bluuebunny/crossref_metadata_2025 huggingface dataset:
Spatio-temporal characteristics of Tuberculosis in Ghana
Authors: Iddrisu Abdul-Karim , A. Amikiya Emmanuel , Kwame Bukari Francis
Published: January 2023

Background: The number of Tuberculosis (TB) cases or deaths is declining, however, the rate of decline is not adequate to meet the World Health Organization's (WHO's) mitigation. TB remains a public health problem in Ghana with a significant economic and health burden on its citizens and health care system.  Consequently, there is a need for further studies about the disease aimed at accelerating the rate of decline in cases.

Methods:  The spatio-temporal characteristics of TB in Ghana using Bayesian spatial and spatio-temporal regression models was analysed in this study. Data were obtained from Ghana National Tuberculosis Programme (NTP) for the 10 regions of Ghana, collected over a six-year period. The study also examines some baseline predictors of TB infections to ascertain their effects on the TB risk across the ten regions in Ghana.

Results: Hot-spots of TB cases are observed in the Upper East, Upper West, Volta, Western, and Central regions and low risk in the Northern, Ashanti, Greater Accra, Brong Ahafo, Eastern and Western regions. The results indicated a clustering of risk between neighboring regions. TB cure rate, TB success rate, knowledge about TB, awareness that TB is airborne, HIV prevalence, percentage of literacy, and high income are important predictors of  detection for this disease across the ten regions of Ghana.

Conclusion: Most regions in Ghana have similar TB risks. A substantial reduction in TB cases  requires measures that will increase  detection, success and cure rates, awareness, knowledge about how this disease spreads as well adequate health facilities with easy access.
Study protocol for a systematic review of the social determinants of mental health and well-being of older migrants aged 50 years and above
Authors: Bhatia Pankhuri , McLaren Helen , Huang Yunong
Published: January 2023

Background: Migration is a milestone event in a person’s life, bringing with it the challenges of settling down in an unfamiliar environment. The age at which migration takes place and the way migrants negotiate their old and new world significantly impacts their mental health.

Thus, this systematic review seeks to analyse and summarize existing research detailing the contexts in which people migrate later in life and the associations between these contexts and social determinants of their mental health and well-being.

Methods: Seven databases including PsycINFO, Web of Science, PubMed, Applied Social Sciences Index, Abstracts: ASSIA, Ageline, CINAHL, and Informit will be searched systematically for original journal articles published in English. In the first screening stage, the first reviewer (PB) will screen all titles and abstracts and mark all potentially eligible texts for full-text screening. The second reviewer (HM) will review the decisions made. Any potential conflicts will be resolved with discussion. Afterward, full texts of potentially eligible studies will be assessed for eligibility by two reviewers (PB and HM). The methodological quality (or risk of bias) of individual studies will be appraised using the Mixed Method Appraisal Tool. The thematic synthesis of the data will be performed using a hybrid approach incorporating deductive (framed against the social determinants of health using intersectionality as a lens) and inductive data-driven processes. The review protocol was registered in the International Prospective Register of Systematic Reviews (PROSPERO) (Reg: CRD42022359881).
­Pharmacokinetics of drugs used to treat uncomplicated malaria in breastfeeding mother-infant pairs: An observational pharmacokinetic study
Authors: Nakijoba Ritah , Nakayiwa Kawuma Aida , Ojara Francis Williams , Tabwenda Jovia C. , Kyeyune Jacqueline , Turyahabwe Christine , Asiimwe Simon Peter , Magoola Johnson , Banda Clifford George , Castelnuovo Barbara , Buzibye Allan , Waitt Catriona
Published: January 2023

Background: Data surrounding the exposure of the breastfed infant to drugs and any associated risks are sparse. Drugs are transferred to milk in small quantities, and many have been used without obviously noticeable infant toxicity for many years – this lack of a ‘safety signal’ has further reduced the interest in studying mother-to-infant transfer of the drugs. In sub-Saharan Africa, pregnant women are at risk of Plasmodium falciparum infection, and one in four women have evidence of placental infection at the time of delivery. Artemisinin-based combination therapies (ACTs), primarily artemether-lumefantrine (AL), are the current first-line treatment for uncomplicated Plasmodium falciparum malaria, with the same dosing recommendations in breastfeeding women as those in the adult population. Dihydroartemisinin-piperaquine (DP) is routinely used as an alternative to AL in Uganda. However, lactation pharmacokinetics (PK) of ACTs are unknown. Pharmacokinetic characterization of anti-malarial transfer to breast milk and breastfed infants is crucial in understanding the potential consequences to the infant, in terms of therapeutic- and prophylactic effects as well as potential toxicity.  

Methods: This observational study will enroll 30 mother-infant pairs, and aims to characterize the breastmilk transfer of antimalarial medications (AL and DP) to infants when these ACTs are administered to mothers as part of treatment for uncomplicated malaria. In addition, we will assess the mental health of the breastfeeding mothers enrolled as well as the well-being of their children.

PK samples of maternal blood, breastmilk and breastfeeding infant’s blood will be obtained at specific times points. Pharmacokinetic data will be analyzed using a population pharmacokinetic approach.

