bluuebunny/crossref_metadata_2025 huggingface dataset:
Heatwave induced health vulnerability assessment in Bangladesh
Authors: Mehrin Maria , Tuz Zuhra Fatema , Rahman Md Mafizur
Published: December 2024

Heatwaves emerge as a substantial environmental hazard, posing a severe threat to public health, especially in the tropical countries of South Asia. Despite Bangladesh’s susceptibility to natural disasters, including unprecedented temperature surge, heat stress lacks official recognition as a disaster. This study aims to assess the spatial distribution of health vulnerability to heat waves at the district level in Bangladesh. Utilizing a framework incorporating exposure, sensitivity, and adaptive capacity, the vulnerability index score for each district was computed. The study selected indicators by first reviewing relevant literature to identify key factors contributing to vulnerability to heatwaves. The final selection of 14 indicators, three for exposure, seven for sensitivity, and four for adaptive capacity, was made independently by the authors after consulting with experts and considering data availability. The entropy weight method, known for its objectivity in decision-making, was applied to assign weights to each indicator. The results indicated that the southwestern region and a portion of the northwestern part of Bangladesh are particularly exposed to heatwaves, with Kurigram identified as the most sensitive to heat. This heightened sensitivity is driven by a high floating population density, significant engagement in agriculture, and high population density. The districts most susceptible to heatwaves due to a combination of high sensitivity and low adaptive capacity include Barisal, Lakshmipur, Kishoreganj, Narayanganj, Narsingdi, Tangail, Jamalpur, Netrakona, Sherpur, Naogaon, Dinajpur, Kurigram, and Rangpur. These areas are likely to face the greatest impact from future heatwaves. This research facilitates strategic resource allocation by by identifying vulnerable districts and offering insights into the underlying causes, thereby supporting policy development and fostering international collaboration.
Three-dimensional disordered alloy metamaterials: a new platform of structure-function integration
Authors: Li Xinxin , Wang Liqiang , Lu Yang
Published: December 2024

Metamaterials have garnered significant interest in recent years due to their unprecedented properties unattainable by natural substances and potential applications in various fields. In this review, we provide an in-depth analysis of a novel class of three-dimensional (3D) disordered alloy metamaterials, including metallic glasses and high/medium entropy alloys metamaterials, which offer a promising platform for the integration of structure and function. These materials are characterized by their unique including disordered atomic structures and alloy compositions modulation, enabling the manipulation of electromagnetic, thermal, and mechanical properties. We begin by discussing the underlying principles and synthesis methods of 3D disordered alloy metamaterials, followed by a comprehensive examination of their distinctive properties and potential applications in the realms of engineering, energy harvesting, and sensing. Furthermore, we delve into the existing challenges and future directions of this burgeoning field, encompassing aspects such as scalability, precision in fabrication, and the evolution of multi-functional materials. 3D disordered alloy metamaterials represent a promising avenue for the advancement of structure-function integration, with potential implications for a broad range of scientific and technological disciplines.
The influence of post-glacial migration and hybridization on the gene pool of marginal Quercus pubescens populations in Central Europe
Authors: Pütz Jil , Jansen Simon , Reutimann Oliver , Rellstab Christian , Bordács Sándor , Neophytou Charalambos
Published: December 2024

Background and Aims

In Central Europe, the drought-tolerant downy oak (Quercus pubescens) is at the northern edge of its natural distribution range, often growing in small and spatially isolated populations. Here, we elucidate how the population genetic structure of Central European Q. pubescens was shaped by geographical barriers, genetic drift and introgression with the closely related sessile oak (Q. petraea).

Methods

In total, 27 Q. pubescens populations from the northern margin of its natural distribution range were sampled. Based on 16 nuclear microsatellite markers (nSSRs), Bayesian clustering and distance-based analyses were performed to determine the intraspecific genetic structure and to identify genetic barriers. To identify drivers of introgression with Q. petraea, generalized linear models were applied to link levels of introgression with environmental conditions. To track post-glacial migration routes, the spatial distribution of haplotypes based on eight chloroplast microsatellite markers (cpSSRs) was investigated.

Key Results

Based on nSSRs, the study populations of Q. pubescens were divided into a western and an eastern genetic cluster. Within these clusters, more pronounced genetic substructure was observed in the west, probably due to a rugged topography and limited gene flow. Introgression from Q. petraea was more prevalent at wetter and north-exposed sites and in the west. The identified cpSSR haplotypes followed known migration pathways.

Conclusions

Our results suggest two late-glacial refugia in or near the southwestern Alps and the southeastern Alps as potential sources for post-glacial migration. Although some genetic exchange is evident in northern Italy, south of the Alps, the two clusters remain distinct at a large scale. Landscape features and introgression with Q. petraea shaped the genetic substructure at a smaller scale. Our study provides a comprehensive overview of the genetic structure of Q. pubescens in Central Europe, relevant for conservation.
Exploratory Analysis of Upper Facial Muscle Interplay During Emotional Expressions: Magnetic Resonance Imaging (MRI) Insights From Young, Caucasian, Toxin-naïve Individuals
Authors: Rams Daniel J , Koziej Mateusz , Shridharani Sachin M , Szczepanek Elżbieta , Gleń Agnieszka , Popiela Tadeusz J , Ostrogórska Monika , Perdikis Galen , Cotofana Mikaela V , Cotofana Sebastian , Alfertshofer Michael
Published: December 2024

Background

Understanding the interplay of muscle activity in the upper face is crucial because it can significantly impact the effectiveness and safety of aesthetic treatments. Traditional injection algorithms typically focus on the general 2-dimensional and 3-dimensional anatomy of muscles, often neglecting the areas where muscles exert the greatest force during facial expressions.

