bluuebunny/crossref_metadata_2025 huggingface dataset:
Implementation of Bandwidth Management in Cafe Billing Systems Using QR Code Authentication
Authors: Rodiyah Afifatur
Published: June 2021

Seeing the high demand for internet, this research will design an implementation of bandwidth management using a user manager, which will be applied to the billing system in public places with internet services. This aims to regulate the bandwidth or internet bandwidth that will be used by each customer in accordance with the total payment. This implementation utilizes a QR Code which will be used as authentication. This QR Code will be printed on the customer's payment receipt / receipt and will be scanned through the application installed on the android mobile phone. The application will be connected to a server which will later connect the customer's smartphone to connect to the internet service. After making the application, it is tested to check the accuracy of the bandwidth received by the customer. From the bandwidth accuracy testing, the results show that the delivery of bandwidth to the customer has an error with an average error in the download bandwidth of 6.5% and the upload bandwidth of 17%. The occurrence of this error is due to the ping and jitter values ??during data transmission, with an average ping of 78.7 ms and a jitter of 82.7 ms. Whereas in reading the QR Code, it was found that when using a camera with a 5MP resolution the QR Code can be read up to a distance of 90 cm and when using a camera with a resolution of 20.7MP, the QR Code can be read up to a distance of 110 cm.
Implementation of Power Line Communication (PLC) for Monitoring Current Use at State Polytechnic of Malang
Authors: Lukitasari Galuh , Hariyadi Aad , Perdana Ridho Hendra Yoga
Published: June 2021

One of the communication technologies that can be used for monitoring current usage is communication technology via electric grids or what is called Power Line Communication (PLC). The advantages of this technology are that the electricity network is already distributed in each building so there is no need for new installations, it is economical and affordable in terms of economics, and is more practical and flexible in its use. In this study, a current usage monitoring system using PLC is proposed which will be applied in every class in the AI ??building of Malang State Polytechnic. The sensor that will be used in measuring the current value is the current sensor SCT-013. By using the KQ330 PLC module as a PLC transmission modem. The implementation of PLC which is applied in each class in the AI ??building has a BER (bit error rate) value of 0.012 in the experiment of sending 1000 data with an error of 12 times at the farthest distance of approximately 15 meters. And have a BER value of 0 or have no error in sending data at the closest distance of approximately 2-5 meters. In this study, the process of sending and receiving data using Power Line Communication allows it to be done at a distance that is not too far away to avoid excessive data errors.
Design of Post Operation Recovery Room Control System Based on Wireless Sensor Network
Authors: Imanniarti Yuni
Published: June 2021

The recovery room is a room in hospital, where patients are treated after they have undergone surgical operations and recovered from the effects of anesthesia. In  recovery room, patients really need a comfort so that they don't experience physical and psychological stress too much. Comfort for everyone is different, but there are several factors that can make the room more comfortable. Therefore, it will take parameters for this research, namely temperature, humidity and lighting.In this study, we will discuss how to design a wireless sensor network system for controlling the recovery room after cesarean operation and how to test sensors on this system and how to display  processing result data to a smartphone.This research will explain about the system description of room temperature and humidity, UV light and room light intensity based on wireless sensor network using 2 types of nodes, namely sink nodes and control sensor nodes and using the HC-12 wireless module as data sender and receiver between nodes. The data taken is related to the measurement result information data that will be accessed and displayed via Android application in realtime.From the system designed, the error value is obtained with an average temperature value on R1 of 1.16%, R2 is 2.64% and R3 is 5.36%, while for the humidity value on R1 is 3.70%, R2 is 9, 32% and R3 10.54%. For testing the communication distance of 10m, the delay value without barrier is 60 seconds, while with barrier, the delay value is 97 seconds.
Central Lock Car Security System Design Using E-KTP Identification
Authors: Santoso Mega Putra Yogia
Published: June 2021

Currently, most motorized vehicle safety technologies, especially cars, still rely heavily on the manufacturer's default safety system from the car system itself. By using a security system from the factory default there are still shortcomings because a motorized vehicle or car can still be used by anyone and there is no age limit in its use. For that, we need a car safety system that is able to prevent the occurrence of car theft and underage drivers. The purpose of this research is to design a central lock security system for motor vehicles, especially cars, using e-KTP identification to improve the security system and reduce underage drivers. For the identification process of e-KTP ID using the RFID reader MFRC522. The RFID reader is connected to the Arduino Nano as a controller. The results of the research used the RFID reader to read e-KTP ID in a vertical and horizontal position with a distance of less than 12 mm. When there is an acrylic barrier and a glass barrier the maximum reading distance is less than 9 mm and the plate barrier cannot be read. The existence of obstacles makes reading the e-KTP card will be reduced.
Monitoring of Soil Media Acidity Detection for Replanting
Authors: Wardah Rufchotuz Zuhrotu
Published: June 2021

