Miracle-dz/UniFAR-FTUs huggingface dataset:
Variability in the density and sound-speed of coastal zooplankton and nekton

Forman, K. A. , and Warren, J. D. 2010. Variability in the density and sound-speed of coastal zooplankton and nekton. - ICES Journal of Marine Science, 67: 10-18.Acoustic sampling techniques provide an advantage over traditional net-sampling by increasing scientist ability to survey a large area in a relatively short period, as well as providing higher-resolution data in the vertical and horizontal dimensions. To convert acoustic data into measures of biological organisms, physics-based scattering models are often used. Such models use several parameters to predict the amount of sound scattered by a fluid-like or weakly scattering animal. Two important input parameters are the density (g) and sound-speed (h) contrasts of the animal and the surrounding seawater. The density and sound-speed contrasts were measured for coastal zooplankton and nekton species including shrimps (Palaemonetes pugio and Crangon septemspinosa), fish (Fundulus majalis and Fundulus heteroclitus), and polychaetes (Nereis succinea and Glycera americana) along with multiple physiological and environmental variables. Factors such as animal size, feeding status, fecundity, gender, and maturity caused variations in g. The variations in g observed for these animals could lead to large differences (or uncertainties) in abundance estimates based on acoustic scattering models and field-collected backscatter data. It may be important to use a range of values for g and h in the acoustic scattering models used to convert acoustic data into estimates of the abundance of marine organisms.
Scalable Network-based Learning Methods for Automated Function Prediction based on the Neo 4 j Graph-database

A recent class of gene/protein function predictors, based on Graph Semi Supervised Learning (GSSL) [1], is able to exploit the functional relationships between genes to propagate existing annotations to unannotated genes that are topologically related in the network. As the prediction of gene functions using network-based methods is frequently performed at whole genome level, the development of scalable methods is of critical importance to make feasible the analysis of very large graphs. Unfortunately GSSL methods scale poorly with the size of the graph [1] and usually have time complexity that becomes quickly prohibitive in large graphs, thus preventing their adoption in whole genome applications. This problem is particularly evident with the prediction of the function of genes in high eukaryotes like mammalians or plants. GSSL methods can be roughly categorized as inductive when they are based on an explicit classification model, or transductive, if the labels are propagated using only information coming from the topology of the network and without training a classification model. Few approaches, aimed at overcoming the scaling limitations of transductive GSSL methods, have been recently proposed: they are based on kernel approximations [2] that trade approximation accuracy for scalability, or on the assumption that graphs have a block structure [3] which is often hard to prove for gene functional networks.
Theoretical analysis of interhemispheric transfer costs in visual word recognition

It is becoming increasingly clear that interhemispheric transfer is an important factor in visual word recognition. One of the two computational models of visual word recognition that includes this aspect, the SERIOL model, is tested on the basis of recently obtained behavioural word naming data. Optimal viewing position (OVP) data were collected from participants with left hemisphere language dominance, right hemisphere language dominance, and bilateral language representation (as determined by fMRI). We employ a mathematical model, which is based on some of the underlying assumptions of SERIOL, to investigate the model's ability to predict our results. We show that this mathematical model, which makes use of the original parameters, is able to perfectly predict the differences in the OVP curves observed in the three groups of participants.
Age Dynamics of Telomere Length of Baikal Gastropods is Sex Specific and Multidirectional

