Miracle-dz/UniFAR-FTUs huggingface dataset:
Evaluation of Serological and Molecular Tests Used for the Identification of Toxoplasma gondii Infection in Patients Treated in an Ophthalmology Clinic of a Public Health Service in São Paulo State, Brazil

Ocular toxoplasmosis is one of the most common complications caused by the infection with the parasite Toxoplasma gondii. The risk of developing eye lesions and impaired vision is considered higher in Brazil than other countries. The clinical diagnosis is difficult and the use of sensitive and specific laboratorial methods can aid to the correct diagnosis of this infection. We compared serological methods ELISA and ELFA, and molecular cPCR, Nested PCR and qPCR for the diagnosis of T. gondii infection in groups of patients clinically evaluated with ocular diseases non-toxoplasma related (G1 = 185) and with lesions caused by toxoplasmosis (G2 = 164) in an Ophthalmology clinic in Brazil. Results were compared by the Kappa index, and sensitivity (S), specificity (E), positive predictive value (PPV), and negative (NPV) were calculated. Serologic methods were in agreement with ELISA more sensitive and ELFA more specific to characterize the acute and chronic infections while molecular methods were discrepant where qPCR presented higher sensitivity, however, lower specificity when compared to cPCR and Nested PCR.
Novel insights into the effect of drought stress on the development of root and caryopsis in barley

Drought is a common natural disaster in barley production, which restricts the growth and development of barley roots and caryopses seriously, thereby decreasing yield and debasing grain quality. However, mechanisms for how drought stress affects barley caryopses and roots development under drought stress are unclear. In this paper, Suluomai1 was treated with drought from flowering to caryopses mature stage. The morphological and structural changes in roots growth and caryopses development of barley were investigated. Drought stress increased root/shoot ratio and eventually led to the 20.16% reduction of ear weight and 7.75% reduction of 1,000-grain weight by affecting the biomass accumulation of roots and caryopses. The barley roots under drought had more lateral roots while the vessel number and volume of roots decreased. Meanwhile, drought stress accelerated the maturation of caryopses, resulting in a decrease in the accumulation of starch but a significant increase of protein accumulation in barley endosperm. There was a significantly positive correlation (0.76) between the area of root vessel and the relative area of protein in endosperm cells under normal condition and drought increased the correlation coefficient (0.81). Transcriptome analysis indicated that drought induced differential expressions of genes in caryopses were mainly involved in encoding storage proteins and protein synthesis pathways. In general, drought caused changes in the morphology and structure of barley roots, and the roots conveyed stress signals to caryopses, inducing differential expression of genes related to protein biosynthesis, ultimately leading to the increase in the accumulation of endosperm protein. The results not only deepen the study on drought mechanism of barley, but also provide theoretical basis for molecular breeding, high-yield cultivation and quality improvement in barley.
South America Climate During the 1970–2001 Pacific Decadal Oscillation Phases Based on Different Reanalysis Datasets

In this paper, circulation and precipitation climate patterns over the South American domain obtained from NCEP-NCAR reanalysis I, JRA-55, and ERA-40 reanalysis datasets were intercompared within the period 1970–2001 in order to verify their climatic association with the Pacific Decadal Oscillation, PDO. Although all three datasets showed similar climatic patterns during each PDO phase, they showed distinct intensities for circulation and precipitation variables. The mean low frequency flow propagation over the South Pacific during negative and positive PDO phases reached central-eastern South America with opposite signals, contributing to the modulation of the local climate. During the negative PDO phases, the northerly flow over South America is intensified, while during the positive phase it is weakened. NCEP-NCAR reanalysis I, in comparison with JRA-55 and ERA-40 values, always indicates the strongest signal for circulation and precipitation variables. NCEP-NCAR reanalysis I meridional wind at the low-level jet area was about 5 and 12% larger than the respective JRA-55 and the ERA-40 values. For the positive and negative PDO phases, only NCEP-NCAR and ERA-40 high-level zonal wind anomalies showed divergent (positive PDO) and convergent (negative PDO) patterns close to 140° W at equatorial latitudes of the Pacific Ocean, respectively. This one indicated distinct representations of the positioning of Walker cells in the three reanalysis datasets. GPCC dataset, NCEP-NCAR, JRA-55, and ERA-40 reanalysis showed, in general, the dipole precipitation pattern over eastern South America, with signs of changes between the central-eastern and southeastern areas during PDO reversal phases. Over the central-eastern South American region, NCEP-NCAR precipitation is, on average, 57% larger than GPCC values, and 35 and 46% larger than JRA-55 and ERA-40 values, respectively. The observed patterns of anomalies for different PDO phases appeared in all reanalysis datasets, leading us to conclude that the physical meaning is independent from the datasets. Even considering the JRA-55 climate signal over South America associated with the PDO influence as the weakest one, the ability of JRA-55 to calculate monthly precipitation provided the highest linear correlation coefficient values in tropical areas, leading us to consider this dataset as the most reliable for the studied area.
Hybrid Antigens Expressing Surface Loops of ZnuD From Acinetobacter baumannii Is Capable of Inducing Protection Against Infection

