bluuebunny/crossref_metadata_2025 huggingface dataset:
Machine learning approaches based on fibroblast morphometry confidently identify stress but have limited ability to predict ALS
Authors: Konrad Csaba , Woo Evan , Bredvik Kirsten , Liu Bangyan , Fuchs Thomas J. , Manfredi Giovanni
Published: October 2022

Objective

Amyotrophic lateral sclerosis (ALS) is a devastating neuromuscular disease with limited therapeutic options. Diagnostic and surrogate endpoint biomarkers are needed for early disease detection, clinical trial design, and personalized medicine.

Methods

We tested the predictive power of a large set of primary skin fibroblast (n=443) from sporadic and familial ALS patients and healthy controls. We measured morphometric features of endoplasmic reticulum, mitochondria, and lysosomes by imaging with vital dyes. We also analysed immunofluorescence images of ALS-linked proteins, including TDP-43 and stress granule components. We studied fibroblasts under basal conditions and under metabolic (galactose medium), oxidative (arsenite), and heat stress conditions. We then employed machine learning (ML) techniques on the dataset to develop biomarkers.

Results

Stress perturbations caused robust changes in the measured features, such as organellar morphology, stress granule formation, and TDP-43 mislocalization. ML approaches were able to predict the perturbation with near perfect performance (ROC-AUC > 0.99). However, when trying to predict disease state or disease groups (e.g., sporadic, or familial ALS), the performance of the ML algorithm was more modest (ROC-AUC Control vs ALS = 0.63). We also detected modest but significant scores when predicting clinical features, such as age of onset (ROC-AUC late vs early = 0.60).

Conclusions

Our findings indicate that the ML morphometry we developed can accurately predict if human fibroblasts are under stress, but the differences between ALS and controls, while statistically significant, are small and pose a challenge for the development of biomarkers for clinical use by these approaches.
SUsPECT: A pipeline for variant effect prediction based on custom long-read transcriptomes for improved clinical variant annotation
Authors: Salz Renee , Saraiva-Agostinho Nuno , Vorsteveld Emil , van der Made Caspar I. , Kersten Simone , Stemerdink Merel , Allen Jamie , Volders Pieter-Jan , Hunt Sarah E. , Hoischen Alexander , ’t Hoen Peter A.C.
Published: October 2022

Our incomplete knowledge of the human transcriptome impairs the detection of disease-causing variants, in particular in transcripts only expressed under certain conditions. These transcripts are often lacking from reference transcript sets, such as Ensembl/GENCODE and RefSeq, and could be relevant for establishing genetic diagnoses. We present SUsPECT (Solving Unsolved Patient Exomes/gEnomes using Custom Transcriptomes), a pipeline based on the Ensembl Variant Effect Predictor (VEP) to predict variant impact on custom transcript sets, such as those generated by long-read RNA-sequencing, for downstream prioritization. Our pipeline predicts the functional consequence and likely deleteriousness scores for missense variants in the context of novel open reading frames predicted from any transcriptome. We demonstrate the utility of SUsPECT by uncovering potential mutational mechanisms of pathogenic variants in ClinVar that are predicted to be benign using the reference transcript annotation. In further support of SUsPECT’s utility, we identified an enrichment of immune-related variants predicted to have a more severe molecular consequence when annotating with a newly generated transcriptome from stimulated immune cells instead of the reference transcriptome. Our pipeline outputs crucial information for further prioritization of potentially disease-causing variants for any disease and will become increasingly useful as more long-read RNA sequencing datasets become available.
RANKL inhibition with denosumab improves fibrous dysplasia by decreasing lesional cell proliferation and increasing osteogenesis
Authors: de Castro Luis F , Whitlock Jarred M , Michel Zachary , Pan Kristen , Taylor Jocelyn , Szymczuk Vivian , Paravastu Sriram S , Saboury Babak , Papadakis Georgios Z , Chernomordik Leonid V , Li Xiaobai , Milligan Kelly , Boyce Brendan , Paul Scott , Martin Daniel , Collins Michael T , Boyce Alison M
Published: October 2022

BACKGROUND

Fibrous dysplasia (FD) is a rare, disabling disease with no established treatments. Growing evidence supports inhibiting the pro-osteoclastic factor receptor activator of nuclear Kappa-B ligand (RANKL) as a potential treatment strategy. We conducted a phase 2 trial evaluating the anti-RANKL drug denosumab in adults with FD, with an emphasis on investigating post-discontinuation bone turnover rebound, and cellular mechanisms underlying anti-RANKL effects on FD osteoprogenitors.

METHODS

Eight subjects received denosumab for 6-months and were observed for 8-months post-discontinuation. Efficacy and safety were evaluated using bone turnover markers,18F-NaF PET/CT, and lesion biopsies. RANKL neutralization effects were assessed by histology, RNASeq, and an FD mouse model. Interplay between osteoclasts and FD osteoprogenitors was assessed in anex vivolesion model.

RESULTS

Denosumab markedly reduced bone turnover and radiographic lesional activity in all subjects. Denosumab was well-tolerated during the treatment period, however post-discontinuation turnover reached or exceeded pre-treatment in six subjects, associated with severe hypercalcemia in one. Histology and whole-exome RNA sequencing showed reduced FD cell proliferation and increased osteogenic maturation, with increased lesional bone formation. Theex vivomodel supported the dependence of FD cell proliferation on osteoclast activation.

