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  1. Article: Prediction of transient and permanent protein interactions using AI methods.

    A, Kiran Kumar / Shayez Karim, Syed Mohammad / Kumar, Mayank / Ravindranath Singh, Rathore

    Bioinformation

    2023  Volume 19, Issue 6, Page(s) 749–753

    Abstract: Protein-protein interactions (PPIs) can be classified as permanent or transient interactions based on their stability or lifetime. Understanding the precise details of such protein interactions will pave the way for the discovery of inhibitors and for ... ...

    Abstract Protein-protein interactions (PPIs) can be classified as permanent or transient interactions based on their stability or lifetime. Understanding the precise details of such protein interactions will pave the way for the discovery of inhibitors and for understanding the nature and function of PPIs. In the present work, 43 relevant physicochemical, geometrical and structural features were calculated for a curated dataset from the literature, comprising of 402 protein-protein complexes of permanent and transient categories, and 5 different Supervised Machine Learning models were developed with
    Language English
    Publishing date 2023-06-30
    Publishing country Singapore
    Document type Journal Article
    ZDB-ID 2203786-X
    ISSN 0973-2063
    ISSN 0973-2063
    DOI 10.6026/97320630019749
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  2. Article ; Online: Pericontusional penumbra in patients with traumatic brain injury

    Amit Agrawal / V Anil Kumar / Luis Rafael Moscote-Salazar / V A Kiran Kumar

    Apollo Medicine, Vol 16, Iss 4, Pp 244-

    2019  Volume 246

    Abstract: Recently, a number of studies have recognized the importance of traumatic pericontusional penumbra as a potential target for therapeutic interventions to prevent the secondary brain damage. We report an illustrative case of a 40-year-old female patient ... ...

    Abstract Recently, a number of studies have recognized the importance of traumatic pericontusional penumbra as a potential target for therapeutic interventions to prevent the secondary brain damage. We report an illustrative case of a 40-year-old female patient who was brought to the emergency room with the alleged history of fall from the bike. Computed tomography scan brain showed left sylvian and left temporoparietal subarachnoid hemorrhage, patchy contusion of the left frontal and temporal lobes, linear fracture of the right temporal bone with edema, mass effect, and mild midline shift. After 6 h of intensive care unit stay, the patient developed pupillary asymmetry and a repeat scan showed significant increase in the size of cerebral contusions with gross pericontusional edema, mass effect, and midline shift. The patient underwent urgent left frontotemporoparietal craniotomy and evacuation of the contused brain and hematoma. Pericontusional penumbra is increasingly recognized and strategies are being suggested to salvage the apparently hypoxic (not yet ischemic) brain to preserve the neurological functions and to improve functional outcome. In future, we need more studies to support the concept of pericontusional penumbra and further characterize the imaging findings for early clinical diagnosis and to plan early appropriate intervention.
    Keywords cerebral contusion ; penumbra ; secondary brain injury ; traumatic brain injury ; Medicine ; R
    Subject code 616
    Language English
    Publishing date 2019-01-01T00:00:00Z
    Publisher Wolters Kluwer Medknow Publications
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  3. Article ; Online: Intraoperative ultrasound in neurosurgical procedures

    V A Kiran Kumar / N A Sai Kiran / B Girija Kumari / Ranabir Pal / V Umamaheswar Reddy / Amit Agrawal

    Apollo Medicine, Vol 17, Iss 4, Pp 246-

    2020  Volume 251

    Abstract: Introduction: The objective of the present study was to study the utility and the effectiveness of intraoperative ultrasound in neurosurgical procedures and to assess the outcome. Material and Methods: In this prospective study, operative procedures by a ...

