bluuebunny/crossref_metadata_2025 huggingface dataset:
A deep learning‐based image captioning method to automatically generate comprehensive explanations of bridge damage
Authors: Chun Pang‐Jo , Yamane Tatsuro , Maemura Yu
Published: November 2021

Photographs of bridges can reveal considerable technical information such as the part of the structure that is damaged and the type of damage. Maintenance and inspection engineers can benefit greatly from a technology that can automatically extract and express such information in readable sentences. This is possibly the first study on developing a deep learning model that can generate sentences describing the damage condition of a bridge from images through an image captioning method. Our study shows that by introducing an attention mechanism into the deep learning model, highly accurate descriptive sentences can be generated. In addition, often multiple forms of damage can be observed in the images of bridges; hence, our algorithm is adapted to output multiple sentences to provide a comprehensive interpretation of complex images. In our dataset, the scores of Bilingual Evaluation Understudy (BLEU)‐1 to BLEU‐4 were 0.782, 0.749, 0.711, and 0.693, respectively, and the percentage of correctly output explanatory sentences is 69.3%. All of these results are better than the model without the attention mechanism. The developed method makes it possible to provide user‐friendly, text‐based explanations of bridge damage in images, making it easier for engineers with relatively little experience and even administrative staff without extensive technical expertise to understand images of bridge damage. Future research in this field is expected to lead to the unification of field expertise with artificial intelligence (AI), which will be the foundation of the evolutionary development of bridge inspection AI.
An expanded agar‐based screening method for azole‐resistant Aspergillus fumigatus
Authors: Lucio Jose , Gonzalez‐Jimenez Irene , Garcia‐Rubio Rocio , Cuetara Maria Soledad , Mellado Emilia
Published: November 2021

Antifungal susceptibility testing is an essential tool for guiding antifungal therapy. Reference methods are complex and usually only available in specialised laboratories. We have designed an expanded agar‐based screening method for the detection of azole‐resistant Aspergillus fumigatus isolates. Normally, identification of resistance mechanisms is obtained only after sequencing the cyp51A gene and promoter. However, our screening method provides azole resistance detection and presumptive resistance mechanisms identification. A previous agar‐based method consisting of four wells containing voriconazole, itraconazole, posaconazole and a growth control, detected azole resistance to clinical azoles. Here, we have modified the concentrations of voriconazole and posaconazole to adapt to the updated EUCAST breakpoints against A. fumigatus. We have also expanded the method to include environmental azoles to assess azole resistance and the azole resistance mechanism involved. We used a collection of A. fumigatus including 54 azole‐resistant isolates with Cyp51A modifications (G54, M220, G448S, TR53, TR34/L98H, TR46/Y121F/T289A, TR34/L98H/S297T/F495I), and 50 azole susceptible isolates with wild‐type Cyp51A. The screening method detects azole‐resistant A. fumigatus isolates when there is growth in any of the azole‐containing wells after 48h. The growth pattern in the seven azoles tested helps determine the underlying azole resistance mechanism. This approach is designed for surveillance screening of A. fumigatus azole‐resistant isolates and can be useful for the clinical management of patients prior to antifungal susceptibility testing confirmation.
Aconitum anhuiense sp. nov. (Ranunculaceae), a new species from Anhui, China
Authors: Yin Min‐Zhen , Peng Hua‐Sheng , Huang Lu‐Qi
Published: November 2021

Aconitum anhuiense, a new species from Anhui Province, China, is described and illustrated. The species is similar to A. hemsleyanum and A. henryi, but can be distinguished by a suit of unique traits such as leaf blade abaxially sparsely puberulent at veins and 3‐parted to 2–4 cm from base, spur circinate, lip shorter, carpels 3 and seeds longer. Detailed information, including morphological descriptions, illustrations and diagnostic comparisons of the new species are provided.
Constraining labour: The integration dynamics of working‐class horticultural migrants in rural areas of Norway, the UK and the US
Authors: Scott Sam , Visser M. Anne
Published: November 2021

This article argues that many low‐wage migrants moving to work in rural areas of the developed world end up in very specific and precarious employment and housing contexts: working in temporary/seasonal jobs within horticultural labour markets and often living in employer‐provided tied accommodation. This context—which we profile by drawing on qualitative case study evidence from Norway, the UK and the US—makes integration virtually impossible. It is only after moving on from precarious temporary/seasonal work and out from tied accommodation that rural integration becomes viable. Yet even then, the integration of these workers is often limited. Migrants are largely ‘quarantined’ and separate and invisible from the host society. Not surprisingly, migrants tend to treat their lack of rural integration as ‘liminal’, that is, a temporary and in‐between life stage. They also engage in ‘transnational simultaneity’ by maintaining family/communal relations back home, whilst focusing largely on work in the host country. This liminality and transnational simultaneity help working‐class migrants survive their quarantined lives.
How Obscurantism Differs from Bullshit: A Proposal
Authors: Bien Eric Nenkia
Published: November 2021

