bluuebunny/crossref_metadata_2025 huggingface dataset:
Anomaly Time
Authors: BOWLES BOONE , REED ADAM V. , RINGGENBERG MATTHEW C. , THORNOCK JACOB R.
Published: July 2024

We examine the timing of returns around the publication of anomaly trading signals. Using a database that captures when information is first publicly released, we show that anomaly returns are concentrated in the first month after information release dates, and these returns decay soon thereafter. We also show that the academic convention of forming portfolios in June underestimates predictability because it uses stale information, which makes some anomalies appear insignificant. In contrast, we show many anomalies do predict returns if portfolios are formed immediately after information releases. Finally, we develop guidance on forming portfolios without using stale information.
Classification system for maxillary fixed dental prostheses
Authors: Zaninovich Michael , Petrucci Cosimo , Drago Carl
Published: July 2024

Purpose

To present an addendum to existing fixed dental prostheses (FDPs) classification system for maxillary prostheses. The new classification identifies the relationships between FP‐1 (fixed prostheses) designs and newly developed clinical interdental gingival contours.

Materials and Methods

Clinical and laboratory descriptions of the various types of full‐arch fixed prostheses are described with photographic illustrations. Benefits and limitations of the various prosthetic designs are explained. Surgical differences in the amount of alveolectomy are illustrated. One clinical case is demonstrated.

Results

A new classification system for maxillary implant fixed complete dentures is presented. The new system will serve as an improved communication aid for clinicians, patients, and laboratory technicians. Treatment of patients with edentulous maxillae and/or terminal dentitions and implant fixed complete dentures include several options relative to design and materials. Restorative space can have a major impact on prosthesis design and longevity. Early on in dental implant therapy, prostheses were generally made with cast metal frameworks, denture bases and denture teeth. Prosthetic complications were widely reported. With increased clinical experience and improved materials, computer‐aided design and computer‐aided manufacturing (CAD‐CAM) protocols were developed that allowed stronger prostheses to be constructed in reduced or small restorative volumes. FP‐1 ceramic implant‐supported fixed prostheses (CISFPs) are designed to replace only the dental hard tissues and to promote preservation and rehabilitation of gingival soft tissues. The physical properties and minimum thickness requirements in full arch prostheses are influenced by several factors including distances between implants and rigid connector sizes.

Conclusion

FP‐1 CISFPs may be the closest prostheses the profession can offer edentulous patients that mimic the look, feel, and function of missing dentitions. Aesthetic outcomes of FP‐1 CISFPs are variable and depend on a multitude of factors. This article presented a classification system that builds on existing classification by identifying the level of papilla heights achieved with FP‐1 CISFPs.
Characterization, phylogenetic analysis and toxigenic potential of Fusarium incarnatum‐equiseti species complex isolates associated with root rot disease in vegetables
Authors: Ghosal Debraj , Datta Bejoysekhar
Published: July 2024

Fusarium incarnatum‐equiseti species complex infects a wide variety of food crops. Six fungal isolates were isolated from rotted roots of Dolichos lablab (hyacinth bean), Trichosanthes dioica (pointed gourd), Momordica dioica (spiny gourd), Capsicum frutescens (chilli) and Pisum sativum (garden pea), and identified as Fusarium spp., belonging to Fusarium incarnatum‐equiseti species complex (FIESC), through conidial morphology, sporodochia on carnation leaf agar medium and sequencing of nuclear ITS‐rRNA and transcription elongation factor 1α gene. Multilocus phylogenetic analysis demonstrated their inclusion within the Incarnatum clade of FIESC. All of them were self‐incompatible and failed to pair with other isolates. Vegetative incompatibility affected their pathogenicity and host specificity. The isolates secreted extracellular cell wall degrading enzymes cellulase (0.033 ± 0.002–0.403 ± 0.020 U.mL−1), polygalacturonase (0.005 ± 0.0001–0.392 ± 0.010 U.mL−1) and pectin‐lyase (0.015 ± 0.001–0.407 ± 0.012 U.mL−1) for direct penetration to root tissue. They also secreted toxic metabolites that inhibited germination of Cicer arietium (chickpea) and Pisum sativum (garden pea) seeds. The isolates exhibited complete pathogenicity on their original hosts (death due to root rotting, Disease Severity Index‐ 100%) but less pathogenicity in other non‐host plants (yellowing of lower leaves without sign of root rot, Disease Severity Index‐ <20%). This study reported the production of plant cell wall degrading enzymes and toxic metabolites by some pathogens belonging to FIESC and three new hosts of the pathogen such as hyacinth bean, spiny gourd and garden pea, from the Indian subcontinent.
Social capital, social heterogeneity, and electoral turnout
Authors: Clark Jeremy , François Abel , Gergaud Olivier
Published: July 2024

Among the many studied determinants of voting, we predict that i) increased social capital will be positively associated with turnout, while increased heterogeneity will be negatively associated; ii) both factors will work through their influence on the costs of information gathering and on the social norms of voting; and iii) that heterogeneity will interact with social capital in its association with turnout. We test these predictions at the extremely fine “meshblock” level by regressing New Zealand voter turnout in its 2017 national election on its 2013 census characteristics. We use roughly 40,000 meshblock volunteering rates to measure social capital, and heterogeneity based primarily on ethnic fragmentation. We find social capital is positively associated with voter turnout, while heterogeneity is negatively associated. We find robust evidence consistent with ethnic heterogeneity working through information costs and social norms, but less so social capital. We also find a robust interaction between social capital and heterogeneity in their association with turnout, consistent with ethnic heterogeneity raising bridging social capital that has a stronger association with turnout than in‐group bonding social capital.
Mental healthcare spaces, ambivalence of caregiving, and Indian memoirs of psychiatric patients
Authors: M S Sree Lekshmi , Das Aratrika
Published: July 2024

