Disentangling the veil line for Brazilian biodiversity: An overview from two long-term research programs reveals huge gaps in ecological data reporting.

The lack of synthesized information regarding biodiversity is a major problem among researchers, leading to a pervasive cycle where ecologists make field campaigns to collect information that already exists and yet has not been made available for a broader audience. This problem leads to long-lasting effects in public policies such as spending money multiple times to conduct similar studies in the same area. We aim to identify this knowledge gap by synthesizing information available regarding two Brazilian long-term biodiversity programs and the metadata generated by them. Using a unique dataset containing 1904 metadata, we identified patterns of metadata distribution and intensity of research conducted in Brazil, as well as where we should concentrate research efforts in the next decades. We found that the majority of metadata were about vertebrates, followed by plants, invertebrates, and fungi. Caating was the biome with least metadata, and that there's still a lack of information regarding all biomes in Brazil, with none of them being sufficiently sampled. We hope that these results will have implications for broader conservation and management guiding, as well as to funding allocation programs.

Pressure-Induced Phase Transformations of Quasi-2D Sr3Hf2O7.

We present an abinitio study of the quasi-2D layered perovskite Sr3Hf2O7 compound, performed within the framework of the density functional theory and lattice dynamics analysis. At high temperatures, this compound takes a I4/mmm centrosymmetric structure (S.G. n. 139); as the temperature is lowered, the symmetry is broken into other intermediate polymorphs before reaching the ground-state structure, which is the Cmc21 ferroelectric phase (S.G. n. 36). One of these intermediate polymorphs is the Ccce structural phase (S.G. n. 68). Additionally, we have probed the C2/c system (S.G n. 15), which was obtained by following the atomic displacements corresponding to the eigenvectors of the imaginary frequency mode localized at the Γ-point of the Ccce phase. By observing the enthalpies at low pressures, we found that the Cmc21 phase is thermodynamically the most stable. Our results show that the I4/mmm and C2/c phases never stabilize in the 0-20 GPa range of pressure values. On the other hand, the Ccce phase becomes energetically more stable at around 17 GPa, surpassing the Cmc21 structure. By considering the effect of entropy and the constant-volume free energies, we observe that the Cmc21 polymorph is energetically the most stable phase at low temperature; however, at 350 K, the Ccce system becomes the most stable. By probing the volume-dependent free energies at 19 GPa, we see that Ccce is always the most stable phase between the two structures and also throughout the studied temperature range. When analyzing the phonon dispersion frequencies, we conclude that the Ccce system becomes dynamically stable only around 19-20 GPa and that the Cmc21 phase is metastable up to 30 GPa.

Local inhomogeneous state in multiferroic SmCrO3.

Rare-earth orthochromites with distorted perovskite structure (e.g. RCrO3, R = Sm, Gd) have been under strong debate with respect to the origin of their ferroelectric order. Of particular interest is the question of whether such orthochromites are, in fact, magnetically driven improper ferroelectrics, as many rare-earth manganites or orthoferrites. Here we show, by studying at the atomic scale the rare-earth SmCrO3 system that a distortion of the Sm local environment emerges within the paramagnetic phase, near room temperature. Our Electric Field Gradient measurements combined with first-principles calculations show that the emergent phase cannot be simply ascribed to the Pna21 structure as reported for GdCrO3 or SmCrO3. Instead a local inhomogeneous state, where regular non-polar and polar distorted environments coexist, develops at low temperatures.

Semen quality is affected by HLA class I alleles together with sexually transmitted diseases.

