Miracle-dz/UniFAR-FTUs huggingface dataset:
Perceptual spatial suppression and sensitivity for motion are weakened in schizophrenia

Perceptual spatial suppression is a phenomenon in which the perceived strength of a stimulus in some region of the space is reduced when the stimulus is surrounded by other stimuli. For contrast perception, several studies suggest that spatial suppression is reduced in patients with schizophrenia. For motion perception, only one study has been conducted in a cohort of 16 patients, suggesting that spatial suppression is reduced. It is unknown, however, whether this reduction is related to the lower intelligence quotient (IQ) that schizophrenic patients usually show; as there is evidence that spatial suppression for motion increases with IQ in healthy individuals. Here, we sought to determine the spatial suppression for motion in a larger cohort of 32 patients with schizophrenia and controlling the results for the IQ of patients. We found a weakened spatial suppression in patients with schizophrenia, consistent with the previous study (effect size g = 0.47 with CI = [0.055, 0.88], combining the previous and our study). For comparison, we performed a meta-analysis on spatial suppression for contrast (7 studies) and found a similar effect size, but with higher evidence (g = 0.56 with CI = [0.40, 0.72]). We found that patients had a lower IQ than controls, but this difference did not explain their weaker spatial suppression. Further, we found that spatial suppression of patients, but not controls increased with their IQ and decreased with age in both groups. Finally, as we estimated lapses of attention, we could estimate motion sensitivity and found that it was decreased in patients. We discuss how this reduced spatial suppression and sensitivity might be related to glutamatergic hypofunction in schizophrenia.
Movements, habitat use, and entrainment of stocked juvenile lake sturgeon in a hydroelectric reservoir system

Identifying movement and habitat use patterns is essential for fish passage efforts and the conservation of threatened species. We used acoustic telemetry to track the movements of 44 juvenile lake sturgeon (Acipenser fulvescens) throughout Kleber Reservoir in northern Michigan. On average, lake sturgeon moved 502 m between telemetry positions, with age-2 lake sturgeon moving longer distances than age-1 lake sturgeon. Areas with high numbers of lake sturgeon detections were clustered near the forebay, while zones with low numbers of detections were clustered toward the head of the reservoir. Analyses showed that 66.4% of the variance in habitat use could be explained by physical habitat features. Reservoir areas with ample deepwater habitat, fine soft substrates, and limited macrophyte vegetation were the most frequently occupied and, thus, may provide suitable habitat conditions to support juvenile lake sturgeon. We observed that 54.4% of the age-1 and 52.8% of the age-2 lake sturgeon stocked into Kleber Reservoir were entrained. Reservoir size, morphology, and the location of suitable habitat in relation to hydroelectric infrastructure may be key factors that affect entrainment rates.
Nutritive effect of dust on microbial biodiversity and productivity of the Arabian Gulf

The Arabian Gulf is exposed to intensive dust storms during summer until early winter. We investigated the nutritive effect of the dust on microbial biodiversity of the water column and the productivity of the Gulf. We collected samples from three sites in a transect perpendicular to the shore in March (before the strong dust storms) and in October (after the dust season) in 2013. At the three sites, we sampled the water column at three depths, and see-floor sediments using a HAPS corer. We also sampled the sand dunes that are the source of the dust. We analyzed the samples for pigments, microbial community composition using a 16S rRNA analysis, and nutrients. Our results showed that species richness and biodiversity were higher in October than in March. The relative abundances of key-player microorganisms were strongly pronounced in October. We assume that the dust rapidly sinks to the seafloor where the nutrients Fe and P are liberated through iron reduction. Assuming that all phosphate diffusing from the seafloor originates from the dust particles after deposition, we estimated a contribution of minimum 30,000 tons of fish produced every year in the Gulf. We found no close temporal coupling between dust storms and productivity. This is because nutrient liberation from the seafloor is slow and its transport from the seafloor to the photic zone by circulation processes is irregular. This study highlights the importance of dust as a source of nutrients in the Gulf ecosystem.
Integrated population model reveals that kestrels breeding in nest boxes operate as a source population

