Miracle-dz/UniFAR-FTUs huggingface dataset:
Local spatial pattern in the occurrence of two congeneric wood-decaying fungi in an old-growth boreal forest

Abstract This paper characterizes spatial patterns in the occurrence of two congeneric wood-decaying fungi (Aphyllophorales: Polyporaceae) in an old-growth boreal forest in eastern Finland. The spatial patterns are used to evaluate indirectly the short-distance dispersal ability of the species. Fomitopsis rosea is a specialist on Picea abies occurring mainly in forests with large amounts of dead wood, whereas Fomitopsis pinicola is a substrate generalist and also abundant in managed forests. Within a forest reserve, a 25 ha study area was divided into 25 m×25 m grid (n=400), and all dead trees and fruiting bodies of the two polypore species were recorded. Spatial patterns were analysed with Spatial Analysis by Distance IndicEs methodology (SADIE). Downed spruce logs were highly aggregated within the study area. After this distribution was accounted for, the spatial pattern of F. pinicola and F. rosea on logs was random. The lack of spatial aggregation suggests that within old-growth forest stands dispersal of the two fungal species is not a limiting factor for their occurrence.
Calcium and oxalate content of the leaves of Phaseolus vulgaris at different calcium supply in relation to calcium oxalate crystal formation

Summary Soluble and insoluble oxalate and insoluble calcium were measured in the leaves of Phaseolus vulgaris. The plants were grown in nutrient solutions with two different concentrations of calcium. Two developmental stages of the leaves were studied. Although the content of insoluble calcium differs widely according to leaf age and growth conditions, the percentage bound in crystals is nearly the same in all cases. In the growing leaves, concentrations of total oxalate are independent of calcium supply, thus, showing that the known rise in numbers of crystals, and of cells containing them, is not induced via oxalate biosynthesis. Fully expanded leaves contain more oxalate when grown in a nutrient solution with higher calcium concentration. Amounts of oxalate in percent of dry weight are similar to those given in the literature for other legume leaves.
Fluorescently labelled, rRNA‐targeted oligonucleotide probes in the study of microbial ecology

In situ hybridization with fluorescently labelled, rRNAtargeted nucleic acid probes is one part of the rRNA approach to microbial ecology. As a whole, encompassing the sequencing and probing of ribosomal RNA (genes) directly retrieved from the environment, this approach facilitates in situ identification and phylogenetic placing of hitherto uncultured micro-organisms. It thereby discloses biodiversity that has not yet been analysed. Molecular studies indicate that currently only a fraction of the extant microbial species have been cultured and characterized. Therefore, even though 165 RNA sequences for about one half of the validly described bacterial species have been determined, true microbial diversity in complex environments might be largely unknown. There are distinct differences between the results that can be obtained by in situ hybridization with rRNA-targeted probes and those of other hybridization techniques. These include information on the exact three-dimensional distribution of microbial populations and the in sifu rRNA content of individual cells. Simultaneous in situ hybridization of one sample with multiple probes marked with different labels allows to control probe specificity even in hghly complex environments in which the true microbial diversity has only been revealed in part. Recent years have shown that in situ hybridization with fluorescently labelled, rRNA-targeted nucleic acid probes is more than a very specialized procedure that allows studies of laboratory cultures. In many examples, microbial populations could be monitored in situ. Aquatic environments, especially nutrient rich ones, have proven less difficult to analyse than soil or sediment.
Fc Receptors on Human T Lymphocytes: Loss of Fcμ and Expression of Fcγ Receptors by T Cells Stimulated in Mixed Lymphocyte Reaction

The consequences of allogeneic stimulation on the expression of Feμ or Feγ receptors were analysed in T‐cell populations responding in mixed lymphocyte reaction (MLR). Unfractionated T‐cell populations were cultured with a pool of irradiated allogeneic T‐depleted cells. The responder E ‐rosetting cells progressively lost Feμ and acquired Fcγ receptors. The change of the original Fc receptor phenotype is not the consequence of a preferential proliferative response of TG versus TM cells but is likely due to a de novo expression of Feγ receptors by T cells lacking detectable Fc receptors (T‐null) and also to the loss of Fcμ and expression of Feγ receptors by TM cells. These data suggest that, after MLR, responder T cells can modify their Fc receptor phenotype.
West Nile Virus-associated Hospitalizations, California, USA, 2004-2017.

