bluuebunny/crossref_metadata_2025_split huggingface dataset:
Host factors associated with vaginal microbiome structure in pregnancy: results from the ECHO cohorts
Authors: McKee Kimberly S. , Bassis Christine M. , Golob Jonathan , Palazzolo Beatrice , Sen Ananda , Comstock Sarah S. , Rosas-Salazar Christian , Stanford Joseph B. , O’Connor Thomas , Gern James E. , Paneth Nigel , Dunlop Anne L. , None Environmental Influences on Child Health Outcomes (ECHO) Pro 
Published: November 2023

Abstract

Using pooled vaginal microbiota data from pregnancy cohorts (N = 683 participants) in the Environmental Influences on Child Health Outcomes (ECHO) Program, we analyzed vaginal 16S rRNA gene amplicon sequences to identify clinical and demographic host factors that associate with vaginal microbiota structure in pregnancy bothwithinandacrossdiverse cohorts. Using PERMANOVA models, we assessed factors associated with vaginal community structure in pregnancy and examined whether host factors were conserved across populations and tested the independent and combined effects of host factors on vaginal community state types (CSTs) using multinomial logistic regression models. Demographic and social factors explained a larger amount of variation in the vaginal microbiome in pregnancy than clinical factors. After adjustment, only lower education remained a robust predictor ofL. inersdominant and Diverse CSTs (OR = 8.44, 95% CI = 4.06–17.6 and OR = 4.18, 95% CI = 1.88–9.26, respectively). In random forest models, we identified specific taxonomic features of host factors, particularly urogenital pathogens associated with pregnancy complications (Aerococcus christenseniiandGardnerella vaginalis) among other facultative anaerobes and key markers of community instability (L. iners). Sociodemographic factors were robustly associated with vaginal microbiota structure in pregnancy and should be considered as sources of variation in human microbiome studies.
Design, Creation, and Use of The Test Us Bank (TUB) COVID-19 Sample Biorepository
Authors: Broach John , Achenbach Chad , Behar Stephanie , O’Connor Laurel , Tarrant Seanan , Ferranto Julia , Wright Colton , Hartin Paul , Orwig Taylor , Nanavati Janvi , Kalibala Benedict , Woods Kelsey , Shaw Bernadette , Flahive Julie , Barton Bruce , Hafer Nathaniel , Herbert Carly , Fahey Nisha , Gibson Laura , Simin Karl , Kowalik Timothy , Ward Doyle , Mirza Agha W , Murphy Rob , Caputo Matthew , Buchholz Bryan , Fantasia Heidi , Koren Ainat , Marchand Lisa , Oludare Simisola , Sogade Felix , Ritland Dana , Davis Cedrice , Grenier Allen , Baron Christi , Brent Ellie , McKenney Jennifer Bacani , Elder Nancy , Michaels LeAnn , Ferrara Laura , Theron Grant , Palmer Zaida , Levy Barcey , Daly Jeanette , Parang Kim , Schmidt Megan , Buxton Denis , Heetderks William , Manabe Yukari C. , Soni Apurv , McManus David 
Published: November 2023

Abstract

Shortly after the first case of SARS-CoV-2 was diagnosed a public health emergency (PHE) was declared and a multi-agency response was initiated within the US federal government to create and propagate testing capacity. As part of this response, an unprecedented program designated Rapid Acceleration of Diagnostics (RADx) Tech was established by the National Institutes of Health (NIH) to facilitate the development of point-of-care tests for the COVID-19. The RADx Tech Clinical Studies Core (CSC), located at the University of Massachusetts Chan Medical School (UMass Chan), with partnering academic, private, and non-governmental organizations around the country, was tasked with developing clinical studies to support this work. This manuscript details development of a biorepository specifically focused on the collection and storage of samples designed for diagnostic platform development. It highlights the unified collection and annotation process that enabled gathering a diverse set of samples. This diversity encompasses the geography and backgrounds of the participants as well as sample characteristics such as variant type and RT-PCR cycle threshold (CT) value of the corresponding reference sample on a uniform clinical reference platform.
Robust compression and detection of epileptiform patterns in ECoG using a real-time spiking neural network hardware framework
Authors: Costa Filippo , Schaft Eline , Huiskamp Geertjan , Aarnoutse Erik , Klooster Maryse van ’t , Krayenbühl Niklaus , Ramantani Georgia , Zijlmans Maeike , Indiveri Giacomo , Sarnthein Johannes 
Published: November 2023

