bluuebunny/crossref_metadata_2025_split huggingface dataset:
Dynamical systems approach to evolution–development congruence: Revisiting Haeckel's recapitulation theory
Authors: Kohsokabe Takahiro , Kaneko Kunihiko 
Published: February 2021

AbstractIt is acknowledged that embryonic development has a tendency to proceed from common toward specific. Ernst Haeckel raised the question of why that tendency prevailed through evolution, and the question remains unsolved. Here, we revisit Haeckel's recapitulation theory, that is, the parallelism between evolution and development through numerical evolution and dynamical systems theory. By using intracellular gene expression dynamics with cell‐to‐cell interaction over spatially aligned cells to represent the developmental process, gene regulation networks (GRN) that govern these dynamics evolve under the selection pressure to achieve a prescribed spatial gene expression pattern. For most numerical evolutionary experiments, the evolutionary pattern changes over generations, as well as the developmental pattern changes governed by the evolved GRN exhibit remarkable similarity. Changes in both patterns consisted of several epochs where stripes are formed in a short time, whereas for other temporal regimes, the pattern hardly changes. In evolution, these quasi‐stationary generations are needed to achieve relevant mutations, whereas, in development, they are due to some gene expressions that vary slowly and control the pattern change. These successive epochal changes in development and evolution are represented as common bifurcations in dynamical systems theory, regulating working network structure from feedforward subnetwork to those containing feedback loops. The congruence is the correspondence between successive acquisitions of subnetworks through evolution and changes in working subnetworks in development. Consistency of the theory with the segmentation gene‐expression dynamics is discussed. Novel outlook on recapitulation and heterochrony are provided, testable experimentally by the transcriptome and network analysis.
Genetic counselors' experiences with transgender individuals in prenatal and preconception settings
Authors: Ruderman Maggie , Berro Tala , Torrey Sosa Lillian , Zayhowski Kimberly 
Published: February 2021

AbstractMany transgender individuals want to have children and are pursuing reproductive care. Limited research has described the experiences of transgender individuals during pregnancy, and no known studies have examined reproductive genetic counseling sessions with this patient population. To understand what topics and considerations are explored within this sector of reproductive care, prenatal and preconception genetic counselors that have seen a transgender patient and/or transgender partner of a patient were recruited through an email blast to members of the National Society of Genetic Counselors. Nine genetic counselors completed phone interviews. Content analysis was used to identify, quantify, and examine the concepts within the transcripts. Six major themes emerged: (1) Trans individuals were referred for common genetic counseling indications, (2) genetic counselors were driven to think of more inclusive language, (3) genetic counselors considered ways to make written materials more inclusive, (4) trans individuals expressed discomforts in the prenatal/preconception setting, (5) genetic counselors observed challenges with the care team, and (6) genetic counselors felt underprepared. This study identifies areas within reproductive spaces of genetic counseling that could be more inclusive, particularly relating to commonly used gendered language and written materials, and provides training recommendations for genetic counselors. Additionally, we outline the reported areas of discrimination for these patients and partners, and discuss ways that genetic counselors can be advocates for respectful and equitable care within their clinics.
Mortality, morbidity, and failure to rescue in hepatopancreatoduodenectomy: An analysis of patients registered in the National Clinical Database in Japan
Authors: Endo Itaru , Hirahara Norimichi , Miyata Hiroaki , Yamamoto Hiroyuki , Matsuyama Ryusei , Kumamoto Takafumi , Homma Yuki , Mori Masaki , Seto Yasuyuki , Wakabayashi Go , Kitagawa Yuko , Miura Fumihiko , Kokudo Norihiro , Kosuge Tomoo , Nagino Masato , Horiguchi Akihiko , Hirano Satoshi , Yamaue Hiroki , Yamamoto Masakazu , Miyazaki Masaru 
Published: February 2021

