bluuebunny/crossref_metadata_2025_split huggingface dataset:
Distinct Intestinal Microbial Signatures Linked to Accelerated Biological Aging in People with HIV
Authors: Singh Shalini , Giron Leila B. , Shaikh Maliha W. , Shankaran Shivanjali , Engen Phillip A. , Bogin Zlata R. , Bambi Simona A. , Goldman Aaron R. , Azevedo Joao L. L. C. , Orgaz Lorena , de Pedro Nuria , González Patricia , Giera Martin , Verhoeven Aswin , Sánchez-López Elena , Pandrea Ivona Vasile , Kannan Toshitha , Tanes Ceylan E. , Bittinger Kyle , Landay Alan L. , Corley Michael J. , Keshavarzian Ali , Abdel-Mohsen Mohamed 
Published: October 2023

Abstract
Background
People with HIV (PWH), even with controlled viral replication through antiretroviral therapy (ART), experience persistent inflammation. This is partly due to intestinal microbial dysbiosis and translocation. Such ongoing inflammation may lead to the development of non-AIDS-related aging-associated comorbidities. However, there remains uncertainty regarding whether HIV affects the biological age of the intestines and whether microbial dysbiosis and translocation influence the biological aging process in PWH on ART. To fill this knowledge gap, we utilized a systems biology approach, analyzing colon and ileal biopsies, blood samples, and stool specimens from PWH on ART and their matched HIV-negative counterparts.
Results
Despite having similar chronological ages, PWH on ART exhibit accelerated biological aging in the colon, ileum, and blood, as measured by various epigenetic aging clocks, compared to HIV-negative controls. Investigating the relationship between microbial translocation and biological aging, PWH on ART had decreased levels of tight junction proteins in the colon and ileum, along with increased microbial translocation. This increased intestinal permeability correlated with faster intestinal and systemic biological aging, as well as increased systemic inflammation. When investigating the relationship between microbial dysbiosis and biological aging, the intestines of PWH on ART had higher abundance of specific pro-inflammatory bacterial genera, such as Catenibacterium and Prevotella. These bacteria significantly correlated with accelerated local and systemic biological aging. Conversely, the intestines of PWH on ART had lower abundance of bacterial genera known for producing short-chain fatty acids and exhibiting anti-inflammatory properties, such as Subdoligranulum and Erysipelotrichaceae, and these bacteria taxa were associated with slower biological aging. Correlation networks revealed significant links between specific microbial genera in the colon and ileum (but not in feces), increased aging, a rise in pro-inflammatory microbial-related metabolites (e.g., those in the tryptophan metabolism pathway), and a decrease in anti-inflammatory metabolites like hippuric acid and oleic acid.
Conclusions
We identified a specific microbial composition and microbiome-related metabolic pathways that are intertwined with both intestinal and systemic biological aging in PWH on ART. A deeper understanding of the mechanisms underlying these connections could potentially offer strategies to counteract premature aging and its associated health complications in PWH.
Osimertinib readministration for central nervous system metastases in non–small cell lung cancer positive for EGFR activating mutations
Authors: Inutsuka Yu , Iwama Eiji , Shiraishi Yoshimasa , Yoneshima Yasuto , Shibahara Daisuke , Tanaka Kentaro , Okamoto Isamu 
Published: October 2023

Abstract
Purpose Osimertinib shows pronounced efficacy for EGFR mutation–positive non–small cell lung cancer (NSCLC) including associated central nervous system (CNS) metastases. Tumors inevitably develop resistance to the drug, however. Osimertinib is sometimes readministered after completion of standard chemotherapy. To clarify which patients might receive benefit from osimertinib readministration, we have retrospectively assessed its efficacy with a focus on CNS metastases.
Methods A retrospective analysis of medical records was performed for 21 patients who underwent osimertinib readministration at Kyushu University Hospital between March 2016 and April 2023. CNS metastases were evaluated according to modified Response Evaluation Criteria in Solid Tumors (RECIST).
Results Among the 21 enrolled patients, 16 individuals had target lesions on the basis of RECIST. One (6.3%) of these 16 patients achieved a partial response to osimertinib readministration, with the remaining 15 patients showing stable or progressive disease. The median overall progression-free survival (PFS) and median overall survival for all 21 patients were 3.8 and 13.9 months, respectively. The efficacy of osimertinib readministration for CNS metastases was evaluable in eight patients including five individuals with leptomeningeal metastases. The objective response rate for CNS metastases and the improvement rate for leptomeningeal metastases were both 100%. The median PFS with regard to CNS or non-CNS lesions for these eight patients was 24.7 and 10.5 months, respectively.
Conclusion Osimertinib readministration showed limited efficacy for non-CNS lesions but excellent efficacy for CNS metastases, suggesting that such treatment is an option for EGFR-mutated NSCLC patients with CNS metastases.
Association between failed eradication of 7-day triple therapy for Helicobacter pylori and untreated dental caries in Japanese adults
Authors: Iwai Komei , Azuma Tetsuji , Yonenaga Takatoshi , Sasai Yasuyuki , Watanabe Kazutoshi , Obora Akihiro , Deguchi Fumiko , Kojima Takao , Tomofuji Takaaki 
Published: October 2023

