bluuebunny/crossref_metadata_2025 huggingface dataset:
Pseudonocardia broussonetiae sp. nov., an endophytic actinomycete isolated from the roots of Broussonetia papyrifera
Authors: Mo Ping , Zhao Yunlin , Liu Jun , Xu Zhenggang , Gao Jian
Published: February 2021

A novel endophytic actinomycete, designated strain Gen 01T, was isolated from the roots of Broussonetia papyrifera and characterized by using a polyphasic approach. The predominant cellular fatty acids were iso-C16 : 0, summed feature 3, iso H-C16 : 1, C16 : 0 and iso-C14 : 0. The polar lipid profile consisted of diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylinositol mannosides, phospholipids of unknown structure containing glucosamine inositol, phosphatidylinositol and unidentified phospholipids. The major menaquinone was MK-8 (H4). The DNA G+C content of the genome sequence, consisting of 7 177 725 bp, was 74.5 mol%. Phylogenetic analysis of the full-length 16S rRNA gene sequences showed that strain Gen 01T belongs to the genus

Pseudonocardia

with the highest sequence similarity to

Pseudonocardia petroleophila

CGMCC 4.1532T (98.9 %) and lower than 98.7 % similarity to other species of the genus

Pseudonocardia

with validly published names. The average nucleotide identity and digital DNA–DNAhybridization values between strain Gen 01T and

P. petroleophila

CGMCC 4.1532T were 84.6 and 30.9 %, respectively. Furthermore, the morphological, physiological and biochemical characteristics were sufficient to categorize strain Gen 01T as being distinct from

P. petroleophila

CGMCC 4.1532T. Consequently, based on phenotypic and genotypic characteristics, strain Gen 01T represents a novel species of the genus

Pseudonocardia

, for which the name Pseudonocardia broussonetiae sp. nov. is proposed. The type strain is Gen 01T (=CICC 24820T=JCM 33840T).
Paracoccus amoyensis sp. nov., isolated from the surface seawater along the coast of Xiamen Island, China
Authors: Lyu Lina , Lai Qiliang , Li Jianyang , Yu Zhiqiang , Shao Zongze
Published: February 2021

Strain 11-3T was isolated from the surface seawater along the coast of Xiamen Island, China. Cells were Gram-stain-negative, oxidase- and catalase-positive, short and rod-shaped, nonmotile, 0.5-1.0 μm in width and 1.0-2.0 μm in length. Growth of strain 11-3T was at temperature of 15–37°C (optimum 28–35°C), at pH of 5.0-11.0 (optimum 7.0-9.0) and at salinity range of 0-10 (optimum 0.5–1). Phylogenetic analysis based on the 16S rRNA gene sequence indicated that strain 11-3T belonged to the genus

Paracoccus

and had the highest similarity with

Paracoccus caeni

MJ17T (98.1 %), followed by

Paracoccus xiamenensis

12-3T (97.1 %),

Paracoccus zeaxanthinifaciens

ATCC 21588T (97.1 %),

Paracoccus aestuarii

DSM 19484T (97.0 %),

Paracoccus liaowanqingii

2251T (97.0 %),

Paracoccus fistulariae

KCTC 22803T (97.0 %) and other species of the genus

Paracoccus

(95.2–96.8 %). The DNA-DNA hybridization values between strain 11-3T and the selected strains (

P. caeni

MJ17T,

P. xiamenensis

12-3T,

P. zeaxanthinifaciens

ATCC 21588T,

P. aestuarii

DSM 19484T and

P. liaowanqingii

2251T) were 19.4, 19.5, 21.6, 19.3 and 19.8 %, respectively. Corresponding, their ANI values were 77.53, 75.61, 75.36, 75.73 and 75.33 %, respectively. The major fatty acid was summed feature 8 (C18:1
ω6c/ω7c). The major respiratory quinone was Q10. The polar lipids included phosphatidylcholine (PC), phosphatidylethanolamine (PE), phosphatidylglycerol (PG), diphosphatidylglycerol (DPG), unidentified glycolipid (GL) and unidentified aminolipid (AL). The DNA G+C content of strain 11-3T was 60.1 %. Based on results of the phylogenetic analysis, phenotypic and chemotaxonomic characteristics, strain 11-3T represents a novel species of the genus

Paracoccus

, for which the name Paracoccus amoyensis sp. nov. is proposed. The type strain is 11-3T (=MCCC 1A16380T=KCTC 72689T).
Bluetongue virus in South America: current status based on phylogenetic analysis
Authors: Legisa Danilo , Dus Santos Maria José
Published: February 2021

Bluetongue (BT) is an insect-borne disease affecting domestic and wild ruminants. Bluetongue virus (BTV) is the causative agent of the BT disease. BT outbreaks have been widely recorded worldwide. However, in the South American subcontinent, accurate information about the disease and molecular epidemiology is still lacking because little effort has been made to cover the region. This study comprises an exhaustive phylogenetic analysis including all BTV sequences available in databases and reports new Argentinean sequences for Seg 8 and Seg 9. Maximum-likelihood phylogenetic analyses were conducted for Seg 2, Seg 3, Seg 6, Seg 7, Seg 8, Seg 9 and Seg 10. Throughout the study, wide circulation and genetic continuity along the American continent were detected. Also, reassortment events are reported, and the historical virus introduction path into and through South America is suggested.
ICTV Virus Taxonomy Profile: Pseudoviridae
Authors: Llorens Carlos , Soriano Beatriz , Krupovic Mart ,   ICTV Report Consortium
Published: February 2021

