Do deep learning models make a difference in the identification of antimicrobial peptides?

In the last few decades, antimicrobial peptides (AMPs) have been explored as an alternative to classical antibiotics, which in turn motivated the development of machine learning models to predict antimicrobial activities in peptides. The first generation of these predictors was filled with what is now known as shallow learning-based models. These models require the computation and selection of molecular descriptors to characterize each peptide sequence and train the models. The second generation, known as deep learning-based models, which no longer requires the explicit computation and selection of those descriptors, started to be used in the prediction task of AMPs just four years ago. The superior performance claimed by deep models regarding shallow models has created a prevalent inertia to using deep learning to identify AMPs. However, methodological flaws and/or modeling biases in the building of deep models do not support such superiority. Here, we analyze the main pitfalls that led to establish biased conclusions on the leading performance of deep models. Also, we analyze whether deep models truly contribute to achieve better predictions than shallow models by performing fair studies on different state-of-the-art benchmarking datasets. The experiments reveal that deep models do not outperform shallow models in the classification of AMPs, and that both types of models codify similar chemical information since their predictions are highly similar. Thus, according to the currently available datasets, we conclude that the use of deep learning could not be the most suitable approach to develop models to identify AMPs, mainly because shallow models achieve comparable-to-superior performances and are simpler (Ockham's razor principle). Even so, we suggest the use of deep learning only when its capabilities lead to obtaining significantly better performance gains worth the additional computational cost.

Handcrafted versus non-handcrafted (self-supervised) features for the classification of antimicrobial peptides: complementary or redundant?

Antimicrobial peptides (AMPs) have received a great deal of attention given their potential to become a plausible option to fight multi-drug resistant bacteria as well as other pathogens. Quantitative sequence-activity models (QSAMs) have been helpful to discover new AMPs because they allow to explore a large universe of peptide sequences and help reduce the number of wet lab experiments. A main aspect in the building of QSAMs based on shallow learning is to determine an optimal set of protein descriptors (features) required to discriminate between sequences with different antimicrobial activities. These features are generally handcrafted from peptide sequence datasets that are labeled with specific antimicrobial activities. However, recent developments have shown that unsupervised approaches can be used to determine features that outperform human-engineered (handcrafted) features. Thus, knowing which of these two approaches contribute to a better classification of AMPs, it is a fundamental question in order to design more accurate models. Here, we present a systematic and rigorous study to compare both types of features. Experimental outcomes show that non-handcrafted features lead to achieve better performances than handcrafted features. However, the experiments also prove that an improvement in performance is achieved when both types of features are merged. A relevance analysis reveals that non-handcrafted features have higher information content than handcrafted features, while an interaction-based importance analysis reveals that handcrafted features are more important. These findings suggest that there is complementarity between both types of features. Comparisons regarding state-of-the-art deep models show that shallow models yield better performances both when fed with non-handcrafted features alone and when fed with non-handcrafted and handcrafted features together.

Isolation by resistance explains genetic diversity in the Arremon brushfinches of northern Mesoamerica.

Genetic differentiation between and within natural populations is the result of the joint effects of neutral and adaptative processes. In addition, the spatial arrangement of the landscape promotes connectivity or creates barriers to gene flow, directly affecting speciation processes. In this study, we carried out a landscape genomics analysis using NextRAD data from a montane forest specialist bird complex, the Mesoamerican Chestnut-capped/Green-striped Brushfinch of the genus Arremon. Specifically, we examined population genomic structure using different assignment methods and genomic differentiation and diversity, and we tested alternative genetic isolation hypotheses at the individual level (e.g., isolation by barrier, IBB; isolation by environment, IBE; isolation by resistance, IBR). We found well-delimited genomic structuring (K = 5) across Mesoamerican montane forests in the studied group. Individual-level genetic distances among major montane ranges were mainly explained by IBR hypotheses in this sedentary Neotropical taxon. Our results uncover genetic distances/differentiation and patterns of gene flow in allopatric species that support the role of tropical mountains as spatial landscape drivers of biodiversity. IBR clearly supports a pattern of conserved niche-tracking of suitable habitat conditions and topographic complexity throughout glacial-interglacial dynamics.

