bluuebunny/crossref_metadata_2025 huggingface dataset:
Minimum complexity integrated photonic architecture for delay-based reservoir computing
Authors: Abdalla Mohab , Zrounba Clément , Cardoso Raphael , Jimenez Paul , Ren Guanghui , Boes Andreas , Mitchell Arnan , Bosio Alberto , O’Connor Ian , Pavanello Fabio
Published: March 2023

Reservoir computing is an analog bio-inspired computation scheme for efficiently processing time-dependent signals, the photonic implementations of which promise a combination of massive parallel information processing, low power consumption, and high-speed operation. However, most of these implementations, especially for the case of time-delay reservoir computing, require extensive multi-dimensional parameter optimization to find the optimal combination of parameters for a given task. We propose a novel, largely passive integrated photonic TDRC scheme based on an asymmetric Mach-Zehnder interferometer in a self-feedback configuration, where the nonlinearity is provided by the photodetector, and with only one tunable parameter in the form of a phase shifting element that, as a result of our configuration, allows also to tune the feedback strength, consequently tuning the memory capacity in a lossless manner. Through numerical simulations, we show that the proposed scheme achieves good performance -when compared to other integrated photonic architectures- on the temporal bitwise XOR task and various time series prediction tasks, while greatly reducing hardware and operational complexity.
40.1-GHz sub-freezing 850-nm VCSEL: microwave extraction of cavity lifetimes and small-signal equivalent circuit modeling
Authors: Cheng Hao-Tien , Wu Cheng-Han , Feng Milton , Wu Chao-Hsin
Published: March 2023

We present an 850-nm vertical-cavity surface-emitting laser (VCSEL) constructed for a wide operating temperature range from 25°C to −50°C sub-freezing temperature, demonstrating 40.1-GHz at −50°C. The optical spectra, junction temperature, and microwave equivalent circuit modeling of a sub-freezing 850-nm VCSEL between −50°C and 25°C are also discussed. Reduced optical losses, higher efficiencies, and shorter cavity lifetimes at sub-freezing temperatures are the leading causes of the improved laser output powers and bandwidths. The e–h recombination lifetime and the cavity photon lifetime are shortened to 113 and 4.1 ps, respectively. Could potentially supercharge VCSEL-based sub-freezing optical links for applications in frigid weather, quantum computing, sensing, aerospace, etc.
65,536-QAM OFDM signal transmission over a fiber-THz system at 320 GHz with delta-sigma modulation
Authors: Shi Junting , Yu Jianjun , Zhang Jiao , Zhu Min , Zhang Long , Wang Kaihui , Zhou Wen , Xie Tangyao , Yu Jianguo
Published: March 2023

The transmission of a 65,536-ary quadrature amplitude modulation (QAM) orthogonal frequency division multiplexing (OFDM) signal supported by a hybrid fiber–terahertz (THz) multiple-input multiple-output (MIMO) system at 320 GHz is experimentally demonstrated in this Letter. We adopt the polarization division multiplexing (PDM) technique to double the spectral efficiency. Based on a 23-GBaud 16-QAM link, 2-bit delta-sigma modulation (DSM) quantization enables 65,536-QAM OFDM signal transmission over a 20-km standard single-mode fiber (SSMF) and a 3-m 2 × 2 MIMO wireless delivery, and satisfies the hard-decision forward error correction (HD-FEC) threshold of 3.8 × 10−3, corresponding to a net rate of 60.5 Gbit/s for THz-over-fiber transport. Meanwhile, below the fronthaul error vector magnitude (EVM) threshold of 0.34%, a maximum signal-to-noise ratio (SNR) of 52.6 dB is achieved. To the best of our knowledge, this is the highest modulation order achievable for DSM applications in THz communication.
Continuous wave multi-pass imaging flow cytometry
Authors: Israel Yonatan , Reynolds Joshua L. , Klopfer Brannon B. , Kasevich Mark A.
Published: March 2023

Biological cells have weak optical properties that limit the sensitivity of measurements and imaging when the total illumination is limited by dynamics or throughput. Multi-pass microscopy enhances the sensitivity of classical light fields to these weak properties. We present a wide-field multi-pass microscope for label-free imaging flow cytometry. By passing the optical field through cells in a high-speed flow up to 4 times, we realize a ×4 enhancement in contrast and signal-to-noise ratio. We show that this technique approaches close to the quantum limit of measurement sensitivity, extending the range of optimal imaging to samples in the weakly absorbing regime. This allows for near optimal imaging sensitivity and throughput in practical scenarios involving dynamic biological samples and surpasses the sensitivity achieved with currently available quantum light sources.
Transport Model for the Propagation of Partially-Coherent, Polarization-Gradient Vector Beams
Authors: Nichols Jonathan , Bucholtz Frank , Nickel Daniel , Rohde Gustavo
Published: March 2023