Acinetobacter baumannii is an important human pathogen causing substantial mortality in hospitalized patients for which treatment with antibiotics has become problematic due to growing antibiotic resistance. In an attempt to develop alternative strategies for dealing with these serious infections surface antigens are being considered as targets for vaccines or immunotherapy. The surface receptor proteins required for zinc acquisition in Gram-negative bacterial pathogens have been proposed as vaccine targets due to their crucial role for growth in the human host. In this study we selected the putative ZnuD outer membrane receptor from A. baumannii as a target for vaccine development. Due to challenges in production of an integral outer membrane protein for vaccine production, we adopted a recently described hybrid antigen approach in which surface epitopes from the Neisseria meningitidis TbpA receptor protein were displayed on a derivative of the C-lobe of the surface lipoprotein TbpB, named the loopless C-lobe (LCL). A structural model for ZnuD was generated and four surface loops were selected for hybrid antigen production by computational approaches. Hybrid antigens were designed displaying the four selected loops (2, 5, 7, and 11) individually or together in a single hybrid antigen. The hybrid antigens along with ZnuD and the LCL scaffold were produced in the E. coli cytoplasm either as soluble antigens or as inclusion bodies, that were used to generate soluble antigens upon refolding. Mice were immunized with the hybrid antigens, ZnuD or LCL and then used in an A. baumannii sepsis model to evaluate their ability to protect against infection. As expected, the LCL scaffold did not induce a protective immune response, enabling us to attribute observed protection to the displayed loops. Immunization with the refolded ZnuD protein protected 63% of the mice while immunization with hybrid antigens displaying individual loops achieved between 25 and 50% protection. Notably, the mice immunized with the hybrid antigen displaying the four loops were completely protected from infection.
Clustering of Brain Function Network Based on Attribute and Structural Information and Its Application in Brain Diseases

At present, the diagnosis of brain disease is mainly based on the self-reported symptoms and clinical signs of the patient, which can easily lead to psychiatrists' bias. The purpose of this study is to develop a brain network clustering model to accurately identify brain diseases based on resting state functional magnetic resonance imaging (fMRI) in the absence of clinical information. We use cosine similarity and sub-network kernels to measure attribute similarity and structure similarity, respectively. By integrating the structure similarity and attribute similarity into one matrix, spectral clustering is used to achieve brain network clustering. Finally, we evaluate this method on three diseases: Alzheimer's disease, Bipolar disorder patients, and Schizophrenia. The performance of methods is evaluated by measuring clustering consistency. Clustering consistency is similar to clustering accuracy, which is used to evaluate the consistency between the clustering labels and clinical diagnostic labels of the subjects. The experimental results show that our proposed method can significantly improve clustering performance, with a consistency of 60.6% for Alzheimer's disease, with a consistency of 100% for Schizophrenia, with a consistency of 100% for Bipolar disorder patients.
Reducing Emissions From Degraded Floodplain Wetlands

Globally, freshwater wetlands are significant carbon sinks; however, altering a wetland’s hydrology can reduce its ability to sequester carbon and may lead to the release of previously stored soil carbon. Rehabilitating a wetland’s water table has the potential to restore the natural process of wetland soil carbon sequestration and storage. Further, little is known about the role of microbial communities that mediate carbon cycling during wetland rehabilitation practices. Here, we examined the carbon emissions and microbial community diversity during a wetland rehabilitation process known as “environmental watering” (rewetting) in an Australian, semi-arid freshwater floodplain wetland. By monitoring carbon dioxide (CO2) and methane (CH4) emissions during dry and wet phases of an environmental watering event, we determined that adding water to a degraded semi-arid floodplain wetland reduces carbon emissions by 28–84%. The watering event increased anoxic levels and plant growth in the aquatic zone of the wetland, which may correlate with lower carbon emissions during and after environmental watering due to lower anaerobic microbial decomposition processes and higher CO2 sequestration by vegetation. During the watering event, areas with higher inundation had lower CO2 emissions (5.15 ± 2.50 g CO2 m–2 day–1) compared to fringe areas surrounding the wetland (11.89 ± 4.25 g CO2 m–2 day–1). CH4 flux was inversely correlated with CO2 emissions during inundation periods, showing a 38% (0.013 ± 0.061 g CO2-e m–2 day–1) increase when water was present in the wetland. During the dry phases of environmental watering, there was CH4 uptake within the fringe and aquatic zones (−0.013 ± 0.063 g CO2-e m–2 day–1). A clear succession of soil microbial community was observed during the dry-wet phases of the environmental watering process. This suggests that wetland hydrology plays a large role in the microbial community structure of these wetland ecosystems, and is consequently linked to CO2 and CH4 emissions. Overall, the total carbon emissions (CO2 + CH4) were reduced within the wetland during and after the environmental watering event, due to increasing vegetative growth and subsequent CO2 sequestration. We, therefore, recommend environmental watering practices in this degraded arid wetland ecosystem to improve conditions for wetland carbon sequestration and storage. Further use of this management practice may improve wetland carbon storage across other arid freshwater wetland ecosystems with similar hydrologic regimes.
Comparative Insights Into the Complete Genome Sequence of Highly Metal Resistant Cupriavidus metallidurans Strain BS1 Isolated From a Gold–Copper Mine

