bluuebunny/crossref_metadata_2025 huggingface dataset:
Investigating the Catalytic Molecular Details of Malonyl‐thioester Decarboxylating Enzymes
Authors: Stunkard Lee Michael , Lohman Jeremy Michael
Published: November 2023

Decarboxylation reactions release the free energy necessary for carbon‐carbon bond formation in the biosynthesis of polyketides and fatty acids. Ketosynthases from fatty acid and polyketide synthases perform a decarboxylative Claisen‐condensation between an acyl‐thioester intermediate and a malonyl‐derived extender unit. However, the molecular details of decarboxylation and C‐C bond formation is not well understood. We are synthesizing and characterizing non‐hydrolyzable and non‐decarboxylatable substrate mimics to capture intermediate catalytic states via X‐ray crystallography. Capturing the substrate mimics in the active site of ketosynthases will yield insight into the mechanism of decarboxylation and polymerization of the two carbon units. Decarboxylation reactions are essentially non‐reversible and have various possible chemical mechanisms, which makes them difficult to study. Ketosynthases are also challenging to study due to their multiple substrates and need for protein‐protein interactions. Therefore, we have begun characterization of our substrate mimics with simpler systems, such as malonyl‐ and methylmalonyl‐CoA decarboxylases (MCD and MMCD), as a proof of principle. We have successfully crystallized E. coli MMCD and the bifunctional acyltransferase/decarboxylase, LnmK, with our substrate mimics. Our substrate mimics preserve the thioester carbonyl as a thioester, ester or amide and have a nitro or sulfonate moiety in place of the carboxylate. Structures of MMCD and LnmK with multiple bound substrate mimics reveals mechanistic insight into decarboxylation. While MMCD and LnmK have no sequence homology to ketosynthases, this study reveals that our substrate mimics indeed inhibit decarboxylation reactions. Therefore, we are beginning to apply this concept to ketosynthases from type III polyketide synthases.

Support or Funding Information

Funding provided by the Department of Biochemistry at Purdue University
How strong is enemy release? A systematic compilation across taxa and approaches
Authors: Zeng Karen , Schembri Jess , Slavich Eve , Moles Angela T.
Published: November 2023

The enemy release hypothesis posits that introduced species escape some of their predators, pathogens and parasites when they move to a new range. We used a systematic review to compile data from 691 quantifications of enemy release spanning plants, animals and algae in aquatic and terrestrial systems worldwide. Data from 311 biogeographic contrasts (between home and new range) revealed that on average, a species experience only 30% as much enemy pressure in their introduced range as they experience in their native range. In contrast, data from 380 community contrasts (between native and introduced species) revealed that introduced species experience on average 57% of the enemy pressure that their native congeners endure. Interestingly, one third (36%) of contrasts showed higher, rather than lower, enemy pressure on the introduced population. Enemy release was consistently strong in contrasts of the diversity of enemies, intermediate in contrasts comparing enemy damage, and not significant in contrasts of host fitness, suggesting that while introduced populations are attacked by fewer enemies, this does not always result in higher fitness. We also found that enemy release was higher in molluscs and fish but lower in insects and algae, indicating that certain taxa may be favoured by enemy release. We hope that an improved understanding of the extent to which introduced species are released from enemy pressures will help managers to identify good opportunities for biocontrol, and to understand the factors likely to be affecting the success of invasive species.
Development and validation of a pharmacogenomics reporting workflow based on the Illumina Global Screening Array chip
Authors: Gan Pamela , Hajis Muhammad Irfan bin , Yumna Mazaya , Haruman Jessline , Matoha Husnul Khotimah , Wahyudi Dian Tri , Silalahi Santha , Oktariani Dwi Rizky , Dela Fitria , Annisa Tazkia , Pitaloka Tessalonika Damaris Ayu , Adhiwijaya Priscilla Klaresza , Pauzi Rizqi Yanuar , Hertanto Robby , Kumaheri Meutia Ayuputeri , Sani Levana , Irwanto Astrid , Pradipta Ariel , Chomchopbun Kamonlawan , Porta Mar Gonzalez
Published: November 2023

Background

Microarrays are a well-established and widely adopted technology capable of interrogating hundreds of thousands of loci across the human genome. Combined with imputation to cover common variants not included in the chip design, they offer a cost-effective solution for large-scale genetic studies. Beyond research applications, this technology can be applied for testing pharmacogenomics, nutrigenetics, and complex disease risk prediction.

However, establishing clinical reporting workflows requires a thorough evaluation of the assay’s performance, which is achieved through validation studies. In this study, we performed pre-clinical validation of a genetic testing workflow based on the Illumina Global Screening Array for 25 pharmacogenomic-related genes.

Methods

To evaluate the accuracy of our workflow, we conducted multiple pre-clinical validation studies. Here, we present the results of accuracy and precision assessments, involving a total of 73 cell lines. These assessments encompass reference materials from the Genome-In-A-Bottle (GIAB), the Genetic Testing Reference Material Coordination Program (GeT-RM) projects, as well as additional samples from the 1000 Genomes project (1KGP). We conducted an accuracy assessment of genotype calls for target loci in each indication against established truth sets.

