Miracle-dz/UniFAR-FTUs huggingface dataset:
On Combining Classical and Numerical Techniques for Extracting the Impedance and Admittance of Cables and Overhead Lines

This paper discuses a general formulation of transmission line parameters for EMT-type programs by combining different computational techniques. The formulation of impedance and admittance matrices are described for various combination of overhead conductors, aerial or underground coaxial cables, pipe-type cables or even certain types of nonconventional cables, etc. The parameters of the transmission line system can be computed by combining different solution techniques to optimize computational speed and memory. Time domain simulations involving electromagnetic transients are carried out for an example consists of an overhead line, a pipetype cable and an aerial pipe cable in parallel. The formulation is also verified with alternative Method of Moment technique for an example case involving a non-conventional cable.
SPECIES RICHNESS, ALPHA AND BETA DIVERSITY OF TREES, SHRUBS AND HERBACEOUS PLANTS IN THE WOODLANDS OF SWAT, PAKISTAN

The variation in species richness and diversity of trees, shrubs and herbs in the mountains of Miandam, Swat, North Pakistan, along an elevation gradient between 1600 m and 3400 m was explored. Field data were collected in 18 altitudinal intervals of 100 m each. Polynomial regression was used to find relations of the different growth forms with elevation. The Shannon index was used for calculating -diversity and the Simpson index for β-diversity. Species richness and -diversity of herbs were unrelated to elevation. Herbaceous species turnover was high, ranging between 0.46 and 0.89, with its maximum between 2700 and 3000 m. Hump-shaped relationship was observed for shrubs with maximum richness between 2000 and 2200 m; and -diversity decreased monotonically. Turnover of shrub species was highest between 2000 and 2500 m. Tree species richness was highest at low elevations, and -diversity was relatively low along the entire gradient. Tree species turnover was also high in the lower zone and again at 2600-2800 m. Species richness of all vascular plants was highest at 2200-2500 m, and diversity was highest in the lower part of the gradient. Beta diversity of all growth forms was quite high ranging between 0.53 and 0.87along the entire gradient reflecting high species and structural turnover.
OWLSIZ: An isiZulu CNL for structured knowledge validation

In iterative knowledge elicitation, engineers are expected to be directly involved in validating the already captured knowledge and obtaining new knowledge increments, thus making the process time consuming. Languages such as English have controlled natural languages than can be repurposed to generate natural language questions from an ontology in order to allow a domain expert to independently validate the contents of an ontology without understanding a ontology authoring language such as OWL. IsiZulu, South Africa’s main L1 language by number speakers, does not have such a resource, hence, it is not possible to build a verbaliser to generate such questions. Therefore, we propose an isiZulu controlled natural language, called OWL Simplified isiZulu (OWLSIZ), for producing grammatical and fluent questions from an ontology. Human evaluation of the generated questions showed that participants’ judgements agree that most (83%) questions are positive for grammaticality or understandability.
Effects of sample mass on gravity recoverable gold test results in low-grade ores

Gravity recoverable gold characterisation methodologies are the single- or three-stage tests, which generally use a standard feed sample mass. A case study of low-grade coarse gold-dominated mineralisation is presented that demonstrates the high variability of test results using different sample masses. Samples were processed using the single-stage test and subsequently entire development rounds were batched through a plant for comparison. Unsurprisingly the results indicate that the small (≤50 kg) test samples grossly understate plant gravity recoverable gold and display poor precision. Larger samples display improved precision, but still understate plant gravity recoverable gold. The small mass samples are unrepresentative as they do not contain the full gold particle size distribution. Poor representivity is enhanced by gold particle clustering. Small samples generally capture finer more abundant and disseminated gold particles, but rarely contain clustered gold. The use of standard GRG test sample masses is challenged. Test work should be based on spatially distributed representative field samples, that if required are split to representative sub-samples for testing. An early stage gold particle size characterisation programme is required to optimise sample mass and improve representivity.
Community genetics in the time of next generation molecular technologies 2 3

