bluuebunny/crossref_metadata_2025_split huggingface dataset:
Tuning charge transport dynamics via clustering of doping in organic semiconductor thin films
Authors: Boyle Connor J. , Upadhyaya Meenakshi , Wang Peijian , Renna Lawrence A. , Lu-Díaz Michael , Pyo Jeong Seung , Hight-Huf Nicholas , Korugic-Karasz Ljiljana , Barnes Michael D. , Aksamija Zlatan , Venkataraman D. 
Published: July 2019

AbstractA significant challenge in the rational design of organic thermoelectric materials is to realize simultaneously high electrical conductivity and high induced-voltage in response to a thermal gradient, which is represented by the Seebeck coefficient. Conventional wisdom posits that the polymer alone dictates thermoelectric efficiency. Herein, we show that doping — in particular, clustering of dopants within conjugated polymer films — has a profound and predictable influence on their thermoelectric properties. We correlate Seebeck coefficient and electrical conductivity of iodine-doped poly(3-hexylthiophene) and poly[2,5-bis(2-octyldodecyl)pyrrolo[3,4-c]pyrrole-1,4(2H,5H)-dione-3,6-diyl)-alt-(2,2′;5′,2′′;5′′,2′′′-quaterthiophen-5,5′′′-diyl)] films with Kelvin probe force microscopy to highlight the role of the spatial distribution of dopants in determining overall charge transport. We fit the experimental data to a phonon-assisted hopping model and found that the distribution of dopants alters the distribution of the density of states and the Kang–Snyder transport parameter. These results highlight the importance of controlling dopant distribution within conjugated polymer films for thermoelectric and other electronic applications.
Modular one-pot assembly of CRISPR arrays enables library generation and reveals factors influencing crRNA biogenesis
Authors: Liao Chunyu , Ttofali Fani , Slotkowski Rebecca A. , Denny Steven R. , Cecil Taylor D. , Leenay Ryan T. , Keung Albert J. , Beisel Chase L. 
Published: July 2019

AbstractCRISPR-Cas systems inherently multiplex through CRISPR arrays—whether to defend against different invaders or mediate multi-target editing, regulation, imaging, or sensing. However, arrays remain difficult to generate due to their reoccurring repeat sequences. Here, we report a modular, one-pot scheme called CRATES to construct CRISPR arrays and array libraries. CRATES allows assembly of repeat-spacer subunits using defined assembly junctions within the trimmed portion of spacers. Using CRATES, we construct arrays for the single-effector nucleases Cas9, Cas12a, and Cas13a that mediated multiplexed DNA/RNA cleavage and gene regulation in cell-free systems, bacteria, and yeast. CRATES further allows the one-pot construction of array libraries and composite arrays utilized by multiple Cas nucleases. Finally, array characterization reveals processing of extraneous CRISPR RNAs from Cas12a terminal repeats and sequence- and context-dependent loss of RNA-directed nuclease activity via global RNA structure formation. CRATES thus can facilitate diverse multiplexing applications and help identify factors impacting crRNA biogenesis.
PRC1 collaborates with SMCHD1 to fold the X-chromosome and spread Xist RNA between chromosome compartments
Authors: Wang Chen-Yu , Colognori David , Sunwoo Hongjae , Wang Danni , Lee Jeannie T. 
Published: July 2019

AbstractX-chromosome inactivation triggers fusion of A/B compartments to inactive X (Xi)-specific structures known as S1 and S2 compartments. SMCHD1 then merges S1/S2s to form the Xi super-structure. Here, we ask how S1/S2 compartments form and reveal that Xist RNA drives their formation via recruitment of Polycomb repressive complex 1 (PRC1). Ablating Smchd1 in post-XCI cells unveils S1/S2 structures. Loss of SMCHD1 leads to trapping Xist in the S1 compartment, impairing RNA spreading into S2. On the other hand, depleting Xist, PRC1, or HNRNPK precludes re-emergence of S1/S2 structures, and loss of S1/S2 compartments paradoxically strengthens the partition between Xi megadomains. Finally, Xi-reactivation in post-XCI cells can be enhanced by depleting both SMCHD1 and DNA methylation. We conclude that Xist, PRC1, and SMCHD1 collaborate in an obligatory, sequential manner to partition, fuse, and direct self-association of Xi compartments required for proper spreading of Xist RNA.
Locus coeruleus-CA1 projections are involved in chronic depressive stress-induced hippocampal vulnerability to transient global ischaemia
Authors: Zhang Qian , Hu Dian Xing , He Feng , Li Chun Yang , Qi Guang Jian , Cai Hong Wei , Li Tong Xia , Ming Jie , Zhang Pei , Chen Xiao Qian , Tian Bo 
Published: July 2019

