bluuebunny/crossref_metadata_2025 huggingface dataset:
Glycans in Virus-Host Interactions: A Structural Perspective
Authors: Miller Nathaniel L. , Clark Thomas , Raman Rahul , Sasisekharan Ram
Published: June 2021

Many interactions between microbes and their hosts are driven or influenced by glycans, whose heterogeneous and difficult to characterize structures have led to an underappreciation of their role in these interactions compared to protein-based interactions. Glycans decorate microbe glycoproteins to enhance attachment and fusion to host cells, provide stability, and evade the host immune system. Yet, the host immune system may also target these glycans as glycoepitopes. In this review, we provide a structural perspective on the role of glycans in host-microbe interactions, focusing primarily on viral glycoproteins and their interactions with host adaptive immunity. In particular, we discuss a class of topological glycoepitopes and their interactions with topological mAbs, using the anti-HIV mAb 2G12 as the archetypical example. We further offer our view that structure-based glycan targeting strategies are ready for application to viruses beyond HIV, and present our perspective on future development in this area.
From System Modeling to System Analysis: The Impact of Resolution Level and Resolution Distribution in the Computer-Aided Investigation of Biomolecules
Authors: Giulini Marco , Rigoli Marta , Mattiotti Giovanni , Menichetti Roberto , Tarenzi Thomas , Fiorentini Raffaele , Potestio Raffaello
Published: June 2021

The ever increasing computer power, together with the improved accuracy of atomistic force fields, enables researchers to investigate biological systems at the molecular level with remarkable detail. However, the relevant length and time scales of many processes of interest are still hardly within reach even for state-of-the-art hardware, thus leaving important questions often unanswered. The computer-aided investigation of many biological physics problems thus largely benefits from the usage of coarse-grained models, that is, simplified representations of a molecule at a level of resolution that is lower than atomistic. A plethora of coarse-grained models have been developed, which differ most notably in their granularity; this latter aspect determines one of the crucial open issues in the field, i.e. the identification of an optimal degree of coarsening, which enables the greatest simplification at the expenses of the smallest information loss. In this review, we present the problem of coarse-grained modeling in biophysics from the viewpoint of system representation and information content. In particular, we discuss two distinct yet complementary aspects of protein modeling: on the one hand, the relationship between the resolution of a model and its capacity of accurately reproducing the properties of interest; on the other hand, the possibility of employing a lower resolution description of a detailed model to extract simple, useful, and intelligible information from the latter.
Nascent Folding of Proteins Across the Three Domains of Life
Authors: Chwastyk Mateusz , Cieplak Marek
Published: June 2021

We study the nascent behavior of three model coarse-grained proteins in six rigid all-atom structures representing ribosomes that come from three domains of life. The synthesis of the proteins is implemented as a growth process. The geometry of the exit tunnel is quantified and shown to differ between the domains of life: both in volume and the size of constriction sites. This results in different characteristic times of capture within the tunnel and various probabilities of the escape. One of the proteins studied is the bacterial YibK which is knotted in its native state. A fraction of the trajectories results in knotting and the probability of doing so is largest for the bacterial ribosomes. Relaxing the condition of the rigidness of the ribosomes should result in a better avoidance of trapping and better proper folding.
The Promising Effect of Nerve Decompression in Trigeminal Autonomic Cephalalgias: Report of Case Series
Authors: Togha Mansoureh , Totonchi Ali , Molaei Hojjat , Ansari Hossein
Published: June 2021

Trigeminal Autonomic Cephalalgias (TAC) are excruciating headaches with limited treatment options. The chronic forms of TACs, including chronic cluster, chronic paroxysmal hemicrania, and hemicrania continua, are disabling conditions. In addition to drug therapy, there are some studies regarding nerve blocking and nerve stimulation with acceptable results. Here we report four cases of decompression nerve surgery with promising results on pain control in these difficult to treat headaches.
Modal-Polar Representation of Evoked Response Potentials in Multiple Arousal States
Authors: El-Zghir Rawan K. , Gabay Natasha C. , Robinson Peter A.
Published: June 2021

An expansion of the corticothalamic transfer function into eigenmodes and resonant poles is used to derive a simple formula for evoked response potentials (ERPs) in various states of arousal. The transfer function corresponds to the cortical response to an external stimulus, which encodes all the information and properties of the linear system. This approach links experimental observations of resonances and characteristic timescales in brain activity with physically based neural field theory (NFT). The present work greatly simplifies the formula of the analytical ERP, and separates its spatial part (eigenmodes) from the temporal part (poles). Within this framework, calculations involve contour integrations that yield an explicit expression for ERPs. The dominant global mode is considered explicitly in more detail to study how the ERP varies with time in this mode and to illustrate the method. For each arousal state in sleep and wake, the resonances of the system are determined and it is found that five poles are sufficient to study the main dynamics of the system in waking eyes-open and eyes-closed states. Similarly, it is shown that six poles suffice to reproduce ERPs in rapid-eye movement sleep, sleep state 1, and sleep state 2 states, whereas just four poles suffice to reproduce the dynamics in slow wave sleep. Thus, six poles are sufficient to preserve the main global ERP dynamics of the system for all states of arousal. These six poles correspond to the dominant resonances of the system at slow-wave, alpha, and beta frequencies. These results provide the basis for simplified analytic treatment of brain dynamics and link observations more closely to theory.
Cassava Orange-Fleshed Sweetpotato Composite Gari: A Potential Source of Dietary Vitamin A
Authors: Atuna Richard Atinpoore , Achaglinkame Matthew Atongbiik , Accorley Trudy Abla Sitsofe , Amagloh Francis Kweku
Published: June 2021