40 Understanding the interactions of co-occurring species within and across trophic levels 41 provides key information needed for understanding the ecological and evolutionary 42 processes that underlie biological diversity. As genetics has only recently been integrated 43 into the study of community-level interactions, the time is right for a critical evaluation 44 of potential new, gene-based approaches to studying communities. Next generation 45 molecular techniques, used in parallel with field-based observations and manipulative 46 experiments across spatio-temporal gradients, are key to expanding our understanding 47 of community-level processes. Here, we introduce a variety of “-omics” tools, with recent 48 studies of plant–insect herbivores and of ectomycorrhizal systems providing a detailed 49 example of how next generation approaches can revolutionize our understanding of 50 interspecific interactions. We suggest ways that novel technologies may convert 51 community genetics from a field that relies on correlative inference to one that reveals 52 causal mechanisms of genetic co-variation and adaptations within communities. 53
Variable Selection and Regularization in Quantile Regression via Minimum Covariance Determinant Based Weights

The importance of variable selection and regularization procedures in multiple regression analysis cannot be overemphasized. These procedures are adversely affected by predictor space data aberrations as well as outliers in the response space. To counter the latter, robust statistical procedures such as quantile regression which generalizes the well-known least absolute deviation procedure to all quantile levels have been proposed in the literature. Quantile regression is robust to response variable outliers but very susceptible to outliers in the predictor space (high leverage points) which may alter the eigen-structure of the predictor matrix. High leverage points that alter the eigen-structure of the predictor matrix by creating or hiding collinearity are referred to as collinearity influential points. In this paper, we suggest generalizing the penalized weighted least absolute deviation to all quantile levels, i.e., to penalized weighted quantile regression using the RIDGE, LASSO, and elastic net penalties as a remedy against collinearity influential points and high leverage points in general. To maintain robustness, we make use of very robust weights based on the computationally intensive high breakdown minimum covariance determinant. Simulations and applications to well-known data sets from the literature show an improvement in variable selection and regularization due to the robust weighting formulation.
USP37 downregulation elevates the Chemical Sensitivity of Human Breast Cancer Cells to Adriamycin

Background: The evolution of adriamycin (ADR) resistance in the treatment of breast cancer often leads to a poor prognosis in patients. Ubiquitin-specific peptidase 37 (USP37) has been recently identified as a modulator in regulating the stemness of breast cancer cells, but its underlying mechanism remains unclear. In this study, we investigated whether USP37 knockdown could hamper the chemical resistance of MCF-7 and MCF-7/ADR cells to adriamycin and elucidated the potential mechanism. Methods: Immunohistochemistry, western blotting, and RT-qPCR assays were performed to detect the USP37 expression in MCF-7 and MCF-7/ADR cells. The efficiency of USP37 knockdown in breast cancer cells was confirmed by western blotting and RT-qPCR assays. We also performed CCK-8 assay, flow cytometry, western blotting, and TUNEL assays to evaluate cell viability and apoptosis in breast cancer cells. In vivo study was performed to detect the tumorigenicity of MCF-7/ADR cells transfected with shScramble or shUSP37#1 under adriamycin treatment. Results: Bioinformatic analysis indicated that USP37 overexpression was positively correlated with adriamycin resistance. The expression levels of USP37 in both MCF-7 and MCF-7/ADR cells increased significantly with the exposure to adriamycin in a dose-dependent manner. It was verified by the observation that USP37 downregulation elevated the inhibitory effects of adriamycin on breast cancer cells, suppressed cell proliferation caused by cell cycle arrest in G1/S transition, as well as induced apoptosis. Furthermore, in vivo study showed that knockdown of USP37 expression also decreased tumorigenicity of MCF-7/ADR cells in mice. TUNEL assay and observation of cell morphology magnified USP37 knockdown synergized with Adriamycin could elevate the apoptosis of MCF-7 and MCF-7/ADR cells. Western blotting assay illustrated that the combination of USP37 knockdown with adriamycin treatment significantly upregulated the expression levels of cleaved caspase 3 and Bax, whereas the expression level of Bcl-2 was inhibited. Conclusion: Knockdown of USP37 gene expression can reverse the resistance of breast cancer cells to adriamycin, and down-regulating USP37 might be a valuable strategy against ADR resistance in breast cancer therapy.
Association analysis between the interaction of RAS family genes mutations and papillary thyroid carcinoma in the Han Chinese population

