Miracle-dz/UniFAR-FTUs huggingface dataset:
Quasispecies Spatial Models for RNA Viruses with Different Replication Modes and Infection Strategies

Empirical observations and theoretical studies suggest that viruses may use different replication strategies to amplify their genomes, which impact the dynamics of mutation accumulation in viral populations and therefore, their fitness and virulence. Similarly, during natural infections, viruses replicate and infect cells that are rarely in suspension but spatially organized. Surprisingly, most quasispecies models of virus replication have ignored these two phenomena. In order to study these two viral characteristics, we have developed stochastic cellular automata models that simulate two different modes of replication (geometric vs stamping machine) for quasispecies replicating and spreading on a two-dimensional space. Furthermore, we explored these two replication models considering epistatic fitness landscapes (antagonistic vs synergistic) and different scenarios for cell-to-cell spread, one with free superinfection and another with superinfection inhibition. We found that the master sequences for populations replicating geometrically and with antagonistic fitness effects vanished at low critical mutation rates. By contrast, the highest critical mutation rate was observed for populations replicating geometrically but with a synergistic fitness landscape. Our simulations also showed that for stamping machine replication and antagonistic epistasis, a combination that appears to be common among plant viruses, populations further increased their robustness by inhibiting superinfection. We have also shown that the mode of replication strongly influenced the linkage between viral loci, which rapidly reached linkage equilibrium at increasing mutations for geometric replication. We also found that the strategy that minimized the time required to spread over the whole space was the stamping machine with antagonistic epistasis among mutations. Finally, our simulations revealed that the multiplicity of infection fluctuated but generically increased along time.
Detection of bone marrow involvement in newly diagnosed post-transplant lymphoproliferative disorder: 18F-fluorodeoxyglucose positron emission tomography/computed tomography versus bone marrow biopsy

Abstract Detecting bone marrow involvement (BMI) in lymphoma is important as it adversely affects stage. Bone marrow biopsy (BMB) remains the standard to detect BMI but is prone to sampling error. We retrospectively investigated whether 18F-fluorodeoxyglucose positron emission tomography with computed tomography (18F-FDG-PET/CT) could identify BMI in patients with post-transplant lymphoproliferative disorder (PTLD) with sufficient accuracy in comparison with staging BMB. Twenty-five patients diagnosed with PTLD who underwent 18F-FDG-PET/CT and BMB within one month were evaluated. Based on our criteria, six patients (24%) were considered positive for BMI on 18F-FDG-PET/CT compared to one by BMB. Although we cannot completely exclude false positive results on 18F-FDG-PET/CT, our data indicate a significantly higher sensitivity of 18F-FDG-PET/CT compared to BMB (100% vs 17%) but similar specificity. These data confirm the high diagnostic performance of 18F-FDG-PET/CT for detecting BMI, but prospective studies are needed to determine whether 18F-FDG-PET/CT could indeed replace staging BMB in PTLD.
Tolerance of Listeria monocytogenes to Quaternary Ammonium Sanitizers Is Mediated by a Novel Efflux Pump Encoded by emrE

ABSTRACT A novel genomic island (LGI1) was discovered in Listeria monocytogenes isolates responsible for the deadliest listeriosis outbreak in Canada, in 2008. To investigate the functional role of LGI1, the outbreak strain 08-5578 was exposed to food chain-relevant stresses, and the expression of 16 LGI1 genes was measured. LGI1 genes with putative efflux (L. monocytogenes emrE [emrELm ]), regulatory (lmo1851), and adhesion (sel1) functions were deleted, and the mutants were exposed to acid (HCl), cold (4°C), salt (10 to 20% NaCl), and quaternary ammonium-based sanitizers (QACs). Deletion of lmo1851 had no effect on the L. monocytogenes stress response, and deletion of sel1 did not influence Caco-2 and HeLa cell adherence/invasion, whereas deletion of emrE resulted in increased susceptibility to QACs (P < 0.05) but had no effect on the MICs of gentamicin, chloramphenicol, ciprofloxacin, erythromycin, tetracycline, acriflavine, and triclosan. In the presence of the QAC benzalkonium chloride (BAC; 5 μg/ml), 14/16 LGI1 genes were induced, and lmo1861 (putative repressor gene) was constitutively expressed at 4°C, 37°C, and 52°C and in the presence of UV exposure (0 to 30 min). Following 1 h of exposure to BAC (10 μg/ml), upregulation of emrE (49.6-fold), lmo1851 (2.3-fold), lmo1861 (82.4-fold), and sigB (4.1-fold) occurred. Reserpine visibly suppressed the growth of the ΔemrELm strain, indicating that QAC tolerance is due at least partially to efflux activity. These data suggest that a minimal function of LGI1 is to increase the tolerance of L. monocytogenes to QACs via emrELm . Since QACs are commonly used in the food industry, there is a concern that L. monocytogenes strains possessing emrE will have an increased ability to survive this stress and thus to persist in food processing environments.
Depression Among Moms: Prevalence, Predictors, and Acting Out among Third Grade Children. Child Trends Research Brief. Publication #2006-19.

