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Comparison of methods for deriving phenotypes from incomplete observation data with an application to age at puberty in dairy cattle

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Journal of Animal Science and Biotechnology 2024年第2期15卷 535-545页

作者： Melissa A.Stephen Chris R.Burke Jennie E.Pryce Nicole M.Steele Peter R.amer Susanne Meier Claire V.C.Phyn Dorian J.Garrick DairyNZ Ltd 605 Ruakura RoadHamilton 3240New Zealand AL Rae Centre for Genetics and Breeding-Massey University RuakuraHamilton 3214New Zealand Agriculture Victoria Research AgriBioCentre for AgriBioscienceBundooraVictoria 3083Australia School of Applied Systems Biology La Trobe UniversityBundooraVictoria 3083Australia AbacusBio DunedinNew Zealand

Background Many phenotypes in animal breeding are derived from incomplete measures,especially if they are challenging or expensive to measure *** include time-dependent traits such as reproductive status,or *** measures for these traits result in phenotypes that are subject to left-,interval-and rightcensoring,where phenotypes are only known to fall below an upper bound,between a lower and upper bound,or above a lower bound *** we compare three methods for deriving phenotypes from incomplete data using age at first elevation(>1 ng/mL)in blood plasma progesterone(AGEP4),which generally coincides with onset of puberty,as an example *** We produced AGEP4 phenotypes from three blood samples collected at about 30-day intervals from approximately 5,000 Holstein–Friesian or Holstein–Friesian×Jersey cross-bred dairy heifers managed in 54 seasonal-calving,pasture-based herds in New *** used these actual data to simulate 7 different visit scenarios,increasing the extent of censoring by disregarding data from one or two of the three *** methods for deriving phenotypes from these data were explored:1)ordinal categorical variables which were analysed using categorical threshold analysis;2)continuous variables,with a penalty of 31 d assigned to right-censored phenotypes;and 3)continuous variables,sampled from within a lower and upper bound using a data augmentation *** Credibility intervals for heritability estimations overlapped across all methods and visit scenarios,but estimated heritabilities tended to be higher when left censoring was *** sires with at least 5 daughters,the correlations between estimated breeding values(EBVs)from our three-visit scenario and each reduced data scenario varied by method,ranging from 0.65 to *** estimated breed effects also varied by method,but breed differences were smaller as phenotype censoring *** Our results indicate that using

关键词： Cattle Gibbs sampler Markov-chain Monte Carlo(MCMC) Puberty

Cardiac evaluation of renal transplant candidates with heart failure

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World Journal of Transplantation 2024年第4期14卷 44-49页

作者： amer Ashaab Belal Alfonso Hernandez Santos Jr Amir Kazory Department of Medicine Division of NephrologyUniversity of Florida College of MedicineGainesvilleFL 32610United States Division of Nephrology Hypertension and Renal TransplantationUniversity of FloridaGainesvilleFL 32608United States

Patients with advanced kidney disease are at elevated risk of developing heart failure and appropriate risk stratification is important to permit them to receive kidney *** american Heart Association and american College of Cardiology joint statement provides guidance on risk stratification for the major cause of heart failure for these patients in its recommendations for coronary heart *** we provide an overview of the available literature on risk strati-fication for nonischemic heart failure and functional heart disease states such as pulmonary *** of these options for optimizing these patients be-fore transplant include optimizing their volume status,often with more agg-ressive *** transplantation remains the treatment of choice for patients with advanced kidney disease and cardiac disease,the correction of the azotemic substances with kidney transplantation has been associated with imp-roved survival than remaining on dialysis *** findings in the studies reviewed here are expected to help clinicians refine current strategies for evalua-ting potential kidney transplant recipients.

关键词： Kidney transplantation Preoperative evaluation Clinical practice guidelines Heart failure Pulmonary hypertension

New Antenna Array Beamforming Techniques Based on Hybrid Convolution/Genetic Algorithm for 5G and Beyond Communications

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Computer Modeling in Engineering & Sciences 2024年第3期138卷 2749-2767页

作者： Shimaa M.amer Ashraf A.M.Khalaf Amr H.Hussein Salman A.Alqahtani Mostafa H.Dahshan Hossam M.Kassem Electronics and Communications Engineering Department Higher Institute of Engineering and TechnologyKafr ElsheikhEgypt Electronics and Electrical Communications Engineering Department Faculty of EngineeringMinia UniversityMiniaEgypt Electronics and Electrical Communications Engineering Department Faculty of EngineeringTanta UniversityTantaEgypt Electronics and Electrical Communications Engineering Department Faculty of EngineeringHorus University EgyptNew DamiettaEgypt Department of Computer Engineering College of computer and Information SciencesKing Saud UniversityRiyadh11543Saudi Arabia School of Computing Mathematics and EngineeringCharles Sturt UniversityBathurstNSW2795Australia

