bluuebunny/crossref_metadata_2025 huggingface dataset:
Surgical skill level classification model development using EEG and eye-gaze data and machine learning algorithms
Authors: Shafiei Somayeh B. , Shadpour Saeed , Mohler James L. , Sasangohar Farzan , Gutierrez Camille , Seilanian Toussi Mehdi , Shafqat Ambreen
Published: October 2023

The aim of this study was to develop machine learning classification models using electroencephalogram (EEG) and eye-gaze features to predict the level of surgical expertise in robot-assisted surgery (RAS). EEG and eye-gaze data were recorded from 11 participants who performed cystectomy, hysterectomy, and nephrectomy using the da Vinci robot. Skill level was evaluated by an expert RAS surgeon using the modified Global Evaluative Assessment of Robotic Skills (GEARS) tool, and data from three subtasks were extracted to classify skill levels using three classification models—multinomial logistic regression (MLR), random forest (RF), and gradient boosting (GB). The GB algorithm was used with a combination of EEG and eye-gaze data to classify skill levels, and differences between the models were tested using two-sample t tests. The GB model using EEG features showed the best performance for blunt dissection (83% accuracy), retraction (85% accuracy), and burn dissection (81% accuracy). The combination of EEG and eye-gaze features using the GB algorithm improved the accuracy of skill level classification to 88% for blunt dissection, 93% for retraction, and 86% for burn dissection. The implementation of objective skill classification models in clinical settings may enhance the RAS surgical training process by providing objective feedback about performance to surgeons and their teachers.
Analyzing Thalamocortical Tract-Tracing Experiments in a Common Reference Space
Authors: Timonidis Nestor , Rubio-Teves Mario , Alonso-Martínez Carmen , Bakker Rembrandt , García-Amado María , Tiesinga Paul , Clascá Francisco
Published: October 2023

Current mesoscale connectivity atlases provide limited information about the organization of thalamocortical projections in the mouse brain. Labeling the projections of spatially restricted neuron populations in thalamus can provide a functionally relevant level of connectomic analysis, but these need to be integrated within the same common reference space. Here, we present a pipeline for the segmentation, registration, integration and analysis of multiple tract-tracing experiments. The key difference with other workflows is that the data is transformed to fit the reference template. As a test-case, we investigated the axonal projections and intranuclear arrangement of seven neuronal populations of the ventral posteromedial nucleus of the thalamus (VPM), which we labeled with an anterograde tracer. Their soma positions corresponded, from dorsal to ventral, to cortical representations of the whiskers, nose and mouth. They strongly targeted layer 4, with the majority exclusively targeting one cortical area and the ones in ventrolateral VPM branching to multiple somatosensory areas. We found that our experiments were more topographically precise than similar experiments from the Allen Institute and projections to the primary somatosensory area were in agreement with single-neuron morphological reconstructions from publicly available databases. This pilot study sets the basis for a shared virtual connectivity atlas that could be enriched with additional data for studying the topographical organization of different thalamic nuclei. The pipeline is accessible with only minimal programming skills via a Jupyter Notebook, and offers multiple visualization tools such as cortical flatmaps, subcortical plots and 3D renderings and can be used with custom anatomical delineations.
A Critical Assessment of Diagnostic Criteria for the Tall Cell Subtype of Papillary Thyroid Carcinoma—How Much? How Tall? And When Is It Relevant?
Authors: Turchini John , Fuchs Talia L. , Chou Angela , Sioson Loretta , Clarkson Adele , Sheen Amy , Delbridge Leigh , Glover Anthony , Sywak Mark , Sidhu Stan , Gill Anthony J.
Published: October 2023

Tall cell papillary thyroid carcinoma (TC-PTC) is considered adverse histology. However, previous studies are confounded by inconsistent criteria and strong associations with other adverse features. It is therefore still unclear if TC-PTC represents an independent prognostic factor in multivariate analysis and, if it does, what criteria should be employed for the diagnosis. We retrospectively reviewed 487 PTCs from our institution (where we have historically avoided the prospective diagnosis of TC-PTC) for both the height of tall cells (that is if the cells were two, or three, times as tall as wide) and the percentage of tall cells. On univariate analysis, there was significantly better disease free survival (DFS) in PTCs with no significant tall cell component (< 30%) compared to PTCs with cells two times tall as wide (p = 0.005). The proportion of tall cells (30–50% and > 50%) was significantly associated with DFS (p = 0.012). In a multivariate model including age, size, vascular space invasion, and lymph node metastasis, the current WHO tall cell criteria, met by 7.8% of PTCs, lacked statistical significance for DFS (p = 0.519). However, in the subset of tumours otherwise similar to the American Thyroid Association (ATA) guidelines low-risk category, WHO TC-PTC demonstrated a highly significant reduction in DFS (p = 0.004). In contrast, in intermediate to high-risk tumours, TC-PTC by WHO criteria lacked statistical significance (p = 0.384). We conclude that it may be simplistic to think of tall cell features as being present or absent, as both the height of the cells (two times versus three times) and the percentage of cells that are tall have different clinical significances in different contexts. Most importantly, the primary clinical significance of TC-PTC is restricted to PTCs that are otherwise low risk by ATA guidelines.
An interdisciplinary journey towards an aesthetics of sonification experience
Authors: Seiça Mariana , Roque Licínio , Martins Pedro , Cardoso F. Amílcar
Published: October 2023

