bluuebunny/crossref_metadata_2025 huggingface dataset:
WebQUAST: online evaluation of genome assemblies
Authors: Mikheenko Alla , Saveliev Vladislav , Hirsch Pascal , Gurevich Alexey
Published: May 2023

Selecting proper genome assembly is key for downstream analysis in genomics studies. However, the availability of many genome assembly tools and the huge variety of their running parameters challenge this task. The existing online evaluation tools are limited to specific taxa or provide just a one-sided view on the assembly quality. We present WebQUAST, a web server for multifaceted quality assessment and comparison of genome assemblies based on the state-of-the-art QUAST tool. The server is freely available at https://www.ccb.uni-saarland.de/quast/. WebQUAST can handle an unlimited number of genome assemblies and evaluate them against a user-provided or pre-loaded reference genome or in a completely reference-free fashion. We demonstrate key WebQUAST features in three common evaluation scenarios: assembly of an unknown species, a model organism, and a close variant of it.
SEanalysis 2.0: a comprehensive super-enhancer regulatory network analysis tool for human and mouse
Authors: Qian Feng-Cui , Zhou Li-Wei , Li Yan-Yu , Yu Zheng-Min , Li Li-Dong , Wang Yue-Zhu , Xu Ming-Cong , Wang Qiu-Yu , Li Chun-Quan
Published: May 2023

Super-enhancers (SEs) play an essential regulatory role in various biological processes and diseases through their specific interaction with transcription factors (TFs). Here, we present the release of SEanalysis 2.0 (http://licpathway.net/SEanalysis), an updated version of the SEanalysis web server for the comprehensive analyses of transcriptional regulatory networks formed by SEs, pathways, TFs, and genes. The current version added mouse SEs and further expanded the scale of human SEs, documenting 1 167 518 human SEs from 1739 samples and 550 226 mouse SEs from 931 samples. The SE-related samples in SEanalysis 2.0 were more than five times that in version 1.0, which significantly improved the ability of original SE-related network analyses (‘pathway downstream analysis’, ‘upstream regulatory analysis’ and ‘genomic region annotation’) for understanding context-specific gene regulation. Furthermore, we designed two novel analysis models, ‘TF regulatory analysis’ and ‘Sample comparative analysis’ for supporting more comprehensive analyses of SE regulatory networks driven by TFs. Further, the risk SNPs were annotated to the SE regions to provide potential SE-related disease/trait information. Hence, we believe that SEanalysis 2.0 has significantly expanded the data and analytical capabilities of SEs, which helps researchers in an in-depth understanding of the regulatory mechanisms of SEs.
Mol* Volumes and Segmentations: visualization and interpretation of cell imaging data alongside macromolecular structure data and biological annotations
Authors: Chareshneu Aliaksei , Midlik Adam , Ionescu Crina-Maria , Rose Alexander , Horský Vladimír , Cantara Alessio , Svobodová Radka , Berka Karel , Sehnal David
Published: May 2023

Segmentation helps interpret imaging data in a biological context. With the development of powerful tools for automated segmentation, public repositories for imaging data have added support for sharing and visualizing segmentations, creating the need for interactive web-based visualization of 3D volume segmentations. To address the ongoing challenge of integrating and visualizing multimodal data, we developed Mol* Volumes and Segmentations (Mol*VS), which enables the interactive, web-based visualization of cellular imaging data supported by macromolecular data and biological annotations. Mol*VS is fully integrated into Mol* Viewer, which is already used for visualization by several public repositories. All EMDB and EMPIAR entries with segmentation datasets are accessible via Mol*VS, which supports the visualization of data from a wide range of electron and light microscopy experiments. Additionally, users can run a local instance of Mol*VS to visualize and share custom datasets in generic or application-specific formats including volumes in .ccp4, .mrc, and .map, and segmentations in EMDB-SFF .hff, Amira .am, iMod .mod, and Segger .seg. Mol*VS is open source and freely available at https://molstarvolseg.ncbr.muni.cz/.
nCoVDock2: a docking server to predict the binding modes between COVID-19 targets and its potential ligands
Authors: Liu Kai , Lu Xufeng , Shi Hang , Xu Xiaojun , Kong Ren , Chang Shan
Published: May 2023

The rapid emergence of SARS-CoV-2 variants with multi-sites mutations is considered as a major obstacle for the development of drugs and vaccines. Although most of the functional proteins essential for SARS-CoV-2 have been determined, the understanding of the COVID-19 target-ligand interactions remains a key challenge. The old version of this COVID-19 docking server was built in 2020, and free and open to all users. Here, we present nCoVDock2, a new docking server to predict the binding modes for targets from SARS-CoV-2. First, the new server supports more targets. We replaced the modeled structures with newly resolved structures and added more potential targets of COVID-19, especially for the variants. Second, for small molecule docking, Autodock Vina was upgraded to the latest version 1.2.0, and a new scoring function was added for peptide or antibody docking. Third, the input interface and molecular visualization were updated for a better user experience. The web server, together with an extensive help and tutorial, are freely available at: https://ncovdock2.schanglab.org.cn.
Rapid Emergence of Potentially Transmissible Severe Acute Respiratory Syndrome Coronavirus 2 With Resistance to Combination Monoclonal Antibody Therapy
Authors: Jacobs Jana L , Haidar Ghady , Naqvi Asma , McCormick Kevin D , Sobolewski Michele , Treat Benjamin R , Heaps Amy L , Simpson Jordan , Kramer Kailey Hughes , McCreary Erin , Bariola J Ryan , Klamar-Blain Cynthia , Macatangay Bernard J C , Dimitrov Dimiter , Li Wei , Marino Christopher C , Raptis Anastasios , Sethi Rahil , Chandran Uma , Barratt-Boyes Simon , Parikh Urvi M , Mellors John W
Published: May 2023