2122 –––––––––––––––––––––––––––––––––––––––– © 2019 The Authors. Ecography published by John Wiley & Sons on behalf of Nordic Society Oikos This is an open access article under the terms of the Creative Commons Attribution License, which permits use, distribution and reproduction in any medium, provided the original work is properly cited. Subject Editor: Jean-Michel Gaillard Editor-in-Chief: Miguel Araújo Accepted 22 August 2019 42: 2122–2131, 2019 doi: 10.1111/ecog.04559 doi: 10.1111/ecog.04559 42 2122–2131
Astyanax paranae (Characiformes, Characidae) da Bacia do Alto Rio Paranaíba: estudos multidisciplinares e conservação da espécie

xi 1-INTRODUÇÃO. 1 1.1) Astyanax paranae: hábito de vida e distribuição. 1 1.2) A Bacia do Paraná e do rio Paranaíba. 2 1.3) Astyanax paranae: diversidade genética e filogenia. 3 1.4) Marcadores moleculares: genes mitocondriais – Citocromo Oxidase b. 5 1.5 ) Morfometria geométrica. 6 2-OBJETIVOS. 7 2.1) Objetivo geral. 7 2.2) Objetivos específicos. 7 3-MATERIAIS E MÉTODOS. 7 3.1) Área de estudo. 7 3.2) Coleta e eutanásia dos indivíduos. 10 3.3) Coleta de tecido e obtenção de DNA dos indivíduos. 10 3.4) Reação em Cadeia da Polimerase PCR e análises moleculares. 10 3.5) Morfometria Geométrica. 12 4-RESULTADOS. 13 4.1) Análises moleculares referente ao gene cyt b. 13 4.2) Análises morfológicas. 17
The effects of β-amyloid on the metabolome of SH-SY5Y cells as a model for the first steps in Alzheimer's disease

11 Declaration. 12 Copyright Statement . 13 Acknowledgements . 14 Chapter 1: Introduction . 15 1.1 Alzheimer’s disease (AD) . 15 1.1.1 History of Dementia and AD . 16 1.1.2 Types of AD and Genetics . 19 1.1.3 AD presentation . 20 1.1. 4 Normal anatomy of the brain and how this is affected in AD . 21 1.1. 5 Pathogenesis of AD . 22 1.1. 6 Amyloid formation . 22 1.1. 7 The role of β-Amyloid in AD . 25 1.1. 8 Clearance of Aβ . 27 1.1. 9 Tau protein and AD . 29 1.1.10 Amyloid cascade hypothesis . 30 1.2 Metabolomics . 32 1.2. 1 Metabolic approaches . 34 1.2. 2 Experimental design, sampling and sample preparation . 36 1.2. 3 Metabolomic analytical techniques and their applications . 37 1.2. 4 Fourier Transform Infrared (FT-IR) Spectroscopy . 40 1.2. 4.1 Benefits, drawbacks and applications of FT-IR spectroscopy . 41 1.2. 5 Mass spectrometry (MS) . 43 1.2. 5.1 Gas Chromatography – Mass Spectrometry (GC-MS) . 44 1.2. 5.2 Liquid Chromatography Mass Spectrometry (LC-MS) . 46 1.2. 5.3 LC-MS vs GC-MS . 48 1.2. 6 Data analysis and interpretation (Chemometrics) . 48 1.2. 6.1 Unsupervised learning . 49 1.2. 6.2 Supervised learning . 50 1.2. 6.3 Model validation . 50 1.3 Importance of metabolomics studies for AD . 51
The complete chloroplast genome sequence of Vitis yeshanensis strain ‘SJTU004’

Abstract This study first released the complete chloroplast genome of Vitis yeshanensis. The circular genome was 161,188 bp in length, composed of a large single-copy region (LSC, 161,100–89,334 bp) and a small single-copy region (SSC, 115,689–134,745 bp), separated by two inverted repeat regions (IRA, 89,335–115,688 bp; IRB, 134,746–161,099 bp). The genome encoded 134 genes, containing 88 protein-coding genes (PCGs), 38 tRNA genes, and 8 rRNA genes. The phylogenetic tree showed a close relationship between V. yeshanensis and V. amurensis.
Characterization of the genetic structure of the brown trout (Salmo trutta) from “Braduljica” fish farm, Serbia

