bluuebunny/crossref_metadata_2025 huggingface dataset:
Validation and verification of the Japanese version of the systemic lupus erythematosus symptom checklist for patient quality of life
Authors: Doi Hiroshi , Ohmura Koichiro , Tabuchi Yuya , Hashimoto Motomu , Takase Yudai , Inaba Ryuta , Kozuki Tomohiro , Iwasaki Takeshi , Taniguchi Masashi , Kitagori Koji , Akizuki Shuji , Murakami Kosaku , Nakashima Ran , Yoshifuji Hajime , Yamamoto Wataru , Tanaka Masao , Akio Morinobu
Published: March 2021

Objective

The systemic lupus erythematosus (SLE) symptom checklist (SSC) is a patient-reported outcome measure consisting of 38 queries. We translated SSC into Japanese and attempted to validate its usefulness for evaluating the quality of life (QOL) of SLE patients and identify factors that affect QOL.

Methods

Data from the Medical Outcomes Study Short-form 36 questionnaire (SF-36), Japanese LupusPRO, the Japanese version of the SSC (SSC-J) questionnaire, SLEDAI-2k, and the physician global assessment (PGA) were obtained on the same day from 226 SLE outpatients of the Kyoto Lupus cohort at Kyoto University Hospital. Relationships between the total scores or each item of SSC-J and SF-36, Japanese LupusPRO, SLEDAI-2k, or PGA were analyzed by Spearman’s rank test.

Results

The total scores of SSC-J correlated with the scores of SF-36 and Japanese LupusPRO. In each item of SSC-J, all 38 items correlated with the physical component summary and mental component summary of SF-36 as well as the Health-Related QOL (HRQOL) scores of Japanese LupusPRO, but not with the non-HRQOL of LupusPRO. SSC-J scores correlated with age, PGA, and corticosteroid doses, but not with SLEDAI-2k.

Conclusions

SSC-J is suitable as a disease-specific QOL assessment tool for SLE.
Breast cancer mortality after eight years of an improved screening program using digital breast tomosynthesis
Authors: Castellano Cristina Romero , Aguilar Angulo Paul Martin , Hernández Lina Cruz , González-Carrato Pilar Sánchez-Camacho , González Rubén Giovanetti , Alvarez Justo , Chacón José Ignacio , Ruiz Juan , Fuentes Guillén Maria Ángeles , Gutiérrez Ávila Gonzalo
Published: March 2021

Objectives

To assess screening quality metrics and to describe mortality rates eight years after redesign of breast cancer screening and diagnosis pathways, and the introduction of digital breast tomosynthesis.

Setting

Breast Unit of the Toledo Health Area in the region of Castilla-La Mancha (Spain).

Methods

We recorded screening metrics and mortality data following the introduction of digital breast tomosynthesis in 2011 for screening and diagnosis pathways. We then compared the mortality between Toledo Health Area and the rest of Castilla-La Mancha, where digital breast tomosynthesis is not available.

Results

All screening quality metrics improved following the introduction of digital breast tomosynthesis. The cancer detection rate significantly increased from 2.3 (95% confidence interval (CI): 1.9–3.6) to 4.5 per 1000 women (95% CI: 3.2–5.2) on average between the periods 2005–2009 and 2015–2018, while the recall rate significantly decreased from 7.0% (95% CI: 6.8%–8.2%) to 2.6% (95% CI: 2.0%–3.6%). Comparing breast cancer mortality rates for 2014–2018 in the Toledo Health Area with the rest of Castilla-La Mancha, which had similar cancer treatment access and management protocols but without digital breast tomosynthesis, the crude mortality rate was 17.79 (95% CI: 15.38 -20.19) vs. 24.76 per 100,000 (95% CI: 26.12–23.39), respectively. The cumulative risk of death was also significantly lower for the Toledo Health Area than for Castilla-La Mancha.

Conclusion

The introduction of digital breast tomosynthesis improved screening quality indicators. Breast cancer mortality simultaneously decreased with respect to the rest of Castilla-La Mancha. Further research is needed to assess the long-term results, and the role that the redesign may have played in reducing mortality.
Why Do People Agree With Both Regular and Reversed Items? A Logical Response Perspective
Authors: Kam Chester Chun Seng , Meyer John P. , Sun Shaojing
Published: March 2021

The current research challenges the received view that misresponses to reversed items are the result of participants’ irrational behavior. On the contrary, for participants at a midpoint level of a trait, it is perfectly logical to agree and disagree with seemingly equivalent statements (e.g., I’m not tall, but neither am I short). For this reason, regular and reversed items for a unidimensional construct were predicted to load on separate factors. Two types of reversed items—polar opposites and negated regular items—were also predicted to load on separate factors, as they are qualitatively different. An empirical study supported this explanation. Differential responding was found to be highest for participants at the mid-level of a trait and diminished toward the ends, revealing a quadratic relationship and a trait × method interaction. Thus, our findings demonstrate that the logical response pattern of individuals at the mid-level of a trait is another previously unrecognized explanation for why the inclusion of regular and reverse-keyed items can contribute to the apparent bi-dimensionality of unidimensional constructs (for data analysis results, see https://osf.io/krh2w/ ).
Multiple-input and multiple-output force control for automobile component road simulation using model predictive control with proportional–integral–derivative
Authors: Na Hong-Cheol , Yuan Hai-Bo , Park Gyuhae , Kim Young-Bae
Published: March 2021