The development of the Indonesian agricultural sector until 2014 according to the Strategic Plan data of the Ministry of Agriculture for 2015–2019 is about 3.90% of the economic sector. One of the most important parameters for improvement efforts is soil. Soil quality on agricultural land is one important thing that needs special attention in its management. It is not easy to create ideal soil conditions for plants. For that, farmers need to know the variables that affect ideal conditions. The easiest way to find out the variable is to measure the pH and humidity of the soil conditions. Evaluation of soil fertility in chili plants is still done manually through visual observation. One of the factors that makes chili plants die before they bear fruit. In this research, a web monitoring system will be made on the planting medium of chilies based on soil acidity and soil moisture using sensors that can be monitored online. Data will be stored in the database and displayed on the web. The results obtained on the growing medium of chili plants produced soil suitable for chili plants, namely soil media sandy which has a moisture value of 7 to 8 and a pH value of 6.5-7.5. The average time needed to communicate between nodes to the website is 344 ms, which in the TIPHON standardization the average value of delay in sending data from the device to the website belongs to the 3rd index, which means that the process is of moderate quality.
Penurunan Nyeri Pada Arthritis Gout Melalui Kompres Hangat Air Rebusan Serai
Authors: Oktavianti Dewi Siti , Anzani Siti
Published: June 2021

Introduction: Gout arthritis is a type of arthritis that caused too much uric acid in the blood and accumulation of uric acid crystals and causing pain. This pain will interfere with activities. The study aims to determine the effect of warm compresses of Boiled lemon Grass reduce the intensity pain of gout. Method: This research used Quasi Experiment design, pre-test and post-test without control. The research samples were 20 respondents who feel pain gout arthritis and have increased levels of uric acid in the blood. The instruments used were the observation sheet and pain intensity scale measurement sheet with Numeric Rating Scale (NRS). The statistical test used the Paired T Test. Results: The results showed that differences in the pain intensity before and after intervention with p value 0.005, meaning  there was a significant effect  warm compressed of Boiled lemon Grass to reduce pain in Gout arthritis. Conclusion: The warm compresses of Boiled lemon Grass can be used as a non-pharmacological therapy to reduce the pain of gout arthritis.
Pengaruh Terapi Kelompok Terapeutik Terhadap Peningkatan Perkembangan Psikososial Dan Emosi Anak Remaja
Authors: Arifuddin Arifuddin , Pangaribuan Helena
Published: June 2021

Penelitian ini bertujuan mengidentiifikasi pengaruh terapi kelompok terapeutik terhadap peningkatan perkembangan psikososial dan emosi, hal ini dilakukan dengan melihat perubahan perkembangan psikososial sebelum dan sesudah dilakukan terapi kelompok terapeuti pada kelompok perlakuan serta menganalisis perbedaan perkembangan psikososisal emosi antara kelompok intervensi yang diberikan terapi kelompok terapeutik dan kelompok kontrolTerapi kelompok adalah suatu bentuk terapi dimana sekelompok klien bertemu secara bersama-sama dengan seorang terapis (Nevid, Rathus, & Greene, 2008). Terapi kelompok terapeutik adalah terapi yang fokus utamanya untuk mencegah gangguan dengan cara mengajarkan cara yang efektif untuk mengatasi stres emosional pada satu situasi atau krisis perkembangan, ( Townsend, 2014). Desain yang digunakan dalam penelitian ini adalah Quasi eksperimen  dengan pendekatan pre test – pos test control group ( Sudigdo, 1995).  Hasil penelitian menunjukkan bahwa terdapat perubahan  skor perkembangan psikosiial sebelum dan sesudah diberikan terapi kelompok terapeutik  dengan signifikansi  dan  terdapat perubahan  skor perkembangan emosi  sebelum dan sesudah diberikan terapi kelompok terapeutik dengan signifikansi  lebih kecil dari , Hasil penelitian menunjukkan bahwa tidak terdapat perubahan  skor perkembangan psikososial kemampuan sebelum dan sesudah diberikan penyuluhan kesehatan hasil uji T berpasangan (paired –sampel T test ) , bahwa tidak terdapat perubahan  skor perkembangan kemampuan emosi sebelum dan sesudah diberikan penyuluhan kesehatan hasil uji T berpasangan ( paired –sampel T test ) , terdapat perbedaan  selisih  skor pre test dan post test  perkembangan psikososial yang bermakna antara kelompok intervensi dan kontrol,   Berdasarkan uji t tidak berpasangan (independent-sampel t test)  menunjukkan nilai t hitung sebesar 5,793 dan nilai signifikansi 0,000 oleh karena t hitung > t tabel  (5,793 > 2,110) dan nilai signifikansi lebih kecil dari 0,05.
Evaluation of Head Injury Criteria for Injury Prediction Effectiveness: Computational Reconstruction of Real-World Vulnerable Road User Impact Accidents
Authors: Wang Fang , Wang Zhen , Hu Lin , Xu Hongzhen , Yu Chao , Li Fan
Published: June 2021

This study evaluates the effectiveness of various widely used head injury criteria (HICs) in predicting vulnerable road user (VRU) head injuries due to road traffic accidents. Thirty-one real-world car-to-VRU impact accident cases with detailed head injury records were collected and replicated through the computational biomechanics method; head injuries observed in the analyzed accidents were reconstructed by using a finite element (FE)-multibody (MB) coupled pedestrian model [including the Total Human Model for Safety (THUMS) head–neck FE model and the remaining body segments of TNO MB pedestrian model], which was developed and validated in our previous study. Various typical HICs were used to predict head injuries in all accident cases. Pearson’s correlation coefficient analysis method was adopted to investigate the correlation between head kinematics-based injury criteria and the actual head injury of VRU; the effectiveness of brain deformation-based injury criteria in predicting typical brain injuries [such as diffuse axonal injury diffuse axonal injury (DAI) and contusion] was assessed by using head injury risk curves reported in the literature. Results showed that for head kinematics-based injury criteria, the most widely used HICs and head impact power (HIP) can accurately and effectively predict head injury, whereas for brain deformation-based injury criteria, the maximum principal strain (MPS) behaves better than cumulative strain damage measure (CSDM0.15 and CSDM0.25) in predicting the possibility of DAI. In comparison with the dilatation damage measure (DDM), MPS seems to better predict the risk of brain contusion.
Differently PEGylated Polymer Nanoparticles for Pancreatic Cancer Delivery: Using a Novel Near-Infrared Emissive and Biodegradable Polymer as the Fluorescence Tracer
Authors: Cai Huazhong , Chen Yanxia , Xu Liusheng , Zou Yingping , Zhou Xiaoliang , Liang Guoxin , Wang Dongqing , Tao Zhimin
Published: June 2021