CONCLUSIONS

Osteoclast inhibition by anti-RANKL decreased FD cell proliferation and lesional activity, enabling osteogenic maturation and bone formation. These findings provide new understanding of FD pathogenesis as driven by crosstalk between osteoclasts and pre-osteoblast/osteoblasts, and support denosumab as a mechanistically-driven treatment strategy. Marked bone turnover rebound with post-discontinuation hypercalcemia occurs in a subset of patients, particularly younger individuals with high disease burden.

TRIAL REGISTRATION

ClinicalTrials.govNCT03571191

FUNDING

This work was supported by the Intramural Research Program of the NIDCR, NICHD, and Clinical Center, National Institutes of Health. Clinical trialNCT03571191was conducted as an investigator-sponsored study supported by Amgen, Inc. This research was supported in part by the NIDCR Genomics and Computational Biology Core: ZIC DC000086 and Veterinary Resources Core: ZIC DE000740-05. Work in MTC lab and LVC labs were supported by the of Research on Women’s Health (ORWH) through the Bench to Bedside Program award #884515.
Association between wasting and feeding practices consumption during 24 hours recall in young children aged 6-23 months in Cambodia: Analysis of Cambodia Demographic and Health Survey 2014
Authors: Um Samnang , Luon Mom , An Yom , Tol Bunkea
Published: October 2022

INTRODUCTION

World Health Organization (WHO), defines wasting as a child’s weight-for-height z-score (WHZ) below minus 2 SD of the Child’s Growth Standards. In Cambodia, the prevalence of wasting among children under five years old increased from 8% in 2005 to 10% in 2014. The WHO divided food into seven categories, including staple foods, legumes, milk, meat, eggs, fruits, and vegetables. It was advised to consume at least four of these categories daily. According to data from the 2014 Cambodia Demographic and Health Survey (CDHS), 48% of kids between the ages of six and 23 months consumed at least four food groups. We aimed to identify the association between feeding practices consumption and wasting in Cambodian children aged 6-23 months.

METHODS

We used existing children’s data from CDHS 2014, two-stage stratified cluster sampling approach to select samples. Data analysis was done by using STATA V16 Survey weights were applied to account for the complex survey design of the CDHS. Descriptive statistics were estimated for key children characteristics, maternal, and household characteristics, geographical regions, and feeding practice consumption. We ran bivariate and multiple logistic regressions to assess the association between wasting and feeding practices consumption in children aged 6-23 months.

RESULTS

A total of 1,415 children aged 6–23 months were eligible for the study. This study did not find an association between wasting and feeding practices consumption. In contrast, children aged 9–11 months had 2.3 times of wasting [AOR = 2.3; 95% CI = 1.0–5.0] compared to children aged 6–8 months. When compared to mothers aged 15–19 years, children born from mothers aged 20–34 years and 35–49 years were protected from 60% of wasting [AOR = 0.3; 95% CI = 0.2–0.6] and [AOR = 0.3; 95% CI = 0.1–0.7], respectively. When compared to children from better-off households, children from the poorest and poorer wealthiest households wasted twice as much time [AOR = 1.9; 95% CI 1.1-3.5].

CONCLUSION

These findings indicate that feeding practices consumption is not significantly associated with wasting in young children aged 6–23 months in Cambodia. It was found in other studies. Children aged 9–11 months and children from the poorest households were the main predictors of child mortality. However, mothers aged 20–49 years old had decreased odds of wasting. Therefore, it is recommended that interventions and policymakers prioritize promoting diverse food consumption among children in Cambodia. Furthermore, interventions to reduce wasting among children aged 6 to 11 months, children from the lowest household quintile, and children of young mothers should be prioritized.
Tuft cells mediate commensal remodeling of the small intestinal antimicrobial landscape
Authors: Fung Connie , Fraser Lisa M. , Barrón Gabriel M. , Gologorsky Matthew B. , Atkinson Samantha N. , Gerrick Elias R. , Hayward Michael , Ziegelbauer Jennifer , Li Jessica A. , Nico Katherine F. , Tyner Miles D.W. , DeSchepper Leila B. , Pan Amy , Salzman Nita H. , Howitt Michael R.
Published: October 2022

Succinate produced by the commensal protistTritrichomonas musculis(T. mu) stimulates chemosensory tuft cells, resulting in intestinal type 2 immunity. Tuft cells express the succinate receptor SUCNR1, yet this receptor does not mediate anti-helminth immunity nor alter protist colonization. Here, we report that microbial-derived succinate increases Paneth cell numbers and profoundly alters the antimicrobial peptide (AMP) landscape in the small intestine. Succinate was sufficient to drive this epithelial remodeling, but not in mice lacking tuft cell chemosensory components required to detect this metabolite. Tuft cells respond to succinate by stimulating type 2 immunity, leading to interleukin-13-mediated epithelial and AMP expression changes. Moreover, type 2 immunity decreases the total number of mucosa-associated bacteria and alters the small intestinal microbiota composition. These findings demonstrate that a single metabolite produced by commensals, likeT. mu, can markedly shift the intestinal AMP profile and suggest that tuft cells utilize SUCNR1 to modulate bacterial homeostasis.
Nature over Nurture: Functional neuronal circuits emerge in the absence of developmental activity
Authors: Barabási Dániel L. , Schuhknecht Gregor F. P. , Engert Florian
Published: October 2022

