Miracle-dz/UniFAR-FTUs huggingface dataset:
Improved Automatic Pharmacovigilance: An Enhancement to the MedWatcher Social System for Monitoring Adverse Events

Traditional pharmacovigilance systems rely on adverse event reports received by regulatory authorities such as the United States Food and Drug Administration (FDA). These traditional systems suffer from underreporting and are not timely due to their reliance on third-party sentinels. To address these issues, the MedWatcher Social system for monitoring adverse events through automated processing of digital social media data and crowdsourcing was launched in 2012 by Boston Children’s Hospital and the FDA. The system is rooted in the well-established FDA MedWatch system. MedWatcher Social uses an indicator score approach to identify adverse events. This study evaluates the MedWatcher Social adverse event classifier’s performance on Twitter data and proposes an enhancement to the indicator score method that results in improved adverse event identification. Our research suggests that automatic pharmacovigilance systems using the original indicator score approach should be updated. Careful consideration of modeling assumptions is critical when designing algorithms for computational epidemiology, and algorithms should be regularly reevaluated to identify enhancements and to remedy concept drift.
Habitat amount drives the functional diversity and nestedness of anuran communities in an Atlantic Forest fragmented landscape

Natural environments disturbed by human activities can suffer from species extinctions, but some can still harbor high taxonomic diversity. However, disturbances may have impacts beyond the species level, if the species lost represent unique functions in the ecosystem. In this study, we evaluated to what extent the amount of habitat can determine the functional diversity and nestedness of amphibian communities in an Atlantic Forest fragmented landscape in Brazil, and if there is a threshold of habitat amount beyond which there is severe loss of functional diversity. As species responses may depend on their habitat type, we performed the analyses for three different sets of species: all species, forest‐dependent species, and generalist species. We also evaluated the relative importance of turnover and nestedness components to total functional dissimilarity among sites. Habitat amount affected functional diversity of frogs, especially for forest‐dependent species where a linear reduction was detected. The functional dissimilarity among sites was mostly explained by the nestedness component. The reduction of functional diversity was mediated by an ordered loss of traits, leading to a functionally nested metacommunity. These sensitive traits were closely related to habits and reproductive modes that depend on rivers and streams. The maintenance of functional diversity of frogs in fragmented landscapes must rely on the conservation of both terrestrial and aquatic environments, as some species and their traits can disappear from remnants of native vegetation lacking some specific habitats (e.g. streams).
Administration of a Synbiotic Containing Enterococcus faecium Does Not Significantly Alter Fecal Microbiota Richness or Diversity in Dogs With and Without Food-Responsive Chronic Enteropathy

Background: Canine chronic enteropathies (CE) are a group of intestinal diseases that can be categorized based on treatment response into diet- or food- responsive enteropathy (FRD), antibiotic-responsive enteropathy, steroid-responsive enteropathy, and non-responsive enteropathy. CE can often be associated with intestinal dysbiosis and thus administration of probiotic or synbiotic products may provide a useful tool for the management of some of these patients. Enterococcus faecium (EF) is a probiotic strain included in a commercially available synbiotic for small animals, however its impact on the microbial communities in dogs with FRD has not yet been evaluated. Hypothesis/Objectives: The administration of a synbiotic will lead to a significant difference of the fecal microbial composition and/or diversity in dogs with FRD, and these changes are not attributable to diet change alone. Animals/Samples: Twelve dogs with FRD fed a hydrolyzed protein diet received either a synbiotic (EF, fructooligosaccharides, gum Arabic) or placebo. Fecal samples were taken before and 6 weeks into treatment. Fecal samples were also acquired from 8 healthy dogs before and 6 weeks after being switched to the same hydrolyzed protein diet as their sole food. Methods: Bacterial DNA was extracted from fecal samples and next generation sequencing based on the 16S rRNA genes was performed. Microbial composition and diversity between groups were compared using QIIME. Results: There was a small increase in species diversity in the feces of dogs with FRD treated with synbiotics. However, there were no significant differences in microbial community composition before and after 6 weeks in either the synbiotic or placebo treated dogs with FRD or the healthy dogs. In all groups, large individual variations were observed. Conclusions: No changes in microbial composition were observed in diseased or healthy dogs with diet change alone. However, administration of a synbiotic increased bacterial richness in both groups.
CoDysAn: A Telemedicine Tool to Improve Awareness and Diagnosis for Patients With Congenital Dyserythropoietic Anemia