When developing an entire vehicle system, testing the structure of the vehicle or each component as a module or individually is necessary to determine the reliability and ensure the endurance of the entire vehicle. Various tests have been conducted to check the durability of the parts. However, the most important part is the verification of the fatigue limit of the load vibration from the road surface when the vehicle is being driven. Verification can be achieved by experimenting while driving on a real road with a prototype vehicle best suited to the actual conditions. However, issues such as problems in time, space, and environmental constraints, inconsistency in driving characteristics of the test driver, and continuous monitoring exist. For testing the load vibration of the road surface in automobile parts in the laboratory, hydraulic servo actuators are used because they provide vibrational loads in multiple directions by configuring them in multiple axes rather than a single axis. In this article, a multiple-input multiple-output model predictive control–proportional–integral–derivative hybrid controller is proposed as the method for optimal control of a multi-axis hydraulic servo actuator used in a random road signal reproduction experiment. Its performance is compared with the simple proportional–integral–derivative controller. A method for obtaining an efficient black box multiple-input multiple-output system model using LabVIEW in a laboratory in the field is also introduced, and the effectiveness of the model predictive control–proportional–integral–derivative hybrid controller is shown by reproducing the actual road load.
STIFF vertical seismic absorbers
Authors: Kapasakalis Konstantinos A , Antoniadis Ioannis A , Sapountzakis Evangelos J
Published: March 2021

Seismic isolation is proven to be an effective technology for seismic protection of building structures, equipment, and industrial facilities. The majority of the existing isolation systems and techniques are related to horizontal ground motions, whereas there are only a few vertical isolation systems. The main reason is because of the conflict concerning the demand for isolation stiffness. More specifically, a vertical isolated system must have sufficient vertical rigidity to sustain the weight of the isolated object/system and retain the static vertical deflection in reasonable limits. On the other hand, the isolated system must also have enough flexibility to isolate the accelerations. In order to overcome this difficulty, a novel vertical seismic absorber system is proposed, that combines negative stiffness-driven absorbers with inerters. The inerter manages to reduce the frequency of the system, without weakening the structure or increasing the seismic load. At the same time, the effective damping is significantly increased with the KDamper. This way, the dynamic behavior of the system is improved, in terms of absolute accelerations, and simultaneously, the static settlements are retained at any desired level. The design of the vertical seismic absorber is based on engineering criteria, and the excitation input is selected according to the seismic design codes. The dynamic performance of the vertical seismic absorber is also evaluated with real earthquake records, using a realistic displacement-dependent configuration for the realization of the negative stiffness element. Finally, the detuning phenomena are observed and discussed via sensitivity analysis.
Effects of Raising Student Teachers’ Metacognitive Awareness of Their Educational Psychological Misconceptions
Authors: Pieschl Stephanie , Budd Janene , Thomm Eva , Archer Jennifer
Published: March 2021

Fostering metacognitive awareness of misconceptions should enhance deep processing of scientifically correct explanations and thereby decrease misconceptions. To explore these potentially beneficial effects, we conducted a field study implemented in a regular educational psychology course in an Australian teacher education program. In a two-by-two within-subject experimental design, student teachers ( n = 119) answered misconception questionnaires, made metacognitive judgments, and participated in awareness activities at the start (T1) and the end (T2) of the semester (within-subject factor: time). Half of the misconception items focused on educational psychology course content, while the other half focused on related topics that were not covered in the course (non-course content). Awareness activities (AA) consisted of providing feedback regarding all misconception items. During the lectures, we provided additional scientifically correct refutational explanations (RE) regarding course content. Thus, we compared the combined AA+RE treatment for course content with the AA treatment for non-course content (within-subject factor: treatment). Our findings confirm that student teachers harbor numerous high-confidence educational psychological misconceptions. Furthermore, awareness activities plus refutational explanations resulted in significant increases in metacognitive awareness and in performance. Additionally, initial metacognitive overconfidence was related to persistent misconceptions, indicating that overconfidence may hinder correction of course content misconceptions.
Bolt damage identification based on orientation-aware center point estimation network
Authors: Zhang Yang , Yuen Ka-Veng
Published: March 2021

With the development of deep learning, object detection algorithms based on horizontal box are widely used in the field of damage identification. However, damages can be in any direction and position, and they are not necessarily horizontal or vertical. This article proposes a bolt damage identification network, namely, orientation-aware center point estimation network, which models a damage as a center point of its rotated bounding box. The proposed orientation-aware center point estimation network uses deep layer aggregation network to search center points and regress to all other damage properties, such as size and angle. A loss function is designed to improve the optimization efficiency of network. Orientation-aware center point estimation network is applied to bolt damage detection, and comparison with the well-known Faster Region-Convolutional Neural Network (a benchmark using horizontal bounding box) demonstrates the accuracy of the proposed method. Finally, videos were utilized to verify the capability of the proposed orientation-aware center point estimation network in real-time detection of bolt damages.
Development of an Interactive Remote Basic Surgical Skills Mini-Curriculum for Medical Students During the COVID-19 Pandemic
Authors: Quaranto Brian R , Lamb Michael , Traversone John , Hu Jinwei , Lukan James , Cooper Clairice , Schwaitzberg Steven
Published: March 2021

