bluuebunny/crossref_metadata_2025 huggingface dataset:
OCRDetector: Accurately Detecting Open Chromatin Regions via Plasma Cell-Free DNA Sequencing Data
Authors: Wang Jiayin , Chen Liubin , Zhang Xuanping , Tong Yao , Zheng Tian
Published: May 2021

Open chromatin regions (OCRs) are special regions of the human genome that can be accessed by DNA regulatory elements. Several studies have reported that a series of OCRs are associated with mechanisms involved in human diseases, such as cancers. Identifying OCRs using ATAC-seq or DNase-seq is often expensive. It has become popular to detect OCRs from plasma cell-free DNA (cfDNA) sequencing data, because both the fragmentation modes of cfDNA and the sequencing coverage in OCRs are significantly different from those in other regions. However, it is a challenging computational problem to accurately detect OCRs from plasma cfDNA-seq data, as multiple factors—e.g., sequencing and mapping bias, insufficient read depth, etc.—often mislead the computational model. In this paper, we propose a novel bioinformatics pipeline, OCRDetector, for detecting OCRs from whole-genome cfDNA sequencing data. The pipeline calculates the window protection score (WPS) waveform and the cfDNA sequencing coverage. To validate the proposed pipeline, we compared the percentage overlap of our OCRs with those obtained by other methods. The experimental results show that 81% of the TSS regions of housekeeping genes are detected, and our results have obvious tissue specificity. In addition, the overlap percentage between our OCRs and the high-confidence OCRs obtained by ATAC-seq or DNase-seq is greater than 70%.
Regulation of Bone Cell Differentiation and Activation by Microbe-Associated Molecular Patterns
Authors: Kwon Yeongkag , Park Chaeyeon , Lee Jueun , Park Dong Hyun , Jeong Sungho , Yun Cheol-Heui , Park Ok-Jin , Han Seung Hyun
Published: May 2021

Gut microbiota has emerged as an important regulator of bone homeostasis. In particular, the modulation of innate immunity and bone homeostasis is mediated through the interaction between microbe-associated molecular patterns (MAMPs) and the host pattern recognition receptors including Toll-like receptors and nucleotide-binding oligomerization domains. Pathogenic bacteria such as Porphyromonas gingivalis and Staphylococcus aureus tend to induce bone destruction and cause various inflammatory bone diseases including periodontal diseases, osteomyelitis, and septic arthritis. On the other hand, probiotic bacteria such as Lactobacillus and Bifidobacterium species can prevent bone loss. In addition, bacterial metabolites and various secretory molecules such as short chain fatty acids and cyclic nucleotides can also affect bone homeostasis. This review focuses on the regulation of osteoclast and osteoblast by MAMPs including cell wall components and secretory microbial molecules under in vitro and in vivo conditions. MAMPs could be used as potential molecular targets for treating bone-related diseases such as osteoporosis and periodontal diseases.
Deep Hybrid Network for Land Cover Semantic Segmentation in High-Spatial Resolution Satellite Images
Authors: Khan Sultan Daud , Alarabi Louai , Basalamah Saleh
Published: May 2021

Land cover semantic segmentation in high-spatial resolution satellite images plays a vital role in efficient management of land resources, smart agriculture, yield estimation and urban planning. With the recent advancement in remote sensing technologies, such as satellites, drones, UAVs, and airborne vehicles, a large number of high-resolution satellite images are readily available. However, these high-resolution satellite images are complex due to increased spatial resolution and data disruption caused by different factors involved in the acquisition process. Due to these challenges, an efficient land-cover semantic segmentation model is difficult to design and develop. In this paper, we develop a hybrid deep learning model that combines the benefits of two deep models, i.e., DenseNet and U-Net. This is carried out to obtain a pixel-wise classification of land cover. The contraction path of U-Net is replaced with DenseNet to extract features of multiple scales, while long-range connections of U-Net concatenate encoder and decoder paths are used to preserve low-level features. We evaluate the proposed hybrid network on a challenging, publicly available benchmark dataset. From the experimental results, we demonstrate that the proposed hybrid network exhibits a state-of-the-art performance and beats other existing models by a considerable margin.
Blockchain and Smart Contracts: A Solution for Payment Issues in Construction Supply Chains
Authors: Nanayakkara Samudaya , Perera Srinath , Senaratne Sepani , Weerasuriya Geeganage Thilini , Bandara Herath Mudiyanselage Nelanga Dilum
Published: May 2021

The construction industry has dynamic supply chains with multiple suppliers usually engaged in short-term relationships. Government legislation, novel types of payment agreements, conventional information technology solutions, and supply chain management best practices have endeavoured to solve payment-related financial issues in the construction industry, which are mainly caused by the complexities of the construction supply chain. Nevertheless, payment-related issues persist as one of the key challenges in the industry. Applications of blockchain technology–a trusted, distributed data storing mechanism–along with smart contracts are gaining focus as solutions for complex interorganisational processes. A smart contract is a self-executing script that codifies a set of rules or agreements between multiple parties and runs across the blockchain network. This paper identifies the suitability of blockchain and smart contract technologies in solving payment issues in the construction industry. An expert forum of construction industry stakeholders served as the primary data collection method through a structured questionnaire. The key finding of the paper is that blockchain and smart contract powered solutions can significantly mitigate the payment and related financial issues in the construction industry, including partial payments, nonpayments, cost of finance, long payment cycle, retention, and security of payments.
Molecular Characterization of Chitin Synthase Gene in Tetranychus cinnabarinus (Boisduval) and Its Response to Sublethal Concentrations of an Insecticide
Authors: Xin Tianrong , Li Zhenzhen , Chen Jia , Wang Jing , Zou Zhiwen , Xia Bin
Published: May 2021