Gari, a fermented granular cassava food product, continues to play a major role in the diets of West Africans. The white cassava commonly used for this product is devoid of provitamin A but may have a significant concentration of cyanogenic compounds. The physicochemical and functional properties of partial substitution of cassava with orange-fleshed sweetpotato (OFSP) to process gari were investigated. Two commonly consumed products “eba” and “soaked gari” were prepared from the various formulations and sensorially assessed. Cassava OFSP composite gari (77% cassava:23% OFSP, 75% cassava:25% OFSP, and 73% cassava:27% OFSP) did not significantly (p > 0.05) influence the moisture content (3.39%−5.42%, p = 0.38), water absorption capacity (589–671 mL/g, p = 0.22), and swelling index (3.75–4.17, p = 0.08) compared with that of 100% cassava gari. Expectedly, increasing the levels of OFSP incorporation significantly (p < 0.001) resulted in color change from white (L* = 83.99, a* = 0.93, b* = 16.35) to orange (L* = 69.26, a* = 7.74, b* = 28.62). For β-carotene, the 73% cassava:27% sample was ~5.2 times more than the level in 100% cassava gari. Also, it had lower residual cyanogenic compounds (0.37 vs. 1.71 mg/kg, p < 0.001, measured as hydrogen cyanide) compared with cassava-only gari. The sensory scores by the 100 panelists using a five-point hedonic scale (1 = dislike extremely to 5 = like extremely) exceeded the minimum threshold (3) for acceptance. Within the limits of this study, OFSP can be composited with cassava up to 27% to process gari that has similar physicochemical properties and sensorial preference as that of cassava only. Furthermore, the OFSP-composited gari contains a significant amount of provitamin A and have a reduced residual cyanogenic compound. Thus, the composited gari could play a significant role in addressing vitamin A deficiency in Ghana compared to the 100% cassava only.
Integrative Analysis of a Novel Eleven-Small Nucleolar RNA Prognostic Signature in Patients With Lower Grade Glioma
Authors: Deng Teng , Gong Yizhen , Liao Xiwen , Wang Xiangkun , Zhou Xin , Zhu Guangzhi , Mo Ligen
Published: June 2021

Objective

The present study used the RNA sequencing (RNA-seq) dataset to identify prognostic snoRNAs and construct a prognostic signature of The Cancer Genome Atla (TCGA) lower grade glioma (LGG) cohort, and comprehensive analysis of this signature.

Methods

RNA-seq dataset of 488 patients from TCGA LGG cohort were included in this study. Comprehensive analysis including function enrichment, gene set enrichment analysis (GSEA), immune infiltration, cancer immune microenvironment, and connectivity map (CMap) were used to evaluate the snoRNAs prognostic signature.

Results

We identified 21 LGG prognostic snoRNAs and constructed a novel eleven-snoRNA prognostic signature for LGG patients. Survival analysis suggests that this signature is an independent prognostic risk factor for LGG, and the prognosis of LGG patients with a high-risk phenotype is poor (adjusted P = 0.003, adjusted hazard ratio = 2.076, 95% confidence interval = 1.290–3.340). GSEA and functional enrichment analysis suggest that this signature may be involved in the following biological processes and signaling pathways: such as cell cycle, Wnt, mitogen-activated protein kinase, janus kinase/signal transducer and activator of tran-ions, T cell receptor, nuclear factor-kappa B signaling pathway. CMap analysis screened out ten targeted therapy drugs for this signature: 15-delta prostaglandin J2, MG-262, vorinostat, 5155877, puromycin, anisomycin, withaferin A, ciclopirox, chloropyrazine and megestrol. We also found that high- and low-risk score phenotypes of LGG patients have significant differences in immune infiltration and cancer immune microenvironment.

Conclusions

The present study identified a novel eleven-snoRNA prognostic signature of LGG and performed a integrative analysis of its molecular mechanisms and relationship with tumor immunity.
Analysis of Applicator Insertion Related Acute Side Effects for Cervical Cancer Treated With Brachytherapy
Authors: Chen Jiajun , Zhang Ning , Liu Ying , Han Dongmei , Mao Zhuang , Yang Wei , Cheng Guanghui
Published: June 2021

Purpose

To report applicator insertion-related acute side effects during brachytherapy (BT) procedure for cervical cancer patients.

Materials and Methods

Between November 2017 and December 2019, 407 BT fractions were performed in 125 patients with locally advanced cervical cancer. Acute side effects recorded comprised anesthesia-related side effects, mechanical-related side effects and infection, whose frequency and degree were recorded. Pain was assessed using numeric rating scale; vaginal bleeding volume was counted by weighing gauze pieces used in packing. The BT procedure comprised eight stages: anesthesia, applicator insertion, image acquisition, transport, waiting for treatment, dose delivery, applicator removal, and removed which denoted 0.5–12.0 h period after removal, with time of each stage recorded. Factors influencing acute side effects were assessed by Spearman correlation and Mann–Whitney U test.

