School Of Basic And Applied Sciences

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Author: search.filters.author.Bhardwaj, Pankaj

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    Global, regional, and national sex differences in the global burden of tuberculosis by HIV status, 1990�2019: results from the Global Burden of Disease Study 2019
    (Elsevier Ltd, 2021-09-23T00:00:00) Ledesma, Jorge R.; Ma, Jianing; Vongpradith, Avina; Maddison, Emilie R.; Novotney, Amanda; Biehl, Molly H.; Legrand, Kate E.; Ross, Jennifer M.; Jahagirdar, Deepa; Bryazka, Dana; Feldman, Rachel; Abolhassani, Hassan; Abosetugn, Akine Eshete; Abu-Gharbieh, Eman; Adebayo, Oladimeji M.; Adnani, Qorinah Estiningtyas Sakilah; Afzal, Saira; Ahinkorah, Bright Opoku; Ahmad, Sajjad Ahmad; Ahmadi, Sepideh; Rashid, Tarik Ahmed; Salih, Yusra Ahmed; Aklilu, Addis; Akunna, Chisom Joyqueenet; Al Hamad, Hanadi; Alahdab, Fares; Alemayehu, Yosef; Alene, Kefyalew Addis; Ali, Beriwan Abdulqadir; Ali, Liaqat; Alipour, Vahid; Alizade, Hesam; Al-Raddadi, Rajaa M.; Alvis-Guzman, Nelson; Amini, Saeed; Amit, Arianna Maever L.; Anderson, Jason A.; Androudi, Sofa; Antonio, Carl Abelardo T.; Antony, Catherine M.; Anwer, Razique; Arabloo, Jalal; Arja, Asrat; Asemahagn, Mulusew A.; Atre, Sachin R.; Azhar, Gulrez Shah; Darshan, B.B.; Babar, Zaheer-Ud-Din; Baig, Atif Amin; Banach, Maciej; Barqawi, Hiba Jawdat; Barra, Fabio; Barrow, Amadou; Basu, Sanjay; Belgaumi, Uzma Iqbal; Bhagavathula, Akshaya Srikanth; Bhardwaj, Nikha; Bhardwaj, Pankaj; Bhattacharjee, Natalia V.; Bhattacharyya, Krittika; Bijani, Ali; Bikbov, Boris; Boloor, Archith; Briko, Nikolay Ivanovich; Buonsenso, Danilo; Nagaraja, Sharath Burugina; Butt, Zahid A.; Carter, Austin; Carvalho, Felix; Charan, Jaykaran; Chatterjee, Souranshu; Chattu, Soosanna Kumary; Chattu, Vijay Kumar; Christopher, Devasahayam J.; Chu, Dinh-Toi; Claassens, Mareli M.; Dadras, Omid; Dagnew, Amare Belachew; Dai, Xiaochen; Dandona, Lalit; Dandona, Rakhi; Daneshpajouhnejad, Parnaz; Darwesh, Aso Mohammad; Dhamnetiya, Deepak; Dianatinasab, Mostafa; Diaz, Daniel; Doan, Linh Phuong; Eftekharzadeh, Sahar; Elhadi, Muhammed; Emami, Amir; Enany, Shymaa; Faraon, Emerito Jose A.; Farzadfar, Farshad; Fernandes, Eduarda; Desideri, Lorenzo Ferro; Filip, Irina; Fischer, Florian; Foroutan, Masoud; Frank, Tahvi D.; Garcia-Basteiro, Alberto L.; Garcia-Calavaro, Christian; Garg, Tushar; Geberemariyam, Biniyam Sahiledengle; Ghadiri, Keyghobad; Ghashghaee, Ahmad; Golechha, Mahaveer; Goodridge, Amador; Gupta, Bhawna; Gupta, Sapna; Gupta, Veer Bala; Gupta, Vivek Kumar; Haider, Mohammad Rifat; Hamidi, Samer; Hanif, Asif; Haque, Shaful; Harapan, Harapan; Hargono, Arief; Hasaballah, Ahmed I.; Hashi, Abdiwahab; Hassan, Shoaib; Hassankhani, Hadi; Hayat, Khezar; Hezam, Kamal; Holla, Ramesh; Hosseinzadeh, Mehdi; Hostiuc, Mihaela; Househ, Mowafa; Hussain, Rabia; Ibitoye, Segun Emmanuel; Ilic, Irena M.; Ilic, Milena D.; Irvani, Seyed Sina Naghibi; Ismail, Nahlah Elkudssiah; Itumalla, Ramaiah; Jaafari, Jalil; Jacobsen, Kathryn H.; Jain, Vardhmaan; Javanmardi, Fatemeh; Jayapal, Sathish Kumar; Jayaram, Shubha; Jha, Ravi Prakash; Jonas, Jost B.; Joseph, Nitin; Joukar, Farahnaz; Kabir, Zubair; Kamath, Ashwin; Kanchan, Tanuj; Kandel, Himal; Katoto, Patrick D.M.C.; Kayode, Gbenga A.; Kendrick, Parkes J.; Kerbo, Amene Abebe; Khajuria, Himanshu; Khalilov, Rovshan; Khatab, Khaled; Khoja, Abdullah T.; Khubchandani, Jagdish; Kim, Min Seo; Kim, Yun Jin; Kisa, Adnan; Kisa, Sezer; Kosen, Soewarta; Koul, Parvaiz A.; Laxminarayana, Sindhura Lakshmi Koulmane; Koyanagi, Ai; Krishan, Kewal; Bicer, Burcu Kucuk; Kumar, Avinash; Kumar, G. Anil; Kumar, Narinder; Kumar, Nithin; Kwarteng, Alexander; Lak, Hassan Mehmood; Lal, Dharmesh Kumar; Landires, Iv�n; Lasrado, Savita; Lee, Shaun Wen Huey; Lee, Wei-Chen; Lin, Christine; Liu, Xuefeng; Lopukhov, Platon D.; Lozano, Rafael; Machado, Daiane Borges; Kunjathur, Shilpashree Madhava; Madi, Deepak; Mahajan, Preetam Bhalchandra; Majeed, Azeem; Malik, Ahmad Azam; Martins-Melo, Francisco Rogerl�ndio; Mehta, Saurabh; Memish, Ziad A.; Mendoza, Walter; Menezes, Ritesh G.; Merie, Hayimro Edemealem; Mersha, Amanual Getnet; Mesregah, Mohamed Kamal; Mestrovic, Tomislav; Mheidly, Nour Mheidly; Misra, Sanjeev; Mithra, Prasanna; Moghadaszadeh, Masoud; Mohammadi, Mokhtar; Mohammadian-Hafshejani, Abdollah; Mohammed, Shafu; Molokhia, Mariam; Moni, Mohammad