bluuebunny/crossref_metadata_2025 huggingface dataset:
Reducing cost with MEMS sensor and improving performance of classifier using probabilistic voting method
Authors: Balaji P Arun , Sugumaran V
Published: October 2023

When developing a solution for fault diagnosis, cost is a critical factor that must be considered to ensure a practical and feasible final product. To reduce expenses, the authors conducted a feasibility study using a low-cost MEMS accelerometer in conjunction with an Arduino Uno. This study aimed to determine the effect of sample length on fault classification by varying it from 50 to 5000 to identify the optimal value for this particular application. After finalizing the parameters, the vibration signal was acquired using the MEMS sensor and Arduino Uno. The resulting classification accuracy using the decision tree was 90.2%, a satisfactory result that can be further improved for industrial applications. To enhance the accuracy of decision tree classifiers, the authors proposed a novel approach known as the probabilistic voting method. By implementing this method and utilizing an Arduino Uno and MEMS sensor (ADXL335), they were able to drastically cut down costs while achieving remarkable classification accuracy. The implementation of the probabilistic voting method further elevated the accuracy to an astounding 98.5%, setting a new benchmark in the field.
A visual SLAM method assisted by IMU and deep learning in indoor dynamic blurred scenes
Authors: Liu Fengyu , Cao Yi , Cheng Xianghong , Liu Luhui
Published: October 2023

Dynamic targets in the environment can seriously affect the accuracy of simultaneous localization and mapping (SLAM) systems. This article proposes a novel dynamic visual SLAM method with inertial measurement unit (IMU) and deep learning for indoor dynamic blurred scenes, which improves the front end of ORB-SLAM2, combining deep learning with geometric constraint to make the dynamic feature points elimination more reasonable and robust. First, a multi-directional superposition blur augmentation algorithm is added to the YOLOv5s network to compensate for errors caused by fast-moving targets, camera shake and camera focus. Then, the fine-tuned YOLOv5s model is used to detect potential dynamic regions. Afterward, IMU measurements are introduced for rotation compensation to calculate the feature point velocity and estimate the motion speed of the camera, in order to estimate the real motion state of potential dynamic targets. Finally, real dynamic points will be removed and potential dynamic points will be reserved for subsequent pose estimation. Experiments are conducted on Technische Universität München dynamic dataset and in the real world. The results demonstrate that the proposed method has significant improvement compared with ORB-SLAM2, and has a more robust performance over some other state-of-the-art dynamic visual SLAM systems.
Extended in-field and out-of-field validation of a compact Monte Carlo model of an IBA PROTEUS®ONE proton beam in TOPAS/GEANT4
Authors: Colson Dries , Blommaert Jeroen , Poels Kenneth , De Saint-Hubert Marijke , Reniers Brigitte , Depuydt Tom
Published: October 2023

Objective: This study evaluates a compact Monte Carlo (MC) model of a pencil beam scanning clinical proton beam using TOPAS to estimate the dose out-of-field (OOF). Compact modelling means that the model starts from a pristine proton beam at the nozzle exit, customised based on acceptance and commissioning data, instead of modelling the full treatment head and room. Approach: First, in-field validation tests were performed. Then, the OOF dose was validated in an RW3 phantom with bubble detectors for personal neutron dosimetry (measuring the neutron dose equivalent) and thermoluminiescent detectors (measuring the absorbed dose by protons and gammas). Measurements were performed at 15 and 35 cm from the distal edge of the field for five different irradiation plans, covering different beam orientations, proton energies and a 40 mm range shifter. TOPAS simulations were performed with QGSP Binary Cascade HP (BIC) and QGSP Bertini HP (Bertini) hadron physics lists. Main results: In-field validation shows that MC simulations agree with point dose measurements within −2.5 % and +1.5 % at locations on- and off-axis and before, in and after the Bragg peak or plateau. The gamma passing rate 2%/3mm of four simulated treatment plans compared to the dose distribution calculated by the TPS exceeds 97 % agreement score. OOF dose simulations showed an average overestimation of 27 % of the neutron dose equivalent for the BIC hadron physics list and an average underestimation of 20 % for the Bertini hadron physics list. The simulated absorbed dose of protons and gammas showed a systematic underestimation which was on average 21 % and 51 % for BIC and Bertini respectively. Significance: Our study demonstrates that a compact MC model can reliably produce in-field data, while out-of-field dose data are within the uncertainties of the detector systems and MC simulations nuclear models, and do so with shorter modelling and faster calculation time.
Optimal batch determination for improved harmonization and prognostication of multi-center PET/CT radiomics feature in head and neck cancer
Authors: Wu Huiqin , Liu Xiaohui , Peng Lihong , Yang Yuling , Zhou Zidong , Du Dongyang , Xu Hui , Lv Wenbing , Lu Lijun
Published: October 2023