Results

The most common acute side effect was pain, followed by vaginal bleeding. The mean scores for pain were highest during removal time, 4.9 ± 1.6 points. The mean vaginal bleeding volume was 44.4 ml during removal time. Mean total procedure time was 218.8 (175–336) min, having positive relationship with frequency of acute side effects. The total procedure time with acute side effects was longer than that without acute side effects. The longest procedure time was waiting time, 113.0 (91.0–132.0) min. More needles generated higher pain scores and larger volume of vaginal bleeding.

Conclusion

Pain and vaginal bleeding were the most common acute side effects, especially during removal time, which physicians should focus on. Shortening patients’ waiting time helps to reduce the total procedure time, thus, reduce acute side effects. While meeting dose requirement, less needles are helpful to reduce acute side effects.
Positive Impact of Organized Physical Exercise on Quality of Life and Fatigue in Children and Adolescents With Cancer
Authors: Spreafico Filippo , Barretta Francesco , Murelli Michele , Chisari Marco , Gattuso Giovanna , Terenziani Monica , Ferrari Andrea , Veneroni Laura , Meazza Cristina , Massimino Maura
Published: June 2021

Background: Cancer and its treatment can cause serious health issues that impair physical and mental well-being in children and adolescents. Exercise may be a valid strategy for managing some symptoms, including fatigue. In the light of our experience, we provide further justification for including exercise as part of routine childhood cancer care.

Methods: Forty-four children and adolescents who had solid cancers not contraindicating their movement were invited to join an in-hospital 6-week supervised exercise program, and asked afterwards to complete validated quality of life and fatigue scales. The program consisted of personalized workout sessions of aerobic, resistance and flexibility exercises. The results obtained on the scales were compared between 21 patients who engaged in the exercise program (GYM group) and 23 who refused (No-GYM group), examining the different dimensions of health-related quality of life (physical, emotional, cognitive, social) and fatigue (general, sleep/rest, cognitive) in the two groups.

Results: Being diagnosed with cancer initially prompted all but one of the respondents to drop-out of previous routine exercise or sports although their continuation had not been contraindicated. After 6 weeks of exercise, the GYM group's scores for quality of life and fatigue showed a statistically significant better perceived emotional functioning, and a trend toward a better social functioning than in the No-GYM group.

Conclusion: We suggest that exercise improves the satisfaction of children and adolescents with cancer with their physical, mental and social functioning. We would emphasize the potential benefits of general practitioners discussing and recommending exercise for their young patients with cancer.
1p36 Deletion Syndrome and Left Ventricular Non-compaction Cardiomyopathy—Two Cases Report
Authors: Jang Subin , Taber Allison , Bateman Michael G. , Steiner Marie E. , Ameduri Rebecca K. , Griselli Massimo
Published: June 2021

1p36 deletion is the most common terminal deletion syndrome in humans. Herein, we report two cases, a 5-month-old female and a 14.5-year-old female, both with 1p36 deletion and left ventricular non-compaction cardiomyopathy. They presented with severely depressed left ventricle function and underwent heart transplantation with excellent outcomes. Given the incidence of heart defects and cardiomyopathy in 1p36 deletion syndrome, it should be recommended that children with this genetic condition have screening for cardiac disease. These cases add to the current literature by demonstrating the potential therapeutic options for non-compaction in 1p36 deletion syndrome and showed the favorable outcomes.
Comparative Analysis for the Performance of Long-Read-Based Structural Variation Detection Pipelines in Tandem Repeat Regions
Authors: Guo Mingkun , Li Shihai , Zhou Yifan , Li Menglong , Wen Zhining
Published: June 2021

There has been growing recognition of the vital links between structural variations (SVs) and diverse diseases. Research suggests that, with much longer DNA fragments and abundant contextual information, long-read technologies have advantages in SV detection even in complex repetitive regions. So far, several pipelines for calling SVs from long-read sequencing data have been proposed and used in human genome research. However, the performance of these pipelines is still lack of deep exploration and adequate comparison. In this study, we comprehensively evaluated the performance of three commonly used long-read SV detection pipelines, namely PBSV, Sniffles and PBHoney, especially the performance on detecting the SVs in tandem repeat regions (TRRs). Evaluated by using a robust benchmark for germline SV detection as the gold standard, we thoroughly estimated the precision, recall and F1 score of insertions and deletions detected by the pipelines. Our results revealed that all these pipelines clearly exhibited better performance outside TRRs than that in TRRs. The F1 scores of Sniffles in and outside TRRs were 0.60 and 0.76, respectively. The performance of PBSV was similar to that of Sniffles, and was generally higher than that of PBHoney. In conclusion, our findings can be benefit for choosing the appropriate pipelines in real practice and are good complementary to the application of long-read sequencing technologies in the research of rare diseases.
Therapeutic Targeting of Transcription Factors to Control the Cytokine Release Syndrome in COVID-19
Authors: Santoso Clarissa S. , Li Zhaorong , Rottenberg Jaice T. , Liu Xing , Shen Vivian X. , Fuxman Bass Juan I.
Published: June 2021