The aesthetic dimension has been proposed as a potential expansion of sonification design, creating listening pieces that reach the goal of effective data communication. However, current views of aesthetics still aim at optimising mapping criteria to convey the ‘right meaning’, maintaining a mostly functional view on what is considered a successful sonification. This paper proposes an interdisciplinary approach to the aesthetics of sonification experience, grounded on theoretical foundations from phenomenology of interaction, post-phenomenology, cross-cultural studies, acoustic ecology and deep listening. From this journey, we present the following design insights: (1) the designofsonifications becomes a designforexperience, (2) co-designed during the interaction with each participant; (3) the sonification artefact gains a mediating role that guides the participant’s intentions in the sonification space; (4) the aesthetics of a sonification experience generates a multistable phenomenon, offering new opportunities to experience multiple perspectives over data; (5) the interaction between human participants and the sonic emanations compose a dialogic space. A call for action to reframe the sonification field into novel design spaces is now open, with aesthetics gaining a transformational role in sonification design and interaction.
Real-Time Defect Monitoring of Laser Micro-drilling Using Reflective Light and Machine Learning Models
Authors: Lee Yong Kwan , Lee Sumin , Kim Sung Hwan
Published: October 2023

Laser micro-drilling is a significant manufacturing method used to drill precise microscopic holes into metals. Quality inspection of micro-holes is costly and redrilling defective holes can lead to imperfection owing to the misalignment in re-aligning the removed specimens. Thus this paper proposes an in-situ, automatic inspection method using photodiode data and machine learning models to detect defects in real-time during the fabrication of SK5 steel plates with 1064 nm Nd:YAG Laser machines to reduce the workload and increase the quality of products. Further, it explores the possibility of generalizing the models to 51 different scenarios of fabrication by classifying unseen data into 51 classes. A dataset of around 1,500,000 time series data points was generated using an optical probe while drilling over 56,000 holes into test specimens. 15 different combinations of thickness and diameter were drilled using suggested parameters. An additional 12 potential defect-prone conditions were designed to obtain data during conditional drilling. Hole quality was measured for each hole using OGP 3D profile microscope measuring machine. Results showed high accuracy in specialized defect detection within each scenario and showed a possibility of classifying photodiode data patterns, offering opportunities to improve the practicality of the proposed solution.
Basque Adaptation of the Reduced Kentucky Inventory of Mindfulness Skills (KIMS-R)
Authors: Olarza Amaiur , Soroa Goretti , Aritzeta Aitor , Mindeguia Rosa
Published: October 2023

Objectives

Mindfulness consists of paying attention to the present moment with curiosity, acceptance and non-judgment. Although several instruments exist for evaluating mindfulness in adults, few have been adapted for children, and even fewer have been adapted to the Basque language. The aim of the present study is to adapt the Reduced Kentucky Inventory of Mindfulness Skills (KIMS-R) questionnaire for use with Basque-speaking children.

Method

A total of 479 children from the last 2 years of primary education (Years 5 and 6), aged between 9 and 12 years, participated in this study. The sample was divided into two subgroups: exploratory subsample (n = 237) and confirmatory subsample (n = 242). In addition to the KIMS-R, we also administered other questionnaires to measure mindfulness, perceived stress, emotional skills, neuroticism and depression.

Results

The analysis showed that the adapted questionnaire was reliable, with scores measuring consistency and stability in acceptable ranges. The analysis revealed a 5-factor structure (Internal observation, External observation, Description, Acting with awareness and Acceptance without judgment). These dimensions showed acceptable internal consistency (α between 0.69 and 0.83; ω between 0.69 and 0.83) and temporal stability (r = 0.54, 0.64, 0.79, 0.40, 0.59). The instrument was also found to have adequate external validity, with associations being observed between mindfulness and emotional abilities, perceived stress, neuroticism and depression.

Conclusions

The Basque version of the KIMS-R will enable scholars to assess the ability of children in the Basque Autonomous Community to be mindful. It will also be useful for evaluating the effectiveness of interventions designed to promote mindfulness skills. This adaptation of the KIMS-R instrument can be considered a step forward in the field of mindfulness research.

Preregistration

This study is not preregistered.
“There should be one spot that you can go:” BRCA mutation carriers’ perspectives on cancer risk management and a hereditary cancer registry
Authors: Hynes J. , Dawson L. , Seal M. , Green J. , Woods M. , Etchegary H.
Published: October 2023

Individuals who carry BRCA1 or BRCA2 pathogenic variants are recommended to have extensive cancer prevention screening and risk-reducing surgeries. Uptake of these recommendations is variable, and there remains room for improvement in the risk management of BRCA carriers. This paper explores female BRCA carriers’ experiences with the current model of care and their perspectives on (and interest in) an inherited cancer registry. Findings can inform the development of a dedicated high-risk screening and management program for these patients. Quantitative and qualitative data were gathered through a provincial descriptive survey and semi-structured qualitative interviews to assess BRCA carriers’ opinions toward risk management services in the province of Newfoundland and Labrador (NL), Canada. Survey (n = 69) and interview data (n = 15) revealed continuity and coordination challenges with the current system of care of high-risk individuals. Respondents suggested an inherited cancer registry would help identify high-risk individuals and provide a centralized system of risk management for identified carriers. Respondents identified concerns about the privacy of their registry data, including who could access it. Findings suggest BRCA carriers see great value in an inherited cancer registry. Specifically, participants noted it could provide a centralized system to help improve the coordination of burdensome, life-long risk management. Important patient concerns about protecting their privacy and their health data confidentiality must be addressed in patient and public information and informed consent documents about a registry.
English RE: under pressure?
Authors: Smalley Paul
Published: October 2023

