bluuebunny/crossref_metadata_2025 huggingface dataset:
Improve hot region prediction by analyzing different machine learning algorithms
Authors: Hu Jing , Zhou Longwei , Li Bo , Zhang Xiaolong , Chen Nansheng
Published: October 2021

Background

In the process of designing drugs and proteins, it is crucial to recognize hot regions in protein–protein interactions. Each hot region of protein–protein interaction is composed of at least three hot spots, which play an important role in binding. However, it takes time and labor force to identify hot spots through biological experiments. If predictive models based on machine learning methods can be trained, the drug design process can be effectively accelerated.

Results

The results show that different machine learning algorithms perform similarly, as evaluating using the F-measure. The main differences between these methods are recall and precision. Since the key attribute of hot regions is that they are packed tightly, we used the cluster algorithm to predict hot regions. By combining Gaussian Naïve Bayes and DBSCAN, the F-measure of hot region prediction can reach 0.809.

Conclusions

In this paper, different machine learning models such as Gaussian Naïve Bayes, SVM, Xgboost, Random Forest, and Artificial Neural Network are used to predict hot spots. The experiment results show that the combination of hot spot classification algorithm with higher recall rate and clustering algorithm with higher precision can effectively improve the accuracy of hot region prediction.
Comparative phenotypic and transcriptomic analyses unravel conserved and distinct mechanisms underlying shade avoidance syndrome in Brassicaceae vegetables
Authors: Nguyen Nguyen Hoai , Sng Benny Jian Rong , Yeo Hock Chuan , Jang In-Cheol
Published: October 2021

Background

Plants grown under shade are exposed to low red/far-red ratio, thereby triggering an array of altered phenotypes called shade avoidance syndrome (SAS). Shade negatively influences plant growth, leading to a reduction in agricultural productivity. Understanding of SAS is crucial for sustainable agricultural practices, especially for high-density indoor farming. Brassicaceae vegetables are widely consumed around the world and are commonly cultivated in indoor farms. However, our understanding of SAS in Brassicaceae vegetables and their genome-wide transcriptional regulatory networks are still largely unexplored.

Results

Shade induced common signs of SAS, including hypocotyl elongation and reduced carotenoids/anthocyanins biosynthesis, in two different Brassicaceae species: Brassica rapa (Choy Sum and Pak Choy) and Brassica oleracea (Kai Lan). Phenotype-assisted transcriptome analysis identified a set of genes induced by shade in these species, many of which were related to auxin biosynthesis and signaling [e.g. YUCCA8 (YUC8), YUC9, and INDOLE-3-ACETIC ACID INDUCIBLE (IAAs)] and other phytohormones signaling pathways including brassinosteroids and ethylene. The genes functioning in plant defense (e.g. MYB29 and JASMONATE-ZIM-DOMAIN PROTEIN 9) as well as in biosynthesis of anthocyanins and glucosinolates were repressed upon shade. Besides, each species also exhibited distinct SAS phenotypes. Shade strongly reduced primary roots and elongated petioles of B. oleracea, Kai Lan. However, these SAS phenotypes were not clearly recognized in B. rapa, Choy Sum and Pak Choy. Some auxin signaling genes (e.g. AUXIN RESPONSE FACTOR 19, IAA10, and IAA20) were specifically induced in B. oleracea, while homologs in B. rapa were not up-regulated under shade. Contrastingly, shade-exposed B. rapa vegetables triggered the ethylene signaling pathway earlier than B. oleracea, Kai Lan. Interestingly, shade induced the transcript levels of LONG HYPOCOTYL IN FAR-RED 1 (HFR1) homolog in only Pak Choy as B. rapa. As HFR1 is a key negative regulator of SAS in Arabidopsis, our finding suggests that Pak Choy HFR1 homolog may also function in conferring higher shade tolerance in this variety.

Conclusions

Our study shows that two Brassicaceae species not only share a conserved SAS mechanism but also exhibit distinct responses to shade, which will provide comprehensive information to develop new shade-tolerant cultivars that are suitable for high-density indoor farms.
Alternative splicing regulation appears to play a crucial role in grape berry development and is also potentially involved in adaptation responses to the environment
Authors: Maillot Pascale , Velt Amandine , Rustenholz Camille , Butterlin Gisèle , Merdinoglu Didier , Duchêne Eric
Published: October 2021

Background

Alternative splicing (AS) produces transcript variants playing potential roles in proteome diversification and gene expression regulation. AS modulation is thus essential to respond to developmental and environmental stimuli. In grapevine, a better understanding of berry development is crucial for implementing breeding and viticultural strategies allowing adaptation to climate changes. Although profound changes in gene transcription have been shown to occur in the course of berry ripening, no detailed study on splicing modifications during this period has been published so far. We report here on the regulation of gene AS in developing berries of two grapevine (Vitis vinifera L.) varieties, Gewurztraminer (Gw) and Riesling (Ri), showing distinctive phenotypic characteristics. Using the software rMATS, the transcriptomes of berries at four developmental steps, from the green stage to mid-ripening, were analysed in pairwise comparisons between stages and varieties.