The highly heavy metal resistant strain Cupriavidus metallidurans BS1 was isolated from the Zijin gold–copper mine in China. This was of particular interest since the extensively studied, closely related strain, C. metallidurans CH34 was shown to not be only highly heavy metal resistant but also able to reduce metal complexes and biomineralizing them into metallic nanoparticles including gold nanoparticles. After isolation, C. metallidurans BS1 was characterized and complete genome sequenced using PacBio and compared to CH34. Many heavy metal resistance determinants were identified and shown to have wide-ranging similarities to those of CH34. However, both BS1 and CH34 displayed extensive genome plasticity, probably responsible for significant differences between those strains. BS1 was shown to contain three prophages, not present in CH34, that appear intact and might be responsible for shifting major heavy metal resistance determinants from plasmid to chromid (CHR2) in C. metallidurans BS1. Surprisingly, the single plasmid – pBS1 (364.4 kbp) of BS1 contains only a single heavy metal resistance determinant, the czc determinant representing RND-type efflux system conferring resistance to cobalt, zinc and cadmium, shown here to be highly similar to that determinant located on pMOL30 in C. metallidurans CH34. However, in BS1 another homologous czc determinant was identified on the chromid, most similar to the czc determinant from pMOL30 in CH34. Other heavy metal resistance determinants such as cnr and chr determinants, located on megaplasmid pMOL28 in CH34, were shown to be adjacent to the czc determinant on chromid (CHR2) in BS1. Additionally, other heavy metal resistance determinants such as pbr, cop, sil, and ars were located on the chromid (CHR2) and not on pBS1 in BS1. A diverse range of genomic rearrangements occurred in this strain, isolated from a habitat of constant exposure to high concentrations of copper, gold and other heavy metals. In contrast, the megaplasmid in BS1 contains mostly genes encoding unknown functions, thus might be more of an evolutionary playground where useful genes could be acquired by horizontal gene transfer and possibly reshuffled to help C. metallidurans BS1 withstand the intense pressure of extreme concentrations of heavy metals in its environment.
Disadvantages of Automated Respiratory Gas Exchange Analyzers

The use of automated gas exchange analysis systems in exercise studies is common throughout the industrialized world and are frequently used in sports medicine laboratories for the measurement of maximal oxygen uptake (VO2max), as an integrative parameter that allows the physical condition to be assessed, in spite of its limitations. Actually, the fundamental principles behind the measurement of respiratory gas exchange (RGE) have not changed for a century. It was used a manual Douglas bag method together with separate chemical analyses. The need for faster and more efficient techniques, has conditioned the traditional procedures and determined the emergence of automated systems. However, the validity and reliability of all these different systems is not well known. The common features associates with these systems, also have disadvantages that must be evaluated at the time of the acquisition of an automated equipment: (1) regular quality control checks, which entails other added economic costs, (2) the validity and reliability of the results, which it is necessary to verify, and (3) the user does not know the equations that determine the values of oxygen consumption and carbon dioxide production. This work aims to clarify the disadvantages of these automated systems. At maximum intensities, the variation of VO2max or VO2peak can be very significant in athletes and even more relevant in sick people undergoing a training program. Therefore, considerable care is needed when comparing RGE data with automated systems. New and Noteworthy Actually, stress tests are more conveniently performed with automated systems. It is necessary to examine the validity and reliability of automated respiratory gas exchange systems. The algorithms incorporated in the software, apart from being a “mystery,” show differences with respect to the data provided.
Electrophile Signaling and Emerging Immuno- and Neuro-modulatory Electrophilic Pharmaceuticals