AbstractBackgroundThe high operative mortality rate after hepatopancreatoduodenectomy (HPD) is still a major issue. The present study explored why operative mortality differs significantly due to hospital volume.MethodSurgical case data were extracted from the National Clinical Database (NCD) in Japan from 2011 to 2014. Surgical procedures were categorized as major (≥2 sections) and minor (<2 sections) hepatectomy. Hospitals were categorized according to the certification system by the Japanese Society of Hepato‐Biliary‐Pancreatic Surgery (JSHBPS) based on the number of major hepato‐biliary‐pancreatic surgeries performed per year. The FTR rate was defined as death in a patient with at least one postoperative complication.ResultsA total of 422 patients who underwent HPD were analyzed. The operative mortality rates in board‐certified A training institutions, board‐certified B training institutions, and non‐certified institution were 7.2%, 11.6%, and 21.4%, respectively. Multiple logistic regression showed that certified A institutions, major hepatectomy, and blood transfusion were the predictors of operative mortality. Failure to rescue rates were lowest in certified A institutions (9.3%, 17.0%, and 33.3% in certified A, certified B, and non‐certified, respectively).ConclusionsTo reduce operative mortality after HPD, further centralization of this procedure is desirable. Future studies should clarify specific ways to improve the failure‐to‐rescue rates in certified institutions.
Proposal of a novel H category‐based classification of colorectal liver metastases based on a Japanese nationwide survey
Authors: Beppu Toru , Imai Katsunori , Honda Goro , Sakamoto Katsunori , Kobayashi Shin , Endo Itaru , Hasegawa Kiyoshi , Kotake Kenjiro , Itabashi Michio , Hashiguchi Yojiro , Kotera Yoshihito , Yamaguchi Tatsuro , Tabuchi Ken , Kobayashi Hirotoshi , Yamaguchi Kensei , Morita Satoshi , Kikuchi Ken , Miyazaki Masaru , Sugihara Kenichi , Yamamoto Masakazu , Takahashi Keiichi ,   Joint Committee for Nationwide Survey on Colorectal Liver Metastasis
Published: February 2021

AbstractBackgroundThe conventional H category‐based classification for colorectal liver metastases (CRLM) was created by equal weighting of tumor number and tumor size; however, our previous nomogram to predict postoperative disease‐free survival demonstrated that CRLM ≥5 as a parameter provided 4.5 times greater impact compared with a largest CRLM size >5 cm.MethodsA total of 3815 patients newly diagnosed with CRLM between 2005 and 2007, including 2220 resectable cases, were investigated. Six groups were created based on largest lesion size (≤ 5 vs >5 cm) and lesion number (1, 2‐4, and ≥5).ResultsThe novel (n) H1, nH2, and nH3 categories were defined as solitary lesions with a size ≤5 cm; lesions other than nH1 or nH3; and ≥5 lesions with any lesion size, respectively. In the resectable cohort, the 5‐year cumulative overall survival rates were 64.0%, 53.5%, and 42.6% in the nH1, nH2, and nH3 groups, respectively (P < .001), and no significant differences were observed between the conventional H2 and H3 categories. In the overall cohort, the discrimination ability of the two classifications were comparable.ConclusionThe novel H category‐based classification might be beneficial in predicting overall survival in patients with CRLM independent of their resectability.
Synthesis of 4H‐chromene‐isoxazole hybrids via ortho‐hydroxy directing cyclization of isoxazole‐styrenes and Michael addition of imino‐chromenes in aqueous medium
Authors: Nagaraju Sakkani , Sathish Kota , Kashinath Dhurke 
Published: February 2021

AbstractA green, efficient, and one‐pot method synthesis of functionalized 4H‐chromene‐isoxazole hybrids is reported via o‐hydroxy group directing cyclization of isoxazole‐styrenes and Michael addition of 3,5‐dimethyl‐4‐nitroisoxazole on 2‐imino‐2H‐chromene‐3‐carbonitrile (independent methods). The developed methodology was further extended for nitromethane, malononitrile, and alkylcyanoacetates as Michael donors.
Attrition in HIV care following HIV diagnosis: a comparison of the pre‐UTT and UTT eras in South Africa
Authors: Onoya Dorina , Hendrickson Cheryl , Sineke Tembeka , Maskew Mhairi , Long Lawrence , Bor Jacob , Fox Matthew P. 
Published: February 2021

