Miracle-dz/UniFAR-FTUs huggingface dataset:
PyPop: A Software Framework for Population Genomics: Analyzing Large-Scale Multi-Locus Genotype Data

Software to analyze multi-locus genotype data for entire populations is useful for estimating haplotype frequencies, deviation from Hardy-Weinberg equilibrium and patterns of linkage disequilibrium. These statistical results are important to both those interested in human genome variation and disease predisposition as well as evolutionary genetics. As part of the 13th International Histocompatibility and Immunogenetics Working Group (IHWG), we have developed a software framework (PyPop). The primary novelty of this package is that it allows integration of statistics across large numbers of data-sets by heavily utilizing the XML file format and the R statistical package to view graphical output, while retaining the ability to inter-operate with existing software. Largely developed to address human population data, it can, however, be used for population based data for any organism. We tested our software on the data from the 13th IHWG which involved data sets from at least 50 laboratories each of up to 1000 individuals with 9 MHC loci (both class I and class II) and found that it scales to large numbers of data sets well.
The Role of NMDARs Ligands on Antinociceptive Effects of Pregabalin in the Tail Flick Test

Background: Pregabalin as a new anticonvulsant has been used in different pain treatments. Objectives: The aim of this study was to investigate the role of N-methyl-D-aspartate (NMDA) ligands in antinociceptive effect of pregabalin in mice using tail flick. Materials and Methods: NMDA (15 and 30 mg/kg) as an agonist or MK801 (0.02 and 0.05 mg/kg) as an antagonist were injected intraperitoneally either alone or 15 minutes before antinociceptive dose of pregabalin (100 mg/kg). Then the latency times and %MPE were measured in the tail flick assay during 75 minutes. Results: NMDA and MK801 had no effects alone. NMDA pretreatment significantly decreased the latency times of pregabalin till 75th minutes. In NMDA pretreated groups, %MPE30 unlike %MPE75 decreased significantly compared to those of pregabalin. MK801 delayed the latency times in pretreated groups, but %MPE30 and %MPE75 did not change significantly compared to pregabalin alone. Conclusions: Our findings support the role of NMDARs in pregabalin antinociception, because the NMDAR agonist, unlike the antagonist, decreased the antinociceptive effect of pregabalin, even if tail flick is not an adequate pain assessment method in this regard.
Parallel and Distributed Systems Report Series An Analysis of Four Long-Term Grid Traces

The Grid computing vision promises to provide the needed platform for a new and more demanding range of applications. For this promise to become true, a number of hurdles, including the design and deployment of adequate resource management and information services, need to be overcome. In this context, understanding the characteristics of real Grid workloads is a crucial step for improving the quality of existing Grid services, and in guiding the design of new solutions. Towards this goal, in this work we present the characteristics of traces of four real Grid environments, namely LCG, Grid3, and TeraGrid, which are among the largest production Grids currently deployed, and the DAS, which is a research Grid. We focus our analysis on virtual organizations, on users, and on individual jobs characteristics. We further attempt to quantify the evolution and the performance of the Grid systems from which our traces originate. Given the incompleteness of the information available for analysis purposes, we discuss the requirements of a new format for Grid traces, and we propose the establishment of a virtual center for workload-based Grid benchmarking data: The Grid Workloads Archive. Finally, we discuss the applicability of our approach in three important areas of Grid research: benchmarking, scheduling, and monitoring.
Influence of genome-scale RNA structure disruption on the replication of murine norovirus—similar replication kinetics in cell culture but attenuation of viral fitness in vivo

