Miracle-dz/UniFAR-FTUs huggingface dataset:
Early estimation of the risk factors for hospitalization and mortality by COVID-19 in Mexico

Background. With its high prevalence of chronic non-degenerative diseases, it is suspected that in Mexico there is a high risk of fatal complications from COVID-19. The present study aims to estimate the risk factors for hospitalisation and death in the Mexican population infected by SARS-CoV-2. Methods and Findings. We used the publicly available data released by the Epidemiological Surveillance System for Viral Respiratory Diseases of the Mexican Ministry of Health (Secretaria de Salud, SS). All records of positive SARS-CoV-2 cases were included. Two multiple logistic regression models were fitted to estimate the association between the hospitalisation and mortality, with other covariables. Data on 10,544 individuals (57.68% men), with mean age 46.47 SD 15.62, were analysed. Men were about 1.54 times as likely to be hospitalized than women (p<0.001, 95% C.I. 1.37-1.74); individuals aged 50-74 and >=74 years were more likely to be hospitalized than people from 25-49 years (OR 2.05, p<0.001, 95% C.I. 1.81-2.32, and OR 23.84, p<0.001, 95% C.I. 2.90-5.15, respectively). People with hypertension, obesity, and diabetes were more likely to be hospitalised than people without these morbidities (p<0.01). Men had more risk of death in comparison to women (OR=1.53, p<0.001, 95% C.I. 1.30-1.81) and individuals aged 50-74 and [≥]75 years were more likely to die than people from 25-49 years (OR 1.96, p<0.001, 95% C.I. 1.63-2.34, and OR 3.74, p<0.001, 95% C.I. 2.80-4.98, respectively). Hypertension, obesity, and diabetes presented in combination, provided a higher risk of dying in comparison to not having these diseases (OR=2.10; p<0.001, 95% C.I. 1.50-2.93). Hospitalisation, intubation and pneumonia conferred a higher risk of dying (OR 5.02, p<0.001, 95% C.I. 3.88-6.50; OR 4.27, p<0.001, 95% C.I. 3.26-5.59, and OR=2.57; p<0.001, 95% C.I. 2.11-3.13, respectively). The main limitation of our study is the lack of information on mild (asymptomatic) or moderate cases of COVID-19. Conclusions. The present study points out that in Mexico, where an important proportion of the population develops two or more chronic conditions simultaneously, high mortality is a sever outcome for those infected by SARS-CoV-2.
Three new species of Cymbellales (Bacillariophyceae) from Réunion Island

Recent surveys of the epilithic diatoms of Reunion Island led to the discovery of three new species: Crucicostulifera bebourensis, Encyonopsis cilaosensis , Encyonopsis palmeti. Crucicostulifera bebourensis is the second species to be included in this recently described genus typified by Crucicostulifera areolata (Hustedt) Taylor & Lange-Bertalot. Both species share the main diagnostic features of the genus. However, Crucicostulifera bebourensis differs from Crucicostulifera areolata (Hustedt) Taylor & Lange-Bertalot in the cingulum composed of at least three open bands whereas the latter species has a single valvocopula on each valve. Encyonopsis cilaosensis and Encyonopsis palmeti can be differentiated from other Encyonopsis species by a combination of characters including valve outline, number of striae in l0 µm, maximum length/breadth ratio, areolae structure and presence or absence of intermissio. Both new species show a particular organization of the cingulum. Crucicostulifera bebourensis occurs in acidic waters with very low conductivity and nutrient concentration. Encyonopsis cilaosensis is found in alkaline waters with high conductivity whereas Encyonopsis palmeti is reported from slighty alkaline waters with low conductivity.
Dispersal Characteristics of Two Native and Two Nonnative Fleshy-Fruited Sympatric Shrubs