Results

In our per-sample analysis, we observed a mean analytical sensitivity of 99.39% and specificity 99.98%. We further assessed the accuracy of star-allele calls by relying on established diplotypes in the GeT-RM catalogue or calls made based on 1KGP genotyping. On average, we detected a diplotype concordance rate of 96.47% across 14 pharmacogenomic-related genes with star allele-calls. Lastly, we evaluated the reproducibility of our findings across replicates and observed 99.48% diplotype and 100 % phenotype inter-run concordance.

Conclusion

Our comprehensive validation study demonstrates the robustness and reliability of the developed workflow, supporting its readiness for further development for applied testing.
Genomic-guided conservation actions to restore the most endangered conifer in the Mediterranean Basin
Authors: del Valle José Carlos , Arista Montserrat , Benítez-Benítez Carmen , Ortiz Pedro Luis , Jiménez-López Francisco J. , Terrab Anass , Balao Francisco
Published: November 2023

Species with extremely small population sizes are critically endangered due to reduced genetic diversity, increased inbreeding, and the added threat of hybridization. Genomic tools significantly advance conservation by revealing genetic insights into endangered species, notably in monitoring frameworks. Sicilian fir is the most endangered conifer in Europe with only 30 adult trees spread across an 84-hectare area. Using 20,824 SNPs from RAD-seq employing the silver fir genome assembly and a custom 120 SNP-array, we evaluated genetic diversity, mating patterns, and effective population size in adult trees, 118 natural seedlings, and 2,064 nursery seedlings from past conservation actions. We assessed introgression from neighboring non-native fir plantations and established an intra-population assisted gene flow program selecting the most genetically dissimilar individuals and investigating the outcome through simulations. Genomic analysis unveiled significant genetic diversity among adult Sicilian firs, comparable to non-endangered Mediterranean firs with larger populations. However, the genetic diversity of the forthcoming generation declined due to high self-fertilization, leading to marked inbreeding (Fis = 0.38) and an alarmingly low effective population size (Ne = 6). Nursery seedling monitoring revealed similar selfing rates but significant introgression (∼50%) from non-native firs. Although intra-population assisted gene flow could help to mitigate genetic loss, it may not alleviate the species vulnerability to imminent environmental challenges, perpetuating the risk of an extinction vortex. Hence, investigating the impact of Sicilian fir population decline and selfing on inbreeding depression, along with exploring the potential of hybrids for genetic load alleviation and future adaptation, is crucial for effective conservation strategies. This study stands as a compelling model for guiding conservation strategies in similarly imperiled species characterized by extremely small populations.
Genomic reconstruction of the successful establishment of a feralized bovine population on the subantarctic island of Amsterdam
Authors: Gautier Mathieu , Micol Thierry , Camus Louise , Moazami-Goudarzi Katayoun , Naves Michel , Guéret Elise , Engelen Stefan , Colas François , Flori Laurence , Druet Tom
Published: November 2023

The feral cattle of the subantarctic island of Amsterdam provide an outstanding case study of a large mammalian population that was established by a handful of founders and thrived within a few generations in a seemingly inhospitable environment. Here, we investigated the genetic history and composition of this population using genotyping and sequencing data. Our inference showed an intense but brief founding bottleneck around the late 19thcentury and revealed contributions from European taurine and Indian Ocean zebu in the founder ancestry. Comparative analysis of whole genome sequences further revealed a moderate reduction in genetic diversity despite high levels of inbreeding. The brief and intense bottleneck was associated with high levels of drift, a flattening of the site frequency spectrum and a slight relaxation of purifying selection on mildly deleterious variants. However, we did not observe any significant purge of highly deleterious variants.

Interestingly, the population’s success in the harsh environment can be attributed to pre-adaptation from their European taurine ancestry, suggesting no strong bioclimatic challenge, and also contradicting evidence for insular dwarfism. Genome scan for footprints of selection uncovered a majority of candidate genes related to nervous system function, likely reflecting rapid feralization driven by behavioral changes and complex social restructuring. This unprecedented case study provides valuable insights into rapid population establishment, feralization, and genetic adaptation in challenging environments. It highlights the importance of preserving the unique genetic legacies of feral populations and raises ethical questions in the eyes of conservation efforts.
AptaBERT: Predicting aptamer binding interactions
Authors: Morsch Flemming , Umasankar Iswarya Lalitha , Moreta Lys Sanz , Latawa Paridhi , Lange Danny B. , Wengel Jesper , Konjen Huram , Code Christian
Published: November 2023

Abstract

Aptamers, short single-stranded DNA or RNA, are promising as future diagnostic and therapeutic agents. Traditional selection methods, such as the Systemic Evolution of Ligands by Exponential Enrichment (SELEX), are not without limitations being both resource-intensive and prone to biases in library construction and the selection phase. Leveraging Dianox’s extensive aptamer database, we introduce a novel computational approach, AptaBERT, built upon the BERT architecture. This method utilizes self-supervised pre-training on vast amounts of data, followed by supervised fine-tuning to enhance the prediction of aptamer interactions with proteins and small molecules. AptaBERT is fine-tuned for binary classification tasks, distinguishing between positive and negative interactions with proteins and small molecules. AptaBERT achieves a ROC-AUC of 96% for protein interactions, surpassing existing models by at least 15%. For small molecule interactions, AptaBERT attains an ROC-AUC of 85%. Our findings demonstrate AptaBERT’s superior predictive capability and its potential to identify novel aptamers binding to targets.
Deep learning-based method to identify disease-resistance proteins inOryza sativaand relative species
Authors: Dhiman Vedikaa , Biswas Soham , Swain Asish Kumar , Sadhukhan Ayan , Yadav Pankaj
Published: November 2023

