bluuebunny/crossref_metadata_2025 huggingface dataset:
FX Comovements and Their Economic Determinants
Authors: Rangel Jose Gonzalo
Published: December 2024

This article models high- and low-frequency dynamic components of FX excess return correlations and examines their relationship with economic fundamentals. A factor pricing model with time-varying betas is used to characterize these correlations. From the low-frequency components, an aggregate comovement measure is derived. This component is countercyclical relative to the U.S., as it is negatively related to economic growth and positively related to both inflation volatility and economic policy uncertainty. Idiosyncratic volatilities also drive currency comovements. I examine their cross-sectional variation and find significant impacts of inflation levels, monetary policy variables, real output growth, trade, and capital flows.
Socioeconomic determinants of cancer screening adherence among cancer survivors: analysis from the 2020 Behavioral Risk Factor Surveillance System
Authors: Beatrici Edoardo , Qian Zhiyu , Filipas Dejan K , Stone Benjamin V , Dagnino Filippo , Labban Muhieddine , Lipsitz Stuart R , Lughezzani Giovanni , Buffi Nicolò M , Cole Alexander P , Trinh Quoc-Dien
Published: December 2024

Background

Factors associated with cancer survivors’ preventive health behaviors are understudied. We hypothesized that socioeconomic and health-care access factors may be associated with adherence to recommended cancer screenings.

Methods

We conducted a cross-sectional analysis using the 2020 Behavioral Risk Factor Surveillance System. Cancer survivors eligible for United States Preventive Services Task Force–recommended breast, cervical, prostate, and colorectal screenings were included. Multivariable logistic regression models were used to identify socioeconomic factors significantly associated with screening adherence.

Results

Overall, 64 958 (weighted national estimate = 29 066 143) cancer survivors were included. Adherence rates varied across cancer types: 80.9% for breast, 88.9% for cervical, 54.1% for prostate, and 84.7% for colorectal cancer. Key predictors of low adherence included lower income (breast: adjusted odds ratio [aOR] = 0.56, 95% confidence interval [CI] = 0.43 to 0.74; cervical: aOR = 0.38, 95% CI = 0.24 to 0.59; prostate: aOR = 0.36, 95% CI = 0.24 to 0.52; colorectal: aOR = 0.74, 95% CI = 0.57 to 0.96), lack of health-care coverage for colorectal cancer (aOR = 0.51, 95% CI = 0.36 to 0.73), time since last checkup between 1 and 2 years prior for breast (aOR = 0.58, 95% CI = 0.45 to 0.75), prostate (aOR = 0.66, 95% CI = 0.47 to 0.91), and colorectal (aOR = 0.69, 95% CI = 0.56 to 0.86) cancer, and no health-care provider for breast (aOR = 0.68, 95% CI = 0.47 to 0.98), prostate (aOR = 0.45, 95% CI = 0.31 to 0.65), and colorectal (aOR = 0.51, 95% CI = 0.40 to 0.66) cancer.

Conclusion

Cancer survivors’ adherence to screening is associated with factors including lack of health-care coverage, lower income, time since the last exam, and having a personal provider. Targeted interventions accounting for such factors may help mitigate these disparities.
Conjoined partners: efficacy and side effects of grafting and dsRNA application on the microbial endophyte population of grapevine plants inoculated with two esca-related fungal pathogens
Authors: Nerva Luca , Gambino Giorgio , Moffa Loredana , Spada Alberto , Falginella Luigi , De Luca Elisa , Zambon Yuri , Chitarra Walter
Published: December 2024

Grafting has been exploited since 7000 BC to enhance productivity, disease resistance, and adaptability of cultivated plants to stressful conditions especially in woody crops such as grapevine (Vitis spp.). In contrast, the application of sequence specific double-stranded RNAs (dsRNAs) to control fungal pathogens and insect pests has only been recently developed. The possibility of combining these approaches to enhance plant resilience, reducing reliance on pesticides, offers new perspectives for a more sustainable agriculture. In this study, we assessed the potential of utilizing dsRNAs to enhance resilience against esca-related wood fungal pathogens in grapevine, considering various rootstock–scion combinations. The results showed that the scion genotype modulates the ability of the rootstock to cope with the inoculated wood fungal pathogens, mainly by altering the efficacy of producing stilbene compounds. Additionally, we found that dsRNAs reduced the growth of two inoculated esca-related fungal pathogens but they did not completely stop their colonization. Furthermore, wood microbiome data showed that the scion genotype (always belonging to Vitis vinifera species) was also able to influence the rootstock-associated microbiota, with a major effect on the fungal community. Lastly, adverse effects on non-target microorganisms are reported, raising questions on the environmental fate of dsRNAs and how dsRNAs can directly or indirectly affect plant-associated microbial communities.
The maize aquaporin ZmPIP1;6 enhances stomatal opening and CO2- and ABA-induced stomatal closure
Authors: Ding Lei , Laurent Maxime J , Milhiet Thomas , Aesaert Stijn , Van Lijsbettens Mieke , Pauwels Laurens , Nelissen Hilde , Inzé Dirk , Chaumont François
Published: December 2024

