Miracle-dz/UniFAR-FTUs huggingface dataset:
Lifestyle Evolution in Cyanobacterial Symbionts of Sponges

ABSTRACT The “Candidatus Synechococcus spongiarum” group includes different clades of cyanobacteria with high 16S rRNA sequence identity (~99%) and is the most abundant and widespread cyanobacterial symbiont of marine sponges. The first draft genome of a “Ca. Synechococcus spongiarum” group member was recently published, providing evidence of genome reduction by loss of genes involved in several nonessential functions. However, “Ca. Synechococcus spongiarum” includes a variety of clades that may differ widely in genomic repertoire and consequently in physiology and symbiotic function. Here, we present three additional draft genomes of “Ca. Synechococcus spongiarum,” each from a different clade. By comparing all four symbiont genomes to those of free-living cyanobacteria, we revealed general adaptations to life inside sponges and specific adaptations of each phylotype. Symbiont genomes shared about half of their total number of coding genes. Common traits of “Ca. Synechococcus spongiarum” members were a high abundance of DNA modification and recombination genes and a reduction in genes involved in inorganic ion transport and metabolism, cell wall biogenesis, and signal transduction mechanisms. Moreover, these symbionts were characterized by a reduced number of antioxidant enzymes and low-weight peptides of photosystem II compared to their free-living relatives. Variability within the “Ca. Synechococcus spongiarum” group was mostly related to immune system features, potential for siderophore-mediated iron transport, and dependency on methionine from external sources. The common absence of genes involved in synthesis of residues, typical of the O antigen of free-living Synechococcus species, suggests a novel mechanism utilized by these symbionts to avoid sponge predation and phage attack. IMPORTANCE While the Synechococcus/Prochlorococcus-type cyanobacteria are widely distributed in the world's oceans, a subgroup has established its niche within marine sponge tissues. Recently, the first genome of sponge-associated cyanobacteria, “Candidatus Synechococcus spongiarum,” was described. The sequencing of three representatives of different clades within this cyanobacterial group has enabled us to investigate intraspecies diversity, as well as to give a more comprehensive understanding of the common symbiotic features that adapt “Ca. Synechococcus spongiarum” to its life within the sponge host. While the Synechococcus/Prochlorococcus-type cyanobacteria are widely distributed in the world's oceans, a subgroup has established its niche within marine sponge tissues. Recently, the first genome of sponge-associated cyanobacteria, “Candidatus Synechococcus spongiarum,” was described. The sequencing of three representatives of different clades within this cyanobacterial group has enabled us to investigate intraspecies diversity, as well as to give a more comprehensive understanding of the common symbiotic features that adapt “Ca. Synechococcus spongiarum” to its life within the sponge host.
Cognitive Decline : An Analysis of the Elderly Population in Isolated Regions of Mexico

Worldwide studies in the last decade have measured the rate of cognitive decline in the elderly population, mainly in Australia, Europe, United States, and Canada. In Mexico, this information is very limited and the population of Hidalgo State has never been studied. Therefore, we decided to perform a transversal study to determine the rate of cognitive decline in this region. We will present an analysis in order to establish the main differences between rural and urban areas, as well as identifying the particular triggers of cognitive decline on each area.
Cx3cr1‐deficiency exacerbates alpha‐synuclein‐A53T induced neuroinflammation and neurodegeneration in a mouse model of Parkinson's disease

