Progress in Biophysics & Molecular Biology最新文献_第8页

Commentary on “A systematic review on machine learning and deep learning techniques in cancer survival prediction”: Validation of survival methods 评论“癌症生存预测中的机器学习和深度学习技术的系统综述”：生存方法的验证。

IF 3.8 3区生物学

Progress in Biophysics & Molecular Biology Pub Date : 2023-10-01 DOI: 10.1016/j.pbiomolbio.2023.08.001

J. Sidorova, J.J. Lozano

引用次数: 0

A systematic review on intracranial aneurysm and hemorrhage detection using machine learning and deep learning techniques 利用机器学习和深度学习技术检测颅内动脉瘤和出血的系统综述。

IF 3.8 3区生物学

Progress in Biophysics & Molecular Biology Pub Date : 2023-10-01 DOI: 10.1016/j.pbiomolbio.2023.07.001

S. Nafees Ahmed, P. Prakasam

{"title":"A systematic review on intracranial aneurysm and hemorrhage detection using machine learning and deep learning techniques","authors":"S. Nafees Ahmed, P. Prakasam","doi":"10.1016/j.pbiomolbio.2023.07.001","DOIUrl":"10.1016/j.pbiomolbio.2023.07.001","url":null,"abstract":"<div><p>The risk of discovering an intracranial aneurysm during the initial screening and follow-up screening are reported as around 11%, and 7% respectively (Zuurbie et al., 2023) to these mass effects, unruptured aneurysms frequently generate symptoms, however, the real hazard occurs when an aneurysm ruptures and results in a cerebral hemorrhage known as a subarachnoid hemorrhage. The objective is to study the multiple kinds of hemorrhage and aneurysm detection problems and develop machine and deep learning models to recognise them. Due to its early stage, subarachnoid hemorrhage, the most typical symptom after aneurysm rupture, is an important medical condition. It frequently results in severe neurological emergencies or even death. Although most aneurysms are asymptomatic and won't burst, because of their unpredictable growth, even small aneurysms are susceptible. A timely diagnosis is essential to prevent early mortality because a large percentage of hemorrhage cases present can be fatal. Physiological/imaging markers and the degree of the subarachnoid hemorrhage can be used as indicators for potential early treatments in hemorrhage. The hemodynamic pathomechanisms and microcellular environment should remain a priority for academics and medical professionals. There is still disagreement about how and when to care for aneurysms that have not ruptured despite studies reporting on the risk of rupture and outcomes. We are optimistic that with the progress in our understanding of the pathophysiology of hemorrhages and aneurysms and the advancement of artificial intelligence has made it feasible to conduct analyses with a high degree of precision, effectiveness and reliability.</p></div>","PeriodicalId":54554,"journal":{"name":"Progress in Biophysics & Molecular Biology","volume":"183 ","pages":"Pages 1-16"},"PeriodicalIF":3.8,"publicationDate":"2023-10-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10273805","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 1

HIF-1α and periodontitis: Novel insights linking host-environment interplay to periodontal phenotypes HIF-1α与牙周炎：将宿主环境相互作用与牙周表型联系起来的新见解。

IF 3.8 3区生物学

Progress in Biophysics & Molecular Biology Pub Date : 2023-09-26 DOI: 10.1016/j.pbiomolbio.2023.09.002

