bluuebunny/crossref_metadata_2025 huggingface dataset:
A Clinicopathologic and Molecular Analysis of Fumarate Hydratase–deficient Pheochromocytoma and Paraganglioma
Authors: Fuchs Talia L. , Luxford Catherine , Clarkson Adele , Sheen Amy , Sioson Loretta , Elston Marianne , Croxson Michael S. , Dwight Trisha , Benn Diana E. , Tacon Lyndal , Field Michael , Ahadi Mahsa S. , Chou Angela , Clifton-Bligh Roderick J. , Gill Anthony J.
Published: August 2022

Up to 40% of pheochromocytomas (PCCs) and paragangliomas (PGLs) are hereditary. Germline mutations/deletions infumarate hydratase(FH) cause hereditary leiomyomatosis and renal cell carcinoma syndrome which manifests predominantly with FH-deficient uterine/cutaneous leiomyomas and renal cell carcinomas (RCCs)—tumors characterized by loss of immunohistochemical (IHC) expression of FH and/or positive staining for S-(2-succino)-cysteine. Occasional patients develop PCC/PGL. We investigated the incidence, morphologic, and clinical features of FH-deficient PCC/PGL. We identified 589 patients with PCC/PGLs that underwent IHC screening for FH and/or S-(2-succino)-cysteine. Eight (1.4%) PCC/PGLs were FH deficient (1.1% in an unselected population). The median age for FH-deficient cases was 55 (range: 30 to 77 y) with 50% arising in the adrenal. All 4 with biochemical data were noradrenergic. Two (25%) metastasized, 1 dying of disease after 174 months. Germline testing was performed on 7 patients, 6 of whom hadFHmissense mutations. None were known to have a significant family history before presentation or developed cutaneous leiomyomas, or FH-deficient RCC at extended follow-up. The patient wild-type forFHon germline testing was demonstrated to have somaticFHmutation and loss of heterozygosity corresponding to areas of subclonal FH deficiency in her tumor. One patient did not undergo germline testing, butFHmutation was demonstrated in his tumor. We conclude that FH-deficient PCC/PGL are underrecognized but can be identified by IHC. FH-deficient PCC/PGL are strongly associated with germline missense mutations but are infrequently associated with leiomyoma or RCC, suggesting there may be a genotype-phenotype correlation. FH-deficient PCC/PGL may have a higher metastatic risk.
Cutaneous Melanocytic Tumor With CRTC1::TRIM11 Translocation
Authors: Hanna John , Ko Jennifer S. , Billings Steven D. , Boivin Felix , Beaudoux Olivia , Pissaloux Daniel , Tirode Franck , Laga Alvaro , Fletcher Christopher D.M. , de la Fouchardiere Arnaud
Published: August 2022

Cutaneous melanocytic tumor with CRTC1::TRIM11 fusion (CMTCT) is a recently described dermally based neoplasm with melanocytic differentiation. It can easily be confused with clear cell sarcoma and metastatic melanoma. Our understanding of this lesion, including its potential for aggressive disease, has been limited by the small number of previously reported cases (13) and the limited clinical follow-up data. Here, we report a series of 41 CMTCT confirmed by molecular studies. We find that the lesion shows highly uniform and reproducible morphologic, immunohistochemical, and genetic features across a wide variety of anatomic locations and age groups. Among 22 cases with follow-up, 1 local recurrence and 1 nodal metastasis were identified. Our data support the classification of CMTCT as a unique nosologic entity and emphasize the importance of distinguishing this entity from its histologic mimics, especially clear cell sarcoma and metastatic melanoma, to guide therapy and establish accurate prognostic expectations.
“Correlation Between Capsular Contracture Rates and Access Incision Location in Vertical Augmentation Mastopexy”
Authors: Bresnick Stephen D.
Published: August 2022

Background:

Plastic surgeons commonly utilize one of three access incisions to place breast implants during vertical augmentation mastopexy, including inframammary, vertical, and periareolar. It is not known whether there is a correlation between capsular contracture and access incision location. The purpose of this study was to investigate in a single-surgeon series, the incidence of capsular contracture associated with access incision locations in silicone vertical augmentation mastopexy.

Methods:

Patients undergoing a vertical augmentation mastopexy between 2013 and 2017 were studied retrospectively. All patients underwent a standardized, dual-plane breast augmentation with smooth surface silicone gel implants. Patients were evaluated one-year postoperatively by the Baker scale.

Results:

A total of 322 patients met study criteria. Eighty-four had periareolar access, 86 had vertical access, and 152 had inframammary access. There were no differences in patient age or mean implant size between the groups. The capsular contracture rate of the periareolar group was 5.36%, while the vertical access group rate was 3.48% and the inframammary access group rate was 1.64%. Capsular contracture rates correlated inversely to the distance to the nipple-areolar complex, with the periareolar access rates the highest, the vertical access rates intermediate, and the inframammary access rates the lowest. Inframammary incisions were associated with lower capsular contracture rates than periareolar incisions when performed in conjunction with vertical augmentation mastopexy (p = 0.043). Vertical access capsular contracture rates were intermediate between periareolar and inframammary.