In line with other research, we find that mothers’ depressive symptoms are related to more acting out behavior problems in their children. For both mothers in general and also for low-income mothers, one reason that depression appears to increase children’s acting out is that depression affects parenting, particularly effective discipline. However, we also find that maternal depressive symptoms are directly related to more acting out behavior.
Study ERCOT fast-responding regulation service using frequency modeling tool

Storage systems are potentially attractive choices for providing frequency Regulation Service in power systems due to their fast-ramping capability. However, despite the speed of response, the duration of their response is limited due to their restricted storage capabilities. Therefore, the deployment logic should be adequately designed for these resources to provide the most benefit to the system. In the Electric Reliability Council of Texas (ERCOT), storage systems can provide Fast-Responding Regulation Service (FRRS). This service was first tested in a pilot project and a deployment logic was mainly designed to demonstrate capabilities of participating storage systems. With the potential of increased storage capacity providing FRRS, the deployment logic designed for the pilot project would need to be reviewed. This paper evaluates the effects of this logic on the system frequency control performance and discusses the potential enhancements. The evaluation is carried out using ERCOT Frequency Modeling and Analysis Tool (EFMAT) developed within this study. The modeling details of the tool are also presented in this paper.
Differentiating and Categorizing of Liposarcoma and Synovial Sarcoma Neoplasms by Fluorescence in Situ Hybridization

Background & Objective: Soft tissue sarcomas (STS) constitute an uncommon and heterogeneous group of tumors of mesenchymal origin and various cytogenetic abnormalities ranging from distinct genomic rearrangements, such as chromosomal translocations and amplifications, to more intricate rearrangements involving multiple chromosomes. Fluorescence in situ hybridization (FISH) can be used to identify these chromosomal translocations and amplifications, and sub classify STS precisely. The current study aimed at investigating the usefulness of FISH, as a diagnostic ancillary aid, to detect cytogenetic abnormalities such as MDM2 (murine double minute 2) amplification and CHOP(C/EBP homologous protein) rearrangement in liposarcoma, as well as SYT (synaptotagmin) rearrangement in synovial sarcoma. Methods: The FISH technique was used to analyze 17 specimens of liposarcoma for MDM2 amplification and CHOP rearrangement, and 10 specimens of synovial sarcoma for SYT rearrangement. The subtypes of liposarcoma and synovial sarcomas were reclassified according to the FISH results and compared with those of the respective histological findings. Results: According to the FISH results in 17 liposarcoma cases, well-differentiated liposarcoma(WDLPS), dedifferentiated liposarcoma (DDLPS), and myxoidliposarcoma (MLPS)subtypes were 41%, 53%, and 6%, respectively. In different subtypes of liposarcoma, a total of 30% mismatches were observed between pathologic and cytogenetic results. According to the histological findings from FISH analysis, SYT rearrangement was found only in three out of 10 (30%) synovial sarcomas. Conclusion: The detection of cytogenetic abnormalities in patients with liposarcoma and synovial sarcoma by FISH technique provides an important objective tool to confirm sarcoma diagnosis and sub classification of specific sarcoma subtypes in such patients.
Tracking the Reorganization of Module Structure in Time-Varying Weighted Brain Functional Connectivity Networks

