bluuebunny/crossref_metadata_2025_split huggingface dataset:
Does the use of intraoperative CT scan improve outcomes in Orthopaedic surgery? A protocol for systematic review and meta-analysis
Authors: Kumar Vishal , Baburaj Vishnu , Patel Sandeep , Sharma Siddhartha , Vaishya Raju 
Published: March 2021

AbstractBackgroundIntraoperative 3D imaging is a valuable tool to visualise complex anatomical structures and position implants optimally. This is an emerging technology and there is a paucity in literature of articles describing the same.ObjectivesThis systematic review aims to compare the outcome of surgeries done under 3D imaging to those done under 2D fluoroscopy by analysing the evidence in literature.MethodsA systematic review will be conducted adhering to the PRISMA guidelines. Electronic databases of PubMed, Embase and Scopus will be searched with a pre-defined search string. A manual search will also be conducted on the references of the included articles. Original research articles published in English that directly compare the outcomes of intraoperative 3D imaging with fluoroscopy will be included. Review articles, conference abstracts and animal studies will be excluded. Outcome measures will be extracted from the selected studies and analysed with the help of appropriate software.
Increased Resistance of SARS-CoV-2 Variant P.1 to Antibody Neutralization
Authors: Wang Pengfei , Casner Ryan G. , Nair Manoj S. , Wang Maple , Yu Jian , Cerutti Gabriele , Liu Lihong , Kwong Peter D. , Huang Yaoxing , Shapiro Lawrence , Ho David D. 
Published: March 2021

SUMMARYThe relative resistance of SARS-CoV-2 variants B.1.1.7 and B.1.351 to antibody neutralization has been described recently. We now report that another emergent variant from Brazil, P.1, is not only refractory to multiple neutralizing monoclonal antibodies, but also more resistant to neutralization by convalescent plasma (3.4 fold) and vaccinee sera (3.8-4.8 fold). The cryo-electron microscopy structure of a soluble prefusion-stabilized spike reveals the P.1 trimer to adopt exclusively a conformation in which one of the receptor-binding domains is in the “up” position, with the functional impact of mutations appearing to arise from local changes instead of global conformational alterations. The P.1 variant threatens current antibody therapies but less so the protective efficacy of our vaccines.
The Disease-Associated ProteinsDrosophilaNab2 and Ataxin-2 Interact with Shared RNAs and Coregulate Neuronal Morphology
Authors: Rounds J. Christopher , Corgiat Edwin B. , Ye Changtian , Behnke Joseph A. , Kelly Seth M. , Corbett Anita H. , Moberg Kenneth H. 
Published: March 2021

ABSTRACTNab2encodes a conserved polyadenosine RNA-binding protein (RBP) with broad roles in post-transcriptional regulation, including in poly(A) RNA export, poly(A) tail length control, transcription termination, and mRNA splicing. Mutation of theNab2human orthologZC3H14gives rise to an autosomal recessive intellectual disability, but understanding of Nab2/ZC3H14 function in metazoan nervous systems is limited, in part because no comprehensive identification of metazoan Nab2/ZC3H14-associated RNA transcripts has yet been conducted. Moreover, many Nab2/ZC3H14 functional protein partnerships likely remain unidentified. Here we present evidence thatDrosophila melanogasterNab2 interacts with the RBP Ataxin-2 (Atx2), a neuronal translational regulator, and implicate these proteins in coordinate regulation of neuronal morphology and adult viability. We then present the first high-throughput identifications of Nab2- and Atx2-associated RNAs inDrosophilabrain neurons using an RNA immunoprecipitation-sequencing (RIP-Seq) approach. Critically, the RNA interactomes of each RBP overlap, and Nab2 exhibits high specificity in its RNA associations in neuronsin vivo, associating with a small fraction of all polyadenylated RNAs. The identities of shared associated transcripts (e.g.drk,me31B,stai) and of transcripts specific to Nab2 or Atx2 (e.g.Arpc2,tea, respectively) promise insight into neuronal functions of and interactions between each RBP. Significantly, Nab2-associated RNAs are overrepresented for internal A-rich motifs, suggesting these sequences may partially mediate Nab2 target selection. Taken together, these data demonstrate that Nab2 opposingly regulates neuronal morphology and shares associated neuronal RNAs with Atx2, and thatDrosophilaNab2 associates with a more specific subset of polyadenylated mRNAs than its polyadenosine affinity alone may suggest.
Comparative analysis of RNA enrichment methods for preparation ofCryptococcus neoformansRNA sequencing libraries
Authors: Telzrow Calla L. , Zwack Paul J. , Righi Shannon Esher , Dietrich Fred S. , Chan Cliburn , Owzar Kouros , Alspaugh J. Andrew , Granek Joshua A. 
Published: March 2021

