bluuebunny/crossref_metadata_2025_split huggingface dataset:
Cega: A Single Particle Segmentation Algorithm to Identify Moving Particles in a Noisy System
Authors: Masucci Erin M. , Relich Peter K. , Ostap E. Michael , Holzbaur Erika L. F. , Lakadamyali Melike 
Published: December 2020

ABSTRACTImprovements to particle tracking algorithms are required to effectively analyze the motility of biological molecules in complex or noisy systems. A typical single particle tracking (SPT) algorithm detects particle coordinates for trajectory assembly. However, particle detection filters fail for datasets with low signal-to-noise levels. When tracking molecular motors in complex systems, standard techniques often fail to separate the fluorescent signatures of moving particles from background noise. We developed an approach to analyze the motility of kinesin motor proteins moving along the microtubule cytoskeleton of extracted neurons using the Kullback-Leibler (KL) divergence to identify regions where there are significant differences between models of moving particles and background signal. We tested our software on both simulated and experimental data and found a noticeable improvement in SPT capability and a higher identification rate of motors as compared to current methods. This algorithm, called Cega, for ‘find the object’, produces data amenable to conventional blob detection techniques that can then be used to obtain coordinates for downstream SPT processing. We anticipate that this algorithm will be useful for those interested in tracking moving particles in complex in vitro or in vivo environments.
Single cell RNA analysis of trunk neural crest cells in zebrafish identifies pre-migratory populations expressing markers of differentiated derivatives
Authors: Lencer Ezra , Prekeris Rytis , Artinger Kristin Bruk 
Published: December 2020

AbstractThe neural crest is a migratory population of stem-like cells that contribute to multiple traits including the bones of the skull, peripheral nervous system, and pigment. How neural crest cells differentiate into diverse cell types is a fundamental question in the study of vertebrate biology. Here, we use single cell RNA sequencing to characterize transcriptional changes associated with neural crest cell development in the zebrafish trunk during the early stages of migration. We show that neural crest cells are transcriptionally diverse, and identify pre-migratory populations already expressing genes associated with differentiated derivatives. Further, we identify a population of Rohon-Beard neurons that are shown to be sources of Fgf signaling in the zebrafish trunk. The data presented identify novel genetic markers for multiple trunk neural crest cell populations and Rohon-Beard neurons providing insight into previously uncharacterized genes critical for vertebrate development.
Single cell multi-omic analysis identifies aTbx1-dependent multilineage primed population in the murine cardiopharyngeal mesoderm
Authors: Nomaru Hiroko , Liu Yang , De Bono Christopher , Righelli Dario , Cirino Andrea , Wang Wei , Racedo Silvia E. , Dantas Anelisa G. , Cai Chenleng , Angelini Claudia , Christiaen Lionel , Kelly Robert G. , Baldini Antonio , Zheng Deyou , Morrow Bernice 
Published: December 2020

AbstractThe poles of the heart and branchiomeric muscles of the face and neck are formed from the cardiopharyngeal mesoderm (CPM) within the pharyngeal apparatus. The formation of the cardiac outflow tract and branchiomeric muscles are disrupted in patients with 22q11.2 deletion syndrome (22q11.2DS), due to haploinsufficiency ofTBX1, encoding a T-box transcription factor. Here, using single cell RNA-sequencing, we identified a multilineage primed population (MLP) within the CPM, marked by theTbx1lineage, which has bipotent properties to form cardiac and skeletal muscle cells. The MLPs are localized within the nascent mesoderm of the caudal lateral pharyngeal apparatus and provide a continuous source of progenitors that undergo TBX1-dependent progression towards maturation.Tbx1also regulates the balance between MLP maintenance and maturation while restricting ectopic non-mesodermal gene expression. We further show that TBX1 confers this balance by direct regulation of MLP enriched genes and downstream pathways, partly through altering chromatin accessibility. Our study thus uncovers a new cell population and reveals novel mechanisms by whichTbx1directs the development of the pharyngeal apparatus, which is profoundly altered in 22q11.2DS.
An open source platform for presenting dynamic visual stimuli
Authors: Swanson Kyra , White Samantha R. , Preston Michael W. , Wilson Joshua , Mitchell Meagan , Laubach Mark 
Published: December 2020