The carmine spider mite, Tetranychus cinnabarinus (Boisduval), is one of the most important acarine pest species. At present, its control remains primarily dependent on using various chemical insecticides/acaricides in agricultural crops worldwide. To clarify the mechanism whereby T. cinnabarinus responds to insecticide exposure, we identified the chitin synthase 1 gene (TcCHS1) and then explored the gene expression levels of TcCHS1 at different developmental stages of T. cinnabarinus. We also investigated the effects of sublethal concentrations of diflubenzuron on the toxicities and survivals of T. cinnabarinus eggs and larvae as well as TcCHS1 expression levels. The full-length cDNA sequence contains an open reading frame (ORF) of 4881 nucleotides that encoded for a 1474 amino acid residues protein. The predicted TcCHS1 protein had a molecular mass of 168.35 kDa and an isoelectric point of 6.26, and its amino acid sequence contained all the signature motifs (EDR, QRRRW and TWGTR) of chitin synthases. The results of phylogenetic analyses demonstrated that the putative CHS1 amino acid sequence of T. cinnabarinus revealed high similarities with chitin synthases in other insects and mites. Additionally, at the molecular level, transcriptional analysis by real-time quantitative PCR in different developmental stages of T. cinnabarinus revealed that TcCHS1 mRNA was expressed in all stages, and highest in eggs and female adults, but lowest in deutonymphs. Furthermore, the results of toxicity bioassays indicated that diflubenzuron treatment resulted in high mortality rates in eggs and larvae of T. cinnabarinus. The mRNA expression levels of TcCHS1 from the eggs and larvae of T. cinnabarinus were up-regulated in response to sublethal concentrations of diflubenzuron exposures. Together, all these results demonstrate that diflubenzuron has ovicidal and larvicidal effects and TcCHS1 may play an important role in the growth and development of T. cinnabarinus and may disrupt the chitin biosynthesis, thereby controlling T. cinnabarinus populations.
Effect of Different Plants on the Growth and Reproduction of Thrips flavus (Thysanoptera: Thripidae)
Authors: Gao Yu , Zhao Yijin , Wang Di , Yang Jing , Ding Ning , Shi Shusen
Published: May 2021

Host plants play an important role in affecting insect development and reproduction. Understanding the host plant preferences is important for pest control. Thrips flavus Schrank (Thysanoptera: Thripidae) is a worldwide phytophagous pest in Palearctic Asian and European countries. We used a life table analysis to study the development duration, population parameters, and population growth of T. flavus on five plant species, including Solanum melongena (Solanaceae), Capsicum annuum (Solanaceae), Glycine max (Leguminosae), Brassica rapa var. glabra (Cruciferae), and Cucumis sativus (Cucurbitaceae). The results showed that T. flavus can survive and reproduce on Cu. sativus and G. max, which were two potentially suitable host plants. T. flavus preferred to oviposit on Cu. sativus with a shorter duration of development (17.8 days) at 25 °C. Therefore, the host plant was an important factor influencing the development and fecundity of T. flavus populations. These results will improve our understanding of the population dynamics of T. flavus and facilitate the development of more scientific and efficient measures to control thrips.
Electrocardiographic Versus Echocardiographic Left Ventricular Hypertrophy in Severe Aortic Stenosis
Authors: Budkiewicz Aleksandra , Surdacki Michał A. , Gamrat Aleksandra , Trojanowicz Katarzyna , Surdacki Andrzej , Chyrchel Bernadeta
Published: May 2021

Although ECG used to be a traditional method to detect left ventricular hypertrophy (LVH), its importance has decreased over the years and echocardiography has emerged as a routine technique to diagnose LVH. Intriguingly, an independent negative prognostic effect of the “electrical” LVH (i.e., by ECG voltage criteria) beyond echocardiographic LVH was demonstrated both in hypertension and aortic stenosis (AS), the most prevalent heart valve disorder. Our aim was to estimate associations of the ECG-LVH voltage criteria with echocardiographic LVH and indices of AS severity. We retrospectively manually analyzed ECG tracings of 50 patients hospitalized in our center for severe isolated aortic stenosis, including 32 subjects with echocardiographic LVH. The sensitivity of single traditional ECG-LVH criteria in detecting echocardiographic LVH was 9–34% and their respective specificity averaged 78–100%. The ability to predict echocardiographic LVH was higher for S-waves than R-waves (mean area under the receiver operating curve (AUC): 0.62–0.70 vs. 0.58–0.65). Among combinations of R- and S-waves, the discriminating ability was highest for the Cornell voltage (AUC: 0.71) compared to the Sokolow–Lyon, Romhilt and Gubner–Ungerleider voltage (AUC: 0.62–0.68). By multiple regression, peak aortic pressure gradient was positively related to the Sokolow–Lyon (β = 1.7 ± 0.5, p = 0.002) and Romhilt voltage (β = 1.3 ± 0.5, p = 0.01), but not Cornell (0.5 ± 0.3, p = 0.2) or Gubner-Ungerleider voltage (β = 0.0 ± 0.5, p > 0.9), regardless of LV mass index. In conclusion, echocardiographic LVH and stenosis severity appear to have distinct associations with traditional ECG-LVH criteria in AS. A moderate diagnostic superiority of the Cornell voltage criterion with regard to anatomic LVH might result from its unique ability to include depolarization vectors in both the frontal and horizontal plane with consequent lesser sensitivity to the confounding effect of obesity.
Usefulness of a Colonoscopy Cap with an External Grid for the Measurement of Small-Sized Colorectal Polyps: A Prospective Randomized Trial
Authors: Han Seul-Ki , Kim Hyunil , Kim Jin-woo , Kim Hyun-Soo , Kim Su-Young , Park Hong-Jun
Published: May 2021