Conclusions: We anticipate that findings from this research will guide to develop a PK model describing lumefantrine and piperaquine disposition and will provide a framework to foster other lactation pharmacokinetic studies in different disease areas.
The genome sequence of the ichneumon wasp Buathra laborator (Thunberg, 1822)
Authors: Broad Gavin R. ,   Natural History Museum Genome Acquisition Lab,   Darwin Tree of Life Barcoding collective,   Wellcome Sanger Institute Tree of Life programme,   Wellcome Sanger Institute Scientific Operations: DNA Pipelines collective,   Tree of Life Core Informatics collective,   Darwin Tree of Life Consortium
Published: January 2023

We present a genome assembly from an individual Buathra laborator (Arthropoda; Insecta; Hymenoptera; Ichneumonidae). The genome sequence is 330 megabases in span. Over 60% of the assembly is scaffolded into 11 chromosomal pseudomolecules. The mitochondrial genome has also been assembled and is 35.8 kilobases in length.
Prison As Paradox: Foucault and the Disciplinary Society
Authors: Kirk Richard
Published: January 2023

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An Environmentalists' Economy: Why Positive Game Economies Appeal to the Modern Gamer
Authors: Marchal Kierstin
Published: January 2023

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A Self-Analysis of My Artistic Journey: Passions and Introspections
Authors: Do Julie
Published: January 2023

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Targeting Advertising Spending and Price on the Hotelling Line
Authors: Moorthy Sridhar , Shahrokhi Tehrani Shervin
Published: January 2023

We examine whether competing firms in a Hotelling model should increase the scope of their targeting from advertising spending or price alone to both advertising spending and price targeting.
Solving Unsplittable Network Flow Problems with Decision Diagrams
Authors: Salemi Hosseinali , Davarnia Danial
Published: January 2023

In unsplittable network flow problems, certain nodes must satisfy a combinatorial requirement that the incoming arc flows cannot be split or merged when routed through outgoing arcs. This so-called no-split no-merge requirement arises in unit train scheduling where train consists should remain intact at stations that lack necessary equipment and manpower to attach/detach them. Solving the unsplittable network flow problems with standard mixed-integer programming formulations is computationally difficult due to the large number of binary variables needed to determine matching pairs between incoming and outgoing arcs of nodes with no-split no-merge constraint. In this paper, we study a stochastic variant of the unit train scheduling problem where the demand is uncertain. We develop a novel decision diagram (DD)-based framework that decomposes the underlying two-stage formulation into a master problem that contains the combinatorial requirements and a subproblem that models a continuous network flow problem. The master problem is modeled by a DD in a transformed space of variables with a smaller dimension, leading to a substantial improvement in solution time. Similar to the Benders decomposition technique, the subproblems output cutting planes that are used to refine the master DD. Computational experiments show a significant improvement in solution time of the DD framework compared with that of standard methods.

History: This paper has been accepted for the Transportation Science Special Issue on Emerging Topics in Transportation Science and Logistics.

Funding: This work was supported by the Iowa Energy Center [Grant 20IEC005].

Supplemental Material: The online appendices are available at https://doi.org/10.1287/trsc.2022.1194 .
The Spatial and Temporal Disparity of Fish Assemblage and Its Association with Environmental Factors Through Multivariate Statistical Analysis in Jammu and Kashmir's Himalayan River System.
Authors: Gupta Chakshu , Langer Seema , Uttam Suneha
Published: January 2023

The goal of this study was to explore the dynamics of the environmental components with fish species assemblages in the Ravi and Chenab rivers of the Himalayan river system during the study period from "July 2020 to June 2021".. To examine the relationship between fish species and environmental parameters, multivariate statistical analyses including canonical correspondence analysis, principal component analysis and cluster analysis were applied to data from fish species. ANOSIM and SIMPER were used to determine whether fish assemblage varied with seasons or streams and to identify the fish species that contributed to this variation between the sampling sites. To study the effect of environmental factors on fish species richness, multiple regression analysis was used. Fish species belonging to 30 species and 12 different families (Cyprinidae, 66.6%) were recorded from three study sites (Bhini, Jhajjar and Chadwal streams) with Chadwal (34.3%) having the most ichthyofaunal population. Hillstream fish species dominated the Bhini stream, while catfish species dominated the Jhajjar stream. The Chadwal Stream was home to a diversity of fish species due to its vast fishing grounds. The values of free carbon dioxide (FCO2), bicarbonates (HCO3-), and habitat structure showed significant variations (p<0.05). The Shannon-Wiener (H'), Simpson dominance, and Margalef index values of fish communities were high. Differences in environmental parameters in each sampling site influenced the fish population in the present study. Our findings showed that environmental factors influenced species composition and provided evidence for the dynamic interaction between environmental variables and fish assemblage in the Ravi and Chenab rivers.
Assessment of Aox Content in Bleaching Effluent of Eucalyptus Tereticornis Kraft Pulps
Authors: Bhatnagar Anju
Published: January 2023