Abstract
IntroductionPolicies for Universal Test & Treat (UTT) and same‐day initiation (SDI) of antiretroviral therapy (ART) were instituted in South Africa in September 2016 and 2017 respectively. However, there is limited evidence on whether these changes have improved patient retention after HIV diagnosis.MethodsWe enrolled three cohorts of newly diagnosed HIV‐infected adults from two primary health clinics in Johannesburg from April to November 2015 (Pre‐UTT, N = 144), May‐September 2017 (UTT, N = 178) and October‐December 2017 (SDI, N = 88). A baseline survey was administered immediately after HIV diagnosis after which follow‐up using clinical records (paper charts, electronic health records and laboratory data) ensued for 12 months. The primary outcome was patient loss to follow‐up (being >90 days late for the last scheduled appointment) at 12 months post‐HIV diagnosis. We modelled attrition across HIV policy periods with Cox proportional hazard regression.ResultsOverall, 410 of 580 screened HIV‐positive patients were enrolled. Overall, attrition at 12 months was 30% lower in the UTT guideline period (38.2%) compared to pre‐UTT (47.2%, aHR 0.7, 95% CI: 0.5 to 1.0). However, the total attrition was similar between the SDI (47.7%) and pre‐UTT cohorts (aHR 1.0, 95% CI: 0.7 to 1.5). Older age at HIV diagnosis (aHR 0.5 for ≥40 vs. 25 to 29 years, 95% CI: 0.3 to 0.8) and being in a non‐marital relationship (aHR 0.5 vs. being single, 95% CI: 0.3 to 0.8) protected against LTFU at 12 months, whereas LTFU rates increased with longer travel time to the diagnosing clinic (aHR 1.8 for ≥30 minutes vs. ≤15 minutes, 95% CI: 1.1 to 3.1). In analyses adjusted for the time‐varying ART initiation status, compared to the pre‐ART period of care, the hazard of on‐ART LTFU was 90% higher among participants diagnosed under the SDI policy compared to pre‐UTT (aHR 1.9, 95% CI: 1.1 to 2.9).ConclusionsOverall, nearly two‐fifths of HIV positive patients are likely to disengage from care by 12 months after HIV diagnosis under the new SDI policy. Furthermore, the increase in on‐ART patient attrition after the introduction of the SDI policy is cause for concern. Further research is needed to determine the best way for rapidly initiating patients on ART and also reducing long‐term attrition from care.
Improved Quantification of Myocardium Scar in Late Gadolinium Enhancement Images: Deep Learning Based Image Fusion Approach
Authors: Fahmy Ahmed S. , Rowin Ethan J. , Chan Raymond H. , Manning Warren J. , Maron Martin S. , Nezafat Reza 
Published: February 2021

BackgroundQuantification of myocardium scarring in late gadolinium enhanced (LGE) cardiac magnetic resonance imaging can be challenging due to low scar‐to‐background contrast and low image quality. To resolve ambiguous LGE regions, experienced readers often use conventional cine sequences to accurately identify the myocardium borders.PurposeTo develop a deep learning model for combining LGE and cine images to improve the robustness and accuracy of LGE scar quantification.Study TypeRetrospective.PopulationA total of 191 hypertrophic cardiomyopathy patients: 1) 162 patients from two sites randomly split into training (50%; 81 patients), validation (25%, 40 patients), and testing (25%; 41 patients); and 2) an external testing dataset (29 patients) from a third site.Field Strength/Sequence1.5T, inversion‐recovery segmented gradient‐echo LGE and balanced steady‐state free‐precession cine sequencesAssessmentTwo convolutional neural networks (CNN) were trained for myocardium and scar segmentation, one with and one without LGE‐Cine fusion. For CNN with fusion, the input was two aligned LGE and cine images at matched cardiac phase and anatomical location. For CNN without fusion, only LGE images were used as input. Manual segmentation of the datasets was used as reference standard.Statistical TestsManual and CNN‐based quantifications of LGE scar burden and of myocardial volume were assessed using Pearson linear correlation coefficients (r) and Bland–Altman analysis.ResultsBoth CNN models showed strong agreement with manual quantification of LGE scar burden and myocardium volume. CNN with LGE‐Cine fusion was more robust than CNN without LGE‐Cine fusion, allowing for successful segmentation of significantly more slices (603 [95%] vs. 562 (89%) of 635 slices; P < 0.001). Also, CNN with LGE‐Cine fusion showed better agreement with manual quantification of LGE scar burden than CNN without LGE‐Cine fusion (%ScarLGE‐cine = 0.82 × %Scarmanual, r = 0.84 vs. %ScarLGE = 0.47 × %Scarmanual, r = 0.81) and myocardium volume (VolumeLGE‐cine = 1.03 × Volumemanual, r = 0.96 vs. VolumeLGE = 0.91 × Volumemanual, r = 0.91).Data ConclusionCNN based LGE‐Cine fusion can improve the robustness and accuracy of automated scar quantification.Level of Evidence3Technical Efficacy1
Assessment of Repeatability, Reproducibility, and Performances of T2 Mapping‐Based Radiomics Features: A Comparative Study
Authors: Crombé Amandine , Buy Xavier , Han Fei , Toupin Solenn , Kind Michèle 
Published: February 2021

