Miracle-dz/UniFAR-FTUs huggingface dataset:
Condições de Referência em riachos de cabeceira tropicais

A definicao de Condicoes de Referencia visa quantificar a variabilidade natural de caracteristicas ambientais e biologicas de ecossistemas minimamente perturbados por acoes antropicas. Riachos de cabeceira no trecho alto da bacia do Rio das Velhas (MG) estao inseridos em uma zona de transicao, que engloba Campos Rupestres e Florestas Estacionais Semi-Desciduais, resultando em alta variabilidade ambiental e biologica. Os objetivos desta dissertacao foram: (i) caracterizar condicoes ambientais e biologicas de referencia em riachos de cabeceira, com base em (a) medidas ambientais em multiplas escalas espaciais, e (b) estrutura de comunidades de macroinvertebrados bentonicos; (ii) testar a hipotese de que a composicao, riqueza e abundância de comunidades bentonicas em areas de campos rupestres e floresta sao diferentes; (iii) apontar quais variaveis ambientais melhor explicam a variacao de riqueza taxonomica. Foram selecionados 21 riachos de cabeceira em areas de mata e 10 em campos rupestres minimamente alterados por atividades humanas. Os riachos foram caracterizados em escalas de microbacia de contribuicao (p. ex.: altitude, litologia, area de drenagem), trecho de riacho (p. ex.: morfologia do canal, tipo de substrato e fluxo) e coluna d'agua (parâmetros fisicos e quimicos da agua). Para caracterizar os trechos de riachos foi realizada uma simplificacao do protocolo de habitats fisicos da Agencia de Protecao Ambiental Norte- Americana (US-EPA). Foram coletados 19.295 macroinvertebrados classificados em 63 familias. A composicao e riqueza de macroinvertebrados foi diferente entre riachos de campos e florestas. Riachos em floresta detem maior numero de taxa (29,9 ± 5,9) do que riachos de campos rupestres (23,6 ± 6,3) (t = 2,69; gl = 29; p = 0,012). Um modelo de regressao linear multipla com tres variaveis (condutividade eletrica, taxa de imersao no sedimento fino e concentracao de nitrito) explicou 42 % da variacao de riqueza entre os riachos. As medidas de condutividade eletrica e taxa de imersao apresentaram correlacao positiva com riqueza, enquanto que a concentracao de nitrito foi negativamente correlacionada. O estudo apontou fatores ambientais que influenciam a estrutura de comunidades de macroinvertebrados bentonicos em riachos de cabeceira. Alem disso, estes dados de referencia podem ser utilizados em planos de monitoramento e restauracao de riachos degradados na regiao do Alto Rio das Velhas, alem de propor um protocolo simplificado de habitat fisico que pode servir como ferramenta de monitoramento de riachos de cabeceira em bacias hidrograficas tropicais.
Losses of human disease-associated genes in placental mammals

Abstract We systematically investigate whether losses of human disease-associated genes occurred in other mammals during evolution. We first show that genes lost in any of 62 non-human mammals generally have a lower degree of pleiotropy, and are highly depleted in essential and disease-associated genes. Despite this under-representation, we discovered multiple genes implicated in human disease that are truly lost in non-human mammals. In most cases, traits resembling human disease symptoms are present but not deleterious in gene-loss species, exemplified by losses of genes causing human eye or teeth disorders in poor-vision or enamel-less mammals. We also found widespread losses of PCSK9 and CETP genes, where loss-of-function mutations in humans protect from atherosclerosis. Unexpectedly, we discovered losses of disease genes (TYMP, TBX22, ABCG5, ABCG8, MEFV, CTSE) where deleterious phenotypes do not manifest in the respective species. A remarkable example is the uric acid-degrading enzyme UOX, which we found to be inactivated in elephants and manatees. While UOX loss in hominoids led to high serum uric acid levels and a predisposition for gout, elephants and manatees exhibit low uric acid levels, suggesting alternative ways of metabolizing uric acid. Together, our results highlight numerous mammals that are ‘natural knockouts’ of human disease genes.
Can chlorination of ballast water reduce biological invasions?