Mental healthcare facilities in hospitals and rehabilitation centres are crucial for providing medical treatment and care. These therapeutic environments manifest as both fulfilled, empathetic spaces of care and as sites tainted by denial of care and exploitation. This article utilises illness memoirs or ‘pathographies’ as an entry point to understand the intricacies of experiential facets of caregiving within mental healthcare spaces. Set against the backdrop of the evolving landscape of psychiatric facilities in India, transitioning from asylums in the pre‐independent era to mental hospitals in the post‐independent era and rehabilitation centres in the 1990s, this article analyses two important postcolonial Indian pathographies: Swadesh Deepak's Maine Mandu Nahin Dekha: Khandit Jeevan ka Collage, 2003 (I Have Not Seen Mandu: A Fractured Soul‐Memoir, 2021), translated by Jerry Pinto and Shreevatsa Nevatia's How to Travel Light: My Memories of Madness and Melancholia (2017). These memoirs allow us to explore the dynamics of caregiving practices within the evolving spatial modalities of mental healthcare spaces in India. Drawing on insights from theorists such as Anne H Hawkins, Sarah Ann Pinto, Arthur Kleinman, Michel Foucault, Erving Goffman and others, the article examines the complex dynamics and ambivalence inherent in the practices of care and denial within mental healthcare spaces. This nuanced analysis contributes to a deeper understanding of the experiential reality of care within distinct mental healthcare spaces of hospitals and rehabilitation centres in India, shedding light on the intricate interplay between individual narratives and broader sociocultural contexts.
Coronavirus disease 2019 vaccination effectiveness based on the 2021 Japanese dialysis registry
Authors: Sugawara Yuka , Iwagami Masao , Kikuchi Kan , Hashiba Toyohiro , Yabushita Sayaka , Ryuzaki Munekazu , Nangaku Masaomi
Published: July 2024

Aim

The effectiveness of the coronavirus disease (COVID‐19) vaccine in Japanese patients undergoing haemodialysis has previously not been evaluated on a large scale. We analyzed data from the Japanese Society for Dialysis Therapy Renal Data Registry (JRDR), covering nearly all Japanese patients undergoing dialysis (~95% coverage), to examine the association between COVID‐19 vaccination and infection or mortality.

Methods

We used data from the JRDR end‐of‐year surveys conducted in 2020 and 2021, including information on the COVID‐19 vaccination and infection months. COVID‐19 infection incidence and its associated mortality rates based on vaccination status (time updated) and odds ratio (OR) (vaccinated vs. unvaccinated) were estimated monthly from April 2021, when vaccination commenced in Japan.

Results

COVID‐19 infection analysis included 228 865 patients (215 941 vaccinated and 12 924 unvaccinated patients at the end of 2021). The age‐ and sex‐adjusted ORs (aORs) were significantly lower in August, September, October and November 2021, especially in September (aOR [95% confidence interval (CI)]: 0.25 [0.18–0.36]). Additional adjustments for past medical history and laboratory results rarely affected these results. Similarly, in the COVID‐19‐related mortality analysis with 228 731 patients, including 216 781 vaccinated and 11 950 unvaccinated at the end of 2021, COVID‐19‐related mortality risk was significantly lower in the vaccinated group in August, September, October and November (aOR [95% CI]: August, 0.32 [0.12–0.84], September, 0.04 [0.01–0.11]; October, 0.10 [0.01–0.81]; November, 0.05 [0.00–0.79]).

Conclusion

In Japanese patients undergoing haemodialysis, the first or second COVID‐19 vaccine dose was significantly associated with decreased COVID‐19 infection and mortality rates, suggesting its effectiveness in this population.

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Framing algorithmic management: Constructed antagonism on HR technology websites
Authors: Williams Penny , Khan Maria Hameed
Published: July 2024

Algorithmic management has been emerging in workplaces through human resource (HR) management technologies that allocate tasks, monitor work activity, and manage the productivity of employees. Growth of HR technologies has coincided with the rise of remote work, yet the role of technology providers in driving demand is under‐researched. Through a frame analysis of the marketing content on six HR technology websites, this article elucidates how technology providers frame algorithmic management and the frame effects for work, employees, managers, and the relations between them. The findings demonstrate that HR technology websites adopt the language of espionage to frame algorithmic management as a managerial imperative required to prevent organisational risks posed by unproductive employees. Applying a labour process lens, this paper demonstrates how the framing exploited tensions in labour–capital relations to place employees and managers in opposing positions, encouraging, and constructing an antagonistic employment relationship.
Identification of the novel HLA‐DQA1*05:03:03 allele by next‐generation sequencing
Authors: Moya‐Quiles María Rosa , Muro Manuel
Published: July 2024

HLA‐DQA1*05:03:03, a novel HLA class II allele detected by next‐generation sequencing.
Development of a novel scoring system to predict mortality in canine patients with infection
Authors: Horridge Mallory V. , Lyons Bridget M. , Stefanovski Darko , Silverstein Deborah C.
Published: July 2024

Objectives

To develop a novel illness severity scoring system to identify canine patients with infection that are at higher risk of mortality.