Accurate measurement of polyp size during colonoscopy is crucial. The usefulness of cap-assisted colonoscopy and external grid application on monitor (gCAP) was evaluated for polyp size measurement in this 3-year, single-center, single-blind, randomized trial. Using the endoscopic forceps width as reference, the discrepancy percent (DP), error rate (ER), and measurement time were compared between gCAP and visual estimation (VE) after randomization. ER was calculated within a 20% and 33% limit. From the 111 patients, 280 polyps were measured. The mean polyp sizes were 4.0 ± 1.7 mm and 4.2 ± 1.8 mm with gCAP and VE, respectively (p = 0.368). Compared with that by the forceps method, DP was significantly lower in the gCAP group than in the VE group. Moreover, ER was significantly lower in the gCAP group within its preset limit. The measurement time was 4 s longer in the gCAP group than in the VE group (8.2 ± 4.8 s vs. 4.2 ± 1.5 s; p < 0.001). However, the forceps method lasted 28 s longer than the others. On subgroup analysis by size, gCAP was more accurate for polyp size ≥ 5 mm. The gCAP method was more accurate for polyp size measurement than VE, especially for polyps ≥ 5 mm, and was more convenient than the forceps method.
State-Level Health Disparity Is Associated with Sarcoidosis Mortality
Authors: Lee Yu-Che , Chang Ko-Yun , Mirsaeidi Mehdi
Published: May 2021

Background: Sarcoidosis is associated with significant morbidity and rising health care utilization, which contribute to the health care burden and disease outcome. In the United States (US), evaluation of sarcoidosis mortality by individual states has not been investigated. Methods: We examined sarcoidosis mortality data for 1999–2018 from the Centers for Disease Control and Prevention (CDC). America’s Health Rankings (AHR) assesses the nation’s health on a state-by-state basis to determine state health rankings. The numbers of certified Sarcoidosis Clinics within the US were obtained from World Association for Sarcoidosis and Other Granulomatous Disorders (WASOG) and Foundation for Sarcoidosis Research (FSR). The associations between sarcoidosis mortality and state health disparities were calculated by linear regression analyses. Results: From 1999 to 2018, the mean age-adjusted mortality rate (AAMR) in all populations, African Americans and European Americans were 2.9, 14.8, and 1.4 per 1,000,000 population, respectively. South Carolina had the highest AAMR for all populations (6.6/1,000,000) and African Americans (20.8/1,000,000). Both Utah and Vermont had the highest AAMR for European Americans (2.6/1,000,000). New York State and South Atlantic had the largest numbers of FSR-WASOG Sarcoidosis Clinics (6 and 13, respectively). States with better health rankings were significantly associated with lower AAMR in all population (R2 = 0.170, p = 0.003) but with higher AAMR in European Americans (R2 = 0.223, p < 0.001). Conclusions: There are significant variations in sarcoidosis mortality within the US. Sarcoidosis mortality was strongly associated with state health disparities. The current study suggests sarcoidosis mortality could be an indicator to reflect the state-level health care disparities in the US.
Inappropriate Use of Oral Antithrombotic Combinations in an Outpatient Setting and Associated Risks: A French Nationwide Cohort Study
Authors: Zerah Lorène , Bonnet-Zamponi Dominique , Ajrouche Aya , Collet Jean-Philippe , De Rycke Yann , Tubach Florence
Published: May 2021

With the increase in prevalence of cardiovascular diseases, multimorbidity, and medical progress, oral antithrombotic (AT) combinations are increasingly prescribed. The aims of this study were to estimate the incidence of oral AT combinations, their appropriateness (defined as indications compliant with guidelines), and the related risk of major bleeding (i.e., leading to hospitalization) or death, among new users. We conducted a 5-year historical cohort study, using the French national healthcare database, including all individuals ≥ 45 years old with a first delivery of oral ATs between 1 January 2013 and 31 December 2017. The cumulative incidence of oral AT combinations was estimated with the Fine and Gray method, taking into account the competitive risk of death. We compared the cumulative incidence of major bleeding according to the type of oral AT treatment initiated at study entry (monotherapy or oral AT combinations). During the study period, 22,220 individuals were included (mean (SD) age 68 (12) years). The cumulative incidence of oral AT combinations at 5 years was 27.8% (95% confidence interval (CI) 26.8–28.9). Overall, 64% of any oral AT combinations did not comply with guidelines. The cumulative incidence of major bleeding and death in the whole cohort at 5 years was 4.1% (95% CI 3.7–4.6) and 10.8% (95% CI 10.1–11.6), respectively. Risk of major bleeding increased among individuals with oral AT combinations versus oral AT monotherapy at study entry (subdistribution hazard ratio sHR: 2.16 (1.01–4.63)); with no difference in terms of death. The use of oral AT combinations among oral AT users is frequent, often inappropriately prescribed, and associated with an increased risk of major bleeding.
The Non-Coding RNA Landscape in IgA Nephropathy—Where Are We in 2021?
Authors: Pawluczyk Izabella Z. A. , Selvaskandan Haresh , Barratt Jonathan
Published: May 2021