AbstractOperant behavior procedures often rely on visual stimuli to cue the initiation or secession of a response, and to provide a means for discriminating between two or more simultaneously available responses. While primate and human studies typically use LCD or OLED monitors and touch screens, rodent studies use a variety of methods to present visual cues ranging from traditional incandescent light bulbs, single LEDs, and, more recently, touch screen monitors. Commercially available systems for visual stimulus presentation are costly, challenging to customize, and are typically closed source. We developed an open-source, highly-modifiable visual stimulus presentation platform that can be combined with a 3D-printed operant response device. The device uses an eight by eight matrix of LEDs, and can be expanded to control much larger LED matrices. Implementing the platform is low-cost (<$70 USD per device in the year 2020). Using the platform, we trained rats to make nosepoke responses and discriminate between two distinct visual cues in a location-independent manner. This visual stimulus presentation platform is a cost-effective way to implement complex visually-guided operant behavior, including the use of moving or dynamically changing visual stimuli.Significance StatementThe design of an open source and low cost device for presenting visual stimuli is described. It is capable of presenting complex visual patterns and dynamically changing stimuli. A practical demonstration of the device is also reported, from an experiment in which rats performed a luminance based visual discrimination. The device has utility for studying visual processing, psychophysics, and decision making in a variety of species.
Quantitative genetics of phosphorus content in the freshwater herbivore, Daphnia pulicaria
Authors: Sherman Ryan E. , Hartnett Rachel , Kiehnau Emily L. , Weider Lawrence J. , Jeyasingh Punidan D. 
Published: December 2020

Abstract

Phosphorus (P) is essential for growth of all organisms, and P content is correlated with growth in most taxa. Although P content was initially considered to be a trait fixed at the species level, there is growing evidence for considerable intraspecific variation. Selection on such variation can thus alter the rates at which P fluxes through food webs.

Nevertheless, prior work describing the sources and extent of intraspecific variation in P content were not genetically explicit, confounded by unknown genetic background and evolutionary history. We constructed an F2 recombinant population of the dominant freshwater grazer, Daphnia pulicaria to mitigate such issues.

F2 recombinants exhibited considerable variation in growth rate, P content (0.49%–1.97%), P use efficiency (PUE; 51–208 mg biomass/mg P), and correlated traits such as hatching time of resting eggs, in common garden conditions.

These results clearly demonstrate the scope of genetic recombination in generating variation in ecologically relevant traits. The absence of environmental selection is a likely component driving such variation not observed in natural settings.

Although phosphoglucose isomerase (PGI) genotype was significantly associated with variation in hatching time of resting eggs, contrary to prior work with less rigorous designs, and allelic variation at the PGI locus did not explain variation in P content and PUE of Daphnia, indicating that such quantitative traits are under polygenic control.

Together, these results suggest that although there is considerable genetic scope for variation in key ecologically relevant traits, such as P content and efficiency of P use, these traits are likely under strong stabilizing selection, most likely due to selection on growth rate and size. Importantly, our observations suggest that anthropogenic alterations to P supply due to eutrophication could alter selection on these traits, thereby rapidly altering the role Daphnia plays in the P cycle of lakes.
Bumblebee colony density on farmland is influenced by late‐summer nectar supply and garden cover
Authors: Timberlake Thomas P. , Vaughan Ian P. , Baude Mathilde , Memmott Jane 
Published: December 2020

Abstract

Floral resources are important in limiting pollinator populations, but they are often highly variable across time and space and the effect of this variation on pollinator population dynamics is not well understood. The phenology (timing) of floral resources is thought to be important in structuring pollinator populations, but few studies have directly investigated this.

Our study quantifies the landscape composition, seasonal nectar and pollen supply and Bombus terrestris colony density of 12 farms in southwest UK to investigate how landscape composition influences the phenology of floral resources and how both these factors affect colony density. We use this information in a spatially explicit predictive model to estimate the effect of different farmland management scenarios on seasonal resource supplies and colony density.