Ali; Al Montasir, Ahmed; Moore, Catrin E.; Nagarajan, Ahamarshan Jayaraman; Nair, Sanjeev; Nair, Suma; Naqvi, Atta Abbas; Swamy, Sreenivas Narasimha; Nayak, Biswa Prakash; Nazari, Javad; Kandel, Sandhya Neupane; Nguyen, Trang Huyen; Nixon, Molly R.; Nnaji, Chukwudi A.; Ntsekhe, Mpiko; Nu�ez-Samudio, Virginia; Oancea, Bogdan; Odukoya, Oluwakemi Ololade; Olagunju, Andrew T.; Oren, Eyal; Mahesh, P.A.; Parthasarathi, Ramakrishnan; Kan, Fatemeh Pashazadeh; Pattanshetty, Sanjay M.; Paudel, Rajan; Paul, Pintu; Pawar, Shrikant; Pepito, Veincent Christian Filipino; Perico, Norberto; Pirestani, Majid; Polibin, Roman V.; Postma, Maarten J.; Pourshams, Akram; Prashant, Akila; Pribadi, Dimas Ria Angga; Radfar, Amir; Rafei, Alireza; Rahim, Fakher; Rahimi-Movaghar, Vafa; Rahman, Mahfuzar; Rahman, Mosiur; Rahmani, Amir Masoud; Ranasinghe, Priyanga; Rao, Chythra R.; Rawaf, David Laith; Rawaf, Salman; Reitsma, Marissa B.; Remuzzi, Giuseppe; Renzaho, Andre M. N.; Reta, Melese Abate; Rezaei, Nima; Rezahosseini, Omid; Rezai, Mohammad Sadegh; Rezapour, Aziz; Roshandel, Gholamreza; Roshchin, Denis O.; Sabour, Siamak; Saif-Ur-rahman, K.M.; Salam, Nasir; Kafl, Hossein Samadi; Samaei, Mehrnoosh; Samy, Abdallah M.; Saroshe, Satish; Sartorius, Benn; Sathian, Brijesh; Sawyer, Susan M.; Senthilkumaran, Subramanian; Seylani, Allen; Shafaat, Omid; Shaikh, Masood Ali; Sharaf, Kiomars; Shetty, Ranjitha S.; Shigematsu, Mika; Shin, Jae Il; Silva, Jo�o Pedro; Singh, Jitendra Kumar; Sinha, Smriti; Skryabin, Valentin Yurievich; Skryabina, Anna Aleksandrovna; Spurlock, Emma Elizabeth; Sreeramareddy, Chandrashekhar T.; Steiropoulos, Paschalis; Sufyan, Mu'awiyyah Babale; Tabuchi, Takahiro; Tadesse, Eyayou Girma; Tamir, Zemenu; Tarkang, Elvis Enowbeyang; Tekalegn, Yohannes; Tesfay, Fisaha Haile; Tessema, Belay; Thapar, Rekha; Tleyjeh, Imad I.; Tobe-Gai, Ruoyan; Tran, Bach Xuan; Tsegaye, Berhan; Tsegaye, Gebiyaw Wudie; Ullah, Anayat; Umeokonkwo, Chukwuma David; Tahbaz, Sahel Valadan; Vo, Bay; Vu, Giang Thu; Waheed, Yasir; Walters, Magdalene K.; Whisnant, Joanna L.; Woldekidan, Mesfn Agachew; Wubishet, Befkadu Legesse; Jabbari, Seyed Hossein Yahyazadeh; Yazie, Taklo Simeneh Yazie; Yeshaw, Yigizie; Yi, Siyan; Yigit, Vahit; Yonemoto, Naohiro; Yu, Chuanhua; Yunusa, Ismaeel; Zastrozhin, Mikhail Sergeevich; Zastrozhina, Anasthasia; Zhang, Zhi-Jiang; Zumla, Alimuddin; Mokdad, Ali H.; Salomon, Joshua A.; Reiner, Robert C.; Lim, Stephen S.; Naghavi, Mohsen; Vos, Theo; Hay, Simon I.; Murray, Christopher J. L.; Kyu, Hmwe Hmwe
    Background: Tuberculosis is a major contributor to the global burden of disease, causing more than a million deaths annually. Given an emphasis on equity in access to diagnosis and treatment of tuberculosis in global health targets, evaluations of differences in tuberculosis burden by sex are crucial. We aimed to assess the levels and trends of the global burden of tuberculosis, with an emphasis on investigating differences in sex by HIV status for 204 countries and territories from 1990 to 2019. Methods: We used a Bayesian hierarchical Cause of Death Ensemble model (CODEm) platform to analyse 21 505 site-years of vital registration data, 705 site-years of verbal autopsy data, 825 site-years of sample-based vital registration data, and 680 site-years of mortality surveillance data to estimate mortality due to tuberculosis among HIV-negative individuals. We used a population attributable fraction approach to estimate mortality related to HIV and tuberculosis coinfection. A compartmental meta-regression tool (DisMod-MR 2.1) was then used to synthesise all available data sources, including prevalence surveys, annual case notifications, population-based tuberculin surveys, and tuberculosis cause-specific mortality, to produce estimates of incidence, prevalence, and mortality that were internally consistent. We further estimated the fraction of tuberculosis mortality that is attributable to independent effects of risk factors, including smoking, alcohol use, and diabetes, for HIV-negative individuals. For individuals with HIV and tuberculosis coinfection, we assessed mortality attributable to HIV risk factors including unsafe sex, intimate partner violence (only estimated among females), and injection