bluuebunny/crossref_metadata_2025_split huggingface dataset:
A simple high efficiency and low costin vitrogrowth system for phenotypic characterization and seed propagation ofArabidopsis thaliana
Authors: Pasternak Taras , Ruperti Benedetto , Palme Klaus 
Published: August 2020

ABSTRACTBackgroundArabidopsis research relies extensively on the use ofin vitrogrowth for phenotypic analysis of the seedlings and characterization of plant responses to intrinsic and extrinsic cues. For this purpose, stress-free optimal growth conditions should be set up and used as a reference especially in studies aimed at characterizing the plant responses to abiotic and biotic stresses. Currently used standardin vitroprotocols for growth and characterization ofArabidopsis thalianaplants often suffer from sub-optimal composition due to an excessively high nutritional content which represents a stress per se and an experimental bias.ResultsWe describe a simple protocol forin vitrogrowth of Arabidopsis plants in which the phenotypic analysis is based on an optimized and nutritionally balanced culture medium. We show that the protocol is robustly applicable for growth of several Arabidopsis mutants, including mutants lacking the root system. This protocol enables rapid high scale seed productionin vitroavoiding soil usage while saving space and time. The optimizedin vitroprotocol aims at: 1) makingin vitrogrowth as close as possible to natural soil conditions by optimizing nutrient balance in the medium; 2) simplifying phenotypic and molecular investigation of individual plants by standardizing all steps of plant growth; 3) enabling seeds formation also in genotypes with severe defect in the root system; 4) minimizing the amount of waste and space for plant growth by avoiding soil usage.ConclusionsHere we report an optimized protocol for optimal growth ofArabidopsis thalianaplants to avoid biases in phenotypic observation of abiotic/biotic stress experiments. The protocol also enables the completion of the whole life cyclein vitrowithin 40-45 days and a satisfactory seed set for further propagation with no need for facilities for plant growth in soil and seed sterilisation.
Focal Electrical Stimulation of Human Retinal Ganglion Cells for Vision Restoration
Authors: Madugula Sasidhar S. , Gogliettino Alex R. , Zaidi Moosa , Aggarwal Gorish , Kling Alexandra , Shah Nishal P. , Vilkhu Ramandeep , Hays Madeline R. , Nguyen Huy , Fan Victoria , Wu Eric G. , Hottowy Pawel , Sher Alexander , Litke Alan M. , Silva Ruwan A. , Chichilnisky E.J. 
Published: August 2020

ABSTRACTVision restoration with retinal implants that electrically stimulate retinal ganglion cells (RGCs), which transmit visual information to the brain, is limited by indiscriminate activation of many cells and cell types. Recent work in isolated macaque retina has demonstrated that direct electrical stimulation of RGCs can be performed with single-cell, single-spike resolution. However, the fidelity of epiretinal stimulation has not been examined in the human retina. Here, electrical activation of the major RGC types was examined using large-scale, multi-electrode recording and stimulation in the human retinaex vivoand compared directly to results from macaque. Targeted activation with single-cell, single-spike resolution was often possible without activating overlying axon bundles, at low stimulation current levels similar to those in macaque. Distinct cell types could be identified and targeted based on their distinct electrical signatures. Simulation based on these measurements revealed that a novel, dynamic stimulation approach would produce a nearly optimal evoked visual signal. These results indicate that high-fidelity control of spiking in human RGCs is achievable with extracellular stimulation and that the macaque retina is an accurate model for vision restoration with epiretinal implants.
pMAT: An Open-Source, Modular Software Suite for the Analysis of Fiber Photometry Calcium Imaging
Authors: Bruno Carissa A. , O’Brien Chris , Bryant Svetlana , Mejaes Jennifer , Pizzano Carina , Estrin David J. , Barker David J. 
Published: August 2020