During development, the complex neuronal circuitry of the brain arises from limited information contained in the genome. After the genetic code instructs the birth of neurons, the emergence of brain regions, and the formation of axon tracts, it is believed that neuronal activity plays a critical role in shaping circuits for behavior. Current AI technologies are modeled after the same principle: connections in an initial weight matrix are pruned and strengthened by activity-dependent signals until the network can sufficiently generalize a set of inputs into outputs. Here, we challenge these learning-dominated assumptions by quantifying the contribution of neuronal activity to the development of visually guided swimming behavior in larval zebrafish. Intriguingly, dark-rearing zebrafish revealed that visual experience has no effect on the emergence of the optomotor response (OMR). We then raised animals under conditions where neuronal activity was pharmacologically silenced from organogenesis onward using the sodium-channel blocker tricaine. Strikingly, after washout of the anesthetic, animals performed swim bouts and responded to visual stimuli with 75% accuracy in the OMR paradigm. After shorter periods of silenced activity OMR performance stayed above 90% accuracy, calling into question the importance and impact of classical critical periods for visual development. Detailed quantification of the emergence of functional circuit properties by brain-wide imaging experiments confirmed that neuronal circuits came ‘online’ fully tuned and without the requirement for activity-dependent plasticity. Thus, we find that complex sensory guided behaviors can be wired up by activity-independent developmental mechanisms.
Auxin-independent effects of apical dominance induce temporal changes in phytohormones
Authors: Cao Da , Barbier Francois , Dun Elizabeth A. , Fichtner Franziska , Dong Lili , Kerr Stephanie C. , Beveridge Christine A.
Published: October 2022

The inhibition of shoot branching by the growing shoot tip of plants, termed apical dominance, was originally thought to be mediated by auxin. Recently the importance of the shoot tip sink strength during apical dominance has re-emerged with recent studies highlighting roles for sugars in promoting branching. This raises many unanswered questions on the relative roles of auxin and sugars in apical dominance. Here we show that auxin regulation of cytokinins, which promote branching, is significant only after an initial stage of branching we call bud release. During this early bud release stage, rapid cytokinin increases are associated with enhanced sugars. Auxin may also act through strigolactones which have been shown to suppress branching after decapitation, but here we show that strigolactones do not have a significant effect on initial bud outgrowth after decapitation. We report here that when sucrose or cytokinin is abundant, strigolactones are less inhibitory during the bud release stage compared to later stages and that strigolactone treatment rapidly inhibits cytokinin accumulation in pea axillary buds of intact plants. After initial bud release, we find an important role of gibberellin in promoting sustained bud growth downstream of auxin. We are therefore able to suggest a model of apical dominance that integrates auxin, sucrose, strigolactones, cytokinins and gibberellins and describes differences in signalling across stages of bud release to sustained growth.
Recognition of Galactose by a Scaffold Protein Recruits a Transcriptional Activator for theGALRegulon Induction inCandida albicans
Authors: Sun Xun , Yu Jing , Zhu Cheng , Sun Qiangqiang , Yang Dandan , Su Chang , Lu Yang
Published: October 2022

TheGALpathway of yeasts has long served as a model system for understanding of how regulatory mode of eukaryotic metabolic pathways evolves. While Gal4 mode has been well-characterized in Saccharomycetaceae clade, little is known about the regulation of theGALpathway in other yeasts. Here, we find that Rep1, a Ndt80-like family transcription factor, serves as a galactose sensor in the commensal-pathogenic fungusCandida albicans. It is presented at theGALgene promoters independent of the presence of galactose. Rep1 recognizes galactose via a direct physical interaction. The net result of this interaction is the recruitment of a transcriptional activator Cga1 (Candida galactose gene activator, orf19.4959) and transcription of theGALgenes proceeds. Rep1 and Cga1 are conserved across the CTG species. Rep1 itself does not possess transcriptional activity. Instead, it provides a scaffold to recruit different factors for transcriptional regulation. Rep1-Cga1 mode of regulation represents a new example of network rewiring in fungi, which provides insight into howC. albicansevolves transcriptional programs to colonize diverse host niches.
Social memory in female mice is rapidly modulated by 17β-estradiol through ERK and Akt modulation of synapse formation
Authors: Sheppard Paul A. S. , Chandramohan Deepthi , Lumsden Alanna , Vellone Daniella , Denley Matthew C. S. , Srivastava Deepak P. , Choleris Elena
Published: October 2022

Background

Social memory is essential to the functioning of a social animal within a group. Estrogens can affect social memory too quickly for classical genomic mechanisms. Previously, 17β-estradiol (E2) rapidly facilitated short-term social memory and increased nascent synapse formation, these synapses being potentiated following neuronal activity. However, what mechanisms underlie and co-ordinate the rapid facilitation of social memory and synaptogenesis are unclear. Here, the necessity of extracellular signal-regulated kinase (ERK) and phosphoinositide 3-kinase (PI3K) signaling for rapid facilitation of short-term social memory and synaptogenesis was tested.

