Miracle-dz/UniFAR-FTUs huggingface dataset:
Growth behavior of evaporated porous thin films

Recent experimental work by a number of researchers has demonstrated that unusual high porosity thin films may be obtained in physical deposition systems by combining glancing angle deposition with in situ substrate motion control. The microstructure of these films consists of isolated columns engineered into shapes such as helices, posts, or chevrons. Due to the isolated nature of the columns, the films present a unique opportunity to study fundamental thin film growth behavior and, in particular, the influence of the self-shadowing mechanism in three dimensions. Apart from this academic motivation, there is the need to characterize the physical constraints imposed on the engineering of these films. In particular, this study will have implications for the realization of isolated, periodically arranged nanostructures envisioned for certain applications such as photonic band gap crystals. Results from an ongoing study of growth dynamics, morphology, porosity, and scaling behavior, and the dependence of these features on deposition parameters are presented.
Proposal : Parallel Balanced Binary Trees Using Just Join

Tree data structures play an important role in almost every area in computer science. Nowadays the explosion of data puts forward a higher demand for the performance of the trees, which requires efficient parallel algorithms for processing large-scale data, as well as a full-featured interface for achieving more functionalities. Traditional algorithm designing on balanced BSTs based on insertions and deletions are plagued with challenges such as being hard to parallelize, single-operand oriented, and varying among different balancing schemes. This thesis proposes a parallel algorithmic framework that overcomes these challenges, which captures all balancing criteria in a single function JOIN. The JOIN-based algorithms are then used for supporting sequences, ordered sets, ordered maps and augmented maps (formally defined in this thesis). A wide variety of functions form a hierarchical interface for these four data types, which are all implemented by join-based algorithms as part of a library PAM (Parallel Augmented Maps). This library is parallel, work-efficient, generic across balancing schemes, persistent, safe for concurrency and applicable to a wide range of applications and queries by proper augmentations. The augmented map structure itself is an abstraction befitting many real applications. The PAM interface greatly simplifies the programming of many applications over direct implementations, such as interval trees, range trees, inverted indices, segment trees, and database snapshot isolations. Experiments show that the implementations of the functions in PAM, as well as all the applications using PAM are practically efficient. Sequentially the code achieves performance that matches or exceeds exiting libraries designed specially for a single application, and the parallel implementation gets speedups ranging from 40 to 90 on 72 cores with 2-way hyperthreading.
RiTE: Providing On-Demand Data for Right-Time Data Warehousing

Data warehouses (DWs) have traditionally been loaded with data at regular time intervals, e.g., monthly, weekly, or daily, using fast bulk loading techniques. Recently, the trend is to insert all (or only some) new source data very quickly into DWs, called near-realtime DWs (right-time DWs). This is done using regular INSERT statements, resulting in too low insert speeds. There is thus a great need for a solution that makes inserted data available quickly, while still providing bulk-load insert speeds. This paper presents RiTE ("Right-Time ETL"), a middleware system that provides exactly that. A data producer (ETL) can insert data that becomes available to data consumers on demand. RiTE includes an innovative main-memory based catalyst that provides fast storage and offers concurrency control. A number of policies controlling the bulk movement of data based on user requirements for persistency, availability, freshness, etc. are supported. The system works transparently to both producer and consumers. The system is integrated with an open source DBMS, and experiments show that it provides "the best of both worlds", i.e., INSERT-like data availability, but with bulk-load speeds (up to 10 times faster).
Transport of Actinides through a Bentonite Backfill

Compacted bentonite has been proposed as a suitable backfill material in the Swedish concept for underground storage of high-level waste. The backfill barrier will serve both as a physical barrier, preventing convective water flow and allowing radionuclide penetration only by diffusion, and as a chemical barrier capable of chemically interacting with the radionuclides.
Protein Structure Prediction Based on Secondary Structure Alignment

In molecular biology, sequence alignment is a fundamental but powerful technique. Biologists find the similarity, the difference and even the function of the input sequences (DNA, RNA and protein sequences) by it. With various purposes, there are many algorithms to align two sequences based on different criteria. Though there are various ways to align macromolecular sequences, a sequence alignment algorithm traditionally considers only the primary structure, which is the amino acid chain. In this paper, we present a new algorithm which aligns sequences with consideration of their secondary structures. When we make use of the information of protein secondary structure such as α helix, β sheet etc., the sensitivity of pairwise alignment can be improved.
Isolation of fusobacteria from the oral cavities of malnourished Nigerian children living in agricultural and herding villages.

