bluuebunny/crossref_metadata_2025 huggingface dataset:
Structural and electronic properties of two-dimensional titanium carbo-oxides
Authors: Hu Yong-Jie , Tandoc Christopher , Barsoum Michel W , Rosen Johanna , Björk Jonas
Published: December 2022

This work was inspired by new experimental findings where we discovered a two-dimensional (2D) material comprised of titanium-oxide-based one-dimensional (1D) sub-nanometer filaments. Preliminary results suggest that the 2D material contains considerable amounts of carbon, C, in addition to titanium, Ti, and oxygen, O. The aim of this study is to investigate the low-energy, stable atomic forms of 2D titanium carbo-oxides as a function of C content. Via a combination of first-principles calculations and an effective structure sampling scheme, the stable configurations of C-substitutions are comprehensively searched by templating different 2D TiO2 polymorphs and considering a two O to one C replacement scheme. Among the searched stable configurations, a structure where the (101) planes of anatase bound the top and bottom surfaces with a chemical formula of

Ti

C

1

/

4

O

3

/

2

was of particularly low energy. Furthermore, the variations in the electronic band structure and chemical bonding environments caused by the high-content C substitution are investigated via additional calculations using a hybrid exchange-correlation functional.
Novel Ni3S4/NiS/NC composite with multiple heterojunctions synthesized through space-confined effect for high-performance supercapacitors
Authors: Wei Wutao , Guo Zijie , Xu Jiaqiang , Fang Zhe , Zhang Jiujun , Jia Yu , Mi Liwei
Published: December 2022

The construction of heterojunctions in composite materials to optimize the electronic structures and active sites of energy materials is considered to be the promising strategy for the fabrication of high-performance electrochemical energy devices. In this paper, a one-step, easy processing and cost-effective technique for generating composite materials with heterojunctions was successfully developed. The composite containing Ni3S4, NiS, and N-doped amorphous carbon (abbreviated as Ni3S4/NiS/NC) with multiple heterojunction nanosheets are synthesized via the space-confined effect of molten salt interface of recrystallized NaCl. Several lattice matching forms of Ni3S4 with cubic structure and NiS with hexagonal structure are confirmed by the detailed characterization of heterogeneous interfaces. The C–S bonds are the key factor in realizing the chemical coupling between nickel sulfide and NC and constructing the stable heterojunction. Density functional theory calculations further revealed that the electronic interaction on the heterogeneous interface of Ni3S4/NiS can contribute to high electronic conductivity. The heterogeneous interfaces are identified to be the good electroactive region with excellent electrochemical performance. The synergistic effect of abundant active sites, the enhanced kinetic process and valid interface charge transfer channels of Ni3S4/NiS/NC multiple heterojunction can guarantee high reversible redox activity and high structural stability, resulting in both high specific capacitance and energy/power densities when it is used as the electrode for supercapacitors. This work offers a new avenue for the rational design of the heterojunction materials with improved electrochemical performance through space-confined effect of NaCl.
Near-unity efficiency in ridge waveguide-based, on-chip single-photon sources
Authors: Wang Y J , Vannucci L , Burger S , Gregersen N
Published: December 2022

We report a numerical design procedure for pursuing a near-unity coupling efficiency in quantum dot (QD)-cavity ridge waveguide single-photon sources (SPSs) by performing simulations with the finite element method. Our optimum design which is based on a 1D nanobeam cavity, achieves a high source efficiency ε

xy
of 97.7% for an isotropic in-plane dipole, together with a remarkable Purcell factor of 38.6. Such a good performance is mainly attributed to the high index contrast of GaAs/SiO2 and a careful cavity design achieving constructive interference and low scattering losses. Furthermore, we analyze the bottleneck of the proposed platform, which is the mode mismatch between the cavity mode and the Bloch mode in the nanobeam. Accordingly, we present the optimization recipe of an arbitrarily high-efficiency on-chip SPS by implementing a taper section, whose high smoothness is beneficial to gradually overcoming the mode mismatch, and therefore leading to a higher Purcell factor and source efficiency. Finally, we see good robustness of the source properties in the taper-nanobeam system under the consideration of realistic fabrication imperfections on the hole variation and QD position deviation.
The trajectory of family caregiving for older adults with dementia: difficulties and challenges
Authors: Tu Jiong , Li Haiyan , Ye Bei , Liao Jing
Published: December 2022

Introduction

As the main source of informal care in China, family members bear a tremendous caregiving burden, particularly in relation to older people with dementia (PwDs). However, the continuous caregiving trajectory of family caregivers was unclear.

Objectives

To investigate the trajectory of PwDs’ family caregivers’ struggles from home care to institutional care, and identify the common tipping points leading to institutional care from their perspectives.

Methods

An ethnographic study was conducted in a long-term care institution in Chengdu, China, from 2019 to 2020. Face-to-face, semi-structured interviews were carried out with 13 family members (i.e. 5 spouses and 8 adult children) of older PwDs during family caregivers’ visits. The interviews were recorded and transcribed, after which the transcripts were analysed using thematic analysis.

Results

The family caregivers’ experiences before and after the PwDs’ institutionalization fell into two distinctive parts, and three subthemes about their caregiving experiences in each period were identified: the mental stress, the physical care burden, and the social and emotional pressure connected to home-based care; the moral pressure and emotional torment, the financial burden, and new worries after institutionalization. The tipping points in between the two stages were major changes or incidents related to the PwDs’ status. Variations in the spouse and older children’s care experiences also emerged.