Methods

Mice performed a short-term social memory task or were used as task-naïve controls. ERK and PI3K pathway inhibitors were infused intra-dorsal hippocampally 5 minutes before E2 infusion. Forty minutes following intrahippocampal E2 or vehicle administration, tissues were collected for quantification of glutamatergic synapse number in the CA1.

Results

Dorsal hippocampal E2 rapid facilitation of short-term social memory depended upon ERK and PI3K pathways. E2 increased glutamatergic synapse number (GluA1/bassoon colocalization) in task-performing mice but decreased synapse number in task-naïve mice. Critically, ERK signaling was required for synapse formation/elimination in task-performing and task-naïve mice, whereas PI3K inhibition blocked synapse formation only in task-performing mice.

Conclusions

Whilst ERK and PI3K are both required for E2 facilitation of short-term social memory and synapse formation, only ERK is required for synapse elimination. This demonstrates previously unknown, bidirectional, rapid actions of E2 on brain and behaviour and underscores the importance of estrogen signaling in the brain to social behaviour.
Semaphorin 4D induced inhibitory synaptogenesis restores benzodiazepine sensitivity in a mouse model of Status Epilepticus
Authors: Adel Susannah S. , Evans-Strong Aidan , Clarke Vernon R.J. , Maguire Jamie , Paradis Suzanne
Published: October 2022

Previously we demonstrated that intra-hippocampal infusion of purified, Semaphorin 4D (Sema4D) extracellular domain into the mouse hippocampus rapidly promotes formation of GABAergic synapses and decreases seizure susceptibility in mice. Given the relatively fast action of Sema4D treatment revealed by these studies, we sought to determine the time course of Sema4D treatment on hippocampal network activity using an acute hippocampal slice preparation. We performed long-term extracellular recordings from area CA1 encompassing a 2 hour application of Sema4D and found that hippocampal excitation is suppressed hours following treatment. We also asked if Sema4D treatment could ameliorate seizures in an acute seizure model: the kainic acid (KA) mouse model of Status Epilepticus (SE). We demonstrate that Sema4D treatment suppresses seizures and lessens benzodiazepine (BZD) insensitivity which is a hallmark of refractory SE. Lastly, we sought to explore alternative methods of Sema4D delivery to hippocampus and thus created an Adeno Associated Virus expressing the extracellular domain of Sema4D. Our data reveal that virally delivered, chronically overexpressed Sema4D extracellular domain promotes GABAergic synapse formation and suppresses seizure activity similar to the actions of purified Sema4D protein. These results provide proof of concept that Sema4D-mediated GABAergic synapse development could combat BZD insensitivity in intractable forms of epilepsy, and that viral delivery of Sema4D is an efficacious and promising delivery method.
Cell types in the mouse amygdala and their transcriptional response to fear conditioning
Authors: Hochgerner Hannah , Tibi Muhammad , Netser Shai , Ophir Osnat , Reinhardt Nuphar , Singh Shelly , Lin Zhige , Wagner Shlomo , Zeisel Amit
Published: October 2022

The amygdala is one of the most widely studied regions in behavioral neuroscience. A plethora of classical, and new paradigms have dissected its precise involvement in emotional and social sensing, learning, and memory. Several important insights resulted from the use of genetic markers – yet, in the age of single cell transcriptomics, the amygdala remains molecularly underdescribed. Here, we present a molecular cell type taxonomy of the full mouse amygdala in fear learning and consolidation. We performed single-cell RNA-seq on naïve and fear conditioned mice, inferred the 130 neuronal cell types distributions in silico using orthogonal spatial transcriptomic datasets, and describe the cell types’ transcriptional responses to learning and memory consolidation. Only a fraction of cells, within a subset of all neuronal types, were transcriptionally responsive to fear learning, memory and retrieval. These activated engram cells upregulated activity-response genes, and processes of synaptic signaling, plasticity, development and neurite outgrowth. Our transcriptome-wide data confirm known actors, and describe several new candidate genes. The atlas may help pinpoint the amygdala’s circuits in performing emotional sensing and integration, and provide new insights to the global cellular processes involved.
Sex-biasing influence of autism-associatedUbe3agene overdosage at connectomic, behavioral and transcriptomic levels
Authors: Montani Caterina , Pagani Marco , De Guzman Elizabeth , Balasco Luigi , Alvino Filomena Grazia , de Felice Alessia , Galbusera Alberto , Nickl-Jockschat Thomas K. , Lau Pierre , Borsotti Noemi , Mattioni Lorenzo , Pasqualetti Massimo , Provenzano Giovanni , Bozzi Yuri , Lombardo Michael V. , Gozzi Alessandro
Published: October 2022