Due to the ecological concerns and preservation of genetic resources, the characterization of genetic structure of the brown trout (Salmo trutta) was carried out on the "Braduljica" fish farm. DNA was isolated from fin clips of 10 individuals, and after that molecular PCR-RFLP methods were used for distinguishing between Atlantic and Danubian lineages based on control region of the mitochondrial DNA (CR mtDNA) and lactate dehydrogenase gene of the nuclear DNA (LDH nDNA). Based on phenotypic characteristics it was estimated that out of 10 individuals included in this study five belonged to the allochtonous Atlantic lineage and remaining five belonged to the native Danubian lineage of brown trout. However, results of molecular analyses showed a high percentage of allochthonous genes among the individuals, which confirms the hybridization between these two lineages. Also, the results showed that the selection based on the phenotype is not adequate. In order to continue with proper broodstock management, it is necessary to eliminate allochtonous individuals of the Atlantic lineage from the broodstock.
Rotational grazing approaches reduces external and internal parasite loads in cattle

We tested whether holistic planned grazing (HPG) and four-camp grazing (FCG) rotational grazing approaches influence beef cattle parasites counts compared with continuous, season-long (SLG) grazing. We expected that parasite counts would increase linearly with increasing camp occupancy by cattle from 1 d (70-camp, HPG) to 21–28 d (four-camp, FCG) to 180 d (one-camp per season, SLG). Tick and faecal egg counts were observed across seasons on 30 steers raised on a private farm in Cedarville, South Africa. Tick species identified were Rhipicephalus evertsi evertsi, Rhipicephalus (Boophilus) decoloratus, Hyalomma spp. and Amblyomma hebreaum with respective prevalences of 32%, 29%, 20% and 19%. Unidentified roundworms had the highest faecal worm egg counts (81.2%) followed by Coccidia (16.4%), Nematodirus (1.2%) and strongyles (1.2%). Overall, prevalence and mean counts for ticks and faecal worm eggs were highest in the hot wet season, with the SLG having greater (P ≤ 0.05) values than either of the rotational approaches. However, increasing camp number and animal densities above four camps did not reduce (P > 0.05) parasite loads compared with HPG. Current results suggest that rotational grazing is a potential strategy to reduce livestock losses caused by high tick and worm loads in cattle, especially in the hot wet season.
South and Central America Cut Flower Production and Postharvest Survey

Imports of cut flowers into the United States have doubled in the last 20 years and come mainly from Colombia and Ecuador. We surveyed the cut flower industry in South and Central America, focusing on Colombia and Ecuador, to determine their production and postharvest problems. We received a total of 51 responses, of which 62% of the respondents had 100 or more employees. The most commonly grown or handled crops were rose (Rosa hybrids), carnation (Dianthus caryophyllus), chrysanthemum (Chrysanthemum ×grandiflorum), alstroemeria (Alstroemeria cultivars), gerbera (Gerbera jamesonii), and hydrangea (Hydrangea species), in order of ranking. The most significant production problem was insect management, with disease management and crop timing the next most important issues. The most important species-specific issues in production were phytosanitary problems, disease (causal organism not specified), leaf miner (Lepidoptera, Symphyta, or Diptera), and thrips (Thysanoptera). The main overall postharvest problem was temperature management, followed by hydration and flower food management and botrytis (Botrytis cinerea). In regard to on-farm postharvest handling, damage to the flowers was the most mentioned issue. For the postharvest during storage and transport phase, temperature management, air transport, damage, and botrytis were the most important problems. The most mentioned customer complaints were damage, botrytis, and phytosanitary problems. The results of this survey can be used by researchers to focus their work on topics of most need. Improved production and postharvest handling will support the continued growth of the cut flower industry.
Choosing the optimal population for a genome-wide association study: a simulation using whole-genome sequences from rice