    Abstract Introduction: The objective of the present study was to study the utility and the effectiveness of intraoperative ultrasound in neurosurgical procedures and to assess the outcome. Material and Methods: In this prospective study, operative procedures by a single surgeon under intraoperative ultrasound localization for basal ganglia/thalamic haematoma or traumatic brain contusions or brain tumours were included. Ultrasound scanning of the brain was performed before and after the excision of the lesion and during the procedure to verify the extent of removal of the lesion. Results: 74 patients underwent surgery for brain tumor/basal ganglia bleed/head injury with hemorrhagic contusion with the help of intraoperative ultrasound. Gross tumor resection was noted in 25 out of 36 cases of brain tumors (69.44%), complete evacuation of hematoma was noted in 14 out of 34 cases(41.2%) of basal ganglia bleed and in 2 out of 4 cases (50%) of intracerebral contusion. As per Modified Rankin scale (MRS)score, among the brain tumor cases, all patients had fared well in recovery and had better MRS scores except in one patient who expired during postoperative period. Conclusions: IoUS is a widely accessible, cheap, portable and less space occupying and reliable imaging tool to follow and modify the surgical plan in real time, and is more accurate and helpful in complete tumor resection, evacuation of intracerebral bleeds and contusions, and biopsy of deep seated lesions. It is easy and safe to handle with no risk of radiation.
    Keywords basal ganglia bleed ; brain tumor ; head injury with brain contusion ; intraoperative ultrasound ; modified rankin scale ; Medicine ; R
    Subject code 616
    Language English
    Publishing date 2020-01-01T00:00:00Z
    Publisher Wolters Kluwer Medknow Publications
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  4. Article ; Online: Efficient Implementation of Dynamic Routing With Security Considerations

    UMADEVI DURVASULA / A KIRAN KUMAR2

    International Journal of Computer Science and Communication Networks, Vol 01, Iss 03, Pp 329-

    2011  Volume 337

    Abstract: Now-a-days security is one of the major issues for data communication over wireless and wired networks. The past work on the designs of cryptography algorithms and system infrastructures. Apart from that the authors proposed a dynamic routing algorithm ... ...

    Abstract Now-a-days security is one of the major issues for data communication over wireless and wired networks. The past work on the designs of cryptography algorithms and system infrastructures. Apart from that the authors proposed a dynamic routing algorithm called improved dynamic routing with security consideration, which is based on the concept of Zone Routing Protocol (ZRP) that could randomize delivery paths for data transmission. The algorithm is easy to implement and compatible with popular routing protocols, such as the Routing Information Protocol (RIP) in wired networks and Destination-Sequenced Distance Vector (DSDV) protocol in wireless networks, without introducing extra control messages. This improves security as well as controls traffic in the network. A clear study on the proposed algorithm is presented, and a series of simulation experiments are conducted to verify the results and to show the capability of the proposed algorithm.
    Keywords Dynamic Routing ; ZRP ; DSDV ; RIP ; Electronic computers. Computer science ; QA75.5-76.95 ; Instruments and machines ; QA71-90 ; Mathematics ; QA1-939 ; Science ; Q ; DOAJ:Computer Science ; DOAJ:Technology and Engineering
    Subject code 629
    Language English
    Publishing date 2011-12-01T00:00:00Z
    Publisher Technopark Publications
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  5. Article ; Online: Cervical pseudomeningocele following posterior cervical spine surgery a cause of neurologic deterioration

    V.A. Kiran Kumar / B.C.M. Prasad / V.V. Ramesh Chandra / M.A. Jagdish Kumar / V. Jayachandar

    Journal of Clinical and Scientific Research, Vol 3, Iss 4, Pp 274-

    2014  Volume 277

    Abstract: Cervical pseudomeningocele causing late onset neurological deterioration is a rare entity. We report our experience with surgical management of a patient with symptomatic cervical pseudomeningocele. A 49-year-old man who underwent posterior cervical ... ...