Results

A total of 305 differential AS (DAS) events, affecting 258 genes, were identified. Interestingly, 22% of these AS events had not been reported before. Among the 80 genes that underwent the most significant variations during ripening, 22 showed a similar splicing profile in Gw and Ri, which suggests their involvement in berry development. Conversely, 23 genes were subjected to splicing regulation in only one variety. In addition, the ratios of alternative isoforms were different in Gw and Ri for 35 other genes, without any change during ripening. This last result indicates substantial AS differences between the two varieties. Remarkably, 8 AS events were specific to one variety, due to the lack of a splice site in the other variety. Furthermore, the transcription rates of the genes affected by stage-dependent splicing regulation were mostly unchanged, identifying AS modulation as an independent way of shaping the transcriptome.

Conclusions

The analysis of AS profiles in grapevine varieties with contrasting phenotypes revealed some similarity in the regulation of several genes with developmental functions, suggesting their involvement in berry ripening. Additionally, many splicing differences were discovered between the two varieties, that could be linked to phenotypic specificities and distinct adaptive capacities. Together, these findings open perspectives for a better understanding of berry development and for the selection of grapevine genotypes adapted to climate change.
Prevalence of cognitive impairment in Chinese older inpatients and its relationship with 1-year adverse health outcomes: a multi-center cohort study
Authors: Yuan Li , Zhang Xiaoming , Guo Na , Li Zhen , Lv Dongmei , Wang Hui , Jin Jingfen , Wen Xianxiu , Zhao Shengxiu , Xu Tao , Jiao Jing , Wu Xinjuan
Published: October 2021

Background

Previous studies on the relationship between cognitive impairment and adverse outcomes among geriatric inpatients are not representative of older inpatients in China because of insufficient sample sizes or single-center study designs. The purpose of our study was to examine the prevalence of cognitive impairment and the relationship between cognitive impairment and 1-year adverse health outcomes in older inpatients.

Methods

This study was a large-scale multi-center cohort study conducted from October 2018 to February 2020. Six tertiary hospitals across China were selected using a two-stage cluster sampling method, and eligible older inpatients were selected for the baseline survey and follow-up. The Mini Cognitive Scale and the FRAIL scale were used to screen for cognitive impairment and frailty, respectively. The EuroQol-5 Dimension-5 Level questionnaire was used to assess health-related quality of life (HRQoL). We used a generalized estimating model to evaluate the relationship between cognitive impairment and adverse outcomes.

Results

The study included 5008 men (58.02%) and 3623 women (41.98%), and 70.64% were aged 65–75 years, and 26.27% were aged 75–85 years. Cognitive impairment was observed in 1756 patients (20.35%). There were significant differences between participants with cognitive impairment and those with normal cognitive function for age, gender, surgery status, frailty, depression, handgrip strength and so on. After adjusting for multiple covariates, compared with patients with normal cognitive function, the odds ratio for 1-year mortality was 1.216 (95% confidence interval [CI]: 1.076–1.375) and for 1-year incidence of frailty was 1.195 (95% CI: 1.037–1.376) in patients with cognitive impairment. Similarly, the regression coefficient of 1-year HRQoL was − 0.013 (95% CI: − 0.024−− 0.002). In the stratified analysis, risk of adverse outcome within 1 year was higher in older patients with cognitive impairment aged over 75 years than those aged 65–74 years.

Conclusions

We revealed that cognitive impairment was highly correlated with occurrence of 1-year adverse health outcomes (death, frailty, and decreased HRQoL) in older inpatients, which provides a basis for formulating effective intervention measures.

Trial registration

Chinese Clinical Trial Registry, ChiCTR1800017682, registered 09 August 2018.
Tear miRNA expression analysis reveals miR-203 as a potential regulator of corneal epithelial cells
Authors: Nakagawa Ayumi , Nakajima Takeshi , Azuma Mitsuyoshi
Published: October 2021

Background

microRNAs (miRNAs) are small noncoding RNAs that negatively regulate gene expression. They are found within cells and in body fluids. Extracellular miRNAs have been shown to associate with the surrounding tissues. Therefore, we predicted that miRNAs in tears may contribute to regulate corneal epithelial cell function. However, information on the miRNA expression profile of tears is limited and the specific functions of tear miRNAs for corneal epithelial cells are still unknown. To study the role of tear miRNAs, we determined which miRNAs are highly expressed in tears and examined the involvement of miRNAs in corneal epithelial cell viability.

Methods

miRNAs extracted from monkey tears and sera were subjected to microarray analysis. miRNAs of which expression levels were higher in tears than in sera were selected, and their expression levels were quantified by quantitative polymerase chain reaction (qPCR). To examine miRNA function, mimics and inhibitors of miRNAs were transfected into human corneal epithelial (HCE-T) cells and incubated for 24 or 48 h. After transfection of miRNA mimics and inhibitors, the viability of HCE-T cells was measured using the water soluble tetrazolium salt (WST) assay, and microarray analysis and qPCR were performed using total RNA extracted from HCE-T cells. siRNAs of the candidate targets for miR-203 were transfected into HCE-T cells and the WST assay was performed. To determine a direct target gene for miR-203, a dual luciferase reporter assay was performed in HCE-T cells using a luciferase reporter plasmid containing 3′-UTR of human IGFBP5.