Rice (Oryza sativa) is a significant agricultural crop consumed by more than half of the global population. Its demand is expected to increase due to rising consumption and a growing global population. Moreover, the rice plant is frequently exposed to disease-causing pathogens, such as bacteria, fungi, viruses, and nematodes. Thus, cultivating disease-resistant varieties is an efficient way of disease control compared to pesticide applications. However, the rice plant has a well-defined defense system to prevent the onset of disease, including Pathogen-associated molecular pattern (PAMP)-triggered immunity (PTI) and effector-triggered immunity (ETI). The defense system is controlled by various disease-resistance proteins, such as resistance (R) proteins and pathogen recognition receptors (PRRs). Therefore, the identification of disease-resistance proteins not only reduces the amount of pesticides used in rice fields but also increases their yield. Though some resistant proteins have been characterized, their rapid identification, precise diagnosis, and appropriate management are still lacking. However, few methods based on sequence-similarity and de novo prediction, such as Machine Learning (ML), usually have low prediction power. In this study, we built a state-of-the-art classifier based on Deep Learning (DL) for the early detection of disease-resistance proteins in rice and related species. We compared the DL-based Multi-layer Perceptron (MLP) model with the five well-established ML-based methods using a protein dataset of rice and its related species. The DL-based MLP model outperformed all of the five classifiers on 10-fold cross-validation. The accuracy, Area Under Receiving Operating Characteristic (ROC) curve (AUC), F1-score, precision, and recall were superior in the DL-based MLP model. In conclusion, the MLP model is an effective DL model for predicting disease-resistance proteins with high scores in performance metrics. This study will provide insight to the breeders in developing disease-resistant rice varieties and assist in transforming traditional rice farming practices into a new age of smart rice farming.
A modular model integrating metabolism, growth, and cell cycle predicts that fermentation is required to modulate cell size in yeast populations
Authors: Vanoni Marco , Palumbo Pasquale , Papa Federico , Busti Stefano , Gotti Laura , Wortel Meike , Teusink Bas , Orlandi Ivan , Pessina Alex , Airoldi Cristina , Brambilla Luca , Vai Marina , Alberghina Lilia
Published: November 2023

For unicellular organisms, the reproduction rate and growth are crucial determinants of fitness and, therefore, essential functional manifestations of the organism genotype. Using the budding yeastSaccharomyces cerevisiaeas a model organism, we integrated metabolism, which provides energy and building blocks for growth, with cell mass growth and cell cycle progression into a low-granularity, multiscale (from cell to population) computational model. This model predicted that cells with constitutive respiration do not modulate cell size according to the growth conditions. We experimentally validated the model predictions using mutants with defects in the upper part of glycolysis or glucose transport. Plugging in molecular details of cellular subsystems allowed us to refine predictions from the cellular to the molecular level. Our hybrid multiscale modeling approach provides a framework for structuring molecular knowledge and predicting cell phenotypes under various genetic and environmental conditions.
Perceived predation risk affects the development of among-individual behavioral variation in a naturally clonal freshwater fish
Authors: Scherer U , Laskowski K , Kressler M , Ehlman S , Wolf M , Bierbach D
Published: November 2023

Predation risk is a key driver of natural selection, influencing various aspects of prey behavior. While many studies focus on how predation risk affects average behavior at population level, less attention has been given to its potential impact on behavioral variation within prey populations. Here, we investigate the effect of perceived predation risk on among-individual behavioral variation in naturally clonal Amazon mollies. Juveniles were raised in two groups: one exposed to a predator during feeding (visual cues only) and the other one serving as a control group. We observed activity and feeding behavior (time spent feeding, visits to feeding spot) over a four-week period. (I) Individuals in the predator-exposed group were on average less active but there was no difference in average feeding behavior between the two groups, suggesting individuals strategically respond to threats based on behavior-specific cost-benefit trade-offs. (II) Among-individual behavioral variation was affected by perceived predation risk: in the absence of the predator, individuals developed pronounced differences in the time spent feeding while no such development was observed in the predator-exposed group. This result has the potential of affecting a wide range of fitness-relevant intraspecific interactions if lower among-individual feeding variation translate into reduced sizes differences. The presence of the predator initially reduced among-individual variation in activity and visits to the feeding spot, but these differences did not persist over time. Our findings highlight the importance of considering both population-level and individual-level responses to predation risk for a more comprehensive understanding of its ecological and evolutionary consequences.
MolLM: A Unified Language Model for Integrating Biomedical Text with 2D and 3D Molecular Representations
Authors: Tang Xiangru , Tran Andrew , Tan Jeffrey , Gerstein Mark B.
Published: November 2023

Motivation

The current paradigm of deep learning models for the joint representation of molecules and text primarily relies on 1D or 2D molecular formats, neglecting significant 3D structural information that offers valuable physical insight. This narrow focus inhibits the models’ versatility and adaptability across a wide range of modalities. Conversely, the limited research focusing on explicit 3D representation tends to overlook textual data within the biomedical domain.