Recently we predicted and experimentally validated a new physical mechanism for altering the propagation path of a monochromatic beam [1]. Specifically, we showed that by properly tailoring the spatial distribution of the linear state of polarization transverse to the direction of propagation, the beam followed a curved trajectory in free space. Here we extend the model to the partially coherent, polychromatic case by redefining the beam amplitude, phase, and polarization angle as appropriate statistical quantities. In particular, the definition of polarization angle represents a fundamentally new quantity in modelling beam propagation, and is shown to be consistent with recent works on energy and momentum flow. In the new model, the beam curvature matches that of our previous work in the fully coherent case, but is predicted to vanish for an unpolarized beam. Simulated beam trajectories are shown for varying levels of initial partial coherence and for different polarization profiles. A new class of non-diffracting beams is also suggested by way of example.
Collagen fiber anisotropy characterization by polarized photoacoustic imaging for just-in-time quantitative evaluation of burn severity
Authors: Zhang Zhenhui , Chen Wei , Cui Dandan , Mi Jie , Mu Gen , Nie Liming , Yang Sihua , Shi Yujiao
Published: March 2023

Just-in-time burn severity assessment plays a vital role in burn treatment and care. However, it is still difficult to quantitatively and promptly evaluate burn severity by existing medical imaging methods via initial burn depth measurement since burn wounds are usually dynamically developed. As an elastic skeleton of skin, the degree of conformational changes of collagen fibers caused by overheating can reflect the burn severity in a timelier manner. Herein, the polarized photoacoustic technique (PPAT) for just-in-time quantitative evaluation of burn severity via collagen fiber anisotropy assessment is proposed. First, phantom experiments demonstrate the ability of PPAT for deep imaging in a transport mean free path and accurately quantify changes in microstructural order by thermal damage. Then, the Pearson correlation coefficient of the PPAT in assessing burn severity is shown to be up to 0.95, validated by burn skin samples. The PPAT provides a just-in-time quantitative strategy for burn severity evaluation.
An AI-guided screen identifies probucol as an enhancer of mitophagy through modulation of lipid droplets
Authors: Moskal Natalia , Visanji Naomi P. , Gorbenko Olena , Narasimhan Vijay , Tyrrell Hannah , Nash Jess , Lewis Peter N. , McQuibban G. Angus
Published: March 2023

Failures in mitophagy, a process by which damaged mitochondria are cleared, results in neurodegeneration, while enhancing mitophagy promotes the survival of dopaminergic neurons. Using an artificial intelligence platform, we employed a natural language processing approach to evaluate the semantic similarity of candidate molecules to a set of well-established mitophagy enhancers. Top candidates were screened in a cell-based mitochondrial clearance assay. Probucol, a lipid-lowering drug, was validated across several orthogonal mitophagy assays. In vivo, probucol improved survival, locomotor function, and dopaminergic neuron loss in zebrafish and fly models of mitochondrial damage. Probucol functioned independently of PINK1/Parkin, but its effects on mitophagy and in vivo depended on ABCA1, which negatively regulated mitophagy following mitochondrial damage. Autophagosome and lysosomal markers were elevated by probucol treatment in addition to increased contact between lipid droplets (LDs) and mitochondria. Conversely, LD expansion, which occurs following mitochondrial damage, was suppressed by probucol and probucol-mediated mitophagy enhancement required LDs. Probucol-mediated LD dynamics changes may prime the cell for a more efficient mitophagic response to mitochondrial damage.
A succession of two viral lattices drives vaccinia virus assembly
Authors: Hernandez-Gonzalez Miguel , Calcraft Thomas , Nans Andrea , Rosenthal Peter B , Way Michael
Published: March 2023

During its cytoplasmic replication, vaccinia virus assembles non-infectious spherical immature virions (IV) coated by a viral D13 lattice. Subsequently, IV mature into infectious brick-shaped intracellular mature virions (IMV) that lack D13. Here, we performed cryo-electron tomography (cryo-ET) of frozen-hydrated vaccinia-infected cells to structurally characterise the maturation process in situ. During IMV formation, a new viral core forms inside IV with a wall consisting of trimeric pillars arranged in a new pseudohexagonal lattice. This lattice appears as a palisade in cross-section. As maturation occurs, which involves a 50% reduction in particle volume, the viral membrane becomes corrugated as it adapts to the newly formed viral core in a process that does not appear to require membrane removal. Our study suggests that the length of this core is determined by the D13 lattice and that the consecutive D13 and palisade lattices control virion shape and dimensions during vaccinia assembly and maturation.
A field-wide assessment of differential expression profiling by high-throughput sequencing reveals widespread bias
Authors: Päll Taavi , Luidalepp Hannes , Tenson Tanel , Maiväli Ülo
Published: March 2023

We assess inferential quality in the field of differential expression profiling by high-throughput sequencing (HT-seq) based on analysis of datasets submitted from 2008 to 2020 to the NCBI GEO data repository. We take advantage of the parallel differential expression testing over thousands of genes, whereby each experiment leads to a large set of p-values, the distribution of which can indicate the validity of assumptions behind the test. From a well-behaved p-value set π0, the fraction of genes that are not differentially expressed can be estimated. We found that only 25% of experiments resulted in theoretically expected p-value histogram shapes, although there is a marked improvement over time. Uniform p-value histogram shapes, indicative of <100 actual effects, were extremely few. Furthermore, although many HT-seq workflows assume that most genes are not differentially expressed, 37% of experiments have π0-s of less than 0.5, as if most genes changed their expression level. Most HT-seq experiments have very small sample sizes and are expected to be underpowered. Nevertheless, the estimated π0-s do not have the expected association with N, suggesting widespread problems of experiments with controlling false discovery rate (FDR). Both the fractions of different p-value histogram types and the π0 values are strongly associated with the differential expression analysis program used by the original authors. While we could double the proportion of theoretically expected p-value distributions by removing low-count features from the analysis, this treatment did not remove the association with the analysis program. Taken together, our results indicate widespread bias in the differential expression profiling field and the unreliability of statistical methods used to analyze HT-seq data.
A mentorship and incubation program using project-based learning to build a professional bioinformatics pipeline in Kenya
Authors: Nanjala Ruth , Nyasimi Festus , Masiga Daniel , Kibet Caleb Kipkurui
Published: March 2023