Objectives

The goal of this study was to analyze the location of greatest morphological change in the upper facial muscles including the procerus muscle (PM), corrugator supercilii muscle (CSM), orbicularis oculi muscle (OOM), and frontalis muscle (FM) during various facial expressions.

Methods

A total of 34 healthy young individuals (17 females, 17 males), with a mean age of 23.6 ± 2.4 years [range 20-30], were examined with magnetic resonance imaging (MRI) to assess the length, thickness, and width of the upper facial muscles (PM, CSM, OOM, and FM) for 5 different facial expressions: repose, anger, joy, surprise, and sadness.

Results

Facial muscle thickness is a key indicator of activity during expressions such as anger, joy, surprise, and sadness. During anger, the PM and CSM decreased in length and width but increased in thickness, whereas the FM passively contracted to stabilize the expression. The OOM showed increased thickness in its medial, inferior, lateral, and superior portions during various expressions, with specific regions activating differently depending on the expression, such as the medial and lateral parts during surprise and the inferior and lateral parts during joy. The medial third of the CSM was the most active region during contraction.

Conclusions

Upper facial muscles—as either agonists or antagonists—act together during facial expressions to stabilize facial expressions, emphasizing the need to assess both groups in neuromodulator treatments. The medial third of the corrugator supercilii shows the most significant MRI changes, making it the primary target for injections.

Level of Evidence: 4 (Therapeutic)
The FunCoup Cytoscape App: multi-species network analysis and visualization
Authors: Buzzao Davide , Steininger Lukas , Guala Dimitri , Sonnhammer Erik L L
Published: December 2024

Motivation

Functional association networks, such as FunCoup, are crucial for analyzing complex gene interactions. To facilitate the analysis and visualization of such genome-wide networks, there is a need for seamless integration with powerful network analysis tools like Cytoscape.

Results

The FunCoup Cytoscape App integrates the FunCoup web service API with Cytoscape, allowing users to visualize and analyze gene interaction networks for 640 species. Users can input gene identifiers and customize search parameters, using various network expansion algorithms like group or independent gene search, MaxLink, and TOPAS. The app maintains consistent visualizations with the FunCoup website, providing detailed node and link information, including tissue and pathway gene annotations. The integration with Cytoscape plugins, such as ClusterMaker2, enhances the analytical capabilities of FunCoup, as exemplified by the identification of the Myasthenia gravis disease module along with potential new therapeutic targets.

Availability and implementation

The FunCoup Cytoscape App is developed using the Java OSGi framework, with UI components implemented in Java Swing and build support from Maven. The App is available as a JAR file at https://bitbucket.org/sonnhammergroup/funcoup_cytoscape/ repository, and can be downloaded from the Cytoscape App store https://apps.cytoscape.org/apps/funcoup.
A nickel metalloradical bearing a phenalenyl-based tridentate ligand
Authors: Noguchi Hikaru , Kodama Takuya , Kikkawa Soichi , Yamazoe Seiji , Tobisu Mamoru
Published: December 2024

A nickel(I) complex 1 bearing a phenalenyl-based tridentate ligand was synthesized. The electronic and spin structures of 1 were elucidated through electronic absorption spectra, electron spin resonance, and X-ray absorption fine structure measurements. Additionally, the metalloradical reactivity of 1 toward diphenyl disulfide and alkyl halides was also demonstrated.
Cyberbullying on Social Media: Definitions, Prevalence, and Impact Challenges
Authors: Ray Geraldine , McDermott Christopher D , Nicho Mathew
Published: December 2024

Cyberbullying on social media is a significant public health concern. This paper systematically reviews the existing literature on cyberbullying to provide a clearer understanding of how it is defined and reported in terms of prevalence and impact. Utilizing the PRISMA search strategy, we examined 71 papers published from 2007 to 2022, offering a comprehensive synthesis of the field’s current understanding. Our findings highlight notable inconsistencies in the definition of cyberbullying across studies, underlining a critical need for a standardized conceptual framework. Additionally, while cyberbullying is shown to be highly prevalent among personalities exhibiting traits of Machiavellianism, psychopathy, and narcissism, our review identifies a crucial research gap: the underexploration of cyberbullying among adult populations. This review synthesizes the breadth of research on cyberbullying and highlights gaps in the existing literature. We have included our proposed standardized definition of cyberbullying.
The association between adverse childhood experiences and adult cardiac function in the UK Biobank
Authors: Quiroz Juan C , Cooper Jackie , McCracken Celeste , Khanji Mohammed Y , Laranjo Liliana , Aung Nay , Lee Aaron Mark , Simon Judit , Murphy Theodore , Biasiolli Luca , Piechnik Stefan K , Maurovich-Horvat Pal , Petersen Steffen E , Raisi-Estabragh Zahra
Published: December 2024

Aims

The importance of early life factors in determining health in later adulthood is increasingly recognized. This study evaluated the association of adverse childhood experiences (ACEs) with cardiovascular magnetic resonance (CMR) phenotypes.

