Miracle-dz/UniFAR-FTUs huggingface dataset:
Expression of flagellin FLjB derived from Salmonella enterica serovar typhimurium in Escherichia coli BL21

Flagellin FljB composes flagellar antigen (H:1,2) of S. Typhimurium. This kind of antigen increases immunogenicity of any conjugated antigen upon administration. Thus, it is supposed to have an enormous potentiality for vaccine development against bacterial infections and cancer diseases. fljB gene (1515 nucleotides) coding for mature FljB was amplified by PCR from genomic DNA of S. Typhimurium and inserted into pET32a(+) for expression in E. coli BL21. The protein FljB was well expressed under the fusion form with Trx, S-tag at N terminal and hexa-histidine at C terminal, thus the recombinant protein was abbreviated to TrxFljB. Study on the impact of temperature on the gene expression showed that TrxFljB was synthesized at lower level at 37 o C comparing to the levels at 22 o C and 25 o C. 13% of the protein synthesized at 37 o C was inclusion body. Lower temperatures used during induction phase increased the solubility of the recombinant protein. About 97% of TrxFljB synthesized at 25 o C was soluble. IPTG concentration had a strong effect on the growth of freshly transformed cells but did not affect on the growth of stored and re-cultivated cells. The increase of IPTG concentration resulted in the decrease of the growth of freshly transformed cells and the TrxFljB productivity. However, 0.05 mM IPTG concentration was found to gain the full TrxFljB expression. TrxFljB productivity declined during storage of cells at 4 o C and re-cultivation. At optimal condition, volumetric productivity of TrxFljB was about 300 mg/ l broth.
Assessment of the spatial variability in particulate organic matter and mineral sinking fluxes in the ocean interior: Implications for the ballast hypothesis

Multiple linear regression analysis (MLRA) applied to sediment trap data has been highly influential in identifying a plausible ‘ballasting’ mechanism that directly links the settling fluxes of particulate organic carbon (POC) to those of denser, inorganic minerals. However, analysis to date has primarily been carried out at the global scale, missing spatial variability in the flux relationships that may be important. In this paper, Geographically Weighted Regression (GWR) is applied to an updated deep (>1500 m) sediment trap database (n = 156), using the MLRA approach of Klaas and Archer (2002) but now allowing the carrying coefficients to vary in space. While the global mean carrying coefficient values for CaCO3, opal, and lithogenics are broadly consistent with previous work, the GWR analysis reveals the existence of substantial and statistically significant spatial variability in all three carrying coefficients. In particular, the absence of a strong globally uniform relationship between CaCO3 and POC in our spatial analysis calls into question whether a simple ballasting mechanism exists. Instead, the existence of coherent spatial patterns in carrying coefficients, which are reminiscent of biogeochemical provinces, points toward differences in specific pelagic ecosystem characteristics as being the likely underlying cause of the flux relationships sampled by sediment traps. Our findings present a challenge to ocean carbon cycle modelers who to date have applied a single statistical global relationship in their carbon flux parameterizations when considering mineral ballasting, and provide a further clue as to how the efficiency of the biological pump in the modern ocean is regulated.
Structural modeling of natural citrus products as potential cross-strain inhibitors of Dengue virus

There are four serotypes of Dengue virus and there are existing drugs used against specific serotype. There is no drug that is effective against all strains of this virus. In this research, bioinformatics tools were used to predict the affinity of natural ligands for the glycoprotein E of Dengue virus by considering the conserved domains. Molecular docking studies were carried out by using Autodock 3.0. Computational analysis which showed that two ligands have the potential to inhibit the site in glycoprotein E and control of all strains is now possible by these ligands.
Integrated scenarios for assessing biodiversity risks

The rapid loss of biodiversity (however measured) constitutes an urgent need to develop policy strategies that reduce the anthropogenic pressures on biodiversity. To go beyond short-term curative measures, such strategies must address the driving forces causing the pressures in an integrated fashion, covering a wide range of policy domains. The development of scenarios and their illustration by modelling are essential tools to study the aggregate human impacts on biodiversity, and to derive well founded policy options to preserve it. However, so far socio-economic, climate and biodiversity models exhibit a wide range of assumptions concerning population development, economic growth and the resulting pressures on biodiversity. This paper summarizes the efforts undertaken in the framework of the ALARM project by an interdisciplinary team of economists, climatologists, land use experts and modellers to identify pressures and drivers, and to derive effective policy strategies. It describes the challenges of such a kind of work, bringing together different world views necessarily inherent to the different fields of investigation, presents preliminary results, indicates necessary policy priorities and suggests urgent issues for future research. Copyright © 2007 John Wiley & Sons, Ltd and ERP Environment.
Does Mycobacterium bovis contribute to the case load of human tuberculosis in Namibia.

