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Self-Expanding Metallic (SEM) Y stents are a newer form of stent that is gaining popularity outside the USA, but still has limited data, especially in a community medicine setting. This study analyzed efficacy and complication rates in 14 patients who had a SEM Y stent placed between August 2022 and June 2024 at Harris Methodist Hospital in Fort Worth, Texas for either central airway obstruction (CAO) or fistulae. Of the 14 patients, 11 were requiring supplemental oxygen or mechanical ventilation prior to stent placement. Post-stenting 42.9% had decreased oxygen requirements, 21.4% unchanged, 14.3% increased, and 21.4% remained on room air. Complications included mucus plugging (42.9%), infection (35.7%), and granulation tissue (14.3%). There was no statistically significant correlation between gender/age and complications (p = 0.879/0.490, respectively). Complication rates were similar when compared to silicone Y stents based on literature review. In conclusion, SEM Y stents are a safe and effective alternative stent intended for palliative treatment with similar success and complications that can be easily and effectively implemented in a community hospital, with the added benefit of being able to be placed with flexible bronchoscopy.

Abstract Objectives The primary metabolite contents of ripe fruits result from complex regulations during their development. For Solanaceae, these regulations have been widely studied in tomato. The fruit metabolite contents of other fruit species, such as pepper (Capsicum annuum L.) and eggplant (Solanum melongena L.), constitute a valuable resource for the community to study the regulation of fruit metabolism and identify common or species-dependent regulations. This dataset about major polar metabolites is part of a larger project that integrates other omics data for pepper and eggplant, and other fruit species for metabolomics and other omics. Data description We provide quantitative metabolite data of pepper and eggplant fruit along development. We sampled pepper and eggplant fruit cultivated in a tunnel or a greenhouse at 10 or 11 stages from anthesis to ripe fruit. We used proton nuclear magnetic resonance (1H-NMR) metabolomic profiling of polar extracts to quantify the major metabolites and expressed the data in µmol per g fresh weight. Twenty-four metabolites were determined in pepper and 27 in eggplant. Nineteen common metabolites were quantified in both fruit species including three soluble sugars and one sugar-alcohol, five organic acids and nine free amino acids. These data can be combined with similar quantitative data on other species or complemented with other omics data to perform cross-species or cross-omics comparisons.

Abstract The sequencing of a kidney sample (KW2013002) from a stranded Megaptera novaeangliae (Humpback whale) calf is the first chromosome-level reference genome for this species1. The calf, a 457 cm and 2,500 lbs male, was found stranded in Hawai’i Kai, HI, in 2013 and was marked as abandoned/orphaned. In 2023, 1 g of kidney was sequenced with PacBio long-read DNA sequencing, chromatin conformation capture (Hi-C), RNA sequencing, and mitochondrial sequencing to comprehensively characterize the genome and transcriptome of M. novaeangliae. Data validation includes a synteny analysis, mitochondrial annotation, and a comparison of BUSCO scores (scaffold v. reference genome and Balaenoptera musculus (Blue whale) v. M. novaeangliae). BUSCO analysis was performed on an M. novaeangliae scaffold-level assembly to determine genomic completeness of the reference genome, with a scaffold BUSCO score of 91.2% versus a score of 95.4%. Synteny analysis was performed using the B. musculus genome as comparison to determine chromosome-level coverage and structure. Further, a time-based phylogenetic tree was constructed using the sequenced data and publicly available genomes.

Abstract Background The composition of ripe fruits depends on various metabolites which content evolves greatly throughout fruit development and may be influenced by the environment. The corresponding metabolism regulations have been widely described in tomato during fruit growth and ripening. However, the regulation of other metabolites that do not show large changes in content have scarcely been studied. Results We analysed the metabolites of tomato fruits collected on different trusses during fruit development, using complementary analytical strategies. We identified the 22 least variable metabolites, based on their coefficients of variation. We first verified that they had a limited functional link with the least variable proteins and transcripts. We then posited that metabolite contents could be stabilized through complex regulations and combined their data with the quantitative proteome or transcriptome data, using sparse partial-least-square analyses. This showed shared regulations between several metabolites, which interestingly remained linked to early fruit development. We also examined regulations in specific metabolites using correlations with individual proteins and transcripts, which revealed that a stable metabolite does not always correlate with proteins and transcripts of its known related pathways. Conclusions The regulation of the least variable metabolites was then interpreted regarding their roles as hubs in metabolic pathways or as signalling molecules.

