Miracle-dz/UniFAR-FTUs huggingface dataset:
Genetic diversity of leafy amaranth (Amaranthus tricolor L.) resources in Vietnam

Leafy amaranths, which are consumed as traditional food in Asia and Africa, are now considered among the most promising vegetables. In Vietnam, leafy amaranths, particularly Amaranthus tricolor L. , are important summer vegetables due to their excellent nutritional values and high tolerance to biotic and abiotic stresses. However, this species has not been subjected to systematic breeding. Here we describe species identification and evaluation of the genetic diversity of Vietnamese amaranth collection by using matK and simple sequence repeats (SSR) markers. Our phylogenetic analysis based on the matK marker classified the species of 68% of the accessions, of which 120 belonged to A. tricolor. We developed 21 SSR markers, which amplified a total of 153 alleles in 294 A. tricolor accessions originating from Vietnam and overseas, with a mean allelic richness of 7.29 per marker, observed heterozygosity of 0.14, expected heterozygosity of 0.38, and polymorphic information content of 0.35. The STRUCTURE and FST analysis indicated a positive relationship between geographic distance and genetic differentiation among most of the overseas groups and the Vietnamese collection, but not among geographic groups within the Vietnamese collection. Vietnamese amaranths could be divided into two major types, one common in East Asia and the other one unique to Vietnam.
Comparison between DNA- and cDNA-based gut microbial community analyses using 16S rRNA gene sequences

† These authors contributed equally to the study. *For correspondence. E-mail: tatsu@jejunu.ac. kr; Tel. : +82-64-754-3354; Fax: +82-64-756-3351 § Supplemental material for this article may be found at http://www.kjom. org. Studies based on microbial community analyses have increased in the recent decade since the development of next generation sequencing technology. Associations of gut microbiota with host’s health are one of the major outcomes of microbial ecology filed. The major approach for microbial community analysis includes the sequencing of variable regions of 16S rRNA genes, which does not provide the information of bacterial activities. Here, we conducted RNA-based microbial community analysis and compared results obtained from DNAand its cDNAbased microbial community analyses. Our results indicated that these two approaches differed in the ratio of Firmicutes and Bacteroidetes, known as an obesity indicator, as well as abundance of some key bacteria in gut metabolisms such as butyrate producers and probiotics strains. Therefore, cDNAbased microbial community may provide different insights regarding roles of gut microbiota compared to the previous studies where DNA-based microbial community analyses were performed.
The early life microbiota protects neonatal mice from pathological small intestinal epithelial cell shedding

The gut microbiota plays a crucial role in regulating and maintaining the epithelial barrier, particularly during early life. Notably, patients with chronic intestinal inflammation have a dysregulated process of renewal and replenishment of the intestinal epithelial cell (IEC) barrier, which is linked to disturbances in the gut microbiota. To date, there are no studies focussed on understanding the impact of inflammatory cell shedding events during the early life developmental window, and which host and microbial factors mediate these responses. Here we sought to determine pathological cell shedding outcomes throughout the postnatal developmental period (day 14, 21, 29 and week 8). Surprisingly neonatal mice (day 14 and 21) were highly refractory to induction of cell shedding after intraperitoneal administration of LPS, with day 29 mice showing strong pathological responses, more similar to those observed in adult mice. These differential responses were not linked to defects in the cellular mechanisms and pathways known to regulate cell shedding responses, although we did observe that neonatal mice had elevated anti-inflammatory (IL-10) responses. Notably, when we profiled microbiota and metabolites from these mice, we observed significant alterations. Neonatal mice had high relative abundances of Streptococcus, Escherichia and Enterococcus and increased primary bile acids. In contrast, older mice were dominated by Candidatus Arthromitus, Alistipes and Lachnoclostridium, and had increased concentrations of SCFAs and methyamines. Faecal microbiota transplant (FMT) and antibiotic studies confirmed the importance of early life gut microbiota in cell shedding responses. In these studies, neonates treated with antibiotics restored LPS-induced small intestinal cell shedding, whereas adult FMT alone had no effect. Our findings further support the importance of the early life window for microbiota-epithelial interactions in the presence of inflammatory stimuli and highlight areas for further investigation to probe underlying mechanisms to drive therapeutic development within the context of chronic inflammatory intestinal diseases.
Antibiotic-resistant Escherichia coli in deer and nearby water sources at Safari parks in Bangladesh

