Miracle-dz/UniFAR-FTUs huggingface dataset:
Chemogenetic inhibition in the dorsal striatum reveals regional specificity of direct and indirect pathway control of action sequencing

Animals engage in intricate action sequences that are constructed during instrumental learning. There is broad consensus that the basal ganglia play a crucial role in the formation and fluid performance of action sequences. To investigate the role of the basal ganglia direct and indirect pathways in action sequencing, we virally expressed Cre-dependent Gi-DREADDs in either the dorsomedial (DMS) or dorsolateral (DLS) striatum during and/or after action sequence learning in D1 and D2 Cre rats. Action sequence performance in D1 Cre rats was slowed down early in training when DREADDs were activated in the DMS, but sped up when activated in the DLS. Acquisition of the reinforced sequence was hindered when DREADDs were activated in the DLS of D2 Cre rats. Outcome devaluation tests conducted after training revealed that the goal-directed control of action sequence rates was immune to chemogenetic inhibition—rats suppressed the rate of sequence performance when rewards were devalued. Sequence initiation latencies were generally sensitive to outcome devaluation, except in the case where DREADD activation was removed in D2 Cre rats that previously experienced DREADD activation in the DMS during training. Sequence completion latencies were generally not sensitive to outcome devaluation, except in the case where D1 Cre rats experienced DREADD activation in the DMS during training and test. Collectively, these results suggest that the indirect pathway originating from the DLS is part of a circuit involved in the effective reinforcement of action sequences, while the direct and indirect pathways originating from the DMS contribute to the goal-directed control of sequence completion and initiation, respectively.
Inhibitory Effects of Gynura procumbens Ethanolic Extract on Nitric Oxide Production and Inducible Nitric Oxide Synthase (iNOS) Protein Expression in Macrophages

Nitric oxide (NO) overproduction by inducible nitric oxide synthase (iNOS) may be associated with acute and chronic inflammations. Macrophages as important cells in the innate immune system are able to be stimulated and can lead to iNOS activation and excessive NO production. Gynura procumbens is a medicinal plant traditionally used in treating various ailments including inflammation but the mechanism of anti-inflammatory activity of this plant is still elusive. This study was carried out to investigate the anti-inflammatory therapeutic effects of Gynura procumbens ethanolic extract on NO production and iNOS protein expression in RAW 264.7 macrophages stimulated with lipopolysaccharide (LPS). Cell viability of RAW 264.7 macrophages treated with Gynura procumbens ethanolic extract was determined by MTT assay. NO production was determined by Griess assay following Gynura procumbens ethanolic extract treatment alone or in combination with LPS stimulation. Protein expression of iNOS was determined by western blot. RAW 264.7 macrophages viability of more than 90% was observed after 24 h treatment with Gynura procumbens ethanolic extract concentration range of 3.9 μg/mL to 500 μg/mL. Significant inhibition of NO production level has been identified in LPS-stimulated RAW 264.7 cells pre-treated with 250 μg/mL Gynura procumbens ethanolic extract (p<0.05) while all selected concentrations of Gynura procumbens ethanolic extract showed no significant alteration of NO production in the absence of LPS stimulation. Pre-treatment of 250 μg/mL Gynura procumbens ethanolic extract also demonstrated significant suppression of iNOS protein expression in LPS-stimulated RAW 264.7 cells (p<0.05). In conclusion, this study demonstrates that Gynura procumbens ethanolic extract exhibits anti-inflammatory potential through inhibition of NO production and iNOS protein expression in LPS-stimulated macrophages, suggesting that this plant could be further researched for its beneficial use in inflammatory disorders.
The Birds of Africa. Volume 1

This is the first of four volumes; when complete the series will be a valuable addition to the ornithological literature. Nearly all species are illustrated in full colour with coverage of age, sex and seasonal differences. In the book's 536 pages resident birds are described in full detail while visitors are also given extensive coverage. The illustrations, by Martin Woodcock and Peter Hayman, are a large-format version of the standard field-guide style; but a field-guide it will never be—the four volumes together will weigh over eight kilogrammes.
Antimicrobial Activities of Desert Truffle Extracts and Their Chemical Identification