ABSTRACTRibosomal RNA (rRNA) is the major RNA constituent of cells, therefore most RNA sequencing (RNA-Seq) experiments involve removal of rRNA. This process, called RNA enrichment, is done primarily to reduce cost: without rRNA removal, deeper sequencing would need to be performed to balance the sequencing reads wasted on rRNA. The ideal RNA enrichment method would remove all rRNA without affecting other RNA in the sample. We have tested the performance of three RNA enrichment methods on RNA isolated fromCryptococcus neoformans, a fungal pathogen of humans. We show that the RNase H depletion method unambiguously outperforms the commonly used Poly(A) isolation method: the RNase H method more efficiently depletes rRNA while more accurately recapitulating the expression levels of other RNA observed in an unenriched “gold standard”. The RNase H depletion method is also superior to the Ribo-Zero depletion method as measured by rRNA depletion efficiency and recapitulation of protein-coding gene expression levels, while the Ribo-Zero depletion method performs moderately better in preserving non-coding RNA (ncRNA). Finally, we have leveraged this dataset to identify novel long non-coding RNA (lncRNA) genes and to accurately map theC. neoformansmitochondrial rRNA genes.ARTICLE SUMMARYWe compare the efficacy of three different RNA enrichment methods for RNA-Seq inCryptococcus neoformans: RNase H depletion, Ribo-Zero depletion, and Poly(A) isolation. We show that the RNase H depletion method, which is evaluated inC. neoformanssamples for the first time here, is highly efficient and specific in removing rRNA. Additionally, using data generated through these analyses, we identify novel long non-coding RNA genes inC. neoformans. We conclude that RNase H depletion is an effective and reliable method for preparation ofC. neoformansRNA-Seq libraries.
redBERT: A Topic Discovery and Deep Sentiment Classification Model on COVID-19 Online Discussions Using BERT NLP Model
Authors: Pandey Chaitanya 
Published: March 2021

AbstractA Natural Language Processing (NLP) method was used to uncover various issues and sentiments surrounding COVID-19 from social media and get a deeper understanding of fluctuating public opinion in situations of wide-scale panic to guide improved decision making with the help of a sentiment analyser created for the automated extraction of COVID-19 related discussions based on topic modelling. Moreover, the BERT model was used for the sentiment classification of COVID-19 Reddit comments. These findings shed light on the importance of studying trends and using computational techniques to assess human psyche in times of distress.
Ammonia-oxidizing archaea possess a wide range of cellular ammonia affinities
Authors: Jung Man-Young , Sedlacek Christopher J. , Dimitri Kits K. , Mueller Anna J. , Rhee Sung-Keun , Hink Linda , Nicol Graeme W. , Bayer Barbara , Lehtovirta-Morley Laura , Wright Chloe , de la Torre Jose R. , Herbold Craig W. , Pjevac Petra , Daims Holger , Wagner Michael 
Published: March 2021