The research aim is to reduce the organochlorine content in bleach plant effluents by modifying conventional (CEHH) bleaching sequences. Majority of pulp and paper mills generally adopted CEHH or CEH bleaching sequences, using chlorine or chlorinated compounds to remove the color from pulps. Organochlorine compounds are mainly generated from chlorination and alkali extraction stages. The purpose of the study is to substitute elemental chlorine in bleaching with oxygen, chlorine dioxide, or peroxide. Investigations of AOX content of various traditional and innovative ECF bleaching sequences were conducted. In this study, kraft pulps of Eucalyptus tereticornis with kappa numbers of 44.91 and 26.46 and its oxygen-delignified pulps of kappa numbers 21.32 and 13.03 were used. In terms of AOX, various ECF bleaching sequences were compared to the reference sequence (CEHH). AOX value was 4.45, 3.42, 2.27 kg/tp for the pulp bleached adopting OCEH, ODEH, ODEP bleaching sequence and 9.24 kg/tp for the pulp bleached adopting CEHH bleaching sequence for the pulp corresponding to Kappa number 44.91. Similarly, the AOX value was 2.60 , 1.78 1.24 Kg/tp for the pulps bleached adopting the OCEH, ODEH, ODEP bleaching sequence and 5.56 Kg/tp for the pulp bleached adopting the CEHH sequence for the pulp corresponding kappa number 26.46. Due to partial-delignification of oxygen, AOX production was reduced up to 50%.
digiRESCUE: A Smart Personal Emergency Rescue System
Authors: Kommey Benjamin , Tamakloe Elvis , Akowuah Bright Yeboah
Published: January 2023

It is of no doubt that, emergencies occur without warning, and one does not predict the outcome. This project seeks to design a personal emergency or panic alert system (digiRESCUE) to aid in inevitable and dangerous situations. The digiRESCUE system has two main parts: the embedded hardware and software application. The hardware part is made up of a button embedded with a chip. This button when pressed triggers the chip, which then activates the software, portion of the system to send an automated message including the individual’s location to the selected contacts saved in the software application. The software part of the system is in the form of a mobile application, which can be downloaded onto a mobile device. This software would allow users to record or write an SOS message and input selected contacts (including friends, family, and authorities) who would be alerted of the user’s predicament when the external button in pressed. This software application can tap into the mobile device’s GPS module to inform the selected contacts of the individual’s location. The hardware would interact with the software application via Bluetooth connectivity therefore making the process of seeking for help, a lot quicker and easier. In situations where the individual is held as a hostage, he or she can easily call for help without drawing attention to oneself
RANKING THE COMPLIANCE OF ISLAMIC BANKING HOME FINANCING PRODUCTS WITH MAQASID SHARIAH USING AHP
Authors: Shahwan Syahidawati , Sapian Safeza Mohd , Ibrahim Norhazlina , Mohammed Mustafa Omar , Agha Ehsanullah , Kanesan Thavamaran
Published: January 2023

Compliance of Islamic banking products with Maqasid Shariah has been a never-ending debate. However, most discussions are merely explorative, descriptive and perceptive in nature. This article aims to evaluate two types of home financing products in Malaysia based on the Maqasid Shariah of the product development process in Islamic banks. To provide a more coherent and concrete decision, the Analytic Hierarchy Process (AHP) has been used. Bay’ Bithaman Ajil (sale with deferred payment) and Tawarruq (monetization) have been chosen to represent sale-based financing and Musharakah Mutanaqiṣah (diminishing partnership) represents partnership-based financing. The overall results demonstrated that partnership-based financing complied with the social requirements of MSPDF (Maqasid Shariah-based product development framework) at 87.5%, while sale-based financing was rated at 12.5%. The findings will assist Shariah advisors, Islamic finance product developers, economic analysts, ﬁnancial engineers and policymakers to incorporate the relevant Shariah objectives in Islamic financial product development.
Simulation and design of a high-speed and high-power modified uni-traveling carrier photodiode based on the electric field distribution in the depletion region
Authors: Wang Xuejie , Huang Yongqing , Ren Ren , Du Jiawei , Yang Mingxi , Liu Kai , Duan Xiaofeng , Ren Xiaomin
Published: January 2023

A modified uni-traveling carrier photodiode with an electric field control layer is proposed to achieve high-speed and high-power performance at a lower bias voltage. By inserting the 10 nm p-type InGaAs electric field control layer between the intrinsic absorption layer and space layer, the electric field distribution in the depleted absorption layer and depleted non-absorption layer can be changed. It is beneficial for reducing power consumption and heat generation, meanwhile suppressing the space-charge effect. Compared with the original structure without the electric field control layer, the 3 dB bandwidth of the 20 µm diameter novel structure, to the best of our knowledge, is improved by 27.1% to 37.5 GHz with a reverse bias of 2 V, and the RF output power reaches 23.9 dBm at 30 GHz. In addition, under 8 V bias voltage, the bandwidth reaches 47.3 GHz.
Joint equalization of EEPN, RSOP, and CD with the sliding window assisted extended Kalman filter for a high baud rate Stokes vector direct detection system
Authors: Cao Lingguo , Xu Hengying , Sun Zukai , Bai Chenglin , Cui Nan , Zhang Yining , Yang Lishan , Sun Weibin , Bi Yanfeng
Published: January 2023