With a lipid-rich environment and elevated oxygen consumption, the central nervous system (CNS) is subject to intricate regulation by lipid-derived electrophiles (LDEs). Investigations into oxidative damage and chronic LDE generation in neural disorders have spurred the development of tools that can detect and catalog the gamut of LDE-adducted proteins. Despite these advances, deconstructing the precise consequences of individual protein-specific LDE modifications remained largely impossible until recently. In this perspective, we first overview emerging toolsets that can decode electrophile-signaling events in a protein/context-specific manner, and how the accumulating mechanistic insights brought about by these tools have begun to offer new means to modulate pathways relevant to multiple sclerosis (MS). By surveying the latest data surrounding the blockbuster MS drug dimethyl fumarate that functions through LDE-signaling-like mechanisms, we further provide a vision for how chemical biology tools probing electrophile signaling may be leveraged toward novel interventions in CNS disease.
A retrospective analysis of NIH-funded digital health research using social media platforms

Objective Social network platforms are increasingly used in digital health research. Our study aimed to 1. qualify and quantify the use of social media platforms in health research supported by the National Institutes of Health (NIH) and document changes occurring between 2011 and 2017 and 2. examine whether institutions hosting these studies provided public-facing guidelines on how to conduct ethical social media health research. Methods The NIH RePORTER (Research Portfolio Online Reporting Tools) database was searched to identify research utilizing Instagram, Pinterest, Facebook, or Twitter. Studies included used social media for observational research, recruitment, intervention delivery or to assess social media as an effective research tool. Abstracts were qualitatively analyzed to describe the population and health topic by year. Websites of organizations receiving funding for this research were searched to identify whether guidance or policy existed. Results Studies (n = 105) were organized by population targeted and health focus. Main “Health” themes were labeled: 1. substance use, 2. disease/diagnosis, 3. psychiatry/mental health, and 4. weight and physical activity. The populations most involved included adolescents and young adults, and men who have sex with men. The number of research studies using social media increased approximately 590% between 2011 and 2017. Studies were linked to 56 organizations of which 21% (n = 12) provided some accessible guidance with 79% (n = 44) offering no guidance specific to social media health research. Conclusions Social media research is conducted with vulnerable populations that are traditionally difficult to reach. There is a compelling need for resources designed to support ethical and responsible social media-enabled research to enable this research to be carried out safely.
Clinical Manifestation and Molecular Characterization of a Novel Member of the Nannizziopsiaceae in a Pulmonary Granuloma From a Galapagos Tortoise (Chelonoidis nigra)

Nannizziopsiaceae is a family of fungal organisms within the order Onygenales containing two genera of important reptile pathogens, Nannizziopsis and Paranannizziopsis. A captive Galapagos tortoise (Chelonoidis nigra) from Boca Raton, Florida, United States, was presented for a clinical history of chronic progressive lethargy and inappetence. At initial presentation, the tortoise had a moderate non-regenerative anemia, leukocytosis, whip-like heterophil projections, erythrocyte fragmentation, and fibrin strands, with the latter two raising concern for disseminated intravascular coagulation. A single large encapsulated pulmonary granuloma was identified through imaging, including plain film radiography and bronchoscopy. Direct intralesional samples were obtained from transcarapacial celioscopy for fungal culture, cytology, histopathology, and polymerase chain reaction. Amplification and sequencing of the ITS2 region of the rRNA genes with Bayesian and maximum likelihood analyses placed the fungus in the family Nannizziopsiaceae within the order Onygenales, representing a novel fungal species.
Microdosimetric quantities of an accelerator-based neutron source used for boron neutron capture therapy measured using a gas-filled proportional counter

Abstract Boron neutron capture therapy (BNCT) is an emerging radiation treatment modality, exhibiting the potential to selectively destroy cancer cells. Currently, BNCT is conducted using a nuclear reactor. However, the future trend is to move toward an accelerator-based system for use in hospital environments. A typical BNCT radiation field has several different types of radiation. The beam quality should be quantified to accurately determine the dose to be delivered to the target. This study utilized a tissue equivalent proportional counter (TEPC) to measure microdosimetric and macrodosimetric quantities of an accelerator-based neutron source. The micro- and macro-dosimetric quantities measured with the TEPC were compared with those obtained via the the particle and heavy ion transport code system (PHITS) Monte Carlo simulation. The absorbed dose from events >20 keV/μm measured free in air for a 1-h irradiation was calculated as 1.31 ± 0.02 Gy. The simulated result was 1.41 ± 0.07 Gy. The measured and calculated values exhibit good agreement. The relative biological effectiveness (RBE) that was evaluated from the measured microdosimetric spectrum was calculated as 3.7 ± 0.02, similar to the simulated value of 3.8 ± 0.1. These results showed the PHITS Monte Carlo simulation can simulate both micro- and macro-dosimetric quantities accurately. The RBE was calculated using a single-response function, and the results were compared with those of several other institutes that used a similar method. However, care must be taken when using such a single-response function for clinical application, as it is only valid for low doses. For clinical dose ranges (i.e., high doses), multievent distribution inside the target needs to be considered.