bluuebunny/crossref_metadata_2025_split huggingface dataset:
DIY caging apparatus to facilitate chronic and continuous stimulation or recording in an awake rodent
Authors: Enam Syed Faaiz , Kang Brian J. , Lyon Johnathan G. , Bellamkonda Ravi V. 
Published: December 2021

AbstractChronic stimulation of and recording from the brain and brain diseases can require expensive apparatus and tedious cycles of inducing rodents with anesthesia. To resolve this, we have designed and fabricated a low-cost (∼$75 vs. $450) DIY rodent caging apparatus consisting of commercially available and 3D-printed components. This apparatus is customizable and can be used to rapidly prototype devices with large rodent sample sizes. Importantly, it enables continuous and chronic stimulation of and recording from the brains of awake and freely moving rodents. It also opens the possibilities of trying complex paradigms of treatment (continuous, intermittent, variable, and chronic). We have successfully used this caging apparatus for chronic intratumoral hypothermia treatment and are currently using it while advancing electrotactic therapies.
isoformant: A visual toolkit for reference-free long-read isoform analysis at single-read resolution
Authors: Le Daniel D. , Stephenson William , Orcales Faye T. 
Published: December 2021

Abstractisoformant is an analytical toolkit for isoform characterization of Oxford Nanopore Technologies (ONT) long-transcript sequencing data (i.e. direct RNA and cDNA). Deployment of these tools using Jupyter Notebook enables interactive analysis of user-defined region-of-interest (ROI), typically a gene. The core module of isoformant clusters sequencing reads by k-mer density to generate isoform consensus sequences without the requirement for a reference genome or prior annotations. The inclusion of differential isoform usage hypothesis testing based on read distribution among clusters enables comparison across multiple samples. Here, as proof-of-principle, we demonstrate the utility of isoformant for analyzing isoform diversity of commercially-available isoform standard mixtures. isoformant is available here: https://github.com/danledinh/isoformant.
Large scale similarity search across digital reconstructions of neural morphology
Authors: Ljungquist Bengt , Akram Masood A. , Ascoli Giorgio A. 
Published: December 2021

AbstractMost functions of the nervous system depend on neuronal and glial morphology. Continuous advances in microscopic imaging and tracing software have provided an increasingly abundant availability of 3D reconstructions of arborizing dendrites, axons, and processes, allowing their detailed study. However, efficient, large-scale methods to rank neural morphologies by similarity to an archetype are still lacking. Using the NeuroMorpho.Org database, we present a similarity search software enabling fast morphological comparison of hundreds of thousands of neural reconstructions from any species, brain regions, cell types, and preparation protocols. We compared the performance of different morphological measurements: 1) summary morphometrics calculated by L-Measure, 2) persistence vectors, a vectorized descriptor of branching structure, 3) the combination of the two. In all cases, we also investigated the impact of applying dimensionality reduction using principal component analysis (PCA). We assessed qualitative performance by gauging the ability to rank neurons in order of visual similarity. Moreover, we quantified information content by examining explained variance and benchmarked the ability to identify occasional duplicate reconstructions of the same specimen. The results indicate that combining summary morphometrics and persistence vectors with applied PCA provides an information rich characterization that enables efficient and precise comparison of neural morphology. The execution time scaled linearly with data set size, allowing seamless live searching through the entire NeuroMorpho.Org content in fractions of a second. We have deployed the similarity search function as an open-source online software tool both through a user-friendly graphical interface and as an API for programmatic access.
Representational drift influences learning of a sensory cortical microstimulation task
Authors: Pancholi Ravi , Ryan Lauren , Peron Simon 
Published: December 2021