Equalization-enhanced phase noise (EEPN) has emerged as one of the major impairments that cannot be ignored for a high baud rate Stokes vector direct detection (SVDD) system. When EEPN interacts with the rotation of state-of-polarization (RSOP) and chromatic dispersion (CD), the joint impairment effects become even more complicated. To achieve the joint equalization of EEPN, RSOP, and CD impairments of a high baud rate SVDD system, this paper first derives a joint impairment model of these three kinds of impairments, and then proposes a joint equalization scheme of EEPN, RSOP, and CD with a sliding window assisted extended Kalman filter (SWA-EKF). The SWA-EKF scheme first tracks RSOP in the time domain, subsequently compensates CD in the frequency domain, and finally performs EEPN mitigation in the time domain again. The effectiveness of the proposed scheme has been verified by a 60 GBaud SVDD-16QAM simulation system. The results show that when these three impairments are jointly equalized, the SWA-EKF scheme can track RSOP as fast as 3 Mrad/s, cumulative dispersion up to 1600 ps/nm, and EEPN caused by laser linewidth up to 3 MHz. In addition, with an optical signal-to-noise ratio penalty of 0.3 dB, it could increase 35 G baud rate under 3 MHz laser linewidth for the SVDD system. More importantly, its total complexity can be reduced to an order of

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Broadband and linearized photonic time-stretch analog-to-digital converter based on a compact dual-polarization modulator
Authors: Yang Bo , Ma Zheng , Yang Shuna , Chi Hao
Published: January 2023

A broadband linearization scheme for a photonic time-stretch (PTS) analog-to-digital converter (ADC) is proposed based on a dual-polarization binary phase-shift keying (DP-BPSK) modulator with complementary parallel single-sideband (SSB) modulation. In this system, two stretched radio frequency signals, corresponding to the two orthogonal polarizations of the DP-BPSK modulator, are complementary, which can realize differential operation to eliminate the second-order harmonic distortion and pulse envelope distortion. Meanwhile, SSB modulation is used to avoid dispersion-induced power fading. Theoretical analysis and simulation results show that the proposed scheme can effectively improve the linear performance of PTS ADC, even considering the polarization-dependent delay deviation and amplitude offset.
Properties of Ni-Al2O3 composite coating by laser-assisted pulse electrodeposition
Authors: Miao Xu , Zhang Haiyun , Zhao Yugang , Han Xingang , Lin Weisheng , Jiang Guangfen , Meng Jianbing , Zhang Zengbo , Zhang Jinjian
Published: January 2023

To study the influence of laser process parameters on the surface properties of the coating,

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composite coatings on 304 stainless-steel sheets with laser-assisted pulsed electrodeposition was proposed in this paper. Laser single pulse energy and scanning speed were selected as research factors. Single-factor experiments were performed to investigate the effect of various factors on the surface morphology, particle mass fraction, microhardness, surface roughness, and corrosion resistance of the composite coating. The experimental results show that the surface properties of the composite coating first increase and then decrease with increasing laser single pulse energy. When the laser single pulse energy is 11 µJ, the minimum surface roughness value is 0.380 µm with a smooth and uniform coating surface and the best surface morphology. Moreover, as the scanning speed increases, the corrosion resistance of the composite coating initially increases and then decreases. The corrosion resistance of the composite coatings is best with a scanning speed of 1000 mm/s. When the scanning speed was 1500 mm/s, the particle mass fraction in the coating reached a maximum of 1.984%; meanwhile, the highest hardness of the composite coating was obtained with the value of 476.38 HV.
Output characteristics of distributed feedback 3.0 terahertz quantum cascade lasers
Authors: Luo Jiawen , Jiang Tao , Zhan Zhiqiang , Wang Xuemin , Yang Qi , Chen Fengwei , Zou Ruijiao , Li Jia , Zeng Yong , Wu Weidong , Xu Lixin
Published: January 2023

Distributed feedback quantum cascade lasers lased at 3.0 THz were prepared and their output performance was analyzed. The optimized grating parameters were obtained by theoretical analyses. Single-mode emission was obtained and a maximum output power of more than 166 mW at 15 K was achieved. The corresponding threshold current density was

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, and the side-mode suppression ratio was more than 15 dB. By changing the input voltage, the frequency was stable with a variation of less than 3 GHz. A beam with obviously fast and slow axis features was observed. Further improvement and the potential application of distributed feedback quantum cascade lasers are discussed.
Magnetic composite fluid optimization for KDP crystal polishing based on a D-optimal mixture design
Authors: Yu XiaoLuo , Yang Wei , Chen ChaoXu , Zhu FanWei
Published: January 2023

The potassium dihydrogen phosphate (KDP) crystal is a kind of electro-optical nonlinear optical crystal with excellent performance, and has attracted much attention from researchers due to its wide application prospects. Some KDP processing techniques have been developed, but polishing KDP with a magnetic composite fluid (MCF) has not been reported, to our knowledge. Accordingly, first, taking the water solubility of KDP into account, a non-water-based MCF is developed based on previous research. Then, orthogonal experiments are used to determine optimal processing parameters of MCF. Finally, a D-optimal mixture design is used to establish a mathematical model of the influence of each component factor on surface roughness, and the ratio of key components in MCF is optimized. The results show that the theoretical optimum ratio is 20 wt.% base liquid (lauryl alcohol and Triton X-100), 39.962 wt.% carbonyl iron particles, and 25.038 wt.%

