Miracle-dz/UniFAR-FTUs huggingface dataset:
Phenotypic Plasticity: From Theory and Genetics to Current and Future Challenges

Phenotypic plasticity is defined as the property of organisms to produce distinct phenotypes in response to environmental variation. While for more than a century, biologists have proposed this organismal feature. Phenotypic plasticity is defined as the property of organisms to produce distinct phenotypes in response to environmental variation. While for more than a century, biologists have proposed this organismal feature to play an important role in evolution and the origin of novelty, the idea has remained contentious. Plasticity is found in all domains of life, but only recently has there been an increase in empirical studies. This contribution is intended as a fresh view and will discuss current and future challenges of plasticity research, and the need to identify associated molecular mechanisms. After a brief summary of conceptual, theoretical, and historical aspects, some of which were responsible for confusion and contention, I will formulate three major research directions and predictions for the role of plasticity as a facilitator of novelty. These predictions result in a four-step model that, when properly filled with molecular mechanisms, will reveal plasticity as a major factor of evolution. Such mechanistic insight must be complemented with comparative investigations to show that plasticity has indeed created novelty and innovation. Together, such studies will help develop a true developmental evolutionary biology.
Paleohistological estimation of bone growth rate in extinct archosaurs

Abstract The clade Archosauria contains two very different sister groups in terms of diversity (number of species) and disparity (phenotypic variation): Crurotarsi (taxa more closely related to crocodiles than to birds) and Ornithodira (pterosaurs and dinosaurs including birds). The extant species of Crurotarsi may constitute a biased sample of past biodiversity regarding growth patterns and metabolic rates. Bone histological characters can be conserved over hundreds of millions of years in the fossil record and potentially contain information about individual age at death, age at sexual maturity, bone growth rates, and basal metabolic rates of extinct vertebrates. Using a sample of extant amniotes, we have constructed a paleobiological model to estimate bone growth rate from bone histological traits. Cross-validation tests show that this model is reliable. We then used it to estimate bone growth rates in a sample of extinct archosaurs including Crurotarsi and Ornithodira. After testing for phylogenetic signal, optimization of femoral growth rates through squared change parsimony onto a time-calibrated tree of amniotes shows two divergent evolutionary trends: whereas bone growth rates increase from the last common ancestor of Ornithodira to extant birds, they decrease from the last common ancestor of Crurotarsi to extant crocodiles. However, we conclude, on the basis of recent evidence for unidirectional airflow in the lungs of alligators, that crocodiles may have retained the capacity of growing at high rates.
A new species of Giovanella Bonatto (Diptera, Calliphoridae, Mesembrinellinae) from Colombia

A new species of Giovanella Bonatto (Diptera, Calliphoridae, Mesembrinellinae) from Colombia. The Mesembrinellinae are exclusively Neotropical, with 33 nominal species distributed in nine genera. Only the genera Mesembrinella, Eumesembrinella, Huascaromusca and Laneella had until now been recorded in Colombia. In this work we present a new species of Giovanella Bonatto, 2005, genus with only one species, G. bolivar Bonatto, differing from the new species G. carvalhoi sp. nov., in the characters: legs entirely dark chestnut; thorax with dorsocentrals setae 1:2; abdomen with T5 with discal bristles poorly differentiated; T6 symmetric and paraphallus not extended and with denticules. Giovanella carvalhoi sp. nov. is from Cordillera Oriental, from the Departments of Caqueta (Amazonian foothills) and Santander, Colombia, collected between 22002400 m. , and associated with decomposing organic matter. A key for the identification of males and females of the two species of Giovanella, illustrations of the genitalia and photographs of male and female of new species are also presented.
Actionable Software Metrics: An Industrial Perspective

Background: Practitioners would like to take action based on software metrics, as long as they find them reliable. Existing literature explores how metrics can be made reliable, but remains unclear if there are other conditions necessary for a metric to be actionable. Context & Method: In the context of a European H2020 Project, we conducted a multiple case study to study metrics' use in four companies, and identified instances where these metrics influenced actions. We used an online questionnaire to enquire about the project participants' views on actionable metrics. Next, we invited one participant from each company to elaborate on the identified metrics' use for taking actions and the questionnaire responses (N=17). Result: We learned that a metric that is practical, contextual, and exhibits high data quality characteristics is actionable. Even a non-actionable metric can be useful, but an actionable metric mostly requires interpretation. However, the more these metrics are simple and reflect the software development context accurately, the less interpretation required to infer actionable information from the metric. Company size and project characteristics can also influence the type of metric that can be actionable. Conclusion: This exploration of industry's views on actionable metrics help characterize actionable metrics in practical terms. This awareness of what characteristics constitute an actionable metric can facilitate their definition and development right from the start of a software metrics program.
Wrist-Worn Wearables for Monitoring Heart Rate and Energy Expenditure While Sitting or Performing Light-to-Vigorous Physical Activity: Validation Study