Results

We present a unified pre-trained language model, MolLM, that concurrently captures 2D and 3D molecular information alongside biomedical text. MolLM consists of a text Transformer encoder and a molecular Transformer encoder, designed to encode both 2D and 3D molecular structures. To support MolLM’s self-supervised pre-training, we constructed 160K molecule-text pairings. Employing contrastive learning as a supervisory signal for cross-modal information learning, MolLM demonstrates robust molecular representation capabilities across 4 downstream tasks, including cross-modality molecule and text matching, property prediction, captioning, and text-prompted molecular editing. Through ablation, we demonstrate that the inclusion of explicit 3D representations improves performance in these downstream tasks.

Availability and implementation

Our code, data, and pre-trained model weights are all available athttps://github.com/gersteinlab/MolLM.
Accountability and the metaverse: unaccounted digital worlds between techwashing mechanisms and new emerging meanings
Authors: Massaro Maurizio , Spanò Rosanna , Kuruppu Sanjaya Chinthana
Published: November 2023

Purpose

This paper aims to understand the main challenges connected with accountability issues across multiple layers of the metaverse, to identify whether and how any techwashing is taking place and to discuss implications for accounting research.

Design/methodology/approach

To develop the research, the authors refer to a critical dialogic accountability framework, operationalized in the current paper by leveraging the perspectives of accountability as virtues and as mechanisms (Bovens, 2010). The authors discuss who is accountable to whom, for what and in what manner in a relatively unregulated and unaccountable world, through the layers of virtual reality introduced by MacKenzieet al. (2013) and Llewellyn (2007). Methodologically, the study concentrates on 32 start-ups working in the metaverse selected from the Crunchbase database and relies on interviews, direct observation in the field and white paper reports analyzed by means of NVivo coding.

Findings

The findings show how metaverse creators deal with accountability as a virtue and accountability as a mechanism. Companies who operate metaverses primarily consider accountability in the virtual-physical domain, which focuses on developing the necessary internal and external architecture to enable a particular metaverse to function. Metaverse companies also emphasize the virtual-agential dimension that concentrates on onboarding, engaging with and incentivizing individuals in virtual worlds. There is an emphasis on outlining the virtues or standards that metaverse companies aspire to, but there is very little detail provided. Similarly, there are uneven and limited discussions of the mechanisms that can support accountability in most layers of a virtual world.

Research limitations/implications

The analysis raises significant questions about the purpose, scope and use of metaverses, which are still a relatively unregulated and unaccountable world. The paper advances the idea that the current creators of metaverses are “techwashing” their projects, providing a utopian ideal of what their universes will look like but obfuscating the realities of their ventures in tech jargon that few people are likely to understand. Therefore, meaning and truth at all levels of the real and virtual worlds remain unaddressed, with implications to be explored in terms of legitimacy and trust of metaverses and the interests that shape them.

Originality/value

This paper is one of the first to address the issue of accountability in metaverses. It advances an analytical framework to guide future accounting and accountability research into virtual worlds.
A review of the status of vultures in the southern state of Karnataka, India
Authors: Gopal Praphul , Kumara Honnavalli N.
Published: November 2023

Vultures are vital scavengers that maintain ecological balance by feeding on carcasses. Among the nine vulture species in India, four are categorised as ‘Critically Endangered’, one as ‘Endangered’, three as ‘Near Threatened’, and one as ‘Least Concern’ as per the IUCN Red List. The vultures have experienced a global decline, while in India, majorly due to the use of diclofenac, a non-steroidal anti-inflammatory drug (NSAID). A review of all available literature on vultures from 1838 to December 2022 and extracting of all sight records from eBird to understand their status, occurrence, and distribution for the Indian state of Karnataka. The study reveals a total of seven vulture species recorded from the state, of them, one was misidentified, two are vagrants, and the other four species, namely Egyptian Vulture, White-rumped Vulture, Indian Vulture, and Red-headed Vulture, are residents. The resident vulture population in the state is experiencing a consistent decrease and has been confined in recent years to in and around Bandipur and Nagarahole tiger reserves, while Egyptian Vulture is mostly observed in human-inhabited areas. In contrast to the gradual recovery of the Gyps vulture population across the country, the population in the Ramadevarabetta Vulture Sanctuary remains relatively low or decreasing. Periodic systematic population assessments and monitoring of nest sites, evaluating breeding patterns, and ensuring the availability of undisturbed carcasses for vultures to feed on are suggested.
Continental fishes of Nicaragua: diversity, distribution and conservation status; with an annotated and illustrated checklist of species and an identification guide to families
Authors: ANGULO ARTURO , BETTS JOEL T. , GONZÁLEZ-ALEMÁN NÉSTOR J. , CASTAÑEDA EDGAR , BERGHE ERIC VAN DEN , ELÍAS DIEGO J. , MCMAHAN CALEB D. , MATAMOROS WILFREDO A.
Published: November 2023

