bluuebunny/crossref_metadata_2025 huggingface dataset:
Clinical practice guideline for the management of hypertension in China
Authors:   Chinese Society of Cardiology, Chinese Medical Association; Hypertension Committee of Cross-Straits Medicine Exchange Association; Cardiovascular Disease Prevention and Rehabilitation Committee, Chinese Association of Rehabilitation Medicine
Published: December 2024

In China, hypertension is the most common chronic non-communicable disease and the most significant risk factor for cardiovascular mortality among urban and rural residents. To standardize the clinical diagnosis and treatment of hypertension and to improve the prevention and control level of hypertension in China, Chinese Society of Cardiology, Chinese Medical Association; Hypertension Committee of Cross-Straits Medicine Exchange Association; Cardiovascular Disease Prevention and Rehabilitation Committee, Chinese Association of Rehabilitation Medicine, jointly collaborated to formulate the Clinical Practice Guideline for Hypertension Management in China. The Grading of Recommendation, Assessment, Development, and Evaluation (GRADE) approach was used to rate the quality of evidence and strength of recommendations, and the reporting items for practice guidelines in healthcare (RIGHT) were followed to establish the guideline. Detailed evidence-based recommendations for the diagnosis, evaluation, and treatment of 44 clinical questions in the field of hypertension, including essential and secondary hypertension, have been provided to guide clinical practice.

Registration:

International Practice Guidelines Registry Platform, http://www.guidelines-registry.cn/, No. IPGRP-2021CN346.
Dose Estimation for Indoor Radon, Occupational Radiation, and Electromagnetic Field Exposure in a Nuclear Medicine Department in Turkiye
Authors: Sahmaran T. , Nur S. , Atılgan H.I. , Peker H.
Published: December 2024

In this study, the occupational radiation dose, radon gas, and non-ionizing radiation doses originating from electromagnetic fields (EMF) to which radiation workers are exposed were monitored and evaluated for 1 y. Using electronic personnel dosimeters (EPD), average daily radiation doses based on the number of patients and annual average effective dose results of radiation workers were obtained over a period of 1 y. Also, the annual effective dose and risk values were calculated for 8 h and 24 h by taking radon gas measurements at 2-mo intervals in the nuclear medicine department. Finally, electric field measurements were made one day a week in the selected areas. All the results obtained were compared with national and international dose limits. The results obtained as a result of EPD, radon gas, and EMF measurements made in the nuclear medicine department were found to be far below the international and national legal dose limits.
Comparing the Waste and Environmental Impact of Blepharoplasty at an Office-based Operating Room Versus an Ambulatory Surgery Center in the United States
Authors: Hu Daniel J. , Rizzuto Philip R.
Published: December 2024

Purpose:

The aim of the study was to evaluate the environmental impact of a blepharoplasty as performed by a single surgeon at an office-based operating room (OR) versus at an ambulatory surgery center.

Methods:

We employed life cycle analyses on routine, uncomplicated bilateral upper lid blepharoplasties as performed by a single surgeon. Life cycle phases of production, use, and end-of-life treatment were included. Study boundaries encompassed all waste products exiting the OR in addition to utility energy and water use. We conducted waste audits to collect data on surgical waste by item, material, and weight. Building energy and water use were approximated using data obtained from utility companies. Environmental impact is reported as global warming potential (GW100a; kg carbon dioxide equivalents).

Results:

The office-based OR generated 784 g of physical waste per blepharoplasty as compared to 1323 g at the ambulatory surgery center. The life cycle analyses found that a blepharoplasty contributed a total of 6.42 kg carbon dioxide equivalents at the office-based OR and 7.78 at the ambulatory surgery center. The production phase contributed the majority of these carbon dioxide equivalents. Plastic supplies contributed the most waste by weight and emissions associated with production. Nonwoven polypropylene contributed the largest waste and emissions by material.

Conclusion:

The ambulatory surgery center produces more waste and carbon dioxide equivalents per blepharoplasty than the office-based OR. Use of supplies including drapes and gowns made of nonwoven polypropylene can be reduced to increase the environmental sustainability of blepharoplasty.
Using the Magnet® Framework to Support a Culture of Excellence
Authors: Lal M. Maureen
Published: December 2024

The American Nurses Credentialing Center's Magnet Recognition Program® is the premier international acknowledgment of nursing excellence in healthcare organizations today. More than 35 years of research continues to support a host of benefits from improved nurse engagement to better patient outcomes. Despite this elite track record, however, myths persist about what is required to earn the coveted credential. In this month's Magnet
®
Perspectives, we tackle some of the biggest misconceptions out there and explore how organizations can use the Magnet framework as a guide and support to create a culture of excellence in 3 key areas: staffing models, education and certification, and engagement.
Development of Clinical Judgment in Prelicensure Nursing Students Through Simulation
Authors: Bussard Michelle E. , Jacobs Lisa A. , Mahoney Sarah A. , Davis Lacey L. , Oberhaus Annette M. , Lavoie Patrick
Published: December 2024

Background:

There is a lack of longitudinal studies measuring student progression in clinical judgment. Previous studies measured gains in clinical judgment after 1 intervention or over 1 semester.

Purpose:

This study evaluated the development and progression of clinical judgment in simulation throughout a prelicensure bachelor of science in nursing (BSN) program using the Lasater Clinical Judgment Rubric (LCJR).