This paper will examine four potential areas of pressure to RE in England in the 2020s: Academisation—and the structural issues arising from ever greater numbers of schools being outside local authority control; the alleged secularisation of the curriculum through the Worldviews Paradigm; the financial situation of Standard Advisory Councils on Religious Education in England; and the teacher recruitment crisis. Taking a historical turn, it will then consider whether these are uniquely challenging to the subject, or whether the RE community might gain solace from a realisation that these challenges have been overcome at other points in history.
Partizipation und Paratext
Authors: Werber Niels , Stein Daniel
Published: October 2023

Lang laufende, populäre Serienerzählungen wie Perry Rhodan (seit 1961) stellen für die Rezeptionsforschung eine besondere Herausforderung dar, weil die vielen über Jahre und Jahrzehnte hinweg in Form von Leserbriefen, Fanzines und Foren publizierten Kommentare genauso wenig zu überblicken sind wie die Abertausenden von Seiten umfassende Heftromanserie; sie bieten aber auch eine einzigartige Chance, da Leser:innen solcher Serien Fans sind, die dazu neigen, ihren eigenen Rezeptionsprozess ausgiebig zu kommentieren. Der quantitativen Herausforderung der populären Serie begegnen wir mit einer Fokussierung auf diejenigen Themen, die auch bei den Fans am meisten Beachtung gefunden haben. Unter dieser Vorgabe untersuchen wir den Paratext der Serie als privilegierten Raum der Leserkommunikation über und der seriellen Auseinandersetzung mit populären Erzählungen. In den Peritexten der »Leserkontaktseite« und den Epitexten des digitalen Fan-Forum lassen sich besonders populäre Aushandlungen zwischen Leser:innen, Autor:innen und Redakteur:innen beobachten und auf die Weiterentwicklung der Serie beziehen. Wie die Serie gelesen und wie sie weitergeschrieben wird, ist eine Frage der paratextuellen Aushandlungen und der Popularität dieser Aushandlungen.
Knowledge of Problem Solving (KOPS) Scale: Design and Evaluation of a Digitally Administered Competence Measure for a Common Practice Element in Task-Shared Youth Mental Health Interventions
Authors: Mathur Sonal , Michelson Daniel , Shetty Tejaswi , Patel Vikram , Field Andy P.
Published: October 2023

There are few reliable and feasible quality assurance methods to support scaling up of psychological interventions delivered by non-specialist providers. This paper reports on the phased development and validation of a digitally administered Knowledge of Problem Solving (KOPS) measure to assess competencies associated with a “task-shared” problem-solving intervention for adolescents with diverse mental health problems in India. Phase 1 established key competencies required to deliver the intervention, followed by item generation for a corresponding knowledge-based competency measure that could be administered efficiently through e-learning systems. In phase 2, items were refined based on responses from an “experienced” reference sample comprising 17 existing counsellors with direct experience of the problem-solving intervention, and a “novice” sample with 14 untrained university students and NGO staff. In phase 3, we evaluated two parallel versions of the measure in a validation sample (N = 277) drawn from universities and NGOs. The resulting 17-item measure was structured around a hypothetical case, followed by multiple-choice questions that asked about the most appropriate response to a practice-based scenario. The difficulty level of the test items was well matched to the ability level of participants (i.e. most items being of moderate difficulty and few items being easy or difficult). Only one item showed a negative discrimination index and was removed from the 17-item forms. The final 16-item version of the KOPS measure provides a scalable digital method to assess key psychotherapeutic competencies among non-specialists, particularly in relation to a transdiagnostic problem-solving intervention. Similar formats could be deployed more widely alongside e-learning programmes to expand the global workforce capable of delivering evidence-based psychological interventions.
In Vitro Cytotoxic Potential of Ethanol Extract of Dictyopteris acrostichoides Against Human Cancer Cells
Authors: Attia Eman Zekry , Abdel-Rahman Iman A. M. , Aly Omar M. , Saber Hani , Rushdi Mohammed I. , Abdelmohsen Usama Ramadan
Published: October 2023

Ethanol extracts of Caulerpa racemose (Forsskål) J.Agardh, 1873, Dictyopteris acrostichoides (J.Agardh) Bornet, 1885, Halimeda opuntia (Linnaeus) J.V.Lamouroux, 1816, and Polycladia myrica (S.G.Gmelin) Draima, Ballesteros, F.Rousseau & T.Thibaut, 2010, were tested for their cytotoxicity against human hepatoma, human breast adenocarcinoma, and human colon adenocarcinoma cell lines. Dictyopteris acrostichoides displayed cytotoxicity against human hepatoma, human breast adenocarcinoma, and human colon adenocarcinoma with IC50 values of 11.65, 9.28, and 16.86 µg/ml, respectively, in comparison to doxorubicin as a positive control (IC50 5.72, 5.17, and 5.81 µg/ml, respectively). Metabolic profiling of the D. acrostichoides extract characterized seventeen metabolites. In silico analysis indicated 1-(3-oxo-undecyldisulfanyl)-undecan-3-one was the most active epidermal growth factor receptor inhibitor, while 1-(3-oxo-undecyldisulfanyl)-undecan-3-one and di(3-acetoxy-5-undecenyl) disulfide were the most active vascular endothelial growth factor inhibitors. Furthermore, the ethanol extract of D. acrostichoides was tested against epidermal growth factor receptor kinase (IC50 0.11 µg/ml) compared to lapatinib as a positive control (IC50 0.03 µg/ml), and against vascular endothelial growth factor (IC50 0.276 µg/ml) compared to sorafenib as a positive control (IC50 0.049 µg/ml).

