Miracle-dz/UniFAR-FTUs huggingface dataset:
The Nothosaur Pachypleurosaurus and the Origin of Plesiosaurs

Description of Pachypleurosaurus edwardsi, from the middle Triassic of Italy and Switzerland, provides a basis for establishing the pattern of aquatic locomotion within the Nothosauria and for determining their relations with more primitive terrestrial reptiles and fully aquatic plesiosaurs. Judging by the proportions of the trunk, limbs and tail, nothosaurs, like modern crocodiles and marine iguanids, relied mainly on lateral undulation of the trunk and tail for aquatic propulsion. The rear limbs probably acted mainly as rudders. Differences in the structure of the pectoral girdles and forelimbs among nothosaurs and the elaboration of the coracoids suggest that the forelimbs were becoming important in propulsion, with emphasis on the back stroke. Pachypleurosaurus has the greatest degree of development of the anterior portion of the shoulder girdle, suggesting that the recovery stroke was of considerable importance. In this feature Pachypleurosaurus approaches the pattern seen in plesiosaurs. It is concluded that the transition between primitive terrestrial diapsids and plesiosaurs occurred via a succession of changes in patterns of aquatic locomotion. Early sauropterygians would have used almost exclusively the axial skeleton and its musculature in swimming. As in the majority of secondarily aquatic reptiles, stereotyped behaviour patterns of terrestrial locomotion would have rendered use of the forelimbs disadvantageous in the water, and they were progressively reduced to limit drag. The hind limbs were also reduced and initially functioned to control changes in depth and direction. The relations of the dermal and endochondral elements of the shoulder girdle in nothosaurs and plesiosaurs differ from those of the majority of early reptiles in having the scapulae superficial to the clavicles and the interclavicle superficial to the clavicles. This may be attributed to a redevelopment of the endochondral and dermal elements subsequent to a period of reduction associated with an early stage in aquatic adaptation. Nothosaurs and plesiosaurs are unique among secondarily aquatic diapsids in the emphasis on the forelimbs for propulsion. In plesiosaurs, both the fore and hind limbs are greatly enlarged and the significance of the tail for propulsion is much reduced. Both limbs may have served in a mode of swimming similar to that practised by the modern sea lions. Although individual vertebrae and bones of the limbs and girdles appear to show a transition from nothosaurs through primitive to advanced plesiosaurs, major differences in the proportions of the trunk, girdles and limbs clearly distinguish nothosaurs and plesiosaurs. This may be attributed to a marked reduction in the amount of lateral undulation of the trunk region and elaboration of the rear limbs as paddles in the immediate ancestors of plesiosaurs.
INCUBATION PERIOD AND SEX RATIO OF TESTUDO hermanni boettgeri

In many tortoise and turtle species the incubation temperature of the egg determines the sex of the hatchling. For Hermann's tortoises (T. hermanni) however, such data are fragmentary or unpublished. In this paper, duration of incubation of hatchlings from 312 eggs laid by a group of 10 female T. hermanni boettgeri are described. This incubation period did not vary linearly with incubation temperature but rather was independent of temperature in the range 29°C to 34°C, being ~57 days throughout. Incubation period changed abruptly to ~83 days for temperatures of 26°C with the transition range of temperatures lying between 26°C and 28°C. No significant correlation between incubation period and other environmental parameters could be detected. Sex ratios were also measured as a function of incubation temperature, with a sex ratio of 50% at a threshold temperature of 31.5°C and an abrupt change from virtually all males to all females over a narrow temperature range.
Effets biocides des alcaloïdes, des saponines et des flavonoïdes extraits de Capsicum frutescens L. (Solanaceae) sur Bemisia tabaci (Gennadius) (Homoptera : Aleyrodidae)