: Desert truffles are edible mushrooms and they belong to groupe of ascomycetes. In Algeria, we find them in arid and semiarid area. They are represented by two most genuses: Tirmania (white terfez) and Terfezia (red terfez). The aim of our work is to present extraction technics of the bioactive substances from gleba (ascoms) of Tirmania pinoyi (Maire) Malençon and from the culture filtrate of mycelium of Terfezia claveryi Chatin. Also, we present antifungal and antibacterial activity of these substances in vitro and their identification. There is antifungal activity of different extracts on solid medium, in vitro , against species of Aspergillus , Fusarium , Gliocladium , Candida . Also, there is antibacterial activity against species of Staphylococus , Streptococcus , Bacillus , Enterococcus , Escherichia , and Salmonella . Results show that extracts inhibition varies according to microbial tested species. Bioactive substances of the different extracts were analyzed by GC (gas chromatography)-mass, RMN (Nuclear Magnetic Resonance) and infrared in order to determine the chemical identity. Results show that these substances contain pyrazines and cyclic compounds like quinones.
Plant hormone profiling in developing seeds of common wheat (Triticum aestivum L.)

This study examined contents of nine plant hormones in developing seeds of field-grown wheat varieties (Triticum aestivum L.) with different seed dormancy using liquid chromatography—mass spectrometry. The varieties showed marked diversity in germination indices at 15°C and 20°C. Contents of the respective hormones in seeds showed a characteristic pattern during seed maturation from 30-day post anthesis to 60-day post anthesis. Principal component analysis and hierarchical clustering analysis revealed that plant hormone profiles were not correlated with dormancy levels, indicating that hormone contents were not associated with preharvest sprouting (PHS) susceptibility. Indole acetic acid (IAA) contents of mature seeds showed positive correlation with the germination index, but no other hormone. Response of embryo-half seeds to exogenous abscisic acid (ABA) indicates that ABA sensitivity is correlated with whole-seed germinability, which can be explained in part by genotypes of MOTHER OF FT AND TFL (MFT) allele modulating ABA signaling of wheat seeds. These results demonstrate that variation in wheat seed dormancy is attributable to ABA sensitivity of mature seeds, but not to ABA contents in developing seeds.
Impact of higher order network structure on emergent cortical activity

Synaptic connectivity between neocortical neurons is highly structured. The network structure of synaptic connectivity includes first-order properties that can be described by pairwise statistics, such as strengths of connections between different neuron types and distance-dependent connectivity, and higher-order properties, such as an abundance of cliques of all-to-all connected neurons. The relative impact of first- and higher-order structure on emergent cortical network activity is unknown. Here, we compare network structure and emergent activity in two neocortical microcircuit models with different synaptic connectivity. Both models have a similar first-order structure, but only one model includes higher-order structure arising from morphological diversity within neuronal types. We find that such morphological diversity leads to more heterogeneous degree distributions, increases the number of cliques, and contributes to a small-world topology. The increase in higher-order network structure is accompanied by more nuanced changes in neuronal firing patterns, such as an increased dependence of pairwise correlations on the positions of neurons in cliques. Our study shows that circuit models with very similar first-order structure of synaptic connectivity can have a drastically different higher-order network structure, and suggests that the higher-order structure imposed by morphological diversity within neuronal types has an impact on emergent cortical activity.
Epidemiological Studies on Toxoplasmosis in Pregnant Women Using Serological Methods in Gezira State-Central Sudan

Objective: To study the relationship between toxoplasmosis and the outcome of pregnancy (full term and abortion) and to find out the epidemiological risk factors. Methods: This case control study was carried out at Wad Medani Teaching hospital, Gezira State, Central Sudan during the period March 2002-May 2004. The cases were 100 pregnant women who presented with abortion between the second and fourth months of gestation, and the controls were 100 full term normally delivered women. Results: ELISA IgG test (n = 94 in each group) revealed 35.1% and 39.4% seroprevalence rates in the study and control groups respectively with no significant difference (p=0.6). When performed on IgG seropositives, ELISA IgM seroprevalence rates were 15.2% and 16.2%, in the study and control groups respectively. Statistically, there was no significant difference between them (p=0.9). When correlated to sociodemographic characteristics and risk factors, Toxoplsma gondii seroprevalence showed significant relationship for age, education, occupation, parity and past history of congenital malformations in both groups. There was significant difference between the two groups for ethnicity. The most important risk factor in both groups was the intake of raw meat (herbivorous viscera). Conclusion: The findings of this study suggests that, ingestion of infected raw meat is an important risk factor for toxoplasmosis. (OR, 3.87; 95%CI, 1.59-9.44) in the study group, while in the control group (OR, 4.41; 95%CI, 1.76-11.09). Key words : Toxoplasmosis, pregnancy, seroepidemiology, risk factors
TEsorter: lineage-level classification of transposable elements using conserved protein domains

