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  1. Article ; Online: AbDb: antibody structure database-a database of PDB-derived antibody structures.

    Ferdous, Saba / Martin, Andrew C R

    Database : the journal of biological databases and curation

    2018  Volume 2018

    Abstract: Database url: www.bioinf.org.uk/abs/abdb/. ...

    Abstract Database url: www.bioinf.org.uk/abs/abdb/.
    MeSH term(s) Animals ; Antibodies/chemistry ; Antibodies/genetics ; Databases, Protein ; Humans ; Protein Domains
    Chemical Substances Antibodies
    Language English
    Publishing date 2018-05-02
    Publishing country England
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 2496706-3
    ISSN 1758-0463 ; 1758-0463
    ISSN (online) 1758-0463
    ISSN 1758-0463
    DOI 10.1093/database/bay040
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  2. Article ; Online: A cfDNA methylation-based tissue-of-origin classifier for cancers of unknown primary.

    Conway, Alicia-Marie / Pearce, Simon P / Clipson, Alexandra / Hill, Steven M / Chemi, Francesca / Slane-Tan, Dan / Ferdous, Saba / Hossain, A S Md Mukarram / Kamieniecka, Katarzyna / White, Daniel J / Mitchell, Claire / Kerr, Alastair / Krebs, Matthew G / Brady, Gerard / Dive, Caroline / Cook, Natalie / Rothwell, Dominic G

    Nature communications

    2024  Volume 15, Issue 1, Page(s) 3292

    Abstract: Cancers of Unknown Primary (CUP) remains a diagnostic and therapeutic challenge due to biological heterogeneity and poor responses to standard chemotherapy. Predicting tissue-of-origin (TOO) molecularly could help refine this diagnosis, with tissue ... ...

    Abstract Cancers of Unknown Primary (CUP) remains a diagnostic and therapeutic challenge due to biological heterogeneity and poor responses to standard chemotherapy. Predicting tissue-of-origin (TOO) molecularly could help refine this diagnosis, with tissue acquisition barriers mitigated via liquid biopsies. However, TOO liquid biopsies are unexplored in CUP cohorts. Here we describe CUPiD, a machine learning classifier for accurate TOO predictions across 29 tumour classes using circulating cell-free DNA (cfDNA) methylation patterns. We tested CUPiD on 143 cfDNA samples from patients with 13 cancer types alongside 27 non-cancer controls, with overall sensitivity of 84.6% and TOO accuracy of 96.8%. In an additional cohort of 41 patients with CUP CUPiD predictions were made in 32/41 (78.0%) cases, with 88.5% of the predictions clinically consistent with a subsequent or suspected primary tumour diagnosis, when available (23/26 patients). Combining CUPiD with cfDNA mutation data demonstrated potential diagnosis re-classification and/or treatment change in this hard-to-treat cancer group.
    MeSH term(s) Humans ; Cell-Free Nucleic Acids/genetics ; Neoplasms, Unknown Primary/genetics ; Biomarkers, Tumor/genetics ; DNA Methylation ; Liquid Biopsy
    Chemical Substances Cell-Free Nucleic Acids ; Biomarkers, Tumor
    Language English
    Publishing date 2024-04-17
    Publishing country England
    Document type Journal Article
    ZDB-ID 2553671-0
    ISSN 2041-1723 ; 2041-1723
    ISSN (online) 2041-1723
    ISSN 2041-1723
    DOI 10.1038/s41467-024-47195-7
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  3. Article: B-cell epitopes: Discontinuity and conformational analysis

    Ferdous, Saba / Baker, Terry S / Kelm, Sebastian / Martin, Andrew C.R / Shi, Jiye

    Molecular immunology. 2019 Oct., v. 114

    2019  

    Abstract: Peptide vaccines have many potential advantages over conventional ones including low cost, lack of need for cold-chain storage, safety and specificity. However, it is well known that approximately 90% of B-cell epitopes (BCEs) are discontinuous in nature ...