Dans la perspective d’elaborer une strategie de gestion integree des ravageurs associes aux cultures maraicheres au Maroc, l’activite biocide des alcaloides, des saponines et des flavonoides extraits des fruits de Capsicum frutescens L. sur la survie des œufs et des adultes de Bemisia tabaci infestant les plants de tomates, Lycopersicon esculentum Mill. var. Daniella, a ete etudiee en conditions controlees. Les alcaloides, saponines et flavonoides dissous dans de l’ethanol a 1 % ont ete appliques a 0, 5, 10 et 20 g.l-1. Par rapport aux temoins, les trois composes affectent significativement la survie des stades suivis, selon la concentration et la duree d’exposition. Pour les œufs, la mortalite corrigee s’echelonne de 35 % a 59 % pour les alcaloides, de 14 % a 31 % pour les saponines et de 10 % a 14 % pour les flavonoides. Chez les adultes, de 29 % a 86 %, de 14 % a 48 % et de 6 % a 29 % meurent intoxiques respectivement par les alcaloides, les saponines et les flavonoides. Oeufs et adultes repondent aux effets toxiques des composes testes lineairement dans le meme sens ; les œufs requierent cependant des concentrations plus elevees que les adultes, la CL50 est de 13,78 contre 6,83 g.l-1 pour les alcaloides, de 98,63 contre 32,28 g.l-1 pour les saponines et non toxique contre 120,65 g.l-1 pour les flavonoides. Ce sont les alcaloides qui se sont averes les plus toxiques par rapport aux saponines et aux flavonoides. Le TL50, estime pour les composes provoquant plus 50 % de morts, ne permet pas d’eviter l’inoculation du TYLCV par des adultes viruliferes. L’utilisation de ces composes en gestion integree des ravageurs associes aux cultures maraicheres merite d’etre approfondie.
In Vitro Effects of the Organochlorine Pesticide β-Hexachlorocyclohexane on Bovine Peripheral Blood Mononuclear Cells

The β-hexachlorocyclohexane (β-HCH) is a very stable and accumulable isomer of Lindane, a well known organochlorine pesticide. The HCHs were banned in all developed countries but to date high concern still exists for environment, animal and human health due to contaminated sites. In this study, several in vitro tests [cell viability (XTT), trypan blue exclusion (TBE), lactate dehydrogenase release (LDH) and bromodeoxyuridine (BrdU) incorporation assays] were performed to investigate the toxic effects of exposure to β- HCH (from 0.1 to 1000 μM) on bovine peripheral blood mononuclear cells (PBMCs). All the trials were performed incubating PBMCs for 2 and 7 days. At high concentrations (i.e. 1000 μM), the β-HCH approximately halved the number of living cells regardless the exposure time, significantly decreased the cell viability assessed by the XTT assay, and compromised the proliferation potential of PBMCs. At lower β-HCH exposure levels (0.1 to 100 μM), particularly after 7 days of exposure, a progressive decrease of cell viability has been observed. These adverse effects were significant at concentrations observed in the blood of cattle reared in polluted areas. The LDH results suggest that β-HCH does not clearly affect the integrity of the cell membrane in the range of exposure levels tested. All in all, these findings warn about the risk posed by the long-term exposure to β-HCH of farm animals reared in rural areas polluted by β-HCH. Further research is needed to deepen our knowledge about the mechanisms through which β-HCH affects the PBMCs functionality.
Production of extracellular alkaline protease from Bacillus subtilis RSKK96 with solid state fermentation

The production of extracellular alkaline protease by producing Bacillus subtilis RSKK96 was studied with solid state fermentation (SSF). Different agro residues as substrate were studied for enzyme production. The highest enzyme production was expressed with lentil husk as units per mass of dry substrate (3937.0 U/mg). Production parameters were optimized as incubation time 120 h, extraction medium Triton-X100 1%, initial moisture content 30%, initial pH 9.0. The high level of alkaline protease was obtained in the medium containing arabinose followed by lactose, galactose, and fructose. Among various nitrogen sources, beef extract was found to be the best inducer of alkaline protease, while other nitrogen sources repressed enzyme production. Among metal salts FeSO4.7H2O and MgSO4.7H2O was found to increase protease production. The maximum enzyme production (5759.2 U/mg) was observed with lentil husk in 1000 mL of fermentation medium volume.
The amount of time female pumas Puma concolor spend with their kittens

