bluuebunny/crossref_metadata_2025_split huggingface dataset:
Distribution of the schistosome intermediate snail host Biomphalaria pfeifferi in East Africa's river systems and the prevalence of Schistosoma mansoni infection
Authors: Magero Victor O , Kisara Sammy , Suleman Mbaruk A , Wade Christopher M 
Published: December 2024

Abstract

Background
There is a need for current and more detailed information on the distribution of Biomphalaria pfeifferi snails in East Africa's river systems. B. pfeifferi is arguably the most important snail intermediate host in the transmission of schistosomiasis, a disease ranked second to malaria in terms of tropical diseases of public health importance.

Methods
We assessed the occurrence and geographical distribution of B. pfeifferi snails in Kenya, Uganda and Tanzania. Maximum entropy modelling was used to predict the potential distribution of B. pfeifferi snails and malacological surveys were conducted guided by MaxEnt predictions and information from previous studies. Malacological surveys were conducted at a total of 172 sites, including streams, rivers, dams, irrigation schemes and springs over a 3-y period from 2018 to 2020, with geospatial, ecological and physicochemical information recorded for each site.

Results
B. pfeifferi snails were found at 23 of the 172 sites and inhabited a variety of habitat types. Of the 23 sites where B. pfeifferi snails were found, 15 (65.2%) were streams, 3 rivers (13.04%), 2 dams (8.7%), 2 springs (8.7%) and 1 an irrigation scheme (4.35%). B. pfeifferi abundance showed a significant positive correlation with increasing water temperature and decreasing water depth. In Kenya, B. pfeifferi snails were found around the Lake Victoria basin, the Mwea irrigation scheme and in parts of the former Eastern Province of Kenya. In Uganda, B. pfeifferi snails were found in Jinja District, Ntoroko District and Soroti District. In Tanzania, B. pfeifferi snails were found in the Iringa, Tabora and Kigoma Regions. We observed moderate to high prevalence of Schistosoma mansoni infection, with S. mansoni–infected snails found at 11 of 23 sites and with an average prevalence of 24.9% at infected sites. In Kenya, S. mansoni–infected snails were found in the Lake Victoria basin (22.5% prevalence at infected sites) and the former Eastern Province (13.5% prevalence at infected sites). In Uganda, infected snails were found in Ntoroko District (100% infected) and Soroti District (20% infected). In Tanzania, infected snails were found in the Kigoma Region, with a prevalence of 10% at the infected site.

Conclusion
This information on the distribution of B. pfeifferi snails and S. mansoni infection in East Africa's river systems can aid in developing better prevention and control strategies for human schistosomiasis. Regular surveys of the river systems for snail intermediate hosts followed by molecular detection of schistosome infection could form a basis for the development of a prompt and cost-effective surveillance system for schistosomiasis in the region.
The Health Burden of E-Waste: The Impact of E-Waste Dumping Sites on Child Mortality
Authors: Lovo Stefania , Rawlings Samantha 
Published: December 2024

Abstract
E-waste is one of the fastest growing global waste streams, and is frequently shipped to poorer nations illegally, leading to contamination of local environments. The impact of e-waste dumping sites on neonatal and infant mortality is investigated, focusing on two major dumpsites in Ghana and Nigeria. Using a difference-in-differences approach, outcomes are compared for children born near and far from dumpsites before and after their creation. E-waste sites increase neonatal and infant mortality for those living closer to sites. Event studies suggest that effects emerge two to three years after site openings, consistent with gradual and systematic accumulation of contaminants in the environment. There is suggestive evidence that contamination of water and of urban farming produce are among the drivers of the observed effects.
Dietary prevention of antibiotic‐induced dysbiosis and mortality upon aging in mice
Authors: Smith Kelsey M. , Francisco Sarah G. , Zhu Ying , LeRoith Tanya , Davis Meredith L. , Crott Jimmy W. , Barger Kathryn , Greenberg Andrew S. , Smith Donald E. , Taylor Allen , Yeruva Laxmi , Rowan Sheldon 
Published: December 2024

