jimnoneill/paper-to-field-training huggingface dataset:
Transposable Elements Contribute to the Regulation of Long Noncoding RNAs in Drosophila melanogaster

Background: Transposable elements (TEs) and noncoding sequences are major components of the genome, yet their functional contributions to long noncoding RNAs (lncRNAs) are not well understood. Although many lncRNAs originating from TEs (TE-lncRNAs) have been identified across various organisms, their characteristics and regulatory roles, particularly in insects, remain largely unexplored. This study integrated multi-omics data to investigate TE-lncRNAs in D. melanogaster, focusing on the influence of transposons across different omics levels. Results: We identified 16,118 transposons overlapping with lncRNA sequences that constitute 2119 TE-lncRNAs (40.4% of all lncRNAs) using 256 public RNA-seq samples and 15 lncRNA-seq samples of Drosophila S2 cells treated with heavy metals. Of these, 67.2% of TE-lncRNAs contain more than one TE. The LTR/Gypsy family was the most common transposon insertion. Transposons preferred to insert into promoters, transcription starting sites, and intronic regions, especially in chromosome ends. Compared with lncRNAs, TE-lncRNAs showed longer lengths, a lower conservation, and lower levels but a higher specificity of expression. Multi-omics data analysis revealed positive correlations between transposon insertions and chromatin openness at the pre-transcriptional level. Notably, a total of 516 TE-lncRNAs provided transcriptional factor binding sites through transposon insertions. The regulatory network of a key transcription factor was rewired by transposons, potentially recruiting other transcription factors to exert regulatory functions under heavy metal stress. Additionally, 99 TE-lncRNAs were associated with m6A methylation modification sites, and 115 TE-lncRNAs potentially provided candidate small open reading frames through transposon insertions. Conclusions: Our data analysis demonstrated that TEs contribute to the regulation of lncRNAs. TEs not only promote the transcriptional regulation of lncRNAs, but also facilitate their post-transcriptional and epigenetic regulation.

Topic: RNA modifications and cancer
Subfield: Molecular Biology
Field: Biochemistry, Genetics and Molecular Biology
Domain: Life Sciences
Susceptibility of Two European strains of Stomoxys calcitrans (L.) to Cypermethrin, Deltamethrin, Fenvalerate, lambda-cyhalothrin, Permethrin and Phoxim

Susceptibility of two French strains of stable flies Stomoxys calcitrans (L.) to six insecticides was assayed, using an exposure technique (1-hour contact) with treated filter papers. Three replicates per insecticide, per concentration (10 concentrations per insecticide), per fly strain (ENVT, Cabanac) and fly category (blood-engorged - non-blood-engorged) were performed using a total of 14,400 adult flies in this trial. The LD50 and LD90 are higher for the blood-engorged flies than the non-blood-engorged flies for both strains of S. calcitrans. The LD90 (mg/m(2)) of the engorged flies for both strains were respectively: cypermethrin (637.9, 54.9), deltamethrin (264.3, 28.1), fenvalerate (2392.5, 125.1), lambda-cyhalothrin (118.2, 41.3), permethrin (353.7, 88.1), and phoxim (194, 226.8). Phoxim, which has not been used in the ENVT for several years, showed the same susceptibility for both strains. The LD90 values obtained for the Cabanac strain (organic farm) were 1 to 4 times lower than the recommended doses of all five pyrethroids. For the ENVT strain (blood-engorged flies), the LD90 was 7.1 and 22.6 times over the recommended doses of both deltamethrin and fenvalerate respectively, which are commonly used insecticides on this site.

Topic: Forensic Entomology and Diptera Studies
Subfield: Insect Science
Field: Agricultural and Biological Sciences
Domain: Life Sciences
Outcomes after incidental dural tears in spine surgery: a systematic review of MIS and OS cohorts