IgA nephropathy (IgAN) is the most commonly diagnosed primary glomerulonephritis worldwide. It is a slow progressing disease with approximately 30% of cases reaching end-stage kidney disease within 20 years of diagnosis. It is currently only diagnosed by an invasive biopsy and treatment options are limited. However, the current surge in interest in RNA interference is opening up new horizons for the use of this new technology in the field of IgAN management. A greater understanding of the fundamentals of RNA interference offers exciting possibilities both for biomarker discovery and, more importantly, for novel therapeutic approaches to target key pathogenic pathways in IgAN. This review aims to summarise the RNA interference literature in the context of microRNAs and their association with the multifaceted aspects of IgA nephropathy.
MiR-126 Is an Independent Predictor of Long-Term All-Cause Mortality in Patients with Type 2 Diabetes Mellitus
Authors: Pordzik Justyna , Eyileten-Postuła Ceren , Jakubik Daniel , Czajka Pamela , Nowak Anna , De Rosa Salvatore , Gąsecka Aleksandra , Cieślicka-Kapłon Agnieszka , Sulikowski Piotr , Filipiak Krzysztof J. , Mirowska-Guzel Dagmara , Siller-Matula Jolanta M. , Postuła Marek
Published: May 2021

MicroRNAs are endogenous non-coding RNAs that are involved in numerous biological processes through regulation of gene expression. The aim of our study was to determine the ability of several miRNAs to predict mortality and response to antiplatelet treatment among T2DM patients. Two hundred fifty-two patients with diabetes were enrolled in the study. Among the patients included, 26 (10.3%) patients died within a median observation time of 5.9 years. The patients were receiving either acetylsalicylic acid (ASA) 75 mg (65%), ASA 150 mg (15%) or clopidogrel (19%). Plasma miR-126, miR-223, miR-125a-3p and Let-7e expressions were assessed by quantitative real time PCR and compared between the patients who survived and those who died. Adjusted Cox-regression analysis was used for prediction of mortality. Differential miRNA expression due to different antiplatelet treatment was analyzed. After including all miRNAs into one multivariate Cox regression model, only miR-126 was predictive of future occurrence of long-term all-cause death (HR = 5.82, 95% CI: 1.3–24.9; p = 0.024). Furthermore, miR-126, Let-7e and miR-223 expressions in the clopidogrel group were significantly higher than in the ASA group (p = 0.014; p = 0.013; p = 0.028, respectively). To conclude, miR-126 expression is a strong and independent predictor of long-term all-cause mortality among patients with T2DM. Moreover, miR-223, miR-126 and Let-7e present significant interactions with antiplatelet treatment regimens and clinical outcomes.
OCT-Derived Plaque Morphology and FFR-Determined Hemodynamic Relevance in Intermediate Coronary Stenoses
Authors: Tomaniak Mariusz , Ochijewicz Dorota , Kołtowski Łukasz , Rdzanek Adam , Pietrasik Arkadiusz , Jąkała Jacek , Slezak Magdalena , Malinowski Krzysztof P. , Zaleska Martyna , Maksym Jakub , Barus Piotr , Roleder Tomasz , Filipiak Krzysztof J. , Opolski Grzegorz , Kochman Janusz
Published: May 2021

Background: optical coherence tomography (OCT) might allow identifying lesion features reportedly associated with plaque vulnerability and increased risk of clinical events. Previous studies on correlation between OCT and functional lesion significance indices reported contradictory results, yet integration of complementary information from both modalities is gaining increased interest. The aim of the study was to compare plaque morphology using OCT in hemodynamically relevant vs. non-relevant lesions by fractional flow reserve (FFR). Methods: consecutive patients with intermediate grade coronary stenoses by angiography were evaluated by both FFR and OCT in this single-center study. Stenoses were labeled hemodynamically relevant in case of the FFR ≤ 0.80. Minimal lumen area (MLA), fibrous cap thickness (FCT), minimal cap thickness over the calcium, angle of the calcium, and necrotic core within the lesions were evaluated. Results: a total of 105 patients (124 vessels) were analyzed. Of them, 65 patients were identified with at least one lesion identified as hemodynamically relevant by FFR (72 vessels, 58.1%). Lesions with FFR ≤0.80 presented with lower mean and minimal lumen area (3.46 ± 1.29 vs. 4.65 ± 2.19, p =0.001 and 1.84 ± 0.97 vs. 2.66 ± 1.40, p = 0.001) compared to patients with FFR > 0.80. No differences were found between groups in the mean and minimal FCT, mean, and maximal necrotic core, calcium angle, as well as the overall rate of calcified and lipid plaques. Conclusion: hemodynamic relevance of intermediate grade lesions correlated moderately with the luminal assessment by OCT. No differences were identified in the plaque morphology between relevant and non-relevant coronary stenoses by FFR.
The Influence of Air Pollution on the Development of Allergic Inflammation in the Airways in Krakow’s Atopic and Non-Atopic Residents
Authors: Czarnobilska Ewa , Bulanda Małgorzata , Bulanda Daniel , Mazur Marcel
Published: May 2021

