julilili42/papers huggingface dataset:
Land Suitability Assessment and Agricultural Production Sustainability Using Machine Learning Models
2020-04-17

Land suitability assessment is essential for increasing production and planning a sustainable agricultural system, but such information is commonly scarce in the semi-arid regions of Iran. Therefore, our aim is to assess land suitability for two main crops (i.e., rain-fed wheat and barley) based on the Food and Agriculture Organization (FAO) “land suitability assessment framework” for 65 km2 of agricultural land in Kurdistan province, Iran. Soil samples were collected from genetic layers of 100 soil profiles and the physical-chemical properties of the soil samples were analyzed. Topography and climate data were also recorded. After calculating the land suitability classes for the two crops, they were mapped using machine learning (ML) and traditional approaches. The maps predicted by the two approaches revealed notable differences. For example, in the case of rain-fed wheat, results showed the higher accuracy of ML-based land suitability maps compared to the maps obtained by traditional approach. Furthermore, the findings indicated that the areas with classes of N2 (≈18%↑) and S3 (≈28%↑) were higher and area with the class N1 (≈24%↓) was less predicted in the traditional approach compared to the ML-based approach. The major limitations of the study area were rainfall at the flowering stage, severe slopes, shallow soil depth, high pH, and large gravel content. Therefore, to increase production and create a sustainable agricultural system, land improvement operations are suggested.
Antimicrobial and antileukemic effects: in vitro activity ofCalyptranthes grandifoliaaqueous leaf extract
2020-04-17

Natural products are still a promising source of bioactive molecules. Food and Drug Administration data showed that approximately 49% of the approved molecules originate naturally or chemically-resemble these substances, of which more than 70% are being used in anticancer therapy. It is noteworthy that at present there are no scientific studies to prove the effectiveness and safety of a number of plants used in folk medicine such as in the case of <i>Calyptranthes grandifolia</i> O. Berg (Myrtaceae) originally from South America. The aim of the present study was to determine the biological potential and toxicological effects of the aqueous leaf extract of <i>C. grandifolia</i>. The main detected phytoconstituents were condensed tannins and flavonoids and a high quantity of polyphenols. Regarding the antimicrobial potential, the extract exerted inhibitory activity against <i>Pseudomonas aeruginosa</i>. The results also revealed the extract induced DNA damage in a concentration-dependent manner in RAW 264.7 cells. In addition, <i>C. grandifolia</i> produced cytotoxicity in leukemia cell lines (HL60 and Kasumi-1) without affecting isolated human lymphocytes but significantly inhibited JAK3 and p38α enzyme activity. Taken together, these findings add important information on the biological and toxicological effects of <i>C. grandifolia</i>, indicating that aqueous extract may be a source of natural antimicrobial and antileukemic constituents.
Biochemical changes of the pericellular matrix and spatial chondrocyte organization—Two highly interconnected hallmarks of osteoarthritis
2020-04-17

Abstract During osteoarthritis, chondrocytes change their spatial arrangement from single to double strings, then to small and big clusters. This change in pattern has recently been established as an image‐based biomarker for osteoarthritis. The pericellular matrix (PCM) appears to degrade together alongside cellular reorganization. The aim of this study was to characterize this PCM‐degradation based on different cellular patterns. We additionally wanted to identify the earliest time point of PCM‐breakdown in this physiopathological model. To this end, cartilage samples were selected according to their predominant cellular pattern. Qualitative analysis of PCM degradation was performed immunohistochemically by analysing five main PCM components: collagen type VI, perlecan, collagen type III, biglycan, and fibrillin‐1 ( n = 6 patients). Their protein content was quantified by enzyme‐linked immunosorbent assay (127 patients). Accompanying spatial cellular rearrangement, the PCM is progressively destroyed, with a pericellular signal loss in fluorescence microscopy for collagen type VI, perlecan, and biglycan. This loss in protein signal is accompanied by a reduction in total protein content from single strings to big clusters ( P &lt; .001 for collagen type VI, P = .003 for perlecan, and P &lt; .001 for biglycan). As a result of an increase in the number of cells from single strings to big clusters, the amount of protein available per cell also decreases for collagen type III and fibrillin‐1, where total protein levels remain constant. Biochemical changes of the PCM and cellular rearrangement are thus highly interconnected hallmarks of osteoarthritis. Interestingly, the earliest point in time for a relevant PCM impairment appears to be at the transition to small clusters.
A novel flow cytometry-based assay to measure compromised B cell receptor signaling as a prognostic factor in chronic lymphocytic leukemia
2020-04-17