1GEOMAR Helmholtz-Zentrum für Ozeanforschung Kiel, Kiel, Germany; 2Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, China; 3University of Chinese Academy of Sciences, Beijing, China; 4Great Lakes Institute for Environmental Research, University of Windsor, Windsor, ON, Canada; 5Museo Argentino de Ciencias Naturales “Bernardino Rivadavia” and Consejo Nacional de Investigaciones Cientı ́ ficas y Técnicas, Buenos Aires, Argentina and 6School of Ecology and Environmental Sciences, Yunnan University, Kunming, China
Effects of Invasive Plant Species on Native Bee Communities in the Southern Great Plains

The worldwide decline of native insect pollinators is of growing concern, as well as the decrease in populations of many flowering forbs. In the southern Great Plains region of the United States, grasslands are one of the most important vegetation types for providing resources to pollinators. Non-native and invasive plant species can alter grassland plant communities, although it is not clear how invasive plants affect native bee populations and communities. We evaluated the response of the native plant community and the native bee community across a gradient of invasion levels for two common invasive plants in the southern Great Plains: Kochia scoparia and Salsola tragus. Study sites were located within four National Parks, with approximately 10 plots representing the gradient of invasion levels sampled at each park, for a total of 40 plots. Pan traps were used to assess the native bee community and both native and non-native plant species and cover classes were recorded for each plot. Data were also recorded on bare ground availability due to its importance for solitary ground-nesting bees. Regression models were used to evaluate how the bee community (richness and abundance) responds to invasive plant species cover and bare ground cover, with an analysis performed for K. scoparia and S. tragus combined, since these two species commonly occur together and are expected to have similar impacts on the native bee community. Our findings suggest grasslands with no or low levels of invasive species support higher bee species richness, but did not affect abundance. Plots with higher levels of bare ground showed a significant correlation with bee richness. Possible factors contributing to the observed patterns could be the lack of floral resources from invasive plants (e.g. K. scoparia and S. tragus), which require limited insect pollination, and reduced abundance and diversity of native forbs. This study suggests that invasive plant species control is important for improving grasslands to support diverse native bee communities.
Wikidata as a FAIR knowledge graph for the life sciences

Wikidata is a community-maintained knowledge base that epitomizes the FAIR principles of Findability, Accessibility, Interoperability, and Reusability. Here, we describe the breadth and depth of biomedical knowledge contained within Wikidata, assembled from primary knowledge repositories on genomics, proteomics, genetic variants, pathways, chemical compounds, and diseases. We built a collection of open-source tools that simplify the addition and synchronization of Wikidata with source databases. We furthermore demonstrate several use cases of how the continuously updated, crowd-contributed knowledge in Wikidata can be mined. These use cases cover a diverse cross section of biomedical analyses, from crowdsourced curation of biomedical ontologies, to phenotype-based diagnosis of disease, to drug repurposing.
Complete chloroplast genome of a widely distributed species in southwest China, Hemiphragma heterophyllum Wall. (Scrophulariaceae)

Abstract Hemiphragma heterophyllum Wall. , a widely distributed species in southwest China, belongs to a monotypic genus, Hemiphragma Wall. in the Scrophulariaceae. To date, there has been no study on its complete chloroplast genome. Hence, we reported the first complete chloroplast genome sequence of H. heterophyllum here. The genome sequences of two individuals were extremely similar except slight differences on sequence lengths (152,707 bp and 152,700 bp, respectively). There was a typical circular quadripartite structure. A total of 113 genes were annotated, including 79 protein-coding genes, 29 tRNA genes, four rRNA genes, and one pseudogene. Among the annotated genes, 16 genes contained one intron, whereas another two genes (ycf3 and clpP) possessed two gene introns. Total GC content is 38.1% in the chloroplast genome. Moreover, a total of 63 simple sequence repeats (SSRs) with five types were detected. Phylogenetic analysis revealed that Hemiphragma was closely related to Veronica L. and Veronicastrum Heist. ex Farbic.
Mesenchymal stem cell therapy for traumatic and degenerative eye disease