Abstract
Helicobacter pylori (H. pylori) infection is a cause of gastric disorders and is treated mainly by pharmacotherapy with antimicrobial agents. An association has been reported between dental caries and H. pylori infection. As antimicrobial agents are less effective inside dental caries because of impaired blood circulation, the presence of untreated dental caries (decayed teeth) may influence the success of H. pylori eradication treatment. In this cross-sectional study, we examined whether failed eradication of H. pylori was associated with decayed teeth in Japanese adults. Enrolled were 226 participants (150 males, 76 females; mean age, 52.7 years) who received dental checkups among those treated for eradication of H. pylori at Asahi University Hospital between April 2019 and March 2021. Treatment efficacy was assessed by urea breath test. Eradication failed in 38/226 participants (17%). Multivariate logistic regression analyses showed that failed eradication of H. pylori was associated with decayed teeth (presence: odds ratio, 2.611; 95% confidence interval, 1.072–6.362) after adjusting for gender, age, and brushing frequency. These results indicate that failed eradication of H. pylori was associated with decayed teeth and suggest that untreated dental caries may impact treatment for eradication of H. pylori.
The interaction mechanism between interstitial-substitutional pairs and defects in nitrogen-added austenitic stainless steels
Authors: Kawahara Yasuhito , Kobatake Shunya , Kaneko Kenji , Sasaki Taisuke , Ohkubo Tadakatsu , Takushima Chikako , Hamada Jun-ichi 
Published: October 2023

Abstract
Interstitial-substitutional pairs have been acknowledged to contribute to the increase in the strengths of steels. For further improvements in mechanical properties, their atomic-scale structures and interaction mechanisms with defects are required to be examined. In this study, both high-resolution transmission electron microscopy and atom-probe tomography were used to correlate interstitial-substitutional pairs with defect characteristics in austenitic stainless steels. Three types of defect core structures are identified and associated with their strain fields as well as N-Cr pairs in the N-added steels. It is revealed that N atoms interact elastically with the defects, followed by the formation of N-Cr pairs via the chemical interaction between N and Cr atoms. This insight significantly improves the understanding of the multiple alloying mechanism in metallic materials such as interstitial alloys and high-entropy alloys.
EDB-FN-Targeted Positron Emission Tomography Imaging of Breast Cancer in Mice
Authors: Zhang Yun , Zheng Xiao-Bin , Huang Yan-Fang , Li Si-Jia , Yang Xiao-Chun , Yang Yi-Ling 
Published: October 2023