Summary Transposable elements (TEs) constitute an import part in eukaryotic genomes, but their classification, especially in the lineage or clade level, is still challenging. For this purpose, we propose TEsorter, which is based on conserved protein domains of TEs. It is easy-to-use, fast with multiprocessing, sensitive and precise to classify TEs especially LTR retrotransposons (LTR-RTs). Its results can also directly reflect phylogenetic relationships and diversities of the classified LTR-RTs. Availability The code in Python is freely available at https://github.com/zhangrengang/TEsorter.
Exploring disturbance as a force for good in motor learning

Disturbance forces facilitate motor learning, but theoretical explanations for this counterintuitive phenomenon are lacking. Smooth arm movements require predictions (inference) about the force-field associated with a workspace. The Free Energy Principle (FEP) suggests that such ‘active inference’ is driven by ‘surprise’. We used these insights to create a formal model that explains why disturbance helps learning. In two experiments, participants undertook a continuous tracking task where they learned how to move their arm in different directions through a novel 3D force field. We compared baseline performance before and after exposure to the novel field to quantify learning. In Experiment 1, the exposure phases (but not the baseline measures) were delivered under three different conditions: (i) robot haptic assistance; (ii) no guidance; (iii) robot haptic disturbance. The disturbance group showed the best learning as our model predicted. Experiment 2 further tested our FEP inspired model. Assistive and/or disturbance forces were applied as a function of performance (low surprise), and compared to a random error manipulation (high surprise). The random group showed the most improvement as predicted by the model. Thus, motor learning can be conceptualised as a process of entropy reduction. Short term motor strategies (e.g. global impedance) can mitigate unexpected perturbations, but continuous movements require active inference about external force-fields in order to create accurate internal models of the external world (motor learning). Our findings reconcile research on the relationship between noise, variability, and motor learning, and show that information is the currency of motor learning.
Herbicides for Control of Wild Garlic in Turfgrass

Wild garlic (Allium vineale) is an annual winter weed in managed turfgrass. Its dark green, upright stems are easily distinguishable among low-lying, dormant warm-season grasses. Experiments were conducted to determine the effectiveness of synthetic auxin and acetolactate synthase (ALS) inhibiting herbicides for post-emergence control of wild garlic. Trials were conducted in 2016 and 2017. Throughout both trial years, synthetic auxin herbicides exhibited visual control quicker than ALS inhibitors at the initial assessment date 20 d after application (DAA). Conversely, at the final assessment date 49 DAA, ALS inhibitors were the only treatments that controlled wild garlic by more than 85%. In 2016, plots treated with 2,4-D + dicamba + mecoprop at 4 pt/acre exhibited 88% visual control when assessed 20 DAA, but this level had decreased to 51% by 49 DAA. Similarly, visual control in plots treated with 2,4-D + mecoprop + dicamba + carfentrazone-ethyl at 4 pt/acre decreased from 59% to 56% and 82% to 18% between assessment dates in 2016 and 2017, respectively. Metsulfuron-methyl at 0.5 fl oz/acre controlled wild garlic 94% and 91% at the 49 DAA assessment date, whereas sulfentrazone + metsulfuron-methyl at 0.41 lb/acre controlled wild garlic 93% and 95% at the same assessment dates in 2016 and 2017, respectively. Future research should consider tank mixes of auxin-mimicking and ALS-inhibiting herbicides as potential routes for quick burndown and season-long control.
Detection Probability of Bats Using Active Versus Passive Monitoring