Objective. To determine the optimal approach for identifying and mitigating batch effects in PET/CT radiomics features, and further improve the prognosis of patients with head and neck cancer (HNC), this study investigated the performance of three batch harmonization methods. Approach. Unsupervised harmonization identified the batch labels by K-means clustering. Supervised harmonization regarding the image acquisition factors (center, manufacturer, scanner, filter kernel) as known/given batch labels, and Combat harmonization was then implemented separately and sequentially based on the batch labels, i.e. harmonizing features among batches determined by each factor individually or harmonizing features among batches determined by multiple factors successively. Extensive experiments were conducted to predict overall survival (OS) on public PET/CT datasets that contain 800 patients from 9 centers. Main results. In the external validation cohort, results show that compared to original models without harmonization, Combat harmonization would be beneficial in OS prediction with C-index of 0.687–0.740 versus 0.684–0.767. Supervised harmonization slightly outperformed unsupervised harmonization in all models (C-index: 0.692–0.767 versus 0.684–0.750). Separate harmonization outperformed sequential harmonization in CT_m+clinic and CT_cm+clinic models with C-index of 0.752 and 0.722, respectively, while sequential harmonization involved clinical features in PET_rs+clinic model further improving the performance and achieving the highest C-index of 0.767. Significance. Optimal batch determination especially sequential harmonization for Combat holds the potential to improve the prognostic power of radiomics model in multi-center HNC dataset with PET/CT imaging.
Optimization of high-temperature superconducting multilayer films using artificial intelligence
Authors: Rivasto Elmeri , Todorović Milica , Huhtinen Hannu , Paturi Petriina
Published: October 2023

We have studied the possibility of utilizing artificial intelligence (AI) models to optimize high-temperature superconducting (HTS) multilayer structures for applications working in a specific field and temperature range. For this, we propose a new vortex dynamics simulation method that enables unprecedented efficiency in the sampling of training data required by the AI models. The performance of several different types of AI models has been studied, including kernel ridge regression (KRR), gradient-boosted decision tree (GBDT) and neural network. From these, the GBDT based model was observed to be clearly the best fitted for the associated problem. We have demonstrated the use of GBDT for finding optimal multilayer structure at 10 K temperature under 1 T field. The GBDT model predicts that simple doped-undoped bilayer structures, where the vast majority of the film is undoped superconductor, provide the best performance under the given environment. The obtained results coincide well with our previous studies providing further validation for the use of AI in the associated problem. We generally consider the AI models as highly efficient tools for the broad-scale optimization of HTS multilayer structures and suggest them to be used as the foremost method to further push the limits of HTS films for specific applications.
Nonlinear dynamics in eyring-powell fluid flow with darcy-forchheimer effects. An asymptotic analysis
Authors: Rahman S , Luis Díaz Palencia José , Reyes Enrique G
Published: October 2023

We provide a mathematical treatment, analytical and numerical, for a fluid constructed as an hybrid of the Eyring-Powell and Darcy-Forchheimer fluid models. The Eyring-Powell model departs from the kinetic theory of liquids and it allows for a description of shear stresses and viscous terms. The Darcy-Forchheimer model permits to describe the fluid effects given in a porous media, and it provides non-linear reaction terms when considered as part of the momentum equations. Hence, it is natural to investigate mathematical characteristics of solutions for a fluid flow formulated as a combination of these two fluid models. First of all, we prove boundedness and uniqueness of solutions arising from rough (i.e. in L
1(R) ∩ L
∞(R)) initial data. This is physically relevant, since it means that we are considering general descriptions of the velocity distribution of the fluid, in a media with particular porosity distributions. Afterwards, stationary profiles are obtained by using a Hamiltonian description, and our construction is supported by numerical validating evidences. Furthermore, asymptotic solutions are explored based on an exponential scaling and a non-linear transport Jacobi equation. Finally, a region of validity for this asymptotic approach is provided, and a numerical validation of our asymptotic analysis is presented. Our main conclusion is that a fluid model combining Eyring-Powell and Darcy-Forchheimer characteristics is indeed possible to introduce, and that solutions of potential physical interest, can be obtained.
An attention-based multi-modal MRI fusion model for major depressive disorder diagnosis
Authors: Zheng Guowei , Zheng Weihao , Zhang Yu , Wang Junyu , Chen Miao , Wang Yin , Cai Tianhong , Yao Zhijun , Hu Bin
Published: October 2023

Objective. Major depressive disorder (MDD) is one of the biggest threats to human mental health. MDD is characterized by aberrant changes in both structure and function of the brain. Although recent studies have developed some deep learning models based on multi-modal magnetic resonance imaging (MRI) for MDD diagnosis, the latent associations between deep features derived from different modalities were largely unexplored by previous studies, which we hypothesized may have potential benefits in improving the diagnostic accuracy of MDD. Approach. In this study, we proposed a novel deep learning model that fused both structural MRI (sMRI) and resting-state MRI (rs-fMRI) data to enhance the diagnosis of MDD by capturing the interactions between deep features extracted from different modalities. Specifically, we first employed a brain function encoder (BFE) and a brain structure encoder (BSE) to extract the deep features from fMRI and sMRI, respectively. Then, we designed a function and structure co-attention fusion (FSCF) module that captured inter-modal interactions and adaptively fused multi-modal deep features for MDD diagnosis. Main results. This model was evaluated on a large cohort and achieved a high classification accuracy of 75.2% for MDD diagnosis. Moreover, the attention distribution of the FSCF module assigned higher attention weights to structural features than functional features for diagnosing MDD. Significance. The high classification accuracy highlights the effectiveness and potential clinical of the proposed model.
Precise image generation on current noisy quantum computing devices
Authors: Rehm Florian , Vallecorsa Sofia , Borras Kerstin , Krücker Dirk , Grossi Michele , Varo Valle
Published: October 2023

