Miracle-dz/UniFAR-FTUs huggingface dataset:
Complete Genome Sequence of Stenotrophomonas maltophilia Siphophage Summit

Stenotrophomonas maltophilia is an opportunistic pathogen exhibiting resistance to multiple antimicrobials. This study reports the complete genome of an S. maltophilia siphophage, Summit. Its genome of 95,728 bp has 148 protein-coding genes and 5 tRNAs, including 1 predicted suppressor tRNA. Possible target genes for the suppressor tRNA are not identified. ABSTRACT Stenotrophomonas maltophilia is an opportunistic pathogen exhibiting resistance to multiple antimicrobials. This study reports the complete genome of an S. maltophilia siphophage, Summit. Its genome of 95,728 bp has 148 protein-coding genes and 5 tRNAs, including 1 predicted suppressor tRNA. Possible target genes for the suppressor tRNA are not identified.
Control System Design of 1 DOF Kinesthetic Interface

The aim of this work is to investigate the performance of closed-loop impedance control in the case of a kinesthetic interface, more precisely to propose this control approach even for devices in which the natural dynamics of the system are relevant. This characteristic can be found in an industrial scenario where commercial components are generally used; hence the system can't be optimized as conversely occurs in a laboratory/ research environment where custom components are generally developed. It is shown that it is possible to guarantee a high dynamic accuracy using the closed-loop impedance control with force feedback and model feedforward. Therefore this approach is suggested as a valid alternative of the most diffused admittance control. The device implemented for the tests and the obtained results are described below.
Coagulopathy and hemostasis management in patients undergoing liver transplantation: Defining a dynamic spectrum across phases of care

Patients with acute and chronic liver disease present with a wide range of disease states and severity that may require liver transplantation (LT). Physiologic alterations occur that are dynamic throughout all phases of perioperative care, creating complex management scenarios that necessitate multidisciplinary clinical care. Specifically, alterations in hemostasis in liver disease can be pronounced and evolve with disease progression over time. Recent studies and society guidance address this emerging paradigm and offer recommendations to assist with hemostatic management in patients with liver disease. However, patients undergoing LT are unique and diverse, often with unstable disease that requires specialized approaches. Our aim is to provide a focused review of hemostatic management of the LT patient, distinguish unique aspects of the three main phases of care (before LT, perioperative, and after LT), and identify knowledge gaps and critical areas of future research.
Identification of immunosuppressive factors in retinoblastoma cell secretomes and aqueous humor from patients

The microenvironment of retinoblastoma, the solid malignancy of the developing retina, is immunosuppressive. To study the interactions between tumor‐associated microglia/macrophages (TAMs) and tumor cells in retinoblastomas, we analyzed immunohistochemistry markers in 23 patient samples and characterized 105 secreted cytokines of 11 retinoblastoma cell models in culture. We detected profuse infiltration of CD163+ protumoral M2‐like polarized TAMs in eyes enucleated due to cancer progression. Previous treatment of patients increased the number of TAMs but did not affect M2‐like polarization. M2‐like microglia/macrophages were almost absent in five eyes obtained from children enucleated due to nontumoral causes. CD8+ tumor‐infiltrating lymphocytes (TILs) were moderately abundant in tumor eyes and very scarce in nontumoral ones. The expression of the immune checkpoint molecule PD‐L1 was absent in 95% of the tumor samples, which is concordant with the finding of FOXP3+ Tregs infiltrating tumors. We confirmed the pathology results using single‐cell transcriptome analysis of one tumor. We identified the cytokines extracellular matrix metalloproteinase inducer (EMMPRIN) and macrophage migration inhibitory factor (MIF), both with reported immunosuppressive activity, secreted at high levels in retinoblastoma primary cell cultures. Gene expression analysis of a large retinoblastoma cohort and single‐cell transcriptome analysis confirmed that MIF and EMMPRIN were significantly upregulated in retinoblastomas, which led us to quantify both proteins by immunoassays in liquid biopsies (aqueous humor obtained from more than 20 retinoblastoma patients). We found a significant increase in the concentration of MIF and EMMPRIN in cancer patients, compared to 12 noncancer ones. Finally, we showed that macrophages derived from peripheral blood mononuclear cells increased the expression of markers of M2‐like polarization upon exposure to retinoblastoma‐conditioned medium or recombinant MIF. Overall, our findings suggest that retinoblastoma cell secretions induce the protumoral phenotype of this tumor. Our results might have clinical impact in the fields of biomarkers and treatment. © 2022 The Pathological Society of Great Britain and Ireland.
Depressive symptoms are no longer a barrier to HCV treatment initiation in the HIV–HCV co-infected population in Canada

