bluuebunny/crossref_metadata_2025 huggingface dataset:
Directed evolution of mesophilic HNA polymerases providing insight into DNA polymerase mechanisms
Authors: Handal-Marquez Paola , Torres Leticia L. , Pinheiro Vitor B.
Published: November 2022

Detailed biochemical characterization of natural and mutant enzymes provides essential clues to understand their mechanisms. There are, however, limits to the throughput of such approaches and they are not without errors. DNA polymerases have benefited from over 50 years of detailed study and remain not fully understood. As such, methods that allow high-throughput interrogation of variants, and viable analysis pipelines to identify relevant variants, become an important tool to accelerate research. Using the DNA polymerase fromB. subtilisPhi29 bacteriophage as a model, we demonstrate how coupling focused libraries, selection and deep sequencing can be combined to identify variants of interest for characterization. As selection parameters can be controlled, different areas of an enzyme’s mechanism can be explored. Focusing selection on faster HNA (1,5-anhydrohexitol nucleic acid) synthesis, we identified P562del as a variant of interest, enriching significantly between rounds. Characterization confirmed its faster HNA synthesis initiation but lower processivity and fidelity. P562 is a non-conserved residue, unlikely to be selected by more traditional approaches, but its deletion recapitulates knowledge on how Phi29 exonuclease, thumb and TPR2 subdomains regulate polymerase function. Our data further support the hypothesis that Phi29 shows a two-state binding to its template: a fast non-replicative complex that transitions to a replication-competent state.
FIRST INSIGHTS IN A NON-RODENT MODEL SPECIES OF THE OLFACTORY LIMBUS. THE RED FOX (Vulpes vulpes) AS A CASE IN POINT
Authors: Ortiz-Leal Irene , Torres Mateo V. , Vargas-Barroso Víctor , Fidalgo Luis Eusebio , López-Beceiro Ana , Larriva-Sahd Jorge , Sanchez-Quinteiro Pablo
Published: November 2022

The mammalian olfactory systems can be divided into several subsystems based on the anatomical location of their neuroreceptor cells and the family of receptors they express. The more in depth studied systems are the main olfactory system and the vomeronasal system, whose first integrative enters are the main and the accessory olfactory bulb, respectively. In addition, there is a range of olfactory subsystems which converge to the transition zone located between the main olfactory bulb and the accessory olfactory bulb., which has been termed as olfactory limbus (OL) and includes specialized glomeruli which receive uncanonical sensory afferences and interact with the MOB and AOB. Beyond the laboratory rodents, there is a lack of information regarding the olfactory subsystems of carnivores. We have focused on the specific study of the olfactory limbus of the fox, performing serial histological sections, general and specific histological stainings, including both double and simple immunohistochemical and lectin-histochemical labeling techniques. As a result, we have been able to determine that the OL of the fox shows an uncommon development with a high degree of development and complexity. This makes this species a novel mammalian model that could provide a wider understanding of non-canonical pathways involved in the processing of chemosensory cues.
Cerebellar granule neurons induce Cyclin D1 in an early stage of Huntington’s disease
Authors: Bauer Susanne , Chen Chwen-Yu , Jonson Maria , Kaczmarczyk Lech , Magadi Srivathsa , Jackson Walker S.
Published: November 2022

Although Huntington’s disease (HD) is predominantly defined by selective vulnerability of striatal projection neurons, there is increasing evidence that cerebellar degeneration modulates clinical symptoms. However, little is known about cell type-specific responses of cerebellar neurons in HD. To dissect early disease mechanisms in the cerebellum and cerebrum, we analyzed translatomes of neuronal cell types from both regions in a new HD mouse model. For this, HdhQ200 knock-in mice were backcrossed with the calm, 129S4 strain, to constrain experimental noise caused by variable hyperactivity of mice in a C57BL/6 background. Behavioral and neuropathological characterization showed that these S4-HdhQ200 mice had very mild behavioral abnormalities starting around 12 months of age that remained mild up to 18 months. By 9 months, we observed abundant Huntingtin-positive neuronal intranuclear inclusions (NIIs) in the striatum and cerebellum. The translatome analysis of GABAergic cells of the cerebrum further confirmed changes typical of HD-induced striatal pathology. Surprisingly, we observed the strongest response with 626 differentially expressed genes in glutamatergic neurons of the cerebellum, a population consisting predominantly of granule cells, a cell type commonly considered disease-resistant. Our findings suggest vesicular fusion and exocytosis, as well as differentiation-related pathways are affected. Furthermore, increased expression of cyclin D1 (Ccnd1) in the granular layer and upregulated expression of polycomb group complex protein genes and cell cycle regulatorsCbx2, Cbx4andCbx8point to a putative role of aberrant cell cycle regulation in cerebellar granule cells in early disease.
Shigellaserotypes associated with carriage in humans establish persistent infection in zebrafish
Authors: Torraca Vincenzo , Brokatzky Dominik , Miles Sydney L. , Chong Charlotte E. , De Silva P. Malaka , Baker Stephen , Jenkins Claire , Holt Kathryn E. , Baker Kate S. , Mostowy Serge
Published: November 2022

