bluuebunny/crossref_metadata_2025_split huggingface dataset:
Population genomics and connectivity of Vazella pourtalesii sponge grounds of the northwest Atlantic with conservation implications of deep sea vulnerable marine ecosystems
Authors: Patova Anna , Ribeiro Pedro A. , Murillo Francisco J. , Riesgo Ana , Taboada Sergi , Pomponi Shirley A. , Rapp Hans Tore , Kenchington Ellen , Xavier Joana R. 
Published: January 2025

AbstractSponges are key ecosystem engineers that shape, structure and enhance the biodiversity of marine benthic communities globally. Sponge aggregations and reefs are recognized as vulnerable marine ecosystems (or VMEs) due to their susceptibility to damage from bottom-contact fishing gears. Ensuring their long-term sustainability, preservation, and ecosystem functions requires the implementation of sound scientific conservation tools. Here, the genetic diversity, structure, and connectivity of the deep-sea glass sponge, Vazella pourtalesii (Schmidt, 1870), was investigated using 1,102 neutral SNPs obtained in RADseq. This species is distributed across the northwest Atlantic from Florida, USA to Nova Scotia, Canada and we sequenced samples covering this full distribution and provided evidence of strong genetic structure with two distinct clusters: Florida together with the Carolina Shelves and the Scotian Shelf. We estimated moderate levels of diversity with low migration across large distances (> 1000 kms) and high connectivity at smaller scales (< 300 kms). Further, fishing pressure on genetic diversity was evaluated, within two Sponge Conservation Areas (SCAs) on the Scotian Shelf. Those areas have different disturbance histories, and cumulative fishing pressure. Slightly lower levels of genetic diversity were found inside the SCAs, and yet they encompassed a high proportion of the diversity observed within the Scotian Shelf. We provide baseline data for future monitoring of the SCAs, discussing our findings in the light of existing area-based management tools.
A retrospective cohort study of the application of Santulli enterostomy in neonatal necrotizing enterocolitis
Authors: Fu Zhe , Zhang Jingmin , Qin Fanyue , Wang Xinru , Huang Hua , Huang Hongwei , Zheng Mingjun , Wang Peng , Zhang Weibo , Shi Hongguang 
Published: January 2025

AbstractThe use of Santulli enterostomy (SE) for necrotizing enterocolitis (NEC) has been limited to a small number of studies involving a small number of patients and no control group. Our study aimed to compare the clinical safety and efficacy of Santulli enterostomy with those of single- or double-lumen enterostomy for neonatal NEC through a retrospective cohort study. One hundred ten patients who met the criteria were divided into an SE group (64 patients) and a conventional enterostomy (CE) group (46 patients). The CE group underwent single- or double-lumen enterostomy. There were no significant differences in complication rates or prognoses between the two groups after either procedure. Although the stoma was positioned higher in the SE group, the length of the unused small intestine (USI) was not significantly different. Multivariate analysis revealed that the length of the USI influenced the likelihood of malnutrition after enterostomy (OR = 1.108, P = 0.008). After stoma closure, compared with those in the CE group, the operation time, intestinal recovery time, fasting time, hospitalization time, intraoperative blood loss volume and the incidence of complications requiring surgical reintervention was significantly lower in the SE group. In conclusion, Santulli enterostomy is not only a safe treatment option for NEC but also an effective method for increasing the length of the small intestine after enterostomy, thereby improving the patient’s postoperative nutritional status. In addition, the procedure is associated with good recovery and a reduced incidence of surgical reintervention after stoma closure.
Silver nanoparticles coated with metabolites of Pseudomonas sp. N5.12 inhibit bacterial pathogens and fungal phytopathogens
Authors: Plokhovska Svitlana , García-Villaraco Ana , Lucas Jose Antonio , Gutierrez-Mañero Francisco Javier , Ramos-Solano Beatriz 
Published: January 2025