Graphical Abstract
Thinking out of the box: revisiting health surveillance based on medical records
Authors: Sampaio Vanderson S. , Lopes Rafael , Ozahata Mina Cintho , Nakaya Helder I. , Sousa Erick , Araújo José D. , Bragatte Marcelo A.S. , Brito Anderson F. , Grespan Regina Maura Zettoni , Capuani Maria Ligia Damato , Domingues Helves Humberto , Pellini Alessandra Cristina Guedes , Mateos Sheila de Oliveira Garcia , Conde Mônica Tilli Reis Pessoa , Eudes Leal Fabio , Sabino Ester , Simão Mariangela , Kalil Jorge
Published: October 2023

Despite the considerable advances in the last years, the health information systems for health surveillance still need to overcome some critical issues so that epidemic detection can be performed in real time. For instance, despite the efforts of the Brazilian Ministry of Health (MoH) to make COVID-19 data available during the pandemic, delays due to data entry and data availability posed an additional threat to disease monitoring. Here, we propose a complementary approach by using electronic medical records (EMRs) data collected in real time to generate a system to enable insights from the local health surveillance system personnel. As a proof of concept, we assessed data from São Caetano do Sul City (SCS), São Paulo, Brazil. We used the “fever” term as a sentinel event. Regular expression techniques were applied to detect febrile diseases. Other specific terms such as “malaria,” “dengue,” “Zika,” or any infectious disease were included in the dictionary and mapped to “fever.” Additionally, after “tokenizing,” we assessed the frequencies of most mentioned terms when fever was also mentioned in the patient complaint. The findings allowed us to detect the overlapping outbreaks of both COVID-19 Omicron BA.1 subvariant and Influenza A virus, which were confirmed by our team by analyzing data from private laboratories and another COVID-19 public monitoring system. Timely information generated from EMRs will be a very important tool to the decision-making process as well as research in epidemiology. Quality and security on the data produced is of paramount importance to allow the use by health surveillance systems.
Using a human-factors engineering approach to evaluate environmental cleaning in Veterans’ Affairs acute and long-term care facilities: A qualitative analysis
Authors: McKinley Linda L. , Goedken Cassie C. , Balkenende Erin C. , Hockett Sherlock Stacey M. , Knobloch Mary Jo , Bartel Rosie , Perencevich Eli N. , Reisinger Heather S. , Safdar Nasia
Published: October 2023

Background:

Environmental cleaning is important in the interruption of pathogen transmission. Although prevention initiatives have targeted environmental cleaning, practice variations exist and compliance is low. Evaluation of human factors influencing variations in cleaning practices can be valuable in developing interventions to standardized practices. We conducted a work-system analysis using a human-factors engineering (HFE) framework to identify barriers and facilitators to environmental cleaning practices in acute and long-term care settings within the Veterans’ Affairs health system.

Methods:

We conducted a qualitative study with key stakeholders at 3 VA facilities. We analyzed transcripts for thematic content and mapped themes to the HFE framework.

Results:

Staffing consistency was felt to improve cleaning practices and teamwork. We found that many environmental management service (EMS) staff were veterans who were motivated to serve fellow veterans, especially to prevent infections. However, hiring veterans comes with regulatory hurdles that affect staffing. Sites reported some form of monitoring their cleaning process, but there was variation in method and frequency. The EMS workload was affected by whether rooms were occupied by patients or were semiprivate rooms; both were reportedly more difficult to clean. Room design and surface finishes were identified as important to cleaning efficiency.

Conclusion:

HFE work analysis identified barriers and facilitators to environmental cleaning. These findings highlight intervention entry points that may facilitate standardized work practices. There is a need to develop task-specific procedures such as cleaning occupied beds and semiprivate rooms. Future research should evaluate interventions that address these determinants of environmental cleaning.
Estimating Three‐Dimensional Structures of Eddy in the South Indian Ocean From the Satellite Observations Based on the isQG Method
Authors: Chen Zhiqiang , Wang Xidong , Liu Lei , Wang Xiaoting
Published: October 2023

By incorporating the high‐resolution satellite remote sensing sea surface temperature (SST) with low‐resolution sea level anomaly and sea surface salinity (SSS), this study explores the reconstructability of the three‐dimensional (3D) eddy structures via the “interior + surface quasigeostrophic” (isQG) method in the South Indian Ocean. We apply the incorporation of high‐resolution SST to improve the spatial resolution of the reconstruction. We also propose a correction scheme for density reconstruction within the mixed layer to offset the absence of mixed layer dynamics in the SQG framework. Comparison against the in situ observations demonstrates a satisfactory reconstructability for subsurface velocity and density anomalies. Statistically, the zonal velocity reconstructability outperforms its meridional counterpart and the corresponding velocity phase. The reconstructed shallow‐layer velocity exhibits a superior skill in eddy‐active regions, when compared with drogued drifter observations. Reconstructed subsurface velocities reproduce the spatial structures of eddy‐induced velocity anomaly along the GO‐SHIP observation transect, although present smaller magnitudes. Results demonstrate the potential applicability of the isQG method for reconstructing mesoscale eddies, particularly in the ocean at mid‐to‐high latitudes, where subsurface dynamics are strongly influenced by barotropic and the first baroclinic modes. With the upcoming high‐advanced satellite observations, the isQG framework is expected to achieve better subsurface estimations.
Prediction of Extraordinarily High Floods Emerging From Heterogeneous Flow Generation Processes
Authors: Mushtaq Sumra , Miniussi Arianna , Merz Ralf , Tarasova Larisa , Marra Francesco , Basso Stefano
Published: October 2023