Shigellarepresents a paraphyletic group of human-adaptedEscherichia colilineages that converged towards the same enteropathogenic pathovar. In low-income countries,Shigellais typically transmitted by ingestion of contaminated water and food, while in high-income countries sexual transmission among men who have sex with men (MSM) is the dominant route of transmission. Although more than 40 different serotypes ofShigellahave been reported globally, within the MSM community the majority of reported cases are attributed to threeShigellaserotypes: theShigella sonneiunique serotype (Ss) and theShigella flexneriserotypes 2a and 3a. Here, using a zebrafish infection model, we demonstrate thatShigellacan establish persistent infectionin vivo. In this case, bacteria are not cleared by the host immune system and become tolerant to therapeutic doses of antibiotics. We show that persistence is dependent on theShigellaO-Antigen, a key constituent of the bacterial cell surface and determinant of serotype classification. Representative isolates of threeShigellaserotypes associated with global dissemination and MSM transmission (S. sonneiSs,S. flexneri2a and 3a) all persist in zebrafish, while a serotype not associated with MSM transmission (S. flexneri5a) does not. Strikingly,Shigellaserotypes which establish persistent infection fail to promote macrophage cell deathin vivo. We conclude that zebrafish can be a valuable platform to illuminate host and pathogen factors underlying the establishment of persistent infection withShigellain humans.

Highlights

Shigellacan establish persistent infection in zebrafish

Establishment of persistent infectionin vivodepends onShigellaserotype

The same serotypes establishing persistent infection in zebrafish are prevalent in a patient group in whom persistent infection is observed

Shigellaserotypes which establish persistent infection fail to promote macrophage cell deathin vivo

In Brief

In high-income countries, sexual transmission among men who have sex with men (MSM) is the dominant cause of domesticShigellatransmission. Torracaet al. discover that three serotypes ofShigellaassociated with MSM transmission also persist in zebrafish. These results indicate thatShigellaserotypes associated with MSM transmission can establish carriage in the host, and highlight the use of zebrafish infection to studyShigellapersistent infection in humans.
Multilevel Modelling of Gaze from Hearing-impaired Listeners following a Realistic Conversation
Authors: Shiell Martha M. , Høy-Christensen Jeppe , Skoglund Martin A. , Keidser Gitte , Zaar Johannes , Rotger-Griful Sergi
Published: November 2022

Purpose

There is a need for outcome measures that predict real-world communication abilities in hearing-impaired people. We outline a potential method for this and use it to answer the question of when, and how much, hearing-impaired listeners look towards a new talker in a conversation.

Method

Twenty-two older hearing-impaired adults followed a pre-recorded two-person audiovisual conversation in the presence of babble noise. We compared their eye-gaze direction to the conversation in two multilevel logistic regression (MLR) analyses. First, we split the conversation into events classified by the number of active talkers within a turn or a transition, and we tested if these predicted the listener’s gaze. Second, we mapped the odds that a listener gazed towards a new talker over time during a conversation transition.

Results

We found no evidence that our conversation events predicted changes in the listener’s gaze, but the listener’s gaze towards the new talker during a silent-transition was predicted by time: The odds of looking at the new talker increased in an s-shaped curve from at least 0.4 seconds before to 1 second after the onset of the new talker’s speech. A comparison of models with different random effects indicated that more variance was explained by differences between individual conversation events than by differences between individual listeners.

Conclusion

MLR modelling of eye-gaze during talker transitions is a promising approach to study a listener’s perception of realistic conversation. Our experience provides insight to guide future research with this method.
PathExpSurv: Pathway Expansion for Explainable Survival Analysis and Disease Gene Discovery
Authors: Hou Zhichao , Leng Jiacheng , Yu Jiating , Xia Zheng , Wu Ling-Yun
Published: November 2022

Motivation

In the field of biology and medicine, the interpretability and accuracy are both important when designing predictive models. The interpretability of many machine learning models such as neural networks is still a challenge. Recently, many researchers utilized prior information such as biological pathways to develop bioinformatics methods based on neural networks, so that the prior information can provide some insights and interpretability for the models. However, the prior biological knowledge may be incomplete and there still exists some unknown information to be explored.

Results

We proposed a novel method, named PathExpSurv, to gain an insight into the black-box model of neural network for cancer survival analysis. We demonstrated that PathExpSurv could not only incorporate the known prior information into the model, but also explore the unknown possible expansion to the existing pathways. We performed downstream analyses based on the expanded pathways and successfully identified some key genes associated with the diseases and original pathways.

Availability

Python source code of PathExpSurv is freely available athttps://github.com/Wu-Lab/PathExpSurv.

