bluuebunny/crossref_metadata_2025_split huggingface dataset:
Identification of a bile acid and bile salt metabolism-related lncRNA signature for predicting prognosis and treatment response in hepatocellular carcinoma
Authors: Cui Hao , Lian Jia , Xu Baiguo , Yu Zhenjun , Xiang Huiling , Shi Jingxiang , Gao Yingtang , Han Tao 
Published: November 2023

AbstractBile acids and salts have been shown to play a role in liver carcinogenesis through DNA damage, inflammation, and tumor proliferation. However, the correlation between bile acid metabolism and hepatocellular carcinoma (HCC) prognosis remains unclear. This study aimed to identify a predictive signature of bile acid and bile salt metabolism-related long non-coding RNAs (lncRNAs) for HCC prognosis and treatment response. The study used HCC RNA-sequencing data and corresponding clinical and prognostic data from The Cancer Genome Atlas. A prognostic model consisting of five bile acid and bile salt metabolism-related lncRNAs was developed and evaluated in a training set, a validation set and an external set. The model demonstrated good performance in predicting HCC prognosis and was shown to be an independent biomarker for prognosis. Additionally, our study revealed a significant association between the signature and immune cell infiltration, as well as its predictive value for therapeutic responses to both immunotherapy and chemotherapy. Furthermore, three LncRNAs (LUCAT1, AL031985.3 and AC015908.3) expression levels in our signature were validated through qRT-PCR in a cohort of 50 pairs of HCC patient tumor samples and corresponding adjacent non-tumor samples, along with 10 samples of normal liver tissue adjacent to benign lesions. These findings suggest that this novel bile acid and bile salt metabolism-related lncRNA signature can independently predict the prognosis of patients with HCC and may be utilized as a potential predictor of response to treatment in this setting.
Phosphorus-solubilizing bacteria improve the growth of Nicotiana benthamiana on lunar regolith simulant by dissociating insoluble inorganic phosphorus
Authors: Xia Yitong , Yuan Yu , Li Chenxi , Sun Zhencai 
Published: November 2023

AbstractIn-situ utilization of lunar soil resources will effectively improve the self-sufficiency of bioregenerative life support systems for future lunar bases. Therefore, we have explored the microbiological method to transform lunar soil into a substrate for plant cultivation. In this study, five species of phosphorus-solubilizing bacteria are used as test strains, and a 21-day bio-improving experiment with another 24-day Nicotiana benthamiana cultivation experiment are carried out on lunar regolith simulant. We have observed that the phosphorus-solublizing bacteria Bacillus mucilaginosus, Bacillus megaterium, and Pseudomonas fluorescens can tolerate the lunar regolith simulant conditions and dissociate the insoluble phosphorus from the regolith simulant. The phosphorus-solubilizing bacteria treatment improves the available phosphorus content of the regolith simulant, promoting the growth of Nicotiana benthamiana. Here we demonstrate that the phosphorus-solubilizing bacteria can effectively improve the fertility of lunar regolith simulant, making it a good cultivation substrate for higher plants. The results can lay a technical foundation for plant cultivation based on lunar regolith resources in future lunar bases.
Vitamin B5 supports MYC oncogenic metabolism and tumor progression in breast cancer
Authors: Kreuzaler Peter , Inglese Paolo , Ghanate Avinash , Gjelaj Ersa , Wu Vincen , Panina Yulia , Mendez-Lucas Andres , MacLachlan Catherine , Patani Neill , Hubert Catherine B. , Huang Helen , Greenidge Gina , Rueda Oscar M. , Taylor Adam J. , Karali Evdoxia , Kazanc Emine , Spicer Amy , Dexter Alex , Lin Wei , Thompson Daria , Silva Dos Santos Mariana , Calvani Enrica , Legrave Nathalie , Ellis James K. , Greenwood Wendy , Green Mary , Nye Emma , Still Emma ,   CRUK Rosetta Grand Challenge Consortium, Kreuzaler Peter , Barry Simon , Goodwin Richard J. A. , Bruna Alejandra , Caldas Carlos , MacRae James , de Carvalho Luiz Pedro Sório , Poulogiannis George , McMahon Greg , Takats Zoltan , Bunch Josephine , Yuneva Mariia 
Published: November 2023