Identification of module structure in brain functional networks is a promising way to obtain novel insights into neural information processing, as modules correspond to delineated brain regions in which interactions are strongly increased. Tracking of network modules in time-varying brain functional networks is not yet commonly considered in neuroscience despite its potential for gaining an understanding of the time evolution of functional interaction patterns and associated changing degrees of functional segregation and integration. We introduce a general computational framework for extracting consensus partitions from defined time windows in sequences of weighted directed edge-complete networks and show how the temporal reorganization of the module structure can be tracked and visualized. Part of the framework is a new approach for computing edge weight thresholds for individual networks based on multiobjective optimization of module structure quality criteria as well as an approach for matching modules across time steps. By testing our framework using synthetic network sequences and applying it to brain functional networks computed from electroencephalographic recordings of healthy subjects that were exposed to a major balance perturbation, we demonstrate the framework's potential for gaining meaningful insights into dynamic brain function in the form of evolving network modules. The precise chronology of the neural processing inferred with our framework and its interpretation helps to improve the currently incomplete understanding of the cortical contribution for the compensation of such balance perturbations.
Crystal Structure of the Heteromolecular Chaperone, AscE-AscG, from the Type III Secretion System in Aeromonas hydrophila

Background The putative needle complex subunit AscF forms a ternary complex with the chaperones AscE and AscG in the type III secretion system of Aeromonas hydrophila so as to avoid premature assembly. Previously, we demonstrated that the C-terminal region of AscG (residues 62–116) in the hetero-molecular chaperone, AscE-AscG, is disordered and susceptible to limited protease digestion. Methodology/Principal Findings Here, we report the crystal structure of the ordered AscG1–61 region in complex with AscE at 2.4 Å resolution. Helices α2 and α3 of AscE in the AscE-AscG1–61 complex assumes a helix-turn-helix conformation in an anti-parallel fashion similar to that in apo AscE. However, in the presence of AscG, an additional N-terminal helix α1 in AscE (residues 4–12) is observed. PscG or YscG in the crystal structures of PscE-PscF-PscG or YscE-YscF-YscG, respectively, assumes a typical tetratricopeptide repeat (TPR) fold with three TPR repeats and one C-terminal capping helix. By comparison, AscG in AscE-AscG1–61 comprises three anti-parallel helices that resembles the N-terminal TPR repeats in the corresponding region of PscG or YscG in PscE-PscF-PscG or YscE-YscF-YscG. Thermal denaturation of AscE-AscG and AscE-AscG1–61 complexes demonstrates that the C-terminal disordered region does not contribute to the thermal stability of the overall complex. Conclusion/Significance The N-terminal region of the AscG in the AscE-AscG complex is ordered and assumes a structure similar to those in the corresponding regions of PscE-PscG-PscF or YscE-YscF-YscG complexes. While the C-terminal region of AscG in the AscE-AscG complex is disordered and will assume its structure only in the presence of the substrate AscF. We hypothesize that AscE act as a chaperone of the chaperone to keep AscG in a stable but partially disordered state for interaction with AscF.
Diversity of 16S-23S rDNA Internal Transcribed Spacer (ITS) Reveals Phylogenetic Relationships in Burkholderia pseudomallei and Its Near-Neighbors

Length polymorphisms within the 16S-23S ribosomal DNA internal transcribed spacer (ITS) have been described as stable genetic markers for studying bacterial phylogenetics. In this study, we used these genetic markers to investigate phylogenetic relationships in Burkholderia pseudomallei and its near-relative species. B. pseudomallei is known as one of the most genetically recombined bacterial species. In silico analysis of multiple B. pseudomallei genomes revealed approximately four homologous rRNA operons and ITS length polymorphisms therein. We characterized ITS distribution using PCR and analyzed via a high-throughput capillary electrophoresis in 1,191 B. pseudomallei strains. Three major ITS types were identified, two of which were commonly found in most B. pseudomallei strains from the endemic areas, whereas the third one was significantly correlated with worldwide sporadic strains. Interestingly, mixtures of the two common ITS types were observed within the same strains, and at a greater incidence in Thailand than Australia suggesting that genetic recombination causes the ITS variation within species, with greater recombination frequency in Thailand. In addition, the B. mallei ITS type was common to B. pseudomallei, providing further support that B. mallei is a clone of B. pseudomallei. Other B. pseudomallei near-neighbors possessed unique and monomorphic ITS types. Our data shed light on evolutionary patterns of B. pseudomallei and its near relative species.
Factory of realities: on the emergence of virtual spatiotemporal structures

