Miracle-dz/UniFAR-FTUs huggingface dataset:
Interaction between a twelve-residue segment of antifreeze protein type I, or its mutants, and water molecules

A molecular dynamics simulation has been carried out for water molecules with a rigid segment of antifreeze protein type I. The segment consists of nine alanine residues, two threonine residues and one asparagine residue. Mutant segments, in which the threonine residues are replaced with valine residues, or serine residues, are also used. It is predicted that the hydrogen site of asparagine residue, and that of threonine residue, play an important role in the hydrogen bond of water molecules in these sites. This hydrogen bond is not noticeable between water molecules and the valine residue, or serine residue. The existence of four hydrophilic sites enhances the mobility of water molecules close to the serine residue of the mutant segment. The difference in the zenith-angle fluctuations of the original segment and the valine-mutant segment is less noticeable in the case of 230 K. This is because the gathering of water molecules due to the hydrophobic hydration is predominant near the alanine residues of the segments at this temperature.
Adaptive decision making or differential mortality: what causes offspring emergence in a gregarious parasitoid?

Hosts represent a limited resource for the developing offspring of parasitic insects laying eggs in or on spatially discrete resources like fruits, seeds, or other insects. The quality of hosts differs with respect to the value and amount of resources they provide for the feeding larvae. Accordingly, the size of a clutch of eggs laid on a given host should be a function of host quality, because severe competition between developing larvae can lead to increased mortality and/or decreased size of the offspring, both causing a fitness loss for the offspring and the mother. Therefore, females should be selected for the ability to estimate host quality and to adjust their clutch size accordingly. Using the parasitic wasp Nasonia vitripennis (Walker) (Hymenoptera: Pteromalidae) this study investigated the respective contribution of developmental mortality of offspring vs. the clutch size decision of the mother as a determinant of final offspring emergence per host. In addition, taking offspring size into account, the study examined the fitness consequences of female oviposition decisions. Developmental mortality was very low in all quality classes of hosts except previously frozen and thus dead host pupae. Females laid reduced clutch sizes on dead, previously parasitized, and smaller hosts. In contrast to offspring number, offspring size did not differ between host qualities. We conclude that females are able to sense the quality of a host and adjust the number of eggs they lay to mitigate larval competition.
High temperature causes arrest of cell cycle in G2 phase in BmN cells derived from the silkworm, Bombyx mori

Abstract The influence of temperature on the insect cell line, BmN, derived from the silkworm, Bombyx mori is investigated. These cells proliferate at an accelerated pace as the temperature increases from 22 to 30 °C, but the growth rate slows at 34 °C, and proliferation stops at 38 °C. At high temperatures, abnormal cellular morphology is observed. Cells treated at 38 °C have cytoplasmic bilateral protrusions and they gradually aggregate and float in the medium. BmN cells without proliferation at 38 °C are viable but have reduced DNA synthesis. At high temperatures, the cell cycle of BmN cells halts at the G2 phase. After heat treatment of the larvae, an accumulation of larval haemocytes with high DNA content is found, which suggests that the cell cycle arrest at G2 also occurs in the silkworm at high temperatures.
The Role of Stock Market Development on Economic Growth in Nigeria: A Time Series Analysis

This study investigated the role of stock market development on economic growth of Nigeria using a 15-year time series data from 1994 - 2008. The method of analysis used is Ordinary Least Square (OLS) techniques. The study measures the relationship between stock market development indices and economic growth. The stock market capitalization ratio was used as a proxy for market size while value traded ratio and turnover ratio were used as proxy for market liquidity. The results show that market capitalization and value traded ratios have a very weak negative correlation with economic growth while turnover ratio has a very strong positive correlation with economic growth. Also, stock market capitalization has a strong positive correlation with stock turnover ratio. This result implies that liquidity has propensity to spur economic growth in Nigeria and that market capitalization influences market liquidity. We should view with caution the notion that stock market size is not significant for economic growth since multicollinearity exists in the data used for this analysis. The government should make policies that boost the interest of domestic investors in Nigeria as this might spur investors’ interest and boost stock market activity. Keywords : Stock Market Development, Economic Growth, Time Series Analysis, Nigeria, Market capitalisation, liquidity.
Control Strategy for Viral Nervous Necrosis of Barfin Flounder

Control Strategy for Viral Nervous Necrosis of Barfin Flounder Ken-ichi Watanabe*1, Shigenori Suzuki*1, Toyohiko Nishizawa*2, Kayo Suzuki*3, Mamoru Yoshimizu*3 and Yoshio Ezura*3 *1Akkeshi Station of Japan Sea-Farming Association, Akkeshi, Hokkaido, 088-1108, Japan *2Laboratory of Fish Pathology, Faculty of Applied and Biological Science, Hiroshima University, Higashi Hiroshima, Hiroshima, 739-8528, Japan *3Laboratory of Microbiology, Faculty of Fisheries, Hokkaido University, Hakodate, Hokkaido, 041-0821, Japan (Received April 24, 1998)
New constructions for secure hash functions: (extended abstract)

