bluuebunny/crossref_metadata_2025 huggingface dataset:
An error‐correction and anti‐interference coding method for tracking big‐data information of commodities
Authors: Wan Jiaxin , Chen Lan , Tong Mei Song
Published: September 2020

The paper presents a novel efficient encoding and decoding method for self‐correction and anti‐interference used in big data product tracing system based on the cyclic code theory. The principle of constructing code set is first illustrated. Then the specific encoding and decoding methods suitable for the algebra rules are invented in sequence for efficiency. At last, to test the new coding system, the paper accelerates the decoding time by OpenMP more than 36 times. The error‐correcting code presents its perfect recovery property with a recovery rate of more than 95% under 60% damage rate. In analyzing its efficiency, the encoding process only costs 0.0045 second in average while the time of decoding method will increase with the damage rate’s ascending, but it can be controlled within 16 seconds. In comparison to other coding patterns in the references, the newly error‐correcting and anti‐interference coding method achieves a balance in complexity, encoding rate, and decoding time with its priority in recovering rate under the damage rate of 60%.
Efficient transient thermal analysis based on spectral element time domain method with curvilinear hexahedrons
Authors: Xue Yilun , Mi Jiamei , Wen Pengfei , Ren Qiang , Zhou Yuanguo
Published: September 2020

In this paper, a three‐dimensional transient thermal simulation algorithm based on spectral element method is proposed. This algorithm uses distorted hexahedron for mesh generation, which not only keeps the high efficiency of hexahedron element calculation, but also improves the flexibility of mesh generation. It supports efficient forward difference and unconditionally stable backward difference in time step. Through practical examples and comparison with commercial software, the reliability and stability of the algorithm are verified, and it has obvious advantages in memory consumption and computing efficiency.
Virtual mechanical tests out‐perform morphometric measures for assessment of mechanical stability of fracture healing in vivo
Authors: Schwarzenberg Peter , Klein Karina , Ferguson Stephen J. , von Rechenberg Brigitte , Darwiche Salim , Dailey Hannah L.
Published: September 2020

Finite element analysis with models derived from computed tomography (CT) scans is potentially powerful as a translational research tool because it can achieve what animal studies and cadaver biomechanics cannot—low‐risk, noninvasive, objective assessment of outcomes in living humans who have actually experienced the injury, or treatment being studied. The purpose of this study was to assess the validity of CT‐based virtual mechanical testing with respect to physical biomechanical tests in a large animal model. Three different tibial osteotomy models were performed on 44 sheep. Data from 33 operated limbs and 20 intact limbs was retrospectively analyzed. Radiographic union scoring was performed on the operated limbs and physical torsional tests were performed on all limbs. Morphometric measures and finite element models were developed from CT scans and virtual torsional tests were performed to assess healing with four material assignment techniques. In correlation analysis, morphometric measures and radiographic scores were unreliable predictors of biomechanical rigidity, while the virtual torsion test results were strongly and significantly correlated with measured biomechanical test data, with high absolute agreement. Overall, the results validated the use of virtual mechanical testing as a reliable in vivo assessment of structural bone healing. This method is readily translatable to clinical evaluation for noninvasive assessment of the healing progress of fractures with minimal risk. Clinical significance: virtual mechanical testing can be used to reliably and noninvasively assess the rigidity of a healing fracture using clinical‐resolution CT scans and that this measure is superior to morphometric and radiographic measures.
Metronidazole and amoxicillin for patients with periodontitis and diabetes mellitus: 5‐year secondary analysis of a randomized controlled trial
Authors: Cruz Daniele Ferreira da , Duarte Poliana Mendes , Figueiredo Luciene Cristina , da Silva Hélio Doyle Pereira , Retamal‐Valdes Belén , Feres Magda , Miranda Tamires Szeremeske
Published: September 2020

Background

The aim of this study was to perform a 5‐year follow‐up analysis of a previously‐published randomized trial (RCT) evaluating the 2‐years effects of metronidazole (MTZ) plus amoxicillin (AMX) as adjuncts to scaling and root planing (SRP) in the treatment of periodontitis in type 2 diabetic patients.

Methods

Volunteers who received periodontal treatment in the aforementioned RCT were selected for clinical and microbiological evaluation. Patients did not receive regular supportive periodontal therapy (SPT) from 2 to 5 years post‐treatment.

Results

Of the patients enrolled in the RCT, 43% entered this study (n = 10/control and 15/test group). Most of clinical parameter values, including the number of sites with probing depth ≥ 5 mm (primary outcome variable), were reduced at 5 years post‐therapy when compared with baseline in the antibiotic‐treated group (P < 0.05), but presented higher values than those at 2 years (P < 0.05). The mean proportions of microbial complexes did not differ between MTZ+AMX+SRP and SRP‐only groups at 5 years post‐treatment (P > 0.05).

