bluuebunny/crossref_metadata_2025 huggingface dataset:
Fluorescence lifetime tracking and imaging of single moving particles assisted by a low-photon-count analysis algorithm
Authors: Chen Pengfa , Kang Qin , Niu JingJing , Jing YingYing , Zhang Xiao , Yu Bin , Qu Junle , Lin Danying
Published: March 2023

Fluorescence lifetime imaging microscopy (FLIM) has been widely used in the field of biological research because of its high specificity, sensitivity, and quantitative ability in the sensing cellular microenvironment. The most commonly used FLIM technology is based on time-correlated single photon counting (TCSPC). Although the TCSPC method has the highest temporal resolution, the data acquisition time is usually long, and the imaging speed is slow. In this work, we proposed a fast FLIM technology for fluorescence lifetime tracking and imaging of single moving particles, named single particle tracking FLIM (SPT-FLIM). We used feedback-controlled addressing scanning and Mosaic FLIM mode imaging to reduce the number of scanned pixels and the data readout time, respectively. Moreover, we developed a compressed sensing analysis algorithm based on alternating descent conditional gradient (ADCG) for low-photon-count data. We applied the ADCG-FLIM algorithm on both simulated and experimental datasets to evaluate its performance. The results showed that ADCG-FLIM could achieve reliable lifetime estimation with high accuracy and precision in the case of a photon count less than 100. By reducing the photon count requirement for each pixel from, typically, 1000 to 100, the acquisition time for a single frame lifetime image could be significantly shortened, and the imaging speed could be improved to a great extent. On this basis, we obtained lifetime trajectories of moving fluorescent beads using the SPT-FLIM technique. Overall, our work offers a powerful tool for fluorescence lifetime tracking and imaging of single moving particles, which will promote the application of TCSPC-FLIM in biological research.
Broadband tunable basic units for nonvolatile field programmable photonic gate array
Authors: Nampoothiri Govindan Nishi , Sadasivan Viswas
Published: March 2023

Field programmable photonic gate arrays (FPPGAs) use 2×2 tunable basic units (TBUs) interconnected as a mesh to achieve various functionalities on the same chip. It is desirable to have TBUs that can retain the state without power and function over a broad bandwidth. Different TBU structures and materials are compared in this work to design a suitable nonvolatile broadband device. An optical phase change material (O-PCM) based Mach–Zehnder interferometer provided the required nonvolatile TBU with a high bandwidth, low insertion loss, and low crosstalk. Among the various O-PCM materials, Sb2S3 provided the lowest insertion loss of <1dB and a low crosstalk of <−25dB. The proposed TBU can enable a low-power FPPGA with a smaller footprint and broader bandwidth compared to their volatile thermo-optic or electro-optic counterparts.
Improved 2 µm broadband luminescence in Tm3+/Ho3+ doping tellurite glass
Authors: Zhu Liqiao , Zhao Dongyi , Li Chengyan , Ding Jiale , Li Jun , Zhou Yaxun
Published: March 2023

Tm3+/Ho3+ doping tellurite glasses (TeO2-ZnO-La2O3) were prepared by applying melt-quenching technique, and the ∼2.0 µm band luminescence characteristics were examined. A broadband and relatively flat luminescence at 1600 to 2200 nm was observed in the tellurite glass co-doped by 1.0 mol% Tm2O3 and 0.085 mol% Ho2O3 under the excitation of 808 nm laser diode (LD), which is the result of spectral overlapping of 1.83 µm band of Tm3+ ions and 2.0 µm band of Ho3+ ions. Further, about 103% enhancement was acquired after the introduction of 0.1 mol% CeO2 and 7.5 mol% WO3 at the same time, which is primarily caused by the cross-relaxation between Tm3+ and Ce3+ ions together with the enhanced energy transfer from the Tm3+:3F4 level to Ho3+:5I7 level due to the increase in phonon energy. Spectral characteristics associated with the radiative transition of Ho3+ and Tm3+ ions on the basis of Judd-Ofelt theory, and the fluorescence decay behaviors after the addition of Ce3+ ions and WO3 component were analyzed to understand the broadband and luminescence enhancement. The findings in this work indicate that tellurite glass with optimal Tm3+-Ho3+-Ce3+ tri-doping combination and appropriate amount of WO3 is a prospective candidate for broadband optoelectronic devices operated in the infrared bands.
Improved design and experimental demonstration of ultrahigh-Q C6-symmetric H1 hexapole photonic crystal nanocavities
Authors: Takata Kenta , Kuramochi Eiichi , Shinya Akihiko , Notomi Masaya
Published: March 2023

