Miracle-dz/UniFAR-FTUs huggingface dataset:
Glutamine Synthetase, Peroxidase and Protease as Indicators of the Ecological State of Higher Aquatic Plants

2 Abstract: The contamination of water by heavy metals leads to conditions of ecological tension in the aquatic systems. In this work we consider to use the peroxidase, protease and glutamine synthetase of aquatic higher plants Typha angustifolia and Lemna polorhyza as indicators of ecological state of the aquatic biocenosis. In response to the 2.5 mg/l lead contamination the glutamine synthetase activity dropped down 10-fold already in 1 hour in the photosynthetic tissues of both plants with following restore up to 70-80% of initial activity values in 3 hours. Also strong inhibition of proteolytic activity without recovery in both L. Polorhyza and T.angustifolia leaves was detected after the lead introduction. By contrast, the peroxidase did not exhibit high sensitivity to the lead contamination and demonstrated 2-fold decreased activity. Taking together, these data demonstrate the possibility to evaluate the ecological state of higher aquatic plants by measuring the activity of the glutamine synthetase, peroxidase and protease in their photosynthetic tissues.
Comment on An additional challenge of Lake Kivu in Central Africa - upward movement of the chemoclines by Finn Hirslund

In a paper published earlier this year, Hirslund suggested to release degassed deepwater from methane harvesting to the surface layer of Lake Kivu in order to counteract an observed slow rising of the chemoclines in the lake. In this comment, we present strong evidence for the presence of subaquatic springs in the lake that maintain the chemoclines at their present levels. Furthermore, the observed changes in the stratification do not call for urgent action. We therefore strongly advise against the proposed measures, which would most probably be harmful for the ecosystem, and instead propose to further monitor the development of the stratification in the lake.
INTERACTIONS OF AN INSECTICIDE WITH COMPETITION AND POND DRYING IN AMPHIBIAN COMMUNITIES

Amphibian populations are often imbedded in agricultural landscapes. Therefore the potential for contamination of their habitat is considerable. Our study examined the effects of an insecticide (carbaryl, a neurotoxin), on larval amphibian communities experiencing natural stresses of competition for resources, predation, and pond drying. In a set of experimental ponds, tadpoles of three anuran species (southern leopard frog [Rana sphenocephala], plains leopard frog [R. blairi], and the Woodhouse's toad [Bufo woodhousii]) were added to 1000-L ponds containing leaf litter, plankton, two newts (Notophthalmus viridescens), and four overwintered green frog (R. clamitans) tadpoles. We manipulated the overall tadpole density (low or high), pond hydroperiod (constant or drying), and chemical exposure (0, 3.5, 5.0, or 7.0 mg/L carbaryl) of the ponds. We measured mass, time, and survival to metamorphosis to determine treatment effects. Carbaryl positively affected Woodhouse's toad survival, although it had a neglig.
Megafaunal assemblages from two shelf stations west of Svalbard

Abstract Megafauna plays an important role in benthic ecosystems and contributes significantly to benthic biomass in the Arctic. The distribution is mostly studied using towed cameras. Here, we compare the megafauna from two sites located at different distances from the Kongsfjord: one station at the entrance to the fjord, another on the outer shelf. Although they are only located 25 km apart and at comparable depth, there were significant differences in their species composition. While the inshore station was characterized by shrimps (2.57±2.18 ind. m−2) and brittlestars (3.21± 3.21 ind. m−2), the offshore site harboured even higher brittlestar densities (15.23±9.32 ind. m−2) and high numbers of the sea urchin Strongylocentrotus pallidus (1.23±1.09 ind. m−2). Phytodetrital concentrations of the upper sediment centimetres were significantly higher inshore compared with offshore. At a smaller scale, there were also differences in the composition of different transect sections. Several taxa were characterized by a patchy distribution along transects. We conclude that these differences were caused primarily by habitat characteristics. The seafloor inshore was characterized by glacial soft sediments, whereas the station offshore harboured large quantities of stones. Although the use of a new web-2.0-based tool, BIIGLE (http://www.BIIGLE.de), allowed us to analyse more images (∼90) than could have been achieved by hand, taxon area curves indicated that the number of images analysed was not sufficient to capture the species inventory fully. New automated image analysis tools would enable a rapid analysis of larger quantities of camera footage.
The Effect of Concentrate Feeding Levels on the Postweanining Performance of Holstein Friesian Calves