Pseudoviridae is a family of reverse-transcribing viruses with long terminal repeats (LTRs) belonging to the order Ortervirales. Pseudoviruses are commonly found integrated in the genomes of diverse plants, fungi and animals and are broadly known as Ty1/Copia LTR retrotransposons. Inside the cell, they form icosahedral virus particles, but unlike most other viruses, do not have an extracellular phase. This is a summary of the ICTV Report on the family Pseudoviridae, which is available at ictv.global/report/pseudoviridae.
Pathogenomic analyses of Mycobacterium microti, an ESX-1-deleted member of the Mycobacterium tuberculosis complex causing disease in various hosts
Authors: Orgeur Mickael , Frigui Wafa , Pawlik Alexandre , Clark Simon , Williams Ann , Ates Louis S. , Ma Laurence , Bouchier Christiane , Parkhill Julian , Brodin Priscille , Brosch Roland
Published: February 2021

Mycobacterium microti

is an animal-adapted member of the

Mycobacterium tuberculosis

complex (MTBC), which was originally isolated from voles, but has more recently also been isolated from other selected mammalian hosts, including occasionally from humans. Here, we have generated and analysed the complete genome sequences of five representative vole and clinical

M. microti

isolates using PacBio- and Illumina-based technologies, and have tested their virulence and vaccine potential in SCID (severe combined immune deficient) mouse and/or guinea pig infection models. We show that the clinical isolates studied here cluster separately in the phylogenetic tree from vole isolates and other clades from publicly available

M. microti

genome sequences. These data also confirm that the vole and clinical

M. microti

isolates were all lacking the specific RD1mic region, which in other tubercle bacilli encodes the ESX-1 type VII secretion system. Biochemical analysis further revealed marked phenotypic differences between isolates in type VII-mediated secretion of selected PE and PPE proteins, which in part were attributed to specific genetic polymorphisms. Infection experiments in the highly susceptible SCID mouse model showed that the clinical isolates were significantly more virulent than the tested vole isolates, but still much less virulent than the

M. tuberculosis

H37Rv control strain. The strong attenuation of the ATCC 35872 vole isolate in immunocompromised mice, even compared to the attenuated BCG (bacillus Calmette–Guérin) vaccine, and its historic use in human vaccine trials encouraged us to test this strain’s vaccine potential in a guinea pig model, where it demonstrated similar protective efficacy as a BCG control, making it a strong candidate for vaccination of immunocompromised individuals in whom BCG vaccination is contra-indicated. Overall, we provide new insights into the genomic and phenotypic variabilities and particularities of members of an understudied clade of the MTBC, which all share a recent common ancestor that is characterized by the deletion of the RD1mic region.
From genotype to phenotype: adaptations of Pseudomonas aeruginosa to the cystic fibrosis environment
Authors: Camus Laura , Vandenesch François , Moreau Karen
Published: February 2021

Pseudomonas aeruginosa

is one of the main microbial species colonizing the lungs of cystic fibrosis patients and is responsible for the decline in respiratory function. Despite the hostile pulmonary environment,

P. aeruginosa

is able to establish chronic infections thanks to its strong adaptive capacity. Various longitudinal studies have attempted to compare the strains of early infection with the adapted strains of chronic infection. Thanks to new ‘-omics’ techniques, convergent genetic mutations, as well as transcriptomic and proteomic dysregulations have been identified. As a consequence of this evolution, the adapted strains of

P. aeruginosa

have particular phenotypes that promote persistent infection.
Ribosome Profiling Reveals a Dichotomy Between Ribosome Occupancy of Nuclear-Encoded and Mitochondrial-Encoded OXPHOS mRNA Transcripts in a Striatal Cell Model of Huntington Disease
Authors: Subramaniam S , Shahani N
Published: February 2021

Huntington disease (HD) is caused by an expanded polyglutamine mutation in huntingtin (mHTT), which promotes a prominent atrophy in the striatum and subsequent psychiatric, cognitive, and choreiform movements. Multiple lines of evidence point to an association between HD and aberrant striatal mitochondrial functions. However, present knowledge about whether (or how) mitochondrial mRNA translation is differentially regulated in HD remains unclear. We have recently applied ribosome profiling (Ribo-Seq), a technique based on the high-throughput sequencing of ribosome-protected mRNA fragments, to analyze detailed snapshots of ribosome occupancy of the mitochondrial mRNA transcripts in control and HD striatal cells. Ribo-seq data revealed almost unaltered ribosome occupancy on the nuclear-encoded mitochondrial transcripts involved in oxidative phosphorylation (OXPHOS) and only a mild reduction in ribosome occupancy on a few selected transcripts (SHDA, Ndufv1, Timm23, Tomm5, and Mrps22) in HD cells. By contrast, ribosome occupancy of mitochondrially encoded OXPHOS mRNAs (mtNd-1, mtNd-2, mtNd-4, mtNd-4l, mtNd-5, mtNd-6, mt-Co1, mtCyt b, and mt-ATP8) was dramatically increased, implying widespread dichotomous effects on ribosome occupancy and OXPHOS mRNA translation in HD. Thus, mHTT may command signals that specifically regulate translation of the mitochondrial OXPHOS transcripts and influence HD pathogenesis.
Improving sequence-based modeling of protein families using secondary structure quality assessment
Authors: Malbranke Cyril , Bikard David , Cocco Simona , Monasson Rémi
Published: February 2021

Motivation

Modeling of protein family sequence distribution from homologous sequence data recently received considerable attention, in particular for structure and function predictions, as well as for protein design. In particular, Direct Coupling Analysis, a method to infer effective pairwise interactions between residues, was shown to capture important structural constraints and to successfully generate functional protein sequences. Building on this and other graphical models, we introduce a new framework to assess the quality of the secondary structures of the generated sequences with respect to reference structures for the family.

