Miracle-dz/UniFAR-FTUs huggingface dataset:
Genetic Variation Analysis of EMS-Induced Chili Pepper (Capsicum frutescens L.) Mutants Using SSR Markers

Mutation induction with chemical mutagen ethyl methane sulfonate (EMS) capable of producing genetic variation in plants. The purpose of this research was to evaluate genetic variation of EMS-induced chili pepper mutants using SSR molecular marker. Various concentration of EMS (0.01%; 0.02%; 0.04%) were applied to chili pepper seeds of Genotypes 2, 7, and 11. The genomic DNA was isolated from mutants and control plants then used for PCR analysis using three SSR primers namely CA26, CA52 and CA96. The three SSR primers were able to detect genetic variation in the three genotypes of EMS-induced chili pepper mutants and control plants. A total of 18 alleles have been identified in all three SSR loci with PIC values ranging from 0.792 to 0.893. The three genotypes of chili pepper plants had different sensitivity to EMS mutation induction. Genotype 11 plants showed higher sensitivity to EMS treatment than genotypes 2 and 7 based on the amount of genomic changes. Dendrogram constructed based on genetic similarity values distributed the mutants and control plants into three main groups with similarity coefficients ranging from 0.34 to 0.90. Similar genotype either control plant or mutants, especially Genotypes 2 and 7 were group into similar group. However, for the Genotype 11 plants, large genome changes cause mutant plants G11K1, G11K2, G11K3 had a low genetic similarity to their control plants, so the mutants were separated in a different group from the control plant. Those indicate that EMS mutation induction capable of increasing genetic variation in chili pepper plants based on SSR molecular marker.
Dietary assessment of age-0 pallid sturgeon and shovelnose sturgeon: implications for surrogacy

Validation is critical when considering potential surrogates for endangered species research. The pallid sturgeon Scaphirhynchus albus is federally endangered in the USA, whereas the congeneric shovelnose sturgeon S. platorynchus is common. Inadequate food availability during early life history is a hypothesized factor limiting recruitment of pallid sturgeon in the lower Missouri River, USA, and an established surrogate relationship with shovelnose sturgeon would dramatically expedite research efforts related to potential food limitation. During 2018, 4 exogenously feeding pallid sturgeon larvae were captured concurrently with multiple shovelnose sturgeon, providing a critical opportunity to evaluate diet surrogacy using individuals captured from the same locations. We found that both species primarily consumed ephemeropterans but chironomids were also frequent prey. Over 90% of the pallid sturgeon prey items belonged to taxa also consumed by shovelnose sturgeon. Additionally, we often observed high diet similarity between these congeners. As for total prey weight, pallid sturgeon consumption was similar or higher compared to similarly sized shovelnose sturgeon. Although the sample size was limited, this study supports the hypothesis that larval pallid sturgeon are capable of finding food in the lower Missouri River and exhibiting diet similarity with shovelnose sturgeon. We also provide the first quantification of prey weight for wild-produced larval pallid sturgeon, which consumed relatively large amounts of prey in the wild during the critical transition from endogenous to exogenous feeding.
Effect of arsenic on growth, lipid peroxidation and antioxidant defence system in cowpea

Arsenic (As) is a toxic ubiquitous metalloid. Exposure of plants to As can result in various morphological, physiological and biochemical variations. Hydroponic experiment was conducted to study the growth response, lipid peroxidation, proline and antioxidant defence system under arsenic (As) stress in the cowpea. Ten day old seedlings of cowpea grown hydroponically, were treated with 0, 25, 50, 75 and 100 µM (Na2HAsO4) sodium arsenate for 7 days and analysed for morphological and biochemical traits under As stress. Significant decline in plant root and shoot length along with biomass was recorded with increased arsenic doses, as compared to control. The As treatment resulted in increased proline and decrease in malondialdehyde (MDA) content in seedlings of cowpea with increased concentration. Enzymatic antioxidants like catalase (CAT), superoxide dismutase (SOD), ascorbate peroxidase (APX) and glutathione reductase (GR) showed increased activity in dose dependant manner over control under As stress. Results indicated lower content of MDA and enhanced activities of the enzymatic antioxidant perform a significant role in As tolerance in cowpea.
The Effects of Motor Modularity on Performance, Generalizability and Learning in Upper-Extremity Reaching: a Computational Analysis