Background Physical activity reduces the incidences of noncommunicable diseases, obesity, and mortality, but an inactive lifestyle is becoming increasingly common. Innovative approaches to monitor and promote physical activity are warranted. While individual monitoring of physical activity aids in the design of effective interventions to enhance physical activity, a basic prerequisite is that the monitoring devices exhibit high validity. Objective Our goal was to assess the validity of monitoring heart rate (HR) and energy expenditure (EE) while sitting or performing light-to-vigorous physical activity with 4 popular wrist-worn wearables (Apple Watch Series 4, Polar Vantage V, Garmin Fenix 5, and Fitbit Versa). Methods While wearing the 4 different wearables, 25 individuals performed 5 minutes each of sitting, walking, and running at different velocities (ie, 1.1 m/s, 1.9 m/s, 2.7 m/s, 3.6 m/s, and 4.1 m/s), as well as intermittent sprints. HR and EE were compared to common criterion measures: Polar-H7 chest belt for HR and indirect calorimetry for EE. Results While monitoring HR at different exercise intensities, the standardized typical errors of the estimates were 0.09-0.62, 0.13-0.88, 0.62-1.24, and 0.47-1.94 for the Apple Watch Series 4, Polar Vantage V, Garmin Fenix 5, and Fitbit Versa, respectively. Depending on exercise intensity, the corresponding coefficients of variation were 0.9%-4.3%, 2.2%-6.7%, 2.9%-9.2%, and 4.1%-19.1%, respectively, for the 4 wearables. While monitoring EE at different exercise intensities, the standardized typical errors of the estimates were 0.34-1.84, 0.32-1.33, 0.46-4.86, and 0.41-1.65 for the Apple Watch Series 4, Polar Vantage V, Garmin Fenix 5, and Fitbit Versa, respectively. Depending on exercise intensity, the corresponding coefficients of variation were 13.5%-27.1%, 16.3%-28.0%, 15.9%-34.5%, and 8.0%-32.3%, respectively. Conclusions The Apple Watch Series 4 provides the highest validity (ie, smallest error rates) when measuring HR while sitting or performing light-to-vigorous physical activity, followed by the Polar Vantage V, Garmin Fenix 5, and Fitbit Versa, in that order. The Apple Watch Series 4 and Polar Vantage V are suitable for valid HR measurements at the intensities tested, but HR data provided by the Garmin Fenix 5 and Fitbit Versa should be interpreted with caution due to higher error rates at certain intensities. None of the 4 wrist-worn wearables should be employed to monitor EE at the intensities and durations tested.
Communications: Bioencapsulation of the Antibacterial Drug Sarafloxacin in Nauplii of the Brine Shrimp Artemia franciscana

Abstract Nauplii of the brine shrimp Artemia franciscana were enriched with the antibacterial drug sarafloxacin hydrochloride to determine if levels effective against four pathogenic strains of Vibrio spp. would accumulate in brine shrimp. Three vibrio strains were Vibrio anguillarum; the fourth was V. vulnifcus. Concentrations of sarafloxacin ranging from 1 to 40% (weight volume) were incorporated into the oil phase of Super Selco brine shrimp diets. Enriched nauplii and controls were sampled at 2-h intervals for 24 h. Antibiotic sensitivity testing was evaluated with a modification of the Kirby–Bauer disk diffusion method. A microbiological assay with Escherichia coli was used to determine the concentration of sarafloxacin per sample of nauplii. The results indicate that sarafloxacin is rapidly taken up by larval brine shrimp and can be detected at 2 h of enrichment by microbiological assay. The efficacy of sarafloxacin appears to depend on the strain of pathogen present.
A morphometric method to assist in defining the South American origins of Microctonus hyperodae Loan (Hymenoptera: Braconidae) established in New Zealand