BACKGROUND West Nile virus (WNV) is the most commonly reported mosquito-borne disease in the United States. California reports more WNV disease than any other state. METHODS We identified WNV-associated hospitalizations from 2004 through 2017 in California and estimated hospitalization incidence using California Patient Discharge Data. We described demographic, geographic, and clinical characteristics of WNV-hospitalizations, identified risk factors for in-hospital death, and tabulated hospitalization charges.Results: From 2004 through 2017, 3,109 Californians were hospitalized with WNV (median: 214 patients per year, range: 72 - 449). The majority were male (1,983; 63.8%) and ≥ 60 years old (1,766; 56.8%). The highest median annual hospitalization rate (0.88 hospitalizations / 100,000 persons) was in the Central Valley, followed by southern California (0.59 hospitalizations / 100,000 persons). Most patients (2,469; 79.4%) had ≥1 underlying condition, including hypertension, cardiovascular disease, diabetes, chronic kidney disease, or immunosuppression due to medications or disease. Median hospitalization length was 12 days (interquartile range: 6-23 days). During hospitalization, 1,317 (42%) patients had acute respiratory failure and/or sepsis/septic shock, 772 (24.8%) experienced acute kidney failure, and 470 (15.1%) had paralysis; 272 (8.8%) patients died. Nearly 47% (1,444) of patients were discharged for additional care. During these 14 years, $838,680,664 (mean $59.9 million / year) was charged for WNV hospitalizations, 73.9% through government payers, a median charge of $142,321 per patient. CONCLUSIONS WNV-associated hospitalizations were substantial and costly in California. Hospitalization incidence was higher in males, elderly persons, and patients with underlying conditions. WNV persists as a costly and severe public health threat to California residents.
What does the germination ecophysiology of the invasive Acacia saligna (Labill.) Wendl. (Fabaceae) teach us for its management?

Acacia saligna is a phanerophyte native to Australia; it was introduced in the 1950s in Sardinia (Italy) for afforestation mainly in coastal areas and at present it is considered naturalized, becoming invasive in sand dune habitats. Seed biology is one of the most important factors contributing to the invasion success of Australian acacias, for this reason the germination ability is an important issue when trying to clarify the invasion dynamics of A. saligna. Germination tests were conducted at the BG-SAR, testing the effect of different temperatures and percentages of NaCl, on seeds belonging to five accessions from four populations of two coastal habitat types. The optimal temperature range for seed germination was 15–20°C; the increase of salt caused a decrease in the final germination percentages. At 1% of NaCl concentration, germination fell at 25–30°C and at 2% it was relatively low (below 40%) and occurred almost only at 15°C. This work represents a contribution to the knowledge of the seed ecology and germination behaviour of the species, providing new data on the interpopulation and interannual variability, and relating them to the invasion dynamics of A. saligna in the coastal Mediterranean habitats.
Growing tall vs growing wide: tree architecture and allometry of Acacia karroo in forest, savanna, and arid environments

In order to investigate how environmental factors other than light availability affect tree architecture, differences in branching architecture and allometry were analysed in populations of Acacia karroo Hein. from three different environments in South Africa: forests, savannas and arid-shrublands. Factors such as fire and herbivory have a large effect on tree life history in certain environments and are likely to have selected for trees that have different architectures from those of forest trees, whose major limitation is light assimilation. Significant differences were found in stem architecture and branching architecture between trees in each environment. Compared with forest trees, trees in savannas had an elongated growth form with small canopy and leaf areas, and tall, thin, unbranched trunks. Trees in arid areas showed opposite trends with wider canopies, and increased lateral branching. Savanna trees had significantly smaller spines than trees in other environments, and both forest and savanna trees showed delayed reproduction. These differences are probably related to a trade-off between an architecture geared towards rapid height-gain and one promoting lateral spread, and can be explained with reference to the different selective pressures in each environment. In forests, vertical and horizontal growth are both important. However, in savannas there is a great pressure for rapid vertical growth to escape fires, while in arid areas a defensive, lateral growth form is selected for. Savanna trees and arid karoo trees have evolved architectures that are more extreme vertically and laterally than the range of architectures displayed in a forest community.
HIV Nef and Antiretroviral Therapy Have an Inhibitory Effect on Autophagy in Human Astrocytes that May Contribute to HIV-Associated Neurocognitive Disorders