Abstract Chronic lymphocytic leukemia (CLL) is the most common leukemia in adults. In the past years, new therapeutic approaches (e.g., ibrutinib or venetoclax) have been established and greatly improved treatment of CLL. However, complete control or cure of the disease have not been reached so far. Thus, reliable prognostic markers are an imperative for treatment decisions. Recent studies have revealed an essential role for B cell receptor (BCR) signaling in the pathogenesis, prognosis, and therapy of CLL. A heterogeneous response to receptor stimulation with anti-IgM treatment culminating in different calcium flux capabilities has been demonstrated by several authors. However, the methods employed have not reached clinical application. Here, we report on a flow cytometry-based assay to evaluate calcium flux capabilities in CLL and demonstrate that compromised BCR signaling with diminished calcium flux is associated with a significantly better clinical outcome and progression free survival. In summary, our data strongly support the role of compromised BCR signaling as an important prognostic marker in CLL and establish a novel diagnostic tool for its assessment in clinical settings.
Heart without ‘the’
2020-04-17

Abstract As one of the most intensely studied literary works, Heart of Darkness has been inviting diversified and conflicting readings for more than one hundred years. Politically or culturally oriented readings are overwhelmingly abundant and often contradict each other. In an effort to incorporate textual evidence as comprehensively and unbiasedly as possible, this paper will pay more attention to how the story is told than to what the story tells. This paper concentrates on the narrative frame. By comparing inner and outer narrative frames, I show that the eavesdropping scene (the inner frame) is a diagrammatic icon of the overall story (the outer frame). A point-by-point resemblance can be constructed between these two frames, in which a quasi-storytelling is set up in a dark world full of voices with rare communication between speakers and listeners. In both frames, Kurtz’s voice, which is embedded within voices of others, can be heard, but “that man” (p. 37) is not fully identified formally and the mysteries surrounding Kurtz are never clearly revealed. The frames are proliferated only to accentuate its hollow core. The inner meaning is pointed at but cannot be pinned down.
Phylogenetic linguistic evidence and the Dene-Yeniseian homeland
2020-04-18

Abstract Sicoli &amp; Holton (2014) (PLoS ONE 9:3, e91722) use computational phylogenetics to argue that linguistic data from the putative, but likely, Dene-Yeniseian macro-family are better compatible with a homeland in Beringia (i.e., northeastern Siberia plus northwestern Alaska) than with one in central Siberia or deeper Asia. I show that a more careful examination of the data invalidates this conclusion: in fact, linguistic data do not support Beringia as the homeland. In the course of showing this, I discuss, without requiring a deep mathematical background, a number of methodological issues concerning computational phylogenetic analyses of linguistic data and drawing inferences from them. The aim is to contribute to making computational phylogenetics less of a black box for historical linguists. I conclude with a brief overview of the current evidence bearing on the Dene-Yeniseian homeland from linguistics, archaeology, folklore studies and genetics, and suggest current best practice for linguistic phylogenetics, the use of which would have helped to avoid some of the problems in Sicoli and Holton’s Dene-Yeniseian study, and in turn the percolation of those problems into subsequent synthetic interdisciplinary research.
Impact of Scientific Scrutiny after the 2016 Braunsbach Flash Flood on Flood-Risk Management in the State of Baden-Württemberg, Germany
2020-04-18

This paper presents interdisciplinary research focusing on the municipality of Braunsbach in the German state of Baden-Württemberg, where, in May 2016, a flash flood attracted media attention and scientific scrutiny that highlighted the fact that certain aspects of flood risk were overlooked during earlier assessments conducted by the municipality, such as sediment transport. Using a network analysis and a focus-group discussion, we traced the flow of knowledge through the reported interactions between governmental, private, and academic actors in the two and a half years after the event. From our analysis, we learned that the extreme event attracted scientists to the formal and informal assessment of the hazard and the associated damages. Most importantly, we found conditions under which scientific scrutiny is not detached from but becomes integrated in a governance setting. While it is through this process that sediment transport has become an integral part of flood-risk management in Baden-Württemberg, with an evident impact on the measures already implemented, the impact of morphological changes, as well as large wood and sediment transport, have not been factored into the risk assessment as of yet. These variations in scientific impact on the assessment can be explained by decision biases that can occur when decision makers are under pressure to tackle vulnerabilities and thus lack the time to deliberate in a way that uses all the available evidence.
Innovation in chimpanzees
2020-04-19