Many neurodevelopmental conditions, including autism, affect males more than females. Genomic mechanisms enhancing risk in males may contribute to this sex-bias. The ubiquitin protein ligase E3A gene (Ube3a) exerts pleiotropic effects on cellular homeostasis via control of protein turnover and by acting as transcriptional coactivator with steroid hormone receptors. Overdosage ofUbe3avia duplication or triplication of chromosomal region 15q11-13 causes 1-2% of autistic cases. Here, we test the hypothesis that increased dosage ofUbe3amay influence autism-relevant phenotypes in a sex-biased manner. We report robust sex-biasing effects on brain connectomics and repetitive behaviors in mice with extra copies of Ube3a. These effects were associated with a profound transcriptional dysregulation of several known autism-associated genes (e.g., FMR1, SCN2A, PTEN, MEF2C, SHANK3, TSC2) as well as differentially-expressed genes identified in human 15q duplication and in autistic patients. Notably, increased Ube3a dosage also affects multiple sex-relevant mechanisms, including genes on the X chromosome, genes influenced by sex steroid hormones, downstream targets of the androgen and estrogen receptors, or genes that are sex-differentially regulated by transcription factors. These results suggest thatUbe3aoverdosage can critically contribute to sex-bias in neurodevelopmental conditions via influence on sex-differential mechanisms.
The study of impact factors on timber trade between Ghana and China
Authors: Kombat Gordon Pasiba , Chen Xiaoqian
Published: October 2022

Purpose

Timber export is an important economic development pillar in Ghana, which has a direct effect on Ghana’s domestic forestry industry development, local communities’ income and sustainable forest management and deforestation. China, as the Ghana’s largest timber export destination, brought significant impacts on Ghana’s timber export. However, there is a lack of quantitative analyses on impact factors of timber trade between the two countries in the past, which this paper sought to do.

Design/methodology/approach

The authors first collected Ghana’s timber exports to China from 1997 to 2017, and then based on the literature review and trade theories, the authors set up a least squares estimate (LSE)-based multiple linear regression (MLR) model to analyse the specific impact factors. In addition, multi-collinearity, autocorrelation and heteroscedasticity issues of the impact factors were checked to guarantee the accuracy of the results.

Findings

The results showed China timber import volume, Ghana cedi (GHC)/US$ exchange rate, Ghana’s gross domestic product (GDP) and China timber consumption volume in construction sector had positive impacts; Ghana timber production volume and Ghana average timber export price had negative impacts. The results confirmed that China’s timber consumption had a positive linkage with Ghana’s timber export. The article also reviewed possible impacts caused by change in timber trade policies, which proved important but was hardly directly quantified. The authors pointed out the importance of optimizing these impact factors to make sure Ghana’s timber export to China went on the sustainable track.

Originality/value

There is no literature about timber trade and its impact factors between Ghana and China, which used econometric models. This paper provided new perspectives on the impact factors in timber trade between the two countries.
Evaluation of safe-to-fail flood solution alternatives and integration of safe-to-fail concept in AEC education to develop resilient coastal cities
Authors: Rahat Rubaya , Pradhananga Piyush , ElZomor Mohamed
Published: October 2022

Purpose

Safe-to-fail (SF) is an emerging resilient design approach that has the potential to minimize the severity of flood damages. The purpose of this study is to explore the SF design strategies to reduce flood disaster damages in US coastal cities. Therefore, this study addresses two research questions: identifying the most suitable SF criteria and flood solution alternatives for coastal cities from industry professionals’ perspective; and investigating the controlling factors that influence the AEC students’ interest to learn about SF concepts through the curricula.

Design/methodology/approach

This study used the analytical hierarchy process to evaluate the SF criteria and flood solutions where data were collected through surveying 29 Department of Transportation professionals from different states. In addition, the study adopted a quantitative methodology by surveying 55 versed participants who reside in a coastal area and have coastal flood experiences. The data analysis included ordinal probit regression and descriptive analysis.

Findings

The results suggest that robustness is the highest weighted criterion for implementing SF design in coastal cities. The results demonstrated that ecosystem restoration is the highest-ranked SF flood solution followed by green infrastructure. Moreover, the results highlighted that age, duration spent in the program and prior knowledge of SF are significantly related to AEC students’ interest to learn this concept.

Originality/value

SF design anticipates failures while designing infrastructures thus minimizing failure consequences due to flood disasters. The findings can facilitate the implementation of the SF design concept during the construction of new infrastructures in coastal cities as well as educate the future workforces to contribute to developing resilient built environments.
Developing positive self-leadership through “Inner Engineering”
Authors: Chang Tracy F. H. , Baelen Rebecca N. , Ramburn Triya Tessa , Purandare Pradeep
Published: October 2022

Purpose

The study evaluated the effect of a comprehensive yogic methodology called “Inner Engineering Online” (IEO) on developing positive self-leadership. The authors hypothesized that IEO would equip participants with knowledge and skills to optimize their functioning in major experiential dimensions of the self (body, mind, emotion, and energy) and produce a synergistic effect in enhancing well-being and positive organizational behavior for employees, leaders, and entrepreneurs.

Design/methodology/approach

The study uses a field quasi-experimental one group design with pre- and post-tests. The sample consists of 97 employees, 84 leaders and 76 entrepreneurs in various industries (N = 264).

Findings

The pairwise t-test results show that IEO has a positive effect on well-being (mindfulness, joy, vitality, and restfulness) and positive organizational behavior (meaningful work, psychological capital, and work engagement).

Research limitations/implications

The study is limited by the lack of a control group. Future research may use a randomized control design to confirm the present findings and explore the mechanisms through which IEO exercises its effect and other positive outcomes.

Practical implications

IEO complements the behavioral and cognitive strategies of self-leadership by including emotional and energetic strategies to produce a synergistic effect on positive outcomes. The program is multi-lingual and scalable and can be implemented in and outside of the organizational settings globally.

