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Article ; Online: RFGR: Repeat Finder for Complete and Assembled Whole Genomes and NGS Reads.

Sukumaran, Rashmi / Shahina, K / Nair, Achuthsankar S

2024

Abstract: ... For NGS reads, RFGR uses the frequency of the repetitive k-mers to determine FASTQ reads containing ...

Abstract	Repetitive DNA sequences cause genomic instability and are important genetic markers. Identification of repeats is a critical step in genome annotation and analysis. On the other hand, repeats also pose a technical challenge for genome assembly and alignment programs using NGS data. RFGR is a comprehensive tool that can find exact repetitive sequences in complete genomes and assembled genomes, as well as NGS reads of prokaryotes. For complete genomes, RFGR uses a suffix trees to find seed repeats of repetitive sequences of fixed length with indels. For assembled genomes, RFGR uses a modified Bowtie aligner to find seed repeats of exact repetitive sequences in the contigs/ scaffolds, which are then extended to maximal repeats. The repeats are classified and for repeats near a gene, RFGR reports the gene as well. For the control dataset of E. coli UTI89 and E. coli K12, RFGR reports 35,141 and 49,352 repeats, respectively. For NGS reads, RFGR uses the frequency of the repetitive k-mers to determine FASTQ reads containing repetitive sequences and removes them from the dataset. An E. coli K12 NGS dataset pre-processed using RFGR, on comparison with the original dataset, gives an improved assembly. The N50 value improves by 22.86% with a decrease in size of the assembly graph by nearly 50%. Thus, with RFGR, we achieve a better assembly with reduced computation. RFGR can be improved in terms of the length of the minimum repeat found, extending to find approximate repeats and to be applicable to Eukaryotes as well.
Language	English
Publishing date	2024-01-12
Publishing country	United States
Document type	Journal Article
ZDB-ID	2168-4
ISSN	1573-4927 ; 0006-2928
ISSN (online)	1573-4927
ISSN	0006-2928
DOI	10.1007/s10528-023-10628-x
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Article ; Online: Biodegradable and 3D printable lysine functionalized polycaprolactone scaffolds for tissue engineering applications.

Naik, Sonali S / Torris, Arun / Choudhury, Namita R / Dutta, Naba K / Sukumaran Nair, Kiran

Biomaterials advances

2024 Volume 159, Page(s) 213816

Abstract: Tissue engineering (TE) has sparked interest in creating scaffolds with customizable properties and functional bioactive sites. However, due to limitations in medical practices and manufacturing technologies, it is challenging to replicate complex porous ...

Abstract	Tissue engineering (TE) has sparked interest in creating scaffolds with customizable properties and functional bioactive sites. However, due to limitations in medical practices and manufacturing technologies, it is challenging to replicate complex porous frameworks with appropriate architectures and bioactivity in vitro. To address these challenges, herein, we present a green approach that involves the amino acid (l-lysine) initiated polymerization of ɛ-caprolactone (CL) to produce modified polycaprolactone (PCL) with favorable active sites for TE applications. Further, to better understand the effect of morphology and porosity on cell attachment and proliferation, scaffolds of different geometries with uniform and interconnected pores are designed and fabricated, and their properties are evaluated in comparison with commercial PCL. The scaffold morphology and complex internal micro-architecture are imaged by micro-computed tomography (micro-CT), revealing pore size in the range of ~300-900 μm and porosity ranging from 30 to 70 %, while based on the geometry of scaffolds the compressive strength varied from 143 ± 19 to 214 ± 10 MPa. Additionally, the degradation profiles of fabricated scaffolds are found to be influenced by both the chemical nature and product design, where Lys-PCL-based scaffolds with better porosity and lower crystallinity degraded faster than commercial PCL scaffolds. According to in vitro studies, Lys-PCL scaffolds have produced an environment that is better for cell adhesion and proliferation. Moreover, the scaffold design affects the way cells interact; Lys-PCL with zigzag geometry has demonstrated superior in vitro vitality (>90 %) and proliferation in comparison to other designs. This study emphasizes the importance of enhancing bioactivity while meeting morphology and porosity requirements in the design of scaffolds for tissue engineering applications.
MeSH term(s)	Tissue Engineering/methods ; Tissue Scaffolds/chemistry ; Lysine ; X-Ray Microtomography ; Polyesters
Chemical Substances	polycaprolactone (24980-41-4) ; Lysine (K3Z4F929H6) ; Polyesters
Language	English
Publishing date	2024-02-28
Publishing country	Netherlands
Document type	Journal Article
ISSN	2772-9508
ISSN (online)	2772-9508
DOI	10.1016/j.bioadv.2024.213816
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Article ; Online: Objective assessment of clinical benefit with ministernotomy more important than anecdotal clinical experience of surgeons.

