Miracle-dz/UniFAR-FTUs huggingface dataset:
Characterizing three Pseudomonas milk isolates and interrogating specific similarities to cystic fibrosis clinical isolate, P. lundensis AU1044

Pseudomonas lundensis are recognized as psychrotrophic bacteria that contribute to cold food spoilage (21). The only existing sequenced genomes of P. lundensis were isolated from spoiled meat until clinical strains of P. lundensis were recovered from the lungs of cystic fibrosis patients in 2018 (21), however the role of P. lundensis in respiratory disease and the overall lung microbiome remains elusive. Novel Pseudomonas species’ dual presence in milk and in disease make it an important area to explore given the discrepancy between the bacteria’s role (pathogenic and non-pathogenic) in each environment. This study aims to characterize three Pseudomonas strains (101, 103, 105) isolated from milk and determine their similarity to Pseudomonas lundensis AU1044, a strain isolated from a cystic fibrosis patient, in order to establish the feasibility that milk could be an environmental source of P. lundensis in the lungs of humans with respiratory disease. Growth morphology, Gram staining, 16S rRNA polymerase chain reaction (PCR), and Pseudomonas specific PCR were utilized to get rough estimates of isolate identities. Isolate identities were strengthened and confirmed by genetic analysis using the combination of 16S rRNA, motA, and rpoB genes as reference in NCBI’s Basic Local Alignment Search Tool (BLAST). Hypotheses concerning isolates’ environmental behavior were formed by looking at genes and proteins within three metabolic systems: respiration, type III secretion, and quorum sensing/biofilm formation. Experimentation showed isolate 103 to be distinct from isolates 101 and 105 in terms of growth morphology, growth temperature preference, and crude identification conclusions made from Pseudomonas specific PCR. Deeper genetic analysis confirmed the phenotype findings and further separated isolate 103 from isolates 101 and 105. Isolates 101 and 105 were identified as the same closely-related P. lundensis strain to P. lundensis AU1044 while isolate 103 was not. In dendrogram analysis, isolates 101 and 105 showed stronger evidence of being closely related P. lundensis strains to P. lundensis AU1044 than isolate 103. Multi-genic analysis suggested that the milk isolates and clinical isolates behave similarly; they prefer aerobic environments, utilize biofilm, and have a limited (or misunderstood) type III secretion system. The majority of Pseudomonas milk isolates exhibited strong similarity to clinical isolate, P. lundensis AU1044, which supports milk as an environmental source for P. lundensis present in respiratory disease. Isolate 103’s distinction from the other milk isolates provides avenues for future directions where similarity to other closely-related Pseudomonas species could be studied for further clinical application.
Fuzzy genetic based dynamic spectrum allocation approach for cognitive radio sensor networks

: Cognitive radio sensor network (CRSN) is known as a distributed network of wireless cognitive radio sensor nodes. Such a system senses an event signal and ensures collaborative dynamic communication processes over the spectrum bands. Here the concept of dynamic spectrum access defines the method of reaching progressively to the unused range of spectrum band. As among the essential CRSN user types, the primary user (PU) has the license to access the spectrum band. On the other hand, the secondary user (SU) tries to access the unused spectrum efficiently, by not disturbing the PU. Considering that issue, this study introduces a fuzzy genetic based dynamic spectrum allocation (FGDSA) system for deciding spectrum allocation in cognitive radio sensor networks. In detail, the primary objective of the FGDSA system is to increase channel use without causing too much interference to the PU. In order to achieve that, some parameters such as signal interference noise ratio (SINR), bit error rate (BER), available channel bandwidth, SU transmission power, and the SU data rate are used as input variables for the fuzzy based inference mechanism taking place in the FGDSA. After development of the system, a performance analysis was done by comparing some metrics such as channel utilization, signal noise interference ratio, and the channel access delay for fuzzy based inference and the fuzzy genetic based inference that are both performing spectrum allocation. It was observed that the hybrid system of FGDSA outperforms fuzzy system by 2% in channel utilization, by also ensuring 16% less SINR, and 41% less channel access delay. The FGDSA was compared with also some existing spectrum allocation techniques such as edge coloring heuristic (ECH) and clique heuristic algorithm (CHA). It was seen that the FGDSA outperforms both ECH and CHA in average channel utilization, with the rates of 6% and 8%, respectively.
Phylogenetic Analysis of Mycoplasma Synoviae Isolated from Commercial Iranian Chicken Farms Compared with Other Genebank Isolate Sequences Based on 16S rRNA Gene