This paper holds the view that althoughbullshitandobscurantismare obviously related phenomena, they should be kept distinct for conceptual reasons. It shows that whereas phenomena of bullshit tend to concentrate on speech acts and a violation of the expectations of relevance therein, obscurantism betrays an indirect move to confound while promising deep content. After an overview of studies on bullshit and a look at the different characteristics and types of obscurantism, this paper investigates why readers retain interest in reading obscure texts. Interpretive charity, which is one of the reasons for this sustained interest, is found to be unsuccessful in making sense of obscurantism. Obscurantism is thus seen to be a vice more cryptic and systematic than bullshit.
Trade policy in Indonesia and Thailand
Authors: Hill Hal , Menon Jayant
Published: November 2021

This paper provides an analytical survey of trade policy in Indonesia and Thailand, in the context of the key findings of the WTO’s 2020 Trade Policy Reviews. These are historically dynamic economies that are integrated within the outward‐looking ASEAN protocols and the China‐centred East Asian trade and investment networks. Over the past decade, there have been no major changes in the two countries’ trade and commercial policy settings, with Thailand maintaining its more open economic settings and Indonesia continuing its more hesitant embrace of globalisation. The major drivers of domestic policy settings have therefore been global factors, including the continuing rise both of China in the regional and global economies and of the increasingly China‐centred global supply chains. Both WTO reports provide comprehensive examinations of trade patterns and policies, although there is room to strengthen the analytical foundations of future reports.
Two ploidy levels present in the invasive Campuloclinium macrocephalum (pompom weed) in South Africa – Implications for biocontrol
Authors: Gitonga Lucy N. , Cron Glynis V. , Glennon Kelsey L. , McConnachie Andrew J. , Byrne Marcus J.
Published: November 2021

The highly invasive Campuloclinium macrocephalum (Asteraceae; ‘pompom weed’), native to South America, was introduced to South Africa where it has flourished and now threatens the native diversity of the grasslands it has invaded. The Argentine C. macrocephalum population is known to comprise at least three ploidy levels, and exhibit aneuploidy. Ploidy levels had not yet been assessed across South African populations of pompom weed and could influence the effectiveness of a biological control (biocontrol) programme. Therefore, we used flow cytometry to estimate ploidy levels of individuals from invaded regions in South Africa and Argentina. Diploids, triploids, tetraploids and aneuploids were detected in the sampled Argentine individuals. In South Africa, only triploid and tetraploid cytotypes were identified, with possible aneuploid variation. Mapping the distribution of these ploidy levels in South Africa revealed that the tetraploids are more widespread across all five sampled provinces, whereas the triploids occur only in Gauteng (the likely origin of the invasion) and neighbouring North West provinces and one sampled area in KwaZulu‐Natal province. Distinct phenotypic variation is evident between Argentine individuals of different ploidy levels. Polyploids have now been confirmed to occur in both the native and introduced ranges. Because triploids and tetraploids are present in both native and introduced ranges, we predict that polyploidy is not likely to be a constraint in effective biocontrol in South Africa as the natural enemies have probably co‐evolved with polyploids in the native range. However, other factors may impact the effectiveness of the biocontrol agents, such as feeding, oviposition (potentially affecting their reproduction), establishment, and spread, therefore, warranting further research.
Gravity-related collapse of the wave function and spontaneous heating: Revisiting the experimental bounds
Authors: Vinante Andrea , Ulbricht Hendrik
Published: November 2021

The possibility that the collapse of the wave function in quantum mechanics is real and ultimately connected to (classical) gravity has been debated for decades with main contributions by Diósi and Penrose (DP). In particular, Diósi proposed a noise-based dynamical reduction model, which captures the same order of magnitudes for the collapse time suggested by Penrose based on heuristic arguments. This is known in the literature as the DP model (Diósi–Penrose). A peculiarity of the DP model is the prediction of spontaneous heating of matter, which can be tested without the need for massive quantum superpositions. Notably, a very similar effect is predicted by recent theoretical approaches to gravity as a classical-only information channel. Here, we reconsider the current constraints on the DP model from spontaneous heating by analyzing experimental situations not properly considered before. We argue that the parameter-free version of the DP model is close to be ruled out by standard heat leak measurements at ultralow temperatures with a conclusive exclusion likely within reach with existing technology. This result would strengthen a recent claim of exclusion inferred by spontaneous x-ray emission experiments, which relies on the somewhat stronger assumption that the DP noise field is white up to x-ray frequencies.
Direct Visualization of Chemical Cues and Cellular Phenotypes throughout Bacillus subtilis Biofilms
Authors: Yannarell Sarah M. , Veličković Dusan , Anderton Christopher R. , Shank Elizabeth A.
Published: November 2021

Bacterial biofilms are complex and heterogeneous structures. Cells within biofilms carry out numerous metabolic processes in a nuanced and organized manner, details of which are still being discovered.
Validation of the Copenhagen Hip and Groin Outcome Score (HAGOS) using modern test theory across different cultures and languages: a cross-sectional study of 452 male athletes with groin pain
Authors: Christensen Karl Bang , Clausen Mikkel Bek , King Enda , Franklyn-Miller Andrew , Harøy Joar , Andersen Thor Einar , Hölmich Per , Thorborg Kristian
Published: November 2021

Bkground

No studies have tested the validity of the Copenhagen Hip and Groin Outcome Score (HAGOS) using modern test theory, across different cultures and languages.

