bluuebunny/crossref_metadata_2025_split huggingface dataset:
Fitness effects of CRISPR endonucleases inDrosophila melanogasterpopulations
Authors: Langmüller Anna M. , Champer Jackson , Lapinska Sandra , Xie Lin , Metzloff Matthew , Liu Jingxian , Xu Yineng , Clark Andrew G. , Messer Philipp W. 
Published: May 2021

AbstractCRISPR/Cas9 systems provide a highly efficient and flexible genome editing technology with numerous potential applications in areas ranging from gene therapy to population control. Some proposed applications involve CRISPR/Cas9 endonucleases integrated into an organism’s genome, which raises questions about potentially harmful effects to the transgenic individuals. One application where this is particularly relevant are CRISPR-based gene drives, which promise a mechanism for rapid genetic alteration of entire populations. The performance of such drives can strongly depend on fitness costs experienced by drive carriers, yet relatively little is known about the magnitude and causes of these costs. Here, we assess the fitness effects of genomic CRISPR/Cas9 expression inDrosophila melanogastercage populations by tracking allele frequencies of four different transgenic constructs, designed to disentangle direct fitness costs due to the integration, expression, and target-site activity of Cas9 from costs due to potential off-target cleavage. Using a maximum likelihood framework, we find a moderate level of fitness costs due to off-target effects but do not detect significant direct costs. Costs of off-target effects are minimized for a construct with Cas9HF1, a high-fidelity version of Cas9. We further demonstrate that using Cas9HF1 instead of standard Cas9 in a homing drive achieves similar drive conversion efficiency. Our results suggest that gene drives should be designed with high-fidelity endonucleases and may have implications for other applications that involve genomic integration of CRISPR endonucleases.
Beyond resting state neuronal avalanches in the somatosensory barrel cortex
Authors: Mariani B. , Nicoletti G. , Bisio M. , Maschietto M. , Oboe R. , Suweis S. , Vassanelli S. 
Published: May 2021

ABSTRACTSince its first experimental signatures, the so called ‘critical brain hypothesis’ has been extensively studied. Yet, its actual foundations remain elusive. According to a widely accepted teleological reasoning, the brain would be poised to a critical state to optimize the mapping of the noisy and ever changing real-world inputs, thus suggesting that primary sensory cortical areas should be critical. We investigated whether a single barrel column of the somatosensory cortex of the anesthetized rat displays a critical behavior. Neuronal avalanches were recorded across all cortical layers in terms of both spikes and population local field potentials, and their behavior during spontaneous activity compared to the one evoked by a controlled single whisker deflection. By applying a maximum likelihood statistical method based on timeseries undersampling to fit the avalanches distributions, we show that neuronal avalanches are power law distributed for both spikes and local field potentials during spontaneous activity, with exponents that are spread along a scaling line. Instead, after the tactile stimulus, activity switches to an across-layers synchronization mode that appears to dominate during cortical representation of the single sensory input.
Syntrophy between fermentative and purple phototrophic bacteria for carbohydrate-based wastewater treatment
Authors: Cerruti Marta , Crosset-Perrotin Guillaume , Ananth Mythili , Rombouts Jules L. , Weissbrodt David G. 
Published: May 2021

ABSTRACTFermentative chemoorganoheterotrophic bacteria (FCB) and purple photoorganoheterotrophic bacteria (PPB) are two interesting microbial guilds to process carbohydrate-rich wastewaters. Their interaction has been studied in axenic pure cultures or co-cultures. Little is known about their metabolic interactions in open cultures. We aimed to harness the competitive and syntrophic interactions between PPB and FCB in mixed cultures. We studied the effect of reactor regimes (batch or continuous, CSTR) and illumination modes (continuous irradiation with infrared light, dark, or light/dark diel cycles) on glucose conversions and the ecology of the process. In batch, FCB outcompeted (>80%) PPB, under both dark and infrared light conditions. In CSTR, three FCB populations of Enterobacteriaceae, Lachnospiraceae and Clostridiaceae were enriched (>70%), while Rhodobacteraceae relatives of PPB made 30% of the community. Fermentation products generated from glucose were linked to the dominant FCB. Continuous culturing at a dilution rate of 0.04 h-1 helped maintain FCB and PPB in syntrophy: FCB first fermented glucose into volatile fatty acids and alcohols, and PPB grew on fermentation products. Direct supply of carboxylates like acetate under infrared light enriched for PPB (60%) independent of reactor regimes. Ecological engineering of FCB- and PPB-based biorefineries can help treat and valorize carbohydrate-based waste feedstocks.GRAPHICAL ABSTRACT
Light at the end of the tunnel: FRAP assay reveals that plant vacuoles start as a tubular network
Authors: Minina Elena A. , Scheuring David , Askani Jana , Krueger Falco , Schumacher Karin 
Published: May 2021

