plantMASST - Community-driven chemotaxonomic digitization of plants.

Understanding the distribution of hundreds of thousands of plant metabolites across the plant kingdom presents a challenge. To address this, we curated publicly available LC-MS/MS data from 19,075 plant extracts and developed the plantMASST reference database encompassing 246 botanical families, 1,469 genera, and 2,793 species. This taxonomically focused database facilitates the exploration of plant-derived molecules using tandem mass spectrometry (MS/MS) spectra. This tool will aid in drug discovery, biosynthesis, (chemo)taxonomy, and the evolutionary ecology of herbivore interactions.

Leaf metabolic traits reveal hidden dimensions of plant form and function.

The metabolome is the biochemical basis of plant form and function, but we know little about its macroecological variation across the plant kingdom. Here, we used the plant functional trait concept to interpret leaf metabolome variation among 457 tropical and 339 temperate plant species. Distilling metabolite chemistry into five metabolic functional traits reveals that plants vary on two major axes of leaf metabolic specialization-a leaf chemical defense spectrum and an expression of leaf longevity. Axes are similar for tropical and temperate species, with many trait combinations being viable. However, metabolic traits vary orthogonally to life-history strategies described by widely used functional traits. The metabolome thus expands the functional trait concept by providing additional axes of metabolic specialization for examining plant form and function.

Reductions in home-range size and social interactions among dehorned black rhinoceroses (Diceros bicornis).

Poaching for horns and tusks is driving declines of megaherbivores worldwide, including the critically endangered African black rhinoceros (Diceros bicornis). By proactively dehorning entire rhinoceros populations, conservationists aim to deter poaching and prevent species loss. However, such conservation interventions may have hidden and underestimated effects on animals' behavior and ecology. Here, we combine >15 y of black rhino-monitoring data across 10 South African game reserves, comprising >24,000 sightings of 368 individuals, to determine the consequences of dehorning for black rhino space use and social interactions. While preventative dehorning at these reserves coincided with a nationwide decrease in black rhino mortality from poaching and did not infer increased natural mortality, dehorned black rhinos decreased their home range area by, on average, 11.7 km2 (45.5%) and were 37% less likely to engage in social encounters. We conclude that dehorning black rhinos as an antipoaching measure alters their behavioral ecology, although the potential population-level effects of these changes remain to be determined.

Biotic Interactions in Soil are Underestimated Drivers of Microbial Carbon Use Efficiency.

Microbial carbon use efficiency (CUE)-the balance between microbial growth and respiration-strongly impacts microbial mediated soil carbon storage and is sensitive to many well-studied abiotic environmental factors. However, surprisingly, little work has examined how biotic interactions in soil may impact CUE. Here, we review the theoretical and empirical lines of evidence exploring how biotic interactions affect CUE through the lens of life history strategies. Fundamentally, the CUE of a microbial population is constrained by population density and carrying capacity, which, when reached, causes species to grow more quickly and less efficiently. When microbes engage in interspecific competition, they accelerate growth rates to acquire limited resources and release secondary chemicals toxic to competitors. Such processes are not anabolic and thus constrain CUE. In turn, antagonists may activate one of a number of stress responses that also do not involve biomass production, potentially further reducing CUE. In contrast, facilitation can increase CUE by expanding species realized niches, mitigating environmental stress and reducing production costs of extracellular enzymes. Microbial interactions at higher trophic levels also influence CUE. For instance, predation on microbes can positively or negatively impact CUE by changing microbial density and the outcomes of interspecific competition. Finally, we discuss how plants select for more or less efficient microbes under different contexts. In short, this review demonstrates the potential for biotic interactions to be a strong regulator of microbial CUE and additionally provides a blueprint for future research to address key knowledge gaps of ecological and applied importance for carbon sequestration.

Lowland plant arrival in alpine ecosystems facilitates a decrease in soil carbon content under experimental climate warming.