SUMMARYSensory cortical representations can be highly dynamic, raising the question of how representational stability impacts perception. We used volumetric two-photon calcium imaging to track neural activity as mice learned an optical microstimulation task. Mice were required to report the number of photostimulation pulses delivered to opsin-expressing neurons in layer 2/3 of primary vibrissal somatosensory cortex. We found that the amount of photostimulus-evoked activity could predict animal choice. Over the course of training, this photostimulus-evoked activity rapidly declined, particularly among highly photoresponsive neurons. Population activity levels across training were similar between animals that learned and those that did not. However, the photoresponsive population exhibited turnover both within and across behavioral sessions that was elevated among animals that failed to learn. Animals that failed to learn also exhibited a faster deterioration in stimulus decoding. Our results show that the rate at which sensory cortical representations change constrains learning and impacts behavior.
Mesoscale cortex-wide neural dynamics predict goal-directed, but not random actions in mice several seconds prior to movement
Authors: Mitelut C. , Zhang Y , Sekino Y , Boyd J , Bolanos F , Swindale N.V. , Silasi G , Saxena S , Murphy T.H. 
Published: December 2021

ABSTRACTVolition - the sense of control or agency over one’s voluntary actions - is widely recognized as the basis of both human subjective experience and natural behavior in non-human animals. Several human studies have found peaks in neural activity preceding voluntary actions, e.g. the readiness potential (RP), and some have shown upcoming actions could be decoded even before awareness. Others propose that random processes underlie and explain pre-movement neural activity. Here we seek to address these issues by evaluating whether pre-movement neural activity in mice contains structure beyond that present in random neural activity. Implementing a self-initiated water-rewarded lever pull paradigm in mice while recording widefield [Ca++] neural activity we find that cortical activity changes in variance seconds prior to movement and that upcoming lever pulls could be predicted between 3 to 5 seconds (or more in some cases) prior to movement. We found inhibition of motor cortex starting at approximately - 5sec prior to lever pulls and activation of motor cortex starting at approximately 2sec prior to a random unrewarded left limb movement. We show that mice, like humans, are biased towards commencing self-initiated actions during specific phases of neural activity but that the pre-movement neural code changes over time in some mice and is widely distributed as behavior prediction improved when using all vs single cortical areas. These findings support the presence of structured multi-second neural dynamics preceding self-initiated action beyond that expected from random processes. Our results also suggest that neural mechanisms underlying self-initiated action could be preserved between mice and humans.
Lipid hydroperoxides promote sarcopenia through carbonyl stress
Authors: Eshima Hiroaki , Shahtout Justin L. , Siripoksup Piyarat , Pearson MacKenzie J. , Mahmassani Ziad S. , Ferrara Patrick J. , Lyons Alexis W. , Maschek J. Alan , Peterlin Alek D. , Verkerke Anthony R. P. , Johnson Jordan M. , Salcedo Anahy , Petrocelli Jonathan J. , Miranda Edwin R. , Anderson Ethan J. , Boudina Sihem , Ran Qitao , Cox James E. , Drummond Micah J. , Funai Katsuhiko 
Published: December 2021

SummaryReactive oxygen species (ROS) accumulation is a cardinal feature of skeletal muscle atrophy. ROS refers to a collection of radical molecules whose cellular signals are vast, and it is unclear which downstream consequences of ROS are responsible for the loss of muscle mass and strength. Here we show that lipid hydroperoxides (LOOH) are increased with age and disuse, and the accumulation of LOOH by deletion of glutathione peroxidase 4 (GPx4) is sufficient to augment muscle atrophy. LOOH promoted atrophy in a lysosomal-dependent, proteasomal-independent manner. In young and old mice, genetic and pharmacologic neutralization of LOOH or their secondary reactive lipid aldehydes robustly prevented muscle atrophy and weakness, indicating that LOOH-derived carbonyl stress mediate age- and disuse-induced muscle dysfunction. Our findings provide novel insights for the role of LOOH in sarcopenia including a therapeutic implication by pharmacologic suppression.
Hepatocyte-specific activity of TSC22D4 triggers progressive NAFLD by impairing mitochondrial function
Authors: Wolff Gretchen , Sakurai Minako , Mhamane Amit , Maida Adriano , Deligiannis Ioannis K. , Yin Kelvin , Weber Peter , Weider Annika , Troullinaki Maria , Zeigerer Anja , Roden Michael , Volk Nadine , Poth Tanja , Hackert Thilo , Wiedmann Lena , De Angelis Rigotti Francesca , Rodriguez-Vita Juan , Fischer Andreas , Mukthavaram Rajesh , Limphong Pattraranee , Tachikawa Kiyoshi , Karmali Priya , Payne Joseph , Chivukula Padmanabh , Ekim-Üstünel Bilgen , Martinez-Jimenez Celia P. , Szendrödi Julia , Nawroth Peter , Herzig Stephan 
Published: December 2021

