bluuebunny/crossref_metadata_2025_split huggingface dataset:
Photoinduced charge carrier dynamics in a ZnSe quantum dot-attached CdTe system
Authors: Saeed Shomaila , Iqbal Azhar , Iqbal Azhar 
Published: March 2020

A new nanohybrid material is prepared by attaching CdTe nanoneedles (NNs) to surface-modified ZnSe quantum dots (QDs). The NNs and QDs are prepared by a colloidal synthesis method in an aqueous alkaline medium. The surface modification and the attachment of nanostructures are achieved by a bifunctional ligand 3-mercaptopropionic acid (3-MPA). The band gap of the ZnSe QDs is varied by controlling the size of the QDs in order to get the maximum overlap between the absorption band of the CdTe NNs and the emission band of the ZnSe QDs, which is a prerequisite for effective charge/energy transfer. The possibility of photoinduced charge transfer (PCT) and Förster resonance energy transfer (FRET) from the donor (QDs) to the acceptor (NNs) has been assessed. Very fast (less than 800 ps) PCT and FRET from QDs to NNs occur because the emission band of QDs overlaps with the absorption band of NNs. The calculated large value of the overlapping integral,
J
(
λ
) ∼4.5 × 10
19
M
−1
cm
−1
nm
4
, of the donor and the acceptor bands proves the feasibility of energy transfer. These findings suggest that the ZnSe QDs can exchange photoinduced energy with the CdTe NNs effectively over a wide distance in a CdTe–ZnSe nanohybrid.
Motif analysis in co-expression networks reveals regulatory elements in plants: The peach as a model
Authors: Ksouri Najla , Castro-Mondragón Jaime A. , Montardit-Tardà Francesc , van Helden Jacques , Contreras-Moreira Bruno , Gogorcena Yolanda 
Published: March 2020

AbstractIdentification of functional regulatory elements encoded in plant genomes is a fundamental need to understand gene regulation. While much attention has been given to model species asArabidopsis thaliana, little is known about regulatory motifs in other plant genera. Here, we describe an accurate bottom-up approach using the online workbench RSAT::Plants for a versatile ab-initio motif discovery takingPrunus persicaas a model. These predictions rely on the construction of a co-expression network to generate modules with similar expression trends and assess the effect of increasing upstream region length on the sensitivity of motif discovery. Applying two discovery algorithms, 18 out of 45 modules were found to be enriched in motifs typical of well-known transcription factor families (bHLH, bZip, BZR, CAMTA, DOF, E2FE, AP2-ERF, Myb-like, NAC, TCP, WRKY) and a novel motif. Our results indicate that small number of input sequences and short promoter length are preferential to minimize the amount of uninformative signals in peach. The spatial distribution of TF binding sites revealed an unbalanced distribution where motifs tend to lie around the transcriptional start site region. The reliability of this approach was also benchmarked inArabidopsis thaliana, where it recovered the expected motifs from promoters of genes containing ChIPseq peaks. Overall, this paper presents a glimpse of the peach regulatory components at genome scale and provides a general protocol that can be applied to many other species. Additionally, a RSAT Docker container was released to facilitate similar analyses on other species or to reproduce our results.One sentence summaryMotifs prediction depends on the promoter size. A proximal promoter region defined as an interval of -500 bp to +200 bp seems to be the adequate stretch to predictde novoregulatory motifs in peach
Corticospinal excitability remains unchanged in the presence of residual force enhancement and does not contribute to increased torque production
Authors: Frischholz Jasmin , Raiteri Brent J. , Cresswell Andrew G. , Hahn Daniel 
Published: March 2020

