Review
Biochemical Research Methods
Lu Yang, Jun Chen
Summary: Differential abundance analysis (DAA) is a crucial statistical task in microbiome data analysis, and a robust DAA tool is important for identifying reliable microbial candidates. However, different DAA tools for correlated microbiome data (DAA-c) often yield inconsistent results. To address this issue, we conducted a comprehensive evaluation of existing DAA-c tools using real data-based simulations. Our findings indicate that linear model-based methods such as LinDA, MaAsLin2, and LDM are more robust than generalized linear models. Among them, LinDA method performs reasonably well even in the presence of strong compositional effects.
BRIEFINGS IN BIOINFORMATICS
(2023)
Article
Mathematics, Applied
Ognyan Kounchev, Hermann Render, Tsvetomir Tsachev
Summary: This paper introduces the classical theory of cubic interpolation splines, which includes an algorithm that requires only O(n) arithmetic operations. Additionally, the smoothing cubic splines can be computed using the Reinsch algorithm, which reduces computation to interpolation cubic splines and also operates with O(n) arithmetic operations. The paper also demonstrates how many characteristics of polynomial cubic splines extend to the larger class of L-splines, where L is a linear differential operator of order 4 with constant coefficients. Criteria are provided for ensuring the associated matrix R is strictly diagonally dominant, implying the existence of a fast interpolation algorithm. An example of two L-splines interpolating S&P500 data is provided.
JOURNAL OF COMPUTATIONAL AND APPLIED MATHEMATICS
(2023)
Article
Microbiology
Lu Yang, Jun Chen
Summary: This study provides a comprehensive evaluation of existing differential abundance analysis (DAA) tools, revealing that none of the evaluated methods are simultaneously robust, powerful, and flexible. To overcome the challenge of selecting the best DAA tool, the researchers designed an optimized procedure called ZicoSeq, which combines the strengths of existing methods and can be applied to diverse microbiome datasets for robust biomarker discovery.
Article
Cardiac & Cardiovascular Systems
Sergi Sayols-Baixeras, Koen F. F. Dekkers, Gabriel Baldanzi, Daniel Joensson, Ulf Hammar, Yi-Ting Lin, Shafqat Ahmad, Diem Nguyen, Georgios Varotsis, Sara Pita, Nynne Nielsen, Aron C. C. Eklund, Jacob B. B. Holm, H. Bjorn Nielsen, Ulrika Ericson, Louise Brunkwall, Filip Ottosson, Anna Larsson, Dan Ericson, Bjoern Klinge, Peter M. M. Nilsson, Andrei Malinovschi, Lars Lind, Goran Bergstrom, Johan Sundstrom, Johan Arnlov, Gunnar Engstrom, J. Gustav Smith, Marju Orho-Melander, Tove Fall
Summary: This study identified associations between gut microbiota composition and coronary atherosclerosis, as well as systemic inflammation markers. The findings suggest a potential role of gut microbiota in the development and progression of atherosclerosis.
Article
Genetics & Heredity
Gabriela E. de Albuquerque, Bruno S. Moda, Marianna S. Serpa, Gabriela P. Branco, Alexandre Defelicibus, Isabella K. T. M. Takenaka, Maria G. de Amorim, Elizabeth C. Miola, Valquiria C. A. Martins, Katia L. Torres, Stephania M. Bezerra, Laura C. L. Claro, Adriane G. Pelosof, Claudia Z. Sztokfisz, Lais L. S. Abrantes, Felipe J. F. Coimbra, Luiz P. Kowalski, Fabio A. Alves, Stenio C. Zequi, Klas I. Udekwu, Israel T. Silva, Diana N. Nunes, Thais F. Bartelli, Emmanuel Dias-Neto
Summary: This study presents a targeted qPCR approach to determine the absolute and relative abundance of bacteria and fungi in different human tissue types. The results show that fungi are more abundant in stool and skin samples, while bacteria are more prevalent in stool, skin, oral swabs, saliva, and gastric fluids.
Article
Biochemical Research Methods
Shulei Wang
Summary: In this study, a new differential abundance test called the MsRDB test is proposed, which embeds the sequences into a metric space and integrates a multiscale adaptive strategy to identify differentially abundant microbes. Compared with existing methods, the MsRDB test can detect differentially abundant microbes at the finest resolution offered by data and is robust to zero counts, compositional effect, and experimental bias in the microbial compositional dataset.