Abstract The wide use of genomic information has enabled the identification of lethal recessive alleles that are the major genetic causes of reduced conception rates, longer calving intervals, or lower survival for live-born animals. This study was carried out to screen the Nellore cattle genome for lethal recessive haplotypes based on deviation from the expected population homozygosity, and to test SNP markers surrounding the lethal haplotypes region for association with heifer rebreeding (HR), post-natal mortality (PNM) and stayability (STAY). This approach requires genotypes only from apparently normal individuals and not from affected embryos. A total of 62,022 animals were genotyped and imputed to a high-density panel (777,962 SNP markers). Expected numbers of homozygous individuals were calculated, and the probabilities of observing 0 homozygotes was obtained. Deregressed genomic breeding values [(G)EBVs] were used in a GWAS to identify candidate genes and biological mechanisms affecting HR, STAY and PNM. In the functional analyses, genes within 100 kb down and upstream of each significant SNP marker, were researched. Thirty haplotypes had high expected frequency, while no homozygotes were observed. Most of the alleles present in these haplotypes had a negative mean effect for PNM, HR and STAY. The GWAS revealed significant SNP markers involved in different physiological mechanisms, leading to harmful effect on the three traits. The functional analysis revealed 26 genes enriched for 19 GO terms. Most of the GO terms found for biological processes, molecular functions and pathways were related to tissue development and the immune system. More phenotypes underlying these putative regions in this population could be the subject of future investigation. Tests to find putative lethal haplotype carriers could help breeders to eliminate them from the population or manage matings in order to avoid homozygous.

Accurate spatial alignment is essential for any population neuroimaging study, and affine (12 parameter linear/translation) or rigid (6 parameter rotation/translation) alignments play a major role. Here we consider intensity based alignment of neuroimages using gradient based optimization, which is a problem that continues to be important in many other areas of medical imaging and computer vision in general. A key challenge is robustness. Optimization often fails when transformations have components with different characteristic scales, such as linear versus translation parameters. Hand tuning or other scaling approaches have been used, but efficient automatic methods are essential for generalizing to new imaging modalities, to specimens of different sizes, and to big datasets where manual approaches are not feasible. To address this we develop a left invariant metric on these two matrix groups, based on the norm squared of optical flow induced on a template image. This metric is used in a natural gradient descent algorithm, where gradients (covectors) are converted to perturbations (vectors) by applying the inverse of the metric to define a search direction in which to update parameters. Using a publicly available magnetic resonance neuroimage database, we show that this approach outperforms several other gradient descent optimization strategies. Due to left invariance, our metric needs to only be computed once during optimization, and can therefore be implemented with negligible computation time.

Acerola (Malpighia emarginata D.C.) is an exotic fruit with high agro-industrial potential due to its high content of ascorbic acid (AA), phenolic compounds, and carotenoid pigments. Acerola fruit is processed into concentrated juice or powder to be incorporated into food supplements. The ascorbic acid content of concentrated juice or powders must be controlled and well assessed. Therefore, the development of optimal methods and procedures for the rapid and accurate determination of the ascorbic acid content in juice concentrate and juice powder remains of considerable commercial interest. NMR spectroscopy is currently a powerful spectroscopic tool for the qualitative and quantitative analysis of molecules of all types and sizes. Firstly, this article presents the NMR-based metabolomic profiling of acerola juice and concentrate powder to describe and compare their composition. Thirty-six metabolites were identified. The AA over choline ratio and the NMR metabolomic profiles could be used for authentication in the future. Secondly, a rapid (8 min), reliable, and non-destructive method for the quantification of ascorbic acid by 1D 1H-NMR spectroscopy was developed and validated. The LOD and LOQ were 0.05 and 0.15 mg/mL, respectively. These two approaches could be combined to better characterize ingredients derived from acerola and incorporated into food supplements.