Congenital Dyserythropoietic Anemia (CDA) is a heterogeneous group of hematological disorders characterized by chronic hyporegenerative anemia and distinct morphological abnormalities of erythroid precursors in the bone marrow. In many cases, a final diagnosis is not achieved due to different levels of awareness for the diagnosis of CDAs and lack of use of advanced diagnostic procedures. Researchers have identified five major types of CDA: types I, II, III, IV, and X-linked dyserythropoietic anemia and thrombocytopenia (XLDAT). Proper management in CDA is still unsatisfactory, as the different subtypes of CDA have different genetic causes and different but overlapping patterns of signs and symptoms. For this reason, we developed a new telemedicine tool that will help doctors to achieve a faster diagnostic for this disease. Using open access code, we have created a responsive webpage named CoDysAn (Congenital Dyserythropoietic Anemia) that includes practical information for CDA awareness and a step-by-step diagnostic tool based on a CDA algorithm. The site is currently available in four languages (Catalan, Spanish, Italian, and English). This telemedicine webpage is available at http://www.codysan. eu.
At a Microsite Scale, Native Vegetation Determines Spatial Patterns and Survival of Pinus contorta Invasion in Patagonia

Research Highlights: The invasive species Pinus contorta, has become a new component of the vegetation in the Patagonian Steppe, invading the complex matrix of bare ground, tussock grasses and cushion plants. At a microsite scale, the type of native vegetation is one of the multiple factors determining the establishment of P. contorta and in some cases, increasing its survival, and as a result, the invasion of the species. Background and Objectives: The presence of trees, particularly pines, where they are naturally absent, represents a clear threat to Patagonian steppe ecosystems. Thus, understanding the interaction between pines and native plant species may be the key to understanding the invasion and applying management actions. Pinus contorta is considered one of the most aggressive among the pines species, with recognized impacts on regions in the southern hemisphere and Europe, and it is one of the main invaders in the Patagonian steppe. Our aim in this study is to determine the influence of surrounding vegetation on P. contorta spatial distribution, its establishment and future development in the Chilean Patagonia. Materials and Methods: We used point pattern analysis to determine the existence of spatial associations between P. contorta and the resident vegetation of the Patagonian steppe. Further, a seeding experiment was carried out to assess the influence of the surrounding vegetation during P. contorta establishment and first growing season. Results: We found that young P. contorta individuals are positively associated with the native cushion plant B. magellanica and also to tussock grasses. Seeding experiments showed that P. contorta is influenced by resident plant species during establishment and is able to establish on any ground cover type in the Patagonian steppe, but some resident plant species increase P. contorta survival chances. Conclusions: Pinus contorta is interacting with native vegetation and becoming an active component of the Patagonian steppe mosaic. Although pines can establish in any type of vegetation in the Patagonian steppe mosaics, native cushion and tussock grasses may be facilitating the process and promoting pine survival, allowing it to survive and thrive in this stressful environment.
Molecular diversity in a germplasm collection of avocado accessions from the tropical and subtropical regions of China

Avocado is an economically important crop and widely cultivated in the tropical and subtropical regions of China, whereas little is known about its genetic diversification. Twenty-six EST-SSR markers were developed based on avocado EST sequences. Molecular characterization was applied to assess the genetic relationships among different accessions. In total, nine gSSRs and nine EST-SSRs were selected to illuminate the genetic relationships within the 92 samples. Diversity parameters associated to the selected markers indicated the relatively low genetic diversity and a certain degree of inbreeding in the 92 avocado accessions. Clustering method and principal coordinate analysis clearly distinguished the accessions in accordance to the botanical races and geographic regions by molecular characterization. Moreover, the botanical race or hybrids of some unknown race accessions from different geographic origins could be determined based on known genotypes in the same cluster.
Prevalence of mobile antimicrobial resistance genes carrying and toxin producing pathogens in retail beef and mutton

Background Food safety has always been the global issue. In addition to food poisoning problems caused by toxin-producing strains, the arising of widely spread antimicrobial resistant bacteria have become a major issue that impacts food safety. The purpose of this study is to assess the safety of retail meat in the last link of sales. Results A total number of 134 samples were collected and 674 strains were isolated. There are different bacterial compositions distributed in meat, environmental and human-derived samples. The major pathogens in meat and environmental or human samples are Klebsiella spp. and Staphylococcus spp. The resistance to amoxicillin + clavulanate (with the resistance rate of 46.78%), tetracycline (44.66%) and erythromycin (32.73%) are major resistant phenotypes of the isolates. According to the whole genome analysis, two K. pneumoniae strains harboring the extended spectrum beta-lactamase genes which are located on mobile elements and two Aeromonas hydrophila isolates carrying mcr-7.1 like genes have been detected. The major toxin genes of Bacillus cereus, and adhesion or invasion related virulence factors were also shared among the isolates. Conclusion There are different pathogens distributed in meat, environment and human source at the final stage of meat consumption. The mobile ARGs are prevalent in strains isolates from meat samples. And toxin-producing strains can be isolated from human source. These factors consist potential risk for public health and need attention.
projectR: An R/Bioconductor package for transfer learning via PCA, NMF, correlation, and clustering