Conclusions:

Surgeons should take into consideration the capsular contracture rates associated with access incision location when planning or performing vertical augmentation mastopexy.
Zygomatic implants through a face-lift approach: Analysis of 30-years experience
Authors: Pelle-Ceravolo Mario , Angelini Matteo
Published: August 2022

Background:

The use of zygomatic implants has been mostly replaced by fat-grafting in rhytidectomy procedures. Further, surgeons using implants prefer the intraoral approach. We aimed to describe and emphasize the usefulness of the preauricular approach as the best approach for this operation and underline the value of cheek implants as an alternative and/or as an adjunct to fat grafting during facelift procedures for midfacial rejuvenation.

Methods:

A retrospective study of 350 patients who underwent facelift procedures with silicone malar implant placement via a preauricular approach was conducted. Postoperative photographs of all patients were examined by two doctors for postoperative volume adequacy, naturalness of appearance, and improvement in asymmetry. Patient satisfaction was evaluated using a questionnaire with an ordinal scale.

Results:

The large majority of patients (338/350, 96.5%) were “completely satisfied” or “satisfied” with the aesthetic outcome. The complication rate was very low and comparable to data reported in current literature.

Conclusions:

The application of cheek implants proved to be a great tool for midfacial volume rejuvenation with or without associated fat-grafting. This conclusion was drawn from the answers reported in the questionnaires completed by the two examiners. The main challenges in this surgery was the choice of the type, shape, and size of the implant. The preauricular approach should be given preference during this procedure because, compared to the other approaches, it is easier, faster, and more comfortable for both the patient and the surgeon.
Pneumothorax, Pneumomediastinum, and Pneumoperitoneum After Combined Abdominoplasty and Liposuction
Authors: Nasr Hani Y. , Levine Jamie P. , Chiu Ernest S.
Published: August 2022

Liposuction is a relatively safe surgical procedure, with most complications being minor in nature. However, there are a few life-threatening complications that should not be underestimated. We present a case of a patient who developed bilateral pneumothoraces, pneumomediastinum, and pneumoperitoneum after combined liposuction and abdominoplasty. Although this presentation is rare, clinicians should keep a high index of suspicion in patients presenting with shortness of breath, chest pain, and/or abdominal pain after liposuction.
Quantification of Facial Allograft Edema During Acute Rejection
Authors: Boczar Daniel , Brydges Hilliard , Rodriguez Colon Ricardo , Onuh Ogechukwu C. , Trilles Jorge , Chaya Bachar F. , Gelb Bruce , Ceradini Daniel J. , Rodriguez Eduardo D.
Published: August 2022

Background

Acute rejection (AR) is a common complication in facial transplant (FT) patients associated with allograft edema and erythema. Our study aims to demonstrate the feasibility of using software-based 3-dimensional (3D) facial analysis to quantify edema as it resolves during/after AR treatment in an FT patient.

Methods

Our patient is a 23-year-old man who underwent a face and bilateral hand allotransplant in August 2020. The Vectra H1 (Canfield, Fairfield, NJ) portable scanner was used to capture 3D facial images at 8 time points between postoperative day (POD) 392 and 539. The images were analyzed with the Vectra Software using a rejection-free image (POD 539) as a control.

Results

Edema increased in the periorbital, lower third, and submandibular regions before AR treatment (POD 392–415). At POD 448, total facial edema was reduced to near baseline values in response to plasmapheresis and thymoglobulin (+156.94 to +28.2 mL). The fastest and most notable response to treatment was seen in the periorbital region, while some edema remained in the submandibular (+19.79 mL) and right lower third (+8.65 mL) regions. On POD 465, after the initial improvement, the edema increased but was resolved with steroid use. Facial edema did not correlate with the histopathological evaluation in our patient.

Conclusions

We demonstrated the feasibility of analyzing 3D facial images to quantify edema during/after AR treatment in an FT patient. Our analysis detected edema changes consistent with AR followed by an improvement after treatment. This technology shows promise for noninvasive monitoring of FT patients.
Auricles Anomalies in Patients With a TCF12 Gene Mutation
Authors: Lacroix Guillaume , Karnoub Melodie-Anne , Vinchon Matthieu , Wolber Alexis , Martinot Véronique , Guerreschi Pierre
Published: August 2022

Craniostenosis is a morphological anomaly affecting about 0.5 of 1000 births and one third of the cases are of genetic origin. Among the syndromes responsible for craniostenosis, there is the Saethre-Chotzen syndrome due to a mutation of the TWIST 1 gene located on chromosome 7. This polymalformative syndrome classically includes a particular morphology of the auricles. The penetrance is variable and results in a phenotypic variability at the origin of “Saethre-Chotzen like” clinical pictures for which the TWIST 1 gene mutation is sometimes not found. Recently, the TCF 12 gene has been implicated in some of these cases. Among the multiple facial malformations, we have carefully examined the particular morphology of the auricle of these patients. The authors found several abnormalities in patients with a TCF 12 gene mutation, namely a thickened and hammered upper pole of the helix, a narrow concha without crux cymbae and a thickened lobe. These morphological features may guide the diagnosis and allow an earlier search for a TCF 12 gene mutation.
EnteroBase: hierarchical clustering of 100 000s of bacterial genomes into species/subspecies and populations
Authors: Achtman Mark , Zhou Zhemin , Charlesworth Jane , Baxter Laura
Published: August 2022