An H1 photonic crystal nanocavity (PCN) is based on a single point defect and has eigenmodes with a variety of symmetric features. Thus, it is a promising building block for photonic tight-binding lattice systems that can be used in studies on condensed matter, non-Hermitian and topological physics. However, improving its radiative quality (Q) factor has been considered challenging. Here, we report the design of a hexapole mode of an H1 PCN with a Q factor exceeding 108. We achieved such extremely high-Q conditions by varying only four structural modulation parameters thanks to the C6 symmetry of the mode, despite the need of more complicated optimizations for many other PCNs. Our fabricated silicon H1 PCNs exhibited a systematic change in their resonant wavelengths depending on the spatial shift of the air holes in units of 1 nm. Out of 26 such samples, we found eight PCNs with loaded Q factors over one million. The best sample was of a measured Q factor of 1.2 × 106, and its intrinsic Q factor was estimated to be 1.5 × 106. We examined the difference between the theoretical and experimental performances by conducting a simulation of systems with input and output waveguides and with randomly distributed radii of air holes. Automated optimization using the same design parameters further increased the theoretical Q factor by up to 4.5 × 108, which is two orders of magnitude higher than in the previous studies. We clarify that this striking improvement of the Q factor was enabled by the gradual variation in effective optical confinement potential, which was missing in our former design. Our work elevates the performance of the H1 PCN to the ultrahigh-Q level and paves the way for its large-scale arrays with unconventional functionalities.
Femtosecond writing of intra-phase-mask volume Bragg gratings
Authors: Talbot Lauris , Bernier Martin
Published: March 2023

In this Letter, we report the first, to the best of our knowledge, femtosecond inscription of volume Bragg gratings (VBGs) directly inside phase-mask substrates. This approach showcases enhanced robustness as both the interference pattern generated by the phase mask and the writing medium are inherently bonded together. The technique is employed with 266-nm femtosecond pulses loosely focused by a 400-mm focal length cylindrical mirror inside fused-silica and fused-quartz phase-mask samples. Such a long focal length reduces the aberrations induced by the refractive-index mismatch at the air/glass interface which allows to inscribe a refractive-index modulation simultaneously over a glass depth reaching 1.5 mm. A decreasing gradient of the modulation amplitude from 5.9 × 10−4 at the surface to 1 × 10−5 at a 1.5-mm depth is observed. This technique has therefore the potential of increasing significantly the inscription depth of femtosecond-written VBGs.
Single-image-source binocular waveguide display based on polarization volume gratings and lenses
Authors: Weng Jiacheng , Li Haifeng , Wu Rengmao , Liu Xu
Published: March 2023

Waveguide displays, a highly competitive solution for augmented reality (AR), have attracted a lot of interest. A polarization-dependent binocular waveguide display using polarization volume lenses (PVLs) and polarization volume gratings (PVGs) as input and output couplers, respectively, is proposed. Light from a single image source is delivered to the left and right eyes independently according to its polarization state. Compared with traditional waveguide display systems, no additional collimation system is needed due to the deflection and collimation capabilities of PVLs. Leveraging the high efficiency, wide angular bandwidth, and polarization selectivity of liquid crystal elements, different images can be independently and accurately produced in the two eyes when the polarization of the image source is modulated. The proposed design paves the way for a compact and lightweight binocular AR near-eye display.
Mechano-biological and bio-mechanical pathways in cutaneous wound healing
Authors: Pensalfini Marco , Tepole Adrian Buganza
Published: March 2023

Injuries to the skin heal through coordinated action of fibroblast-mediated extracellular matrix (ECM) deposition, ECM remodeling, and wound contraction. Defects involving the dermis result in fibrotic scars featuring increased stiffness and altered collagen content and organization. Although computational models are crucial to unravel the underlying biochemical and biophysical mechanisms, simulations of the evolving wound biomechanics are seldom benchmarked against measurements. Here, we leverage recent quantifications of local tissue stiffness in murine wounds to refine a previously-proposed systems-mechanobiological finite-element model. Fibroblasts are considered as the main cell type involved in ECM remodeling and wound contraction. Tissue rebuilding is coordinated by the release and diffusion of a cytokine wave,e.g.TGF-β, itself developed in response to an earlier inflammatory signal triggered by platelet aggregation. We calibrate a model of the evolving wound biomechanics through a custom-developed hierarchical Bayesian inverse analysis procedure. Further calibration is based on published biochemical and morphological murine wound healing data over a 21-day healing period. The calibrated model recapitulates the temporal evolution of: inflammatory signal, fibroblast infiltration, collagen buildup, and wound contraction. Moreover, it enablesin silicohypothesis testing, which we explore by: (i) quantifying the alteration of wound contraction profiles corresponding to the measured variability in local wound stiffness; (ii) proposing alternative constitutive links connecting the dynamics of the biochemical fields to the evolving mechanical properties; (iii) discussing the plausibility of a stretch-vs.stiffness-mediated mechanobiological coupling. Ultimately, our model challenges the current understanding of wound biomechanics and mechanobiology, beside offering a versatile tool to explore and eventually control scar fibrosis after injury.
Spatial evaluation of healthcare accessibility across archipelagic communities of Maluku Province, Indonesia
Authors: Leosari Yanti , Uelmen Johnny Albert , Carney Ryan Marc
Published: March 2023

The Maluku Province is an underdeveloped region in Indonesia with over 1,340 scattered islands. Due to the limited health facilities and transportation infrastructure, access to healthcare is very challenging. Here, we combined data from various sources to locate the population clusters, health facilities, roads, and ports/docks, and then utilize geographic information systems (GIS) to estimate distances from residents to health facilities. Health workforce distribution data was then integrated to elucidate overall healthcare equity among districts in the province. The average distances to puskesmas (primary health clinics) were 8.89 km (by land) and 18.43 km (by land and water) respectively, and the average distances to hospitals were 56.19 km (by land) and 73.09 km (by land and water), with large disparities within and among districts. Analysis of health workforce data shows that 65% of 207 puskesmas lack physicians, while 49% lack midwives. Ambon, Tual, and Southeast Maluku have the highest health equity, while East Ceram, Buru, and South Buru have the lowest. In general, this study demonstrates the utility of GIS and spatial analyses, which can help identify problem areas in healthcare accessibility and equity in archipelago settings, and provide recommendations to stakeholders such as public health officials and district administrators.
Identification of key genes involved in secondary metabolite biosynthesis in Digitalis purpurea
Authors: Amiri Fatemeh , Moghadam Ali , Tahmasebi Ahmad , Niazi Ali
Published: March 2023

