bluuebunny/crossref_metadata_2025 huggingface dataset:
Twenty years of advances in prediction of nucleic acid-binding residues in protein sequences
Authors: Basu Sushmita , Yu Jing , Kihara Daisuke , Kurgan Lukasz
Published: January 2025

Computational prediction of nucleic acid-binding residues in protein sequences is an active field of research, with over 80 methods that were released in the past 2 decades. We identify and discuss 87 sequence-based predictors that include dozens of recently published methods that are surveyed for the first time. We overview historical progress and examine multiple practical issues that include availability and impact of predictors, key features of their predictive models, and important aspects related to their training and assessment. We observe that the past decade has brought increased use of deep neural networks and protein language models, which contributed to substantial gains in the predictive performance. We also highlight advancements in vital and challenging issues that include cross-predictions between deoxyribonucleic acid (DNA)-binding and ribonucleic acid (RNA)-binding residues and targeting the two distinct sources of binding annotations, structure-based versus intrinsic disorder-based. The methods trained on the structure-annotated interactions tend to perform poorly on the disorder-annotated binding and vice versa, with only a few methods that target and perform well across both annotation types. The cross-predictions are a significant problem, with some predictors of DNA-binding or RNA-binding residues indiscriminately predicting interactions with both nucleic acid types. Moreover, we show that methods with web servers are cited substantially more than tools without implementation or with no longer working implementations, motivating the development and long-term maintenance of the web servers. We close by discussing future research directions that aim to drive further progress in this area.
PHPGAT: predicting phage hosts based on multimodal heterogeneous knowledge graph with graph attention network
Authors: Liu Fu , Zhao Zhimiao , Liu Yun
Published: January 2025

Antibiotic resistance poses a significant threat to global health, making the development of alternative strategies to combat bacterial pathogens increasingly urgent. One such promising approach is the strategic use of bacteriophages (or phages) to specifically target and eradicate antibiotic-resistant bacteria. Phages, being among the most prevalent life forms on Earth, play a critical role in maintaining ecological balance by regulating bacterial communities and driving genetic diversity. Accurate prediction of phage hosts is essential for successfully applying phage therapy. However, existing prediction models may not fully encapsulate the complex dynamics of phage–host interactions in diverse microbial environments, indicating a need for improved accuracy through more sophisticated modeling techniques. In response to this challenge, this study introduces a novel phage–host prediction model, PHPGAT, which leverages a multimodal heterogeneous knowledge graph with the advanced GATv2 (Graph Attention Network v2) framework. The model first constructs a multimodal heterogeneous knowledge graph by integrating phage–phage, host–host, and phage–host interactions to capture the intricate connections between biological entities. GATv2 is then employed to extract deep node features and learn dynamic interdependencies, generating context-aware embeddings. Finally, an inner product decoder is designed to compute the likelihood of interaction between a phage and host pair based on the embedding vectors produced by GATv2. Evaluation results using two datasets demonstrate that PHPGAT achieves precise phage host predictions and outperforms other models. PHPGAT is available at https://github.com/ZhaoZMer/PHPGAT.
High-volume lactated Ringer’s solution with human albumin versus standard-volume infusion as a prophylactic treatment for post-endoscopic retrograde cholangiopancreatography pancreatitis: randomized clinical trial
Authors: Shatsnimitkul Ekaphan , Laopeamthong Issaree , Tansawet Amarit , Techapongsatorn Suphakarn , Kasetsermwiriya Wisit , Leungon Poramet , Sukhvibul Pakkapol
Published: January 2025

Background

Adverse events after endoscopic retrograde cholangiopancreatography (ERCP) are rare, and post-ERCP pancreatitis is a serious adverse event. This study aimed to determine the role of aggressive intravenous hydration with lactated Ringer’s solution at a specific volume with 20% human albumin before ERCP in reducing the incidence of post-ERCP pancreatitis.

Methods

This study was a single-centre randomized clinical trial. The participants were randomly assigned to two groups: those who received aggressive intravenous hydration with 20% human albumin and lactated Ringer's solution (intervention group), and those who received standard-volume intravenous hydration with lactated Ringer's solution (control group). The primary endpoint was post-ERCP pancreatitis. Participants and outcome assessors were blinded to treatment allocation. Comparison was performed using the chi-square, the Fisher’s exact, the Student’s t, or the Mann–Whitney U tests, where appropriate.

Results

Of 300 randomized participants, 149 and 144 participants from the intervention and control group were included in the analysis. There was no significant difference in the post-ERCP pancreatitis rate (n = 10; 6.7% versus n = 9; 6.3%, P = 0.873) between the intervention and control groups. High-risk procedures (that is pancreatic duct wiring, pancreatic duct injection, precut sphincterotomy, and balloon dilation of the ampulla) were significantly associated with post-ERCP pancreatitis compared with low-risk procedures (n = 15; 15% versus n = 4; 2.1%, P < 0.001). In the high-risk procedures population, the intervention and control groups had increased post-ERCP pancreatitis rates (P = 0.716). Two participants in each group developed pulmonary congestion.

Conclusion

Aggressive peri-ERCP intravenous hydration with lactated Ringer's solution combined with 50 ml of 20% human albumin did not prevent post-ERCP pancreatitis. None of the subgroups presented with prophylactic effects.

