bluuebunny/crossref_metadata_2025 huggingface dataset:
Discovery of Potential Compounds Against Nipah Virus: A Molecular Docking and Dynamics Simulation Approaches
Authors: Bhuiyan Maruf Ahmed , Keya Nawshin Atia , Mou Farha Susan , Imon Raihan Rahman , Alam Rahat , Samad Abdus , Ahammad Foysal
Published: March 2022

Nipah virus (NiV) is a zoonotic pathogen that causes Nipah encephalitis. it was thought to have transmitted from bats to pigs and ultimately to humans. Infected humans may experience an asymptomatic infection or mild to deadly symptoms. The coordinated actions of envelope attachment glycoprotein led to viral entry. NiV has been classified as a pandemic potential virus due to the lack of specialized vaccinations or treatments, as well as its high pathogenicity. In Computer-Aided Drugs Design study, active site prediction, ADMET properties, molecular docking assist to select five suitable small molecular compounds including control compound against NiV attachment glycoprotein(G) chain A to suppress its function. Binding affinity scores of selected compounds were distributed between -6.2 to -6.5 kcal/mol. All the selected compounds had desirable non-toxic and good pharmacokinetics properties. In Molecular Dynamic (MD) simulation, the ligands Amb33921182, Amb35795905, Amb22736116, and Amb28974637 are all potential drug candidates, but Amb33921182 is the most acceptable. This in-silico method has the potential to help with drug discovery and development in a short period of time against Nipah virus.
Infodemiology of autoimmune encephalitis: An analysis of online search behavior using Google Trends
Authors: Roberto Katrina Torres , Jamora Roland Dominic G. , Moalong Kevin Michael C. , Espiritu Adrian I.
Published: March 2022

BackgroundPatients and their caregivers, including clinicians and educators, use web-based search engines to access healthcare-related information from the internet. Online search behavior analysis has been used to obtain insights on health information demand.ObjectivesWe aimed to describe the online search behavior for autoimmune encephalitis worldwide over time through the analysis of search volumes made on Google.MethodsIn this infodemiological study, we retrieved search volume indices for the keyword “autoimmune encephalitis (disease)” based on worldwide search data from January 01, 2004 to October 31, 2021, using Google Trends. We performed a descriptive analysis of search volume patterns, including related topics and queries.ResultsThere was a progressive increase in search volume numbers over time for the keyword “autoimmune encephalitis (disease)” with no annual seasonal variation. Peak search volume was recorded in July 2018. The greatest search volume was recorded in Singapore, followed by Australia, the United States of America, the Philippines, and New Zealand. The most searched topics were related to autoimmune encephalitis definition, causes, symptoms, diagnosis, and treatment. All related topics and queries increased in volume by more than 5000-fold over time.ConclusionsThis study showed an uptrend in the online search interest on autoimmune encephalitis over time, which may reflect the increased awareness on the condition by the public and the medical community. Information on online health information-seeking behavior may be obtained from Google Trends data despite its limitations.
An investigation into mental distress among students at Universities in the Eastern Cape, South Africa
Authors: Mutinta Given
Published: March 2022

IntroductionMental distress is a global health concern. Studies show that the prevalence of mental distress is higher in students’ population than in the general population. Therefore, there is need to understand the extent and predictors of mental distress among students to help policymakers and practitioners in South Africa. Aim of the studyTh­e study was designed to investigate into the prevalence and predictors of mental distress among students at universities in the Eastern Cape Province, South Africa. MethodsA cross-sectional research design and quantitative research method guided this study. The data were collected from 844 students from four universities in the Eastern Cape Province using an online self-reporting questionnaire-20 to assess mental distress of students. Multivariable logistic regression modelling determined the association between socio-demographic and psychosocial factors with students’ mental distress.Findings The prevalence of mental distress among students was 53.3% (95% CI: 47.0%, 58.1%). Female students were more prone to mental distress than male students ([AOR]: 4.67; 95% CI: 2.82, 7.72). Poor sleep quality (AOR: 2.24; 95% CI: 1.13, 3.67) and using cannabis (AOR: 3.10; 95% CI: 1.755, 5.51) were significantly correlated with students’ mental distress.Conclusion and recommendations The study found the level of mental distress to be higher among students than what is reported in most of the previous studies in South Africa. Being a female student, a user of cannabis, and having poor sleep quality were predictors of mental distress. Findings point to the need to devise evidence-driven interventions and strategies to prevent and reduce the problem of mental distress among students.
Complexin-1 Regulated Assembly of Single Neuronal SNARE Complex Revealed by Dual-Trap Optical Tweezers
Authors: Hao Tongrui , Feng Nan , Gong Fan , Yu Yang , Liu Jiaquan , Ren Yu-Xuan
Published: March 2022