Methods and results

UK Biobank participants who had completed CMR and the self-reported questionnaire on traumatic childhood experiences were included. Images were analysed using automated pipelines to extract measures of left and right ventricular (LV and RV) structure and function, myocardial character, and arterial compliance. Multivariable linear regression was used to estimate the association of childhood adversity with CMR phenotypes adjusting for age, sex, deprivation, education, obesity, smoking, alcohol intake, exercise level, diabetes, hypertension, and hypercholesterolaemia. Amongst 30 814 participants analysed, 6023 (19.5%) experienced physical abuse, 2746 (8.9%) sexual abuse, 4685 (15.2%) emotional abuse, 6822 (22.1%) emotional neglect, and 4534 (14.7%) physical neglect. Except for physical abuse, women reported greater rates of childhood adversity than men. Collectively, all types of childhood adversity were associated with smaller LV and RV volumes, greater LV mass, a concentric pattern of LV remodelling, poorer LV and RV function, lower aortic compliance, and greater arterial stiffness. Sexual abuse was associated with unhealthy CMR phenotypes in age- and sex-adjusted models, but these relationships were attenuated in fully adjusted models. Physical neglect had the most prominent pattern of adverse cardiovascular remodelling.

Conclusion

ACEs were associated with unhealthy cardiovascular remodelling in adulthood, independent of traditional cardiovascular risk factors. These findings support the consideration of early life factors in cardiovascular disease risk assessment.
Aligning rhetoric with reality: a qualitative analysis of multistakeholder initiatives in the global food system
Authors: van den Akker Amber , Gilmore Anna B , Fabbri Alice , Knai Cecile , Rutter Harry
Published: December 2024

Global food system governance increasingly relies on multistakeholder initiatives (MSIs) that aim to include those who are affected by and/or affected by an issue. Multistakeholderism’s perceived legitimacy is premised on both its outcomes (output legitimacy) and processes (input legitimacy), the latter in turn based on four key rationales: inclusiveness, procedural fairness, consensual orientation and transparency. To date, evidence on the ineffectiveness of MSI’s outcomes undermines its claims to output legitimacy. While individual case study assessments have also raised concerns over their processes, documenting instances of power asymmetries and corporate capture, there has hitherto been no comprehensive assessment of the input legitimacy of multistakeholderism. This work addresses that gap through interviews with 31 participants working either in or on MSIs. Participants noted significant challenges related to input legitimacy, including that (i) inclusion was often based on pre-existing networks of an MSI’s founders—most of whom were based in the global North—and risked excluding less well-resourced or marginalized actors; (ii) pre-existing power imbalances, both internal and external to the MSI, considerably influenced its processes and structures; (iii) goal-setting was complicated by conflicts of interest and (iv) reliance on informal processes limited transparency. The similarities in challenges across MSIs indicate that these are not attributable to shortcomings of individual MSIs but are instead indicative of wider system constraints. Rather than rely on multistakeholderism as a ‘good’ governance norm, our findings add to evidence that MSIs do not meet output legitimacy and signal that the legitimacy of MSIs in their current form should be questioned.
Adolescent health literacy: sociodemographic determinants and its relationship with substance use avoidance
Authors: Fleary Sasha A , Rastogi Somya , Srivastava Venya
Published: December 2024

Adolescence is a critical period for health literacy (HL) development and for decision-making regarding substance use behaviors. Little is known about which sociodemographic factors are related to the three major components of HL (i.e. functional, interactive, critical HL) and the extent to which these components of HL moderate the relationship between sociodemographic determinants of substance use avoidance and avoidance for adolescents. This study aimed to identify sociodemographic determinants of functional, interactive, critical and composite HL among adolescents, and to assess HL’s role as a determinant and moderator of substance use avoidance. Data were collected from 675 adolescents (mean age = 15.5 years, ~53% girls, ~32% Hispanic/Latine) through Qualtrics survey panels and in school settings. Participants completed surveys on social and demographic factors, HL, and substance use. Binary and multinomial logistic regressions were used to address the study aims. In adjusted analyses, adolescents who were girls, Hispanic/Latine (vs. White), food secure, English proficient, had private communications with health providers, and those without impaired decision-making had higher odds of having high HL. Having higher functional, interactive and composite HL increased the odds of substance use avoidance and moderated the effect of age, with younger adolescents with higher HL (vs. low HL) having greater odds of substance use avoidance. Our findings suggest that HL may act as a protective factor against the initiation of substance use in younger adolescents. Thus, HL may be a good intervention strategy to delay substance use initiation for younger adolescents.
Public Attitudes toward On-Going Transitional Justice in Latvia: Sometimes More Isn’t Better
Authors: Horne Cynthia M
Published: December 2024