The quantum angle generator (QAG) is a new full quantum machine learning model designed to generate accurate images on current noise intermediate scale quantum devices. Variational quantum circuits form the core of the QAG model, and various circuit architectures are evaluated. In combination with the so-called MERA-upsampling architecture, the QAG model achieves excellent results, which are analyzed and evaluated in detail. To our knowledge, this is the first time that a quantum model has achieved such accurate results. To explore the robustness of the model to noise, an extensive quantum noise study is performed. In this paper, it is demonstrated that the model trained on a physical quantum device learns the noise characteristics of the hardware and generates outstanding results. It is verified that even a quantum hardware machine calibration change during training of up to 8% can be well tolerated. For demonstration, the model is employed in indispensable simulations in high energy physics required to measure particle energies and, ultimately, to discover unknown particles at the large Hadron Collider at CERN.
Physics-informed neural networks for solving forward and inverse Vlasov–Poisson equation via fully kinetic simulation
Authors: Zhang Baiyi , Cai Guobiao , Weng Huiyan , Wang Weizong , Liu Lihui , He Bijiao
Published: October 2023

The Vlasov–Poisson equation is one of the most fundamental models in plasma physics. It has been widely used in areas such as confined plasmas in thermonuclear research and space plasmas in planetary magnetospheres. In this study, we explore the feasibility of the physics-informed neural networks for solving forward and inverse Vlasov–Poisson equation (PINN-Vlasov). The PINN-Vlasov method employs a multilayer perceptron (MLP) to represent the solution of the Vlasov–Poisson equation. The training dataset comprises the randomly sampled time, space, and velocity coordinates and the corresponding distribution function. We generate training data using the fully kinetic PIC simulation rather than the analytical solution to the Vlasov–Poisson equation to eliminate the correlation between data and equations. The Vlasov equation and Poisson equation are concurrently integrated into the PINN-Vlasov framework using automatic differentiation and the trapezoidal rule, respectively. By minimizing the residuals between the reconstructed distribution function and labeled data, and the physically constrained residuals of the Vlasov–Poisson equation, the PINN-Vlasov method is capable of dealing with both forward and inverse problems. For forward problems, the PINN-Vlasov method can solve the Vlasov–Poisson equation with given initial and boundary conditions. For inverse problems, the completely unknown electric field and equation coefficients can be predicted with the PINN-Vlasov method using little particle distribution data.
Phylogeography and chromosome number variation in Micranthes nelsoniana and related species (Saxifragaceae) in Northeast Asia
Authors: Fukuda Tomoko , Ishikawa Naoko , Chernyagina Olga A , Barkalov Vyacheslav Y , Taran Aleksandr A , Yakubov Valentin V , Marchuk Elena A , Linnik Elena V , Tamaki Ichiro
Published: October 2023

Micranthes nelsoniana possesses multiple different variants and numerous chromosomes. Based on the internal transcribed spacer (ITS) and chloroplast (cp)DNA sequences, the phylogeography of M. nelsoniana and its relatives in Northeast Asia was investigated, with extensive sampling around the Kuril Islands. The Arctic–Asian continent and a clade of marginal islands were the two main groupings that comprised the ITS phylogenetic tree. The island clade was separated into five well-supported clades: Kamchatka and Hokkaido highlands, Kuril–Aleutian Islands, southern Kuril Islands, Japanese archipelago, and Primorye region. Micranthes fusca was found in Japan and in the southern Kuril Islands. It is a separate species that created several types of hybrids between M. nelsoniana in the centre of the Kuril Islands based on a comparison of the ITS and cpDNA networks. Micranthes nelsoniana and M. ohwii appear to have hybridized in the northern Kuril Islands. Cytological investigation on the local species of M. nelsoniana showed that the chromosomal numbers are: 2n = 24, 26, 28, 30, 50, and 80. Among them, two usual numbers to this area, 2n = 24 and 50, appear to encourage interspecific gene exchange. The genomes of Hokkaido plants with high chromosome counts were cloned, revealing that they contained genes of both continental and marginal origins. This study revealed the crucial role of marginal islands along Northeast Asia in the genetic diversity of M. nelsoniana and related species.
The Political Economy of Australian Militarism: On the Emergent Military–Industrial–Academic Complex
Authors: Troath Sian
Published: October 2023

