bluuebunny/crossref_metadata_2025_split huggingface dataset:
SILK+ Preventing Latency Spikes in Log-Structured Merge Key-Value Stores Running Heterogeneous Workloads
Authors: Balmau Oana , Dinu Florin , Zwaenepoel Willy , Gupta Karan , Chandhiramoorthi Ravishankar , Didona Diego 
Published: May 2020

Log-Structured Merge Key-Value stores (LSM KVs) are designed to offer good write performance, by capturing client writes in memory, and only later flushing them to storage. Writes are later compacted into a tree-like data structure on disk to improve read performance and to reduce storage space use. It has been widely documented that compactions severely hamper throughput. Various optimizations have successfully dealt with this problem. These techniques include, among others, rate-limiting flushes and compactions, selecting among compactions for maximum effect, and limiting compactions to the highest level by so-called fragmented LSMs.
In this article, we focus on latencies rather than throughput. We first document the fact that LSM KVs exhibit high tail latencies. The techniques that have been proposed for optimizing throughput do not address this issue, and, in fact, in some cases, exacerbate it. The root cause of these high tail latencies is interference between client writes, flushes, and compactions. Another major cause for tail latency is the heterogeneous nature of the workloads in terms of operation mix and item sizes whereby a few more computationally heavy requests slow down the vast majority of smaller requests.
We introduce the notion of an Input/Output (I/O) bandwidth scheduler for an LSM-based KV store to reduce tail latency caused by interference of flushing and compactions and by workload heterogeneity. We explore three techniques as part of this I/O scheduler: (1) opportunistically allocating more bandwidth to internal operations during periods of low load, (2) prioritizing flushes and compactions at the lower levels of the tree, and (3) separating client requests by size and by data access path. SILK+ is a new open-source LSM KV that incorporates this notion of an I/O scheduler.
Scene Grammars, Factor Graphs, and Belief Propagation
Authors: Chua Jeroen , Felzenszwalb Pedro F. 
Published: May 2020

We describe a general framework for probabilistic modeling of complex scenes and for inference from ambiguous observations. The approach is motivated by applications in image analysis and is based on the use of priors defined by stochastic grammars. We define a class of grammars that capture relationships between the objects in a scene and provide important contextual cues for statistical inference. The distribution over scenes defined by a probabilistic scene grammar can be represented by a graphical model, and this construction can be used for efficient inference with loopy belief propagation.We show experimental results with two applications. One application involves the reconstruction of binary contour maps. Another application involves detecting and localizing faces in images. In both applications, the same framework leads to robust inference algorithms that can effectively combine local information to reason about a scene.
Movement patterns, maximum distances traveled and microhabitat selection of spadefoot toad tadpoles in temporary ponds
Authors: Pinero-Rodríguez María Jesús , Díaz-Paniagua Carmen , Gomez-Mestre Ivan 
Published: May 2020

Abstract
Understanding the movement of individuals across natural habitats is important to determine fundamental aspects of their ecology, from dispersal patterns and habitat selection to interactions with predators, pathogens or conspecifics. Amphibian larvae are key to aquatic systems, playing fundamental roles as both consumers and prey, affecting nutrient cycling and even physico-chemical properties of the water bodies they occupy. Nevertheless, despite an extensive body of literature on most other aspects of their ecology, we know very little about spatial movements of amphibian larvae in their natural habitats, and the little information we have is restricted to lotic systems. Here we use a mark-and-recapture procedure using elastomers to determine movement patterns and microhabitat selection of western spadefoot toad tadpoles (Pelobates cultripes) in two large ponds in southwestern Spain. We observed maximum distances moved by these tadpoles of >67 m and >245 m, depending on the pond. These distances coincided with the maximum cross distance in each pond, suggesting that they could potentially move even farther in larger wetlands. Mean distances moved were 29.7 and 105 m in each pond. We sampled at two, four and nine days after release of tagged individuals, and we observed a stable, not expanding, movement pattern across sampling dates, suggesting that tadpoles resumed normal activity immediately after release. Tadpoles showed preference for deeper and more densely vegetated areas of the ponds, especially associated with plant species such as Ranunculus peltatus and Potamogeton pectinatus.
The Patarei Sea Fort: Perspectives on Heritage, Memory and Identity Politics in Post-Soviet Estonia
Authors: Novak Onessa , Plets Gertjan 
Published: May 2020