ABSTRACT∞

This article explores Latvia’s continued use of citizenship requirements and language policies as forms of transitional justice to redress vestiges of the Soviet past. This article presents an original 1,000-person survey conducted in June 2023 of Latvian residents’ attitudes toward these measures, which have been on-going for more than 30 years and have been amplified following Russia’s war in Ukraine. Despite the connections made between Russia’s war in Ukraine and potential domestic security threats from resident Russophones and Soviet-era migrants, there was only moderate agreement that transitional justice measures were needed to redress lingering problems of the past. There was lukewarm support for the use of measures to address corruption linked to lingering Soviet-era networks. Instead, respondents overwhelmingly thought the government should focus more on solving current problems than on dealing with the consequences of Soviet-era injustices. Within these trends, divisions emerged between Latvian and ethnic Russians, raising concerns that elongated measures could exacerbate political polarization along socioeconomic and ethnic lines. Generational responses yielded some unexpected results, with the youngest cohort more supportive of continued retributive measures than older cohorts. The survey findings suggest the utility and resonance of these measures might have run their course, and worse, that they could even exacerbate societal divisions.
Assessing Adherence to the PRISMA-DTA Guideline in Diagnostic Test Accuracy Systematic Reviews: A Five-Year Follow-up Analysis
Authors: Salameh Jean-Paul , Moher David , McGrath Trevor A , Frank Robert A , Sharifabadi Anahita Dehmoobad , Islam Nabil , Lam Eric , Adamo Robert , Dawit Haben , Kashif Al-Ghita Mohammed , Levis Brooke , Thombs Brett D , Bossuyt Patrick M , McInnes Matthew D F
Published: December 2024

Background

We evaluated reporting of diagnostic test accuracy (DTA) systematic reviews using Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA)-DTA and PRISMA-DTA for abstracts.

Methods

We searched MEDLINE for recent DTA systematic reviews (September 2023–Mar 2024) to achieve a sample size of 100. Analyses evaluated adherence to PRISMA-DTA (and abstracts), on a per-item basis. Association of reporting with journal, country, impact factor (IF), index-test type, subspecialty area, use of supplemental material, PRISMA citation, word count, and PRISMA adoption was evaluated. Comparison to the baseline evaluation from 2019 was done. Protocol: https://doi.org/10.17605/OSF.IO/P25TE.

Results

Overall adherence (n = 100) was 78% (20.3/26.0 items, SD = 2.0) for PRISMA-DTA and 52% (5.7/11.0 items, SD = 1.6) for abstracts. Infrequently reported items (<33% of studies): eligibility criteria, definitions for data extraction, synthesis of results, and characteristics of the included studies. Infrequently reported items in abstracts were characteristics of the included studies, strengths and limitations, and funding. Reporting completeness for full text was minimally higher in studies in higher IF journals [20.7 vs 19.8 items; 95% confidence interval (95%CI) (0.09; 1.77)], as well as studies that cited PRISMA [21.1 vs 20.1 items; 95%CI (0.04; 1.95)], or used supplemental material (20.7 vs 19.2 items; 95%CI (0.63; 2.35)]. Variability in reporting was not associated with author country, journal, abstract word count limitations, PRISMA adoption, structured abstracts, study design, subspecialty, open-access status, or index test. No association with word counts was observed among full text or abstracts. Compared to the baseline evaluation, reporting was improved for full texts [71% to 78%; 95%CI (1.18; 2.26)] but not for abstracts [50% to 52%; 95%CI (−0.20; 0.60)].

Conclusions

Compared to the baseline evaluation published in 2019, we observed modest improved adherence to PRISMA-DTA and no improvement in PRISMA-DTA for abstracts reporting.
A case and review of FGF23-mediated hypophosphatemic osteomalacia in the absence of pathogenic PHEX variants
Authors: Park Yeung-Ae , Gong Joanna Y , Chiang Cherie , Trainer Alison H , Yates Christopher J
Published: December 2024

We report an atypical case of fibroblast growth factor-23 (FGF23)-mediated hypophosphatemic osteomalacia without a pathogenic variant (PV) of PHEX, who improved biochemically, clinically and radiologically post burosumab treatment. We present a narrative review of FGF23-mediated hypophosphatemic osteomalacia and propose a roadmap for investigating the etiology of hypophosphatemia to guide therapy.

A 29-year-old female with FGF23-mediated hypophosphatemic osteomalacia experienced multiple insufficiency fractures, including bilateral femoral diaphyseal fractures and delayed healing. This occurred on a background of juvenile enthesitis-related arthritis, narcolepsy and brittle dentition since her early teens. Whole-body magnetic resonance imaging and Gallium-68 DOTATATE positron emission tomography scans were unremarkable, making tumor-induced osteomalacia highly unlikely. No hypophosphatemic PVs were found using massively parallel sequencing. Despite phosphate and calcitriol therapy, mild hypophosphatemia persisted with minimal improvement in fracture healing or pain. One dose of 60 mg burosumab, an anti-FGF23 antibody, led to hyperphosphatemia requiring dose titration and three doses of burosumab normalized renal tubular maximum reabsorption rate of phosphate relative to glomerular filtration rate. Burosumab led to fracture healing with callus formation corresponding with improved pain at fracture sites.