Australia is undergoing a process of substantial militarization. This article argues that one of the key forces underpinning Australia’s militarization is an emergent military–industrial–academic complex (MIAC), comprised of increasingly close relationships between universities, defense, and defense industry. The connections between the three have rapidly intensified since 2016 due to changes in defense industry policy, pessimism regarding the strategic environment, the ongoing malaise of the neoliberal university, and the motivations of key individuals. This article demonstrates that each of the three groups is actively seeking closer relationships with the other, driven by a patchwork of competing economic and strategic motivations, and powered by ideals of innovation and the entrepreneurial spirit. Each needs the other—for military advantage, for profits, and for survival. Australia’s emergent but rapidly expanding MIAC raises concerns about the pace, nature, and necessity of Australia’s militarization, the impact on the role of the university in society, and the hollowness of Australian strategic policy. Furthermore, it has substantial implications for strategic competition in the Indo-Pacific, Australia’s alliances, and the Australia-UK-US (AUKUS) partnership.
First-Line Antituberculosis Drug Concentrations in Infants With HIV and a History of Recent Admission With Severe Pneumonia
Authors: Chabala Chishala , Jacobs Tom G , Moraleda Cinta , Ndaferankhande John M , Mumbiro Vivian , Passanduca Alfeu , Namuziya Natasha , Nalwanga Damalie , Musiime Victor , Ballesteros Alvaro , Domínguez-Rodríguez Sara , Chitsamatanga Moses , Cassia Uneisse , Nduna Bwendo , Bramugy Justina , Sacarlal Jahit , Madrid Lola , Nathoo Kusum J , Colbers Angela , Burger David M , Mulenga Veronica , Buck W Chris , Mujuru Hilda A , te Brake Lindsey H M , Rojo Pablo , Tagarro Alfredo , Aarnoutse Rob E ,   EMPIRICAL clinical trial group, Sidat Muhammad , Manjate Elias , Martins Sónia , Langa Stella , Nipaco Natália , Machava Sara , Chirindza Anastância , Martins Luzidina , Nhaca Mércia , Nathoo Kusum J , Chitsamatanga Moses , Marange Ruth , Mudzingwa Shepherd , Murungu Dorothy , Zulu Idah , Shankalala Perfect , Mukubesa Mulima , Namwinwa Juliet , Chibuye Chalwe , Chipoya Terence , Simunyola Bwalya , Tembo John , Inambao Muleya , Chitondo Salome , Mumba Wyclef , Mankushe Endreen , Musukwa Henry , Sondashi Davies , Kamugisha Albert , Econi Karen , Kiggwe Andrew , Beinomugisha Judith , Nkinzi Sharafat , Kakooza Lawrence , Namisanvu Henriator , Lajara Mark Nancy , Mwesige Josam Thembo , Segawa Ivan , Ssessanga Joseph , Mbavu Paul , Kafufu Bosco , Nansera Denis , Najjingo Elizabeth , Mbabazi Bashira T , Lugemwa Abbas , Kasozi Mariam , Ankunda Rogers , Manukyan Lilit
Published: October 2023

Optimal antituberculosis therapy is essential for favorable clinical outcomes. Peak plasma concentrations of first-line antituberculosis drugs in infants with living HIV receiving WHO-recommended dosing were low compared with reference values for adults, supporting studies on increased doses of first-line TB drugs in infants.
Working with Afghan Evacuees: Field Reflections on Five Useful Supervision Questions for Crisis Intervention Workers
Authors: Adhyaru Jai Shree , Guchait Ankita
Published: October 2023

This field reflection is a reflective dialogue between a supervisor and supervisee focusing on work with Afghan evacuees undertaken by the Centre for Anxiety, Stress & Trauma within Central and North West London NHS Foundation Trust. This field reflection focuses on five themes that emerged between the supervisor and supervisee during clinical supervision. The themes are posed as questions that may help others working in the context of a humanitarian crisis to utilize supervision to effectively support both staff and the target population. The reflections conclude with recommendations on how supervision can support staff well-being and, in turn, offer a supportive service to people feeling their homeland in the context of war.
TAGADA: a scalable pipeline to improve genome annotations with RNA-seq data
Authors: Kurylo Cyril , Guyomar Cervin , Foissac Sylvain , Djebali Sarah
Published: October 2023

Genome annotation plays a crucial role in providing comprehensive catalog of genes and transcripts for a particular species. As research projects generate new transcriptome data worldwide, integrating this information into existing annotations becomes essential. However, most bioinformatics pipelines are limited in their ability to effectively and consistently update annotations using new RNA-seq data. Here we introduce TAGADA, an RNA-seq pipeline for Transcripts And Genes Assembly, Deconvolution, and Analysis. Given a genomic sequence, a reference annotation and RNA-seq reads, TAGADA enhances existing gene models by generating an improved annotation. It also computes expression values for both the reference and novel annotation, identifies long non-coding transcripts (lncRNAs), and provides a comprehensive quality control report. Developed using Nextflow DSL2, TAGADA offers user-friendly functionalities and ensures reproducibility across different computing platforms through its containerized environment. In this study, we demonstrate the efficacy of TAGADA using RNA-seq data from the GENE-SWiTCH project alongside chicken and pig genome annotations as references. Results indicate that TAGADA can substantially increase the number of annotated transcripts by approximately $300\%$ in these species. Furthermore, we illustrate how TAGADA can integrate Illumina NovaSeq short reads with PacBio Iso-Seq long reads, showcasing its versatility. TAGADA is available at github.com/FAANG/analysis-TAGADA.
Conserved structured domains in plant non-coding RNA enod40, their evolution and recruitment of sequences from transposable elements
Authors: Gultyaev Alexander P , Koster Celine , van Batenburg Diederik Cames , Sistermans Tom , van Belle Niels , Vijfvinkel Daan , Roussis Andreas
Published: October 2023

Plant long noncoding RNA enod40 is involved in the regulation of symbiotic associations with bacteria, in particular, in nitrogen-fixing root nodules of legumes, and with fungi in phosphate-acquiring arbuscular mycorrhizae formed by various plants. The presence of enod40 genes in plants that do not form such symbioses indicates its other roles in cell physiology. The molecular mechanisms of enod40 RNA function are poorly understood. Enod40 RNAs form several structured domains, conserved to different extents. Due to relatively low sequence similarity, identification of enod40 sequences in plant genomes is not straightforward, and many enod40 genes remain unannotated even in complete genomes. Here, we used comparative structure analysis and sequence similarity searches in order to locate enod40 genes and determine enod40 RNA structures in nitrogen-fixing clade plants and in grasses. The structures combine conserved features with considerable diversity of structural elements, including insertions of structured domain modules originating from transposable elements. Remarkably, these insertions contain sequences similar to tandem repeats and several stem-loops are homologous to microRNA precursors.
Critiquing Trends and Identifying Gaps in the Literature on LGBTQ Refugees and Asylum-Seekers
Authors: García Rodríguez Diego
Published: October 2023