Contact:

lywu@amss.ac.cn

Supplementary information

Supplementary data are available atBioinformaticsonline.
Dynamic changes in the transcriptome of oocytes during adolescent-onset PCOS in mice
Authors: Danfeng Du , Ke Deng , Dengxuan Fan , Congjian Xu
Published: November 2022

(1) Background: This study aimed to explore temporal changes in the transcriptome of oocytes in an adolescent-onset polycystic ovarian syndrome (PCOS) mouse model. (2) Methods: An adolescent-onset PCOS mouse model was established using DHEA. Genes with a similar expression trend over time were identified using trend analysis. KEGG pathway enrichment analysis and gene regulatory network diagrams were examined for signaling pathways to identify potential hub genes related to the pathogenesis of PCOS. (3) Results: Four main trends of gene expression were extracted, of which six combinations of Venn diagrams were generated. Differentially expressed genes were mainly enriched in oxidative phosphorylation, cell cycle, P53 signaling pathway. Cell cycle-related genes (Skp1, Ccnb1, Orc1 and 5, Wee2, Mapk3, Cdc20) were abnormally down-regulated in the DHEA group. Ptges3 was the top1 DEGs at the initial stage of PCOS modeling. (4) Conclusion: This study provides a novel insight into the altered transcriptome of oocytes from PCOS mice. mtDNA-related genes and Cell cycle-related genes play the most important role in the development of PCOS. Ptges3 was the one of the top DEGs which was up-regulated in DHEA group at the initial stage of modeling, which suggested it may play an important role in the early stage of PCOS.
Volumetric microscopy of CD9 and CD63 reveals distinct subpopulations and novel structures of extracellular vesiclesin situin triple negative breast cancer cells
Authors: White Elizabeth D. , Walker Nykia D. , Yi Hannah , Dinner Aaron R. , Scherer Norbert F. , Rosner Marsha Rich
Published: November 2022

Secreted extracellular vesicles (EVs) are now known to play multifaceted roles in biological processes such as immune responses and cancer. The two primary classes of EVs are defined in terms of their origins: exosomes are derived from the endosomal pathway while microvesicles (ectosomes) bud from the cell membrane. However, it remains unclear whether the contents, sizes, and localizations of subpopulations of EVs can be used to associate them with the two primary classes. Here, we use confocal microscopy and high-resolution volumetric imaging to study intracellular localization of the EV markers CD9 and CD63 prior to EV export from cells. We find significantly different spatial expression of CD9 and CD63. CD9 is primarily localized in microvesicles, while CD63 is detected exclusively in exosomes. We also observe structures in which CD63 forms a shell that encapsulates CD9 and interpret them to be multi-vesicular bodies. The morphology and location within the endoplasmic reticulum of these shell-like structures are consistent with a role in differential sorting and export of exosomes and microvesicles. Ourin situimaging allows unambiguous identification and tracking of EVs from their points of origin to cell export, and suggest that CD9 and CD63 can be used as biomarkers to differentiate subpopulations of EVs.
Analysis of alternative polyadenylation from long-read or short-read RNA-seq with LAPA
Authors: Çelik Muhammed Hasan , Mortazavi Ali
Published: November 2022

Motivation

Alternative polyadenylation (APA) is a major mechanism that increases transcriptional diversity and regulates mRNA abundance. Existing computational tools to analyze APA have low precision because these tools are designed for short-read RNA-seq, which is a suboptimal data source to study APA. Long-read RNA-seq (LR-RNA-seq) accurately detects complete transcript isoforms with poly(A)-tails, providing an ideal data source to study APA. However, current computational tools are incompatible with LR-RNA-seq.

Results

Here, we introduce LAPA, a computational toolkit to study alternative polyadenylation (APA) from diverse data sources such as LR-RNA-seq and short-read 3’ sequencing (3’-seq). LAPA counts and clusters reads with poly(A)-tail, then performs peak-calling to detect poly(A)-site in a data source agnostic manner. The resulting peaks are annotated based on genomics features and regulatory sequence elements such as presence of a poly(A)-signal. Finally, LAPA can perform robust statistical testing and multiple testing correction to detect differential APA.

We analyzed ENCODE LR-RNA-seq data from human WTC11, mouse C2C12 myoblast, and C2C12-derived differentiated myotube cells using LAPA. Comparing LR-RNA-seq from different platforms and library preparation methods against 3’-seq shows that LR-RNA-seq detects poly(A)-sites with a performance of 75% precision at 57% recall. Moreover, LAPA consistently improved TES validation by at least 25% over the baseline transcriptome annotation generated by TALON, independent of protocol or platform. Differential APA analysis detected 788 statistically significant genes with unique polyadenylation signatures between undifferentiated myoblast and differentiated myotube cells. Among these genes, 3’ UTR elongation is significantly associated with higher expression, while shortening is linked with lower expression. This analysis reveals a link between cell state/identity and APA. Overall, our results show that LR-RNA-seq is a reliable data source for the study of post-transcriptional regulation by providing precise information about alternative polyadenylation.

Availability

LAPA is publicly available athttps://github.com/mortazavilab/lapaand PyPI.