The influences of different levels of concentrate on the growth characteristics of Holstein Friesian calves reared under an original calf-rearing program were investigated in this study. Forty-one new-born calves (20 male and 21 female) were allocated to the four concentrate groups: 2, 2.5, 3 kg/calf and ad libitum. The calves were weaned at 5 weeks of age, and the trial lasted for 6 months. The results with regard to weights at 6 months of age revealed that an increasing amount of concentrate supplementation resulted in a significantly (P < 0.01) higher live weight. Furthermore, daily weight gains between birth and 6 months of age was also significantly higher (P < 0.01) in the ad libitum group than in the 2, 2.5 and 3 kg/day groups. The highest overall gains in body measurements, for example body length and heart girth, were obtained from calves fed concentrate ad libitum. However, feed efficiency ratios were not significantly influenced by the various amounts of concentrate offered to calves. The overall results suggest that the appropriate level of concentrate for the new calf-rearing program should be ad libitum.
Clinical and Genetic Diversity of PMP22 Mutations in a Large Cohort of Chinese Patients With Charcot-Marie-Tooth Disease

Charcot-Marie-Tooth (CMT) disease is a clinically and genetically heterogeneous group of inherited neuropathies. The purpose of this study is to identify the clinical and genetic diversity of peripheral myelin protein 22 (PMP22) in Chinese patients with CMT disease and evaluate their correlations with the clinical manifestations. Using the multiplex ligation-dependent probe amplification (MLPA) technique and Sanger sequencing of PMP22 in a cohort of 465 Chinese families between 2007 and 2019, we identified 137 pedigrees with PMP22 duplications (29.5%), 26 pedigrees with PMP22 deletions (5.6%), and 10 pedigrees with point mutations (2.2%). By comparing our data with the results from other CMT centers in China, we estimate that the frequency of PMP22 mutation in mainland China is ~23.3% (261/1120). We confirmed de novo mutations in 40% (4/10) of PMP22 point mutations. We have also identified two severely affected patients who are compound heterozygotes for recessive PMP22 mutations (novel mutation c.320-1 G>A and R157W mutation) and a 1.5 Mb deletion in 17p11.2-p12, suggesting that c.320-1 G>A might be another recessive allele contributing to DSS in addition to the T118M and R157W mutations. A de novo mutation of S79P in PMP22 was also identified concomitantly with the R94W mutation in mitofusin2 (MFN2). Our study highlights the phenotypic variability associated with PMP22 mutations in mainland China. The results provide valuable insights into the current strategy of genetic testing for CMT disease. NGS technology has increased the potential for efficient detection of variants of unknown significance (VUS) and concurrent causative genes. Greater cooperation between neurologists and molecular biologists is needed in future investigations.
Low plasma 25(OH) vitamin D level is associated with increased risk of COVID‐19 infection: an Israeli population‐based study

Vitamin D deficiency is a worldwide pandemic. The aim of this study was to evaluate associations of plasma 25(OH)D levels with the likelihood of coronavirus disease 2019 (COVID‐19) infection and hospitalization. The study population included the 14 000 members of Leumit Health Services, who were tested for COVID‐19 infection from February 1st to April 30th, 2020, and who had at least one previous blood test for the plasma 25(OH)D level. ‘Suboptimal’ or ‘low’ plasma 25(OH)D level was defined as plasma 25‐hydroxyvitamin D, or 25(OH)D, concentration below the level of 30 ng/mL. Of 7807 individuals, 782 (10.02%) were COVID‐19‐positive, and 7025 (89.98%) COVID‐19‐negative. The mean plasma vitamin D level was significantly lower among those who tested positive than negative for COVID‐19 [19.00 ng/mL (95% confidence interval (CI) 18.41–19.59) vs. 20.55 (95% CI: 20.32–20.78)]. Univariate analysis demonstrated an association between the low plasma 25(OH)D level and increased likelihood of COVID‐19 infection [crude odds ratio (OR) of 1.58 (95% CI: 1.24–2.01, P < 0.001)], and of hospitalization due to the SARS‐CoV‐2 virus [crude OR of 2.09 (95% CI: 1.01–4.30, P < 0.05)]. In multivariate analyses that controlled for demographic variables, and psychiatric and somatic disorders, the adjusted OR of COVID‐19 infection [1.45 (95% CI: 1.08–1.95, P < 0.001)] and of hospitalization due to the SARS‐CoV‐2 virus [1.95 (95% CI: 0.98–4.845, P = 0.061)] were preserved. In the multivariate analyses, age over 50 years, male gender and low–medium socioeconomic status were also positively associated with the risk of COVID‐19 infection; age over 50 years was positively associated with the likelihood of hospitalization due to COVID‐19. We concluded that low plasma 25(OH)D levels appear to be an independent risk factor for COVID‐19 infection and hospitalization.
Effect of plant growth regulator on in vitro micropropagation of 'Bitter Yam' (Dioscorea hispida Dennst.)