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. The KDP surface roughness (Ra) after 60 min of polishing converges to 7.5 nm, consistent with expected estimates, indicating that the formulation optimized by this method is effective and reliable.
Multiple-scattering simulator-trained neural network for intensity diffraction tomography
Authors: Matlock Alex , Zhu Jiabei , Tian Lei
Published: January 2023

Recovering 3D phase features of complex biological samples traditionally sacrifices computational efficiency and processing time for physical model accuracy and reconstruction quality. Here, we overcome this challenge using an approximant-guided deep learning framework in a high-speed intensity diffraction tomography system. Applying a physics model simulator-based learning strategy trained entirely on natural image datasets, we show our network can robustly reconstruct complex 3D biological samples. To achieve highly efficient training and prediction, we implement a lightweight 2D network structure that utilizes a multi-channel input for encoding the axial information. We demonstrate this framework on experimental measurements of weakly scattering epithelial buccal cells and strongly scattering C. elegans worms. We benchmark the network’s performance against a state-of-the-art multiple-scattering model-based iterative reconstruction algorithm. We highlight the network’s robustness by reconstructing dynamic samples from a living worm video. We further emphasize the network’s generalization capabilities by recovering algae samples imaged from different experimental setups. To assess the prediction quality, we develop a quantitative evaluation metric to show that our predictions are consistent with both multiple-scattering physics and experimental measurements.
Nonlocal effects investigation via the coupling between localized and acoustic plasmons
Authors: Deng Kaifu , Zeng Xiaodong
Published: January 2023

A scheme to investigate nonlocal effects in metal using the coupling between localized graphene plasmons (GPs) and acoustic plasmons (APs) is proposed. Because of the extremely strong field confinement property, the APs on a configuration consisting of monolayer graphene and a metal film have different dispersions when the nonlocal response is considered or not. A graphene nanoribbon array can efficiently couple incident light to the localized GPs on the ribbons and subsequently the APs. The strong coupling between the two kinds of plasmon, equivalent to electric field dipole interaction, is highly related to the acoustic plasmonic dispersion and induces different absorption spectra, depending on the dispersion. Using a very simple model, nonlocal effects can be extracted from the spectra. The investigation provides a promising platform to manipulate nanophotonics and study nonlocal effects. © 2022 Optica Publishing Group
Fabrication of engineered dopant profiles in Er/Lu:YAG transparent laser ceramics via additive manufacturing
Authors: Osborne Ross A. , Wineger Tyler J. , Yee Timothy D. , Cherepy Nerine J. , Seeley Zachary M. , Gaume Romain , Dubinskii Mark , Payne Stephen A.
Published: January 2023

Transparent ceramic Er:YAG laser rods were fabricated via the direct ink write (DIW) method with engineered doping profiles featuring an Er-doped core with endcaps and core-clad structures. Laser rods up to 11 cm in length were produced which required development of a scalable process. To achieve this, multiple improvements were implemented, including printing the rods horizontally on a substrate, rather than vertically, eliminating the need for an external support structure and using a sacrificial drying layer to mitigate warping and defects. Highly transparent rods were achieved with optical scatter levels as low as 0.5%/cm (at 543 nm). A small refractive index difference of 5.7 ppm was measured at the interface between the Er-doped core and the Lu-doped endcaps and cladding. These results demonstrate DIW as a straightforward method for making good optical quality laser rods with engineered doping profiles to improve laser performance.
RCFGL: Rapid Condition adaptive Fused Graphical Lasso and application to modeling brain region co-expression networks
Authors: Seal Souvik , Li Qunhua , Basner Elle Butler , Saba Laura M. , Kechris Katerina
Published: January 2023

Inferring gene co-expression networks is a useful process for understanding gene regulation and pathway activity. The networks are usually undirected graphs where genes are represented as nodes and an edge represents a significant co-expression relationship. When expression data of multiple (p) genes in multiple (K) conditions (e.g., treatments, tissues, strains) are available, joint estimation of networks harnessing shared information across them can significantly increase the power of analysis. In addition, examining condition-specific patterns of co-expression can provide insights into the underlying cellular processes activated in a particular condition. Condition adaptive fused graphical lasso (CFGL) is an existing method that incorporates condition specificity in a fused graphical lasso (FGL) model for estimating multiple co-expression networks. However, with computational complexity ofO(p2KlogK), the current implementation of CFGL is prohibitively slow even for a moderate number of genes and can only be used for a maximum of three conditions. In this paper, we propose a faster alternative of CFGL named rapid condition adaptive fused graphical lasso (RCFGL). In RCFGL, we incorporate the condition specificity into another popular model for joint network estimation, known as fused multiple graphical lasso (FMGL). We use a more efficient algorithm in the iterative steps compared to CFGL, enabling faster computation with complexity ofO(p2K) and making it easily generalizable for more than three conditions. We also present a novel screening rule to determine if the full network estimation problem can be broken down into estimation of smaller disjoint sub-networks, thereby reducing the complexity further. We demonstrate the computational advantage and superior performance of our method compared to two non-condition adaptive methods, FGL and FMGL, and one condition adaptive method, CFGL in both simulation study and real data analysis. We used RCFGL to jointly estimate the gene co-expression networks in different brain regions (conditions) using a cohort of heterogeneous stock rats. We also provide an accommodatingCandPythonbased package that implements RCFGL.
Novel modelling approaches to predict the role of antivirals in reducing influenza transmission
Authors: Asher Jason , Lemenuel-Diot Annabelle , Clay Matthew , Durham David P. , Mier-y-Teran-Romero Luis , Arguello Carlos J. , Jolivet Sebastien , Wong Diana Y. , Kuhlbusch Klaus , Clinch Barry , Charoin Jean-Eric
Published: January 2023

