An Interactive Visual Database for American Sign Language Reveals How Signs are Organized in the Mind

We are four researchers who study psycholinguistics, linguistics, neuroscience and deaf education. Our team of deaf and hearing scientists worked with a group of software engineers to create the ASL-LEX database that anyone can use for free. We cataloged information on nearly 3,000 signs and built a visual, searchable and interactive database that allows scientists and linguists to work with ASL in entirely new ways

The ASL-LEX 2.0 Project: A Database of Lexical and Phonological Properties for 2,723 Signs in American Sign Language

ASL-LEX is a publicly available, large-scale lexical database for American Sign Language (ASL). We report on the expanded database (ASL-LEX 2.0) that contains 2,723 ASL signs. For each sign, ASL-LEX now includes a more detailed phonological description, phonological density and complexity measures, frequency ratings (from deaf signers), iconicity ratings (from hearing non-signers and deaf signers), transparency (“guessability”) ratings (from non-signers), sign and videoclip durations, lexical class, and more. We document the steps used to create ASL-LEX 2.0 and describe the distributional characteristics for sign properties across the lexicon and examine the relationships among lexical and phonological properties of signs. Correlation analyses revealed that frequent signs were less iconic and phonologically simpler than infrequent signs and iconic signs tended to be phonologically simpler than less iconic signs. The complete ASL-LEX dataset and supplementary materials are available at https://osf.io/zpha4/ and an interactive visualization of the entire lexicon can be accessed on the ASL-LEX page: http://asl-lex.org/

Microbial dark matter sequences verification in amplicon sequencing and environmental metagenomics data

Although microorganisms constitute the most diverse and abundant life form on Earth, in many environments, the vast majority of them remain uncultured. As it is based on information gleaned mainly from cultivated microorganisms, our current body of knowledge regarding microbial life is partial and does not reflect actual microbial diversity. That diversity is hidden in the uncultured microbial majority, termed by microbiologists as “microbial dark matter” (MDM), a term borrowed from astrophysics. Metagenomic sequencing analysis techniques (both 16S rRNA gene and shotgun sequencing) compare gene sequences to reference databases, each of which represents only a small fraction of the existing microorganisms. Unaligned sequences lead to groups of “unknown microorganisms” that are usually ignored and rarefied from diversity analysis. To address this knowledge gap, we analyzed the 16S rRNA gene sequences of microbial communities from four different environments—a living organism, a desert environment, a natural aquatic environment, and a membrane bioreactor for wastewater treatment. From those datasets, we chose representative sequences of potentially unknown bacteria for additional examination as “microbial dark matter sequences” (MDMS). Sequence existence was validated by specific amplification and re-sequencing. These sequences were screened against databases and aligned to the Genome Taxonomy Database to build a comprehensive phylogenetic tree for additional sequence classification, revealing potentially new candidate phyla and other lineages. These putative MDMS were also screened against metagenome-assembled genomes from the explored environments for additional validation and for taxonomic and metabolic characterizations. This study shows the immense importance of MDMS in environmental metataxonomic analyses of 16S rRNA gene sequences and provides a simple and readily available methodology for the examination of MDM hidden behind amplicon sequencing results

The first Neanderthal remains from an open-air Middle Palaeolithic site in the Levant

The late Middle Palaeolithic (MP) settlement patterns in the Levant included the repeated use of caves and open landscape sites. The fossil record shows that two types of hominins occupied the region during this period - Neandertals and Homo sapiens. Until recently, diagnostic fossil remains were found only at cave sites. Because the two populations in this region left similar material cultural remains, it was impossible to attribute any open-air site to either species. In this study, we present newly discovered fossil remains from intact archaeological layers of the open-air site 'Ein Qashish, in northern Israel. The hominin remains represent three individuals: EQH1, a nondiagnostic skull fragment; EQH2, an upper right third molar (RM3); and EQH3, lower limb bones of a young Neandertal male. EQH2 and EQH3 constitute the first diagnostic anatomical remains of Neandertals at an open-air site in the Levant. The optically stimulated luminescence ages suggest that Neandertals repeatedly visited 'Ein Qashish between 70 and 60 ka. The discovery of Neandertals at open-air sites during the late MP reinforces the view that Neandertals were a resilient population in the Levant shortly before Upper Palaeolithic Homo sapiens populated the region

Proline Metabolism is Essential for Trypanosoma brucei brucei Survival in the Tsetse Vector

Adaptation to different nutritional environments is essential for life cycle completion by all Trypanosoma brucei sub-species. In the tsetse fly vector, L-proline is among the most abundant amino acids and is mainly used by the fly for lactation and to fuel flight muscle. The procyclic (insect) stage of T. b. brucei uses L-proline as its main carbon source, relying on an efficient catabolic pathway to convert it to glutamate, and then to succinate, acetate and alanine as the main secreted end products. Here we investigated the essentiality of an undisrupted proline catabolic pathway in T. b. brucei by studying mitochondrial Δ1-pyrroline-5- carboxylate dehydrogenase (TbP5CDH), which catalyzes the irreversible conversion of gamma-glutamate semialdehyde (γGS) into L-glutamate and NADH. In addition, we provided evidence for the absence of a functional proline biosynthetic pathway. TbP5CDH expression is developmentally regulated in the insect stages of the parasite, but absent in bloodstream forms grown in vitro. RNAi down-regulation of TbP5CDH severely affected the growth of procyclic trypanosomes in vitro in the absence of glucose, and altered the metabolic flux when proline was the sole carbon source. Furthermore, TbP5CDH knocked-down cells exhibited alterations in the mitochondrial inner membrane potential (ΔΨm), respiratory control ratio and ATP production. Also, changes in the proline-glutamate oxidative capacity slightly affected the surface expression of the major surface glycoprotein EP-procyclin. In the tsetse, TbP5CDH knocked-down cells were impaired and thus unable to colonize the fly's midgut, probably due to the lack of glucose between bloodmeals. Altogether, our data show that the regulated expression of the proline metabolism pathway in T. b. brucei allows this parasite to adapt to the nutritional environment of the tsetse midgut