Conclusion

Our study provides a nuanced analysis of the trajectory of family caregiving for PwDs. The plight of family caregivers at all stages should be recognized and supported with adequate medical and social resources, with a further consideration of the caregivers’ relationships with the older PwDs.
Microbiome Toolbox: methodological approaches to derive and visualize microbiome trajectories
Authors: Banjac Jelena , Sprenger Norbert , Dogra Shaillay Kumar
Published: December 2022

Motivation

The gut microbiome changes rapidly under the influence of different factors such as age, dietary changes or medications to name just a few. To analyze and understand such changes, we present a Microbiome Toolbox. We implemented several methods for analysis and exploration to provide interactive visualizations for easy comprehension and reporting of longitudinal microbiome data.

Results

Based on the abundance of microbiome features such as taxa as well as functional capacity modules, and with the corresponding metadata per sample, the Microbiome Toolbox includes methods for (i) data analysis and exploration, (ii) data preparation including dataset-specific preprocessing and transformation, (iii) best feature selection for log-ratio denominators, (iv) two-group analysis, (v) microbiome trajectory prediction with feature importance over time, (vi) spline and linear regression statistical analysis for testing universality across different groups and differentiation of two trajectories, (vii) longitudinal anomaly detection on the microbiome trajectory and (viii) simulated intervention to return anomaly back to a reference trajectory.

Availability and implementation

The software tools are open source and implemented in Python. For developers interested in additional functionality of the Microbiome Toolbox, it is modular allowing for further extension with custom methods and analysis. The code, python package and the link to the interactive dashboard of Microbiome Toolbox are available on GitHub https://github.com/JelenaBanjac/microbiome-toolbox

Supplementary information

Supplementary data are available at Bioinformatics online.
Poisson hurdle model-based method for clustering microbiome features
Authors: Qiao Zhili , Barnes Elle , Tringe Susannah , Schachtman Daniel P , Liu Peng
Published: December 2022

Motivation

High-throughput sequencing technologies have greatly facilitated microbiome research and have generated a large volume of microbiome data with the potential to answer key questions regarding microbiome assembly, structure and function. Cluster analysis aims to group features that behave similarly across treatments, and such grouping helps to highlight the functional relationships among features and may provide biological insights into microbiome networks. However, clustering microbiome data are challenging due to the sparsity and high dimensionality.

Results

We propose a model-based clustering method based on Poisson hurdle models for sparse microbiome count data. We describe an expectation–maximization algorithm and a modified version using simulated annealing to conduct the cluster analysis. Moreover, we provide algorithms for initialization and choosing the number of clusters. Simulation results demonstrate that our proposed methods provide better clustering results than alternative methods under a variety of settings. We also apply the proposed method to a sorghum rhizosphere microbiome dataset that results in interesting biological findings.

Availability and implementation

R package is freely available for download at https://cran.r-project.org/package=PHclust.

Supplementary information

Supplementary data are available at Bioinformatics online.
TransFlow: a Snakemake workflow for transmission analysis ofMycobacterium tuberculosiswhole-genome sequencing data
Authors: Pan Junhang , Li Xiangchen , Zhang Mingwu , Lu Yewei , Zhu Yelei , Wu Kunyang , Wu Yiwen , Wang Weixin , Chen Bin , Liu Zhengwei , Wang Xiaomeng , Gao Junshun
Published: December 2022

Motivation

Whole-genome sequencing (WGS) is increasingly used to aid the understanding of Mycobacterium tuberculosis (MTB) transmission. The epidemiological analysis of tuberculosis based on the WGS technique requires a diverse collection of bioinformatics tools. Effectively using these analysis tools in a scalable and reproducible way can be challenging, especially for non-experts.

Results

Here, we present TransFlow (Transmission Workflow), a user-friendly, fast, efficient and comprehensive WGS-based transmission analysis pipeline. TransFlow combines some state-of-the-art tools to take transmission analysis from raw sequencing data, through quality control, sequence alignment and variant calling, into downstream transmission clustering, transmission network reconstruction and transmission risk factor inference, together with summary statistics and data visualization in a summary report. TransFlow relies on Snakemake and Conda to resolve dependencies among consecutive processing steps and can be easily adapted to any computation environment.

Availability and implementation

TransFlow is free available at https://github.com/cvn001/transflow.

Supplementary information

Supplementary data are available at Bioinformatics online.
Cervical cancer screening history among women diagnosed with cervical cancer in Estonia 2017–18
Authors: Orumaa Madleen , Innos Kaire , Suurna Maria , Veerus Piret
Published: December 2022

Background

Despite the national cervical cancer screening programme launched in 2006, Estonia has one of the highest cervical cancer incidence rates in Europe. While the overall coverage of cervical cytology is high, the factors related to cancer screening history prior to cancer diagnosis need to be studied.

Methods

In this study, we aimed to examine the 10-year screening history of women diagnosed with cervical cancer in Estonia in 2017–18, using data collected from laboratory reports from 2007 to 2018. From each report, we extracted information on the date and result of cytology and on the laboratory where the sample was assessed. We analysed these data across cancer histology, the time interval between the last test result and cancer diagnosis and the laboratory type (local or regional).

