bluuebunny/crossref_metadata_2025 huggingface dataset:
Prevalence of drugs used for chronic conditions after diagnosis of thyroid cancer: a register-based cohort study
Authors: Hegvik Tor-Arne , Zhou YanYan , Brauckhoff Katrin , Furu Kari , Hjellvik Vidar , Bjørge Tone , Engeland Anders
Published: July 2024

Objective

Little is known about thyroid cancer survivors' risk of chronic conditions. We, therefore, investigated the prevalence of drugs used for chronic conditions among thyroid cancer patients using population-wide register data.

Methods

We linked data from the Cancer Registry of Norway to the Norwegian Prescription Database and other databases for a study population of 3.52 million individuals, including 3486 individuals with thyroid cancer diagnosed during 2005-2019. Prevalence ratios (PRs) with 95% CIs of reimbursed prescribed drugs in thyroid cancer patients up to 15 years after thyroid cancer diagnosis were estimated by log-binomial regression, with the cancer-free population as reference.

Results

Individuals (both males and females) with thyroid cancer had higher use of drugs for several chronic conditions in the years after diagnosis; eg, 5 years after thyroid cancer diagnosis, there was elevated use of drugs for hypoparathyroidism (PRmales = 35.4, 95% CI, 25.2-49.7; PRfemales = 42.8, 95% CI, 34.2-53.6), hypertension (PRfemales = 1.20, 95% CI, 1.12-1.28), anxiety and tension (PRmales = 4.01, 95% CI, 1.80-8.92; PRfemales = 2.01, 95% CI, 1.15-3.52), gastric acid disorders (PRmales = 1.52, 95% CI, 1.22-1.91; PRfemales = 1.45, 95% CI, 1.27-1.66), and pain (PRmales = 1.48, 95% CI, 1.11-1.97; PRfemales = 1.24, 95% CI, 1.08-1.42) as compared with the cancer-free population. In addition, males with thyroid cancer had long-term elevated use of drugs for depression (eg, year 10+, PRmales = 1.66, 95% CI, 1.06-2.59). Individuals with thyroid cancer also had higher use of drugs for several conditions prior to the thyroid cancer diagnosis, eg, hypertension, gastric acid disorders, and pain.

Conclusions

Individuals diagnosed with thyroid cancer had elevated long-term use of drugs for several chronic conditions, as compared with the cancer-free population.
The ‘war of images’ between Louis XIV and Leopold I: Jean-Baptiste Lully’s music and Il pomo d’oro in Vienna in 1667
Authors: Burke Devin
Published: July 2024

The current article uncovers a new concordance for an enigmatic dance suite titled Balletti francesi that was copied in Vienna in 1667, showing that all eight dances are arrangements of Lully’s music from Hercule amoureux. This finding has permitted new insights into how and why Lully’s music appeared in Vienna so early. I argue that the unusual titles of the suite, particularly the four dances for animated statues, connect it to the iconography of the opera Il pomo d’oro and to the political rivalry between Austria and France. Statue iconographies in opera and ballet differed between the imperial and French courts as part of complex strategies of monarchical representation. While much remains uncertain about the transmission and performance of the Lully Balletti francesi, the suite opens a new window on how the dominant two states of Europe engaged in strategies of cultural appropriation and political theatre, while mobilizing music within a so-called ‘war of images’.
Same-day discharge vs. overnight stay following catheter ablation for atrial fibrillation: a comprehensive review and meta-analysis by the European Heart Rhythm Association Health Economics Committee
Authors: Zylla Maura M , Imberti Jacopo F , Leyva Francisco , Casado-Arroyo Ruben , Braunschweig Frieder , Pürerfellner Helmut , Merino José L , Boriani Giuseppe
Published: July 2024

Aims

Same-day discharge (SDD) after catheter ablation of atrial fibrillation (AF) may address the growing socio-economic health burden of the increasing demand for interventional AF therapies. This systematic review and meta-analysis analyses the current evidence on clinical outcomes in SDD after AF ablation compared with overnight stay (ONS).

Methods and results

A systematic search of the PubMed database was performed. Pre-defined endpoints were complications at short-term (24–96 h) and 30-day post-discharge, re-hospitalization, and/or emergency room (ER) visits at 30-day post-discharge, and 30-day mortality. Twenty-four studies (154 716 patients) were included. Random-effects models were applied for meta-analyses of pooled endpoint prevalence in the SDD cohort and for comparison between SDD and ONS cohorts. Pooled estimates for complications after SDD were low both for short-term [2%; 95% confidence interval (CI): 1–5%; I2: 89%) and 30-day follow-up (2%; 95% CI: 1–4%; I2: 91%). There was no significant difference in complications rates between SDD and ONS [short-term: risk ratio (RR): 1.62; 95% CI: 0.52–5.01; I2: 37%; 30 days: RR: 0.65; 95% CI: 0.42–1.00; I2: 95%). Pooled rates of re-hospitalization/ER visits after SDD were 4% (95% CI: 1–10%; I2: 96%) with no statistically significant difference between SDD and ONS (RR: 0.86; 95% CI: 0.58–1.27; I2: 61%). Pooled 30-day mortality was low after SDD (0%; 95% CI: 0–1%; I2: 33%). All studies were subject to a relevant risk of bias, mainly due to study design.