AbstractThe synthesis of nanomaterials from PGPB is an exciting approach and it’s often used in agriculture as nano-fertilizers and nano-pesticides. The present study reports a new approach to biosynthesis of silver nanoparticles (AgNP), using bacterial metabolites as agents to reduce Ag+, which will remain as coating agents able to prevent microbial growth. Silver NP were biosynthesized using the bacterial metabolites produced by the beneficial strain Pseudomonas sp. N5.12. Optimization of physicochemical parameters (temperature, pH, and AgNO3 concentration) for the synthesis of AgNP was carried out. In each condition, success on AgNP synthesis was determined by UV–Visible spectra showing peaks between 400 and 450 nm. TEM analysis showed that the AgNP are spherical in shape with an average particle size ranging from 13.75 ± 0.47 nm to 20.71 ± 0.43 nm, covered with a unique organic matter corona of bacterial metabolites. The best parameters for AgNP biosynthesis by Pseudomonas sp. N5.12 occurred with 24 h bacterial metabolites, temperature of 37 °C, pH 9 and a ratio of 2:4 (v: v; bacterial supernatant: 1 mM AgNO3). The biosynthesized AgNP inhibited growth of human pathogenic bacteria better than equivalent AgNO3 concentration. Growth of bacterial and fungal phytopathogens was also inhibited with striking effects on Alternaria sp. (74% inhibition) and Stemphylium sp. (52% inhibition), appearing as promising tools to biocontrol fungal diseases in agriculture.
A CRISPR-Cas9 system protecting E. coli against acquisition of antibiotic resistance genes
Authors: Lee Danna , Muir Petra , Lundberg Sara , Lundholm August , Sandegren Linus , Koskiniemi Sanna 
Published: January 2025

AbstractAntimicrobial resistance (AMR) is an increasing problem worldwide, and new treatment options for bacterial infections are direly needed. Engineered probiotics show strong potential in treating or preventing bacterial infections. However, one concern with the use of live bacteria is the risk of the bacteria acquiring genes encoding for AMR or virulence factors through horizontal gene transfer (HGT), and the transformation of the probiotic into a superbug. Therefore, we developed an engineered CRISPR-Cas9 system that protects bacteria from horizontal gene transfer. We synthesized a CRISPR locus targeting eight AMR genes and cloned this with the Cas9 and transacting tracrRNA on a medium copy plasmid. We next evaluated the efficiency of the system to block HGT through transformation, transduction, and conjugation. Our results show that expression of the CRISPR-Cas9 system successfully protects E. coli MG1655 from acquiring the targeted resistance genes by transformation or transduction with 2–3 logs of protection depending on the system for transfer and the target gene. Furthermore, we show that the system blocks conjugation of a set of clinical plasmids, and that the system is also able to protect the probiotic bacterium E. coli Nissle 1917 from acquiring AMR genes.
Trees shape the soil microbiome of a temperate agrosilvopastoral and syntropic agroforestry system
Authors: Vaupel Anna , Küsters Max , Toups Julia , Herwig Nadine , Bösel Benedikt , Beule Lukas 
Published: January 2025

Abstract
Agroforestry systems are multifunctional land-use systems that promote soil life. Despite their large potential spatio-temporal complexity, the majority of studies that investigated soil organisms in temperate cropland agroforestry systems focused on rather non-complex systems. Here, we investigated the topsoil and subsoil microbiome of two complex and innovative alley cropping systems: an agrosilvopastoral system combining poplar trees, crops, and livestock and a syntropic agroforestry system combining 35 tree and shrub species with forage crops. Increasing soil depth resulted in a decline of bacterial and fungal richness and a community shift towards oligotrophic taxa in both agroforestry systems, which we attribute to resource-deprived conditions in subsoil. At each soil depth, the microbiome of the tree rows was compositionally distinct from the crop rows. We detected a shift towards beneficial microorganisms as well as a decline in putative phytopathogens under the trees as compared to the crop rows. Finally, based on our results on community dissimilarity, we found that compared to an open cropland without trees, spatial heterogeneity introduced by the tree rows in the agrosilvopastoral system translated into a compositionally less homogeneous soil microbiome, highlighting the potential of agroforestry to counteract the homogenization of the soil microbiome through agriculture.
Human iPSC-derived microglial cells protect neurons from neurodegeneration in long-term cultured adhesion brain organoids
Authors: Chen Xianwei , Sun Guoqiang , Feng Lizhao , Tian E , Shi Yanhong 
Published: January 2025

