bluuebunny/crossref_metadata_2025 huggingface dataset:
Seabed classification and source localization from ship spectrograms using deep learning models
Authors: Castro-Correa Jhon A. , Escobar-Amado Christian D. , Badiey Mohsen , Neilsen Tracianne B. , Knobles David P.
Published: November 2021

An 18-layer residual neural network (ResNet-18) and a convolutional neural network (CNN) are used for source localization and seabed classification using broadband spectrograms obtained from ship-radiated noise. The propagation of the broadband noise from those ships of opportunity (SOO) contains significant information about the waveguide and seafloor. In this work, a ResNet-18 and a CNN are trained using multi-task learning to estimate the closest point of approach, ship speed, and seabed type. Training data are simulated using a range-independent normal modes model and several sediment profiles obtained by inversions in different regions. The input data samples correspond to 20 min long broadband spectrograms in the 300–1500 Hz band. During the training stage, data augmentation techniques are also applied to evaluate their effects on the predictions. The metrics used to evaluate performance are accuracy for seabed classification and root mean square error for source localization. Results demonstrate the ability of deep learning models to estimate source localization and seabed classification along with the impact of data augmentation techniques using SOO spectrograms. [Work supported by ONR, Contract No. N00014-19-C-2001.]
Three-dimensional cavitation mapping in shock wave and laser lithotripsy
Authors: Li Mucong , Sankin Georgy , Vu Tri , Jing Yun , Zhong Pei , Yao Junjie
Published: November 2021

Shock wave lithotripsy (SWL) and laser lithotripsy (LL) have been widely used for non-invasive treatment of kidney stones. Cavitation plays an important role in stone fragmentation, yet it may also contribute to renal injury during SWL and LL. It is therefore crucial to determine the spatiotemporal distributions of cavitation activities to maximize stone fragmentation while minimizing tissue injury. Traditional cavitation detection methods include high-speed optical imaging, active cavitation mapping (ACM), and passive cavitation mapping (PCM), among which PCM has most practical applications in biological tissues. To image the dynamics of cavitation bubble collapse, we have developed tri-modality cavitation imaging that includes 3D high-speed optical imaging, ACM, and PCM seamlessly integrated in a single imaging system. We also developed a transient angular spectrum approach for PCM reconstruction, which is ten times faster than the traditional delay-and-sum method. Using the tri-modality system, we imaged and analyzed laser-induced single cavitation bubbles in both free field and constricted space and shock wave-induced cavitation clusters. Collectively, our results have demonstrated the high reliability and spatial-temporal accuracy of the 3D PCM approach, which paves the way for future in vivo applications in large animals and human studies during SWL and LL.
Particle swarm optimization of the manipulation of acoustic waves through nonhomogeneous, anisotropic mediums for application in shock wave lithotripsy
Authors: Roemhildt Joseph J. , Fan Jiadi , Wang Ziping , Sang Sheng
Published: November 2021

Shock Wave Lithotripsy is the most widely used treatment for kidney stones, a fragmentation process using shock waves generated outside the body that are focused onto the stone. However, the nonhomogenous, anisotropic nature of the human body causes the waves to be refracted, which can lead to less efficient fracturing of the kidney stone, requiring longer or more frequent treatment sessions, and increased risks of side effects from treatment. In this paper, a Particle Swarm Optimization (PSO) algorithm was utilized to program wave generators using a swarm of individual particles representing element configurations, such as amplitude, phase difference, and stimulation parameters. A Finite Element Model of the area between the shockwave generator and the kidneys used to demonstrate how the PSO algorithm can efficiently optimize a multi-objective function that maximizes predictions of activation in the kidney stone (Region of Interest, ROI) and minimizes predictions of activation in the surrounding sensitive tissues (Regions of Avoidance, ROA).
Flexible ultrasound-based system for clinical trial of burst wave lithotripsy and pushing of kidney stones
Authors: Kuznetsova Ekaterina , Bailey Michael R. , Cunitz Bryan W. , Dunmire Barbrina , Kim Ga Won , Lynch Elizabeth , Maxwell Adam
Published: November 2021

Fragmentation of kidney stones by burst-wave lithotripsy (BWL) has shown promising results in preclinical and clinical trials. Based on initial findings, the system was upgraded to enhance imaging, target stones at deeper depths, fragment small stones, and potentially conduct dusting of stones. A 64-element, single-crystal, phased-array imaging probe is coaxially aligned with the therapy probe for image guidance and therapy feedback. Imaging is controlled through a Verasonics Vantage research ultrasound engine capable of harmonic imaging to enhance stone resolution and contrast. These features improve targeting and endpoint detection, particularly for small stones and fragments. New therapy probes were added to effectively target stones with greater skin-to-stone distance, including a higher (800 kHz) frequency transducer to effectively break <4mm stones into sub-millimeter fragments to facilitate passage. The amplifier was upgraded to a custom class D/E design with increased power required by the therapy transducers and is capable of ultrasonic propulsion and real time monitoring of electrical power. This system will provide capabilities to treat a larger patient population as we begin trials breaking and expelling stones in the clinic setting. [Work supported by NIH-P01-DK043881.]
Antiaging diets: Separating fact from fiction
Authors: Lee Mitchell B. , Hill Cristal M. , Bitto Alessandro , Kaeberlein Matt
Published: November 2021

