bluuebunny/crossref_metadata_2025_split huggingface dataset:
Parental Holocaust Exposure, Related PTSD Symptoms and Subjective Aging Across the Generations
Authors: Shrira Amit 
Published: January 2019

Abstract

Objectives
Traumatic exposure and posttraumatic stress disorder (PTSD) are related to less favorable perceptions of aging. The current study examined parental PTSD and perceptions of aging among old Holocaust survivor (HS) parents and their middle-aged offspring.

Method
Parents (mean age = 81.79) and their offspring (mean age = 55.41) reported PTSD symptoms, attitudes toward aging and subjective age. Offspring also rated how they perceive both their parents’ aging and subjective age. Dyads were divided into three groups: HS with probable PTSD (n = 21 dyads), HS without probable PTSD (n = 65 dyads), and comparison parents without probable PTSD (n = 57 dyads).

Results
Relative to parents and offspring from other groups, HS parents with probable PTSD and their offspring had both less favorable attitudes toward their own aging as well as reporting feeling older. Offspring of posttraumatic HS also held less favorable attitudes toward parents’ aging and perceived their own parents as being older. Serial mediation models showed that the effect of parental PTSD on offspring’s subjective aging was serially mediated by parental subjective aging and offspring’s perception of parents’ aging.

Discussion
The study provides the first evidence that posttraumatic distress is related to less favorable perceptions of aging across generations in HS families. Possible mechanisms for such intergenerational effect and the implication for interventions are discussed.
Direct synthesis of EM-visible gold nanoparticles on genetically encoded tags for single-molecule visualization in cells
Authors: Jiang Zhaodi , Jin Xiumei , Li Yuhua , Liu Sitong , Liu Xiao-Man , Wang Ying-Ying , Zhao Pei , Cai Xinbin , Liu Ying , Tang Yaqi , Sun Xiaobin , Liu Yan , Hu Yanyong , Li Ming , Cai Gaihong , Qi Xiangbing , Chen She , Du Li-Lin , He Wanzhong 
Published: January 2019

AbstractSingle-molecule visualization in cells with genetically encoded tags for electron microscopy (EM) has been a long-awaited but unimplemented tool for cell biologists. Here, we report an approach for directly synthesizing EM-visible gold nanoparticles (AuNPs) on cysteine-rich tags for single-molecule visualization in cells. We first uncovered an auto-nucleation suppression mechanism that allows specific synthesis of AuNPs on isolated cysteine-rich tags. We next exploited this mechanism to develop an approach for single-molecule detection of proteins in prokaryotic cells and achieved an unprecedented labeling efficiency. We then expanded it to more complicated eukaryotic cells and successfully detected the proteins targeted to various organelles, including the membranes of endoplasmic reticulum (ER) and nuclear envelope, ER lumen, nuclear pores, spindle pole bodies, and mitochondrial matrix. Thus, our implementation of genetically encoded tags for EM should allow cell biologists to address an enormous range of biological questions at single-molecule level in diverse cellular ultrastructural contexts without using antibodies.
Endogenous pioneer neutrophils release NETs during the swarming response in zebrafish
Authors: Isles Hannah M. , Loynes Catherine A. , Hamilton Noémie , Muir Clare F. , Kadochnikova Anastasia , Henry Katherine M. , Kadirkamanathan Visakan , Renshaw Stephen A. , Elks Philip M. 
Published: January 2019

AbstractNeutrophils are rapidly recruited to inflammatory sites where they coordinate their migration to form clusters, a process termed neutrophil swarming. The factors which modulate neutrophil swarming during its early stages are not fully understood, requiring the development of newin vivomodels. Using transgenic zebrafish larvae to study endogenous neutrophil migration in a tissue damage model, we demonstrate that neutrophil swarming is a conserved process in zebrafish immunity, sharing essential features with mammalian systems. We show that neutrophil swarms initially develop around a pioneer neutrophil, in a three-phase sequence of events. By adopting a high-resolution confocal microscopy approach, we observed the release of cell fragments by early swarming neutrophils. We developed a neutrophil specific histone H2A transgenic reporter lineTgBAC(mpx:GFP)i114;Tg(lyz:H2A-mCherry)sh530to study neutrophil extracellular traps (NETs), and found that endogenous neutrophils recruited to sites of tissue damage released NETs at the start of the swarming process. The optical transparency achieved using the zebrafish model has provided some of the highest resolution imaging of NET releasein vivoto date. Using a combination of transgenic reporter lines and DNA intercalating agents, we demonstrate that pioneer neutrophils release extracellular traps during the swarming response, suggesting that cell death signalling via NETosis might be important in driving the swarming response.
On the Complexity of Sequence to Graph Alignment
Authors: Jain Chirag , Zhang Haowen , Gao Yu , Aluru Srinivas 
Published: January 2019