Results

We introduce two scoring functions characterizing the likeliness of the secondary structure of a protein sequence to match a reference structure, called Dot Product and Pattern Matching. We test these scores on published experimental protein mutagenesis and design dataset, and show improvement in the detection of non-functional sequences. We also show that use of these scores help rejecting non-functional sequences generated by graphical models (Restricted Boltzmann Machines) learned from homologous sequence alignments.

Availability

Supplementary Materials, Data and Code available athttps://github.com/CyrilMa/ssqa.

Contact

cyril.malbranke@ens.fr

Abstract Figure
Tools enabling flexible approaches to high-resolution subtomogram averaging
Authors: Burt Alister , Gaifas Lorenzo , Dendooven Tom , Gutsche Irina
Published: February 2021

Cryo-electron tomography and subtomogram averaging are increasingly used for macromolecular structure determinationin situ. Here we introduce a set of computational tools and resources designed to enable flexible approaches to subtomogram averaging. In particular, our tools simplify metadata handling, increase automation, and interface theDynamosoftware package with theWarp-Relion-Mpipeline. We provide a framework forab initioand geometrical approaches to subtomogram averaging combining tools from these packages. We illustrate the power of working within the framework enabled by our developments by applying it toEMPIAR-10164, a publicly available dataset containing immature HIV-1 virus-like particles, and a challengingin situdataset containing chemosensory arrays in bacterial minicells. Additionally, we establish an open and collaborative online platform for sharing knowledge and tools related to cryo-electron tomography data processing. To this platform, we contribute a comprehensive guide to obtaining state-of-the-art results fromEMPIAR-10164.
Modelling TGFβR and Hh pathway regulation of prognostic matrisome molecules in ovarian cancer
Authors: Delaine-Smith Robin M. , Maniati Eleni , Malacrida Beatrice , Nichols Sam , Roozitalab Reza , Jones Roanne R. , Lecker Laura , Pearce Oliver M.T. , Knight Martin M. , Balkwill Frances R.
Published: February 2021

In a multi-level ‘deconstruction’ of omental metastases, we previously identified a prognostic matrisome gene expression signature in high-grade serous ovarian cancer (HGSOC) and twelve other malignancies. Here, our aim was to understand how six of these extracellular matrix, ECM, molecules, COL11A1, COMP, FN1, VCAN, CTSB and COL1A1, are up-regulated in cancer. Using biopsies, we identified significant associations between TGFβR activity, Hedgehog signalling and these ECM molecules and then studied the associations in mono-, co- and tri-culture. Activated omental fibroblasts produced more matrix than malignant cells, directed by TGFβR and Hedgehog signalling crosstalk. We ‘reconstructed’ omental metastases in tri-culture of HGSOC cells, omental fibroblasts and adipocytes. This combination was sufficient to generate all six ECM proteins and the matrisome expression signature. TGFβR and Hedgehog inhibitor combinations attenuated fibroblast activation, gel remodelling and ECM remodelling in these models. The tri-culture model reproduces key features of omental metastases and allows study of diseased-associated ECM.
Terpenoid components, antioxidant and antibacterial activities of essential oils from fresh immature and mature leaves ofBlumea balsamifera,extracted with different hydrodistillation periods
Authors: Jirakitticharoen Sirinapha , Wisuitiprot Wudtichai , Jitareerat Pongphen , Wongs-Aree Chalermchai
Published: February 2021

Volatiles and antioxidant capacities in essential oils (EOs) from fresh immature and mature leaves ofBlumea balsamifera,extracted with different extraction periods of hydrodistillation, were investigated. There were seven major terpenoid compounds in the leaf extracts, including 2 monoterpenes of camphor and L-borneol, and 5 sesquiterpenes of silphiperfol-5-ene, 7-epi-silphiperfol-5-ene, ß-caryophyllene, ɤ-eudesmol, and α-eudesmol. Different hydrodistillation periods resulted in different quantitates and compositions of the terpenoids in EOs. The yield of EOs from the immature leaves was 1.4 times higher than the mature ones, whereas 73% of the yield was collected from the first 6 h of hydrodistillation. Camphor and L-borneol were almost collected in the first 6 h, while ß-caryophyllene, silphiperfolene, and 7-epi-silphiperfolene were above 80%, but ɤ-eudesmol and α-eudesmol were only 32 and 54% released. ß-Caryophyllene, ɤ-eudesmol, and α-eudesmol were found higher in the mature leaf EOs. Antioxidant capacities in EOs were positively related to terpenoid contents. Antibacterial activity of EOs from the immature leaves was subsequently tested. Although EOs from the hydrodistillation period of 12-18 h contained fewer terpenoid compositions, it showed the same minimum inhibitory concentration (MIC) and minimum bactericidal concentration (MBC) onEscherichia coliandPseudomonas aeruginosa,compared to 0-6 h EOs.
Synthetic Antigen-Presenting Cells for Adoptive T Cell Therapy
Authors: Dahotre Shreyas N. , Romanov Anna M. , Su Fang-Yi , Kwong Gabriel A.
Published: February 2021