Until now, the simultaneous influence of air pollution assessed by measuring the objective marker of exposition (1-hydroxypirene, 1-OHP) and atopy on the development of allergic airway diseases has not been studied. The aim of this study was to determine the pathomechanism of the allergic response to PM2.5 in atopic and non-atopic patients. We investigated the changes in peripheral blood basophil activity of patients after stimulation with the birch pollen allergen alone, the allergen combined with PM2.5 (BP), PM2.5 alone, a concentration of 1-OHP in urine, and a distance of residence from the main road in 30 persons. Activation by dust alone was positive for all concentrations in 83% of atopic and 75% of non-atopic assays. In the group of people with atopy, the simultaneous activation of BP gave a higher percentage of active basophils compared to the sum of activation with dust and birch pollen alone (B + P) for all concentrations. The difference between BP and B + P was 117.5 (p = 0.02) at a PM concentration of 100 μg. Such a relationship was not observed in the control group. The correlation coefficient between the distance of residence from major roads and urinary 1-OHP was 0.62. A Pearson correlation analysis of quantitative variables was performed, and positive correlation results were obtained in the atopy group between BP and 1-OH-P. Exposure to birch pollen and PM2.5 has a synergistic effect in sensitized individuals. The higher the exposure to pollutants, the higher the synergistic basophil response to the allergen and PM in atopic patients.
HspB4/αA-Crystallin Modulates Neuroinflammation in the Retina via the Stress-Specific Inflammatory Pathways
Authors: Nath Madhu , Shan Yang , Myers Angela M. , Fort Patrice Elie
Published: May 2021

Purpose: We have previously demonstrated that HspB4/αA-crystallin, a molecular chaperone, plays an important intrinsic neuroprotective role during diabetes, by its phosphorylation on residue 148. We also reported that HspB4/αA-crystallin is highly expressed by glial cells. There is a growing interest in the potential causative role of low-grade inflammation in diabetic retinopathy pathophysiology and retinal Müller glial cells’ (MGCs’) participation in the inflammatory response. MGCs indeed play a central role in retinal homeostasis via secreting various cytokines and other mediators. Hence, this study was carried out to delineate and understand the regulatory function of HspB4/αA-crystallin in the inflammatory response associated with metabolic stresses. Methods: Primary MGCs were isolated from knockout HspB4/αA-crystallin mice. These primary cells were then transfected with plasmids encoding either wild-type (WT), phosphomimetic (T148D), or non-phosphorylatable mutants (T148A) of HspB4/αA-crystallin. The cells were exposed to multiple metabolic stresses including serum starvation (SS) or high glucose with TNF-alpha (HG + T) before being further evaluated for the expression of inflammatory markers by qPCR. The total protein expression along with subcellular localization of NF-kB and the NLRP3 component was assessed by Western blot. Results: Elevated levels of IL-6, IL-1β, MCP-1, and IL-18 in SS were significantly diminished in MGCs overexpressing WT and further in T148D as compared to EV. The HG + T-induced increase in these inflammatory markers was also dampened by WT and even more significantly by T148D overexpression, whereas T148A was ineffective in either stress. Further analysis revealed that overexpression of WT or the T148D, also led to a significant reduction of Nlrp3, Asc, and caspase-1 transcript expression in serum-deprived MGCs and nearly abolished the NF-kB induction in HG + T diabetes-like stress. This mechanistic effect was further evaluated at the protein level and confirmed the stress-dependent regulation of NLRP3 and NF-kB by αA-crystallin. Conclusions: The data gathered in this study demonstrate the central regulatory role of HspB4/αA-crystallin and its modulation by phosphorylation on T148 in retinal MGCs. For the first time, this study demonstrates that HspB4/αA-crystallin can dampen the stress-induced expression of pro-inflammatory cytokines through the modulation of multiple key inflammatory pathways, therefore, suggesting its potential as a therapeutic target for the modulation of chronic neuroinflammation.
Bone Lengthening with a Motorized Intramedullary Nail in 34 Patients with Posttraumatic Limb Length Discrepancies
Authors: Teulières Maxime , Langlais Tristan , de Gauzy Jérôme Sales , Rölfing Jan Duedal , Accadbled Franck
Published: May 2021

The Fitbone® motorized nail system has been used to correct limb length discrepancies (LLD) for several years. This study focuses on its application in posttraumatic limb lengthening surgery, its outcome and challenges. Materials and methods: A prospective, single center study was conducted between 2010 and 2019 in patients treated with motorized lengthening nails. The inclusion criteria were symptomatic LLD of 20 mm or more. An imaging analysis was done using TraumaCad® software (Brainlab AG, Munich, Germany) to compare frontal alignment angles and limb length discrepancy (LLD) on preoperative and latest follow-up radiographs of the lower limbs. Results: Thirty-four patients were included with a mean age of 28.8 ± 9.7 years, a mean follow-up of 27.8 ± 13 months and a mean hospital stay of 4.4 ± 1.7 days. The mean LLD was 44 ± 18 mm in 29 femoral and 32 ± 8 mm in 4 tibial cases, which was reduced to less than 10 mm in 25/34 (74%) patients. The mean healing index was 84.6 ± 62.5 days/cm for femurs and 92 ± 38.6 days/cm for tibias. The mean time to resume full weight-bearing without walking aids was 226 days ± 133. There was no significant difference between preoperative and final follow-up alignment angles and range of motion. The mechanical lateral distal femoral angle (mLDFA) was corrected in the subgroup of 10 LLD patients with varus deformity of the femur (preoperative 95.7° (±5.0) vs. postoperative 91.5° (±3.4), p = 0.008). According to Paley’s classification, there were 14 problems, 10 obstacles and 2 complications. Discussion: Six instances of locking screw pull out, often requiring reoperation, raise the question of whether a more systematic use of blocking screws that provide greater stability might be indicated. Lack of compliance can lead to poor outcomes, patient selection in posttraumatic LLD patients is therefore important. Conclusion: Limb lengthening with a motorized lengthening nail for posttraumatic LLD is a relatively safe and reliable procedure. Full patient compliance is crucial. In-depth knowledge of lengthening and deformity correction techniques is essential to prevent and manage complications.
Improvements in Hearing and in Quality of Life after Sequential Bilateral Cochlear Implantation in a Consecutive Sample of Adult Patients with Severe-to-Profound Hearing Loss
Authors: Sivonen Ville , Sinkkonen Saku T. , Willberg Tytti , Lamminmäki Satu , Jääskelä-Saari Hilkka , Aarnisalo Antti A. , Dietz Aarno
Published: May 2021