Methods:

This retrospective longitudinal study evaluated clinical judgment using the LCJR over 4 semesters, with a sample of 53 prelicensure nursing students. Each student had 18 simulation scores recorded during the study. A linear mixed model was employed to compare LCJR average scores from the beginning to the end of the program and across each semester.

Results:

Eighteen simulations were reviewed among 4 nursing courses. LCJR scores increased progressively from the first to the fourth semester.

Conclusions:

Students showed progression of clinical judgment throughout a BSN curriculum using the LCJR as an assessment tool.
Association of chronic pain with incidence and progression of cardiometabolic multimorbidity in middle-aged and older populations: a multicohort study
Authors: You Yating , Zhou Yaguan , Chen Hui , Kancheva Angelina Kirilova , Carrillo-Larco Rodrigo Martin , Yuan Changzheng , Xu Xiaolin
Published: December 2024

Introduction:

Chronic pain is associated with single cardiometabolic diseases (CMDs). Less is known about the association of chronic pain with the co-occurrence of multiple CMDs, known as cardiometabolic multimorbidity (CMM).

Objectives:

This study aims to examine the association between chronic pain and incidence of CMM and if it existed, to what extent chronic pain relates to the progression of specific CMD-related multimorbidity (MM).

Methods:

We pooled individual-level data of 59,134 participants from 4 cohort studies across 18 countries between 2010 and 2020. Participants aged 45 years or older, free of CMDs (diabetes, heart diseases, and stroke), and with self-reported chronic pain status at baseline were included. Multinomial logistic regression was performed on the association of chronic pain with incident CMM and the progression of specific CMD-related MM.

Results:

One-third (21,204) of participants reported chronic pain at baseline. After 8 to 9 years, 1344 (2.3%) developed CMM. Chronic pain was associated with the onset of each CMD (odds ratio [OR] range 1.12–1.37) and CMM combinations (OR range 1.57–2.09). It is also linked with the increased odds of more CMDs (1, 2, and 3) during the follow-up. For example, OR increased from 1.31 for individuals with one CMD, to 1.57 for those with 2 CMDs, to 2.09 for those with 3 CMDs. Chronic pain was also associated with developing all CMD-related MM (OR range 1.26–1.88). Compared with those with diabetes only, participants with chronic pain were more likely to progress to diabetes and heart diseases, as well as diabetes, heart diseases, and stroke.

Conclusion:

Chronic pain is associated with incidence and progression of CMM, whose management should be considered in primary and secondary prevention of CMM among middle-aged and older populations.
Temporal characteristics of foot rollover of amputee walking gait when using an Energy Storage and Return prosthesis
Authors: Muñoz-Larrosa Eugenia Soledad , Garcia-Añino Eloisa , Schlotthauer Gaston , Shaheen Aliah F. , Oldfield Matthew , Catalfamo-Formento Paola
Published: December 2024

Background:

Energy Storage and Return (ESAR) prosthetic feet provide improved walking when compared with previous designs. However, it may not mimic the unimpaired smooth and progressive movement of the foot on the floor (foot rollover).

Objective:

To characterize the temporal foot rollover of participants with unilateral transtibial amputation using an ESAR prosthetic foot.

Study design:

Cross-sectional.

Methods:

Plantar pressure data were collected from 11 participants with unilateral transtibial amputation using ESAR prostheses (2 females, mean age 37 ± 10 years, activity levels K2-K4) and 9 unimpaired participants (3 females, mean age 33 ± 10 years). The Initial Contact, Final Contact, and Total Contact times of 7 areas of the feet (unimpaired, intact, and prosthetic feet) were studied together with the duration of the Heel Rocker, Ankle Rocker, and Forefoot Rocker. Results were compared using a mixed analysis of the variance test.

Results:

Statistical analysis revealed an interaction (P < 0.05) between foot and areas. The contact times were different (P < 0.05) between unimpaired and prosthetic feet for most foot areas. Furthermore, the prosthetic foot showed the longest duration of Heel Rocker (21.1 ± 8.5% of stance phase vs. 17.7 ± 10.2% for the intact foot and 15.7 ± 8.8% for the unimpaired feet, P < 0.05) and the shortest duration of Ankle Rocker (43.8 ± 18.1% vs. 47.2 ± 16.9% for the intact foot and 50.0 ± 13.4% for the unimpaired feet, P < 0.05).

Conclusions:

Results suggest that the ESAR foot does not mimic the unimpaired foot rollover, especially in the contact pattern and the heel and ankle rockers. This might have an impact on efficiency and stability of gait.
High Voltage Pulsed Radiofrequency Combined With Duloxetine on the Treatment of Glossopharyngeal Neuralgia
Authors: Xu Geng , Xu Ziqi , Ren Zhanjie
Published: December 2024

The incidence of glossopharyngeal neuralgia (GPN) is low, but the pain of GPN is severe and seriously affects the patient’s life. We report a case with GPN, who had pain relief after treatment with high-voltage pulsed radiofrequency (PRF) combined with duloxetine. This case indicates that high-voltage PRF combined with duloxetine may be an effective approach for reducing pain in patients with GPN, and duloxetine may have a potential advantage for patients with evoked pain.
Selective nonoperative management of abdominal gunshot wounds: What you need to know
Authors: Matsushima Kazuhide , Inaba Kenji
Published: December 2024

