bluuebunny/crossref_metadata_2025_split huggingface dataset:
Backpressure control with estimated queue lengths for urban network traffic
Authors: Li Li , Okoth Victor , Jabari Saif Eddin 
Published: January 2021

AbstractBackpressure (BP) control was originally used for packet routing in communications networks. Since its first application to network traffic control, it has undergone different modifications to tailor it to traffic problems with promising results. Most of these BP variants are based on an assumption of perfect knowledge of traffic conditions throughout the network at all times, specifically the queue lengths (more accurately, the traffic volumes). However, it has been well established that accurate queue length information at signalized intersections is never available except in fully connected environments. Although connected vehicle technologies are developing quickly, a fully connected environment in the real world is still far. This paper tests the effectiveness of BP control when incomplete or imperfect knowledge about traffic conditions is available. BP control is combined with a speed/density field estimation module suitable for a partially connected environment. The proposed system is referred to as a BP with estimated queue lengths (BP‐EQ). The robustness of BP‐EQ is tested to varying levels of connected vehicle penetration, and BP‐EQ is compared with the original BP (i.e. assuming accurate knowledge of traffic conditions), a real‐world adaptive signal controller, and optimized fixed timing control using microscopic traffic simulation with field calibrated data. These results show that with a connected vehicle penetration rate as little as 10%, BP‐EQ can outperform the adaptive controller and the fixed timing controller in terms of average delay, throughput, and maximum stopped queue lengths under high demand scenarios.
The IO–PS in the context of GVC-related policymaking: The case of the South African automotive industry
Authors: Bam Wouter G. , De Bruyne Karolien , Laing Mare 
Published: January 2021

AbstractRecent years have seen renewed interest in evaluating the effectiveness of industrial policy, especially in the context of global value chains. One approach that might add a complementary view in this domain is product space analysis. To date, product space-based value chain analyses have focused on theoretical debates only, or on empirical applications for a single year. In this paper, we employ the input–output product space (IO–PS) framework combined with a time dimension. We thereby evaluate the effectiveness of industrial policies within a value chain over time. The paper focuses on the case of the South African automotive value chain for the years 1995 to 2017. We evaluate ex post the implemented industrial policies and confirm their (partial) success. We then use the framework to make ex ante recommendations to improve the current policy approach and find that it might pay off to target specific sub-sectors in the future. The results illustrate how the framework can be used to evaluate industrial policies and to identify which parts of the global value chain should be targeted to foster both short- and long-term growth. We also highlight shortcomings of the approach which might limit its application.
RedefiningRhynchosporasectionTenues(Cyperaceae), a phylogenetic approach
Authors: Silva Filho Pedro J S , Thomas William W , Boldrini Ilsi I 
Published: January 2021

AbstractRhynchospora is one of the most species-rich genera of Cyperaceae, comprising c. 400 species in 28 sections. Rhyncospora section Tenues is one of the largest sections and one of the most problematic. Because it is morphologically similar to sections Laevinuces, Luzuliformes and Spermodontes, the characters traditionally used to distinguish section Tenues cannot be reliably used to place species into one of these four sections. These four sections are included in the Psilocarya group of Rhynchospora subgenus Rhynchospora with sections Psilocarya and Dichromena. Previous molecular studies of Rhynchospora indicate that species of the Psilocarya group form a clade and are sister to at least some species of the sections being studied here. Since only 11 of the estimated 41 species in these four sections were included in earlier phylogenetic studies, the relationships among these sections remain unclear. To elucidate these relationships, we conducted a molecular phylogenetic analysis for Rhynchospora, based on plastid trnL-F and nuclear ETS and ITS markers, emphasizing species in these four sections. Results show that sections Laevinuces, Spermodontes and Tenues are individually not monophyletic but, grouped together, form a well-supported clade, Rhynchospora section Tenues s.l. Rhynchospora section Luzuliformes is monophyletic but is not a sister clade of section Tenues.
Two mutations in a maize bronze-1 allele caused by transposable elements of the Ac-Ds family alter the quantity and quality of the gene product.
Authors: Schiefelbein J W , Furtek D B , Dooner H K , Nelson O E 
Published: January 2021

