bluuebunny/crossref_metadata_2025_split huggingface dataset:
Simultaneous Multislice Diffusion-Weighted Imaging of the Kidneys at 3 T
Authors: Tavakoli Andrej , Krammer Julia , Attenberger UIrike I. , Budjan Johannes , Stemmer Alto , Nickel Dominik , Kannengiesser Stephan , Morelli John N. , Schoenberg Stefan O. , Riffel Philipp 
Published: January 2020

Purpose
The aim of this study was to compare respiratory-triggered diffusion-weighted imaging with simultaneous-multislice acceleration (SMS-RT-DWI) to a standard free-breathing echoplanar DWI (s-DWI) for 3 T renal imaging with respect to image quality and artifacts.

Materials and Methods
A total of 40 patients who had undergone renal magnetic resonance imaging were included in this retrospective analysis of a prospectively planned cohort study. All examinations were performed on a 3 T whole-body magnetic resonance system. Both s-DWI and SMS-RT-DWI were obtained and images were independently reviewed by 2 radiologists on a 5-point Likert scale with respect to overall preference and image quality, renal edge and parenchymal sharpness, cortico-medullary differentiation, and sequence-related artifacts. Furthermore, discernibility of renal lesions was assessed. The signal-to-noise ratio (SNR) was measured from SNR maps. The derived mean apparent diffusion coefficients were also compared. Qualitative parameters were assessed with the Wilcoxon rank-sum test, and quantitative parameters, with the Student t test.

Results
Overall image quality, renal edge, and parenchymal sharpness of SMS-RT-DWI were rated as superior to s-DWI by the readers, with fewer sequence-related artifacts (P < 0.01 for all). Lesion discernibility was significantly improved for SMS-RT-DWI (P < 0.01). Both readers preferred SMS-RT-DWI to s-DWI in all cases (40/40). The acquisition time for SMS-RT-DWI was 30% shorter than for s-DWI. Mean SNR heterogeneity of SMS-RT-DWI at b = 800 s/mm2 was statistically significantly lower than s-DWI, whereas mean SNR was significantly higher for SMS-RT-DWI. Mean apparent diffusion coefficient values from both sequences were comparably homogeneous throughout the kidneys.

Conclusion
Simultaneous multislice DWI of the kidney at 3 T with respiratory triggering yields substantially improved image quality and lesion discernibility compared with standard single-shot echoplanar DWI with a 30% reduction in scan acquisition time.
Constructing plasticity phenotypes to classify experience-dependent development of the visual cortex
Authors: Balsor Justin L. , Jones David G. , Murphy Kathryn M. 
Published: January 2020

AbstractMany neural mechanisms regulate experience-dependent plasticity in the visual cortex (V1) and new techniques for quantifying large numbers of proteins or genes are transforming how plasticity is studied into the era of big data. With those large data sets comes the challenge of extracting biologically meaningful results about visual plasticity from data-driven analytical methods designed for high-dimensional data. In other areas of neuroscience, high-information content methodologies are revealing more subtle aspects of neural development and individual variations that give rise to a richer picture of brain disorders. We have developed an approach for studying V1 plasticity that takes advantage of the known functions of many synaptic proteins for regulating visual plasticity and using that to rebrand the results of high-dimensional analyses into a plasticity phenotype. Here we provide a primer for analyzing experience-dependent plasticity in V1 using example R code to identify high-dimensional changes in a group of proteins. We describe using PCA to classify high-dimensional plasticity features and use them to construct a plasticity phenotype. In the examples, we show how the plasticity phenotype can be visualized and used to identify neurobiological features in V1 that change during development or after different visual rearing conditions. We include an R package “v1hdexplorer” that aggregates the various coding packages and custom visualization scripts written in R Studio.
Spatiotemporal Genetic Diversity of Lions
Authors: Curry Caitlin J. , Davis Brian W. , Bertola Laura D. , White Paula A. , Murphy William J. , Derr James N. 
Published: January 2020