BACKGROUND: The human leukocyte antigen (HLA) locus includes several genes with key roles in antigen presentation and immune response, some of them inclusively found to be associated with non-obstructive azoospermia. Still, HLA connections to other infertility phenotypes such as semen hyperviscosity (SHV), asthenozoospermia (AST), and oligozoospermia (OLI) have been often neglected. OBJECTIVES: In this work, we aimed to evaluate the association of HLA class I and II genes with SHV, AST, and OLI phenotypes while exploring a possible role in an adaptive immune response to sexually transmitted diseases (STD). MATERIALS AND METHODS: Whole-exome sequencing was performed in a Portuguese cohort of 71 infertility cases and 68 controls, followed by HLA typing using a specific software-HLA*PRG:LA tool. Molecular screenings of seven STD were carried out in a subset of 72 samples (30 cases and 42 controls). RESULTS: Statistical tests uncovered three protective alleles: HLA-A*11:01, associated with all forms of male infertility (p = 0.0006); HLA-DQB1*03:02 with SHV and OLI (PSHV  = 0.0303, POLI  = 0.0153); and HLA-A*29:02 with OLI (p = 0.0355), which was found to interfere in sperm number together with HPV (p = 0.0313). Five risk alleles were also identified: two linked with SHV (HLA-B*50:01, p = 0.0278; and HLA-C*06:02, p = 0.0461), another one with both SHV and OLI (HLA-DQA1*05:01, PSHV  = 0.0444 and POLI =0.0265), and two with OLI (HLA-C*03:03, p = 0.0480; and HLA-DQB1*03:01, p = 0.0499). Here, HLA-C*03:03 carriers tend to be HPV infected. CONCLUSIONS: The application of HLA*PRG:LA tool to the study of male infertility provided novel insights for an HLA correlation with semen quality, namely among SHV and OLI phenotypes. The discovery of an HLA-A*29:02/HPV crosstalk, together with former reports of HLA alleles conferring resistance-susceptibility to diverse human pathogens, raises the hypothesis of a mechanistic link between male infertility, HLA polymorphism, and host response to STD.

An update on enzymatic cocktails for lignocellulose breakdown.

Alternative energy sources have received increasing attention in recent years. The possibility of adding value to agricultural wastes, by producing biofuels and other products with economic value from lignocellulosic biomass by enzymatic hydrolysis, has been widely explored. Lignocellulosic biomass, as well as being an abundant residue, is a complex recalcitrant structure that requires a consortium of enzymes for its complete degradation. Pools of enzymes with different specificities acting together usually produce an increase in hydrolysis yield. Enzymatic cocktails have been widely studied due to their potential industrial application for the bioconversion of lignocellulosic biomass. This review presents an overview of enzymes required to degrade the plant cell wall, paying particular attention to the latest advances in enzymatic cocktail production and the main results obtained with cocktails used to degrade a variety of types of biomass, as well as some future perspectives within this field.

Insights into the evolution of the new variant rabbit haemorrhagic disease virus (GI.2) and the identification of novel recombinant strains.

Rabbit haemorrhagic disease (RHD) is a viral disease that affects the European rabbit. RHD was detected in 1984 in China and rapidly disseminated worldwide causing a severe decline in wild rabbit populations. The aetiological agent, rabbit haemorrhagic disease virus (RHDV), is an RNA virus of the family Caliciviridae, genus Lagovirus. Pathogenic (G1-G6 or variants GI.1a-GI.1d) and non-pathogenic strains (GI.4) have been characterized. In 2010, a new variant of RHDV, RHDV2/RHDVb/GI.2, was detected in France. GI.2 arrived to the Iberian Peninsula in 2011, and several recombination events were reported. Here, we sequenced full genomes of 19 samples collected in Portugal between 2014 and 2016. New GI.2 recombinant strains were detected, including triple recombinants. These recombinants possess a non-structural protein p16 related to a non-pathogenic strain. Evolutionary analyses were conducted on GI.2 VP60 sequences. Estimated time to the most recent common ancestor (tMRCA) suggests an emergence of GI.2 in July 2008, not distant from its first detection in 2010. This is the first study on GI.2 evolution and highlights the need of continued monitoring and characterization of complete genome sequences when studying lagoviruses' evolution.

Epidemiology of RHDV2 (Lagovirus europaeus/GI.2) in free-living wild European rabbits in Portugal.