Results

Among 319 women with cervical cancer, 181 (56.7%) did not have any cytology reports available. Among 138 women with at least one cytology, 60% had 1–3, 24% 4–6 and 16% ≥7 tests (mean 3.7) before cancer. In 78% of women, the last test was performed less than 5 years before cancer diagnosis and 62% of these tests did not report any abnormalities. The last cytology results differed significantly between the regional and local laboratories (P = 0.028).

Conclusion

Women received the cervical cancer diagnosis in Estonia despite having several screening tests 10 years prior to the diagnosis. The proportion of cytology tests without any abnormalities less than 5 years before the diagnosis was worryingly high and needs further investigation together with the difference between laboratory types.
Determining Whether Older Adults Use Similar Strategies to Young Adults in Theory of Mind Tasks
Authors: Krendl Anne C , Mannering Willa , Jones Michael N , Hugenberg Kurt , Kennedy Daniel P
Published: December 2022

Objectives

Theory of mind—the ability to infer others’ mental states—declines over the life span, potentially due to cognitive decline. However, it is unclear whether deficits emerge because older adults use the same strategies as young adults, albeit less effectively, or use different or no strategies. The current study compared the similarity of older adults’ theory of mind errors to young adults’ and a random model.

Methods

One hundred twenty older adults (MAge = 74.68 years; 64 female) and 111 young adults (MAge = 19.1; 61 female) completed a novel theory of mind task (clips from an episode of the sitcom The Office®), and a standard measure of cognitive function (Logical Memory II). Monte Carlo resampling estimated the likelihood that older adults’ error patterns were more similar to young adults’ or a random distribution.

Results

Age deficits emerged on the theory of mind task. Poorer performance was associated with less similarity to young adults’ response patterns. Overall, older adults’ response patterns were ~2.7 million times more likely to match young adults’ than a random model. Critically, one fourth of older adults’ errors were more similar to the random distribution. Poorer memory ability contributed to this relationship.

Discussion

Age deficits in theory of mind performance may be driven by a subset of older adults and be related to disparities in strategy use. A certain amount of cognitive ability may be necessary for older adults to engage similar strategies to young adults’ during theory of mind.
Crossing disciplinary boundaries: motivations, challenges, and enablers for early career marine researchers moving from natural to social sciences
Authors: Shellock R J , Cvitanovic C , Badullovich N , Catto D , DelBene J A , Duggan J , Karcher D B , Ostwald A , Tuohy P
Published: December 2022

Recent years have seen increasing calls to better document and understand the human dimensions of the marine and coastal environment and to incorporate this knowledge into decision-making. Human dimensions of the marine and coastal environment are best investigated through the application of marine social science. Individuals within marine social science are not solely “pure” social scientists, but rather are a diverse and interdisciplinary community, including many who have moved from the natural sciences to pursue a career in marine social science. This is particularly the case for early career researchers, with many moving from natural to social science earlier in their academic careers than their predecessors, and thus developing stronger interdisciplinary skills than previous generations of social scientists. In this perspective, we draw on our experiences, highlighting our main motivations for moving from natural to social science, the barriers we have faced and our top tips for early career researchers faced with similar opportunities and challenges. The ten tips include: “Work with like-minded researchers,” “Learn from and be inspired by academic heroes,” “Learn about and engage with research philosophy, positionality and reflexivity,” “Value your own skillset and perspective,” and “Be patient and kind to yourself.”
Discrete and continuum models for the coevolutionary dynamics between CD8+ cytotoxic T lymphocytes and tumour cells
Authors: Almeida Luís , Audebert Chloe , Leschiera Emma , Lorenzi Tommaso
Published: December 2022

We present an individual-based model for the coevolutionary dynamics between CD8+ cytotoxic T lymphocytes (CTLs) and tumour cells. In this model, every cell is viewed as an individual agent whose phenotypic state is modelled by a discrete variable. For tumour cells, this variable represents a parameterization of the antigen expression profiles, while for CTLs it represents a parameterization of the target antigens of T-cell receptors (TCRs). We formally derive the deterministic continuum limit of this individual-based model, which comprises a non-local partial differential equation for the phenotype distribution of tumour cells coupled with an integro-differential equation for the phenotype distribution of CTLs. The biologically relevant homogeneous steady-state solutions of the continuum model equations are found. The linear-stability analysis of these steady-state solutions is then carried out in order to identify possible conditions on the model parameters that may lead to different outcomes of immune competition and to the emergence of patterns of phenotypic coevolution between tumour cells and CTLs. We report on computational results of the individual-based model, and show that there is a good agreement between them and analytical and numerical results of the continuum model. These results shed light on the way in which different parameters affect the coevolutionary dynamics between tumour cells and CTLs. Moreover, they support the idea that TCR-tumour antigen binding affinity may be a good intervention target for immunotherapy and offer a theoretical basis for the development of anti-cancer therapy aiming at engineering TCRs so as to shape their affinity for cancer targets.
Simulating and Analyzing aggressive car-following behavior for testing autonomous vehicles
Authors: Tang Li , Gupta Abhishek , Liu Ziyi , Qiao Chunming , He Qing
Published: December 2022

