Miracle-dz/UniFAR-FTUs huggingface dataset:
Ticks and Tick-borne Diseases

Rhipicephalus appendiculatus is an important tick vector of several pathogens and parasitizes domestic and wild animals across eastern and southern Africa. However, its inherent genetic variation and population structure is poorly understood. To investigate whether mammalian host species, geographic separation and resulting reproductive isolation, or a combination of these, deﬁne the genetic structure of R. appendiculatus , we analyzed multi-locus genotype data from 392 individuals from 10 geographic locations in Kenya generated in an earlier study. These ticks were associated with three types of mammalian host situations; (1) cattle grazing systems, (2) cattle and wildlife co-grazing systems (3) wildlife grazing systems without livestock. We also analyzed data from 460 individuals from 10 populations maintained as closed laboratory stocks and 117 individuals from ﬁve other species in the genus Rhipicephalus. The pattern of genotypes observed indicated low levels of genetic differentiation between the ten ﬁeld populations ( F ST = 0.014 ± 0.002) and a lack of genetic divergence corresponding to the degree of separation of the geographic sampling locations. There was also no clear association of particular tick genotypes with speciﬁc host species. This is consistent with tick dispersal over large geographic ranges and lack of host speciﬁcity. In contrast, the 10 laboratory populations ( F ST = 0.248 ± 0.015) and the ﬁve other species of Rhipicephalus ( F ST = 0.368 ± 0.032) were strongly differentiated into distinct genetic groups. Some laboratory bred populations diverged markedly from their ﬁeld counterparts in spite of originally being sampled from the same geographic locations. Our results demonstrate a lack of deﬁned population genetic differentiation in ﬁeld populations of the generalist R. appendiculatus in Kenya, which may be a result of the frequent anthropogenic movement of livestock and mobility of its several wildlife hosts between different locations.
Middle Miocene paleoclimate change at Bryce Burn, southern New Zealand

Abstract New Zealand's isolated position in the Southwest Pacific and the quality of its marine and terrestrial sedimentary record make it a valuable source of information for studies of global climate change. A section at Bryce Burn in Southland, South Island, provides a record of middle Miocene global cooling associated with buildup of an extensive semi‐permanent ice sheet on Antarctica. The section yielded δ18O, δ13C, lithological, clay mineral, foraminiferal, and pollen data that have been linked to a high‐resolution age model based on magnetostratigraphy and foraminiferal dating. The sequence exhibits evidence for a δ18O c. 0.6‰ positive baseline shift consistent with the age and magnitude of the E3/ Mi3 isotope excursion around 13.9 Ma, carbon maxima 4–6 δ13C excursions, probable orbitally controlled changes in clay mineralogy, and short‐term changes in terrestrial vegetation. This is the first time these stable isotopic events have been recognised in outcrop sequences in New Zealand. There appears to be no clear, long‐term shift in the data associated with middle Miocene oceanic cooling, apart from the stable isotope evidence, though Milankovitch‐scale, short‐term fluctuations are present.
firm size

We show theoretically that when larger firms pay higher wages and are more likely to be caught defaulting on labor taxes, then large-high wage firms will be in the formal and small-low wage firms will be in the informal sector. The formal sector wage premium is thus just a firm size wage differential. Using data from Ecuador we illustrate that firm size is indeed the key variable determining whether a formal sector premium exists.
An Assessment of Impacts of African Elephants (Loxodonta africana) onthe Structure of Mopane (Colophospermum mopane) in the North EasternLake Kariba Shore, Zimbabwe