drug use. We present 95% uncertainty intervals for all estimates. Findings: Globally, in 2019, among HIV-negative individuals, there were 1�18 million (95% uncertainty interval 1�08�1�29) deaths due to tuberculosis and 8�50 million (7�45�9�73) incident cases of tuberculosis. Among HIV-positive individuals, there were 217 000 (153 000�279 000) deaths due to tuberculosis and 1�15 million (1�01�1�32) incident cases in 2019. More deaths and incident cases occurred in males than in females among HIV-negative individuals globally in 2019, with 342 000 (234 000�425 000) more deaths and 1�01 million (0�82�1�23) more incident cases in males than in females. Among HIV-positive individuals, 6250 (1820�11 400) more deaths and 81 100 (63 300�100 000) more incident cases occurred among females than among males in 2019. Age-standardised mortality rates among HIV-negative males were more than two times greater in 105 countries and age-standardised incidence rates were more than 1�5 times greater in 74 countries than among HIV-negative females in 2019. The fraction of global tuberculosis deaths among HIV-negative individuals attributable to alcohol use, smoking, and diabetes was 4�27 (3�69�5�02), 6�17 (5�48�7�02), and 1�17 (1�07�1�28) times higher, respectively, among males than among females in 2019. Among individuals with HIV and tuberculosis coinfection, the fraction of mortality attributable to injection drug use was 2�23 (2�03�2�44) times greater among males than females, whereas the fraction due to unsafe sex was 1�06 (1�05�1�08) times greater among females than males. Interpretation: As countries refine national tuberculosis programmes and strategies to end the tuberculosis epidemic, the excess burden experienced by males is important. Interventions are needed to actively communicate, especially to men, the importance of early diagnosis and treatment. These interventions should occur in parallel with efforts to minimise excess HIV burden among women in the highest HIV burden countries that are contributing to excess HIV and tuberculosis coinfection burden for females. Placing a focus on tuberculosis burden among HIV-negative males and HIV and tuberculosis coinfection among females might help to diminish the overall burden of tuberculosis. This strategy will be crucial in reaching both equity and burden targets outlined by global health milestones. Funding: Bill & Melinda Gates Foundation. � 2022 The Author(s). Published by Elsevier Ltd. This is an Open Access article under the CC BY 4.0 license
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    Transcriptome Analysis Revealed Behavior Complexity of Senescence Responses in Himalayan Tree Species Ulmus wallichiana
    (Springer, 2023-05-17T00:00:00) Singh, Amandeep; Majeed, Aasim; Sharma, Vikas; Gadri, Hari Shankar; Chowdhary, Md. Asif; Bhardwaj, Pankaj
    The Himalayas present a highly contrasting environment for the organisms that inhabit it, with summer and winter being the most disparate seasons. As winter approaches, the temperature drops, and deciduous plants, such as Ulmus wallichiana Planch., undergo senescence. In this study, we used the RNA-seq approach to generate a de novo transcriptome assembly of U. wallichiana, consisting of 300,067 unigenes. We investigated the differential expression pattern of these unigenes under changing climatic conditions, with a focus on the contrast between winter and summer. We observed that 2746 unigenes were differentially expressed, with a fold change of ? 2 and an FDR-adjusted p-value of ? 0.001. Among these unigenes, 37 were found to be related to senescence. We also identified nine DREB unigenes in the U. wallichiana transcriptome, which exhibited more or less contrasting patterns between summer and winter. These DREB unigenes may play an important role in regulating the plant�s tolerance to cold and/or drought stress. Our findings shed light on the complex and dynamic process of transcriptomic reprogramming that enables U. wallichiana to cope with seasonal changes. Furthermore, this study highlights the urgent need for further research on U. wallichiana, as this endangered plant species remains largely unexplored at the genomic level. � 2023, The Author(s), under exclusive licence to Springer Science+Business Media, LLC, part of Springer Nature.
