bluuebunny/crossref_metadata_2025_split huggingface dataset:
CryoEM Structures of the Human HIV-1 Restriction Factor SERINC3 and Function as a Lipid Transporter
Authors: Leonhardt Susan A. , Purdy Michael D. , Grover Jonathan R. , Yang Ziwei , Poulos Sandra , McIntire William E. , Tatham Elizabeth A. , Erramilli Satchal , Nosol Kamil , Lai Kin Kui , Ding Shilei , Lu Maolin , Uchil Pradeep D. , Finzi Andrés , Rein Alan , Kossiakoff Anthony A. , Mothes Walther , Yeager Mark 
Published: July 2022

AbstractThe host proteins SERINC3 and SERINC5 are HIV-1 restriction factors that reduce infectivity when incorporated into the viral envelope. The HIV-1 accessory protein Nef abrogates incorporation of SERINCs via binding to intracellular loop 4 (ICL4). CryoEM maps of full-length human SERINC3 and an ICL4 deletion construct reveal that hSERINC3 is comprised of twoα- helical bundles connected by a ∼40-residue, tilted, “crossmember” helix. The design resembles non-ATP-dependent lipid transporters. Consistently, purified hSERINCs reconstituted into proteoliposomes flip phosphatidylserine (PS), phosphatidylethanolamine and phosphatidylcholine. SERINC3 and SERINC5 reduce infectivity and expose PS on the surface of HIV-1 and also MLV, which is counteracted by Nef and GlycoGag, respectively. Antiviral activities by SERINCs and the scramblase TMEM16F correlate with the exposure of PS and with altered conformation of the envelope glycoprotein. We conclude that SERINCs are lipid transporters, and we demonstrate that lipid flipping is directly correlated with loss of infectivity.One Sentence SummaryThe HIV-1 restriction factor SERINC3 has a molecular design similar to non-ATP dependent lipid transporters, a function supported by the observation of flipping activity in proteoliposomes and exposure of phosphatidylserine on HIV-1 and MLV particles, which is correlated with loss of infectivity.
Tracing back primed resistance in cancer via sister cells
Authors: Dai Jun , Zheng Shuyu , Falco Matías M. , Bao Jie , Eriksson Johanna , Pikkusaari Sanna , Forstén Sofia , Jiang Jing , Wang Wenyu , Gao Luping , Perez-Villatoro Fernando , Dufva Olli , Saeed Khalid , Wang Yinyin , Amiryousefi Ali , Färkkilä Anniina , Mustjoki Satu , Kauppi Liisa , Tang Jing , Vähärautio Anna 
Published: July 2022

AbstractExploring non-genetic evolution of cell states during cancer treatments has become attainable by recent advances in lineage-tracing methods. However, transcriptional changes that drive cells into resistant fates may be subtle, necessitating high resolution analysis. We developed ReSisTrace that uses shared transcriptomic features of synchronised sister cells to predict the states that prime treatment resistance. We applied ReSisTrace in ovarian cancer cells perturbed with olaparib, carboplatin or natural killer (NK) cells. The pre-resistant phenotypes were defined by cell cycle and proteostatic features, reflecting the traits enriched in the upcoming subclonal selection. Furthermore, DNA repair deficiency rendered cells susceptible to both DNA damaging agents and NK killing in a context-dependent manner. Finally, we leveraged the pre-resistance profiles to predict and validate small molecules driving cells to sensitive states prior to treatment. In summary, ReSisTrace resolves pre-existing transcriptional features of treatment vulnerability, facilitating both molecular patient stratification and discovery of synergistic pre-sensitizing therapies.
PAT mRNA decapping factors function specifically and redundantly during development inArabidopsis
Authors: Zuo Zhangli , Roux Milena Edna , Dagdas Yasin F. , Rodriguez Eleazar , Petersen Morten 
Published: July 2022