Background Psychiatric illness was a major barrier for HCV treatment during the Interferon (IFN) treatment era due to neuropsychiatric side effects. While direct acting antivirals (DAA) are better tolerated, patient-level barriers persist. We aimed to assess the effect of depressive symptoms on time to HCV treatment initiation among HIV–HCV co-infected persons during the IFN (2003–2011) and second-generation DAA (2013–2020) eras. Methods We used data from the Canadian Co-infection Cohort, a multicentre prospective cohort, and its associated sub-study on Food Security (FS). We predicted Center for Epidemiologic Studies Depression Scale-10 (CES-D-10) classes for depressive symptoms indicative of a depression risk using a random forest classifier and corrected for misclassification using predictive value-based record-level correction. We used marginal structural Cox proportional hazards models with inverse weighting for competing risks (death) to assess the effect of depressive symptoms on treatment initiation among HCV RNA-positive participants. Results We included 590 and 1127 participants in the IFN and DAA eras. The treatment initiation rate increased from 9 (95% confidence interval (CI): 7–10) to 21 (95% CI: 19–22) per 100 person-years from the IFN to DAA era. Treatment initiation was lower among those with depressive symptoms compared to those without in the IFN era (hazard ratio: 0.81 (95% CI: 0.69–0.95)) and was higher in the DAA era (1.19 (95% CI: 1.10–1.27)). Conclusion Depressive symptoms no longer appear to be a barrier to HCV treatment initiation in the co-infected population in the DAA era. The higher rate of treatment initiation in individuals with depressive symptoms suggests those previously unable to tolerate IFN are now accessing treatment.
Lytic Phages against ST11 K47 Carbapenem-Resistant Klebsiella pneumoniae and the Corresponding Phage Resistance Mechanisms

Carbapenem-resistant Klebsiella pneumoniae (CRKP) is a major challenge for infection control and clinical management. Alternative therapies to antimicrobial agents are urgently needed and bacteriophages (phages) are an attractive option. ABSTRACT We isolated and characterized a novel phage from hospital sewage, P13, able to lyse ST11 K47 carbapenem-resistant Klebsiella pneumoniae (CRKP), a major CRKP lineage. P13 formed a large lytic plaque (3.0 to 6.0 mm in diameter) in double-layer LB agar after overnight coculture with its host bacterial strain. A translucent halo formed when the culture was prolonged to 48 h. P13 showed a narrow host range only lysing ST11 K47 CRKP with a burst size of around 167 PFU/cell and exhibited broad pH and thermal stability. Genome sequencing showed that P13 contains no virulence, lysogenic or antimicrobial resistance genes, making this lytic phage a potential agent for phage therapy. Transmission electron microscopy showed that P13 exhibited typical morphology of the family Podoviridae with an isometric head and a short noncontracted tail. Genomic analysis showed that P13 belongs to a novel species of the genus Przondovirus, subfamily Studiervirinae, family Autographiviridae. P13-resistant mutants of bacteria emerged after 4 h exposure to the phage. Interruptions of wbaP (encoding capsule polysaccharide synthesis) by insertion sequence IS903B mediated P13 resistance. The rapid emergence of resistant mutants represents a disadvantage for P13 as a therapeutic phage and highlights the need for recovery of a range of phages binding to different surface receptors of host bacteria to further extend their utility as a potential tool against CRKP. IMPORTANCE Carbapenem-resistant Klebsiella pneumoniae (CRKP) is a major challenge for infection control and clinical management. Alternative therapies to antimicrobial agents are urgently needed and bacteriophages (phages) are an attractive option. However, more novel lytic phages and more studies to reveal phage-resistant mechanisms are needed to overcome phage resistance. In this study, we isolated and characterized a novel species of lytic phage active against CRKP. We found this phage exhibited delayed formation of halo, which is atypical compared to other characterized similar phages, and we provide an explanation for this phenotype based on genomic analysis. We also identified mechanisms mediating resistance to the phage.
The role of relaxation and retardation phenomenon of Oldroyd-B fluid flow through Stehfest’s and Tzou’s algorithms

Abstract Delayed response (delay of the elasticity) and time needed for initial stress can lead to relaxation and retardation phenomenon; this is because of the consistent behavior of viscoelastic fluid on thermodynamic principles. In this context, the aim of this article is to investigate the unsteady, incompressible, and Oldroyd-B viscoelastic fluid under wall slip conditions to know the hidden aspects of relaxation and retardation. The motion of the liquid is assumed over a flat vertical plate which moves through an oscillating velocity. A fractional model is developed by using the modern definition of the non-singular kernel proposed by Caputo and Fabrizio. We have obtained a semi-analytical solution of the non-dimensional model by using the Laplace transformation that satisfies our imposed suitable boundary conditions. We have tackled the Laplace inverse by employing Stehfest’s and Tzou’s algorithms. The velocity is enhanced by decreasing the estimations of relaxation time λ as well as slip parameter, and the temperature is also increasing for a considerable measure of the fractional factor. The effects of different fractional and physical parameters are plotted using Mathcad software based on the relaxation and retardation phenomenon of Oldroyd-B viscoelastic fluid.
Open Problems in Software Test Coverage