The medicinal plantDigitalis purpureaproduces cardiac glycosides that are useful in the pharmaceutical industry. These bioactive compounds are in high demand due to ethnobotany’s application to therapeutic procedures. Recent studies have investigated the role of integrative analysis of multi-omics data in understanding cellular metabolic status through systems metabolic engineering approach, as well as its application to genetically engineering metabolic pathways. In spite of numerous omics experiments, most molecular mechanisms involved in metabolic pathways biosynthesis inD.purpurearemain unclear. Using R Package Weighted Gene Co-expression Network Analysis, co-expression analysis was performed on the transcriptome and metabolome data. As a result of our study, we identified transcription factors, transcriptional regulators, protein kinases, transporters, non-coding RNAs, and hub genes that are involved in the production of secondary metabolites. Since jasmonates are involved in the biosynthesis of cardiac glycosides, the candidate genes forScarecrow-Like Protein 14(SCL14),Delta24-sterol reductase(DWF1),HYDRA1(HYD1), and Jasmonate-ZIM domain3 (JAZ3) were validated under methyl jasmonate treatment (MeJA, 100 μM). Despite early induction ofJAZ3, which affected downstream genes, it was dramatically suppressed after 48 hours.SCL14, which targetsDWF1, andHYD1, which induces cholesterol and cardiac glycoside biosynthesis, were both promoted. The correlation between key genes and main metabolites and validation of expression patterns provide a unique insight into the biosynthesis mechanisms of cardiac glycosides inD.purpurea.
A new gene tree algorithm employing DNA sequences of bovine genome using discrete Fourier transformation
Authors: Abadeh Roxana , Aminafshar Mehdi , Ghaderi-Zefrehei Mostafa , Chamani Mohammad
Published: March 2023

Within the realms of human thoughts on nature, Fourier analysis is considered as one of the greatest ideas currently put forwarded. The Fourier transform shows that any periodic function can be rewritten as the sum of sinusoidal functions. Having a Fourier transform view on real-world problems like the DNA sequence of genes, would make things intuitively simple to understand in comparison with their initial formal domain view. In this study we used discrete Fourier transform (DFT) on DNA sequences of a set of genes in the bovine genome known to govern milk production, in order to develop a new gene clustering algorithm. The implementation of this algorithm is very user-friendly and requires only simple routine mathematical operations. By transforming the configuration of gene sequences into frequency domain, we sought to elucidate important features and reveal hidden gene properties. This is biologically appealing since no information is lost via this transformation and we are therefore not reducing the number of degrees of freedom. The results from different clustering methods were integrated using evidence accumulation algorithms to provide in insilico validation of our results. We propose using candidate gene sequences accompanied by other genes of biologically unknown function. These will then be assigned some degree of relevant annotation by using our proposed algorithm. Current knowledge in biological gene clustering investigation is also lacking, and so DFT-based methods will help shine a light on use of these algorithms for biological insight.
Deuterium isotope probing (DIP) on Listeria innocua: Optimisation of labelling and impact on viability state
Authors: Trigueros Sylvain , Brauge Thomas , Dedole Tommy , Debuiche Sabine , Rebuffel Véronique , Morales Sophie , Marcoux Pierre R. , Midelet Graziella
Published: March 2023

An innovative approach, Raman microspectroscopy coupled with deuterium isotope probing (Raman-DIP), can be used to evaluate the metabolism of deuterated carbon source in bacteria and also to presume different anabolic pathways. This method requires the treatment of cells with heavy water that could affect the bacterial viability state at higher concentration. In this study, we evaluated the effect of heavy water incorporation on the viability state of Listeria innocua cells. We exposed the L. innocua suspensions to different heavy water concentrations (0%, 25%, 50% and 75%) from 30 minutes to 72 h of incubation times at 37°C. The total, viable and viable culturable populations were quantified by qPCR, PMA-qPCR and plate count agar respectively. We analyzed heavy water incorporation by Raman-DIP. The exposure of L. innocua cells to different concentrations of heavy water did not alter their cell viability to 24 h incubation time. In addition, the maximum intensity for C-D band, specific for the incorporation of heavy water, was reached after 2 h of exposure in a media containing 75% v/v D2O but an early detection of the labelling was possible at t = 1 h 30 min. In conclusion, the use of D2O as a metabolic marker was validated and can be developed for the detection of L. innocua cell viability state.
Oral and emotional health experience of refugees’ in the state of Massachusetts - A mixed methods approach
Authors: Aldukhail Shaikha , Shukla Anubhuti , Khadra Mohammad Tareq , Al Hennawi Ziad , Jordan Samantha , Cadet Tamara J. , Alqaderi Hend
Published: March 2023

Objectives

In this study, we aimed to explore the oral and emotional health challenges experienced by a sample of refugees in Massachusetts across different stages of resettlement using a mixed methods approach.

