Miracle-dz/UniFAR-FTUs huggingface dataset:
Freakish patterns - species and species concepts in apomicts

Apomict groups keep challenging taxonomists, in classifications as well as in more fundamental question about the nature of apomictic species. The latter question is not just an academic one, because the outcome influences practical decisions on biodiversity and conservation. A historical overview over the species problem shows that a period of confusion and proliferation of species concepts between 1940 and 1990 was followed by an increasing consensus at the end of the 20th century that the species category is heterogeneous. Species come in kinds, which is understandable in light of their different evolutional histories. Recently, Wilkins stated that we do not need a generally applicable species concept, because species are not an a priori category into which all biological organisms must fit, but salient phenomena that are to be explained. Not only biparental, but also asexual organisms often form such species-as-phenomena, explained as some combination of adaptation to an ecological niche and reproductive compatibility. The above is illustrated by historical and current studies in three well-studied apomict groups, viz. Ranunculus cassubicus agg. , Rubus subgen. Rubus and Hieracium (subgen. Hieracium and Pilosella). Species in the Ranunculus cassubicus aggregate are the few existing sexuals, which are surrounded by a hybrid swarm of only partial apomictic forms, whereas in Rubus subgen. Rubus and Hieracium s.s. sexuals as well as numerous apomicts form well defined species. How species should be circumscribed in Pilosella is yet to be clarified. Largely, the differences between these groups can be contributed to their different modes of apomixis and the associated retained sexuality. From this review it is clear that the question is not so much ‘What is a species? ‘, but ‘What is a species in this particular group? ‘ To answer this question a thorough knowledge and understanding of the biology of the genus in question is required.
Simulation of digestion in cattle fed sugarcane: model development

SUMMARY A dynamic model of digestion and absorption of nutrients in cattle fed sugarcane-based diets is described. There are 11 rumen state variables, and four zero pools representing absorbed nutrients. The rumen state variables represent nitrogen, carbohydrate, long chain fatty acid, microbial and volatile fatty acid pools. The zero pools relate to absorbed amino acids, glucose, long chain fatty acids, and volatile fatty acids. The flux equations are described by mass-action and Michaelis-Menten forms. Wherever possible, data derived from trials with cattle fed sugarcane-based diets were used to parameterize the model. Sensitivity analyses revealed that stability and behaviour of the model was generally satisfactory. The model was most sensitive to changes in fractional passage and substratehydrolysis rates and to the microbial maintenance requirement. Within the limited information available for comparison, the simulations agreed with observations of fibre flows and ammonia and volatile fatty acid concentrations in rumen fluid. Duodenal non-ammonia nitrogen flow was consistently underpredicted and reasons for this underprediction are suggested.
Fostering STEAM education using computers and information technologies

The academic world is witnessing the new opportunities offered by information and computer technologies for STEAM education (Science, Technology, Engineering, Arts and Mathematics). These STEAM subjects, studied in integrated form, are considered essential in the education of citizens of a modern society. This paper addresses the development and support of STEAM education that our research team has carried out in recent years in different educational environments that include engineering studies, training of future teachers, primary and secondary education, and outreach to society. We will describe a set of activities that promote STEAM education, including courses (face-to-face courses, online courses, and MOOC courses), and scientific and informative conferences. We make use a set of applications of information and computing technologies in the creation and delivery of courses and conferences that include programming languages (ie Matlab, WolframAlpha - Computational Intelligent, Snap and Scratch), learning platforms (Moodle, MiriadaX), resources / tools to interact with the student (motivate face-to-face sessions, e.g. Socrative, video conferences and online tutorials e.g. Blackboard Collaborate, remote desktop connection, and website portals, among other resources). This paper presents real cases carried out in university educational centers, and in primary and secondary schools. These are examples that show cases of integration of computer science, engineering and education in which information and computer technologies are used to promote STEAM education.
GENETIC CONTROL OF TEST-DAY MILK YIELD IN SAHIWAL CATTLE