This article delivers a comprehensive review of the English-language literature concerning the experiences of lesbian, gay, bisexual, transgender, transsexual, and queer (LGBTQ) refugees and asylum-seekers. Through an incisive synthesis and analysis, it identifies five pivotal themes: 1) journey and settlement; 2) legislation, policy, and charitable intervention; 3) health; 4) creative expression; and 5) religion, faith, and spirituality. This analysis uncovers gaps in the existing body of knowledge, charting innovative paths for future research and policy. This work transcends the boundaries of a traditional scholarly review to offer actionable recommendations aimed at guiding policy and practice. This involves pushing for strategies that are not just inclusive, but also rooted in overcoming Western-centric approaches to gender and sexual identities.
Using the matrixed multiple case study methodology to understand site differences in the outcomes of a Hybrid Type 1 trial of a peer-led healthy lifestyle intervention for people with serious mental illness
Authors: Tuda Daniela , Bochicchio Lauren , Stefancic Ana , Hawes Mark , Chen Jun-Hong , Powell Byron J , Cabassa Leopoldo J
Published: October 2023

Site differences in implementation trial outcomes are common but often not examined. In a Hybrid Type 1 trial examining the effectiveness-implementation of a peer-led group life-style balance (PGLB) intervention for people with serious mental illness (SMI) in three supportive housing agencies, we found that PGLB recipients’ physical health outcomes differed by study sites. The matrixed multiple case study methodology was used to explore how implementation outcomes and changes in context of usual care (UC) services contributed to these site differences. Two implementation outcomes (i.e. PGLB fidelity ratings and intervention recipients’ acceptability of PGLB and UC) and changes in healthcare services integration at the study sites were examined. ANOVAs were used to examine site differences in fidelity ratings and client satisfaction. Directed content analysis was used to analyze leadership interviews to identify changes in the context of UC services. Site 3 showed a trend approaching significance (P = .05) towards higher fidelity ratings. High levels of satisfaction with PGLB were reported at all sites. Significant differences in PGLB recipients’ satisfaction with UC were found, with Site 3 reporting the lowest levels of satisfaction. Agency leaders reported an increase in prioritizing client’s health throughout the trial with sites differing in how these priorities were put into action. Differences in PGLB recipients’ satisfaction with UC, and changes in healthcare service integration seemed to have contributed to the site differences in our trial. The matrixed multiple case study methodology is a useful approach to identify implementation outcomes contributing to the heterogeneity of multisite implementation trial results.
Convergent evolution of dark, ultraviolet-absorbing cuticular pigmentation in a new Afro-Oriental Echiniscus brunus species complex (Heterotardigrada: Echiniscidae)
Authors: Dey Pritam K , Gąsiorek Piotr , Michalczyk Łukasz
Published: October 2023

Green, brown and black pigments are uncommon in the otherwise typically yellow to orange Echiniscidae. Viridiscus, a genus currently represented by a handful of species, in which cuticular coloration varies from a light green through dark green to almost black, has been an exception. Here, we uncover a new echiniscid lineage from the primeval subtropical and tropical rainforests of India and Tanzania, comprising three species with a caramel/brown body. Given that both Viridiscus and the new species complex lack dorsolateral trunk appendages and share dark cuticular pigmentation, they may be mistaken for each other. However, a closer inspection of the dorsal cuticular sculpture and molecular phylogenetic analyses indicate that the new complex belongs within the Echiniscus spinulosus morphogroup. Thus, the presence of dark pigments in two indirectly related lineages is evidence for the convergence of dark cuticular coloration in limno-terrestrial heterotardigrades. We detected three species in the new complex: Echiniscus brunus sp. nov., from the Western Ghats (Tamil Nadu, India), and two other candidate species, Echiniscus aff. brunus sp. can. 1 and Echiniscus aff. brunus sp. can. 2, from India and Tanzania, respectively. We refrain from describing the two latter species formally because they exhibit little or no morphological differences, which is yet another clear case of the crucial role of DNA barcoding in an accurate estimation of tardigrade species richness.
Chinese Neonatal Nurses' Lived Experiences of Providing End-of-Life Care in the NICU
Authors: Tong-Hui Suo , Qi Lu , Xiao-Li Rui , Guo-Qin Yang , Li-Ping Wang , Lin Wang
Published: October 2023

Background:

Although end-of-life care (EOLC) has been well-studied, the experience of neonatal intensive care unit (NICU) nurses in China, where little EOLC training is provided, requires further investigation.

Purpose:

To explore the lived experience of EOLC delivery among NICU nurses, to provide evidence to enhance nurses' EOLC skills and improve their overall quality.

Methods:

This qualitative study adopted a phenomenological approach. A total of 11 NICU nurses participated in semistructured in-depth interviews between June and July 2022 at the First Affiliated Hospital of University of Science and Technology of China (USTC). Colaizzi's 7-step method was used to analyze the data.

Results:

Five main themes were identified: (a) multiple emotions are experienced during EOLC delivery; (b) EOLC delivery is stressful from various sources for nurses; (c) expressing empathy and compassion is important; (d) ethical and clinical decision-making are key components of EOLC delivery; and (e) there are challenges in improving neonatal EOLC understanding and delivery.