Mechanisms by which certain RNA viruses, such as hepatitis C virus, establish persistent infections and cause chronic disease are of fundamental importance in viral pathogenesis. Mammalian positive-stranded RNA viruses establishing persistence typically possess genome-scale ordered RNA secondary structure (GORS) in their genomes. Murine norovirus (MNV) persists in immunocompetent mice and provides an experimental model to functionally characterize GORS. Substitution mutants were constructed with coding sequences in NS3/4- and NS6/7-coding regions replaced with sequences with identical coding and (di-)nucleotide composition but disrupted RNA secondary structure (F1, F2, F1/F2 mutants). Mutants replicated with similar kinetics to wild-type (WT) MNV3 in RAW264.7 cells and primary macrophages, exhibited similar (highly restricted) induction and susceptibility to interferon-coupled cellular responses and equal replication fitness by serial passaging of co-cultures. In vivo, both WT and F1/F2 mutant viruses persistently infected mice, although F1, F2 and F1/F2 mutant viruses were rapidly eliminated 1–7 days post-inoculation in competition experiments with WT. F1/F2 mutants recovered from tissues at 9 months showed higher synonymous substitution rates than WT and nucleotide substitutions that potentially restored of RNA secondary structure. GORS plays no role in basic replication of MNV but potentially contributes to viral fitness and persistence in vivo.
Increase in soil organic carbon by agricultural intensification in northern China

Abstract. Agricultural intensification has contributed greatly to the sustained food supply of China's population of 1.3 billion over the 30-year period from 1982 to 2011. Intensification has several and widely recognized negative environmental impacts including depletion of water resources, pollution of water bodies, greenhouse gas emissions and soil acidification. However, there have been few studies over this period on the impacts of intensification on soil organic carbon (SOC) at the regional level. The present study was conducted in Huantai County, a typical intensive farming region in northern China, to analyze the temporal dynamics of SOC influenced by climate and farming practices. The results indicate that from 1982 to 2011, SOC content and density in the 0–20 cm layer of the cropland increased from 7.8 ± 1.6 to 11.0 ± 2.3 g kg−1 (41%) and from 21.4 ± 4.3 to 33.0 ± 7.0 Mg ha−1 (54%), respectively. The SOC stock (0–20 cm) of the farmland for the entire county increased from 0.75 to 1.2 Tg (59%). Correlation analysis revealed that incorporation of crop residues significantly increased SOC, while an increase in the mean annual temperature decreased the SOC level. Therefore, agricultural intensification has increased crop productivity and contributed to SOC sequestration in northern China. In the near future, more appropriate technologies and practices must be developed and implemented for a maintenance or enhancement of SOC in this region and elsewhere in northern China, which also reduce non-CO2 greenhouse gas emissions, since the climate benefit from the additional SOC storage is estimated to be smaller than the negative climate impacts of N2O from N fertilizer additions.
Effectiveness of biphasic calcium phosphate block bone substitutes processed using a modified extrusion method in rabbit calvarial defects

Purpose This study evaluated the mechanical and structural properties of biphasic calcium phosphate (BCP) blocks processed using a modified extrusion method, and assessed their in vivo effectiveness using a rabbit calvarial defect model. Methods BCP blocks with three distinct ratios of hydroxyapatite (HA):tricalcium phosphate (TCP) were produced using a modified extrusion method:HA8 (8%:92%), HA48 (48%:52%), and HA80 (80%:20%). The blocks were examined using scanning electron microscopy, X-ray diffractometry, and a universal test machine. Four circular defects 8 mm in diameter were made in 12 rabbits. One defect in each animal served as a control, and the other three defects received the BCP blocks. The rabbits were sacrificed at either two weeks (n=6) or eight weeks (n=6) postoperatively. Results The pore size, porosity, and compressive strength of the three types of bone block were 140-170 µm, >70%, and 4-9 MPa, respectively. Histologic and histomorphometric observations revealed that the augmented space was well maintained, but limited bone formation was observed around the defect base and defect margins. No significant differences were found in the amount of new bone formation, graft material resorption, or bone infiltration among the three types of BCP block at either of the postoperative healing points. Conclusions Block bone substitutes with three distinct compositions (i.e., HA:TCP ratios) processed by a modified extrusion method exhibited limited osteoconductive potency, but excellent space-maintaining capability. Further investigations are required to improve the processing method. Graphical Abstract
Low-carbon routing algorithms for cloud computing services in IP-over-WDM networks