Abstract In the sport hunting of pumas Puma concolor, most states and provinces of the United States and Canada do not allow the killing of females with kittens. However, female pumas can be away from their kittens and, if detected by hunters at these times, can be mistakenly killed. To assess the extent to which females with kittens might mistakenly be killed we need to have estimates of the percent of time female pumas are with their kittens on a daily basis. Previous estimates range within 52-83%, but are based on simultaneous locations taken during the day when pumas are least active. To provide a more accurate assessment of the amount of time females spend with their young, we analyzed telemetry data collected over 24, 24-hour blocks for 15 females and their kittens. We collected data from June to September during 1989-1999 in southeastern Idaho and northwestern Utah. We found that females with 7-12 month-old kittens were within 200 m of their kittens an average 16.2±3.8% (N=12) of the time. These females were >1.0 km from their kittens 30.9±6.7% of the time. Three females with kittens in dens were near their dens 10.3, 12.2 and 2.3% of the time. Females were within 200 m of their kittens the least amount of time (5.1±2.1%, N=8) during 11:00-14:30 and the most amount of time during 23:00-01:30 (29.4±3.0, N=6) and 07:00–10:30 (23.2±3.1%). We conclude that the probability that a hunter would encounter a female without her kittens was >80%.
Combined effects of life‐history traits and human impact on extinction risk of freshwater megafauna

Megafauna species are intrinsically vulnerable to human impact. Freshwater megafauna (i.e., freshwater animals ≥30 kg, including fishes, mammals, reptiles, and amphibians) are subject to intensive and increasing threats. Thirty‐four species are listed as critically endangered on the International Union for Conservation of Nature (IUCN). Red List of Threatened Species, the assessments for which are an important basis for conservation actions but remain incomplete for 49 (24%) freshwater megafauna species. Consequently, the window of opportunity for protecting these species could be missed. Identifying the factors that predispose freshwater megafauna to extinction can help predict their extinction risk and facilitate more effective and proactive conservation actions. Thus, we collated 8 life‐history traits for 206 freshwater megafauna species. We used generalized linear mixed models to examine the relationships between extinction risk based on the IUCN Red List categories and the combined effect of multiple traits, as well as the effect of human impact on these relationships for 157 classified species. The most parsimonious model included human impact and traits related to species’ recovery potential including life span, age at maturity, and fecundity. Applying the most parsimonious model to 49 unclassified species predicted that 17 of them are threatened. Accounting for model predictions together with IUCN Red List assessments, 50% of all freshwater megafauna species are considered threatened. The Amazon and Yangtze basins emerged as global diversity hotspots of threatened freshwater megafauna, in addition to existing hotspots, including the Ganges‐Brahmaputra and Mekong basins and the Caspian Sea region. Assessment and monitoring of those species predicted to be threatened are needed, especially in the Amazon and Yangtze basins. Investigation of life‐history traits and trends in population and distribution, regulation of overexploitation, maintaining river connectivity, implementing protected areas focusing on freshwater ecosystems, and integrated basin management are required to protect threatened freshwater megafauna in diversity hotspots.
Association of Thyroid Peroxidase Gene polymorphisms and serum anti-TPO levels in Egyptian Patients with Autoimmune Hypothyroidism.

BACKGROUND Thyroid peroxidase (TPO) gene mutation leads to change in enzyme built structure result in the anti-TPO autoantibodies production that may cause thyroid destruction. AIM to evaluate the association of three single nucleotide polymorphisms (SNPs) of the TPO gene and anti TPO- levels in Egyptian patients with autoimmune hypothyroidism and correlate them with the disease severity. METHODS Two hundred patients with newly discovered autoimmune hypothyroidism were included in the study (100 with subclinical hypothyroidism and 100 of them with overt hypothyroidism) and100 healthy individuals as a control group were genotyped by PCR-REFLP. RESULTS The TT genotype of rs2071400 C/T and the T allele were significantly more frequent in patients with subclinical hypothyroidism and overt hypothyroidism than in control group. But there were no significant difference in the TT genotype and T allele between subclinical and overt hypothyroidism patient. As regards TPO rs732609 A/C polymorphism, the CC genotype of rs732609 A/C and the C allele were significantly increased in patients with subclinical hypothyroidism and overt hypothyroidism than in controls. There was significant difference in the CC genotype and C allele between subclinical and overt hypothyroidism patients. CONCLUSION We found an association of rs2071400 C/T and rs732609A/C polymorphisms with autoimmune hypothyroidism and correlated anti-TPO levels with different genotypes in hypothyroid patients. Also we found an association of rs732609A/C polymorphism with the disease severity.
Determination of Dose Rate of Florfenicol in Feed for Control of Mortality in Channel Catfish Ictalurus punctatus (Rafinesque) Infected with Edwardsiella ictaluri, Etiological Agent of Enteric Septicemia

