Miracle-dz/UniFAR-FTUs huggingface dataset:
Early role of Fsp1 in epithelial-mesenchymal transformation.

A seamless plasticity exists among cells shifting between epithelial and mesenchymal phenotypes during early development and again later, in adult tissues, following wound repair or organ remodeling in response to injury. Fsp1, a gene encoding a fibroblast-specific protein associated with mesenchymal cell morphology and motility, is expressed during epithelial-mesenchymal transformations (EMT) in vivo. In the current study, we identified several cytokines that induce Fsp1 in cultured epithelial cells. A combination of these factors, however, was most efficacious at completing the process of EMT. The optimal combination identified were two of the cytokines classically associated with fibrosis, i.e., transforming growth factor-β1 (TGF-β1) and epidermal growth factor (EGF). To confirm that it was the induction of Fsp1 by these cytokines mediating EMT, we used antisense oligomers to block Fsp1 production and subsequently measured cell motility and markers of EMT phenotype. The antisense oligomers suppressed Fsp1 expression and epithelial transformation; therefore, we conclude that the appearance of Fsp1 is an important early event in the pathway toward EMT.
Spinal Lewy body pathology in older adults without an antemortem diagnosis of Parkinson's disease

To test the hypothesis that Lewy body pathology (LBs) is present in the spinal cord of older community‐dwelling adults without a clinical diagnosis of Parkinson's disease (PD). We studied 162 prospective autopsies from older adults with PD (N = 6) and without PD (N = 156). We documented the presence of LBs in cerebrum and brainstem structures from each of the six regions used for Braak PD staging and four spinal cord levels (C5/6, T7, L4/5 and S4/5). Parkinsonism proximate to death was based on a previously validated measure present if two or more of the four signs of parkinsonism were present based on a modified version of the Unified Parkinson's Disease Rating Scale (UPDRS). Fifty‐three of 156 individuals without PD (34%) had LBs in a least one site within the CNS. About half of cases with LBs in the cerebrum or brainstem, (25/53, 47%) also had spinal LBs. Almost 90% (22/25, 88%) of cases with spinal LBs had LBs in the cerebrum (Braak stages 4–6) and about 10% (3/25, 12%) had only brainstem LBs (Braak stages 1–3). Four of six cases with PD showed LBs in cerebrum, brainstem and spinal cord. Individuals with LBs in the spinal cord were more likely to have clinical parkinsonism proximate to death compared to individuals with LBs in brainstem and cerebrum alone (52% vs. 32%; Chi‐Square x2 = 5.368, d.f. = 1, P = 0.0.021) and more severe nigral neuronal loss (48% vs. 11%; Chi‐Square x2 = 9.049, d.f. = 1, P = 0.003). These findings were unchanged when we included cases with a history of PD. Older community‐dwelling adults without a clinical diagnosis of PD have evidence of LBs throughout the CNS including the spinal cord which is associated with parkinsonism and more severe nigral neuronal loss.
Broad Consent for Research on Biospecimens: The Views of Actual Donors at Four U.S. Medical Centers

Commentators are concerned that broad consent may not provide biospecimen donors with sufficient information regarding possible future research uses of their tissue. We surveyed with interviews 302 cancer patients who had recently provided broad consent at four diverse academic medical centers. The majority of donors believed that the consent form provided them with sufficient information regarding future possible uses of their biospecimens. Donors expressed very positive views regarding tissue donation in general and endorsed the use of their biospecimens in future research across a wide range of contexts. Concerns regarding future uses were limited to for-profit research and research by investigators in other countries. These results support the use of broad consent to store and use biological samples in future research.
Trade-offs between survival, longevity, and reproduction, and variation of survival tolerance in Mediterranean Bemisia tabaci after temperature stress

