Chemical data evaluation: general considerations and approaches for IUPAC projects and the chemistry community (IUPAC Technical Report).

The International Union of Pure and Applied Chemistry (IUPAC) has a long tradition of supporting the compilation of chemical data and their evaluation through direct projects, nomenclature and terminology work, and partnerships with international scientific bodies, government agencies and other organizations. The IUPAC Interdivisional Subcommittee on Critical Evaluation of Data (ISCED) has been established to provide guidance on issues related to the evaluation of chemical data. In this first report we define the general principles of the evaluation of scientific data and describe best practices and approaches to data evaluation in chemistry.

PI3K-AKT, JAK2-STAT3 pathways and cell-cell contact regulate maspin subcellular localization.

BACKGROUND: Maspin (SERPINB5) is a potential tumor suppressor gene with pleiotropic biological activities, including regulation of cell proliferation, death, adhesion, migration and gene expression. Several studies indicate that nuclear localization is essential for maspin tumor suppression activity. We have previously shown that the EGFR activation leads to maspin nuclear localization in MCF-10A cells. The present study investigated which EGFR downstream signaling molecules are involved in maspin nuclear localization and explored a possible role of cell-cell contact in this process. METHODS: MCF-10A cells were treated with pharmacological inhibitors against EGFR downstream pathways followed by EGF treatment. Maspin subcellular localization was determined by immunofluorescence. Proteomic and interactome analyses were conducted to identify maspin-binding proteins in EGF-treated cells only. To investigate the role of cell-cell contact these cells were either treated with chelating agents or plated on different cell densities. Maspin and E-cadherin subcellular localization was determined by immunofluorescence. RESULTS: We found that PI3K-Akt and JAK2-STAT3, but not MAP kinase pathway, regulate EGF-induced maspin nuclear accumulation in MCF-10A cells. We observed that maspin is predominantly nuclear in sparse cell culture, but it is redistributed to the cytoplasm in confluent cells even in the presence of EGF. Proteomic and interactome results suggest a role of maspin on post-transcriptional and translation regulation, protein folding and cell-cell adhesion. CONCLUSIONS: Maspin nuclear accumulation is determined by an interplay between EGFR (via PI3K-Akt and JAK2-STAT3 pathways) and cell-cell contact. Video Abstract.

Pituitary neuroendocrine tumors and differentiated thyroid cancer: do metabolic and inflammatory risk factors play roles?

PURPOSE: It is postulated that patients with different types of pituitary neuroendocrine tumors (PitNETs) may present a higher incidence of cancer. Factors underlying individuals becoming overweight, such as insulin resistance, hyperleptinemia, and low-grade inflammation, may play a role in the risk of differentiated thyroid carcinoma (DTC) in such patients. This study aimed to investigate the frequency of and obesity-related risk factors associated with DTC in patients with PitNETs. METHODS: This cross-sectional study involved 149 patients with nonacromegalic PitNETs (AG group), 71 patients with acromegaly (ACRO group), and 156 controls (CG group). All participants underwent insulin and blood glucose measurements with the determination of the homeostatic model assessment-insulin resistance (HOMA-IR) index, leptin, and high-sensitivity C-reactive protein (hsCRP), and they also underwent thyroid ultrasound. Clinically significant nodules were biopsied for subsequent cytopathological evaluation, and participants were operated on when indicated. RESULTS: Patients in the AG group had high levels of insulin resistance and significantly higher levels of leptin and hsCRP compared with those of patients in the ACRO group. There were no cases of DTC in the AG group; two findings, one incidental, of DTC occurred in the CG group, and three cases of DTC were present in the ACRO group. Acromegaly was associated with DTC after adjusted analysis. CONCLUSIONS: Our findings in patients with nonacromegalic PitNETs do not indicate a high risk for DTC despite the presence of metabolic and inflammatory risk factors for neoplastic events. In contrast, acromegaly promotes a greater risk of DTC.

Acquired hepatocerebral degeneration and hepatic encephalopathy: one or two entities?