Heritabilities of test-day (TD) and 305-day milk yield were estimated using performance records of 780 first lactation Sahiwal cows, following two models. In the first model, estimated 305-day lactation milk yields were analyzed through an individual animal model with period-season of calving as fixed effect and additive genetic effect as random factor. The second model was a repeatability model where monthly milk yield records were analyzed using period-season of calving as fixed effect and additive genetic effect and permanent environmental effect as random factors. The age at calving, ratio of days in milk to 305-day (as linear and quadratic components) and their reciprocal logs were used as covariables. The heritability estimates for 305-day and TD milk yields were 0.082 and 0.024, respectively. Heritability estimates of individual TDs ranged from 0 to 0.274. The relative proportion of permanent environment variance to total variance was 0.498. Heritability of individual test-day milk yield was highest in the mid-lactation (TD6TD8). Lower genetic control of test day and lactation milk yield in the present study needs validation using larger data sets with accurate pedigree recording.
W-net: A Network Structure for Automatic Segmentation of Organs at Risk in Thorax Computed Tomography

Accurate segmentation of Organs at Risk (OAR) on Computed Tomography (CT) images is a crucial step in radiotherapy treatment planning. In this paper, we propose a novel W-Net structure combining a U-Net segmentation network and an adversarial network (GAN) to reconstruct the OAR. With the reconstruction loss, W-Net can better learn effective features and get more accuracy segmentation result than U-Net. We test our method in the SegTHOR challenge which focus on 4 thoracic OAR: esophagus, heart, trachea and aorta. The average Dice Similarity Coefficient (%) of W-Net and U-Net on these 4 OAR are 80.6 versus 79.6, 93.8 versus 93.4, 88.3 versus 88.1, and 91.5 versus 90.6. The Hausdorff Distance (HD) are 0.5905 versus 0.6923, 0.2055 versus 0.2215, 0.7162 versus 0.7374, and 0.8061 versus 0.9290.
Bacillus subtilis α-Phosphoglucomutase Is Required for Normal Cell Morphology and Biofilm Formation

ABSTRACT Mutations designated gtaC and gtaE that affect α-phosphoglucomutase activity required for interconversion of glucose 6-phosphate and α-glucose 1-phosphate were mapped to the Bacillus subtilis pgcA (yhxB) gene. Backcrossing of the two mutations into the 168 reference strain was accompanied by impaired α-phosphoglucomutase activity in the soluble cell extract fraction, altered colony and cell morphology, and resistance to phages φ29 and ρ11. Altered cell morphology, reversible by additional magnesium ions, may be correlated with a deficiency in the membrane glycolipid. The deficiency in biofilm formation in gtaC and gtaE mutants may be attributed to an inability to synthesize UDP-glucose, an important intermediate in a number of cell envelope biosynthetic processes.
UndersTAndinG smALL-sCALe disTUrbAnCes in GUAy AnA's mon TAne ForesTs: GAp CHArACTeriZATion in THe sierrA de LemA, VeneZUeLA

Summary This case study describes the structure of gaps in a montane forest in Sierra de Lema, Bolivar State, Venezuela. The sizes of the gaps were measured in the forest canopy (canopy gaps) and at ground level (extended gaps), and the corresponding micro habitats assessed. The trees involved in the formation of gaps were recorded, and their basal areas and volumes calculated. a distinction was made between gap makers and those trees that were brought down by gap makers. The mode of fall was record ed for all fallen trees. The main gap formation mode was the up rooting of trees, bringing about multiple tree-falls. The gap sizes observed (canopy gaps: 31-896m², extended gaps: 83-1235m²) were 30-90% larger than those reported for most tropical forests. Gap formation resulted in a loss to the basal area and volume of the stand of ~5.8 and ~0.5%, respectively. Canopy gaps occupied 1.4% of the forest area, which is in the range reported for tropi cal forests. The microhabitat ‘undisturbed ground’ accounted for the largest area within the gaps. The predominance of uproot ing as a cause of gap formation in the forests of the Sierra de Lema was probably due to the superficial rooting of the trees. The larger gap area is explained by the frequent occurrence of multiple tree-falls. From the large gap sizes and the high pro portion of undisturbed ground in the gaps, high survival rates of advanced regeneration, and of numerous new maidens of pioneer species, might reasonably be expected.
Epigenetic regulation of lytic and latent herpes simplex virus 1 infection