Climate warming is releasing carbon from soils around the world, constituting a positive climate feedback. Warming is also causing species to expand their ranges into new ecosystems. Yet, in most ecosystems, whether range expanding species will amplify or buffer expected soil carbon loss is unknown. Here, we used two whole-community transplant experiments and a follow-up glasshouse experiment to determine whether the establishment of herbaceous lowland plants in alpine ecosystems influences soil carbon content under warming. We found that warming (transplantation to low elevation) led to a negligible decrease in alpine soil carbon content, but its effects became significant and 52% ± 31% (mean ± 95% confidence intervals) larger after lowland plants were introduced at low density into the ecosystem. We present evidence that decreases in soil carbon content likely occurred via lowland plants increasing rates of root exudation, soil microbial respiration, and CO2 release under warming. Our findings suggest that warming-induced range expansions of herbaceous plants have the potential to alter climate feedbacks from this system, and that plant range expansions among herbaceous communities may be an overlooked mediator of warming effects on carbon dynamics.

In a terrestrial ecosystem, the carbon cycle primarily represents the balance between plants consuming carbon dioxide from the atmosphere and soil microbes releasing carbon stored in the soil into the atmosphere (mostly as carbon dioxide). Given that carbon dioxide traps heat in the atmosphere, the balance of carbon inputs and outputs from an ecosystem can have important consequences for climate change. Rising temperatures caused by climate warming have led plants from lowland ecosystems to migrate uphill and start growing in alpine ecosystems, where temperatures are lower and most carbon is stored in the soil. Soil microbes use carbon stored in the soil and exuded from plants to grow, and they release this carbon ­ in the form of carbon dioxide ­ into the atmosphere through respiration. Walker et al. wanted to know how the arrival of lowland plants in alpine ecosystems under climate warming would affect carbon stores in the soil. To answer this question, Walker et al. simulated warmer temperatures by moving turfs (plants and soil) from alpine ecosystems to a warmer downhill site and planting lowland plants into the turfs. They compared the concentration of soil carbon in these turfs to that of soil in alpine turfs that had not been moved downhill and had no lowland plants. Their results showed that the warmed turfs containing lowland plants had a lower concentration of soil carbon. This suggests that climate warming will lead to more soil carbon being released into the atmosphere if lowland plants also migrate into alpine ecosystems. Walker et al. also wanted to know the mechanism through which lowland plants were decreasing soil carbon concentration under warming. They find that lowland plants probably release more small molecules into the soil than alpine plants. Soil microbes use the carbon and nutrients in these molecules to break down more complex molecules in the soil, thereby releasing nutrients and carbon that can then be used in respiration. This finding suggests that soil microbes breakdown and respire native soil carbon faster in the presence of lowland plants, releasing more carbon dioxide into the atmosphere and reducing carbon stores in the soil. Walker et al.'s results reveal a new mechanism through which uphill migration of lowland plants could increase the effects of climate change, in a feedback loop. Further research as to whether this mechanism occurs in different regions and ecosystems could help to quantify the magnitude of this feedback and allow scientists to make more accurate predictions about climate change.

Tessier 30 Facial Clefts-A Literature Review of 72 Cases (1996-2020), Suggested Treatment Protocol, Outcome Measures, Minimum Dataset for Future Case Reports, and Registries.

INTRODUCTION: Tessier 30 facial cleft is a rare anomaly presenting in the soft and hard tissues over the central lower face. Owing to the rarity of cases and difficulty of treatment, there is no universally accepted surgical management strategy. The last comprehensive literature review of Tessier 30 clefts was in 1996. This report aims to update the literature to inform decision-making on treating Tessier 30 cases. METHODOLOGY: A literature search was performed. PubMed, SCOPUS, and OVID databases were searched. A total of 72 cases in 51 articles were analyzed, looking at demographics, extent of cleft, parent health, family history, procedures, follow-up, existence of other anomalies, and stages of repair. RESULTS: Surgeons are increasingly choosing to repair Tessier 30 defects in one rather than multiple stages. Of the 72 cases studied, only 31 had documented the completed repair of the cleft. All completed soft tissue only defects were repaired in 1 stage of repair (n = 11). Where both soft tissue and mandible was involved (n = 20), 55% (n = 11) had undergone 1-stage repair to address the Tessier 30 cleft. DISCUSSION: We argue that a single-stage approach is preferable to multistage. Primary mucogingivoperiosteoplasty should be undertaken in children at the time of management of the soft tissue cleft. The timing of this procedure should be in the latter half of the first year of life, as this is when mandibular symphyseal fusion normally occurs. We have suggested a treatment protocol and we hope that future case reports use our minimum data set.