The dynamic assembly of the Synaptic-soluble N-ethylmaleimide-sensitive factor Attachment REceptor (SNARE) complex is crucial to the membrane fusion. Traditional ensemble studies lack the information of dynamic assembly of the protein complex. Here, we apply minute force on a tethered protein complex through dual-trap optical tweezers and study the folding dynamics of SNARE complex under mechanical force regulated by complexin-1 (CpxI). We reconstructed the clamp and facilitate functions of CpxI in vitro. Specially, the 1–83 amino acids (aa) of CpxI mainly implement the facilitate function, while the N-terminal domain (NTD) plays a dominant role. CTD is mainly related to Clamping, and separate 1-83aa and C-terminal domain (CTD) of CpxI can efficiently reconstitute the inhibitory signal identical to that the full-length CpxI functions. Our observation identifies the important chaperone role of the CpxI molecule in the dynamic assembly of SNARE complex under mechanical tension, and elucidates the specific function of each fragment of CpxI molecules in the chaperone process. Additionally, the developed technique may also be applied to study the mechanobiology and folding dynamics of single molecular protein complex.
Applicability of AC impedance method for measuring time-variant corrosion rate to cracked and crack-repaired reinforced concrete
Authors: Kanemitsu Toshinori , Takaya Satoshi
Published: March 2022

Purpose

Several models of the time-variant corrosion rate (CR) have been proposed to predict the service life of reinforced concrete (RC) structures based on polarization resistance (PR) monitoring. However, few of them have verified the accuracy by comparing the estimated corrosion weight loss (CWL) obtained from the PR monitoring with the actual CWL. In addition, few studies have measured the time-variant CR on crack-repaired RC specimens, and the evaluation of repair efficacy is clearly an essential step in the maintenance of the structures. This study aims to clarify the applicability of the alternating current (AC) impedance method, one of the PR methods, to cracked and crack-repaired RC.

Methods

The CRs in such RC in an accelerated corrosion environment were measured every one to three months over three years using the AC impedance method. To confirm accuracy, the corroded area and CWL of the steel bars were measured.

Results

The results clarify that the measurement area of the AC impedance method was almost equal to the corroded area, which indicates that the corrosion area should be calculated in addition to the CWL for accuracy verification. The results also show that the AC impedance method can be applied to cracked and crack-repaired RC for measuring time-variant CR.

Conclusion

The CR increases rapidly after crack initiation but becomes constant with time, and early crack repair can delay corrosion progress in cracked RC to the same extent as in uncracked concrete.
Galla chinensis exhibits anticancer activity in HPV-16 infected cervical cancer cells
Authors: Zhang XuXuan , Ma XiaoPing , Wang Zhe , Dang Hongwei , Yu Wei , Han Bo , Ren Yan
Published: March 2022

Background
Cervical cancer induced by the human papillomavirus (HPV) is one of the most common cancers in women in developing countries. Novel treatments for cervical cancer are focused on bioactive metabolites obtained from natural sources.
Materials and Methods
The biological effects of Galla Chinensis on HPV16 + cells were analyzed by cell scratch and plate cloning, and the cycle process was evaluated by flow cytometry; PCR, WB and immunofluorescence techniques were used to explore its mechanism
Results
It was shown that compared to a blank control group, Galla chinensis is less toxic to cervical cancer cells and exhibits prominent inhibitory effects on the growth, cloning, and migration of SiHa adherent cells. The effects of Galla chinensis also included cell cycle arrest in the S phase, and our obtained results suggest that its mechanism of action may involve the downregulation of the HPV E6 oncoprotein and the reconstruction of the p53 functional protein.
Conclusion
It is proved that Galla chinensis can effectively eliminate HPV16 + cells and inhibit the development of cervical cancer. It can down regulate oncoprotein E6 and up regulate tumor suppressor protein p53.
Effects of Non-symmetrical Current Distribution Controlled by Capacitor Placement in Loop Coils at 300 MHz MRI
Authors: Hernandez Daniel , Kim Donghyuk , Jeong Yonghwa , Nam Taewoo , Kim Kyoung-Nam
Published: March 2022

In this work, we present a study on the effects of the non-symmetric electrical design of radiofrequency (RF) coils for magnetic resonance imaging (MRI) operating at ultra-high frequency (UHF). A typical loop coil used in MRI consists of symmetrically distributed capacitors along the coil; this design is able to produce uniform current distributions inside the coil. However, in UHF conditions, the magnetic flux density (|B1|) field produced by this setup may exhibit field distortion, requiring a method of controlling the field distribution and improving the field intensity of the circular loop coil. The control mechanism investigated in this study is based on the position of the tuning capacitor in the circular coil. We performed comparisons against a reference coil that is based on a circular coil with four symmetrically distributed tuning capacitors. We performed electromagnetic (EM) simulations and MRI at 7 T to determine the effects of variations in the position of the capacitor and confirmed that unbalanced current distributions were created.
Robot Arm Grasping Using Learning-Based Template Matching and Self-Rotation Learning Network
Authors: Le Minh-Tri , Lien Jenn-Jier James
Published: March 2022

Applying deep neural network models to robot-arm grasping tasks requires the laborious and time-consuming annotation of a large number of representative examples in the training process. Accordingly, this work proposes a two-stage grasping model, in which the first stage employs learning-based template matching (LTM) algorithm for estimating the object position, and a self-rotation learning (SRL) network is then proposed to estimate the rotation angle of the grasping objects in the second stage. The LTM algorithm measures similarity between the feature maps of the search and template images which are extracted by a pre-trained model. While the SRL network performs the automatic rotation and labelling of the input data for training purposes. Therefore, the proposed model does not consume an expensive human-annotation process. The experimental results show that the proposed model obtains 92.6% when testing on 2400 pairs of the template and target images. Moreover, in performing practical grasping tasks on a NVidia Jetson TX2 developer kit, the proposed model achieves a higher accuracy (88.5%) than other grasping approaches on a split of Cornell-grasp dataset.
Liquefaction and Reliquefaction Characteristics of Cement Mixing Pile Strengthening Aeolian Sand Subgrade
Authors: Zhou Yuan , Wu Honggang , Ma Zhigang , Sun Hao
Published: March 2022