Caution around the fountain of youth

The scientific and popular literature is full of claims for diets that delay or reverse the aging process (at least in model organisms). But how do these interventions work? Is it the amount of food, the timing of food intake, the proportion of certain macronutrients? In a Review, Lee
et al
. explore the fact and fiction of dietary prescriptions for a healthier and longer life. They propose that one unifying concept may be convergence on the signaling pathway mediated by the protein kinase mTOR (mechanistic target of rapamycin). Another conclusion is that the efficacy and safety of these diets for humans largely remain to be established. —LBR
Response to Comment on “A global environmental crisis 42,000 years ago”
Authors: Cooper Alan , Turney Chris S. M. , Palmer Jonathan , Hogg Alan , McGlone Matt , Wilmshurst Janet , Lorrey Andrew M. , Heaton Timothy J. , Russell James M. , McCracken Ken , Anet Julien G. , Rozanov Eugene , Friedel Marina , Suter Ivo , Peter Thomas , Muscheler Raimund , Adolphi Florian , Dosseto Anthony , Faith J. Tyler , Fenwick Pavla , Fogwill Christopher J. , Hughen Konrad , Lipson Matthew , Liu Jiabo , Nowaczyk Norbert , Rainsley Eleanor , Bronk Ramsey Christopher , Sebastianelli Paolo , Souilmi Yassine , Stevenson Janelle , Thomas Zoe , Tobler Raymond , Zech Roland
Published: November 2021

Our study on the exact timing and the potential climatic, environmental, and evolutionary consequences of the Laschamps Geomagnetic Excursion has generated the hypothesis that geomagnetism represents an unrecognized driver in environmental and evolutionary change. It is important for this hypothesis to be tested with new data, and encouragingly, none of the studies presented by Picin
et al
. undermine our model.
Antigenic evolution of dengue viruses over 20 years
Authors: Katzelnick Leah C. , Coello Escoto Ana , Huang Angkana T. , Garcia-Carreras Bernardo , Chowdhury Nayeem , Maljkovic Berry Irina , Chavez Chris , Buchy Philippe , Duong Veasna , Dussart Philippe , Gromowski Gregory , Macareo Louis , Thaisomboonsuk Butsaya , Fernandez Stefan , Smith Derek J. , Jarman Richard , Whitehead Stephen S. , Salje Henrik , Cummings Derek A. T.
Published: November 2021

Variations in disease enhancement

Secondary Dengue virus (DENV) infections can be dangerous if levels of antibodies from prior infection are inadequate to clear the virus. This RNA flavivirus exploits the presence of lower levels of heterotypic antibodies to infect immunoglobulin Fcγ receptor–bearing cells. Many RNA viruses also exhibit antigenic variation, which classically allows evasion of immune responses. Katzelnick
et al
. investigated whether antigenic variation in DENV has a biological function in a virus that courts immune responses to enhance replication (see the Perspective by Rohani and Drake). Using antigenic cartography on a panel of more than 400 DENV1-4 subtype samples isolated in Bangkok, Thailand, the authors found that antigenic variation in virus populations oscillated between similarity and dissimilarity across subtypes over time, with outbreaks correlating with periods of antigenic dissimilarity within serotypes. This pattern may be at least in part a result of the conflicting evolutionary pressures of immune evasion and immune enhancement. —CA
A molecular double-slit experiment
Authors: Wang Xingan , Yang Xueming
Published: November 2021

Quantum interaction similar to light interference is observed in molecular collisions
Glasgow pact leaves 1.5°C goal on life support
Authors: O’Grady Cathleen
Published: November 2021

Goal of preventing dangerous warming slipping away, but nations boost emissions cuts
To fight Lyme disease, vaccine targets ticks
Authors: Wadman Meredith
Published: November 2021

Ticks fed poorly, transmitted pathogen less often to guinea pigs given mRNA vaccine
Complete Genome Sequences of Four Soil-Derived Isolates for Studying Synthetic Bacterial Community Assembly
Authors: Lozano-Andrade Carlos N. , Strube Mikael Lenz , Kovács Ákos T.
Published: November 2021

Here, we report the complete genome sequences of four bacterial soil isolates,
Chryseobacterium
sp.,
Stenotrophomonas indicatrix
,
Pedobacter
sp., and
Rhodococcus globerulus
. These isolates can be used for studying microbial interactions and community assembly
in vitro
.
Complete Genome Resequencing of Thermus thermophilus Strain TMY by Hybrid Assembly of Long- and Short-Read Sequencing Technologies
Authors: Miyazaki Kentaro , Tokito Natsuko
Published: November 2021

Complete genome resequencing was conducted for
Thermus thermophilus
strain TMY by hybrid assembly of Oxford Nanopore Technologies long-read and MGI short-read data. Errors in the previously reported genome sequence determined by PacBio technology alone were corrected, allowing for high-quality comparative genomic analysis of closely related
T. thermophilus
genomes.
From crisis to normal science, and back again: Coming full “Kuhn cycle” in the career of Warren B. Hamilton
Authors: Rossetter Thomas
Published: November 2021