Based on a combination of intensive literature review, electronic database searches, re-identification of museum specimens, and fieldwork, we provide an updated checklist of the continental fishes of Nicaragua. This checklist, systematically arranged at the ordinal and familial level, includes nomenclatural revisions, distributional information, conservation status, and when appropriate, cross-references to previous lists and revisionary works on the fish fauna of the country and region (Central America); illustrations and descriptions to the family level and color photographs of some representative species are also included. According to our results, the native Nicaraguan continental fish fauna is composed of 244 species, divided into 111 genera, 45 families, 24 orders, and two classes; increasing by 60 (i.e., 32.6%) the number of species originally reported by Villa (1982; i.e., the most comprehensive work published to date). The majority of the Nicaraguan native continental fish species, according to their supposed tolerance to salinity, are peripheral (68.9%), followed by secondary freshwater fishes (23.8%), and primary freshwater fishes (only 7.4%). Fish diversity in the 19 major river basins ranged between 21 and 90 species (mean = 58 species, median = 60); the Escondido (Es; 87 species), in the Atlantic, and the Pacífico de Nicaragua (PN; 90), in the Pacific, presented the highest species richness. Most species (188) are restricted to elevations between 0 and 100 meters above sea level (masl); only a few species (18), in contrast, were found at elevations greater than 500 masl (up to 780 masl). Fourteen species in this revision are listed as endemic to Nicaragua. Regarding their conservation status, 22 species (9.0%) are categorized, according to the International Union for Conservation of Nature (IUCN), as Data Deficient, 186 (76.2%) as Least Concern, and seven (2.9%) as Near Threatened; while 24 species (9.8%) are listed as Threatened, thirteen (5.3%) as Vulnerable, two (0.8%) as Endangered, and nine (3.7%) as Critically Endangered. Five species (2.0%) have not yet been evaluated. Six exotic species are also reported. Our results provide a framework for future taxonomic and biogeographic works on fishes from this country and region (Central America), particularly by providing up-to-date knowledge on nomenclature and distributions. In addition, the data provided in this revision will help to monitor fish distributional changes in the future due to human introductions and global change and will aid in conservation decisions concerning Nicaraguan continental fishes.
An illustrated guide to the lady beetles (Coleoptera: Coccinellidae) of the Indian Subcontinent. Part II. Tribe Chilocorini
Authors: POORANI J.
Published: November 2023

An illustrated guide to the lady beetles of the tribe Chilocorini (Coleoptera: Coccinellidae: Coccinellinae) of the Indian region is presented. Brief diagnostic accounts of six genera and 31 species are given with supporting illustrations of the diagnostic characters, including genitalia, wherever possible. Details of distribution, host insects / plant associations, and seasonal occurrences are provided for the first time based on extensive collections, label data and published literature. Chilocorus keralensis sp. n. is described from the Western Ghats, South India. Brumoides lineatus sensu Kapur 1967, recorded from the Andaman Islands, is found to be distinct from B. lineatus Weise 1885, and described and illustrated as B. andamanensis sp. n. Phaenochilus indicus Miyatake, 1970 and P. flaviceps Miyatake, 1970 are transferred to Chilocorus Leach (comb. n.) following the latest phylogenetic generic classification of Chilocorini. Three species, Chilocorus albomarginalis (Li & Wang), Chilocorus nigricaeruleus Li & Wang and Chilocorus yunlongensis Cao & Xiao, all originally described from China, are added to the Indian fauna of Chilocorini based on material examined from the north-eastern Indian states of Assam, Meghalaya, and Manipur, respectively. For nine species, illustrations of the life stages are included to facilitate their field identification. A key to the genera and an updated and revised checklist of the Chilocorini of the Indian subcontinent are also provided.
Scanning electron microscopy study of Lars Silén’s cheilostome bryozoan type specimens in the historical collections of natural history museums in Sweden
Authors: MARTINO EMANUELA DI
Published: November 2023

The type specimens of 42 cheilostome bryozoan species introduced by Lars Silén between 1938 and 1954 and housed at three different Swedish institutions (the Swedish Museum of Natural History in Stockholm, the Biological Museum in Lund and the Museum of Evolution in Uppsala) are here revised using scanning electron microscopy, with two exceptions, for the first time. As a result of this revision, new morphological observations were made for some species, such as ooecia in Antropora erecta, a costal pseudopore in Jullienula hippocrepis, intracolonial variation in the number of intracostal windows in Costaticella gisleni, and oral spines in Triphyllozoon mauritzoni. Some other observations confirmed the presence of structures/polymorphs in type material that had previously only been noted in non-type specimens, such as spinose interzooidal kenozooids in Retevirgula triangulata and putative brooding zooids in Bugulina kiuschiuensis. Structures originally interpreted as hydroid tube openings on the dorsal side of Triphyllozoon microstigmatum were confirmed to be avicularia, while the supposed kenozooidal attachment rootlet of Fedora nodosa might be the polypide tube of a coronate scyphozoan. In addition, the original combination Heliodoma goesi is here reinstated after Lagaaij assigned the species to Setosellina in 1963. The following new combinations are also proposed: Labioporella aviculifera for Siphonoporella aviculifera; Mangana canui and Mangana incrustata for Callopora canui and Tegella incrustata, respectively; Sphaerulobryozoon ovum for Fedora ovum. Lectotypes were selected when appropriate. This work clarifies the exact identity of some species that have never been recorded after their first description, such as Stylopoma magnovicellata and three species of Triphyllozoon, and contributes to the current increasing effort to digitize historical key specimens in natural history museum collections.
Book review: V. Srinivas, G20@2023: The Roadmap to Indian Presidency, One Earth. One Family. One Future
Authors: Barua Shrabana
Published: November 2023

V. Srinivas, G20@2023: The Roadmap to Indian Presidency, One Earth. One Family. One Future. Pentagon Press, 2023, pp. 290, ₹995, ISBN 9789390095742.
Does the requirement for an interpreter impact experience with telehealth modalities, acceptability and trust in telehealth? Results from a national survey including people requiring interpreter services
Authors: Gallegos-Rejas Victor M , Kelly Jaimon T , Snoswell Centaine L , Haydon Helen M , Banbury Annie , Thomas Emma E , Major Taylor , Caffery Liam J , Smith Anthony C , de Camargo Catapan Soraia
Published: November 2023