Mycoplasma synoviae (M. synoviae) is an important avian and extracellular pathogen which causes great economic losses in poultry industry. We have performed a phylogenetic analysis of M. synoviae isolates derived from commercial chicken farms in Iran based on 16S rRNA gene. Partial sequences of 16S rRNA genes obtained from 19 isolates of central region of Iran were amplified by PCR in 207bp fragment, then sequenced and next compared with the 16S rRNA gene of M. synoviae sequences that were available in GeneBank. Sequences were aligned using the ClustalW method, the UPGMA algorithm was used to create the phylogenetic tree. Phylogenetic analysis of these sequences demonstrated that all 19 M. synoviae isolated from Iran were most closely related to sequences of M. synoviae from Brazil. Variations, polymorphisms, and differences between nucleotides of all isolates were observed. The results of this study suggest that the close relationship, different molecular structure and heterogeneity among M. synoviae isolated may be explained by the transmission of mutations and variations between countries due to trading or to the stabilisation of spontaneous mutations because of regional conditions.
Anthropometric profiles of elite athletes

Quantifying body composition is central to monitoring performance and training in athletes, however limited sport-specific anthropometric reference data, assessed and reported in a standardised manner, is available. This study provides anthropometric profiles in elite male athletes from different sports. Elite male athletes (n = 73) from National squads of boxing (n = 10), cricket (n = 21), swimming (n = 23), hockey (n = 10) and eventing (n = 9) were assessed for body mass, height, eight skinfolds (triceps, subscapular, biceps, iliac crest, supraspinal, abdominal, thigh and medial calf), body circumferences (arm, waist, hip, thigh and calf) and muscle circumferences (arm, thigh, calf) using ISAK standardised guidelines. For all athletes, large variability exists for measures of skinfold thickness at each skinfold site. Swimming (64.6 ± 16.1 mm) and boxing (63.5 ± 16.1 mm) were similar for the sum of eight skinfolds (∑8SKF) but swimming had lower ∑8SKF compared to cricket (86.1 ± 21.3 mm; p = .011) and eventing (89.9 ± 30.7 mm; p = .028). Hockey (81.9 ± 26.3 mm) and eventing had the most varied ∑8SKF. Thigh body (p=.006) and muscle circumferences (p = .005) were significantly reduced in boxing compared to hockey. No differences were seen between sports for arm (p = .346; ES = .06) and calf (p = .382; ES = .06) muscle circumferences. The anthropometric profiles for elite athletes from various sports during pre-season training will be a useful resource for sports professionals when monitoring and interpreting body composition data. Large variation exists in anthropometric profiles between the different athletes and different sports, highlighting the necessity to have sport-specific normative ranges available to allow optimal monitoring of individual athletes particularly varying across sports as well as age, training status and position.
A MULTI-SCALE METHODOLOGY FOR EXPLAINING DATA STREAMS

This paper presents a novel, multi-scale, framework, for the simultaneous analysis of multiple data streams, called StreamStory. The framework models the data streams as a hierarchical Markovian model by automatically learning states and transitios, and aggregating them into a hierarchy of Markov chains. This approach aims to compensate the gap between low-level streaming observations and high-level output/alerts which provide a value for higher levels of streaming data analysis, like inference and prediction, and provides ground for qualitative interpretation of the data.
Smart Type-Ahead Search in XML

: Now a day in this digital world, internet search keyword paradigm are much popularized. However the search engine that uses html based model does not capture more semantics. But the xml model captures more semantics and navigates into document and displays more relevant information. The keyword search is alternative method to search in xml data, which is user friendly, user no need to know about the knowledge of xml data. This paper focuses on the survey of techniques used to retrieve the top k results from the xml document more efficiently. In addition to this, focus is given how to improve search performance by using data view. Data view is maintained after every successful search which will increase search performance as other searches will first begin with data view. Our proposed method has the following features: 1) Search as you type: It extends Auto-complete by supporting queries with multiple keywords in XML data.2) Fuzzy: It can find high-quality answers that have keywords matching query keywords approximately. 3) Intelligent: Our effective index structures, searching algorithms and data view can achieve a very high interactive speed. Answering queries using data views has shown significant performance benefits.
Human-in-the-loop Language-agnostic Extraction of Medication Data from Highly Unstructured Electronic Health Records

