Miracle-dz/UniFAR-FTUs huggingface dataset:
Implementing ecological intensification in fish farming: definition and principles from contrasting experiences

Ecological intensification is a new concept in agriculture that addresses the double challenge of maintaining a level of production sufficient to support needs of human populations and respecting the environment in order to conserve the natural world and human quality of life. This article adapts this concept to fish farming using agroecological principles and the ecosystem services framework. The method was developed from the study of published literature and applications at four study sites chosen for their differences in production intensity: polyculture ponds in France, integrated pig and pond polyculture in Brazil, the culture of striped catfish in Indonesia and a recirculating salmon aquaculture system in France. The study of stakeholders' perceptions of ecosystem services combined with environmental assessment through Life Cycle Assessment and Emergy accounting allowed development of an assessment tool that was used as a basis for co-building evolution scenarios. From this experience, ecological intensifica-tion of aquaculture was defined as the use of ecological processes and functions to increase productivity, strengthen ecosystem services and decrease disservices. It is based on aquaecosystem and biodiversity management and the use of local and traditional knowledge. Expected consequences for farming systems consist of greater autonomy, efficiency and better integration into their surrounding territories. Ecological intensification requires territorial governance and helps improve it from a sustainable development perspective.
Use of orange by-products (dry peel) as an alternative gelling agent for marmalade production: Evaluation of antioxidant activity and inhibition of HMF formation during different storage temperature

In this study, dry orange peel was added to an orange marmalade as an alternative for pectin. The product stability and the antioxidant effect on shelf life of this enriched marmalade were evaluated. In particular, the hydroxymethylfurfural formation in correlation with major bioactive compounds, antioxidant assay, total phenols and anthocyans were estimated during storage at 20 and 35 °C for 150 days. The level of phenols ranged from 73.65 to 147.67 mg/100 g for control samples and from 110.09–157.32 mg/100 g for enriched samples. The initial HMF content was 0.09 mg/100 g for the control marmalade and 0.16 mg/100 g for enriched samples and during storage, the level increased. Obtained data show that incorporation of orange peel in marmalade production can be a valid use of this by-product. After storage, the enriched samples at 20 °C maintained the analytical parameters better than the samples stored at 35 °C. Practical applications The citrus fruit residues, which are usually discarded as waste can be used as nutraceutical resources. The utilization of these bioactive rich citrus residues can serve for the production of novel products or for the improvement of those already in use. Orange peel contains significant amounts of phenolic compounds especially phenolic acids and flavonoids, thus we can consider it a potential material for the formulation of nutraceuticals and food preservatives and may be used as a possible functional ingredient in alimentary products such as marmalade.
Diversity of arboreal ants in a Brazilian tropical dry forest: effects of seasonality and successional stage.

In tropical systems, habitat heterogeneity and resource availability have been reported as important factors driving ant species richness and composition. For this reason, these variables have been widely used as indicators of forest disturbance. The aim of this study was to compare the composition and richness of arboreal ants between the dry and wet seasons in three successional stages of a tropical dry forest at the Parque Estadual da Mata Seca, northern Minas Gerais state, Brazil. Ant sampling was performed in 15 plots in three different forest secondary stages: early, intermediate and late. Ants were sampled during the wet and dry seasons, using five pitfall traps per plot. We collected 43 ant species, distributed in 19 genera. Our results indicated a change on ant species composition along the successional gradient (p 0.05) and was not affected by the variables used here as surrogates to habitat heterogeneity (tree richness) and resource availability (tree density) (p > 0.05). Ant composition did not change significantly between the dry and wet seasons for the early successional stage, but plots from the intermediate and late stages were clearly segregated according to seasons. We suggest that 1 Departamento de Biologia Geral, Universidade Estadual de Montes Claros, Montes Claros-Minas Gerais, Brazil, Campus Darcy Ribeiro, 39401-089, frederico.neves@unimontes.br 2 Ecologia Evolutiva & Biodiversidade/DBG, CP 486, ICB/Universidade Federal de Minas Gerais, 30161 970 Belo Horizonte Minas Gerais, Brazil. rodrigo.fagundes@yahoo.com. br 3 Departamento de Biologia, Setor Ecologia, Universidade Federal de Lavras, Campus Universitario, CP 3037, 37200-000, Lavras, Minas Gerais, Brazil. 4 Laboratorio de Mirmecologia, Convenio CEPEC/UESC, Centro de Pesquisa do Cacau, CEPLAC, 45.600-000 Itabuna, Bahia, Brazil, jacques.delabie@gmail.com 5 Earth and Atmospheric Sciences Department, University of Alberta, Edmonton, Alberta, Canada T6G 2E3 1 2 Sociobiology Vol. 56, No. 1, 2010 it is likely that 25 years of forest regeneration are enough to restore most of the arboreal ant communities in tropical dry forests, strengthening the importance of secondary habitats to biodiversity maintenance. Key-words: habitat heterogeneity, resource availability, secondary succession, species richness, species composition.
Evaluation of Cyto‐genotoxicity of Perfluorooctane Sulfonate (PFOS) to Allium cepa