Conclusion

In this meta-analysis including a large contemporary cohort, SDD after AF ablation was associated with low prevalence of post-discharge complications, re-hospitalizations/ER visits and mortality, and a similar risk compared with ONS. Due to limited quality of current evidence, further prospective, randomized trials are needed to confirm safety of SDD and define patient- and procedure-related prerequisites for successful and safe SDD strategies.
Atrial cardiomyopathy revisited—evolution of a concept: a clinical consensus statement of the European Heart Rhythm Association (EHRA) of the ESC, the Heart Rhythm Society (HRS), the Asian Pacific Heart Rhythm Society (APHRS), and the Latin American Heart Rhythm Society (LAHRS)
Authors: Goette Andreas , Corradi Domenico , Dobrev Dobromir , Aguinaga Luis , Cabrera Jose-Angel , Chugh Sumeet S , de Groot Joris R , Soulat-Dufour Laurie , Fenelon Guilherme , Hatem Stephane N , Jalife Jose , Lin Yenn-Jiang , Lip Gregory Y H , Marcus Gregory M , Murray Katherine T , Pak Hui-Nam , Schotten Ulrich , Takahashi Naohiko , Yamaguchi Takanori , Zoghbi William A , Nattel Stanley , Mont Lluis , Akar Joseph G , Akoum Nazem , Althoff Till , Diaz Juan Carlos , Guichard Jean-Baptiste , Jadidi Amir , Kalman Jonathan , Lim Han , Teixeira Ricardo Alkmim
Published: July 2024

Aims

The concept of “atrial cardiomyopathy” (AtCM) had been percolating through the literature since its first mention in 1972. Since then, publications using the term were sporadic until the decision was made to convene an expert working group with representation from four multinational arrhythmia organizations to prepare a consensus document on atrial cardiomyopathy in 2016 (EHRA/HRS/APHRS/SOLAECE expert consensus on atrial cardiomyopathies: definition, characterization, and clinical implication). Subsequently, publications on AtCM have increased progressively.

Methods and results

The present consensus document elaborates the 2016 AtCM document further to implement a simple AtCM staging system (AtCM stages 1–3) by integrating biomarkers, atrial geometry, and electrophysiological changes. However, the proposed AtCM staging needs clinical validation. Importantly, it is clearly stated that the presence of AtCM might serve as a substrate for the development of atrial fibrillation (AF) and AF may accelerates AtCM substantially, but AtCM per se needs to be viewed as a separate entity.

Conclusion

Thus, the present document serves as a clinical consensus statement of the European Heart Rhythm Association (EHRA) of the ESC, the Heart Rhythm Society (HRS), the Asian Pacific Heart Rhythm Society (APHRS), and the Latin American Heart Rhythm Society (LAHRS) to contribute to the evolution of the AtCM concept.
Nitrogen reduces calcium availability by promoting oxalate biosynthesis in apple leaves
Authors: Xing Yue , Feng Zi-Quan , Zhang Xin , Cao Hong-Xing , Liu Chun-Ling , Qin Han-Han , Jiang Han , Zhu Zhan-Ling , Ge Shun-Feng , Jiang Yuan-Mao
Published: July 2024

N and Ca are essential nutrients for apple growth and development. Studies have found that Ca content was not low under high N conditions but was poorly available. However, the underlying physiological mechanism through which N regulates Ca availability remains unclear. In this study, apple plants were supplied with N and Ca to analyse the content, in situ distribution, and forms of Ca using noninvasive micro-test technique, electron probe microanalysis, Fourier transform infrared spectroscopy, and transcriptome analysis. A potential interaction was observed between N and Ca in apple leaves. The application of high N and Ca concentration led to a CaOx content of 12.51 g/kg, representing 93.54% of the total Ca in the apple leaves. Electron probe microanalysis revealed that Ca deposited in the phloem primarily existed as CaOx rhombus-shaped crystals. Additionally, high N positively regulated oxalate accumulation in the leaves, increasing it by 40.79 times compared with low N concentration. Specifically, N induced oxalate synthesis in apple leaves by upregulating the MdICL, MdOXAC, and MdMDH genes, while simultaneously inhibiting degradation through downregulation of the MdAAE3 gene. Transcriptome and correlation analyses further confirmed oxaloacetate as the precursor for the synthesis of CaOx crystals in the apple leaves, which were produced via the ‘photosynthesis/glycolysis -oxaloacetate -oxalate -CaOx’ pathway. WGCNA identified potential regulators of the CaOx biosynthesis pathway triggered by N. Overall, the results provide insights into the regulation of Ca availability by N in apple leaves and support the development of Ca efficient cultivation technique.
PpBBX32 and PpZAT5 modulate temperature-dependent and tissue-specific anthocyanin accumulation in peach fruit
Authors: Huang Dan , Xue Lei , Lu Yueqin , Liu Mengfei , Lin-Wang Kui , Allan Andrew C , Zhang Bo , Chen Kunsong , Xu Changjie
Published: July 2024

Anthocyanins are important compounds for fruit quality and nutrition. The R2R3 MYB transcription factor PpMYB10.1 is known to be critical for regulating anthocyanin accumulation in peach. However, regulatory factors upstream of PpMYB10.1 which control temperature-dependent, cultivar-contrasted and tissue-specific anthocyanin accumulation remain to be determined. In this study, differential anthocyanin accumulation in the outer flesh near the peel (OF) of peach [Prunus persica (L.) Batsch] was observed between cultivars ‘Zhonghuashoutao’ and ‘Dongxuemi’, as well as among different storage temperatures and different fruit tissues of ‘Zhonghuashoutao’. By cross-comparisons of RNA-Seq data of samples with differential anthocyanin accumulation, transcription factor genes PpBBX32 and PpZAT5 were identified. These were functionally characterized as two positive regulators for anthocyanin accumulation via transient expression and genetic transformation. Various interaction assays revealed that both PpBBX32 and PpZAT5 can directly activate the PpMYB10.1 promoter and meanwhile interact at protein level as a PpZAT5-PpBBX32-PpMYB10.1 complex. Furthermore, the results of in silico analysis and exogenous application of methyl jasmonate (MeJA) indicated that MeJA favored anthocyanin accumulation, while it was also found that anthocyanin accumulation as well as PpBBX32 and PpZAT5 expression correlated significantly with endogenous JA and JA-Ile in different fruit tissues. In summary, PpBBX32 and PpZAT5 are upstream activators of PpMYB10.1, allowing JAs to take part in temperature-dependent and tissue-specific anthocyanin accumulation by modulating their expression. This work enriches the knowledge of the transcriptional regulatory mechanisms for differential anthocyanin accumulation under internal and external factors.
Multiaspect analysis and optimization of a power and cooling cogeneration plant integrated with a multilevel waste heat recovery system
Authors: Hai Tao , Omar Ihab , El-Sharkawy Mohamed R , Kassim Murizah , Rajab Husam , Said Esraa Ahmed , Hussein Abbas Hameed Abdul , Hassan Alhaidry Wesam Abed AL , Idan Ameer Hassan , Alizadeh Mehrsam
Published: July 2024