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    Transcriptome characterization and generation of marker resource for Himalayan vulnerable species, Ulmus wallichiana
    (Springer Science and Business Media B.V., 2021-01-14T00:00:00) Singh, Amandeep; Majeed, Aasim; Bhardwaj, Pankaj
    Ulmus wallichiana is a traditional medicinal plant listed as a vulnerable in the IUCN red list data. Genomic and transcriptomic resources for this species are lacking, hindering its genetic exploration. Further, no polymorphic marker resource is available for this species, thus limiting the elucidation of its underlying genetic diversity, which is a pre-requisite for its conservation. This study was therefore aimed to generate a functionally annotated transcriptomic resource and screen it for SSR regions. We used paired-end Illumina based RNAseq technology and trinity based de novo assembly approach to generate full length transcripts, which were screened for SSR regions and functionally annotated. Around 6.6 million raw reads were de novo assembled transcripts, which were clustered into 146,083 unigenes. 19,909 transcripts were provided with 3986 unique KEGG ids, 70,519 transcripts with 6621 unique Pfam domains, and 45,125 transcripts with 7302 unique INTERPRO domains. 1456 transcripts were identified as transcriptions factors (TFs). Further, 8868 unique GO terms were obtained for the unigenes. The transcripts mapped to 23,056 known pre-determined orthology clusters in the eggNOG database. A total of 16,570 SSRs were identified from the unigenes. Out of the 90 SSRs selected for characterization on 20 genotypes, 28 were polymorphic. Mean effective alleles (Ne) of 2.53, mean observed heterozygosity (Ho) of 0.77, and average polymorphic information content (PIC) of 0.57 were found. This study may facilitate the genetic exploration of this species. The polymorphic SSRs would prove useful to explore its genetic diversity patterns, required for its conservation. � 2021, The Author(s), under exclusive licence to Springer Nature B.V. part of Springer Nature.
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    Codon usage pattern in Gnetales evolved in close accordance with the Gnetifer hypothesis
    (Oxford University Press, 2021-01-06T00:00:00) Majeed, Aasim; Kaur, Harpreet; Kaur, Amitozdeep; Das, Sreemoyee; Joseph, Josepheena; Bhardwaj, Pankaj
    The evolution of Gnetales is ambiguous, and their phylogenetic position is still debated. The biological and molecular processes may evolve with the evolutionary history of a species or a clade. The molecular/biological processes of phylogenetically similar lineages closely follow their evolutionary pattern. If Gnetales evolved as a sister to Pinaceae, cupressophytes or Coniferales as a whole, then it is expected that the molecular or biological processes may reflect this pattern of evolution. In light of this, we deciphered the codon usage pattern of Gnetales, compared it with angiosperms, Pinaceae, cupressophytes and Coniferales as a whole. We evaluated whether this important molecular process has evolved in agreement with the Anthophyte, Gnepine, Gnecup or Gnetifer hypothesis. We observed that Gnetales prefer A/U-ending codons to G/C-ending codons like other lineages. Natural selection plays a dominant role in governing the codon usage bias (CUB). The CpA/CpT dinucleotides were over-represented, whereas the CpG dinucleotide was suppressed. Hierarchical clustering (HC) and correspondence analysis (CA) on relative synonymous codon usage values of 59 synonymous codons showed Gnetales as a sister clade to Coniferales as a whole and revealed that the codon usage pattern in Gnetales has evolved in close accordance with the Gnetifer hypothesis. � 2021 The Linnean Society of London, Botanical Journal of the Linnean Society.
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    Transcribing molecular and climatic data into conservation management for the Himalayan endangered species, Taxus contorta (Griff.)
    (Springer Science and Business Media B.V., 2020-11-12T00:00:00) Majeed, Aasim; Singh, Amandeep; Bhardwaj, Pankaj
    Owing to the changing climatic scenario globally, and human overexploitation, the risk of extinction of Himalayan endangered species has increased many folds. Taxus contorta, an endangered gymnosperm has reached a decisive state in the Western Himalayas, thus, demands immediate attention to rescue it. This study aims to elucidate population and landscape genetics of T. contorta to plan a successful conservation strategy. We used SSR genotyping to identify genetic diversity hotspots, and ecological niche modeling to reveal climatic hotspots of T. contorta in the Indian Western Himalayas. We observed a substantial genetic diversity, and a negligible level of inbreeding among T. contorta populations. A genetic bottleneck was observed in several populations. We propose that changing climate can cause a failure of an entire conservation management plan if the shift produces a degraded environment in the future, at the sites of conservation. Further, the conservation management is futile if it fails to enhance or conserve the genetic diversity. We propound that use of germplasm from genetic diversity hotspots for propagation in climatic hotspots, and prioritization of these hotspot patches for conservation would ensure greater genetic variability under a safe environment. This integrative approach of translating molecular and climatic data into conservation planning would save our efforts, time, and capital investment, and ensure greater success in managing the revival of T. contorta in the Western Himalayas. � 2020, Springer Nature B.V.
