bluuebunny/crossref_metadata_2025_split huggingface dataset:
Automated formal synthesis of provably safe digital controllers for continuous plants
Authors: Abate Alessandro , Bessa Iury , Cordeiro Lucas , David Cristina , Kesseli Pascal , Kroening Daniel , Polgreen Elizabeth 
Published: December 2019

Abstract
We present a sound and automated approach to synthesizing safe, digital controllers for physical plants represented as time-invariant models. Models are linear differential equations with inputs, evolving over a continuous state space. The synthesis precisely accounts for the effects of finite-precision arithmetic introduced by the controller. The approach uses counterexample-guided inductive synthesis: an inductive generalization phase produces a controller that is known to stabilize the model but that may not be safe for all initial conditions of the model. Safety is then verified via bounded model checking: if the verification step fails, a counterexample is provided to the inductive generalization, and the process further iterates until a safe controller is obtained. We demonstrate the practical value of this approach by automatically synthesizing safe controllers for physical plant models from the digital control literature.
Revealing factors determining immunodominant responses against dominant epitopes
Authors: Ritmahan Wannisa , Kesmir Can , Vroomans Renske M.A. 
Published: December 2019

AbstractUpon recognition of peptide-MHC complexes by T cell receptors (TCR), the cognate T cells expand and differentiate into effector T cells to generate protective immunity. Despite the fact that any immune response generates a diverse set of TCR clones against a particular epitope, only a few clones are highly expanded in any immune response. Previous studies observed that the highest frequency clones usually control viral infections better than subdominant clones, but the reasons for this dominance among T cell clones are still unclear. Here, we used publicly available TCR amino acid sequences to study which factors determine whether a response becomes immunodominance (ID) per donor; we classified the largest T cell clone as the epitope-specific dominant clone and all the other clones as subdominant responses (SD). We observed a distinctively hydrophobic CDR3 in ID responses against a dominant epitope from influenza A virus, compared to the SD responses. The common V-J combinations were shared between ID and SD responses, suggesting that the biased V-J recombination events are restricted by epitope specificity; thus, the immunodominance is not directly determined by a bias combination of V and J genetic segments. Our findings reveal a close similarity of global sequence properties between dominant and subdominant clones of epitope-specific responses but detectable distinctive amino acid enrichments in ID. Taken together, we believe this first comparative study of immunodominant and subdominant TCR sequences can guide further studies to resolve factors determining the immunodominance of antiviral as well as tumor-specific T cell responses.
Hierarchical stochastic graphlet embedding for graph-based pattern recognition
Authors: Dutta Anjan , Riba Pau , Lladós Josep , Fornés Alicia 
Published: December 2019

AbstractDespite being very successful within the pattern recognition and machine learning community, graph-based methods are often unusable because of the lack of mathematical operations defined in graph domain. Graph embedding, which maps graphs to a vectorial space, has been proposed as a way to tackle these difficulties enabling the use of standard machine learning techniques. However, it is well known that graph embedding functions usually suffer from the loss of structural information. In this paper, we consider the hierarchical structure of a graph as a way to mitigate this loss of information. The hierarchical structure is constructed by topologically clustering the graph nodes and considering each cluster as a node in the upper hierarchical level. Once this hierarchical structure is constructed, we consider several configurations to define the mapping into a vector space given a classical graph embedding, in particular, we propose to make use of the stochastic graphlet embedding (SGE). Broadly speaking, SGE produces a distribution of uniformly sampled low-to-high-order graphlets as a way to embed graphs into the vector space. In what follows, the coarse-to-fine structure of a graph hierarchy and the statistics fetched by the SGE complements each other and includes important structural information with varied contexts. Altogether, these two techniques substantially cope with the usual information loss involved in graph embedding techniques, obtaining a more robust graph representation. This fact has been corroborated through a detailed experimental evaluation on various benchmark graph datasets, where we outperform the state-of-the-art methods.
Single and ensemble classifiers for defect prediction in sheet metal forming under variability
Authors: Dib M. A. , Oliveira N. J. , Marques A. E. , Oliveira M. C. , Fernandes J. V. , Ribeiro B. M. , Prates P. A. 
Published: December 2019