Spironolactone as a potential new pharmacotherapy for alcohol use disorder: convergent evidence from rodent and human studies.

Evidence suggests that spironolactone, a nonselective mineralocorticoid receptor (MR) antagonist, modulates alcohol seeking and consumption. Therefore, spironolactone may represent a novel pharmacotherapy for alcohol use disorder (AUD). In this study, we tested the effects of spironolactone in a mouse model of alcohol drinking (drinking-in-the-dark) and in a rat model of alcohol dependence (vapor exposure). We also investigated the association between spironolactone receipt for at least 60 continuous days and change in self-reported alcohol consumption, using the Alcohol Use Disorders Identification Test-Consumption (AUDIT-C), in a pharmacoepidemiologic cohort study in the largest integrated healthcare system in the US. Spironolactone dose-dependently reduced the intake of sweetened or unsweetened alcohol solutions in male and female mice. No effects of spironolactone were observed on drinking of a sweet solution without alcohol, food or water intake, motor coordination, alcohol-induced ataxia, or blood alcohol levels. Spironolactone dose-dependently reduced operant alcohol self-administration in dependent and nondependent male and female rats. In humans, a greater reduction in alcohol consumption was observed among those who received spironolactone, compared to propensity score-matched individuals who did not receive spironolactone. The largest effects were among those who reported hazardous/heavy episodic alcohol consumption at baseline (AUDIT-C ≥ 8) and those exposed to ≥ 50 mg/day of spironolactone. These convergent findings across rodent and human studies demonstrate that spironolactone reduces alcohol use and support the hypothesis that this medication may be further studied as a novel pharmacotherapy for AUD.

The Rise and Rise of Lupus.

Despite how difficult the early diagnosis of systemic lupus erythematosus (SLE) is, which is mainly due to the heterogeneity and non-specificity of its clinical manifestations, SLE is currently being diagnosed more frequently than in past decades. In fact, there has been an increase in the incidence and prevalence of SLE over the last four decades; this can be explained by a number of reasons including a better knowledge of the pathogenesis of the disease which allows its earlier diagnosis, the rising ethnic and racial diversity of the world population, the use of the 2019 EULAR/ACR criteria that allows classifying patients earlier, and improvements in survival over the last decades, which results in an increase in the prevalent cases of SLE. In this article, we will also review the genetic, environmental, and lifestyle factors, that are reported to increase the risk of developing SLE and how preventive strategies through a clinical care pathway may prevent or delay the development of SLE and improve these patients' outcomes.

Lupus enteritis: A 10-year experience in a single Latin American center.

OBJECTIVE: The objective is to compare the clinical and laboratory characteristics of systemic lupus erythematosus (SLE) patients with and without lupus enteritis (LE) and to identify the factors associated with the occurrence of LE. METHODS: We performed a retrospective, case-control study in hospitalized patients with SLE who were admitted to our tertiary hospital between January 2012 and December 2021. Sixteen LE patients (cases) were matched (1:3 ratio) for sex and birth year with 48 non-LE patients (controls). Univariable and multivariable logistic regression analyses were used to identify the variables associated with LE. RESULTS: Of 2,479 SLE patients who were admitted to our hospital as inpatients, 16 (0.65%) were diagnosed as having LE. All patients, cases and controls, were of Mestizo ethnicity. SLE was diagnosed simultaneously with the first episode of LE in 10 (62.5%) patients. The median time from SLE diagnosis to the first episode of LE was 7 (IQR 0-78) months. LE patients had a shorter median disease duration [7 (0-78) vs 34 (9.5-79) months], and a significantly longer hospital stay (28.3 ± 15.8 vs 6.5 ± 7.9 days, p < 0.001) than non-LE patients. Most LE patients (93.8%) had concomitant lupus nephritis. LE patients had higher SLEDAI-2K scores than those without LE (20.5 ± 9.4 vs 9.8 ± 10.4, p < 0.001). By multivariable analysis, a higher SLEDAI-2K score (OR 1.10, 95% CI 1.02-1.18; p = 0.015) was independently associated with LE occurrence after adjusting for cutaneous involvement, lymphocyte count, serum creatinine, and serum complement C4. Recurrence was observed in two patients (12.5%), both with a bowel wall thickening > 8 mm. The two patients with large intestine-dominant LE developed intestinal pseudo-obstruction. No patient had life-threatening complications (intestinal hemorrhage, infarction, or perforation), and there were no deaths induced directly by LE itself. CONCLUSION: In patients of Mestizo ethnicity, LE occurs during the early course of SLE, frequently is one of the presenting manifestations of SLE, and in most cases, it presents with concomitant lupus nephritis. Higher levels of disease activity at diagnosis were independently associated with LE occurrence and when recurrences occur, they do so in the context of severe wall thickness.