In this paper, I use Thomas S. Kuhn’s model of scientific change to frame a brief, broad-brushed biographical sketch of the career of Warren B. Hamilton. I argue that Hamilton’s career can usefully be interpreted as encompassing a full “Kuhn cycle,” from a period of crisis in his early work, to one of normal science in midcareer, and back to something resembling crisis in his later research. Hamilton entered the field around mid-twentieth century when earth science can plausibly be described as being in a period of crisis. The then dominant fixist paradigm was facing an increasing number of difficulties, an alternative mobilist paradigm was being developed, and Hamilton played an important role in its development. The formulation of plate tectonics in the 1960s saw the overthrow of the fixist paradigm. This inaugurated a new phase of normal science as scientists worked within the new paradigm, refining it and applying it to different regions and various geological phenomena. Hamilton’s mid-career work fits largely into this category. Later, as the details of the plate-tectonic model became articulated more fully, and several of what Hamilton perceived as weakly supported conjectures became incorporated into the paradigm, problems began again to accumulate, and earth science, in Hamilton’s estimation, entered a new period of crisis. Radically new frameworks were now required, and Hamilton’s later work was dedicated principally to developing and articulating these frameworks and to criticizing mainstream views.
Effect of the Pore Size on the Biological Activity of β-Ca3(PO4)2-Based Resorbable Macroporous Ceramic Materials Obtained by Photopolymerization
Authors: Evdokimov P. V. , Tikhonova S. A. , Kiseleva A. K. , Filippov Ya. Yu. , Novoseletskaya E. S. , Efimenko A. Yu. , Putlayev V. I.
Published: November 2021

The effect of the pore size of macroporous ceramic materials based on β-Ca3(PO4)2 on their biological activity was studied. The formation conditions of macroporous ceramics with a porosity of >50% and a specified pore size were determined. The effect of components of the light-curing emulsion on the pore size in the final macroporous ceramics was studied. The biocompatibility of β-Ca3(PO4)2-based macroporous ceramics was demonstrated in in vitro biomedical assays. The effect of pore size of macroporous ceramic materials on mesenchymal stromal cell proliferation and viability was established.
Extramedullary relapse in a patient with multiple myeloma: a rare cause of gastrointestinal perforation and massive bleeding
Authors: Rene Christoffer Galletta , Achiam Michael Patrick , Salomo Morten , Penninga Luit
Published: November 2021

Multiple myeloma (MM) patients live longer due to more effective treatment, and we now see previously uncommon manifestations of MM, like extramedullary disease. We present a case of a 74-year-old man known with MM that relapsed with extramedullary manifestations at different locations. One of them as a gastric plasmacytoma (GP). He was successfully treated with chemoradiotherapy (Daratumumab, Bortezomib and Dexamethasone), which resulted in clinical response for 8 months, confirmed by biopsy and histopathology. Perforation of the GP occurred, and he underwent partial gastrectomy (Billroth II gastrojejunostomy). The patient’s disease progressed again 5 months after surgery, and he did not want any additional treatment. He accepted palliative care and died 10 months after the operation. A lack of knowledge about the characteristics and treatment of extramedullary MM exists, and prospective studies to investigate incidence, prognosis and treatment for extramedullary MM are needed for improving the poor prognosis of this manifestation.
Using experience-based codesign to coproduce aphasia rehabilitation services: study protocol
Authors: Anemaat Lisa , Palmer Victoria J , Copland David A , Mainstone Kathryn , Druery Kent , Druery Julia , Aisthorpe Bruce , Binge Geoffrey , Mainstone Penelope , Wallace Sarah J
Published: November 2021

Introduction

Aphasia is an impairment of language that occurs in 30%–40% of stroke survivors. This often chronic condition results in poor outcomes for the individual with aphasia and their family. Long-term aphasia management is limited, with few people receiving sufficient services by 6–12 months postonset. We present a protocol for the development of coproduced aphasia service elements. We will use experience-based codesign (EBCD), an approach that enables service users and providers to collaboratively develop services and care pathways. Drawing on the experiences of people with aphasia, their families and clinicians we will establish priorities for the development of new services and later work together to codesign them.

Methods and analysis

This research will be coproduced with people with aphasia (n=30–60), their families (n=30–60) and speech pathologists (n=30–60) in Queensland, Australia, using EBCD. A consumer advisory committee will provide oversight and advice throughout the research. In phase 1, we will use semistructured interviews and the nominal group technique to explore experiences and unmet needs in aphasia rehabilitation. Data will be analysed using thematic analysis and the resulting themes will be prioritised in multistakeholder focus groups. Outcomes of phase 1 will inform future research (phase 2) to codesign services. Financial costs and participant experiences of EBCD will be measured.

Ethics and dissemination

Human Research Ethics Committee approval for phase 1 has been obtained (HREC/2020/QRBW/61368). Results will be reported in peer-reviewed journal articles, presented at relevant conferences and, following EBCD suggested best practice, fed back to participants and community members at a celebratory event at completion of the project. The inclusion of service users in all stages of research will facilitate an integrated approach to knowledge translation. A summary of research findings will be made available to participating sites.
Factors related to educational adaptations and social life at school experienced by young people with CFS/ME: a qualitative study
Authors: Similä Wenche Ann , Nøst Torunn Hatlen , Helland Ingrid B , Rø Torstein Baade
Published: November 2021

Objectives

To explore factors perceived as positive or negative among young people with chronic fatigue syndrome/myalgic encephalomyelitis (CFS/ME) in relation to school and everyday life.

