Miracle-dz/UniFAR-FTUs huggingface dataset:
BRAF mutation, TERT promoter mutation, and HER2 amplification in sporadic or neurofibromatosis‐related neurofibromas and malignant peripheral nerve sheath tumors: do these molecules have a signature in malignant transformation?

Peripheral nerve sheath tumors may occur sporadically or related to neurofibromatosis (NF). Unless the mechanisms of tumorigenesis in NF related malignant peripheral nerve sheath tumors (MPNST) are better understood, it remained unclear in sporadic cases. We aimed to investigate the genetic route for malignancy in both individuals with NF‐1 and sporadic ones to open a way for targeted therapies in the future. We investigated the role of HER2 with Dual ISH DNA Probe Cocktail test, BRAF mutation (exon 15) and TERT promoter mutation frequency with Sanger sequencing method in respectively 25 sporadic neurofibromas, 25 NF‐1 related neurofibromas and 25 MPNST cases from two institutes. Categorical data were analyzed and summarized as frequency and percentage. Statistical analysis was done with SPSS v.22 statistical package, and the statistical significance level was considered as 0.05. We identified TERT promoter mutation only in one sporadic MPNST (4%) and no BRAF mutation in any case. HER2 amplification is found in 10/25 (40%) MPNST cases. No mutations or gene amplification detected in neurofibromas (p < 0.001). MPNSTs are sarcomas with poor prognosis and limited treatment options. TERT promoter mutations and HER2 amplification may play a putative role in therapeutic purposes.
Evaluation of Stoffenmanager and a New Exposure Model for Estimating Occupational Exposure to Styrene in the Fiberglass Reinforced Plastics Lamination Process

This study aims to evaluate occupational exposure models by comparing model estimations of Stoffenmanager, version 8.2, and exposure scores calculated using a new exposure model with personal exposure measurements for styrene used in the fiberglass-reinforced plastic (FRP) lamination processes in Korea. Using the collected exposure measurements (n = 160) with detailed contextual information about the type of process, working conditions, local exhaust ventilation, respiratory protections, and task descriptions, we developed a new model algorithm to estimate the score for occupational exposures on situation level. We assumed that the source of exposure originates from the near field only (within the breathing zone of workers). The new model is designed as a simple formula of multiplying scores for job classification, exposure potential, engineering controls, chemical hazard, and exposure probability and then dividing the score for workplace size. The final score is log-transformed, ranging from 1 to 14, and the exposure category is divided into four ratings: no exposure (1), low (2), medium (3), and high (4) exposures. Using the contextual information, all the parameters and modifying factors are similarly entered into the two models through direct translation and coding processes with expert judgement, and the exposure estimations and scores using the two models are calculated for each situation. Overall bias and precision for Stoffenmanager are −1.00 ± 2.07 (50th) and −0.32 ± 2.32 (90th) for all situations (n = 36), indicating that Stoffenmanager slightly underestimated styrene exposures. Pearson’s correlation coefficients are significantly high for Stoffenmanager (r = 0.87) and the new model (r = 0.88), and the correlation between the two models is significantly high (r = 0.93) (p < 0.01). Therefore, the model estimations using Stoffenmanager and the new model are significantly correlated with the styrene exposures in the FRP lamination process. Further studies are needed to validate and calibrate the models using a larger number of exposure measurements for various substances in the future.
Role of institutional and socio-economic factors on adoption, dis-adoption and non-adoption of soil and water conservation technologies: Empirical evience from the North Western Ethiopia highlands.