Energy consumption in telecommunication networks keeps growing rapidly, mainly due to emergence of new Cloud Computing (CC) services that need to be supported by large data centers that consume a huge amount of energy and, in turn, cause the emission of enormous quantity of CO2. Given the decreasing availability of fossil fuels and the raising concern about global warming, research is now focusing on novel “low-carbon” telecom solutions. E.g., based on today telecom technologies, data centers can be located near renewable energy plants and data can then be effectively transferred to these locations via reconfigurable optical networks, based on the principle that data can be moved more efficiently than electricity. This paper focuses on how to dynamically route on-demand optical circuits that are established to transfer energy-intensive data processing towards data centers powered with renewable energy. Our main contribution consists in devising two routing algorithms for connections supporting CC services, aimed at minimizing the CO2 emissions of data centers by following the current availability of renewable energy (Sun and Wind). The trade-off with energy consumption for the transport equipments is also considered. The results show that relevant reductions, up to about 30% in CO2 emissions can be achieved using our approaches compared to baseline shortest-path-based routing strategies, paying off only a marginal increase in terms of network blocking probability.
On the Cohomology of the Steenrod algebra

L etA be the dual of the mod p Steenrod algebra. A = Fp(1;:::). Let A(n) be the subalgebra generated by 1;::: ;n. We show that there exists a family of nite p-groups G(n;r) whose group algebra Fp(G(n;r)) is a quotient Hopf al- gebra ofA(n) and the restriction map on the cohomology is an isomorphism up to certain level depending on r.
Homogeneous orbit closures and applications

Abstract We give new classes of examples of orbits of the diagonal group in the space of unit volume lattices in ℝd for d≥3 with nice (homogeneous) orbit closures, as well as examples of orbits with explicitly computable but irregular orbit closures. We give Diophantine applications to the former; for instance, we show that, for all γ,δ∈ℝ, \[ \liminf _{|n|\to \infty }|n|\langle n \sqrt [3]{2}-\gamma \rangle \langle n \sqrt [3]{4}-\delta \rangle =0, \] where 〈c〉 denotes the distance of a real number c to the integers.
Visual knowledge transfer among multiple cameras for people counting with occlusion handling

We present a framework to count the number of people in an environment where multiple cameras with different angles of view are available. We consider the visual cues captured by each camera as a knowledge source, and carry out cross-camera knowledge transfer to alleviate the difficulties of people counting, such as partial occlusions, low-quality images, clutter backgrounds, and so on. Specifically, this work distinguishes itself with the following contributions. First, we overcome the variations of multiple heterogeneous cameras with different perspective settings by matching the same groups of pedestrians taken by these cameras, and present an algorithm for accomplishing cross-camera correspondence. Second, the proposed counting model is composed of a pair of collaborative regressors. While one regressor measures people counts by the features extracted from intra-camera visual evidences, the other recovers the yielded residual by taking the conflicts among inter-camera predictions into account. The two regressors are elegantly coupled, and jointly lead to an accurate counting system. Additionally, we provide a set of manually annotated pedestrian labels on the PETS 2010 videos for performance evaluation. Our approach is comprehensively tested in various settings and compared with competitive baselines. The significant improvement in performance manifests the effectiveness of the proposed approach.
Explicit phonetic instruction vs. implicit attention to native exposure: phonological awareness of English schwa in CLIL

Abstract The present study aims at determining whether instruction in the form of explicit phonetic training and of implicit exposure to native input impacted Content and Language Integrated Learning (CLIL) students’ phonological awareness of the occurrence of English schwa in unstressed syllables of content words (bacon). Four intact CLIL groups were administered a perception task immediately before and after an intervention period of one month in which two groups underwent explicit instruction on the incidence of reduced vowels versus full vowels in English disyllabic words while another group was exposed to native input in their CLIL sessions. A fourth CLIL group with neither explicit intervention nor native teacher input served as control group. All four groups tended to judge both schwas and full vowels as correct in the pre-test, indicating that they were not knowledgeable of the general pattern of vowel reduction occurrence in unstressed syllables in English prior to intervention. In the post-test, the three experimental groups significantly improved their ability to identify full vowels as incorrect, the groups receiving explicit instruction exhibiting higher gains than the group which was implicitly exposed to native input.
Effects of dietary crude protein level on odour from pig manure.