The age dynamics of telomeres are affected by various internal and external factors. We examined the age dynamics of relative telomere length (RTL) and telomerase activity in freshwater dioecious gastropod species from Lake Baikal (Benedictia fragilis, B. baicalensis and Kobeltocochlea martensiana). They differ in habitats, growth rate, size of mature specimens, reproductive strategy and degree of phylogenetic relatedness, but do not possess sexual dimorphism and, irrespective of sex, they have a similar lifespan (~8 years) and time to maturity (~4 years). Sex specificity in changes of telomere with age was observed in each species of benedectiids. Immature specimens do not differ in telomere size irrespective of sex. However, when they become mature, we recorded differences and similarities in telomere length between females and males. Telomeres are longer in 4-6 year-old adult females than in males. At the age of 7-8 years, sex differences in telomere sizes are leveled in B. fragilis and K. martensiana, while in B. baicalensis the difference remains. Sex differences in the telomere age dynamics of B. baicalensis have also been revealed between the embryonic and mature stages of development. Telomeres in mature males are shorter than in embryos and mature females. In females after the embryonic stage, telomeres shorten rapidly, and then at the age of 4-8 years telomere length is restored up to the embryonic level. Active telomerase was revealed in all species irrespective of sex and developmental stage. The multidirectionality of sex-dependent age dynamics of telomere size may be attributed to the combined effect of internal and external factors on telomeres during ontogenesis.
Diffusion and Short‐Term Efficacy of Botulinum Toxin A After the Addition of Hyaluronidase and Its Possible Application for the Treatment of Axillary Hyperhidrosis

BACKGROUND Botulinum toxin adequately treats hyperkinetic facial lines and hyperhidrosis. Higher doses of botulinum toxin appear to enhance efficacy and longevity possibly through greater evenness of diffusion; however, recurrent treatments with higher doses are expensive. OBJECTIVE To admix botulinum toxin with hyaluronidase and to test whether there is maintenance of efficacy, a spread of effect, and possibly a decrease in required dose compared with botulinum toxin. METHODS Six patients participated in a double-blinded side-to-side comparison pilot study with photographic analysis for frontalis overactivity and Minor's iodine and gravimetric testing for axillary hyperhidrosis. RESULTS Initial efficacy of botulinum with admixed hyaluronic acid appeared maintained with possibly increased diffusion when hyaluronic acid is added. No difference was evident on short-term review of patients treated with 50 U of botulinum in one axilla compared with the contralateral side injected with 25 U with admixed hyaluronidase. CONCLUSION There may be a role for hyaluronic acid in aiding diffusion and decreasing the required dose of botulinum toxin in hyperhidrosis axillaris.
Two new millipede genera from northwest Tasmania, Australia (Diplopoda: Polydesmida: Dalodesmidae)

Setoisenoton pallidus n. gen., n. sp. and Dysmicodesmus jeekeli n. gen., n. sp. occupy small ranges (<5000 km 2 ) in the forests of northwest Tasmania. Both have a head+19 rings, metatergites lacking posterior corner extensions, and long, rigid gonopod telopodites reaching at least to legpair 4 when retracted. S. pallidus resembles Notonesiotes aucklandensis Johns, 1970 from the subantarctic Auckland Islands, but differs in gonopod details. D. jeekeli is unusual in the Tasmanian dalodesmid fauna in having basally fused telopodites.
Characterization of a Salt-Tolerant and Cold-Adapted Xylanase from Bacillus cellulosilyticus

A xylanase (Xyn10A) gene from the saline-alkali-tolerant microorganism Bacillus cellulosilyticus DSM 2522 was cloned and expressed in Escherichia coli BL21 (DE3). The open reading frame was composed of 1008 base pairs, and it encoded 335 amino acid residues belonging to glycosyl hydrolase family 10. The optimal temperature and pH of the purified Xyn10A were 40 °C and 8.0, respectively. The Xyn10A was sensitive to heat and showed obvious cold-adapted activity, retaining 38.3%, 55.7%, and 82.9% of the optimal activity at 4, 20, and 30 °C, respectively. Xyn10A also showed a high level of NaCl tolerance. The highest activity was observed with 1.5 M NaCl. The specific enzyme activity of Xyn10A was as much as 163.8 U/mg. Kinetic assays showed that Km, Vmax, and Kcat were 2.56 mg/mL, 202.5 μM/min/mg, and 132.6 /s, respectively. Additionally, the main hydrolysis products using birchwood xylan as substrate were xylobiose, xylotriose, and xylotetraose, as determined by thin layer chromatography analysis. As a cold-adapted and salt-tolerant enzyme, Xyn10A is an ideal candidate for further research and biotechnological applications.
Materials and Methods Association between Urinary Polycyclic Aromatic Hydrocarbon Metabolites and Sperm Dna Damage: a Population Study in Chongqing, China

