bluuebunny/crossref_metadata_2025 huggingface dataset:
The Making of Future Scientists: Faculty Mentor Cultural Awareness and Inclusive Science Labs
Authors: Hernandez Ivan A. , Segura Oliva Mota , Gonzalez Rosalva Romero , Flores Lilibeth , Villodas Miguel T. , Sohl Christal D. , Smith Jessi L. , Thoman Dustin B.
Published: August 2024

Student researchers from racially marginalized and minoritized backgrounds who perceived their faculty research mentor to be more culturally aware experienced more positive social climates in the lab and were more identified as scientists. Increased science identity, in turn, predicted their motivation to pursue STEM careers three months later.
Human Leukocyte Antigen Mismatching and Survival in Contemporary Hematopoietic Cell Transplantation for Hematologic Malignancies
Authors: Arrieta-Bolaños Esteban , Bonneville Edouard F. , Crivello Pietro , Robin Marie , Gedde-Dahl Tobias , Salmenniemi Urpu , Kröger Nicolaus , Yakoub-Agha Ibrahim , Crawley Charles , Choi Goda , Broers Annoek E.C. , Forcade Edouard , Carre Martin , Poiré Xavier , Huynh Anne , Lenhoff Stig , Ciceri Fabio , Tholouli Eleni , Schroeder Thomas , Deconinck Eric , Carlson Kristina , de Wreede Liesbeth C. , Hoogenboom Jorinde D. , Malard Florent , Ruggeri Annalisa , Fleischhauer Katharina ,   on behalf of the Cellular Therapy and Immunobiology Working Party of the EBMT
Published: August 2024

PURPOSE

Human leukocyte antigen (HLA) mismatching can reduce survival of patients with blood cancer after hematopoietic cell transplantation (HCT). How recent advances in HCT practice, in particular graft-versus-host disease (GVHD) prophylaxis by post-transplantation cyclophosphamide (PTCy), influence HLA risk associations is unknown.

PATIENTS AND METHODS

The study included 17,292 unrelated HCTs with 6-locus high-resolution HLA typing, performed mainly for acute leukemia or related myeloid neoplasms between 2016 and 2020, including 1,523 transplants with PTCy. HLA risk associations were evaluated by multivariable Cox regression models, with overall survival (OS) as primary end point.

RESULTS

OS was lower in HLA mismatched compared with fully matched transplants (hazard ratio [HR], 1.23 [99% CI, 1.14 to 1.33];
P
< .001). This was driven by class I HLA-A, HLA-B, HLA-C (HR, 1.29 [99% CI, 1.19 to 1.41];
P
< .001) but not class II HLA-DRB1 and HLA-DQB1 (HR, 1.07 [99% CI, 0.93 to 1.23];
P
= .19). Class I antigen-level mismatches were associated with worse OS than allele-level mismatches (HR, 1.36 [99% CI, 1.24 to 1.49];
P
< .001), as were class I graft-versus-host peptide-binding motif (PBM) mismatches compared with matches (HR, 1.42 [99% CI, 1.28 to 1.59];
P
< .001). The use of PTCy improved GVHD, relapse-free survival compared with conventional prophylaxis in HLA-matched transplants (HR, 0.77 [0.66 to 0.9];
P
< .001). HLA mismatching increased mortality in PTCy transplants (HR, 1.32 [1.04 to 1.68];
P
= .003) similarly as in non-PTCy transplants (interaction
P
= .43).

CONCLUSION

Class I but not class II HLA mismatches, especially at the antigen and PBM level, are associated with inferior survival in contemporary unrelated HCT. These effects are not significantly different between non-PTCy compared with PTCy transplants. Optimized HLA matching should still be considered in modern HCT.
Prospects for the use of plasmonic vortices to control nanosystems
Authors: Quinteiro Rosen G. F. , Tamborenea P. I.
Published: August 2024

Fueled by the rapid pace of technological advancements, the convergence of ideas from optics and solid-state physics is yielding valuable insights into the fundamental principles governing interactions between light and matter at the nanoscale, as well as paving the way for future technologies. In this review, we explore a burgeoning avenue that investigates the synergy between plasmonics and optical vortex concepts. The excitation of plasmon modes with phase dislocations, occasionally referred to as plasmonic vortices, has revealed novel facets of physics. One particularly promising expansion of this field pertains to the manipulation of nearby nanostructures. Consequently, we provide commentary on the associated research, which offers innovative solutions to a variety of technological challenges.
VitelloTag: a tool for high-throughput cargo delivery into oocytes
Authors: Clarke D. Nathaniel , Kane Akshay , Perillo Margherita , Lowe Christopher J. , Swartz S. Zachary
Published: August 2024

Delivering molecular tools into oocytes is essential for developmental and reproductive biology. Microinjection, the conventional method, is equipment intensive, often technically challenging and has a low yield, and is impractical in species with delicate oocytes or restricted spawning seasons. To overcome these limitations, we developed VitelloTag, a cost-effective, high-throughput system using vitellogenin-derived fusion proteins to enable efficient cargo delivery via receptor-mediated endocytosis. We demonstrate its utility by delivering Cas9/sgRNA complexes in two distantly related species for gene knockout.
The role of kinesin-1 in neuronal dense core vesicle transport, locomotion and lifespan regulation in C. elegans
Authors: Gavrilova Anna , Boström Astrid , Korabel Nickolay , Fedotov Sergei , Poulin Gino B. , Allan Victoria J.
Published: August 2024