The present study reports a highly efficient and cost effective protocol for high frequency plantlet regeneration from nodal explants of Dioscorea hispida. Nodal vine segments from 40 days old plants of Dioscorea hispida were cultured on Murashige and Skoog’s (MS) medium supplemented with different concentration and combination of cytokinin i.e. 6-Benzyl Aminopurine (BAP) and auxin i.e. α-naphthalene acetic acid (NAA) to evaluate optimum condition for multiple shoot proliferation. The highest number of multiple shoot proliferation was obtained with explants cultured on MS medium supplemented with 2.0 mg/l BAP+0.5 mg/l NAA +100mg/l ascorbic acid. Shoot multiplication rate was maintained by repeated sub culturing on to fresh media containing same growth regulators. When elongated invitro shootlets were inoculated to half-strength MS basal media supplemented with 2.0 mg/l NAA+2 g/l activated charcoal, rooting was more profuse. Rooted shoots were transplanted in the green house for hardening and their survival was 90% in the field conditions.
RICE STRIPE VIRUS

Rice stripe disease has become a widespread and destructive virus disease coinciding with the extension of early planting of the rice crop in Japan. The disease has been reported in every rice growing area except the northern parts of Tohoku district in . Tapan. Rice stripe virus (RSV), the causal agent, is transmitted by leafhoppers such as Laodelpha:r striatellu8, Unkanocles sapporonus, Ribau.todelphax albifascia, and Terthron albovittatus. A high rate of transovarial passage of the virus and serial passage of the virus by micro-injection method showed virus multiplication in vector insects. Leafhopper transmission or varietal resistance has been studied by many workers. Prior to the perfect purification of RSV, Yasuo and Yanagita (1963) succeeded in preparing the antiserum against the virus by injecting the crude sap from RSV-infected rice leaves into rabbits. Okuyama (1959) first reported the purification of RSV from RSV-infetced rice leaves. They found spherical particles of 30-50 nm in diameter in the purified preparation. Saito et al. (1964) also purified RSV and demonstrated that RSV was a spherical virus of about 30 nm in diameter. Kitani and Kiso (1968) isolated RSV as spherical particles of the same size which showed infectivity in micro-injection tests into Laodelphax striatellus. In a preliminary experiment, the author could not find any spherical virus particle in preparations obtained by the method described by Kitani and Kiso (1968). So the author attempted to isolate and find RSV particles.
In-Depth Bioinformatic Analyses of Nidovirales Including Human SARS-CoV-2, SARS-CoV, MERS-CoV Viruses Suggest Important Roles of Non-canonical Nucleic Acid Structures in Their Lifecycles

Non-canonical nucleic acid structures play important roles in the regulation of molecular processes. Considering the importance of the ongoing coronavirus crisis, we decided to evaluate genomes of all coronaviruses sequenced to date (stated more broadly, the order Nidovirales) to determine if they contain non-canonical nucleic acid structures. We discovered much evidence of putative G-quadruplex sites and even much more of inverted repeats (IRs) loci, which in fact are ubiquitous along the whole genomic sequence and indicate a possible mechanism for genomic RNA packaging. The most notable enrichment of IRs was found inside 5′UTR for IRs of size 12+ nucleotides, and the most notable enrichment of putative quadruplex sites (PQSs) was located before 3′UTR, inside 5′UTR, and before mRNA. This indicates crucial regulatory roles for both IRs and PQSs. Moreover, we found multiple G-quadruplex binding motifs in human proteins having potential for binding of SARS-CoV-2 RNA. Non-canonical nucleic acids structures in Nidovirales and in novel SARS-CoV-2 are therefore promising druggable structures that can be targeted and utilized in the future.
Nitrospina-Like Bacteria Are Potential Mercury Methylators in the Mesopelagic Zone in the East China Sea