AbstractEvolutionarily conserved PAT1 proteins activate mRNA decay through binding mRNA and recruiting decapping enzymes and other factors hence optimize transcriptional reprogramming during development. Here, we generated multiple mutants ofpat1(Protein Associated with Topoisomerase II),path1andpath2and inspected their growth and leaf morphology phenotype.pattriple mutants exhibit extreme stunted growth and all mutants withpat1exhibit leaf serration while mutants withpat1andpath1all display short petioles. All 3 PATs can be found localized to Prossessing Bodies (PBs) upon auxin treatment and RNA-seq analysis indicate that all 3 PATs redundantly regulate auxin responses. Moreover, shade avoidance and NAC genes are misregulated inpat1path1double andpattriple mutants suggesting PAT1 and PATH1 function in petiole elongation and leaf patterning. In conclusion, PAT proteins exhibit both specific and overlapping functions during different stages of plant growth and our observations underpin the importance of the mRNA decay machinery for proper development.
Genomic diversity and molecular epidemiology of a multidrug resistantPseudomonas aeruginosaDMC30b isolated from hospitalized burn patient in Bangladesh
Authors: Hoque M. Nazmul , Jahan M. Ishrat , Hossain M. Anwar , Sultana Munawar 
Published: July 2022

AbstractObjectivesPseudomonas aeruginosais a key opportunistic pathogen causing a wide range of community- and hospital-acquired infections in immunocompromised or catheterized patients. Here, we report the complete genome sequence of a multidrug resistant (MDR)P. aeruginosaDMC30b in order to elucidate the genetic diversity, molecular epidemiology, and underlying mechanisms for antimicrobial resistance and virulence.MethodsP. aeruginosaDMC30b was isolated from septic wound swab of a severe burn patient. Whole-genome sequencing (WGS) was performed under Ion Torrent platform. The genome was annotated using the SPAdes v. 3.12.01 in an integrated Genome Analysis Platform (IonGAP) for Ion Torrent sequence data. The genome was annotated using the NCBI Prokaryotic Genome Annotation Pipeline (PGAP).In-silicopredictions of antimicrobial resistance genes (ARGs), virulence factor genes (VFGs) and metabolic functional potentials were performed using different curated bioinformatics tools.ResultsP. aeruginosaDMC30b was classified as MDR and belongs to sequence type 244 (ST244). The complete genome size is 6,994,756 bp with a coverage of 76.76x, G+C content of 65.7% and a BUSCO (Benchmarking Universal Single-Copy Orthologs) score of 100. The genome ofP. aeruginosaDMC30b harboured two plasmids (e,g., IncP-6 plasmid p10265-KPC; 78,007 bp and ColRNAI_pkOIISD1; 9,359 bp), 35 resistomes (ARGs) conferring resistance to 18 different antibiotics (including four beta-lactam classes), and 214 VFGs. It was identified as the 167thST244 strain among ∼ 5,800 whole-genome sequences ofP. aeruginosaavailable in the NCBI database.ConclusionP. aeruginosaDMC30b belongs to ST244 and was identified as the 167thsuch isolate to be submitted to NCBI, and the first complete ST244 genome from Bangladesh. The complete genome data with high genetic diversity and underlying mechanisms for antimicrobial resistance and virulence ofP. aeruginosaDMC30b (ST244) will aid in understanding the evolution and phylogeny of such high-risk clones and provide a solid basis for further research on MDR or extensively drug resistant strains.
FOXP2confers oncogenic effects in prostate cancer through activating MET signalling
Authors: Zhu Xiaoquan , Chen Chao , Wei Dong , Xu Yong , Liang Siying , Jia Wenlong , Li Jian , Qu Yanchun , Zhai Jianpo , Zhang Yaoguang , Wu Pengjie , Hao Qiang , Zhang Linlin , Zhang Wei , Yang Xinyu , Pan Lin , Qi Ruomei , Li Yao , Wang Feiliang , Yi Rui , Yang Ze , Wang Jianye , Zhao Yanyang 
Published: July 2022