    Abstract Peptide vaccines have many potential advantages over conventional ones including low cost, lack of need for cold-chain storage, safety and specificity. However, it is well known that approximately 90% of B-cell epitopes (BCEs) are discontinuous in nature making it difficult to mimic them for creating vaccines. In this study, the degree of discontinuity in B-cell epitopes and their conformational nature is examined. The discontinuity of B-cell epitopes is analyzed by defining ‘regions’ (consisting of at least three antibody-contacting residues each separated by ≤3 residues) and small fragments (antibody-contacting residues that do not satisfy the requirements for a region). Secondly, an algorithm has been developed that classifies each region's shape as straight, curved or folded on the basis that straight and folded regions are more likely to retain their native conformation as isolated peptides. We have investigated the structures of 488 B-cell epitopes from which 1282 regions and 1018 fragments have been identified. 90% of epitopes have five or fewer regions and five or fewer fragments with 14% containing only one region and 4% being truly linear (i.e. having one region and no fragments). Of the 1282 regions, 508 are straight in shape, 626 are curved and 148 are folded.
    Keywords algorithms ; B-lymphocytes ; cold chain ; epitopes ; molecular conformation ; peptides ; subunit vaccines
    Language English
    Dates of publication 2019-10
    Size p. 643-650.
    Publishing place Elsevier Ltd
    Document type Article
    ZDB-ID 424427-8
    ISSN 1872-9142 ; 0161-5890
    ISSN (online) 1872-9142
    ISSN 0161-5890
    DOI 10.1016/j.molimm.2019.09.014
    Database NAL-Catalogue (AGRICOLA)

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  4. Article ; Online: B-cell epitopes: Discontinuity and conformational analysis.

    Ferdous, Saba / Kelm, Sebastian / Baker, Terry S / Shi, Jiye / Martin, Andrew C R

    Molecular immunology

    2019  Volume 114, Page(s) 643–650

    Abstract: Peptide vaccines have many potential advantages over conventional ones including low cost, lack of need for cold-chain storage, safety and specificity. However, it is well known that approximately 90% of B-cell epitopes (BCEs) are discontinuous in nature ...

    Abstract Peptide vaccines have many potential advantages over conventional ones including low cost, lack of need for cold-chain storage, safety and specificity. However, it is well known that approximately 90% of B-cell epitopes (BCEs) are discontinuous in nature making it difficult to mimic them for creating vaccines. In this study, the degree of discontinuity in B-cell epitopes and their conformational nature is examined. The discontinuity of B-cell epitopes is analyzed by defining 'regions' (consisting of at least three antibody-contacting residues each separated by ≤3 residues) and small fragments (antibody-contacting residues that do not satisfy the requirements for a region). Secondly, an algorithm has been developed that classifies each region's shape as straight, curved or folded on the basis that straight and folded regions are more likely to retain their native conformation as isolated peptides. We have investigated the structures of 488 B-cell epitopes from which 1282 regions and 1018 fragments have been identified. 90% of epitopes have five or fewer regions and five or fewer fragments with 14% containing only one region and 4% being truly linear (i.e. having one region and no fragments). Of the 1282 regions, 508 are straight in shape, 626 are curved and 148 are folded.
    MeSH term(s) Antibodies/chemistry ; Antibodies/immunology ; Epitope Mapping/methods ; Epitopes, B-Lymphocyte/chemistry ; Epitopes, B-Lymphocyte/immunology ; Protein Conformation
    Chemical Substances Antibodies ; Epitopes, B-Lymphocyte
    Language English
    Publishing date 2019-09-20
    Publishing country England
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 424427-8
    ISSN 1872-9142 ; 0161-5890
    ISSN (online) 1872-9142
    ISSN 0161-5890
    DOI 10.1016/j.molimm.2019.09.014
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  5. Article ; Online: Temporal dynamics of land use/land cover change and its prediction using CA-ANN model for southwestern coastal Bangladesh.

    Rahman, M Tauhid Ur / Tabassum, Faheemah / Rasheduzzaman, Md / Saba, Humayra / Sarkar, Lina / Ferdous, Jannatul / Uddin, Syed Zia / Zahedul Islam, A Z M

    Environmental monitoring and assessment

    2017  Volume 189, Issue 11, Page(s) 565

    Abstract: Change analysis of land use and land cover (LULC) is a technique to study the environmental degradation and to control the unplanned development. Analysis of the past changing trend of LULC along with modeling future LULC provides a combined opportunity ... ...

