bluuebunny/crossref_metadata_2025_split huggingface dataset:
Synchronous Epidermodysplasia Verruciformis and Intraepithelial Lesion of the Vulva is Caused by Coinfection with α-HPV and β-HPV Genotypes and Facilitated by Mutations in Cell-Mediated Immunity Genes
Authors: Ribeiro Renan Ribeiro e , Sung C , Quddus M Ruhul 
Published: August 2022

Abstract
There have been exceedingly few reports of epidermodysplasia verruciformis (EV) or EV-like lesions in the vulva. We describe the first case series featuring vulvar lesions displaying synchronous EV-like histologic changes and conventional high-grade intraepithelial lesion (VIN 3), a finding hitherto unreported in medical literature. We hypothesized that this could be caused by coinfection with α-HPV and β-HPV genotypes. Cases were retrospectively selected from our institutional archive. Detailed review of clinical information, histologic examination and whole genome sequencing (WGS) were performed in 5 samples from 4 different patients. Three of four patients had a history of either iatrogenic immune suppression or prior immune deficiency, and all featured classic VIN 3 and EV changes within the same lesion. The fourth patient had no history of immune disorders, presented with EV-like changes and multinucleated atypia of the vulva, and was the sole patient without conventional high-grade intraepithelial lesion. By WGS, several uniquely mappable reads pointed towards infection with multiple HPV genotypes including both α-HPVs and β-HPVs. Mutations in genes implicated in cell-mediated immunity, such as DOCK8, CARMIL2, MST1 and others, were also found. Our findings provide novel insight into EV and HPV pathogenesis, vulvar precancerous lesions and expand the clinicopathological spectrum of genetic alterations linked to unconventional immune deficiencies.
Maternal septic shock secondary to amniocentesis at mid-gestation: A summary of 19 cases, including 2 new Chinese cases, and a literature review
Authors: He Xiaobo , Chen Aner , Zhou Junjun , Hong Xunyu , Li Dongmei 
Published: August 2022

Abstract
BACKGROUND: Amniocentesis is commonly performed to obtain a prenatal diagnosis. The most common indications for amniocentesis are abnormal foetal ultrasonography findings, followed by an increased risk of Down syndrome and advanced maternal age. The incidence of intra-amniotic infection is approximately 0.1%, and the risk of subclinical infection development after serial amniocentesis is no more than 0.5%. Septic shock is an unusual complication among cases of foetal loss associated with amniocentesis. Here, we report two cases of septic shock and multiple organ failure (MOF) after amniocentesis at mid-gestation. PRESENTATION OF CASES: Two women underwent genetic amniocentesis due to chromosomal aneuploidy. Prior to amniocentesis, the temperature, routine blood count, CRP and ultrasound findings were all normal. Genetic amniocentesis was performed under sterile conditions and without difficulty at 3P.M. A 22-gauge needle was passed into the right lower quadrant of the uterus, and 30 mL of clear ﬂuid was extracted during the ﬁrst attempt. They all complained of fever and chills and presented to the hospital within 48 hours after the amniocentesis. Foetal demise was found, and the patients rapidly developed septic shock. Despite vaginal delivery, curettage and antibiotic therapy, the patients deteriorated with the onset of MOF (myocardial damage, hypotension, renal insufficiency, low platelets). Blood cultures, discharge cultures and some tissue from the foetus all revealed Escherichia coli. The foul-smelling placenta was evacuated. There was gradual improvement with intensive monitoring. CONCLUSION: Uterine infection after amniocentesis leading to maternal sepsis is associated with a high morbidity and mortality rate. Our patients were able to survive without a hysterectomy due to the rapid administration of antibiotics and surgical intervention while being evaluated. Genetic counsellors and obstetric care providers should be aware of potential serious maternal morbidity and mortality that may occur subsequent to uncomplicated amniocentesis.
Controlled Finite Frames
Authors: Alijani Azadeh , Heidarpour Zohreh , Parizi Maryam Naderi 
Published: August 2022