AbstractThe combined development of new technologies for neuronal recordings and the development of novel sensors for recording both cellular activity and neurotransmitter binding has ushered in a new era for the field of neuroscience. Among these new technologies is fiber photometry, a technique wherein an implanted fiber optic is used to record signals from genetically encoded fluorescent sensors in bulk tissue. Fiber photometry has been widely adapted due to its cost-effectiveness, ability to examine the activity of neurons with specific anatomical or genetic identities, and the ability to use these highly modular systems to record from one or more sensors or brain sites in both superficial and deep-brain structures. Despite these many benefits, one major hurdle for laboratories adopting this technique is the steep learning curve associated with the analysis of fiber photometry data. This has been further complicated by a lack of standardization in analysis pipelines. In the present communication, we present pMAT, a ‘photometry modular analysis tool’ that allows users to accomplish common analysis routines through the use of a graphical user interface. This tool can be deployed in MATLAB and edited by more advanced users, but is also available as an independently deployable, open-source application.
Neuron-class specific responses govern adaptive remodeling of myelination in the neocortex
Authors: Yang Sung Min , Michel Katrin , Jokhi Vahbiz , Nedivi Elly , Arlotta Paola 
Published: August 2020

AbstractMyelination plasticity plays a critical role in neurological function, including learning and memory. However, it is unknown whether this plasticity is enacted through uniform changes across all neuronal subtypes, or whether myelin dynamics vary between neuronal classes to enable fine-tuning of adaptive circuit responses. We performedin vivotwo-photon imaging to investigate the dynamics of myelin sheaths along single axons of both excitatory callosal projection neurons and inhibitory parvalbumin+interneurons in layer 2/3 of adult mouse visual cortex. We find that both neuron types show dynamic, homeostatic myelin remodeling under normal vision. However, monocular deprivation results in experience-dependent adaptive myelin remodeling only in parvalbumin+interneurons, but not in callosal projection neurons. Monocular deprivation induces an initial increase in elongation events in myelin segments of parvalbumin+interneurons, followed by a contraction phase affecting a separate cohort of segments. Sensory experience does not alter the generation rate of new myelinating oligodendrocytes, but can recruit pre-existing oligodendrocytes to generate new myelin sheaths. Parvalbumin+interneurons also show a concomitant increase in axonal branch tip dynamics independent from myelination events. These findings suggest that adaptive myelination is part of a coordinated suite of circuit reconfiguration processes, and demonstrate that distinct classes of neocortical neurons individualize adaptive remodeling of their myelination profiles to diversify circuit tuning in response to sensory experience.
Size matters: optimal mask diameter and box size for single-particle cryogenic electron microscopy
Authors: Moriya Toshio , Adachi Naruhiko , Kawasaki Masato , Yamada Yusuke , Shinoda Akira , Koiwai Kotaro , Yumoto Fumiaki , Senda Toshiya 
Published: August 2020

AbstractRecently it has been demonstrated that single-particle cryogenic electron microscopy (cryo-EM) at 200 keV is capable of determining protein structures, including those smaller than 100 kDa, at sub-3.0 Å resolutions, without using significant defocus or a phase plate. However, the majority of near-atomic resolution cryo-EM structures has been determined using 300 keV. Consequently, many typical parameter settings for the cryo-EM computational image processing steps, especially those associated with the contrast transfer function, are based on the accumulated experience of 300 kV cryo-EM. We have therefore revised these parameters, established theoretical bases for criteria to find an optimal mask diameter and box size for a given dataset irrespective of acceleration voltage or protein size, and proposed a protocol. Considering the defocus distributions of the datasets, merely optimizing the mask diameters and box sizes yielded meaningful resolution improvements for the reconstruction of < 200 kDa proteins using 200 kV cryo-EM.
Calling small variants with universality and Bayesian-frequentist hybridism
Authors: Zhao Xiaofei , Hu Allison , Wang Sizhen , Wang Xiaoyue 
Published: August 2020