Conclusion

Diabetic patients treated with adjunctive MTZ+AMX were better maintained over a period of 5 years than those treated with SRP only. However, the clinical and microbiological benefits obtained up to 2 years post‐treatment were not fully sustained in these patients who did not receive SPT between 2 and 5 years post‐treatment.
Modelling Last Glacial Maximum ice cap with the Parallel Ice Sheet Model to infer palaeoclimate in south‐west Turkey
Authors: Candaş Adem , Sarikaya M. Akif , KÖSE Oğuzhan , Şen Ömer L. , Çiner Attila
Published: September 2020

Modelling palaeoglaciers in mountainous terrain is challenging due to the need for detailed ice flow computations in relatively narrow and steep valleys, high‐resolution climate estimations, knowledge of pre‐ice topography, and proxy‐based palaeoclimate forcing. The Parallel Ice Sheet Model (PISM), a numerical model that approximates glacier sliding and deformation to simulate large ice sheets such as Greenland and Antarctica, was recently adapted to alpine environments. In an attempt to reconstruct the climate conditions during the Last Glacial Maximum (LGM) on Mount Dedegöl in SW Turkey, we used PISM and explored palaeoglacier dynamics at high spatial resolution (100 m) in a relatively small domain (225 km2). Palaeoice‐flow fields were modelled as a function of present temperature and precipitation. Nine different palaeoclimate simulations were run to reach the steady‐state glacier extents and the modelled glacial areas were compared with the field‐based and chronologically well‐established ice extents. Although our results provide a non‐unique solution, best‐fit scenarios indicate that the LGM climate on Mount Dedegöl was between 9.2 and 10.6 °C colder than today, while precipitation levels were the same as today. More humid (20% wetter) or arid (20% drier) conditions than today bring the palaeotemperature estimates to 7.7–8.8 or 11.5–13.2 °C lower than present, respectively.
Sedimentary evidence and luminescence and ESR dating of Early Pleistocene high lake levels of Megalake Tengger, northwestern China
Authors: Yuxin Fan , Zhenjun Li , Guangliang Yang , Shuangwen Yi , Qingsong Zhang , Wenhao Liu , Xuesong Mou
Published: September 2020

The timing of high lake‐level stands during the Late Pleistocene in western China remains controversial. Here we report new results from Megalake Tengger based on a study of palaeo‐shorelines and a drill core from Baijian Lake in the northwestern Tengger Desert. Multiple dating methods, based on luminescence signals (quartz optically stimulated luminescence, K‐feldspar post infrared‐infrared stimulated luminescence) and electron spin resonance signals of quartz, were used to date beach sands from palaeo‐shoreline profiles at altitudes of ~1310 m (+20 m above lake level), ~1320 m (+30 m) and ~1350 m (+60 m), and from the top 20 m of sandy sediments from the drill core obtained from the modern beach of Baijian Lake. The dating results show that high lake‐level stands associated with the previously reported Megalake Tengger (~1310–1320 m) occurred during the late Early to Middle Pleistocene, which is much earlier than previously reported. In addition, no geomorphological evidence of shorelines and sedimentary evidence from the drill core profile were found to support the previously reported Late Pleistocene lake levels. Our results indicate that the exact age of the previously reported ‘high lake level event’ in a large part of northwestern China during the Late Pleistocene needs to be re‐evaluated.
Influence of Quartz, Kaolin, and Organic Matter on the Critical Micelle Concentration of Tween Surfactants and their Application in Diesel‐Contaminated Soil Washing
Authors: Jantanaprasartporn Angkana , Tongcumpou Chantra , Tuntiwiwattanapun Nattapong
Published: September 2020

Surfactant solutions are commonly used for the remediation of petroleum‐contaminated soil due to their good petroleum removal performance, time‐saving capability, and cost effectiveness. However, applying surfactants in excess concentrations could make oil recovery difficult. Moreover, residual surfactants in soil are toxic to microorganisms and plants. Thus, it is crucial to identify a suitable surfactant concentration for soil washing applications. The main objective of this study was to evaluate the effect of soil minerals (quartz and kaolin) and organic matter (OM) on the critical micelle concentration (CMC) of polyethoxylated sorbitan ester surfactants (Tween 20, 40, 60, and 80) and its effect on diesel removal from diesel‐contaminated soil by soil washing. The results showed that Tween surfactants with shorter carbon chain lengths required higher CMC for diesel removal from quartz, while those with longer chains needed higher CMC for kaolin cleanup. FTIR results illustrated that oxygenated functional groups of Tween surfactants played an important role in their adsorption on quartz, while alkyl chains of Tween surfactants were responsible for their adsorption on kaolin. At a certain OM concentration, quartz and OM exhibited antagonistic effects, resulting in CMC reduction. In soil washing application, maximum diesel removal could be achieved from kaolin, in the presence of which surfactants exhibited the highest CMC. Based on FTIR results, the adsorbed surfactant could reduce the hydrophobicity of the kaolin surface, thus preventing the re‐deposition of detached diesel.
Intelligent pH indicator films containing anthocyanins extracted from blueberry peel for monitoring tilapia fillet freshness
Authors: Shi Ce , Zhang Jiaran , Jia Zhixin , Yang Xinting , Zhou Zhongyun
Published: September 2020

BACKGROUND

Fish spoilage leads to an increase in the pH value of the fish. A colorimetric pH indicator can be used to monitor fish spoilage and has been exploited in intelligent packaging because of its simplicity, practicality and low cost. The aim of this study was to develop two pH‐indicator films comprising starch (S), tara gum (TG), polyvinyl alcohol (PVA) and anthocyanins extracted from blueberry peel and the films were then used to monitor the freshness of tilapia fillets during storage at 25 and 4 °C.

RESULTS

The ultraviolet‐visible (UV‐visible) spectra and color of anthocyanins changed within pH 2–10. Fourier‐transform infrared spectroscopy, UV‐visible spectrophotometry and scanning electron microscopy certified that blueberry peel extract (BPE) had been introduced into the S/PVA and TG/PVA matrices. Visual color changes in the films occurred at pH 2–8. A freshness application test was conducted in tilapia fillets stored at 4 and 25 °C, and visual color changes in the films were observed. The TG/PVA/BPE film had a greater color difference (ΔE) from pink and transparent to dark yellow at 25 °C and to dark purple at 4 °C than ΔE of S/PVA/BPE film, which sufficiently correlated with the change of total volatile base nitrogen (TVB‐N) and total aerobic counts (TACs) of fillets.

