bluuebunny/crossref_metadata_2025_split huggingface dataset:
A comparative study of next-generation sequencing and fragment analysis for the detection and allelic ratio determination of FLT3 internal tandem duplication
Authors: Kim Jin Ju , Lee Kwang Seob , Lee Taek Gyu , Lee Seungjae , Shin Saeam , Lee Seung-Tae 
Published: January 2022

Abstract
Background
Currently, FLT3 internal tandem duplication (ITD) is tested by fragment analysis. With next-generation sequencing (NGS), however, not only FLT3 ITD but also other mutations can be detected, which can provide more genetic information on disease.

Methods
We retrospectively reviewed the results of two tests—fragment analysis and a custom-designed, hybridization capture-based, targeted NGS panel—performed simultaneously. We used the Pindel algorithm to detect FLT3 ITD mutations.

Results
Among 277 bone marrow aspirate samples tested by NGS and fragment analysis, the results revealed 99.6% concordance in FLT3 ITD detection. Overall, the allele frequency (AF) attained by NGS positively correlated with the standard allelic ratio (AR) attained by fragment analysis, with a Spearman correlation coefficient (r) of 0.757 (95% confidence interval: 0.627–0.846; p < 0.001). It was concluded that an AF of 0.11 attained by NGS is the most appropriate cutoff value (with 85.3% sensitivity and 86.7% specificity) for high mutation burden criterion presented by guidelines.

Conclusion
Sensitive FLT3 ITD detection with comprehensive information of other mutation offered by NGS could be a useful tool in clinical laboratories. Future studies will be needed to evaluate and standardize NGS AF cutoff to predict actual clinical outcomes.
Human embryonic mesenchymal lung-conditioned medium promotes differentiation to myofibroblast and loss of stemness phenotype in lung adenocarcinoma cell lines
Authors: Canals Jordi , Navarro Alfons , Vila Cristina , Canals Josep M. , Díaz Tania , Acosta-Plasencia Melissa , Cros-Font Coralí , Han Bing , He Yangyi , Monzó Mariano 
Published: January 2022

Abstract
Background
When genes responsible for normal embryonic development are abnormally expressed in adults, it can lead to tumor development. This can suggest that the same mechanism that controls embryonic differentiation can also control tumor differentiation. We hypothesize that the malignant phenotype of lung cancer cells could acquire benign characteristics when in contact with an embryonic lung microenvironment. We cultured two lung cancer cell lines in embryonic lung mesenchyme-conditioned medium and evaluated morphological, functional and molecular changes.

Methods
The human embryonic mesenchymal lung-conditioned medium (hEML-CM) was obtained by culturing lung cells from embryos in the pseudoglandular stage of development. The NSCLC cell lines A549 and H1299 we cultured in the hEML-CM and in a tumor-conditioned medium. Morphological changes were analyzed with optical and transmission electron microscopy. To evaluate the functional effect of conditioned medium in tumor cells, we analyzed cell proliferation, migration, colony formation capacity in 2D and 3D and in vivo tumor growth capacity. The expression of the pluripotency genes OSKM, the adenocarcinoma marker NKX2-1, the lung surfactant proteins SFTP, the myofibroblast marker MYH and DNMT3A/3B was analyzed with qRT-PCR and the presence of the myofibroblast markers vimentin and α-SMA with immunofluorescence. Transcriptomic analysis was performed using Affymetrix arrays.

Results
The A549 and H1299 cells cultured in hEML-CM lost their epithelial morphology, acquired mesodermal characteristics, and decreased proliferation, migration, and colony formation capacity in 2D and 3D, as well as reduced its capacity to growth in vivo. The expression of OSKM, NKX2-1 and SFTP decreased, while that of DNMT3A/3B, vimentin, α-SMA and MYH increased. Distant matrix analysis based on transcriptomic profile showed that conditioned cells were closer to myoblast and human lung fibroblast than to normal epithelial immortalized lung cells. A total of 1631 for A549 and 866 for H1299 differentially expressed genes between control and conditioned cells were identified.