Fast axonal transport is crucial for neuronal function and is driven by kinesins and cytoplasmic dynein. Here, we investigated the role of kinesin-1 in dense core vesicle (DCV) transport in C. elegans, using mutants in the kinesin light chains (klc-1 and klc-2) and the motor subunit (unc-116) expressing an ida-1::gfp transgene that labels DCVs. DCV transport in both directions was greatly impaired in an unc-116 mutant and had reduced velocity in a klc-2 mutant. In contrast, the speed of retrograde DCV transport was increased in a klc-1 mutant whereas anterograde transport was unaffected. We identified striking differences between the klc mutants in their effects on worm locomotion and responses to drugs affecting neuromuscular junction activity. We also determined lifespan, finding that unc-116 mutant was short-lived whereas the klc single mutant lifespan was wild type. The ida-1::gfp transgenic strain was also short-lived, but surprisingly, klc-1 and klc-2 extended the ida-1::gfp lifespan beyond that of wild type. Our findings suggest that kinesin-1 not only influences anterograde and retrograde DCV transport but is also involved in regulating lifespan and locomotion, with the two kinesin light chains playing distinct roles.
Pediatric residency milestone performance is not predicted by the United States Medical Licensing Examination Step 2 Clinical Knowledge
Authors: Miller Benjamin , Nowalk Andrew , Ward Caroline , Walker Lorne , Dewar Stephanie
Published: August 2024

Objectives This study aims to show whether correlation exists between pediatric residency applicants’ quantitative scores on the United States Medical Licensing Exam Step 2 Clinical Knowledge examination and their subsequent performance in residency training based on the Accreditation Council for Graduate Medical Education Milestones, which are competency-based assessments that aim to determine residents’ ability to work unsupervised after postgraduate training. No previous literature has correlated Step 2 Clinical Knowledge scores with pediatric residency performance assessed by Milestones. Methods In this retrospective cohort study, the United States Medical Licensing Exam Step 2 Clinical Knowledge Scores and Milestones data were collected from all 188 residents enrolled in a single categorical pediatric residency program from 2012 - 2017. Pearson correlation coefficients were calculated amongst available test and milestone data points to determine correlation between test scores and clinical performance. Results Using Pearson correlation coefficients, no significant correlation was found between quantitative scores on the Step 2 Clinical Knowledge exam and average Milestones ratings (r = -0.1 for post-graduate year 1 residents and r = 0.25 for post-graduate year 3 residents). Conclusions These results demonstrate that Step 2 scores have no correlation to success in residency training as measured by progression along competency-based Milestones. This information should limit the importance residency programs place on quantitative Step 2 scores in their ranking of residency applicants. Future studies should include multiple residency programs across multiple specialties to help make these findings more generalizable.
Long-Term Impact of a Medical School Course on the Intersection of Art and Medical History
Authors: Coller Bobbi G. , Slamovits Gabriel , Coller Barry S.
Published: August 2024

Background One recent trend in medical education is the integration of humanities into the curriculum, including viewing works of art in museums, with analysis of short-term, but not long-term, impact. We developed a course for medical students, trainees, and faculty at the Icahn School of Medicine at Mount Sinai co-taught by an art historian and a physician/medical historian that features images of great works of art to make connections between art and medical history with the following goals: 1. To encourage the students to make careful and systematic observations, describe what they see to others in the group, and exchange their views respectfully, 2. To sensitize students to the patient’s experience of illness by discussing artists’ depictions of patients and the impact of their illness on family and friends, and 3. To highlight milestones in medical history by focusing on artworks that epitomize the state of medical care and science at a defined point in time. We have taught the course for more than a decade and so wanted to assess whether participating in the course had a long-term impact. Methods We created and deployed a five-question survey to 167 students and received responses from 35 of those students. Results 97% of respondents answered that they still think about the course, and large majorities of the respondents indicated that the course, had an impact on how they viewed works of art (91%), their appreciation of the history of medicine (89%), and their observational skills (80%). More than half the students responded that the course sensitized them to the patient’s perspective of illness (63%) and had an impact on how they viewed their role as a physician (51%). Conclusions Our course has had a long-term impact on the respondents across a wide range of professional and personal characteristics.
Trends and Cross-National Differences in Educational Homogamy in Europe: The Role of Educational Composition
Authors: Uunk Wilfred
Published: August 2024

