Miracle-dz/UniFAR-FTUs huggingface dataset:
The origin, dynamics, and molecular evolution of transmissible cancers

Three transmissible cancers are known to have emerged naturally in the wild: canine transmissible venereal tumor (CTVT); Tasmanian devil facial tumor disease (DFTD); and a recently discovered leukemia-like cancer in soft-shell clams (Mya arenaria). These cancers have all acquired the ability to pass between individuals. DFTD emerged approximately 20 years ago and has decimated the Tasmanian devil population. CTVT arose over 10,000 years ago in an ancient breed of dog. The clam cancer is believed to have evolved at least 40 years ago. In this manuscript, we review CTVT and DFTD, the two transmissible mammalian cancers, and provide an overview of the leukemia-like cancer of clams. We showcase how genetics and genomics have enhanced our understanding of the unique biology, origins, and evolutionary histories of these rare cancers.
A call-up for circuit-switched NoCs in the Dark-Silicon Era

Networks-on-Chip (NoCs) are the backbone of communications in MPSoCs and future Many-Cores. The approaching thousand cores technology, together with the dark silicon era, put energy-efficiency on top of the challenges for future NoC-based multicore chips, where NoCs significantly contribute to the total chip power. This paper explores the use of circuit-switched (CS) NoCs as a low complexity energy-efficient solution for future platforms in the Dark-Silicon (Si) era. We present a thorough analysis for circuit-switched NoCs from hardware synthesis perspective at different threshold voltage (Vth) and supply levels. Based on this analysis, we further propose a Dark-si inspired multilayered-CS-NoC architecture. The proposed NoC is implemented as a mixed Vth double layered design, where each layer is optimized for a frequency level at a different supply voltage. Layer switching is explored on a per-router-port granularity level; links are either reserved on the fast or the slow layer based on the speed requirements, while the other layer is kept dark. The proposed NoC architecture is synthesized using Synopsys Design Compiler for SAED90nm technology. The obtained results show energy savings up to 34% compared to conventional single-layer single supply CS-NoCs.
Physiological Recording in the MRI Environment (PRiME): MRI-Compatible Hemodynamic Recording System

Hemodynamic recording during interventional cardiovascular procedures is essential for procedural guidance, monitoring patient status, and collection of diagnostic information. Recent advances have made interventions guided by magnetic resonance imaging (MRI) possible and attractive in certain clinical scenarios. However, in the MRI environment, electromagnetic interference (EMI) can cause severe distortions and artifacts in acquired hemodynamic waveforms. The primary aim of this paper was to develop and validate a system to minimize EMI on electrocardiogram (ECG) and invasive blood pressure (IBP) signals. A system was developed which incorporated commercial MRI compatible ECG leads and pressure transducers, custom electronics, user interface, and adaptive signal processing. Measurements were made on pediatric patients (N = 6) during MRI-guided catheterization. Real-time interactive scanning, which is known to produce significant EMI due to fast gradient switching and varying imaging plane orientations, was selected for testing. The effectiveness of the adaptive algorithms was determined by measuring the reduction of noise peaks, amplitude of noise peaks, and false QRS triggers. During real-time gradient-intensive imaging sequences, peak noise amplitude was reduced by 80% and false QRS triggers were reduced to a median of 0. There was no detectable interference on the IBP channels. A hemodynamic recording system front-end was successfully developed and deployed, which enabled high-fidelity recording of ECG and IBP during MRI scanning. The schematics and assembly instructions are publicly available to facilitate implementation at other institutions. Researchers and clinicians are provided a critical tool in investigating and implementing MRI guided interventional cardiovascular procedures.
Three-Dimensional Microfluidic Tri-Culture Model of the Bone Marrow Microenvironment for Study of Acute Lymphoblastic Leukemia

Acute lymphoblastic leukemia (ALL) initiates and progresses in the bone marrow, and as such, the marrow microenvironment is a critical regulatory component in development of this cancer. However, ALL studies were conducted mainly on flat plastic substrates, which do not recapitulate the characteristics of marrow microenvironments. To study ALL in a model of in vivo relevance, we have engineered a 3-D microfluidic cell culture platform. Biologically relevant populations of primary human bone marrow stromal cells, osteoblasts and human leukemic cells representative of an aggressive phenotype were encapsulated in 3-D collagen matrix as the minimal constituents and cultured in a microfluidic platform. The matrix stiffness and fluidic shear stress were controlled in a physiological range. The 3-D microfluidic as well as 3-D static models demonstrated coordinated cell-cell interactions between these cell types compared to the compaction of the 2-D static model. Tumor cell viability in response to an antimetabolite chemotherapeutic agent, cytarabine in tumor cells alone and tri-culture models for 2-D static, 3-D static and 3-D microfluidic models were compared. The present study showed decreased chemotherapeutic drug sensitivity of leukemic cells in 3-D tri-culture models from the 2-D models. The results indicate that the bone marrow microenvironment plays a protective role in tumor cell survival during drug treatment. The engineered 3-D microfluidic tri-culture model enables systematic investigation of effects of cell-cell and cell-matrix interactions on cancer progression and therapeutic intervention in a controllable manner, thus improving our limited comprehension of the role of microenvironmental signals in cancer biology.
Vault: Fast Bootstrapping for Cryptocurrencies