This study focuses on the development and improvement of a new combined power and cooling system called the power-cooling cogeneration system (PCCS). The PCCS incorporates a tri-tier waste heat recovery system that includes an organic Rankine cycle (ORC) system and an ejector-driven refrigeration mechanism. The cogeneration system design incorporates a thorough assessment of thermodynamic efficiency, cost-efficiency, and environmental consequences. A dual-objective optimization technique is developed to decrease expenses while simultaneously improving exergy efficiency. In addition, the complex behavior of PCCS is compared to a standard system that uses a one-stage recovery-ORC system and a compressor-based refrigeration approach. Also, the effectiveness of the PCCS was evaluated through the utilization of several environmentally friendly refrigerants. Environmental evaluations employ two metrics: total equivalent-warming impact (TE-WI) and life cycle-climate performance (LC-CP), emphasizing substantial reductions in environmental harm through improved waste heat recovery. The results demonstrate that the R1234-yf refrigerant achieves the best possible performance in both configurations, resulting in a significant increase of roughly 10.1% in exergetic efficiency compared to the standard system. Simultaneously, the PCCS experiences a decrease in exergy loss and annual costs of around 7.25% and 21.16%, respectively, as compared to the baseline. Incorporating an ejector into the refrigeration cycle has the potential to reduce carbon dioxide emissions by up to 11.41 × 106 kg.
Comparison of Predictive Models for Severe Dengue: Logistic Regression, Classification Tree, and the Structural Equation Model
Authors: Lee Hyelan , Srikiatkhachorn Anon , Kalayanarooj Siripen , Farmer Aaron R , Park Sangshin
Published: July 2024

Background

This study aimed to compare the predictive performance of 3 statistical models—logistic regression, classification tree, and structural equation model (SEM)—in predicting severe dengue illness.

Methods

We adopted a modified classification of dengue illness severity based on the World Health Organization’s 1997 guideline. We constructed predictive models using demographic factors and laboratory indicators on the day of fever occurrence, with data from 2 hospital cohorts in Thailand (257 Thai children). Different predictive models for each category of severe dengue illness were developed employing logistic regression, classification tree, and SEM. The model’s discrimination abilties were analyzed with external validation data sets from 55 and 700 patients not used in model development.

Results

From external validation based on predictors on the day of presentation to the hospital, the area under the receiver operating characteristic curve was from 0.65 to 0.84 for the regression models from 0.73 to 0.85 for SEMs. Classification tree models showed good results of sensitivity (0.95 to 0.99) but poor specificity (0.10 to 0.44).

Conclusions

Our study showed that SEM is comparable to logistic regression or classification tree, which was widely used for predicting severe forms of dengue.
Effects of Habitat and Fruit Scent on the Interactions between Short-tailed Fruit Bats and Piper Plants
Authors: Sil S , Visconti F , Chaverri G , Santana S E
Published: July 2024

Synopsis

Piper is a mega-diverse genus of pioneer plants that contributes to the maintenance and regeneration of tropical forests. In the Neotropics, Carollia bats use olfaction to forage for Piper fruit and are a main disperser of Piper seeds via consumption and subsequent defecation during flight. In return, Piper fruits provide essential nutrients for Carollia year-round. There is evidence that the types and diversity of Piper frugivores are influenced by the primary habitat type of different Piper species (forest and gap), with forest Piper depending more on bats for seed dispersal; however, this pattern has not been tested broadly. We aimed to characterize and compare the interactions between Carollia and Piper across forested and gap habitats, and further investigate whether differences in fruit traits relevant to bat foraging (i.e., scent) could underlie differences in Carollia-Piper interactions. We collected nightly acoustic ultrasonic recordings and 24 h camera trap data in La Selva, Costa Rica across 12 species of Piper (six forest, six gap) and integrated this information with data on Carollia diet and Piper fruit scent. Merging biomonitoring modalities allowed us to characterize ecological interactions in a hierarchical manner: from general activity and presence of bats, to visitations and inspections of plants, to acquisition and consumption of fruits. We found significant differences in Carollia-Piper interactions between forested and gap habitats; however, the type of biomonitoring modality (camera trap, acoustics, diet) influenced our ability to detect these differences. Forest Piper were exclusively visited by bats, whereas gap Piper had a more diverse suite of frugivores; the annual diet of Carollia, however, is dominated by gap Piper since these plants produce fruit year-round. We found evidence that fruit scent composition significantly differs between forest and gap Piper, which highlights the possibility that bats could be using chemical cues to differentially forage for gap vs. forest Piper. By integrating studies of Piper fruit scent, plant visitation patterns, and Carollia diet composition, we paint a clearer picture of the ecological interactions between Piper and Carollia, and plant-animal mutualisms more generally.
Reversed oxidative TCA (roTCA) for carbon fixation by an Acidimicrobiia strain from a saline lake
Authors: Gao Lei , Liu Lan , Lv Ai-Ping , Fu Lin , Lian Zheng-Han , Nunoura Takuro , Hedlund Brian P , Xu Qing-Yu , Wu Dildar , Yang Jian , Ali Mukhtiar , Li Meng-Meng , Liu Yong-Hong , Antunes André , Jiang Hong-Chen , Cheng Lei , Jiao Jian-Yu , Li Wen-Jun , Fang Bao-Zhu
Published: July 2024

