bluuebunny/crossref_metadata_2025 huggingface dataset:
Rapid molecular species identification of mammalian scat samples using nanopore adaptive sampling
Authors: Frank Lexi E. , Lindsey Laramie L. , Kipp Evan J. , Faulk Christopher , Stone Suzanne , Roerick Tanya M. , Moore Seth A. , Wolf Tiffany M. , Larsen Peter A.
Published: June 2023

Abstract

Accurate species identification is essential to mammalogy. Despite this necessity, rapid and accurate identification of cryptic, understudied, and elusive mammals remains challenging. Traditional barcoding of mitochondrial genes is standard for molecular identification but requires time-consuming wet-lab methodologies. Recent bioinformatic advancements for nanopore sequencing data offer exciting opportunities for non-invasive and field-based identification of mammals. Nanopore adaptive sampling (NAS), a PCR-free method, selectively sequences regions of DNA according to user-specified reference databases. Here, we utilized NAS to enrich mammalian mitochondrial genome sequencing to identify species. Fecal DNA extractions were sequenced from nine mammals, several collected in collaboration with Minnesota Tribal Nations, to demonstrate utility for NAS-barcoding of non-invasive samples. By mapping to the entire National Center for Biotechnology Information (NCBI) mammalian mitochondrial reference genome database and bioinformatically analyzing highly similar matches, we successfully produced species identifications for all of our fecal samples. Eight of nine species identifications matched previous PCR or animal/fecal morphological identifications. For the ninth species, our genetic data indicate a misidentification stemming from the original study. Our approach has a range of applications, particularly field-based wildlife research, conservation, disease surveillance, and monitoring of wildlife trade. Of importance to Minnesota tribes is invasive species monitoring, detections, and confirmation as climate impacts causes changes in biodiversity and shifts in species distributions. The rapid assessment techniques described here will be useful as new introductions and range expansions of native and invasive species may first be detected by the presence of signs such as scat rather than direct observations and will be helpful for chronically understaffed tribal natural resources agencies.
cudaMMC - GPU-enhanced Multiscale Monte Carlo Chromatin 3D Modelling
Authors: Wlasnowolski Michał , Grabowski Paweł , Roszczyk Damian , Kaczmarski Krzysztof , Plewczynski Dariusz
Published: June 2023

Motivation

Investigating the 3D structure of chromatin provides new insights into transcriptional regulation. With the advancements in 3C new-sequencing techniques such as ChiA-PET and Hi-C, there has been a substantial increase in the volume of collected data, necessitating faster algorithms for chromatin spatial modelling. This study presents the cudaMMC method, which utilises the Simulated Annealing Monte Carlo approach extended by GPU-accelerated computing to generate ensembles of chromatin 3D structures efficiently.

Results

ThecudaMMCcalculations demonstrate significantly faster performance and lower (better) model scores compared to our previous method on the same workstation.cudaMMCsubstantially reduces the computation time required for generating ensembles of large chromatin models, making it an invaluable tool for studying chromatin spatial conformation.

Availability

Open-source software and manual and sample data are freely available onhttps://github.com/SFGLab/cudaMMC

Contact

Dariusz.Plewczynski@pw.edu.pl
Improving modelling for epidemic responses: reflections from members of the UK infectious disease modelling community on their experiences during the COVID-19 pandemic
Authors: Sherratt Katharine , Carnegie Anna C. , Kucharski Adam , Cori Anne , Pearson Carl A. B. , Jarvis Christopher I. , Overton Christopher , Weston Dale , Hill Edward M. , Knock Edward , Fearon Elizabeth , Nightingale Emily , Hellewell Joel , Edmunds W. John , Arenas Julián Villabona , Prem Kiesha , Pi Li , Baguelin Marc , Kendall Michelle , Ferguson Neil , Davies Nicholas , Eggo Rosalind M. , van Elsland Sabine , Russell Timothy , Funk Sebastian , Liu Yang , Abbott Sam
Published: June 2023

The COVID-19 pandemic both relied and placed significant burdens on the experts involved from research and public health sectors. The sustained high pressure of a pandemic on responders, such as healthcare workers, can lead to lasting psychological impacts including acute stress disorder, post-traumatic stress disorder, burnout, and moral injury, which can impact individual wellbeing and productivity. As members of the infectious disease modelling community, we convened a reflective workshop to understand the professional and personal impacts of response work on our community and to propose recommendations for future epidemic responses. The attendees represented a range of career stages, institutions, and disciplines. This piece was collectively produced by those present at the session based on our collective experiences. Key issues we identified at the workshop were lack of institutional support, insecure contracts, unequal credit and recognition, and mental health impacts. Our recommendations include rewarding impactful work, fostering academia-public health collaboration, decreasing dependence on key individuals by developing teams, increasing transparency in decision-making, and implementing sustainable work practices. Despite limitations in representation, this workshop provided valuable insights into the UK COVID-19 modelling experience and guidance for future public health crises. Recognising and addressing the issues highlighted is crucial, in our view, for ensuring the effectiveness of epidemic response work in the future.
Blind cavefish evolved food-searching behavior without changing sensory modality compared with sighted conspecies in the dark
Authors: Kuball Kyleigh , Fernandes Vânia Filipa Lima , Takagi Daisuke , Yoshizawa Masato
Published: June 2023