Hypophosphatemic osteomalacia manifests with varus deformity of the lower limbs, gait disturbance, muscle weakness, enthesopathy, and dental necrosis. Evaluation of the etiology is crucial and requires an algorithmic approach to determine whether hypophosphatemia is renally-mediated, FGF23-mediated, acquired or inherited. The most common inherited cause of FGF23-mediated hypophosphatemic osteomalacia is X-linked hypophosphatemia (XLH) secondary to a PV of the PHEX gene. However, the absence of a PHEX PVs does not exclude a diagnosis of hereditary FGF23-mediated hypophosphatemic osteomalacia. Other inherited causes of this disorder include autosomal dominant and autosomal recessive hypophosphatemic rickets, fibrous dysplasia-McCune-Albright syndrome, cutaneous skeletal hypophosphatemia syndrome and osteoglophonic dysplasia. Burosumab significantly improves serum phosphate and fracture healing in XLH and may effectively treat other forms of FGF23-mediated hypophosphatemia.
Six-month rehabilitation following surgical hip dislocation for femoroacetabular impingement restores the preoperative strength of most hip muscles, except for external rotators
Authors: Servant Guillaume , Bothorel Hugo , Pernoud Anthony , Mayes Susan , Fourchet François , Christofilopoulos Panayiotis
Published: December 2024

The aim of this study was to evaluate the bilateral changes in hip muscle strength after a 6-month rehabilitation period for patients undergoing surgical hip dislocation (SHD) to treat femoroacetabular impingement syndrome (FAIS). We conducted a retrospective analysis on a cohort of 22 patients (mean ± SD age: 26 ± 7, 68% male) who underwent SHD for FAIS between March 2020 and January 2023 at La Tour Hospital. Bilateral isometric strength of eight hip muscle groups (abductors, adductors, hamstrings, quadriceps, extensors, flexors, internal, and external rotators) was assessed using a handheld dynamometer before surgery, and at 3 and 6 months postoperatively. After 6 months of rehabilitation, only the external rotators were weaker compared to preoperative levels (−13% ± 23%, P = .021). Strength levels were similar to preoperative levelsfor adductors (−2% ± 21%, P = .309), internal rotators (0% ± 25%, P = .444), quadriceps (0%± 23%, P = .501), hamstrings (7%± 20%, P = .232), extensors (7%± 19%, P = .336), flexors (8%± 34%, P = .781), and abductors (8% ± 25%, P = .266). At 6 months, 59% (abductors) to 82% (adductors) of patients did not achieve a clinically relevant strength improvement (>15%) compared to their preoperative status for aforementioned muscles. Additionally, 50% of the cohort experienced a clinically relevant loss of strength in the external rotators at 6 months post-surgery. To conclude, after SHD, most FAIS patients regained their preoperative strength for all muscle groups except the external rotators with a 6-month rehabilitation program. However, the effectiveness of the rehabilitation protocol varies on an individual level.
Genome-wide identification of bacterial genes contributing to nucleus-forming jumbo phage infection
Authors: Harding Kate R , Malone Lucia M , Kyte Natalie A P , Jackson Simon A , Smith Leah M , Fineran Peter C
Published: December 2024

The Chimalliviridae family of bacteriophages (phages) form a proteinaceous nucleus-like structure during infection of their bacterial hosts. This phage ‘nucleus’ compartmentalises phage DNA replication and transcription, and shields the phage genome from DNA-targeting defence systems such as CRISPR-Cas and restriction-modification. Their insensitivity to DNA-targeting defences makes nucleus-forming jumbo phages attractive for phage therapy. However, little is known about the bacterial gene requirements during the infectious cycle of nucleus-forming phages or how phage resistance may emerge. To address this, we used the Serratia nucleus-forming jumbo phage PCH45 and exploited a combination of high-throughput transposon mutagenesis and deep sequencing (Tn-seq), and CRISPR interference (CRISPRi). We identified over 90 host genes involved in nucleus-forming phage infection, the majority of which were either involved in the biosynthesis of the primary receptor, flagella, or influenced swimming motility. In addition, the bacterial outer membrane lipopolysaccharide contributed to PCH45 adsorption. Other unrelated Serratia-flagellotropic phages used similar host genes as the nucleus-forming phage, indicating that phage resistance can lead to cross-resistance against diverse phages. Our findings demonstrate that resistance to nucleus-forming jumbo phages can readily emerge via bacterial surface receptor mutation and this should be a major factor when designing strategies for their use in phage therapy.
R-DeeP/TripepSVM identifies the RNA-binding OB-fold-like protein PatR as regulator of heterocyst patterning
Authors: Brenes-Álvarez Manuel , Ropp Halie R , Papagiannidis Dimitrios , Potel Clement M , Stein Frank , Scholz Ingeborg , Steglich Claudia , Savitski Mikhail M , Vioque Agustín , Muro-Pastor Alicia M , Hess Wolfgang R
Published: December 2024