In natural environments, the production of neurotoxic and bioaccumulative methylmercury (MeHg) is mediated by microorganisms carrying the genes hgcA and hgcB. However, the contribution of these microorganisms to mercury (Hg) methylation or MeHg accumulation in the ocean is poorly understood. Here we determined the total Hg (THg) and MeHg concentrations in seawater samples and conducted a metagenomic survey of the hgcAB genes and functional modules involved in metabolic pathways in the East China Sea (ECS). In the metagenomic analyses, we used paired-end reads and assembled contigs for hgcAB enumeration and phylogenetic analyses in the seawater column. To evaluate the relative abundance of hgcAB in the metagenomic data, we estimated the abundance of recA (single-copy gene of bacteria) as well and then compared them. Moreover, the profiles of prokaryotic community composition were analyzed by 16S rRNA gene (V4 region) deep-sequencing. In the mesopelagic layers, the hgcA sequences were detected, and there was a positive correlation between hgcA abundance relative to the recA and MeHg concentrations. Thus, the quantification of the hgcA sequences could provide valuable information to evaluate the potential environments of microbial MeHg accumulation in the seawater column. A phylogenetic analysis using the assembled contigs revealed that all of the hgcA sequences in the mesopelagic layers were affiliated with Nitrospina-like sequences. The 16S rRNA gene analysis revealed that Nitrospinae were abundant in the mesopelagic layers. Although the lineages of Deltaproteobacteria, Firmicutes, and Spirochaetes were detected in the seawater column, their hgcAB sequences were not detected in our metagenomes, despite the fact that they are closely related to previously identified Hg methylators. The metabolic pathway analysis revealed that the modules related to sulfur and methane metabolism were prominent in the mesopelagic layers. However, no hgcA sequences affiliated with sulfate-reducing bacteria (SRB) or methanogens were detected in these layers, suggesting that these bacteria could not be strongly involved in the Hg accumulation in the seawater column. Our results indicate that Nitrospina-like bacteria with hgcAB genes could play a critical role in microbial Hg accumulation in the oxygenated mesopelagic layers of the ECS.
Weaving relationships in areas of cultural contacts: production, use and consumption of loom weights in pre-Roman Sicily

This paper emerges from a wider research program ‘Tracing Networks. Craft traditions in the ancient Mediterranean and beyond’. Our specifi c project within the program (‘Weaving relationships’) concerns loom weights in the ancient Mediterranean, with particular attention to southern Italy and Greece. These objects have rarely been the subject of careful analysis, although they provide important information about weaving, an activity typically associated with women in this area in antiquity. Their systematic and contextual study allows us: 1) to increase our knowledge of technologies of textile production and weaving; 2) to understand better the manufacturing processes and life histories of loom weights, which are far more complex than has generally been recognised; 3) to explore the socio-cultural relationships and emotional ties between women, as well as personal, familial and group identities. In this paper we investigate what interaction existed between the traditions of making and using loom weights in Sicily, a paradigmatic example of intense and deep contacts between the Greeks and the indigenous communities. We explore: 1) the signifi cance of morphological and technical characteristics, including decoration, for understanding social links; 2) how objects travel through time and accumulate histories; 3) how innovations may be met by adaptation and ‘resistance’.
Anatomical and histological changes during the oestrous cycle in the mare

The mares chosen for the investigation of the changes in the reproductive organs during the oestrous cycle were kept under observation for some time before they were killed. The duration of the heat period in these animals was 7 days and the length of the dioestrus was 16 days. Ovulation takes place at about a day before the end of oestrus. The size of the ovary during the oestrous cycle is chiefly influenced by the growing Graafian follicle. The number of follicles present at different stages varies greatly. The numerous small follicles present at the beginning of oestrus disappear later in the cycle; it is suggested that this may be due to the lack of follicle-stimulating hormone. The colour of the corpus luteum varies greatly at different stages of the cycle. The rupture of the follicle is associated with some bleeding. The active stage of the corpus luteum is very short, and the maximum diameter of the corpus luteum seems to be always below that of the Graafian follicle. The greater development of the Graafian follicle, with its secretion of oestrin, in the mare leads to its playing a more important role than in the cow and the sow, in which species the corpus luteum takes a m ore dominant part in the cycle. It appears that the much longer oestrus in the mare than in the cow is due to the longer time required by the follicle to come to the surface and to break through. This is probably due to the peculiar structure of the ovary in the mare, since the ovulation, which is spontaneous, can only occur in the small ovulation fossa. No pronounced secretion stage occurs during oestrus in the Fallopian tubes.
Genetic Divergence and Chimerism within Ancient Asexually Propagated Winegrape Cultivars