In nature, animals must navigate to forage according to their sensory inputs. Different species use different sensory modalities to locate food efficiently. For teleosts, food emits visual, mechanical, chemical, and/or possibly weak-electrical signals, which can be detected by optic, auditory/lateral line, and olfactory/taste buds sensory systems. However, how fish respond to and use different sensory inputs when locating food, as well as the evolution of these sensory modalities, remain unclear. We examined the Mexican tetra,Astyanax mexicanus, which is composed of two different morphs: a sighted riverine (surface fish) and a blind cave morph (cavefish). Compared with surface fish, cavefish have enhanced non-visual sensory systems, including the mechanosensory lateral line system, chemical sensors comprising the olfactory system and taste buds, and the auditory system to help navigate toward food sources. We tested how visual, chemical, and mechanical stimuli evoke food-seeking behavior. In contrast to our expectations, both surface fish and cavefish did not follow a gradient of chemical stimulus (food extract) but used it as a cue for the ambient existence of food. Surface fish followed visual cues (red plastic beads and food pellets), but, in the dark, were likely to rely on mechanosensors—the lateral line and/or tactile sensor—as cavefish did. Our results indicate cavefish used similar sensory modality to surface fish in the dark, while adherence levels to stimuli were higher in cavefish. In addition, cavefish evolved an extended circling strategy to capture food, which may yield a higher chance to capture food by swimming-by the food multiple times instead of once through zigzag motion. In summary, we propose ancestors of cavefish similar to surface fish may have needed little modification in food-seeking strategy to adapt to the dark.
AMPK Drives Both Glycolytic and Oxidative Metabolism in T Cells During Graft-versus-host Disease
Authors: Ramgopal Archana , Braverman Erica L , Sun Lee-Kai , Monlish Darlene , Wittmann Christopher , Ramsey Manda J. , Caitley Richard , Hawse William , Byersdorfer Craig A.
Published: June 2023

Allogeneic T cells reprogram their metabolism during acute graft-versus-host disease (GVHD) in a process reliant on the cellular energy sensor AMP-activated protein kinase (AMPK). Deletion of AMPK in donor T cells limits GVHD but still preserves homeostatic reconstitution and graft-versus-leukemia (GVL) effects. In the current studies, murine T cells lacking AMPK decreased oxidative metabolism at early timepoints post-transplant and were also unable to mediate a compensatory increase in glycolysis following inhibition of the electron transport chain. Human T cells lacking AMPK gave similar results, with glycolytic compensation impaired bothin vitroand following expansionin vivoin a modified model of GVHD. Immunoprecipitation of proteins from day 7 allogeneic T cells, using an antibody specific to phosphorylated AMPK targets, recovered lower levels of multiple glycolysis-related proteins including the glycolytic enzymes aldolase, enolase, pyruvate kinase M (PKM), and glyceraldehyde 3-phosphate dehydrogenase (GAPDH). Functionally, murine T cells lacking AMPK exhibited impaired aldolase activity following anti-CD3/CD28 stimulation and a decrease in GAPDH activity on day 7 post-transplant. Importantly, these changes in glycolysis correlated with an impaired ability of AMPK KO T cells to produce significant amounts of interferon gamma (IFNγ) upon antigenic re-stimulation. Together these data highlight a significant role for AMPK in controlling oxidative and glycolytic metabolism in both murine and human T cells during GVHD and endorse further study of AMPK inhibition as a potential target for future clinical therapies.

KEY POINTS

AMPK plays a key role in driving both and oxidative and glycolytic metabolism in T cells during graft-versus-host disease (GVHD)

Absence of AMPK simultaneously impairs both glycolytic enzyme activity, most notably by aldolase, and interferon gamma (IFNγ) production
The Genetics of Aerotolerant Growth in a Naturally Reduced Genome Alphaproteobacterium
Authors: Enright Amy L. , Banta Amy B. , Ward Ryan D. , Vazquez Julio Rivera , Felczak Magdalena M. , Wolfe Michael B. , TerAvest Michaela A. , Amador-Noguez Daniel , Peters Jason M.
Published: June 2023

Reduced genome bacteria are genetically simplified systems that facilitate biological study and industrial use. The free-living Alphaproteobacterium,Zymomonas mobilis, has a naturally reduced genome containing fewer than 2000 protein coding genes. Despite its small genome, Z. mobilis thrives in diverse conditions including the presence or absence of atmospheric oxygen. However, insufficient characterization of essential and conditionally essential genes has limited broader adoption ofZ. mobilisas a model Alphaproteobacterium. Here, we use genome-scale CRISPRi-seq to systematically identify and characterizeZ. mobilisgenes that are conditionally essential for aerotolerant or anaerobic growth, or are generally essential across both conditions. Comparative genomics revealed that the essentiality of most “generally essential” genes was shared betweenZ. mobilisand other Alphaproteobacteria, validatingZ. mobilisas reduced genome model. Among conditionally essential genes, we found that the DNA repair gene, recJ, was critical only for aerobic growth but reduced the mutation rate under both conditions. Further, we show that genes encoding the F1FOATP synthase and Rnf respiratory complex are required for anaerobic growth ofZ. mobilis. Combining CRISPRi partial knockdowns with metabolomics and membrane potential measurements, we determined that the ATP synthase generates membrane potential that is consumed by Rnf to power downstream processes. Rnf knockdown strains accumulated isoprenoid biosynthesis intermediates, suggesting a key role for Rnf in powering essential biosynthetic reactions. Our work establishesZ. mobilisas a streamlined model for alphaproteobacterial genetics, has broad implications in bacterial energy coupling, and informsZ. mobilisgenome manipulation for optimized production of valuable isoprenoid-based bioproducts.