AbstractThis paper presents an approach, based on machine learning techniques, to predict the occurrence of defects in sheet metal forming processes, exposed to sources of scatter in the material properties and process parameters. An empirical analysis of performance of ML techniques is presented, considering both single learning and ensemble models. These are trained using data sets populated with numerical simulation results of two sheet metal forming processes: U-Channel and Square Cup. Data sets were built for three distinct steel sheets. A total of eleven input features, related to the mechanical properties, sheet thickness and process parameters, were considered; also, two types of defects (outputs) were analysed for each process. The sampling data were generated, assuming that the variability of each input feature is described by a normal distribution. For a given type of defect, most single classifiers show similar performances, regardless of the material. When comparing single learning and ensemble models, the latter can provide an efficient alternative. The fact that ensemble predictive models present relatively high performances, combined with the possibility of reconciling model bias and variance, offer a promising direction for its application in industrial environment.
Embedded axonal fiber tracts improve finite element model predictions of traumatic brain injury
Authors: Hajiaghamemar Marzieh , Wu Taotao , Panzer Matthew B. , Margulies Susan S. 
Published: December 2019

AbstractWith the growing rate of traumatic brain injury (TBI), there is an increasing interest in validated tools to predict and prevent brain injuries. Finite element models (FEM) are valuable tools to estimate tissue responses, predict probability of TBI, and guide the development of safety equipment. In this study, we developed and validated an anisotropic pig brain multi-scale FEM by explicitly embedding the axonal tract structures and utilized the model to simulate experimental TBI in piglets undergoing dynamic head rotations. Binary logistic regression, survival analysis with Weibull distribution, and receiver operating characteristic curve analysis, coupled with repeated k-fold cross-validation technique, were used to examine 12 FEM-derived metrics related to axonal/brain tissue strain and strain rate for predicting the presence or absence of traumatic axonal injury (TAI). All 12 metrics performed well in predicting of TAI with prediction accuracy rate of 73–90%. The axonal-based metrics outperformed their rival brain tissue-based metrics in predicting TAI. The best predictors of TAI were maximum axonal strain times strain rate (MASxSR) and its corresponding optimal fraction-based metric (AF-MASxSR7.5) that represents the fraction of axonal fibers exceeding MASxSR of 7.5 s−1. The thresholds compare favorably with tissue tolerances found in in–vitro/in–vivo measurements in the literature. In addition, the damaged volume fractions (DVF) predicted using the axonal-based metrics, especially MASxSR (DVF = 0.05–4.5%), were closer to the actual DVF obtained from histopathology (AIV = 0.02–1.65%) in comparison with the DVF predicted using the brain-related metrics (DVF = 0.11–41.2%). The methods and the results from this study can be used to improve model prediction of TBI in humans.
Complex origins of chloroplast membranes with photosynthetic machineries: multiple transfers of genes from divergent organisms at different times or a single endosymbiotic event?
Authors: Sato Naoki 
Published: December 2019