Value of choice.

Accounts of the value of patient choice in contemporary medical ethics typically focus on the act of choosing. Being the one to choose, it is argued, can be valuable either because it enables one to bring about desired outcomes, or because it is a way of enacting one's autonomy. This paper argues that all such accounts miss something important. In some circumstances, it is having the opportunity to choose, not the act of choosing, that is valuable. That is because in many situations whether one has, or is denied, that opportunity conveys how one is seen. In particular, it conveys whether or not one is seen as an equal and competent member of society. Adequately recognising this fact has implications for what healthcare professionals should do, ones that require a move away from the current focus on autonomy. The paper draws out these implications by focusing on patients who may struggle to be recognised as competent and equal members of society, and whose autonomy may thus itself sometimes be in question.

Open and reusable annotated mass spectrometry dataset of a chemodiverse collection of 1,600 plant extracts.

As privileged structures, natural products often display potent biological activities. However, the discovery of novel bioactive scaffolds is often hampered by the chemical complexity of the biological matrices they are found in. Large natural extract collections are thus extremely valuable for their chemical novelty potential but also complicated to exploit in the frame of drug-discovery projects. In the end, it is the pure chemical substances that are desired for structural determination purposes and bioactivity evaluation. Researchers interested in the exploration of large and chemodiverse extract collections should thus establish strategies aiming to efficiently tackle such chemical complexity and access these structures. Establishing carefully crafted digital layers documenting the spectral and chemical complexity as well as bioactivity results of natural extracts collections can help prioritize time-consuming but mandatory isolation efforts. In this note, we report the results of our initial exploration of a collection of 1,600 plant extracts in the frame of a drug-discovery effort. After describing the taxonomic coverage of this collection, we present the results of its liquid chromatography high-resolution mass spectrometric profiling and the exploitation of these profiles using computational solutions. The resulting annotated mass spectral dataset and associated chemical and taxonomic metadata are made available to the community, and data reuse cases are proposed. We are currently continuing our exploration of this plant extract collection for drug-discovery purposes (notably looking for novel antitrypanosomatids, anti-infective and prometabolic compounds) and ecometabolomics insights. We believe that such a dataset can be exploited and reused by researchers interested in computational natural products exploration.

Hematological Paraneoplastic Syndrome and Heparin-Induced Thrombocytopenia in Untreated Parotid Acinic Cell Carcinoma - A Case Report.

RATIONALE: Acinic cell carcinoma (ACC) is a rare and indolent malignancy commonly found in the parotid gland. This can give rise to paraneoplastic syndromes, which represent the clinical manifestations of indirect and remote events produced by tumour metabolites. PATIENT CONCERNS: A 38-year-old Afro-Caribbean female suffered an indolent parotid mass. She only presented to our tertiary center when it started to ulcerate and bleed. DIAGNOSIS: She was diagnosed with advanced parotid ACC. She also went on to develop an hematological paraneoplastic syndrome resulting in venous thrombi. This was complicated by her developing heparin-induced thrombocytopenia (HIT). TREATMENT: A difficult multidisciplinary decision was made to proceed with surgery despite her extremely poor condition. OUTCOMES: After the surgery, the patient made a full recovery. TAKE-AWAY LESSONS: ACC is a relatively uncommon and indolent malignancy that is usually found in the parotid gland. It can be associated with a hematological paraneoplastic syndrome and further complicated by iatrogenic HIT.

Spatial and evolutionary predictability of phytochemical diversity.

To cope with environmental challenges, plants produce a wide diversity of phytochemicals, which are also the source of numerous medicines. Despite decades of research in chemical ecology, we still lack an understanding of the organization of plant chemical diversity across species and ecosystems. To address this challenge, we hypothesized that molecular diversity is not only related to species diversity, but also constrained by trophic, climatic, and topographical factors. We screened the metabolome of 416 vascular plant species encompassing the entire alpine elevation range and four alpine bioclimatic regions in order to characterize their phytochemical diversity. We show that by coupling phylogenetic information, topographic, edaphic, and climatic variables, we predict phytochemical diversity, and its inherent composition, of plant communities throughout landscape. Spatial mapping of phytochemical diversity further revealed that plant assemblages found in low to midelevation habitats, with more alkaline soils, possessed greater phytochemical diversity, whereas alpine habitats possessed higher phytochemical endemism. Altogether, we present a general tool that can be used for predicting hotspots of phytochemical diversity in the landscape, independently of plant species taxonomic identity. Such an approach offers promising perspectives in both drug discovery programs and conservation efforts worldwide.