Chao Shan , YuNing Xia , Zeyu Wu , Jin Zhao

{"title":"HIF-1α and periodontitis: Novel insights linking host-environment interplay to periodontal phenotypes","authors":"Chao Shan , YuNing Xia , Zeyu Wu , Jin Zhao","doi":"10.1016/j.pbiomolbio.2023.09.002","DOIUrl":"10.1016/j.pbiomolbio.2023.09.002","url":null,"abstract":"<div><p><span>Periodontitis, the sixth most prevalent epidemic disease globally, profoundly impacts oral aesthetics and masticatory functionality. Hypoxia-inducible factor-1α (HIF-1α), an oxygen-dependent transcriptional activator<span>, has emerged as a pivotal regulator in periodontal tissue and alveolar bone metabolism, exerts critical functions in angiogenesis, </span></span>erythropoiesis<span><span>, energy metabolism, and cell fate determination. Numerous essential phenotypes regulated by HIF are intricately associated with bone metabolism in periodontal tissues. Extensive investigations have highlighted the central role of HIF and its downstream target genes and pathways in the coupling of angiogenesis and osteogenesis. Within this concise perspective, we comprehensively review the cellular phenotypic alterations and microenvironmental dynamics linking HIF to periodontitis. We analyze current research on the HIF pathway, elucidating its impact on bone repair and regeneration, while unraveling the involved cellular and molecular mechanisms. Furthermore, we briefly discuss the potential application of targeted interventions aimed at HIF in the field of bone </span>tissue regeneration engineering. This review expands our biological understanding of the intricate relationship between the HIF gene and bone angiogenesis in periodontitis and offers valuable insights for the development of innovative therapies to expedite bone repair and regeneration.</span></p></div>","PeriodicalId":54554,"journal":{"name":"Progress in Biophysics & Molecular Biology","volume":"184 ","pages":"Pages 50-78"},"PeriodicalIF":3.8,"publicationDate":"2023-09-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"41158378","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Piezo1：the potential new therapeutic target for fibrotic diseases Piezo1：纤维疾病的潜在新治疗靶点。

IF 3.8 3区生物学

Progress in Biophysics & Molecular Biology Pub Date : 2023-09-16 DOI: 10.1016/j.pbiomolbio.2023.09.001

Xin Liu , Weipin Niu , Shuqing Zhao , Wenjuan Zhang , Ying Zhao , Jing Li

{"title":"Piezo1：the potential new therapeutic target for fibrotic diseases","authors":"Xin Liu , Weipin Niu , Shuqing Zhao , Wenjuan Zhang , Ying Zhao , Jing Li","doi":"10.1016/j.pbiomolbio.2023.09.001","DOIUrl":"10.1016/j.pbiomolbio.2023.09.001","url":null,"abstract":"<div><p>Fibrosis is a pathological process that occurs in various organs, characterized by excessive deposition of extracellular matrix (ECM), leading to structural damage and, in severe cases, organ failure. Within the fibrotic microenvironment, mechanical forces play a crucial role in shaping cell behavior and function, yet the precise molecular mechanisms underlying how cells sense and transmit these mechanical cues, as well as the physical aspects of fibrosis progression, remain less understood. Piezo1, a mechanosensitive ion channel protein, serves as a pivotal mediator, converting mechanical stimuli into electrical or chemical signals. Accumulating evidence suggests that Piezo1 plays a central role in ECM formation and hemodynamics in the mechanical transduction of fibrosis expansion. This review provides an overview of the current understanding of the role of Piezo1 in fibrosis progression, encompassing conditions such as myocardial fibrosis, pulmonary fibrosis, renal fibrosis, and other fibrotic diseases. The main goal is to pave the way for potential clinical applications in the field of fibrotic diseases.</p></div>","PeriodicalId":54554,"journal":{"name":"Progress in Biophysics & Molecular Biology","volume":"184 ","pages":"Pages 42-49"},"PeriodicalIF":3.8,"publicationDate":"2023-09-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10673539","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Application of nanomaterials as potential quorum quenchers for disease: Recent advances and challenges 纳米材料作为疾病潜在群体猝灭剂的应用：最新进展和挑战。

IF 3.8 3区生物学

Progress in Biophysics & Molecular Biology Pub Date : 2023-09-02 DOI: 10.1016/j.pbiomolbio.2023.08.005

Saad Alghamdi , Krisha Khandelwal , Soumya Pandit , Arpita Roy , Subhasree Ray , Ahad Amer Alsaiari , Abdulelah Aljuaid , Mazen Almehmadi , Mamdouh Allahyani , Rohit Sharma , Jigisha Anand , Ahmad Adnan Alshareef