Software testing is concerned with the production and maintenance of high quality systems. Test coverage is one major component in software testing. It gives a meaningful description of how much testing is required. The level of test coverage is an indicator of testing thoroughness, which in turn helps testers decide when to stop testing. Several studies addressed coverage criteria effectiveness and adequacy. However, there are several interesting open problems. We identify nine open problems in test coverage and discuss what issues need to be addressed. The objective of this paper is to direct the attention of researchers and testers toward the areas that need to be investigated.
Research on Topology Evolution of Autonomous System Network

After investigating the study about autonomous system level networks, we found that the latest data analysis used is open data provided in 2013. Thus, based on the open-source network BGP routing information provided by RouteViews from 2000 to 2020, this paper designs the calculation and analysis methods of the topological characteristic parameters of autonomous system level network combing the research theories and methods of Complex Network. Using these methods, the scale and topological characteristic parameters of the autonomous system-level network are calculated monthly from the global level and the national levels. And the evolution of the network scale and topological characteristics in the past 21 years are analyzed. Through analyzing the evolution of the number of connections, the number of network segments, the number of IP addresses, the number of nodes, the number of cores, the number of betweenness, and the average length of the path, and so on. Some regularities of network evolution are summarized. Firstly, some characteristics of the network are strongly correlated with each other. Since 2012, this kind of node has resumed its main part in the network whose number of degrees is 1, because the nodes of countries with late network development have gradually increased their influence. The evolution of the national autonomous system network characteristics is self-similar to the global network, but there are certain differences in different countries. These conclusions provide method support for the macro-level understanding of the Internet's topological characteristics and further inference of its evolutionary trend.
Implementation of Elastic IP for Public Cloud

A VPC (Virtual Private Cloud) in a public cloud often allocates private IP addresses which are not globally routable, to virtual resources, e.g., ECSs (Elastic Cloud Server), ELBs (Elastic Load Balancer) and so on. An EIP (Elastic IP) is a static IP that can be mapped to a private IP address of virtual resource deployed in VPC to make it reachable from outside of a public cloud, e.g., from a client in the Internet. As a public cloud usually holds millions of EIPs which can be dynamically allocated to virtual entities inside of VPCs, legacy firewall or router-based NAT (Network Address Translation) solutions cannot fulfil the requirements of public cloud in dynamicity, flexibility, scalability, and some other aspects. In this paper we propose a hierarchically clustered EIP implementation system for public cloud. The system implements the translation from private IP to EIP in two stages, and stage 1 performs the translation from a private IP to a floating IP which is in a locally routable IP space while stage 2 performs the translation from a floating IP to an EIP which is allocated from IANA (Internet Assigned Numbers Authority) directly or from an Internet service provider and can be accessed from the Internet. This hierarchically clustered implementation system brings many benefits such as good scalability to support millions of EIPs, more flexibility to apply access control to the traffic between different VPCs, support of dynamically allocating an EIP to different virtual entities when needed.
Inhibition is a prevalent mode of activity in the neocortex around awake hippocampal ripples in mice

Coordinated peri-ripple activity in the hippocampal-neocortical network is essential for mnemonic information processing in the brain. Hippocampal ripples likely serve different functions in sleep and awake states. Thus, the corresponding neocortical activity patterns may differ in important ways. We addressed this possibility by conducting voltage and glutamate wide-field imaging of the neocortex with concurrent hippocampal electrophysiology in awake mice. Contrary to our previously published sleep results, deactivation and activation were dominant in post-ripple neocortical voltage and glutamate activity, respectively, especially in the agranular retrosplenial cortex (aRSC). Additionally, the spiking activity of aRSC neurons, estimated by two-photon calcium imaging, revealed the existence of two subpopulations of excitatory neurons with opposite peri-ripple modulation patterns: one increases and the other decreases firing rate. These differences in peri-ripple spatiotemporal patterns of neocortical activity in sleep versus awake states might underlie the reported differences in the function of sleep versus awake ripples.
Study on search performance of subarray multi-channel phased array radar based on multiple received beams