Application of the Lomb-Scargle Periodogram to InvestigateHeart Rate Variability during Haemodialysis.

Short-term cardiovascular compensatory responses to perturbations in the circulatory system caused by haemodialysis can be investigated by the spectral analysis of heart rate variability, thus providing an important variable for categorising individual patients' response, leading to a more personalised treatment. This is typically accomplished by resampling the irregular heart rate to generate an equidistant time series prior to spectral analysis, but resampling can further distort the data series whose interpretation can already be compromised by the presence of artefacts. The Lomb-Scargle periodogram provides a more direct method of spectral analysis as this method is specifically designed for large, irregularly sampled, and noisy datasets such as those obtained in clinical settings. However, guidelines for preprocessing patient data have been established in combination with equidistant time-series methods and their validity when used in combination with the Lomb-Scargle approach is missing from literature. This paper examines the effect of common preprocessing methods on the Lomb-Scargle power spectral density estimate using both real and synthetic heart rate data and will show that many common techniques for identifying and editing suspect data points, particularly interpolation and replacement, will distort the resulting power spectrum potentially misleading clinical interpretations of the results. Other methods are proposed and evaluated for use with the Lomb-Scargle approach leading to the main finding that suspicious data points should be excluded rather than edited, and where required, denoising of the heart rate signal can be reliably accomplished by empirical mode decomposition. Some additional methods were found to be particularly helpful when used in conjunction with the Lomb-Scargle periodogram, such as the use of a false alarm probability metric to establish whether spectral estimates are valid and help automate the assessment of valid heart rate records, potentially leading to greater use of this powerful technique in a clinical setting.

Patients' perception of using a smartphone light source in the clinical environment.

Introduction A satisfactory light source is of paramount importance during an oral head and neck examination. It has become common practice for the light source on a smartphone to be used during inpatient intra-oral examination. We determined if patients identified the use of a smartphone as a light source, during head and neck examinations, as unprofessional.Methods and materials A clinical photograph illustrating professional errors was presented to patients as a pilot survey (n = 10); a smartphone camera flash being used as a light source was featured. Patients were then asked which aspects they considered unprofessional. Following staff training and improvements to the survey wording, the same photo was presented to patients (n = 150) as the main study.Results Of the patients surveyed, 97% considered the use of a smartphone in the staged clinical photograph as unprofessional. They also noted: a clinician sitting on the bed (88%), clinicians not wearing gloves (81%), lack of privacy/curtain not drawn (62%), long hair not tied back (50%), a clinician's name badge not visible (23%), clinician bare below the elbows (15%) and clinician not wearing a tie (12%).Conclusions This is the first piece of research into the use of a smartphone light source within clinical examination. The use of a smart phone light source during clinical examination was the most reported 'error' and was recognised more than a clinician not wearing gloves. Eighty-five percent of patients considered the use of a smartphone light source unprofessional. Authors, therefore, do not advocate the use of a smartphone light source in the clinical care of patients.

Ecometabolomics for a Better Understanding of Plant Responses and Acclimation to Abiotic Factors Linked to Global Change.