AbstractPlant vacuoles play key roles in cellular homeostasis performing catabolic and storage functions, regulating pH and ion balance. The essential role of vacuoles for plant cell viability makes them a notoriously difficult subject to study impeding reaching the consensus on the mechanism of vacuolar establishment and the source of membrane material for it. Our previous suggestion of endoplasmic reticulum being the main membrane contributor for the tubular network of young vacuoles was recently challenged in a study proposing that young plant vacuoles comprise a set of individual vesicles that are formed de novo via homotypic fusion of multivesicular bodies (MVBs).To resolve these seemingly contradictory observations we have carefully revaluated both hypotheses. Here we provide a systematic overview of successive vacuolar biogenesis stages in Arabidopsis root, starting from the youngest cells proximate to the quiescent center. We validate our previous conclusions by demonstrating that the vacuolar dye BCECF is fully suitable for studying the organelle’s morphology and provide 3D models of vacuoles at all developmental stages. Furthermore, we established a customized FRAP assay and proved that even at the earliest stages of biogenesis, vacuoles comprise a connected network. Finally, we summarized the new and pre-existing evidence substantiating that vacuolar structures cannot originate solely from MVBs.
Data Independent Acquisition Mass Spectrometry of the Human Lens Enhances Spatiotemporal Measurement of Fiber Cell Aging
Authors: Cantrell Lee S , Schey Kevin L 
Published: May 2021

AbstractThe ocular lens proteome undergoes post-translational and progressive degradation as fiber cells age. The oldest fiber cells and the proteins therein are present at birth and are retained through death. Transparency of the lens is maintained in part by the high abundance crystallin family proteins (up to 300 mg/mL), which establishes a high dynamic range of protein abundance. As a result, previous Data Dependent Analysis (DDA) measurements of the lens proteome are less equipped to identify the lowest abundance proteins. In an attempt to probe more deeply into the lens proteome, we measured the insoluble lens proteome of an 18-year-old human with DDA and newer Data Independent Analysis (DIA) methods. By applying library free DIA search methods, 4,564 protein groups, 48,474 peptides and 5,577 deamidation sites were detected: significantly outperforming the quantity of identifications in using DDA and Pan-Human DIA library searches. Finally, by segmenting the lens into multiple fiber cell-age related regions, we uncovered cell-age resolved changes in proteome composition and putative function.
Paternal chromosome elimination and X non-disjunction on asymmetric spindles inSciaramale meiosis
Authors: de Saint Phalle Brigitte , Oldenbourg Rudolf , Kubai Donna F. , Salmon E. D. , Gerbi Susan A. 
Published: May 2021