—Decentralized cryptocurrencies rely on participants to keep track of the state of the system in order to verify new transactions. As the number of users and transactions grows, this requirement places a signiﬁcant burden on the users, as they need to download, verify, and store a large amount of data in order to participate. Vaultisanew cryptocurrency designed to minimize these storage and bootstrapping costs for participants. Vault builds on Algorand’s proof-of-stake consensus protocol and uses several techniques to achieve its goals. First, Vault decouples the storage of recent transactions from the storage of account balances, which enables Vault to delete old account state. Second, Vault allows sharding state across participants in a way that preserves strong security guarantees. Finally, Vault introduces the notion of stamping certiﬁcates that allow a new client to catch up securely and efﬁciently in a proof-of-stake system without having to verify every single block. Experiments with a prototype implementation of Vault’s data structures shows that Vault reduces the bandwidth cost of joining the network as a full client by 99.7% compared to Bitcoin and 90.5% compared to Ethereum when downloading a ledger containing 500 million transactions.
Multiple System Atrophy: An Oligodendroglioneural Synucleinopathy

Multiple system atrophy (MSA) is an orphan, fatal, adult-onset neurodegenerative disorder of uncertain etiology that is clinically characterized by various combinations of parkinsonism, cerebellar, autonomic, and motor dysfunction. MSA is an α-synucleinopathy with specific glioneuronal degeneration involving striatonigral, olivopontocerebellar, and autonomic nervous systems but also other parts of the central and peripheral nervous systems. The major clinical variants correlate with the morphologic phenotypes of striatonigral degeneration (MSA-P) and olivopontocerebellar atrophy (MSA-C). While our knowledge of the molecular pathogenesis of this devastating disease is still incomplete, updated consensus criteria and combined fluid and imaging biomarkers have increased its diagnostic accuracy. The neuropathologic hallmark of this unique proteinopathy is the deposition of aberrant α-synuclein in both glia (mainly oligodendroglia) and neurons forming glial and neuronal cytoplasmic inclusions that cause cell dysfunction and demise. In addition, there is widespread demyelination, the pathogenesis of which is not fully understood. The pathogenesis of MSA is characterized by propagation of misfolded α-synuclein from neurons to oligodendroglia and cell-to-cell spreading in a “prion-like” manner, oxidative stress, proteasomal and mitochondrial dysfunction, dysregulation of myelin lipids, decreased neurotrophic factors, neuroinflammation, and energy failure. The combination of these mechanisms finally results in a system-specific pattern of neurodegeneration and a multisystem involvement that are specific for MSA. Despite several pharmacological approaches in MSA models, addressing these pathogenic mechanisms, no effective neuroprotective nor disease-modifying therapeutic strategies are currently available. Multidisciplinary research to elucidate the genetic and molecular background of the deleterious cycle of noxious processes, to develop reliable biomarkers and targets for effective treatment of this hitherto incurable disorder is urgently needed.
Dynamic knowledge integration into HBD knowledge presentation model

We aim to construct adequate models of knowledge presentation. Language is one of the main spaces of knowledge transfer, thus we have developed a model based on main dimensions of verbs in English “have”, “be”, “do” (HBD). Below we purpose ways to enhance the existing HBD model to provide more flexible knowledge acquisition of it by integration of dynamic types.
Strong Association of 677 C>T Substitution in the MTHFR Gene with Male Infertility - A Study on an Indian Population and a Meta-Analysis

Background Methylenetetrahydrofolate reductase (MTHFR) is an important enzyme of folate and methionine metabolism, making it crucial for DNA synthesis and methylation. The objective of this study was to analyze MTHFR gene 677C>T polymorphism in infertile male individuals from North India, followed by a meta-analysis on our data and published studies. Methodology/Principal Findings We undertook genotyping on a total of 837 individuals including well characterized infertile (N = 522) and confirmed fertile (N = 315) individuals. The SNP was typed by direct DNA sequencing. Chi square test was done for statistical analysis. Published studies were searched using appropriate keywords. Source of data collection for meta-analysis included ‘Pubmed’, ‘Ovid’ and ‘Google Scholar’. Those studies analyzing 677C>T polymorphism in male infertility and presenting all relevant data were included in meta-analysis. The genotype data for infertile subjects and fertile controls was extracted from each study. Chi square test was done to obtain odds ratio (OR) and p-value. Meta-analysis was performed using Comprehensive Meta-analysis software (Version 2). The frequency of mutant (T) allele (p = 0.0025) and genotypes (CT+TT) (p = 0.0187) was significantly higher in infertile individuals in comparison to fertile controls in our case-control study. The overall summary estimate (OR) for allele and genotype meta-analysis were 1.304 (p = 0.000), 1.310 (p = 0.000), respectively, establishing significant association of 677C>T polymorphism with male infertility. Conclusions/Significance 677C>T substitution associated strongly with male infertility in Indian population. Allele and genotype meta-analysis also supported its strong correlation with male infertility, thus establishing it as a risk factor.
Prognostic value of tissue and circulating levels of IMP3 in prostate cancer