Abstract
Interictal Epileptiform Discharges (IED) and High Frequency Oscillations (HFO) in intraoperative electrocorticography (ECoG) may guide the surgeon by delineating the epileptogenic zone. We designed a modular spiking neural network (SNN) in a mixed-signal neuromorphic device to process the ECoG in real-time. We exploit the variability of the inhomogeneous silicon neurons to achieve efficient sparse and de-correlated temporal signal encoding. We interface the full-custom SNN device to the BCI2000 real-time framework and configure the setup to detect HFO and IED co-occurring with HFO (IED-HFO). We validate the setup on pre-recorded data and obtain HFO rates that are concordant with a previously validated offline algorithm (Spearman’s ρ = 0.75, p = 1e-4), achieving the same postsurgical seizure freedom predictions for all patients. In a remote on-line analysis, intraoperative ECoG recorded in Utrecht was compressed and transferred to Zurich for SNN processing and successful IED-HFO detection in real-time. These results further demonstrate how automated remote real-time detection may enable the use of HFO in clinical practice.
Design Method for Unbalanced Ternary Logic Family Based on Binary Memristors
Authors: Wang Xiaoyuan , Sun Yingfei , Zhou Jiawei , Chen Xinhui , Kang Sung Mo , Iu Herbert Ho- 
Published: November 2023

Abstract
This paper proposes a design method for unbalanced ternary logic family based on hybrid design of binary memristors and CMOS transistors, building on the foundational positive ternary logic circuits. By using the symmetry of negative and positive ternary logics, negative ternary TAND, TOR, TI, 1-3 decoder and 2-9 decoder are derived from the previously designed positive ternary basic logic gate circuits. Furthermore, negative ternary XOR, XNOR, 3-1 encoder, and 9-2 encoder are design-improved. For the first time, unbalanced ternary priority encoders is proposed, including a 3-1 priority encoder and a 9-2 priority encoder，of which the former is implemented with only 7 memristors. The functionalities of these circuits are demonstrated through LTSpice simulations. Finally, hardware experiments were performed on a stable 20×20 ZnO-based resistive switch array. Subsequent design of more complex digital logic circuits can benefit from this work.
Diatom-Inspired Silicification Process for Development of Green Flexible Silica Composite Aerogels
Authors: Maleki Hajar , Tan Valerie , Berg Florian 
Published: November 2023

Abstract
In this study, we have developed novel biomimetic silica composite aerogels and cryogels for the first time, drawing inspiration from the natural diatom's silicification process. Our biomimetic approach involved the modification of tyrosinase-mediated oxidized silk fibroin (SFO) surfaces with polyethyleneimine (PEI). This modification introduced ample amine groups onto the SF polymer, which catalyzed the silicification of the SFO-PEI gel surface with silicic acid. This process emulates the catalytic function of long-chain polyamines and silaffin proteins found in diatoms, resulting in a silica network structure on the primary SFO-PEI network gel's surface. The SFO-PEI gel matrix played a dual role in this process: 1) It provided numerous amine functional groups that directly catalyzed the silicification of silicic acid on the porous structure's exterior surface, without encapsulating the created silica network in the gel. 2) It served as a flexible mechanical support facilitating the creation of the silica network. As a result, the final ceramic composite exhibits a mechanically flexible nature (e.g., cyclic compressibility up to 80% strain), distinguishing it from conventional composite aerogels. By mimicking the diatom's silicification process, we were able to simplify the development of silica-polymer composite aerogels. It eliminates the need for surfactants, multi-step procedures involving solvent exchange, and gel washing. Instead, the reaction occurs under mild conditions, streamlining the composite aerogels fabrication process.
Later initiation of ECMO is associated with intracranial hemorrhage in COVID-19 patients
Authors: Saiydoun Gabriel , Bapst Blanche , Teiger Emmanuel , Folliguet Thierry , Gallet Romain , Palfi Stéphane , Mekantso-Dessap Armand , Mongardon Nicolas , Rancière Fanny , Faillot Matthieu 
Published: November 2023