The definition of bacterial species is traditionally a taxonomic issue while bacterial populations are identified by population genetics. These assignments are species specific, and depend on the practitioner. Legacy multilocus sequence typing is commonly used to identify sequence types (STs) and clusters (ST Complexes). However, these approaches are not adequate for the millions of genomic sequences from bacterial pathogens that have been generated since 2012. EnteroBase (
http://enterobase.warwick.ac.uk
) automatically clusters core genome MLST allelic profiles into hierarchical clusters (HierCC) after assembling annotated draft genomes from short-read sequences. HierCC clusters span core sequence diversity from the species level down to individual transmission chains. Here we evaluate HierCC's ability to correctly assign 100 000s of genomes to the species/subspecies and population levels for
Salmonella, Escherichia, Clostridoides, Yersinia, Vibrio
and
Streptococcus
. HierCC assignments were more consistent with maximum-likelihood super-trees of core SNPs or presence/absence of accessory genes than classical taxonomic assignments or 95% ANI. However, neither HierCC nor ANI were uniformly consistent with classical taxonomy of
Streptococcus.
HierCC was also consistent with legacy eBGs/ST Complexes in
Salmonella
or
Escherichia
and with O serogroups in
Salmonella
. Thus, EnteroBase HierCC supports the automated identification of and assignment to species/subspecies and populations for multiple genera.

This article is part of a discussion meeting issue ‘Genomic population structures of microbial pathogens’.
Scalable Bayesian phylogenetics
Authors: Fisher Alexander A. , Hassler Gabriel W. , Ji Xiang , Baele Guy , Suchard Marc A. , Lemey Philippe
Published: August 2022

Recent advances in Bayesian phylogenetics offer substantial computational savings to accommodate increased genomic sampling that challenges traditional inference methods. In this review, we begin with a brief summary of the Bayesian phylogenetic framework, and then conceptualize a variety of methods to improve posterior approximations via Markov chain Monte Carlo (MCMC) sampling. Specifically, we discuss methods to improve the speed of likelihood calculations, reduce MCMC burn-in, and generate better MCMC proposals. We apply several of these techniques to study the evolution of HIV virulence along a 1536-tip phylogeny and estimate the internal node heights of a 1000-tip SARS-CoV-2 phylogenetic tree in order to illustrate the speed-up of such analyses using current state-of-the-art approaches. We conclude our review with a discussion of promising alternatives to MCMC that approximate the phylogenetic posterior.

This article is part of a discussion meeting issue ‘Genomic population structures of microbial pathogens’.
Recent progress on methods for estimating and updating large phylogenies
Authors: Zaharias Paul , Warnow Tandy
Published: August 2022

With the increased availability of sequence data and even of fully sequenced and assembled genomes, phylogeny estimation of very large trees (even of hundreds of thousands of sequences) is now a goal for some biologists. Yet, the construction of these phylogenies is a complex pipeline presenting analytical and computational challenges, especially when the number of sequences is very large. In the past few years, new methods have been developed that aim to enable highly accurate phylogeny estimations on these large datasets, including divide-and-conquer techniques for multiple sequence alignment and/or tree estimation, methods that can estimate species trees from multi-locus datasets while addressing heterogeneity due to biological processes (e.g. incomplete lineage sorting and gene duplication and loss), and methods to add sequences into large gene trees or species trees. Here we present some of these recent advances and discuss opportunities for future improvements.

This article is part of a discussion meeting issue ‘Genomic population structures of microbial pathogens’.
Impact of vaccination with SCB-2019 COVID-19 vaccine on transmission of SARS-CoV-2 infection: a household contact study in the Philippines
Authors: Tadesse Birkneh Tilahun , Bravo Lulu , Marks Florian , Aziz Asma Binte , You Young Ae , Sugimoto Jonathan , Li Ping , Garcia Joyce , Rockhold Frank , Clemens Ralf ,   the HHC study group
Published: August 2022

Background

An exploratory household transmission study was nested in SPECTRA, the phase 2/3 efficacy study of the adjuvanted recombinant protein-based COVID-19 vaccine SCB-2019. We compared occurrence of confirmed COVID-19 infections between households and household contacts of infected SPECTRA participants who were either placebo or SCB-2019 recipients.

Methods

SPECTRA trial participants at eight study sites in the Philippines who developed rRT-PCR-confirmed COVID-19 were contacted by a study team blinded to assignment of index cases to vaccine or placebo groups to enroll in this household transmission study. Enrolled households and household contacts were monitored for three weeks using rRT-PCR and rapid antigen testing to detect new COVID-19 infections.

Results

Observation of the households of 154 eligible COVID-19 index cases, 130 symptomatic and 24 asymptomatic at diagnosis, revealed household secondary attack rates for any COVID-19 infection of SCB-2019 index cases of 0.76% (90% CI: 0.15–3.90) compared with 5.88% (90% CI: 3.20–10.8) in placebo index case households, a relative risk reduction of 79% (90% CI: -28–97). The relative risk reduction of symptomatic COVID-19 was 84% (90% CI: 28–97) for household contacts of all COVID-19 infected index cases, and 80% (90% CI: 7–96) for household contacts of index cases with symptomatic COVID-19.

