Miracle-dz/UniFAR-FTUs huggingface dataset:
A mutation in integrase can compensate for mutations in the simian immunodeficiency virus att site

Sequences at the left terminus of U3 in the left long terminal repeat (LTR) and at the right terminus of U5 in the right LTR are important for integration of retroviral DNA. In the infectious pathogenic molecular clone of simian immunodeficiency virus strain mac239 (SIVmac239), 10 of the 12 terminal base pairs form an imperfect inverted repeat structure (5' TGGAAGGGATTT 3' [nucleotides 1 to 12] and 3' ACGATCCCTAAA 5' [nucleotides 10279 to 10268]). Nineteen different mutant forms of SIVmac239 proviral DNA with changes at one or more of the positions in each of the 12-terminal-base-pair regions were constructed. Viral replication was severely or completely compromised with nine of these mutants. Revertants appeared 40 to 50 days after transfection in two independent experiments with mutant 7, which contained changes of AGG to TAC at positions 5 to 7 in U3 and TCC to GAA at positions 10275 to 10273 in U5. Virus produced at these times from mutant 7 transfection replicated upon reinfection with only a slight delay when compared to the wild type. Sequence analysis of the LTR and integrase regions from infected cultures revealed two predominant changes: G to A at position 10275 in U5 and Glu to Lys at position 136 in integrase. Derivatives of clone 7 in which these changes were introduced individually and together were constructed by site-specific mutagenesis. Each change individually restored replication capacity only partially. However, the combination of both mutations restored replicative capacity to that of the original revertants. These results indicate that changes in integrase can compensate for mutations in the terminal nucleotides of the SIV LTR. The results further indicate that resistance to integrase inhibitors may include both integrase and LTR mutations.
Characterization of a functional NF-kappa B site in the human interleukin 1 beta promoter: evidence for a positive autoregulatory loop

The -300 region of the interleukin 1 beta (IL-1 beta) promoter contains a functional NF-kappa B binding site composed of the decamer sequence 5'-GGGAAAATCC-3'. Probes representing the -300 region or the NF-kappa B site alone interacted with NF-kappa B proteins present in phorbol myristate acetate-, lipopolysaccharide-, or Sendai virus-induced myeloid cell extracts as well as recombinant NFKB1 (p50) and RelA (p65); furthermore, NF-kappa B protein-DNA complex formation was dissociated in vitro by the addition of recombinant I kappa B alpha. Mutation of the NF-kappa B site in the context of the IL-1 beta promoter reduced the responsiveness of the IL-1 beta promoter to various inducers, including phorbol ester, Sendai virus, poly(rI-rC), and IL-1 beta. A 4.4-kb IL-1 beta promoter fragment linked to a chloramphenicol acetyltransferase reporter gene was also preferentially inducible by coexpression of individual NF-kappa B subunits compared with a mutated IL-1 beta promoter fragment. When multiple copies of the IL-1 beta NF-kappa B site were linked to an enhancerless simian virus 40 promoter, this element was able to mediate phorbol ester- or lipopolysaccharide-inducible gene expression. In cotransfection experiments, RelA (p65) and c-Rel (p85) were identified as the main subunits responsible for the activation of the IL-1 beta NF-kappa B site; also, combinations of NFKB1 (p50) and RelA (p65) or c-Rel and RelA were strong transcriptional activators of reporter gene activity. The presence of a functional NF-kappa B binding site in the IL-1 beta promoter suggests that IL-1 positively autoregulates its own synthesis, since IL-1 is a strong inducer of NF-kappa B binding activity. Thus, the IL-1 beta gene may be considered as an important additional member of the family of cytokine genes regulated in part by the NF-kappa B/rel family of transcription factors.
Fabrication and characterization of a titanium dioxide (TiO2) nanoparticles reinforced bio-nanocomposite containing Miswak (Salvadora persica L.) extract – the antimicrobial, thermo-physical and barrier properties