In this study, a chemically synthetic polymer, benzo[1,2-b:4,5-b′]difuran(BDF)-based donor–acceptor copolymer PBDFDTBO, was individually coated by amphiphilic poly(ethylene oxide)-block-poly(ε-caprolactone) (PEO-PCL) and 1,2-distearoyl-sn-glycero-3-phosphoethanolamine-N-methoxy(polyethylene glycol) (DSPE-PEG or PEG-DSPE), to form stably fluorescent nanoparticles in the near-infrared (NIR) window. The physicochemical properties of the synthesized nanoparticles were characterized and compared, including their size, surface charge, and morphology. In addition, in vitro studies were also performed using two pancreatic cancer cell lines, assessing the cell viability of the PBDFDTBO-included PEGylated nanoparticles formulations. Moreover, in vivo studies were also conducted, using subcutaneous murine cancer models to investigate the polymeric nanoparticles’ circulation time, tumor accumulation, and preferred organ biodistribution. The overall results demonstrated that even with the same PEGylated surface, the hydrophobic composition anchored on the encapsulated PBDFDTBO core strongly affected the biodistribution and tumor accumulation of the nanoparticles, to a degree possibly determined by the hydrophobic interactions between the hydrophobic segment of amphiphilic polymers (DSPE or PCL moiety) and the enwrapped PBDFDTBO. Both PEGylated nanoparticles were compared to obtain an optimized coating strategy for a desired biological feature in pancreatic cancer delivery.
m5C-Related lncRNAs Predict Overall Survival of Patients and Regulate the Tumor Immune Microenvironment in Lung Adenocarcinoma
Authors: Pan Junfan , Huang Zhidong , Xu Yiquan
Published: June 2021

Long non-coding RNAs (lncRNAs), which are involved in the regulation of RNA methylation, can be used to evaluate tumor prognosis. lncRNAs are closely related to the prognosis of patients with lung adenocarcinoma (LUAD); thus, it is crucial to identify RNA methylation-associated lncRNAs with definitive prognostic value. We used Pearson correlation analysis to construct a 5-Methylcytosine (m5C)-related lncRNAs–mRNAs coexpression network. Univariate and multivariate Cox proportional risk analyses were then used to determine a risk model for m5C-associated lncRNAs with prognostic value. The risk model was verified using Kaplan–Meier analysis, univariate and multivariate Cox regression analysis, and receiver operating characteristic curve analysis. We used principal component analysis and gene set enrichment analysis functional annotation to analyze the risk model. We also verified the expression level of m5C-related lncRNAs in vitro. The association between the risk model and tumor-infiltrating immune cells was assessed using the CIBERSORT tool and the TIMER database. Based on these analyses, a total of 14 m5C-related lncRNAs with prognostic value were selected to build the risk model. Patients were divided into high- and low-risk groups according to the median risk score. The prognosis of the high-risk group was worse than that of the low-risk group, suggesting the good sensitivity and specificity of the constructed risk model. In addition, 5 types of immune cells were significantly different in the high-and low-risk groups, and 6 types of immune cells were negatively correlated with the risk score. These results suggested that the risk model based on 14 m5C-related lncRNAs with prognostic value might be a promising prognostic tool for LUAD and might facilitate the management of patients with LUAD.
SUN5 Interacting With Nesprin3 Plays an Essential Role in Sperm Head-to-Tail Linkage: Research on Sun5 Gene Knockout Mice
Authors: Zhang Yunfei , Yang Linfei , Huang Lihua , Liu Gang , Nie Xinmin , Zhang Xinxing , Xing Xiaowei
Published: June 2021

Acephalic spermatozoa syndrome is a rare genetic and reproductive disease. Recent studies have shown that approximately 33–47% of patients with acephalic spermatozoa syndrome have SUN5 mutations, but the molecular mechanism underlying this phenomenon has not been elucidated. In this study, we generated Sun5 knockout mice and found that the head-to-tail linkage was broken in Sun5–/– mice, which was similar to human acephalic spermatozoa syndrome. Furthermore, ultrastructural imaging revealed that the head-tail coupling apparatus (HTCA) and the centrosome were distant from the nucleus at steps 9–10 during spermatid elongation. With the manchette disappearing at steps 13–14, the head and the tail segregated. To explore the molecular mechanism underlying this process, bioinformatic analysis was performed and showed that Sun5 may interact with Nesprin3. Further coimmunoprecipitation (Co-IP) and immunofluorescence assays confirmed that Sun5 and Nesprin3 were indeed bona fide interaction partners that formed the linker of the nucleoskeleton and cytoskeleton (LINC) complex participating in the connection of the head and tail of spermatozoa. Nesprin3 was located posterior and anterior to the nucleus during spermiogenesis in wild-type mice, whereas it lost its localization at the implantation fossa of the posterior region in Sun5–/– mice. Without correct localization of Nesprin3 at the nuclear membrane, the centrosome, which is the originator of the flagellum, was distant from the nucleus, which led to the separation of the head and tail. In addition, isobaric tag for relative and absolute quantitation results showed that 47 proteins were upregulated, and 56 proteins were downregulated, in the testis in Sun5–/– mice, and the downregulation of spermatogenesis-related proteins (Odf1 and Odf2) may also contribute to the damage to the spermatozoa head-to-tail linkage. Our findings suggested that Sun5 is essential for the localization of Nesprin3 at the posterior nuclear membrane, which plays an essential role in the sperm head-tail connection.
Transforming Growth Factor-β Signaling Regulates Tooth Root Dentinogenesis by Cooperation With Wnt Signaling
Authors: Zhang Ran , Lin Jingting , Liu Yang , Yang Shurong , He Qi , Zhu Liang , Yang Xiao , Yang Guan
Published: June 2021