BACKGROUND AND PURPOSE: Acquired hepatocerebral degeneration (AHD) and hepatic encephalopathy (HE) are neurological complications of chronic liver disease (CLD) with portosystemic shunt. While HE is common, AHD is a rare entity, and the clinical imaging relationships observed in small series lack validation in large patient cohorts. The aim of this study was to characterize a cohort of AHD patients and to explore possible associations with HE coexistence. METHODS: We performed a retrospective analysis of patients with a working AHD diagnosis, between 2008 and 2019. Clinical, laboratory, imaging and neuropsychological results at first neurological observation were reviewed and compared between the 'AHD' group and the 'AHD with HE' group. RESULTS: A total of 76 patients were recruited. The most frequent neurological manifestations were neuropsychiatric (93.4%) and extrapyramidal (84.2%). Only 38% of patients had hypermanganesemia. Compared with the AHD group, the AHD with HE group had more hyperkinetic movement disorders (71.4% vs. 38.5%; P = 0.05), a higher number of patients on the dementia spectrum (57.7% vs. 20%; P = 0.04), higher median ammonia levels (P = 0.014) and more widespread cortico-subcortical and pyramidal involvement on brain magnetic resonance imaging. Nineteen patients underwent liver transplantation, with significantly improved survival (P = 0.006). DISCUSSION: Hepatic encephalopathy and AHD often coexist in the same patient. Seventy-six patients with CLD and AHD were evaluated, making this one of the largest reported AHD cohorts. Blood manganese level was a weak diagnostic marker in AHD. Early liver function restoration through liver transplantation improved survival. Our report provides a detailed description of the phenotype and long-term outcome of AHD, with relevance for diagnosis and treatment.

Negative impact on the reproductive potential of blue jack mackerel Trachurus picturatus by Kudoa infection of the ovary.

Reproduction of Trachurus picturatus off the western Portuguese coast was studied over 1 yr. During histological analyses, the presence of Kudoa sp. was detected in advanced vitellogenic oocytes. Kudoa infections are known to cause economic loss through the induction of post-mortem liquefaction of fish muscles, but ovarian infection as reported in this study will seriously affect the reproductive potential of the species and thus impact fisheries productivity. Only females showed gonad infection which led to total degradation of advanced vitellogenic oocytes. No macroscopic, somatic or condition indices revealed differences between infected and uninfected females, rendering this infection event a concealed suppression of reproduction.

Phylogenetic diversity of aerobic spore-forming Bacillalles isolated from Brazilian soils.

The phylum Firmicutes comprises seven classes where most species are either aerobic or anaerobic endospore former. Inside Firmicutes, species allocated in the genus Bacillus and related genera are collectively named aerobic endospore-forming bacteria (AEFB), and the soil is their major reservoir. AEFB have great importance in health, agriculture, and biotechnology although the more studied species are Bacillus subtilis and the human pathogens Bacillus cereus and Bacillus anthracis. AEFB have great importance in health, agriculture, and biotechnology; although the knowledge about these organisms is based on few species, notably, Bacillus subtilis, Bacillus cereus, and Bacillus anthracis. In this work, we generated partial 16S rRNA gene sequences of both strands of 192 AEFB strains isolated from soils of Distrito Federal, Brazil (SDF strains). The resulting consensus sequences were used to obtain taxonomic assignment and establish the phylogenetic relationships among these strains. Through this approach, we could observe that classified SDF strains were distributed among genera Bacillus (169 strains; 88.02%), Paenibacillus (11; 5.73%), Lysinibacillus (6; 3.13%), Brevibacillus (4; 2.08%), Terribacillus (1; 0.52%), and Rummeliibacillus (1; 0.52%). Phylogenetic trees revealed these 192 SDF strains can be segregated into eight groups spanning families Bacillaceae and Paenibacillaceae belonging to the order Bacillales. To expand the knowledge about the diversity of these SDF strains, further studies regarding characterization with different methodologies are underway.

Spatial clustering, social vulnerability and risk of leprosy in an endemic area in Northeast Brazil: an ecological study.

BACKGROUND: Despite the global decline in the detection of leprosy cases, its incidence has remained unchanged in certain settings and requires the determination of the factors linked to its persistence. We examined the spatial and space-time distribution of leprosy and the influence of social vulnerability on the occurrence of the disease in an endemic area of Northeast Brazil. METHODS: We performed an ecological study of all leprosy cases reported by Sergipe state, Northeast Brazil from 2001 to 2015, to examine the association of the Social Vulnerability Index and the prevalence and persistence of leprosy among the State's municipalities. Socio-economic and leprosy surveillance information was collected from the Brazilian information systems, and a Bayesian empirical local model was used to identify fluctuations of the indicators. Spatial and space-time clusters were identified using scan spatial statistic tests and to measure the municipalities' relative risk of leprosy. RESULTS: Leprosy clusters and burden of disease had a strong statistical association with the municipalities' Social Vulnerability Index. Municipalities with a high social vulnerability had higher leprosy incidence, multibacillary leprosy and newly diagnosed cases with grade 2 disability than areas with low social vulnerability. CONCLUSION: Social vulnerability is strongly associated with leprosy transmission and maintenance of disease incidence. Leprosy control programmes should be targeted to the populations with high social vulnerability.