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    Adaptability of Rhododendrons in high altitude habitats
    (Northeast Forestry University, 2020-01-03T00:00:00) Choudhary, Shruti; Thakur, Sapna; Majeed, Aasim; Bhardwaj, Pankaj
    Tree species dominate many ecosystems throughout the world and their response to climate, in light of global warming, is a matter of primary concern. This review describes past and ongoing research in Rhododendron, an ecologically important and well-adapted genus of more than 1000 species, occupying diverse habitats. Research to date indicates survival ability and mechanisms, with an emphasis on cold tolerance. The capability of long-distance gene flow in these species increases their genetic variability which in turn enhances their adaptability to newer niches as well as to environmental gradients (mainly temperature). Attempts to explain the molecular basis of morphological and behavioural changes in Rhododendron against cold-induced damage has been made. Gradual advances in �omics� have led to an enriched genomic resource dissecting the role and interaction of multiple molecular factors participating in cold adaptability. However, fewer genetic studies are available on species with an inherent or a default cold-tolerance ability. Considering this fact, understanding specific features of an adapted species can provide insights on overriding the effects of desiccation and determining phase transitions in other plants as well. We propose to integrate ecological and evolutionary studies with functional genomics to improve predictions of tree responses to their environment. � 2020, Northeast Forestry University.
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    Global, regional, and national sex differences in the global burden of tuberculosis by HIV status, 1990�2019: results from the Global Burden of Disease Study 2019
    (Elsevier Ltd, 2021-09-23T00:00:00) Ledesma, Jorge R.; Ma, Jianing; Vongpradith, Avina; Maddison, Emilie R.; Novotney, Amanda; Biehl, Molly H.; Legrand, Kate E.; Ross, Jennifer M.; Jahagirdar, Deepa; Bryazka, Dana; Feldman, Rachel; Abolhassani, Hassan; Abosetugn, Akine Eshete; Abu-Gharbieh, Eman; Adebayo, Oladimeji M.; Adnani, Qorinah Estiningtyas Sakilah; Afzal, Saira; Ahinkorah, Bright Opoku; Ahmad, Sajjad Ahmad; Ahmadi, Sepideh; Rashid, Tarik Ahmed; Salih, Yusra Ahmed; Aklilu, Addis; Akunna, Chisom Joyqueenet; Al Hamad, Hanadi; Alahdab, Fares; Alemayehu, Yosef; Alene, Kefyalew Addis; Ali, Beriwan Abdulqadir; Ali, Liaqat; Alipour, Vahid; Alizade, Hesam; Al-Raddadi, Rajaa M.; Alvis-Guzman, Nelson; Amini, Saeed; Amit, Arianna Maever L.; Anderson, Jason A.; Androudi, Sofa; Antonio, Carl Abelardo T.; Antony, Catherine M.; Anwer, Razique; Arabloo, Jalal; Arja, Asrat; Asemahagn, Mulusew A.; Atre, Sachin R.; Azhar, Gulrez Shah; Darshan, B.B.; Babar, Zaheer-Ud-Din; Baig, Atif Amin; Banach, Maciej; Barqawi, Hiba Jawdat; Barra, Fabio; Barrow, Amadou; Basu, Sanjay; Belgaumi, Uzma Iqbal; Bhagavathula, Akshaya Srikanth; Bhardwaj, Nikha; Bhardwaj, Pankaj; Bhattacharjee, Natalia V.; Bhattacharyya, Krittika; Bijani, Ali; Bikbov, Boris; Boloor, Archith; Briko, Nikolay Ivanovich; Buonsenso, Danilo; Nagaraja, Sharath Burugina; Butt, Zahid A.; Carter, Austin; Carvalho, Felix; Charan, Jaykaran; Chatterjee, Souranshu; Chattu, Soosanna Kumary; Chattu, Vijay Kumar; Christopher, Devasahayam J.; Chu, Dinh-Toi; Claassens, Mareli M.; Dadras, Omid; Dagnew, Amare Belachew; Dai, Xiaochen; Dandona, Lalit; Dandona, Rakhi; Daneshpajouhnejad, Parnaz; Darwesh, Aso Mohammad; Dhamnetiya, Deepak; Dianatinasab, Mostafa; Diaz, Daniel; Doan, Linh Phuong; Eftekharzadeh, Sahar; Elhadi, Muhammed; Emami, Amir; Enany, Shymaa; Faraon, Emerito Jose A.; Farzadfar, Farshad; Fernandes, Eduarda; Desideri, Lorenzo Ferro; Filip, Irina; Fischer, Florian; Foroutan, Masoud; Frank, Tahvi D.; Garcia-Basteiro, Alberto L.; Garcia-Calavaro, Christian; Garg, Tushar; Geberemariyam, Biniyam Sahiledengle; Ghadiri, Keyghobad; Ghashghaee, Ahmad; Golechha, Mahaveer; Goodridge, Amador; Gupta, Bhawna; Gupta, Sapna; Gupta, Veer Bala; Gupta, Vivek Kumar; Haider, Mohammad Rifat; Hamidi, Samer; Hanif, Asif; Haque, Shaful; Harapan, Harapan; Hargono, Arief; Hasaballah, Ahmed I.; Hashi, Abdiwahab; Hassan, Shoaib; Hassankhani, Hadi; Hayat, Khezar; Hezam, Kamal; Holla, Ramesh; Hosseinzadeh, Mehdi; Hostiuc, Mihaela; Househ, Mowafa; Hussain, Rabia; Ibitoye, Segun Emmanuel; Ilic, Irena M.; Ilic, Milena D.; Irvani, Seyed Sina Naghibi; Ismail, Nahlah Elkudssiah; Itumalla, Ramaiah; Jaafari, Jalil; Jacobsen, Kathryn