Abstract The invasive Mediterranean Bemisia tabaci (Gennadius) (Hemiptera: Aleyrodidae) has emerged as one of the most common agricultural pests in the world. In the present study, we examined the cross-tolerance, fitness costs, and benefits of thermal tolerance and the variation in the responses of life history traits after heat-shock selection. The results showed that survival and longevity of Mediterranean B. tabaci were decreased significantly after direct or cross temperature stress and that the number of eggs per female was not reduced significantly. Furthermore, heat-shock selection dramatically increased the survival of Mediterranean B. tabaci within two generations, and it did not significantly affect the egg number per female within five generations. These results indicated that there was a trade-off between survival, longevity, and reproduction in Mediterranean B. tabaci after temperature stress. The improvement in reproduction was costly in terms of decreased survival and longevity, and there was a fitness consequence to temperature stress. In addition, heat tolerance in Mediterranean B. tabaci increased substantially after selection by heat shock, indicating a considerable variation for survival tolerance in this species. This information could help us better understand the thermal biology of Mediterranean B. tabaci within the context of climate change.
Host Adaptation of Soybean Dwarf Virus Following Serial Passages on Pea (Pisum sativum) and Soybean (Glycine max)

Soybean Dwarf Virus (SbDV) is an important plant pathogen, causing economic losses in soybean. In North America, indigenous strains of SbDV mainly infect clover, with occasional outbreaks in soybean. To evaluate the risk of a US clover strain of SbDV adapting to other plant hosts, the clover isolate SbDV-MD6 was serially transmitted to pea and soybean by aphid vectors. Sequence analysis of SbDV-MD6 from pea and soybean passages identified 11 non-synonymous mutations in soybean, and six mutations in pea. Increasing virus titers with each sequential transmission indicated that SbDV-MD6 was able to adapt to the plant host. However, aphid transmission efficiency on soybean decreased until the virus was no longer transmissible. Our results clearly demonstrated that the clover strain of SbDV-MD6 is able to adapt to soybean crops. However, mutations that improve replication and/or movement may have trade-off effects resulting in decreased vector transmission.
The Application of Dehydroepiandrosterone on Improving Mitochondrial Function and Reducing Apoptosis of Cumulus Cells in Poor Ovarian Responders

Poor ovarian responders (PORs) pose a great challenge for in vitro fertilization (IVF). Previous studies have suggested that dehydroepiandrosterone (DHEA) may improve IVF outcomes in PORs. The current study attempted to investigate the clinical benefits of DHEA in PORs and the possible mechanisms of DHEA on cumulus cells (CCs). This was a prospective study performed at one tertiary center from January 2015 to March 2016. A total of 131 women who underwent IVF treatment participated, including 59 normal ovarian responders (NORs) and 72 PORs. PORs were assigned to receive DHEA supplementation or not before the IVF cycle. For all patients, CCs were obtained after oocyte retrieval. In the CCs, mRNA expression of apoptosis-related genes and mitochondrial transcription factor A (TFAM) gene, terminal deoxynucleotidyl transferase dUTP nick end labeling assay, mitochondrial dehydrogenase activity and mitochondrial mass were measured. The results indicated that PORs with DHEA supplementation produces a great number of top-quality embryos at day 3 and increased the number of transferred embryos and fertilization rate compared with those without DHEA supplementation. Additionally, supplementation with DHEA in PORs decreased DNA damage and apoptosis in CCs while enhancing the mitochondrial mass, mitochondrial dehydrogenase activity and TFAM expression in CCs. In conclusion, our results showed that the benefits of DHEA supplementation on IVF outcomes in PORs were significant, and the effects may be partially mediated by improving mitochondrial function and reducing apoptosis in CCs.
Genotypic and Lipid Analyses of Strains From the Archaeal Genus Halorubrum Reveal Insights Into Their Taxonomy, Divergence, and Population Structure