AbstractBrain organoid models have greatly facilitated our understanding of human brain development and disease. However, key brain cell types, such as microglia, are lacking in most brain organoid models. Because microglia have been shown to play important roles in brain development and pathologies, attempts have been made to add microglia to brain organoids through co-culture. However, only short-term microglia-organoid co-cultures can be established, and it remains challenging to have long-lasting survival of microglia in organoids to mimic long-term residency of microglia in the brain. In this study, we developed an adhesion brain organoid (ABO) platform that allows prolonged culture of brain organoids (greater than a year). Moreover, the long-term (LT)-ABO system contains abundant astrocytes and can support prolonged survival and ramification of microglia. Furthermore, we showed that microglia in the LT-ABO could protect neurons from neurodegeneration by increasing synaptic density and reducing p-Tau level and cell death in the LT-ABO. Therefore, the microglia-containing LT-ABO platform generated in this study provides a promising human cellular model for studying neuron-glia and glia-glia interactions in brain development and the pathogenesis of neurodegenerative diseases such as Alzheimer’s disease.
State-level policies alone are insufficient to meet the federal food waste reduction goal in the United States
Authors: Kakadellis Sarah , Mao Selena , Harwood Asch , Spang Edward S. 
Published: January 2025

Abstract
The United States Food Loss and Waste Reduction Goal seeks to reduce national food waste by 50%, down to 74 kg per capita, by 2030. Here we investigate state policies’ alignment with the federal goal across four policy categories. We develop a policy scoring matrix and apply it to wasted food solutions listed in the non-profit ReFED’s database to derive ranges of food waste diversion potential and projected generation across states. On the basis of state policies alone, no state can meet the federal target. We estimated a diversion potential of 5–14 kg per capita and a food waste generation of 149 kg per capita nationally in 2022, equivalent to the 2016 baseline. Without additional intervention at the state and federal level promoting a shift from food waste recycling towards prevention, rescue and repurposing, food generation in the United States will probably remain high.
RNA dysregulation in neurodegenerative diseases
Authors: Li Yini , Sun Shuying 
Published: January 2025

Abstract
Dysregulation of RNA processing has in recent years emerged as a significant contributor to neurodegeneration. The diverse mechanisms and molecular functions underlying RNA processing underscore the essential role of RNA regulation in maintaining neuronal health and function. RNA molecules are bound by RNA-binding proteins (RBPs), and interactions between RNAs and RBPs are commonly affected in neurodegeneration. In this review, we highlight recent progress in understanding dysregulated RNA-processing pathways and the causes of RBP dysfunction across various neurodegenerative diseases. We discuss both established and emerging mechanisms of RNA-mediated neuropathogenesis in this rapidly evolving field. Furthermore, we explore the development of potential RNA-targeting therapeutic approaches for the treatment of neurodegenerative diseases.
Acidic pH can attenuate immune killing through inactivation of perforin
Authors: Hodel Adrian W , Rudd-Schmidt Jesse A , Noori Tahereh , Lupton Christopher J , Cheuk Veronica C T , Trapani Joseph A , Hoogenboom Bart W , Voskoboinik Ilia 
Published: January 2025

Abstract
Cytotoxic lymphocytes are crucial to our immune system, primarily eliminating virus-infected or cancerous cells via perforin/granzyme killing. Perforin forms transmembrane pores in the plasma membrane, allowing granzymes to enter the target cell cytosol and trigger apoptosis. The prowess of cytotoxic lymphocytes to efficiently eradicate target cells has been widely harnessed in immunotherapies against haematological cancers. Despite efforts to achieve a similar outcome against solid tumours, the immunosuppressive and acidic tumour microenvironment poses a persistent obstacle. Using different types of effector cells, including therapeutically relevant anti-CD19 CAR T cells, we demonstrate that the acidic pH typically found in solid tumours hinders the efficacy of immune therapies by impeding perforin pore formation within the immunological synapse. A nanometre-scale study of purified recombinant perforin undergoing oligomerization reveals that pore formation is inhibited specifically by preventing the formation of a transmembrane β-barrel. The absence of perforin pore formation directly prevents target cell death. This finding uncovers a novel layer of immune effector inhibition that must be considered in the development of effective immunotherapies for solid tumours.
Oncolytic viruses expressing MATEs facilitate target-independent T-cell activation in tumors
Authors: Peter Malin , Mundt Bettina , Menze Arne , Woller Norman , Volk Valery , Ernst Amanda M , Öhler Leon A , Talbot Steven R , Wedemeyer Heiner , Falk Christine , Feuerhake Friedrich , Wirth Thomas C , Kühnel Florian 
Published: January 2025

