The origin and speciation of orchids

SummaryOrchids constitute one of the most spectacular radiations of flowering plants. However, their origin, spread across the globe, and hotspots of speciation remain uncertain due to the lack of an up-to-date phylogeographic analysis.We present a new Orchidaceae phylogeny based on combined high-throughput and Sanger sequencing data, covering all five subfamilies, 17/22 tribes, 40/49 subtribes, 285/736 genera, and c. 7% (1921) of the 29 524 accepted species, and use it to infer geographic range evolution, diversity, and speciation patterns by adding curated geographical distributions from the World Checklist of Vascular Plants.The orchids' most recent common ancestor is inferred to have lived in Late Cretaceous Laurasia. The modern range of Apostasioideae, which comprises two genera with 16 species from India to northern Australia, is interpreted as relictual, similar to that of numerous other groups that went extinct at higher latitudes following the global climate cooling during the Oligocene. Despite their ancient origin, modern orchid species diversity mainly originated over the last 5 Ma, with the highest speciation rates in Panama and Costa Rica.These results alter our understanding of the geographic origin of orchids, previously proposed as Australian, and pinpoint Central America as a region of recent, explosive speciation

Finishing the euchromatic sequence of the human genome

The sequence of the human genome encodes the genetic instructions for human physiology, as well as rich information about human evolution. In 2001, the International Human Genome Sequencing Consortium reported a draft sequence of the euchromatic portion of the human genome. Since then, the international collaboration has worked to convert this draft into a genome sequence with high accuracy and nearly complete coverage. Here, we report the result of this finishing process. The current genome sequence (Build 35) contains 2.85 billion nucleotides interrupted by only 341 gaps. It covers ∼99% of the euchromatic genome and is accurate to an error rate of ∼1 event per 100,000 bases. Many of the remaining euchromatic gaps are associated with segmental duplications and will require focused work with new methods. The near-complete sequence, the first for a vertebrate, greatly improves the precision of biological analyses of the human genome including studies of gene number, birth and death. Notably, the human enome seems to encode only 20,000-25,000 protein-coding genes. The genome sequence reported here should serve as a firm foundation for biomedical research in the decades ahead

The Changing Landscape for Stroke\ua0Prevention in AF: Findings From the GLORIA-AF Registry Phase 2

Background GLORIA-AF (Global Registry on Long-Term Oral Antithrombotic Treatment in Patients with Atrial Fibrillation) is a prospective, global registry program describing antithrombotic treatment patterns in patients with newly diagnosed nonvalvular atrial fibrillation at risk of stroke. Phase 2 began when dabigatran, the first non\u2013vitamin K antagonist oral anticoagulant (NOAC), became available. Objectives This study sought to describe phase 2 baseline data and compare these with the pre-NOAC era collected during phase 1. Methods During phase 2, 15,641 consenting patients were enrolled (November 2011 to December 2014); 15,092 were eligible. This pre-specified cross-sectional analysis describes eligible patients\u2019 baseline characteristics. Atrial fibrillation disease characteristics, medical outcomes, and concomitant diseases and medications were collected. Data were analyzed using descriptive statistics. Results Of the total patients, 45.5% were female; median age was 71 (interquartile range: 64, 78) years. Patients were from Europe (47.1%), North America (22.5%), Asia (20.3%), Latin America (6.0%), and the Middle East/Africa (4.0%). Most had high stroke risk (CHA2DS2-VASc [Congestive heart failure, Hypertension, Age  6575 years, Diabetes mellitus, previous Stroke, Vascular disease, Age 65 to 74 years, Sex category] score  652; 86.1%); 13.9% had moderate risk (CHA2DS2-VASc = 1). Overall, 79.9% received oral anticoagulants, of whom 47.6% received NOAC and 32.3% vitamin K antagonists (VKA); 12.1% received antiplatelet agents; 7.8% received no antithrombotic treatment. For comparison, the proportion of phase 1 patients (of N = 1,063 all eligible) prescribed VKA was 32.8%, acetylsalicylic acid 41.7%, and no therapy 20.2%. In Europe in phase 2, treatment with NOAC was more common than VKA (52.3% and 37.8%, respectively); 6.0% of patients received antiplatelet treatment; and 3.8% received no antithrombotic treatment. In North America, 52.1%, 26.2%, and 14.0% of patients received NOAC, VKA, and antiplatelet drugs, respectively; 7.5% received no antithrombotic treatment. NOAC use was less common in Asia (27.7%), where 27.5% of patients received VKA, 25.0% antiplatelet drugs, and 19.8% no antithrombotic treatment. Conclusions The baseline data from GLORIA-AF phase 2 demonstrate that in newly diagnosed nonvalvular atrial fibrillation patients, NOAC have been highly adopted into practice, becoming more frequently prescribed than VKA in Europe and North America. Worldwide, however, a large proportion of patients remain undertreated, particularly in Asia and North America. (Global Registry on Long-Term Oral Antithrombotic Treatment in Patients With Atrial Fibrillation [GLORIA-AF]; NCT01468701

