Miracle-dz/UniFAR-FTUs huggingface dataset:
PTSD blood transcriptome mega-analysis: Shared inflammatory pathways across biological sex and modes of traumas

Transcriptome-wide screens of peripheral blood during the onset and development of posttraumatic stress disorder (PTSD) indicate widespread immune dysregulation. However, little is known as to whether biological sex and the type of traumatic event influence shared or distinct biological pathways in PTSD. We performed a combined analysis of five independent PTSD blood transcriptome studies covering seven types of trauma in 229 PTSD and 311 comparison individuals to synthesize the extant data. Analyses by trauma type revealed a clear pattern of PTSD gene expression signatures distinguishing interpersonal (IP)-related traumas from combat-related traumas. Co-expression network analyses integrated all data and identified distinct gene expression perturbations across sex and modes of trauma in PTSD, including one wound-healing module down-regulated in men exposed to combat traumas, one IL12-mediated signaling module up-regulated in men exposed to IP-related traumas, and two modules associated with lipid metabolism and MAPK-activity up-regulated in women exposed to IP-related traumas. Remarkably, a high degree of sharing of transcriptional dysregulation across sex and modes of trauma in PTSD was also observed converging on common signaling cascades, including cytokine, innate immune and type I interferon pathways. Collectively, these findings provide a broad view of immune dysregulation in PTSD and demonstrate inflammatory pathways of molecular convergence and specificity, which may inform mechanisms and diagnostic biomarkers for the disorder.
Migratory pathways, stopover zones and wintering destinations of Western European Nightjars Caprimulgus europaeus

Little is known about the wintering distribution of the European Nightjar Caprimulgus europaeus. We combined geolocator and GPS-logger data from different sites in Western Europe to analyse migration routes and migration timing of this trans-equatorial migrant. Nightjars followed a loop migration route during which they cross two ecological barriers, and converged near common stopover zones in Northern, Central and Western Africa, where they stayed for two to three weeks. Nightjars used the same stopover sites as several other European migrants, relying on small and discrete wintering areas within the Democratic Republic of Congo. This confirms the importance of these specific zones and highlights the vulnerability of Western European populations to habitat loss in their non-breeding areas. This article is protected by copyright. All rights reserved.
Immune Responses to LcrV, A Plague Baboons Generate Vigorous Humoral An Age-Old Paradigm Challenged: Old

Immune senescence in the elderly results in decreased immunity with a concomitant increase in susceptibility to infection and diminished efﬁcacy of vaccination. Nonhuman primate models have proven critical for testing of vaccines and therapeutics in the general population, but a model using old animals has not been established. Toward that end, immunity to LcrV, a protective Ag from Yersinia pestis , was tested in young and old baboons. Surprisingly, there was no age-associated loss in immune competence; LcrV elicited high-titer, protective Ab responses in the older individuals. The primary responses in the younger baboons were lower, but they did show boosting upon secondary immunization to the levels achieved in the old animals. The LcrV Ag was also tested in mice and, as expected, age-associated loss of immunity was seen; older animals responded with lower-titer Abs and, as a result, were more susceptible to Yersinia challenge. Thus, although age-related loss in immune function has been observed in humans, rodents, and some nonhuman primates, baboons appear to be unusual; they age without losing immune competence. The Journal of Immunology, 2008, 181: 109–115.
Trinucleotide Repeat Instability Is Modulated by DNA Base Lesions and DNA Base Excision Repair

Base excision repair (BER) of an oxidized base within a trinucleotide repeat (TNR) tract can lead to TNR expansions that are associated with over 40 human neurodegenerative diseases. This occurs as a result of DNA secondary structures such as hairpins formed during repair. We have previously shown that BER in a TNR hairpin loop can lead to removal of the hairpin, attenuating or preventing TNR expansions. Here, we further provide the first evidence that AP endonuclease 1 (APE1) prevented TNR expansions via its 3’-5’ exonuclease activity and stimulatory effect on DNA ligation during BER in a hairpin loop. Coordinating with flap endonuclease 1, the APE1 3’-5’ exonuclease activity cleaves the annealed upstream 3’-flap of a double-flap intermediate resulting from 5’incision of an abasic site in the hairpin loop. Furthermore, APE1 stimulated DNA ligase I to resolve a long double-flap intermediate, thereby promoting hairpin removal and preventing TNR expansions.
Re-evaluating models for estimating prey consumption by leopards