Since the 1990s, there has been a slow but steady adoption of selective nonoperative management (SNOM) for abdominal gunshot wounds (GSW). Multiple studies have shown that SNOM is feasible and can be performed safely, even at trauma centers with low penetrating trauma volumes. The principles of SNOM for abdominal GSW consists of (1) careful patient selection, (2) diagnostic workup with CT, and (3) clinical observation. By implementing SNOM, the number of patients undergoing a nontherapeutic laparotomy can significantly be improved to less than 10%. Overall, approximately one third of patients with abdominal GSW can be managed nonoperatively. This review article provides a practical approach to the management of patients with an abdominal GSW.
Namibian fairy circles: Hostile territory for soil nematodes
Authors: Treonis Amy M. , Bell L. Andrew , Marais Eugene , Maggs-Kölling Gillian
Published: December 2024

Fairy circles are rings of grass with centers of bare soil that are found in some arid grasslands. Above- and belowground chemical and biological attributes of fairy circles have been explored in an ongoing debate about the ultimate causes of this pattern. We studied the soil nematode communities associated withStipagrostisfairy circles along a 900-km range in the Namib Desert of Namibia in southern Africa. Nematode abundance and diversity were highest in soils along the vegetation rings that define fairy circles and in soils in the vegetated matrix surrounding the bare circles, demonstrating the positive impact of plant-derived resources on nematode communities. In contrast, soils from the bare centers of fairy circles had lower organic matter content and were nearly defaunated, averaging only 9.9 ± 1.7 nematodes 100 g−1soil. Bacterial-feedingAcrobeloidesnematodes were the only taxa over-represented in center soils in comparison to ring soils. Our results indicate that nematode communities are influenced by the unique soil environments that the fairy circle vegetation pattern generates and suggest that the soils at the centers of fairy circles are uniquely hostile habitat for soil organisms as well as plants. Co-occurrence network analysis of nematode communities elucidated relationships among the taxa. For example, the abundances of dorylaims andNothacrobeleswere positively correlated across all soil positions, suggesting they have overlapping ecological niches. In ring soils, the abundances of fungal-feedingAphelenchoides,Ditylenchus, andHexatyluswere positively correlated, likely due to enhanced fungal communities in these plant-influenced soils.Panagrobelusdemonstrated niche specialization by being negatively correlated to two other bacterial-feeding taxa (Elaphonemain matrix soils andAcrobeloidesin ring soils). The co-occurrence patterns revealed by these relatively low diversity communities provide insights into the potential roles of nematode interactions as well as environmental factors in community assembly.
Low mutation rate but high male-bias in the germline of a short-lived opossum
Authors: Peña-Garcia Yadira , Wang Richard J. , Raveendran Muthuswamy , Harris R. Alan , Samollow Paul B. , Rogers Jeffrey , Hahn Matthew W.
Published: December 2024

Age and sex have been found to be important determinants of the mutation rate per generation in mammals, but the mechanisms underlying these factors are still unclear. One approach to distinguishing between alternative mechanisms is to study species that reproduce at very young ages, as competing hypotheses make different predictions about patterns of mutation in these organisms. Here, we study the germline mutation rate in the gray short-tailed opossum, Monodelphis domestica, a laboratory model species that becomes reproductively mature at less than six months of age. Whole-genome sequencing of 22 trios reveals the lowest mutation rate per generation found in mammals thus far (0.26 × 10-8 per base pair per generation at an average parental age of 313 days), which is expected given their early reproduction. We also examine the mutation spectrum and find fewer mutations at CpG sites in opossums than in humans, consistent with the lower CpG content in the opossum genome. We observe that two-thirds of mutations are inherited from the male parent in opossums, slightly lower than the degree of male bias observed in organisms that reproduce at much older ages. Nevertheless, the very young age at reproduction in opossums suggests that ongoing spermatogonial divisions in males after puberty are not the primary driver of the observed male mutation bias. These findings contribute to a growing body of evidence that the differences between male and female germline mutation may arise from mechanisms other than cell division post-puberty.

Article Summary

This study investigates the germline mutation rate in the gray short-tailed opossum, a marsupial with early reproductive maturity. By sequencing 22 families, we report the lowest mutation rate recorded in mammals but a typical male mutation bias. These findings add to growing evidence that challenges the traditional view that continuing cell division is the primary driver of male-biased mutations. Instead, the study suggests that alternative mechanisms, such as differences in DNA repair, may influence sex-specific mutation rates.
Diploid origins, adaptation to polyploidy, and the beginning of rediploidization in allotetraploid Arabidopsis suecica
Authors: Burns Robin , Kulkarni Aboli , Glushkevich Anna , Kolesnikova Uliana K , Kolar Filip , Scott Alison Dawn , Novikova Polina Yu.
Published: December 2024