Per‐ and polyfluoroalkyl substances (PFAS) have emerged as contaminants of global concern. Among several PFAS, perfluorooctanoic acid (PFOA) and perfluorooctane sulfonate (PFOS) are persistent and bioaccumulative compounds. We investigated the cyto‐genotoxic potential of PFOS to Allium cepa root meristem cells. The A. cepa root tips were exposed to 6 different concentrations (1–100 mg L−1) of PFOS for 48 h. Reduction in mitotic index and chromosomal aberrations was measured as genotoxic endpoints in meristematic root cells. Exposure to PFOS significantly affected cell division by reducing the miotic index at higher concentrations (>10 mg L−1). The median effect concentration of PFOS to elicit cytotoxicity based on the mitotic index was 43.2 mg L−1. Exposure to PFOS significantly increased chromosomal aberrations at concentrations >25 mg L−1. The common aberrations were micronuclei, vagrant cells, and multipolar anaphase. The alkaline comet assay revealed a genotoxic potential of PFOS with increased tail DNA percentage at concentrations >25 mg L−1. To our knowledge, this is the first study to report the cyto‐genotoxic potential of PFOS in higher plants. Environ Toxicol Chem 2021;40:792–798. © 2020 SETAC
Arterial Steal to the Penumbra Area in Patients with Acute MCA Occlusion: A Quantitative Angiographic Analysis

Purpose In acute middle cerebral artery (MCA) occlusion, collateral vessels provide retrograde supply to the occluded territory. We hypothesized that such collateral flow reduces perfusion of the non-occluded donor region (steal effect). Materials and Methods Patients with an MCA occlusion with opacification of both ipsi- and contralateral anterior cerebral arteries (ACA) on angiography prior to endovascular treatment were selected. Arteriovenous transit time (AVTT) for both ACA territories was compared for different grades of collateral supply to the MCA territory. In addition, the influence of diabetes and hypertension was analyzed. After successful revascularization, AVTT was re-assessed to determine reversibility. Results Forty-one patients were analyzed. An AVTT of 8.6 seconds (standard deviation [SD] 2.4 seconds) was seen in the ACA territory of the affected hemisphere in comparison to 6.6 seconds (SD 2.1 seconds) for the contralateral side (P<0.001). A more prolonged (but not significant) AVTT was seen in cases with a higher collateral grade. No difference in AVTT was seen in patients with diabetes or hypertension. After successful MCA revascularization, AVTT delay was 7.4 seconds (SD 2.1 seconds). Conclusion A cerebral steal effect occurs in patients with an acute MCA occlusion, probably related to augmented flow to the penumbra area.
Automated Hippocampal Subfield Volumetric Analyses in Atypical Alzheimer's Disease.

BACKGROUND Posterior cortical atrophy (PCA) and logopenic progressive aphasia (LPA) are two of the most common variants of atypical Alzheimer's disease (AD). Both PCA and LPA are associated with relative sparing of hippocampus compared to neocortex, although hippocampal atrophy is observed. It is unclear whether regional patterns of hippocampal subfield involvement differ between PCA and LPA, and whether they differ from typical AD. OBJECTIVE To assess volume of specific subfields of the hippocampus in PCA, LPA, and typical AD. METHODS Fifty-nine patients with PCA and 77 patients with LPA were recruited and underwent T1-weighted MRI and Pittsburgh Compound B (PiB) PET at Mayo Clinic. Thirty-six probable AD patients and 100 controls were identified from the Alzheimer's Disease Neuroimaging Initiative. Hippocampal subfield volumes were calculated using Freesurfer, and volumes were compared between PCA, LPA, AD, and controls using Kruskal-Wallis and Dunn tests. RESULTS The LPA and PCA groups both showed the most striking abnormalities in CA4, presubiculum, molecular layer of the hippocampus, molecular and granule cell layers of the dentate gyrus, and the hippocampal-amygdala transition area, although atrophy was left-sided in LPA. PCA showed smaller volume of right presubiculum compared to LPA, with trends for smaller volumes of right parasubiculum and fimbria. LPA showed a trend for smaller volumes of left CA1 compared to PCA. The AD group showed smaller volumes of the right subiculum, CA1, and presubiculum compared to LPA. CONCLUSION Patterns of hippocampal subfield atrophy differ across the different syndromic variants of AD.
The role of Bacteroides Host Factor A in CTnDOT integration and Holliday junction resolution