Epigenetic regulation plays a major role in whether the herpes simplex virus 1 (HSV-1) will initiate viral gene expression and lytic infection or instead suppress its gene expression and establish a latent infection. Prior to this study, it was known that cells respond to naked DNA by assembling chromatin to silence foreign genetic material. However, during lytic infection of epithelial cells, viral proteins VP16 and ICP0 have been implicated in limiting chromatin association and promoting euchromatic histone modifications on the HSV-1 genome. We hypothesized that the viral genome would also be subject to silencing by heterochromatin modification during lytic infection. To test this we examined the association of chromatin and heterochromatic modifications during lytic infection with WT viruses and ICP0-null mutant viruses. We found that heterochromatin modifications H3K9me3 and H3K27me3 associate initially with all viruses, but were removed rapidly during infection with WT HSV-1. ICP0-null viruses were not able to remove histones or heterochromatin, indicating a role for ICP0 in reversing epigenetic silencing. In latent infection, HSV-1 undergoes epigenetic silencing as a means to suppress gene expression and persist in neurons. Surprisingly, in this study, we find that ICP0null viruses accumulate less heterochromatin on lytic gene promoters relative to WT
Effects of Substance P and Vasoactive Intestinal Polypeptide on Gastrointestinal Blood Flow in the Atlantic Cod Gadus Morhua

The cardiovascular effects of vasoactive intestinal polypeptide (VIP) and substance P (SP) in vivo were studied in the Atlantic cod Gadus morhua . Special interest was focused on the distribution of blood to the gastrointestinal circulation. VIP increased the blood flow to the gut by increasing cardiac output and by decreasing resistance in the vascular bed supplied by the coeliac artery. In addition, VIP had an inhibitory effect on spontaneous stomach motility. SP induced a triphasic response in the coeliac artery blood flow. An initial increase was followed by a rapid decrease, to the control level or below, and a second increase in flow. The triphasic response was not changed after vagotomy, while atropine blocked the second phase, the decrease, indicating that a local cholinergic mechanism is involved. The significance of this temporary decrease in flow remains to be elucidated. SP also caused an increase in cardiac output and in mesenteric artery blood flow. In addition to the increase in cardiac output, the increase in gastrointestinal blood flow produced by SP is accomplished by a decreased resistance in the coeliac and mesenteric vascular beds.
Combining Crop Growth Modeling With Trait-Assisted Prediction Improved the Prediction of Genotype by Environment Interactions

Plant breeders evaluate their selection candidates in multi-environment trials to estimate their performance in contrasted environments. The number of genotype/environment combinations that can be evaluated is strongly constrained by phenotyping costs and by the necessity to limit the evaluation to a few years. Genomic prediction models taking the genotype by environment interactions (GEI) into account can help breeders identify combination of (possibly unphenotyped) genotypes and target environments optimizing the traits under selection. We propose a new prediction approach in which a secondary trait available on both the calibration and the test sets is introduced as an environment specific covariate in the prediction model (trait-assisted prediction, TAP). The originality of this approach is that the phenotyping of the test set for the secondary trait is replaced by crop-growth model (CGM) predictions. So there is no need to sow and phenotype the test set in each environment which is a clear advantage over the classical trait-assisted prediction models. The interest of this approach, called CGM-TAP, is highest if the secondary trait is easy to predict with CGM and strongly related to the target trait in each environment (and thus capturing GEI). We tested CGM-TAP on bread wheat with heading date as secondary trait and grain yield as target trait. Simple CGM-TAP model with a linear effect of heading date resulted in high predictive abilities in three prediction scenarios (sparse testing, or prediction of new genotypes or of new environments). It increased predictive abilities of all reference GEI models, even those involving sophisticated environmental covariates.
Nanotechnology in Chronic Pain Relief