Design

A qualitative study with semistructured individual interviews performed at the local hospital or at the informants’ homes between September 2017 and January 2018, with an additional telephone interview to collect data on experiences from the COVID-19 pandemic, conducted in September 2020. Data were analysed using a grounded theory approach.

Setting

The informants were recruited from two university hospitals that offer interdisciplinary assessments of young people with CFS/ME from various parts of Norway.

Participants

Five males and 13 females aged 13–21 years with CFS/ME diagnosed 3–56 months prior to the interviews participated.

Results

The informants were concerned about a lack of educational adaptations and missed social life at school. Educational and social adaptations could improve schooling and health among young people with CFS/ME. Negative experiences were related to a lack of knowledge about CFS/ME among school personnel and young people’s difficulties to limit activities. Online teaching as experienced during the COVID-19 pandemic was described as positive both for education and social life.

Conclusions

Young people with CFS/ME can benefit from better educational adaptations and increased social interaction with peers. From the participants’ view, factors that limit learning and socialisation include a lack of knowledge about CFS/ME among teachers and school personnel, expectations from teachers of doing more than they could manage at school, feeling alone coping with the disease and not recognising their own limitations regarding what they are able to do. Suggested factors perceived to enhance learning and socialisation were a better understanding of the disease among school personnel and peers, suitable educational adaptations and being able to socialise with peers.
Supporting population mental health and wellness during the COVID-19 pandemic in Canada: protocol for a sequential mixed-method study
Authors: Risling Tracie , Carlberg Courtney , Kassam Iman , Moss Tyler , Janssen Patricia , Iduye Steve , Strudwick Gillian
Published: November 2021

Introduction

The global COVID-19 pandemic has reported to have a negative impact on the mental health and well-being of individuals around the world. Mental health system infrastructure, primarily developed to support individuals through in-person care, struggled to meet rising demand for services even prior to COVID-19. With public health guidelines requiring the use of physical distancing during the pandemic, digital mental health supports may be one way to address the needs of the population. Despite this, barriers exist in promoting and supporting access to existing and emerging digital resources. Text messaging may address some of these barriers, extending the potential reach of these digital interventions across divides that may separate some vulnerable or disadvantaged groups from essential mental health supports. Building on an existing knowledge synthesis project identifying key digital resources for improved mental health, this research will establish low-tech connections to assess need and better match access to services for those who need it most. The aim of this study is to codesign a customised two-way texting service to explore need and better align access to mental health supports for Canadians located in Saskatchewan during the COVID-19 pandemic.

Methods and analysis

This study will be completed in Saskatchewan, Canada. For this project, the RE-AIM (reach, effectiveness, adoption, implementation, maintenance) framework will be used to support three phases of a sequential mixed-method study. An advisory committee of Saskatchewan residents will guide this work with the study team. A 10-week service will be launched to connect individuals with appropriately suited digital mental health interventions through the use of text messaging. In phase 1, implementation and prototyping will be conducted with collaborative codesign for key elements related to features of an enrolment survey and initial messaging content. Phase 2 will focus on advancing the effectiveness of the service using quantitative user data. In phase 3, an embedding approach will be used to integrate both qualitative and quantitative data collected to understand the overall acceptability, satisfaction and perceived benefit of the text messaging service. Thematic analysis and descriptive statistics will be used as analytic methods.

Ethics and dissemination

This study has received approval from the Research Ethics Board at the University of Saskatchewan. A knowledge dissemination plan has been developed that includes traditional academic approaches such as conference presentations, and academic publications, as well as mainstream approaches such as social media, radio and dissemination through the advisory committee.
Use of peripheral neutrophil to lymphocyte ratio and peripheral monocyte levels to predict survival in fibrotic hypersensitivity pneumonitis (fHP): a multicentre retrospective cohort study
Authors: Barratt Shaney L , Creamer Andrew W , Adamali Huzaifa I , Duckworth Anna , Fallon Janet , Fidan Silan , Nancarrow Tom , Wollerton Rebecca , Steward Matthew , Gooptu Bibek , Gibbons Michael , Woodhead Felix Alexander , Scotton Chris
Published: November 2021

The factors determining disease course and survival in fibrotic hypersensitivity pneumonitis (fHP) have not been fully elucidated.

The aim of this study was to describe the characteristics of patients with fHP in a real-world cohort and investigate factors associated with worse outcomes. We aimed to explore the use of neutrophil to lymphocyte ratio (NLR) and peripheral blood monocyte levels in predicting mortality.

Methods

A retrospective, multicentre, observational UK cohort study.

Results

Patients with fHP were significantly younger than those with idiopathic pulmonary fibrosis (IPF) (median age fHP 73 vs IPF 75 years) and were much more likely to be woman (fHP 61% vs IPF 26%). In almost half of all fHP cases (49%, n=104/211), no causative antigen was identified from either the history or specific antigen testing. Overall, fHP was associated with a better survival than IPF, although median survival of both groups was poor (fHP 62 months vs IPF 52 months).

IPF survival in patients with a high NLR was significantly lower than those with a low NLR (44 vs 83 months). A monocyte count ≥0.95 K/uL also predicted significantly poorer outcomes for patients with IPF compared with <0.95 K/uL (33 vs 57 months). In contrast, NLR and monocyte count did not predict survival in the fHP cohort.