    Abstract Cervical pseudomeningocele causing late onset neurological deterioration is a rare entity. We report our experience with surgical management of a patient with symptomatic cervical pseudomeningocele. A 49-year-old man who underwent posterior cervical laminectomy for cervical ossified posterior longitudinal ligament had neurological deterioration 7 years after undergoing surgery. On evaluation, magnetic resonance imaging of the cervical spine showed cervical pseudomeningocele extending from C2-C6 level causing cord compression at C2-C7 levels. He underwent C2, C7 laminectomy and excision of pseudomeningocele and closure of the communication with dural tube. The post-operative course was uneventful. We present this rare case specially emphasizing the pathogenesis, clinical features and management issues concerning late onset pseudomeningocele. Awareness of this rare possibility of late onset neurological deterioration from posterior cervical pseudomeningocele and its treatment options can help in early diagnosis and treatment.
    Keywords Pseudomeningocele ; Dural tear ; Complication ; Laminectomy ; Cerebrospinal fluid ; Medicine ; R
    Language English
    Publishing date 2014-10-01T00:00:00Z
    Publisher Wolters Kluwer Medknow Publications
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  6. Article ; Online: EFFECTIVENESS OF CONCENTRIC AND ECCENTRIC RESISTANCE TRAINING OF QUADRICEPS AND HAMSTRINGS ON MUSCLE STRENGTH, ROM, AND PAIN IN ACL RECONSTRUCTED SUBJECTS

    G. Haribabu / Sreekar Kumar Reddy .R / A. Kiran Kumar / Dr. M. O. Krishna Murthy / J. Sushma Anand

    International Journal of Physiotherapy, Vol 1, Iss

    2014  Volume 4

    Abstract: Background: Ligament injury accounts for nearly 40% of all injury problems in anterior cruciate ligament injury constitute nearly 50% of all knee ligament injuries. Anterior cruciate ligament deficiency affects not only the mobility, self-confidence and ... ...

    Abstract Background: Ligament injury accounts for nearly 40% of all injury problems in anterior cruciate ligament injury constitute nearly 50% of all knee ligament injuries. Anterior cruciate ligament deficiency affects not only the mobility, self-confidence and lifestyle of the affected persons in short term but also causes arithmetic changes in the affected knee in the long run. Purpose of study to find the effectiveness of concentric and eccentric for post anterior cruciate ligament reconstruction subjects on muscle strength, joint range of motion and pain. Methods: 24 samples with age group of 35 years were randomly assigned to two groups Concentric and Eccentric groups. The Concentric group, performed 9 (3sets) concentric contractions for knee extensors and 9 concentric contractions for knee flexor muscles. The eccentric group done 9 (3 sets) eccentric contractions for knee extensors and 9 eccentric contractions for knee flexors. Results: Pain is significantly decreased in concentric group. But not significantly decreased in eccentric group (t = 2.85, P = 0.009; and t = 1.40; P = 0.17). The range of motion is significantly increased in both concentric knee extension and flexion and eccentric knee extension and flexion (t = 3.53, P = 0.0023; and t = 4.55; P < 0.001). The quadriceps muscle strength is significantly improved in both concentric and eccentric groups at 60° / sec and 90° / sec. Conclusion: The eccentric exercises are better than concentric exercises in improving the strength of hamstring and quadriceps muscles.
    Keywords Concentric ; Eccentric ; Hamstring ; Quadriceps ; ACL ; Medicine (General) ; R5-920
    Subject code 796
    Language English
    Publishing date 2014-10-01T00:00:00Z
    Publisher IJPHY
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  7. Article ; Online: A machine learning-based approach to determine infection status in recipients of BBV152 (Covaxin) whole-virion inactivated SARS-CoV-2 vaccine for serological surveys.