AbstractThe paradigm “cyanobacterial origin of chloroplasts” is currently viewed as an established fact. However, we may have to re-consider the origin of chloroplast membranes, because membranes are not replicated by their own. It is the genes for lipid biosynthetic enzymes that are inherited. In the current understandings, these enzymes became encoded by the nuclear genome as a result of endosymbiotic gene transfer from the endosymbiont. However, we previously showed that many enzymes involved in the synthesis of chloroplast peptidoglycan and glycolipids did not originate from cyanobacteria. Here I present results of comprehensive phylogenetic analysis of chloroplast enzymes involved in fatty acid and lipid biosynthesis, as well as additional chloroplast components related to photosynthesis and gene expression. Four types of phylogenetic relationship between chloroplast enzymes (encoded by the chloroplast and nuclear genomes) and cyanobacterial counterparts were found: type 1, chloroplast enzymes diverged from inside of cyanobacterial clade; type 2, chloroplast and cyanobacterial enzymes are sister groups; type 3, chloroplast enzymes originated from homologs of bacteria other than cyanobacteria; type 4, chloroplast enzymes diverged from eukaryotic homologs. Estimation of evolutionary distances suggested that the acquisition times of chloroplast enzymes were diverse, indicating that multiple gene transfers accounted for the chloroplast enzymes analyzed. Based on the results, I try to relax the tight logic of the endosymbiotic origin of chloroplasts involving a single endosymbiotic event by proposing alternative hypotheses. The hypothesis of host-directed chloroplast formation proposes that glycolipid synthesis ability had been acquired by the eukaryotic host before the acquisition of chloroplast ribosomes. Chloroplast membrane system could have been provided by the host, whereas cyanobacteria contributed to the genes for the genetic and photosynthesis systems, at various times, either before or after the formation of chloroplast membranes. The origin(s) of chloroplasts seems to be more complicated than the single event of primary endosymbiosis.
circRNAs expressed in human peripheral blood are associated with human aging phenotypes, cellular senescence and mouse lifespan
Authors: Haque Shahnaz , Ames Ryan M. , Moore Karen , Pilling Luke C. , Peters Luanne L. , Bandinelli Stefania , Ferrucci Luigi , Harries Lorna W. 
Published: December 2019

AbstractCircular RNAs (circRNAs) are an emerging class of non-coding RNA molecules that are thought to regulate gene expression and human disease. Despite the observation that circRNAs are known to accumulate in older organisms and have been reported in cellular senescence, their role in aging remains relatively unexplored. Here, we have assessed circRNA expression in aging human blood and followed up age-associated circRNA in relation to human aging phenotypes, mammalian longevity as measured by mouse median strain lifespan and cellular senescence in four different primary human cell types. We found that circRNAs circDEF6, circEP300, circFOXO3 and circFNDC3B demonstrate associations with parental longevity or hand grip strength in 306 subjects from the InCHIANTI study of aging, and furthermore, circFOXO3 and circEP300 also demonstrate differential expression in one or more human senescent cell types. Finally, four circRNAs tested showed evidence of conservation in mouse. Expression levels of one of these, circPlekhm1, was nominally associated with lifespan. These data suggest that circRNA may represent a novel class of regulatory RNA involved in the determination of aging phenotypes, which may show future promise as both biomarkers and future therapeutic targets for age-related disease.
Boundary Crossing Support in Part-Time Higher Professional Education Programs
Authors: Arts Margit , Bronkhorst Larike H. 
Published: December 2019

AbstractAs learning societies necessitate continuous education, a growing number of part-time programs are being offered. A key challenge for part-time programs is adequately supporting students in connecting their learning within the program to their work life, which in contrast to dual education is not part of the program. To better understand such boundary-crossing support in part-time higher professional education, this explanatory sequential mixed-methods study was conducted. A large-scale study, consisting of quantitative data analysis of the Dutch National Student Survey, confirmed that part-time programs (n = 600) differ in perceived boundary crossing, with a medium effect size of η2 = .13, and that factors postulated in the literature are related. An in-depth cross-case analysis of the boundary-crossing support provided in four purposefully selected part-time higher education programs (with high and low perceived support) indicated that brokers, boundary objects, hybrid practices, boundary interactions, degrees of freedom, degrees of clarity, and supervision are ways to support boundary crossing. These findings provide actionable strategies by which part-time higher professional education programs can support student learning across contexts.
Complement C5 Contributes to Brain Injury After Subarachnoid Hemorrhage
Authors: van Dijk Bart J. , Meijers Joost C.M. , Kloek Anne T. , Knaup Veronique L. , Rinkel Gabriel J.E. , Morgan B. Paul , van der Kamp Marije J. , Osuka Koji , Aronica Eleonora , Ruigrok Ynte M. , van de Beek Diederik , Brouwer Matthijs , Pekna Marcela , Hol Elly M. , Vergouwen Mervyn D.I. 
Published: December 2019

