Miracle-dz/UniFAR-FTUs huggingface dataset:
Characterization of Cu-rich aggregates in neurogenic niches of the rodent brain by X-ray fluorescence microscopy

Sullivan, Brendan T. PhD, Purdue University, May 2016. Characterization of Cu-rich aggregates in neurogenic niches of the rodent brain by X-ray fluorescence microscopy. Major Professor: Yulia Pushkar. Copper is an essential element in the brain playing several critical roles ranging from neurotransmitter synthesis to ATP production. As Cu is typically present in micromolar concentrations and has a spatially capricious distribution in the brain, determining concentrations has historically been challenging. X-ray fluorescence microscopy (XRF) offers excellent spatial resolution (down to 30 nm) and detection limits (sub parts per million), making it an excellent tool for analyzing metal distributions in the brain. Using XRF, it is demonstrated that Cu-rich aggregates with concentrations in the hundreds of millimolar are present in the subventricular zone of rats and mice. As the subventricular zone is a neurogenic niche in the adult brain, the hippocampal dentate gyrus and rostral migratory stream were also examined to see if these aggregates were present. It is shown that rats, but not mice, have Cu accumulations in the rostral migratory stream and dentate gyrus, which may be related to the fact that the rat hippocampus produces more neurons and new neurons are integrated more readily into neural circuits. In addition, these aggregates are found in glial fibrillary acidic protein-positive cells and a lack of co-localization with bromodeoxyuridine suggests they are specifically in type-B progenitor cells in the SVZ. Co-localization experiments with lysosomal associated membrane protein 1 and ubiquitin suggest that Cu aggregates are not simply awaiting autophagy but likely serve some purpose. (XANES) spectra recorded directly from Cu aggregates in tissue show that Cu is present as a CuxSy multimetallic cluster and has the oxidation state Cu . Consistent with being bound as a cuprous-thiolate cluster, Cu aggregates consistently co-localize with sulfur with a molar ratio of [S]/[Cu] = 1.66 ± 0.07. By co-localizing
Movement correlates of lizards’ dorsal pigmentation patterns

Summary Understanding the ecological function of an animal's pigmentation pattern is an intriguing research challenge. We used quantitative information on lizard foraging behaviour to search for movement correlates of patterns across taxa. We hypothesized that noticeable longitudinal stripes that enhance escape by motion dazzle are advantageous for mobile foragers that are highly detectable against the stationary background. Cryptic pigmentation patterns are beneficial for less-mobile foragers that rely on camouflage to reduce predation. Using an extensive literature survey and phylogenetically controlled analyses, we found that striped lizards were substantially more mobile than lizards with cryptic patterns. The percentage of time spent moving was the major behavioural index responsible for this difference. We provide empirical support for the hypothesized association between lizard dorsal pigmentation patterns and foraging behaviour. Our simple yet comprehensive explanation may be relevant to many other taxa that present variation in body pigmentation patterns.
Effects of Probiotics on the Expression of Cathelicidins in Response to Stimulation by Salmonella Minnesota Lipopolysaccharides in the Proventriculus and Cecum of Broiler Chicks

The aim of this study was to determine whether probiotic-feeding affected the expression of cathelicidins (CATHs), a major family of antimicrobial peptides, in response to lipopolysaccharides (LPS) challenge in the proventriculus and cecum of broiler chicks. One-day-old male Chunky broiler chicks were fed with or without 0.4% probiotics for 7 days (P-group and non-P-group, respectively). Then, they were orally challenged with no LPS (0-LPS), 1 µg LPS (1-LPS), or 100 µg LPS (100-LPS) (n=5 in all groups) in Experiment 1, and with no LPS or 1 µg LPS (n=6 in all groups) in Experiment 2. Five hours after LPS challenge, the proventriculi and ceca were collected to analyze CATHs expression. Expression of CATHs was examined at first by reverse transcription-polymerase chain reaction (RT-PCR) using the 0-LPS chicks of non-P-group. The differences in CATHs expression upon probiotics-feeding and LPS were analyzed by real time-PCR. All four CATHs (CATH1, 2, 3 and 4) were expressed in the proventriculus and cecum of chicks. In the proventriculus, the expression of CATHs after LPS challenge did not show significant differences between non-P and P-groups in Experiment 1 and 2. In the cecum, the interactions of the effects of probiotics and LPS on the expression of CATH2 in Experiment 1 and CATH1 and 2 in Experiment 2 were significant, and their expression in 1-LPS chicks was higher in P-group than in non-P-group. However, CATH3 and 4 did not show any significant differences between non-P- and P-groups challenged with LPS. These results suggest that probiotics-feeding may stimulate the immunodefense system mediated by CATH2 and possibly CATH1 against infection by Gram-negative bacteria in the cecum.
Virulence of the invasive ash pathogen Hymenoscyphus fraxineus in old and recently established populations