The demand for well-trained bioinformaticians to support genomics research continues to rise. Unfortunately, undergraduate training in Kenya does not prepare students for specialization in bioinformatics. Graduates are often unaware of the career opportunities in bioinformatics, and those who are may lack mentors to help them choose a specialization. The Bioinformatics Mentorship and Incubation Program seeks to bridge the gap by laying the foundation for a bioinformatics training pipeline using project-based learning. The program selects six participants through an intensive open recruitment exercise for highly competitive students to join the program for four months. The six interns undergo intensive training within the first one and a half months before being assigned to mini-projects. We track the progress of the interns weekly through code review sessions and a final presentation at the end of the four months. We have trained five cohorts, most of whom have secured master’s scholarships within and outside the country and job opportunities. We demonstrate the benefit of structured mentorship using project-based learning in filling the training gap after undergraduate programs to generate well-trained bioinformaticians who are competitive in graduate programs and bioinformatics jobs.
Assembling the perfect bacterial genome using Oxford Nanopore and Illumina sequencing
Authors: Wick Ryan R. , Judd Louise M. , Holt Kathryn E.
Published: March 2023

A perfect bacterial genome assembly is one where the assembled sequence is an exact match for the organism’s genome—each replicon sequence is complete and contains no errors. While this has been difficult to achieve in the past, improvements in long-read sequencing, assemblers, and polishers have brought perfect assemblies within reach. Here, we describe our recommended approach for assembling a bacterial genome to perfection using a combination of Oxford Nanopore Technologies long reads and Illumina short reads: Trycycler long-read assembly, Medaka long-read polishing, Polypolish short-read polishing, followed by other short-read polishing tools and manual curation. We also discuss potential pitfalls one might encounter when assembling challenging genomes, and we provide an online tutorial with sample data (github.com/rrwick/perfect-bacterial-genome-tutorial).
The effect of supervision on community health workers’ effectiveness with households in rural South Africa: A cluster randomized controlled trial
Authors: Rotheram-Borus Mary Jane , le Roux Karl W. , Norwood Peter , Stansert Katzen Linnea , Snyman Andre , le Roux Ingrid , Dippenaar Elaine , Tomlinson Mark
Published: March 2023

Background

Community health workers (CHWs) can supplement professional medical providers, especially in rural settings where resources are particularly scarce. Yet, outcomes of studies evaluating CHWs effectiveness have been highly variable and lack impact when scaled nationally. This study examines if child and maternal outcomes are better when existing government CHWs, who are perinatal home visitors, receive ongoing enhanced supervision and monitoring, compared to standard care.

Methods and findings

A cluster randomized controlled effectiveness trial was conducted comparing outcomes over 2 years when different supervision and support are provided. Primary health clinics were randomized by clinic to receive monitoring and supervision from either (1) existing supervisors (Standard Care (SC);n= 4 clinics, 23 CHWs, 392 mothers); or (2) supervisors from a nongovernmental organization that provided enhanced monitoring and supervision (Accountable Care [AC];n =4 clinic areas, 20 CHWs, 423 mothers). Assessments were conducted during pregnancy and at 3, 6, 15, and 24 months post-birth with high retention rates (76% to 86%). The primary outcome was the number of statistically significant intervention effects among 13 outcomes of interest; this approach allowed us to evaluate the intervention holistically while accounting for correlation among the 13 outcomes and considering multiple comparisons.

The observed benefits were not statistically significant and did not show the AC’s efficacy over the SC. Only the antiretroviral (ARV) adherence effect met the significance threshold established a priori (SC mean 2.3, AC mean 2.9,p< 0.025; 95% CI = [0.157, 1.576]). However, for 11 of the 13 outcomes, we observed an improvement in the AC compared to the SC. While the observed outcomes were not statistically significant, benefits were observed for 4 outcomes: increasing breastfeeding for 6 months, reducing malnutrition, increasing ARV adherence, and improving developmental milestones. The major study limitation was utilizing existing CHWs and being limited to a sample of 8 clinics. There were no major study-related adverse events.

Conclusions

Supervision and monitoring were insufficient to improve CHWs’ impact on maternal and child outcomes. Alternative strategies for staff recruitment and narrowing the intervention outcomes to the specific local community problems are needed for consistently high impact.