Treatment of the cytokine release syndrome (CRS) has become an important part of rescuing hospitalized COVID-19 patients. Here, we systematically explored the transcriptional regulators of inflammatory cytokines involved in the COVID-19 CRS to identify candidate transcription factors (TFs) for therapeutic targeting using approved drugs. We integrated a resource of TF-cytokine gene interactions with single-cell RNA-seq expression data from bronchoalveolar lavage fluid cells of COVID-19 patients. We found 581 significantly correlated interactions, between 95 TFs and 16 cytokines upregulated in the COVID-19 patients, that may contribute to pathogenesis of the disease. Among these, we identified 19 TFs that are targets of FDA approved drugs. We investigated the potential therapeutic effect of 10 drugs and 25 drugs combinations on inflammatory cytokine production, which revealed two drugs that inhibited cytokine production and numerous combinations that show synergistic efficacy in downregulating cytokine production. Further studies of these candidate repurposable drugs could lead to a therapeutic regimen to treat the CRS in COVID-19 patients.
Cefdinir and β-Lactamase Inhibitor Independent Efficacy Against Mycobacterium tuberculosis
Authors: Srivastava Shashikant , Thomas Tania , Howe Dave , Malinga Lesibana , Raj Prithvi , Alffenaar Jan-Willem , Gumbo Tawanda
Published: June 2021

Background: There is renewed interest in repurposing β-lactam antibiotics for treatment of tuberculosis (TB). We investigated efficacy of cefdinir, that withstand the β-lactamase enzyme present in many bacteria, against drug-susceptible and multi-drug resistant (MDR) Mycobacterium tuberculosis (Mtb).

Methods: Minimum inhibitory concentration (MIC) experiments were performed with Mtb H37Ra, eight drug-susceptible, and 12 MDR-TB clinical isolates with and without the β-lactamase inhibitor, avibactam at 15 mg/L final concentration. Next, we performed dose-response study with Mtb H37Ra in test-tubes followed by a sterilizing activity study in the pre-clinical hollow fiber model of tuberculosis (HFS-TB) study using an MDR-TB clinical strain. Inhibitory sigmoid Emax model was used to describe the relationship between the drug exposure and bacterial burden.

Results: Cefdinir MIC for Mtb H37Ra was 4 and 2 mg/L with or without avibactam, respectively. The MIC of the clinical strains ranged between 0.5 and 16 mg/L. In the test-tube experiments, cefdinir killed 4.93 + 0.07 log10 CFU/ml Mtb H37Ra in 7 days. In the HFS-TB studies, cefdinir showed dose-dependent killing of MDR-TB, without combination of avibactam. The cefdinir PK/PD index linked to the Mtb sterilizing efficacy was identified as the ratio of area under the concentration-time curve to MIC (AUC0–24/MIC) and optimal exposure was calculated as AUC0–24/MIC of 578.86. There was no resistance emergence to cefdinir in the HFS-TB.

Conclusion: In the HFS-TB model, cefdinir showed efficacy against both drug susceptible and MDR-TB without combination of β-lactamase inhibitor. However, clinical validation of these findings remains to be determined.
Solving the Problem of Assessing Synergy and Antagonism for Non-Traditional Dosing Curve Compounds Using the DE/ZI Method: Application to Nrf2 Activators
Authors: Repash Elizabeth M. , Pensabene Kaitlin M. , Palenchar Peter M. , Eggler Aimee L.
Published: June 2021

Multi-drug combination therapy carries significant promise for pharmacological intervention, primarily better efficacy with less toxicity and fewer side effects. However, the field lacks methodology to assess synergistic or antagonistic interactions for drugs with non-traditional dose response curves. Specifically, our goal was to assess small-molecule modulators of antioxidant response element (ARE)-driven gene expression, which is largely regulated by the Nrf2 transcription factor. Known as Nrf2 activators, this class of compounds upregulates a battery of cytoprotective genes and shows significant promise for prevention of numerous chronic diseases. For example, sulforaphane sourced from broccoli sprouts is the subject of over 70 clinical trials. Nrf2 activators generally have non-traditional dose response curves that are hormetic, or U-shaped. We introduce a method based on the principles of Loewe Additivity to assess synergism and antagonism for two compounds in combination. This method, termed Dose-Equivalence/Zero Interaction (DE/ZI), can be used with traditional Hill-slope response curves, and it also can assess interactions for compounds with non-traditional curves, using a nearest-neighbor approach. Using a Monte-Carlo method, DE/ZI generates a measure of synergy or antagonism for each dosing pair with an associated error and p-value, resulting in a 3D response surface. For the assessed Nrf2 activators, sulforaphane and di-tert-butylhydroquinone, this approach revealed synergistic interactions at higher dosing concentrations consistently across data sets and potential antagonistic interactions at lower concentrations. DE/ZI eliminates the need to determine the best fit equation for a given data set and values experimentally-derived results over formulated fits.
Structural Health Monitoring Method of Pantograph–Catenary System Based on Strain Response Inversion
Authors: Liu Sheng , Wei Yibo , Yin Yongxin , Feng Tangzheng , Lin Jinbao
Published: June 2021

