bluuebunny/crossref_metadata_2025 huggingface dataset:
THE ROLE OF ROTATION IN TOTAL ANKLE ARTHROPLASTY
Authors: Najefi A-A. , Ghani Y. , Goldberg A.
Published: May 2024

Background

The importance of total ankle replacement (TAR) implant orientation in the axial plane is poorly understood with major variation in surgical technique of implants on the market. Our aims were to better understand the axial rotational profile of patients undergoing TAR.

Methods

In 157 standardised CT Scans of end-stage ankle arthritis patients planning to undergo primary TAR surgery, we measured the relationship between the knee posterior condylar axis, the tibial tuberosity, the transmalleolar axis(TMA) and the tibiotalar angle. The foot position was measured in relation to the TMA with the foot plantigrade. The variation between medial gutter line and the line bisecting both gutters was assessed.

Results

The mean external tibial torsion was 34.5±10.3°(11.8–62°). When plantigrade the mean foot position relative to the TMA was 21±10.6°(0.7–38.4°) internally rotated. As external tibial torsion increased, the foot position became more internally rotated relative to the TMA(pearson correlation 0.6;p< 0.0001). As the tibiotalar angle became more valgus, the foot became more externally rotated relative to the TMA(pearson correlation −0.4;p< 0.01). The mean difference between the medial gutter line and a line bisecting both gutters was 4.9±2.8°(1.7°-9.4°). More than 51% of patients had a difference greater than 5°. The mean angle between the medial gutter line and a line perpendicular to the TMA was 7.5°±2.6°(2.8°-13.7°).

Conclusion

There is a large variation in rotational profile of patients undergoing TAR, particularly between the medial gutter line and the transmalleolar axis. Surgeon designers and implant manufacturers need to develop consistent methods to guide surgeons towards judging appropriate axial rotation of their implanton an individual basis. We recommend careful clinical assessment and CT scanspre-operatively to enable the correct rotation to be determined.
THE DEEP DELTOID LIGAMENT AND STABILITY AFTER ANKLE FRACTURE: A CADAVERIC STUDY
Authors: McCormack D. , Kirmani S. , Aziz S. , Faroug R. , Solan M. , Mangwani J.
Published: May 2024

Background

Supination-external rotation (SER) injuries make up 80% of all ankle fractures. SER stage 2 injuries (AITFL and Weber B) are considered stable. SER stage 3 injury includes disruption of the posterior malleolus (or PITFL). In SER stage 4 there is either medial malleolus fracture or deltoid injury too. SER 4 injuries have been considered unstable, requiring surgery. The deltoid ligament is a key component of ankle stability, but clinical tests to assess deltoid injury have low specificity. This study specifically investigates the role of the components of the deep deltoid ligament in SER ankle fractures.

Aim

To investigate the effect of deep deltoid ligament injury on SER ankle fracture stability.

Methods

Four matched pairs (8 specimens) were tested using a standardised protocol. Specimens were sequentially tested for stability when axially loaded with a custom rig with up to 750N. Specimens were tested with: ankle intact; lateral injury (AITFL and Weber B); additional posterior injury (PITFL); additional anterior deep deltoid; additional posterior deep deltoid; lateral side ORIF. Clinical photographs and radiographs were recorded. In addition, dynamic stress radiographs were performed after sectioning the deep deltoid and then after fracture fixation to assess tilt of the talus in eversion.

Results

All specimens with an intact posterior deep deltoid ligament were stable when loaded and showed no talar tilt on dynamic assessment. Once the posterior deep deltoid ligament was sectioned there was instability in all specimens. Surgical stabilisation of the lateral side prevented talar shift but not talar tilt.

Conclusion

If the posterior deep deltoid ligament is intact SER fractures may be managed without surgery in a plantigrade cast. Without immobilisation the talus may tilt, risking deltoid incompetence.
Nonlinear Schrödinger equation for integrated photonics
Authors: Gravesen Kevin Bach , Brimnes Gardner Asger , Ulsig Emil Zanchetta , Stanton Eric J. , Torrild Hansen Mikkel , Thomsen Simon Thorndahl , Ahler Lucas , Volet Nicolas
Published: May 2024

The foundations of nonlinear optics are revisited, and the formalism is applied to waveguide modes. The effects of loss and dispersion are included rigorously along with the vectorial nature of the modes, and a full derivation of a new version of the nonlinear Schrödinger (NLS) equation is presented. This leads to more general expressions for the group index, for the group-index dispersion (GVD), and for the Kerr coefficient. These quantities are essential for the design of waveguides suitable for, e.g., the generation of optical frequency combs and all-optical switches. Examples are given using the silicon nitride material platform. Specifically, values are extracted for the coefficients of the chi-3 tensor based on measurements of Kerr coefficients and mode simulations.
Fast reconstruction of laser beam near-field and focal spot profiles using deep neural network and numerical propagation
Authors: He Xiaoliang , Tao Hua , Veetil Suhas P. , Chang Chencheng , Liu Cheng , Zhu Jianqiang
Published: May 2024

Inertial confinement fusion (ICF) experiments demand precise knowledge of laser beam parameters on high-power laser facilities. Among these parameters, near-field and focal spot distributions are crucial for characterizing laser beam quality. While iterative phase retrieval shows promise for laser beam reconstruction, its utility is hindered by extensive iterative calculations. To address this limitation, we propose an online laser beam reconstruction method based on deep neural network. In this method, we utilize coherent modulation imaging (CMI) to obtain labels for training the neural network. The neural network reconstructs the complex near-field distribution, including amplitude and phase, directly from a defocused diffraction pattern without iteration. Subsequently, the focal spot distribution is obtained by propagating the established complex near-field distribution to the far-field. Proof-of-principle experiments validate the feasibility of our proposed method.
WASP: weighted average of sequential projections for ptychographic phase retrieval
Authors: Maiden Andrew M , Mei Wenjie , Li Peng
Published: May 2024