<title>Abstract</title> <bold>Background:</bold> Incidental dural tears (IDTs) are established complications in spinal surgery, yet the outcomes associated with early mobilization following IDTs differ between minimally invasive spine surgery (MISS) and open spine surgery (OSS), with limited clarity on best practices. <bold>Objective:</bold> This systematic review examines the differential outcomes of IDTs after MISS versus OSS, with a focus on hospital length of stay (LOS), rates of major and minor complications, and reoperation frequency. <bold>Methods:</bold> Following PRISMA guidelines, a comprehensive review of the literature was conducted across PubMed, Embase, and Cochrane databases through October 2022, with the quality of evidence evaluated per a modified version of Sackett’s Criteria. Twelve studies met the inclusion criteria, including 1 Level I study, 3 Level II studies, and 8 Level IV studies. Statistical comparisons were performed using unpaired t-tests and chi-squared tests to assess significance. <bold>Results:</bold> A total of 653 OSS patients (mean age 60.7 ± 3.5 years) and 179 MISS patients (mean age 61.6 ± 1.5 years), all mobilized within 24 hours were included. Dural repairs were performed in 95% of OSS cases and 98% of MISS cases. Although MISS patients experienced a shorter LOS (mean 2.0 ± 1.8 days) than OSS patients (mean 5.7 ± 2.9 days). Major complications were observed in 6.0% of OSS cases and 3.9% of MISS case, while minor complications were significantly reduced in MISS (2.2%) compared to OSS (6.0%). Although Dural repairs were performed in a similar percentage of patients in both groups (95% in OSS vs. 98% in MISS), the <bold>mean number of primary repairs per patient</bold>was significantly lower in the MISS group (3.5 ± 1.1) than in the OSS group (4.2 ± 1.3, p = 0.0283). This likely reflects fewer complex or multi-layered repairs needed in MISS, despite the high overall repair rate. Moreover, Reoperation rates were substantially lower in MISS (mean 5.6% ± 1.9%) relative to OSS (mean 8.5% ± 2.1%). The follow-up periods were statistically different between the OSS (10.5 ± 2.6 months) and MISS (9.1 ± 1.7 months) groups. <bold>Conclusion:</bold> MISS demonstrates potential significant benefits over OSS following IDT, with markedly lower minor complications and reoperation rates, as well as reduced need for primary repairs, and a trend toward shorter hospital stays.

Topic: Spine and Intervertebral Disc Pathology
Subfield: Pathology and Forensic Medicine
Field: Medicine
Domain: Health Sciences
Analytical Evaluation of Chunk-Based Tractable Multi-cell OFDMA system

This paper evaluates thoroughly the performance of multi-cell OFDMA system. The two types of deployment in multi-cell OFDMA system, such as Strict Fractional Frequency Reuse (FFR) and Soft FFR (SFR) were evaluated. In order to model the base station locations, homogeneous Poisson point processes were used, i.e. tractable model instead of hexagonal grid was considered. In order to reduce complexity, chunk-based resource allocation scheme was embedded. Each cell divides the users into the users of the central cell area and the users of the cell edge area according to their average received Signal to Interference and Noise Ratio (SINR) compared with FFR threshold. The primary stage of the analysis includes the spectral efficiency’s expression deriving from these two deployment scenarios, followed by the analysis with the use of coverage probability. However, the improvement of spectral efficiency is achieved in the case of SFR. On the contrary, coverage probability is far improved by using strict FFR scheme. Through numerical anaysis, We have shown that the optimal FFR threshold to achieve the highest spectral efficiency was 12 dB for both Strict FFR as well as SFR.

Topic: Advanced MIMO Systems Optimization
Subfield: Electrical and Electronic Engineering
Field: Engineering
Domain: Physical Sciences
Inferring Structural Variability Using Modal Analysis in a Bayesian Framework

Dynamic systems with different geometric configurations may present remarkable distinct dynamic behaviour. However, variability is identifiable in the measured modal shapes and modal frequencies. This paper explores a Bayesian framework in order to infer structural variability based on modal parameters. This is relevant in cases of difficult access for inspection in finished products/structures. An approach using a radial basis neural network benchmarked by a Gaussian process metamodel is developed and then followed by a test case with experimental data. It is concluded that the proposed methodology shows promise in solving this kind of problems.

Topic: Probabilistic and Robust Engineering Design
Subfield: Statistics, Probability and Uncertainty
Field: Decision Sciences
Domain: Social Sciences
The great Edwardian gardens of Harold Peto: from the archives of Country life

Harold Peto (1854-1933) was one of the great landscape designers of the Edwardian era. A great exponent of the ultra-romantic Italianate style so fashionable in the first two decades of the twentieth century, he was also influenced by the Arts and Crafts movement. Much admired by both Gertrude Jekyll and Edwin Lutyens, he was recognised as one of the most successful garden designers of his generation, building up a formidable reputation for his work both in England and the South of France. Garden historian Robin Whalley's illuminating commentary is brought to life by 200 dazzling photographs from the Country Life archive, showing many of Peto's gardens in their heyday. Among those featured are: Iford Manor, Peto's own house and garden; Easton Lodge, the garden of Daisy, Countess of Warwick, with its pergola, water garden and Japanese tea house; West Dean, which boasts a 300-foot pergola; and Ilnacullin in Eire, one of his best-known gardens. This latest volume in the acclaimed Country Life series is of great appeal to garden historians, designers and amateur enthusiasts alike.