Introduction. Teaching surgical skills has historically been a hands-on activity, with instructors and learners in close physical proximity. This paradigm was disrupted by the COVID-19 pandemic, requiring innovative solutions to surmount the challenges of teaching surgical skills remotely. In this work, we describe our institution’s path and early results of developing an interactive remote surgical skills course for medical students in the surgical clerkship. Methods. 31 third-year medical students were distributed a set of surgical equipment and 3D printed phone dock. Each participant completed a baseline questionnaire and underwent 3 structured interactive remote sessions on surgical instruments, knot tying, and suturing techniques. Students were instructed on sharing their first-person viewpoint and received real-time feedback on their knot tying and suturing techniques from the course instructor. Pre- and post-session surveys were conducted and analyzed. Results. All students were able to complete the remote surgical skills course successfully, as defined by visually demonstrating successful two-handed knot and simple suture techniques. Students’ aggregate confidence score in their knot tying ability (pretest mean 7.9, SD 0.7 vs posttest mean 9.7, SD 0.9, t-statistic −2.3, P = .03) and suturing ability (pretest mean 8.0, SD 1.3 vs posttest mean 13.8, SD 0.9 t-statistic −5.5, P < .001) significantly improved after the intervention. Qualitative feedback from the students underscored the utility of the first-person perspective for teaching surgical technique. Conclusion. This study demonstrates that remote teaching of knot tying and simple suturing to medical students can be effectively implemented using a remote learning curriculum that was well received by the learners.
Multicomponent Informed Consent with Marshallese Participants
Authors: Purvis Rachel S. , Ayers Britni L. , Bogulski Cari A. , Kaminicki Kyle F. , Haggard-Duff Lauren K. , Riklon Lynda A. , Iban Anita , Mejbon-Samuel Rotha , Lakmis Rumina , Riklon Sheldon , Thompson Joseph W. , McElfish Pearl A.
Published: March 2021

Pacific Islanders are the second fastest-growing population in the United States; however, Pacific Islanders, and Marshallese specifically, are underrepresented in health research. A community-based participatory research (CBPR) approach was used to engage Marshallese stakeholders and build an academic-community research collaborative to conduct health disparities research. Our CBPR partnership pilot tested a multicomponent consent process that provides participants the option to control the use of their data. Consent forms used concise plain language to describe study information, including participant requirements, risks, and personal health information protections, and were available in both English and Marshallese. This study demonstrates that when provided a multicomponent consent, the vast majority of consenting study participants (89.6%) agreed to all additional options, and only five (10.4%) provided consent for some but not all options. Our description of the development and implementation of a multicomponent consent using a CBPR approach adds a specific example of community engagement and may be informative for other indigenous populations.
L-ascorbyl 6-palmitate as lead compound targeting SphK1: an in silico and in vitro investigation
Authors: Chen HaiJiao , Yang Xinmei , Sun Peng , Zhi Ying , Yao Qingqiang , Liu Bo
Published: March 2021

Sphingosine kinases (SphKs) are a class of lipid kinases, that have received extensive attention as important rate-limiting enzyme in tumor. Inhibition of the activity of SphK1 can lead to an anticancer effect. Herein, we describe the discovery process and biological characteristics of a new SphK1 inhibitor, ascorbyl palmitate, discovered through computer-aided drug design. Biochemical experiments show that ascorbyl palmitate has a strong inhibitory effect on SphK1, with an IC50 value of 6.4 μM. The MTT experiment showed that ascorbyl palmitate had anti-cancer effects toward the U87, A549, 22RV1, and A375 cell lines. Among them, ascorbyl palmitate has prominent inhibitory activity against the 22RV1 cell line, with an IC50 value of 41.57 μM. To explore the structure–activity relationship, four ascorbyl palmitate derivatives were synthesized and tested for kinase activity. The outstanding effect of ascorbyl palmitate toward SphK1 and its known non-toxicity suggest that ascorbyl palmitate may be a lead compound for the development of effective SphK1 anti-cancer inhibitors.
Implementation fidelity of an Integrated Healthy Lifestyle Service: a process evaluation
Authors: Sanders GJ , Griffiths C , Flint S , Christensen A , Gately P
Published: March 2021

Aims:

The current study aimed to evaluate implementation fidelity of an Integrated Healthy Lifestyle Service (IHLS).

Methods:

A pragmatic sample of 28 individual interviews and 11 focus groups were conducted. This resulted in a total of 81 (22 male) individuals comprising key stakeholders (n = 18), as well as intervention staff across senior management (n = 4), team lead (n = 14) and practitioner (n = 11) roles, and intervention clients (n = 34).

