bluuebunny/crossref_metadata_2025_split huggingface dataset:
A simple, inexpensive and multi-scale 3-D fluorescent test sample for optical sectioning microscopies
Authors: Olevsko Ilya , Szederkenyi Kaitlin , Corridon Jennifer , Au Aaron , Delhomme Brigitte , Bastien Thierry , Fernandes Julien , Yip Christopher , Oheim Martin , Salomon Adi 
Published: April 2021

ABSTRACTFluorescence standards allow for quality control and for the comparison of data sets across instruments and laboratories in applications of quantitative fluorescence. For example, users of microscopy core facilities expect a homogenous and time-invariant illumination and a uniform detection sensitivity, which are prerequisites for quantitative imaging analysis, particle tracking or fluorometric pH or Ca2+-concentration measurements. Similarly, confirming the three-dimensional (3-D) resolution of optical sectioning micro-scopes prior to volumetric reconstructions calls for a regular calibration with a standardised point source. Typically, the test samples required for such calibration measurements are different ones, and they depend much on the very microscope technique used. Also, the ever-increasing choice among these techniques increases the demand for comparison and metrology across instruments. Here, we advocate and demonstrate the multiple uses of a surprisingly versatile and simple 3-D test sample that can complement existing and much more expensive calibration samples: simple commercial tissue paper labelled with a fluorescent highlighter pen. We provide relevant sample characteristics and show examples ranging from the sub-µm to cm scale, acquired on epifluorescence, confocal, image scanning, two-photon (2P) and light-sheet microscopes.Graphical abstractPyranine-labeled tissue paper, imaged upon 405-nm epifluorescence excitation through a 455LP LP dichroic and 465LP emission filter. Objective ×20/NA0.25. Overlaid are the normalised absorbance (dashed) and emission spectra (through line), respectively. In the present work we show that this “primitive” and inexpensive three-dimensional (3-D) test sample is a surprisingly versatile and powerful tool for quality assessment, comparison across microscopes as well as routine metrology for optical sectioning techniques, both for research labs and imaging core facilities.Research highlights-highlighter-pen marked tissue paper is a surprisingly powerful and versatile test sample for 3-D fluorescence microscopies-standard tissue paper presents features ranging from 400 nm to centimetres-our sample can simultaneously be used for testing intensity, field homogeneity, resolution, optical sectioning and image contrast-it is easy to prepare, versatile, photostable and inexpensive
Cognitive impairment and metabolite profile alterations in the hippocampus and cortex of male and female mice exposed to a fat and sugar-rich diet are normalized by diet reversal
Authors: Garcia-Serrano Alba M. , Mohr Adélaïde A. , Spégel Peter , Duarte João M.N. 
Published: April 2021

AbstractDiabetes impacts on brain metabolism, structure and function. Alterations in brain metabolism have been observed in obesity and diabetes models induced by exposure to diets rich in saturated fat and/or sugar, and have been linked to memory impairment. However, it remains to be determined whether brain dysfunction induced by obesogenic diets results from permanent brain alterations. We tested the hypothesis that an obesogenic diet (high-fat and high-sucrose diet; HFHSD) causes reversible changes in hippocampus and cortex metabolism and alterations in behavior. To test this hypothesis, mice were exposed to HFHSD for 24 weeks or for 16 weeks followed by 8 weeks of diet normalization. Development of the metabolic syndrome, changes in behavior, and brain metabolite profiles by1H magnetic resonance spectroscopy (MRS) were assessed longitudinally. Control mice were fed an ingredient-matched low-fat and low-sugar diet. Mice fed a HFHSD developed obesity, glucose intolerance and insulin resistance, with a more severe phenotype in male than female mice. Relative to controls, both male and female HFHSD-fed mice showed increased anxiety-like behavior, impaired memory in object recognition tasks, but preserved working spatial memory as evaluated by spontaneous alternation in a Y-maze. Alterations in the metabolite profiles were observed both in the hippocampus and cortex, but were more distinct in the former. HFHSD-induced metabolic changes included altered levels of lactate, glutamate, GABA, glutathione, taurine,N-acetylaspartate, creatine and choline. Notably, HFHSD-induced metabolic syndrome, anxiety, memory impairment, and brain metabolic alterations recovered upon diet normalization for 8 weeks. We conclude that cortical and hippocampal derangements induced by long-term HFHSD consumption are reversible rather than being the result of permanent tissue damage.
Probabilistic solvers enable a straight-forward exploration of numerical uncertainty in neuroscience models
Authors: Oesterle Jonathan , Krämer Nicholas , Hennig Philipp , Berens Philipp 
Published: April 2021