In 1991, Microctonus hyperodae Loan (Hymenoptera: Braconidae, Euphorinae), collected from eight diverse South American locations, was released in New Zealand as a biological control agent of the pasture pest Listronotus bonariensis (Kuschel) (Coleoptera: Curculionidae). Equal numbers of each South American geographical population of this thelytokous endoparasitoid of adult hosts were released in New Zealand. A morphometric method described in this paper provided a means of classifying M. hyperodae adults as originating from either east or west of the Andes. Analysis revealed that, on average, specimens collected in Chile had significantly more antennal segments, narrower stigmas and longer radial cells than those collected in Brazil, Uruguay and Argentina. Significant differences between populations originating from each side of the Andes were also recorded in the dimensions of metasomal tergum one and basitarsus three. The morphometric method should, therefore, assist in defining the origins of M. hypero.
Advance Directives in the Neurocritically Ill: A Systematic Review.

OBJECTIVES To determine the frequency of advance directives or directives disclosed by healthcare agents and their influence on decisions to withdraw/withhold life-sustaining care in neurocritically ill adults. DATA SOURCES PubMed, Embase, and Cochrane databases. STUDY SELECTION Screening was performed using predefined search terms to identify studies describing directives of neurocritically ill patients from 2000 to 2019. The review was registered prior to the screening process (International Prospective Register of Systematic Reviews [PROSPERO]-Identification number 149185). DATA EXTRACTION Data were collected using standardized forms. Primary outcomes were the frequency of directives and associated withholding/withdrawal of life-sustaining care. DATA SYNTHESIS Out of 721 articles, 25 studies were included representing 35,717 patients. The number of studies and cohort sizes increased over time. A median of 39% (interquartile range, 14-72%) of patients had directives and/or healthcare agents. The presence of directives was described in patients with stroke, status epilepticus, neurodegenerative disorders, neurotrauma, and neoplasms, with stroke patients representing the largest subgroup. Directives were more frequent among patients with neurodegenerative disorders compared with patients with other illnesses (p = 0.043). In reference to directives, care was adapted in 71% of European, 50% of Asian, and 42% of American studies, and was withheld or withdrawn more frequently over time with a median of 58% (interquartile range, 39-89%). Physicians withheld resuscitation in reference to directives in a median of 24% (interquartile range, 22-70%). CONCLUSIONS Studies regarding the use and translation of directives in neurocritically ill patients are increasing. In reference to directives, care was adapted in up to 71%, withheld or withdrawn in 58%, and resuscitation was withheld in every fourth patient, but the quality of evidence regarding their effects on critical care remains weak and the risk of bias high. The limited number of patients having directives is worrisome and studies aiming to increase the use and translation of directives are scarce. Efforts need to be made to increase the perception, use, and translation of directives of the neurocritically ill.
Ecological and genomic analyses of candidate phylum WPS-2 bacteria in an unvegetated soil.

Members of the bacterial candidate phylum WPS-2 (or Eremiobacterota) are abundant in several dry, bare soil environments. In a bare soil deposited by an extinct iron-sulfur spring, we found that WPS-2 comprised up to 24% of the bacterial community and up to 108 cells per g of soil based on 16S rRNA gene sequencing and quantification. A single genus-level cluster (Ca. Rubrimentiphilum) predominated in bare soils, but was less abundant in adjacent forest. Nearly complete genomes of Ca. Rubrimentiphilum were recovered as single amplified genomes (SAGs) and metagenome-assembled genomes (MAGs). Surprisingly, given the abundance of WPS-2 in bare soils, the genomes did not indicate any capacity for autotrophy, phototrophy, or trace gas metabolism. Instead, they suggest a predominantly aerobic organoheterotrophic lifestyle, perhaps based on scavenging amino acids, nucleotides, and complex oligopeptides, along with lithotrophic capacity on thiosulfate. Network analyses of the entire community showed that some species of Chloroflexi, Actinobacteria, and candidate phylum AD3 (or Dormibacterota) co-occurred with Ca. Rubrimentiphilum, and may represent ecological or metabolic partners. We propose that Ca. Rubrimentiphilum act as efficient heterotrophic scavengers. Combined with previous studies, these data suggest that the phylum WPS-2 includes bacteria with diverse metabolic capabilities.
Nop9 recognizes structured and single-stranded RNA elements of preribosomal RNA