To aid understanding of the effect of antiviral treatment on population-level influenza transmission, we used a novel pharmacokinetic–viral kinetic transmission model to test the correlation between nasal viral load and infectiousness, and to evaluate the impact that timing of treatment with the antivirals oseltamivir or baloxavir has on influenza transmission. The model was run under three candidate profiles whereby infectiousness was assumed to be proportional to viral titer on a natural-scale, log-scale, or dose–response model. Viral kinetic profiles in the presence and absence of antiviral treatment were compared for each individual (N = 1000 simulated individuals); subsequently, viral transmission mitigation was calculated. The predicted transmission mitigation was greater with earlier administration of antiviral treatment, and with baloxavir versus oseltamivir. When treatment was initiated 12–24 hours post symptom onset, the predicted transmission mitigation was 39.9–56.4% for baloxavir and 26.6–38.3% for oseltamivir depending on the infectiousness profile. When treatment was initiated 36–48 hours post symptom onset, the predicted transmission mitigation decreased to 0.8–28.3% for baloxavir and 0.8–19.9% for oseltamivir. Model estimates were compared with clinical data from the BLOCKSTONE post-exposure prophylaxis study, which indicated the log-scale model for infectiousness best fit the observed data and that baloxavir affords greater reductions in secondary case rates compared with neuraminidase inhibitors. These findings suggest a role for baloxavir and oseltamivir in reducing influenza transmission when treatment is initiated within 48 hours of symptom onset in the index patient.
A quantitative model for human neurovascular coupling with translated mechanisms from animals
Authors: Sten Sebastian , Podéus Henrik , Sundqvist Nicolas , Elinder Fredrik , Engström Maria , Cedersund Gunnar
Published: January 2023

Neurons regulate the activity of blood vessels through the neurovascular coupling (NVC). A detailed understanding of the NVC is critical for understanding data from functional imaging techniques of the brain. Many aspects of the NVC have been studied both experimentally and using mathematical models; various combinations of blood volume and flow, local field potential (LFP), hemoglobin level, blood oxygenation level-dependent response (BOLD), and optogenetics have been measured and modeled in rodents, primates, or humans. However, these data have not been brought together into a unified quantitative model. We now present a mathematical model that describes all such data types and that preserves mechanistic behaviors between experiments. For instance, from modeling of optogenetics and microscopy data in mice, we learn cell-specific contributions; the first rapid dilation in the vascular response is caused by NO-interneurons, the main part of the dilation during longer stimuli is caused by pyramidal neurons, and the post-peak undershoot is caused by NPY-interneurons. These insights are translated and preserved in all subsequent analyses, together with other insights regarding hemoglobin dynamics and the LFP/BOLD-interplay, obtained from other experiments on rodents and primates. The model can predict independent validation-data not used for training. By bringing together data with complementary information from different species, we both understand each dataset better, and have a basis for a new type of integrative analysis of human data.
A role for BCL2L13 and autophagy in germline purifying selection of mtDNA
Authors: Kremer Laura S. , Bozhilova Lyuba V. , Rubalcava-Gracia Diana , Filograna Roberta , Upadhyay Mamta , Koolmeister Camilla , Chinnery Patrick F. , Larsson Nils-Göran
Published: January 2023

Mammalian mitochondrial DNA (mtDNA) is inherited uniparentally through the female germline without undergoing recombination. This poses a major problem as deleterious mtDNA mutations must be eliminated to avoid a mutational meltdown over generations. At least two mechanisms that can decrease the mutation load during maternal transmission are operational: a stochastic bottleneck for mtDNA transmission from mother to child, and a directed purifying selection against transmission of deleterious mtDNA mutations. However, the molecular mechanisms controlling these processes remain unknown. In this study, we systematically tested whether decreased autophagy contributes to purifying selection by crossing the C5024T mouse model harbouring a single pathogenic heteroplasmic mutation in the tRNAAlagene of the mtDNA with different autophagy-deficient mouse models, including knockouts ofParkin,Bcl2l13,Ulk1, andUlk2. Our study reveals a statistically robust effect of knockout ofBcl2l13on the selection process, and weaker evidence for the effect ofUlk1and potentiallyUlk2, while no statistically significant impact is seen for knockout ofParkin. This points at distinctive roles of these players in germline purifying selection. Overall, our approach provides a framework for investigating the roles of other important factors involved in the enigmatic process of purifying selection and guides further investigations for the role of BCL2L13 in the elimination of non-synonymous mutations in protein-coding genes.
A qualitative enquiry of health care workers’ narratives on knowledge and sources of information on principles of Respectful Maternity Care (RMC)
Authors: Lusambili Adelaide M. , Wisofschi Stefania , Wade Terrance J. , Temmerman Marleen , Obure Jerim
Published: January 2023