Trial registration

Thai Clinical Trials Registry (TCTR20240405003)
Safety and Tolerability of Pivmecillinam During More Than Four Decades of Clinical Experience: A Systematic Review
Authors: Kaye Keith S , Santerre Henriksen Anne , Sommer Morten , Frimodt-Møller Niels
Published: January 2025

The recent US Food and Drug Administration approval of pivmecillinam—an oral prodrug of the amidinopenicillin antibiotic mecillinam—presents a valuable opportunity to address the need for new treatments for uncomplicated urinary tract infection (uUTI). We report findings of a systematic literature review of the safety profile of pivmecillinam/mecillinam based on more than 40 years’ experience, mainly in Europe and Canada, to describe its tolerability profile and identify any important safety signals. In total, 110 eligible publications were identified describing use of pivmecillinam/mecillinam as monotherapy or in combination, for treatment of uUTI or other infectious conditions. These studies revealed a benign safety and tolerability profile, awareness of which will inform treatment decisions as pivmecillinam is made available in the United States. Together with the evidence for efficacy of, and minimal resistance to, pivmecillinam, the findings of this review support the position of pivmecillinam as a first-line treatment for uUTI.
Complicated infective endocarditis of the bioprosthetic mitral valve following the transcatheter mitral valve-in-valve procedure: a case report and literature review
Authors: Sahebjam Mohammad , Karimi Yeganeh , Fallah Flora
Published: January 2025

Background

Since the transcatheter valve-in-valve (ViV) procedure was introduced in 2007, a few cases of infective endocarditis (IE) following the ViV procedure have been reported, which can be predisposed by older age, pre-existing medical conditions, and procedural techniques. Paravalvular abscesses constitute a rare complication of IE, resulting from extending IE beyond the valve annulus, less commonly caused by Klebsiella species. This complication is more common in prosthetic valves, particularly bioprosthetic valves.

Case summary

We describe a 75-year-old woman with Churg–Strauss syndrome and diabetes mellitus who underwent surgical replacement of bioprosthetic aortic and mitral valves 11 years ago. One year ago, she had a transcatheter mitral ViV procedure due to bioprosthetic mitral valve degeneration. The patient was referred to our centre with fatigue and fever, alongside elevated white blood cell count, erythrocyte sedimentation rate, and C-reactive protein. Blood and urine cultures tested positive for Klebsiella oxytoca. Echocardiographic assessments revealed a paravalvular abscess (13 × 8 mm) in the posterolateral side of the bioprosthetic mitral valve, fistulized into the left ventricle. The patient received treatment with vancomycin, meropenem, and colistin and was a candidate for surgery. Eleven days after the patient’s admission, she passed away.

Discussion

This study underscores the novelty of IE complicated with paravalvular abscess following the ViV procedure. In such cases, a multidisciplinary approach and timely surgical interventions are crucial for optimal patient outcomes.
Re-sheathing failure with Navitor during transcatheter aortic valve implantation: a case report
Authors: Onoda Hiroshi , Ueno Hiroshi , Hida Yuki , Imamura Teruhiko , Kinugawa Koichiro
Published: January 2025

Background

Self-expanding valves used in transcatheter aortic valve implantation (TAVI) are designed to allow recapture and repositioning, facilitating optimal placement and mitigating conduction disturbances and paravalvular leakage. Here, we present a rare case in which the Navitor (Abbott Structural Heart, Santa Clara, CA, USA) could not be recaptured.

Case summary

An 81-year-old Japanese woman with very severe aortic stenosis and a massively calcified nodule at the non-coronary cusp (NCC) underwent TAVI with a 25 mm Navitor valve. During the initial deployment attempt, non-uniform expansion (NUE) was observed on the NCC side when the valve was 80% deployed. An attempt was made to recapture and reposition the valve, but the delivery system capsule failed to fully re-sheath the prosthesis, leaving approximately one-third of the valve outside the capsule and preventing complete recapture. The Navitor was promptly redeployed while still within the basal ring. Following redeployment, the NUE resolved, and the valve was successfully positioned 3 mm below the basal ring on the NCC side and 4 mm below the left coronary cusp. We hypothesized that interference between the capsule tip and the calcified nodule on the NCC leaflet inhibited the re-sheathing process.

Conclusion

This report documents a rare complication involving the failure to recapture the Navitor valve. In cases with large calcified nodules on the leaflet, caution is essential during the re-sheathing process. We strongly recommend re-deploying the prosthesis rather than attempting to remove it from the basal ring to minimize procedural risks and ensure proper valve placement.
The risk of failure of subcutaneous implantable cardioverter defibrillator therapy: from PRAETORIAN score to clinical practice
Authors: Ziacchi Matteo , Ottaviano Luca , Checchi Luca , Viani Stefano , Nigro Gerardo , Bianchi Valter , De Bonis Silvana , De Filippo Paolo , Francia Pietro , Rapacciuolo Antonio , Vitulano Gennaro , Perego Giovanni Battista , Schillaci Vincenzo , Lavalle Carlo , Migliore Federico , Pisanò Ennio C L , Compagnucci Paolo , Palmisano Pietro , Botto Gianluca , Rordorf Roberto , Lovecchio Mariolina , Valsecchi Sergio , Biffi Mauro
Published: January 2025

Aims

The subcutaneous implantable cardioverter defibrillator (S-ICD) is an alternative to traditional ICDs. The PRAETORIAN score, based on chest radiographs, has been validated to predict the probability of successful S-ICD defibrillation testing by assessing factors like fat thickness between the coil and sternum and generator placement. This study evaluated the correlation between the PRAETORIAN score and clinical characteristics, as well as implantation variables.