Background and Aim: The emergence and rapid dissemination of multidrug-resistant (MDR) bacteria in different ecosystems is a growing concern to human health, animal health, and the environment in recent years. The study aimed to determine the antibiotic resistance in Escherichia coli from deer and nearby water sources at two different Safari parks in Bangladesh. Materials and Methods: A number of 55 fresh fecal samples of deer and six water samples from nearby lakes were collected from two Safari parks. Samples were processed, cultured, and carried out biochemical tests for E. coli. The antibiotic susceptibility was determined by disk diffusion method. To identify the resistance genes, polymerase chain reaction was performed. Results: A total of 32 E. coli isolates from 55 fecal samples and 6 of 6 E. coli isolates from lake water were isolated. From fecal E. coli isolates, ampicillin and sulfamethoxazole were 90.63% (n=29/32) resistant and 87.5% (n=28/32) were resistant to tetracycline and nalidixic acid. High resistance was also observed to other antibiotics. On the contrary, all E. coli isolates from water sources were 100% (n=6/6) resistant to ampicillin, tetracycline, sulfamethoxazole, and nalidixic acid. MDR was revealed in all water samples, whereas 96.88% (n=31/32) was found in fecal isolates. A number of blaTEM, tet A, and Sul2 genes were detected from both isolates. Conclusion: This study for the 1st time highlights, a significant proportion of E. coli isolates in wildlife deer and nearby water sources were MDR in Bangladesh.
Mating changes the genital microbiome in both sexes of the common bedbug Cimex lectularius across populations

Many bacteria live on host surfaces, in cells, and specific organ systems. Although gut microbiomes of many organisms are well-documented, the bacterial communities of reproductive organs, i.e. genital microbiomes, have received little attention. During mating, male and female genitalia interact and copulatory wounds can occur, providing an entrance for sexually transmitted microbes. Besides being potentially harmful to the host, invading microbes might interact with resident genital microbes and affect immunity. While sexual transmission of individual symbiont species is relatively well-understood, few studies have addressed how mating changes genital microbiomes. Here, we characterize male and female genital microbiomes in four different populations of the common bedbug Cimex lectularius and investigate mating-induced changes. We dissected reproductive organs from virgin and mated individuals to sequence their genital microbiomes. We show that mating changes genital microbiomes, suggesting bacteria are sexually transmitted. This raises the question how the host’s physiological and immunological mechanisms control mating-induced changes in their genital microbiomes. Also, genital microbiomes varied between populations and the sexes. This provides evidence for local and sex-specific adaptation of bacteria and hosts, again suggesting that bacteria might play an important role in shaping the evolution of reproductive traits. Coadaptation of genital microbiomes and reproductive traits might further lead to reproductive isolation between populations, giving reproductive ecology an important role in speciation. Future studies should investigate the transmission dynamics between the sexes and populations to uncover potential reproductive barriers.
Modeling behaviorally relevant neural dynamics enabled by preferential subspace identification (PSID)