When the line project passes through a large area of aeolian sand, cement mixing piles are often used to reinforce the subgrade, which can effectively improve the bearing capacity of the subgrade, but its anti-liquefaction effect is worthy of in-depth evaluation. Intermittent earthquakes cause more than one liquefaction of aeolian sand subgrade, so it is worth further research on the re-liquefaction characteristics of cement mixing piles in treatment of aeolian sand subgrade. In this paper, a real-time comparative test (pile reinforced area and unreinforced area) is carried out through a shaking table, and the liquefaction and re-liquefaction characteristics of the reinforced subgrade are mainly explored. The experimental model will produce the following results under 0.4g EL Centro wave excitation:(1) The pore pressure will have multiple peaks, causing the surface of the model to float or sink. The phenomenon will be weakened by experiencing multiple earthquakes of the same level or using pile reinforcement;(2) The deeper the burial depth, the longer the time for the pore pressure to reach the maximum peak value. After multiple vibrations, the corresponding time of the shallow layer in the unreinforced area and the deep layer in the reinforced area doubles;(3) The cement mixing pile can improve the liquefaction and re-liquefaction resistance of aeolian sand foundation, and the effect is best in the shallow foundation, with an increase of more than 30%, and the deeper the burial depth, the lower the effect;(4) After the subgrade has experienced a strong earthquake, its resistance to liquefaction will be improved, but the acceleration response during the next earthquake will increase significantly.
Designing a zero-order energy transition model: a guide for creating a Starter Data Kit
Authors: Cannone Carla , Allington Lucy , Barron Karla Cervantes , Charbonnier Flora , Walker Miriam Zachau , Halloran Claire , Yeganyan Rudolf , Tan Naomi , Cullen Jonathan M , Harrison John , To Long Seng , Howells Mark
Published: March 2022

The Paris Agreement was signed by 192 Parties, who committed to reducing emissions. Reaching such commitments by developing national decarbonisation strategies requires significant analyses and investment. Analyses for such strategies are often delayed due to a lack of accurate and up-to-date data for creating energy transition models. The Starter Data Kits address this issue by providing open-source, zero-level country datasets to accelerate the energy planning process. There is a strong demand for replicating the process of creating Starter Data Kits because they are currently only available for 69 countries in Africa, Asia, and South America. Using an African country as an example, this paper presents the methodology to create a Starter Data Kit from data collection to the creation of tool-agnostic data repositories. The paper illustrates the steps involved, provides additional information for conducting similar work in Asia and South America, and highlights the limitations of the current version of the Starter Data Kits. Future development is proposed to expand the datasets, including new and more accurate data and new energy sectors.
4-oxo-2-thioxo-1,2,3,4-tetrahydropyrimidine-5-carbohydrazide (TC) based materials; DFT, NBO analysis, Fukui function analysis, photovoltaic and solar
Authors: Sakr Mahmoud , Sherbiny Farag , El-Etrawy Abd-Allah
Published: March 2022

Due to numerous pharmaceutical and biological activities 4-oxo-2-thioxo-1,2,3,4-tetrahydropyrimidine-5-carbohydrazide (TC) based materials, it was important to investigate Density functional theory (DFT) calculations, natural bond orbital (NBO) analysis, molecular electrostatic potential (MESP), and local reactivity usage Fukui function for six TC derivatives compounds. DFT, NBO, MESP, and local reactivity calculations were obtained via utilizing CAM-Becke's three-parameter functional and Leee Yange Parr (CAM-B3LYP) functional and 6-311G++(2d, 2p) basis set. Optimized molecular structures for all studied compounds were obtained usage the DFT/CAM-B3LYP/6-311G++(2d, 2p) method. In addition, the highest occupied molecular orbital (HOMO), lowest unoccupied molecular orbital (LUMO), energy gap (Eg), light harvest efficiency (LHE), and open-circuit voltage (Voc) of all studied MSs are calculated and illustrated. These properties indicate that these molecular modeling structures as good candidates for utilization in organic DSSCs.
Spatial transcriptomic revealed intratumor heterogeneity and cancer stem cell enrichment in colorectal cancer metastasis
Authors: Zhou Leqi , Wen Rongbo , Yu Guanyu , Zheng Kuo , Li Zhixuan , Yu Yue , Zhu Xiaoming , Sui Jinke , Gong Haifeng , Lou Zheng , Hao Liqiang , Bai Chenguang , Yang Fu , Zhang Wei
Published: March 2022