CONCLUSION

It can be concluded that the color changes of TG/PVA/BPE films were corresponded with TVB‐N and TAC values of tilapia fillets, which presented great potential as a visual package label to monitor fish freshness at ambient and chilled temperatures. © 2020 Society of Chemical Industry
Reoperation cascade in postmastectomy breast reconstruction and its associated factors: Results from a long‐term population‐based study
Authors: Roberts Amanda , Baxter Nancy N. , Sutradhar Rinku , Lau Cindy , Zhong Toni
Published: September 2020

Background

Unplanned surgeries following postmastectomy breast reconstruction (PMBR) may be required to treat complications or to revise the reconstructed breast. The primary objective of this study was to examine factors that influenced unplanned reoperations after PMBR.

Methods

A retrospective cohort study using provincial databases in Ontario, Canada, was completed. Patients with breast cancer underwent mastectomy between April 2002 and March 2012 followed by immediate or delayed PMBR. Primary outcome was time from PMBR to unplanned reoperations measured in years. The Anderson‐Gill counting process model was used to estimate the risk of recurrent unplanned reoperations over time. Univariate and multivariate analyses were completed to examine the association between covariates.

Results

A total of 3066 women underwent PMBR and 51.7% had at least one unplanned reoperation. Unplanned breast reoperation was significantly associated with microsurgical tissue vs implant‐based reconstruction (hazard ratio [HR]: 1.27), radiation after PMBR (HR: 1.22), surgery at a nonteaching hospital (HR: 1.16), patient comorbidity score (HR: 1.02), and prior unplanned reoperations (HR: 1.25).

Conclusions

Our study provides important long‐term population‐level data regarding factors influencing unplanned reoperations after PMBR. Patients undergoing microsurgical PMBR or postmastectomy radiation had a higher rate of additional procedures. Every additional reoperation also increases the likelihood of unplanned reoperations resulting in a “reoperation cascade.”
Imaging the local biochemical content of native and injured intervertebral disc using Fourier transform infrared microscopy
Authors: Sloan Stephen R. , Wipplinger Christoph , Kirnaz Sertaç , Delgado Robert , Huang Steven , Shvets Gennady , Härtl Roger , Bonassar Lawrence J.
Published: September 2020

Alterations to the biochemical composition of the intervertebral disc (IVD) are hallmarks of aging and degeneration. Methods to assess biochemical content, such as histology, immunohistochemistry, and spectrophotometric assays, are limited in their ability to quantitatively analyze the spatial distribution of biochemical components. Fourier transform infrared (FTIR) microscopy is a biochemical analysis method that can yield both quantitative and high‐resolution data about the spatial distribution of biochemical components. This technique has been largely unexplored for use with the IVD, and existing methods use complex analytical techniques that make results difficult to interpret. The objective of the present study is to describe an FTIR microscopy method that has been optimized for imaging the collagen and proteoglycan content of the IVD. The method was performed on intact and discectomized IVDs from the sheep lumbar spine after 6 weeks in vivo in order to validate FTIR microscopy in healthy and degenerated IVDs. FTIR microscopy quantified collagen and proteoglycan content across the entire IVD and showed local changes in biochemical content after discectomy that were not observed with traditional histological methods. Changes in collagen and proteoglycans content were found to have strong correlations with Pfirrmann grades of degeneration. This study demonstrates how FTIR microscopy is a valuable research tool that can be used to quantitatively assess the local biochemical composition of IVDs in development, degeneration, and repair.
Methods to determine the kinetic performance limit of contemporary chromatographic techniques
Authors: Broeckhoven Ken , Desmet Gert
Published: September 2020

By combining separation efficiency data as a function of flow rate with the column permeability, the kinetic plot method allows to determine the limits of separation power (time vs. efficiency) of different chromatographic techniques and methods. The technique can be applied for all different types of chromatography (liquid, gas, or supercritical fluid), for different types of column morphologies (packed beds, monoliths, open tubular, micromachined columns), for pressure and electro‐driven separations and in both isocratic and gradient elution mode. The present contribution gives an overview of the methods and calculations required to correctly determine these kinetic performance limits and their underlying limitations.
A Gel Pad Designed to Measure Muscle Volume Using Freehand 3‐Dimensional Ultrasonography
Authors: Thomare Julien , Lacourpaille Lilian , McNair Peter J. , Crouzier Marion , Ellis Richard , Nordez Antoine
Published: September 2020

We developed an innovative gel pad that covers the entire lower leg to remove artifacts due to the pressure of the transducer in freehand 3‐dimensional ultrasonography. In comparison to the reference method in water, this study showed that this new method was valid (bias, 3.4 mL; limit of agreement, 7.7 mL for a volume of ≈220 mL) and reliable (coefficient of variation, <1.1%) for the measurement of gastrocnemius medialis muscle volume. Considering that it is easier to use than the water tank technique, it has much promise for volumetric measurement of many muscles.
How often are basic details of the research process mentioned in social science research papers?
Authors: Coates Adam
Published: September 2020