Importance

The inherent complexity of biological systems is a major barrier to our understanding of cellular physiology. Bacteria with markedly fewer genes than their close relatives, or reduced genome bacteria, are promising biological models with less complexity. Reduced genome bacteria can also have superior properties for industrial use, provided the reduction does not overly restrict strain robustness. Naturally reduced genome bacteria, such as the Alphaproteobacterium,Zymomonas mobilis, have fewer genes but remain environmentally robust. In this study, we show thatZ. mobilisis a simplified genetic model for Alphaproteobacteria, a class with important impacts on the environment, human health, and industry. We also identify genes that are only required in the absence of atmospheric oxygen, uncovering players that maintain and utilize the cellular energy state. Our findings have broad implications for the genetics of Alphaproteobacteria and industrial use ofZ. mobilisto create biofuels and bioproducts.
GDmicro: classifying host disease status with GCN and Deep adaptation network based on the human gut microbiome data
Authors: Liao Herui , Shang Jiayu , Sun Yanni
Published: June 2023

Motivation

With advances in metagenomic sequencing technologies, there are accumulating studies revealing the associations between the human gut microbiome and some human diseases. These associations shed light on using gut microbiome data to distinguish case and control samples of a specific disease, which is also called host disease status classification. Importantly, using learning-based models to distinguish the disease and control samples is expected to identify important biomarkers more accurately than abundance-based statistical analysis. However, available tools have not fully addressed two challenges associated with this task: limited labeled microbiome data and decreased accuracy in cross-studies. The confounding factors such as the diet, technical biases in sample collection/sequencing across different studies/cohorts often jeopardize the generalization of the learning model.

Results

To address these challenges, we develop a new tool GDmicro, which combines semi-supervised learning and domain adaptation to achieve a more generalized model using limited labeled samples. We evaluated GDmicro on human gut microbiome data from 10 cohorts covering 5 different diseases. The results show that GDmicro has better performance and robustness than state-of-the-art tools. In particular, it improves the AUC from 0.783 to 0.949 in identifying inflammatory bowel disease. Furthermore, GDmicro can identify potential biomarkers with greater accuracy than abundance-based statistical analysis methods. It also reveals the contribution of these biomarkers to the host’s disease status.

Availability and implementation

https://github.com/liaoherui/GDmicro

Contact

yannisun@cityu.edu.hk

Supplementary information

Supplementary data are available at XXX online
Building a genetic and epigenetic predictive model of breast cancer intrinsic subtypes using large-scale data and hierarchical structure learning
Authors: Xie Jiemin , Yang Binyu , Li Keyi , Gao Lixin , Liu Xuemei , Xiong Yunhui , Chen Wen , Xia Li C.
Published: June 2023

Breast cancer subtyping is a difficult clinical and scientific challenge. The prevalent Prediction Analysis of Microarray of 50 genes (PAM50) system and its Immunohistochemistry (IHC) surrogate showed significant inconsistencies. This is because of the limited training samples, highly variable molecular features and in-efficient strategies used in these classifiers. The rapid development of early screening technologies, especially in the field of circulating tumor DNA, has also challenged the subtyping of breast cancer at the DNA level. By integrating large-scale DNA-level data and using a hierarchical structure learning algorithm, we developed Unified Genetic and Epigenetic Subtyping (UGES), a new intrinsic subtype classifier. The benchmarks showed that the use of all classes of DNA alterations worked much better than single classes, and that the multi-step hierarchical learning is crucial, which improves the overall AUC score by 0.074 compared to the one-step multi-classification method. Based on these insights, the ultimate UGES was trained as a three-step classifier on 50831 DNA features of 2065 samples, including mutations, copy number aberrations, and methylations. UGES achieved overall AUC score 0.963, and greatly improved the clinical stratification of patients, as each strata’s survival difference became statistically more significant p-value=9.7e-55 (UGES) vs 2.2e-47 (PAM50). Finally, UGES identified 52 subtype-level DNA biomarkers that can be targeted in early screening technology to significantly expand the time window for precision care. The analysis code is freely available athttps://github.com/labxscut/UGES.
Crystal structure of 1-(4-bromophenyl)but-3-yn-1-one
Authors: Siddiqui Shaziyaparveen K. , Ramana C. V. , Gonnade Rajesh G.
Published: June 2023

The title compound, 1-(4-bromophenyl)but-3-yn-1-one, C10H7BrO, crystallizes in the monoclinic space group P21/n with one molecule in the asymmetric unit. The structure displays a planar geometry. The crystal structure is consolidated by C—H...O hydrogen bonding and a short C=O...C[triple-bond]C (acetylene) contacts. Hirshfeld surface analysis indicates that H...H, C...H/H...C and H...Br/Br...H interactions play a more important role in consolidating the crystal structure compared to H...O/O...H and C...C contacts.
What motivates viewers to purchase recommended products in live streaming? The moderating role of extroversion–introversion personality
Authors: Chang Chun-Ming , Yen Chiahui , Chou Szu-Yu , Lo Wen-Wan
Published: June 2023

Purpose

This study aims to investigate the factors driving viewers' purchase intention in live-streaming by incorporating stimuli–organism–response (S–O–R) framework and extroversion–introversion personality perspectives.