Originality/value

The study proposes the concept of positive self-leadership and is the first study to investigate the potentiality of an emerging program for developing positive self-leadership.
Review of quality issues and mitigation strategies for metal powder bed fusion
Authors: Ravalji Jaydeepsinh M. , Raval Shruti J.
Published: October 2022

Purpose

Selective laser melting and electron beam melting processes are well-known for the additive manufacturing of metal parts. Metal powder bed fusion (MPBF) is a common term for them. The MPBF process can empower the manufacturing of intricate shapes by reducing the use of special tools, shortening the supply chain and allowing small batches. However, the MPBF process suffers from many quality issues. In literature, several works are recorded for qualification of the MPBF part. The purpose of this study is to recollect those works done for quality control and report their helpful findings for further research and development.

Design/methodology/approach

A systematic literature review was conducted to highlight the major quality issues in the MPBF process and its root causes. Further, the works reported in the literature for mitigation of these issues are classified and discussed in five categories: experimental investigation, finite element method-based numerical models, physics-based analytical models, in-situ control using artificial intelligence (AI) and machine learning (ML) methods and statistical approaches. A comparison is also prepared among these strategies based on their suitability and limitations. Additionally, improvements in MPBF printers are pointed out to enhance the part quality.

Findings

Analytical models require less computational time to simulate the MPBF process and need a smaller number of experiments to confirm the results. They can be used as an efficient process parameter planning tool to print metal parts for noncritical applications. The AI-ML based quality control is also suitable for MPBF processes as it can control many processing parameters that may affect the quality of the MPBF part. Moreover, capabilities of MPBF printers like thinner layer thickness, smaller beam diameter, multiple lasers and high build temperature range can help in quality control.

Research limitations/implications

This study converts the piecemeal data on MPBF part qualification methods into interesting information and presents it in tabular form under each strategy. This tabular information provides the basis for further quality improvement efforts in the MPBF process.

Originality/value

This study references researchers and practitioners on recent quality control efforts and their significant findings for a better quality of MPBF part.
Environmental, social, and governance (ESG) investing and commodities: dynamic connectedness and risk management strategies
Authors: Cagli Efe C. Caglar , Mandaci Pinar Evrim , Taşkın Dilvin
Published: October 2022

Purpose

The purpose of this study is to examine the dynamic connectedness and volatility spillovers between commodities and corporations exhibiting the best environmental, social and governance (ESG) practices. In addition, the authors determine the optimal hedge ratios and portfolio weights for ESG and commodity investors and portfolio managers.

Design/methodology/approach

This study uses the novel frequency connectedness framework to point out volatility spillover between ESG indices covering the USA, developed and emerging markets and commodity indices, including energy (crude oil, natural gas and heating oil), industrial metals (aluminum, copper, zinc, nickel and lead) and precious metals (gold and silver) by using daily data between January 3, 2011 and May 26, 2021, covering significant socio-economic developments and the COVID-19 outbreak.

Findings

The results of this study suggest a total connectedness index at a mediocre level, mainly driven by the shocks creating uncertainty in the short term. And the results indicate that all ESG indices are net volatility transmitters, and all commodity indices other than crude oil and copper are net volatility receivers.

Practical implications

The results imply statistically significant hedging and portfolio diversification opportunities to investors and portfolio managers across the asset classes, proven by the hedging effectiveness analyses.

Social implications

This study provides implications for policymakers focusing on the risk of contagion among the commodity and ESG markets during turbulent periods to ensure international financial stability.

Originality/value

This study contributes to the existing literature by differentiating ESG portfolios as the USA, developed and developing markets and examining dynamic connectedness and volatility spillovers between ESG portfolios and commodities with a different technique. This study also contributes by considering COVID-19 outbreak.
Common‐offset domain reflection–diffraction separation with deep learning
Authors: Zwartjes Paul , Yoo Jewoo
Published: October 2022

Separation of diffracted from reflected events in seismic data is still challenging due to the relatively low amplitude of the diffracted wavefield compared to the reflected wavefield as well as the overlap in the kinematics of reflection and diffraction events. A workflow based on deep learning can be a simple and fast alternative, but using training data made by physics‐based modelling is expensive and lacks diversity in terms of noise, amplitude, frequency content and wavelet. This results in poor generalization beyond the training data without retraining and transfer learning. In this paper, we demonstrate successful applications of reflection–diffraction separation using a conventional U‐net architecture. The novelty of our approach is that we do not use synthetic data created from physics‐based modelling, but instead use only synthetic data built from basic geometric shapes. Our domain of application is the pre‐migration common‐offset domain where reflected events resemble local geology and the diffracted wavefield consists of downward convex hyperbolic diffraction patterns. Both patterns were randomly perturbed in many ways while maintaining their intrinsic features. This approach is inspired by the common practice of data augmentation in deep learning for machine vision applications. Since many of the standard data augmentation techniques lack a geophysical motivation, we have instead perturbed our synthetic training data in ways to make more sense from a signal processing perspective or given our ‘domain knowledge’ of the problem at hand. We did not have to retrain the network to show good results on the field data set. The large variety and diversity in examples enabled to trained neural networks to show encouraging results on synthetic and field data sets that were not used in training.
Soundscape enrichment enhances recruitment and habitat building on new oyster reef restorations
Authors: McAfee Dominic , Williams Brittany R. , McLeod Lachlan , Reuter Andreas , Wheaton Zak , Connell Sean D.
Published: October 2022

Marine soundscapes provide important navigational cues to dispersing larvae in search of suitable habitat. Yet, widespread habitat loss has degraded marine soundscapes and their functional role in recruitment. Habitat restoration efforts can provide suitable substrate for habitat regeneration, such as constructing reefs to facilitate recruitment and habitat growth by oysters, but typically occur where soundscapes are degraded and recruitment is limited. Enhancing marine soundscapes on newly constructed reefs using speaker technology may ensure sufficient recruitment to establish a trajectory of recovery for the desired habitat.