This study investigated whether basic details of the research process are mentioned in social science research articles. Five hundred empirical articles were sampled from the Social Sciences Citation Index. The frequency of omitted details was mixed. For central essential details, omission rates were: 0% for research purpose, 2% for data collection method, 8% for sample size, 20% for data analysis method, and 48% for sampling strategy. The analysis found that 56% of articles were missing one or more of these five details. For more peripheral details, omission rates were: 36% for limitations, 55% for ethical considerations, and 94% for foundational philosophy. Prevalence rates were varied when compared across different disciplines and between qualitative, quantitative, and mixed methods approaches. Possible causes for these findings include the use of secondary data, the view that certain details are not essential, and traditions in ethnographic writing. Those involved in academic publishing are invited to reflect on the basic details that are essential for their specialism and how reporting standards are enforced.
The Monocyte to High‐Density Lipoprotein Cholesterol Ratio in the Prediction for Atherosclerosis: A Retrospective Study in Adult Chinese Participants
Authors: Zhou Yaqing , Wang Liyi , Jia Limei , Lu Baojin , Gu Guoqiang , Bai Long , Cui Wei
Published: September 2020

The ratio of monocyte to high‐density lipoprotein cholesterol level (MHR) was a newly proposed inflammatory and oxidative stress marker. This study aimed to explore the association between MHR and Brachial‐ankle pulse wave velocity (Ba‐PWV) in adult Chinese participants. A total of 2029 participants were divided into two groups according to the Ba‐PWV: a high Ba‐PWV group (Ba‐PWV ≥1400 cm/s) and a low Ba‐PWV group (Ba‐PWV < 1400 cm/s). According to the cut‐off points of quartile of MHR, the participants were divided into four groups. The relationship between MHR and Ba‐PWV was analyzed. After adjusting for potential confounders, a non‐linear relationship between MHR and Ba‐PWV was found in the participants, and the inflection point was 7.78 in the non‐linear curve. On the left of the inflection point, MHR had a positive correlation with Ba‐PWV (OR = 1.17, 95% confidence interval (CI): 1.08 to 1.28, p < 0.01). However, there was no obvious relationship between MHR and Ba‐PWV on the right of the inflection point (OR = 0.96, 95% CI: 0.90 to 1.01, p = 0.117). Further demographic analysis demonstrated that the positive relationship between MHR and Ba‐PWV was found in the female participants with hypertension family history, but without a current history of hypertension, smoking, or drinking (p < 0.05). An increased MHR is a risk factor of atherosclerosis, which may predict the potential development of atherosclerosis. When the MHR is close to 7.78, it has the highest predictive value for the risk of atherosclerosis occurrence.
Constructing a Biomaterial to Simulate Extracellular Drug Transport in Solid Tumors
Authors: Huayamares Sebastian G. , Song Jimmy Y. , Huang Aric , Crowl Samuel R. , Groer Chad E. , Forrest M. Laird , Berkland Cory J.
Published: September 2020

Designing an in vitro model of the tumor extracellular microenvironment to screen intratumoral drugs is an active challenge. As recent clinical successes of human intratumoral therapies stimulate research on intratumoral delivery, a need for a 3D tumor model to screen intratumoral therapies arises. When injecting the drug formulation directly into the tumor, the biophysics affecting intratumoral retention must be considered; especially for biologic therapies, which may be dominated by extracellular transport mechanisms. Fibrotic regions in solid tumors are typically rich in collagen I fibers. Using shear rheology, head and neck tumors with higher collagen density show a higher stiffness. Similarly, the stiffness of the hyaluronic acid (HA) hydrogel models is increased by adding collagen fibers to model the bulk biomechanical properties of solid tumors. HA hydrogels are then used as intratumoral injection site simulators to model in vitro the retention of glatiramer acetate (GA) and polyethylene glycol (PEG) administered intratumorally. Both compounds are also injected in murine tumors and retention is studied ex vivo for comparison. Retention of GA in the hydrogels is significantly longer than PEG, analogous to the solid tumors, suggesting the utility of HA hydrogels with collagen I fibers for screening extracellular drug transport after intratumoral administration.
Organocatalytic Synthesis of Alkyne‐Functional Aliphatic Polycarbonates via Ring‐Opening Polymerization of an Eight‐Membered‐N‐Cyclic Carbonate
Authors: Bexis Panagiotis , De Winter Julien , Arno Maria C. , Coulembier Olivier , Dove Andrew P.
Published: September 2020

The synthesis of well‐defined propargyl‐functional aliphatic polycarbonates is achieved via the organocatalytic ring‐opening polymerization of prop‐2‐yn‐1‐yl 2‐oxo‐1,3,6‐dioxazocane‐6‐carboxylate (P‐8NC) using a wide variety of commercially available or readily made, shelf‐stable organocatalysts. The resulting homopolymers show low dispersities and end‐group fidelity, with the versatility of the system being demonstrated by the synthesis of telechelic copolymers and block copolymers with molar mass up to 40 kDa.
A preliminary examination of the bacterial, archaeal, and fungal rhizosphere microbiome in healthy and Phellinus noxius‐infected trees
Authors: Tsang Karen Sze Wing , Cheung Man Kit , Lam Regent Yau Ching , Kwan Hoi Shan
Published: September 2020

