Miracle-dz/UniFAR-FTUs huggingface dataset:
CoVDB: a comprehensive database for comparative analysis of coronavirus genes and genomes

The recent SARS epidemic has boosted interest in the discovery of novel human and animal coronaviruses. By July 2007, more than 3000 coronavirus sequence records, including 264 complete genomes, are available in GenBank. The number of coronavirus species with complete genomes available has increased from 9 in 2003 to 25 in 2007, of which six, including coronavirus HKU1, bat SARS coronavirus, group 1 bat coronavirus HKU2, groups 2c and 2d coronaviruses, were sequenced by our laboratory. To overcome the problems we encountered in the existing databases during comparative sequence analysis, we built a comprehensive database, CoVDB (http://covdb.microbiology.hku.hk), of annotated coronavirus genes and genomes. CoVDB provides a convenient platform for rapid and accurate batch sequence retrieval, the cornerstone and bottleneck for comparative gene or genome analysis. Sequences can be directly downloaded from the website in FASTA format. CoVDB also provides detailed annotation of all coronavirus sequences using a standardized nomenclature system, and overcomes the problems of duplicated and identical sequences in other databases. For complete genomes, a single representative sequence for each species is available for comparative analysis such as phylogenetic studies. With the annotated sequences in CoVDB, more specific blast search results can be generated for efficient downstream analysis.
The β-Catenin/T-Cell Factor/Lymphocyte Enhancer Factor Signaling Pathway Is Required for Normal and Stress-Induced Cardiac Hypertrophy

ABSTRACT In cells capable of entering the cell cycle, including cancer cells, β-catenin has been termed a master switch, driving proliferation over differentiation. However, its role as a transcriptional activator in terminally differentiated cells is relatively unknown. Herein we utilize conditional, cardiac-specific deletion of the β-catenin gene and cardiac-specific expression of a dominant inhibitory mutant of Lef-1 (Lef-1Δ20), one of the members of the T-cell factor/lymphocyte enhancer factor (Tcf/Lef) family of transcription factors that functions as a coactivator with β-catenin, to demonstrate that β-catenin/Tcf/Lef-dependent gene expression regulates both physiologic and pathological growth (hypertrophy) of the heart. Indeed, the profound nature of the growth impairment of the heart in the Lef-1Δ20 mouse, which leads to very early development of heart failure and premature death, suggests β-catenin/Tcf/Lef targets are dominant regulators of cardiomyocyte growth. Thus, our studies, employing complementary models in vivo, implicate β-catenin/Tcf/Lef signaling as an essential growth-regulatory pathway in terminally differentiated cells.
Assuring Assured Retaliation: China's Nuclear Posture and U.S.-China Strategic Stability

Abstract Whether China will abandon its long-standing nuclear strategy of assured retaliation for a first-use posture will be a critical factor in future U.S.-China strategic stability. In the past decade, advances in U.S. strategic capabilities, especially missile defenses and enhanced long-range conventional strike capacity, could undermine China's nuclear retaliatory capability, which is based on a relatively small force and second-strike posture. An exhaustive review of Chinese writings on military affairs indicates, however, that China is unlikely to abandon its current nuclear strategy of assured retaliation. Instead, China will modestly expand its arsenal, increase the sophistication of its forces, and allow limited ambiguity regarding its pledge not to use nuclear weapons first. This limited ambiguity allows China to use the threat of nuclear retaliation to deter a conventional attack on its nuclear arsenal, without significantly increasing the size of its nuclear forces and triggering a costly arms race. Nevertheless, China's effort to maintain its strategy of assured retaliation while avoiding an arms race could backfire. Those efforts increase the risk that nuclear weapons could be used in a crisis between the United States and China, even though China views this possibility as much less likely than the United States does.
Mitigation of organic compound movement in landfills by shredded tires