Proper differentiation of odontoblasts is crucial for the development of tooth roots. Previous studies have reported the osteogenic/odontogenic potential of pre-odontoblasts during root odontoblast differentiation. However, the underlying molecular pathway that orchestrates these processes remains largely unclear. In this study, ablation oftransforming growth factor-βreceptor type 2(Tgfbr2) in root pre-odontoblasts resulted in abnormal formation of root osteodentin, which was associated with ectopic osteogenic differentiation of root odontoblasts. Disrupting TGF-β signaling caused upregulation of Wnt signaling characterized by increasedWnt6,Wnt10a,Tcf-1, andAxin2expression. Interestingly, inhibiting Wnt signaling by deletingWntless(wls) inOsteocalcin(Ocn)-Cre; Tgfbr2fl/fl; Wlsfl/flmice or overexpressing the Wnt antagonistDkk1inOcn-Cre; Tgfbr2fl/fl; ROSA26Dkk1mice decreased ectopic osteogenic differentiation and arrested odontoblast differentiation. Our results suggest that TGF-β signaling acts with Wnt signaling to regulate root odontogenic differentiation.
The Impact of Aging on Macroautophagy in the Pre-ovulatory Mouse Oocyte
Authors: Peters Alexandra E. , Caban Shandelle J. , McLaughlin Eileen A. , Roman Shaun D. , Bromfield Elizabeth G. , Nixon Brett , Sutherland Jessie M.
Published: June 2021

Accompanying the precipitous age-related decline in human female fertility is an increase in the proportion of poor-quality oocytes within the ovary. The macroautophagy pathway, an essential protein degradation mechanism responsible for maintaining cell health, has not yet been thoroughly investigated in this phenomenon. The aim of this study was to characterize the macroautophagy pathway in an established mouse model of oocyte aging using in-depth image analysis-based methods and to determine mechanisms that account for the observed changes. Three autophagy pathway markers were selected for assessment of gene and protein expression in this model: Beclin 1; an initiator of autophagosome formation, Microtubule-associated protein 1 light chain 3B; a constituent of the autophagosome membrane, and lysosomal-associated membrane protein 1; a constituent of the lysosome membrane. Through quantitative image analysis of immunolabeled oocytes, this study revealed impairment of the macroautophagy pathway in the aged oocyte with an attenuation of both autophagosome and lysosome number. Additionally, an accumulation of amphisomes greater than 10 μm2in area were observed in aging oocytes, and this accumulation was mimicked in oocytes treated with lysosomal inhibitor chloroquine. Overall, these findings implicate lysosomal dysfunction as a prominent mechanism by which these age-related changes may occur and highlight the importance of macroautophagy in maintaining mouse pre-ovulatory oocyte quality. This provides a basis for further investigation of dysfunctional autophagy in poor oocyte quality and for the development of therapeutic or preventative strategies to aid in the maintenance of pre-ovulatory oocyte health.
Deep Cavitand Calixarene–Solubilized Fullerene as a Potential Photodynamic Agent
Authors: Zhang Tian-Xing , Li Juan-Juan , Li Hua-Bin , Guo Dong-Sheng
Published: June 2021

Fullerene has attracted much attention in biomedical research due to its unique physical and chemical properties. However, the hydrophobic nature of fullerene is limited to deploy in the body, given that the biofluids are mainly water. In this study, a water-soluble supramolecular nanoformulation based on a deep cavitand calixarene (SAC4A) and fullerene is developed to overcome the hydrophobicity of fullerene and is used as a potential photodynamic agent. SAC4A solubilizes fullerene very well with a simple grinding method. The significantly increased water solubility of fullerene enables efficient activation of reactive oxygen species. The host–guest strategy to solubilize fullerene can not only provide a new method to achieve water solubility but also expand the biomedical applications of fullerene.
Induction of Protective Immunity by a Single Low Dose of a Master Cell Bank cGMP-rBCG-P Vaccine Against the Human Metapneumovirus in Mice
Authors: Soto Jorge A. , Gálvez Nicolás M. S. , Pacheco Gaspar A. , Canedo-Marroquín Gisela , Bueno Susan M. , Kalergis Alexis M.
Published: June 2021