ABSTRACT In order to combat land degradation in the form of water erosion and fertility depletion in the Central Rift Valley (CRV) of Ethiopia farmers are of crucial importance. If they perceive land degradation as a problem they will be more willing to invest in land management measures. This study presents farmers’ perceptions of land degradation, respective investments, and factors influencing their investments in land. In this study, water erosion and fertility depletion are taken as main indicators of land degradation. Results show that farmers perceive water erosion and soil fertility depletion as problems that have intensified over the last decade. However, despite awareness of these problems, farmers’ investments to control soil erosion and soil fertility depletion are very limited. This study shows that the major factors that positively influence farmers’ investments in land management practices are households’ resource endowments, access to information, social capital and availability of family labor. For sustainable land management strategies this implies that these should (i) be integrated within a comprehensive rural development strategy that generates improvements of farmers’ livelihoods and their financial capacity, (ii) trigger social capital and create enabling conditions for farmers to participate in different groups, cross site visits and farmer-to-farmer experience sharing, and (iii) stimulate collective action within the villages in order to enhance access to labor which is crucial for carrying out land management practices. Key words: Land degradation, farmers’ investments, sustainable land management, socioeconomic factors, factor analysis
New insights on the functions of carbon-calcium-inclusions in plants.

The carbon-calcium-inclusions (CCaIs) either as calcium oxalate crystals (CaOx) or amorphous calcium carbonate cystoliths are spread among most photosynthetic organisms. They represent dynamic structures with a significant construction cost and their appearance during evolution indicates an ancient origin. Both types of inclusions share some similar functional characteristics providing adaptive advantages, such as the regulation of Ca level, and the release of CO2 and water molecules upon decomposition. The latter seems to be essential under drought conditions and explains the intense occurrence of these structures in plants thriving in dry climates. It seems, however, that for plants CaOx may represent a more prevalent storage system compared to CaCO3 due to the multifunctionality of oxalate. This compound participates in a number of important soil biogeochemical processes, creates endosymbiosis with beneficial bacteria and provides tolerance against a combination of abiotic (nutrient deprivation, metal toxicity) and biotic (pathogens, herbivores) stress factors. We suggest a reevaluation of the roles of these fascinating plant structures under a new and holistic approach that could enhance our understanding of carbon sequestration at the whole plant level and provide future perspectives.
Prealbumin as a Predictor of Prognosis in Patients With Coronavirus Disease 2019

Background: The predictive value of prealbumin for the prognosis of coronavirus disease 2019 (COVID-19) has not been extensively investigated. Methods: A total of 1,115 patients with laboratory-confirmed COVID-19 were enrolled at Tongji hospital from February to April 2020 and classified into fatal (n = 129) and recovered (n = 986) groups according to the patient's outcome. Prealbumin and other routine laboratory indicators were measured simultaneously. Results: The level of prealbumin on admission was significantly lower in fatal patients than in recovered patients. For predicting the prognosis of COVID-19, the performance of prealbumin was better than most routine laboratory indicators, such as albumin, lymphocyte count, neutrophil count, hypersensitive C-reactive protein, d-dimer, lactate dehydrogenase, creatinine, and hypersensitive cardiac troponin I. When a threshold of 126 mg/L was used to discriminate between fatal and recovered patients, the sensitivity and specificity of prealbumin were, respectively, 78.29 and 90.06%. Furthermore, a model based on the combination of nine indexes showed an improved performance in predicting the death of patients with COVID-19. Using a cut-off value of 0.19, the prediction model was able to distinguish between fatal and recovered individuals with a sensitivity of 86.82% and a specificity of 90.37%. Conclusions: A lower level of prealbumin on admission may indicate a worse outcome of COVID-19. Immune and nutritional status may be vital factors for predicting disease progression in the early stage of COVID-19.
Review: Effects of feeding sugars on productivity of lactating dairy cows

Oba, M. 2011. Review: Effects of feeding sugars on productivity of lactating dairy cows. Can. J. Anim. Sci. 91: 37–46. Sugars are water-soluble carbohydrates that are readily available in the rumen. Although sugars ferment faster than starch or fibre in the rumen, the rates of disaccharide hydrolysis and monosaccharide fermentation vary greatly depending on the type of sugar and rumen environment. Despite rapid fermentation in the rumen and their potential to provide greater fermentable energy to enhance microbial protein production, feeding sugars in place of dietary starch sources may not decrease rumen pH or improve N utilization efficiency and milk protein production in dairy cows. However, feeding high-sugar diets often increases dry matter intake, butyrate concentration in the rumen, and milk fat yield. These nutritional characteristics of sugars may allow us to use high-sugar feedstuffs as an alternative energy source for lactating dairy cows to increase dietary energy density with reduced risk of .
Distribution and molecular characterization of the root endophyte Phialocephala fortinii along an environmental gradient in the boreal forest of Alberta