The plasma membrane aquaporin ZmPIP1;6 is expressed in maize stomatal complexes, with higher expression during the day than at night. To elucidate the role of ZmPIP1;6 in gas exchange and stomatal movement, it was expressed in maize (inbred line B104) under the control of the p35S promoter (overexpression) or its native promoter fused with mYFP (monomeric yellow fluorescent protein) cDNA (mYFP-ZmPIP1;6). In stomatal complexes of the mature zone of the leaf, mYFP–ZmPIP1;6 showed higher expression in subsidiary cells than in guard cells, and light and dark treatments influenced its subcellular localization. Notably, ZmPIP1;6 internalization increased in dark conditions compared with light. Stomatal opening was greater in ZmPIP1;6 overexpression plants than in the wild type, while closure exhibited greater sensitivity to elevated CO2 concentration or abscisic acid (ABA) treatment. Our findings revealed that reactive oxygen species (H2O2) were involved in ABA-induced stomatal closure, while ZmPIP1;6 was unable to facilitate H2O2 diffusion when expressed in yeast. Finally, ZmPIP1;6 overexpression and mYFP-ZmPIP1;6 transgenic plants exhibited higher abaxial stomatal density than the wild type. Overall, these results indicate that ZmPIP1;6 plays important roles in stomatal opening and CO2- and ABA-induced stomatal closure.
Cracking the code of aldosterone synthase deficiency: bridging genetics and biochemistry: a case report
Authors: Kamarajan Lekha Priyadharshini , Mahto Mala , Kumar Sushil , Kumar Pradeep
Published: December 2024

Objective

Aldosterone synthase deficiency (ASD) is a rare autosomal recessive inherited disease with an overall clinical phenotype of failure to thrive, vomiting, severe dehydration, hyperkalemia, and hyponatremia. Mutations in the CYP11B2 gene encoding AS are responsible for the occurrence of ASD. Defects in CYP11B2 gene have only been reported in a limited number of cases worldwide. Due to this potential life-threatening risk, a comprehensive hormonal investigation followed by genetic confirmation is essential for the clinical management of offspring.

Methods

We report a case of a newborn who was found to have persistent hyponatremia, hyperkalemia, low aldosterone level, raised renin levels, normal cortisol, and normal 17 hydroxyprogesterone level, suggesting the diagnosis of isolated ASD.

Results

Genetic report was suggestive of isolated ASD caused by a novel base pair deletion in exon 3, homozygous CYP11B2 variant (chr8:g.142915123_142915125del; depth: 124x d) (p.Lys175del; ENST00000323110.2). After initial steps of rehydration and salt restoration, the child was started on oral tablet fludrocortisone. The child responded well and showed a good gain in growth and development.

Discussion

We elaborate on the biochemical and genetic work-up performed and describe potential pitfalls in CYP11B2 sequencing due to its homology to CYP11B1.
Updates in Human Papillomavirus Vaccination to Improve Medical Readiness in Active Duty Service Members
Authors: Hope Erica R , Kopelman Zachary A , Darcy Kathleen M , Penick Emily R
Published: December 2024

Human papillomavirus (HPV) is the most common sexually transmitted infection in the United States and is associated with the development of genital warts, precancerous lesions, and cancers of the oropharynx, anus, penis, vulva, vagina, and cervix. HPV-associated diseases are preventable through vaccination. An Australian nationwide vaccination program will effectively eliminate cervical cancer as a public health concern by the year 2035. Despite safety and efficacy data, vaccination against HPV is not mandatory for military service members. Active duty service women are more likely to test positive for HPV when compared to dependents, and veterans diagnosed with HPV-associated cancers have higher health care resource utilization and costs. Even if a patient has a prior HPV infection, vaccination at the time of HPV diagnosis or following treatment can reduce recurrence of HPV and dysplasia. In addition, patients with a history of cancer have a higher incidence of secondary HPV-associated malignancies and should be offered vaccination or re-vaccination if they received a hematopoietic stem-cell transplant. Improving HPV vaccination rates within the military health system requires a multidisciplinary approach. Providers should use every opportunity to recommend HPV vaccination, including recommending HPV vaccines for individuals who do not have a record of HPV vaccination. The electronic health record can be utilized to generate prompts for vaccine reminders, and clinics should stock HPV vaccines to allow for easy administration. Additionally, adoption of an opt-out policy for HPV vaccines rather than mandatory vaccination may be an acceptable alternative to increase HPV vaccination while allowing active duty service members to retain autonomy.
Mortality patterns in candidemia: Insights from a multispecies analysis using a global research network
Authors: Thompson III George R , Chastain Daniel B , Ferraz Carolina , Alhayek Soubhi , Salinas Jorge L , Sillau Stefan , Stenehjem Edward A , Henao-Martínez Andrés F
Published: December 2024

Understanding the impact of different Candida species on patient outcomes is crucial for effective management and treatment strategies. This study aims to comprehensively analyze the association between Candida species and mortality in documented candidemia. We queried TriNetX, a global research network database, to identify patients diagnosed with candidemia through polymerase chain reaction from 2020 to 2023. The primary outcome was mortality in candidemia patients, categorized by Candida species at 90 days and 1 year. The time to death was assessed using Kaplan–Meier plots. Cox proportional hazard (PH) models were also used for comparative analysis, unadjusted and adjusted for demographic and comorbidity covariates. We captured 1234 candidemia episodes during the study period. The 90-day and 1-year mortality rates for the various Candida species were as follows: C. tropicalis (33.9% and 35.6%), C. glabrata (28.3% and 34%), multispecies (27.7% and 36.4%), C. parapsilosis (25.8% and 31.8%), C. krusei (21.4% and 28.6%), C. albicans (21.1% and 23.9%), and C. auris (13.3% and 15.9%). The unadjusted Kaplan–Meier Survival analysis showed that multispecies candidemia, followed by C. tropicalis, had the lowest survival. The adjusted multivariable Cox PH model found that C.albicans, C. glabrata, C. parapsilosis, C. tropicalis, and multispecies candidemia had significantly higher mortality rates than C. auris. Age and a higher Charlson comorbidity index value emerged as independent predictors of increased mortality. Among patients with candidemia, we found an overall 1-year mortality of 28%. Multispecies candidemia, C. tropicalis, older age, and a higher comorbidity burden were associated with the highest mortality rates.
Detection and characterization of giant planets with Gaia astrometry
Authors: Wallace A L , Casey A R , Brown A G A , Castro-Ginard A
Published: December 2024