ABSTRACTThe Scramble for Africa in the late 1800s marked the beginning of increased human population growth in Africa. Here, we determined the genetic architecture of both historical and modern lions to identify changes in genetic diversity that occurred during this period of landscape and anthropogenic change. We surveyed microsatellite and mitochondrial genetic variation from 143 high-quality museum specimens of known provenance and combined them with data from recently published nuclear and mitochondrial studies. Analysis of variation at 9 microsatellites and 280 polymorphic mitogenome SNPs indicate the presence of male-mediated gene flow and recent isolation of local subpopulations, likely due to habitat fragmentation. Nuclear markers showed a significant decrease in genetic diversity from the historical (HE=0.833) to the modern (HE=0.796) populations, while mitochondrial genetic diversity was maintained (Hd=0.98 for both). While the historical population appears to have been panmictic based on nDNA data, hierarchical structure analysis identified four tiers of fine structure in modern populations, able to detect most sampling locations. Mitochondrial analyses identified 4 clusters: Southern, Mixed, Eastern, and Western; and were consistent between modern and historically sampled haplotypes. Within the last century, habitat fragmentation caused lion subpopulations to become more isolated as human expansion changed the African landscape. This resulted in an increase in fine-scale nuclear genetic structure and loss of genetic diversity as subpopulations became more differentiated, while mitochondrial structure and diversity was maintained over time.
Unequal contribution of two paralogous centromeric histones to function the cowpea centromere
Authors: Ishii Takayoshi , Juranić Martina , Maheshwari Shamoni , de Oliveira Bustamante Fernanda , Vogt Maximilian Moritz , Salinas-Gamboa Rigel , Dreissig Steven , Gursanscky Nial , How Tracy , Fuchs Joerg , Schubert Veit , Spriggs Andrew , Vielle-Calzada Jean-Philippe , Comai Luca , Koltunow Anna M. G. , Houben Andreas 
Published: January 2020

AbstractThe legume cowpea (Vigna unguiculata, 2n=2x=22) has significant tolerance to drought and heat stress. Here we analysed and manipulated cowpea centromere-specific histone H3 (CENH3) genes, aiming to establish a centromere-based doubled-haploid method for use in genetic improvement of this dryland crop in future. Cowpea encodes two functional CENH3 variants (CENH3.1 and CENH3.2) and two CENH3 pseudogenes. Phylogenetic analysis suggests that gene duplication of CENH3 occurred independently during the speciation ofV. unguiculataand the relatedV. mungowithout a genome duplication event. Both functional cowpeaCENH3variants are transcribed, and the corresponding proteins are intermingled in subdomains of different types of centromere sequences in a tissue-specific manner together with the outer kinetochore protein CENPC. CENH3.2 is removed from the generative cell of mature pollen, while CENH3.1 persists. Differences between both CENH3 paralogs are restricted to the N-terminus. The complete CRISPR/Cas9-based inactivation ofCENH3.1resulted in delayed vegetative growth and sterility, indicating that this variant is needed for plant development and reproduction. By contrast,CENH3.2knockout individuals did not show obvious defects during vegetative and reproductive development, suggesting that the gene is an early stage of subfunctionalization or pseudogenization.One-sentence summaryThe two paralogous centromeric histones (CENH3) of cowpea contribute unequal to the function of the centromere.
Metacognition and memory of emotional information: Judgments of learning predict the affectivity congruence effect in free recall
Authors: Siedlecka Marta , Blaut Agata , Paulewicz Borys , Kłosowska Joanna 
Published: January 2020

AbstractMemory of emotional information often depends on the current mood and the dominant affective state. For example, studies show that people tend to recall emotional information of valence that is congruent with their affective traits. However, not much is known about whether this tendency is captured by metacognitive judgments of learning (JOLs). The aim of this study was to find out how people who score low or high on affectivity scales assess their memory of emotional material. We used a free-recall task with self-referential neutral, positive, and negative adjectives. The results show the affectivity congruence effect: the number of negative words recalled is related to affectivity; it increases with Negative Affectivity (NA) and decreases with Positive Affectivity (PA). Metacognitive assessment of future recall is also related to affectivity. Higher PA is related to higher JOLs for positive words and lower JOLs for negative words. Higher NA is related to higher JOLs for negative words and lower JOLs for positive words. The results suggest that metacognitive processes are sensitive to affective trait-specific memory bias.
Work horse strainClostridioides difficile630Δermis oblivious to its anaerobic lifestyle
Authors: Troitzsch Daniel , Zhang Hao , Dittmann Silvia , Düsterhöft Dorothee , Michel Annika-Marisa , Jänsch Lothar , Riedel Katharina , Borrero-de Acuña José Manuel , Jahn Dieter , Sievers Susanne 
Published: January 2020

