bluuebunny/crossref_metadata_2025_split huggingface dataset:
Impact of cancer and other causes of death on mortality of cancer patients: A study based on Japanese population‐based registry data
Authors: Charvat Hadrien , Fukui Keisuke , Matsuda Tomohiro , Katanoda Kota , Ito Yuri 
Published: June 2023

AbstractCancer registry data provide a very important source of information for improving our understanding of the epidemiology of various cancers. In this work, we estimated the 5‐year crude probabilities of death from cancer and from other causes for five common cancers, namely stomach, lung, colon‐rectum, prostate and breast, in Japan, using population‐based registry data. Based on data on 344 676 patients diagnosed with one of these cancers between 2006 and 2008 in 21 prefectures participating in the Monitoring of Cancer Incidence in Japan (MCIJ) and followed‐up for at least 5 years, we used a flexible excess hazard model to compute the crude probabilities of death for different combinations of sex, age and stage at diagnosis. For tumours diagnosed at the distant stage, as well as for regional lung tumours, the vast majority of deaths at 5 years in cancer patients were attributable to the disease itself (although this proportion was only around 60% in older prostate cancer patients). For localised and most regional tumours, the impact of other causes of death on the total mortality increased with age at diagnosis, especially for localised breast, colorectal and gastric cancer. By allowing the partition of the mortality experience of cancer patients into a cancer‐ and an other‐cause‐specific component, crude probability of death estimates provide insight into how the impact of cancer on mortality might differ among populations with different background mortality risks. This might be useful for informing discussions between clinicians and patients about treatment options.
Evaluation of pregnancy and neonatal outcomes according to the phenotypic types of polycystic ovary syndrome: A prospective study
Authors: Eralp Berat , Ibanoglu Mujde Can , Engin‐Ustun Yaprak 
Published: June 2023

AbstractObjectiveWe aimed to compare pregnancy and neonatal outcomes in the phenotypic subtypes of patients with polycystic ovary syndrome (PCOS).MethodsThis prospective cohort included the patients with PCOS (n = 121) diagnosed according to the presence of androgen excess, ovulatory dysfunction, and/or polycystic ovary morphology and healthy controls (n = 125). We stratified PCOS as phenotype A (n = 45), phenotype B (n = 8), phenotype C (n = 32) and phenotype D (n = 35) and followed throughout pregnancy, comparing their outcomes.ResultsThe study population had a mean age of 28.7 ± 4.9 years and a mean BMI of 31.6 kg/m2 with no difference between the groups. Primary cesarean deliveries were significantly more common in PCOS patients (23.3%) than in the control group (17.6%, P = 0.021). The phenotype A group had significantly higher rates of gestational diabetes mellitus (GDM) (42.2%, P < 0.001) and fetal macrosomia (14.6%, P = 0.002) compared with the control group (4.8% and 0.8%m respectively). We detected a significantly lower rate of normal risk score on the double screening test in the PCOS group (59.0%) than in the control group (75.4%) and in the other groups (P = 0.001).ConclusionThe rates of GDM, fetal macrosomia, and cesarean section were higher in the PCOS group, depending on the phenotype. We observed changes in risk calculation according to phenotypic types at aneuploidy screening.
ViWrap: A modular pipeline to identify, bin, classify, and predict viral–host relationships for viruses from metagenomes
Authors: Zhou Zhichao , Martin Cody , Kosmopoulos James C. , Anantharaman Karthik 
Published: June 2023

AbstractViruses are increasingly being recognized as important components of human and environmental microbiomes. However, viruses in microbiomes remain difficult to study because of the difficulty in culturing them and the lack of sufficient model systems. As a result, computational methods for identifying and analyzing uncultivated viral genomes from metagenomes have attracted significant attention. Such bioinformatics approaches facilitate the screening of viruses from enormous sequencing data sets originating from various environments. Although many tools and databases have been developed for advancing the study of viruses from metagenomes, there is a lack of integrated tools enabling a comprehensive workflow and analysis platform encompassing all the diverse segments of virus studies. Here, we developed ViWrap, a modular pipeline written in Python. ViWrap combines the power of multiple tools into a single platform to enable various steps of virus analyses, including identification, annotation, genome binning, species‐ and genus‐level clustering, assignment of taxonomy, prediction of hosts, characterization of genome quality, comprehensive summaries, and intuitive visualization of results. Overall, ViWrap enables a standardized and reproducible pipeline for both extensive and stringent characterization of viruses from metagenomes, viromes, and microbial genomes. Our approach has flexibility in using various options for diverse applications and scenarios, and its modular structure can be easily amended with additional functions as necessary. ViWrap is designed to be easily and widely used to study viruses in human and environmental systems. ViWrap is publicly available via GitHub (https://github.com/AnantharamanLab/ViWrap). A detailed description of the software, its usage, and interpretation of results can be found on the website.
Sampling volume assessment for wearable multimodal optical diagnostic device
Authors: V. Zharkikh Elena , V. Dremin Viktor , V. Dunaev Andrey 
Published: June 2023