Phialocephala fortinii is a common root endophytic fungus with a wide geographic distribution and little, if any, host specificity. Little is known about its habitat specificity, although there is evidence to suggest that high water tables may restrict the occurrence of P. fortinii in wetlands. We tested this hypothesis by determining the distribution of P. fortinii along a sand dune – wetland complex. Isolates of P. fortinii, identified on the basis of cultural and morphological characteristics, were obtained from the roots of vascular plants across the moisture gradient. Three ‘cultural groups’ were recognized among these isolates. Thirty-three of these isolates were compared among themselves and to strains of known identity using PCR/RFLP analysis of the ITS region and a portion of the 28S subunit of rDNA. The restriction digest profiles of all isolates were identical to those of P. fortinii for 4 restriction enzymes. DNA sequences, from a subset of these strains, showed a low percent sequence divergence confirming the reliability of the RFLP data. The same analyses were done with two strains of Leptodontidium orchidicola a culturally similar root endophyte, to ensure that this taxon was not among the transect isolates. DNA data showed a clear difference between P. fortinii and L. orchidicola but did not discriminate among cultural groups. Thus, P. fortinii showed no habitat specificity and occurred in both xeric and hydric sites. RFLP profiles and ITS sequences showed little variation among isolates of P. fortinii and among the isolates of L. orchidicola.
Structuration de la diversité génétique et analyse des patrons de déséquilibre de liaison de l'espèce Coffea canephora Pierre ex. Froehner

La recherche d'associations entre marqueurs moleculaires et les variations de caracteres d'interet agronomique est un enjeu majeur du developpement de la selection assistee par marqueurs, notamment pour des especes perennes. La connaissance de la diversite genetique et de la structure de celle-ci est un prealable indispensable a la mise en place de telles etudes. Au meme titre, la connaissance de l'etendue et de l'intensite du desequilibre de liaison au sein des populations considerees est egalement necessaire. Nous avons donc entrepris de confirmer et de preciser la diversite et la structure genetique de Coffea canephora Pierre afin d'evaluer les potentialites d'etudes d'association sur cette espece. Nous avons pose les bases d'une caracterisation rapide des collections de ressources genetiques de cette espece a l'aide de marqueurs microsatellites et precise l'origine genetique d'une population jusqu'a present non etudiee. Cette base pourra egalement servir au developpement de futures cores-collections. L'evaluation de la structure et de l'etendue du desequilibre de liaison a differentes echelles et au niveau de differentes populations ou groupes de diversite a l'aide de 108 marqueurs repartis sur l'ensemble du genome nous a permis de proposer des populations utilisables pour les 2 types d'approches de genetique d'associations, scan genome entier ou region candidate. Un premier essai d'etude d'association a montre les potentialites importantes de ces approches pour notre espece. Les implications de l'importance de la diversite genetique et de sa structure ainsi que de la structure du desequilibre de liaison au sein de nos populations pour l'amelioration sont discutees.
Clostridium difficile infection and intestinal microbial ecology

For many microorganisms, including Clostridium difficile, mucosal association is an important factor influencing intestinal colonisation and subsequent infection. Inhibition of adhesion of C. difficile to intestinal mucosa could be a new promising strategy for prevention and treatment of antibiotic-associated diarrhoea. We investigated the possibilities of influencing the adhesion of C. difficile by xylitol and bovine colostrum whey. Caco-2 cells and C. difficile cells were incubated with 1%, 5% and 10% solutions of xylitol and colostrum. Our study revealed that both xylitol and colostrum inhibited the adhesion of C. difficile to Caco-2 cells. Inhibition by xylitol was dose-dependent. When compared to the control, the count of adherent C. difficile decreased 3.4 times when treated with 1% xylitol, 12 times when 5% xylitol was applied, and 18.7 times when treated with 10% xylitol. The inhibition of adherence by colostrum was partially dose-depen­ dent: 3.1 times in the case of 1%, and 5.5 times in the cases of 5% and 10% colostrum. Further experimental and clinical studies are needed for the application of xylitol and colostrum in the treatment and prophylaxis of pseudomembraneous
Stable integration of an optimized inducible promoter system enables spatiotemporal control of gene expression throughout avian development