Abstract
The occurrence of severe intracranial hemorrhage under venovenous extracorporeal membrane oxygenation (VV-ECMO) is a diagnostic and therapeutic challenge. The aim of this retrospective study is to determine factors associated with the occurrence of severe intracranial hemorrhage under VV-ECMO in patients with SARS-CoV-2 infection.
Among the 43 COVID-19 VV-ECMO patients included (seven women, median age: 55 years), eight patients(19%) presented an intracranial hemorrhage during VV-ECMO treatment, and 10 patients didn’t show any signs of intracranial hemorrhage on brain imaging. Twenty-five patients didn’t have imaging during or after VV-ECMO treatment. Kaplan-Meier analysis showed that the delay from hospital admission to VV-ECMO initiation was longer in patients with intracranial hemorrhage than in patients without intracranial hemorrhage(log-rank test P=0.03). Minute ventilation before cannulation was significantly lower in patients with intracranial hemorrhage compared to patients without intracranial hemorrhage: median(range)= 7.7L/min (3.9–14.0) vs. 12.1L/min(8.3–16.0);P=0.04. Arterial lactate values were higher in patients with intracranial hemorrhage compared to patients without intracranial hemorrhage: median(range)= 3.0mmol/L(1.1–6.6) vs. 1.9mmol/L(1.1–2.8);P=0.03.
The occurrence of intracranial hemorrhage was associated with a longer period from hospitalization to VV-ECMO initiation, as well as hypoventilation and higher arterial lactate levels before VV-ECMO treatment.
Self-Reporting Photodynamic Nanobody Conjugate for Precise and Sustainable Large-Volume Tumor Treatment
Authors: Fan Jiangli , Chen Yingchao , Xiong Tao , Peng Qiang , Du Jianjun , Sun Wen , Peng xiaojun 
Published: November 2023

Abstract

Nanobodies (Nbs), the smallest antigen-binding fragments with high stability and affinity, bring a new opportunity to improve the specificity of photosensitizers for tumor tissue in photodynamic therapy (PDT) through an active targeting strategy. Nonetheless, the rapid metabolism of Nbs in vivo restricts the accumulation and retention of the photosensitizer at the tumor site, especially in large-volume tumors. Herein, we developed photodynamic conjugates, MNB-Pyra Nbs, through site-specific modification of 7D12 Nbs with the type I photosensitizer MNB-Pyra in a 1:2 ratio. The π − π stacking interactions of MNB-Pyra molecules within the conjugate causes fluorescence quenching, while the photosensitizer with long-term retention could be released by reactive oxygen species (ROS) cleavage, which is accompanied by fluorescence recovery for self-reporting. Moreover, the conjugation of MNB-Pyra and Nbs greatly improved the metabolism of the benzophenothiazine photosensitizer in vivo, leading to the clearance of MNB-Pyra Nbs in 24 h without illumination. Ultimately, a single dose of MNB-Pyra Nbs demonstrated highly effective tumor suppression (tumor inhibition rate > 95%) with high biosafety in the large-volume tumor model after three rounds of PDT. This self-reporting photodynamic nanobody conjugate is expected to promote the development of personalized precision PDT.
Pancancer Analysis of the Prognostic and immunological Role of FANCD2: A Potential Target for Carcinogenesis and Survival
Authors: zhao zedan , Wang Ruyu , Wang Ruixue , Song Jialing , Ma Fengjun , Pan Huafeng , Gao Cuiyun , Wang Deqiang , Chen Xuemei , Fan Xiangzhen 
Published: November 2023

Abstract

Recent evidence has shed light on the significant role of FANCD2 in cancer initiation, development, and progression. However, a comprehensive pan-cancer analysis of FANCD2 has been lacking. In this study, we have conducted a thorough investigation into the expression profiles and prognostic significance of FANCD2, as well as its correlation with clinicopathological parameters and immune cell infiltration, using advanced bioinformatic techniques. The results demonstrate that FANCD2 is significantly upregulated in various common cancers and is associated with prognosis. Notably, higher expression levels of FANCD2 are linked to poor overall survival, as indicated by Cox regression and Kaplan-Meier analyses. Additionally, we have observed a decrease in the methylation of FANCD2 DNA in some cancers, and this decrease is inversely correlated with FANCD2 expression. Genetic alterations in FANCD2 predominantly manifest as mutations, which are associated with overall survival, disease-specific survival, disease-free survival, and progression-free survival in certain tumor types. Moreover, FANCD2 exhibits a strong correlation with infiltrating cell levels, immune checkpoint genes, tumor mutation burden (TMB), and microsatellite instability (MSI). Enrichment analysis further highlights the potential impact of FANCD2 on Fanconi anemia (FA) pathway and cell cycle regulation. Through this comprehensive pan-cancer analysis, we have gained a deeper understanding of the functions of FANCD2 in oncogenesis and metastasis across different types of cancer.
Fisetin suppresses chondrocyte senescence and attenuates osteoarthritis progression by targeting SIRT6
Authors: Wang Xuezhong , Li Xuyang , Zhou Jianlin , Lei Zheng , Yang Xiaoming 
Published: November 2023