In a mixed traffic flow, evaluating the operation safety of autonomous vehicles (AVs) is crucial under different aggressive car-following behavior of surrounding human driven-vehicles (HVs). To pursue this goal, this paper develops a machine-learning-based simulation method accompanied by a traditional car-following model. We integrate the unsupervised learning method, Approximate Bayesian computation, and Gipps car-following model to obtain different parameter distributions of the Gipps model. After utilizing the key parameter distribution, this paper employs a supervised learning method to predict the aggressive index of human-driven vehicles in each individual car-following event. Further, we verify the outputs of this simulation model with the NGSIM I-80 traffic dataset. After the validation, we develop an AV simulation study to analyze Avs’ performance in different aggressive HVs scenarios. The result indicates that the higher penetration rate of AV is essential for stabilizing AVs’ performance in terms of velocity and the probability of involving in a crash. Additionally, aggressive HV drivers significantly impact scenarios of low AV penetration rate regarding safety issues.
Evidence for Early Mesozoic diversification of Hypsimetopidae Nicholls, 1943 (Isopoda), with the description of a new genus from Andhra Pradesh and notes on threats to Indian cave environments
Authors: Wilson George D , Shaik Shabuddin
Published: December 2022

A new phreatoicidean isopod, Speonastes venkataramanigen., sp. nov. is described from Borra Cave in northeastern Andhra Pradesh, India. This new taxon has features seen in most phreatoicideans such as ventrally projecting pleonal pleurae, but also has features characteristic of the hypogean family Hypsimetopidae, such as an elongated pleotelson with a medially rotating uropod that has protopodal denticles or denticulate setae opposing the denticulate margin of the pleotelson, as well as the distal article of the antennula being minute and the penultimate article elongated and somewhat inflated. Robustness-tested phylogenetic analyses of character data from exemplars from nearly all phreatoicidean genera and four non-phreatoicidean outgroups finds that this species is the earliest derived member of Hypsimetopidae. These analyses have substantial implications for both relationships among Phreatoicidea, but within the family as well. The body form of the Phreatoicidea basal to the hypsimetopid clade resembles the form seen in fossils or by recent taxa such as CrenisopusWilson & Keable, 1999. Ancestors of Speonastesgen. nov. may have independently colonized India from those of the Nichollsia-Andhracoides clade. An early Mesozoic diversification of Hypsimetopidae and related taxa along continental rifts in eastern Gondwana between Antarctica, India, and Australia is one implication of the phylogeny. Although the caves of Andhra Pradesh and other Indian states have biologically unique and scientifically important taxa, India provides no protection for any cave. This exposes the fauna to negative impacts such as quarrying or illegal mining, over-exploitation of water resources, and damage from unconstrained tourist visitation.
Classification and characterization of alternative promoters in 26 lung adenocarcinoma cell lines
Authors: Hamaya Yamato , Suzuki Ayako , Suzuki Yutaka , Tsuchihara Katsuya , Yamashita Riu
Published: December 2022

Background

Genome-wide landscape of alternative promoter use remains unknown. We determined expression profiles of promoters in 26 lung adenocarcinoma cell lines using the transcriptional start site-sequencing data and proposed an index ‘canonical promoter usage’ to quantify the diversity of alternative promoter usage.

Methods

Transcriptional start site-sequencing and other datasets were obtained from the DataBase of Transcriptional Start Sites. Transcriptional start site-sequencing read clusters were mapped onto RefGene to determine the promoters. Commonly used promoters were designated as canonical promoters. The sequence logos, CpG islands, DNA methylation and histone modifications of canonical and non-canonical promoters were examined. Canonical promoter usage was calculated by dividing ‘read counts of a canonical promoter’ by ‘read counts of all the units of promoters’ on each gene. The expressed genes were subjected to hierarchical clustering according to their canonical promoter usage.

Results

Among 104 455 promoters for 14 297 genes, 8659 canonical and 68 197 non-canonical promoters were identified. Corresponding to higher expression, canonical promoters showed core promoter sequences, higher CpG island positivity, less DNA methylation and higher transcription-promoting histone modifications. Gene ontology enrichment analysis revealed that the clusters with lower canonical promoter usage were related to signalling pathways, whereas clusters of tightly regulated genes with higher canonical promoter usage were related to housekeeping genes.

Conclusion

Canonical promoters were regulated by conventional transcriptional machinery, while non-canonical promoters would be targets of ‘leaky’ expression. Further investigation is warranted to analyse the correlation between alternative promoter usage and biological characteristics contributing to carcinogenesis.
Networking the Counterrevolution: The École Supérieure de Guerre, Transnational Military Collaboration, and Cold War Counterinsurgency, 1955–1975
Authors: Peterson Terrence G
Published: December 2022

Over the past several decades, scholars have devoted considerable attention to tracing the influence of French counterinsurgency practices developed in Indochina and Algeria on other militaries during the Cold War. This article builds on that literature to offer an explanation for why French counterrevolutionary knowledge circulated so broadly, and to connect the French military more concretely to an emerging literature on anticommunist internationalism. At the center of French efforts, this article argues, stood the Army’s École Supérieure de Guerre (ESG) in Paris, which trained growing numbers of high-ranking foreign officers after 1945. The ESG taught counterrevolutionary warfare directly, but as this article argues, it also helped constitute an audience abroad for such ideas by cultivating affective bonds, strategic preferences, and personal connections over the longer term. In tracing the partnerships cultivated through the ESG in this period, this article also illustrates the broader entanglements between counterinsurgency, international military cooperation, and professionalization at midcentury. For military partners seeking to professionalize their own forces, the attractiveness of French doctrines lay as much in the easily accessible set of materials, training, and expertise the French military offered as in their capacity to combat subversion. By tracing the transnational networks of exchange knit together by military academies in this period, this article concludes, scholars can better historicize the rise of counterinsurgency as a key paradigm of cold warfare.
Type 1 von Willebrand Disease in a Pediatric Patient Caused by a Novel Heterozygous Deletion of Exons 1 to 6 of the von Willebrand Factor Gene: A Case Report
Authors: Lapić Ivana , Radić Antolic Margareta , Rogić Dunja , Dejanović Bekić Sara , Coen Herak Désirée , Bilić Ernest , Zadro Renata
Published: December 2022

