completeness means that every packet satisfies at least one rule in the firewall, and compactness means that the firewall has no redundant rules. Our method starts by designing a firewall decision diagram (FDD, for short) whose consistency and completeness can be checked systematically (by an algorithm). We then apply a sequence of five algorithms to this FDD to generate, reduce and simplify the target firewall rules while maintaining the consistency and completeness of the original FDD.
Improving high temperature properties of alumina based ceramic cores containing yttria by vacuum impregnating

Abstract Ceramic cores used in investment casting for directional solidification and single crystal blades must have excellent high temperature properties. A strengthening process was developed to improve high temperature properties of alumina based ceramic cores containing yttria. Besides, different parameters, including reinforcing agent, the number of times of vacuum impregnating, were investigated. The experimental results showed that aqueous yttria sol can improve the high temperature properties of ceramic cores through multiple impregnating, which made it a suitable reinforcing agent. Considering the effects of the strengthening process on the apparent porosity and sintered shrinkage of ceramic cores, the optimal vacuum impregnating process was determined. Furthermore, the strengthening mechanism was revealed by using X-ray diffraction and electron spectroscopy analysis. The high temperature properties of the strengthened ceramic cores can meet the requirements of directional solidification and single crystal casting, which benefits the production of turbine blades.
Information Divergence Based Saliency Detection with a Global Center-Surround Mechanism

In this paper a novel technique for saliency detection called Global Information Divergence is proposed. The technique is based on the diversity in information between two regions. Initially patches are extracted at multi-scales from the input images. This is followed by reducing the dimensionality of the extracted patches using Principal Component Analysis. After that the information divergence is evaluated between the reduced dimensionality patches, and calculated between a center and a surround region. Our technique uses a global method for defining the center patch and the surround patches collectively. The technique is tested on four competitive and complex datasets both for saliency detection and segmentation. The results obtained show a good performance in terms of quality of the saliency maps and speed compared with 16 state-of-the-art techniques.
A 5.8 GHz 1.7 dB NF fully integrated differential low noise amplifier in CMOS

This work presents a fully integrated differential 5.8 GHz low-noise amplifier (LNA). The LNA is fabricated in a 90 nm RF-CMOS process and has a power gain of 12.5 dB, an IIP3 of 4dBm, and a noise figure of 1.7 dB consuming 14 mA from a 1.2 V supply. Compared to previously reported differential CMOS designs this LNA show lower noise figure and better linearity.
Evolution of chemical, biological, and physical water properties in the northern California Current in 2005: Remote or local wind forcing?

The spring onset of persistent upwelling‐favorable winds was later than usual in the northern California Current system in 2005, resulting in delayed provision of inorganic nutrients to the upper waters of the coastal ocean. This study uses water column measurements to illustrate the evolution of temperature, salinity, nitrate and chlorophyll a prior to and after the onset of persistent local upwelling‐favorable winds, including recovery to “typical” conditions. Warm, nutrient‐ and chlorophyll‐depleted surface conditions similar to those in an El Niño were observed from Vancouver Island to central Oregon, and extended to depths greater than 500 m. Return to typical conditions was more rapid than suggested by time‐integrated local wind stress but consistent in timing with “remote” forcing of water properties in this region by upwelling‐favorable winds off northern California. Alongshore advection also likely contributed to the observed recovery, but was much less effective than upwelling.
HippDB: a database of readily targeted helical protein-protein interactions

SUMMARY HippDB catalogs every protein-protein interaction whose structure is available in the Protein Data Bank and which exhibits one or more helices at the interface. The Web site accepts queries on variables such as helix length and sequence, and it provides computational alanine scanning and change in solvent-accessible surface area values for every interfacial residue. HippDB is intended to serve as a starting point for structure-based small molecule and peptidomimetic drug development. AVAILABILITY AND IMPLEMENTATION HippDB is freely available on the web at http://www.nyu.edu/projects/arora/hippdb. The Web site is implemented in PHP, MySQL and Apache. Source code freely available for download at http://code.google. com/p/helidb, implemented in Perl and supported on Linux. CONTACT arora@nyu.edu.
The Effect of Nano-Sized β-Tricalcium Phosphate on Remineralization in Glass Ionomer Dental Luting Cement

This study aimed to evaluate the anticariogenic and remineralization effects of the glass ionomer dental luting cement containing nano-β-TCP in vitro. The β-Tricalcium Phosphate (β-TCP) are the components of dental enamel and bone mineral as biological apatites. In addition, β-TCP contains a significant amount of calcium and phosphate, which can promote remineralization of enamel subsurface lesions in animal and human. RelyXTM glass ionomer cement(3M/ESPE, USA) was used as dental luting cement. Film thickness, setting time, and compressive strength was measured for each group of pure glass GIC, 15% nano-β-TCP GIC. Human molars were prepared in box-shaped cavities that were filled with the GIC with and without the 15% nano-β-TCP were placed in 25ml of pH 5.0 acid buffer for 4 days at 37°C. After 4 days, longitudinal sections (1007m) were obtained through the center of each restoration. The sections were analyzed using a scanning electronic microscope (SEM) and confocal laser scanning microscopy (CLSM) to identify the change in the enamel surface. A significant difference in the CLSM images between pure GIC and nano-β-TCP-GIC. CLSM allows the demineralized surface layers of sound enamel to be visualized down to approximately 100 μm. The pure GIC specimens had a relatively thick fluorescent layer. On the other hand, the fluorescent layer of the nano-β-TCP-GIC specimens were thinner. The SEM images of micro surfaces demonstrate that nano-β-TCP-GIC is less rough than pure GIC. Therefore, the addition of nano-β-TCP enhanced protection against acid demineralization and promoted remineralization of enamel surface.
Causal Structure Learning and Inference: A Selective Review