Polyploidization or whole-genome duplication (WGD), followed by genome downsizing is a recurring evolutionary cycle with a significant impact on genome structure. Polyploidy originates from a cell cycle error and in species without a dedicated germline, mitotic as well as meiotic errors can be stably inherited. After the origin, polyploids face immediate challenges, particularly the need to adapt meiotic machinery to prevent improper chromosome pairing and segregation, such as multivalent formation. Over evolutionary timescales, surviving polyploids undergo rediploidization, reorganizing their genomes back to a diploid state. This study focuses on the evolution of a young allotetraploid Arabidopsis suecica, a hybrid species derived from A. thaliana and A. arenosa. Our genomic analyses reveal that A. suecica originated from diploid A. arenosa, contrary to earlier suggestions of a tetraploid origin, indicating that WGD in A. suecica likely occurred somatically rather than being inherited via unreduced gametes. Ecological niche modeling traces the geographic origin of A. suecica to the southeastern edge of the European glacier during the last ice age. We explore how A. suecica adapted to allopolyploidy from diploid ancestors and find evidence of positive selection on meiotic cell cycle genes in the A. arenosa sub-genome. Several of these genes overlap with those involved in autopolyploid adaptation in A. arenosa, but have distinct haplotypes. We also show that purifying selection is relaxed in A. suecica, however, functional compensation between homeologous gene pairs persists, with fewer gene pairs than expected having loss-of-function mutations in both copies. This is consistent with early signs of rediploidization just after ~16K years since the origin of A. suecica. Our study covers three key aspects of the evolution of allopolyploid A. suecica: origin, meiotic adaptation, and the beginning of rediploidization.
Linking multiple serological assays to infer dengue virus infections from paired samples using mixture models
Authors: Hamins-Puértolas Marco , Buddhari Darunee , Salje Henrik , Huang Angkana T. , Hunsawong Taweewun , Cummings Derek A.T. , Fernandez Stefan , Farmer Aaron , Kaewhiran Surachai , Khampaen Direk , Srikiatkhachorn Anon , Iamsirithaworn Sopon , Waickman Adam , Thomas Stephen J. , Endy Timothy , Rothman Alan L. , Anderson Kathryn B. , Rodriguez-Barraquer Isabel
Published: December 2024

Dengue virus (DENV) is an increasingly important human pathogen, with already half of the globe’s population living in environments with transmission potential. Since only a minority of cases are captured by direct detection methods (RT-PCR or antigen tests), serological assays play an important role in the diagnostic process. However, individual assays can suffer from low sensitivity and specificity and interpreting results from multiple assays remains challenging, particularly because interpretations from multiple assays may differ, creating uncertainty over how to generate finalized interpretations. We develop a Bayesian mixture model that can jointly model data from multiple paired serological assays, to infer infection events from paired serological data. We first test the performance of our model using simulated data. We then apply our model to 677 pairs of acute and convalescent serum collected as a part of illness and household investigations across two longitudinal cohort studies in Kamphaeng Phet, Thailand, including data from 232 RT-PCR confirmed infections (gold standard). We compare the classification of the new model to prior standard interpretations that independently utilize information from either the hemagglutination inhibition assay (HAI) or the enzyme-linked immunosorbent assay (EIA). We find that additional serological assays improve accuracy of infection detection for both simulated and real world data. Models incorporating paired IgG and IgM data as well as those incorporating IgG, IgM, and HAI data consistently have higher accuracy when using PCR confirmed infections as a gold standard (87-90% F1 scores, a combined metric of sensitivity and specificity) than currently implemented cut-point approaches (82-84% F1 scores). Our results provide a probabilistic framework through which multiple serological assays across different platforms can be leveraged across sequential serum samples to provide insight into whether individuals have recently experienced a DENV infection. These methods are applicable to other pathogen systems where multiple serological assays can be leveraged to quantify infection history.
Tumor break load quantitates structural variant-associated genomic instability with biological and clinical relevance across cancers
Authors: Lakbir Soufyan , de Wit Renske , de Bruijn Ino , Kundra Ritika , Madupuri Ramyasree , Gao Jianjiong , Schultz Nikolaus , Meijer Gerrit A. , Heringa Jaap , Fijneman Remond J. A. , Abeln Sanne
Published: December 2024

While structural variants (SVs) are a clear sign of genomic instability, they have not been systematically quantified per patient. Therefore, the biological and clinical impact of high numbers of SVs in patients is unknown. We introduce tumor break load (TBL), defined as the sum of unbalanced SVs, as a measure for SV-associated genomic instability. Using pan-cancer data from TCGA, PCAWG, and CCLE, we show that a high TBL is associated with significant changes in gene expression in 26/31 cancer types that consistently involve upregulation of DNA damage repair and downregulation of immune response pathways. Patients with a high TBL show a higher risk of recurrence and shorter median survival times for 5/15 cancer types. Our data demonstrate that TBL is a biologically and clinically relevant feature of genomic instability that may aid patient prognostication and treatment stratification. For the datasets analyzed in this study, TBL has been made available in cBioPortal.
ROS1 immunohistochemistry as a potential predictive biomarker for ROS1-targeted therapy in breast cancer: impact of antibody clone selection
Authors: Sokolova Anna , Joshi Vaibhavi , Chittoory Haarika , Walsh Michael , Lim Malcolm , Kutasovic Jamie R. , Ferguson Kaltin , Simpson Peter T. , Lakhani Sunil R. , McCart Reed Amy E.
Published: December 2024

Aims

Invasive lobular carcinoma (ILC) may show targetable vulnerabilities secondary to the characteristic loss of the cell adhesion protein E-cadherin. Specifically, a synthetic lethal interaction was identified between E-cadherin loss and ROS1 inhibition. Several clinical trials are currently underway to assess the efficacy of ROS1 inhibitors in ILC, however, ROS1 expression has not been confirmed in ILC tumours and ROS1 has not been validated as a biomarker in the breast cancer setting. This study aimed to (i) examine ROS1 expression in a large cohort of breast cancer cases and (ii) investigate the biology and clinical significance of ROS1 positivity in breast cancer.