Human metapneumovirus (hMPV) is an emergent virus, which mainly infects the upper and lower respiratory tract epithelium. This pathogen is responsible for a significant portion of hospitalizations due to bronchitis and pneumonia in infants and the elderly worldwide. hMPV infection induces a pro-inflammatory immune response upon infection of the host, which is not adequate for the clearance of this pathogen. The lack of knowledge regarding the different molecular mechanisms of infection of this virus has delayed the licensing of effective treatments or vaccines. As part of this work, we evaluated whether a single and low dose of a recombinant Mycobacterium bovis Bacillus Calmette-Guérin (BCG) expressing the phosphoprotein of hMPV (rBCG-P) can induce a protective immune response in mice. Immunization with the rBCG-P significantly decreased neutrophil counts and viral loads in the lungs of infected mice at different time points. This immune response was also associated with a modulated infiltration of innate cells into the lungs, such as interstitial macrophages (IM) and alveolar macrophages (AM), activated CD4+ and CD8+ T cells, and changes in the population of differentiated subsets of B cells, such as marginal zone B cells and plasma cells. The humoral immune response induced by the rBCG-P led to an early and robust IgA response and a late and constant IgG response. Finally, we determined that the transfer of cells or sera from immunized and infected mice to naïve mice promoted an efficient viral clearance. Therefore, a single and low dose of rBCG-P can protect mice from the disease caused by hMPV, and this vaccine could be a promising candidate for future clinical trials.
The Gut Microbiota of Critically Ill Patients With COVID-19
Authors: Gaibani Paolo , D’Amico Federica , Bartoletti Michele , Lombardo Donatella , Rampelli Simone , Fornaro Giacomo , Coladonato Simona , Siniscalchi Antonio , Re Maria Carla , Viale Pierluigi , Brigidi Patrizia , Turroni Silvia , Giannella Maddalena
Published: June 2021

The SARS-CoV-2-associated COVID-19 pandemic has shaken the global healthcare system. Although the best-known symptoms are dry cough and pneumonia, viral RNA has been detected in the stool and about half of COVID-19 patients exhibit gastrointestinal upset. In this scenario, special attention is being paid to the possible role of the gut microbiota (GM). Fecal samples from 69 COVID-19 patients from three different hospitals of Bologna (Italy) were analyzed by 16S rRNA gene-based sequencing. The GM profile was compared with the publicly available one of healthy age- and gender-matched Italians, as well as with that of other critically ill non-COVID-19 patients. The GM of COVID-19 patients appeared severely dysbiotic, with reduced diversity, loss of health-associated microorganisms and enrichment of potential pathogens, particularly Enterococcus. This genus was far overrepresented in patients developing bloodstream infections (BSI) and admitted to the intensive care unit, while almost absent in other critically ill non-COVID-19 patients. Interestingly, the percentage of patients with BSI due to Enterococcus spp. was significantly higher during the COVID-19 pandemic than in the previous 3 years. Monitoring the GM of critically ill COVID-19 patients could help clinical management, by predicting the onset of medical complications such as difficult-to-treat secondary infections.
The Complete Mitochondrial DNA of Trypanosoma cruzi: Maxicircles and Minicircles
Authors: Callejas-Hernández Francisco , Herreros-Cabello Alfonso , del Moral-Salmoral Javier , Fresno Manuel , Gironès Núria
Published: June 2021

The mitochondrial DNA of Trypanosomatids, known as the kinetoplast DNA or kDNA or mtDNA, consists of a few maxicircles and thousands of minicircles concatenated together into a huge complex network. These structures present species-specific sizes, from 20 to 40 Kb in maxicircles and from 0.5 to 10 Kb in minicircles. Maxicircles are equivalent to other eukaryotic mitochondrial DNAs, while minicircles contain coding guide RNAs involved in U-insertion/deletion editing processes exclusive of Trypanosomatids that produce the maturation of the maxicircle-encoded transcripts. The knowledge about this mitochondrial genome is especially relevant since the expression of nuclear and mitochondrial genes involved in oxidative phosphorylation must be coordinated. In Trypanosoma cruzi (T. cruzi), the mtDNA has a dual relevance; the production of energy, and its use as a phylogenetic marker due to its high conservation among strains. Therefore, this study aimed to assemble, annotate, and analyze the complete repertoire of maxicircle and minicircle sequences of different T. cruzi strains by using DNA sequencing. We assembled and annotated the complete maxicircle sequence of the Y and Bug2148 strains. For Bug2148, our results confirm that the maxicircle sequence is the longest assembled to date, and is composed of 21 genes, most of them conserved among Trypanosomatid species. In agreement with previous results, T. cruzi minicircles show a conserved structure around 1.4 Kb, with four highly conserved regions and other four hypervariable regions interspersed between them. However, our results suggest that the parasite minicircles display several sizes and numbers of conserved and hypervariable regions, contrary to those previous studies. Besides, this heterogeneity is also reflected in the three conserved sequence blocks of the conserved regions that play a key role in the minicircle replication. Our results using sequencing technologies of second and third-generation indicate that the different consensus sequences of the maxicircles and minicircles seem to be more complex than previously described indicating at least four different groups in T. cruzi minicircles.
Understanding Cybersecurity Threat Trends Through Dynamic Topic Modeling
Authors: Sleeman Jennifer , Finin Tim , Halem Milton
Published: June 2021