BackgroundMagnetic resonance imaging (MRI)‐based radiomics features (RFs) quantify tumors radiological phenotypes but are sensitive to postprocessing parameters, including the intensity harmonization technique (IHT), while mappings enable objective quantitative assessment.PurposeTo investigate whether T2 mapping could improve repeatability, reproducibility, and performances of radiomics compared to conventional T2‐weighted imaging (T2WI).Study TypeProspective.SubjectsTwenty‐six healthy adults.Field Strength/SequenceRespiratory‐trigged radial turbo spin echo (TSE) multiecho T2 mapping (prototype) and conventional TSE T2WI of the abdomen were acquired twice at 1.5 T.AssessmentT2 maps were reconstructed using a two‐parameter exponential fitting model. Volumes‐of‐interest (VOIs) were manually drawn in six tissues: liver, kidney, pancreas, muscle, bone, and spleen. After co‐registration, conventional T2WIs were processed with two IHTs (standardization [std] and histogram‐matching [HM]) resulting in four paired input image types: initial T2WI, T2WIstd, T2WIHM, and T2‐map. VOIs were propagated to extract 45 RFs from MRI‐1 and MRI‐2 of each image type (LIFEx, v5.10).Statistical TestsInfluence of the input data type on RF values was evaluated with analysis of variance. RFs test–retest repeatability and reproducibility over multiple segmentations were evaluated with intra‐class correlation coefficient (ICC). Correlations between k‐means clusters and the six tissues depending on the RFs dataset were investigated with adjusted‐Rand‐index (ARI).ResultsAbout 41 of 45 (91.1%) RFs were significantly influenced by the input image type (P values < 0.05), which was the most influential factor on repeatability of RFs (P‐value < 0.05). Repeatability ICCs from T2‐map displayed intermediate values between the initial T2WI (range: 0.407–0.736) and the T2WIHM (range: 0.724–0.817). The number of RFs with interobserver and intraobserver reproducibility ICCs ≥ 0.90 was 37/45 (82.2%) for T2WIHM, 33/45 (73.3%) for T2WIstd, 31/45 (68.9%) for T2 map, and 25/45 (55.6%) for the initial T2WI. T2 map provided the best tissue discrimination (ARI = 0.414 vs. 0.157 with T2WIHM).Data ConclusionT2 mapping provided RFs with moderate to substantial repeatability and reproducibility ICCs, along with the most preserved discriminative information.Level of Evidence1Technical Efficacy1
Progression of Plaque Burden of Intracranial Atherosclerotic Plaque Predicts Recurrent Stroke/Transient Ischemic Attack: A Pilot Follow‐Up Study Using Higher‐Resolution MRI
Authors: Shi Zhang , Li Jing , Zhao Ming , Zhang Xuefeng , Degnan Andrew J. , Mossa‐Basha Mahmud , Saloner David , Lu Jianping , Liu Qi , Zhu Chengcheng 
Published: February 2021

BackgroundPatients with intracranial atherosclerotic disease (ICAD) have a high frequency of stroke recurrence. However, there has been little investigation into the prognostic value of higher‐resolution magnetic resonance imaging (HR‐MRI).PurposeTo investigate the use of intracranial atherosclerotic plaques features in predicting risk of recurrent cerebrovascular ischemic events using HR‐MRI.Study TypeProspective.PopulationFifty‐eight patients with acute/subacute stroke (N = 46) or transient ischemic attack (N = 12).Field Strength/SequenceA 3.0 T, 3D time‐of‐flight gradient echo sequence and T1‐ and T2‐weighted fast spin echo sequences with 0.31 x 0.39 mm2 in‐plane resolution, twice (with >3 months between scans) following the initial event.AssessmentPatients were also followed clinically for recurrent ischemic events for up to 48 months or until a subsequent event occurred. The degree of stenosis, plaque burden (PB), minimal lumen area (MLA), and contrast enhancement ratio were assessed at each scanning session and the percentage change of each over time was calculated.Statistical TestsUnivariable and multivariable Cox regression analyses were used to calculate the hazard ratio (HR) and 95% confidence interval (CI) for predicting recurrent events.ResultsThe mean time interval between baseline and follow‐up MRI scans was 6.2 ± 4.1 months. After the second MRI scan, 20.7% of patients (N = 12) had experienced ipsilateral recurrent TIA/stroke within 10.9 ± 9.2 months. Univariable analyses showed that baseline triglyceride, percentage change of PB, and progression of PB were significantly associated with recurrent events (all P < 0.05). Multivariable Cox regression indicated that progression of PB (HR, 6.293; 95% CI, 1.620–24.444; P < 0.05) was a significant independent imaging feature for recurrent ischemic events.Data ConclusionProgression of PB was independently associated with recurrent ischemic cerebrovascular events. HR‐MRI may help risk stratification of patients at risk of recurrent stroke.Level of Evidence2Technical EfficacyStage 4
Brain Abscess Apparent Diffusion Coefficient is Associated With Microbial Culture Yields
Authors: Toh Cheng Hong , Siow Tiing Yee , Wong Alex Mun‐Ching , Castillo Mauricio 
Published: February 2021