AbstractIdentification oncogenes is fundamental to revealing the molecular basis of cancer. Here, we found thatFOXP2is overexpressed in human prostate cancer cells and prostate tumors, but its expression is absent in normal prostate epithelial cells and low in benign prostatic hyperplasia. To date, little is known regarding the link ofFOXP2to prostate cancer. We observed that highFOXP2expression and frequent amplification are significantly associated with high Gleason score. Ectopic expression ofFOXP2induces malignant transformation of mouse NIH3T3 fibroblasts and human prostate epithelial cell RWPE-1. Conversely,FOXP2knockdown suppresses the proliferation of prostate cancer cells. Transgenic overexpression ofFOXP2in the mouse prostate causes prostatic intraepithelial neoplasia. Overexpression ofFOXP2aberrantly activates oncogenic MET signalling and inhibitors targeting MET signalling effectively reverts theFOXP2-induced oncogenic phenotype. Additionally, the novel recurrentFOXP2-CPED1fusion identified in prostate tumors results in high expression of truncated FOXP2, which exhibit a similar capacity for malignant transformation. Together, our data demonstrate for the first time thatFOXP2is an oncogene involved in tumorigenicity of prostate.
NvPrdm14d-expressing neural progenitor cells contribute to non-ectodermal neurogenesis in Nematostella vectensis
Authors: Lemaître Quentin I. B. , Bartsch Natascha , Kouzel Ian U. , Busengdal Henriette , Richards Gemma Sian , Steinmetz Patrick R. H. , Rentzsch Fabian 
Published: July 2022

ABSTRACTNeurogenesis has been studied extensively in the ectoderm, from which most animals generate the majority of their neurons. Neurogenesis from non-ectodermal tissue is, in contrast, poorly understood. Here we use the cnidarian Nematostella vectensis as a model to provide new insights into the molecular regulation of non-ectodermal neurogenesis. We show that the transcription factor NvPrdm14d is expressed in a subpopulation of NvSoxB(2)-expressing endodermal progenitor cells and their NvPOU4-expressing progeny. Using a new transgenic reporter line, we show that NvPrdm14d-expressing cells give rise to neurons in the body wall and in close vicinity of the longitudinal retractor muscles. RNA-sequencing of NvPrdm14d::GFP-expressing cells and gene knockdown experiments provide candidate genes for the development and function of these neurons. Together, the identification of a population of endoderm-specific neural progenitor cells and of previously undescribed putative motoneurons in Nematostella provide new insights into the regulation of non-ectodermal neurogenesis.
Improved analysis of (e)CLIP data with RCRUNCH yields a compendium of RNA-binding protein binding sites and motifs
Authors: Katsantoni Maria , van Nimwegen Erik , Zavolan Mihaela 
Published: July 2022

AbstractWe present RCRUNCH, an end-to-end solution to CLIP data analysis for identification of binding sites and sequence specificity of RNA-binding proteins. RCRUNCH can analyze not only reads that map uniquely to the genome, but also those that map to multiple genome locations or across splice boundaries, and can consider various types of background in the estimation of read enrichment. By applying RCRUNCH to the eCLIP data from the ENCODE project, we have constructed a comprehensive and homogeneous resource ofin vivo-bound RBP sequence motifs. RCRUNCH automates the reproducible analysis of CLIP data, enabling studies of post-transcriptional control of gene expression.
stuart: an R package for the curation of SNP genotypes from experimental crosses
Authors: Bourdon Marie , Montagutelli Xavier 
Published: July 2022

AbstractGenetic mapping in two-generation crosses requires genotyping, usually performed with SNP markers arrays which provide high-density genetic information. However, genetic analysis on raw genotypes can lead to spurious or unreliable results due to defective SNP assays or wrong genotype interpretation. Here we introduce stuart, an open-source R package which analyzes raw genotyping data to filter SNP markers based on informativeness, Mendelian inheritance pattern and consistency with parental genotypes. Functions of this package provide a curation pipeline and formatting adequate for genetic analysis with the R/qtl package. stuart is available with detailed documentation fromhttps://gitlab.pasteur.fr/mouselab/stuart/.
Cisplatin toxicity is mediated by direct binding to TLR4 through a mechanism that is distinct from metal allergens
Authors: Domingo Ivan K. , Groenendyk Jody , Michalak Marek , Bhavsar Amit P. 
Published: July 2022