AbstractOral antibiotic use is both widespread and frequent in older adults and has been linked to dysbiosis of the gut microbiota, enteric infection, and chronic diseases. Diet and nutrients, particularly prebiotics, may modify the susceptibility of the gut microbiome to antibiotic‐induced dysbiosis. We fed 12‐month‐old mice a high glycemic (HG) or low glycemic (LG) diet with or without antibiotics (ampicillin and neomycin) for an additional 11 months. The glycemic index was modulated by the ratio of rapidly digested amylopectin starch to slowly digested amylose, a type‐2‐resistant starch. We observed a significant decrease in survival of mice fed a HG diet containing antibiotics (HGAbx) relative to those fed a LG diet containing antibiotics (LGAbx). HGAbx mice died with an enlarged and hemorrhagic cecum, which is associated with colonic hyperplasia and goblet cell depletion. Gut microbiome analysis revealed a pronounced expansion of Proteobacteria and a near‐complete loss of Bacteroidota and Firmicutes commensal bacteria in HGAbx, whereas the LGAbx group maintained a population of Bacteroides and more closely resembled the LG microbiome. The predicted functional capacity for bile salt hydrolase activity was lost in HGAbx mice but retained in LGAbx mice. An LG diet containing amylose may therefore be a potential therapeutic to prevent antibiotic‐induced dysbiosis and morbidity.
False and Misleading Claims of Scientific Misconduct in Early Research into Radiation Dose-response: Part 1. Overlooking Key Historical Text
Authors: Beyea Jan 
Published: December 2024

Abstract
In reviewing a video series that they created for the website of the Health Physics Society (HPS), past leaders of the Health Physics Society have treated as authoritative and trustworthy the scientific misconduct theories of University of Massachusetts Professor Edward Calabrese. No mention is made of detailed critiques of Calabrese’s work. I show that Calabrese’s historical work as presented by HPS’s authors is unreliable because it overlooks key historical text and key statistical concepts about the limits of an early atomic bomb genetics study. When these errors are corrected, claims of scientific misconduct on the part of historical figures evaporate. Claims of threshold behavior in early radiation genetic experiments are wrong for atomic bomb data. Calabrese’s unique claims about thresholds in early animal genetic data are not credible for human cancer, given the doses at which they were carried out (>30 R). Recent epidemiological studies of both acute and protracted exposure in humans fail to show dose-rate effects or a dose threshold above 30 R. Such results from human data should be more relevant for most regulators and review committees than Calabrese’s claims about old data on animals. Disclaimers, errata, and links to critiques should be added to the HPS webpage hosting the 22-part video series. Failure to do so can cause damage to reputations and historical accuracy because it erroneously validates Calabrese’s inflammatory claims of scientific misconduct against past scientists, including three Nobel Prize winners, members of the NAS, and presidents of the AAAS.
Harold Ridley and the Invention of the Intraocular Lens: a Reappraisal
Authors: Maloney Robert K. , Mahone Sloan 
Published: December 2024

Abstract
Harold Ridley permanently implanted the first intraocular lens (IOL) in 1950. The widely accepted narrative is that Ridley and his invention received a hostile reception from Stewart Duke-Elder and other ophthalmic thought leaders. Ridley suffered greatly but was eventually vindicated as later IOL designs were widely accepted. This narrative casts Ridley as a prophetic innovator who suffered and eventually triumphed against the forces of animosity, jealousy and close-mindedness arrayed against him. We argue that this narrative is biased because it was told by Ridley himself and amplified by his biographer and close friend, David Apple. There were good reasons to be skeptical of Ridley’s invention. Ridley had not done pre-clinical studies, so his first patients suffered avoidable complications. He worked in secret at a time when openness was the norm. Ridley’s IOL had a high percentage of poor outcomes. The cautious approach that Duke-Elder and others had towards IOLs is understandable. The accurate history is a story of a clash of worldviews between an inventor who was focused on innovating quickly to solve a major clinical problem and established leaders who were concerned about the harm to patients from a flawed invention. The skepticism of established thought leaders remains a valuable check on aggressive innovation today.
Using the Expertise of a Clinical Nurse Specialist to Lead a Neonatal Peripherally Inserted Central Catheter Team to Central Line–Associated Bloodstream Infection Reduction and Cost-Efficiency Through Quality Improvement
Authors: Bedwell Susan , Oberlechner Myka , Pogribna Ulana , Sekar Kris 
Published: December 2024

OBJECTIVE
This quality improvement project aimed to reduce central line bacteremias (central line–associated bloodstream infections [CLABSIs]) in a neonatal ICU (NICU) to a CLABSI rate of zero using a clinical nurse specialist (CNS)–led neonatal peripherally inserted central catheter (PICC) team.