Pantograph-catenary system provides electric energy for the subway lines; its health status is essential to the serviceability of the vehicle. In this study, a real-time structural health monitoring method based on strain response inversion is proposed to calculate the magnitude and position of the dynamic contact force between the catenary and pantograph. The measurement principle, calibration, and installation detail of the fiber Bragg grating (FBG) sensors are also presented in this article. Putting this monitoring system in use, an application example of a subway with a rigid overhead catenary is given to demonstrate its performance. The pantograph was monitored and analyzed, running underground at a maximum speed of 80 km/h. The results show that the strain response inversion method has high measurement accuracy, good data consistency, and flexibility on sensor installation. It can accurately calculate the magnitude and location of the contact force exerted on the pantograph.
Presence of Left Atrial Fibrosis May Contribute to Aberrant Hemodynamics and Increased Risk of Stroke in Atrial Fibrillation Patients
Authors: Paliwal Nikhil , Ali Rheeda L. , Salvador Matteo , O’Hara Ryan , Yu Rebecca , Daimee Usama A. , Akhtar Tauseef , Pandey Pallavi , Spragg David D. , Calkins Hugh , Trayanova Natalia A.
Published: June 2021

Atrial fibrillation (AF) patients are at high risk of stroke, with the left atrial appendage (LAA) found to be the most common site of clot formation. Presence of left atrial (LA) fibrosis has also been associated with higher stroke risk. However, the mechanisms for increased stroke risk in patients with atrial fibrotic remodeling are poorly understood. We sought to explore these mechanisms using fluid dynamic analysis and to test the hypothesis that the presence of LA fibrosis leads to aberrant hemodynamics in the LA, contributing to increased stroke risk in AF patients. We retrospectively collected late-gadolinium-enhanced MRI (LGE-MRI) images of eight AF patients (four persistent and four paroxysmal) and reconstructed their 3D LA surfaces. Personalized computational fluid dynamic simulations were performed, and hemodynamics at the LA wall were quantified by wall shear stress (WSS, friction of blood), oscillatory shear index (OSI, temporal directional change of WSS), endothelial cell activation potential (ECAP, ratio of OSI and WSS), and relative residence time (RRT, residence time of blood near the LA wall). For each case, these hemodynamic metrics were compared between fibrotic and non-fibrotic portions of the wall. Our results showed that WSS was lower, and OSI, ECAP, and RRT was higher in the fibrotic region as compared to the non-fibrotic region, with ECAP (p = 0.001) and RRT (p = 0.002) having significant differences. Case-wise analysis showed that these differences in hemodynamics were statistically significant for seven cases. Furthermore, patients with higher fibrotic burden were exposed to larger regions of high ECAP, which represents regions of low WSS and high OSI. Consistently, high ECAP in the vicinity of the fibrotic wall suggest that local blood flow was slow and oscillating that represents aberrant hemodynamic conditions, thus enabling prothrombotic conditions for circulating blood. AF patients with high LA fibrotic burden had more prothrombotic regions, providing more sites for potential clot formation, thus increasing their risk of stroke.
RAGE Differentially Altered in vitro Responses in Vascular Smooth Muscle Cells and Adventitial Fibroblasts in Diabetes-Induced Vascular Calcification
Authors: Kennon Amber M. , Stewart James A.
Published: June 2021

The Advanced Glycation End-Products (AGE)/Receptor for AGEs (RAGE) signaling pathway exacerbates diabetes-mediated vascular calcification (VC) in vascular smooth muscle cells (VSMCs). Other cell types are involved in VC, such as adventitial fibroblasts (AFBs). We hope to elucidate some of the mechanisms responsible for differential signaling in diabetes-mediated VC with this work. This work utilizes RAGE knockout animals and in vitro calcification to measure calcification and protein responses. Our calcification data revealed that VSMCs calcification was AGE/RAGE dependent, yet AFBs calcification was not an AGE-mediated RAGE response. Protein expression data showed VSMCs lost their phenotype marker, α-smooth muscle actin, and had a higher RAGE expression over non-diabetics. RAGE knockout (RKO) VSMCs did not show changes in phenotype markers. P38 MAPK, a downstream RAGE-associated signaling molecule, had significantly increased activation with calcification in both diabetic and diabetic RKO VSMCs. AFBs showed a loss in myofibroblast marker, α-SMA, due to calcification treatment. RAGE expression decreased in calcified diabetic AFBs, and P38 MAPK activation significantly increased in diabetic and diabetic RKO AFBs. These findings point to potentially an alternate receptor mediating the calcification response in the absence of RAGE. Overall, VSMCs and AFBs respond differently to calcification and the application of AGEs.
Characterization of Histone H3 Lysine 4 and 36 Tri-methylation in Brassica rapa L.
Authors: Mehraj Hasan , Takahashi Satoshi , Miyaji Naomi , Akter Ayasha , Suzuki Yutaka , Seki Motoaki , Dennis Elizabeth S. , Fujimoto Ryo
Published: June 2021