Abstract
Purpose The Breast Imaging Reporting and Data System (BI-RADS) and 2-deoxy-2-[18F]fluoro-D-glucose ([18F]F-FDG) positron emission tomography (PET) have some limitations in the diagnosis of breast cancer. The extra domain B splice variant of fibronectin (EDB-FN), which is overexpressed in several cancer types, including breast cancer, is an approved diagnostic and therapeutic target of EDB-FN-positive cancers. Herein, we provide the EDB-FN-targeted peptide EDBp as a noninvasive oncological imaging modality for the molecular imaging of breast cancer.Procedures The binding of the peptide EDBp-Cy5 to EDB-positive breast cancer cells was investigated by flow cytometry and confocal microscopy. Near-Infrared Fluorescence (NIRF) imaging was performed at 48 hours after 1 µmol EDBp-Cy5 was intravenously injected into subcutaneous MDA-MB-231 breast cancer model mice or pulmonary metastasis model mice. Model mice were intravenously injected with approximately 100 µCi of [18F]-EDBp, and PET/CT scanning was performed after 2 hours of in vivo circulation.Results Our results demonstrate that EDBp-Cy5 had a strong binding ability to the MDA-MB-231 cells. EDBp-Cy5 exhibited specific tumor accumulation in MDA-MB-231 subcutaneous and pulmonary metastasis model mice. Importantly, we proposed and validated an EDBp peptide-based radiotracer [18F]-EDBp for PET imaging. [18F]-EDBp provided excellent diagnostic value for PET imaging of breast cancer, especially in subcutaneous tumors. The uptake of [18F]-EDBp in subcutaneous tumors (6.53 ± 0.89%, ID/g) was unexpectedly higher than that in the kidney (4.96 ± 0.20, %ID/g), which is the main metabolic organ of peptides. In the pulmonary metastasis model mice, PET/CT imaging showed that [18F]-EDBp moderately accumulated in the pulmonary metastases.Conclusion The high tumor uptake of this radiotracer in mice suggests its potential for application in PET imaging of EDB-FN-positive breast cancer for disease staging of regional and distant metastases and relapse monitoring.
Host-specific co-evolution likely driven by diet in Buchnera aphidicola
Authors: Burger N Francois V , Nicolis Vittorio F , Botha Anna-Maria 
Published: October 2023

Abstract
Background Russian wheat aphid (Diuraphis noxia Kurd.) is a severe pest to wheat, and even though resistance varieties are available to curb this pest, they are becoming obsolete with the development of new virulent aphid populations. Unlike many other aphids, D noxia only harbours a single endosymbiont, Buchnera aphidicola. Considering the importance of Buchnera, this study aimed to elucidate commonalities and dissimilarities between various hosts, to better understand its distinctiveness within its symbiotic relationship with D. noxia. To do so, the genome of the D. noxia’s Buchnera was assembled and compared to those of other aphid species that feed on diverse host species.Results The overall importance of several features such as gene length and percentage GC content was found to be critical for the maintenance of Buchnera genes when compared to their closest free-living relative, Escherichia coli. Buchnera protein coding genes were found to have percentage GC contents that tended towards a mean of ~ 26% which had strong correlation to their identity to their E. coli homologs. Several SNPs were identified between different aphid populations and multiple isolates of Buchnera were confirmed in single aphids.Conclusions Establishing the strong correlation of percentage GC content of protein coding genes and gene identity will allow for identifying which genes will be lost in the continually shrinking Buchnera genome. This is also the first report of a parthenogenically reproducing aphid that hosts multiple Buchnera strains in a single aphid, raising questions regarding the benefits of maintaining multiple strains. We also found preliminary evidence for post-transcriptional regulation of Buchnera genes in the form of polyadenylation.
New Quantum LDPC Codes Based on Euclidean Geometry
Authors: Feng Ya’nan , Tang Chuchen , Bai Chenming 
Published: October 2023

Abstract
With the development of quantum error correction techniques, quantum low density parity check (QLDPC) codes become a promising area in quantum error correction codes. In this paper, the requirements of QLDPC codes based on points except the origin and lines not passing through the origin of Euclidean geometry are given. QLDPC codes based on all the lines and parallel classes are obtained respectively.
Detection of pharmaceutically active compounds in tap water samples by direct injection HPLC/MS-MS: A danger signal in deficiency in residue management
Authors: Peregrina-Lucano Alejandro Aarón , Mendoza-Michel Judith , Rodríguez-Arreola Ariana , Peña-Velasco Gabriela 
Published: October 2023