Objective

To validate the Danish, English and Norwegian versions of HAGOS and its six subscales (Symptoms (S, Item 1–7), Pain (P, Item 1–10), activities of daily living (Item 1–5), Sport and recreation (Sport/rec, Item 1–8), Participation in physical activity (item 1–2) and quality of life (item 1–5)) by evaluating differential item functioning (DIF) and measurement invariance across the three language versions in male multidirectional team athletes with groin pain. Second, to modify subscales depending on goodness-of-fit to the item response theory models and calculate conversion tables if language DIF was observed.

Methods

We included individual responses to the Danish (n=157), English (n=146) and Norwegian (n=149) language versions of HAGOS from 452 athletes (median age 24 years old, range 20–28) with groin pain. Overall fit, model fit, individual item fit, local response dependence and measurement invariance was examined using confirmatory factor analysis and graphical Rasch models.

Results

The removal of seven misfitting items (S2, P1, P2, A4, SP1, SP5, Q3) resulted in 6 HAGOS subscales with acceptable psychometric properties. For the Symptoms, Pain and Sports subscales evidence of DIF was disclosed between the three different language-versions of HAGOS and conversion tables were created.

Conclusions

A revised HAGOS derived using modern test theory provides valid measurements for male multidirectional athletes with groin pain across different cultures and languages. Conversion tables must be applied to compare HAGOS scores from Danish, Norwegian and English language versions.
Japanese newspaper advertisements for dietary supplements before and after COVID-19: a content analysis
Authors: Okuhara Tsuyoshi , Yokota Rie , Shirabe Ritsuko , Iye Reina , Okada Hiroko , Kiuchi Takahiro , Chiba Tsuyoshi , Akamatsu Rie
Published: November 2021

Objectives

Public health institutions have alerted consumers about advertising for dietary supplements with false claims of preventing or treating COVID-19. We quantitatively and qualitatively examined newspaper advertisements for dietary supplements before and after the COVID-19 spread.

Design

Content analysis.

Participants

We analysed advertisements for dietary supplements in two major Japanese newspapers in February–July 2019 and February–July 2020. Our analysis covered 2167 advertisements.

Results

The number of advertisements for dietary supplements that claimed to be effective in infection prevention (p=0.009) and improving joint (p=0.002) and digestive functions (p=0.002) significantly increased after the spread of COVID-19 compared with before. Dietary supplements that claimed to be effective in preventing infection were advertised in combination with recommendations for gargling and handwashing. Such terms as ‘defence’ and ‘prevent’ were used to promote the preventive effect.

Conclusions

False and misleading claims in advertising for dietary supplements may result in consumer harm, such as overdosing and failure to take preventive behaviour. While the pandemic continues, there will be an increasing need for disseminating accessible information about the appropriate use of dietary supplements, consumer education and warnings to manufacturers.
Uterine Fibroid Symptom and Quality of Life questionnaire (UFS-QOL NL) in the Dutch population: a validation study
Authors: Keizer Alieke L , van Kesteren Paul J M , Terwee Caroline , de Lange Maria E , Hehenkamp Wouter J K , Kok Helen S
Published: November 2021

Objective

Uterine fibroids can cause a variety of symptoms in women, from heavy menstrual bleeding and dysmenorrhea to bulk symptoms. The Uterine Fibroid Symptom and health-related Quality Of Life questionnaire (UFS-QOL) is a patient-reported outcome measure developed for assessing fibroid-related symptoms in a standardised way. Our aim was to translate and validate the UFS-QOL in Dutch.

Design

Validation study.

Setting

Patients were recruited by a gynaecologist at the outpatient clinic.

Participants

Women with uterine fibroids.

Methods

The UFS-QOL was translated into Dutch (UFS-QOL NL) and validated through testing construct validity (comprising of structural validity and hypotheses testing), reliability, responsiveness and interpretability, assessing floor and ceiling effects and minimal important change. An option to answer ‘not applicable’ was added to the translated questionnaire.

Results

191 women with uterine fibroids completed the UFS-QOL NL at baseline, after 2 weeks and after 3 months. The questionnaire retained the same factor structure after translation (Comparative Fit Index 0.94–0.95; Tucker-Lewis fit Index 0.93–0.95; Root Mean Square Error of Approximation 0.10–0.11) and correlations to other questionnaires (RAND 36, Hospital Anxiety and Depression Scale and Golombok Rust Inventory of Sexual Satisfaction) were generally moderate, as hypothesised (Pearson’s r 0.3–0.7). We found a sufficient reliability with intraclass correlation coefficients of approximately 0.8–0.9 for all subscales. Responsiveness was sufficient when testing hypotheses comparing women who had surgery with those who did not. Cronbach’s alpha was higher than 0.7 for all subscales, indicating sufficient internal consistency and there were no concerns about floor or ceiling effects. Minimal important change could not be calculated due to low correlation between the different subscales and the anchor question.

Conclusions

The results support the measurement properties of the Dutch UFS-QOL for assessing fibroid-related symptoms and health-related quality of life in Dutch women with uterine fibroids.
Protocol for a multicentre, parallel-group, open-label randomised controlled trial comparing ferric carboxymaltose with the standard of care in anaemic Malawian pregnant women: the REVAMP trial
Authors: Mwangi Martin N , Mzembe Glory , Moya Ernest , Braat Sabine , Harding Rebecca , Robberstad Bjarne , Simpson Julie , Stones William , Rogerson Stephen , Biselele Kabeya , Chinkhumba Jobiba , Larson Leila , Ataíde Ricardo , Phiri Kamija S , Pasricha Sant-Rayn
Published: November 2021

Introduction

Anaemia in pregnancy remains a critical global health problem, affecting 46% of pregnant women in Africa and 49% in Asia. Oral iron therapy requires extended adherence to achieve correction of anaemia and replenishment of iron stores. Ferric carboxymaltose (FCM) is a recently established intravenous iron formulation associated with substantial advantages in safety, speed of delivery and total dose deliverable in a single infusion. We aim to determine whether FCM given once during the second trimester of pregnancy compared with standard oral iron distributed through routine antenatal services is effective and safe for treatment of moderate to severe maternal anaemia in sub-Saharan Africa.