Conclusions

In this prospective household contact study vaccination with SCB-2019 reduced SARS-CoV-2 transmission in households, so decreasing infections of household contacts, compared with placebo.
Costing analysis to introduce a Contrast Enhanced Mammography service in place of existing breast MRI service for local staging of breast cancer
Authors: Savaridas Sarah L , Jin Huajie
Published: August 2022

Introduction

Contrast-enhanced spectral mammography (CESM) is a functional imaging technique with comparable accuracy to MRI for loco-regional staging of breast cancer. This study assesses the cost impact of switching from CE-MRI to CESM for loco-regional staging of breast cancer from a public healthcare perspective.

Methods

The CE-MRI cost was obtained from NHS reference cost. The CESM cost was calculated using a bottom-up approach including use of the machine, pump injector, contrast, image storage and clinical staff’s time for reporting and cannulation. The cost of upgrading existing machines to CESM or purchasing new mammographic machines were obtained via national procurement. Other costs were obtained from local pharmacy, published unit cost data, or estimated based on surveys.

Results

For large health boards in Scotland (≥500 cancers diagnosed/annum), the cost savings of switching from CE-MRI to CESM range from £64,069 to £81,570. For small health boards (<500 cancers diagnosed/annum), the cost savings of switching from CE-MRI to CESM range from £6,453 to £23,953. The cost savings are most sensitive to the number of tests conducted per year, and whether the existing mammography machine can be upgraded to CESM or not.

Conclusion

Switching from CE-MRI to CESM for loco-regional staging of breast cancer is likely to be cost saving for both large and small health boards in Scotland. Further research is urgently needed to confirm the non-inferiority of CESM to CE-MRI as a locoregional staging technique. The input data of this analysis can be updated when such results become available.

Highlights

Switching from CE-MRI to CESM for locoregional staging is likely to be cost saving

For large health boards, estimated annual savings range from £64,069 to £81,570

For a small health boards, estimated annual savings range from £6,453 to £23,953

Cost is driven by number of imaging studies and equipment upgrade vs replacement

Research to confirm the non-inferiority of CESM for locoregional staging is needed
Neural network facilitated ab initio derivation of linear formula: A case study on formulating the relationship between DNA motifs and gene expression
Authors: Liu Chengyu , Wang Wei
Published: August 2022

Developing models with high interpretability and even deriving formulas to quantify relationships between biological data is an emerging need. We propose here a framework for ab initio derivation of sequence motifs and linear formula using a new approach based on the interpretable neural network model called contextual regression model. We showed that this linear model could predict gene expression levels using promoter sequences with a performance comparable to deep neural network models. We uncovered a list of 300 motifs with important regulatory roles on gene expression and showed that they also had significant contributions to cell-type specific gene expression in 154 diverse cell types. This work illustrates the possibility of deriving formulas to represent biology laws that may not be easily elucidated. (https://github.com/Wang-lab-UCSD/Motif_Finding_Contextual_Regression)
Transcriptional landscapes and signaling pathways of chloroquine-treated Esophageal squamous cell carcinoma
Authors: Wang Wei (David) , Qian Zhiwen
Published: August 2022

Esophageal squamous cell carcinoma (ESCC) is one of the human malignancies worldwide, but the mechanism of ESCC development is still unclear. Chloroquine has the anti-tumor function by the inhibition of autophagy and thereby contributing to apoptosis. In our study, we analyzed the RNA-seq data of Chloroquine-treated ESCC cells and identified the transcriptional landscapes. We then used the gene enrichment methods such as KEGG and GO to further analyze the potential signaling pathways. In addition, we constructed the PPI network and Reactome map to further identified the biological processes. We identified the top two signaling pathways that were involved in the chloroquine-treated ESCC: Cell cycle and Glycerophospholipid metabolism. We identified the top ten interactive genes including ATM, CCNB1, FN1, CCT6A, VEGFA, PA2G4, CCT2, CDKN1A, BRIX1, and CDC20. Our study may provide new insights into the mechanisms for the Chloroquine-treated ESCC cells.
Overview of the SARS-CoV-2 genotypes circulating in Latin America during 2021
Authors: Molina-Mora Jose Arturo , Reales-González Jhonnatan , Camacho Erwin , Duarte-Martínez Francisco , Tsukayama Pablo , Soto-Garita Claudio , Brenes Hebleen , Cordero-Laurent Estela , dos Santos Andrea Ribeiro , Salgado Cláudio Guedes , Silva Caio Santos , de Souza Jorge Santana , Nunes Gisele , Negri Tatiane , Vidal Amanda , Oliveira Renato , Oliveira Guilherme , Muñoz-Medina José Esteban , Salas Lais Angel Gustavo , Mireles-Rivera Guadalupe , Sosa Ezequiel , Turjanski Adrián , Monzani María Cecilia , Carobene Mauricio G. , Lenicov Federico Remes , Schottlender Gustavo , Do Porto Darío A. Fernández , Kreuze Jan Frederik , Sacristán Luisa , Guevara-Suarez Marcela , Cristancho Marco , Campos-Sánchez Rebeca , Herrera-Estrella Alfredo
Published: August 2022

Latin America is one of the regions in which the COVID-19 pandemic has had a stronger impact, with more than 72 million reported infections and 1.6 million deaths until June 2022. Since this region is ecologically diverse and is affected by enormous social inequalities, efforts to identify genomic patterns of the circulating SARS-CoV-2 genotypes are necessary for the suitable management of the pandemic.