Results

Microarray and qPCR analyses showed that miR-184 and miR-203 were expressed significantly more highly in tears than in sera (165,542.8- and 567.8-fold, respectively, p < 0.05). Of these two miRNAs, transfection of a miR-203 mimic significantly reduced the viability of HCE-T cells (p < 0.05), while a miR-203 inhibitor significantly increased this viability (p < 0.05). miR-203 mimic downregulated insulin-like growth factor-binding protein 5 (IGFBP5) and nuclear casein kinase and cyclin-dependent kinase substrate 1 (NUCKS1), while miR-203 inhibitor upregulated these two genes. Transfection of IGFBP5-siRNA decreased the viability of HCE-T cells. miR-203 mimic significantly diminished the luciferase reporter activity.

Conclusions

In this study, we identified miRNAs that are highly expressed in tears, and the inhibition of miR-203 increases the viability of corneal epithelial cells. Our results suggest that miR-203 contributes to regulating the homeostasis of corneal epithelial cells.
Expression of FRS2 in atypical lipomatous tumor/well-differentiated liposarcoma and dedifferentiated liposarcoma: an immunohistochemical analysis of 182 cases with genetic data
Authors: Jing Wenyi , Lan Ting , Qiu Yan , Peng Ran , Lu Yang , Chen Huijiao , Chen Min , He Xin , Chen Chen , Zhang Hongying
Published: October 2021

Background

The fibroblast growth factor receptor substrate 2 (FRS2) gene is located close to MDM2 and CDK4 within the 12q13-15 chromosomal region. FRS2 gene was recently found to be consistently amplified in atypical lipomatous tumor (ALT)/well-differentiated liposarcoma (WDL) and dedifferentiated liposarcoma (DDL), suggesting the detection of FRS2 amplification could be a diagnostic tool for ALT/WDL/DDLs. However, the expression of FRS2 protein and diagnostic value of FRS2 immunohistochemistry (IHC) has not been evaluated in a large cohort of ALT/WDL/DDLs.

Methods

A SNOMED search of hospital surgical pathology files from January 2007 to July 2020 identified 182 ALT/WDL/DDLs with available materials. FRS2 fluorescence in situ hybridization (FISH) and IHC were performed on 182 ALT/WDL/DDLs and 64 control samples. The expression of FRS2 was also compared with that of classic immunomarkers (MDM2 and CDK4) of this tumor entity.

Results

This study included 91 ALT/WDLs and 91 DDLs. The FISH results showed 172 of 182 (94.5%) cases were FRS2-amplified, and 10 cases were FRS2-nonamplified. Immunostaining results showed 171 (94.0%) ALT/WDL/DDLs were positive for FRS2 and 11 cases (6.0%) were FRS2-immunonegative. In 172 FRS2-amplified cases, 166 (96.5%) were FRS2-immunopositive, and 6 (3.5%) were negative. Among 10 FRS2-nonamplified ALT/WDL/DDL cases, 5 cases were FRS2-immunonegative, and 5 tumors displayed 1+ staining for this marker. In 64 control cases, none of them exhibited FRS2 amplification. Forty-seven (73.5%) control cases were negative for FRS2 immunostaining, while 17 cases (26.5%) were FRS2-immunopositive. Fifteen of these false positive samples (15/17, 88.2%) showed 1+ positivity and only 2 cases (2/17, 11.8%) displayed 2+ positivity. In ALT/WDL/DDLs, the sensitivity of FRS2 immunostaining was slightly lower than MDM2 (FRS2 vs. MDM2: 94.0% vs 100.0%) and CDK4 (FRS2 vs. CDK4: 94.0% vs 97.0%). However, the specificity of FRS2 (73.5%) was slightly higher than that of MDM2 (67.8%) and CDK4 (64.4%).

Conclusion

This study indicated that FRS2 IHC had relatively good consistency with FRS2 FISH, suggesting that FRS2 immunostaining could be utilized as an additional screening tool for the diagnosis of ALT/WDL/DDL. It must be emphasized that MDM2/CDK4/FRS2 especially MDM2 FISH remains the gold standard and the most recommended method to diagnose this entity.
The geometry of colors in van Gogh’s Sunflowers
Authors: Liao Shuting , Koehl Patrice , Schultens Jennifer , Hsieh Fushing
Published: October 2021

“Paintings fade like flowers”: van Gogh’s prediction on the impact of age on paintings came true for most of his paintings. We have studied the consequences of this aging on the Sunflowers in a vase with a yellow background series, namely its original, F454, currently in London, and two replicates, F457, in Tokyo, and F458, in Amsterdam, which van Gogh painted using the original as a model. The background and flower renditions in those paintings have faded and turned brown, making them less vibrant that van Gogh had most likely intended. We have attempted to restore van Gogh’s intent using a computational approach based on data science. After identifications of regions of interest (ROI) within the three paintings F454, F457, and F458 that capture the flowers, stems of the flowers, and background, respectively, we studied the geometry of the color space (in RGB representation) occupied by those ROIs. By comparing those color spaces with those occupied by similar ROIs in photographs of real sunflowers, we identified shifts in all three color coordinates, R, G, and B, with the positive shift in the blue coordinate being the more salient. We have proposed two algorithms, PCR-1 and PCR-2, for correcting that shift in blue and generate representations of the paintings that aim to restore their original conditions. The reduction of the blue component in the yellow hues has lead to more vibrant and less brownish digital rendition of the three Sunflowers in a vase with a yellow background.
“The City of Combat”
Authors: Nesci Catherine
Published: October 2021