Papillary thyroid carcinoma (PTC) is the major subtype of thyroid cancer, accounting for 75%-85% of all thyroid malignancies. This study aimed to identify the association between the interactions of single nucleotide polymorphisms (SNPs) in RAS family genes and PTC in the Han Chinese population, to provide clues to the pathogenesis and potential therapeutic targets for PTC. Hap Map and NCBI-db SNP databases were used to retrieve SNPs. Haploview 4.2 software was used to filter SNPs based on specific parameters, six SNPs of RAS gene (KRAS-rs12427141, KRAS-rs712, KRAS-rs7315339, HRAS-rs12628, NRAS-rs14804 and NRAS-rs2273267) were genotyped by matrix-assisted laser desorption/ionization time of flight mass spectrometry (MALDI-TOF-MS) in 673 PTC patients and 657 healthy controls, the interactive effect was evaluated by crossover analysis, logistic regression and GMDR software. We found that genetic mutation in rs712 have significant associations with PTC risk after Bonferroni correction (p<0.001). The interaction between KRAS-rs12427141 and HRAS-rs12628 increased the risk of PTC (U=-2.119, p<0.05), the interaction between KRAS-rs2273267 and HRAS-rs7315339 reduced the risk of PTC (U=2.195, p<0.05). GMDR analysis showed that the two-factor model (KRAS-rs712, NRAS-rs2273267) was the best (p=0.0107). Summarily, there are PTC-related interactions between RAS family genes polymorphisms in the Han Chinese population.
Identification of Compounds With Glucocorticoid Sparing Effects on Suppression of Chemokine and Cytokine Production by Rheumatoid Arthritis Fibroblast-Like Synoviocytes

In recent years target based drug discovery has expanded our therapeutic armamentarium in the treatment of inflammatory and autoimmune diseases. Despite these advances and adverse effects, glucocorticoids remain reliable agents that are used in many of these diseases. The anti-inflammatory mechanisms of glucocorticoids include the suppression of transcription factor activity like nuclear factor kappa B (NF-κB). By reanalyzing data from two prior high throughput screens (HTS) that utilized a NF-κB reporter construct in THP-1 cells, we identified 1824 small molecule synthetic compounds that demonstrated NF-κB suppressive activities similar to the glucocorticoids included in the original >134,000 compound libraries. These 1824 compounds were then rescreened for attenuating NF-κB activity at 5 and 16 h after LPS stimuli in the NF-κB THP-1 reporter cells. After a “Top X” selection approach 122 hit compounds were further tested for toxicity and suppression of LPS induced CXCL8 release in THP-1 cells. Excluding cytotoxic compounds, the remaining active compounds were grouped into chemotype families using Tanimoto based clustering. Promising representatives from clustered chemotype groups were commercially purchased for further testing. Amongst these index compounds a lead chemotype: 1H-pyrazolo [3,4 d] pyrimidin-4-amine, effectively suppressed CXCL8, and TNF production by THP-1 cells when stimulated with LPS, TNF or IL-1ß. Extending these studies to primary cells, these lead compounds also reduced IL-6 and CXCL8 production by TNF stimulated fibroblast-like synoviocytes (FLS) from rheumatoid arthritis (RA) patients. Importantly a lead 1H-pyrazolo [3,4 d] pyrimidin-4-amine compound demonstrated synergistic effects with dexamethasone when co-administered to TNF stimulated THP-1 cells and RA FLS in suppressing chemokine production. In summary, a cell based HTS approach identified lead compounds that reduced NF-κB activity and chemokine secretion induced by potent immunologic stimuli, and one lead compound that acted synergistically with dexamethasone as an anti-inflammatory agent showing a dose-sparing effect.
Draft Genome Sequence of Enterobacter sp. AS-1, a Potential Eurytrophic Recombination Host