Astrometric observations with Gaia are expected to play a valuable role in future exoplanet surveys. With current data from Gaia’s third data release (DR3), we are sensitive to periods from less than 1 yr to more than 4 yr but, unlike radial velocity (R.V.) are not as restricted by the orbital inclination of a potential planet. The presence and potential properties of a companion affect the primary’s renormalized unit weight error (RUWE) making this a valuable quantity in the search for exoplanets. Using this value and the fitted astrometric tracks from Gaia, we use Bayesian inference to constrain the mass and orbital parameters of companions in known systems. Combining this with R.V. measurements, we show it is possible to independently measure mass and inclination and suggest HD 66141 b is a possible brown dwarf with maximum mass 23.9$^{+7.2}_{-6.4}$ $\mathrm{ M}_{\mathrm{J}}$. We show how this method may be applied to directly imaged planets in the future, using $\beta$-Pictoris c as an example but note that the host star is bright and active, making it difficult to draw clear conclusions. We show how the next Gaia data release, which will include epoch astrometry, will allow us to accurately constrain orbital parameters from astrometric data alone, revolutionizing future searches for exoplanets. Combining predicted observational limits on planet mass with theoretical distributions, we estimate the probability that a star with a given RUWE will host a detectable planet, which will be highly valuable in planning future surveys.
SN 2023tsz: a helium-interaction-driven supernova in a very low-mass galaxy
Authors: Warwick B , Lyman J , Pursiainen M , Coppejans D L , Galbany L , Jones G T , Killestein T L , Kumar A , Oates S R , Ackley K , Anderson J P , Aryan A , Breton R P , Chen T W , Clark P , Dhillon V S , Dyer M J , Gal-Yam A , Galloway D K , Gutiérrez C P , Gromadzki M , Inserra C , Jiménez-Ibarra F , Kelsey L , Kotak R , Kravtsov T , Kuncarayakti H , Magee M R , Matilainen K , Mattila S , Müller-Bravo T E , Nicholl M , Noysena K , Nuttall L K , O’Brien P , O’Neill D , Pallé E , Pessi T , Petrushevska T , Pignata G , Pollacco D , Ragosta F , Ramsay G , Sahu A , Sahu D K , Singh A , Sollerman J , Stanway E , Starling R , Steeghs D , Teja R S , Ulaczyk K
Published: December 2024

SN 2023tsz is a Type Ibn supernova (SN Ibn), an uncommon subtype of stripped-envelope core-collapse supernovae (SNe), discovered in an extremely low-mass host. SNe Ibn are characterized by narrow helium emission lines in their spectra and are believed to originate from the collapse of massive Wolf–Rayet (WR) stars, though their progenitor systems still remain poorly understood. In terms of energetics and spectrophotometric evolution, SN 2023tsz is largely a typical example of the class, although line profile asymmetries in the nebular phase are seen, which may indicate the presence of dust formation or unshocked circumstellar material. Intriguingly, SN 2023tsz is located in an extraordinarily low-mass host galaxy that is in the second percentile for stripped-envelope SN host masses and star formation rates (SFRs). The host has a radius of 1.0 kpc, a g-band absolute magnitude of $-12.72 \pm 0.05$, and an estimated metallicity of $\log (Z_{*}/{\rm Z}_{\odot }) \approx -1.6$. The SFR and metallicity of the host galaxy raise questions about the progenitor of SN 2023tsz. The low SFR suggests that a star with sufficient mass to evolve into a WR would be uncommon in this galaxy. Further, the very low metallicity is a challenge for single stellar evolution to enable H and He stripping of the progenitor and produce an SN Ibn explosion. The host galaxy of SN 2023tsz adds another piece to the ongoing puzzle of SNe Ibn progenitors, and demonstrates that they can occur in hosts too faint to be observed in contemporary sky surveys at a more typical SN Ibn redshift.
Structural plasticity of the coiled–coil interactions in human SFPQ
Authors: Koning Heidar J , Lai Jia Y , Marshall Andrew C , Stroeher Elke , Monahan Gavin , Pullakhandam Anuradha , Knott Gavin J , Ryan Timothy M , Fox Archa H , Whitten Andrew , Lee Mihwa , Bond Charles S
Published: December 2024