This essay builds on Priscilla Parkhurst Ferguson’s pioneering inquiry on reading and writing Paris as the site of a democratizing and modernizing process and, more specifically, on her approach to Jules Vallès’s “performance of politics” in Le Tableau de Paris and L’Insurgé. I examine the ways in which Vallès’s reading of the Paris of the early 1880s and excavation of the multilayered city’s past and cultural representations help foster the return of repressed voices and collective memories. Using the trope of the city as palimpsest, I argue that the critical power of nostalgia for revolutionary Paris aims to generate a new street aesthetics and an egalitarian public sphere.
Long-Term Passive Leg Stretch Improves Systemic Vascular Responsiveness as Much as Single-Leg Exercise Training
Authors: CÈ EMILIANO , VENTURELLI MASSIMO , BISCONTI ANGELA VALENTINA , LONGO STEFANO , PEDRINOLLA ANNA , CORATELLA GIUSEPPE , SCHENA FEDERICO , ESPOSITO FABIO
Published: October 2021

Purpose

The current study compared the local and systemic vascular responsiveness after small muscle mass endurance training or passive stretching training (PST).

Methods

Thirty-six sex-matched healthy participants underwent 8-wk single-leg knee extension (SLKE) (n = 12) training or PST (n = 12), or no intervention (control, n = 12). Before and after the intervention, local and systemic vascular responsiveness was assessed by Doppler ultrasound at the femoral (local effect) and brachial artery (systemic effect) during single passive leg movement and brachial flow-mediated dilation (FMD) test, respectively.

Results

After training, delta femoral blood flow (representing the local vascular responsiveness) increased after SLKE and PST by +54 (7)% (effect size, 2.72; P < 0.001) and +20 (2)% (effect size, 2.43; P < 0.001), respectively, albeit with a greater extent in SLKE (post-SLKE vs post-PST: +56 [8]% [effect size, 2.92; P < 0.001]). Interestingly, the %FMD (standing for the systemic effect) increased after SLKE and PST by +12 (2)% (effect size, 0.68; P < 0.001) and +11 (1)% (effect size, 0.83; P < 0.001), respectively, without any between-groups difference (P > 0.05). No changes occurred in control.

Conclusions

The present findings revealed that both active and passive training modalities induced similar improvements in the brachial artery dilatation capacity, whereas the former was more effective in improving femoral artery blood flow. Passive stretching could be used in people with limited mobility to improve vascular responsiveness both at the local and systemic level and in this latter case has similar effects as small muscle mass endurance training.
Promoting Physical Activity in Rural Settings: Effectiveness and Potential Strategies
Authors: Smith Whitney J. , Martin Michelle Y. , Pisu Maria , Oster Robert A. , Qu Haiyan , Shewchuk Richard M. , Sheffield Mary E. , Minter Alex , Baumann Ana A. , Rogers Laura Q.
Published: October 2021

Implementing efficacious physical activity interventions in real-world rural settings is needed because rural cancer survivors are more physically inactive and experience poorer health. To address this gap, this study evaluated the effectiveness of an evidenced-based physical activity program (Better Exercise Adherence after Treatment for Cancer [BEAT Cancer]) for rural women cancer survivors when implemented by community-based nonresearch staff. Sixteen rural women cancer survivors received BEAT Cancer implemented by a rural community organization and nonresearch staff; physical activity, patient-reported outcomes, and social cognitive constructs were measured at baseline and postprogram. Cancer survivors and interventionists completed program evaluations postprogram. Cancer survivor mean age was 58 ± 12 yr; 62% were White. Mean months since diagnosis was 54 ± 72; 69% had breast cancer. Significant improvements from pre- to postprogram occurred for self-report weekly minutes of moderate to vigorous physical activity (mean change [M] = 146 ± 186, P = 0.009), anxiety (M = −1.3 ± 1.8, P = 0.016), depression (M = −2.1 ± 2.0, P = 0.001), self-efficacy (M = 20.9 ± 30.5, P = 0.019), barriers interference (M = −15.0 ± 14.1, P = 0.001), and social support (M = 5.0 ± 7.4, P = 0.02). Cancer survivors ranked the program highly, identified strategies that were helpful (e.g., group activities, personalized exercise plan, etc.), and suggested additional implementation strategies (e.g., guide for home-based phase, etc.). Interventionists identified strategies (e.g., logistics, staff training and certification, cost, etc.) for enhancing organizational readiness for program delivery. Evidence-based physical activity programs can be effective when implemented by nonresearch staff in rural settings. Further research testing strategies that improve implementation are needed. Effectiveness and identified strategies supporting delivery when implemented by a rural organization can improve physical activity promotion for rural at-risk populations.
Popularization of the History of Kazan Journalism by Students of the Higher School of Journalism and Media Communications of Kazan (Volga Region) Federal University as a Communication Project: Achievements and Problems
Authors: Bakanov Roman
Published: October 2021