BACKGROUND
The NICU at the study site was experiencing more than twice the National Healthcare Safety Network average CLABSI rate at 2.2 per 1000 line-days with an estimated cost of $2 072 806 to the organization.

METHODS
In early 2009, the CNS guided the unit from on-demand PICC placement to a dedicated team of PICC certified nurses who assumed total care of PICC line insertion and maintenance. The project used a continual, rapid cycle quality improvement model to incorporate the current evidence-based practices.

RESULTS
The CNS-led PICC team has maintained a zero CLABSI rate for 9 years with only 1 CLABSI since June 2022.

CONCLUSIONS
The adoption of a CNS-led PICC team was instrumental in achieving a zero CLABSI rate over a prolonged period.
The Dynamics of Shape Changes in the Tongue Base during Respiration, Chewing and Swallowing
Authors: Salazar Doris Haydee Rosero , Ly Amy , Dong Yikang , Simnhoung Alexander Veasna , Liu Zi-Jun 
Published: December 2024

AbstractThis study aimed to analyze dimensional deformations of the tongue base during respiration, chewing, and swallowing. Eight 7-8-month-old Yucatan minipigs were used. Under deep sedation, eight 2mm ultrasonic piezoelectric (SONO) crystals were implanted in the tongue base forming a cubic-shaped configuration, representing right/left dorsal and ventral lengths, anterior/posterior dorsal and ventral widths, and right/left anterior and posterior thicknesses. Next, 8 pairs of electromyographic (EMG) microelectrodes were inserted into the tongue, jaw, hyoid, pharyngeal, and palatal muscles. SONO and EMG signals during respiration were recorded. Then, minipigs were allowed to wake-up for unrestrained feeding. The feeding sessions were recorded with synchronized EMG and videofluoroscopy to confirm the phases of jaw movement in chewing, and swallowing episodes. Amplitudes, durations, and timings for each dimension of the SONO crystal-circumscribed region were measured from the start of the jaw opening. Findings during respiration showed elongated lengths, anterior widths and anterior thickness (p<0.05). For chewing, the width elongated up to 17% while the length and thickness shortened (12-33% and 10-32% respectively, p<0.05). Onsets of deformational changes in length and thickness occurred 10-30% earlier than in width. The cycle duration was 0.55 ± 0.11seconds chewing, and 0.69 ± 0.16seconds swallowing. During swallowing, the dorsal length (5-12%) and posterior width (10-14%) elongated whereas the posterior thickness (9-15%) and ventral length (4-10%) shortened. Explicit 3D-kinematic patterns in relation to specific functions characterize the tongue base deformation. The findings of this analysis will contribute to a better understanding of the oropharyngeal biomechanics upon abnormal conditions.
Nanoparticle Accumulation and Penetration in 3D Tumor Models: the Effect of Size, Shape, and Surface Charge
Authors: Cybulski Pierre , Bravo Maria , Chen Jim Jui-Kai , Van Zundert Indra , Krzyzowska Sandra , Taemaitree Farsai , Uji-i Hiroshi , Hofkens Johan , Rocha Susana , Fortuni Beatrice 
Published: December 2024

AbstractPreclinical studies have demonstrated that nanoparticles (NPs) hold significant potential for advancing cancer therapy by enhancing therapeutic efficacy while reducing side effects. Their effectiveness in solid tumors is, however, often constrained by insufficient accumulation and penetration. Understanding how the physicochemical properties of NPs – such as size, shape, and surface charge – influence their interaction with cells within the tumor is critical for optimizing NP design. In this study, we addressed the challenge of inconsistent NP behavior by systematically evaluating NP uptake in both 2D and 3D tumor models, and NP penetration in spheroids. Our results showed that larger NPs exhibited higher internalization rates in 2D models but limited penetration in 3D spheroids. Furthermore, negatively charged NPs consistently achieved superior accumulation and deeper penetration than neutral and positively charged NPs. Spherical NPs outperformed rod-shaped NPs in tumor accumulation and penetration. These findings underscore the importance of carefully tailoring NP properties to the complex tumor microenvironment for improved therapeutic outcomes in real tumors.
HIPSTR: highest independent posterior subtree reconstruction in TreeAnnotator X
Authors: Baele Guy , Carvalho Luiz M. , Brusselmans Marius , Dudas Gytis , Ji Xiang , McCrone John T. , Lemey Philippe , Suchard Marc A. , Rambaut Andrew 
Published: December 2024

