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Background: The bryophytes are a plant group that is smaller than and not as well known as the vascular plants. They are less used and are almost completely neglected in ethnobotanical studies. Traditional nativity scenes depicting the birth of Christ are commonly decorated with both vascular plants and bryophytes. The aim of this study was to document the diversity of decorative bryophytes sold during the Advent season at farmers' markets in Croatia (Southeastern Europe, Balkan Peninsula). Methods: Twenty-eight farmers' markets in the two largest Croatian cities (Zagreb in the continental part and Split in the Mediterranean part) were studied in the search for local vendors selling bryophytes during the pre-Christmas season. The bryophytes collected were identified and analysed with respect to families, growth type, life forms and threat status. Results: Among 275 collected specimens, 43 moss and four liverwort species were identified. The mean number of species per vendor was 3.5. The most frequent species were Hypnum cupressiforme, Homalothecium sericeum and Ctenidium molluscum. Mats, wefts and tufts were the most common life-forms, while pleurocarpous prevailed over acrocarpous mosses, as they are usually pinnately branched and form large carpets, suitable for decorations. The overall selection of bryophytes and the decorations made of them were more diverse and abundant in inland Croatia, where 49 vendors at 15 farmers' markets sold goods containing 43 species. In Mediterranean Croatia, at six farmers' markets only 29 vendors sold goods, which contained 18 species. A considerable number of species that are less attractive to harvesters were collected non-intentionally, entangled in carpets of other, more frequent species. Among them, Rhodobryum ontariense and Loeskeobryum brevirostre are rare and insufficiently recorded in Croatia so far. Conclusions: The present study provided a first perspective on the use of bryophytes in traditional nativity scenes in Croatia and Southeastern Europe, contributing to scarce ethnobotanical documentation of the decorative use of bryophytes in Christmas festivities in Europe and globally. [ABSTRACT FROM AUTHOR]

Selected papers from the 13th International Conference on Bioinformatics (InCoB2014), July 31-2 August, 2014 in Sydney, Australia have been compiled in this supplement. These range from network analysis and gene regulatory networks to systems level biological analysis, providing the 2014 update to InCoB's computational systems biology research. [ABSTRACT FROM AUTHOR]

Background: Structural variants (SVs), including deletions, insertions, duplications, and inversions, are relatively long genomic variations implicated in a diverse range of processes from human disease to ecology and evolution. Given their complex signatures, tendency to occur in repeated regions, and large size, discovering SVs based on short reads is challenging compared to single-nucleotide variants. The increasing availability of long-read technologies has greatly facilitated SV discovery; however, these technologies remain too costly to apply routinely to population-level studies. Here, we combined short-read and long-read sequencing technologies to provide a comprehensive population-scale assessment of structural variation in a panel of Canadian soybean cultivars. Results: We used Oxford Nanopore long-read sequencing data (~12× mean coverage) for 17 samples to both benchmark SV calls made from Illumina short-read data and predict SVs that were subsequently genotyped in a population of 102 samples using Illumina data. Benchmarking results show that variants discovered using Oxford Nanopore can be accurately genotyped from the Illumina data. We first use the genotyped deletions and insertions for population genetics analyses and show that results are comparable to those based on single-nucleotide variants. We observe that the population frequency and distribution within the genome of deletions and insertions are constrained by the location of genes. Gene Ontology and PFAM domain enrichment analyses also confirm previous reports that genes harboring high-frequency deletions and insertions are enriched for functions in defense response. Finally, we discover polymorphic transposable elements from the deletions and insertions and report evidence of the recent activity of a Stowaway MITE. Conclusions: We show that structural variants discovered using Oxford Nanopore data can be genotyped with high accuracy from Illumina data. Our results demonstrate that long-read and short-read sequencing technologies can be efficiently combined to enhance SV analysis in large populations, providing a reusable framework for their study in a wider range of samples and non-model species. [ABSTRACT FROM AUTHOR]

Background: Plants in cliff habitats may evolve specific reproductive strategies to cope with harsh environments, and unraveling these reproductive characteristics can improve our understanding of survival strategies and lithophyte evolution. This understanding is especially important for efforts to protect rare and endemic plants. Here, we investigated the reproductive biology of Lonicera oblata, an endangered lithophytic shrub that is scattered in highly fragmented and isolated cliff habitats of the Taihang and Yan mountains in North China. Results: Flowers of L. oblata are herkogamous and protandrous, characteristics that can prevent autogamy at the single-flower level, and insects are necessary for pollination. The outcrossing index, pollen/ovule ratio, and the results of hand pollination were measured and all revealed a mixed mating system for L. oblata, that combines cross-fertilization and partial self-fertilization. The floral traits of L. oblata of zygomorphic and brightly yellowish corolla, heavy fragrance, and rich nectar, suggest an entomophilous pollination system. Sweat bees were observed as the most effective pollinators but their visiting frequencies were not high. Pollen limitation may limit the reproductive success of L. oblata. Conclusions: We determined the reproductive characteristics of L. oblata, a critically endangered species endemic to cliffs in North China, providing insight into its endangerment and suggesting conservation strategies. L. oblata has highly pollinator-dependent self-fertilization as part of a mixed mating system. Floral features such as low-flowering synchrony, asynchronous anthers dehiscence, and high duration of stigma receptivity, improve pollination efficiency in the case of low pollinator service. Our work provides reference information to understand the survival strategies and conservation of L. oblata and other lithophytes. [ABSTRACT FROM AUTHOR]