Neural activity exhibits dynamics that in addition to a behavior of interest also relate to other brain functions or internal states. Understanding how neural dynamics explain behavior requires dissociating behaviorally relevant and irrelevant dynamics, which is not achieved with current neural dynamic models as they are learned without considering behavior. We develop a novel preferential subspace identification (PSID) algorithm that models neural activity while dissociating and prioritizing its behaviorally relevant dynamics. Applying PSID to large-scale neural activity in two monkeys performing naturalistic 3D reach-and-grasps uncovered new features for neural dynamics. First, PSID revealed the behaviorally relevant dynamics to be markedly lower-dimensional than otherwise implied. Second, PSID discovered distinct rotational dynamics that were more predictive of behavior. Finally, PSID more accurately learned the behaviorally relevant dynamics for each joint and recording channel. PSID provides a general new tool to reveal behaviorally relevant neural dynamics that can otherwise go unnoticed.
At-sea movements of wedge-tailed shearwaters during and outside the breeding season from four colonies in New Caledonia

The wedge-tailed shearwater (WTS) population of New Caledonia is one of the largest in the world, yet its biology and foraging ecology are poorly known. We studied WTS from 4 colonies in New Caledonia. We examined foraging behaviour and habitats using GPS receivers and light sensors during and outside the breeding season, respectively, and compared our findings with those from other WTS populations worldwide. During breeding, New Caledonian WTS alternated short foraging trips close to the colony over the lagoon, or off the reef edge, with longer trips over distant, deep waters. Whereas neighboring colonies overlapped at sea, especially during short trips, there was a clear separation of foraging zones between the pairs of colonies located in the southern versus northwestern parts of New Caledonia. Although WTS actively foraged and commuted to foraging zones during the day, they mainly returned to the colony or rested at night, indicating that they feed mainly during the day. Active foraging did not take place in more productive areas, suggesting that it may instead be related to the presence of sub-surface predators. Outside the breeding season, birds from 3 colonies had similar trans-equatorial migratory behaviour. All left New Caledonia at the same time of the year with a fast, northeasterly movement and wintered over deep waters in the same sector of the northwestern tropical Pacific Ocean. At overwintering sites, they spent most of their non-foraging time presumably sitting on the water, especially at night, making a slow westward movement before returning to New Caledonia. WTS from New Caledonia forage over warm, oligotrophic deep waters throughout their life cycle, and the species appears to have a flexible foraging strategy adapted to the various environmental conditions encountered across its wide tropical range.
THE ROLE OF CD8 T CELL IMMUNODOMINANCE AND REGULATORY T CELLS IN NEONATAL IMMUNITY TO INFLUENZA VIRUS

OF DISSERTATION THE ROLE OF CD8 T CELL IMMUNODOMINANCE AND REGULATORY T CELLS IN NEONATAL IMMUNITY TO INFLUENZA VIRUS Neonates are more susceptible to influenza virus infection than adults, resulting in increased morbidity and mortality as well as delayed clearance of the virus. Efforts to improve influenza infection outcomes in neonates typically center on prevention, although current vaccines fall short of complete protection and can only be administered in humans after 6 months of life. We propose that as the neonatal immune system responds differently than the adult immune system, interventions that are efficacious or tolerable in adults cannot be guaranteed to perform the same in neonates. T cell vaccines that target conserved influenza virus epitopes have been proposed for conferring protection to multiple influenza virus strains, but if T cell vaccines will be used in infants and adults, neonates must be able to respond to the same T cell antigens as adults. Mouse pups responded to influenza virus peptide PA224-233 but not NP366-374 during influenza virus infection in contrast to the codominant adult response. Mice infected as pups also generated diminished T cell memory compared to mice infected as adults and displayed skewed immunodominance during secondary infection. Adult bone marrow derived dendritic cells (BMDCs) improved viral clearance when loaded with influenza virus and promoted NP366-374-specific CD8+ T cell responses in infected pups. BMDC peptide vaccination could stimulate PA224-233-specific but not NP366-374-specific CD8+ T cell responses in pups, but, PA224-233 vaccination offered no protection to pups during lethal infection. These data suggest that altered immunodominance must be considered when stimulating CD8+ T cell responses in adults and neonates. Immaturity and active suppression of immune responses are both factors in neonatal vulnerability to disease. Specifically, active suppression of neonatal immunity by regulatory T cells (Tregs) has been proposed as a driving factor in diminished neonatal immunity, but removing these cells can compromise viral defense or increase deleterious inflammation. Mice that lacked Tregs displayed compromised anti-influenza antibody responses and decreased lymph node responses during influenza virus infection. A high proportion of pup Tregs also expressed Gata3. Transgenic pups with a Treg specific Gata3 knockout displayed an increase in Tbet expression in both conventional and regulatory T cells and an increase in IFNγ producing CD4+ T cells in the lungs during infection. These data suggest that Tregs are required for effective humoral responses to influenza virus and that Gata3 expression influences Treg suppressive function in neonates.
Climatic niche limits and community‐level vulnerability of obligate symbioses