We find that farmland nectar supply during September is a strong predictor of B. terrestris colony density in the following year, explaining over half of all the variation in colony density; no other period of resource availability showed a significant association. Semi‐natural habitat cover was not a good proxy for nectar or pollen supply and showed no significant association with colony density. However, the proportional cover of gardens in the landscape was significantly associated with colony density.

The predictive model results suggest that increasing the area of semi‐natural flowering habitat has limited effect on bumblebee populations. However, improving the quality of these habitats through Environmental Stewardship and other management options is predicted to reduce the late‐summer resource bottleneck and increase colony density.

Synthesis and Applications. Our study demonstrates the importance of considering the phenology of resources, rather than just total resource availability, when designing measures to support pollinators. Late summer appears to be a resource bottleneck for bumblebees in UK farmland, and consequently management strategies which increase late‐summer nectar availability may be the most effective. These include mowing regimes to delay flowering of field margins until September, planting late‐flowering cover crops such as red clover and supporting late‐flowering wild plant species such as Hedera helix. Our results also suggest that rural gardens may play an important role in supporting farmland bumblebee populations.
Just what is critical race theory, and what is it doing in British sociology? From “BritCrit” to the racialized social system approach
Authors: Meghji Ali 
Published: December 2020

AbstractCritical race theory is growing in popularity in Britain. However, critics and advocates of critical race theory (CRT) in Britain have neglected the racialized social system approach. Through ignoring this approach, critics have thus “missed the target” in their rebuttals of CRT, while advocates of CRT have downplayed the strength of critical race analysis. By contrast, in this paper, I argue that that through the racialized social system approach, critical race theory has the conceptual flexibility to study British society. As a practical social theory, critical race theory provides us with the tools to study the realities and reproduction of racial inequality. To demonstrate this strength of CRT, and to demonstrate its theoretical nature, I discuss the conceptual framework of the racialized social system approach, paying specific attention to the notions of social space, the racial structure and racial interests; the racialized interaction order, racialized emotions, and structure and agency; and racial ideology, racial grammar, and racialized cognition.
Craft beer: An overview
Authors: Baiano Antonietta 
Published: December 2020

AbstractThe purpose of the work was to provide an overview on craft beer. Details and issues concerning history and legal definition market, fiscal policy, innovation, safety, healthiness, consumer profile, and sustainability are supplied. The term “craft brewery” generally refers to a brewery able to produce low volumes of beer, often made with traditional ingredients—for emulating historic styles—but also with the addition of nontraditional ingredients as a distinctiveness sign of the master brewer. In many countries, the importance of the company size is related to the opportunity to take advantage of reduced excise rates for low production volumes. In several countries, another important requisite of a craft brewery is represented by its independence from other alcohol industry members. Even in the presence of a great heterogeneity of the size of craft breweries in the various countries, their number in the world is around 17,000. Craft beer is mainly consumed in restaurants and bars. Innovation of craft beer concerns aspects, such as ingredients, alcohol content, aging, and packaging, and the profile of the typical craft beer drinker is that of a young man, with a higher education and a medium‐high income. Craft beers are often not filtered/not pasteurized and, for these reasons, they are beverages rich in health compounds but with a reduced shelf life. As in the case of larger breweries, the environmental impact of craft breweries is mainly represented by water consumption and production of liquid and solid wastes.
Courting Informal Workers: Exclusion, Forbearance, and the Left
Authors: Feierherd Germán 
Published: December 2020