Key Findings

Mentation (Modified Glasgow Coma Scale and the Acute Patient Physiologic and Laboratory Evaluation mentation score), heart rate, pH, Pvco2, potassium, and total plasma protein were found to be associated with mortality on univariate analysis. Logistic regression found that mentation, heart rate, and Pvco2 combined to form the following score: [(100 × mentation score) + (3 × heart rate) + (10 × Pvco2], which was predictive of mortality (area under the receiver operating characteristic curve: 0.88). A cutoff of 900 provided a sensitivity of 80% and a specificity of 80%. If the cutoff was changed to 800, the sensitivity was 100% and the specificity was 50%.

Significance

A novel scoring system was developed to predict mortality in hospitalized dogs with confirmed or suspected infection. Further prospective evaluation in a larger patient cohort is necessary to validate this score.
Unilocus delimitation methods reveal the underestimated species diversity of Thomasomys (Rodentia, Cricetidae)
Authors: Ruelas Dennisse , Pacheco Víctor , Pérez José , Diaz‐Nieto Juan , Fabre Pierre‐Henri
Published: July 2024

Thomasomys is the most diverse genus of the Sigmodontinae subfamily, comprising at least 51 species. Despite recent systematic advances, the monophyly of this genus, the proposed species groups and their content, and the species limits are not yet firmly established. Using a well‐sampled mitochondrial dataset, we aim to test the monophyly of the genus, infer phylogenetic relationships among species and species groups and test the limits between valid species and candidate species. For this, we used a large matrix of 272 partial non‐redundant sequences of the cytochrome b mitochondrial gene from 40 valid and 20 candidate species. Using probabilistic approaches on this dataset, we inferred Thomasomys phylogenetic relationships and explored species boundaries using four unilocus species delimitation methods (ABGD, ASAP, bPTP and GMYC). Thomasomys sensu stricto was recovered monophyletic and well‐supported, excluding a Peruvian lineage misidentified as part of the genus. Analyses consistently recovered 10 well‐supported major clades and several paraphyletic or polyphyletic species. Delimitation methods and genetic divergences estimated that Thomasomys comprises between 81 and 93 putative species, thus potentially doubling the species diversity of Thomasomys. Such a result clearly calls for an urgent taxonomic revision of this genus and the use of further molecular loci within an integrative taxonomic approach to describe its diversity and understand its evolutionary history.
Subvarieties of a very general logarithmic projective space
Authors: Abe Takeshi
Published: July 2024

Let be a very general degree hypersurface and be a subvariety of not contained in . When , we show that the pair is of log‐general type unless is a union of lines that either meet set‐theoretically in at most two points or are contained in .
Wake Dynamics of Complex Turning Vanes Using Time-Resolved Particle Image Velocimetry Measurements
Authors: Hayden Andrew P. , Gillespie John , Hefner Cole , Lowe K. Todd , Untaroiu Alexandrina
Published: July 2024

The use of turning vanes spans multiple engineering disciplines such as aerospace, ocean, and biomedical to effectively turn an otherwise uniform flowfield and achieve desired downstream flow angles. The presented work investigates the wake dynamics generated by sets of complex turning vanes which contained nonaxisymmetric geometries, spanwise variations in turning angle, and multiple vane junctions. Time-resolved particle image velocimetry (TR-PIV) measurements were performed to collect three-component velocity data downstream of the vane pack geometries. As the vanes contained blunt trailing edges (TEs), large-scale periodic structures (von Kármán vortices) dominated the unsteady wakes. Two postprocessing methods, proper orthogonal decomposition (POD) and dynamic mode decomposition (DMD), were employed to extract the wake energy or enstrophy content, corresponding spatial modes, and associated frequencies. This was completed for various parameters such as Reynolds number, vane turning angle, and vane trailing edge thickness. Spatial POD analyses showed that zero-turning vanes contained similar dynamics to that of a circular cylinder, and the total wake energy distributions were affected by freestream velocity. A spectral POD analysis in the wake of vane junctions found that the junction flow contained significant coherent content and gave some insight into the mean flow. Finally, vane parameters such as turning angle and TE thickness were found to play a large role in modifying the enstrophy content of the large-scale shedding modes.
Effect of the Material Properties and Knee Position to the Bone Bruise Pattern in Skeletally Mature and Immature Subjects
Authors: Yamakawa Satoshi , Fu Freddie H. , Musahl Volker , Debski Richard E.
Published: July 2024