AbstractUnderstanding neural computation on the mechanistic level requires models of neurons and neuronal networks. To analyze such models one typically has to solve coupled ordinary differential equations (ODEs), which describe the dynamics of the underlying neural system. These ODEs are solved numerically with deterministic ODE solvers that yield single solutions with either no, or only a global scalar bound on precision. It can therefore be challenging to estimate the effect of numerical uncertainty on quantities of interest, such as spike-times and the number of spikes. To overcome this problem, we propose to use recently developed sampling-based probabilistic solvers, which are able to quantify such numerical uncertainties. They neither require detailed insights into the kinetics of the models, nor are they difficult to implement. We show that numerical uncertainty can affect the outcome of typical neuroscience simulations, e.g. jittering spikes by milliseconds or even adding or removing individual spikes from simulations altogether, and demonstrate that probabilistic solvers reveal these numerical uncertainties with only moderate computational overhead.
QPromoters: Sequence based prediction of promoter strength inSaccharomyces cerevisiae
Authors: Liya Devang Haresh , Elanchezhian Mirudula , Pahari Mukulika , Anand Nithishwer Mouroug , Suresh Shivani , Balaji Nivedha , Jainarayanan Ashwin Kumar 
Published: April 2021

AbstractPromoters play a key role in influencing transcriptional regulation for fine-tuning expression of genes. Heterologous promoter engineering has been a widely used concept to control the level of transcription in all model organisms. The strength of a promoter is mainly determined by its nucleotide composition. Many promoter libraries have been curated but few have attempted to develop theoretical methods to predict the strength of promoters from its nucleotide sequence.Such theoretical methods are not only valuable in the design of promoters with specified strength, but are also meaningful to understand the mechanism of promoters in gene transcription. In this study, we present a theoretical model to describe the relationship between promoter strength and nucleotide sequence inSaccharomyces cerevisiae. We infer from our analysis that the −49 to 10 sequence with respect to the Transcription Start Site represents the minimal region that can be used to predict the promoter strength. We present an online toolhttps://qpromoters.com/that takes advantage of this fact to quickly quantify the strength of the promoters.
Plant detection and counting from high-resolution RGB images acquired from UAVs: comparison between deep-learning and handcrafted methods with application to maize, sugar beet, and sunflower
Authors: David Etienne , Daubige Gaëtan , Joudelat François , Burger Philippe , Comar Alexis , de Solan Benoit , Baret Frédéric 
Published: April 2021