The proteins SFPQ (splicing Factor Proline/Glutamine rich) and NONO (non-POU domain-containing octamer-binding protein) are mammalian members of the Drosophila Behaviour/Human Splicing (DBHS) protein family, which share 76% sequence identity in their conserved 320 amino acid DBHS domain. SFPQ and NONO are involved in all steps of post-transcriptional regulation and are primarily located in mammalian paraspeckles: liquid phase-separated, ribonucleoprotein sub-nuclear bodies templated by NEAT1 long non-coding RNA. A combination of structured and low-complexity regions provide polyvalent interaction interfaces that facilitate homo- and heterodimerisation, polymerisation, interactions with oligonucleotides, mRNA, long non-coding RNA, and liquid phase-separation, all of which have been implicated in cellular homeostasis and neurological diseases including neuroblastoma. The strength and competition of these interaction modes define the ability of DBHS proteins to dissociate from paraspeckles to fulfil functional roles throughout the nucleus or the cytoplasm. In this study, we define and dissect the coiled–coil interactions which promote the polymerisation of DBHS proteins, using a crystal structure of an SFPQ/NONO heterodimer which reveals a flexible coiled–coil interaction interface which differs from previous studies. We support this through extensive solution small-angle X-ray scattering experiments using a panel of SFPQ/NONO heterodimer variants which are capable of tetramerisation to varying extents. The QM mutant displayed a negligible amount of tetramerisation (quadruple loss of function coiled-coil mutant L535A/L539A/L546A/M549A), the Charged Single Alpha Helix (ΔCSAH) variant displayed a dimer-tetramer equilibrium interaction, and the disulfide-forming variant displayed constitutive tetramerisation (R542C which mimics the pathological Drosophila nonAdiss allele). We demonstrate that newly characterised coiled–coil interfaces play a role in the polymerisation of DBHS proteins in addition to the previously described canonical coiled–coil interface. The detail of these interactions provides insight into a process critical for the assembly of paraspeckles as well as the behaviour of SFPQ as a transcription factor, and general multipurpose auxiliary protein with functions essential to mammalian life. Our understanding of the coiled coil behaviour of SFPQ also enhances the explanatory power of mutations (often disease-associated) observed in the DBHS family, potentially allowing for the development of future medical options such as targeted gene therapy.
PRMT1-mediated methylation regulates MLL2 stability and gene expression
Authors: An Dongju , Kim Jihyun , Moon Byul , Kim Hyoungmin , Nguyen Hoa , Park Sunghu , Lee J Eugene , Kim Jung-Ae , Kim Jaehoon
Published: December 2024

The interplay between multiple transcription factors precisely regulates eukaryotic transcription. Here, we report that the protein methyltransferases, MLL2/KMT2B and PRMT1, interact directly and act collectively to regulate gene expression. PRMT1 binds to the N-terminal region of MLL2, considered an intrinsically disordered region, and methylates multiple arginine residues within its RGG/RG motifs. Notably, overexpression of PRMT1 decreased poly-ubiquitylation of MLL2, whereas mutations on methylation sites in MLL2 increased MLL2 poly-ubiquitylation, suggesting that PRMT1-mediated methylation stabilizes MLL2. MLL2 and PRMT1 cooperatively stimulated the expression of a chromosomal reporter gene in a PRMT1-mediated, MLL2-methylation-dependent manner. RNA-seq analysis found that MLL2 and PRMT1 jointly regulate the expression of genes involved in cell membrane and extracellular matrix functions, and depletion of either resulted in impaired cell migration and invasion. Our study provides evidence that PRMT1-mediated MLL2 methylation regulates MLL2 protein stability and the expression of their target genes.
Mining single-cell data for cell type–disease associations
Authors: Chen Kevin G , Farley Kathryn O , Lassmann Timo
Published: December 2024

A robust understanding of the cellular mechanisms underlying diseases sets the foundation for the effective design of drugs and other interventions. The wealth of existing single-cell atlases offers the opportunity to uncover high-resolution information on expression patterns across various cell types and time points. To better understand the associations between cell types and diseases, we leveraged previously developed tools to construct a standardized analysis pipeline and systematically explored associations across four single-cell datasets, spanning a range of tissue types, cell types and developmental time periods. We utilized a set of existing tools to identify co-expression modules and temporal patterns per cell type and then investigated these modules for known disease and phenotype enrichments. Our pipeline reveals known and novel putative cell type–disease associations across all investigated datasets. In addition, we found that automatically discovered gene co-expression modules and temporal clusters are enriched for drug targets, suggesting that our analysis could be used to identify novel therapeutic targets.
GRAViTy-V2: a grounded viral taxonomy application
Authors: Mayne Richard , Aiewsakun Pakorn , Turner Dann , Adriaenssens Evelien M , Simmonds Peter
Published: December 2024

Taxonomic classification of viruses is essential for understanding their evolution. Genomic classification of viruses at higher taxonomic ranks, such as order or phylum, is typically based on alignment and comparison of amino acid sequence motifs in conserved genes. Classification at lower taxonomic ranks, such as genus or species, is usually based on nucleotide sequence identities between genomic sequences. Building on our whole-genome analytical classification framework, we here describe Genome Relationships Applied to Viral Taxonomy Version 2 (GRAViTy-V2), which encompasses a greatly expanded range of features and numerous optimisations, packaged as an application that may be used as a general-purpose virus classification tool. Using 28 datasets derived from the ICTV 2022 taxonomy proposals, GRAViTy-V2 output was compared against human expert-curated classifications used for assignments in the 2023 round of ICTV taxonomy changes. GRAViTy-V2 produced taxonomies equivalent to manually-curated versions down to the family level and in almost all cases, to genus and species levels. The majority of discrepant results arose from errors in coding sequence annotations in INDSC records, or from inclusion of incomplete genome sequences in the analysis. Analysis times ranged from 1-506 min (median 3.59) on datasets with 17-1004 genomes and mean genome length of 3000–1 000 000 bases.
Infiltrative classical monocyte-derived and SPP1 lipid-associated macrophages mediate inflammation and fibrosis in ANCA-associated glomerulonephritis
Authors: Vegting Yosta , Jongejan Aldo , Neele Annette E , Claessen Nike , Sela Gal , Prange Koen H M , Kers Jesper , Roelofs Joris J T H , van der Heijden Joost W , de Boer Onno J , Remmerswaal Ester B M , Vogt Liffert , Bemelman Frederike J , de Winther Menno P J , Moerland Perry D , Hilhorst Marc L
Published: December 2024