Conclusions
To the best of our knowledge, this is the first study to report that stimuli from the embryonic lung can modulate the malignant phenotype of lung cancer cells, control their growth capacity and activate their differentiation into myofibroblasts. These findings could lead to new strategies for lung cancer management.
Species-resolved sequencing of low-biomass or degraded microbiomes using 2bRAD-M
Authors: Sun Zheng , Huang Shi , Zhu Pengfei , Tzehau Lam , Zhao Helen , Lv Jia , Zhang Rongchao , Zhou Lisha , Niu Qianya , Wang Xiuping , Zhang Meng , Jing Gongchao , Bao Zhenmin , Liu Jiquan , Wang Shi , Xu Jian 
Published: January 2022

AbstractMicrobiome samples with low microbial biomass or severe DNA degradation remain challenging for amplicon-based or whole-metagenome sequencing approaches. Here, we introduce 2bRAD-M, a highly reduced and cost-effective strategy which only sequences ~ 1% of metagenome and can simultaneously produce species-level bacterial, archaeal, and fungal profiles. 2bRAD-M can accurately generate species-level taxonomic profiles for otherwise hard-to-sequence samples with merely 1 pg of total DNA, high host DNA contamination, or severely fragmented DNA from degraded samples. Tests of 2bRAD-M on various stool, skin, environmental, and clinical FFPE samples suggest a successful reconstruction of comprehensive, high-resolution microbial profiles.
Transcutaneous auricular vagus nerve stimulation (taVNS) for the treatment of pediatric nephrotic syndrome: a pilot study
Authors: Merchant Kumail , Zanos Stavros , Datta-Chaudhuri Timir , Deutschman Clifford S. , Sethna Christine B. 
Published: January 2022

Abstract
Background
Children with frequently relapsing nephrotic syndrome (FRNS) and steroid resistant nephrotic syndrome (SRNS) are exposed to immunosuppressant medications with adverse side effects and variable efficacy. Transcutaneous auricular vagus nerve stimulation (taVNS) modulates the immune system via the inflammatory reflex and has become a therapy of interest for treating immune-mediated illnesses.

Methods
An open-label, pilot study of tavNS for five minutes daily for 26 weeks via a TENS 7000 unit was conducted.

Results
Three FRNS participants and 4 SRNS participants had a mean age of 9.5±4.2 years (range 4 to 17). Those with FRNS remained relapse-free during the study period; two participants continued treatment and remained in remission for 15 and 21 months, respectively. Three SRNS participants experienced a reduction in first morning UPC (mean of 42%, range 25-76%). Although UPC decreased (13.7%) in one SRNS participant with congenital nephrotic syndrome, UPC remained in nephrotic range. All but one participant (non-compliant with treatment) experienced a reduction in TNF (7.33pg/mL vs. 5.46pg/mL, p=0.03). No adverse events or side effects were reported.

Conclusions
taVNS was associated with clinical remission in FRNS and moderately reduced proteinuria in non-congenital SRNS. Further study of taVNS as a treatment for nephrotic syndrome in children is warranted.
ClinicalTrials.gov Identifier: NCT04169776, Registered November 20, 2019, https://clinicaltrials.gov/ct2/show/NCT04169776.
New definition for torsional irregularity based on floors rotations of reinforced concrete buildings
Authors: Alaa Khaled M. , El-Kashif Khaled F. , Salem Hamed M. 
Published: January 2022

AbstractEarthquake investigations confirm that un-symmetric buildings suffer more damage than their symmetric counterparts. Torsional vibrations due to irregularity are one of the main factors which cause damage to buildings. Seismic codes include provisions to consider the torsional vibrations in the design of structures. However, the design of the stiff side elements may be unconservative. In this study, a total of 15 Dual system buildings were analyzed using nonlinear dynamic analysis to propose a new definition for torsional irregularity considering the effects of plan asymmetry on the earthquake response of mid-rise dual system buildings. Based on the analysis results, two new equations were derived using nonlinear regression analysis to check the torsional irregularity and the torsional amplification. Afterward, the proposed torsional irregularity provisions were compared with the torsional irregularity provisions of Europe code (EC-8), Japanese code & ASCE 7-16 code, and the results indicate that the torsional irregularity provisions of all the codes are unconservative. The current investigation proposes new equations to be used in the existing codes for torsional irregularity design considerations to improve the accuracy of the current codes' torsional irregularity provisions.
A cutoff time scaling of 1/f noise in a sandpile
Authors: Yadav Avinash Chand , Kumar Naveen 
Published: January 2022