A 6-year-old boy was referred to a hematologist due to excessive mucocutaneous bleeding. Diagnostic assessment for von Willebrand disease (VWD) was indicated and included both coagulation and genetic testing. Laboratory testing revealed proportionally decreased von Willebrand factor (VWF) glycoprotein Ib-binding activity (23.6%) compared to VWF antigen (24.7%), similarly decreased VWF collagen-binding activity (24.2%), and normally distributed VWF multimers, with decreased intensity of all fractions. Diagnosis of type 1 VWD was established. Genetic analysis by means of next-generation sequencing (NGS) of VWF and coagulation factor VIII genes did not identify any causative mutations. Additionally, multiplex ligation-dependent probe amplification (MLPA) of VWF gene exons revealed a heterozygous deletion of exons 1 to 6, which is reported in type 1 VWD for the first time. Application of MLPA was crucial for revealing the genetic basis of type 1 VWD in this case, which would have remained undetected if only NGS was used.
A high-resolution spectroscopic search for multiple populations in the 2 Gyr old cluster NGC 1846
Authors: Oh W S , Nordlander T , Da Costa G S , Mackey A D
Published: December 2022

We present detailed C, O, Na, Mg, Si, Ca, Ti, V, Fe, Zr, Ba, and Eu abundance measurements for 20 red giant branch (RGB) stars in the Large Magellanic Cloud (LMC) star cluster NGC 1846 ([Fe/H] = −0.59). This cluster is 1.95 Gyr old and lies just below the supposed lower age limit (2 Gyr) for the presence of multiple populations in massive star clusters. Our measurements are based on high- and low-resolution VLT/FLAMES spectra combined with photometric data from Hubble Space Telescope (HST). Corrections for non-local thermodynamic equilibrium effects are also included for O, Na, Mg, Si, Ca, Fe, and Ba. Our results show that there is no evidence for multiple populations in this cluster based on the lack of any intrinsic star-to-star spread in the abundances of Na and O: We place 95  per cent confidence limits on the intrinsic dispersion for these elements of ≤0.07 and ≤0.09 dex, respectively. However, we do detect a significant spread in the carbon abundances, indicating varying evolutionary mixing occurring on the RGB that increases with luminosity. Overall, the general abundance patterns for NGC 1846 are similar to those seen in previous studies of intermediate-age LMC star clusters and field stars.
Clinical features and outcomes of spine surgery in patients with ankylosing spondylitis
Authors: Nakao Yuki , Sakuraba Koji , Harimaya Katsumi , Terada Kazuo , Kobara Nobuo , Kawaguchi Ken-Ichi , Hayashida Mitsumasa , Iida Keiichiro , Nakashima Yasuharu , Fukushi Jun-Ichi
Published: December 2022

Objectives

The study aimed to comprehend the clinical features and outcomes of surgical treatments for spinal disorders in patients with ankylosing spondylitis (AS).

Methods

This retrospective study enrolled patients with AS who underwent spine surgery between 2000 and 2019 in our facility.

Results

Thirteen patients with AS underwent spine surgeries. The mean age was 56.2 years, and the mean disease duration was 25.1 years at the time of surgery. Nine patients had vertebral fracture, two had kyphotic deformity, and two had myelopathy due to the spinal ligament ossification. Fracture cases included five patients with secondary pseudarthrosis/delayed palsy due to conservative treatment failure. Spinal fixation was performed in all patients. Pedicle subtraction osteotomy for kyphosis and laminectomy for myelopathy were also conducted. All patients improved after surgeries. One patient with kyphotic deformity underwent additional surgery of bilateral hip prosthesis, which resulted in better spine alignment. Four cases of perioperative complications were observed.

Conclusion

Myelopathy was newly found as the aetiology requiring surgery in patients with AS. This summarized case series could help physicians to identify patients with surgically treatable spinal disorders among patients with AS.
Bispecific antibodies—effects of point mutations on CH3-CH3 interface stability
Authors: Pomarici Nancy D , Fernández-Quintero Monica L , Quoika Patrick K , Waibl Franz , Bujotzek Alexander , Georges Guy , Liedl Klaus R
Published: December 2022

A new format of therapeutic proteins is bispecific antibodies, in which two different heavy chains heterodimerize to obtain two different binding sites. Therefore, it is crucial to understand and optimize the third constant domain (CH3-CH3) interface to favor heterodimerization over homodimerization, and to preserve the physicochemical properties, as thermal stability. Here, we use molecular dynamics simulations to investigate the dissociation process of 19 CH3-CH3 crystal structures that differ from each other in few point mutations. We describe the dissociation of the dimeric interface as a two-steps mechanism. As confirmed by a Markov state model, apart from the bound and the dissociated state, we observe an additional intermediate state, which corresponds to an encounter complex. The analysis of the interdomain contacts reveals key residues that stabilize the interface. We expect that our results will improve the understanding of the CH3-CH3 interface interactions and thus advance the developability and design of new antibodies formats.
Editing Aspergillus terreus using the CRISPR-Cas9 system
Authors: Shih Sra-Yh , Mortensen Uffe Hasbro , Chang Fang-Rong , Tsai HsinYuan
Published: December 2022