RNA-binding proteins (RBPs) are central components of gene regulatory networks. The differentiation of heterocysts in filamentous cyanobacteria is an example of cell differentiation in prokaryotes. Although multiple non-coding transcripts are involved in this process, no RBPs have been implicated thus far. Here we used quantitative mass spectrometry to analyze the differential fractionation of RNA–protein complexes after RNase treatment in density gradients yielding 333 RNA-associated proteins, while a bioinformatic prediction yielded 311 RBP candidates in Nostoc sp. PCC 7120. We validated in vivo the RNA-binding capacity of six RBP candidates. Some participate in essential physiological aspects, such as photosynthesis (Alr2890), thylakoid biogenesis (Vipp1) or heterocyst differentiation (PrpA, PatU3), but their association with RNA was unknown. Validated RBPs Asl3888 and Alr1700 were not previously characterized. Alr1700 is an RBP with two oligonucleotide/oligosaccharide-binding (OB)-fold-like domains that is differentially expressed in heterocysts and interacts with non-coding regulatory RNAs. Deletion of alr1700 led to complete deregulation of the cell differentiation process, a striking increase in the number of heterocyst-like cells, and was ultimately lethal in the absence of combined nitrogen. These observations characterize this RBP as a master regulator of the heterocyst patterning and differentiation process, leading us to rename Alr1700 to PatR.
Spatial transcriptomics in breast cancer reveals tumour microenvironment-driven drug responses and clonal therapeutic heterogeneity
Authors: Jiménez-Santos María José , García-Martín Santiago , Rubio-Fernández Marcos , Gómez-López Gonzalo , Al-Shahrour Fátima
Published: December 2024

Breast cancer patients are categorized into three subtypes with distinct treatment approaches. Precision oncology has increased patient outcomes by targeting the specific molecular alterations of tumours, yet challenges remain. Treatment failure persists due to the coexistence of several malignant subpopulations with different drug sensitivities within the same tumour, a phenomenon known as intratumour heterogeneity (ITH). This heterogeneity has been extensively studied from a tumour-centric view, but recent insights underscore the role of the tumour microenvironment in treatment response. Our research utilizes spatial transcriptomics data from breast cancer patients to predict drug sensitivity. We observe diverse response patterns across tumour, interphase and microenvironment regions, unveiling a sensitivity and functional gradient from the tumour core to the periphery. Moreover, we find tumour therapeutic clusters with different drug responses associated with distinct biological functions driven by unique ligand-receptor interactions. Importantly, we identify genetically identical subclones with different responses depending on their location within the tumour ducts. This research underscores the significance of considering the distance from the tumour core and microenvironment composition when identifying suitable treatments to target ITH. Our findings provide critical insights into optimizing therapeutic strategies, highlighting the necessity of a comprehensive understanding of tumour biology for effective cancer treatment.
PyNetCor: a high-performance Python package for large-scale correlation analysis
Authors: Long Shibin , Xia Yan , Liang Lifeng , Yang Ying , Xie Hailiang , Wang Xiaokai
Published: December 2024

The development of multi-omics technologies has generated an abundance of biological datasets, providing valuable resources for investigating potential relationships within complex biological systems. However, most correlation analysis tools face computational challenges when dealing with these high-dimensional datasets containing millions of features. Here, we introduce pyNetCor, a fast and scalable tool for constructing correlation networks on large-scale and high-dimensional data. PyNetCor features optimized algorithms for both full correlation coefficient matrix computation and top-k correlation search, outperforming other tools in the field in terms of runtime and memory consumption. It utilizes a linear interpolation strategy to rapidly estimate P-values and achieve false discovery rate control, demonstrating a speedup of over 110 times compared to existing methods. Overall, pyNetCor supports large-scale correlation analysis, a crucial foundational step for various bioinformatics workflows, and can be easily integrated into downstream applications to accelerate the process of extracting biological insights from data.
Exploring transcription modalities from bimodal, single-cell RNA sequencing data
Authors: Regényi Enikő , Mashreghi Mir-Farzin , Schütte Christof , Sunkara Vikram
Published: December 2024

There is a growing interest in generating bimodal, single-cell RNA sequencing (RNA-seq) data for studying biological pathways. These data are predominantly utilized in understanding phenotypic trajectories using RNA velocities; however, the shape information encoded in the two-dimensional resolution of such data is not yet exploited. In this paper, we present an elliptical parametrization of two-dimensional RNA-seq data, from which we derived statistics that reveal four different modalities. These modalities can be interpreted as manifestations of the changes in the rates of splicing, transcription or degradation. We performed our analysis on a cell cycle and a colorectal cancer dataset. In both datasets, we found genes that are not picked up by differential gene expression analysis (DGEA), and are consequently unnoticed, yet visibly delineate phenotypes. This indicates that, in addition to DGEA, searching for genes that exhibit the discovered modalities could aid recovering genes that set phenotypes apart. For communities studying biomarkers and cellular phenotyping, the modalities present in bimodal RNA-seq data broaden the search space of genes, and furthermore, allow for incorporating cellular RNA processing into regulatory analyses.
Osteomyelitis and Septic Arthritis in the Darwin Prospective Melioidosis Study
Authors: Campbell Stuart , Hicks Dane , Shetty Rajendra P , Currie Bart J
Published: December 2024

Background

Melioidosis is a multisystem infectious disease caused by the environmental bacterium Burkholderia pseudomallei. Osteomyelitis (OM) and septic arthritis (SA) are uncommon primary presentations for melioidosis but important secondary foci, often requiring prolonged therapy and multiple surgeries. We characterized the epidemiology, presentation, treatment, and outcomes of patients from 24 years of the Darwin Prospective Melioidosis Study (DPMS).

