bluuebunny/crossref_metadata_2025_split huggingface dataset:
MOSS I: Double radio relics in the Saraswati supercluster
Authors: Parekh V , Kincaid R , Thorat K , Hugo B , Sankhyayan S , Kale R , Oozeer N , Smirnov O , Heywood I , Makhathini S , van der Heyden K 
Published: October 2021

ABSTRACT
Superclusters are the largest objects in the Universe, and they provide a unique opportunity to study how galaxy clusters are born at the junction of the cosmic web as well as the distribution of magnetic fields and relativistic particles beyond cluster volume. The field of radio astronomy is going through an exciting and important era of the Square Kilometer Array (SKA). We now have the most sensitive functional radio telescopes, such as the MeerKAT, which offers high angular resolution and sensitivity towards diffuse and faint radio sources. To study the radio environments around supercluster, we observed the (core part of) Saraswati supercluster with the MeerKAT. From our MeerKAT Observation of the Saraswati Supercluster (MOSS) project, the initial results of the pilot observations of two massive galaxy clusters, A2631 and ZwCl2341.1+0000, which are located around the dense central part of the Saraswati supercluster, were discussed. In this paper, we describe the observations and data analysis details, including direction-dependent calibration. In particular, we focus on the ZwCl2341.1+0000 galaxy cluster, which hosts double radio relics and puzzling diffuse radio source in the filamentary network. We have imaged these double radio relics in our high resolution and sensitive L-band MeerKAT observation and a puzzling radio source, located between relics, in the low-resolution image. We also derived the spectra of double radio relics using MeerKAT and archival GMRT observations. The following papers will focus on the formation of radio relics and halo, as well as radio galaxy properties in a supercluster core environment.
Bipolar molecular outflow from M17
Authors: Sofue Yoshiaki 
Published: October 2021

ABSTRACT
Kinematics of the molecular clouds in the star-forming complex M17 is studied using the high-resolution CO-line mapping data at resolution (20 arcsec ∼ 0.2 pc) with the Nobeyama 45-m telescope. The northern molecular cloud of M17, which we call the molecular ‘lobe’, is shown to have an elongated shell structure around a top-covered cylindrical cavity. The lobe is expanding at ∼5 km s−1 in the minor axis direction, and at ∼3/cos  i km s−1 in the major axis direction, where i is the inclination of the major axis. The kinetic energy of the expanding motion is on the order of ∼3 × 1049 erg. We show that the lobe is a backyard structure having the common origin to the denser molecular ‘horn’ flowing out from NGC 6618 toward the south, so that the lobe and horn compose a bipolar outflow. Intensity distributions across the lobe and horn show a double-peak profile typical for a cylinder around a cavity. Position–velocity diagrams (PVD) across the lobe and horn exhibit open-ring structure with the higher and/or lower-velocity side(s) being lacking or faded. This particular PVD behaviour can be attributed to outflow in a conical cylinder with the flow velocity increasing toward the lobe and horn axes.
Radio emission from colliding outflows in high-mass X-ray binaries with strongly magnetized neutron stars
Authors: Chatzis Margaritis , Petropoulou Maria , Vasilopoulos Georgios 
Published: October 2021

Abstract
We present a toy model for radio emission in HMXBs with strongly magnetized NSs where a wind-collision region is formed by the NS outflow and the stellar wind of the massive companion. Radio emission is expected from the synchrotron radiation of shock-accelerated electrons and the free-free emission of the stellar wind. We found that the predicted relation between the GHz luminosity (LR) and the accretion X-ray luminosity (LX) can be written as $L_R \propto L_X^b$ for most parameters. No correlation with X-rays is expected (b = 0) when the thermal emission of the stellar wind dominates in radio. We typically find a steep correlation (b = 12/7) for sub-Eddington X-ray luminosities and a more shallow one (b = 2(p − 1)/7) for super-Eddington X-ray luminosities, where p is the power-law index of accelerated electrons. The maximum predicted radio luminosity is independent of the NS properties, while it depends on the stellar wind momentum, binary separation distance, and the minimum electron Lorentz factor. Using a Bayesian approach we modelled the radio observations of Swift J0243.6+6124 that cover a wide range of mass accretion rates. Our results support a shock origin for the radio detections at sub-Eddington X-ray luminosities. However, no physically meaningful parameters could be found for the super-Eddington phase of the outburst, suggesting a different origin. Future observations with more sensitive instruments might reveal a large number of HMXBs with strongly magnetized NSs in radio, allowing determination of the slope in the LR − LX relation, and putting the wind-collision scenario into test.
m5C-Atlas: a comprehensive database for decoding and annotating the 5-methylcytosine (m5C) epitranscriptome
Authors: Ma Jiongming , Song Bowen , Wei Zhen , Huang Daiyun , Zhang Yuxin , Su Jionglong , de Magalhães João Pedro , Rigden Daniel J , Meng Jia , Chen Kunqi 
Published: October 2021