The ubiquitous nature of modern Information Retrieval and Virtual World give rise to new realities. To what extent are these "realities" real? Which "physics" should be applied to quantitatively describe them? In this essay I dwell on few examples. The first is Adaptive neural networks, which are not networks and not neural, but still provide service similar to classical ANNs in extended fashion. The second is the emergence of objects looking like Einsteinian spacetime, which describe the behavior of an Internet surfer like geodesic motion. The third is the demonstration of nonclassical and even stronger-than-quantum probabilities in Information Retrieval, their use. Immense operable datasets provide new operationalistic environments, which become to greater and greater extent "realities". In this essay, I consider the overall Information Retrieval process as an objective physical process, representing it according to Melucci metaphor in terms of physical-like experiments. Various semantic environments are treated as analogs of various realities. The readers' attention is drawn to topos approach to physical theories, which provides a natural conceptual and technical framework to cope with the new emerging realities.
A 280μW dynamic-zoom ADC with 120dB DR and 118dB SNDR in 1kHz BW

Micro-power ADCs with high linearity and dynamic range (DR) are required in several applications, such as smart sensors, biomedical imaging, and portable instrumentation. Since the signals of interest are then often small (tens of μν) and slow (<1kHz BW), such ADCs should also exhibit low offset and flicker noise. Noise-shaping SAR [1] and incremental ADCs [2] have been proposed for such applications, but their DR is limited to about 100dB. Although the ΔΣ modulator (ΔΣM) proposed in [3] achieves 136dB DR, it is at the expense of high power consumption (12.7mW). The incremental zoom ADC proposed in [4] combines a coarse SAR ADC and a fine ΔΣ ADC to efficiently achieve 119.8dB DR, but is limited to DC signals. The dynamic zoom ADC in [5] solves this problem, but requires external filtering to cope with out-of-band interference. This paper describes an interferer-robust dynamic zoom ADC that consumes 280μW while achieving 120.3dB DR and 118.1dB SNDR in 1kHz BW, resulting in a Schreier FoM of 185.8dB. It also achieves a maximum offset of 30μν and a 1/f corner of 7Hz. These advances are achieved by the combination of dynamic error-correction techniques, an asynchronous SAR ADC and a fully differential inverter-based ΔΣ ADC.
Five Cases of Familial Mediterranean Fever in Japan: The Relationship with MEFV Mutations

Familial Mediterranean fever (FMF) is the most common genetic autoinflammatory disease, but it has been considered a rare disease in Japan. We herein describe five patients with FMF who were diagnosed both clinically and genetically at a single Japanese institute. A genetic investigation of Mediterranean fever (MEFV) detected heterozygosity for the compound mutations L110P/E148Q (n=2) and L110P/148Q/P369S/R406Q (n=1), and heterozygosity for M694I (n=1) and S503C (n=1). Colchicine prevented febrile attacks and accompanying symptoms in four patients. One patient with an S503C mutation showed resistance. Physicians should be aware of the characteristic symptoms, as well as the more unusual symptoms such as headache, when diagnosing FMF.
Energy forecasting tools and services

The increasing complexity of the power grid and the continuous integration of volatile renewable energy systems on all aspects of it have made more precise forecasts of both energy supply and demand necessary for the future Smart Grid. Yet, the ever increasing volume of tools and services makes it difficult for users (e.g., energy utility companies) and researchers to obtain even a general sense of what each tool or service offers. The present contribution provides an overview and categorization of several energy‐related forecasting tools and services (specifically for load and volatile renewable power), as well as general information regarding principles of time series, load, and volatile renewable power forecasting. WIREs Data Mining Knowl Discov 2018, 8:e1235. doi: 10.1002/widm.1235
Extracting information on urban impervious surface from GF-1 data in Tianjin City of China