Methods

ROS1 immunohistochemistry was performed on a large cohort of ILC (n=274) and invasive carcinoma of no special type (NST; n=431) cases with extensive clinicopathological data. The staining performance of four ROS1 antibody clones was compared.

Results

There was marked variation in ROS1 status according to antibody clone. D4D6 and SP384 were negative in almost all breast cancer cases, whereas EP282 and EPMGHR2 were positive in 37% and 47% of ILC cases, and 49% and 74% of NST cases, respectively. Only data from clones D4D6 and SP384 were highly concordant, while EP282 and EPMGHR2 were positive in distinct breast cancer subtypes.

Conclusions

Assessment of ROS1 status in breast cancer appears to be highly antibody clone dependent. ROS1 antibody clone selection will be an important consideration in the design of clinical trials investigating the clinical validity of ROS1 as a predictive biomarker in breast cancer.
Early-life infectious disease exposure, the “hygiene hypothesis”, and lifespan: evidence from hookworm
Authors: Lawton Ralph I.
Published: December 2024

Exposure to infectious disease in early life may have long-term ramifications for health and lifespan. However, reducing pathogen exposure may not be uniformly beneficial. The rise of modern sanitation and reduction of infectious diseases has been implicated in increasing levels of allergy and immune dysregulation: termed, the “hygiene hypothesis.” This study leverages quasi-experimental variation from combining pre-campaign hookworm exposure with the Rockefeller Sanitary Commission’s de-worming campaign in the early 20th century to rigorously examine the impacts of childhood hookworm exposure on adult lifespan and morbidity. Findings show de-worming before age five leads to 2.5 additional months of life in a large sample of adult death records. Further, decreasing hookworm exposure is related to improvements in biomarkers for inflammation and skin-tested allergies, in contrast to predictions of the “hygiene hypothesis”. Placebo tests using health outcomes that should not be affected by de-worming do not show similar patterns. Overall, childhood de-worming leads to improvements in morbidity and lifespan decades later.
Genomic and proteomic characterization of sulfate-reducing symbionts of gutless marine annelids
Authors: D’Angelo Grace , Kleiner Manuel , Mankowski Anna , Cifuentes-Anticevic Jerónimo , Violette Marlene J. , Anda Valerie De , Kröber Eileen , Dubilier Nicole , Liebeke Manuel
Published: December 2024

Sulfate-reducing bacteria inhabit marine and terrestrial environments, forming syntrophic associations with other bacteria, archaea and eukaryotes. A notable example is the symbiosis between sulfate-reducing bacteria (SRB) and gutless oligochaete worms found in marine sediments worldwide. These endosymbionts participate in a syntrophic sulfur exchange with the primary endosymbiont of gutless oligochaetes, a sulfur-oxidizing bacterium, thus providing otherwise inaccessible metabolic capabilities to the animal host. Here, we used a combination of metagenomic and metaproteomic analysis to describe the metabolic functions of SRBs from gutless annelids. Identified as members of the Desulfobacteria class, closely related to theDesulfococcusandDesulfosarcinagenera, these SRB symbionts exhibit a range of common and unique metabolic capabilities. Our analyses revealed their core metabolism of complete oxidation of acetate to CO2 via the Wood-Ljungdahl pathway, glyoxylate bypass of the TCA cycle, degradation of glycine as a nitrogen source, and presence of transporters for essential nutrients. A large-scale genome comparison revealed that the sulfate-reducing endosymbionts, named here "CandidatusDesulfoconcordia", have metabolic distinctions with respect to their free-living counterparts that could indicate adaptation to the energy and nutrient requirements of their symbiotic niche. The enrichment of functions like peptidases and amino acid transporters together with their abundant expression in the proteomes and the reduction of sugar and sulfur scavenging functions in the symbiotic genomes indicate a symbiosis-driven ecological role distinct from free-living SRBs. Our study revealed the metabolic capabilities that have enabled "CandidatusDesulfoconcordia" to adapt to their multi-domain associations.
A skewed picture of functional diversity in global drylands
Authors: Tordoni Enrico , Puglielli Giacomo , Beccari Eleonora , Carmona Carlos P.
Published: December 2024

Recently, Gross et al. (Nature 632, 808-814) found that plant phenotypic diversity dramatically increases with aridity globally, challenging conventional environmental filtering theories. However, some methodological choices by Gross et al. might overestimate the effect of aridity on phenotypic diversity: (i) We detected a skewed distribution of sampling sites towards the arid end of the analyzed gradient; (ii) We posited that fine-tuning of some statistical parameters might further challenge their estimates. We reanalyzed Gross et al. data accounting for these effects and found a substantially reduced change of phenotypic diversity with increasing aridity. Gross et al. surely represents a cornerstone for future research on trait diversity in a drier world, but their interpretations need to be considered alongside our findings. Importantly, the points raised by our reanalysis provide general guidelines for future research on plant phenotypic diversity changes along environmental gradients.
Current transcriptome database and biomarker discovery for immunotherapy by immune checkpoint blockade
Authors: Zhang Han , Lu Binfeng , Lu Xinghua , Saeed Anwaar , Chen Lujia
Published: December 2024