Parkinson's disease (PD) is the second most common neurodegenerative disorder characterized by the degeneration of dopaminergic neurons of the substantia nigra and the accumulation of protein aggregates, called Lewy bodies, where the most abundant is alpha‐synuclein (α‐SYN). Mutations of the gene that codes for α‐SYN (SNCA), such as the A53T mutation, and duplications of the gene generate cases of PD with autosomal dominant inheritance. As a result of the association of inflammation with the neurodegeneration of PD, we analyzed whether overexpression of wild‐type α‐SYN (α‐SYNWT) or mutated α‐SYN (α‐SYNA53T) are involved in the neuronal dopaminergic loss and inflammation process, along with the role of the chemokine fractalkine (CX3CL1) and its receptor (CX3CR1). We generated in vivo murine models overexpressing human α‐SYNWT or α‐SYNA53T in wild type (Cx3cr1+/+) or deficient (Cx3cr1–/–) mice for CX3CR1 using unilateral intracerebral injection of adeno‐associated viral vectors. No changes in CX3CL1 levels were observed by immunofluorescence or analysis by qRT‐PCR in this model. Interestingly, the expression α‐SYNWT induced dopaminergic neuronal death to a similar degree in both genotypes. However, the expression of α‐SYNA53T produced an exacerbated neurodegeneration, enhanced in the Cx3cr1–/– mice. This neurodegeneration was accompanied by an increase in neuroinflammation and microgliosis as well as the production of pro‐inflammatory markers, which were exacerbated in Cx3cr1–/– mice overexpressing α‐SYNA53T. Furthermore, we observed that in primary microglia CX3CR1 was a critical factor in the modulation of microglial dynamics in response to α‐SYNWT or α‐SYNA53T. Altogether, our study reveals that CX3CR1 plays an essential role in neuroinflammation induced by α‐SYNA53T.
H-Reflex Up-Conditioning Encourages Recovery of EMG Activity and H-Reflexes after Sciatic Nerve Transection and Repair in Rats

Operant conditioning of the spinal stretch reflex or its electrical analog, the H-reflex, produces spinal cord plasticity and can thereby affect motoneuron responses to primary afferent input. To explore whether this conditioning can affect the functional outcome after peripheral nerve injury, we assessed the effect of up-conditioning soleus (SOL) H-reflex on SOL and tibialis anterior (TA) function after sciatic nerve transection and repair. Sprague Dawley rats were implanted with EMG electrodes in SOL and TA and stimulating cuffs on the posterior tibial nerve. After control data collection, the sciatic nerve was transected and repaired and the rat was exposed for 120 d to continued control data collection (TC rats) or SOL H-reflex up-conditioning (TU rats). At the end of data collection, motoneurons that had reinnervated SOL and TA were labeled retrogradely. Putative primary afferent terminals [i.e., terminals containing vesicular glutamate transporter-1 (VGLUT1)] on SOL motoneurons were studied immunohistochemically. SOL (and probably TA) background EMG activity recovered faster in TU rats than in TC rats, and the final recovered SOL H-reflex was significantly larger in TU than in TC rats. TU and TC rats had significantly fewer labeled motoneurons and higher proportions of double-labeled motoneurons than untransected rats. VGLUT1 terminals were significantly more numerous on SOL motoneurons of TU than TC rats. Combined with the larger H-reflexes in TU rats, this anatomical finding supports the hypothesis that SOL H-reflex up-conditioning strengthened primary afferent reinnervation of SOL motoneurons. These results suggest that H-reflex up-conditioning may improve functional recovery after nerve injury and repair.
The Northern χ-Orionid meteoroid stream and possible association with the potentially hazardous asteroid 2008XM1

We present new orbital data and dynamic results pointing towards the origin of the Northern χ -Orionid meteoroid stream, which is a part of the Taurid meteoroid complex. A new software package was developed to establish the potential parent bodies of meteoroid streams based on the similarity of their orbits. The analysis of a Northern χ -Orionid fireball observed on 2011 December 6 identified two potential parent bodies: the near-Earth object (NEO) 2002XM35 (previously proposed as the parent of this meteoroid stream) and the more recently discovered potentially hazardous asteroid 2008XM1. The calculation of the evolution of the orbital elements performed by using the Mercury 6 symplectic integrator supports the idea that 2008XM1 is a better parent body. Our data sample was expanded by including also in the calculations the mean orbit of the χ -Orionid stream. The results are consistent with the fragmentation of a larger body in the past that could give rise to both NEOs and the Northern χ -Orionid stream. To confirm this, further observations to improve the orbital elements of these asteroids should be attempted before the objects are lost. The analysis of the emission spectrum recorded for this fireball supports a primitive nature for these meteoroids.
Fabrication and Strengthening Mechanisms of Al/WC Particles Composite Prepared by Accumulative Roll Bonding

