Miracle-dz/UniFAR-FTUs huggingface dataset:
The Antarctic lichen Cetraria subscutata is a synonym of Nephromopsis chlorophylla

The Parmeliaceae is a highly diverse family among the lichenized Ascomycota, both in terms of species number, with more than 2500 species distributed worldwide (Thell et al. 2012; Jaklitsch et al. 2016), and morphological and anatomical variation (Blanco et al. 2006; Crespo et al. 2007). It also has a complex taxonomy which dates back to the time of Acharius and has been studied by some of the most well-known lichenologists of the 20th century (Thell et al. 2012). Generic concepts and delimitation have often undergone dramatic changes (Crespo et al. 2007; Nelsen et al. 2011) but in recent years molecular phylogenetics have helped to establish a more natural classification (Thell et al. 2009; Crespo et al. 2011; Miadlikowska et al. 2014; Divakar et al. 2017). Within the informal group of “cetrarioid” species, the most recent classification includes only two genera, Cetraria and Nephromopsis (Divakar et al. 2017). However, as pointed out by Randlane et al. (2013), there are still some poorly known species in this group with an unresolved taxonomy. One such case is the Antarctic species Cetraria subscutata D. C. Linds. , described from collections made during the 1964 British Antarctic Surveys in the Argentine Islands Archipielago, west Antarctic Peninsula (Lindsay 1973). It was included in Cetraria Ach. , the most important genus within the “cetrarioid group” at that time, mainly due to the similarity in external morphology and its chemistry, despite the lack of apothecia. Lindsay compared it with two other Cetraria species, namely C. chlorophylla (Wild.) Vain. (now in Nephromopsis Müll. Arg.), from which it was distinguished by the lack of soredia, and with C. antarctica Zalhbr. [=Pseudocyphellaria glabra (Hook f. & Taylor) C. W. Dodge] (Lindsay 1973). Later, Øvstedal & LewisSmith (2001) re-examined Lindsay’s species as part of their Antarctic Flora and kept it in Cetraria, although with some hesitation, stating that it would probably be better placed under Tuckermannopsis (a genus resurrected by Lai (1980), now included in Nephromopsis) but the observation of sexual structures was needed for confirmation. So far, the species has been collected in Antarctica only four times; all these sterile specimens were studied by Lindsay (1973) and by Øvstedal & Lewis-Smith (2001). As a result, it has never been included in any of the recent molecular studies and is currently considered as an enigmatic species of unknown taxonomic position (Randlane et al. 2013). During the 2014 Argentine Antarctic Survey, we identified some sterile specimens as “C. subscutata” and these were used for molecular phylogenetic studies. The results confirmed that the species belongs toNephromopsis and is conspecific withN. chlorophylla (Willd.) Divakar et al. However, the specimens from Antarctica show some differences with collections from other regions, which are discussed below.
Combining biological and socio‐political criteria to set spatial conservation priorities for the endangered African wild dog

The effectiveness of biodiversity conservation projects is influenced by socio‐political context, a reality overlooked by traditional prioritization schemes that use only measures of biological value and threat when deciding where to invest limited conservation resources. We combined ecological and socio‐political criteria to illuminate options for prioritizing investment in African wild dog Lycaon pictus conservation among countries and subpopulations. Countries and subpopulations were assigned scores for conservation priority (based on their wild dog populations) and conservation likelihood (based on their governance quality and other indicators of the likelihood of effective conservation action for wild dogs). Seven of the 19 wild dog countries scored above the median value for both priority and likelihood and supported 74% of the total wild dog population. Investment in these ‘higher priority, higher likelihood’ countries may offer the greatest returns on conservation investment. The intention of this study is not, however, to be prescriptive, nor to suggest abandoning disadvantaged countries, but to provide a tool for understanding and managing trade‐offs between where conservation is most needed for wild dogs and where it is most feasible. The prioritization framework presented in this paper may easily and profitably be applied to other taxa, extending the scope of our results.
Association of the CSN1S1 gene polymorphism with milk composition traits in Jamunapari goat