The extent of educational homogamy has important consequences for social inequalities and social cohesion. However, little is known about current trends, cross-national differences, and the drivers of educational homogamy in Europe. This study aims to fill this gap by (a) describing trends in absolute educational homogamy (i.e., the share of similarly educated partners) and relative educational homogamy (i.e., homogamy corrected for the distribution of spouses’ education) for European countries; and (b) examining the association between a population’s educational composition and the level of absolute and relative educational homogamy. Given the large changes in the educational composition of European populations and the presumed consequences for absolute and relative educational homogamy, this focus on educational composition is warranted. Our aggregate-level regression analyses covering 36 countries and five birth cohorts (1940-1989) from the European Social Survey show that absolute and relative educational homogamy has not changed. However, this obscures variation by education group and country. We find that the extent of absolute educational homogamy in a country cohort is strongly associated with educational composition and observe statistical effects of educational expansion (positive for the higher educated), educational heterogeneity (negative), educational gender symmetry (positive), educational income inequality (positive), and educational reproduction (positive). Relative educational homogamy is only weakly associated with a population’s educational composition, and its effects are confined to gender symmetry (positive) and educational reproduction (positive). Our findings suggest that changes in educational composition in Europe affect educational homogamy in various directions and indicate that these effects come from structural opportunities rather than changing preferences for educational homogamy.
* This article belongs to a special issue on “Changes in Educational Homogamy and Its Consequences”.
Modern Methods Of Glucose Monitoring In The Context Of Physical Activity - Review Study
Authors: Jędrasek Aleksandra , Jędrasek Tomasz , Pogoda Julia , Piotrowski Jan , Hądzlik Izabela , Biały-Karbowniczek Julia , Słychan Katarzyna , Łuczak Blanka , Bulska Klaudia , Sławek Konrad
Published: August 2024

Introduction: In the last few years, with over 422 million cases of diabetes worldwide and with an overload of healthcare, the development of new glucose monitoring approaches has become a crucial subject. This paper set out to explore the effectiveness of current glucose monitoring methods, their usage in the context of physical activity, and prospects for the future.
Review methods: We conducted our study as a literature review, with data being gathered via PubMed and Embase.
The state of knowledge: Currently, the two most popular methods of glucose monitoring are self-monitoring (SMBG) and continuous glucose monitoring (CGM) with real-time devices such as Dexcom G6, and Medtronic Guardian Connect System, and intermittent devices such as Freestyle Libre 2. Both approaches are invasive and can cause allergic reactions and dermatitis. As a result, many researchers propose non-invasive methods including optical coherence tomography, spectroscopy, and fluorescence. The growing accessibility leads to the usage of CGM devices in everyday life not only by patients with diabetes melitus. 
Conclusions: Advancements in diabetes technologies allow patients to maintain glucose homeostasis and improve their Quality of life. CGM devices are constantly being developed to be more accessible and easy to use, which may help adjust the training programs and diets for individual needs.
Infections of the Central Nervous System
Authors: Dobosz Mateusz , Arciszewska Klaudia , Bogoń Aleksandra , Buczkowski Jakub , Pieniążek Jakub Maciej , Padkowska Aleksandra , Paprocki Michał , Mataczyńska Anna , Laskowska Aleksandra
Published: August 2024

Central nervous system infections are among the most devastating infections in the world. Pathogens may enter the central nervous system as a result of dissemination from the upper respiratory tract or other primary site via blood and then crossing the blood-brain barrier. Pathogens present in health care facilities are not an exception. In addition, the neurosurgical procedures performed there are an additional way of entering the central nervous system. Moreover, nosocomial infections are characterized by very high morbidity and mortality, therefore their early diagnosis and treatment is important.
The aim of the study is to review the current knowledge and guidelines on the most common healthcare-associated infections of the central nervous system, their diagnosis and treatment.
Information searches were carried out in online databases, scientific and educational editions.
The most common healthcare-associated infection of the central nervous system is meningitis, followed by a subdural empyema and a brain abscess. The greatest risk factor is neurosurgery. In all of the most common infections of the central nervous system listed, rapid implementation of empiric antibiotic therapy is essential. Further antibiotic therapy depends on the identified etiological factor. As a rule, surgical treatment is required for subdural empyema and brain abscesses.
Healthcare-related central nervous system infections remain a significant problem. Due to the risk posed by them to the patient's health, prophylaxis, prompt diagnosis and treatment are essential.
Distributed Ledgers and Secure Multiparty Computation for Financial Reporting and Auditing
Authors: Cao Sean Shun , Cong Lin William , Yang Baozhong
Published: August 2024

To understand the disruption and implications of distributed ledger technologies for financial reporting and auditing, we analyze firm misreporting, auditor monitoring and competition, and regulatory policy in a unified model. A federated blockchain for financial reporting and auditing can improve verification efficiency not only for transactions in private databases but also for cross-chain verifications through privacy-preserving computation protocols. Despite the potential benefit of blockchains, private incentives for firms and first-mover advantages for auditors can create inefficient under-adoption or partial adoption that favors larger auditors. Although a regulator can help coordinate the adoption of technology, endogenous choice of transaction partners by firms can still lead to adoption failure. Our model also provides an initial framework for further studies of the costs and implications of the use of distributed ledgers and secure multiparty computation in financial reporting, including the positive spillover to discretionary auditing and who should bear the cost of adoption.

This paper was accepted by David Simchi-Levi, finance.

Funding: The authors gratefully acknowledge research support from the FinTech Laboratory at J. Mack Robinson College of Business at Georgia State University, the Center for Research in Security Prices at the University of Chicago, the Ripple University Blockchain Research Initiative, and the Smith AI Initiative for Capital Market Research at the University of Maryland.