ABSTRACT The study of innovation in non‐human animals (henceforth: animals) has recently gained momentum across fields including primatology, animal behaviour and cultural evolution. Examining the rate of innovations, and the cognitive mechanisms driving these innovations across species, can provide insights into the evolution of human culture. Especially relevant to the study of human culture is one of our closest living relatives, the chimpanzee ( Pan troglodytes ). Both wild and captive chimpanzees demonstrate an impressive ability to innovate solutions to novel problems, but also a striking level of conservatism in some contexts, creating a unique and at times puzzling, picture of animal innovation. Whilst the animal innovation field is rife with potential for expanding our knowledge of human and non‐human cognition and problem‐solving, it is undermined by a lack of consistency across studies. The field is yet to settle on a definition of the term ‘innovation’, leading to studies being incomparable across and even within the same species. Here, we fill two gaps in the literature. First, we discuss some of the most prevalent definitions of ‘innovation’ from different fields, highlighting similarities and differences between them. Secondly, we provide an up‐to‐date review of accounts of innovations in both wild and captive chimpanzees. We hope this review will provide a resource for researchers interested in the study of innovation in chimpanzees and other animals, as well as emphasising the need for consistency in the way in which innovations are reported.
Host preference and sorus location correlate with parasite phylogeny in the smut fungal genus Microbotryum (Basidiomycota, Microbotryales)
2020-04-19

Abstract The smut fungal genus Microbotryum (Microbotryales, Pucciniomycotina) contains species that parasitize plants from many different lineages of euasterids, with host specificity of individual parasite species in general being exceptionally high. Additionally, it has been shown that the location of spore production in some species is related to spore dispersal. In this phylogenetic study based on ITS and LSU rDNA data of 57 Microbotryum spp., host spectra and sorus location are mapped on the phylogeny of Microbotryum species in order to understand the macroevolutionary patterns of these two traits. We find that monophyletic parasite clades correspond well with monophyletic host clades and also that monophyletic parasite groups in general produce their spores in the same plant organ. Ancestral state reconstruction inferred the most probable ancestral trait for sorus location being leaves and the most probable ancestral host family for the genus Microbotryum as being the Polygonaceae. According to molecular analyses, a newly sequenced specimen of Ustilago ducellieri , a seed parasite on Arenaria leptoclados , previously treated as synonym of Microbotryum duriaeanum , belongs to a lineage distinct from specimens of M. duriaeanum . A new combination, Microbotryum ducellieri , is accordingly proposed. Taxonomic implications of the presented analyses for the genera Bauhinus and Haradaea are briefly discussed.
Brain substrate metabolism and ß‐cell function in humans: A positron emission tomography study
2020-04-19

Abstract Aims Recent clinical studies have shown enhanced brain glucose uptake during clamp and brain fatty acid uptake in insulin‐resistant individuals. Preclinical studies suggest that the brain may be involved in the control of insulin secretion. The aim of this study was to investigate whether brain metabolism assessed as brain glucose and fatty acid uptake is associated with the parameters of β‐cell function in humans. Materials and methods We analysed cross‐sectional data of 120 subjects across a wide range of BMI and insulin sensitivity. Brain glucose uptake (BGU) was measured during euglycaemic‐hyperinsulinaemic clamp (n = 67) and/or during fasting (n = 45) using [ 18 F]‐fluorodeoxyglucose (FDG) positron emission tomography (PET). In another group of subjects (n = 34), brain fatty acid uptake was measured using [ 18 F]‐fluoro‐6‐thia‐heptadecanoic acid (FTHA) PET during fasting. The parameters of β ‐ cell function were derived from OGTT modelling. Statistical analysis was performed with whole‐brain voxel‐based statistical parametric mapping. Results In non‐diabetics, BGU during euglycaemic hyperinsulinaemic clamp correlated positively with basal insulin secretion rate ( r = 0.51, P = .0008) and total insulin output ( r = 0.51, P = .0008), whereas no correlation was found in type 2 diabetics. BGU during clamp correlated positively with potentiation in non‐diabetics ( r = 0.33, P = .02) and negatively in type 2 diabetics ( r = −0.61, P = .02). The associations in non‐diabetics were not explained with whole‐body insulin sensitivity or BMI. No correlations were found between baseline (fasting) BGU and basal insulin secretion rate, whereas baseline brain fatty acid uptake correlated directly with basal insulin secretion rate ( r = 0.39, P = .02) and inversely with potentiation ( r = −0.36, P = .04). Conclusions Our study provides coherent, though correlative, evidence that, in humans, the brain may be involved in the control of insulin secretion independently of insulin sensitivity.
Lung cryobiopsy and interstitial lung disease: What is its role in the era of multidisciplinary meetings and antifibrotics?
2020-04-19

ABSTRACT Diagnosing ILD can be complex, and despite detailed evaluation and HRCT imaging, many patients require lung biopsy to help classify their disease. SLB has served as the reference standard for histopathology in ILD, since initial classification schemes were created more than 50 years ago. Frequently, patients are too unwell to undertake SLB and remain unclassifiable, despite the input of expert MDD. This can limit access to therapy and establishment of prognosis. TBLC is an emerging procedure for sampling lung tissue with promising results in research and clinical settings. Although diagnostic yield is not as high as SLB, the risk profile looks to be more acceptable and the accuracy appears to be good. There is increasing evidence for the utility of cryobiopsy in ILD diagnosis, particularly within the MDD. Cryobiopsy serves as an important adjunct for the diagnosis of ILD, enhancing the diagnostic confidence of treating clinicians.
Market structure, common ownership, and coordinated manager compensation
2020-04-19