We aimed to assess if experience with telehealth modalities, acceptability and levels of trust in telehealth vary with the need for an interpreter using a cross-sectional survey of telehealth consumers in Australia. Non-parametric tests were used to compare the means and percentages between those who required an interpreter and those who did not. A total of N = 1,116 completed the survey; 5% ( n = 56) represented people needing an interpreter for telehealth services. Of those needing interpreters, 14.29% had experienced only phone consultations whereas 63.21% of those who did not need interpreters had experienced only phone consultations. Trust in telehealth with allied health professionals was significantly higher among people needing interpreters (mean 4.12 ± 1.02) than those with no interpreter required (mean 3.70 ± 1.30), p = 0.03. People requiring interpreters had non-significantly higher acceptability towards video consultation than those who did not (mean 3.60 ± 0.61 vs mean 3.51 ± 0.80, p = 0.42), similar to telephone consultations (mean 3.71 ± 0.95 vs mean 3.48 ± 0.79, p = 0.38). The need for interpreters does not appear to impact acceptability or trust in telehealth with doctors. However, experience with telehealth modalities and trust in telehealth with allied health varied significantly among groups. Increasing exposure to telehealth modalities, trust and acceptability is crucial to promote equitable access to telehealth.
From Competition to Inclusion: Assessing the Nature of the South Asian Labour Market from the Perspective of International Core Labour Standards and the Sustainable Development Goals
Authors: Islam Iyanatul
Published: November 2023

The textbook construct of a competitive labour market represents an ideal world in which workers and employers have equal bargaining power. Such a construct yields powerful conclusions: Wages are aligned with productivity; employers earn a normal rate of return; there is no involuntary unemployment and working poverty; regulations—such as minimum wages and the presence of unions—impedes the efficient functioning of the labour market. Yet, these conclusions—which have influenced, academic economists, policymakers and redoubtable international agencies—are impaired in the presence of unequal bargaining power of workers and employers. In such circumstances, unscrupulous employers can exploit the vulnerability of workers leading to such deleterious outcomes as working poverty, unsafe working conditions, use of child labour and so forth. This creates the rationale for appropriately designed regulations that seek to create a level playing field between workers and employers and thus facilitate the transition to an ‘inclusive’ labour market.
Book review: Harsh Mander, Between Memory and Forgetting: Massacre and the Modi Years in Gujarat, Harsh Mander, Partitions of the Heart: Unmaking the Idea of India and Harsh Mander, Locking Down the Poor: The Pandemic and India’s Moral Centre
Authors: Habib Irfan
Published: November 2023

Harsh Mander, Between Memory and Forgetting: Massacre and the Modi Years in Gujarat (New Delhi: Yoda Press), 2019, 292 pp., ₹450 (Pb).

Harsh Mander, Partitions of the Heart: Unmaking the Idea of India (Gurgaon: Penguin-Viking), 2018, 290 pp., ₹599 (Hb).

Harsh Mander, Locking Down the Poor: The Pandemic and India’s Moral Centre (New Delhi: Speaking Tiger Books), 2021, 231 pp., ₹399 (Pb).
Book review: Ratttan Lal Hangloo, Enquiries in Medieval India: Religion, Society, Culture and Polity
Authors: Moosvi Shireen
Published: November 2023

Ratttan Lal Hangloo, Enquiries in Medieval India: Religion, Society, Culture and Polity (Delhi: Primus Books), 2022, 199 pp., ₹1,125 (Hb).
Prognostic potential of whole exome sequencing in the clinical management of metachronous colorectal cancer liver metastases
Authors: Heczko Lucie , Hlaváč Viktor , Holý Petr , Dvořák Pavel , Liška Václav , Vyčítal Ondřej , Fiala Ondřej , Souček Pavel
Published: November 2023

Background

Colorectal cancer is a highly prevalent and deadly. The most common metastatic site is the liver. We performed a whole exome sequencing analysis of a series of metachronous colorectal cancer liver metastases (mCLM) and matched non-malignant liver tissues to investigate the genomic profile of mCLM and explore associations with the patients’ prognosis and therapeutic modalities.

Methods

DNA samples from mCLM and non-malignant liver tissue pairs (n = 41) were sequenced using whole exome target enrichment and their germline and somatic genetic variability, copy number variations, and mutational signatures were assessed for associations with relapse-free (RFS) and overall survival (OS).

Results

Our genetic analysis could stratify all patients into existing targeted therapeutic regimens. The most commonly mutated genes in mCLM were TP53, APC, and KRAS together with PIK3CA and several passenger genes like ABCA13, FAT4, PCLO, and UNC80. Patients with somatic alterations in genes from homologous recombination repair, Notch, and Hedgehog pathways had significantly prolonged RFS, while those with altered MYC pathway genes had poor RFS. Additionally, alterations in the JAK-STAT pathway were prognostic of longer OS. Patients bearing somatic variants in VIPR2 had significantly shorter OS and those with alterations in MUC16 prolonged OS. Carriage of the KRAS-12D variant was associated with shortened survival in our and external datasets. On the other hand, tumor mutation burden, mismatch repair deficiency, microsatellite instability, mutational signatures, or copy number variation in mCLM had no prognostic value.