Methods and results

We retrospectively analysed data from 1253 patients who had undergone implantation of an S-ICD across 33 centres. The intermuscular positioning of the pulse generator was adopted in all patients. Post-implantation posterior–anterior and lateral chest radiographs were analysed to calculate the PRAETORIAN score. A total of 95.7% of patients had a PRAETORIAN score < 90, indicative of a low risk of conversion failure. Body mass index (BMI) was the only independent predictor of a score ≥ 90, and all patients with BMI < 25 kg/m2 (normal weight or underweight) had a score < 90. The intermuscular positioning technique resulted in optimal posterior placement of the device in all patients and significant sub-generator fat in only 3% of cases. A shock impedance value > 88 Ohm enabled to detect a PRAETORIAN score ≥ 90 with 98% (95% CI 97–99%) negative predictive value.

Conclusion

In contemporary practice, the PRAETORIAN score can be simplified. By adopting an intermuscular approach, two of the three steps of the score—evaluating the adequate posterior positioning of the generator and measuring the sub-generator fat—become superfluous, and impedance may serve as a reliable surrogate of sub-coil fat thickness. Furthermore, our data suggest that for non-obese patients, a favourable PRAETORIAN score is assured, making the score evaluation potentially unnecessary.

Clinical trial registration

URL: http://clinicaltrials.gov/ Identifier: NCT02275637.
Public knowledge, attitudes, and practices regarding antibiotics use and resistance in Montenegro
Authors: Raicevic Maja , Labovic Barjaktarovic Snezana , Milic Dejana , Nedovic Vukovic Mirjana , Bajceta Natasa
Published: January 2025

A drug consumption monitoring revealed that Montenegro is one of the major consumers of antimicrobial drugs in Europe. The aim of this study is to obtain the first data on the knowledge, attitudes, and practices of the general population in Montenegro regarding antibiotics use. This cross-sectional study was designed according to the methodology of Eurobarometer survey on antimicrobial resistance, created by the European Commission. The standardized questionnaire was conducted in Podgorica, in October–November 2022. A total of 532 participants completed the questionnaire. More than a half of responders (60.9%) have received antibiotics within the last 12 months and among them 33.4% was missing a medical prescription, nor the antibiotic was administered by a medical practitioner. The rest of the responders mostly had some antibiotics left over from a previous course (13.0%), had taken it from a pharmacy (11.4%), or elsewhere without a prescription. The most frequent reasons for antimicrobial therapy were “cold” (22.5%), “sore throat” (21.0%), “cough” (19.4%), and “COVID-19” (coronavirus disease 2019) (17.9%). Throat swab, blood test, urine test, or other test that could identify the cause of the illness preceded antimicrobial therapy in 46.3% participants. Only one-half of the participants were convinced that antibiotics are ineffective in viral infection treatment. This study is the first report on public knowledge, attitudes and practices regarding antibiotics use and resistance in Montenegro and it highlights the need for the knowledge improvement among general population, better regulations for antibiotics procurement and a campaign regarding appropriate antibiotics use among youth.
Effectiveness of the AZD1222 vaccine against COVID-19 hospitalization in Europe: final results from the COVIDRIVE test-negative case–control study
Authors: de Munter Leonie , Meeraus Wilhelmine , Dwivedi Akshat , Mitratza Marianna , Wyndham-Thomas Chloé , Carty Lucy , Ouwens Mario , Hartig-Merkel Wendy , Drikite Laura , Rebry Griet , Casas Irma , Mira-Iglesias Ainara , Icardi Giancarlo , Otero-Romero Susana , Baumgartner Sebastian , Martin Charlotte , Holemans Xavier , ten Kate Gerrit Luit , Bollaerts Kaatje , Taylor Sylvia
Published: January 2025

Marketing authorization holders of vaccines typically need to report brand-specific vaccine effectiveness (VE) to the regulatory authorities as part of their regulatory obligations. COVIDRIVE (now id. DRIVE) is a European public–private partnership for respiratory pathogen surveillance and studies of brand-specific VE with long-term follow-up. We report the final VE results from a two-dose primary series AZD1222 (ChAdOx1 nCoV-19) vaccine schedule in ≥18-year-old individuals not receiving boosters. Patients (N = 1,333) hospitalized with severe acute respiratory infection at 14 hospitals in Austria, Belgium, Italy, and Spain were included in the test-negative case–control study in 2021–2023. Absolute VE was calculated using generalized additive model (GAM), generalized estimating equation (GEE), and spline-based area under the curve (AUC, measuring VE up to 6 months after the last dose of AZD1222). Overall VE (against coronavirus disease 2019 [COVID-19] hospitalization) of an AZD1222 primary series was estimated as 65% using GEE (95% confidence interval [CI]: 52.9–74.5), and 69% using GAM (95% CI: 50.1–80.9) over the 22-month study period (comparator group: unvaccinated patients). The AUC of the spline-based VE estimate was 74.1% (95% CI: 60.0–88.3). VE against hospitalization in study participants who received their second AZD1222 dose 2 months or less before hospitalization was 86% using GEE (95% CI: 77.8–91.4), 93% using GAM (95% CI: 67.2–98.6). During this study period, where mainly the severe acute respiratory syndrome coronavirus 2 Omicron variant was circulating, a two-dose primary series AZD1222 vaccination conferred protection against COVID-19 hospitalization up to at least 6 months after the last dose.
Increasing incidence and prevalence of Hodgkin’s lymphoma in Finland: a population-based registry study
Authors: Antikainen Tessa , Hannuksela Noora , Anttalainen Anna , Partanen Anu , Rönkä Aino , Kuitunen Hanne , Ukkola-Vuoti Liisa , Toppila Iiro , Miettinen Tatu , Kuittinen Outi
Published: January 2025

