Article
Biochemistry & Molecular Biology
Cody Coyotee Howard, Andrew A. Crowl, Timothy S. Harvey, Nico Cellinese
Summary: This study provides the first phylogenomic perspective into the Ledebouriinae group, revealing a rapid radiation and incomplete lineage sorting within the group. The study also suggests potential historical hybridization between Drimiopsis and a subclade within Ledebouria Clade A.
MOLECULAR PHYLOGENETICS AND EVOLUTION
(2022)
Article
Plant Sciences
Isma Il Eker
Summary: This study re-evaluates the taxonomic status of Muscari wallii, previously considered as a synonym of Muscari tenuiflorum, based on morphological and chorological studies. It is morphologically similar to M. tenuiflorum and M. babachii, but can be distinguished by seed characteristics and other features.
Article
Statistics & Probability
Gregor Zens, Sylvia Fruehwirth-Schnatter, Helga Wagner
Summary: This paper introduces a novel latent variable representation based on Polya-Gamma random variables for Bayesian models of binary and categorical data. New Gibbs sampling algorithms and marginal data augmentation strategies are derived to improve the efficiency of Bayesian methods in this context. Extensive simulations and real data applications illustrate the merits of this approach.
JOURNAL OF THE AMERICAN STATISTICAL ASSOCIATION
(2023)
Article
Infectious Diseases
Tianyi Luo, Jiaojiao Wang, Quanyi Wang, Xiaoli Wang, Pengfei Zhao, Daniel Dajun Zeng, Qingpeng Zhang, Zhidong Cao
Summary: The study aims to reconstruct the complete transmission chain of the COVID-19 outbreak in Beijing's Xinfadi Market using epidemiological investigation data, contributing to understanding transmission dynamics and risk factors. Results show that the transmission rate of COVID-19 within households is 9.2%, and older people are more susceptible. The accuracy of the reconstructed transmission chain is 67.26%. In the Beef and Mutton Trading Hall of Xinfadi market, most transmission occurs within 20 meters, with an average transmission distance of 13.00 meters and the deepest transmission generation being the 9th.
INTERNATIONAL JOURNAL OF INFECTIOUS DISEASES
(2022)
Article
Plant Sciences
Brita Stedje, Antonius J. H. Rulkens, Andrew J. Hankey
Summary: A new genus Occultia, distinct from Ledebouria and closely related genera, is described from Malawi and Mozambique based on its unique characteristics of flower and fruit.
Article
Plant Sciences
Ismail Eker, Hasan Yildirim
Summary: A new species of Muscari, Muscari inundatum from Turkey, has been described and illustrated. It is morphologically similar to two existing species but can be differentiated mainly by its unique flowers. This study provides a comprehensive description, diagnostic characters, original photographs, detailed illustrations, geographical distribution, conservation assessment, identification key, and taxonomic comments on the new species.
Article
Plant Sciences
Sayantani Nath, Sayantika Sarkar, Sayali D. Patil, Partha Sarathi Saha, Manoj M. Lekhak, Sudipta Ray, Satyawada Rama Rao, S. R. Yadav, R. C. Verma, Manoj K. Dhar, S. N. Raina, Sumita Jha
Summary: The family Asparagaceae, specifically the subfamily Scilloideae, is a group of deciduous bulbous geophytes with a long history of medicinal use. However, there is still uncertainty in the delimitation of genera and species within this family due to a lack of reliable discriminating characters. Detailed cytogenetic characterization and comparative analysis in this group are limited, but can provide taxonomical data and a basis for further genomic studies. By studying different tribes within the subfamily, diverse cytogenetic characters have been observed, but more species need to be investigated to predict trends in chromosomal diversity.
Article
Ecology
Yiming Ma, Chungkun Shih, Dong Ren, Yongjie Wang
Summary: A new species of the Kempyninae insect family is described from Inner Mongolia, China, and a classification key to extinct and extant genera of the family is provided. Phylogenetic analyses of extant and fossil genera reveal the complex evolutionary scenario of Kempyninae, with three distinct clades and independent evolution of extant kempynines from their northern Mesozoic relatives. The study also suggests a northern and prepangean origin of Kempyninae.
FRONTIERS IN ECOLOGY AND EVOLUTION
(2022)
Article
Anatomy & Morphology
Burcu Yilmaz Citak, Tuna Uysal, Meryem Bozkurt, Hakki Demirelma, Ahmet Aksoy, Kuddisi Ertugrul
Summary: This study examines the palynomorphological traits of the genus Muscari and its relatives. The research finds that there is no significant difference in pollen structures among these taxa, indicating a high similarity in terms of germ cells or microspores. Common pollen types can be used to differentiate closely related species or taxonomic groups.