Nair, Sukumaran K

The Journal of thoracic and cardiovascular surgery

2019 Volume 157, Issue 4, Page(s) e132–e133

MeSH term(s)	Aortic Valve/surgery ; Heart Valve Prosthesis Implantation ; Humans ; Surgeons
Language	English
Publishing date	2019-02-13
Publishing country	United States
Document type	Letter ; Comment
ZDB-ID	3104-5
ISSN	1097-685X ; 0022-5223
ISSN (online)	1097-685X
ISSN	0022-5223
DOI	10.1016/j.jtcvs.2018.11.083
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Article: Governance and upgrading opportunities in beef industry in Botswana

Sukumaran Nair, M. K

International journal of business policy and economics Vol. 9, No. 2 , p. 137-152

a global commodity chain approach

2016 Volume 9, Issue 2, Page(s) 137–152

Author's details	M. K. Sukumaran Nair
Keywords	Botswana ; global commodity chain analysis ; SPS requirements ; upgrading
Language	English
Dates of publication	2016-9999
Publisher	Serials Publ.
Publishing place	New Delhi
Document type	Article
ZDB-ID	2548332-8
ISSN	0973-5801
Database	ECONomics Information System

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Article ; Online: Structural Modifications on Chalcone Framework for Developing New Class of Cholinesterase Inhibitors.

George, Ginson / Koyiparambath, Vishal Payyalot / Sukumaran, Sunitha / Nair, Aathira Sujathan / Pappachan, Leena K / Al-Sehemi, Abdullah G / Kim, Hoon / Mathew, Bijo

International journal of molecular sciences

2022 Volume 23, Issue 6

Abstract: Due to the multifaceted pharmacological activities of chalcones, these scaffolds have been considered one of the most privileged frameworks in the drug discovery process. Structurally, chalcones are α, β-unsaturated carbonyl functionalities with two aryl ...

Abstract	Due to the multifaceted pharmacological activities of chalcones, these scaffolds have been considered one of the most privileged frameworks in the drug discovery process. Structurally, chalcones are α, β-unsaturated carbonyl functionalities with two aryl or heteroaryl units. Amongst the numerous pharmacological activities explored for chalcone derivatives, the development of novel chalcone analogs for the treatment of Alzheimer's disease (AD) is among the research topics of most interest. Chalcones possess numerous advantages, such as smaller molecular size, opportunities for further structural modification thereby altering the physicochemical properties, cost-effectiveness, and convenient synthetic methodology. The present review highlights the recent evidence of chalcones as a privileged structure in AD drug development processes. Different classes of chalcone-derived analogs are summarized for the easy understanding of the previously reported analogs as well as the importance of certain functionalities in exhibiting cholinesterase inhibition. In this way, this review will shed light on the medicinal chemistry fraternity for the design and development of novel promising chalcone candidates for the treatment of AD.
MeSH term(s)	Alzheimer Disease/drug therapy ; Chalcone ; Chalcones/chemistry ; Cholinesterase Inhibitors/chemistry ; Drug Discovery ; Humans ; Structure-Activity Relationship
Chemical Substances	Chalcones ; Cholinesterase Inhibitors ; Chalcone (5S5A2Q39HX)
Language	English
Publishing date	2022-03-14
Publishing country	Switzerland
Document type	Journal Article ; Review
ZDB-ID	2019364-6
ISSN	1422-0067 ; 1422-0067 ; 1661-6596
ISSN (online)	1422-0067
ISSN	1422-0067 ; 1661-6596
DOI	10.3390/ijms23063121
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Article ; Online: In Situ Synthesis of Silver Nanospheres, Nanocubes, and Nanowires over Boron-Doped Graphene Sheets for Surface-Enhanced Raman Scattering Application and Enzyme-Free Detection of Hydrogen Peroxide.

Nair, Anju K / Sukumaran Nair, Kala Moolepparambil / Thomas, Sabu / Rouxel, Didier / Alwarappan, Subbiah / Kalarikkal, Nandakumar

Langmuir : the ACS journal of surfaces and colloids

2018 Volume 34, Issue 45, Page(s) 13603–13614

Abstract: An effective in situ synthesis strategy is demonstrated for the preparation of silver nanostructures (nanospheres (NSs), nanocubes (NCs), and nanowires (NWs)) on the surface of boron-doped graphene (BG). Further, these functional nanomaterials are ... ...