AbstractThe accuracy of variant calling is crucially important in clinical settings, as the misdiagnosis of a genetic disease such as cancer can compromise patient survival. Although many variant callers were developed, variant-calling accuracy is still insufficient for clinical applications.Here we describe UVC, a method for calling small variants of germline or somatic origin. By combining contrary assumptions with sublation, we found two principles to improve variant calling. First, we discovered the following power-law universality: allele fraction is inversely proportional to the cubic root of variant-calling error rate. Second, we found that zero inflation can combine Bayesian and frequentist models of sequencing bias.We evaluated UVC with other state-of-the-art variant callers by considering a variety of calling modes (germline, somatic, tumor-only, and cell-free DNA with unique molecular identifiers (UMIs)), sequencing platforms (Illumina, BGI, and IonTorrent), sequencing types (whole-genome, whole-exome, and PCR-amplicon), human reference genomes (hg19, hs37d5, and GRCh38), aligners (BWA and NovoAlign), and representative sequencing depths and purities for both tumor and normal. UVC generally outperformed other germline variant callers on the GIAB germline truth sets. UVC strongly outperformed other somatic variant callers on 192 scenarios ofin silicomixtures simulating 192 combinations of tumor/normal sequencing depths and tumor/normal purities. UVC strongly outperformed other somatic variant callers on the GIAB somatic truth sets derived from physical mixture and on the SEQC2 somatic reference sets derived from the breast-cancer cell-line HCC1395. UVC achieved 100% concordance with the manual review conducted by multiple independent researchers on a Qiagen 71-gene-panel dataset derived from 16 patients with colon adenoma. Additionally, UVC outperformed Mageri and smCounter2, the state-of-the-art UMI-aware variant callers, on the tumor-only datasets used for publishing these two variant callers. Performance is measured by using sensitivity-specificity trade off for all called variants. The improved variant calls generated by UVC from previously published UMI-based sequencing data are able to provide additional biological insight about DNA damage repair.UVC enables highly accurate calling of small variants from a variety of sequencing data, which can directly benefit patients in clinical settings. UVC is open-sourced under the BSD 3-Clause license athttps://github.com/genetronhealth/uvcandquay.io/genetronhealth/gcc-6-3-0-uvc-0-6-0-441a694.
Deviation of Dyar’s rule in the post-embryonic development in millipedes – a comprehensive analysis
Authors: Bhakat Somnath 
Published: August 2020

AbstractDyar’s value on the basis of length and width of nine polydesmid and 15 non-polydesmid millipede species were calculated. The value of polydesmid millipede ranged from 1.50 to 1.78 and that of non-polydesmid millipede ranged from 1.08 to 1.45. Weight progression factor was determined for nine species of millipede (two polydesmid and seven non-polydesmids). The result showed that the mean weight progression factor in polydesmid is 2.54 while that of non-polydesmid is 1.95. Both the results showed that Dyar’s value in polydesmida is significantly higher compared to that of non-polydesmida. In polydesmida, the number of stadium is only eight with higher Dyar’s value (mean 1.61) while in non-polydesmida, where number of stadium is more than eight have lower Dyar’s value (mean 1.23). As in other arthropods, Dyar’s value is inversely proportional to the number of stadium in millipede.The present study also affirmed Enders’ hypothesis in favour of adaptive importance of Dyar’s rule. Deviations from Dyar’s constant in these two group also support Crossby’s growth rule. The variation of Dyar’s value in these two groups of millipede is related to the development time and habitat utilization. The variation of weight progression factor in these two groups is also linked to the development time as observed in other arthropods.
MRE11 is crucial for malaria transmission and its absence affects expression of interconnected networks of key genes essential for life
Authors: Guttery David S. , Ramaprasad Abhinay , Ferguson David J. P. , Zeeshan Mohammad , Pandey Rajan , Brady Declan , Holder Anthony A. , Pain Arnab , Tewari Rita 
Published: August 2020