A study on impacts of African elephants (Loxodonta africana) on the structure of C. mopane was done on the north eastern Lake Kariba shore, Zimbabwe. The objectives of the study were to determine the structure and abundance of C. mopane, determine the levels of elephant induced damage on C. mopane along a distance gradient from the lake and to determine the relationship between elephant induced damage on C. mopane trees and distance from the north eastern Lake Kariba shore. C. mopane trees were sampled in May 2013. Four belt transects were demarcated extending from the lake towards the ZESA pylons. Eight plots measuring 20 m x 30 m were systematically placed at 100 m, 500 m, 1000 m and 2000 m distances from the lake shore within each belt. C. mopane variables, that is, tree height, basal area, tree density, shrub density, number of stems per plant, density of damaged plants and number of dead trees were recorded within each plot. Damage was also assessed and rated depending on the intensity of damage. A total of 479 C. mopane trees were sampled in 32 plots. Data was analysed using STATISTICA Version 7 Results from Kruskal-Wallis ANOVA test (KWH test), indicated that Height (P=0.5423), basal area (P=0.9463), tree density (P=0.2465), shrub density (P=0.3027), number of stems per plant (0.7503, density of damaged plants (P=0.1802) and density of dead trees (P=0.4603) were not significantly different across all distances from the lake. The results also indicated no significant difference in the level of damage (P=0.8050) across all distances from the lake. PCA indicated that trees were densely populated in areas close to the lakeshore (100 m and 500 m) and it is within this area where the highest number of damaged and dead trees was recorded. HCA showed that plots within 2000 m recorded the highest average sapling density, plots within 1000 m recorded the highest average tree height and shrub density and plots within 100 m recorded the highest of density of damaged trees and basal area. Findings from linear regression showed that distance from water create an herbivory gradient of C. mopane utilization though the herbivory gradient might not lead to overall degradation of C. mopane. Management should focus on maintaining herbivore populations within ranges that does not lead to C. mopane woodland degradation.
Flora vascolare e vegetazione della Riserva Naturale Regionale “Foce del Fiume Crati” (Calabria, Italia meridionale)

Riassunto Sono presentati i risultati di uno studio sulla flora e sulla vegetazione effettuato nella Riserva Naturale della Foce del Crati, zona umida caratterizzata da una notevole biodiversità, minacciata dalla presenza di attività agricole e pastorali condotte irrazionalmente e dall'espansione di complessi turistici edificati proprio a contatto con le cenosi costiere più sensibili all'antropizzazione. La flora, costituita soprattutto da elementi mediterranei, consiste di 482 taxa, comprendenti 15 specie nuove per la Calabria e 18 specie inserite nelle Liste Rosse regionali. Notevole risulta la presenza di specie sinantropiche. La vegetazione è rappresentata dalle fitocenosi della geoserie psammofila litoranea, da quelle tipiche delle paludi salmastre, da vegetazione prettamente alofila e da cenosi delle zone umide dulciacquicole prossime al corso del fiume. Essa è differenziata notevolmente in funzione anche di piccole variazioni del contenuto salino o di umidità del suolo. Nel complesso, sono state individuate 46 tipologie di vegetazione, spesso distribuite su superfici molto limitate. Alcune associazioni sono nuove per la Calabria o per l'Italia Meridionale, altre sono degne di nota per la particolare rarità, quali i pioppeti a Clematis scandens e le associazioni della geoserie alofila. Nonostante le vaste superfici rimboschite ad eucalipti e pini, la riserva mantiene ancora un elevato grado di naturalità. Tuttavia, le misure di protezione devono essere rinforzate ed estese anche alle aree limitrofe, onde garantire la migliore conservazione di un così fragile ecosistema.
Nomenclature BB Building Block DSM Design Structure Matrix QAP Quadratic Assignment Problem