Methods and analysis

The randomized controlled trial of the effect of intravenous iron on anaemia in Malawian pregnant women (REVAMP) is a two-arm confirmatory individually randomised trial set in Blantyre and Zomba districts in Malawi. The trial will randomise 862 women in the second trimester of pregnancy with a capillary haemoglobin concentration below 100.0 g/L. The study comprises two arms: (a) intravenous FCM (20 mg/kg up to 1000 mg) given once at randomisation, and (b) standard of care oral iron (65 mg elemental iron two times per day) for 90 days (or the duration of pregnancy, whichever is shorter) provided according to local healthcare practices. Both arms receive sulfadoxine-pyrimethamine as intermittent preventive treatment in pregnancy. The primary outcome is the prevalence of anaemia (Hb <110.0 g/L) at 36 weeks’ gestation. Secondary outcomes include birth weight, gestation duration and safety outcomes, including clinical malaria, serious perinatal events and postpartum haematologic and health-related outcomes in the mother and child.

Ethics and dissemination

Ethical approval was granted by the Research Ethics Committee (COMREC P.02/18/2357) in Malawi and the Human Research Ethics Committee (WEHI: 18/02), Melbourne, Australia. The protocol is registered with the Australian and New Zealand Clinical Trials Registry. The results will be shared with the local community that enabled the research, and also to the international fora.

Trial registration number

ACTRN12618001268235; Pre-results.
Feasibility of allied health assistant management of people with acute hip fracture: protocol for a feasibility randomised controlled trial
Authors: Snowdon David A , Vincent Peggy , Callisaya Michele L , Collyer Taya A , Wang Yi Tian , Taylor Nicholas F
Published: November 2021

Introduction

Guidelines for hip fracture care state that patients with hip fracture should be mobilised on the day after surgery and at least once a day thereafter. However, compliance with these guidelines is poor. One approach that would assist physiotherapists to meet mobility guidelines after hip fracture is to delegate the provision of daily mobilisation to allied health assistants under their supervision. Therefore, we plan to conduct a randomised controlled trial to determine the feasibility of an allied health assistant providing daily inpatient rehabilitation to patients with hip fracture.

Methods and analysis

Using a parallel group randomised controlled design with one-to-one allocation, participants will be randomly allocated to an experimental group (allied health assistant management) or a comparison group (physiotherapist management). Inclusion criteria are: adult with diagnosis of hip fracture; inpatient in acute hospital; walked independently pre-hip fracture and able to communicate in conversational English. The experimental group will receive routine physiotherapy rehabilitation, including daily mobilisation, from an allied health assistant following initial physiotherapist assessment. The comparison group will receive routine rehabilitation from a physiotherapist. The primary outcome will be the feasibility of allied health assistant management of patients with hip fracture. Feasibility will be determined using the following areas of focus in Bowen’s feasibility framework: acceptability (patient satisfaction), demand (proportion of patients who participate), implementation (time allied health assistant/physiotherapist spends with participant, occasions of service) and practicality (cost, adverse events). Staff involved in the implementation of allied health assistant care will be interviewed to explore their perspectives on feasibility. Secondary outcomes include compliance with daily mobilisation guidelines, discharge destination, hospital readmission, falls, functional activity and length of stay. We aim to recruit 50 participants. Descriptive statistics will be used to describe feasibility and mobilisation rates will be calculated using Cox proportional hazards regression to compare compliance with mobilisation guidelines.

Ethics and dissemination

Ethics approval was obtained from the Peninsula Health human research ethics committee (HREC/63 005/PH-2020). The findings will be disseminated in peer-reviewed journals and conference presentations.

Trail registration number

Australian and New Zealand Clinical Trial Registry; ACTRN12620000877987; Pre-results.
MRI-based 3D retinal shape determination
Authors: van Vught Luc , Shamonin Denis P , Luyten Gregorius P M , Stoel Berend C , Beenakker Jan-Willem M
Published: November 2021

Objective

To establish a good method to determine the retinal shape from MRI using three-dimensional (3D) ellipsoids as well as evaluate its reproducibility.

Methods and analysis

The left eyes of 31 volunteers were imaged using high-resolution ocular MRI. The 3D MR-images were segmented and ellipsoids were fitted to the resulting contours. The dependency of the resulting ellipsoid parameters on the evaluated fraction of the retinal contour was assessed by fitting ellipsoids to 41 different fractions. Furthermore, the reproducibility of the complete procedure was evaluated in four subjects. Finally, a comparison with conventional two-dimensional (2D) methods was made.