Biomass regression models and associated correction factors derived from feeding trials are essential to convert frequency of prey occurrence from scats into biomass and numbers of prey individuals consumed by carnivores. These dietary analyses form a substantial part of many research projects on predator–prey relationships and human–carnivore conflicts. So far, diet studies of leopard (Panthera pardus) applied the linear biomass model developed for puma (Puma concolor). Recent works, however, suggested that non-linear biomass models are more meaningful for estimating prey biomass and numbers, and presented a generalized model of biomass consumption for all tropical felids. This model accounted for partial consumption of prey, but did not include ecological factors limiting prey consumption by felids. Hence, using 35 feeding trials we developed a leopard specific regression equation by setting a consumption limit for leopard per prey. This new correction factor takes into account the proportion of inedible matter of prey and daily food intake. Besides refining the leopard specific biomass models, our study also showed the saturation in scat production with consumption of larger prey, which was described in recent studies. A reanalysis of prey consumption by leopards from published diet studies by using our new regression models suggests a significant decrease in estimated absolute numbers of prey individuals consumed. This finding and the higher share of larger prey in leopard diet may affect subsequent analyses using prey profiles, and may affect decisions made in biodiversity conservation and management, especially in the area of human–carnivore conflict.
Characterizations of juvenile stages of some semaeostome Scyphozoa (Cnidaria), with recognition of a new family (Phacellophoridae)

Phacellophora camtschatica has long been assigned to the semaeostome scyphozoan family Ulmaridae. Early stages (scyphistomae, strobilae, ephyrae, postephyrae, and young medusae) of the species were compared with those of several other semaeostomes currently assigned to Ulmaridae, Pelagiidae, and Cyaneidae. Juveniles of P. camtschatica did not strictly conform with characters of those of any of these families, and appeared intermediate between Cyaneidae and Ulmaridae. A new family, Phacellophoridae, is proposed to accommodate P. camtschatica.
Targeted selective treatment strategies for sustainable nematode control and delay of anthelmintic resistance in adult Merino sheep in a Mediterranean environment

‘Targeted selective treatment’ (TST) is the concept of targeting anthelmintic treatments to individual animals that will benefit from treatment, rather than giving whole flock treatments. The purpose of TST is to delay the onset of anthelmintic resistance in nematode populations. Two key issues that have delayed the utilization of TST are; a) the need for a convenient and reliable method for identifying animals less likely to cope with nematode challenge; and b) the risk that some animals will be left with nematode burdens sufficient to cause sub-clinical disease that compromises production and welfare. To investigate these issues, this thesis tested the hypothesis that body condition can indicate the ability of mature sheep to better cope with nematodes (and therefore remain untreated), thereby providing a convenient selection method for TST strategies in a Mediterranean climate, where Trichostrongylus spp. and Teladorsagia circumcincta are the predominant nematode parasites. The risk of loss of production and welfare by leaving some animals untreated was examined by modelling simulations, based on data derived from field studies, and on computer models, with various proportions of the flock remaining untreated to determine the threshold proportions of sheep to leave untreated. This approach indicated the trade-offs between delaying anthelmintic resistance with production loss and animal welfare associated with nematode burdens resultant from leaving animals untreated. Further to this, an investigation of Western Australian sheep producers (farmers) identified factors associated with the acceptance of sustainable nematode control practices, especially those likely to facilitate the adoption of TST and act as the basis for the development of communication strategies to producers. The findings of this research provide evidence-based recommendations for the sheep industry regarding sustainable nematode management strategies utilising TST in Mediterranean environments and the facilitation of adoption of TST strategies. In conclusion, the general hypothesis was shown to be applicable, that a body condition score-based TST control program can be practical to implement and will delay anthelmintic resistance in adult Merino sheep in a Mediterranean environment.
Inventory and Assessment of the Pan troglodytes (Blumenbach, 1799) Skeletal Collection Housed at the Yale Peabody Museum

Abstract Museum collections are critical resources for examining comparative anatomy, developmental biology and life history hypotheses. Evaluation of skeletal collections provides insight into spatiotemporal, species, population and individual variation associated with environmental, social and epidemiological history. For endangered species such as primates, these collections provide data that are nearly impossible to replicate today. In this first in a series of papers reviewing the great ape holdings of the Peabody Museum of Natural History at Yale University, we describe the Pan troglodytes skeletal collection. Although most of the collection is from Central Africa's Atlantic coast, it includes several Pan troglodytes subspecies. Multiple age and sex classes are present, with craniodental and postcranial elements available for each age class. All material was assessed for developmental, disease, trauma and socioecological indicators. Multiple indicators of metabolic stress are present and likely associated with nutritional and epidemiological factors. Instances of trauma and injury, ranging from antemortem to perimortem events, are described. For some individuals, these injuries are likely associated with intraspecific and intrasexual competition and violence, whereas others are suggestive of infanticide attempts. Other injuries associated with interspecific violence are of value for forensic examination. Our evaluation of the Yale Peabody Museum collection provides a baseline for future research and testable hypotheses for alternate techniques, such as isotopic analyses of calculus and noninvasive genetic testing. Museum collections continue to provide new insights into taxonomic and individual variation and environmental cues, and ultimately allow for comparisons between modern and historical environmental and behavioral variables.
Why phylogenies do not always predict ecological differences