We introduce the weighted average of sequential projections, or WASP, an algorithm for ptychography. Using both simulations and real-world experiments, we test this new approach and compare performance against several alternative algorithms. These tests indicate that WASP effectively combines the benefits of its competitors, with a rapid initial convergence rate, robustness to noise and poor initial conditions, a small memory footprint, easy tuning, and the ability to reach a global minimum when provided with noiseless data. We also show how WASP can be parallelised to split operation across several different computation nodes.
Monolayer directional metasurface for all-optical image classifier doublet: publisher’s note
Authors: Xia Rui , Wu Lin , Tao Jin , Zhao Ming , Yang ZhenYu
Published: May 2024

This publisher’s note contains a correction to Opt. Lett. 49, 2505 (2024)10.1364/OL.520642.
Coupling ideality of standing-wave supermode microresonators
Authors: Wang Min , Lei Yuechen , Hu Zhi-Gang , Lao Chenghao , Wang Yuanlei , Zhou Xin , Li Jincheng , Yang Qi-Fan , Li Bei-Bei
Published: May 2024

Standing-wave supermode microresonators that are created through the strong coupling between counter-propagating modes have emerged as versatile platforms for sensing and nonlinear optics. For example, these microresonators have shown potential in nanoparticle sizing and counting, as well as enhancing the single-photon optomechanical coupling rate of stimulated Brillouin scattering. However, it has been observed that the relation between the mode linewidth and on-resonance transmission of the split supermodes differs obviously from that of the non-split modes. This behavior is typically quantified by the coupling ideality (I), which remains inadequately explored for the standing-wave supermodes. In this study, we theoretically and experimentally investigate the coupling ideality of standing-wave supermodes in a commonly employed configuration involving a SiO2 microresonator side-coupled to a tapered fiber. Our findings demonstrate that, even with a single-mode tapered fiber, the coupling ideality of the standing-wave supermodes is limited to 0.5, due to the strong backscattering-induced energy loss into the counter-propagating direction, resulting in an additional equivalent parasitic loss. While achieving a coupling ideality of 0.5 presents challenges for reaching over-coupled regimes, it offers a convenient approach for adjusting the total linewidth of the modes while maintaining critically-coupled conditions.
Robust genetic codes enhance protein evolvability
Authors: Rozhoňová Hana , Martí-Gómez Carlos , McCandlish David M. , Payne Joshua L.
Published: May 2024

The standard genetic code defines the rules of translation for nearly every life form on Earth. It also determines the amino acid changes accessible via single-nucleotide mutations, thus influencing protein evolvability—the ability of mutation to bring forth adaptive variation in protein function. One of the most striking features of the standard genetic code is its robustness to mutation, yet it remains an open question whether such robustness facilitates or frustrates protein evolvability. To answer this question, we use data from massively parallel sequence-to-function assays to construct and analyze 6 empirical adaptive landscapes under hundreds of thousands of rewired genetic codes, including those of codon compression schemes relevant to protein engineering and synthetic biology. We find that robust genetic codes tend to enhance protein evolvability by rendering smooth adaptive landscapes with few peaks, which are readily accessible from throughout sequence space. However, the standard genetic code is rarely exceptional in this regard, because many alternative codes render smoother landscapes than the standard code. By constructing low-dimensional visualizations of these landscapes, which each comprise more than 16 million mRNA sequences, we show that such alternative codes radically alter the topological features of the network of high-fitness genotypes. Whereas the genetic codes that optimize evolvability depend to some extent on the detailed relationship between amino acid sequence and protein function, we also uncover general design principles for engineering nonstandard genetic codes for enhanced and diminished evolvability, which may facilitate directed protein evolution experiments and the bio-containment of synthetic organisms, respectively.
Nuclear export is a limiting factor in eukaryotic mRNA metabolism
Authors: Müller Jason M. , Moos Katharina , Baar Till , Maier Kerstin C. , Zumer Kristina , Tresch Achim
Published: May 2024

The eukaryotic mRNA life cycle includes transcription, nuclear mRNA export and degradation. To quantify all these processes simultaneously, we perform thiol-linked alkylation after metabolic labeling of RNA with 4-thiouridine (4sU), followed by sequencing of RNA (SLAM-seq) in the nuclear and cytosolic compartments of human cancer cells. We develop a model that reliably quantifies mRNA-specific synthesis, nuclear export, and nuclear and cytosolic degradation rates on a genome-wide scale. We find that nuclear degradation of polyadenylated mRNA is negligible and nuclear mRNA export is slow, while cytosolic mRNA degradation is comparatively fast. Consequently, an mRNA molecule generally spends most of its life in the nucleus. We also observe large differences in the nuclear export rates of different 3’UTR transcript isoforms. Furthermore, we identify genes whose expression is abruptly induced upon metabolic labeling. These transcripts are exported substantially faster than average mRNAs, suggesting the existence of alternative export pathways. Our results highlight nuclear mRNA export as a limiting factor in mRNA metabolism and gene regulation.
Liebig’s law of the minimum in the TGF-β/SMAD pathway
Authors: Li Yuchao , Deng Difan , Höfer Chris Tina , Kim Jihye , Do Heo Won , Xu Quanbin , Liu Xuedong , Zi Zhike
Published: May 2024