Abstract
5-Methylcytosine (m5C) is one of the most prevalent covalent modifications on RNA. It is known to regulate a broad variety of RNA functions, including nuclear export, RNA stability and translation. Here, we present m5C-Atlas, a database for comprehensive collection and annotation of RNA 5-methylcytosine. The database contains 166 540 m5C sites in 13 species identified from 5 base-resolution epitranscriptome profiling technologies. Moreover, condition-specific methylation levels are quantified from 351 RNA bisulfite sequencing samples gathered from 22 different studies via an integrative pipeline. The database also presents several novel features, such as the evolutionary conservation of a m5C locus, its association with SNPs, and any relevance to RNA secondary structure. All m5C-atlas data are accessible through a user-friendly interface, in which the m5C epitranscriptomes can be freely explored, shared, and annotated with putative post-transcriptional mechanisms (e.g. RBP intermolecular interaction with RNA, microRNA interaction and splicing sites). Together, these resources offer unprecedented opportunities for exploring m5C epitranscriptomes. The m5C-Atlas database is freely accessible at https://www.xjtlu.edu.cn/biologicalsciences/m5c-atlas.
Availability and role of clinical pharmacists in ambulatory neuro-oncology
Authors: Patel Mallika P , Lipp Eric S , Miller Elizabeth S , Healy Patrick N , Herndon James E , Peters Katherine B 
Published: October 2021

Abstract

Background
Outpatient clinics treating neuro-oncology patients are becoming more multidisciplinary. Utilization of all team members is critical for the holistic care of these complex patients. Specifically, the role of clinical pharmacist (CP) in the ambulatory clinic remains undefined and will likely evolve as more therapeutics are developed for CNS malignancies. We queried the Society for Neuro-Oncology (SNO) membership about the availability of a CP in their ambulatory setting and, if present, the role of that CP.

Methods
In an IRB-exempt study, we surveyed the SNO community and analyzed responses to queries about CPs in the ambulatory setting.

Results
Of the 65 SNO members who responded, 52 were clinical members. Of these 52 clinicians, the majority were physicians (88.5%, n = 46). Of these physicians, most were in academic practices (93.5%, n = 43). Over half of the 52 clinical respondents (51.9%, n = 27) reported that they saw ≥30 primary brain tumor patients per month, thus typifying busy clinics. Despite having busy clinics, only 12 (28.6%) of 42 providers with access to a CP reported that their CP was solely dedicated to neuro-oncology patients. For the respondents who had access to a CP, only ~two-thirds of those CPs had direct patient interaction. The top 3 roles of the CP included medication review, chemotherapy dosing/modifications, and practice guideline development; none of which involve direct patient interaction.

Conclusions
We found that while our surveyed population of SNO clinical members have demanding outpatient practices, most do not have the support or expertise of dedicated neuro-oncology CPs.
Misregulation of MYB16 expression causes stomatal cluster formation by disrupting polarity during asymmetric cell divisions
Authors: Yang Shao-Li , Tran Ngan , Tsai Meng-Ying , Ho Chin-Min Kimmy 
Published: October 2021

Abstract
Stomatal pores and the leaf cuticle regulate evaporation from the plant body and balance the tradeoff between photosynthesis and water loss. MYB16, encoding a transcription factor involved in cutin biosynthesis, is expressed in stomatal lineage ground cells, suggesting a link between cutin biosynthesis and stomatal development. Here, we show that the downregulation of MYB16 in meristemoids is directly mediated by the stomatal master transcription factor SPEECHLESS (SPCH) in Arabidopsis thaliana. The suppression of MYB16 before an asymmetric division is crucial for stomatal patterning, as its overexpression or ectopic expression in meristemoids increased stomatal density and resulted in the formation of stomatal clusters, as well as affecting the outer cell wall structure. Expressing a cutinase gene in plants ectopically expressing MYB16 reduced stomatal clustering, suggesting that cutin affects stomatal signaling or the polarity setup in asymmetrically dividing cells. The clustered stomatal phenotype was rescued by overexpressing EPIDERMAL PATTERNING FACTOR2, suggesting that stomatal signaling was still functional in these plants. Growing seedlings ectopically expressing MYB16 on high-percentage agar plates to modulate tensile strength rescued the polarity and stomatal cluster defects of these seedlings. Therefore, the inhibition of MYB16 expression by SPCH in the early stomatal lineage is required to correctly place the polarity protein needed for stomatal patterning during leaf morphogenesis.
Knowledge, attitudes and control practices regarding venomous arthropods among staff and students in a Nigerian public university campus
Authors: Ogbusu Vivian Onyinyechukwu , Onyido Angus Ejidikeme , Okechukwu Chidiebere Emmanuel , Okwelogu Izunna Somadina 
Published: October 2021

