bluuebunny/crossref_metadata_2025 huggingface dataset:
Extracting Phonetic Features From Natural Classes: A Mismatch Negativity Study of Mandarin Chinese Retroflex Consonants
Authors: Fu Zhanao , Monahan Philip J.
Published: March 2021

How speech sounds are represented in the brain is not fully understood. The mismatch negativity (MMN) has proven to be a powerful tool in this regard. The MMN event-related potential is elicited by a deviant stimulus embedded within a series of repeating standard stimuli. Listeners construct auditory memory representations of these standards despite acoustic variability. In most designs that test speech sounds, however, this variation is typically intra-category: All standards belong to the same phonetic category. In the current paper, inter-category variation is presented in the standards. These standards vary in manner of articulation but share a common phonetic feature. In the standard retroflex experimental block, Mandarin Chinese speaking participants are presented with a series of “standard” consonants that share the feature [retroflex], interrupted by infrequent non-retroflex deviants. In the non-retroflex standard experimental block, non-retroflex standards are interrupted by infrequent retroflex deviants. The within-block MMN was calculated, as was the identity MMN (iMMN) to account for intrinsic differences in responses to the stimuli. We only observed a within-block MMN to the non-retroflex deviant embedded in the standard retroflex block. This suggests that listeners extract [retroflex] despite significant inter-category variation. In the non-retroflex standard block, because there is little on which to base a coherent auditory memory representation, no within-block MMN was observed. The iMMN to the retroflex was observed in a late time-window at centro-parieto-occipital electrode sites instead of fronto-central electrodes, where the MMN is typically observed, potentially reflecting the increased difficulty posed by the added variation in the standards. In short, participants can construct auditory memory representations despite significant acoustic and inter-category phonological variation so long as a shared phonetic feature binds them together.
Automatic Detection of Microsleep Episodes With Deep Learning
Authors: Malafeev Alexander , Hertig-Godeschalk Anneke , Schreier David R. , Skorucak Jelena , Mathis Johannes , Achermann Peter
Published: March 2021

Brief fragments of sleep shorter than 15 s are defined as microsleep episodes (MSEs), often subjectively perceived as sleepiness. Their main characteristic is a slowing in frequency in the electroencephalogram (EEG), similar to stage N1 sleep according to standard criteria. The maintenance of wakefulness test (MWT) is often used in a clinical setting to assess vigilance. Scoring of the MWT in most sleep-wake centers is limited to classical definition of sleep (30 s epochs), and MSEs are mostly not considered in the absence of established scoring criteria defining MSEs but also because of the laborious work. We aimed for automatic detection of MSEs with machine learning, i.e., with deep learning based on raw EEG and EOG data as input. We analyzed MWT data of 76 patients. Experts visually scored wakefulness, and according to recently developed scoring criteria MSEs, microsleep episode candidates (MSEc), and episodes of drowsiness (ED). We implemented segmentation algorithms based on convolutional neural networks (CNNs) and a combination of a CNN with a long-short term memory (LSTM) network. A LSTM network is a type of a recurrent neural network which has a memory for past events and takes them into account. Data of 53 patients were used for training of the classifiers, 12 for validation and 11 for testing. Our algorithms showed a good performance close to human experts. The detection was very good for wakefulness and MSEs and poor for MSEc and ED, similar to the low inter-expert reliability for these borderline segments. We performed a visualization of the internal representation of the data by the artificial neuronal network performing best using t-distributed stochastic neighbor embedding (t-SNE). Visualization revealed that MSEs and wakefulness were mostly separable, though not entirely, and MSEc and ED largely intersected with the two main classes. We provide a proof of principle that it is feasible to reliably detect MSEs with deep neuronal networks based on raw EEG and EOG data with a performance close to that of human experts. The code of the algorithms (https://github.com/alexander-malafeev/microsleep-detection) and data (https://zenodo.org/record/3251716) are available.
In silico Analysis of Polymorphisms in microRNAs Deregulated in Alzheimer Disease
Authors: Moraghebi Mahta , Maleki Reza , Ahmadi Mohsen , Negahi Ahmad Agha , Abbasi Hossein , Mousavi Pegah
Published: March 2021

Background

Alzheimer’s disease (AD) is a degenerative condition characterized by progressive cognitive impairment and dementia. Findings have revolutionized current knowledge of miRNA in the neurological conditions. Two regulatory mechanisms determine the level of mature miRNA expression; one is miRNA precursor processing, and the other is gene expression regulation by transcription factors. This study is allocated to the in-silico investigation of miRNA’s SNPs and their effect on other cell mechanisms.