We present new, efficient and practical schemes for construction of collision-resistant hash functions, and analyze some simple methods for combining existing hash-function designs so as to enhance their security. In our new constructions, we first map the input to a slightly longer string using a primitive we introduce called secure stretch functions. These are length-increasing almost surely injective one-way functions that sufficiently randomize their inputs so that it is hard for an adversary to force the outputs to fall into a target set. Then we apply a compression function to the output of the stretch function. We analyze the security of these constructions under different types of assumptions on both stretch and compression functions. These assumptions combine random-function models, intractability of certain biasing tasks, and the degeneracy structure of compression functions. The use of stretching seems to allow reduced requirements on the compression function, and may be of independent interest. These constructions allow one to use popular and efficient primitives such as MD5, SHA-1, and RIPEMD that may exhibit weaknesses as collision-resistant functions. But no attacks are currently known on their one-way and randomizing properties, when they are used as stretch functions as in our constructions. There are several collision-resistant hash functions based on DES for which there are no known effective attacks, but which are too slow for most practical applications. Our use of stretch functions enable us to base our compression function on DES so that the resulting hash function achieves practical speeds: a test implementation runs at 40% of the speed of MD5. We also suggest some imperfect random-oracle models, showing how to build better primitives from given imperfect ones. In this vein, we also analyze how to defend against a collision-finding adversary for a given primitive by building independent primitives.
An online method for condition monitoring and prognostics of hydraulic systems

Engineering systems, such as aircrafts, hydraulic, electronic and electrical systems are becoming more complex and are subjected to failure modes that impact adversely their reliability, availability, safety and maintainability. In particular, hydraulic systems are challenging from the condition monitoring point of view due to the non-linear equations that describe behavior of the fluid. For this reason, numerous efforts have been made to improve the reliability of hydraulic system, leading to the development of complex algorithms for diagnostics and prognostics. In the present research, both diagnostic and prognostic algorithms have been developed, considering the case of an hydraulic crane available at the Purdue's Maha Fluid Power Research Center. Based on the architecture, three components have been analyzed as possible faults in the system: the fixed-displacement pump, the meter-in valve and the cylinder. Among all the modern approaches, a data-driven, neural network based method has been exploited based on a simulation model of the machine through which the behavior of the system is predicted. Moreover, a realistic simulation has been designed, in order to be as close as possible to the real system set-up. Then, a validation of this approach has been performed on the target machine. In summary, the diagnostic algorithm is capable to understand the intensity of the fault and to discern which is the component that is failing also during simultaneous failures; the prognostic algorithm can properly estimate the Remaining Useful Life (RUL) based on the Weibull distribution. Notably, both algorithms use a limited set of sensors taking also advantage of the implemented controller.
PSO active learning of XGBoost and spatiotemporal data for PM2.5 sensor calibration

Ambient PM2.5 concentrations affect human health and natural environment. Government-built PM2.5 monitoring supersites are accurate but cannot provide a dense coverage of the air quality index (AQI) monitoring. Broadly-distributed PM2.5 microsite sensors can complement supersites for fine-grained monitoring. However, due to the low cost of microsite sensors, the accuracy of the raw AQI measurements is not high enough for monitoring purpose. Calibration of low-cost sensors is thus a necessary processing step to enhance measurement fidelity. This paper presents a particle swarm optimization (PSO) based active learning of optimal configurations of XGBoost and spatiotemporal data for PM2.5 microsite sensor calibration. The experimental results show that PSO active learning of the optimal configurations of XGBoost and spatiotemporal data can calibrate low-cost PM2.5 microsite sensors to achieve high accuracy by reference to governmental supersites.
Analyzing the Pacific-North American teleconnection pattern and its relationship to climate using RegCM3, a high-resolution regional climate model

recognized as a robust feature of Northern Hemisphere atmospheric circulation, and more specifically represents the structure of the quasi-stationary wave field over the North Pacific and North America. The PNA is a strong control of interand intra-annual climate variability over North America. This study presents an assessment of the influence of the PNA on past, present, and future climate and surface hydrology in North America. Analyzing the Pacific-North American teleconnection pattern and its relationship to climate using RegCM3, a high resolution regional climate model Andrea M. Allan1§, and Steven W. Hostetler2, and Jay Alder1 1Oregon State University, College of Earth, Ocean, and Atmospheric Sciences, Corvallis OR 97331 2U.S. Geological Survey, College of Earth, Ocean, and Atmospheric Sciences, Corvallis OR 97331 §Contact: andrea.allan@geo.oregonstate. edu
PIONIER: A Four-telescope Instrument for the VLTI