Research Polycyclic aromatic hydrocarbons (PAHs) are a large family of environmental pollutants generated from the incomplete combustion of coal, wood, oil, gas, garbage, or other organic substances. PAH exposure is a major public health concern worldwide, because the active metabolites of PAHs are believed to act as mutagens and carcinogens and because PAHs are associated with an increased risk for developing many types of cancers, including lung, prostate, skin, lymphatic, and hematopoietic malignancies [Armstrong et al. 2004; Agency for Toxic Substances and Disease Registry (ATSDR) 1995; Rybicki et al. 2008]. Accumulating evidence has also suggested that PAH exposure has harmful effects on reproductive health. Early studies demonstrate that intraperitoneal injection of benzo(a)pyrene into adult rats resulted in the atrophy of seminiferous tubules and a lack of spermatids and spermatozoa (Payne 1958). In utero exposure to benzo(a)pyrene (10 mg/kg body weight) markedly impairs the fertility of F1 male mice (MacKenzie and Angevine 1981). Moreover, subacute exposure of male rats to inhaled benzo(a)pyrene leads to reduced testosterone concentrations and impaired epididymal function (Inyang et al. 2003; Ramesh et al. 2008). More recent reports have also suggested that certain PAHs or their metabolites can interact with the estrogen receptor (ER) and initiate ER signal-ing pathways in vitro and in vivo (Kummera et al. 2008; Vinggaard et al. 2000). Similar effects for PAHs on the male reproductive system have been reported among infertility clinic clients or occupational populations. For example, a recent study (Xia et al. 2009) reported that exposure to PAHs at environmental levels is associated with an increased risk of male idiopathic infertility. Hsu et al. (2006) reported that the ambient PAH levels of occupationally exposed individuals are associated with decreased sperma-tozoa quality. However, the biological effects of PAHs on the reproductive system have not been confirmed in the general population. Our study was designed to investigate the relationships between PAH exposure and male reproductive function in a general population in the city of Chongqing, China. Chongqing is one of the largest cities with heavy industries along the Yangtze River. In our earlier study, we found that PAHs were some of the most ubiquitous environmental contaminants in the Chongqing of southwestern China and that the levels of PAHs in this city were higher than those in other cities (Guo et al. 2006; Shu et al. 2002; Tian et al. 2003). In another study, Li et al. (2009) found that 61.1% of male …
Kinetic bottlenecks to chemical exchange rates for deep-sea animals II : Carbon dioxide

fluid properties (∆pH, ∆[ ∑ CO2] etc.) as the critical variable and with a major focus on carbonate shell dissolution. Here we describe the rate problem for animals that must export CO2 at about the same rate at which O2 is consumed. We analyze the basic properties controlling CO2 export within the diffusive boundary layer around marine animals in an ocean changing in temperature (T ) and CO2 concentration in order to 10
The Nostrum backbone-a communication protocol stack for Networks on Chip

We propose a communication protocol stack to be used in Nostrum, our Network on Chip (NoC) architecture. In order to aid the designer in the selection process of what parts of protocols, and their respective facilities, to include, a layered approach to communication is taken. A nomenclature for describing the individual layers' interfaces and service definitions of the layers in the protocol stack is suggested and used. The concept includes support for best effort traffic packet delivery as well as support for guaranteed bandwidth traffic, using virtual circuits. Furthermore an application to NoC adapter is defined, as part of the Resource to Network Interface, and is used to communicate between the Nostrum protocol stack and the application. An industrial example has been implemented, simulated, and the results justifies the suggested layered approach.
The Journal of Systems and Software