AbstractNitrification, the oxidation of ammonia to nitrate, is an essential process in the biogeochemical nitrogen cycle. The first step of nitrification, ammonia oxidation, is performed by three, often co- occurring guilds of chemolithoautotrophs: ammonia-oxidizing bacteria (AOB), archaea (AOA), and complete ammonia oxidizers (comammox). Substrate kinetics are considered to be a major niche-differentiating factor between these guilds, but few AOA strains have been kinetically characterized. Here, the ammonia oxidation kinetic properties of 12 AOA representing all major phylogenetic lineages were determined using microrespirometry. Members of the genusNitrosocosmicushave the lowest substrate affinity of any characterized AOA, which are similar to previously determined affinities of AOB. This contrasts previous assumptions that all AOA possess much higher substrate affinities than their comammox or AOB counterparts. The substrate affinity of ammonia oxidizers correlated with their cell surface area to volume ratios. In addition, kinetic measurements across a range of pH values strongly supports the hypothesis that – like for AOB – ammonia and not ammonium is the substrate for the ammonia monooxygenase enzyme of AOA and comammox. Together, these data will facilitate predictions and interpretation of ammonia oxidizer community structures and provide a robust basis for establishing testable hypotheses on competition between AOB, AOA, and comammox.
Deriving accurate molecular indicators of protein synthesis through Raman-based sparse classification
Authors: Pavillon N. , Smith N. I. 
Published: March 2021

AbstractRaman spectroscopy has the ability to retrieve molecular information from live biological samples non-invasively through optical means. Coupled with machine learning, it is possible to use the large amount of information contained in a Raman spectrum to create models that can predict the state of new samples based on statistical analysis from previous measurements. Furthermore, in case of linear models, the separation coefficients can be used to interpret which bands are contributing to the discrimination between experimental conditions, which correspond here to single-cell measurements of macrophages underin vitroimmune stimulation. We here evaluate a typical linear method using discriminant analysis and PCA, and compare it to regularized logistic regression (Lasso). We find that the use of PCA is not beneficial to the classification performance. Furthermore, the Lasso approach yields sparse separation vectors, since it suppresses spectral coefficients which do not improve classification, making interpretation easier. To further evaluate the approach, we apply the Lasso technique to a well-defined case where protein synthesis is inhibited, and show that the separating features are consistent with RNA accumulation and protein levels depletion. Surprisingly, when Raman features are selected purely in terms of their classification power (Lasso), the selected coefficients are contained in side bands, while typical strong Raman peaks are not present in the discrimination vector. We propose that this occurs because large Raman bands are representative of a wide variety of cellular molecules and are therefore less suited for accurate classification.
Non-canonical function of theSex-lethalgene controls the protogyny phenotype inDrosophila melanogaster
Authors: Seong Ki-Hyeon , Kang Siu 
Published: March 2021

AbstractMany animal species exhibit sex differences in the time period prior to reaching sexual maturity. However, the underlying mechanism for such biased maturation remains poorly understood. Females of the fruit flyDrosophila melanogastereclose 4 h faster on average than males, owing to differences in the pupal period between the sexes; this characteristic is referred to as the protogyny phenotype. Here, we aimed to elucidate the mechanism underlying the protogyny phenotype in the fruit fly using our newly developedDrosophilaIndividual Activity Monitoring and Detecting System (DIAMonDS), which can continuously detect the precise timing of both pupariation and eclosion of individual flies. Via this system, following the laying of eggs, we detected the precise time points of pupariation and eclosion of a large number of individual flies simultaneously and succeeded in identifying the tiny differences in pupal duration between females and males. We first explored the role of physiological sex by establishing transgender flies via knockdown of the sex-determination gene,transformer(tra) and its co-factortra2, which retained the protogyny phenotype. In addition, disruption of dosage compensation bymale-specific lethal(msl-2) knockdown did not affect the protogyny phenotype. TheDrosophilamaster sex switch gene—Sxlpromotes female differentiation viatraand turns off male dosage compensation through the repression ofmsl-2.However, we observed that stage-specific whole-body knockdown and mutation ofSxlinduced disturbance of the protogyny phenotype. These results suggest that an additional, non-canonical function ofSxlinvolves establishing the protogyny phenotype inD. melanogaster.Author summaryA wide variety of animals show differences in time points of sexual maturation between sexes. For example, in many mammals, including human beings, females mature faster than males. This maturation often takes several months or years, and precisely detecting the time point of maturation is challenging, because of the continuity of growth, especially in mammals. Moreover, the reason behind the difference in sexual maturation time points between sexes is not fully understood. The fruit flyDrosophila—a model organism—also shows biased maturation between the sexes, with females emerging 4 h faster than males (a characteristic known as the protogyny phenotype). To understand the mechanism underlying the protogyny phenotype, we used our newly developed system,DrosophilaIndividual Activity Monitoring and Detecting System (DIAMonDS), to detect the precise eclosion point in individual fruit flies. Surprisingly, our analysis of transgender flies obtained by knockdown and overexpression techniques indicated that a physiological gender might not be necessary requirement for protogyny and that a non-canonical novel function of the fruit fly master sex switch gene,Sxl, regulates protogyny in fruit flies.
Pathogenic LRRK2 control of primary cilia and Hedgehog signaling in neurons and astrocytes of mouse brain
Authors: Khan Shahzad S. , Sobu Yuriko , Dhekne Herschel S. , Tonelli Francesca , Berndsen Kerryn , Alessi Dario R. , Pfeffer Suzanne R. 
Published: March 2021