The long-term effect of a plant (P)-based diet was assessed by proton nuclear magnetic resonance (1H-NMR) metabolomics in rainbow trout fed a marine fish meal (FM)–fish oil (FO) diet (M), a P-based diet and a control commercial-like diet (C) starting with the first feeding. Growth performances were not heavily altered by long-term feeding on the P-based diet. An 1H-NMR metabolomic analysis of the feed revealed significantly different soluble chemical compound profiles between the diets. A set of soluble chemical compounds was found to be specific either to the P-based diet or to the M diet. Pterin, a biomarker of plant feedstuffs, was identified both in the P-based diet and in the plasma of fish fed the P-based diet. 1H-NMR metabolomic analysis on fish plasma and liver and muscle tissues at 6 and 48 h post feeding revealed significantly different profiles between the P-based diet and the M diet, while the C diet showed intermediate results. A higher amino acid content was found in the plasma of fish fed the P-based diet compared with the M diet after 48 h, suggesting either a delayed delivery of the amino acids or a lower amino acid utilisation in the P-based diet. This was associated with an accumulation of essential amino acids and the depletion of glutamine in the muscle, together with an accumulation of choline in the liver. Combined with an anticipated absorption of methionine and lysine supplemented in free form, the present results suggest an imbalanced essential amino acid supply for protein metabolism in the muscle and for specific functions of the liver.

The SHARC Interest Group of the Research Data Alliance was established to improve research crediting and rewarding mechanisms for scientists who wish to organise their data (and material resources) for community sharing. This requires that data are findable and accessible on the Web, and comply with shared standards making them interoperable and reusable in alignment with the FAIR principles. It takes considerable time, energy, expertise and motivation. It is imperative to facilitate the processes to encourage scientists to share their data. To that aim, supporting FAIR principles compliance processes and increasing the human understanding of FAIRness criteria – i.e., promoting FAIRness literacy – and not only the machine-readability of the criteria, are critical steps in the data sharing process. Appropriate human-understandable criteria must be the first identified in the FAIRness assessment processes and roadmap. This paper reports on the lessons learned from the RDA SHARC Interest Group on identifying the processes required to prepare FAIR implementation in various communities not specifically data skilled, and on the procedures and training that must be deployed and adapted to each practice and level of understanding. These are essential milestones in developing adapted support and credit back mechanisms not yet in place.

A large body of research has shown that human adults are fast and accurate at enumerating arrays of ~1-4 items. This phenomenon has been called subitizing. Above this range, enumeration is slower and less accurate. The subitizing range has been related to individual differences in variables such as mathematical abilities, working memory, etc. The two most common methods for calculating subitizing range today – bilinear fit and sigmoid fit – have their strengths and weaknesses. By combining these two methods, we overcome their biggest limitations and come up with a novel way for calculating Individual Subitizing Range (ISR). This paper introduces this new method as well as empirical studies designed to test the new method. We replicated classic effects from the literature and obtain a high correlation with the sigmoid fit method. This paper includes a Matlab code for easy calculation of ISR as well as a ready-to-use experimental file for testing ISR. We hope that these tools would be of use to researchers studying individual differences in the subitizing range.