A bone bruise is generated by a bony collision that could occur when the anterior cruciate ligament (ACL) is injured, and its pattern reflects the injury mechanism and skeletal maturity. Thus, the bone bruise pattern is useful to predict a subject-specific injury mechanism, although the sensitivity and/or effect of the material property and the knee position at injury is still unclear. The objective of the present study was to determine the effect of the material property and knee position on the bone bruise pattern in skeletally mature and immature subjects using finite element analysis. Finite element models were created from a magnetic resonance (MR) image in the sagittal plane of a skeletally mature (25 y. o.) and immature (9 y. o.) male subject. The femur and tibia were collided at 2 m/s to simulate the impact trauma and determine the maximum principal stress. The analysis was performed at 15, 30, and 45 deg of knee flexion, and neutral, 10 mm anterior and posterior translated position at each knee flexion angle. Although high stress was distributed toward the metaphysis area in the mature model, the stress did not cross the growth plate in the immature model. The size of the stress area was larger in the mature model than those in the immature model. The location of the stress area changed depending on the joint position. Young's modulus of cartilage and trabecular bone also affected the location of the stress area. The Young's modulus for the cartilage affected peak stress during impact, while the size of the stress area had almost no change. These results indicate that the bone bruise pattern is strongly associated with subject-specific parameters. In addition, the bone bruise pattern was affected not only by knee position but also by tissue qualities. In conclusion, although the bone bruise distribution was generally called footprint of the injury, the combined evaluation of the quality of the structure and the bone bruise distribution is necessary for properly diagnosing tissue injury based on the MR imaging.
Characterization of rigid open-cell foams using direct ultrasonic simulation
Authors: Sachan Swati , Ramamoorthy Sripriya
Published: July 2024

An ultrasonic simulation technique based on the direct fluid model is proposed as an alternative to the analogous experimental technique to determine the tortuosity and characteristic lengths for high pore-density foams. It is beneficial as it reduces cost and almost eliminates the signal-to-noise issues encountered in the experiment. The proposed method is demonstrated for periodic microlattices with three different unit-cell configurations, 75%–90% porosity, and a pore size of about 200 microns. The technique is also applicable to high-resolution computed tomography (CT) scans of open-cell foams with a priori unknown microporous structure. An acoustic simulation software, ACTRAN® (Hexagon AB, Stockholm, Sweden), is used to model and perform analysis of the ultrasonic pulse propagation through the foam. Based on through-transmission by foam saturated with two different mediums, the tortuosity, and characteristic lengths are estimated from the high-frequency asymptotic behavior of the square of the propagation index (Nr2) versus the inverse square root of frequency (1/f). The predicted parameters are validated by comparing them with those determined by solving the electric conduction boundary value problem for the same configuration. Further, detailed parametric sensitivity analysis reveals the sensitivity of the Johnson–Champoux–Allard parameters to errors in Nr2 and so the effect of these errors on the acoustic absorption behavior of the rigid porous sample.
Sparse reconstruction of sound field using pattern-coupled Bayesian compressive sensing
Authors: Xiao Yue , Yuan Lei , Liu Yuan , Wang Jun-Yu , Hu Wen-Xin , Sun Rui-Min , Liu Yong-Jin , Ni Peng
Published: July 2024

Conventional near-field acoustic holography based on compressive sensing either does not fully exploit the underlying block-sparse structures of the signal or suffers from a mismatch between the actual and predefined block structure due to the lack of prior information about block partitions, resulting in poor accuracy in sound field reconstruction. In this paper, a pattern-coupled Bayesian compressive sensing method is proposed for sparse reconstruction of sound fields. The proposed method establishes a hierarchical Gaussian-Gamma probability model with a pattern-coupled prior based on the equivalent source method, transforming the sound field reconstruction problem into recovering the sparse coefficient vector of the equivalent source strengths within the compressive sensing framework. A set of hyperparameters is introduced to control the sparsity of each element in the sparse coefficient vector of the equivalent source strengths, where the sparsity of each element is determined by both its own hyperparameters and those of its immediate neighbors. This approach enables the promotion of block sparse solutions and achieves better performance in solving for the sparse coefficient vector of the equivalent source strengths without prior information of block partitions. The effectiveness and superiority of the proposed method in reconstructing sound fields are verified by simulations and experiments.
Birds optimize fruit size consumed near their geographic range limits
Authors: Martins Lucas P. , Stouffer Daniel B. , Blendinger Pedro G. , Böhning-Gaese Katrin , Costa José Miguel , Dehling D. Matthias , Donatti Camila I. , Emer Carine , Galetti Mauro , Heleno Ruben , Menezes Ícaro , Morante-Filho José Carlos , Muñoz Marcia C. , Neuschulz Eike Lena , Pizo Marco Aurélio , Quitián Marta , Ruggera Roman A. , Saavedra Francisco , Santillán Vinicio , Schleuning Matthias , da Silva Luís Pascoal , Ribeiro da Silva Fernanda , Tobias Joseph A. , Traveset Anna , Vollstädt Maximilian G. R. , Tylianakis Jason M.
Published: July 2024

Animals can adjust their diet to maximize energy or nutritional intake. For example, birds often target fruits that match their beak size because those fruits can be consumed more efficiently. We hypothesized that pressure to optimize diet—measured as matching between fruit and beak size—increases under stressful environments, such as those that determine species’ range edges. Using fruit-consumption and trait information for 97 frugivorous bird and 831 plant species across six continents, we demonstrate that birds feed more frequently on closely size-matched fruits near their geographic range limits. This pattern was particularly strong for highly frugivorous birds, whereas opportunistic frugivores showed no such tendency. These findings highlight how frugivore interactions might respond to stressful conditions and reveal that trait matching may not predict resource use consistently.
The human mitochondrial mRNA structurome reveals mechanisms of gene expression
Authors: Moran J. Conor , Brivanlou Amir , Brischigliaro Michele , Fontanesi Flavia , Rouskin Silvi , Barrientos Antoni
Published: July 2024