Abstract

The growing and decelerated presence of pharmaceutically active compounds in water samples is further studied due to the risks to the environment and the health public. Evidence suggests that antibiotics, oncologic, and endocrine disruptor compounds classified as emerging pollutants have been released into the aquatic environment and maintained in diverse aquatic compartments until networks of tap water are affected. Therefore, an HPLC–MS/MS method is developed for the simultaneous determination of 16 active pharmaceutical compounds in tap water samples of the metropolitan area of Guadalajara: amoxicillin, ampicillin, cephalexin, cefotaxime, cefuroxime, ciprofloxacin, clarithromycin, clindamycin, chloramphenicol, cyproterone, erythromycin, flutamide, spironolactone, sulfamethoxazole, tamoxifen, and trimethoprim, using a direct injection technique. The implemented method obtained results of linearity determination coefficients (r2) higher than 0.998; limits of detection (LOD) of 0.3–15 µg/L and quantification limits (LOQ) from 1.5 to 50 µg/L, recoveries percentages in the range of 70–125% and time retentions ≤ 2.2 min. The methodology developed allowed the analysis of a total of 22 tap water samples where the highest concentrations corresponding to amoxicillin (147 mg/L) and ciprofloxacin (44 mg/L). Overall, most tap water samples analyzed presented more than six pharmaceutical active compounds at diverse levels of concentrations. The alternative methodology proposed in this research work and its findings could be a precedent for framework regulatory and establishing safe levels of these compounds in water associated with significant human health and environmental risks, as well as increasing the standards for quality tap water represents a main source of diseases in terms of the health public.
Comparative Investigation of the Antimicrobial Properties of the Root, Leaf, and Seed Oils of Carrot Plant Growing in Sierra Leone
Authors: Vandy Ahmed , Kamara Marie-kholipha , Mattia Sia Christiana , Buffa Tamba , Marah Foday , Conteh Eugene , Lahai Michael , Marah Mohamed , Suma Kadiatu M. , Kamara Fatmata S. , Sower Hawanatu , Gbla Zainab , Sheriff Matilda S. , Ogaya Jericho , Comabig Rey , III Don Eliseo Lucero-Prisno 
Published: October 2023

Abstract
Daucus carota L. (Carrot) is a biennial herbaceous plant which has various nutritional, cosmetic, and medicinal benefits. This study determined the antimicrobial activity of the oil extract from the leaves, roots, and seeds of carrot plants against four selected bacterial isolates. The leaves, roots, and seeds of the carrot plant were weighed and the oils were extracted by hydrodistillation using the Clevenger apparatus. The antimicrobial susceptibility testing was performed by disc and well diffusion methods against Streptococcus pneumoniae, Staphylococcus aureus, Salmonella typhi, and Pseudomonas aeruginosa. Nigella sativa oil was used as the positive control. The extraction process of essential oils from the part of the carrot plants yielded varying quantities of oil, spanning from the roots (0.3%), the leaves (0.4%) and the seeds (0.8%). The results of the study showed that all the extracted essential oils had some activity against the selected bacterial isolates, with varying degrees of inhibition. The root oil showed the highest antimicrobial activity (14mm) against Streptococcus Pneumoniae, matching the control oil using the well diffusion method and a higher activity (17mm) than the control when the disc diffusion method was used. The seed oil had the highest activity (15mm) against Pseudomonas aeruginosa, which is slightly less than the control oil using the disc diffusion method. The zones of inhibition were generally higher by the disc diffusion method than the well diffusion method for most of the isolates. The essential oils extracted from Daucus carota L. oils had antimicrobial activity against the four bacterial isolates used, with higher activity against gram-positive bacteria than gram-negative. The antimicrobial activity varied according to the extracted plant parts, the bacterial isolate and the susceptibility test methods used.
Few-shot Adaptation of Multi-modal Foundation Models: A Survey
Authors: Liu Fan , Zhang Tianshu , Dai Wenwen , Cai Wenwen , Zhou Xiaocong , Chen Delong 
Published: October 2023

Abstract

Multi-modal models, such as CLIP, are replacing traditional supervised pre-training models (e.g., ImageNet-based pre-training) as the new generation of foundational visual models. These multi-modal models with robust and aligned semantic representations from billions of internet image-text pairs and can be applied to various downstream zero-shot tasks. However, in some fine-grained domains like medical imaging and remote sensing, the performance of multi-modal foundation models often leaves much to be desired. Consequently, many researchers have begun to explore few-shot adaptation methods for multi-modal foundation models, gradually deriving three technical approaches: 1) prompt-based fine-tuning adaptation methods, 2) adapter-based fine-tuning adaptation methods, and 3) adaptation methods based on external knowledge. Nevertheless, this rapidly developing field has produced numerous results without a comprehensive survey to systematically organize the research progress. Therefore, in this paper, we provide an extensive survey and analysis of the research advancements in few-shot adaptation methods for multi-modal models, summarizing commonly used datasets and experimental setups, and comparing the results of different methods. In addition, due to the lack of reliable theoretical support for existing methods, we derive the few-shot adaptation generalization error bound for multi-modal models. The theorem reveals that the generalization error of multi-modal foundation models is constrained by three factors: domain gap, model capacity, and sample size. Based on this, we propose three possible solutions from the following aspects: 1) domain distribution adaptation, 2) model selection adaptation, and 3) knowledge utilization adaptation.
On fast iterative methods for solving the split fixed point problem of multiple output sets involving demicontractive mappings
Authors: Majee Prashanta , Bai Sonu , Padhye Sahadeo 
Published: October 2023

