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Article ; Online: Genome assembly of the hybrid grapevine Vitis ‘Chambourcin’

Sagar Patel / Zachary N. Harris / Jason P. Londo / Allison Miller / Anne Fennell

GigaByte (2023)

2023

Abstract: Chambourcin’ is a French-American interspecific hybrid grape grown in the eastern and midwestern United States and used for making wine. Few genomic resources are available for hybrid grapevines like ‘Chambourcin’. Here, we assembled the genome of ‘ ... ...

Abstract	‘Chambourcin’ is a French-American interspecific hybrid grape grown in the eastern and midwestern United States and used for making wine. Few genomic resources are available for hybrid grapevines like ‘Chambourcin’. Here, we assembled the genome of ‘Chambourcin’ using PacBio HiFi long-read, Bionano optical map, and Illumina short-read sequencing technologies. We generated an assembly for ‘Chambourcin’ with 26 scaffolds, with an N50 length of 23.3 Mb and an estimated BUSCO completeness of 97.9%. We predicted 33,791 gene models and identified 16,056 common orthologs between ‘Chambourcin’, V. vinifera ‘PN40024’ 12X.v2, VCOST.v3, Shine Muscat and V. riparia Gloire. We found 1,606 plant transcription factors from 58 gene families. Finally, we identified 304,571 simple sequence repeats (up to six base pairs long). Our work provides the genome assembly, annotation and the protein and coding sequences of ‘Chambourcin’. Our genome assembly is a valuable resource for genome comparisons, functional genomic analyses and genome-assisted breeding research.
Keywords	Electronic computers. Computer science ; QA75.5-76.95
Language	English
Publishing date	2023-07-01T00:00:00Z
Publisher	GigaScience Press
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Data related to architectural bone parameters and the relationship to Ti lattice design for powder bed fusion additive manufacturing

Martine McGregor / Sagar Patel / Stewart McLachlin / Mihaela Vlasea

Data in Brief, Vol 39, Iss , Pp 107633- (2021)

2021

Abstract: The data included in this article provides additional supporting information on our publication (McGregor et al. [1]) on the review of the natural lattice architecture in human bone and its implication towards titanium (Ti) lattice design for laser ... ...

Abstract	The data included in this article provides additional supporting information on our publication (McGregor et al. [1]) on the review of the natural lattice architecture in human bone and its implication towards titanium (Ti) lattice design for laser powder bed fusion and electron beam powder bed fusion. For this work, X-ray computed tomography was deployed to understand and visualize a Ti-6Al-4V lattice structure manufactured by laser powder bed fusion. This manuscript includes details about the manufacturing of the lattice structure using laser powder bed fusion and computed tomography methods used for analyzing the lattice structure. Additionally, a comprehensive literature review was conducted to understand how lattice parameters are controlled in additively manufactured Ti and Ti-alloy parts aimed at replacing or augmenting human bone. From this literature review, lattice design information was collected and is summarized in tabular form in this manuscript.
Keywords	Additive manufacturing ; X-ray computed tomography ; Laser powder bed fusion ; Lattice design ; Bone replacement ; Orthopaedic design ; Computer applications to medicine. Medical informatics ; R858-859.7 ; Science (General) ; Q1-390
Language	English
Publishing date	2021-12-01T00:00:00Z
Publisher	Elsevier
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Porcine respiratory disease complex (PRDC) in Indian pigs: a slaughterhouse survey.

Thakor, Jigarji Chaturji / Sahoo, Monalisa / Karam Pal Singh / Rajendra Singh / Salauddin Qureshi / Ajay Kumar / Pradeep Kumar / Sagar Patel / Rohit Singh / Nihar Ranjan Sahoo

Veterinaria italiana

2023 Volume 59, Issue 1, Page(s) 23–38

Abstract: Porcine Respiratory Disease Complex (PRDC) is an unequivocally leading cause of economic losses to the pig industry. To investigate the pathogens associated with PRDC, a total of 900 lungs with gross lesions and 125 lungs with no appreciable gross ... ...