Increasing awareness of chronic pain due to both injury and disease have encouraged drug companies and pharmaceutical researchers alike to design and fabricate better, more specific drugs for pain relief. However, overuse of clinically available pain medication has caused a multitude of negative repercussions, including drug tolerance, addiction, and other severe side effects, which can prolong suffering and reduce pain mediation. Applications of nanotechnology to the field of drug delivery has sought to enhance the treatment efficiency, lower side effects, and mitigate the formation of tolerance. The use of nanomaterials has several advantages for chronic pain relief, such as controlled release, prolonged circulation time, and limited side effects. With the development of nanotechnology, strategies for chronic pain relief have also bourgeoned utilizing a variety of nanomaterials and targeting surface modifications. In addition to using these materials as carriers for drug delivery, nanomaterials can also be designed to have inherent properties that relieve chronic pain. This minireview covers the current status of designed nanomaterials for pain relief and provides a discussion of future considerations for nanotechnology designed for relieving chronic pain.
Taxonomy of Cardamine amara (Cruciferae) in the Iberian Peninsula

Summary Lihova, J., Marhold, K. & Neuffer, B. : Taxonomy of Cardamine amara (Cruciferae) in the Iberian Peninsula. – Taxon 49: 747–763. 2000. – ISSN 0040-0262. Cardamine amara is represented in the Iberian Peninsula by two subspecies: the diploid (2n = 16) subsp. pyrenaea, occurring in the Eastern Pyrenees, and the tetraploid (2n = 32) subsp. olotensis, concentrated at the lower altitudes in Catalonia, N and NE of Barcelona. Morphometric analysis of populations of these taxa and four other subspecies of C. amara, which occur in other parts of Europe, supported their subspecific distinctness. RAPD (Random Amplified Polymorphic DNA) analysis of a ll six European subspecies of C. amara provided more evidence supporting this taxonomic treatment. Lectotypes were designated for the following names: C. amara var. parviflora Cadevall, C. amara subsp. pyrenaea Sennen, C. amara subsp. siifolia Sennen, and C. amporitana Sennen & Pau.
Compartmentalization: A Conceptual Framework for Understanding How Trees Grow and Defend Themselves

The purpose of this chapter is to describe a conceptual framework for understanding how trees grow and how they and other perennial plants defend themselves. The concept of compartmentalization has developed over many years, a synthesis of ideas from a number of investigators. It is derived from detailed studies of the gross morphology and cellular anatomy of the wood and bark of roots and stems in healthy angiosperms and gymnosperms. It is based on research in tree physiology and the chemistry of wood and bark. It is founded on observations of trees injured in the field by wind, snow, ice, fire, animals, and insects, as well as during pruning, coppicing, sugaring, and other forest and orchard management practices. It is based on experimental studies of natural and artificial wounds with and without controlled inoculations with selected pathogenic and saprophytic microorganisms. These microbes have included wood-decaying Basidiomycetes and Ascomycetes, wood-staining Ascomycetes and Fungi Imperfecti, canker fungi, and a myriad of woodinhabiting bacteria. The end result of all these studies is an integrating concept that involves defenses laid down by trees prior to injury and defenses laid down by trees after injury.
Breeding for Resistance Against Some of the Major Insects of Cowpea and Pigeon Pea