Acidimicrobiia are widely distributed in nature and suggested to be autotrophic via the Calvin–Benson–Bassham (CBB) cycle. However, direct evidence of chemolithoautotrophy in Acidimicrobiia is lacking. Here, we report a chemolithoautotrophic enrichment from a saline lake, and the subsequent isolation and characterization of a chemolithoautotroph, Salinilacustristhrix flava EGI L10123T, which belongs to a new Acidimicrobiia family. Although strain EGI L10123T is autotrophic, neither its genome nor Acidimicrobiia metagenome-assembled genomes from the enrichment culture encode genes necessary for the CBB cycle. Instead, genomic, transcriptomic, enzymatic, and stable-isotope probing data hinted at the activity of the reversed oxidative TCA (roTCA) coupled with the oxidation of sulfide as the electron donor. Phylogenetic analysis and ancestral character reconstructions of Acidimicrobiia suggested that the essential CBB gene rbcL was acquired through multiple horizontal gene transfer events from diverse microbial taxa. In contrast, genes responsible for sulfide- or hydrogen-dependent roTCA carbon fixation were already present in the last common ancestor of extant Acidimicrobiia. These findings imply the possibility of roTCA carbon fixation in Acidimicrobiia and the ecological importance of Acidimicrobiia. Further research in the future is necessary to confirm whether these characteristics are truly widespread across the clade.
Dynamics and activity of an ammonia-oxidizing archaea bloom in South San Francisco Bay
Authors: Rasmussen Anna N , Francis Christopher A
Published: July 2024

Transient or recurring blooms of ammonia-oxidizing archaea (AOA) have been reported in several estuarine and coastal environments, including recent observations of AOA blooms in South San Francisco Bay. Here, we measured nitrification rates, quantified AOA abundance, and analyzed both metagenomic and metatranscriptomic data to examine the dynamics and activity of nitrifying microorganisms over the course of an AOA bloom in South San Francisco Bay during the autumn of 2018 and seasonally throughout 2019. Nitrification rates were correlated with AOA abundance in quantitative polymerase chain reaction (PCR) data, and both increased several orders of magnitude between the autumn AOA bloom and spring and summer seasons. From bloom samples, we recovered an extremely abundant, high-quality Candidatus Nitrosomarinus catalina-like AOA metagenome-assembled genome that had high transcript abundance during the bloom and expressed >80% of genes in its genome. We also recovered a putative nitrite-oxidizing bacteria metagenome-assembled genome from within the Nitrospinaceae that was of much lower abundance and had lower transcript abundance than AOA. During the AOA bloom, we observed increased transcript abundance for nitrogen uptake and oxidative stress genes in non-nitrifier metagenome-assembled genomes. This study confirms AOA are not only abundant but also highly active during blooms oxidizing large amounts of ammonia to nitrite—a key intermediate in the microbial nitrogen cycle—and producing reactive compounds that may impact other members of the microbial community.
Effectiveness of direct delabelling of allergy labels in type A adverse drug reactions to penicillin: a multicentre hospitalwide prospective cohort study
Authors: Drummond Kate , Vogrin Sara , Lambros Belinda , Trubiano Jason A , Mitri Elise
Published: July 2024

Background

Patient-reported penicillin allergy labels (PALs) are associated with adverse patient outcomes and inappropriate antibiotic prescribing. Removal of PALs via direct oral challenge (DOC) is associated with increased penicillin utilization post removal.

Objectives

To assess the impact of direct delabelling (allergy label removal via medical reconciliation alone) of type A adverse drug reaction (ADR) PALs on inpatient prescribing.

Methods

From January 2019 to December 2022 at two tertiary hospitals in Melbourne, patients aged ≥18 years with type A ADR PALs, as defined by the validated Antibiotic Allergy Assessment Tool, were offered direct delabelling or single-dose DOC. The primary endpoint was antibiotic use pre- and post-assessment (during index admission and 90 days post assessment). The secondary endpoint was the proportion of patients delabelled in the direct delabelling and DOC cohorts in the electronic medical record at 90 days post assessment.

Results

Allergy labels (n = 4108) were assessed for 488 participants, with 490 individual type A ADR PAL assessments included. Three hundred and thirty-seven patients were directly delabelled, 69 underwent DOC and 84 were not delabelled. There was increased use of any penicillin following direct delabelling (OR 19.19, 95% CI 2.48–148.36) and DOC (OR 56.98, 95% CI 6.82–476.19) during the index admission, higher in the DOC group compared with direct delabelling (OR 2.97, 95% CI 1.39–6.37). Relabelling at 90 days was low with no statistically significant difference between direct delabelling (5/337; 1.5%) and DOC (0/69; 0%).