Electronic health records contain important information written in free-form text. They are often highly unstructured and ungrammatical and contain misspellings and abbreviations, making it difficult to apply traditional natural language processing techniques. Annotated data is hard to come by due to restricted access, and supervised models often don't generalize well to other datasets. We propose a language-agnostic human-in-the-loop approach for extracting medication names from a large set of highly unstructured electronic health records, where we reach almost 97% recall on our test set after the second iteration while maintaining 100% precision. Starting with a bootstrap lexicon we perform a context based dictionary expansion curated by a human reviewer. The method can handle ambiguous lexicon entries and efficiently find fuzzy matches without producing false positives. The human review step ensures a high precision, which is especially important in healthcare, and is not subject to disagreements with annotations from an external source. The code is available online 11https://github.com/FrankRuis/medical_concept_extraction.
Space use and multi-scale habitat selection of adult raccoons in Central Mississippi

Raccoons (Procyon lotor) are important furbearers and ecological generalists that exist in a variety of landscapes. Numerous studies have examined raccoon space and macrohabitat use, but information detailing these parameters within pine-dominated landscapes is lacking. Furthermore, no studies using radiotracking have examined raccoon habitat use at multiple spatial scales. We radiomonitored 131 adult raccoons (99 M, 32 F) during 1991-1997 in central Mississippi, USA. We subsequently assessed space use and habitat selection at 3 spatial scales. Males maintained larger home ranges and core areas than females. Size of home ranges differed by season, but raccoons maintained similar-size core areas across seasons. Habitat use differed by gender only at the coarsest spatial scale. Raccoons consistently used mature (>30 years old) pine and hardwood habitats over other available habitats at all spatial scales. Although hardwood-dominated habitats were important to raccoons, our findings suggest that in pine-dominated landscapes, raccoons select multiple seral stages of pine. Raccoons also readily used ≤8-year-old pine habitats, likely because of increased foraging opportunities within these habitats, particularly, during spring and summer. Our findings illustrate the importance of juxtaposition of habitat types for raccoons in pine-dominated landscapes, specifically the availability of mature pine and hardwood habitats, as well as early-successional habitats capable of providing beneficial foraging resources. Additionally, our findings offer evidence that prescribed burning may alter landscape use by raccoons, providing the potential that manipulating burning frequencies may allow managers to manage raccoon habitat-use patterns.
Transient streaming potential measurements on fluid‐saturated porous structures: An experimental verification of Biot’s slow wave in the quasi‐static limit

The time behavior of the streaming potential is identical to that of differential fluid pressure when local laminar flow is maintained and electromagnetic relaxation is not important. The time evolution of the streaming potential waveform resulting from the application of a pressure pulse to one face of a cylindrical water‐saturated porous structure is found to depend on the elastic properties of the fluid and rock frame and on the porosity and permeability of the core. The analysis of this quasi‐static flow based on Biot’s soil consolidation work [Biot, J. Appl. Phys. 12, 155 (1941)] and advanced by J.R. Rice and M.P. Cleary [Rev. Geophys. Space Phys. 14, 227 (1976)] is completely equivalent to that obtained from Biot’s slow wave model [M.A. Biot, J. Acoust. Soc. Am. 28, 168 (1956)] in the limit of zero frequency. Both analyses result in a homogeneous diffusion equation in pore pressure (and streaming potential) where the diffusivity is expressed in terms of the bulk moduli of the fluid and solid constit.
OLD-FOREST DISTRIBUTION AROUND SPOTTED OWL NESTS IN THE CENTRAL CASCADE MOUNTAINS, OREGON