Incidence and visual outcomes of acute endophthalmitis post intravitreal injection of anti-vascular endothelial growth factors in a single referral center.

BACKGROUND: To describe the incidence and factors predicting visual outcome in patients with infectious endophthalmitis following intravitreal anti-VEGF injection. METHODS: Retrospective, single-site, cohort study. Patients with acute endophthalmitis within 6 weeks of intravitreal anti-VEGF injection who were referred to our practice after inciting injection or were injected by us between January 2010 and July 2017 were included. All patients received intravitreal antibiotics with either vitreous/anterior chamber tap (TAP) or pars plana vitrectomy. Visual outcomes pre/post treatment, baseline variables (age, gender, ocular disease) and cultures results were studied. RESULTS: Seventy eyes of 69 patients were included. Presenting VA was the strongest factor associated with final visual outcome after adjusting for other variables including culture status and baseline VA (p = .0002). Cultures were positive in 62.8% of eyes and were associated with worse visual outcome (p = .0087). Growth of Streptococcus or microorganisms other than coagulase negative Staphylococci (CNS) was also associated with worse prognosis, regardless of baseline and presenting VA (p = .0002). The crude incidence of post-injection endophthalmitis was 0.028% in our practice (40 eyes in 143,628 injections) during the study time. No significant difference was found between pre-filled bevacizumab versus ranibizumab or aflibercept drawn from a vial. CONCLUSIONS: In a large, single center, retrospective study, the incidence of acute endophthalmitis post anti-VEGF injection was relatively low. Worse visual acuity at presentation of endophthalmitis and growth of Streptococcus or organisms other than CNS were associated with the worst visual outcomes.

The tangled evolutionary history of a long-debated Mesoamerican taxon: The Velazquez Woodpecker (Melanerpes santacruzi, Aves: Picidae).

The Velazquez Woodpecker Melanerpes santacruzi is a highly polytypic species distributed from east-central Mexico to northern Nicaragua. The ample variation in body size, barring of the plumage, and the coloration of nasal tufts, neck, and belly have fueled debates about the taxonomy and evolutionary history of the species; however, the processes generating these patterns of variation and the underlying population dynamics throughout the species' distribution remain poorly understood. Here, we employed reduced representation genome sequencing (NextRAD) and Ecological Niche Modeling methods to test the distinctiveness of the Velazquez Woodpecker based on this new set of genomic data and analyze the correspondence of the genetic structure and ecological differentiation with phenotypic variation and geographic distribution. From phylogenetic and demographic analyses including the Golden-Fronted (M. aurifrons) and Red-bellied Woodpecker (M. carolinus), we obtained results congruent with previous molecular phylogenies. The clades of M. santacruzi and M. carolinus-M. aurifrons are reciprocally monophyletic, although the sister group relationship of M. aurifrons is ambiguous. Using genetic and ecological analyses, we found that the species is structured into three genetically and ecologically differentiated groups comprising the subspecies (1) M. s. santacruzi, (2) M. s. dubius and (3) M. s. grateloupensis-polygrammus-veraecrucis. These groups diverged recently, with two splits between 250,000 and 150,000 years ago, and show a significant genetic admixture among them, especially in their current contact zones. Ecological and demographic models suggest the existence of intermittent areas of sympatry and connectivity among populations of M. santacruzi since the Last Interglacial period. We also found evidence of bi-directional gene flow between the species M. aurifrons and the nearby populations of M. santacruzi (M. s. grateloupensis), along the Sierra Madre Oriental in northeastern Mexico. Gene flow seems to be uneven, with prevalence of movement in the direction from M. aurifrons to M. s. grateloupensis.

Addressing health disparities as a function of ethnicity in systemic lupus erythematosus patients.