Topic: Landscape and Cultural Studies
Subfield: Archeology
Field: Arts and Humanities
Domain: Social Sciences
The Childhood Executive Functioning Inventory (CHEXI) Parent and Teacher Form: Factor Structure and Cognitive Correlates in Spanish-speaking Children from Argentina

The aims of the present study were: (1) to explore the CHEXI factor structure parent (<i>n</i> = 183) and teacher (<i>n</i> = 206) forms in Spanish-speaking children aged 6 to 11 years, (2) to analyze the relationship between parent- and teacher-rated data and performance-based measures of EF (including working memory, inhibition, and cognitive flexibility tasks) and academic achievement and (3) to examine the association between parents and teachers reports. Confirmatory Factor analysis (CFA) showed that the two-factor model including (1) Working memory and (2) Inhibition best fit the data. McDonald's Omega coefficient was adequate for both the total parents (ω = .98). and teachers' (ω = .98) scales. In addition, low and selective associations were found between performance and rater-based assessments. However, stronger associations were observed between CHEXI and academic performance with differences according to the informant (parents vs. teachers). Finally, low correlations were found between parents and teachers reports. Taken together, our results suggest that the CHEXI is a reliable measure to assess EF in Argentinean Spanish-speaking children, supporting existing evidence that proposes that ratings and performance-based measures would assess different underlying mental constructs. Clinical and educational implications for considering both perspectives during neuropsychological assessment, further including parent- and teacher-rated reports are discussed.

Topic: Attention Deficit Hyperactivity Disorder
Subfield: Psychiatry and Mental health
Field: Medicine
Domain: Health Sciences
Electrical properties of p-Zn1 − x Cd x GeAs 2 〈Mn〉

The electrical resistivity and Hall coefficient of the high-temperature ferromagnetic semiconductor p-Zn1 − x Cd x GeAs2〈Mn〉 have been measured as a function of pressure near room temperature. The features in the curves obtained attest to a structural phase transition at particular pressures. With increasing manganese content, the phase transition shifts to lower pressure. The features observed in the pressure-dependent Hall coefficient of the crystals containing more than 0.06 wt % manganese, in which ferromagnetic behavior is more pronounced, are probably due to the anomalous component of the Hall effect and its modulation in the presence of narrow impurity bands.

Topic: Semiconductor Quantum Structures and Devices
Subfield: Atomic and Molecular Physics, and Optics
Field: Physics and Astronomy
Domain: Physical Sciences
Description and Postharvest Physiology of Some Slow-ripening Nectarine Genotypes

Abstract The postharvest behavior of several slow-ripening nectarine genotypes that originated from ‘Fantasia’ was investigated. These fruit were firmer and greener than ‘Fantasia’, had higher phenolic compounds and soluble solids contents, a higher pH, lower titratable acidity, and equal or greater levels of total and reducing sugars. Changes in flesh color and firmness during storage were much slower than in ‘Fantasia’, but the rate of softening varied among the genotypes. Although all of the genotypes tested seemed to be climacteric-type fruit, the preclimacteric period at 20°C could exceed 1 month, and C 2 H 4 production was much lower than in ‘Fantasia’. Application of C 2 H 4 during the preclimacteric period stimulated respiration rates, with the maximum response occurring at 10 ppm. A 2nd application of C 2 H 4 resulted in a 2nd increase in respiration, as with nonclimacteric fruit. Incidence of internal breakdown generally was severe compared to ‘Fantasia’ following 4 weeks of storage at 5°, although the genotype P19-11 appeared to be somewhat resistant to chilling injury.