ABSTRACT Aspects of the dispersal characteristics of two nonnative shrubs, Elaeagnus umbellata and Ligustrum sinense, were compared with those of two native shrubs, Cornus amomum and Frangula caroliniana, to identify factors that contribute to successful invasion of the nonnative species. For each species, the following aspects were examined: shrub abundance, physical characteristics and nutritional values of fruits, arrangement of fruits along the stem and number of fruits per branch, phenology of fruit maturation and foliage coloration, and animal interactions. The two native shrubs and E. umbellata were similar in abundance, but L. sinense was significantly more abundant than the others. Cornus amomum and F. caroliniana present bicolored displays of fruits that are rapidly dispersed during autumn avian migration. Elaeagnus umbellata produces moisture- and protein-rich fruits during summer that are also rapidly removed. In contrast, L. sinense produces high numbers of fruits in late autumn that remain available to frugivores throughout the winter. The large quantities and prolonged availability of L. sinense fruits enable the dispersal of this shrub by a diverse array of frugivores and contribute at least partially to its successful invasion of new habitat and its observed abundance.
Effects of Compressive and Tensile Strain on Macrophages during Simulated Orthodontic Tooth Movement

During orthodontic tooth movement (OTM) to therapeutically correct the position of misaligned teeth, thus improving oral health and quality of life, fibroblasts, macrophages, and other immune cells within the periodontal ligament (PDL), which connects a tooth to its surrounding bone, are exposed to compressive and tensile strain. While it is known that PDL fibroblasts are critically involved in the biological regulation of OTM by a mechanotransductively triggered release of cytokines, it is unclear whether macrophages also react to pressure and tension in a similar manner thus impacting on or mediating OTM. RAW264.7 macrophages were seeded onto conventional 6-well cell culture plates for pressure or on Bioflex plates for tension assays and preincubated for 24 h. For in vitro simulation of physiological orthodontic compressive or tensile strain for 2 h, 4 h, 24 h, and 48 h, glass discs (2 g/cm2) were placed or adherent macrophages isotropically stretched for 16%, respectively. We determined cell number, cytotoxicity, and gene/protein expression of Vegf-a/VEGF-A (macrophage-mediated angiogenesis), Mmp-8/9 (extracellular matrix reorganization), and Cox-2/PG-E2, Il-6/IL-6, and Tnf-α/TNF-α (proinflammatory mediators) by RT-qPCR and ELISA. Compressive but not tensile strain resulted in a significant reduction in cell number after only 2 h. Mmp-8 and Mmp-9 expression was significantly enhanced within 24 h of compressive and in part tensile strain. Significantly increased Vegf-a/VEGF-A expression was detected within 4 h of pressure, but not during application of tensile strain. Expression of proinflammatory mediators Cox-2/PG-E2, Il-6/IL-6, and Tnf-α/TNF-α was significantly increased as early as 2-4 h after application of compressive or tensile strain. Our results indicate that macrophages respond early on to compressive and tensile strain occurring during OTM with an enhanced gene expression of proinflammatory cytokines, which could affect PDL fibroblasts, osteoblasts, and immune cells triggering or enhancing the biological mechanisms and osteoclastogenesis underlying OTM.
Genome-wide analysis of the superoxide dismutase (SOD) gene family in Zostera marina and expression profile analysis under temperature stress

Superoxide dismutases (SODs) serve as the first line of defense in the plant antioxidant enzyme system, and play a primary role in the removal of reactive oxygen species (ROS). However, our understanding of the functions of the SOD family in Zostera marina is limited. In this study, a systematic analysis was conducted on the characteristics of the SOD genes in Z. marina at the whole-genome level. Five SOD genes were identified, consisting of two Cu/ZnSODs, two FeSODs, and one MnSOD. Phylogenetic analysis showed that ZmSOD proteins could be divided into two major categories (Cu/ZnSODs and Fe-MnSODs). Sequence motifs, gene structure, and the 3D-modeled protein structures further supported the phylogenetic analysis, with each subgroup having similar motifs, exon-intron structures, and protein structures. Additionally, several cis-elements were identified that may respond to biotic and abiotic stresses. Transcriptome analysis revealed expression diversity of ZmSODs in various tissues. Moreover, qRT-PCR analysis showed that the expression level of most ZmSOD genes trended to decreased expression with the increase of temperature, indicating that heat stress inhibits expression of ZmSODs and may result in reduced ability of ZmSODs to scavenge ROS. Our results provide a basis for further functional research on the SOD gene family in Z. marina, which will help to determine the molecular mechanism of ZmSOD genes in response to environmental stress.
Dacus oleae (Gmel.) ovipositing in olive drupes (Diptera, Tephrytidae) 1