Abstract
The finite frame theory is a very important part offrame theory due to its significant relevance in various branchesof mathematical applications. Studying controlled inite frames isthe goal of the work. To this end, we introduce controlled framesin a inite-dimensional Hilbert space and study some properties ofthem. The main class of inite frames in frame applied problemsis Parseval frames. By viewpoint to this, a brief discussion aboutParseval frames is presented and also Parseval controlled framesare investigated. Afterward, the paper characterizes all operatorsthat construct controlled inite frames. Furthermore, controlledinite frames are also considered as a proper subset of dual framesby the equivalency relation between frames.
Vaccination with an HIV T-cell immunogen induces alterations in the mouse gut microbiota
Authors: Borgognone Alessandra , Elizalde-Torrent Aleix , Casadellà Maria , Romero Luis , Escribà Tuixent , Parera Mariona , Català-Moll Francesc , Noguera-Julian Marc , Brander Christian , Olvera Alex , Paredes Roger 
Published: August 2022

Abstract
The gut microbiota is emerging as a crucial factor modulating vaccine responses; however, few studies have investigated if vaccines, in turn, can alter the microbiota and to what extent such changes may improve vaccine efficacy. To understand the effect of T-cell vaccination on the gut microbiome, we administered an HIV-1 T-cell immunogen (HTI arm) or PBS (control) to C57Bl/6 mice following a heterologous prime-boost scheme. The longitudinal dynamics of the mice gut microbiota were characterized by 16S ribosomal RNA sequencing in fecal samples collected from cages, as well as from three gut sections (caecum, small and large intestine). Serum and spleen cells were obtained at the study endpoint to assess immune correlates using IFNγ ELISPOT and cytokine Luminex® assays. Compared with PBS, HTI vaccination increased several Clostridiales genera associated with anti-inflammatory responses, such as Eubacterium xylanophilum group, Roseburia and Ruminococcus. Such shifts were observed after the first HTI dose and remained throughout the study follow-up (18 weeks). Hoverer, the enriched Clostridiales specific genera were different between feces and gut sections. The abundance of HTI-enriched bacteria positively correlated with the magnitude of vaccine-induced responses and a set of pro-inflammatory cytokines, especially IL-6. This longitudinal analysis reveals that, in mice, T-cell vaccination promotes the increase of anti-inflammatory gut bacteria in parallel to significant associations with proinflammatory cytokines, suggesting an adaptation of the gut microbial milieu to T-cell-induced systemic inflammation.
DNA methylation patterns suggest the involvement of DNMT3B and TET1 in osteosarcoma development
Authors: Pires Sara Ferreira , de Barros Juliana Sobral , Costa Silvia Souza , Scliar Marília Oliveira , Lengert André Helvoort , Boldrini Érica , Silva Sandra Regina Morini , Tasic Ljubica , Vidal Daniel Onofre , Krepischi Ana Cristina Victorino , Maschietto Mariana 
Published: August 2022

Abstract
Osteosarcomas commonly arise during the bone growth and remodeling in puberty, making it plausible to infer the involvement of epigenetic alterations in their development. We investigated DNA methylation and related genetic variants in 28 primary osteosarcomas aiming to identify deregulated driver pathways. Methylation and genomic data was obtained using the Illumina HM450K beadchips and the TruSight One sequencing panel, respectively. Aberrant DNA methylation was spread throughout the osteosarcomas genomes. We identified 3,146 differentially methylated CpGs comparing osteosarcomas and bone tissue samples, with high methylation heterogeneity, global hypomethylation and focal hypermethylation at CpG islands. Differentially methylated regions (DMR) were detected in 585 loci (319 hypomethylated and 266 hypermethylated), mapped to the promoter regions of 350 genes. These DMR-genes were enriched for biological processes related to skeletal system morphogenesis, proliferation, inflammatory response and signal transduction. Six tumor suppressor genes harbored deletions or promoter hypermethylation (DLEC1, GJB2, HIC1, MIR149, PAX6, WNT5A), and four oncogenes presented gains or hypomethylation (ASPSCR1, NOTCH4, PRDM16, RUNX3). Our analysis also revealed hypomethylation at 6p22, a region that contains several histone genes. DNMT3B gain was found to be a recurrent copy number change in osteosarcomas, providing a possible explanation for the observed phenotype of CpG island hypermethylation. While the detected open-sea hypomethylation likely contributes to the well-known osteosarcoma genomic instability, enriched CpG island hypermethylation suggests an underlying mechanism possibly driven by overexpression of DNMT3B likely resulting in silencing of tumor suppressors and DNA repair genes.
Measurements of decaying grid turbulence with various initial conditions
Authors: Zhao Yongfei , Yang Yang , Li Mingshui , Lei Yongfu , Peng Yuxuan 
Published: August 2022