Abstract
This paper studies the struggle over the rehabilitation of the Patarei Sea Fort in Tallinn (Estonia), a former prison where during the Soviet period political prisoners were held and corralled before deportation to Siberia. We explore how three groups of stakeholders assemble and define the future of the site: The Estonian State; ngo Eesti Muinsuskaiste Selts (the Estonian Heritage Society); and Europa Nostra. Each of these groups have a competing future for the site in mind. The struggle over the Patarei Sea fort is connected to discussions over heritage politics in those countries that entered the European Union around the early 2000s. In comparison to other memory practices in the region, the Patarei Sea Fort is not instrumentalized by the state to support a national historical narrative othering the Russian Federation. Rather the state’s engagement with the site is restricted and textured by ambitions to gentrify the district it is situated in. Not the state, but an ngo, assisted by a European heritage association, promotes a heritage discourse geared at strengthening the Estonian national narrative.
Creativity and Complexity: Creative Solutions are Complex and Need Time
Authors: Heiligensetzer Sarah A. , Schmittlutz Thorsten H. , Carbon Claus-Christian 
Published: May 2020

Abstract
To create art means to be creative, but how creativity is gained, how we can induce and train creativity and how we can validly measure creative potential is a matter of still unsolved research. In our exploratory study, 49 participants had to create figures by using a double set of Tangram puzzles — so to say: to create something with an infinite degree of freedoms but that is still based on just a few defined and simple basic elements. In total, participants created 708 different figures. Creativity and complexity of these creations were then assessed in a subsequent study by five further raters in two randomly ordered blocks. We observed a strong correlation between the ratings of creativity and complexity on basis of average as well as individual data level. Interestingly, highly productive people, sometimes misinterpreted as ‘creatives’ due to their sheer quantitative output, actually produced simpler scenes that were also evaluated as less creative. We could also reveal that the level of creativity in the produced items remained very similar over the course of the test, pointing to relatively stable creativity traits (at least during the study phase). Our approach could lead to a deeper and more differentiated understanding of the concept of creativity and creative potential, specifically by combining it with qualitative analyses of the complexity of the created figures.
Accuracy Assessment of MERRA-2 and ERA-Interim Sea Surface Temperature, Air Temperature, and Humidity Profiles over the Atlantic Ocean Using AEROSE Measurements
Authors: Luo Bingkun , Minnett Peter J. , Szczodrak Malgorzata , Nalli Nicholas R. , Morris Vernon R. 
Published: June 2020

AbstractSatellite and in situ measurements of the sea surface and the atmosphere often have inadequate sampling frequencies and often lack consistent global coverage. Because of such limitations, reanalysis model output is frequently used in atmospheric and oceanographic research endeavors to complement satellite and in situ data. The National Aeronautics and Space Administration’s (NASA’s) Goddard Earth Sciences Modern-Era Retrospective Analysis for Research and Applications version 2 (MERRA-2) and the European Centre for Medium-Range Weather Forecasts (ECMWF) interim reanalysis (ERA-Interim) datasets provide accurate, complete fields through the assimilation of many atmospheric and surface observations. Still, the reanalysis output data must be rigorously and continuously evaluated to understand their strengths and weaknesses. To this end, this study evaluates sea surface skin temperature (SSTskin) and atmospheric temperature and humidity profiles in MERRA-2 and ERA-Interim data through comparisons with independent Marine-Atmospheric Emitted Radiance Interferometer (M-AERI) and radiosonde data from the Aerosols and Ocean Science Expeditions (AEROSE) cruises, focusing on the representation of spatial and temporal variability. SSTskinvalues are generally in good agreement with corresponding M-AERI measurements, with the average differences on the order of 0.1 K. Comparisons between MERRA-2 and ERA-Interim relative humidity and air temperature profiles with a total of 553 radiosondes that have been withheld from data assimilation schemes show good correspondence below 500 hPa: the average air temperature difference is <2 K and the average relative humidity discrepancy is within 10%. These results support the use of these MERRA-2 and ERA-Interim reanalysis fields in a variety of research applications.
Along-Stream Evolution of Gulf Stream Volume Transport
Authors: Heiderich Joleen , Todd Robert E. 
Published: June 2020