    Abstract Change analysis of land use and land cover (LULC) is a technique to study the environmental degradation and to control the unplanned development. Analysis of the past changing trend of LULC along with modeling future LULC provides a combined opportunity to evaluate and guide the present and future land use policy. The southwest coastal region of Bangladesh, especially Assasuni Upazila of Satkhira District, is the most vulnerable to natural disasters and has faced notable changes in its LULC due to the combined effects of natural and anthropogenic causes. The objectives of this study are to illustrate the temporal dynamics of LULC change in Assasuni Upazila over the last 27 years (i.e., between 1989 and 2015) and also to predict future land use change using CA-ANN (cellular automata and artificial neural network) model for the year 2028. Temporal dynamics of LULC change was analyzed, employing supervised classification of multi-temporal Landsat images. Then, prediction of future LULC was carried out by CA-ANN model using MOLUSCE plugin of QGIS. The analysis of LULC change revealed that the LULC of Assasuni had changed notably during 1989 to 2015. "Bare lands" decreased by 21% being occupied by other land uses, especially by "shrimp farms." Shrimp farm area increased by 25.9% during this period, indicating a major occupational transformation from agriculture to shrimp aquaculture in the study area during the period under study. Reduction in "settlement" area revealed the trend of migration from the Upazila. The predicted LULC for the year 2028 showed that reduction in bare land area would continue and 1595.97 ha bare land would transform into shrimp farm during 2015 to 2028. Also, the impacts of the changing LULC on the livelihood of local people and migration status of the Upazila were analyzed from the data collected through focus group discussions and questionnaire surveys. The analysis revealed that the changing LULC and the occupational shift from paddy cultivation to shrimp farming were related to each other. Around 31.3% of the total respondents stated that at least one of their family members had migrated. Climate-driven southwestern coastal people usually migrate from the vulnerable rural areas towards the nearest relatively safe city due to adverse effects of natural disasters. To control the unplanned development and reduce the internal migration in Assasuni and other coastal areas, a comprehensive land use management plan was suggested that would accommodate the diversified uses of coastal lands and eventually lessen the threats to the life and livelihood of the local people.
    Language English
    Publishing date 2017-10-17
    Publishing country Netherlands
    Document type Journal Article
    ZDB-ID 782621-7
    ISSN 1573-2959 ; 0167-6369
    ISSN (online) 1573-2959
    ISSN 0167-6369
    DOI 10.1007/s10661-017-6272-0
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  6. Article ; Online: Glycyrrhetinic acid and E.resveratroloside act as potential plant derived compounds against dopamine receptor D3 for Parkinson's disease: a pharmacoinformatics study.

    Mirza, Muhammad Usman / Mirza, A Hammad / Ghori, Noor-Ul-Huda / Ferdous, Saba

    Drug design, development and therapy

    2015  Volume 9, Page(s) 187–198

    Abstract: Parkinson's disease (PD) is caused by loss in nigrostriatal dopaminergic neurons and is ranked as the second most common neurodegenerative disorder. Dopamine receptor D3 is considered as a potential target in drug development against PD because of its ... ...