MICROSCOPY RESEARCH AND TECHNIQUE
(2022)
Article
Biochemical Research Methods
Lucille Lopez-Delisle, Jean-Baptiste Delisle
Summary: This study introduces a new tool called baredSC, which uses a Gaussian mixture model to infer the intrinsic expression distribution in scRNA-seq data. The tool can be used to obtain the expression distribution of individual genes and pairs of genes, as well as estimate the correlation between the expressions of two genes. The effectiveness of baredSC is demonstrated through application on simulated data and real biological datasets.
BMC BIOINFORMATICS
(2022)
Article
Biochemistry & Molecular Biology
Iris van Kleinwee, Isabel Larridon, Toral Shah, Kenneth Bauters, Pieter Asselman, Paul Goetghebeur, Frederik Leliaert, Emily Veltjen
Summary: Sansevierias, commonly known as low maintenance houseplants, are a diverse group of flowering plants native to Africa, Madagascar, the Arabian Peninsula, and the Indian subcontinent. Recent research has merged the genus Sansevieria with the larger Dracaena genus, causing taxonomic uncertainties. This study used genome skimming to generate datasets and reconstruct a phylogenetic hypothesis, uncovering evolutionary relationships and morphological evolution. The findings revealed a recent radiation with five main clades, confirming previously defined groups and showing convergent evolution in other groups. The study contributes to our understanding of the Sansevieria Clade's evolution and has implications for taxonomy and conservation efforts.
MOLECULAR PHYLOGENETICS AND EVOLUTION
(2022)
Article
Statistics & Probability
Yves Atchade, Liwei Wang
Summary: This paper proposes a fast approximate Markov chain Monte Carlo sampling framework for a large class of sparse Bayesian inference problems. The computational cost per iteration in several regression models is of order O(n(s+J)), which can be further reduced by data sub-sampling. The algorithm is an extension of the asynchronous Gibbs sampler and can be viewed as a form of Bayesian iterated sure independent screening.
JOURNAL OF THE ROYAL STATISTICAL SOCIETY SERIES B-STATISTICAL METHODOLOGY
(2023)
Article
Plant Sciences
Azarnoosh Jafari, Jamil Vaezi, Mohammad Mahdi Forghanifard, Felix Forest, John C. Manning
Summary: The traditional sections within the genus Bellevalia are not monophyletic based on phylogenetic analysis, leading to a recommendation to reduce the current four sections and six subsections to two sections. The study highlights the importance of characteristics such as cilia on the leaf margin, green veins in the perianths lobes, and the colour of the anthers in determining relationships among species within the genus.
Article
Mathematics, Interdisciplinary Applications
Aliaksandr Hubin, Georg Heinze, Riccardo De Bin
Summary: This paper proposes a framework for fitting multivariable fractional polynomial models as special cases of Bayesian generalized nonlinear models. By applying an adapted version of the genetically modified mode jumping Markov chain Monte Carlo algorithm, the Bayesian version of fractional polynomials can be used in any supervised learning task.
FRACTAL AND FRACTIONAL
(2023)
Article
Automation & Control Systems
Liam Hodgkinson, Robert Salomone, Fred Roosta
Summary: Implicit integrators from theta-method discretization of overdamped Langevin diffusion SDE were studied for sampling from a log-concave density. The resulting sampling methods were analyzed for theta in [0,1] and various step sizes. Generalizing and extending prior works, geometric ergodicity and stability were proven for theta >= 1/2 across all step sizes. Subsequent sample generation was shown to involve solving a strongly-convex optimization problem, feasible with existing methods, supported by numerical examples.
JOURNAL OF MACHINE LEARNING RESEARCH
(2021)
Article
Biochemistry & Molecular Biology
Zainib Babar, Mazhar Khan, Mubeen Zahra, Munazza Anwar, Kashif Noor, Huma Farooque Hashmi, Muhammad Suleman, Muhammad Waseem, Abdullah Shah, Shahid Ali, Syed Shujait Ali
Summary: The outbreak of the recent coronavirus poses significant risks to public health, and researchers have identified potential drug candidates that can inhibit SARs-CoV-2 by targeting key residues. Experimental testing is recommended to confirm their antiviral effects.
JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS
(2022)
Article
Biochemistry & Molecular Biology
Shahzeb Khan, Syed Shujait Ali, Iqra Zaheer, Shoaib Saleem, Ziaullah, Nasib Zaman, Arshad Iqbal, Muhammad Suleman, Abdul Wadood, Ashfaq Ur Rehman, Asghar Khan, Abbas Khan, Dong-Qing Wei
Summary: This study identified three potential vaccine candidate proteins for Porphyromonas gingivalis using subtractive proteomics and reverse vaccinology approaches. Epitopes were predicted for the candidate proteins and molecular docking was performed. A computer-simulated vaccine was constructed and molecular dynamics simulations were conducted. Future experimental validation is required, but the developed vaccine has the potential to protect against P. gingivalis infections.
JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS
(2022)
Article
Biology
Abbas Khan, Sarfaraz Hussain, Sajjad Ahmad, Muhammad Suleman, Imrana Bukhari, Taimoor Khan, Farooq Rashid, Abul Kalam Azad, Muhammad Waseem, Wajid Khan, Zahid Hussain, Asghar Khan, Syed Shujait Ali, Qiyao Qin, Dong-Qing Wei
Summary: This study focuses on the importance of the spike protein of SARS-CoV-2 and the host ACE2 receptor in cell entry, especially on the structural variants of the hotspot residue 501, the impact of mutations on binding affinity, and the potential consequences. Results suggest that the N501I, N501T, and N501V variants may worsen the situation, raising questions about the relationship between viral fitness and binding affinity.
COMPUTERS IN BIOLOGY AND MEDICINE
(2022)
Article
Biology
Abdullah Shah, Saira Rehmat, Iqra Aslam, Muhmmad Suleman, Farah Batool, Abdul Aziz, Farooq Rashid, Midrarullah, Muhmmad Asif Nawaz, Syed Shujait Ali, Muhammad Junaid, Abbas Khan, Dong-Qing Wei
Summary: The study revealed that the nucleocapsid protein is the most frequently mutated protein in Pakistani isolates of SARS-CoV-2, while the spike protein exhibits the highest mutation rate globally. Mutations in the spike protein enhance its binding with the ACE2 receptor, leading to increased infectivity.
COMPUTERS IN BIOLOGY AND MEDICINE
(2022)
Article
Food Science & Technology
Safwan Ahmad Abdullah Murshed, Muhammad Rizwan, Fazal Akbar, Nasib Zaman, Muhammad Suleman, Syed Shujait Ali
Summary: The study found that levels of Aflatoxin M1 contamination in traditional Taizi cheese and commercial cheeses in Yemen exceeded the acceptable limit set by the European Commission, indicating a serious public health concern.
INTERNATIONAL JOURNAL OF DAIRY TECHNOLOGY
(2022)
Article
Environmental Sciences
Muhammad Idrees, Muhammad Yasir Noorani, Kalim Ullah Altaf, Eid A. Alatawi, Faris F. Aba Alkhayl, Khaled S. Allemailem, Ahmad Almatroudi, Murad Ali Khan, Muhammad Hamayun, Taimoor Khan, Syed Shujait Ali, Abbas Khan, Dong-Qing Wei
Summary: A protein-wide annotation approach was used to identify three essential vaccine targets for Elizabethkingia meningoseptica, and a multi-epitope immunogenic construct was designed. Computational predictions indicated high antigenicity and multiple interactions with immune receptors. Molecular dynamics simulations confirmed stable binding and good dynamic properties, with the computationally modelled immune response showing strong immunity induction and antigen neutralization after multiple doses.
INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH
(2022)
Article
Agronomy
Zahid Hussain, Habiba Khan, Muhammad Imran, Muhmmad Kashif Naeem, Sabir Hussain Shah, Arshad Iqbal, Syed Shujait Ali, Muhammad Rizwan, Shahid Ali, Muhammad Atif Muneer, Emilie Widemann, Sarfraz Shafiq
Summary: This study identified and analyzed 33 putative CPA genes in tomato and found that they play a crucial role in maintaining ionic balance and pH homeostasis, promoting plant development, and responding to salt stress. Further analysis revealed the characteristics of CPA genes in terms of gene structure, distribution pattern, and co-localization. The diverse functions of these CPA genes provide comprehensive information for exploring new candidate genes for salt tolerance in tomato.
Article
Biochemistry & Molecular Biology
Abbas Khan, Hira Waris, Memoona Rafique, Muhammad Suleman, Anwar Mohammad, Syed Shujait Ali, Taimoor Khan, Yasir Waheed, Chenguang Liao, Dong-Qing Wei
Summary: This study provides a basis for understanding the impact of novel mutations on the structure, function, and binding of the new SARS-CoV-2 variants, and serves as a strong impetus for the development of novel drugs against them.
INTERNATIONAL JOURNAL OF BIOLOGICAL MACROMOLECULES
(2022)
Article
Genetics & Heredity
Fazal Akbar, Muhammad Suleman, Muhammad Israr, Syed Shujait Ali, Nasib Zaman, Owais Khan, Jawad Ali, Waqar Ahmad, Murad Ali Rahat, Akhtar Rasool, Muzafar Shah, Zahid Hussain, Mohammad Ali
Summary: The study found that COVID-19 cases in highly infected provinces of Pakistan were mainly concentrated in June, with a higher incidence at higher temperatures and humidity. However, the correlation between temperature, humidity, and the COVID-19 pandemic was not significant, suggesting the need for stricter control measures despite the indirect association with temperature variation and humidity in the transmission of COVID-19.