Side lobe level reduction(SLL)of antenna arrays significantly enhances the signal-to-interference ratio and improves the quality of service(QOS)in recent and future wireless communication systems starting from 5G up to ***,it improves the array gain and directivity,increasing the detection range and angular resolution of radar *** study proposes two highly efficient SLL reduction *** techniques are based on the hybridization between either the single convolution or the double convolution algorithms and the genetic algorithm(GA)to develop the Conv/GA andDConv/GA,*** convolution process determines the element’s excitations while the GA optimizes the element *** M elements linear antenna array(LAA),the convolution of the excitation coefficients vector by itself provides a new vector of excitations of length N=(2M−1).This new vector is divided into three different sets of excitations including the odd excitations,even excitations,and middle excitations of lengths M,M−1,andM,*** the same element spacing as the original LAA is used,it is noticed that the odd and even excitations provide a much lower SLL than that of the LAA but with amuch wider half-power beamwidth(HPBW).While the middle excitations give the same HPBWas the original LAA with a relatively higher *** the increased HPBWof the odd and even excitations,the element spacing is optimized using the ***,the synthesized arrays have the same HPBW as the original LAA with a two-fold reduction in the ***,for extreme SLL reduction,the DConv/GA is *** this technique,the same procedure of the aforementioned Conv/GA technique is performed on the resultant even and odd excitation *** provides a relatively wider HPBWthan the original LAA with about quad-fold reduction in the SLL.

关键词： Array synthesis convolution process genetic algorithm(GA) half power beamwidth(HPBW) linear antenna array(LAA) side lobe level(SLL) quality of service(QOS)

Physiological phenotypes differ among color morphs in introduced common wall lizards(Podarcis muralis)

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Integrative Zoology 2024年第3期19卷 505-523页

作者： Ali amer Sierra SPEARS Princeton L.VAUGHN Cece COLWELL Ethan H.LIVINGSTON Wyatt MCQUEEN Anna SCHILL Dustin G.REICHARD Eric J.GANGLOFF Kinsey M.BROCK Department of Biological Sciences Ohio Wesleyan UniversityDelawareOhioUSA Department of Ecology and Evolutionary Biology Princeton UniversityPrincetonNew JerseyUSA Department of Biology Idaho State UniversityPocatelloIdahoUSA Department of Environmental Science Policyand ManagementCollege of Natural ResourcesUniversity of CaliforniaBerkeleyUSA Museum of Vertebrate Zoology University of CaliforniaBerkeleyUSA

Many species exhibit color polymorphisms which have distinct physiological and behavioral ***,the consistency of morph trait covariation patterns across species,time,and ecological contexts remains *** trait covariation is especially relevant in the context of invasion biology and urban ***,physiological traits pertaining to energy maintenance are crucial to fitness,given their immediate ties to individual reproduction,growth,and population *** investigated the physiological traits of Podarcis muralis,a versatile color polymorphic species that thrives in urban environments(including invasive populations in Ohio,USA).We measured five physiological traits(plasma corticosterone and triglycerides,hematocrit,body condition,and field body temperature),which compose an integrated multivariate *** then tested variation among co-occurring color morphs in the context of establishment in an urban *** found that the traits describing physiological status and strategy shifted across the active season in a morph-dependent manner—the white and yellow morphs exhibited clearly different multivariate physiological phenotypes,characterized primarily by differences in plasma *** suggests that morphs have different strategies in physiological regulation,the flexibility of which is crucial to urban *** white-yellow morph exhibited an intermediate phenotype,suggesting an intermediary energy maintenance *** morphs also exhibited distinct phenotypes,but the low prevalence of this morph in our study populations precludes clear *** work provides insight into how differences among stable polymorphisms exist across axes of the phenotype and how this variation may aid in establishment within novel environments.

关键词： color polymorphism physiological status seasonal variation thermoregulation urban habitat

Advancing Early Detection of Colorectal Adenomatous Polyps via Genetic Data Analysis: A Hybrid Machine Learning Approach

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Journal of Computer and Communications 2024年第7期12卷 23-38页

作者： Ahmed S. Maklad Mohamed A. Mahdy amer Malki Noboru Niki Abdallah A. Mohamed Computer Science Department College of Computer Science and Engineering in Yanbu Taibah University Medina Saudi Arabia Information Systems Department Faculty of Computers and Artificial Intelligence Beni-Suef University Beni-Suif Egypt Computer Science Department Faculty of Computers and Artificial Intelligence Beni-Suef University Beni-Suif Egypt Institute of Advanced Science and Technology Tokushima University Tokushima Japan Information Systems Department College of Computer Science and Engineering in Yanbu Taibah University Medina Saudi Arabia Mathematics and Computer Science Department Faculty of Science Menoufia University Menoufia Egypt