Background

Kidney macrophage infiltration is a histological hallmark of vasculitic lesions and is strongly linked to disease activity in anti-neutrophil cytoplasmic antibodies (ANCA)-associated glomerulonephritis (AGN). The precise mechanisms by which kidney macrophages influence local inflammation and long-term damage remain largely unknown.

Methods

Here, we investigate kidney macrophage diversity using single-cell transcriptome analysis of 25 485 freshly retrieved unfrozen, high-quality kidney CD45+ immune cells from five AGN patients during active disease, a lupus nephritis and a nephrectomy control. Detailed subclustering of myeloid cells was performed to identify disease-specific macrophage subtypes. Next, transcriptome differences between macrophage subsets and disease serotypes were assessed. Findings were validated by immunostainings of an extended cohort of kidney biopsies and flow cytometric analysis of peripheral blood monocytes.

Results

Four main macrophage subsets were identified, including a classical monocyte-derived macrophage (MDM) subset expressing a chemotactic (CXCL2, CXCL3, CXCL8, CCL3) and pro-inflammatory (IL1β, TNF) set of markers and an osteopontin/SPP1+ lipid-associated macrophage (SPP1 LAMs) subtype exhibiting distinctive upregulation of fibrotic genesets. AGN samples revealed a markedly increased proportion of CD163+ macrophages, predominantly composed of classical MDMs, accompanied by resident-like C1Q macrophages, and SPP1 LAMs. An analogous trend was observed in the expansion of peripheral blood classical monocytes during active disease. The proteinase 3 (PR3)-AGN subtype exhibited heightened classical MDM and SPP1 LAM infiltration and markers of acute inflammation, while interferon signaling and markers of chronicity were reduced compared with myeloperoxidase-AGN.

Conclusions

Our findings highlight the expression of inflammatory and fibrotic genes by kidney macrophage subsets in AGN. Classical monocyte dysregulation might contribute to inflammation in the pathogenesis of AGN. Targeting these specific monocyte/macrophage subsets may potentially control the inflammatory cascade and attenuate resulting fibrosis in AGN and kidney disease in general.
Recovery of Mycobacterium tuberculosis Complex Isolates Including Pre–Extensively Drug-Resistant Strains From Cattle at a Slaughterhouse in Chennai, India
Authors: Ramanujam Harini , Refaya Ahmed Kabir , Thiruvengadam Kannan , Pazhanivel Natesan , Kandasamy Devika , Shanmugavel Ashokkumar , Radhakrishnan Ammayappan , Radhika Golla , Ravi Rajkumar , Ravi Neelakandan , Palanisamy Maheswaran , Shanmugam Sivakumar , Stuber Tod P , Kapur Vivek , Palaniyandi Kannan
Published: December 2024

Background

India has the highest global burden of human tuberculosis (TB) and the largest cattle herd with endemic bovine TB (bTB). However, the extent of cross-species transmission and the zoonotic spillover risk, including drug-resistant Mycobacterium tuberculosis complex (MTBC) strains circulating in cattle, remain uncharacterized.

Methods

To address this major knowledge gap, we investigated tissue samples from 500 apparently healthy cattle at a slaughterhouse in Chennai, India. Whole genome sequencing was performed to characterize the isolates.

Results

Sixteen animals (32 per 1000 [95% confidence interval, 16–47]) were MTBC-positive, a rate that is nearly an order of magnitude greater than the reported human TB incidence in the region. Thirteen isolates were identified as Mycobacterium orygis and 3 were M tuberculosis: 1 was a mixed infection of M tuberculosis lineage 1 and M orygis, and the other 2 had pure growth of M tuberculosis lineage 2, in both cases pre–extensively drug-resistant (pre-XDR) with identical resistance patterns and separated by 7 single-nucleotide polymorphisms. The results confirm that bTB in this region is primarily due to M orygis and M tuberculosis, and not Mycobacterium bovis.