Hodgkin’s lymphoma (HL) is a lymphoid malignancy with an emphasized incidence in developed countries. This study aimed to assess the changes in the epidemiology of HL in Finland at the population level by utilizing data from six nationwide healthcare registries. A total of 2912 patients with HL, diagnosed and treated between 2000 and 2019 were matched by controls and divided into younger (<50 years) and older cohorts (≥50 years) for analysis. A slightly increasing trend in incidence per age group was observed. For the younger patients, the mean annual incidence was 3.19 for males and 2.89 for females. For the older patients, it was 3.07 and 1.59, respectively. Finland has higher incidence rates than other Scandinavian countries possibly due to unique human leucocyte antigen allele distribution. There was a notable increase in prevalence. For females, this was particularly emphasized between the ages of 30–50 years, while among males, it was more evenly distributed across all ages. As a result of improved disease management, the proportion of HL survivors is increasing.
Delayed feeding disrupts diurnal oscillations in the gut microbiome of a neotropical bat in captivity
Authors: Melville Dominik W , Meyer Magdalena , Kümmerle Corbinian , Alvarado-Barrantes Kevin A , Wilhelm Kerstin , Sommer Simone , Tschapka Marco , Risely Alice
Published: January 2025

Diurnal rhythms of the gut microbiota are emerging as an important yet often overlooked facet of microbial ecology. Feeding is thought to stimulate gut microbial rhythmicity, but this has not been explicitly tested. Moreover, the role of the gut environment is entirely unexplored, with rhythmic changes to gut pH rather than feeding per se possibly affecting gut microbial fluctuations. In this study, we experimentally manipulated the feeding schedule of captive lesser long-nosed bats, Leptonycteris yerbabuenae, to dissociate photic and feeding cues, and measured the faecal microbiota and gut pH every 2 h. We detected strong diurnal rhythms in both microbial alpha diversity and beta diversity as well as in pH within the control group. However, a delay in feeding disrupted oscillations of gut microbial diversity and composition, but did not affect rhythms in gut pH. The oscillations of some genera, such as Streptococcus, which aid in metabolizing nutrients, shifted in accordance with the delayed-feeding cue and were correlated with pH. For other bacterial genera, oscillations were disturbed and no connection to pH was found. Our findings suggest that the rhythmic proliferation of bacteria matches peak feeding times, providing evidence that diurnal rhythms of the gut microbiota likely evolved to optimize their metabolic support to the host’s circadian phenotype.
Co-inoculation with Bacillus thuringiensis RZ2MS9 and rhizobia improves the soybean development and modulates soil functional diversity
Authors: Fonseca de Souza Leandro , Oliveira Helena Gutierrez , Pellegrinetti Thierry Alexandre , Mendes Lucas William , Bonatelli Maria Leticia , Dumaresq Aline Silva Romão , Sinatti Vanessa V C , Pinheiro José Baldin , Azevedo João Lucio , Quecine Maria Carolina
Published: January 2025

Despite the beneficial effects of plant growth-promoting rhizobacteria on agriculture, understanding the consequences of introducing foreign microbes into soil taxonomic and functional diversity is necessary. This study evaluated the effects co-inoculation of soybean with Bacillus thuringiensis (Bt) RZ2MS9 and commercial rhizobia on the natural microbial community structure and functional potential. Our results indicated that soybean development was positively influenced by co-inoculation, plants exhibited greater height and a higher number of pods, and no reductions in productivity estimates. Soil prokaryotic diversity and community structure remained unchanged by Bt RZMS9 inoculation or co-inoculation with rhizobia 147 days after sowing. However, functional diversity was influenced by sole Bt inoculation, potentially due to community quorum sensing disruption by N-acyl homoserine lactone hydrolases. The genes enriched by co-inoculation were mostly related to soil phosphorus cycling, with gcd showing the most pronounced increase. The nifA genes increased when rhizobia alone were inoculated, suggesting that this pathway could be affected by Bt RZ2MS9 inoculation. This study demonstrates the synergistic activity of rhizobia and Bt RZ2MS9 on soybean development, without significantly interfering with natural microbial community, presenting a promising approach for sustainable crop management.
Sanctuary policies and type 2 diabetes medication prescription trends among community health center patients
Authors: Goglichidze Salome , Wang Wanjiang , Smith Louisa H , Ezekiel-Herrera David , Heintzman John D , Marino Miguel , Lucas Jennifer A , Crookes Danielle M
Published: January 2025