ABSTRACT

Background
The objectives of this study were to assess the knowledge, attitudes and control practices among the staff and students of Nnamdi Azikiwe University (NAU), Awka, Anambra State, Nigeria, regarding venomous arthropods.

Methods
The knowledge, attitudes and control practices regarding venomous arthropods were assessed in 350 participants.

Results
The respondents were aware of the presence of venomous arthropods at NAU and they had seen them on campus, with spiders (40.44%) being the most common and electric ants (1.39%) being the least common. The control practices applied to limit the activities of these arthropods included keeping the environment clean (40.80%), the use of insecticides (37.33%), the use of repellents (8.68%), spraying houses with kerosene (7.81%), spraying of fuel on the arthropods (3.47%), screening of houses (1.39%) and the use of bed nets (0.52%).

Conclusions
An assessment and determination of knowledge, attitudes and control practices regarding venomous arthropods among the staff and students of NAU is necessary in order to improve the preventive measures to reduce injuries caused by venomous arthropod encounters, which are some of the most underestimated health hazards in tropical regions, including southeastern Nigeria, affecting primarily rural communities. According to the findings of our study, students and staff at NAU are rarely involved in life-threatening incidents as a result of their encounters with venomous arthropods and most apply several globally accepted standard practices for the control of venomous arthropods.
Clinical Transition: RN to BSN Students’ Perceptions of Their Abilities to Meet Program Outcomes
Authors: Connerton Charlotte S. , Hand Mikel W. , Wooton Angela K. 
Published: October 2021

Abstract
The purpose of this study was to analyze RN to BSN students’ perceptions of their abilities to meet program outcomes through their clinical experiences with a clinical teaching associate and after assuming responsibility for planning and directing clinical learning activities. A mixed-methods approach was used. Most students (87 percent) reported achievement of program outcome measures. Students demonstrated real-world learning and application through clinical experiences and successfully met program outcomes.
Preparing for Next Generation NCLEX® Through Team-Based Learning: Student Perspectives
Authors: Rhodes Kathleen A. , Carr Kayla , McElwain Sharon , Stewart Mary W. 
Published: October 2021

Abstract
The Next Generation NCLEX® requires higher levels of understanding for new registered nurses to practice safely. Team-based learning (TBL) offers a rigorous but pragmatic approach to achieve that aim. TBL employs collaborative strategies for structured problem-solving, a key focus of contemporary nurse educators. In this prospective study, a faculty team at a second-degree, accelerated baccalaureate nursing program within the southeast United States evaluated student perspectives of TBL. Overall findings revealed positive student experiences (n = 30, with three students on an alternate plan of study) in all aspects of the method.
Undibacterium baiyunense sp. nov., Undibacterium curvum sp. nov., Undibacterium fentianense sp. nov., Undibacterium flavidum sp. nov., Undibacterium griseum sp. nov., Undibacterium hunanense sp. nov., Undibacterium luofuense sp. nov., Undibacterium nitidum sp. nov., Undibacterium rivi sp. nov., Undibacterium rugosum sp. nov. and Undibacterium umbellatum sp. nov., isolated from streams in China
Authors: Lu Huibin , Liu Fei , Deng Tongchu , Xu Meiying 
Published: October 2021

Twelve Gram-stain-negative, catalase- and oxidase-positive, rod-shaped and motile strains (CY7WT, CY18WT, CY22WT, FT31WT, FT137WT, FT147WT, BYS50W, BYS107WT, LFS511WT, LX15WT, LX22WT and NL8WT) were isolated from streams in China. Comparisons based on 16S rRNA gene sequences indicated that these strains take species of genus

Undibacterium

as close neighbours. The reconstructed phylogenetic and phylogenomic trees also showed that these strains cluster with species of genus