Results:

A mixed degree of implementation fidelity was demonstrated throughout the five a priori fidelity domains of study design, provider training, intervention delivery, intervention receipt, and enactment. Stakeholders, staff and clients alike noted a high degree of intervention receipt across all services offered. Contrastingly, practitioners noted that they received minimal formal operational, data systems, clinical, and curriculum training as well as a lack of personal development opportunities. Consequently, practitioners reported low confidence in delivering sessions and collecting and analysing any data. A top-down approach to information dissemination within the service was also noted among practitioners which affected motivation and overall team morale.

Conclusion:

Results can be used to conceptualise best practices as a process to further strengthen the design, delivery and recruitment strategies of the IHLS.
Motion Direction Discrimination with Tactile Random-Dot Kinematograms
Authors: Kuroki Scinob , Nishida Shin’ya
Published: March 2021

Motion detection is a fundamental sensory function for multiple modalities, including touch, but the mechanisms underlying tactile motion detection are not well understood. While previous findings supported the existence of high-level feature tracking, it remains unclear whether there also exist low-level motion sensing that directly detects a local spatio-temporal correlation in the skin-stimulation pattern. To elucidate this mechanism, we presented, on braille displays, tactile random-dot kinematograms, similar to those widely used in visual motion research, which enables us to independently manipulate feature trackability and various parameters of local motion. We found that a human observer is able to detect the direction of difficult-to-track tactile motions presented to the fingers and palms. In addition, the direction-discrimination performance was better when the stimuli were presented along the fingers than when presented across the fingers. These results indicate that low-level motion sensing, in addition to high-level tracking, contribute to tactile motion perception.
Fibroblast growth factor 21 is associated with increased serum total antioxidant capacity and oxidized lipoproteins in humans with different stages of chronic kidney disease
Authors: Gómez-Sámano Miguel Ángel , Vargas-Abonce Valerie Paola , Martínez-Sánchez Froylan David , Palacios-Báez Lucía , Vera-Zertuche Juan Mauricio , Navarro-Flores María Fernanda , Morales-García Mariana Guadalupe , Fonseca-Correa Jorge Ignacio , Zuarth-Vázquez Julia María , Vega-Vega Olynka , Correa-Rotter Ricardo , Rincón-Pedrero Rodolfo , Morales-Buenrostro Luis E. , Alberú-Gómez Josefina , Ramírez-González Julia Berenice , Pacheco-Domínguez Reyna Lizette , López-Cervantes Malaquías , Mendoza-de-la-Garza María de los Ángeles , Baeza-Arias Yolanda Victoria , Espinosa-Cuevas Ángeles , López-Carrasco Guadalupe , López-Estrada Angelina , Guillén-Pineda Luz Elizabeth , Gómez-Pérez Francisco Javier , Cuevas-Ramos Daniel
Published: March 2021

Background and aims:

Oxidative stress (OS) induces the production of fibroblast growth factor 21 (FGF21). Previous data have revealed that FGF21 protects cells from OS injury and death, making it a potential therapeutic option for many diseases with increased OS. However, the association of this growth factor with OS markers in humans with chronic kidney disease (CKD) remains unknown. This study aims to evaluate the association of serum FGF21 with serum total antioxidant capacity (TAC) and oxidized low-density lipoproteins (OxLDL) in subjects in different stages of kidney disease.

Methods:

This is a cross-sectional study that included 382 subjects with different stages of CKD, irrespective of type 2 diabetes (T2D) diagnosis. Associations of serum FGF21 with OxLDL, TAC, sex, age, body mass index (BMI), fasting plasma glucose, estimated glomerular filtration rate (eGFR), T2D, and smoking, were evaluated through bivariate and partial correlation analyses. Independent associations of these variables with serum FGF21 were evaluated using multiple linear regression analysis.

Results:

Serum FGF21 was significantly and positively correlated with age ( r = 0.236), TAC (lnTAC) ( r = 0.217), and negatively correlated with eGFR ( r = −0.429) and male sex ( r = −0.102). After controlling by age, sex, BMI, T2D, smoking, and eGFR; both TAC and OxLDL were positively correlated with FGF21 ( r = 0.117 and 0.158 respectively, p < 0.05). Using multiple linear regression analysis, eGFR, male sex, T2D, OxLDL, and TAC were independently associated with serum FGF21 (STDβ = −0.475, 0.162, −0.153, 0.142 and 0.136 respectively; p < 0.05 for all) adjusted for age, BMI, smoking, and fasting plasma glucose.

Conclusion:

A positive association between serum FGF21 and OS has been found independently of renal function in humans. Results from the present study provide novel information for deeper understanding of the role of FGF21 in OS in humans with CKD and T2D; mechanistic studies to explain the association of serum FGF21 with oxidative stress in CKD are needed.
From Consumer Satisfaction to Recommendation of Mobile App–Based Services: An Overview of Mobile Taxi Booking Apps
Authors: Siyal Abdul Waheed , Hongzhuan Chen , Gang Chen
Published: March 2021