Prolonged coronavirus disease 2019 may generate new viral variants. We report an immunocompromised patient treated with monoclonal antibodies who experienced rebound of viral RNA and emergence of an antibody-resistant (>1000-fold) variant containing 5 mutations in the spike gene. The mutant virus was isolated from respiratory secretions, suggesting the potential for secondary transmission.
The adaptive significance of off-lek sociality in birds: A synthetic review, with evidence for the reproductive benefits hypothesis in Long-wattled Umbrellabirds
Authors: Anderson H Luke , Olivo Jorge , Karubian Jordan
Published: May 2023

Anecdotal evidence suggests that lekking birds exhibit considerable variation in form and degree of sociality away from the lek, yet this phenomenon has received very little theoretical or empirical research attention. Here, we provide the first synthetic literature review of off-lek sociality in birds and develop a conceptual framework for the potential adaptive function of off-lek sociality across lekking taxa. We then present a case study of the Long-wattled Umbrellabird (Cephalopterus penduliger), where we find support for the hypothesis that off-lek sociality is primarily driven by male reproductive incentives for coordinating lek attendance during the breeding season. During periods of high lekking activity, male umbrellabirds depart the lek in highly coordinated groups and maintain larger off-lek social groups relative to periods of low lekking activity. These seasonal differences in off-lek sociality do not occur in females, are not explained by patterns of foraging behavior, and are expected to confer individual-level benefits for participating males. Both the literature review and empirical study of umbrellabirds suggest that off-lek interactions and behavioral strategies may shape sexual selection processes at leks in important ways. Further research into this historically understudied area of lekking species’ behavioral ecology will likely deepen our understanding of the evolutionary dynamics of lek mating.
Conclusions
Authors: Michelson David A.
Published: May 2023

This final chapter suggests how the study of East Syrian contemplative reading can serve as framework for future scholarship. The chapter begins by summarizing the findings of the book as a whole in the form of answers to the questions about Syriac contemplative reading posed in Chapter 1. Next, the chapter demonstrates how the East Syrian tradition of contemplative reading offers a new historical context for the study of Isaac of Nineveh, John of Dalyatha, and other mystical authors in later centuries in the Church of the East. The chapter notes the wider legacies and implications of the East Syrian contemplative reading tradition. The works of ʿEnanishoʿ and Dadishoʿ circulated in Sogdian, West Syrian, Melkite, and Ethiopian monastic libraries where the East Syrian theology of contemplative ascetic reading was adapted to new contexts. Moreover, the East Syrian practice offers comparative insights into the closely related traditions of Latin lectio divina as well as Greek and Slavonic hesychasm. Finally, the chapter concludes by calling for other scholars to examine what this tradition could reveal about connections between Jewish, Christian, and Muslim mystical theologies in medieval Mesopotamia.
The Origin of Ultramafic Complexes with Melilitolites and Carbonatites: A Petrological Comparison of the Gardiner (E Greenland) and Kovdor (Russia) Intrusions
Authors: Gudelius Dominik , Marks Michael W , Markl Gregor , Nielsen Troels F D , Kolb Jochen , Walter Benjamin
Published: May 2023

In many alkaline complexes, large amounts of ultramafic rocks occur together with carbonatites, melilitolites and other alkaline silicate rocks. There is an ongoing debate if and how these contrasting lithologies were formed by differentiation of a common, mantle-derived silicate magma or rather by metasomatic processes between carbonatite and country rocks. In order to find petrological evidence for one or the other, two key examples, the Gardiner (E Greenland) and Kovdor (Russia) complexes are compared in this study. Despite their similar tectonic setting and succession of rock types, they show significant differences in the texture and mineral composition of ultramafic rocks. Ultramafic rocks from Kovdor include calcite- and biotite-rich dunites and pyroxenites without typical cumulate textures. They consist of Ni-poor forsterite, Cr-poor diopside and Ni-Cr-poor spinel and are possibly metasomatic reaction products between mantle-derived carbonatite melts and silicic host rocks. Similar ultramafic rocks are associated with carbonatites e. g. at Palabora (South Africa), Afrikanda (Russia), and Salitre (Brazil). In contrast, the ultramafic rocks from Gardiner show well-preserved cumulate textures and consist of Ni-rich forsterite, Cr-rich diopside as well as Cr-Ni-Ti-rich spinel and also contain F-Cl-rich apatite. They record an increase in aSiO2 from dunite to pyroxenite at similar fO2 (ΔFMQ ~ +1.2, with FMQ = fayalite-magnetite-quartz buffer), indicating that these rocks represent cumulates of an evolving, moderately oxidized mafic melt derived from a Ti-rich mantle source, similar to other rocks of the North Atlantic igneous province. In contrast to systems like Kovdor where carbonatite metasomatism is likely dominant, Ti-rich parental silicate magmas can abundantly crystallize Ti phases, as recorded by massive perovskite cumulates in Gardiner melilitolites. This can effectively scavenge HFSE from the magmatic system early in its evolution and likely explains HFSE-barren carbonatites at Gardiner, while those from Kovdor are highly HFSE-enriched. In summary, the results of our study provide strong textural and mineral chemical evidence that ultramafic rocks in alkaline complexes can be of both cumulate and metasomatic origin; the specific type has an important bearing on their HFSE enrichment and on the types of ores present in such complexes.
The transcriptional hub SHORT INTERNODES1 integrates hormone signals to orchestrate rice growth and development
Authors: Duan Erchao , Lin Qibing , Wang Yihua , Ren Yulong , Xu Huan , Zhang Yuanyan , Wang Yunlong , Teng Xuan , Dong Hui , Wang Yupeng , Jiang Xiaokang , Chen Xiaoli , Lei Jie , Yang Hang , Chen Rongbo , Jiang Ling , Wang Haiyang , Wan Jianmin
Published: May 2023