It has been hypothesized that the central nervous system simplifies the production of movement by limiting motor commands to a small set of modules known as muscle synergies. Recently, investigators have questioned whether a low-dimensional controller can produce the rich and flexible behaviors seen in everyday movements. We implemented muscle synergies in a biomechanically realistic human upper extremity model and performed computational experiments to determine whether synergies introduced task performance deficits, generalized to different movements, and facilitated the learning of new movements as occurs during motor skill acquisition. We used dynamic optimization to solve for control patterns (i.e., muscle excitations) to achieve a varied set of reaching tasks. We derived sets of synergies from the muscle excitations our dynamic optimization framework computed for a nominal task (reaching in a plane). Then we compared the performance and learning rates of a controller that activated muscles independently to controllers that activated the synergies derived from the nominal reaching task. We found that a controller based on synergies was able to achieve a variety of reaching tasks with low performance errors. For example, target errors for a controller based on 8 synergies were within 1 cm of the full-dimensional controller for new targets in the same plane as the nominal reaching task. The synergy-based controllers could also accomplish new tasks–such as reaching to targets on a higher or lower plane, starting from an alternate initial pose, moving at a faster velocity, and holding a light weight–with average errors similar to a full-dimensional controller. We also found that for new tasks, the synergy-based controllers converged to good solutions (as defined by a cost-function threshold) with lower computational cost than a full-dimensional controller. Our results show that a modular architecture based on muscle synergies can generate a wide variety of reaching behaviors for a high-dimensional musculoskeletal system without a significant degradation in performance.
Hippocampal neural stem cells facilitate access from circulation via apical cytoplasmic processes

Blood vessels (BVs) are considered an integral component of neural stem cells (NSCs) niches. NSCs in the dentate gyrus (DG) have enigmatic elaborated apical cellular processes that are associated with BVs. Whether this contact serves as a mechanism for delivering circulating molecules is not known. Here we uncovered a previously unrecognized communication route allowing exclusive direct access of blood-borne substances to hippocampal NSCs in defiance of an intact blood-brain barrier (BBB). BBB-impermeable fluorescent tracer injected transcardially is selectively uptaken by DG NSCs within a minute, via the vessel-associated apical processes. These processes, measured >30nm in diameter, establish direct membrane-to-membrane contact with endothelial cells in areas devoid of the endothelial basement membrane. Doxorubicin, a brain-impermeable chemotherapeutic agent, is also readily and selectively uptaken by NSCs and reduces their proliferation, which might explain its problematic anti-neurogenic or cognitive side-effect. The newly-discovered NSC-BV communication route explains how circulatory neurogenic mediators are ‘sensed’ by NSCs.
PLANTING DATE, CINNAMIC ACID AND N FERTILIZER AFFECT GROWTH AND METABOLITES OF Pimpinella anisum

Two field experiments were conducted, to determine the effect of planting anise plant on late date (25 th Dec.) in addition to the control date (25 th Oct.) on growth parameters, photosynthetic pigments, carbohydrates and nitrogen content of Pimpinella anisum L. treated with cinnamic acid (CA) and/ or urea. In general the obtained data showed that, treating anise plant with different concentrations of CA (1mM, 5mM and 10mM) decreased all the growth parameters, photosynthetic pigments, carbohydrate and nitrogen contents during the two dates of cultivation. On the other hand the two used levels of urea fertilizer (50% and 100%) especially 100%, increased all the growth parameters, photosynthetic pigments, carbohydrate and nitrogen contents during the two dates of cultivation. In general, the results obtained by CA and urea; either alone or together in case of control date of cultivation were much better than those obtained on the late date of cultivation.
Chromatiblock: scalable whole-genome visualization of structural differences in prokaryotes

Summary Chromatiblock is a Python application for visualizing the presence, absence and arrangement of syntenic blocks across large numbers of complete bacterial genomes. Availability Chromatiblock is freely available under a GPL license, for macOS, GNU/Linux and and Microsoft Windows from https://github.com/mjsull/chromatiblock/ Contact harm.vanbakel@mssm.edu
Pressure Ulcers in Home Care Settings: Is It Overlooked?