H.; Jain, Vardhmaan; Javanmardi, Fatemeh; Jayapal, Sathish Kumar; Jayaram, Shubha; Jha, Ravi Prakash; Jonas, Jost B.; Joseph, Nitin; Joukar, Farahnaz; Kabir, Zubair; Kamath, Ashwin; Kanchan, Tanuj; Kandel, Himal; Katoto, Patrick D.M.C.; Kayode, Gbenga A.; Kendrick, Parkes J.; Kerbo, Amene Abebe; Khajuria, Himanshu; Khalilov, Rovshan; Khatab, Khaled; Khoja, Abdullah T.; Khubchandani, Jagdish; Kim, Min Seo; Kim, Yun Jin; Kisa, Adnan; Kisa, Sezer; Kosen, Soewarta; Koul, Parvaiz A.; Laxminarayana, Sindhura Lakshmi Koulmane; Koyanagi, Ai; Krishan, Kewal; Bicer, Burcu Kucuk; Kumar, Avinash; Kumar, G. Anil; Kumar, Narinder; Kumar, Nithin; Kwarteng, Alexander; Lak, Hassan Mehmood; Lal, Dharmesh Kumar; Landires, Iv�n; Lasrado, Savita; Lee, Shaun Wen Huey; Lee, Wei-Chen; Lin, Christine; Liu, Xuefeng; Lopukhov, Platon D.; Lozano, Rafael; Machado, Daiane Borges; Kunjathur, Shilpashree Madhava; Madi, Deepak; Mahajan, Preetam Bhalchandra; Majeed, Azeem; Malik, Ahmad Azam; Martins-Melo, Francisco Rogerl�ndio; Mehta, Saurabh; Memish, Ziad A.; Mendoza, Walter; Menezes, Ritesh G.; Merie, Hayimro Edemealem; Mersha, Amanual Getnet; Mesregah, Mohamed Kamal; Mestrovic, Tomislav; Mheidly, Nour Mheidly; Misra, Sanjeev; Mithra, Prasanna; Moghadaszadeh, Masoud; Mohammadi, Mokhtar; Mohammadian-Hafshejani, Abdollah; Mohammed, Shafu; Molokhia, Mariam; Moni, Mohammad Ali; Al Montasir, Ahmed; Moore, Catrin E.; Nagarajan, Ahamarshan Jayaraman; Nair, Sanjeev; Nair, Suma; Naqvi, Atta Abbas; Swamy, Sreenivas Narasimha; Nayak, Biswa Prakash; Nazari, Javad; Kandel, Sandhya Neupane; Nguyen, Trang Huyen; Nixon, Molly R.; Nnaji, Chukwudi A.; Ntsekhe, Mpiko; Nu�ez-Samudio, Virginia; Oancea, Bogdan; Odukoya, Oluwakemi Ololade; Olagunju, Andrew T.; Oren, Eyal; Mahesh, P.A.; Parthasarathi, Ramakrishnan; Kan, Fatemeh Pashazadeh; Pattanshetty, Sanjay M.; Paudel, Rajan; Paul, Pintu; Pawar, Shrikant; Pepito, Veincent Christian Filipino; Perico, Norberto; Pirestani, Majid; Polibin, Roman V.; Postma, Maarten J.; Pourshams, Akram; Prashant, Akila; Pribadi, Dimas Ria Angga; Radfar, Amir; Rafei, Alireza; Rahim, Fakher; Rahimi-Movaghar, Vafa; Rahman, Mahfuzar; Rahman, Mosiur; Rahmani, Amir Masoud; Ranasinghe, Priyanga; Rao, Chythra R.; Rawaf, David Laith; Rawaf, Salman; Reitsma, Marissa B.; Remuzzi, Giuseppe; Renzaho, Andre M. N.; Reta, Melese Abate; Rezaei, Nima; Rezahosseini, Omid; Rezai, Mohammad Sadegh; Rezapour, Aziz; Roshandel, Gholamreza; Roshchin, Denis O.; Sabour, Siamak; Saif-Ur-rahman, K.M.; Salam, Nasir; Kafl, Hossein Samadi; Samaei, Mehrnoosh; Samy, Abdallah M.; Saroshe, Satish; Sartorius, Benn; Sathian, Brijesh; Sawyer, Susan M.; Senthilkumaran, Subramanian; Seylani, Allen; Shafaat, Omid; Shaikh, Masood Ali; Sharaf, Kiomars; Shetty, Ranjitha S.; Shigematsu, Mika; Shin, Jae Il; Silva, Jo�o Pedro; Singh, Jitendra Kumar; Sinha, Smriti; Skryabin, Valentin Yurievich; Skryabina, Anna Aleksandrovna; Spurlock, Emma Elizabeth; Sreeramareddy, Chandrashekhar T.; Steiropoulos, Paschalis; Sufyan, Mu'awiyyah Babale; Tabuchi, Takahiro; Tadesse, Eyayou Girma; Tamir, Zemenu; Tarkang, Elvis Enowbeyang; Tekalegn, Yohannes; Tesfay, Fisaha Haile; Tessema, Belay; Thapar, Rekha; Tleyjeh, Imad I.; Tobe-Gai, Ruoyan; Tran, Bach Xuan; Tsegaye, Berhan; Tsegaye, Gebiyaw Wudie; Ullah, Anayat; Umeokonkwo, Chukwuma David; Tahbaz, Sahel Valadan; Vo, Bay; Vu, Giang Thu; Waheed, Yasir; Walters, Magdalene K.; Whisnant, Joanna L.; Woldekidan, Mesfn Agachew; Wubishet, Befkadu Legesse; Jabbari, Seyed Hossein Yahyazadeh; Yazie, Taklo Simeneh Yazie; Yeshaw, Yigizie; Yi, Siyan; Yigit, Vahit; Yonemoto, Naohiro; Yu, Chuanhua; Yunusa, Ismaeel; Zastrozhin, Mikhail Sergeevich; Zastrozhina, Anasthasia; Zhang, Zhi-Jiang; Zumla, Alimuddin; Mokdad, Ali H.; Salomon, Joshua A.; Reiner, Robert C.; Lim, Stephen S.; Naghavi, Mohsen; Vos, Theo; Hay, Simon I.; Murray, Christopher J. L.; Kyu, Hmwe Hmwe