AbstractThe process and results of numerical Monte Carlo simulation of optical radiation propagation in laser Doppler flowmetry (LDF) and fluorescence spectroscopy (FS) channels of a wearable diagnostic multimodal device are described in this paper. To achieve the goal, a multilayer skin model with different parameters of blood and melanin content and different distances between sources and radiation receivers was designed. The changes in the sampling (diagnostic) volume depending on the anatomical features of the biological tissues, as well as on the technical parameters of the device were shown. Depending on the scattering media optical properties and the source‐detector configuration of the device, the diagnostic volume can range from 2 to 7 mm3. The obtained results allow the formation of specialized medical and technical requirements for wearable multimodal devices implementing LDF and FS channels.
Extracellular vesicles from human plasma dampen inflammation and promote tissue repair functions in macrophages
Authors: Adamczyk Alan M. , Leicaj María Luz , Fabiano Martina Paula , Cabrerizo Gonzalo , Bannoud Nadia , Croci Diego O. , Witwer Kenneth W. , Remes Lenicov Federico , Ostrowski Matías , Pérez Paula Soledad 
Published: June 2023

AbstractAlthough inflammation is a vital defence response to infection, if left uncontrolled, it can lead to pathology. Macrophages are critical players both in driving the inflammatory response and in the subsequent events required for restoring tissue homeostasis. Extracellular vesicles (EVs) are membrane‐enclosed structures released by cells that mediate intercellular communication and are present in all biological fluids, including blood. Herein, we show that extracellular vesicles from plasma (pEVs) play a relevant role in the control of inflammation by counteracting PAMP‐induced macrophage activation. Indeed, pEV‐treatment of macrophages simultaneously with or prior to PAMP exposure reduced the secretion of pro‐inflammatory IL‐6 and TNF‐α and increased IL‐10 response. This anti‐inflammatory activity was associated with the promotion of tissue‐repair functions in macrophages, characterized by augmented efferocytosis and pro‐angiogenic capacity, and increased expression of VEGFa, CD300e, RGS2 and CD93, genes involved in cell growth and tissue remodelling. We also show that simultaneous stimulation of macrophages with a PAMP and pEVs promoted COX2 expression and CREB phosphorylation as well as the accumulation of higher concentrations of PGE2 in cell culture supernatants. Remarkably, the anti‐inflammatory activity of pEVs was abolished if cells were treated with a pharmacological inhibitor of COX2, indicating that pEV‐mediated induction of COX2 is critical for the pEV‐mediated inhibition of inflammation. Finally, we show that pEVs added to monocytes prior to their M‐CSF‐induced differentiation to macrophages increased efferocytosis and diminished pro‐inflammatory cytokine responses to PAMP stimulation. In conclusion, our results suggest that pEVs are endogenous homeostatic modulators of macrophages, activating the PGE2/CREB pathway, decreasing the production of inflammatory cytokines and promoting tissue repair functions.
Power amplifier circuit defect detection based on improved PatchSVDD
Authors: Xie Zhonghui , Kong Wa , Zhou Xinyu , Zhang Wence , Zhong Yujie , Xia Jing 
Published: June 2023

AbstractIn the manufacturing process of power amplifier (PA), various defects on the circuit surface will seriously affect the circuit performance and its operation. To solve the above problems, this article proposes a circuit defect detection method based on improved patch‐based support vector data description algorithm (Patch SVDD), which uses contrastive learning to enhance the feature extraction ability of neural network. An image calibration algorithm is used for calibration preprocessing to enhance the robustness of the model. The Euclidean distance between a query image patch and its nearest normal patch is defined to be an anomaly score. For verification, three defects in the PA circuit, including components missing, solder contamination and component orientation dislocation, were detected. The experimental results show that, compared with conventional method, the area under receiver operating characteristic (AUROC) of the improved anomaly detection model increased from 90.1% to 95.1%, which improves the detection accuracy effectively.
Understanding the extremely wet autumn over West China in 2017 from intraseasonal oscillation perspective
Authors: Guo Quanling , Wang Lu , Ma Jing , Sun Ming , Cheng Yifeng , Zhou Xuan 
Published: June 2023