Objective: The microbial, physico-chemical and optical corruptions threaten a variety of foods and drugs and consequently the human biological safety and its accessible resources. The humanbeing’s tendency towards bio-based materials and natural plant-extracts led to an increase in the usage of antimicrobial biocomposites based on medicinal herbs. Miswak (Salvadora persica L.) extract (SPE) has been proved effective for its antimicrobial and other biological activities. Therefore, in this study, titanium dioxide (TiO2) nanoparticles (TONP) and SPE were applied to fabricate antimicrobial carboxymethyl cellulose (Na-CMC) based bio-nanocomposites which would simultaneously promote some thermo-physical and barrier properties. Methods: CMC-neat film (C1), CMC/TONP-2% (C2) and CMC/TONP-2% with 150, 300 and 450 mg/mL SPE (SPE150, SPE30 and SPE450, respectively) were fabricated. The physical and mechanical properties; elemental mapping analysis (MAP), X-ray diffraction (XRD), scanning electron microscopy (SEM), thermal gravimetric analysis (TGA-DTG); fourier transform infrared (FTIR), energy-dispersive X-ray (EDX) and UV-vis spectroscopies were done to further validate the results. Results: Addition of TONP (2%) improved the blocking of UV light at 280 nm while SPE-containing nanocomposites completely blocked it. FTIR, XRD and SEM confirmed the formation of homogeneous films and high miscibility of applied materials. TONP led to an increase in Young’s modulus (YM) and stress at break (SB) while SPE decreased them and enhanced the elongation to break (EB) (flexibility) of the active nanocomposites. Compared to CMC-film, the thermo-gravimetric analysis (TGA-DTG) showed a higher thermal stability for CMC/TONP and CMC/TONP/SPE nanocomposites. The EDX spectroscopy and elemental mapping analysis (MAP) proved the existence and well-distributedness of Na, K, Cl, S, Ti, F and N elements in SPE-activated nanocomposites. The pure SPE and SPE-activated nanocomposites showed a favorable antimicrobial activity against both gram-positive (Staphylococcus aureus) and negative (Escherichia coli) bacteria. Conclusion: The CMC-TiO2-SPE nanocomposites were homogeneously produced. Combination of TiO2 nanoparticles and dose-dependent SPE led to an improvement of thermal stability, and high potential in antimicrobial and UV-barrier properties. These results can generally highlight the role of the fabricated antimicrobial bio-nanocomposites as a based for different applications especially in food/drug packaging or coating.
La «s» sonora prevocálica en el español moderno

A semejanza de lo que ocurre hoy día en portugués y catalán, en el español medieval había una distinción fonológica entre sibilantes sordas y sonoras, al principio de sílaba. Las grafías // y s, en posición intervocálica, representaban una fricativa ápicoalveolar sorda y una sonora: passo, casa; las grafías g y z, una africada predorsoalveolar o predorsodental sorda y una sonora: caga, dezir; las grafías x y /, o g ante vocal palatal, una fricativa palatal sorda y una africada o fricativa palatal sonora: mexilla, joven, coger. Como norma general, las sibilantes sonoras medievales se ensordecieron en español \ Hay o había hasta muy recientemente algunas excepciones. En el dialecto judeo-español se conserva la distinción fonológica de sordez y sonoridad en las sibilantes, con algunos cambios. Las africadas predorsales g y z evolucionaron a fricativas, y las fricativas ápicoalveolares se hicieron predorsales, confundiéndose con los resultados de g y z. En la comarca de Miranda, situada en el nordeste de Portugal, existe una habla española que mantiene casi inalterado el sistema medieval de sibilantes, excepto que las africadas g y z pasaron a fricativas. En Petisqueira y Deiláo, dos poblaciones situadas al norte de Miranda, el fonema / z / evolucionó a /I/, pero se conserva la distinción entre la sibilante fricativa ápicoalveolar sorda y la sonora, la fricativa predorsoalveolar sorda y la sonora. En Enguera, una población de habla
Novel Wi-Fi - LTE Real-Time Traffic Steering - First Field Measurement Results