The human mitochondrial genome encodes crucial oxidative phosphorylation system proteins, pivotal for aerobic energy transduction. They are translated from nine monocistronic and two bicistronic transcripts whose native structures remain unexplored, posing a gap in understanding mitochondrial gene expression. In this work, we devised the mitochondrial dimethyl sulfate mutational profiling with sequencing (mitoDMS-MaPseq) method and applied detection of RNA folding ensembles using expectation-maximization (DREEM) clustering to unravel the native mitochondrial messenger RNA (mt-mRNA) structurome in wild-type (WT) and leucine-rich pentatricopeptide repeat–containing protein (LRPPRC)–deficient cells. Our findings elucidate LRPPRC’s role as a holdase contributing to maintaining mt-mRNA folding and efficient translation. mt-mRNA structural insights in WT mitochondria, coupled with metabolic labeling, unveil potential mRNA-programmed translational pausing and a distinct programmed ribosomal frameshifting mechanism. Our data define a critical layer of mitochondrial gene expression regulation. These mt-mRNA folding maps provide a reference for studying mt-mRNA structures in diverse physiological and pathological contexts.
Live chromosome identifying and tracking reveals size-based spatial pathway of meiotic errors in oocytes
Authors: Takenouchi Osamu , Sakakibara Yogo , Kitajima Tomoya S.
Published: July 2024

Meiotic errors of relatively small chromosomes in oocytes result in egg aneuploidies that cause miscarriages and congenital diseases. Unlike somatic cells, which preferentially mis-segregate larger chromosomes, aged oocytes preferentially mis-segregate smaller chromosomes through unclear processes. Here, we provide a comprehensive three-dimensional chromosome identifying-and-tracking dataset throughout meiosis I in live mouse oocytes. This analysis reveals a prometaphase pathway that actively moves smaller chromosomes to the inner region of the metaphase plate. In the inner region, chromosomes are pulled by stronger bipolar microtubule forces, which facilitates premature chromosome separation, a major cause of segregation errors in aged oocytes. This study reveals a spatial pathway that facilitates aneuploidy of small chromosomes preferentially in aged eggs and implicates the role of the M phase in creating a chromosome size–based spatial arrangement.
A hard fruit to swallow
Authors: Hargreaves Anna L. , Alexander Jake M.
Published: July 2024

Foraging niches become more specialized toward bird range limits
In Science Journals
Authors: Grocholski Brent , Szuromi Phil , Yeston Jake S. , Smith Jesse , Walia Ankit , Norton Melissa L. , Funk Michael A. , Isles Hannah M. , Jiang Di , Ash Caroline , Nusinovich Yevgeniya , Lopez Bianca , Baek Amy E.
Published: July 2024

Highlights from the
Science
family of journals
Making fusion pay
Authors: Cho Adrian
Published: July 2024

To fund its vision of generating power from fusion, SHINE Technologies aims first to revolutionize medical isotope production
High bar for famine declaration delays food aid
Authors: Roberts Leslie
Published: July 2024

Lack of humanitarian action during early stages of acute food insecurity takes a heavy toll
Cimicifugin, a broad-spectrum inhibitor of
Theileria annulata
and
Plasmodium falciparum
CDK7
Authors: Kar Prajna Parimita , Araveti Prasanna Babu , Saxena Kanika , Borah Atlanta , Sijwali Puran , Srivastava Anand
Published: July 2024

Cyclin-dependent kinase 7 is an attractive therapeutic target for the treatment of cancers, and a previous report suggested that
Plasmodium falciparum
CDK7 is a potential drug target for developing new anti-malarial drugs. In this study, we aimed to characterize and evaluate the drug target potential of
Theileria annulata
CDK7.
Theileria annulata
is responsible for tropical theileriosis, which induces a phenotype similar to cancerous cells like immortalization, hyperproliferation, and dissemination. Virtual screening of the MyriaScreen II library predicted 14 compounds with high binding energies to the ATP-binding pocket of TaCDK7. Three compounds (cimicifugin, ST092793, and ST026925) of these 14 compounds were non-cytotoxic to the uninfected bovine cells (BoMac cells). Cimicifugin treatment led to the activation of the extrinsic apoptosis pathway and induced autophagy in
T. annulata
-infected cells. Furthermore, cimicifugin also inhibited the growth of
P. falciparum
, indicating that it has both anti-theilerial and anti-malarial activities and that TaCDK7 and PfCDK7 are promising drug targets.
Mutual regulation of novel transcription factors RsrD and RsrE positively modulates the production of raw-starch-degrading enzyme in
Penicillium oxalicum
Authors: Guo Hao , Mo Li-Xiang , Luo Xue-Mei , Zhao Shuai , Feng Jia-Xun
Published: July 2024