Plants have evolved sophisticated mechanisms to coordinate their growth and stress responses via integrating various phytohormone signaling pathways. However, the precise molecular mechanisms orchestrating integration of the phytohormone signaling pathways remain largely obscure. In this study, we found that the rice (Oryza sativa) short internodes1 (shi1) mutant exhibits typical auxin-deficient root development and gravitropic response, brassinosteroid (BR)-deficient plant architecture and grain size as well as enhanced abscisic acid (ABA)-mediated drought tolerance. Additionally, we found that the shi1 mutant is also hyposensitive to auxin and BR treatment but hypersensitive to ABA. Further, we showed that OsSHI1 promotes the biosynthesis of auxin and BR by activating the expression of OsYUCCAs and D11, meanwhile dampens ABA signaling by inducing the expression of OsNAC2, which encodes a repressor of ABA signaling. Furthermore, we demonstrated that 3 classes of transcription factors, AUXIN RESPONSE FACTOR 19 (OsARF19), LEAF AND TILLER ANGLE INCREASED CONTROLLER (LIC), and OsZIP26 and OsZIP86, directly bind to the promoter of OsSHI1 and regulate its expression in response to auxin, BR, and ABA, respectively. Collectively, our results unravel an OsSHI1-centered transcriptional regulatory hub that orchestrates the integration and self-feedback regulation of multiple phytohormone signaling pathways to coordinate plant growth and stress adaptation.
A phase-separated CO2-fixing pyrenoid proteome determined by TurboID in Chlamydomonas reinhardtii
Authors: Lau Chun Sing , Dowle Adam , Thomas Gavin H , Girr Philipp , Mackinder Luke C M
Published: May 2023

Phase separation underpins many biologically important cellular events such as RNA metabolism, signaling, and CO2 fixation. However, determining the composition of a phase-separated organelle is often challenging due to its sensitivity to environmental conditions, which limits the application of traditional proteomic techniques like organellar purification or affinity purification mass spectrometry to understand their composition. In Chlamydomonas reinhardtii, Rubisco is condensed into a crucial phase-separated organelle called the pyrenoid that improves photosynthetic performance by supplying Rubisco with elevated concentrations of CO2. Here, we developed a TurboID-based proximity labeling technique in which proximal proteins in Chlamydomonas chloroplasts are labeled by biotin radicals generated from the TurboID-tagged protein. By fusing 2 core pyrenoid components with the TurboID tag, we generated a high-confidence pyrenoid proxiome that contains most known pyrenoid proteins, in addition to new pyrenoid candidates. Fluorescence protein tagging of 7 previously uncharacterized TurboID-identified proteins showed that 6 localized to a range of subpyrenoid regions. The resulting proxiome also suggests new secondary functions for the pyrenoid in RNA-associated processes and redox-sensitive iron–sulfur cluster metabolism. This developed pipeline can be used to investigate a broad range of biological processes in Chlamydomonas, especially at a temporally resolved suborganellar resolution.
Cholesterol twists the transmembrane Di-Gly region of amyloid-precursor protein
Authors: Wang David Tzu-Wei , Tang Tiffany Y C , Kuo Chun-Ting , Yu Yun-Ting , Chen Eric H L , Lee Ming-Tao , Tsai Ruei-Fong , Chen Hung-Ying , Chiang Yun-Wei , Chen Rita P Y
Published: May 2023

Nearly 95% of Alzheimer's disease (AD) occurs sporadically without genetic linkage. Aging, hypertension, high cholesterol content, and diabetes are known nongenomic risk factors of AD. Aggregation of Aβ peptides is an initial event of AD pathogenesis. Aβ peptides are catabolic products of a type I membrane protein called amyloid precursor protein (APP). Aβ40 is the major product, whereas the 2-residue-longer version, Aβ42, induces amyloid plaque formation in the AD brain. Since cholesterol content is one risk factor for sporadic AD, we aimed to explore whether cholesterol in the membrane affects the structure of the APP transmembrane region, thereby modulating the γ-secretase cutting behavior. Here, we synthesized several peptides containing the APP transmembrane region (sequence 693–726, corresponding to the Aβ22–55 sequence) with one or two Cys mutations for spin labeling. We performed three electron spin resonance experiments to examine the structural changes of the peptides in liposomes composed of dioleoyl phosphatidylcholine and different cholesterol content. Our results show that cholesterol increases membrane thickness by 10% and peptide length accordingly. We identified that the di-glycine region of Aβ36–40 (sequence VGGVV) exhibits the most profound change in response to cholesterol compared with other segments, explaining how the presence of cholesterol affects the γ-secretase cutting site. This study provides spectroscopic evidence showing how cholesterol modulates the structure of the APP transmembrane region in a lipid bilayer.
Discourses of growth in megaproject-based urban development: a comparative study of Poland and Finland
Authors: Rek-Woźniak Magdalena
Published: May 2023