As the detection of the first outbreak of a novel aetiological agent of rabbit haemorrhagic disease commonly called RHDV2 or RHDVb (Lagovirus europaeus/GI.2, henceforth GI.2) in France in 2010, the virus rapidly spread throughout continental Europe and nearby islands such as Great Britain, Sardinia, Sicily, the Azores and the Canary Islands among others. The outbreaks of this new lagovirus cause important economic losses in rabbitries, and ecological disruptions by affecting the conservation of rabbit-sensitive top predators. We analysed 550 rabbit carcasses collected in the field between May 2013 and March 2016, to investigate the epidemiology of GI.2 in free-living populations and to perform a comparative analysis with the epidemiology of classical rabbit haemorrhagic disease virus forms (RHDV, henceforth GI.1) in Portugal. Rabbits were sexed, aged and liver and blood samples were collected for subsequent RHDV screening and serology. A total of 172 samples were PCR-positive to GI.2, whereas GI.1 strains were not detected in any of the samples. The outbreaks of GI.2 revealed a marked seasonality, with peaks during the breeding season (November-May). We also found that approximately, one-third of free-ranging European rabbits in Portugal have seroconverted to GI.2. We demonstrate that the GI.2 lagovirus is currently widespread in wild populations in Portugal and is affecting a high proportion of adults and juveniles. Therefore, ongoing monitoring and surveillance are required to assess the effects of GI.2 on wild rabbit populations, its evolution, and to guide management actions aimed at mitigating the impacts of rabbit declines in the ecosystem and in rural economies.

Ordered La0.7Sr0.3MnO3 nanohole arrays fabricated on a nanoporous alumina template by pulsed laser ablation.

Highly ordered nanohole arrays of [Formula: see text] manganite have been synthesized using pulsed laser deposition on nanoporous alumina template. Their structure and phase formation were characterized by scanning electron microscopy (SEM), atomic force microscopy (AFM), energy dispersive x-ray spectroscopy (EDX) and x-ray diffraction (XRD). The magnetic measurements were performed with respect to temperature and field and exhibit a ferromagnetic to paramagnetic transition at 284 K. In addition, the temperature dependence of electrical resistance was measured at different magnetic fields and an insulating phase throughout all the temperatures was observed. The low temperature ferromagnetic insulating state is discussed by the presence of a canted ferromagnetic state induced by the nanoholes. The present work shows the feasibility of combining both the nanoporous alumina template and pulsed laser ablation for the fabrication of perovskite manganite nanohole arrays which can also be extended to fabricate other multicomponent oxide nanohole materials.

Rare double sex and mab-3-related transcription factor 1 regulatory variants in severe spermatogenic failure.

The double sex and mab-3-related transcription factor 1 (DMRT1) gene has long been linked to sex-determining pathways across vertebrates and is known to play an essential role in gonadal development and maintenance of spermatogenesis in mice. In humans, the genomic region harboring the DMRT gene cluster has been implicated in disorders of sex development and recently DMRT1 deletions were shown to be associated with non-obstructive azoospermia (NOA). In this work, we have employed different methods to screen a cohort of Portuguese NOA patients for DMRT1 exonic insertions and deletions [by multiplex ligation probe assay (MLPA); n = 68] and point mutations (by Sanger sequencing; n = 155). We have found three novel patient-specific non-coding variants in heterozygosity that were absent from 357 geographically matched controls. One of these is a complex variant with a putative regulatory role (c.-223_-219CGAAA>T), located in the promoter region within a conserved sequence involved in Dmrt1 repression. Moreover, while DMRT1 domains are highly conserved across vertebrates and show reduced levels of diversity in human populations, two rare synonymous substitutions (rs376518776 and rs34946058) and two rare non-coding variants that potentially affect DMRT1 expression and splicing (rs144122237 and rs200423545) were overrepresented in patients when compared with 376 Portuguese controls (301 fertile and 75 normozoospermic). Overall our previous and present results suggest a role of changes in DMRT1 dosage in NOA potentially also through a process of gene misregulation, even though DMRT1 deleterious variants seem to be rare.