Conclusions

Both direct delabelling and DOC of type A ADR PALs increased penicillin usage; however, the impact was greatest with DOC. Most patients remain delabelled at 90 days.
Genomic analysis of enterococci carrying optrA, poxtA, and vanA resistance genes from wild boars, Italy
Authors: Cinthi Marzia , Coccitto Sonia Nina , Massacci Francesca Romana , Albini Elisa , Binucci Giorgia , Gobbi Marco , Tentellini Michele , D'Avino Nicoletta , Ranucci Alice , Papa Paola , Magistrali Chiara Francesca , Brenciani Andrea , Giovanetti Eleonora
Published: July 2024

Aims

To investigate enterococci carrying linezolid and vancomycin resistance genes from fecal samples recovered from wild boars

Methods and results

Florfenicol- and vancomycin-resistant enterococci, isolated on selective agar plates, were screened by PCR for the presence of linezolid and vancomycin resistance genes. Five isolates carried optrA or poxtA linezolid resistance genes; one strain was resistant to vancomycin for the presence of vanA gene. All isolates were tested for their antibiotic susceptibility and subjected to Whole Genome Sequencing (WGS) analysis. In Enterococcus faecalis (E. faecalis) V1344 and V1676, the optrA was located on the new pV1344-optrA and pV1676-optrA plasmids, respectively, whereas in Enterococcus faecium (E. faecium) V1339 this gene was on a 22 354-bp chromosomal genetic context identical to the one detected in a human E. faecium isolate. In both E. faecium V1682 and E. durans V1343, poxtA was on the p1818-c plasmid previously found in a human E. faecium isolate. In E. faecium V1328, the vanA gene was on the Tn1546 transposon in turn located on a new pV1328-vanA plasmid. Only E. faecium V1682 successfully transferred the poxtA gene to an enterococcal recipient in filter mating assays.

Conclusions

The occurrence of genetic elements carrying linezolid and vancomycin resistance genes in enterococci from wild boars is a matter of concern, moreover, the sharing of plasmids and transposons between isolates from wild animals, human, and environment indicates an exchange of genetic material between these settings.
Sequential post-translational modifications regulate damaged DNA-binding protein DDB2 function
Authors: Kaneoka Hidenori , Arakawa Kazuhiko , Masuda Yusuke , Ogawa Daiki , Sugimoto Kota , Fukata Risako , Tsuge-Shoji Maasa , Nishijima Ken-ichi , Iijima Shinji
Published: July 2024

Nucleotide excision repair (NER) is a major DNA repair system and hereditary defects in this system cause critical genetic diseases (e.g. xeroderma pigmentosum, Cockayne syndrome and trichothiodystrophy). Various proteins are involved in the eukaryotic NER system and undergo several post-translational modifications. Damaged DNA-binding protein 2 (DDB2) is a DNA damage recognition factor in the NER pathway. We previously demonstrated that DDB2 was SUMOylated in response to UV irradiation; however, its physiological roles remain unclear. We herein analysed several mutants and showed that the N-terminal tail of DDB2 was the target for SUMOylation; however, this region did not contain a consensus SUMOylation sequence. We found a SUMO-interacting motif (SIM) in the N-terminal tail that facilitated SUMOylation. The ubiquitination of a SUMOylation-deficient DDB2 SIM mutant was decreased, and its retention of chromatin was prolonged. The SIM mutant showed impaired NER, possibly due to a decline in the timely handover of the lesion site to XP complementation group C. These results suggest that the SUMOylation of DDB2 facilitates NER through enhancements in ubiquitination.
Benefits of Targeted Vibration for Bone Strength and Bone Density in Postmenopausal Women with Osteopenia: A Randomized, Sham-Controlled Trial
Authors: Bilek Laura D , Flores Laura E , Waltman Nancy , Mack Lynn R , Smith Kara , Kelly Colleen , Keaveny Tony M , Hillstrom Derek , Griffin Meghan , Yecies Laura , Jaasma Michael J
Published: July 2024

Postmenopausal women are at increased risk of fractures due to higher bone turnover that accompanies reduced estrogen production. Vibration may be an effective intervention for maintaining bone strength and bone density. The Osteoboost Belt is a wearable, home-use device that delivers targeted vibration to the lumbar spine and hips. This randomized, sham-controlled trial evaluated the safety and effectiveness of targeted vibration on bone strength and density in postmenopausal women with osteopenia. Participants (n = 126) were randomized (1:1) to receive the Active (vibration therapy device) or Sham (inactive device) treatment for 30 minutes/day over 12 months. At baseline and 12 months, computed tomography scans of the lumbar spine were analyzed to measure finite element analysis-assessed vertebral bone compressive strength (vertebral strength) and volumetric bone mineral density (vBMD) of the L1 vertebra. The primary endpoint, the difference in percentage change of vertebral strength between the Active (-1.40%, [95% CI: -2.73, -0.08]) and Sham (-2.74% [-4.04, -1.43]) groups in the modified intent-to-treat population, did not reach statistical significance (relative benefit: +1.33% [-0.57, 3.24], P=.17). However, a statistically significant benefit of targeted vibration was observed for participants who met the prespecified per-protocol compliance criterion (averaged ≥3 treatment sessions/week): -0.48% [-2.12, 1.17]) and -2.84% [-4.21, -1.47] (n = 73, P=.028) for Active and Sham groups, respectively. Similarly, in this compliant cohort, targeted vibration provided a statistically significant benefit on vertebral bone density, with the percentage change in vBMD of -0.29% [-1.28, 0.70] and -1.97% [-2.92, -1.01] (P=.016) for the Active and Sham groups, respectively. The vibration therapy was well-tolerated, and there were no serious device-related adverse events. These results demonstrate that targeted vibration is safe and, in adherent individuals, can significantly mitigate the decline in vertebral bone strength and vertebral bone density in postmenopausal women with osteopenia.
New okra genotypes for the management of aphids (Hemiptera: Aphididae) in the diverse ecological landscapes of Central Africa
Authors: Abang Albert Fomumbod , Ramasamy Srinivasan , Hanna Rachid , Kekeunou Sevillor , Fotso Kuate Apollin , Tenkouano Abdou , Fiaboe Komi Kouma Mokpokpo , Bilong Bilong Charles-Félix
Published: July 2024