Bilateral cochlear implantation is increasing worldwide. In adults, bilateral cochlear implants (BICI) are often performed sequentially with a time delay between the first (CI1) and the second (CI2) implant. The benefits of BICI have been reported for well over a decade. This study aimed at investigating these benefits for a consecutive sample of adult patients. Improvements in speech-in-noise recognition after CI2 were followed up longitudinally for 12 months with the internationally comparable Finnish matrix sentence test. The test scores were statistically significantly better for BICI than for either CI alone in all assessments during the 12-month period. At the end of the follow-up period, the bilateral benefit for co-located speech and noise was 1.4 dB over CI1 and 1.7 dB over CI2, and when the noise was moved from the front to 90 degrees on the side, spatial release from masking amounted to an improvement of 2.5 dB in signal-to-noise ratio. To assess subjective improvements in hearing and in quality of life, two questionnaires were used. Both questionnaires revealed statistically significant improvements due to CI2 and BICI. The association between speech recognition in noise and background factors (duration of hearing loss/deafness, time between implants) or subjective improvements was markedly smaller than what has been previously reported on sequential BICI in adults. Despite the relatively heterogeneous sample, BICI improved hearing and quality of life.
Molecular Tests for Risk-Stratifying Cytologically Indeterminate Thyroid Nodules: An Overview of Commercially Available Testing Platforms in the United States
Authors: Nishino Michiya , Bellevicine Claudio , Baloch Zubair
Published: May 2021

The past decade has witnessed significant advances in the application of molecular diagnostics for the pre-operative risk-stratification of cytologically indeterminate thyroid nodules. The tests that are currently marketed in the United States for this purpose combine aspects of tumor genotyping with gene and/or microRNA expression profiling. This review compares the general methodology and clinical validation studies for the three tests currently offered in the United States: ThyroSeq v3, Afirma GSC and Xpression Atlas, and ThyGeNEXT/ThyraMIR.
A Decision-Making Method for Autonomous Collision Avoidance for the Stand-On Vessel Based on Motion Process and COLREGs
Authors: Wang Bing , He Yixiong , Hu Weixuan , Mou Junmin , Li Liling , Zhang Ke , Huang Liwen
Published: May 2021

A great number of collision accidents can be attributed to incongruous collision-avoidance actions between the give-way vessel and the stand-on vessel in a crossing or overtaking situation. If the give-way vessel does not take appropriate collision-avoidance action according to international regulations for preventing collisions at sea, the last barrier to pass safely is the appropriate and effective collision-avoidance action taken by the stand-on vessel. To find the proper autonomous collision-avoidance action of the stand-on vessel, a method is proposed that combines quantitative analysis rules of collision-avoidance with the deduction of nonlinear maneuvering motion process based on the mathematical model group, which conformity can reach 90%. This research presents a method to calculate the timing and most effective collision-avoidance actions for the stand-on vessel based on the four-stage theory of encountering vessels and the characteristics of vessel motion. The accuracy of the latest-action timing and the action amplitude for the stand-on vessel can be increased to the level of second and degree, respectively. A novel model of collision risk index is constructed by the latest time of the feasible collision-avoidance action on the precise of different course-altering amplitude. Methods to find the stand-on vessel’s proper collision-avoidance actions in the open sea are presented. The simulation indicates the proposed method for the stand-on vessel can make correct collision-avoidance decisions autonomously.
Quantification of Measurement and Model Effects in Monopile Foundation Scour Protection Experiments
Authors: Wu Minghao , De Vos Leen , Arboleda Chavez Carlos Emilio , Stratigaki Vasiliki , Streicher Maximilian , Troch Peter
Published: May 2021