Unlike previous spotted owl (Strix occidentalis) habitat association studies, we restricted our inquiry to the old-forest type and thus explored the association of spotted owls with habitat distribution as opposed to habitat type. We compared old-forest distribution around 126 northern spotted owl (S. o. caurina) nests in 70 pair territories, 14 nonreproductive spotted owl activity centers, and 104 points drawn randomly from old forest (closed canopy, >80 yr) in the central Cascade Mountains of Oregon. We quantified the percentage of old forest within 50 concentric circular plots (0.1-5.0-km radii) centered on each analyzed point, and we used logistic regression to make spatially explicit inferences. Owl nests were surrounded by more old forest in plots with 0.2-0.8-km radii (P < 0.05). Results suggested the landscape scales most pertinent to northern spotted owl nest-site positioning in this study were (in descending order) (1) the surrounding 15 ha (approx 200-m radius), (2) the surrounding 30-115 ha (approx 300-600-m radius), (3) the surrounding 200 ha (800-m radius), and (4) possibly the surrounding 700 ha (1,500-m radius). Nests were associated with higher proportions of old forest near the nest, implying that the arrangement of habitat was important for nest-site selection, posi- tioning, or both. The 70 territories of nesting owls had more old forest on average than did the 14 nonrepro- ductive owl sites, and the probability that a pair nested at least once during the study was positively associated with area of old-forest habitat in all radii studied. Because spotted owls in the central Cascade Mountains of Oregon are known to have home ranges that average 1,769 ha, our results apply to nest-site location on the landscape and not to the amount of habitat necessary for pair persistence or successful reproduction.
Intercomparison of freshwater fluxes over ocean and investigations into water budget closure

Abstract. The development of algorithms for the retrieval of water cycle components from satellite data – such as total column water vapor content (TCWV), precipitation (P), latent heat flux, and evaporation (E) – has seen much progress in the past 3 decades. In the present study, we compare six recent satellite-based retrieval algorithms and ERA5 (the European Centre for Medium-Range Weather Forecasts' fifth reanalysis) freshwater flux (E−P) data regarding global and regional, seasonal and interannual variation to assess the degree of correspondence among them. The compared data sets are recent, freely available, and documented climate data records (CDRs), developed with a focus on stability and homogeneity of the time series, as opposed to instantaneous accuracy. One main finding of our study is the agreement of global ocean means of all E−P data sets within the uncertainty ranges of satellite-based data. Regionally, however, significant differences are found among the satellite data and with ERA5. Regression analyses of regional monthly means of E, P, and E−P against the statistical median of the satellite data ensemble (SEM) show that, despite substantial differences in global E patterns, deviations among E−P data are dominated by differences in P throughout the globe. E−P differences among data sets are spatially inhomogeneous. We observe that for ERA5 long-term global E−P is very close to 0 mm d−1 and that there is good agreement between land and ocean mean E−P, vertically integrated moisture flux divergence (VIMD), and global TCWV tendency. The fact that E and P are balanced globally provides an opportunity to investigate the consistency between E and P data sets. Over ocean, P (nearly) balances with E if the net transport of water vapor from ocean to land (approximated by over-ocean VIMD, i.e., ∇⋅(vq)ocean) is taken into account. On a monthly timescale, linear regression of Eocean-∇⋅(vq)ocean with Pocean yields R2=0.86 for ERA5, but smaller R2 values are found for satellite data sets. Global yearly climatological totals of water cycle components (E, P, E−P, and net transport from ocean to land and vice versa) calculated from the data sets used in this study are in agreement with previous studies, with ERA5 E and P occupying the upper part of the range. Over ocean, both the spread among satellite-based E and the difference between two satellite-based P data sets are greater than E−P, and these remain the largest sources of uncertainty within the observed global water budget. We conclude that, for a better understanding of the global water budget, the quality of E and P data sets needs to be improved, and the uncertainties more rigorously quantified.
Estimation of turbulence in fan-rotor wakes for broadband noise prediction during acoustic preliminary design

When calculating broadband fan noise caused by rotor-stator wake interaction analytically, information about the airflow, particularly about the turbulence in the rotorwakes, is necessary. During the pre-design phase, two-dimensional streamline methods are commonly used. These provide only general flow quantities like mean-flow velocities or total-pressure losses. Turbulent parameters such as turbulent kinetic energy and turbulent integral length scale need to be deduced from these quantities. There are several models mentioned in the literature which correlate the wake size with the wake turbulence. But they usually comprise calibration factors that need to be assessed empirically by numerical simulations or measurements. The contribution of the paper is to present an updated semi-empirical model for rotor-wake turbulence quantities, derived on the basis of an extensive comparison of the model with measurements and numerical simulations on four different turbofan stages. A recalibration of the empirical factors improved the noise prediction by 8 dB, reaching an accuracy of 2 dB. In addition, it is shown, that the endwall flow is responsible for large variance in the noise prediction, and may have a contribution of up to 2 dB to the overall sound power.
Cattle production in silvopastoral systems compared to monoculture pasture in the Brazilian Cerrado