AbstractPrevious studies showed that complement activation is associated with poor functional outcome after aneurysmal subarachnoid hemorrhage (SAH). We investigated whether complement activation is underlying brain injury after aneurysmal SAH (n = 7) and if it is an appropriate treatment target. We investigated complement expression in brain tissue of aneurysmal SAH patients (n = 930) and studied the role of common genetic variants in C3 and C5 genes in outcome. We analyzed plasma levels (n = 229) to identify the functionality of a single nucleotide polymorphism (SNP) associated with outcome. The time course of C5a levels was measured in plasma (n = 31) and CSF (n = 10). In an SAH mouse model, we studied the extent of microglia activation and cell death in wild-type mice, mice lacking the C5a receptor, and in mice treated with C5-specific antibodies (n = 15 per group). Brain sections from aneurysmal SAH patients showed increased presence of complement components C1q and C3/C3b/iC3B compared to controls. The complement component 5 (C5) SNP correlated with C5a plasma levels and poor disease outcome. Serial measurements in CSF revealed that C5a was > 1400-fold increased 1 day after aneurysmal SAH and then gradually decreased. C5a in plasma was 2-fold increased at days 3–10 after aneurysmal SAH. In the SAH mouse model, we observed a ≈ 40% reduction in both microglia activation and cell death in mice lacking the C5a receptor, and in mice treated with C5-specific antibodies. These data show that C5 contributes to brain injury after experimental SAH, and support further study of C5-specific antibodies as novel treatment option to reduce brain injury and improve prognosis after aneurysmal SAH.
Transition zones analysis using empirical capillary pressure model from well logs and 3D seismic data on ‘Stephs’ field, onshore, Niger Delta, Nigeria
Authors: Abiola O. , Obasuyi F. O. 
Published: December 2019

AbstractCapillary pressure is an important characteristic that indicates the zones of interaction between two-phase fluids or fluid and rock occurring in the subsurface. The analysis of transition zones (TZs) using Goda (Sam) et al.’s empirical capillary pressure from well logs and 3D seismic data in ‘Stephs’ field, Niger Delta, was carried out to remove the effect of mobile water above the oil–water contact in reservoirs in the absence of core data/information. Two reservoirs (RES B and C) were utilized for this study with net thicknesses (NTG) ranging from 194.14 to 209.08 m. Petrophysical parameters computed from well logs indicate that the reservoirs’ effective porosity ranges from 10 to 30% and the permeability ranges from 100 to > 1000 mD, which are important characteristics of good hydrocarbon bearing zone. Checkshot data were used to tie the well to the seismic section. Faults and horizons were mapped on the seismic section. Time structure maps were generated, and a velocity model was used to convert the time structure maps to its depth equivalent. A total of six faults were mapped, three of which are major growth faults (F1, F4 and F5) and cut across the study area. Reservoir properties were modelled using SIS and SGS. The capillary pressure log, curves and models generated were useful in identifying the impact of mobile water in the reservoir as they show the trend of saturating and interacting fluids. The volume of oil estimated from reservoirs B and C without taking TZ into consideration was 273 × 106 and 406 × 106 mmbbls, respectively, and was found to be higher than the volume of oil estimated from the two reservoirs while taking TZ into consideration which was 242 × 106 and 256 × 106 mmbbls, respectively. The results have indicated the presence of mobile water, which have further established that conventionally recoverable hydrocarbon (RHC) is usually overestimated; hence, TZ analysis has to be performed for enhancing RHC for cost-effective extraction and profit maximization.
Efficiency of induction of Shiga-toxin lambdoid prophages in Escherichia coli due to oxidative and antibiotic stress depends on the combination of prophage and the bacterial strain
Authors: Filipiak Michalina , Łoś Joanna M. , Łoś Marcin 
Published: December 2019