Phellinus noxius is a pathogenic fungus that causes brown root rot disease, resulting in a widespread tree and crop mortality in the tropics and subtropics. Early stages of this disease are largely asymptomatic, hindering early diagnosis and effective treatment. We hypothesized that P. noxius infection would alter the rhizosphere microbiome of infected trees, based on which diagnostic biomarkers could be developed. Here, we examined for the first time the bacterial, archaeal, and fungal rhizosphere microbiome in four species of healthy and P. noxius‐infected trees (Ficus microcarpa, Celtis sinensis, Mallotus paniculatus, and Cinnamomum camphora) using high‐throughput amplicon sequencing. Results revealed the dominance of Proteobacteria and Actinobacteria in bacteria, Crenarchaeota and Euryarchaeota in archaea, and Ascomycota and Basidiomycota in fungi. Phellinus noxius infection did not affect the alpha diversity of the bacterial rhizosphere microbiome in all four tree species but affected that of archaea and fungi in a tree species‐dependent manner. Infection with P. noxius only affected the bacterial rhizosphere composition in M. paniculatus but not the other three tree species. By contrast, P. noxius infection affected the composition of the archaeal and fungal rhizosphere microbiome in all four tree species. Collectively, these results suggest that potential diagnostic biomarkers for brown root rot disease are tree species‐specific and should be developed based on different taxonomic groups. Our study has provided insights into the rhizosphere microbiome in healthy and P. noxius‐infected trees and laid a solid foundation for future comprehensive studies.
Disease causing property analyzation of variants in 12 Chinese families with polycystic kidney disease
Authors: Dong Kexian , Liu Xiaogang , Jia Xueyuan , Miao Huanhuan , Ji Wei , Wu Jie , Huang Yun , Xu Lidan , Zhang Xuelong , Su Hui , Ji Guohua , Liu Peng , Guan Rongwei , Bai Jing , Fu Songbin , Zhou Xianli , Sun Wenjing
Published: September 2020

Background

Polycystic kidney disease (PKD) is an inherited disease that is life‐threatening. Multiple cysts are present in the bilateral kidneys of PKD patients. The progressively enlarged cysts cause structural damage and loss of kidney function.

Methods

This study examined and analyzed 12 families with polycystic kidney disease. Whole exome sequencing (WES) or whole genome sequencing (WGS) of the probands was performed to detect the pathogenic genes. The candidate gene segments for lineal consanguinity in the family were amplified by the nest PCR followed by Sanger sequencing. The variants were assessed by pathogenic and conservational property prediction analysis and interpreted according to the American College of Medical Genetics and Genomics.

Results

Nine of the 12 pedigrees were identified the disease causing variants. Among them, four novel variants in PKD1, c.6930delG:p.C2311Vfs*3, c.1216T>C:p.C406R, c.8548T>C:p.S2850P, and c.3865G>A:p.V1289M (NM_001009944.2) were detected. After assessment, the four novel variants were considered to be pathogenic variants and cause autosomal dominant polycystic kidney disease in family. The detected variants were interpreted.

Conclusion

The four novel variants in PKD1, c.6930delG:p.C2311Vfs*3, c.1216T>C:p.C406R, c.8548T>C:p.S2850P, and c.3865G>A:p.V1289M (NM_001009944.2) are pathogenic variants and cause autosomal dominant polycystic kidney disease in family.
Genomic study of dilated cardiomyopathy in a group of Mexican patients using site‐directed next generation sequencing
Authors: Carnevale Alessandra , Rosas‐Madrigal Sandra , Rosendo‐Gutiérrez Rigoberto , López‐Mora Enrique , Romero‐Hidalgo Sandra , Avila‐Vazzini Nydia , Jacobo‐Albavera Leonor , Domínguez‐Pérez Mayra , Vargas‐Alarcón Gilberto , Pérez‐Villatoro Fernando , Navarrete‐Martínez Juana Inés , Villarreal–Molina María Teresa
Published: September 2020

Background

Dilated cardiomyopathy (DCM) is a major cause of nonischemic heart failure and death in young adults. Next generation sequencing (NGS) has become part of the diagnostic workup in idiopathic and familial DCM. More than 50 DCM genes have been identified, revealing great molecular heterogeneity and variable diagnostic yield. Interpretation of variant pathogenicity is challenging particularly in underrepresented populations, as pathogenic variant databases include studies mainly from European/Caucasian populations. To date, no studies on genomic diagnosis of DCM have been conducted in Mexico.

Methods

We recruited 55 unrelated DCM patients, 22 familial (F‐DCM), and 33 idiopathic (I‐DCM), and performed site‐directed NGS seeking causal mutations. Diagnostic yield was defined as the proportion of individuals with at least one pathogenic (P) or likely pathogenic (LP) variant in DCM genes.

Results

Overall diagnostic yield was 47.3%, and higher in F‐DCM (63.6%) than in I‐DCM (36.4%, p = 0.047). Overall, NGS disclosed 41 variants of clinical interest (61.0% novel), 27 were classified as P/LP and 14 of unknown clinical significance. Of P/LP variants, 10 were A‐band region TTN truncating variants, five were found in DSP (18.5%), five in MYH7 (18.5%), two in LMNA (7.4%), and one in RBM20, ABCC9, FKTN, ACTA1, and TNNT2. NGS findings suggested autosomal recessive inheritance in three families, two with DSP loss of function mutations in affected individuals. The increasing number of mutation reports in DCM, increasing knowledge on the functional consequences of mutations, mutational hotspots and functional domains of DCM‐related proteins, the recent refinement ACMG/ClinGen Guidelines, and co‐segregation analysis in DCM families helped increase the diagnostic yield.

Conclusion

This is the first NGS study performed in a group of Mexican DCM patients, contributing to understand the mutational spectrum and complexity of DCM molecular diagnosis.
Association of a novel homozygous mutation in the HMGCS2 gene with an HMGCSD in an Iranian patient
Authors: Heidari Masoud , Soleyman‐Nejad Morteza , Isazadeh Alireza , Shapouri Javad , Taskhiri Mohammad Hossein , Ahangari Roghayyeh , Mohamadi Ali Reza , Ebrahimi Masoumeh , Karimi Hadi , Bolhassani Manzar , Karimi Zahra , Heidari Mansour
Published: September 2020

Background

3‐Hydroxy‐3‐methylglutaryl‐CoA (HMG‐CoA) synthase 2 gene (HMGCS2) encodes a mitochondrial enzyme catalyzing the first reaction of ketogenesis metabolic pathway which provides lipid‐derived energy for various organs during times of carbohydrate deprivation, such as fasting. Mutations in this gene are responsible for HMG‐CoA synthase deficiency (HMGCSD). The aim of present study was to investigate the association of mutation in the HMGCS2 gene with HMGCSD in a patient with atypical symptoms.