The broad variability of Cucumis melo (melon, Cucurbitaceae) presents a challenge to conventional classification and organization within the species. To shed further light on the infraspecific relationships within C. melo, we compared genotypic and metabolomic similarities among 44 accessions representative of most of the cultivar-groups. Genotyping-by-sequencing (GBS) provided over 20,000 single-nucleotide polymorphisms (SNPs). Metabolomics data of the mature fruit flesh and rind provided over 80,000 metabolomic and elemental features via an orchestra of six complementary metabolomic platforms. These technologies probed polar, semi-polar, and non-polar metabolite fractions as well as a set of mineral elements and included both flavor- and taste-relevant volatile and non-volatile metabolites. Together these results enabled an estimate of “metabolomic/elemental distance” and its correlation with the genetic GBS distance of melon accessions. This study indicates that extensive and non-targeted metabolomics/elemental characterization produced classifications that strongly, but not completely, reflect the current and extensive genetic classification. Certain melon Groups, such as Inodorous, clustered in parallel with the genetic classifications while other genome to metabolome/element associations proved less clear. We suggest that the combined genomic, metabolic, and element data reflect the extensive sexual compatibility among melon accessions and the breeding history that has, for example, targeted metabolic quality traits, such as taste and flavor.

Nutrition of high trophic species in aquaculture is faced with the development of sustainable plant-based diets. Insects seem particularly promising for supplementing plant-based diets. However, the complex effect of whole insect meal on fish metabolism is not well understood, and even less is known about insect meal extracts. The purpose of this work was to decipher the metabolic utilization of a plant-based diet supplemented with the gradual addition of an insect protein extract (insect hydrolysate at 0%, 5%, 10% and 15%). 1H-NMR profiling was used to assess metabolites in experimental diets and in fish plasma, liver and muscle. A significant dose-dependent increase in growth and feed efficiency with increasing insect extract amounts was observed. The incremental incorporation of the insect extract in diet had a significant and progressive impact on the profile of dietary soluble compounds and trout metabolome. The metabolites modulated by dietary insect extracts in plasma and tissues were involved in protein and energy metabolism. This was associated with the efficient metabolic use of dietary free amino acids toward protein synthesis through the concomitant supply of balanced free amino acids and energy substrates in muscle. The findings provide new insights into how the dietary food metabolome affects fish metabolism.

Se investigó el uso de plantas medicinales en la Comunidad San Jacinto, provincia de Los Ríos (Ecuador). Se estableció qué partes de las plantas son usadas, el tipo de administración, la preparación, las categorías de uso medicinal tradicional y el conocimiento por sexo y por rangos de edad. Se determinó el valor de uso (IVU), el conocimiento relativo (RVU) y el nivel de uso significativo Tramil (UST). Se registran 33 plantas que tuvieron uso medicinal; las hojas fueron las estructuras más utilizadas (87,9%); la forma de preparación principal fue la infusión (66,7%) y la vía de administración más empleada fue la bebida (87,9%). La categoría de uso medicinal mejor representada está relacionada con el sistema gastrointestinal (36,4%). No se encontró diferencias significativas en el conocimiento de las especies de acuerdo al sexo y al rango de edad de los informantes. Las plantas medicinales más importantes para la población local fueron: la sábila (Aloe vera), la hoja del aire (Kalanchoe pinnata), la ruda de gallinazo (Ruta graveolens), el toronjil (Melissa officinalis), la valeriana (Valeriana officinalis), la hierba luisa (Cymbopogon citratus) y el orégano (Origanum vulgare).

Soil microbial biomass (SMB) plays an important role in nutrient cycling in agroecosystems, and is limited by several factors, such as soil water availability. This study assessed the effects of soil water availability on microbial biomass and its variation over time in the Latossolo Amarelo concrecionário of a secondary forest in eastern Amazonia. The fumigation-extraction method was used to estimate the soil microbial biomass carbon and nitrogen content (SMBC and SMBN). An adaptation of the fumigation-incubation method was used to determine basal respiration (CO2-SMB). The metabolic quotient (qCO2) and ratio of microbial carbon:organic carbon (CMIC:CORG) were calculated based on those results. Soil moisture was generally significantly lower during the dry season and in the control plots. Irrigation raised soil moisture to levels close to those observed during the rainy season, but had no significant effect on SMB. The variables did not vary on a seasonal basis, except for the microbial C/N ratio that suggested the occurrence of seasonal shifts in the structure of the microbial community.