Since MTB has been deemed as the business model of 21st century but its long-term sustainability depends on level of consumer satisfaction with its applicability in their everyday life. Therefore, current research aims to highlight factors which could shape consumers’ satisfaction and further trigger their intuition to recommend it in their circle of influence. Unified theory of acceptance and use of technology 2 (utaut2) was modified and extended to fit the purpose. Data were collected from prevailing MTB users and analyzed in PLS-SEM. Results reveal that utaut2 factors signify their effects on consumer satisfaction which further trigger their instinct to recommend MTB. Current research modified utaut2 with mediating role of consumer satisfaction with MTB which further stimulates their instinct to recommend it. The modified framework adds value to the theoretical horizon of utaut2 and further extends its applicability in a novel setting like MTB. The study offers insightful implications to MTB companies for effective design and implementation of future strategies. Moreover, limitations and suggestions for future researchers are also discussed.
Posterior tibial slope is a modifiable predictor of relatively large extension gaps in total knee arthroplasty for degenerative osteoarthritis
Authors: Shin Kyun-Ho , Kim Sang-Bum , Jang Ki-Mo , Lee Chul-Soo , Han Seung-Beom
Published: March 2021

Background:

During total knee arthroplasty (TKA) for osteoarthritis, the sagittal gap imbalance (SGI) with a relatively large extension gap is an important surgical challenge. We determined the predictors of SGI with a relatively large extension gap and evaluated the surgical outcomes of knees with SGI.

Methods:

551 consecutive cases of primary TKA for osteoarthritis were retrospectively reviewed. The cohort was divided into two groups according to the SGI and statistically matched according to baseline characteristics via the inverse probability of treatment weighting method. Multiple linear and logistic regression analyses were performed to determine the predictors of sagittal gap difference (SGD) and SGI. Intergroup differences in clinical and radiological outcomes were analyzed.

Results:

Of all the knees included, 8.5% (n = 45) presented with SGI with a relatively large extension gap and required femoral sagittal balancing to manage SGI. The hyperextension angle (HA), preoperative joint line convergence angle (JLCA), and the change in posterior tibial slope (PTS) significantly correlated to SGD and predicted SGI with a relatively large extension gap. SGI group showed significant changes in femoral posterior condylar offset and joint line height compared to those without SGI (1.48 vs −0.45, 1.37 vs −0.51, respectively). Postoperative ROM and knee society knee scores were lower in SGI group.

Conclusion:

Knees requiring sagittal balancing to manage SGI with a relatively large extension gap is not uncommon in TKA for osteoarthritic knees. The change in PTS is an independent and modifiable predictor of SGI.
Short Term Stock Price Prediction in Indian Market: A Neural Network Perspective
Authors: Banerjee Soham , Mukherjee Diganta
Published: March 2021

In recent times there has been an increasing level of debate whether patterns do exist in equity market movements and whether they can be predicted. In order to overcome the shortcomings of traditional time series models, we have focused our study on the application of non-parametric paradigms like stacked multi-layer perceptrons (MLP), long short term memory (LSTM), gated recurrent unit (GRU), bidirectional long short term memory (BLSTM) and gated bidirectional recurrent unit (BGRU) on three NSE listed banks to predict short term stock price, and compared their performance with a shallow neural network benchmark. We have predicted equity ‘Close Prices’ five minutes into the future, using a sliding window approach and have observed that average error in predictions of MLP, LSTM, GRU, BLSTM and BGRU models, varied between 0.09% and 0.1%, indicating their superior performance with regard to benchmark baseline of 0.88%. We have used the aforementioned predictions to determine price trends, which successfully outperformed the random walk baseline accuracy of 50%.

JEL Classification: C45, C58, G11, G14
Factor graph-aggregated heterogeneous network embedding for disease-gene association prediction
Authors: He Ming , Huang Chen , Liu Bo , Wang Yadong , Li Junyi
Published: March 2021

Background

Exploring the relationship between disease and gene is of great significance for understanding the pathogenesis of disease and developing corresponding therapeutic measures. The prediction of disease-gene association by computational methods accelerates the process.

Results

Many existing methods cannot fully utilize the multi-dimensional biological entity relationship to predict disease-gene association due to multi-source heterogeneous data. This paper proposes FactorHNE, a factor graph-aggregated heterogeneous network embedding method for disease-gene association prediction, which captures a variety of semantic relationships between the heterogeneous nodes by factorization. It produces different semantic factor graphs and effectively aggregates a variety of semantic relationships, by using end-to-end multi-perspectives loss function to optimize model. Then it produces good nodes embedding to prediction disease-gene association.

Conclusions

Experimental verification and analysis show FactorHNE has better performance and scalability than the existing models. It also has good interpretability and can be extended to large-scale biomedical network data analysis.
Genome-wide identification and expression analysis of the B-box transcription factor gene family in grapevine (Vitis vinifera L.)
Authors: Zhang Xiuming , Zhang Li , Ji Miaomiao , Wu Yifei , Zhang Songlin , Zhu Yanxun , Yao Jin , Li Zhi , Gao Hua , Wang Xiping
Published: March 2021

Background

B-box (BBX) zinc-finger transcription factors play important roles in plant growth, development, and stress response. Although these proteins have been studied in model plants such as Arabidopsis thaliana or Oryza sativa, little is known about the evolutionary history or expression patterns of BBX proteins in grapevine (Vitis vinifera L.).