Abstract
The Dissociation (Ds) mutant, Bz-wm, of the maize bronze-1 (bz) locus conditions a leaky phenotype. Plants carrying this mutant allele synthesize a low amount of an altered Bz gene product, which leads to reduced anthocyanin pigmentation in the seed. The molecular analysis reported here shows that the Bz-wm mutant has a 406-bp Ds1 insertion located 63 bp 5' to the start of Bz transcription. Furthermore, the Bz-wm allele contains three additional base pairs within the second exon, relative to the wild-type Bz allele. These additional nucleotides are believed to be derived from the 8-bp target site duplication created by an Activator (Ac) element in a previous allele in the series. The biochemical and molecular analyses of Bz-wm and revertants of Bz-wm indicate that the three additional nucleotides are responsible for the altered enzyme stability, while the Ds1 element affects the steady-state level of Bz-specific protein and RNA. Since the two mutations present in the Bz-wm mutant were each caused by the action of the Ac-Ds transposable element system, these results provide new insights into the ways that transposable elements can modify maize gene expression.
Evolution by gene duplication and compensatory advantageous mutations.
Authors: Ohta T 
Published: January 2021

Abstract
Relaxation of selective constraint is thought to play an important role for evolution by gene duplication, in connection with compensatory advantageous mutant substitutions. Models were investigated by incorporating gene duplication by unequal crossing over, selection, mutation and random genetic drift into Monte Carlo simulations. Compensatory advantageous mutations were introduced, and simulations were carried out with and without relaxation, when genes are redundant on chromosomes. Relaxation was introduced by assuming that deleterious mutants have no effect on fitness, so long as one or more genes free of such mutations remain in the array. Compensatory mutations are characterized by the intermediate deleterious step of their substitutions, and therefore relaxation by gene redundancy is important. Through extensive Monte Carlo simulations, it was found that compensatory mutant substitutions require relaxation in addition to gene duplication, when mutant effects are large. However when mutant effects are small, such that the product of selection coefficient and population size is around unity, evolution by compensatory mutation is enhanced by gene duplication even without relaxation.
Chloroplast DNA diversity in populations of wild and cultivated barley.
Authors: Neale D B , Saghai-Maroof M A , Allard R W , Zhang Q , Jorgensen R A 
Published: January 2021

Abstract
Chloroplast DNA (cpDNA) diversity was found within and among populations (245 accessions total) of wild barley, Hordeum vulgare L. ssp. spontaneum Koch from Israel and Iran. Three polymorphic restriction sites (HindIII, EcoRI, BclI) which define three distinct cpDNA lineages were detected. One lineage is common to populations in the Hule Valley and Kinneret of northern Israel, and in Iran. The second lineage is found predominantly in the Lower Jordan Valley and Negev. The distribution of the third lineage is scattered but widespread throughout Israel. Sixty two accessions of cultivated barleys, H. vulgare L., were found, with two exceptions, to belong to just one cpDNA lineage of wild barley, indicating that the cpDNA of cultivated barley is less variable than its wild ancestor. These results demonstrate the need for assessing intraspecific cpDNA variability prior to choosing single accessions for phylogenetic constructions at the species level and higher.
Mechanisms of mutagenesis by a bulky DNA lesion at the guanine N7 position.
Authors: Sambamurti K , Callahan J , Luo X , Perkins C P , Jacobsen J S , Humayun M Z 
Published: January 2021

Abstract
In order to examine the mechanisms of mutagenesis by a bulky DNA lesion at the guanine N7 position, the replicative form DNA of phage M13AB28 (mp8 without the amber codons in phage genes) was modified in vitro with aflatoxin B1-2,3-dichloride and transfected into appropriate Escherichia coli cells. Forward mutations in the lacZ alpha-complementing gene segment were identified as light blue or colorless plaques on appropriate indicator plates, isolated, and defined by DNA sequencing. Transfection of modified DNA into uvrA-/mucAB+ cells without prior UV (SOS) induction increased mutation frequency eight-fold over untreated DNA, whereas this increase was 12-fold upon SOS induction. Transfection of modified DNA after conversion of the primary guanine-aflatoxin lesions to the stable imidazole ring-opened formamidopyrimidine-aflatoxin suggested that these lesions were nearly equally mutagenic. A majority of point mutations under all conditions affected G:C bp. Base substitutions were in the majority, but significant frameshift mutagenesis was also detected in SOS-induced cells. Both G-to-T transversions and G-to-A transitions were produced at equal efficiency and together accounted for virtually all of the base substitutions induced by the primary lesions. Point mutations occurred predominantly at predicted damage hotspots. The characteristics of base substitution and frameshift mutations, together with available information point to multiple mechanisms of mutagenesis by this class of mutagens. The data indicate that primary lesions have the properties of both a noninstructional and pseudo-instructional lesion. In addition, the sequence context appears to play a role in determining whether a frameshift or a base substitution is induced by this bulky lesion.
A MUTANT AFFECTING MEIOSIS IN NEUROSPORA
Authors: Smith David A 
Published: January 2021