Abstract
Background
Osteoarthritis (OA), the most common type of arthritis, is a highly prevalent age-related joint disease particularly in subjects over 65 years old. The chronic rise of senescent cells closely correlates with age-related diseases including OA, and the senescence-associated secretory phenotype (SASP) is implicated in the pathogenesis of OA cartilage degeneration. Sirtuin 6 (SIRT6) is probable to be a key senescence-related regulator. Fisetin (FST), a natural flavonol of the flavonoid family, is recommended to be a senolytic that extends health and lifespan. However, the potential chondroprotective effects of FST on OA rats remain largely unclarified. This study aimed to investigate the ameliorative effects of FST on OA joint cartilage and the relationship with SIRT6, and the detailed mechanisms from both anti-inflammatory and anti-senescent perspectives.
Methods
Rats were subjected to destabilization of the medial meniscus (DMM) surgery to induce the experimental OA model in vivo. Chondrocytes treated with IL-1β were utilized to mimic the OA cell model in vitro. Intra-articular injection of FST, OSS_128167 (OSS, SIRT6 inhibitor), and MDL800 (MDL, SIRT6 agonist) in vivo or incubation with IL-1β-induced rat chondrocytes in vitro were performed to determine the effects of FST on OA and the link with SIRT6.
Results
SIRT6 level was negatively correlated with OA severity. SIRT6 downregulation was validated in joint cartilages of DMM rats and IL-1β-treated chondrocytes. Of note, We demonstrated FST could activate SIRT6. Both the administration of FST and activation of SIRT6 using MDL rescued cartilage erosion, decreased extracellular matrix (ECM) degradation, prevented cartilage from apoptosis, and improved detrimental senescence-related phenotype. The alleviative effects of FST against inflammation, ECM degradation, apoptosis, and senescence were also confirmed in IL-1β-stimulated chondrocytes.
Conclusion
SIRT6 loss occurs in articular cartilage in the pathogenesis of OA, which is linked to aging. FST attenuates injury-induced aging-related phenotype changes in chondrocytes by targeting SIRT6.
Digital Twin-Driven Lifecycle Management for Motorized Spindle
Authors: Kai-Guo Fan , Liu Jiahui 
Published: November 2023

Abstract

A digital twin-driven lifecycle management system for motorized spindle is proposed to monitor the lifespan of motorized spindle. The lifecycle management system is designed and developed based on the combined programming of MATLAB, ANSYS and LabVIEW. The lifespan prediction models are built according to the digital twin data of thermal characteristics of motorized spindle. The digital twin for thermal characteristics is realized through correcting the thermal boundary conditions according to the thermal boundary correction models which are established according to the measured and simulated temperatures at thermal key points. The temperature domain model of cooling channel is constructed to monitor the working status of the cooling system. The experimental results show that the digital twin-driven lifecycle management system can effectively monitor the status and remaining lifespan of the motorized spindle, which provides a basis for lifecycle management of motorized spindle.
The use of shear wave elastography in the diagnosis of erectile dysfunction: a feasibility study
Authors: Zhang Da-Kun , Li Yunlin , Guan Jing-Bo , Li Zhi-Xuan , Sun Min 
Published: November 2023