Abstract
The uniform grid is widely used for the aim of generating the approximately homogeneous and isotropic turbulence. Although many previousstudies have investigated the influence of initial conditions of the uniform square grids, including the Reynolds number, mesh size, bar size,cross-section of bar and solidities, on the statistical characteristics ofthe grid turbulence, the influence of mesh shape has rarely been studied. Compared to the traditional uniform square grid, the present workinvestigates the influence of different mesh shapes (the uniform non-square grid) on the grid turbulence, and this change of mesh shape canbe easily achieved based on the traditional uniform square grid. Thework found that in the cases of uniform non-square grid, the distance ofturbulence needs to fully develop is shorten, the low frequency components of fluctuating velocity increase while high frequency componentsdecrease, leading to the difference of energy distribution. Meanwhile, theuse of uniform non-square grid reduces the anisotropies of decaying turbulence to a certain extent. The skewness is much closer to the theoreticalvalue 0, while the flatness almost remains unchanged. The decay exponents and power-law coefficients obtained are affected by the mesh shapeand the decay exponent could be much closer to 1. Furthermore, largerintegral length scales can be obtained at the same downstream position by using the uniform non-square grid, compared to traditional uniformsquare grid. This may better meet requirements of large-scale turbulence in some engineering communities, such as the wind engineering
Freeze-and-Mutate: Abnormal Sample Identification for DL Applications through Model Core Analysis
Authors: Wang Huiyan , Chen Ziqi , Xu Chang 
Published: August 2022

Abstract
Deep learning (DL) applications, representing an emerging form of new software, are gaining increasing popularity by their intelligent and adaptive services. However, their service reliability depends highly on the prediction accuracy of their internally-integrated DL models. In practice, DL models are often observed to suffer from ill predictions upon abnormal inputs (e.g., adversarial attacking samples, out-of-distribution (OOD) samples, and etc.), and this could easily lead to unexpected behaviors or even catastrophic consequences (e.g., system crash). One promising way to guard the application reliability is to reveal such abnormal inputs in time before they are fed to the DL models integrated in the concerned applications. Then remedy actions (e.g., discarding or fixing these inputs) can be done to protect applications from acting abnormally. Existing work addressed this revealing problem by either making sample distance-comparison based analysis or generating sufficient model mutants for comparative analysis. However, such treatments caused a restricted focus on samples only, while overlooking the DL models themselves, or had to analyze massive mutants, incurring non-negligible overheads to applications. In this article, we propose a novel approach, NetChopper, to conducting a core analysis on the target DL model, and then partitioning it into two parts, one associating closely with the training knowledge being the model core (expected to be important and thus stable), and the other being the remaining part (expected to be immaterial and thus changeable). Based on such partitioning, NetChopper proceeds to preserve (or freeze) the model core, but mutate the remaining part to produce only a small number of model mutants. Later, NetChopper becomes able to reveal abnormal inputs from normal ones by exploiting these model-relevant and light-weight mutants only. We experimentally evaluated NetChopper by widely-used DL subjects (e.g., MNIST+LeNet4, and CIFAR10+VGG16) and typical abnormal inputs (e.g., adversarial and OOD samples). The results reported NetChopper's promising AUROC scores in revealing the abnormal degrees of inputs, generally and stably outperforming, or comparably effective as, state-of-the-art techniques (e.g., mMutant, Surprise, and Mahalanobis), and also confirmed its high effectiveness and efficiency (with only marginal online overhead).
Topology and adenocarcinoma cell localization dataset on the labyrinthin diapeutic biomarker
Authors: Sharma Ankit , Babich Michael , Li Tianhong , Radosevich James A. 
Published: August 2022