ABSTRACT
Many mutants affecting meiosis increase the occurrence of aneuploid meiotic products. In Neurospora, mutants of this type cause ascospore abortion which is reflected by an increase in the proportion of ascospores failing to develop black pigment. The usefulness of the criterion white-ascospore-production as a signal for the presence of a mutant affecting meiosis is demonstrated by the recovery of several such mutants. One of these is mei-1 (meiotic-1), a recessive mutant on linkage group IV. Crosses homozygous for mei-1 produce 90% white ascospores (vs. 5% in wild-type crosses). Viable ascospores, invariably black, are always disomic for one or more linkage groups; the chromatids assorted into viable ascospores do not engage in crossing over in meiosis. The distribution of viable ascospores in individual asci suggests that all meioses are defective in the first meiotic division, and that most meioses are defective in both divisions.
CHEMOTAXIS-DEFECTIVE MUTANTS OF THE NEMATODE CAENORHABDITIS ELEGANS
Authors: Dusenbery David B , Sheridan Robert E , Russell Richard L 
Published: January 2021

ABSTRACT
The technique of countercurrent separation has been used to isolate 17 independent chemotaxis-defective mutants of the nematode Caenorhabditis elegans. The mutants, selected to be relatively insensitive to the normally attractive salt NaCl, show varying degrees of residual sensitivity; some are actually weakly repelled by NaCl. The mutants are due to single gene defects, are autosomal and recessive, and identify at least five complementation groups.
Data-driven measures to mitigate the impact of COVID-19 in South America: how do regional programmes compare to best practice?
Authors: Blauth Taís Fernanda , Gstrein Oskar Josef 
Published: January 2021

Abstract
• This article analyses data-driven measures used in South America to mitigate the impact of COVID-19. Based on a broad review of relevant programmes in the region three selected cases from Argentina (Cuidar App), Brazil (use of personal data by IBGE), and Chile (CoronApp) are evaluated against best regional and international practices.
• Our findings suggest that programmes in South America mirror approaches in other global regions and as such face many similar challenges. There is no clearly defined purpose, a lack of transparency, and the need for readjustment soon after initial development.
• While the region is heavily affected by COVID-19, the three case-studies analysed demonstrate that policy makers in the region failed to establish trust in the measures. This can be deducted from low penetration rates of the programmes in Argentina and Chile.
• Finally, there are serious concerns regarding the long-term impact of these programmes upon human rights (especially privacy) and human dignity.
Empirical Results for High-definition Video and Augmented Reality Content Delivery in Hyper-connected Cars
Authors: Schipor Ovidiu-Andrei , Vatavu Radu-Daniel 
Published: January 2021