AbstractFollowing active muscle stretch, muscle force is enhanced, which is known as residual force enhancement (rFE). As earlier studies found apparent corticospinal excitability modulations in the presence of rFE, this study aimed to test whether corticospinal excitability modulations contribute to rFE. Fourteen participants performed submaximal plantar flexion stretch-hold and fixed-end contractions at 30% of their maximal voluntary soleus muscle activity in a dynamometer. During the steady state of the contractions, participants either received subthreshold or suprathreshold transcranial magnetic stimulation (TMS) of their motor cortex, while triceps surae muscle responses to stimulation were obtained via electromyography (EMG), and net ankle joint torque was recorded. B-mode ultrasound imaging was used to confirm muscle fascicle stretch during stretch-hold contractions in a subset of participants. Following stretch of the plantar flexors, an average rFE of 7% and 11% was observed for contractions with subthreshold and suprathreshold TMS, respectively. 41-46 ms following subthreshold TMS, triceps surae muscle activity was suppressed by 19-25%, but suppression was not significantly different between stretch-hold and fixed-end contractions. Similarly, the reduction in plantar flexion torque following subthreshold TMS was not significantly different between contraction conditions. Motor evoked potentials, silent periods and superimposed twitches following suprathreshold TMS were also not significantly different between contraction conditions. As TMS of the motor cortex did not result in any differences between stretch-hold and fixed-end contractions, we conclude that rFE is not linked to changes in corticospinal excitability, making rFE a muscle mechanical property rather than a combined neuro-muscular property.
Implementing an algorithm for controlling for female MC phase for clinical neuroscience
Authors: Herrold Amy A. , Gallagher Virginia T. , Chen Yufen , Majaanes Jeffery , Kramer Natalie , Vesci Brian , Colegrove Danielle , Reilly James , McCloskey Leanne , Breiter Hans 
Published: March 2020

AbstractBackgroundRecent research suggests that hormones and/or menstrual cycle (MC) phase at time of study may significantly affect clinical neuroscience outcomes of interest. Prior research puts forth sound methods for characterizing MC phase in women not using hormonal contraceptives (HC). However, an estimated 40% of premenopausal women in the United States use some form of HC. We developed an algorithm for characterizing hormone levels and MC phase among women both using and not using HC. We have employed this algorithm among female collegiate athletes post-mild traumatic brain injury (mTBI) as female athletes are understudied in the sports mTBI field, MC phase may have important effects on mTBI-related outcomes and controlling for MC phase has not been employed in this population.MethodsThirty female collegiate athletes were studied. Fifteen incurred a mTBI 3-10 days prior to assessment and sixteen were age, ethnicity, and menstrual cycle (MC) phase matched to the injured athletes. MC matching was conducted with retrospective and prospective self-report MC tracking, self-report of HC use, and serum progesterone testing.Results53% (16/30) of females were on HC and 47% (14/30) were not. Of the non-HC users, seven female pairs were in the follicular and one was in the luteal phase. Among the non-HC users, there was 50% agreement in MC phase identification between self-report and progesterone measures and a κ = 0.138. Of the HC users, eight were in the inactive and six were in the active phase of their medication. Among the HC users, average progesterone levels indicated medication compliance (.58ng/mL).ConclusionsThis study provides important methodology and proof-of-concept that MC phase can be used as a control variable for time-sensitive prospective clinical neuroscience studies including those involving brain injury. When studying females, it is important to properly examine and control for the sex-specific factor of MC phase in order to have a full understanding of brain behavior relationships in translational research.
Applying a gene-suite approach to examine the physiological status of wild-caught walleye (Sander vitreus)
Authors: Jeffrey Jennifer D. , Carlson Hunter , Wrubleski Dale , Enders Eva C. , Treberg Jason R. , Jeffries Ken M. 
Published: March 2020

AbstractMolecular techniques have been increasingly used in a conservation physiology framework to provide valuable information regarding the mechanisms underlying responses of wild organisms to environmental and anthropogenic stressors. In the present study, we developed a reference gill transcriptome for walleye (Sander vitreus) allowing us to pair a gene-suite approach with multivariate statistics to examine the physiological status of wild-caught walleye. For molecular analyses of wild fish, the gill is a useful target for conservation studies, not only because of its importance as an indicator of the physiological status of fish but also because it can be biopsied non-lethally. Walleye were non-lethally sampled following short- (∼1.5 month) and long-term (∼3.5 month) holding in the Delta Marsh, that is located south of Lake Manitoba in Manitoba, Canada. Large-bodied walleye are held in the Delta Marsh from late April to early August by exclusion screens used to protect the marsh from invasive common carp (Cyprinus carpio), exposing fish to potentially stressful water quality conditions. Principal components analysis (PCA) revealed patterns of transcript abundance consistent with exposure of fish to increasingly high temperature and low oxygen conditions with longer holding in the marsh. For example, longer-term holding in the marsh was associated with increases in the mRNA levels of heat shock proteins and a shift in the mRNA abundance of aerobic to anaerobic metabolic genes. Overall, the results of the present study suggest that walleye held in the Delta Marsh may be exhibiting sub-lethal responses to high temperature and low oxygen conditions and provides valuable information for managers invested in mediating these impacts to a local species of conservation concern. More broadly, we highlight the usefulness of pairing transcriptomic techniques with multivariate statistics to address potential confounding factors that can affect measured physiological responses of wild-caught fish.Lay summaryNon-lethal molecular techniques were used to assess the physiological status of wild-caught walleye confined in the Delta Marsh, Manitoba, Canada, because of common carp exclusion screens. Walleye sampled during the warmest months of the year exhibited responses to elevated temperature and low oxygen conditions, suggesting sub-lethal effects of local conditions.
Heme A-containing oxidases evolved in the ancestors of iron oxidizing bacteria
Authors: Degli Esposti Mauro , Garcia-Meza Viridiana , Ceniceros Gómez Agueda E. , Moya-Beltrán Ana , Quatrini Raquel , Hederstedt Lars 
Published: March 2020