Filamentous fungi can produce raw-starch-degrading enzyme, however, regulation of production of raw-starch-degrading enzyme remains poorly understood thus far. Here, two novel transcription factors raw-starch-degrading enzyme regulator D (RsrD) and raw-starch-degrading enzyme regulator E (RsrE) were identified to participate in the production of raw-starch-degrading enzyme in
Penicillium oxalicum
. Individual knockout of
rsrD
and
rsrE
in the parental strain Δ
ku70
resulted in 31.1%–92.9% reduced activity of raw-starch-degrading enzyme when cultivated in the presence of commercial starch from corn. RsrD and RsrE contained a basic leucine zipper and a Zn2Cys6-type DNA-binding domain, respectively, but with unknown functions. RsrD and RsrE dynamically regulated the expression of genes encoding major amylases over time, including raw-starch-degrading glucoamylase gene
PoxGA15A
and α-amylase gene
amy13A
. Interestingly, RsrD and RsrE regulated each other at transcriptional level, through binding to their own promoter regions; nevertheless, both failed to bind to the promoter regions of
PoxGA15A
and
amy13A
, as well as the known regulatory genes for regulation of amylase gene expression. RsrD appears to play an epistatic role in the module RsrD-RsrE on regulation of amylase gene expression. This study reveals a novel regulatory pathway of fungal production of raw-starch-degrading enzyme.

IMPORTANCE

To survive via combating with complex extracellular environment, filamentous fungi can secrete plant polysaccharide-degrading enzymes that can efficiently hydrolyze plant polysaccharide into glucose or other mono- and disaccharides, for their nutrients. Among the plant polysaccharide-degrading enzymes, raw-starch-degrading enzymes directly degrade and convert hetero-polymeric starch into glucose and oligosaccharides below starch gelatinization temperature, which can be applied in industrial biorefinery to save cost. However, the regulatory mechanism of production of raw-starch-degrading enzyme in fungi remains unknown thus far. Here, we showed that two novel transcription factors raw-starch-degrading enzyme regulator D (RsrD) and raw-starch-degrading enzyme regulator E (RsrE) positively regulate the production of raw-starch-degrading enzyme by
Penicillium oxalicum
. RsrD and RsrE indirectly control the expression of genes encoding enzymes with amylase activity but directly regulate each other at transcriptional level. These findings expand diversity of gene expression regulation in fungi.
AlgU mediates hyperosmotic tolerance in
Pseudomonas protegens
SN15-2 by regulating membrane stability, ROS scavenging, and osmolyte synthesis
Authors: Wang Jian , Wang Yaping , Lu Shouquan , Lou Haibo , Wang XiaoBing , Wang Wei
Published: July 2024

Pseudomonas protegens
can serve as an agricultural biocontrol agent.
P. protegens
often encounters hyperosmotic stress during industrial production and field application. The ability of
P. protegens
to withstand hyperosmotic stress is important for its application as a biocontrol agent. AlgU is a global regulator responsible for stress response and biocontrol ability. However, the specific regulatory role of AlgU in the hyperosmotic adaptation of
P. protegens
is poorly understood. In this study, we found that the AlgU mutation disrupted the hyperosmotic tolerance of
P. protegens
. Many genes and metabolites related to cell envelope formation were significantly downregulated in Δ
algU
compared with that in the wild-type (WT) strain under hyperosmotic conditions, and we found that the
algU
mutation caused membrane integrity to be compromised and increased membrane permeability. Further experiments revealed that the cell envelope integrity protein TolA, which is regulated by AlgU, contributes to cell membrane stability and osmotic tolerance in
P. protegens
. In addition, several genes related to oxidative stress response were significantly downregulated in Δ
algU
, and higher levels of intracellular reactive oxygen species were found in Δ
algU
. Furthermore, we found that the synthesis of N-acetyl glutaminyl glutamine amide is directly regulated by AlgU and contributes to the hyperosmotic adaptation of
P. protegens
. This study revealed the mechanisms of AlgU’s participation in osmotic tolerance in
P. protegens
, and it provides potential molecular targets for research on the hyperosmotic adaptation of
P. protegens
.

IMPORTANCE

In this study, we found that the extracytoplasmic function sigma factor AlgU is essential for the survival of
P. protegens
under hyperosmotic conditions. We provided evidence supporting the roles of AlgU in influencing cell membrane stability, intracellular reactive oxygen species (ROS) accumulation, and dipeptide N-acetylglutaminylglutamine amide (NAGGN) synthesis in
P. protegens
under hyperosmotic conditions. Our findings revealed the mechanisms of AlgU’s participation in hyperosmotic stress tolerance in
P. protegens,
and they provide potential molecular targets for research on the hyperosmotic adaptation of
P. protegens
, which is of value in improving the biocontrol ability of
P. protegens
.
The polinton-like supergroup of viruses: evolution, molecular biology, and taxonomy
Authors: Koonin Eugene V. , Fischer Matthias G. , Kuhn Jens H. , Krupovic Mart
Published: July 2024