Across two of the largest oyster reef restorations in Australia, we deployed low‐cost marine speakers at four sites and at three times throughout the recruitment season to test whether soundscape enrichment could boost recruitment and habitat formation by oysters. In the presence and absence of soundscape playback, we compared oyster recruitment rates to settlement panels across space and time, and oyster habitat cover and three‐dimensional habitat building on newly constructed boulder reefs.

On the settlement panels deployed across the two reef restorations, soundscape playback significantly increased oyster recruitment at 8 of the 10 sites by an average (±1 SE) 5.1 ± 1.9 times (5281 ± 1384 more larvae per m2), and by as much as 18 times.

On boulders atop newly constructed reefs, where the restoration goal is for oysters to form three‐dimensional habitat, the surface area covered by oysters after 5 months did not differ between speaker and control treatments. However, soundscape playback appeared to influence the earlier recruitment of oysters, resulting in significantly more large oysters per boulder that formed significantly more three‐dimensional habitat building by an average 4.3 ± 1.2 times relative to nonspeaker controls.

Synthesis and applications. Our results show that using speakers to enrich marine soundscapes at new restoration sites can boost oyster recruitment, resulting in more larger oysters that form more three‐dimensional habitat atop reef restorations. In accelerating the formation of these vertical growth forms, which provide the ecological functions that motivate restoration efforts, the early application of speaker technology on new reef restorations may help steer ecological succession on a trajectory of desired habitat recovery, potentially reducing the substantial cost of ongoing intervention.
Direct and indirect effects of management and landscape on biological pest control and crop pest infestation in apple orchards
Authors: Daelemans Robin , Hulsmans Eva , Laenen Emily , Remy Serge , Beliën Tim , Honnay Olivier
Published: October 2022

Biological pest control, relying on naturally occurring predator–prey dynamics, is considered a key element to achieve more sustainable farming systems. However, the combined effects of local management and landscape factors on communities of natural enemies as well as the cascading effects on pest infestations are rarely addressed, especially in perennial crops.

Here, we used Piecewise Structural Equation Modelling (PSEM) to test direct and indirect effects of landscape composition, landscape configuration and local management practices on natural enemy communities, the pest control services they provide and ultimately on pest infestation and pest‐related yield damage in apple crops. To this end, we surveyed 12 organic and 12 Integrated Pest Management (IPM) orchards during three consecutive years, and we also established a semi‐natural benchmark to quantify the extent to which predator communities in the orchards were degraded.

Natural enemies had a different community composition and were more abundant in organic orchards compared with IPM orchards. This had a small and positive effect on sentinel egg predation rates in organic orchards, but overall had very little impact on actual apple pest infestation. On the contrary, apple pest infestation levels were directly and positively affected by organic management practices and by increasing semi‐natural habitat cover and landscape edge density. Compared with a semi‐natural benchmark, both agricultural management systems showed degraded predator communities, which translated into an impaired delivery of biological control services.

Synthesis and applications. Our results indicate that organic management and habitat conservation can enhance natural enemies and stimulate pest control, but also show that these factors can enhance pest infestations and can even lead to an overall increase in pest‐related crop damage. Our study thus highlights the complex interplay of ecosystem services and disservices provided by biodiversity, which should be taken into account when advising farmers, policy makers and land managers on effective and sustainable strategies to control pest species and safeguard crop production.
On Islam and Portraiture: Lithography, Glass Painting, and Photography in Senegal
Authors: Paoletti Giulia
Published: October 2022

Scholars have for decades challenged the popular belief that Islam is intrinsically and implacably hostile to anthropomorphic art. Rooted in this literature, this essay argues that Islam was responsible for popularizing portraiture in Senegal, which previously featured none. With the founding of local Sufi brotherhoods such as the Mouridiyya in the 1880s, the eminence of religious leaders led to an unprecedented demand for their portraits. Glass painting became the privileged medium for reproducing images that appeared in other media, such as lithographs or photographs. Inspired by the respect for Muslim saints inherent in Sufi practices, the widespread desire to display portraits in one's home and for one's personal devotional practices made this genre indispensable. Rather than concentrating on any one medium, this essay focuses on the theoretical and formal interaction among chromolithographs, photographs, and glass paintings, and the migration of images across the three between the 1910s and the 1950s.
Impact of the combination of sintilimab and chemotherapy on the tumor and paratumor PD‐L1, IDO, TIM‐3, FOXP3+ and CD8 expressions in patients with advanced esophageal squamous cell carcinoma
Authors: Zhang Shifa , Cai Haibo , Huang Junjun , Wang Gongchao
Published: October 2022

Background

Anti‐PD‐1/PD‐L1 therapeutics have been widely used in the clinic in various tumors, including advanced esophageal cancer, showing remarkable treatment efficacy. Factors determining the response to anti‐PD‐1/PD‐L1 therapeutics are numerous, including the tumor microenvironment, such as CD8+ T cells and expression of PD‐1/PD‐L1. Our study aimed to explore the effect of chemoimmunotherapy on the expression of CD8+ T cells, TIM‐3, and FOXP3+ in tumor, paratumor tissues, and the expression of PD‐L1, IDO, in tumor, paratumor tissues, and lymph nodes, and analyze the correlation among these markers.