Results

The mean distance between the fitted ellipsoids and the segmented retinal contour was 0.03±0.01 mm (mean±SD) for the central retina and 0.13±0.03 mm for the peripheral retina. For the central retina, the resulting ellipsoid radii were 12.9±0.9, 13.7±1.5 and 12.2±1.2 mm along the horizontal, vertical and central axes. For the peripheral retina, these radii decreased to 11.9±0.6, 11.6±0.4 and 10.4±0.7 mm, which was accompanied by a mean 1.8 mm posterior shift of the ellipsoid centre. The reproducibility of the ellipsoid fitting was 0.3±1.2 mm for the central retina and 0.0±0.1 mm for the peripheral retina. When 2D methods were used to fit the peripheral retina, the fitted radii differed a mean 0.1±0.1 mm from the 3D method.

Conclusion

An accurate and reproducible determination of the 3D retinal shape based on MRI is provided together with 2D alternatives, enabling wider use of this method in the field of ophthalmology.
Time for change in practice of in-patient oxygen therapy: a period-limited, multidimensional approach to improve oxygen prescription compliance: quality improvement project at Hamad General Hospital, Qatar
Authors: Rose Samman , Sardar Sundus , Sasi Sreethish , Al Mohanadi Dabia Hamad S H , Al-Mohammed Ahmed Ali A A , Zahid Muhammad
Published: November 2021

Prescription of oxygen therapy has traditionally poor compliance across the globe and mostly given to patients on verbal orders leading to under or overuse. The British Thoracic Society (BTS) guidelines (2017) recommend that oxygen therapy must be prescribed. Our study aimed to assess the prescription practice of oxygen therapy for patients admitted to acute medical assessment unit and general medical wards at Hamad General Hospital, Qatar and to achieve 80% compliance of valid oxygen therapy prescription implementing the quality improvement model against the BTS guidelines.

The prescription practice of oxygen therapy was audited between April 2019 and August 2019. Using a Plan, Do, Study, Act (PDSA) model of improvement and multiple interventions was performed in the eight PDSA cycles, including (1) educational sessions for residents/fellows/nurses, (2) introduction of electronic prescription, (3) emails, posters/flyers, (4) nurse-led reminders and (5) re-enforced teaching for new residents. Data were then collected using a questionnaire assessing electronic prescriptions and documentation. Our baseline study regarding oxygen therapy showed limited awareness of BTS guidelines regarding the documentation of initiation and further adjustment of oxygen therapy. There was a lack of compliance with oxygen prescription; none of the patients had a valid prescription on our computer-based prescription (Cerner). The duration, target range and indications of Oxygen therapy were documented in 25% (18/72), 45.8% (33/72) and 42% (30/72) patients, respectively. Oxygen was initiated by communication order only. In a total of 16 weeks period, the repeated PDSA cycles showed significant improvement in safe oxygen prescription practices. Following intervention, oxygen electronic prescription, documentation of indications for oxygen therapy, target oxygen saturation and wean-off plan improved to 93%, 85%, 86 % and 80 %, respectively.

We concluded that poor compliance to oxygen therapy Orders is a universal issue, which can be successfully managed using small-scale PDSA cycles to ensure sustained improvement through multidimensional interventions, continuous reinforcement and frequent reassessments.
COVID-19 and child marriage in Bangladesh: emergency call to action
Authors: Hossain Md. Jamal , Soma Mahfuza Afroz , Bari Md. Sazzadul , Emran Talha Bin , Islam Md. Rabiul
Published: November 2021

The social burden of Bangladesh’s already prevalent child marriage problem has further flared up amid the ongoing COVID-19 pandemic. We aim to briefly report on the current scenario of underage marriage in Bangladesh from available sources and highlight concerns. The prevalence of child marriage has increased by at least 13% due to pandemic-enforced long-term school closure throughout the country, while many cases remain unreported. Exacerbated financial crisis, the prolonged shutdown of educational institutions and social insecurities are the principal triggering factors for such a high pace of child marriages. We urge the government and local administrations to address the current situation through concerted and integrated efforts to combat the early marriage crisis in Bangladesh.
Pan-cancer landscape ofCD274(PD-L1) rearrangements in 283,050 patient samples, its correlation with PD-L1 protein expression, and immunotherapy response
Authors: Kelly Andrew D , Murugesan Karthikeyan , Kuang Zheng , Montesion Meagan , Ross Jeffrey S , Albacker Lee A , Huang Richard S P , Lin Douglas I , Demirci Umut , Creeden James
Published: November 2021

Background

Immune checkpoint inhibitors (ICIs) benefit patients with multiple cancer types, however, additional predictive biomarkers of response are needed.CD274(programmed cell death ligand-1, PD-L1) gene rearrangements are positively associated with PD-L1 expression and may confer benefit to ICI, thus a pan-cancer characterization of these alterations is needed.

Methods

We analyzed 283,050 patient samples across multiple tumor types that underwent comprehensive genomic profiling for activatingCD274rearrangements and other alterations. The DAKO 22C3 Tumor Proportion Scoring (TPS) method was used for PD-L1 immunohistochemistry (IHC) testing in a small subset with available data (n=55,423). A retrospective deidentified real-world clinico-genomic database (CGDB) was examined for ICI treatment outcomes. We also report a detailed case ofCD274-rearranged metastatic rectal adenocarcinoma.