The paper aims to add to the debate on the varieties of neoliberalism and the homogenizing effects of megaproject-based urban development. It examines the acculturation of the growth imperative as the master discourse that supports the development and implementation of two projects aimed at transforming the centers of Tampere, Finland, and Łódź, Poland. The selected cities shared similar traits as industrial centers in the past, but their current socioeconomic situation is entirely different. Tampere holds the title of “Finland’s most likeable city,” while rapidly depopulating Łódź was labeled the “Polish Detroit.” Nevertheless, both municipalities became attracted by the idea of boosting their development through implementing large-scale infrastructural investments to reshape their centers. Inspired by discursive institutionalism, which defines discourse as a set of policy ideas and values, and interactive policy communication and formulation processes, the paper reconstructs and compares the strategic visions of Tampere’s “Five Star City Centre” and “The New Centre of Łódź.” It demonstrates how the proponents of the projects discursively forced consent around proposed ideas. Namely, it shows how the issues of complexity, risk, and potential conflict of the two megaprojects have been addressed. On a conceptual level, the paper shows how policy convergence can be discursively facilitated in different socioeconomic, cultural, and political circumstances.
Phosphoserine enhanced Cu-doped bioactive glass dynamic dual-network hydrogel for craniofacial bone defect repair
Authors: Liu Yuwei , Wang Gang , Luo Huitong , Zhao Bangjiao , Liao Muheng , Dai Qiyuan , Li Maocai , Li Qingtao , Cao Xiaodong
Published: May 2023

Flexible hydrogels containing various osteogenic inorganic constituents, which can accommodate complicated shape variations, are considered as ideal grafts for craniofacial bone defect reconstruction. However, in most hybrid hydrogels, poor interaction between the polymer network and particles has detrimental effects on hydrogel rheological and structural properties, clinical manipulation and repair efficacy. In this article, we designed and prepared a series of hyaluronic acid composite hydrogel containing Cu-doped bioactive glass (CuBG) and phosphoserine (PS), in which hyaluronic acid was modified by methacrylate groups and phenylboronic acid groups to form a double crosslinked network. PS acted as an interaction bridge of CuBG particles and HAMA-PBA network to improve the mechanical properties of the composite hydrogels. The CuBG/PS hydrogels exhibited suitable rheological properties (injectable, self-healing, shape-adaptable), bone tissue integrating ability and anti-bacterial property. Meanwhile, we found that CuBG and PS have synergistic effect on improving osteogenic efficiency both in vitro and in vivo, particularly when the ratio of CuBG to PS is lower than 3 (9CB/3PS). This work provided a versatile and scalable approach to enhanced the interaction within inorganic particles and polymer network in hydrogels without extra modification on components.
Effects of the windshield inclination angle on head/brain injuries in car-to-pedestrian collisions using computational biomechanics models
Authors: Wang Fang , Wang Mingliang , Hu Lin , Peng Ke , Yin Jiajie , Wang Danqi , Shi Liangliang , Zhou Zhou
Published: May 2023

Car-to-pedestrian collision (CPC) accidents occur frequently, and pedestrians often suffer serious head/brain injuries. One major cause is the primary impact with the windshield. Here, we use a numerical simulation method to study the influence of the windshield inclination angle of a passenger car on pedestrian head/brain injury due to CPC accidents. The range of the windshield inclination angle was set at 24°–50°, with an interval of 2°. The results show that the windshield angle significantly affects the pedestrian kinematics and exerts different effects on the head injury when evaluating with various head injury criteria. Regarding the head peak linear/rotational acceleration and acceleration-based head injury criterion (HIC)/rotational injury criterion (RIC), the predictions at the secondary impact stage have no clear relationship with the windshield angle (R2=0.04, 0.07, 0.03 and 0.26, respectively) and their distributions are scattered. In the primary impact, the peak linear acceleration and HIC show a weak trend of first decreasing and then increasing with the increasing of the windshield angle, and the rotational acceleration and RIC tend to remain relatively constant. Regarding the cumulative strain damage measure (CSDM) criterion, the predictions at the primary impact are slightly lower than those at the secondary impact, and the trend of first decreasing and then increasing with the increase in the windshield angle is observed at both impact stages. When the windshield inclination angle is approximately 32°–40°, the head injury severity in both impact phases is generally lower than that predicted at other windshield angles.
Systemic Colonization of Xanthomonas fragariae Strain YL19 Causing Dry Cavity Rot of Strawberry Crown Tissue in China
Authors: Wang Dan-Juan , Shi Jian-Cheng , Fan Li , Wang Ruo-Jing , Wei Feng , Ma Yang-Yang , Cai Xiao-Lin , Fan Si-Hao , Liang Xia , Yang Hong-Liang , Xing Kun , Qiu Li-Juan , Lu Li-Juan , Li Xi-Xuan , Wen Ying-Qiang , Feng Jia-Yue
Published: May 2023

Xanthomonas fragariae usually causes angular leaf spot (ALS) of strawberry, a serious bacterial disease in many strawberry-producing regions worldwide. Recently, a new strain of X. fragariae (YL19) was isolated from strawberry in China and has been shown to cause dry cavity rot in strawberry crown. In this study, we constructed a green fluorescent protein (GFP)-labeled Xf YL19 (YL19-GFP) to visualize the infection process and pathogen colonization in strawberries. Foliar inoculation of YL19-GFP resulted in the pathogen migrating from the leaves to the crown, whereas dip inoculation of wounded crowns or roots resulted in the migration of bacteria from the crowns or roots to the leaves. These two invasion types both resulted in the systematic spread of YL19-GFP, but inoculation of a wounded crown was more harmful to the strawberry plant than foliar inoculation. Results increased our understanding of the systemic invasion of X. fragariae, and the resultant crown cavity caused by Xf YL19.
Discovery of Novel Small Molecule Growth Inhibitors to Manage Pseudomonas Leaf Spot Disease on Peppers (Capsicum sp.)
Authors: Ranjit Sochina , Deblais Loïc , Rotondo Francesca , Shannon Brandon , Johnson Reed , Miller Sally A. , Rajashekara Gireesh
Published: May 2023