Following its introduction from Asia in the 1990s, the ascomycete Hymenoscyphus fraxineus has caused a severe dieback of Fraxinus excelsior in Europe. In this study we assess and compare the virulence of 200 H. fraxineus isolates equally representing (i) two geographically distant populations with a different disease history (Switzerland, recently established populations at the epidemic front vs. Lithuania, old established populations), and (ii) two different types of host tissue (necrotic bark lesions as dead-end tissue vs. fallen leaf petioles as primary host tissue). Inoculations conducted on 3-year-old F. excelsior seedlings showed that the vast majority of the isolates (98%) were able to induce necrotic bark lesions after 10 months. Although a high variation in virulence was observed among isolates, no significant differences were detected between the older and the epidemic-front populations. Decline in virulence of populations of invasive organisms is generally assumed with increasing age of epidemics. This, however, does not appear to hold true for H. fraxineus. Either the Lithuanian population is still too young (15–20-years-old) to show a decline in virulence, or the size of the host population may still not be critical for pathogen survival. Given that bark lesions represent an epidemiological dead end and do not benefit the survival of H. fraxineus, a trend towards reduced “bark virulence” of isolates originating from leaf petioles compared to isolates from the bark lesions was expected. Such a trend, however, was observed neither in old, nor in recently established populations. This article is protected by copyright. All rights reserved.
Deep Learning With Electronic Health Records for Short-Term Fracture Risk Identification: Crystal Bone Algorithm Development and Validation

Background Fractures as a result of osteoporosis and low bone mass are common and give rise to significant clinical, personal, and economic burden. Even after a fracture occurs, high fracture risk remains widely underdiagnosed and undertreated. Common fracture risk assessment tools utilize a subset of clinical risk factors for prediction, and often require manual data entry. Furthermore, these tools predict risk over the long term and do not explicitly provide short-term risk estimates necessary to identify patients likely to experience a fracture in the next 1-2 years. Objective The goal of this study was to develop and evaluate an algorithm for the identification of patients at risk of fracture in a subsequent 1- to 2-year period. In order to address the aforementioned limitations of current prediction tools, this approach focused on a short-term timeframe, automated data entry, and the use of longitudinal data to inform the predictions. Methods Using retrospective electronic health record data from over 1,000,000 patients, we developed Crystal Bone, an algorithm that applies machine learning techniques from natural language processing to the temporal nature of patient histories to generate short-term fracture risk predictions. Similar to how language models predict the next word in a given sentence or the topic of a document, Crystal Bone predicts whether a patient’s future trajectory might contain a fracture event, or whether the signature of the patient’s journey is similar to that of a typical future fracture patient. A holdout set with 192,590 patients was used to validate accuracy. Experimental baseline models and human-level performance were used for comparison. Results The model accurately predicted 1- to 2-year fracture risk for patients aged over 50 years (area under the receiver operating characteristics curve [AUROC] 0.81). These algorithms outperformed the experimental baselines (AUROC 0.67) and showed meaningful improvements when compared to retrospective approximation of human-level performance by correctly identifying 9649 of 13,765 (70%) at-risk patients who did not receive any preventative bone-health-related medical interventions from their physicians. Conclusions These findings indicate that it is possible to use a patient’s unique medical history as it changes over time to predict the risk of short-term fracture. Validating and applying such a tool within the health care system could enable automated and widespread prediction of this risk and may help with identification of patients at very high risk of fracture.
Numerical evaluation of the direct method for cohesive law extraction in shear by the End-Notched Flexure test

With adhesive bonding, design can be oriented towards lighter structures, not only regarding the direct weight saving advantages of the joint over fastened or welded joints, but also because of flexibility to joint different materials. Cohesive Zone Models (CZM) are a powerful design tool, although the CZM laws of the adhesive bond in tension and shear are required as input in the models. This work evaluated the shear fracture toughness and CZM laws of bonded joints. The End-Notched Flexure (ENF) test geometry was used with this purpose. The experimental work consisted on the shear fracture characterization of the bond by conventional and the J-integral techniques. Additionally, by the J-integral technique, the precise shape of the cohesive law was defined. Numerical Finite Element (FE) simulations were carried out in Abaqus to assess the accuracy of the obtained CZM laws in predicting the experimental behaviour of the ENF tests, with positive results. As output of this work, fracture data is provided in shear for the selected adhesive, allowing the subsequent strength prediction of bonded joints. © 2015 The Authors. Published by Elsevier Ltd. Peer-review under responsibility of INEGI Institute of Science and Innovation in Mechanical and Industrial Engineering.
Distribution, habitat and movement of juvenile smooth hammerhead sharks (Sphyrna zygaena) in northern New Zealand