Methods

We collaborated with two Federally Qualified Health Centers to identify and recruit participants for either surveys (n = 69) or semi-structured interviews (n = 12). Data collection was conducted in 2018. We performed descriptive statistics using STATA 14, and analyzed the interviews using qualitative methods.

Results

Overall, cost and lack of structure were the largest barriers identified for accessing dental care in participants’ home and host countries. In the US, participants reported receiving state-provided public health insurance, but still experienced disrupted access to dental care due to coverage limitations. We identified several mental health risk factors that may affect participants’ oral health, including trauma, depression, and sleeping problems. Despite these challenges, participants also identified areas of resilience and adaptability in both attitude and actions.

Conclusions

The themes identified in our study suggest that refugees have attitudes, beliefs, and experiences that contribute to their perspectives on oral health care. While some of the reported barriers to access dental care were attitudinal, others were structural. Access to dental care in the US was reported to be structured and available, but with limited coverage issues. This paper underscores the oral and emotional health aspects of refugees for future considerations and planning of appropriate, affordable and cost-effective policies in the global health care systems.
Predictive simulation of single-leg landing scenarios for ACL injury risk factors evaluation
Authors: Moustridi Evgenia , Risvas Konstantinos , Moustakas Konstantinos
Published: March 2023

The Anterior Cruciate Ligament (ACL) rupture is a very common knee injury during sport activities. Landing after jump is one of the most prominent human body movements that can lead to such an injury. The landing-related ACL injury risk factors have been in the spotlight of research interest. Over the years, researchers and clinicians acquire knowledge about human movement during daily-life activities by organizing complex in vivo studies that feature high complexity, costs and technical and most importantly physical challenges. In an attempt to overcome these limitations, this paper introduces a computational modeling and simulation pipeline that aims to predict and identify key parameters of interest that are related to ACL injury during single-leg landings. We examined the following conditions: a) landing height, b) hip internal and external rotation, c) lumbar forward and backward leaning, d) lumbar medial and lateral bending, e) muscle forces permutations and f) effort goal weight. Identified on related research studies, we evaluated the following risk factors: vertical Ground Reaction Force (vGRF), knee joint Anterior force (AF), Medial force (MF), Compressive force (CF), Abduction moment (AbdM), Internal rotation moment (IRM), quadricep and hamstring muscle forces and Quadriceps/Hamstrings force ratio (Q/H force ratio). Our study clearly demonstrated that ACL injury is a rather complicated mechanism with many associated risk factors which are evidently correlated. Nevertheless, the results were mostly in agreement with other research studies regarding the ACL risk factors. The presented pipeline showcased promising potential of predictive simulations to evaluate different aspects of complicated phenomena, such as the ACL injury.
“In an ideal world that would be a multiagency service because you need everybody’s expertise.” Managing hoarding disorder: A qualitative investigation of existing procedures and practices
Authors: Haighton Catherine , Caiazza Roberta , Neave Nick
Published: March 2023

Hoarding disorder is characterised by the acquisition of, and failure to discard large numbers of items regardless of their actual value, a perceived need to save the items and distress associated with discarding them, significant clutter in living spaces that render the activities associated with those spaces very difficult causing significant distress or impairment in functioning. To aid development of an intervention for hoarding disorder we aimed to identify current practice by investigating key stakeholders existing practice regarding identification, assessment and intervention associated with people with hoarding disorder. Two focus groups with a purposive sample of 17 (eight male, nine female) stakeholders representing a range of services from housing, health, and social care were audio recorded, transcribed verbatim and analysed thematically. There was a lack of consensus regarding how hoarding disorder was understood and of the number of cases of hoarding disorder however all stakeholders agreed hoarding disorder appeared to be increasing. The clutter image rating scale was most used to identify people who needed help for hoarding disorder, in addition to other assessments relevant to the stakeholder. People with hoarding disorder were commonly identified in social housing where regular access to property was required. Stakeholders reported that symptoms of hoarding disorder were often tackled by enforced cleaning, eviction, or other legal action however these approaches were extremely traumatic for the person with hoarding disorder and failed to address the root cause of the disorder. While stakeholders reported there was no established services or treatment pathways specifically for people with hoarding disorder, stakeholders were unanimous in their support for a multi-agency approach. The absence of an established multiagency service that would offer an appropriate and effective pathway when working with a hoarding disorder presentation led stakeholders to work together to suggest a psychology led multiagency model for people who present with hoarding disorder. There is currently a need to examine the acceptability of such a model.
A cross-sectional analysis of the predictors of COVID-19 vaccine uptake and vaccine hesitancy in Iraq
Authors: Alatrany Saad S. J. , Falaiyah Ashraf Muwafa , Zuhairawi Raheem Hammlee Maarij , Ogden Ruth , ALi Sayyid ALdrraji ‏Hasan , Alatrany Abbas S. S. , Al-Jumeily Dhiya
Published: March 2023

Background

Vaccine hesitancy poses a significant risk to global recovery from COVID-19. To date however, there is little research exploring the psychological factors associated with vaccine acceptability and hesitancy in Iraq.

Aim

To explore attitudes towards COVID-19 vaccination in Iraq. To establish the predictors of vaccine uptake and vaccine hesitancy in an Iraqi population.