Contact::ali.mortazavi@uci.edu
ToDD: Topological Compound Fingerprinting in Computer-Aided Drug Discovery
Authors: Demir Andac , Coskunuzer Baris , Segovia-Dominguez Ignacio , Chen Yuzhou , Gel Yulia , Kiziltan Bulent
Published: November 2022

In computer-aided drug discovery (CADD), virtual screening (VS) is used for identifying the drug candidates that are most likely to bind to a molecular target in a large library of compounds. Most VS methods to date have focused on using canonical compound representations (e.g., SMILES strings, Morgan fingerprints) or generating alternative fingerprints of the compounds by training progressively more complex variational autoencoders (VAEs) and graph neural networks (GNNs). Although VAEs and GNNs led to significant improvements in VS performance, these methods suffer from reduced performance when scaling to large virtual compound datasets. The performance of these methods has shown only incremental improvements in the past few years. To address this problem, we developed a novel method using multiparameter persistence (MP) homology that produces topological fingerprints of the compounds as multidimensional vectors. Our primary contribution is framing the VS process as a new topology-based graph ranking problem by partitioning a compound into chemical substructures informed by the periodic properties of its atoms and extracting their persistent homology features at multiple resolution levels. We show that the margin loss fine-tuning of pretrained Triplet networks attains highly competitive results in differentiating between compounds in the embedding space and ranking their likelihood of becoming effective drug candidates. We further establish theoretical guarantees for the stability properties of our proposed MP signatures, and demonstrate that our models, enhanced by the MP signatures, outperform state-of-the-art methods on benchmark datasets by a wide and highly statistically significant margin (e.g., 93% gain for Cleves-Jain and 54% gain for DUD-E Diverse dataset).
Density-dependent selection during range expansion affects expansion load in life-history traits
Authors: Urquhart-Cronish Mackenzie , Angert Amy L. , Otto Sarah P. , MacPherson Ailene
Published: November 2022

Models of range expansion have independently explored fitness consequences of life-history trait evolution and increased rates of genetic drift—or “allele surfing”—during spatial spread, but no previous model has examined the interactions between these two processes. Here, we explore an ecologically complex range expansion scenario that combines density-dependent selection with allele surfing, using spatially explicit simulations to asses the genetic and fitness consequences of density-dependent selection on the evolution of life-history traits. We demonstrate that density-dependent selection on the range edge acts differently depending on the life-history trait and can either diminish or enhance allele surfing. Specifically, we show that selection on the range edge is always weaker at sites affecting competitive ability (K-selected traits) than intrinsic growth rate ((r-selected traits). We then link differences in the frequency of deleterious mutations to differences in the efficacy of selection and rate of mutation accumulation across distinct life-history traits. Finally, we demonstrate the fitness consequences of accumulated deleterious mutations for different life-history traits are related to the population density in which they are expressed. Our work highlights the complex relationship between ecology and expressed genetic load, which will be important to consider when interpreting both experimental and field studies of range expansion.
Translational fusion of terpene synthases enhances metabolic flux by increasing protein stability
Authors: Cheah Li Chen , Liu Lian , Stark Terra , Plan Manuel R. , Peng Bingyin , Lu Zeyu , Schenk Gerhard , Sainsbury Frank , Vickers Claudia E.
Published: November 2022

The end-to-end fusion of enzymes that catalyse successive steps in a reaction pathway is a metabolic engineering strategy that has been successfully applied in a variety of pathways and is particularly common in terpene bioproduction. Despite its popularity, limited work has been done to interrogate the mechanism of metabolic enhancement from enzyme fusion. We observed a remarkable >110-fold improvement in nerolidol production upon translational fusion of nerolidol synthase (a sesquiterpene synthase) to farnesyl diphosphate synthase. This delivered a titre increase from 29.6 mg/L up to 4.2 g/L nerolidol in a single engineering step. Whole-cell proteomic analysis revealed that nerolidol synthase levels in the fusion strains were greatly elevated compared to the non-fusion control. Similarly, the fusion of nerolidol synthase to non-catalytic domains also produced comparable increases in titre, which coincided with improved enzyme expression. When farnesyl diphosphate synthase was fused to other terpene synthases, we observed more modest improvements in terpene titre (1.9- and 3.8-fold), which corresponds to increases of a similar magnitude in terpene synthase expression. Therefore, increasedin vivoenzyme levels – resulting from improved expression and/or stability – is likely to be a major driver of catalytic enhancement from enzyme fusion.
Schlafen 12 restricts HIV-1 latency reversal by a codon-usage dependent post-transcriptional block in CD4+ T cells
Authors: Kobayashi-Ishihara Mie , Smutná Katarína Frazão , Alonso Florencia E. , Argilaguet Jordi , Esteve-Codina Anna , Geiger Kerstin , Genescà Meritxell , Grau-Expósito Judith , Duran-Castells Clara , Rogenmoser Selina , Böttcher René , Jungfleisch Jennifer , Oliva Baldomero , Martinez Javier P. , Li Manqing , David Michael , Yamagishi Makoto , Ruiz-Riol Marta , Brander Christian , Tsunetsugu-Yokota Yasuko , Buzon Maria J. , Díez Juana , Meyerhans Andreas
Published: November 2022