Implications for Practice and Research:

The experience of EOLC among Chinese NICU nurses is multidimensional and intensive. Institutions or units must establish and implement related protocols and guidelines to address differences between clinical practice and ideal protocols for neonatal EOLC. Educational programs that consider nurses' personal and interpersonal factors, including local culture, must be developed. Neonatal nurses in Western countries encountering Chinese-born parents who have lost their infants can gain an understanding of parents' perceptions from this study. Future research should focus on developing and testing interventions to train and support NICU nurses working with end-of-life neonates.
Comparison of Melanocyte-Associated Immunohistochemical Markers in Acral Lentiginous Melanoma and Acral Benign Nevi
Authors: Kim Jin Cheol , Choi Jee Woong , Kim You Chan
Published: October 2023

Acral lentiginous melanoma (ALM) is a relatively rare clinicopathologic subtype of cutaneous malignant melanoma, but it is the most common type of melanoma among Asians. Although the research to identify immunohistochemical (IHC) markers to differentiate nevi from melanoma is being conducted, specific markers for ALM are not well-known. Therefore, we aimed to analyze and compare the differences in the expression of melanocyte-associated IHC markers between ALM and acral benign nevi (ABN). Two independent groups of 53 and 19 paraffin-embedded specimens (from patients with pathologically confirmed ALM and ABN, respectively) were subjected to IHC staining for MART-1, preferentially expressed antigen in melanoma (PRAME), SOX10, HMB-45, Ki-67, and p16. We performed a quantitative analysis of PRAME, SOX10, KI-67, and p16 expression and gradient pattern analysis of HMB-45 expression for each specimen. The PRAME (60.1% and 28.5%, P < 0.05) and Ki-67 (7.8% and 3.5%, P < 0.05) expression levels were significantly higher in the ALM group than in the ABN group. The p16 expression was significantly lower (14.2% and 19.4%, P < 0.05), and the absence of HMB-45 gradient was more frequent in the ALM group than in the ABN group. However, no statistical significance was noted in SOX10 (54.8% and 44.7%). Receiver operating characteristic curves showed that PRAME had the highest area under the curve value. In summary, among various IHC markers, PRAME was the most valuable marker for the diagnosis of ALM; however, further large-scale studies are needed to validate these findings.
Prophylactic Absorbable Antibiotic Beads for High-risk, Implant-based Prepectoral Reconstruction
Authors: Ahmed Shahnur , Lee Jason T. C. , Roth Dylan , Sinha Mithun , Fisher Carla , Fan Betty , Imeokparia Folasade , Ludwig Kandice , Lester Mary E. , Hassanein Aladdin H.
Published: October 2023

Infections are problematic in postmastectomy implant-based reconstruction with infection rates as high as 30%. Strategies to reduce the risk of infection have demonstrated various efficacies. A prolonged course of systemic, oral antibiotics has not shown evidence-based benefit. Although absorbable antibiotic beads have been described for orthopedic procedures and pressure wounds, their use has not been well studied during breast reconstruction, particularly for prepectoral implant placement. The purpose of this study was to evaluate the selective use of prophylactic absorbable calcium sulfate antibiotic beads during high-risk implant-based, prepectoral breast reconstruction after mastectomy. Patients who underwent implant-based, prepectoral breast reconstruction between 2019 and 2022 were reviewed. Groups were divided into those who received antibiotic beads and those who did not. Outcome variables included postoperative infection at 90 days. A total of 148 patients (256 implants) were included: 15 patients (31 implants) who received biodegradable antibiotic beads and 133 patients (225 implants) in the control group. Patients who received antibiotic beads were more likely to have a history of infection (66.7%) compared with the control group (0%) (P < 0.01). Surgical site infection occurred in 3.2% of implants in the antibiotic bead group compared with 7.6%, but this did not reach statistical significance. The incidence of infection in high-risk patients who have absorbable antibiotic beads placed during the time of reconstruction seems to be normalized to the control group in this pilot study. We present a novel use of prophylactic absorbable antibiotic beads in prepectoral breast implant reconstruction.
Reflecting upon the Long-term Impact of COVID-19 on Cosmetic Plastic Surgery and Education
Authors: Krupp James , Menon Ambika , Shauly Orr , Losken Albert
Published: October 2023

As we enter a new year, this article serves as an opportunity to ponder on the impact of a worldwide pandemic on physicians and the field of plastic surgery, which began 4 years ago in January 2020. When looking at the data in the general-surgery and reconstructive literature, the surgical treatment of patients with COVID-19 appears safest 8 weeks after infection. It was also found that the so-called Zoom-boom crush of cosmetic surgery cases following pandemic lockdown appeared to be largely due to a backlog of cases. Cosmetic surgery, particularly facial cosmetic surgery, continues to increase in popularity year over year. However, the effects on plastic surgery training remain unclear. Even so, those affected by the pandemic seem more driven than ever to find job stability and security.
Nocardia paucivorans Endophthalmitis and Cerebral Abscesses in an Immunocompetent Patient
Authors: Thakkar Heeral , Rama Raj Palaniraj , Howard-Jones Annaleise R. , Adler Paul , Menon Vidthiya
Published: October 2023