AbstractAvailability of extensive genetics data across multiple individuals and populations is driving the growing importance of graph based reference representations. Aligning sequences to graphs is a fundamental operation on several types of sequence graphs (variation graphs, assembly graphs, pan-genomes, etc.) and their biological applications. Though research on sequence to graph alignments is nascent, it can draw from related work on pattern matching in hypertext. In this paper, we study sequence to graph alignment problems under Hamming and edit distance models, and linear and affine gap penalty functions, for multiple variants of the problem that allow changes in query alone, graph alone, or in both. We prove that when changes are permitted in graphs either standalone or in conjunction with changes in the query, the sequence to graph alignment problem is -complete under both Hamming and edit distance models for alphabets of size ≥ 2. For the case where only changes to the sequence are permitted, we present an O(|V| + m|E|) time algorithm, where m denotes the query size, and V and E denote the vertex and edge sets of the graph, respectively. Our result is generalizable to both linear and affine gap penalty functions, and improves upon the run-time complexity of existing algorithms.
Comparative analysis of mitochondrial genome between UG93A and UG93B reveal common feature of 5’-end heterogeneity in mitochondrial genes of kenaf
Authors: Liao Xiaofang , Zhao Yanhong , Khan Aziz , Kong Xiangjun , Zhou Bujin , Li Min , Wei Meiling , Peng Shuangshuang , Munsif Fazal , Zhou Ruiyang 
Published: January 2019

AbstractPlant cytoplasmic male sterility (CMS) being maternal phenomenon trait that result from pollen abortion and closely linked with mitochondrial DNA rearrangement in many crops including kenaf. However, the molecular mechanism in kenaf is poorly known. In present work, we described the mitochondrial genome in isonuclear CMS line UG93A and its maintainer line UG93B. Findings of the current study revealed that a total of 398 SNPs and 230 InDels were identified in UG93A mtDNA. Total of 26 SNPs variations and three InDels were identified in the coding region of atp6, indicating its active role in mitochondrial genome re-arrangement. Northern blot analysis showed that the transcripts of atp1, atp4, atp6, cox3 and sdh4 in F1 were consistent with UG93A but different for UG93B. The transcript of atp9 was found similar between UG93B and F1 while different for UG93A, which depict that atp9 may be regulated by nuclear genes in F1 hybrid. The expression of atp9 in UG93A was substantially lower compared with UG93B, suggesting its key role for energy supplying in microspore development of kenaf. Circularized RNA (CR)-RT-PCR revealed that mitochondrial RNAs with heterogeneous 5’-ends but uniform 3’ - ends are common feature in kenaf mitochondrial genes, and the promoter architecture analysis showed that the promoter sequences in kenaf mitochondrial genome are highly diverged in comparison to those in other plants. Our data highlight that the translation of mitochondrial genes in kenaf is closely associated with heterogeneity of the 5’-end of plant mRNA. The present result provides the basic information in understanding the transcription of kenaf mitochondrial genome and can be used as reference in other plants.
Single-neuron representations of spatial targets in humans
Authors: Tsitsiklis Melina , Miller Jonathan , Qasim Salman E. , Inman Cory S. , Gross Robert E. , Willie Jon T. , Smith Elliot H. , Sheth Sameer A. , Schevon Catherine A. , Sperling Michael R. , Sharan Ashwini , Stein Joel M. , Jacobs Joshua 
Published: January 2019