Background & Aims Metastasis is the main cause of mortality in colorectal cancer (CRC) patients. Exploring the mechanisms of metastasis is of great importance in both clinical and fundamental CRC research. CRC is a highly heterogeneous disease with variable therapeutic outcomes of treatment. Approach & Results In this study, we applied spatial transcriptomics (ST) to generate a tissue-wide transcriptome from two primary colorectal cancer tissues and their matched liver metastatic tissues. Spatial RNA information showed intratumoral heterogeneity (ITH) of both primary and metastatic tissues. The comparison of gene expressions across tissues revealed an apparent enrichment of cancer stem cells (CSCs) in metastatic tissues and identified FOXD1 as a novel metastatic CSC marker. Trajectory and pseudo-time analyses revealed distinct evolutionary trajectories and a dedifferentiation-differentiation process during metastasis. CellphoneDB analysis suggested a dominant interaction of CD74-MIF with tumor cells in metastatic tissues. FOXD1 was also found to be an independent risk factor and predictor of patient survival. Conclusions Our study found ITH of primary and metastatic tissues and provides novel insights into the cellular mechanisms underlying liver metastasis of CRC and foundations for therapeutic strategies for CRC metastasis.
Sigmoid colon metastasis after radical nephrectomy for clear cell renal carcinoma: a case report and literature review
Authors: Che Hao , Li Zhenjun , Yao Yuechao , Ying Xiaojiang , Wang Zian , Chen Zhiliang , Tian GuoJiang , Lu Zengxin , Liu Xibo
Published: March 2022

Background: Metastasis of renal cell carcinoma most commonly occurs in the lungs, lymph nodes, bones, liver, and brain. It is rare for CCRCC to metastasize to the sigmoid colon after radical nephrectomy, which often signifies systemic metastasis and poor prognosis. Case Presentation: A 65-year-old woman was hospitalized for bloody stools, and she had a radical nephrectomy eight years ago after being diagnosed with CCRCC. The preoperative colonoscopic biopsy failed to clarify the nature of the mass, and the imaging examination suggested that the mass may be malignant. Following surgery to remove the mass, it was diagnosed as sigmoid metastatic CCRCC according to histopathology and immunohistochemistry. At present, she was in good health, and no clinical or radiological evidence of metastasis was found in her 11-month follow-up after surgery. Conclusion: Metastasis may take a long time to appear after radical nephrectomy, so it is essential to actively follow up and review patients who have undergone renal cancer surgery, and early detection and treatment of metastases remain crucial.
Clonal and Seasonal Variation of Major Essential Oil Components of Salvia fruticosa Clones
Authors: Uysal Fatma , Gölükçü Muharrem , Alan Murat , Alım Esra , Turgut Kenan
Published: March 2022

Anatolian sage (Salvia fruticosa MILL.) is widely used in many sectors such as food, cosmetics, and pharmaceuticals. The components in an essential oil species are important criteria to determine the usage area. This study was carried out to determine the differences in essential oil components and seasonal changes in the components of six clonally selected C-clones and one natural population. Samples were collected monthly from C-clones for two years, and essential oil ratios were determined. Assessment of all clones revealed that the time of monthly harvests had a significant effect on essential oil components. The highest β-caryophyllene content of clones was recorded in December or February and for essential oil in August. The clone and harvest time interaction caused significant differences in essential oil components, and clones reached the highest values in different months. The highest 1.8 cineole content of clones was recorded between March and June. High variation in the components, the differences in harvest times, and high correlations between components indicated that clones developed by selection have a significant production potential.
Single track formation of pure copper in directed energy deposition using a blue laser
Authors: Yamaguchi Mitsugu , Yamazaki Masamichi , Funada Yoshinori , Yachi Taisei , Saikai Ayahito , Furmoto Tatsuaki
Published: March 2022

Additive manufacturing (AM) techniques, including directed energy deposition (DED), have been developed and applied in the copper parts manufacturing. DED processes with conventional infrared lasers require more energy owing to the low laser absorptivity of copper. Moreover, local thermal gradients cause large residual stresses, resulting in cracks, deformation, and failure of parts. This study focused on the DED process of pure copper using a blue laser with a wavelength of 445 nm and addressed the following deficiencies. Firstly, the influence of process parameters on the geometry and surface defects of the built structure, such as meandering, distortion, and cracking, were investigated. Secondly, the chemical composition of cross-sections of the built structure was analyzed using an electron probe microanalyzer (EPMA). Finally, a prediction of surface defect-free building conditions was presented. The results indicated that the laser power directly affected the built width and penetration depth, while the built height varied with the rate of powder supplied, and that the traverse speed was inversely proportional to the built height and width. The meandering and distortion of the built structure may be attributed to changes in the melting of the powder and process instability due to obstructions in the optical path of the laser. Meanwhile, the cracks generated owing to shrinkage during solidification when the molten area was formed by laser irradiation are insufficient. A structure without defects can be obtained at a powder feed rate of 20 mg/s, laser power between 60–270 W, and traverse speeds between 10–20 mm/s.
Performance of the EULAR/ACR 2019 classification criteria for systemic lupus erythematous in monogenic lupus
Authors: Al-Mayouf Sulaiman M , Akbar Lujayn , Abdwani Reem , Ginesi Giulia , Volpi Stefano , Gattorno Marco , Bakry Reima , AlHashim Samia , Alsaleem Alhanouf
Published: March 2022