Precisely altering gene expression is critical for understanding molecular processes of embryogenesis. Although some tools exist for transgene misexpression in developing chick embryos, we have refined and advanced them by simplifying and optimizing constructs for spatiotemporal control. To maintain expression over the entire course of embryonic development we use an enhanced piggyBac transposon system that efficiently integrates sequences into the host genome. We also incorporate a DNA targeting sequence to direct plasmid translocation into the nucleus and a D4Z4 insulator sequence to prevent epigenetic silencing. We designed these constructs to minimize their size and maximize cellular uptake, and to simplify usage by placing all of the integrating sequences on a single plasmid. Following electroporation of stage HH8.5 embryos, our tetracycline-inducible promoter construct produces robust transgene expression in the presence of doxycycline at any point during embryonic development in ovo or in culture. Moreover, expression levels can be modulated by titrating doxycycline concentrations and spatial control can be achieved using beads or gels. Thus, we have generated a novel, sensitive, tunable, and stable inducible-promoter system for high-resolution gene manipulation in vivo.
Unveiling the mysteries of phytoplankton life cycles: patterns and opportunities behind complexity

Life cycles of phytoplankton species have been selected over a long evolutionary history and represent a key element for our understanding of their ecology and natural history and for improving our comprehension of ocean functioning. A species can alternate in its life cycle between four distinct major phases: growth, sex, quiescence and cell death. This implies that the population of a phytoplankton species found in any particular water sample will contain cells that undergo different fates, have strong differentiation in physiology and have different functional roles even if they are genetically identical. The factors regulating transitions among the different phases are still largely unknown but have direct impacts on the ecological distribution of species and on their biogeochemical function. Focused research efforts in recent years have begun to reveal emerging patterns in the variability of phytoplankton life cycle traits. This research has relied both on careful observations in culture and at sea and on making use of new genomics-and transcriptomics-based tools. The study of phytoplankton in the context of their life cycle characteristics opens up new opportunities to address fundamental questions about the physiology and cell biology of these important organisms and creates a new evolutionary and ecological framework for defining phytoplankton functional groups.
The intercellular distribution of vacuolar solutes in the epidermis and mesophyll of barley leaves changes in response to NaCl

Concentrations of inorganic and organic solutes were measured in sap extracted from individual mesophyll and epidermal cells of the third leaf of barley. During the development of the third leaf plants were grown in various salt solutions (NaCI; 2, 50,100, and 150 mM, KCI; 100 mM or KN03; 100 mM). Leaves were analysed 2-4 d after full expansion. Cell-sap was extracted using a modified pressure probe and analysed for its osmolality, concentrations of P, Na+, K + , Ca 2+, and C\ and, in some cases, of nitrate, hexoses and total amino acids. Salt treatment caused differential changes in the concentrations of solutes in mesophyll and epidermal cells, but did not affect the basic pattern of solute compartmentation between these tissues. Calcium was found at osmotically significant concentrations only in the epidermis, whereas P and organic solutes were almost exclusively found in the mesophyll. Chloride and Na+ accumulated preferentially in the epidermis, although mesophyll concentrations also increased considerably. At 150 mM external NaCI, mesophyll cells contained 302 mM Na + and 167 mM Cr, compared to 29 mM Na+ and 16 mM CI" in the control. Mesophyll CI" levels were even higher in the 100 mM KCI treatment (216 mM) where mesophyll and epidermal K+ accumulated to 424 and 491 mM, respectively. These huge increases in mesophyll Na + , Cl~ and K+ were not associated with a breakdown in leaf performance since net rates of photosynthesis decreased only by less than 20%. Under control (2 mM NaCI) conditions, solutes followed patterned gradients between the various epidermal cell types. The extent of these gradients changed with leaf age. During 50 mM NaCI treatment, gradients in Cr, nitrate and malate concentrations progressively disappeared, with malate concentrations approaching zero. Potassium and Na+ exhibited altered distribution profiles, whereas Ca2+ distribution was unaffected. NaCI-dependent increases in osmolalities differed between cells. Exposure of plants to 150 mM NaCI caused qualitatively similar changes in both epidermal solute and osmolality profiles, although absolute values differed from those at 50 mM NaCI. In particular, epidermal CI' and Na+ increased to about 500 mM and K+ disappeared (^5mM) from the vacuole of certain epidermal cell types completely.
Ações sustentáveis na produção de ovos