Design/methodology/approach

Data collected from 228 users on live-streaming platforms in Taiwan were used to test the proposed model. The partial least squares method was used to test the measurement and the structural models.

Findings

Product attractiveness and trust in streamer significantly impacts purchase intention. The results also reveal that interactivity, breadth of information and uniqueness of information significantly impact product attractiveness, whereas social presence, breadth of information and uniqueness of information positively affect trust in streamer. Furthermore, streamer attractiveness has a greater effect on the purchase intention of extroverts.

Originality/value

This study investigates how the features of media, message and streamer impact purchase intention through their reactions to live-streaming. This research is also one of the earliest studies to examine the moderating role of extroversion–introversion personality on purchase intention and its antecedents in live-streaming commerce.
A transdisciplinary framework for university-industry collaboration in establishing a social business model
Authors: Cheah Jeffrey S. S. , Amran Azlan , Kirubakaran Mahendran , Lang Daniel J. , Su Pek-Fuen , Chu Jenn-Weng
Published: June 2023

Purpose

This study aims to illuminate the limited understanding of viable social business among corporate actors in developing countries. It addresses pressing environmental and societal problems, emphasizing the need for corporate participation in sustainable solutions. Additionally, the study explores the transformational business notion linking company achievement with social progress, an increasingly studied concept in management.

Design/methodology/approach

Based on a transdisciplinary case study (i.e. a university-industry collaboration [UIC]), this study proposed a structural framework and guiding principles to integrate the academic and practitioners’ different but complementary resources and expertise.

Findings

The outcomes could provide insights for social entrepreneurs to perform highly optimal decisions on their organisational strategies, in which the financial-then-social pathway could be an effective social business success mechanism.

Originality/value

Besides, the case study also generates each five learning lessons and challenges coping strategies that provide practical guidance on operationalising an effective UIC. The empirical findings contribute to social entrepreneurship and sustainability science literature.
Exploring barriers and facilitators to knowledge transfer and learning processes through a cross-departmental collaborative project in a municipal organization
Authors: Sunnemark Fredrik , Lundqvist Westin Wilma , Al Saad Tamy , Assmo Per
Published: June 2023

Purpose

This study aims to explore barriers and facilitators for knowledge transfer and learning processes by examining a cross-departmental collaborative project in the municipal organization. It is based on a R&D collaboration between University West and a Swedish municipality.

Design/methodology/approach

To explore the barriers and facilitators, the data collection was made through observation of the project implementation process, as well as 20 interviews with public servants and external actors. To conduct a systematic qualitative-oriented content analysis, the article constructs and applies a theoretical analytical framework consisting of different factors influencing knowledge transfer and learning processes within a municipal organizational setting.

Findings

This study explores the facilitators and barriers to knowledge transfer and learning processes, specifically focusing on strategic communication, individual roles, common goals, time pressure, group learning, trust and relationships and absorptive capability. Lack of communication affected the group learning process, while the close relation between time pressure, group learning and trust in colleagues is also pointed out as crucial areas. Trust developed through dialogue efforts helped overcome project fatigue. Coaching with a human rights-based approach improved organizational absorptive capabilities.

Originality/value

The study gives important insights into organizational learning within a municipality in Sweden for the successful implementation of collaborative projects. Knowledge must be transferred for the organization to learn to develop and tackle future challenges and its complex responsibilities. The theoretical analytical framework provided in this article has proven to be effective and is therefore transferable to other organizations in both the public and private sectors.
Identifying reliable ions for the statistical differentiation of structurally similar fentanyl analogs
Authors: Sacha Andrew M. , Willis Isaac C. , McGuffin Victoria L. , Waddell Smith Ruth
Published: June 2023

Definitive identification of fentanyl analogs based on mass spectral comparison is challenging given the high degree of structural and, hence, spectral similarity. To address this, a statistical method was previously developed in which two electron‐ionization (EI) mass spectra are compared using the unequal variance t‐test. Normalized intensities of corresponding ions are compared, testing the null hypothesis (H0) that the difference in intensity is equal to zero. If H0 is accepted at all m/z values, the two spectra are statistically equivalent at the specified confidence level. If H0 is not accepted at any m/z value, then there is a significant difference in intensity at that m/z value between the two spectra. In this work, the statistical comparison method is applied to distinguish EI spectra of valeryl fentanyl, isovaleryl fentanyl, and pivaloyl fentanyl. Spectra of the three analogs were collected over a 9‐month period and at different concentrations. At the 99.9% confidence level, the spectra of corresponding isomers were statistically associated. Spectra of different isomers were statistically distinct, and ions responsible for discrimination were identified in each comparison. To account for inherent instrument variations, discriminating ions for each pairwise comparison were ranked based on the magnitude of the calculated t‐statistic (tcalc) value. For a given comparison, ions with higher tcalc values are those with the greatest difference in intensity between the two spectra and, therefore, are considered more reliable for discrimination. Using these methods, objective discrimination among the spectra was achieved and ions considered most reliable for discrimination of these isomers were identified.
Slovakia: Political Developments and Data in 2022
Authors: LÁŠTIC ERIK
Published: June 2023