To gain a better understanding of how divergence occurs, and how taxonomy can benefit from studying natural populations, we isolated and examined 25 closely related Halorubrum strains obtained from different hypersaline communities and compared them to validly named species and other reference strains using five taxonomic study approaches: phylogenetic analysis using the 16S rRNA gene and multilocus sequencing analysis (MLSA), polar lipid profiles (PLP), average nucleotide identity (ANI) and DNA-DNA hybridization (DDH). 16S rRNA gene sequence could not differentiate the newly isolated strains from described species, while MLSA grouped strains into three major clusters. Two of those MLSA clusters distinguished candidates for new species. The third cluster with concatenated sequence identity equal to or greater than 97.5% was comprised of strains from Aran-Bidgol Lake (Iran) and solar salterns in Namibia and Spain, and two previously described species isolated from Mexico and Algeria. PLP and DDH analyses showed that Aran-Bidgol strains formed uniform populations, and that strains isolated from other geographic locations were heterogeneous and divergent, indicating that they may constitute different species. Therefore, applying only sequencing approaches and similarity cutoffs for circumscribing species may be too conservative, lumping concealed diversity into a single taxon. Further, our data support the interpretation that local populations experience unique evolutionary homogenization pressures, and once relieved of insular constraints (e.g., through migration) are free to diverge.
GAGAN: Geometry-Aware Generative Adversarial Networks

Deep generative models learned through adversarial training have become increasingly popular for their ability to generate naturalistic image textures. However, aside from their texture, the visual appearance of objects is significantly influenced by their shape geometry; information which is not taken into account by existing generative models. This paper introduces the Geometry-Aware Generative Adversarial Networks (GAGAN) for incorporating geometric information into the image generation process. Specifically, in GAGAN the generator samples latent variables from the probability space of a statistical shape model. By mapping the output of the generator to a canonical coordinate frame through a differentiable geometric transformation, we enforce the geometry of the objects and add an implicit connection from the prior to the generated object. Experimental results on face generation indicate that the GAGAN can generate realistic images of faces with arbitrary facial attributes such as facial expression, pose, and morphology, that are of better quality than current GAN-based methods. Our method can be used to augment any existing GAN architecture and improve the quality of the images generated.
Mechanisms of Adaptive Immunity to Porcine Reproductive and Respiratory Syndrome Virus

The adaptive immune response is necessary for the development of protective immunity against infectious diseases. Porcine reproductive and respiratory syndrome virus (PRRSV), a genetically heterogeneous and rapidly evolving RNA virus, is the most burdensome pathogen of swine health and wellbeing worldwide. Viral infection induces antigen-specific immunity that ultimately clears the infection. However, the resulting immune memory, induced by virulent or attenuated vaccine viruses, is inconsistently protective against diverse viral strains. The immunological mechanisms by which primary and memory protection are generated and used are not well understood. Here, we summarize current knowledge regarding cellular and humoral components of the adaptive immune response to PRRSV infection that mediate primary and memory immune protection against viruses.
Ethics of treatment interruption trials in HIV cure research: addressing the conundrum of risk/benefit assessment

Though antiretroviral therapy is the standard of care for people living with HIV, its treatment limitations, burdens, stigma and costs lead to continued interest in HIV cure research. Early-phase cure trials, particularly those that include analytic treatment interruption (ATI), involve uncertain and potentially high risk, with minimal chance of clinical benefit. Some question whether such trials should be offered, given the risk/benefit imbalance, and whether those who choose to participate are acting rationally. We address these questions through a longitudinal decision-making study nested in a Thai acute HIV research cohort. In-depth interviews revealed central themes about decisions to join. Participants felt they possessed an important identity as members of the acute cohort, viewing their bodies as uniquely suited to both testing and potentially benefiting from HIV cure approaches. While acknowledging risks of ATI, most perceived they were given an opportunity to interrupt treatment, to test their own bodies and increase normalcy in a safe, highly monitored circumstance. They were motivated by potential benefits to themselves, the investigators and larger acute cohort, and others with HIV. They believed their own trial experiences and being able to give back to the community were sufficient to offset participation risks. These decisions were driven by the specific circumstances experienced by our participants. Judging risk/benefit ratios without appreciating these lived experiences can lead to false determinations of irrational decision- making. While this does not minimise vital oversight considerations about risk reduction and protection from harm, it argues for inclusion of a more participant-centered approach.
Vanadate and triclosan synergistically induce alginate production by Pseudomonas aeruginosa strain PAO1