Trial registration

Clinicaltrials.gov,NCT02957799.
Qualitative evaluation of rapid implementation of remote blood pressure self-monitoring in pregnancy during Covid-19
Authors: Paterson Charlotte , Jack Elaine , McKinstry Brian , Whyte Sonia , Denison Fiona C. , Cheyne Helen
Published: March 2023

In March 2020, the World Health Organisation named the severe acute respiratory syndrome coronavirus 2 (Sars-CoV-2), which causes corona virus disease 2019 (COVID –19), as a pandemic. Pregnant women were considered at increased risk of developing severe COVID-19 after viral infection. In response maternity services reduced face-to-face consultations with high-risk pregnant women by supplying blood pressure monitors for supported self-monitoring. This paper explores the experiences of patients and clinicians of the rapid roll-out of supported self-monitoring programme in Scotland during the first and second wave of the COVID-19 pandemic. We conducted semi-structured telephone interviews with high-risk women and healthcare professionals who were using supported self-monitoring of blood pressure (BP) In four case studies during the COVID-19 pandemic. 20 women, 15 midwives and 4 obstetricians took part in the interviews. Interviews with healthcare professionals showed that while implementation occurred at pace and at scale across the National Health Service (NHS) in Scotland, implementation differed locally, resulting in mixed experiences. Study Participants observed several barriers and facilitators to implementation. Women value the simplicity of use and convenience of the digital communications platforms while health professionals were more interested in their impact on reducing workload for both women and health professionals largely found self-monitoring acceptable, with only a few exceptions. These results show that rapid change can occur in the NHS at a national level when there is a shared motivation. While self-monitoring is acceptable to most women, decisions regarding self-monitoring should be made jointly and on an individual basis.
Impact of gender on mid-term prognosis of patients undergoing coronary artery bypass grafting
Authors: Jang Woo Jin , Choi Ki Hong , Kim Jihoon , Yang Jeong Hoon , Hahn Joo-Yong , Choi Seung-Hyuk , Gwon Hyeon-Cheol , Cho Yang Hyun , Sung Kiick , Kim Wook Sung , Jeong Dong Seop , Song Young Bin
Published: March 2023

Objectives

We evaluated the impact of sex on mid-term prognosis in patients who underwent coronary artery bypass grafting (CABG). Data on gender differences in current management or clinical outcomes after CABG are controversial, and there have been limited data focusing on them.

Methods

This was a retrospective and prospective, single-center, observational study. Between January 2001 and December 2017, 6613 patients who underwent CABG were enrolled from an institutional registry of Samsung Medical Center, Seoul, Korea (Clinicaltrials.gov, NCT03870815) and divided into two groups according to sex (female group, n = 1679 vs. male group, n = 4934). The primary outcome was cardiovascular death or myocardial infarction (MI) at 5 years. Propensity score matching analysis was performed to reduce confounding factors.

Results

During a mean follow-up duration of 54 months, a total of 252 cardiovascular death or MIs occurred (female, 78 [7.5%] vs. male, 174 [5.7%]). Multivariate analysis revealed no significant difference in the incidence of cardiovascular death or MI at 5 years between female and male groups (hazard ratio [HR] 1.05; 95% confidence interval [CI] 0.78 to 1.41; p = 0.735). After propensity score matching, the incidence of cardiovascular death or MI was still similar between the two groups (HR 1.08; 95% CI 0.76 to 1.54; p = 0.666). The similarity of long-term outcomes between the two groups was consistent across various subgroups. There was also no significant difference in the risk of 5-year cardiovascular death or MI between males and females according to age (pre- and postmenopausal status) (p for interaction = 0.437).

Conclusions

After adjusting for baseline differences, sex does not appear to influence long-term risk of cardiovascular death or MI in patients undergoing CABG.

Clinical trials.gov number

NCT03870815.
Vascular density and macular sensitivity in eyes after scleral buckling surgery for macula-on rhegmatogenous retinal detachment
Authors: Zabel Przemyslaw , Zabel Katarzyna , Kazmierczak Karolina , Stankiewicz Martyna , Jaworski Damian , Suwala Karolina , Buszko Katarzyna , Stafiej Joanna , Malukiewicz Grazyna , Kaluzny Jakub J.
Published: March 2023

Purpose

To investigate the structure and function of the retina after scleral buckling (SB) surgery due to macula-on rhegmatogenous retinal detachment (RRD).

Methods

Twenty eyes with repaired macula-on RRD and 20 fellow eyes were included. All patients within 6–12 months of the procedure, were examined to evaluate retinal structure using spectral domain optical coherence tomography (SD-OCT) and vessel density (VD) by OCT angiography (OCTA). Best corrected visual acuity (BCVA) and microperimetry (MP) tests were used to assess retinal function.

Results

Analysis of the microvascular network using OCTA between the operated and healthy fellow eyes showed a significant reduction on VD in superficial vascular plexus (SVP), deep vascular plexus (DVP) and radial peripapillary capillaries (RPC) (p< 0.001, p = 0.019 and p = 0.008, respectively). Comparison of retinal structure in SD-OCT showed no significant differences on thickness in ganglion cell complex (GCC) and peripaillary retinal nerve fiber layer (pRNFL) (p> 0.05) between examined eyes. Retinal function analysis by MP examination showed a decrease of retinal sensitivity (p = 0.0013) whereas postoperative BCVA showed no differences (p = 0.62) in the operated eyes. Significant Pearson’s correlations were observed between retinal sensitivity and VD in SVP, RPC (p< 0.05).