Covalent modifications of histone proteins act as epigenetic regulators of gene expression. We report the distribution of two active histone marks (H3K4me3 and H3K36me3) in 14-day leaves in two lines of Brassica rapa L. by chromatin immunoprecipitation sequencing. Both lines were enriched with H3K4me3 and H3K36me3 marks at the transcription start site, and the transcription level of a gene was associated with the level of H3K4me3 and H3K36me3. H3K4me3- and H3K36me3-marked genes showed low tissue-specific gene expression, and genes with both H3K4me3 and H3K36me3 had a high level of expression and were constitutively expressed. Bivalent active and repressive histone modifications such as H3K4me3 and H3K27me3 marks or antagonistic coexistence of H3K36me3 and H3K27me3 marks were observed in some genes. Expression may be susceptible to changes by abiotic and biotic stresses in genes having both H3K4me3 and H3K27me3 marks. We showed that the presence of H3K36me3 marks was associated with different gene expression levels or tissue specificity between paralogous paired genes, suggesting that H3K36me3 might be involved in subfunctionalization of the subgenomes.
Genetic Mapping and Validation of Loci for Kernel-Related Traits in Wheat (Triticum aestivum L.)
Authors: Qu Xiangru , Liu Jiajun , Xie Xinlin , Xu Qiang , Tang Huaping , Mu Yang , Pu Zhien , Li Yang , Ma Jun , Gao Yutian , Jiang Qiantao , Liu Yaxi , Chen Guoyue , Wang Jirui , Qi Pengfei , Habib Ahsan , Wei Yuming , Zheng Youliang , Lan Xiujin , Ma Jian
Published: June 2021

Kernel size (KS) and kernel weight play a key role in wheat yield. Phenotypic data from six environments and a Wheat55K single-nucleotide polymorphism array–based constructed genetic linkage map from a recombinant inbred line population derived from the cross between the wheat line 20828 and the line SY95-71 were used to identify quantitative trait locus (QTL) for kernel length (KL), kernel width (KW), kernel thickness (KT), thousand-kernel weight (TKW), kernel length–width ratio (LWR), KS, and factor form density (FFD). The results showed that 65 QTLs associated with kernel traits were detected, of which the major QTLs QKL.sicau-2SY-1B, QKW.sicau-2SY-6D, QKT.sicau-2SY-2D, and QTKW.sicau-2SY-2D, QLWR.sicau-2SY-6D, QKS.sicau-2SY-1B/2D/6D, and QFFD.sicau-2SY-2D controlling KL, KW, KT, TKW, LWR, KS, and FFD, and identified in multiple environments, respectively. They were located on chromosomes 1BL, 2DL, and 6DS and formed three QTL clusters. Comparison of genetic and physical interval suggested that only QKL.sicau-2SY-1B located on chromosome 1BL was likely a novel QTL. A Kompetitive Allele Specific Polymerase chain reaction (KASP) marker, KASP-AX-109379070, closely linked to this novel QTL was developed and used to successfully confirm its effect in two different genetic populations and three variety panels consisting of 272 Chinese wheat landraces, 300 Chinese wheat cultivars most from the Yellow and Huai River Valley wheat region, and 165 Sichuan wheat cultivars. The relationships between kernel traits and other agronomic traits were detected and discussed. A few predicted genes involved in regulation of kernel growth and development were identified in the intervals of these identified major QTL. Taken together, these stable and major QTLs provide valuable information for understanding the genetic composition of kernel yield and provide the basis for molecular marker–assisted breeding.
The Arabidopsis AAC Proteins CIL and CIA2 Are Sub-functionalized Paralogs Involved in Chloroplast Development
Authors: Li Mingjiu , Ruwe Hannes , Melzer Michael , Junker Astrid , Hensel Goetz , Tschiersch Henning , Schwenkert Serena , Chamas Sindy , Schmitz-Linneweber Christian , Börner Thomas , Stein Nils
Published: June 2021

The Arabidopsis gene Chloroplast Import Apparatus 2 (CIA2) encodes a transcription factor that positively affects the activity of nuclear genes for chloroplast ribosomal proteins and chloroplast protein import machineries. CIA2-like (CIL) is the paralogous gene of CIA2. We generated a cil mutant by site-directed mutagenesis and compared it with cia2 and cia2cil double mutant. Phenotype of the cil mutant did not differ from the wild type under our growth conditions, except faster growth and earlier time to flowering. Compared to cia2, the cia2cil mutant showed more impaired chloroplast functions and reduced amounts of plastid ribosomal RNAs. In silico analyses predict for CIA2 and CIL a C-terminal CCT domain and an N-terminal chloroplast transit peptide (cTP). Chloroplast (and potentially nuclear) localization was previously shown for HvCMF3 and HvCMF7, the homologs of CIA2 and CIL in barley. We observed nuclear localization of CIL after transient expression in Arabidopsis protoplasts. Surprisingly, transformation of cia2 with HvCMF3, HvCMF7, or with a truncated CIA2 lacking the predicted cTP could partially rescue the pale-green phenotype of cia2. These data are discussed with respect to potentially overlapping functions between CIA2, CIL, and their barley homologs and to the function of the putative cTPs of CIA2 and CIL.
Molecular Mechanisms and Biochemical Pathways for Micronutrient Acquisition and Storage in Legumes to Support Biofortification for Nutritional Security
Authors: Roorkiwal Manish , Pandey Sarita , Thavarajah Dil , Hemalatha R. , Varshney Rajeev K.
Published: June 2021