Deriving extra-functional properties (e.g., performance, security, reliability) from software architectural models is the cornerstone of software development as it supports the designers with quantitative predictions of system qualities. However, the problem of interpreting results from quantitative analysis of extra-functional properties is still challenging because it is hard to understand how the analysis results (e.g., response time, data conﬁdentiality, mean time to failure) trace back to the architectural model elements (i.e., software components, interactions among components, deployment nodes). The goal of this paper is to automate the traceability between software architectural models and extra-functional results, such as performance and security, by investigating the uncertainty while bridging these two domains. Our approach makes use of extra-functional patterns and antipatterns, such as performance antipatterns and security patterns, to deduce the logical consequences between the architectural elements and analysis results and automatically build a graph of traces, thus to identify the most critical causes of extra-functional ﬂaws. We developed a tool that jointly considers SOftware and Extra-Functional concepts (SoEfTraceAnalyzer), and it automatically builds model-to-results traceability links. This paper demonstrates the effectiveness of our automated and tool supported approach on three case studies, i.e., two academic research projects and one industrial system.
Cephalopod fauna of subantarctic islands: new information from predators

Using top predators as biological samplers, we collected information on the poorly known— but ecologically important —cephalopod fauna of the Southern Ocean. A total of 4527 cephalopod beaks were identified from stomach contents of Patagonian toothfish caught in slope waters at Crozet and Kerguelen Islands (Indian Ocean). Main prey were the squid Gonatus antarcti- cus and Kondakovia longimana at both localities, Taonius sp. B (Voss) and Slosarczykovia circum- antarctica at Crozet, and Chiroteuthis veranyi and Mastigoteuthis psychrophila at Kerguelen. Fish diet together with the feeding habits of sharks and seabirds show that at least 36 and 38 different cephalopod species inhabit Crozet and Kerguelen waters, respectively. Oegopsid squid dominate the assemblages (29 and 32 taxa at Crozet and Kerguelen, respectively) over octopods (7 and 5 taxa), 1 species of sepiolid occurring at Kerguelen. These rich communities include pelagic squid, bentho- pelagic cirrate octopods and a few endemic benthic octopodids. The results emphasize the impor- tance of onychoteuthids and gonatids in the nutrition of top consumers in the Southern Ocean and they shed new light on the role of chiroteuthids, mastigoteuthids and cirrate octopods in the trophic web of the marine ecosystems.
Effect of Preoperative Inspiratory Muscle Training on Alveolar-Arterial Oxygen Gradients After Coronary Artery Bypass Surgery

Purpose: Gas exchange abnormalities and inspiratory muscle dysfunction are common postoperative pulmonary complications after cardiac surgery. The aim of this study was to investigate the changes in the alveolar arterial oxygen gradients and inspiratory muscle power after preoperative inspiratory muscle training (IMT) followed by postoperative IMT and early mobilization after coronary artery bypass graft surgery. Methods: Patients were randomly assigned to the intervention group (n = 20) or the usual care group (n = 20). The intervention group received preoperative IMT by a threshold load inspiratory muscle trainer and education followed by postoperative IMT and early mobilization. The usual care group received preoperative education and postoperative routine physical therapy care. Alveolar-arterial oxygen gradients and oxygen saturation were measured before induction of anesthesia and postoperatively immediately after extubation, at 24 hours, 48 hours, and on day 8 postsurgery. Inspiratory muscle power was measured before surgery, after 48 hours, and on day 8. Results: Forty male patients underwent coronary artery bypass graft surgery. The intervention group showed significant (P < .05) improvement of alveolar arterial-oxygen gradients and inspiratory muscle power at all measurement points. The mean of inspiratory muscle power at discharge was significantly higher than at baseline but not statistically significantly different from the preoperative measurement. Conclusion: Pre- and postoperative IMT by the threshold load inspiratory muscle trainer resulted in improvement of inspiratory muscle power, alveolar-arterial gradient, and oxygen saturation.
Effects of Substrate on the Structure,Morphology and Optical Properties of Vertically Aligned ZnO Nanorod Arrays Grown by Low-temperature CBD Method