Methods

DPMS patients from October 1, 1999, until September 30, 2023, were included if they had a primary or secondary diagnosis of OM or SA. Epidemiological, risk factor, clinical, and outcome data were retrieved from the DPMS database. Antibiotic and surgical data were collated from patient records.

Results

From 1129 consecutive patients with culture-confirmed melioidosis, 122 (10.8%) had OM and/or SA, with 115 evaluable. Ninety-four of 1129 (8.3%) had OM, and 62/1129 (5.5%) had SA, with 41/115 (35.7%) of these having both OM and SA. Many combined infections involved contiguous bone and joints or soft tissue. Fifty-nine (51.3%) were male, and only 4.3% were ≤16 years old. Diabetes mellitus was present in 69.6%, and only 12.2% had no identifiable clinical risk factor. There were 8 deaths (7.0%) and 20 (17.4%) recurrent infections. Seventy-one (61.7%) had operative management, with combined infection associated with more procedures and longer length of stay.

Conclusions

The current paradigm of care for osteoarticular melioidosis involves prolonged intravenous antibiotics in conjunction with timely and complete operative management, and in our setting where these are available, outcomes are good. In many melioidosis-endemic regions these resources are limited, and mortality remains high.
Symmetry Relationships between Crystal Structures
Authors: Müller Ulrich , de la Flor Gemma
Published: December 2024

In crystal chemistry and crystal physics, the relations between the symmetry groups (space groups) of crystalline solids are of special importance. Part 1 of this book presents the necessary mathematical foundations and tools: the fundamentals of crystallography with special emphasis on symmetry, the theory of the crystallographic groups, and the formalisms of the needed crystallographic computations. Part 2 gives an insight into applications to problems in crystal chemistry. With the aid of numerous examples, it is shown how crystallographic group theory can be used to make evident relationships between crystal structures, to set up a systematic order in the huge amount of known crystal structures, to predict crystal structures, to analyse phase transitions and topotactic reactions in the solid state, to understand the formation of domains and twins in crystals, and to avoid errors in crystal structure determinations. Part 3 goes more deeply into some special topics, namely the isomorphic subgroups of space groups, the theory of phase transitions, and computer programs dedicated to crystallographic group theory.
Basics of crystallography, part 1
Authors: Müller Ulrich , de la Flor Gemma
Published: December 2024

Crystals are described by a vector lattice that is periodical in three dimensions. Three non-coplanar basis vectors span a crystallographic basis (unit cell) and define a coordinate system. The lengths of the basis vectors and the angles between them are the lattice parameters. Planes across the vector lattice are designated by integral Miller indices hkl. The metric tensor serves to calculate distances and angles.
Equivalent descriptions of crystal structures and chirality
Authors: Müller Ulrich , de la Flor Gemma
Published: December 2024

By application of certain rules a standardized description of crystal structures is achieved. Frequently, often for good reasons, these rules are not observed, and for the consideration of symmetry relations they may even be inconvenient. Usually there are several different sets of coordinates to describe the very same crystal structure. The different sets of coordinates can be determined with the aid of the Euclidean normalizer. A chiral crystal structure can only adopt one of the 65 Sohncke space-group types. These have no reflections, glide reflections, rotoinversions or inversions. If these symmetry operations are also excluded for the Euclidean normalizer, the space group itself belongs to one of the 11 pairs of chiral (enantiomorphic) pairs of space-group types. The crystal structures of two compounds are isotypic it their atoms are distributed in a like manner and if they have the same space groups.
Derivation of crystal structures from closest packings of spheres
Authors: Müller Ulrich , de la Flor Gemma
Published: December 2024

A large number of crystal structures can be derived by partial occupation of interstices in closest packings of spheres. Examples are the rhombohedral, hexagonal and trigonal hettotypes that result from the partial occupation of octahedral voids in the hexagonal-closest packing of spheres. Other examplers are the hettotypes of the NaCl structure with a doubled unit cell and partial occupation of the octahedral voids, and the hetttotypes of the CaF2 type with a doubled unit cell and partial occupation of the tetrahedral voids.
Topotactic reactions
Authors: Müller Ulrich , de la Flor Gemma
Published: December 2024

A topotactic chemical reaction takes place in the solid state such that the orientation of the product crystal depends on the orientation of the initial material. Sometimes there is a group—subgroup relation between the involved space groups. When lanthanoid subhalides LnnCl2n+1 crystallize from a melt, they form topotactic mixtures such as DyCl2 + Dy7Cl15 whose structures can be derived from the fluorite type.
Facets of the Soviet
Authors: Titus Joan
Published: December 2024

Chapter 3 (“Facets of the Soviet”) provides an examination of Shostakovich’s scores to three disparate films representing three different film types of the late 1930s–early 1940s: Great Citizen (Velikiy grazhdanin, dir. Fridrikh Ermler, Parts 1 and 2, 1937 and 1938–1939), Man with a Gun (Chelovek s ruzh’yom, dir. Sergey Yutkevich, 1938), and Adventures of Korzinkina (Priklyucheniya Korzinkinoy, dir. Klimentiy Mints, 1940–1941). Each film and its score represent an approach to particular genres—the speech-focused propaganda film, a feature film, and a short comedy. Analyses of each film score demonstrate Shostakovich’s ability to negotiate multiple styles and genres in scores for diverse film types during the prewar period.
The Long Walk: Spring 1569
Authors: Snow Dean
Published: December 2024