In the article is telling with the use of modern digital technologies when students of the Higher School of Journalism and Media Communications of Kazan (Volga Region) Federal University master some disciplines related to the history of regional journalism, as well as the language and creative style of local publicists. These were the first attempts of creative and project activities of students, the information occasion for which was the 210th anniversary of Kazan journalism. This anniversary is celebrated in 2021, but there will not be a wide celebration for various reasons. Using the methods of included observation, meaningful, structural and comparative analysis of each of the student online projects, using the example of educational project activities of fourth-year students studying in the direction of "Journalism", the author identified the reasons why the anniversary of Kazan journalism has not yet gone beyond the professional journalistic circle, studied the course and dynamics, as well as the pros and cons of implementing the creative process within the existing administrative, managerial and material and technical conditions for training a modern journalist as a versatile creative person. While working on this creative task, students had the opportunity to try their hand at such media fields of activity as a correspondent, photojournalist, director of photography, screenwriter, director, author of stories, infographer, bild editor, editor, videographer, producer and reviewer and understand in which of them each student feels more confident and comfortable. In this article, we studied how well the media projects created by students showed and realized their communicative function: with the help of what creative techniques or the modern digital means used, students managed (and whether they managed) to interest the audience and cause a response from it. The author of the article also concludes that during their preparation, students of the Higher School of Journalism and Media Communications of KFU experienced difficulties of both a technical and organizational and creative nature. The insufficient thematic and intellectual background also made itself felt and manifested itself in the created projects in the form of some factual inaccuracies and errors. However, in general, the first experience of students' creative activity in the implementation of a communicative project can be considered successful.
Institutional changes in politics
Authors: Mieleszko Anna
Published: October 2021

Motivation: Institutions are a set of rules of the game, norms and values that constitute a fundamental element of any social and political system. Political institutions are an important object of theoretical considerations and a number of attempts at explanations in political science. in their research, they put more emphasis on the effects of political institutions than on issues related to their genesis and the changes taking place. This article is in the trend of New Institutionalism which focuses on the causal role and the limited ability to design new tools, as well as a strong intention in this area.

Aim: The aim of the article is to provide a synthetic overview of the causes and effects of continuity and changes in formal political institutions within the interdisciplinary area — new institutionalism. The research methods used during the preparation of the article include the analysis and criticism of the literature

Results: The article focuses on presenting the role of institutions in political life, showing the dysfunctionality of the institutional sphere in the face of pressure from interest groups and the game of political actors. The explanation of these aspects was served by logical constructions and analyzes, primarily of a historical and sociological study, emphasizing the importance of determinants of informal institutions on the durability and institutional change.
Directional Necessary Optimality Conditions for Bilevel Programs
Authors: Bai Kuang , Ye Jane J.
Published: October 2021

The bilevel program is an optimization problem in which the constraint involves solutions to a parametric optimization problem. It is well known that the value function reformulation provides an equivalent single-level optimization problem, but it results in a nonsmooth optimization problem that never satisfies the usual constraint qualification, such as the Mangasarian–Fromovitz constraint qualification (MFCQ). In this paper, we show that even the first order sufficient condition for metric subregularity (which is, in general, weaker than MFCQ) fails at each feasible point of the bilevel program. We introduce the concept of a directional calmness condition and show that, under the directional calmness condition, the directional necessary optimality condition holds. Although the directional optimality condition is, in general, sharper than the nondirectional one, the directional calmness condition is, in general, weaker than the classical calmness condition and, hence, is more likely to hold. We perform the directional sensitivity analysis of the value function and propose the directional quasi-normality as a sufficient condition for the directional calmness. An example is given to show that the directional quasi-normality condition may hold for the bilevel program.
More planning and slower discharge: a qualitative study of the facilitators of and barriers to a smooth discharge for stroke patients
Authors: Freaney Sharon
Published: October 2021

Background:

It is likely that one-third of people that experience a stroke will be dependent on others for their care after discharge from hospital.

Aims:

This study aims to explore the perspectives of a range of stakeholders about the challenges impacting on a smooth transition from hospital to home following a stroke.

Methods:

A qualitative study was conducted, which involved people living with stroke (n=3), family carers (n=3) and senior nurses (n=5) from one health trust in the UK. Face-to-face interviews, telephone interviews and open response questionnaires were used for data collection. An inductive approach informed data analysis.

Findings:

The three main themes that emerged from the data analysis were 1) communication and information, 2) support mechanisms, and 3) organisational issues. The findings indicate a gap between what the service is presently delivering and what patients and carers require for a smooth care transition from hospital to home.