Abstract
Software architecture and applications for the connected car can process and share a variety of digital content, among which high-definition video and augmented reality (AR) content, toward enhanced driving assistance, navigation and infotainment systems and services. However, several technical challenges need to be overcome to make such systems and services viable and efficient, including dealing effectively with a variety of types of systems, devices and platforms, either installed inside the vehicle or represented by the personal mobile and wearable devices of the drivers and passengers. In this paper, we outline these technical challenges and propose a software solution in the form of an event-based middleware layer by modeling the smart, connected car as a specific type of a smart environment. We employ an adapted version of Euphoria, a recently introduced software architecture for general-purpose smart environments, to implement asynchronous communications among heterogeneous input/output devices inside the vehicle. We also adapt Euphoria to fit into the four-layer infrastructure model of the connected car. We conduct a technical evaluation of the request-response time performance achieved with the Euphoria middleware for streaming digital content from 1 Mbps (360p@30fps) to 32 Mbps (4K@30fps) on various devices, either integrated in the vehicle, not integrated but used inside the vehicle and devices outside the vehicle (the control condition). Our results show effective live streaming achieved for 2K content at 30fps with the 600 Mbps network (i.e., the connected car) and for 4K content at 30fps with the 1.7 Gbps network envisioned for hyper-connected vehicles. These results open up opportunities for high-definition video and AR applications in the automotive industry.
KINETIC SIMULATIONS OF THE THERMOLUMINESCENCE CHARACTERISTICS OF LIF:MG, TI INCORPORATING LOCALISED AND DELOCALISED RECOMBINATION
Authors: Eliyahu I , Oster L 
Published: January 2021

ABSTRACT
Kinetic simulations of the thermoluminescence characteristics of LiF:Mg, Ti are reviewed in the framework of conduction band/valence band models. Delocalised recombination models have been mainly applied to the simulation of glow peak shapes, although comparison with experimental data has proven difficult if not impossible due to the scarcity of materials with demonstrably proven ‘single-peak’ glow curves. The delocalised models are incapable of the simulation of TL dose response linear/supralinear behaviour and the dependence of the supralinearity on particle energy. These characteristics require the incorporation of localised, nanodosimetric, recombination processes in the TL mechanisms. These investigations have simulated many of the TL characteristics of LiF:Mg, Ti in kinetic models based on a mixture of both delocalised and localised recombination.
Cis-regulatory Element Hijacking by Structural Variants Overshadows Higher-Order Topological Changes in Prostate Cancer
Authors: Hawley James R. , Zhou Stanley , Arlidge Christopher , Grillo Giacomo , Kron Ken , Hugh-White Rupert , van der Kwast Theodorus , Fraser Michael , Boutros Paul C. , Bristow Robert G. , Lupien Mathieu 
Published: January 2021

AbstractProstate cancer is a heterogeneous disease whose progression is linked to genome instability. However the impact of this instability on the three-dimensional chromatin organization and how this drives progression is unclear. Using primary benign and tumour tissue, we find a high concordance in the higher-order three-dimensional genome organization across normal and prostate cancer cells. This concordance argues for constraints to the topology of prostate tumour genomes. Nonetheless, we identify changes to focal chromatin interactions and show how structural variants can induce these changes to guidecis-regulatory element hijacking. Such events result in opposing differential expression on genes found at antipodes of rearrangements. Collectively, our results argue thatcis-regulatory element hijacking from structural variant-induced altered focal chromatin interactions overshadows higher-order topological changes in the development of primary prostate cancer.
SARS-CoV-2 RBD in vitro evolution follows contagious mutation spread, yet generates an able infection inhibitor
Authors: Zahradník Jiří , Marciano Shir , Shemesh Maya , Zoler Eyal , Chiaravalli Jeanne , Meyer Björn , Rudich Yinon , Dym Orly , Elad Nadav , Schreiber Gideon 
Published: January 2021

AbstractSARS-CoV-2 is continually evolving, with more contagious mutations spreading rapidly. Using in vitro evolution to affinity maturate the receptor-binding domain (RBD) of the spike protein towards ACE2 resulted in the more contagious mutations, S477N, E484K, and N501Y, to be among the first selected, explaining the convergent evolution of the “European” (20E-EU1), “British” (501.V1),”South African” (501.V2), and ‘‘Brazilian” variants (501.V3). Plotting the binding affinity to ACE2 of all RBD mutations against their incidence in the population shows a strong correlation between the two. Further in vitro evolution enhancing binding by 600-fold provides guidelines towards potentially new evolving mutations with even higher infectivity. For example, Q498R epistatic to N501Y. Nevertheless, the high-affinity RBD is also an efficient drug, inhibiting SARS-CoV-2 infection. The 2.9Å Cryo-EM structure of the high-affinity complex, including all rapidly spreading mutations, provides a structural basis for future drug and vaccine development and for in silico evaluation of known antibodies.
Simultaneous readout of multiple FRET pairs using photochromism
Authors: Roebroek Thijs , Vandenberg Wim , Sipieter François , Hugelier Siewert , Stove Christophe , Zhang Jin , Dedecker Peter 
Published: January 2021