Pseudomonas leaf spot (PLS) disease in peppers caused by Pseudomonas syringae pv. syringae (Pss) is an emerging seedborne phytopathogen. Pss infection can severely reduce the marketable yield of peppers in favorable environmental conditions and cause significant economic losses. The intensive use of copper-sulfate and streptomycin-sulfate to control PLS and other bacterial diseases is associated with antimicrobial-resistant Pss strains, making these control methods less effective. So, there is an urgent need to develop novel antimicrobials effective against Pss in peppers. Several studies, including those done in our laboratory, have shown that small molecule (SM) antimicrobials are ideal candidates as they can be effective against multidrug resistant bacteria. Therefore, our study aims to identify novel SM growth inhibitors of Pss, assess their safety, and evaluate their efficacy on Pss-infected pepper seeds and seedlings. Using high-throughput screening, we identified 10 SMs (PC1 to PC10) that inhibited the growth of Pss strains at 200 µM or lower concentrations. These SMs were effective against both copper- and streptomycin-resistant as well as biofilm-embedded Pss. These SMs were effective against other plant pathogens (n = 22) at low concentrations (<200 μM) and had no impact on beneficial phytobacteria (n = 12). Furthermore, these SMs showed better or equivalent antimicrobial activity against Pss in infested pepper seeds and inoculated seedlings compared with copper-sulfate (200 μM) and streptomycin (200 μg/ml). Additionally, none of the SMs were toxic to pepper tissues (seeds, seedlings, or fruits), human Caco-2 cells, and pollinator honeybees at 200 μM. Overall, the SMs identified in this study are promising alternative antimicrobials for managing PLS in pepper production.
Bridging Access to Pediatric Pain Care
Authors: Sepsey Amber M. , Sokol Olivia E. , Huestis Samantha E. , Bhandari Rashmi P.
Published: May 2023

Objectives:

To evaluate subsequent shifts to patient access to tertiary pain management care following shelter-in-place (SIP) and increased telehealth during the COVID-19 pandemic.

Materials and Methods:

Retrospective naturalistic design was used. Data for this study were extracted from a retrospective review of the Pediatric-Collaborative Health Outcomes Information Registry, with additional demographic information collected using chart review. Participants were 906 youth who received an initial evaluation either in-person (n=472) within the 18 months before SIP or through telehealth (n=434) within the 18 months after SIP during the COVID-19 pandemic. Patient variables to assess access included geographic distance from the clinic, ethnic and racial diversity, and patient’s insurance type. Descriptive characteristics for each group were analyzed using χ2 test, percentage change, and t-test analyses.

Results:

Data indicated that transitioning to telehealth resulted in maintained access rates between groups as measured by race and ethnic diversity as well as distance traveled from the clinic. A trend toward increase in government-funded insurance was found, though no statistically significant differences were identified between telehealth and in-person visits. Though the majority of participants (in-person: 52.75%; telehealth 55.81%) lived within 50 miles of the clinic, results indicated that telehealth allowed for a statistically significant increase in evaluation access for families living further from the clinic within a 50-mile radius.

Discussion:

Overall, accessibility to pediatric pain management through telehealth during SIP was maintained despite significant declines in overall access to health care, with some trends in increased accessibility for patients with government insurance.
Diagnosis of Developmental Dysplasia of the Hip by Ultrasound Imaging Using Deep Learning
Authors: Kinugasa Maki , Inui Atsuyuki , Satsuma Shinichi , Kobayashi Daisuke , Sakata Ryosuke , Morishita Masayuki , Komoto Izumi , Kuroda Ryosuke
Published: May 2023

Background:

A timely diagnosis of developmental dysplasia of the hip (DDH) is important for satisfactory clinical outcomes. Ultrasonography is a useful tool for DDH screening; however, it is technically demanding. We hypothesized that deep learning could assist in the diagnosis of DDH. In this study, several deep-learning models were assessed to diagnose DDH on ultrasonograms. This study aimed to evaluate the accuracy of diagnoses made by artificial intelligence (AI) using deep learning on ultrasound images of DDH.

Methods:

Infants who were up to 6 months old with suspected DDH were included. DDH diagnosis using ultrasonography was performed according to the Graf classification. Data on 60 infants (64 hips) with DDH and 131 healthy infants (262 hips) obtained from 2016 to 2021 were retrospectively reviewed. For deep learning, a MATLAB deep learning toolbox (MathWorks, Natick, MA, US) was used, and 80% of the images were used as training data, with the rest as validation data. Training images were augmented to increase data variation. In addition, 214 ultrasound images were used as test data to evaluate the AI’s accuracy. Pre-trained models (SqueezeNet, MobileNet_v2, and EfficientNet) were used for transfer learning. Model accuracy was evaluated using a confusion matrix. The region of interest of each model was visualized using gradient-weighted class activation mapping (Grad-CAM), occlusion sensitivity, and image LIME.

Results:

The best scores for accuracy, precision, recall, and F-measure were all 1.0 in each model. In DDH hips, the region of interest for deep learning models was the area lateral to the femoral head, including the labrum and joint capsule. However, for normal hips, the models highlighted the medial and proximal areas where the lower margin of the os ilium and the normal femoral head exist.