Conclusions

Although fHP has a statistically lower mortality than IPF, absolute survival time of both conditions is poor. High baseline NLR and absolute monocyte counts predict worse survival in IPF but not in fHP, highlighting the potential for divergence in their pathogenic mechanisms.
Nasal fentanyl and buccal midazolam carer administration ‘as needed’ for breakthrough symptom control in a specialist palliative care unit: a nested qualitative study
Authors: Perkins Paul , Parkinson Anne , Taylor Vanessa , Husbands Emma
Published: November 2021

Introduction

When people are dying and unable to take oral medication, injectable medication is commonly used, usually administered by healthcare professionals. There may be delays to symptom relief due to travel to the person’s home. In a randomised controlled trial (RCT) previously reported, nasal fentanyl (NF) or buccal midazolam (BM) were administered by lay carers in a hospice.

Objective

(1) To report experiences of lay carers who administered NF and BM for symptom control and (2) To use feedback to develop guidance informing a future definitive RCT to determine whether NF and BM administered by lay carers can lead to timely, improved symptom control for people dying at home and fewer ‘emergency’ community nursing visits than standard breakthrough medication administered by healthcare professionals.

Material and methods

Semistructured interviews with lay carers who gave trial medication were conducted. Interview data were analysed using a stage by stage method to code and categorise transcripts.

Findings

The six themes were: (1) Participation—lay carers welcomed the opportunity to administer medication; (2) Ease of use—lay carers found preparations easy to use; (3) How things could have been done differently—lay carers would have liked access to trial drugs at home; (4) Training—lay carers were happy with the training they received; (5) Timing—lay carers liked the immediacy of trial drugs and (6) Evaluation—assessing symptom intensity and drug efficacy.

Conclusions

Participation was acceptable to patients and lay carers, and beneficial for symptom relief. The findings will inform planning for a future community-based study.
A Machine learning model trained on dual-energy CT radiomics significantly improves immunotherapy response prediction for patients with stage IV melanoma
Authors: Brendlin Andreas Stefan , Peisen Felix , Almansour Haidara , Afat Saif , Eigentler Thomas , Amaral Teresa , Faby Sebastian , Calvarons Adria Font , Nikolaou Konstantin , Othman Ahmed E
Published: November 2021

Background

To assess the additive value of dual-energy CT (DECT) over single-energy CT (SECT) to radiomics-based response prediction in patients with metastatic melanoma preceding immunotherapy.

Material and methods

A total of 140 consecutive patients with melanoma (58 female, 63±16 years) for whom baseline DECT tumor load assessment revealed stage IV and who were subsequently treated with immunotherapy were included. Best response was determined using the clinical reports (81 responders: 27 complete response, 45 partial response, 9 stable disease). Individual lesion response was classified manually analogous to RECIST 1.1 through 1291 follow-up examinations on a total of 776 lesions (6.7±7.2 per patient). The patients were sorted chronologically into a study and a validation cohort (each n=70). The baseline DECT was examined using specialized tumor segmentation prototype software, and radiomic features were analyzed for response predictors. Significant features were selected using univariate statistics with Bonferroni correction and multiple logistic regression. The area under the receiver operating characteristic curve of the best subset was computed (AUROC). For each combination (SECT/DECT and patient response/lesion response), an individual random forest classifier with 10-fold internal cross-validation was trained on the study cohort and tested on the validation cohort to confirm the predictive performance.

Results

We performed manual RECIST 1.1 response analysis on a total of 6533 lesions. Multivariate statistics selected significant features for patient response in SECT (min. brightness, R²=0.112, padj. ≤0.001) and DECT (textural coarseness, R²=0.121, padj. ≤0.001), as well as lesion response in SECT (mean absolute voxel intensity deviation, R²=0.115, padj. ≤0.001) and DECT (iodine uptake metrics, R²≥0.12, padj. ≤0.001). Applying the machine learning models to the validation cohort confirmed the additive predictive power of DECT (patient response AUROC SECT=0.5, DECT=0.75; lesion response AUROC SECT=0.61, DECT=0.85; p<0.001).

Conclusion

The new method of DECT-specific radiomic analysis provides a significant additive value over SECT radiomics approaches for response prediction in patients with metastatic melanoma preceding immunotherapy, especially on a lesion-based level. As mixed tumor response is not uncommon in metastatic melanoma, this lends a powerful tool for clinical decision-making and may potentially be an essential step toward individualized medicine.
Impact of tumor mutational burden on checkpoint inhibitor drug eligibility and outcomes across racial groups
Authors: Hsiehchen David , Espinoza Magdalena , Valero Cristina , Ahn Chul , Morris Luc G T
Published: November 2021

The FDA approval of immune checkpoint inhibitors for cancers with tumor mutation burden (TMB) of at least 10 mut/Mb is postulated to reduce healthcare disparities by broadly expanding treatment eligibility. In a cohort of 39,400 patients with available genomic and race data, black and Asian patients were less likely to have TMB-high cancers in multiple types of malignancies based on the currently approved cut-off. Decreasing TMB thresholds preferentially increased the eligibility of minority patients for immune checkpoint inhibitors while retaining predictive value of treatment benefit in a cohort of immune checkpoint inhibitor treated patients. This study highlights differing distributions of TMB-high cancers between racial groups and provides guidance in developing more rational eligibility criteria for immune checkpoint inhibitors.
Combining fixed-location count data and movement data to estimate abundance of a lake sturgeon spawning run: a framework for riverine migratory species
Authors: Izzo Lisa K. , Zydlewski Gayle Barbin , Parrish Donna L.
Published: November 2021