Latency is a major barrier towards virus elimination in HIV-1-infected individuals. Yet, the mechanisms that contribute to the maintenance of HIV-1 latency are incompletely understood. Here we describe the Schlafen 12 protein (SLFN12) as an HIV-1 restriction factor that establishes a post-transcriptional block in HIV-1-infected cells and thereby inhibits HIV-1 replication and virus reactivation from latently infected cells. The inhibitory activity is dependent on the HIV-1 codon usage and on the SLFN12 RNase active sites. Within HIV-1- infected individuals,SLFN12expression in PBMCs correlated with HIV-1 plasma viral loads and proviral loads suggesting a link with the general activation of the immune system. Using an RNA FISH-Flow HIV-1 reactivation assay, we demonstrate that SLFN12 expression is enriched in infected cells positive for HIV-1 transcripts but negative for HIV-1 proteins. Thus, codon-usage dependent translation inhibition of HIV-1 proteins participates in HIV-1 latency and can restrict the amount of virus release after latency reversal.
Lorentz factor for time-of-flight neutron Bragg and total scattering
Authors: Zhang Yuanpeng , Liu Jue , Tucker Matthew G.
Published: November 2022

The three fundamental origins of the Lorentz factor for neutron time-of-flight powder diffraction are revisited. A detailed derivation of the Lorentz factor is presented in the context of diffuse scattering modelling in reciprocal space when perfect periodicity is assumed, and the total scattering pattern is constructed in its discrete form – the factor in this case becomes 1/Q
2 (or d
2). Discussion is also presented with respect to practical data reduction where a vanadium measurement is usually taken as the normalization factor (to account for various factors such as detector efficiency), and it is shown that the existence of the Lorentz factor is independent of such a normalization process.
Calculating a life: classification, valuation and compensation in the British abolition of slavery
Authors: Jeacle Ingrid
Published: November 2022

Purpose

This paper examines the calculative practices used by the Slave Compensation Commission to value a slave for the purposes of compensating slave owners on the abolishment of slavery across the British colonies in 1833. It contributes to accounting research in the field of valuation, particularly to understanding the practices of valuing human life.

Design/methodology/approach

The methodology is primarily archival and draws on the records of the Slave Compensation Commission held at the British National Archives (Kew).

Findings

The paper makes two contributions to the literature. Firstly, it contributes to the valuation studies literature by suggesting the significance of understanding the practice of valuation as a product of the dynamics of strategic action fields (Fligstein and McAdam, 2012). Secondly, it contributes to the theory of strategic action fields by revealing the role of calculative technologies in supporting the organizational apparatus of valuation within the Slave Compensation Commission, and therefore suggests the powerful role of accounting in stabilizing a strategic action field.

Originality/value

The paper provides novel insights into the monetary commensuration of life and the role of calculative technologies in that valuation process.
Crowdfunding and innovation: a bibliometric review and future research agenda
Authors: Bargoni Augusto , Ferraris Alberto , Bresciani Stefano , Camilleri Mark Anthony
Published: November 2022

Purpose

This article aims to investigate the status of and the trends in the intertwining of crowdfunding and innovation literature by identifying, evaluating and synthesizing the findings from previous research. This paper provides a bibliometric meta-analysis of the already substantial and growing literature on innovation and crowdfunding research.

Design/methodology/approach

Using a bibliometric approach, this research scrutinizes all articles that include terms related to “crowdfunding” and “innovation” (in their title, abstract or keywords) in Elsevier’s Scopus database. VosViewer and Bibliometrix package in R have been used to analyse 150 articles.

Findings

The results suggest that there are three main research clusters in the innovation and crowdfunding literature. The first cluster highlights the role of crowdfunding in fostering radical and incremental innovation. The second cluster focuses on the concept of openness and its effect on innovation in crowdfunding campaigns, while the third cluster explains the role of platforms’ innovation in crowdfunding success.

Originality/value

Taking a holistic perspective, this contribution advances new knowledge on the intertwining of crowdfunding and innovation research fields. It implies that crowdfunding is facilitating the flow of knowledge between different stakeholders, including project initiators and crowd investors, among others, as they all benefit from open innovation platforms.
Indoor environmental quality (IEQ) in the home workplace in relation to mental well-being
Authors: Boegheim Bouke , Appel-Meulenbroek Rianne , Yang Dujuan , Loomans Marcel
Published: November 2022

Purpose

This paper aims to study employee mental health in relation to workplace design and indoor environmental quality (IEQ) when working from home, which has received little attention. The trend toward hybrid working urges for more knowledge.

Design/methodology/approach

Through a mixed data collection method, this study analyzed potential relationships (between mental health, workplace design and IEQ) from information obtained through a cross-sectional survey, repeated point-in-time surveys and desk-based IEQ sensors at home. Data were collected in April 2020 during a national COVID-19 lockdown in The Netherlands amongst 36 subjects. They all worked full time from home in this period and together completed 321 point-in-time surveys. The three data sets were combined and analyzed using bivariate and path analysis.