The frequency of pressure ulcers in patients living at home is not well-defined. To quantify the extent of this issue, surveillance was conducted in 2009 within 45 community health sites across the Hunter New England Area Health Service of New South Wales (NSW). This is the first community pressure ulcer prevalence study completed in NSW. Seven hundred and ninety-six randomly selected patients cared for by community nurses participated in the study. A pressure ulcer prevalence rate of 8.9% (n=71, 95% CI=7.1 - 11.1%) was recorded, 6.5% (n=52, 95% CI=5.0 - 8.5%) if stage I pressure ulcers were excluded. A total of 111 pressure ulcers were identified on 71 clients, with 35.3% of the patients classified as high risk of developing pressure ulcers. Of the patients with pressure ulcers, 40.8% developed the ulcers during their care by community nursing staff. Similar portions of patients acquired their ulcers during hospitalisation or before admitted to the community nursing services. Issues requiring action from the survey include improving documentation of risk, improving speed and access to pressure redistributing devices, which were absent in 50% of the patients with pressure ulcers.
Structural Analysis and Distribution Patterns in Lowland Tropical Forest, Eastern Amazon

Floristic surveys allow us to make a momentary assessment of the structure and degree of conservation of the vegetation, supporting future actions for the sustainable use of forest resources. The aim of this work was to study the floristic and structural composition of fragments of floodplain forest in the Cajari River Extractive Reserve, Amapá state, Brazil. Systematic sampling was applied with the allocation of 27 plots of dimensions 10 m x 100 m each, with inclusion level of individuals greater than or equal to 10 cm in diameter at chest height. The floristic diversity of species was determined by the Shannon Diversity Indexes and Pielou Equability. The characterization of the horizontal structure was determined by the parameters: density, frequency and relative and absolute dominance, values of ecological importance and the diametrical distribution. The families Fabaceae and Euphorbiaceae were the ones that obtained the highest richness of species and number of individuals. The species Virola surinamensis Warb. , Hevea brasiliensis (HBK) Muell. Arg. , Pentaclethra macroloba (Willd.) Kuntze and Mora paraensis (Ducke) Ducke, were the most abundant. The várzea forest fragments presented high diversity and high ecological dominance of species. The J-inverted diametric distribution, characteristic of natural forests, indicates that it is a mature forest component with an expressive group of dominating (hyperdominant) species, such as the species V. surinamensis and M. paraensis. Most species presented aggregate distribution. It is hoped that these results may serve the environmental control and control bodies as strategies for the use of forest resources and in the design of the management plan of Resex.
IMPMD: An Integrated Method for Predicting Potential Associations Between miRNAs and Diseases

Background With the rapid development of biological research, microRNAs (miRNAs) have increasingly attracted worldwide attention. The increasing biological studies and scientific experiments have proven that miRNAs are related to the occurrence and development of a large number of key biological processes which cause complex human diseases. Thus, identifying the association between miRNAs and disease is helpful to diagnose the diseases. Although some studies have found considerable associations between miRNAs and diseases, there are still a lot of associations that need to be identified. Experimental methods to uncover miRNA-disease associations are time-consuming and expensive. Therefore, effective computational methods are urgently needed to predict new associations. Methodology In this work, we propose an integrated method for predicting potential associations between miRNAs and diseases (IMPMD). The enhanced similarity for miRNAs is obtained by combination of functional similarity, gaussian similarity and Jaccard similarity. To diseases, it is obtained by combination of semantic similarity, gaussian similarity and Jaccard similarity. Then, we use these two enhanced similarities to construct the features and calculate cumulative score to choose robust features. Finally, the general linear regression is applied to assign weights for Support Vector Machine, K-Nearest Neighbor and Logistic Regression algorithms. Results IMPMD obtains AUC of 0.9386 in 10-fold cross-validation, which is better than most of the previous models. To further evaluate our model, we implement IMPMD on two types of case studies for lung cancer and breast cancer. 49 (Lung Cancer) and 50 (Breast Cancer) out of the top 50 related miRNAs are validated by experimental discoveries. Conclusion We built a software named IMPMD which can be freely downloaded from https://github.com/Sunmile/IMPMD.
On islands, evolutionary but not functional originality is rare