SummaryThe hippocampus and surrounding medial-temporal-lobe (MTL) structures are critical for both memory and spatial navigation, but we do not fully understand the neuronal representations used to support these behaviors. Much research has examined how the MTL neurally represents spatial information, such as with “place cells” that represent the current location or “head-direction cells” that code for the current heading. In addition to behaviors that require an animal to attend to the current spatial location, navigating to remote destinations is a common part of daily life. To examine the neural basis of these behaviors we recorded single-neuron activity from neurosurgical patients playing Treasure Hunt, a virtual-reality spatial-memory task. By analyzing how the activity of these neurons related to behavior in Treasure Hunt, we found that the firing rates of many MTL neurons during navigation significantly changed depending on the position of the current spatial target. In addition, we observed neurons whose firing rates during navigation were tuned to specific heading directions in the environment, and others whose activity changed depending on the timing within the trial. By showing that neurons in our task represent remote locations rather than the subject’s own position, our results suggest that the human MTL can represent remote spatial information according to task demands.
Ultra-fast fit-free analysis of complex fluorescence lifetime imaging via deep learning
Authors: Smith Jason T. , Yao Ruoyang , Sinsuebphon Nattawut , Rudkouskaya Alena , Mazurkiewicz Joseph , Barroso Margarida , Yan Pingkun , Intes Xavier 
Published: January 2019

AbstractFluorescence lifetime imaging (FLI) provides unique quantitative information in biomedical and molecular biology studies, but relies on complex data fitting techniques to derive the quantities of interest. Herein, we propose a novel fit-free approach in FLI image formation that is based on Deep Learning (DL) to quantify complex fluorescence decays simultaneously over a whole image and at ultra-fast speeds. Our deep neural network (DNN), named FLI-Net, is designed and model-based trained to provide all lifetime-based parameters that are typically employed in the field. We demonstrate the accuracy and generalizability of FLI-Net by performing quantitative microscopic and preclinical experimental lifetime-based studies across the visible and NIR spectra, as well as across the two main data acquisition technologies. Our results demonstrate that FLI-Net is well suited to quantify complex fluorescence lifetimes, accurately, in real time in cells and intact animals without any parameter settings. Hence, it paves the way to reproducible and quantitative lifetime studies at unprecedented speeds, for improved dissemination and impact of FLI in many important biomedical applications, especially in clinical settings.
Affective reactivity during adolescence: Associations with age, puberty and testosterone
Authors: Vijayakumar Nandita , Pfeifer Jennifer H. , Flournoy John C. , Hernandez Leanna M. , Dapretto Mirella 
Published: January 2019

AbstractAdolescence is a period of heightened social engagement that is accompanied by normative changes in neural reactivity to affective stimuli. It is also a period of concurrent endocrine and physical changes associated with puberty. A growing body of research suggests that hormonal shifts during adolescence impact brain development, but minimal research in humans has examined the relationship between intra-individual changes in puberty and brain function. The current study examines linear and nonlinear changes in affective reactivity in a longitudinal sample of 82 adolescents who underwent three fMRI sessions between the ages of 9 and 18 years. Changes in response to affective facial stimuli were related to age, pubertal stage, and testosterone levels. Using multilevel modelling, we highlight extensive nonlinear development of socio-emotional responsivity across the brain. Results include mid-pubertal peaks in amygdala and hippocampus response to fearful expressions, as well as sex differences in regions subserving social and self-evaluative processes. However, testosterone levels exhibited inverse patterns of association with neural response compared to pubertal stage in females (e.g. U-shaped relationship with the amygdala and hippocampus). Findings highlight potentially unique roles of age, pubertal stage and testosterone on socio-emotional development during adolescence, as well as sex differences in these associations.
Changes in fungal communities across a forest disturbance gradient
Authors: Shi Lingling , Dossa Gbadamassi G.O. , Paudel Ekananda , Zang Huadong , Xu Jianchu , Harrison Rhett D. 
Published: January 2019