River floods are generated by various processes that, if disregarded, may induce errors in flood hazard assessment. This is particularly relevant where events extraordinarily larger than the typical floods have been observed, that is, for rivers with a flood divide in their flood‐frequency curves. We identify 11 such cases in a large set of German catchments and test a statistical approach that accounts for different runoff‐generation processes to predict the magnitude and frequency of extraordinarily high floods. We observe that in catchments with a flood divide, ordinary peaks are generated by different runoff‐generation processes and the distribution of at least one process is heavy‐tailed. By accounting for the different tail behaviors of multiple processes, we can reproduce flood‐frequency curves in these catchments. Our findings shed light on the origin of flood divides and set a method to improve the estimation of high flood quantiles in these high‐risk cases.
Room-temperature continuous-wave topological Dirac-vortex microcavity lasers on silicon
Authors: Ma Jingwen , Zhou Taojie , Tang Mingchu , Li Haochuan , Zhang Zhan , Xi Xiang , Martin Mickael , Baron Thierry , Liu Huiyun , Zhang Zhaoyu , Chen Siming , Sun Xiankai
Published: October 2023

Robust laser sources are a fundamental building block for contemporary information technologies. Originating from condensed-matter physics, the concept of topology has recently entered the realm of optics, offering fundamentally new design principles for lasers with enhanced robustness. In analogy to the well-known Majorana fermions in topological superconductors, Dirac-vortex states have recently been investigated in passive photonic systems and are now considered as a promising candidate for robust lasers. Here, we experimentally realize the topological Dirac-vortex microcavity lasers in InAs/InGaAs quantum-dot materials monolithically grown on a silicon substrate. We observe room-temperature continuous-wave linearly polarized vertical laser emission at a telecom wavelength. We confirm that the wavelength of the Dirac-vortex laser is topologically robust against variations in the cavity size, and its free spectral range defies the universal inverse scaling law with the cavity size. These lasers will play an important role in CMOS-compatible photonic and optoelectronic systems on a chip.
The social cognitive and neural mechanisms that underlie social functioning in individuals with schizophrenia – a review
Authors: Lemmers-Jansen Imke , Velthorst Eva , Fett Anne-Kathrin
Published: October 2023

In many individuals with a diagnosis of schizophrenia social functioning is impaired across the lifespan. Social cognition has emerged as one of the possible factors that may contribute to these challenges. Neuroimaging research can give further insights into the underlying mechanisms of social (cognitive) difficulties. This review summarises the evidence on the associations between social cognition in the domains of theory of mind and emotion perception and processing, and individuals’ social functioning and social skills, as well as associated neural mechanisms. Eighteen behavioural studies were conducted since the last major review and meta-analysis in the field (inclusion between 7/2017 and 1/2022). No major review has investigated the link between the neural mechanisms of social cognition and their association with social functioning in schizophrenia. Fourteen relevant studies were included (from 1/2000 to 1/2022). The findings of the behavioural studies showed that associations with social outcomes were slightly stronger for theory of mind than for emotion perception and processing. Moreover, performance in both social cognitive domains was more strongly associated with performance on social skill measures than questionnaire-based assessment of social functioning in the community. Studies on the underlying neural substrate of these associations presented mixed findings. In general, higher activation in various regions of the social brain was associated with better social functioning. The available evidence suggests some shared regions that might underlie the social cognition-social outcome link between different domains. However, due to the heterogeneity in approaches and findings, the current knowledge base will need to be expanded before firm conclusions can be drawn.
Long non-coding RNA NRSN2-AS1 promotes ovarian cancer progression through targeting PTK2/β-catenin pathway
Authors: Wu Yi-Bo , Li Shen-Yi , Liu Jin-Yan , Xue Jia-Jia , Xu Jin-Fu , Chen Ting , Cao Tian-Yue , Zhou Hui , Wu Tian-Tian , Dong Chun-Lin , Qian Wei-Feng , Qiao Long-Wei , Hou Shun-Yu , Wang Ting , Shen Cong
Published: October 2023