Nop9 is an essential factor in the processing of preribosomal RNA. Its absence in yeast is lethal, and defects in the human ortholog are associated with breast cancer, autoimmunity, and learning/language impairment. PUF family RNA-binding proteins are best known for sequence-specific RNA recognition, and most contain eight α-helical repeats that bind to the RNA bases of single-stranded RNA. Nop9 is an unusual member of this family in that it contains eleven repeats and recognizes both RNA structure and sequence. Here we report a crystal structure of Saccharomyces cerevisiae Nop9 in complex with its target RNA within the 20S preribosomal RNA. This structure reveals that Nop9 brings together a carboxy-terminal module recognizing the 5′ single-stranded region of the RNA and a bifunctional amino-terminal module recognizing the central double-stranded stem region. We further show that the 3′ single-stranded region of the 20S target RNA adds sequence-independent binding energy to the RNA–Nop9 interaction. Both the amino- and carboxy-terminal modules retain the characteristic sequence-specific recognition of PUF proteins, but the amino-terminal module has also evolved a distinct interface, which allows Nop9 to recognize either single-stranded RNA sequences or RNAs with a combination of single-stranded and structured elements.
A checklist of British and Irish freshwater fish parasites with notes on their distribution

One hundred and sixty eight species of parasite are listed from 36 species of freshwater fish from Britain and Ireland, and notes on their distribution are provided. A list of hosts together with the parasites recorded from them is also given. Although almost twice as many species are listed as in the most recent published reference list, the parasite fauna of Britain appears to be considerably poorer in number of species than that of mainland Europe, and that of Ireland poorer still. The distribution of most species, apart from two endemic species and a very few which have clearly been introduced into Britain in recent years from America or the mainland of Europe, appears to show no peculiarities and is probably contiguous with that of their hosts.
Prevalence and Factors Associated with Current Cigarette Smoking among Ethiopian University Students: A Systematic Review and Meta-Analysis

Background Although tobacco use is highest in high-income countries, most tobacco-related deaths occur in low- and middle-income countries with the highest number of deaths recorded in East Africa. The aim of this systematic review and meta-analysis is to determine the pooled prevalence and associated factors of current cigarette smoking among Ethiopian university students. Methods The authors searched databases from PubMed, PsycINFO, Google Scholar, EMBASE, and Web of Sciences. The publications included in the analysis were inclusive, the literature was searched from January 2011 to December 2018. The JBI-MAStARI critical appraisal tool was applied to 13 publications identified by the database search. I2 statistics were used to indicate heterogeneity. Publication bias was evaluated using the visual funnel plot. A p value < 0.1 was considered as indicative of statistically significant publication bias. A random effect meta-analysis model was computed to estimate the pooled prevalence of cigarette smoking, and the variables associated with cigarette smoking were examined. Results The meta-analysis of 13 studies showed that the pooled prevalence of current cigarette smoking was found to be 12.55% (95% CI: 10.39–14.72; I2 = 94.0%) with no publication bias according to Egger's test (p = 0.007) for cigarette smoking by 2.05 (95% CI: 1.52–2.75). Factors associated with cigarette smoking were peer influence 2.79 (95% CI: 1.62–4.82; I2 = 35.7), khat chewing (95% CI: 2.81–15.26; I2 = 82.5), and alcohol use 11.16 (95% CI: 7.46–16.71). Conclusion Our findings indicate a high prevalence of cigarette smoking among Ethiopian university students as compared to the general population. Gender, peer influence, khat chewing, and current alcohol use were significantly associated with cigarette smoking. The authors recommend promoting antismoking campaigns, emphasizing health hazard public service announcements about cigarettes, and integrating health education on smoking in youth-friendly services, especially targeting higher educational institutions.
LncRNA ST8SIA6-AS1 promotes colorectal cancer cell proliferation, migration and invasion by regulating the miR-5195/PCBP2 axis.