Abstract	Porcine Respiratory Disease Complex (PRDC) is an unequivocally leading cause of economic losses to the pig industry. To investigate the pathogens associated with PRDC, a total of 900 lungs with gross lesions and 125 lungs with no appreciable gross lesions were collected from the abattoirs and subjected to pathological investigation for distribution of lesions/and types of exudates, as well as to molecular confirmation of bacterial and viral pathogens by PCR. The pneumonic lungs showed the higher prevalence of Mycoplasma spp. (31.22%), with evidence of M. hyorhinis, P. multocida (21.33%), S. suis (18.66%), B. bronchiseptica (16.77%), and viral pathogens as porcine circovirus type 2 (PCV2) (28.11%), porcine reproductive and respiratory syndrome virus (PRRSV) (2.7%) and swine influenza virus (SIV) (1.2%). On histopathological examination, high prevalence of bronchopneumonia (37.88%) followed by enzootic pneumonia‑like lung lesions (11.44%), and interstitial pneumonia (7.44%) was recorded in the majority of affected pigs. The winter season was found to be more conducive for highest prevalence of pneumonia as compared to other seasons. The present study reports the high prevalence of PRDC in slaughtered pigs of India. M. hyorhinis showing the EP‑like lesions, PCV2 and their combination were likely to be the prime contributors of PRDC in Indian pigs.
MeSH term(s)	Swine ; Animals ; Abattoirs ; Porcine respiratory and reproductive syndrome virus ; Swine Diseases/epidemiology ; Respiratory Tract Diseases/epidemiology ; Respiratory Tract Diseases/veterinary ; Circovirus ; Pasteurella multocida ; Pneumonia/veterinary
Language	English
Publishing date	2023-03-31
Publishing country	Italy
Document type	Journal Article
ZDB-ID	2536397-9
ISSN	1828-1427 ; 0505-401X
ISSN (online)	1828-1427
ISSN	0505-401X
DOI	10.12834/VetIt.2935.20591.2
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article ; Online: Exploring medically-related Canadian summer student research programs

Sagar Patel / Catharine M. Walsh / Jacob A. Udell

BMC Medical Education, Vol 19, Iss 1, Pp 1-

a National Cross-sectional Survey Study

2019 Volume 9

Abstract: Abstract Background Summer student research programs (SSRPs) serve to generate student interest in research and a clinician-scientist career path. This study sought to understand the composition of existing medically-related Canadian SSRPs, describe the ... ...

Abstract	Abstract Background Summer student research programs (SSRPs) serve to generate student interest in research and a clinician-scientist career path. This study sought to understand the composition of existing medically-related Canadian SSRPs, describe the current selection, education and evaluation practices and highlight opportunities for improvement. Methods A cross-sectional survey study among English-language-based medically-related Canadian SSRPs for undergraduate and medical students was conducted. Programs were systematically identified through academic and/or institutional websites. The survey, administered between June–August 2016, collected information on program demographics, competition, selection, student experience, and program self-evaluation. Results Forty-six of 91 (50.5%) identified programs responded. These SSRPs collectively offered 1842 positions with a mean 3.76 applicants per placement. Most programs (78.3%, n = 36/46) required students to independently secure a research supervisor. A formal curriculum existed among 61.4% (n = 27/44) of programs. Few programs (5.9%, n = 2/34) offered an integrated clinical observership. Regarding evaluation, 11.4% (n = 5/44) of programs tracked subsequent research productivity and 27.5% (n = 11/40) conducted long-term impact assessments. Conclusions Canadian SSRPs are highly competitive with the responsibility of selection primarily with the individual research supervisor rather than a centralized committee. Most programs offered students opportunities to develop both research and communication skills. Presently, the majority of programs do not have a sufficient evaluation component. These findings indicate that SSRPs may benefit from refinement of selection processes and more robust evaluation of their utility. To address this challenge, the authors describe a logic model that provides a set of core outcomes which can be applied as a framework to guide program evaluation of SSRPs.
Keywords	Medical education ; Medical student ; Medical careers ; Summer student research programs ; Clinician-scientists ; Special aspects of education ; LC8-6691 ; Medicine ; R
Subject code	420
Language	English
Publishing date	2019-05-01T00:00:00Z
Publisher	BMC
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: A review of recent advances in the diagnosis of cardiac amyloidosis, treatment of its cardiac complications, and disease-modifying therapies [version 1; peer review