At the northern tip of Chesapeake Bay, the three men left Eastern Algonquian territory to visit a large Northern Iroquoian town on the lower Susquehanna River. Ingram called the town “Balma,” and they remained there for a week, longer than any other place they rested. Balma was a town having large multifamily Iroquoian longhouses. Here Ingram saw fields of maize, beans, and squash. He was invited to witness masked curing ceremonies and was offered trade goods in exchange for the shell beads and other southern goods he carried. Here the travelers learned of the feared Mohawks who lived northward in the interior, their source for valued quartz crystals. Ingram returned to Eastern Algonquian country, following trails closer to the coast from eastern Pennsylvania to southern New England. There they passed through villages that had been visited described by Verrazzano in 1524.
Ingram’s Legacy
Authors: Snow Dean
Published: December 2024

It is unavoidable that David Ingram was a participant in English race-based slavery. However, although he was probably illiterate, the evidence shows that he was a sympathetic and accurate reporter of the environments and cultures of Africa, the Caribbean, and North America. Most important, the evidence also shows that Ingram was not a travel liar. Historians have dismissed his observations for four centuries because they have depended upon Richard Hakluyt’s poorly edited published version of Ingram’s 1582 testimony. A curious postscript is that William Shakespeare apparently used some of Ingram’s testimony as a source for his play The Tempest, which he published in 1623.
Land Concentration
Authors: Berry Albert
Published: December 2024

Land concentration has been a central feature of the history of all empires, regions, and countries, and has underpinned the creation of the state and of inegalitarian and elitist societies. It is the key part of a “monopolization model” whereby a small group has access to the bulk of the available land and as much labor as it needs to achieve a high level of wealth. Access to that labor can occur either through slavery or through a sufficiently large supply of labor to keep its market price very low; this latter condition is fostered by the core group having nearly all the land such that little is left for the rest of the population. The degree of land concentration and elite control of labor have varied across cultures and over time, as have the means of concentration, including physical violence. The main early manifestation of the monopolization model was feudalism, in which both lord and serf had some rights and some obligations. It later morphed into market-based capitalism. When an economy “develops” beyond the phase in which the great majority of output and employment is found in agriculture to a more industrial and service-oriented system, the level of inequality characterizing it at the beginning of this transition tends to persist long after the country is no longer mainly agricultural.
Land Concentration and Agrarian Reform in Recent World History
Authors: Berry Albert
Published: December 2024

The twentieth century saw most countries of the world at early and/or middle stages of economic development with agriculture playing a dominant economic role. Most would have benefited from significant transfers of land from large to small family units. Only a few, most notably the East Asian Tigers, achieved maximum success from such transfers, in the form of fast, equitable growth that quickly did away with poverty. All socialist countries made the initial mistake of switching to state or collective farms. In China, this choice plus Mao’s other mistakes, in particular the “great leap forward,” brought a huge death toll. Both China and Vietnam achieved greater agricultural success and very fast poverty reduction when they eventually delegated decision-making authority to the farm families themselves. These five Asian experiences, plus a few others, constituted the century’s big successes. Failures included blocked reform attempts (Brazil and others); attempts accompanied by much violence (Colombia); and promising attempts that could have brought great benefits but were sabotaged by foreign interests, leading to political and social disasters (Iran and Guatemala). For the many countries where egalitarian agrarian systems could, in principle, still bring many benefits—mostly now found in Sub-Saharan Africa—a major lesson is to avoid letting land concentration reach the levels at which redistributive reform becomes necessary for political and/or societal welfare reasons.
British-Irish Relations in the Twenty-First Century
Authors: Tannam Etain
Published: December 2024

The book examines the impact of the Belfast/Good Friday Agreement and Brexit on Northern Ireland, and British–Irish relations from 1998 to 2023, highlighting not only the Agreement’s successes but also its failures. It highlights the conflicting assumptions about the meaning of sovereignty that fuelled division and were exemplified by Brexiteers. It argues that these differences are likely to intensify over time, given that Brexit placed the constitutional future of Northern Ireland in focus and given the possibility of a referendum on a united Ireland. It is also argued that British and Irish governments consistently underestimated the salience of ethno-national identity politics in Northern Ireland in the decades after the Agreement. A joint intergovernmental strategy will be needed to manage the dual tasks of managing identity politics and supporting those who place pragmatic policy before the constitutional future of Northern Ireland.
From the Anglo-Irish Agreement to the 1998 Agreement
Authors: Tannam Etain
Published: December 2024

In this chapter, the road to the 1998 Belfast/Good Friday Agreement is examined and the role of the Anglo-Irish Agreement (AIA) in 1985 is highlighted as being part of a long-term process that led to the 1998 Agreement. In particular, the role of John Hume, the then leader of the Social Democratic and Labour Party, his work on the three-strands model (Northern Ireland’s consociational devolved government island, institutionalised North–South cooperation on the island of Ireland, and institutionalised East–West cooperation between the islands, including between UK and Irish governments), and his strategy for conflict resolution are highlighted as being key to the development of strategy and statecraft in Northern Ireland and integral to both the AIA and the 1998 Agreement.