ABSTRACTMeiosis in maleSciarais unique with a single centrosome. A monopolar spindle forms in meiosis I, but a bipolar spindle forms in meiosis II. The imprinted paternal chromosomes are eliminated in meiosis I; there is non-disjunction of the X in meiosis II. Despite differences in spindle construction and chromosome behavior, both meiotic divisions are asymmetric, producing a cell and a small bud. Observations of live spermatocytes made with the LC-PolScope, differential interference contrast optics and fluorescence revealed maternal and paternal chromosome sets on the monopolar spindle in meiosis I and formation of an asymmetric monastral bipolar spindle in meiosis II where all chromosomes except the X congress to the metaphase plate. The X remains near the centrosome after meiosis I and stays with it as the spindle forms in meiosis II. Electron microscopy revealed amorphous material between the X and the centrosome. Immunofluorescence with an antibody against the checkpoint protein Mad2 stains the centromeres of the maternal X dyad in late meiosis I and in meiosis II where it fails to congress to the metaphase plate. Mad2 is also present throughout the paternal chromosomes destined for elimination in meiosis I, suggesting a possible role in chromosome imprinting. If Mad2 on the X dyad mediates a spindle checkpoint in meiosis II, it may delay metaphase to facilitate formation of the second half spindle through a non-centrosomal mechanism.
Alkaline intracellular pH activates AMPK-mTORC2 signaling to promote cell survival during growth factor limitation
Authors: Kazyken D , Lentz SI , Fingar DC 
Published: May 2021

AbstractmTORC2 controls cell metabolism and promotes cell survival, yet its upstream regulation by diverse cellular cues remains poorly defined. While considerable evidence indicates that mTORC1 but not mTORC2 responds dynamically to amino acid levels, several studies reported activation of mTORC2 signaling by amino acids, a paradox that remains unresolved. Following amino acid starvation, we noted that addition of a commercial amino acid solution but not re-feeding with DMEM containing amino acids increased mTORC2 signaling. Interestingly, the pH of the amino acid solution was ∼ 10. These key observations enabled us to discover that alkaline intracellular pH (pHi) represents a previously unknown activator of mTORC2. Using a fluorescent pH-sensitive dye (cSNARF-1-AM) coupled to live-cell imaging, we demonstrate that alkaline extracellular pH (pHe) increases intracellular pHi, which increases mTORC2 catalytic activity and downstream signaling to Akt. Alkaline pHi also activates AMPK, a sensor of energetic stress. Functionally, alkaline pHi attenuates apoptosis caused by growth factor withdrawal, which requires AMPK in part and mTOR in full. Collectively, these findings reveal that alkaline pHi increases AMPK-mTORC2 signaling to promote cell survival during growth factor limitation. As elevated pHi represents an under-appreciated hallmark of cancer cells, alkaline pH sensing by AMPK-mTORC2 may contribute to tumorigenesis.One Sentence SummaryAlkaline intracellular pH activates mTORC2
Chromatin loading of MCM hexamers is associated with di-/tri-methylation of histone H4K20 toward S phase entry
Authors: Hayashi-Takanaka Yoko , Hayashi Yuichiro , Hirano Yasuhiro , Miyawaki-Kuwakado Atsuko , Ohkawa Yasuyuki , Obuse Chikashi , Kimura Hiroshi , Haraguchi Tokuko , Hiraoka Yasushi 
Published: May 2021

AbstractDNA replication is a key step in initiating cell proliferation. Loading hexameric complexes of minichromosome maintenance (MCM) helicase onto DNA replication origins during the G1 phase is essential for initiating DNA replication. Here, we examined MCM hexamer states during the cell cycle in human hTERT-RPE1 cells using multicolor immunofluorescence-based, single-cell plot analysis, and biochemical size fractionation. Experiments involving cell-cycle arrest at the G1 phase and release from the arrest revealed that a double MCM hexamer was formed via a single hexamer during G1 progression. A single MCM hexamer was recruited to chromatin in the early G1 phase. Another single hexamer was recruited to form a double hexamer in the late G1 phase. We further examined relationship between the MCM hexamer states and the methylation levels at lysine 20 of histone H4 (H4K20) and found that the double MCM hexamer state was correlated with di/trimethyl-H4K20 (H4K20me2/3). Inhibiting the conversion from monomethyl-H4K20 (H4K20me1) to H4K20me2/3 retained the cells in the single MCM hexamer state. Non-proliferative cells, including confluent cells or Cdk4/6 inhibitor-treated cells, also remained halted in the single MCM hexamer state. We propose that the single MCM hexamer state is a halting step in the determination of cell cycle progression.
Regulatory compliance and environmental sustainability practices of manufacturing entrepreneurial ventures in Uganda
Authors: Sendawula Kasimu , Turyakira Peter , Ikiror Cathy Mbidde , Bagire Vincent 
Published: May 2021

Purpose
The purpose of this paper is to establish whether all the dimensions of regulatory compliance matter for environmental sustainability practices of manufacturing small and medium entrepreneurial ventures (SMEVs) using evidence from Uganda.