Motivation Dimension reduction techniques are widely used to interpret high-dimensional biological data. Features learned from these methods are used to discover both technical artifacts and novel biological phenomena. Such feature discovery is critically import to large single-cell datasets, where lack of a ground truth limits validation and interpretation. Transfer learning (TL) can be used to relate the features learned from one source dataset to a new target dataset to perform biologically-driven validation by evaluating their use in or association with additional sample annotations in that independent target dataset. Results We developed an R/Bioconductor package, projectR, to perform TL for analyses of genomics data via TL of clustering, correlation, and factorization methods. We then demonstrate the utility TL for integrated data analysis with an example for spatial single-cell analysis. Availability projectR is available on Bioconductor and at https://github.com/genesofeve/projectR. Contact gsteinobrien@jhmi.edu; ejfertig@jhmi.edu
Nest site selection and nest survival of Black-backed Woodpeckers after wildfire

ABSTRACT Recently burned coniferous forests host wildlife communities that respond to variation in burn severity, post-fire habitat structure, and patch configuration. Habitat selection theory predicts that birds inhabiting these variable post-fire landscapes will select nesting locations that confer an adaptive advantage through increased fitness and reproductive success. Understanding the effect of post-fire habitat on avian nesting ecology can provide valuable information to guide restoration and management after wildfire. The Black-backed Woodpecker (Picoides arcticus) is strongly associated with recently burned forests in the western United States, where it is used as an indicator species for the effects of post-fire forest management. Between 2011 and 2018, we located and monitored 118 Black-backed Woodpecker nests in burned forests of northern California. We evaluated the influence of habitat and nest characteristics on nest site selection and daily nest survival. Our results demonstrate a pattern of neutral congruence between habitat selection and fitness. Blackbacked Woodpeckers showed strong selection for each of the nest habitat variables that we measured: woodpeckers selected moderately sized trees in areas of high snag density burned at high severity, but also in areas relatively close to low-severity or unburned edges. However, only nest initiation date affected nest survival, with decreased survival in late-season nests. Our results suggest that management actions aimed at maintaining breeding habitat for Black-backed Woodpeckers should prioritize retention and creation of pyrodiverse landscapes that include dense stands of snags (>5 snags per 100 m2) within ~500 m of forest that burned at low severity or remained unburned.
Potency of some Photosensitizing Compounds against the Cotton Leaf Worm, Spodoptera littoralis (Boisduval) in Relation to some Biochemical Aspects

The present study aimed to evaluate the toxicological as well as biochemical effects of the three photosensitizer compounds; rose bengal, eosin yellow lactone and methylene blue on the fourth larval instar of the cotton leaf worm, Spodoptera littoralis (Boisd.). Results of insecticidal activity against the fourth larval instar of S. littoralis revealed that rose bengal is the most toxic photosensitizer compound followed by eosin yellow lactone, then methylene blue. The corresponding LC50 values were 37X10 M, 81X10M and 136X10M; respectively. Concerning, the photodynamic process of the thee photosensitizer compounds to control the 4 instar larvae of S. littoralis , the LT50 values of the lowest concentrations of rose bengal, eosin yellow lactone and methylene blue were >4hrs for each. On the other hand, the LT50 values of the highest concentrations were 2.2, 3.25 and 2.50 hrs; respectively. This indicates that rose bengal was the most active compound. On the light of the median lethal effects of the three tested photosensitizer compounds on the total protein ,total lipids and total carbohydrates content in the tested fourth larval instar of the cotton leaf worm, the results proved that the three photosensitizer compounds decreased these biochemical contents except methylene blue slighty increased total protein content relative to control.
Gotta Trace ‘em All: A Mini-Review on Tools and Procedures for Segmenting Single Neurons Toward Deciphering the Structural Connectome