Article
Biotechnology & Applied Microbiology
Lucas R. van Dijk, Bruce J. Walker, Timothy J. Straub, Colin J. Worby, Alexandra Grote, Henry L. Schreiber, Christine Anyansi, Amy J. Pickering, Scott J. Hultgren, Abigail L. Manson, Thomas Abeel, Ashlee M. Earl
Summary: This article introduces a toolkit called Strain Genome Explorer (StrainGE), which can deconvolve strain mixtures and characterize component strains at the nucleotide level from short-read metagenomic sequencing with higher sensitivity and resolution than other tools.
Article
Horticulture
Hongfei Li, Fang Song, Xiaoxiao Wu, Chongling Deng, Qiang Xu, Shu'ang Peng, Zhiyong Pan
Summary: The study identified significant changes in rhizosphere and root bacterial genera in response to CLas infection, with particular impacts on carbohydrate metabolism and phosphoinositide signaling pathways.
Article
Biochemical Research Methods
Matteo Calgaro, Chiara Romualdi, Davide Risso, Nicola Vitulo
Summary: This article presents benchdamic, a Bioconductor package for benchmarking methods for the identification of differentially abundant taxa.
Article
Microbiology
Victoria Pascal Andreu, Hannah E. Augustijn, Koen van den Berg, Justin J. J. van der Hooft, Michael A. Fischbach, Marnix H. Medema
Summary: Microbial gene clusters encoding biosynthesis of metabolites are crucial for microbial ecosystems. BiG-MAP is a bioinformatic tool that profiles gene cluster abundance and expression levels in microbiome samples, allowing for hypothesis generation on functional roles and associations with phenotypes of interest.
Article
Health Care Sciences & Services
Souad Kartti, Houda Bendani, Nasma Boumajdi, El Mehdi Bouricha, Oumaima Zarrik, Hajar EL Agouri, Mohamed Fokar, Youssef Aghlallou, Rachid EL Jaoudi, Lahcen Belyamani, Basma Elkhannoussi, Azeddine Ibrahimi
Summary: This study analyzed the differences in bacterial composition between tumor and adjacent tissues in breast cancer patients in Morocco. The results showed that tumor tissues had a higher abundance of Bacilli and Actinobacteria, while adjacent tissues had a higher abundance of Gammaproteobacteria. Additionally, different microbial communities were identified in different breast cancer subtypes. These findings have implications for diagnosis and treatment strategies for breast cancer.
JOURNAL OF PERSONALIZED MEDICINE
(2023)
Article
Microbiology
Zhicheng Ji, Li Ma
Summary: In analyzing metatranscriptomics data, it is important to control for both DNA and taxa abundances to eliminate their strong correlation with RNA abundance.
Article
Microbiology
Joann Phan, Divya Nair, Suneer Jain, Thibaut Montagne, Demi Valeria Flores, Andre Nguyen, Summer Dietsche, Saurabh Gombar, Philip Cotter
Summary: Irritable bowel syndrome (IBS) is characterized by abdominal discomfort and irregular bowel movements, with the gut microbiome posited to play a significant role. This study analyzed stool samples from individuals with IBS and without IBS and found differences in microbial features, with synbiotic supplementation showing potential to impact these features. Further research is needed to determine the relationship between microbiome changes and improvement in IBS symptoms.
Article
Microbiology
Andrew L. Neal, Timothy McLaren, Mariana Lourenco Campolino, David Hughes, Antonio Marcos Coelho, Ubiraci Gomes de Paula Lana, Eliane Aparecida Gomes, Sylvia Morais de Sousa
Summary: The study found that different phosphorus fertilizer sources did not significantly affect crop performance, but did influence the accumulation of fertilizer phosphorus into organic soil pools. Phosphatase activity was the only biological parameter influenced by phosphorus fertilization. Differences in rhizosphere microbiomes were observed due to crop type, not fertilization.
FEMS MICROBIOLOGY ECOLOGY
(2021)
Article
Biochemistry & Molecular Biology
Zhiyin Chen, Baogui Liu, Zhihua Gong, Hua Huang, Yihui Gong, Wenjun Xiao
Summary: By studying the effects of EGCG@beta-CD NPs on the gut microbiota, it was found that continuous administration of EGCG@beta-CD NPs could reduce serum cholesterol and lipoprotein levels in rats, while increasing the levels of antioxidant enzymes and apolipoprotein-A1 in the liver. In addition, EGCG@beta-CD NPs could alter the ratio of bacterial phyla in the gut, particularly by increasing the abundance of Akkermansia muciniphila.