    Abstract Parkinson's disease (PD) is caused by loss in nigrostriatal dopaminergic neurons and is ranked as the second most common neurodegenerative disorder. Dopamine receptor D3 is considered as a potential target in drug development against PD because of its lesser side effects and higher degree of neuro-protection. One of the prominent therapies currently available for PD is the use of dopamine agonists which mimic the natural action of dopamine in the brain and stimulate dopamine receptors directly. Unfortunately, use of these pharmacological therapies such as bromocriptine, apomorphine, and ropinirole provides only temporary relief of the disease symptoms and is frequently linked with insomnia, anxiety, depression, and agitation. Thus, there is a need for an alternative treatment that not only hinders neurodegeneration, but also has few or no side effects. Since the past decade, much attention has been given to exploitation of phytochemicals and their use in alternative medicine research. This is because plants are a cheap, indispensable, and never ending resource of active compounds that are beneficial against various diseases. In the current study, 40 active phytochemicals against PD were selected through literature survey. These ligands were docked with dopamine receptor D3 using AutoDock and AutoDockVina. Binding energies were compared to docking results of drugs approved by the US Food and Drug Administration against PD. The compounds were further analyzed for their absorption, distribution, metabolism, and excretion-toxicity profile. From the study it is concluded that glycyrrhetinic acid and E.resveratroloside are potent compounds having high binding energies which should be considered as potential lead compounds for drug development against PD.
    MeSH term(s) Binding Sites/drug effects ; Dose-Response Relationship, Drug ; Drug Evaluation, Preclinical ; Glucosides/chemistry ; Glucosides/metabolism ; Glucosides/pharmacology ; Glycyrrhetinic Acid/chemistry ; Glycyrrhetinic Acid/metabolism ; Glycyrrhetinic Acid/pharmacology ; Humans ; Ligands ; Models, Molecular ; Molecular Docking Simulation ; Parkinson Disease/drug therapy ; Parkinson Disease/metabolism ; Phytotherapy ; Plants/chemistry ; Receptors, Dopamine D3/antagonists & inhibitors ; Stilbenes/chemistry ; Stilbenes/metabolism ; Stilbenes/pharmacology ; Structure-Activity Relationship
    Chemical Substances 3,5,4'-trihydroxystilbene-4'-O-glucoside ; Glucosides ; Ligands ; Receptors, Dopamine D3 ; Stilbenes ; Glycyrrhetinic Acid (P540XA09DR)
    Language English
    Publishing date 2015
    Publishing country New Zealand
    Document type Journal Article
    ZDB-ID 2451346-5
    ISSN 1177-8881 ; 1177-8881
    ISSN (online) 1177-8881
    ISSN 1177-8881
    DOI 10.2147/DDDT.S72794
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  7. Article ; Online: Mutually exclusive binding of APPL(PH) to BAR domain and Reptin regulates β-catenin dependent transcriptional events.

    Rashid, Sajid / Parveen, Zahida / Ferdous, Saba / Bibi, Nousheen

    Computational biology and chemistry

    2013  Volume 47, Page(s) 48–55

    Abstract: Reptin functions in a wide range of biological processes including chromatin remodelling, nucleolar organization and transcriptional regulation of WNT signalling. As β-catenin dependent transcriptional repression and activation events involve binding of ... ...

    Abstract Reptin functions in a wide range of biological processes including chromatin remodelling, nucleolar organization and transcriptional regulation of WNT signalling. As β-catenin dependent transcriptional repression and activation events involve binding of Reptin and histone deacetylase 1 to APPL endocytic proteins, this complex has become an important target to identify molecules governing endocytic processes and WNT signalling. Here, we describe the structural basis of APPL binding to Reptin to explore their mode of binding in context with APPL1/APPL2 dimerization. There is an evidence that both PH and BAR domains of APPL proteins exhibit alternately conserved regions involved in hetero-dimerization process and our in-silico data also corroborate this fact. Moreover, APPL2(PH) domain binds to the BAR domain region encompassing a nuclear localization signal. We conclude that APPL(PH) binding to BAR domain and Reptin is mutually exclusive which regulates the nucleocytoplasmic shuttling of Reptin. Furthermore, Reptin is unable to bind with membrane-associated APPL proteins. These observations were further expanded by experimental approaches where we identified a novel point mutation D316N lying in the APPL1(PH) domain which resulted in a significantly reduced binding with Reptin. By luciferase assays, we observed that overexpression of APPL1(D316N) and APPL1(WT) stimulated β-catenin/TCF dependent transcriptional activity in a similar manner which suggested that binding of Reptin to APPL1 is not necessary for β-catenin dependent target gene expression. Overall, our data attempt to highlight a comparative role of APPL proteins in controlling β-catenin dependent transcription mechanism which may improve our understanding of gene regulation.
    MeSH term(s) ATPases Associated with Diverse Cellular Activities ; Adaptor Proteins, Signal Transducing/chemistry ; Adaptor Proteins, Signal Transducing/genetics ; Adaptor Proteins, Signal Transducing/metabolism ; Algorithms ; Amino Acid Sequence ; Binding Sites ; Carrier Proteins/chemistry ; Carrier Proteins/genetics ; Carrier Proteins/metabolism ; DNA Helicases/chemistry ; DNA Helicases/genetics ; DNA Helicases/metabolism ; HEK293 Cells ; Humans ; Models, Molecular ; Molecular Sequence Data ; Protein Binding ; Protein Structure, Tertiary ; Sequence Alignment ; Transcription, Genetic ; Transcriptional Activation/genetics ; beta Catenin/metabolism
    Chemical Substances APPL1 protein, human ; APPL2 protein, human ; Adaptor Proteins, Signal Transducing ; Carrier Proteins ; beta Catenin ; ATPases Associated with Diverse Cellular Activities (EC 3.6.4.-) ; DNA Helicases (EC 3.6.4.-) ; RUVBL2 protein, human (EC 3.6.4.12)
    Language English
    Publishing date 2013-12
    Publishing country England
    Document type Journal Article
    ISSN 1476-928X
    ISSN (online) 1476-928X
    DOI 10.1016/j.compbiolchem.2013.05.005
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  8. Article ; Online: Prevalence of gastrointestinal parasitic infections in wild mammals of a safari park and a zoo in Bangladesh.