Pigeon pea (Cajanus cajan L. Millsp.) and cowpea (Vigna unguiculata L. Walp) are the major grain legumes grown in the semi-arid areas of Kenya. Heavy losses in grain yield occur due to their vulnerability to a large number of insect pests in the field as well as damage by weevil during storage. Aphids, thrips, pod-borers and pod-sucking bugs are common insect pests to both pigeon pea and cowpea. Pod fly mostly attacks pigeon pea, and apion beetle is a serious pest of cowpea. Use of chemical control in the semi-arid areas is expensive and beyond the reach of the small-scale farmers. Work on development of less susceptible or tolerant crop varieties has been initiated at the National Dryland Farming Research Station (NDFRS) at Katumani. Results of preliminary screening against major insect pests are reported in this paper.The sources of resistance against aphids and thrips in cowpea, were received from the International Institute of Tropical Agriculture (UTA), Nigeria, and information on their reaction to these insects under field conditions has been discussed. In pigeon pea, resistance against pod-sucking bug, which appear to be of the antibiosis type, has been identified in the early maturing group of the local germplasm. Implications of breeding for insect resistance and pest management in the two crops are discussed. RésuméLe pois cajan (Cajanus cajan L. Millsp.) et le niébé (Vigna unguiculata L. Walp) sont les principales légumineuses à grains cultivées dans les régions semi-arides du Kenya. Elles subissent de lourdes pertes en grains en raison de leur vulnérabilité aux attaques d’un grand nombre d’insectes, aussi bien en plein champs que durant le stockage. Parmi les insectes communs au niébé et au pois cajan il faut signaler des aphides, des thrips, des foreurs et des punaises des gousses. La mouche de gousses attaque principalement le pois cajan, et l’apion est un ennemi sérieux du niébé. De par son coût élevé, n’est pas à la portée du petit paysan.Des travaux sur le développement de variétés moins susceptibles ou tolérantes aux principaux insectes ont été commencés au National Dryland Farming Research Station (NDFRS) à Katumani. Le présent article porte sur les résultats obtenus au cours des essais préliminaires. Le matériel ayant servi aux études de résistance contre les aphides et les thrips du niébé a été obtenu de l’IITA au Nigéria; le comportement de ce matériel vis-à-vis de ces insectes est discuté. Chez le pois cajan, la résistance à la punaise des gousses semble être du type antibiose et elle a été identifiée dans le groupe précoce des variétés locales. Les implications de la sélection de ces cultures pour la résistance et l’aménagement des ravageurs sont discutées.
EXPERIMENTS ON THE COLONIZATION OF POTATO PLANTS BY APTEROUS AND BY ALATE APHIDS IN RELATION TO THE SPREAD OF VIRUS DISEASES

Batches of potato plants in pots were placed in the field for limited periods among plants infected with potato virus Y and leaf roll virus. Some of the potted plants were surrounded by sticky boards which prevented apterous aphids from reaching them. Almost as many plants within the boards as without became infected, indicating that most of the spread of virus was by winged aphids. Apterae were probably responsible for spreading the viruses throughout a hill after one or more stems were infected. They may carry infection to neighbouring plants, but most of these will have been infected already by alatae. The number of plants contracting infection was unaffected by watering.
Depletion of ATP Limits Membrane Excitability of Skeletal Muscle by Increasing Both ClC1-Open Probability and Membrane Conductance

Activation of skeletal muscle contractions require that action potentials can be excited and propagated along the muscle fibers. Recent studies have revealed that muscle fiber excitability is regulated during repeated firing of action potentials by cellular signaling systems that control the function of ion channel that determine the resting membrane conductance (Gm). In fast-twitch muscle, prolonged firing of action potentials triggers a marked increase in Gm, reducing muscle fiber excitability and causing action potential failure. Both ClC-1 and KATP ion channels contribute to this Gm rise, but the exact molecular regulation underlying their activation remains unclear. Studies in expression systems have revealed that ClC-1 is able to bind adenosine nucleotides, and that low adenosine nucleotide levels result in ClC-1 activation. In three series of experiments, this study aimed to explore whether ClC-1 is also regulated by adenosine nucleotides in native skeletal muscle fibers, and whether the adenosine nucleotide sensitivity of ClC-1 could explain the rise in Gm muscle fibers during prolonged action potential firing. First, whole cell patch clamping of mouse muscle fibers demonstrated that ClC-1 activation shifted in the hyperpolarized direction when clamping pipette solution contained 0 mM ATP compared with 5 mM ATP. Second, three-electrode Gm measurement during muscle fiber stimulation showed that glycolysis inhibition, with 2-deoxy-glucose or iodoacetate, resulted in an accelerated and rapid >400% Gm rise during short periods of repeated action potential firing in both fast-twitch and slow-twitch rat, and in human muscle fibers. Moreover, ClC-1 inhibition with 9-anthracenecarboxylic acid resulted in either an absence or blunted Gm rise during action potential firing in human muscle fibers. Third, Gm measurement during repeated action potential firing in muscle fibers from a murine McArdle disease model suggest that the rise in Gm was accelerated in a subset of fibers. Together, these results are compatible with ClC-1 function being regulated by the level of adenosine nucleotides in native tissue, and that the channel operates as a sensor of skeletal muscle metabolic state, limiting muscle excitability when energy status is low.