Conclusions

The detection of pre-XDR M tuberculosis in cattle highlights a potential public health concern, since controlling human TB alone may be insufficient without addressing bovine TB. Overall, our findings underscore an urgent need for targeted interventions to mitigate zoonotic tuberculosis transmission in regions where bTB is endemic.
Ideas of Closure
Authors: Caplin William E.
Published: December 2024

This chapter surveys general concepts of closure in everyday life, gestalt psychology, and literature, especially poetry. Important for the latter are the concepts of terminal modification, a significant change in the final lines of a poem, as well as formal circularity, created by bringing back the opening lines of a poem to conclude it. The chapter shows how these ideas resonate in discussions on closure by music theorists. Some of their formulations are relatively abstract, while others are more pertinent to the topic of cadential closure specifically. Leonard Meyer discusses how closure is created foremost by syntactical parameters (harmony, melody, meter); Kofi Agawu differentiates between closure and ending; Robert Hatten proposes a notion of dramatic closure; Patrick McCreless relates musical closure to a more general sense of narrative closure; Mark Anson-Cartwright offers three definitions of musical closure, all of which characterize it as expressing differing modes of ending and finality.
Cadential Deviations
Authors: Caplin William E.
Published: December 2024

This chapter investigates how promised cadences may fail to be realized by means of cadential deviations. Three deviation types—deceptive cadence, evaded cadence, and abandoned cadence—are associated with authentic cadences, whereas an implied half cadence may bring in its place various kinds of dominant arrival. Each deviation type is defined by how its harmonic content and grouping structure disrupt the norms of genuine cadential closure. The deviations normally involve processes that loosen the formal organization. Especially typical is how a cadential deviation functions as a way station on the road to an eventual perfect authentic cadence, thus helping to defer that cadence in time and making its arrival a strongly articulated rhetorical event. Dominant arrivals are shown to be manifest by a variety of harmonic means, as well as by how they often appear in a manner that seems premature to the actual closing of various thematic processes.
Cadential Expansion
Authors: Caplin William E.
Published: December 2024

This chapter examines various techniques for cadential expansion from both morphological and form-functional perspectives. Whereas a simple, relatively compact cadence typically lasts one or two measures, a cadence supported by an expanded cadential progression (ECP) occupies four or more measures and supports one or more phrases of a theme. In that the means of expansion are essentially harmonic, the chapter treats, in turn, how the initial tonic, pre-dominant, and dominant harmonies of a cadence can undergo significant lengthening, often accompanied by extensive chromaticism. It assesses as well the extent to which the theory of cadential melody introduced in Chapter 3 is applicable to ECPs, especially in the context of highly embellished melodic lines. The chapter considers how cadential deviations work in connection with phrase expansion techniques and concludes by analyzing some remarkable expanded cadences in Beethoven’s symphonic oeuvre.
Mappings
Authors: Müller Ulrich , de la Flor Gemma
Published: December 2024

A mapping which maps parallel straight lines onto parallel straight lines is an affine mapping. It is represented by a set of equations that relate the coordinates of an initial point with the coordinates of its image point. For a concise notation, the equations are recorded as matrix—column pairs (W,w). An isometry is an affine mapping that leaves distances and angles unchanged. If, in addition, the object is mapped onto itself, it is a symmetry operation and it is a crystallogtaphic symmetry operation if the object is a crystal. The set of all symmetry operations of a crystal is its space group. Changes of the coordinate system entail changes of the coordinates that are calculated by equations similar to those of affine mappings.
Group theory
Authors: Müller Ulrich , de la Flor Gemma
Published: December 2024

A group is set of elements that fulfils the group axioms. A subset that also fulfils the axioms is a subgroup. According to certain rules, the elements of a group can be decomposed to a subgroup and i −1 cosets; i is the index of the subgroup. Two subgroups of a symmetry group G are conjugate if they are transformed one to another by some other symmetry operation of the same group G. If a symmetry group G acts on a point (or atom) X, it yields a set of symmetry-equivalent points called the orbit of X under G.
Conjugate subgroups and normalizers of space groups
Authors: Müller Ulrich , de la Flor Gemma
Published: December 2024

Conjugate subgroups of space groups together form a conjugacy class. Conjugate maximal subgroups of space groups show either orientational conjugation or translational conjugation. In a group—subgroup pair G > H, the normalizer of H in G is the group of all elements of G that map H onto itself. The Euclidean normalizer of a space group is a supergroup of the space group that maps all symmetry elements of the space group onto equal symmetry elements; it exhibits the ‘symmetry of the symmetry’. Subgroups on a par belong to different conjugacy classes, have the same lattice dimensions and the same space-group type.
Historical remarks
Authors: Müller Ulrich , de la Flor Gemma
Published: December 2024

Historical development of the theory of space groups, the symmetry principle, and the use of group—subgroup relations of space groups.
Symmetry species
Authors: Müller Ulrich , de la Flor Gemma
Published: December 2024

A table of the symbols for most important irreducible representations is given.
Early childhood contexts for learning mathematics
Authors: Barkai Ruthi , Levenson Esther , Tsamir Pessia , Tirosh Dina
Published: December 2024

It is well known that children enter the first grade with mathematical skills, conceptions, and misconceptions. Thus, early childhood mathematics research can inform elementary school mathematics educators. This chapter reviews plenary talks, research reports, posters, and workshops presented at the Symposium on Elementary Mathematics Teaching (SEMT) over the past 30 years, regarding children who have not yet entered the first grade. Tthe chapter focuses on early childhood contexts for learning number concepts, geometry, spatial reasoning, and patterns and generalization. These contexts often involve the senses, employing sight, hearing, and touch. Furthermore, reviewing past studies also showed that the same context may be used for promoting different mathematical concepts and skills. Most of the early childhood studies reported at past SEMTs occurred in preschools or elementary schools. Recognizing the importance of out-of-school settings as contexts for early mathematical learning, we next describe current research with adults who are not preschool teachers.
Learning to solve word problems with understanding
Authors: Vondrová Naďa
Published: December 2024