Aims The aim of this PhD research project was to investigate the application of dental pulp stem cells (DPSC) as a treatment for traumatic and degenerative eye diseases. The accuracy and reliability of counting retinal ganglion cells (RGC) in radial retinal section was also assessed. Methods Numbers of RGC in radial retinal sections were compared to numbers in retinal wholemounts. DPSC were cultured with RGC and survival and neuritogenesis were quantified. DPSC were also transplanted intravitreally into rat models of optic neuropathy (optic nerve crush) and glaucoma and surviving RGC and regenerated axons were quantified in radial retinal sections. Results Quantifying RGC in radial retinal sections was as reliable and accurate as the current gold standard Thus, retinal wholemounts with Brn3a proved to be the most reliable marker for RGC. DPSC protected RGC from optic nerve crush-/glaucoma-induced death, promoting significant regeneration of RGC axons in the former and preserving visual function (as measured by electroretinography) in the latter. The mechanism of action, as determined in vitro, appeared to be through the secretion of multiple neurotrophic factors (NTF). Conclusions In conclusion, DPSC is a potent cell therapy in the treatment of traumatic and degenerative eye disease.
Quantitative Analysis of Nursing Observation Employing a Portable Eye-Tracker

Background: Observation is an important skill for making appropriate nursing decisions and engaging in good practice. However, experts’ observation behavior and cognitive processes cannot be easily verbalized or documented in an objective and accurate manner. Quantitative analysis of the observation behavior of nurses with rich clinical experience will yield effective educational data for fostering and improving nursing students’ observation skills. Objectives: To improve nursing assessment education, the differences in the information gathering processes between clinical nurses and nursing students were analyzed by using a portable eye-tracker. Design: An experimental study. Settings: The experiment was performed at a university in Japan. Participants: The participants were 11 clinical nurses with at least 5 years of clinical experience for postoperative patients, and 10 fourth-year nursing students. Methods: In a mock hospital room, wherein we recreated a situation where a patient in postoperative day 1 was confined to a bed, participants wore an eye-tracking camera and engaged in nursing observation to make an early postoperative ambulation assessment of the patient. Participants’ gaze points and gaze fixation durations were extracted from the gaze measurement data and compared. Results: Clinical nurses had shorter observation times and gaze durations than did nursing students, and focused more on the patient chart, intravenous drip, and indwelling drain. Students gazed for longest at the measuring devices for vital signs. Conclusions: We quantitatively analyzed differences in nursing observation according to clinical experience. Although no significant difference was found in gaze points, nursing students had a greater tendency to focus on information that was numerically displayed. Nurses with clinical experience conducted observations by gazing at information that they needed to focus on the most according to the patients’ postoperative course.
Molecular mechanism of attenuation of heat shock transcription factor 1 activity

The heat shock response is a universal transcriptional response to proteotoxic stress orchestrated by heat shock transcription factor Hsf1 in all eukaryotic cells. Despite over 40 years of intense research, the mechanism of HSF1 activity regulation remains poorly understood at a molecular level. In metazoa Hsf1 trimerizes upon heat shock through a leucin-zipper domain and binds to DNA. How Hsf1 is dislodged from DNA and monomerized remained enigmatic. Here, we demonstrate that trimeric Hsf1 is dissociated from DNA in vitro by Hsc70 and DnaJB1. Hsc70 acts at two distinct sites on Hsf1. Hsf1 trimers are monomerized by successive cycles of entropic pulling, unzipping the triple leucine-zipper. This process directly monitors the concentration of Hsc70 and DnaJB1. During heat shock adaptation Hsc70 first binds to the transactivation domain leading to partial attenuation of the response and subsequently, at higher concentrations, Hsc70 removes Hsf1 from DNA to restore the resting state.
Assessment of Fuel Properties Produced From Tamarix nilotica and Pluchea dioscoridis Plants

NOWADAYS, there is a great demand concerning searching about renewable energy sources. Therefore, wild plants such as Tamarix nilotica and Pluchea dioscoridis could be used as fossil fuel-alternative to meet the huge increments in the energy demand. The aerial parts of T. nilotica were collected from the Cairo–Suez road, while those of P. dioscoridis were collected from Wadi Hagul, Egypt. The biofuel generating compounds including lipids, carbohydrates, cellulose, pectin and lignin were assayed. The physico-chemical properties of the produced biodiesel were calculated. The obtained results indicated that, the high cellulose content (25.02%) of T. nilotica increases its potentiality for bioethanol production. The GC-MS analysis showed that P. dioscoridis displayed the highest levels of saturated fatty acid (SFAs) and a desirable degree of unsaturation (DU). The biodiesel properties in terms of iodine value (IV), saponification number (SN), cetane number (CN), oxidative stability (OS), high heating value (HHV), kinematic viscosity (η) and density (ρ) for both species were within the recommended standards and mostly met the criteria required to be a diesel substitute compared with the international biodiesel standards. Particularly biodiesel produced from P. dioscoridis has good and suitable engine parameters (SN 196.3, IV 76.81 and CN 114.18).
Staphylococcus aureus bones and joints infections: in vivo studies and host immune response