Immigrants in the United States are at increased risk of diabetes-related complications due to delayed diagnoses compared with US-born individuals. Immigration-related federal policies may support immigration enforcement activities and restrict some immigrants' access to health insurance and other publicly funded resources. Conversely, state and county-level sanctuary policies may reduce the fear of deportation and increase mobility in the community, improving the accessibility of essential pharmacological treatment for type 2 diabetes patients. This retrospective cohort study estimated the odds of receiving glucose-lowering medication prescriptions by the county's sanctuary policy environment for patients within a nationwide network of community health centers. We did not find statistically significant associations between sanctuary policies and annual prescription rates. The associations were not modified by nativity or race/ethnicity. Notably, compared to US-born patients, immigrants had higher odds of receiving prescriptions regardless of the sanctuary policy environment, emphasizing other potential influences on the receipt of anti-diabetes prescriptions for community health center patients.
A fast algorithm for smooth convex minimization problems and its application to inverse source problems
Authors: Quy Muoi Pham , Quang Duy Vo , Vinh Khanh Chau , Trung Thành Nguyen
Published: January 2025

In this paper, we propose a fast algorithm for smooth convex minimization problems in a real Hilbert space whose objective functionals have Lipschitz continuous Fréchet derivatives. The main advantage of the proposed algorithm is that it has the optimal-order convergence rate and faster than Nesterov’s algorithm with the best setting. To demonstrate the efficiency of the proposed algorithm, we compare it with Nesterov’s algorithm in several examples, including inverse source problems for elliptic and hyperbolic PDEs. The numerical tests show that the proposed algorithm converges faster than Nesterov’s algorithm.
Tolerance to land-use changes through natural modulations of the plant microbiome
Authors: Zieschank Vincent , Muola Anne , Janssen Stefan , Lach Alexander , Junker Robert R
Published: January 2025

Land-use changes threaten ecosystems and are a major driver of species loss. Plants may adapt or migrate to resist global change, but this can lag behind rapid anthropogenic changes to the environment. Our data show that natural modulations of the microbiome of grassland plants in response to experimental land-use change in a common garden directly affect plant phenotype and performance, thus increasing plant tolerance. In contrast, direct effects of fertilizer application and mowing on plant phenotypes were less strong. Land-use intensity-specific microbiomes caused clearly distinguishable plant phenotypes also in a laboratory experiment using gnotobiotic strawberry plants in absence of environmental variation. Therefore, natural modulations of the plant microbiome may be key to species persistence and ecosystem stability. We argue that a prerequisite for this microbiome-mediated tolerance is the availability of diverse local sources of microorganisms facilitating rapid modulations in response to change. Thus, conservation efforts must protect microbial diversity, which can help mitigate the effects of global change and facilitate environmental and human health.
Dietary phytosterols increased the rate of weight gain, antioxidant capacity and growth of beneficial strains of bacteria in the gut and suppressed the population of potentially pathogenic bacteria in largemouth bass (Micropterus salmoides)
Authors: Shi Haisong , Pan Zhongchao , Chen Yufei , Ai Qinghui , Ouyang Paihuai , Sun Fenggang , Qu Kangyuan , Liu Yucheng , Tan Beiping , Xie Shiwei
Published: January 2025

This study was to evaluate the effects of dietary adding of phytosterol (PS) on growth, antioxidant capacity, tissue morphology and gut microbiota of largemouth bass (Micropterus salmoides). A total of 540 largemouth bass (13.75 ± 0.37g) were selected and randomly divided into six groups and fed with diets supplemented with 0, 0.01 %, 0.02 %, 0.03 %, 0.04 % and 0.05 % of PS (ontrol, PS1-PS5) for 56 d. The results showed that the rate of weight gain (WGR) and condition factor (CF) of largemouth bass increased significantly (P < 0.05) with the increasing PS addition levels. In addition, PS significantly increased the activities of superoxide dismutase (SOD) and catalase (CAT) in serum compared to group C (P < 0.05), as well as increased relative expression of pituitary Insulin-like growth factor (igf1ra, igf1rb, and igf2r), hypothalamic growth hormone gh and insulin receptor ir, compared with group C (P < 0.05). Histopathological analysis showed that the addition of 0.04 % PS to the feed resulted in a tighter cellular arrangement and a significant reduction in vacuolisation in the liver of largemouth bass. It also significantly increased intestinal fold width and muscle wall thickness (P < 0.05). Analysis of the intestinal flora showed a significant decrease in the α-diversity of the flora in the PS4 group compared to the C group (P < 0.05). Notably, at the phylum level, the addition of PS to feed significantly reduced the relative abundance of Proteobacteria and Bacteroidota. At the genus level, PS significantly increased the relative abundance of Cetobacterium (P < 0.05). The addition of 0.04 % PS to the feed promotes growth, antioxidant capacity, improved tissue morphology and increased abundances of beneficial gut microbiotas in largemouth bass.
Relevance of mouse and human IBD patients-derived colon organoids to investigate intestinal macrophage differentiation
Authors: Costa Maxime , Pottier Muriel , Jacob Marie , Zarnitzky Pauline , Segain Benjamin , Figeac Martin , Sebda Shéhérazade , Leprêtre Frédéric , Meresse Bertrand , Demaret Julie , Foligné Benoit , Standaert Annie , Bertin Benjamin
Published: January 2025