Article
Multidisciplinary Sciences
Ammal M. Metwally, Dalia M. Elmosalami, Hazem Elhariri, Lobna A. El Etreby, Ahmed Aboulghate, Marwa M. El-Sonbaty, Amira Mohsen, Rehan M. Saleh, Ghada A. Abdel-Latif, Sahar Samy, Sherif E. El Deeb, Asmaa M. Fathy, Mohab M. Salah, Mohamed A. Abdel Mawla, Hanaa M. Imam, Nihad A. Ibrahim, Fatma A. Shaaban, Reham Y. Elamir, Mohamed Abdelrahman, Manal H. El-Sayed
Summary: This study aimed to assess the dominance of risk practices associated with HCV endemicity in Egypt and detect the behavioral development level concerning different aspects of HCV risk behaviors with respect to age and gender. The survey revealed that cost-effective strategies could accelerate HCV elimination in Egypt by focusing on motivating the adoption of risk-reduction behaviors, tackling misconceptions, and reinforcing social support.
Article
Surgery
Markus Quante, Jasper Iske, Hirofumi Uehara, Koichiro Minami, Yeqi Nian, Ryochi Maenosono, Tomohisa Matsunaga, Yang Liu, Haruhito Azuma, David Perkins, Maria-Luisa Alegre, Hao Zhou, Abdallah Elkhal, Stefan G. Tullius
Summary: The study reveals the impact of obesity and bariatric surgery on transplant rejection and allograft survival in obese mice. Sleeve gastrectomies prior to transplantation attenuate T cell-derived alloimmune responses, prolonging allograft survival. Administration of taurodeoxycholic acid and valine increases graft survival and reduces donor-specific antibody levels in transplant patients.
AMERICAN JOURNAL OF TRANSPLANTATION
(2022)
Article
Multidisciplinary Sciences
Ammal M. Metwally, Hala A. Amer, Hend I. Salama, Safaa I. Abd El Hady, Raefa R. Alam, Ahmed Aboulghate, Hanan A. Mohamed, Hanan M. Badran, Amal A. Saadallah, Marwa M. El-Sonbaty, Eman Eltahlawy, Walaa Saad, Amira Mohsen, Ghada A. Abdel-Latif, Asmaa M. Fathy, Amal I. Hassanain, Abdelmoneim Eldali
Summary: The study found that there is significant variation in IC implementation across different healthcare facilities in Egypt. The top three purposes of current IC practices include helping patient/guardian decide, documenting patient's/guardian's decision, and having shared decision. The perceived purposes for IC practices in the future include informing the patient/guardian, ensuring patient/guardian understand, and documenting patients/guardians decisions.
Article
Statistics & Probability
Keren Li, Jie Yang
Summary: The proposed representative approach is a fast and efficient strategy for big data analysis with generalized linear models, aiming to improve computational efficiency and accuracy by constructing representative data points for each data block to fit the target model.
ELECTRONIC JOURNAL OF STATISTICS
(2022)
Article
Genetics & Heredity
Nan Sun, Jie Yang, Stephen S. -T. Yau
Summary: Mutation is the driving force of species evolution and can provide selective competitive advantages for organisms to adapt to environmental changes. However, it can also lead to diseases. Identifying gene regions with high mutation rates is crucial. This study proposes a mathematical formula based on natural vectors to measure the difference in nucleotide distribution over time and investigates the mutation of human immunodeficiency virus using gene sequences from twenty HIV-infected patients. The results demonstrate that certain genes or gene segments in the genome exhibit varying mutation rates during the infection period, with the Env gene showing the highest mutation rate.
Article
Pediatrics
Ammal M. Metwally, Ali M. Abdallah, Ebtissam M. Salah El-Din, Zeinab Khadr, Ehab R. Abdel Raouf, Nahed A. Elghareeb, Rehan M. Saleh, Manal H. Abuelela, Hala A. Amer, Hasanin M. Hasanin, Mohamed A. Abdel Mawla, Sara F. Sallam, Inas R. El-Alameey, Samia M. Sami, Ghada A. Abdel-Latif, Mohamed Abdelrahman, Manal A. Shehata
Summary: This study examined the prevalence and associated risk factors of developmental delays among 41,640 Egyptian children. The overall prevalence was 6.7%, with communication deficit being the most common type. Risk factors included parental education, health problems during pregnancy, and family structure.