Functionally and evolutionary original species are those whose traits or evolutionary history are shared by few others in a given set. These original species promote ecosystem multifunctionality, the ability to cope with an uncertain future, future benefits to society and therefore have a high conservation value. A potential signal of their extinction risks is their rarity (stating for geographic range-restriction in this study). On islands, life in isolation conducted to the rise of a multitude of original forms and functions as well as to high rates of endemism. Not only patterns and processes of insular originality are unexplained but the relationship between originality and rarity is still unknown. The aim of this study is to assess how original insular species are, to explore whether original species are rare or not and to investigate the factors that may explain the rarity of original species. We first compared the functional and evolutionary originality of monocotyledon species and whether continental or insular species were more original. We found that species restricted to islands were more original than continental species and, although functionally and evolutionary original species were dissimilar, many occurred on similar territories so that regional conservation strategies may allow to conserve these distinct forms. Yet, evolutionary original species were significantly more range-restricted than those which were distinct in their traits. Reflecting their rarity, evolutionary original species had low dispersal abilities and were found on islands where settlement may have been facilitated. On the opposite, functionally original species could reach a wider set of islands by being transported on long-distances. While some mechanisms may both explain rarity and originality such as extinctions, others may be specific to each of these biodiversity facets, in particular diversification, niche shift and expansion, and dispersal power. Implications for conservation are huge: original species are range-restricted and mostly found in the most threatened systems of the world, i.e. islands, endangering the reservoir of features against an uncertain future.
Antioxidant and antibacterial activities of C-phycocyanin from common name Spirulina platensis

In this study, the antibacterial and antioxidant properties of C-phycocyanin (C-PC) from Spirulina platensis were evaluated. The extraction and purification of C-PC were carried out using lyzosyme and ammonium sulphate precipitation, respectively. DPPH radical-scavenging activity, ferric reducing antioxidant power (FRAP)and Fe2+-chelating activity were used for evaluation of antioxidant properties of C-PC. Antibacterial activity was also performed using agar well diffusion and microdilution [minimal inhibitory concentration (MIC) and minimal bactericidal concentration (MBC)]. The selected bacteria were Escherichia coli, Staphylococcus aureus, Listeria monocytogenes, Streptococcus iniae and Yersinia ruckeri. The results showed that the biomass production was 1120 mg L-1 and C-PC concentration in crude extracts and purified by (NH4)2SO4 were also 1.815 and 3.75 mg ml-1, respectively. The results of DPPH, FRAP and Fe2+-chelating activitiesof C-PC was 45.75%, 0.051 mg TAE g-1 and 40.23% at zero time and 41.56%, 0.046 mg TAE g-1 and 36.56% after 60 days at -18°C, respectively. The results of agar well diffusion indicated that L. monocytogenes and S. iniae were the most sensitive and resistant, respectively among examined bacteria in different concentrations of C-PC (0- 25 µg ml-1) and the mean of inhibition zones were also 7.50-22.11mm. The results of MIC and MBC of C-PC (as µg ml-1) were 50-500 and 100-500, respectively. As a conclusion, C-PC from S. platensis had high potential of antioxidant activity in vitro and it can be used as natural antioxidants in variety of foods. Antibacterial activity of C-PC was lower than other algal pigments (such as astaxanthin and C-PC in other cyanobacteria).
Avaliação do gene CYP1B1 e da ancestralidade genômica no glaucoma congênito primário