Conclusions

The results encourage further molecular profiling for personalized treatment of colorectal cancer liver metastases discerning metachronous from synchronous scenarios.
The effects of ARID1A mutation in gastric cancer and its significance for treatment
Authors: Lu Shan , Duan Ruifeng , Cong Liang , Song Ying
Published: November 2023

Gastric cancer (GC) has emerged as a significant issue in public health all worldwide as a result of its high mortality rate and dismal prognosis. AT-rich interactive domain 1 A (ARID1A) is a vital component of the switch/sucrose-non-fermentable (SWI/SNF) chromatin remodeling complex, and ARID1A mutations occur in various tumors, leading to protein loss and decreased expression; it then affects the tumor biological behavior or prognosis. More significantly, ARID1A mutations will likely be biological markers for immune checkpoint blockade (ICB) treatment and selective targeted therapy. To provide theoretical support for future research on the stratification of individuals with gastric cancer with ARID1A as a biomarker to achieve precision therapy, we have focused on the clinical significance, predictive value, underlying mechanisms, and possible treatment strategies for ARID1A mutations in gastric cancer in this review.
Monetary shocks and production network in the G7 countries
Authors: Simionescu Mihaela , Schneider Nicolas
Published: November 2023

Understanding the structure and properties of production networks is essential to identify the transmission channels from monetary shocks. While growingly studied, this literature keeps displaying critical caveats from which the investigation of G-7 economies is not spared. To fill this gap, this paper applies a version of Time-Varying Parameters Bayesian Vector-Autoregressions models (TVP-VAR) and investigates the responses of production networks (upstream and downstream dynamics) to endogeneous monetary shocks on key macro-level indicators (GDP, GDP deflator, exchange rate, short-term and long-term interest rates). Two distinct time-lengths are considered: a test (i.e., 2000–2014) and a treated period (i.e., 2007–2009,”the Great Recession”). Prior, key statistical conditions are checked using a stepwise stationary testing framework including the Kwiatkowski–Phillips–Schmidt–Shin (Kapetanios et al. in J Economet 112(2):359–379, 2003—KPSS) and panel Breitung (Nonstationary panels, panel cointegration, and dynamic panels. Emerald Group Publishing Limited, London, 2001) unit root tests; followed by the Pesaran (General diagnostic tests for cross section dependence in panels, 2004) Cross-sectional Dependence (CD) test; and the Im–Pesaran–Shin (Im et al. in J Economet 115(1):53–74, 2003—IPS) test for unit root in the presence of heterogenous slope coefficients. Panel Auto-Regressive Distributed Lag Mean Group estimates (PARDL-MG) offer interesting short- and long-run monetary shocks-production networks response functions, stratified by country and sector. Findings clearly indicate that upstreamness forces dominated downstremness dynamics during the period 2000–2014, whereas the financial sector ermeges as the clear transmission channel through which monetary shocks affected the productive economy during the Great Recession. In general, we conclude that the prioduction structure influences the transmission of monetary shocks in the G-7 economies. Adequate policy implications are supplied, along with a methodological note on the forecasting potential of TVP-VAR methodologies when dealing with series exhibiting structural breaks.
Curriculum Reconstruction: Alignment of Profile, Body of Knowledge, and Learning Outcomes of the Indonesian Islamic Education Study Program
Authors: Eva Latipah  , Hasan Noorhaidi
Published: November 2023

Purpose – The misalignment between the profile with the body of knowledge (BoK) and the graduates’ learning outcomes (LO) of the PAI Study Program has caused the unclear educational objectives of the PAI study program, requiring the reconstruction of the PAI curriculum. This study aims to examine the reconstruction process of the PAI curriculum including the Profile, BoK, and LO of the PAI.

Design/methods/approach –The research was conducted qualitatively using survey, interview, and documentation methods packaged in seminars, guest lectures, workshops, and Focus Group Discussions. The subjects in this study were 83 PAI Study Program managers from Sumatra, Jakarta and Jabodetabek, DIY and Central Java, East Java, and the Eastern regions; the interviews were carried out with 15 study program managers. The obtained data was processed through the stages of reduction, display, and interpretation.

Findings – The results showed: 1) there are 6 profiles of Indonesian PAI after being reduced from 51 profiles, namely PAI teachers in schools/madrasahs, educational consultants, research assistants, administrators of educational institutions, Da’i/muballigh, and edupreneurs, 2) PAI’s Body of Knowledge consists of four scientific families: PAI science (what to teach), teaching science (how to teach), education and psychology (how to discipline), Research methodology, philosophy, language, technology, edupreneur (how to produce), 3) Graduate learning outcomes include in-depth mastery of PAI science, teaching, pedagogic, and PAI development, as well as how to teach PAI science effectively.

Research implications/limitations – This research has implications for the importance of preparing graduate profiles based on tracer studies, rather than based on ‘personal wishes’; and Learning outcomes must be adjusted to the standardized BoK of the Study Program.