Labdhi Sanghvi / Akhil Jain / Sajid Siddiq / Kamal Sharma / Maharshi Raval / Rupak Desai / Kanishka Uttam Chandani / Dhriti Patel / Sagar Patel / Jaahnavee Trivedi

F1000Research, Vol

2 approved]

2023 Volume 12

Abstract: Cardiac amyloidosis (CA), a significant condition resulting in infiltrative cardiomyopathy and heart failure with preserved ejection fraction (HFpEF), is caused by extracellular deposition of amyloid fibrils in the heart. Even though this has been known ... ...

Abstract	Cardiac amyloidosis (CA), a significant condition resulting in infiltrative cardiomyopathy and heart failure with preserved ejection fraction (HFpEF), is caused by extracellular deposition of amyloid fibrils in the heart. Even though this has been known for an extended period, its prevalence in elderly patients with heart failure is increasingly being recognized. Recent advances in diagnosis with non-invasive methods like technetium pyrophosphate-labeled cardiac scintigraphy (i.e., Tc-PYP scan) and treatment options with tafamidis have played a pivotal role in awareness of the burden of this disease. Management of cardiac complications like heart failure, atrial arrhythmias, conduction block, ventricular arrhythmias, coronary artery disease, and aortic stenosis is now more critical than ever. We aim to review and outline the recent advances in diagnoses of CA. We also review management strategies for cardiac complications of CA with a brief summary of disease-modifying therapies.
Keywords	cardiac amyloidosis ; heart failure ; bone scintigraphy ; ATTR amyloidosis ; AL amyloidosis ; tafamidis ; eng ; Medicine ; R ; Science ; Q
Subject code	610
Language	English
Publishing date	2023-02-01T00:00:00Z
Publisher	F1000 Research Ltd
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: The authentication and repatriation of a ceremonial tsantsa to its country of origin (Ecuador)

Craig D. Byron / Adam M. Kiefer / Joanna Thomas / Sagar Patel / Amy Jenkins / Anthony L. Fratino / Todd Anderson

Heritage Science, Vol 9, Iss 1, Pp 1-

2021 Volume 13

Abstract: Abstract Tsantsas, commonly referred to as “shrunken heads”, are unique and valuable antiquities that were produced by the Shuar, Achuar, Awajún/Aguaruna, Wampís/Huambisa, and Candoshi-Shampra (SAAWC) peoples until the mid twentieth century. Originally ... ...

Abstract	Abstract Tsantsas, commonly referred to as “shrunken heads”, are unique and valuable antiquities that were produced by the Shuar, Achuar, Awajún/Aguaruna, Wampís/Huambisa, and Candoshi-Shampra (SAAWC) peoples until the mid twentieth century. Originally used with ceremonial purpose during important social group functions, tsantsas became monetarily valuable as keepsakes and curios during the nineteenth century as a result of Western/European cultural encroachment. Unmet demand resulted in the production of convincing forgeries that created confusion about the authenticity of existing collections. Ceremonial tsantsas are both human remains and valuable cultural items. Their production and purpose were negatively influenced by colonialism and the outside curio market; as such many institutions may choose to repatriate them to their places of origin. Herein, we report on the authentication and repatriation of a ceremonial tsantsa recently rediscovered in a university’s natural history collection. The personal memoirs of the original collector describe that it originated in the Ecuadorean Amazon. In consultation with the government of Ecuador, it was determined that authentication was required prior to repatriation. The tsantsa was compared to a list of thirty-three distinct characteristics shared by ceremonial tsantsas. These criteria were taken from those provided by Ecuador’s National Cultural Heritage Institute and those found in prior studies from the academic literature; they include notable skin and hair features, structure and facial anatomy, and evidence of traditional fabrication and modification. We were able to affirm 30 of the 33 authenticating indicators. As part of our protocol the tsantsa was scanned with a CT-imaging system. The resulting 3D images were invaluable in discerning subtle and difficult-to-visualize characteristics regarding the skin and patterns of modification, although there are limitations related to the small size of filamentous structures. The results of the authentication were ...
Keywords	Tsantsa ; Jivaro ; SAAWC peoples ; Ecuador ; Repatriation ; Computed tomography ; Fine Arts ; N ; Analytical chemistry ; QD71-142
Language	English
Publishing date	2021-05-01T00:00:00Z
Publisher	SpringerOpen
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Correction to