Background: Neurological disability progression occurs across the spectrum of people living with multiple sclerosis (MS). Although there are a handful of disease-modifying treatments approved for use in progressive phenotypes of MS, there are no treatments that substantially modify the course of clinical progression in MS. Characterizing the determinants of clinical progression can inform the development of novel therapeutic agents and treatment approaches that target progression in MS, which is one of the greatest unmet needs in clinical practice. Canada, having one of the world's highest rates of MS and a publicly-funded health care system, represents an optimal country to achieve in-depth analysis of progression. Accordingly, the overarching aim of the Canadian Prospective Cohort Study to Understand Progression in MS (CanProCo) is to evaluate a wide spectrum of factors associated with the clinical onset and rate of disease progression in MS, and to describe how these factors relate to one another to influence progression.Methods: CanProCo is a prospective, observational cohort study with investigators specializing in epidemiology, neuroimaging, neuroimmunology, health services research and health economics. CanProCo's study design was approved by an international review panel, comprised of content experts and key stakeholders. One thousand individuals with radiologically-isolated syndrome, relapsing-remitting MS, and primary-progressive MS within 10-15 years of disease onset will be recruited from 5 academic MS centres in Canada. Participants will undergo detailed clinical evaluation annually over 5 years (including advanced, app-based clinical data collection). In a subset of participants within 5-10 years of disease onset (n = 500), blood, cerebrospinal fluid, and research MRIs will be collected allowing an integrated, in-depth evaluation of factors contributing to progression in MS from multiple perspectives. Factors of interest range from biological measures (e.g. single-cell RNA-sequencing), MRI-based microstructural assessment, participant characteristics (self-reported, performance-based, clinician-assessed, health-system based), and micro and macro-environmental factors.Discussion: Halting the progression of MS remains a fundamental need to improve the lives of people living with MS. Achieving this requires leveraging transdisciplinary approaches to better characterize why clinical progression occurs. CanProCo is a pioneering multi-dimensional cohort study aiming to characterize these determinants to inform the development and implementation of efficacious and effective interventions. [ABSTRACT FROM AUTHOR]

Background: In Ethiopia, about 92.3% of all the fuelwood (firewood and/or charcoal) is consumed for cooking, heating and lighting purposes by domestic households and the demand is growing from 10 to 14%. However, there are little/no practical experiences or documented indigenous knowledge on how traditional people identify and select high fuelwood producing plant species with short rotation periods at Boset District. Therefore, the present study was aimed at: (1) selecting and documenting high fuelwood producing plant species at Boset District; (2) identifying major predictor variables that influence the prioritization and selection of species; and (3) develop a Generalized Linear Model (GLM) to predict the selection of species. Methods: A total of 96 informants comprising 59 men and 37 women between the ages of 18 and 81 were sampled. Data were collected using structured interviews, guided field walk, discussions and field observations. Results: Collected data indicated that 88.5% of the informants involved in firewood collection, while 90% practiced charcoal making. A total of 1533.60 Birr per household on average was earned annually from this activity. A total of 25 fuelwood producing plant species were identified and documented at Boset District. Of these, Acacia senegal, Acacia tortilis and Acacia robusta were the three best prioritized and selected indigenous high fuelwood producing species. Prosopis juliflora, Parthenium hysterophorus, Azadirachta indica, Calotropis procera, Cryptostegia grandiflora, Lantana camara and Senna occidentalis further grouped under introduced fuelwood species. Prediction of GLM assured sampled Kebeles and source of income generated from fuelwood species positively and significantly (p < 0.001) related to selection of species. Higher efficiency to provide energy and heat; little or no smoke or soot; easier to cut and split the wood and easier availability were some of the main selection criteria. Conclusions: This study provides valuable information in selecting and documenting of high fuelwood producing plant species for proper management and sustainable use at Boset District. The three most selected species (A. senegal, A. tortilis and A. robusta) should be further evaluated at laboratory to determine their calorific value and combustion characteristics. [ABSTRACT FROM AUTHOR]