Originality/value – the importance of profile mapping based on tracer studies, the significance of PAI’s body of knowledge in achieving PAI goals, and the importance of graduate learning outcomes for the expertise of PAI graduates.
Synthesis and Structure of Tricymantrenyltin Oxide
Authors:   South Ural State University, Chelyabinsk, Russian Federation, Sharutin V. , Senchurin V.
Published: November 2023

Interaction of tricymantrenyltin chloride with sodium hydroxide in an acetone-water solu-tion leads to formation of tricymantrenyltin oxide {[(CO)3MnС5H4]3Sn}2O (1), yielding 72 %. The structure of the obtained compound has been investigated by IR spectroscopy and X-ray diffraction analysis. The IR spectrum of complex 1 contains the characteristic absorption bands related to stretching vibrations of carbonyl groups at 1921 and 2019 cm–1. According to the X-ray analysis data, obtained on an automatic diffractometer D8 Quest Bruker (MoK-radiation, λ = 0.71073 Å, graphite monochromator) at 293 K, compound 1 is crystallized in a monoclinic crystal lattice, the spatial group is P21/c. Cell parameters: a = 12.651(6) Å, b = 35.000(16) Å, c = 12.297(7) Å,  =  = 90.00, β = 113.44(3) degrees, V = 5251(4) Å3, Z = 4, (sub.)= 1.861 g/cm3, F(000) = 2856.0, the crystal size is 0.690.530.33 mm; the 2 range of data collection is 5.78–54.4 degrees, the ranges of refraction indices are 16 ≤ h ≤ 16, 44 ≤ k ≤ 44, 16 ≤ l ≤ 16; total reflections 50910; independent reflections 11625; refinement variables 676; GOOF 1.122; R1 = 0.0596; wR2 = 0.1321; the residual electron density equals 4.29/2.57 e/Å3. The tin atoms in 1 have a distorted tetrahedral coordination; the CSnC angles are 102.3(2)120.1(2), the Sn–C bond lengths change within the range 2.107(6)2.119(7) Å, the Sn–O distances are 1.945(4) and 1.959(4) Å. The structural organization of the complex 1 crystal is controlled by in-termolecular bonds С–HO≡С (2.572.71 Å).
Synthesis and Structure Features of Triphenylbismuth Dicarboxylates
Authors:   South Ural State University, Chelyabinsk, Russian Federation, Koshcheeva L.
Published: November 2023

The interaction of triphenylbismuth with chloroacetic acid and pentafluorobenzoic acid in the presence of tert-butyl hydroperoxide or hydrogen peroxide in ether has led totriphenylbismuthbis(chloroacetate) (1) and triphenylbismuthbis(2,3,4,5,6-pentafluorobenzoate) (2). The X-ray diffraction pattern for the crystal 1has been obtained at 293 K on an automatic diffractometer D8 Quest Bruker (MoKα-radiation, λ = 0.71073 Å, graphite monochromator), the results are [C22H19O4Cl2Bi, M 627.25, the triclinic syngony, the symmetry group P–1; cell parameters: a = 8.891(5), b = 10.401(5), c = 12.452(5) Å; α = 86.38(2) degrees,β = 73.97(2) degrees., γ = 87.15(3) degrees.; V = 1104.0(9) Å3; the crystal size is 0.41×0.28×0.1 mm; intervals of reflection indexes are –15 ≤ h ≤ 15, –17 ≤ k ≤ 17, –21 ≤ l ≤ 21; total reflections 76809; independent reflections 11945; Rint 0.0525; GOOF 1.041; R1 = 0.0330, wR2 = 0.0665; residual electron density 1.30/–2.28 e/Å3], and 2 [C32H15O4F10Bi, M 862.42, the triclinic syngony, the symmetry group P–1; cell parameters: a = 12.168(8), b = 12.260(8), c = 12.720(8) Å; α = 72.43(3) degrees, β = 63.39(3) degrees, γ = 61.46(2) degrees.; V = 1481.0(16) Å3; the crystal size is 0.37×0.2×0.1 mm; intervals of reflection indexes are –16 ≤ h ≤ 16, –16 ≤ k ≤ 16, –16 ≤ l ≤ 16; total reflections 51260; independent reflections 7342; Rint 0.0416; GOOF 1.047; R1 = 0.0251, wR2 = 0.0524; residual electron density 0.84/–0.91 e/Å3]the bismuth atoms have a distorted trigonal-bipyramidal coordination. The OBiO axial angles are 173.07(7) degrees and 172.24(8) degrees; the sums of the CBiC angles in the equatorial plane are 359.93 degrees and 359.92 degrees. The Bi–O bond lengths are 2.303(2), 2.323(2) Å, and 2.272(3), 2.315(3) Å .The intervals of variation in the Bi–C equatorial bond lengths are 2.190(3)–2.214(3)Å and 2.194(3)–2.206(3)Å. Structures 1 and 2 contain intermolecular contacts between the bismuth atoms and the oxygen atoms of the carboxylate groups. The Bi•••O=С distances equal 2.904(3), 2.908(3) Å (1), and 2.947(4), 3.167(4) Å (2), which is less than the sum of the Van der Waals radii of bismuth and oxygen (3.59 Å). The Cl∙∙∙Cl intermolecular contacts (3.43 Å) and H∙∙∙O (2.43, 2.57 Å) are present in crystal 1; while only H∙∙∙O (2.50 Å) is presentin crystal 2. Complete tables of coordinates of atoms, bond lengths and valence angles for the structure are deposited at the Cambridge Structural Data Bank (No. 1991198 (1); No. 2042930 (2); deposit@ccdc.cam.ac.uk; http: //www.ccdc.cam.ac.uk).