AbstractDepression and transient ischaemic attack represent the common psychological and neurological diseases, respectively, and are tightly associated. However, studies of depression-affected ischaemic attack have been limited to epidemiological evidences, and the neural circuits underlying depression-modulated ischaemic injury remain unknown. Here, we find that chronic social defeat stress (CSDS) and chronic footshock stress (CFS) exacerbate CA1 neuron loss and spatial learning/memory impairment after a short transient global ischaemia (TGI) attack in mice. Whole-brain mapping of direct outputs of locus coeruleus (LC)-tyrosine hydroxylase (TH, Th:) positive neurons reveals that LC-CA1 projections are decreased in CSDS or CFS mice. Furthermore, using designer receptors exclusively activated by designer drugs (DREADDs)-based chemogenetic tools, we determine that Th:LC-CA1 circuit is necessary and sufficient for depression-induced aggravated outcomes of TGI. Collectively, we suggest that Th:LC-CA1 pathway plays a crucial role in depression-induced TGI vulnerability and offers a potential intervention for preventing depression-related transient ischaemic attack.
A genetically encoded probe for imaging nascent and mature HA-tagged proteins in vivo
Authors: Zhao Ning , Kamijo Kouta , Fox Philip D. , Oda Haruka , Morisaki Tatsuya , Sato Yuko , Kimura Hiroshi , Stasevich Timothy J. 
Published: July 2019

AbstractTo expand the toolbox of imaging in living cells, we have engineered a single-chain variable fragment binding the linear HA epitope with high affinity and specificity in vivo. The resulting probe, called the HA frankenbody, can light up in multiple colors HA-tagged nuclear, cytoplasmic, membrane, and mitochondrial proteins in diverse cell types. The HA frankenbody also enables state-of-the-art single-molecule experiments in living cells, which we demonstrate by tracking single HA-tagged histones in U2OS cells and single mRNA translation dynamics in both U2OS cells and neurons. Together with the SunTag, we also track two mRNA species simultaneously to demonstrate comparative single-molecule studies of translation can now be done with genetically encoded tools alone. Finally, we use the HA frankenbody to precisely quantify the expression of HA-tagged proteins in developing zebrafish embryos. The versatility of the HA frankenbody makes it a powerful tool for imaging protein dynamics in vivo.
Gate-reflectometry dispersive readout and coherent control of a spin qubit in silicon
Authors: Crippa A. , Ezzouch R. , Aprá A. , Amisse A. , Laviéville R. , Hutin L. , Bertrand B. , Vinet M. , Urdampilleta M. , Meunier T. , Sanquer M. , Jehl X. , Maurand R. , De Franceschi S. 
Published: July 2019

AbstractSilicon spin qubits have emerged as a promising path to large-scale quantum processors. In this prospect, the development of scalable qubit readout schemes involving a minimal device overhead is a compelling step. Here we report the implementation of gate-coupled rf reflectometry for the dispersive readout of a fully functional spin qubit device. We use a p-type double-gate transistor made using industry-standard silicon technology. The first gate confines a hole quantum dot encoding the spin qubit, the second one a helper dot enabling readout. The qubit state is measured through the phase response of a lumped-element resonator to spin-selective interdot tunneling. The demonstrated qubit readout scheme requires no coupling to a Fermi reservoir, thereby offering a compact and potentially scalable solution whose operation may be extended above 1 K.
Adult stem cell deficits drive Slc29a3 disorders in mice
Authors: Nair Sreenath , Strohecker Anne M. , Persaud Avinash K. , Bissa Bhawana , Muruganandan Shanmugam , McElroy Craig , Pathak Rakesh , Williams Michelle , Raj Radhika , Kaddoumi Amal , Sparreboom Alex , Beedle Aaron M. , Govindarajan Rajgopal 
Published: July 2019