AbstractDeforestation has a substantial impact on above ground biodiversity, but the response of below ground soil fungi remains poorly understood. In a tropical montane rainforest in southwestern China, plots were established along a forest degradation gradient ranging from mature and regenerated forests to open land to examine the impacts of forest degradation and deforestation on ecosystem diversity and function. Here, we evaluate the changes in below ground fungal diversity and community composition using a metabarcoding approach. Soil saprotrophic fungal richness declined with increasing forest disturbance. For example, Penicillium spp. (Phosphorus (P) solubilizing fungi) dominated in mature forest, but were less abundant in regenerating forest and showed the lowest abundance in open land sites. Conversely, the abundance of facultative pathogenic fungi increased along the disturbance gradient. The decline in soil saprophytic fungi may be a direct result of forest disturbance or it may be associated with increased availability of soil phosphorus indirectly through an increase in soil pH. The increase in abundance of facultative pathogenic fungi may be related to reduce competition with saprotrophic fungi, changes in microclimate or increased spore rain. These results demonstrate a loss of dominant P solubilizing saprotrophic fungi along the disturbance gradient, indicated a change from soil P limitation in mature tropical forest to soil C limitation in deforested sites. The increased prevalence of pathogenic fungi may inhibit plant succession following deforestation. Overall, this research demonstrates that soil fungi can be used as a sensitive indicator for soil health to evaluate the consequences of forest disturbance.ImportanceThe soil fungal functional group changes in response to forest disturbance indicated a close interaction between the above-ground plant community and the below-ground soil biological community. Soil saprotrophic fungi declined in relative abundance with increasing forest disturbance. At the same time, the relative abundance of facultative pathogenic fungi increased. The loss of saprotrophic fungal richness and abundance may have been a direct result of forest disturbance or an indirect result of changes in soil pH and soil P. Furthermore, the dominant P solubilizing saprotrophic fungi was replaced by diverse facultative pathogenic fungi, which have weaker C decomposition ability. These changes potentially indicate a shift from soil phosphate limitation to carbon limitation following deforestation. This study suggests that changes in fungal functional group composition can be used as an indicator of the effects of forest disturbance on soil carbon and nutrients.
Metabolic rates of prokaryotic microbes may inevitably rise with global warming
Authors: Smith Thomas P. , Thomas Thomas J. H. , García-Carreras Bernardo , Sal Sofía , Yvon-Durocher Gabriel , Bell Thomas , Pawar Samrāt 
Published: January 2019

AbstractUnderstanding how the metabolic rates of prokaryotes respond to temperature is fun-damental to our understanding of how ecosystem functioning will be altered by climate change, as these micro-organisms are major contributors to global carbon efflux. Ecological metabolic theory suggests that species living at higher temperatures evolve higher growth rates than those in cooler niches due to thermodynamic constraints. Here, using a global prokaryotic dataset, we find that maximal growth rate at thermal optimum increases with temperature for mesophiles (temperature optima ≲ 45°C), but not thermophiles (≳ 45°C). Furthermore, short-term (within-day) thermal responses of prokaryotic metabolic rates are typically more sensitive to warming than those of eukaryotes. Given that climatic warming will mostly impact ecosystems in the mesophilic temperature range, we conclude that as microbial communities adapt to higher temperatures, their metabolic rates and therefore, carbon efflux, will inevitably rise. Using a mathematical model, we illustrate the potential global impacts of these findings.
No evidence that portion size influences food consumption in male Sprague Dawley rats
Authors: Naneix Fabien , Pinder Sophie C. , Summers Megan Y. , Rouleau Renee M. , Robinson Eric , Myers Kevin P. , McCutcheon James E. 
Published: January 2019