INTRODUCAO: O glaucoma congenito primario e uma trabeculodisgenesia isolada que resulta na obstrucao do escoamento do humor aquoso e no consequente aumento da pressao intraocular, sendo uma importante causa de cegueira pediatrica. E a forma mais comum de glaucoma na infância e tem sido associada a alteracoes no gene CYP1B1. Em escala bem menor, o gene LTBP2 tambem tem sido relatado como causa da doenca. OBJETIVOS: Investigar a contribuicao de mutacoes no gene CYP1B1 e avaliar a ancestralidade genomica em criancas portadoras de glaucoma congenito primario. METODO: Trinta criancas com glaucoma congenito primario com um seguimento minimo de seis meses apos a ultima cirurgia e 60 controles foram submetidos a coleta de sangue e exame oftalmologico. Dados clinicos e cirurgicos foram coletados, o DNA, extraido, e o gene CYP1B1, sequenciado. O estudo da ancestralidade genomica foi realizado utilizando-se 40 marcadores de insercao-delecao (indels). RESULTADOS: Foram encontradas 10 mutacoes no CYP1B1 em 11 pacientes (36,7%), sendo tres delas novas mutacoes (p.Gln109Stop, p.Ser476Pro e fs.1416delC). As criancas com GCP apresentaram proporcao ancestral de europeus, africanos e amerindios de 0,784±0,044 (media ± SE), 0,149±0,035 e 0,067±0,023, respectivamente, e a do grupo-controle foi 0,730±0,048, 0,132±0,034 e 0,138±0,032, respectivamente. As diferencas nas proporcoes entre probandos e controles nao foram significativas (p>0,05). Nao foram observadas diferencas estatisticamente significativas dos componentes da ancestralidade entre os probandos com mutacoes e sem mutacoes no CYP1B1. Um maior indice de ancestralidade africana foi associado a um pior prognostico da doenca. CONCLUSOES: CYP1B1 e o principal gene causador do glaucoma congenito primario. Entretanto, ausencia de mutacoes em 63,3% das criancas com glaucoma congenito primario sugere o envolvimento de outro(s) gene(s) ou causas moleculares ainda desconhecidas na patogenese dessa doenca. O componente ancestral africano parece influenciar os algoritmos, agindo talvez como um fator de risco, quando presente em alta proporcao. Novas pesquisas sao necessarias para revelar o papel da ancestralidade genomica no glaucoma congenito primario em populacoes miscigenadas como a brasileira.
Integrated proteomics reveals brain-based cerebrospinal fluid biomarkers in asymptomatic and symptomatic Alzheimer’s disease

Integrative proteomic analysis identifies CSF biomarker panels linked to brain-based pathophysiologies in Alzheimer’s disease. Alzheimer’s disease (AD) lacks protein biomarkers reflective of its diverse underlying pathophysiology, hindering diagnostic and therapeutic advancements. Here, we used integrative proteomics to identify cerebrospinal fluid (CSF) biomarkers representing a wide spectrum of AD pathophysiology. Multiplex mass spectrometry identified ~3500 and ~12,000 proteins in AD CSF and brain, respectively. Network analysis of the brain proteome resolved 44 biologically diverse modules, 15 of which overlapped with the CSF proteome. CSF AD markers in these overlapping modules were collapsed into five protein panels representing distinct pathophysiological processes. Synaptic and metabolic panels were decreased in AD brain but increased in CSF, while glial-enriched myelination and immunity panels were increased in brain and CSF. The consistency and disease specificity of panel changes were confirmed in >500 additional CSF samples. These panels also identified biological subpopulations within asymptomatic AD. Overall, these results are a promising step toward a network-based biomarker tool for AD clinical applications.
EFFICACY OF SOME BIOAGENTS AND NEMASTOP COMPOUND IN CONTROLLING ROOT KNOT DISEASE ON PEANUT.

Biological control of plant diseases especially root knot nematode has been handled in many scientific papers. Bacillus subtilis, Trichoderma harzianum (T1), T. viride (T2), mixture of both (T1andT2) in addition to the commercial product Nemastop were used under field conditions to control root knot nematode, Meloidogyne javanica Chitwood on peanut plants which was the most frequent extracted from soil and roots . The efficacy of the treatments at different concentrations was also assayed under laboratory conditions as percentage of juvenile mortality and inhibition of egg hatching. All treatments revealed good effect in controlling root-knot at the highest concentrations, Nemastop was the most effective at(1:10), whereas, B. subtilis was the lowest one. Results obtained from field experiments were in harmony with those obtained from laboratory compared with control. Efficacy of the treatment also positively correlated with number of application time. The plot treated with any one of the bioagents tested three times achieved highest effect in controlling root knot nematode and increased peanut yield. Under field condition mixture of Trichoderma isolates was the most effective followed by Nemastop.