The war in Ukraine and its fallout dominated politics in Slovakia throughout 2022. The coalition split up after the summer, leaving the Cabinet in a fragile position in Parliament. This led to chaotic parliamentary sessions in October and November that ended on 15 December, when the Heger II Cabinet lost a no‐confidence vote initiated by a former coalition party Freedom and Solidarity, SaS. As no new parliamentary majority formed, the Heger II Cabinet continued in office under the supervision of President Z. Čaputová, with parliamentary political parties unable to compromise on early elections.
The effect of the COVID‐19 pandemic on substance use patterns and physiological dysregulation in pregnant and postpartum women
Authors: Ruyak Sharon , Roberts Melissa H. , Chambers Stephanie , Ma Xingya , DiDomenico Jared , De La Garza Richard , Bakhireva Ludmila N.
Published: June 2023

Background

The SARS‐CoV‐2/COVID‐19 pandemic has been associated with increased stress levels and higher alcohol use, including in pregnant and postpartum women. In the general population, alcohol use is associated with dysregulation in the autonomic nervous system (ANS), which is indexed by heart rate variability (HRV). The objectives of this study were to: (1) characterize changes in substance use during the SARS‐CoV‐2/COVID‐19 pandemic via a baseline self‐report survey followed by mobile ecological momentary assessment (mEMA) of substance use; and (2) examine the associations between momentary substance use and ambulatory HRV measures in pregnant and postpartum women.

Methods

Pregnant and postpartum women were identified from the ENRICH‐2 prospective cohort study. Participants were administered a baseline structured phone interview that included the Coronavirus Perinatal Experiences (COPE) survey and ascertained the prevalence of substance use. Over a 14‐day period, momentary substance use was assessed three times daily, and HRV measurements were captured via wearable electronics. Associations between momentary substance use and HRV measures (root mean square of successive differences [RMSSD] and low frequency/high frequency [LF/HF] ratio) were examined using a mixed effects model that included within‐subject (WS) and between‐subject (BS) effects and adjusted for pregnancy status and participant age.

Results

The sample included 49 pregnant and 22 postpartum women. From a combination of a baseline and 14‐day mEMA surveys, 21.2% reported alcohol use, 16.9% reported marijuana use, and 8.5% reported nicotine use. WS effects for momentary alcohol use were associated with the RMSSD (β = −0.14; p = 0.005) and LF/HF ratio (β = 0.14; p = 0.01) when controlling for pregnancy status and maternal age. No significant associations were observed between HRV measures and instances of marijuana or nicotine use.

Conclusions

These findings highlight the negative effect of the SARS‐CoV‐2/COVID‐19 pandemic on the psychological health of pregnant and postpartum women associated with substance use, and in turn, ANS dysregulation, which potentially puts some women at risk of developing a substance use disorder.
Long‐term follow‐up of single‐visit pulp revascularisation for the dens evaginatus and dens invaginatus: Cases report
Authors: Kim Hyeon‐Cheol , Kwak Sang Won , Cheung Gary Shun‐Pan
Published: June 2023

This article documents cases of single‐visit pulp revascularisation for dens evaginatus and dens invaginatus, without using intracranial medicaments or antibiotics, aiming to provide a potentially applicable protocol for pulp revascularisation procedure in a single‐visit. Two patients with chief complaints of pain and swelling visited a dental hospital. Radiographs revealed that the causative teeth had an open apex and periapical radiolucency, and the teeth were diagnosed as pulp necrosis and acute apical abscess or symptomatic apical periodontitis. For both cases, single‐visit revascularisation was completed without intracanal medicaments or antibiotics. The patients were periodically recalled to evaluate periapical healing after treatment. The apical lesion healed, and the root dentin thickening was observed. The single‐visit pulp revascularisation procedure without using specific intracanal medicaments can produce clinically favourable results for these dental anomalies.
‘Fixing’ destitute children: The relational geography of an early twentieth century children's home through its archives
Authors: Cope Meghan
Published: June 2023

Drawing from early twentieth century documents from the Home for Destitute Children in Burlington, Vermont, USA, I explore the notion of the archive as a site of knowledge, politics, and ethics. Despite the absence of children's own perspectives in this archive, I propose taking a geographical relational poverty approach to gain insights by examining power relations between middle‐class adult women and ‘destitute’ children. Specifically, I use records generated by women in charge of the Home (the matrons and the Board of Directors) to identify three dimensions of relational relevance. First, the women exerted power in constructing the Home as a place through ordering temporal rhythms, influencing sensory experiences, and imposing social boundaries and material conditions. Second, I review discourses such as the ‘desirable child’, ‘innocence’, and eugenicist notions of ‘feeblemindedness’ employed by the women to ‘fix’ children, both to repair them and to keep them in place. Third, I provide a reflection on the possibilities of combining manuscript archives with digitized sources such as the census to uncover adults' production and containment of ‘destitute children’.
Environmental influences on ophthalmic conditions: A scoping review
Authors: Heilenbach Noah , Hu Galen , Lamrani Ryan , Prasad Jaideep , Ogunsola Titilola , Iskander Mina , Elgin Cansu Yuksel , McGowan Richard , Vieira Dorice , Al‐Aswad Lama A.
Published: June 2023

Background

Environmental factors have been implicated in various eye pathologies. The purpose of this review is to synthesise the published research on environmental effects on eye disease.