Conclusion

In the eyes after SB surgery due to macula-on RRD, changes in retinal sensitivity were accompanied by impairment of the microvascular network assessed by the OCTA.
The mediating role of anxiety between negative feelings and depression among students with congenital physical disabilities
Authors: Uwimbabazi Marie Paule , Muziki Jean d’Amour , Muhayisa Assumpta , Uwera Thaoussi , Mutabaruka Jean
Published: March 2023

Congenital physical disability is associated with various psychological challenges, including negative feelings, anxiety, and stress. These challenges will, in turn, predict significant negative emotional well-being among students with congenital physical disabilities, but the mechanisms of these effects are not well known. This study examined whether Negative Emotional Wellbeing Anxiety (NEWA) would mediate the effect of Negative Feelings (NF) and Negative Emotional Wellbeing Depression (NEWD) among students with congenital physical disabilities. Forty-six students with congenital physical disabilities (mean age: 20 years, SD = 2.05; 45.65% females) completed self-rating measures that included sociodemographic variables (age and sex), emotional state for Children to assess negative feelings, and an emotional distress protocol to assess NEWA and NEWD. Results show that NF was positively correlated with NEWA (r = .69, p < .001) and NEWD (r = .69, p < .001), and NEWA was positively correlated with NEWD (r = .86, p < .001). Findings further reported that NEWA significantly mediated the positive relationship between NF and NEWD (a*b = .37, Bootstrap CI95 = .23 and .52) [Sobel test statistic of 4.82 (p < .001)] among students with congenital physical disabilities. The results highlight the importance of screening students with congenital physical disabilities for common psychological challenges and providing suitable interventions.
Imaging breast malignancies with the Twente Photoacoustic Mammoscope 2
Authors: Schoustra S. M. , De Santi B. , op ’t Root T. J. P. M. , Klazen C. A. H. , van der Schaaf M. , Veltman J. , Steenbergen W. , Manohar S.
Published: March 2023

Clinical measurements on breast cancer patients were performed with a three-dimensional tomographic photoacoustic prototype imager (PAM 2). Patients with a suspicious lesion, visiting the center for breast care of a local hospital, were included in the study. The acquired photoacoustic images were compared to conventional clinical images. Of 30 scanned patients, 19 were diagnosed with one or more malignancies, of which a subset of four patients was selected for detailed analysis. Reconstructed images were processed to enhance image quality and the visibility of blood vessels. Processed photoacoustic images were compared to contrast-enhanced magnetic resonance images where available, which aided in localizing the expected tumoral region. In two cases, spotty high-intensity photoacoustic signals could be seen in the tumoral region, attributable to the tumor. One of these cases also displayed a relatively high image entropy at the tumor site, likely related to the chaotic vascular networks associated with malignancies. For the other two cases, it was not possible to identify features indicative of malignancy, because of limitations in the illumination scheme and difficulties in locating the region of interest in the photoacoustic image.
Pentraxin 3 in the cerebrospinal fluid during central nervous system infections: A retrospective cohort study
Authors: Thomsen Martin Munthe , Munthe-Fog Lea , Trier Petersen Pelle , Hillig Thore , Friis-Hansen Lennart Jan , Roed Casper , Harboe Zitta Barrella , Brandt Christian Thomas
Published: March 2023

The present study describes diagnostic and prognostic abilities of Cerebrospinal fluid (CSF) Pentraxin 3 (PTX3) in central nervous system (CNS) infections. CSF PTX3 was measured retrospectively from 174 patients admitted under suspicion of CNS infection. Medians, ROC curves and Youdens index was calculated. CSF PTX3 was significantly higher among all CNS infections and undetectable in most of the patients in the control group, and significantly higher in bacterial infections compared to viral and Lyme infections. No association was found between CSF PTX3 and Glasgow Outcome Score. PTX3 in the CSF can distinguish bacterial infection from viral and Lyme infections and non-CNS infections. Highest levels were found in bacterial meningitis. No prognostic abilities were found.
Robust framework for COVID-19 identication from a multicenter dataset of chest CT scans
Authors: Khademi Sadaf , Heidarian Shahin , Afshar Parnian , Enshaei Nastaran , Naderkhani Farnoosh , Rafiee Moezedin Javad , Oikonomou Anastasia , Shafiee Akbar , Babaki Fard Faranak , plataniotis Konstantinos N. , Mohammadi Arash
Published: March 2023