Results

We identified a total of 25 VviBBX genes in the grapevine genome and named them according to the homology with Arabidopsis. These proteins were classified into five groups on the basis of their phylogenetic relationships, number of B-box domains, and presence or absence of a CCT domain or VP motif. BBX proteins within the same group showed similar exon-intron structures and were unevenly distributed in grapevine chromosomes. Synteny analyses suggested that only segmental duplication events contributed to the expansion of the VviBBX gene family in grapevine. The observed syntenic relationships between some BBX genes from grapevine and Arabidopsis suggest that they evolved from a common ancestor. Transcriptional analyses showed that the grapevine BBX genes were regulated distinctly in response to powdery mildew infection and various phytohormones. Moreover, the expression levels of a subset of BBX genes in ovules were much higher in seedless grapevine cultivars compared with seeded cultivars during ovule development, implying a potential role in seed abortion. Additionally, VviBBX8, VquBBX15a and VquBBX29b were all located in the nucleus and had transcriptional activity except for VquBBX29b.

Conclusions

The results of this study establish the genome-wide analysis of the grapevine BBX family and provide a framework for understanding the biological roles of BBX genes in grapevine.
Telomere-to-telomere assembly of the genome of an individual Oikopleura dioica from Okinawa using Nanopore-based sequencing
Authors: Bliznina Aleksandra , Masunaga Aki , Mansfield Michael J. , Tan Yongkai , Liu Andrew W. , West Charlotte , Rustagi Tanmay , Chien Hsiao-Chiao , Kumar Saurabh , Pichon Julien , Plessy Charles , Luscombe Nicholas M.
Published: March 2021

Background

The larvaceanOikopleura dioicais an abundant tunicate plankton with the smallest (65–70 Mbp) non-parasitic, non-extremophile animal genome identified to date. Currently, there are two genomes available for the Bergen (OdB3) and Osaka (OSKA2016)O. dioicalaboratory strains. Both assemblies have full genome coverage and high sequence accuracy. However, a chromosome-scale assembly has not yet been achieved.

Results

Here, we present a chromosome-scale genome assembly (OKI2018_I69) of the OkinawanO. dioicaproduced using long-read Nanopore and short-read Illumina sequencing data from a single male, combined with Hi-C chromosomal conformation capture data for scaffolding. The OKI2018_I69 assembly has a total length of 64.3 Mbp distributed among 19 scaffolds. 99% of the assembly is contained within five megabase-scale scaffolds. We found telomeres on both ends of the two largest scaffolds, which represent assemblies of two fully contiguous autosomal chromosomes. Each of the other three large scaffolds have telomeres at one end only and we propose that they correspond to sex chromosomes split into a pseudo-autosomal region and X-specific or Y-specific regions. Indeed, these five scaffolds mostly correspond to equivalent linkage groups in OdB3, suggesting overall agreement in chromosomal organization between the two populations. At a more detailed level, the OKI2018_I69 assembly possesses similar genomic features in gene content and repetitive elements reported for OdB3. The Hi-C map suggests few reciprocal interactions between chromosome arms. At the sequence level, multiple genomic features such as GC content and repetitive elements are distributed differently along the short and long arms of the same chromosome.

Conclusions

We show that a hybrid approach of integrating multiple sequencing technologies with chromosome conformation information results in an accurate de novo chromosome-scale assembly ofO. dioica’s highly polymorphic genome. This genome assembly opens up the possibility of cross-genome comparison betweenO. dioicapopulations, as well as of studies of chromosomal evolution in this lineage.
Genome-wide identification and functional characterization of the PheE2F/DP gene family in Moso bamboo
Authors: Li Long , Shi Qianqian , Li Zhouqi , Gao Jian
Published: March 2021

Background

E2F/DP proteins have been shown to regulate genes implicated in cell cycle control and DNA repair. However, to date, research into the potential role of the Moso bamboo E2F/DP family has been limited.

Results

Here, we identified 23 E2F/DPs in the Moso bamboo genome, including nine E2F genes, six DP genes, eight DEL genes and one gene with a partial E2F domain. An estimation of the divergence time of the paralogous gene pairs suggested that the E2F/DP family expansion primarily occurred through a whole-genome duplication event. A regulatory element and coexpression network analysis indicated that E2F/DP regulated the expression of cell cycle-related genes. A yeast two-hybrid assay and expression analysis based on transcriptome data and in situ hybridization indicated that the PheE2F-PheDP complex played important roles in winter Moso bamboo shoot growth. The qRT-PCR results showed that the PheE2F/DPs exhibited diverse expression patterns in response to drought and salt treatment and diurnal cycles.

Conclusion

Our findings provide novel insights into the Moso bamboo E2F/DP family and partial experimental evidence for further functional verification of the PheE2F/DPs.
Risk factors leading to trabeculectomy surgery of glaucoma patient using Japanese nationwide administrative claims data: a retrospective non-interventional cohort study
Authors: Shirai Chikako , Tsuda Satoru , Tarasawa Kunio , Fushimi Kiyohide , Fujimori Kenji , Nakazawa Toru
Published: March 2021

Background

Early recognition and management of baseline risk factors may play an important role in reducing glaucoma surgery burdens. However, no studies have investigated them using real-world data in Japan or other countries. This study aimed to clarify the risk factors leading to trabeculectomy surgery, which is the most common procedure of glaucoma surgery, of glaucoma patient using the Japanese nationwide administrative claims data associated with the diagnosis procedure combination (DPC) system.