ABSTRACTObjectiveFibrotic organ responses have recently been identified as long-term complication in diabetes. Indeed, insulin resistance and aberrant hepatic lipid accumulation represent driving features of progressive non-alcoholic fatty liver disease (NAFLD), ranging from simple steatosis and non-alcoholic steatohepatitis (NASH) to fibrosis. Effective pharmacological regimens to stop progressive liver disease are still lacking to-date.MethodsBased on our previous discovery of transforming growth factor beta-like stimulated clone (TSC)22D4 as a key driver of insulin resistance and glucose intolerance in obesity and type 2 diabetes, we generated a TSC22D4-hepatocyte specific knockout line (TSC22D4-HepaKO) and exposed mice to control or NASH diet models. Mechanistic insights were generated by metabolic phenotyping and single cell liver sequencing.ResultsHepatic TSC22D4 expression was significantly correlated with markers of liver disease progression and fibrosis in both murine and human livers. Indeed, hepatic TSC22D4 levels were elevated in human NASH patients as well as in several murine NASH models. Specific genetic deletion of TSC22D4 in hepatocytes led to reduced liver lipid accumulation, improvements in steatosis and inflammation scores and decreased apoptosis in mice. Single cell RNA sequencing revealed a distinct gene signature identifying an upregulation of mitochondrial-related processes. An enrichment of genes involved in the TCA cycle, mitochondrial organization, and triglyceride metabolism underscored the hepatocyte-protective phenotype and overall decreased liver damage as seen in mouse models.ConclusionsTogether, our data uncover a new connection between targeted depletion of TSC22D4 and intrinsic metabolic processes in progressive liver disease. Cell-specific reduction of TSC22D4 improves hepatic steatosis, inflammation and promotes hepatocyte survival thus paving the way for further preclinical therapy developments.
Cerebellar associative learning underlies skilled reach adaptation
Authors: Calame Dylan J. , Becker Matthew I. , Person Abigail L. 
Published: December 2021

AbstractCerebellar output has been shown to enhance movement precision by scaling the decelerative phase of reaching movements in mice. We hypothesized that during reach, initial kinematics cue late-phase adjustments through cerebellar associative learning. We identify a population-level response in mouse PCs that scales inversely with reach velocity, suggesting a candidate mechanism for anticipatory control to target limb endpoint. We next interrogate how such a response is generated by combining high-density neural recordings with closed-loop optogenetic stimulation of cerebellar mossy fiber afferents originating in the pontine nuclei during reach, using perturbation schedules reminiscent of classic adaptation paradigms. We found that reach kinematics and PC electrophysiology adapt to position-locked mossy fiber perturbations and exhibit aftereffects when stimulation is removed. Surprisingly, we observed partial adaptation to position-randomized stimulation schedules but no opposing aftereffect. A model that recapitulated these findings provided novel insight into how the cerebellum deciphers cause-and-effect relationships to adapt.
Identification and characterization of the WYL BrxR protein and its gene as separable regulatory elements of a BREX phage restriction system
Authors: Luyten Yvette A. , Hausman Deanna E. , Young Juliana C. , Doyle Lindsey A. , Higashi Kerilyn M. , Ubilla-Rodriquez Natalia C. , Lambert Abigail R. , Arroyo Corina S. , Forsberg Kevin J. , Morgan Richard D. , Stoddard Barry L. , Kaiser Brett K. 
Published: December 2021