Cells use signaling pathways to sense and respond to their environments. The transforming growth factor-β (TGF-β) pathway produces context-specific responses. Here, we combined modeling and experimental analysis to study the dependence of the output of the TGF-β pathway on the abundance of signaling molecules in the pathway. We showed that the TGF-β pathway processes the variation of TGF-β receptor abundance using Liebig’s law of the minimum, meaning that the output-modifying factor is the signaling protein that is most limited, to determine signaling responses across cell types and in single cells. We found that the abundance of either the type I (TGFBR1) or type II (TGFBR2) TGF-β receptor determined the responses of cancer cell lines, such that the receptor with relatively low abundance dictates the response. Furthermore, nuclear SMAD2 signaling correlated with the abundance of TGF-β receptor in single cells depending on the relative expression levels of TGFBR1 and TGFBR2. A similar control principle could govern the heterogeneity of signaling responses in other signaling pathways.
Interpretable online network dictionary learning for inferring long-range chromatin interactions
Authors: Rana Vishal , Peng Jianhao , Pan Chao , Lyu Hanbaek , Cheng Albert , Kim Minji , Milenkovic Olgica
Published: May 2024

Dictionary learning (DL), implemented via matrix factorization (MF), is commonly used in computational biology to tackle ubiquitous clustering problems. The method is favored due to its conceptual simplicity and relatively low computational complexity. However, DL algorithms produce results that lack interpretability in terms of real biological data. Additionally, they are not optimized for graph-structured data and hence often fail to handle them in a scalable manner.

In order to address these limitations, we propose a novel DL algorithm calledonline convex network dictionary learning(online cvxNDL). Unlike classical DL algorithms, online cvxNDL is implemented via MF and designed to handle extremely large datasets by virtue of its online nature. Importantly, it enables the interpretation of dictionary elements, which serve as cluster representatives, through convex combinations of real measurements. Moreover, the algorithm can be applied to data with a network structure by incorporating specialized subnetwork sampling techniques.

To demonstrate the utility of our approach, we apply cvxNDL on 3D-genome RNAPII ChIA-Drop data with the goal of identifying important long-range interaction patterns (long-range dictionary elements). ChIA-Drop probes higher-order interactions, and produces data in the form of hypergraphs whose nodes represent genomic fragments. The hyperedges represent observed physical contacts. Our hypergraph model analysis has the objective of creating an interpretable dictionary of long-range interaction patterns that accurately represent global chromatin physical contact maps. Through the use of dictionary information, one can also associate the contact maps with RNA transcripts and infer cellular functions.

To accomplish the task at hand, we focus on RNAPII-enriched ChIA-Drop data fromDrosophila MelanogasterS2 cell lines. Our results offer two key insights. First, we demonstrate that online cvxNDL retains the accuracy of classical DL (MF) methods while simultaneously ensuring unique interpretability and scalability. Second, we identify distinct collections of proximal and distal interaction patterns involving chromatin elements shared by related processes across different chromosomes, as well as patterns unique to specific chromosomes. To associate the dictionary elements with biological properties of the corresponding chromatin regions, we employ Gene Ontology (GO) enrichment analysis and perform multiple RNA coexpression studies.
Persuasive technologies design for mental and behavioral health platforms: A scoping literature review
Authors: Idrees Abdul Rahman , Kraft Robin , Mutter Agnes , Baumeister Harald , Reichert Manfred , Pryss Rüdiger
Published: May 2024

This review investigates persuasive design frameworks within eHealth, concentrating on methodologies, their prevalence in mental and behavioral health applications, and identifying current research gaps. An extensive search was conducted across 8 databases, focusing on English publications with full text available. The search prioritized primary research articles, post-2011 applications, and eHealth platforms emphasizing treatment or support. The inclusion process was iterative, involving multiple authors, and relied on detailed criteria to ensure the relevance and contemporaneity of selected works. The final review set comprised 161 articles, providing an overview of persuasive design frameworks in eHealth. The review highlights the state of the art in the domain, emphasizing the utilization and effectiveness of these frameworks in eHealth platforms. This review details the restricted adoption of persuasive design frameworks within the field of eHealth, particularly in the mental and behavioral sectors. Predominant gaps include the scarcity of comparative evaluations, the underrepresentation of tailored interventions, and the unclear influence of persuasive components on user experience. There is a notable requirement for further scrutiny and refinement of persuasive design frameworks. Addressing these concerns promises a more substantial foundation for persuasive design in eHealth, potentially enhancing user commitment and platform efficiency.
Inhibitory effect of doxycycline conjugated with deoxycholic acid and polyethylenimine conjugate on nasal fibroblast differentiation and extracellular production
Authors: Shin Jae-Min , Yang Hyun-Woo , Lim Su-yeon , Jeong Ji-hoon , Park Il-Ho
Published: May 2024

Background

Chronic rhinosinusitis (CRS) is an inflammatory disease affecting the sinuses or nose. Persistent inflammatory responses can lead to tissue remodeling, which is a pathological characteristics of CRS. Activation of fibroblasts in the nasal mucosal stroma, differentiation and collagen deposition, and subepithelial fibrosis have been associated with CRS.

Objectives

We aimed to assess the inhibitory effects of doxycycline and deoxycholic acid-polyethyleneimine conjugate (DA3-Doxy) on myofibroblast differentiation and extracellular matrix (ECM) production in nasal fibroblasts stimulated with TGF-β1.