Strain AS-1 was isolated from laboratory-scale activated sludge collected in Japan. This strain not only grows on rich medium, including R2A medium, but also forms colonies on medium lacking organic matter other than agar (water agar), indicating it could be used as a eurytrophic recombinant host in material production processes. Here, we present a draft genome sequence of Enterobacter sp. AS-1, which consists of a total of 24 contigs containing 5,207,146 bp, with a GC content of 55.64%, and comprising 4,921 predicted coding sequences. Based on 16S rRNA gene sequence analysis, strain AS-1 was designated as Enterobacter sp. AS-1.
Redox-Responsive Nanocarrier for Controlled Release of Drugs in Inflammatory Skin Diseases

A synthetic route for redox-sensitive and non-sensitive core multi-shell (CMS) carriers with sizes below 20 nm and narrow molecular weight distributions was established. Cyclic voltammetric measurements were conducted characterizing the redox potentials of reduction-sensitive CMS while showcasing its reducibility through glutathione and tris(2-carboxyethyl)-phosphine as a proof of concept. Measurements of reduction-initiated release of the model dye Nile red by time-dependent fluorescence spectroscopy showed a pronounced release for the redox-sensitive CMS nanocarrier (up to 90% within 24 h) while the non-sensitive nanocarriers showed no release in PBS. Penetration experiments using ex vivo human skin showed that the redox-sensitive CMS nanocarrier could deliver higher percentages of the loaded macrocyclic dye meso-tetra (m-hydroxyphenyl) porphyrin (mTHPP) to the skin as compared to the non-sensitive CMS nanocarrier. Encapsulation experiments showed that these CMS nanocarriers can encapsulate dyes or drugs with different molecular weights and hydrophobicity. A drug content of 1 to 6 wt% was achieved for the anti-inflammatory drugs dexamethasone and rapamycin as well as fluorescent dyes such as Nile red and porphyrins. These results show that redox-initiated drug release is a promising strategy to improve the topical drug delivery of macrolide drugs.
Inter- and Intra-Day Comparisons of Smartphone-Derived Heart Rate Variability across Resistance Training Overload and Taper Microcycles

The purposes of this study were: (1) to determine if smartphone-derived heart rate variability (HRV) could detect changes in training load during an overload microcycle and taper, and (2) to determine the reliability of HRV measured in the morning and measured immediately prior to the testing session. Twelve powerlifters (male = 10, female = 2) completed a 3-week resistance training program consisting of an introduction microcycle, overload microcycle, and taper. Using a validated smartphone application, daily measures of resting, ultra-short natural logarithm of root mean square of successive differences were recorded in the morning (LnRMSSDM) and immediately before the test session (LnRMSSDT) following baseline, post-overload, and post-taper testing. LnRMSSDM decreased from baseline (82.9 ± 13.0) to post-overload (75.0 ± 9.9, p = 0.019), while post-taper LnRMSSDM (81.9 ± 7.1) was not different from post-overload (p = 0.056) or baseline (p = 0.998). No differences in LnRMSSDT (p < 0.05) were observed between baseline (78.3 ± 9.0), post-overload (74.4 ± 10.2), and post-taper (78.3 ± 8.0). LnRMSSDM and LnRMSSDT were strongly correlated at baseline (ICC = 0.71, p < 0.001) and post-overload (ICC = 0.65, p = 0.010), whereas there was no relationship at post-taper (ICC = 0.44, p = 0.054). Bland–Altman analyses suggest extremely wide limits of agreement (Bias ± 1.96 SD) between LnRMSSDM and LnRMSSDT at baseline (4.7 ± 15.2), post-overload (0.5 ± 16.9), and post-taper (3.7 ± 15.3). Smartphone-derived HRV, recorded upon waking, was sensitive to resistance training loads across an overload and taper microcycles in competitive strength athletes, whereas the HRV was taken immediately prior to the testing session was not.
Athlete concussion history recall is underestimated: a validation study of self-reported concussion history among current professional rugby union players