A genome-wide association study (GWAS) needs to have a suitable population. The factors that affect a GWAS, e.g. population structure, sample size, and sequence analysis and field testing costs, need to be considered. Mixture populations containing subpopulations of different genetic backgrounds may be suitable populations. We conducted simulation experiments to see if a population with high genetic diversity, e.g., a diversity panel, should be added to a target population, especially when the target population harbors small genetic diversity. The target population was 112 accessions of Oryza sativa subsp. japonica, mainly developed in Japan. We combined the target population with three populations that had higher genetic diversities. These were 100 indica accessions, 100 japonica accessions, and 100 accessions with various genetic backgrounds. The results showed that the GWAS power with a mixture population was generally higher than with a separate population. Also, the GWAS optimal population varied depending on the fixation index FST of the quantitative trait nucleotide (QTN) and its polymorphism of QTN in each population. When a QTN is polymorphic in a target population, a target population combined with a higher diversity population improves the QTN detection power. Investigating FST and the expected heterozygosity He as factors influencing the detection power, we showed that SNPs with high FST or low He are less likely to be detected by GWAS with mixture populations. Sequenced/genotyped germplasm collections can improve the GWAS detection power by using a subset of them with a target population. Core ideas (3-5 impact statements, 85 char max for each) - Genome-wide association studies with mixture populations are expected to improve the detection power of novel genes due to the increase of the sample size although the influence of population structure is a concern. - When a quantitative trait nucleotide (QTN) is polymorphic in a target population, a combination of the target population and a population with higher diversity than the target population improves the detection power of the QTN. - We found that the fixation index (FST) and the expected heterozygosity (He) were strongly related to the detection power of QTNs. - Germplasm collections which have been already sequenced/genotyped are useful for improving the detection power of GWAS without any addition of sequence costs by using a subset of them with a target population.
Sleep Promotes Downward Firing Rate Homeostasis

Homeostatic plasticity is hypothesized to regulate neuronal activity around a stable set point to compensate for learning-related plasticity. This regulation is predicted to be bidirectional but only upward firing rate homeostasis (FRH) has been demonstrated in vivo. We combined chronic electrophysiology in freely behaving animals with a protocol that induces robust plasticity in primary visual cortex (V1) to induce downward FRH and show that neurons bidirectionally regulate firing rates around an individual set point. Downward FRH did not require N-methyl-D-aspartate receptor (NMDAR) signaling and was associated with homeostatic scaling down of synaptic strengths. Like upward FRH, downward FRH was gated by vigilance state, but in the opposite direction: it occurred during sleep and not during wake. In contrast, FR changes associated with Hebbian plasticity happened independently of sleep and wake. Thus, we find that sleep’s impact on neuronal plasticity depends on the particular forms of plasticity that are engaged.
Drought Superimposes the Positive Effect of Silver Fir on Water Relations of European Beech in Mature Forest Stands

Research Highlights: Investigations of evapotranspiration in a mature mixed beech-fir forest stand do not indicate higher resilience towards intensified drying-wetting cycles as compared with pure beech stands. Background and Objectives: Forest management seeks to implement adaptive measures, for example, the introduction of more drought resistant species into prevailing monospecific stands to minimize forest mortality and monetary losses. In Central Europe this includes the introduction of native silver fir (Abies alba) into monospecific beech (Fagus sylvatica) stands. In order to determine, if the introduction of fir would improve the resilience against drier conditions, this study investigates water relations of a mature pure beech and a mature mixed beech-fir stand under natural as well as reduced water availability. Materials and Methods: Sap flow rates and densities were measured in two consecutive years using the heat ratio method and scaled using stand inventory data and modeling. Results: Transpiration rates estimated from sap flow were significantly higher for beech trees as compared with silver fir which was attributed to the more anisohydric water-use strategy of the beech trees. We estimate that stand evapotranspiration was slightly higher for mixed stands due to higher interception losses from the mixed stand during times of above average water supply. When precipitation was restricted, beech was not able to support its transpiration demands, and therefore there was reduced sap flow rates in the mixed, as well as in the pure stand, whereas transpiration of fir was largely unaffected, likely due to its more isohydric behavior toward water use and access to moister soil layers. Thus, we found the rates of evapotranspiration in the mixed beech-fir stand to be smaller during times with no precipitation as compared with the pure beech stand, which was accountable to the severely reduced transpiration of beech in the mixed stand. Conclusions: We conclude that smaller evapotranspiration rates in the mixed beech-fir stand might not be the result of increased water use efficiency but rather caused by restricted hydraulic conductivity of the root system of beech, making mixed beech-fir stands at this site less resilient towards drought.
Transient Reprogramming of Neonatal Cardiomyocytes to a Proliferative Dedifferentiated State