ZnO nanorods were grown on different substrates(quartz glass,Si and ITO glass) by the wet chemical bath deposition(CBD) method at a relatively low temperature of 95℃. X-ray diffraction(XRD) and scanning electron microscope(SEM) results illustrate that the ZnO nanorod arrays with hexagonal wurtzite structure are grown densely and vertically on all the substrates,whereas the average diameter and length are found to be closely related to the substrates nature.High intensity near-band edge ultraviolet(UV) emission peak are observed in room temperature photoluminescence(PL) spectra for the ZnO nanorod arrays on all substrates,yet the usually observed defect related deep level emissions are nearly undetectable regardless of crystalline or amorphous,indicating high optical quality ZnO nanorod arrays can be achieved via this low temperature easy process chemical approach.Moreover,the small shift in the UV emission among different substrates is interpreted in terms of compress stress,which is further demonstrated by the Raman spectra measurement results.
Effects of Internet Popular Opinion Leaders (iPOL) Among Internet-Using Men Who Have Sex With Men

Background The Internet has become a popular venue for facilitating sex networking for men who have sex with men (MSM). Objective The study aimed to evaluate the effectiveness of Internet popular opinion leaders (iPOL) in disseminating information about the human immunodeficiency virus (HIV), increasing the frequency of HIV testing, and reducing risky behaviors among MSM in Taiwan. Methods A quasi-experimental study with a nonequivalent control website for comparison was used to estimate the effectiveness of iPOL. A community-level intervention, iPOL, was conducted at the Facebook social networking website and at top1069 as a control. The iPOLs actively disseminated HIV-related information via the platform of Internet opinion leaders and AIDS information center, and discussed and responded to questions or replied to Internet-using MSM. Results A total of 369 iPOLs posted 432 articles and 503 replies to others, influencing 959,088 persons on Facebook. A total of 1037 MSM, 552 (53.23%) from an intervention website and 485 (46.76%) from a control website, participated in the follow-up study survey (response rate 96%). At the 6-month follow-up after the intervention was conducted, MSM who visited the intervention website were more likely to receive HIV-related information (25.49% versus 10.47%, P<.001), discuss HIV issues with others (41.88% versus 23.79%, P<.001), review articles about HIV (90.58% versus 79.73%, P<.001), and be asked about or discuss HIV-related questions (51.11% versus 31.78%, P<.001) than those on the control website. In addition, MSM were more likely to have HIV tests within 6 months (43.89% versus 22.31%, P<.001) and consistently use condoms during anal sex with online sex partners than those using the control website (34.15% versus 26.19%, P=.004). Conclusions The study showed the feasibility and effectiveness of the iPOL intervention as an online HIV prevention program. These findings underscore the importance of disseminating HIV information online, as well as the challenges inherent in the efforts of iPOL to reduce HIV-related risky behaviors among Internet-using MSM.
Assessment of liver viscoelasticity using multifrequency MR elastography

MR elastography (MRE) allows the noninvasive assessment of the viscoelastic properties of human organs based on the organ response to oscillatory shear stress. Shear waves of a given frequency are mechanically introduced and the propagation is imaged by applying motion‐sensitive gradients. An experiment was set up that introduces multifrequency shear waves combined with broadband motion sensitization to extend the dynamic range of MRE from one given frequency to, in this study, four different frequencies. With this approach, multiple wave images corresponding to the four driving frequencies are simultaneously acquired and can be evaluated with regard to the dispersion of the complex modulus over the respective frequency. A viscoelastic model based on two shear moduli and one viscosity parameter was used to reproduce the experimental wave speed and wave damping dispersion. The technique was applied in eight healthy volunteers and eight patients with biopsy‐proven high‐grade liver fibrosis (grade 3–4). Fibrotic liver had a significantly higher (P < 0.01) viscosity (14.4 ± 6.6 Pa · s) and elastic moduli (2.91 ± 0.84 kPa; 4.83 ± 1.77 kPa) than the viscosity (7.3 ± 2.3 Pa · s) and elastic moduli (1.16 ± 0.28 kPa; 1.97 ± 0.30 kPa) of normal volunteers. Multifrequency MRE is well suited for the noninvasive differentiation of normal and fibrotic liver as it allows the measurement of rheologic material properties. Magn Reson Med 60:373–379, 2008. © 2008 Wiley‐Liss, Inc.