The genetic polymorphism of the CSN1S1 (casein alpha-s1) locus was investigated in Jamunapari goat breed by Sodium Dodicyle Sulphate – Poly Acrylamide Gel Electrophoresis (SDS-PAGE) and Polymerase Chain Reaction – Restriction Fragment Length Polymorphism (PCR-RFLP). A total of 122 milk and blood samples were collected. The SDS-PAGE pattern revealed the presence of four variants of CSN1S1 locus namely, A, B, E and F. The A allele of a-s1 – casein was observed in the majority of goats. The genotypic frequency of the AA, BB, BE, AF and FF genotypes of CSN1S1 locus were 0.437, 0.175, 0.250, 0.125 and 0.012, respectively. The PCR-RFLP was performed, six different variant groups of F allele (224)bp, the B/E allelic pair (161+63) bp, A/0 allelic pair (150+63) bp, AD allelic pair (212+150+63) bp, AF allelic pair (224+150+63) bp and BF allelic pair (224+160+63) were obtained after restriction digestion with XmnI. The genotypic frequency of AA, AD, AF, BB, BE, BF and BC genotypes were 0.274, 0.114, 0.147, 0.098, 0.163, 0.081 and 0.163, respectively. The allelic frequency of A, B, C, D, E and F were 0.360, 0.303, 0.081, 0.057, 0.081 and 0.114, respectively. The present study showed that AA genotype had significant effect on total protein content on the milk and AD genotype had significant effect on 90 day milk yield in Jamunapari goat. Thus the CSN1S1 genotype information in Jamunapari could be utilised in selection strategies, in order to select genetic stock for the production of goat milk with higher protein content in marker assisted selection to increase the rate of genetic gain.
Switch costs in inhibitory control and voluntary behavior: A computational study of the antisaccade task

An integral aspect of human cognition is the ability to inhibit habitual responses in order to initiate complex, rule-guided actions. Moreover, humans have also the ability to alternate between different sets of rules or tasks, at the cost of degraded performance when compared to repeating the same task, a phenomenon called the ‘task switch cost’. While it is recognized that switching between tasks requires often to inhibit habitual responses, the interaction between these two forms of cognitive control has been much less studied than each of them separately. Here, we use a computational model to draw a bridge between inhibitory control and voluntary action generation and thereby provide a novel account of seemingly paradoxical findings in the task switch literature. We investigated task switching in the mixed antisaccade task, in which participants are cued to saccade either in the same or in the opposite direction to a peripheral stimulus. Our model demonstrates that stopping a habitual action leads to increased inhibitory control that persists on the next trial. However, enhanced inhibition affects only the probability of generating habitual responses, and, contrary to previous accounts, cannot be characterized as proactive task interference. In addition, our model demonstrates that voluntary actions (but not habitual responses) are slower and more prompt to errors on switch trials compared to repeat trials. We conclude that precisely the interaction between these two effects explains a variety of contradictory findings reported in the literature.
Contributions to Turkish Flora: taxonomic and distributional notes on the poorly known Noccaea (Brassicaceae) species.

Herein the taxonomical status of some poorly known Noccaea (Brassicaceae) species is revised. Moreover, the morphological, distributional and ecological properties of these species are updated. Some overlooked species in Turkey such as Noccaea versicolor and N. aptera are recollected and their descriptions emended and discussed. N. huber-morathii is also recollected from its type locality after its first collection. The description and distribution of N. huber-morathii are also updated. New distribution areas for N. tatiaae and N. aghrica , which have been insufficiently known species in Turkey, are also given.
Layer-specific integration of locomotion and concurrent wall touching in mouse barrel cortex