Polintons are 15–20 kb-long self-synthesizing transposons that are widespread in eukaryotic, and in particular protist, genomes. Apart from a transposase and a protein-primed DNA polymerase, polintons encode homologs of major and minor jelly-roll capsid proteins, DNA-packaging ATPases, and proteases involved in capsid maturation of diverse eukaryotic viruses of kingdom
Bamfordvirae
. Given the conservation of these structural and morphogenetic proteins among polintons, these elements are predicted to alternate between transposon and viral lifestyles and, although virions have thus far not been detected, are classified as viruses (class
Polintoviricetes
) in the phylum
Preplasmiviricota
. Related to polintoviricetes are vertebrate adenovirids; unclassified polinton-like viruses (PLVs) identified in various environments or integrated into diverse protist genomes; virophages (
Maveriviricetes
), which are part of tripartite hyperparasitic systems including protist hosts and giant viruses; and capsid-less derivatives, such as cytoplasmic linear DNA plasmids of fungi and transpovirons. Phylogenomic analysis indicates that the polinton-like supergroup of viruses bridges bacterial tectivirids (preplasmiviricot class
Tectiliviricetes
) to the phylum
Nucleocytoviricota
that includes large and giant eukaryotic DNA viruses. Comparative structural analysis of proteins encoded by polinton-like viruses led to the discovery of previously undetected functional domains, such as terminal proteins and distinct proteases implicated in DNA polymerase processing, and clarified the evolutionary relationships within
Polintoviricetes
. Here, we leverage these insights into the evolution of the polinton-like supergroup to develop an amended megataxonomy that groups
Polintoviricetes
, PLVs (new class ‘
Aquintoviricetes
’), and virophages (renamed class ‘
Virophaviricetes
’) together with
Adenoviridae
(new class ‘
Pharingeaviricetes
’) in a preplasmiviricot subphylum ‘
Polisuviricotina
’ sister to a subphylum including
Tectiliviricetes
(‘
Prepoliviricotina
’).
Supplemental Material: Evolution of magma compositions and phosphorus availability in early Earth’s crust: New constraints from zircon-melt partitioning experiments
Authors: Shang Sheng , Lin Yanhao , al. et
Published: July 2024

Experimental and analytical methods, lattice strain model fitting of 3+ trace element partitioning data, criteria used to filter natural zircon data for primary (unaltered) crystals, Figures S1–S4, and Tables S1–S8.  
Cellular immunotherapies and immune cell depleting therapies in inflammatory bowel diseases: the next magic bullet?
Authors: Neurath Markus Friedrich , Sands Bruce Eric , Rieder Florian
Published: July 2024

Despite significant advances in biologic and small molecule treatments and the emergence of combination therapies to treat inflammatory bowel diseases (IBD) a large unmet need remains to control intestinal inflammation. New approaches targeting several pathways simultaneously with a favorable safety profile and agents that trigger anti-inflammatory pathways to drive durable resolution of inflammation are needed. This article discusses novel cellular immunotherapies and immune cell depleting therapies in IBD, including CAR-T cell approaches, Tr1 and T regulatory (Treg) cells and cell depleting antibodies such as rosnilimab. These novel approaches have the potential to overcome current therapeutic limitations in the treatment of IBD.
Risk factors of falls in rural elderly of Ningxia in China: a prospective cohort study
Authors: Wang Qingan , Wang Guoqi , Wang Binxia , Li Xiaoxia , Liu Xiuying , Yin Ting , Jing Jinyun , Zhao Yi
Published: July 2024

Objectives

To identify risk factors associated with falls in older people in rural China.

Methods

A prospective cohort study was conducted across 27 villages in the rural areas of Ningxia, China. After excluding individuals younger than 60 years, a total of 758 out of the initial 822 participants were ultimately included for the collection of baseline information. Participants were followed up through telephone calls or face-to-face interviews at 3rd, 6th and 12th months following the baseline investigation. The Cox proportional hazards regression model was used to examine risk factors of falls.

Results

A total of 758 participants underwent baseline information surveys, and all samples were included in the Cox model analysis. The study found that being woman (RR=1.879, 95% CI: 1.313 to 2.668), smoking (RR=1.972, 95% CI: 1.238 to 3.143), use of painkillers (RR=1.700, 95% CI: 1.226 to 2.356) and higher systolic blood pressure (SBP) (RR=1.081, 95% CI: 1.013 to 1.154) were associated with higher risk of falls among the elderly in rural China. After excluding those who were lost to follow-up or deceased, 738 participants completed the follow-up. There were 341 men (46.2%) and 397 women (53.8%), with an average age of 66.8±5.0 years. The fall rate in study area was 23.8% during the follow-up period.

Conclusions

The fall rate among the elderly in rural China was higher than other areas. Our findings revealed that being woman, smoking, medication usage, elevated SBP and people with a higher body mass index were risk factors for developing falls.
Cycle safe or cycle cool? Adolescents’ views on bicycle helmet use and injury prevention campaigns in Belgium
Authors: Verlinde Liesbeth , Verlinde Femke , Van Doren Shauni , De Coninck David , Toelen Jaan
Published: July 2024

Objectives

Although cycling is a healthy, ecological and practical way of transportation, it is not without risk. The effect of bicycle helmets to prevent head injuries on crashing has been extensively investigated. Nonetheless, the overall use of helmets by adolescents remains low. While various interventions to increase helmet use have been adopted, adolescents’ perspectives on these interventions have not been extensively explored. In our study, we aim to understand the facilitators and barriers to bicycle helmet use by adolescents and their perspectives on injury prevention campaigns.

Methods

A qualitative methodology was selected. A convenience sample of three schools in Belgium was selected for participation. 12 focus groups were conducted with a total of 84 adolescents aged 12–17 years in the second, third or fourth year of secondary school.

Results

Four key themes regarding adolescents’ views on safe cycling practices emerged from the analysis: external motivation, internal motivation, factors specific to the helmet and the cycling environment. The main barriers to bicycle helmet use identified by adolescents were peer pressure, appearance and discomfort. The perceived risks of cycling without a helmet among adolescents were low. Mandatory bicycle helmet laws and non-legislative programmes were considered to be an effective strategy by the study participants. Parental strategies, including strict parental rules and parental helmet use, further contributed to wear a bicycle helmet.

