Miracle-dz/UniFAR-FTUs huggingface dataset:
Genomic Variant Analyses in Pyrethroid Resistant and Susceptible Malaria Vector, Anopheles sinensis

Anopheles sinensis is a major malaria vector in Southeast Asia. Resistance to pyrethroid insecticides in this species has impeded malaria control in the region. Previous studies found that An. sinensis populations from Yunnan Province, China were highly resistant to deltamethrin and did not carry mutations in the voltage-gated sodium channel gene that cause knockdown resistance. In this study, we tested the hypothesis that other genomic variants are associated with the resistance phenotype. Using paired-end whole genome sequencing (DNA-seq), we generated 108 Gb of DNA sequence from deltamethrin -resistant and -susceptible mosquito pools with an average coverage of 83.3× depth. Using a stringent filtering method, we identified a total of 916,926 single nucleotide variants (SNVs), including 32,240 non-synonymous mutations. A total of 958 SNVs differed significantly in allele frequency between deltamethrin -resistant and -susceptible mosquitoes. Of these, 43 SNVs were present within 37 genes that code for immunity, detoxification, cuticular, and odorant proteins. A subset of 12 SNVs were randomly selected for genotyping of individual mosquitoes by polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) and showed consistent allele frequencies with the pooled DNA-seq derived allele frequencies. In addition, copy number variations (CNVs) were detected in 56 genes, including 33 that contained amplification alleles and 23 that contained deletion alleles in resistant mosquitoes compared to susceptible mosquitoes. The genomic variants described here provide a useful resource for future studies on the genetic mechanism of insecticide resistance in this important malaria vector species.
Management of Adult Inpatient Otolaryngologic Consultations During the COVID-19 Pandemic: A Proposed Tier-Based Triage System

The coronavirus disease 2019 (COVID-19) pandemic has placed tremendous strain on health care systems, leading to unprecedented challenges and obstacles in the delivery of patient care. Otolaryngologists are frequently called on for inpatient consultations for an array of pathologies, ranging from chronic benign conditions to acutely life-threatening processes. Professional otolaryngologic societies across the world have proposed limiting patient care to time-sensitive and urgent matters; however, limited literature is available to describe how this transient change in philosophy may translate to clinical practice. Here we present a structured algorithm that allows for rapid triage of otolaryngologic consults during the ongoing pandemic, in efforts to minimize infectious spread and protect clinicians while preserving high-quality patient care. Considerations for managing these consults are presented, with a commentary on practical and ethical considerations.
Modulation of β‐catenin levels regulates cranial neural crest patterning and dispersal into first pharyngeal arch

Vertebrate cranial neural crest cells (CNCCs) are multipotent, proximal to the source CNCC form the cranial ganglia. Distally, in the pharyngeal arches, they give rise to the craniofacial skeleton and connective tissues. Fate choices are made as CNCC pattern into distinct destination compartments. In spite of this importance, the mechanism patterning CNCC is poorly defined.
Epigenetic regulation of TLR2-mediated periapical inflammation.

AIM o determine the methylation pattern of TLR2 gene promoter and its association with the transcriptional regulation of periapical inflammatory and angiogenic responses in symptomatic and asymptomatic forms of apical periodontitis. METHODOLOGY Cross-sectional study. Apical lesions were obtained from volunteers with asymptomatic apical periodontitis (AAP) (n=17) and symptomatic apical periodontitis (SAP) (n=17) scheduled for tooth extraction, and both total RNA and DNA were extracted. DNA was bisulfite-treated, a region of CpG island within the TLR2 gene was amplified by qPCR and the products were sequenced. Additionally, mRNA expression of TLR2, TLR4, IL6, IL12 TNFalpha, IL23, IL10 and TGFbeta, VEGFA, CDH5 were analyzed by qPCR. The data were analyzed with chi-square tests, Mann-Whitney or unpaired T-tests, and Spearman's correlation; variable adjustments were performed using multiple linear regression (p <0.05). RESULTS TLR2 depicted a hypomethylated DNA profile at the CpG island in SAP when compared with AAP, along with up-regulated expression of TLR2, with pro-inflammatory cytokines IL6 and IL23, and the angiogenesis marker CDH5 (p <0.05). TLR2 methylation percentage negatively correlated with mRNA levels of IL-23 and CDH5 in apical periodontitis. Lower methylation frequencies of single CpG dinucleotides -8 and -10 localized in close proximity to nuclear factor κB (NFκB) binding within the TLR2 promoter were identified in SAP versus AAP (p<0.05). Finally, unmethylated -10 and -8 single sites demonstrated up-regulation of IL23, IL10 and CDH5 transcripts compared to their methylated counterparts (p<0.05). CONCLUSIONS TLR2 gene promoter hypomethylation is linked to transcriptional activity of pro-inflammatory cytokines and angiogenic markers in exacerbated periapical inflammation. Moreover, unmethylated single sites in close proximity to NFκB binding were involved in active transcription of IL23, IL10 and CDH5.
Ancient Genomic Regulatory Blocks Are a Source for Regulatory Gene Deserts in Vertebrates after Whole-Genome Duplications