This study speaks about the relationship between olive fly (D. oleae) ovipositing and certain physical parameters of drupes. During the first period of observation weight was the most important parameter statistically. Subsequently, this relationship became less important because of the remarcable increase in the density of population and because of the presence in the olives of particular substances which induce the female to select the smaller drupes for ovipositing.
Diversity of Soil Filamentous Fungi Influenced by Marine Environment in São Luís, Maranhão, Brazil

Introduction In recent decades, there has been an intensification of environmental problems, which are becoming increasingly critical and frequent due to population growth. Microorganisms, including soilborne fungi, play an essential role in maintaining and balancing the environment. One of the most impacted ecosystems in São Luís, Maranhão, Brazil, is the Jansen Lagoon State Park, an important tourist spot, which has suffered anthropogenic actions such as the dumping of household waste (sewage) in its body of water. As a consequence, these pollutants can accumulate in the adjacent soil, since the body of water is near this substrate. The objectives were to isolate and identify filamentous fungi from the soil of the Jansen Lagoon State Park. Methods Monthly soil samples were collected and later processed using the modified suspension technique according to Clark (1965). Results The isolated genera were Aspergillus, Penicillium, Trichoderma, Absidia, and Fusarium. Aspergillus is the fungal genus of greater dominance in the soil of the Jansen Lagoon State Park. Aspergillus niger was the dominant species (37%), followed by A. tamarii (21.6%). Conclusion The main isolated fungi from the Jansen Lagoon State Park were Aspergillus niger and Aspergillus tamrii. These fungi can be used as biological markers of pollution and as biodegraders and/or bioremediators to improve the area studied.
Prediction of CD4 T-Lymphocyte Count Using WHO Clinical Staging among ART-Naïve HIV-Infected Adolescents and Adults in Northern Ethiopia: A Retrospective Study

Background WHO clinical staging has long been used to assess the immunological status of HIV-infected patients at initiation of antiretroviral therapy and during treatment follow-up. In setups where CD4 count determination is not readily available, WHO clinical staging is a viable option. However, correlation between CD4 count and WHO clinical staging is not known in an Ethiopian setting, and hence, the main aim of this study was to assess predictability of CD4 T-lymphocyte count using WHO clinical staging among ART-naïve HIV-infected adolescents and adults in northern Ethiopia. Methods A retrospective cross-sectional study was done in the Tigray Region, Ethiopia, from April 2015 to January 2019 from a secondary database of 19525 HIV-infected patients on antiretroviral treatment. Analysis was done using STATA-14.0 to estimate the frequencies, mean, and median of CD4 T-cell count in each WHO stages. Sensitivity, specificity, positive predictive value, negative predictive value, kappa test, and correlations were calculated to show the relationships between WHO stages and CD T-cell count. Results The sensitivity of WHO clinical staging to predict CD4 T-cell counts of <200 cells/μl was 94.17% with a specificity of 3.62%. The PPV was 49.03%, and the NPV was 3.62%. The sensitivity of WHO clinical staging to predict CD4 T-cell counts of <350 cells/μl was 94.75% with a specificity of 3.00%. The PPV was 75.81%, and the NPV was 15.09%. Similarly, the sensitivity of WHO clinical staging to predict CD4 T-cell counts of <500 cells/μl was 95.03% with a specificity of 2.73% and the PPV and NPV were 88.32% and 6.62%, respectively. The kappa agreement of WHO clinical stages was also insignificant when compared with the disaggregated CD4 counts in different categories. The correlation of WHO clinical staging was inversely associated with the CD4 count, and the magnitude of the correlation was 5.22%. Conclusions The WHO clinical staging had high sensitivity but low specificity in predicting patients with CD4 count <200 cells/μl, <350 cells/μl, and <500 cells/μl. There was poor correlation and agreement between CD4 T-lymphocyte count and WHO clinical staging. Therefore, WHO clinical staging alone may not provide accurate information on the immunological status of patients, and hence, it is better to use the CDC definition rather than the WHO clinical definition.
On the importance of spatial scales on beta diversity of coral assemblages: a study from Venezuelan coral reefs