Adoptive T cell therapies are transforming the treatment of solid and liquid tumors, yet their widespread adoption is limited in part by the challenge of generating functional cells. T cell activation and expansion using conventional antigen-presenting cells (APCs) is unreliable due to the variable quality of donor-derived APCs. As a result, engineered approaches using nanomaterials presenting T cell activation signals are a promising alternative due to their ability to be robustly manufactured with precise control over stimulation cues. In this work, we design synthetic APCs that consist of liposomes surface-functionalized with peptide-major histocompatibility complexes (pMHC). Synthetic APCs selectively target and activate antigen-specific T cell populations to levels similar to conventional protocols using non-specific αCD3 and αCD28 antibodies without the need for costimulation signals. T cells treated with synthetic APCs produce effector cytokines and demonstrate cytotoxic activity when co-cultured with tumor cells presenting target antigenin vitro. Following adoptive transfer into tumor-bearing mice, activated cells control tumor growth and improve overall survival compared to untreated mice. Synthetic APCs could potentially be used in the future to improve the accessibility of adoptive T cell therapies by removing the need for conventional APCs during manufacturing.
Motor cortex activity across movement speeds is predicted by network-level strategies for generating muscle activity
Authors: Saxena Shreya , Russo Abigail A. , Cunningham John P. , Churchland Mark M.
Published: February 2021

Learned movements can be skillfully performed at different paces. What neural strategies produce this flexibility? Can they be predicted and understood by network modeling? We trained monkeys to perform a cycling task at different speeds, and trained artificial recurrent networks to generate the empirical muscle-activity patterns. Network solutions reflected the principle that smooth well-behaved dynamics require low trajectory tangling. Network solutions had a consistent form, which yielded quantitative and qualitative predictions. To evaluate predictions, we analyzed motor cortex activity recorded during the same task. Responses supported the hypothesis that the dominant neural signals reflect not muscle activity, but network-level strategies for generating muscle activity. Single-neuron responses were better accounted for by network activity than by muscle activity. Similarly, neural population trajectories shared their organization not with muscle trajectories, but with network solutions. Thus, cortical activity could be understood based on the need to generate muscle activity via dynamics that allow smooth, robust control over movement speed.
Stochastic dynamics of consumer-resource interactions
Authors: Singh Abhyudai
Published: February 2021

The interaction between a consumer (such as, a predator or a parasitoid) and a resource (such as, a prey or a host) forms an integral motif in ecological food webs, and has been modeled since the early 20thcentury starting from the seminal work of Lotka and Volterra. While the Lotka-Volterra predator-prey model predicts a neutrally stable equilibrium with oscillating population densities, a density-dependent predator attack rate is known to stabilize the equilibrium. Here, we consider a stochastic formulation of the Lotka-Volterra model where the prey’s reproduction rate is a random process, and the predator’s attack rate depends on both the prey and predator population densities. Analysis shows that increasing the sensitivity of the attack rate to the prey density attenuates the magnitude of stochastic fluctuations in the population densities. In contrast, these fluctuations vary non-monotonically with the sensitivity of the attack rate to the predator density with an optimal level of sensitivity minimizing the magnitude of fluctuations. Interestingly, our systematic study of the predator-prey correlations reveals distinct signatures depending on the form of the density-dependent attack rate. In summary, stochastic dynamics of nonlinear Lotka-Volterra models can be harnessed to infer density-dependent mechanisms regulating consumer-resource interactions. Moreover, these mechanisms can have contrasting consequences on population fluctuations, with predator-dependent attack rates amplifying stochasticity, while prey-dependent attack rates countering to buffer fluctuations.
Targeted therapy forLIMD1-deficient non-small cell lung cancer subtypes
Authors: Davidson Kathryn , Grevitt Paul , Contreras G. Maria F. , Bridge Katherine S. , Hermida Miguel , Shah Kunal M. , Mardakheh Faraz K , Stubbs Mark , Clarke Paul A. , Burke Rosemary , Casado-Izquierdo Pedro , Cutillas Pedro R. , Martin Sarah A. , Sharp Tyson V.
Published: February 2021

An early event in lung oncogenesis is loss of the tumour suppressor geneLIMD1 (LIM domains containing 1);this encodes a scaffold protein, which suppresses tumourigenesis via a number of different mechanisms. Approximately 45% of non-small cell lung cancers (NSCLC) are deficient in LIMD11, yet this subtype of NSCLC has been overlooked in preclinical and clinical investigations. Defining therapeutic targets in these LIMD1 loss-of-function patients is difficult due to a lack of ‘druggable’ targets, thus alternative approaches are required. To this end, we performed the first drug repurposing screen to identify compounds that confer synthetic lethality with LIMD1 loss in NSCLC cells. PF-477736 was shown to selectively target LIMD1 deficient cellsin vitrothrough inhibition of multiple kinases, inducing cell death via apoptosis. Furthermore, PF-477736 was effective in treating LIMD1−/−tumors in subcutaneous xenograft models, with no significant effect in LIMD1+/+cells. We have identified a novel drug tool with significant preclinical characterization that serves as an excellent candidate to explore and define LIMD1-deficient cancers as a new therapeutic subgroup of critical unmet need.