Abstract We investigated how the two rounds of whole-genome duplication that occurred at the base of the vertebrate lineage have impacted ancient microsyntenic associations involving developmental regulators (known as genomic regulatory blocks, GRBs). We showed that the majority of GRBs identified in the last common ancestor of chordates have been maintained as a single copy in humans. We found evidence that dismantling of the duplicated GRB copies occurred early in vertebrate evolution often through the differential retention of the regulatory gene but loss of the bystander gene’s exonic sequences. Despite the large evolutionary scale, the presence of duplicated highly conserved noncoding regions provided unambiguous proof for this scenario for multiple ancient GRBs. Remarkably, the dismantling of ancient GRB duplicates has contributed to the creation of large gene deserts associated with regulatory genes in vertebrates, providing a potentially widespread mechanism for the origin of these enigmatic genomic traits.
Spatial mapping of polymicrobial communities reveals a precise biogeography associated with human dental caries

Significance Dental caries remains an unresolved public health problem. The etiology is poorly understood, as the oral cavity harbors diverse communities of microorganisms. Using multiple imaging modalities on human teeth from patients with caries, we discovered a microbial community precisely arranged in a corona-like architecture. Moreover, this organization is mediated by the pathogen Streptococcus mutans through production of an extracellular scaffold that directs positioning of other oral microbes. We developed a methodology to quantify the spatial structure of microbial communities at the micron scale and found a precise spatial patterning of bacteria associated with localized caries onset. These findings are relevant as we approach the post-microbiome era, whereby quantifying the community structural organization may be essential for understanding microbiome function. Tooth decay (dental caries) is a widespread human disease caused by microbial biofilms. Streptococcus mutans, a biofilm-former, has been consistently associated with severe childhood caries; however, how this bacterium is spatially organized with other microorganisms in the oral cavity to promote disease remains unknown. Using intact biofilms formed on teeth of toddlers affected by caries, we discovered a unique 3D rotund-shaped architecture composed of multiple species precisely arranged in a corona-like structure with an inner core of S. mutans encompassed by outer layers of other bacteria. This architecture creates localized regions of acidic pH and acute enamel demineralization (caries) in a mixed-species biofilm model on human teeth, suggesting this highly ordered community as the causative agent. Notably, the construction of this architecture was found to be an active process initiated by production of an extracellular scaffold by S. mutans that assembles the corona cell arrangement, encapsulating the pathogen core. In addition, this spatial patterning creates a protective barrier against antimicrobials while increasing bacterial acid fitness associated with the disease-causing state. Our data reveal a precise biogeography in a polymicrobial community associated with human caries that can modulate the pathogen positioning and virulence potential in situ, indicating that micron-scale spatial structure of the microbiome may mediate the function and outcome of host–pathogen interactions.
A diversity of beta diversities: straightening up a concept gone awry. Part 2. Quantifying beta diversity and related phenomena

The present two-part review aims to put the different phenomena that have been called "beta diversity" over the years into a common conceptual framework and to explain what each of them measures. The first part (Tuomisto 2010) discussed basic definitions of "beta diversity". Each arises from a different way of combining a definition of "diversity" with a definition of its alpha component and with a mathematical relationship between the alpha and gamma components. This second part assumes that an appropriate basic definition of a beta component (which may or may not be true beta diversity) has been chosen, and the focus here will be on how to quantify it for a given dataset. About twenty different approaches have been used for this purpose. It turns out that only two of these approaches accurately quantify the selected beta component: one does so for the entire dataset, and the other for two sampling units at a time. The other approaches actually quantify other phenomena, such as mean species turnover between sampling units, compositional gradient length (with or without reference to an external gradient), distinctness of a focal sampling unit, rate of species accumulation with increasing sampling effort, rate of compositional turnover along an external gradient, or the rate of decay in compositional similarity with increasing geographical distance. Although most of these phenomena can be expressed as a function of a beta component of diversity, they do not equal a beta component of diversity. Many of these derived variables are not even numerically correlated with the beta component on which they are based, which needs to be taken into account when interpreting the results. The effects of sampling decisions when results are extrapolated beyond the available data will also be discussed.
Hemisphere opposite to vascular trunk deviation is earlier affected by glaucomatous damage in myopic high-tension glaucoma