Background: The formation of the Bicoid (Bcd) gradient in the early Drosophila is one of the most fascinating observations in biology and serves as a paradigm for gradient formation, yet its mechanism is still not fully understood. Two distinct models were proposed in the past, the SDD and the ARTS model. Results: We define novel cis- and trans-acting factors that are indispensable for gradient formation. The first one is the poly A tail length of the bcd mRNA where we demonstrate that it changes not only in time, but also in space. We show that posterior bcd mRNAs possess a longer poly tail than anterior ones and this elongation is likely mediated by wispy (wisp), a poly A polymerase. Consequently, modulating the activity of Wisp results in changes of the Bcd gradient, in controlling downstream targets such as the gap and pair-rule genes, and also in influencing the cuticular pattern. Attempts to modulate the Bcd gradient by subjecting the egg to an extra nuclear cycle, i.e. a 15th nuclear cycle by means of the maternal haploid (mh) mutation showed no effect, neither on the appearance of the gradient nor on the control of downstream target. This suggests that the segmental anlagen are determined during the first 14 nuclear cycles. Finally, we identify the Cyclin B (CycB) gene as a trans-acting factor that modulates the movement of Bcd such that Bcd movement is allowed to move through the interior of the egg. Conclusions: Our analysis demonstrates that Bcd gradient formation is far more complex than previously thought requiring a revision of the models of how the gradient is formed. [ABSTRACT FROM AUTHOR]

Background: While vector-borne diseases (VBDs) pose an important public health problem worldwide, there is a limited and conflicting knowledge about such illnesses in rural or urban settings. The present study aimed to explore the social representations (SRs) held by people in the state of Puebla, Mexico on insects and the diseases they transmit. Understood as the group of ideas held and shared by a group of human beings which enable them to understand and interpret the world, SRs constitute what could be called a collective science or knowledge of everyday life. Methods: The present study was conducted in six municipalities in the state of Puebla, wherein an open-ended questionnaire was applied with three age ranges. A total of 360 questionnaires were applied with people dedicated to a variety of activities. The survey data was analyzed to identify the SR's structure (the central nucleus of the SR and its peripheral system) and the level of organization in order to explore the degree to which the ideas that constitute it are shared and based on consensus. To describe the structure of the SR, a network analysis was conducted and complemented by a correspondence analysis, which also enables the differences between social groups to be identified. Results: Popular knowledge on insects and VBDs is often limited, even in communities in which more than one-vector insect is found. The elements that were most frequently mentioned in the data, as pertaining to the insect–disease relationship, were mosquitoes and dengue fever, with scorpions (which are arachnids and not insects) receiving the second-highest number of mentions, while other insects such as kissing bugs, flies, and cockroaches were also mentioned as transmitting VBDs. While television was the main information source on VBDs for the residents of these communities, biology books were also mentioned. Chemical control measures (insect repellents) were the most used prevention method, and traditional medicine was the remedy most commonly used to treat insect bites and transmitted diseases. Entomophobia was the main cause for the respondents' fear and rejection of insects. Beyond the deleterious effects of many insects, those surveyed also recognized a positive relationship with insects due to economic and nutritional benefits they provide. Conclusions: The present study provides relevant information on how insects and the diseases they transmit are perceived by rural and urban communities. Although the population is aware of dengue fever and the role of mosquitoes in transmitting it, information campaigns are required for other historically neglected VBDs, such as leishmaniasis, Chagas disease, and, even, rickettsiosis. As it is important to understand the impact that these illnesses have on communities further research is required to ensure that better information and guidance is provided on VBDs in order to develop a culture of illness prevention in not only the rural but also the metropolitan communities of the state of Puebla. [ABSTRACT FROM AUTHOR]

The cellular complexity of glioblastoma microenvironments is still poorly understood. In-depth, cell-resolution tissue analyses of human material are rare but highly necessary to understand the biology of this deadly tumor. Here we present a unique 3D visualization revealing the cellular composition of human GBM in detail and considering its critical association with the neo-vascular niche. Our images show a complex vascular map of human 3D biopsies with increased vascular heterogeneity and altered spatial relationship with astrocytes or glioma-cell counterparts. High-resolution analysis of the structural layers of the blood brain barrier showed a multilayered fenestration of endothelium and basement membrane. Careful examination of T cell position and migration relative to vascular walls revealed increased infiltration corresponding with tumor proliferation. In addition, the analysis of the myeloid landscape not only showed a volumetric increase in glioma-associated microglia and macrophages relative to GBM proliferation but also revealed distinct phenotypes in tumor nest and stroma. Images and data sets are available on demand as a resource for public access. [ABSTRACT FROM AUTHOR]

Future radiation oncology encompasses a broad spectrum of topics ranging from modern clinical trial design to treatment and imaging technology and biology. In more detail, the application of hybrid MRI devices in modern image-guided radiotherapy; the emerging field of radiomics; the role of molecular imaging using positron emission tomography and its integration into clinical routine; radiation biology with its future perspectives, the role of molecular signatures in prognostic modelling; as well as special treatment modalities such as brachytherapy or proton beam therapy are areas of rapid development. More clinically, radiation oncology will certainly find an important role in the management of oligometastasis. The treatment spectrum will also be widened by the rational integration of modern systemic targeted or immune therapies into multimodal treatment strategies. All these developments will require a concise rethinking of clinical trial design. This article reviews the current status and the potential developments in the field of radiation oncology as discussed by a panel of European and international experts sharing their vision during the "X-Change" symposium, held in July 2019 in Munich (Germany). [ABSTRACT FROM AUTHOR]