To contribute to the genomic surveillance of the SARS-CoV-2 in Latin America, we extended the number of SARS-CoV-2 genomes available from the region by sequencing and analyzing the viral genome from COVID-19 patients from seven countries (Argentina, Brazil, Costa Rica, Colombia, Mexico, Bolivia and Peru). Subsequently, we analyzed the genomes circulating mainly during 2021 including records from GISAID database from Latin America.

A total of 1534 genome sequences were generated from seven countries, demonstrating the laboratory and bioinformatics capabilities for genomic surveillance of pathogens that have been developed locally. For Latin America, patterns regarding several variants associated with multiple re-introductions, a relatively low percentage of sequenced samples, as well as an increment in the mutation frequency since the beginning of the pandemic, are in line with worldwide data. Besides, some variants of concern (VOC) and variants of interest (VOI) such as Gamma, Mu and Lambda, and at least 83 other lineages have predominated locally with a country-specific enrichments.

This work has contributed to the understanding of the dynamics of the pandemic in Latin America as part of the local and international efforts to achieve timely genomic surveillance of SARS-CoV-2.
The Association of Postoperative Anaemia with Outcomes in Cardiac Surgical Patients Eligible for Patient Blood Management: A Single Institution Retrospective Cohort Study
Authors: Bartoszko Justyna , Li Michelle , Callum Jeannie , Yi Sujung , Ouzounian Maral , McCluskey Stuart A. , Miles Sarah , Lin Yulia , Karkouti Keyvan
Published: August 2022

Background

Anaemia is prognostically important and affects 30-40% of cardiac surgical patients. The objective of this study was to examine the association of pre- and postoperative anaemia with outcomes in cardiac surgical patients.

Methods

This was a single-institution retrospective cohort study including cardiac surgical patients from October 26, 2020 to December 3, 2021. Patients were classified as preoperatively non-anaemic (hemoglobin ≥ 130 g/L), anaemic, or treated with IV Iron. The main predictors of interest were nadir haemoglobin on postoperative days 1-2 and preoperative anaemia and receipt of IV iron therapy. The primary outcome was number of red blood cell units (RBC) transfused on postoperative days 1-7. Secondary outcomes included acute kidney injury, hospital length of stay, and 30 day in-hospital mortality. Regression models, adjusted for demographics, comorbidities, and surgical characteristics, examined the association between predictors and outcomes.

Results

A total of 844 patients were included [528 (63%) non-anaemic, 276 (33%) anaemic, and 40 (5%) anaemic, treated with IV iron]. There was no difference between groups in RBC transfusion or mortality, however anaemic patients had a higher adjusted risk for acute kidney injury [aOR 2.69 (95% CI, 1.37 to 5.30), p=0.004] and longer hospital length of stay [aRR 1.38 (95% CI, 1.24 to 1.54), p<0.0001] compared to non-anaemic patients. Patients treated with IV iron did not have the same increased risk. A lower postoperative haemoglobin nadir was significantly associated with increased risk for all outcomes.

Conclusions

Postoperative anaemia confers additional risk regardless of preoperative anaemia status. Further research is needed to better clarify these associations.
Genomic and transcriptional profiling stratifies VQ myeloma lines into two clusters with distinct risk signatures and drug responses
Authors: Flietner Evan , Yu Mei , Rajagopalan Adhithi , Zhou Yun , Feng Yubin , Veltri Anthony J. , Lasho Terra , Wen Zhi , Sun Yuqian , Patnaik Mrinal M. , Callander Natalie S. , Asimakopoulos Fotis , Wang Demin , Zhang Jing
Published: August 2022

Multiple myeloma (MM) is a cancer of malignant plasma cells in the bone marrow and extramedullary sites. We previously characterized a VQ model for human high-risk MM. Different VQ lines display distinct disease phenotypes and survivals, suggesting significant intra-model variation. Here, we use whole exome sequencing and copy number variation (CNV) analysis coupled with RNA-Seq to stratify VQ lines into corresponding clusters: Cluster I VQ cells carried recurrent amplification of chromosome (chr) 3 and displayed upregulation of growth pathways and high-risk myeloma gene signatures, whereas Cluster II cells had monosomy chr5 and overexpressed genes and pathways associated with positive response to bortezomib (Btz) treatment in human MM patients. Consistently, in sharp contrast to Cluster II VQ cells that showed short-term response to Btz, Cluster I VQ cells were de novo resistant to Btzin vivo. Our study highlights Cluster I VQ lines as highly representative of human high-risk MM subset.
MoTERNN: Classifying the Mode of Cancer Evolution Using Recursive Neural Networks
Authors: Edrisi Mohammadamin , Ogilvie Huw A. , Li Meng , Nakhleh Luay
Published: August 2022