CTnDOT is a conjugative transposon found in Bacteroides species. It encodes multiple antibiotic resistances and is stimulated to transfer by exposure to tetracycline. CTnDOT integration into the host chromosome requires IntDOT and a previously unknown host factor. We have identified a protein, designated BHFa (Bacteroides host factor A), that participates in integrative recombination. BHFa is the first host factor identified for a site-specific recombination reaction in the CTnDOT family of integrative and conjugative elements. Based on the amino acid sequence of BHFa, the ability to bind specifically to 4 sites in the attDOT DNA, and its activity in the integration reaction, BHFa is a member of the IHF/HU family of nucleoid-associated proteins. Other DNA bending proteins that bind DNA nonspecifically can substitute for BHFa in the integration reaction.
Learning in non‐avian reptiles 40 years on: advances and promising new directions

Recently, there has been a surge in cognition research using non‐avian reptile systems. As a diverse group of animals, non‐avian reptiles [turtles, the tuatara, crocodylians, and squamates (lizards, snakes and amphisbaenids)] are good model systems for answering questions related to cognitive ecology, from the role of the environment on the brain, behaviour and learning, to how social and life‐history factors correlate with learning ability. Furthermore, given their variable social structure and degree of sociality, studies on reptiles have shown that group living is not a pre‐condition for social learning. Past research has demonstrated that non‐avian reptiles are capable of more than just instinctive reactions and basic cognition. Despite their ability to provide answers to fundamental questions in cognitive ecology, and a growing literature, there have been no recent systematic syntheses of research in this group. Here, we systematically, and comprehensively review studies on reptile learning. We identify 92 new studies investigating learning in reptiles not included in previous reviews on this topic – affording a unique opportunity to provide a more in‐depth synthesis of existing work, its taxonomic distribution, the types of cognitive domains tested and methodologies that have been used. Our review therefore provides a major update on our current state of knowledge and ties the collective evidence together under nine umbrella research areas: (i) habituation of behaviour, (ii) animal training through conditioning, (iii) avoiding aversive stimuli, (iv) spatial learning and memory, (v) learning during foraging, (vi) quality and quantity discrimination, (vii) responding to change, (viii) solving novel problems, and (ix) social learning. Importantly, we identify knowledge gaps and propose themes which offer important future research opportunities including how cognitive ability might influence fitness and survival, testing cognition in ecologically relevant situations, comparing cognition in invasive and non‐invasive populations of species, and social learning. To move the field forward, it will be immensely important to build upon the descriptive approach of testing whether a species can learn a task with experimental studies elucidating causal reasons for cognitive variation within and among species. With the appropriate methodology, this young but rapidly growing field of research should advance greatly in the coming years providing significant opportunities for addressing general questions in cognitive ecology and beyond.
Chemical short-range order in derivative Cr-Ta-Ti-V-W high entropy alloys from the first-principles thermodynamic study.