Methods

Four databases were searched for terms relating to environmental exposures and ophthalmic disease. Titles and abstracts were screened followed by full‐text review. Data was extracted from 118 included studies. Quality assessment was conducted for each study.

Results

Air pollutants, including nitrogen dioxide, nitrites, sulphur dioxide, particulate matter, carbon monoxide, ozone and hydrocarbons are associated with ocular conditions ranging from corneal damage to various retinopathies, including central retinal artery occlusion. Certain chemicals and metals, such as cadmium, are associated with increased risk of age‐related macular degeneration. Climate factors, such as sun exposure, have been associated with the development of cataracts. Living in rural areas was associated with various age‐related eye diseases whereas people living in urban settings had higher risk for dry eye disease and uveitis.

Conclusion

Environmental exposures in every domain are associated with various ophthalmic conditions. These findings underscore the importance of continued research on the interplay between the environment and eye health.
Development and validation of a novel nomogram to predict the impact of the polymorphism of the ICAM‐1 gene on the prognosis of ischemic cardiomyopathy
Authors: Naman Tuersunjiang , Abuduhalike Refukaiti , Abudouwayiti Aihaidan , Sun Juan , Mahemuti Ailiman
Published: June 2023

The current study investigated the association between polymorphisms of the ICAM‐1 gene and prognosis of Ischemic cardiomyopathy (ICM), and developed a prognostic nomogram for ICM on the basis of ICAM‐1 gene variants. The current study included totally 252 patients with ICM. In addition, PCR‐RFLP (polymerase chain reaction‐restriction fragment length polymorphism) was used to genotype SNPs in the ICAM‐1 gene in the patients. Later, the nomogram model was built by combining clinical data and ICAM‐1 gene variants. This study used the least absolute shrinkage and selection operator (LASSO) regression model to optimize feature selection into an ICM prognostic model. Furthermore, multivariate Cox‐regression was applied to build the prognostic model, which included clinical and gene features chosen by the LASSO regression model. Following that, the receiver operating characteristic (ROC) curve, C‐index, calibration plot analyses and decision curve analysis (DCA) were carried out to evaluate the discrimination ability, consistency, and clinical utility of the prognostic model, and the bootstrap method was adopted for internal validation. predicting factors rs112872667, treating by PCI or CABG, ventricular arrhythmia, left ventricular end‐diastolic diameter (LVDD), use of β‐blockers, systolic blood pressure (SBP), heart rate (HR), and serum sodium were incorporated into the prognostic nomogram. The constructed nomogram performed well in discrimination ability, as observed by the time‐dependent C‐index. Furthermore, as shown by calibration curves, our nomogram's predicted probabilities were highly consistent with measured values. With threshold probabilities, DCA suggested that our nomogram could be useful in the clinic. mutation of rs112872667 have critical predictive value on the prognosis of ICM, ICM patients with the mutant genotype (CT or TT) have higher survival probability than those with the wild genotype (CC). Mutation of rs112872667 in ICAM‐1 gene have critical predictive value on the prognosis of ICM, ICM patients with the mutant genotype (CT or TT) have higher survival probability than those with the wild genotype (CC).
Influence of obesity on osseointegration of implants with different surface treatments: A preclinical study
Authors: Silva Bruno Luís Graciliano , Sánchez‐Puetate Julio Cesar , Pinotti Felipe Eduardo , Marcantonio Camila Chierici , Pedroso Gabriel Gimenez , Junior Elcio Marcantonio , Marcantonio Rosemary Adriana Chierici
Published: June 2023

Objective

The aim of the present study was to evaluate the effect of obesity on the osseointegration of implants with hydrophobic and hydrophilic surfaces.

Materials and Methods

Sixty‐four male rats were distributed among four experimental groups: H‐HB (Healthy/Hydrophobic): healthy animals with hydrophobic implants; H‐HL (Healthy/Hydrophilic): healthy animals with hydrophilic implants; O‐HB (Obese/Hydrophobic): animals with induced obesity and hydrophobic implants; O‐HL (Obese/Hydrophilic): animals with induced obesity and hydrophilic implants. One hundred and twenty‐eight implants were installed in the tibiae of the animals bilaterally (64 on the left tibiae and 64 on the right one) after 75 days of a specific diet (standard or high‐fat diet) and euthanasia was performed in the experimental periods of 15 and 45 days after implant placement. Bone formation was assessed by biomechanical analysis (on the left tibiae of each animal), and microtomographic and histomorphometric analyses (on the right tibiae of each animal). Statistical analysis was performed using the Shapiro–Wilk test for normality and ANOVA followed by Tukey test to observe whether there was a significant difference between groups (p < 0.05); the t‐test was used to compare the animals' body weight.

Results

The biomechanical analysis showed an increase in the removal torque value of animals after 45 days in comparison to after 15 days, with the exception of O‐HB groups. The microtomographic analysis demonstrated no significant differences in the mineralized bone tissue volume between the groups. In the histomorphometric analysis, the H‐HL/45 day group/period demonstrated higher bone‐implant contact, in comparison to H‐HL/15 days and the O‐HL/45 day group/period showed an increase in bone area between the implant threads, in comparison to O‐HL/15 days.