In product design, it is critical to perform project activities in an appropriate sequence. Otherwise, essential information will not be available when it is needed, and activities that depend on it will proceed using assumptions instead. Later, when the real information is finally available, comparing it with the assumptions made often precipitates a cascade of rework, and thus cost and schedule overruns for the project. Information flow models have been used to sequence the engineering design process to minimize feedback and iteration—i.e., to maximize the availability of real information where assumptions might otherwise be made instead. In this paper, we apply Genetic Algorithms (GAs) to an information flow model to find an optimized sequence for a set of design activities. The optimality of a solution depends on the objective of rearrangement. In an activity sequencing context, objectives vary: reducing iteration/feedback, increasing concurrency, reducing development lead-time and cost, or some combination of these. We adopt a matrix-based representation scheme, the design structure matrix (DSM), for the information flow models. Our tests indicate that certain DSM characteristics (e.g. size, sparseness, and sequencing objective) cause serious problems for simple Genetic Algorithm (SGA) designs. To cope with the SGA deficiency, we investigate the use of a competent GA: the Ordering messy GA (OmeGA). Tests confirm the superiority of the OmeGA over a SGA for hard DSM problems. Extensions enhancing the efficiency of both a SGA and the OmeGA, in particular niching and hybridization with a local search method, are also investigated. Nomenclature BB Building Block DSM Design Structure Matrix QAP Quadratic Assignment Problem SCC Strongly Connected Components of a graph a Number of arcs/edges/relationships in a digraph; number of off-diagonal marks in a DSM c Constant factor d Signal difference between the best and the second-best BB I Selection intensity k Order or size of BBs l Current chromosome length m Number of BBs n Number of activities in a design process; number of vertices or nodes in a graph; DSM block size npop Population size p Probability to pick the best fit chromosome of a tournament during the Tournament Selection phase pc Crossover probability pcut Cut probability in the OmeGA pκ Bitwise cut probability in the OmeGA pm Mutation probability ps Slice probability in the OmeGA s Size of tournament used in the Tournament Selection phase SP Selection pressure tc Convergence time α Selection error φ Number of SCCs in a graph or iterative/coupled blocks in a DSM μ Calibration coefficient σ2 Average fitness variance π Ludolph ́s number ψ A DSM sequence φ A DSM sequence
Molecular Action of Tamoxifen in the Ovaries of Rats with Mammary Neoplasia

Tamoxifen (TAM) is a drug commonly used in patients with breast cancer. The anticancer effect of TAM occurs via its ability to antagonize estrogen-dependent growth of mammary epithelial cells. Previously, we demonstrated that TAM prevented the chemotherapy-induced loss of ovarian follicular reserves in both cancer-free rats and rats with cancer. Such follicular loss is a main cause of infertility in young women treated for cancer. The current study was undertaken to discover the molecules and intracellular pathways involved in the action of TAM in the ovaries of rats with mammary tumors. To meet this goal we used transcriptomic (RNA-Seq) and proteomic (2D-DIGE/MS) approaches. TAM inhibited the expression of genes and lncRNAs involved in ovarian steroidogenesis. Moreover, TAM altered the expression of genes related to primordial follicle activation or arrest. In addition, proteomic screening indicated the importance of basic metabolic processes in the ovarian actions of TAM. Although simple extrapolation of these data to humans is not possible, the results of this study emphasize the need to explore the ability of TAM to affect ovarian function in women undergoing cancer treatment.
Physicochemical Properties, Antioxidant Activity and Organoleptic of Yogurt with The Addition of Red Dragon Fruit Juice (Hylocereus polyrhizus)

Yogurt is dairy product with high nutritional content, is obtained by fermentation process on fresh milk or milk solution with lactic acid bacteria. Yoghurt has a sour taste, to increase the sourness, natural flavourings from fruit juice are added. Red dragon fruit (Hylocereus polyrhizus) is one of thefruits that can be added to yogurt. Red dragon fruit (Hylocereus polyrhizus) is a fruit that contains antioxidants. The aim of this study was to determine the physicochemical characteristic, antioxidant activity and sensory properties of red dragon yogurt. The results showed that physical properties (pH,Aw, Viscosity and Total Titratable Acid) and chemical properties of ash content in red dragon yogurt has been accordance with SNI. The addition of red dragon fruit juice (Hylocereus polyrhizus) had significant affects (P<0.05) on the pH value, protein content, sensory properties of aroma, color, and taste. However, the addition of red dragon fruit juice (Hylocereus polyrhizus) did not give significant affect (P>0.05) to the Aw value, viscosity, total acid titration, ash content, color hedonic characteristics, texture, taste, texture hedonic quality characteristics. Yogurt with the concentration 10% of red dragon fruit juice had the best formulation compared to other concentration.
Feature Line Smoothing and Adaptive Optimizing Method for 3 D Models

