bluuebunny/crossref_metadata_2025_split huggingface dataset:
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

Abstract
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

Abstract
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

Abstract
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

Abstract
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

Abstract
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

Abstract
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

Abstract
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

Abstract
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

Abstract
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

Abstract
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

Abstract
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.
Circulating levels of PCSK9, ANGPTL3 and Lp(a) in stage III breast cancers
Authors: Chong Émilie Wong , Joncas France-Hélène , Seidah Nabil G , Calon Frédéric , Diorio Caroline , Gangloff Anne 
Published: March 2022

Abstract

Background/ Synopsis: Cholesterol plays an important role in sustaining tumor growth and metastasis in a large variety of cancers. New and powerful cholesterol-lowering drugs are being used in combination to treat cardiovascular diseases. Thus, it becomes intuitive to verify whether these drugs could be combined to induce a cholesterol shortage sufficient to impede tumor progression. Circulating levels of the targets of a new generation of lipid-lowering drugs have not been fully investigated in cancers. Given that drugs directed against PCSK9 (evolocumab, alirocumab, inclisiran), ANGPTL3 (evinacumab) and Lp(a) (pelacarsen) are available, it becomes important to assess circulating levels of these drug targets and their role in cancers. Objective/Purpose: To compare circulating levels of PCSK9, ANGPTL3, and Lp(a) in women with stage III breast cancer versus women with premalignant or benign breast lesions. Methods: Twenty-three plasma samples from women diagnosed with a stage III breast cancer (ductal, lobular or mixed) were matched for age with twenty-three plasma samples from women bearing premalignant (stage 0, n=9) or benign (n= 14) breast lesions. The lipid profile (Apo B, total cholesterol, HDL cholesterol and triglycerides levels) and Lp(a) were measured on a Roche Modular analytical platform, whereas LDL levels were calculated with the Friedewald formula. ANGPTL3 and PCSK9 plasma levels were quantitated by ELISA. All statistical analyses were performed using SAS software version 9.4. Results: PCSK9 levels were significantly higher in women with stage III breast cancer compared to age-matched counterparts presenting a benign lesion (95.9 +/- 27.1 ng/mL vs. 78.5 +/- 19.3 ng/mL, p<0.05, n=14). Moreover, PCSK9 levels positively correlated with breast disease severity (benign, stage 0, stage III) (Rho=0.34, p<0.05, n=46). In contrast, ANGPTL3 and Lp(a) plasma levels did not display any association with breast disease status and lipids did not correlate with disease severity. Conclusion: In this cohort of 46 women, PCSK9 levels increased along with the severity of breast disease. Given that PCSK9 plays an important role in maintaining cholesterolemia and has been shown to degrade MHC-I on tumor cells, impeding immune T-cells response to tumors, the association between PCSK9 levels and breast disease severity needs to be further investigated in larger studies.
Dynamics of the Delta and Omicron variants of SARS-CoV-2 in the United States: the battle of supremacy in the presence of vaccination, mask usage and antiviral treatment
Authors: Ngonghala Calistus N , Taboe Hemaho B , Gumel Abba B 
Published: March 2022

Abstract
The effectiveness of control interventions against COVID-19 is threatened by the emergence of SARS-CoV-2 variants of concern. We present a mathematical model for studying the transmission dynamics of two of these variants (Delta and Omicron) in the United States, in the presence of vaccination, treatment of individuals with clinical symptoms of the disease and the use of face masks. Using current daily case data for COVID-19, we showed that the predominant Omicron variant can be eliminated if current control measures are maintained at their baseline levels. Vaccine-derived herd immunity can be achieved (so that the pandemic will be eliminated) if at least 68% of the population is fully-vaccinated. We showed that elimination is feasible by June 2022 if current baseline level of full vaccination coverage is increased by about 20%. The prospect of pandemic elimination is significantly improved if vaccination is combined with a face mask strategy that prioritizes moderately effective and high-quality masks. Having a high percentage of the populace wearing the moderately-effective surgical mask is more beneficial to the community than having low percentage of the populace wearing the highly-effective N95 masks. We showed that waning natural and vaccine-derived immunity (if considered individually) offer marginal impact on disease burden, except for the case when they wane at a much faster rate (e.g., within three months), in comparison to the baseline (estimated to be within 9 months to a year). Treatment of symptomatic individuals has marginal effect in reducing daily cases of SARS-CoV-2, in comparison to the baseline, but it has significant impact in reducing daily hospitalizations. Further, while treatment significantly reduces hospitalization, the prospects of COVID-19 elimination in the United States is more significantly enhanced if investments in control resources are focused on mask usage and vaccination rather than on treatment.