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Fulltext Haplotype divergence and multiple candidate genes at Rphq2, a partial resistance QTL of barley to Puccinia hordei

Yeo FK, Wang Y, Vozabova T, Huneau C, Leroy P, Chalhoub B, et al.

Theor Appl Genet, 2016 Feb;129(2):289-304.
PMID: 26542283 DOI: 10.1007/s00122-015-2627-5

Rphq2, a minor gene for partial resistance to Puccinia hordei , was physically mapped in a 188 kbp introgression with suppressed recombination between haplotypes of rphq2 and Rphq2 barley cultivars.
Fulltext Call of the wild rice: Oryza rufipogon shapes weedy rice evolution in Southeast Asia

Vigueira CC, Qi X, Song BK, Li LF, Caicedo AL, Jia Y, et al.

Evol Appl, 2019 Jan;12(1):93-104.
PMID: 30622638 DOI: 10.1111/eva.12581

Agricultural weeds serve as productive models for studying the genetic basis of rapid adaptation, with weed-adaptive traits potentially evolving multiple times independently in geographically distinct but environmentally similar agroecosystems. Weedy relatives of domesticated crops can be especially interesting systems because of the potential for weed-adaptive alleles to originate through multiple mechanisms, including introgression from cultivated and/or wild relatives, standing genetic variation, and de novo mutations. Weedy rice populations have evolved multiple times through dedomestication from cultivated rice. Much of the genomic work to date in weedy rice has focused on populations that exist outside the range of the wild crop progenitor. In this study, we use genome-wide SNPs generated through genotyping-by-sequencing to compare the evolution of weedy rice in regions outside the range of wild rice (North America, South Korea) and populations in Southeast Asia, where wild rice populations are present. We find evidence for adaptive introgression of wild rice alleles into weedy rice populations in Southeast Asia, with the relative contributions of wild and cultivated rice alleles varying across the genome. In addition, gene regions underlying several weed-adaptive traits are dominated by genomic contributions from wild rice. Genome-wide nucleotide diversity is also much higher in Southeast Asian weeds than in North American and South Korean weeds. Besides reflecting introgression from wild rice, this difference in diversity likely reflects genetic contributions from diverse cultivated landraces that may have served as the progenitors of these weedy populations. These important differences in weedy rice evolution in regions with and without wild rice could inform region-specific management strategies for weed control.
Fulltext Convolutional neural network optimized by differential evolution for electrocardiogram classification

Chen SW, Wang SL, Qi X, Ng TF, Ibrahim H

Multimed Tools Appl, 2023 Apr 26.
PMID: 37362685 DOI: 10.1007/s11042-023-15407-9

The Coronavirus disease 2019, or COVID-19, has shifted the medical paradigm from face-to-face to telehealth. Telehealth has become a vital resource to contain the virus spread and ensure the continued care of patients. In terms of preventing cardiovascular diseases, automating electrocardiogram (ECG) classification is a promising telehealth intervention. The healthcare service ensures that patient care is appropriate, comfortable, and accessible. Convolutional neural networks (CNNs) have demonstrated promising results in ECG categorization, which require high accuracy and short training time to ensure healthcare quality. This study proposes a one-dimensional-CNN (1D-CNN) arrhythmia classification based on the differential evolution (DE) algorithm to optimize the accuracy of ECG classification and training time. The performance of 1D-CNNs of different activation functions are optimized based on the standard DE algorithm. Finally, based on MIT-BIH and SCDH arrhythmia databases, the performances of optimized and unoptimized 1D-CNN are compared and analysed. Results show that the 1D-CNN optimized by the DE has higher accuracy in heartbeats classification. The optimized 1D-CNN improves from 97.6% to 99.5% on MIT-BIH and from 80.2% to 88.5% on SCDH. Therefore, the optimized 1D-CNN shows improvements of 1.9% and 8.3% in the two datasets, respectively. In addition, compared with the unoptimized 1D-CNN based on the same parameter settings, the optimized 1D-CNN has less training time. Under the conditions of ReLU function and 10 epochs, the training takes 9.22 s on MIT-BIH and 10.35 s on SCDH, reducing training time by 67.2% and 64.2%, respectively.
Estrogen directly stimulates LHb expression at the pituitary level during puberty in female zebrafish

Li G, Tang H, Chen Y, Yin Y, Ogawa S, Liu M, et al.