AbstractWest China experienced an extremely wet autumn in 2017, and the amount of September–October precipitation is the greatest during 1961–2018. This study explored the physical processes responsible for two primary intraseasonal precipitation events which contribute greatly to such an extremely wet season. The first event peaking in early September is induced by the southward movement of a frontal system from the northern China, which is attributed to the southward displacement of an intraseasonal anticyclonic anomaly. The northerly anomaly associated with the anticyclone advects cold air into West China and thus triggers frontal precipitation. The second event peaking in early October is related to the northward shift and intensification of an intraseasonal anticyclonic anomaly centred over the northwestern Pacific Ocean. The southerly anomaly along the western flank of the anticyclone transports moisture to West China and thus triggers precipitation. The different initiation processes for the two precipitation events may be due to the distinct dynamical and thermal‐dynamical conditions in September and October. West China has sufficient moisture but less dynamical disturbances in September, while it has adequate dynamical disturbances but less moisture in October.
A novel antibacterial compound decreases MRSA biofilm formation without the use of antibiotics in a murine model
Authors: Bouloussa Houssam , Durand Zoe , Gibon Emmanuel , Chen Antonia F. , Grant Matthew , Saleh‐Mghir Azzam , Mirza Mohsin , Stutzman Bradley , Vergari Claudio , Yue James , Anzala Nelson , Bonnot Dorian , Albac Sandrine , Bouloussa Othman , Croisier Delphine 
Published: June 2023

AbstractDespite significant advancements in material science, surgical site infection (SSI) rates remain high and prevention is key. This study aimed to demonstrate the in vivo safety and antibacterial efficacy of titanium implants treated with a novel broad‐spectrum biocidal compound (DBG21) against methicillin‐resistant Staphylococcus aureus (MRSA). Titanium (Ti) discs were covalently bound with DBG21. Untreated Ti discs were used as controls. All discs were implanted either untreated for 44 control mice or DBG21‐treated for 44 treated mice. After implantation, 1 × 107 colony forming units (CFU) of MRSA were injected into the operating site. Mice were killed at 7 and 14 days to determine the number of adherent bacteria (biofilm) on implants and in the peri‐implant surrounding tissues. Systemic and local toxicity were assessed. At both 7 and 14 days, DBG21‐treated implants yielded a significant decrease in MRSA biofilm (3.6 median log10 CFU [99.97%] reduction [p < 0.001] and 1.9 median log10 CFU [98.7%] reduction [p = 0.037], respectively) and peri‐implant surrounding tissues (2.7 median log10 CFU/g [99.8%] reduction [p < 0.001] and 5.6 median log10 CFU/g [99.9997%] reduction [p < 0.001], respectively). There were no significant differences between control and treated mice in terms of systemic and local toxicity. DBG‐21 demonstrated a significant decrease in the number of biofilm bacteria without associated toxicity in a small animal implant model of SSI. Preventing biofilm formation has been recognized as a key element of preventing implant‐related infections.
Circ‐MALAT1 accelerates cell proliferation and epithelial mesenchymal transformation of colorectal cancer through regulating miR‐506‐3p/KAT6B axis
Authors: Yang Feng‐Shuai , Gong Shuang‐Xi , Qiu Dong‐Da 
Published: June 2023