Abstract	An effective in situ synthesis strategy is demonstrated for the preparation of silver nanostructures (nanospheres (NSs), nanocubes (NCs), and nanowires (NWs)) on the surface of boron-doped graphene (BG). Further, these functional nanomaterials are employed for the surface-enhanced Raman scattering (SERS) and non-enzymatic electrochemical detection of H
Language	English
Publishing date	2018-11-01
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2005937-1
ISSN	1520-5827 ; 0743-7463
ISSN (online)	1520-5827
ISSN	0743-7463
DOI	10.1021/acs.langmuir.8b02005
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Article: COVID-19 and haematology services in a cancer centre from a middle-income country: adapting service delivery, balancing the known and unknown during the pandemic.

Radhakrishnan, Vivek S / Nair, Reghu K Sukumaran / Goel, Gaurav / Ramanan, Venkatraman / Chandy, Mammen / Nair, Reena

Ecancermedicalscience

2020 Volume 14, Page(s) 1110

Abstract: The COVID-19 pandemic has caused major disruptions in multiple spheres of healthcare delivery in the world. Developing nations have had to tackle this unanticipated crisis in the midst of various other healthcare delivery issues and resource constraints. ...

Abstract	The COVID-19 pandemic has caused major disruptions in multiple spheres of healthcare delivery in the world. Developing nations have had to tackle this unanticipated crisis in the midst of various other healthcare delivery issues and resource constraints. As a tertiary level cancer care provider located in an eastern Indian city, a COVID-19 hotspot, we share our experience from the perspective of haematology and haematopoietic stem cell transplantation (HSCT) services. The primary challenges related to infection control included infection screening and decreasing exposure among patients and healthcare workers. Logistic challenges include maintaining essential patient care services, personnel redeployment, blood bank inventory constraints and maintaining the supply chain for a continuum of care. Clinical management challenges were dealt with by rationalising treatment delivery by modification of treatment regimens, risk-based deferral of HSCT, management of COVID-19 in patients, and staggering the follow-up schedules in survivors and those on maintenance therapies, among other strategies. These challenges were compounded by the restrictions imposed by a countrywide lockdown in the initial period of the pandemic, which also affected the socio-economic aspects of treatment delivery. As a training institution, this period also impacted academics and research activities. This overview details our response to these challenges during the COVID-19 pandemic, which has many unknowns.
Keywords	covid19
Language	English
Publishing date	2020-09-24
Publishing country	England
Document type	Journal Article
ISSN	1754-6605
ISSN	1754-6605
DOI	10.3332/ecancer.2020.1110
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Article: Implementation GAP or absorptive capacity constraint?

Sukumaran Nair, M. K / Galebotswe, O

Asian African journal of economics and econometrics Vol. 15, No. 1 , p. 65-75

a study of underspending of budgets in Botswana

2015 Volume 15, Issue 1, Page(s) 65–75

Author's details	M. K. Sukumaran Nair and O. Galebotswe
Keywords	Absorptive capacity constraint ; Botswana ; budgeted expenditure ; capital consumption ; economic diversification ; liquid assets ; total factor productivity
Language	English
Publisher	Serials Publ.
Publishing place	New Delhi
Document type	Article
ZDB-ID	2471806-3
ISSN	0972-3986
Database	ECONomics Information System

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Article: Relapsed Refractory Hodgkin Lymphoma and Brentuximab Vedotin-Bendamustine Combination Therapy as a Bridge to Transplantation: Real-World Evidence From a Middle-Income Setting and Literature Review.

Radhakrishnan, Vivek S / Bajaj, Rajat / Raina, Vasundhara / Kumar, Jeevan / Bhave, Saurabh J / Sukumaran Nair, Reghu K / Nag, Arijit / Arun, Indu / Zameer, Lateef / Dey, Debdeep / Arora, Neeraj / Parihar, Mayur / Das, Jayanta / Achari, Rimpa B / Mishra, Deepak K / Chandy, Mammen / Nair, Reena

Frontiers in oncology

2022 Volume 11, Page(s) 796270

Abstract: Introduction: Despite high cure rates with standard treatment, 30% patients with Hodgkin lymphoma develop relapsed or refractory (R/R) disease. Salvage therapy followed by autologous hematopoietic cell transplantation (HCT) is considered standard of ... ...