Purpose To investigate whether the position of the central vascular trunk, as a surrogate of lamina cribrosa (LC) shift, is associated with the initial hemisphere of visual field defect in myopic high-tension glaucoma (HTG) eyes. Methods The deviation of the central vascular trunk was measured from the center of the Bruch’s membrane opening (BMO), which was delineated by OCT imaging. The angular deviation was measured with the horizontal nasal midline as 0° and the superior location as a positive value. The initial hemisphere developing visual field defect was defined as three connected abnormal points (having a P value with less than 0.5% probability of being normal) appearing in only one hemisphere in pattern deviation plots. If those points were observed in both hemispheres initially, the eye was classified as bi-hemispheric visual field defect. Results Initially, 36 eyes (44%) had superior visual field defects, 27 (33%) inferior visual field defects, and 18 (22%) bi-hemispheric visual field defects. After a mean follow-up of 5 years, the number of bi-hemispheric visual field defects had increased to 34 (42%). A logistic regression analysis revealed that inferior deviation of vascular trunk was the only factor associated with initial inferior visual field defect (P = 0.001), while initial bi-hemispheric visual field defects were associated with worse mean deviation at initial visits (P<0.001). A conditional inference tree analysis showed that both the angular deviation (P<0.001) and initial mean deviation (P = 0.025) determined the initial hemispheres developing visual field defect. Conclusions Although both hemispheres were involved as glaucoma progression, the axons on the side counter to the vascular trunk deviation were damaged earlier in HTG. This finding implies the LC shift could add additional stress to axons exposed to high intraocular pressure.
Changes in the Electrical Characteristics of Perovskite Solar Cells with Aging Time

The last decade has witnessed the impressive progress of perovskite solar cells (PSCs), with power conversion efficiency exceeding 25%. Nevertheless, the unsatisfactory device stability and current–voltage hysteresis normally observed with most PSCs under operational conditions are bottlenecks that hamper their further commercialization. Understanding the electrical characteristics of the device during the aging process is important for the design and development of effective strategies for the fabrication of stable PSCs. Herein, electrochemical impedance spectroscopical (IS) analyses are used to study the time-dependent electrical characteristics of PSC. We demonstrate that both the dark and light ideality factors are sensitive to aging time, indicating the dominant existence of trap-assisted recombination in the investigated device. By analyzing the capacitance versus frequency responses, we show that the low-frequency capacitance increases with increasing aging time due to the accumulation of charges or ions at the interfaces. These results are correlated with the observed hysteresis during the current–voltage measurement and provide an in-depth understanding of the degradation mechanism of PSCs with aging time.
Parent–child communication about sexual and reproductive health: perspectives of Jordanian and Syrian parents

Abstract Young people throughout the world face considerable challenges related to their sexual and reproductive health (SRH). The parent–child relationship is fundamental to shaping children’s trajectories through adolescence and suggests considerable potential to improve youth SRH knowledge. Lack of parent–child sexual communication (PCSC) may cause youth to turn instead to questionable information sources, such as peers, the internet and social media. The limited research in this area, and specifically in the Middle East, led us to explore how parents discuss SRH issues with their children and pinpointed the potential role for parents in supporting their children’s SRH needs. A qualitative research approach was used, with 20 focus groups stratified by nationality and sex of participants from four major communities in Jordan. Thematic coding and analysis was used. Parents described their willingness to “break the culture of shame. ” Three primary strategies emerged: (1) the gender match, (2) mothers as a safe space and (3) seeking help from others, which included two sub-themes: incorporating others, and relying on the delivery of SRH information in schools. Strengths and challenges were inherent within each strategy, and discussion topics varied according to the strategy used. Evidence from this study provides an opportunity for future research and programming to improve adolescent health outcomes within conservative milieus to break the intergenerational cycle of shame. Interventions are suggested to target parents’ knowledge and self-confidence to help youth achieve their sexual development. Using gender-matched PCSC strategies, school-based platforms and religious institutions are ways to destigmatise such topics.
A preliminary overview of raptor monitoring in Slovenia – an overview of methodologies, current monitoring status and future perspectives

Abstract Among 48 raptor species (birds of prey, owls, shrikes) recorded recently in Slovenia, some long-term monitoring activities are being conducted for more than half of them, mainly for conservation and research purposes. However, national coverage is achieved only in 15% of the species, whereas other monitoring programmes are more or less local. Two monitoring approaches are considered, the species specific approach and assemblage approach. Current ongoing monitoring programmes for raptors in Slovenia lack monitoring of breeding success, which is now confined to only a few owl species. Use of nestboxes should therefore be considered more broadly in the future for some species at least
Relating species abundance distributions to species‐area curves in two Mediterranean‐type shrublands

