bluuebunny/crossref_metadata_2025_split huggingface dataset:
Multi-class semantic segmentation of breast tissues from MRI images using U-Net based on Haar wavelet pooling
Authors: Yang Kwang Bin , Lee Jinwon , Yang Jeongsam 
Published: January 2023

Abstract
MRI images for breast cancer diagnosis are inappropriate for reconstructing the natural breast shape in a standing position because they are taken in a lying position. Some studies have proposed methods to present the breast shape in a standing position using ordinary differential equation of the finite element method. However, it is difficult to obtain meaningful results because breast tissues have different elastic moduli. This study proposed a multi-class semantic segmentation method for breast tissues to reconstruct breast shape using U-Net based on Haar wavelet pooling. First, a dataset was constructed by labeling the skin, fat, and fibro-glandular tissues and the background from MRI images taken in a lying position. Next, multi-class semantic segmentation was performed using U-Net based on Haar wavelet pooling to improve the segmentation accuracy for breast tissues. The U-Net based on Haar wavelet pooling effectively extracted breast tissue features while reducing information loss of the image in a subsampling stage using multiple sub-bands. In addition, the proposed network is robust to overfitting. The proposed network showed an mIOU of 87.48 for segmenting breast tissues. The proposed networks showed high-accuracy segmentation for breast tissue with different elastic moduli to reconstruct the natural breast shape.
Perceived parenting before adolescence is associated with adult attachment among Japanese women during the perinatal period: a path models comparison
Authors: Zain Ekachaeryanti , Fukui Naoki , Watanabe Yuichiro , Hashijiri Koyo , Motegi Takaharu , Ogawa Maki , Egawa Jun , Someya Toshiyuki 
Published: January 2023

Abstract
This study aimed to determine how paternal and maternal parenting before adolescence affects adult attachment to a partner during the perinatal period, using three different models of attachment. We used the Parental Bonding Instrument (PBI) and the Relationship Questionnaire (RQ) to examine perceived parenting practices and adult attachment styles, respectively. The participants included 4586 Japanese women who were pregnant and who had given birth, up until one month after childbirth. We performed structural equation modeling analysis between PBI and RQ scores with three different category models, including the four-category model (secure, fearful, preoccupied, and dismissing attachment) as Model 1, the two-category model (model of the self and others) as Model 2, and the single-category model (total attachment style) as Model 3. Models 1 and 2 showed a good fit. Both path models showed a significant association between adult attachment style and perceived paternal and maternal parenting before adolescence, where high care and low overprotection from both paternal and maternal parents predicted adult attachment. Our findings indicate that attachment styles are best described using the four-category and two-category models, suggesting that both paternal and maternal overprotection and care are important in forming adult attachment with a partner during the perinatal period.
Generation of rat offspring using spermatids produced through in vitro spermatogenesis
Authors: Matsumura Takafumi , Katagiri Kumiko , Yao Tatsuma , Ishikawa-Yamauchi Yu , Nagata Shino , Hashimoto Kiyoshi , Sato Takuya , Kimura Hiroshi , Shinohara Takashi , Sanbo Makoto , Hirabayashi Masumi , Ogawa Takehiko 
Published: January 2023

Abstract
An in vitro spermatogenesis method using mouse testicular tissue to produce fertile sperm was established more than a decade ago. Although this culture method has generally not been effective in other animal species, we recently succeeded in improving the culture condition to induce spermatogenesis of rats up to the round spermatid stage. In the present study, we introduced acrosin-EGFP transgenic rats in order to clearly monitor the production of haploid cells during spermatogenesis in vitro. In addition, a metabolomic analysis of the culture media during cultivation revealed the metabolic dynamics of the testis tissue. By modifying the culture media based on these results, we were able to induce rat spermatogenesis repeatedly up to haploid cell production, including the formation of elongating spermatids, which was confirmed histologically and immunohistochemically. Finally, we performed a microinsemination experiment with in vitro produced spermatids, which resulted in the production of healthy and fertile offspring. This is the first demonstration of the in vitro production of functional haploid cells that yielded offspring in animals other than mice. These results are expected to provide a basis for the development of an in vitro spermatogenesis system applicable to many other mammals.
Evaluation of The Treatment Outcome of Cleft Palate Patients Treated with Differential Opening Expander with Alt-RAMEC Protocol and Facemask : (a cohort clinical study )
Authors: Khalil Sarah S , Salama Ahmed E. , Mohammad Maha M. , Awad Maiada M 
Published: January 2023