As technology has evolved, bat researchers have relied more heavily on using acoustic techniques to collect data on bat communities. Acoustic data can be collected actively, where the researcher is present at the sampling point and follows the bat with the detector, or passively, where the researcher is not present and the detector is set out by itself. Active sampling can yield longer, clearer calls, and is only conducted during part of the night (usually from sunset to about 02:00 hours) for short bouts (20 minutes). By contrast, passive sampling can yield lower quality calls, but procedures are easily repeatable and data can be used to measure temporal variation in activity throughout the night and detect individuals and species that are missed during active sampling. Researchers are increasingly attempting to monitor and compare bat communities over time, including sites where both active and passive sampling have occurred. However, these two techniques can yield different detection probabilities and the extent to which data collected using these two techniques can be compared is unclear. Thus, in July 2017 we simultaneously collected acoustic data actively and passively to compare detection probabilities of bats at the Savannah River Site, South Carolina, USA. Using Anabat Express detectors, we detected five species or species groups (Eptesicus fuscus/Lasiurus cinereus, L. borealis/L. seminolus, Perimyotis subflavus, Myotis austroriparius, and Nycticeius humeralis) using each method. Using single season occupancy modeling, we found that method (passive vs. active sampling) had a significant effect on detection probabilities of all species, and that passively sampling throughout the night yielded the highest detection probability for all species. As a result, if differences in detection probability are not taken into account, comparison of historical active datasets with current passive datasets could lead to different insights into habitat use by similar bat communities. Based on our findings, we recommend that researchers use passive sampling throughout the night when studying and monitoring bat communities.
Influence of stage of harvesting and zinc application on yield and zinc uptake in cluster bean [Cyamopsis tetragonoloba (L.) TAUB]

The field experiment entitled, “Influence of stage of harvesting and zinc application on yield and zinc uptake in cluster bean (Cyamopsis tetragonoloba L.)” was conducted during Kharif 2016 at Forage Research Farm, Agronomy Section, ICAR-National Dairy Research Institute, Karnal, Haryana. The experiment was laid out in split plot design with three replications. The main plot treatments comprised of four stages of harvesting [50, 60, 70 and 80 DAS] and under sub plot treatments four levels of Zinc application (Control, 10 kg ZnSO4, 20 kg ZnSO4 and 0.5 % Zinc spray at 30 DAS) were taken. The soil of the experimental field was sandy clay loam in texture with neutral pH, low in available nitrogen and zinc, medium in available phosphorus and higher in available potassium. The growth parameters viz. plant height, leaf length, number of leaves, stem girth and leaf: stem ratio were significantly higher at 80 DAS over other harvesting stages. In sub plot treatments application of zinc through zinc sulphate @ 20 kgha-1 significantly improved all growth parameters except stem girth over other treatments. Positive interaction effect was recorded between Stage of harvesting and zinc application for stem girth and plant height. Highest plant height was recorded under treatment combination of 80 DAS and zinc application @ 20 kg ha-1over other harvesting date and zinc level combinations. A significant increase in green fodder yield (GFY) and dry matter yield (DMY) was obtainedup to harvest at 80 DAS and zinc application @ 20 kg ha-1whereas significantly highest OM content was recorded at 50 DAS (Day after sowing). Maximum zinc uptake was noticed at 80 DAS stage and application rate of 20 kg ZnSO4ha-1 among other treatments.
Extrafloral nectaries in Leguminosae: phylogenetic distribution, morphological diversity and evolution