{"title":"Application of nanomaterials as potential quorum quenchers for disease: Recent advances and challenges","authors":"Saad Alghamdi , Krisha Khandelwal , Soumya Pandit , Arpita Roy , Subhasree Ray , Ahad Amer Alsaiari , Abdulelah Aljuaid , Mazen Almehmadi , Mamdouh Allahyani , Rohit Sharma , Jigisha Anand , Ahmad Adnan Alshareef","doi":"10.1016/j.pbiomolbio.2023.08.005","DOIUrl":"10.1016/j.pbiomolbio.2023.08.005","url":null,"abstract":"<div><p>Chemical signal molecules are used by bacteria to interact with one another. Small hormone-like molecules known as autoinducers<span><span> are produced, released, detected, and responded to during chemical communication. Quorum Sensing (QS) is the word for this procedure; it allows bacterial populations to communicate and coordinate group behavior. Several research has been conducted on using inhibitors to prevent QS and minimize the detrimental consequences. Through the enzymatic breakdown of the autoinducer component, by preventing the formation of autoinducers, or by blocking their reception by adding some compounds (inhibitors) that can mimic the autoinducers, a technique known as “quorum quenching” (QQ) disrupts microbial communication. Numerous techniques, including colorimetry, electrochemistry, </span>bioluminescence<span><span>, chemiluminescence, fluorescence, chromatography-mass </span>spectroscopy, and many more, can be used to test QS/QQ. They all permit quantitative and qualitative measurements of QS/QQ molecules. The mechanism of QS and QQ, as well as the use of QQ in the prevention of biofilms, are all elaborated upon in this writing, along with the fundamental study of nanoparticle (NP)in QQ. Q.</span></span></p></div>","PeriodicalId":54554,"journal":{"name":"Progress in Biophysics & Molecular Biology","volume":"184 ","pages":"Pages 13-31"},"PeriodicalIF":3.8,"publicationDate":"2023-09-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10227317","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

A revised central dogma for the 21st century: All biology is cognitive information processing 21世纪修正后的中心教条：所有生物学都是认知信息处理

IF 3.8 3区生物学

Progress in Biophysics & Molecular Biology Pub Date : 2023-09-01 DOI: 10.1016/j.pbiomolbio.2023.05.005

William B. Miller Jr. , František Baluška , Arthur S. Reber

{"title":"A revised central dogma for the 21st century: All biology is cognitive information processing","authors":"William B. Miller Jr. , František Baluška , Arthur S. Reber","doi":"10.1016/j.pbiomolbio.2023.05.005","DOIUrl":"10.1016/j.pbiomolbio.2023.05.005","url":null,"abstract":"<div><p>Crick's Central Dogma has been a foundational aspect of 20th century biology, describing an implicit relationship governing the flow of information in biological systems in biomolecular terms. Accumulating scientific discoveries support the need for a revised Central Dogma to buttress evolutionary biology's still-fledgling migration from a Neodarwinian canon. A reformulated Central Dogma to meet contemporary biology is proposed: all biology is cognitive information processing. Central to this contention is the recognition that life is the self-referential state, instantiated within the cellular form. Self-referential cells act to sustain themselves and to do so, cells must be in consistent harmony with their environment. That consonance is achieved by the continuous assimilation of environmental cues and stresses as information to self-referential observers. All received cellular information must be analyzed to be deployed as cellular problem-solving to maintain homeorhetic equipoise. However, the effective implementation of information is definitively a function of orderly information management. Consequently, effective cellular problem-solving is information processing and management. The epicenter of that cellular information processing is its self-referential internal measurement. All further biological self-organization initiates from this obligate activity. As the internal measurement by cells of information is self-referential by definition, self-reference is biological self-organization, underpinning 21st century Cognition-Based Biology.</p></div>","PeriodicalId":54554,"journal":{"name":"Progress in Biophysics & Molecular Biology","volume":"182 ","pages":"Pages 34-48"},"PeriodicalIF":3.8,"publicationDate":"2023-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9878032","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 2