Estimating abundance of migrating fishes is challenging. While sonars can be deployed continuously, improper assumptions about unidirectional migration and complete spatial coverage can lead to inaccurate estimates. To address these challenges, we present a framework for combining fixed-location count data from a dual-frequency identification sonar (DIDSON) with movement data from acoustic telemetry to estimate spawning run abundance of lake sturgeon (Acipenser fulvescens). Acoustic telemetry data were used to estimate the probability of observing a lake sturgeon on the DIDSON and to determine the probability that a lake sturgeon passing the DIDSON site had passed the site previously during the season. Combining probabilities with DIDSON counts, using a Bayesian integrated model, we estimated the following abundances: 99 (42–215 credible interval, CI) in 2017, 131 (82–248 CI) in 2018, and 92 (47–184 CI) in 2019. Adding movement data generated better inferences on count data by incorporating fish behavior (e.g., multiple migrations in a single season) and its uncertainty into abundance estimates. This framework can be applied to count and movement data to estimate abundance of spawning runs of other migratory fishes in riverine systems.
Use of biochar for alleviating negative impact of salinity stress in corn grown in arid soil
Authors: Alotaibi Khaled D.
Published: November 2021

Tremendous benefits of biochar (BC) amendment to soil have been reported, including their role in alleviating the impact of salinity stress in plants. The aim of this study was to evaluate the effects of BC produced at 300 °C (BC300) and 700 °C (BC700) on the germination rate (GR) and selected growth characteristics of corn plants irrigated with salinized water over a growth period of 6 weeks. The experimental treatments included three biochar treatments: BC0 (control, without biochar addition), BC300, and BC700. The treatments also included three salinity levels of irrigation water: 0, 3, and 6 dS·m−1. The biochar was applied at a rate of 3%. The GR decreased with increasing salinity level, which was more evident in the first week. This stress impact was reduced when treated with the BC700 relative to the saline treatments without BC. Both BC treatments demonstrated contrasting effects on corn growth, nutrient uptake, and Na+ and K+ content in plant tissue. The effect of BC700 treatment on plant height and root length was limited, but the impact of salinity stress on chlorophyll meter readings, chlorophyll fluorescence parameter (Fv/Fm), dry matter yield, and N and P uptake were largely mitigated. It also increased K+ and decreased Na+ content in plant tissue. However, the BC300 treatment adversely affected plant growth parameters at each salinity level. Overall, the BC produced at a higher temperature significantly alleviated the impact of salinity stress on plant growth characteristics, which is probably attributed to their higher surface area and porosity, enhancing their salt ion sorption capacity.
Performance of the ReD TPC, a novel double-phase LAr detector with silicon photomultiplier readout
Authors: Agnes P. , Albergo S. , Albuquerque I. , Arba M. , Ave M. , Boiano A. , Bonivento W. M. , Bottino B. , Bussino S. , Cadeddu M. , Caminata A. , Canci N. , Cappello G. , Caravati M. , Cariello M. , Castellano S. , Catalanotti S. , Cataudella V. , Cereseto R. , Cesarano R. , Cicalò C. , Covone G. , de Candia A. , De Filippis G. , De Rosa G. , Davini S. , Dionisi C. , Dolganov G. , Fiorillo G. , Franco D. , Giovanetti G. K. , Galbiati C. , Gulino M. , Ippolito V. , Kemmerich N. , Kochanek I. , Korga G. , Kuss M. , La Commara M. , La Delfa L. , Leyton M. , Li X. , Lissia M. , Mari S. M. , Martoff C. J. , Masone V. , Matteucci G. , Musico P. , Oleynikov V. , Pallavicini M. , Pandola L. , Razeto A. , Rescigno M. , Rode J. , Rossi N. , Sablone D. , Sanfilippo S. , Scapparone E. , Sosa A. , Suvorov Y. , Testera G. , Tricomi A. , Tuveri M. , Wada M. , Wang H. , Wang Y. , Westerdale S.
Published: November 2021