Conclusions:

Ultrasound imaging with deep learning can assess DDH with high accuracy. This system could be refined for a convenient and accurate diagnosis of DDH.

Level of Evidence:

Level—Ⅳ.
Intracranial activity of first-line immune checkpoint inhibitors combined with chemotherapy in advanced non-small cell lung cancer
Authors: Huang Zhe , Wu Fang , Xu Qinqin , Song Lianxi , Zhang Xiangyu , Wang Zhan , Deng Li , Zhang Yongchang , Zeng Liang , Yang Nong
Published: May 2023

Background:

Immune checkpoint inhibitors (ICIs) are increasingly used as first-line therapy for patients with advanced non-small cell lung cancer (NSCLC) harboring no actionable mutations; however, data on their efficacy among patients presenting with intracranial lesions are limited. This study aimed to explore the efficacy and safety of ICIs combined with chemotherapy in advanced NSCLC patients with measurable brain metastasis at initial diagnosis.

Methods:

Our study retrospectively analyzed clinical data of a total of 211 patients diagnosed with driver gene mutation-negative advanced NSCLC with measurable, asymptomatic brain metastasis at baseline from Hunan Cancer Hospital between January 1, 2019 and September 30, 2021. The patients were stratified into two groups according to the first-line treatment regimen received: ICI combined with chemotherapy (n = 102) or chemotherapy (n = 109). Systemic and intracranial objective response rates (ORRs) and progression-free survival (PFS) were analyzed. Adverse events were also compared between the groups.

Results:

Compared with the chemotherapy-based regimen, the ICI-containing regimen was associated with a significantly higher intracranial (44.1% [45/102] vs. 28.4% [31/109], χ
2 = 5.620, P = 0.013) and systemic (49.0% [50/102] vs. 33.9% [37/109], χ
2 = 4.942, P = 0.019) ORRs and longer intracranial (11.0 months vs. 7.0 months, P <0.001) and systemic (9.0 months vs. 5.0 months, P <0.001) PFS. Multivariable analysis consistently revealed an independent association between receiving ICI plus platinum-based chemotherapy as a first-line regimen and prolonged intracranial PFS (hazard ratio [HR] = 0.52, 95% confidence interval [CI]: 0.37–0.73, P <0.001) and systemic PFS (HR = 0.48, 95% CI: 0.35–0.66, P <0.001). No unexpected serious adverse effects were observed.

Conclusion:

Our study provides real-world clinical evidence that ICI combined with chemotherapy is a promising first-line treatment option for driver gene mutation-negative advanced NSCLC patients who present with brain metastasis at initial diagnosis.

Clinical trial registration:

https://www.clinicaltrials.gov/, OMESIA, NCT05129202.
Association between weekend catch-up sleep and hyperuricemia with insufficient sleep in postmenopausal Korean women: a nationwide cross-sectional study
Authors: Son Soo Min , Park Eun-Ju , Kwon Ryuk Jun , Cho Young Hye , Lee Sang Yeoup , Choi Jung In , Lee Youngin , Lee Sae Rom , Kim Yun Jin , Lee Jeong Gyu , Yi Yu Hyeon , Tak Young Jin , Lee Seung Hun , Kim Gyu Lee , Ra Young Jin
Published: May 2023

Objective

Hyperuricemia is associated with metabolic and cardiovascular diseases and mortality. Efforts to lower the risk of hyperuricemia in various ways are needed as the prevalence of these diseases increases in postmenopausal women. Studies have shown that one of these methods is associated with adequate sleep duration, which is related to a low risk of hyperuricemia. Considering that it is difficult for people to get enough sleep in modern society, this study hypothesized that weekend catch-up sleep could be an alternative. To our knowledge, no past study has investigated the relation between weekend catch-up sleep and hyperuricemia in postmenopausal women. Hence, the aim of this research was to estimate the relation between weekend catch-up sleep and hyperuricemia with insufficient sleep in postmenopausal women during weekday or workday.

Methods

This study included 1,877 participants extracted from the Korea National Health and Nutrition Examination Survey VII. The study population was divided into weekend catch-up sleep and non–weekend catch-up sleep groups. Odds ratios with 95% confidence intervals were derived using multiple logistic regression analysis.

Results

Weekend catch-up sleep had a significantly lower prevalence of hyperuricemia after adjusting for confounders (odds ratio, 0.758 [95% confidence interval, 0.576-0.997]). In a subgroup analysis, weekend catch-up sleep of 1 to 2 hours was significantly correlated with a lower prevalence of hyperuricemia after adjusting for confounders (odds ratio: 0.522 [95% confidence interval, 0.323-0.845]).

Conclusions

Weekend catch-up sleep had a decreased prevalence of hyperuricemia in postmenopausal women with sleep deprivation.
Investigating the efficacy and feasibility of using a whole-of-diet approach to lower circulating levels of C-reactive protein in postmenopausal women: a mixed methods pilot study
Authors: Cowan Stephanie , Dordevic Aimee , Sinclair Andrew J. , Truby Helen , Sood Surbhi , Gibson Simone
Published: May 2023

Objective

Chronic inflammation is associated with obesity and is an underlying pathophysiology for cardiovascular disease (CVD) development in postmenopausal women. This study aims to determine feasibility and efficacy of an anti-inflammatory dietary intervention to lower levels of C-reactive protein in weight stable postmenopausal women with abdominal obesity.