OBJECTIVE Long non-coding RNAs (lncRNAs) have been reported to play a vital role in the development and progression of various cancers, including colorectal cancer (CRC). Although the dysregulation of lncRNA ST8SIA6-AS1 participates in the development of multiple malignancies, the underlying molecular mechanisms of ST8SIA6-AS1 in regulating CRC progression remain to be fully discovered. PATIENTS AND METHODS The expression level of lncRNA ST8SIA6-AS1 was examined in the tumor tissues and paracancerous tissues of CRC patients. Quantitative Real Time-Polymerase Chain Reaction (qRT-PCR) was utilized to examine the expression levels of ST8SIA6-AS1, miR-5195, and Poly-(C) Binding Protein 2 (PCBP2). The protein expression level of PCBP2 was detected by Western blotting. MTT assay was performed to measure the proliferation of HCT-116 and SW480 cells. Cell migration and invasion abilities were measured by transwell assay. Luciferase reporter assay was used to examine the interaction between miR-5195 and ST8SIA6-AS1 or PCBP2. RESULTS This study revealed that lncRNA ST8SIA6-AS1 was upregulated in CRC tissues and cells. Knockdown of ST8SIA6-AS1 inhibited proliferation, migration, and invasion of CRC cells. Moreover, ST8SIA6-AS1 was proved to inhibit miR-5195 expression by directly targeting miR-5195. In addition, it was demonstrated that overexpression of miR-5195 inhibited CRC progression. Furthermore, PCBP2 was shown to enhance sh-ST8SIA6-AS1 and miR-5195 mimics-attenuated cell proliferation, migration, and invasion by directly binding to miR-5195. CONCLUSIONS Our study revealed that ST8SIA6-AS1 promoted CRC progression via the miR-5195/PCBP2 axis. This study may provide an improved understanding of the pathogenesis of CRC.
Estimating the generation interval for coronavirus disease (COVID-19) based on symptom onset data, March 2020

Background Estimating key infectious disease parameters from the coronavirus disease (COVID-19) outbreak is essential for modelling studies and guiding intervention strategies. Aim We estimate the generation interval, serial interval, proportion of pre-symptomatic transmission and effective reproduction number of COVID-19. We illustrate that reproduction numbers calculated based on serial interval estimates can be biased. Methods We used outbreak data from clusters in Singapore and Tianjin, China to estimate the generation interval from symptom onset data while acknowledging uncertainty about the incubation period distribution and the underlying transmission network. From those estimates, we obtained the serial interval, proportions of pre-symptomatic transmission and reproduction numbers. Results The mean generation interval was 5.20 days (95% credible interval (CrI): 3.78–6.78) for Singapore and 3.95 days (95% CrI: 3.01–4.91) for Tianjin. The proportion of pre-symptomatic transmission was 48% (95% CrI: 32–67) for Singapore and 62% (95% CrI: 50–76) for Tianjin. Reproduction number estimates based on the generation interval distribution were slightly higher than those based on the serial interval distribution. Sensitivity analyses showed that estimating these quantities from outbreak data requires detailed contact tracing information. Conclusion High estimates of the proportion of pre-symptomatic transmission imply that case finding and contact tracing need to be supplemented by physical distancing measures in order to control the COVID-19 outbreak. Notably, quarantine and other containment measures were already in place at the time of data collection, which may inflate the proportion of infections from pre-symptomatic individuals.
Global Trends in YouTube and Google Search Activity for Psoriasis and Atopic Eczema: Detecting Geographic Hot Spots, Blind Spots and Treatment Strategies

To date, the geographical distribution and global trends of search activities on psoriasis and atopic eczema on Google and YouTube are widely unknown. The aim of this study was to identify geographic and temporal trends in YouTube and Google search activities for psoriasis and atopic eczema. We used specific filter settings on Google Trends to indicate the global search activity for (“Psoriasis”) and (“Atopic Eczema”) on Google and YouTube between January 1st, 2008 and August 7th, 2019. The four resulting data sets were analyzed and compared with respect to geographic distribution and temporal trends. Apart from a few “blind spots” (eg, Chad, Uzbekistan) the term “Psoriasis” was queried geographically fairly evenly distributed. The opposite was true for “Atopic Eczema”, which was predominantly queried from a few “hot spots” (eg, United States, Commonwealth of Nations and Sweden). Since 2008, the search activity on YouTube for “Psoriasis” has tripled, while that for “Atopic Eczema” has decreased. On Google, by contrast, search activity has risen for both “Psoriasis” and “Atopic Eczema. ” Google Trends can be a useful tool to track people's/patients' interests and search search behavior over time, enabling, for instance, regionally tailored information and prevention campaigns.