ABSTRACT The smooth hammerhead shark, Sphyrna zygaena, occurs in warm temperate waters around the northern North Island of New Zealand. Commercial fishing records and research trawl survey data were used to determine their distribution. Highest catch rates were recorded in relatively sheltered bays and coastlines along the northeast coast of North Island. Neonate and juvenile sharks use shallow coastal waters and large harbours and estuaries as nursery areas up to an age of two years and total length of 150 cm. Five sharks were electronically tagged but two apparently died and three (137–160 cm total length) returned useful data. Two tagged sharks remained in or near the Bay of Islands for 6–55 days after tagging, moving extensively through the bay. A third shark moved about 155 km southeast in 250 days. That shark spent 70 days mostly shallower than 10 m (94% of time) with occasional dives to 40 m. Thereafter, it oscillated between the surface and depths of 60−80 m, with most time (55%) being spent at 40−60 m. Maximum recorded depth was 144 m.
Differential plant species responses to interactions of sand burial, precipitation enhancement and climatic variation promote co‐existence in Chinese steppe vegetation

Aims Sand burial and precipitation play important roles in vegetation of inland deserts and desertified areas, and both are under strong influence of climate and land-use change. Sand deposition and precipitation both vary greatly in space and time, and different plant species, with diverse adaptations, occupy different niches along spatial gradients in the combination of sand and water availability dynamics. We hypothesized that species specificity in spatial and temporal niche occupation along such gradients is a mechanism for their co-existence and, thereby, a driver and stabilizer of biodiversity in dry, sandy areas. Location Ordos Plateau, China. Methods We conducted a 2-yr field experiment with factorial treatments of precipitation (control, slight enhancement, strong enhancement) and sand addition (control, medium addition, large addition). Plant cover of the six dominant species was followed over different seasons, as we expected different species to benefit from different treatments in different seasons and years with different weather regimes. Results Sand burial alone significantly affected plant cover of all six dominant species, while precipitation enhancement had no significant effect. Effects of sand burial on plant cover changed overall during the two hydrologically contrasting years. Our key finding was that there were multiple significant two- and three-way interactions between species, sand burial and precipitation enhancement on plant cover, while there were also multiple two- and three-way interactions involving species, sand burial or precipitation treatment with year and/or season. Conclusion Our results supported our hypothesis, i.e. the co-existence of species in a semi-arid sand dune can be explained from the different niches they occupy in terms of seasonal and year-to-year variation in precipitation in combination with sand deposition regime. The interactions of these drivers on plant cover with experimental enhancement of precipitation, mimicking a realistic scenario for this region, suggest that shifts in species composition are to be expected this century. More generally, our findings advance our understanding of what drives species co-existence and thereby biodiversity, now and in the future.
Homology and synapomorphy‐symplesiomorphy—neither synonymous nor equivalent but different perspectives on the same phenomenon

In a recent debate, either synapomorphy and symplesiomorphy or only synapomorphy have been claimed to be synonymous or equivalent to homology. In my view, exactly the same relationship exists between homology supported by a congruence test on the one hand and synapomorphy as well as symplesiomorphy on the other hand. Both conditions become established at the same time with the process of rooting of an unrooted topology. I, however, do not consider the concept of homology equal or synonymous to that of synapomorphy and symplesiomorphy. In my view, they represent different perspectives on the same phenomenon, i.e. correspondence by common origin. Homology has no implication on the direction of transformation, whereas symplesiomorphy as “primitive” condition and synapomorphy as “derived” condition refer directly to phylogenesis, the real historical evolutionary process of speciation and transformation. In addition, synapomorphy and symplesiomorphy might also refer to a character state that refers to the absence of a structure/organ, which creates problems with traditional homology concepts. Hennig's terms synapomorphy and symplesiomorphy are necessary and sufficient for the evolutionary interpretation of character states. For what is corroborated in an unrooted topology as the result of a congruence test, I suggest as a new term “synmorphy” because it can well be applied also to those characters where one state represents the absence of a structure/organ. The place for homology in morphological cladistics, however, is restricted to the characterization of the relationship between different character states of one transformation series (i.e. character).
The need to include phylogeny in trait-based analyses of community composition