    Singh, Prateek / Ujjainiya, Rajat / Prakash, Satyartha / Naushin, Salwa / Sardana, Viren / Bhatheja, Nitin / Singh, Ajay Pratap / Barman, Joydeb / Kumar, Kartik / Gayali, Saurabh / Khan, Raju / Rawat, Birendra Singh / Tallapaka, Karthik Bharadwaj / Anumalla, Mahesh / Lahiri, Amit / Kar, Susanta / Bhosale, Vivek / Srivastava, Mrigank / Mugale, Madhav Nilakanth /
    Pandey, C P / Khan, Shaziya / Katiyar, Shivani / Raj, Desh / Ishteyaque, Sharmeen / Khanka, Sonu / Rani, Ankita / Promila / Sharma, Jyotsna / Seth, Anuradha / Dutta, Mukul / Saurabh, Nishant / Veerapandian, Murugan / Venkatachalam, Ganesh / Bansal, Deepak / Gupta, Dinesh / Halami, Prakash M / Peddha, Muthukumar Serva / Veeranna, Ravindra P / Pal, Anirban / Singh, Ranvijay Kumar / Anandasadagopan, Suresh Kumar / Karuppanan, Parimala / Rahman, Syed Nasar / Selvakumar, Gopika / Venkatesan, Subramanian / Karmakar, Malay Kumar / Sardana, Harish Kumar / Kothari, Anamika / Parihar, Devendra Singh / Thakur, Anupma / Saifi, Anas / Gupta, Naman / Singh, Yogita / Reddu, Ritu / Gautam, Rizul / Mishra, Anuj / Mishra, Avinash / Gogeri, Iranna / Rayasam, Geethavani / Padwad, Yogendra / Patial, Vikram / Hallan, Vipin / Singh, Damanpreet / Tirpude, Narendra / Chakrabarti, Partha / Maity, Sujay Krishna / Ganguly, Dipyaman / Sistla, Ramakrishna / Balthu, Narender Kumar / A, Kiran Kumar / Ranjith, Siva / Kumar, B Vijay / Jamwal, Piyush Singh / Wali, Anshu / Ahmed, Sajad / Chouhan, Rekha / Gandhi, Sumit G / Sharma, Nancy / Rai, Garima / Irshad, Faisal / Jamwal, Vijay Lakshmi / Paddar, Masroor Ahmad / Khan, Sameer Ullah / Malik, Fayaz / Ghosh, Debashish / Thakkar, Ghanshyam / Barik, S K / Tripathi, Prabhanshu / Satija, Yatendra Kumar / Mohanty, Sneha / Khan, Md Tauseef / Subudhi, Umakanta / Sen, Pradip / Kumar, Rashmi / Bhardwaj, Anshu / Gupta, Pawan / Sharma, Deepak / Tuli, Amit / Ray Chaudhuri, Saumya / Krishnamurthi, Srinivasan / Prakash, L / Rao, Ch V / Singh, B N / Chaurasiya, Arvindkumar / Chaurasiyar, Meera / Bhadange, Mayuri / Likhitkar, Bhagyashree / Mohite, Sharada / Patil, Yogita / Kulkarni, Mahesh / Joshi, Rakesh / Pandya, Vaibhav / Mahajan, Sachin / Patil, Amita / Samson, Rachel / Vare, Tejas / Dharne, Mahesh / Giri, Ashok / Paranjape, Shilpa / Sastry, G Narahari / Kalita, Jatin / Phukan, Tridip / Manna, Prasenjit / Romi, Wahengbam / Bharali, Pankaj / Ozah, Dibyajyoti / Sahu, Ravi Kumar / Dutta, Prachurjya / Singh, Moirangthem Goutam / Gogoi, Gayatri / Tapadar, Yasmin Begam / Babu, Elapavalooru Vssk / Sukumaran, Rajeev K / Nair, Aishwarya R / Puthiyamadam, Anoop / Valappil, Prajeesh Kooloth / Pillai Prasannakumari, Adrash Velayudhan / Chodankar, Kalpana / Damare, Samir / Agrawal, Ved Varun / Chaudhary, Kumardeep / Agrawal, Anurag / Sengupta, Shantanu / Dash, Debasis

    Computers in biology and medicine

    2022  Volume 146, Page(s) 105419

    Abstract: Data science has been an invaluable part of the COVID-19 pandemic response with multiple applications, ranging from tracking viral evolution to understanding the vaccine effectiveness. Asymptomatic breakthrough infections have been a major problem in ... ...