AbstractIn Bayesian phylogenetic and phylodynamic studies it is common to summarise the posterior distribution of trees with a time-calibrated consensus phylogeny. While the maximum clade credibility (MCC) tree is often used for this purpose, we here show that a novel consensus tree method – the highest independent posterior subtree reconstruction, or HIPSTR – contains consistently higher supported clades over MCC. We also provide faster computational routines for estimating both consensus trees in an updated version of TreeAnnotator X, an open-source software program that summarizes the information from a sample of trees and returns many helpful statistics such as individual clade credibilities contained in the consensus tree. HIPSTR and MCC reconstructions on two Ebola virus and two SARS-CoV-2 data sets show that HIPSTR yields consensus trees that consistently contain clades with higher support compared to MCC trees. The MCC trees regularly fail to include several clades with very high posterior probability (≥ 0.95) as well as a large number of clades with moderate to high posterior probability (≥ 0.50), whereas HIPSTR achieves near-perfect performance in this respect. HIPSTR also exhibits favorable computational performance over MCC in TreeAnnotator X. Comparison to the recently developed CCD0-MAP algorithm yielded mixed results, and requires more in-depth exploration in follow-up studies. TreeAnnotator X – which is part of the BEAST X (v10.5.0) software package – is available athttps://github.com/beast-dev/beast-mcmc/releases.
DNA duplication-mediated activation of a two-component regulatory system serves as a bet-hedging strategy forBurkholderia thailandensis
Authors: Lowrey Lillian C. , Mote Katlyn B. , Cotter Peggy A. 
Published: December 2024

AbstractBurkholderia thailandensisstrain E264 (BtE264) and close relatives stochastically duplicate a 208.6 kb region of chromosome I via RecA-dependent recombination between two nearly identical insertion sequence elements. Because homologous recombination occurs at a constant, low level, populations ofBtE264 are always heterogeneous, but cells containing two or more copies of the region (Dup+) have an advantage, and hence predominate, during biofilm growth, while those with a single copy (Dup–) are favored during planktonic growth. Moreover, only Dup+ bacteria form ‘efficient’ biofilms within 24 hours in liquid medium. We determined that duplicate copies of a subregion containing genes encoding an archaic chaperone-usher pilus (aplFABCDE) and a two-component regulatory system (bubSR) are necessary and sufficient for generating efficient biofilms and for conferring a selective advantage during biofilm growth. BubSR functionality is required, as deletion of eitherbubSorbubR, or a mutation predicted to abrogate phosphorylation of BubR, abrogates biofilm formation. However, duplicate copies of theaplFABCDEgenes are not required. Instead, we found that BubSR controls expression ofaplFABCDEandbubSRby activating a promoter upstream ofaplFduring biofilm growth or when the 208.6 kb region, or justbubSR, are duplicated. Single cell analyses showed that duplication of the 208.6 kb region is sufficient to activate BubSR in 75% of bacteria during planktonic (BubSR ‘OFF’) growth conditions. Together, our data indicate that the combination of deterministic two-component signal transduction and stochastic, duplication-mediated activation of that TCS form a bet-hedging strategy that allowsBtE264 to survive when conditions shift rapidly from those favoring planktonic growth to those requiring biofilm formation, such as may be encountered in the soils of Southeast Asia and Northern Australia. Our data highlight the positive impact that transposable elements can have on the evolution of bacterial populations.Author summaryTransposable elements naturally accumulate within genomes in all kingdoms of life. When present in the same orientation, a pair of homologous elements can act as substrates for DNA recombination reactions that can duplicate and delete intervening sequences – giving rise to genetically heterogenous populations. We showed here thatBurkholderia thailandensisstrain E264 uses this mechanism to amplify genes encoding a two-component regulatory system and an archaic chaperone usher pilus, priming the cells for rapid biofilm formation. The formation of a small subpopulation of biofilm-ready bacteria serves as a bet- hedging strategy, ensuring overall population survival should conditions change rapidly from those in which planktonic growth is optimal to those in which adherence and biofilm formation is required.
Human gut archaea collection from Estonian population
Authors: Pantiukh Kateryna , Org Elin 
Published: December 2024