In total, 25 clones of Vitis vinifera 'Pinot noir' and 22 clones of 'Chardonnay' were analyzed with 100 microsatellite markers, selected from an initial screening of 228 markers. Of the 100 markers, 17 detected polymorphism within one or both of the cultivars. In 'Pinot noir', 15 polymorphic markers detected 15 different genotypes, uniquely distinguished 12 clones out of the 25 and separated the remaining 13 clones into 3 groups. In 'Chardonnay', 9 polymorphic markers detected 9 genotypes and uniquely distinguished 6 clones out of the 22. The remaining 16 clones were separated into 3 groups. For markers that were polymorphic in 'Pinot noir' and 'Chardonnay', none of the variant alleles were common to both cultivars. It is inferred from this result that the natural cross that produced 'Chardonnay' probably occurred when 'Pinot' was still relatively young. Many of the variant genotypes were expressed as three alleles. Further analysis revealed the presence of chimeras in which the third allele was present in leaf but not root or wood tissues, confirming that the grape apical meristem is functionally two-layered. Some clones that share the same microsatellite genotype are documented to have originated in the same locality, suggesting that the origins of undocumented clones may be traced by comparing their microsatellite genotypes with those of well-documented clones. Because clones of 'Pinot noir' and 'Chardonnay' are often visually indistinguishable, microsatellite genotyping may also be useful to detect identification errors in collections and nurseries. Because winemakers have strong preferences for certain clones, it has become increasingly important to be able to identify them. Morphological differences between clones are slight at best and are often obscured by environmental variables and cultural practices. An objective means by which to distinguish them has long been sought.
Figural Memory Impairment in Conjunction With Neuropsychiatric Symptoms in IgLON5 Antibody-Associated Autoimmune Encephalitis

Background IgLON5 disease is an autoimmune disorder that shares neuropathological aspects with a tauopathy. Its clinical spectrum is heterogeneous, and figural memory impairment as an initial phenomenon of IgLON5 syndrome has not yet been described. The rationale of this report is to highlight symptoms related to IgLON5 disease that have not been reported to date. This case report will thereby emphasize how important it is to initiate thorough diagnostic methods including cerebrospinal fluid analysis (CSF) before starting early immunotherapy. Methods We examined a 65-year-old Caucasian male via neuropsychological tests, magnetic resonance imaging (MRI), electroencephalography (EEG), neurography and polysomnography. He also underwent two lumbar punctures from which we determined specific autoantibodies in cerebrospinal (CSF) and peripheral blood (PB). Results The patient presented initially complaining of memory loss, gradual dysphagia and sleeping dysfunction. Neuropsychological testing at first presentation and follow-up revealed subtle figural and working memory impairment. At onset and at his 6-month follow-up, we detected IgLON5 antibodies in CSF and PB. Furthermore, we identified in the CSF a blood–brain barrier disturbance at disease onset and follow-up, and markers of neuroaxonal damage such as mildly elevated phosphorylated Tau-181 protein with 86 pg/ml (normal range ≤ 61 pg/ml) at onset. Three months after his initial presentation, he was suffering from axonal neuropathy and transient ataxia in the extremities. Assuming a definitive autoimmune encephalitis-associated with anti-IgLON5 antibodies, we applied high-dose steroids monthly (1g methylprednisolone i.v. for five consecutive days) and his memory complaints, ataxia of extremities and peripheral neuropathy as well as sleeping dysfunction decreased. Conclusions Our findings broaden IgLON5 disease’s clinical spectrum to include predominant and discrete figural memory impairment together with sleeping dysfunction at disease onset. In addition, our report illustrates how important taking an elaborated diagnostic approach is to assuring an accurate diagnosis and the appropriate therapy if a patient presents with a persisting figural memory impairment and sleeping abnormalities so as to avoid overlooking IgLON5 disease and a potentially poor outcome.