Background: Open air markets hold an important position for ethnobiologists. In Southeast Asia, they are seriously understudied, in spite of their incredible biocultural diversity. In order to fill this gap we recorded plants and fungi sold in the open air markets of Luang Prabang, Lao PDR. Methods: The markets were visited 38 times in four seasons: the dry season, early monsoon, mid-monsoon, and end-of-monsoon, at least 8 times per season. All items were photographed and voucher specimens were collected. Fungi were identified using DNA barcoding techniques. Results: We recorded 110 species of wild edible plants and 54 species of fungi, including 49 wild-collected species. The sold plants included 86 species of green vegetables, 18 species of fruits and 3 species of flowers. Products from woody species constitute around half of all taxa sold. These include the young shoots of tree leaves, which are used for salads—an interesting feature of Lao cuisine. A large number of extremely rare Russula, with no reference sequences represented in databases or even species unknown to science is present on sale in the markets. Conclusions: Luang Prabang markets are some of the richest in species of wild edible plants and fungi in Asia, and indeed in the whole world. It is worth pointing out the exceptionally long list of wild edible mushrooms which are sold in Luang Prabang (and probably elsewhere in Laos). We view the Morning Market of Luang Prabang as a cultural treasure that unites the traditions of eating a large number of living species with very diverse flora and fauna. Measures should be taken to strike a balance between local foraging traditions and nature conservation priorities. [ABSTRACT FROM AUTHOR]

The International Association for Intelligent Biology and Medicine (IAIBM) is a nonprofit organization that promotes intelligent biology and medical science. It hosts an annual International Conference on Intelligent Biology and Medicine (ICIBM), which was initially established in 2012. Due to the coronavirus (COVID-19) pandemic, the ICIBM 2020 was held for the first time as a virtual online conference on August 9 to 10. The virtual conference had ~ 300 registered participants and featured 41 online real-time presentations. ICIBM 2020 received a total of 75 manuscript submissions, and 12 were selected to be published in this special issue of BMC Bioinformatics. These 12 manuscripts cover a wide range of bioinformatics topics including network analysis, imaging analysis, machine learning, gene expression analysis, and sequence analysis. [ABSTRACT FROM AUTHOR]

Background: The discovery of biomarkers of ageing has led to the development of predictors of impending natural death and has paved the way for personalised estimation of the risk of death in the general population. This study intends to identify the ethical resources available to approach the idea of a long-lasting dying process and consider the perspective of death prediction. The reflection on human mortality is necessary but not sufficient to face this issue. Knowledge about death anticipation in clinical contexts allows for a better understanding of it. Still, the very notion of prediction and its implications must be clarified. This study outlines in a prospective way issues that call for further investigation in the various fields concerned: ethical, psychological, medical and social.Methods: The study is based on an interdisciplinary approach, a combination of philosophy, clinical psychology, medicine, demography, biology and actuarial science.Results: The present study proposes an understanding of death prediction based on its distinction with the relationship to human mortality and death anticipation, and on the analogy with the implications of genetic testing performed in pre-symptomatic stages of a disease. It leads to the identification of a multi-layered issue, including the individual and personal relationship to death prediction, the potential medical uses of biomarkers of ageing, the social and economic implications of the latter, especially in regard to the way longevity risk is perceived.Conclusions: The present study work strives to propose a first sketch of what the implications of death prediction as such could be - from an individual, medical and social point of view. Both with anti-ageing medicine and the transhumanist quest for immortality, research on biomarkers of ageing brings back to the forefront crucial ethical matters: should we, as human beings, keep ignoring certain things, primarily the moment of our death, be it an estimation of it? If such knowledge was available, who should be informed about it and how such information should be given? Is it a knowledge that could be socially shared? [ABSTRACT FROM AUTHOR]

Cancer is a complex disease in which both genetic defects and microenvironmental components contribute to the development, progression, and metastasization of disease, representing major hurdles in the identification of more effective and safer treatment regimens for patients. Three-dimensional (3D) models are changing the paradigm of preclinical cancer research as they more closely resemble the complex tissue environment and architecture found in clinical tumors than in bidimensional (2D) cell cultures. Among 3D models, spheroids and organoids represent the most versatile and promising models in that they are capable of recapitulating the heterogeneity and pathophysiology of human cancers and of filling the gap between conventional 2D in vitro testing and animal models. Such 3D systems represent a powerful tool for studying cancer biology, enabling us to model the dynamic evolution of neoplastic disease from the early stages to metastatic dissemination and the interactions with the microenvironment. Spheroids and organoids have recently been used in the field of drug discovery and personalized medicine. The combined use of 3D models could potentially improve the robustness and reliability of preclinical research data, reducing the need for animal testing and favoring their transition to clinical practice. In this review, we summarize the recent advances in the use of these 3D systems for cancer modeling, focusing on their innovative translational applications, looking at future challenges, and comparing them with most widely used animal models. [ABSTRACT FROM AUTHOR]