CRISPR-Cas9 technology has been utilized in different organisms for targeted mutagenesis, offering a fast, precise and cheap approach to speed up molecular breeding and study of gene function. Until now, many researchers have established the demonstration of applying the CRISPR/Cas9 system to various fungal model species. However, there are very few guidelines available for CRISPR/Cas9 genome editing in Aspergillus terreus. In this study, we present CRISPR/Cas9 genome editing in A. terreus. To optimize the guide ribonucleic acid (gRNA) expression, we constructed a modified single-guide ribonucleic acid (sgRNA)/Cas9 expression plasmid. By co-transforming an sgRNA/Cas9 expression plasmid along with maker-free donor deoxyribonucleic acid (DNA), we precisely disrupted the lovB and lovR genes, respectively, and created targeted gene insertion (lovF gene) and iterative gene editing in A. terreus (lovF and lovR genes). Furthermore, co-delivering two sgRNA/Cas9 expression plasmids resulted in precise gene deletion (with donor DNA) in the ku70 and pyrG genes, respectively, and efficient removal of the DNA between the two gRNA targeting sites (no donor DNA) in the pyrG gene. Our results showed that the CRISPR/Cas9 system is a powerful tool for precise genome editing in A. terreus, and our approach provides a great potential for manipulating targeted genes and contributions to gene functional study of A. terreus.
Medical Counseling on Sexual Enrichment Aids: Women’s Preferences and Medical Practitioner Expertise
Authors: Collar Amanda L. , Brakey Heidi Rishel , Fuentes Jesus E. , Frietze Kathryn M.
Published: December 2022

(Abstracted from Obstet Gynecol 2022;140:489–498)

Use of sexual enrichment aids such as sex toys is increasing among sexually active women. Nearly 80% of women aged 18 to 35 years reported previous use.
Impact of Anesthetic Exposures on the Neurocognitive Profiles of Pediatric Brain Tumor Survivors: A New Direction for Research and Multidisciplinary Collaboration
Authors: Eisler Lisa , Jackson William M. , Sun Lena S. , Sands Stephen A.
Published: December 2022

Primary brain tumors are the most commonly diagnosed solid tumors in children, and pediatric brain tumor survivors experience lasting, pervasive deficits of neurocognitive functioning. Repeated exposure to anesthetic drugs is a necessary component not only of surgical resection but also of multimodal cancer care for the youngest patients with brain tumors. The potential for anesthetic neurotoxicity to worsen neurocognitive outcomes in this vulnerable group, therefore, warrants our attention and further study through multi-disciplinary collaboration. This review discusses neurocognitive functioning in pediatric brain tumor survivors, highlighting the findings of a recent study of children with tumors of the posterior fossa which identified treatment-related risk factors for neurocognitive difficulties, with those undergoing multimodal therapies (eg, chemotherapy and irradiation) experiencing the greatest deficits compared with healthy controls. The role of anesthetic neurotoxicity in long-term outcomes among pediatric brain tumor survivors is also reviewed.
Activating transcription factor 4 protects mice against sepsis-induced intestinal injury by regulating gut-resident macrophages differentiation
Authors: Wen Zhenliang , Chen Dechang , Xiong Xi , Shao Lujing , Tang Xiaomeng , Shen Xuan , Zhang Sheng , Huang Sisi , Zhang Lidi , Chen Yizhu , Zhang Yucai , Wang Chunxia , Liu Jiao
Published: December 2022

Background:

Gut-resident macrophages (gMacs) supplemented by monocytes-to-gMacs differentiation play a critical role in maintaining intestinal homeostasis. Activating transcription factor 4 (ATF4) is involved in immune cell differentiation. We therefore set out to investigate the role of ATF4-regulated monocytes-to-gMacs differentiation in sepsis-induced intestinal injury.

Methods:

Sepsis was induced in C57BL/6 wild type (WT) mice and Atf4-knockdown (Atf4

+/−) mice by cecal ligation and puncture or administration of lipopolysaccharide (LPS). Colon, peripheral blood mononuclear cells, sera, lung, liver, and mesenteric lymph nodes were collected for flow cytometry, hematoxylin and eosin staining, immunohistochemistry, quantitative reverse transcription polymerase chain reaction, and enzyme-linked immunosorbent assay, respectively.

Results:

CD64, CD11b, Ly6C, major histocompatibility complex-II (MHC-II), CX3CR1, Ly6G, and SSC were identified as optimal primary markers for detecting the process of monocytes-to-gMacs differentiation in the colon of WT mice. Monocytes-to-gMacs differentiation was impaired in the colon during sepsis and was associated with decreased expression of ATF4 in P1 (Ly6Chi monocytes), the precursor cells of gMacs. Atf4 knockdown exacerbated the impairment of monocytes-to-gMacs differentiation in response to LPS, resulting in a significant reduction of gMacs in the colon. Furthermore, compared with WT mice, Atf4

+/−
mice exhibited higher pathology scores, increased expression of inflammatory factor genes (TNF-α, IL-1β), suppressed expression of CD31 and vascular endothelial-cadherin in the colon, and increased translocation of intestinal bacteria to lymph nodes and lungs following exposure to LPS. However, the aggravation of sepsis-induced intestinal injury resulting from Atf4 knockdown was not caused by the enhanced inflammatory effect of Ly6Chi monocytes and gMacs.