A previous study demonstrated the presence and possible involvement of Fusobacterium necrophorum in the pathogenesis of noma lesions of children living in agricultural and herding villages in northwestern Nigeria. In order to determine if F. necrophorum was part of the oral flora of malnourished children with no noma lesions, a study of the fusobacteria present in the oral cavities of 30 children, 2-6 years of age in Sokoto State, was undertaken. Swabs taken of the oral cavity were cultured on selective fusobacteria medium using conventional anaerobic microbiological techniques. F. nucleatum was recovered from each child and F. necrophorum was isolated from the oral cavity of only one child. The presence of F. nucleatum and the lack of F. necrophorum, except in one case, suggests that the latter is not normal flora in the children at risk for noma. F. necrophorum, a putative trigger organism for noma may gain a foothold only when certain staging conditions (i.e., lowered host resistance and/or oral lesion) are present.
A Model-based Approach to Interdependency between Safety and Security in ICS

Wide use of modern ICT technologies brings not only communication efficiency, but also security vulnerabilities into industrial control systems. Traditional physically-isolated systems are now required to take cyber security into consideration, which might also lead to system failures. However, integrating security and safety analysis has always been a challenging issue and the various interdependencies between them make it even more difficult, because they might mutually enhance, or undermine. The paper proposes an integrating framework to (i) formalise the desired and undesired properties to be safe(unsafe) or secure(insecure), including the dependencies between them, (ii) evaluate if a query state reaches a safe(unsafe) or secure(insecure) state, and further quantify how safe or secure the state is. In this way, we can accurately capture the benign and harmful relations between safety and security, particularly detecting and measuring conflicting impacts on them. Finally, this framework is implemented by answer set programming to enable automatic evaluation, which is demonstrated by a case study on pipeline transportation.
Modeling Flash Crowd Performance in Peer-to-Peer File Distribution

Given the growing popularity of peer-to-peer file distribution in commercial applications, it is important to understand the challenges of using p2p file-sharing protocols for file distribution, and how extreme conditions such as flash crowds affect the efficiency of file distribution. In this light, there is a need to understand the impact of the utilization of available bandwidth on the performance of peer-assisted file distribution systems. With a simple measurement study on PlanetLab, we identified distinct phases in peer bandwidth utilization over the download duration. Based on the evolution of the utilization of available peer bandwidth over time, we formulated an analytical model for flash crowds in homogeneous and heterogeneous bandwidth swarms. The model estimates the instantaneous download rate and the average file download time with 10 percent error for swarms up to 160 peers. Our model can be used to predict the scalability of the system when the number of peers increases, and to provision for flash crowds by estimating the server bandwidth to achieve a minimum quality of service. Lastly, we demonstrate how our model is applied to new p2p protocols to understand their design and performance problems.
Guiding Properties of 1.31-and 1.55-μm-Wavelength Surface Plasmon Polaritons on Striped Waveguides on Silicon and Their Wavelength-Selective Detection