Methods

We used databases which annotate the functional effect of SNPs on mRNA-miRNA and miRNA-RBP interaction. Also, we investigated SNPs which are located on the promoter or UTR region.

Results

miRNA SNP3.0 database indicated several SNPs in miR-339 and miR-34a in the upstream and downstream of pre-miRNA and mature miRNAs. While, for some miRNAs miR-124, and miR-125, no polymorphism was observed, and also miR-101 with ΔG -3.1 and mir-328 with ΔG 5.8 had the highest and lowest potencies to produce mature microRNA. SNP2TFBS web-server presented several SNPs which altered the Transcription Factor Binding Sites (TFBS) or generated novel TFBS in the promoter regions of related miRNA. At last, RBP-Var database provided a list of SNPs which alter miRNA-RBP interaction pattern and can also influence other miRNAs’ expression.

Discussion

The results indicated that SNPs microRNA affects both miRNA function and miRNA expression. Our study expands molecular insight into how SNPs in different parts of miRNA, including the regulatory (promoter), the precursor (pre-miRNA), functional regions (seed region of mature miRNA), and RBP-binding motifs, which theoretically may be correlated to the Alzheimer’s disease.
Clinical and Neurobiological Aspects of TAO Kinase Family in Neurodevelopmental Disorders
Authors: Hu Chun , Feng Pan , Yang Qian , Xiao Lin
Published: March 2021

Despite the complexity of neurodevelopmental disorders (NDDs), from their genotype to phenotype, in the last few decades substantial progress has been made in understanding their pathophysiology. Recent accumulating evidence shows the relevance of genetic variants in thousand and one (TAO) kinases as major contributors to several NDDs. Although it is well-known that TAO kinases are a highly conserved family of STE20 kinase and play important roles in multiple biological processes, the emerging roles of TAO kinases in neurodevelopment and NDDs have yet to be intensively discussed. In this review article, we summarize the potential roles of the TAO kinases based on structural and biochemical analyses, present the genetic data from clinical investigations, and assess the mechanistic link between the mutations of TAO kinases, neuropathology, and behavioral impairment in NDDs. We then offer potential perspectives from basic research to clinical therapies, which may contribute to fully understanding how TAO kinases are involved in NDDs.
A Synaptic Framework for the Persistence of Memory Engrams
Authors: Rao-Ruiz Priyanka , Visser Esther , Mitrić Miodrag , Smit August B. , van den Oever Michel C.
Published: March 2021

The ability to store and retrieve learned information over prolonged periods of time is an essential and intriguing property of the brain. Insight into the neurobiological mechanisms that underlie memory consolidation is of utmost importance for our understanding of memory persistence and how this is affected in memory disorders. Recent evidence indicates that a given memory is encoded by sparsely distributed neurons that become highly activated during learning, so-called engram cells. Research by us and others confirms the persistent nature of cortical engram cells by showing that these neurons are required for memory expression up to at least 1 month after they were activated during learning. Strengthened synaptic connectivity between engram cells is thought to ensure reactivation of the engram cell network during retrieval. However, given the continuous integration of new information into existing neuronal circuits and the relatively rapid turnover rate of synaptic proteins, it is unclear whether a lasting learning-induced increase in synaptic connectivity is mediated by stable synapses or by continuous dynamic turnover of synapses of the engram cell network. Here, we first discuss evidence for the persistence of engram cells and memory-relevant adaptations in synaptic plasticity, and then propose models of synaptic adaptations and molecular mechanisms that may support memory persistence through the maintenance of enhanced synaptic connectivity within an engram cell network.
The Effects of a 6-Week Controlled, Hypocaloric Ketogenic Diet, With and Without Exogenous Ketone Salts, on Body Composition Responses
Authors: Buga Alex , Kackley Madison L. , Crabtree Christopher D. , Sapper Teryn N. , Mccabe Lauren , Fell Brandon , LaFountain Rich A. , Hyde Parker N. , Martini Emily R. , Bowman Jessica , Pan Yue , Scandling Debbie , Brownlow Milene L. , O'Connor Annalouise , Simonetti Orlando P. , Kraemer William J. , Volek Jeff S.
Published: March 2021