During navigation rodents continually sample the environment with their whiskers. How locomotion modulates neuronal activity in somatosensory cortex and how self-motion is integrated with whisker touch remains unclear. Here, we used calcium imaging in mice running in a tactile virtual reality to investigate modulation of neurons in layer 2/3 (L2/3) and L5 of barrel cortex. About a third of neurons in both layers increased activity during running and concomitant whisking, in the absence of touch. Fewer neurons were modulated by whisking alone (<10%). Whereas L5 neurons responded transiently to wall-touching during running, L2/3 neurons showed sustained activity after touch onset. Consistently, neurons encoding running-with-touch were more abundant in L2/3 compared to L5. Few neurons across layers were also sensitive to abrupt perturbations of tactile flow. We propose that L5 neurons mainly report changes in touch conditions whereas L2/3 neurons continually monitor ongoing tactile stimuli during running.
TMEM135 is an LXR-Inducible Regulator of Peroxisomal Metabolism

The liver x receptors (LXRs) are key regulators of systemic lipid metabolism. We identified transmembrane protein 135 (TMEM135), a peroxisomal protein with an unknown function, as an LXR target gene. The LXRs induce TMEM135 transcription in humans via an LXR response element located downstream of the putative transcriptional start site, but do not increase Tmem135 in murine cells. Functionally, knockdown of TMEM135 in hepatocytes in vitro and in vivo results in fatty acid accumulation due to reduced peroxisomal β-oxidation, which was most pronounced with elevated fatty acid loading. Mechanistically, proteomic and Western blot analyses indicated that TMEM135 mediates import of peroxisome matrix proteins necessary for β-oxidation and bile acid synthesis. These findings indicate that the LXRs regulate peroxisomal metabolism via transcriptional control of TMEM135, and TMEM135 mediates an auxiliary matrix protein import pathway and thus may serve as a therapeutic target for metabolic and aging disorders associated with peroxisome dysfunction.
Compositional Generalization with Tree Stack Memory Units.

We study compositional generalization, viz., the problem of zero-shot generalization to novel compositions of concepts in a domain. Standard neural networks fail to a large extent on compositional learning. We propose Tree Stack Memory Units (Tree-SMU) to enable strong compositional generalization. Tree-SMU is a recursive neural network with Stack Memory Units (\SMU s), a novel memory augmented neural network whose memory has a differentiable stack structure. Each SMU in the tree architecture learns to read from its stack and to write to it by combining the stacks and states of its children through gating. The stack helps capture long-range dependencies in the problem domain, thereby enabling compositional generalization. Additionally, the stack also preserves the ordering of each node's descendants, thereby retaining locality on the tree. We demonstrate strong empirical results on two mathematical reasoning benchmarks. We use four compositionality tests to assess the generalization performance of Tree-SMU and show that it enables accurate compositional generalization compared to strong baselines such as Transformers and Tree-LSTMs.
RainBlock: Faster Transaction Processing in Public Blockchains

Public blockchains like Ethereum use Merkle trees to verify transactions received from untrusted servers before applying them to the blockchain. We empirically show that the low throughput of such blockchains is due to the I/O bottleneck associated with using Merkle trees for processing transactions. We present RAINBLOCK, a new architecture for public blockchains that increases throughput without affecting security. RAINBLOCK achieves this by tackling the I/O bottleneck on two fronts: first, decoupling transaction processing from I/O, and removing I/O from the critical path; second, reducing I/O amplification by customizing storage for blockchains. RAINBLOCK uses a novel variant of the Merkle tree, the Distributed Sharded Merkle tree (DSM-TREE) to store system state. We evaluate RAINBLOCK using workloads based on public Ethereum traces (including smart contracts) and show that RAINBLOCK processes 20K transactions per second in a geo-distributed setting with four regions spread across three continents.
Mechanisms of immunity and pathology during canine leishmaniasis: Leading the way to prevention and treatment