AbstractThe laboratory reference strain 630Δermof the anaerobic human pathogenClostridioides difficileis characterized by a remarkable high oxygen tolerance. We show that an amino acid exchange in the DNA binding domain of the hydrogen peroxide sensor PerR results in a constitutive derepression of PerR-controlled genes and thus in an oxidative stress response even under anaerobic conditions. This questions the model status, strain 630Δermclaims inC. difficileresearch.
ERBB2 drives YAP activation and EMT-like processes during cardiac regeneration
Authors: Aharonov Alla , Shakked Avraham , Umansky Kfir Baruch , Savidor Alon , Kain David , Lendengolts Daria , Revach Or-Yam , Morikawa Yuka , Dong Jixin , Levin Yishai , Geiger Benjamin , Martin James F. , Tzahor Eldad 
Published: January 2020

SummaryCardiomyocyte (CM) loss after injury results in adverse remodelling and fibrosis, which inevitably lead to heart failure. ERBB2-Neuregulin and Hippo-YAP signaling pathways are key mediators of CM proliferation and regeneration, yet the crosstalk between these pathways is unclear. Here, we demonstrate in adult mice that transient over-expression (OE) of activated ERBB2 in CMs promotes cardiac regeneration in a heart failure model. OE CMs present an EMT-like regenerative response manifested by cytoskeletal remodelling, junction dissolution, migration, and ECM turnover. Molecularly, we identified YAP as a critical mediator of ERBB2 signaling. In OE CMs, YAP interacts with nuclear envelope and cytoskeletal components, reflecting the altered mechanic state elicited by ERBB2. Hippo-independent activating phosphorylation on YAP at S352 and S274 were enriched in OE CMs, peaking during metaphase, and viral overexpression of YAP phospho-mutants dampened the proliferative competence of OE CMs. Taken together, we demonstrate a potent ERBB2-mediated YAP mechanosensory signaling, involving EMT-like characteristics, resulting in heart regeneration.HighlightsERBB2-driven regeneration of scarred hearts recapitulates core-EMT processesYAP is activated and required downstream to ERBB2 signaling in CMsYAP activity is mechanically driven by cytoskeleton and nuclear envelope remodelingYAP S274 and S352 phosphorylation is essential for CM mitosis
The Latent Genetic Structure of Impulsivity and its Relation to Internalizing Psychopathology
Authors: Gustavson Daniel E. , Friedman Naomi P. , Fontanillas Pierre , Elson Sarah L. ,   the 23andMe Research Team, Palmer Abraham A. , Sanchez-Roige Sandra 
Published: January 2020

AbstractFactor analyses suggest that impulsivity traits that capture tendencies to act prematurely or take risks tap partially distinct constructs. We applied genomic structure equation modeling to evaluate the genetic factor structure of two well-established impulsivity questionnaires, using published genome-wide association study statistics from up to 22,861 participants. We also tested the hypotheses that delay discounting would be genetically separable from other impulsivity factors, and that emotionally-triggered facets of impulsivity (urgency) would be those most strongly genetically correlated with an internalizing latent factor. A five-factor model best fit the impulsivity data. Delay discounting was genetically distinct from these five factors. As expected, the two urgency subscales were most strongly related to an Internalizing Psychopathology latent factor. These findings provide empirical genetic evidence that impulsivity can be disarticulated into distinct categories of differential relevance for internalizing psychopathology. They also demonstrate how measured genetic markers can be used to inform theories of psychology/personality.
Atomistic basis of microtubule dynamic instability assessed via multiscale modeling
Authors: Hemmat Mahya , Odde David J. 
Published: January 2020

AbstractMicrotubule “dynamic instability,” the abrupt switching from assembly to disassembly caused by the hydrolysis of GTP to GDP within the β subunit of the αβ-tubulin heterodimer, is necessary for vital cellular processes such as mitosis and migration. Despite existing high-resolution structural data, the key mechanochemical differences between the GTP and GDP states that mediate dynamic instability behavior remain unclear. Starting with a published atomic-level structure as an input, we used multiscale modeling to find that GTP hydrolysis results in both longitudinal bond weakening (~4 kBT) and an outward bending preference (~1.5 kBT) to both drive dynamic instability and give rise to the microtubule tip structures previously observed by light and electron microscopy. More generally, our study provides an example where atomic level structural information is used as the sole input to predict cellular level dynamics without parameter adjustment.
siRNA-mediatedde novosilencing ofAc/Dstransposons is initiated by alternative transposition in maize
Authors: Wang Dafang , Zhang Jianbo , Zuo Tao , Lisch Damon , Zhao Meixia , Peterson Thomas 
Published: January 2020