Methods

It was a retrospective, non-interventional cohort study. Data were collected from patients who were admitted to DPC participating hospitals, nationwide acute care hospitals and were diagnosed with glaucoma between 2012 to 2018. The primary outcome was the risk factors associated with trabeculectomy surgery. The association between baseline characteristics and trabeculectomy surgery was identified using multivariable logistic regression analysis by comparing patients with and without trabeculectomy surgery. Meanwhile, the secondary outcomes included the rate of comorbidities, the rate of concomitant drug use and the treatment patterns of glaucoma eye drops at the index admission. Among patients with trabeculectomy surgery, the risk factors leading to cataract surgery were also evaluated as subgroup analysis.

Results

A total of 29,599 patients included in the analysis, 12,038 and 17,561 patients were in the glaucoma surgery and non-glaucoma surgery cohorts, respectively. The factors associated with the increase in trabeculectomy surgery were having allergies, taking concomitant drugs including cancer, depression, ischemic heart disease and peptic ulcer, being diagnosed with primary open-angle glaucoma and longer length of stay in hospital. In contrast, the factors associated with the decrease in trabeculectomy surgery were having hypertension, taking hypertension drug, age ≥ 80 and female.

Conclusions

Special focus on Japanese patients with glaucoma who have allergy-related comorbidities or take immune, nervous, circulatory or gastrointestinal system-related concomitant drugs seems to be desirable.
Axenfeld‐Rieger syndrome combined with a foveal anomaly in a three‐generation family: a case report
Authors: Gołaszewska Kinga , Dub Natalia , Saeed Emil , Mariak Zofia , Konopińska Joanna
Published: March 2021

Background

Axenfeld-Rieger syndrome (ARS) is a rare autosomal dominant eye disorder that can also affect other organs of the human body. The condition is primarily characterized by the anterior segmental abnormalities of the eye. Here, we present an observational case series of a three-generation family with ARS and unexpected foveal anomaly.

Case presentation

A 33-year-old woman was admitted to an Ophthalmology Clinic in Bialystok for left eye congenital cataract surgery. The patient (proband) was diagnosed with visual deterioration, multiple defects of iris, corectopia, displacement of the Schwalbe’s line, and phenotypic characteristics of ARS. A perimetric examination indicated peripheral visual field loss and signs typical for glaucoma. Based on the phenotypic symptoms and genetic test, the patient was diagnosed with Axenfeld Rieger Syndrome. However, the optical coherence tomography of the macula showed foveal anomaly (absence of the physiological pit), which is not typically associated with this genetic disorder. The patient’s family history revealed that her two daughters were undergoing treatment for congenital glaucoma, and one of the daughters also had foveal anomaly the same as her mother. Interestingly, an examination of the patient’s mother showed typical phenotypic features of ARS such as a defect of the iris, posterior embryotoxon, and coloboma, as well as foveal anomaly. A genetic test confirmed PITX2 mutation in both, proband’s two daughters and mother.

Conclusions

This study highlights the occurrence of ARS with unusual ophthalmic features such as foveal anomaly (absence of the physiological pit) in a three-generation family. Although ARS is known to represent the developmental defects of the anterior segment of the eye, it is very important to perform fundus evaluation to identify associated posterior segment anomalies that may affect visual acuity. The presence of ocular defects not typically associated with ARS suggests a wide spectrum of mutations within PITX2 gene which are required to identify in order to determine genotype- phenotype correlation in ARS affected individuals.
The national rate of intensive care units-acquired infections, one-year retrospective study in Iran
Authors: Izadi Neda , Eshrati Babak , Mehrabi Yadollah , Etemad Korosh , Hashemi-Nazari Seyed-Saeed
Published: March 2021

Background

Hospital-acquired infections (HAIs) in intensive care units (ICUs) are among the avoidable morbidity and mortality causes. This study aimed at investigating the rate of ICU-acquired infections (ICU-AIs) in Iran.

Methods

For the purpose of this multi-center study, the rate of ICU-AIs calculated based on the data collected through Iranian nosocomial infections surveillance system and hospital information system. The data expanded based on 12 months of the year (13,632 records in terms of “hospital-ward-month”), and then, the last observation carried forward method was used to replace the missing data.

Results

The mean (standard deviation) age of 52,276 patients with HAIs in the ICUs was 47.37 (30.78) years. The overall rate of ICU-AIs was 96.61 per 1000 patients and 16.82 per 1000 patient-days in Iran’s hospitals. The three main HAIs in the general ICUs were ventilator-associated events (VAE), urinary tract infection (UTI), and pneumonia events & lower respiratory tract infection (PNEU & LRI) infections. The three main HAIs in the internal and surgical ICUs were VAE, UTI, and bloodstream infections/surgical site infections (BSI/SSI). The most prevalent HAIs were BSI, PNEU & LRI and eye, ear, nose, throat, or mouth (EENT) infections in the neonatal ICU and PNEU & LRI, VAE, and BSI in the PICU. Device, catheter, and ventilator-associated infections accounted for 60.96, 18.56, and 39.83% of ICU-AIs, respectively. The ventilator-associated infection rate was 26.29 per 1000 ventilator-days. Based on the Pabon Lasso model, the lowest rates of ICU-AIs (66.95 per 1000 patients and 15.19 patient-days) observed in zone III, the efficient area.