Abstract
We show that for fluctuations in a sandpile with

spectrum, the power may also exhibit a scaling with its cutoff time. Despite significant progress, this generic behaviour remains so far overlooked and poorly understood. An intriguing example is the power spectrum of a simple random walk (normal diffusive process) on a ring with L sites, showing

behaviour instead of

(Brownian noise) in the frequency regime

. We address the intriguing problem by scaling method and discuss its relevance in the context of the sandpile system and a class of stochastic processes.
Determinants of Dropout from and Variation in Adherence to an Exercise Intervention: The STRRIDE Randomized Trials
Authors: Collins Katherine A. , Huffman Kim M. , Wolever Ruth Q. , Smith Patrick J. , Siegler Ilene C. , Ross Leanna M. , Hauser Elizabeth R. , Jiang Rong , Jakicic John M. , Costa Paul T. , Kraus William E. 
Published: January 2022

ABSTRACT

Purpose
This study aimed to characterize the timing and self-reported determinants of exercise dropout among sedentary adults with overweight or obesity. We also sought to explore variations in adherence among individuals who completed a 6- to 8-month structured exercise intervention.

Methods
A total of 947 adults with dyslipidemia (STRRIDE I, STRRIDE AT/RT) or prediabetes (STRRIDE-PD) were enrolled to either control or to 1 of 10 exercise interventions, ranging from doses of 8 to 23 kcal·kg−1·wk−1, intensities of 50% to 75% V˙O2 peak, and durations of 6 to 8 months. Two groups included resistance training, and one included dietary intervention (7% weight loss goal). Dropout was defined as an individual who withdrew from the study because of a variety of determinants. Timing of intervention dropout was defined as the last session attended and categorized into phases. Exercise training adherence was calculated by dividing weekly minutes or total sets of exercise completed by weekly minutes or total sets of exercise prescribed. General linear models were used to characterize the associations between timing of dropout and determinant category.

Results
Compared with exercise intervention completers (n = 652), participants who dropped out (n = 295) were on average non-White (98% vs 80%, P < 0.01), had higher body mass index (31.0 vs 30.2 kg·m−2, P < 0.01), and were less fit at baseline (25.0 vs 26.7 mL·kg−1·min−1, P < 0.01). Of those who dropped out, 67% did so before the start of or while ramping up to the prescribed exercise volume and intensity. The most commonly reported reason for dropout was lack of time (40%). Notably, among individuals who completed the ramp training period, subsequent exercise intervention adherence did not waiver over the ensuing 6–8 months of training.

Conclusions
These findings are some of the first to delineate associations between the timing of dropout and dropout determinants, providing guidance for future exercise interventions to better support individuals at risk for dropout.
Personalized Retail Promotions Through a Directed Acyclic Graph–Based Representation of Customer Preferences
Authors: Jagabathula Srikanth , Mitrofanov Dmitry , Vulcano Gustavo 
Published: January 2022

A Framework to Run Personalized Promotions The availability of individual-level transaction data allows retailers to implement personalized operational decisions. Although such decisions have been around for several years now in online platforms, recent technological developments open new opportunities to extend similar practices to bricks-and-mortar settings (e.g., by using electronic price tags to show different prices to different customers or by using beacon-based technology to send promotion offers to targeted customers). In “Personalized Retail Promotions through a DAG-Based Representation of Customer Preferences,” Jagabathula, Mitrofanov, and Vulcano propose a back-to-back procedure for running customized promotions in retail operations contexts, from the construction of a nonparametric choice model where customer preferences are represented by directed acyclic graphs to the formulation of the promotion optimization problem. The empirical validation of their proposal on real supermarket data shows the promising performance of their approach over state-of-the-art benchmarks.
Type II Abernethy Malformation: A Rare Cause of Hepatic Encephalopathy in Adulthood
Authors: Gonçalves Inês , Barros Daniela , Araújo Margarida , Machado Ana Isabel , Oliveira Camila , Pinto Luisa 
Published: January 2022

Abernethy malformation is a rare congenital extrahepatic portosystemic shunt with variable clinical manifestations, mainly associated with the portosystemic shunt. Hepatic encephalopathy can be the first manifestation. We present the case of a 50-year-old woman with hepatic encephalopathy without liver dysfunction. Further evaluation with contrast-enhanced abdominal computed tomography was performed, showing a large-calibre portocaval shunt from the left portal branch, suggestive of type 2 Abernethy malformation. The patient improved with lactulose and rifaximin but maintained rare encephalopathy episodes. She is therefore currently awaiting surgical treatment. Despite being a rare cause of hepatic encephalopathy, Abernethy malformation should be considered in patients with unexplained hyperammonaemia. Since it is potentially reversible, and early diagnosis and treatment may improve outcome, raising awareness of this malformation is essential.
Construções típicas são um aborto? Presentismo e germanidade nos conflitos da passagem de Roberto Burle Marx por Blumenau
Authors: Machado Ricardo 
Published: January 2022

