Miracle-dz/UniFAR-FTUs huggingface dataset:
Genetic population structure of the common sole, Solea solea Linnaeus, 1758 (Pisces, Pleuronectiformes) along the southern shores of the Mediterranean Sea (Tunisian coasts)

Abstract We studied the genetic differentiation among Solea solea populations, collected from both sides of the Siculo-Tunisian Strait (northeast and southeast Tunisian coasts), which is considered to be a boundary area between the eastern and western Mediterranean basins. Seven polymorphic enzyme loci (MDH-2*, MDH-3*, PGM*, PGI-1*, PGI-2*, GOT-2* and SOD*) were used in this study. Significant departure from the Hardy–Weinberg equilibrium, especially along the southeast Tunisian coast, was observed. Null alleles and inbreeding in populations subjected to overexploitation pressure can explain this result. No heterogeneity was detected between localities of both sides of the Siculo-Tunisian Strait, which reflects a continuous gene flow between northeast and southeast Tunisian coast populations. This result agrees with the biological characteristics of the species that favour the gene flow. In order to position Tunisian populations in the Mediterranean context, published data from eastern and western basins were integrated. Homogeneity was detected in the western Mediterranean basin and a high level of east-west differentiation was detected only with the extreme east Mediterranean populations (Aegean Sea and Egypt).
Human B lymphoblast cell lines defective of Stat6 signaling produce high levels of proinflammatory cytokines IL-12, TNFα and IFNγ

Based on Stat6 gene knockout animal models, the Stat6 signaling pathway has been suggested to play a role in carcinogenesis and Th1/Th2 cytokine balance. Using a semiquantitative EMSA assay and EBV-transformed human B lymphoblast cell lines, we have previously identified three Stat6 activational phenotypes, termed as Stat6high, Stat6low, and Stat6null. A genetic mechanism has been proposed which determines the IL-4-induced activation of the human Stat6 signaling. With respect to the contribution of variant phenotypes to human disease, we further hypothesize that the Stat6null phenotype may result from a partial defect in Stat6 signaling which resembles Stat6 knockout animals in several functional aspects. The characterization of the human Stat6null phenotype stably displayed by the EBV-B cell lines is easily assailable and possesses important implications with respect to Th1/Th2 cytokine imbalance in diseases such as cancer development/metastasis and inflammatory diseases. In this study, we have extended our investigation to the downstream regulatory consequences associated with these Stat6 phenotypes. Production of three important proinflammatory cytokines, IL-12, TNFalpha and IFNgamma was examined in spontaneous EBV-B cell culture using ELISA methodology. Individual cell lines defined as Stat6null produced significantly higher levels of IL-12, TNFalpha and IFNgamma on day 4 in spontaneous culture in comparison with cell lines characterized as Stat6high and Stat6low. These observations of the human Stat6null phenotype, together with those accruing from Stat6 knockout mouse model studies, suggest that the Stat6 signaling pathway may play a role in maintaining the Th1/Th2 cytokine balance by directly and indirectly down-regulating the production of proinflammatory cytokines, a regulatory process which appears to go awry in inflammatory diseases. Moreover, observations from signal transduction studies in our human B lymphocyte model may be compatible with those in the chosen mouse B lymphocyte for establishing signaling networks by the Alliance for Cellular Signaling (AfCS).
Scale Methods for Discriminating between Great Lakes Stocks of Wild and Hatchery Rainbow Trout, with a Measure of Natural Recruitment in Lake Ontario

Abstract Growth characteristics of scales were used to discriminate between rainbow trout Oncorhynchus mykiss of hatchery and wild origin and to provide a measure of natural recruitment in Lake Ontario. Scale samples were collected in 1971, 1974, and 1989–1992 from 20 sources that included three hatcheries and Lakes Ontario, Huron, and Superior and their tributaries. Spacing of the circuli about the first annulus has been shown to separate wild and hatchery rainbow trout. However, criteria for recognizing and locating the first annulus are lacking, which leads to subjectivity and general imprecision. We developed methods that use the first two scale checks (breaks in the configuration of the circuli) regardless of designation, incorporate differences in the thickness of the circuli, and detect regenerated nuclei so that these scales could be eliminated from the analysis. The dichotomous key we developed provides specific criteria that makes it easy to locate a diagnostic check and discriminate origin of t.
Predation of Nabis punctipennis on Acyrthosiphon pisum in the presence of the alternative prey Aphis craccivora in alfalfa