Methods

To enhance efficacy, we prepared DA3-Doxy using a conjugate of low-molecular-weight polyethyleneimine (PEI) (MW 1800) and deoxycholic acid (DA) and Doxy. The synthesis of the DA3-Doxy polymer was confirmed using nuclear magnetic resonance, and the critical micelle concentration required for cationic micelle formation through self-assembly was determined. Subsequently, the Doxy loading efficiency of DA3 was assessed. The cytotoxicity of Doxy, DA3, PEI, and DA-Doxy in nasal fibroblasts was evaluated using the WST-1 assay. The anti-tissue remodeling and anti-inflammatory effects of DA3-Doxy and DA3 were examined using real-time polymerase chain reaction (Real-time PCR), immunocytochemistry, western blot, and Sircol assay.

Results

Both DA3 and DA3-Doxy exhibited cytotoxicity at 10 μg/ml in nasal fibroblasts. Doxy partially inhibited α-smooth muscle actin, collagen types I and III, and fibronectin. However, DA3-Doxy significantly inhibited α-SMA, collagen types I and III, and fibronectin at 5 μg/ml. DA3-Doxy also modulated TGF-β1-induced changes in the expression of MMP 1, 2, and 9. Nonetheless, TGF-β1-induced expression of MMP3 was further increased by DA3-Doxy. The expression of TIMP 1 and 2 was partially reduced with 5 μg/ml DA3-Doxy.

Conclusions

Although initially developed for the delivery of genetic materials or drugs, DA3 exhibits inhibitory effects on myofibroblast differentiation and ECM production. Therefore, it holds therapeutic potential for CRS, and a synergistic effect can be expected when loaded with CRS treatment drugs.
Navigating regulatory landscape: A qualitative exploration of medical devices and in vitro diagnostic medical devices oversight in Zimbabwe through key stakeholder perspectives
Authors: Chiku Charles , Maruta Talkmore , Mbiba Fredrick , Manasa Justen
Published: May 2024

Medical devices and In Vitro Diagnostics (IVDs) are vital for public health and accessible healthcare. Still, there is an imbalance in high-quality products in Low and Middle-Income Countries (LMICs). Zimbabwe’s regulatory framework for medical devices and IVDs is unclear, leading to ineffective compliance and surveillance. As a result, there are knowledge gaps regarding pre-market and post-market regulatory elements to ensure the safety, quality and performance of medical devices and IVDs used in Zimbabwe. Our study aimed to explore the current status of medical devices and IVD regulations in Zimbabwe. Semi-structured interviews were conducted with 12 regulators from the Medicines Control Authority of Zimbabwe (MCAZ) National Microbiology Reference Laboratory (NMRL), Medical Laboratory and Clinical Scientists Council (MLCScCZ) to understand the current status of medical devices and IVD regulations in Zimbabwe. Three participants completed a questionnaire to understand the regulatory landscape in Zimbabwe. Three key informant interviews were conducted with three regulators from the South African Health Products Regulatory Authority (SAHPRA), Tanzanian Medicines and Medical Devices Authority (TMDA), and World Health Organization Regulatory Systems Strengthening (WHO RSS) to learn best practices to create a roadmap for Zimbabwe. We analyzed qualitative data using a thematic analysis. The findings reveal significant deficiencies and gaps in the legal framework for regulating medical devices and IVDs, highlighting the need for a legal framework and the absence of more comprehensive regulations. Regulatory entities face capacity limitations, especially in regulating medical devices and IVDs. Conformity assessment processes, medical devices, IVD classification criteria, and post-market surveillance also represent challenges, highlighting the need for a well-defined framework and regulatory procedures. The Zimbabwean regulatory system pathway is reactive, prompting several regulatory initiatives to address needs. Despite facing challenges, there is recognition of the importance of collaboration among regulatory authorities, emphasizing a shared commitment to improving and strengthening medical devices and IVD regulations for improved patient safety. By advocating for a proactive, comprehensive, and legally sound approach, indicating the potential for collaboration and synergy, this study provides a foundation for well-informed policy recommendations to guide enhancements and build a framework for a resilient, efficient, and transparent regulatory environment in the Zimbabwe and African regions as a whole.
Assessing operational readiness: Regulatory landscape and compliance in zimbabwe for medical devices and in vitro diagnostic medical devices
Authors: Chiku Charles , Maruta Talkmore , Mbiba Fredrick , Manasa Justen
Published: May 2024