The objective of this study was to determine the effects of dietary crude protein (CP) level on odour emission, odour intensity, hedonic tone, and ammonia emission from pig manure and on manure composition (pH, total nitrogen, ammonium, volatile fatty acids, indolic, phenolic and sulphur-containing compounds). An experiment was conducted with growing pigs (n = 18) in a randomised complete-block design with three treatments in six blocks. Treatment groups were 12%, 15% and 18% CP diets. Barley was exchanged for soya-bean meal. Crystalline amino acids (AA) were included in the 12% CP diet up to the level of pigs' requirement; the same amount of AA was added to the 15% and 18% CP diets. Pigs with an initial body weight (BW) of 36.5 ± 3.4 kg (mean ± s.d.) were individually penned in partly slatted floor pens and offered a daily feed allowance of 2.8 × maintenance requirement for net energy (NE: 293 kJ/kg BW0.75). Feed was mixed with water, 1/2.5 (w/w). Faeces and urine of each pig were accumulated together in a separate manure pit under the slatted floor. After an adaptation period of 2 weeks, the manure pits were cleaned and manure was collected. In the 5th week of the collection period, air samples for odour and ammonia analyses, and manure samples were collected directly from each manure pit. Air samples were analysed for odour concentration and for hedonic value and intensity above odour detection threshold. Manure samples were analysed for volatile fatty acids, and indolic, phenolic and sulphurous compounds, ammonium and total nitrogen concentrations. Reducing dietary CP from 18% to 12% lowered odour emission ( P < 0.05) and ammonia emission ( P = 0.01) from pig manure by 80% and 53%, respectively. Reduced dietary CP decreased total nitrogen, methyl sulphide, carbon disulphide, ethanethiol, phenol, 4-ethyl phenol, indole and 3-methyl indole concentrations in the manure ( P < 0.05). Volatile fatty acids and cresols concentrations in the manure of pigs fed different dietary CP levels were similar. A reduction of dietary CP and at the same time providing essential AA is an option to reduce odour emission as well as ammonia emission from pig manure.
Application of a Constraints-Led Approach to pedagogy in schools: embarking on a journey to nurture Physical Literacy in primary physical education

ABSTRACT Background: Oversimplified, reductionist approaches to operationalising Physical Literacy (PL) have been a barrier to the development of a complex, dynamic and embodied understanding of the individual Physical Literacy journey. Further, there has been no appropriate approach that might allow practitioners to integrate Physical Literacy in Physical Education (PE). Whilst popular approaches, such as Teaching Games for Understanding (TGfU) and Game Sense (GS), for operationalising learner-centred and problem-based learning, have gained professional traction in the last three decades, the development of a comprehensive theoretical basis to underpin pedagogical principles has been neglected – particularly in Physical Education. Pedagogical approaches grounded in play have gained popularity as a vehicle for Physical Literacy development in Physical Education. Despite the prominence of a Constraint-Led Approach (CLA) in sport pedagogy to assist in developing ‘the intelligent, autonomous individual’ in sport, application to Physical Education is limited. Purpose: In this article, we propose key pedagogical principles of a Constraints-Led Approach (CLA) in primary physical education, underpinned by the theoretical framework of Ecological Dynamics (ED). Driven by the challenge of designing affordance landscapes for learning, we present our reflections on a recently designed PE curriculum for primary schools, Boing, which could facilitate the development of movement capacities in play-based curricula designed to nurture the Physical Literacy journey for individuals. An articulation of support for the key theoretical ideas is provided in this paper. Design: This is achieved through reflections on the play-based curriculum (BOING) founded on the principles of Ecological Dynamics (ED) underpinning a Constraints-Led approach (CLA) to better serve the implementation of a Physical Literacy focussed Physical Education in a Primary school setting based on key principles for delivery. Findings: Summarising the findings, the we were able to highlight the importance of developing key principles for delivering a theoretically informed curriculum that elicits key principles of Physical Literacy. Whilst movement skills are key, these approaches are able to elicit the intended outcomes in learners of confidence, motivation and competence (Whitehead 2010, 2016). Conclusions: A CLA affords the theoretical design of play-based curricula beyond just play or sport towards purposeful, inclusive learning environments. Practitioners should look to underpin their practice with key theoretical ideas. This paper is of particular interest to those coaches and teachers tasked with designing practical environments for learning beyond the rhetoric of skill development in sport.
Antibacterial Activity of Salvadora persica L. (Miswak) Extracts against Multidrug Resistant Bacterial Clinical Isolates