Conclusion

In conclusion, obesity does not interfere with the osseointegration of hydrophobic and hydrophilic implants.
Neurotensin and energy balance
Authors: Gereau Graydon B. , Garrison Sy’Keria D. , McElligott Zoe A.
Published: June 2023

The neurotensin system spans across the central nervous system, to the enteric nervous system (gut), and the periphery to govern behaviors and physiological responses that tune energy balance to maintain homeostasis. Neurotensin transmission is not only modulated by metabolic signals, neurotensin transmission itself can also impact metabolic state by exerting control over consumption, physical activity, and satiety signals. Many responses to sensory experiences and sleep processes are dictated by neurotensinergic activity via mechanisms that allow the organism to balance energy seeking and utilization to thrive in its environment. Given the broad reach neurotensin signaling has across the homeostatic landscape, understanding this system as a whole and examining new ways to target this system for therapeutic efficacy across many different conditions is necessary.

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Maternal cortisol levels in third trimester and early language development: A study of 1093 mother–child pairs from the Odense Child Cohort
Authors: Mumm Hanne , Dreyer Anja Fenger , Bleses Dorthe , Glintborg Dorte , Jensen Tina Kold , Boye Henriette , Trecca Fabio , Andersen Marianne Skovsager
Published: June 2023

Language development during early childhood is considered an important marker of fetal neurodevelopment. Prenatal cortisol exposure plays a critical role in maturation of the fetal brain; however, the effect on offspring language development needs further investigation. In this prospective observational study we aimed to evaluate the association between maternal third trimester cortisol and early longitudinal offspring language development in the Odense Child Cohort (OCC) and to test whether there were sex differences in the association. The study cohort included 1093 mother–child dyads (570 boys and 523 girls). Fasting morning serum (s‐) cortisol was collected from third trimester (gestational week 26–28) pregnant women and measured by liquid chromatography–tandem mass spectrometry. Offspring receptive and productive vocabulary assessments by MacArthur‐Bates Communicative Development Inventories parent reports were completed every third month from children age 12–37 months. Levels of cortisol were higher in women carrying a girl (858 ± 214 nmol/L) than in women carrying a boy (820 ± 222 nmol/L). Higher third trimester maternal cortisol levels showed a positive association with development of productive vocabulary in boys at age 12–21 months (OR = 1.23, SE = 0.07, p = .005) and age 22–37 months (OR = 1.09, SE = 0.06, p = .967). Higher maternal cortisol levels in the third trimester were positively associated with receptive vocabulary in girls at 12–21 months of age (OR = 1.16, SE = 0.05, p = .002). Maternal third trimester s‐cortisol levels were positively associated with early language development in children at age 12–37 months.
Comparison between ultrasound and magnetic resonance imaging of the temporomandibular joint in juvenile idiopathic arthritis: A systematic review
Authors: Rotolo Rossana Patricia , d'Apuzzo Fabrizia , Femiano Felice , Nucci Ludovica , Minervini Giuseppe , Grassia Vincenzo
Published: June 2023

Objectives

The objectives of this systematic review were to evaluate the correlation between Ultrasound (US) and Magnetic Resonance Imaging (MRI) in patients with JIA and to investigate the association with Temporomandibular Disorders (TMD).

Materials and Methods

The protocol was registered in PROSPERO (CRD42022312734). Databases Medline, Embase, Cochrane Central Register of Controlled Trials, Scopus, Web of Science, Latin American and Caribbean Health Sciences Literature were searched. Eligibility criteria were patients with JIA subjected to diagnostic evaluation using US and MRI. No language restrictions were applied. After duplicate study selection, data extraction and risk of bias assessment according to Cochrane were conducted. Data extraction of patients was conducted by two independent authors.

Results

Five observational studies were included with 217 participants (153 females and 64 males; mean age 11.3 years). The quality of the studies was overall satisfactory. The correlation between US and MRI in children with JIA was ‘moderate’ in acute arthritis while the chronic arthritis correlated positively in two studies.

Conclusions

Even if MRI remains the more accurate imaging modality for the detection of TMJ of patients with JIA, US may be useful to early detect pathological conditions and to address the patient with JIA and putative TMJ involvement to a more accurate diagnosis with MRI and consequent appropriate treatment management.

Clinical Relevance

MRI should be deemed necessary only secondary to less‐invasive assessments with US just to confirm the diagnosis or to increase sensitivity, accuracy of positive predictive values detected.
Exogenous application of a Burkholderia sp. and jasmonic acid at the postharvest stage for management of anthracnose in dessert banana (Musa acuminata)
Authors: Kumara U. M. Aruna , Costa Devika M. De
Published: June 2023