Results

We identified 145 samples with functional rearrangements inCD274. There were significant enrichments forPIK3CA,JAK2,PDCD1LG2,CREBBP, andPBRM1co-mutations (ORs=2.1, 16.7, 17.8, 3.6, and 3.4, respectively, p<0.01). Genomic human papillomavirus (HPV)-16, Epstein-Barr virus, and mismatch repair genes also co-occurred (OR=6.2, 8.4, and 4.3, respectively, p<0.05). Median tumor mutational burden (TMB) was higher compared withCD274wild-type samples (7.0 vs 3.5 mutations/Mb, p=1.7e-11), with disease-specific TMB enrichment in non-small cell lung, colorectal, unknown primary, and stomach cancers. PD-L1 IHC skewed toward positivity (N=39/43 samples with ≥1% positivity). Of eight patients from the CGDB, three remained on ICI treatment after 6 months. Separately, one patient with metastatic rectal adenocarcinoma experienced a pathologic complete response on chemoimmunotherapy.

Conclusions

CD274gene rearrangements are associated with increased PD-L1 IHC scores, higher TMB, and potential clinical benefit in ICI-treated patients with cancer.
CHA2DS2-VASc score stratifies mortality risk in patients with and without atrial fibrillation
Authors: Harb Serge C , Wang Tom Kai Ming , Nemer David , Wu Yuping , Cho Leslie , Menon Venu , Wazni Osama , Cremer Paul C , Jaber Wael
Published: November 2021

Objectives

The CHA2DS2-VASc score is the preferred risk model for anticoagulation decision-making in atrial fibrillation (AF) patients. Recent studies have found this score to have prognostic value in other cardiovascular diseases. We assessed the relationships between CHA2DS2-VASc score and long-term mortality in adults referred for stress testing,

Methods

165 184 consecutive patients from January 1991 to December 2014 from a prospective registry were studied, with CHA2DS2-VASc score calculated for all patients, and AF and anticoagulation status were recorded. The primary endpoint was all-cause mortality.

Results

In this cohort, 12 450 (7.5%) patients had AF and mean CHA2DS2-VASc score was 2.2±1.2. There were 22 152 (18.4%) deaths during mean follow-up of 6.1±4.8 years. In multivariable analysis, CHA2DS2-VASc score, presence of AF and anticoagulation use, along with end-stage renal failure and smoking were all independently associated with mortality with HRs (95% CIs) of 1.23 (1.21 to 1.25), 1.18 (1.10 to 1.27) and 1.50 (1.40 to 1.60), respectively. Higher CHA2DS2-VASc score was incrementally associated with worse survival both in patients with and without AF (log-rank p<0.001). Anticoagulation use was associated with reduced survival in non-AF patients with alternative anticoagulation indications at all CHA2DS2-VASc score categories, and AF patients with lower CHA2DS2-VASc score 0–2, but was protective in AF patients with higher CHA2DS2-VASc score 4–9.

Conclusion

Incrementally higher CHA2DS2-VASc score, a simple clinical tool, is associated with mortality in patients regardless of presence of AF and anticoagulation status. Anticoagulation use was associated with worse survival in non-AF patients and AF patients with low CHA2DS2-VASc scores, but was protective in AF patients with high CHA2DS2-VASc scores.
Third-order optical nonlinearity of DSR13/THF solutions under CW He–Ne laser irradiation using Z-scan method
Authors: Abbas Bassam , Alshikh Khalil Mohammad
Published: November 2021

The Z-scan technique was employed to explore the third-order nonlinear optical properties of disperse red 13 organic chromophore solutions in tetrahydrofuran. A continuous-wave He–Ne laser (632.8 nm) was used as a source of irradiation. The nonlinear absorption and nonlinear refractive index coefficients of this dye were investigated. The results showed that this dye has a good nonlinear response with its real and imaginary quantities of third-order susceptibility. The solutions showed negative nonlinear refraction. The best obtained value of the third-order susceptibility was 6.37 × 10–3 esu at a dye concentration of 3.15 × 10–4 mol/L. Moreover, the nonlinear optical properties were enhanced with higher dye concentrations, and an elevated trend in nonlinear absorption and nonlinear refractive index coefficients was observed. Also, it was found that the reverse saturable absorption was the main mechanism responsible for the two-photon absorption effect in DSR13/THF samples.
Identification of topology changes in power grids via reduced admittance matrix
Authors: Lin Ling , Ding Li , Kong Zhengmin , Chen Chaoyang
Published: November 2021

Frequent changes in power grid topology bring risks to the stable operation of power systems. It is essential to identify changes in the power grid topology quickly and accurately. This paper presents a novel method named network reduction-based topology change identification (NR-TCI) algorithm to identify topology changes in multi-machine power systems. The proposed algorithm can quickly identify power grid topology changes using only phasor measurement unit (PMU) data sampled during the system’s transient process. The NR-TCI algorithm uses the network order reduction method to reduce the order of a bus admittance matrix and then uses PMU measurement data to estimate the reduced admittance matrix by least square method. Finally, the reduced admittance matrix is adopted to find topological information, and the Sherman–Morrison formula is utilized to identify the topology changes. The effectiveness of the proposed NR-TCI algorithm is verified with a case study of a 3 machine 9 bus system in Matlab. In addition, the influence of PMU sampling frequency on the effectiveness of the proposed algorithm is also studied.
Bifurcation Analysis of a Diffusive SIR Model with Saturated Treatment in a Heterogeneous Environment
Authors: Avila-Vales Eric , Pérez Ángel G. C.
Published: November 2021