Impact of COVID-19 on cardiovascular testing in the United States versus the rest of the world

Objectives: This study sought to quantify and compare the decline in volumes of cardiovascular procedures between the United States and non-US institutions during the early phase of the coronavirus disease-2019 (COVID-19) pandemic. Background: The COVID-19 pandemic has disrupted the care of many non-COVID-19 illnesses. Reductions in diagnostic cardiovascular testing around the world have led to concerns over the implications of reduced testing for cardiovascular disease (CVD) morbidity and mortality. Methods: Data were submitted to the INCAPS-COVID (International Atomic Energy Agency Non-Invasive Cardiology Protocols Study of COVID-19), a multinational registry comprising 909 institutions in 108 countries (including 155 facilities in 40 U.S. states), assessing the impact of the COVID-19 pandemic on volumes of diagnostic cardiovascular procedures. Data were obtained for April 2020 and compared with volumes of baseline procedures from March 2019. We compared laboratory characteristics, practices, and procedure volumes between U.S. and non-U.S. facilities and between U.S. geographic regions and identified factors associated with volume reduction in the United States. Results: Reductions in the volumes of procedures in the United States were similar to those in non-U.S. facilities (68% vs. 63%, respectively; p = 0.237), although U.S. facilities reported greater reductions in invasive coronary angiography (69% vs. 53%, respectively; p < 0.001). Significantly more U.S. facilities reported increased use of telehealth and patient screening measures than non-U.S. facilities, such as temperature checks, symptom screenings, and COVID-19 testing. Reductions in volumes of procedures differed between U.S. regions, with larger declines observed in the Northeast (76%) and Midwest (74%) than in the South (62%) and West (44%). Prevalence of COVID-19, staff redeployments, outpatient centers, and urban centers were associated with greater reductions in volume in U.S. facilities in a multivariable analysis. Conclusions: We observed marked reductions in U.S. cardiovascular testing in the early phase of the pandemic and significant variability between U.S. regions. The association between reductions of volumes and COVID-19 prevalence in the United States highlighted the need for proactive efforts to maintain access to cardiovascular testing in areas most affected by outbreaks of COVID-19 infection

Chapter 13 - Business Continuity as a Means to Strengthen Disaster Risk Reduction in a Coastal Community of Oyster Farmers

The Philippines is located in a region where climate and geological hazards often lead to disasters affecting many lives of its citizens. This paper discusses how business continuity initiatives were used to introduce and strengthen DRR for a community of oyster farmers in the Philippines; that are among the poor and marginalized sectors vulnerable to coastal hazards. The geological hazards that may affect the livelihood of those oyster farmers were assessed and the appropriate business continuity and DRR initiatives were recommended. The success of these initiatives depends on a strong collaboration between the partner community organization of oyster farmers; business sector; government and higher educational institutions

Three questions for identifying chemically intolerant individuals in clinical and epidemiological populations: The Brief Environmental Exposure and Sensitivity Inventory (BREESI).