Significance Statement

Here we provide the first proof-of-concept data validating the scope for development of a targeted therapy against the non-small cell lung cancers (NSCLC) subtypes deficient in expression of the LIMD1 tumor suppressor gene. Approximately 45% of NSCLC are deficient in LIMD11representing at least 1.2 million lung cancer patients worldwide; yet this subtype has been ignored in preclinical and clinical investigations with no targeted therapies available. This seminal study applied synthetic lethality drug screening to target the loss/reduction of LIMD1 in lung cancer and normal cell lines, identifying and validating the multi-kinase inhibitor PF-477736 as a selectively cytotoxic compound towards LIMD1 deficient cells. This study provides rationale for further investigation into targeting LIMD1 loss in lung cancer, thereby addressing a critical unmet need for therapeutic approached to targeting LIMD1-deficent cancer subtypes.
ESD1 Affects Seed Setting Rate in Rice by Controlling Embryo Sac Development
Authors: Wang Tiankang , Li Yixing , Song Shufeng , Qiu Mudan , Zhang Licheng , Li Chengxia , Dong Hao , Li Lei , Wang Jianlong , Li Li
Published: February 2021

Seed setting rate is one of the critical factors that determine rice yield. Grain formation is a complex biological process, whose molecular mechanism is yet to be improved. Here we investigated the function of an OVATE family protein, Embryo Sac Development 1 (ESD1), in the regulation of seed setting rate in rice (Oryza sativa) by examining its loss-of-function mutants generated via CRISPR/Cas9 technology.ESD1was predominantly expressed at stage 6 of panicle development, especially in the ovules.esd1mutants displayed reduced seed setting rates with normal stamen development and pollen tube growth but abnormal pistil group. Investigation of embryo sacs revealed that during the mitosis of functional megaspores, some egg cells degraded during differentiation inesd1mutants, thereby hindering subsequent fertilization process and reducing seed setting rate. In addition, the transcriptional level ofOsAPC6,a reported embryo sac developing gene, was found to be significantly reduced inesd1mutants. These results support that ESD1 is an important modulator of embryo sac development and seed setting rate in rice. Together, this finding demonstrates that ESD1 positively regulates the seed setting rate by controlling embryo sac development in rice, and has implications for the improvement of rice yield.
Structural insights into the intermolecular interaction of the adhesin SdrC in the pathogenicity of Staphylococcus aureus
Authors: Wang Junchao , Zhang Min , Wang Mingzhu , Zang Jianye , Zhang Xuan , Hang Tianrong
Published: February 2021

Staphylococcus aureus is an opportunistic disease-causing pathogen that is widely found in the community and on medical equipment. A series of virulence factors secreted by S. aureus can trigger severe diseases such as sepsis, endocarditis and toxic shock, and thus have a great impact on human health. The transformation of S. aureus from a colonization state to a pathogenic state during its life cycle is intimately associated with the initiation of bacterial aggregation and biofilm accumulation. SdrC, an S. aureus surface protein, can act as an adhesin to promote cell attachment and aggregation by an unknown mechanism. Here, structural studies demonstrate that SdrC forms a unique dimer through intermolecular interaction. It is proposed that the dimerization of SdrC enhances the efficiency of bacteria–host attachment and therefore contributes to the pathogenicity of S. aureus.
Crystal structure of cis-(1,4,8,11-tetraazacyclotetradecane-κ4
N)bis(thiocyanato-κN)chromium(III) bromide from synchrotron X-ray diffraction data
Authors: Moon Dohyun , Choi Jong-Ha
Published: February 2021

The crystal structure of the title complex, cis-[Cr(NCS)2(cyclam)]Br (cyclam = 1,4,8,11-tetraazacyclotetradecane, C10H24N4), has been determined from synchrotron X-ray data. The asymmetric unit contains one [Cr(NCS)2(cyclam)]+ cation and one bromide anion. The CrIII ion of the complex cation is coordinated by the four N atoms of the cyclam ligand and by two N-coordinating NCS groups in a cis arrangement, displaying a distorted octahedral coordination sphere. The Cr—N(cyclam) bond lengths are in the range 2.075 (3) to 2.081 (3) Å while the average Cr—N(NCS) bond length is 1.996 (16) Å. The macrocyclic cyclam moiety adopts the most stable cis-V conformation. The crystal structure is stabilized by intermolecular hydrogen bonds involving the cyclam N—H groups as donor groups, and the bromide anion and the S atom of one of the NCS ligands as acceptor groups.
Social media use by first-generation college students and two forms of social capital: a revealed causal mapping approach
Authors: Deng Xuefei (Nancy) , Fernández Yesenia , Zhao Meng
Published: February 2021

Purpose

The purpose of this study is to examine social media use and its impacts on first generation students by answering the two questions: how do FGS use social media on college campuses, compared to their peers? How does the use of social media affect their academic experiences?

Design/methodology/approach

This qualitative study adopted social capital theory as a sensitizing framework for understanding the social media (SM) use and the resources valued by first-generation students (FGS) and used a revealed causal mapping method to analyze the narratives of 96 informants to identify key constructs and linkages on SM use and perceived outcomes.

Findings

The revealed causal mapping (RCM) analysis revealed nine key constructs that shaped the SM use and academic experience of FGS and their peers. The linkages among the nine constructs: three types of social capital (bridging, family bonding and friend bonding), three types of SM use (social, cognitive and hedonic) and three outcomes (academic support, emotional support and distraction to work) were different between FGS and their peers. Among FGS, SM use and perceptions differed by gender.