BackgroundObtaining pus for microbial cultures is one of the surgical aims in patients with brain abscess. Predictors of microbial yields are necessary as they help in treatment planning.PurposeTo investigate the relationship between microbial culture yields of brain abscesses and their apparent diffusion coefficient (ADC) values and clinical characteristics.Study TypeRetrospective.SubjectsEighty‐four patients diagnosed with brain abscess by surgery and histopathology (59 with positive abscess cultures).Field Strength/SequenceDiffusion‐weighted, T2‐weigthed, and contrast‐enhanced T1‐weighted imaging at 1.5 T and 3 T.AssessmentContrast‐enhanced T1‐weighted images were co‐registered to ADC maps. Three neuroradiologists determined abscess imaging characteristics (distribution, location, and ventricular rupture), and two measured abscess volumes and ADC values. Clinical characteristics collected included sex, age, fever, underlying diseases, infection sources, white blood cell count, percentage of segmented neutrophils, C‐reactive protein level, regimen and duration of empirical antibiotics, and types of surgery.Statistical TestsInterobserver differences were assessed with Fleiss kappa and intraclass correlation coefficients. The differences in clinical and imaging factors between the positive and negative culture groups were compared with Chi‐square analysis or Student's t test. All factors were subjected to multivariable logistic regression analysis to assess their associations with microbial culture yields, and factors with statistical significance were evaluated with receiver operating characteristic curve analysis to assess their diagnostic performance in discriminating the two groups.ResultsMean ADC (×10−6 mm2/s) of culture‐negative abscesses (841 ± 173) was significantly higher (P < 0.05) than that of culture‐positive abscesses (536 ± 90). On multivariable analysis, mean ADC was the only significant factor (P < 0.05) related to culture yields. With 660 as the cutoff value, the sensitivity, specificity, and accuracy of ADC for discriminating culture yields were 93.2%, 88.0%, and 91.7%, respectively.Data ConclusionADC could be used to discriminate between culture‐positive and culture‐negative abscesses.Evidence Level4Technical EfficacyStage 2
LC‐MALDI‐TOF ISD MS analysis is an effective, simple and rapid method of investigation for histones characterization: Application to EBV lymphoblastoid cell lines
Authors: De Benedittis Selene , Gaspari Marco , Magariello Angela , Spadafora Patrizia , Citrigno Luigi , Romeo Nelide , Qualtieri Antonio 
Published: February 2021

AbstractThis contribution is the result of our progressive engagement to develop and to apply a top‐down liquid chromatography (LC) matrix‐assisted laser desorption/ionization (MALDI) time‐of‐flight (TOF) (LC‐MALDI‐TOF) analysis for the histone post‐translational modifications (PTMs) and variants characterization, mainly in order to provide comprehensive and fast results. The histone post‐translational modifications and the differential expression of the histone variants play an essential role both in the DNA packaging mechanism in chromosomes and in the regulation of gene expression in different cellular processes, also in response to molecular agents of environmental origin. This epigenetic mechanism is widely studied in different field such as cellular differentiation, development and in the understanding of mechanisms underlying diseases. The characterization of histone PTMs has traditionally performed by antibodies‐based assay, but immunological methods have significant limits, and today systems that use mass spectrometry are increasingly employed. We evaluated an in‐source decay (ISD) analysis for the histone investigation on human lymphoblastoid cells, and by this approach, we were able to identify and quantify several PTMs such as the di‐methylation in the lysine 20 and the acetylation in the lysine 16 in H4 and the mono‐methylation, di‐methylation and trimethylations at K9 of the histone H3.1. Moreover, we detected and quantified in the same H2B spectrum the prevalent H2B 1C/2E type but also the minor H2B 1D, 1M and 1B/1L/1N, 1O/2F, 1J/1K variants. In this work, we show that MALDI‐ISD represents an excellent methodology to obtain global information on histone PTMs and variants from cells in culture, with rapidity and simplicity of execution. Finally, this is a useful approach to get label‐free relative quantitative data of histone variants and PTMs.