As a common malignant tumor among women, ovarian cancer poses a serious threat to their health. This study demonstrates that long non-coding RNA NRSN2-AS1 is over-expressed in ovarian cancer tissues using patient sample and tissue microarrays. In addition, NRSN2-AS1 is shown to promote ovarian cancer cell proliferation and metastasis both in vitro and in vivo. Mechanistically, NRSN2-AS1 stabilizes protein tyrosine kinase 2 (PTK2) to activate the β-catenin pathway via repressing MG-53-mediated ubiquitinated degradation of PTK2, thereby facilitating ovarian cancer progression. Rescue experiments verify the function of the NRSN2-AS1/PTK2/β-catenin axis and the effects of MG53 on this axis in ovarian cancer cells. In conclusion, this study demonstrates the key role of the NRSN2-AS1/PTK2/β-catenin axis for the first time and explores its potential clinical applications in ovarian cancer.
Exogenous H2S initiating Nrf2/GPx4/GSH pathway through promoting Syvn1-Keap1 interaction in diabetic hearts
Authors: Wang Mengyi , Tang Jingyuan , Zhang Shiwu , Pang Kemiao , Zhao Yajun , Liu Ning , Huang Jiayi , Kang Jiaxin , Dong Shiyun , Li Hongxia , Tian Zhen , Duan Binhong , Lu Fanghao , Zhang Weihua
Published: October 2023

Excessive ROS accumulation contributes to cardiac injury in type 2 diabetes mellitus. Hydrogen sulfide (H2S) is a vital endogenous gasotransmitter to alleviate cardiac damage in diabetic cardiomyopathy (DCM). However, the underlying mechanisms remain unclear. In this study, we investigated the effects of NaHS administration in db/db mice via intraperitoneal injection for 20 weeks and the treatment of high glucose (HG), palmitate (PA) and NaHS in HL-1 cardiomyocytes for 48 h, respectively. H2S levels were decreased in hearts of db/db mice and HL-1 cardiomyocytes exposed to HG and PA, which were restored by NaHS. Exogenous H2S activated the nuclear factor erythroid 2-related factor 2 (Nrf2)/glutathione peroxidase 4 (GPx4)/glutathione (GSH) pathway, suppressed ferroptosis and mitigated mitochondrial apoptosis in db/db mice. However, these effects were abrogated after Nrf2 knockdown. NaHS treatment elevated the ubiquitination level of Kelch-like ECH-associated protein (Keap1) by preserving its E3 ligase synoviolin (Syvn1), resulting in Nrf2 nuclear translocation. H2S facilitated the sulfhydration of Syvn1-cys115 site, a post-translational modification. Transfecting Syvn1 C115A in cardiomyocytes exposed to HG and PA partially attenuated the effects of NaHS on Nrf2 and cell death. Our findings suggest that exogenous H2S regulates Nrf2/GPx4/GSH pathway by promoting the Syvn1-Keap1 interaction to reduce ferroptosis and mitochondrial apoptosis in DCM.
Ectopic expression of human TUBB8 leads to increased aneuploidy in mouse oocytes
Authors: Dong Jie , Jin Liping , Bao Shihua , Chen Biaobang , Zeng Yang , Luo Yuxi , Du Xingzhu , Sang Qing , Wu Tianyu , Wang Lei
Published: October 2023

Aneuploidy seriously compromises female fertility and increases incidence of birth defects. Rates of aneuploidy in human eggs from even young women are significantly higher than those in other mammals. However, intrinsic genetic factors underlying this high incidence of aneuploidy in human eggs remain largely unknown. Here, we found that ectopic expression of humanTUBB8in mouse oocytes increases rates of aneuploidy by causing kinetochore–microtubule (K–MT) attachment defects. Stretched bivalents in mouse oocytes expressingTUBB8are under less tension, resulting in continuous phosphorylation status of HEC1 by AURKB/C at late metaphase I that impairs the established correct K–MT attachments. This reduced tension in stretched bivalents likely correlates with decreased recruitment of KIF11 on meiotic spindles. We also found that ectopic expression ofTUBB8without its C-terminal tail decreases aneuploidy rates by reducing erroneous K–MT attachments. Importantly, variants in the C-terminal tail ofTUBB8were identified in patients with recurrent miscarriages. Ectopic expression of an identifiedTUBB8variant in mouse oocytes also compromises K–MT attachments and increases aneuploidy rates. In conclusion, our study provides novel understanding for physiological mechanisms of aneuploidy in human eggs as well as for pathophysiological mechanisms involved in recurrent miscarriages.
Integrated radiogenomics models predict response to neoadjuvant chemotherapy in high grade serous ovarian cancer
Authors: Crispin-Ortuzar Mireia , Woitek Ramona , Reinius Marika A. V. , Moore Elizabeth , Beer Lucian , Bura Vlad , Rundo Leonardo , McCague Cathal , Ursprung Stephan , Escudero Sanchez Lorena , Martin-Gonzalez Paula , Mouliere Florent , Chandrananda Dineika , Morris James , Goranova Teodora , Piskorz Anna M. , Singh Naveena , Sahdev Anju , Pintican Roxana , Zerunian Marta , Rosenfeld Nitzan , Addley Helen , Jimenez-Linan Mercedes , Markowetz Florian , Sala Evis , Brenton James D.
Published: October 2023