The feeding behavior of the generalist predator Nabis punctipennis Blanchard (Nabidae) on Acyrthosiphon pisum Harris (Aphididae), two hemipterans common in alfalfa in Chile, was studied in a laboratory experiment using A. pisum, and Aphis craccivora Koch (Aphididae) as alternative prey, which is another common aphid in alfalfa. The presence of A. craccivora did not affect the predation of A. pisum by N. punctipennis. This finding on the predatory behavior of N. punctipennis is valuable to evaluate the potential of this nabid as a biological control agent of A. pisum.
Review: Confirmation of Resistance to Herbicides and Evaluation of Resistance Levels

Abstract As cases of resistance to herbicides escalate worldwide, there is increasing demand from growers to test for weed resistance and learn how to manage it. Scientists have developed resistance-testing protocols for numerous herbicides and weed species. Growers need immediate answers and scientists are faced with the daunting task of testing an increasingly large number of samples across a variety of species and herbicides. Quick tests have been, and continue to be, developed to address this need, although classical tests are still the norm. Newer methods involve molecular techniques. Whereas the classical whole-plant assay tests for resistance regardless of the mechanism, many quick tests are limited by specificity to an herbicide, mode of action, or mechanism of resistance. Advancing knowledge in weed biology and genomics allows for refinements in sampling and testing protocols. Thus, approaches in resistance testing continue to diversify, which can confound the less experienced. We aim to help weed science practitioners resolve questions pertaining to the testing of herbicide resistance, starting with field surveys and sampling methods, herbicide screening methods, data analysis, and, finally, interpretation. More specifically, this article discusses approaches for sampling plants for resistance confirmation assays, provides brief overviews on the biological and statistical basis for designing and analyzing dose–response tests, and discusses alternative procedures for rapid resistance confirmation, including molecular-based assays. Resistance confirmation procedures often need to be slightly modified to suit a specific situation; thus, the general requirements as well as pros and cons of quick assays and DNA-based assays are contrasted. Ultimately, weed resistance testing research, as well as resistance management decisions arising from research, needs to be practical, feasible, and grounded in science-based methods.
Calibration of the APSIM-Lucerne model for ‘Grasslands Kaituna’ lucerne crops grown in New Zealand

This study used results from field experiments to calibrate the Agricultural Production Systems Simulator (APSIM) model for ‘Grasslands Kaituna’ lucerne (Medicago sativa L.) crops grown in the cool temperate climate of New Zealand. The field data allowed refinement of functions related to the seasonality of crop phenology and above- and below-ground growth. The model structure was adequate to accommodate the calibration of reproductive development in response to temperature and photoperiod in both release and calibrated versions (root mean squared deviation [RMSD] from 14% to 3% of the mean, respectively). Similarly, vegetative development, characterised by the rate of appearance of main-stem nodes, was simulated with acceptable accuracy (RMSD from 28% to 25% of the mean). Analysis showed a lack of current field data to accurately represent the number of main-stem nodes at the beginning of each regrowth cycle, which is required to further improve the accuracy of leaf appearance simulations. The simulation of leaf area index (LAI) was slightly more accurate when using a site-specific empirical canopy modelling approach for ‘Grassland Kaituna’ (RMSD = 34% of the mean) than with the more mechanistic approach in the release version used for Australian cultivars (RMSD = 40% of the mean). This is particularly important before canopy closure, when LAI has the greatest influence on light interception and biomass accumulation. ‘Grassland Kaituna’ showed a seasonal pattern of change in leaf size and specific leaf area that could not be parameterised using the approach in the release version. Finally, the model structure of the calibrated version was adapted to explicitly simulate the seasonal flow of biomass to shoots and roots. For that, the ‘shoot’ radiation use efficiency (RUE) was modified to a ‘whole plant’ RUE of 1.6 g/MJ total solar radiation and a seasonal rate of below-ground biomass turnover (i.e. respiration plus senescence) was incorporated to correct for the initial offset observed between simulated and observed root biomass. These changes improved the RMSD from 53% to 38% for shoot biomass and 29% to 18% of the mean for roots. This calibration illustrates the heuristic aspect of applying crop models to identify knowledge gaps for guiding future experimentation, including time of node appearance on basal buds and leaf area index dynamics of contrasting lucerne cultivars.
Colorings of Plane Graphs Without Long Monochromatic Facial Paths