Immune checkpoint blockade (ICB) has revolutionized the current immuno-oncology and significantly improved clinical outcome for cancer treatment. Despite the advancement in clinics, only a small subset of patients derives immune response to the ICB therapy. Therefore, a robust predictive biomarker that identifies potential candidate becomes increasingly crucial in delivering this technology to the public. In this review, we first discuss the biomarkers that focus on tumor genome, tumor microenvironment and tumor-host interaction. Then, we compare existing databases for biomarker discovery for ICB response. We also present IOhub - an interactive web portal that incorporates 36 bulk and 10 single-cell transcriptome datasets for benchmark analysis of the current biomarkers. Finally, we highlight the trending interest in antibody drug conjugate and combination treatment and their use in precision immuno-oncology.
Changes in urinary proteome of rats before and after noise exposure
Authors: Yang Minhui , Zhao Chenyang , Gao Youhe
Published: December 2024

This study established an acute noise exposure model in which 10 rats were exposed to a 119 dB noise environment for 9 hours daily over a period of 7 consecutive days. Proteomic analysis was performed on urine samples collected from the rats. A comparison of protein expression profiles before and after noise exposure identified 219 differentially expressed proteins, 30 of which are known to be associated with hearing loss. Notably, Gelsolin plays a critical role in regulating the growth and stability of the mechanosensory hair bundles in mammalian cochlear outer hair cells. Deficiency of Lysosome-associated membrane glycoprotein 1 has been reported to cause vacuolization and structural alterations in lysosomal membrane proteins in cochlear marginal cells, leading to hearing loss in mice. Similarly, SLIT and NTRK-like family member 6 deficiency is linked to delayed synaptogenesis and auditory dysfunction in mice. These findings indicate that high-decibel noise exposure induces significant changes in urinary protein expression, many of which are associated with auditory damage as previously reported.
Gender–specific Single Transcript Level Atlas of Vasopressin and its Receptor (AVPR1a) in the Mouse Brain
Authors: Gumerova Anisa , Pevnev Georgii , Korkmaz Funda , Cheliadinova Uliana , Burganova Guzel , Vasilyeva Darya , Cullen Liam , Barak Orly , Sultana Farhath , Zhou Weibin , Sims Steven , Laurencin Victoria , Frolinger Tal , Kim Se-Min , Goosens Ki A. , Yuen Tony , Zaidi Mone , Ryu Vitaly
Published: December 2024

Vasopressin (AVP), a nonapeptide synthesized predominantly by magnocellular hypothalamic neurons, is conveyed to the posterior pituitaryviathe pituitary stalk, where AVP is secreted into the circulation. Known to regulate blood pressure and water homeostasis, it also modulates diverse social behaviors, such as pair–bonding, social recognition and cognition in mammals including humans. Importantly, AVP modulates social behaviors in a gender–specific manner, perhaps, due to gender differences in the distribution in the brain of AVP and its main receptor AVPR1a. There is acorpusof integrative studies for the expression of AVP and AVPR1a in various brain regions, and their functions in modulating central and peripheral actions. In order to purposefully address sexually dimorphic and novel roles of AVP on central and peripheral functions through its AVPR1a, we utilized RNAscope to mapAvpandAvpr1asingle transcript expression in the mouse brain. As the most comprehensive atlas of AVP and AVPR1a in the mouse brain, this compendium highlights the importance of newly identified AVP/AVPR1a neuronal nodes that may stimulate further functional studies.
High-Resolution Transcriptional Impact of AIRE: Effects of Pathogenic Variants p.Arg257Ter, p.Cys311Tyr, and Polygenic Risk Variant p.Arg471Cys
Authors: Berger Amund Holte , Oftedal Bergithe Eikeland , Wolff Anette Susanne Bøe , Husebye Eystein Sverre , Knappskog Per Morten , Bratland Eirik , Johansson Stefan
Published: December 2024

The Autoimmune Regulator, AIRE, acts as a transcriptional regulator in the thymus, facilitating ectopic expression of thousands of genes important for the process of negative T-cell selection and immunological tolerance to self. Pathogenic variants in the gene encoding AIRE are causing Autoimmune polyendocrine syndrome type 1 (APS-1), defined by multiorgan autoimmunity and chronic mucocutaneous candidiasis. More recently, Genome Wide Association Studies (GWAS) have also implicated AIRE in several common organ-specific autoimmune diseases including Autoimmune primary adrenal insufficiency, type 1 diabetes and pernicious anemia. We developed a highly sensitive cell-system approach based on HEK293FT cells transfected withAIREthat allowed us to characterise and functionally evaluate the transcriptional potential of genetic variants in theAIREgene. We confirm that our cell system recapitulates the expression of the vast majority of known AIRE induced genes including well-characterised tissue restricted antigens (TRAs), but also increases the total number of identified AIRE induced genes by an order of magnitude compared to previously published strategies. The approach differentiates between categories ofAIREvariants on the transcriptional level, including the nonsense variant p.R257* (near complete loss of function), the p.C311Y variant associated with dominantly inherited APS-1 (severely impaired function), and the polygenic risk variant p.R471C (slightly increased function) linked to common organ-specific autoimmunity. The increased activity of p.R471C compared to wildtype indicates different molecular mechanisms for monogenic and polygenic AIRE related autoimmunity.
Simple and rapid lectin-based detection of native glycoRNAs
Authors: Li Yong , Qian Yisong , Lei Tianhua , Monaghan-Nichols Paula , Fu Mingui
Published: December 2024