Findings

Outcomes indicate that subjective and objective IEQ conditions, workplace suitability and distraction affect employee mental health in the home workplace in a similar way as in the office. Being satisfied with the noise level increases concentration, self-reported well-being and engagement. High sound pressure levels (>58 dB) increased tension or nervous feelings.

Originality/value

To the best of the authors’ knowledge, this study is one of the first to explore employee mental health in relation to simultaneously assessed (perceived and measured) multiple IEQ parameters in the home workplace.
Crop diversity and farm income: evidence from a large-scale national survey
Authors: Sehgal Vandana
Published: November 2022

Purpose

This study aims to evaluate the effectiveness of crop diversification in increasing the income of farm households. In addition, this study introduces the impact of natural disasters in the analysis to determine how diversification helps mitigate the negative effect of disasters on farm income. More importantly, the study also analyses the effect of diversification on farm income by farm class to see where the benefits of diversification are concentrated.

Design/methodology/approach

This study uses a linear model, in which agricultural income is expressed as a function of diversification, natural disasters and several control variables. Diversification is measured using the Simpson index of diversification. The linear model is enhanced with the inclusion of an interaction term of natural disasters with the diversification index to shed light on the role of diversification in negating their harmful effect on agricultural income. Finally, to analyze the impact of institutional variables on farm income, the interactions of diversification with irrigation, insurance, usage of technical information and formal training are incorporated in the linear model.

Findings

The study highlights the importance of demographic, farm and institutional variables in raising farm income. The study suggests that an increase in education level, irrigation, usage of technical information and possession of Kisan Credit Card (KCC) have a positive impact on agricultural income. The study reveals that crop diversification has a positive impact on farm income and the benefits of diversification are conditioned by institutional factors. Thus, there is a need for policy intervention to ensure increased irrigation facilities along with extension services to provide information to the farm households. It has been found that small farmers gain more from crop diversification than larger farmers. Furthermore, the results show that natural disasters negatively impact farm income, but their impact can be mitigated by higher levels of diversification.

Originality/value

The results of the study are based on the recent unit-level data from the 77th Round of the National Sample Survey Office survey. The survey covers a large number of farm households and reports information for the year 2018–2019.
Developing cash waqf models for Baitul Maal wat Tamwil as integrated Islamic social and commercial microfinance
Authors: Ascarya Ascarya , Sukmana Raditya , Rahmawati Siti , Masrifah Atika Rukminastiti
Published: November 2022

Purpose

This study aims to develop cash waqf models for Baitul Maal wat Tamwil (BMT), a special Islamic microfinance institution in Indonesia, combining Islamic social finance in Baitul Maal (house of wealth) division and Islamic commercial finance in Baitut Tamwil (house of asset development) division, as integrated Islamic social and commercial microfinance in Indonesia, to achieve triple bottom-line, including outreach, sustainability and welfare impact.

Design/methodology/approach

This study uses Delphi and analytic network process methods, with three groups of relevant respondents, including experts (academic), BMT practitioners and regulators.

Findings

The results show that the best cash waqf model for BMT is “BMT as Nazir (waqf manager) and also as cash waqf receiver Lembaga Keuangan Syariah Penerima Wakaf Uang (LKSPWU)”, followed by “BMT Association as representative Nazir of several certified BMTs”. Moreover, “long-term investment deposit” is the best to account cash waqf in the BMT balance sheet. With regard to financing, the most preferred one is “financing to regular Micro and Small Enterprises” of BMT members.

Research limitations/implications

Having allowed BMT to be Nazir (waqf manager), this research might only benefit Indonesian policymakers, such as the Financial Services Authority and the Ministry of Cooperatives, BMTs and the National Waqf Board. But it may also benefit other countries which have similar characteristics.

Practical implications

BMTs could adopt several alternatives of best models in managing cash waqf most appropriate for their specific conditions.

Social implications

The management of cash waqf by BMT could help the social activities of the Baitul Maal through social cash waqf and, indirectly, by productive cash waqf.

Originality/value

Studies have been limited, and to the best of the authors’ knowledge, there is no specific study discussing the integrated cash waqf model, cash waqf account and cash waqf investment appropriate for BMT.
The relationship between creative developments and place: a position paper
Authors: Afsari Bajestani Sepideh , Stupples Polly , Kiddle Rebecca
Published: November 2022

Purpose

The purpose of this paper is to explore and clarify the relationship between creative developments and the concepts of place and placemaking.

Design/methodology/approach

This paper systematically reviews scholarly literature on the relationship between creative developments and the concepts of place, and critically analyzes the extent to which creative developments acknowledge different aspects of place.

Findings

The findings demonstrate that the relationship between creative development and place is multifaceted, and combines physical, cultural and social aspects of place. However, the literature also calls for the greater valuation of particular facets of place, including the daily experiences of communities and local cultural producers, alongside symbolic and imagined aspects of place, all of which inform either positive or negative perceptions of urban form. In addition, the authors argue that the cultural value of the creative industries needs to be better acknowledged in creative developments, implying support for a range of cultural practitioners.