ABSTRACT Objective: To assess the concurrent validity and test re-test reliability of the Michigan Traumatic Brain Injury Identification Method (MTBIIM). The psychometric properties of this concussion index were investigated by comparing the agreement between player self-reported diagnosed concussions and medical record diagnosed concussions among professional rugby union players. Study Design: Cross-sectional study i) validation and ii) test re-test reliability. Methods: The MTBIIM was administered via a structured interview to obtain the number and nature of player self-reported concussion histories from players, while contracted to the host club. Self-reported concussion history information was compared to medically recorded data captured between 2008 and 2017. A mixed-effects logistic regression model explored predictors of player self-report accuracy. Results: Data from 62 players (25.39[4.36] years) included 99 unique rugby related concussions. Medically documented concussions (n = 92) per player (1.48 [1.96]) were 30% more than the mean number of self-reported diagnosed (n = 63) concussions per player (1.02 [1.21] events). Overall, self-reported diagnosed concussions and medical record diagnosed concussion histories had a ‘fair’ level of agreement (k=0.274; SE [0.076]), p=. 001). Self-reported lifetime concussion history was signicantly negatively correlated with recall of concussions. Conclusions: Initial concurrent validity of the MTBIIM was found to be fair with the average athlete under-reporting the number of clinically diagnosed concussions.
Enteral broad-spectrum antibiotics antagonize the effect of fecal microbiota transplantation in preterm pigs

ABSTRACT Preterm infants are at risk of multiple morbidities including necrotizing enterocolitis (NEC). Suspected NEC patients receive intravenous antibiotics (AB) to prevent sepsis, although enteral AB is arguably more effective at reducing NEC but is rarely used due to the risk of AB resistance. Fecal microbiota transplantation (FMT) has shown protective effects against NEC in animal experiments, but the interaction between AB and FMT has not been investigated in neonates. We hypothesized that administration of enteral AB followed by rectal FMT would effectively prevent NEC with negligible changes in AB resistance and systemic immunity. Using preterm piglets, we examined host and gut microbiota responses to AB, FMT, or a sequential combination thereof, with emphasis on NEC development. In a saline-controlled experiment, preterm piglets (n = 67) received oro-gastric neomycin (50 mg/kg/d) and amoxicillin-clavulanate (50/12.5 mg/kg/d) (hereafter AB) for four days after cesarean delivery, and were subsequently given rectal FMT from healthy suckling piglet donors. Whereas AB protected the stomach and small intestine, and FMT primarily protected the colon, the sequential combination treatment surprisingly provided no NEC protection. Furthermore, minor changes in the gut microbiota composition were observed in response to either treatment, although AB treatment decreased species diversity and increased AB resistance among coliform bacteria and Enterococci, which were both partly reversed by FMT. Besides, enteral AB treatment suppressed cellular and functional systemic immune development, which was not prevented by subsequent FMT. We discovered an antagonistic relationship between enteral AB and FMT in terms of NEC development. The outcome may depend on choice of AB compounds, FMT composition, doses, treatment duration, and administration routes, but these results challenge the applicability of enteral AB and FMT in preterm infants.
Suppressing Grating Lobes for Transcranial Focused Ultrasound System by Frequency-Modulated Excitation

Transcranial focused ultrasound is a novel noninvasive therapeutic modality for glioblastoma and other disorders of the brain. However, because the phase aberrations caused by the skull need to be corrected with computed tomography (CT) images, the transcranial transducer is tightly fixed on the patient’s head to avoid any variation in the relative position, and the focus shifting relies mainly on the capacity for electronic beam steering. Due to the presence of grating lobes and the rapid degradation of the focus quality with increasing focus-shifting distance, transcranial focus-shifting sonication may damage healthy brain tissue unintentionally. To reduce the risks associated with transcranial focused ultrasound therapy, linear frequency-modulated (FM) excitation is proposed. The k-space corrected pseudospectral time domain (PSTD) and acoustic holography approach based on the Rayleigh integral are combined to calculate the distribution of the deposited acoustic power. The corresponding simulation was performed with axial/lateral focus shifting at different distances. The distributions of the deposited acoustic power show that linear FM excitation can effectively suppress undesired prefocal grating lobes without compromising focus quality.