High grade serous ovarian carcinoma (HGSOC) is a highly heterogeneous disease that typically presents at an advanced, metastatic state. The multi-scale complexity of HGSOC is a major obstacle to predicting response to neoadjuvant chemotherapy (NACT) and understanding critical determinants of response. Here we present a framework to predict the response of HGSOC patients to NACT integrating baseline clinical, blood-based, and radiomic biomarkers extracted from all primary and metastatic lesions. We use an ensemble machine learning model trained to predict the change in total disease volume using data obtained at diagnosis (n = 72). The model is validated in an internal hold-out cohort (n = 20) and an independent external patient cohort (n = 42). In the external cohort the integrated radiomics model reduces the prediction error by 8% with respect to the clinical model, achieving an AUC of 0.78 for RECIST 1.1 classification compared to 0.47 for the clinical model. Our results emphasize the value of including radiomics data in integrative models of treatment response and provide methods for developing new biomarker-based clinical trials of NACT in HGSOC.
Recognition and coacervation of G-quadruplexes by a multifunctional disordered region in RECQ4 helicase
Authors: Papageorgiou Anna C. , Pospisilova Michaela , Cibulka Jakub , Ashraf Raghib , Waudby Christopher A. , Kadeřávek Pavel , Maroz Volha , Kubicek Karel , Prokop Zbynek , Krejci Lumir , Tripsianes Konstantinos
Published: October 2023

Biomolecular polyelectrolyte complexes can be formed between oppositely charged intrinsically disordered regions (IDRs) of proteins or between IDRs and nucleic acids. Highly charged IDRs are abundant in the nucleus, yet few have been functionally characterized. Here, we show that a positively charged IDR within the human ATP-dependent DNA helicase Q4 (RECQ4) forms coacervates with G-quadruplexes (G4s). We describe a three-step model of charge-driven coacervation by integrating equilibrium and kinetic binding data in a global numerical model. The oppositely charged IDR and G4 molecules form a complex in the solution that follows a rapid nucleation-growth mechanism leading to a dynamic equilibrium between dilute and condensed phases. We also discover a physical interaction with Replication Protein A (RPA) and demonstrate that the IDR can switch between the two extremes of the structural continuum of complexes. The structural, kinetic, and thermodynamic profile of its interactions revealed a dynamic disordered complex with nucleic acids and a static ordered complex with RPA protein. The two mutually exclusive binding modes suggest a regulatory role for the IDR in RECQ4 function by enabling molecular handoffs. Our study extends the functional repertoire of IDRs and demonstrates a role of polyelectrolyte complexes involved in G4 binding.
Cu-catalyzed asymmetric regiodivergent electrosynthesis and its application in the enantioselective total synthesis of (-)-fumimycin
Authors: Xie Tian , Huang Jianming , Li Juan , Peng Lingzi , Song Jin , Guo Chang
Published: October 2023

Quaternary amino acids are one of the essential building blocks and precursors of medicinally important compounds. Various synthetic strategies towards their synthesis have been reported. On the other hand, developing core-structure-oriented cross-dehydrogenative coupling (CDC) reactions, is a largely unsolved problem. Herein, we describe a copper-catalyzed regiodivergent electrochemical CDC reaction of Schiff bases and commercially available hydroquinones to obtain three classes of chiral quaternary amino acid derivatives for the efficient assembly of complex scaffolds with excellent stereocontrol. The electrochemical anodic oxidation process with slow releasing of quinones serves as an internal syringe pump and provides high levels of reaction efficiency and enantiomeric control. The utility of this strategy is highlighted through the synthetic utility in the asymmetric total synthesis of (-)-fumimycin.
PAPγ associates with PAXT nuclear exosome to control the abundance of PROMPT ncRNAs
Authors: Contreras Xavier , Depierre David , Akkawi Charbel , Srbic Marina , Helsmoortel Marion , Nogaret Maguelone , LeHars Matthieu , Salifou Kader , Heurteau Alexandre , Cuvier Olivier , Kiernan Rosemary
Published: October 2023

Pervasive transcription of the human genome generates an abundance of RNAs that must be processed and degraded. The nuclear RNA exosome is the main RNA degradation machinery in the nucleus. However, nuclear exosome must be recruited to its substrates by targeting complexes, such as NEXT or PAXT. By proteomic analysis, we identify additional subunits of PAXT, including many orthologs of MTREC found in S. pombe. In particular, we show that polyA polymerase gamma (PAPγ) associates with PAXT. Genome-wide mapping of the binding sites of ZFC3H1, RBM27 and PAPγ shows that PAXT is recruited to the TSS of hundreds of genes. Loss of ZFC3H1 abolishes recruitment of PAXT subunits including PAPγ to TSSs and concomitantly increases the abundance of PROMPTs at the same sites. Moreover, PAPγ, as well as MTR4 and ZFC3H1, is implicated in the polyadenylation of PROMPTs. Our results thus provide key insights into the direct targeting of PROMPT ncRNAs by PAXT at their genomic sites.
New diffusive interface model for pitting corrosion
Authors: Li Bohan , Xing Hui , Jing Hanxu
Published: October 2023

In this paper, a diffusive interface model for pitting corrosion is proposed, which can be used to simulate diffusion- and activation-controlled pitting corrosion with the pit morphologies and the distribution of metal cation concentration. The diffusive interface equation is derived from the general interface advection-like equation coupled with the description of the normal velocity of the moving pitting boundary from the sharp interface model. The corrosion rate is expressed in an explicit way through the diffusion field in the diffusion-controlled regime, and the activation-controlled corrosion is expressed by introducing the interface kinetic parameter, which greatly simplifies the model. The curvature effect can be subtracted back out directly by introducing a counter term. Predicted results from numerical simulations are compared with the analytical solution to determine numerical parameter in one-dimensional pencil electrode test. The effect of local curvature on simulated semicircle corrosion is discussed. Then, the application scenarios of the model including electropolishing, single and multiple corrosion, corrosion with composite materials are presented.
All-photonic one-way quantum repeaters with measurement-based error correction
Authors: Niu Daoheng , Zhang Yuxuan , Shabani Alireza , Shapourian Hassan
Published: October 2023