Abstract In this paper we give a review of recent causal inference methods. First, we discuss methods for causal structure learning from observational data when confounders are not present and have a close look at methods for exact identifiability. We then turn to methods which allow for a mix of observational and interventional data, where we also touch on active learning strategies. We also discuss methods which allow arbitrarily complex structures of hidden variables. Second, we present approaches for estimating the interventional distribution and causal effects given the (true or estimated) causal structure. We close with a note on available software and two examples on real data.
Rainfall seasonality and pest pressure as determinants of tropical tree species' distributions

Drought and pests are primary abiotic and biotic factors proposed as selective filters acting on species distributions along rainfall gradients in tropical forests and may contribute importantly to species distributional limits, performance, and diversity gradients. Recent research demonstrates linkages between species distributions along rainfall gradients and physiological drought tolerance; corresponding experimental examinations of the contribution of pest pressure to distributional limits and potential interactions between drought and herbivory are limited. This study aims to quantitate differential performance and herbivory as a function of species range limits across a climatic and floristic transition in Southeast Asia. Khao Chong Botanical Garden, Thailand and Pasoh Forest Reserve, Malaysia straddle the Kangar-Pattani Line. A reciprocal transplantation across a seasonality gradient was established using two groups of species (“widespread” taxa whose distributions include seasonally dry forests and “aseasonal” taxa whose distributions are limited to aseasonal forests). Growth, biomass allocation, survival, and herbivory were monitored for 19 months. Systematic differences in performance were a function of species distribution in relation to rainfall seasonality. In aseasonal Pasoh, aseasonal species had both greater growth and survivorship than widespread species. These differences were not a function of differential herbivory as widespread and aseasonal species experienced similar damage in the aseasonal forest. In seasonally dry Khao Chong, widespread species showed higher survivorship than aseasonal species, but these differences were only apparent during drought. We link this differential performance to physiological mechanisms as well as differential tolerance of biotic pressure during drought stress. Systematic decreases in seedling survival in aseasonal taxa during drought corresponded with previously documented physiological differences and may be exacerbated by herbivore damage. These results have important implications for tropical diversity and community composition in light of predicted increases in the frequency and severity of drought in hyperdiverse tropical forests.
Physicians, Primary Caregivers and Topical Repellent: All Under-Utilised Resources in Stopping Dengue Virus Transmission in Affected Households

Background Primary health care facilities frequently manage dengue cases on an ambulatory basis for the duration of the patient’s illness. There is a great opportunity for specific messaging, aimed to reduce dengue virus (DENV) transmission in and around the home, to be directly targeted toward this high-risk ambulatory patient group, as part of an integrated approach to dengue management. The extent however, to which physicians understand, and can themselves effectively communicate strategies to stop focal DENV transmission around an ambulatory dengue case is unknown; the matter of patient comprehension and recollection then ensues. In addition, the effectiveness of N,N-diethyl-3-methylbenzamide (DEET)-based insect repellent in protecting dengue patients from Aedes aegypti mosquitoes’ bites has not been investigated. Methodology A knowledge, attitude and practice (KAP) survey, focusing on the mechanisms of DENV transmission and prevention, was performed using semi-structured questionnaires. This survey was targeted towards the patients and family members providing supportive care, and physicians routinely involved in dengue patient management in Southern Vietnam. An additional clinical observational study was conducted to measure the efficacy of a widely-used 13% DEET-based insect repellent to repel Ae. aegypti mosquitoes from the forearms of dengue cases and matched healthy controls. Principal Findings Among both the physician (n = 50) and patient (n = 49) groups there were several respondents lacking a coherent understanding of DENV transmission, leading to some inappropriate attitudes and inadequate acute preventive practices in the household. The application of insect repellent to protect patients and their relatives from mosquito bites was frequently recommended by majority of physicians (78%) participating in the survey. Nevertheless, our tested topical application of 13% DEET conferred only ~1hr median protection time from Ae. aegypti landing. This is notably shorter than that advertised on the manufacturer’s label. No differences in landing time between febrile dengue cases or matched healthy controls (n = 19 experiments) were observed. Conclusion/Significance Our study identifies missed opportunities for primary care physicians to improve public health through communication of strategies that could prevent focal dengue transmission in and around a case household. We advocate better access to more efficient communication methods for physicians and auxilliary health workers, supporting to educate those at high risk of DENV transmission. Our empirical testing of a widely-available 13% DEET-based repellent was limited in its protective efficacy against Ae. aegypti mosquito bites, and therefore DENV transmission, suggesting more frequent application is necessary to be beneficial.