Estimating variability across spatial scales has been a major issue in ecology because the description of patterns in space is extremely valuable to propose specific hypotheses to unveil key processes behind these patterns. This paper aims to estimate the variability of the coral assemblage structure at different spatial scales in order to determine which scales explain the largest variability on β-diversity. For this, a fully-nested design including a series of hierarchical-random factors encompassing three spatial scales: (1) regions, (2) localities and (3) reefs sites across the Venezuelan territory. The variability among spatial scales was tested with a permutation-based analysis of variance (Permanova) based on Bray-Curtis index. Dispersion in species presence/absence across scales (i.e., β-diversity) was tested with a PermDisp analysis based on Jaccard’s index. We found the highest variability in the coral assemblage structure between sites within localities (Pseudo-F = 5.34; p-value = 0.001, CV = 35.10%). We also found that longitude (Canonical corr = 0.867, p = 0.001) is a better predictor of the coral assemblage structure in Venezuela, than latitude (Canonical corr = 0.552, p = 0.021). Largest changes in β-diversity of corals occurred within sites (F = 2.764, df1= 35, df2 = 107, p = 0.045) and within localities (F = 4.438, df1= 6, df2 = 29, p = 0.026). Our results suggest that processes operating at spatial scales of hundreds of meters and hundreds of kilometers might both be critical to shape coral assemblage structure in Venezuela, whereas smaller scales (i.e., hundreds of meters) showed to be highly- important for the species turnover component of β-diversity. This result highlights the importance of creating scale-adapted management actions in Venezuela and likely across the Caribbean region.
The old and the large may suffer disproportionately during episodes of high temperature: evidence from a keystone zooplankton species

Abstract Widespread declines in the body size of aquatic ectotherms have been attributed to the poorer ability of older, larger individuals to tolerate high temperature. Here, using the thermal death time curve framework, we investigate the relationship between temperature tolerance and size/age by measuring the change in heat tolerance of the keystone zooplankton species Daphnia magna across a range of temperature intensities (and hence exposures of varying duration) among individuals that differed up to 3-fold in size and thus varied in age also. Across the gradient of exposure temperatures, younger, smaller individuals were more tolerant than older, larger individuals. This suggests that the young and the small may be better equipped to withstand temperature challenges that are both intense/brief and more moderate/prolonged. Our study generalizes results obtained from more acute tolerance assays, providing physiological evidence consistent with the observed reductions in ectotherm body size as a response to warming in aquatic systems.
Association of Brain-Gut Peptides with Inflammatory Cytokines in Moyamoya Disease

Systemic inflammation has been shown to play a pivotal role in the pathogenesis of moyamoya disease (MMD). Brain-gut peptides exhibit regulatory effects in the secretion of proinflammatory cytokines. To investigate the association between brain-gut peptides and inflammation in the occurrence of MMD, 41 patients with MMD, as well as 74 age- and sex-matched healthy individuals were enrolled. The levels of four brain-gut peptides (vasoactive intestinal polypeptide (VIP), cholecystokinin (CCK), somatostatin (SST), substance P (SP)) and three proinflammatory cytokines (interleukin-1β (IL-1β), tumor necrosis factor-α (TNF-α), IL-12) in the serum and cerebrospinal fluid (CSF) were measured using the enzyme-linked immunosorbent assay. The associations between brain-gut peptides and proinflammatory cytokines were estimated according to the multiple linear regression and correlation analyses. MMD patients exhibited significantly lower levels of VIP, CCK, and SST and higher levels of IL-1β, TNF-α, and IL-12 in the serum compared with healthy controls. Multiple logistic regression analysis showed that decreased VIP, CCK, and SST levels were independent predictors of the occurrence of MMD. Negative correlations were observed between the VIP and proinflammatory cytokines, including IL-1β, TNF-α, and IL-12 (serum vs. CSF). Significant negative correlations were also found between CCK and IL-1β, as well as IL-12 (serum vs. CSF). SST was negatively correlated with IL-1β and TNF-α in the serum and IL-1β only in the CSF. In addition, the levels of VIP, CCK, SST, and proinflammatory cytokines IL-1β and TNF-α in the serum were correlated with those measured in the CSF. Collectively, lower levels of VIP, CCK, and SST may be associated with the pathogenesis of MMD and act as clinically useful biomarkers along with the levels of proinflammatory cytokines.
Clinicoradiological features of resected serous cystic neoplasms according to morphological subtype and preoperative tentative diagnosis: can radiological characteristics distinguish serous cystic neoplasms from other lesions?