Conclusions

HAIs are common in the internal ICU wards. In fact, VAE and ventilator-related infections are more prevalent in Iran. HAIs in the ICUs leads to an increased risk of ICU-related mortality. Therefore, to reduce ICU-AIs, the specific and trained personnel must be responsible for the use of the devices (catheter use and ventilators), avoid over use of catheterization when possible, and remove catheters earlier.
Health workers’ perspectives on informed consent for caesarean section in Southern Malawi
Authors: Bakker Wouter , Zethof Siem , Nansongole Felix , Kilowe Kelvin , van Roosmalen Jos , van den Akker Thomas
Published: March 2021

Objective

Informed consent is a prerequisite for caesarean section, the commonest surgical procedure in low- and middle-income settings, but not always acquired to an appropriate extent. Exploring perceptions of health care workers may aid in improving clinical practice around informed consent. We aim to explore health workers’ beliefs and experiences related to principles and practice of informed consent.

Methods

Qualitative study conducted between January and June 2018 in a rural 150-bed mission hospital in Southern Malawi. Clinical observations, semi-structured interviews and a focus group discussion were used to collect data. Participants were 22 clinical officers, nurse-midwives and midwifery students involved in maternity care. Data were analysed to identify themes and construct an analytical framework.

Results

Definition and purpose of informed consent revolved around providing information, respecting women’s autonomy and achieving legal protection. Due to fear of blame and litigation, health workers preferred written consent. Written consent requires active participation by the consenting individual and was perceived to transfer liability to that person. A woman’s refusal to provide written informed consent may pose a dilemma for the health worker between doing good and respecting autonomy. To prevent such refusal, health workers said to only partially disclose surgical risks in order to minimize women's anxiety. Commonly perceived barriers to obtain a fully informed consent were labour pains, language barriers, women’s lack of education and their dependency on others to make decisions.

Conclusions

Health workers are familiar with the principles around informed consent and aware of its advantages, but fear of blame and litigation, partial disclosure of risks and barriers to communication hamper the process of obtaining informed consent. Findings can be used to develop interventions to improve the informed consent process.
Evaluation of a shared decision-making strategy with online decision aids in surgical and orthopaedic practice: study protocol for the E-valuAID, a multicentre study with a stepped-wedge design
Authors: Thunnissen Floris M. , Schreurs Bernhard W. , Latenstein Carmen S. S. , Meinders Marjan J. , Adang Eddy M. , Elwyn Glyn , Boersma Doeke , Bosmans Bas , Bosscha Koop , Ginsel Bastiaan L. , Hazebroek Eric J. , Nieuwenhuis Jeroen J. , Staarink Maarten , Verhallen Dries , Wagener Marc L. , Atsma Femke , de Reuver Philip R.
Published: March 2021

Background

Inguinal hernia repair, gallbladder removal, and knee- and hip replacements are the most commonly performed surgical procedures, but all are subject to practice variation and variable patient-reported outcomes. Shared decision-making (SDM) has the potential to reduce surgery rates and increase patient satisfaction. This study aims to evaluate the effectiveness of an SDM strategy with online decision aids for surgical and orthopaedic practice in terms of impact on surgery rates, patient-reported outcomes, and cost-effectiveness.

Methods

The E-valuAID-study is designed as a multicentre, non-randomized stepped-wedge study in patients with an inguinal hernia, gallstones, knee or hip osteoarthritis in six surgical and six orthopaedic departments. The primary outcome is the surgery rate before and after implementation of the SDM strategy. Secondary outcomes are patient-reported outcomes and cost-effectiveness. Patients in the usual care cluster prior to implementation of the SDM strategy will be treated in accordance with the best available clinical evidence, physician’s knowledge and preference and the patient’s preference. The intervention consists of the implementation of the SDM strategy and provision of disease-specific online decision aids. Decision aids will be provided to the patients before the consultation in which treatment decision is made. During this consultation, treatment preferences are discussed, and the final treatment decision is confirmed. Surgery rates will be extracted from hospital files. Secondary outcomes will be evaluated using questionnaires, at baseline, 3 and 6 months.

Discussion

The E-valuAID-study will examine the cost-effectiveness of an SDM strategy with online decision aids in patients with an inguinal hernia, gallstones, knee or hip osteoarthritis. This study will show whether decision aids reduce operation rates while improving patient-reported outcomes. We hypothesize that the SDM strategy will lead to lower surgery rates, better patient-reported outcomes, and be cost-effective.

Trial registration: The Netherlands Trial Register, Trial NL8318, registered 22 January 2020. URL: https://www.trialregister.nl/trial/8318.