CHILD AND ADOLESCENT PSYCHIATRY AND MENTAL HEALTH
(2022)
Article
Pediatrics
Ammal M. Metwally, Sara F. Sallam, Mohamed A. Abdel Mawla, Khadija M. Alian, Ghada A. Abdel-Latif, Hasanin M. Hasanin, Ayat N. Kamal, Carine Hanna, Salwa M. El Shebini, Nihad H. Ahmed, Hoda B. Mabrok, Maha H. Mahmoud, Ahmed S. Ismail, Samia A. W. Boseila, Inas R. El-Alameey, Nermine N. Mahfouz, Fatma A. Shaaban, Nihad A. Ibrahim, Nayera E. Hassan, Sahar A. El-Masry, Maie M. Naga, Aya Khalil
Summary: By closely communicating with targeted communities and respecting parents' beliefs and cultural norms, the use of Communication for Development (C4D) principles significantly improves weaning practices and infant growth.
Article
Virology
Wangfei Wang, Anirban Sinha, Rene Lutter, Jie Yang, Christian Ascoli, Peter J. Sterk, Nicole K. Nemsick, David L. Perkins, Patricia W. Finn
Summary: In this study, the temporal behavior of circulating exosomal microRNAs (ExoMiRNAs) in asthmatics and healthy controls inoculated with rhinovirus was characterized. Differentially expressed (DE) miRNAs were identified between the two groups, showing a unique Cluster of Upregulated and Downregulated DE ExoMiRNAs in asthmatic subjects. These clusters were correlated with specific cytokines, pulmonary function measurements, and inflammatory biomarkers.
Article
Surgery
Zhipeng Li, Luqiu Chen, Martin Sepulveda, Peter Wang, Mladen Rasic, Stefan G. Tullius, David Perkins, Maria-Luisa Alegre
Summary: Obesity is associated with dysbiosis and chronic inflammation, which contribute to the development of metabolic diseases. This study found that antibiotic treatment can prolong graft survival and reduce fasting glycemia in high-fat diet (HFD)-fed mice, suggesting a role for the microbiota in promoting accelerated graft rejection and hyperglycemia induced by diet-induced obesity (DIO). Additionally, the impact of high-fat diet on transplant outcomes is not only dependent on the microbiota but also independent of obesity and hyperglycemia. Supplementation of the gut commensal Alistipes onderdonkii can alleviate HFD-induced inflammation and glucose intolerance, leading to a reduction in hyperglycemia in DIO mice.
AMERICAN JOURNAL OF TRANSPLANTATION
(2023)
Article
Pediatrics
Ammal M. Metwally, Ali M. Abdallah, Ebtissam M. Salah El-Din, Dina Abu Zeid, Zeinab Khadr, Ghada A. Elshaarawy, Alshaimaa A. Elkhatib, Amal Elsaied, Engy A. Ashaat, Nahed A. Elghareeb, Mohamed H. Abdou, Asmaa M. Fathy, Sherif E. Eldeeb, Mohamed Abdallah, Muhammed Al-tohamy Soliman, Rokia AbdElshafy S. El Banna, Abdelrahman K. Hassanein, Thanaa M. Rabah, Mohamed Abdelrahman, Sara F. Sallam
Summary: This study aimed to assess the types and prevalence of developmental delays (DDs) among Egyptian preschool children and explore the determinants of these delays based on sociodemographic, epidemiological, maternal, and child perinatal risk factors. The study found that perinatal factors were among the most common determinants of DD in preschool children and many of these risk factors are preventable.