Conclusion:

ATF4, as a novel regulator of monocytes-to-gMacs differentiation, plays a critical role in protecting mice against sepsis-induced intestinal injury, suggesting that ATF4 might be a potential therapeutic target for sepsis treatment.
Considerations for genetic testing in individuals with autosomal dominant polycystic kidney disease
Authors: Noce Elyssa M.
Published: December 2022

Autosomal dominant polycystic kidney disease (ADPKD) is a systemic, irreversible, genetic condition caused by mutations in the PKD1 and PKD2 genes, and the most common form of inherited kidney disease in the United States, affecting more than 600,000 individuals. Because the condition is autosomal dominant, there is a 50% chance that each child of an affected adult will also have the pathogenic genetic mutation. PKD1 mutation accounts for approximately 85% of ADPKD cases and is characterized by an earlier onset of disease with more rapid progression, whereas PKD2 mutation accounts for the remaining 15% of cases and is characterized by a less severe and less rapid disease course. Genetic testing is not consistently used in the management of individuals with ADPKD, although it can provide invaluable information regarding disease progression and prognosis. Genetic data are necessary to effectively communicate disease progression with patients, use current prognostic calculators, and play a role in family planning. Increasing clinician knowledge in primary care and nephrology providers will contribute to improved care for individuals affected by ADPKD.
Social Vulnerability Index and Surgical Management of Abnormal Uterine Bleeding in Reproductive-Age Women
Authors: Fakas Steliana , Lu Anjanique Mariquit Rosete , Shahani Disha , Blitz Matthew J. , Rodriguez-Ayala Gianni
Published: December 2022

(Abstracted from J Minim Invasive Gynecol 2022;29:1104–1109)

Abnormal uterine bleeding (AUB) is common and affects 10% to 50% of reproductive-age women. A large number of nonmedical factors in the social and physical environment have a strong effect on health outcomes in patients with AUB and other disorders/diseases.
Linzagolix With and Without Hormonal Add-Back Therapy for the Treatment of Symptomatic Uterine Fibroids: Two Randomized, Placebo-Controlled, Phase 3 Trials
Authors: Donnez Jacques , Taylor Hugh S. , Stewart Elizabeth A. , Bradley Linda , Marsh Erica , Archer David , Al-Hendy Ayman , Petraglia Felice , Watts Nelson , Gotteland Jean-Pierre , Bestel Elke , Terrill Paul , Loumaye Ernest , Humberstone Andrew , Garner Elizabeth
Published: December 2022

(Abstracted from Lancet 2022;400:896–907)

Uterine fibroids occur in 50% to 60% of women and are symptomatic in 30% of patients by causing abnormal uterine bleeding and pelvic pressure. Treatment of uterine fibroids involves surgical and radiological interventions, as well as progestogens and other medical therapies.
Using Drain-Free Flap Fixation Techniques Versus Traditional Wound Closure With Drain Placement to Prevent Seroma Formation and Its Complications in Breast Cancer Patients Undergoing Mastectomy: A Systematic Review and Meta-analysis
Authors: Soltani Hamidreza , Kargar Saeid , Jafari-Nedooshan Jamal , Dehghan Hamidreza , Akhavan-Tafti Yasamin , Heiranizadeh Naeimeh , Neshan Mehdi
Published: December 2022

During the past decade, there has been some controversy related to using flap fixation techniques instead of conventional wound closure methods and drain placement during mastectomy procedures. The purpose of our study was to address this controversy using a systematic review and meta-analysis of current published literature. Nineteen studies met our inclusion criteria. Our sample population consisted of 2,956 participants divided into two groups. The study group (SG) consisted of 1,418 individuals and the control group (CG) consisted of 1,538 participants. We found there was a significant reduction in the incidence of seroma formation (odds ratio [OR] = 0.35; 95% confidence interval, CI [0.3, 0.42]; p < .000) and surgical site infection (OR = 0.65; 95% CI [0.48, 0.88]; p = .006) in the SG compared with the CG. The length of hospital stay was also significantly reduced in the SG (0.59 days; 95% CI [0.73, 0.46]; χ2[6, N = 502] = 52.88; p < .000) compared with the CG. The results of our study show that using a flap fixation technique after mastectomy can decrease the patient's risk for seroma formation and surgical site infection while reducing their length of hospital stay. Further studies with longer follow-up periods are warranted to evaluate long-term complications associated with using a flap fixation technique compared with using conventional wound closure techniques and drain placement.
Addressing Body Image After Reconstructive Surgery in Adult Patients with Cancer
Authors: Williams Tish
Published: December 2022