Complete genome sequence of two rabbit hemorrhagic disease virus variant b isolates detected on the Iberian Peninsula.

We report the complete genome sequences of two isolates (RHDV-N11 and CBVal16) of variant rabbit hemorrhagic disease virus (RHDVb). Isolate N11 was detected in young domestic animals during a rabbit hemorrhagic disease (RHD) outbreak that occurred in 2011 on a rabbit farm in Navarra, Spain, while CBVal16 was isolated from a wild rabbit found dead in Valpaços, Northern Portugal, a year later. The viral sequences reported show 84.8-85.1 % and 78.3-78.5 % identity to RHDVAst/89 and RCV-A1 MIC-07, representative members of the pathogenic genogroup 1 RHDV and apathogenic rabbit calicivirus, respectively. In comparison with other RHDV isolates belonging to the previously known genogroups 1-6, RHDVb shows marked phenotypic differences, as it causes disease preferentially in young rabbits under 40 days of age and shows modified red blood cell agglutination profiles as well as antigenic differences that allow this variant to escape protection by the currently available vaccines.

Hyperfine local probe study of alkaline-earth manganites SrMnO3 and BaMnO3.

We report perturbed angular correlation measurements with (111m)Cd/(111)Cd and (111)In/(111)Cd probes, at the ISOLDE-CERN facility, in the manganite compounds BaMnO3, with the 6H and 15R polymorphs, and SrMnO3, with the 4H polymorph. The electric field gradient (EFG) is measured, and found approximately constant in a large temperature range for all the compounds. The EFG is also calculated from first principles with density functional theory, and compared with experimental results by considering diluted substitutional Cd impurities. Based on the results, we assign as sites for the probes the Ba (for BaMnO3-6H, 15R) and Sr (for SrMnO3-4H) sites, apart from fractions of undetermined origin in the case of BaMnO3-6H. We predict the hyperfine parameters in the recently synthesized multiferroic manganite Sr(0.5)Ba(0.5)MnO3, and its variation with the structure and electric polarization, which is found to be very small.

Jahn-Teller distortion relaxation across the LaMnO3+Δ phase diagram.

The evolution of the local Jahn-Teller distortion across the LaMnO3+Δ phase diagram was obtained using the perturbed angular correlation local probe technique. We found that upon doping, the local distortion decreases continuously with increasing doping and that no fully Jahn-Teller distorted Mn(3+)O6 octahedra are observed within the orthorhombic insulating phase. A local single-phase scenario is established for the orbital disordered orthorhombic crystallographic structure. We also show that the continuous weakening of the Jahn-Teller distortions is not limited to a single-phase environment and occurs in a similar manner within an undistorted rhombohedric matrix upon lowering the temperature.

Rapid synthesis of ordered manganite nanotubes by microwave irradiation in alumina templates.

Highly ordered La2/3Ca1/3MnO3 nanotube arrays were successfully synthesized by a simple and rapid process, combining nanoporous alumina template-assisted synthesis with microwave irradiation. The method offers a quick hands-on route to produce manganite bulk sample and nanotube arrays at relative low-temperatures. We obtain thin wall nanotubes of uniform diameter of 80 nm. The growth mechanism of nanotubes is briefly discussed. Magnetic measurements indicate that the ferromagnetic transition temperature T(c) of the nanotubes is depleted with respect to its bulk counterpart possibly due to the geometric confinement imposed by the thin wall of the nanotubes.

New phase transition in the Pr1-xCaxMnO3 system: evidence for electrical polarization in charge ordered manganites.

In this Letter a detailed study of the electric field gradient (EFG) across the Pr(1-x)Ca(x)MnO(3) phase diagram and its temperature dependence is given. Clearly, distinct EFG behavior for samples outside or inside the charge order (CO) region are observed. The EFG temperature dependence evidences a new phase transition occurring over the broad CO region of the phase diagram. This transition is discontinuous and occurs at temperatures between the charge ordering and the Néel temperatures. The prominent features observed in the EFG are associated with polar atomic vibrations which eventually lead to a spontaneous local electric polarization below CO transition.