The Messenger 146 – December 2011 wavelength channel and one closure amplitude, whereas a three-telescope combiner only provides three visibilities and one closure phase. The remarkable success of the four-telescope (4T) CHARA inter ferometer ( Monnier et al., 2007) has demonstrated that such an increase in uv-plane coverage significantly improves the capability to reconstruct a “modelindependent” image from the observables, so-called aperture synthesis imaging.
Sex- and Age-specific Patterns of Mineral Lick Use by White-tailed Deer (Odocoileus virginianus)

Abstract Little is known regarding the influence of sex- and age-specific factors on mineral lick use by white-tailed deer (Odocoileus virginianus). We recorded 1020 visits to mineral licks by deer between April and September, of which we could classify 922 by sex and age (yearling or adult). We observed a relationship between the frequency of mineral lick visitation and both sex and age of users. No relationship was found between visitation frequency and time interval of use. Adult females used licks more frequently than other sex/age classes. Visitation frequencies were similar for adult males and yearling males and females. We detected no relationship between lick sodium (Na) content and sex or age of visitors. Greater lick use by adult females may have reflected an increased need for Na associated with gestation and lactation. The majority of male visitors were yearlings, which require Na for antler production and rapid somatic growth. In areas where Na concentration in forage is below dietary requirements and Na-conserving mechanisms are compromised and/or additional production demands occur, available mineral licks may ameliorate the potential negative impact of limited Na on pregnancy/lactation.
An Economical PDF-Based Turbulence Closure Model for Cloud-Resolving Models and Global Climate Models

• SAM-PDF includes these desirable features: • A diagnostic higher-order closure with assumed double Gaussian joint PDF. • A turbulence length scale that depends on SGS TKE and large-eddy length scales. • It can realistically represent many boundary layer cloud regimes in models with dx ~ 0.5 km or larger, with virtually no dependence on horizontal grid size. • It is economical, with potential for easy portability to other explicit-convection models (e.g., WRF, GCRMs) and GCMs. In MMF-PDF, shallow Cu are improved by the new turbulence model but Sc are still severely underrepresented, likely due to inadequate vertical resolution. Preliminary Test of Closure within MMF • Code implemented in the embedded CRMs within the MMF. • SGS cloud fraction and liquid water content passed to radiation code (computed on the CRM grid every 15 minutes). • SPCAM & SPCAM-PDF run in T42 configuration with 30 vertical levels (embedded CRM: dx = 4 km, dz ~ 200-300 m in boundary layer). • Preliminary results below are from June, July, August (JJA) simulation (with one month spin-up).
Statistical Emulation of a landslide-generated tsunami model

Due to the catastrophic consequences of tsunamis, early warnings need to be issued quickly in order to mitigate the hazard. Additionally, there is a need to represent the uncertainty in the predictions of tsunamis’ characteristics corresponding to the uncertain trigger features (e.g. either position, shape and speed of a landslide, or sea ﬂoor deformation associated with an earthquake). Unfortunately, computer models are expensive to run. This leads to signiﬁcant delays in predictions and makes the uncertainty quantiﬁcation impractical. Statistical emulators run almost instantaneously and may represent well the outputs of the computer model. In this paper, we employ the Outer Product Emulator to build a fast statistical surrogate of a landslide-generated tsunami computer model. This Bayesian framework enables us to build the emulator by combining prior knowledge of the computer model properties with a few carefully chosen model evaluations. The good performance of the emulator is validated using the Leave-One-Out method.
FOOD LIMITATION OF PLANKTOTROPHIC MARINE INVERTEBRATE LARVAE: DOES IT CONTROL RECRUITMENT SUCCESS?

Article de synthese sur l'etude de l'influence des insuffisances dans la quantite de nourriture larvaire sur un jeune alimentaire et la vraisemblance que cela puisse constituer un facteur primordial dans la regulation du succes de recrutement des larves du zoobenthos marin
A Methodology to Determine SMR Build Schedule and the Impact of Modularisation