Pain and quality of life in knee osteoarthritis, chronic low back pain and fibromyalgia: a comparative cross-sectional study.

The objective of our study was to compare pain and health-related quality of life among patients with knee osteoarthritis (OA), chronic nonspecific low back pain (CNLBP) and fibromyalgia (FM). This cross-sectional study included 87 subjects, who were divided into three groups according to their diagnosis: knee OA (n=29), CNLBP (n=29) and FM (n=29), between March 2013 and March 2014. Pain intensity was measured using the Numeric Pain Rating Scale (NPRS), quality of pain using the McGill Pain Questionnaire (MPQ) and health-related quality of life using the 36-item Short-Form Health Survey (SF-36). Painful body areas were marked on a pain map. No statistically significant differences between groups were found for NPRS. Regarding MPQ, the knee OA group presented a lower pain-rating index in contrast to the CNLBP and FM groups, and no significant differences were found between the CNLBP and FM groups. A greater number of characteristic pain descriptors and painful locations were found in the FM group than in the CNLBP or knee OA groups. Regarding SF-36, the FM group presented statistically significant lower values for bodily pain in contrast to the knee OA group. Even though the global pain intensity was similar between groups, the findings suggest that the FM group presented the worst pain experience and a lower health-related quality of life than the knee OA group in terms of bodily pain. They also suggest that the pain experience was worse for the CNLBP group than for the knee OA group but health-related quality of life was similar.

The land morphology approach to flood risk mapping: An application to Portugal.

In the last decades, the increasing vulnerability of floodplains is linked to societal changes such as population density growth, land use changes, water use patterns, among other factors. Land morphology directly influences surface water flow, transport of sediments, soil genesis, local climate and vegetation distribution. Therefore, the land morphology, the land used and management directly influences flood risks genesis. However, attention is not always given to the underlying geomorphological and ecological processes that influence the dynamic of rivers and their floodplains. Floodplains are considered a part of a larger system called Wet System (WS). The WS includes permanent and temporary streams, water bodies, wetlands and valley bottoms. Valley bottom is a broad concept which comprehends not only floodplains but also flat and concave areas, contiguous to streams, in which slope is less than 5%. This will be addressed through a consistent method based on a land morphology approach that classifies landforms according to their hydrological position in the watershed. This method is based on flat areas (slopes less than 5%), surface curvature and hydrological features. The comparison between WS and flood risk data from the Portuguese Environmental Agency for the main rivers of mainland Portugal showed that in downstream areas of watersheds, valley bottoms are coincident with floodplains modelled by hydrological methods. Mapping WS has a particular interest in analysing river ecosystems position and function in the landscape, from upstream to downstream areas in the watershed. This morphological approach is less demanding data and time-consuming than hydrological methods and can be used as the preliminary delimitation of floodplains and potential flood risk areas in situations where there is no hydrological data available. The results were also compared with the land use/cover map at a national level and detailed in Trancão river basin, located in Lisbon metropolitan area, an urbanized basin that suffered heavy flooding in the last decades. This study also contributes to a better understanding of the basin morphology at a local-scale and the effects of soil sealing in downstream flood risks. This work will contribute to the understanding of the morphology, ecology and land use of watersheds that could be used to reduce runoff and downstream flood risk. This can be accomplished by using natural water retention and infiltration methods or higher-level based planning instead of a reaction to local decisions on flood hazards. This morphological approach to map landforms, including wet system, is a valuable tool to assist policy makers and planners in flood risk and land use management, floodplain restoration, agricultural land management practices, and location of human activities according to ecological suitability.

Reproductive dynamics shapes genomotype composition in an allopolyploid complex.