Abstract Let G be a plane graph. A facial path of G is a subpath of the boundary walk of a face of G. We prove that each plane graph admits a 3-coloring (a 2-coloring) such that every monochromatic facial path has at most 3 vertices (at most 4 vertices). These results are in a contrast with the results of Chartrand, Geller, Hedetniemi (1968) and Axenovich, Ueckerdt, Weiner (2017) which state that for any positive integer t there exists a 4-colorable (a 3-colorable) plane graph Gt such that in any its 3-coloring (2-coloring) there is a monochromatic path of length at least t. We also prove that every plane graph is 2-list-colorable in such a way that every monochromatic facial path has at most 4 vertices.
Pembrolizumab (and friends) in pediatric malignancies: should we consider Hodgkin lymphoma a world of its own?

Department of Pediatric Hematology and Oncology, Scientific Institute for Research and Healthcare (IRCCS), Bambino Gesù Children’s Hospital, Rome, Italy; Sapienza University of Rome, Rome, Italy Correspondence to: Franco Locatelli. Director, Department of Pediatric Hematology and Oncology, IRCCS Ospedale Pediatrico Bambino Gesù, Piazza Sant'Onofrio, 4 00165 Rome, Italy. Email: franco.locatelli@opbg.net. Provenance and Peer Review: This article was commissioned by the editorial office, Annals of Translational Medicine. The article did not undergo external peer review. Comment on: Geoerger B, Kang HJ, Yalon-Oren M, et al. Pembrolizumab in paediatric patients with advanced melanoma or a PD-L1-positive, advanced, relapsed, or refractory solid tumour or lymphoma (KEYNOTE-051): interim analysis of an open-label, single-arm, phase 1–2 trial. Lancet Oncol 2020;21:121-33.
EFFECT OF SEEDING RATE ON HEIGHT, YIELD AND QUALITY OF LARGE-SEEDED AND SEMI-DWARF BUCKWHEAT GENOTYPES

Two large-seeded buckwheat (Fagopyrum esculentum Moench.) cultivars, Mancan and Manor, and semi-dwarf lines, were grown at Morden and Portage la Prairie in the years 1979–1982 at seeding rates of 15, 30, 45 and 60 kg/ha. There was no consistent effect of seeding rate on plant height, seed weight (g/1000 seeds) or seed density. In six of the eight location-years there was no interaction of genotype × seeding rate for seed yield, indicating that, generally, the cultivars and lines reacted similarly to differences in seeding rate. It was concluded that a seeding rate of from 30 to 45 kg/ha would ensure optimum yield in most years.Key words: Buckwheat, Fagopyrum esculentum Moench. , seeding rates
Consumer Preference Heterogeneity and Preference Segmentation: The Case of Ecolabeled Salmon in Danish Retail Sales