O artigo problematiza as transformações urbanísticas e arquitetônicas em Blumenau, Santa Catarina, nas últimas décadas do século XX através do conflito gerado pela passagem de Roberto Burle Marx na cidade. O paisagista teria afirmado na imprensa de que as formas adotadas a partir dos anos 1970 seriam um aborto arquitetônico, gerando um intenso conflito que se estendeu por alguns meses, mobilizando a opinião do poder público, dos intelectuais e da imprensa local. Essa contenda trouxe visibilidade a uma questão mais geral relativa ao debate sobre as políticas da memória, invenções identitárias e usos do passado no tempo presente.
Application of autologous platelet-rich plasma to graft donor sites to reduce pain and promote healing
Authors: Gupta Samarth , Jain Rakesh Kumar 
Published: January 2022

Objective: Platelet-rich plasma (PRP) is widely used for wound healing in medical care because of the numerous growth factors it contains. Traditionally, donor sites are left to heal with a primary dressing so wounds are not left open. However, a delay in healing accompanied by pain at a donor site is often seen. This study primarily throws light on the use of autologous PRP over split-thickness skin graft (STSG) donor sites to promote healing and reduce pain. Method: The patients enrolled in this study in 2018–2019 were divided into two groups: the intervention group received autologous PRP applied topically at the donor site; in the control group, the wound was dressed traditionally. Pain scales were measured in the immediate postoperative period at six hours, 10 hours and 16 hours. The dressing was opened on the postoperative day 14 and observed for healing by an independent observer. Results: A total of 100 patients were included in the study. Patients in the PRP group showed statistically significant faster healing at postoperative day 14 compared with the control group (p<0.05), who required dressings for 3-4 weeks postoperatively. Pain scale scores in the postoperative period were significantly less in the PRP group at six hours postoperatively compared with the control group (p<0.05). There was a reduced incidence of hypertrophic scar formation in the small number of patients in the PRP group who had developed hypertrophic scar previously. Conclusion: Application of PRP is a safe, cost-effective and easy method to achieve faster healing in graft donor site areas that are troublesome to both patients and doctors. It also reduces postoperative pain at donor sites. The authors recommend PRP is used more often in the management of donor sites for STSGs.
Characterization of surface defects using a phase retrieval technique in a high-power laser system
Authors: Lehmann Lucien , Bouillet Stéphane , Leymarie Christophe , Ameil-Schuh Christel , Benoit Melusine , Rouyer Claude 
Published: January 2022

In the framework of high-power lasers, surface defects on optics can generate strong light intensification and induce damage sites on downstream optics. To evaluate this intensification during high-energy laser shots, a three-step method is proposed. First, a dedicated measurement bench is designed to measure the intensification induced by defects on a wide variety of optics, including amplifier slabs, KDP crystals, mirrors, gratings, and vacuum windows, for propagation distances up to 2000 mm. A multi-resolution single-beam multiple-intensity reconstruction phase retrieval algorithm is then used to reconstruct a model of the defect, in both amplitude and phase, from a set of intensification measurements. Finally, the impact of the modeled defect on downstream optics is evaluated with a simulation of the high-power laser system. This method is experimentally validated through a case study of damage identified on one of the Laser Mégajoule (LMJ) beams, characterized with the method presented in this paper. The long-distance impact on the LMJ beam is estimated by simulation and compared to a direct near-field measurement.
Non-communicable diseases (NCDs) and vulnerability to COVID-19: The case of adult patients with hypertension or diabetes mellitus in Gamo, Gofa, and South Omo zones in Southern Ethiopia
Authors: Bojola Fikre , Taye Wondimagegn , Samuel Habtamu , Mulatu Bahiru , Kawza Aknaw , Mekuria Aleme 
Published: January 2022

Background
A growing body of evidence demonstrating that individuals with Non-Communicable Disease (NCD) are more likely to have severe forms of COVID-19 and subsequent mortality. Hence, our study aimed to assess the knowledge of vulnerability and preventive practices towards COVID-19 among patients with hypertension or diabetes in Southern Ethiopia.

Objective
To assess the knowledge and preventive practices towards COVID-19 among patients with hypertension or diabetes mellitus in three zones of Southern Ethiopia, 2020.