AbstractPreviously, we showed that cholinergic interneurons of the dorsal striatum lose cilia in mice harboring the Parkinson’s disease associated, kinase activating, R1441C LRRK2 mutation (Dhekne et al., 2018). Here we show that this phenotype is also seen in two mouse strains carrying the most common human G2019S LRRK2 mutation. Heterozygous loss of the PPM1H phosphatase that is specific for LRRK2-phosphorylated Rab GTPases (Berndsen et al., 2019) yields the same cilia loss phenotype, strongly supporting a connection between Rab GTPase phosphorylation and cilia loss. In addition, astrocytes throughout the striatum show a ciliation defect in LRRK2 and PPM1H-/+mutant models. Hedgehog signaling requires cilia, and loss of cilia correlates here with a loss in induction of Hedgehog signaling as monitored by in situ hybridization ofGli1transcripts. These data support a model in which LRRK2 and PPM1H mutant mice struggle to receive and respond to critical Hedgehog signals in the nigral-striatal pathway.
Death comes for us all: an interplay of habitat selection, movement, and social behavior relate to cause specific mortality among grey wolves
Authors: Turner Julie W. , Prokopenko Christina M. , Kingdon Katrien A. , Dupont Daniel L. J. , Zabihi-Seissan Sana , Wal Eric Vander 
Published: March 2021

AbstractAvoiding death infects biological processes, including behavior. Habitat selection, movement, and sociality are highly flexible behaviors that influence the mortality risks and subsequent fitness of individuals. In the Anthropocene, animals are experiencing increased risks from direct human causes and increased spread of infectious diseases. Using integrated step selection analysis, we tested how the habitat selection, movement, and social behaviors of grey wolves vary as an individual dies due to humans or canine distemper virus (CDV) and how those behaviors may vary in the lead up to death. Behaviors that changed prior to death were strongly related to how an animal eventually died. Wolves killed by humans moved slower than wolves that survived and selected to be nearer roads closer in time to their death. Wolves that died due to CDV moved progressively slower as they neared death and reduced their avoidance of wet habitats. All animals, regardless of dying or not maintained strong selection to be near packmates across time, which seemingly contributed to disease dynamics in the packs that became infected with CDV. Habitat selection, movement, and sociality interact to put individuals and groups at greater risks, influencing their cause-specific mortality.Lay SummaryNot much is known about behaviors prior to death in wild animals. Grey wolves killed by humans selected to be in riskier areas increasingly prior to their deaths. Wolves that died due to disease moved slower and changed their habitat selection to be in areas with more water as they became sicker. Sick wolves also continued to select for packmates, increasing the chances that the whole pack would succumb to the disease.
A pro-endocrine pancreatic transcriptional program established during development is retained in human gallbladder epithelial cells
Authors: Joglekar Mugdha V. , Sahu Subhshri , Wong Wilson KM , Satoor Sarang N. , Dong Charlotte X. , Farr Ryan J , Williams Michael D. , Pandya Prapti , Jhala Gaurang , Yang Sundy N.Y. , Vee Chew Yi , Hetherington Nicola , Thiruchevlam Dhan , Mitnala Sasikala , Rao Guduru V , Nageshwar Reddy Duvvuru , Loudovaris Thomas , Hawthorne Wayne J. , Elefanty Andrew G. , Joglekar Vinay M. , Stanley Edouard G. , Martin David , Thomas Helen E. , Tosh David , Dalgaard Louise T. , Hardikar Anandwardhan A. 
Published: March 2021