Fruit is a complex organ containing seeds and several interconnected tissues with dedicated roles. However, most biochemical or molecular studies about fleshy fruit development concern the entire fruit, the fruit without seeds, or pericarp only. We studied tomato (Solanum lycopersicum) fruit at four stages of development (12, 20, 35, and 45 days post-anthesis). We separated the seeds and the other tissues, exocarp, mesocarp, columella with placenta and locular tissue, and analyzed them individually using proton NMR metabolomic profiling for the quantification of major polar metabolites, enzymatic analysis of starch, and LC-DAD analysis of isoprenoids. Pericarp tissue represented about half of the entire fruit mass only. The composition of each fruit tissue changed during fruit development. An ANOVA-PCA highlighted common, and specific metabolite trends between tissues e.g., higher contents of chlorogenate in locular tissue and of starch in columella. Euclidian distances based on compositional data showed proximities within and between tissues. Several metabolic regulations differed between tissues as revealed by the comparison of metabolite networks based on correlations between compounds. This work stressed the role of specific tissues less studied than pericarp but that impact fruit organoleptic quality including its shape and taste, and fruit processing quality.

A maioria dos estudos de sucessão em florestas secundárias na Amazônia avalia sítios de diferentes idades, que representam uma cronoseqüência sucessional, em vez de monitorar um único sítio por vários anos pelo inventário contínuo. Este estudo comparou a composição e estrutura florísticas de espécies arbóreas com diâmetro a 1,3 m de altura (DAP) ≥ 1 cm, em sítios com 4 e 12 anos na Amazônia Oriental, e avaliou a mortalidade e o recrutamento em ambos os sítios baseados em dados de inventário contínuo durante 4 anos de estudo. As áreas de estudo foram abandonadas após múltiplos ciclos de uso agrícola de 7 a 10 anos, desde ~1940. Ambos os sítios são dominados pelas espécies arbóreas Lacistema pubescens e Vismia guianensis, com densidade de indivíduos, diâmetro, altura, área basal e riqueza de espécies significativamente maiores no sítio de 12 anos. A densidade de indivíduos, ao longo do tempo, foi crescente no sítio de 4 anos e decrescente no de 12 anos; o diâmetro, a altura e a área basal aumentaram nos dois sítios. No sítio de 4 anos, foi constatada uma taxa de recrutamento líquido crescente entre 2000-2001 e 2001-2002, que diminuiu entre 2002-2003, indicando redução gradual na colonização. No sítio de 12 anos, foi observada alta mortalidade líquida (13 e 11%), sobretudo nas duas primeiras avaliações, indicando o processo de autodesbaste. A combinação dos métodos de cronoseqüência e inventário contínuo aumenta substancialmente o entendimento do desenvolvimento sucessional.

Forest regrowth occupies an extensive and increasing area in the Amazon basin, but accurate assessment of the impact of regrowth on carbon and nutrient cycles has been hampered by a paucity of available allometric equations. We develop pooled and species-specific equations for total aboveground biomass for a study site in the eastern Amazon that had been abandoned for 15 years. Field work was conducted using randomized branch sampling, a rapid technique that has seen little use in tropical forests. High consistency of sample paths in randomized branch sampling, as measured by the standard error of individual paths (14%), suggests the method may provide substantial efficiencies when compared to traditional procedures. The best fitting equations in this study used the traditional form Y=a×DBHb, where Y is biomass, DBH is diameter at breast height, and a and b are both species-specific parameters. Species-specific equations of the form Y=a(BA×H), where Y is biomass, BA is tree basal area, H is tree height, and a is a species-specific parameter, fit almost as well. Comparison with previously published equations indicated errors from -33% to +29% would have occurred using off-site relationships. We also present equations for stemwood, twigs, and foliage as biomass components.Florestas secundárias ocupam uma área extensa e crescente na bacia Amazônica, porém determinações acuradas do impacto dessas florestas nos ciclos de carbono e nutrientes têm sido dificultadas pelo número reduzido de equações alométricas. Neste estudo, nós desenvolvemos equações em nível de comunidade e espécies individuais para estimar a biomassa total da parte aérea de uma floresta secundária com 15 anos de idade na Amazônia oriental. O trabalho de campo utilizou amostragem aleatória de ramos, que é uma técnica rápida, porém pouco utilizada em florestas tropicais. Baseada no erro padrão da série de segmentos individuais (14%), a consistência da série de segmentos totais amostrados foi considerada elevada, sugerindo que o método pode ser eficiente em comparação com procedimentos tradicionais. Os melhores ajustes foram obtidos com a equação tradicional Y=a×DBHb, onde Y é a biomassa, DBH é o diâmetro à altura do peito, e a e b são parâmetros para cada espécie arbórea. Ajustes razoáveis também foram alcançados com equações da forma Y=a(BA×H), onde Y é a biomassa, BA é a área basal, H é a altura e a é um parâmetro específico para cada espécie arbórea. Comparações com equações disponíveis na literatura indicaram uma faixa de erro provável de -33% a +29% usando-se relações desenvolvidas para outros sítios. Nós também apresentamos equações para os seguintes componentes da biomassa da parte aérea: tronco, ramos e folhas.