Abstract The aim of this work was the development of a murine model of septic arthrosynovitis and osteomyelitis caused by Staphylococcus aureus, which could mimic the natural disease occurring in humans and which could be suitable for testing preventive and therapeutic interventions. This model could be particularly useful since S. aureus-mediated joints and bones infections are relevant in humans, both in terms of frequency and severity. Our attention focused in tracking bacterial infiltration in joints and bones over time using different microbiological and hystopathological tools, which allowed us to have a complete overview of the situation and to evaluate the immunological actions undertaken by the host to contain or eradicate the bacterial infection. Antibodies and cytokines profiles, as well as recruitment of host immune cells at joints of immunized and infected mice were therefore monitored for a time period that allowed us to study both the acute and the chronic phases of the disease in situ. Finally the Novartis vaccine formulation proposed against S. aureus infections was tested for its capacity to protect immunized mice from joints infections, and the preventive immunization was compared to a standard antibiotic prophylaxis. The availability of powerful tools to study specific bacterial-mediated diseases is nowadays an important requirement for the scientific community to shed light on the complex interactions between host and pathogens and to test treatments for preventing or contrasting infections. We believe that our work significantly contributes to the overall knowledge in the field of S. aureus-dependent pathologies, opening the possibility for further investigations in several fields of study.
Should Upper Limit of Available Water be Based on Field Capacity?

Plant-available water is usually determined from laboratory measurements as the difference between field capacity (undisturbed soil samples) and wilting point (disturbed samples), both of which are determined at arbitrary applied pressures. How much soil water is actually available to plants? The purpose of this report is to demonstrate that data are inconsistent with the concept of field capacity at a pressure head being the upper limit of available water. Existing field studies were re-examined. Literature shows that a considerable portion of transpired water often comes from below the root zone. A site that had water table depths ranging from near the surface to 3 m deep showed that tensiometer pressure heads in the root zone rarely got as dry as -333 cm pressure head (approximate limit of field capacity). Another study showed that as surface soil dried, the roots were able to take up water from deeper soil, showing the flexibility of the root zone depth. Still other studies suggest that transpiration might start between 3 and 10 h after a rain ends, even while the soil is still draining. Together these studies strongly suggest that roots take up water under conditions wetter than -333 cm pressure head; therefore, laboratory-determined field capacity should not be considered the upper cutoff of available water.
Morphological and molecular analysis of Laxus oneistus juveniles and their bacterial ectosymbiont

Diplomarbeit enthalt Bilder! Marine Nematoden aus der Unterfamilie der Stilbonematinae sind durch ihre Fahigkeit, sehr spezifische Assoziationen mit schwefeloxidierenden Bakterien einzugehen, charakterisiert. Bei der Spezies Laxus oneistus bedecken diese fast die gesamte Oberflache der Kutikula jedes erwachsenen Nematoden, mit Ausnahme der ausersten Spitze des Schwanzes und des Vorderkorpers. Dies ist die erste Studie, die sich ausschlieslich mit juvenilen Individuen von L. oneistus befasst. Morphologische Analysen durch Licht-, Elektronen- und Konfokalmikroskopie zeigten, dass auch juvenile Nematoden, die zum ersten frei lebenden Entwicklungsstadium (J1/2) gehoren, einen bakteriellen Uberzug aufweisen. Seine raumliche Begrenzung und Architektur ist die gleiche wie bei adulten Exemplaren. Zusammen mit der Detektion des ektosymbiontbindenden Proteins „Mermaid“ wird eine Ektosymbiontrekrutierung in J1/2 Stadien oder sogar vorher vermutet. Die Bakterien wurden molekular charakterisiert indem eine 16S rRNA-Gen- Bibliothek angelegt und Fluoreszenz in situ Hybridisierung angewandt wurde. Mit Hilfe von 16S rRNA-Gen-spezifischen Sonden konnten zum ersten Mal Ektosymbiontzellen im Darm molekular identifiziert werden. Zusatzlich zum Ektosymbiont wurde eine neuartige, filamentose Mikrobe entdeckt, die meistens, wenn nicht sogar ausschlieslich, mit den Offnungen der epidermalen Drusen von juvenilen Nematoden verbunden ist. Die filamentose Mikrobe wurde zum Stamm der Planctomyceten unter Anwendung von 16S rRNA Klonbibliotheken und FISH mit spezifischen Sonden zugeordnet. Datenbankanalysen ergaben, dass die 16S-rRNA-Gene nur zu 91% identisch mit dem am nachsten verwandten Planctomyceten Bakterium ist. Aufgrund des Lokalisierungsmusters wird vermutet, dass dieses filamentose Bakterium die sekretorischen und oder auch exkretorischen Produkte nutzen kann. Wurde sich das letztere Szenario als wahr erweisen, konnte der Wirt uberdies von diesen, mit den Planctomyceten verwandten Bakterien, profitieren.
Effectiveness of a low-dose Norgestomet ear implant in short-term protocols to induce estrus in ewes during the non-breeding season in Brazil.