AbstractThe origin of oxygen respiration in bacteria has long intrigued biochemists, microbiologists and evolutionary biologists. The earliest enzymes that consume oxygen to extract energy did not evolve in the same lineages of photosynthetic bacteria that released oxygen on primordial earth, leading to the great oxygenation event (GOE). A widespread type of such enzymes is proton pumping cytochromecoxidase (COX) that contains heme A, a unique prosthetic group for these oxidases. Here we show that the most ancestral proteins for the biosynthesis of heme A are present in extant acidophilic Fe2+-oxidizing Proteobacteria. Acidophilic Fe2+-oxidizers lived on emerged land around the time of the GOE, as suggested by the earliest geochemical evidence for aerobic respiration on paleoproterozoic earth. The gene for heme A synthase in acidophilic Fe2+-oxidizing Proteobacteria is associated with the COX gene cluster for iron oxidation. Compared to many other soil bacteria, the COX subunits encoded by this gene cluster are early diverging. Our data suggest that the ancient bacterial lineage which first evolved heme A-containing COX was related to the ancestors of present acidophilic Fe2+-oxidizers such asAcidiferrobacterandAcidithiobacillusspp. The copper leaching activity of such bacteria might have constituted a key ecological factor to promote COX evolution.
Absent from DNA and protein: genomic characterization of nullomers and nullpeptides across functional categories and evolution
Authors: Georgakopoulos-Soares Ilias , Barnea Ofer Yizhar , Mouratidis Ioannis , Hemberg Martin , Ahituv Nadav 
Published: March 2020

AbstractNullomers and nullpeptides are short DNA or amino acid sequences that are absent from a genome or proteome, respectively. One potential cause for their absence could be that they have a detrimental impact on an organism. Here, we identified all possible nullomers and nullpeptides in the genomes and proteomes of over thirty species and show that a significant proportion of these sequences are under negative selection. We assign nullomers to different functional categories (coding sequences, exons, introns, 5’UTR, 3’UTR and promoters) and show that nullomers from coding sequences and promoters are most likely to be selected against. Utilizing variants in the human population, we annotate variant-associated nullomers, highlighting their potential use as DNA ‘fingerprints’. Phylogenetic analyses of nullomers and nullpeptides across evolution shows that they could be used to build phylogenetic trees. Our work provides a catalog of genomic and proteome derived absent k-mers, together with a novel scoring function to determine their potential functional importance. In addition, it shows how these unique sequences could be used as DNA ‘fingerprints’ or for phylogenetic analyses.
Dynamic cell wall modifications in brassicas during clubroot disease
Authors: Badstöber Julia , Ciaghi Stefan , Neuhauser Sigrid 
Published: March 2020