ObjectiveTo evaluate the application of the EULAR/ACR-2019 criteria to monogenic lupus patients and compare its performance against the SLICC-2012 criteria. Methods In a multicenter retrospective cohort study, consecutive patients with monogenic lupus from three tertiary lupus clinics were enrolled. The diagnosis of monogenic lupus was based on the expert physician’s opinion or fulfilling the SLICC-2012 criteria. All enrolled patients had genetic variants. A control group of sporadic childhood SLE (cSLE) and non-SLE patients, were included. A descriptive data analysis was conducted, and the EULAR/ACR-2019 and SLICC-2012 criteria were applied to both groups.Results Forty-nine patients with monogenic lupus with a median age at diagnosis of 6.0 (IQR 3.0-10.8) years, and 104 controls (55 patients with cSLE and 49 non-lupus patients with a median age at diagnosis of 10.0 and 5.0 respectively) were included. Forty-four (89.8%) patients with monogenic lupus fulfilled the EULAR/ACR-2019 with a mean score of 22.3±8.9. The most frequent domains were immunologic (93.9%), musculoskeletal and renal (each 57.1%), and mucocutaneous (55.1%). Fifty-four (98.2%) cSLE patients and six (12.2%) non-lupus patients met the EULAR/ACR-2019 criteria with a mean score of 22.5±9.2 and 8.5±5.2, respectively. The sensitivity of the EULAR/ACR-2019 criteria in monogenic lupus was 95.6% (95% CI: 0.8-0.9) while the specificity was 75.0% (95% CI: 0.5- 0.9). ConclusionThis is the first and largest cohort of monogenic lupus patients testing the performance of the 2019-EULAR/ACR criteria. It efficiently classifies monogenic lupus patients, irrespective of the underlying genetic variants. Further studies are needed before these criteria are adopted worldwide.
Clinical Features And Incidence Of Visual Improvement Following Systemic Antibiotic Treatment In Patients With Syphilitic Uveitis
Authors: Sittivarakul Wantanee , Aramrungroj Sukrita , Seepongphun Usanee
Published: March 2022

Purpose: To describe the clinical features, longitudinal pattern, and incidence rate of improvement of visual acuity (VA) following antibiotic therapy in patients with syphilitic uveitis.Methods: A total of 36 patients were included in this retrospective study from 2009 to 2020. The longitudinal patterns of mean VA values during follow-up were analyzed using a linear mixed model.Results: Most patients were men with HIV coinfection (81%) and presented with panuveitis (49%). The mean VA at baseline improved from 0.97 to 0.39 logMAR at 6 months and remained stable thereafter. The cumulative incidence of VA ≥20/25 achieved by 2 years was 70%. Receiving antibiotic therapy within four weeks of the onset of ocular symptoms (adjusted hazard ratio [aHR] 3.4, P = 0.012), absence of HIV coinfection (aHR 8.2, P<0.001), absence of neurosyphilis (aHR 6.5, P = 0.037), better presenting VA (aHR 5.0, P = 0.003), and intermediate uveitis as opposed to panuveitis (aHR 11.5, P = 0.013) were predictive of achieving VA ≥20/25.Conclusions: Men with HIV coinfection represented the majority of our patients. Visual outcomes, in response to antibiotics, were favorable. Delayed treatment, poor presenting VA, presence of HIV coinfection, and concomitant neurosyphilis decreased the likelihood of VA restoration.
InSAR-Derived Source Characteristics of Iranian Blind Reverse-Fault Earthquakes and Their Implications for Seismic Hazard Evaluation
Authors: Ghayournajarkar Nematollah , Fukushima Yo , Nakahara Hisashi
Published: March 2022

Investigating fault characteristics is necessary for seismic hazard evaluation and can provide useful insights for municipalities to optimize their investments in safer buildings and more resilient infrastructure. The location and the geometry of the faults, especially their relationship with sedimentary layer thickness, and the amount of stress drop are critical components when evaluating strong ground motions caused by earthquakes. Interferometric Synthetic Aperture Radar (InSAR) is a powerful tool for accurately determining fault parameters of shallow inland earthquakes and investigating their characteristics in terms of seismic hazards. In this study, based on our earlier results from InSAR data inversions conducted on five Iranian shallow blind reverse-fault earthquakes, we particularly exploited the resolving power of InSAR to investigate fault characteristics and discussed their implications for seismic hazard evaluation in Iran. For all studied Iranian earthquakes, the InSAR-derived fault was deeper than the sedimentary layer. This may indicate that these earthquakes did not rupture the entire seismogenic layer, likely leaving a significant seismic potential. Moreover, the average stress drop of the Iranian earthquakes was relatively large (13.4 MPa), which might be related to their immature blind reverse faults, leading to a possibility of generating stronger short-period ground motions, which should receive greater consideration in future seismic hazard analyses. As InSAR data can be easily accessed, this study presents a cost-effective method to provide fault parameters that can be used for the evaluation of strong ground motions caused by earthquakes, even in countries where observation networks of strong ground motions are not well developed.
Deep learning architecture optimization with metaheuristic algorithms for predicting BRCA1 / BRCA2 pathogenicity NGS analysis
Authors: PELLEGRINO Eric , Brunet Theo , Pissier Christel , Camilla Clara , Abbou Norman , Beaufils Nathalie , Nanni Isabelle , Metellus Philippe , Ouafik L’Houcine
Published: March 2022