The present work introduces an analysis of the measurement and model effects that exist in monopile scour protection experiments with repeated small scale tests. The damage erosion is calculated using the three dimensional global damage number S3D and subarea damage number S3D,i. Results show that the standard deviation of the global damage number σ(S3D)=0.257 and is approximately 20% of the mean S3D, and the standard deviation of the subarea damage number σ(S3D,i)=0.42 which can be up to 33% of the mean S3D. The irreproducible maximum wave height, chaotic flow field and non-repeatable armour layer construction are regarded as the main reasons for the occurrence of strong model effects. The measurement effects are limited to σ(S3D)=0.039 and σ(S3D,i)=0.083, which are minor compared to the model effects.
A Multiomic Approach to Understand How Pleurotus eryngii Transforms Non-Woody Lignocellulosic Material
Authors: Peña Ander , Babiker Rashid , Chaduli Delphine , Lipzen Anna , Wang Mei , Chovatia Mansi , Rencoret Jorge , Marques Gisela , Sánchez-Ruiz María Isabel , Kijpornyongpan Teeratas , Salvachúa Davinia , Camarero Susana , Ng Vivian , Gutiérrez Ana , Grigoriev Igor V. , Rosso Marie-Noëlle , Martínez Angel T. , Ruiz-Dueñas Francisco J.
Published: May 2021

Pleurotus eryngii is a grassland-inhabiting fungus of biotechnological interest due to its ability to colonize non-woody lignocellulosic material. Genomic, transcriptomic, exoproteomic, and metabolomic analyses were combined to explain the enzymatic aspects underlaying wheat–straw transformation. Up-regulated and constitutive glycoside–hydrolases, polysaccharide–lyases, and carbohydrate–esterases active on polysaccharides, laccases active on lignin, and a surprisingly high amount of constitutive/inducible aryl–alcohol oxidases (AAOs) constituted the suite of extracellular enzymes at early fungal growth. Higher enzyme diversity and abundance characterized the longer-term growth, with an array of oxidoreductases involved in depolymerization of both cellulose and lignin, which were often up-regulated since initial growth. These oxidative enzymes included lytic polysaccharide monooxygenases (LPMOs) acting on crystalline polysaccharides, cellobiose dehydrogenase involved in LPMO activation, and ligninolytic peroxidases (mainly manganese-oxidizing peroxidases), together with highly abundant H2O2-producing AAOs. Interestingly, some of the most relevant enzymes acting on polysaccharides were appended to a cellulose-binding module. This is potentially related to the non-woody habitat of P. eryngii (in contrast to the wood habitat of many basidiomycetes). Additionally, insights into the intracellular catabolism of aromatic compounds, which is a neglected area of study in lignin degradation by basidiomycetes, were also provided. The multiomic approach reveals that although non-woody decay does not result in dramatic modifications, as revealed by detailed 2D-NMR and other analyses, it implies activation of the complete set of hydrolytic and oxidative enzymes characterizing lignocellulose-decaying basidiomycetes.
Potential Usage of Edible Mushrooms and Their Residues to Retrieve Valuable Supplies for Industrial Applications
Authors: Kumar Harsh , Bhardwaj Kanchan , Sharma Ruchi , Nepovimova Eugenie , Cruz-Martins Natália , Dhanjal Daljeet Singh , Singh Reena , Chopra Chirag , Verma Rachna , Abd-Elsalam Kamel A. , Tapwal Ashwani , Musilek Kamil , Kumar Dinesh , Kuča Kamil
Published: May 2021

Currently, the food and agricultural sectors are concerned about environmental problems caused by raw material waste, and they are looking for strategies to reduce the growing amount of waste disposal. Now, approaches are being explored that could increment and provide value-added products from agricultural waste to contribute to the circular economy and environmental protection. Edible mushrooms have been globally appreciated for their medicinal properties and nutritional value, but during the mushroom production process nearly one-fifth of the mushroom gets wasted. Therefore, improper disposal of mushrooms and untreated residues can cause fungal disease. The residues of edible mushrooms, being rich in sterols, vitamin D2, amino acids, and polysaccharides, among others, makes it underutilized waste. Most of the published literature has primarily focused on the isolation of bioactive components of these edible mushrooms; however, utilization of waste or edible mushrooms themselves, for the production of value-added products, has remained an overlooked area. Waste of edible mushrooms also represents a disposal problem, but they are a rich source of important compounds, owing to their nutritional and functional properties. Researchers have started exploiting edible mushroom by-products/waste for value-added goods with applications in diverse fields. Bioactive compounds obtained from edible mushrooms are being used in media production and skincare formulations. Furthermore, diverse applications from edible mushrooms are also being explored, including the synthesis of biosorbent, biochar, edible films/coating, probiotics, nanoparticles and cosmetic products. The primary intent of this review is to summarize the information related to edible mushrooms and their valorization in developing value-added products with industrial applications.
In Vitro and In Vivo Antifungal Activity of Sorbicillinoids Produced by Trichoderma longibrachiatum
Authors: Ngo Men Thi , Nguyen Minh Van , Han Jae Woo , Park Myung Soo , Kim Hun , Choi Gyung Ja
Published: May 2021