AbstractTheMeioticRecombination 11 protein (MRE11) plays a key role in DNA damage response and maintenance of genome stability. However, little is known about its function during development of the malaria parasitePlasmodium. Here, we present a functional, ultrastructural and transcriptomic analysis ofPlasmodiumMRE11 during its life-cycle in both mammalian and mosquito vector hosts. Genetic disruption ofPlasmodium berghei mre11(PbMRE11) results in significant retardation of oocyst development in the mosquito midgut associated with cytoplasmic and nuclear degeneration, along with concomitant ablation of sporogony and subsequent parasite transmission. Further, absence of PbMRE11 results in significant transcriptional downregulation of genes involved in key interconnected biological processes that are fundamental to all eukaryotic life including ribonucleoprotein biogenesis, spliceosome function and iron-sulphur cluster assembly. Overall, our study provides a comprehensive functional analysis of MRE11’s role inPlasmodiumdevelopment during the mosquito stages and offers a potential target for therapeutic intervention during malaria parasite transmission.
Dynamic hormone control of stress and fertility
Authors: Zavala Eder , Voliotis Margaritis , Zerenner Tanja , Tabak Joël , Walker Jamie J , Li Xiao Feng , Terry John R , Lightman Stafford L , O’Byrne Kevin , Tsaneva-Atanasova Krasimira 
Published: August 2020

ABSTRACTNeuroendocrine axes display a remarkable diversity of dynamic signalling processes relaying information between the brain, endocrine glands, and peripheral target tissues. These dynamic processes include oscillations, elastic responses to perturbations, and plastic long term changes observed from the cellular to the systems level. While small transient dynamic changes can be considered physiological, larger and longer disruptions are common in pathological scenarios involving more than one neuroendocrine axes, suggesting that a robust control of hormone dynamics would require the coordination of multiple neuroendocrine clocks. The idea of apparently different axes being in fact exquisitely intertwined through neuroendocrine signals can be investigated in the regulation of stress and fertility. The stress response and the reproductive cycle are controlled by the Hypothalamic-Pituitary-Adrenal (HPA) axis and the Hypothalamic-Pituitary-Gonadal (HPG) axis, respectively. Despite the evidence surrounding the effects of stress on fertility, as well as of the reproductive cycle on stress hormone dynamics, there is a limited understanding on how perturbations in one neuroendocrine axis propagate to the other. We hypothesize that the links between stress and fertility can be better understood by considering the HPA and HPG axes as coupled systems. In this manuscript, we investigate neuroendocrine rhythms associated to the stress response and reproduction by mathematically modelling the HPA and HPG axes as a network of interlocked oscillators. We postulate a network architecture based on physiological data and use the model to predict responses to stress perturbations under different hormonal contexts: normal physiological, gonadectomy, hormone replacement with estradiol or corticosterone (CORT), and high excess CORT (hiCORT) similar to hypercortisolism in humans. We validate our model predictions against experiments in rodents, and show how the dynamic responses of these endocrine axes are consistent with our postulated network architecture. Importantly, our model also predicts the conditions that ensure robustness of fertility to stress perturbations, and how chronodisruptions in glucocorticoid hormones can affect the reproductive axis’ ability to withstand stress. This insight is key to understand how chronodisruption leads to disease, and to design interventions to restore normal rhythmicity and health.
Cortical activity evoked by voice pitch changes: a combined fNIRS and EEG study
Authors: Steinmetzger Kurt , Megbel Esther , Shen Zhengzheng , Andermann Martin , Rupp André 
Published: August 2020