Abstract
Tumors are intrinsically heterogeneous and it is well established that this directs their evolution, hinders their classification and frustrates therapy1–3. Consequently, spatially resolved omics-level analyses are gaining traction4–9. Despite considerable therapeutic interest, tumor metabolism has been lagging behind this development and there is a paucity of data regarding its spatial organization. To address this shortcoming, we set out to study the local metabolic effects of the oncogene c-MYC, a pleiotropic transcription factor that accumulates with tumor progression and influences metabolism10,11. Through correlative mass spectrometry imaging, we show that pantothenic acid (vitamin B5) associates with MYC-high areas within both human and murine mammary tumors, where its conversion to coenzyme A fuels Krebs cycle activity. Mechanistically, we show that this is accomplished by MYC-mediated upregulation of its multivitamin transporter SLC5A6. Notably, we show that SLC5A6 over-expression alone can induce increased cell growth and a shift toward biosynthesis, whereas conversely, dietary restriction of pantothenic acid leads to a reversal of many MYC-mediated metabolic changes and results in hampered tumor growth. Our work thus establishes the availability of vitamins and cofactors as a potential bottleneck in tumor progression, which can be exploited therapeutically. Overall, we show that a spatial understanding of local metabolism facilitates the identification of clinically relevant, tractable metabolic targets.
Spatial and single-cell profiling of the metabolome, transcriptome and epigenome of the aging mouse liver
Authors: Nikopoulou Chrysa , Kleinenkuhnen Niklas , Parekh Swati , Sandoval Tonantzi , Ziegenhain Christoph , Schneider Farina , Giavalisco Patrick , Donahue Kat-Folz , Vesting Anna Juliane , Kirchner Marcel , Bozukova Mihaela , Vossen Christian , Altmüller Janine , Wunderlich Thomas , Sandberg Rickard , Kondylis Vangelis , Tresch Achim , Tessarz Peter 
Published: November 2023

AbstractTissues within an organism and even cell types within a tissue can age with different velocities. However, it is unclear whether cells of one type experience different aging trajectories within a tissue depending on their spatial location. Here, we used spatial transcriptomics in combination with single-cell ATAC-seq and RNA-seq, lipidomics and functional assays to address how cells in the male murine liver are affected by age-related changes in the microenvironment. Integration of the datasets revealed zonation-specific and age-related changes in metabolic states, the epigenome and transcriptome. The epigenome changed in a zonation-dependent manner and functionally, periportal hepatocytes were characterized by decreased mitochondrial fitness, whereas pericentral hepatocytes accumulated large lipid droplets. Together, we provide evidence that changing microenvironments within a tissue exert strong influences on their resident cells that can shape epigenetic, metabolic and phenotypic outputs.
Analysis of microbial composition and sharing in low-biomass human milk samples: a comparison of DNA isolation and sequencing techniques
Authors: Spreckels Johanne E , Fernández-Pato Asier , Kruk Marloes , Kurilshikov Alexander , Garmaeva Sanzhima , Sinha Trishla , Ghosh Hiren , Harmsen Hermie , Fu Jingyuan , Gacesa Ranko , Zhernakova Alexandra 
Published: November 2023

Abstract
Human milk microbiome studies are currently hindered by low milk bacterial/human cell ratios and often rely on 16S rRNA gene sequencing, which limits downstream analyses. Here, we aimed to find a method to study milk bacteria and assess bacterial sharing between maternal and infant microbiota. We tested four DNA isolation methods, two bacterial enrichment methods and three sequencing methods on mock communities, milk samples and negative controls. Of the four DNA isolation kits, the DNeasy PowerSoil Pro (PS) and MagMAX Total Nucleic Acid Isolation (MX) kits provided consistent 16S rRNA gene sequencing results with low contamination. Neither enrichment method substantially decreased the human metagenomic sequencing read-depth. Long-read 16S-ITS-23S rRNA gene sequencing biased the mock community composition but provided consistent results for milk samples, with little contamination. In contrast to 16S rRNA gene sequencing, 16S-ITS-23S rRNA gene sequencing of milk, infant oral, infant faecal and maternal faecal DNA from 14 mother-infant pairs provided sufficient resolution to detect significantly more frequent sharing of bacteria between related pairs compared to unrelated pairs. In conclusion, PS or MX kit-DNA isolation followed by 16S rRNA gene sequencing reliably characterises human milk microbiota, and 16S-ITS-23S rRNA gene sequencing enables studies of bacterial transmission in low-biomass samples.
The grade of individual prostate cancer lesions predicted by magnetic resonance imaging and positron emission tomography
Authors: Nilsson Erik , Sandgren Kristina , Grefve Josefine , Jonsson Joakim , Axelsson Jan , Lindberg Angsana Keeratijarut , Söderkvist Karin , Karlsson Camilla Thellenberg , Widmark Anders , Blomqvist Lennart , Strandberg Sara , Riklund Katrine , Bergh Anders , Nyholm Tufve 
Published: November 2023

Abstract
Background
Multiparametric magnetic resonance imaging (mpMRI) and positron emission tomography (PET) are widely used for the management of prostate cancer (PCa). However, how these modalities complement each other in PCa risk stratification is still largely unknown. We aim to provide insights into the potential of mpMRI and PET for PCa risk stratification.