In the search for antifungal agents from marine resources, we recently found that the culture filtrate of Trichoderma longibrachiatum SFC100166 effectively suppressed the development of tomato gray mold, rice blast, and tomato late blight. The culture filtrate was then successively extracted with ethyl acetate and n-butanol to identify the fungicidal metabolites. Consequently, a new compound, spirosorbicillinol D (1), and a new natural compound, 2′,3′-dihydro-epoxysorbicillinol (2), together with 11 known compounds (3–13), were obtained from the solvent extracts. The chemical structures were determined by spectroscopic analyses and comparison with literature values. The results of the in vitro antifungal assay showed that of the tested fungal pathogens, Phytophthora infestans was the fungus most sensitive to the isolated compounds, with MIC values ranging from 6.3 to 400 µg/mL, except for trichotetronine (9) and trichodimerol (10). When tomato plants were treated with the representative compounds (4, 6, 7, and 11), bisvertinolone (6) strongly reduced the development of tomato late blight disease compared to the untreated control. Taken together, our results revealed that the culture filtrate of T. longibrachiatum SFC100166 and its metabolites could be useful sources for the development of new natural agents to control late blight caused by P. infestans.
A System Pharmacology Multi-Omics Approach toward Uncontrolled Pediatric Asthma
Authors: Abdel-Aziz Mahmoud , Neerincx Anne , Vijverberg Susanne , Hashimoto Simone , Brinkman Paul , Gorenjak Mario , Toncheva Antoaneta , Harner Susanne , Brandstetter Susanne , Wolff Christine , Perez-Garcia Javier , Hedman Anna , Almqvist Catarina , Corcuera-Elosegui Paula , Korta-Murua Javier , Sardón-Prado Olaia , Pino-Yanes Maria , Potočnik Uroš , Kabesch Michael , Kraneveld Aletta , Maitland-van der Zee Anke ,   on behalf of the SysPharmPediA Consortium
Published: May 2021

There is a clinical need to identify children with poor asthma control as early as possible, to optimize treatment and/or to find therapeutic alternatives. Here, we present the “Systems Pharmacology Approach to Uncontrolled Pediatric Asthma” (SysPharmPediA) study, which aims to establish a pediatric cohort of moderate-to-severe uncontrolled and controlled patients with asthma, to investigate pathophysiological mechanisms underlying uncontrolled moderate-to-severe asthma in children on maintenance treatment, using a multi-omics systems medicine approach. In this multicenter observational case–control study, moderate-to-severe asthmatic children (age; 6–17 years) were included from four European countries (Netherlands, Germany, Spain, and Slovenia). Subjects were classified based on asthma control and number of exacerbations. Demographics, current and past patient/family history, and clinical characteristics were collected. In addition, systems-wide omics layers, including epi(genomics), transcriptomics, microbiome, proteomics, and metabolomics were evaluated from multiple samples. In all, 145 children were included in this cohort, 91 with uncontrolled (median age = 12 years, 43% females) and 54 with controlled asthma (median age = 11.7 years, 37% females). The two groups did not show statistically significant differences in age, sex, and body mass index z-score distribution. Comprehensive information and diverse noninvasive biosampling procedures for various omics analyses will provide the opportunity to delineate underlying pathophysiological mechanisms of moderate-to-severe uncontrolled pediatric asthma. This eventually might reveal novel biomarkers, which could potentially be used for noninvasive personalized diagnostics and/or treatment.
Metrics and Equivalence in Conservation Banking
Authors: Grimm Marie
Published: May 2021

Offsets are increasingly used to compensate for unavoidable development impacts on species and habitats. Many offset programs pursue no net loss, but research on the success of these programs is lacking, including research on conservation banking’s success in conserving protected species under the US Endangered Species Act. This article provides a case study analysis of two conservation banks in the state of California, comparing the conservation gains provided by banks with the losses from development impacts. It provides an analysis of credits and metrics to determine whether the gains are equal to the losses in terms of type, condition, and amount. Results do show that the gains exceed the losses in terms of acreage. However, the program uses indirect metrics (acreage), and the equivalence of the losses and gains, besides habitat type and size, is not reflected. Banks provide a baseline in their documentation and conduct monitoring of species abundance and habitat quality, but they do not use it to measure additional conservation gains. More detailed metrics and transparent indices to certify the acres in production could allow for a quantification of conservation benefits and an evaluation of program success. However, selecting standardized metrics is challenging because they need to be species-specific to reflect the goal of species recovery, and still be operational in practice.
Novel Exploratory Spatiotemporal Analysis to Identify Sociospatial Patterns at Small Areas Using Property Transaction Data in Dublin
Authors: Rabiei-Dastjerdi Hamidreza , McArdle Gavin
Published: May 2021

The residential real estate market is very important because most people’s wealth is in this sector, and it is an indicator of the economy. Real estate market data in general and market transaction data, in particular, are inherently spatiotemporal as each transaction has a location and time. Therefore, exploratory spatiotemporal methods can extract unique locational and temporal insight from property transaction data, but this type of data are usually unavailable or not sufficiently geocoded to implement spatiotemporal methods. In this article, exploratory spatiotemporal methods, including a space-time cube, were used to analyze the residential real estate market at small area scale in the Dublin Metropolitan Area over the last decade. The spatial patterns show that some neighborhoods are experiencing change, including gentrification and recent development. The extracted spatiotemporal patterns from the data show different urban areas have had varying responses during national and global crises such as the economic crisis in 2008–2011, the Brexit decision in 2016, and the COVID-19 pandemic. The study also suggests that Dublin is experiencing intraurban displacement of residential property transactions to the west of Dublin city, and we are predicting increasing spatial inequality and segregation in the future. The findings of this innovative and exploratory data-driven approach are supported by other work in the field regarding Dublin and other international cities. The article shows that the space-time cube can be used as complementary evidence for different fields of urban studies, urban planning, urban economics, real estate valuations, intraurban analytics, and monitoring sociospatial changes at small areas, and to understand residential property transactions in cities. Moreover, the exploratory spatiotemporal analyses of data have a high potential to highlight spatial structures of the city and relevant underlying processes. The value and necessity of open access to geocoded spatiotemporal property transaction data in social research are also highlighted.