Abstract
Oncolytic viruses (OV) expressing bispecific T-cell engagers (BiTEs) are promising tools for tumor immunotherapy but the range of target tumors is limited. To facilitate effective T-cell stimulation with broad-range applicability, we established membrane-associated T-cell engagers (MATEs) harboring the protein transduction domain of the HIV-Tat protein to achieve non-selective binding to target cells. In vitro, MATEs effectively activated murine T cells and improved killing of MC38 colon carcinoma cells. Similarly, humanized MATEs activated T cells in PBMCs from human donors. In MC38-tumors in mice, MATE-expression by the oncolytic adenovirus Ad5/11 facilitated intratumoral T-cell activation, reduced tumor growth and prolonged survival accompanied by infiltration of tumor-directed CD8+ T cells and improved CD8/CD4 T-cell ratio. Absence of early T-cell activation in tumor draining lymph nodes suggests the safe applicability of this strategy. Furthermore, MATE-expression by Ad5/11 was capable of breaking resistance to αPD-1 checkpoint therapy thereby promoting T-cell/tumor cell proximity and clustering of CD8+ and CD4+ T cells. In summary, we demonstrated that MATE expressing OVs are powerful T-cell activating tools suitable for local immunotherapy of a broad range of tumors.
Effects of F1–F2 Frequency Spacing on Spectral Integration in Combined Electric and Acoustic Stimulation
Authors: Jaisinghani Priyanka , Yoon Yang-Soo 
Published: January 2025

Purpose:
The aim of this study was to measure the effects of frequency spacing (i.e., F2 minus F1) on spectral integration for vowel perception in simulated bilateral electric–acoustic stimulation (BiEAS), electric–acoustic stimulation (EAS), and bimodal hearing.

Method:
Twenty listeners with typical hearing participated in synthetic vowel recognition. Four vowels were used with varying frequency spacings (/ͻ/: 270 Hz, /ʊ/: 653 Hz, /æ/: 1040 Hz, and /I/: 1607 Hz). F1 was acoustically simulated with a band-pass filtering, while F2 was electrically simulated using an eight-channel sine wave vocoder with matched input and output frequency range. Vowel recognition was measured in five listening conditions: BiEAS (F1 and F2 in both ears), EAS (F1 and F2 in the left ear), bimodal (F1 and F2 in opposite ears), cochlear implant alone (F2 alone in the left ear), and hearing aid alone (F1 alone in the left ear).

Results:
In EAS, spectral integration was significantly better at a 270-Hz spacing, while in bimodal hearing, spectral integration was significantly poorer at a 1607-Hz frequency compared to other frequency spacings. BiEAS conditions offered the best spectral integration, regardless of frequency spacing. Vowel confusion remained consistent and below chance level across the first three listening conditions. Bimodal interference occurred for the /I/ vowel when the cochlear implant ear perceives the dominant cue and the hearing aid ear perceives the nondominant cue. The F2 place cue is transmitted significantly better than the F1 height cue in BiEAS, EAS, and bimodal conditions.

Conclusions:
EAS and bimodal hearing integrates narrower frequency ranges better than wider spacings. EAS hearing provided greater outcomes over bimodal hearing, suggesting that within-ear (EAS) integration is more effective than across-ear (bimodal) integration. Bimodal interference may be a factor for variability in bimodal performance. Cautious interpretation and further research with real EAS and bimodal users are suggested to validate and extend these findings.

Supplemental Material:

https://doi.org/10.23641/asha.28127249
Exploring the Feasibility of Self-Reported Cognitive Fatigue in Children With and Without Traumatic Brain Injury After Functional Experimental Tasks
Authors: Riccardi Jessica Salley , Underhill Brooke 
Published: January 2025

Purpose:
The overall purpose of this study was to explore the feasibility of collecting subjective measures of cognitive fatigue in children with and without traumatic brain injury (TBI) before and after functional, experimental tasks.

Method:
Seven participants (i.e., two children with TBI and five children without TBI) completed the experimental tasks for this study. Demographics, injury information, and executive functioning were collected through an online, parent-reported survey. Self-reported ratings of cognitive fatigue were collected from children through an online survey and before and after four in-person experimental tasks, including two high-demand and two low-demand tasks.