Methods
We analyzed data from 55 consecutive patients with elevated prostate-specific antigen and biopsy-proven PCa enrolled in a prospective study between December 2016 and December 2019. [68Ga]PSMA-11 PET (PSMA-PET), [11C]Acetate PET (Acetate-PET) and mpMRI were co-registered with whole-mount histopathology. Lower- and higher-grade lesions were defined by International Society of Urological Pathology (ISUP) grade groups (IGG). We used PET and mpMRI data to differentiate between grades in two cases: IGG 3 vs. IGG 2 (case 1) and IGG ≥ 3 vs. IGG ≤ 2 (case 2). The performance was evaluated by receiver operating characteristic (ROC) analysis.

Results
We find that the maximum standardized uptake value (SUVmax) for PSMA-PET achieves the highest area under the ROC curve (AUC), with AUCs of 0.72 (case 1) and 0.79 (case 2). Combining the volume transfer constant, apparent diffusion coefficient and T2-weighted images (each normalized to non-malignant prostatic tissue) results in AUCs of 0.70 (case 1) and 0.70 (case 2). Adding PSMA-SUVmax increases the AUCs by 0.09 (p < 0.01) and 0.12 (p < 0.01), respectively.

Conclusions
By co-registering whole-mount histopathology and in-vivo imaging we show that mpMRI and PET can distinguish between lower- and higher-grade prostate cancer, using partially discriminative cut-off values.
Understanding intracranial aneurysm sounds via high-fidelity fluid-structure-interaction modelling
Authors: Bruneau David A. , Steinman David A. , Valen-Sendstad Kristian 
Published: November 2023

Abstract
Background
Since the 1960s, the origins of intracranial aneurysm bruits and musical murmurs have been debated, with proposed mechanisms ranging from self-excitation (i.e., resonance) by stable pulsatile flow, to vibration caused by unstable (laminar vortex shedding or turbulent) flow. This knowledge gap has impeded the use of intracranial sounds a marker of aneurysm remodelling or rupture risk. New computational techniques now allow us to model these phenomena.

Methods
We performed high-fidelity fluid-structure interaction simulations capable of understanding the magnitude and mechanisms of such flow-induced vibrations, under pulsatile flow conditions. Six cases from a previous cohort were used.

Results
In five cases, underlying flow instabilities present as broad-band, random vibrations, consistent with previously-described bruits, while the sac also exhibits resonance, rocking back and forth in different planes of motion, consistent with previously described musical murmurs. Both types of vibration have amplitudes in the range of 0.1 to 1 μm. The murmurs extend into diastole, after the underlying flow instability has dissipated, and do not exhibit the characteristic repeating frequency harmonics of previously hypothesized vortex-shedding mechanisms. The remaining case with stable pulsatile flow does not vibrate. Spectrograms of the simulated vibrations are consistent with previously reported microphone and Doppler ultrasound recordings.

Conclusions
Our results provide a plausible explanation for distinct intracranial aneurysm sounds and characterize the mechanical environment of a vibrating aneurysm wall. Future work should aim to quantify the deleterious effects of these overlooked stimuli on the vascular wall, to determine which changes to the wall makeup are associated with vibration.
Noble metal-free bimetallic phosphide-decorated Zn0.5Cd0.5S with efficient photocatalytic H2 evolution
Authors: Chen Lu , Chen Feng , Xia Yuzhou , Liang Ruowen , Huang Renkun , Yan Guiyang , Ying Shaoming 
Published: November 2023

The 7% NiCoP/Zn0.5Cd0.5S photocatalyst exhibits a remarkable photocatalytic hydrogen evolution rate of 19.5 mmol g−1 h−1, which is 27 times higher than that of pristine Zn0.5Cd0.5S.
Blockchain privacy: Fundamental aspects and challenges for the future Internet data sharing
Authors: Kapsoulis Nikolaos , Psychas Alexandros , Litke Antonios , Varvarigou Theodora 
Published: November 2023