Undibacterium

together. The genome G+C contents of these strains were in the range of 45.3 to 53.3 mol%. The calculated pairwise OrthoANIu values and digital DNA–DNA hybridization values among these strains and related strains were in the range of 70.4 to 94.1% and 19.3 to 55.3% except that the values between strains CY7WT and BYS50W were 99.0 and 91.8 %, respectively. Q-8 was their predominant respiratory quinone. C16 : 1
ω7c and C16 : 0 were their major fatty acids. Their polar lipids profiles were similar, including phosphatidylglycerol, phosphatidylethanolamine, one unidentified phospholipid and two kinds of unidentified aminolipids. Combining polyphasic taxonomic characteristics and phylogenetic relationships, twelve strains should represent eleven independent novel species of genus

Undibacterium

, for which the names Undibacterium baiyunense sp. nov. (type strain BYS107WT=GDMCC 1.2453T=KCTC 82653T), Undibacterium curvum sp. nov. (type strain CY22WT=GDMCC 1.1906T=KACC 21951T), Undibacterium fentianense sp. nov. (type strain FT137WT=GDMCC 1.2456T=KCTC 82656T), Undibacterium flavidum sp. nov. (type strain LX15WT=GDMCC 1.1910T=JCM 34286T), Undibacterium griseum sp. nov. (type strain FT31WT=GDMCC 1.1908T=KACC 21953T), Undibacterium hunanense sp. nov. (type strain CY18WT=GDMCC 1.1904T=KACC 21949T), Undibacterium luofuense sp. nov. (type strain LFS511WT=GDMCC 1.2458T=KCTC 82658T), Undibacterium nitidum sp. nov. (type strain LX22WT=GDMCC 1.1912T=KACC 21957T), Undibacterium rivi sp. nov. (type strain FT147WT=GDMCC 1.2457T=KCTC 82657T), Undibacterium rugosum sp. nov. (type strain CY7WT=GDMCC 1.1903T=KACC 21961T) and Undibacterium umbellatum sp. nov. (type strain NL8WT=GDMCC 1.1915T=KACC 21960T) are proposed.
Dysregulation of circulating protease activity in Covid-19-associated superinfection
Authors: Dos Santos Fernando , Li Joyce B. , Juocys Nathalia , Mazor Rafi , Beretta Laura , Coufal Nicole G. , Lam Michael T.Y. , Odish Mazen F. , Irigoyen Maria C. , O’Donoghue Anthony J. , Aletti Federico , Kistler Erik B. 
Published: October 2021

AbstractInfection by SARS-CoV-2 and subsequent COVID-19 can cause viral sepsis and septic shock. Several complications have been observed in patients admitted to the intensive care unit (ICU) with COVID-19, one of those being bacterial superinfection. Based on prior evidence that dysregulated systemwide proteolysis is associated with death in bacterial septic shock, we investigated whether protease activity and proteolysis could be elevated in COVID-19-induced sepsis with bacterial superinfection. In particular, we sought to assess the possible implications on the regulation of protein systems, such as for instance the proteins and enzymes involved in the clotting cascade.Blood samples collected at multiple time points during the ICU stay of four COVID-19 patients were analyzed to quantify: a) the circulating proteome and peptidome by mass spectrometry; b) plasma enzymatic activity of trypsin-like substrates and five clotting factors (plasmin, thrombin, factor VII, factor IX, factor X) by a fluorogenic assay.Of the four patients, one was diagnosed with bacterial superinfection on day 7 after beginning of the study and later died. The other three patients all survived (ICU length-of-stay 11.25±6.55 days, hospital stay of 15.25±7.18 days). Spikes in protease activity (factor VII, trypsin-like activity) were detected on day 7 for the patient who died. Corresponding increases in the total intensity of peptides derived by hydrolysis of plasma proteins, especially of fibrinogen degradation products, and a general reduction of coagulation proteins, were measured as well. A downregulation of endogenous enzymatic inhibitors, in particular trypsin inhibitors, characterized the non-surviving patient throughout her ICU stay. Enzymatic activity was stable in the patients who survived.Our study highlights the potential of multiomics approaches, combined with quantitative analysis of enzymatic activity, to i) shed light on proteolysis as a possible pathological mechanism in sepsis and septic shock, including COVID-19-induced sepsis; ii) provide additional insight into malfunctioning protease-mediated systems, such as the coagulation cascade; and iii) describe the progression of COVID-19 with bacterial superinfection.
Diamond Raman Laser and Yb Fiber Amplifier for In Vivo Multiphoton Fluorescence Microscopy
Authors: Engelmann Shaun A. , Zhou Annie , Hassan Ahmed M. , Williamson Michael R. , Jarrett Jeremy W. , Perillo Evan P. , Spence David J. , Jones Theresa A. , Dunn Andrew K. 
Published: October 2021