The gastrointestinal tract is a remarkable example of complex biology, with a constant dialogue between the intestinal epithelium, in close contact with the microbiota, and the immune cells that protect the gut from infection. Organoids have revolutionized our approach to modelling the intestinal cellular compartment and have opened new avenues for unravelling the mechanisms involved in intestinal homeostasis and chronic pathogenesis such as inflammatory bowel disease. To date, few models have been established to explore the role of the colon, which is however the main site of inflammation in ulcerative colitis (UC). Here, we used conditioned media produced by colon organoids (OCM) from mice or human (control and UC patients) to investigate the relationship between macrophages and the colon epithelium. We addressed transcriptomic profiles of OCM-stimulated bone marrow-derived macrophages and found that these cells exhibited a unique anti-inflammatory signature distinct from that of conventional in vitro IL-4/IL-13 M2 differentiated macrophages. In addition, OCM induced a clear CD5 antigen-like-mediated immunoregulatory effect characterized by a significant reduction in LPS-induced iNOS expression. In line, OCM from human colons inhibited LPS-dependent inflammatory cytokine expression in human monocytes-derived macrophages. Interestingly, the inflammatory marker CD68 was reduced by OCM from control patients but not from UC patients, suggesting epithelial dysfunction in UC patients. Our results report new regulatory mechanisms in the colon and highlight the importance of developing new in vitro models to better characterize the relationship between the intestinal epithelium and immune mucosal cells.
Flow cytometric measurement of CFTR-mediated chloride transport in human neutrophils
Authors: Montanez-Barragan Alejandra , Robledo-Avila Frank H , Rascon Raul , McCoy Karen S , Kopp Benjamin T , Partida-Sanchez Santiago
Published: January 2025

Immune cells express a variety of ion channels and transporters in the plasma membrane and intracellular organelles, responsible of the transference of charged ions across hydrophobic lipid membrane barriers. The correct regulation of ion transport ensures proper immune cell function, activation, proliferation, and cell death. Cystic fibrosis (CF) is a genetic disease in which the Cystic Fibrosis Transmembrane Conductance Regulator (CFTR) chloride channel gene is defective, consequently, the CFTR protein is dysfunctional, and the chloride efflux in CF cells is markedly impaired. Cystic fibrosis is characterized by chronic inflammation in the airways, mainly triggered by neutrophilic infiltration and recurring bacterial infections, causing the decline of lung function and eventually respiratory failure. Novel modulator-based therapies have improved lung function in people with Cystic Fibrosis (pwCF) by increasing expression and function of CFTR in the plasma membrane of lung cells, however, the effects of these drugs in the lung recruited inflammatory cells, specifically neutrophils, remains unknown. Given the complex biology of neutrophils and their short lifespan, we aimed to develop a fluorometric method to evaluate CFTR-mediated chloride transport in human neutrophils by using flow cytometry and the intracellular chloride-binding MQAE dye. Our results show that CFTR-mediated chloride transport in human neutrophils or human neutrophil-like cell lines can be consistently evaluated in vitro by this methodology. Additionally, this assay measured increased chloride efflux in neutrophils collected from pwCF under modulator therapy, as compared to healthy donors, indicating this method can evaluate restoration of CFTR-mediated chloride transport in CF neutrophils.
Comparative analysis of bacterial microbiota in Aedes aegypti (Diptera: Culicidae): insights from field and laboratory populations in Colombia
Authors: Gómez Marcela , Martínez David , Luna Nicolás , Vega Laura , Yepez-Pérez Yoelis , Cantillo-Barraza Omar , Camargo Milena , Patiño Luz H , Muñoz Marina , Ramírez Juan David
Published: January 2025

Comparative studies of the microbiota in whole-body mosquitoes from natural populations and laboratory-reared specimens are scarce, particularly in tropical countries like Colombia, where understanding microbial patterns is critical for effective disease control and vector management. This study examines the bacterial microbiota of Aedes aegypti by comparing field-collected mosquitoes from 3 Colombian regions (Southern Amazon, Central Andean region, and Northern Caribbean coast) with laboratory strains (Rockefeller, Otanche, and Tolima). These regions are highly endemic for dengue and are associated with lineage 1 of Ae. aegypti, known for its elevated vector competence. Using next-generation sequencing of the 16S rRNA gene with Illumina technology, we found that field-collected mosquitoes exhibited significantly higher alpha and beta diversity compared to laboratory-reared specimens. Field mosquitoes were enriched with bacterial families such as Acetobacteraceae, Lactobacillaceae, and Bacillaceae, while laboratory mosquitoes showed a greater abundance of Enterobacteriaceae. Differential abundance analysis revealed that Acetobacter and Bacillus predominated in field mosquitoes, whereas Asaia, Cedacea, and Chryseobacterium were more common in laboratory specimens. Notably, Pseudomonas and Acinetobacter were consistently abundant across all samples. Our findings suggest that environmental factors, such as habitat and diet, significantly influence the bacterial composition and diversity of Ae. aegypti in Colombia. Future research should further explore how these factors, alongside genetic components, shape mosquito–microbiota interactions and their implications for disease transmission and vector competence.
Pronounced temporal velocity variations within the fault fracture zone in response to Earth tide modes
Authors: Sun Tenghui , Yao Huajian , Yang Hongfeng , Yu Chang , Luo Song , Sheng Yixiao
Published: January 2025