Decoding the morphology and physical connections of all the neurons populating a brain is necessary for predicting and studying the relationships between its form and function, as well as for documenting structural abnormalities in neuropathies. Digitizing a complete and high-fidelity map of the mammalian brain at the micro-scale will allow neuroscientists to understand disease, consciousness, and ultimately what it is that makes us humans. The critical obstacle for reaching this goal is the lack of robust and accurate tools able to deal with 3D datasets representing dense-packed cells in their native arrangement within the brain. This obliges neuroscientist to manually identify the neurons populating an acquired digital image stack, a notably time-consuming procedure prone to human bias. Here we review the automatic and semi-automatic algorithms and software for neuron segmentation available in the literature, as well as the metrics purposely designed for their validation, highlighting their strengths and limitations. In this direction, we also briefly introduce the recent advances in tissue clarification that enable significant improvements in both optical access of neural tissue and image stack quality, and which could enable more efficient segmentation approaches. Finally, we discuss new methods and tools for processing tissues and acquiring images at sub-cellular scales, which will require new robust algorithms for identifying neurons and their sub-structures (e.g., spines, thin neurites). This will lead to a more detailed structural map of the brain, taking twenty-first century cellular neuroscience to the next level, i.e., the Structural Connectome.
Climate Warming, Resource Availability, and the Metabolic Meltdown of Ectotherms

Climate warming may lower environmental resource levels, growth, and fitness of many ectotherms. In a classic experiment, Brett and colleagues documented that growth rates of salmon depended strikingly on both temperature and food levels. Here we develop a simple bioenergetic model that explores how fixed temperatures and food jointly alter the thermal sensitivity of net energy gain. The model incorporates differing thermal sensitivities of energy intake and metabolism. In qualitative agreement with Brett’s results, it predicts that decreased food intake reduces growth rates, lowers optimal temperatures for growth, and lowers the highest temperatures sustaining growth (upper thermal limit). Consequently, ectotherms facing reduced food intake in warm environments should restrict activity to times when low body temperatures are biophysically feasible, but—in a warming world—that will force ectotherms to shorten activity times and thus further reduce food intake. This “metabolic meltdown” is a consequence of declining energy intake coupled with accelerating metabolic costs at high temperatures and with warming-imposed restrictions on activity. Next, we extend the model to explore how increasing mean environmental temperatures alter the thermal sensitivity of growth: when food intake is reduced, optimal temperatures and upper thermal limits for growth are lowered. We discuss our model’s key assumptions and caveats as well as its relationship to a recent model for phytoplankton. Both models illustrate that the deleterious impacts of climate warming on ectotherms will be amplified if food intake is also reduced, either because warming reduces standing food resources or because it restricts foraging time.
Complementary functions of the mechanosensitive factors egr1, klf2b and klf2a instruct the endocardial program

Mechanical forces are key modulators of valvulogenic developmental programs. However, the mechanosensitive gene network underlying this process remains unclear. It is well established that contractile and flow forces activate endocardial expression of the transcription factor klf2a during valve morphogenesis. We report two novel transcription factors with a function in heart valve formation in zebrafish: egr1 and klf2b. Genome-wide analysis of gene expression reveals that the endocardial transcriptional programs modulated by klf2a, klf2b, and egr1 mainly contain non-redundant targets. Several of these targets have been implicated in endothelial-to-mesenchymal transition (EMT). Many of the deregulated genes exhibit changes in chromatin accessibility pointing to potential direct effects of these factors. Finally, in vivo phenotypic analyses show that VEGF receptor 1 (flt1) is a target of egr1 and klf2b during early valvulogenesis. These findings suggest that klf2a, klf2b, and egr1 cooperate for the activation of EMT program in response to mechanosensitive inputs. We propose that the combinatorial action of these factors mediates flow mechanotransduction to control the endocardial program, especially for valve development.
The Effect of Drying Methods on Color and Chlorophyll Content of Parsley Leaves

Parsley leaves (Petroselinum crispum L.) weighing 100 ± 0.09 g were dehydrated from moisture content of 82.24 ± 0.07% to 10.01 ± 0.02 % (wet basis) using the microwave (MD), convective (CD), solar oven (SOD), sun (SD) and natural (ND) drying. Drying in MD, CD, SOD, SD, and ND was completed at 18±1.15, 61±0.58, 255±10, 330±5.29, and 1530±11.55 min, respectively. The energy consumption of MD and CD was measured as 0.213±0.009 and 0.427±0.015 kWh, respectively. In microwave drying, 700 W microwave output power was applied while convective drying was used with 50Â°C temperature and 1m/s air velocity. The sun and solar oven drying processes were carried out under the same conditions at the same time. The average temperature of the system during the solar oven drying was 81.7±1. 5Â°C whereas the airflow in the system was 0.5 m/s. The data obtained from the experiments were also modeled using twelve different thin-layer drying equations, and thus the theoretical data were obtained. According to these theoretical data, the best model in the microwave and natural drying was Alibas‘s equation while the most suitable model in the solar and convective drying was modified Henderson and Pabis‘s model. On the other hand, it was seen that the best model in the solar oven drying was the Page equation. As a result, considering both quality and drying parameters, it was determined that MD and SOD were the most suitable method for drying of parsley leaves.