Methods

The clinical and genetic features of an 8‐months‐old girl with HMGCSD were evaluated. Molecular genetic testing was conducted using whole‐exome sequencing (WES) in order to identify potential disease‐causing mutation. The WES finding was confirmed by the polymerase chain reaction (PCR) amplification of the target sequence carried out for the patient and her parents. The PCR products were subjected to direct sequencing using forward and reverse specific primers corresponding to the HMGCS2 gene.

Results

A novel homozygous missense mutation (c.266G>A p.Gly89Asp) was detected in the HMGCS2 gene. Sanger sequencing along with co‐segregation analysis of all family members confirmed this novel pathogenic germline mutation. The mutant gene was found to be pathogenic by bioinformatics analysis.

Conclusion

To our best knowledge, this is the first report of HMGCSD in Iran which would expand our knowledge about the mutational spectrum of the HMGCS2 gene and the phenotype variations of the disease.
Independent reaction times method in Geant4‐DNA: Implementation and performance
Authors: Ramos‐Méndez José , Shin Wook‐Geun , Karamitros Mathieu , Domínguez‐Kondo Jorge , Tran Ngoc Hoang , Incerti Sebastien , Villagrasa Carmen , Perrot Yann , Štěpán Václav , Okada Shogo , Moreno‐Barbosa Eduardo , Faddegon Bruce
Published: September 2020

Purpose

The simulation of individual particle tracks and the chemical stage following water radiolysis in biological tissue is an effective means of improving our knowledge of the physico‐chemical contribution to the biological effect of ionizing radiation. However, the step‐by‐step simulation of the reaction kinetics of radiolytic species is the most time‐consuming task in Monte Carlo track‐structure simulations, with long simulation times that are an impediment to research. In this work, we present the implementation of the independent reaction times (IRT) method in Geant4‐DNA Monte Carlo toolkit to improve the computational efficiency of calculating G‐values, defined as the number of chemical species created or lost per 100 eV of deposited energy.

Methods

The computational efficiency of IRT, as implemented, is compared to that from available Geant4‐DNA step‐by‐step simulations for electrons, protons and alpha particles covering a wide range of linear energy transfer (LET). The accuracy of both methods is verified using published measured data from fast electron irradiations for •OH and for time‐dependent G‐values. For IRT, simulations in the presence of scavengers irradiated by cobalt‐60 γ‐ray and 2 MeV protons are compared with measured data for different scavenging capacities. In addition, a qualitative assessment comparing measured LET‐dependent G‐values with Geant4‐DNA calculations in pure liquid water is presented.

Results

The IRT improved the computational efficiency by three orders of magnitude relative to the step‐by‐step method while differences in G‐values by 3.9% at 1 μs were found. At 7 ps, •OH and yields calculated with IRT differed from recent published measured data by 5% ± 4% and 2% ± 4%, respectively. At 1 μs, differences were 9% ± 5% and 6% ± 7% for •OH and , respectively. Uncertainties are one standard deviation. Finally, G‐values at different scavenging capacities and LET‐dependent G‐values reproduced the behavior of measurements for all radiation qualities.

Conclusion

The comprehensive validation of the Geant4‐DNA capabilities to accurately simulate the chemistry following water radiolysis is an ongoing work. The implementation presented in this work is a necessary step to facilitate performing such a task.
Quantifying the effect of dobutamine stress on myocardial Pi and pH in healthy volunteers: A 31P MRS study at 7T
Authors: Apps Andrew , Valkovič Ladislav , Peterzan Mark , Lau Justin Y. C. , Hundertmark Moritz , Clarke William , Tunnicliffe Elizabeth M. , Ellis Jane , Tyler Damian J. , Neubauer Stefan , Rider Oliver J. , Rodgers Christopher T. , Schmid Albrecht Ingo
Published: September 2020

Purpose

Phosphorus spectroscopy (31P‐MRS) is a proven method to probe cardiac energetics. Studies typically report the phosphocreatine (PCr) to adenosine triphosphate (ATP) ratio. We focus on another 31P signal: inorganic phosphate (Pi), whose chemical shift allows computation of myocardial pH, with Pi/PCr providing additional insight into cardiac energetics. Pi is often obscured by signals from blood 2,3‐diphosphoglycerate (2,3‐DPG). We introduce a method to quantify Pi in 14 min without hindrance from 2,3‐DPG.

Methods

Using a 31P stimulated echo acquisition mode (STEAM) sequence at 7 Tesla that inherently suppresses signal from 2,3‐DPG, the Pi peak was cleanly resolved. Resting state UTE‐chemical shift imaging (PCr/ATP) and STEAM 31P‐MRS (Pi/PCr, pH) were undertaken in 23 healthy controls; pH and Pi/PCr were subsequently recorded during dobutamine infusion.

Results

We achieved a clean Pi signal both at rest and stress with good 2,3‐DPG suppression. Repeatability coefficient (8 subjects) for Pi/PCr was 0.036 and 0.12 for pH. We report myocardial Pi/PCr and pH at rest and during catecholamine stress in healthy controls. Pi/PCr was maintained during stress (0.098 ± 0.031 [rest] vs. 0.098 ± 0.031 [stress] P = .95); similarly, pH did not change (7.09 ± 0.07 [rest] vs. 7.08 ± 0.11 [stress] P = .81). Feasibility for patient studies was subsequently successfully demonstrated in a patient with cardiomyopathy.