A novel algorithm, real-time two-way traffic steering, has been developed to address the issue in mixed cellular-wireless deployments that current commercial terminals switch from cellular access to wireless access regardless of the expected bitrate in the wireless cell. In contrast to terminal-controlled traffic steering mechanisms, no changes on the terminal side are needed in order to benefit from the proposed algorithm. The algorithm was tested in an end-to-end test network and very promising results were obtained for both a single user and for multiple users. Two scenarios were considered: In the first scenario, real-time two-way traffic steering was demonstrated for one single moving user. Here the capability of selecting the best access was demonstrated. In the latter scenario, multiple users were moving together mimicking users arriving to and leaving from a train station. Here the load balancing capabilities of the algorithm were demonstrated and it was also seen that the pro-posed algorithm distributes the resources in a fair way between the users.
Sexual Violence Against Older People: A Review of the Empirical Literature

Aging and sexual violence are both established areas of research, but little attention has been paid to research into sexual violence against older people. This article presents a critical review of the literature reporting empirical research in three overlapping fields of inquiry: elder abuse, domestic violence, and sexual violence, identifying points of theoretical and methodological similarity and difference across academic disciplines. Using a range of search terms combining age, sexual violence, and elder abuse, the following databases were searched: EBSCOHOST, Ingenta-Ingenta connect, and JSTOR. In total, the databases searches returned 31 relevant articles and an additional 9 relevant articles were found through manual searches of bibliographies and Google searches, which were grouped into three categories: elder abuse, domestic violence in later life, and sexual violence against older people. Four themes common across these fields emerged: prevalence, characteristics of victims and risk factors, impacts and coping strategies, and perpetrator and assault characteristics. The findings in each area are discussed in detail, exposing gaps in knowledge and understandings of sexual violence against older women. The article ends by defining a future research agenda for this underexplored phenomenon that is of increasing importance in a context of global aging.
GATE as a GEANT4-based Monte Carlo platform for the evaluation of proton pencil beam scanning treatment plans

Active scanning delivery systems take full advantage of ion beams to best conform to the tumor and to spare surrounding healthy tissues; however, it is also a challenging technique for quality assurance. In this perspective, we upgraded the GATE/GEANT4 Monte Carlo platform in order to recalculate the treatment planning system (TPS) dose distributions for active scanning systems. A method that allows evaluating the TPS dose distributions with the GATE Monte Carlo platform has been developed and applied to the XiO TPS (Elekta), for the IBA proton pencil beam scanning (PBS) system. First, we evaluated the specificities of each dose engine. A dose-conversion scheme that allows one to convert dose to medium into dose to water was implemented within GATE. Specific test cases in homogeneous and heterogeneous configurations allowed for the estimation of the differences between the beam models implemented in XiO and GATE. Finally, dose distributions of a prostate treatment plan were compared. In homogeneous media, a satisfactory agreement was generally obtained between XiO and GATE. The maximum stopping power difference of 3% occurred in a human tissue of 0.9 g cm−3 density and led to a significant range shift. Comparisons in heterogeneous configurations pointed out the limits of the TPS dose calculation accuracy and the superiority of Monte Carlo simulations. The necessity of computing dose to water in our Monte Carlo code for comparisons with TPSs is also presented. Finally, the new capabilities of the platform are applied to a prostate treatment plan and dose differences between both dose engines are analyzed in detail. This work presents a generic method to compare TPS dose distributions with the GATE Monte Carlo platform. It is noteworthy that GATE is also a convenient tool for imaging applications, therefore opening new research possibilities for the PBS modality.
Thermophilic anaerobic digestion of sugars in upflow anaerobic sludge blanket reactors.