Tissue levels of the oncofetal protein insulin‐like growth factor 2 (IGF2) messenger RNA‐binding protein 3 (IMP3) have been associated with poor prognosis in multiple human malignancies. However, its circulating levels have not yet been analyzed. Therefore, the aim of this study was to assess the prognostic value of both serum and tissue levels of IMP3 in prostate cancer (PC). IMP3 protein expression was analyzed in 124 PC and 13 benign prostate hyperplasia (BPH) patients using immunohistochemistry. Gene expression levels of IMP3 and its molecular target IGF2 were analyzed in 29 frozen and 26 paraffin‐embedded PC tissues using real‐time polymerase chain reaction and immunohistochemistry. Serum IMP3 levels were assessed in 94 PC and 20 BPH patients as well as in 20 controls using enzyme‐linked immunosorbent assay. IMP3 immunostaining was present in 0% (0/13) of BPHs, 15% (15/101) of clinically localized PCs and 65% (15/23) of palliatively treated metastatic PCs (p < 0.001). Accordingly, serum IMP3 concentrations were significantly higher in PC compared to BPH patients which were higher than those in controls (p < 0.001 each). The highest concentrations were detected in metastatic PC patients (p = 0.036). In patients who underwent radical prostatectomy high IMP3 serum levels were independently associated with poor cancer‐specific survival. IMP3 gene and protein expressions were not correlated with those of IGF2. In conclusion, we found enhanced IMP3 levels in tissue and serum samples of PC patients compared to non‐PC men. Moreover, IMP3 was associated with metastasis and PC‐specific survival. The tumor promoting effect of IMP3 appears to be independent from its regulatory role on IGF2 in PC.
Comparison of Life History Characteristics of the Genetically Modified OX513A Line and a Wild Type Strain of Aedes aegypti

The idea of implementing genetics-based insect control strategies modelled on the traditional SIT (Sterile Insect Technique), such as RIDL (Release of Insects carrying a Dominant Lethal), is becoming increasingly popular. In this paper, we compare a genetically modified line of Aedes aegypti carrying a tetracycline repressible, lethal positive feedback system (OX513A) with a genetically similar, unmodified counterpart and their respective responses to increasing larval rearing density using a constant amount of food per larva. The parameters that we examined were larval mortality, developmental rate (i.e., time to pupation), adult size and longevity. Analysis revealed some statistically significant differences between the life history traits we examined. The genetically modified OX513A line overall showed 5% lower larval survival as well as reduced adult longevity (20 vs 24 days mean lifespan) compared to the unmodified line. Furthermore, the OX513A line pupated about one day sooner, which could be advantageous in mass-rearing, but produced somewhat smaller adults than the unmodified line; this effect was more pronounced in females than in males. Increasing the larval rearing density delayed pupation, decreased adult longevity and reduced adult size in both lines. While the delay in pupation and the decrease in longevity were similar between the two lines, the decrease in adult size was more pronounced for OX513A males. Our study shows that in a controlled laboratory situation the transgenic sterile OX513A line may have somewhat reduced performance compared to its unmodified counterpart and that high rearing densities may further reduce performance. Laboratory-based cage trials as well as field trials are necessary to assess how the differences in life history traits documented here impact the males' success upon release. Furthermore, this paper highlights the potential value of optimisation of mass-rearing systems as optimised rearing methods may be able to alleviate performance issues associated with specific lines or with lab-adapted lines in general.
Sebacinales Everywhere: Previously Overlooked Ubiquitous Fungal Endophytes