    Background: Tuberculosis is a major contributor to the global burden of disease, causing more than a million deaths annually. Given an emphasis on equity in access to diagnosis and treatment of tuberculosis in global health targets, evaluations of differences in tuberculosis burden by sex are crucial. We aimed to assess the levels and trends of the global burden of tuberculosis, with an emphasis on investigating differences in sex by HIV status for 204 countries and territories from 1990 to 2019. Methods: We used a Bayesian hierarchical Cause of Death Ensemble model (CODEm) platform to analyse 21 505 site-years of vital registration data, 705 site-years of verbal autopsy data, 825 site-years of sample-based vital registration data, and 680 site-years of mortality surveillance data to estimate mortality due to tuberculosis among HIV-negative individuals. We used a population attributable fraction approach to estimate mortality related to HIV and tuberculosis coinfection. A compartmental meta-regression tool (DisMod-MR 2.1) was then used to synthesise all available data sources, including prevalence surveys, annual case notifications, population-based tuberculin surveys, and tuberculosis cause-specific mortality, to produce estimates of incidence, prevalence, and mortality that were internally consistent. We further estimated the fraction of tuberculosis mortality that is attributable to independent effects of risk factors, including smoking, alcohol use, and diabetes, for HIV-negative individuals. For individuals with HIV and tuberculosis coinfection, we assessed mortality attributable to HIV risk factors including unsafe sex, intimate partner violence (only estimated among females), and injection drug use. We present 95% uncertainty intervals for all estimates. Findings: Globally, in 2019, among HIV-negative individuals, there were 1�18 million (95% uncertainty interval 1�08�1�29) deaths due to tuberculosis and 8�50 million (7�45�9�73) incident cases of tuberculosis. Among HIV-positive individuals, there were 217 000 (153 000�279 000) deaths due to tuberculosis and 1�15 million (1�01�1�32) incident cases in 2019. More deaths and incident cases occurred in males than in females among HIV-negative individuals globally in 2019, with 342 000 (234 000�425 000) more deaths and 1�01 million (0�82�1�23) more incident cases in males than in females. Among HIV-positive individuals, 6250 (1820�11 400) more deaths and 81 100 (63 300�100 000) more incident cases occurred among females than among males in 2019. Age-standardised mortality rates among HIV-negative males were more than two times greater in 105 countries and age-standardised incidence rates were more than 1�5 times greater in 74 countries than among HIV-negative females in 2019. The fraction of global tuberculosis deaths among HIV-negative individuals attributable to alcohol use, smoking, and diabetes was 4�27 (3�69�5�02), 6�17 (5�48�7�02), and 1�17 (1�07�1�28) times higher, respectively, among males than among females in 2019. Among individuals with HIV and tuberculosis coinfection, the fraction of mortality attributable to injection drug use was 2�23 (2�03�2�44) times greater among males than females, whereas the fraction due to unsafe sex was 1�06 (1�05�1�08) times greater among females than males. Interpretation: As countries refine national tuberculosis programmes and strategies to end the tuberculosis epidemic, the excess burden experienced by males is important. Interventions are needed to actively communicate, especially to men, the importance of early diagnosis and treatment. These interventions should occur in parallel with efforts to minimise excess HIV burden among women in the highest HIV burden countries that are contributing to excess HIV and tuberculosis coinfection burden for females. Placing a focus on tuberculosis burden among HIV-negative males and HIV and tuberculosis coinfection among females might help to diminish the overall burden of tuberculosis. This strategy will be crucial in reaching both equity and burden targets outlined by global health milestones. Funding: Bill & Melinda Gates Foundation. � 2022 The Author(s). Published by Elsevier Ltd. This is an Open Access article under the CC BY 4.0 license
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    Transcriptome Analysis Revealed Behavior Complexity of Senescence Responses in Himalayan Tree Species Ulmus wallichiana
    (Springer, 2023-05-17T00:00:00) Singh, Amandeep; Majeed, Aasim; Sharma, Vikas; Gadri, Hari Shankar; Chowdhary, Md. Asif; Bhardwaj, Pankaj