AbstractFörster resonant energy transfer (FRET) is a powerful mechanism to probe associationsin situ. Simultaneously performing more than one FRET measurement can be challenging due to the spectral band-width required for the donor and acceptor fluorophores. We present an approach to distinguish overlapping FRET pairs based on the photochromism of the donor fluorophores, even if the involved fluorophores display essentially identical absorption and emission spectra. We develop the theory underlying this method and validate our approach using numerical simulations. To apply our system, we develop rsAKARev, a photochromic biosensor for cAMP-dependent kinase (PKA), and combine it with the spectrally-identical biosensor EKARev, a reporter for ERK kinase activity, to deliver simultaneous readout of both activities in the same cell. We further perform multiplexed PKA, ERK, and calcium measurements by including a third, spectrally-shifted biosensor. Our work demonstrates that exploiting donor photochromism in FRET can be a powerful approach to simultaneously read out multiple associations within living cells.
TRPM2 ion channels steer neutrophils towards a source of hydrogen peroxide
Authors: Morad Hassan , Luqman Suaib , Tan Chun-Hsiang , Swann Victoria , McNaughton Peter A. 
Published: January 2021

AbstractNeutrophils must navigate accurately towards pathogens in order to destroy invaders and thus defend our bodies against infection. Here we show that hydrogen peroxide, a potent neutrophil chemoattractant, guides chemotaxis by activating calcium-permeable TRPM2 ion channels and thus generating an intracellular leading-edge calcium “pulse”. The thermal sensitivity of TRPM2 activation means that chemotaxis towards hydrogen peroxide is strongly promoted by small temperature elevations, suggesting that an important function of fever may be to enhance neutrophil chemotaxis by facilitating calcium influx through TRPM2. Chemotaxis towards conventional chemoattractants such as LPS, CXCL2 and C5a does not depend on TRPM2 but is driven in a similar way by leading-edge calcium pulses. Other proposed initiators of neutrophil movement, such as PI3K, Rac andlyn, influence chemotaxis by modulating the amplitude of calcium pulses. We propose that intracellular leading-edge calcium pulses are universal drivers of the motile machinery involved in neutrophil chemotaxis.
Expression and processing of polycistronic artificial microRNAs andtrans-acting siRNAs inSolanum lycopersicumandNicotiana benthamiana
Authors: Lunardon Alice , Kariuki Samwel Muiruri , Axtell Michael J. 
Published: January 2021

AbstractTargeted gene silencing using small regulatory RNAs is a widely used technique for genetic studies in plants. Artificial microRNAs are one common approach; they have the advantage of producing just a single functional small RNA which can be designed for high target specificity and low off-target effects. Simultaneous silencing of multiple targets with artificial microRNAs can be achieved by producing polycistronic microRNA precursors. Alternatively, specializedtrans-acting short interfering RNA (tasiRNA) precursors can be designed to produce several specific tasiRNAs at once. Here we tested several artificial microRNA- and tasiRNA-based methods for multiplexed gene silencing inSolanum lycopersicum(tomato) andNicotiana benthamiana. Small RNA sequencing analyses revealed that many previously described approaches resulted in poor small RNA processing. The 5’-most microRNA precursor hairpins on polycistronic artificial microRNA precursors were generally processed more accurately than precursors at the 3’ end. Polycistronic artificial microRNAs where the hairpin precursors were separated by transfer RNAs had the best processing precision. Strikingly, artificial tasiRNA precursors failed to be processed in the expected phased manner in our system. These results highlight the need for further development of multiplexed artificial microRNA and tasiRNA strategies. The importance of small RNA sequencing, as opposed to single-target assays such as RNA blots or real-time PCR, is also discussed.Significance statementSeveral strategies for multiplexed gene silencing using artificial microRNAs or tasiRNAs have been described. We find that many result in imprecise processing, and thus low accumulation of the intended small RNAs. Our findings highlight the importance of small RNA sequencing to fully analyze gene silencing experiments, and also the need for continued methodological development of these methods.