Nocardia spp are an uncommon cause of central nervous system infections and particularly endophthalmitis. In this case report, we present the first documented case of endogenous Nocardia paucivorans endophthalmitis and subretinal abscesses. We also provide a brief summary of the literature regarding ocular and cerebral nocardiosis. Early diagnosis and management improve outcomes; hence, clinicians should be cognizant of Nocardia infection as a differential diagnosis in cases of cerebral abscess or endophthalmitis, including in the immunocompetent.
Dental Screening and Referral during Prenatal Care
Authors: Spencer Michelle , Idzik Shannon K.
Published: October 2023

Background:

Oral health is an important aspect of overall health and should be maintained during pregnancy. Due to complex physiological changes during pregnancy, the pregnant woman is at risk for developing periodontal disease and dental caries which are associated with poor birth outcomes including preterm births and low birthweight infants. Evidence-based guidelines developed by several professional organizations recommend oral screening be included in the first prenatal visit. The purpose of this quality improvement project was to implement a dental screening tool during prenatal care to identify pregnant patients with oral health needs and provide subsequent referrals to a dentist.

Methods:

The project was implemented over a 14-week period and included an oral health screening using a valid and reliable tool to identify oral health needs. Patients were screened and received a referral for dental care.

Results:

N = 826 pregnant women were screened. Of those screened 36.3% (n = 300) had not had their teeth cleaned in the past 12 months. More than 30% of pregnant patients (n = 316) reported some type of dental problem, 29.5% (n = 244) were screened during the first prenatal visit, and 36.7% (n = 303) were enrolled in Medicaid. At project completion, 74.6% (n = 616) of patients received dental referrals.

Conclusion:

Conducting oral health screenings during the first prenatal visit is important for identifying pregnant women at risk for oral health problems and improving birth outcomes and allows the patient time to visit the dentist prior to birth. Integration of an oral health screening and referral process can be successfully implemented during prenatal care to meet the needs of childbearing women.
Using Machine Learning to Select Breast Implant Volume
Authors: Basile Filipe V. , Oliveira Thais S.
Published: October 2023

Background:

In breast augmentation surgery, selection of the appropriate breast implant size is a crucial step that can greatly affect patient satisfaction and the outcome of the procedure. However, this decision is often based on the subjective judgment of the surgeon and the patient, which can lead to suboptimal results. The authors aimed to develop a machine-learning approach that can accurately predict the size of breast implants selected for breast augmentation surgery.

Methods:

The authors collected data on patient demographic characteristics, medical history, and surgeon preferences from a sample of 1000 consecutive patients who underwent breast augmentation. This information was used to train and test a supervised machine-learning model to predict the size of breast implant needed.

Results:

The study demonstrated the effectiveness of the algorithm in predicting breast implant size, achieving a Pearson correlation coefficient of 0.9335 (P < 0.001). The model generated accurate predictions in 86% of instances, with a mean absolute error of 27.10 mL. Its effectiveness was confirmed in the reoperation group, in which 36 of 57 patients (63%) would have received a more suitable implant size if the model’s suggestion had been followed, potentially avoiding reoperation.

Conclusions:

The findings show that machine learning can accurately predict the needed size of breast implants in augmentation surgery. By integrating the artificial intelligence model into a decision support system for breast augmentation surgery, essential guidance can be provided to surgeons and patients. This approach not only streamlines the implant selection process but also facilitates enhanced communication and decision-making, ultimately leading to more reliable outcomes and improved patient satisfaction.
Identifying perturbations that boost T-cell infiltration into tumours via counterfactual learning of their spatial proteomic profiles
Authors: Wang Zitong Jerry , Farooq Abdullah S. , Chen Yu-Jen , Bhargava Aman , Xu Alexander M. , Thomson Matt W.
Published: October 2023

Cancer progression can be slowed down or halted via the activation of either endogenous or engineered T cells and their infiltration of the tumour microenvironment. Here we describe a deep-learning model that uses large-scale spatial proteomic profiles of tumours to generate minimal tumour perturbations that boost T-cell infiltration. The model integrates a counterfactual optimization strategy for the generation of the perturbations with the prediction of T-cell infiltration as a self-supervised machine-learning problem. We applied the model to 368 samples of metastatic melanoma and colorectal cancer assayed using 40-plex imaging mass cytometry, and discovered cohort-dependent combinatorial perturbations (CXCL9, CXCL10, CCL22 and CCL18 for melanoma, and CXCR4, PD-1, PD-L1 and CYR61 for colorectal cancer) that support T-cell infiltration across patient cohorts, as confirmed via in vitro experiments. Leveraging counterfactual-based predictions of spatial omics data may aid the design of cancer therapeutics.
IFIH1loss-of-function predisposes to inflammatory and SARS-CoV-2-related infectious diseases
Authors: Najm Rania , Yavuz Lemis , Jain Ruchi , El Naofal Maha , Ramaswamy Sathishkumar , Abuhammour Walid , Loney Tom , Nowotny Norbert , Alsheikh-Ali Alawi , Abou Tayoun Ahmad , Kandasamy Richard K.
Published: October 2023