The world faces a grave situation of nutrient deficiency as a consequence of increased uptake of calorie-rich food that threaten nutritional security. More than half the world’s population is affected by different forms of malnutrition. Unhealthy diets associated with poor nutrition carry a significant risk of developing non-communicable diseases, leading to a high mortality rate. Although considerable efforts have been made in agriculture to increase nutrient content in cereals, the successes are insufficient. The number of people affected by different forms of malnutrition has not decreased much in the recent past. While legumes are an integral part of the food system and widely grown in sub-Saharan Africa and South Asia, only limited efforts have been made to increase their nutrient content in these regions. Genetic variation for a majority of nutritional traits that ensure nutritional security in adverse conditions exists in the germplasm pool of legume crops. This diversity can be utilized by selective breeding for increased nutrients in seeds. The targeted identification of precise factors related to nutritional traits and their utilization in a breeding program can help mitigate malnutrition. The principal objective of this review is to present the molecular mechanisms of nutrient acquisition, transport and metabolism to support a biofortification strategy in legume crops to contribute to addressing malnutrition.
Religion as Meaning-Making Resource in Understanding Suicidal Behavior in Ghana and Uganda
Authors: Knizek Birthe Loa , Andoh-Arthur Johnny , Osafo Joseph , Mugisha James , Kinyanda Eugene , Akotia Charity , Hjelmeland Heidi
Published: June 2021

Suicidal behavior is condemned by religions and tradition, and suicide attempts are criminalized by law in several African countries, including Ghana and Uganda. Suicide and suicide attempts may have severe consequences for both the entire family and the community. Religion is known to act as a protective coping force that helps people to make meaning and find comfort when dealing with stressful life events or situations like suicide. In this article, we focus on the cultural interpretations of the dominating religion in Ghana and Uganda, Christianity, and whether these affect attitudes toward suicidal behavior, meaning making, and coping possibilities for people who have attempted suicide or are bereaved by suicide. This article is based on data material from previous studies on the mentioned topics by the authors.
Bribery and the Role of Public Service Motivation and Social Value Orientation: A Multi-Site Experimental Study in Belgium, Germany and the Netherlands
Authors: De Waele Lode , Weißmüller Kristina S. , van Witteloostuijn Arjen
Published: June 2021

Bribery is a complex phenomenon rooted in both individual motives and the greater institutional context. Experimental research into causal mechanisms that drive bribing behavior is still scarce. To date, there is no empirical evidence on how the society-regarding motivational survey measure of Public Service Motivation (PSM) and the other-oriented motivational measure of Social Value Orientation (SVO) can help explain why some people are more susceptible to engage in the act of bribing than others. Based on a multi-site triple-replication, and a vignette-based research design, quasi-experimental evidence from Belgium, Germany, and the Netherlands shows that both measures interact and that—paradoxically—people with higher SVO are more likely to be willing to engage in bribery.
“Have You Taken the A4 Challenge?” Correlates and Impact of a Thin Ideal Expression From Chinese Social Media
Authors: Jackson Todd , Ye Xiaoxuan , Hall Brian J. , Chen Hong
Published: June 2021

In three studies, we assessed knowledge, correlates, and effects of the A4 challenge, an expression of the thin ideal from Chinese social media. In Study 1, gender differences in familiarity with the A4 challenge were assessed among 225 women and 151 men. Compared to men, women and female peers from participant social networks were more familiar with and likely to have taken the challenge themselves. In Study 2, body image experiences of women who passed the A4 challenge (N = 45) and average weight peers who did not pass the challenge (N = 75) were assessed. The former group reported fewer weight concerns and less social pressure to lose weight but no group differences were observed with respect to binge-eating, dieting, or other compensatory weight loss behaviors. As such, eating disorder symptoms did not account for the experience of passing the A4 challenge. In Study 3, changes in state body dissatisfaction were assessed among 205 women randomly assigned to view images of (1) thin peers successfully passing the challenge vs. (2) thin or (3) average size controls. The absence of condition differences in post-exposure state body dissatisfaction indicated exposure to A4 challenge portrayals per se did not cause increases in negative appearance self-evaluations for women in general. However, among women who were exposed to A4 challenge images, but not control group women exposure to other images, trait body dissatisfaction predicted increased post-exposure state dissatisfaction, independent of pre-exposure state dissatisfaction. Implications are discussed in relation to effects of exposure to the A4 challenge and conceptualizing the task as a “challenge.”
Influence of the Quality Perceived of Service of a Higher Education Center on the Loyalty of Students
Authors: Del Río-Rama María de la Cruz , Álvarez-García José , Mun Nam Kwon , Durán-Sánchez Amador
Published: June 2021