AbstractIn the study presented here, we tested, how large a fraction of lysogenic culture was undergoing filamentation, which could indicate triggering of the SOS response or SOS-independent prophage induction that is also known to cause cell filamentation. Here, antibiotic stress was triggered by adding mitomycin C and oxidative stress was induced by hydrogen peroxide. Observation of bacterial cells under an optical microscope revealed more filamenting cells for lysogenic Escherichia coli than for strains not carrying a prophage. Moreover, the amount of filamenting cells depended not only on the stress agents used and the type of the prophage, but also on the host. During induction of the 933W prophage, the resulting phage titer and the amount of elongating cells were different when using E. coli O157:H7 EDL933 clinical isolate and the E. coli MG1655 laboratory strain. The amount of filamenting cells correlates well with the observed phage titers.
The Ellis semigroup of certain constant-length substitutions
Authors: STAYNOVA PETRA 
Published: December 2019

In this article, we calculate the Ellis semigroup of a certain class of constant-length substitutions. This generalizes a result of Haddad and Johnson [IP cluster points, idempotents, and recurrent sequences. Topology Proc.22 (1997) 213–226] from the binary case to substitutions over arbitrarily large finite alphabets. Moreover, we provide a class of counterexamples to one of the propositions in their paper, which is central to the proof of their main theorem. We give an alternative approach to their result, which centers on the properties of the Ellis semigroup. To do this, we also show a new way to construct an almost automorphic–isometric tower to the maximal equicontinuous factor of these systems, which gives a more particular approach than the one given by Dekking [The spectrum of dynamical systems arising from substitutions of constant length. Z. Wahrscheinlichkeitstheor. Verw. Geb.41(3) (1977/78) 221–239].
Antibiotic stewardship teams and Clostridioides difficile practices in United States hospitals: A national survey in The Joint Commission antibiotic stewardship standard era
Authors: Vaughn Valerie M. , Greene M. Todd , Ratz David , Fowler Karen E. , Krein Sarah L. , Flanders Scott A. , Dubberke Erik R. , Saint Sanjay , Patel Payal K. 
Published: December 2019

Abstract

Objective:
Clostridioides difficile infection (CDI) can be prevented through infection prevention practices and antibiotic stewardship. Diagnostic stewardship (ie, strategies to improve use of microbiological testing) can also improve antibiotic use. However, little is known about the use of such practices in US hospitals, especially after multidisciplinary stewardship programs became a requirement for US hospital accreditation in 2017. Thus, we surveyed US hospitals to assess antibiotic stewardship program composition, practices related to CDI, and diagnostic stewardship.

Methods:
Surveys were mailed to infection preventionists at 900 randomly sampled US hospitals between May and October 2017. Hospitals were surveyed on antibiotic stewardship programs; CDI prevention, treatment, and testing practices; and diagnostic stewardship strategies. Responses were compared by hospital bed size using weighted logistic regression.

Results:
Overall, 528 surveys were completed (59% response rate). Almost all (95%) responding hospitals had an antibiotic stewardship program. Smaller hospitals were less likely to have stewardship team members with infectious diseases (ID) training, and only 41% of hospitals met The Joint Commission accreditation standards for multidisciplinary teams. Guideline-recommended CDI prevention practices were common. Smaller hospitals were less likely to use high-tech disinfection devices, fecal microbiota transplantation, or diagnostic stewardship strategies.

Conclusions:
Following changes in accreditation standards, nearly all US hospitals now have an antibiotic stewardship program. However, many hospitals, especially smaller hospitals, appear to struggle with access to ID expertise and with deploying diagnostic stewardship strategies. CDI prevention could be enhanced through diagnostic stewardship and by emphasizing the role of non–ID-trained pharmacists and clinicians in antibiotic stewardship.