Word problems have been investigated in mathematics education research for many decades and standpoints. Topics researched by SEMT authors roughly fit into four broad categories. The first investigates the characteristics of pupils and how these affect their ability to solve these problems (e.g. being strong or weak in mathematics). The second focuses on variables that make word problems difficult (e.g. order of the data, context, language consistency). The most attention has been given to the third category, studies on the effect of different instructional methods on pupils’ problem-solving ability. The fourth category is lack of attention to effects of classroom-related conditions on pupils’ ability to solve word problems. This chapter summarizes the main results of SEMT presentations on word problems in which methodology is presented. These results are discussed against outcomes from international research. Three meta-analyses of studies of word problems are used towards this aim.
Elementary mathematics teaching: Relevance, conceptualizations, and research
Authors: Višňovská Jana , Luis Cortina José , Vale Pamela
Published: December 2024

In classroom situations, teaching and learning are closely connected. Through examples drawn from contributions to the SEMT over time, this chapter explores and illustrates ways in which research on mathematics learning has implicitly and explicitly addressed this connection, and how research on mathematics teaching emerged as an area of focus in its own right. It then specifically attends to interventionist work (design research informed by Realistic Mathematics Education instructional design theory) as a thread within SEMT endeavours, within which the authors took part in a shift in focus from student learning, first to a focus on their teaching, and then to one on supporting the teaching of others. They view this chapter as an invitation to discuss the future of research into mathematics teaching as an area with the overt aim of supporting the work of teachers.
From variation pedagogy and Lesson Study to cultural transposition
Authors: Bussi Maria Bartolini , Ramploud Alessandro
Published: December 2024

This chapter reconstructs the research trajectory of the authors, an academic researcher and a primary school teacher who worked as a full-time supervisor for the practicum of prospective primary school teachers at SEMT 2011. An early introduction to variation pedagogy was given, reporting some Italian experiments in primary school. The two authors together introduced a version of Lesson Study to Italian teachers, drawing on their experience in China and Japan, where these models of teacher education and development are implemented systematically. Drawing on their experience, the second author, in collaboration with a small group of Italian researchers, carried on the elaboration of the theoretical construct of cultural transposition. The aim of this chapter is to reconstruct the recent story of variation pedagogy, as interpreted by the Italian community, through the lenses of cultural transposition, to be interpreted both as a design and an analytical tool.
Japanese Lesson Study: Insights from SEMT
Authors: Doig Brian , Groves Susie
Published: December 2024

Looking at past SEMT papers, it now seems strange that the now internationally well-known Japanese Lesson Study, and the structured problem-solving approach in mathematics, were unfamiliar in some European countries. However, looking back at three different presentations at SEMT, it would appear that the idea was not only novel, but also well received. This chapter looks at three very different presentations—a plenary address, a paper presentation, and a workshop—all with a focus on this topic. While the authors of these different presentations take different perspectives on their topics, the fundamental basis is the Japanese Lesson Study tradition, with a particular emphasis on the structured problem-solving mathematics lesson within the framework of Lesson Study. The three papers that this chapter is based upon come from two different SEMT symposia, and have very different substantive bases. However, despite this, they offer the reader insights into how one foreign pedagogical culture can be implemented in another. While some of the examples included here provide more information than others, the sum of them gives sufficient information for an interested reader to start their own journey in this pedagogically fruitful field.
Democracy in Action
Authors: Dzur Albert W. , Hendriks Carolyn M.
Published: December 2024

Around the globe citizens are leading practical experimental civil society efforts to solve complex problems in areas such as crime and punishment, energy, care, environmental conservation, planning, food security, and substance use. This book casts light on these spaces of citizens’ governance and draws out their potential benefits and risks for democracy. Drawing on more than 30 case studies from diverse regions and policy domains, the book shows how citizens in these bottom-up initiatives often interconnect their governance work with public and private sector actors; while keeping their agency, they draw resources and authority on the one hand, and model innovation and change on the other. The book renders more visible the citizen motivations, associational form, knowledge production, and democratic work of these spaces, and considers key lessons they hold for boosting and deepening political participation in modern systems of democracy. Citizen spaces reset expectations for citizen action and break down conventional understandings of crystalized divisions of labor in governance between citizen, official, and market.
Citizen Action in Uncertain Times: Contextualizing Citizens’ Governance Spaces
Authors: Dzur Albert W. , Hendriks Carolyn M.
Published: December 2024

This chapter introduces the key ideas in the book and elaborates on the concept of citizens’ governance spaces, stressing its analytic and practical value for understanding sources of social innovation and political participation in civil society. Also considered is the political context in which these spaces emerge and operate, focusing in on three broad trends in contemporary democracies: decentered governance, rising distrust, and polarization. The chapter lays out the book’s methodological approach which is grounded in over 30 empirical cases of citizen-led governance from around the globe. The final section explores normative characteristics, distinguishing between “good” citizen governance practices that identify and respond to basic needs and increase democratic governance from “bad” practices that are exclusionary and allow coercion and deception. It then outlines the arguments of the five chapters that follow.
Living in a Materials World
Authors: Addison Tony , Roe Alan
Published: December 2024