Abstract

The aim of this study was to explore the value of SWE in evaluating vascular and nonvascular erectile dysfunction. In this study, ED patients enrolled (n = 114) received SWE and PCUD exams. The PSV and EDV were used as the classification standard. The performance of the SWE was assessed with the receiver operating characteristic curve, sensitivity and specificity. The rigidity alterations of corpus cavernosum penis with age was also investigated. SWE values of CCP before ICI negatively correlated with age of patients in vascular ED group (r = -0.288, P<0.05). In erectile or flaccid state, the SWE value of vascular ED was significantly larger than non-vascular ED. When the cut-off value for SWE values of CCP 0.88 m/s in erectile state and 2.32 m/s in flaccid state, the areas under the ROC curve were 0.700 (sensitivity: 77.78%, specificity: 60.00%) and 0.612(sensitivity: 68.52%, specificity: 51.67%) in erectile or flaccid state, respectively. This study provides preliminary evidence that SWE in flaccid state could be non-invasive methods used to moderate predict vascular ED.
Bacterial succession during terrestrial and marine decomposition in fish and pig models to estimate Post- Mortem Interval: Death and Decomposition
Authors: Zedi Saniya , Khandeparkar Rakhee , Render Riya , Gracias Magaly 
Published: November 2023

Abstract

Marine forensics is emerging rapidly with an aim to legally protect the aquatic wild life from pollution and anthropogenic activities along with scientific investigation of human and non-human death in any sort of water body. The fate of a carcass is not well understood in marine system yet a large amount of body deposition and recreation death could be seen. The study is conducted to identify time-dependent microbial biomarkers of decomposition in non-human models (Fish and Pig) to determine Post Mortem Interval (PMI). Shift in the bacterial community from fresh stage to active decay stage in both models till skeletisation on terrestrial and marine environment was observed, which was supported by change in nutrient profile of the area keeping a note of traditional changes like early death changes, livor, algor, rigor mortis and entomological evidences. Bacteria from genusAcinetobacter, Enterobacter, Citrobacter, Pantoea, Aeromonas, Klebsiella, Wohlfahrtiimonas, Brachybacterium, Myroides, Bacillus, Kurthia, Staphylococcus, MetalysinibacillusandPlanococcuswere isolated from different organs of fish including some pathogenic bacteria likeKlebsiella pneumonia, Staphylococcus arlettaeandBacillus cereuspresent in the gills, tissue, liver andClostridium perfringensfrom pig. In pig during marine decomposition bacteria of genusKlebsiella, Cytobacillus, Bacillus, Pseudomonas, Pseudoalteromonas, Shewanella, Clostridium, Tenacibaculum, Aeromonas, andPsychrobacterwere isolated. The bacterial community from both the models were identified using 16s rRNA gene sequencing. Much attention has been given to dissolved organic matter (DOM) and particulate organic matter (POM) during the early stages of decomposition in aquatic environment which attracts scavangers and microbes, their enhanced breakdown activity is depicted by the increased ammonia levels and high phosphorus release in water. Terrestrial skeletonization is achieved in 7 days on contrary marine environment pose a great challenge due to high scavenging activity resulted in loss of tissue in 3 days merely during the study and it is observed that the decomposition studies in marine environment greatly rely on the ecosystem of the area especially the allochthonous and autochthonous bacteria.
Phytochemical compositions and in vitro anticancer effects of ethanolic extracts from Syrian hawthorn fruit on the human breast cell line MDA-MB-231
Authors: assaad Thaer , Al-Mardini Mohammad Amer , darouish Manal , Yousif Manhal , Youssef Aeham , nasser Anas , Mohammed Roua , Zahra Rema , Abass Layana , moulla Ali , assaad Lana 
Published: November 2023

Abstract
Hawthorn is an important medicinal plant among other wide spread herbal species. Only few studies have been performed to exhibit therapeutic effects of hawthorn extracts on cancer cell lines. Herein, three types of hawthorn fruits were collected from different places in Syria, samples were air dried until reaching a constant dry weight and then powdered. Hawthorn bioactive compounds were extracted from the powder with absolute ethanol. Qualitative phytochemical analysis confirmed the presence of flavonoids, alkaloids, tannins, saponins and glycosides in the three types of hawthorn fruits. The red hawthorn contained anthracene derivatives, unlike both yellow and green hawthorns. FT-IR analysis revealed the presence of functional groups such as alcohols, alkanes, alkyl halides, aromatic groups and alkenes. UV‒Visible analysis represents the absorption spectrum and shows a broad absorption band at 350–400 nm and a peak at approximately 300 nm. Chromatography–mass spectrometry (GC/MS) analysis showed 13, 5 and 22 chemical constituents representing an average of 100% in the EOs of yellow, green and red hawthorn respectively. Cell proliferation assessment results showed that hawthorn inhibits cell viability of MDA-MB-231 cancer cells lines, which was strongly related to increasing concentration of hawthorn.