–A dose titration study was conducted to determine the appropriate dosage of florfenicol in feed to control mortality in channel catfish Ictalurus punctatus associated with enteric septicemia of catfish caused by Edwardsiella ictaluri. Six tanks (20 fish/ tank) were assigned to each of the following treatment: 1) not challenged with E. ictaluri and fed unmedicated feed; 2) challenged with E. ictaluri and fed unmedicated feed; 3) challenged and fed 5-mg florfenicol/kg body weight (kg bw); 4) challenged and fed 10-mg florfenicol/kg bw; or 5) challenged and fed 15-mg florfenicol/kg bw. Treatment was initiated the day after inoculation, and feed was administered by hand at 2.5% body weight for 10 consecutive days. Feeding activity was scored for all groups and was noted to be significantly less than the challenged, unmedicated group. Cumulative mortality in the challenged untreated group was 60%. The mortality in the unchallenged untreated group was 0%, and in die 5-, 10-, 15-mg florfenicol/kg bw group was 2.5%, 0.8%, and 2.5%, respectively. The mortality in each challenged, treated group and the non-challenged control group was significantly less than the challenged, unmedicated controls (P < 0.0001 for each contrast). There were no pairwise statistically significant contrasts among the florfenicol treated groups and the non-challenged control group. All 600 fish in the study were necropsied, cultured for bacteria, and examined by gross pathology. No specific lesions that could be associated with the antibiotic were observed. The efficacy of the 10 mg/kg dosage was confirmed in a separate dose confirmation study. In this study, fish in 30 tanks (20 fish/ tank) were infected with E. icraluri by immersion. Two days post-inoculation, fish in 15 tanks were hand-fed unmedicated feed, and 15 tanks were hand-fed medicated feed at a dosage of 10-mg florfenicol/kg bw at 2.5% body weight for 10 d. Feeding activity was scored and was noted to be significantly less than the challenged, unmedicated group. Cumulative mortality in the florfenicol group (14%) was significantly less than cumulative mortality in the untreated group (87.3%) (P < 0.0001). All 600 fish were submitted for bacterial culture, necropsied. and examined for gross pathology, and once again, no specific lesions that could be associated with the antibiotic were observed. The minimum inhibitory concentration of florfenicol against E. ictaluri in both studies was 0.25 ug/mL. Florfenicol was palatable, safe, and efficacious for control of mortality due to infection by E. ictaluri in catfish.
Deep Physiological Model for Blood Glucose Prediction in T1DM Patients

Accurate estimations for the near future levels of blood glucose are crucial for Type 1 Diabetes Mellitus (T1DM) patients in order to be able to react on time and avoid hypo and hyper-glycemic episodes. Accurate predictions for blood glucose are the base for control algorithms in glucose regulating systems such as the artificial pancreas. Numerous research studies have already been conducted in order to provide predictions for blood glucose levels with particularities in the input signals and underlying models used. These models can be categorized into two major families: those based on tuning glucose physiological-metabolic models and those based on learning glucose evolution patterns based on machine learning techniques. This paper reviews the state of the art in blood glucose predictions for T1DM patients and proposes, implements, validates and compares a new hybrid model that decomposes a deep machine learning model in order to mimic the metabolic behavior of physiological blood glucose methods. The differential equations for carbohydrate and insulin absorption in physiological models are modeled using a Recurrent Neural Network (RNN) implemented using Long Short-Term Memory (LSTM) cells. The results show Root Mean Square Error (RMSE) values under 5 mg/dL for simulated patients and under 10 mg/dL for real patients.
Network analysis of barley seed flows in Tigray, Ethiopia: supporting the design of strategies that contribute to on-farm management of plant genetic resources