    Abstract Data science has been an invaluable part of the COVID-19 pandemic response with multiple applications, ranging from tracking viral evolution to understanding the vaccine effectiveness. Asymptomatic breakthrough infections have been a major problem in assessing vaccine effectiveness in populations globally. Serological discrimination of vaccine response from infection has so far been limited to Spike protein vaccines since whole virion vaccines generate antibodies against all the viral proteins. Here, we show how a statistical and machine learning (ML) based approach can be used to discriminate between SARS-CoV-2 infection and immune response to an inactivated whole virion vaccine (BBV152, Covaxin). For this, we assessed serial data on antibodies against Spike and Nucleocapsid antigens, along with age, sex, number of doses taken, and days since last dose, for 1823 Covaxin recipients. An ensemble ML model, incorporating a consensus clustering approach alongside the support vector machine model, was built on 1063 samples where reliable qualifying data existed, and then applied to the entire dataset. Of 1448 self-reported negative subjects, our ensemble ML model classified 724 to be infected. For method validation, we determined the relative ability of a random subset of samples to neutralize Delta versus wild-type strain using a surrogate neutralization assay. We worked on the premise that antibodies generated by a whole virion vaccine would neutralize wild type more efficiently than delta strain. In 100 of 156 samples, where ML prediction differed from self-reported uninfected status, neutralization against Delta strain was more effective, indicating infection. We found 71.8% subjects predicted to be infected during the surge, which is concordant with the percentage of sequences classified as Delta (75.6%-80.2%) over the same period. Our approach will help in real-world vaccine effectiveness assessments where whole virion vaccines are commonly used.
    MeSH term(s) COVID-19/epidemiology ; COVID-19/prevention & control ; COVID-19 Vaccines/therapeutic use ; Humans ; Machine Learning ; Pandemics ; SARS-CoV-2 ; Vaccines, Inactivated ; Viral Vaccines ; Virion
    Chemical Substances COVID-19 Vaccines ; Vaccines, Inactivated ; Viral Vaccines
    Language English
    Publishing date 2022-04-25
    Publishing country United States
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 127557-4
    ISSN 1879-0534 ; 0010-4825
    ISSN (online) 1879-0534
    ISSN 0010-4825
    DOI 10.1016/j.compbiomed.2022.105419
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  8. Article ; Online: A machine learning-based approach to determine infection status in recipients of BBV152 whole virion inactivated SARS-CoV-2 vaccine for serological surveys

    Singh, Prateek / Ujjainiya, Rajat / Prakash, Satyartha / Naushin, Salwa / Sardana, Viren / Bhatheja, Nitin / Singh, Ajay Pratap / Barman, Joydeb / Kumar, Kartik / Khan, Raju / Tallapaka, Karthik Bharadwaj / Anumalla, Mahesh / Lahiri, Amit / Kar, Susanta / Bhosale, Vivek / Srivastava, Mrigank / Mugale, Madhav Nilakanth / Pandey, C.P / Khan, Shaziya /
    Katiyar, Shivani / Raj, Desh / Ishteyaque, Sharmeen / Khanka, Sonu / Rani, Ankita / Promila / Sharma, Jyotsna / Seth, Anuradha / Dutta, Mukul / Saurabh, Nishant / Veerapandian, Murugan / Venkatachalam, Ganesh / Bansal, Deepak / Gupta, Dinesh / Halami, Prakash M / Peddha, Muthukumar Serva / Sundaram, Gopinath M / Veeranna, Ravindra P / Pal, Anirban / Singh, Ranvijay Kumar / Anandasadagopan, Suresh Kumar / Karuppanan, Parimala / Rahman, Syed Nasar / Selvakumar, Gopika / Venkatesan, Subramanian / Karmakar, MalayKumar / Sardana, Harish Kumar / Kothari, Animika / Parihar, DevendraSingh / Thakur, Anupma / Saifi, Anas / Gupta, Naman / Singh, Yogita / Reddu, Ritu / Gautam, Rizul / Mishra, Anuj / Mishra, Avinash / Gogeri, Iranna / Rayasam, Geethavani / Padwad, Yogendra / Patial, Vikram / Hallan, Vipin / Singh, Damanpreet / Tirpude, Narendra / Chakrabarti, Partha / Maity, Sujay Krishna / Ganguly, Dipyaman / Sistla, Ramakrishna / Balthu, Narender Kumar / A, Kiran Kumar / Ranjith, Siva / Kumar, Vijay B / Jamwal, Piyush Singh / Wali, Anshu / Ahmed, Sajad / Chouhan, Rekha / Gandhi, Sumit G / Sharma, Nancy / Rai, Garima / Irshad, Faisal / Jamwal, Vijay Lakshmi / Paddar, MasroorAhmad / Khan, Sameer Ullah / Malik, Fayaz / Ghosh, Debashish / Thakkar, Ghanshyam / Barik, Saroj K / Tripathi, Prabhanshu / Satija, Yatendra Kumar / Mohanty, Sneha / Khan, Md. Tauseef / Subudhi, Umakanta / Sen, Pradip / Kumar, Rashmi / Bhardwaj, Anshu / Gupta, Pawan / Sharma, Deepak / Tuli, Amit / Chaudhuri, Saumya Ray / Krishnamurthi, Srinivasan / L, Prakash / Rao, Ch V / Singh, B N / Chaurasiya, Arvindkumar / Chaurasiyar, Meera / Bhadange, Mayuri / Likhitkar, Bhagyashree / Mohite, Sharada / Patil, Yogita / Kulkarni, Mahesh / Joshi, Rakesh / Pandya, Vaibhav / Patil, Amita / Samson, Rachel / Vare, Tejas / Dharne, Mahesh / Giri, Ashok / Paranjape, Shilpa / Sastry, G. Narahari / Kalita, Jatin / Phukan, Tridip / Manna, Prasenjit / Romi, Wahengbam / Bharali, Pankaj / Ozah, Dibyajyoti / Sahu, Ravi Kumar / Dutta, Prachurjya / Singh, Moirangthem Goutam / Gogoi, Gayatri / Tapadar, Yasmin Begam / Babu, Elapavalooru VSSK / Sukumaran, Rajeev K / Nair, Aishwarya R / Puthiyamadam, Anoop / Valappil, PrajeeshKooloth / Pillai Prasannakumari, Adrash Velayudhan / Chodankar, Kalpana / Damare, Samir / Agrawal, Ved Varun / Chaudhary, Kumardeep / Agrawal, Anurag / Sengupta, Shantanu / Dash, Debasis