Methods

This mixed-methods pilot study used a single arm pre-post design. Thirteen women followed a 4-week anti-inflammatory, dietary intervention, optimizing consumption of healthy fats, low glycemic index wholegrains, and dietary antioxidants. Quantitative outcomes included change in inflammatory and metabolic markers. Focus groups were undertaken and thematically analyzed to explore participants lived experience of following the diet.

Results

There was no significant change in plasma high-sensitivity C-reactive, protein. Despite discouraging weight loss, median (Q1–Q3) body weight decreased by −0.7 (−1.3 to 0 kg, P = 0.02). This was accompanied by reductions in plasma insulin (0.90 [−0.05 to 2.20] mmol/L), Homeostatic Model Assessment of Insulin Resistance (0.29 [−0.03 to 0.59]), and low-density lipoprotein:high-density lipoprotein ratio (0.18 [−0.01 to 0.40]) (P ≤ 0.023 for all). Thematic analysis revealed that postmenopausal women have a desire to improve meaningful markers of health status that do not focus on weight. Women were highly engaged with learning about emerging and innovative nutrition topics, favoring a detailed and comprehensive nutrition education style that challenged their proficient health literacy and cooking skills.

Conclusions

Weight-neutral dietary interventions targeting inflammation can improve metabolic markers and may be a viable strategy for CVD risk reduction in postmenopausal women. To determine effects on inflammatory status, a fully powered and longer-term randomized controlled trial is required.
Barriers to hormone therapy following prophylactic bilateral salpingo-oophorectomy in BRCA1/2 mutation carriers
Authors: DiSilvestro Jessica B. , Haddad Jessica , Robison Katina , Beffa Lindsey , Laprise Jessica , Scalia-Wilbur Jennifer , Raker Christina , Clark Melissa , Lokich Elizabeth , Hofstatter Erin , Dalela Disha , Brown Amy , Bradford Leslie , Toland Maris , Stuckey Ashley
Published: May 2023

Objective

This study aimed to identify barriers to hormone therapy (HT) use among women with BRCA1/2 mutations after prophylactic bilateral salpingo-oophorectomy (BSO).

Methods

A cross-sectional, electronic survey was conducted of BRCA1/2 mutation carriers at Women and Infants Hospital, Yale Medical Center, Hartford Healthcare, and Maine Medical Center. This study was a subanalysis of a subset of female BRCA1/2 mutation carriers who had undergone a prophylactic BSO. Data were analyzed using the Fisher's exact test or t test.

Results

We performed a subanalysis of 60 BRCA mutation carriers who underwent a prophylactic BSO. Only 24 women (40%) reported ever using HT. HT use was higher in women who underwent their prophylactic BSO at age younger than 45 years (51% vs. 25%, P = 0.06). Among all women who had a prophylactic BSO, the majority (73%) reported that a provider talked to them about using HT. Two thirds reported having seen contradictory information in the media about long-term consequences of HT. Seventy percent listed their provider as the primary influence in their decision to start HT. The most common reasons for not starting HT included it not being recommended by their physician (46%) and that it was not necessary (37%).

Conclusions

BRCA mutation carriers frequently undergo prophylactic BSO at young ages, and less than half report using HT. This study highlights barriers to HT use, such as patient fears and physician discouragement, and identifies potential areas to improve educational efforts.
Hysteroscopic alterations in women with infertility or recurrent spontaneous abortion in case of normal transvaginal ultrasonography
Authors: Zhang Ya-nan , Liu Peng , Qi Dan , Zhao Sheng-rui , Chen Zi-Jiang , Han Ting , Yan Lei
Published: May 2023

Introduction:

Whether hysteroscopy should routinely be conducted before embryo transfer remains uncertain especially when transvaginal ultrasonography (TVS) is normal. We aimed to investigate the hysteroscopic findings for patients with infertility or recurrent spontaneous abortion and with normal TVS.

Methods:

Patients who underwent TVS and hysteroscopy in the hospital from January 2014 to May 2019 were enrolled. Propensity score matching (1:1) was carried out for TVS positive and negative result groups. The positive results of hysteroscopy in the primary and secondary infertility patients were further compared. The prevalence rates of various diseases in different age groups were summarized and analyzed.

Results:

A total of 1532 individuals were enrolled in the study group and 19,118 cases in the control group. A total of 1495 cases with TVS positive results were matched using propensity score matching (1:1). The prevalence of uterine diseases in the TVS positive group was significantly higher than that in the TVS negative group (P<0.001).The prevalence of endometrial polyps and endometrial hyperplasia in patients with primary infertility was significantly higher than that with secondary infertility (P<0.001). The diagnostic sensitivity of TVS for major uterine cavity diseases, confirmed by hysteroscopy was relatively low (12.7%; 11.9%–13.6%).

Conclusions:

Hysteroscopy can detect a considerable number of uterine lesions even after normal TVS results. The sensitivity of TVS for the diagnosis of intrauterine lesions is relatively low. We suggest that hysteroscopy be recommended for patients with infertility or recurrent spontaneous abortion.
Association Between Solid Fuel Use and the Risk of Hypertension in China
Authors: Fu Ziwei , Wang Shuang , Xie Hongwei , Xie Yuxin , Wen Xilin , Zheng Jing , Shi Yu , Li Yichong
Published: May 2023

Objective

The aim of the study is to assess the association between solid fuel use for cooking or heating and the risk of hypertension among individuals older than 45 years.

Methods

Baseline questionnaires were used to collect self-reported primary cooking and heating fuel usage. Outcomes were defined as the time of first diagnosis of hypertension. Data were analyzed using Cox proportional hazards models.