A contradiction between the searching time and the beam-shape loss exists when the phased array radar is searching targets. According to this problem, this paper has presented a method for improving the sub-array multi-channel phased array radar's search performance based on multiple received beams. This method still applies single beam in transmit, but applies digital multi-beam forming technology to form multiple instantaneous beams in receive. It has reduced received beam-shape loss without increasing the searching time. Moreover, by optimizing the average beam-shape loss and the maximum beam-shape loss of received beams, this method has determined the optimal received beam number and beam layout. In the end, the computer simulation result has shown that the method is effective. (6 pages)
Modernizing the NEURON Simulator for Sustainability, Portability, and Performance

The need for reproducible, credible, multiscale biological modeling has led to the development of standardized simulation platforms, such as the widely-used NEURON environment for computational neuroscience. Developing and maintaining NEURON over several decades has required attention to the competing needs of backwards compatibility, evolving computer architectures, the addition of new scales and physical processes, accessibility to new users, and efficiency and flexibility for specialists. In order to meet these challenges, we have now substantially modernized NEURON, providing continuous integration, an improved build system and release workflow, and better documentation. With the help of a new source-to-source compiler of the NMODL domain-specific language we have enhanced NEURON’s ability to run efficiently, via the CoreNEURON simulation engine, on a variety of hardware platforms, including GPUs. Through the implementation of an optimized in-memory transfer mechanism this performance optimized backend is made easily accessible to users, providing training and model-development paths from laptop to workstation to supercomputer and cloud platform. Similarly, we have been able to accelerate NEURON’s reaction-diffusion simulation performance through the use of just-in-time compilation. We show that these efforts have led to a growing developer base, a simpler and more robust software distribution, a wider range of supported computer architectures, a better integration of NEURON with other scientific workflows, and substantially improved performance for the simulation of biophysical and biochemical models.
Compositionally Constrained Sites Drive Long-Branch Attraction

Accurate phylogenies are fundamental to our understanding of the pattern and process of evolution. Yet, phylogenies at deep evolutionary timescales, with correspondingly long branches, have been fraught with controversy resulting from conflicting estimates from models with varying complexity and goodness of fit. Analyses of historical as well as current empirical datasets, such as alignments including Microsporidia, Nematoda or Platyhelminthes, have demonstrated that inadequate modeling of across-site compositional heterogeneity, which is the result of biochemical constraints that lead to varying patterns of accepted amino acids along sequences, can lead to erroneous topologies that are strongly supported. Unfortunately, models that adequately account for across-site compositional heterogeneity remain computationally challenging or intractable for an increasing fraction of contemporary datasets. Here, we introduce “compositional constraint analysis”, a method to investigate the effect of site-specific constraints on amino acid composition on phylogenetic inference. We show that more constrained sites with lower diversity and less constrained sites with higher diversity exhibit ostensibly conflicting signal under models ignoring across-site compositional heterogeneity that lead to long branch attraction artifacts and demonstrate that more complex models accounting for across-site compositional heterogeneity can ameliorate this bias. We present CAT-PMSF, a pipeline for diagnosing and resolving phylogenetic bias resulting from inadequate modeling of across-site compositional heterogeneity based on the CAT model. CAT-PMSF is robust against long branch attraction in all alignments we have examined. We suggest using CAT-PMSF when convergence of the CAT model cannot be assured. We find evidence that compositionally constrained sites are driving long branch attraction in two metazoan datasets and recover evidence for Porifera as the sister group to all other animals.
Reduced childhood social attention in autism model marmosets predicts impaired social skills and inflexible behavior in adulthood

Autism spectrum disorder (ASD) is a neurodevelopmental disorder characterized by social and communication impairments and restricted and repetitive behavior. Although currently no established cure exists for ASD, early intervention to the deficits of attention to other individuals is expected to reduce the progression of ASD symptoms in later life. In order to confirm this hypothesis and improve early therapeutic interventions, it is desirable to develop an animal model of ASD in which social attention is impaired in childhood and ASD-like social behavior is observed in adulthood. However, rodent models of ASD have difficulty in recapitulating the deficit of gaze-based social attention. In this study, we examined the direction of gaze towards other conspecifics during childhood and puberty in a three-chamber test setting using an ASD model of marmoset produced by maternal exposure to valproic acid (VPA). We also conducted a reversal learning test in an adult VPA-exposed marmoset as an indicator of perseveration, a core symptom of ASD that has not previously been investigated in this model. The results showed that time spent gazing at other conspecifics was reduced in VPA-exposed marmosets in childhood, and adults displayed rigidity of response. In a longitudinal study using the same animals, deficits in social attention in childhood correlated well with ASD-like social disturbance (inequity aversion and third-party reciprocity) and inflexible behavior in adulthood. Since VPA-exposed marmosets exhibit these diverse ASD-like behaviors that are coherent from childhood to adulthood, VPA-exposed marmosets will provide a valuable opportunity to elucidate mechanisms for early intervention and contribute to the development of early therapies.