Cybersecurity threats continue to increase and are impacting almost all aspects of modern life. Being aware of how vulnerabilities and their exploits are changing gives helpful insights into combating new threats. Applying dynamic topic modeling to a time-stamped cybersecurity document collection shows how the significance and details of concepts found in them are evolving. We correlate two different temporal corpora, one with reports about specific exploits and the other with research-oriented papers on cybersecurity vulnerabilities and threats. We represent the documents, concepts, and dynamic topic modeling data in a semantic knowledge graph to support integration, inference, and discovery. A critical insight into discovering knowledge through topic modeling is seeding the knowledge graph with domain concepts to guide the modeling process. We use Wikipedia concepts to provide a basis for performing concept phrase extraction and show how using those phrases improves the quality of the topic models. Researchers can query the resulting knowledge graph to reveal important relations and trends. This work is novel because it uses topics as a bridge to relate documents across corpora over time.
Holdout-Based Empirical Assessment of Mixed-Type Synthetic Data
Authors: Platzer Michael , Reutterer Thomas
Published: June 2021

AI-based data synthesis has seen rapid progress over the last several years and is increasingly recognized for its promise to enable privacy-respecting high-fidelity data sharing. This is reflected by the growing availability of both commercial and open-sourced software solutions for synthesizing private data. However, despite these recent advances, adequately evaluating the quality of generated synthetic datasets is still an open challenge. We aim to close this gap and introduce a novel holdout-based empirical assessment framework for quantifying the fidelity as well as the privacy risk of synthetic data solutions for mixed-type tabular data. Measuring fidelity is based on statistical distances of lower-dimensional marginal distributions, which provide a model-free and easy-to-communicate empirical metric for the representativeness of a synthetic dataset. Privacy risk is assessed by calculating the individual-level distances to closest record with respect to the training data. By showing that the synthetic samples are just as close to the training as to the holdout data, we yield strong evidence that the synthesizer indeed learned to generalize patterns and is independent of individual training records. We empirically demonstrate the presented framework for seven distinct synthetic data solutions across four mixed-type datasets and compare these then to traditional data perturbation techniques. Both a Python-based implementation of the proposed metrics and the demonstration study setup is made available open-source. The results highlight the need to systematically assess the fidelity just as well as the privacy of these emerging class of synthetic data generators.
Modeling Challenge Data to Quantify Endogenous Lactate Production
Authors: Stefanovski Darko , Wilkins Pamela A. , Boston Raymond C.
Published: June 2021

With the intention of isolating the susceptibility of modeling methodology to influence our investigation of the infusion data, we used three kinetic approaches to our models: a simple approach, a unit approach, and a novel approach. The simple approach used exclusively built-in modeling features of the software in terms of units of the infusion dilution (mmol/L), as well as in terms of the precision of switching the infusion on and off. The unit approach used the same switching mechanism as the simple approach, but the units were modeled in those of the infusion (e.g., mmol/kg). Thirdly with the novel approach, we used an automated approach to controlling the infusion, in the sense that as the modeling mechanism sensed the slowdown of the infusion, it was gradually turned off. The units of the analysis for the novel approach were exactly the same as those deployed in the unit approach. Our objective here was to see if common pharmacokinetic parameters were seriously impacted by the particular modeling method.
Epigenetic Marks and Variation of Sequence-Based Information Along Genomic Regions Are Predictive of Recombination Hot/Cold Spots in Saccharomyces cerevisiae
Authors: Liu Guoqing , Song Shuangjian , Zhang Qiguo , Dong Biyu , Sun Yu , Liu Guojun , Zhao Xiujuan
Published: June 2021

Characterization and identification of recombination hotspots provide important insights into the mechanism of recombination and genome evolution. In contrast with existing sequence-based models for predicting recombination hotspots which were defined in a ORF-based manner, here, we first defined recombination hot/cold spots based on public high-resolution Spo11-oligo-seq data, then characterized them in terms of DNA sequence and epigenetic marks, and finally presented classifiers to identify hotspots. We found that, in addition to some previously discovered DNA-based features like GC-skew, recombination hotspots in yeast can also be characterized by some remarkable features associated with DNA physical properties and shape. More importantly, by using DNA-based features and several epigenetic marks, we built several classifiers to discriminate hotspots from coldspots, and found that SVM classifier performs the best with an accuracy of ∼92%, which is also the highest among the models in comparison. Feature importance analysis combined with prediction results show that epigenetic marks and variation of sequence-based features along the hotspots contribute dominantly to hotspot identification. By using incremental feature selection method, an optimal feature subset that consists of much less features was obtained without sacrificing prediction accuracy.
The Role of the IL-23/IL-17 Axis in Disease Initiation in Spondyloarthritis: Lessons Learned From Animal Models
Authors: Mandour Mohamed , Chen Sijia , van de Sande Marleen G. H.
Published: June 2021

Spondyloarthritis (SpA) is a spectrum of chronic inflammatory joint diseases that frequently presents with inflammation of the axial skeleton, peripheral joints, entheses, skin, and gut. Understanding SpA pathogenesis has been proven challenging due to the limited availability of human target tissues. In recent years, the interleukin (IL)-23/IL-17 pathway has been implicated in the pathogenesis of SpA, in addition to the Tumor Necrosis Factor Alpha (TNF-α) cytokine. The underlying molecular mechanisms by which the IL-23/IL-17 pathway triggers disease initiation, both in the joints as well as at extra-musculoskeletal sites, are not precisely known. Animal models that resemble pathological features of human SpA have provided possibilities for in-depth molecular analyses of target tissues during various phases of the disease, including the pre-clinical initiation phase of the disease before arthritis and spondylitis are clinically present. Herein, we summarize recent insights gained in SpA animal models on the role of the IL-23/IL-17 pathway in immune activation across affected sites in SpA, which include the joint, entheses, gut and skin. We discuss how local activation of the IL-23/IL-17 axis may contribute to the development of tissue inflammation and the onset of clinically manifest SpA. The overall aim is to provide the reader with an overview of how the IL-23/IL-17 axis could contribute to the onset of SpA pathogenesis. We discuss how insights from animal studies into the initiation phase of disease could instruct validation studies in at-risk individuals and thereby provide a perspective for potential future preventive treatment.
Expression and Function Analysis of Interleukin-17A/F1, 2, and 3 Genes in Yellow Catfish (Pelteobagrus fulvidraco): Distinct Bioactivity of Recombinant IL-17A/F1, 2, and 3
Authors: Zhou Xu , Zhang Gui-Rong , Ji Wei , Shi Ze-Chao , Ma Xu-Fa , Luo Zun-Lan , Wei Kai-Jian
Published: June 2021