In this paper, we propose a diffusive SIR model with general incidence rate, saturated treatment rate and spatially heterogeneous diffusion coefficients. We first prove the global existence of bounded solutions for the model and compute the basic reproduction number. We study the local and global stabilities of the disease-free equilibrium and the uniform persistence. In the case when the diffusion rate of infected individuals is constant, we carry out a bifurcation analysis of equilibria by considering the maximal treatment rate as the bifurcation parameter. Finally, we perform some numerical simulations, which show that the solutions to our model present periodic oscillations for certain values of the parameters.
A Stochastic Hierarchical Population System: Excitement, Extinction and Transition to Chaos
Authors: Bashkirtseva Irina , Perevalova Tatyana , Ryashko Lev
Published: November 2021

A problem of the mathematical modeling and analysis of noise-induced transformations of complex oscillatory regimes in hierarchical population systems is considered. As a key example, we use a three-dimensional food chain dynamical model of the interacting prey, predator, and top predator. We perform a comparative study of the impacts of random fluctuations on three key biological parameters of prey growth, predator mortality, and the top predator growth. A detailed investigation of the stochastic excitement, noise-induced transition from order to chaos, and various scenarios of extinction is carried out. Constructive abilities of the semi-analytical method of confidence domains in the analysis of the noise-induced extinction are demonstrated.
Bifurcations and Exact Solitary Wave, Compacton and Pseudo-Peakon Solutions in a Modified Generalized KdV Equation
Authors: Shi Jianping , Li Jibin
Published: November 2021

A modified generalized KdV equation is considered in this paper. Under the given parameter conditions, the corresponding traveling wave system is a singular planar dynamical system with three singular straight lines. The bifurcations and traveling wave solutions of the system are investigated in the parameter space from the perspective of dynamical systems. The existence of solitary wave solutions, periodic peakon solutions, pseudo-peakon solutions, kink and anti-kink wave solutions and compactons is proved. Furthermore, possible exact explicit parametric representations of various solutions are given. Particularly, the model has uncountably infinite many solitary wave and pseudo-peakon solutions.
A THEORETICAL STUDY ON FRACTIONAL EBOLA HEMORRHAGIC FEVER MODEL
Authors: MOMANI SHAHER , CHAUHAN R. P. , KUMAR SUNIL , HADID SAMIR
Published: November 2021

The Ebola virus infection (EVI), generally known as Ebola hemorrhagic fever, is a major health concern. The occasional outbreaks of virus occur primarily in certain parts of Africa. Many researches have been devoted to the study of the Ebola virus disease. In this paper, we have taken susceptible-infected-recovered-deceased-environment (SIRDP) system to investigate the dynamics of Ebola virus infection. We adopted fractional operators for a better illustration of model dynamics and memory effects. Initially, the Ebola disease model is modified with Caputo–Fabrizio arbitrary operator in Caputo sense (CFC) and we employed the fixed-point results for the existence and uniqueness of the solution of the fractional system. Further, we adopted the arbitrary fractional conformable and [Formula: see text]-conformable derivatives to the alternative representation of the model. For the numerical approximation of the system, we show a numerical technique based on the fundamental theorem of fractional calculus for CFC derivative and a numerical scheme called the Adams–Moulton for conformable derivatives. Finally, for the validation of theoretical results, the numerical simulations are displayed.
A STUDY ON THE RELATION BETWEEN MORPHOLOGICAL AND CHEMICAL CHANGES AND WETTABILITY MODIFICATION OF POLYETHERSULFONE SURFACE AFTER IRRADIATION WITH A PULSED KrF LASER
Authors: PAZOKIAN HEDIEH , RASHIDIAN VAZIRI MOHAMMAD REZA
Published: November 2021

Laser irradiation is used for surface modification of polymers aiming to improve their properties for different applications. The wettability of a polymeric surface can significantly affect its performance for biological applications. In this paper, the interaction of high-energy KrF laser photons in the two above- and below-threshold regimes with polyethersulfone polymer is studied. The role of morphological and chemical changes of the irradiated polymer and their correlation in the modification of the wetting property of this polymer is investigated. The obtained results show that the morphological parameter of surface roughness is the dominant mechanism in the below-threshold regime, while in the above-threshold region, the competition between this parameter and the carbonization amount of the surface determines the final hydrophilic response.
Application of BP Neural Network Based on Petrophysical Big Data Mining
Authors: Ding Yu , Yuan Shixiong , Deng Rui , Luo Chenxiang
Published: November 2021

Based on the big data mining method of petrophysical data, this paper studies the method and application of BP neural network to establish nonlinear interpretation model in distributed cloud computing environment. The nonlinear mapping relationship between the relative objective logging response and actual formation component is established by extracting the data mining result model, which overcomes existing deficiencies of the conventional logging interpretation procedure based on the homogeneity theory, linear hypothesis and the use of statistical experience simplifying model and parameters. The results show that network prediction model has been improved and has superior reference value for solving practical problems of interpretation under complex geological conditions.
High-OrderAb InitioValence Force Field with Chemical Pattern-Based Parameter Assignment
Authors: Yang Xudong , Liu Chengwen , Ren Pengyu
Published: November 2021