With the advent of single-cell DNA sequencing, it is now possible to infer the evolutionary history of thousands of tumor cells obtained from a single patient. This evolutionary history, which takes the shape of a tree, reveals the mode of evolution of the specific cancer under study and, in turn, helps with clinical diagnosis, prognosis, and therapeutic treatment. In this study we focus on the question of determining the mode of evolution of tumor cells from their inferred evolutionary history. In particular, we employ recursive neural networks that capture tree structures to classify the evolutionary history of tumor cells into one of four modes—linear, branching, neutral, and punctuated. We trained our model, MoTERNN, using simulated data in a supervised fashion and applied it to a real phylogenetic tree obtained from single-cell DNA sequencing data. MoTERNN is implemented in Python and is publicly available at https://github.com/NakhlehLab/MoTERNN.
Determinants of institutional agricultural credit access and its linkage with farmer satisfaction in India: a moderated-mediation analysis
Authors: Dey Shiladitya , Singh Piyush Kumar , Mhaskar Megha Deepak
Published: August 2022

Purpose

The study assesses the relationship between institutional credit access and farmer satisfaction using contextual mediating and moderating variables. This study identifies various socioeconomic, service features and service quality determinants impacting institutional credit access.

Design/methodology/approach

The authors used the stratified random sampling method and selected 512 farmers from 40 villages in Maharashtra, India. Initially, the study employed probit regression analysis to identify the credit adoption determinants. Subsequently, the relationship between institutional credit and farmer satisfaction is identified through moderated-mediation analysis using the Statistical Package for the Social Sciences and Analysis of a Moment Structures (SPSS - AMOS model).

Findings

Probit model's results suggest that socioeconomic variables like education and bank distance; service quality variables like prompt service and employee behavior; and service characteristics variables like the interest rate, loan sanction time, repayment period, and documents for loan application significantly affect institutional credit adoption across the smallholders. Subsequently, the results of the moderating-mediation analysis show that working capital, perceived value and risk perception partially mediate the association between credit adoption and farmer satisfaction. The mediated effects are further moderated by farm advisory services and financial knowledge and skills.

Research limitations/implications

The study is restricted in opportunity due to primary data, and it considers only farmers' perspectives to measure service quality and service features as constraints for institutional credit access.

Practical implications

The government, nongovernment organizations, civil societies and private institutions should provide sufficient financial knowledge and training to the farmers via extension services to utilize the borrowed capital effectively to bring economic welfare and mental satisfaction.

Originality/value

The existing literature rarely considered banking service quality and service features (demand side) variables as determinants of credit access. Further, the study brings novelty in examining how the capital management cognitive factors of the formal credit adopters influence the relationship between credit access and satisfaction.
Investment and inclusive growth in sub-Saharan Africa
Authors: Adeosun Opeoluwa Adeniyi , Olomola Philip Akani , Tabash Mosab I. , Anagreh Suhaib
Published: August 2022

Purpose

This paper examined the inclusive growth position of sub-Saharan Africa (SSA) through the metrics of poverty-gap, bottom20 and employment. Through these indicators, the study investigated the effects of domestic-investment on inclusive-growth and established the moderating impact of governance in the domestic investment-inclusive growth nexus. It further accounted for potential nonlinearity and investigated the governance threshold that moderates domestic investment-inclusive growth relationships.

Design/methodology/approach

Using a sample of 41-SSA countries, the paper employed the fixed effect (FE) with the Driscoll and Kraay nonparametric consistent covariance matrix estimator, the generalized method of moments (GMM) and the dynamic-panel threshold techniques.

Findings

The poverty-gap metric showed that with increasing GDP-growth, the income of the poor falls below the poverty-line, suggesting that GDP-growth episodes may have widened the poverty-gap and contributed minimally to reducing it. Findings revealed insignificant effects of GDP-growth on the bottom-20 metric while the employment-metric indicated that the “jobless-growth” phenomenon remained valid. The authors essentially established that economic growth has not been inclusive but the complementary roles played by domestic-investments and governance are essential requirements for achieving inclusive growth. The threshold-modeling indicated that countries in the upper-regime of governance gained more in reducing poverty gaps, increasing income shared by the bottom-quintile and improving employment for every percentage increase in investment. The authors confirmed nonlinearity and showed that there exists a governance threshold that respective governments in Africa must reach for domestic-investment to enhance inclusive growth.

Originality/value

The paper accounted for cross-sectional dependence, nonlinearity and the governance threshold needed for domestic-investment to stimulate inclusive growth.
Gender differences among teenagers: healthy and unhealthy lifestyle habits and eating behaviours, food involvement and packaging cues
Authors: Kuster-Boluda Ines , Vila-Lopez Natalia
Published: August 2022

Purpose

The aim of this paper is the analysis of teenage consumers with varying degrees of healthy and unhealthy lifestyle habits and different healthy and unhealthy eating behaviours and food involvement, and its effects on packaging cues. At the same time, the paper tries to analyse the moderating role of gender.

Design/methodology/approach

With a sample of 589 (316 girls and 273 boys) young consumers (14–17 years old) and using SEM methodology, this paper tested a theoretical model related to the association between health, food, packaging cues and gender differences.