ABSTRACTIn studies of eating behavior that have been conducted in humans, the tendency to consume more when given larger portions of food, known as the portion size effect (PSE), is one of the most robust and widely replicated findings. Despite this, the mechanisms that underpin it are still unknown. In particular, it is unclear whether the PSE arises from higher-order social and cognitive processes that are unique to humans or, instead, reflects more fundamental processes that drive feeding, such as conditioned food-seeking. Importantly, studies in rodents and other animals have yet to show convincing evidence of a PSE. In this series of studies, we used several methods to test for a PSE in adult male Sprague Dawley rats. Our approaches included using visually identifiable portions of a palatable food; training on a plate cleaning procedure; providing portion sizes of food pellets that were signaled by auditory and visual food-predictive cues; providing food with amorphous shape properties; and providing standard chow diet portions in home cages. In none of these manipulations did larger portions increase food intake. In summary, our data provide no evidence that a PSE is present in male Sprague Dawley rats, and if it is, it is more nuanced, dependent on experimental procedure, and/or smaller in size than it is in humans. In turn, these findings suggest that the widely-replicated PSE in humans may be more likely to reflect higher-order cognitive and social processes than fundamental conditioned behaviors.HighlightsPortion size effect (PSE) refers to increased food intake induced by large portions.Although widely replicated in human feeding studies, it may not exist animals.Presence of a PSE in animals would shed light on mechanisms, which are not known.Here, we find no evidence of PSE in male Sprague Dawley rats under a number of experimental conditions.This suggests that the human PSE is more likely due to socio-cognitive processes.
An encoding of genome content for machine learning
Authors: Viehweger A. , Krautwurst S. , Parks D. H. , König B. , Marz M. 
Published: January 2019

AbstractAn ever-growing number of metagenomes can be used for biomining and the study of microbial functions. The use of learning algorithms in this context has been hindered, because they often need input in the form of low-dimensional, dense vectors of numbers. We propose such a representation for genomes callednanotextthat scales to very large data sets.The underlying model is learned from a corpus of nearly 150 thousand genomes spanning 750 million protein domains. We treat the protein domains in a genome like words in a document, assuming that protein domains in a similar context have similar “meaning”. This meaning can be distributed by a neural net over a vector of numbers.The resulting vectors efficiently encode function, preserve known phylogeny, capture subtle functional relationships and are robust against genome incompleteness. The “functional” distance between two vectors complements nucleotide-based distance, so that genomes can be identified as similar even though their nucleotide identity is low.nanotextcan thus encode (meta)genomes for direct use in downstream machine learning tasks. We show this by predicting plausible culture media for metagenome assembled genomes (MAGs) from theTara Oceans Expeditionusing their genome content only.nanotextis freely released under a BSD licence (https://github.com/phiweger/nanotext).
Postnatal development of skeletal muscle in IUGR pigs: morphofunctional phenotype and molecular mechanisms
Authors: Pereira A.D. , Felicioni F. , Caldeira-Brant A.L. , Magnabosco D. , Bortolozzo F.P. , Tsoi S.C. , Dyck M. K. , Dixon W.T. , Martinelli P.M. , Jorge E.C. , Chiarini-Garcia H. , Almeida F.R.C.L. 
Published: January 2019

AbstractIntrauterine growth restriction (IUGR) is a serious condition which impairs the achievement of the fetus full growth potential and occurs in a natural and severe manner in pigs. Knowledge on skeletal muscle morphofunctional phenotype and its molecular regulation in IUGR pigs is important to understand postnatal muscle development and may help the establishment of therapies to improve skeletal muscle growth in those individuals. To investigate the impairment of skeletal muscle postnatal development due to IUGR, we evaluated the histomorphometrical pattern of the semitendinosus muscle, the Myosin Heavy Chain (embryonic, I, IIa, IIb and IIx MyHC) fiber composition and the relative expression of genes related to myogenesis, adipogenesis and growth during three specific periods: postnatal myogenesis (newborn to 100 days of age), postnatal development (newborn to 150 days of age), and hypertrophy (100 days to 150 days of age), comparing IUGR and normal birth weight (NW) pigs. Growth restriction in utero affected muscle fiber diameter, total fiber number and muscle cross sectional area which were smaller in IUGR pigs at birth (P < 0.05). Even though the percentage of MyHC-I myofibers was higher in IUGR females at birth (P < 0.05), in older gilts, a lower percentage of MyHC-IIx isoform (P < 0.05) and the presence of emb-MyHC were also observed in that experimental group. Regarding the pattern of gene expression in the postnatal myogenesis period, growth restriction in utero led to a down regulation of myogenic factors, which delayed the expression of signals that induces skeletal muscle myogenesis (PAX7, MYOD, MYOG, MYF5 and DES). Taken together, the muscle morphofunctional aspects described and their ontogenetic regulation define the possible molecular origins of the notorious damage to the postnatal musculature development in IUGR pigs.