The regulation of medical devices and In Vitro Diagnostic (IVD) medical devices have lagged significantly, especially in low- and middle-income countries. Disparities in regulating medical and IVD medical devices in Africa are below the global average. This may translate to poor access to quality-assured medical and IVD devices, resulting in undesirable health outcomes. Operational readiness to regulate medical and IVD devices at the Medicines Control Authority of Zimbabwe (MCAZ) was assessed. The aim was to determine the strengths and gaps and propose an action plan that can be monitored and evaluated to assess progress over time. We used the World Health Organization (WHO) Global Benchmarking Tool for medical devices and IVDs methodology to evaluate regulatory oversight of these products. Purposive sampling was used for data collection using researcher-administered global benchmarking tool factsheets and document reviews to evaluate the implementation of the regulatory functions. The regulatory functions assessed were the National Regulatory System, Registration and Market Authorization, Vigilance, Market Surveillance and Control, Licensing Establishment, Regulatory Inspection, Laboratory Testing, and Clinical Trials Oversight. The MCAZ attained maturity level 1, with a regulatory system score of 79%, registration and market authorization 44%, vigilance 27%, market surveillance and control 40%, licensing establishment 62%, regulatory inspection 68%, laboratory testing 88%, and clinical trials 18%. Condoms and gloves were the only regulated medical devices in Zimbabwe. IVDs were not regulated by the MCAZ. This review showed that the regulatory system is not robust, fit for purpose, responsive, transparent, or proportionate to the risk classification of medical devices and IVDs. It is crucial to amend the Medicines and Allied Substance Control Act to incorporate the definition and classification of medical devices and IVDs, regulatory authority establishment, licensing and registration, quality management system, conformity assessment, post-market surveillance, labeling and instructions for use, capacity building and training, and international harmonization.
Symptoms of depression among outpatients with suspected COVID-19 in metropolitan Local Government Areas of Kaduna State, Nigeria
Authors: Umeh Gregory C. , Cleenwerck de Kiev Laurent , Mamza Jabani , Atiku Aliyu , Mohammed Suleiman , Hananiya Dauda S. , Onoh Moses , Yahaya Habibu B. , Adeoti Basirat , Musa Rabiat T. , Adegbite Mutiu , Audu Sunday , Daikwo Jeremiah , Iliyasu Neyu , Baloni Amina Mohammed
Published: May 2024

Background

The novel SARS-CoV-2 virus that causes Coronavirus disease (COVID-19) has redefined global health and response to Acute Respiratory Infection (ARI). The outbreak of a cluster of influenza-like illnesses in Wuhan, China, has morphed into a pandemic in the last quarter of 2019, stretching from South East Asia to Europe, The Americas, Africa, and the Australian subcontinent. We evaluated the prevalence of depression among outpatients diagnosed with ARI.

Materials and methods

We utilized a cross-sectional, observational design and investigated the prevalence of symptoms of depression among outpatients with ARI and described the characteristics of outpatients with ARI in Kaduna State.

Results

The prevalence of symptoms of depression was 19.6% for respondents with symptoms of ARI and 14.4% for those without symptoms of ARI. On no risk of depression, we had a higher proportion of the respondents without symptoms of ARI (86%) than those with symptoms of depression (80%) (M = 318.4, SD = 29.62 case, and M = 344.0, SD = 14.2 control, r = 0.88, CI = 13.5 to 6.5, P = 0.000952). Likewise, in the category with mild risk of depression, respondents without symptoms of ARI were fewer (10%) than those with symptoms of depression (15%) (M = 58.4, SD = 26.0 case, and M = 42.1, SD = 12.7 control, r = 0.86, CI = 11.8 to 5.8, P = 0.0136. There was no significant difference between respondents with symptoms of ARI and without symptoms of ARI in the categories of moderate (M = 13.6, SD = 5.1 case, and M = 11.6, SD = 4.6 control, r = 0.87, CI = 2.3 to 2.1, P = 0.178) and high (M = 5.6, SD = 2.5 case, and M = 4.4, SD = 3.2 control, r = 0.61, CI = 1.2 to 1.5, P = 0.174) risk of depression.

Conclusion

Symptoms of depression were commoner among respondents who presented with symptoms of Acute Respiratory Infection (ARI) at the Outpatient Department (OPD). However, further explanatory research is needed to establish causality.
COVID-19 hotspot detection in a university setting
Authors: Duncan Garrett , Christensen William F. , Handley Camilla
Published: May 2024

The onset of the COVID-19 pandemic commenced an era of widespread disruptions in the academic world, including shut downs, periodic shifts to online learning, and disengagement from students. In an effort to transition back to in-person learning, many universities and schools tried to implement policy that balanced student learning with community health. While academic administrators have little control over some aspects of COVID-19 spread, they often choose to use temporary shutdowns of in-person teaching based on perceived hotspots of COVID-19. Specifically, if administrators have substantial evidence of within-group transmission for a class or other academic unit (a “hotspot”), the activities of that class or division of the university might be temporarily moved online. In this article, we describe an approach used to make these types of decisions. Using demographic information and weekly COVID-19 testing outcomes for university students, we use an XGBoost model that produces an estimated probability of testing positive for each student. We discuss variables engineered from the demographic information that increased model fit. As part of our approach, we simulate semesters under the null hypothesis of no in-class transmission, and compare the distribution of simulated outcomes to the observed group positivity rates to find an initial p-value for each group (e.g., section, housing area, or major). Using a simulation-based modification of a standard false discovery rate procedure, we identify possible hot spots—classes or groups whose COVID-19 rates exceed the levels expected for the demographic mix of students in each group of interest. We use simulation experiments and an anonymized example from Fall 2020 to illustrate the performance of our approach. While our example is based on hotspot detection in a university setting, the approach can be used for monitoring the spread of infectious disease within any interconnected organization or population.
Mapping sedentary behaviour (MAPS-B) in winter and spring using wearable sensors, indoor positioning systems, and diaries in older adults who are pre-frail and frail: A feasibility longitudinal study
Authors: Rodrigues Isabel B. , Tariq Suleman , Kouroukis Alexa , Swance Rachel , Adachi Jonathan , Bray Steven , Fang Qiyin , Ioannidis George , Kobsar Dylan , Rabinovich Alexander , Papaioannou Alexandra , Zheng Rong
Published: May 2024