AbstractWhile microbiota plays a crucial role in maintaining overall health, archaea, a component of microbiota, remain relatively unexplored. Here, we present a newly assembled set of archaeal metagenome-assembled genomes (MAGs) from 1,887 fecal microbiome samples. These archaeal MAGs were recovered for the first time from the Estonian population, specifically from the Estonian Microbiome Deep (EstMB-deep) cohort. In total, we identified 273 archaeal MAGs, representing 21 species and 144 strains (“EstMB MAGdb Archaea-273” MAGs collection). Of these 21 species, 12 species belonged to the orderMethanobacterialesandMethanomassilicicoccales, other 9 species fromMethanomassiliicoccaleswere novel. Notably, 7 of the 9 new species belonged to theUBA71genus. Given that the latest version of the Unified Human Gastrointestinal Genome (UHGG v2.0.2) database includes 27 archaeal species, we expanded the known archaeal diversity at the species level by 30%.
Rhodococcus parequisp. nov., a new species isolated from equine farm soil closely related to the pathogenRhodococcus equi
Authors: Vázquez-Boland José A. , Val-Calvo Jorge , Duquesne Fabien , Decorosi Francesca , Viti Carlo , Petry Sandrine , Scortti Mariela 
Published: December 2024

ABSTRACTWe present the description of the new species,Rhodococcus(Prescottella)parequi, found during phylogenomic investigations of a global collection of strains identified asRhodococcus(Prescottella)equi. Strain PAM 2766 was isolated from horse-breeding farm soil in Normandy, France, and was indistinguishable fromR. equibased on the usual identification tests. Whole-genome phylogenetic analyses located PAM 2766 in the sameRhodococcussublineage asR. equi, together withRhodococcus agglutinans,Rhodococcus defluvii,Rhodococcus soli,Rhodococcus subtropicus,Rhodococcus spongiicolaandRhodococcus xishaensis. PAM 2766 is most closely related to, but sufficiently distinct fromR. equiDSM 20307Tto be considered as a separate species. Average Nucleotide Identity (ANI) and Average Amino Acid Identity (AAI) values are 88.60% and 92.35, respectively, well below the species cutoff. The PAM 2766 draft genome is ∼5.3 Mb in size with 68.98% G+C mol content. PAM 2766Tis aerobic, non-motile, and produces smooth creamy to buff-coloured colonies very similar to those ofR. equi. It phenotypically differs from the latter by the ability to grow at 5°C, a strongly positive urease test at 24 h, and specificities in the carbon and nitrogen source utilization profile as determined by phenotype microarray screens. Our data indicate that PAM 2766 belongs to a novel species, for which the nameRhodococcus parequisp. nov. is proposed.R. parequiwas avirulent in macrophage infection assays and is assumed to be non-pathogenic. The type strain is PAM 2766T(=CETC 30995T= NCTC 14987T).
More Structure, Less Accuracy: ESM3’s Binding Prediction Paradox
Authors: Loux Thomas , Wang Dianzhuo , Shakhnovich Eugene I. 
Published: December 2024

AbstractThis paper investigates the impact of incorporating structural information into the protein-protein interaction predictions made by ESM3, a multimodal protein language model (pLM). We utilized various structural variants as inputs and compared three widely used structure acquisition pipelines—EvoEF2, Gromacs, and Rosetta Relax—to assess their effects on ESM3’s performance. Our findings reveal that the use of a consistent identical structure, regardless of whether it is relaxed or variant, consistently enhances model performance across various datasets. This improvement is striking in few-show learning. However, performance deteriorates when different relaxed mutant structures are used for each variant. Based on these results, we advise caution when integrating distinct mutant structures into ESM3 and similar models.This study highlights the critical need for careful consideration of structural inputs in protein binding affinity prediction.