AbstractThe Gulf Stream affects global climate by transporting water and heat poleward. The current’s volume transport increases markedly along the U.S. East Coast. An extensive observing program using autonomous underwater gliders provides finescale, subsurface observations of hydrography and velocity spanning more than 15° of latitude along the path of the Gulf Stream, thereby filling a 1500-km-long gap between long-term transport measurements in the Florida Strait and downstream of Cape Hatteras. Here, the glider-based observations are combined with shipboard measurements along Line W near 68°W to provide a detailed picture of the along-stream transport increase. To account for the influences of Gulf Stream curvature and adjacent circulation (e.g., corotating eddies) on transport estimates, upper- and lower-bound transports are constructed for each cross–Gulf Stream transect. The upper-bound estimate for time-averaged volume transport above 1000 m is 32.9 ± 1.2 Sv (1 Sv ≡ 106 m3 s−1) in the Florida Strait, 57.3 ± 1.9 Sv at Cape Hatteras, and 75.6 ± 4.7 Sv at Line W. Corresponding lower-bound estimates are 32.3 ± 1.1 Sv in the Florida Strait, 54.5 ± 1.7 Sv at Cape Hatteras, and 69.9 ± 4.2 Sv at Line W. Using the temperature and salinity observations from gliders and Line W, waters are divided into seven classes to investigate the properties of waters that are transported by and entrained into the Gulf Stream. Most of the increase in overall Gulf Stream volume transport above 1000 m stems from the entrainment of subthermocline waters, including upper Labrador Sea Water and Eighteen Degree Water.
Overturning Circulation Pathways in a Two-Basin Ocean Model
Authors: Nadeau Louis-Philippe , Jansen Malte F. 
Published: June 2020

AbstractA toy model for the deep ocean overturning circulation in multiple basins is presented and applied to study the role of buoyancy forcing and basin geometry in the ocean’s global overturning. The model reproduces the results from idealized general circulation model simulations and provides theoretical insights into the mechanisms that govern the structure of the overturning circulation. The results highlight the importance of the diabatic component of the meridional overturning circulation (MOC) for the depth of North Atlantic Deep Water (NADW) and for the interbasin exchange of deep ocean water masses. This diabatic component, which extends the upper cell in the Atlantic below the depth of adiabatic upwelling in the Southern Ocean, is shown to be sensitive to the global area-integrated diapycnal mixing rate and the density contrast between NADW and Antarctic Bottom Water (AABW). The model also shows that the zonally averaged global overturning circulation is to zeroth-order independent of whether the ocean consists of one or multiple connected basins, but depends on the total length of the southern reentrant channel region (representing the Southern Ocean) and the global ocean area integrated diapycnal mixing. Common biases in single-basin simulations can thus be understood as a direct result of the reduced domain size.
On the utility of the trail making test in migraine with and without aura: a meta-analysis
Authors: Vallesi Antonino 
Published: June 2020

AbstractThis meta-analytical review assesses the utility of the Trail Making Test (TMT), versions A and B, in detecting migraine-related cognitive deficits. A comprehensive literature search was performed in two electronic databases and other sources to obtain relevant studies administering TMT to migraine patients. Search terms included “migraine” and “Trail Making”. Only studies in which the TMT-A, TMT-B or both were administered to adult patients suffering from migraine with and without aura were included. All pooled meta-analyses were based on random effects models. A total of 14 studies for TMT-A and 15 for TMT-B met inclusion criteria and were subjected to meta-analyses. Results showed that performance is worse in migraine patients than in controls for both the TMT-A (Hedges’ g = −.28) and TMT-B (g = −.37), with no difference between migraine with and without aura. This study demonstrates the sensitivity of the TMT in detecting cognitive alterations in migraine. This test should be considered for inclusion in cognitive batteries assessing patients with migraine.
Hysteroscopic treatment of retained placental tissue: a case report
Authors: Angelos Daniilidis , Anastasios Liberis , Panagiotis Papandreou , Konstantinos Sidiropoulos , George Pratilas , Konstantinos Dinas 
Published: June 2020