A significant number of people living with HIV (PLWH) develop HIV-associated neurocognitive disorders (HAND) despite highly effective antiretroviral therapy (ART). Dysregulated macroautophagy (autophagy) is implicated in HAND pathogenesis. The viral protein Nef, expressed even with suppressive ART, and certain antiretrovirals affect autophagy in non-CNS cells. Astrocytes, vital for CNS microenvironment homeostasis and neuronal health, require autophagy for their own homeostasis. We hypothesized that extracellular Nef and/or ART impact astrocyte autophagy, thus contributing to HAND. We studied in-bulk and selective autophagic flux in primary human astrocytes treated with extracellular Nef and/or a combination of tenofovir+emtricitabine+raltegravir (ART) using Western blotting, a tandem fluorescent LC3 reporter, and transmission electron microscopy/morphometry. We show that after 24 h treatment, Nef and ART decrease autophagosomes through different mechanisms. While Nef accelerates autophagosome degradation without inducing autophagosome formation, ART inhibits autophagosome formation. Combination Nef+ART further depletes autophagosomes by inducing both abnormalities. Additionally, extracellular Nef and/or ART inhibit lysosomal degradation of p62, indicating Nef and/or ART affect in-bulk and selective autophagy differently. Dysregulation of both autophagic processes is maintained after 7 days of Nef and/or ART treatment. Persistent autophagy dysregulation due to chronic Nef and/or ART exposure may ultimately result in astrocyte and neuronal dysfunction, contributing to HAND.
The Role of ERα36 in Development and Tumor Malignancy

Estrogen nuclear receptors, represented by the canonical forms ERα66 and ERβ1, are the main mediators of the estrogen-dependent pathophysiology in mammals. However, numerous isoforms have been identified, stimulating unconventional estrogen response pathways leading to complex cellular and tissue responses. The estrogen receptor variant, ERα36, was cloned in 2005 and is mainly described in the literature to be involved in the progression of mammary tumors and in the acquired resistance to anti-estrogen drugs, such as tamoxifen. In this review, we will first specify the place that ERα36 currently occupies within the diversity of nuclear and membrane estrogen receptors. We will then report recent data on the impact of ERα36 expression and/or activity in normal breast and testicular cells, but also in different types of tumors including mammary tumors, highlighting why ERα36 can now be considered as a marker of malignancy. Finally, we will explain how studying the regulation of ERα36 expression could provide new clues to counteract resistance to cancer treatments in hormone-sensitive tumors.
In vitro hydrolysis of oligomannosyl oligosaccharides by the lysosomal α-d-mannosidases

In vitro incubation of the oligomannosyl oligosaccharides Man9GlcNAc and Man5GlcNAc with isolated disrupted lysosomes yields different oligosaccharide isomers resulting from mannosidase hydrolysis. These isomers were isolated by HPLC and characterized by 1H-NMR spectroscopy. The first steps of the degradation involve an (α1-2)mannosidase activity and lead to the formation of one Man8GlcNAc, one Man7GlcNAc, two Man6GlcNAc and two Man5GlcNAc isomers. These reactions do not require Zn2+ as activator. On the other hand, the following steps, which lead to the formation of Man3GlcNAc and Man2GlcNAc, are Zn2+-dependent. This process is characterized by the preferential action of an (α1-3)mannosidase activity, and the formation of Man(α1-6)Man(α1-6)Man(β1-4)GlcNAc and Man(α1-6)Man(β1-4)GlcNAc. Therefore, the digestion of Man9GlcNAc inside the lysosome appears to follow a very specific pathway, since only nine intermediate compounds can be identified instead of the 38 possible isomers. Our results are consistent both with the existence of several specific enzymes for α1-2, α1-3 and α1-6 linkages, and with the presence of a unique enzyme whose specificity would be dependent either on Zn2+ or on the spatial conformation of the glycan. Nevertheless, previous work on the structural analysis of oligosaccharides excreted in the urine of patients suffering from mannosidosis, demonstrates the absence of the core α1-6-linked mannosyl residue in the major storage product derived from oligomannosyl oligosaccharides. This observation indicates the presence of a specific (α1-6)mannosidase form, unaffected in mannosidosis.
Evaluating Learner-Centeredness Course Pedagogy in Project Management Syllabi Using a Content Analysis Approach