Popularity of sustainably produced food products has grown rapidly in recent years. Ecolabels are used to indicate the environmental sustainability of products and have been implemented in the seafood market, with the leading ecolabel being that of the Marine Stewardship Council (MSC) for wild fish. However, the effect of ecolabels in consumer decision making remains unclear in regard to actual purchasing behavior. This study analyzes scanner data from a household panel in Denmark, accounting for consumer heterogeneity using random parameter and latent class logit models to identify the effect of ecolabels. The results indicate substantial consumer preference heterogeneity with respect to important salmon attributes. Salmon attributes that confer convenience to household fish consumption appear to be very important in consumer choices. Ecolabeling has a significant effect on household decision making, but the majority of consumers are more likely to choose non-labeled products, which may be due to the low availability of ecolabeled products. Five consumer segments are identified, revealing one consumer segment with a preference for organic labeled salmon, comprising 15% of households. However, a consumer segment for MSC-labeled salmon is not identified. The implication is that management can rely on a segment of consumers to implement organic principles in salmon farming, but the preference for sustainable salmon fishing is inconclusive due to uncertain confounding effects.
The integration of GPS, vegetation mapping and GIS in ecological and behavioural studies

Global Positioning System (GPS) satellite navigation receivers are increasingly being used in ecological and behavioural studies to track the movements of animals in relation to the environments in which they live and forage. Concurrent recording of the animal's foraging behaviour (e.g. from jaw movement recording) allows foraging locations to be determined. By combining the animal GPS movement and foraging data with habitat and vegetation maps using a Geographical Information System (GIS) it is possible to relate animal movement and foraging location to landscape and habitat features and vegetation types. This powerful approach is opening up new opportunities to study the spatial aspects of animal behaviour, especially foraging behaviour, with far greater precision and objectivity than before. Advances in GPS technology now mean that sub-metre precision systems can be used to track animals, extending the range of application of this technology from landscape and habitat scale to paddock and patch scale studies. As well as allowing ecological hypotheses to be empirically tested at the patch scale, the improvements in precision are also leading to the approach being increasing extended from large scale ecological studies to smaller (paddock) scale agricultural studies. The use of sub-metre systems brings both new scientific opportunities and new technological challenges. For example, fitting all of the animals in a group with sub-metre precision GPS receivers allows their relative inter-individual distances to be precisely calculated, and their relative orientations can be derived from data from a digital compass fitted to each receiver. These data, analyzed using GIS, could give new insights into the social behaviour of animals. However, the improvements in precision with which the animals are being tracked also needs equivalent improvements in the precision with which habitat and vegetation are mapped. This needs some degree of automation, as vegetation mapping at a fine spatial scale using the traditional manual approach is far too time consuming. This paper explores these issues, discussing new applications as well as approaches to overcoming some of the associated problems.
Eggshell penetration by Salmonella: a review

Intact eggs can become contaminated with Salmonella as a result of infections of the reproductive tissues of the laying hens but also by penetration through the shell. In this paper, the penetration of Salmonella through the shell of hen eggs is reviewed. A description is given of the advantages and disadvantages of the various methods used to study bacterial penetration through the shell and membranes. The possibility of Salmonella contamination of the shell after lay is included because shell contamination is the first requisite for penetration. Various factors affect the probability of bacterial penetration. Both the intrinsic and extrinsic factors are highlighted. For the extrinsic factors, the influence of bacterial strain and number of organisms, temperature, moisture and immersion and storage conditions on the probability of Salmonella penetration through the shell is described. With regard to intrinsic factors, the presence of cuticle, shell characteristics (shell quality, porosity, shell defects) and membrane properties are summarized.
Raman spectroscopic signature of life in a living yeast cell

We have discovered a Raman spectroscopic signature that sharply reflects the metabolic activity of a mitochondrion in a living yeast cell. Raman mapping experiments on a GFP-labeled yeast cell showed that this signature originated exclusively from mitochondria. Addition of KCN caused a rapid decrease and subsequent disappearance of the signature followed by gradual changes of the phospholipid Raman bands, indicating that respiration was first inhibited by KCN and then lowered metabolic activity gradually deteriorated the double-membrane structure of a mitochondrion. We can now monitor the life and death of a single cell by time- and space-resolved Raman spectroscopy. Copyright © 2004 John Wiley & Sons, Ltd.
The benefit of computational modelling in physics teaching: a historical overview