Aluminium metal matrix composites reinforced with WC ceramic particles were manufactured through warm accumulative roll bonding (ARB) in this study. The microstructures of the composites exhibited excellent particles distribution in the matrices. Compared with the mechanical properties of ARB monolithic pure Al, the Al/WC composites exhibited higher tensile strength. The shear lag theory modified was used in considering the yield strength of the composites. The results indicated that the effects of WC particles in Al/WC composite lead to the thermal expansion dislocation strengthening, small subgrain strengthening, Orowan strengthening and geometrically necessary dispersion strengthening.
Weakly Paired Multimodal Fusion for Object Recognition

The ever-growing development of sensor technology has led to the use of multimodal sensors to develop robotics and automation systems. It is therefore highly expected to develop methodologies capable of integrating information from multimodal sensors with the goal of improving the performance of surveillance, diagnosis, prediction, and so on. However, real multimodal data often suffer from significant weak-pairing characteristics, i.e., the full pairing between data samples may not be known, while pairing of a group of samples from one modality to a group of samples in another modality is known. In this paper, we establish a novel projective dictionary learning framework for weakly paired multimodal data fusion. By introducing a latent pairing matrix, we realize the simultaneous dictionary learning and the pairing matrix estimation, and therefore improve the fusion effect. In addition, the kernelized version and the optimization algorithms are also addressed. Extensive experimental validations on some existing data sets are performed to show the advantages of the proposed method.Note to Practitioners—In many industrial environments, we usually use multiple heterogeneous sensors, which provide multimodal information. Such multimodal data usually lead to two technical challenges. First, different sensors may provide different patterns of data. Second, the full-pairing information between modalities may not be known. In this paper, we develop a unified model to tackle such problems. This model is based on a projective dictionary learning method, which efficiently produces the representation vector for the original data by an explicit form. In addition, the latent pairing relation between samples can be learned automatically and be used to improve the classification performance. Such a method can be flexibly used for multimodal fusion with full-pairing, partial-pairing and weak-pairing cases.
Refractory pancolitis: a novel presentation of idiopathic myointimal hyperplasia of mesenteric veins.

Idiopathic myointimal hyperplasia of mesenteric veins (IMHMV) is a rare condition that primarily affects middle-aged men. IMHMV is typically associated with symptoms of abdominal pain, rectal bleeding, and diarrhea and endoscopic findings of severe inflammation, ulceration, and pseudopolyps. However, these clinical symptoms and endoscopic findings are also suggestive of ulcerative colitis and Crohn’s disease, which are much more common than IMHMV. Thus, patients with IMHMV are often misdiagnosed with inflammatory bowel disease that is refractory to medical treatment. IMHMV can be definitively differentiated from inflammatory bowel disease only after histologic examination of specimens from the resected colon. In most IMHMV patients, disease is restricted to the sigmoid colon, but this case reports IMHMV in a patient with pancolitis.
Expression Templates Revisited: A Performance Analysis of Current Methodologies

In the last decade, expression templates (ETs) have gained a reputation as an efficient performance optimization tool for C++ codes. This reputation builds on several ET-based linear algebra frameworks focused on combining both elegant and high-performance C++ code. However, on closer examination the assumption that ETs are a performance optimization technique cannot be maintained. In this paper we compare the performance of several generations of ET-based frameworks. We analyze different ET methodologies and explain the inability of some ET implementations to deliver high performance for dense and sparse linear algebra operations. Additionally, we introduce the notion of “smart” ETs, which truly allow for a combination of high performance code with the elegance and maintainability of a domain-specific language.
Governance-default risk relationship and the demand for intermediated and non-intermediated debt