Findings

Among teenagers, healthy habits (sports) and healthy eating behaviours affect positively food involvement (p < 0.01 in both cases), and food involvement is positively related to informative packaging cues (p < 0.05). There are some differences between girls and boys. For example (1) there is a significant relationship between your consumers' sports activities and food involvement, and young consumers' healthy eating behaviours and food involvement. (2) More food-involved teenagers are those consumers that significantly read more carefully the packaging labels. Or (3) gender could be considered as a variable able to moderate the relationships between health and unhealthy lifestyle habits and eating behaviours, food involvement and packaging decisions.

Originality/value

The present paper tries to fulfil some literature gaps by developing a study with teenage consumers to solve three main questions/objectives: (1) Do healthy behaviours affect teenagers' food involvement? (2) Does teenagers' food involvement affect teenagers' packaging perceptions? and (3) Do girls and boys differ in their food packaging perceptions?
Factors affecting contractors’ bid or no-bid and mark-up decisions: a case of the Jilin province, China
Authors: Zhang Yixi , Oo Bee Lan , Lim Benson Teck-Heng
Published: August 2022

Purpose

Contractors of different scales, operating in different construction industries of varying institutional and economic settings, have different considerations when making bid or no-bid and mark-up decisions. Focusing on the large and medium-sized contractors in the Jilin province, China, the purpose of this study is to examine important factors affecting their decision to bid (d2b) and mark-up decisions and investigate differences between large and medium-sized contractors in evaluating the importance of the various factors affecting their d2b and mark-up decisions.

Design/methodology/approach

This study used a survey design for timely data collection from a large population. Contractors’ bidding attitudes was collected using an online survey questionnaire with a list of 40 key factors. Statistical analytical methods were applied for comparing the two groups of contractors.

Findings

The results of this study indicate that factors related to client conditions are most critical for both large and medium-sized contractors in their d2b and mark-up decisions. The results also show statistically significant differences between the two groups of contractors on a subset of factors affecting their d2b and mark-up decisions. The large contractors have placed more emphasis on projects' potential financial and strategic benefits. Another notable finding is that both groups of contractors have placed great emphasise on “government legislations” in their d2b and mark-up decisions.

Research limitations/implications

These findings should be interpreted in consideration of several limitations. Firstly, the sample size is relatively small, and the focus was on a single province in the China construction industry. Next, this study only explores differences between large and medium-sized contractors in evaluating the importance of the various factors affecting their d2b and mark-up decisions.

Practical implications

Contractors could refer list of critical factors in competing for jobs in Jilin province or other provinces of similar institutional and economic settings. Construction clients, on the other hand, should consider the list of critical factors in the formulation of their competitive tendering procedures, thus enhancing the efficiency in their procurement of construction services.

Originality/value

Research on contractors’ bidding decision-making in the context of Chinese construction industry remains scarce; the research findings have implications for the industry stakeholders.
“If your voice isn't accepted, does it mean you stop talking?” Exploring a woman leader’s reversal of postfeminist confidence discourses
Authors: Yoong Melissa
Published: August 2022

Purpose

This study offers a lens for exploring women leaders’ production of resistance through postfeminist discourses. Through the case study of Bozoma Saint John, a high-profile Black C-Suite executive, this study examines micro-acts of subversion and considers the extent they can promote feminist thinking in the corporate world and the implications for feminist theorising about women in leadership.

Design/methodology/approach

Interviews with Saint John were collected from YouTube and examined using feminist critical discourse analysis informed by intersectionality, feminist poststructuralism and Foucault’s notion of “reverse discourse”.

Findings

Saint John reproduces elements of the postfeminist confidence discourse to defy stereotypes of Black women, while simultaneously reversing the individualistic conception of confidence in favour of corporate and collective action. This has the potential to facilitate positive change, albeit within the boundaries of the confidence culture.

Research limitations/implications

Combining reverse discourse, intersectionality and feminist poststructuralism with a micro-level analysis of women leaders’ language use can help to capture the ways postfeminist concepts are given new subversive meanings.

Originality/value

Whereas existing studies have focused on how elite women’s promotion of confidence sustains the status quo, this study shifts the research gaze to the resistance realised through rearticulations of confidence, illustrating how women-in-leadership research can advance feminist theorising without vilifying senior women even as they participate in postfeminist logics of success.
Institutional isomorphism and sustainable HRM adoption: a conceptual framework
Authors: Anlesinya Alex , Amponsah-Tawiah Kwesi , Dartey-Baah Kwasi , Adeti Sampson Kudjo , Brefo-Manuh Adwoa Benewaa
Published: August 2022

Purpose

There is a major lacuna in sustainable human resource management (HRM) research regarding the theoretical context of its adoption or implementation. Consequently, the purpose of this study is to examine the relative influence and interactive effects of different levels of institutional isomorphisms on sustainable HRM adoption.

Design/methodology/approach

This study applies the conceptual method and anchors the discussions on the institutional theory and the extant literature on the antecedents of sustainable HRM implementation.

Findings

Internal and external institutional isomorphisms will have complementary (synergies) or substitution (trade-offs) effects on sustainable HRM adoption. Furthermore, external institutional isomorphic pressures related to societal values and culture and stakeholders’ sustainability demands are likely to have greater influence on sustainable HRM implementation relative to the internal institutional isomorphic pressures related to managerial sustainability values and attitudes; sustainability-related HRM competencies; resource availability; and perceived sustainability benefits.