Methods

Using a cross-sectional design, 7,778 participants completed an online questionnaire exploring their vaccination status, likelihood of infection, perceived severity infection, benefits of vaccine, barriers to vaccine, anticipated regret, subjective norms, and trust in government.

Findings

Vaccination rates increased with age and were greater in males, those who were married, divorced or widowed, those with children and those with underlying conditions. Vaccine hesitancy was widespread with 61.40% of unvaccinated individuals reported an unwillingness to receive a COVID-19 vaccine. In unvaccinated groups, vaccine hesitancy was associated with lower trust in the government, more negative social norms, greater perceived barriers to vaccination and reduced perceived benefits.

Conclusions

There is significant COVID-19 vaccine hesitancy in Iraq. Public health institutions should be aware of the influence of demographic factors, as well as personal beliefs and social norms, on individuals’ decisions to vaccinate. Public health messaging should therefore aim to be tailored to address the concerns of citizens.
spmodel: Spatial statistical modeling and prediction in R
Authors: Dumelle Michael , Higham Matt , Ver Hoef Jay M.
Published: March 2023

spmodelis anRpackage used to fit, summarize, and predict for a variety spatial statistical models applied to point-referenced or areal (lattice) data. Parameters are estimated using various methods, including likelihood-based optimization and weighted least squares based on variograms. Additional modeling features include anisotropy, non-spatial random effects, partition factors, big data approaches, and more. Model-fit statistics are used to summarize, visualize, and compare models. Predictions at unobserved locations are readily obtainable.
Shedding light on participant selection bias in Ecological Momentary Assessment (EMA) studies: Findings from an internet panel study
Authors: Stone Arthur A. , Schneider Stefan , Smyth Joshua M. , Junghaenel Doerte U. , Wen Cheng , Couper Mick P. , Goldstein Sarah
Published: March 2023

Although the potential for participant selection bias is readily acknowledged in the momentary data collection literature, very little is known about uptake rates in these studies or about differences in the people that participate versus those who do not. This study analyzed data from an existing Internet panel of older people (age 50 and greater) who were offered participation into a momentary study (n = 3,169), which made it possible to compute uptake and to compare many characteristics of participation status. Momentary studies present participants with brief surveys multiple times a day over several days; these surveys ask about immediate or recent experiences. A 29.1% uptake rate was observed when all respondents were considered, whereas a 39.2% uptake rate was found when individuals who did not have eligible smartphones (necessary for ambulatory data collection) were eliminated from the analyses. Taking into account the participation rate for being in this Internet panel, we estimate uptake rates for the general population to be about 5%. A consistent pattern of differences emerged between those who accepted the invitation to participate versus those who did not (in univariate analyses): participants were more likely to be female, younger, have higher income, have higher levels of education, rate their health as better, be employed, not be retired, not be disabled, have better self-rated computer skills, and to have participated in more prior Internet surveys (all p < .0026). Many variables were not associated with uptake including race, big five personality scores, and subjective well-being. For several of the predictors, the magnitude of the effects on uptake was substantial. These results indicate the possibility that, depending upon the associations being investigated, person selection bias could be present in momentary data collection studies.
Prevalence and factors associated with pediatric HIV therapy failure in a tertiary hospital in Asmara, Eritrea: A 15-year retrospective cohort study
Authors: Mengistu Samuel Tekle , Ghebremeskel Ghirmay Ghebrekidan , Achila Oliver Okoth , Abrehe Miriam Berhane , Tewelde Samuel Fisseha , Idris Mahmud Mohammed , Tikue Tsegereda Gebrehiwot , Mesfin Araia Berhane
Published: March 2023

Introduction

Treatment failure (TF) in HIV infected children is a major concern in resource-constrained settings in Sub-Saharan Africa (SSA). This study investigated the prevalence, incidence, and factors associated with first-line cART failure using the virologic (plasma viral load), immunologic and clinical criteria among HIV-infected children.

Methods

A retrospective cohort study of children (<18 years of age on treatment for a period of > 6 months) enrolled in the pediatric HIV/AIDs treatment program at Orotta National Pediatric Referral Hospital from January 2005 to December 2020 was conducted. Data were summarized using percentages, medians (± interquartile range (IQR)), or mean ± standard deviation (SD). Where appropriate, Pearson Chi-Squire (χ2) tests or Fishers exacts test, Kaplan–Meier (KM) estimates, and unadjusted and adjusted Cox-proportional hazard regression models were employed.

Results

Out of 724 children with at least 24 weeks’ follow-up 279 experienced therapy failure (TF) making prevalence of 38.5% (95% CI 35–42.2) over a median follow-up of 72 months (IQR, 49–112 months), with a crude incidence of failure of 6.5 events per 100- person-years (95% CI 5.8–7.3). In the adjusted Cox proportional hazards model, independent factors of TF were suboptimal adherence (Adjusted Hazard Ratio (aHR) = 2.9, 95% CI 2.2–3.9, p < 0.001), cART backbone other than Zidovudine and Lamivudine (aHR = 1.6, 95% CI 1.1–2.2, p = 0.01), severe immunosuppression (aHR = 1.5, 95% CI 1–2.4, p = 0.04), wasting or weight for height z-score < -2 (aHR = 1.5, 95% CI 1.1–2.1, p = 0.02), late cART initiation calendar years (aHR = 1.15, 95% CI 1.1–1.3, p < 0.001), and older age at cART initiation (aHR = 1.01, 95% CI 1–1.02, p < 0.001).