In this study, a hybrid machine learning (HML)-based approach, incorporating Genetic data analysis (GDA), is proposed to accurately identify the presence of adenomatous colorectal polyps (ACRP) which is a crucial early detector of colorectal cancer (CRC). The present study develops a classification ensemble model based on tuned hyperparameters. Surpassing accuracy percentages of early detection approaches used in previous studies, the current method exhibits exceptional performance in identifying ACRP and diagnosing CRC, overcoming limitations of CRC traditional methods that are based on error-prone manual examination. Particularly, the method demonstrates the following CRP identification accuracy data: 97.7 ± 1.1, precision: 94.3 ± 5, recall: 96.0 ± 3, F1-score: 95.7 ± 4, specificity: 97.3 ± 1.2, average AUC: 0.97.3 ± 0.02, and average p-value: 0.0425 ± 0.07. The findings underscore the potential of this method for early detection of ACRP as well as clinical use in the development of CRC treatment planning strategies. The advantages of this approach are highly expected to contribute to the prevention and reduction of CRC mortality.

关键词： Colorectal Adenoma Detection Colorectal Cancer Diagnosis Hybrid Machine Learning Genetics Analysis

Assessment the effect of Dapoxetine and/or Acetaminophen in rats;neurochemicals and oxidative stress biomarkers evaluation

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Brain Science Advances 2024年第1期10卷 57-71页

作者： Gehan S.Georgy Ibrahim M.Ibrahim Laila Mohamed E.amer Ebtehal Mohammad F. Pharmacology Department Egyptian Drug Authority(EDA)Giza P.O.29Egypt Molecular Drug Evaluation Department Egyptian Drug Authority(EDA)Giza P.O.29Egypt Histology Department Faculty of MedicineAl-Azhar UniversityDamietta P.O.11651Egypt

Dapoxetine is a newer anti-depressant that is used for severe forms of depression via selective serotonin reuptake inhibition *** aimed to evaluate the effect of different doses of dapoxetine lonely or with acetaminophen(AMP).Seven groups of albino rats were used where dapoxetine was administered orally at the doses of 3,5,and 8 mg/kg body weight for a period of 14 days in groups 2,4,and 6,***(67.5 mg/kg body weight)was co-administered with dapoxetine(3,5,and 8 mg/kg body weight)for 14 days in groups 3,5 and 7,*** in mid and high dose plus AMP increased body weight and hematological *** and rearing were declined with mid and high doses of dapoxetine+AMP,contrary to *** was decreased with high doses of dapoxetine+*** dose of dapoxetine+AMP induced lowering of serotonin and dopamine as well as increasing of *** derived neurotrophic factor was decreased in all *** stress biomarkers were augmented with high dose of dapoxetine+*** doses of dapoxetine and/or AMP induced loss of the Purkinje cell layer at *** high dose of dapoxetine+AMP denotes behavioral,histopathological and neurochemical alterations,even though no serotonin syndrome occurs.

关键词： acetaminophen dapoxetine neurotransmitters oxidative stress biomarkers

Severe asthma exacerbation:Changes in patient characteristics,management,and outcomes from 1997 to 2016 in 40 ICUs in the greater Paris area

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Journal of Intensive Medicine 2024年第2期4卷 209-215页

作者： Romy Younan Jean Loup Augy Bertrand Hermann Bertrand Guidet Philippe Aegerter Emmanuel Guerot Ana Novara Caroline Hauw-Berlemont amer Hamdan Clotilde Bailleul Francesca Santi Jean-Luc Diehl Nicolas Peron Nadia Aissaoui Intensive Care Unit AP-HPGeorges Pompidou European HospitalUniversitéde ParisParisFrance Intensive Care Unit AP-HPSaint Antoine HospitalUniversités de SorbonneUniversitéPierre et Marie CurieParisFrance INSERM U1136 ParisFrance Versailles Saint-Quentin-en-Yvelines University INSERM U1018Groupe Interrégional de Recherche Clinique et d'InnovationÎle-de-FranceFrance Respiratory Medicine Department AP-HPGeorges Pompidou European HospitalUniversitéde ParisParisFrance Innovative Therapies in Hemostasis INSERM UMR-S1140Universitéde ParisParisFrance Intensive Care Unit and Biosurgical Research Lab(Carpentier Foundation) AP-HPGeorges Pompidou European HospitalParisFrance Paris-Cardiovascular-Research-Center INSERM U970ParisFrance