Method versatility in RNA extraction-free PCR detection of SARS-CoV-2 in saliva samples 唾液样本中严重急性呼吸系统综合征冠状病毒2型无RNA提取PCR检测方法的多功能性

IF 3.8 3区生物学

Progress in Biophysics & Molecular Biology Pub Date : 2023-09-01 DOI: 10.1016/j.pbiomolbio.2023.06.004

Orchid M. Allicock, Devyn Yolda-Carr, Rebecca Earnest, Mallery I. Breban, Noel Vega, Isabel M. Ott, Chaney Kalinich, Tara Alpert, Mary E Petrone, Anne L. Wyllie

{"title":"Method versatility in RNA extraction-free PCR detection of SARS-CoV-2 in saliva samples","authors":"Orchid M. Allicock, Devyn Yolda-Carr, Rebecca Earnest, Mallery I. Breban, Noel Vega, Isabel M. Ott, Chaney Kalinich, Tara Alpert, Mary E Petrone, Anne L. Wyllie","doi":"10.1016/j.pbiomolbio.2023.06.004","DOIUrl":"10.1016/j.pbiomolbio.2023.06.004","url":null,"abstract":"<div><p>Early in the pandemic, a simple, open-source, RNA extraction-free RT-qPCR protocol for SARS-CoV-2 detection in saliva was developed and made widely available. This simplified approach (SalivaDirect) requires only sample treatment with proteinase K prior to PCR testing. However, feedback from clinical laboratories highlighted a need for a flexible workflow that can be seamlessly integrated into their current health and safety requirements for the receiving and handling of potentially infectious samples. To address these varying needs, we explored additional pre-PCR workflows. We built upon the original SalivaDirect workflow to include an initial incubation step (95 °C for 30 min, 95 °C for 5 min or 65 °C for 15 min) with or without addition of proteinase K. The limit of detection for the workflows tested did not significantly differ from that of the original SalivaDirect workflow. When tested on de-identified saliva samples from confirmed COVID-19 individuals, these workflows also produced comparable virus detection and assay sensitivities, as determined by RT-qPCR analysis. Exclusion of proteinase K did not negatively affect the sensitivity of the assay. The addition of multiple heat pretreatment options to the SalivaDirect protocol increases the accessibility of this cost-effective SARS-CoV-2 test as it gives diagnostic laboratories the flexibility to implement the workflow which best suits their safety protocols.</p></div>","PeriodicalId":54554,"journal":{"name":"Progress in Biophysics & Molecular Biology","volume":"182 ","pages":"Pages 103-108"},"PeriodicalIF":3.8,"publicationDate":"2023-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10290768/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10257264","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 5

Investigation of thermal stability characteristic in family A DNA polymerase - A theoretical study A家族DNA聚合酶热稳定性特征的研究——一项理论研究。

IF 3.8 3区生物学

Progress in Biophysics & Molecular Biology Pub Date : 2023-09-01 DOI: 10.1016/j.pbiomolbio.2023.05.003