Conclusions

Seven in one hundred children on first-line cART are likely to develop TF every year. To address this problem, access to viral load tests, adherence support, integration nutritional care into the clinic, and research on factors associated with suboptimal adherence should be prioritized.
Redundancy-aware unsupervised ranking based on game theory: Ranking pathways in collections of gene sets
Authors: Balestra Chiara , Maj Carlo , Müller Emmanuel , Mayr Andreas
Published: March 2023

In Genetics, gene sets are grouped in collections concerning their biological function. This often leads to high-dimensional, overlapping, and redundant families of sets, thus precluding a straightforward interpretation of their biological meaning. In Data Mining, it is often argued that techniques to reduce the dimensionality of data could increase the maneuverability and consequently the interpretability of large data. In the past years, moreover, we witnessed an increasing consciousness of the importance of understanding data and interpretable models in the machine learning and bioinformatics communities. On the one hand, there exist techniques aiming to aggregate overlapping gene sets to create larger pathways. While these methods could partly solve the large size of the collections’ problem, modifying biological pathways is hardly justifiable in this biological context. On the other hand, the representation methods to increase interpretability of collections of gene sets that have been proposed so far have proved to be insufficient. Inspired by this Bioinformatics context, we propose a method to rank sets within a family of sets based on the distribution of the singletons and their size. We obtain sets’ importance scores by computing Shapley values; Making use of microarray games, we do not incur the typical exponential computational complexity. Moreover, we address the challenge of constructing redundancy-aware rankings where, in our case, redundancy is a quantity proportional to the size of intersections among the sets in the collections. We use the obtained rankings to reduce the dimension of the families, therefore showing lower redundancy among sets while still preserving a high coverage of their elements. We finally evaluate our approach for collections of gene sets and apply Gene Sets Enrichment Analysis techniques to the now smaller collections: As expected, the unsupervised nature of the proposed rankings allows for unremarkable differences in the number of significant gene sets for specific phenotypic traits. In contrast, the number of performed statistical tests can be drastically reduced. The proposed rankings show a practical utility in bioinformatics to increase interpretability of the collections of gene sets and a step forward to include redundancy-awareness into Shapley values computations.
Antibiotic—Lysobacter enzymogenes proteases combination as a novel virulence attenuating therapy
Authors: Suaifan Ghadeer A. R. Y. , Abdel Rahman Diana M. A. , Abu-Odeh Ala’ M. , Abu Jbara Fahid , Shehadeh Mayadah B. , Darwish Rula M.
Published: March 2023

Minimizing antibiotic resistance is a key motivation strategy in designing and developing new and combination therapy. In this study, a combination of the antibiotics (cefixime, levofloxacin and gentamicin) with Lysobacter enzymogenes (L. enzymogenes) bioactive proteases present in the cell- free supernatant (CFS) have been investigated against the Gram-positive methicillin-sensitive Staphylococcus aureus (MSSA), methicillin-resistant Staphylococcus aureus (MRSA) and the Gram-negative Escherichia coli (E. coli O157:H7). Results indicated that L. enzymogenes CFS had maximum proteolytic activity after 11 days of incubation and higher growth inhibitory properties against MSSA and MRSA compared to E. coli (O157:H7). The combination of L. enzymogenes CFS with cefixime, gentamicin and levofloxacin at sub-MIC levels, has potentiated their bacterial inhibition capacity. Interestingly, combining cefixime with L. enzymogenes CFS restored its antibacterial activity against MRSA. The MTT assay revealed that L. enzymogenes CFS has no significant reduction in human normal skin fibroblast (CCD-1064SK) cell viability. In conclusion, L. enzymogenes bioactive proteases are natural potentiators for antimicrobials with different bacterial targets including cefixime, gentamicin and levofloxacin representing the beginning of a modern and efficient era in the battle against multidrug-resistant pathogens.
Research of the impact of economic decline on air quality in Wuhan under COVID-19 epidemic
Authors: Qiu Junda , Li Peng , You Congzhe , Fan Honghui
Published: March 2023

A novel economic impact model is proposed by this paper to analyze the impact of economic downturn on the air quality in Wuhan during the epidemic period, and to explore the effective solutions to improve the urban air pollution. The Space Optimal Aggregation Model (SOAM) is used to evaluate the air quality of Wuhan from January to April in 2019 and 2020. The analysis results show that the air quality of Wuhan from January to April 2020 is better than that of the same period in 2019, and it shows a gradually better trend. This shows that although the measures of household isolation, shutdown and production stoppage adopted during the epidemic period in Wuhan caused economic downturn, it objectively improved the air quality of the city. In addition, the impact of economic factors on PM2.5, SO2 and NO2 is 19%, 12% and 49% respectively calculated by the SOMA. This shows that industrial adjustment and technology upgrading for enterprises that emit a large amount of NO2 can greatly improve the air pollution situation in Wuhan. The SOMA can be extended to any city to analyze the impact of the economy on the composition of air pollutants, and it has extremely important application value at the level of industrial adjustment and transformation policy formulation.
Guided-deconvolution for correlative light and electron microscopy
Authors: Ma Fengjiao , Kaufmann Rainer , Sedzicki Jaroslaw , Cseresnyés Zoltán , Dehio Christoph , Hoeppener Stephanie , Figge Marc Thilo , Heintzmann Rainer
Published: March 2023