Methods

A total of 18 patients were allocated into two treatment groups: a treatment group and a concurrent control group. A total of 38 tissue samples, 114 slides (tumor, paratumor, and lymph node) were collected in the treatment group, and 37 tissue samples, 111 slides (tumor, paratumor, and lymph node) were collected in the concurrent control group.

Results

The expression of PD‐L1, CD8+, FOXP3+, TIM‐3, and IDO in tumors, paratumor tissues, but not lymph nodes, was significantly affected by chemoimmunotherapy. Compared with patients without chemoimmunotherapy, the expression of CD8+ T cells, IDO, and PD‐L1 was significantly decreased in tumor and paratumor tissues after chemoimmunotherapy, while FOXP3+ expression was significantly decreased only in tumor tissues, and TIM‐3 expression was significantly decreased only in paratumor tissues. Moreover, the correlation between these markers was also completely altered after chemoimmunotherapy. In addition, N staging was associated with high expression of CD8 in advanced esophageal squamous cell carcinoma in the concurrent control group.

Conclusion

This study provides new insight into the effects of CI treatment on isolated CD8+ T cell infiltration, PD‐L1, IDO, FOXP3+ and TIM‐3 expression as well as their cross‐talk in different tissues enabling a better understanding of the impact of CI treatment on the immune microenvironment.
Liver resection versus microwave ablation for hepatocellular carcinoma in ideal candidates for ablation per Barcelona Clinic Liver Cancer staging: a propensity score matching and inverse probability of treatment weighting analysis
Authors: Tong Yao , Cai Ran , Li Jun‐Xiang , Chang De‐Hua , Wang Li‐Zhou , Cai Wen‐Wu , Xiao Yu‐Dong
Published: October 2022

Background

Liver resection (LRE) and microwave ablation (MWA) for hepatocellular carcinoma (HCC) have been widely compared.

Aims

To compare the therapeutic outcomes of percutaneous MWA and LRE for HCC in ideal candidates for ablation according to Barcelona Clinic Liver Cancer (BCLC) staging

Methods

Between August 2013 and November 2020, 483 consecutive patients meeting criteria for “ideal candidates for ablation” per the BCLC staging initially treated with MWA (n = 168) or LRE (n = 315) were included. Patients were further divided into BCLC‐0 (n = 116) and BCLC‐A (n = 367) groups. Overall survival (OS), recurrence‐free survival (RFS) and post‐procedure‐related complication rates were compared before and after propensity score matching (PSM) and inverse probability of treatment weighting (IPTW) in the overall population and subgroups. Multivariate Cox regression analysis was performed to determine whether the treatment modality was an independent prognostic factor.

Results

LRE had a better RFS and similar OS and post‐procedure‐related complication rates compared to MWA in the overall population and in the BCLC‐A subgroup both before and after PSM and IPTW. However, the OS, RFS and post‐procedure‐related complication rates were equivalent between the two groups before and after PSM and IPTW in patients with BCLC‐0 disease. The multivariate Cox regression analysis showed that LRE was associated with better RFS over MWA in overall population (p = 0.003; HR = 0.67; 95% CI: 0.51–0.87) and BCLC‐A disease (p = 0.046; HR = 0.74; 95% CI: 0.56–0.99), while it did not differ in OS.

Conclusion

An ‘ideal candidate for ablation’ according to the BCLC staging system may not be an ideal candidate for MWA. However, patients with BCLC‐0 may be the optimal population for MWA.
Statistical Inference and Power Analysis for Direct and Spillover Effects in Two-Stage Randomized Experiments
Authors: Jiang Zhichao , Imai Kosuke , Malani Anup
Published: October 2022

Two-stage randomized experiments become an increasingly popular experimental design for causal inference when the outcome of one unit may be affected by the treatment assignments of other units in the same cluster. In this paper, we provide a methodological framework for general tools of statistical inference and power analysis for two-stage randomized experiments. Under the randomization-based framework, we consider the estimation of a new direct effect of interest as well as the average direct and spillover effects studied in the literature. We provide unbiased estimators of these causal quantities and their conservative variance estimators in a general setting. Using these results, we then develop hypothesis testing procedures and derive sample size formulas. We theoretically compare the two-stage randomized design with the completely randomized and cluster randomized designs, which represent two limiting designs. Finally, we conduct simulation studies to evaluate the empirical performance of our sample size formulas. For empirical illustration, the proposed methodology is applied to the randomized evaluation of the Indian National Health Insurance Program. An open-source software package is available for implementing the proposed methodology.