In mammals, Interleukin-17 cytokine family plays critical roles in both acute and chronic inflammatory responses. In fish species, three Interleukin-17A/F (IL-17A/F) genes have been identified to be homologous to mammalian IL-17A and IL-17F, but little is known about their functional activity. In this study, Pf_IL-17A/F1, 2 and 3 genes were cloned from yellow catfish (Pelteobagrus fulvidraco) and they differed in protein structure and exon length, implying that they may have divergent bioactivity. Real-time quantitative PCR analyses revealed that three Pf_IL-17A/F genes were highly expressed in blood and mucosal tissues (skin+mucus and gill) from healthy adult fish. The mRNA expressions of Pf_IL-17A/F1, 2 and 3 genes were significantly up-regulated in the gill, skin+mucus, head kidney and spleen after challenge with Edwardsiella ictaluri and in the isolated peripheral blood leucocytes (PBLs) of yellow catfish after stimulation with phytohaemagglutinin (PHA), lipopolysaccharides (LPS), peptidoglycan (PGN) and polyinosinic-polycytidylic acid (Poly I:C). These results indicate that Pf_IL-17A/F1, 2 and 3 genes may play a vital role in the regulation of immune against pathogens. Additionally, the recombinant (r) Pf_IL-17A/F1, 2 and 3 proteins significantly induced the mRNA expressions of proinflammatory cytokines, chemokines and antibacterial peptides genes, and the rPf_IL-17A/F 2 and 3 proteins promoted phagocytosis of PBLs more powerfully than the rPf_IL-17A/F1. Furthermore, the rPf_IL-17A/F1, 2 and 3 proteins might activate the NF-κB and MAPK signal pathways by IL-17RA, ACT1, TRAF6, TRAF2, TRAF5 and TAK1, indicating that the three Pf_IL-17A/F proteins may play different roles in promoting inflammatory response.
EVA1C Is a Potential Prognostic Biomarker and Correlated With Immune Infiltration Levels in WHO Grade II/III Glioma
Authors: Hu Zhicheng , Qu Shanqiang
Published: June 2021

Background

Immunotherapy is an effective therapeutic approach for multiple human cancer types. However, the correlations between EVA1C and patients’ prognosis as well as immune infiltration remain obscure. Herein, we employed transcriptomic and clinical data extracted from two independent databases to systematically investigate the role of EVA1C in the oncological context.

Methods

The differential expression of EVA1C was analyzed via TCGA and Oncomine databases. We evaluated the influence of EVA1C on clinical prognosis using Kaplan-Meier plotter. We then used the expression profiler to calculate stromal score, immune score, and ESTIMATE score based on the ESTIMATE algorithm. The abundance of infiltrating immune cells was calculated via TIMER. The correlations between EVA1C expression and immune infiltration levels were analyzed in two independent cohorts.

Results

In patients with World Health Organization (WHO) grade II/III glioma, high EVA1C expression was associated with malignant clinicopathological features and poor overall survival in both cohorts. EVA1C expression was positively associated with immune infiltration levels of B cell, CD4+ T cell, neutrophil, macrophage, and dendritic cells (DCs). Besides, EVA1C expression strongly correlated with diverse immune marker sets. And the predictive power of EVA1C was better than that of other indicators in predicting high immune infiltration levels in glioma.

Conclusions

For the first time, we identified the overexpression of EVA1C in glioma, which was tightly correlated with the high infiltration levels of multiple immune cells as well as poor prognosis. Meanwhile, EVA1C might be a potential biomarker for predicting high immune infiltration in WHO grade II/III gliomas.
Limitations of a Commercial Assay as Diagnostic Test of Autoimmune Encephalitis
Authors: Ruiz-García Raquel , Muñoz-Sánchez Guillermo , Naranjo Laura , Guasp Mar , Sabater Lidia , Saiz Albert , Dalmau Josep , Graus Francesc , Martinez-Hernandez Eugenia
Published: June 2021