Systemic lupus erythematosus (SLE) is an autoimmune disorder with significant health disparities, as it disproportionately and more severely affects vulnerable and disadvantaged population groups in the United States and around the world, that is, women, ethnic minorities, individuals living in poverty, less educated, and lacking medical insurance. Both, genetic and non-genetic factors, contribute to these disparities. To overcome these health disparities and reduce poor outcomes among disadvantaged SLE populations, interventions on non-genetic amendable factors, especially on social health determinants, are necessary.

Effect of the variation in the extracellular concentration of l-arginine in the physiology of Leishmania (Viannia) braziliensis and its susceptibility to some antileishmanial drugs.

The knowledge about amino acid metabolism in trypanosomatids is a valuable source of new therapeutic targets. l-arginine is an essential amino acid for Leishmania parasites, and it participates in the synthesis of polyamines, a group of essential nutrients used for nucleic acids, proteins biosynthesis, and redox modulation necessary for proliferation. In the present study, we evaluated the effect of changes in the availability of this amino acid on promastigotes and intracellular amastigotes on U937 macrophages and showed that the absence of l-arginine in culture medium negatively influences the growth and infectivity of Leishmania (Viannia) braziliensis, causing a decrease in the percentage of the infected cells and parasite load tested through light microscopy. In addition, the absence of l-arginine resulted in the parasite's inability to regulate its reactive oxygen species (ROS) production, which persisted for up to 24 h by flow cytometry following the probe H2DCF-DA dye. Moreover, the differentiation of promastigote to amastigote in axenic culture was more significant at low concentrations of l-arginine suggesting that this depletion induces a stress environment to increase this transformation under axenic conditions. No association was established between the availability of l-arginine and the effectiveness of antileishmanial drugs. All these results confirm the importance of l-arginine in L. braziliensis life cycle vital processes, such as its replication and infectivity, as documented in other Leishmania species. Based on these results, we proposed that the l-arginine uptake/metabolism route is possible in exploring new antileishmanial drugs.

Synthesis and Evaluation of Trypanocidal Activity of Chromane-Type Compounds and Acetophenones.

American trypanosomiasis (Chagas disease) caused by the Trypanosoma cruzi parasite, is a severe health problem in different regions of Latin America and is currently reported to be spreading to Europe, North America, Japan, and Australia, due to the migration of populations from South and Central America. At present, there is no vaccine available and chemotherapeutic options are reduced to nifurtimox and benznidazole. Therefore, the discovery of new molecules is urgently needed to initiate the drug development process. Some acetophenones and chalcones, as well as chromane-type substances, such as chromones and flavones, are natural products that have been studied as trypanocides, but the relationships between structure and activity are not yet fully understood. In this work, 26 compounds were synthesized to determine the effect of hydroxyl and isoprenyl substituents on trypanocide activity. One of the compounds showed interesting activity against a resistant strain of T. cruzi, with a half effective concentration of 18.3 µM ± 1.1 and an index of selectivity > 10.9.

Subtotal content and geochemical fractionation of potential toxic elements in agricultural soils from Mocorito River basin in NW Mexico: environmental and health implications.

Agricultural soils were collected from Mocorito river basin, to determine potentially toxic elements (PTEs) subtotal concentrations and geochemical fractionation, and evaluate their environmental and health risks. All sites showed low As and Cr concentrations. Subtotal concentrations (mg/kg) ranged between 6.8 and 25.6 for As, 1.9 and 2.5 for Cd and 22.5 and 55.1 for Cr. These values were classified as moderately contaminated for As, while a considerable contamination was presented for Cd and Cr. Geochemical partitioning revealed that PTEs are strongly linked with residual phase. Arsenic was associated with amorphous Fe-oxyhydroxides. Ecotoxicological indices showed from low (As and Cr) to considerable (Cd) potential ecological risk factors; potential non-carcinogenic risks by As, Cd and Cr, and potential carcinogenic risks by As and Cr. Lithogenic and anthropogenic sources were identified. Arsenic and Cr showed lithogenic influence, while Cd increased, caused by nearby activities, representing an environmental and health risk.

A proposal of an algorithm for the diagnosis and treatment of recurrence or treatment failure of retinopathy of prematurity after anti-VEGF therapy based on a large case series.