AbstractRetained placenta tissue is a rare condition, and its diagnosis and surgical treatment are often challenging. Conventionally, the surgical management of such cases is largely performed using blind dilation and curettage. Our case demonstrates that the successful complete removal of retained placental tissues can be achieved with operative hysteroscopy with minimal use of electrosurgery in order to minimize the short- and long-term complications. This was achieved using the loop of the bipolar resectoscope as a curette performing cold dissection.
The green-brown polymorphism of the club-legged grasshopper Gomphocerus sibiricus is heritable and appears genetically simple
Authors: Schielzeth Holger , Dieker Petra 
Published: June 2020

AbstractBackgroundLocal coexistence of distinct, genetically determined color morphs can be unstable and transitional. Stable, long-term coexistence requires some form of balancing selection to protect morphs from getting lost by directional selection or genetic drift. However, not all phenotypic polymorphism need to have a genetic basis. We here report on the genetic basis of two color polymorphisms in the club-legged grasshopperGomphocerus sibiricus: a green-brown polymorphism that is phylogenetically and geographically widespread among orthopteran insects and a pied-brown pattern polymorphism that is shared among many gomphocerine grasshoppers.ResultsWe found a remarkably clear outcome of matings within and between morph that suggest not only that the green-brown polymorphism is heritable in this species, but that results can be most parsimoniously explained by a single autosomal locus with two alleles in which the green allele is dominant over the brown allele. A few individuals did not match this pattern and suggest the existence of genetic modifiers and/or developmental phenocopies. We also show that the pied-brown polymorphism is highly heritable, although the evidence for the involvement of one or more loci is less clear-cut.ConclusionsOverall, our data demonstrate that the two polymorphisms are heritable in the club-legged grasshopper and appear genetically simple, at least with respect to green morphs. The results are consistent with the idea that the synthesis or transport of a pigment involved in the production of green coloration (likely biliverdin) is lost by homozygosity for loss-of-function alleles in brown individuals. The apparently simple genetic architecture of the green-brown polymorphism offer potential for studying balancing selection in the field and for genetic mapping in this species.
Precursor peptide-targeted mining of more than one hundred thousand genomes expands the lanthipeptide natural product family
Authors: Walker Mark C. , Eslami Sara M. , Hetrick Kenton J. , Ackenhusen Sarah E. , Mitchell Douglas A. , van der Donk Wilfred A. 
Published: June 2020

Abstract
Background
Lanthipeptides belong to the ribosomally synthesized and post-translationally modified peptide group of natural products and have a variety of biological activities ranging from antibiotics to antinociceptives. These peptides are cyclized through thioether crosslinks and can bear other secondary post-translational modifications. While lanthipeptide biosynthetic gene clusters can be identified by the presence of genes encoding characteristic enzymes involved in the post-translational modification process, locating the precursor peptides encoded within these clusters is challenging due to their short length and high sequence variability, which limits the high-throughput exploration of lanthipeptide biosynthesis. To address this challenge, we enhanced the predictive capabilities of Rapid ORF Description & Evaluation Online (RODEO) to identify members of all four known classes of lanthipeptides.

Results
Using RODEO, we mined over 100,000 bacterial and archaeal genomes in the RefSeq database. We identified nearly 8500 lanthipeptide precursor peptides. These precursor peptides were identified in a broad range of bacterial phyla as well as the Euryarchaeota phylum of archaea. Bacteroidetes were found to encode a large number of these biosynthetic gene clusters, despite making up a relatively small portion of the genomes in this dataset. A number of these precursor peptides are similar to those of previously characterized lanthipeptides, but even more were not, including potential antibiotics. One such new antimicrobial lanthipeptide was purified and characterized. Additionally, examination of the biosynthetic gene clusters revealed that enzymes installing secondary post-translational modifications are more widespread than initially thought.