Seddigheh Borhani, Seyed Shahriar Arab

{"title":"Investigation of thermal stability characteristic in family A DNA polymerase - A theoretical study","authors":"Seddigheh Borhani, Seyed Shahriar Arab","doi":"10.1016/j.pbiomolbio.2023.05.003","DOIUrl":"10.1016/j.pbiomolbio.2023.05.003","url":null,"abstract":"<div><p><span>DNA polymerases create complementary DNA strands<span><span> in living cells and are crucial to genome transmission and maintenance. These enzymes<span> possess similar human right-handed folds which contain thumb, fingers, and palm subdomains and contribute to polymerization activities. These enzymes are classified into seven evolutionary families, A, B, C, D, X, Y, and RT, based on amino acid sequence analysis and biochemical characteristics. Family A DNA polymerases exist in an extended range of organisms including mesophilic, thermophilic, and hyper-thermophilic bacteria, participate in DNA replication and repair, and have a broad application in </span></span>molecular biology<span> and biotechnology. In this study, we attempted to detect factors that play a role in the thermostability properties of this family member despite their remarkable similarities in structure and function. For this purpose, similarities and differences in </span></span></span>amino acid sequences<span>, structure, and dynamics of these enzymes have been inspected. Our results demonstrated that thermophilic and hyper-thermophilic enzymes have more charged, aromatic, and polar residues than mesophilic ones and consequently show further electrostatic and cation-pi interactions. In addition, in thermophilic enzymes, aliphatic residues tend to position in buried states more than mesophilic enzymes. These residues within their aliphatic parts increase hydrophobic core packing and therefore enhance the thermostability of these enzymes. Furthermore, a decrease in thermophilic cavities volumes assists in the protein compactness enhancement. Moreover, molecular dynamic simulation results revealed that increasing temperature impacts mesophilic enzymes further than thermophilic ones that reflect on polar and aliphatic residues surface area and hydrogen bonds changes.</span></p></div>","PeriodicalId":54554,"journal":{"name":"Progress in Biophysics & Molecular Biology","volume":"182 ","pages":"Pages 15-25"},"PeriodicalIF":3.8,"publicationDate":"2023-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10256746","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Towards solving the mystery of spiral phyllotaxis 解开螺旋叶序之谜

IF 3.8 3区生物学

Progress in Biophysics & Molecular Biology Pub Date : 2023-09-01 DOI: 10.1016/j.pbiomolbio.2023.04.004

Boris Rozin

引用次数: 0

Biological evolution requires an emergent, self-organizing principle 生物进化需要一个紧急的、自组织的原则

IF 3.8 3区生物学

Progress in Biophysics & Molecular Biology Pub Date : 2023-09-01 DOI: 10.1016/j.pbiomolbio.2023.06.001

Olen R. Brown , David A. Hullender

{"title":"Biological evolution requires an emergent, self-organizing principle","authors":"Olen R. Brown , David A. Hullender","doi":"10.1016/j.pbiomolbio.2023.06.001","DOIUrl":"10.1016/j.pbiomolbio.2023.06.001","url":null,"abstract":"<div><p><span>In this perspective review, we assess fundamental flaws in Darwinian evolution, including its modern versions. Fixed mutations ‘explain’ microevolution but not macroevolution including speciation events and the origination of all the major body plans of the Cambrian explosion. Complex, multifactorial change is required for speciation events and inevitably requires self-organization beyond what is accomplished by known mechanisms. The assembly of ribosomes and ATP synthase are specific examples. We propose their origin is a model for what is unexplained in biological evolution. Probability of evolution is modeled in Section 9 and values are absurdly improbable. Speciation and higher taxonomic changes become exponentially less probable as the number of required, genetically-based events increase. Also, the power required of the proposed selection mechanism (survival of the fittest) is nil for any biological advance requiring multiple changes, because they regularly occur in multiple generations (different genomes) and would not be selectively conserved by the concept survival of the fittest (a concept ultimately centered on the individual). Thus, survival of the fittest cannot ‘explain’ the origin of the millions of current and </span>extinct species. We also focus on the inadequacies of laboratory chemistry to explain the complex, required biological self-organization seen in cells. We propose that a ‘bioelectromagnetic’ field/principle emerges in living cells. Synthesis by self-organization of massive molecular complexes involves biochemical responses to this emergent field/principle. There are ramifications for philosophy, science, and religion. Physics and mathematics must be more strongly integrated with biology and integration should receive dedicated funding with special emphasis for medical applications; treatment of cancer and genetic diseases are examples.</p></div>","PeriodicalId":54554,"journal":{"name":"Progress in Biophysics & Molecular Biology","volume":"182 ","pages":"Pages 75-102"},"PeriodicalIF":3.8,"publicationDate":"2023-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9883515","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 1