The main objective of this study is to develop a robust deep learning-based framework to distinguish COVID-19, Community-Acquired Pneumonia (CAP), and Normal cases based on volumetric chest CT scans, which are acquired in different imaging centers using different scanners and technical settings. We demonstrated that while our proposed model is trained on a relatively small dataset acquired from only one imaging center using a specific scanning protocol, it performs well on heterogeneous test sets obtained by multiple scanners using different technical parameters. We also showed that the model can be updated via an unsupervised approach to cope with the data shift between the train and test sets and enhance the robustness of the model upon receiving a new external dataset from a different center. More specifically, we extracted the subset of the test images for which the model generated a confident prediction and used the extracted subset along with the training set to retrain and update the benchmark model (the model trained on the initial train set). Finally, we adopted an ensemble architecture to aggregate the predictions from multiple versions of the model. For initial training and development purposes, an in-house dataset of 171 COVID-19, 60 CAP, and 76 Normal cases was used, which contained volumetric CT scans acquired from one imaging center using a single scanning protocol and standard radiation dose. To evaluate the model, we collected four different test sets retrospectively to investigate the effects of the shifts in the data characteristics on the model’s performance. Among the test cases, there were CT scans with similar characteristics as the train set as well as noisy low-dose and ultra-low-dose CT scans. In addition, some test CT scans were obtained from patients with a history of cardiovascular diseases or surgeries. This dataset is referred to as the “SPGC-COVID” dataset. The entire test dataset used in this study contains 51 COVID-19, 28 CAP, and 51 Normal cases. Experimental results indicate that our proposed framework performs well on all test sets achieving total accuracy of 96.15% (95%CI: [91.25–98.74]), COVID-19 sensitivity of 96.08% (95%CI: [86.54–99.5]), CAP sensitivity of 92.86% (95%CI: [76.50–99.19]), Normal sensitivity of 98.04% (95%CI: [89.55–99.95]) while the confidence intervals are obtained using the significance level of 0.05. The obtained AUC values (One class vs Others) are 0.993 (95%CI: [0.977–1]), 0.989 (95%CI: [0.962–1]), and 0.990 (95%CI: [0.971–1]) for COVID-19, CAP, and Normal classes, respectively. The experimental results also demonstrate the capability of the proposed unsupervised enhancement approach in improving the performance and robustness of the model when being evaluated on varied external test sets.
Hospital-wide survey of clinical experience with artificial intelligence applied to daily chest radiographs
Authors: Shin Hyun Joo , Lee Seungsoo , Kim Sungwon , Son Nak-Hoon , Kim Eun-Kyung
Published: March 2023

Purpose

To assess experience with and perceptions of clinical application of artificial intelligence (AI) to chest radiographs among doctors in a single hospital.

Materials and methods

A hospital-wide online survey of the use of commercially available AI-based lesion detection software for chest radiographs was conducted with all clinicians and radiologists at our hospital in this prospective study. In our hospital, version 2 of the abovementioned software was utilized from March 2020 to February 2021 and could detect three types of lesions. Version 3 was utilized for chest radiographs by detecting nine types of lesions from March 2021. The participants of this survey answered questions on their own experience using AI-based software in daily practice. The questionnaires were composed of single choice, multiple choices, and scale bar questions. Answers were analyzed according to the clinicians and radiologists using paired t-test and the Wilcoxon rank-sum test.

Results

One hundred twenty-three doctors answered the survey, and 74% completed all questions. The proportion of individuals who utilized AI was higher among radiologists than clinicians (82.5% vs. 45.9%, p = 0.008). AI was perceived as being the most useful in the emergency room, and pneumothorax was considered the most valuable finding. Approximately 21% of clinicians and 16% of radiologists changed their own reading results after referring to AI, and trust levels for AI were 64.9% and 66.5%, respectively. Participants thought AI helped reduce reading times and reading requests. They answered that AI helped increase diagnostic accuracy and were more positive about AI after actual usage.

Conclusion

Actual adaptation of AI for daily chest radiographs received overall positive feedback from clinicians and radiologists in this hospital-wide survey. Participating doctors preferred to use AI and regarded it more favorably after actual working with the AI-based software in daily clinical practice.
Creation of an ustekinumab external control arm for Crohn’s disease using electronic health records data: A pilot study
Authors: Rudrapatna Vivek A. , Cheng Yao-Wen , Feuille Colin , Mosenia Arman , Shih Jonathan , Shi Yongmei , Roberson Olivia , Rubin Benjamin , Butte Atul J. , Mahadevan Uma , Skomrock Nicholas , Erondu Ngozi , Chehoud Christel , Rahim Saquib , Apfel David , Curran Mark , Khan Najat S. , O’Brien Christopher , Terry Natalie , Martini Benjamin D.
Published: March 2023

Background

Randomized trials are the gold-standard for clinical evidence generation, but they can sometimes be limited by infeasibility and unclear generalizability to real-world practice. External control arm (ECA) studies may help address this evidence gaps by constructing retrospective cohorts that closely emulate prospective ones. Experience in constructing these outside the context of rare diseases or cancer is limited. We piloted an approach for developing an ECA in Crohn’s disease using electronic health records (EHR) data.

Methods

We queried EHR databases and manually screened records at the University of California, San Francisco to identify patients meeting the eligibility criteria of TRIDENT, a recently completed interventional trial involving an ustekinumab reference arm. We defined timepoints to balance missing data and bias. We compared imputation models by their impacts on cohort membership and outcomes. We assessed the accuracy of algorithmic data curation against manual review. Lastly, we assessed disease activity following treatment with ustekinumab.

Results

Screening identified 183 patients. 30% of the cohort had missing baseline data. Nonetheless, cohort membership and outcomes were robust to the method of imputation. Algorithms for ascertaining non-symptom-based elements of disease activity using structured data were accurate against manual review. The cohort consisted of 56 patients, exceeding planned enrollment in TRIDENT. 34% of the cohort was in steroid-free remission at week 24.