This paper explores the impact of corporate governance on the demand for intermediated debt (asset finance, bank debt, non-bank private debt) and non-intermediated debt (public debt) in the Australian debt market. Relative to other countries the Australian debt market is characterised by higher proportions of intermediated or private debt with a lower inherent level of information asymmetry in that private lenders have greater access to financial information (Gray, Koh & Tong 2009). Our firm level, cross-sectional evidence suggests that higher corporate governance impacts demand for debt via the mitigation of default risk. However, this relationship is not uniform across all debt types. Intermediated debt such as bank and asset finance debt are more responsive to changes in governance-default risk relationship than non-bank and non-intermediated debt. The implication is that a firm’s demand for different debt types will reflect its governance-default risk profile.
The E ects of Information and Application Assistance : Experimental Evidence from SNAP Amy Finkelstein and Matthew

This paper develops a framework for evaluating the welfare impact of various interventions designed to increase take-up of social safety net programs in the presence of potential behavioral biases. We then calibrate key parameters using a randomized eld experiment in which 30,000 elderly individuals not enrolled in but likely eligible for the Supplemental Nutrition Assistance Program (SNAP) are either provided with information that they are likely eligible or provided with this information and also o ered assistance in applying; a status quo control group receives no contact. Only 6 percent of the control group enrolls in SNAP over the next 9 months, compared to 11 percent of the Information Only group and 18 percent of the Information Plus Assistance group. The individuals who apply or enroll in response to either intervention receive lower bene ts and are less sick than the average enrollee in the control group. Despite the poor targeting properties of the interventions, our rough calculations suggest that they are nonetheless a cost-e ective way to redistribute to low-income individuals relative to other safety net programs. JEL codes: C93; H53; I38
Utilization of aspirin and statin in management of coronary artery disease in patients with cirrhosis undergoing liver transplant evaluation

Coronary artery disease (CAD) assessment is a vital part of liver transplantation (LT) evaluation, as it allows for identification and medical optimization prior to transplantation. Although aspirin and statins are standard of care for CAD, they are not universally used in cirrhosis due to concerns about adverse events. Per protocol, coronary angiography was performed as part of the LT evaluation in all patients over the age of 50 years or with CAD risk factors, even if they were younger than 50. Optimal CAD medical management was defined as the use of both statin and aspirin, unless a contraindication was documented. Impact of these medications on hepatic decompensation, renal function, gastrointestinal bleeding, and need for transfusion was evaluated. CAD was detected in 84/228 (36.8%) patients. Lipid profile was similar in patients with and without CAD. In patients with CAD, statins were started in 19 (23%), while aspirin was used in 30 (36%) patients. In patients with obstructive or multivessel CAD, statin therapy was used only in 41% and 65%, respectively. Statins were more likely to be prescribed in patients with diabetes (32% versus 15%, P = 0.05) and history of dyslipidemia (38% versus 15%, P = 0.02). Use of statin therapy was not linked to hepatic decompensation, hospitalization, or rise in Model for End‐Stage Liver Disease (MELD). Similarly, use of aspirin therapy was not associated with increased risk acute variceal hemorrhage, gastrointestinal bleeding, or worsening anemia. In conclusion, in decompensated cirrhosis, lipid profile alone is unable to risk stratify patients with CAD. Statin and aspirin appear to be safe. However, they are significantly underutilized for the management of CAD in this patient population. Liver Transplantation 24 872–880 2018 AASLD.
Ensuring reproducibility and ethics in animal experiments reporting in Korea using the ARRIVE guideline