AbstractBiotic interactions of plants and microbial pathogens can cause drastic changes in cell wall composition in response to developmental reprogramming caused as consequence of an infection. Clubroot disease, caused by the biotrophic plant pathogenPlasmodiophora brassicae(Phytomyxea, Rhizaria), is the economically most important disease of Brassica crops worldwide. The disease is best known by the characteristic hypertrophied roots (root galls, clubroots). Amongst a series of physiological changes of the host tissue, the formation of the characteristic root galls leads to cell wall modification and reorganization. Cell wall chemistry and the hosts genetic repertoire are discussed to play a role in the resilience of plants against clubroot disease. Plant cells infected withP. brassicaeare markedly enlarged, and look very differently from uninfected, healthy cells. Here we systematically review cell wall related processes that lead to the typical clubroot phenotype and provide novel insights howP. brassicaeuses these modifications to benefit its own development. An infection withP. brassicaeimpacts on nearly all cell wall related processes, but all alterations are meaningful for successful growth and development ofP. brassicae.Processes related to cell wall stability and rigidity (e.g. cellulose, pectin or lignin synthesis) are down-regulated, while cell wall degrading enzymes or processes that increase the flexibility of the host cell wall (e.g. expansin) are up-regulated. The here presented findings indicate thatP. brassicaeweakens the structural stability of its host cell while it increases its elasticity, which in consequence allowsP. brassicaeto grow bigger and ultimately to develop more resting spores. Consequently, the understanding of the modification of the host cell wall is important for the formation of the characteristic root galls but also to better understand clubroot disease.
Bridging parametric and nonparametric measures of species interactions unveils new insights of non-equilibrium dynamics
Authors: Song Chuliang , Saavedra Serguei 
Published: March 2020

AbstractA central theme in ecological research is to understand how species interactions contribute to community dynamics. Species interactions are the basis of parametric (model-driven) and nonpara-metric (model-free) approaches in theoretical and empirical work. However, despite their different interpretations across these approaches, these measures have occasionally been used interchangeably, limiting our opportunity to use their differences to gain new insights about ecological systems. Here, we revisit two of the most used measures across these approaches: species interactions measured asconstant directeffects (typically used in parametric approaches) andlocal aggregatedeffects (typically used in nonparametric approaches). We show two fundamental properties of species interactions that cannot be revealed without bridging these definitions. First, we show that the local aggregated intraspecific effect summarizes all potential pathways through which one species impacts itself, which are likely to be negative even without any constant direct self-regulation mechanism. This property has implications for the long-held debate on how communities can be stabilized when little evidence of self-regulation has been found among higher-trophic species. Second, we show that a local aggregated interspecific effect between two species is correlated with the constant direct interspecific effect if and only if the population dynamics do not have any higher-order direct effects. This other property provides a rigorous methodology to detect direct higher-order effects in the field and experimental data. Overall, our findings illustrate a practical route to gain further insights about non-equilibrium ecological dynamics and species interactions.
UC2 – A Versatile and Customizable low-cost 3D-printed Optical Open-Standard for microscopic imaging
Authors: Diederich Benedict , Lachmann René , Carlstedt Swen , Marsikova Barbora , Wang Haoran , Uwurukundo Xavier , Mosig Alexander , Heintzmann Rainer 
Published: March 2020

AbstractWith UC2 (You-See-Too) we present an inexpensive 3D-printed microscopy toolbox. The system is based on concepts of modular development, rapid-prototyping and all-time accessibility using widely available off-the-shelf optic and electronic components. We aim to democratize microscopy, reduce the reproduction crisis and enhance trust into science by making it available to everyone via an open-access public repository. Due to its versatility the aim is to boost creativity and non-conventional approaches. In this paper, we demonstrate a development cycle from basic blocks to different microscopic techniques. First, we build a bright-field system and stress-test it by observing macrophage cell differentiation, apoptosis and proliferation incubator-enclosed for seven days with automatic focussing to minimize axial drift. We prove versatility by assembling a system using the same components to a fully working fluorescence light-sheet system and acquire a 3D volume of a GFP-expressing living drosophila larvae. Finally, we sketch and demonstrate further possible setups to draw a picture on how the system can be used for reproducible prototyping in scientific research. All design files for replicating the experimental setups are provided via an open-access online repository (https://github.com/bionanoimaging/UC2-GIT) to foster widespread use.
A Decoy Library Uncovers U-box E3 Ubiquitin Ligases that Regulate Flowering Time in Arabidopsis
Authors: Feke Ann M. , Hong Jing , Liu Wei , Gendron Joshua M. 
Published: March 2020