Conclusions:

The author recommends timely, coordinated discharge planning that actively involves the patient and family carer, the implementation of day leave and weekend leave, and the involvement of the family carer in providing some aspects of care for their relative in the hospital environment.
Maintaining chromatic dispersion and signal gain performances in a chalcogenide buffer step-index optical fiber
Authors: Tong Hoang Tuan , Koumura Ayaka , Nakatani Asuka , Suzuki Takenobu , Ohishi Yasutake
Published: October 2021

Aiming at maintaining the chromatic dispersion properties and fiber optical parametric amplification (FOPA) performance when fiber core fluctuation occurs, we propose a buffer step-index optical fiber. The AsSe2 chalcogenide glass is employed as the core material due to its high nonlinearity and broad transmission spectrum. The calculated results in this study show that the chromatic dispersion variation due to the change of core diameter can be greatly suppressed and a continuous and very broad FOPA signal gain spectrum can be obtained and maintained by carefully controlling the core, buffer and cladding properties such as refractive index and diameters. The calculated results in this study showed that by using the proposed 3-cm-long fiber pumped at 5.02 µm, a broad signal gain bandwidth from 3 to 14 µm at about 15 dB is attainable although the fiber core diameter Dc drastically fluctuated from 2 to 5 µm and the buffer diameter Db varies from 8.9 to 9.3 µm. Moreover, when Dc varies in smaller range from 3 to 4 µm, the FOPA signal gain spectra calculated at different fixed values of Db in the range from 8.9 to 9.3 µm are highly maintained. When Db is kept at 9.0 µm and Dc varies from 3 to 4 µm, the calculated FOPA signal gain spectra at different pump wavelengths from 4.98 to 5.02 µm are also nearly identical in the wavelength range from 3 up to 13 µm.
High-efficient subwavelength-scale optofluidic waveguides with tapered microstructured optical fibers
Authors: Yu Ruowei , Wang Caoyuan , Jiang Wei , Shen Zihao , Yan Zhengyu , Hao Yang , Shi Yuzhi , Yu Fei , Hua Ping , Schötz Gerhard , Liu Ai Qun , Xiao Limin
Published: October 2021

Microstructured optical fibers (MOFs) have attracted intensive research interest in fiber-based optofluidics owing to their ability to have high-efficient light-microfluid interactions over a long distance. However, there lacks an exquisite design guidance for the utilization of MOFs in subwavelength-scale optofluidics. Here we propose a tapered hollow-core MOF structure with both light and fluid confined inside the central hole and investigate its optofluidic guiding properties by varying the diameter using the full vector finite element method. The basic optical modal properties, the effective sensitivity, and the nonlinearity characteristics are studied. Our miniature optofluidic waveguide achieves a maximum fraction of power inside the core at 99.7%, an ultra-small effective mode area of 0.38 µm2, an ultra-low confinement loss, and a controllable group velocity dispersion. It can serve as a promising platform in the subwavelength-scale optical devices for optical sensing and nonlinear optics.
All-optical intensity fluctuation magnification using Kerr effect: erratum
Authors: Vanus Benoit , Baker Chams , Chen Liang , Bao Xiaoyi
Published: October 2021

We provide a correction to a figure in our published paper [Opt. Express 28, 3789 (2020)10.1364/OE.384004].
Complexity and diversity in sparse code priors improve receptive field characterization of Macaque V1 neurons
Authors: Wu Ziniu , Rockwell Harold , Zhang Yimeng , Tang Shiming , Lee Tai Sing
Published: October 2021

System identification techniques—projection pursuit regression models (PPRs) and convolutional neural networks (CNNs)—provide state-of-the-art performance in predicting visual cortical neurons’ responses to arbitrary input stimuli. However, the constituent kernels recovered by these methods are often noisy and lack coherent structure, making it difficult to understand the underlying component features of a neuron’s receptive field. In this paper, we show that using a dictionary of diverse kernels with complex shapes learned from natural scenes based on efficient coding theory, as the front-end for PPRs and CNNs can improve their performance in neuronal response prediction as well as algorithmic data efficiency and convergence speed. Extensive experimental results also indicate that these sparse-code kernels provide important information on the component features of a neuron’s receptive field. In addition, we find that models with the complex-shaped sparse code front-end are significantly better than models with a standard orientation-selective Gabor filter front-end for modeling V1 neurons that have been found to exhibit complex pattern selectivity. We show that the relative performance difference due to these two front-ends can be used to produce a sensitive metric for detecting complex selectivity in V1 neurons.
Prevalence of depression and associated factors among patients with epilepsy at the University of Gondar Comprehensive Specialized Hospital, Northwest Ethiopia, 2019
Authors: Addis Banchlay , Wolde Maereg , Minyihun Amare , Aschalew Andualem Yalew
Published: October 2021

Introduction

Depression is a commonly overwhelming problem among patients with epilepsy which compromises their quality of life especially in developing countries. Previously limited studies were conducted using Becks Depression Inventory tool in Ethiopia. The aim of this study’s objective was to determine the prevalence of depression and associated factors among patients with epilepsy.

Methods

Institution based cross-sectional study was employed at the University of Gondar Comprehensive Specialized Hospital from March 01–30, 2019.A total of 370 participants were selected using an interview administered structured questionnaire. Hospital Anxiety and Depression Scale was used to assess the prevalence of depression.Multivariable logistic regression analysis was done to investigate potential predictors and variables with a P-value of < 0.05 and a 95% confidence interval were considered statistically significant.