Continuous monitoring of seismogenic faults can advance our understanding of the evolution process, holding important keys in forecasting future earthquakes. We report here seismic velocity variations around the Anninghe fault zone in southwest China based on seismic interferometry techniques. We observed that tidal forces significantly impact velocity changes within the fault fracture zone, inducing periodic changes in seismic velocity on diurnal, semidiurnal, and monthly scales. Moreover, the response to Earth tides is notably more pronounced in the fault fracture zone compared to other areas. This can be attributed to tidal forces affecting the opening and closing of cracks in the subsurface medium. Due to the higher density of fractures within the fault fracture zone, it becomes more sensitive to tidal forces. Our findings underscore the crucial role of tidal forces in perturbing stress within the fault zone during periods when earthquakes have not occurred.
Mass shootings durably increase the sale of alcohol in American communities
Authors: Buttrick Nicholas , Yang Shiyu , Okada Sosuke
Published: January 2025

Mass shootings are devastating events. Communities can cope with the ensuing trauma in a number of ways, including changing their behavioral patterns. Using point-of-sale data from 35,000 individual retailers, including more than half of all American grocery and drugstore purchases, and all American mass shootings from 2006 to 2019, we find, in a set of two-way fixed-effects counterfactual analyses, that a mass shooting in a given community (the area covered by the ZIP-3 code) predicts a significant increase in the sales of alcohol that lasts at least 2 years past the shooting. The effect is especially strong for the subset of mass shootings that take place in public settings, whereas we find no evidence for an increase in alcohol sales in the aftermath of mass shootings that take place in private homes or residences. As alcohol is an accelerant for violence, especially firearm-related violence, we suggest the importance of whole-community approaches to addressing the trauma of mass shootings.
Collaborative optimization of high-speed railway ticket allocation and stopping plan based on time-period stochastic demands
Authors: Zhou Wenliang , Yan Qianqian
Published: January 2025

Ticket allocation and train stopping plans are important parts of railway transportation organization. At present, most of the ticket allocation plans are based on fixed train stopping plans, which limit the scope of ticket allocation. Trains can only serve passenger demands between stopping stations, leading to a loss of passenger demands at non-stopping stations, resulting in low seat occupancy rates and low revenue for railway enterprise. In order to better meet passenger demands, improve seat occupancy rates, and increase revenue of railway enterprise, this paper constructs a collaborative optimization model of ticket allocation and stopping plan based on stochastic demand and passenger choice behaviors in different time periods. Combined with CPLEX solver, the simulated annealing algorithm is designed to solve the problem. At the same time, new neighborhood solution generation strategies of train stopping plans and ticket allocation plans under given stopping plan are designed, respectively. The experimental results show that in small-scale experiments and large-scale experiments, the proposed method increases revenue by 0.14% and 9.09%, respectively, and effectively improves seat occupancy rates.
Clinical characteristics of acute epiphyseal osteomyelitis and acute metaphyseal osteomyelitis of long bones in children
Authors: Jia Haiting , Liu Tao
Published: January 2025

This study aimed to summarize the clinical characteristics of acute epiphyseal osteomyelitis and acute metaphyseal osteomyelitis of long bones in children. Data of 43 children with acute osteomyelitis of long bones diagnosed and treated from November 2017 to January 2021 were retrospectively analyzed. Medical records, laboratory results, and MRI were reviewed. Surgical drainage of lesions was done to retrieve infective fluid and tissue for examination. There were 12 cases of metaphyseal and epiphysis involvement, including five boys and seven girls, aged from 1 to 12 years old, and the length of hospitalization was 21–45 days. There were six cases of distal femur, five cases of proximal tibia, and one case of distal humerus. The pathogenic microorganisms were methicillin-sensitive Staphylococcus aureus (MSSA) in six cases and methicillin-resistant Staphylococcus aureus (MRSA) in six cases. No complications were reported during the follow-up. Thirty-one cases of simple metaphyseal involvement, including 20 boys and 11 girls, aged 19 days to 12 years, and the length of hospitalization was 18–60 days. Twelve cases of distal femur, 11 cases of proximal tibia, three cases of distal humerus, two cases of proximal tibiofibular, two cases of proximal fibula, and one case of proximal ulna. The pathogenic microorganism was MSSA in 26 cases and MRSA in five cases. One patient with knee contracture during follow-up. Epiphyseal osteomyelitis is rare but can occur in older children. The prognosis is good with aggressive surgical treatment.
Interobserver reliability of Pirani scoring for idiopathic clubfoot in walking-age children
Authors: Agarwal Anil , Upadhyay Ashish , Garg Varun , Sachdeva Kishmita , KS Ankitha , Salot Jainam
Published: January 2025

Pirani scoring system is one of the most commonly used tools to assess the initial deformity, monitor the treatment progression, and identify relapse in clubfoot. The method has been demonstrated to correlate well with the sequential correction of deformity for children under age 1 year. We conducted a study to examine the interobserver reliability of Pirani scores in children of walking-age. The retrospective study focused on children >1 year age with idiopathic clubfoot presenting for primary treatment. The Pirani scores at presentation charted by pediatric orthopedic consultant and orthopedic registrars were compared and the intergroup reliability calculated using Cohen’s kappa. Thirty-five feet in 22 clubfoot children (13 bilateral) were analyzed. The mean child’s age was 3.9 years. The mean Pirani score for the consultant was 3.2 and for the registrars was 3.6. The overall reliability of Pirani score was 0.3 (‘fair’). The highest reliability was calculated for the head of talus (0.55), rigid equinus (0.48), and lateral border (0.44) (moderate). A lower kappa was recorded for medial crease (0.28), posterior crease (0.34), and empty heel (0.4). The registrars graded the clubfoot deformity in the walking-age child as more severe compared to the consultant. The mean Pirani scores for medial and posterior crease subcomponents were low. Contrary to the common perception, empty heel manifested even in this age group. Looking to the statistics of ‘fair’ reliability of Pirani score for older child, further research is warranted to develop more reliable scores for assessment and treatment of clubfoot.
Development of a prediction model based on Hemoglobin, Albumin, Lymphocyte count, and Platelet-score for lymph node metastasis in rectal cancer
Authors: Liu Huanhui , Zou Qian , Zhang Hanjing , Ma Xiaojie
Published: January 2025