    medRxiv

    Abstract: Data science has been an invaluable part of the COVID-19 pandemic response with multiple applications, ranging from tracking viral evolution to understanding the effectiveness of interventions. Asymptomatic breakthrough infections have been a major ... ...

    Abstract Data science has been an invaluable part of the COVID-19 pandemic response with multiple applications, ranging from tracking viral evolution to understanding the effectiveness of interventions. Asymptomatic breakthrough infections have been a major problem during the ongoing surge of Delta variant globally. Serological discrimination of vaccine response from infection has so far been limited to Spike protein vaccines used in the higher-income regions. Here, we show for the first time how statistical and machine learning (ML) approaches can discriminate SARS-CoV-2 infection from immune response to an inactivated whole virion vaccine (BBV152, Covaxin, India), thereby permitting real-world vaccine effectiveness assessments from cohort-based serosurveys in Asia and Africa where such vaccines are commonly used. Briefly, we accessed serial data on Anti-S and Anti-NC antibody concentration values, along with age, sex, number of doses, and number of days since the last vaccine dose for 1823 Covaxin recipients. An ensemble ML model, incorporating a consensus clustering approach alongside the support vector machine (SVM) model, was built on 1063 samples where reliable qualifying data existed, and then applied to the entire dataset. Of 1448 self-reported negative subjects, 724 were classified as infected. Since the vaccine contains wild-type virus and the antibodies induced will neutralize wild type much better than Delta variant, we determined the relative ability of a random subset of such samples to neutralize Delta versus wild type strain. In 100 of 156 samples, where ML prediction differed from self-reported uninfected status, Delta variant, was neutralized more effectively than the wild type, which cannot happen without infection. The fraction rose to 71.8% (28 of 39) in subjects predicted to be infected during the surge, which is concordant with the percentage of sequences classified as Delta (75.6%-80.2%) over the same period.
    Keywords covid19
    Language English
    Publishing date 2021-12-17
    Publisher Cold Spring Harbor Laboratory Press
    Document type Article ; Online
    DOI 10.1101/2021.12.16.21267889
    Database COVID19

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