Older adults who are frail are likely to be sedentary. Prior interventions to reduce sedentary time in older adults have not been effective as there is little research about the context of sedentary behaviour (posture, location, purpose, social environment). Moreover, there is limited evidence on feasible measures to assess context of sedentary behaviour in older adults. The aim of our study was to determine the feasibility of measuring context of sedentary behaviour in older adults with pre-frailty or frailty using a combination of objective and self-report measures. We defined “feasibility process” using recruitment (20 participants within two-months), retention (85%), and refusal (20%) rates and “feasibility resource” if the measures capture context and can be linked (e.g., sitting-kitchen-eating-alone) and are all participants willing to use the measures. Context was assessed using a wearable sensor to assess posture, a smart home monitoring system for location, and an electronic or hard-copy diary for purpose and social context over three days in winter and spring. We approached 80 potential individuals, and 58 expressed interest; of the 58 individuals, 37 did not enroll due to lack of interest or medical mistrust (64% refusal). We recruited 21 older adults (72±7.3 years, 13 females, 13 frail) within two months and experienced two dropouts due to medical mistrust or worsening health (90% retention). The wearable sensor, indoor positioning system, and electronic diary accurately captured one domain of context, but the hard copy was often not completed with enough detail, so it was challenging to link it to the other devices. Although not all participants were willing to use the wearable sensor, indoor positioning system, or electronic diary, we were able to triage the measures of those who did. The use of wearable sensors and electronic diaries may be a feasible method to assess context of sedentary behaviour, but more research is needed with device-based measures in diverse groups.
Gene flow from Fraxinus cultivars into natural stands of Fraxinus pennsylvanica occurs range-wide, is regionally extensive, and is associated with a loss of allele richness
Authors: Abhainn Everett A. , Shirley Devin L. , Stanley Robert K. , Scarpato Tatum , Koch Jennifer L. , Romero-Severson Jeanne
Published: May 2024

In North America, a comparatively small number ofFraxinus(ash) cultivars were planted in large numbers in both urban and rural environments across the entire range ofFraxinus pennsylvanicaMarsh (green ash) over the last 80 years. Undetected cultivar gene flow, if extensive, could significantly lower genetic diversity within populations, suppress differentiation between populations, generate interspecific admixture not driven by long-standing natural processes, and affect the impact of abiotic and biotic threats. In this investigation we generated the first range-wide genetic assessment ofF.pennsylvanicato detect the extent of cultivar gene flow into natural stands. We used 16 EST-SSR markers to genotype 48 naturally regenerated populations ofF.pennsylvanicadistributed across the native range (1291 trees), 19F.pennsylvanicacultivars, and oneF.americanaL. (white ash) cultivar to detect cultivar propagule dispersal into these populations. We detected first generation cultivar parentage with high confidence in 171 individuals in 34 of the 48 populations and extensive cultivar parentage (23–50%) in eight populations. The incidence of cultivar parentage was negatively associated with allele richness (R2= 0.151, p = 0.006). The evidence for a locally high frequency of cultivar propagule dispersal and the interspecific admixture in eastern populations will informFraxinusgene pool conservation strategies and guide the selection of individuals for breeding programs focused on increasing resistance to the emerald ash borer (Agrilus planipennisFairmaire), an existential threat to theFraxinusspecies of North America.
Enhancing rice growth and yield with weed endophytic bacteria Alcaligenes faecalis and Metabacillus indicus under reduced chemical fertilization
Authors: Fatema Kaniz , Mahmud Nur Uddin , Gupta Dipali Rani , Siddiqui Md. Nurealam , Sakif Tahsin Islam , Sarker Aniruddha , Sharpe Andrew G. , Islam Tofazzal
Published: May 2024

Endophytic bacteria, recognized as eco-friendly biofertilizers, have demonstrated the potential to enhance crop growth and yield. While the plant growth-promoting effects of endophytic bacteria have been extensively studied, the impact of weed endophytes remains less explored. In this study, we aimed to isolate endophytic bacteria from native weeds and assess their plant growth-promoting abilities in rice under varying chemical fertilization. The evaluation encompassed measurements of mineral phosphate and potash solubilization, as well as indole-3-acetic acid (IAA) production activity by the selected isolates. Two promising strains, tentatively identified as Alcaligenes faecalis (BTCP01) from Eleusine indica (Goose grass) and Metabacillus indicus (BTDR03) from Cynodon dactylon (Bermuda grass) based on 16S rRNA gene phylogeny, exhibited noteworthy phosphate and potassium solubilization activity, respectively. BTCP01 demonstrated superior phosphate solubilizing activity, while BTDR03 exhibited the highest potassium (K) solubilizing activity. Both isolates synthesized IAA in the presence of L-tryptophan, with the detection of nifH and ipdC genes in their genomes. Application of isolates BTCP01 and BTDR03 through root dipping and spraying at the flowering stage significantly enhanced the agronomic performance of rice variety CV. BRRI dhan29. Notably, combining both strains with 50% of recommended N, P, and K fertilizer doses led to a substantial increase in rice grain yields compared to control plants receiving 100% of recommended doses. Taken together, our results indicate that weed endophytic bacterial strains BTCP01 and BTDR03 hold promise as biofertilizers, potentially reducing the dependency on chemical fertilizers by up to 50%, thereby fostering sustainable rice production.
Study protocol: Close Assessment and Testing for Chronic Graft-vs.-Host disease (CATCH)
Authors: Pidala Joseph , Carpenter Paul A. , Onstad Lynn , Pavletic Steven Z. , Hamilton Betty K. , Chen George L. , Farhadfar Nosha , Hall Marcie , Lee Stephanie J.
Published: May 2024