Liquid-liquid extraction of commercial and biosynthesized nisin by aqueous two-phase micellar systems.

Nisin is a natural additive for conservation of food, and can also be used as a therapeutic agent. Nisin inhibits the outgrowth of spores, the growth of a variety of Gram-positive and Gram-negative bacteria. In this paper we present a potentially scalable and cost-effective way to purify commercial and biosynthesized in bioreactor nisin, including simultaneously removal of impurities and contaminants, increasing nisin activity. Aqueous two-phase micellar systems (ATPMS) are considered promising for bioseparation and purification purposes. Triton X-114 was chosen as the as phase-forming surfactant because it is relatively mild to proteins and it also forms two coexisting phases within a convenient temperature range. Nisin activity was determined by the agar diffusion assay utilizing Lactobacillus sake as a sensitive indicator microorganism. Results indicated that nisin partitions preferentially to the micelle rich-phase, despite the surfactant concentration tested, and its antimicrobial activity increases. The successful implementation of this peptide partitioning, from a suspension containing other compounds, represents an important step towards developing a separation method for nisin, and more generally, for other biomolecules of interest.

Avaliação da adesão às normas da portaria 344/98 svs/ms utilizando notificações e receitas oriundas da cidade de Salto / SP / Assessment of adherence to regulatory decree 344/98 by study of notifications and prescriptions in the city of Salto, SP, Brazil

Ações controladoras do consumo de entorpecentes constituem uma constante preocupação das sociedades há muito tempo. Neste trabalho optou-se por avaliar se de fato estão sendo cumpridas as exigências feitas pelo ordenamento jurídico no que se refere à prescrição e dispensão de medicamentos sujeitos ao controle especial normatizados pela Portaria 344/98 da então Secretaria de Vigilância Sanitária do Ministério da Saúde. Assim, esta pesquisa conduzida em 13 drogarias, na cidade de Salto/SP, avaliou os documentos compostos por Notificação de Receita B (NRB) e Receita de Controle Especial (RCE), disponibilizados no local, no período de outubro a dezembro de 2002, sendo estes selecionados por amostragem sistemática. Os 230 RCE e 154 NRB que foram analisados de acordo com a presença dos elementos de receitas descritos na Portaria que incluem aqueles de competência do prescritor, do farmacêutico e do estabelecimento e a adesão ao modelo oficial do tipo do documento preconizado pela ANVISA. Os resultados mostram que tanto nos documentos RCE e NRB provenientes do SUS e privado há ausência de itens de responsabilidade tanto dos prescritores, quanto farmacêuticos e estabelecimento. Concluiu-se que as exigências estabelecidas por esta Portaria não estão sendo cumpridas devidamente, podendo permitir comércio ilegal, mostrando que isso ocorre por falta de fiscalização mais pontual

Optimum conditions for growth in liquid medium of Oscillatoria formosa Bory used as the principal food in laboratory culture of intermediate hosts for schistosomosis and fasciolosis.

The rearing of snails, intermediate hosts of Schistosoma haematobium, S. intercalatum, S. bovis and Fasciola hepatica is the first step to maintain the life cycle of these parasites in laboratory in order to have biological material for the different studies, namely on the systematic biology and immunodiagnostic of schistosomosis and fasciolosis. According to the traditional method, the alga Oscillatoria formosa Bory (Cyanobacteria), principal food source for the snails, was cultivated in soil extract (Sampaio Xavier et al., 1968). However, it was sometimes very difficult to find the proper soil extract and the material was also contaminated by protozoa and fungi. In our work, using a new medium having as a base the Mineral Medium II (modified from Hughes et al., 1958) we found that O. formosa had a better growth response than in the soil extract medium. Snails fed on O. formosa reached three times the size of others at the same age, and they also reached sex maturity earlier, having more egg-masses per snail and, in addition, the rate of survival as well as the number of generations per year under laboratory conditions significantly increased. This culture was also easier to perform, and the axenic conditions easier to maintain.