A maioria dos estudos de sucessão em florestas secundárias na Amazônia avalia sítios de diferentes idades, que representam uma cronoseqüência sucessional, em vez de monitorar um único sítio por vários anos pelo inventário contínuo. Este estudo comparou a composição e estrutura florísticas de espécies arbóreas com diâmetro a 1,3 m de altura (DAP) ≥ 1 cm, em sítios com 4 e 12 anos na Amazônia Oriental, e avaliou a mortalidade e o recrutamento em ambos os sítios baseados em dados de inventário contínuo durante 4 anos de estudo. As áreas de estudo foram abandonadas após múltiplos ciclos de uso agrícola de 7 a 10 anos, desde ~1940. Ambos os sítios são dominados pelas espécies arbóreas Lacistema pubescens e Vismia guianensis, com densidade de indivíduos, diâmetro, altura, área basal e riqueza de espécies significativamente maiores no sítio de 12 anos. A densidade de indivíduos, ao longo do tempo, foi crescente no sítio de 4 anos e decrescente no de 12 anos; o diâmetro, a altura e a área basal aumentaram nos dois sítios. No sítio de 4 anos, foi constatada uma taxa de recrutamento líquido crescente entre 2000-2001 e 2001-2002, que diminuiu entre 2002-2003, indicando redução gradual na colonização. No sítio de 12 anos, foi observada alta mortalidade líquida (13 e 11%), sobretudo nas duas primeiras avaliações, indicando o processo de autodesbaste. A combinação dos métodos de cronoseqüência e inventário contínuo aumenta substancialmente o entendimento do desenvolvimento sucessional.

Most published studies of secondary forest succession in the Amazon examine stands of different ages that represent a successional chronosequence, rather than monitoring a single stand over the long-term. This study compares floristic composition and structure of tree species with diameter at 1.3 m height (DBH) ≥ 1 cm in a 4-year-old and a 12-year-old re-growth stand in the Eastern Amazon, and examines mortality and recruitment occurring within both stands based on repeated sampling carried out annually for four years. The study areas were abandoned after multiple agricultural cicles that lasted 7 to 10 years, beginning in ~1940. Both stands are largely dominated by the same tree species Lacistema pubescens and Vismia guianensis, with significantly higher stem density, diameter, height, basal area and species richness in the 12-year-old stand. In the 4-year-old stand there were measured an increase in annual net recruitment during the first two data collection periods but relatively lower net recruitment during the last evaluation period, indicating on-going but gradually weakening colonization. There were registered a high net mortality during the first two data collection periods in the 12-years-old stand with a relatively lower net mortality during the last evaluation indicating rapid self thinning. When used in combination, the chronosequence and the longitudinal approaches significantly strengthen the understanding of successional development.