Abstract
Objective:
The discovery and characterization of tumor associated antigens is increasingly important to advance the field of immuno-oncology. In this regard, labyrinthin has been implicated as a neo-antigen found on the cell surface of adenocarcinomas. Data on the 1) topology, 2) amino acid (a.a.) homology analyses and 3) cell surface localization of labyrinthin by fluorescent activated cell sorter (FACS) are studied in support of labyrinthin as a novel, pan-adenocarcinoma marker.
Results:
Bioinformatics analyses predict labyrinthin as a type II protein with calcium binding domain(s), N-myristoylation sites, and kinase II phosphorylation sites. Sequence homologies for labyrinthin (255 a.a.) were found vs. the intracellular aspartyl/asparaginyl beta-hydroxylase (ASPH; 758 a.a.) and the ASPH-gene related protein junctate (299 a.a.), which are both type II proteins. Labyrinthin was detected by FACS on only non-permeablized A549 human lung adenocarcinoma cells, but not on normal WI-38 human lung fibroblasts nor primary cultures of normal human glandular-related cells. Microscopic images of immunofluorescent labelled MCA 44-3A6 binding to A549 cells at random cell cycle stages complement the FACS results by further showing that labyrinthin persisted on the cell surfaces along with some cell internalization within 20 minutes.
An Automated System for Cephalometric Soft-tissue Landmark Detection
Authors: Elaiwat Said , Azad Mohammad , Alam Mohammad 
Published: August 2022

Abstract
The ability to detect cephalometric landmarks in x-ray images plays a crucial role in several medical applications, including orthodontics and maxillofacial surgery. The manual annotation of landmarks is time-consuming and prone to inaccuracy. These limitations can be overcome by building a system for automated landmark detection. Towards this goal, we propose a fully automated system for the task of soft-tissue landmark detection. The proposed method combines two different types of descriptors, Haar-like features and spatial features, to build a strong classifier using Adaboost technique. In order to evaluate the proposed method, we introduce a new dataset for soft-tissue landmark detection task along with two evaluation protocols to define detection rate. The first protocol represents the detection rate within mean radial error (MRE) while the second protocol represents the detection rate within a predefined confidence region R. Reported experiments demonstrate the superior performance of the proposed method compared to state-of-the-art.
Effects of combination treatment using arsenic trioxide and resveratrol on human breast cancer (MCF-7) cells
Authors: Hu Hongye , Zhu Xiaofang , Zhang Xiaohua , Huang Guanli 
Published: August 2022

Abstract
Background: Arsenic trioxide (ATO) has shown remarkable efficacy in the treatment of cancer. Resveratrol (RSV) has anti-tumor, anti-aging, and anti-inflammatory properties. We examined the anti-cancer effects of using ATO plus RSV together against human breast cancer (MCF-7) cells.Methods: MCF-7 cells were treated with ATO (0–16 μM) alone or combined with RSV (0–100 μM). Cell viability and percent apoptosis were estimated using Cell Counting Kit-8, the TUNEL assay and microscopy. mRNA and protein expression of caspase-3, caspase-7, Bax, and B-cell lymphoma (Bcl)-2 were assessed by real-time reverse transcription-quantitative polymerase chain reaction (RT-qPCR) and western blotting. Chromatin immunoprecipitation (ChIP) was adopted to determine the histone acetylation of the promoter regions of caspase-3, caspase-7, Bax, and Bcl-2.Results: Combined treatment was more efficacious than treatment of ATO alone or RSV alone in suppressing the viability of MCF-7 cells. The intracellular mechanisms of cytotoxicity of ATO+RSV treatment were revealed to be a relative increase in mRNA and protein expression of caspase-3, caspase-7, and Bax, and relative decrease in Bcl-2, in MCF-7 cells. ChIP results showed that combined treatment increased the acetylation of histone H3K27 in the promoter region of caspase-3, caspase-7, and Bax, but decreased the acetylation of histone H3K27 in Bcl-2.Conclusion: Combination therapy using ATO and RSV could be employed for BC treatment.
Mentorship matters: the example of mentoring by Dr. Alberto F. García – a role model for future Colombian academic trauma and emergency surgeons
Authors: Manzano-Nunez Ramiro 
Published: August 2022