Research from sub-Saharan Africa indicate that many women experience varied forms of disrespectful maternity care, which amount to a violation of their rights and dignity. Notably, there is little research that sheds light on health care workers (HCWs) training and knowledge of principles of respectful maternity care (RMC). Formulating appropriate interventional strategies to promote the respectful provision of services for women during pregnancy, childbirth, and postpartum period requires an understanding of the current state of knowledge and sources of information on respectful maternity care among HCWs. This paper reports findings from a qualitative study that examined the knowledge and sources of information on the Respectful Maternity Care Charter among HCWs in rural Kisii and Kilifi counties in Kenya. Between January and March 2020, we conducted 24 in-depth interviews among HCWs in rural Kisii and Kilifi health facilities. Data were analyzed using a mixed deductive and inductive thematic analysis guided by Braun’s [2006] six stages of analysis. We found that from the seven globally accepted principles of respectful maternity care, at least half of the HCWs were aware of patients right to consented care, confidentiality and privacy, and the right to non-discriminatory care based on specific attributes. Knowledge of the right to no physical and emotional abuse, abandonment of care, and detentions in the facilities was limited to a minority of health care workers but only after prompting. Sources of information on respectful maternity care were largely limited to continuous medical and professional training and clinical mentorship. The existing gap shows the need for training and mentorship of HCWs on the Respectful Maternity Care Charter as part of pre-service medical and nursing curricula and continuing clinical education to bridge this gap. At the policy level, strategies are necessary to support the integration of respectful maternity care into pre-service training curricula.
Maternal hypertensive mother’s knowledge, attitudes and misconceptions on hypertension in pregnancy: A multi-center qualitative study in Ghana
Authors: Tamma Evelyn , Adu-Bonsaffoh Kwame , Nwameme Adanna , Dako-Gyeke Phyllis , Srofenyoh Emmanuel , Browne Joyce
Published: January 2023

Hypertension in pregnancy is one of the commonest complications of pregnancy and a leading cause of maternal and perinatal morbidity and mortality globally, with the highest burden in low and middle income countries. Pregnant women’s knowledge about hypertension in pregnancy facilitates early health seeking behavior, which can result in early diagnosis and treatment. This study therefore explored the knowledge, misconceptions and attitudes of Ghanaian women who were affected by hypertension in pregnancy. A qualitative study was carried out across five referral hospitals in the Greater Accra Region of Ghana. In-depth interviews (IDIs) and focus group discussions (FGDs) were used to explore the women’s knowledge on hypertensive disorders of pregnancy (HDP), and particularly preeclampsia. Women of at least 16 years, admitted with a HDP to the maternity ward with gestational ages from 26–34 weeks were eligible for participation. The inductive approach was used to develop a code book and the dataset was coded using Nvivo version 12 software. A total of 72 women participated in the study. Fifty IDIs and 3 FGDs involving 22 women were conducted. Although most of the women had regular antenatal visits, several had never heard of “pre-eclampsia”. More common terminology used by women (i.e. “Bp”) referred to any of the hypertensive disorders (e.g. pre-eclampsia, gestational hypertension and chronic hypertension). Women also perceived that pre-eclampsia may be inherited or caused by “thinking too much”. The study revealed that the knowledge about hypertension in pregnancy is limited among the affected women despite regular antenatal attendance with some form of health education. There should be more education programs on hypertensive disorders of pregnancy including pre-eclampsia with revised strategies.
Mechanical ventilation for COVID-19: Outcomes following discharge from inpatient treatment
Authors: Butler Mark J. , Best Jennie H. , Mohan Shalini V. , Jonas Jennifer A. , Arader Lindsay , Yeh Jackson
Published: January 2023

Though mechanical ventilation (MV) is used to treat patients with severe coronavirus disease 2019 (COVID-19), little is known about the long-term health implications of this treatment. Our objective was to determine the association between MV for treatment of COVID-19 and likelihood of hospital readmission, all-cause mortality, and reason for readmission. This study was a longitudinal observational design with electronic health record (EHR) data collected between 3/1/2020 and 1/31/2021. Participants included 17,652 patients hospitalized for COVID-19 during this period who were followed through 6/30/2021. The primary outcome was readmission to inpatient care following discharge. Secondary outcomes included all-cause mortality and reason for readmission. Rates of readmission and mortality were compared between ventilated and non-ventilated patients using Cox proportional hazards regression models. Differences in reasons for readmission by MV status were compared using multinomial logistic regression. Patient characteristics and measures of illness severity were balanced between those who were mechanically ventilated and those who were not utilizing 1-to-1 propensity score matching. The sample had a median age of 63 and was 47.1% female. There were 1,131 (6.4%) patients who required MV during their initial hospitalization. Rates (32.1% versus 9.9%) and hazard of readmission were greater for patients requiring MV in the propensity score–matched samples [hazard ratio (95% confidence interval) = 3.34 (2.72–4.10)]. Rates (15.3% versus 3.4%) and hazard [hazard ratio (95% confidence interval) = 3.12 (2.32–4.20)] of all-cause mortality were also associated with MV status. Ventilated patients were more likely to be readmitted for reasons which were classified as COVID-19, infectious diseases, and respiratory diagnoses compared to non-ventilated patients. Mechanical ventilation is a necessary treatment for severely ill patients. However, it may be associated with adverse outcomes including hospital readmission and death. More intense post-discharge monitoring may be warranted to decrease this associational finding.
Fluorescence lifetime distribution in phakic and pseudophakic healthy eyes
Authors: Dysli Chantal , Dysli Muriel , Wolf Sebastian , Zinkernagel Martin
Published: January 2023

Purpose

To investigate the influence of the lens status and to describe fundus autofluorescence lifetimes (FLT) in a large cohort of healthy eyes across a wide age range.