Conclusion

We piloted an approach for creating an ECA in Crohn’s disease from EHR data by using a combination of informatics and manual methods. However, our study reveals significant missing data when standard-of-care clinical data are repurposed. More work will be needed to improve the alignment of trial design with typical patterns of clinical practice, and thereby enable a future of more robust ECAs in chronic diseases like Crohn’s disease.
Development of retinal structure in perinatally HIV-infected children and adolescents: A longitudinal and cross-sectional assessment
Authors: van Genderen Jason G. , Verkade Charissa R. , Van den Hof Malon , Demirkaya Nazli , Schrantee Anouk G. M. , Verbraak Frank D. , Pajkrt Dasja
Published: March 2023

In perinatally HIV-infected (PHIV) children, cross-sectional studies reported on subtle structural retinal differences and found associations between the retina and structural brain changes. Our objective is to investigate whether neuroretinal development in PHIV children is similar to the development in healthy matched controls and to explore associations with the brain structure. We measured RT using optical coherence tomography (OCT) on two occasions in 21 PHIV children or adolescents and 23 matched controls–all with good visual acuity–with a mean interval of 4.6 years (SD 0.3). We also included 22 participants (11 PHIV children and 11 controls) together with the follow-up group for a cross-sectional assessment using a different OCT device. Magnetic resonance imaging (MRI) was used to assess the white matter microstructure. We used linear (mixed) models to assess changes in RT and its determinants (over time), adjusting for age and sex. The development of the retina was similar between the PHIV adolescents and controls. In our cohort, we found that changes in the peripapillary RNFL was significantly associated with changes in WM microstructural makers: fractional anisotropy (coefficient = 0.030, p = 0.022) and radial diffusivity (coefficient = -0.568, p = 0.025). We found comparable RT between groups. A thinner pRNFL was associated with lower WM volume (coefficient = 0.117, p = 0.030). PHIV children or adolescents appear to have a similar development of the retinal structure. In our cohort, the associations between RT and MRI biomarkers underscore the relation between retina and brain.
YOLOv5-LiNet: A lightweight network for fruits instance segmentation
Authors: Lawal Olarewaju Mubashiru
Published: March 2023

To meet the goals of computer vision-based understanding of images adopted in agriculture for improved fruit production, it is expected of a recognition model to be robust against complex and changeable environment, fast, accurate and lightweight for a low power computing platform deployment. For this reason, a lightweight YOLOv5-LiNet model for fruit instance segmentation to strengthen fruit detection was proposed based on the modified YOLOv5n. The model included Stem, Shuffle_Block, ResNet and SPPF as backbone network, PANet as neck network, and EIoU loss function to enhance detection performance. YOLOv5-LiNet was compared to YOLOv5n, YOLOv5-GhostNet, YOLOv5-MobileNetv3, YOLOv5-LiNetBiFPN, YOLOv5-LiNetC, YOLOv5-LiNet, YOLOv5-LiNetFPN, YOLOv5-Efficientlite, YOLOv4-tiny and YOLOv5-ShuffleNetv2 lightweight model including Mask-RCNN. The obtained results show that YOLOv5-LiNet having the box accuracy of 0.893, instance segmentation accuracy of 0.885, weight size of 3.0 MB and real-time detection of 2.6 ms combined together outperformed other lightweight models. Therefore, the YOLOv5-LiNet model is robust, accurate, fast, applicable to low power computing devices and extendable to other agricultural products for instance segmentation.
Fluoropyrimidine combination therapy versus fluoropyrimidine monotherapy for gemcitabine-refractory advanced pancreatic cancer: A systematic review and meta-analysis of randomized controlled trials
Authors: Tian Wei , Zhang Lina , Liu Xiao , Ma Xiao , Wang Rui
Published: March 2023

Objectives

Fluoropyrimidine-based regimens have been investigated as the second line chemotherapy in patients with advanced pancreatic cancer refractory to gemcitabine. We conducted this systematic review and meta-analysis to evaluate the efficacy and safety profile of fluoropyrimidine combination therapy versus fluoropyrimidine monotherapy in such patients.

Methods

The databases of MEDLINE, EMBASE, Cochrane Central Register of Controlled Trials, ASCO Abstracts and ESMO Abstracts were systematically searched. Randomized controlled trials (RCTs) that compared fluoropyrimidine combination therapy versus fluoropyrimidine monotherapy in patients with gemcitabine-refractory advanced pancreatic cancer were included. The primary outcome was overall survival (OS). Secondary outcomes included progression-free survival (PFS), overall response rate (ORR) and serious toxicities. Statistical analyses were performed by using Review Manager 5.3. Egger’s test was performed to assess the statistical evidence of publication bias by using stata 12.0.

Results

A total of 1183 patients from six randomized controlled trials were included for this analysis. Fluoropyrimidine combination therapy increased ORR [RR 2.82 (1.83–4.33), p<0.00001] and PFS [HR 0.71 (0.62–0.82), p<0.00001], without significant heterogeneity. Fluoropyrimidine combination therapy improved OS [HR 0.82 (0.71–0.94), p = 0.006], with significant heterogeneity (I2 = 76%, p = 0.0009). The significant heterogeneity might have been caused by the different administration regimens and baseline characteristics. Peripheral neuropathy and diarrhea were more common in the regimens containing oxaliplatin and irinotecan, respectively. No publication bias was detected by Egger’s tests.