Article
Plant Sciences
Mario Martinez-Azorin, Manuel B. Crespo, Maria Angeles Alonso-Vargas, Michael Pinter, Neil R. Crouch, Anthony P. Dold, Ladislav Mucina, Martin Pfosser, Wolfgang Wetschnig
Summary: The taxonomy and systematics of Urgineoideae have been controversial, but this study provides a comprehensive analysis using morphological and DNA data to resolve the classification. Phylogenetic analysis reveals well-defined clades corresponding to known genera, and consistent character syndromes support genus recognition. The forthcoming revised classification of Urgineoideae is outlined.
JOURNAL OF SYSTEMATICS AND EVOLUTION
(2023)
Article
Immunology
Muhammad Suleman, Ali Raza Balouch, AsfandYar Waheed Randhawa, Taimoor Khan, Maria Muddassir, Asad Ullah, Amin Ullah Jan, Muhammad Amir Zia, Syed Shujait Ali, Abbas Khan
Summary: In this study, a multi-epitopes subunit vaccine was designed using specific and proteome-wide epitopes mapping. The constructed vaccine demonstrated strong antigenicity and non-allergic behavior, and showed good binding with Toll-like receptor 7 (TLR7). Immune simulation experiments also showed a stronger neutralization effect of the proteome-wide vaccine construct on the antigen.
MICROBIAL PATHOGENESIS
(2022)
Article
Biology
Muhammad Suleman, Uzair Asad, Shafia Arshad, Ayaz ur Rahman, Fazal Akbar, Haji Khan, Zahid Hussain, Syed Shujait Ali, Anwar Mohammad, Abbas Khan, Liaqat Ali, Dong-Qing Wei
Summary: In this study, a computational meta-analysis approach combined with immunoinformatics was used to design multi-epitopes vaccines for the treatment of SFTS. The best epitopes were selected and combined to construct vaccines for specific proteins and the proteome. Molecular docking validation showed that the designed vaccines had good binding potential with TLR3. The injection of the multi-epitopes vaccines significantly stimulated the immune response and enhanced the anti-toxicity of antibodies. In vivo trials are needed to confirm the effectiveness of the constructed vaccine against SFTS.
COMPUTERS IN BIOLOGY AND MEDICINE
(2022)
Article
Pharmacology & Pharmacy
Muhammad Suleman, Syeda Umme-I-Hani, Muhammad Salman, Mohammed Aljuaid, Abbas Khan, Arshad Iqbal, Zahid Hussain, Syed Shujait Ali, Liaqat Ali, Hassan Sher, Yasir Waheed, Dong-Qing Wei
Summary: This study utilized different machine learning algorithms to screen deleterious nonsynonymous single nucleotide polymorphisms (nsSNPs) in the IDH1 gene, and used structure-based prediction methods to validate the destabilization caused by some of these mutations. Molecular docking and simulation analysis revealed variations in dynamics features and reduced binding of small molecules in these deleterious mutations compared to the wild type. Principal component analysis and free energy landscape analysis showed that these mutations caused different arrangements for small molecule binding and decreased total internal motion, resulting in minimal binding effects.
FRONTIERS IN PHARMACOLOGY
(2022)
Article
Chemistry, Multidisciplinary
Abbas Khan, AsfandYar Waheed Randhawa, Ali Raza Balouch, Naila Mukhtar, Abrar Mohammad Sayaf, Muhammad Suleman, Taimoor Khan, Shahid Ali, Syed Shujait Ali, Yanjing Wang, Anwar Mohammad, Dong-Qing Wei
Summary: A computational study identified four compounds that showed potential as antiviral agents against the omicron variant of SARS-CoV-2. These compounds demonstrated good antiviral properties, stability, and structural compactness.
Article
Biochemistry & Molecular Biology
Irfan Ahmad, Syed Shujait Ali, Bisma Zafar, Huma Farooque Hashmi, Ismail Shah, Shahzeb Khan, Muhammad Suleman, Mazhar Khan, Saif Ullah, Shahid Ali, Jafar Khan, Mohammad Ali, Abbas Khan, Dong-Qing Wei
Summary: This study aims to develop an effective vaccine against human Norovirus infection. B and T cell epitopes of proteins were predicted using immunoinformatics tools and selected for subunit vaccine. The vaccine structure was modelled and validated, and its stability was evaluated through docking and MD simulation. Experimental validation is necessary for the vaccine developed in this study.
JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS
(2022)