AbstractObjectivePancreatic islet β-cells are factories for insulin production; however ectopic expression of insulin is also well recognized. The gallbladder is a next-door neighbour to the developing pancreas. Here, we wanted to understand if gallbladders contain functional insulin-producing cells.DesignWe compared developing and adult mouse as well as human gallbladder epithelial cells and islets using immunohistochemistry, flow cytometry, ELISAs, RNA-sequencing, real-time PCR, chromatin immunoprecipitation and functional studies.ResultsWe demonstrate that the epithelial lining of developing, as well as adult mouse and human gallbladders naturally contain interspersed cells that retain the capacity to actively transcribe, translate, package, and release insulin. We show for the first time that human gallbladders also contain functional insulin-secreting cells with the potential to naturally respond to glucosein vitroandin situ. Notably, in a NOD mouse model of type 1 diabetes, we observed that insulin-producing cells in the gallbladder are not targeted by autoimmune cells. Conclusion: In summary, our biochemical, transcriptomic, and functional data in human gallbladder epithelial cells collectively demonstrate their potential for insulin-production under pathophysiological conditions, and open newer areas for type 1 diabetes research and therapy.Significance of the studyWhat is already known about this subject?Developing pancreas and gallbladder are next-door neighbours and share similar developmental pathways.Human Gallbladder-derived progenitor cells were shown to differentiate into insulin-producing cells.What are the new findings?Gallbladder epithelium contains interspersed cells that can transcribe, translate, package and secrete insulin.Insulin-producing cells in the gallbladder are not destroyed by immune cells in an animal model of type 1 diabetes (T1D).Our studies demonstrating the absence of insulin splice variants in human gallbladder cells, and higher splice forms in human islets, suggest a potential mechanism (via defective ribosomal products) in escaping islet autoimmunity.How might it impact clinical practice?Deciphering mechanisms of protection of insulin-producing cells from immune cells in the gallbladder could help in developing strategies to prevent islet autoimmunity in T1D.
What do customers want? The impact of pricing tactic persuasion knowledge and frequency of exposure
Authors: Chen Yen-Ting , Lan Li-Chi , Fang Wen-Chang 
Published: March 2021

PurposePrevious research has shown that consumers prefer a bonus pack to a price discount for virtue foods, whereas they prefer a price discount to a bonus pack for vice foods. Acting as a guilt-mitigating mechanism, a price discount justifies consumers' purchasing behavior, allowing them to save money and consume less vice foods. However, for virtue foods, neither the anticipated post-consumption guilt nor the resulting need for justification lead consumers to prefer a bonus pack to a price discount. This study investigates whether product promotions remain effective with other moderating variables.Design/methodology/approachThe authors use pricing tactic persuasion knowledge (PTPK), which refers to the consumer persuasion knowledge of marketers' pricing tactics, as a lens to understand whether the power of these promotions could be enhanced or mitigated. The authors inferred that increasing the frequency of exposure to these foods could positively influence consumers' purchasing choices. They conducted three studies to examine these effects. In Study 1, using pearl milk tea (vice food) and sugar-free tea (virtue food), the authors contended that consumers would prefer a price discount when purchasing pearl milk tea, but a bonus pack when purchasing sugar-free tea. In Studies 2 and 3, the authors varied the participants' frequency of exposure to photographs of people in everyday situations with vice (virtue) foods.FindingsIn Study 1, PTPK was shown to be more predictive of consumer choices regarding price discounts and bonus packs. In Studies 2 and 3, the authors contended that increased exposure to vice (virtue) foods increases the selection of vice (virtue) foods by participants who were unaware of having been exposed to vice (virtue) foods.Originality/valueThis research has not only made quite managerial and policy implications for marketing but also brought the theoretical contributions for marketing researches. This research demonstrates that either for vice foods or virtue foods, a price discount is preferred to a bonus pack.