In recent years numerous designs have been developed for the high-rate anaerobic treatment of wastewater. '-6 All these processes have their advantages and drawbacks, which have been discussed repeatedly (see, for example, ref. 7). Of these processes, the upflow anaerobic sludge blanket (UASB) process is currently the most widely applied, at least in Western Europe. It is successfully applied in the treatment of wastewaters from maize and potato starch industries and sugar beet and potato processing industries. ' Perhaps the main advantage of the UASB process is that no specific support material is required. However, this main advantage may sometimes be a serious drawback: the absence of support material necessitates the availability of a sludge with very good settling properties. Whenever such a sludge is obtained, or can be maintained, successful operation of the UASB process is readily achieved. Under certain circumstances the settleability of the sludge in UASB reactors is greatly improved because bacterial growth is in the form of spherical flocs with a quite consistent structure, normally referred to as granular sludge.6 Although already considerable research has been performed on factors considered to be important in the phenomenon of gran~lation,~-" the knowledge on this matter is still relatively poor. Thermophilic anaerobic digestion may become an attractive alternative for mesophilic digestion because of the higher growth rates of the bacteria involved and, consequently, the higher maximum activities per unit of biomass. As the specific growth rates of the methane-forming bacteria of the genus Methanothrix, which are believed to be the predominant acetoclastic methanogens in methane digestion processes with a high biomass retention time,L2313 is ca. 2.5 times as high at 55°C as at 30°C,'2. '3 also a 2.5 times higher methanogenic acitivity per unit of biomass may be expected. Also, in thermophilic sewage sludge digestion a Methanosarcina was found to be the predominant acetoclastic methanogen, which even has a higher specific growth rate than the thermophilic Methanothrix. l 4 The successful operation of high-rate thermophilic systems requires a high activity per unit of volume, and therefore a high biomass retention is a prerequisite. In view of the successful use under mesophilic conditions, we investigated the thermophilic UASB process for this purpose. Glucose was chosen as the substrate because granulation is reported to occur in UASB reactors when it is the substrate for a acid-formation process. "
Solving One-dimensional Cutting-Stock Problem Based on Ant Colony Optimization

One-dimensional cutting-stock is one of the classic NP-hard problems in combinatorial optimization. It is widely applied in engineering technology and industrial production. In this paper, an improved ant colony optimization is proposed based on the optimized one-dimensional cutting-stock model. Aiming at the specific characteristics of the problem, a series of improvement strategies are proposed, including part encoding, solution path, state transition probability and pheromone updating rules. Then the concrete steps of algorithm are described. Through the analysis and comparison of experimental results, this method is proved high efficiency.
Interaction of the Clostridium difficile Binary Toxin CDT and Its Host Cell Receptor, Lipolysis-stimulated Lipoprotein Receptor (LSR)*

Background: Clostridium difficile binary toxin CDT enters host cells via its receptor LSR. Results: Regions responsible for the CDT-LSR interaction were identified. Conclusion: An immunoglobulin-like domain of LSR and amino acids 757–866 of the binding component of CDT determine the toxin-receptor interaction. Significance: Knowledge of the toxin-receptor interaction is key to the development of anti-toxin strategies. CDT (Clostridium difficile transferase) is a binary, actin ADP-ribosylating toxin frequently associated with hypervirulent strains of the human enteric pathogen C. difficile, the most serious cause of antibiotic-associated diarrhea and pseudomembranous colitis. CDT leads to the collapse of the actin cytoskeleton and, eventually, to cell death. Low doses of CDT result in the formation of microtubule-based protrusions on the cell surface that increase the adherence and colonization of C. difficile. The lipolysis-stimulated lipoprotein receptor (LSR) is the host cell receptor for CDT, and our aim was to gain a deeper insight into the interplay between both proteins. We show that CDT interacts with the extracellular, Ig-like domain of LSR with an affinity in the nanomolar range. We identified LSR splice variants in the colon carcinoma cell line HCT116 and disrupted the LSR gene in these cells by applying the CRISPR-Cas9 technology. LSR truncations ectopically expressed in LSR knock-out cells indicated that intracellular parts of LSR are not essential for plasma membrane targeting of the receptor and cellular uptake of CDT. By generating a series of N- and C-terminal truncations of the binding component of CDT (CDTb), we found that amino acids 757–866 of CDTb are sufficient for binding to LSR. With a transposon-based, random mutagenesis approach, we identified potential LSR-interacting epitopes in CDTb. This study increases our understanding about the interaction between CDT and its receptor LSR, which is key to the development of anti-toxin strategies for preventing cell entry of the toxin.
Assessing the online outpatient booking system