Correlative light and electron microscopy is a powerful tool to study the internal structure of cells. It combines the mutual benefit of correlating light (LM) and electron (EM) microscopy information. The EM images only contain contrast information. Therefore, some of the detailed structures cannot be specified from these images alone, especially when different cell organelle are contacted. However, the classical approach of overlaying LM onto EM images to assign functional to structural information is hampered by the large discrepancy in structural detail visible in the LM images. This paper aims at investigating an optimized approach which we call EM-guided deconvolution. This applies to living cells structures before fixation as well as previously fixed sample. It attempts to automatically assign fluorescence-labeled structures to structural details visible in the EM image to bridge the gaps in both resolution and specificity between the two imaging modes. We tested our approach on simulations, correlative data of multi-color beads and previously published data of biological samples.
Integration of evidence into Theory of Change frameworks in the healthcare sector: A rapid systematic review
Authors: Romão Davi Mamblona Marques , Setti Cecilia , Arruda Leo Heikiti Maeda , de Melo Roberta Crevelário , de Araujo Bruna Carolina , Tan Audrey R. , DeMaio Peter Nichols , Kuchenmüller Tanja
Published: March 2023

Background

Theory of Change (ToC) has become an established approach to design and evaluate interventions. While ToC should—in line with the growing international focus on evidence-informed health decision-making–consider explicit approaches to incorporate evidence, there is limited guidance on how this should be done. This rapid review aims to identify and synthesize the available literature on how to systematically use research evidence when developing or adapting ToCs in the health sector.

Methods

A rapid review methodology using a systematic approach, was designed. Eight electronic databases were consulted to search for peer-reviewed and gray publications detailing tools, methods, and recommendations promoting the systematic integration of research evidence in ToCs. The included studies were compared, and the findings summarized qualitatively into themes to identify key principles, stages, and procedures, guiding the systematic integration of research evidence when developing or revising a ToC.

Results

This review included 18 studies. The main sources from which evidence was retrieved in the ToC development process were institutional data, literature searches, and stakeholder consultation. There was a variety of ways of finding and using evidence in ToC. Firstly, the review provided an overview of existing definitions of ToC, methods applied in ToC development and the related ToC stages. Secondly, a typology of 7 stages relevant for evidence integration into ToCs was developed, outlining the types of evidence and research methods the included studies applied for each of the proposed stages.

Conclusion

This rapid review adds to the existing literature in two ways. First, it provides an up-to-date and comprehensive review of the existing methods for incorporating evidence into ToC development in the health sector. Second, it offers a new typology guiding any future endeavors of incorporating evidence into ToCs.
An exact bifurcation diagram for ap-qLaplacian boundary value problem
Authors: Acharya Ananta , Munoz Victor , Nichols Dustin , Shivaji Ratnasingham
Published: March 2023

We study positive solutions to thep–qLaplacian two-point boundary value problem:{−μ[(u′)p−1]′−[(u′)q−1]′=λu(1−u)on (0,1)u(0)=0=u(1)whenp=4andq=2. Hereλ>0is a parameter andμ≥0is a weight parameter influencing the higher-order diffusion term. Whenμ=0(the Laplacian case) the exact bifurcation diagram for a positive solution is well-known, namely, whenλ≤π2there are no positive solutions, and forλ>π2there exists a unique positive solutionuλ,μsuch that‖uλ,μ‖∞→0asλ→π2and‖uλ,μ‖∞→1asλ→∞. Here, we will prove that for allμ>0similar bifurcation diagrams preserve, and they all bifurcate from(λ,u)=(π2,0). Our results are established via the method of sub-super solutions and a quadrature method. We also present computational evaluations of these bifurcation diagrams for various values ofμand illustrate how they evolve whenμvaries.
On the Vortical Structures in a Linear Blade Cascade
Authors: Flídr E. , Jelínek T. , Němec M.
Published: March 2023

Paper deals with the investigation of the vortical structures in a linear blade cascade, more specifically this work is focused on the vortical structures in the end-wall region of the cascade. The effects of three different inlet flow angles ( α₁ = -25° ; 5° and 30° ) were studied under the constant isentropic Mach number (M₂,ᵢₛ = 0.4) and Reynolds number (Re₂,ᵢₛ = 4.5 × 10⁵).
Mixing Characteristics of a Magnetically Driven Rushton Turbine in an Unbaffled Stirred Tank Reactor
Authors: Idžakovičová K. , Haidl J. , Gebouský O. , Isoz M.
Published: March 2023