Much effort has focused on examining the inhibitory effect of Salvadora persica (miswak) on oral microorganisms, but information concerning its antibacterial activity against other human pathogens, particularly multidrug resistant (MDR) isolates, is scarce. Therefore, this study aimed to assess the in vitro antibacterial activities of Salvadora persica L. extracts against 10 MDR bacterial clinical isolates other than oral pathogens. The antibacterial activity of aqueous and methanol miswak extracts was assessed using the agar dilution and minimum inhibitory concentration (MIC) methods. Overall, the 400 mg/mL of miswak extract was the most effective on all strains. The methanol extract exhibited a stronger antibacterial activity against Gram-negative (3.3–13.6 mm) than Gram-positive (1.8–8.3 mm) bacteria. The lowest MIC value was seen for E. coli (0.39, 1.56 µg/mL), followed by Streptococcus pyogenes (1.56 µg/mL). The highest MIC value (6.25, 12.5 µg/mL) was recorded for methicillin-resistant Staphylococcus aureus (MRSA), Acinetobacter baumannii, and Stenotrophomonas maltophilia. This study demonstrates, for the first time, the moderate to strong antibacterial activity of miswak extracts against all tested MDR-pathogens. Methanol extract appears to be a potent antimicrobial agent that could be considered as complementary and alternative medicine against resistant pathogens. Further studies on a large number of MDR organisms are necessary to investigate and standardize the inhibitory effect of miswak extracts against these emerging pathogens.
Characterization of Listeria monocytogenes Expressing Anthrolysin O and Phosphatidylinositol-Specific Phospholipase C from Bacillus anthracis

ABSTRACT Two virulence factors of Listeria monocytogenes, listeriolysin O (LLO) and phosphatidylinositol-specific phospholipase C (PI-PLC), mediate escape of this pathogen from the phagocytic vacuole of macrophages, thereby allowing the bacterium access to the host cell cytosol for growth and spread to neighboring cells. We characterized their orthologs from Bacillus anthracis by expressing them in L. monocytogenes and characterizing their contribution to bacterial intracellular growth and cell-to-cell spread. We generated a series of L. monocytogenes strains expressing B. anthracis anthrolysin O (ALO) and PI-PLC in place of LLO and L. monocytogenes PI-PLC, respectively. We found that ALO was active at both acidic and neutral pH and could functionally replace LLO in mediating escape from a primary vacuole; however, ALO exerted a toxic effect on the host cell by damaging the plasma membrane. B. anthracis PI-PLC, unlike the L. monocytogenes ortholog, had high activity on glycosylphosphatidylinositol-anchored proteins. L. monocytogenes expressing B. anthracis PI-PLC showed significantly decreased efficiencies of escape from a phagosome and in cell-to-cell spread. We further compared the level of cytotoxicity to host cells by using mutant strains expressing ALO in combination either with L. monocytogenes PI-PLC or with B. anthracis PI-PLC. The results demonstrated that the mutant strain expressing the combination of ALO and B. anthracis PI-PLC caused less damage to host cells than the strain expressing ALO and L. monocytogenes PI-PLC. The present study indicates that LLO and L. monocytogenes PI-PLC has adapted for L. monocytogenes intracellular growth and virulence and suggests that ALO and B. anthracis PI-PLC may have a role in B. anthracis pathogenesis.