Communities with many species at their climatic niche limits may be vulnerable to species losses, suggesting that niche‐based measures can inform vulnerability assessments. We aimed to quantify spatial variation in community‐level vulnerability indices based on niche limits, not just central tendencies, to predict where climate changes will produce rapid, pronounced shifts in ecological communities.
Genetic differentiation in Alewife populations using microsatellite loci

2 ACKNOWLEDGEMENTS. 3 LIST OF TABLES . 5 LIST OF FIGURES. 6 CHAPTER 1. 7-24 A Review of the ecology, genetics and management of fish populations . 7 Introduction . 7 Genetic variation in natural populations . 7 Fish biology. 8 Molecular markers.12 Population genetics and fisheries policy . 21 CHAPTER 2.25-37 Genetic differentiation in alewife populations using microsatellite loci.25 Introduction . 25 Materials and Methods . 27 Results.30 Discussion . 37 CHAPTER 3.38-42 Implications of the study on management of fish populations . 38 REFERENCES.43-51 APPENDIX A: Unedited and edited genotyping data for the 5 microsatellite loci in alewife.52-70 APPENDIX B: Microsatellite allele frequencies for alewife from all sampling locations. 71-72
Dimensionality, information and learning in prefrontal cortex

Learning leads to changes in population patterns of neural activity. In this study we wanted to examine how these changes in patterns of activity affect the dimensionality of neural responses and information about choices. We addressed these questions by carrying out high channel count recordings in dorsal-lateral prefrontal cortex (dlPFC; 768 electrodes) while monkeys performed a two-armed bandit reinforcement learning task. The high channel count recordings allowed us to study population coding while monkeys learned choices between actions or objects. We found that the dimensionality of neural population activity was higher across blocks in which animals learned the values of novel pairs of objects, than across blocks in which they learned the values of actions. The increase in dimensionality with learning in object blocks was related to less shared information across blocks, and therefore patterns of neural activity that were less similar, when compared to learning in action blocks. Furthermore, these differences emerged with learning, and were not a simple function of the choice of a visual image or action. Therefore, learning the values of novel objects increases the dimensionality of neural representations in dlPFC.
Investigation of a low-stress and low-contamination clamping method for large-aperture optics

Motivated by the need to decrease initial contact seal stress on Nd:glass coated with SiO2 sol–gel film and effectively control the surface contaminants from film debris induced by stress in the assembly process, a novel vacuum clamping method is studied to achieve the purpose of low stress and low contamination. In this article, theoretical analyses, numerical simulations, and field experiments are used to verify the feasibility of this method. Mechanical simulation results indicate that under the same radial compression conditions, the higher the hollowness of the O-ring rubber, the less the contact stress on Nd:glass. In addition, microstructures of the SiO2 sol–gel film are observed by scanning electron microscopy, and the damage mechanism is analyzed in order to optimize assembly stress. By optimizing the distribution of hollowness, the honeycomb structure is proved to have lower contact stress due to its larger deformation. Finally, experimental results verify that the low-stress vacuum clamping method can meet the strict surface cleanliness requirements of Nd:glass. This study also provides a promising method for clean assembly of other large-aperture optics.
Woody plants constructing tundra soils