Results

Solid fuel use for cooking was associated with a higher risk of hypertension. The association between solid fuel for cooking and hypertension remained significant among residents in north China, individuals aged 45 to 65 years, urban residents, and nonsmokers. Solid fuel for heating was associated with a higher risk of hypertension only in South China.

Conclusions

Solid fuel use may result in an increased risk of hypertension. Our findings further emphasize the health hazards of solid fuel for cooking and heating.
Career Development Needs of Physician Associates in the United Kingdom: A Qualitative Study
Authors: Carey Frances , Newton Philip M.
Published: May 2023

Introduction

The physician associate (PA) profession is relatively new to the United Kingdom (UK) with the first UK-trained PAs graduating in 2008. Unlike other UK health professions, there is currently no well-established career framework after graduating as a PA. This pragmatic research aimed primarily to provide useful information for the future development of a PA career framework that will best support the career development needs of the PA profession.

Methods

The current study used qualitative 1:1 interviews to understand senior PAs' aspirations, postgraduate education, career progression, development opportunities, and perceptions for a career framework. Where are they now? What are they doing? What are their expectations for the future? What subsequent changes do senior PAs think a career framework might bring to the profession?

Results

Most PAs support a career framework and the opportunity to highlight and facilitate the PA's unique ability to transfer specialties; both generalist and specialized PA experience should be recognized. All participants supported a postgraduate standardization of PA practice citing patient safety and equal opportunities for the PA workforce. Furthermore, although the PA profession was introduced to the UK with lateral rather than vertical progression, the current study demonstrates the existence of hierarchical roles within the PA workforce.

Discussion

A postqualification framework is needed in the UK, one that supports the current flexibility of the PA workforce.
Three- versus two-rows circular staplers for left-sided colorectal anastomosis: a propensity score-matched analysis of the iCral 2 and 3 prospective cohorts
Authors: Catarci Marco , Guadagni Stefano , Masedu Francesco , Ruffo Giacomo , Viola Massimo Giuseppe , Borghi Felice , Baldazzi Gianandrea , Scatizzi Marco ,   on behalf of the the Italian ColoRectal Anastomotic Leakage (iCral) study group
Published: May 2023

Background:

Since most anastomoses after left-sided colorectal resections are performed with a circular stapler, any technological change in stapling devices may influence the incidence of anastomotic adverse events. The aim of the present study was to analyze the effect of a three-rows circular stapler on anastomotic leakage and related morbidity after left-sided colorectal resections.

Materials and Methods:

A circular stapled anastomosis was performed in 4,255 (50.9%) out of 8,359 patients enrolled in two prospective multicenter studies in Italy, and, after exclusion criteria to reduce heterogeneity, 2,799 (65.8%) cases were retrospectively analyzed through a 1:1 propensity score-matching model including 20 covariates relative to patient characteristics, to surgery and to perioperative management. Two well balanced groups of 425 patients each were obtained: group (A) – true population of interest, anastomosis performed with a 3-rows circular stapler; group (B), – control population, anastomosis performed with a 2-rows circular stapler. The target of inferences was the average treatment effect in the treated (ATT). The primary endpoints were overall and major anastomotic leakage, and overall anastomotic bleeding; the secondary endpoints were overall and major morbidity, and mortality rates. The results of multiple logistic regression analyses for the outcomes, including the 20 covariates selected for matching, were presented as odds ratios (OR) and 95% confidence intervals (95%CI).

Results:

Group A vs. group B showed a significantly lower risk of overall anastomotic leakage [2.1 vs. 6.1%; OR 0.33; 95%CI 0.15–0.73; P=.006], major anastomotic leakage [2.1 vs. 5.2%; OR 0.39; 95%CI 0.17–0.87; P=.022], and major morbidity [3.5 vs. 6.6% events; OR 0.47; 95%CI 0.24–0.91; P=.026].

Conclusion:

The use of 3-rows circular staplers independently reduced the risk of anastomotic leakage and related morbidity after left-sided colorectal resection. Twenty-five patients were required to avoid one leakage.
Influence of General and Local Anesthesia on Postoperative Pain After a Loop Electrosurgical Excision Procedure
Authors: Güngördük Kemal , Türkmen Hilal Ezgi , Gülseren Varol , Küçükler Berfin , Çelikkol Özgü , Özdemir İsa Aykut
Published: May 2023

Objective

To compare patient satisfaction, histopathologic results, and short-term morbidity in patients undergoing loop electrosurgical excision procedure (LEEP) under local anesthesia (LA) versus general anesthesia (GA).

Methods

Participants who met the inclusion criteria were randomly allocated in a 1:1 ratio to the LA group or GA group. Pain was determined by both objective (faces pain scale-revised) and subjective (visual analog scale score) methods.

Results

Data from 244 patients (123 in the LA group and 121 in the GA group) were analyzed. The median cone volume was 2.0 (0.4–4.7) cm3in the LA group and 2.4 (0.3–4.8) cm3in the GA group. There was no difference in margin involvement or repeat conization between the groups. The procedure time, time to complete hemostasis, intraoperative blood loss, and early postoperative blood loss were similar between the groups. The visual analog scale scores were higher in the LA group at 1, 2, and 4 hours postoperatively, but the differences between the groups were not significant. In addition, the median faces pain scale-revised scores at 1, 2, and 4 hours postoperatively were not significantly different between the LA and GA groups.

Conclusions

The present study showed no difference in pain during the postoperative period, need for additional analgesia, volume of the extracted cone specimens, rate of positive surgical margin, bleeding volume, or operation time in women undergoing loop electrosurgical excision procedure under LA versus GA.