Background: Herpes simplex virus (HSV) can cause encephalitis. Its infected cell polypeptide 47 (ICP47), encoded by immediate-early gene US12, promotes immune escape. ICP47 was modified in the clinically approved oncolytic HSV (oHSV) T-Vec. However, transcription regulatory sequence (TRS) and transcription regulatory factor (TRF) of HSV US12 are seldom reported. Methods: Previously, our laboratory isolated a new HSV strain named HSV-1-LXMW from a male patient with oral herpes in Beijing, China. Firstly, the genetic tree was used to analyze its genetic relationship. The US12 TRS and TRF in HSV-1-LXMW were found by using predictive software. Secondly, the further verification by the multi-sequence comparative analysis shown that the upstream DNA sequence of HSV US12 gene contained the conserved region. Finally, the results of literature search shown that the expression of transcription factors was related to the tissue affinity of HSV-1 and HSV-2, so as to increase the new understanding of the transcriptional regulation of HSV biology and oncolytic virus (OVs) therapy. Results: Here we reported the transcriptional regulation region sequence of our new HSV-1-LXMW, and its close relationship with HSV-1-CR38 and HSV-1-17. Importantly we identified eight different kinds of novel TRSs and TRFs of HSV US12 for the first time, and found they are conserved among HSV-1 (c-Rel, Elk-1, Pax-4), HSV-2 (Oct-1, CF2-II, E74A, StuAp) or both HSVs (HNF-4). The TRFs c-Rel and Oct-1 are biologically functional respectively in immune escape and viral replication during HSV infection. Conclusions: Our findings have important implication to HSV biology, infection, immunity and oHSVs. [ABSTRACT FROM AUTHOR]

Background: The Mulam are an ethnic group native to Guangxi, and nearly 80% of the Mulam population lives in Luocheng Mulam Autonomous County, northern Guangxi, southern China. They have accumulated rich medicinal folk knowledge through practice and experience in their long-term struggles with disease and the harsh natural environment. However, their traditional medicinal knowledge is threatened due to a lack of written records, conservative inheritance patterns, and rapid economic development. Therefore, the investigation and documentation of medicinal plants and their associated indigenous wisdom are necessary. Method: Ethnobotanical data were collected from 12 villages and five communities in Luocheng County from January 2013 to April 2017. A total of 128 informants were interviewed through semistructured interviews, field observations, group discussions, and guided field walks. Quantitative indices such as use categories, preference ranking exercises, the informant consensus factor (ICF), and the fidelity level (FL) were used to evaluate the importance of medicinal plant species. Additionally, group discussions were conducted about the conservation of and threats to medicinal plants and traditional knowledge. Results: A total of 456 medicinal plant species from 350 genera and 132 families were recorded and documented in our ethnobotanical investigation. Most of them (335 species, 73.47%) were obtained from wild habitats. Most of the documented species (246) were herbaceous (54%), followed by shrubs, with 76 species (17%), lianas, with 75 species (16%), and trees, with 59 species (13%). The most common method of administration was oral administration, which was used for 390 species (62.70%). The most common method of preparation was decoction (316 species, 54.11%). The plants were used to treat 312 human diseases in 12 disease categories, and most of the categories had a high ICF value. The highest ICF value was recorded for gynecological ailments (0.92), followed by nervous and psychosomatic problems (0.90) and digestive system diseases (0.89). Traditional medicinal knowledge and medicinal plants are under threat due to conservative inheritance processes and anthropogenic pressures for various reasons. Conclusion: A rich diversity of medicinal plants is distributed in the Mulam area, and these plants play an important role in healthcare among the Mulam people. Mulam people are skilled in using the plants in their surroundings to treat diseases in their daily lives. However, their traditional medicinal knowledge and medicinal plants are greatly threatened by rapid economic development for various reasons. Thus, policies and practices for the conservation of medicinal plants and the associated traditional knowledge are necessary. [ABSTRACT FROM AUTHOR]

Background: Cashmere goat is known for its precious undercoat. Being photoperiod-dictated, cashmere growth has been studied focusing mainly on hair follicle cycle phases (anagen, catagen and telogen). An accurate molecular knowledge of the goat hair follicle cycle, disentangling gene expression changes during phases and recognizing timing boundaries, could be useful to improve cashmere goat management and ultimately cashmere production. Results: To better describe goat's hair follicle transcriptome we applied RNA-sequencing to isolated hair follicles from five Italian cashmere goats, during the anagen and catagen phase, identifying total of 214 differentially expressed genes (DEGs): 97 were up-regulated while 117 were down-regulated in catagen with respect to anagen. Gene Ontology and pathway analysis were performed. We detected 144 significant pathways spanning from estrogen, pluripotency of stem cells, thermogenesis and fatty acid metabolism that were strongly expressed during the hair follicle phases analysed. Finally, we validated promising DEGs by RT-qPCR in the same set of samples as well as in hair follicles and entire skin biopsies of another cashmere goats cohort accounting for early anagen, anagen, early catagen, and catagen phases. Conclusions: As in the isolated hair follicles, some target genes were homogenously modulated during the four hair follicle phases. Ceruloplasmin (CP) and Keratin 4 (K4), confirmed their clear cut expression between growing and resting phase. In fact, K4 was almost absent in catagen phases while CP was barely expressed in anagen phases. In particular, the strong expression of K4 in early anagen makes it an eligible marker to track the beginning of a new hair cycle, and therefore defining the optimum time for cashmere harvesting. [ABSTRACT FROM AUTHOR]