A busca por indicadores de sustentabilidade nas cadeias produtivas tornou-se urgente em funcao da crescente exigencia dos consumidores por informacoes que antes nao eram consideradas na escolha de um produto, levando-se em conta as implicacoes eticas e ambientais na producao de um alimento, agora observados como atributos essenciais de qualidade e seguranca alimentar. Como definicao geral e simplificada, os sistemas sustentaveis de producao de alimentos devem ser socialmente responsaveis, economicamente viaveis, garantir a saude e o bem-estar humanos e animal, e a protecao ao meio-ambiente. Dentro desse contexto, as agroindustrias vem adaptando-se as mudancas, no sentido de atender as exigencias dos mercados atraves da implementacao de praticas sustentaveis na producao de alimentos. Acoes objetivas para alcance dos propositos de sustentabilidade na producao de alimentos devem basear-se em principios de boas-praticas de producao (BPP) considerando a abordagem integral (“
RESUSCITATED VARIATION MODEL FOR IMAGE DEHAZING

-------------------------------------------------------------------------- ABSTRACT: Fuzzy-view photography usually suffers from low-contrast, which reduces the visibility of the scene. The performance of single-image dehumidification methods is limited by the priests or the restrictions. In this paper, we present an effective method for fog removal, which uses retrieved correlated fog-free images as external information. The proposed variable model includes two `1-standard regularization rules to prevent visual transmission and transverse visual illumination, which are best applied in the image dehumidification area. In contrast to the traditional two-stage framework, our proposed
Udder health in organic dairy cattle in Northern Spain

This paper presents first data on the udder health status of organic dairy farms in Northern Spain and analyses some management and productive characteristics related to milk production comparing with the conventional sector. Five certified organic farms from the Cantabrian Region were monitored monthly from February 2006 to January 2008 and individual samples of all lactating cows were taken from parturition to the end of lactation. Although organic farms in our study showed a great individual variability, overall these were small (<50 lactating cows) traditional farms, with a high degree of pasture (66-82% dry matter intake) and a milk production (average milk yield: 5950 L) 23% lower compared with the reference conventional sector (<50 cow farms). The organic farms had higher ( p <0.05) average number of calves per cow (3.93) and a lower number of first-lactation cows (16.9%) than the comparable conventional farms (2.47 calves per cow and 33.1% first-lactation cows). Organic farms showed higher ( p <0.05) somatic cell counts (SCC) than the reference conventional farms (mean log 10 ±SD for all cows: 5.25±0.49 and 5.06±0.59, respectively). Detailed analysis of the SCC depending on the number of lactation and % of monthly SCC tests with linear scores indicative of udder infection suggest that while the heifers’ sanitary condition at the beginning of their productive cycle was similar in both types of farms, this seems to become worse along the productive cycle in the organics. This could be related to a low use of antibiotics for prophylaxis and treatment of udder infections and merits further investigation.
Cotton Leaf Reddening in the Irrigated Gezira

Summary Cotton leaf reddening was studied in irrigated vertisols at the Gezira Research Farm over three seasons. The percentage leaf reddening was negatively correlated with seed cotton yield. Plants showing symptoms of reddening produced smaller and fewer leaves which did not persist long enough to sustain the reproductive parts. Deficiencies of nitrogen and phosphorus were found to be responsible for the reddening symptoms. Nitrogen application, late August sowing and frequent control of insect pests all significantly reduced the incidence of reddening. Other possible remedies are discussed.