The standard and well-researched stirred vessel configuration comprises a tank equipped with one or more impellers positioned in the vessel’s axis and multiple wall-mounted baffles preventing the central vortex creation. However, particular industries, such as biotechnology, have an increased need for a sterile environment that often results in the usage of atypical stirred vessel configurations. An example of a commonly equipped atypical stirred vessel is an unbaffled stirred tank with an eccentric magnetically driven impeller. However, there is only a little knowledge about the mixing characteristics of such designs. In this work, we list experimental results for both the standard and atypical stirred vessel configurations. Furthermore, we present a CFD model of the atypical configuration. The model is used to calculate its mixing characteristics that are subsequently compared against our experimental results. It is shown that for the liquid height (H) to the vessel diameter (T) ratio H/T ≲ 1.2, the characteristics of both the standard and atypical designs coincide. For higher liquid heights (i) the characteristics of the atypical design decrease dramatically, and (ii) the characteristics estimates based on approaches developed for the standard configuration become unreliable.
Properties and Characteristics of the Fluid Flow Model With Non-Equilibrium Thermodynamic Pressure
Authors: Kardaś D.
Published: March 2023

The paper presents a model of fluid flow with non-equilibrium pressure and the pressure evolution equation. The equation takes into account the dynamics of pressure changes caused by the difference between hydrodynamic and thermodynamic pressure as well as bulk viscosity effects. For the model of one-dimensional fluid flow, consisting of the conservation equations and the pressure evolution equation, the disturbances velocity was determined using the method of characteristics. Even though there occurs viscosity in the equations, the perturbation velocities are finite. The evolution equation for pressure makes it possible to understand pressure as an independent component of a vector of unknowns, similarly to density, velocity and internal energy. Thanks to this, the integration of the non-equilibrium pressure over time is performed as it is an other unknown. The fluid flow solution is controlled by the presence of thermodynamic pressure in the form of an equilibrium equation of state.
Model Order Reduction for Particle-Laden Flows: Systems with Rotations and Discrete Transport Operators
Authors: Kovárnová A. , Isoz M.
Published: March 2023

In the present work, we concentrate on particle-laden flows as an example of industry-relevant transport-dominated systems. Our previously-developed framework for data-driven model order reduction (MOR) of such systems, the shifted proper orthogonal decomposition with interpolation via artificial neural networks, is further extended by improving the handling of general transport operators. First, even with intrusive MOR approaches, the underlying numerical solvers can provide only discrete realizations of transports linked to the movement of individual particles in the system. On the other hand, our MOR methodology requires continuous transport operators. Thus, the original framework was extended by the possibility to reconstruct continuous approximations of known discrete transports via another artificial neural network. Second, the treatment of rotation-comprising transports was significantly improved.
Modified Navier-Stokes Equations: An Overview and Numerical Aspects
Authors: Pozorski J. , Kajzer A.
Published: March 2023

The Navier-Stokes equations represent a well established, commonly accepted and amply validated model of Newtonian fluid flows. However, there has been a debate about its possible inconsistencies in the context of compressible viscous flow modelling. Alternative models have been put forward that, in particular, feature the density diffusive term in the equation of mass conservation. We briefly revisit physical arguments of that debate and recall a proposal of an alternative flow model, formulated by M. Svärd (2018), resulting in a purely parabolic type of the governing equation system. We present some discussion of the Sv¨ard model and an overview of its numerical aspects. We also recall our recent simplification of the model to handle low Mach number isothermal flows in the weakly compressible approach. From the purely numerical standpoint, the presence of mass diffusion in the continuity equation is beneficial as it reduces dispersive errors of simple centred discretisation schemes (numerical diffusion free). This has been confirmed in the benchmark simulations, including a doubly-periodic shear layer at low Mach numbers. The results have demonstrated high accuracy and efficiency of the mass diffusive flow model that has proven well suited for effective parallelisation.
FATORES AMBIENTAIS ASSOCIADOS A HOSPITALIZAÇÕES E ÓBITOS POR DOENÇAS CEREBROVASCULARES NO MUNICÍPIO DE NOVA IGUAÇU
Authors: Moura Paulo Henrique de , Silva Esthefany Evelyn Araújo , Sobreira Paula Guidone Pereira , Silva Fabricio Polifke da , Dias Luciana Armada , Maia Luiz Francisco Pires Guimarães , Moreno Adalgiza Mafra
Published: March 2023

Objetivo: associar fatores ambientais com as hospitalizações e óbitos por doença cerebrovascular nos residentes do município de Nova Iguaçu. Métodos: estudo observacional, retrospectivo e analítico. Foram utilizados bases de dados de qualidade do ar (PM10) do INEA, dados de hospitalizações e óbitos do DATASUS, por Doenças Cerebrovasculares (DCBV) contidos no CID X (subcapítulos I63-I66 e I69). A inferência estatística utilizou as causas de hospitalizações e óbitos por DCBV dividida por sexo considerando o valor de p ≤ 0,05. Os fatores ambientais foram correlacionados as hospitalizações e óbitos por DCBV. As análises estatísticas utilizaram software SPSS IBM 25 e a confecção gráfica o Excel e R studio. Resultados: A média das médias anuais de PM10 ultrapassou em 4,4 vezes os padrões do CONAMA. O sexo masculino apresentou maior número de hospitalizações e óbitos por doenças cerebrovasculares, e em faixas etárias inferiores as mulheres. A correlação entre a poluição do ar e hospitalizações foi positiva muito forte (r = 0,990; p < 0,000) e com os óbitos foi positiva e fraca (r = 0,300; p < 0,000). Conclusão: Apesar da redução das concentrações de PM10 ao longo dos anos, os valores excederam os padrões do CONAMA, correlacionando-se com o aumento das hospitalizações e óbitos por DCBV no município.