Topic: Postharvest Quality and Shelf Life Management
Subfield: Plant Science
Field: Agricultural and Biological Sciences
Domain: Life Sciences
ARCHIVEIT-1443-WEEKLY-MVKHNS-20120619132539-00000-crawling212.us.archive.org-6683.warc.gz

recurrence=WEEKLY, maxDuration=259200, maxDocumentCount=1100, isTestCrawl=false, seedCount=11, accountId=351, organizationName="American University in Cairo", collectionId=1443, collectionName="American University in Cairo"

Topic: Smart Agriculture and AI
Subfield: Plant Science
Field: Agricultural and Biological Sciences
Domain: Life Sciences
Trade Integration in Turbulent Times

The WTO has been going through an existential crisis, from which it is like that it will not exit unscathed. If it is to remain an organization of universal membership, it will have to content itself to shallow integration. Its continuing policy relevance, will largely depend on the choices it will make about the nature of its own integration process. The good news is that no one can simply walk away from globalization. The downside (for the WTO) is that globalization is being increasingly administered through bilateral contracts.

Topic: Magnetic confinement fusion research
Subfield: Nuclear and High Energy Physics
Field: Physics and Astronomy
Domain: Physical Sciences
Weak localization in p-type heterostructures in the presence of parallel magnetic field

Theory of weak localization is developed for two-dimensional holes in the presence of in-plane magnetic field. The Zeeman splitting even in the hole momentum results in the spin-dependent phase changing the quantum interference. The negative correction to the conductivity is shown to decrease by a factor of two by the in-plane magnetic field. The positive magnetoconductivity in a classically weak perpendicular field caused by the weak localization is calculated for both quadratic and quartic in momentum Zeeman hole splittings. Calculations show that the conductivity corrections are very close to each other in these two cases of low and high hole density.

Topic: Quantum and electron transport phenomena
Subfield: Atomic and Molecular Physics, and Optics
Field: Physics and Astronomy
Domain: Physical Sciences
The importance of organic phosphorus sources, transfers and impacts across the agricultural continuum

This thesis investigates the risks posed by organic phosphorus (P) from agriculture to river and stream chemical water quality and the ecology. Organic P compounds have received limited attention in past research, due to the agronomic focus on inorganic P and the analytical challenges of quantifying organic P in environmental matrices. Through laboratory and field experiments, this thesis aimed to: (i) characterise organic P within fresh and stored livestock slurry; (ii) quantify organic P export within overland flow and leachate from grasslands, including following livestock slurry application; and (iii) determine the benthic microbial responses to organic P compounds in rivers and streams. Finally, a coupled terrestrial-aquatic modelling approach was developed to quantify the impact of diffuse agricultural P mitigation measures on river water quality. The organic P pool in fresh livestock slurry was substantial and dominated by monoesters, including glycerophosphates, other labile monoesters (e.g. ATP) and inositol-6-phosphates. Storage drove significant changes in the chemical and physical fractionation of P within slurry. Organic P was observed in overland flow and leachate from grassland soil. Significant increases in organic P concentrations within leachate followed slurry application, predominantly in the form of glycerophosphates and inositol-6-phosphates. Within streams, heterotrophic responses to glycerophosphates and inositol-6-phosphate were observed, although these varied depending on background stream P concentrations. However, under certain stream conditions, inhibitory effects of organic P on the autotrophic community were observed. Modelling the efficacy of agricultural P mitigation suggested a best-case scenario in which annual river total P loads decreased by 7.5%, yet this increased to 19.4-25.1% when wastewater effluent was addressed alongside agricultural sources of P. The outcomes of this thesis present an opportunity to develop an organic P focus to the P transfer continuum, alongside highlighting a range of future research priorities related to organic P in the environment.

Topic: Microbial Natural Products and Biosynthesis
Subfield: Pharmacology
Field: Medicine
Domain: Health Sciences
Bacteriologic Profile and Antibiogram of Blood Culture Isolates in a Pediatric Care Unit

ABSTRACT Background / Aims: Septicemia is one of the important causes of mortality and morbidity in neonates and children. Blood culture is the gold standard for the diagnosis. Emergence of multidrug resistant bacterial strains is a major problem in the management of sepsis. Present study was undertaken to identify the common bacterial pathogens associated with pediatric sepsis and to determine their antibiotic susceptibility pattern. Materials and Methods: Blood cultures from 185 suspected cases of sepsis were examined. The growths from the subcultures were identified by conventional biochemical tests. Antibiotic susceptibility testing was performed by modified Kirby-Bauer disk diffusion method and drug resistant strains in primary screening were further processed for extended spectrum beta lactamases (ESBL) and methicillin resistant Staphylococcus aureus (MRSA) status by combination disk method (ESBL) and oxacillin disk diffusion method (MRSA). Results: Out of the 185 cultures obtained from suspected cases, 81 (44%) were culture positive. Fifty-two (35%) of the culture isolates were Gram negative bacilli. Twenty-eight (64%) of the isolates were Gram positive cocci. One case was of mixed infection. The prevalence of MRSA in 41 strains of S. aureus was found to be 29% (12 strains). The overall prevalence of ESBL producers among 28 Gram negative bacterial isolates was found to be 32% (9 strains). Conclusion: This study stresses the need for the continuous screening and surveillance for antibiotic resistance in pediatric care unit.