Purpose Serous cystic neoplasm (SCN) of the pancreas is considered benign in most cases. However, some SCN patients undergo surgical resection because lesions could not be differentiated preoperatively. This study evaluated causes of resection for SCN, investigated clinical and radiological features of surgically resected SCNs, and compared characteristics of SCNs diagnosed accurately and those misdiagnosed. Methods One hundred patients, who underwent surgery for pancreatic cystic tumors with pathological confirmation of SCN between 2000 and 2014 were retrospectively analyzed. Results The mean patient age was 52.9 years, 67 (67%) were female, and most lesions (72%) were located in the pancreatic body or tail. Fifty-one (51%) pathologically confirmed SCNs were preoperatively diagnosed as non-SCNs. Patients underwent surgery due to uncertain diagnosis (58%) or symptomatology (18%). According to radiological examination, most lesions were macrocystic (85%), exhibited septation (58%), or were enhancing lesions (48%). Compared with preoperatively diagnosed non-SCNs, accurately diagnosed SCNs exhibited septation (75.5% vs. 41.2%, P = 0.001) and central scar (36.7% vs. 11.8%, P = 0.003) more frequently in radiological examinations. In terms of macrocystic tumors (n = 85), most parameters did not differentiate preoperative diagnoses, although lesions accurately diagnosed as SCN exhibited septation more frequently than those preoperatively misdiagnosed as mucinous cystic neoplasm or intraductal papillary mucinous neoplasm (70.7% vs. 38.9% vs. 33.3%, respectively, P = 0.009). Conclusion It is difficult to accurately distinguish macrocystic SCNs from other cystic tumors using conventional radiological methods. For more accurate diagnosis, new biomarkers and/or other diagnostic modalities are needed and warrant further investigation.
First assessment of hoary fox (Lycalopex vetulus) seasonal ovarian cyclicity by non-invasive hormonal monitoring technique

Abstract Reproduction is key to species survival, and reproductive physiology represents a high priority investigative area for conservation biology, as it provides a basic understanding of critical life-history traits, information that is helpful for the establishment of management strategies. Here, we generated knowledge about the reproductive endocrinology of the hoary fox (Lycalopex vetulus), a small canid (2.5–4 kg) endemic to open areas of the Brazilian Cerrado and listed in the Brazilian National List of Endangered species. Specifically, we utilized non-invasive hormone monitoring methods to assess oestrogen and progestagen metabolites from eight female hoary foxes housed in five zoological institutions in the state of São Paulo—Brazil. We observed the elevations of oestrogen and progestagen metabolites between July and September in six of the eight females. No significant evidence of ovarian activity was observed during other months. Two females, who shared the same enclosure, did not show a pattern of reproductive cyclicity. Based on these characteristics, we concluded that captive hoary foxes are seasonal monoestric, with the beginning of the oestrus cycle occurring mainly in July followed by 2 months of the luteal phase when conception does not occur. We suggest the dosage of faecal metabolites of estradiol and progesterone could be used to differentiate the reproductive period from a non-reproductive period in Lycalopex vetulus females, providing relevant information about their reproductive biology that may contribute to species conservation and management strategies, such as increased ex situ reproductive success.