Methods
A community-based cross-sectional study design was used with a multi-stage random sampling technique to select 682 patients with hypertension or diabetes mellitus from 10th -17th July 2020 at the three zones of Southern Ethiopia. Logistic regression analysis with a 95% confidence interval was fitted to identify independent predictors of knowledge and preventive practices towards COVID-19. The adjusted odds ratio (AOR) was used to determine the magnitude of the association between the outcome and independent variables. P-value <0.05 is considered statistically significant.

Results
The Multi-dimensional knowledge (MDK) analysis of COVID-19 revealed that 63% of study subjects had good knowledge about COVID-19. The overall preventive practice towards COVID -19 was 26.4%. Monthly income (AOR = 1.42; 95% CI: 1.04, 1.94) significantly predicted knowledge towards COVID-19. Ninety-five percent of the study subjects knew that the COVID-19 virus spreads via respiratory droplets of infected individuals. One hundred and ten (16.2%) of study subjects correctly responded to the questions that state whether people with the COVID-19 virus who do not have a fever can infect the other. Knowledge about COVID-19 (AOR = 1.47; 95% CI: 1.03, 2.1) became the independent predictor of preventive practice.

Conclusions
In this study, the knowledge of the respondents towards the COVID-19 pandemic was good. But the preventive practice was very low. There was a significant gap between knowledge and preventive practices towards the COVID-19 pandemic among the study subjects. Monthly income was significantly associated with knowledge of COVID-19. Knowledge of COVID-19 was found to be an independent predictor of preventive practice towards COVID-19. Community mobilization and improving COVID-19- related knowledge and practice are urgently recommended for those patients with hypertension or diabetes mellitus.
Clinical, anamnestic, and sociodemographic predictors of positive SARS-CoV-2 testing in children: A cross sectional study in a tertiary hospital in Italy
Authors: Armocida Benedetta , Zamagni Giulia , Magni Elena , Monasta Lorenzo , Comar Manola , Zanotta Nunzia , Cason Carolina , Argentini Giorgia , Urriza Marianela , Cassone Andrea , Vascotto Fulvia , Buzzetti Roberto , Barbi Egidio , Del Pin Massimo , Pani Paola , Knowles Alessandra , Carletti Claudia , Concina Federica , Milinco Mariarosa , Ronfani Luca 
Published: January 2022

Objectives
We aimed to identify clinical, anamnestic, and sociodemographic characteristics associated with a positive swab for SARS-CoV2, and to provide a predictive score to identify at risk population in children aged 2–14 years attending school and tested for clinical symptoms of COVID-19.

Design
Cross sectional study.

Setting
Outpatient clinic of the IRCCS Burlo Garofolo, a maternal and child health tertiary care hospital and research centre in Italy.

Data collection and analysis
Data were collected through a predefined form, filled out by parents, and gathered information on sociodemographic characteristics, and specific symptoms, which were analysed to determine their association with a positive SARS-CoV-2 swab. The regression coefficients of the variables included in the multivariate analysis were further used in the calculation of a predictive score of the positive or negative test.

Results
Between September 20th and December 23rd 2020, from 1484 children included in the study, 127 (8.6%) tested positive. In the multivariate analysis, the variables retained by the model were the presence of contact with a cohabiting, non-cohabiting or unspecified symptomatic case (respectively OR 37.2, 95% CI 20.1–68.7; 5.1, 95% CI 2.7–9.6; 15.6, 95% CI 7.3–33.2); female sex (OR 1.49, 95% CI 1.0–2.3); age (6–10 years old: OR 3.2, 95% CI 1.7–6.1 p<0.001; >10 years old: OR 4.8, 95% CI 2.7–8.8 p<0.001); fever (OR 3.9, 95% CI 2.3–6.4); chills (OR 1.9, 95% CI 1.1–3.3); headache (OR 1.45, 95% CI 0.9–2.4); ageusia (OR 1.3, 95% CI 0.5–4.0); sore throat (OR 0.48, 95% CI 0.3–0.8); earache (OR 0.4, 95% CI 0.1–1.3); rhinorrhoea (OR 0.8, 95% CI 0.5–1.3); and diarrhoea (OR 0.52, 95% CI 0.2–1.1). The predictive score based on these variables generated 93% sensitivity and 99% negative predictive value.

Conclusions
The timely identification of SARS-CoV2 cases among children is useful to reduce the dissemination of the disease and its related burden. The predictive score may be adopted in a public health perspective to rapidly identify at risk children.