The merger of phylogenies with ecology has given rise to the field of “community phylogenetics” predicated on the assumption that ecological differences among species can be estimated from phylogenetic relationships (the phylogenetic distance/ecological difference, PDED, hypothesis). A number of studies have failed to find strong support for this assumption, thus challenging the utility of phylogenetic approaches. This gap might highlight the fact that the PDED relationship is not useful for community assembly, but it is difficult to know because the lack of a relationship might also be due to a number of biological or methodological reasons, including inappropriate phylogenies, skewed distributions of phylogenetic distances, the lack of consideration of models of trait evolution, or the absence of sufficient niche space in experimental and observational venues. Each of these limitations, separately or combined, may confound recent experimental or observational results that examine relationships between phylogenetic distance and ecological differences. Notably, common evolutionary models can support alternative conclusions about the relationship between evolutionary distances and ecological differences than typically assumed and can change interpretations of community-based phylogenetic analyses. Here we review a number of issues that may lead to confounded effects in community phylogenetic analyses. In light of these potential pitfalls, we provide a number of guidelines for researchers to follow and stress that they need to address methodological shortcomings before concluding that ecological differences are unrelated to phylogenetic distances. This article is protected by copyright. All rights reserved.
Comparative Phytochemical and Antioxidant Properties of Costus pictus and C. speciosus

Introduction: C. pictus, known as spiral ginger, an ornamental plant which has its origin in Mexico, but cultivated in Indian state of Kerala. C. speciosus could be collected from its natural habitat, but due to ruthless and indiscriminate collection it is endangered. These species are used in many of the indigenous preparation, mainly known for anti-diabetic and anti-hyperlipidaemic properties. The current study is an attempt to compare the phytochemical and antioxidant potential of the two species. Methods: Phytochemical test was carried out in order to figure out the constituents present in the two species of Costus. Further antioxidant activity was carried out in ethanolic extracts by DPPH radical scavenging assay and reducing power assay in vitro by standardised chemical methods using ascorbic acid as standard. Preliminary phytochemical tests and WHO recommended parameters of standardisation were performed. HPTLC fingerprinting profile of the leaf was also been carried out. Results: Antioxidant potential of C. speciosus and C. pictus is attributed to mainly phytoconstituents such as tannins, phenols, flavonoids. Both the species showed equally good antioxidant potential, C. speciosus was better radical scavenger in DPPH assay while C. pictus had a better reducing power. Conclusion: The study has provided evidence of good antioxidant in the species of Costus investigated.
Breeding system evolution in relation to adult sex ratios

The study of breeding system evolution has been prolific given the broad subjects that it embraces, from the social environment and sexual selection to courtship behaviour and parental care. The general objective of this dissertation was to test empirically ideas shown in recent models of breeding system evolution. Using plovers Charadrius spp. as model organisms, which show remarkable variation in breeding systems, I investigate how adult sex ratio (ASR) and operational sex ratio (OSR) are linked together and relate to two major components of breeding systems: courtship behaviour and parental care. Experimental studies have led to equate ASR and OSR, but they are not necessarily the same and the way they correlate in nature is unknown. Here I show that in a wild polygamous plover population these ratios seem to be uncorrelated (Chapter 2). Differences in the social environment and the degree of mating competition between monogamous and polygamous populations could also be reflected in their courtship behaviour; higher courtship rates in a polygamous plover than in a monogamous closely-related plover support this prediction (Chapter 3). OSR may be more variable throughout time than ASR, and therefore be less reliable as a cue to the social environment. In support of this prediction ASR was better than OSR at predicting the duration of female brood care in a polygamous plover where females have variable care (Chapter 4). Sex-specific timing of breeding could differ according to the social environment and the level of mating competition in a population, I compared six populations of five closely-related plover species with varying breeding systems (Chapter 5); only one polygamous population showed sex-specific differences in arrival date and the length of time spent in the breeding grounds. Finally, I discuss the contribution of these results to the understanding of breeding system evolution and suggest potential future lines of research.
Pre-B Cell Colony-enhancing Factor (PBEF) Promotes Neutrophil Inflammatory Function through Enzymatic and Non-enzymatic Mechanisms