This paper evaluates the feasibility of using shredded tires for removal of organic compounds from landfill leachate. From the batch sorption isotherm experiments, tire chips were found to have 1.4% to 5.6% of the sorption capacity of granular activated carbon on a volume basis. The sorption equilibrium occurred within 2 days for 0.6-, 1.3-, and 2.5-cm size tire chips. The capacity of tire chips to adsorb organic compounds in a multisolute system was almost equal to that in single-solute systems. Only 3.4% to 7.9% of the organic compounds sorbed in tire chips were desorbed. A design method was proposed to estimate the thickness of a tire layer required for a target organic compound removal from the landfill leachate based on a structure-activity relationship obtained from laboratory tests.
Memory Management Strategies for Single-Pass Index Construction in Text Retrieval Systems

Many text retrieval systems construct their index by accumulating postings in main memory until there is no more memory available and then creating an on-disk index from the in-memory data. When the entire text collection has been read, all on-disk indices are combined into one big index through a multiway merge process. This paper discusses several ways to arrange postings in memory and studies the eects on memory requirements and indexing performance. Starting from the traditional approach that holds all postings for one term in a linked list, we examine strategies for combining consecutive postings into posting groups and arranging these groups in a linked list in order to reduce the number of pointers in the linked list. We then extend these techniques to compressed posting lists and nally evaluate the eects they have on overall indexing performance for both static and dynamic text collections. Substantial improvements are achieved over the initial approach.
Very low-cost internet access using KioskNet

Rural Internet kiosks in developing regions can cost-effectively provide communication and e-governance services to the poorest sections of society. A variety of technical and non-technical issues have caused most kiosk deployments to be economically unsustainable [1]. KioskNet addresses the key technical problems underlying kiosk failure by using robust 'mechanical backhaul' for connectivity [2], and by using low-cost and reliable kiosk-controllers to support services delivered from one or more recycled PCs. KioskNet also addresses related issues such as security, user management, and log collection. In this paper, we describe the KioskNet system, outlining its hardware, software, and security architecture. We describe a pilot deployment, and how we used lessons from this deployment to re-design our initial proto-type.
Hot flushes in healthy aging men differ from those in men with prostate cancer and in menopausal women

Calcitonin gene-related peptide (CGRP) seems to be involved in hot flushes in women and in castrated men. Therefore, we studied whether the plasma concentrations of CGRP changed during flushes in a group of healthy aging men. Twelve men (49–71 years) with no history of current or former prostate cancer or hormonal treatment reporting ≥20 flushes/week were investigated. Blood samples were drawn during and between flushes for analysis of CGRP and also androgen concentrations, that is, testosterone and bioavailable testosterone were analysed. Skin temperature and skin conductance were monitored. Thirty-five flushes were reported by 10 men. The plasma concentrations of CGRP did not increase during flushes. No significant change in skin temperature or conductance was found. CGRP is probably not involved in the mechanisms of flushes in healthy aging men. Therefore, flushes in aging healthy men seem to be different from flushes in men and women deprived of sex steroids where CGRP increases during flushes.
Specificity of synaptic regeneration in the spinal cord of the larval sea lamprey.