En este artículo se analizan las principales causas de mortalidad entre los varones jóvenes de México, a saber: los accidentes, homicidios y suicidios, a la luz de la perspectiva de género. Este enfoque permite mostrar el peso del modelo hegemónico de masculinidad en las prácticas de riesgo que conducen hacia estas causas y cuestionar la socialización de género como un proceso desencadenante de riesgo para la relación de los varones con las mujeres y consigo mismos.

O objetivo deste trabalho foi estudar a sucessão florestal pela análise florística e estrutural de floresta em três estágios sucessionais (4, 8 e 12 anos), localizadas no município de Castanhal-PA. Consideraram-se duas classes de DAP: Classe I (DAP>1cm) e classe II (DAPThe objective of this study is to understand secondary forest succession through florisitc and structural analysis of a forest in three successional stages (4, 8 and 12 years) located in Castanhal in the state of Pará. This study considers wood species divided into two DBH classes: class I (DBH>1cm) and class II (DBH

O presente trabalho descreve o ingresso e a mortalidade em uma floresta em diferentes estágios sucessionais, no município de Castanhal, Pará. A área de estudo está localizada na Estação Experimental da Universidade Federal Rural da Amazônia. As parcelas foram implantadas em áreas de florestas sucessionais de diferentes idades (4, 8 e 12 anos). Nas florestas sucessionais de 4 e 8 anos foram utilizadas quatro parcelas de 10m x 10m e na floresta de 12 anos foram, 12 parcelas de 10m x 10m. Realizaram duas medições de todos os indivíduos com DAP>1cm, em intervalos de 12 meses, nas florestas sucessionais de 4 e 8 anos; e intervalo de 18 meses na floresta de 12 anos. Foram calculadas as taxas de ingresso e de mortalidade. Na floresta de 4 anos o ingresso foi maior que a mortalidade. Nas florestas sucessionais de 8 e 12 anos as densidades diminuíram, perdendo mais indivíduos por mortalidade do que ganhando por ingresso. Lacistema pubescens, Myrcia silvatica, Vismia guianensis, Rollinia exsucca e Miconia ciliata apresentaram muitos indivíduos mortos nas florestas estudadas.The present work describe recruitment and mortality in a forest in different successional stages in Castanhal, Pará. The study area is located at the Experimental Research Station of the Universidade Federal Rural da Amazônia. Twelve 10m x 10m study plots were established in a 12-year-old secondary forest, and four 10m x 10m study plots were demarcated in a 4-year-old and an 8-year-old secondary forest. We measured diameter and height of all individuals with DBH>1cm at a 12-month interval in the 4 and 8-year-old stands, and an 18-month interval in the 12-year-old stand. Using this inventory data we calculated recruitment and mortality rates. In the 4-year-old forest, recruitment was greater than mortality, while in the 8 and 12-year-old forests experienced net mortality, as density declined over the measurement interval. Lacistema pubescens, Myrcia sylvatica, Vismia guianensis, Rollinia exsucca and Miconia ciliata displayed the greatest number of dead individuals in the studied successional forests.

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Human populations differ reliably in the degree to which people favor family, friends and community members over strangers and outsiders. In the last decade, researchers have begun to propose several economic and evolutionary hypotheses for these cross-population differences in parochialism. In this paper, we outline major current theories and review recent attempts to test them. We also discuss the key methodological challenges in assessing these diverse economic and evolutionary theories for cross-population differences in parochialism.