Namibia has one of the highest infection rates of human tuberculosis (TB) in the world. The causative agent is generally asserted to be Mycobacterium tuberculosis. Renewed concerns have been raised globally in the last decades regarding the emergence of Mycobacterium bovis as a contributor to human TB. The pathogen is harbored by a number of mammalian animal species and, hence has a high zoonotic potential. Numerous investigations in recent years show evidence of the spread of M. bovis from the wildlifelivestock interface to humans in southern African countries. Rural communities in these regions are most at risk since livestock can easily be infected. Namibia is considered to be free of bovine TB in cattle because no cases have been reported since 1995. However the disease may be under-diagnosed in single cases especially in remote areas because of the slow and chronic course. Weakened animals might be slaughtered privately, with contaminated meat and raw milk from infected cows or goats being consumed. The aim of this review is to discuss the complex issues of diagnosis and epidemiology, and to highlight the importance of the dierentiation of mycobacteria species in the medical laboratory for the outcome of patient treatment. M. bovis is clinically indistinguishable from human TB, possesses intrinsic resistance to at least one of the four first-line anti TB drugs, and shows a tendency to develop multidrug resistance. It poses a high risk predominantly for immuno-compromised individuals, as HIV-patients for example. Since Namibia has both - a high case load of HIV and TB - the occurrence and risk of zoonotic M. bovis in southern Africa should be discussed.
Far-field spectral characterization of conical emission and filamentation in Kerr media

By use of an imaging spectrometer we map the far-field (theta-lambda) spectra of 200-fs optical pulses that have undergone beam collapse and filamentation in a Kerr medium. By studying the evolution of the spectra with increasing input power and by using a model based on an asymptotic linear superposition of stationary wave modes (rather than the exact instantaneous solution), we are able to trace a consistent model of optical beam collapse highlighting the interplay between conical emission, multiple pulse splitting, and other effects such as spatial chirp.
Role of Organizational and Personal Factors on Work Stress Among the Managers of State Owned Enterprises in Kenya

The current stagnation of both the public and private enterprise sectors in Kenya’s economy, suggests among other things that, Kenyan managers/leaders may not be performing to their full managerial and leadership potential. This observation engenders the need for further investigations. Managerial work stress is a major organizational problem that has not been adequately addressed neither by organizations nor researchers despite concerted attempts. This paper sought to examine how work stress may be impacted by organizational and personal factors in Kenya commercial State Owned Enterprises (SOEs). To achieve this, the paper examined how the organizational and personal factors affect work stress among top managers of commercial SOEs in Kenya. Primary data was collected using questionnaires administered to 175 senior managers of SOEs in Kenya. Using random sampling, the paper collected data from 162 managers representing a response rate of 93 percent. The paper found out that organizational factors significantly influenced work stress while organizational structure and climate were major sources of stress. The paper recommended that organization structures and work environment should be streamlined so as to reduce work stress among top managers of commercial SOEs in Kenya. Keywords: State-owned enterprises, work stress, personal factors, organizational factors.
Mitochondrial DNA Diversity and Origin of Red Chittagong Cattle

To determine the origin and genetic diversity of Red Chittagong (RC) cattle in Bangladesh, we analyzed mitochondrial DNA displacement loop (D-loop) sequences of 48 samples along with 22 previously published sequences from Bos indicus and Bos taurus breeds. Twenty five haplotypes were identified in RC cattle that were defined by 44 polymorphic sites and nucleotide diversity was 0.0055±0.0026. The estimated sequence divergence times between RC and other zebu cattle breeds studied ranged between 22,700-26,900 years before present (YBP) which, it is suggested, predate domestication of RC cattle. Furthermore, it is assumed that introgressions have occurred in this breed mainly from Indian zebu breeds in the recent millennia. The phylogenetic studies showed RC cattle clustered with Bos indicus lineage with two distinct haplogroups representing high genetic variability of this breed. These findings can be used for designing proper breeding and conservation strategies for RC cattle in Bangladesh.
Developing methods for strategic evaluation in agricultural research and production

We analyze instruments to evaluate investment strategies as new options for co-operatives within the wheat production chain. Using a value-based management the extension of our concept, a “cooperative balanced scorecard” is discussed as we propose the further differentiation of the scorecard’s financial perspective. This is a market development-driven approach as cooperatives may be regarded as commodity-price-intermediators for their members. Proposing this approach we use a simple model of conjoint-hedging in intermediating firms within agribusiness.
FIBERLINES FOR BLEACHED EUCALYPTUS KRAFT PULPS - IMPACT ON BLEACHABILITY AND PULP PROPERTIES