Light-water cooled Small Modular Reactors (SMRs) are a potential game-changing technology for energy supply. The potential benefits of SMRs are however conditional on solving the key standardisation and construction issues that have troubled large reactor (LR) projects, which have in turn led to high build costs and long project durations. Initiatives to determine the build schedule of SMRs are hindered by a lack of SMR construction experience and related data. The methodology used in this paper, to deal with the lack of SMR-specific data, draws conclusions about SMRs based on data from actual large pressurised water reactor (PWR) construction experience. It is expected that SMR build schedules can be greatly reduced because of the smaller physical size of structures, fewer components, and other size-related features. However, the construction work space will be more constrained, which could negatively impact build durations. As a result, simple geometric scaling and reduction arguments cannot necessarily be applied to SMR schedules. This paper defines the key areas in which SMR construction differs from LRs, such as smaller geometries as well as modularised and standardised build processes, and describes how these differences might be expected to impact build duration quantitatively. The model developed in this paper presents an approach to determining SMR build schedule durations for a range of reactor sizes. It starts with an LR build schedule based on real data from the UK’s only PWR, Sizewell B. The available data are used to establish a reference point for a non-modular, stick-built SMR schedule. This scheduling approach assumes that, for each major element, part of the time spent on fabrication and installation tasks will vary with reactor size while the remaining fraction will remain constant regardless of reactor size (e.g. due to quality assurance and commissioning tasks). The accuracy of the model generated here is assessed against available construction data and models from a range of actual reactor build projects. The objective of this work is to consider how modularisation can reduce build schedule of SMRs of varying size, by employing modular design and construction principles to both remove tasks that are of long duration from the critical path and to improve construction productivity. Mechanisms by which modularisation reduces build schedule are investigated. Build reduction scenarios are presented based on analysis and subsequent modularisation of the SMR critical path and are compared with other related analyses.
A Comparative Analysis of Market Orientation in the Commercial Fish Processing Industries of Atlantic Canada and The New England States

This paper provides a comparative analysis of market orientation in the New England States Commercial Fish Processing Sector to that of Atlantic Canada. Part I is an exploratory analysis of market orientation in the New England setting. Part II is concerned with the construction of a parsimonious seasonal market orientation model for the North-Eastern Atlantic Commercial Fish Processing Sector. Using structural equation modeling, the author provides an interpretable solution of market orientation in this broad industry setting. The paper concludes with a discussion of limitations on the research, and recommendations for future research initiatives.
Cysticercosis in experimentally and naturally infected pigs: parasitological and immunological diagnosis

Our objective was to evaluate the diagnosis of swine cysticercosis by examining "ante mortem" (inspection of the tongue), "post mortem" (inspection and detailed necropsy) and ELISA for research in serum of antibodies (Ab-ELISA) and antigens (Ag-ELISA). Seven (7) pigs were experimentally infected orally with eggs of Taenia solium and another 10 were naturally infected. In the pigs experimentally infected, inspection of the tongue was negative in all animals, in the routine inspection detailed necropsy and cysticercis were identified in all of them. In pigs with heavy natural infection, inspection of the tongue identified cysticerci in two (20%), while at inspection with necropsy the parasites were identified in large quantities in all animals. In ELISA for antibody search (Ab-ELISA) TS-14 recombinant protein was used, and in search for antigen (Ag-ELISA) a monoclonal antibody against this protein. In animals experimentally infected, blood was collected weekly for 140 days. The Ab-ELISA identified an increase in titers of antibody to cysticerci 21 days after infection, and at the end of the experimental period six animals (86%) were positive to the test. The search for circulating antigens (Ag-ELISA) was positive in two pigs 28 to 91 days after infection. All naturally infected pigs were positive for Ag-ELISA and Ab-ELISA. The search for antibodies and antigens by ELISA in serum from 30 pigs of a local farm and without history of cysticercosis was negative. Thus, the use of TS-14 antigen in ELISA test (Ab-ELISA) can be useful for the diagnosis of cysticercosis in pigs with low infection.
Chromatin Remodeling in Transgenic Mouse Brain: Implications for the Neurobiology of Depression: A Dissertation

Histone lysine methylation is an important epigenetic mark for regulation of gene expression and chromatin organization. Setdb1 (Set domain, bifurcate 1), one of the histone lysine methyltransferases, specifically methylates histone H3 at lysine 9 (H3K9) and participates in transcriptional repression and heterochromatin formation. The major task of my thesis work was to investigate the epigenetic roles of Setdb1 in regulating brain functions. I started my thesis work by examining Setdb1 expression pattern during mouse brain development. The most robust signal of Setdb1 was detected in the fetal brains at embryonic day 12.5, with a ubiquitous distribution in all the proliferative zones, as well as the cortical plate and other regions comprised of postmitotic neurons. The expression of Setdb1 decreased as the brain developed, and this downregulation profile was correlated to neuronal maturation as examined in a primary culture model of mouse cortical neurons. I then generated CK-Setdb1 transgenic mice, in which a myc-tagged full length mouse Setdb1 was constantly expressed in postmitotic neurons under the control of the CaMK II alpha promoter (CK). The expression of mycSetdb1 was detected in NeuN positive cells throughout most forebrain regions including cerebral cortex, striatum and hippocampus. A sustained increase of Setdb1 in CK-Setdb1 transgenics was verified at both mRNA and protein levels. Furthermore, an increase of H3K9 trimethylation was detected at major satellite DNA repeats in CK-Setdb1 forebrains, which indicated that transgene-expressed mycSetdb1 was functionally active in adult brains.