AbstractMutations exclusively in equilibrative nucleoside transporter 3 (ENT3), the only intracellular nucleoside transporter within the solute carrier 29 (SLC29) gene family, cause an expanding spectrum of human genetic disorders (e.g., H syndrome, PHID syndrome, and SHML/RDD syndrome). Here, we identify adult stem cell deficits that drive ENT3-related abnormalities in mice. ENT3 deficiency alters hematopoietic and mesenchymal stem cell fates; the former leads to stem cell exhaustion, and the latter leads to breaches of mesodermal tissue integrity. The molecular pathogenesis stems from the loss of lysosomal adenosine transport, which impedes autophagy-regulated stem cell differentiation programs via misregulation of the AMPK-mTOR-ULK axis. Furthermore, mass spectrometry-based metabolomics and bioenergetics studies identify defects in fatty acid utilization, and alterations in mitochondrial bioenergetics can additionally propel stem cell deficits. Genetic, pharmacologic and stem cell interventions ameliorate ENT3-disease pathologies and extend the lifespan of ENT3-deficient mice. These findings delineate a primary pathogenic basis for the development of ENT3 spectrum disorders and offer critical mechanistic insights into treating human ENT3-related disorders.
Adipocyte β-arrestin-2 is essential for maintaining whole body glucose and energy homeostasis
Authors: Pydi Sai P. , Jain Shanu , Tung Wesley , Cui Yinghong , Zhu Lu , Sakamoto Wataru , Jain Shalini , Abel Brent S. , Skarulis Monica C. , Liu Jie , Huynh Thanh , Pacak Karel , Caron Marc G. , Gavrilova Oksana , Finkel Toren , Wess Jürgen 
Published: July 2019

Abstractβ-Arrestins are major regulators of G protein-coupled receptor-mediated signaling processes. Their potential roles in regulating adipocyte function in vivo remain unexplored. Here we report the novel finding that mice lacking β-arrestin-2 (barr2) selectively in adipocytes show significantly reduced adiposity and striking metabolic improvements when consuming excess calories. We demonstrate that these beneficial metabolic effects are due to enhanced signaling through adipocyte β3-adrenergic receptors (β3-ARs), indicating that barr2 represents a potent negative regulator of adipocyte β3-AR activity in vivo. Interestingly, essentially all beneficial metabolic effects caused by adipocyte barr2 deficiency are absent in adipocyte barr2-PRDM16 double KO mice, indicating that the metabolic improvements caused by the lack of barr2 in adipocytes are mediated by the browning/beiging of white adipose tissue. Our data support the novel concept that ‘G protein-biased’ β3-AR agonists that do not promote β3-AR/barr2 interactions may prove useful for the treatment of obesity and related metabolic disorders.
A dataset of egg size and shape from more than 6,700 insect species
Authors: Church Samuel H. , Donoughe Seth , de Medeiros Bruno A. S. , Extavour Cassandra G. 
Published: July 2019

AbstractOffspring size is a fundamental trait in disparate biological fields of study. This trait can be measured as the size of plant seeds, animal eggs, or live young, and it influences ecological interactions, organism fitness, maternal investment, and embryonic development. Although multiple evolutionary processes have been predicted to drive the evolution of offspring size, the phylogenetic distribution of this trait remains poorly understood, due to the difficulty of reliably collecting and comparing offspring size data from many species. Here we present a dataset of 10,449 morphological descriptions of insect eggs, with records for 6,706 unique insect species and representatives from every extant hexapod order. The dataset includes eggs whose volumes span more than eight orders of magnitude. We created this dataset by partially automating the extraction of egg traits from the primary literature. In the process, we overcame challenges associated with large-scale phenotyping by designing and employing custom bioinformatic solutions to common problems. We matched the taxa in this dataset to the currently accepted scientific names in taxonomic and genetic databases, which will facilitate the use of these data for testing pressing evolutionary hypotheses in offspring size evolution.
A multimodal dataset of human gait at different walking speeds established on injury-free adult participants
Authors: Schreiber Céline , Moissenet Florent 
Published: July 2019