ABSTRACTCisplatin is an effective chemotherapeutic agent, yet its use is limited by several adverse drug reactions, known as cisplatin-induced toxicities (CITs). We recently demonstrated that cisplatin could elicit pro-inflammatory responses associated with CITs through Toll-like Receptor 4 (TLR4). TLR4 is best recognized for binding bacterial lipopolysaccharide (LPS) via its coreceptor, MD-2. TLR4 is also proposed to directly bind transition metals, such as nickel. Little is known about the nature of the cisplatin-TLR4 interaction. Here, we show that soluble TLR4 was capable of blocking cisplatin-induced, but not LPS-induced TLR4 activation. Cisplatin and nickel, but not LPS, were able to directly bind soluble TLR4 in a microscale thermophoresis binding assay. Interestingly, TLR4 histidine variants that abolish nickel binding, reduced, but did not eliminate, cisplatin-induced TLR4 activation. This was corroborated by binding data that showed cisplatin, but not nickel, could directly bind mouse TLR4 that lacks these histidine residues. Altogether, our findings suggest that TLR4 can directly bind cisplatin in a manner that is enhanced by, but not dependent on, histidine residues that facilitate binding to transition metals.
Virtual learning environment factors as predictors of students' learning satisfaction during COVID-19 period in Nigeria
Authors: Adewale Sulaimon , Tahir Muyideen Babatunde 
Published: July 2022

PurposeThe onus of this study was to find out the role played by virtual learning environment factors on students' satisfaction during the COVID-19 period in Nigeria. A survey was carried out on students in higher education institutions in Nigeria to actualize this purpose.Design/methodology/approachSimple random sampling techniques with the aid of Krejcie and Morgan's (1970) sample determinant and the Snowball sampling technique were adopted to sample 270 students in higher education institutions in Nigeria. An adapted questionnaire was used. Cronbach alpha coefficients were calculated for the two sections of the independent and dependent variables. Virtual learning environment factors yielded 0.89, while students' satisfaction yielded 0.87. Data were analyzed using descriptive statistics, Pearson product–moment correlation, two-way ANOVA and linear regression analysis.FindingsThe results of the ANOVA, F (df 4, 265) = 50.905, p < 0.000, indicate a statistically significant relationship (stronger than 0.05) between the independent variables (virtual learning environment factors) and the dependent variable (students' satisfaction). It was found among others that instructors' support and collaboration factors predicted students' satisfaction with virtual learning experiences during the COVID-19 period.Originality/valueVirtual learning during COVID-19 caught both lecturers and students unprepared. Most developing countries especially Africans were used to the traditional face-to-face learning, more so, the use of virtual means to learn was still at a nascent stage. This study, therefore, contributed to the role of the learning environment in virtual learning satisfaction.
Analysis and optimization of Dual Parallel Partition Sorting with OpenMP
Authors: Ketchaya Sirilak , Rattanatranurak Apisit 
Published: July 2022

PurposeSorting is a very important algorithm to solve problems in computer science. The most well-known divide and conquer sorting algorithm is quicksort. It starts with dividing the data into subarrays and finally sorting them.Design/methodology/approachIn this paper, the algorithm named Dual Parallel Partition Sorting (DPPSort) is analyzed and optimized. It consists of a partitioning algorithm named Dual Parallel Partition (DPPartition). The DPPartition is analyzed and optimized in this paper and sorted with standard sorting functions named qsort and STLSort which are quicksort, and introsort algorithms, respectively. This algorithm is run on any shared memory/multicore systems. OpenMP library which supports multiprocessing programming is developed to be compatible with C/C++ standard library function. The authors’ algorithm recursively divides an unsorted array into two halves equally in parallel with Lomuto's partitioning and merge without compare-and-swap instructions. Then, qsort/STLSort is executed in parallel while the subarray is smaller than the sorting cutoff.FindingsIn the authors’ experiments, the 4-core Intel i7-6770 with Ubuntu Linux system is implemented. DPPSort is faster than qsort and STLSort up to 6.82× and 5.88× on Uint64 random distributions, respectively.Originality/valueThe authors can improve the performance of the parallel sorting algorithm by reducing the compare-and-swap instructions in the algorithm. This concept can be used to develop related problems to increase speedup of algorithms.
INS/CNS/DNS/XNAV deep integrated navigation in a highly dynamic environment
Authors: Hu Jintian , Liu Jin , Wang Yidi , Ning Xiaolin 
Published: July 2022

Purpose
This study aims to address the problem of the divergence of traditional inertial navigation system (INS)/celestial navigation system (CNS)-integrated navigation for ballistic missiles. The authors introduce Doppler navigation system (DNS) and X-ray pulsar navigation (XNAV) to the traditional INS/CNS-integrated navigation system and then propose an INS/CNS/DNS/XNAV deep integrated navigation system.