The number of ecometabolomic studies, which use metabolomic analyses to disentangle organisms' metabolic responses and acclimation to a changing environment, has grown exponentially in recent years. Here, we review the results and conclusions of ecometabolomic studies on the impacts of four main drivers of global change (increasing frequencies of drought episodes, heat stress, increasing atmospheric carbon dioxide (CO2) concentrations and increasing nitrogen (N) loads) on plant metabolism. Ecometabolomic studies of drought effects confirmed findings of previous target studies, in which most changes in metabolism are characterized by increased concentrations of soluble sugars and carbohydrate derivatives and frequently also by elevated concentrations of free amino acids. Secondary metabolites, especially flavonoids and terpenes, also commonly exhibited increased concentrations when drought intensified. Under heat and increasing N loads, soluble amino acids derived from glutamate and glutamine were the most responsive metabolites. Foliar metabolic responses to elevated atmospheric CO2 concentrations were dominated by greater production of monosaccharides and associated synthesis of secondary metabolites, such as terpenes, rather than secondary metabolites synthesized along longer sugar pathways involving N-rich precursor molecules, such as those formed from cyclic amino acids and along the shikimate pathway. We suggest that breeding for crop genotypes tolerant to drought and heat stress should be based on their capacity to increase the concentrations of C-rich compounds more than the concentrations of smaller N-rich molecules, such as amino acids. This could facilitate rapid and efficient stress response by reducing protein catabolism without compromising enzymatic capacity or increasing the requirement for re-transcription and de novo biosynthesis of proteins.

Examination of the neck when a patient complains of shoulder pain: a global survey of current practice (2019).

BACKGROUND: Shoulder pain is a common musculoskeletal problem. Despite this, much uncertainty still exists regarding diagnosis, prognosis and effectiveness of treatments. One diagnostic challenge is determining the role of the neck when a patient complains of shoulder pain. The aim of this survey was to investigate healthcare professionals' indications for examining the neck in this case and subsequent methods used. METHODS: An online survey was developed and distributed via Twitter and the authors' professional networks. Responses were collected over a 4-week period in 2019. RESULTS: In total, 918 respondents replied; 804 completed the full survey. The majority were physiotherapists. Over 80% would examine the neck of patients presenting with shoulder pain. The most commonly used method was neck active range-of-movement testing (n = 822/95.3%), followed by neurological examination (n = 713/78.1%). Less commonly used tests were neck resistance testing, palpation of the neck and Spurling's test. Fewer numbers (n = 176/22%) resorted to using diagnostic tests such as imaging. CONCLUSIONS: This survey provides some insight as to how healthcare practitioners examine the neck when a patient complains of shoulder pain. Most would examine based on anterolateral shoulder pain, using variable combinations of movement, resistance, neurological and palpation/other testing. A minority would perform diagnostics or imaging. The results of the survey highlight that practice in this area is mixed, which may be due to uncertainty regarding optimal methods. This highlights the need for further work to understand this clinical dilemma better.

Increased microbial growth, biomass, and turnover drive soil organic carbon accumulation at higher plant diversity.

Species-rich plant communities have been shown to be more productive and to exhibit increased long-term soil organic carbon (SOC) storage. Soil microorganisms are central to the conversion of plant organic matter into SOC, yet the relationship between plant diversity, soil microbial growth, turnover as well as carbon use efficiency (CUE) and SOC accumulation is unknown. As heterotrophic soil microbes are primarily carbon limited, it is important to understand how they respond to increased plant-derived carbon inputs at higher plant species richness (PSR). We used the long-term grassland biodiversity experiment in Jena, Germany, to examine how microbial physiology responds to changes in plant diversity and how this affects SOC content. The Jena Experiment considers different numbers of species (1-60), functional groups (1-4) as well as functional identity (small herbs, tall herbs, grasses, and legumes). We found that PSR accelerated microbial growth and turnover and increased microbial biomass and necromass. PSR also accelerated microbial respiration, but this effect was less strong than for microbial growth. In contrast, PSR did not affect microbial CUE or biomass-specific respiration. Structural equation models revealed that PSR had direct positive effects on root biomass, and thereby on microbial growth and microbial biomass carbon. Finally, PSR increased SOC content via its positive influence on microbial biomass carbon. We suggest that PSR favors faster rates of microbial growth and turnover, likely due to greater plant productivity, resulting in higher amounts of microbial biomass and necromass that translate into the observed increase in SOC. We thus identify the microbial mechanism linking species-rich plant communities to a carbon cycle process of importance to Earth's climate system.

A systemic overreaction to years versus decades of warming in a subarctic grassland ecosystem.