Visceral leishmaniasis (VL) caused by certain species of the genus Leishmania results in a significant disease burden worldwide. This is most pronounced in some of the world’s poorest communities. In South America and the Mediterranean basin, dogs are the major domestic reservoir for Leishmania infantum, one cause of human VL. In addition, dogs infected with L. infantum have an immune response and pathophysiology similar to human cases, making them a representative naturally-occurring animal model of VL. Chronic infection with Leishmania infantum can result in asymptomatic infection for a long period of time, or symptomatic, potentially life-threatening visceralizing disease. Immunopathology that contributes to the precipitation of clinical disease during natural infection is incompletely understood. The goal of the research presented in this thesis was to evaluate immunopathology potentially contributing to the onset of symptomatic VL and to evaluate a potential candidate for canine vaccination against Leishmania infantum. Using a prospective cohort of dogs naturally infected with L. infantum, we identified the presence of both CD4+ and CD8+ T cell exhaustion during symptomatic VL, mediated through coinhibitory receptor Programmed Death 1 (PD-1). Blockage of the interaction of PD-1 and one of it’s ligands, B7 homolog 1 (B7.H1), partially recovered proliferation and IFN production in both CD4+ and CD8+ T cells. Furthermore, the blockage of PD-1/B7.H1 improved superoxide production in canine monocyte-derived phagocytes, and resulted in improved parasite clearance from peripheral blood after 7 days of culture. This data significantly contributes to knowledge of immunopathology during VL. In dogs with Leishmania-associated glomerulopathy, we evaluated glomerular lesions, describing the occurrence of a type I membranoproliferative glomerulonephritis, with expansion of the mesangium and podocyte retraction with
Cell Boundary Confinement Sets the Size and Position of the E. coli Chromosome

While the spatiotemporal structure of the genome is crucial to its biological function, many basic questions remain unanswered on the morphology and segregation of chromosomes. Here, we experimentally show in Escherichia coli that spatial confinement plays a dominant role in determining both the chromosome size and position. In non-dividing cells with lengths up to 10 times normal, single chromosomes are observed to expand more than 4 fold in size, an effect only modestly influenced by deletions of various nucleoid-associated proteins. Chromosomes show pronounced internal dynamics but exhibit a robust positioning where single nucleoids reside strictly at mid-cell, while two nucleoids self-organize at ¼ and ¾ cell positions. Molecular dynamics simulations of model chromosomes recapitulate these phenomena and indicate that these observations can be attributed to depletion effects induced by cytosolic crowders. These findings highlight boundary confinement as a key causal factor that needs to be considered for understanding chromosome organization.
Effect of distance to edge and edge interaction on seedling regeneration and biotic damage in tropical rainforest fragments: A long‐term experiment

In forest fragments, edge effects can influence forest regeneration, but little is known about how edge effects influence seedling performance and the interaction between seedlings and their natural enemies over time. In central Amazonia, we recorded survival and growth (in height and leaf number) and damage by insect herbivores and leaf‐fungal pathogens of Chrysophyllum pomiferum (Sapotaceae) seedlings that were exposed to different numbers of edges and to different distances from the forest edge. Grown seedlings were transplanted into one‐square‐metre plots within 1‐ha blocks located in the centre (no edge), the edge (one edge), and the corner (two edges), and at different distances from the edge towards the interior (i.e., 20, 40, 60, 80, and 100 m) of two rectangular fragments (10‐ and 100‐ha in size). Plots were visited once every 2 months for 1 year (1992–1993) and thereafter every 2 years for almost 8 years (1993–2001). Overall, results showed that seedling survival, height, leaf number, and biotic damage varied over time with the presence of nearby edges and with the distance from the edge. Survival was lower in fragment edges and corners than in centres. Increase in height was similar for all positions within the 100‐ha fragment, whereas in the 10‐ha fragment seedling height had a greater increase at the edge and corner than in the centre. Furthermore, survival increased with distance from the edge as did leaf number, whereas height showed a lower increase closer to the edge than farther away. Regarding biotic damage, for both fragments herbivory was greater at the centres and decreased with edge proximity over time, whereas leaf‐fungal damage was greater at the corners than in the edges and increased significantly over time. Biotic damage was correlated with seedling size. Small seedlings were more susceptible to fungal attack, whereas larger seedlings were so to herbivores. Synthesis. This study demonstrated that despite stochastic environmental factors seedling survival, growth, and biotic damage by herbivores and fungal pathogens varied with the level of edge exposure and proximity, which may threaten forest regeneration in the long term.
Mean Performance of Knolkhol (Brassica oleracea var. gongylodes L.) Genotypes for Various Quantitative Traits under Sub Tropical Conditions of Jammu