Results

A total of 370 study participants participated with a response rate of 92%. From the total respondents 37% experienced depression. Perceived stigma (AOR = 3.89, CI: 2.27, 6.68), educational status (AOR = 0.48, CI: 0.25, 0.92), residence (AOR = 0.5, CI: 0.28, 0.89), frequency of seizure (AOR = 2.07, CI: 1.01, 4.23) and social support (AOR = 2.73, CI: 1.41–5.31) were significantly associated with depression status.

Conclusion

This study revealed that prevalence of depression among Epileptic patients was high. Perceived stigma, educational status, residence, frequency of seizure and social support were significantly associated with depression status. Thus, health care workers better to give more emphasis to patients with perceived stigma, higher number of seizure frequency and to those with poor level of social support.
Single nucleotide polymorphisms and copy-number variations in the Trypanosoma brucei repeat (TBR) sequence can be used to enhance amplification and genotyping of Trypanozoon strains
Authors: Van Reet Nick , Patient Pyana Pati , Dehou Sara , Bebronne Nicolas , Deborggraeve Stijn , Büscher Philippe
Published: October 2021

The Trypanosoma brucei repeat (TBR) is a tandem repeat sequence present on the Trypanozoon minichromosomes. Here, we report that the TBR sequence is not as homogenous as previously believed. BLAST analysis of the available T. brucei genomes reveals various TBR sequences of 177 bp and 176 bp in length, which can be sorted into two TBR groups based on a few key single nucleotide polymorphisms. Conventional and quantitative PCR with primers matched to consensus sequences that target either TBR group show substantial copy-number variations in the TBR repertoire within a collection of 77 Trypanozoon strains. We developed the qTBR, a novel PCR consisting of three primers and two probes, to simultaneously amplify target sequences from each of the two TBR groups into one single qPCR reaction. This dual probe setup offers increased analytical sensitivity for the molecular detection of all Trypanozoon taxa, in particular for T.b. gambiense and T. evansi, when compared to existing TBR PCRs. By combining the qTBR with 18S rDNA amplification as an internal standard, the relative copy-number of each TBR target sequence can be calculated and plotted, allowing for further classification of strains into TBR genotypes associated with East, West or Central Africa. Thus, the qTBR takes advantage of the single-nucleotide polymorphisms and copy number variations in the TBR sequences to enhance amplification and genotyping of all Trypanozoon strains, making it a promising tool for prevalence studies of African trypanosomiasis in both humans and animals.
Developing a logic model of change for the determinants of parental nurturance in the first 1000 days: A mixed-method study protocol
Authors: Goldschmidt Tessa , Adebiyi Babatope O. , Roman Nicolette V.
Published: October 2021

Background

Parents play a key role in providing nurturance and nurturing care to their child during the first 1000 days which is important for optimal child development. Various factors have been found to influence parenting but the contribution of these factors toward parental nurturance within the first 1000 days is not yet known in the South African context. This paper describes a protocol for a project that aims to develop a logic model of change for the determinants of parental nurturance in the first 1000 days in the South African context.

Method

This study will apply a mixed methods approach with a sequential design within an intervention mapping framework. The study will occur in two phases. The first phase will identify the problem, which will be done via a scoping review, a policy review and a needs assessment for parents and stakeholders. This phase will recruit approximately 35 participants (20 parents and 15 stakeholders) for the qualitative component and then approximately 398 participants for the quantitative component. Data will be collected via semi-structured interviews and with questionnaires (Home Observation for Measurement of the Environment Inventory, the Depression and Anxiety Scale, and the Multidimensional Perceived Social Support Scale). Data will be thematically analysed, and the Statistical Package for Social Science (SPSS) will be used to determine descriptive statistics, both of which will inform the development of the model in phase 2. The second phase will be the development of a logic model of change for determinants for parental nurturance in the first thousand days. This phase will consist of one stage- a consensus workshop which will be attended by approximately 20 participants (5 parents, 5 pregnant woman/new mothers, and 10 stakeholders). The data collected in this stage will be thematically analysed and will contribute to the refinement of the model.

Discussion

The first thousand days (FTD) is a period in which rapid growth occurs in all domains of development. If children do not receive sensitive and responsive care in an environment that is conducive for their optimal development, children may not reach their full developmental potential.
Accuracy of Kinovea software in estimating body segment movements during falls captured on standard video: Effects of fall direction, camera perspective and video calibration technique
Authors: Shishov Nataliya , Elabd Karam , Komisar Vicki , Chong Helen , Robinovitch Stephen N.
Published: October 2021