A double-phase argon Time Projection Chamber (TPC), with an active mass of 185 g, has been designed and constructed for the Recoil Directionality (ReD) experiment. The aim of the ReD project is to investigate the directional sensitivity of argon-based TPCs via columnar recombination to nuclear recoils in the energy range of interest (20–$$200\,\hbox {keV}_{nr}$$200keVnr) for direct dark matter searches. The key novel feature of the ReD TPC is a readout system based on cryogenic Silicon Photomultipliers (SiPMs), which are employed and operated continuously for the first time in an argon TPC. Over the course of 6 months, the ReD TPC was commissioned and characterised under various operating conditions using$$\gamma $$γ-ray and neutron sources, demonstrating remarkable stability of the optical sensors and reproducibility of the results. The scintillation gain and ionisation amplification of the TPC were measured to be$$g_1 = (0.194 \pm 0.013)$$g1=(0.194±0.013)photoelectrons/photon and$$g_2 = (20.0 \pm 0.9)$$g2=(20.0±0.9)photoelectrons/electron, respectively. The ratio of the ionisation to scintillation signals (S2/S1), instrumental for the positive identification of a candidate directional signal induced by WIMPs, has been investigated for both nuclear and electron recoils. At a drift field of 183 V/cm, an S2/S1 dispersion of 12% was measured for nuclear recoils of approximately 60–$$90\,\hbox {keV}_{nr}$$90keVnr, as compared to 18% for electron recoils depositing 60 keV of energy. The detector performance reported here meets the requirements needed to achieve the principal scientific goals of the ReD experiment in the search for a directional effect due to columnar recombination. A phenomenological parameterisation of the recombination probability in LAr is presented and employed for modeling the dependence of scintillation quenching and charge yield on the drift field for electron recoils between 50–500 keV and fields up to 1000 V/cm.
3D multi-scale modelling of plasma-based seeded soft X-ray lasers
Authors: Oliva Eduardo , Fernández-Tello Elisa V. , Cotelo Manuel , Martínez Gil Pablo , Moreno José Antonio , Velarde Pedro
Published: November 2021

Modelling plasma-based seeded soft X-ray lasers from the creation of the plasma to the propagation of a femtosecond high-order harmonic (HOH) seed throughout several millimetres of inhomogeneous plasma is a complex challenge. Different spatio-temporal scales from the hydrodynamic evolution of the plasma (hundreds of micrometres and nanoseconds) to the propagation of pulses through the plasma (millimetres and tens of picoseconds), electron collisions (picoseconds or even shorter) and the evolution of the envelope of the seeded HOH (tens of femtoseconds) must be tackled in order to fully understand these systems. In this paper, we will present the multi-scale computational paradigm that we have used to perform a full ab initio simulation of a dense, Ni-like Krypton plasma amplifier of soft X-rays. Results of the modelling and expected future applications will also be shown.
A new neural network approach to density calculation on ceramic materials
Authors: Mitic Vojislav V. , Ribar Srdjan , Randjelovic Branislav M. , Aleksic Dejan , Fecht Hans , Vlahovic Branislav
Published: November 2021

The materials’ consolidation, especially ceramics, is very important in advanced research development and industrial technologies. Science of sintering with all incoming novelties is the base of all these processes. A very important question in all of this is how to get the more precise structure parameters within the morphology of different ceramic materials. In that sense, the advanced procedure in collecting precise data in submicro-processes is also in direction of advanced miniaturization. Our research, based on different electrophysical parameters, like relative capacitance, breakdown voltage, and [Formula: see text], has been used in neural networks and graph theory successful applications. We extended furthermore our neural network back propagation (BP) on sintering parameters’ data. Prognosed mapping we can succeed if we use the coefficients, implemented by the training procedure. In this paper, we continue to apply the novelty from the previous research, where the error is calculated as a difference between the designed and actual network output. So, the weight coefficients contribute in error generation. We used the experimental data of sintered materials’ density, measured and calculated in the bulk, and developed possibility to calculate the materials’ density inside of consolidated structures. The BP procedure here is like a tool to come down between the layers, with much more precise materials’ density, in the points on morphology, which are interesting for different microstructure developments and applications. We practically replaced the errors’ network by density values, from ceramic consolidation. Our neural networks’ application novelty is successfully applied within the experimental ceramic material density [Formula: see text] [kg/m3], confirming the direction way to implement this procedure in other density cases. There are many different mathematical tools or tools from the field of artificial intelligence that can be used in such or similar applications. We choose to use artificial neural networks because of their simplicity and their self-improvement process, through BP error control. All of this contributes to the great improvement in the whole research and science of sintering technology, which is important for collecting more efficient and faster results.
Minimal degree of standard identities of matrix algebras with symplectic graded involution
Authors: Bessades D. C. L. , dos Santos R. B. , Vieira A. C.
Published: November 2021

Let [Formula: see text] be a field of characteristic zero and [Formula: see text] the algebra of [Formula: see text] matrices over [Formula: see text]. By the classical Amitsur–Levitzki theorem, it is well known that [Formula: see text] is the smallest degree of a standard polynomial identity of [Formula: see text]. A theorem due to Rowen shows that when the symplectic involution [Formula: see text] is considered, the standard polynomial of degree [Formula: see text] in symmetric variables is an identity of [Formula: see text]. This means that when only certain kinds of matrices are considered in the substitutions, the minimal degree of a standard identity may not remain being the same. In this paper, we present some results about the minimal degree of standard identities in skew or symmetric variables of odd degree of [Formula: see text] in the symplectic graded involution case. Along the way, we also present the minimal total degree of a double Capelli polynomial identity in symmetric variables of [Formula: see text] with transpose involution.
Modeling of Risk Measure Bonds Using the Beta Model
Authors: Hachicha Fatma , Hachicha Ahmed , Masmoudi Afif
Published: November 2021