Temperature governs most biotic processes, yet we know little about how warming affects whole ecosystems. Here we examined the responses of 128 components of a subarctic grassland to either 5-8 or >50 years of soil warming. Warming of >50 years drove the ecosystem to a new steady state possessing a distinct biotic composition and reduced species richness, biomass and soil organic matter. However, the warmed state was preceded by an overreaction to warming, which was related to organism physiology and was evident after 5-8 years. Ignoring this overreaction yielded errors of >100% for 83 variables when predicting their responses to a realistic warming scenario of 1 °C over 50 years, although some, including soil carbon content, remained stable after 5-8 years. This study challenges long-term ecosystem predictions made from short-term observations, and provides a framework for characterization of ecosystem responses to sustained climate change.

Secretion of functionally active complement factor H related protein 5 (FHR5) by primary tumour cells derived from Glioblastoma Multiforme patients.

The complement system is an important humoral immune surveillance mechanism against tumours. However, many malignant tumours are resistant to complement mediated lysis. Here, we report secretion of complement factor H related protein 5 (FHR5) by primary tumour cells derived from Glioblastoma multiforme (GBM) patients. We investigated whether the secreted FHR5 exhibited functional activity similar to factor H, including inhibition of complement mediated lysis, acting as a co-factor for factor I mediated cleavage of C3b, and decay acceleration of C3 convertase. Immunoblotting analysis of primary GBM cells (B30, B31 and B33) supernatant showed the active secretion of FHR5, but not of Factor H. ELISA revealed that the secretion of soluble GBM-FHR5 by cultured GBM cells increased in a time-dependent manner. Primary GBM-FHR5 inhibited complement mediated lysis, possessed co-factor activity for factor I mediated cleavage and displayed decay acceleration of C3 convertase. In summary, we detected the secretion of FHR5 by primary GBM cells B30, B31 and B33. The results demonstrated that GBM-FHR5 shares biological function with FH as a mechanism primary GBM cells potentially use to resist complement mediated lysis.

Screening of the cervical spine in subacromial shoulder pain: A systematic review.

BACKGROUND: Subacromial shoulder pain is a common clinical presentation with much diagnostic uncertainty. Some of this uncertainty relates to the involvement of the cervical spine as a source or contribution to subacromial shoulder pain. Currently, there is no accepted method of screening of the cervical spine in the presence of subacromial shoulder pain, which risks patients receiving misguided and/or ineffective interventions. OBJECTIVE: To evaluate approaches used to screen the cervical spine in patients with subacromial shoulder pain. DESIGN: Systematic review of randomized controlled trials. METHODS: Electronic searches of PEDro and MEDLINE to December 2016 were conducted. Randomized controlled trials evaluating the effectiveness of interventions within the current scope of physiotherapy comprising of adult patients complaining of subacromial shoulder pain were included. Data relating to the method of cervical spine screening were extracted and synthesized categorically. RESULTS: One hundred and two studies were included. Twenty-six (25.5%) were categorized as "No method of screening undertaken or reported," 49 (48.0%) were categorized as "Localized cervical spine symptoms and/or radiculopathy/radicular pain," nine (8.8%) were categorized as "Cervical examination," two (2.0%) were categorized as "Manual testing," two (2.0%) were categorized as "History of cervical surgery," and 14 (13.7%) were categorized as using "Combined approaches." CONCLUSION: Examination of the cervical spine in patients with subacromial shoulder pain is variable in randomized controlled trials. In many instances, no or minimal attempts to screen were undertaken or reported. This has potential research and management implications and further research is indicated to facilitate development of this aspect of examination.

Tessier 30 Median Mandibular Hard and Soft Tissue Cleft, One-Stage Reconstruction Using a Template-Guided Resorbable "U"-Shaped Plate.

Midline clefts of the lower lip, tongue, and mandible are a rare type of facial cleft classified as "Tessier 30." We present the case of a female patient with an isolated Tessier 30 facial cleft affecting the tongue, lower lip, and mandibular symphysis with ankyloglossia. This was reconstructed with a template-guided resorbable "U"-shaped plate at 10 months of age. The procedure was carried out in one stage, which avoided the need for a repeat general anesthetic for the patient. We had a successful outcome with normal dental eruption and we believe such an approach could be considered as a relevant treatment modality for future cases.