ABSTRACTTargeted degradation of proteins is mediated by E3 ubiquitin ligases and is important for the execution of many biological processes. Previously, we created and employed a large library of E3 ubiquitin ligase decoys to identify regulators of the circadian clock (Feke et al., 2019). In tandem with the screen for circadian regulators, we performed a flowering time screen using our U-box-type E3 ubiquitin ligase decoy transgenic library. We identified five U-box decoy transgenic populations that have defects in flowering time or the floral development program. We used additional genetic and biochemical studies to validatePLANT U-BOX 14(PUB14),MOS4-ASSOCIATED COMPLEX 3A (MAC3A),andMAC3Basbona fideregulators of flowering time. This work reinforces the utility of the decoy library in identifying regulators of important developmental transitions in plants and expands the scope of the technique beyond our previous studies.
CDKN2Chomozygous loss identifies a distinct subtype ofTP53/RB1-wildtype leiomyosarcoma with frequentCICgenomic alterations and 1p/19q-codeletion
Authors: Williams Erik A. , Sharaf Radwa , Decker Brennan , Werth Adrienne J. , Toma Helen , Montesion Meagan , Sokol Ethan S. , Pavlick Dean C. , Shah Nikunj , Venstrom Jeff M. , Alexander Brian M. , Ross Jeffrey S. , Albacker Lee A. , Lin Douglas I , Ramkissoon Shakti H. , Elvin Julia A. 
Published: March 2020

AbstractPurposeLeiomyosarcomas (LMS) harbor frequent inactivation ofTP53andRB1, and extensive DNA copy number alterations. Here, we describe a distinct recurrent genomic signature inTP53/RB1-wildtype uterine LMS.MethodsTissues from 276,645 unique advanced cancers, including 2,570 uterine and soft tissue LMS were sequenced by hybrid-capture-based next-generation DNA and RNA sequencing/comprehensive genomic profiling of up to 406 genes. We characterized clinicopathologic features of relevant cases.ResultsWe identified 77 LMS with homozygous copy loss ofCDKN2Cat chromosome 1p32.3 (3.0% of LMS). Genomic alterations (GAs) inTP53, RB1, andATRXwere rare in comparison with the remainder of the LMS cohort (11.7% vs 73.4%, 0% vs 54.5%, 2.6% vs 24.5%, all p<0.0001).CDKN2C-null LMS cases were significantly enriched for GAs inCIC(40.3% vs 1.4%) at 19q13.2,CDKN2A(46.8% vs 7.0%), andRAD51B(16.9% vs 1.7%; all p<0.0001). Chromosome arm-level aneuploidy analysis of available LMS cases (n=1,251) found that 85% (n=33/39) ofCDKN2C-null LMS cases exhibited 1p/19q-codeletion, with significant enrichment in comparison to the remainder of the evaluated LMS cohort (85% vs. 5.1%, p<0.0001).99% ofCDKN2C-null cases were in females; median age was 61 years at surgery (range, 36-81 years). 55 cases were of uterine primary, 4 cases non-uterine, and the remaining 18 of uncertain primary site. 6 patients had a prior history of leiomyomatosis or uterine smooth muscle tumor of uncertain malignant potential. 60% of cases showed at least focal epithelioid variant histology. Most cases were of known advanced stage, with 62% of confirmed uterine primary cases at FIGO stage IVB.ConclusionThe identification of this novel genomic subset may have prognostic and/or therapeutic clinical relevance, including use of specific cyclin-dependent kinase inhibitors.
Ongoing exposure to peritoneal dialysis fluid alters resident peritoneal macrophage phenotype and activation propensity
Authors: Sutherland Tara E. , Shaw Tovah N. , Lennon Rachel , Herrick Sarah E. , Rückerl Dominik 
Published: March 2020

AbstractPeritoneal dialysis (PD) is a more continuous alternative to haemodialysis, for patients with chronic kidney disease, with considerable initial benefits for survival, patient independence and healthcare costs. However, longterm PD is associated with significant pathology, negating the positive effects over haemodialysis. Importantly, peritonitis and activation of macrophages is closely associated with disease progression and treatment failure. However, recent advances in macrophage biology suggest opposite functions for macrophages of different cellular origins. While monocyte-derived macrophages promote disease progression in some models of fibrosis, tissue resident macrophages have rather been associated with protective roles. Thus, we aimed to identify the relative contribution of tissue resident macrophages to PD induced inflammation in mice. Unexpectedly, we found an incremental loss of homeostatic characteristics, anti-inflammatory and efferocytic functionality in peritoneal resident macrophages, accompanied by enhanced inflammatory responses to external stimuli. Moreover, presence of glucose degradation products within the dialysis fluid led to markedly enhanced inflammation and almost complete disappearance of tissue resident cells. Thus, alterations in tissue resident macrophages may render longterm PD patients sensitive to developing peritonitis and consequently fibrosis/sclerosis.