Extrafloral nectaries (EFNs) mediating ecologically important ant–plant protection mutualisms are especially common and unusually diverse in the Leguminosae. We present the first comprehensively curated list of legume genera with EFNs, detailing and illustrating their systematic and phylogenetic distributions, locations on the plant, morphology and anatomy, on the basis of a unified classification of EFN categories and a time-calibrated phylogeny, incorporating 710 of the 768 genera. This new synthesis, the first since Mckey (1989)’s seminal paper, increases the number of genera with EFNs to 153 (20% of legumes), distributed across subfamilies Cercidoideae (1), Detarioideae (19), Caesalpinioideae (87) and Papilionoideae (46). EFNs occur at nine locations, and are most prevalent on vegetative plant parts, especially leaves (74%) and inflorescence axes (26%). Four main categories (with eight subcategories) are recognised and include the following: formless, trichomatic (exposed, hollow), parenchymatic (embedded, pit, flat, elevated) and abscission zone EFNs (non-differentiated, swollen scars). Phylogenetic reconstruction of EFNs suggests independent evolutionary trajectories of different EFN types, with elevated EFNs restricted almost exclusively to Caesalpinioideae (where they underwent spectacular morphological disparification), flat EFNs in Detarioideae, swollen scar EFNs in Papilionoideae, and Cercidoideae is the only subfamily bearing intrastipular EFNs. We discuss the complex evolutionary history of EFNs and highlight future research directions.
Characterisation of AmpC Hyper-Producing Escherichia coli from Humans and Dairy Farms Collected in Parallel in the Same Geographical Region

Objectives To characterise putative AmpC hyper-producing 3rd generation cephalosporin-resistant E. coli from dairy farms and their phylogenetic relationships as well as to identify risk factors for their presence; to assess evidence for their zoonotic transmission into the local human population Methods Proteomics was used to explain differences in antimicrobial susceptibility. Whole genome sequencing allowed phylogenetic analysis. Multilevel, multivariable logistic regression modelling was used to identify risk factors. Results Increased use of amoxicillin-clavulanate was associated with an increased risk of finding AmpC hyper-producers on farms. Expansion of cephalosporin resistance in AmpC hyper-producers was seen in farm isolates with marR mutations (conferring cefoperazone resistance) or when AmpC was mutated (conferring 4th generation cephalosporin and cefoperazone resistance). Phylogenetic analysis confirmed the dominance of ST88 amongst farm AmpC hyper-producers but there was no evidence for acquisition of farm isolates by members of the local human population. Conclusions In this two-year surveillance study of 53 dairy farms, AmpC hyper-production was the cause of cefotaxime resistance in 46.2% of E. coli. There was evidence of recent farm-to-farm transmission and of adaptive mutations to expand resistance. Whilst there was no evidence of isolates entering the local human population, efforts to reduce 3rd generation cephalosporin resistance on dairy farms must address the high prevalence of AmpC hyper-producers. The finding that amoxicillin-clavulanate use was associated with increased risk of finding AmpC hyper-producers is important because this is not currently categorised as a highest-priority critically important antimicrobial and so is not currently targeted for specific usage restrictions in the UK.
Reduced fronto-striatal volume in ADHD in two cohorts across the lifespan

Objective Neuroimaging studies have associated Attention-Deficit/Hyperactivity Disorder (ADHD) with altered brain anatomy. However, small and heterogeneous study samples, and the use of region-of-interest and tissue-specific analyses have limited the consistency and replicability of these effects. The present study uses a fully data-driven multivariate approach to investigate alterations in both gray and white matter simultaneously, and capture neuroanatomical features associated with ADHD in two large, independent, demographically different cohorts. Methods The study comprised two ADHD cohorts with structural magnetic resonance imaging data: the Dutch NeuroIMAGE cohort (n=890, average age 17.2 years, discovery sample) and the Brazilian IMpACT cohort (n=180, average age 44.2 years, cross validation sample). Using independent component analysis of whole-brain morphometry images in the NeuroIMAGE cohort, 375 independent components of neuroanatomical variations were extracted and assessed their association with ADHD. Afterwards, ADHD-associated components were cross validated in the Brazilian IMpACT cohort. Results In both discovery (corrected- p=0.020) and validation (p=0.033) cohorts, ADHD diagnosis was significantly associated with reduced brain volume in a component mapping to frontal lobes, striatum, and their interconnecting white-matter tracts. The most pronounced case-control differences were localized in white matter adjacent to the orbitofrontal cortex. Conclusion Independent component analysis is a sensitive approach to uncover neuroanatomical alterations in ADHD and avoid bias attributable to a priori region-of-interest based methods. Current results provide further evidence for the role of the fronto-striatal circuit in ADHD. The fact that the two cohorts are from different continents and comprising different age ranges highlights the robustness of the findings.