BRCA1 and BRCA2 are genes with tumor suppressor activity, and they are involved ina considerable number of biological processes allowing the regulation of the cellreplication cycle. A mutation in one of these two genes has a significant probability ofcausing cancer. We have set up within the platform a machine learning algorithm basedon the random forest to predict pathogenicity in colorectal, melanoma, lung, and gliomacancer. but this algorithm has revealed its limits when we want to predict on morecomplex genes like BRCA1 and BRCA2. To help the biologist in the classification oftumors, we decided to develop a deep learning algorithm.The question we ask ourselves when we want to construct a neural network is howmany hidden layers and neurons should we use. If the number of inputs and outputs isdefined by the problem that we require to resolve, the number of hidden layers andneurons is difficult to define because there is no pre-established rule. The number ofhidden layers and neurons that make up each layer of the neural network has aninfluence on the performance of system predictions. There are different methods forfinding the optimal architecture like grid search or based on empirical equations. Allthese techniques can be very time-consuming. In this paper, we will present the twopackages that we have developed, the genetic algorithm (GA) and the particle swarmoptimization (PSO) to optimize the parameters of the neural network for the predictionof the pathogenicity of the BRCA1 and BRCA2 genes. We will compare the resultsobtained by the two algorithms. We used datasets collected from our NGS analysis ofBRCA1 and BRCA2 genes to train deep learning models. This represents a datacollection of 11,875 BRCA1 and BRCA2 variants (BRCA1 benign 2,632, BRCA1pathogenic 2,660, BRCA2 benign 3,446, BRCA2 pathogenic 3,137). Our preliminaryresults show that the PSO provided the most significant architecture in terms of hiddenlayers and the number of neurons compared to grid search and GA. The optimalarchitecture found by the PSO algorithm is composed of 6 hidden layers with 275 hiddennodes with an accuracy of 0.98, precision 0.99, recall 0.98, and a specificity of 0.99.
Double Batched DNA Sequencing is a reliable, cost-effective and scalable approach to genomic population screening
Authors: Stoltze Ulrik , Hagen Christian , Hansen Thomas , Byrjalsen Anna , Gerdes Anne-Marie , Yakimov Victor , Rasmussen Simon , Bækvad-Hansen Marie , Hougaard David , Schmiegelow Kjeld , Hjalgrim Henrik , Wadt Karin , Bybjerg-Grauholm Jonas
Published: March 2022

Next-generation sequencing (NGS) based population screening holds great promise for disease prevention and earlier diagnosis, but associated sequencing costs remain prohibitive. We developed double batched sequencing (DoBSeq) and tested it on neonatal blood spot DNA in an explorative (n = 100) and a validation (n = 100) cohort selected from a nation-wide childhood cancer whole genome sequencing (WGS) study. Each cohort was enriched for loss-of-function/pathogenic variants in cancer predisposition syndrome genes. Using a commercial 113-gene panel benchmarked against individual WGS data, we demonstrated replicable detection of deleterious and pathogenic variants, with positive and negative predictive values of 100% (95%CI 0.91-1.00 & 95%CI 0.98-1.00, respectively). Pathogenic variants were detected in RB1, TP53, BRCA2, APC, and 19 other genes. Analyses of larger batches (n = 24, 48, 72 & 96) indicate that DoBSeq is highly scalable and thus a promising, cost-effective method for realizing the potential of population-scale NGS-based screening.
Evaluation of the effect of the application of combined pretreatments and inoculum with high alkalinity on food residues through BMP tests.
Authors: Alanis-Silva Edgar Daniel , Chávez-Parga Ma. del Carmen , Cortés José Apolinar
Published: March 2022

The management and control of food waste is currently seen as a growing concern, anaerobic digestion is a promising alternative for the valorization of food waste. This study evaluates the effect of the application of three pretreatments (grinding, pH control, thermal treatment) and organic load control, employing a high alkalinity inoculum for methane production through BMP tests, using a Taguchi L 8 experimental design of 4 factors and 2 levels, resulting in the best performance (65.91 NmL ·g -1 TVS) with pretreatment conditions of grinding with fine particle size, pH 11, thermal pretreatment at 60 °C and a concentration of 14 g TVS ·L -1 , which represents an improvement of 34.66% in comparation with the food waste without pretreatments.
Robustness of the long-term nonlinear evolution of global sea surface temperature trend
Authors: Xu Zhenhao , Huang Gang , Ji Fei , Liu Bo , Chang Fei
Published: March 2022

The multi-scale variability of global sea surface temperature (GSST), which is often dominated by secular trends, significantly impacts global and regional climate change. Previous studies are mainly carried out under linear assumptions, even if the nonlinear trend features are discussed based on annual data, the conclusions of which are still incomplete due to several factors such as the sampling frequency and the time interval selection. Here, based on the Ensemble Empirical Mode Decomposition (EEMD) method, the robustness of GSST trends is further explored. The main features derived from the annual data are still maintained. However, monthly and seasonal data lag and mute the cooling in the equatorial central Pacific and the Southern Ocean in the Pacific sector while emphasizing more warming over most North Pacific in both magnitude and surface area. The results also highlight that early data causes a minimal effect on secular trends except for the portion near the left endpoint of the interval due to the local temporal nature of EEMD. Our research also clarifies that quadratic fitting cannot reveal all the meaningful evolution patterns, even as a nonlinear solution.
Immunotherapy for Type 1 Diabetes Mellitus by Adjuvant-Free Schistosoma Japonicum-Egg Tip-Loaded Asymmetric Microneedle Patch (STAMP)
Authors: Huang Haoming , Hu Dian , Chen Zhuo , Xu Jiarong , Xu Rengui , Gong Yusheng , Fang Zhengming , Wang Ting , Chen Wei
Published: March 2022