In tundra, woody plants are expanding towards higher latitudes and altitudes due to increasingly favourable climatic conditions. Their expansion may also occur through increases in the coverage and height of the plants. These shifts may cascade further across the ecosystem, such as in the foundations of tundra: that is, in the soils. Yet, little is known about the effects woody plants have on local soil conditions. Here, we examined if the coverage and height of woody plants affect the growing-season soil moisture and temperature as well as soil organic carbon stocks. We carried out a field observation study in a dwarf shrub–dominated tundra and built a hierarchical model. We found that, after controlling for other possible factors influencing woody plants and soil conditions (namely, topography, snow, and the overall plant coverage), the coverage of woody plants inversely correlated with all three soil conditions. Yet, we found no link between the woody plant height to the soil variables. This indicates that woody plants affect local soil conditions in various ways, depending upon whether their expansion occurs though the growth of coverage or their height. Nevertheless, woody plants likely alter the very ground of the entire tundra system and feedback into the global climate system through the water, energy, and carbon cycles of tundra.
Salinity regulation of copepod egg production in a large microtidal estuary

Salinity is a key variable for ecological processes in estuaries. Acartia tonsa is a typical estuarine copepod whose responses to salinity have been thoroughly studied in the laboratory. However, results cannot be extrapolated to the field, and formal comparisons between lab and field responses to salinity were not attempted. Here we compare lab-based with field copepod egg production rates (EPR) from the Río de la Plata estuary (RPE), with focus on A. tonsa . Field work was conducted between 2009 and 2011 in the mixing zone of the RPE. Water temperature, salinity and chlorophyll-a varied over ample ranges (temperature: 10.54 - 24.56ºC, salinity: 2.83 - 32.99, chlorophyll-a: 0.62 - 7.27 mg m -3 ). A. tonsa was the strongly dominant species. EPR ranged between 6.7 and 95.7 eggs female -1 day -1 , and correlated to salinity, temperature (weakly), but not to chlorophyll. The relationship between A. tonsa’s EPR (EPR AT ) and salinity was consistent with that obtained under laboratory conditions: a humped pattern with a maximum at intermediate salinities. However, differences were also evident, e.g., higher EPR AT was measured in the field. We speculate that discrepancies derive from nutritional differences between field and reference (laboratory) data sets. Besides salinity, food quality and quantity may be first order drivers of A. tonsa’s productivity in the RPE. Descriptors: Copepods, Estuary, Acartia tonsa , Egg production rate, Río de la Plata.
Seat belt syndrome: a global issue

Background: The seat belt does not alter the amount of force sustained in an accident, but it does alter the distribution of that force, in attempting to place it across the less vulnerable pelvic area. Its greatest usefulness is in the rollover type accidents and in preventing ejection from the vehicle. The aim of the present study was to review the literature about the sea-belt. Methods: An extensive literature search was performed aiming to identify and review research studies that investigate the causes and the consequences of the seat belt syndrome during the last 25 years. The databases that were searched were: the Cochrane Library, Medline and PubMed. Results: There are a number of significant risk factors associated with seat-belt nonuse in the general public: male gender, young age, passenger status, risk-taking rural living, low level of education, black or hispanic ethnicity, having few dependents or children, smoking, speeding, alcohol consumption before driving and travelling on secondary roads late in the day. The seat belt syndrome is most commonly associated with using a lap belt, but has also been reported in occupants using three-point restraints. In these cases the patient often has cutaneous signs of injury with a lap belt mark. The seatbelt syndrome itself is characterized by injuries in the plane of the lap portion of the belt particularly with laceration of the colon, small bowel and occasionally the stomach, laceration of the liver and spleen, occasional injury of the pancreas, major vascular injuries. Some spinal injuries, such as lumbar spine or spinal cord injury are included in the 'seat-belt syndrome', but it is not clear whether or not these injuries are caused directly by the belt. Conclusions: Seat belts are effective in reducing the incidence of major and fatal injuries in automobile accidents.