Adoption of silvopastoral systems (SS) in Brazil has been stimulated in the last decade. This work aimed to evaluate beef production under SS with eucalyptus using densities of 178 and 441 trees per ha and to compare it to a traditional monoculture Piatã grass pasture (PM) in the Brazilian Cerrado. Shading caused by the two tree densities, in the third year of the systems implementation did not cause changes neither on forage mass nor on its nutritive value. As consequence, results show that both SS did not differ from the PM for beef cattle production in the period studied, allowing better thermal comfort for grazing cattle, besides wood production and greenhouse gases mitigation.
Thermoelectric properties of novel clathrates Ba 8 T x T ' y Ge 46-x-y (

und Kurzfassung Abstract In the present diploma thesis the thermoelectric properties of cubic type I Ba-Ge-based clathrates are studied, where Ge in Ba8Ge43 3 ( is a vacancy) is substituted by Ag → Ba8AgxGe46−x x = 2, 3, 4, 5 Pd & Zn → Ba8PdxZnyGe46−x−y Cu & Zn → Ba8CuxZnyGe46−x−y Si & Zn → Ba8SixZnyGe46−x−y.In the present diploma thesis the thermoelectric properties of cubic type I Ba-Ge-based clathrates are studied, where Ge in Ba8Ge43 3 ( is a vacancy) is substituted by Ag → Ba8AgxGe46−x x = 2, 3, 4, 5 Pd & Zn → Ba8PdxZnyGe46−x−y Cu & Zn → Ba8CuxZnyGe46−x−y Si & Zn → Ba8SixZnyGe46−x−y. The speci c compositions discussed in this diploma thesis are summarised in the Table on page iii. The synthesis of these materials as well as the structural investigations were conducted by Navida Nasir and Isolde Zeiringer at the Institute of Physical Chemistry, University of Vienna. The structural investigations in all cases con rmed cubic primitive symmetry consistent with the space group type Pm3̄n of a typical type I clathrate structure with lattice parameters ranging from a ≈ 1.05 nm to a ≈ 1.08 nm. Thermoelectric properties (electrical resistivity, thermal conductivity and Seebeck coe cient) were measured in a broad temperature range from 4.2 to about 800 K, demonstrating that substitution allows ne tuning of the charge carrier density, shifting the materials into the proximity of a metal-to-insulator transition. This is evidenced from giant thermopower reaching values of about 400μV/K in the case of Ba8Cu5.2Zn0. 8Ge40.0 at temperatures well below room temperature (T S max ≈ 150 K).
Possibility for bio-control of harmful diatom blooms in Coscinodiscus wailesii by marine bacteria

In recent years, increasing interest has focused on bacteria that affect the physiology and ecology of microalgae such as survival and sexual reproduction. In the Japanese coastal sea areas such as Harima-Nada, the giant diatom Coscinodiscus wailesii can cause serious damage to Nori (Porphyra) culture during the autumn and following spring. A marine bacterium Alteromonas sp. , lethal to C. wailesii, was isolated from eastern Seto Inland Sea, Japan. The existence of bacteria that induce sperm formation in this diatom was also confirmed in the coastal area. To try to regulate those harmful algal blooms by microorganisms, the interactions between these bacteria and microalgae have been investigated. Namely, the lethal processes, the algicidal ranges, the effects of incubation conditions such as temperature, irradiance, cell densities of bacteria on these bacterial activities, and the chemicals produced by bacteria were studied. These studies strongly suggest that these bacteria play an important role in the development and decomposition of algal blooms, and in the usual succession of microalgal community structures. Since, there is a possibility of controlling the occurrence and extermination of these harmful algal blooms such as C. wailesii, the efforts should be offered to investigate these microorganisms.