Originality/value

Leveraging social media is critical for universities to enhance FGS persistence, yet knowledge remains limited. This study showed FGS differed from their counterparts in the SM use and perceptions. Among FGS, the SM use and perceptions differed by gender. The research contributions are: (1) SM technology can empower FGS by building social capital, impacting their academic experiences and psychological well-being and (2) the intersection of gender and student generation status is worth investigation. This paper enriches FGS research by proposing a model of SM use and social capital.
Comparison of post‐operative pain in short versus long stitch technique for abdominal wall closure after elective laparotomy: a double‐blind randomized controlled trial
Authors: Lai Larry Weng‐Hong , Roslani April Camilla , Yan Yang‐Wai , Bhojwani Kavita M. , Jamaluddin Mohamad Fadhil Hadi
Published: February 2021

Background

Conventional mass closure uses suture‐to‐wound length ratio of 4:1 (‘long stitch’, LS). ‘Short stitch’ (SS) has a suture‐to‐wound length ratio of more than 4 and incorporates only the linea alba, which may reduce tension and pain. We compared the post‐operative pain after laparotomy closure using LS and SS.

Methods

Patients undergoing elective midline laparotomy through standardized incisions in two tertiary hospitals from February 2017 to September 2018 were randomized to either LS or SS. The primary outcome was post‐operative patient‐controlled analgesia morphine usage at 24 h. Secondary outcomes were presence of surgical site infection and length of hospital stay (LOHS). Categorical variables were analysed using chi‐squared analysis. Outcomes of study were tested for normal distribution. Skewed data were analysed using Mann–Whitney U‐test.

Results

Eighty‐six patients were recruited (42 SS and 44 LS). The median age was 66 (interquartile range (IQR) 15). Majority were males (62.8%) and Chinese (50%). The median incision length was 17 cm in both groups. The median patient‐controlled analgesia morphine usage 24 h post‐operatively did not differ significantly (SS 21 mg, IQR 28.3; LS 18.5 mg, IQR 33.8, P = 0.829). The median pain score at rest (SS 1, IQR 1; LS 1, IQR 2, P = 0.426) and movement (SS 3, IQR 1; LS 3, IQR 2, P = 0.307) did not differ significantly. LOHS was shorter in the SS group (SS 6, IQR 4; LS 8, IQR 5, P = 0.034). The rate of surgical site infection trended lower in the SS group with no statistical difference.

Conclusion

There were no differences in post‐operative pain between SS and LS but we found that there were shorter LOHS in SS arm as secondary outcome.
Challenges in diagnosis and management of a spiradenocarcinoma: a comprehensive literature review
Authors: Wagner Katy , Jassal Karishma , Lee James C. , Ban Ee‐Jun , Cameron Rhoda , Serpell Jonathan
Published: February 2021

Background

Spiradenocarcinoma is a rare skin adnexal neoplasm that may behave aggressively. It is often associated with a benign slow‐growing spiradenoma that has undergone malignant transformation. Given the paucity of cases in the literature, there is a lack of consensus on treatment.

Methods

The terms ‘malignant spiradenoma’ or ‘spiradenocarcinoma’ were systematically used to search the PubMed, MEDLINE and Google Scholar databases. A total of 182 cases of spiradenocarcinoma were identified as eligible for this comprehensive literature review.

Results

Spiradenocarcinoma was commoner in older age and Caucasian race. In most cases, surgical excision for local disease is the mainstay of treatment. Lymph node dissection is usually reserved for those with suspected or confirmed lymph node metastases. High rates of local recurrence (20.8%), metastasis (37.4%) and mortality (19.1%) were identified, prompting some authors to suggest regular follow up including chest X‐rays and liver function tests.

Conclusions

Patients with spiradenocarcinoma may benefit from a magnetic resonance imaging and fluorodeoxyglucose‐positron emission tomography/computed tomography to establish the extent of disease. We recommend wide local excision as the treatment of choice to achieve surgical margins of ≥1 cm, with node resection to be determined on a case‐to‐case basis. Regular follow up is important given the high rate of local recurrence, metastasis and mortality. This should include an examination of the regional lymph nodes. Further research is required to refine an evidence‐based approach to spiradenocarcinoma.
Incidence of catheter‐associated right atrial thrombus detected by transthoracic echocardiogram
Authors: Clark Jeffrey R. , Hoffman Steven C. , Shlobin Nathan A. , Bavishi Aakash , Narang Akhil
Published: February 2021

Introduction

The development of right atrial (RA) thrombus (RAT) is a known complication of central venous catheter insertion (CVC). Deeper insertion of CVC within the RA may increase the risk for RAT development versus those placed at the superior vena cava (SVC)‐RA junction. We sought to evaluate the incidence of catheter‐associated RAT as detected by transthoracic echocardiograms (TTEs), characterize thrombi though multimodal imaging, and evaluate thrombi management with follow‐up imaging.

Methods

A retrospective analysis was conducted of consecutive TTEs from our institution between October 1, 2018, and January 1, 2020, in which a venous catheter was visualized in the RA. Studies were reviewed in detail to determine the presence of suspected RAT. Demographic data, comorbidities, laboratory values, characteristics of the catheter and the thrombus, subsequent imaging and management, and outcomes were collected.

Results

A total of 364 TTEs were performed in 290 patients with a venous catheter visualized in the RA. Of these 290 patients, 15 had an imaging suspicion for RAT yielding an incidence of 5.2%. Management strategies included anticoagulation in 13 (86.7%) patients and catheter removal in 11 (73.3%) patients. At eight months of follow‐up, 11 (73.3%) patients had resolution of RAT based on subsequent imaging.