Hybrid complexes are composed of organisms with multiple combinations of parental genomes (genomotypes) that interconnect through nets of crosses. Although several such complexes are well established without speciation or extinction, mechanisms shaping their dynamics remain poorly understood. In this study, we quantified the reproductive success of the allopolyploid Iberian fish Squalius alburnoides in experimental free-access and directional crosses involving the most common genomotypes. Specifically, we analysed the paternity of the offspring produced when females had free access to male genomotypes and quantified variations in egg allocation, fertilization rate, and offspring survival among crosses involving each male genomotype. The composition of the offspring produced from free-access crosses varied significantly from that expected from random mating, suggesting that offspring production and viability are not independent of parental male genomotype. Moreover, directional crosses producing the genomotype most commonly found in wild populations appeared to be the most successful, with females laying more eggs, and fertilization rate and offspring survival being the highest. These results suggest that reproductive dynamics plays a relevant role in structuring the genomotype composition of populations and opens a path to future research on the ecology and evolutionary biology of allopolyploids and their multiplicity of possible evolutionary pathways.

Neonatal detection of Turner syndrome by real-time PCR gene quantification of the ARSE and MAGEH1 genes.

Turner syndrome (TS) is characterized by the presence of one full X chromosome and total or partial deletion of the second sex chromosome. Diagnosis of TS is often delayed, resulting in inappropriate treatment. Early diagnosis of TS using a neonatal screening test may improve preventive measures and treatment, thus improving patient quality of life. The goal of this study was to standardize a neonatal TS screening algorithm. Two study genes (ARSE and MAGEH1) and 1 normalizing gene (HBB) were used to detect the second X chromosome. We screened 996 newborns whose peripheral blood was collected and stored in filter paper. In addition, samples from 20 patients with confirmed diagnosis of TS were included in the study. Relative amounts of ARSE/HBB were determined using real-time polymerase chain reaction. The cutoff at the 5th percentile was arbitrarily set to indicate repetition of the test. The test was repeated in 51/1016 patients with ARSE/HBB < 0.81. For 10 samples with values persistently <0.81, we quantified the MAGEH1/HBB ratio. Values below the 95th percentile in TS patients (MAGEH1/HBB < 1.24) were considered to be inadequate. Only 6/996 NB showed inadequate values for the 2 studied genes, which were recalled for clinical evaluation and karyotype testing. Analysis of 20 patients diagnosed with TS allowed for identification of false-negatives and true-positives, establishing 95% sensitivity when the indicated cutoff values were used. In conclusion, our algorithm reached 95% detection sensitivity with an acceptable recall rate (0.6%), allowing for the detection of suspected TS cases in the neonatal period.

In situ crosslinkable multi-functional and cell-responsive alginate 3D matrix via thiol-maleimide click chemistry.

In vivo, cells interact with the extracellular matrix (ECM), which provides a multitude of biophysical and biochemical signals that modulate cellular behavior. Inspired by this, we explored a new methodology to develop a more physiomimetic polysaccharide-based matrix for 3D cell culture. Maleimide-modified alginate (AlgM) derivatives were successfully synthesized using DMTMM to activate carboxylic groups. Thiol-terminated cell-adhesion peptides were tethered to the hydrogel network to promote integrin binding. Rapid and efficient in situ hydrogel formation was promoted by thiol-Michael addition "click" chemistry via maleimide reaction with thiol-flanked protease-sensitive peptides. Alginate derivatives were further ionically crosslinked by divalent ions present in the medium, which led to greater stability and allowed longer cell culture periods. By tailoring alginate's biofunctionality we improved cell-cell and cell-matrix interactions, providing an ECM-like 3D microenvironment. We were able to systematically and independently vary biochemical and biophysical parameters to elicit specific cell responses, creating custom-made 3D matrices. DMTMM-mediated maleimide incorporation is a promising approach to synthesizing AlgM derivatives that can be leveraged to produce ECM-like matrices for a broad range of applications, from in vitro tissue modeling to tissue regeneration.

Local environment and fragmentation by drought and damming shape different components of native and non-native fish beta diversity across pool refuges.

Pool refuges are critical for maintaining stream fish diversity in increasingly intermittent streams. Yet, the patterns and drivers of beta diversity of native and non-native fish in pool refuges remain poorly known. Focusing on Mediterranean streams, we decomposed beta diversity of native and non-native fish into richness difference (RichDiff) and species replacement (Repl), and local (LCBD, LCBDRichDiff and LCBDRepl) and species (SCBD) contributions. We assessed the influence of environmental and spatial factors associated with drought and damming fragmentations on beta diversity components and LCBDs, and of local species richness and occupancy on LCBDs and SCBD, respectively. Overall, non-native species showed a more limited occupancy of pool refuges than native fish. RichDiff dominated beta diversity, though it was influenced by drought and damming fragmentations for native fish and local environment for non-native fish. Repl for native fish was slightly influenced by local environment, but for non-native fish was largely driven by drought and damming, albeit with a contribution of local environment as well. LCBD and LCBDRichDiff increased in pools in low order streams for native fish and at low elevations for non-native fish, and with high or low species richness. SCBD was higher for native species with intermediated pool occupancy, but for non-native species with low occupancy. Our results suggest that stream fragmentation may drive native species loss and non-native species replacement in pool refuges, and that environmental filtering may shape non-native species loss. Pools in lower order streams harbouring unique species-rich or species-poor assemblages should be prioritize for conservation and restoration, respectively, and pools at low elevation with unique non-native assemblages should deserve control efforts. We encourage the partitioning of beta diversity and individual analysis of native and non-native fish in intermittent streams, which may be key in stressing the importance of pool refuges in safeguarding native fish diversity.