Research limitations/implications

The authors argue that embracing a more holistic understanding of place in creative development has the potential to minimize the negative impacts sometimes associated with such developments (like gentrification and social displacement) while generating greater social and cultural benefits to people and place. The study findings raise questions that frame a critical research agenda for creative-led developments and creative placemaking in this context.

Originality/value

By examining the broader relationship between creative developments and place and identifying areas neglected by researchers, this research contributes to an articulation of “creative placemaking” that moves creative city policy toward enhancing community development.
House energy efficiency retrofits and loan maturity
Authors: Drivas Kyriakos , Vlamis Prodromos
Published: November 2022

Purpose

The purpose of this study is to examine how households opt for their loan’s duration when it comes to energy efficiency retrofits (EERs). The primary focus is on the time horizon that these types of EERs will provide benefits to the households.

Design/methodology/approach

This study examines the second wave of the largest EER support program in Greece in recent years. The authors exploit an idiosyncrasy of the support program which offered interest-free loans. The baseline sample of this study includes approximately 18,000 households awarded the support and opted for a loan. To provide robustness and complement the analysis, the authors also use data from 38,000 households that were awarded support from the first wave of the EER program.

Findings

This study finds that EER investments that are likely to deliver longer-term benefits, in the form of energy savings, are positively associated with longer duration. This finding implies that households view such EERs as long-term investments that will consistently provide benefits in the future, thereby tolerating a longer period of incurring the inconvenience of paying monthly installments.

Practical implications

This study posits that an EER can be perceived by the household as an investment that saves money in the long term because of more efficient energy use. To this end, the authors bring forward the duration of the benefits accrued to the household as a driving factor to the household’s decision over the length of the loan.

Originality/value

This study expands on prior literature that has focused on consumer and loans for durables (e.g. cars) by examining EERs. However, EERs are different, as they can save households money in future periods. In addition, house EERs are at the forefront of energy policies and the design of future support programs at the epicenter of several initiatives.
Review article: Early steroid administration for traumatic haemorrhagic shock: A systematic review
Authors: Hogarty Joseph P , Jones Morgan E , Jassal Karishma , Hogarty Daniel T , Mitra Biswadev , Udy Andrew A , Fitzgerald Mark C
Published: November 2022

Haemorrhagic shock after trauma is a leading cause of death worldwide, particularly in young individuals. Despite advances in trauma systems and resuscitation strategies, mortality from haemorrhagic shock has not declined over the previous two decades. A proportion of shocked trauma patients may experience a deficiency of cortisol relative to the severity of their injury. The benefit of exogenous steroid administration in patients suffering haemorrhagic shock as a result of injury is unclear. A systematic review of four databases (Ovid Medline, Ovid Embase, Cochrane, Scopus) was undertaken. Inclusion and exclusion criteria were pre‐determined and two reviewers independently screened the articles with disagreements arbitrated by a third reviewer. The primary outcome variable was 28‐day mortality. Quality of studies were assessed using the Cochrane‐risk‐of‐bias (RoB 2) tool. Of the 2919 studies yielded by the search strategy, 1274 duplicates were removed and 1645 screened on title and abstract. After the full text of 33 studies were assessed, two articles were included. Both studies were over 30 years old with small numbers of participants and with primary outcomes not including mortality. Of the data available, no statistically significant difference in mortality was detected. Hospital length of stay, reversal of shock or adverse events were not reported. Both studies were at risk of bias. There are no high quality or recent studies in the English literature investigating the use of steroids for haemorrhagic shocked trauma patients. PROSPERO: CRD42021239656.
Target enrichment of long open reading frames and ultraconserved elements to link microevolution and macroevolution in non‐model organisms
Authors: Ortiz‐Sepulveda Claudia M. , Genete Mathieu , Blassiau Christelle , Godé Cécile , Albrecht Christian , Vekemans Xavier , Van Bocxlaer Bert
Published: November 2022

Despite the increasing accessibility of high‐throughput sequencing, obtaining high‐quality genomic data on non‐model organisms without proximate well‐assembled and annotated genomes remains challenging. Here, we describe a workflow that takes advantage of distant genomic resources and ingroup transcriptomes to select and jointly enrich long open reading frames (ORFs) and ultraconserved elements (UCEs) from genomic samples for integrative studies of microevolutionary and macroevolutionary dynamics. This workflow is applied to samples of the African unionid bivalve tribe Coelaturini (Parreysiinae) at basin and continent‐wide scales. Our results indicate that ORFs are efficiently captured without prior identification of intron‐exon boundaries. The enrichment of UCEs was less successful, but nevertheless produced substantial data sets. Exploratory continent‐wide phylogenetic analyses with ORF supercontigs (>515,000 parsimony informative sites) resulted in a fully resolved phylogeny, the backbone of which was also retrieved with UCEs (>11,000 informative sites). Variant calling on ORFs and UCEs of Coelaturini from the Malawi Basin produced ~2000 SNPs per population pair. Estimates of nucleotide diversity and population differentiation were similar for ORFs and UCEs. They were low compared to previous estimates in molluscs, but comparable to those in recently diversifying Malawi cichlids and other taxa at an early stage of speciation. Skimming off‐target sequence data from the same enriched libraries of Coelaturini from the Malawi Basin, we reconstructed the maternally‐inherited mitogenome, which displays the gene order inferred for the most recent common ancestor of Unionidae. Overall, our workflow and results provide exciting perspectives for integrative genomic studies of microevolutionary and macroevolutionary dynamics in non‐model organisms.
Career Concerns and the Dynamics of Electoral Accountability
Authors: Iaryczower Matias , Lopez‐Moctezuma Gabriel , Meirowitz Adam
Published: November 2022