AbstractColorectal cancer (CRC) is a prevalent malignant tumor of the digestive tract. Circular RNAs may play important roles in the progression of CRC. In this study, we investigated the roles and mechanisms of action of circ‐MALAT1 in CRC. Gene expression and protein abundance were determined using qRT‐PCR and western blot, respectively. Cell proliferation and migration were assessed by MTT, clone formation, and wound‐healing assays. The interactions among the long non‐coding RNA metastasis‐associated lung adenocarcinoma transcript 1 (circ‐MALAT1), miR‐506‐3p, and lysine acetyltransferase 6B (KAT6B) were predicted using the StarBase software and confirmed by the luciferase activity assay. Circ‐MALAT1 and KAT6B were upregulated, while miR‐506‐3p was downregulated in CRC cells. We validated that knocking down of circ‐MALAT1 suppressed proliferation, migration, and epithelial–mesenchymal transition (EMT) of CRC cells, and these effects were abolished by miR‐506‐3p downregulation or KAT6B sufficiency. Our study suggests that circ‐MALAT1 could sponge miR‐506‐3p to regulate the expression of KAT6B. Moreover, KAT6B sufficiency could neutralize miR‐506‐3p‐dependent growth arrest, migration, and EMT. Circ‐MALAT1 promotes cell proliferation, migration, and EMT of CRC cells via the miR‐506‐3p/KAT6B axis, thereby acting as a novel potential therapeutic target for the treatment of colorectal cancer.
Parametrically Driven Inertial Sensing in Chip‐Scale Optomechanical Cavities at the Thermodynamical Limits with Extended Dynamic Range
Authors: Flor Flores Jaime Gonzalo , Yerebakan Talha , Wang Wenting , Yu Mingbin , Kwong Dim‐Lee , Matsko Andrey , Wong Chee Wei 
Published: June 2023

AbstractRecent scientific and technological advances have enabled the detection of gravitational waves, autonomous driving, and the proposal of a communications network on the Moon (Lunar Internet or LunaNet). These efforts are based on the measurement of minute displacements and their corresponding force transduction, which enables acceleration, velocity, and position determination for navigation. State‐of‐the‐art accelerometers use capacitive or piezoresistive techniques and micro‐electromechanical systems (MEMS) via integrated circuit (IC) technologies to drive transducers and convert their output for electric readout. In recent years, laser optomechanical transduction and readout have enabled highly sensitive detection of motional displacement. Here the theoretical framework is further examined for the novel mechanical frequency readout technique of optomechanical transduction when the sensor is driven into oscillation mode. Theoretical and physical agreements are demonstrated, and the most relevant performance parameters are characterized by a device with a 1.5 mg Hz−1acceleration sensitivity, a 2.5 fm Hz−1/2displacement resolution corresponding to a 17.02 µg Hz−1/2force‐equivalent acceleration, and a 5.91 Hz nW−1power sensitivity, at the thermodynamical limits. In addition, a novel technique is presented for dynamic range extension while maintaining the precision sensing sensitivity. This inertial accelerometer is integrated on‐chip and enabled for packaging, with a laser‐detuning‐enabled approach.
Hydrogels as Scaffolds in Bone‐Related Tissue Engineering and Regeneration
Authors: Jurczak Przemyslaw , Lach Slawomir 
Published: June 2023

AbstractSeveral years have passed since the medical and scientific communities leaned toward tissue engineering as the most promising field to aid bone diseases and defects resulting from degenerative conditions or trauma. Owing to their histocompatibility and non‐immunogenicity, bone grafts, precisely autografts, have long been the gold standard in bone tissue therapies. However, due to issues associated with grafting, especially the surgical risks and soaring prices of the procedures, alternatives are being extensively sought and researched. Fibrous and non‐fibrous materials, synthetic substitutes, or cell‐based products are just a few examples of research directions explored as potential solutions. A very promising subgroup of these replacements involves hydrogels. Biomaterials resembling the bone extracellular matrix and therefore acting as 3D scaffolds, providing the appropriate mechanical support and basis for cell growth and tissue regeneration. Additional possibility of using various stimuli in the form of growth factors, cells, etc., within the hydrogel structure, extends their use as bioactive agent delivery platforms and acts in favor of their further directed development. The aim of this review is to bring the reader closer to the fascinating subject of hydrogel scaffolds and present the potential of these materials, applied in bone and cartilage tissue engineering and regeneration.
Integral Ricci curvature and the mass gap of Dirichlet Laplacians on domains
Authors: Ramos Olivé Xavier , Rose Christian , Wang Lili , Wei Guofang 
Published: June 2023

AbstractWe obtain a fundamental gap estimate for classes of bounded domains with quantitative control on the boundary in a complete manifold with integral bounds on the negative part of the Ricci curvature. This extends the result of Oden, Sung, and Wang [Trans. Amer. Math. Soc. 351 (1999), no. 9, 3533–3548] to ‐Ricci curvature assumptions, . To achieve our result, it is shown that the domains under consideration are John domains, what enables us to obtain an estimate on the first nonzero Neumann eigenvalue, which is of independent interest.
Improving high‐tech enterprises' new product development performance through digital transformation: A configurational analysis based on fuzzy‐set qualitative comparative analysis (fsQCA)
Authors: Liu Jingyan , Yang Yiyan 
Published: June 2023