AbstractHere we introduce a fiber amplifier and a diamond Raman laser that output high powers (6.5 W, 1.3 W) at valuable wavelengths (1060 nm, 1250 nm) for multiphoton excitation of red-shifted fluorophores. These custom excitation sources are both simple to construct and cost-efficient in comparison to similar custom and commercial alternatives. Furthermore, they operate at a repetition rate (80 MHz) that allows fast image acquisition using resonant scanners. We demonstrate our system’s compatibility with fast resonant scanning, the ability to acquire neuronal images, and the capability to image vasculature at deep locations (>1 mm) within the mouse cerebral cortex.
Plasticity of Neural Connections Underlying Oxytocin-mediated Parental Behaviors of Male Mice
Authors: Inada Kengo , Hagihara Mitsue , Tsujimoto Kazuko , Abe Takaya , Konno Ayumu , Hirai Hirokazu , Kiyonari Hiroshi , Miyamichi Kazunari 
Published: October 2021

SummaryThe adult brain can flexibly adapt behaviors to specific life-stage demands. For example, while sexually naïve male mice are aggressive to the conspecific young, they start to provide caregiving to infants around the time when their own young are expected. How such behavioral plasticity is implemented at the level of neural connections remains poorly understood. Using viral-genetic approaches, here we establish hypothalamic oxytocin neurons as key regulators of parental caregiving behaviors of male mice. We then used rabies virus-mediated unbiased screen to identify excitatory neural connections originating from the lateral hypothalamus to the oxytocin neurons to be drastically strengthened when male mice become fathers. These connections are functionally relevant, as their activation suppresses pup-directed aggression in virgin males. These results demonstrate the life-stage associated, long-distance, and cell-type-specific plasticity of neural connections in the hypothalamus, the brain region classically assumed to be hard-wired.Highlight–OT is indispensable for parental caregiving behavior of male mice–Activation of OT neurons triggers paternal caregiving behavior in otherwise infanticidal sexually-naïve male mice partly via OT ligand–Unbiased rabies virus-mediated screening reveals enhanced connectivity originated from excitatory LHA neurons to OT neurons in fathers.–This structural plasticity can support behavioral plasticity
GAMES: A dynamic model development workflow for rigorous characterization of synthetic genetic systems
Authors: Dray Kate E. , Muldoon Joseph J. , Mangan Niall M. , Bagheri Neda , Leonard Joshua N. 
Published: October 2021

AbstractMathematical modeling is invaluable for advancing understanding and design of synthetic biological systems. However, the model development process is complicated and often unintuitive, requiring iteration on various computational tasks and comparisons with experimental data. Ad hoc model development can pose a barrier to reproduction and critical analysis of the development process itself, reducing potential impact and inhibiting further model development and collaboration. To help practitioners manage these challenges, we introduceGAMES: a workflow forGeneration andAnalysis ofModels forExploringSynthetic systems that includes both automated and human-in-the-loop processes. We systematically consider the process of developing dynamic models, including model formulation, parameter estimation, parameter identifiability, experimental design, model reduction, model refinement, and model selection. We demonstrate the workflow with a case study on a chemically responsive transcription factor. The generalizable workflow presented in this tutorial can enable biologists to more readily build and analyze models for various applications.Graphical Abstract
Escherichia coli ribosomal protein S1 enhances the kinetics of ribosome biogenesis and RNA decay
Authors: Duval Mélodie , Prévost Karine , Bandyra Katarzyna J. , Helfer Anne Catherine , Korepanov Alexey , Bakhti Latifa , Kuhn Lauriane , Springer Mathias , Romby Pascale , Luisi Ben F. , Massé Eric , Marzi Stefano 
Published: October 2021

SummaryEscherichia coli ribosomal protein S1 is essential for translation initiation of mRNAs and for cellular viability. Two oligonucleotide binding (OB)-fold domains located in the C-terminus of S1 are dispensable for growth, but their deletion causes a cold-shock phenotype, loss of motility and deregulation of RNA mediated stress responses. Surprisingly, the expression of the small regulatory RNA RyhB and one of its repressed target mRNA, sodB, are enhanced in the mutant strain lacking the two OB domains. Using in vivo and in vitro approaches, we show that RyhB retains its capacity to repress translation of target mRNAs in the mutant strain but becomes deficient in triggering rapid turnover of those transcripts. In addition, the mutant is defective in of the final step of the RNase E-dependent maturation of the 16S rRNA. This work unveils an unexpected function of S1 in facilitating ribosome biogenesis and RyhB-dependent mRNA decay mediated by the RNA degradosome. Through its RNA chaperone activity, S1 participates to the coupling between ribosome biogenesis, translation, and RNA decay.