Various aphid species, including Aphis gossypii Glover (Hemiptera: Aphididae), are considered important pests of okra and other vegetables. Previous studies under 1 environment in Cameroon, Central Africa, had found multiple okra genotypes with resistance to A. gossypii. However, the stability and yield performance of the “resistant” genotypes across different environments were unknown. Ten previously identified aphid-resistant okra genotypes along with 1 commercial variety and a local landrace (specific to a given location) were compared during 2 seasons in replicated trials in 4 agro-ecological zones of Cameroon that also represent large areas of Central Africa. Aphid populations and okra yield parameters were evaluated. Breeding values were predicted using a linear mixed model for all data, and genotypes by location interactions were identified. The area under the infestation pressure curve (AUIPC) was calculated using aphid count data and subjected to resistance analysis. The Local—the most susceptible with the highest breeding value (+2.33)—and VI060794—one of the moderately resistant—genotypes had the highest yield per hectare. The only resistant genotype VI036213 had the lowest breeding value (–2.20). Genotype × location interactions were significant for yield, pod width, and plant height, while location variance was significant for all parameters evaluated. When considering that higher aphid densities could lead to greater pesticide use and, therefore higher production and environmental costs, the high-yielding VI060794—with moderate aphid resistance across multiple environments—presents an alternative or substitute for local landraces across multiple agro-ecologies of Cameroon and (by extension) Central Africa.
A method for assessing the operational status of a microseismic monitoring system using energy distribution changes of observed data
Authors: Zeng Han , Ye Fang , Cai Jinhui , Xu Yiwen
Published: July 2024

The operational status of geophones plays a pivotal role in ensuring the accuracy and reliability of microseismic monitoring systems. However, conventional techniques used to evaluate the operational status of geophones require human intervention or significant time delays. To address this issue, we propose a method for online monitoring of geophone status using observed data obtained from a microseismic system. First, the energy features of the preprocessed observation data are extracted via wavelet packet decomposition. Subsequently, the distribution parameters of energy features are obtained through log-logistic distribution fitting. These parameters are then applied to a change-point detection model, enabling the online monitoring of seismic geophones. In addition, we select a long short-term memory network to classify the operational status of the geophones, which is trained using the obtained energy distribution data and the time-frequency characteristics of the observed data. The experimental results indicate that the model achieves an accuracy of 98.33%, surpassing the 89.58% accuracy of the support vector machine. The proposed method not only contributes to online monitoring and precise determination of the operating status of detectors, but also has enormous application potential in other fields that require monitoring and evaluating the operating status of instruments.
Dual role of PpV in Drosophila crystal cell proliferation and survival
Authors: Luo Wang , Zhang Fang , Zhao Fangzhen , Fang Yang , Zhao Long , Su Ying
Published: July 2024

Drosophila melanogaster crystal cells are a specialized type of blood cells for innate immune process upon injury. Under normal conditions, crystal cells rarely proliferate and constitute a small proportion of fly blood cells. Notch signaling has been known to guide the cell fate determination of crystal cells and maintain their survival. Here, we reported that protein phosphatase V (PpV), the unique catalytic subunit of protein phosphatase 6 in Drosophila, is a novel regulator of crystal cell proliferation and integrity. We found that PpV proteins highly accumulated in crystal cells in the larval hematopoietic organ termed the lymph gland. Silencing PpV using RNA interference led to increased crystal cell proliferation in a Notch-independent manner and induced crystal cell rupture dependent on Notch signaling. Moreover, additive PpV prevented the rupture of crystal cells in lymph glands upon a needle injury, suggesting the involvement of PpV in wound healing. Altogether, our results indicated that PpV plays a dual role in lymph glands, preventing crystal cell proliferation to limit the cell number, as well as inhibiting crystal cell rupture to maintain their survival.
Antibacterial mechanism of the methanol extract of Thamnolia subuliformis (Ehrh.) W. Culb against Staphylococcus aureus
Authors: Liu Menglong , Tian Hongqiao , Zhu Jiana , Ding Haiyan
Published: July 2024

Thamnolia subuliformis (Ehrh.) W. Culb is a species of lichen with edible and medicinal applications in China. Our previous studies demonstrated that the methanol extract of Thamnolia subuliformis (METS) exhibits broad antibacterial activity and stability against foodborne pathogens. This study aimed to investigate the antibacterial mechanism of METS against Staphylococcus aureus using nontargeted metabolomics, focusing on cell wall and membrane damage. The results revealed that the minimum inhibitory concentration (MIC) was 0.625 mg ml−1 and that METS had good biosafety at this concentration. METS caused significant damage to the cell wall and membrane integrity, based on both morphological observation by electron microscopy and the leakage of alkaline phosphatase, protein, and nucleic acid in the cell cultures. Treatment with METS at the MIC disrupted the lipid metabolism of S. aureus, causing a decrease in the metabolism of various phospholipids and sphingolipids in the cell membrane and an increase in the ratio of saturated fatty acids to unsaturated fatty acids. Moreover, it influenced intracellular amino acid and energy metabolism. These results shed light on the antibacterial mechanism of METS against S. aureus while also serving as a reference for the further development of natural antibacterial compounds derived from Thamnolia subuliformis.
The XAI system for answer set programming xASP2
Authors: Alviano Mario , Ly Trieu Ly , Cao Son Tran , Balduccini Marcello
Published: July 2024