The Quick Environmental Exposure and Sensitivity Inventory (QEESI) is a validated questionnaire used worldwide to assess intolerances to chemicals, foods, and drugs, and has emerged as the gold standard for assessing chemical intolerance (CI). Despite a reported prevalence of 8-33%, epidemiological studies and routine primary care clinics rarely assess CI. To help address this gap, we developed the Brief Environmental Exposure and Sensitivity Inventory (BREESI)-a 3-item CI screening tool. We tested the BREESI's potential to predict whether an individual is likely to be classified as chemically intolerant if administered the 50-item QEESI. We recruited 293 participants from a university-based primary care clinic and through online participation. The statistical sensitivity, specificity, and positive and negative predictive values of the BREESI were calculated against the validated QEESI. Ninety percent (90%) of participants answering "yes" to all three items on the BREESI fit the QEESI criteria for being very suggestive of CI based upon their chemical intolerance and symptom scores (positive predictive value = 90%). For participants endorsing two items, 93% were classified as either very suggestive (39%) or suggestive (54%) of CI (positive predictive value = 87%). Of those endorsing only one item, 13% were classified as very suggestive of CI, and 70% as suggestive. Of those answering "No" to all of the BREESI items, 95% were classified as not suggestive of CI (i.e., negative predictive value = 95%). The BREESI is a versatile screening tool for assessing potential CI useful for clinical and epidemiological applications, based upon individuals' past adverse responses in a variety of settings. Just as health care professionals routinely inquire about latex allergy to prevent adverse reactions, the BREESI provides an essential screen for CI. Together, the BREESI and QEESI provide new diagnostic tools that may help predict and prevent future adverse reactions to chemicals, foods, and drugs

What initiates chemical intolerance? Findings from a large population-based survey of U.S. adults

Abstract Background Worldwide observations point to a two-stage theory of disease called Toxicant-Induced Loss of Tolerance (TILT): Stage I, Initiation by an acute high-level or repeated lower-level chemical exposures, followed by Stage II, Triggering of multisystem symptoms by previously tolerated, structurally diverse chemical inhalants, foods/food additives and drugs. Until recently, there was no known biological mechanism that could explain these observations. In 2021, we published a plausible and researchable two-stage biomechanism for TILT involving mast cells: Stage I, Initiation via mast cell sensitization; Stage II, Triggering of mast cell degranulation by previously tolerated exposures, resulting in the release of thousands of mediators, including histamine and a host of inflammatory molecules. The objective of this study was to identify common TILT initiators. Methods A randomized, population-based sample of 10,981 U.S. adults responded to a survey which included items concerning medical diagnoses, personal exposures, antibiotic use, and several possible initiators of Chemical Intolerance (CI). CI was assessed using the internationally validated Quick Environmental Exposure and Sensitivity Inventory (QEESI). Participants identified as chemically intolerant were asked to recall when their intolerances began and what they felt had initiated their condition. Results Twenty percent met QEESI criteria for TILT, approximately half of whom identified one or more initiating exposures. Initiators in order of frequency were mold (15.6%), pesticides (11.5%), remodeling/new construction (10.7%), medical/surgical procedures (11.3%), fires/combustion products (6.4%), and implants (1.6%). Protracted antibiotic use for infections involving the prostate, skin, tonsils, gastrointestinal tract, and sinuses were strongly associated with TILT/CI (OR > 2). Discussion Participants identified two broad classes of TILT initiators: 1) fossil fuel-derived toxicants (i.e., from coal, oil, natural gas), their combustion products, and/or synthetic organic chemical derivatives, e.g., pesticides, implants, drugs/antibiotics, volatile organic compounds (VOCs); and 2) biogenic toxicants, e.g., particles and VOCs from mold or algal blooms. One in four primary care patients suffers from Medically Unexplained Symptoms (MUS). Doctors in primary care, neurology, psychiatry, psychology, occupational medicine, and allergy/immunology would be well-advised to include TILT in their differential diagnosis of patients with so-called MUS. Because 20% of U.S. adults meet QEESI criteria for CI, the role of contemporary exposures in initiating and exacerbating these conditions via mast cells needs our immediate attention. There is a concomitant need for policies and practices that reduce initiating exposures as well as ubiquitous and often unavoidable triggers such as fragranced personal care, cleaning, and laundry products in multi-occupant housing, workplaces, medical settings, schools, places of worship, and all public buildings—literally anywhere air is shared. Fossil fuels are assaulting humans and other animal species both from within via mast cell sensitization, and from without via climate change