Abstract
Objectives: The purpose of this study was to assess the effectiveness of the expander with differential opening (EDO) with alternate rapid maxillary expansion and contraction (Alt-RAMEC), and Facemask Protraction in patients with cleft lip and palate using cone beam computed tomography (CBCT) records.
Material and methods: Eight cleft lip and palate patients, ages 8 to12 years, were selected. All patients had maxillary permanent first molars and displayed a constricted maxillary arch, Primary lip adhesion and palatal closure were done in early childhood. All patients treated with the Alt-RAMEC protocol used EDO and a protraction facemask. CBCT scans were taken both before and six months after treatment. Maxillary transverse dimensions were measured, including the nasal cavity width, maxillary width, alveolar crest width, arch width, inclination of the molar teeth, alveolar width, alveolar crest level, and buccal and palatal bone plate thickness. A paired sample t-test for significance was used when comparing related samples. Pearson's correlation coefficient (r) test was used to assess the degree of association between two sets of variables.
Results: All maxillary transverse measurements increased significantly at the molar and premolar regions (p<0.05). Alveolar crest level and buccal bone plate thickness were slightly decreased (0.57mm) and 0.5 mm, respectively; (p<0.05). The molar teeth showed a significant increase in buccal inclination (6.36°) (P<0.001). Forward movement of the maxilla was seen in lateral cephalometric extracted from CBCT.
Conclusion: Significant maxillary expansion and advancement were achieved while using the EDO with Alt-RAMEC and facemask protraction, while there was a slight decrease in buccal bone thickness and height and significant increase in buccal molar inclination.
Registration : This trial was registered in the ClinicalTrials.gov Identifier: NCT04970095 and the date of registration was July 16, 2021.
Clinical Relevance: This innovative treatment approach corrects anterior and posterior crossbite in patients with cleft lip and palate who have dentoskeletal anomalies.
Brain metastasis originated from gastric cancer: its clinicopathological characteristics and survival outcome
Authors: Zhao Bochao , Wang Jingchao , Ma Zhicheng , Wang Weiqiang , Meng Kewei , Yang Tao 
Published: January 2023

Abstract
Objective
The frequency and prognostic factors of brain metastasis(BM) originated from gastric cancer(GC) remain unclear. The purpose of this study was to clarify the current knowledge of BM and determine its risk factors and survival outcome.
Methods
A total of 9,278 stage IV GC patients were retrospectively identified from the Surveillance, Epidemiology, and End Results(SEER) database. Clinicopathological features and survival outcomes between patients with and without BM were compared, and significant prognostic factors were determined.
Results
The frequency of BM in stage IV patients was 2.2%(203/9,278), and 52.7%(107/203) of BM patients presented synchronous extracranial metastases at the time of diagnosis. Younger age(< 65 years old) and proximal GC were significantly associated with BM. The patients with BM had a shorter median cancer-specific survival(CSS)(3.0 months [95% CI: 2.21–3.79] vs 7.0 months [95% CI:6.73–7.27], P < 0.001) and overall survival(OS)(3.0 months [95%CI:2.27–3.73] vs 6.0 months [95%CI:5.77–6.23], P < 0.001) than those without BM. For patients with BM, the presence of synchronous extracranial metastases was significantly associated with shorter median CSS(3.0 months [95%CI: 2.30–3.70] vs 4.0 months [95%CI: 2.69–5.31], P = 0.031). However, there was no correlation between the number of extracranial metastatic organs and survival outcomes. Poorly differentiated/undifferentiated adenocarcinoma(HR:1.876, 95%CI:1.231–2.858, P = 0.003) and the presence of extracranial metastasis(HR:1.420, 95%CI:1.003–2.010, P = 0.048) were independent predictive factors for poor survival of patients with BM.
Conclusions
Brain metastasis originated from GC was not common, but survival outcome was extremely poor. For early detection of brain metastasis, it is necessary to pay more attention to patients with risk factors.
Development of Scalable and Generalizable Machine Learned Force Field for Polymers
Authors: Mohanty Shaswat , Stevenson James , Browning Andrea , Jacobson Leif , Leswing Karl , Halls Mathew , Afzal Mohammad Atif Faiz 
Published: January 2023