Conclusion
Lanthipeptide biosynthetic gene clusters are more widely distributed and the precursor peptides encoded within these clusters are more diverse than previously appreciated, demonstrating that the lanthipeptide sequence-function space remains largely underexplored.
Discovering candidate imprinted genes and imprinting control regions in the human genome
Authors: Bina Minou 
Published: May 2020

Abstract
Background
Genomic imprinting is a process thereby a subset of genes is expressed in a parent-of-origin specific manner. This evolutionary novelty is restricted to mammals and controlled by genomic DNA segments known as Imprinting Control Regions (ICRs) and germline Differentially Methylated Regions (gDMRs). Previously, I showed that in the mouse genome, the fully characterized ICRs/gDMRs often includes clusters of 2 or more of a set of composite-DNA-elements known as ZFBS-morph overlaps.

Results
Because of the importance of the ICRs to regulating parent-of-origin specific gene expression, I developed a genome-wide strategy for predicting their positions in the human genome. My strategy consists of creating plots to display the density of ZFBS-morph overlaps along the entire chromosomal DNA sequences. In initial evaluations, I found that peaks in these plots pinpointed several of the known ICRs/gDMRs along the DNA in chromosomal bands. I deduced that in density-plots, robust peaks corresponded to actual or candidate ICRs in the DNA. By locating the genes in the vicinity of candidate ICRs, I could discover potential imprinting genes. Additionally, my assessments revealed a connection between several of the potential imprinted genes and human developmental anomalies. Examples include Leber congenital amaurosis 11, Coffin-Siris syndrome, progressive myoclonic epilepsy-10, microcephalic osteodysplastic primordial dwarfism type II, and microphthalmia, cleft lip and palate, and agenesis of the corpus callosum.

Conclusion
With plots displaying the density of ZFBS-morph overlaps, researchers could locate candidate ICRs and imprinted genes. Since the datafiles are available for download and display at the UCSC genome browser, it is possible to examine the plots in the context of Single nucleotide polymorphisms (SNPs) to design experiments to discover novel ICRs and imprinted genes in the human genome.
Silicon-induced thermotolerance in Solanum lycopersicum L. via activation of antioxidant system, heat shock proteins, and endogenous phytohormones
Authors: Khan Adil , Khan Abdul Latif , Imran Muhammad , Asaf Sajjad , Kim Yoon-Ha , Bilal Saqib , Numan Muhammad , Al-Harrasi Ahmed , Al-Rawahi Ahmed , Lee In-Jung 
Published: June 2020

Abstract
Background
Abiotic stresses (e.g., heat or limited water and nutrient availability) limit crop production worldwide. With the progression of climate change, the severity and variation of these stresses are expected to increase. Exogenous silicon (Si) has shown beneficial effects on plant growth; however, its role in combating the negative effects of heat stress and their underlying molecular dynamics are not fully understood.

Results
Exogenous Si significantly mitigated the adverse impact of heat stress by improving tomato plant biomass, photosynthetic pigments, and relative water content. Si induced stress tolerance by decreasing the concentrations of superoxide anions and malondialdehyde, as well as mitigating oxidative stress by increasing the gene expression for antioxidant enzymes (peroxidases, catalases, ascorbate peroxidases, superoxide dismutases, and glutathione reductases) under stress conditions. This was attributed to increased Si uptake in the shoots via the upregulation of low silicon (SlLsi1 and SlLsi2) gene expression under heat stress. Interestingly, Si stimulated the expression and transcript accumulation of heat shock proteins by upregulating heat transcription factors (Hsfs) such as SlHsfA1a-b, SlHsfA2-A3, and SlHsfA7 in tomato plants under heat stress. On the other hand, defense and stress signaling-related endogenous phytohormones (salicylic acid [SA]/abscisic acid [ABA]) exhibited a decrease in their concentration and biosynthesis following Si application. Additionally, the mRNA and gene expression levels for SA (SlR1b1, SlPR-P2, SlICS, and SlPAL) and ABA (SlNCEDI) were downregulated after exposure to stress conditions.

Conclusion
Si treatment resulted in greater tolerance to abiotic stress conditions, exhibiting higher plant growth dynamics and molecular physiology by regulating the antioxidant defense system, SA/ABA signaling, and Hsfs during heat stress.