Unexplained elevated midtrimester maternal serum levels of alpha fetoprotein, human chorionic gonadotropin, or low unconjugated estriol: recurrence risk and association with adverse perinatal outcome.

OBJECTIVE: To determine if women experiencing an unexplained elevated maternal serum alpha fetoprotein (MSAFP; > or =2.0 MoM) or human chorionic gonadotropin (hCG; > or =2.0 MoM), or low unconjugated estriol (E3; < or =0.5 MoM) in one pregnancy are at increased risk for similar results in a subsequent pregnancy, and to determine if recurrence of these analyte extremes is associated with adverse perinatal outcome. METHODS: We identified all women delivering two consecutive singleton pregnancies at one hospital between 1992-1997 for whom second trimester trisomy 21 serum screen was performed in each pregnancy. All screens were performed in a single laboratory. Each pregnancy delivered after 20 weeks and had gestational age confirmed by ultrasound prior to 24 weeks. Subjects were excluded if a fetal anomaly or aneuploidy was present. Adverse outcomes included abruption, oligohydramnios, preeclampsia, preterm membrane rupture, preterm delivery, stillbirth, birthweight <10th centile, and admission to neonatal intensive care unit (NICU). RESULTS: A total of 538 women had 1,076 pregnancies meeting inclusion criteria; 12/515 (2.3%) of women with a normal MSAFP, 28/470 (6.0%) with a normal hCG, and 11/504 (2.2%) with a normal E3 in the first pregnancy had an anomalous result for the respective analyte in the second pregnancy. In contrast, only 4/23 (17.4%) patients with an elevated MSAFP (P = 0.003), 14/44 (31.8%) with an elevated hCG (P < 0.001), and 2/10 (20.0%) with a low E3 (P < 0.025) in the first pregnancy had the same analyte anomaly recur in the second pregnancy. The odds ratios for recurrent elevated MSAFP, hCG, and low E3 were 7.5, 5.3, and 9.2, respectively. Adverse perinatal outcomes occurred with similar frequency, regardless of MSAFP, hCG, or E3 results in consecutive pregnancies, using women with normal MSAFP, hCG, and E3 results in one or both pregnancies as controls. CONCLUSIONS: Women experiencing an anomalous serum analyte in one pregnancy are at significant risk to experience the same analyte result in a subsequent pregnancy.

Development of compensatory thermogenesis in response to overfeeding in hypothyroid rats.

Intact or surgically thyroidectomized (Tx) adult male Wistar rats, weighing 150-200 g, were fed a standard chow diet (approximately 1.8 Cal/g) or a high calorie (approximately 3.8 Cal/g) diet (cafeteria diet) for up to 30 days. Daily energy intake was about 5-fold higher in the rats fed the cafeteria diet regardless of their thyroid status. The cafeteria diet caused the retroperitoneal white fat pad to increase by approximately 2-fold, the volume of isolated white adipocytes to increase by 2-fold, and the total body fat to increase by a factor of approximately 3, again regardless of thyroid status. It also increased basal metabolic rate by about 20% in intact rats and by about 50% in Tx rats. The brown fat thermal response to norepinephrine (NE) infusion was approximately 2-fold increased in the intact rats fed the cafeteria diet. However, in the Tx rats, the brown fat thermal response to NE was blunted regardless of the dietary regimen adopted. In both intact and Tx rats, the cafeteria diet increased total brown fat mitochondria, uncoupling protein percentage, and total brown fat uncoupling protein by about 3-, 2-, and 5-fold, respectively. Serum leptin levels also increased approximately 4-fold in intact rats fed the cafeteria diet. However, in Tx rats, leptin levels did not change significantly during overfeeding. In conclusion, hypothyroidism caused the brown fat to become unresponsive to NE, even after 1 month on the cafeteria diet. However, these rats were able to increase basal metabolic rate and, as assessed by several different parameters, did not gain fat beyond that observed in intact controls kept on a similar overfeeding schedule.