Falls are a major cause of unintentional injuries. Understanding the movements of the body during falls is important to the design of fall prevention and management strategies, including exercise programs, mobility aids, fall detectors, protective gear, and safer environments. Video footage of real-life falls is increasingly available, and may be used with digitization software to extract kinematic features of falls. We examined the validity of this approach by conducting laboratory falling experiments, and comparing linear and angular positions and velocities measured from 3D motion capture to estimates from Kinovea 2D digitization software based on standard surveillance video (30 Hz, 640x480 pixels). We also examined how Kinovea accuracy depended on fall direction, camera angle, filtering cut-off frequency, and calibration technique. For a camera oriented perpendicular to the plane of the fall (90 degrees), Kinovea position data filtered at 10 Hz, and video calibration using a 2D grid, mean root mean square errors were 0.050 m or 9% of the signal amplitude and 0.22 m/s (7%) for vertical position and velocity, and 0.035 m (6%) and 0.16 m/s (7%) for horizontal position and velocity. Errors in angular measures averaged over 2-fold higher in sideways than forward or backward falls, due to out-of-plane movement of the knees and elbows. Errors in horizontal velocity were 2.5-fold higher for a 30 than 90 degree camera angle, and 1.6-fold higher for calibration using participants’ height (1D) instead of a 2D grid. When compared to 10 Hz, filtering at 3 Hz caused velocity errors to increase 1.4-fold. Our results demonstrate that Kinovea can be applied to 30 Hz video to measure linear positions and velocities to within 9% accuracy. Lower accuracy was observed for angular kinematics of the upper and lower limb in sideways falls, and for horizontal measures from 30 degree cameras or 1D height-based calibration.
S-farnesylation is essential for antiviral activity of the long ZAP isoform against RNA viruses with diverse replication strategies
Authors: Kmiec Dorota , Lista María José , Ficarelli Mattia , Swanson Chad M. , Neil Stuart J. D.
Published: October 2021

The zinc finger antiviral protein (ZAP) is a broad inhibitor of virus replication. Its best-characterized function is to bind CpG dinucleotides present in viral RNAs and, through the recruitment of TRIM25, KHNYN and other cofactors, target them for degradation or prevent their translation. The long and short isoforms of ZAP (ZAP-L and ZAP-S) have different intracellular localization and it is unclear how this regulates their antiviral activity against viruses with different sites of replication. Using ZAP-sensitive and ZAP-insensitive human immunodeficiency virus type I (HIV-1), which transcribe the viral RNA in the nucleus and assemble virions at the plasma membrane, we show that the catalytically inactive poly-ADP-ribose polymerase (PARP) domain in ZAP-L is essential for CpG-specific viral restriction. Mutation of a crucial cysteine in the C-terminal CaaX box that mediates S-farnesylation and, to a lesser extent, the residues in place of the catalytic site triad within the PARP domain, disrupted the activity of ZAP-L. Addition of the CaaX box to ZAP-S partly restored antiviral activity, explaining why ZAP-S lacks antiviral activity for CpG-enriched HIV-1 despite conservation of the RNA-binding domain. Confocal microscopy confirmed the CaaX motif mediated localization of ZAP-L to vesicular structures and enhanced physical association with intracellular membranes. Importantly, the PARP domain and CaaX box together jointly modulate the interaction between ZAP-L and its cofactors TRIM25 and KHNYN, implying that its proper subcellular localisation is required to establish an antiviral complex. The essential contribution of the PARP domain and CaaX box to ZAP-L antiviral activity was further confirmed by inhibition of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) replication, which replicates in double-membrane vesicles derived from the endoplasmic reticulum. Thus, compartmentalization of ZAP-L on intracellular membranes provides an essential effector function in ZAP-L-mediated antiviral activity against divergent viruses with different subcellular replication sites.
Recloning and Characterization of C2C12 Myoblast and Its Clonal Derivatives
Authors: Prasetyaningrum Pekik Wiji , Septisetyani Endah Puji , Suyoko Ahmad , Santoso Adi
Published: October 2021

The C2C12 myoblasts are adult murine muscle stem cells which isolated after injury to induce muscle regeneration. The cells are widely used in pharmaceutical and biological researches to represent skeletal muscle cells. In our laboratory, we utilize the cells for glucose uptake assay after insulin treatment and studying the muscle regeneration. In this study we conducted recloning of C2C12 cells by limiting dilution cloning (LDC) and investigated the biological properties incuding cell proliferation, adhesion and differentiation of the clonal cells in comparison to the parental cells. Cell proliferation rate had been determined by WST assay, cell adhesion had been observed after cell detachment by EDTA and cell differentiation into multinucleated myotube had been investigated after induction and incubation with horse serum. As results, two clonal derivatives of C2C12 myoblast cells had been retrieved by LDC and used for cell assays. Moreover, the results indicated that parental cells showed faster proliferation rate and better differentiation ability than that of clonal cells. In the contrary the parental cells exhibited weaker adhesion rate than clonal cells. To conclude, C2C12 parental cells are better for performing the glucose uptake or muscle regeneration assays since they showed better differentiation capability.Keywords: C2C12 cells, cells differentiation, myoblast, myotube, recloning.
Transition from the Taylor rule to the zero lower bound
Authors: Hurn Stan , Johnson Nicholas , Silvennoinen Annastiina , Teräsvirta Timo
Published: October 2021

This paper examines the Taylor rule in the context of United States monetary policy since 1965, particularly with respect to the zero-lower-bound era of the federal funds rate from 2009 to 2016. A nonlinear Taylor rule is developed which features smooth transitions in the first two moments of the federal funds rate. This flexible specification is found to usefully capture observed nonlinearity, while accounting for the well-documented structural changes in monetary policy formation at the Federal Reserve in the last 50 years, and especially in the recent zero-lower-bound era.