Background: Ketogenic diets (KDs) that elevate beta-hydroxybutyrate (BHB) promote weight and fat loss. Exogenous ketones, such as ketone salts (KS), also elevate BHB concentrations with the potential to protect against muscle loss during caloric restriction. Whether augmenting ketosis with KS impacts body composition responses to a well-formulated KD remains unknown.

Purpose: To explore the effects of energy-matched, hypocaloric KD feeding (<50 g carbohydrates/day; 1.5 g/kg/day protein), with and without the inclusion of KS, on weight loss and body composition responses.

Methods: Overweight and obese adults were provided a precisely defined hypocaloric KD (~75% of energy expenditure) for 6 weeks. In a double-blind manner, subjects were randomly assigned to receive ~24 g/day of a racemic BHB-salt (KD + KS; n = 12) or placebo (KD + PL; n = 13). A matched comparison group (n = 12) was separately assigned to an isoenergetic/isonitrogenous low-fat diet (LFD). Body composition parameters were assessed by dual x-ray absorptiometry and magnetic resonance imaging.

Results: The KD induced nutritional ketosis (>1.0 mM capillary BHB) throughout the study (p < 0.001), with higher fasting concentrations observed in KD + KS than KD + PL for the first 2 weeks (p < 0.05). There were decreases in body mass, whole body fat and lean mass, mid-thigh muscle cross-sectional area, and both visceral and subcutaneous adipose tissues (p < 0.001), but no group differences between the two KDs or with the LFD. Urine nitrogen excretion was significantly higher in KD + PL than LFD (p < 0.01) and trended higher in KD + PL compared to KD + KS (p = 0.076), whereas the nitrogen excretion during KD + KS was similar to LFD (p > 0.05).

Conclusion: Energy-matched hypocaloric ketogenic diets favorably affected body composition but were not further impacted by administration of an exogenous BHB-salt that augmented ketosis. The trend for less nitrogen loss with the BHB-salt, if manifested over a longer period of time, may contribute to preserved lean mass.
Trans Fat Free by 2023—A Building Block of the COVID-19 Response
Authors: Bösch Simone , Westerman Lucinda , Renshaw Nina , Pravst Igor
Published: March 2021

COVID-19 has brought to center stage the most important health issue of our era, largely ignored by policymakers and the public to date: non-communicable diseases (NCDs), the cause of 71% of deaths per year worldwide. People living with NCDs, and particularly those living with cardiovascular disease (CVD), are at higher risk of severe symptoms and death from COVID-19. As a result, the urgent need for policy measures to protect cardiovascular health is more apparent than ever. One example of “low-hanging fruit” in the prevention of CVD is the elimination of industrially-produced trans fatty acids (iTFA). Their removal from the global food supply could prevent up to 17 million deaths by 2040 and would be the first time an NCD risk factor has been eliminated.
Optimal Surgery Type and Adjuvant Therapy for T1N0M0 Lung Large Cell Neuroendocrine Carcinoma
Authors: Peng Kunwei , Cao Huijiao , You Yafei , He Wenzhuo , Jiang Chang , Wang Lei , Jin Yanan , Xia Liangping
Published: March 2021

Background

The appropriate treatment strategy for T1N0M0 lung large cell neuroendocrine carcinoma (LCNEC) was not well illustrated. We evaluated the efficacy of different surgery types and adjuvant therapy on patients with T1N0M0 LCNEC.

Methods

Patients diagnosed T1N0M0 LCNEC from 2004 to 2016 were identified in the surveillance, epidemiology, and end results (SEER) database. Clinical characteristics, treatment and survival data were collected. The efficacy of surgery type and adjuvant therapy stratified by tumor size was assessed. Overall survival(OS) was evaluated by the Kaplan-Meier method, and relevant survival variables were identified by the Cox proportional hazard model.