AbstractThis paper investigates conditional configurations for improving high‐tech enterprises' new product development (NPD) performance under complex environment of digital era in China. The results indicate that digital transformation is neither sufficient nor necessary for high NPD performance but a significant component of those configurations for high NPD performance. Through the fuzzy‐set qualitative comparative analysis (fsQCA) approach, four configurations for high NPD performance and four configurations for non‐high NPD performance are generated from complex nonlinear interactions among five antecedent conditions of NPD performance. Our findings enrich the literature on NPD performance and provide references on enterprises' decision making on digital transformation.
Clinical report and genetic analysis of a neonate with genitourinary and/or brain malformation syndrome caused by a non‐coding sequence variant of PPP1R12A
Authors: Diao Yanxia , Sun Weiwei , Zhang Zhen , Zhao Bing , Chen Xin 
Published: June 2023

AbstractBackgroundGenitourinary and/or brain malformation syndrome (GUBS) is a recently discovered syndrome involving abnormalities of the neurological or urogenital system. PPP1R12A may be the pathological gene causing this syndrome. Currently, to our knowledge, there is only one study related to GUBS in the world. Here, we report a clinical case of a Chinese newborn with congenital micropenis caused by a non‐coding sequence pathogenic variant of PPP1R12A, providing additional evidence on genetic causes of genital malformation.MethodsThe genetic cause of the patient's malformation was detected using trio‐whole exome sequencing and Sanger sequencing, and reverse transcription‐PCR analysis was performed by constructing the minigene mutant plasmid in vitro.ResultsGenetic testing revealed a novel heterozygous variant, c.2666+3A>G, of the PPP1R12A gene of the patient. The parents at this site were wild‐type, indicating that this might be a de novo variant. The minigene experiment showed that the c.2666+3A>G plasmid led to the deletion of 17 bp in exon 20, and a new mRNA product c.2650_2666del (p.Thr884IleTer2) with skipping of exon 20 was produced. This may lead to PPP1R12A haploinsufficiency and cause biological harm.ConclusionsTo our knowledge, this is the first clinical study on a rare variant of PPP1R12A in the Chinese population. The c.2666+3A>G may lead to external genitalia malformation, such as congenital micropenis in male neonates. The results of this study further verified the correlation between GUBS and PPP1R12A haploinsufficiency and revealed the important role of a non‐coding sequence variant in the pathogenesis of the disease.
Zebrafish Danio rerio exhibit positive growth profiles when fed dietary yeast and bacterial-based single-cell protein as a replacement for fish protein hydrolysate
Authors: Williams Michael B. , Lawrence Addison L. , Chehade Sophie B. , Yuan Yuan , Fowler Adele L. , Barry Robert J. , Powell Mickie L. , Watts Stephen A. 
Published: June 2023

Abstract

Objective
The value of Zebrafish Danio rerio as a preclinical biomedical model has increased as nutritionally complete diets are being developed. Consequently, nutrients and nutrient sources can be used in evaluating the health status of Zebrafish, providing information that can be translated to human health. We have investigated the impact of commercially produced bacterial (MRD-Pro) and yeast (DY-Pro) single-cell protein sources in formulated Zebrafish diets.

Methods
Thirty-five days after fertilization Zebrafish were randomized to one of five dietary treatments including FPH100 (a control diet with primarily fish protein hydrolysate [FPH] as the protein source), MRD50 and MRD100 (diets that replaced half or all of the FPH with MRD, a bacterial protein), or DY50 and DY100 (diets that replaced half or all of the FPH with DY, a yeast protein) for 8 weeks (n = 8 tanks/diet treatment, 14 fish/tank).

Result
Female terminal wet weight was the same among all diets; however, male terminal wet weight was increased in fish consuming MRD diets. In addition, carcass lipid content was significantly lower in females consuming the DY and MRD diets than those fed FPH. Male lipid content was the same among all diets.

Conclusion
Results demonstrate that single-cell protein sources are suitable replacements for FPH and, in female populations, may impart health benefits related to lean matter production and reduced adiposity.