Background: The syphilis epidemic continues to cause substantial morbidity and mortality worldwide, particularly in low- and middle-income countries, despite several recent disease control initiatives. Though our understanding of the pathogenesis of this disease and the biology of the syphilis agent, Treponema pallidum subsp. pallidum has improved over the last two decades, further research is necessary to improve clinical diagnosis and disease management protocols. Additionally, such research efforts could contribute to the identification of possible targets for the development of an effective vaccine to stem syphilis spread.Methods: This study will recruit two cohorts of participants with active syphilis infection, one with de novo infection, one with repeat infection. Whole blood specimens will be collected from each study participant at baseline, 4, 12, 24, 36, and 48 weeks, to track specific markers of their immunological response, as well as to compare humoral reactivity to Treponema pallidum antigens between the two groups. Additionally, we will use serum specimens to look for unique cytokine patterns in participants with early syphilis. Oral and blood samples, as well as samples from any syphilitic lesions present, will also be collected to sequence any Treponema pallidum DNA found.Discussion: By furthering our understanding of syphilis pathogenesis and human host immune response to Treponema pallidum, we will provide important data that will help in development of new point-of-care tests that could better identify active infection, leading to improved syphilis diagnosis and management. Findings could also contribute to vaccine development efforts. [ABSTRACT FROM AUTHOR]

The landscape of multiple myeloma (MM) has changed considerably in the past two decades regarding new treatments, insight into disease biology and innovation in the techniques available to assess measurable residual disease (MRD) as the most accurate method to evaluate treatment efficacy. The sensitivity and standardization achieved by these techniques together with unprecedented rates of complete remission (CR) induced by new regimens, raised enormous interest in MRD as a surrogate biomarker of patients' outcome and endpoint in clinical trials. By contrast, there is reluctance and general lack of consensus on how to use MRD outside clinical trials. Here, we discuss critical aspects related with the implementation of MRD in clinical practice. [ABSTRACT FROM AUTHOR]

Background: In Europe and the Mediterranean, over-exploitation and destructive harvesting techniques have been identified as two critical threats affecting the sustainable harvesting of wild medicinal plant (WMP) species. However, unsustainable harvesting is not an issue everywhere and localized assessments are needed. Local knowledge has been praised for its potential for local short-term assessments. In this study, we aimed to register the known, harvested, and locally utilized WMP species and understand local knowledge of harvesters about the ecological sustainability of WMP harvesting and the perceived changes of WMP availability. Materials and methods: This study was conducted on Lemnos island, Greece, in July and August 2018. Sixteen harvesters knowledgeable about gathering and using WMP were chosen through purposeful and snowball sampling. Successive free-lists provided insights on the taxa known, harvested, and utilized by harvesters and subsequent semi-structured interviews served to understand harvesting practices and perceived changes of WMP availability. Participant observation during seven harvesting walks allowed for additional insights and facilitated the collection of voucher specimens. Results: In total, 144 different plant taxa were listed as useful and 81 had been harvested in the prior 4 years. Medicinal applications were mainly related to digestive and respiratory system issues. A number of favorable harvesting practices suggested a high potential towards an ecologically sustainable harvest. Although, a decreased availability for certain plant taxa and harvesting sites was reported and mainly attributed to external factors such as pollution, unusually dry weather, intentional pastureland burning or chemicals in agriculture, but also destructive harvesting by less knowledgeable harvesters. Conclusions: Knowledgeable harvesters of Lemnos gather and use a considerable number of WMP taxa and possess local knowledge that supports an ecologically sustainable harvest. However, certain plant taxa and areas of the island were indicated to be under pressure from harvesting, unusual climatic conditions, and agricultural practices. Our approach confirmed that local knowledge should be taken into account for assessing the sustainability of WMP harvesting. [ABSTRACT FROM AUTHOR]

Background: Network motifs are connectivity structures that occur with significantly higher frequency than chance, and are thought to play important roles in complex biological networks, for example in gene regulation, interactomes, and metabolomes. Network motifs may also become pivotal in the rational design and engineering of complex biological systems underpinning the field of synthetic biology. Distinguishing true motifs from arbitrary substructures, however, remains a challenge. Results: Here we demonstrate both theoretically and empirically that implicit assumptions present in mainstream methods for motif identification do not necessarily hold, with the ramification that motif studies using these mainstream methods are less able to effectively differentiate between spurious results and events of true statistical significance than is often presented. We show that these difficulties cannot be overcome without revising the methods of statistical analysis used to identify motifs. Conclusions: Present-day methods for the discovery of network motifs, and, indeed, even the methods for defining what they are, are critically reliant on a set of incorrect assumptions, casting a doubt on the scientific validity of motif-driven discoveries. The implications of these findings are therefore far-reaching across diverse areas of biology. [ABSTRACT FROM AUTHOR]