Conclusion

The results of this qualitative study add to the literature by expanding the understanding of motivation for bicycle helmet use and should be considered when designing interventions to promote bicycle helmet use.
‘We may need some help; we are just parents who have chosen to engage in football’: a qualitative study on amateur coaches’ experiences of use of and support for injury prevention training in Sweden
Authors: Lindblom Hanna , Sonesson Sofi , Hägglund Martin
Published: July 2024

Introduction

Achieving sufficient adherence with injury prevention exercise programmes is a challenge. The aim was to explore how amateur football coaches experience the use of and support for injury prevention training using theKnee Controlprogrammes as examples.

Methods

Semistructured interviews with 20 amateur football coaches around experiences of injury prevention training, facilitators and barriers, and perceived support, analysed with qualitative content analysis. Participants coached male and female, junior and senior teams. Experience of having used theKnee Controlprogrammes was an inclusion criteria.

Results

Four main categories were developed:Why are we really doing this?,How do we make it work?,What are our drivers and challenges?andWhat could be improved?Coaches were motivated for injury prevention training but faced challenges such as limited access to football grounds and low player motivation. To make the prevention programme work for them, they integrated it and used exercises in the pauses during football-specific drills, or used as a warm-up. Many conducted prevention routines from an early player age. Coaches believed preventive training use could be further enhanced by education and practical support, and by football associations and clubs working together to reduce injuries.

Conclusion

Coaches were motivated and creatively worked with the prevention programme to make it fit their team. Even coaches with long-term experience of using prevention programmes wanted support, indicating that present implementation strategies targeting those about to start using prevention programmes should be complemented by continuous support for maintained use. These strategies should preferably target both coaches and players.
Gone but not forgotten: expanding the spectrum of ORISE (submucosal lifting agent) associated diagnostic pitfalls and complications
Authors: Dhorajiya Pooja , Mahmood Sultan , Fabrizio Anne , Deshpande Vikram , Vyas Monika
Published: July 2024

Aims

A synthetic lifting agent, ORISE, used for endoscopic mucosal resections, has been recalled from the market since November 2022 due to clinical complications. Despite this, the impact of ORISE-associated complications is expected to persist in the foreseeable future. We present a large single institutional series of therapeutic resections from patients for whom ORISE was used for initial endoscopic procedures, highlighting the pitfalls and complications associated with its use.

Methods

All specimens showing lifting agent granulomata (LAGs) associated with the use of ORISE were identified. The H&E slides were reviewed to define the morphological characteristics and extent of LAG in the intestinal wall and other organs. The clinical impression and gross findings were compared with the final pathological diagnosis.

Results

34 cases (28 resections and 6 repeat endoscopic mucosal resection specimens) showed LAG. On microscopy, 20.5% showed no residual disease, 64.7% also showed residual precursor lesion and 14.7% also showed malignancy. In 64.2% of cases, a mass lesion was seen grossly but no malignancy was identified microscopically. ORISE was present in vascular spaces (n=9), lymph nodes (n=2), other organs such as appendix (n=1) and omentum/peritoneum (n=1). The major discordance between clinical impression (mass/neoplasm) and final pathology (no residual malignancy) was seen in 4/34 (11.8%) cases. LAGs were seen up to 10 months after the use of ORISE in the prior endoscopic procedure.

Conclusion

ORISE deposits may mimic residual/disseminated neoplasm and prompt inadvertent changes in surgical decisions. Awareness of this pitfall is essential to prevent unwarranted surgical resections in patients undergoing follow-up for endoscopically resected lesions.
Pitfalls in the diagnosis and management of acid–base disorders in humans: a laboratory medicine perspective
Authors: Carlton Henry , Shipman Kate E
Published: July 2024

Diagnostic errors affect patient management, and as blood gas analysis is mainly performed without the laboratory, users must be aware of the potential pitfalls. The aim was to provide a summary of common issues users should be aware of.

A narrative review was performed using online databases such as PubMed, Google Scholar and reference lists of identified papers. Language was limited to English.

Errors can be pre-analytical, analytical or post-analytical. Samples should be analysed within 15 min and kept at room temperature and taken at least 15–30 min after changes to inspired oxygen and ventilator settings, for accurate oxygen measurement. Plastic syringes are more oxygen permeable if chilled. Currently, analysers run arterial, venous, capillary and intraosseous samples, but variations in reference intervals may not be appreciated or reported. Analytical issues can arise from interference secondary to drugs, such as spurious hyperchloraemia with salicylate and hyperlactataemia with ethylene glycol, or pathology, such as spurious hypoxaemia with leucocytosis and alkalosis in hypoalbuminaemia. Interpretation is complicated by result adjustment, for example, temperature (alpha-stat adjustment may overestimate partial pressure of carbon dioxide (pCO2) in hypothermia, for example), and inappropriate reference intervals, for example, in pregnancy bicarbonate, and pCO2ranges should be lowered.

Lack of appreciation for patient-specific and circumstance-specific reference intervals, including extremes of age and altitude, and transformation of measurements to standard conditions can lead to inappropriate assumptions. It is vitally important for users to optimise specimen collection, appreciate the analytical methods and understand when reference intervals are applicable to their specimen type, clinical question or patient.