Results:
All participants successfully completed the experimental tasks including self-rating cognitive fatigue before beginning the experiment and after each experimental task. While cognitive fatigue patterns were inconsistent across participants, changes in self-ratings were observed, demonstrating the feasibility of the tasks and measure for children with and without TBI.

Conclusion:
The findings from this preliminary study of a small sample support the feasibility of and continued research on self-ratings to better understand, assess, and manage cognitive fatigue after childhood TBI.
Collaborative optimization method for scalable prosumers’ participation in frequency regulation ancillary services
Authors: Pan Xi'an , Ai Xin , Gao Fei , Hu Junjie , Zhang Yingnan 
Published: January 2025

AbstractAs the demand for frequency regulation resources in power systems increases, collaborative optimization of flexible resources with rapid frequency regulation response capabilities, particularly by enabling scalable prosumers in local areas to participate in the frequency regulation ancillary service market, can effectively enhance safety, stability, and frequency regulation ability of power system. Therefore, this paper first establishes a collaborative optimization framework for scalable prosumers in frequency regulation and describes the operation model of prosumers. Considering the uncertainties that can impact prosumers' power decisions during frequency regulation, a scenario‐augmented dataset generation method based on a denoising diffusion probabilistic model is proposed to improve decision adaptability under extreme scenarios with insufficient regulation capabilities. Additionally, to enhance the scalability and applicability of the training method in scalable prosumer collaborative optimization scenarios, a multi‐agent attention proximal policy optimization algorithm combined with a global attention mechanism is introduced. The effectiveness of the proposed method in improving decision timeliness, operation benefits, scalability, and policy adaptability during scalable prosumers’ participation in frequency regulation ancillary services is validated using the IEEE standard node test system under various scales and scenarios.
Research on the registration of infrared and visible images based on phase consistency and edge extreme points
Authors: Li Jie , Zhou Rougang , Ruan Zhenchao , Chien Chou Jay Tsai , Zhu Junjie 
Published: January 2025

AbstractDue to the significant differences in the imaging principles of infrared images and visible images, the feature points and descriptors between the two cannot be effectively matched directly by traditional feature extraction methods such as SIFT. To solve this problem, this study proposes a registration algorithm for infrared and visible images based on phase information and edge information. The algorithm extracts the feature points of the infrared image and the visible image through the principle of phase agreement and the edge binary map of the image and then calculates the descriptors of the gradient images of the infrared image and the visible image, and the descriptor calculation draws on some SIFT principles. Finally, the cosine similarity was used to match the feature points, and the improved random sample consensus algorithm was used to screen out the correct registration points. Experiments show that this method can effectively register between infrared and visible images and is also suitable for the registration of infrared and visible images with different rotation angles and similar structures.
Edge‐computing‐based operations for automated vehicles with different cooperation classes at stop‐controlled intersections
Authors: Soleimaniamiri Saeid , Yao Handong , Ghiasi Amir , Li Xiaopeng , Bujanović Pavle , Vadakpat Govindarajan , Lochrane Taylor W. P. 
Published: January 2025

AbstractCooperation classes have been defined by SAE International to differentiate the communication capabilities between vehicles and infrastructure. To advance understanding of the impact of cooperation classes on autonomous cooperative driving and optimize traffic operations, this article proposes an edge‐computing‐based operations framework for cooperative‐automated driving system (C‐ADS)‐equipped vehicles at a stop‐controlled intersection. First, a critical time points estimation component estimates a set of critical time points for each C‐ADS‐equipped vehicle. Second, a trajectory‐smoothing component is called at each C‐ADS‐equipped vehicle in a decentralized manner to control C‐ADS‐equipped vehicle trajectories based on the estimated critical time points and its cooperation behavior. Notably, this study represents a first‐time investigation of different cooperation classes for stop‐controlled intersections. Simulation results show that the proposed framework can reduce stop‐and‐go traffic, yielding significant improvements in mobility and energy efficiency, as the cooperation class increases. Results also demonstrate that the proposed framework is suitable for real‐time applications by distributing computational burden in different entities. Further, results verify that the proposed framework can handle varying speed errors without significant loss in performance.