Abstract
This paper aims to formulate some novel inertial-type iterative methods for approximating the solution of a split fixed point problem involving demicontractive mappings in real Hilbert spaces. We construct the iterative methods with the help of two selection techniques of stepsize. One type of iterative method is introduced with fixed stepsize, and the other type of method is introduced with the help of variable stepsize. First, we prove weak convergence of the proposed methods with the mild conditions on the control parameters. Then, we establish strong convergence results for approximating the solution of the split fixed point problem. Finally, we give some numerical examples to justify the validity and efficiency of the proposed iterative methods.
MSC Classification: 47H09 , 47H10 , 47J05
Age-of-Information in Distributed Systems caused by Asynchronous Computing Modeled as Parallel Renewal Processes
Authors: Redder Adrian , Karl Holger 
Published: October 2023

Abstract
We consider methods where processors from a distributed computing (DC) infrastructure compute updates for a set of parameters asynchronously. In such scenarios, the parameter updates can experience practically unbounded stochastic processing times caused by effects like queuing, processor sharing, priorities, preemption, or heavy-tailed traffic. As a result, processors will update parameters multiple times while one processor observes the parameters and calculates a new parameter update based on it. The resulting error between the current parameter and the older version used to calculate the parameter update is thus a function of a discrete information delay that we call Age-of-Information (AoI). To counter the errors caused by AoI, predict the performance of asynchronous algorithms, and effectively solve problems in machine learning and artificial intelligence, it is important to know AoI properties. To do this, we model the processing times in a DC system as parallel renewal processes. For this model, we derive the distribution and moment bounds for the discrete AoI affecting asynchronous algorithms executed on the DC system. We also derive exact expressions for the asymptotic mean and sharp bounds for the asymptotic variance.
Spatiotemporal coordination in children with unilateral cerebral palsy: insights from a bimanual goal-directed task
Authors: Mailleux Lisa , Decraene Lisa , Kalkantzi Alexandra , Kleeren Lize , Crotti Monica , Campenhout Anja Van , Verheyden Geert , Ortibus Els , Green Dido , Klingels Katrijn , Feys Hilde 
Published: October 2023

Abstract

Background: In children with unilateral cerebral palsy (uCP), bimanual assessments mostly focus on qualitative assessments of the impaired upper limb during bimanual tasks, which do not capture the spatiotemporal coordination between both hands. Hence, we aimed to advance our understandings in spatiotemporal coordination in children with uCP compared to typically developing children (TDC) using a bimanual goal-directed task. Participants and methodology: In this observational study, thirty-seven children with uCP (11y8m±2y10m, 20 males, 16 right-sided uCP, Manual Ability Classification System level I=23, II=11, III=3) and 37 age and sex-matched TDC opened a box with one hand and pressed a button inside using the opposite hand. Spatiotemporal bimanual (movement time, temporal coupling, movement overlap, goal synchronisation) and unimanual (movement time, path length and smoothness) parameters were extracted. Between groups comparisons were investigated using a two-way mixed ANCOVA with age as covariate (α<0.05). Additionally, correlation coefficients between unimanual and bimanual parameters were calculated. Results: Compared to TDC, children with uCP did not differ in bimanual coupling relative to their movement time (p>0.31, ηp2<0.03). However, they were slower (p=0.01, ηp2=0.13) and presented with unimanual spatiotemporal deficits bilaterally (p<0.03, ηp2>0.10), which worsened in children with lower manual abilities (p<0.04, ηp2>0.19). Moreover, slower movement time was related with increased unimanual spatiotemporal deficits bilaterally (r=0.34-0.80, p<0.001-0.04), suggesting that reduced performance at both sides contributes to bimanual difficulties in children with uCP. Conclusions: The bilateral reduced spatiotemporal coordination, related to longer bimanual movement time, stresses the importance to assess and treat both upper limbs in children with uCP.