A multitude of options is available when considering designing an "ultimate" fiberline for bleached eucalyptus kraft pulps. With a flexible cooking plant there are excellent opportunities to optimise cooking and oxygen delignification for improved yield and bleachability and for tailor making pulps with special properties. Hot acid treatment prior to bleaching or a hot first chlorine dioxide stage decreases brightness reversion and chlorine dioxide consumption. A drawback is increased effluent emissions, lower yield and impaired paper making properties. Milder conditions in the hot (D/A) stage decrease but do not eliminate these negative effects. The best choice is a first high consistency ozone stage that efficiently decrease chlorine dioxide consumption and effluent emissions, while retaining strength properties of the unbleached pulp. Evidence is presented that the discoloration of eucalyptus pulp measured after thermal yellowing is not permanent. The initial brightness of the bleached pulp can almost fully be recovered by simply washing with water. This raises the question whether brightness reversion, measured after thermal yellowing of standard brightness sheets, is a real problem or a virtual one.
AIRCRAFT SEGMENTATION IN SAR IMAGES BASED ON IMPROVED ACTIVE SHAPE MODEL

Abstract. In SAR image interpretation, aircrafts are the important targets arousing much attention. However, it is far from easy to segment an aircraft from the background completely and precisely in SAR images. Because of the complex structure, different kinds of electromagnetic scattering take place on the aircraft surfaces. As a result, aircraft targets usually appear to be inhomogeneous and disconnected. It is a good idea to extract an aircraft target by the active shape model (ASM), since combination of the geometric information controls variations of the shape during the contour evolution. However, linear dimensionality reduction, used in classic ACM, makes the model rigid. It brings much trouble to segment different types of aircrafts. Aiming at this problem, an improved ACM based on ISOMAP is proposed in this paper. ISOMAP algorithm is used to extract the shape information of the training set and make the model flexible enough to deal with different aircrafts. The experiments based on real SAR data shows that the proposed method achieves obvious improvement in accuracy.
Monoids of upper triangular boolean matrices

We study the variety W generated by monoids of upper-triangular boolean matrices. First, we present W as a natural extension of the variety J of finite J-trivial monoids and we give a description of the family of recognizable languages whose syntactic monoids are in W. Then we show that W can be described in terms of the generalized Schutzenberger product of finite monoids. We also show that W is generated by the power monoids of members of J. Finally we consider the membership problem for W and the connection with the dot-depth hierarchy in language theory. Although the majority of our results are purely "semigroup-theoretic" we use recognizable languages constantly in the proofs.
NIDS using Machine Learning Classifiers on UNSW-NB15 and KDDCUP99 Datasets

: The benchmark KDD dataset for intrusion detection system generated a decade ago has become outdated as it does not reflect modern normal behaviors and contemporary synthesized attack activities. In this paper we have used a new UNSW-NB15 data set for NIDS. Pre-processing on this datasets is done using Central Points of attribute values with apriori algorithm to select high ranked feature and remove irrelevant features which causes high false alarm rate. The evaluation of the dataset is performed using machine learning classifiers algorithm: Naïve Bayes and Logistic Regression. The results show that the decrease in false alarm rate and detection accuracy is improved even after reducing the dataset by eliminating the features and further more reduce in the processing time.
PFP-RFSM: Protein fold prediction by using random forests and sequence motifs

Protein tertiary structure is indispensible in revealing the biological functions of proteins. De novo perdition of protein tertiary structure is dependent on protein fold recognition. This study proposes a novel method for prediction of protein fold types which takes primary sequence as input. The proposed method, PFP-RFSM, employs a random forest classifier and a comprehensive feature representation, including both sequence and predicted structure descriptors. Particularly, we propose a method for generation of features based on sequence motifs and those features are firstly employed in protein fold prediction. PFP-RFSM and ten representative protein fold predictors are validated in a benchmark dataset consisting of 27 fold types. Experiments demonstrate that PFP-RFSM outperforms all existing protein fold predictors and improves the success rates by 2%-14%. The results suggest sequence motifs are effective in classification and analysis of protein sequences.
Child Abuse and Dissociation in Patients with Complex Regional Pain Syndrome

>OBJECTIVE: In the absence of a proven medical explanation for the chronic pain syndrome Complex Regional Pain Syndrome type I (CRPS I), this study explored a hypothetical link between childhood physical and sexual abuse, and the subsequent development of CRPS I. The hypothesis predicts the existence of a subpopulation of CRPS I patients with a high frequency of dissociative experiences corresponding to a history of childhood trauma.
A Compact Physical Model for Critical Quantum Mechanical Effects in Bulk MOSFETs