Computational modelling is not only an important element in scientific research, it also has a rich history in physics education and its application in the classroom has changed greatly over the last few decades. To explain why computational modelling is used in physics education, we discuss its use in teaching and the benefits to the teaching and learning process. Secondly, historical developments are highlighted, and different methods of computational modelling are discussed in more detail, developing the desired features of modern software for classroom computational modelling. A review of the research in this field was conducted, showing what is known about the effects of computational modelling on students’ conceptual understanding, systemic thinking, views about nature of science and interest in physics, among others variables. Derived from the research results, recommendations are given about the use of computational modelling in physics education and research recommendations are presented with the goal to better understand the interaction between the student and computational modelling process.
Monitoring bird migration with a fixed-beam radar and a thermal-imaging camera

Previous studies using thermal imaging cameras (TI) have used target size as an indicator of target altitude when radar was not available, but this approach may lead to errors if birds that differ greatly in size are actually flying at the same altitude. To overcome this potential difficulty and obtain more accurate measures of the flight altitudes and numbers of individual migrants, we have developed a technique that combines a vertically pointed stationary radar beam and a vertically pointed thermal imaging camera (VERTRAD/TI). The TI provides accurate counts of the birds passing through a fixed, circular sampling area in the TI display, and the radar provides accurate data on their flight altitudes. We analyzed samples of VERTRAD/TI video data collected during nocturnal fall migration in 2000 and 2003 and during the arrival of spring trans-Gulf migration during the daytime in 2003. We used a video peak store (VPS) to make time exposures of target tracks in the video record of the TI and developed criteria to distinguish birds, foraging bats, and insects based on characteristics of the tracks in the VPS images and the altitude of the targets. The TI worked equally well during daytime and nighttime observations and best when skies were clear, because thermal radiance from cloud heat often obscured targets. The VERTRAD/TI system, though costly, is a valuable tool for measuring accurate bird migration traffic rates (the number of birds crossing 1609.34 m (1 statute mile) of front per hour) for different altitudinal strata above 25 m. The technique can be used to estimate the potential risk of migrating birds colliding with man-made obstacles of various heights (e.g., communication and broadcast towers and wind turbines)? a subject of increasing importance to conservation biologists.
GnRH agonis short protocol versus GnRH antagonist flexible protocols in poor responder undergoing in vitro fertilization treatment.

Objective: To compare the short agonist and flexible antagonist protocols in the management of poor responders to standerd long down regulation protocol. Design: Randomized prospective comparative study. Setting: private IVF center(Engab). Patient(s): One hundred poor-responder (IVF)(ICSI), who responded poorly to the standerd long down- regulation protocol in their first treatment cycle. Intervention(s): Peak serum E2 was assayed on the day of hCG administration. Main Outcome Measure(s): primary outcome: number of HMG ampoules used, peak E2 at the triggering day, number of oocytes retrieved, number of metaphase II oocytes, fertilization rate, embryo quality and number of embryos transferred.cycle cancellation. secondary outcome: pregnancy rate , miscarriage rate . Result(s): GnRH-antagonist protocol shows increased – non significant- pregnancy rate and decreased - non significant - miscarriage rate than agonist short protocol, however agonist short protocol appears to be more effective than the GnRH-antagonist protocol in terms of number of FSH ampules, peak E2 level, fertilization rate, and top-quality embryos transferred in poor-responder. Conclusion(s): The probability of pregnancy might be better with the use of the antagonist protocol, also flexible antagonist protocol is a simpler and more patient friendly method of ovarian stimulation compared with the short agonist protocol.
Modified k-string in composition vector method for DNA sequence comparison based on maximum entropy principle

Abstract The Composition Vector method is a type of alignment-free methods for sequence comparison. The proposed method is based on modified k-string method, which uses the ratio of frequencies of all possible sub-words of length k in a DNA sequence to compare two sequences. We have proposed a scheme based on modified formulas for sequence comparison considering principle of maximum entropy. There exist several formulas for the purpose however the one maximizing the entropy was selected for the study. It leads to a unified approach for sequence comparison. The obtained results have been analyzed and compared with existing composition vector and K-string methods by drawing phylogenetic trees. The results show that the proposed scheme performs better in comparison to existing methods.