Background Despite advances in asthma treatments,severe asthma exacerbation(SAE)remains a life-threatening condition in adults,and there is a lack of data derived from adult patients admitted to intensive care units(ICUs)for *** current study investigated changes in adult patient characteristics,management,and outcomes of SAE over a 20-year period in 40 ICUs in the greater Paris *** In this retrospective observational study,admissions to 40 ICUs in the greater Paris area for SAE from January 1,1997,to December 31,2016 were *** primary outcome was the proportion of ICU admissions for SAE during 5-year *** outcomes were ICU and hospital mortality,and the use of mechanical ventilation and *** analysis was performed to assess factors associated with ICU *** A total of 7049 admissions for SAE were *** each 5-year period,the proportion decreased over time,with SAE accounting for 2.84%of total ICU admissions(n=2841)between 1997 and 2001,1.76%(n=1717)between 2002 and 2006,1.05%(n=965)between 2007 and 2011,and 1.05%(n=1526)between 2012 and *** median age was 46 years(interquartile range[IQR]:32–59 years),55.41%were female,the median Simplified Acute Physiology Score II was 20(IQR:13–28),and 19.76%had mechanical *** use of mechanical ventilation remained infrequent throughout the 20-year period,whereas the use of catecholamine *** and hospital mortality rates *** associated with ICU mortality were renal replacement therapy,catecholamine,cardiac arrest,pneumothorax,acute respiratory distress syndrome,sepsis,and invasive mechanical ventilation(IMV).Non-survivors were older,had more severe symptoms,and were more likely to have received *** ICU admission for SAE remains uncommon,and the proportion of cases decreased over *** a slight increase in symptom severity during a 20-year period,ICU and hospital mortality *** requirin

关键词： Epidemiology Intensive care unit Mechanical ventilation Severe asthma exacerbation

Eczema herpeticum vs dermatitis herpetiformis as a clue of dedicator of cytokinesis 8 deficiency diagnosis:A case report

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World Journal of Clinical Cases 2022年第29期10卷 10735-10741页

作者： amer Alshengeti Department of Pediatrics College of MedicineTaibah UniversityDepartment of Infection prevention and controlPrince Mohammad Bin Abdulaziz HospitalNational Guard Health AffairsAl-Madinah 41491Saudi Arabia

BACKGROUND Dedicator of cytokinesis 8(DOCK 8) deficiency,also known as autosomal recessive hyper immunoglobulin E(IgE) syndrome,is a combined immunodeficiency disease that was first recognized in *** is caused by genetic alterations(mutations or deletions) in the DOCK 8 gene and is characterized by multiple allergies,elevated IgE levels,and susceptibility to viral and bacterial *** diagnosis is critical to optimize the success of stem cell *** SUMMARY This study reports the case of a pediatric patient with DOCK 8 deficiency who had negative genetic testing using multiplex primary immunodeficiency(PID) panel and whole-exome sequencing(WES) with a next-generation sequencing *** presented with chronic diarrhea and was managed as celiac disease based on previous negative workup for immunodeficiency and duodenal *** developed a generalized vesicular rash which was thought to be dermatitis herpetiformis associated with celiac ***,it turned out to be Eczema herpeticum based on positive herpes simplex virus from blood and *** diagnosis was re-evaluated after the child was found to have multiple viral,bacterial,and parasitic co-infections(herpes simplex virus,cytomegalovirus,Epstein-Barr virus,Salmonella,and cryptosporidiosis).Re-evaluation with target gene testing with copy number variation(CNV) analysis and Multiplex Ligation Probe Amplification(MLPA) showed a large homozygous deletion in the DOCK 8 gene,confirming the diagnosis of DOCK 8 *** Targeted gene testing with CNV analysis might detect deletions that can be missed by WES for diagnosing patients with PID.

关键词： Immunoglobulin E Whole-exome sequencing Infections Dedicator of cytokinesis 8 Case report

Application of machine learning algorithms to predict tubing pressure in intermittent gas lift wells

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Petroleum Research 2022年第2期7卷 246-252页

作者： Nagham amer Sami Department of Petroleum Engineering Faculty of Earth ScienceUniversity of Miskolc3515MiskolcHungary

Tubing pressure at gas injection depth in intermittent wells is one of the most critical parameters for production engineers to evaluate the performance of the ***,monitoring of the tubing pressure is not usually carried out in real *** has been realized that the generally used correlations are not effective enough due to complexity of the intermittent process which involve many parameters and assumptions to develop such *** focus of this study is to utilize machine learning(ML)algorithms to develop a model that can accurately predict tubing pressure in artificial intermittent gas lift *** algorithms built on the field data provide a solution that is easy to use and universally applicable to the complex *** non-linear regression ML methods are employed in this study,namely,Decision Tree-regression(DT),Random Forest-regression(RF)and K Nearest Neighbors-regression(KNN).All the tubing pressures obtained from ML models were compared with the actual values to ensure the effectiveness of the *** developed models show that it can predict the pressure with more than 99.9%*** is an interesting result,as such outcome accuracy has not been reported usually in the open literature.

关键词： Machine learning Artificial intelligence Intermittent gas lift Tubing pressure Random forest Decision tree KNN