AbstractProgresses in agronomy rely on accurate measurement of the experimentations conducted to improve the yield component. Measurement of the plant density is required for a number of applications since it drives part of the crop fate. The standard manual measurements in the field could be efficiently replaced by high-throughput techniques based on high-spatial resolution images taken from UAVs. This study compares several automated detection of individual plants in the images from which the plant density can be estimated. It is based on a large dataset of high resolution Red/Green/Blue (RGB) images acquired from Unmanned Aerial Vehicules (UAVs) during several years and experiments over maize, sugar beet and sunflower crops at early stages. A total of 16247 plants have been labelled interactively on the images. Performances of handcrafted method (HC) were compared to those of deep learning (DL). The HC method consists in segmenting the image into green and background pixels, identifying rows, then objects corresponding to plants thanks to knowledge of the sowing pattern as prior information. The DL method is based on the Faster Region with Convolutional Neural Network (Faster RCNN) model trained over 2/3 of the images selected to represent a good balance between plant development stage and sessions. One model is trained for each crop.Results show that simple DL methods generally outperforms simple HC, particularly for maize and sunflower crops. A significant level of variability of plant detection performances is observed between the several experiments. This was explained by the variability of image acquisition conditions including illumination, plant development stage, background complexity and weed infestation. The image quality determines part of the performances for HC methods which makes the segmentation step more difficult. Performances of DL methods are limited mainly by the presence of weeds. A hybrid method (HY) was proposed to eliminate weeds between the rows using the rules developed for the HC method. HY improves slightly DL performances in the case of high weed infestation. When few images corresponding to the conditions of the testing dataset were complementing the training dataset for DL, a drastic increase of performances for all the crops is observed, with relative RMSE below 5% for the estimation of the plant density.
Identification and Characterization of Human Activation-Induced ChAT+CD4+T Cells
Authors: Tarnawski L , Gallina AL , Kort EJ , Shavva VS , Zhuge Z , Martínez-Enguita D , Weiland M , Caravaca AS , Schmidt S , Wang FH , Färnert A , Weitzberg E , Gustafsson M , Eberhardson M , Hult H , Kehr J , Malin SG , Carlström M , Jovinge S , Olofsson PS 
Published: April 2021

AbstractVasodilation is a cornerstone of inflammation physiology. By regulating vasodilation and tissue entry of T cells, CD4+T lymphocytes expressing choline acetyltransferase (ChAT), a key enzyme for biosynthesis of the vasorelaxant acetylcholine (ACh), critically link immunity with vascular biology in mice. However, the characterization of primary human ChAT+T cells remained elusive. Here, we identified human ChAT+T cells and report thatChATmRNA was induced by activation. Functional studies demonstrated that T cell-derived ACh increased muscarinic ACh-receptor dependent NO-synthase activity and vasorelaxation. Further, single-cell RNA-sequencing revealedChAT+CD4+T cells in blood from patients with severe circulatory failure and a high relative frequency ofChAT+CD4+T cells correlated with better 30-day survival in this cohort. Our findings provide the first insights into ChAT biology in primary human T cells, linking ChAT+T cells with vasorelaxation as well as survival in a cohort of critically ill patients.
Molecular mechanism of proton-coupled ligand translocation by the bacterial efflux pump EmrE
Authors: Jurasz Jakub , Czub Jacek , Bagiński Maciej , Wieczór Miłosz 
Published: April 2021

AbstractThe current surge in bacterial multi-drug resistance (MDR) is one of the largest challenges to public health, threatening to render ineffective many therapies we rely on for treatment of serious infections. Understanding different factors that contribute to MDR is hence crucial from the global “one health” perspective. In this contribution, we focus on the prototypical broad-selectivity proton-coupled antiporter EmrE, one of the smallest known ligand transporters that confers resistance to aromatic cations in a number of clinically relevant species. As an asymmetric homodimer undergoing an “alternating access” protomer-swap conformational change, it serves as a model for the mechanistic understanding of more complex drug transporters. Here, we present a free energy and solvent accessibility analysis that indicates the presence of two complementary ligand translocation pathways that remain operative in a broad range of conditions. Our simulations show a previously undescribed desolvated apo state and anticorrelated accessibility in the ligand-bound state, explaining on a structural level why EmrE does not disrupt the pH gradient through futile proton transfer. By comparing the behavior of a number of model charged and/or aromatic ligands, we also explain the origin of selectivity of EmrE towards a broad class of aromatic cations. Finally, we explore unbiased pathways of ligand entry and exit to identify correlated structural changes implicated in ligand binding and release, as well as characterize key intermediates of occupancy changes.
Ppargdrives luminal differentiation and luminal tumor formation in the urothelium
Authors: Tate Tiffany , Xiang Tina , Zhou Mi , Kim William Y. , Chen Xiao , Kim Hyunwoo , Batourina Ekatherina , Lin Chyuan-Sheng , Lu Chao , Wobker Sara E. , Mckiernan James M. , Mendelsohn Cathy Lee 
Published: April 2021