Knolkhol (Brassica oleracea var. gongylodes L.) 2n=18 belongs to family Brassicacea is a cool season vegetable crop. It has its primary centre of origin in Northern Europe. It is also called as kohl rabi (German word) i.e. cabbage turnip, since it resemble an above ground turnip. It has importance for both leaves and knobs consumption in India and only knobs in Europe. In India it is widely grown in Jammu and Kashmir, West Bengal and to a limited extent as a rare exotic vegetable in some parts of Maharashtra, Assam, Uttar Pradesh and Punjab (Thamburaj and Singh, 2010). Of late demand for knolkhol has gained momentum in National Capital Region of Delhi and adjoining states because of its wholesome utility as fresh vegetable and value addition products which support the food needs of the people. In Jammu and Kashmir it is a popular vegetable both among rich and poor and International Journal of Current Microbiology and Applied Sciences ISSN: 2319-7706 Volume 7 Number 06 (2018) Journal homepage: http://www.ijcmas. com
Forage productivity of cowpea [Vigna unguiculata (L.) Walp] cultivars improves by optimization of spatial arrangements

Sustainable production of quality forages in sufficient quantities constitutes one of the biggest challenges for profitable dairy farming. Forage legumes including cowpea offer a feasible solution to meet this task but planting geometry for spreading and erect types of varieties needs to be optimized. Two cowpea varieties (P-518 and Rawan-2003) were sown to different row spacing (30, 45 and 60 cm), while broadcasted crops were kept for comparison. Factorial arrangement of randomized complete block design (RCBD) was employed to carry out the field trial with four replicates. Dry matter biomass, quality variables, net income and benefit-cost ratio were taken as experimental variables. Rawan-2003 (spreading type) sown at 45 cm spaced rows gave significantly ( P ≤0.01) higher dry matter biomass (8.26 and 9.03 t ha -1 in 2013 and 2014, respectively) along with significantly ( P ≤0.05) improved forage quality (especially higher crude protein and lower crude fiber contents). The same variety and spatial arrangement resulted in the highest net income and benefit-cost ratio (BCR) (4.66 and 4.85 in 2013 and 2014 respectively). P-518 (erect type) gave better results with closer inter-row spacing (30 cm spaced rows), while broadcasting of both cowpea varieties proved to be inferior to all other spatial arrangements.
Human cytochrome P450 enzyme inhibition profile of three flavonoids isolated from Psoralea corylifolia: in silico predictions and experimental validation

Cytochrome P450 enzyme (CYP)-associated metabolic studies in vitro have been considered cost-effective for predicting potential clinical drug/herb–drug interactions (DDI/HDI). There is an increasing use of computational approaches to investigate CYPs and their interactions with ligands. In silico studies will help us to significantly reduce the number of potential false positive hypotheses and decrease the running times of the experiments. They can also better predict and comprehend the molecular nature of binding interactions. Bavachin, neobavaisoflavone and corylifol A are the bioactive flavonoids of Psoralea corylifolia, which have been found to be associated with osteoarthritis treatment. In this study, molecular docking (CDOCKER) together with molecular dynamic simulation (MD) methods was used to predict the binding mode of these three flavonoids with CYP1A2/2C9/2C19/2D6/3A4/2E1. The IC50 shift and GSH-trapping experiments were conducted to validate the computational results as well as to identify the inhibition mechanism. The binding abilities predicted by CDOCKER and MD simulation with CYPs were in good agreement with the experimental data. Further inhibitory mechanism studies showed that bavachin and neobavaisoflavone might be mechanism-based inhibitors of CYP1A2 and CYP2C19. These results suggest that the flavonoids obtained from Psoralea corylifolia may participate in interactions with drugs that act as substrates for CYP2C9, CYP2C19 and CYP1A2, and the combination of CDOCKER and MD simulation may be a useful tool to identify potential CYP inhibitors from herbal medicines.