Bonded (or valence) interactions, which directly determine the local structures of the molecules, are fundamental parts of molecular mechanics force fields (FFs). Most popular classical FFs adopt the simple harmonic models for bond stretching and angle bending and ignore cross-coupling effects among the valence terms. This may lead to less accurate vibrational properties and configurations in molecular dynamics (MD) simulations. AMOEBA models utilize an MM3(MM4)-style bonded interaction model, in which the vibrational anharmonicity, the coupling effects among different energy terms, and the out-of-plane bending for sp2-hybridized atoms are considered. In this work, we report the development of bonded interaction parameters for a wide range of chemistry based on quantum mechanics (QM). About 270 atomic types defined by SMARTS strings were used to model the valence interactions. Our results indicate that the resulting valence parameters produce accurate vibrational frequencies (RMSD from QM is less than ∼36.6cm−1) over a large set of molecules with diverse functional groups (445 molecules). By contrast, the harmonic models usually give an RMS error greater than 60cm−1. Meanwhile, this model accurately reflects the potential energy surface of the out-of-plane bending. Our model can generally be applied to the AMOEBA family and any MM3(MM4)-based molecular mechanics FFs.
Impact of Electronic Polarization on Preformed, β-Strand Rich Homogenous and Heterogeneous Amyloid Oligomers
Authors: King Kelsie M. , Sharp Amanda K. , Davidson Darcy S. , Brown Anne M. , Lemkul Justin A.
Published: November 2021

Amyloids are a subset of intrinsically disordered proteins (IDPs) that self-assemble into cross-[Formula: see text] oligomers and fibrils. The structural plasticity of amyloids leads to sampling of metastable, low-molecular-weight oligomers that contribute to cytotoxicity. Of interest are amyloid-[Formula: see text] (A[Formula: see text] and islet amyloid polypeptide (IAPP), which are involved in the pathology of Alzheimer’s disease and Type 2 diabetes mellitus, respectively. In addition to forming homogenous oligomers and fibrils, these species have been found to cross-aggregate in heterogeneous structures. Biophysical properties, including electronic effects, that are unique or conserved between homogenous and heterogeneous amyloids oligomers are thus far unexplored. Here, we simulated homogenous and heterogeneous amyloid oligomers of A[Formula: see text] and IAPP[Formula: see text] fragments using the Drude oscillator model to investigate the impact of electronic polarization on the structural morphology and stability of preformed hexamers. Upon simulation of preformed, [Formula: see text]-strand rich oligomers with Drude, structural rearrangement occurred causing some loss of [Formula: see text]-strand structure in favor of random coil content for all oligomers. Homogenous A[Formula: see text] was the most stable system, deriving stability from low polarization in hydrophobic residues and through salt bridge formation. Changes in polarization were observed primarily for A[Formula: see text] residues in heterogeneous cross-amyloid systems, displaying a decrease in charged residue dipole moments and an increase in hydrophobic sidechain dipole moments. This work is the first study utilizing the Drude-2019 force field with amyloid oligomers, providing insight into the impact of electronic effects on oligomer structure and highlighting the importance of different microenvironments on amyloid oligomer stability.
A Review on Fact Extraction and Verification
Authors: Bekoulis Giannis , Papagiannopoulou Christina , Deligiannis Nikos
Published: November 2021

We study the fact-checking problem, which aims to identify the veracity of a given claim. Specifically, we focus on the task of Fact Extraction and VERification (FEVER) and its accompanied dataset. The task consists of the subtasks of retrieving the relevant documents (and sentences) from Wikipedia and validating whether the information in the documents supports or refutes a given claim. This task is essential and can be the building block of applications such as fake news detection and medical claim verification. In this article, we aim at a better understanding of the challenges of the task by presenting the literature in a structured and comprehensive way. We describe the proposed methods by analyzing the technical perspectives of the different approaches and discussing the performance results on the FEVER dataset, which is the most well-studied and formally structured dataset on the fact extraction and verification task. We also conduct the largest experimental study to date on identifying beneficial loss functions for the sentence retrieval component. Our analysis indicates that sampling negative sentences is important for improving the performance and decreasing the computational complexity. Finally, we describe open issues and future challenges, and we motivate future research in the task.
Vulnerabilities of Unattended Face Verification Systems to Facial Components-based Presentation Attacks: An Empirical Study
Authors: Qin Le , Peng Fei , Long Min , Ramachandra Raghavendra , Busch Christoph
Published: November 2021

As face presentation attacks (PAs) are realistic threats for unattended face verification systems, face presentation attack detection (PAD) has been intensively investigated in past years, and the recent advances in face PAD have significantly reduced the success rate of such attacks. In this article, an empirical study on a novel and effective face impostor PA is made. In the proposed PA, a facial artifact is created by using the most vulnerable facial components, which are optimally selected based on the vulnerability analysis of different facial components to impostor PAs. An attacker can launch a face PA by presenting a facial artifact on his or her own real face. With a collected PA database containing various types of artifacts and presentation attack instruments (PAIs), the experimental results and analysis show that the proposed PA poses a more serious threat to face verification and PAD systems compared with the print, replay, and mask PAs. Moreover, the generalization ability of the proposed PA and the vulnerability analysis with regard to commercial systems are also investigated by evaluating unknown face verification and real-world PAD systems. It provides a new paradigm for the study of face PAs.