Abstract
Understanding and predicting the properties of polymers is vital to developing tailored polymer molecules for desired applications. Classical force fields may fail to capture key properties, for example, the transport properties of certain polymer systems such as polyethylene glycol. As a solution, we present an alternative potential energy surface, a charge recursive neural network (QRNN) model trained on DFT calculations made on smaller atomic clusters that generalizes well to oligomers comprising larger atomic clusters or longer chains. We demonstrate the validity of the polymer QRNN workflow by modeling the oligomers of ethylene glycol. We apply two rounds of active learning (addition of new training clusters based on current model performance) and implement a novel model training approach that uses partial charges from a semi-empirical method. Our developed QRNN model for polymers produces stable molecular dynamics (MD) simulation trajectory and captures the dynamics of polymer chains as indicated by the striking agreement with experimental values. Our model allows working on much larger systems than allowed by DFT simulations, at the same time providing a more accurate force field than classical force fields which provides a promising avenue for large-scale molecular simulations of polymeric systems.
Bayesian network-based risk factors analysis for diabetic retinopathy: A cross-sectional study
Authors: Gao Jian , Zhang Ruimin , Feng Yongliang , Song Wenzhu , Zhang Peigang , Chen Jing 
Published: January 2023

Abstract
Background: Diabetic retinopathy (DR) represents one of the common complications of diabetes mellitus, which not only affects the quality of life of patients, but also poses a huge economic burden to their families and society.We aim to construct a Bayesian networks (BNs) to detect risk factors associated with DR, exploring their complicated network relationships, thus, providing a scientific reference for risk prediction and prevention of DR.
Methods: A questionnaire survey and clinical data were collected from 1745 patients with type 2 diabetes from 4 randomly selected communities in four regions of Shanxi Province, China. Afterwards, Elastic Net was employed to make a feature selection, after which, BNs with MMHC algorithms was constructed to discuss risk factors related to DR and their probabilistic dependencies.
Results: After feature selection, 11 variables were incorporated into BNs construction. BNs suggested that the prior probability of DR stands at 0.155. Besides, BNs showed that systolic blood pressure, fasting blood glucose, glycosylated haemoglobin represent parental nodes for DR, and urea nitrogen and urine protein to creatinine ratio constitute child nodes of DR. When the above parameters leaves at abnormal, the probability of DR reaches at 0.741. Besides, marital status and duration of diabetes are indirectly related to DR. Separated marital status indirectly relates to DR by affecting pressure; duration of diabetes indirectly increases the risk of DR through glycated haemoglobin.
Conclusion: The BNs constructed in this study reveals the complex network linkages between DR and its associated factors, and provides a probabilistic model of the risk for DR, allowing physicians and patients to target risk prediction and to take preventive control of DR complicated by type 2 diabetes.
Empagliflozin reduces arrhythmogenic effects in rat neonatal and human iPSC-derived cardiomyocytes and improves cytosolic calcium handling at least partially independent of NHE1
Authors: Santos Danúbia Silva , Turaça Lauro Thiago , Coutinho Keyla Cristiny Silva , Barbosa Raiana Andrade Quintanilha , Polidoro Juliano Zequini , Brunswick Tais Hanae Kasai , Carvalho Antonio Carlos Campos , Girardi Adriana Castello Costa 
Published: January 2023