AbstractAlthough Transposable Elements (TEs) comprise a major fraction of many higher eukaryotic genomes, most TEs are silenced by host defense mechanisms. The means by which otherwise active TEs are recognized and silenced remains poorly understood. Here we analyzed two independent cases of spontaneous silencing of the active maizeAc/Dstransposon system. This silencing was initiated by Alternative Transposition (AT), a type of aberrant transposition event that engages the termini of two nearby separate TEs. AT during DNA replication can generate Composite Insertions (CIs) that contain inverted duplications of the transposon sequences. We show that the inverted duplications of two CIs are transcribed to produce dsRNAs that trigger the production of two distinct classes of siRNAs: a 24-nt class complementary to the TE terminal inverted repeats (TIRs) and non-coding sub-terminal regions, and a 21-22 nt class corresponding to the TE transcribed regions. Plants containing these siRNA-generating CIs exhibit decreased levels ofActranscript and heritable repression ofAc/Dstransposition. This study documents the first case of TE silencing attributable to transposon self-initiated AT and may represent a general initiating mechanism for silencing of DNA transposons.Article summaryTransposable Elements (TEs) are often silenced by their hosts, but how TEs are initially recognized for silencing remains unclear. Here we describe two independent loci that inducede novoheritable silencing of maizeAc/Dstransposons. Plants containing these loci produce dsRNA andAc-homologous small interfering RNAs, and exhibit decreased levels ofActranscript and heritable repression ofAc/Dstransposition. We show that these loci comprise inverted duplications of TE sequences generated by Alternative Transposition coupled with DNA re-replication. This study documents the first case of transposon silencing induced by AT and may represent a general initiating mechanism for TE silencing.
Genomic surveillance enables suitability assessment ofSalmonellagene targets used for culture-independent diagnostic testing
Authors: Rockett Rebecca J. , Arnott Alicia , Wang Qinning , Howard Peter , Sintchenko Vitali 
Published: January 2020

ABSTRACTSalmonellais a highly diverse genus consisting of over 2600 serovars responsible for high-burden food- and water-borne gastroenteritis worldwide. Sensitivity and specificity of PCR-based culture-independent diagnostic testing (CIDT) systems forSalmonella, which depend on a highly conserved gene target, can be affected by single nucleotide polymorphisms (SNPs), indels and genomic rearrangements within primer and probe sequences. This report demonstrates the value of prospectively collected genomic data for verifying CIDT targets.We utilised the genomes of 3165Salmonellaisolates prospectively collected and sequenced in Australia. The sequence ofSalmonellaCIDT PCR gene targets (ttrA, spaOandinvA) were systematically interrogated to measure nucleotide dissimilarity. Analysis of 52 different serovars and 79 MLST types demonstrated dissimilarity within and between PCR gene targets ranging between 0 – 81.3 SNP/Kbp (0 and 141 SNPs). Lowest average dissimilarity was observed in thettrAtarget gene used by the Roche LightMix at 2.0 SNP/Kbp [range 0 – 46.7]), however entropy across the gene demonstrates it may not be the most stable CIDT target.While debate continues over the benefits and pitfalls of replacing bacterial culture with molecular assays, the growing volumes of genomic surveillance data enable periodic regional reassessment and validation of CIDT targets against both prevalent and emerging serovars. If PCR systems are to become the primary screening and diagnostic tool for laboratory diagnosis of salmonellosis, ongoing monitoring of the genomic diversity in PCR target regions is warranted as is the potential inclusion of twoSalmonellaPCR targets into frontline diagnostic systems.
ALPPL2 is a highly specific and targetable tumor cell surface antigen
Authors: Su Yang , Zhang Xin , Bidlingmaier Scott , Behrens Christopher R. , Lee Nam-Kyung , Liu Bin 
Published: January 2020