Results

From 2004 to 2016, 425 patients were included in this study, 253 (59.5%) patients received lobectomy, and 236 (55.5%) patients had 4 or more lymph nodes removed. Patients received lobectomy had better survival than those received sublobar resection(P=0.000). No matter tumor size less than 2 cm or 2 to 3 cm, lobectomy was significantly prolonged survival. Compared with no lymph nodes removed, lymph nodes dissection was associated with more remarkable OS(P<0.000). 4 or more regional lymph nodes dissection predicted better OS compared with 1 to 3 regional lymph nodes dissection(P=0.014). After surgery, adjuvant chemotherapy did not contribute to extended survival in patients with tumor less than 2 cm(P=0.658), and possibly for tumor 2 to 3 cm(P=0.082). Multivariate analysis showed that age and lobectomy were independent prognostic factors(P=0.000).

Conclusion

Our results suggest that lobectomy and lymph nodes dissection were associated with significantly better survival. Extensive regional lymph node dissection(4 or more) was more effective in prolonging survival than 1 to 3 lymph nodes dissection. Adjuvant chemotherapy was not associated with extended survival for tumor less than 2 cm, and possibly for tumor 2 to 3 cm.
Prognostic Value of Postoperative Neutrophil and Albumin: Reassessment One Month After Gastric Cancer Surgery
Authors: Guner Ali , Cho Minah , Kim Yoo-Min , Cheong Jae-Ho , Hyung Woo Jin , Kim Hyoung-Il
Published: March 2021

Objective

The prognostic value of postoperative parameters reflecting the inflammatory and nutritional status of patients undergoing cancer surgery has been rarely studied. This study investigated the prognostic value of inflammatory and nutritional parameters measured preoperatively and 1 month after curative gastrectomy for gastric cancer.

Methods

Data from a prospectively maintained database of 1,194 patients with gastric cancer who underwent curative surgery in 2009–2018 were retrospectively reviewed. Demographics, clinicopathologic characteristics, operative data, survival data, and laboratory parameters were extracted. Neutrophil counts, lymphocyte counts, and albumin levels before surgery and 1 month postoperatively were analyzed.

Results

In multivariable analysis adjusted for age, sex, and pathologic stage, high neutrophil count (hazard ratio [HR] 1.09, 95% confidence interval [CI] 1.01–1.17, p = 0.022) and low albumin (HR 0.45, 95% CI 0.27–0.74, p = 0.002) 1 month postoperatively were independent prognostic factors for overall survival. High neutrophil count (HR 1.09, 95% CI 1.02–1.16, p = 0.015) 1 month postoperatively was also an independent prognostic factor for recurrence-free survival after adjusting for age, sex, body mass index, extent of gastrectomy, and pathologic stage. Patients were classified into risk groups based on thresholds of 4.2 × 103 cells/mm3 and 4.1 g/dl for 1-month neutrophil count and albumin. High-risk groups had a significantly worse prognosis than low-risk groups for overall survival (HR 5.87, 95% CI 3.28–10.51, p <0.001) and recurrence-free survival (HR 1.52, 95% CI 1.07–2.16, p = 0.021).

Conclusions

Neutrophil count and albumin level 1 month after curative surgery reflect long-term prognosis better than preoperative values. These parameters can be used to stratify patients with the same stage into different prognostic groups.
A Four-Gene-Based Prognostic Model Predicts Overall Survival in Patients With Cutaneous Melanoma
Authors: Tong Xiaoxia , Qu Xiaofei , Wang Mengyun
Published: March 2021

Background

Cutaneous melanoma (CM) is one of the most aggressive cancers with highly metastatic ability. To make things worse, there are limited effective therapies to treat advanced CM. Our study aimed to investigate new biomarkers for CM prognosis and establish a novel risk score system in CM.