Abstract
The antidiabetic agent class of sodium-glucose cotransporter 2 (SGLT2) inhibitors confer unprecedented cardiovascular benefits beyond glycemic control, including reducing the risk of fatal ventricular arrhythmias. However, the impact of SGLT2 inhibitors on the electrophysiological properties of cardiomyocytes exposed to stimuli other than hyperglycemia remains elusive. This investigation tested the hypothesis that the SGLT2 inhibitor empagliflozin (EMPA) affects cardiomyocyte electrical activity under normoxic and hypoxic conditions. Rat neonatal and human iPSC-derived cardiomyocytes incubated or not with the hypoxia-mimetic agent CoCl2 were treated with EMPA (1 µM) or vehicle for 24 h. Action potential records obtained using intracellular microelectrodes demonstrated that EMPA reduced the action potential duration at 30%, 50%, and 90% repolarization and arrhythmogenic events in rat and human cardiomyocytes under normoxia and hypoxia. Analysis of Ca2+ transients using Fura-2-AM and contractility kinetics showed that EMPA increased Ca2+ transient amplitude and decreased the half-time to recover Ca2+ transients and relaxation time in rat neonatal cardiomyocytes. We also observed that the combination of EMPA with the NHE1 inhibitor cariporide (10 µM) exerted a more pronounced effect on Ca2+ transients and contractility than either EMPA or cariporide alone. Besides, EMPA, but not cariporide, increased phospholamban phosphorylation at serine 16. Collectively, our data reveal that EMPA reduces arrhythmogenic events, decreases the action potential duration in rat neonatal and human cardiomyocytes under normoxic or hypoxic conditions, and improves cytosolic calcium handling at least partially independent of NHE1. Moreover, we provided further evidence that SGLT2 inhibitor-mediated cardioprotection may be partly attributed to its cardiomyocyte electrophysiological effects.
Investigations of the spin-Hamiltonian parameters and defect structure for the (TiO 4 ) 5− tetrahedral clusters in ZrSiO 4 : Ti 3+ crystal
Authors: Mei Yang 
Published: January 2023

Abstract
The spin-Hamiltonian parameters (g factors g//, g⊥ and hyperfine structure constants 47Ai, 49Ai, where i = // or ⊥, 47Ai and 49Ai denote the values of isotopes 47Ti3+ and 49Ti3+) of the Ti3+ ions at the tetrahedral Si4+ sites in ZrSiO4 crystal are computed from the high-order perturbation formulas based on the cluster approach where the contributions due to both the d orbitals of central dn ion and p orbitals of ligand ion are considered. The calculated results are reasonably coincident with the experimental values. The defect structure of (TiO4)5− impurity cluster which differs from the replaced host (SiO4)4− cluster in ZrSiO4 is evaluated in the calculation. The results are discussed.
HepaRG cells undergo increased levels of post-differentiation patterning in physiologic conditions when maintained as 3D cultures in paper-based scaffolds
Authors: Diprospero Thomas J. , Brown Lauren G. , Fachko Trevor D. , Lockett Matthew R. 
Published: January 2023

Abstract

Monolayer cultures of hepatocytes lack many aspects of the liver sinusoid, including a tissue-level organization that results from extracellular matrix interactions and gradients of soluble molecules that span from the portal triad to the central vein. We measured the activity and transcript levels of drug-metabolizing enzymes in HepaRG cells maintained in three different culture configurations: as monolayers, seeded onto paper scaffolds that were pre-loaded with a collagen matrix, and when seeded directly into the paper scaffolds as a cell-laden gel. Drug metabolism was significantly decreased in the presence of the paper scaffolds compared to monolayer configurations when cells were exposed to standard culture conditions. Despite this decreased function, transcript levels suggest the cells undergo increased polarization and adopt a biliary-like character in the paper scaffolds, including the increased expression of transporter proteins (e.g.,ABCB11andSLOC1B1) and theKRT19cholangiocyte marker. When exposed to representative periportal or perivenous culture conditions, we observed in vivo zonal-like patterns, including increased cytochrome P450 (CYP) activity and transcript levels in the perivenous condition. This increased CYP activity is more pronounced in the laden configuration, supporting the need to include multiple aspects of the liver microenvironment to observe the post-differentiation processing of hepatocytes.
IGF2BP3 is associated with HPV status and tight junction in HPV-related cervical cancer
Authors: Han Xiu , Han# Qignzhen , Wu Xiangwei , Geng Haiying , Wang Lin , Gong Aihua 
Published: January 2023