We study oligopolistic competition in product markets where the firms' quantity decisions are delegated to managers. Some firms are commonly owned by shareholders such as index funds, whereas the other firms are owned by independent shareholders. Under such an asymmetric ownership structure, the common owners have an incentive to coordinate when designing the manager compensation schemes. This implicit collusion induces a less aggressive output behavior by the coordinated firms and a more aggressive behavior by the noncoordinated firms. The profits of the noncoordinated firms are increasing in the number of coordinated firms. The profits of the coordinated firms exceed the profits without coordination if at least 80% of the firms are commonly owned.
Learning Model-Agnostic Counterfactual Explanations for Tabular Data
2020-04-20

Counterfactual explanations can be obtained by identifying the smallest\\nchange made to a feature vector to qualitatively influence a prediction; for\\nexample, from 'loan rejected' to 'awarded' or from 'high risk of cardiovascular\\ndisease' to 'low risk'. Previous approaches often emphasized that\\ncounterfactuals should be easily interpretable to humans, motivating sparse\\nsolutions with few changes to the feature vectors. However, these approaches\\nwould not ensure that the produced counterfactuals be proximate (i.e., not\\nlocal outliers) and connected to regions with substantial data density (i.e.,\\nclose to correctly classified observations), two requirements known as\\ncounterfactual faithfulness. These requirements are fundamental when making\\nsuggestions to individuals that are indeed attainable. Our contribution is\\ntwofold. On one hand, we suggest to complement the catalogue of counterfactual\\nquality measures [1] using a criterion to quantify the degree of difficulty for\\na certain counterfactual suggestion. On the other hand, drawing ideas from the\\nmanifold learning literature, we develop a framework that generates attainable\\ncounterfactuals. We suggest the counterfactual conditional heterogeneous\\nvariational autoencoder (C-CHVAE) to identify attainable counterfactuals that\\nlie within regions of high data density.\\n
The ENIGMA Stroke Recovery Working Group: Big data neuroimaging to study brain–behavior relationships after stroke
2020-04-20

Abstract The goal of the Enhancing Neuroimaging Genetics through Meta‐Analysis (ENIGMA) Stroke Recovery working group is to understand brain and behavior relationships using well‐powered meta‐ and mega‐analytic approaches. ENIGMA Stroke Recovery has data from over 2,100 stroke patients collected across 39 research studies and 10 countries around the world, comprising the largest multisite retrospective stroke data collaboration to date. This article outlines the efforts taken by the ENIGMA Stroke Recovery working group to develop neuroinformatics protocols and methods to manage multisite stroke brain magnetic resonance imaging, behavioral and demographics data. Specifically, the processes for scalable data intake and preprocessing, multisite data harmonization, and large‐scale stroke lesion analysis are described, and challenges unique to this type of big data collaboration in stroke research are discussed. Finally, future directions and limitations, as well as recommendations for improved data harmonization through prospective data collection and data management, are provided.
COVID-19: Limiting the Risks for Eye Care Professionals
2020-04-20

After the outbreak of the disease COVID-19, it has reached pandemic proportions within a very short time. It is mainly transmitted human-to-human through direct contact with secretions from an infected person or through inhalation of droplets containing SARS-CoV-2. It is controversial whether the virus may be transmitted via tears. Exposed ocular surface can serve as a gateway in transmission and acquiring respiratory diseases. Considering the reported cases on healthcare workers indicating nosocomial transmission and the anatomical and physiological aspects it is perceived that ophthalmic healthcare professionals are at higher risk of contracting the virus by virtue of their job. In this narrative review we discuss current evidence around detection of SARS-CoV-2 in human tears and forms of transmissions reported to date. We also provide a comprehensive approach that may be implemented in an ophthalmic care facility to protect healthcare personnel, as well as patients, from contracting the virus.
PCARE and WASF3 regulate ciliary F-actin assembly that is required for the initiation of photoreceptor outer segment disk formation
2020-04-20

Significance The photoreceptor outer segments are primary cilia, modified for phototransduction by incorporation of stacked opsin-loaded membrane disks that are continuously regenerated. This process is disrupted in several types of inherited retinal dystrophy, but the driving force remained unclear. We show that C2orf71/PCARE (photoreceptor cilium actin regulator), associated with inherited retinal dystrophy subtype RP54, efficiently recruits the Arp2/3 complex activator WASF3 to the cilium. This activates an actin dynamics-driven expansion of the ciliary tip, resembling membrane evagination in lamellipodia formation. Colocalization of this actin dynamics module to the base of the outer segments, and absence thereof in Pcare −/− mice, suggests PCARE-regulated actin dynamics as a critical process in outer segment disk formation.