Inconspicuous basidiomycetes from the order Sebacinales are known to be involved in a puzzling variety of mutualistic plant-fungal symbioses (mycorrhizae), which presumably involve transport of mineral nutrients. Recently a few members of this fungal order not fitting this definition and commonly referred to as ‘endophytes’ have raised considerable interest by their ability to enhance plant growth and to increase resistance of their host plants against abiotic stress factors and fungal pathogens. Using DNA-based detection and electron microscopy, we show that Sebacinales are not only extremely versatile in their mycorrhizal associations, but are also almost universally present as symptomless endophytes. They occurred in field specimens of bryophytes, pteridophytes and all families of herbaceous angiosperms we investigated, including liverworts, wheat, maize, and the non-mycorrhizal model plant Arabidopsis thaliana. They were present in all habitats we studied on four continents. We even detected these fungi in herbarium specimens originating from pioneering field trips to North Africa in the 1830s/40s. No geographical or host patterns were detected. Our data suggest that the multitude of mycorrhizal interactions in Sebacinales may have arisen from an ancestral endophytic habit by specialization. Considering their proven beneficial influence on plant growth and their ubiquity, endophytic Sebacinales may be a previously unrecognized universal hidden force in plant ecosystems.
Long-Term Survival of Hydrated Resting Eggs from Brachionus plicatilis

Background Several organisms display dormancy and developmental arrest at embryonic stages. Long-term survival in the dormant form is usually associated with desiccation, orthodox plant seeds and Artemia cysts being well documented examples. Several aquatic invertebrates display dormancy during embryonic development and survive for tens or even hundreds of years in a hydrated form, raising the question of whether survival in the non-desiccated form of embryonic development depends on pathways similar to those occurring in desiccation tolerant forms. Methodology/Principal Findings To address this question, Illumina short read sequencing was used to generate transcription profiles from the resting and amictic eggs of an aquatic invertebrate, the rotifer, Brachionus plicatilis. These two types of egg have very different life histories, with the dormant or diapausing resting eggs, the result of the sexual cycle and amictic eggs, the non-dormant products of the asexual cycle. Significant transcriptional differences were found between the two types of egg, with amictic eggs rich in genes involved in the morphological development into a juvenile rotifer. In contrast, representatives of classical “stress” proteins: a small heat shock protein, ferritin and Late Embryogenesis Abundant (LEA) proteins were identified in resting eggs. More importantly however, was the identification of transcripts for messenger ribonucleoprotein particles which stabilise RNA. These inhibit translation and provide a valuable source of useful RNAs which can be rapidly activated on the exit from dormancy. Apoptotic genes were also present. Although apoptosis is inconsistent with maintenance of prolonged dormancy, an altered apoptotic pathway has been proposed for Artemia, and this may be the case with the rotifer. Conclusions These data represent the first transcriptional profiling of molecular processes associated with dormancy in a non-desiccated form and indicate important similarities in the molecular pathways activated in resting eggs compared with desiccated dormant forms, specifically plant seeds and Artemia.
Role of buoyant flame dynamics in wildfire spread

Significance Wildfires burn millions of hectares per year on every inhabited continent, but the physical mechanism governing spread is not known. Models of wildfire spread are widely used for prediction, firefighter training, and ecological research but have assumed various formulations of known heat transfer processes (radiation and convection) absent a definitive theory of their organization. New experimental evidence reported here reveals how buoyancy generated by the fire induces vorticity and instabilities in the flame zone that control the convective heating needed to ignite fuel particles and produce spread. Large wildfires of increasing frequency and severity threaten local populations and natural resources and contribute carbon emissions into the earth-climate system. Although wildfires have been researched and modeled for decades, no verifiable physical theory of spread is available to form the basis for the precise predictions needed to manage fires more effectively and reduce their environmental, economic, ecological, and climate impacts. Here, we report new experiments conducted at multiple scales that appear to reveal how wildfire spread derives from the tight coupling between flame dynamics induced by buoyancy and fine-particle response to convection. Convective cooling of the fine-sized fuel particles in wildland vegetation is observed to efficiently offset heating by thermal radiation until convective heating by contact with flames and hot gasses occurs. The structure and intermittency of flames that ignite fuel particles were found to correlate with instabilities induced by the strong buoyancy of the flame zone itself. Discovery that ignition in wildfires is critically dependent on nonsteady flame convection governed by buoyant and inertial interaction advances both theory and the physical basis for practical modeling.
Proteolytic Remodeling of Perineuronal Nets: Effects on Synaptic Plasticity and Neuronal Population Dynamics

The perineuronal net (PNN) represents a lattice-like structure that is prominently expressed along the soma and proximal dendrites of parvalbumin- (PV-) positive interneurons in varied brain regions including the cortex and hippocampus. It is thus apposed to sites at which PV neurons receive synaptic input. Emerging evidence suggests that changes in PNN integrity may affect glutamatergic input to PV interneurons, a population that is critical for the expression of synchronous neuronal population discharges that occur with gamma oscillations and sharp-wave ripples. The present review is focused on the composition of PNNs, posttranslation modulation of PNN components by sulfation and proteolysis, PNN alterations in disease, and potential effects of PNN remodeling on neuronal plasticity at the single-cell and population level.