PURPOSE: To provide a diagnostic algorithm of recurrence and treatment failure after intravitreal bevacizumab (IVB) injection for retinopathy of prematurity type 1 (ROP1) and the stepwise therapeutic approach for both conditions. METHODS: Retrospective chart review of all patients diagnosed with ROP1 initially treated with IVB in 6 tertiary referral centers of Toluca and Mexico City from 2005 to 2017. Treatment failure was defined as persistence or progression of neovascularization, elevation of the ridge, worsening of plus disease, or retinal crunch within the first week after treatment. Recurrence was defined as the new appearance of plus disease, an elevated ridge, or pathological new vessels after an initial regression of ROP following treatment. Therapy was observation, switch of anti-VEGF agent, retinal photocoagulation, vitrectomy, or a combination of two or more, depending on the severity of findings. RESULTS: A total of 672 patients who received intravitreal bevacizumab injection for ROP1 treatment were included. Of these, 2.5% (17 patients) failed to treatment, 6.8% (46 patients) developed a recurrence for ROP, and 5.5% (37 patients) carried a misdiagnosis of recurrence and were diagnosed with other than ROP1 after examination. Based on the severity of findings, patients with recurrence or treatment failure were further treated by observation, repeat anti-VEGF intravitreal injection (bevacizumab or other), laser photocoagulation, vitrectomy, or a combination of these. Based on the treatment results, a therapeutic algorithm was created. CONCLUSIONS: Intravitreal injection of anti-VEGFs for the treatment of ROP warrants close follow-up as some of these patients may have treatment failure or recurrence of the disease. It is crucial to differentiate between them to avoid a misdiagnosis and offer the correct treatment. We propose a novel algorithm for the follow-up and treatment approach of ROP1 following initial treatment with IVB. This algorithm offers a summary of our recommendations based on a large case series of ROP1 patients. It is meant to grow and expand as more clinical evidence becomes available.

Effect of substituents in the A and B rings of chalcones on antiparasite activity.

Chalcones are a group of natural products with many recognized biological activities, including antiparasitic activity. Although a lot of chalcones have been synthetized and assayed against parasites, the number of structural features known to be involved in this biological property is small. Thus, in the present study, 21 chalcones were synthesized to determine the effect of substituents in the A and B rings on the activity against Leishmania braziliensis, Trypanosoma cruzi, and Plasmodium falciparum. The compounds were active against L. braziliensis in a structure-dependent manner. Only one compound was very active against T. cruzi, but none of them had a significant antiplasmodial activity. The electron-donating substituents in ring B and the hydrogen bonds at C-2' with carbonyl affect the antiparasitic activity.

Synthesis of ZnO Nanorod Film Deposited by Spraying with Application for Flexible Piezoelectric Energy Harvesting Microdevices.

Industry 4.0 and the Internet of Things have significantly increased the use of sensors and electronic products based on flexible substrates, which require electrical energy for their performance. This electrical energy can be supplied by piezoelectric vibrational energy harvesting (pVEH) devices. These devices can convert energy from ambient mechanical excitations into electrical energy. In order to develop, these devices require piezoelectric films fabricated with a simple and low-cost process. In this work, we synthesize ZnO nanorod film by a solvothermal method and deposit by spraying on ITO (indium-tin-oxide)/PET (polyethylene terephthalate) flexible substrate for a pVEH microdevice. The results of the characterization of the ZnO nanorod film using X-ray diffraction (XRD) confirm the typical reflections for this type of nanomaterial (JCPDS 36-145). Based on transmission electron microscopy (TEM) images, the size of the nanorod film is close to 1380 nm, and the average diameter is 221 ± 67 nm. In addition, the morphological characteristics of the ZnO nanorod film are obtained using atomic force microscopy (AFM) tapping images. The pVEH microdevice has a resonant frequency of 37 Hz, a generated voltage and electrical power of 9.12 V and 6.67 µW, respectively, considering a load resistance of 107.7 kΩ and acceleration of 1.5 g. The ZnO nanorod film may be applied to pVEH microdevices with flexible substrates using a low-cost and easy fabrication process.