Conclusion

We introduced a method that can resolve Pi using 7 Tesla STEAM 31P‐MRS. We demonstrate the stability of Pi/PCr and myocardial pH in volunteers at rest and during catecholamine stress. This protocol is feasible in patients and potentially of use for studying pathological myocardial energetics.
Dynamic distortion correction for functional MRI using FID navigators
Authors: Wallace Tess E. , Polimeni Jonathan R. , Stockmann Jason P. , Hoge W. Scott , Kober Tobias , Warfield Simon K. , Afacan Onur
Published: September 2020

Purpose

To develop a method for slice‐wise dynamic distortion correction for EPI using rapid spatiotemporal B0 field measurements from FID navigators (FIDnavs) and to evaluate the efficacy of this new approach relative to an established data‐driven technique.

Methods

A low‐resolution reference image was used to create a forward model of FIDnav signal changes to enable estimation of spatiotemporal B0 inhomogeneity variations up to second order from measured FIDnavs. Five volunteers were scanned at 3 T using a 64‐channel coil with FID‐navigated EPI. The accuracy of voxel shift measurements and geometric distortion correction was assessed for experimentally induced magnetic field perturbations. The temporal SNR was evaluated in EPI time‐series acquired at rest and with a continuous nose‐touching action, before and after image realignment.

Results

Field inhomogeneity coefficients and voxel shift maps measured using FIDnavs were in excellent agreement with multi‐echo EPI measurements. The FID‐navigated distortion correction accurately corrected image geometry in the presence of induced magnetic field perturbations, outperforming the data‐driven approach in regions with large field offsets. In functional MRI scans with nose touching, FIDnav‐based correction yielded temporal SNR gains of 30% in gray matter. Following image realignment, which accounted for global image shifts, temporal SNR gains of 3% were achieved.

Conclusions

Our proposed application of FIDnavs enables slice‐wise dynamic distortion correction with high temporal efficiency. We achieved improved signal stability by leveraging the encoding information from multichannel coils. This approach can be easily adapted to other EPI‐based sequences to improve temporal SNR for a variety of clinical and research applications.
A multicenter study on radiomic features from T2‐weighted images of a customized MR pelvic phantom setting the basis for robust radiomic models in clinics
Authors: Bianchini Linda , Santinha João , Loução Nuno , Figueiredo Mário , Botta Francesca , Origgi Daniela , Cremonesi Marta , Cassano Enrico , Papanikolaou Nikolaos , Lascialfari Alessandro
Published: September 2020

Purpose

To investigate the repeatability and reproducibility of radiomic features extracted from MR images and provide a workflow to identify robust features.

Methods

T2‐weighted images of a pelvic phantom were acquired on three scanners of two manufacturers and two magnetic field strengths. The repeatability and reproducibility of features were assessed by the intraclass correlation coefficient and the concordance correlation coefficient, respectively, and by the within‐subject coefficient of variation, considering repeated acquisitions with and without phantom repositioning, and with different scanner and acquisition parameters. The features showing intraclass correlation coefficient or concordance correlation coefficient >0.9 were selected, and their dependence on shape information (Spearman’s ρ > 0.8) analyzed. They were classified for their ability to distinguish textures, after shuffling voxel intensities of images.

Results

From 944 two‐dimensional features, 79.9% to 96.4% showed excellent repeatability in fixed position across all scanners. A much lower range (11.2% to 85.4%) was obtained after phantom repositioning. Three‐dimensional extraction did not improve repeatability performance. Excellent reproducibility between scanners was observed in 4.6% to 15.6% of the features, at fixed imaging parameters. In addition, 82.4% to 94.9% of the features showed excellent agreement when extracted from images acquired with echo times 5 ms apart, but decreased with increasing echo‐time intervals, and 90.7% of the features exhibited excellent reproducibility for changes in pulse repetition time. Of nonshape features, 2.0% was identified as providing only shape information.

Conclusion

We showed that radiomic features are affected by MRI protocols and propose a general workflow to identify repeatable, reproducible, and informative radiomic features to ensure robustness of clinical studies.
The “chronic immune polyradiculopathies”: Diverse but maybe just CIDP after all
Authors: Rajabally Yusuf A.
Published: September 2020

See article on pages 99–103 in this issue.
Stock Assessment of the Lemon Shark off the Southeast United States
Authors: Hansell Alexander C. , Curtis Tobey H. , Carlson John , Cortés Enric , Fay Gavin , Cadrin Steven X.
Published: September 2020

The Lemon Shark Negaprion brevirostris is a large coastal shark that commonly occurs in the shallow nearshore waters of the tropical western Atlantic Ocean. There are conservation concerns for this species due to fisheries exploitation, low productivity, anthropogenic disturbance at nursery sites, and the depleted status of other large coastal sharks, but no quantitative assessment of Lemon Shark stock status is available. We synthesized available data to develop a stock assessment of the Lemon Shark in the western North Atlantic. All information on stock identity was considered to define a fishery management unit off the southeastern United States. Stock abundance and trends in fishing mortality were estimated from 1981 to 2017 using a Bayesian state–space surplus production model. The model incorporated prior knowledge of Lemon Shark demography, catches, and a combination of 11 indices of abundance. Seven model configurations that fit the data well and produced plausible estimates were used to evaluate the sensitivity of posterior estimates to assumed priors and data decisions. Results suggested that Lemon Shark stock abundance has been relatively stable since the mid-1990s, with some estimates of prior depletion. Estimates of relative fishing mortality indicate earlier periods of overfishing, with a decrease in fishing mortality since the early 2000s. These estimates of population trends provide information for future fisheries management and conservation.
A branch‐and‐dive heuristic for single vehicle snow removal
Authors: Hajizadeh Roghayeh , Holmberg Kaj
Published: September 2020