ABSTRACTBacteriophage exclusion (‘BREX’) phage restriction systems are found in a wide range of bacteria. Various BREX systems encode unique combinations of proteins that usually include a site-specific methyltransferase; none appear to contain a nuclease. Here we describe the identification and characterization of a Type I BREX system from Acinetobacter and the effect of deleting each BREX ORF on growth, methylation, and restriction. We identified a previously uncharacterized gene in the BREX operon that is dispensable for methylation but involved in restriction. Biochemical and crystallographic analyses of this factor, which we term BrxR (‘BREX Regulator’), demonstrate that it forms a homodimer and specifically binds a DNA target site upstream of its transcription start site. Deletion of the BrxR gene causes cell toxicity, reduces restriction, and significantly increases the expression of BrxC. In contrast, the introduction of a premature stop codon into the BrxR gene, or a point mutation blocking its DNA binding ability, has little effect on restriction, implying that the BrxR coding sequence and BrxR protein play independent functional roles. We speculate that the BrxR coding sequence is involved in cis regulation of anti-phage activity, while the BrxR protein plays an additional regulatory role, perhaps during horizontal transfer.
Insights into the organic labelling effect: the special case of wine
Authors: Macht Janine , Klink-Lehmann Jeanette , Piqueras-Fiszman Betina , Hartmann Monika 
Published: December 2021

PurposeWhile research shows that organic labels are perceived positively for most food products, the findings are more ambiguous for wine. This may be due to the complexity of the product. Accordingly, the labelling effect might be influenced by people's prior knowledge of wines and their attitudes towards organic wines and thus be more pronounced for certain consumer groups. Providing insights into those moderators could help to steer people towards sustainable wine consumption. Therefore, this paper aims to investigate the effect of organic labelling on consumers' liking of, and their willingness to pay (WTP) for white wine, and the role of potential moderators.Design/methodology/approachA wine tasting experiment was conducted using a within-subjects design (n = 214). The mediating role of expected liking and the moderating roles of subjective knowledge and attitude towards organic wine were analysed using the MEMORE macro in SPSS.FindingsThe results do not confirm an overall positive halo effect of labelling on liking of organic wine. Nevertheless, a positive halo effect on actual liking was observed for those respondents who have a positive attitude towards organic wine. Furthermore, an overall positive effect of organic labelling on WTP was found. Mediation effects could not be confirmed.Originality/valueThis study used an experimental design that considers not only expected liking but also actual liking and WTP for organic wines. Using a moderation-mediation framework helps to better understand consumers' quality evaluation and WTP for organic wine. Finally, it could be shown that the organic halo is more complex for the product category of wine than others have previously stated.
Development of a knowledge scale for nutrients of tropical and traditional fruits
Authors: Ozgen Leyla , Güllü Mehmet , Ozturk Elif Esra 
Published: December 2021

PurposeThe aim of this study is to develop a knowledge scale for nutrients of tropical and traditional fruits for university students and conduct its validity and reliability. Another purpose of the study is to determine whether or not the students' knowledge mean scores about nutrients of tropical and traditional fruits vary based on their demographic information.Design/methodology/approachThe design of the study was the survey model. While the population consisted of 1,551 students studying in the faculty of health sciences, Gazi University, the sample consisted of 668 students who were determined based on criterion sampling.FindingsWhen examining in terms of gender of the students, it was determined that even though mean score of the knowledge scale for nutritional values of tropical and traditional fruits was slightly higher in female students (X¯ = 8.12) than male students (X¯ = 7.71), there was an insignificant difference between them (t(666) = 1.25, p > 0.05). A significant difference was determined between the students' knowledge mean scores of the knowledge scale for nutritional values of tropical and traditional fruits in terms of residence place (t(666) = 2.86, p < 0.5). While the nutritional value mean score of the students residing in Ankara was low (X¯ = 7.67), the nutritional value mean score of the students residing out of Ankara was high (X¯ = 8.58).Originality/valueWhen the scale developed in this study is analysed according to demographic information, it can be asserted that the students had knowledge about the nutrients of tropical and traditional fruits. Although tropical fruits are expensive, they still prefer these fruits. It can be stated that the students had knowledge about the diversity, nutritional compounds and antioxidant content of tropical and traditional fruits.
The determinants of ESG in the banking sector of MENA region: a trend or necessity?
Authors: El Khoury Rim , Nasrallah Nohade , Alareeni Bahaaeddin 
Published: December 2021

Purpose
As reporting environmental, social and governance (ESG) information is not yet mandatory in all countries, it is intriguing to understand ESG’s underlying driving mechanisms. This study aims to investigate ESG determinants in the banking sector of the Middle East and North Africa countries.