Feature lines, especially viewand scaleindependent ridge-valley lines can indicate most prominent characteristics on surface. Mathematically, ridge-valley lines are defined as local extrema of principle curvatures along corresponding principle directions. When detecting ridge-valley lines on 3D mesh model, estimation of the curvature and first even higher order curvature derivatives is necessary. This may often yields to squiggly and noisy result since the estimation is sensitive against unwanted surface noises. We present an adaptive algorithm to obtain smooth and noiseless ridge-valley lines based on graph theory model. After an iteration procedure acting on local ridge (or valley) vertices and their previous and next neighbors on connected lines is applied to smooth feature lines, each separate feature line is considered as an undirected weighted graph which is called as Feature Graph. With a correct root node choosing, the minimal spanning tree of the feature graph is computed. We can automatically get rid of most noises and preserve meaningful feature lines through optimizing those minimal spanning trees.
University of Per-arnt-sim (PAS) domain-containing protein kinase is downregulated in human islets in type 2 diabetes and regulates glucagon secretion

Aims/hypothesis We assessed whether per-arnt-sim (PAS) domain-containing protein kinase (PASK) is involved in the regulation of glucagon secretion. Methods mRNA levels were measured in islets by quantitative PCR and in pancreatic beta cells obtained by laser capture microdissection. Glucose tolerance, plasma hormone levels and islet hormone secretion were analysed in C57BL/6 Pask homozygote knockout mice ( Pask − / − ) and control littermates. Alpha-TC1-9 cells, human islets or cultured E13.5 rat pancreatic epithelia were transduced with anti- Pask or control small interfering RNAs, or with adenoviruses encoding enhanced green fluorescent protein or PASK. Results PASK expression was significantly lower in islets from human type 2 diabetic than control participants. PASK mRNA was present in alpha and beta cells from mouse islets. In Pask − / − mice, fasted blood glucose and plasma glucagon levels were 25±5% and 50±8% (mean ± SE) higher, respectively, than in control mice. At inhibitory glucose concentrations (10 mmol/l), islets from Pask − / − mice secreted 2.04±0.2-fold ( p <0.01) more glucagon and 2.63±0.3-fold ( p <0.01) less insulin than wild-type islets. Glucose failed to inhibit glucagon secretion from PASK-depleted alpha-TC1-9 cells, whereas PASK overexpression inhibited glucagon secretion from these cells and human islets. Extracellular insulin (20 nmol/l) inhibited glucagon secretion from control and PASK-deficient alpha-TC1-9 cells. PASK-depleted alpha-TC1-9 cells and pancreatic embryonic explants displayed increased expression of the preproglucagon ( Gcg ) and AMP-activated protein kinase (AMPK)-alpha2 ( Prkaa2 ) genes, implying a possible role for AMPK-alpha2 downstream of PASK in the control of glucagon gene expression and release. Conclusions/interpretation PASK is involved in the regulation of glucagon secretion by glucose and may be a useful target for the treatment of type 2 diabetes.
The role of the tropical West Pacific in the extreme Northern Hemisphere winter of 2013/2014

In the 2013/2014 winter, the eastern U.S. was exceptionally cold, the Bering Strait region was exceptionally warm, California was in the midst of drought, and the UK suffered severe flooding. It has been suggested that elevated sea surface temperatures (SSTs) in the tropical West Pacific (TWPAC) were partly to blame due to them producing a Rossby wave train that propagated into the extratropics. We find that seasonal forecasts with the tropical atmosphere relaxed toward a reanalysis give 2013/2014 winter mean anomalies with strong similarities to those observed in the Northern Hemisphere, indicating that low‐latitude anomalies had a role in the development of the extremes. Relaxing just the TWPAC produces a strong wave train over the North Pacific and North America in January, but not in the winter mean. This suggests that anomalies in this region alone had a large influence but cannot explain the extremes through the whole winter. We also examine the response to applying the observed TWPAC SST anomalies in two atmospheric general circulation models. We find that this does produce winter mean anomalies in the North Pacific and North America resembling those observed and that the tropical forcing of Rossby waves due to the applied SST anomalies appears stronger than that in reanalysis, except in January. Therefore, both experiments indicate that the TWPAC influence was important, but the true strength of the TWPAC influence is uncertain. None of the experiments indicate a strong systematic impact of the TWPAC anomalies on Europe.
On the use of an high order perturbation method for numerical time integration in structural dynamics.