This chapter sketches out the scope and structure of the book Resources Matter: Ending Poverty While Protecting Nature. The book aims to broaden the development debate around the extractive industries. And within that debate, the narrative focuses on transparency in the collection and use of the revenues arising from mining and oil and gas extraction to combat the resource curse traditionally associated with the sector. Confining discussion to transparency is insufficient because any discussion of the extractive sector must also grapple with the industries’ pivotal role in relation to climate change; not only as a supplier of the critical materials necessary if the net-zero transition is to be achieved but also as a source of the fossil fuels that contribute so much to the growth of emissions. Readers will find discussions on transparency, as well as those of economic management, together with those of climate and the sector’s impact on nature more broadly.
Seizing the Opportunities
Authors: Addison Tony , Roe Alan
Published: December 2024

This chapter focuses on the three main transformations required—in economies, states, companies—and the related attitudes and policies that are necessary to seize the opportunities while also managing the risks. Huge investments in mining are underway, not least to meet the material needs of net zero, and judicious complementary investments and policy reforms can deliver greater benefit to national economies. The resource curse is not inevitable. At the same time, the chapter reinforces Chapter 3’s message that renewable natural capital has the greatest long-run economic value. Successful economic transformation requires success in transforming the state: ensuring transparency and reducing corruption and building the capacities of local and central government—especially in project selection and management. Effective partnerships can then be built with companies, the best of which are now delivering more community benefit, decarbonization, and minimal environmental impact.
Values, Knowledge, and Interests
Authors: Addison Tony , Roe Alan
Published: December 2024

This chapter concludes the book by restating and summarizing its main arguments under three headings. The first is values, and specifically the value that societies assign to ending poverty, versus the value assigned to protecting nature. Given their limited finances, the governments of poor countries tend to prioritize poverty over nature. The second is knowledge: we now have a great deal more evidence about how to improve the developmental role of the extractive industries. Knowledge also encompasses scientific and technological advances which have the capacity to upturn markets for metals, materials, and fuels with major consequences for the fortunes of nations. The third is interests: groups within society can oppose or promote desirable reforms. Additionally, nation states have interests and compete with each other; we have now entered a new geopolitical era characterized by heightened conflict—which will surely have profound implications for the prospects of the extractive industries.
Introduction
Authors: Rutter Tom
Published: December 2024

This chapter provides a justification for considering Shakespeare’s engagement with scientific themes, as well as addressing the potential objection that science in its modern sense did not exist during his lifetime. It discusses the terminology used to describe the study of nature in Shakespeare’s time, summarizes the debate over whether a ‘scientific revolution’ began in the seventeenth century, and outlines how Shakespeare has been positioned in relation to science by recent critics. It then summarizes the contents of the chapters that follow, as well as the book’s contribution to its field: namely, the range of topics it synthesizes, the evidence it supplies for Shakespeare’s extensive interest in science, and its emphasis on the importance of dramatic form and performance in Shakespeare’s engagement with the topic.
Matter
Authors: Rutter Tom
Published: December 2024

This chapter considers the multiple ways of thinking about matter upon which Shakespeare draws. It begins by showing how the Sonnets are variously informed by elemental theory, Ovidian ideas of matter as continually changing, the language of alchemy, and the miraculous behaviour of matter in the Eucharist. It goes on to discuss the extent of Shakespeare’s familiarity with atomism, a model extensively set out in Lucretius’s poem De rerum natura, focusing in particular on Hamlet, Antony and Cleopatra, and King Lear. Finally, it considers The Tempest, a play that brings questions of matter and materiality to the fore as well as thematizing the relationship between science, magic, and colonization.
Sufi Devotional Performances in Multan, Pakistan, a “City of Saints”
Authors: Gillani Karim
Published: December 2024

Multan is an ancient capital and crossroads with a significant Muslim presence since the tenth century. As one of the most important trading centers of medieval Islamic India, it attracted Sufi mystics and became known as Madinat al-Awliya, a “city of saints,” and a vibrant center for learning and teaching. Its Sufi saints and shrines attract large numbers of devotees throughout the year. Besides various Sufi orders, the city has also attracted many mystics, the most significant among them Bahauddin Zakariya, Pir Shams Sabzwari, and Shah Rukn-e-Alam. This chapter examines the performance of qawwali at Bahauddin Zakariya and Shah Rukn-e-Alam shrines, which serves to arouse mystical love and remembrance (dhikr) of the divine: the core experience of Sufism. In two examples, drawn from field research in 2002, this chapter demonstrates contexts through which people of Multan experience and accept a variety of religious beliefs and teachings in their daily lives.
Sindhi Kafi and Vernacular Islam in Western India
Authors: Bond Brian E.
Published: December 2024

This chapter discusses contemporary practice of the Sindhi-language kafi genre, in which singers perform metaphorical Sufi poetry based on the rich narrative tradition of the Indus Valley, continuing the Sufi tradition of transmitting Islam through affectively powerful stories. In Kachchh, Gujarat, a borderland in western India adjacent to Sindh, Pakistan, amateur Muslim singers from agriculturalist and pastoralist communities learned to sing Sindhi repertoire by imitating singers they heard on cross-border Pakistani radio and Pakistani cassettes. This chapter discusses the musico-poetic repertoire of Sindh’s most important poet-saint, Shah ʿAbdul Latif Bhitai, who allegorized over a dozen regional narratives and indelibly imbued them with Islamic meaning. It focuses on the poignant tale of ʿUmar and Marui to explore how poetry enthusiasts and performers bring this story and Shah Bhitai’s poetry based on it to bear emotional meaning in multiple dimensions of their lives.