In this paper, a compact physical model is developed to incorporate the critical quantum mechanical effects (QME) in bulk MOSFETs. This new model gives close agreement with the numerical simulation down to 20 nm effective channel length. For the 20 nm channel length MOSFET with the gate dielectric equivalent oxide thickness (EOT) of 0.5 nm, QME lead to the increase of subthreshold swing ( S ) from 74 mV/decade to 105 mV/decade. The scaling limit of bulk MOSFETs is then discussed based on two considerations: short-channel effects (SCE) controllability and power consumption constraint for tunneling current. For 30 nm channel length MOSFETs with tolerable SCE and tunneling current density, the appropriate range of EOT for SiO2 is only 0.1 nm and less than the thickness of one atom layer of SiO2. This indicates high dielectric constant (N ) gate material should be applied to extend the scaling of bulk MOSFETs for the 30 nm technology generation and beyond.
Performance of Foreign and Global Mutual Funds: The Role of Security Selection, Region‐Shifting, and Style‐Shifting Abilities

We examine the performance of U.S.-based foreign and global funds after controlling for their regional and style exposure. We show that, on average, the total performance (TP) and security selection abilities of both foreign and global funds are significantly negative and exhibit short-term predictability. Additionally, R-super-2 reflects funds’ security selection abilities, consistent with previous findings for domestic mutual funds. Investors can earn higher abnormal returns and TP in the short run by purchasing past winners with low R-super-2 than by purchasing past losers with high R-super-2. However, there is no evidence of predictability in the funds' region-shifting and style-shifting abilities.
Piezoelectric scavengers in MEMS technology : fabrication and simulation

A robust process flow for fabricating piezoelectric devices in MEMS technology is presented. In this process several devices of different dimensions and electric connections (single and series) are fabricated. The devices range of resonance frequencies is 300-1000 Hz. For the piezoelectric layer two different piezoelectric materials (AlN, PZT) are alternatively used. Moreover a model for the piezoelectric devices based on finite element calculations is presented. According to calculations with this model the predicted power output of the devices is in the range of 1 100 μW
THE ADJOINT METHOD APPLIED TO TIME–DISTANCE HELIOSEISMOLOGY

For a given misfit function, a specified optimality measure of a model, its gradient describes the manner in which one may alter properties of the system to march toward a stationary point. The adjoint method, arising from partial-differential-equation-constrained optimization, describes a means of extracting derivatives of a misfit function with respect to model parameters through finite computation. It relies on the accurate calculation of wavefields that are driven by two types of sources, namely, the average wave-excitation spectrum, resulting in the forward wavefield, and differences between predictions and observations, resulting in an adjoint wavefield. All sensitivity kernels relevant to a given measurement emerge directly from the evaluation of an interaction integral involving these wavefields. The technique facilitates computation of sensitivity kernels (Fréchet derivatives) relative to three-dimensional heterogeneous background models, thereby paving the way for nonlinear iterative inversions. An algorithm to perform such inversions using as many observations as desired is discussed.
Estimation of the Wenchuan Earthquake Rupture Sequence Utilizing Teleseismic Records and Coseismic Displacements

For the 12 May 2008 Mw 7.9 Wenchuan earthquake, two imbricate faults, Beichuan fault and Pengguan fault, have ruptured simultaneously. Special attention should be paid to the point of 40 km northeast of the epicenter, in which the Xiaoyudong fault intersects the above two faults, creating a complex fault structure. Surface rupture data from field surveys and previous research of dynamics studies indicate that an important transformation may take place at the intersection. But, few studies about inversion of source rupture process have focused on this issue. We establish a multiple-segment, variable-slip, finite-fault model to reproduce the rupture process and distinguish rupture sequence. Based on the nonnegative least square method and multiple-time-window approach, the spatial and temporal distribution of slip for three rupture sequences are exhibited, using teleseismic records and coseismic displacements. The conformity between synthetic and observed teleseismic records as well as the slip value of the shallowest subfaults and the coseismic displacements is utilized to calibrate the model. The results are as follows: (1) The teleseismic records inversion alone could not distinguish different rupture sequences. However, in order to make the slip of the Hongkou and Yingxiu area coincide with the field investigation, only the Beichuan fault has a bilateral rupture on the point of intersection of Xiaoyudong fault. So the possible rupture sequence is that the earthquake started at the low dip angle part of southern Beichuan fault, and then it propagated to the Pengguan fault, which caused the rupture of Xiaoyudong fault. Then the southern part of Beichuan fault with high dip angle is triggered by the Xiaoyudong fault. (2) The coseismic displacements constraint can control the slip of subfaults near the surface and has little impact on the deeper subfaults. (3) The maximum slip on the fault is located near the Yingxiu and Beichuan area; moreover, the slip is mainly distributed at the shallow region rather than at the deep, which led to serious disasters. Meanwhile, majority of the aftershocks occur in the periphery of large slip.