Quantum repeater is the key technology enabler for long-distance quantum communication. To date, most of the existing quantum repeater protocols are designed based on specific quantum codes or graph states. In this paper, we propose a general framework for all-photonic one-way quantum repeaters based on the measurement-based error correction, which can be adapted to any Calderbank–Shor–Steane code including the recently discovered quantum low-density parity check (QLDPC) codes. We present a decoding scheme, where the error correction process is carried out at the destination based on the accumulated data from the measurements made across the network. This procedure not only outperforms the conventional protocols with independent repeaters but also simplifies the local quantum operations at repeaters. As an example, we numerically show that the [[48, 6, 8]] generalized bicycle code (as a small but efficient QLDPC code) has an equally good performance while reducing the resources by at least an order of magnitude.
Non-pharmaceutical interventions to combat COVID-19 in the Americas described through daily sub-national data
Authors: Touchton Michael , Knaul Felicia Marie , Arreola-Ornelas Héctor , Porteny Thalia , Carniado Óscar Méndez , Faganello Marco , Hummel Calla , Otero Silvia , Insua Jorge , Patino Fausto , Undurraga Eduardo , Pérez-Cruz Pedro , Sanchez-Talanquer Mariano , Velasco Guachalla V. Ximena , Nelson-Nuñez Jami , Boulding Carew , Calderon-Anyosa Renzo , Garcia Patricia J , Vargas Enciso Valentina
Published: October 2023

This dataset covers national and subnational non-pharmaceutical interventions (NPI) to combat the COVID-19 pandemic in the Americas. Prior to the development of a vaccine, NPI were governments’ primary tools to mitigate the spread of COVID-19. Variation in subnational responses to COVID-19 is high and is salient for health outcomes. This dataset captures governments’ dynamic, varied NPI to combat COVID-19 for 80% of Latin America’s population from each country’s first case through December 2021. These daily data encompass all national and subnational units in Argentina, Bolivia, Brazil, Chile, Colombia, Ecuador, Mexico, and Peru. The dataset includes individual and aggregate indices of nine NPI: school closures, work suspensions, public event cancellations, public transport suspensions, information campaigns, local travel restrictions, international travel controls, stay-at-home orders, and restrictions on the size of gatherings. We also collected data on mask mandates as a separate indicator. Local country-teams drew from multiple data sources, resulting in high-quality, reliable data. The dataset thus allows for consistent, meaningful comparisons of NPI within and across countries during the pandemic.
Macroeconomic dynamics in a finite world based on thermodynamic potential
Authors: Herbert Éric , Giraud Gaël , Louis-Napoléon Aurélie , Goupil Christophe
Published: October 2023

This paper presents a conceptual model describing the medium and long term co-evolution of natural and socio-economic subsystems of Earth. An economy is viewed as an out-of-equilibrium dissipative structure that can only be maintained with a flow of energy and matter. The distinctive approach emphasized here consists in capturing the economic impact of natural ecosystems’ depletion by human activities via a pinch of thermodynamic potentials. This viewpoint allows: (i) the full-blown integration of a limited quantity of primary resources into a non-linear macrodynamics that is stock-flow consistent both in terms of matter-energy and economic transactions; (ii) the inclusion of natural and forced recycling; (iii) the inclusion of a friction term which reflects the impossibility to produce (and recycle)goods and services without exuding energy and matter wastes, and (iv) the computation of the anthropically produced entropy as a function of metabolizing intensity and frictions. Analysis and numerical computations confirm the role played by intensity and frictions as key factors for sustainability by contrast with real gdp growth—as well as the interplay between resource scarcity, income inequality, and inflation. A more egalitarian society with moderate inflation turns out to be more sustainable than an unequal society with low inflation. Our approach is flexible enough to allow for various economic models to be embedded into our thermodynamic framework. Finally, we propose the open source EcoDyco software as a first complete realization implementing economic dynamics in a multi-resource environment.
Landscape genetics identified conservation priority areas for blue sheep (Pseudois nayaur) in the Indian Trans-Himalayan Region
Authors: Dolker Stanzin , Jabin Gul , Singh Sujeet Kumar , Joshi Bheem Dutt , Singh Vinaya Kumar , Dalui Supriyo , Chandra Kailash , Sharma Lalit Kumar , Thakur Mukesh
Published: October 2023

The trans-Himalayan region of India, although have xeric features, still supports a unique assemblage of biodiversity, including some of the charismatic and endemic species. In the present study, we studied blue sheep (Pseudois nayaur) across the distribution range in the Western trans Himalayas of India and found about 18,775 km2 area suitable for blue sheep. The explicit Bayesian based spatial and non-spatial population structure analysis assigned blue sheep into two genetic populations, i.e., Ladakh and Lahaul-Spiti. We found relatively high genetic divergence in blue sheep which is also supported by the low current flow in Circuitscape model. With the multiple evidences, we explain landscape resistance facilitated by the landscape heterogeneity, and large patches of unsuitable habitats forced population divergence and poor functional connectivity. We found that blue sheep population has been demographically stable in the past, but showed a slight decline within the last few decades. This study is the first range-wide attempt to exhibit landscape features in shaping the spatial distribution, genetic structure and demography patterns of blue sheep in Western Himalayas, and will be of use in the conservation and management planning of blue sheep.