Abstract. Based on both theoretical and empirical studies there is evidence that different species abundance distributions underlie different species‐area relationships. Here I show that Australian and Californian shrubland communities (at the scale from 1 to 1000 m2) exhibit different species‐area relationships and different species abundance patterns. The species‐area relationship in Australian heathlands best fits an exponential model and species abundance (based on both density and cover) follows a narrow log normal distribution. In contrast, the species‐area relationship in Californian shrublands is best fit with the power model and, although species abundance appears to fit a log normal distribution, the distribution is much broader than in Australian heathlands. I hypothesize that the primary driver of these differences is the abundance of small‐stature annual species in California and the lack of annuals in Australian heathlands. Species‐area is best fit by an exponential model in Australian heathlands because the bulk of the species are common and thus the species‐area curves initially rise rapidly between 1 and 100 m2. Annuals in Californian shrublands generate very broad species abundance distributions with many uncommon or rare species. The power function is a better model in these communities because richness increases slowly from 1 to 100 m2 but more rapidly between 100 and 1000 m2 due to the abundance of rare or uncommon species that are more likely to be encountered at coarser spatial scales. The implications of this study are that both the exponential and power function models are legitimate representations of species‐area relationships in different plant communities. Also, structural differences in community organization, arising from different species abundance distributions, may lead to different species‐area curves, and this may be tied to patterns of life form distribution.
Strategies for the Improvement of Pet Health and Welfare in Portugal Based on a Pilot Survey on Husbandry, Opinion, and Information Needs

Simple Summary This study examined husbandry practices in companion animals being conducted in Portugal in order to understand the health and welfare issues which can be improved. One of the more important findings is that, despite adopting most pets, pet owners do not adopt from animal shelters, possibly due to the large bureaucratic process. Veterinary practice is viewed as expensive and identification of animals with microchip is frequently disregarded. These issues may result in important threats to animal welfare and health and should be addressed at societal level. Several strategies based on results are proposed to improve pet health and welfare in Portugal, focusing on showcasing the importance of veterinary care, reducing the number of lost or abandoned animals, and improving awareness and education. Abstract Pets are present in half of the homes across Portugal. However, little is known about the husbandry, opinion, and information needs of Portuguese pet owners. Thus, the objective of this work was to clarify this information providing the basis for suggesting potential improvements. Responses were collected through an online survey, including inhabitants from different regions of Portugal (n = 111). Cats and dogs are the most popular pets and the majority are adopted, fed commercial diets, live indoors, are vaccinated, dewormed, and treated for external parasites, and occasionally visit the veterinary practice. Portuguese owners are interested in improving their pet’s health, and would like to learn more about welfare, health assessment, and diet from veterinarians. However, microchip and municipal registration are often overlooked. Lack of adoption from animal shelters as well as expectations over the cost of veterinary practice were other difficulties identified in this study. Strategies for the improvement of pet health and welfare in Portugal were proposed as improving the perception of the value and importance of veterinary care, reducing the number of lost and abandoned pets, and improving awareness and education. Thus, Portuguese stakeholders and authorities must take the required measures to improve these issues.
Psychological Distress of Patients Experiencing Different Types of Road Traffic Injuries in Vietnam

Road-related injuries are often catastrophic, and the eighth leading cause of all-aged mortality. While psychological problems, including anxiety, driving phobia, and post-traumatic stress have been found to be common among injured survivors, the literature in this area is still limited. This study aimed to evaluate the prevalence of distress between different types of road injuries among 413 patients in Thai Binh hospitals from October to December 2018. The Kessler Psychological Distress Scale (K6) was used to assess mental health status. Sociodemographic and clinical characteristics were also collected. The results of Multiple Logistic and Tobit regression models were utilized. Psychological issues were found in 13.8% of the participants. In terms of K6 profile, nervous, restless/fidgety, and “everything was an effort” were the three most frequently endorsed aspects. Having soft-tissue injuries had a 0.32-time lower likelihood of psychological distress compared to those having other injuries. Additionally, patients who were diagnosed with fractures were 4.5-times more likely to report psychological distress. Our finding highlights the need for psychological screening to reduce disabilities associated with non-fatal injury related to road traffic crashes.
Spatial and habitat-related patterns of temperate reef fish assemblages: implications for the design of Marine Protected Areas

Patterns of rocky reef fish assemblages (composition and relative abundance of species) were examined to provide data on the design of Marine Protected Areas (MPAs), which aim to protect these organisms. A hierarchical design was used to investigate changes in fish assemblages at scales of metres to kilometres along-shore, and among reef habitat types within two 10-km areas on the central coast of New South Wales, Australia. Influences of physical and biological attributes of a reef on assemblages of fish were also examined. The greatest variation in fish assemblages occurred at scales of 2–6 km along-shore. Eighty percent of species recorded were found within a 6-km section of coastline. The most predictable differences in assemblages were found between reef habitats (urchin-grazed barrens, Ecklonia forest and sponge habitat), and between depths. Marine Protected Areas should ideally incorporate all available habitats over the entire depth range at which they occur. This may require MPAs larger than 2–6 km, or multiple MPAs that have been specifically located to include these features, as representation of habitats was found to vary at scales of kilometres to tens of kilometres along shore.