Supplemental Material: The online appendix is available at https://doi.org/10.1287/mnsc.2023.02577 .
Prediction of Antenna Performance based on Scalable Data-informed Machine Learning Methods
Authors: Chen Yiming , Demir Veysel , Bhupatiraju Srirama , Elsherbeni Atef Z. , Gavilan Joselito , Stoynov Kiril
Published: August 2024

This paper proposes a scalable architecture for predicting antenna performance using various data-informed machine learning (DIML) methods. By utilizing the computation power of graphics processing units (GPUs), the architecture takes advantage of hardware (HW) acceleration from the beginning of electromagnetic (EM) full-wave simulation to the final machine learning (ML) validation. A total of 49152 full-wave simulations of a classical microwave patch antenna forms the ML dataset. The dataset contains the performance of patch antenna on six commonly used materials and two standard thicknesses in a wide frequency range from 0.1 to 20 GHz. A total of 13 base ML models are stacked and ensembled in a tabular workflow with performance as 0.970 and 0.933 F1 scores for two classification models, as well as 0.912 and 0.819 R2 scores for two regression models. Moreover, an image-based workflow is proposed. The image-based workflow yields the 0.823 R2 score, indicating a near real-time prediction for all S11 values from 0.1 to 20 GHz. The proposed architecture requires neither the fine-tuned hyperparameters in the ML-assisted optimization (MLAO) model for specified antenna design nor the pre-knowledge required in the physics-informed models. The fully automated process with data collection and the customized ML pipeline provides the architecture with robust scalability in future work where more antenna types, materials, and performance requirements can be involved. Also, it could be wrapped as a pre-trained ML model as a reference for other antenna designs.
Optimal Synthesis of Unequally Spaced Linear Arrays under Multiple Constraints
Authors: Zhao Zhong-Hui
Published: August 2024

This paper proposes a differential evolution modified with adaptive ε-constraint handling and whale optimization algorithm (ε-WOA-DE) for the synthesis of unequally spaced linear arrays under array layout constraints and array pattern characteristics constraints. In particular, the success history based adaptive differential evolution with linear population reduction (LSHADE) serves as the basic search engine in this study. To ensure the searching ability of LSHADE under multiple constraints, an adaptive ε-constraint handling technique is implemented in LSHADE, in which the epsilon level is adjusted dynamically to make the solution scalable to the feasible region when it is in the infeasible region. In addition, the WOA mutation is implemented in the LSHADE to enhance the local search capability. Two array synthesis examples with multiple constraints are chosen to demonstrate the effectiveness of the proposed algorithm. The simulation results comparison and the convergence analysis of the ε-WOA-DE illustrate the superior capability of the proposed method.
Research on Variable Direction Wireless Power Transfer System based on Auxiliary Coils:
Authors: Xiao Feihang , Qiang Hao
Published: August 2024

In complex environments such as mines and pipelines, wireless power transfer (WPT) technology stands as a safe and convenient method for supplying power. However, in practical applications, the unavoidable angular misalignment between the sending and receiving coils results in decreased power. To address this issue, this paper proposes a variable direction WPT design method based on auxiliary coils. The mutual inductance of the system is analyzed with coils placed at different positions and incorporating multiple auxiliary coils. This paper conducts simulation and experimental analysis based on a 45∘ angle between the horizontal shaft and the slant shaft, showing a 14.92% increase in received power. The effectiveness of the proposed design method validates the feasibility of the technology and offers substantial support for practical applications.
A Mississippian limestone platform at the southwestern margin of the South Munster Basin
Authors: Sevastopulo George D. , Naylor David
Published: August 2024

Abstract: Core holes have demonstrated that the anomalous limestone erratics of the Bantry area of west Cork were derived by ice plucking of local in-situ deposits. The boulders had been deposited during the Mississippian into basinal sediments proximal to, or within, a fault zone trending along the south coast of Bantry Bay. Samples were collected from all the known occurrences of limestone erratics and from Geological Survey Ireland core hole GSI 99-4. A micropalaeontological and petrological study was carried out on all the samples. Evidence is presented that a carbonate platform was present over Sheep's Head, and an area to the south, from Ivorian to Brigantian time.
Sexual Sin in Orderic Vitalis's Historia Ecclesiastica : Performative Purgation in the Penitential Parade
Authors: White Christopher
Published: August 2024

Abstract: Orderic Vitalis's 'Historia Ecclesiastica' is an important source for scholars of the Norman demesne in the late eleventh and early twelfth centuries. The 'Historia' is a chronicle of the history of Normandy, but also details social mores and customs. The 'Historia' also contains wonder tales, and one of these is the focus of this article—the narrative of 'Herlechin's Hunt'. This article addresses a key element of the symbolism of the story that has been largely overlooked by modern scholarship. In doing so, it argues that the narrative is as much about illicit sex and the sexual mores of the monks of Saint-Évroul as it is about anger and violence, as it has traditionally been understood.
Low-voltage-tunable electromechanical photonic directional coupler in silicon nitride for telecom wavelengths
Authors: Sommer Timo , Haas Kevin-Jeremy , Hoch David , Poot Menno
Published: August 2024

Silicon nitride is a low-loss photonic integrated circuit (PIC) platform. However, silicon nitride also shows small nonlinear optical properties and is dielectric, which makes the implementation of programmability challenging. Typically, the thermo-optic effect is used for this, but modulators based on this effect are often slow and cross talk-limited. Here, we present a different approach to programmability in silicon nitride photonics. Micro-electromechanical elements are added to a photonic directional coupler, forming two H-shaped structures. The coupling can be changed by applying a voltage to electrodes placed onto the H-structure, which are then attracted by an electrostatic force. These suspended directional couplers show an insertion loss of 0.67 dB and demonstrate switching with 1.1±0.1 µs rise times, representing a valuable addition to the thermal photonic modulators in silicon nitride technology that offer higher modulation speeds while keeping a comparable insertion loss.
Low photon-number stand-off speckle holography at kHz frame rates
Authors: Wolley O. , Gregory T. , Mekhail S. P. , Archibald R. , Padgett M. J.
Published: August 2024