This paper deals with planning of a tour for a vehicle to clear a certain set of streets in a city of snow. Our previous results on the problem contain a heuristic based on reformulation to an asymmetric traveling salesman problem (ATSP) which yields feasible solutions and upper bounds, and a relaxation of a MIP model for obtaining lower bounds. The goal now is to try to improve the solutions and bounds. In this paper we describe a branch‐and‐dive heuristic which is based on branch‐and‐bound principles. We discuss how branching can be done so that the fixations can be utilized in both the relaxation and the ATSP model, and how the search for better solutions can be done. The heuristic has been implemented and applied to real life city networks. The method is shown to outperform two other heuristics for the ATSP with precedence constraints.
Prognostic Implications of Tumor Differentiation in Clinical T1N0 Gastric Adenocarcinoma
Authors: Margalit Ofer , Shacham-Shmueli Einat , Yang Yu-Xiao , Lawerence Yaacov R. , Levy Idan , Reiss Kim A. , Golan Talia , Halpern Naama , Aderka Dan , Giantonio Bruce , Mamtani Ronac , Boursi Ben
Published: September 2020

Background

Current guidelines recommend neoadjuvant chemotherapy in patients with locoregional gastric adenocarcinoma. Patients diagnosed with early stage gastric adenocarcinoma are usually managed with upfront surgical intervention. However, pathologic staging in a subset of these clinically staged patients identifies more advanced locoregional disease requiring adjuvant treatment. Therefore, identifying these patients prior to surgical intervention is critical to ensure employment of the appropriate treatment paradigm. The aim of the current study was to define patient characteristics associated with clinical understaging in early gastric cancer.

Methods

Using the National Cancer Database (2004–2014) we identified 3,892 individuals with clinical T1N0 gastric adenocarcinoma who underwent upfront definitive surgery, had negative surgical margins, and did not receive preoperative chemotherapy or radiotherapy. Patient characteristics were compared between those with pathologic stage T1N0 disease and those who were upstaged upon surgery.

Results

Twenty-seven percent of clinical T1N0 gastric adenocarcinomas had a change in stage because of pathologically defined ≥T2 disease or positive lymph nodes. Individuals who were upstaged had a higher tumor grade compared with those with pathologic stage T1N0 disease. Specifically, 41.9% (530/1,264) of individuals with a poorly differentiated tumor were upstaged, compared with only 10.7% (70/656) with a well-differentiated tumor. Approximately 75% of cases involved upstaging because of T misclassification. The highest percentage of upstaging was shown for tumors located at the fundus and body of the stomach.

Conclusion

Upstaging of clinical T1N0 gastric adenocarcinoma is characterized by higher tumor grade and is mostly a result of a change in T stage. These findings mandate thorough workup in order to identify patients with clinically staged T1N0 disease requiring preoperative chemotherapy.

Implications for Practice

Upstaging of clinical T1N0 gastric adenocarcinoma is characterized by higher tumor grade and is mostly a result of a change in T stage. These findings mandate thorough workup in order to identify patients with clinically staged T1N0 disease requiring preoperative chemotherapy.
Ultrasound measures of abdominal fat layers correlate with metabolic syndrome features in patients with obesity
Authors: Cuatrecasas Guillem , de Cabo Francisco , Coves Maria Josep , Patrascioiu Ioana , Aguilar Gerardo , March Sonia , Balfegó Mariona , Bretxa Clara , Calbo Marta , Cuatrecasas Gabriel , Aranda Gloria , Orois Aida , Bové Isabel , Munoz‐Marron Elena , García‐Lorda Pilar
Published: September 2020

Objective

Abdominal fat ultrasound (US) is a simple clinical tool that may allow measures of fat depots not visible using common dual‐energy X‐ray absorptiometry (DEXA) or computerized tomography (CT) imaging. The aim of this study was to validate the technique, give measures of superficial and profound subcutaneous, preperitoneal, omental and perirenal (retroperitoneal) fat and correlate them with MS markers.

Methods

Sequential US measures of these five abdominal fat layers were done at 397 adults. Blood pressure (BP), body mass index (BMI), waist, body fat %, HOMA‐IR index (homeostatic model assessment of insulin resistance), lipid profile and leptin were recorded. Metabolic syndrome (MS) was defined according to Cholesterol education programme adult treatment panel III (ATPIII) criteria.

Results

Subcutaneous and omental fat were increased among people with obesity, whereas preperitoneal and perirenal fat did not show any difference according to BMI or waist. Women showed thicker subcutaneous fat (both superficial and profound), whereas men had bigger omental fat. Both postmenopausal and diabetic patients had changes in omental fat only, whereas patients with fatty liver showed thicker preperitoneal and perirenal fat, as well. MS patients showed both thicker perirenal and omental fat. A cut‐off of 54 mm in male (M)/34 mm in female (F) of omental fat and 22.5 mm (M)/12.5 mm (F) of perirenal fat could be predictive of later MS onset.

Conclusions

US is a valid method to measure all different abdominal fat depots. Omental and perirenal fat measures may classify patients at risk for MS. Preperitoneal fat depot may also correlate with fatty liver disease.