The current detection methods for glycoRNAs include metabolic labeling of living cells or animals and rPAL that directly detects native glycoRNAs by periodate oxidation and aldehyde ligation. Both of them have some limitations. Here we reported a simple and rapid detection of native glycoRNAs by using lectins. The method involves in several simple procedures: isolation of total RNA, northern blotting and detection with lectins. The advantages of this method include high sensitivity, very simple procedures and broader applications. We used this method detecting glycoRNA expression in the RNA samples from different species. We also detect the glycoRNA expression across the varieties of mouse and human tissues and compared with other detection methods. We are in the first to detect free glycoRNAs in the varieties of human biofluids. Overall, this simple and rapid method will provide a new tool for study of glycoRNA biology and clinical diagnosis in future.
Mapping and characterization of a novel powdery mildew resistance locus (PM2) inCannabis sativaL
Authors: Seifi Soren , Leckie Keegan M. , Giles Ingrid , O’Brien Taylor , MacKenzie John O. , Todesco Marco , Rieseberg Loren H. , Baute Gregory J. , Celedon Jose M.
Published: December 2024

Breeding genetic resistance to economically important crop diseases is the most sustainable strategy for disease management and enhancing agricultural and horticultural productivity, particularly where the application of synthetic pesticides is prohibited. Powdery mildew disease, caused by the biotrophic fungal pathogenGolovinomyces ambrosiae, is one of the most prevalent threats to the cannabis and hemp industry worldwide. In this study, we used bulk-segregant analysis (BSA) combined with high-throughput sequencing to identify and map a novel single dominant resistance (R) locus (designatedPM2), that strongly suppresses powdery mildew infection and sporulation inCannabis sativa. Histochemical analysis revealed that PM2-induced resistance is mediated by a highly localized hypersensitive response mainly in the epidermal cells of the host. Importantly, genetic markers capable of tracking PM2 resistance in breeding populations were developed using associated SNPs identified in this study.
Nonlinear gauge-Higgs
CP
violation
Authors: Bhardwaj Akanksha , Englert Christoph , Gonçalves Dorival , Navarro Alberto
Published: December 2024

A critical element of the LHC physics program is the search for an additional source of CP violation. This is largely unexplored in the context of nonlinear Higgs physics, which is naturally described in Higgs effective field theory (HEFT). Relevant new higher-dimensional operators modify the production rate and branching ratios of the Higgs boson, decorrelating different Higgs multiplicities. In this work, we consider single Higgs and Higgs pair production via weak boson fusion from the perspective of gauge-Higgs CP violation through the lens of Higgs nonlinearity. This generalizes existing rate-based searches and analyses by the ATLAS and CMS experiments. Particular focus is given to the phenomenological differences in the expected beyond Standard Model (BSM) sensitivity pattern when comparing HEFT constraints with Standard Model effective field theory (SMEFT) limits.

Published by the American Physical Society
2024
Superdiffusive Thermal Transport in Polymer-Grafted Nanoparticle Melts
Authors: Liu Bohai , Jhalaria Mayank , Ruzicka Eric , Benicewicz Brian C. , Kumar Sanat K. , Fytas George , Xu Xiangfan
Published: December 2024

In contrast to normal diffusion processes, thermal conduction in one-dimensional systems is anomalous. The thermal conductivity is found to vary with the length as κ∼Lα(α>0), but there is a long-standing debate on the value α. Here, we present a canonical example of this behavior in polymer-grafted spherical nanoparticle (GNP) melts at fixed grafting density and nanoparticle radius. For long chains (chain length N≥945), the experimental κ(N) of GNP melts decreases with N, i.e., polymer concentration. For N<945, however, κ(N) unexpectedly increases with N with a maximum near N∼945. For these systems, the extensional free energy per polymer chain is predicted to be maximized near Nmax≈940 for σ≈0.47  chains/nm2, which indicates the dominance of extended conformations at short N and Gaussian-like conformation for longer N. In the former regime, the thermal conductivity of extended polymer chains increases with N and follows κp∼Ndry0.46±0.02, which provides experimental evidence of a novel class of superdiffusive thermal transport with α=1/2.

Published by the American Physical Society
2024
Cell Sorting in an Active Nematic Vertex Model
Authors: Rozman Jan , Yeomans Julia M.
Published: December 2024

We study a mixture of extensile and contractile cells using a vertex model extended to include active nematic stresses. The two cell populations phase separate over time. While phase separation strengthens monotonically with an increasing magnitude of contractile activity, the dependence on extensile activity is nonmonotonic, so that sufficiently high values reduce the extent of sorting. We interpret this by showing that extensile activity renders the system motile, enabling cells to undergo neighbor exchanges. Contractile cells that come into contact as a result are then more likely to stay connected due to an effective attraction arising from contractile activity.