Quantifying the value that legislators give to reelection relative to policy is crucial to understanding electoral accountability. We estimate the preferences for office and policy of members of the U.S. Senate, using a structural approach that exploits variation in polls, position‐taking, and advertising throughout the electoral cycle. We then combine these preference estimates with estimates of the electoral effectiveness of policy moderation and political advertising to quantify electoral accountability in competitive and uncompetitive elections. We find that senators differ markedly in the value they give to securing office relative to policy gains: While over a fourth of senators are highly ideological, a sizable number of senators are willing to make relatively large policy concessions to attain electoral gains. Nevertheless, electoral accountability is only moderate on average, due to the relatively low impact of changes in senators' policy stance on voter support.
Inherited cancer predisposing mutations in patients with therapy‐related myeloid neoplasms
Authors: Shih Andrew J. , Jun Tomi , Skol Andrew D. , Bao Riyue , Huang Lei , Vora Sapana , McNerney Megan E. , Hungate Eric A. , Le Beau Michelle M. , Larson Richard A. , Elliott Aaron , Lu Hsiao‐Mei , Huether Robert , Hernandez Felicia , Stölzel Friedrich , Allan James M. , Onel Kenan
Published: November 2022

Some patients with therapy‐related myeloid neoplasms (t‐MN) may have unsuspected inherited cancer predisposition syndrome (CPS). We propose a set of clinical criteria to identify t‐MN patients with high risk of CPS (HR‐CPS). Among 225 t‐MN patients with an antecedent non‐myeloid malignancy, our clinical criteria identified 52 (23%) HR‐CPS patients. Germline whole‐exome sequencing identified pathogenic or likely pathogenic variants in 10 of 27 HR‐CPS patients compared to 0 of 9 low‐risk CPS patients (37% vs. 0%, p = 0.04). These simple clinical criteria identify t‐MN patients most likely to benefit from genetic testing for inherited CPS.
Arylnitro monocarbonyl curcumin analogues: Synthesis and in vitro antitubercular evaluation
Authors: du Preez Charné , Legoabe Lesetja J. , Jordaan Audrey , Jesumoroti Omobolanle J. , Warner Digby F. , Beteck Richard M.
Published: November 2022

Curcumin is a natural product that has been reported to exhibit myriad pharmacological properties, one of which is antitubercular activity. It demonstrates antitubercular activity by directly inhibiting Mycobacterium tuberculosis (M.tb) and also enhances immune responses that ultimately lead to the elimination of M.tb by macrophages. This natural product is, however, unstable, and several analogues, noticeably monocarbonyl analogues, have been synthesized to overcome this challenge. Curcumin and its monocarbonyl analogues reported so far exhibit moderate antitubercular activity in the range of 7 to 16 μM. Herein, we report a straightforward synthesis of novel monocarbonyl curcumin analogues, their antitubercular activity, and the structure–activity relationship. The hit compound from this study, 3a, exhibits potent MIC90 values in the range of 0.2 to 0.9 μM in both ADC and CAS media.
Effects of Amazonian flying rivers on frog biodiversity and populations in the Atlantic rainforest
Authors: Ferrante Lucas , Getirana Augusto , Baccaro Fabricio Beggiato , Schöngart Jochen , Leonel Ana Cristina Monteiro , Gaiga Renato , Garey Michel Varajão , Fearnside Philip Martin
Published: November 2022

Given the speed at which humans are changing the climate, species with high degrees of endemism may not have time to avoid extinction through adaptation. We investigated through teleconnection analysis the origin of rainfall that determines the phylogenetic diversity of rainforest frogs and the effects of microclimate differences in shaping the morphological traits of isolated populations (which contribute to greater phylogenetic diversity and speciation). We also investigated through teleconnection analysis how deforestation in Amazonia can affect ecosystem services that are fundamental to maintaining the climate of the Atlantic rainforest biodiversity hotspot. Seasonal winds known as flying rivers carry water vapor from Amazonia to the Atlantic Forest, and the breaking of this ecosystem service could lead Atlantic Forest species to population decline and extinction in the short term. Our results suggest that the selection of morphological traits that shape Atlantic Forest frog diversity and their population dynamics are influenced by the Amazonian flying rivers. Our results also suggest that the increases of temperature anomalies in the Atlantic Ocean due to global warming and in the Amazon forest due to deforestation are already breaking this cycle and threaten the biodiversity of the Atlantic Forest hotspot.