Explainable artificial intelligence (XAI) aims at addressing complex problems by coupling solutions with reasons that justify the provided answer. In the context of Answer Set Programming (ASP) the user may be interested in linking the presence or absence of an atom in an answer set to the logic rules involved in the inference of the atom. Such explanations can be given in terms of directed acyclic graphs (DAGs). This article reports on the advancements in the development of the XAI system xASP by revising the main foundational notions and by introducing new ASP encodings to compute minimal assumption sets, explanation sequences, and explanation DAGs. DAGs are shown to the user in an interactive form via the xASP navigator application, also introduced in this work.
Discovery of a split stellar stream in the periphery of the Small Magellanic Cloud
Authors: Nidever David L
Published: July 2024

I report the discovery of a stellar stream (Sutlej) using Gaia DR3 (third data release) proper motions and XP metallicities located $\sim$15° north of the Small Magellanic Cloud (SMC). The stream is composed of two parallel linear components (‘branches’) approximately $\sim$8° × 0.6° in size and separated by 2.5°. The stars have a mean proper motion of ($\mu _{\rm RA},\mu _{\rm Dec.}$) = (+0.08 mas yr−1, −1.41 mas yr−1), which is quite similar to the proper motion of stars on the western side of the SMC. The colour–magnitude diagram of the stream stars has a clear red giant branch, horizontal branch, and main-sequence turn-off that are well matched by a parsec isochrone of 10 Gyr, [Fe/H] = −1.8 at 32 kpc, and a total stellar mass of $\sim$33 000 M$_{\odot }$. The stream is spread out over an area of 9.6 deg2 and has a surface brightness of 32.5 mag arcsec−2. The metallicity of the stream stars from Gaia XP spectra extends over $-2.5$$\le$ [M/H] $\le$$-1.0$ with a median of [M/H] = −1.8. The tangential velocity of the stream stars is 214 km s−1 compared to the values of 448 km s−1 for the Large Magellanic Cloud and 428 km s−1 for the SMC. While the radial velocity of the stream is not yet known, a comparison of the space velocities using a range of assumed radial velocities shows that the stream is unlikely to be associated with the Magellanic Clouds. The tangential velocity vector is misaligned with the stream by nearly 90°, which might indicate an important gravitational influence from the nearby Magellanic Clouds.
Two distinct molecular cloud populations detected in massive galaxies
Authors: Rose Tom , McNamara B R , Combes F , Edge A C , McDonald M , O’Sullivan Ewan , Russell H , Fabian A C , Ferland G , Salomé P , Tremblay G
Published: July 2024

We present new ALMA observations of CO, CN, CS, HCN, and HCO$^{+}$ absorption seen against the bright and compact radio continuum sources of eight galaxies. Combined with archival observations, they reveal two distinct populations of molecular clouds, which we identify by combining CO emission and absorption profiles to unambiguously reveal each cloud’s direction of motion and likely location. In galaxy discs, we see clouds with low velocity dispersions, low line-of-sight velocities, and a lack of any systemic inflow or outflow. In galactic cores, we find high velocity dispersion clouds inflowing at up to 550 km s−1. This provides observational evidence in favour of cold accretion on to galactic centres, which likely contributes to the fuelling of active galactic nuclei. We also see a wide range in the CO(2-1)/CO(1-0) ratios of the absorption lines. This is likely the combined effect of hierarchical substructure within the molecular clouds and continuum sources which vary in size with frequency.
Signatures of gas flows – I. Connecting the kinematics of the H i circumgalactic medium to galaxy rotation
Authors: Nateghi Hasti , Kacprzak Glenn G , Nielsen Nikole M , Murphy Michael T , Churchill Christopher W , Muzahid Sowgat , Sameer  , Charlton Jane C
Published: July 2024

The circumgalactic medium (CGM) hosts many physical processes with different kinematic signatures that affect galaxy evolution. We address the CGM–galaxy kinematic connection by quantifying the fraction of H i that is aligned with galaxy rotation with the equivalent width co-rotation fraction, $f_{\rm EWcorot}$. Using 70 quasar sightlines having Hubble Space Telescope/Cosmic Origins Spectrograph H i absorption (${12\lt \log (N(\rm{{\rm H}\,{\small I}})/{\rm cm}^{-2})\lt 20}$) within $5R_{\rm vir}$ of $z\lt 0.6$ galaxies we find that $f_{\rm EWcorot}$ increases with increasing H i column density. $f_{\rm EWcorot}$ is flat at $\sim 0.6$ within $R_{\rm vir}$ and decreases beyond $R_{\rm vir}$ to $f_{\rm EWcorot}$$\sim 0.35$. $f_{\rm EWcorot}$ also has a flat distribution with azimuthal and inclination angles within $R_{\rm vir}$, but decreases by a factor of two outside of $R_{\rm vir}$ for minor axis gas and by a factor of 2 for edge-on galaxies. Inside $R_{\rm vir}$, co-rotation dominated H i is located within $\sim 20$ deg of the major and minor axes. We surprisingly find equal amounts of H i absorption consistent with co-rotation along both major and minor axes within $R_{\rm vir}$. However, this co-rotation disappears along the minor axis beyond $R_{\rm vir}$, suggesting that if this gas is from outflows, then it is bound to galaxies. $f_{\rm EWcorot}$ is constant over two decades of halo mass, with no decrease for log(M$_{\rm h}/{\rm M}_{\odot })\gt 12$ as expected from simulations. Our results suggest that co-rotating gas flows are best found by searching for higher column density gas within $R_{\rm vir}$ and near the major and minor axes.
P-based referencing for correcting tissue artifacts in laser ablation-inductively coupled plasma-mass spectrometry imaging of cancer samples
Authors: Kronenberg Katharina , Hoffmann Emily , Hiddeßen Lena , Maus Bastian , Gerwing Mirjam , Faber Cornelius , Sperling Michael , Wildgruber Moritz , Karst Uwe
Published: July 2024

