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Multiple immunoinformatic tools have been developed to predict T-cell epitopes from protein amino acid sequences for different major histocompatibility complex (MHC) alleles. These prediction tools output hundreds of potential peptide candidates which require further processing; however, these tools are either not graphical or not friendly for non-programming users. We present Epitope-Evaluator, a web tool developed in the Shiny/R framework to interactively analyze predicted T-cell epitopes. Epitope-Evaluator contains six tools providing the distribution of epitopes across a selected set of MHC alleles, the promiscuity and conservation of epitopes, and their density and location within antigens. Epitope-Evaluator requires as input the fasta file of protein sequences and the output prediction file coming out from any predictor. By choosing different cutoffs and parameters, users can produce several interactive plots and tables that can be downloaded as JPG and text files, respectively. Using Epitope-Evaluator, we found the HLA-B*40, HLA-B*27:05 and HLA-B*07:02 recognized fewer epitopes from the SARS-CoV-2 proteome than other MHC Class I alleles. We also identified shared epitopes between Delta, Omicron, and Wuhan Spike variants as well as variant-specific epitopes. In summary, Epitope-Evaluator removes the programming barrier and provides intuitive tools, allowing a straightforward interpretation and graphical representations that facilitate the selection of candidate epitopes for experimental evaluation. The web server Epitope-Evaluator is available at https://fuxmanlab.shinyapps.io/Epitope-Evaluator/., Competing Interests: The authors have declared that no competing interests exist.

Newly discovered hydrothermal systems in the Pescadero Basin (PB) and the neighboring Pescadero Transform Fault (PTF) at the mouth of the Gulf of California disclosed a diverse macrofauna assemblage. The trophic structure of both ecosystems was assessed using carbon (δ13C), nitrogen (δ15N), and sulfur (δ34S) stable isotopes. The δ13C ranged from -40.8 to -12.1‰, revealing diverse carbon sources and its assimilation via Calvin-Benson-Bassham and the reductive tricarboxylic acid cycles. The δ15N values were between -12.5 and 18.3‰, corresponding to primary and secondary consumers. The δ34S values fluctuated from -36.2 to 15.1‰, indicating the sulfide assimilation of biogenic, magmatic, and photosynthetic sources. In PB high-temperature vents, primary consumers including symbiont-bearing, bacterivores and filter-feeders predominated. The secondary consumers within the scavengers/detritivores and predator guilds were scarce. The siboglinid Oasisia aff alvinae dominated the macrofauna assemblage at PB, but rather than playing a trophic role, it provides a substrate to vent dwellers. In PTF low-temperature vents, only symbiont-bearing primary consumers were analyzed, displaying the lowest δ34S values. This assemblage was dominated by the coexisting siboglinids Lamellibrachia barhami and Escarpia spicata. δ34S values allowed to distinguish between PB and PTF vent communities, to exclude the presence of methanotrophic organisms, and the detection of photosynthetic organic matter input., Competing Interests: The authors have declared that no competing interests exist.

Numerous animals have declining populations due to habitat loss, illegal wildlife trade, and climate change. The cotton-top tamarin (Saguinus oedipus) is a Critically Endangered primate species, endemic to northwest Colombia, threatened by deforestation and illegal trade. In order to assess the current state of this species, we analyzed changes in the population of cotton-top tamarins and its habitat from 2005 to 2012. We used a tailor-made "lure strip transect" method to survey 43 accessible forest parcels that represent 30% of the species' range. Estimated population size in the surveyed region was approximately 2,050 in 2005 and 1,900 in 2012, with a coefficient of variation of approximately 10%. The estimated population change between surveys was -7% (a decline of approximately 1.3% per year) suggesting a relatively stable population. If densities of inaccessible forest parcels are similar to those of surveyed samples, the estimated population of cotton-top tamarins in the wild in 2012 was 6,946 individuals. We also recorded little change in the amount of suitable habitat for cotton-top tamarins between sample periods: in 2005, 18% of surveyed forest was preferred habitat for cotton-top tamarins, while in 2012, 17% percent was preferred. We attribute the relatively stable population of this Critically Endangered species to increased conservation efforts of Proyecto Tití, conservation NGOs, and the Colombian government. Due to continued threats to cotton-top tamarins and their habitat such as agriculture and urban expansion, ongoing conservation efforts are needed to ensure the long-term survival of cotton-top tamarins in Colombia., Competing Interests: Disney's Animals, Science and Environment supported the salaries of authors AS, KLF, and MP and provided financial resources to support the survey (covered expenses related to equipment and travel). This does not alter our adherence to PLOS ONE policies on sharing data and materials.

The surficial sediments recovered from 12 sites located near the channel axis of the Florida Straits and the lower slope off NW Cuba were analyzed for total organic carbon (TOC), nitrogen (TN), phosphorus (TP), elemental C:N:P ratios, C and N isotopic values, and 14C dating. The depth profiles of TOC, TN, and TP (0-18 cm) displayed a downcore trend and a significant variation. The TOC values were low (0.15 to 0.62%; 66 to 516 µmol g(-1)). Sites near the island's lower slope had lower TOC average concentrations (158-333 µmol g(-1)) than those closer to the channel axis (averaging 341-516 µmol g(-1); p <0.05). The TN concentrations near the lower slope attained 0.11% (80 µmol g(-1)), whereas, towards the channel axis, they decreased to 0.07% (55 µmol g(-1); p<0.05). The C:N ratios ranged from 1.9 to 10.2. The mean molar C:N ratio (5.4) indicated a marine hemipelagic deposition. The TP was lower at sites near the lower slope (38.4 to 50.0 µmol gv; 0.12% to 0.16%) than those near the channel axis (50.0 to 66 µmol g(-1); 0.15 to 0.21%). C:P fluctuated from 7.7 to 14.1 in the surficial sediment layer. The bulk organic δ13Corg and δ15N values confirmed pelagic organic sources, and the 14C dating revealed that the sediments were deposited during the Holocene (1000-5000 yr BP). We suggest that the hydrodynamic conditions in the Straits influence vertical and advective fluxes of particulate organic material trapped in the mixed-layer, which reduces the particulate matter flux to the seabed.