Craig D. Byron / Adam M. Kiefer / Joanna Thomas / Sagar Patel / Amy Jenkins / Anthony L. Fratino / Todd Anderson

Heritage Science, Vol 9, Iss 1, Pp 1-

The authentication and repatriation of a ceremonial tsantsa to its country of origin (Ecuador)

2021 Volume 1

Abstract: An amendment to this paper has been published and can be accessed via the original article. ...

Abstract	An amendment to this paper has been published and can be accessed via the original article.
Keywords	Fine Arts ; N ; Analytical chemistry ; QD71-142
Language	English
Publishing date	2021-05-01T00:00:00Z
Publisher	SpringerOpen
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Role of RBCs alloimmunization in multiple transfused thalassaemia patients

Amita Sagar Patel / Sejal Gamit / Mayuri Gohil

International Journal of Research in Medical Sciences, Vol 4, Iss 3, Pp 822-

2016 Volume 828

Abstract: Background: Appropriate and regular red cell transfusion remains the main treatment of choice for a large number of patients with multiple transfusions. This study has been carried out to assess the prevalence of and to provide frequency and distribution ...

Abstract	Background: Appropriate and regular red cell transfusion remains the main treatment of choice for a large number of patients with multiple transfusions. This study has been carried out to assess the prevalence of and to provide frequency and distribution patterns of various types of irregular red cell alloantibodies in thalassaemia major patients. Methods: 50 patients of thalassemia major were studied. The saline method, Albumin method, indirect coombs' and Three cell panel test used for detection of red blood cell alloantibody. The variables studied were rate of red cell alloimmunization, type and specificity of RBCs alloantibodies and factors contributes to development of RBCs alloimmunization like age, gender, age at start of transfusion, number of packed cell received and ethnicity. Results: Out 50 patients of thalassemia major, 4 patients (8%) developed red cell alloantibodies respectively. The red cell alloantibodies were against Rh, Kidd, Kell, Duffy, Lewis, MNS and P system. Results of this study (P value >0.05) indicate low frequency of RBCs alloimmunization. Conclusions: Low alloimmunization rate implies that there is homogeneity of red cell antigens in blood donors and recipients. RBCs alloantibody formation was not influenced by gender, age at start of transfusions and number of packed cells received. Already alloimmunized patients get benefits from leucodepleted packed cells. Specific recommendation given on routine pre-transfusion antibody screening to ensure safer transfusion. [Int J Res Med Sci 2016; 4(3.000): 822-828]
Keywords	Antibody screening ; Thalassaemia ; Red cell alloimmunization ; Leucodepleted packed cells ; Medicine (General) ; R5-920 ; Medicine ; R
Subject code	610 ; 616
Language	English
Publishing date	2016-03-01T00:00:00Z
Publisher	Medip Academy
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Primary outcome reporting in adolescent depression clinical trials needs standardization

Andrea Monsour / Emma J. Mew / Sagar Patel / Alyssandra Chee-a-tow / Leena Saeed / Lucia Santos / Darren B. Courtney / Priya N. Watson / Suneeta Monga / Peter Szatmari / Martin Offringa / Nancy J. Butcher

BMC Medical Research Methodology, Vol 20, Iss 1, Pp 1-

2020 Volume 15

Abstract: Abstract Background Evidence-based health care is informed by results of randomized clinical trials (RCTs) and their syntheses in meta-analyses. When the trial outcomes measured are not clearly described in trial publications, knowledge synthesis, ... ...