The geography of evolutionary divergence in the highly endemic avifauna from the Sierra Madre del Sur, Mexico.

BACKGROUND: Mesoamerica is a remarkable region with a high geological and ecological complexity. Within northern Mesoamerica, the biotic province of the Sierra Madre del Sur (SMS) in southwestern Mexico harbors exceptionally high avian endemism and diversity. Herein, we searched for spatially and temporally concordant phylogeographic patterns, in four bird genera from three distinct avian orders co-distributed across Mesoamerica and investigated their causes through hypothesis testing regarding historical processes. Selected species include endemic and differentiated populations across the montane forests of Mesoamerica, and particularly within the SMS. RESULTS: We gathered mitochondrial DNA sequences for at least one locus from 177 individuals across all species. We assessed genetic structure, demographic history, and defined a framework for the coalescent simulations used in biogeographic hypothesis testing temporal and spatial co-variance. Our analyses suggested shared phylogeographic breaks in areas corresponding to the SMS populations, and between the main montane systems in Mesoamerica, with the Central Valley of Oaxaca and the Nicaragua Depression being the most frequently shared breaks among analyzed taxa. Nevertheless, dating analyses and divergence patterns observed were consistent with the hypothesis of broad vicariance across Mesoamerica derived from mechanisms operating at distinct times across taxa in the SMS. CONCLUSIONS: Our study provides a framework for understanding the evolutionary origins and historical factors enhancing speciation in well-defined regions within Mesoamerica, indicating that the evolutionary history of extant biota inhabiting montane forests is complex and often idiosyncratic.

Enhancing Acute Oral Toxicity Predictions by using Consensus Modeling and Algebraic Form-Based 0D-to-2D Molecular Encodes.

Quantitative structure-activity relationships (QSAR) are introduced to predict acute oral toxicity (AOT), by using the QuBiLS-MAS (acronym for quadratic, bilinear and N-Linear maps based on graph-theoretic electronic-density matrices and atomic weightings) framework for the molecular encoding. Three training sets were employed to build the models: EPA training set (5931 compounds), EPA-full training set (7413 compounds), and Zhu training set (10 152 compounds). Additionally, the EPA test set (1482 compounds) was used for the validation of the QSAR models built on the EPA training set, while the ProTox (425 compounds) and T3DB (284 compounds) external sets were employed for the assessment of all the models. The k-nearest neighbor, multilayer perceptron, random forest, and support vector machine procedures were employed to build several base (individual) models. The base models with REPA-training ≥ 0.75 ( R = correlation coefficient) and MAEEPA-training ≤ 0.5 (MAE = mean absolute error) were retained to build consensus models. As a result, two consensus models based on the minimum operator and denoted as M19 and M22, as well as a consensus model based on the weighted average operator and denoted as M24, were selected as the best ones for each training set considered. According to the applicability domain (AD) analysis performed, model M19 (built on the EPA training set) has MAEtest-AD = 0.4044, MAEProTox-AD = 0.4067 and MAET3DB-AD = 0.2586 on the EPA test set, ProTox external set, and T3DB external set, respectively; whereas model M22 (built on the EPA-full set) and model M24 (built on the Zhu set) present MAEProTox-AD = 0.3992 and MAET3DB-AD = 0.2286, and MAEProTox-AD = 0.3773 and MAET3DB-AD = 0.2471 on the two external sets accounted for, respectively. These outcomes were compared and statistically validated with respect to 14 QSAR methods (e.g., admetSAR, ProTox-II) from the literature. As a result, model M22 presents the best overall performance. In addition, a retrospective study on 261 withdrawn drugs due to their toxic/side effects was performed, to assess the usefulness of prospectively using the QSAR models proposed in the labeling of chemicals. A comparison with regard to the methods from the literature was also made. As a result, model M22 has the best ability of labeling a compound as toxic according to the globally harmonized system of classification and labeling of chemicals. Therefore, it can be concluded that the models proposed, especially model M22, constitute prominent tools for studying AOT, at providing the best results among all the methods examined. A freely available software was also developed to be used in virtual screening tasks ( http://tomocomd.com/apps/ptoxra ).

Complex biogeographic scenarios revealed in the diversification of the largest woodpecker radiation in the New World.