Chronic graft-versus-host disease (GVHD) is an immune-mediated disorder that causes significant late morbidity and mortality following allogeneic hematopoietic cell transplantation. The “Close Assessment and Testing for Chronic GVHD (CATCH)” study is a multi-center Chronic GVHD Consortium prospective, longitudinal cohort study designed to enroll patients before hematopoietic cell transplantation and follow them closely to capture the development of chronic GVHD and to identify clinical and biologic biomarkers of chronic GVHD onset. Data are collected pre-transplant and every two months through one-year post-transplant with chart review thereafter. Evaluations include clinician assessment of chronic GVHD and its manifestations, patient-reported outcomes, multiple biospecimens (blood, saliva, tears, buccal mucosa and fecal samples, biopsies of skin and mouth), laboratory testing, and medical record abstraction. This report describes the rationale, design, and methods of the CATCH study, and invites collaboration with other investigators to leverage this resource.

trial registration: This study is registered at www.clinicaltrials.gov as NCT04188912.
PPARgamma dependent PEX11beta counteracts the suppressive role of SIRT1 on neural differentiation of HESCs
Authors: Esmaeili Maryam , Nasr-Esfahani Mohammad Hossein , Shoaraye Nejati Alireza , Safaeinejad Zahra , Atefi Atefeh , L. Megraw Timothy , Ghaedi Kamran
Published: May 2024

The membrane peroxisomal proteins PEX11, play a crucial role in peroxisome proliferation by regulating elongation, membrane constriction, and fission of pre-existing peroxisomes. In this study, we evaluated the function of PEX11B gene in neural differentiation of human embryonic stem cell (hESC) by inducing shRNAi-mediated knockdown of PEX11B expression. Our results demonstrate that loss of PEX11B expression led to a significant decrease in the expression of peroxisomal-related genes including ACOX1, PMP70, PEX1, and PEX7, as well as neural tube-like structures and neuronal markers. Inhibition of SIRT1 using pharmacological agents counteracted the effects of PEX11B knockdown, resulting in a relative increase in PEX11B expression and an increase in differentiated neural tube-like structures. However, the neuroprotective effects of SIRT1 were eliminated by PPAR inhibition, indicating that PPARɣ may mediate the interaction between PEX11B and SIRT1. Our findings suggest that both SIRT1 and PPARɣ have neuroprotective effects, and also this study provides the first indication for a potential interaction between PEX11B, SIRT1, and PPARɣ during hESC neural differentiation.
Changing trends in traumatic spinal cord injury in an aging society: Epidemiology of 1152 cases over 15 years from a single center in Japan
Authors: Yokota Kazuya , Sakai Hiroaki , Kawano Osamu , Morishita Yuichiro , Masuda Muneaki , Hayashi Tetsuo , Kubota Kensuke , Ideta Ryosuke , Ariji Yuto , Koga Ryuichiro , Murai Satoshi , Ifuku Ryusei , Uemura Masatoshi , Kishimoto Junji , Watanabe Hiroko , Nakashima Yasuharu , Maeda Takeshi
Published: May 2024

Traumatic spinal cord injury (TSCI) causes an insult to the central nervous system, often resulting in devastating temporary or permanent neurological impairment and disability, which places a substantial financial burden on the health-care system. This study aimed to clarify the up-to-date epidemiology and demographics of patients with TSCI treated at the largest SCI center in Japan. Data on all patients admitted to the Spinal Injuries Center with TSCI between May 2005 and December 2021 were prospectively collected using a customized, locally designed SCI database named the Japan Single Center Study for Spinal Cord Injury Database (JSSCI-DB). A total of 1152 patients were identified from the database. The study period was divided into the four- or five-year periods of 2005–2009, 2010–2013, 2014–2017, and 2018–2021 to facilitate the observation of general trends over time. Our results revealed a statistically significant increasing trend in age at injury. Since 2014, the average age of injury has increased to exceed 60 years. The most frequent spinal level affected by the injury was high cervical (C1-C4: 45.8%), followed by low cervical (C5-C8: 26.4%). Incomplete tetraplegia was the most common cause or etiology category of TSCI, accounting for 48.4% of cases. As the number of injuries among the elderly has increased, the injury mechanisms have shifted from high-fall trauma and traffic accidents to falls on level surfaces and downstairs. Incomplete tetraplegia in the elderly due to upper cervical TSCI has also increased over time. The percentage of injured patients with an etiology linked to alcohol use ranged from 13.2% (2005–2008) to 19% (2014–2017). Given that Japan has one of the highest aging populations in the world, epidemiological studies in this country will be very helpful in determining health insurance and medical costs and deciding strategies for the prevention and treatment of TSCI in future aging populations worldwide.
Interaction of sedentary behaviour and educational level in breast cancer risk
Authors: Pinto-Carbó Marina , Vanaclocha-Espí Mercedes , Ibañez Josefa , Martín-Pozuelo Javier , Romeo-Cervera Paula , Nolasco Andreu , Besó-Delgado María , Castán-Cameo Susana , Salas Dolores , Molina-Barceló Ana
Published: May 2024

Objective

This cross-sectional study aims to analyse the relationship between sedentary behaviour and breast cancer (BC) risk from a social perspective.