Abstract

Purpose Little is known about the current status of mentoring and mentorship programs in the Colombian surgical community. This report aims to present the example of Dr. Alberto Federico García's mentoring to inform Colombian surgeons interested in mentoring young individuals who desire to pursue a surgical career. To this end, this paper describes Dr. Garcia's mentees' academic trajectory since they started working with him. Methods The academic trajectory of Dr. Garcia’s mentees was descriptively analyzed. Results Since 2015, 5 young physicians worked under the mentorship of Dr. Garcia at FVL university hospital in Cali, Colombia. All the mentees had a considerable rise in their research outputs since they started working with Dr. Garcia. Overall, the mentees submitted and presented abstracts in surgical meetings and got accepted into a residency program in general surgery. Conclusion This paper depicts a consistent improvement in the academic performance of Dr. Garcia's mentees during the period they worked with him, including research output and the mentees' personal goal of getting admitted to a general surgery residency program.
Predictive Risk Model for the Development of Encephalopathy in Patients with Nutritional Pancreatic Necrosis
Authors: Mikhin V. S , Burchuladze N. Sh. , Popov A. S. , Turovets M. I. , Mikhin I. V. , Kitaeva A. V. 
Published: August 2022

The objective: to develop a predictive model for assessing the risk of developing encephalopathy (EP) in patients with nutritional pancreatic necrosis.Subjects and Methods. A single-center prospective cohort study was conducted at Faculty Surgery Clinic of Volgograd State Medical University from 2010 to 2020. Logistic regression analysis was used to build a model for predicting the risk of developing EP.Results. A total of 429 patients were included in the study. It was determined that in the majority of patients EP manifested in the first three days after hospitalization. A statistically significant predictive model of correlation of the risk to develop EP with clinical and demographic variables showed that an increase in the severity of the patient's condition (according to the SOFA scale) by 1 point increased the risk by 1.9 times, and an increase in bilirubin levels by 1 μmol/l, and urea by 1 mmol/l increased the risk of AED by 8.0% and 28.0%, respectively. In non-alcoholic pancreatic necrosis, compared with the alcoholic genesis of the disease, and when using early (before day 3) enteral nutrition, there was a significant reduction in the risk of developing EP by 175.5% and 137% of cases. The specificity and sensitivity of the model were 78.7% and 82.8%, respectively.Conclusions. In nurtitional pancreatic necrosis, an increase in the severity of the patient's condition, alcoholic genesis of the disease, progression of signs of liver and kidney failure significantly increased the risk of developing EP. At the same time, early enteral nutrition contributed to a significant reduction in the risk of this complication. The presented predictive model is recommended to be used in routine clinical practice.
Comparison of Effectiveness of Pressure Support and Mandatory Ventilation Modes at the End of General Combined Anesthesia
Authors: Pyzhov V. A. , Khrapov K. N. , Miroshkina V. M. 
Published: August 2022

The objective: to compare effectiveness of pressure support and mandatory ventilation modes at the final stage of general anesthesia.Subjects and Methods. 58 patients were included in the study. All patients underwent laparoscopic or open surgery under combined general anesthesia with muscle relaxants and tracheal intubation. At the end of the operation, after suturing the muscle layer, patients were randomly divided into two groups, depending on the further mode of ventilation: the mandatory mode group with dual control until extubation (n = 29) and the spontaneous breathing mode group with pressure support (n = 29). The time of awakening, the severity of post-extubation cough, hemodynamic parameters and oxygenation immediately before and 5 minutes after extubation were assessed.Results. In the groups of patients, statistically significant differences were observed in the time of awakening (252 ± 67 sec and 426 ± 71 sec in PSV and PCV-VG Groups, respectively), extubation (287 ± 55 sec and 464 ± 67 sec in the PSV and PCV-VG groups, respectively), and transfer from the operating room (473 ± 60 sec and 687 ± 77 sec in the PSV and PCV-VG groups, respectively) (p < 0.0001). Also, patients receiving PSV respiratory support had higher saturation levels 5 minutes after extubation (p < 0.0001), and heart rate and mean arterial pressure immediately before extubation were lower than in the mandatory ventilation group (p = 0.013 and p < 0.0001, respectively). In addition, in the mode of spontaneous breathing with pressure support, a lower severity of post-extubation cough was observed (p = 0.003).Conclusion. The use of a spontaneous breathing mode with pressure support at the end of general combined anesthesia has several advantages versus mandatory ventilation mode. These advantages include faster awakening, extubation and transfer of the patient to the ward, lower severity of post-extubation cough, as well as better gas exchange after extubation, lower intensity of hypertension and tachycardia before it.