AbstractPrivacy concerns the majority of individuals, governments, and organizations that share data over dissimilar networks of nodes. Every kind of participant requires awareness of the data journey that unfolds inside a blockchain network with its own trustworthy rules of data management and accessibility. This paper provides a methodological approach on privacy for data sharing within blockchain environments. Specific technological aspects of blockchains that relate to on‐chain privacy such as network nature, party join, smart contracts, blockchain states, transactions, and ledger flows, are analysed with respect to the involvement and impact of privacy in distributed ledgers. A high‐level architectural approach is suggested that is intended to address significant privacy concerns on data sharing among different kinds of users in the context of blockchain networks deployment and the broader Web 3.0 ecosystem building. Simultaneously, many pertinent challenges are discussed regarding network nature, configurable privacy, ownership, confidentiality, secured computation, and data monetization that appear in the field and ought to be carefully tackled for the future mass adoption of privacy‐matured distributed ledgers that interconnect delivering the future Internet.
Electromagnetic analysis of moving structures in a moving reference frame
Authors: Marvasti M. , Boutayeb H. 
Published: November 2023

AbstractIn this work, the finite‐difference time‐domain (FDTD) method is employed to study electromagnetic problems with moving bodies in a moving system. The proposed approach consists in modeling objects with time‐varying positions and using the direct discretization of Maxwell's equations in space and time domains. Doppler effects are investigated for problems with moving observer, source, or reflector, in a moving frame. A distinction is also made between a high‐impedance or low‐impedance plane wave source in motion. The full‐wave electromagnetic simulations are compared with closed‐form equations that agree with wave theory. The proposed analysis shows that, for Doppler radars used every day, the motion of the Earth relative to the Cosmic Microwave Background has a negligible effect and only relative motions in the Earth frame are relevant.
Telemedizin, Kratom und
Autismus-Spektrum-Störung
Authors: Mulert Christoph 
Published: November 2023

Liebe Kolleginnen und Kollegen,es freut mich sehr, Ihnen in der aktuellen Ausgabe interessante Beiträge
vorzustellen zu können, die entweder aus neurologischen oder psychiatrischen
Arbeitsgruppen kommen, aber jeweils auch von besonderem Interesse für das
andere Fachgebiet sind.
The French Experience with a Population-Based Esophageal Atresia Registry (RENATO)
Authors: Sfeir Rony , Aumar Madeleine , Sharma Dyuti , Labreuche Julien , Dauchet Luc , Gottrand Frederic 
Published: November 2023

AbstractThis paper presented a national register for esophageal atresia (EA) started in January 2008. We report our experience about the conception of this database and its coordination. Data management and data quality are also detailed. In 2023, more than 2,500 patients with EA are included. Prevalence of EA in France was calculated at 1.8/10,000 live birth. Main clinical results are listed with scientific publications issued directly from the register.
Acylative and Silylative Dynamic Kinetic Resolutions of 6-Hydroxy-2H-pyran-3(6H)-one Catalyzed by Chiral Guanidines
Authors: Nakata Kenya , Miyazaki Kanako 
Published: November 2023

AbstractChiral guanidine-catalyzed acylative and silylative dynamic kinetic resolutions of 6-hydroxy-2H-pyran-3(6H)-one were achieved. We succeeded in developing a non-enzymatic acylative dynamic kinetic resolution of 6-hydroxy-2H-pyran-3(6H)-one with high enantioselectivity, which could be improved by recrystallization. In contrast, the non-enzymatic silylative dynamic kinetic resolution of 6-hydroxy-2H-pyran-3(6H)-one was accomplished with a moderate selectivity for the first time.
Anthropometric, Metabolic, and Endocrine Parameters as Predictors of
Estimated Average Glucose and Other Biomarkers of Dysglycemia in Women with
Different Phenotypes of Polycystic Ovary Syndrome
Authors: de Medeiros Sebastião Freitas , Winck Yamamoto de Medeiros Ana Lin , Souto de Medeiros Matheus Antônio , da Silva Carvalho Anna Bethany , Yamamoto Marcia W. , M. Soares José , Baracat Edmund C. 
Published: November 2023