Background: Appointment scheduling is considered as one of the important aspects of patient flow management. Today, the advent of Internet into the realm of health care has paved the way for employing an internet-based booking system for visiting physicians. Therefore, this study aimed at assessing the online outpatient booking system in Iranian hospitals. Methods: The present study was an applied descriptive study. In this study, all outpatient appointment booking websites in Iranian hospitals were evaluated. The methods of outpatients booking in the hospitals (N = 598) were determined based on information available at their active websites. Finally, 31 active online booking systems were identified and investigated using a localized checklist, including 59 items in 6 sections. Results: The results showed that only 13.03% of Iranian hospitals had an active online booking system. All the online booking systems had a weak quality based on the total score percentage (17.10%). The highest score percentages were related to sections of online security features (45%) and details of health insurance (42%), while the clinical data section received the lowest score (7.25%). The most frequent item was the patient’s name in the patient demographics section (27 websites). Conclusions: The outpatient appointment system in Iranian hospitals is done more traditionally through walk-ins to the health centers. The online outpatient booking systems have poor quality. Hence, codification and communication of national standards for designing hospital websites, periodical evaluation of appointment booking websites by ministry of health, and survey of the users of this method can enhance the qualitative level of these websites.
Application of WGS data for O-specific antigen analysis and in silico serotyping of Pseudomonas aeruginosa isolates

Accurate typing methods are required for efficient infection control. The emergence of whole genome sequencing (WGS) technologies has enabled the development of genomics-based methods applicable for routine typing and surveillance of bacterial pathogens. In this study, we developed the Pseudomonas aeruginosa serotyper (PAst) program, which enabled in silico serotyping of P. aeruginosa isolates using WGS data. PAst has been made publically available as a web-service, and aptly facilitate high-throughput serotyping analysis. The program overcomes critical issues such as the loss of in vitro typeability often associated with P. aeruginosa isolates from chronic infections, and quickly determines the serogroup of an isolate based on the sequence of the O-specific antigen (OSA) gene cluster. Here, PAst analysis of 1649 genomes resulted in successful serogroup assignments in 99.27% of the cases. This frequency is rarely achievable by conventional serotyping methods. The limited number of non-typeable isolates found using PAst was the result of either complete The serotyping technique has been one of the standard tools for epidemiological studies and infection controls for many decades. The available historical records of P. aeruginosa serotypes offer a vast amount of information about P. aeruginosa and population structures Although problems with non- typeable isolates have been described since the implementation of the method, the serotype information is still applicable today for outbreak tracking, strain typing, and studies of LPS structure and evolution. The present study presents a newly developed Web Server tool called PAst, which is user friendly, reliable, and high- throughput for in silico serotyping of P. aeruginosa isolates.
Speciation below ground: Tempo and mode of diversification in a radiation of endogean ground beetles

Dispersal is a critical factor determining the spatial scale of speciation, which is constrained by the ecological characteristics and distribution of a species’ habitat and the intrinsic traits of species. Endogean taxa are strongly affected by the unique qualities of the below‐ground environment and its effect on dispersal, and contrasting reports indicate either high dispersal capabilities favoured by small body size and mediated by passive mechanisms, or low dispersal due to restricted movement and confinement inside the soil. We studied a species‐rich endogean ground beetle lineage, Typhlocharina, including three genera and more than 60 species, as a model for the evolutionary biology of dispersal and speciation in the deep soil. A time‐calibrated molecular phylogeny generated from >400 individuals was used to delimit candidate species, to study the accumulation of lineages through space and time by species–area–age relationships and to determine the geographical structure of the diversification using the relationship between phylogenetic and geographic distances across the phylogeny. Our results indicated a small spatial scale of speciation in Typhlocharina and low dispersal capacity combined with sporadic long distance, presumably passive dispersal events that fuelled the speciation process. Analysis of lineage growth within Typhlocharina revealed a richness plateau correlated with the range of distribution of lineages, suggesting a long‐term species richness equilibrium mediated by density dependence through limits of habitat availability. The interplay of area‐ and age‐dependent processes ruling the lineage diversification in Typhlocharina may serve as a general model for the evolution of high species diversity in endogean mesofauna.