1. Pairs of central neurones in large larval sea lampreys were impaled with micro‐electrodes and studied for synaptic connexions in both unoperated control animals and animals which had recovered from complete spinal transection. Two identified classes of neurones served as post‐synaptic targets: giant interneurones (g.i.s) and lateral cells (l.c.s). Several identified neurone types were tested as potential sources of presynaptic input. 2. When synaptic potentials had short, fixed latencies they also persisted during activation of the presynaptic cell at 3.3‐33.3 Hz and were not eliminated after addition of lamprey saline containing high (20 mM) Ca2+. These presumably represented monosynaptic connexions. Variable‐latency responses were eliminated by faster rates of stimulation of the presynaptic cell and were mediated via polysynaptic pathways. 3. In control animals, g.i. s received monosynaptic input from more caudal g.i. s in fourteen of thirty‐two tested cell pairs. These excitatory post‐synaptic potentials (e.p.s.p.s) were composite electrochemical responses. The amplitudes of the earlier electrical component averaged 1.66 +/‐ 0.24 mV (mean +/‐ S.E. of mean) and the amplitude of the later chemical component averaged 0.79 +/‐ 0.05 mV. 4. In operated larvae, eight of forty‐seven g.i. ‐g.i. pairs separated by the transection scar were connected by monosynaptic composite e.p.s.p.s. In these pairs the electrical component averaged 0.84 +/‐ 0.17 mV (P less than 0.05 vs. control) and the chemical component averaged 1.56 +/‐ 0.40 mV. The average conduction velocity between these cells was less than that in control g.i. ‐g.i. pairs (0.93 +/‐ 0.11 vs. 1.61 +/‐ 0.25 m/s; P less than 0.01). 5. The l.c. s showed monosynaptic e.p.s.p.s after activation of a subset of the bulbar Müller neurones (B2‐4) in seven of twelve pairs. In behaviourally recovered larvae three of twenty‐two similar pairs separated by the transection scar were also connected via monosynaptic e.p.s.p.s. The average conduction velocity between these experimental neurones was also less than that in control bulbar‐l.c. pairs (1.03 +/‐ 0.03 vs. 1.58 +/‐ 0.09 m/s; P less than 0.001). 6. Several types of neurones were either infrequently linked or never connected to g.i. s or to l.c. s in control larvae. In animals which had recovered from a spinal transection, no synaptic connexions were found from such neurones on to g.i. s or l.c. s respectively, in 124 tested cell pairs. In addition, dorsal cells (intraspinal primary sensory neurones) received no synaptic input upon stimulation of the spinal cord before or after transection. (ABSTRACT TRUNCATED AT 400 WORDS)
Bisphosphonates in oncology: evidence for the prevention of skeletal events in patients with bone metastases

Bone metastases frequently occur in patients with advanced solid tumors, particularly breast and prostate cancers, and nearly all patients with multiple myeloma have some degree of skeletal involvement. The strides made in treating these primary tumors have extended median survival times and thereby increased patient risk for skeletal-related events (SREs), including pathologic fractures, spinal cord compression, need for palliative radiation therapy or surgery to bone, and hypercalcemia. Bisphosphonates, inhibitors of osteoclastic bone resorption that were first established as treatment of osteoporosis, have been shown to prevent and/or delay SREs related to malignancy. The results of a large, randomized phase 3 study comparing zoledronic acid and pamidronate in breast cancer or multiple myeloma patients with osteolytic lesions showed that the incidence of SREs, time to first SRE, and risk of developing a SRE were similar between treatment groups. However, in patients with solid tumors (excluding breast or prostate cancer) metastatic to the bone, only zoledronic acid has demonstrated clinical efficacy. Although bone turnover marker levels, such as N-telopeptide of type I collagen, have been shown to correlate with clinical response, additional studies are needed to validate their ability to predict response to bisphosphonate therapy.
Connexin Specificity of Second Messenger Permeation: Real Numbers At Last

Harris 2008. J. Gen. Physiol. doi:10.1085/jgp.200809998 [OpenUrl][1][FREE Full Text][2] [1]: {openurl}? query=rft_id%253Dinfo%253Adoi%252F10.1085%252Fjgp.200809998%26rft_id%253Dinfo%253Apmid%252F18378797%26rft.genre%253Darticle%26rft_val_fmt%253Dinfo%253Aofi%252Ffmt%253Akev%253Amtx%253Ajournal%
Centrilobular nodules correlate with air trapping in diffuse panbronchiolitis during erythromycin therapy.