Stand-off imaging using active illumination is challenging as the intensity of the backscattered light drops with the square of the distance to the target. Homodyne or heterodyne detection, by interfering with the low intensity signal with a much stronger reference, is capable of amplifying the signal above the noise floor of a detector. However, the low spatial coherence of the backscattered light from an optically rough surface makes imaging the spatially resolved interference problematic. We deliberately over-resolve the image so that each speckle in the back-scattered light falls across many pixels and then by using off-axis holography we can reconstruct phase-images even when the collected light signal is below the noise floor of the detector. We achieve a sensitivity of ∼1 photon per pixel per frame at a frame rate of up to 50 kHz. We demonstrate how the phase imaging capability of the system can be applied to stand-off vibrometry measurements, and extend their range by being able to reconstruct the phase below the noise floor of the camera, achieving a signal-to-noise ratio of 22.4±0.5 dB at a range of 6 m.
Infrared quantum ghost imaging of living and undisturbed plants
Authors: Ryan Duncan P. , Meier Kristina , Seitz Kati , Hanson David , Morales Demosthenes , Palmer David M. , Hanson Buck , Goodwin Peter M. , Newell Raymond , Holmes Rebecca M. , Thompson David , Werner James
Published: August 2024

Quantum ghost imaging (QGI) is a method that measures absorption at extremely low light intensities. Nondegenerate QGI probes a sample at one wavelength while forming an image with correlated photons at a different wavelength. This spectral separation alleviates the need for imaging detectors with high sensitivity in the near-infrared (NIR) region, thereby reducing the required illumination intensity. Using NCam, a single-photon detector, we demonstrated nondegenerate QGI with unprecedented sensitivity and contrast, obtaining images of living plants with less than 1% light transmission. The plants experienced 3aW/cm2 of light during imaging, orders of magnitude below starlight. This realization of QGI expands the method to extremely low-light bioimaging and imaging of light-sensitive samples, where minimizing illumination intensity is crucial to prevent phototoxicity or sample degradation.
The ion channel Anoctamin 10/TMEM16K coordinates organ morphogenesis across scales in the urochordate notochord
Authors: Liang Zonglai , Dondorp Daniel Christiaan , Chatzigeorgiou Marios
Published: August 2024

During embryonic development, tissues and organs are gradually shaped into their functional morphologies through a series of spatiotemporally tightly orchestrated cell behaviors. A highly conserved organ shape across metazoans is the epithelial tube. Tube morphogenesis is a complex multistep process of carefully choreographed cell behaviors such as convergent extension, cell elongation, and lumen formation. The identity of the signaling molecules that coordinate these intricate morphogenetic steps remains elusive. The notochord is an essential tubular organ present in the embryonic midline region of all members of the chordate phylum. Here, using genome editing, pharmacology and quantitative imaging in the early chordate Ciona intestinalis we show that Ano10/Tmem16k, a member of the evolutionarily ancient family of transmembrane proteins called Anoctamin/TMEM16 is essential for convergent extension, lumen expansion, and connection during notochord morphogenesis. We find that Ano10/Tmem16k works in concert with the plasma membrane (PM) localized Na+/Ca2+ exchanger (NCX) and the endoplasmic reticulum (ER) residing SERCA, RyR, and IP3R proteins to establish developmental stage specific Ca2+ signaling molecular modules that regulate notochord morphogenesis and Ca2+ dynamics. In addition, we find that the highly conserved Ca2+ sensors calmodulin (CaM) and Ca2+/calmodulin-dependent protein kinase (CaMK) show an Ano10/Tmem16k-dependent subcellular localization. Their pharmacological inhibition leads to convergent extension, tubulogenesis defects, and deranged Ca2+ dynamics, suggesting that Ano10/Tmem16k is involved in both the “encoding” and “decoding” of developmental Ca2+ signals. Furthermore, Ano10/Tmem16k mediates cytoskeletal reorganization during notochord morphogenesis, likely by altering the localization of 2 important cytoskeletal regulators, the small GTPase Ras homolog family member A (RhoA) and the actin binding protein Cofilin. Finally, we use electrophysiological recordings and a scramblase assay in tissue culture to demonstrate that Ano10/Tmem16k likely acts as an ion channel but not as a phospholipid scramblase. Our results establish Ano10/Tmem16k as a novel player in the prevertebrate molecular toolkit that controls organ morphogenesis across scales.
iCRBP-LKHA: Large convolutional kernel and hybrid channel-spatial attention for identifying circRNA-RBP interaction sites
Authors: Yuan Lin , Zhao Ling , Lai Jinling , Jiang Yufeng , Zhang Qinhu , Shen Zhen , Zheng Chun-Hou , Huang De-Shuang
Published: August 2024