Body image or how a person views their body and the way it functions ultimately influences their quality of life and functional well-being in their daily environments. The changes to appearance or to body structures and functions that occur as a result of cancer and its treatment can cause individuals to become dissatisfied with their body image where maladaptive emotions, thought processes, and behaviors develop and may lead to deleterious consequences including social avoidance and isolation. Although reconstructive surgery is restorative in nature, it does not guarantee the mitigation of body image dissatisfaction when treating adults with cancer. The majority of adults who undergo reconstructive surgery for the treatment of cancer demonstrate some level of body image dissatisfaction during or after the reconstructive process. Therefore, a need exists for nurses and other oncological team members to recognize and address body image dissatisfaction and the detrimental emotional and behavioral consequences associated with it. This article provides guidance for nurses to address body image by understanding the effects of cancer and its treatment on body image, by recognizing the impact of reconstructive surgery on body image when treating cancer in adults, and by integrating body image assessment and interventions into practice.
Potential Role of 68Ga-NOTA-Duramycin PET/CT Imaging for Early Response Evaluation in a Lymphoma Patient
Authors: Kaur Gurvinder , Shukla Jaya , Sood Ashwani , Prakash Gaurav , Krishnaraju Venkata Subramanian , Rana Nivedita , Pandey Somit , Singh Harmandeep , Kumar Rajender , Bal Amanjit , Mittal Bhagwant Rai
Published: December 2022

Duramycin, a 19 amino acids peptide, is known for its potential to target phosphatidylethanolamine. During cell death (apoptosis), rearrangement of membrane phospholipids results in the externalization of phosphatidylethanolamine to the outer leaflet of the cell membrane, which can be imaged using 68Ga-NOTA-duramycin. We report 68Ga-NOTA-duramycin imaging in a 50-year-old man with biopsy-proven diffuse large B-cell lymphoma planned for anthracycline-based chemotherapy. 68Ga-NOTA-duramycin PET/CT imaging along with 18F-FDG PET/CT was performed before and after 2 cycles of chemotherapy. The tracer avidity in interim 68Ga-NOTA-duramycin PET/CT showed its diagnostic potential to assess early response to chemotherapy.
7T Small Animal MRI Research for Hepatic Alveolar Echinococcosis
Authors: Zhang Guanmi , Mou Yalin , Fan Haining , Li Weixia , Cao Yuntai , Bao Haihua
Published: December 2022

Objectives:

7T small animal magnetic resonance imaging (MRI) was used to analyze the growth characteristics of hepatic alveolar echinococcosis (HAE).

Methods:

A mouse model of HAE was established by intraperitoneal injection of alveolar Echinococcus tissue suspension. Ten mouse models successfully inoculated by ultrasound screening were selected. The mouse model was scanned with T1-weighted imaging (T1WI), T2-weighted imaging (T2WI), and diffusion-weighted imaging (DWI) sequence by 7T small animal MRI. Size, morphology, boundary, signal, and relationship with surrounding tissues of the lesions were recorded as characteristic alterations. Mice were killed at the end of the experiment, and the pathological specimens were taken for routine hematoxylin and eosin staining.

Results:

Lesions were mainly located in the right lobe of the liver. The multivesicular structure is the characteristic manifestation of this disease. In the liver, lesions invaded the portal vein and were mainly distributed at the hepatic hilum. The left branch of the portal vein was mainly invaded. The mean diameter of the lesions in the left lobe of the liver was larger than in other parts of the liver. The mean diameter of the cystic solid lesions was greater than the multilocular cystic lesions. HAE showed hypointense on T1WI, hyperintense on T2WI, and hypointense on DWI; the marginal zone of the lesion showed hyperintensity on DWI and grew toward the hilum. The MRI features of intraperitoneal lesions were similar to those of intrahepatic lesions. Intraperitoneal lesions increased faster than intrahepatic lesions in the same period.

Conclusion:

Polyvesicular structure is a characteristic manifestation of hepatic alveolar echinococcosis in mice. The noninvasive monitoring of liver HAE in mice by 7T small animal MRI provides a visual basis for the diagnosis and treatment integration of HAE.
Comparative Study on Nosocomial Biliary Tract Infection Rate Between Biliary Stent Loaded with Radioactive 125I Seeds and Conventional Biliary Stent in the Treatment of Distal Malignant Biliary Obstruction
Authors: An Jianli , Dong Yanchao , Niu Hongtao , Li Yanguo , Han Xiaoyu , Zou Zibo , Wu Jingpeng , Tian Ye , Chen Zhuo
Published: December 2022

Background:

The purpose of this prospective randomized study was to compare the nosocomial biliary tract infection rate of biliary stent implantation with a biliary stent loaded with radioactive 125I seeds (radioactive biliary stent, RBS) and conventional biliary stent (CBS); additionally, to preliminary discuss the causes of postoperative cholangitis. Moreover, the results will provide clinical evidence for the prevention of postoperative biliary tract infection.

Materials and Methods:

We prospectively analyzed the nosocomial infection rate of the distal malignant biliary obstruction (MBO) treatment by stent implantation with RBS and CBS. All MBO patients who initially visited our tertiary hospital between July 2015 and December 2019 (n= 196) were evaluated, enrolled, and randomly divided into 2 groups, RBS (n=97) and CBS (n=99) group. χ2 test was used to evaluate the categorical data, and t test was used to evaluate the numerical data.

Results:

Our analysis of the study showed the incidence of postoperative infections of a biliary tract of the RBS group (23.7%) was significantly higher than the CBS group (11.1%). The difference was statistically significant (χ2=5.425, P=0.020). Our study also showed the most common pathogenic bacteria after surgery was Escherichia coli (26.5%).

Conclusion:

Treatment for distal MBO with biliary stent loaded with radioactive 125I seeds had a higher nosocomial infection rate, and the most common pathogenic bacteria was E coli., Supplemental Digital Content 1, http://links.lww.com/sle/A350