Design/methodology/approach
The authors gather data for 38 listed banks for the period 2011–2019. The data used is threefold as follows: data related to ESG; firm-level; and country-level data. While ESG and firm’s level data are taken from Refinitiv, country-level data are extracted from the World Bank. Using panel regression, the authors test the effect of firm- and country-specific variables on the overall ESG score and its pillars.

Findings
Results indicate that banks’ ESG scores are negatively affected by performance and positively affected by size. The level of economic development exerts a negative impact on the environmental pillar while the social development exerts a positive impact on ESG and governance pillar. Corruption is the only country-level that gathers a homogenous effect on ESG scores. Finally, the three pillars follow heterogeneous patterns.

Originality/value
This study extends the scope of previous studies by introducing new country-level independent variables to contribute to the understanding of ESG antecedents.
Tackling organizational innovativeness through strategic orientation: strategic alignment and moderating role of strategic flexibility
Authors: Nassani Abdelmohsen A. , Aldakhil Abdullah Mohammed 
Published: December 2021

PurposeThe purpose of the research was to examine the effect of strategic orientation on organizational innovativeness of small and medium enterprises (SMEs). Moreover, in order to highlight the constructive role of strategic orientation, the study also observes the intervening role of strategic alignment and moderating role of strategic flexibility.Design/methodology/approachData were collected from 209 owner/managers of SMEs through self-administered questionnaires. Descriptive statistics, correlation and hierarchical regression were used for testing the study hypotheses.FindingsResults revealed that strategic orientation is positively related to SMEs innovativeness. Strategic alignment mediates between the strategic orientation and innovativeness link. Furthermore, the findings also established that the association between strategic orientation and strategic alignment is stronger when SMEs are strategically flexible.Originality/valueOrganizational innovativeness is of vital importance for SMEs strength, especially in the context of developing economies. Although researchers have acknowledged several antecedents of SMEs innovativeness, however, it is still unclear how strategic orientation influences organizational innovativeness. Moreover, the study focuses on another important element of strategic alignment through the integration of goals and strategies to achieve innovativeness.
The role of healthcare supply chain management in the wake of COVID-19 pandemic: hot off the press
Authors: Sriyanto Sriyanto , Lodhi Muhammad Saeed , Salamun Hailan , Sardin Sardin , Pasani Chairil Faif , Muneer Gulnaz , Zaman Khalid 
Published: December 2021

Purpose
The study aims to examine the role of health-care supply chain management during the COVID-19 pandemic in a cross-section of 42 selected sub-Saharan African (SSA) countries.

Design/methodology/approach
The study used cross-sectional robust least square regression for parameter estimates.

Findings
The results confirmed the N-shaped relationship between the health-care logistics performance index (HLPI) and COVID-19 cases. It implies that initially HLPI increases along with an increase in COVID-19 cases. Later down, it decreases COVID-19 cases by providing continued access to medical devices and personal protective equipment. Again, it increases due to resuming economic activities across countries.

Practical implications
The continuing health-care supply chain is crucial to minimize COVID-19 cases. The international support from the developed world in providing health-care equipment, debt resettlement and resolving regional conflicts is deemed desirable to escape the SSA countries from the COVID-19 pandemic.

Originality/value
The importance of the health-care supply chain during the COVID-19 pandemic is evident in the forecasting estimates, which shows that from August 2021 to April 2022, increasing the health-care supply chain at their third-degree level would reduce coronavirus registered cases. The results conclude that SSA countries required more efforts to contain coronavirus cases by thrice increasing their health-care logistics supply chain.