We have analyzed the propagation behavior of 1.31-and 1.55-μm-wavelength-band surface plasmon polaritons (SPPs) for three simple Si-based plasmonic waveguides: the Au stripe waveguide, the SiO2 stripe waveguide, and the Au/SiO2 stripe waveguide on a Si substrate. The SPP propagation length in the waveguide varied depending on the waveguide structure and propagation lengths for waveguides with different structural parameters are summarized. The energy that was required for SPP detection after propagation along the waveguides for the 1.31- and 1.55-μm-wavelength bands was calculated for intensity-modulation direct-detection and heterodyne frequency-shift keying systems. The results demonstrate that SPPs can propagate with lower energy consumption than conventional electric wiring below a specific interconnect length. A wavelength-selective structure for SPPs that comprised nano-slits in an Au film on an Si substrate was fabricated. The device can selectively detect 1.31-μm-wavelength SPPs as electrical signals and transmit 1.55-μm-wavelength SPPs. Experimental photoresponses and transmittances were measured and compared with calculated results. Magnitude correlation of the measured and calculated photoresponses and transmittances showed good agreement. Evaluation of the SPP propagation behavior and the wavelength-selective structure are important considerations for the development of optoelectronic integrated circuits that use SPPs and electrons as signal carriers.
Chloroquine susceptibility and reversibility in a Plasmodium falciparum genetic cross

Mutations in the Plasmodium falciparum chloroquine (CQ) resistance transporter (PfCRT) are major determinants of verapamil (VP)‐reversible CQ resistance (CQR). In the presence of mutant PfCRT, additional genes contribute to the wide range of CQ susceptibilities observed. It is not known if these genes influence mechanisms of chemosensitization by CQR reversal agents. Using quantitative trait locus (QTL) mapping of progeny clones from the HB3 × Dd2 cross, we show that the P. falciparum multidrug resistance gene 1 (pfmdr1) interacts with the South‐East Asia‐derived mutant pfcrt haplotype to modulate CQR levels. A novel chromosome 7 locus is predicted to contribute with the pfcrt and pfmdr1 loci to influence CQR levels. Chemoreversal via a wide range of chemical structures operates through a direct pfcrt‐based mechanism. Direct inhibition of parasite growth by these reversal agents is influenced by pfcrt mutations and additional loci. Direct labelling of purified recombinant PfMDR1 protein with a highly specific photoaffinity CQ analogue, and lack of competition for photolabelling by VP, supports our QTL predictions. We find no evidence that pfmdr1 copy number affects CQ response in the progeny; however, inheritance patterns indicate that an allele‐specific interaction between pfmdr1 and pfcrt is part of the complex genetic background of CQR.
Acidic Residues in the Nucleotide-binding Site of the Bacteriophage T7 DNA Primase*

DNA primases catalyze the synthesis of oligoribonucleotides to initiate lagging strand DNA synthesis during DNA replication. Like other prokaryotic homologs, the primase domain of the gene 4 helicase-primase of bacteriophage T7 contains a zinc motif and a catalytic core. Upon recognition of the sequence, 5′-GTC-3′ by the zinc motif, the catalytic site condenses the cognate nucleotides to produce a primer. The TOPRIM domain in the catalytic site contains several charged residues presumably involved in catalysis. Each of eight acidic residues in this region was replaced with alanine, and the properties of the altered primases were examined. Six of the eight residues (Glu-157, Glu-159, Asp-161, Asp-207, Asp-209, and Asp-237) are essential in that altered gene 4 proteins containing these mutations cannot complement T7 phage lacking gene 4 for T7 growth. These six altered gene 4 proteins can neither synthesize primers de novo nor extend an oligoribonucleotide. Despite the inability to catalyze phosphodiester bond formation, the altered proteins recognize the sequence 5′-GTC-3′ in the template and deliver preformed primer to T7 DNA polymerase. The alterations in the TOPRIM domain result in the loss of binding affinity for ATP as measured by surface plasmon resonance assay together with ATP-agarose affinity chromatography.
One-Step Carbon Coating and Polyacrylamide Functionalization of Fe3O4 Nanoparticles for Enhancing Magnetic Adsorptive-Remediation of Heavy Metals