The aim of this research is to validate the explanatory model of how the quality of service perceived by students of a higher education center influences their loyalty (retaining and attracting new students) through mediating variables: perceived value, expectations, and satisfaction. The methodology used to validate the measurement scales is exploratory, and confirmatory factor analysis and the structural equation modeling (SEM) technique are applied to analyze the causal relationships proposed in the model. The results show that the key variables to improve student's loyalty to the center are the quality of the service provided and the satisfaction perceived by the students. Both variables are postulated as a major source of competitive advantages. It is also observed that service quality is one of the three key variables to achieve student's satisfaction together with expectations and perceived value. This research and its results allow us to understand the relationship between quality and satisfaction with loyalty and to identify the background variables of satisfaction (perceived service quality, perceived value, and expectations), as well as to obtain evidence of the importance that expectations have within the model for the formation of both perceived quality and satisfaction.
Repetition and Aesthetic Judgment in Post-tonal Music for Large Ensemble and Orchestra
Authors: Touizrar Moe , Knoll Anna Lena , Siedenburg Kai
Published: June 2021

Post-tonal music often poses perceptual and cognitive challenges for listeners, potentially related to the use of relatively uncommon and unfamiliar musical material and compositional processes. As a basic compositional device, repetition affects memory for music and is structured by composers in very different ways across tonal and post-tonal musical repertoires. Of particular concern is whether post-tonal music exhibits mnemonic affordances that allow listeners to experience a sense of global coherence, and whether repetition correlates strongly with aesthetic judgment. Although previous research suggests that repetition impacts aesthetic preference, empirical research has not mapped out the relationship between repetition and aesthetic judgments across a broad set of post-tonal music. Presenting 14 excerpts, grouped into three categories: tonal, modernist, and post-1970, we observed that indications of repetitions in the music for a group of 60 listeners, with and without musical training, showed significant periods of interindividual synchronization. Aesthetic judgments were assessed by means of ratings for the following parameters: familiarity with the piece, confidence of repetition responses, judgments of affordances for easy listening, coherence, similarity of moments, and recognition, as well as listeners’ liking and interest. A principal component analysis (PCA) on the joint question data and the repetition responses suggested that two factors account for 92% of variance in the data. These factors were interpreted as dominated by aesthetic judgment and repetition strength. Linear mixed-effects regression indicated that repetition strength generally differed across excerpt category, with modernist excerpts featuring lower repetition strength compared to both post-1970 and tonal excerpts. Aesthetic preference, on the other hand, was lower for excerpts in both the modernist and post-1970 categories when compared to tonal excerpts. The analysis did not reveal difference in response behavior for repetition responses as a function of musical training, though it indicated higher preference of modernist excerpts with increasing levels of musical training. Overall, the results suggest that the two factors, aesthetic judgment and repetition strength, act as independent determinants in the experience of post-tonal music.
Teams in Transition: A Three-Wave Longitudinal Study of Reflection, Implicit and Explicit Coordination and Performance Improvements
Authors: Konradt Udo , Schippers Michaéla C. , Krys Sabrina , Fulmer Ashley
Published: June 2021

Research has shown that team reflection is a critical transition process for coordination processes and team performance, but our understanding of its dynamics and relationship to action processes and performance is incomplete. The goal of the present study was to examine the long-term change in reflection in teams over time and explore whether these changes are related to implicit and explicit coordination processes and performance improvement. Drawing on the recurring phase model of team processes and team reflexivity theory, we hypothesized that team reflection is at least stable or increases over time for dissimilar tasks, that reflection trajectories are positively associated with implicit and negatively associated with explicit coordination in the later phases, and that implicit coordination mediates the relationship between team reflection and performance improvement. This model was tested in a three-wave longitudinal study (N = 175 teams) over a 2-months period. Results from growth curve modeling and structural equation modeling provided support for our hypotheses.
Supporting Learner Success: Revisiting Strategic Competence Through Developing an Inventory for Computer-Assisted Speaking Assessment
Authors: Zhang Weiwei , Zhang Lawrence Jun , Wilson Aaron John
Published: June 2021

This study investigated English-as-a-foreign-language (EFL) learners' strategic competence in the computer-assisted integrated speaking tests (CAIST) through the development and validation of the Strategic Competence Inventory for Computer-assisted Speaking Assessment (SCICASA). Based on our review of the literature on the CAIST, strategic competence, and available instruments for measuring the construct, we defined EFL learners' strategic competence in the CAIST as learners' use of four metacognitive strategies: Planning, problem-solving, monitoring, and evaluating, with each of them consisting of various components. These metacognitive strategies formulated the four factors and scale items of the SCICASA under validation. An exploratory factor analysis of responses from 254 EFL students and the subsequent confirmatory factor analysis of data collected on another sample of 242 students generated 23 items under the four factors. The high validity and reliability of the SCICASA reveal that EFL learners' strategic competence operates in the forms of the four metacognitive strategies in the CAIST. This will lend some new supporting evidence for Bachman and Palmer's (2010) strategic competence model while providing implications for metacognitive instructions and test development. Concomitantly, the findings show the inventory as a valid instrument for measuring strategic competence in computer-assisted foreign/second language (L2) speaking assessment and relevant research arenas and beyond.