Phylogenetic relationships and patterns of evolution within Melanerpes, one of the most diverse groups of New World woodpeckers (22-23 lineages), have been complicated due to complex plumages and morphological adaptations. In an attempt to resolve these issues, we obtained sequence data from four nuclear introns and two mitochondrial protein-coding genes for 22 of the 24 currently recognized species in the genus. We performed phylogenetic analyses involving Maximum Likelihood and Bayesian Inference, species-tree divergence dating, and biogeographic reconstructions. Tree topologies from the concatenated and species-tree analyses of the mtDNA and nDNA showed broadly similar patterns, with three relatively well-supported groups apparent: (a) the Sphyrapicus clade (four species); (b) the typical Melanerpes clade, which includes temperate and subtropical dry forest black-backed species; and (c) the mostly barred-backed species, here referred to as the "Centurus" clade. The phylogenetic position of Melanerpes superciliaris regarding the rest of Melanerpes is ambiguous as it is recovered as sister to the rest of Melanerpes or as sister to a group including Sphyrapicus+Melanerpes. Our species tree estimations recovered the same well-delimited highly-supported clades. Geographic range evolution (estimated in BioGeoBEARS) was best explained by a DIVALIKE+j model, which includes vicariance, founder effect speciation, and anagenetic dispersal (range expansion) as important processes involved in the diversification of the largest radiation of woodpeckers in the New World.

CONSTRUCT AND FACE VALIDITY OF THE EYESI INDIRECT OPHTHALMOSCOPE SIMULATOR.

PURPOSE: To evaluate construct and face validity of the Eyesi Binocular Indirect Ophthalmoscope Simulator. METHODS: The performance of 25 medical students (Group A) was compared with that of 17 ophthalmology and optometry trainees (Group B) on the Eyesi Binocular Indirect Ophthalmoscope Simulator. During the course of a single session, each participant viewed an orientation module followed by an instruction session and a demonstration case, and performed 6 cases of progressively increasing difficulty (4 levels) and a 10-question face validity questionnaire. Outcomes included total score, total examination time, percent retina examined, and duration of eye exposure to light. RESULTS: Group B achieved significantly better total scores than Group A on all difficulty levels (P = 0.02, P = 0.001, P = 0.001, and P = 0.0001, for Levels 1-4, respectively) and had a significantly faster mean duration of examination (8 minutes 58 seconds vs. 5 minutes 21 seconds, P < 0.0001). Medical students reported higher scores in the face validity questionnaire for the simulator experience being helpful at orienting them to true indirect ophthalmology, and that further training on the simulator would improve their skills in the clinic (P = 0.03 for all). CONCLUSION: The Eyesi Binocular Indirect Ophthalmoscope Simulator has significant construct and face validity and shows promise for medical education.

Surface chemistry allows for abiotic precipitation of dolomite at low temperature.

Although the mineral dolomite is abundant in ancient low-temperature sedimentary systems, it is scarce in modern systems below 50 °C. Chemical mechanism(s) enhancing its formation remain an enigma because abiotic dolomite has been challenging to synthesize at low temperature in laboratory settings. Microbial enhancement of dolomite precipitation at low temperature has been reported; however, it is still unclear exactly how microorganisms influence reaction kinetics. Here we document the abiotic synthesis of low-temperature dolomite in laboratory experiments and constrain possible mechanisms for dolomite formation. Ancient and modern seawater solution compositions, with identical pH and pCO2, were used to precipitate an ordered, stoichiometric dolomite phase at 30 °C in as few as 20 d. Mg-rich phases nucleate exclusively on carboxylated polystyrene spheres along with calcite, whereas aragonite forms in solution via homogeneous nucleation. We infer that Mg ions are complexed and dewatered by surface-bound carboxyl groups, thus decreasing the energy required for carbonation. These results indicate that natural surfaces, including organic matter and microbial biomass, possessing a high density of carboxyl groups may be a mechanism by which ordered dolomite nuclei form. Although environments rich in organic matter may be of interest, our data suggest that sharp biogeochemical interfaces that promote microbial death, as well as those with high salinity may, in part, control carboxyl-group density on organic carbon surfaces, consistent with origin of dolomites from microbial biofilms, as well as hypersaline and mixing zone environments.