This paper concerns numerical simulations of time-dependent problems in computational solid mechanics. A perturbation method, with the time as perturbation parameter, is proposed to solve two classical problems: an elastic bar excited by an end force and the dynamic buckling of a cylindrical panel. Specific quadratic recast of the equations is proposed to solve the nonlinear problems. Numerical results show that asymptotic time expansions is robust, e ffi cient and gives more accurate solutions than the ones obtained with classical time-integration schemes (implicit or explicit), even when the considered meshes are coarse.
OLD INDUSTRIAL MASONRY CHIMNEYS : REPAIRING AND MAINTENANCE

The aim of this paper is present a review of the current state of research in industrial masonry chimneys and a deeper approach to them to facilitate their knowledge. For this, the first part of the paper is devoted to review the history of these chimneys, why and how they were constructed, the shape and dimensions and having pathologies or causes that may lead to the need for repair or strengthening. A detailed description of the main problems on these structures is presented: inclination, vertical cracks, alteration of the masonry mortar joints, and expansion of mortar due corrosion of steel elements, etc. This description includes a possible origin of these structural pathologies. The second part of the paper presents the preliminary results of a case of study: The chimney of the factory “La Paz” in Agost (Alicante-Spain). This construction is in phase to be declared local monument by the City Council of Agost. This structure presents examples of all the previously described pathologies and shows a severe crack pattern. A 3D numerical model with the actual deformation of this structure and with the main crack patterns is developed to obtain the actual stability of the structure under self weight and extreme wind loads. Finally a general description of possible repairing actuation for each pathology is presented with some real examples.
Effect of recombinant human nerve growth factor treatment on corneal nerve regeneration in patients with neurotrophic keratopathy

Introduction Neurotrophic Keratopathy (NK) is a neurodegenerative corneal disease that results in diminished corneal sensation. Previous studies have found that Cenegermin 0.002%, a recombinant human nerve growth factor (rhNGF), improves corneal epithelial healing in stage 2 and 3 NK patients. However, rhNGF effect on corneal sensation and nerve regeneration has not been well established. Thus, this study aims to analyze the effect of rhNGF on corneal nerve regeneration using in vivo confocal microscopy (IVCM) and on corneal sensitivity in NK patients. Methods This is a retrospective, longitudinal, case–control study that included patients with NK, treated with rhNGF for at least 4 weeks, with pre- and post-treatment IVCM images available for analysis. Chart reviews were conducted documenting prior medical and surgical history, clinical signs and symptoms, and corneal sensation using Cochet-Bonnet esthesiometry. Corneal nerve parameters were assessed by IVCM. Sex- and age-matched reference controls were selected from a database of healthy subjects for comparison. Results The study included 25 patients, with 22 (88%) stage 1, two (8%) stage 2, and 1 (4%) stage 3 NK patients, with a median age of 64 years (range: 30–93 years). Total, main, and branch nerve densities [median (range) in mm/mm2] were lower in the NK group pre-treatment [2.3 (0.0–21.1); 1.7 (0.0–13.0); 0.5 (0.0–10.2); respectively] vs. controls [22.3 (14.9–29.0); 10.1 (3.2–15.4); and 12.1 (6.2–18.4), (p < 0.0001 for all), respectively]. Post-treatment nerve densities increased compared to pre-treatment to 5.3 (0.0–19.4, p = 0.0083) for total, 3.5 (0.0–13.2, p = 0.0059) for main, and 2.0 (0.0–10.4, p = 0.0251) for branch nerves, but remained lower than controls (p < 0.0001 for all). Corneal sensation increased from 2.3 ± 1.1 cm pre-treatment to 4.1 ± 1.4 cm post-treatment (p = 0.001). Median best corrected visual acuity significantly increased following rhNGF treatment from 0.4 (0.0–1.6) to 0.12 (−0.1 to 1.6) (p = 0.007). Conclusion Patients with NK treated with at least 4 weeks of rhNGF, showed a significant increase in corneal nerve densities after treatment. A significant increase in corneal sensation, as well as best corrected visual acuity, was observed following treatment.