The present study was conducted to determine the potential of controlling natural (latent) and wound infections of anthracnose using a biological control agent (Burkholderia sp. [BS]) and jasmonic acid (JA). Exogenous application of BS (1 × 108 cfu/mL) and JA (0.2 mM) reduced both types of anthracnose in banana cultivars Kolikuttu and Seenikesel within a range of 67.6%–100%. Due to BS and JA treatments, three selected defence genes (β‐1,3‐glucanase, PR‐1 and chitinase) were up‐regulated in the fruit peels of the two banana cultivars over a period of 144 h after treatment (HAT), indicating the ability to induce host plant resistance by the two treatments. BS treatment resulted in a 1.5‐ to 2.5‐fold increase of the above gene transcripts under natural infection in both cultivars. The findings revealed that induction of the three selected defence genes varies depending on the type of the treatment and infection. JA‐treated fruits with natural infections showed a 1‐day delay of ripening and resulted in the lowest ripening indices till 6th day after treatment in comparison to the BS‐ and untreated banana. BS and JA concentrations used in the study, significantly reduced mycelial growth and spore production of C. musae. Lowering of the ripening index, reduction of mycelial growth and spore production of the fungal pathogen and increased expression of the three selected defence genes by BS and JA treatments reduced the disease progression and lesion development of anthracnose in the two banana cultivars under natural and wound infections of C. musae.
Exploring factors associated with parent‐reported early childhood caries with Alaska's childhood understanding behaviors survey data
Authors: Grage Laura , Wise Frances , Meyer Jennifer
Published: June 2023

Objectives

Early Childhood Caries (ECC) can negatively impact the lives of young children, despite being preventable. The purpose of this study was to utilize available data in Alaska to describe changes in parent reports of ECC, and identify factors related to ECC.

Methods

The Childhood Understanding Behaviors Survey (CUBS) is a population‐based survey of parents of 3‐year‐old children and was utilized to describe changes in: parent‐reported ECC among children with a dental visit, access to and or utilization of dental care, and consumption of three or more cups of sweetened beverages between 2009–2011 and 2016–2019. Logistic regression modeling was used to explore factors associated with parent‐reported ECC among children with a dental visit.

Results

Over time, a significantly smaller proportions of parents whose 3‐year‐old child had seen a dental professional reported ECC. Additionally, a smaller proportion of parents reported three or more cups of sweetened beverage consumption by their child, while larger proportions had seen a dental professional by age 3. Factors associated with parent‐reported ECC included consumption of three or more cups of sweetened beverages, and enrollment in Medicaid or Tribal health care insurance, while protective factors included a parent earning a college degree, and military insurance.

Conclusions

Although at the statewide level, improvements were observed in parent‐reported measures over time, regional disparities were apparent. Social and economic factors as well as excessive consumption of sweetened beverages appear to play important roles in ECC. CUBS data can help identify trends in ECC within Alaska.
Sex chromosome heteromorphism and the Fast‐X effect in poeciliids
Authors: Darolti Iulia , Fong Lydia J. M. , Sandkam Benjamin A. , Metzger David C. H. , Mank Judith E.
Published: June 2023

Fast‐X evolution has been observed in a range of heteromorphic sex chromosomes. However, it remains unclear how early in the process of sex chromosome differentiation the Fast‐X effect becomes detectible. Recently, we uncovered an extreme variation in sex chromosome heteromorphism across poeciliid fish species. The common guppy, Poecilia reticulata, Endler's guppy, P. wingei, swamp guppy, P. picta and para guppy, P. parae, appear to share the same XY system and exhibit a remarkable range of heteromorphism. Species outside this group lack this sex chromosome system. We combined analyses of sequence divergence and polymorphism data across poeciliids to investigate X chromosome evolution as a function of hemizygosity and reveal the causes for Fast‐X effects. Consistent with the extent of Y degeneration in each species, we detect higher rates of divergence on the X relative to autosomes, a signal of Fast‐X evolution, in P. picta and P. parae, species with high levels of X hemizygosity in males. In P. reticulata, which exhibits largely homomorphic sex chromosomes and little evidence of hemizygosity, we observe no change in the rate of evolution of X‐linked relative to autosomal genes. In P. wingei, the species with intermediate sex chromosome differentiation, we see an increase in the rate of nonsynonymous substitutions on the older stratum of divergence only. We also use our comparative approach to test for the time of origin of the sex chromosomes in this clade. Taken together, our study reveals an important role of hemizygosity in Fast‐X evolution.
Scaffold protein RACK1 regulates BR signaling by modulating the nuclear localization of BZR1
Authors: Li Zhiyong , Fu Yajuan , Wang Yuzhu , Liang Jiansheng
Published: June 2023

Brassinosteroids (BRs) are a group of plant‐specific steroid hormones, which induces the rapid nuclear localization of the positive transcriptional factors BRASSINAZOLE RESISTANT1/2 (BZR1/2). However, the mechanisms underlying the regulation of nucleocytoplasmic shuttling of BZR1 remain to be fully elucidated.

In this study, we show that the scaffold protein Receptor for Activated C Kinase 1 (RACK1) from Arabidopsis is involved in BR signaling cascades through mediating the nuclear localization of BZR1, which is tightly retained in the cytosol by the conserved scaffold protein 14‐3‐3s.

RACK1 can interact with BZR1 and competitively decrease the 14‐3‐3 interaction with BZR1 in cytosol, which efficiently enhances the nuclear localization of BZR1. 14‐3‐3 also retains RACK1 in cytosol through their interaction. Conversely, BR treatment enhances the nuclear localization of BZR1 by disrupting the 14‐3‐3 interaction with RACK1 and BZR1.

Our study uncovers a new mechanism that integrates two kinds of conserved scaffold proteins (RACK1 and 14‐3‐3) coordinating BR signaling event.