Posted Online: 3 March 2020 Published: 4 June 2020 Full terms and conditions of access and use, archived papers, submission instructions, a search tool, and much more can be found on the JISE website: http://jise.org ISSN: 2574-3872 (Online) 1055-3096 (Print) Evaluating Learner-Centeredness Course Pedagogy in Project Management Syllabi Using a Content Analysis
Graph-based Patterns for Local Coherence Modeling

Coherence is an essential property of well-written texts. It distinguishes a multi-sentence text from a sequence of randomly strung sentences. The task of local coherence modeling is about the way that sentences in a text link up one another. Solving this task is beneficial for assessing the quality of texts. Moreover, a coherence model can be integrated into text generation systems such as text summarizers to produce coherent texts. In this dissertation, we present a graph-based approach to local coherence modeling that accounts for the connectivity structure among sentences in a text. Graphs give our model the capability to take into account relations between non-adjacent sentences as well as those between adjacent sentences. Besides, the connectivity style among nodes in graphs reflects the relationships among sentences in a text. We first employ the entity graph approach, proposed by Guinaudeau and Strube (2013), to represent a text via a graph. In the entity graph representation of a text, nodes encode sentences and edges depict the existence of a pair of coreferent mentions in sentences. We then devise graph-based features to capture the connectivity structure of nodes in a graph, and accordingly the connectivity structure of sentences in the corresponding text. We extract all subgraphs of entity graphs as features which encode the connectivity structure of graphs. Frequencies of subgraphs correlate with the perceived coherence of their corresponding texts. Therefore, we refer to these subgraphs as coherence patterns. In order to complete our approach to coherence modeling, we propose a new graph representation of texts, rather than the entity graph. Our approach employs lexico-semantic relations among words in sentences, instead of only entity coreference relations, to model relationships between sentences via a graph. This new lexical graph representation of texts plus our method for mining coherence patterns make our coherence model. We evaluate our approach on the readability assessment task because a primary factor of readability is coherence. Coherent texts are easy to read and consequently demand less effort from their readers. Our extensive experiments on two separate readability assessment datasets show that frequencies of coherence patterns in texts correlate with the readability ratings assigned by human judges. By training a machine learning method on our coherence
Analyse automatique par transitions pour l'identification des expressions polylexicales. (Automatic transition-based analysis for multiword expression identification)