AbstractPparg, a nuclear receptor, is downregulated in basal subtype bladder cancers that tend to be muscle invasive and amplified in luminal subtype bladder cancers that tend to be non-muscle invasive. Bladder cancers derive from the urothelium, one of the most quiescent epithelia in the body which is composed of basal, intermediate, and superficial cells. We find that expression of an activated form of Pparg (VP16;Pparg) in basal progenitors induces formation of superficial cells in situ, that exit the cell cycle, and do not form tumors. Expression in basal progenitors that have been activated by mild injury however, results in luminal tumor formation. We find that tumors are immune deserted, which may be linked to downregulation of Nf-kb, a Pparg target. Interestingly, some luminal tumors begin to shift to basal subtype tumors with time, downregulating Pparg and other luminal markers. Our findings have important implications for treatment and diagnosis bladder cancer.
Immune microenvironment subtypes and association with tumor cell mutations and antigen expression in follicular lymphoma
Authors: Han Guangchun , Deng Qing , Dai Enyu , Dang Minghao , Ma John , Yang Haopeng , Kudryashova Olga , Meerson Mark , Isaev Sergey , Kotlov Nikita , Nomie Krystle , Bagaev Alexander , Parmar Simrit , Hagemeister Fredrick , Ahmed Sairah , Iyer Swami , Samaniego Filepe , Steiner Raphael , Fayad Luis , Lee Hun , Fowler Nathan , Vega Francisco , Flowers Christopher R. , Strati Paolo , Westin Jason R. , Neelapu Sattva S. , Nastoupil Loretta J. , Wang Linghua , Green Michael R. 
Published: April 2021

AbstractFollicular lymphoma (FL) is a B-cell lymphoma with a complex tumor microenvironment that is rich in non-malignant immune cells. We applied single-cell RNA-sequencing to characterize the diverse tumor and immune cell populations of FL and identified major phenotypic subsets of FL T-cells including a novel cytotoxic CD4 T-cell population. Their relative proportions of T-cells defined four major FL subtypes, characterized by differential representation or relative depletion of distinct T-cell subsets. By integrating exome sequencing, we observed that somatic mutations are associated with, but not definitive for, reduced antigen presentation on FL cells. In turn, expression of MHC class II genes by FL cells was associated with significant differences in the proportions and targetable immunophenotypic characteristics. This provides a classification framework of the FL microenvironment, their association with FL genotypes and antigen presentation, and informs different potential immunotherapeutic strategies based upon tumor cell MHC class II expression.Statement of significanceWe have characterized the FL-infiltrating T-cells, identified cytotoxic CD4 T-cells as an important component, showed that the abundance of these T-cell populations is associated with tumor-cell-intrinsic characteristics, and identified sets of targetable immune checkpoints on T-cells that differed between FLs with normal versus low antigen presentation.
Evaluating performance management of COVID-19 reality in three European countries: a pragmatic constructivist study
Authors: Mitchell Falconer , Nørreklit Hanne , Nørreklit Lennart , Cinquini Lino , Koeppe Frederik , Magnacca Fabio , Mauro Sara Giovanna , Jakobsen Morten , Korhonen Tuomas , Laine Teemu , Liboriussen Jakob Mathias 
Published: April 2021

PurposeThe study aims to assess the COVID-19 event in three European countries (Germany, Italy and the UK) by investigating the quality of their performance management of it.Design/methodology/approachPragmatic constructivism (PC) is employed as a lens through which the performance management of each country can be examined and compared over a period encompassing the first wave of COVID-19.FindingsOfficial statistics show that one of the countries has a significantly lower death rate. It developed and operated a more detailed and precise system of performance management. From the perspective of PC, this system supported efforts to build a functioning reality construction integrating facts, possibilities, values and communication.Originality/valueThe evaluation of different national approaches to the performance management of the COVID-19 reality is novel to the literature on management accounting. PC is used as a diagnostic tool to pinpoint strengths and weaknesses of the performance management of public sector activities in different countries.
Occupants' perceived importance and satisfaction with the indoor environmental quality of a green building
Authors: Agyekum Kofi , Hammond Samuel Fiifi , Salgin Burcu 
Published: April 2021