Mol Cell Endocrinol, 2018 02 05;461:1-11.
PMID: 28801227 DOI: 10.1016/j.mce.2017.08.003

The LHb expression is up-regulated during puberty in female zebrafish. However, the molecular mechanism underlying how LHb expression is regulated during puberty remains largely unknown. In this study, we found that the mRNA expression levels of lhb, fshb and cyp19a1b were up-regulated along with the puberty onset in zebrafish. Among the three nuclear estrogen receptors (nERs), the esr2b is the only type whose expression is significantly up-regulated during puberty onset in the pituitary. However, in situ hybridization results revealed that lhb mRNA was colocalized with esr1 and esr2a but not esr2b. Exposure to estradiol (E2) significantly stimulates LHb expression in both wild-type and kiss1-/-;kiss2-/-;gnrh3-/- triple knockout pubertal zebrafish. Moreover, exposure of cultured pituitary cells to E2 increased the LHb expression, indicating that the estrogenic effect on LHb expression could be acted at the pituitary level. Finally, we cloned and analyzed the promoter of lhb by luciferase assay. Our results indicated that the E2 responsive regions of lhb promoter for ERα and ERβ2 are identical, suggesting that ERα and ERβ2 could bind to the same half ERE region of the promoter of lhb, exhibiting a classical ERE-dependent pathway. In summary, we demonstrate that E2 could directly act on the pituitary level to stimulate LHb transcription during puberty in zebrafish.
Fulltext Goals, challenges and strategies for wound and bleeding management in total knee arthroplasty: A modified Delphi method

Lyons M, Nunley RM, Ahmed Shokri A, Doneley T, Han HS, Harato K, et al.

J Orthop Surg (Hong Kong), 2022;30(3):10225536221138985.
PMID: 36374258 DOI: 10.1177/10225536221138985

BACKGROUND: Surgical techniques related to soft tissue management play critical roles in optimizing surgical outcomes and patient satisfaction in total knee arthroplasty (TKA). Despite the importance of wound closure and bleeding management approaches, no published guidelines/consensus are available.
METHODS: Twelve orthopedic surgeons participated in a modified Delphi panel consisting of 2 parts (each part comprising two rounds) from September-October 2018. Questionnaires were developed based on published evidence and guidelines on surgical techniques/materials. Questionnaires were administered via email (Round 1) or at a face-to-face meeting (subsequent rounds). Panelists ranked their agreement with each statement on a five-point Likert scale. Consensus was achieved if ≥70% of panelists selected 4/5, or 1/2. Statements not reaching consensus in Round 1 were discussed and repeated or modified in Round 2. Statements not reaching consensus in Round 2 were excluded from the final consensus framework.
RESULTS: Consensus was reached on 13 goals of wound management. Panelists agreed on 38 challenges and 71 strategies addressing surgical techniques or wound closure materials for each tissue layer, and management strategies for blood loss reduction or deep vein thrombosis prophylaxis in TKA. Statements on closure of capsular and skin layers, wound irrigation, dressings and drains required repeat voting or modification to reach consensus.
CONCLUSION: Consensus from Asia-Pacific TKA experts highlights the importance of wound management in optimizing TKA outcomes. The consensus framework provides a basis for future research, guidance to reduce variability in patient outcomes, and can help inform recommendations for wound management in TKA.
Fulltext Pre-existing liver disease is associated with poor outcome in patients with SARS CoV2 infection; The APCOLIS Study (APASL COVID-19 Liver Injury Spectrum Study)

Sarin SK, Choudhury A, Lau GK, Zheng MH, Ji D, Abd-Elsalam S, et al.

Hepatol Int, 2020 Sep;14(5):690-700.
PMID: 32623632 DOI: 10.1007/s12072-020-10072-8

BACKGROUND AND AIMS: COVID-19 is a dominant pulmonary disease, with multisystem involvement, depending upon comorbidities. Its profile in patients with pre-existing chronic liver disease (CLD) is largely unknown. We studied the liver injury patterns of SARS-Cov-2 in CLD patients, with or without cirrhosis.
METHODS: Data was collected from 13 Asian countries on patients with CLD, known or newly diagnosed, with confirmed COVID-19.
RESULTS: Altogether, 228 patients [185 CLD without cirrhosis and 43 with cirrhosis] were enrolled, with comorbidities in nearly 80%. Metabolism associated fatty liver disease (113, 61%) and viral etiology (26, 60%) were common. In CLD without cirrhosis, diabetes [57.7% vs 39.7%, OR = 2.1 (1.1-3.7), p = 0.01] and in cirrhotics, obesity, [64.3% vs. 17.2%, OR = 8.1 (1.9-38.8), p = 0.002] predisposed more to liver injury than those without these. Forty three percent of CLD without cirrhosis presented as acute liver injury and 20% cirrhotics presented with either acute-on-chronic liver failure [5 (11.6%)] or acute decompensation [4 (9%)]. Liver related complications increased (p
Correction to: Acute-on-chronic liver failure: consensus recommendations of the Asian Pacific association for the study of the liver (APASL): an update

Sarin SK, Choudhury A, Sharma MK, Maiwall R, Al Mahtab M, Rahman S, et al.