Methods

Gene expression data of CM from Gene Expression Omnibus (GEO) datasets were downloaded and analyzed to identify differentially expressed genes (DEGs). The overlapped DEGs were then verified for prognosis analysis by univariate and multivariate COX regression in The Cancer Genome Atlas (TCGA) datasets. Based on the gene signature of multiple survival associated DEGs, a risk score model was established, and its prognostic and predictive role was estimated through Kaplan-Meier (K-M) analysis and log-rank test. Furthermore, the correlations between prognosis related genes expression and immune infiltrates were analyzed via Tumor Immune Estimation Resource (TIMER) site.

Results

A total of 103 DEGs were obtained based on GEO cohorts, and four genes were verified in TCGA datasets. Subsequently, four genes (ADAMDEC1, GNLY, HSPA13, and TRIM29) model was developed by univariate and multivariate Cox regression analyses. The K-M plots showed that the high-risk group was associated with shortened survival than that in the low-risk group (P < 0.0001). Multivariate analysis suggested that the model was an independent prognostic factor (high-risk vs. low-risk, HR= 2.06, P < 0.001). Meanwhile, the high-risk group was prone to have larger breslow depth (P< 0.001) and ulceration (P< 0.001).

Conclusions

The four-gene risk score model functions well in predicting the prognosis and treatment response in CM and will be useful for guiding therapeutic strategies for CM patients. Additional clinical trials are needed to verify our findings.
Dihydrocapsaicin Inhibits Cell Proliferation and Metastasis in Melanoma via Down-regulating β-Catenin Pathway
Authors: Shi Shaomin , Li Chongyang , Zhang Yanli , Deng Chaowei , Liu Wei , Du Juan , Li Qian , Ji Yacong , Guo Leiyang , Liu Lichao , Hu Huanrong , Liu Yaling , Cui Hongjuan
Published: March 2021

Dihydrocapsaicin (DHC) is one of the main components of capsaicinoids in Capsicum. It has been reported that DHC exerts anti-cancer effects on diverse malignant tumors, such as colorectal cancer, breast cancer, and glioma. However, studies focused on the effect of DHC upon melanoma have rarely been done. In the present study, melanoma A375 and MV3 cell lines were treated with DHC and the cell proliferation, migration, and invasion were significantly suppressed. Furthermore, DHC effectively inhibited xenograft tumor growth and pulmonary metastasis of melanoma cells in NOD/SCID mice model. It was identified that β-catenin, which plays significant roles in cell proliferation and epithelial-mesenchymal transition, was down-regulated after DHC treatment. In addition, cyclin D1, c-Myc, MMP2, and MMP7, which are critical in diverse cellular process regulation as downstream proteins of β-catenin, were all decreased. Mechanistically, DHC accelerates ubiquitination of β-catenin and up-regulates the beta-transducin repeat containing E3 ubiquitin protein ligase (BTRC) in melanoma cells. The DHC induced suppression of cell proliferation, migration, and invasion were partly rescued by exogenous β-catenin overexpression, both in vitro and in vivo. Taken together, DHC may serve as a candidate natural compound for human melanoma treatment through β-catenin pathway.
Polysaccharide Isolated From Tetrastigma hemsleyanum Activates TLR4 in Macrophage Cell Lines and Enhances Immune Responses in OVA-Immunized and LLC-Bearing Mouse Models
Authors: Zhou Fang-mei , Chen Yu-chi , Jin Chao-ying , Qian Chao-dong , Zhu Bing-qi , Zhou Ying , Ding Zhi-shan , Wang Yi-qi
Published: March 2021