The development of high-entropy alloys (HEAs) focuses on exploring compositional regions in multi-component systems with all alloy elements in equal or near-equal atomic concentrations. Initially it was based on the main idea that high mixing configurational entropy contributions to the alloy free energy could promote the formation of a single solid solution phase. By using the ab-initio based Cluster Expansion (CE) Hamiltonian model constructed for the quinary bcc Cr-Ta-Ti-V-W system in combination with Monte Carlo (MC) simulations, we show that the phase stability and chemical short-range order (SRO) of the equiatomic quinary and five sub-quaternary systems, as well as their derivative alloys, can dramatically change the order-disorder transition temperatures (ODTT) as a function of alloy compositions. In particular, it has been found, that the equiatomic quaternary Ta-Ti-V-W and Cr-Ta-Ti-W alloys had the lowest order-disorder transition temperature (500 K) among all the analysed equiatomic compositions. In all investigated alloy systems, the strongest chemical ordering has been observed between Cr and V, which led to the conclusion that decreasing the concentration of either Cr or V might be beneficial in terms of decreasing the ODTT. It also predicts that increasing concentration of Ti significantly decreases the ODTT. Our analysis of chemical SRO as a function of alloy composition allows to understand the microstructure evolution of HEAs as a function of temperature in excellent agreement with available experimental observations. Importantly, our free energy of mixing and SRO calculations predict that the origin of precipitates formed by Cr- and V-rich in the sub-quaternary Cr-Ta-V-W system is driven by the thermodynamics. The modelling results are in an excellent agreement with experimental observation of Cr and V segregation in the W0.38Ta0. 36Cr0.15V0. 11 alloy which in turns shows an exceptional radiation resistance.
Neurobiological Investigations of Dimensionally Conceptualized Personality Pathology: Mapping a Way Forward for the Clinical Neuroscience of Personality Disorders.

Despite significant efforts, relatively limited progress has been made in attempts to fully understand the links between personality dysfunction and neurobiology. A growing consensus, buttressed by a reliable empirical literature, is that advancement has been impeded by a reliance on the categorical classification of personality disorders (PDs) as described by earlier versions of the Diagnostic and Statistical Manual of Mental Disorders (DSM) and the International Statistical Classification of Diseases and Related Health Problems (ICD) rather than an inherent limitation in the endeavor. As described briefly below, and demonstrated through the series of articles included in this special section of the Journal of Personality Disorders, dimensional models of personality pathology offer a promising strategy for addressing these challenges and accelerating the clinical neuroscience of personality disorders.
Evaluation of fresh semen quality and predicting the number of frozen semen doses in Jaffrabadi buffalo bull

Scientific information on frozen semen characteristics of Jaffrabadi buffaloes (Bubalis bubalis) is scanty and centre to this research is to evaluate frozen semen characteristics in Jaffrabadi buffalo bulls. The study included six buffalo bulls with average age 95.83±5.47 months and average body weight of 834.16±47.63 kg maintained at Cattle Breeding Farm, Junagadh Agricultural University, Junagadh. A total of 206 ejaculates were collected during the period of study. Ejaculates collected from the six Jaffrabadi buffalo bulls were clean, dense to very dense (D = 67.2%, DD = 32.8%) and milky white (72.5%) to creamy (27.5%) in colour. During this observatory study average (Mean±SE) semen parameter like, ejaculatory volume, mass activity, sperm concentration, initial progressive sperm motility and total sperm number per ejaculate were 5.11±0.17 ml, +3.43±0.04, 838.30±25.74×106 /ml, 79.41±0.60% and 4053.99±150.56×106 spermatozoa, respectively. Average dilution rate in 0.5 ml medium straw (40 million sperm/straw) was found to be ideal at 10.48±0.32 ml. In a year expected number of ejaculates that could be frozen from the 6 bulls was 34.34±6.43 and correspondingly, the expected number of frozen doses produced from bulls could be 3546.46±540.30 numbers.
External Validation of the Long Short-Term Memory Artificial Neural Network-Based SCaP Survival Calculator for Prediction of Prostate Cancer Survival

Purpose Decision-making for treatment of newly diagnosed prostate cancer (PCa) is complex due to the multiple initial treatment modalities available. We aimed to externally validate the SCaP (Severance Study Group of Prostate Cancer) Survival Calculator that incorporates a long short-term memory artificial neural network (ANN) model to estimate survival outcomes of PCa according to initial treatment modality. Materials and Methods The validation cohort consisted of clinicopathological data of 4,415 patients diagnosed with biopsy-proven PCa between April 2005 and November 2018 at three institutions. Area under the curves (AUCs) and time-to-event calibration plots were utilized to determine the predictive accuracies of the SCaP Survival Calculator in terms of progression to castration-resistant PCa (CRPC)–free survival, cancer-specific survival (CSS), and overall survival (OS). Results Excellent discrimination was observed for CRPC-free survival, CSS, and OS outcomes, with AUCs of 0.962, 0.944, and 0.884 for 5-year outcomes and 0.959, 0.928, and 0.854 for 10-year outcomes, respectively. The AUC values were higher for all survival endpoints compared to those of the development cohort. Calibration plots showed that predicted probabilities of 5-year survival endpoints had concordance comparable to those of the observed frequencies. However, calibration performances declined for 10-year predictions with an overall underestimation. Conclusion The SCaP Survival Calculator is a reliable and useful tool for determining the optimal initial treatment modality and for guiding survival predictions for patients with newly diagnosed PCa. Further modifications in the ANN model incorporating cases with more extended follow-up periods are warranted to improve the ANN model for long-term predictions.
Comparative effects of angiotensin II on the contractility of muscularis mucosae and detrusor in the pig urinary bladder