Published by the American Physical Society
2024
Markov State Model Approach to Simulate Self-Assembly
Authors: Trubiano Anthony , Hagan Michael F.
Published: December 2024

Computational modeling of assembly is challenging for many systems, because their timescales can vastly exceed those accessible to simulations. This article describes the multiMSM, which is a general framework that uses Markov state models (MSMs) to enable simulating self-assembly and self-organization of finite-sized structures on timescales that are orders of magnitude longer than those accessible to brute-force dynamics simulations. As with traditional MSM approaches, the method efficiently overcomes free energy barriers and other dynamical bottlenecks. In contrast to previous MSM approaches to simulating assembly, the framework describes simultaneous assembly of many clusters and the consequent depletion of free subunits or other small oligomers. The algorithm accounts for changes in transition rates as concentrations of monomers and intermediates evolve over the course of the reaction. Using two model systems, we show that the multiMSM accurately predicts the concentrations of the full ensemble of intermediates on timescales required to reach equilibrium. Importantly, after constructing a multiMSM for one system concentration, yields at other concentrations can be approximately calculated without any further sampling. This capability allows for orders of magnitude additional speedup. In addition, the method enables highly efficient calculation of quantities such as free energy profiles, nucleation timescales, flux along the ensemble of assembly pathways, and entropy production rates. Identifying contributions of individual transitions to entropy production rates reveals sources of kinetic traps. The method is broadly applicable to systems with equilibrium or nonequilibrium dynamics and is trivially parallelizable and, thus, highly scalable.

Published by the American Physical Society
2024
Crystal structure of luliconazole
Authors: Ben Anna , Chęcińska Lilianna
Published: December 2024

The crystal structure of luliconazole {LCZ; C14H9Cl2N3S2; systematic name: (E)-[(4R)-4-(2,4-dichlorophenyl)-1,3-dithiolan-2-ylidene](1H-imidazol-1-yl)acetonitrile} is reported. In the molecule of the title compound, the dithiolane ring adopts an envelope conformation, while the dichlorophenyl ring exhibits disorder. In the crystal packing of luliconazole, only two intermolecular C–H...N hydrogen bonds are observed. Hirshfeld surface analysis reveals that the most dominant contacts are H...N/N...H, H...Cl/Cl...H, H...H and C...H/H...C.
3-(2-Hydroxyethyl)-1-(4-nitrophenyl)-1H-benzo[d]imidazol-3-ium bromide
Authors: Ibrahim Halliru , Zamisa Sizwe J. , Bala Muhammad D. , Ntola Pinkie , Friedrich Holger B.
Published: December 2024

The cation of the title salt, C15H14N3O3
+·Br−, has a dihedral angle of 24.26 (6)° between its fused imidazole and 4-nitrophenyl rings and the N—C—C—O torsion angle associated with the hydroxyethyl substituent is 60.15 (17)°. In the crystal, the bromide ions act as double acceptors for hydrogen bonds from a hydroxyl group (O—H...Br) and a fused imidazolium moiety (C—H...Br). Additionally, C—H...O hydrogen bonds between the phenyl group and hydroxyl oxygen atom create a two-dimensional supramolecular network extending diagonally in the crystallographic bc plane.
Sn(SO4)2·2H2O from synchrotron powder data
Authors: Fjellvåg Øystein Slagtern , Fjellvåg Helmer
Published: December 2024

Tin(IV) sulfate dihydrate, Sn(SO4)2·2H2O, was prepared in a reflux of sulfuric acid under oxidizing conditions. Its crystal structure was determined from powder synchrotron X-ray diffraction data and is constructed of (100) layers of [SnO4(H2O)2] octahedra (point group symmetry 1) corner-connected by sulfate tetrahedra. Hydrogen bonds of moderate strength between the water molecules and sulfate O atoms hold the layers together.
Factors hindering the implementation of PPP in Iraq
Authors: Al-Tameemi Khaldoon Shehab , Alfaiz Sundus Khaleel , Al-Sadoon Nidhal
Published: December 2024

Purpose

It is a worldwide phenomenon that infrastructure development is considered a catalyst for a country’s economic growth, enhanced service delivery and improved quality of life. Iraq has a considerable lack of necessary infrastructure. Many developing and developed nations utilise public-private partnerships (PPPs) as a means to address their infrastructure investment requirements. This study, however, uniquely investigates the specific factors hindering the implementation of PPP in Iraq, focusing on Iraq’s distinct political, economic and legislative challenges.

Design/methodology/approach

A thorough literature review, guided by systematic principles similar to Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA), has been conducted to understand PPP and highlight the factors that can facilitate the effective implementation of PPP around the globe. Afterwards, a questionnaire survey was deployed to relevant stakeholders in Iraq to examine these factors in the specific context of Iraq. Subsequently, in-depth interviews with key Iraqi decision-makers were carried out to discuss the questionnaire results in more detail and pinpoint particular barriers impeding successful PPP implementation in Iraq. These data were then rigorously analysed to highlight Iraq’s unique challenges, and the results were discussed to provide a contextual understanding. Based on these insights, conclusions and recommendations are drawn accordingly.

Findings

The results revealed that one of the main factors hindering the implementation of PPP in Iraq is the absence of a legal and regulatory framework that can give PPP implementation its legitimacy in Iraq. Other factors include the overall reluctance of several Iraqi legislators towards the PPP system and the unavailability of an environment attractive to investors.

Originality/value

The findings and recommendations set forth in this research can aid champions of the PPP system within the government of Iraq in devising an effective plan. Unlike similar studies, this paper addresses barriers specific to Iraq, such as political reluctance and regulatory gaps, providing new insights to guide policy. This plan is intended to foster a PPP mindset among relevant lawmakers, ensuring the successful approval of PPP laws and regulatory frameworks.