Abstract
Background
Although m6A modification was known to have broad effects on malignant tumors by participating in tumor proliferation, differentiation, tumorigenesis, invasion and metastasis, as oncogenes or anti-oncogenes, their effects of microbes in cancers have been rarely disputed. To investigate the function of IGF2BP3, one of the indispensable regulators of m6A, in HPV virus invading and transmitting, integrative analyses was performed in this study and identified that it was highly expressed in tumors and was related to the poor prognosis in CESC.
Methods
We investigate the expresseion level of IGF2BP3 and its prognostic value in CESC via multiple datasets including TCGA, GTEx datasets and TIMER. Gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analyses of differentially expressed genes were performed using GOplot, org.Hs.eg.db and clusterProfiler packages and visualized using the ggplot2 package
Results
In HPV-positive tumors, IGF2BP3 was positively associated with tumor HPV status. Further analysis demonstrated that IGF2BP3 high status was correlated with signaling pathways related to cell-cell and cell-ECM interactions, including receptor ligand activity, neuroactive ligand receptor interaction and chemical carcinogenesis receptor activation. Moreover, correlation analysis showed that IGF2BP3 would impair the formation of cell polarity and cell-cell contacts by dysregulating the expression of tight junction molecules.
Conclusions
Our results identified that IGF2BP3 high status, is associated with poor prognosis and HPV status, and IGF2BP3 serves as a mediator of the tight junction formation in HPV-associated cancer, which provides a promising therapeutic target for anti-cancer schedule.
Improved metamodels for predicting high-dimensional outputs by accounting for the dependence structure of the latent variables: application to marine flooding
Authors: Rohmer Jeremy , Sire Charlie , Lecacheux Sophie , Idier Deborah , Pedreros Rodrigo 
Published: January 2023

Abstract
Metamodelling techniques have shown high performance to overcome the computational burden of numerical hydrodynamic models for fast prediction of key indicators of marine flooding (e.g. total flooded area). To predict flood maps (e.g. spatial distribution of maximum value of water depth during a flood event), a commonly-used approach is to rely on principal component analysis to reduce the high dimensionality of the flood map (related to the number of pixels typically of several 1,000s) by transforming the spatial output into a low number of latent variables (typically <10). One commonly-used approach is to build one metamodel per latent variable by assuming independence between the latent variables. Using two real cases of marine flooding, we show that the predictive performance of the metamodelling approach (relying on kriging metamodels) can significantly be improved when the dependence structure of the latent variables is accounted for. Our tests show that the most efficient approach relies on the clustering in the space of the latent variables (here with k-means algorithm). Complementing the approach with a kriging metamodel specifically dedicated to handle vector-valued variables allows an additional increase of predictability for the case with the larger size of the training dataset.
Anthropogenic Contamination in the Free Aquifer of the San Luis Potosi Valley
Authors: Rivera Sonia Torres , Hernández José Ramón Torres , Lozada Simón Eduardo Carranco , Arreola María Elena García , Doncel Rubén Alfonso López 
Published: January 2023

Abstract
The valley of San Luis Potosí is an endorheic basin formed by three aquifers: shallow hanging, alluvial material on a hardened horizon known as "tepetate", two deep, free and confined type. Population growth has led to gradual contamination of the surface aquifer. Recent studies documented anthropogenic, biogenic and heavy metal contamination. A recent phenomenon of settlement has affected houses and buildings in the urban area, extending to parts of the valley that are still used for agriculture, developing "faults" affecting the tepetate that supports the superficial aquifer, facilitating the infiltration of contaminated water into the aquifer. free type. This investigation reports detection of nitrogen (N-NO3), with a concentration of 15 mg/L (milligram liter) its maximum allowable limit is 10 mg/L. Twelve samples with fecal coliforms from 5 to 17 MPN/100 (the most probable number in one hundred milliliters of the sample). Thirteen samples showed total coliform concentrations, one sample reported a too high concentration of 150 NMP/100, compared to the rest with concentrations of 5 to 17 NMP/100, indicating less contamination. Some trace elements with concentrations in parts per million (ppm) that were also detected were manganese (Mn), arsenic (As), cadmium (Cd), and mercury (Hg). Results that give the first sign of attention to the contamination of the deep free aquifer, derived from anthropic activity in the valley of San Luis Potosí.