Magnetic nanoparticles are used in adsorptive removal of heavy metals from polluted wastewater. However, their poor stability in an acidic medium necessitates their protection with a coating layer. Coating magnetic nanoparticles with carbon showed proper protection but the heavy metal removal efficiency was slightly weak. However, to boost the removal efficiencies of surface functionalization, polyacrylamide was applied to carbon-coated Fe3O4 nanoparticles. In this paper, to facilitate the synthesis process, one-step carbon coating and polyacrylamide functionalization were conducted using the hydrothermal technique with the aim of enhancing the adsorptive removal capacity of Fe3O4 nanoparticles towards some heavy metals such as Cu(II), Ni(II), Co(II), and Cd(II). The results showed that the one-step process succeeded in developing a carbon coating layer and polyacrylamide functionality on Fe3O4 nanoparticles. The stability of the magnetic Fe3O4 nanoparticles as an adsorbent in an acidic medium was improved due to its resistance to the dissolution that was gained during carbon coating and surface functionalization with polyacrylamide. The adsorptive removal process was investigated in relation to various parameters such as pH, time of contact, metal ion concentrations, adsorbent dose, and temperature. The polyacrylamide functionalized Fe3O4 showed an improvement in the adsorption capacity as compared with the unfunctionalized one. The conditions for superior adsorption were obtained at pH 6; time of contact, 90 min; metal solution concentration, 200 mg/L; adsorbent dose, 0.3 g/L. The modeling of the adsorption data was found to be consistent with the pseudo-second-order kinetic model, which suggests a fast adsorption process. However, the equilibrium data modeling was consistent with both the Langmuir and Freundlich isotherms. Furthermore, the thermodynamic parameters of the adsorptive removal process, including ΔG°, ΔH°, and ΔS°, indicated a spontaneous and endothermic sorption process. The developed adsorbent can be utilized further for industrial-based applications.
The Association of Initiation Factor 4F with Poly(A)-binding Protein Is Enhanced in Serum-stimulated Xenopus Kidney Cells*

Serum stimulation of cultured Xenopuskidney cells results in enhanced phosphorylation of the translational initiation factor (eIF) 4E and promotes a 2.8-fold increase in the binding of the adapter protein eIF4G to eIF4E, to form the functional initiation factor complex eIF4F. Here we demonstrate the serum-stimulated co-isolation of the poly(A)-binding protein (PABP) with the eIF4F complex. This apparent interaction of PABP with eIF4F suggests that a mechanism shown to be important in the control of translation in the yeast Saccharomyces cerevisiae also operates in vertebrate cells. We also present evidence that the signaling pathways modulating eIF4E phosphorylation and function inXenopus kidney cells differ from those in several mammalian cell types studied previously. Experiments with the immunosuppressant rapamycin suggest that the mTOR signaling pathway is involved in serum-promoted eIF4E phosphorylation and association with eIF4G. Moreover, we could find little evidence for regulation of eIF4E function via interaction with the specific binding proteins 4E-BP1 or 4E-BP2 in these cells. Although rapamycin abrogated serum-enhanced rates of protein synthesis and the interaction of eIF4G with eIF4E, it did not prevent the increase in association of eIF4G with PABP. This suggests that serum stimulates the interaction between eIF4G and PABP by a distinct mechanism that is independent of both the mTOR pathway and the enhanced association of eIF4G with eIF4E.
A Short Review on Chitosan Membrane for Biomolecules Immobilization

Chitosan is an important natural polymer that occurs in the world. Chitosan is soluble in acidic aqueous media and it can be obtained in various forms. It is widely used for many applications. Hence, we briefly describe the role of chitosan in membrane form, an important area of research in which a variety of synthetic methods has been proposed and their significance is explained. Thus, this review emphasizes the papers on the high value-added applications of these chitosan membranes in diverse fields such as medicine, biological, cosmetics and nanotechnology.
Accurate Automated Protein NMR Structure Determination Using Unassigned NOESY Data