AbstractLeftist governments with strong links to organized labor are expected to increase the number of people protected by job security rules. But do they? I explore whether the Left in power at the local level in Brazil cracks down on enterprises that employ noncontract, informal‐sector workers, and implements policies aimed at reducing the size of the informal sector. With a close‐election regression‐discontinuity design, I show that mayors from the Workers' Party (PT) in fact slow down enforcement and improve conditions in the informal sector, rather than encouraging a shift to formal jobs. This reflects a challenge that leftist parties face across the world: how to simultaneously improve the employment prospects and conditions of workers in precarious employment and those in full‐time jobs in the context of increased global competition, segmented labor markets and, in Latin America, truncated welfare states.
Effect of early use of ivabradine on left ventricular remodeling after primary percutaneous coronary intervention in patients with acute ST‐segment elevation myocardial infarction: A pilot test
Authors: Xu Yan , Zhang Wenying , Zhong Xinbo , Yan Shaodi , Chen Haijun , Guo Ruirui , Luo Xinlin , Liu Qiang 
Published: December 2020

AbstractObjectiveTo investigate the effect of early use of ivabradine on left ventricular remodeling after primary percutaneous coronary intervention (PCI) in patients with acute ST‐segment elevation myocardial infarction (STEMI).MethodsA total of 66 STEMI patients with sinus rhythm and the resting heart rate ≥80 bpm after successful emergency PCI were included. The patients in the test group were treated with ivabradine combined with metoprolol at 12 hr after PCI, while the control group was given only metoprolol orally. Their resting heart rate was controlled to <70 bpm at discharge and followed for 180 days. Heart rate and blood pressure were measured regularly. Echocardiogram was performed. N‐terminal pro‐B‐type natriuretic peptide (NT‐proBNP), high sensitivity troponin T, high sensitivity troponin I, and high sensitivity C‐reactive protein were measured. The major adverse cardiovascular events during hospitalization and follow‐up period were recorded.ResultsCompared with the control group, the heart rate of the test group decreased significantly (p < .05). Compared with the control group, the left ventricular end‐diastolic volume and left ventricular end‐systolic volume were significantly decreased while left ventricular ejection fraction was significantly increased in the test group at 90 days after operation. NT‐proBNP of the test group was significantly lower than that of the control group at 7 days after operation (p < .05).ConclusionFor STEMI patients, early use of ivabradine combined with standard therapy such as β‐blocker after successful reperfusion can achieve effective heart rate control, with great safety and tolerance. But the effect of ivabradine on left ventricular remodeling is uncertain.
MicroRNA‐2355‐5p regulates γ‐globin expression in human erythroid cells by inhibiting KLF6
Authors: Cheng Yi , Shang Xuan , Chen Diyu , Pang Dejian , Zhao Cunyou , Xu Xiangmin 
Published: December 2020

SummaryKrüppel‐like factors (KLFs) are a highly conserved family of transcription factors. We analysed expression profile data of KLFs and identified KLF6 as a new potential regulator of erythropoiesis. Knocking down the expression of KLF6 significantly raised γ‐globin mRNA and protein levels in the erythroid cell line HUDEP‐2 and haematopoietic progenitor (CD34+) cells. We found that overexpression of microRNA (miR)‐2355‐5p in HUDEP‐2 and CD34+ cells correlated with increased γ‐globin synthesis by suppressing expression of KLF6. Our discovery that the interaction between miR‐2355‐5p and KLF6 affects the expression of γ‐globin may provide more information for the clinical management of β‐thalassaemia patients.
Memory at Play: Examining Relations Between Episodic and Semantic Memory in a Children’s Museum
Authors: Sipe Sarah J. , Pathman Thanujeni 
Published: December 2020

The relation between episodic and semantic memory was examined by testing how semantic knowledge influences children’s episodic memory for events and their locations. Five‐, six‐, and seven‐year‐olds (N = 87) engaged in events in a children’s museum designed as a town. Events were semantically congruent or incongruent with the spatial location (e.g., sorting mail at post office vs. grocery store). In addition to this experimental paradigm, a semantic interview assessed children’s semantic knowledge about real‐world locations. Accuracy in the experimental paradigm showed that children’s semantic memory influenced memory for locations. Interviews revealed age‐related improvements in children’s semantic knowledge. Regression analyses examined factors that best supported episodic memory. These results provide novel insights and highlight the utility of research in naturalistic settings.
Assessment of Autism Symptoms From 6 to 18 Months of Age Using the Autism Observation Scale for Infants in a Prospective High‐Risk Cohort
Authors: Zwaigenbaum Lonnie , Bryson Susan E. , Brian Jessica , Smith Isabel M. , Sacrey Lori , Armstrong Vickie , Roberts Wendy , Szatmari Peter , Garon Nancy , Vaillancourt Tracy , Roncadin Caroline 
Published: December 2020