Cette these porte sur l'identification des expressions polylexicales, abordee au moyen d'une analyse par transitions. Une expression polylexicale (EP) est une construction linguistique composee de plusieurs elements dont la combinaison montre une irregularite a un ou plusieurs niveaux linguistiques. La tâche d'identification d'EPs consiste a annoter en contexte les occurrences d'EPs dans des textes, i.e a detecter les ensembles de tokens formant de telles occurrences. L'analyse par transitions est une approche celebre qui construit une sortie structuree a partir d'une sequence d'elements, en appliquant une sequence de «transitions» choisies parmi un ensemble predefini, pour construire incrementalement la sortie. Dans cette these, nous proposons un systeme par transitions dedie a l'identification des EPs au sein de phrases representees comme des sequences de tokens, et etudions diverses architectures pour le classifieur qui selectionne les transitions a appliquer, permettant de construire l'analyse de la phrase. La premiere variante de notre systeme utilise un classifieur lineaire de type machine a vecteur support. Les variantes suivantes utilisent des modeles neuronaux: un simple perceptron multicouche, puis des variantes integrant une ou plusieurs couches recurrentes. Le scenario privilegie est une identification d'EPs n'utilisant pas d'informations syntaxiques, alors meme que l'on sait les deux tâches liees. Nous etudions ensuite une approche par apprentissage multitâche, realisant conjointement l’etiquetage morphosyntaxique, l’identification des EPs par transitions et l’analyse syntaxique en dependances par transitions. La these comporte une partie experimentale importante. Nous avons d'une part etudie quelles techniques de re-echantillonnage des donnees permettent une bonne stabilite de l'apprentissage malgre des initialisations aleatoires. D'autre part, nous avons propose une methode de reglage des hyperparametres de nos modeles par analyse de tendances au sein d'une recherche aleatoire de combinaison d'hyperparametres. Nous utilisons en effet de maniere privilegiee les donnees des deux competitions internationales PARSEME des EPs verbales. Nos variantes produisent de tres bons resultats, et notamment les scores d’etat de l’art pour de nombreuses langues de PARSEME. L’une des variantes s'est classee premiere pour la plupart des langues de PARSEME 1.0. Pourtant, nos modeles ont des performances faibles sur les EPs non vues a l'apprentissage.
Sediment Toxicity of Industrialized Coastal Areas of Korea Using Bioluminescent Marine Bacteria

The quality of marine sediments from the industrialized coastal areas of Korea (Ulsan Bay, Masan Bay, and artificial Lake Shihwa) was investigated using a bacterial bioluminescence toxicity test. Sediment toxicity results were compared with the levels of chemical contamination (trace metals, organic wastewater markers, acid volatile sulfides, total organic carbon). Effective concentration 50% (EC50) of sediments ranged from 0.014 to 1.126 mg/mL, which is comparable to or lower than values in contaminated lakes, rivers, and marine sediments of other countries. Sediment reference index (SRI) ranged from 13 to 1044, based on the EC50 of the negative control sample. Mean average SRI values in Masan Bay and Lake Shihwa were approximately 8 and 9 times as high as that in Ulsan Bay, indicating higher sediment toxicity and greater contamination in the two former regions. Sediment toxicity were strongly associated with the concentrations of some chemicals, suggesting that this test may be useful for determining potential chemical contamination in sediments.
Psychological Distress among College Students: Role of Food Insecurity and Other Social Determinants of Mental Health

Food insecurity is a major social determinant of health and an assessment of how it may impact college students’ mental health is imperative, as well as differential associations by self-identified gender. A cross-sectional survey was used among college students of a mid-size minority-serving institution with a final sample size of 302 participants aged 18 years or above. Descriptive, bivariate, and multivariable regressions were conducted, by gender, to assess the role of food insecurity (United States Department of Agriculture (USDA) six-item questionnaire), on mental health outcomes (Kessler-6 scale and self-perception). All the statistical analyses were conducted in SPSS version 24 (IBM, Corp.; Armonk, NY, USA) with an alpha less than 0.05 used to denote significance. Among those with food insecurity, the odds of reporting psychological distress (odds ratio (OR) = 3.645, p < 0.05) and an average to very poor self-perceived mental health status (OR = 2.687, p <0.05) were higher compared to their food-secure counterparts, with the results consistent in a gender-specific analysis as well. Compared to men, however, women had higher odds of psychological distress (OR = 2.280, p < 0.05), as well as reporting average to very poor self-perceived mental health statuses (OR = 2.700, p < 0.05). Among women, any alcohol use in the past 12 months (OR = 2.505, p < 0.05) and a low self-perceived physical health status (OR = 3.601, p < 0.05) were associated with an average to very poor self-perceived mental health status. Among men, a low perceived physical health status was associated with higher odds of psychological distress (OR = 3.477, p < 0.05). The results of our study highlight that food insecurity should be considered a social determinant of mental health wellbeing. In addition, gender-specific trends in mental health highlight the need for targeted interventions for prevention and treatment.