Methods

Women aged 45–70 who participated in the Valencia Region Breast Cancer Screening Programme (2018–2019) were included, with a total of 121,359 women analysed, including 506 with cancer and 120,853 without cancer. The response variable was BC (screen-detected) and the main explanatory variable was sedentary behaviour (≤2 / >2-≤3 / >3-≤5 / >5 hours/day, h/d). Nested logistic regression models (M) were estimated: M1: sedentary behaviour adjusted for age and family history of BC; M2: M1 + hormonal/reproductive variables (menopausal status, number of pregnancies, hormone replacement therapy; in addition, months of breastfeeding was added for a subsample of women with one or more live births); M3: M2 + lifestyle variables (body mass index, smoking habits); M4: M3 + socioeconomic variables (educational level, occupation); Final model: M4 + gender variables (childcare responsibilities, family size). Interaction between sedentary behaviour and educational level was analysed in the Final model. Moreover, for the whole sample, postmenopausal women and HR+ BC, the Final model was stratified by educational level.

Results

Sedentary behaviour was associated with an increased risk of BC with a nearly statistically significant effect in the Final model (>2-≤3 h/d: OR = 1.22 (0.93–1.61); >3-≤5 h/d: OR = 1.14 (0.86–1.52); >5: OR = 1.19 (0.89–1.60)). For women with a low educational level, sitting more than 2 h/d was associated with an increased risk of BC in the whole sample (>2-≤3 h/d OR = 1.93 (1.19–3.21); in postmenopausal women (>2-≤3 h/d, OR = 2.12 (1.18–2.96), >5h/d OR = 1.75 (1.01–3.11)) and in HR+ BC (>2-≤3h/d, OR = 2.15 (1.22–3.99)). Similar results were observed for women with one or more live births.

Conclusions

Sitting >2 h/d is associated with BC risk in women with low educational level, especially in postmenopausal women and those with live births.
Metagenomic analysis of sewage for surveillance of bacterial pathogens: A release experiment to determine sensitivity
Authors: Kohle Simon , Petersen Thomas N. , Vigre Håkan , Johansson Markus Hans Kristofer , Aarestrup Frank M.
Published: May 2024

Accurate monitoring of gastro-enteric and other diseases in large populations poses a challenge for public health management. Sewage represents a larger population, is freely obtainable and non-subject to ethical approval. Metagenomic sequencing offers simultaneous, multiple-target analysis. However, no study has demonstrated the sensitivity of metagenomics for detecting bacteria in sewage. In this study, we spot-released 1013 colony-forming units (CFU) of Staphyloccus hyicus (non-pathogenetic strain 842J-88). The strain was flushed down a toilet into the sewer in the catchment area of a public wastewater treatment plant (WWTP), serving a population of 36,000 people. Raw sewage was continuously sampled at the WWTP’s inlet over 30- and 60-minute intervals for a total period of seven hours. The experiment was conducted twice with one week in-between release days and under comparable weather conditions. For the metagenomics analyses, the pure single isolate of S. hyicus was sequenced, assembled and added to a large database of bacterial reference sequences. All sewage samples were analyzed by shotgun metagenome sequencing and mapped against the reference database. S. hyicus was identified in duplicate samples at both of two release days and these sequence fragment counts served as a proxy to estimate the minimum number of sick people or sensitivity required in order to observe at least one sick person at 95% probability. We found the sensitivity to be in the range 41–140 and 16–36 sick people at release days 1 and 2, respectively. The WWTP normally serves 36,000 people giving a normalized sensitivity in the range of one in 257 to 2,250 persons.
Individual and community level determinants of delayed antenatal care initiation in Ethiopia: A multilevel analysis of the 2019 Ethiopian Mini Demographic Health Survey
Authors: Alemu Addisu Alehegn , Zeleke Liknaw Bewket , Jember Desalegn Abebaw , Kassa Getachew Mullu , Khajehei Marjan
Published: May 2024

Background

Antenatal care (ANC) is essential health care and medical support provided to pregnant women, with the aim of promoting optimal health for both the mother and the developing baby. Pregnant women should initiate ANC within the first trimester of pregnancy to access a wide range of crucial services. Early initiation of ANC significantly reduces adverse pregnancy outcomes, yet many women in Sub-Saharan Africa delay its initiation. The aim of this study was to assess prevalence and determinants of delayed ANC initiation in Ethiopia.

Methods

We conducted a secondary data analysis of the 2019 Ethiopian Mini Demographic and Health Survey (EMDHS). The study involved women of reproductive age who had given birth within the five years prior to the survey and had attended ANC for their most recent child. A total weighted sample of 2,895 pregnant women were included in the analysis. Due to the hierarchical nature of the data, we employed a multi-level logistic regression model to examine both individual and community level factors associated with delayed ANC initiation. The findings of the regressions were presented with odds ratios (OR), 95% confidence intervals (CI), and p-values. All the statistical analysis were performed using STATA—14 software.

Results

This study showed that 62.3% (95% CI: 60.5, 64.1) of pregnant women in Ethiopia delayed ANC initiation. Participants, on average, began their ANC at 4 months gestational age. Women with no education (AOR = 2.1; 95% CI: 1.4, 3.0), poorest wealth status (AOR = 1.9; 95% CI: 1.3, 2.8), from the Southern Nations, Nationalities, and Peoples (SNNP) region (AOR = 2.1; 95% CI: 1.3, 3.3), and those who gave birth at home (AOR = 1.4; 95% CI: 1.1, 1.7) were more likely to delay ANC initiation.

Conclusions

The prevalence of delayed ANC initiation in Ethiopia was high. Enhancing mothers’ education, empowering them through economic initiatives, improving their health-seeking behavior towards facility delivery, and universally reinforcing standardized ANC, along with collaborating with the existing local community structure to disseminate health information, are recommended measures to reduce delayed ANC initiation.