Zebrafish and urodele amphibians are capable of extraordinary myocardial regeneration thanks to the ability of their cardiomyocytes to undergo transient dedifferentiation and proliferation. Somatic cells can be temporarily reprogrammed to a proliferative, dedifferentiated state through transient expression of Oct3/4, Sox2, Klf4 and c-Myc (OSKM) transcription factors. Here, we utilized an OSKM-encoding non-integrating vector to induce transient reprogramming of mammalian cardiomyocytes in vitro. Reprogramming factor expression in neonatal rat cardiomyocytes triggered rapid cell dedifferentiation characterized by downregulation of cardiomyocyte specific gene and protein expression, sarcomere dis-assembly and loss of autorhythmic contractile activity. Concomitantly, a significant increase in cell cycle related gene expression and Ki67 positive cells was observed, indicating that dedifferentiated cardiomyocytes possess an enhanced proliferative capacity. A small proportion of cardiomyocytes progressed through mesenchymal to epithelial transition, further indicating the initiation of cell reprogramming. However, complete reprogramming to a pluripotent-like state was not achieved for the duration of the study (20 days), both in standard and embryonic stem cell culture media conditions. The transient nature of this partial reprogramming response was confirmed as cardiomyocyte-specific cell morphology, gene expression and contractile activity were recovered by day 15 after viral transduction. Further investigations into the complete downstream biological effects of ectopic OSKM expression in cardiomyocytes and the fate of these reprogrammed cells are warranted. Our results to date suggest that transient reprogramming could be a feasible strategy to recapitulate regenerative mechanisms of lower vertebrates and inform direct gene therapy approaches to cardiac regenerative medicine.
Characterization of novel regulators for heat stress tolerance in tomato from Indian sub-continent

The footprint of tomato cultivation, a cool region crop that exhibits heat stress (HS) sensitivity, is increasing in the tropics/sub-tropics. Knowledge of novel regulatory hot-spots from varieties growing in the Indian sub-continent climatic zones could be vital for developing HS-resilient crops. Comparative transcriptome-wide signatures of a tolerant (CLN1621L) and sensitive (CA4) cultivar-pair short-listed from a pool of varieties exhibiting variable thermo-sensitivity using physiological, survival and yield-related traits revealed redundant to cultivar-specific HS-regulation with more up-regulated genes for CLN1621L than CA4. The anatgonisiticly-expressing genes include enzymes; have roles in plant defense and response to different abiotic stresses. Functional characterization of three antagonistic genes by overexpression and TRV-VIGS silencing established Solyc09g014280 (Acylsugar acyltransferase) and Solyc07g056570 (Notabilis), that are up-regulated in tolerant cultivar, as positive regulators of HS-tolerance and Solyc03g020030 (Pin-II proteinase inhibitor), that is down-regulated in CLN1621L, as negative regulator of thermotolerance. Transcriptional assessment of promoters of these genes by SNPs in stress-responsive cis-elements and promoter swapping experiments in opposite cultivar background showed inherent cultivar-specific orchestration of transcription factors in regulating transcription. Moreover, overexpression of three ethylene response transcription factors (ERF.C1/F4/F5) also improved HS-tolerance in tomato. This study identifies several novel HS-tolerance genes and provides proof of their utility in tomato-thermotolerance. Highlight Novel heat stress regulatory pathways uncovered by comparative transcriptome profiling between contrasting tomato cultivars from Indian sub-continent for improving thermotolerance. (20/30)