Topic: Bacterial Identification and Susceptibility Testing
Subfield: Clinical Biochemistry
Field: Biochemistry, Genetics and Molecular Biology
Domain: Life Sciences
Visual and Optical Analyses of XM-29 and M-24 Protective Masks.

USAARL was tasked to provide medical guidance and assessment relative to visual and optical aspects in the development of the XM-29 protective mask. In fulfillment of this responsibility, complete optical and visual tests have been completed on the new mask prior to its validation. To provide baseline and comparison information, identical optical testing was also performed on the M-24 aviator's protective mask, and visual performance testing was completed with the XM-29 mask, the M-24 mask, and unobstructed vision.

Topic: Hermeneutics and Narrative Identity
Subfield: Philosophy
Field: Arts and Humanities
Domain: Social Sciences
Prediction of Pavement Concrete Strength Development, Joint Sawing, and Opening Time Using FEMLAB

This paper describes a new model using Finite Element Modeling Laboratory (FEMLAB). The model can be used to predict pavement strength development and consequently the pavement joint-sawing and opening times. The strength prediction was based on the temperature history of the concrete pavement, which was determined by the rate of heat generation and the heat exchange between the pavement and the environment. Pavement joint-sawing and opening times were defined as the times when concrete strength reached 4.3 and 24.1 MPa (megapascals), respectively. Using this model, the effects of weather conditions, fly ash and slag replacement, concrete placement time and temperature, and pavement thickness on concrete strength, joint-sawing time, and pavement opening time were evaluated. Results showed that weather conditions and the use of fly ash and slag had a significant effect on strength development, joint-sawing time, and pavement opening time. Based on the prediction, this model can be used to optimize the concrete mix design to select the appropriate concrete placement temperature and paving time for the optimal concrete construction and strength development under certain environmental condition.

Topic: Concrete and Cement Materials Research
Subfield: Civil and Structural Engineering
Field: Engineering
Domain: Physical Sciences
Dairy cows – an opportunity in the research field of non-genetic inheritance?

More than 1 billion cattle are raised annually for meat and milk production. Dairy cows are repeatedly impregnated and separated from their calves, usually within the first 24 h after birth. Here, I suggest that dairy cows undergo a procedure comparable to the 'Maternal separation combined with unpredictable maternal stress' paradigm (MSUS), which is used to study the non-genetic inheritance (NGI) of phenotypes in rodents. I discuss what research on dairy cows may bring to the research field of NGI. The resulting research findings are likely to have benefits to our understanding of MSUS, NGI and consumer safety.

Topic: Animal Behavior and Welfare Studies
Subfield: Small Animals
Field: Veterinary
Domain: Health Sciences
The National Insurance (Increase of Benefit and Miscellaneous Provisions) Regulations 1974

The Secretary of State for Social Services, in exercise of powers conferred by sections 45, 49(l)(a) and 50(l)(a)(ii) of the National Insurance Act 1965 and paragraphs 17 and 18 of Schedule 11 to that Act, section 11(1) of the National Insurance Act 1966, as amended by section 6(1) of the National Insurance Act 1972 and paragraph 13 of Schedule 4 to the National Insurance Act 1974, paragraph 3 of Schedule 6 to the National Insurance Act 1969 and section 1 of the National Insurance Act 1970, and of all other powers enabling her in that behalf, and in conjunction with the Treasury so far as relates to matters with regard to which the Treasury have so directed, hereby makes the following regulations, which contain no provisions other than such as are made in consequence of the National Insurance Act 1974 and which accordingly, by virtue of paragraph 2(l)(a) of Schedule 5 to that Act, are exempt from the requirements of section 108 of the National Insurance Act 1965 (reference to the National Insurance Advisory Committee):—

Topic: Legal Issues in South Africa
Subfield: Law
Field: Social Sciences
Domain: Social Sciences