AbstractIt has been challenging to identify tumor-specific cell surface antigens as the vast majority of tumor-associated antigens are also expressed by some normal tissues. In the course of our study on mesothelioma, we identified a highly specific tumor cell surface antigen that can be targeted for therapy development. Mesothelioma is caused by malignant transformation of the mesothelium, incurable and categorized into three histological subtypes, epithelioid, biphasic and sarcomatoid. To identity novel mesothelioma cell surface antigens with broad subtype coverage and high tissue specificity, we have previously selected phage antibody display libraries on live mesothelioma cells and tissues following counter-selection on normal cells, and identified a panel of human antibodies that bind all subtypes of mesothelioma but not normal mesothelium. One of the antibodies, M25, showed high specificity, and we hereby report the identification of the M25 antigen as ALPPL2. We performed immunohistochemistry on normal human tissues and found that ALPPL2 is expressed only on placental trophoblasts but not any other normal tissues. This exquisite tissue specificity and broad tumor type coverage suggests that ALPPL2 could be an excellent cell surface target for therapeutic development against mesothelioma. To evaluate therapeutic potential of ALPPL2 targeting, we developed an ALPPL2-targeted antibody-drug conjugate and demonstrated potent and specific tumor killingin vitroandin vivoagainst both epithelioid and sarcomatoid mesothelioma. Thus ALPPL2 belongs to a rare class of cell surface antigens that can be said as being truly tumor specific and is well suited for therapy development against ALPPL2 expressing tumors.
Homogeneous multifocal excitation for high-throughput super-resolution imaging
Authors: Mahecic Dora , Gambarotto Davide , Douglass Kyle M. , Fortun Denis , Banterle Niccoló , Le Guennec Maeva , Ibrahim Khalid , Gönczy Pierre , Hamel Virginie , Guichard Paul , Manley Suliana 
Published: January 2020

AbstractSuper-resolution microscopies, which allow features below the diffraction limit to be resolved, have become an established tool in biological research. However, imaging throughput remains a major bottleneck in using them for quantitative biology, which requires large datasets to overcome the noise of the imaging itself and to capture the variability inherent to biological processes. Here, we develop a multi-focal flat illumination for field independent imaging (mfFIFI) module, and integrate it into an instant structured illumination microscope (iSIM). Our instrument extends the field of view (FOV) to >100×100 µm2without compromising image quality, and maintains high-speed (100 Hz), multi-color, volumetric imaging at double the diffraction-limited resolution. We further extend the effective FOV by stitching multiple adjacent images together to perform fast live-cell super-resolution imaging of dozens of cells. Finally, we combine our flat-fielded iSIM setup with ultrastructure expansion microscopy (U-ExM) to collect 3D images of hundreds of centrioles in human cells, as well as of thousands of purifiedChlamydomonas reinhardtiicentrioles per hour at an effective resolution of ∼35 nm. We apply classification and particle averaging to these large datasets, allowing us to map the 3D organization of post-translational modifications of centriolar microtubules, revealing differences in their coverage and positioning.
Sucrose promotes etiolated stem branching through activation of cytokinin accumulation followed by vacuolar invertase activity
Authors: Salam Bolaji Babajide , Barbier Francois , Danieli Raz , Ziv Carmit , Spíchal Lukáš , Teper-Bamnolker Paula , Jiang Jiming , Ori Naomi , Beveridge Christine , Eshel Dani 
Published: January 2020

ABSTRACTThe potato (Solanum tuberosumL.) tuber is a swollen stem. Sprouts growing from the tuber nodes represent dormancy release and loss of apical dominance. We recently identified sucrose as a key player in triggering potato stem branching. To decipher the mechanisms by which sucrose induces stem branching, we investigated the nature of the inducing molecule and the involvement of vacuolar invertase (VInv) and the plant hormone cytokinin (CK) in this process. Sucrose was more efficient at enhancing lateral bud burst and elongation than either of its hexose moieties (glucose and fructose), or a slowly metabolizable analog of sucrose (palatinose). Sucrose feeding induced expression of the sucrose transporter geneSUT2, followed by enhanced expression and activity of VInv in the lateral bud prior to its burst. We observed a reduction in the number of branches on stems ofVInv-RNA interference lines during sucrose feeding, suggesting that sucrose breakdown is needed for lateral bud burst. Sucrose feeding led to increased CK content in the lateral bud base prior to bud burst. Inhibition of CK synthesis or perception inhibited the sucrose-induced bud burst, suggesting that sucrose induces stem branching through CK. Together, our results indicate that sucrose is transported to the bud, where it promotes bud burst by inducing CK accumulation and VInv activity.