Design/methodology/approach
This study is cross-sectional and correlational. Data was collected through a questionnaire survey of 106 manufacturing SMEVs. Data was analyzed using Statistical Package for Social Sciences (SPSS) version 23.

Findings
The results indicate that controls, legitimacy and deterrence do matter for environmental sustainability practices of the manufacturing SMEVs in Uganda, unlike social norms and values.

Originality/value
This study fosters the understanding of environmental sustainability practices, as it provides insights on whether all the dimensions of regulatory compliance do matter for environmental sustainability practices of manufacturing SMEVs in Uganda.
Entrepreneurial intentions on perceived behavioral control and personal attitude: moderated by structural support
Authors: Otchengco Jr. Alberto Magtoto , Akiate Yuri Walter Dulay 
Published: May 2021

Purpose
This study aims to explore the association between the tricycle drivers’ personal attitude and perceived behavioral control and their entrepreneurial intention. Moreover, the study was conducted to determine whether such a relationship is moderated by structural support.

Design/methodology/approach
A total of 349 tricycle drivers in the Philippines were randomly selected and served as the respondents of this study. To determine if there is a significant relationship between the variables, structural equation modeling was used.

Findings
Tricycle drivers denoted that the more positive their perceived behavior control and personal attitude is, the greater their entrepreneurial intention is likely to be. Hence, the relationship of perceived behavioral control and personal attitude on entrepreneurial intention is moderated by perceived structural support.

Originality/value
By learning individuals’ perceived behavioral control, personal attitude and their entrepreneurial intention of specific classes of people, specifically tricycle drivers, it is possible to assess the feasibility of entrepreneurial efforts initiated by the government even before it is implemented, avoiding wastage of both times, resources and effort.
University-industry collaborations in Pakistan: current challenges and future opportunities
Authors: Malik Khaleel , Bashir Tariq , Ali Tariq Mahmood 
Published: May 2021

Purpose
This paper aims to identify current challenges that hinder university–industry (U-I) collaboration in Pakistan and presents future opportunities for promoting such collaborations in developing countries.

Design/methodology/approach
This exploratory study presents new empirical evidence obtained from Pakistan via a questionnaire survey of 24 universities, 25 interviews with key stakeholders including industry managers and outputs from a high level workshop event.

Findings
Although there is limited evidence of U-I engagement in Pakistan, the findings show that a lack of coordination between government, universities and industrial firms has hindered knowledge transfer between universities and industry. Such steps as utilising intermediaries to help broker effective collaborations and building trust-based relationships can help in socialising these types of scientific activities.

Research limitations/implications
Any overall conclusions drawn from this exploratory study can only be tentative, as the findings represent a snapshot of current U-I collaboration initiatives in Pakistan.

Practical implications
Less stringent policy interventions from government entities, as well as more universities willing to invite industry input on their board of studies might enable co-development of some university curriculums with industry partners. U-I collaborations could also help to boost innovation efforts in developing country firms.

Originality/value
This paper also offers awareness into benefits of teaching activity collaboration with industry partners, which has been an under explored area of past U-I collaboration studies. The findings should be of interest for both innovation policy and higher education policy researchers.
Understanding the core elements of event portfolio strategy: lessons from Auckland and Dunedin
Authors: Antchak Vladimir , Lück Michael , Pernecky Tomas 
Published: May 2021

Purpose
An event portfolio is a vital part of economic and socio-cultural processes designed around the use of public events in cities and destinations around the world. The purpose of this paper is to suggest a new research framework for comparative studies of diverse event portfolio strategies.

Design/methodology/approach
The discussion in this paper is based on a review of the literature and content analysis of event strategies from two New Zealand cities: Auckland and Dunedin.

Findings
The paper suggests an empirically tested framework for exploring event portfolios. It entails such dimensions as the event portfolio strategy, event portfolio focus, portfolio objectives and evaluation tools and event portfolio configuration.