Conclusion

In patients with deeply placed CVC catheters, the incidental detection of RAT by TTE was not trivial. Anticoagulation and catheter removal and replacement, if deemed safe, were effective methods of thrombus management. RAT as a complication of CVCs must be accounted for when addressing factors that influence depth of CVC insertion.
Financial flexibility demand and corporate financial decisions
Authors: Byoun Soku
Published: February 2021

I develop a hypothesis that predicts nonlinear patterns of leverage and cash holdings over firms' financial flexibility (FF) demand stages. The hypothesis also predicts distinctive financing patterns over the FF demand stages. The empirical results support the hypothesis: Flexibility‐building firms maintain low leverage by issuing equity in order to raise cash; flexibility‐utilizing firms increase debt and use reserved cash to exercise investment options; and flexibility‐recharging firms repay debt and increase cash using internal funds. The pronounced nonlinear patterns in financial decisions over the FF demand stages have important implications for previously documented empirical regularities and for future theoretical considerations.
Critical amino acids in the TM2 of EAAT2 are essential for membrane‐bound localization, substrate binding, transporter function and anion currents
Authors: Mai Dongmei , Chen Rongqing , Wang Ji , Zheng Jiawei , Zhang Xiuping , Qu Shaogang
Published: February 2021

Excitatory amino acid transporter 2 (EAAT2), the gene of which is known as solute carrier family 1 member 2 (SLC1A2), is an important membrane‐bound transporter that mediates approximately 90% of the transport and clearance of l‐glutamate at synapses in the central nervous system (CNS). Transmembrane domain 2 (TM2) of EAAT2 is close to hairpin loop 2 (HP2) and far away from HP1 in the inward‐facing conformation. In the present study, 14 crucial amino acid residues of TM2 were identified via alanine‐scanning mutations. Further analysis in EAAT2‐transfected HeLa cells in vitro showed that alanine substitutions of these residues resulted in a decrease in the efficiency of trafficking/targeting to the plasma membrane and/or reduced functionality of membrane‐bound, which resulted in impaired transporter activity. After additional mutations, the transporter activities of some alanine‐substitution mutants recovered. Specifically, the P95A mutant decreased EAAT2‐associated anion currents. The Michaelis constant (Km) values of the mutant proteins L85A, L92A and L101A were increased significantly, whereas R87 and P95A were decreased significantly, indicating that the mutations L85A, L92A and L101A reduced the affinity of the transporter and the substrate, whereas R87A and P95A enhanced this affinity. The maximum velocity (Vmax) values of all 14 alanine mutant proteins were decreased significantly, indicating that all these mutations reduced the substrate transport rate. These results suggest that critical residues in TM2 affect not only the protein expression and membrane‐bound localization of EAAT2, but also its interactions with substrates. Additionally, our findings elucidate that the P95A mutant decreased EAAT2‐related anion currents. Our results indicate that the TM2 of EAAT2 plays a vital role in the transport process. The key residues in TM2 affect protein expression in the membrane, substrate transport and the anion currents of EAAT2.
Anwulignan is a novel JAK1 inhibitor that suppresses non‐small cell lung cancer growth
Authors: Xie Xiaomeng , Wang Xiangyu , Shi Xiaodan , Zhang Yuanyuan , Laster Kyle Vaughn , Liu Kangdong , Dong Zigang , Kim Dong Joon
Published: February 2021

Anwulignan is a monomer compound derived from Schisandra sphenanthera lignans. It has been reported to possess a spectrum of pharmacological activities, including anti‐bacterial, anti‐inflammatory, anticancer and hepatoprotective properties. However, its anticancer capacity and molecular mechanism(s) against non‐small cell lung cancer (NSCLC) have not been fully elucidated. Anwulignan significantly inhibited cell growth and increased G1‐phase cell cycle arrest in NSCLC cells. Anwulignan strongly attenuates the JAK1/STAT3 signalling pathway by directly targeting JAK1 protein kinase activity in vitro. The anticancer activity by Anwulignan is dependent upon the JAK1 protein expression. Remarkably, Anwulignan strongly inhibited tumour growth in vivo. In conclusion, Anwulignan is a novel JAK1 inhibitor that may have therapeutic implications for NSCLC management.
Knowledge of and Attitudes Toward Perinatal Home Visiting in Women with High‐Risk Pregnancies
Authors: Barkin Jennifer L. , Bloch Joan Rosen , Smith Katherine E.R. , Telliard Sarah N. , McGreal Analise , Sikes Chris , Ezeamama Amare , Buoli Massimiliano , Serati Marta , Bridges Christy C.
Published: February 2021

Introduction

Published research indicates that some perinatal home visiting programs are highly effective. However, there is a dearth of information regarding how these services apply to women experiencing a high‐risk pregnancy. The aim of this study was to determine the potential acceptability of home visiting services within this vulnerable population and identify what services women want.

Methods

Four focus groups (N = 32) were conducted with a population of low‐income, pregnant individuals in medically underserved central Georgia (United States). Participants were evaluated based on their current exposure to home visiting, receptiveness to home visiting, and reasons for apprehension regarding home visiting.

Results

The results of this study were mixed, with women expressing both interest in and reluctance about home visiting programs. Themes of distrust and fear of judgment or persecution existed. Women also varied with regard to what home visiting services they would like offered. Those discussed included assistance with maternal or infant medical needs, maternal function tasks, household tasks, and child care.