Article
Psychiatry
Ammal M. Metwally, Mona A. Helmy, Ebtissam Salah M. El-Din, Rehan M. Saleh, Ehab Abdel R. Raouf, Ali M. Abdallah, Zeinab Khadr, Amal Elsaied, Mostafa M. El-Saied, Randa I. Bassiouni, Dina A. Nagi, Manal A. Shehata, Inas R. El-Alameey, Hazem M. El-Hariri, Somia I. Salama, Thanaa M. Rabah, Ghada A. Abdel-Latif, Lobna A. El Etreby, Dalia M. Elmosalami, Samia M. Sami, Eman Eltahlawy, Nihad A. Ibrahim, Nahed A. Elghareeb, Hala Y. Badawy, Eman M. Dewdar, Engy A. Ashaat
Summary: This study aimed to estimate the national prevalence of the high risk of autism spectrum disorder (ASD) and identify its determinants. The study conducted a national screening survey for 41,640 Egyptian children aged 1 to 12 years in two phases. The overall prevalence of children at high risk of ASD was 3.3% (95% CI: 3.1%-3.5%). Children living without mothers, having a history of convulsions, cyanosis after birth, or low birth weight (LBW) were more likely to be at high risk of ASD.
Article
Psychiatry
Ammal M. Metwally, Ahmed Aboulghate, Ghada A. Elshaarawy, Ali M. Abdallah, Ehab R. Abdel Raouf, Ebtissam M. Salah El-Din, Zeinab Khadr, Mostafa M. El-Saied, Mona A. Elabd, Maysa S. Nassar, Marwa W. Abouelnaga, Engy A. Ashaat, Mohamed M. El-Sonbaty, Hala Y. Badawy, Eman M. Dewdar, Somia I. Salama, Mohamed Abdelrahman, Aida M. Abdelmohsen, Sherif E. Eldeeb, Maie M. Naga, Nada H. Elshamy, Fatma A. Shaaban, Amira S. ElRifay
Summary: This study investigated the prevalence and associated factors of seven types of disabilities among Egyptian children aged 1-6 years. The findings revealed a high prevalence of disabilities, with male sex, preterm birth, and low birth weight being risk factors.
Article
Public, Environmental & Occupational Health
Ammal M. Metwally, Ebtissam M. Salah M. El-Din, Ghada A. Abdel-Latif, Dina A. Nagi, Lobna A. El Etreby, Ali M. Abdallah, Zeinab Khadr, Randa I. Bassiouni, Ehab A. Abdel R. Raouf, Amal Elsaied, Alshaimaa A. Elkhatib, Sara F. Sallam, Marwa M. El-Sonbaty, Manal A. Shehata, Nahed A. Elghareeb, Hala Y. Badawy, Doaa E. Ahmed, Nihad A. Ibrahim, Hanaa Emam, Soha M. Abd El Dayem, Asmaa M. Fathy
Summary: This study aimed to determine the prevalence of disability domains among Egyptian children aged 6-12 years and to assess their socio-demographic, epidemiological, and perinatal predictors. A national population-based cross-sectional household survey was conducted, and the prevalence of children with at least one type of disability was found to be 9.2%. Learning/ comprehension was the most common type, followed by speech/communication, physical/mobility and seizures, intellectual impairment, visual, and hearing disabilities.
Article
Multidisciplinary Sciences
Ammal M. Metwally, Maysa S. Nassar, Ebtissam M. Salah El-Din, Ali M. Abdallah, Zeinab Khadr, Marwa W. Abouelnaga, Engy A. Ashaat, Mostafa M. El-Saied, Ahmed M. Elwan, Randa I. Bassiouni, Zeinab M. Monir, Hala Y. Badawy, Eman M. Dewdar, Hazem M. El-Hariri, Ahmed Aboulghate, Carine Hanna, Thanaa M. Rabah, Amira Mohsen, Mona A. Elabd
Summary: This study aimed to estimate the national prevalence of developmental delays (DDs) and their determinants among Egyptian children aged 6 to 12 years. The study used the Vineland Adaptive Behavior Scales to assess various skills and used logistic regression analysis to identify factors associated with DDs. The study found that 7.4% of the surveyed children had at least one delay, with communication deficits being the most common. Factors such as convulsions, male gender, low birth weight, maternal health problems, incubator stay, less educated fathers, and middle social class were associated with a higher likelihood of DDs.
Article
Biotechnology & Applied Microbiology
Niloufar Dousti Mousavi, Hani Aldirawi, Jie Yang
Summary: In this study, a statistical procedure based on multinomial logistic regression analysis is introduced for analyzing high-dimensional sparse data, particularly in the field of omics. The procedure includes variable screening, model selection, order selection for response categories, and variable selection. Application of the procedure on gene expression data resulted in three recommended models, one of which achieved extremely low cross-entropy loss and zero predictive error rate.