AbstractThe aim of the study was to evaluate the efficacy of anthropometric, metabolic,
and endocrine abnormalities as predictors of estimated average glucose and other
biomarkers of dysglycemia in women with different phenotypes of polycystic ovary
syndrome (PCOS). This cross-sectional study included 648 women with PCOS and 330
controls. A single protocol of investigation was applied for all subjects. PCOS
women were divided by phenotypes according to the Rotterdam criteria. Biomarkers
of dysglycemia were considered dependent variables and anthropometric, lipid,
and hormone alterations as independent variables using univariate and
multivariate logistic regressions. Univariate logistic regression analysis,
controlled for age and BMI, showed that many biomarkers of dysglycemia could be
predicted by anthropometric, lipid, and endocrine variables. Multivariate
logistic models showed that in non-PCOS women estimated average glucose (eAG)
was predicted by lower TSH levels (OR=0.39; p=0.045); fasting
glucose was predicted by increased T (OR=2.3). For PCOS, phenotype A,
eAG was predicted by decreased HDL-C (OR=0.17, p=0.023) and high
levels of free estradiol (OR=7.1, p<0.001). Otherwise, in PCOS,
phenotype D, eAG was predicted by higher levels of HDL-C. The current study
demonstrated that eAG was poorly predicted by anthropometric, lipid, and hormone
parameters. Nevertheless, without adding significant benefits, it was comparable
with other established markers of dysglycemia in women with different PCOS
phenotypes.
Reliability of Anaerobic Contributions during a Single Exhaustive
Knee-extensor Exercise
Authors: Luches-Pereira Gabriel , Kalva-Filho Carlos Augusto , Bertucci Danilo Rodrigues , de Carvalho Carlos Dellavechia , Barbieri Ricardo Augusto , Papoti Marcelo 
Published: November 2023

AbstractThe total anaerobic contribution (AC[La-]+PCr) is a valid and
reliable methodology. However, the active muscle mass plays an important role in
the AC[La-]+PCr determination, which might influence its
reliability. Thus, this study aimed to investigate the effects of two exhaustive
intensities on the reliability of the AC[La-]+PCr during a
one-legged knee extension (1L-KE) exercise. Thirteen physically active males
were submitted to a graded exercise to determine the peak power output (PPO) in
the 1L-KE. Then, two constant-load exercises were conducted to task failure at
100% (TTF100) and 110% (TTF110) of PPO,
and the exercises were repeated on a third day. The blood lactate accumulation
and the oxygen uptake after exercise were used to estimate the anaerobic lactic
and alactic contributions, respectively. Higher values of
AC[La-]+PCr were found after the TTF100
compared to TTF110 (p=0.042). In addition, no significant
differences (p=0.432), low systematic error (80.9 mL), and a
significant ICC (0.71; p=0.004) were found for
AC[La-]+PCr in the TTF100. However, an
elevated coefficient of variation was found (13.7%). In conclusion, we
suggest the use of the exhaustive efforts performed at 100% of the PPO
with the 1L-KE model, but its elevated individual variability must be carefully
considered in future studies.
Social and Health Information Platform: Piloting a Standards-Based, Digital Platform Linking Social Determinants of Health Data into Clinical Workflows for Community-Wide Use
Authors: Khurshid Anjum , Hautala Matti , Oliveira Eliel , Lakshminarayanan Vidya , Abrol Vishal , Collier Joshua , Rosseau Justin , Granado Linda , Nallaparaju Shreya , Mitra Kanishka , Sohail Rania 
Published: November 2023

Abstract
Background Social determinants of health (SDoH)a are increasingly recognized as a main contributor to clinical health outcomes, but the technologies and workflows within clinics make it difficult for health care providers to address SDoH needs during routine clinical visits.
Objectives Our objectives were to pilot a digital platform that matches, links, and visualizes patient-level information and community-level deidentified data from across sectors; establish a technical infrastructure that is scalable, generalizable, and interoperable with new datasets or technologies; employ user-centered codesign principles to refine the platform's visualizations, dashboards, and alerts with community health workers, clinicians, and clinic administrators.
Methods We used privacy-preserving record linkage (PPRL) tools to ensure that all identifiable patient data were encrypted, only matched and displayed with consent, and never accessed or stored by the data intermediary. We used limited data sets (LDS) to share nonidentifiable patient data with the data intermediary through a health information exchange (HIE) to take advantage of existing partner agreements, technical infrastructure, and community clinical data.
Results The platform was successfully piloted in two Federally Qualified Health Clinics by 26 clinic staff. SDoH and demographic data from findhelp were successfully linked, matched, and displayed with clinical and demographic data from the HIE, Connxus. Pilot users tested the platform using real-patient data, guiding the refinement of the social and health information platform's visualizations and alerts. Users emphasized the importance of visuals and alerts that gave quick insights into individual patient SDoH needs, survey responses, and clinic-level trends in SDoH service referrals.
Conclusion This pilot shows the importance of PPRL, LDS, and HIE-based data intermediaries in sharing data across sectors and service providers for scalable patient-level care coordination and community-level insights. Clinic staff are integral in designing, developing, and adopting health technologies that will enhance their ability to address SDoH needs within existing workflows without adding undue burdens or additional stress.