Abstract	Introduction: Despite high cure rates with standard treatment, 30% patients with Hodgkin lymphoma develop relapsed or refractory (R/R) disease. Salvage therapy followed by autologous hematopoietic cell transplantation (HCT) is considered standard of care. Brentuximab Vedotin (Bv) in combination with Bendamustine (B) has been tested in the salvage setting with promising results. Materials and methodology: We conducted a single centre retrospective chart review of patients who received BBv salvage therapy to determine its activity and safety in patients with R/R classical Hodgkin lymphoma (HL). Between May 2011- December 2019, 179 patients were diagnosed with R/R HL. Results: Thirty patients received BBv [median age: 30 (15-59) years, females (n=15)]. Primary refractory disease in 19 patients (63%), and 26 patients (87%) had advanced stage at treatment. Most patients received BBv after 2 prior lines of therapy [n=16 (53%)]. The median number of cycles of BBv were 3 (1-6). The number of BBv cycles delivered as outpatient was 63%. The most common Grade III/IV hematological adverse event was neutropenia [n=21, (70%)], while grade III/IV non-hematological toxicities included infections in 4 (13%), neuropathy in 4(13%), skin rash in 2 (7%), GI toxicities in 3 (10%) and liver dysfunction in 2 (7%) patients. The ORR and CR rates were 79% and 62%, respectively. Seventeen patients (57%) underwent an autologous HCT and 8 (26%) underwent an Allogeneic HCT (all haploidentical). The median follow up time from BBv administration was 12 months. Six patients died: 2 = disease progression, and 4 = non-relapse causes (Infection and sepsis = 2, GVHD=2). In addition to this, one patient progressed soon after HCT and another patient relapsed 22 months post HCT. Three year Overall survival (OS) and Event free survival (EFS) probability post-BBv treatment was 75% and 58%, respectively. OS and EFS analysis based on response (viz., CMR) to BBv demonstrated that patients in CMR had better survival probability [93% (p=0.0022) 3yr-OS and 72% (p=0.038) 3yr-EFS probability]. Conclusions: BBv is an active and well-tolerated salvage treatment for patients with R/R HL, even in refractory and advanced settings. In middle-income settings, cost constraints and access determine patient uptake of this regimen.
Language	English
Publishing date	2022-01-21
Publishing country	Switzerland
Document type	Journal Article
ZDB-ID	2649216-7
ISSN	2234-943X
ISSN	2234-943X
DOI	10.3389/fonc.2021.796270
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Article ; Online: Low-grade papillary adenocarcinoma of nasopharynx with expression of thyroid transcription factor-1: Case report and review of literature.

Rajeswari, Binitha / Sukumaran Nair, Reghu K / Parukuttyamma, Kusumakumary / Mathews, Anitha

Indian journal of pathology & microbiology

2016 Volume 59, Issue 4, Page(s) 518–520

Abstract: Low-grade papillary adenocarcinomas with expression of thyroid transcription factor-1 (TTF-1) are rare tumors of the nasopharynx, with only a few cases reported in the literature. These tumors have an excellent prognosis following complete surgical ... ...

Abstract	Low-grade papillary adenocarcinomas with expression of thyroid transcription factor-1 (TTF-1) are rare tumors of the nasopharynx, with only a few cases reported in the literature. These tumors have an excellent prognosis following complete surgical excision. We report a 13-year-old boy with this rare tumor in the nasopharynx. The patient underwent complete surgical excision of the tumor and was on follow-up without evidence of recurrence.
MeSH term(s)	Adenocarcinoma, Papillary/diagnosis ; Adenocarcinoma, Papillary/pathology ; Adenocarcinoma, Papillary/surgery ; Adolescent ; Biomarkers, Tumor/analysis ; Head/diagnostic imaging ; Histocytochemistry ; Humans ; Immunohistochemistry ; Male ; Microscopy ; Nasopharyngeal Neoplasms/diagnosis ; Nasopharyngeal Neoplasms/pathology ; Nasopharyngeal Neoplasms/surgery ; Nasopharynx/pathology ; Nuclear Proteins/analysis ; Thyroid Nuclear Factor 1 ; Tomography, X-Ray Computed ; Transcription Factors/analysis ; Treatment Outcome
Chemical Substances	Biomarkers, Tumor ; NKX2-1 protein, human ; Nuclear Proteins ; Thyroid Nuclear Factor 1 ; Transcription Factors
Language	English
Publishing date	2016-10
Publishing country	India
Document type	Case Reports ; Journal Article ; Review
ZDB-ID	197621-7
ISSN	0974-5130 ; 0377-4929
ISSN (online)	0974-5130
ISSN	0377-4929
DOI	10.4103/0377-4929.191809
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