Microplastics Contamination in the Fishes of Selected Sites in Pasig River and Marikina River in the Philippines

Microplastics (MPs), \u3c5 mm in size, are a concerning pollutant in bodies of water because they can be ingested by biological organisms, posing risks to humans and the environment. This study assessed the extent of MPs contamination in various fish species (Oreochromis niloticus, Arius manillensis, and Pterygoplichthys spp.) in selected sites along two major river systems in the Philippines – Pasig and Marikina Rivers. An optimized Raman microspectroscopy technique was used for imaging and identification of MPs using a mean laser spot size of about 1 μm, which is advantageous in the identification of fibers which have small diameters (\u3c50 μm). It also allowed the simultaneous identification of MPs and their pigment additives, which in turn enabled the tracing of possible sources of these MPs. This is important because the fate and accumulation of MPs in rivers systems, as well as its toxicity is dependent on various factors including polymer type and surface chemistry. Majority of the MPs identified from all the fish species were composed of polypropylene and polyethylene in the form of fragments, which reflects both the widespread use of these polymers for packaging and their environmental fate as riverine plastic debris. Moreover, the detection of MPs in the fish species may affect the food chain and eventually pose health risks for humans. The study could provide guidance on waste and environmental water management in the surrounding region

Submarine Groundwater Discharge Releases CO2 to a Coral Reef

Submarine groundwater discharge (SGD) flows into coral reefs. In volcanically active areas; the incoming groundwater is typically CO2-rich which can alter the carbon balance and views on how coral reefs function at prevailing high CO2. We quantified dynamic hydrothermal SGD and CO2 fluxes to a Philippine coral reef over a spring-neap tidal cycle. SGD rates; with mean of 35 cm d−1 and 5−95% range of 0−147.8 cm d−1 . The groundwater-CO2 fluxes (266 mmol m d−1; range: 0−1111 mmol m2 d−1) were up to ∼300-fold larger than evasion of CO2 to the atmosphere. The reef seawater pCO2 (493 μatm; range: 421−680 μatm) remained above atmospheric values and spanned the upper end of the range of atmospheric levels (400−500 μatm) expected for the next century. Because of the hydrothermal SGD; the reef has prevailing above-atmospheric CO2 and is a source to the atmosphere and nearby waters

Submarine Groundwater and Vent Discharge in a Volcanic Area Associated With Coastal Acidification

We investigated submarine groundwater discharge (SGD) in a volcanic coastal area that hosts the world\u27s most biodiverse reefs. Measurements of 222Rn activity in coastal seawater, a tracer for groundwater, indicated prevalent SGD. In areas where seawater 222Rn activity was generally higher, we discovered hydrothermal springs emitting acidic waters (pH ~5.4–6.0) and venting magmatic CO2 that brought local pCO2 levels up to 95,000 ppm. The collection of vents raised CO2 and lowered pH over 1–2 km of coastline. The hydrogen and oxygen isotope compositions of water and chloride concentration revealed that the springs discharge recirculated seawater mixed variably with terrestrial groundwater. Shallower springs and pore water have a higher proportion of terrestrial groundwater than deeper springs, which emit mostly recirculated seawater. This suggests that different SGD mechanisms are present. The SGD could be contributing to the evolution and function of the biodiverse ecosystem, but it also represents myriad pathways for contamination