Circular RNAs (circRNAs) play vital roles in transcription and translation. Identification of circRNA-RBP (RNA-binding protein) interaction sites has become a fundamental step in molecular and cell biology. Deep learning (DL)-based methods have been proposed to predict circRNA-RBP interaction sites and achieved impressive identification performance. However, those methods cannot effectively capture long-distance dependencies, and cannot effectively utilize the interaction information of multiple features. To overcome those limitations, we propose a DL-based model iCRBP-LKHA using deep hybrid networks for identifying circRNA-RBP interaction sites. iCRBP-LKHA adopts five encoding schemes. Meanwhile, the neural network architecture, which consists of large kernel convolutional neural network (LKCNN), convolutional block attention module with one-dimensional convolution (CBAM-1D) and bidirectional gating recurrent unit (BiGRU), can explore local information, global context information and multiple features interaction information automatically. To verify the effectiveness of iCRBP-LKHA, we compared its performance with shallow learning algorithms on 37 circRNAs datasets and 37 circRNAs stringent datasets. And we compared its performance with state-of-the-art DL-based methods on 37 circRNAs datasets, 37 circRNAs stringent datasets and 31 linear RNAs datasets. The experimental results not only show that iCRBP-LKHA outperforms other competing methods, but also demonstrate the potential of this model in identifying other RNA-RBP interaction sites.
The Mycetoma Research Center, University of Khartoum, Sudan’s experience in community engagement initiatives spans 3 decades
Authors: Fahal Ahmed Hassan , Ahmed Eiman Siddig , Mahmoud Ahmed Hussein , Saaed Ali Awadella
Published: August 2024

Mycetoma profoundly affects marginalised communities, especially in impoverished and remote areas with limited access to healthcare. This chronic and debilitating inflammatory disease highlights the typical issues of neglected tropical diseases (NTDs), such as insufficient attention, funding, and resources, which perpetuate neglect and suffering. Patients often delay seeking medical help, leading to advanced disease stages, severe complications, and lasting disabilities. The lack of medical infrastructure and skilled healthcare professionals worsens the situation, causing delays in diagnosis and inadequate treatment. Engaging affected communities in tailored interventions is essential to tackle these challenges, promote collaboration, raise awareness, and mobilise resources to improve healthcare access and enhance diagnostic and treatment capabilities. Since 1991, the Mycetoma Research Center (MRC) at the University of Khartoum, Sudan, has led community engagement initiatives aimed at improving the quality of life for mycetoma-affected individuals through education, advocacy, and local collaboration. In this communication, the MRC shares its extensive experience in community engagement to benefit mycetoma-affected communities.
Unsupervised clustering analysis of trauma/non-trauma centers using hospital features including surgical care
Authors: Sun Xiaonan , Liu Shan , Mock Charles , Vavilala Monica , Bulger Eileen , Maine Rebecca G.
Published: August 2024

Background

Injuries are a leading cause of death in the United States. Trauma systems aim to ensure all injured patients receive appropriate care. Hospitals that participate in a trauma system, trauma centers (TCs), are designated with different levels according to guidelines that dictate access to medical and research resources but not specific surgical care. This study aimed to identify patterns of injury care that distinguish different TCs and hospitals without trauma designation, non-trauma centers (non-TCs).

Study design

We extracted hospital-level features from the state inpatient hospital discharge data in Washington state, including all TCs and non-TCs, in 2016. We provided summary statistics and tested the differences of each feature across the TC/non-TC levels. We then conducted 3 sets of unsupervised clustering analyses using the Partition Around Medoids method to determine which hospitals had similar features. Set 1 and 2 included hospital surgical care (volume or distribution) features and other features (e.g., the average age of patients, payer mix, etc.). Set 3 explored surgical care without additional features.

Results

The clusters only partially aligned with the TC designations. Set 1 found the volume and variation of surgical care distinguished the hospitals, while in Set 2 orthopedic procedures and other features such as age, social vulnerability indices, and payer types drove the clusters. Set 3 results showed that procedure volume rather than the relative proportions of procedures aligned more, though not completely, with TC designation.

Conclusion

Unsupervised machine learning identified surgical care delivery patterns that explained variation beyond level designation. This research provides insights into how systems leaders could optimize the level allocation for TCs/non-TCs in a mature trauma system by better understanding the distribution of care in the system.
Real-time AIoT platform for monitoring and prediction of air quality in Southwestern Morocco
Authors: Bekkar Abdellatif , Hssina Badr , ABEKIRI Najib , Douzi Samira , Douzi Khadija
Published: August 2024

Urbanization and industrialization have led to a significant increase in air pollution, posing a severe environmental and public health threat. Accurate forecasting of air quality is crucial for policymakers to implement effective interventions. This study presents a novel AIoT platform specifically designed for PM2.5 monitoring in Southwestern Morocco. The platform utilizes low-cost sensors to collect air quality data, transmitted via WiFi/3G for analysis and prediction on a central server. We focused on identifying optimal features for PM2.5 prediction using Minimum Redundancy Maximum Relevance (mRMR) and LightGBM Recursive Feature Elimination (LightGBM-RFE) techniques. Furthermore, Bayesian optimization was employed to fine-tune hyperparameters of popular machine learning models for the most accurate PM2.5 concentration forecasts. Model performance was evaluated using Root Mean Square Error (RMSE), Mean Absolute Error (MAE), and the coefficient of determination (R2). Our results demonstrate that the LightGBM model achieved superior performance in PM2.5 prediction, with a significant reduction in RMSE compared to other evaluated models. This study highlights the potential of AIoT platforms coupled with advanced feature selection and hyperparameter optimization for effective air quality monitoring and forecasting.
Divergent effects of azithromycin on purple corn (Zea mays L.) cultivation: Impact on biomass and antioxidant compounds
Authors: Mamani Ramos Yoselin , Huamán Castilla Nils Leander , Colque Ayma Elvis Jack , Mamani Condori Noemi , Campos Quiróz Clara Nely , Vilca Franz Zirena
Published: August 2024