Tetrastigmahemsleyanum Diels et Gilg is a valuable Chinese medicinal herb with a long history of clinical application. Our previous study isolated and characterized a purified polysaccharide from the aerial part of Tetrastigma hemsleyanum (SYQP) and found it having antipyretic and antitumor effects in mice. A preliminary mechanistic study suggests these effects may be related to the binding of toll-like receptor (TLR4). The objective of this study is to further explore the detailed stimulating characteristics of SYQP on TLR4 signaling pathway and its in vivo immune regulating effect. We use HEK-BLUE hTLR4, mouse and human macrophage cell lines, as research tools. In vitro results show SYQP activated HEK-BLUE hTLR4 instead of HEK-BLUE Null cells. The secretion and the mRNA expression of cytokines related to TLR4 signaling significantly increased after SYQP treatment in both PMA-induced THP-1 and RAW264.7 macrophage cell lines. The TLR4 antagonist TAK-242 can almost completely abolish this activation. Furthermore, molecules such as IRAK1, NF-κB, MAPKs, and IRF3 in both the MyD88 and TRIF branches were all activated without pathway selection. In vivo results show SYQP enhanced antigen-specific spleen lymphocyte proliferation and serum IgG levels in OVA-immunized C57BL/6 mice. Orally administered 200 mg/kg SYQP induced obvious tumor regression, spleen weight increase, and the upregulation of the mRNA expression of TLR4-related cytokines in Lewis lung carcinoma–bearing mice. These results indicate SYQP can act as both a human and mouse TLR4 agonist and enhance immune responses in mice (p < 0.05). This study provides a basis for the development and utilization of SYQP as a new type of TLR4 agonist in the future.
Oleuropein Attenuates Lipopolysaccharide-Induced Acute Kidney Injury In Vitro and In Vivo by Regulating Toll-Like Receptor 4 Dimerization
Authors: Cui Yushun , Gao Hongwei , Han Shan , Yuan Renyikun , He Jia , Zhuo Youqiong , Feng Yu-Lin , Tang Meiwen , Feng Jianfang , Yang Shilin
Published: March 2021

Acute kidney injury (AKI) is a common critical illness that involves multiple systems and multiple organs with a rapid decline in kidney function over short period. It has a high mortality rate and presents a great treatment challenge for physicians. Oleuropein, the main active constituent of Ilex pubescens Hook. et Arn. var. kwangsiensis Hand.-Mazz. displays significant anti-inflammatory activity, although oleuropein’s therapeutic effect and mechanism of action in AKI remain to be elucidated. The present study aimed to further clarify the mechanism by which oleuropein exerts effects on inflammation in vitro and in vivo. In vitro, the inflammatory effect and mechanism were investigated through ELISA, Western blotting, the thermal shift assay, co-immunoprecipitation, and immunofluorescence staining. Lipopolysaccharide (LPS) induced acute kidney injury was employed in an animal model to investigate oleuropein’s therapeutic effect on AKI and mechanism in vivo. The underlying mechanisms were investigated by Western blot analysis of kidney tissue. In LPS-stimulated macrophages, our data demonstrated that oleuropein significantly reduced the expression of inflammatory mediators like NO, IL-6, TNF-α, iNOS, and COX-2. Moreover, oleuropein inhibited NF-κB/p65 translocation, and had a negative regulatory effect on key proteins in the NF-κB and MAPK pathways. In addition, the thermal shift and co-immunoprecipitation assays revealed that oleuropein played an essential role in binding to the active sites of TLR4, as well as inhibiting TLR4 dimerization and suppressing the binding of TLR4 to MyD88. Oleuropein markedly alleviated LPS induced acute kidney injury, decreased serum creatinine and blood urea nitrogen (BUN) levels and proinflammatory cytokines. More importantly, the TLR4-MyD88-NF-κB/MAPK pathways were confirmed to play an important role in the oleuropein treatment of AKI. In this study, oleuropein exhibited excellent anti-inflammatory effects by regulating TLR4-MyD88-NF-κB/MAPK axis in vitro and in vivo, suggesting oleuropein as a candidate molecule for treating AKI.
COVID-19: Famotidine, Histamine, Mast Cells, and Mechanisms
Authors: Malone Robert W. , Tisdall Philip , Fremont-Smith Philip , Liu Yongfeng , Huang Xi-Ping , White Kris M. , Miorin Lisa , Moreno Elena , Alon Assaf , Delaforge Elise , Hennecker Christopher D. , Wang Guanyu , Pottel Joshua , Blair Robert V. , Roy Chad J. , Smith Nora , Hall Julie M. , Tomera Kevin M , Shapiro Gideon , Mittermaier Anthony , Kruse Andrew C. , García-Sastre Adolfo , Roth Bryan L. , Glasspool-Malone Jill , Ricke Darrell O.
Published: March 2021