The aim of this study is to evaluate the reporting quality of animal experiments in Korea using the Animals in Research: Reporting In Vivo Experiments (ARRIVE) guideline developed in 2010 to overcome the reproducibility problem and to encourage compliance with replacement, refinement and reduction of animals in research (3R's principle). We reviewed 50 papers published by a Korean research group from 2013 to 2016 and scored the conformity with the 20-items ARRIVE guideline. The median conformity score was 39.50%. For more precise evaluation, the 20 items were subdivided into 57 sub-items. Among the sub-items, status of experimental animals, housing and husbandry were described under the average level. Microenvironment sub-items, such as enrichment, bedding material, cage type, number of companions, scored under 10%. Although statistical methods used for the studies were given in most publications (84%), sample size calculation and statistical assumption were rarely described. Most publications mentioned the IACUC approval, but only 8% mentioned welfare-related assessments and interventions, and only 4% mentioned any implications of experimental methods or findings for 3R. We may recommend the revision of the present IACUC proposal to collect more detailed information and improving educational program for animal researchers according to the ARRIVE guideline.
Genetics of hypertrophic cardiomyopathy: A review of current state

Hypertrophic cardiomyopathy (HCM) is the most common inherited cardiovascular disease. HCM is a highly complex and heterogeneous disease regarding not only the number of associated mutations but also the severity of phenotype, symptom burden, and the risk of complications, such as heart failure and sudden death. The penetrance is incomplete and it is age and gender dependent. It is accepted as a disease of the sarcomere. Sixty percent of HCM cases carry mutations in 1 of 8 sarcomere protein genes, mainly non‐sense MYBPC3 and missense MYH7 variants. Young patients with severe phenotype and other clinical features are included in proposed scores for prediction of high positive genetic result. The number of genes reported as disease‐causing has increased in the last few years, in some cases without robust evidence. Currently available in silico tools are not always useful for differentiation between benign and deleterious variants. There is enough information on genotype‐phenotype correlations to start understanding the mechanisms of the disease. Genetic and environmental modifiers have been explored with some interesting insights from miRNA studies with potential as biomarkers and therapeutic agents. There is an additional value of genetic testing in HCM for prognosis. Knowledge about genetics and functional studies are the basis of near future therapies.
Seasonality of soil moisture mediates responses of ecosystem phenology to elevated CO2 and warming in a semi‐arid grassland

Vegetation greenness, detected using digital photography, is useful for monitoring phenology of plant growth, carbon uptake and water loss at the ecosystem level. Assessing ecosystem phenology by greenness is especially useful in spatially extensive, water‐limited ecosystems such as the grasslands of the western United States, where productivity is moisture dependent and may become increasingly vulnerable to future climate change. We used repeat photography and a novel means of quantifying greenness in digital photographs to assess how the individual and combined effects of warming and elevated CO2 impact ecosystem phenology (greenness and plant cover) in a semi‐arid grassland over an 8‐year period. Climate variability within and among years was the proximate driver of ecosystem phenology. Individual and combined effects of warming and elevated CO2 were significant at times, but mediated by variation in both intra‐ and interannual precipitation. Specifically, warming generally enhanced plant cover and greenness early in the growing season but often had a negative effect during the middle of the summer, offsetting the early season positive effects. The individual effects of elevated CO2 on plant cover and greenness were generally neutral. Opposing seasonal variations in the effects of warming and less so elevated CO2 cancelled each other out over an entire growing season, leading to no net effect of treatments on annual accumulation of greenness. The main effect of elevated CO2 dampened quickly, but warming continued to affect plant cover and plot greenness throughout the experiment. The combination of warming and elevated CO2 had a generally positive effect on greenness, especially early in the growing season and in later years of the experiment, enhanced annual greenness accumulation. However, interannual precipitation variation had larger effect on greenness, with two to three times greater greenness in wet years than in dry years. Synthesis. Seasonal variation in timing and amount of precipitation governs grassland phenology, greenness and the potential for carbon uptake. Our results indicate that concurrent changes in precipitation regimes mediate vegetation responses to warming and elevated atmospheric CO2 in semi‐arid grasslands. Even small changes in vegetation phenology and greenness in response to warming and rising atmospheric CO2 concentrations, such as those we report here, can have large consequences for the future of grasslands.