    Ferdous, Sabrina / Chowdhury, Joya / Hasan, Tanjila / Dutta, Pronesh / Rahman, Md Mizanur / Hassan, Mohammad Mahmudul / Faruque, Md Rayhan / Alim, Mohammad Abdul

    Veterinary medicine and science

    2023  Volume 9, Issue 3, Page(s) 1385–1394

    Abstract: In safari parks and zoos, wild animals are kept mainly for recreational purposes. Animals in these enclosures are also crucial for the education, research, and conservation aspect. To ensure better management and good health of wild animals in captivity, ...

    Abstract In safari parks and zoos, wild animals are kept mainly for recreational purposes. Animals in these enclosures are also crucial for the education, research, and conservation aspect. To ensure better management and good health of wild animals in captivity, it is essential to monitor the occurrence of gastrointestinal (GI) parasitic (helminths and protozoa) infections. The current investigation was undertaken to investigate the prevalence of GI parasitic infections in wild mammals at Bangabandhu Sheikh Mujib (BSM) safari park and Chattogram (CTG) zoo of Bangladesh. A total of 72 individual faecal samples were collected from 25 species of wild mammals. Routine qualitative (e.g. direct smear, sedimentation, and flotation) and quantitative (e.g. McMaster technique) tests were performed to identify the eggs or oocysts of helminths and protozoa. Results demonstrated that wild mammals of both BSM safari park and CTG zoo were infected with a total of 17 genera/species of helminths and protozoa. The overall prevalence of GI parasitic infections in wild mammals of both zoological parks was 65.3% (95% confidence interval [CI]: 53.14-76.12), whereas it was 72.4% (95% CI: 52.76-87.27) in the BSM safari park and 60.5% (95% CI: 44.41-75.02) in the CTG zoo. In both zoological parks, infection with nematodes was more frequent compared to other helminth into the wild mammals. The herbivores were more infected with GI parasites than carnivores and omnivores of both BSM safari park and CTG zoo. The mean eggs/oocysts per gram of faeces was the highest in the carnivores compared to herbivores and omnivores of both enclosures. The findings of the current study demonstrated that wild mammals of both BSM safari park and CTG zoo suffered from various GI parasitic infections. Regular monitoring along with proper therapeutic measures may reduce the severe consequences of GI parasitic infections in captive wild animals.
    MeSH term(s) Animals ; Parasites ; Prevalence ; Bangladesh/epidemiology ; Mammals/parasitology ; Intestinal Diseases, Parasitic/epidemiology ; Intestinal Diseases, Parasitic/veterinary ; Intestinal Diseases, Parasitic/parasitology ; Helminths ; Animals, Wild ; Gastrointestinal Diseases/parasitology ; Gastrointestinal Diseases/veterinary
    Language English
    Publishing date 2023-02-06
    Publishing country England
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 2819409-3
    ISSN 2053-1095 ; 2053-1095
    ISSN (online) 2053-1095
    ISSN 2053-1095
    DOI 10.1002/vms3.1093
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  9. Article ; Online: Publisher Correction: Pulmonary venous circulating tumor cell dissemination before tumor resection and disease relapse.