Originality/value

This study proposes a novel multi-level conceptual model on the implementation context of sustainable HRM for testing empirically. Furthermore, this study generates insight on how different levels of institutional isomorphic pressures relatively and interactively (synergies versus trade-offs) affect sustainable HRM adoption. This is significant because there is a view that HRM as a discipline is theoretically weak. Although the field has advanced theoretically, one of the areas that need more theorisation is the context of HRM. Hence, this study advances the theoretical context of sustainable HRM implementation through the perspectives of the institutional theory.
Emergency medical services on the frontlines of the opioid overdose crisis: the role of mental health, substance use, and burnout
Authors: Beaugard Corinne A. , Hruschak Valerie , Lee Christina S. , Swab Jenifer , Roth Sheila , Rosen Daniel
Published: August 2022

Purpose

Emergency medical service (EMS) workers are at risk for burnout related to the opioid overdose crisis because they are frequently present during overdose events. The study’s aims were twofold: 1) to determine whether variables related to the opioid crisis were associated with burnout and 2) to explore the relationship between mental health, sleep, substance use, social support, and attitudes about working during the opioid overdose crisis with burnout.

Design/methodology/approach

In a cross-sectional web-based study, surveys were distributed by supervisors to EMS workers in Pennsylvania (winter 2018). Participants (n = 214) completed measures on burnout, social support, mental health, substance use, and sleep quality and reported their frequency of naloxone administration and their attitudes about working during the opioid overdose crisis. Bivariate and multivariable analyses were run to determine correlates of burnout.

Findings

The sample was 65.4% male, 91.5% white, and 43% were between 36–55 years old. In the regression model (n = 177), depression, anxiety, post-traumatic stress disorder (PTSD), sleep, attitudes about working during the opioid crisis, cannabis use, social support, age, hours worked each week, and frequency of naloxone administration were significantly correlated with burnout.

Originality/value

This study contributes to the emergent literature on burnout and EMS professionals during the opioid overdose crisis by finding that attitudes about working during the opioid overdose crisis are correlated with burnout. While the relationship should be explored in future research, the authors believe that interventions to prevent EMS burnout could incorporate training to improve attitudes about supporting individuals during overdose events.
3D SLAM based on NDT matching and ground constraints for ground robots in complex environments
Authors: Jiang Yi , Wang Ting , Shao Shiliang , Wang Lebing
Published: August 2022

Purpose

In large-scale environments and unstructured scenarios, the accuracy and robustness of traditional light detection and ranging (LiDAR) simultaneous localization and mapping (SLAM) algorithms are reduced, and the algorithms might even be completely ineffective. To overcome these problems, this study aims to propose a 3D LiDAR SLAM method for ground-based mobile robots, which uses a 3D LiDAR fusion inertial measurement unit (IMU) to establish an environment map and realize real-time localization.

Design/methodology/approach

First, we use a normal distributions transform (NDT) algorithm based on a local map with a corresponding motion prediction model for point cloud registration in the front-end. Next, point cloud features are tightly coupled with IMU angle constraints, ground constraints and gravity constraints for graph-based optimization in the back-end. Subsequently, the cumulative error is reduced by adding loop closure detection.

Findings

The algorithm is tested using a public data set containing indoor and outdoor scenarios. The results confirm that the proposed algorithm has high accuracy and robustness.

Originality/value

To improve the accuracy and robustness of SLAM, this method proposed in the paper introduced the NDT algorithm in the front-end and designed ground constraints and gravity constraints in the back-end. The proposed method has a satisfactory performance when applied to ground-based mobile robots in complex environments experiments.
Consequences of Russian invasion on Ukraine: evidence from foreign exchange rates
Authors: Aliu Florin , Hašková Simona , Bajra Ujkan Q.
Published: August 2022

Purpose

The stability of exchange rates facilitates international trade, diminishes portfolio risk, and ensures that economic policies are effective. The war in Ukraine is showing that the European financial system is still fragile to external shocks. This paper examines the consequences of the Russian invasion of Ukraine on five Euro exchange rates. The final goal is to empirically test whether the ruble caused the euro to depreciate with the Russian invasion of Ukraine.

Design/methodology/approach

The exchange rates analyzed are Euro/Russian Ruble, Euro/US Dollar, Euro/Japanese Yen, Euro/British Pound, and Euro/Chinese Yuan. The data collected are daily and cover the period from November 1, 2021, to May 1, 2022. In this context, the changes in the FX rates reflect two months of the ongoing war in Ukraine. The FX rates used in the study contain 137 observations indicating five months of daily series.

Findings

The results from impulse response function, variance decomposition, SVAR, and VECM indicate that the EUR/RUB significantly influenced the Euro devaluation. On the other side, the FX rates used in our work altogether hold long-run cointegration. The situation is different in the short run, where only EUR/RUB, EUR/USD, and EUR/CNY possess significant relations with other parities.

Originality/value

The Ruble is not among hard currencies, but its position strengthened during this period due to the importance of Russian gas to the Eurozone. The results indicate that even weak currencies can be influential depending on the geopolitical and economic situation. To this end, diversification remains a valid concept not only in portfolio construction but also for the preservation of the national economy.