Duration and convexity are important measures in fixed-income portfolio management. In this paper, we analyze this measure of the bonds by applying the beta model. The general usefulness of the beta probability distribution enhances its applicability in a wide range of reliability analyses, especially in the theory and practice of reliability management. We estimate the beta density function of the duration/convexity. This estimate is based on two important and simple models of short rates, namely, Vasicek and CIR (Cox, Ingersoll, and Ross CIR). The models are described and then their sensitivity of the models with respect to changes in the parameters is studied. We generate the stochastic interest rate on the duration and convexity model. The main results show that the beta probability distribution can be applied to model each phase of the risk function. This distribution approved its effectiveness, simplicity and flexibility. In this paper, we are interested in providing a decision-making tool for the manager in order to minimize the portfolio risk. It is helpful to have a model that is reasonably simple and suitable to different maturity of bonds. Also, it is widely used by investors for choosing bond portfolio immunization through the investment strategy. The finding also shows that the probability of risk measured by the reliability function is to highlight the relationship between duration/convexity and different risk levels. With these new results, this paper offers several implications for investors and risk management purposes.
Reflected and doubly reflected BSDEs driven by RCLL martingales
Authors: Nie Tianyang , Rutkowski Marek
Published: November 2021

We prove some new results on reflected BSDEs and doubly reflected BSDEs driven by a multi-dimensional RCLL martingale. The goal is to develop a general multi-asset framework encompassing a wide spectrum of nonlinear financial models, including as particular cases the setups studied by Peng and Xu [BSDEs with random default time and their applications to default risk, working paper, preprint (2009), arXiv:0910.2091] and Dumitrescu et al. [BSDEs with default jump, in Computation and Combinatorics in Dynamics, Stochastics and Control, Abel Symposia, Vol. 13, eds. E. Celledoni, G. Di Nunno, K. Ebrahimi-Fard and H. Munthe-Kaas (Springer, Cham, 2018), pp. 233–263] who examined BSDEs driven by a one-dimensional Brownian motion and a purely discontinuous martingale with a single jump. Our results are not covered by existing literature on reflected and doubly reflected BSDEs driven by a Brownian motion and a Poisson random measure.
Formal aspects of parametrized topological complexity and its pointed version
Authors: García-Calcines J. M.
Published: November 2021

The notion of parametrized topological complexity, introduced by Cohen, Farber and Weinberger, is extended to fiberwise spaces which are not necessarily Hurewicz fibrations. After exploring some formal properties of this extension we also introduce the pointed version of parametrized topological complexity. Finally, we give sufficient conditions so that both notions agree.
Developing a Cross-lingual Semantic Word Similarity Corpus for English–Urdu Language Pair
Authors: Fatima Ghazeefa , Nawab Rao Muhammad Adeel , Khan Muhammad Salman , Saeed Ali
Published: November 2021

Semantic word similarity is a quantitative measure of how much two words are contextually similar. Evaluation of semantic word similarity models requires a benchmark corpus. However, despite the millions of speakers and the large digital text of the Urdu language on the Internet, there is a lack of benchmark corpus for the Cross-lingual Semantic Word Similarity task for the Urdu language. This article reports our efforts in developing such a corpus. The newly developed corpus is based on the SemEval-2017 task 2 English dataset, and it contains 1,945 cross-lingual English–Urdu word pairs. For each of these pairs of words, semantic similarity scores were assigned by 11 native Urdu speakers. In addition to corpus generation, this article also reports the evaluation results of a baseline approach, namely “Translation Plus Monolingual Analysis” for automated identification of semantic similarity between English–Urdu word pairs. The results showed that the path length similarity measure performs better for the Google and Bing translated words. The newly created corpus and evaluation results are freely available online for further research and development.
Subclinical Atrial Fibrillation: A Silent Threat with Uncertain Implications
Authors: Kashou Anthony H. , Adedinsewo Demilade A. , Noseworthy Peter A.
Published: November 2021

Atrial fibrillation (AF) is one of the most common cardiac arrhythmias. Implantable and wearable cardiac devices have enabled the detection of asymptomatic AF episodes—termed subclinical AF (SCAF). SCAF, the prevalence of which is likely significantly underestimated, is associated with increased cardiovascular and all-cause mortality and a significant stroke risk. Recent advances in machine learning, namely artificial intelligence–enabled ECG (AI-ECG), have enabled identification of patients at higher likelihood of SCAF. Leveraging the capabilities of AI-ECG algorithms to drive screening protocols could eventually allow for earlier detection and treatment and help reduce the burden associated with AF.
Innate Immunity and Cancer Pathophysiology
Authors: Maiorino Laura , Daßler-Plenker Juliane , Sun Lijuan , Egeblad Mikala
Published: November 2021

Chronic inflammation increases the risk of several cancers, including gastric, colon, and hepatic cancers. Conversely, tumors, similar to tissue injury, trigger an inflammatory response coordinated by the innate immune system. Cellular and molecular mediators of inflammation modulate tumor growth directly and by influencing the adaptive immune response. Depending on the balance of immune cell types and signals within the tumor microenvironment, inflammation can support or restrain the tumor. Adding to the complexity, research from the past two decades has revealed that innate immune cells are highly heterogeneous and plastic, with variable phenotypes depending on tumor type, stage, and treatment. The field is now on the cusp of being able to harness this wealth of data to ( a) classify tumors on the basis of their immune makeup, with implications for prognosis, treatment choice, and clinical outcome, and ( b) design therapeutic strategies that activate antitumor immune responses by targeting innate immune cells.