Conclusions

Compared with fluoropyrimidine monotherapy, fluoropyrimidine combination therapy had a higher response rate and longer PFS in patients with gemcitabine-refractory advanced pancreatic cancer. Fluoropyrimidine combination therapy could be recommended in the second line setting. However, due to concerns about toxicities, the dose intensities of chemotherapy drugs should be carefully considered in patients with weakness.
cnm-positive Streptococcus mutans is associated with galactose-deficient IgA in patients with IgA nephropathy
Authors: Misaki Taro , Naka Shuhei , Suzuki Hitoshi , Lee Mingfeng , Aoki Ryosuke , Nagasawa Yasuyuki , Matsuoka Daiki , Ito Seigo , Nomura Ryota , Matsumoto-Nakano Michiyo , Suzuki Yusuke , Nakano Kazuhiko
Published: March 2023

The presence of Streptococcus mutans expressing Cnm protein encoded by cnm (cnm-positive S. mutans) in the oral cavity is associated with immunoglobulin A (IgA) nephropathy (IgAN). However, the precise mechanism by which cnm-positive S. mutans is involved in the pathogenesis of IgAN remains unclear. The present study evaluated glomerular galactose-deficient IgA1 (Gd-IgA1) to clarify the association between the presence of cnm-positive S. mutans and glomerular Gd-IgA1 in patients with IgAN. The presence of S. mutans and cnm-positive S. mutans was evaluated by polymerase chain reaction in saliva specimens from 74 patients with IgAN or IgA vasculitis. Immunofluorescent staining of IgA and Gd-IgA1 using KM55 antibody in clinical glomerular tissues was then performed. There was no significant association between the glomerular staining intensity of IgA and the positive rate of S. mutans. However, there was a significant association between the glomerular staining intensity of IgA and the positive rate of cnm-positive S. mutans (P < 0.05). There was also a significant association between the glomerular staining intensity of Gd-IgA1 (KM55) and the positive rate of cnm-positive S. mutans (P < 0.05). The glomerular staining intensity of Gd-IgA1 (KM55) was not associated with the positive rate of S. mutans. These results suggest that cnm-positive S. mutans in the oral cavity is associated with the pathogenesis of Gd-IgA1 in patients with IgAN.
Toward characterizing cardiovascular fitness using machine learning based on unobtrusive data
Authors: Frade Maria Cecília Moraes , Beltrame Thomas , Gois Mariana de Oliveira , Pinto Allan , Tonello Silvia Cristina Garcia de Moura , Torres Ricardo da Silva , Catai Aparecida Maria
Published: March 2023

Cardiopulmonary exercise testing (CPET) is a non-invasive approach to measure the maximum oxygen uptake (V˙O2−max), which is an index to assess cardiovascular fitness (CF). However, CPET is not available to all populations and cannot be obtained continuously. Thus, wearable sensors are associated with machine learning (ML) algorithms to investigate CF. Therefore, this study aimed to predict CF by using ML algorithms using data obtained by wearable technologies. For this purpose, 43 volunteers with different levels of aerobic power, who wore a wearable device to collect unobtrusive data for 7 days, were evaluated by CPET. Eleven inputs (sex, age, weight, height, and body mass index, breathing rate, minute ventilation, total hip acceleration, walking cadence, heart rate, and tidal volume) were used to predict the V˙O2−max by support vector regression (SVR). Afterward, the SHapley Additive exPlanations (SHAP) method was used to explain their results. SVR was able to predict the CF, and the SHAP method showed that the inputs related to hemodynamic and anthropometric domains were the most important ones to predict the CF. Therefore, we conclude that the cardiovascular fitness can be predicted by wearable technologies associated with machine learning during unsupervised activities of daily living.
Exploring the experiences and views of doctors working with Artificial Intelligence in English healthcare; a qualitative study
Authors: Ganapathi Shaswath , Duggal Sandhya
Published: March 2023

Background

The National Health Service (NHS) aspires to be a world leader of Artificial Intelligence (AI) in healthcare, however, there are several barriers facing translation and implementation. A key enabler of AI within the NHS is the education and engagement of doctors, however evidence suggests that there is an overall lack of awareness of and engagement with AI.

Research aim

This qualitative study explores the experiences and views of doctor developers working with AI within the NHS exploring; their role within medical AI discourse, their views on the implementation of AI more widely and how they consider the engagement of doctors with AI technologies may increase in the future.

Methods

This study involved eleven semi-structured, one-to-one interviews conducted with doctors working with AI in English healthcare. Data was subjected to thematic analysis.

Results

The findings demonstrate that there is an unstructured pathway for doctors to enter the field of AI. The doctors described the various challenges they had experienced during their career, with many arising from the differing demands of operating in a commercial and technological environment. The perceived awareness and engagement among frontline doctors was low, with two prominent barriers being the hype surrounding AI and a lack of protected time. The engagement of doctors is vital for both the development and adoption of AI.

Conclusions

AI offers big potential within the medical field but is still in its infancy. For the NHS to leverage the benefits of AI, it must educate and empower current and future doctors. This can be achieved through; informative education within the medical undergraduate curriculum, protecting time for current doctors to develop understanding and providing flexible opportunities for NHS doctors to explore this field.