The objectives were to characterize behavioral signs of autism spectrum disorder (ASD) in younger siblings of diagnosed children (high‐risk; HR) and examine classification features of the Autism Observation Scale for Infants (AOSI). Participants (501 HR and 180 low‐risk [LR]) were assessed between 6 and 18 months using the AOSI and at age 3 for ASD diagnoses. Total AOSI scores differentiated HR infants later diagnosed with ASD starting at 12 months. ROC analyses identified 12‐ and 18‐month cutoff scores associated with 0.52 sensitivity and 0.74 specificity and 0.73 sensitivity and 0.65 specificity, respectively. Although classification accuracy does not support use as a standalone screen, the AOSI identifies features associated with ASD starting at 6 months and differentiates HR infants with ASD by 12 months.
Associated positive patch test reactions to standard contact allergens: 10‐year data from the Slovenian E‐Surveillance System
Authors: Dugonik Aleksandra , Dugonik Bogdan , Podgorelec Vili , Brezočnik Lucija 
Published: December 2020

AbstractBackgroundA considerable share of patients tested with a baseline patch test series respond with a positive reaction to more than one allergen, and some associations between synchronous positive reactions to distinct baseline patch allergens have been described in the literature.ObjectivesTo evaluate the prevalence of sensitization to haptens of the European baseline series as well as the prevalence of oligosensitization and polysensitization and the most significant associated positive patch test reactions in Slovenia.MethodsPatch testing data collected by the Slovenian E‐Surveillance System from January 2008 to December 2017 were retrospectively analysed.ResultsOf a total of 15 171 patients analysed, 39.29% showed at least one positive reaction. The highest prevalences were noted for metals (nickel[II]sulfate hexahydrate: 16.33%) and fragrances (fragrance mix I: 6.70%). The correlation analysis showed the strongest correlation between mercapto mix and 2‐mercaptobenzothiazole (61.2%), fragrance Mix II and hydroxyisohexyl 3‐cyclohexene carboxaldehyde (50.5%), and potassium dichromate and cobalt(II) chloride hexahydrate (33.3%).ConclusionsSensitization prevalences to the most common haptens were described, and their strongest correlations on a national level quantified. A comparison with other European results confirms already known associations between allergens in terms of cross‐reactivity.
Built to last a day: The function and benefits of spider mound nests
Authors: Raboin Maggie , Elias Damian O. 
Published: December 2020

AbstractNests are crucial to the survival of offspring and reproductive success of the animals that build them. These benefits are subject to change over time due to fluctuating conditions inside and outside of nests. For many species, nests are assumed to benefit offspring until they disperse and therefore, nest destruction prior to offspring dispersal results in reduced reproductive success for parents. However, the consequences of nest destruction to reproductive success, or lack thereof, remain largely unstudied across diverse taxa. Here, we experimentally investigate the function and benefits of nests of a mound‐building spider. Mason spiders (Castianeirasp.) are wandering spiders that build intricate nests (mounds) on top of their egg sacs. Their offspring inhabit egg sacs at nest sites for up to 7 months, including through winter. We find that despite requiring hundreds of collecting trips and many hours to construct, mason spider nests remain for a small portion of time that offspring occupy nest sites. Our study finds that nest benefits change over time, likely explaining this dynamic. Nests greatly reduce the rate of predation and parasitism of egg sacs by 19.1% and offspring mortality within egg sacs due to abiotic factors by 19.9%. These effects are only present the few days following nest construction. Our study illuminates the idea that nest destruction does not always result in reduced reproductive success for nest builders. We suggest that nest durability, the ability of a nest to withstand environmental conditions, may be subject to natural selection and a critical, yet understudied, aspect of parental care.