Originality/value
This exploratory research provides a comparative analysis of diverse portfolio contexts and offers insights on developing sustainable event strategies while considering diverse local contexts. Core conditions and processes shaping event portfolio design and management are evaluated and strategic factors articulated.
Justice in arbitration: the consumer perspective
Authors: Ghodoosi Farshad , Sharif Monica M. 
Published: May 2021

Purpose
Arbitration – a binding private third-party adjudication – has been the primary legal way for resolution of consumer disputes. Consumers, however, rarely use arbitration to resolve their disputes while evidence suggests that their disputes remain unresolved. Contrary to the current prevailing emphasis on who is winning in arbitration, this study aims to establish that consumers believe that the court is more just than arbitration, regardless of the outcome. This study further establishes that consumers’ perceived poor legitimacy and lack of familiarity, not cost calculation, are what drive their justice perception.

Design/methodology/approach
In three experimental studies, participants were presented with scenarios in which they were to envision themselves amid a consumer dispute. The scenarios were followed by survey questions that examined individuals’ perceptions of justice. Three mediating variables of legitimacy, cost and familiarity were also examined.

Findings
The results suggest that consumers hold a high perception of justice for court as opposed to arbitration. Even though a favorable outcome increases consumers’ perception of justice, the results suggest that consumers find courts to be fairer regardless of the outcome. Familiarity and legitimacy mediate this relationship, not cost.

Originality/value
Current research does not provide an adequate explanation for consumers’ underutilization of arbitration nor does it focus on correct factors. Studies in psychology and law primarily focus on ex post feelings of individuals after dispute resolution, ex post favorable outcomes and ex ante cost–benefit analysis. To the best of the authors’ knowledge, the present study for the first time analyzes ex ante consumer perception of justice.
A generalizable sentiment analysis method for creating a hotel dictionary: using big data on TripAdvisor hotel reviews
Authors: Bagherzadeh Sayeh , Shokouhyar Sajjad , Jahani Hamed , Sigala Marianna 
Published: May 2021

PurposeResearch analyzing online travelers’ reviews has boomed over the past years, but it lacks efficient methodologies that can provide useful end-user value within time and budget. This study aims to contribute to the field by developing and testing a new methodology for sentiment analysis that surpasses the standard dictionary-based method by creating two hotel-specific word lexicons.Design/methodology/approachBig data of hotel customer reviews posted on the TripAdvisor platform were collected and appropriately prepared for conducting a binary sentiment analysis by developing a novel bag-of-words weighted approach. The latter provides a transparent and replicable procedure to prepare, create and assess lexicons for sentiment analysis. This approach resulted in two lexicons (a weighted lexicon, L1 and a manually selected lexicon, L2), which were tested and validated by applying classification accuracy metrics to the TripAdvisor big data. Two popular methodologies (a public dictionary-based method and a complex machine-learning algorithm) were used for comparing the accuracy metrics of the study’s approach for creating the two lexicons.FindingsThe results of the accuracy metrics confirmed that the study’s methodology significantly outperforms the dictionary-based method in comparison to the machine-learning algorithm method. The findings also provide evidence that the study’s methodology is generalizable for predicting users’ sentiment.Practical implicationsThe study developed and validated a methodology for generating reliable lexicons that can be used for big data analysis aiming to understand and predict customers’ sentiment. The L2 hotel dictionary generated by the study provides a reliable method and a useful tool for analyzing guests’ feedback and enabling managers to understand, anticipate and re-actively respond to customers’ attitudes and changes. The study also proposed a simplified methodology for understanding the sentiment of each user, which, in turn, can be used for conducting comparisons aiming to detect and understand guests’ sentiment changes across time, as well as across users based on their profiles and experiences.Originality/valueThis study contributes to the field by proposing and testing a new methodology for conducting sentiment analysis that addresses previous methodological limitations, as well as the contextual specificities of the tourism industry. Based on the paper’s literature review, this is the first research study using a bag-of-words approach for conducting a sentiment analysis and creating a field-specific lexicon.