Background
Type 1 diabetes mellitus (T1DM) is an autoimmune disease mediated by autoreactive T cells and dominated by Th1 response polarization. Insulin replacement therapy faces great challenges to this autoimmune disease, requiring highly frequent daily administration. Intriguingly, the progression of T1DM has proven to be prevented or attenuated by helminth infection or worm antigens for a relatively long term. However, the inevitable problems of low safety and poor compliance arise from infection with live worms or direct injection of antigens. Microneedles would be a promising candidate for local delivery of intact antigens, thus providing an opportunity for the clinical immunotherapy of parasitic products.
Methods
We developed a Schistosoma japonicum-egg tip-loaded asymmetric microneedle patch (STAMP) system, which serves as a new strategy to combat TIDM. In order to improve retention time and reduce contamination risk, a specific imperfection was introduced on the STAMP (asymmetric structure), which allows the tip to quickly separate from the base layer, improving reaction time and patient’s comfort. After loading Schistosoma japonicum-egg as the immune regulator, the effects of STAMP on blood glucose control and pancreatic pathological progression improvement were evaluated in vivo. Meanwhile, the immunoregulatory mechanism and biosafety of STAMP were confirmed by histopathology, qRT-PCR, ELISA and Flow cytometric analysis.
Results
Here, the newly developed STAMP was able to significantly reduce blood glucose and attenuate the pancreatic injury in T1DM mice independent of the adjuvants. The isolated Schistosoma japonicum-eggs micron slowly degraded in the skin and continuously released egg antigen for at least 2 weeks, ensuring localization and safety of antigen stimulation. This phenomenon should be attributed to the shift of Th2 immune response to reduce Th1 polarization.
Conclusion
Our results exhibited that STAMP could significantly regulate the blood glucose level and attenuate pancreatic pathological injury in T1DM mice by balancing the Th1/Th2 immune responses, which is independent of adjuvants. This technology opens a new window for the application of parasite products in clinical immunotherapy.
Tunable Four-Port MIMO/Self-Multiplexing THz Graphene Patch Antenna with High Isolation
Authors: Ali Mohd Farman , Bhattacharya Rajarshi , Varshney Gaurav
Published: March 2022

A tunable terahertz four-port multiple-input-multiple-output (MIMO) graphene microstrip patch antenna with self-multiplexing ability is designed and numerically studied. The top layer of the four-port patch antenna, which is a symmetric cross-shaped graphene patch, is patterned using a cross-slot. Insertion of this cross-slot improved the level of isolation to the order of 50-70 dB in the MIMO mode of operation. The frequency of impedance matching at each port of the designed antenna could be tuned independently by applying an electrostatic potential on the corresponding graphene patch enabling its usage as a MIMO self-diplexing and quadruplexing antenna. The MIMO performance parameters like envelope correlation coefficient, diversity gain, mean effective gain, etc. are found within the acceptable limits. An equivalent circuit model is presented to provide insight into the radiation mechanism and validate the results.
Learning the arm-leg coordination in breaststroke swimming: Identifying exploration of movement dynamics with drifting Markov Models
Authors: Komar John , Seifert Ludovic , Vergne Nicolas , Newell Karl M.
Published: March 2022

Constraints on practice can benefit motor learning by guiding the learner towards efficient coordination patterns, but can also narrow the potential solution space of coordination and control. The aim of this paper was to investigate whether narrowing the solution space through more restrictive task constraints limits the expression of potential exploratory behaviours during the learning process, identified using Drifting Markov Models. The change in interlimb coordination of 7 learners practicing for 16 lessons over 2 months was analysed to quantify motor exploration and identify periods of metastable regimes of coordination. Results showed that the observed exploratory dynamics were highly individual both in terms of range of exploration and in the patterns of search. The more restrictive task constraints did not impair the range of exploration but rather channelled the exploration around a few selected patterns. In addition, restraining the nature of the exploratory process increased the inter-individual differences of the learning rate. Although manipulating the task constraints during learning can help learners to escape from the behavioural consequences of their intrinsic dynamics, maintaining a broad solution space for a diversity of coordination patterns to emerge was key to fostering effective exploration of individual coordination solutions.
Radial Basis Function Neural Network with Extreme Learning Machine Algorithm for Solving Ordinary Differential Equations
Authors: Liu Min , Peng Wenping , Hou Muzhou , Tian Zhongchu
Published: March 2022

We present a novel numerical method for solving ordinary differential equations (ODEs) using Radial Basis Function (RBF) Network with Extreme Learning Machine Algorithm. A single layer Radial Basis Functional Link Neural Network (RBFNN) model has been developed for the proposed method. The weight from the hidden layer to the output layer can be calculated efficiently by Extreme Learning Machine algorithm. The experimental comparison of various methods proves that the proposed method shows better performance than the existing methods.
Deresuscitation during continuous renal replacement therapy: A before-after pilot study (The EARLY DRY COHORT)
Authors: Ruste Martin , Sghaier Raouf , Chesnel Delphine , Didier Léa , Fellahi Jean-Luc , Jacquet-Lagrèze Matthias
Published: March 2022