A referencing strategy based on the element P is presented to compensate for cryosectioning tissue artifacts in laser ablation-inductively coupled plasma-mass spectrometry (LA-ICP-MS) data. The study examines how the gadolinium-based contrast agent Gadofosveset is distributed in murine cancer tissue, and illustrates how referenced images can compensate for tissue artifacts like folds, overlaps, and density variations. Compared to non-referenced images that provide information on the absolute distribution of the analyte, referenced images allow for the representation of the analyte distribution relative to the amount of material introduced into the instrument, which in this case is correlated to the P signal. Tissue artifacts were corrected in referenced images for both Gadofosveset and endogenous elements, such as Fe and Zn. Additionally, the referencing approach provides valuable information on the Gd uptake relative to the tissue density in necrotic compared to vital tumor areas, which is not obtained from in vivo magnetic resonance imaging (MRI) data. However, validation of in vivo MRI and ex vivo LA-ICP-MS methods was possible by establishing a mean ratio of necrotic to vital tumor areas in the T1-weighted image post Gadofosveset injection and the non-referenced LA-ICP-MS image of Gd. In summary, P-based correction of LA-ICP-MS imaging data allows for a more accurate spatial representation of certain elements, including endogenous and exogenous elements such as injected contrast agents.
Solution structures and effects of a platinum compound successively bound MYC G-quadruplex
Authors: Liu Wenting , Zhu Bo-Chen , Liu Liu-Yi , Xia Xiao- Yu , Jang Jinho , Dickerhoff Jonathan , Yang Danzhou , Mao Zong-Wan
Published: July 2024

G-quadruplex (G4) structures play integral roles in modulating biological functions and can be regulated by small molecules. The MYC gene is critical during tumor initiation and malignant progression, in which G4 acts as an important modulation motif. Herein, we reported the MYC promoter G4 recognized by a platinum(II) compound Pt-phen. Two Pt-phen–MYC G4 complex structures in 5 mM K+ were determined by NMR. The Pt-phen first strongly binds the 3′-end of MYC G4 to form a 1:1 3′-end binding complex and then binds 5′-end to form a 2:1 complex with more Pt-phen. In the complexes, the Pt-phen molecules are well-defined and stack over four bases at the G-tetrad for a highly extensive π–π interaction, with the Pt atom aligning with the center of the G-tetrad. The flanking residues were observed to rearrange and cover on top of Pt-phen to stabilize the whole complex. We further demonstrated that Pt-phen targets G4 DNA in living cells and represses MYC gene expression in cancer cells. Our work elucidated the structural basis of ligand binding to MYC promoter G4. The platinum compound bound G4 includes multiple complexes formation, providing insights into the design of metal ligands targeting oncogene G4 DNA.
Quantifying allele-specific CRISPR editing activity with CRISPECTOR2.0
Authors: Assa Guy , Kalter Nechama , Rosenberg Michael , Beck Avigail , Markovich Oshry , Gontmakher Tanya , Hendel Ayal , Yakhini Zohar
Published: July 2024

Off-target effects present a significant impediment to the safe and efficient use of CRISPR-Cas genome editing. Since off-target activity is influenced by the genomic sequence, the presence of sequence variants leads to varying on- and off-target profiles among different alleles or individuals. However, a reliable tool that quantifies genome editing activity in an allelic context is not available. Here, we introduce CRISPECTOR2.0, an extended version of our previously published software tool CRISPECTOR, with an allele-specific editing activity quantification option. CRISPECTOR2.0 enables reference-free, allele-aware, precise quantification of on- and off-target activity, by using de novo sample-specific single nucleotide variant (SNV) detection and statistical-based allele-calling algorithms. We demonstrate CRISPECTOR2.0 efficacy in analyzing samples containing multiple alleles and quantifying allele-specific editing activity, using data from diverse cell types, including primary human cells, plants, and an original extensive human cell line database. We identified instances where an SNV induced changes in the protospacer adjacent motif sequence, resulting in allele-specific editing. Intriguingly, differential allelic editing was also observed in regions carrying distal SNVs, hinting at the involvement of additional epigenetic factors. Our findings highlight the importance of allele-specific editing measurement as a milestone in the adaptation of efficient, accurate, and safe personalized genome editing.
Engineered transcription activator-like effector dimer proteins confer DNA loop-dependent gene repression comparable to Lac repressor
Authors: Becker Nicole A , Peters Justin P , Lewis Elizabeth , Daby Camden L , Clark Karl , Maher L James
Published: July 2024

Natural prokaryotic gene repression systems often exploit DNA looping to increase the local concentration of gene repressor proteins at a regulated promoter via contributions from repressor proteins bound at distant sites. Using principles from the Escherichia coli lac operon we design analogous repression systems based on target sequence-programmable Transcription Activator-Like Effector dimer (TALED) proteins. Such engineered switches may be valuable for synthetic biology and therapeutic applications. Previous TALEDs with inducible non-covalent dimerization showed detectable, but limited, DNA loop-based repression due to the repressor protein dimerization equilibrium. Here, we show robust DNA loop-dependent bacterial promoter repression by covalent TALEDs and verify that DNA looping dramatically enhances promoter repression in E. coli. We characterize repression using a thermodynamic model that quantitates this favorable contribution of DNA looping. This analysis unequivocally and quantitatively demonstrates that optimized TALED proteins can drive loop-dependent promoter repression in E. coli comparable to the natural LacI repressor system. This work elucidates key design principles that set the stage for wide application of TALED-dependent DNA loop-based repression of target genes.