The present study assessed the impact of using irrigation water contaminated with Azithromycin (AZM) residues on the biomass and antioxidant compounds of purple corn; for this purpose, the plants were cultivated under ambient conditions, and the substrate used consisted of soil free from AZM residues, mixed with compost in a ratio of 1:1 (v/v). The experiment was completely randomized with four replications, with treatments of 0, 1, 10, and 100 μg/L of AZM. The results indicate that the presence of AZM in irrigation water at doses of 1 and 10 μg/L increases the weight of dry aboveground biomass, while at an amount of 100 μg/L, it decreases. Likewise, this study reveals that by increasing the concentration of AZM from 1 to 10 μg/L, total polyphenols and monomeric anthocyanins double, in contrast, with an increase to 100 μg/L, these decrease by 44 and 53%, respectively. It has been demonstrated that purple corn exposed to the antibiotic AZM at low doses has a notable antioxidant function in terms of DPPH and ORAC. The content of flavonols, phenolic acids, and flavanols increases by 57, 28, and 83%, respectively, when the AZM concentration is from 1 to 10 μg/L. However, with an increase to 100 μg/L, these compounds decrease by 17, 40, and 42%, respectively. On the other hand, stem length, root length, and dry weight of root biomass are not significantly affected by the presence of AZM in irrigation water.
The application effect of the Rasch measurement model combined with the CRF model: An analysis based on English discourse
Authors: Wang Yunxia
Published: August 2024

To analyze English discourse more accurately and provide more detailed feedback information, this study applies Rasch measurement and Conditional Random Field (CRF) models to English discourse analysis. The Rasch measurement model is widely used to evaluate and quantify the potential traits of individuals, and it has remarkable advantages in measurement and evaluation. By combining the CRF model, the Rasch model is employed to model the structural and semantic information in the discourse and use this model to carry out sequence labeling, to enhance the ability to capture the internal relations of the discourse. Finally, this study conducts comparative experiments on integrating the Rasch measurement and CRF models, comparing the outcomes against traditional scoring methods and the standalone CRF model. The research findings indicate that: (1) The discourse component syntactic analysis model on the Penn Treebank (PTB) database obtained Unlabeled Attachment Score (UAS) values of 94.07, 95.76, 95.67, and 95.43, and Labeled Attachment Score (LAS) values of 92.47, 92.33, 92.49, and 92.46 for the LOC, CRF, CRF2O, and MFVI models, respectively. After adding the Rasch measurement model, the UAS values of the four models on the PTB database are 96.85, 96.77, 96.92, and 96.78 for the LOC, CRF, CRF2O, and MFVI models, respectively, with LAS values of 95.33, 95.34, 95.39, and 95.32, all showing significant improvement. (2) By combining contextual information with CRF models, students can better understand their discourse expression, capture the connections between English discourse sentences, and analyze English discourse more comprehensively. This study provides new ideas and methods for researchers in English language education and linguistics.
Evaluating research ethics committees in Vietnam and Laos: Results of a validated self-assessment tool
Authors: Sattah Nathan Gabriel , D’Anniballe Vincent , Le Hoang Tu , Le Luyen Thi , Le Thanh Ngoc , Vu Thom Thi , Louangpradith Viengsakhone , Lee Walter T.
Published: August 2024

Background

There is an increase in human subject research in developing countries and conducting them in an ethical manner depends on the research ethics oversight in these countries. The purpose of this study is to evaluate the operational, financial, and educational characteristics of research ethics committees (RECs) at institutions in Vietnam and Laos.

Methods

A validated self-assessment tool designed to assess nine major characteristics of RECs was translated into Vietnamese and Laotian. The translated surveys were delivered to and completed by representatives from RECs at institutions in Vietnam and Laos. The surveys were collected, translated back into English, and scored. The data was analyzed to identify potential areas of strength and areas for improvement.

Results

The mean survey score for the 19 RECs surveyed was 165.3 out of a maximum of 200 points with a standard deviation of 22.9. Committees scored the highest in the review of specific protocol items (95.6%), submission arrangements and materials (89.5%), and the policies referring to review procedures (85.6%) domains. RECs scored the lowest in the resources domain (65.5%), with only 26.3% of committees having an annual budget. Nearly all RECs have standard operating procedures (94.7%) and policies for disclosing conflicts of interest (89.5%). Most committees use prior ethics training as a criterion to select REC chairs (78.9%) and members (73.7%), with the majority of committees requiring a training course in ethics (76.5%). 68.4% of committees have continuing education in ethics for members and only 42.1% of committees have a budget for member training.