Background: Active fluid removal has been suggested to improve prognosis following the resolution of acute circulatory failure. To standardize the deresuscitation strategy, we have implemented a routine care protocol to guide fluid removal during continuous renal replacement therapy (CRRT). We designed a before-after pilot study to evaluate the impact of this deresuscitation strategy on the cumulative fluid balance.Methods: Consecutive ICU patients suffering from fluid overload and undergoing CRRT for acute kidney injury underwent a perfusion-based deresuscitation protocol combining a restrictive intake, continuous net ultrafiltration (UFnet) of 2 mL/kg/h, and both clinical and laboratory monitoring of perfusion (early dry group, N=42) and were compared to an historical group managed according to usual practices (control group, N=45). The primary outcome was the cumulative fluid balance at day 5 or at discharge. Secondary outcomes addressed the protocol safety. Adjustments were done with inverse probability of treatment weighting propensity score analysis.Results: Adjusted cumulative fluid balance was significantly lower in the early dry group (median [IQR]: -7784 [-11833 to -2933] mL) compared to the control group (-3492 [-9935 to -1736] mL, p=0.04). The difference was mainly driven by a greater daily UFnet (31 [22-46] mL/kg/day vs. 24 [15-32] mL/kg/day, p=0.01). There was no significant difference between both groups regarding maximal arterial lactate level and maximal norepinephrine dose requirement. Conclusion: Our perfusion-based deresuscitation protocol achieved a greater negative cumulative fluid balance compared to standard practices and was hemodynamically well tolerated. Those data suggest the feasibility of an interventional randomized clinical trial using a similar protocol.
Prognostic Value of Neutrophil-to-lymphocyte Ratio and Prognostic Nutrition Index in Patients with Non-small Cell Lung Cancer Receiving Pulmonary Resection
Authors: Motono Nozomu , Ishikawa Masahito , Iwai Shun , Iijima Yoshihito , Uramoto Hidetaka
Published: March 2022

Background: The prognostic value of neutrophil-to-lymphocyte ratio (NLR) and prognostic nutritional index (PNI) for patients with early-stage non-small cell lung cancer (NSCLC) has not been elucidated. In the present study, we retrospectively evaluated the prognostic value of NLR and PNI for patients with NCSLC received pulmonary resection, even early-stage patients.Methods: The clinical data of 739 patients who underwent pulmonary resection for NSCLC were collected, and the prognostic value of NLR and PNI were analyzed.Results: Coexistence of interstitial lung disease (ILD) (p<0.01), coexistence of arrhythmia (p=0.04), smoking status (p=0.02), carcinoembryonic antigen (CEA) (p=0.04), NLR>1.75 (p=0.01), and pathological stage (p<0.01) were revealed as significant factors for progression free survival (PFS) in the multivariate analysis. Coexistence of ILD (p=0.03), smoking status (p<0.01), CEA (p<0.04), PNI<47.97 (p=0.01), and pathological stage (p<0.01) were revealed as significant factors for overall survival in the multivariate analysis. Furthermore, smoking status (p=0.01), CEA (p=0.03), NLR>4.04 (p<0.01), pathological stage (p=0.01), and lobectomy (p<0.01) were revealed as significant factors for PFS in pathological stage I NSCLC patients. Smoking status (p<0.01), PNI<49.19 (p=0.02), pathological stage (p=0.01), and wedge resection (p=0.01) were revealed as significant factors for OS in pathological stage I NSCLC patients.Conclusions: NLR was revealed as the significant factor for PFS in NSCLC patients received surgical treatment, even patients with pathological stage I. Furthermore, PNI was revealed as a significant factor of OS for NSCLC patients received surgical treatment. Trial registration: The Institutional Review Board of Kanazawa Medical University approved the protocol of this retrospective study (approval number: I392), and written informed consent was obtained from all patients.
Effect of ergonomic intervention on cognitive function of office workers
Authors: Mottaghi Zahra , Halvani Gholamhossein , Jambarsang Sara , Mehrparvar Amir Houshang
Published: March 2022

Introduction: This study was designed to assess the effect of an ergonomic training intervention on the cognitive function of office workers.Materials and methods: This was a before-after study performed in 2020 in Yazd, Iran on female office workers. Cognitive function (working memory, attention and response time) was assessed by Wechsler working memory and Stroop test before and after the intervention. Ergonomic intervention consisted of ergonomic modification of the workstation and a training program about ergonomic principles of office work. Data were analyzed by SPSS (ver. 24) using paired T-test and multiple regression linear model. Results: Mean age and work experience of the participants was 35.38±1.60 yr., and 8.54± 1.24 yr., respectively. Forward visual memory, response time and interference time were significantly changed after the intervention, but the change in other aspects of cognitive function (i.e. memory span, backward visual memory, and interference score) was not statistically significant. Marital status, age and working hours significantly affected working memory, test duration and response time, and number of errors, respectively. Conclusion: This study showed that ergonomic intervention (modification of workstation and training) may significantly affect some aspects of cognitive function in office workers.