To explore contractile actions of angiotensin II (ATII) on the muscularis mucosae (MM) of the bladder, ATII‐induced contractions were compared between MM and the detrusor smooth muscle (DSM) of the pig bladder by isometric tension recordings. Effects of ATII on spontaneous Ca2+ transients in MM were visualized using Cal‐520 fluorescence. ATII receptor type 1 (ATR1) expression in MM and DSM was also examined by immunohistochemistry. ATII (1 nM–1 μM) caused phasic contractions of MM in a concentration‐dependent manner, while ATII (10 nM–10 μM) had no or marginal effects on DSM contractility. ATII (100 nM)‐induced MM contractions had an amplitude of approximately 70% of carbachol (1 μM)‐induced or 90% of U46619 (100 nM)‐induced contractions. Candesartan (10 nM), an ATR1 blocker, prevented the contractile effects of ATII (1 nM) in MM, while ATR1 immunofluorescence was greater in MM than DSM. ATII (10–100 pM) increased the frequency but not the amplitude of spontaneous Ca2+ transients in MM. Both urothelium‐intact and ‐denuded MM strips developed comparable spontaneous phasic contractions, but ATII, carbachol and U46619‐induced contractions were significantly larger in urothelium‐denuded than urothelium‐intact MM strips. In conclusion, the MM appears to have a much greater sensitivity to ATII compared with DSM that could well sense circulating ATII, suggesting that MM may be the predominant target of contractile actions induced by ATII in the bladder while the urothelium appears to inhibit MM contractility.
A comparative whole genome analysis of Helicobacter pylori from a human dense South Asian setting

Helicobacter pylori, a Gram‐negative bacterium, is associated with a wide range of gastric diseases such as gastritis, duodenal ulcer, and gastric cancer. The prevalence of H pylori and risk of disease vary in different parts of the world based on the prevailing bacterial lineage. Here, we present a contextual and comparative genomics analysis of 20 clinical isolates of H pylori from patients in Bangladesh. Despite a uniform host ethnicity (Bengali), isolates were classified as being part of the HpAsia2 (50%) or HpEurope (50%) population. Out of twenty isolates, eighteen isolates were cagA positive, with two HpEurope isolates being cagA negative, three EPIYA motif patterns (AB, AB‐C, and ABC‐C) were observed among the cagA‐positive isolates. Three vacA genotypes were observed with the s1m1i1dic1 genotype observed in 75% of isolates; the s1m2i1d1c2 and s2m2i2d2c2 genotypes were found to be 15% and 10% of isolates, respectively. The non‐virulent genotypes s2m2i2d2c2 was only observed in HpEurope population isolates. Genotypic analysis of oipA gene, present in all isolates, revealed five different patterns of the CT repeat; all HpAsia2 isolates were in “ON” while 20% of HpEurope isolates were genotypically “OFF. ” The three blood group antigen binding adhesins encoded genes (bab genes) examined and we observed that the most common genotype was (babA/babB/‐) found in eight isolates, notably six were HpAsia2 isolates. The babA gene was found in all HpAsia2 isolates but present in only half of the HpEurope isolates. In silico antibiotic susceptibility analysis revealed that 40% of the strains were multi‐drug resistant. Mutations associated with resistance to metronidazole, fluoroquinolone, and clarithromycin were detected 90%, 45%, and 5%, respectively, in H pylori strain. In conclusion, it is evident that two populations of H pylori with similar antibiotic profiles are predominant in Bangladesh, and it appears that genotypically the HpAisa2 isolates are potentially more virulent than the HpEurope isolates.