Mycoplasma hominis is an opportunistic human mycoplasma. Two other pathogenic human species, M. genitalium and Ureaplasma parvum, reside within the same natural niche as M. hominis: the urogenital tract. These three species have overlapping, but distinct, pathogenic roles. They have minimal genomes and, thus, reduced metabolic capabilities characterized by distinct energy-generating pathways. Analysis of the M. hominis PG21 genome sequence revealed that it is the second smallest genome among self-replicating free living organisms (665,445 bp, 537 coding sequences (CDSs)). Five clusters of genes were predicted to have undergone horizontal gene transfer (HGT) between M. hominis and the phylogenetically distant U. parvum species. We reconstructed M. hominis metabolic pathways from the predicted genes, with particular emphasis on energy-generating pathways. The Embden-Meyerhoff-Parnas pathway was incomplete, with a single enzyme absent. We identified the three proteins constituting the arginine dihydrolase pathway. This pathway was found essential to promote growth in vivo. The predicted presence of dimethylarginine dimethylaminohydrolase suggested that arginine catabolism is more complex than initially described. This enzyme may have been acquired by HGT from non-mollicute bacteria. Comparison of the three minimal mollicute genomes showed that 247 CDSs were common to all three genomes, whereas 220 CDSs were specific to M. hominis, 172 CDSs were specific to M. genitalium, and 280 CDSs were specific to U. parvum. Within these species-specific genes, two major sets of genes could be identified: one including genes involved in various energy-generating pathways, depending on the energy source used (glucose, urea, or arginine) and another involved in cytadherence and virulence. Therefore, a minimal mycoplasma cell, not including cytadherence and virulence-related genes, could be envisaged containing a core genome (247 genes), plus a set of genes required for providing energy. For M. hominis, this set would include 247+9 genes, resulting in a theoretical minimal genome of 256 genes.

Mycoplasmas are commonly described as the simplest self-replicating organisms, whose evolution was mainly characterized by genome downsizing with a proposed evolutionary scenario similar to that of obligate intracellular bacteria such as insect endosymbionts. Thus far, analysis of mycoplasma genomes indicates a low level of horizontal gene transfer (HGT) implying that DNA acquisition is strongly limited in these minimal bacteria. In this study, the genome of the ruminant pathogen Mycoplasma agalactiae was sequenced. Comparative genomic data and phylogenetic tree reconstruction revealed that approximately 18% of its small genome (877,438 bp) has undergone HGT with the phylogenetically distinct mycoides cluster, which is composed of significant ruminant pathogens. HGT involves genes often found as clusters, several of which encode lipoproteins that usually play an important role in mycoplasma-host interaction. A decayed form of a conjugative element also described in a member of the mycoides cluster was found in the M. agalactiae genome, suggesting that HGT may have occurred by mobilizing a related genetic element. The possibility of HGT events among other mycoplasmas was evaluated with the available sequenced genomes. Our data indicate marginal levels of HGT among Mycoplasma species except for those described above and, to a lesser extent, for those observed in between the two bird pathogens, M. gallisepticum and M. synoviae. This first description of large-scale HGT among mycoplasmas sharing the same ecological niche challenges the generally accepted evolutionary scenario in which gene loss is the main driving force of mycoplasma evolution. The latter clearly differs from that of other bacteria with small genomes, particularly obligate intracellular bacteria that are isolated within host cells. Consequently, mycoplasmas are not only able to subvert complex hosts but presumably have retained sexual competence, a trait that may prevent them from genome stasis and contribute to adaptation to new hosts.

The sequencing of a kidney sample (KW2013002) from a stranded Megaptera novaeangliae (Humpback whale) calf is the first chromosome-level reference genome for this species1. The calf, a 457 cm and 2,500 lbs male, was found stranded in Hawai'i Kai, HI, in 2013 and was marked as abandoned/orphaned. In 2023, 1 g of kidney was sequenced with PacBio long-read DNA sequencing, chromatin conformation capture (Hi-C), RNA sequencing, and mitochondrial sequencing to comprehensively characterize the genome and transcriptome of M. novaeangliae. Data validation includes a synteny analysis, mitochondrial annotation, and a comparison of BUSCO scores (scaffold v. reference genome and Balaenoptera musculus (Blue whale) v. M. novaeangliae). BUSCO analysis was performed on an M. novaeangliae scaffold-level assembly to determine genomic completeness of the reference genome, with a scaffold BUSCO score of 91.2% versus a score of 95.4%. Synteny analysis was performed using the B. musculus genome as comparison to determine chromosome-level coverage and structure. Further, a time-based phylogenetic tree was constructed using the sequenced data and publicly available genomes. [ABSTRACT FROM AUTHOR]