Abstract	Abstract Background Evidence-based health care is informed by results of randomized clinical trials (RCTs) and their syntheses in meta-analyses. When the trial outcomes measured are not clearly described in trial publications, knowledge synthesis, translation, and decision-making may be impeded. While heterogeneity in outcomes measured in adolescent major depressive disorder (MDD) RCTs has been described, the comprehensiveness of outcome reporting is unknown. This study aimed to assess the reporting of primary outcomes in RCTs evaluating treatments for adolescent MDD. Methods RCTs evaluating treatment interventions in adolescents with a diagnosis of MDD published between 2008 and 2017 specifying a single primary outcome were eligible for outcome reporting assessment. Outcome reporting assessment was done independently in duplicate using a comprehensive checklist of 58 reporting items. Primary outcome information provided in each RCT publication was scored as “fully reported”, “partially reported”, or “not reported” for each checklist item, as applicable. Results Eighteen of 42 identified articles were found to have a discernable single primary outcome and were included for outcome reporting assessment. Most trials (72%) did not fully report on over half of the 58 checklist items. Items describing masking of outcome assessors, timing and frequency of outcome assessment, and outcome analyses were fully reported in over 70% of trials. Items less frequently reported included outcome measurement instrument properties (ranging from 6 to 17%), justification of timing and frequency of outcome assessment (6%), and justification of criteria used for clinically significant differences (17%). The overall comprehensiveness of reporting appeared stable over time. Conclusions Heterogeneous reporting exists in published adolescent MDD RCTs, with frequent omissions of key details about their primary outcomes. These omissions may impair interpretability, replicability, and synthesis of RCTs that inform clinical guidelines and decision-making in this field. Consensus on the minimal criteria for outcome reporting in adolescent MDD RCTs is needed.
Keywords	Major depressive disorder ; Adolescent ; Randomized clinical trial ; Outcome reporting ; Primary outcomes ; Medicine (General) ; R5-920
Subject code	333
Language	English
Publishing date	2020-05-01T00:00:00Z
Publisher	BMC
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Nodular Regenerative Hyperplasia of the Liver in Rheumatic Disease

Prarthana Jain DO, MPH / Sagar Patel MD / Heather N. Simpson MD / Richard M. Silver MD / David N. Lewin MD / Ruth C. Campbell MD, MSPH / Marcelo Guimaraes MD, MBA / Katherine C. Silver MD, MSCR

Journal of Investigative Medicine High Impact Case Reports, Vol

Cases and Review of the Literature

2021 Volume 9

Abstract: Nodular regenerative hyperplasia (NRH) is a rare disease that is characterized by benign transformation of the hepatic parenchyma into small nodules with little to no fibrosis. Nodular regenerative hyperplasia is a cause of noncirrhotic portal ... ...

Abstract	Nodular regenerative hyperplasia (NRH) is a rare disease that is characterized by benign transformation of the hepatic parenchyma into small nodules with little to no fibrosis. Nodular regenerative hyperplasia is a cause of noncirrhotic portal hypertension. Symptoms can range from asymptomatic disease to more serious complications of portal hypertension such as esophageal varices and ascites. Nodular regenerative hyperplasia has been described in association with a variety of different rheumatologic, hematologic, and oncologic diseases, as well as in immune deficiency states and with exposures to certain toxins. Diagnosis is made by histology, and the treatment involves addressing the underlying disease. The first description of this rare disease was actually described in a patient with rheumatoid arthritis, neutropenia, and splenomegaly (Felty’s Syndrome). We describe 2 cases of NRH associated with underlying rheumatic disorders, in one of which NRH was actually the presenting feature of the patient’s underlying autoimmune condition. Subsequently, we provide a brief review of the literature of NRH in autoimmune disease with respect to epidemiology, cause, clinical manifestations, diagnosis, and treatment.
Keywords	Medicine (General) ; R5-920 ; Pathology ; RB1-214
Subject code	610
Language	English
Publishing date	2021-09-01T00:00:00Z
Publisher	SAGE Publishing
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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