BACKGROUND Low-dose erythromycin therapy improves airflow limitation and airway inflammation in patients with diffuse panbronchiolitis (DPB). However, to our knowledge there has been no study to determine whether physiologic improvement during erythromycin therapy correlates with radiologic findings. STUDY OBJECTIVE To clarify whether improvement in pulmonary function correlates with specific changes on chest CT. DESIGN The relationship between five CT findings and five pulmonary function parameters was evaluated before and 3 months after low-dose erythromycin therapy in 24 patients with DPB retrospectively. RESULTS After erythromycin therapy, the predicted percentage of vital capacity (%VC; 87.0 +/- 3.07% vs 98.9 +/- 3.39%; p = 0.00006) and 50% of the maximum midexpiratory flow rate of FVC (1.41 +/- 0.26 L/s vs 1.61 +/- 0.27 L/s; p = 0.03) significantly increased, and the residual volume/total lung capacity ratio (RV/TLC%; 44.5 +/- 1.93% vs 40.7 +/- 1.83%; p = 0.0019) significantly decreased, but the FEV(1) to FVC ratio and 25% of the maximum expiratory flow rate of FVC did not. In five CT findings, centrilobular nodules (3.7 +/- 0.4 vs 1.5 +/- 0.3; p = 0.0001), peripheral bronchiolar wall thickness (3.8 +/- 0.3 vs 2.6 +/- 0.4; p = 0.0007), and peripheral bronchiolectasis (2.8 +/- 0.3 vs 2.2 +/- 0.4; p = 0.0058) had significantly improved, whereas low attenuation area and central bronchiectasis had not. There were positive correlations of improved scores of centrilobular nodules with improved %VC (r = 0.58, p = 0.0062) and RV/TLC% (r = 0.64, p = 0.0022). CONCLUSIONS Decreased air trapping in DPB correlates with an improvement of centrilobular nodules, which reflects the obstructive lesions of bronchioles during the erythromycin therapy.
Effects of Connectivity and Recurrent Local Disturbances on Community Structure and Population Density in Experimental Metacommunities

Metacommunity theory poses that the occurrence and abundance of species is a product of local factors, including disturbance, and regional factors, like dispersal among patches. While metacommunity ideas have been broadly tested there is relatively little work on metacommunities subject to disturbance. We focused on how localized disturbance and dispersal interact to determine species composition in metacommunities. Experiments conducted in simple two-patch habitats containing eight protozoa and rotifer species tested how dispersal altered community composition in both communities that were disturbed and communities that connected to refuge communities not subject to disturbance. While disturbance lowered population densities, in disturbed patches connected to undisturbed patches this was ameliorated by immigration. Furthermore, species with high dispersal abilities or growth rates showed the fastest post-disturbance recovery in presence of immigration. Connectivity helped to counteract the negative effect of disturbances on local populations, allowing mass-effect-driven dispersal of individuals from undisturbed to disturbed patches. In undisturbed patches, however, local population sizes were not significantly reduced by emigration. The absence of a cost of dispersal for undisturbed source populations is consistent with a lack of complex demography in our system, such as age- or sex-specific emigration. Our approach provides an improved way to separate components of population growth from organisms' movement in post-disturbance recovery of (meta)communities. Further studies are required in a variety of ecosystems to investigate the transient dynamics resulting from disturbance and dispersal.
Dust aerosol vertical structure measurements using three MPL lidars during 2008 China-U.S. joint dust field experiment

[1] The 2008 China-U.S. joint dust field experiment, which aims to estimate the effect of dust on radiative forcing and its associated climatic impacts, was conducted during the dust-intensive period from March to June of 2008 over the Loess Plateau of northwest China. Dust aerosol vertical profiles and long-range transport of dust storm were measured with the three MPL-net Micro-Pulse Lidar (MPL) systems as well as other ground-based instruments and spaceborne remote sensing techniques. In this study, to ensure the effectiveness of the retrieval results, an effective algorithm was introduced for retrieving aerosol optical properties and vertical profiles from Mie lidar measurements. The advantage of this algorithm is that Aerosol Optical Depth (AOD) retrieval from lidar measurements can be accomplished without the use of the so-called lidar ratio for the corresponding quantities obtained from the AERONET Sun photometer. Dust aerosol vertical profiles are derived successfully from three MPL lidar systems using this algorithm. A dust storm that affected a large part of northwest China on 2 May 2008 was studied using measurements obtained from the three ground-based lidar systems, satellite-borne instruments and NCEP reanalysis data. The results show that different aerosol vertical structures were present at each site, and the colder Siberia air mass and stronger and longer cyclones around Mongolia are key features leading to the dust storm.
Harmony Graph, a Social-Network-Like Structure, and Its Applications to Music Corpus Visualization, Distinguishing and Music Generation