Hepatol Int, 2019 11;13(6):826-828.
PMID: 31595462 DOI: 10.1007/s12072-019-09980-1

The article Acute-on-chronic liver failure: consensus recommendations of the Asian Pacific association for the study of the liver (APASL): an update, written by [Shiv Sarin], was originally published electronically on the publisher's internet portal (currently SpringerLink) on June 06, 2019 without open access.
Fulltext Acute-on-chronic liver failure: consensus recommendations of the Asian Pacific association for the study of the liver (APASL): an update

Sarin SK, Choudhury A, Sharma MK, Maiwall R, Al Mahtab M, Rahman S, et al.

Hepatol Int, 2019 Jul;13(4):353-390.
PMID: 31172417 DOI: 10.1007/s12072-019-09946-3

The first consensus report of the working party of the Asian Pacific Association for the Study of the Liver (APASL) set up in 2004 on acute-on-chronic liver failure (ACLF) was published in 2009. With international groups volunteering to join, the "APASL ACLF Research Consortium (AARC)" was formed in 2012, which continued to collect prospective ACLF patient data. Based on the prospective data analysis of nearly 1400 patients, the AARC consensus was published in 2014. In the past nearly four-and-a-half years, the AARC database has been enriched to about 5200 cases by major hepatology centers across Asia. The data published during the interim period were carefully analyzed and areas of contention and new developments in the field of ACLF were prioritized in a systematic manner. The AARC database was also approached for answering some of the issues where published data were limited, such as liver failure grading, its impact on the 'Golden Therapeutic Window', extrahepatic organ dysfunction and failure, development of sepsis, distinctive features of acute decompensation from ACLF and pediatric ACLF and the issues were analyzed. These initiatives concluded in a two-day meeting in October 2018 at New Delhi with finalization of the new AARC consensus. Only those statements, which were based on evidence using the Grade System and were unanimously recommended, were accepted. Finalized statements were again circulated to all the experts and subsequently presented at the AARC investigators meeting at the AASLD in November 2018. The suggestions from the experts were used to revise and finalize the consensus. After detailed deliberations and data analysis, the original definition of ACLF was found to withstand the test of time and be able to identify a homogenous group of patients presenting with liver failure. New management options including the algorithms for the management of coagulation disorders, renal replacement therapy, sepsis, variceal bleed, antivirals and criteria for liver transplantation for ACLF patients were proposed. The final consensus statements along with the relevant background information and areas requiring future studies are presented here.
Fulltext Guidelines for the use and interpretation of assays for monitoring autophagy (3rd edition)

Klionsky DJ, Abdelmohsen K, Abe A, Abedin MJ, Abeliovich H, Acevedo Arozena A, et al.

Autophagy, 2016;12(1):1-222.
PMID: 26799652 DOI: 10.1080/15548627.2015.1100356
Fulltext Guidelines for the use and interpretation of assays for monitoring autophagy (4th edition)1

Klionsky DJ, Abdel-Aziz AK, Abdelfatah S, Abdellatif M, Abdoli A, Abel S, et al.

Autophagy, 2021 Jan;17(1):1-382.
PMID: 33634751 DOI: 10.1080/15548627.2020.1797280

In 2008, we published the first set of guidelines for standardizing research in autophagy. Since then, this topic has received increasing attention, and many scientists have entered the field. Our knowledge base and relevant new technologies have also been expanding. Thus, it is important to formulate on a regular basis updated guidelines for monitoring autophagy in different organisms. Despite numerous reviews, there continues to be confusion regarding acceptable methods to evaluate autophagy, especially in multicellular eukaryotes. Here, we present a set of guidelines for investigators to select and interpret methods to examine autophagy and related processes, and for reviewers to provide realistic and reasonable critiques of reports that are focused on these processes. These guidelines are not meant to be a dogmatic set of rules, because the appropriateness of any assay largely depends on the question being asked and the system being used. Moreover, no individual assay is perfect for every situation, calling for the use of multiple techniques to properly monitor autophagy in each experimental setting. Finally, several core components of the autophagy machinery have been implicated in distinct autophagic processes (canonical and noncanonical autophagy), implying that genetic approaches to block autophagy should rely on targeting two or more autophagy-related genes that ideally participate in distinct steps of the pathway. Along similar lines, because multiple proteins involved in autophagy also regulate other cellular pathways including apoptosis, not all of them can be used as a specific marker for bona fide autophagic responses. Here, we critically discuss current methods of assessing autophagy and the information they can, or cannot, provide. Our ultimate goal is to encourage intellectual and technical innovation in the field.