ABSTRACTNumerous studies have investigated the cortical representation and time course of responses to auditory signals with and without pitch. However, little is known regarding the responses evoked by pitch changes. To study the spatial as well as temporal characteristics of cortical activity elicited by voice pitch changes, combined functional near-infrared spectroscopy (fNIRS) and electroencephalography (EEG) data were obtained from normal-hearing listeners presented with continuous vowel sequences in which the prosodic contours either varied between the individual vowels or were the same throughout. The fNIRS topographies and the EEG source reconstructions indicated additional right-hemispheric activity anterior to the primary auditory cortex and in the superior temporal sulcus for sequences with variable prosody. Additionally, the time courses of the fNIRS signals showed that activity was more sustained in response to sequences with changing prosodic contours. The EEG data revealed a similar pattern for the P2 amplitude, which was smaller during the second half for blocks with fixed prosody, whereas the P1 was consistently larger for sequences with variable prosody. Moreover, the sources of the P2, but not the P1, were lateralised to the right, suggesting that the hemispheric asymmetry in the processing of voice pitch changes develops over time.
Designing enhanced labeling information to increase consumer willingness to pay for genetically modified foods
Authors: Zhan Jintao , Ma Yubei , Deng Pengcheng , Li Yinqiu , Xu Meng , Xiong Hang 
Published: August 2020

PurposeThe regulations for qualitative genetically modified (GM) food labeling do not effectively eliminate the information asymmetries pertaining to the consumption of GM products. China's GM food labeling law requires the presentation of certain categories of GM products on GMO labels on packages. Such information is invaluable for understanding whether the disclosure of more information on GM foods can help alleviate information asymmetry while reducing consumer fear and risk perceptions of GM foods, and thus cause changes in their behaviors. The purpose of this paper is to explore the heterogeneity of consumer preferences for enhanced GM food labeling, how consumer preferences are influenced by labeling information, and how these preferences vary in different consumers.Design/methodology/approachBoth descriptive statistics and econometric techniques, including the multivariate ordered Probit model, were applied to a sample of 566 urban consumers in the Yangtze River Delta region of China. All respondents were divided into two groups: people who would definitely not buy GM foods before selecting enhanced labeling information (“consumer group 1”, sample size 282) and people who would definitely not object to buying GM foods before selecting enhanced labeling information (“consumer group 2”, sample size 274).FindingsThe findings suggest that urban consumers have a preference for different types of enhanced labeling information about GM foods, that such a preference significantly influences their willingness to pay for GM foods, that there exists a large difference in the preferences of different consumer groups, and that enhanced GM food labeling information has a greater impact on those consumers who would not accept GM foods.Originality/valueThis research identifies the GM information disclosures that most affect consumer preferences and how these preferences vary across different segments of consumers, which is a current gap in the literature. The study has demonstrated that enhanced labels of GM foods with diverse information would not alter a consumer's WTP for GM foods who does not perceive the value of information from the enhanced labels, but change positively consumers with uncertainty willingness to pay before disclosure.
Why competitive productivity sometimes goes too far: a multilevel evolutionary model of “karoshi”
Authors: Timming Andrew R. 
Published: August 2020

PurposeThe aim of this paper is to outline an innovative multilevel conceptual model capable of explaining “karoshi” (death from overwork) and its relationship to molecular-, micro-, meso- and macro-competitive productivity (CP).Design/methodology/approachA theoretical model, grounded in the evolutionary biological, psychological, organizational and sociological literatures, is provided.FindingsKaroshi is a function of molecular (genetic), micro (individual), meso (organizational) and macro (cultural) evolutionary forces. It is also demonstrated to be a function of time, geography, agri-climate and cultural and ethnic homogeneity.Research limitations/implicationsThe analysis is purely theoretical and its theoretically informed hypotheses are not tested empirically. As such, further data-driven research is indicated. Additional analyses are also needed to further unpack the recursive nature of the relationship between karoshi and CP and the subtle differences between genetic evolution and cultural and organizational evolution.Practical implicationsKaroshi-related deaths are a public health epidemic and increasingly a major obstacle to sustainable CP. As such, organizations can leverage these analyses to help them implement interventions aimed at reducing incidents of work-related deaths, not only in Japan, but across the world.Originality/valueThis multilevel conceptual framework makes a unique contribution to the cross-cultural and strategic management literatures. More specifically, it constitutes a new and innovative contribution to one’s current understanding of CP by uniquely integrating biology, psychology, organization studies and cultural studies into one overarching model.