Efeito do açúcar de coco na cariogenicidade do streptococcus mutans

Aim: The consumption of foods rich in sugar is linked to several non-communicable diseases, including dental caries. Coconut sugar has systemic benefits due to its lower glycemic indexes (GI) than other table sugars. However, there is currently no data regarding its cariogenic potential. This study aimed to evaluate the effect of coconut sugar on acidogenicity and adhesion of Streptococcus mutans in vitro, compared to sugarcane products. Materials and methods: Aliquots of cultures of S. mutans UA159 were resuspended in a buffer solution enriched with coconut sugar, crystal sugar (refined sugar), and minimally processed sugarcane (demerara light brown sugar and maskavo dark brown sugar), as well as positive (sucrose) and negative controls. The decrease in pH and its corresponding area under the curve (AUC; cm2) were evaluated for the analysis of acidogenicity. S. mutans was incubated in BHI supplemented with each sugar and the percentages of microbial adhesion were calculated. After testing data normality, the one-way ANOVA test (Bonferroni post hoc) was used to compare the AUC and the proportion of adhesion of each group. Results: Regarding the acidogenic potential, statistical differences were found only between the negative control versus all other groups (p<0.001). Likewise, no significant difference in adhesion was found between the tested sugars (p>0.05). Discussion: Although the tested sugars are marketed as “healthy products,” their amount and frequency of usage should be controlled. Conclusion: Coconut sugar presents a similar cariogenic potential to that of sugarcane products when acidogenicity and adhesion are evaluated. Coconut sugar is not indicated as a substitute for sucrose in the control of cariogenic activity.Objetivo: O consumo de alimentos ricos em açúcar está associado a diversas doenças não transmissíveis, incluindo a doença cárie. O açúcar de coco tem benefícios sistêmicos devido aos seus índices glicêmicos (IG) mais baixos do que outros açúcares de mesa. No entanto, atualmente não há dados sobre seu potencial cariogênico. Esse estudo teve como objetivo avaliar o efeito do açúcar do coco na acidogenicidade e adesão de Streptococcus mutans in vitro, em comparação com produtos derivados da cana-de-açúcar. Materiais e métodos: alíquotas de culturas de S. mutans UA159 foram suspensas em solução tampão enriquecida com açúcar de coco, açúcar cristal (açúcar refinado) e cana-de-açúcar minimamente processada (açúcar mascavo demerara claro e açúcar mascavo), além de controles positivo (sacarose) e negativo. A diminuição do pH e correspondente área sob a curva (AUC; cm2) foram avaliadas na análise de acidogenicidade. S. mutans foi incubado em BHI suplementado com cada tipo de açúcar e as porcentagens de adesão microbiana foram calculadas. Após testar a normalidade dos dados, o teste ANOVA de uma via (Bonferroni post hoc) foi utilizado para comparar a AUC e a proporção de adesão de cada grupo. Resultados: Em relação ao potencial acidogênico, diferenças estatísticas foram encontradas apenas entre o controle negativo versus todos os outros grupos (p <0,001). Não foi encontrada diferença significativa na adesão entre os açúcares testados (p> 0,05). Discussão: Apesar dos açúcares testados serem comercializados como “produtos saudáveis”, sua quantidade e frequência de consumo deve ser controlada. Conclusão: O açúcar do coco apresenta potencial cariogênico semelhante à dos produtos da cana-de-açúcar quanto a acidogenicidade e a adesão. O açúcar de coco não é indicado como substituto da sacarose no controle da atividade cariogênica

Airway microbiota-host interactions regulate secretory leukocyte protease inhibitor levels and influence allergic airway inflammation

Homeostatic mucosal immune responses are fine-tuned by naturally evolved interactions with native microbes, and integrating these relationships into experimental models can provide new insights into human diseases. Here, we leverage a murine-adapted airway microbe, Bordetella pseudohinzii (Bph), to investigate how chronic colonization impacts mucosal immunity and the development of allergic airway inflammation (AAI). Colonization with Bph induces the differentiation of interleukin-17A (IL-17A)-secreting T-helper cells that aid in controlling bacterial abundance. Bph colonization protects from AAI and is associated with increased production of secretory leukocyte protease inhibitor (SLPI), an antimicrobial peptide with anti-inflammatory properties. These findings are additionally supported by clinical data showing that higher levels of upper respiratory SLPI correlate both with greater asthma control and the presence of Haemophilus, a bacterial genus associated with AAI. We propose that SLPI could be used as a biomarker of beneficial host-commensal relationships in the airway

The gut microbiota of people with asthma influences lung inflammation in gnotobiotic mice

The gut microbiota in early childhood is linked to asthma risk, but may continue to affect older patients with asthma. Here, we profile the gut microbiota of 38 children (19 asthma, median age 8) and 57 adults (17 asthma, median age 28) by 16S rRNA sequencing and find individuals with asthma harbored compositional differences from healthy controls in both adults and children. We develop a model to aid the design of mechanistic experiments in gnotobiotic mice and show enterotoxigeni