Materials and methods

FLT data were acquired from healthy phakic and pseudophakic eyes using fluorescence lifetime imaging ophthalmoscopy (FLIO). Retinal autofluorescence was excited with a 473 nm laser and emitted autofluorescence was detected in a short and a long spectral channel (SSC: 498–560 nm; LSC: 560–720 nm).

Results

141 healthy eyes from 141 participants (56 ± 18 years) were included. The shortest mean FLTs were measured within the macular center, followed by the temporal inner and outer ETDRS (Early Treatment Diabetic Retinopathy Study) grid segments, and the remaining areas of the inner and the outer ETDRS ring. In phakic participants (81%), mean, short and long FLTs correlated with the age (SSC: r2 = 0.54; LSC: r2 = 0.7; both p<0.0001) with an increase of about 33 ps in the SSC resp. 28 ps in the LSC per decade. In pseudophakic subjects (19%), mean FLTs only correlated with age in the long spectral channel (r2 = 0.44; p = 0.0002) but not in the short spectral channel (r2 = 0.066; p = 0.2).

Conclusions

Fundus autofluorescence lifetimes are age dependent. FLTs in the SSC are more susceptible to lens opacities but less dependent on age changes, whereas FLTs in the LSC are largely independent of the lens status but display a higher degree of age dependency.

Study registry

ClinicalTrials.gov NCT01981148.
An adaptive spatiotemporal correlation filtering visual tracking method
Authors: Liu Yuhan , Yan He , Zhang Wei , Li Mengxue , Liu Lingkun
Published: January 2023

Discriminative correlation filter (DCF) tracking algorithms are commonly used for visual tracking. However, we observed that different spatio-temporal targets exhibit varied visual appearances, and most DCF-based trackers neglect to exploit this spatio-temporal information during the tracking process. To address the above-mentioned issues, we propose a three-way adaptive spatio-temporal correlation filtering tracker, named ASCF, that makes fuller use of the spatio-temporal information during tracking. To be specific, we extract rich local and global visual features based on the Conformer network, establish three correlation filters at different spatio-temporal locations during the tracking process, and the three correlation filters independently track the target. Then, to adaptively select the correlation filter to achieve target tracking, we employ the average peak-to-correlation energy (APCE) and the peak-to-sidelobe ratio (PSR) to measure the reliability of the tracking results. In addition, we propose an adaptive model update strategy that adjusts the update frequency of the three correlation filters in different ways to avoid model drift due to the introduction of similar objects or background noise. Extensive experimental results on five benchmarks demonstrate that our algorithm achieves excellent performance compared to state-of-the-art trackers.
Immune environment and antigen specificity of the T cell receptor repertoire of malignant ascites in ovarian cancer
Authors: Yoshida-Court Kyoko , Karpinets Tatiana V. , Mitra Aparna , Solley Travis N. , Dorta-Estremera Stephanie , Sims Travis T. , Delgado Medrano Andrea Y. , El Alam Molly B. , Ahmed-Kaddar Mustapha , Lynn Erica J. , Sastry K. Jagannadha , Zhang Jianhua , Futreal Andrew , Nick Alpa , Lu Karen , Colbert Lauren E. , Klopp Ann H.
Published: January 2023

We evaluated the association of disease outcome with T cell immune-related characteristics and T cell receptor (TCR) repertoire in malignant ascites from patients with high-grade epithelial ovarian cancer. Ascitic fluid samples were collected from 47 high-grade epithelial ovarian cancer patients and analyzed using flow cytometry and TCR sequencing to characterize the complementarity determining region 3 TCR β-chain. TCR functions were analyzed using the McPAS-TCR and VDJ databases. TCR clustering was implemented using Grouping of Lymphocyte Interactions by Paratope Hotspots software. Patients with poor prognosis had ascites characterized by an increased ratio of CD8+ T cells to regulatory T cells, which correlated with an increased productive frequency of the top 100 clones and decreased productive entropy. TCRs enriched in patients with an excellent or good prognosis were more likely to recognize cancer antigens and contained more TCR reads predicted to recognize epithelial ovarian cancer antigens. In addition, a TCR motif that is predicted to bind theTP53neoantigen was identified, and this motif was enriched in patients with an excellent or good prognosis. Ascitic fluid in high-grade epithelial ovarian cancer patients with an excellent or good prognosis is enriched with TCRs that may recognize ovarian cancer-specific neoantigens, including mutatedTP53andTEAD1. These results suggest that an effective antigen-specific immune response in ascites is vital for a good outcome in high-grade epithelial ovarian cancer.