Detection of neuronal surface antibodies (NSAb) is important for the diagnosis of autoimmune encephalitis (AE). Although most clinical laboratories use a commercial diagnostic kit (Euroimmun, Lübeck, Germany) based on indirect immunofluorescence on transfected cells (IIFA), clinical experience suggests diagnostic limitations. Here, we assessed the performance of the commercial IIFA in serum and CSF samples of patients with suspected AE previously examined by rat brain immunohistochemistry (Cohort A). Of 6213 samples, 404 (6.5%) showed brain immunostaining suggestive of NSAb: 163 (40%) were positive by commercial IIFA and 241 (60%) were negative. When these 241 samples were re-assessed with in-house IIFA, 42 (18%) were positive: 21 (9%) had NSAb against antigens not included in the commercial IIFA and the other 21 (9%) had NSAb against antigens included in the commercial kit (false negative results). False negative results occurred more frequently with CSF (29% vs 10% in serum) and predominantly affected GABABR (39%), LGI1 (17%) and AMPAR (11%) antibodies. Results were reproduced in a separate cohort (B) of 54 AE patients with LGI1, GABABR or AMPAR antibodies in CSF which were missed in 30% by commercial IIFA. Patients with discordant GABABR antibody results (positive in-house but negative commercial IIFA) were less likely to develop full-blown clinical syndrome; no significant clinical differences were noted for the other antibodies. Overall, NSAb testing by commercial IIFA led to false negative results in a substantial number of patients, mainly those affected by anti-LG1, GABABR or AMPAR encephalitis. If these disorders are suspected and commercial IIFA is negative, more comprehensive antibody studies are recommended.
The Mid-Atlantic Bight Dissolved Inorganic Carbon System Observed in the March 1996 DOE Ocean Margins Program (OMP)—A Baseline Study
Authors: Huang Ting-Hsuan , Cai Wei-Jun , Vlahos Penny , Wallace Douglas W. R. , Lewis Ernie R. , Chen Chen-Tung Arthur
Published: June 2021

The United States Department of Energy (DOE)’s Ocean Margins Program (OMP) cruise EN279 in March 1996 provides an important baseline for assessing long-term changes in the carbon cycle and biogeochemistry in the Mid-Atlantic Bight (MAB) as climate and anthropogenic changes have been substantial in this region over the past two decades. The distributions of O2, nutrients, and marine inorganic carbon system parameters are influenced by coastal currents, temperature gradients, and biological production and respiration. On the cross-shelf direction, pH decreases seaward, but carbonate saturation state (ΩArag) does not exhibit a clear trend. In contrast, ΩArag increases from north to south, while pH has no clear spatial patterns in the along-shelf direction. In order to distinguish between the effects of physical mixing of various water masses and those of biological activities on the marine inorganic carbon system, we use the potential temperature-salinity diagram to identify water masses, and differences between observations and theoretical mixing concentrations to measure the non-conservative (primarily biological) effects. Our analysis clearly shows the degree to which ocean margin pH and ΩArag are regulated by biological activities in addition to water mass mixing, gas exchange, and temperature. The correlations among anomalies in dissolved inorganic carbon, phosphate, nitrate, and apparent oxygen utilization agree with known biological stoichiometry. Biological uptake is substantial in nearshore waters and in shelf-slope mixing areas. This work provides valuable baseline information to assess the more recent changes in the marine inorganic carbon system and the status of coastal ocean acidification.
Quantitative Monitoring of Bolt Looseness Using Multichannel Piezoelectric Active Sensing and CBAM-Based Convolutional Neural Network
Authors: Chen Yixuan , Jiang Jian , Qin Xiaojun , Feng Qian
Published: June 2021

The bolted connection is widely utilized in engineering to practically and rigidly couple structural components. The integrity of the connection is paramount to the safety of the structure and has prompted the development of many monitoring methods, including the piezoelectricity-based active sensing method. However, the active sensing method cannot quantify bolt looseness due to the unclear relationship between bolt looseness and the single monitoring index typically used in the active sensing method. Thus, the authors propose the unique combination of a one-dimensional convolutional neural network (1DCNN) and multichannel active sensing for quantitative monitoring of bolted connections. In an experiment, piezoelectric ceramic transducer (PZT) patches are bonded on steel plates connected by a bolt. Each patch is wired to a multichannel active sensing monitoring system. After obtaining multichannel stress wave signals at different looseness levels, a looseness vector is calculated to generate training and validation datasets. A baseline 1DCNN model and a novel model improved using the convolutional block attention module (CBAM) are used to monitor the bolt looseness. Finally, the authors verify that the multichannel active sensing method combined with the 1DCNN model can accurately perform quantitative monitoring of bolt looseness, and the monitoring accuracy of the baseline 1DCNN model is above 91.07% in three different specimens. Compared with the baseline 1DCNN model, the monitoring accuracy of the CBAMCNN model improved by approximately 5%. Overall, the method proposed in this article offers a new and highly accurate approach for quantitative monitoring of bolted connections.
Proliferation Increasing Genetic Engineering in Human Corneal Endothelial Cells: A Literature Review
Authors: Arras Wout , Vercammen Hendrik , Ní Dhubhghaill Sorcha , Koppen Carina , Van den Bogerd Bert
Published: June 2021

The corneal endothelium is the inner layer of the cornea. Despite comprising only a monolayer of cells, dysfunction of this layer renders millions of people visually impaired worldwide. Currently, corneal endothelial transplantation is the only viable means of restoring vision for these patients. However, because the supply of corneal endothelial grafts does not meet the demand, many patients remain on waiting lists, or are not treated at all. Possible alternative treatment strategies include intracameral injection of human corneal endothelial cells (HCEnCs), biomedical engineering of endothelial grafts and increasing the HCEnC density on grafts that would otherwise have been unsuitable for transplantation. Unfortunately, the limited proliferative capacity of HCEnCs proves to be a major bottleneck to make these alternatives beneficial. To tackle this constraint, proliferation enhancing genetic engineering is being investigated. This review presents the diverse array of genes that have been targeted by different genetic engineering strategies to increase the proliferative capacity of HCEnCs and their relevance for clinical and research applications. Together these proliferation-related genes form the basis to obtain a stable and safe supply of HCEnCs that can tackle the corneal endothelial donor shortage.