AbstractHuman motion capture is used in various fields to analyse, understand and reproduce the diversity of movements that are required during daily-life activities. The proposed dataset of human gait has been established on 50 adults healthy and injury-free for lower and upper extremities in the most recent six months, with no lower and upper extremity surgery in the last two years. Participants were asked to walk on a straight level walkway at 5 speeds during one unique session: 0–0.4 m.s−1, 0.4–0.8 m.s−1, 0.8–1.2 m.s−1, self-selected spontaneous and fast speeds. Three dimensional trajectories of 52 reflective markers spread over the whole body, 3D ground reaction forces and moment, and electromyographic signals were simultaneously recorded. For each participants, a minimum of 3 trials per condition have been made available in the dataset for a total of 1143 trials. This dataset could increase the sample size of similar datasets, lead to analyse the effect of walking speed on gait or conduct unusual analysis of gait thanks to the full body markerset used.
Exotic Halophila stipulacea is an introduced carbon sink for the Eastern Mediterranean Sea
Authors: Apostolaki Eugenia T. , Vizzini Salvatrice , Santinelli Veronica , Kaberi Helen , Andolina Cristina , Papathanassiou Evangelos 
Published: July 2019

AbstractCarbon and nitrogen storage in exotic Halophila stipulacea were compared to that in native Posidonia oceanica and Cymodocea nodosa meadows and adjacent unvegetated sediments of the Eastern Mediterranean Sea and to that in native H. stipulacea of the Red Sea at sites with different biogeochemical conditions and level of human pressure. Exotic H. stipulacea possessed considerable storing capacity, with 2-fold higher Corg stock (0.71 ± 0.05 kg m−2 in the top 20 cm of sediment) and burial (14.78 gCorg m−2 y−1) than unvegetated areas and C. nodosa meadows and, surprisingly, comparable to P. oceanica. N (0.07 ± 0.01 kg m−2) and Cinorg (14.06 ± 8.02 kg m−2) stocks were similar between H. stipulacea and C. nodosa or unvegetated sediments, but different to P. oceanica. Corg and N stocks were higher in exotic than native H. stipulacea populations. Based on isotopic mixing model, organic material trapped in H. stipulacea sediments was mostly allochthonous (seagrass detritus 17% vs seston 67%). Corg stock was similar between monospecific and invaded C. nodosa meadows by H. stipulacea. Higher stocks were measured in the higher human pressure site. H. stipulacea introduction may contribute in the increase of carbon sequestration in the Eastern Mediterranean.
An optimised tissue disaggregation and data processing pipeline for characterising fibroblast phenotypes using single-cell RNA sequencing
Authors: Waise Sara , Parker Rachel , Rose-Zerilli Matthew J. J. , Layfield David M. , Wood Oliver , West Jonathan , Ottensmeier Christian H. , Thomas Gareth J. , Hanley Christopher J. 
Published: July 2019

AbstractSingle-cell RNA sequencing (scRNA-Seq) provides a valuable platform for characterising multicellular ecosystems. Fibroblasts are a heterogeneous cell type involved in many physiological and pathological processes, but remain poorly-characterised. Analysis of fibroblasts is challenging: these cells are difficult to isolate from tissues, and are therefore commonly under-represented in scRNA-seq datasets. Here, we describe an optimised approach for fibroblast isolation from human lung tissues. We demonstrate the potential for this procedure in characterising stromal cell phenotypes using scRNA-Seq, analyse the effect of tissue disaggregation on gene expression, and optimise data processing to improve clustering quality. We also assess the impact of in vitro culture conditions on stromal cell gene expression and proliferation, showing that altering these conditions can skew phenotypes.
Membrane mediated motor kinetics in microtubule gliding assays
Authors: Lopes Joseph , Quint David A. , Chapman Dail E. , Xu Melissa , Gopinathan Ajay , Hirst Linda S. 
Published: July 2019

AbstractMotor-based transport mechanisms are critical for a wide range of eukaryotic cell functions, including the transport of vesicle cargos over long distances. Our understanding of the factors that control and regulate motors when bound to a lipid substrate is however incomplete. We used microtubule gliding assays on a lipid bilayer substrate to investigate the role of membrane diffusion in kinesin-1 on/off binding kinetics and thereby transport velocity. Fluorescence imaging experiments demonstrate motor clustering on single microtubules due to membrane diffusion in the absence of ATP, followed by rapid ATP-induced dissociation during gliding. Our experimental data combined with analytical modeling show that the on/off binding kinetics of the motors are impacted by diffusion and, as a consequence, both the effective binding and unbinding rates for motors are much lower than the expected bare rates. Our results suggest that motor diffusion in the membrane can play a significant role in transport by impacting motor kinetics and can therefore function as a regulator of intracellular transport dynamics.
The Route to ‘Chemobrain’ - Computational probing of neuronal LTP pathway
Authors: Fahim Ammad , Rehman Zaira , Bhatti Muhammad Faraz , Virk Nasar , Ali Amjad , Rashid Amir , Paracha Rehan Zafar 
Published: July 2019