Background: Due to the influence of several factors on the hunting of game meat, we investigated how the seasonality of the environment, the abundance, and the biomass of wild animals, as well as the proximity to these resources, can affect the hunting. Methods: The research was developed with the Fulni-ô people in the municipality of Águas Belas, Agreste of Pernambuco, Northeast of Brazil. In order to do this, we applied snowball sampling to select the participants. Data from potentially useful game species were obtained from lists and semi-structured interviews to register their particular kind of uses, capture periods (daytime, night, or both), preferences, and perceived abundance. The hunters who allowed their game meat captured to be weighed and identified were followed for 1 year. Results: Our records pointed to a vast repertoire of potentially hunting animals. However, we did not verify relationships between the abundance, seasonality, and biomass of the animals that were hunted by the Fulni-ô. We observed a total of 209,866 (kg) of game meat hunted in the studied group, belonging to 23 species, distributed in three taxonomic groups, the birds being the most representative group with 59% of total reported. Conclusion: Such consumption by the group is well below in terms of biomass when compared to other ethnic or local groups in other regions of Brazil, or in Caatinga areas, characterizing an activity much more of cultural character than subsistence. Also, the use of game meat among the Fulni-ô seems to be actively directed to the preferred species, suggesting that in the case of an urbanized indigenous community, where other sources of income are available, the demand for game meat is lower when compared to other ethnic groups. [ABSTRACT FROM AUTHOR]

Background: Halyomorpha halys (Stål), the brown marmorated stink bug, is a highly invasive insect species due in part to its exceptionally high levels of polyphagy. This species is also a nuisance due to overwintering in human-made structures. It has caused significant agricultural losses in recent years along the Atlantic seaboard of North America and in continental Europe. Genomic resources will assist with determining the molecular basis for this species' feeding and habitat traits, defining potential targets for pest management strategies. Results: Analysis of the 1.15-Gb draft genome assembly has identified a wide variety of genetic elements underpinning the biological characteristics of this formidable pest species, encompassing the roles of sensory functions, digestion, immunity, detoxification and development, all of which likely support H. halys' capacity for invasiveness. Many of the genes identified herein have potential for biomolecular pesticide applications. Conclusions: Availability of the H. halys genome sequence will be useful for the development of environmentally friendly biomolecular pesticides to be applied in concert with more traditional, synthetic chemical-based controls. [ABSTRACT FROM AUTHOR]

Phosphatidylserine (PS) is an anionic phospholipid found on the membranes of a variety of organelles throughout the cell, most notably the plasma membrane. Under homeostatic conditions, PS is typically restricted to the inner leaflet of the plasma membrane. However, during cellular activation and/or induction of cell death, PS is externalized on the outer surface via the activation of phospholipid scramblases. Externalized PS not only changes the biochemical and biophysical properties of the plasma membrane but also initiates a series of interactions between endogenous extracellular proteins as well as receptors on neighboring cells to stimulate engulfment (efferocytosis) that influence the surrounding immune milieu. In this thematic series published in Cell Communication and Signaling, we feature review articles that highlight recent work in the field of PS biology, including the biochemistry and physiological significance of PS externalization, therapeutic applications and efforts to target PS, as well as posit open questions that remain in the field. [ABSTRACT FROM AUTHOR]

Background: Due to historical perceptions of Liangshan Yi Autonomous Prefecture (Sichuan Province, China) as being a violent place, and due to its rugged terrain, cultural differences, and relative inaccessibility, few researchers have conducted in-depth ethnobotanical investigations in Liangshan. But wild edible plants (WEPs) are widely consumed by the Yi people of Liangshan, and their associated ethnobotanical knowledge remains relatively unknown, especially outside of China. This study aimed to (1) investigate the WEPs used by the Liangshan Yi, (2) document the traditional knowledge held about these plants, (3) analyze their special preparation methods and consumption habits, and (4) identify species with important cultural significance to the Liangshan Yi. Methods: During 2016-2017, 396 Yi individuals were interviewed in 1 county-level city and 6 counties across Liangshan. Prior informed consent was obtained, and multiple ethnographic methods were utilized, including direct observation, semi-structured interviews, key informant interviews, informal discussions, and field visits. Market surveys were conducted in April, July, and August 2017 by interviewing 38 Yi merchants selling WEPs in 6 Liangshan traditional markets. We collected information about the parts consumed, preparation methods, consumption habits, growth pattern of species, collection months, market prices, and other uses of WEPs. Use values (UVs) were calculated to analyze the relative cultural importance of each WEP. Results: In total, 105 plant species belonging to 97 genera and 62 families were recorded. Rosaceae was the family with the largest number of species (14), and herbs (58 species) were the dominant growth form reported. Fruits (34 species), roots (21 species), and tender shoots (20 species) were the primary plant parts used for snacking and cooking. There were 6 main preparation and consumption methods of WEPs reported, ranging from primary food, famine food, snack, spice, culinary coagulant, and medicine, among a few other uses. The Liangshan Yi mainly collect WEPs from March to October, seldom collecting from November to February. There were 35 species of WEPs sold in the markets we visited in Liangshan. The price of medicinal plants was much higher than the price of food and fruits. In total, we documented 49 species of edible medicinal plants in Liangshan, accounting for 44.7% of all WEPs. They can be used for treating 27 medical conditions, including cough, diarrhea, injury, and headaches. The plants with the highest UVs were Berberis jamesiana (1.92), Pyracantha fortuneana (1.87), and Artemisia capillaris (1.44) indicating that these species are the most commonly used and important to the Liangshan Yi's traditional life and culture. Conclusions: The traditional knowledge of WEPs from the accumulated experience of the Yi people's long period residing in Liangshan reflects the cultural richness of the Yi and the plant diversity of the region. Future research on the nutrition, chemical composition, and bioactivity of the WEPs are needed. Some species with high medicinal value but with sharp wild population decline should be surveyed for resource assessment, conservation, and domestication potential. [ABSTRACT FROM AUTHOR]