Conclusion

This study demonstrated that RECs in Vietnam and Laos have strong foundational review processes for research protocols. Important areas of improvement include improved institutional oversight, financial and administrative resources, and the continued ethics education for current committee members.
Early detection of critical urban events using mobile phone network data
Authors: Lemaire Pierre , Furno Angelo , Rubrichi Stefania , Bondu Alexis , Smoreda Zbigniew , Ziemlicki Cezary , El Faouzi Nour-Eddin , Gaume Eric
Published: August 2024

Network Signalling Data (NSD) have the potential to provide continuous spatio-temporal information about the presence, mobility, and usage patterns of cell phone services by individuals. Such information is invaluable for monitoring large urban areas and supporting the implementation of decision-making services. When analyzed in real time, NSD can enable the early detection of critical urban events, including fires, large accidents, stampedes, terrorist attacks, and sports and leisure gatherings, especially if these events significantly impact mobile phone network activity in the affected areas. This paper presents empirical evidence that advanced NSD can detect anomalies in mobile traffic service consumption, attributable to critical urban events, with fine spatial (a spatial resolution of a few decameters) and temporal (minutes) resolutions. We introduce two methodologies for real-time anomaly detection from multivariate time series extracted from large-scale NSD, utilizing a range of algorithms adapted from the state-of-the-art in unsupervised machine learning techniques for anomaly detection. Our research includes a comprehensive quantitative evaluation of these algorithms on a large-scale dataset of NSD service consumption for the Paris region. The evaluation uses an original dataset of documented critical or unusual urban events. This dataset has been built as a ground truth basis for assessing the algorithms’ performance. The obtained results demonstrate that our framework can detect unusual events almost instantaneously and locate the affected areas with high precision, largely outperforming random classifiers. This efficiency and effectiveness underline the potential of NSD-based anomaly detection in significantly enhancing emergency response strategies and urban planning. By offering a proactive approach to managing urban safety and resilience, our findings highlight the transformative potential of leveraging NSD for anomaly detection in urban environments.
Differential lung gene expression identified Zscan2 and Bag6 as novel tissue repair players in an experimental COPD model
Authors: Sánchez Carretero Laura , Cardeñosa Pérez Àdele Chole , Peces-Barba Germán , Pérez-Rial Sandra
Published: August 2024

Chronic obstructive pulmonary disease is a common chronic lung disease with an ever-increasing incidence. Despite years of drug research and approvals, we are still not able to halt progress or restore normal lung function. Our previous studies have demonstrated that liver growth factor—LGF has an effect on the repair of the affected tissue in a mouse model of cigarette smoke exposure, but by what pathways it achieves this is unknown. The present study aimed to identify differentially expressed genes between emphysematous mice treated with LGF to identify potential therapeutic targets for the treatment of pulmonary emphysema. The emphysema mouse model was induced by prolonged exposure to cigarette smoke. To determine the gene expression profile of the lung in smokers treated or not with LGF, lung messenger RNA gene expression was assessed with the Agilent Array platform. We carried out differentially expressed gene analysis, functional enrichment and validated in treated mouse lung samples. The treated group significantly improved lung function (~35%) and emphysema level (~20%), consistent with our previous published studies. Microarray analysis demonstrated 290 differentially expressed genes in total (2.0-fold over or lower expressed). Injury repair-associated genes and pathways were further enhanced in the lung of LGF treated mice. The expression trends of two genes (Zscan2 and Bag6) were different in emphysematous lungs treated with LGF compared to untreated lungs. Therefore, Zscan2 and Bag6 genes could play a role in regulating inflammation and the immune response in the lung that undergoes partial lung regeneration. However, further studies are necessary to demonstrate this causal relationship.
The assembly of neutrophil inflammasomes during COVID-19 is mediated by type I interferons
Authors: Cabrera Luz E. , Jokiranta Suvi T. , Mäki Sanna , Miettinen Simo , Kant Ravi , Kareinen Lauri , Sironen Tarja , Pietilä Jukka-Pekka , Kantele Anu , Kekäläinen Eliisa , Lindgren Hanna , Mattila Pirkko , Kipar Anja , Vapalahti Olli , Strandin Tomas
Published: August 2024

The severity of COVID-19 is linked to excessive inflammation. Neutrophils represent a critical arm of the innate immune response and are major mediators of inflammation, but their role in COVID-19 pathophysiology remains poorly understood. We conducted transcriptomic profiling of neutrophils obtained from patients with mild and severe COVID-19, as well as from SARS-CoV-2 infected mice, in comparison to non-infected healthy controls. In addition, we investigated the inflammasome formation potential in neutrophils from patients and mice upon SARS-CoV-2 infection. Transcriptomic analysis of polymorphonuclear cells (PMNs), consisting mainly of mature neutrophils, revealed a striking type I interferon (IFN-I) gene signature in severe COVID-19 patients, contrasting with mild COVID-19 and healthy controls. Notably, low-density granulocytes (LDGs) from severe COVID-19 patients exhibited an immature neutrophil phenotype and lacked this IFN-I signature. Moreover, PMNs from severe COVID-19 patients showed heightened nigericin-induced caspase1 activation, but reduced responsiveness to exogenous inflammasome priming. Furthermore, IFN-I emerged as a priming stimulus for neutrophil inflammasomes. These findings suggest a potential role for neutrophil inflammasomes in driving inflammation during severe COVID-19. Altogether, these findings open promising avenues for targeted therapeutic interventions to mitigate the pathological processes associated with the disease.