This study aimed to evaluate the ability of the preoperative Hemoglobin, Albumin, Lymphocyte count, and Platelet (HALP) score to predict lymph node metastasis (LNM) in patients with rectal cancer (RC) and improve prediction accuracy by incorporating clinical parameters. Data from 263 patients with RC were analyzed. The receiver operating characteristic (ROC) curve was used to determine the optimal cutoff value (OCV) for the HALP score in predicting LNM. Based on this cutoff value, patients were divided into two groups. A baseline analysis was conducted to identify independent factors linked to LNM. A support vector machine (SVM) prediction model was developed, and its performance was evaluated using ROC, calibration curves, decision curve analysis, and Kolmogorov–Smirnov curve. The OCV for HALP score was 45.979. Patients were then classified into a low HALP group (n = 182) and a high HALP group (n = 81). The analysis found 21 clinical factors significantly associated with LNM. Among them, the key risk factors included high inflammatory status, poor nutritional condition, and a low HALP score. The SVM model incorporated these factors and showed robust predictive performance, with area under the curve values of 0.897, 0.813, and 0.750 for the training, validation, and testing datasets, respectively. The HALP score was significantly associated with LNM in RC patients. A machine learning model integrating the HALP score and inflammatory markers may be an effective tool for predicting LNM in RC.
Effectiveness of simultaneous electroacupuncture stimulation on the tibial and ilioinguinal-iliohypogastric nerves in the treatment of refractory overactive bladder syndrome in women
Authors: Lv Tingting , Fang Weilin , Si Junwen , Ji Xiang , Li Ziwei , Song Xin , Huang Jin , Weng Zhijun , Lv Jianwei
Published: January 2025

Objectives

The aim of this study was to observe the clinical effectiveness of simultaneous electroacupuncture stimulation on the tibial nerve (TN) and ilioinguinal-iliohypogastric nerve (IIN/IHN) in the treatment of refractory overactive bladder (OAB) in women.

Materials and methods

A prospective study was conducted involving 94 female patients with a diagnosis of OAB in the Urology Department of our hospital from September 2022 to October 2023. The patients were randomly divided into a TN-IIN/IHN group and a control group, each comprising 47 cases. All patients in both groups had received anticholinergic muscarinic receptor antagonists (tolterodine/solifenacin), β3 receptor agonists, flupentixol/melitracen, and other basic treatment regimens with poor results. The TN-IIN/IHN group received simultaneous electroacupuncture on the TN and IIN/IHN, whereas the control group received pelvic floor muscle biofeedback electrical stimulation. Both groups underwent treatment 3 times a week for a total of 4 weeks. Bladder symptoms (24-hour voiding diary), OAB Symptom Score, OAB-Quality of Life Questionnaire, and anxiety and depression scores were compared and analyzed before treatment, after treatment, and at a 3-month follow-up. Clinical efficacy was also assessed.

Results

Both groups showed significant improvement in voiding frequency, nocturia, urgency, OAB Symptom Score, and average voiding volume after treatment and at follow-up (p < 0.01). The TN-IIN/IHN group showed significantly superior results compared with the control group (p < 0.01). Quality of life scores and anxiety and depression scores significantly decreased (p < 0.01), with the TN-IIN/IHN group scores significantly lower than those of the control group (p < 0.01). The treatment success rate in the TN-IIN/IHN group was 84.78%, whereas that in the control group was 28.89%, showing a statistically significant difference (p < 0.01). No significant adverse reactions occurred in either group during the treatment period.

Conclusions

Simultaneous electroacupuncture on the TN and IIN/IHN is effective in treating refractory OAB in women and has good long-term efficacy. This therapy is safe, convenient, and free of significant adverse reactions, providing a new approach for the clinical treatment of refractory OAB in these patients. It significantly improves bladder symptoms and alleviates anxiety and depression, thereby markedly enhancing the patients' quality of life.
Association between cystitis glandularis and bladder neck leiomyoma: A case report and literature review
Authors: Zhang Caixia , Fan Longlong , Li Kuiqing , Huang Li , Chen Lingjiao , Yao Yousheng
Published: January 2025

This article reported the diagnosis and treatment of cystitis glandularis (CG) co-occurring with bladder neck leiomyomas. We retrospectively analyzed the clinical data of a single case of CG with bladder neck leiomyoma. A 31-year-old Chinese woman was given a diagnosis of CG and bladder neck leiomyoma. The mass and surrounding bladder mucosal lesions were entirely excised via transurethral resection, leaving a clean margin of healthy tissue. Histopathological analyses confirmed the diagnosis of CG and bladder neck leiomyoma. The patient remained asymptomatic throughout the follow-up period, with no indication of recurrence. Cystitis glandularis co-occurring with bladder neck leiomyoma requires careful examination, and surgery remains the best treatment option for these diseases.