Pre-B Cell Colony-Enhancing Factor (PBEF) is a cytokine-like molecule that functions as a nicotinamide phosphoribosyl transferase (Nampt) in a salvage pathway of NAD biosynthesis. PBEF has well-characterized activity as an extracellular inflammatory mediator and has been proposed to signal through the insulin receptor (IR). As neutrophils are key effectors of the innate immune response to infection and injury, we hypothesized that PBEF promotes proinflammatory function in neutrophils and that these pro-inflammatory effects may occur through interactions with the neutrophil IR or through PBEF’s enzymatic Nampt activity. Our studies focused on two important facets of neutrophil inflammatory function: their ability to generate reactive oxygen species (ROS) and undergo constitutive apoptosis. We found that, although PBEF does not activate oxidative burst on its own, it primes for ROS generation through the NADPH oxidase. PBEF promotes membrane translocation of cytosolic NADPH oxidase subunits p40 phox and p47 phox , but not p67 phox , induces p40 phox phosphorylation and activates Rac. Priming, translocation and phosphorylation are dependent on activation of p38 and ERK mitogen activated protein kinases. PBEF priming of neutrophils occurs independent of its Nampt capacity or of interactions with IR. We next
Efficient CRISPR/Cas-mediated homologous recombination in the model diatom Thalassiosira pseudonana

CRISPR/Cas enables targeted genome editing in many different plant and algal species including the model diatom Thalassiosira pseudonana. However, efficient gene targeting by homologous recombination (HR) to date is only reported for photosynthetic organisms in their haploid life-cycle phase and there are no examples of efficient nuclease-meditated HR in any photosynthetic organism. Here, a CRISPR/Cas construct, assembled using Golden Gate cloning, enabled highly efficient HR for the first time in a diploid photosynthetic organism. HR was induced in T. pseudonana by means of sequence specific CRISPR/Cas, paired with a donor matrix, generating substitution of the silacidin gene by a resistance cassette (FCP:NAT). Approximately 85% of NAT resistant T. pseudonana colonies screened positive for HR using a nested PCR approach and confirmed by sequencing of the PCR products. The knockout of the silacidin gene in T. pseudonana caused a significant increase in cell size, confirming the role of this gene for cell-size regulation in centric diatoms. Highly efficient gene targeting by HR makes T. pseudonana as genetically tractable as Nannochloropsis and Physcomitrella, hence rapidly advancing functional diatom biology, bionanotechnology and any biotechnological application targeted on harnessing the metabolic potential of diatoms.
Understanding the developmental basis of grain yield potential in bread wheat

Grain yield potential in wheat is a complex trait controlled by sub-traits like grain number, grain size, and assimilate partitioning. To achieve further understanding of grain yield potential, this thesis combines physiological and genetic dissection of wheat development. In particular, how the length of developmental phases can be optimized in favour of increased partitioning of assimilates to the spike, in order to reduce abortion rates of florets. The physiological section of the thesis (Chapter 2 and 3) comprises the in depth study of the CIMCOG panel (CIMMYT Core Germplasm). In this section the variation in patterns of floret and phenological development was determined, ascertaining how these differences affect the number of fertile florets. The differences in floret development were clear in the intermediate florets (floret primordia 3, 4, and 5 from the rachis). Floret survival was found to be positively related to the length of the period of floret development. Also fruiting efficiency, using the frontier concept, show a positive relationship with the stem elongation period. The genetic section (Chapter 4 and 5) involves the use of quantitative trait locus (QTL) analysis with a segregating population to determine the chromosomal locations affecting key developmental traits. A Buster x Charger doubled haploid population provided a crucial contrast between similar genetic background and differences in length of phenological phases. The results show that a QTL on chromosome 7A has an effect on the time to terminal spikelet phase, i.e. the onset of stem elongation, and QTL affecting time to heading was found on chromosomes 2D and 4A. Furthermore, this population also varies in lodging resistance. A major QTL was found on chromosome 2D affecting height and providing lodging resistance. These studies provide the basis to optimise wheat developmental patterns and, therefore, maximize spike fertility.
Snail Hosts of Schistosomiasis and Other Snail-Transmitted Diseases in Tropical America: A Manual: by Emile A. Malek. ix + 325 pages, illustrated. Pan American Health Organization, 525 23rd Street, N.W., Washington, DC 20037. 1985. $12.00

Dr. Malek has, with this manual, updated the 1968 PAHO publication A Guide for the Identification of the Snail Intermediate Hosts of Schistosomiasis in the Americas. The 1968 work has been expanded to cover snail hosts of fascioliasis, paragonimiasis, and angio-strongyliasis. The manual is primarily concerned with schistosomiasis in the Neotropics, i.e., Schistosoma mansoni transmitted by various planorbid snails. This topic is the forte of the author and is covered with excellence. Schistosomiasis and snail hosts of Schistosoma mansoni occupies some 25% of the manual. This section includes the anatomy and ecology of the planorbid intermediate hosts and a key to the 18 species of neotropical Biomphalaria. An additional 13% of the manual covers how to collect, preserve and store snails, to rear and maintain living snails, and to control snails. Some 6% of the manual deals with lymnaeid snails and fascioliasis, 15% with hydrobioid snails and paragonimiasis, and 15% with land snails and angiostrongyliasis.