Discussion

Home visiting programs can be effective for improving maternal and child health outcomes. However, not all home visiting programs effectively reach their target population. More research is needed to determine what women who have high‐risk conditions during pregnancy want help with and how to increase receptiveness. The results of this study could be informative to health care providers who treat persons with high‐risk conditions in identifying adjunctive services for those in need of additional support.
Role of insulin in the neuroendocrine control of reproduction
Authors: Evans Maggie C. , Hill Jennifer W. , Anderson Greg M.
Published: February 2021

Infertility associated with insulin resistance is characterised by abnormal hormone secretion by the hypothalamus, pituitary gland and gonads. These endocrine tissues can maintain insulin sensitivity even when tissues such as the muscle and liver become insulin‐resistant, resulting in excessive insulin stimulation as hyperinsulinaemia develops. Experiments conducted to determine the role of neuronal insulin signalling in fertility were unable to recapitulate early findings of hypogonadotrophic hypogonadism in mice lacking insulin receptors throughout the brain. Rather, it was eventually shown that astrocytes critically mediate the effects of insulin on puberty timing and adult reproductive function. However, specific roles for neurones and gonadotrophs have been revealed under conditions of hyperinsulinaemia and by ablation of insulin and leptin receptors. The collective picture is one of multiple insulin‐responsive inputs to gonadotrophin releasing hormone neurones, with astrocytes being the most important player.
Junzi living in liberal democracy: What role could Confucianism play in political liberalism?
Authors: Wong Baldwin
Published: February 2021

It has been widely argued that East Asian governments should be permitted to promote Confucian values. Recently, Zhuoyao Li rejected this view and advocates that East Asian governments should be neutral to all cultures and religions, including Confucianism. Nevertheless, Li believes that Confucianism does not loses its significance in a political liberal state because Confucians can still propose laws and policies, so long as their proposals are justified by public reason. In this paper, I argue that Li misunderstands the true significance of Confucianism in his model. Under the constraint of public reason, Confucians can hardly give any novel input in public deliberation. Rather, I believe that the contribution of Confucianism is to educate citizens to become fully just in the private sphere. Citizens may learn to be unjust if injustices are common in the private sphere. However, a political liberal state would be criticized as being overly invasive if it directly regulates the private sphere. Hence, I propose a division of educational labour between political liberalism and Confucianism in the public and private sphere. Finally, I use the Confucian workplace as an example to show how rituals in the workplace can enhance citizens’ sense of justice in the private sphere.
Word frequency effect in written production: Evidence from ERPs and neural oscillations
Authors: Wang Cheng , Zhang Qingfang
Published: February 2021

It has been widely documented that word frequency (WF) modulates language processing in various input and output modalities. WF effect has also been reported in the domain of written production; however, how WF affects written production is a controversial issue. The present study attempts to investigate the time course of and neural oscillation underlying the WF effect in handwritten production. Participants were asked to handwrite pictures names of high versus low WF, while concurrently recording EEG. EEG trials were extracted time‐locked to picture onsets and then submitted to event‐related potential analysis and time–frequency analysis. WF affected ERPs in the time windows of around 98–160 and 282–360 ms after picture onsets. More importantly, WF modulated the evoked and induced theta‐band (4–8 Hz) neural oscillations in the time window of around 36–240 and 244–472 ms, respectively. Considering the time course of language production and the role of theta‐band oscillation in long‐term memory retrieval, we suggest that the two stages of the WF effect, respectively, reflect conceptual preparation and retrieval of orthographic word‐forms in written production.
Recognizing Ourselves in Others: A Reply to Bauer and Svolba in SJP 55.1
Authors: Witonsky Abe
Published: February 2021

In “Justice at the Margins: The Social Contract and the Challenge of Marginal Cases” (Southern Journal of Philosophy, 55.1), Nathan Bauer and David Svolba appeal to a concept of recognition found in social contract theory to argue that all humans, including humans who lack certain unique cognitive abilities, so‐called marginal cases, have rights that nonhuman animals lack. The main reason is that we can recognize ourselves in all humans, but not in nonhuman animals. I argue (i) that it is unclear that we can recognize ourselves in certain types of marginal cases, such as corpses and embryos; (ii) that Bauer and Svolba’s reason for why we cannot recognize ourselves in nonhuman animals is questionable; and (iii) if we can recognize ourselves in any types of marginal cases, then we should be able to recognize ourselves in nonhuman animals.
Abundant Monovalent Ions as Environmental Signposts for Pathogens during Host Colonization
Authors: Tan Shumin
Published: February 2021

Host colonization by a pathogen requires proper sensing and response to local environmental cues, to ensure adaptation and continued survival within the host. The ionic milieu represents a critical potential source of environmental cues, and indeed, there has been extensive study of the interplay between host and pathogen in the context of metals such as iron, zinc, and manganese, vital ions that are actively sequestered by the host.
Genomic Diversity of Burkholderia pseudomallei in Ceara, Brazil
Authors: Gee Jay E. , Gulvik Christopher A. , Castelo-Branco Debora S. C. M. , Sidrim José J. C. , Rocha Marcos F. G. , Cordeiro Rossana A. , Brilhante Raimunda S. N. , Bandeira Tereza J. P. G. , Patrício Iracema , Alencar Lucas P. , da Costa Ribeiro Ana Karoline , Sheth Mili , Deka Mark A. , Hoffmaster Alex R. , Rolim Dionne
Published: February 2021

B. pseudomallei
causes significant morbidity and mortality, but its geographic prevalence and genetic diversity are not well characterized, especially in the Western Hemisphere. A better understanding of the genetic relationships among clinical and environmental isolates will improve knowledge of the population structure of this bacterium as well as the ability to conduct epidemiological investigations of cases of melioidosis.
Supplemental Material 1: Geomorphic expression and slip rate of the Fairweather fault, southeast Alaska, and evidence for predecessors of the 1958 rupture
Authors: Witter R.C. , al. et
Published: February 2021

GIS material includes four shapefiles depicting geomorphic lines, fault lines, unit contacts, and geologic units mapped on lidar-based digital elevation models and in the field as explained in the paper.