The urban impervious surface, an important part in the city system, has a great influence on theecologicalenvironment in urban areas. The coverage of it is an important indicator for the evaluation ofurbanization. TheRemotesensing data has prominent features such as information-rich and accurate and it can provide data basis for large area extraction of impervious surface. GF-1 satellite is the first satellite of high-resolution earth observation system in China. With the homemade GF-1 satellite remote sensing image date as a resolution, this research, by the combination of V-I-S model and linear spectral mixture model, has first made estimation on the impervious surface of Tianjin City and then employed the remote sensingimage date with high resolution to test the precision of the estimated results. The results not only show that this method will make high precision available, but also reveal that Tianjin City has a wide coverage of impervious surface in general level, especially a high coverage rate both in the center and the coastal areas. The average coverage of impervious surface of the Tianjin city is very high and the coverage of impervious surface in the center and the coastal areas of Tianjin city reach seventy percent.City managers can use these data to guide city management and city planning.
Mathematical Model and Algorithm for Link Community Detection in Bipartite Networks

In the past ten years, community detection in complex networks has attracted more and more attention of researchers. Communities often correspond to functional subunits in the complex systems. In complex network, a node community can be defined as a subgraph induced by a set of nodes, while a link community is a subgraph induced by a set of links. Although most researches pay more attention to identifying node communities in both unipartite and bipartite networks, some researchers have investigated the link community detection problem in unipartite networks. But current research pays little attention to the link community detection problem in bipartite networks. In this paper, we investigate the link community detection problem in bipartite networks, and formulate it into an integer programming model. We proposed a genetic algorithm for partition the bipartite network into overlapping link communities. Simulations are done on both artificial networks and real-world networks. The results show that the bipartite network can be efficiently partitioned into overlapping link communities by the genetic algorithm.
Allium Roseum L. Extract Exerts Potent Suppressive Activities on Chronic Myeloid Leukemia K562 Cell Viability Through the Inhibition of BCR-ABL, PI3K/Akt, and ERK1/2 Pathways and the Abrogation of VEGF Secretion

ABSTRACT Use of plant extracts, alone or combined to the current chemotherapy as chemosensitizers, has emerged as a promising strategy to overcome tumor drug resistance. Here, we investigated the anticancer activity of Allium roseum L. extracts, a wild edible species in North Africa, on human Chronic Myeloid Leukemia (CML) K562 cells. The dehydrated aqueous extract (DAE) disturbed the cell cycle progression and induced the apoptosis of K562 cells. Chemical analysis of DAE showed a diversity of organosulfur compounds S-alk(en)yl-cysteine sulfoxides (RCSO) and high amount of allicin, suggesting that such molecule may be behind its antitumor effect. DAE was efficient in inhibiting K562 cell viability. DAE inhibitory effect was associated with the dephosphorylation of the BCR-ABL kinase and interfered with ERK1/2, Akt, and STAT5 pathways. Furthermore, we found that DAE-induced inactivation of Akt kinase led to the activation of its target FOXO3 transcription factor, enhancing the expression of FOXO3-regulated proapoptotic effectors, Bim and Bax, and cell cycle inhibitor p27. Finally, we found that DAE reduced the secretion of vascular endothelial growth factor. Overall, our data suggest that A. roseum extract has great potential as a nontoxic cheap and effective alternative to conventional chemotherapy.
Deletion of ghrelin prevents aging‐associated obesity and muscle dysfunction without affecting longevity

During aging, decreases in energy expenditure and locomotor activity lead to body weight and fat gain. Aging is also associated with decreases in muscle strength and endurance leading to functional decline. Here, we show that lifelong deletion of ghrelin prevents development of obesity associated with aging by modulating food intake and energy expenditure. Ghrelin deletion also attenuated the decrease in phosphorylated adenosine monophosphate‐activated protein kinase (pAMPK) and downstream mediators in muscle, and increased the number of type IIa (fatigue resistant, oxidative) muscle fibers, preventing the decline in muscle strength and endurance seen with aging. Longevity was not affected by ghrelin deletion. Treatment of old mice with pharmacologic doses of ghrelin increased food intake, body weight, and muscle strength in both ghrelin wild‐type and knockout mice. These findings highlight the relevance of ghrelin during aging and identify a novel AMPK‐dependent mechanism for ghrelin action in muscle.