Design/methodology/approach
DNS and XNAV can provide velocity and position information, respectively. In addition to providing velocity information directly, DNS suppresses the impact of the Doppler effect on pulsar time of arrival (TOA). A pulsar TOA with drift bias is observed during the short navigation process. To solve this problem, the pulsar TOA drift bias model is established. And the parameters of the navigation filter are optimised based on this model.

Findings
The experimental results show that the INS/CNS/DNS/XNAV deep integrated navigation can suppress the drift of the accelerometer to a certain extent to improve the precision of position and velocity determination. In addition, this integrated navigation method can reduce the required accuracy of inertial navigation, thereby reducing the cost of missile manufacturing and realising low-cost and high-precision navigation.

Originality/value
The velocity information provided by the DNS can suppress the pulsar TOA drift, thereby improving the positioning accuracy of the XNAV. This reflects the “deep” integration of these two navigation methods.
Bending and torsional vibration attenuation of multi-panel deployable solar array using reaction wheel actuators
Authors: Wang Cunfu , Chen Bifa 
Published: July 2022

Purpose
This paper aims to present a multi-axis actuating approach to attenuate the bending and torsional vibration of the solar array through the reaction wheel (RW) actuators.

Design/methodology/approach
The motion equation of the solar array with the RW actuators is derived in modal coordinates for controller design. The reaction torques, induced by the speed change of the RW actuators, are controlled for vibration attenuation through the constraints on the actuators’ rotating speed. The proposed control approach is firstly verified with numerical simulation on the finite element model of a full-scale solar array. Experimental study of a simplified elastic plate model is subsequently performed for feasibility and validity investigation.

Findings
Both the numerical and experimental studies demonstrated the success of adopting RW as the actuator. Results from numerical simulation reveal that the vibration response peak can be reduced by 80% with 2% of mass increase by using the RW actuators.

Practical implications
It is demonstrated that the multi-axis actuating method using RW actuators has a great potential in vibration attenuation of the multi-panel deployable solar array.

Originality/value
An approach to reduce bending and torsional vibration of solar array based on RW actuators is investigated. Theoretical analysis, numerical simulation and experimental study are conducted to demonstrate the validity of the proposed vibration attenuation approach and its potential application in the spacecraft design.
“From the beginning, I think it was a stretch” – teachers’ perceptions and practices in teaching multiliteracies
Authors: Lim Fei Victor , Chia Alexius , Nguyen Thi Thu Ha 
Published: July 2022

PurposeThe purpose of this study is to examine five Secondary English Language teachers’ perceptions and practices of multiliteracies teaching in the context of a decade after multiliteracies was introduced into the English Language syllabus in Singapore.Design/methodology/approachAdopting a case study approach, the authors observed 12 multiliteracies lessons taught by the five teacher participants across three secondary schools. The classroom data included field notes and video-recordings of the lessons. The authors also conducted pre-lesson and post-lesson interviews with the teachers to understand their beliefs and the rationale behind their classroom practices. The video-recordings of the lessons and audio-recordings of the interviews were transcribed verbatim and analysed using thematic coding.FindingsThe authors identify an essentialising of multiliteracies to the skills of viewing and representing with multimodal texts, as well as a sense of uncertainty amongst the teachers towards the teaching of multiliteracies. In terms of practices, the authors observed an attempt to connect with the students’ life-worlds through the use of authentic materials, but often only in service of language learning. The authors also highlight the constraining influence of assessment on shaping multiliteracies learning. The findings of this study resonate with the conclusions that some of the earlier studies reported on teachers’ perceptions and practices of multiliteracies teaching. This resonation suggests perennial issues and challenges which remain unresolved.Research limitations/implicationsThis study is limited by the number of participants as well as the selected lessons the authors observed. The schools, while selected because they were considered as mid-range public schools in Singapore, were also not representative of all Singapore schools. As such, the authors acknowledge that the generalisability of the findings from this study is limited.Practical implicationsThe issues raised in this study resonate with the findings from previous studies both from Singapore and around the world. The persistence of these concerns over time and space that remain unresolved demands attention and concerted action from policymakers, curriculum developers and education researchers, to address the challenges in multiliteracies teaching and learning.Originality/valueThis study was conducted a decade after the launch of the English Language Syllabus 2010, which first incorporated multiliteracies into the curriculum. This study examines the teachers’ perceptions and practices in relation to the policy intent. The implications from this study are relevant to educators interested in integrating multiliteracies in the literacy curriculum internationally.