    The Himalayas present a highly contrasting environment for the organisms that inhabit it, with summer and winter being the most disparate seasons. As winter approaches, the temperature drops, and deciduous plants, such as Ulmus wallichiana Planch., undergo senescence. In this study, we used the RNA-seq approach to generate a de novo transcriptome assembly of U. wallichiana, consisting of 300,067 unigenes. We investigated the differential expression pattern of these unigenes under changing climatic conditions, with a focus on the contrast between winter and summer. We observed that 2746 unigenes were differentially expressed, with a fold change of ? 2 and an FDR-adjusted p-value of ? 0.001. Among these unigenes, 37 were found to be related to senescence. We also identified nine DREB unigenes in the U. wallichiana transcriptome, which exhibited more or less contrasting patterns between summer and winter. These DREB unigenes may play an important role in regulating the plant�s tolerance to cold and/or drought stress. Our findings shed light on the complex and dynamic process of transcriptomic reprogramming that enables U. wallichiana to cope with seasonal changes. Furthermore, this study highlights the urgent need for further research on U. wallichiana, as this endangered plant species remains largely unexplored at the genomic level. � 2023, The Author(s), under exclusive licence to Springer Science+Business Media, LLC, part of Springer Nature.
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    Transcriptome characterization and generation of marker resource for Himalayan vulnerable species, Ulmus wallichiana
    (Springer Science and Business Media B.V., 2021-01-14T00:00:00) Singh, Amandeep; Majeed, Aasim; Bhardwaj, Pankaj
    Ulmus wallichiana is a traditional medicinal plant listed as a vulnerable in the IUCN red list data. Genomic and transcriptomic resources for this species are lacking, hindering its genetic exploration. Further, no polymorphic marker resource is available for this species, thus limiting the elucidation of its underlying genetic diversity, which is a pre-requisite for its conservation. This study was therefore aimed to generate a functionally annotated transcriptomic resource and screen it for SSR regions. We used paired-end Illumina based RNAseq technology and trinity based de novo assembly approach to generate full length transcripts, which were screened for SSR regions and functionally annotated. Around 6.6 million raw reads were de novo assembled transcripts, which were clustered into 146,083 unigenes. 19,909 transcripts were provided with 3986 unique KEGG ids, 70,519 transcripts with 6621 unique Pfam domains, and 45,125 transcripts with 7302 unique INTERPRO domains. 1456 transcripts were identified as transcriptions factors (TFs). Further, 8868 unique GO terms were obtained for the unigenes. The transcripts mapped to 23,056 known pre-determined orthology clusters in the eggNOG database. A total of 16,570 SSRs were identified from the unigenes. Out of the 90 SSRs selected for characterization on 20 genotypes, 28 were polymorphic. Mean effective alleles (Ne) of 2.53, mean observed heterozygosity (Ho) of 0.77, and average polymorphic information content (PIC) of 0.57 were found. This study may facilitate the genetic exploration of this species. The polymorphic SSRs would prove useful to explore its genetic diversity patterns, required for its conservation. � 2021, The Author(s), under exclusive licence to Springer Nature B.V. part of Springer Nature.
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    Adaptability of Rhododendrons in high altitude habitats
    (Northeast Forestry University, 2020-01-03T00:00:00) Choudhary, Shruti; Thakur, Sapna; Majeed, Aasim; Bhardwaj, Pankaj
    Tree species dominate many ecosystems throughout the world and their response to climate, in light of global warming, is a matter of primary concern. This review describes past and ongoing research in Rhododendron, an ecologically important and well-adapted genus of more than 1000 species, occupying diverse habitats. Research to date indicates survival ability and mechanisms, with an emphasis on cold tolerance. The capability of long-distance gene flow in these species increases their genetic variability which in turn enhances their adaptability to newer niches as well as to environmental gradients (mainly temperature). Attempts to explain the molecular basis of morphological and behavioural changes in Rhododendron against cold-induced damage has been made. Gradual advances in �omics� have led to an enriched genomic resource dissecting the role and interaction of multiple molecular factors participating in cold adaptability. However, fewer genetic studies are available on species with an inherent or a default cold-tolerance ability. Considering this fact, understanding specific features of an adapted species can provide insights on overriding the effects of desiccation and determining phase transitions in other plants as well. We propose to integrate ecological and evolutionary studies with functional genomics to improve predictions of tree responses to their environment. � 2020, Northeast Forestry University.