The genetic landscape of mitochondrial diseases in the next-generation sequencing era: a Portuguese cohort study.

Introduction: Rare disorders that are genetically and clinically heterogeneous, such as mitochondrial diseases (MDs), have a challenging diagnosis. Nuclear genes codify most proteins involved in mitochondrial biogenesis, despite all mitochondria having their own DNA. The development of next-generation sequencing (NGS) technologies has revolutionized the understanding of many genes involved in the pathogenesis of MDs. In this new genetic era, using the NGS approach, we aimed to identify the genetic etiology for a suspected MD in a cohort of 450 Portuguese patients. Methods: We examined 450 patients using a combined NGS strategy, starting with the analysis of a targeted mitochondrial panel of 213 nuclear genes, and then proceeding to analyze the whole mitochondrial DNA. Results and Discussion: In this study, we identified disease-related variants in 134 (30%) analyzed patients, 88 with nuclear DNA (nDNA) and 46 with mitochondrial DNA (mtDNA) variants, most of them being pediatric patients (66%), of which 77% were identified in nDNA and 23% in mtDNA. The molecular analysis of this cohort revealed 72 already described pathogenic and 20 novel, probably pathogenic, variants, as well as 62 variants of unknown significance. For this cohort of patients with suspected MDs, the use of a customized gene panel provided a molecular diagnosis in a timely and cost-effective manner. Patients who cannot be diagnosed after this initial approach will be further selected for whole-exome sequencing. Conclusion: As a national laboratory for the study and research of MDs, we demonstrated the power of NGS to achieve a molecular etiology, expanding the mutational spectrum and proposing accurate genetic counseling in this group of heterogeneous diseases without therapeutic options.

Identification of three new variants of SDHx genes in a cohort of Portuguese patients with extra-adrenal paragangliomas.

BACKGROUND: Extra-adrenal paragangliomas (PGL) are rare neoplasms occurring in sporadic and familial forms, the latter mostly in association with germline mutations of SD- HB, SDHC or SDHD genes. AIM: Characterize frequency and spectrum of germline mutations among a cohort of Portuguese patients with extra-adrenal PGL. DESIGN: Molecular and clinical data were reviewed on 44 patients referred for genetic testing by a single laboratory. RESULTS: Genetic analysis identified 11 patients with head and neck PGL (30.6%) positive for SD- Hx gene mutations (6 SDHD, 4 SDHB, 1 SDHC) and 4 patients with abdominal or pelvic PGL (50%) positive for SDHx gene mutations (4 SDHB). Large deletions made up about 20% of the mutations detected. Mutation carriers were younger and more frequently had multiple or malignant PGL than patients without mutations. Only 11% of the head and neck PGL were secretory. In contrast, 100% of the abdominal or pelvic PGL were secretory. Five patients had a malignant PGL (4 SDHB, 1 apparently sporadic). Three novel mutations were identified: two in the SDHD gene (c.411delT [p.Leu139PhefsX29] and c.371_390del20insGG [p.Ala124_Ala130delinsGly]), one in the SDHB gene (c.49A>G [p.Thr17Ala]). The SDHD variant c.411delT [p.Leu139PhefsX29] was present in 3 apparently unrelated patients. Molecular genetic testing of 22 relatives disclosed 16 mutation carriers. CONCLUSIONS: Genetic analysis identified 15 patients (34.1%) and 16 at-risk individuals (72.7%) positive for SDHx gene mutations. The finding of three novel mutations broadens the mutational profile of the mitochondrial complex II succinate dehydrogenase genes reported in other large European series of patients with paragangliomas. Further studies are needed to clarify whether the high frequency of the SDHD variant c.411delT [p.Leu139PhefsX29] corresponds to a founder mutation.