PurposeThis study examines occupants' satisfaction with the indoor environmental quality (IEQ) of a green-certified building [The Green Star South Africa (SA) Building] in Ghana.Design/methodology/approachViews of 300 respondents are solicited on 15 IEQ (obtained through a critical review of the literature and complemented with a pilot interview on the subject) parameters. Data obtained are analysed using both descriptive and inferential statistics.FindingsFindings suggest that occupants are generally satisfied with five critical aspects of IEQ. The results also indicate that the occupants perceive five key IEQ parameters to have high levels of importance. Further inferential analysis of the parameters revealed that two core IEQs require the highest levels of improvement actions.Research limitations/implicationsThe study was conducted in Ghana and analysed occupants' perceptions of working within one green-certified building. Again, the collection of the occupants' responses was not linked with the direct measurement of physical characteristics of the IEQ parameters of the building. Hence, the findings cannot be generalised.Practical implicationsPractically, the study contributes to providing all stakeholders involved in the Green Star SA Ghana certification system with the relevant feedback for their decision-making on current and future projects to be certified under this certification system.Originality/valueThis study provides valuable information on the performance of IEQ parameters of the building and points out potential IEQ areas that need improvement efforts, especially concerning current and future facilities certified under this certification system.
Social entrepreneurship education: changemaker training at the university
Authors: García-González Abel , Ramírez-Montoya María Soledad 
Published: April 2021

PurposeThis study aims to contribute to the body of scientific knowledge about teaching and promoting social entrepreneurship in higher education institutions (HEIs) based on a measurement before and after concluding an educational experience.Design/methodology/approachIt tests hypotheses to draw conclusions from analyzing the pre- and post-test results of three study cases with different training experiences, to know the characteristics of the 304 participants.FindingsThe study indicated that incorporating transversal social entrepreneurship projects in various courses resulted in students feeling more capable regarding their social entrepreneurship potential.Originality/valueThe study presents the analysis of social entrepreneur training in three different curricular study cases. The information obtained adds value to social entrepreneurship education research that takes social entrepreneurship beyond business schools.
Essential employable skill sets in management graduates for finance job roles in India
Authors: Srinivasan Shruti , Thangaraj Ravikumar 
Published: April 2021

PurposeThere has been an increase in the number of highly qualified management graduates specialized in finance from various esteemed universities in India, thus increasing the competition for finance job roles in the country. This, therefore, brings in the need for the employees or the prospective candidates to mold their soft skills so as to make them desirable by the companies and hence employable. The purpose of this paper is to provide a list of skills required by management graduates to become employable for finance job roles from the perspective of corporate executives. This list will enable prospective candidates to prepare themselves for a career in the field of finance.Design/methodology/approachThe research was carried out through the collection of data from 117 finance professionals with a minimum work experience of 5 years with the help of structured questionnaires. This was then analyzed through factor analysis and the list of 15 factors was obtained.FindingsA list of 15 essential factors was obtained through the analysis of the data. The essential skills included empathetic and judicious behavior, professional etiquette and employee well-being, ethical behavior, conflict management, change analysis and prediction; practicality and organizational presence of mind; social and moral presence of mind; self-confidence and effective written communication; effective interpersonal communication and employee value systems; responsibility and self-awareness; problem diagnosis and problem-solving; real-time work and activity experience; professional development and advancement; technology rationalization and effective information generation. The findings also included that a candidate should be able to effectively present crucial information and should possess practical advisory skills.Originality/valueThe study will be highly beneficial for management graduates who have specialized in finance to secure finance job roles in India. This paper will enable the students to prepare themselves in the essential soft skills required for these job roles apart from technical knowledge and hard skills.