Conventional NMR structure determination requires nearly complete assignment of the cross peaks of a refined NOESY peak list. Depending on the size of the protein and quality of the spectral data, this can be a time-consuming manual process requiring several rounds of peak list refinement and structure determination. Programs such as Aria, CYANA, and AutoStructure can generate models using unassigned NOESY data but are very sensitive to the quality of the input peak lists and can converge to inaccurate structures if the signal-to-noise of the peak lists is low. Here, we show that models with high accuracy and reliability can be produced by combining the strengths of the high-resolution structure prediction program Rosetta with global measures of the agreement between structure models and experimental data. A first round of models generated using CS-Rosetta (Rosetta supplemented with backbone chemical shift information) are filtered on the basis of their goodness-of-fit with unassigned NOESY peak lists using the DP-score, and the best fitting models are subjected to high resolution refinement with the Rosetta rebuild-and-refine protocol. This hybrid approach uses both local backbone chemical shift and the unassigned NOESY data to direct Rosetta trajectories toward the native structure and produces more accurate models than AutoStructure/CYANA or CS-Rosetta alone, particularly when using raw unedited NOESY peak lists. We also show that when accurate manually refined NOESY peak lists are available, Rosetta refinement can consistently increase the accuracy of models generated using CYANA and AutoStructure.
Morphology and Characterization of Clay-reinforced EPDM Nanocomposites

The clay-reinforced ethylene propylene diene terpolymer (EPDM) nanocomposites with organo-montmorillonite (OMMT) and EPDM-clay conventional composites with pristine MMT are compared in terms of their morphology, mechanical properties, and solvent resistance. The maleic anhydride grafted EPDM (MAH-g-EPDM) is used as the compatiblizer for preparing clay-reinforced EPDM nanocomposites via a melt intercalation process. The formation of exfoliated nano-composites is confirmed by X-ray diffraction (XRD) and transmission electron microscopy (TEM). Furthermore, the morphological change during the mixing times of vulcanization process through exerting shearing force on clay particles is discussed. The mechanical properties and solvent resistance of clay-reinforced EPDM nanocomposites are examined as a function of the organoclay content in the matrix of the polymer, the result shows remarkable improvement relative to that of conventional composites.
Dendritic cells from different tissues induce production of different T cell cytokine profiles

The precise role of antigen‐presenting cells (APC) in regulating the balance of T‐helper type 1 (Th1) and T‐helper type 2 (Th2) cytokine production is unclear. Dendritic cells (DC), the most potent APC for activation of naive T cells, were found to regulate Th1 and Th2 cytokine profiles in a fashion dependent upon their tissue of origin. Spleen (systemic) DC induce mainly Th1 cytokines and Peyer's patch (mucosal) DC induce predominantly Th2 cytokines. These findings support the current concept that different tissues, each with its distinct microenvironment of cytokines, hormones, and cellular elements, are involved in the selection, promotion, and/or maintenance of different immune responses. With regard to DC, it is apparent that the tissue of DC origin determines the cytokine profiles produced by T cells and that DC from different tissues favor either cellular versus humoral immune responses by influencing T cell cytokine production.
Determinants of Postconflict Symptoms in Albanian Kosovars

During the period from 1998 to 1999, more than 1 million civilians from the province of Kosovo in the Balkans were displaced as a consequence of organized violence and war. The aim of the present study was to determine the prevalence of posttraumatic stress disorder (PTSD) in a sample of the Albanian Kosovar population more than 2 years after the end of the conflict and to assess the effect of exposure to war-related events. A total of 340 households were randomly selected among 12,900 families returned from a country of asylum (Switzerland). All adults in each household were invited to participate (N = 996). The following instruments were used: the Albanian translations of the PTSD section of the Mini International Neuropsychiatric Interview and of the Medical Outcomes Study 36-Item Short Form, and a list of traumatic events adapted from the Harvard Trauma Questionnaire. The overall prevalence of PTSD was 23.5%. A strong cumulative effect of trauma was observed, with odds ratios for PTSD rising steeply with the number of events to which people were exposed. After taking into account traumatic events, multivariable analysis indicated that female gender, older age, and having left Kosovo during the conflict were significantly associated with higher frequency of PTSD, whereas significant heterogeneity among municipalities was observed. Stratified analysis for people who stayed and left the province during the war suggested that different patterns of trauma may be relevant in the two subsamples, with forced separation and isolation strongly associated with PTSD in people who stayed in Kosovo. PTSD diagnosis was also significantly associated with lower scores on all dimensions of the Medical Outcomes Study 36-Item Short Form and lower economic status. The results suggest that responding to medium-term and long-term mental health consequences of conflict is a necessary task for the global rehabilitation of health care systems in a war devastated country.