In this research project, we propose a model, the Harmony Graph, to decompose music into a social-network-like structure according to its harmonies. The whole Harmony Graph network represents the harmony progressions in music. The Harmony Graph is utilized to visualize, distinguish, and generate music for four prepared corpora using social network techniques. We experimented on different characteristics in social network analysis, and we found significant differences among the Harmony Graphs of the four corpora. A new measure called Agglomeration is created to characterize the agglomerating phenomenon that cannot be described sufficiently by existing measures. A corpus-based music composition method is also proposed in this research. By performing random-walk in a Harmony Graph, we generated new music that differs from yet reflects the style of music pieces in the corpus. With the link prediction technique, we also generated music more pleasant aurally than simply using random walks.
E-Cigarettes and Adolescents’ Risk Status

The prevalence of e-cigarette use was only in the low single digits a few years ago but currently reaches ≥30% among high school students, and at least half are regular users.1,2 This rapid explosion of e-cigarette use has caught the field by surprise, and researchers are scrambling to understand the implications for public health. In their paper “Adolescent Risk Behaviors and Use of Electronic Vapor Products and Cigarettes,” Demissie et al3 provide a useful new perspective on this phenomenon. The researchers showed that 16% of the adolescent population used e-cigarettes only, 3% only smoked cigarettes, and 8% were dual users (cigarettes and e-cigarettes). The good news is that 73% of the adolescent population did not use any tobacco-related product (nonusers). However, that 27% of adolescents still do is not comforting to public health researchers and advocates. Here I bring out 3 points about how this paper helps us understand how e-cigarette use is related to adolescents’ risk status overall. The pattern of results in Demissie et al3 shows that youth … Address correspondence to Thomas A. Wills, PhD, Cancer Prevention and Control Program, University of Hawaii Cancer Center, 701 Ilalo St, Room 528, Honolulu, HI 96813. E-mail: twills{at}cc.hawaii. edu
Building Robust Crowdsourcing Systems with Reputation-aware Decision Support Techniques

Crowdsourcing refers to the arrangement in which contributions are solicited from a large group of unrelated people. Due to this nature, crowdsourcers (or task requesters) often face uncertainty about the workers' capabilities which, in turn, affects the quality and timeliness of the results obtained. Trust is a mechanism used by people to facilitate interactions in human societies where risk and uncertain are common. The crucial challenge to building a robust crowdsourcing system is how to make trust-aware task delegation decisions to efficiently utilize the capacities of workers (or trustee agents) to achieve high social welfare? This book presents the research addressing this challenge. It goes beyond the existing trust management research framework by removing a widespread assumption implicitly adopted by existing research: that a trustee agent can process an unlimited number of interaction requests per discrete time unit without compromising its performance as perceived by the task requesters (or truster agents). Decision support in crowdsourcing is re-formalized as a multi-agent trust game based on the principles of the Congestion Game, which is solved by two trust-aware interaction decision-making approaches: 1) the Social Welfare Optimizing approach for Reputation-aware Decision-making (SWORD) approach, and 2) the Distributed Request Acceptance approach for Fair utilization of Trustee agents (DRAFT). SWORD is designed for centralized systems, while DRAFT is designed for fully distributed systems. Theoretical analyses have shown that the social welfare produced by these two approaches can be made closer to optimal by adjusting only one key parameter. With these two approaches, the framework of research for crowdsourcing systems can be enriched to handle more realistic scenarios where workers have varied and limited capabilities.