Background: To understand biology and differences among various tissues or cell types, one typically searches for molecular features that display characteristic abundance patterns. Several specificity metrics have been introduced to identify tissue-specific molecular features, but these either require an equal number of replicates per tissue or they can't handle replicates at all. Results: We describe a non-parametric specificity score that is compatible with unequal sample group sizes. To demonstrate its usefulness, the specificity score was calculated on all GTEx samples, detecting known and novel tissue-specific genes. A webtool was developed to browse these results for genes or tissues of interest. An example python implementation of SPECS is available at https://github.com/celineeveraert/SPECS. The precalculated SPECS results on the GTEx data are available through a user-friendly browser at specs.cmgg.be. Conclusions: SPECS is a non-parametric method that identifies known and novel specific-expressed genes. In addition, SPECS could be adopted for other features and applications. [ABSTRACT FROM AUTHOR]

Background: Colorectal cancer (CRC) is a heterogeneous disease with a complex biology and a wide number of altered genes such as BRAF, KRAS and PIK3CA. Advances with new-targeted therapies have been achieved and available treating options have prolonged patient's survival. However, BRAF-mutated CRC patients remain unresponsive to available therapies with RAF inhibitors (RAFi) alone or combined with ErbB inhibitors (ErbBi). These unmet needs require further exploitation of oncogenic signaling in order to set up individualized treatments.Methods: To this end, we tested the efficacy of single agent or combined treatments using the BRAFi, vemurafenib and two different ErbBi: panitumumab and afatinib in CRC cells characterized by different molecular phenotypes.Results: Combination strategies with BRAFi and ErbBi achieved a better response in BRAFV600E mutated cells expressing high levels of ErbB2.Conclusions: Our findings support the importance of ErbB2 evaluation in BRAF-mutated CRC patients and its role as a positive predictor factor of response to BRAFi/ErbBi combination. [ABSTRACT FROM AUTHOR]

The vasculature not only transports oxygenated blood, metabolites, and waste products but also serves as a conduit for hormonal communication between distant tissues. Therefore, it is important to maintain homeostasis within the vasculature. Recent studies have greatly expanded our understanding of the regulation of vasculature development and vascular-related diseases at the epigenetic level, including by protein posttranslational modifications, DNA methylation, and noncoding RNAs. Integrating epigenetic mechanisms into the pathophysiologic conceptualization of complex and multifactorial vascular-related diseases may provide promising therapeutic approaches. Several reviews have presented detailed discussions of epigenetic mechanisms not including histone methylation in vascular biology. In this review, we primarily discuss histone methylation in vascular development and maturity, and in vascular diseases. [ABSTRACT FROM AUTHOR]

Background: Understanding the forces that maintain diversity across a range of scales is at the very heart of biology. Frequency-dependent processes are generally recognized as the most central process for the maintenance of ecological diversity. The same is, however, not generally true for genetic diversity. Negative frequency dependent selection, where rare genotypes have an advantage, is often regarded as a relatively weak force in maintaining genetic variation in life history traits because recombination disassociates alleles across many genes. Yet, many regions of the genome show low rates of recombination and genetic variation in such regions (i.e., supergenes) may in theory be upheld by frequency dependent selection. Results: We studied what is essentially a ubiquitous life history supergene (i.e., mitochondrial DNA) in the fruit fly Drosophila subobscura, showing sympatric polymorphism with two main mtDNA genotypes co-occurring in populations world-wide. Using an experimental evolution approach involving manipulations of genotype starting frequencies, we show that negative frequency dependent selection indeed acts to maintain genetic variation in this region. Moreover, the strength of selection was affected by food resource conditions. Conclusions: Our work provides novel experimental support for the view that balancing selection through negative frequency dependency acts to maintain genetic variation in life history genes. We suggest that the emergence of negative frequency dependent selection on mtDNA is symptomatic of the fundamental link between ecological processes related to resource use and the maintenance of genetic variation. [ABSTRACT FROM AUTHOR]