Alginate overproduction by P. aeruginosa strains, also known as mucoidy, is associated with chronic lung infections in cystic fibrosis (CF). It is not clear how alginate induction occurs in the wild‐type (wt) mucA strains. When grown on Pseudomonas isolation agar (PIA), P. aeruginosa strains PAO1 and PA14 are non‐mucoid, producing minimal amounts of alginate. Here we report the addition of ammonium metavanadate (AMV), a phosphatase inhibitor, to PIA (PIA‐AMV) induced mucoidy in both these laboratory strains and early lung colonizing non‐mucoid isolates with a wt mucA. This phenotypic switch was reversible depending on the availability of vanadate salts and triclosan, a component of PIA. Alginate induction in PAO1 on PIA‐AMV was correlated with increased proteolytic degradation of MucA, and required envelope proteases AlgW or MucP, and a two‐component phosphate regulator, PhoP. Other changes included the addition of palmitate to lipid A, a phenotype also observed in chronic CF isolates. Proteomic analysis revealed the upregulation of stress chaperones, which was confirmed by increased expression of the chaperone/protease MucD. Altogether, these findings suggest a model of alginate induction and the PIA‐AMV medium may be suitable for examining early lung colonization phenotypes in CF before the selection of the mucA mutants.
Anti-inflammatory ω-3 endocannabinoid epoxides

Significance The health benefits of ω-3 fatty acids are mediated, in part, through metabolic conversion to bioactive epoxides. Here we detail the discovery and initial characterization of naturally occurring ω-3–derived endocannabinoid epoxides that are formed via enzymatic oxidation of ω-3 endocannabinoids by cytochrome P450s. These dual functional ω-3 endocannabinoid epoxides are anti-inflammatory and vasodilatory and reciprocally modulate platelet aggregation. By virtue of their physiological properties, they are expected to play important roles in neuroinflammation and in cerebrovascular diseases such as stroke. Clinical studies suggest that diets rich in ω-3 polyunsaturated fatty acids (PUFAs) provide beneficial anti-inflammatory effects, in part through their conversion to bioactive metabolites. Here we report on the endogenous production of a previously unknown class of ω-3 PUFA–derived lipid metabolites that originate from the crosstalk between endocannabinoid and cytochrome P450 (CYP) epoxygenase metabolic pathways. The ω-3 endocannabinoid epoxides are derived from docosahexaenoic acid (DHA) and eicosapentaenoic acid (EPA) to form epoxyeicosatetraenoic acid-ethanolamide (EEQ-EA) and epoxydocosapentaenoic acid-ethanolamide (EDP-EA), respectively. Both EEQ-EAs and EDP-EAs are endogenously present in rat brain and peripheral organs as determined via targeted lipidomics methods. These metabolites were directly produced by direct epoxygenation of the ω-3 endocannabinoids, docosahexanoyl ethanolamide (DHEA) and eicosapentaenoyl ethanolamide (EPEA) by activated BV-2 microglial cells, and by human CYP2J2. Neuroinflammation studies revealed that the terminal epoxides 17,18-EEQ-EA and 19,20-EDP-EA dose-dependently abated proinflammatory IL-6 cytokines while increasing anti-inflammatory IL-10 cytokines, in part through cannabinoid receptor-2 activation. Furthermore the ω-3 endocannabinoid epoxides 17,18-EEQ-EA and 19,20-EDP-EA exerted antiangiogenic effects in human microvascular endothelial cells (HMVEC) and vasodilatory actions on bovine coronary arteries and reciprocally regulated platelet aggregation in washed human platelets. Taken together, the ω-3 endocannabinoid epoxides’ physiological effects are mediated through both endocannabinoid and epoxyeicosanoid signaling pathways. In summary, the ω-3 endocannabinoid epoxides are found at concentrations comparable to those of other endocannabinoids and are expected to play critical roles during inflammation in vivo; thus their identification may aid in the development of therapeutics for neuroinflammatory and cerebrovascular diseases.
Multispecies coalescent delimits structure, not species