AbstractChemotherapy causes deleterious side effects during the course of cancer management. The toxic effects may be extended to CNS chronically resulting in altered cognitive function like learning and memory. The present study follows a computational assessment of 64 chemotherapeutic drugs for their off-target interactions against the major proteins involved in neuronal long term potentiation pathway. The cancer chemo-drugs were subjected to induced fit docking followed by scoring alignment and drug-targets interaction analysis. The results were further probed by electrostatic potential computation and ligand binding affinity prediction of the top complexes. The study identified novel off-target interactions by Dactinomycin, Temsirolimus, and Everolimus against NMDA, AMPA, PKA and ERK2, while Irinotecan, Bromocriptine and Dasatinib were top interacting drugs for CaMKII. This study presents with basic foundational knowledge regarding potential chemotherapeutic interference in LTP pathway which may modulate neurotransmission and synaptic plasticity in patient receiving these chemotherapies.
Visuospatial task-related prefrontal activity is correlated with negative symptoms in schizophrenia
Authors: Curtin Adrian , Sun Junfeng , Zhao Qiangfeng , Onaral Banu , Wang Jijun , Tong Shanbao , Ayaz Hasan 
Published: July 2019

AbstractControl of attention is thought to be specifically impaired in schizophrenia due to abnormal function in the prefrontal cortex (PFC). The PFC plays a critical role in the identification of relevant stimuli and the development of appropriate biases for the identified signals, including selection of an appropriate attentional ‘zoom’. We examined how demands associated with changes in attentional requirements in a Sustained Attention Task (SAT) may contribute to differences in functional involvement of the PFC and relation to clinical status. A group of 24 individuals with schizophrenia and 16 healthy controls (N = 40) performed the SAT and a visuospatial condition (vSAT) while activity in the bilateral anterior PFC was monitored using functional Near Infrared Spectroscopy (fNIRS). The results confirm that the right frontopolar region plays a role in control of attention for both patients and healthy controls. However, patients with schizophrenia exhibited a general attentional deficit and inefficient right-medial PFC activation. Additionally, we observed a strong regional association between left Middle Frontal Gyrus (MFG) activity during the vSAT task and the PANSS score driven by the negative symptom subscale. The presence of aberrant activation differences within the left-MFG region may describe a dysregulation of attentional networks linked to the clinical expression of negative and general symptoms.
Precipitation Biases in CMIP5 Models over the South Asian Region
Authors: Pathak Raju , Sahany Sandeep , Mishra Saroj Kanta , Dash S. K. 
Published: July 2019

AbstractUsing data from 33 models from the CMIP5 historical and AMIP5 simulations, we have carried out a systematic analysis of biases in total precipitation and its convective and large-scale components over the south Asian region. We have used 23 years (1983–2005) of data, and have computed model biases with respect to the PERSIANN-CDR precipitation (with convective/large-scale ratio derived from TRMM 3A12). A clustering algorithm was applied on the total, convective, and large-scale precipitation biases seen in CMIP5 models to group them based on the degree of similarity in the global bias patterns. Subsequently, AMIP5 models were analyzed to conclude if the biases were primarily due to the atmospheric component or due to the oceanic component of individual models. Our analysis shows that the set of individual models falling in a given group is somewhat sensitive to the variable (total/convective/large-scale precipitation) used for clustering. Over the south Asian region, some of the convective and large-scale precipitation biases are common across groups, emphasizing that although on a global scale the bias patterns may be sufficiently different to cluster the models into different groups, regionally, it may not be true. In general, models tend to overestimate the convective component and underestimate the large-scale component over the south Asian region, although with spatially varying magnitudes depending on the model group. We find that the convective precipitation biases are largely governed by the closure and trigger assumptions used in the convection parameterization schemes used in these models, and to a lesser extent on details of the individual cloud models. Using two different methods: (i) clustering, (ii) comparing the bias patterns of models from CMIP5 with their AMIP5 counterparts, we find that, in general, the atmospheric component (and not the oceanic component through biases in SSTs and atmosphere-ocean feedbacks) plays a major role in deciding the convective and large-scale precipitation biases. However, the oceanic component has been found important for one of the convective groups in deciding the convective precipitation biases (over the maritime continent).