TheIFIH1gene, encoding melanoma differentiation-associated protein 5 (MDA5), is an indispensable innate immune regulator involved in the early detection of viral infections. Previous studies described MDA5 dysregulation linking it to weakened immunological responses, and increased susceptibility to microbial infections and autoimmune disorders. Monoallelic gain-of-function of theIFIH1gene has been associated with multisystem disorders, namely Aicardi-Goutieres and Singleton-Merten syndromes, while biallelic loss of this gene causes immunodeficiency. In this study, nine patients suffering from different cases of recurrent infections, inflammatory diseases, severe COVID-19, or multisystem inflammatory syndrome in children (MIS-C) were identified with putative loss-of-functionIFIH1variants by whole exome sequencing. All patients revealed signs of lymphopenia and an increase in inflammatory markers, including CRP, amyloid A, ferritin, and IL-6. One patient with a pathogenic homozygous variant c.2807+1G>A was the most severe case showing immunodeficiency and glomerulonephritis. The c.1641+1G>C variant was identified in the heterozygous state in patients suffering from periodic fever, COVID-19, or MIS-C, while the c.2016delA variant was identified in two patients with inflammatory bowel disease or MIS-C. Expression analysis showed that PBMCs of one patient with a c.2016delA variant had a significant decrease inISG15,IFNAandIFNGtranscript levels, compared to normal PBMCs, upon stimulation with poly(I:C), suggesting that MDA5 receptor truncation disrupts the immune response. Our findings accentuate the implication of rare monogenicIFIH1loss-of-function variants in altering the immune response, and severely predisposing patients to inflammatory and infectious diseases, including SARS-CoV-2 related disorders.
Genetic predisposition to altered blood cell homeostasis is associated with glioma risk and survival
Authors: Kachuri Linda , Guerra Geno A. , Wendt George A. , Hansen Helen M. , Molinaro Annette M. , Bracci Paige , McCoy Lucie , Rice Terri , Wiencke John K. , Eckel-Passow Jeanette E. , Jenkins Robert B. , Wrensch Margaret , Francis Stephen S.
Published: October 2023

Glioma is a highly fatal brain tumor comprised of molecular subtypes with distinct clinical trajectories. Observational studies have suggested that variability in immune response may play a role in glioma etiology. However, their findings have been inconsistent and susceptible to reverse causation due to treatment effects and the immunosuppressive nature of glioma. We applied genetic variants associated (p<5×10−8) with blood cell traits to a meta-analysis of 3418 glioma cases and 8156 controls. Genetically predicted increase in the platelet to lymphocyte ratio (PLR) was associated with an increased risk of glioma (odds ratio (OR)=1.25, p=0.005), especially in IDH-mutant (IDHmutOR=1.38, p=0.007) and IDHmut1p/19q non-codeleted (IDHmut-noncodelOR=1.53, p=0.004) tumors. However, reduced glioma risk was observed for higher counts of lymphocytes (IDHmut-noncodelOR=0.70, p=0.004) and neutrophils (IDHmutOR=0.69, p=0.019; IDHmut-noncodelOR=0.60, p=0.009), which may reflect genetic predisposition to enhanced immune-surveillance. In contrast to susceptibility, there was no association with survival in IDHmut-noncodel;however, in IDHmut1p/19q co-deleted tumors, we observed higher mortality with increasing genetically predicted counts of lymphocytes (hazard ratio (HR)=1.65, 95% CI: 1.24-2.20), neutrophils (HR=1.49, 1.13-1.97), and eosinophils (HR=1.59, 1.18-2.14). Polygenic scores for blood cell traits were also associated with tumor immune microenvironment features, with heterogeneity by IDH status observed for 17 signatures related to interferon signaling, PD-1 expression, and T-cell/Cytotoxic responses. In summary, we identified novel, immune-mediated susceptibility mechanisms for glioma with potential disease management implications.

SIGNIFICANCE

This study suggests that genetic determinants of peripheral blood cell counts influence subtype-specific glioma susceptibility and mortality, with potential effects on the tumor immune microenvironment. These findings may have disease management implications.
A splicing-based multi-tissue joint transcriptome-wide association study identifies susceptibility genes for breast cancer
Authors: Gao Guimin , McClellan Julian , Barbeira Alvaro N. , Fiorica Peter N. , Li James L. , Mu Zepeng , Olopade Olufunmilayo I. , Huo Dezheng , Im Hae Kyung
Published: October 2023

Splicing-based transcriptome-wide association studies (splicing-TWASs) of breast cancer have the potential to identify new susceptibility genes. However, existing splicing-TWASs test association of individual excised introns in breast tissue only and have thus limited power to detect susceptibility genes. In this study, we performed a multi-tissue joint splicing-TWAS that integrated splicing-TWAS signals of multiple excised introns in each gene across 11 tissues that are potentially relevant to breast cancer risk. We utilized summary statistics from a meta-analysis that combined genome-wide association study (GWAS) results of 424,650 European ancestry women. Splicing level prediction models were trained in GTEx (v8) data. We identified 240 genes by the multi-tissue joint splicing-TWAS at the Bonferroni corrected significance level; in the tissue-specific splicing-TWAS that combined TWAS signals of excised introns in genes in breast tissue only, we identified 9 additional significant genes. Of these 249 genes, 88 genes in 62 loci have not been reported by previous TWASs and 17 genes in 7 loci are at least 1 Mb away from published GWAS index variants. By comparing the results of our spicing-TWASs with previous gene expression-based TWASs that used the same summary statistics and expression prediction models trained in the same reference panel, we found that 110 genes in 70 loci identified by our splicing-TWASs were not reported in the expression-based TWASs. Our results showed that for many genes, expression quantitative trait loci (eQTL) did not show significant impact on breast cancer risk, while splicing quantitative trait loci (sQTL) showed strong impact through intron excision events.