Significance Despite its widespread application to the species delimitation problem, our study demonstrates that what the multispecies coalescent actually delimits is structure. The current implementations of species delimitation under the multispecies coalescent do not provide any way for distinguishing between structure due to population-level processes and that due to species boundaries. The overinflation of species due to the misidentification of general genetic structure for species boundaries has profound implications for our understanding of the generation and dynamics of biodiversity, because any ecological or evolutionary studies that rely on species as their fundamental units will be impacted, as well as the very existence of this biodiversity, because conservation planning is undermined due to isolated populations incorrectly being treated as distinct species. The multispecies coalescent model underlies many approaches used for species delimitation. In previous work assessing the performance of species delimitation under this model, speciation was treated as an instantaneous event rather than as an extended process involving distinct phases of speciation initiation (structuring) and completion. Here, we use data under simulations that explicitly model speciation as an extended process rather than an instantaneous event and carry out species delimitation inference on these data under the multispecies coalescent. We show that the multispecies coalescent diagnoses genetic structure, not species, and that it does not statistically distinguish structure associated with population isolation vs. species boundaries. Because of the misidentification of population structure as putative species, our work raises questions about the practice of genome-based species discovery, with cascading consequences in other fields. Specifically, all fields that rely on species as units of analysis, from conservation biology to studies of macroevolutionary dynamics, will be impacted by inflated estimates of the number of species, especially as genomic resources provide unprecedented power for detecting increasingly finer-scaled genetic structure under the multispecies coalescent. As such, our work also represents a general call for systematic study to reconsider a reliance on genomic data alone. Until new methods are developed that can discriminate between structure due to population-level processes and that due to species boundaries, genomic-based results should only be considered a hypothesis that requires validation of delimited species with multiple data types, such as phenotypic and ecological information.
Semantics and implementation of schema evolution in object-oriented databases

Object-oriented programming is well-suited to such data-intensive application domains as CAD/CAM, AI, and OIS (office information systems) with multimedia documents. At MCC we have built a prototype object-oriented database system, called ORION. It adds persistence and sharability to objects created and manipulated in applications implemented in an object-oriented programming environment. One of the important requirements of these applications is schema evolution, that is, the ability to dynamically make a wide variety of changes to the database schema. In this paper, following a brief review of the object-oriented data model that we support in ORION, we establish a framework for supporting schema evolution, define the semantics of schema evolution, and discuss its implementation.
Delocalized Photomechanical Effects of UV ns Laser Ablation on Polymer Substrates Captured by Optical Holography Workstation: An overview on Experimental Result

A brief overview of results from an experimental investigation performed on polymer materials to examine delocalized photomechanical effects generated due to UV laser ablation is provided. Delocalized structural modifications were observed in PMMA, PS by means of optical holographic interferometry. The integrity of samples was examined before and after irradiation in 193 and 248 nm (15 ns) above and below ablation threshold, F = 0.1–1.0 J/cm2. A value of structural continuity was initially determined for each sample by generation of a reference holographic image before irradiation. Microscopic discontinuities were intentionally induced to act as preexistent defects. Sequential holographic recording monitored the growth of morphological alterations according to the number of pulses in the neighbor as well as far from the preexistent discontinuities. The imposed alterations are visually observable at the whole extent of the irradiated sample in distances far off the ablation spot as local cracks and voids. The induced flaws cannot be classified as transient or instantly generated. Fracture follows a long-term emergence and deterioration pattern. Extensively fluctuated long-term effects were also observed in laser-assisted varnish removal of multilayered technical samples simulating Byzantine icons with decrease of effect duration and fluctuation being according to increase in sample homogeneity.