    Chemi, Francesca / Rothwell, Dominic G / McGranahan, Nicholas / Gulati, Sakshi / Abbosh, Chris / Pearce, Simon P / Zhou, Cong / Wilson, Gareth A / Jamal-Hanjani, Mariam / Birkbak, Nicolai / Pierce, Jackie / Kim, Chang Sik / Ferdous, Saba / Burt, Deborah J / Slane-Tan, Daniel / Gomes, Fabio / Moore, David / Shah, Rajesh / Al Bakir, Maise /
    Hiley, Crispin / Veeriah, Selvaraju / Summers, Yvonne / Crosbie, Philip / Ward, Sophia / Mesquita, Barbara / Dynowski, Marek / Biswas, Dhruva / Tugwood, Jonathan / Blackhall, Fiona / Miller, Crispin / Hackshaw, Allan / Brady, Ged / Swanton, Charles / Dive, Caroline

    Nature medicine

    2020  Volume 26, Issue 7, Page(s) 1147

    Abstract: An amendment to this paper has been published and can be accessed via a link at the top of the paper. ...

    Abstract An amendment to this paper has been published and can be accessed via a link at the top of the paper.
    Language English
    Publishing date 2020-06-03
    Publishing country United States
    Document type Published Erratum
    ZDB-ID 1220066-9
    ISSN 1546-170X ; 1078-8956
    ISSN (online) 1546-170X
    ISSN 1078-8956
    DOI 10.1038/s41591-020-0865-9
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  10. Article: Sociodemographic determinants of child mortality based on mothers' attitudes toward partner violence: Evidence from Bangladesh.

    Ara, Ferdous / Sultana, Mir Misnad / Naoshin, Sabrina / Sultana, Israth / Hoq, Mohammad Nazmul / Hossain, Mohammad Emdad

    Heliyon

    2023  Volume 9, Issue 3, Page(s) e13848

    Abstract: Bangladesh, a lower-middle-income country in South Asia, has achieved a significant reduction in child mortality over the last three decades from 151 to 40 per 1000 live births. However, child mortality is still considered high, which may be attributed ... ...

    Abstract Bangladesh, a lower-middle-income country in South Asia, has achieved a significant reduction in child mortality over the last three decades from 151 to 40 per 1000 live births. However, child mortality is still considered high, which may be attributed to a lack of awareness among mothers regarding the risk factors, particularly their perceptions of intimate partner violence (IPV). To investigate the effect of demographic and socioeconomic factors of women on child mortality, this study extracted data from the cross-sectional survey of Bangladesh Multiple Indicator Cluster Survey (MICS) 2019. The data were analyzed using a Poisson regression model to assess women's perceptions and exposure to physical violence in the last three years preceding the survey and their impact on the risk of child mortality. The results indicated that approximately 26% of the participants justified domestic violence under certain circumstances. Moreover, the prevalence of child mortality was higher among those who thought that IPV is acceptable than among those who considered such violence to be unjustified. Among women who are strongly averse to partner violence, the risk of child mortality was significantly lower in those who had higher levels of education, higher household income, internet usage experience, first child at 20 years or later, frequent access to mass media, and one or two children ever born. Moreover, child mortality rates also varied across geographical areas, with children from Sylhet and Mymenshing being the most vulnerable. The data indicates women's intolerable attitudes toward partner violence not only improve their status but also increase the survival chances of their young children.
    Language English
    Publishing date 2023-02-25
    Publishing country England
    Document type Journal Article
    ZDB-ID 2835763-2
    ISSN 2405-8440
    ISSN 2405-8440
    DOI 10.1016/j.heliyon.2023.e13848
    Database MEDical Literature Analysis and Retrieval System OnLINE

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