A growing number of studies incorporate functional trait information to analyse patterns and processes of community assembly. These studies of trait-environment relationships generally ignore phylogenetic relationships among species. When functional traits and the residual variation in species distributions among communities have phylogenetic signal, however, analyses ignoring phylogenetic relationships can decrease estimation accuracy and power, inflate type I error rates, and lead to potentially false conclusions. Using simulations, we compared estimation accuracy, statistical power, and type I error rates of linear mixed models (LMM) and phylogenetic linear mixed models (PLMM) designed to test for trait-environment interactions in the distribution of species abundances among sites. We considered the consequences of both phylogenetic signal in traits and phylogenetic signal in the residual variation of species distributions generated by an unmeasured (latent) trait with phylogenetic signal. When there was phylogenetic signal in the residual variation of species among sites, PLMM provided better estimates (closer to the true value) and greater statistical power for testing whether the trait-environment interaction regression coefficient differed from zero. LMM had unacceptably high type I error rates when there was phylogenetic signal in both traits and the residual variation in species distributions. When there was no phylogenetic signal in the residual variation in species distributions, LMM and PLMM had similar performances. LMMs that ignore phylogenetic relationships can lead to poor statistical tests of trait-environment relationships when there is phylogenetic signal in the residual variation of species distributions among sites, such as caused by unmeasured traits. Therefore, phylogenies and PLMMs should be used when studying how functional traits affect species abundances among communities in response to environmental gradients.
Purification, Characterization of a Novel Fibrinolytic Enzyme from Paenibacillus sp. IND8, and its in Vitro Thrombolytic Activity

In the present study, a fibrinolytic enzyme from Paenibacillus sp. IND8 was isolated and characterized. This enzyme was purified by 12.4-fold using ammonium sulphate precipitation, diethyl amino ethyl-cellulose, and casein–agarose column chromatography. The purified enzyme showed homogenous in terms of sodium dodecyl sulfate-polyacrylamide gel electrophoresis with a molecular weight of 44 kDa. This enzyme depicted an optimal pH of 7.0 and was stable at pH 7.0–9.0. The optimal temperature was found to be 40°C and was highly stable at this temperature. The enzyme activity was inhibited by the addition of tested ions. The fibrinolytic enzyme dissolved fibrin net of blood clot completely in vitro, which may have potent application in the treatment of myocardial infarction.
Systematic Palaeontology (Vertebrate Palaeontology) The earliest Muntiacus (Artiodactyla, Mammalia) from the Late Miocene of Yuanmou, southwestern China

The extended excavations from 1998 to 2000 in Yuanmou, Yunnan Province, southwestern China, resulted in the discovery of a new Late Miocene (ca 9–7 Ma) hominoid locality with associated mammalian fauna at Leilao. It includes a new muntjak, Muntiacus leilaoensis sp. nov. It has similar morphology to the extant forms and is the earliest record of the Muntiacus. This discovery shows that the Muntiacus are a persistent and conservative group in contrast with the other rapidly evolving cervids
Competition and facilitation determine dwarf mistletoe infection dynamics

Interspecific interactions have a fundamental role in plant population dynamics, as they may set the conditions for species coexistence. Parasitic plants, like dwarf mistletoes, offer the opportunity to study competition for resources that are different from those consumed by most plants, allowing for a better understanding of the interaction. We explored how interspecific interactions between two dwarf mistletoe species (Arceuthobium), co‐infecting the same host species (even sharing the same individual tree of Pinus hartwegii) affect their infection dynamics at two different stages of population development (colonization of new hosts and subsequent growth), and if heterogeneity in resource availability (host density and size structure) affects these interactions. For that purpose, we integrated these processes into a spatially explicit model of density‐dependent population growth. We found that self‐regulation (density‐dependence) was strong for both species; however, the intensity and sign of interspecific interactions changed depending on host size and demographic process. Population growth in Arceuthobium globosum was reduced by competition, except for smaller hosts where A. globosum growth was facilitated by Arceuthobium vaginatum. Arceuthobium vaginatum was facilitated by A. globosum regardless of host size. Colonization of new hosts by A. globosum was enhanced by previous infection by the other species, showing intraguild facilitation. Demographic importance of interactions depended on stand structure: in homogeneous, low‐density forests, facilitation predominates, increasing the population sizes of both species, whereas the opposite occurs in heterogeneous and dense forests. Both species achieved stable coexistence, fulfilling the invasibility criterion because each mistletoe species can invade a forest that is already infected by the other species. Synthesis. Despite the fundamentally different mechanisms underlying the interactions between mistletoes compared with non‐parasitic plants, our results reveal that their behaviour at the population level is similar. Stabilizing mechanisms, like strong self‐limiting population growth, allow dwarf mistletoe coexistence. Interactions shift as populations develop, and they depend largely on environmental factors such as forest structure. Intraguild mutualism is shown as a relevant process for colonization of new spaces, highlighting the complexity of competitive/facilitative interactions between parasitic plants, a formerly unexplored subject. Interactions can only be fully understood when integrating all their components at the population level. Analysing these interactions may contribute to the understanding of plant–plant interactions in general, and convey interesting implications for forest management.