For maintaining food security and livelihood, farmers in marginal areas of production environments make use of high levels of crop genetic diversity. The exchange of seed and varieties among villagers, and also the relative isolation of local varieties in their production environments, contributes to the continued existence of locally adapted genotypes. In Tigray, one of the major barley-growing regions of Ethiopia, local varieties and local seed systems are dominant. The annual barley seed requirement is met with seed produced, saved and exchanged by farmers. In order to understand the flows of seed and varieties within and between villages, a study was conducted using a survey to gather information from 130 respondents in seven villages. Seed network analysis was used as an analytical tool to assess flows of seed and varieties and to identify farmers who play different roles in the seed system. Within the major seed exchange network, nodal or connector farmers linked seed subnetworks. The flow within villages was much more dominant than beyond. Rare varieties appeared to be sourced from farms that maintain a broad variety portfolio. Varieties seemed to disseminate informally across farms, in their target environments, following participatory varietal selection. The methodology of social seed network analysis proved to be a powerful tool for monitoring seed and variety flows. Furthermore, it identified farmers as critical partners in the conservation and on-farm management of plant genetic resources, recognized the role of plant breeders in participatory varietal selection and that of seed experts, engaged in strengthening local seed supply and in disseminating quality seed of superior varieties.
Ultra-structural study of the indomethacin-induced apoptosis and autophagy in rat gastric parietal cells

ABSTRACT Background and aim of the work Indomethacin (IND), a non-steroidal anti-inflammatory drug, can induce gastric mucosal ulcerations. To date, the ultra-structural changes in the parietal cells (PCs) of the gastric mucosa following the intake of IND are mostly unknown. We carried out the current investigation to get insights into this issue. Materials and methods We established an animal model consisting of 35 adult male Sprague Dawley rats. The animals were divided into three groups, including; control (normal feeding), fasting, and indomethacin-treated groups. After treatment of 18-h fasting rats with IND, they were sacrificed at 3, 6, and 12-h intervals. The morphological features, including the apoptotic, and autophagic changes in the gastric mucosa PCs were examined using transmission electron microscopy. Results In normal feeding animals (control group), the gastric PCs were present in various stages of activity. Fasting was associated with the predominance of the inactive parietal cells with features of up-regulated autophagy. In the IND -treated animals (at 3-h interval), PCs showed prominent autophagic changes, and subtle apoptotic cell death. In the IND -treated animals (at 6–12-h interval), PCs showed prominent apoptotic changes, and subtle autophagic features. Conclusions Our study indicates that IND treatment could induce gastropathy through time-dependent alterations in the autophagic and apoptotic machinery of PCs. Further studies are needed to examine the underlying molecular mechanisms.
Time-varying natural mortality in fisheries stock assessment models: identifying a default approach

Center for the Advancement of Population Assessment Methodology, 8901 La Jolla ShoresDrive,La Jolla, CA 92037, USA*Corresponding author: tel: +1 206 543 4270; fax: +1 206 685 7471; e-mail: kfjohns@uw.eduJohnson,K.F. ,Monnahan,C.C. ,McGilliard,C.R. ,Vert-pre,K.A. ,Anderson,S.C. ,Cunningham,C.J.,Hurtado-Ferro,F. ,Licandeo,R.R. ,Muradian,M.L. ,Ono,K. ,Szuwalski,C.S. ,Valero,J.L. ,Whitten,A.R. ,andPunt,A.E. Time-varyingnaturalmortalityinﬁsheriesstockassessmentmodels:identifyingadefaultapproach. – ICESJournalofMarineScience,doi:10.1093/icesjms/fsu055.Received4 September 2013; revised 1 March 2014; accepted 3 March 2014.A typical assumption used in most ﬁshery stock assessments is that natural mortality (M) is constant across time and age. However, M is rarelyconstant in reality as a result of the combined impacts of exploitation history, predation, environmental factors, and physiological trade-offs. Misspeciﬁcation or poor estimation of M can lead to bias in quantities estimated using stock assessment methods, potentially resulting inbiasedestimatesofﬁsheryreferencepointsandcatchlimits,withthemagnitudeofbiasbeinginﬂuencedbylifehistoryandtrendsinﬁshingmor-tality. Monte Carlo simulations were used to evaluate the ability of statistical age-structured population models to estimate spawning-stockbiomass,ﬁshingmortality,andtotalallowablecatchwhenthetrueMwasage-invariant,buttime-varying. Conﬁgurationsofthestockassessmentmethod,implementedinStockSynthesis,includedasingleage-andtime-invariantMparameter,speciﬁedatoneofthethreelevels(high,medium,andlow)oranestimatedM.Themin–max(i.e.mostrobust)approachtospecifyingMwhenitisthoughttovaryacrosstimewastoestimateM.The least robust approach for most scenarios examined was to ﬁx M at a high value, suggesting that the consequences of misspecifying M areasymmetric.Keywords: model misspeciﬁcation, natural mortality,population models, reference points, simulation, Stock Synthesis, time-varying.