ABSTRACT The objective of this study was to evaluate the reproductive performance of ewes subjected to a short-term protocol for estrus induction using 1 mg of Norgestomet during the non-breeding season in Brazil. A total of 84 ewes were randomly divided into two equal groups (n = 42 per group). Controlled Internal Drug Release (CIDR) containing 330 mg progesterone was inserted into the vagina in the first 42 ewes, and for the other 42 ewes in the second group, 1 [. ]
Seagrass ecosystem metabolic carbon capture in response to green turtle grazing across Caribbean meadows

Increasing green turtle abundance will lead to increased grazing within seagrass habitats—ecosystems that are important for carbon sequestration and storage. However, it is not well understood how carbon dynamics in these ecosystems respond to grazing and whether a response differs among meadows or locations. We measured seagrass ecosystem metabolism in grazed and ungrazed areas of Thalassia testudinum meadows with established green turtle foraging areas across the Greater Caribbean and Gulf of Mexico. We sampled meadows from five locations that differed in seagrass and environmental characteristics. Established meadows of the invasive seagrass Halophila stipulacea were also present at two of these locations, and we measured ecosystem metabolism in these meadows for comparison to grazed and ungrazed areas of the native T. testudinum. Across all individual sites, rates of net ecosystem production (NEP) ranged from 56% to 96% lower in grazed areas than ungrazed areas of T. testudinum meadows. Rates of NEP were also strongly, positively correlated with above‐ground seagrass biomass across sites. While metabolic carbon capture rates were lower in grazed areas, heterotrophic respiration was not stimulated, and grazing therefore did not result in significant metabolic remineralization of carbon in these meadows. NEP in H. stipulacea meadows was similar to rates in T. testudinum meadows at all three sites, suggesting that metabolic carbon capture may remain similar in Caribbean meadows where this invasive seagrass is replacing native species. Synthesis. Our results show that there is a consistent response in metabolic carbon dynamics to green turtle grazing in T. testudinum meadows across the Greater Caribbean region. An increase in grazing will not likely stimulate remineralization of carbon as these important habitats are returned to a natural grazed state.
Late ERP amplitude for self-face perception positively associated with heartbeat perception accuracy

Perception of yourself involves the integration of information from various sources. In a number of studies, it was found that the perception of one’s own face is accompanied by an increase in the accuracy of perception of heartbeats and the amplitude of brain potentials caused by heart beats. In this study, subjects had to do a heartbeat count test to determine the accuracy of the interception. Then, the subjects were presented with the faces of an unknown person, a friend and the subject’s own face. The simultaneous registration of EEG was organized. We analyzed the relationship between the amplitude of the evoked potentials when viewing these faces and the accuracy of interoception. It was found that the amplitude of the late EP component (850 - 1106 ms) has a positive correlation with IAcc in the central and right parietal and occipital areas when perceiving one’s own face. According to the localization of distributed sources of activity, it was found that the connection is localized in the right anterior upper temporal cortex. Thus, the association between exteroceptive perception of one’s own face and IAcc occurs in the late period of EP. Moreover it is localized in the right temporal region of the cortex, associated with multisensory integration and recognition of personal information.