SARS-CoV-2 infection is required for COVID-19, but many signs and symptoms of COVID-19 differ from common acute viral diseases. SARS-CoV-2 infection is necessary but not sufficient for development of clinical COVID-19 disease. Currently, there are no approved pre- or post-exposure prophylactic COVID-19 medical countermeasures. Clinical data suggest that famotidine may mitigate COVID-19 disease, but both mechanism of action and rationale for dose selection remain obscure. We have investigated several plausible hypotheses for famotidine activity including antiviral and host-mediated mechanisms of action. We propose that the principal mechanism of action of famotidine for relieving COVID-19 symptoms involves on-target histamine receptor H2 activity, and that development of clinical COVID-19 involves dysfunctional mast cell activation and histamine release. Based on these findings and associated hypothesis, new COVID-19 multi-drug treatment strategies based on repurposing well-characterized drugs are being developed and clinically tested, and many of these drugs are available worldwide in inexpensive generic oral forms suitable for both outpatient and inpatient treatment of COVID-19 disease.
Storage, Splitting, and Routing of Optical Peregrine Solitons in a Coherent Atomic System
Authors: Shou Chong , Huang Guoxiang
Published: March 2021

We propose a scheme to realize the storage and retrieval of optical Peregrine solitons in a coherent atomic gas via electromagnetically induced transparency (EIT). We show that optical Peregrine solitons with very small propagation loss, ultraslow motional velocity, and extremely low generation power can be created in the system via EIT. We also show that such solitons can be stored, retrieved, split, and routed with high efficiency and fidelity through the manipulation of control laser fields. The results reported here are useful for the active control of optical Peregrine solitons and promising for applications in optical information processing and transmission.
Nicotinamide Mononucleotide Attenuates Renal Interstitial Fibrosis After AKI by Suppressing Tubular DNA Damage and Senescence
Authors: Jia Yan , Kang Xin , Tan Lishan , Ren Yifei , Qu Lei , Tang Jiawei , Liu Gang , Wang Suxia , Xiong Zuying , Yang Li
Published: March 2021

Acute kidney injury (AKI) is a worldwide health problem currently lacking therapeutics that directly promote renal repair or prevent the occurrence of chronic fibrosis. DNA damage is a feature of many forms of kidney injury, and targeting DNA damage and repair might be effective strategies for kidney protection in AKI. Boosting nicotinamide adenine dinucleotide (NAD+) levels is thought to have beneficial effects on DNA damage repair and fibrosis in other organs. However, no kidney-related studies of such effects have been performed to date. Here, we have shown that NMN (an NAD+ precursor) administration could significantly reduce tubular cell DNA damage and subsequent cellular senescence induced by hydrogen peroxide and hypoxia in human proximal tubular cells (HK-2 cells). The DNA damage inhibition, antiaging and anti-inflammatory effects of NMN were further confirmed in a unilateral ischemia-reperfusion injury (uIRI) mouse model. Most importantly, the antifibrosis activity of NMN was also shown in ischemic AKI mouse models, regardless of whether NMN was administered in advance or during the recovery phase. Collectively, these results suggest that NMN could significantly inhibit tubular cell DNA damage, senescence and inflammation. NMN administration might be an effective strategy for preventing or treating kidney fibrosis after AKI.
Nutations in Plant Shoots: Endogenous and Exogenous Factors in the Presence of Mechanical Deformations
Authors: Agostinelli Daniele , DeSimone Antonio , Noselli Giovanni
Published: March 2021

We present a three-dimensional morphoelastic rod model capable to describe the morphogenesis of growing plant shoots driven by differential growth. We discuss the evolution laws for endogenous oscillators, straightening mechanisms, and reorientations to directional cues, such as gravitropic reactions governed by the avalanche dynamics of statoliths. We use this model to investigate the role of elastic deflections due to gravity loading in circumnutating plant shoots. We show that, in the absence of endogenous cues, pendular and circular oscillations arise as a critical length is attained, thus suggesting the occurrence of an instability triggered by exogenous factors. When also oscillations due to endogenous cues are present, their weight relative to those associated with the instability varies in time as the shoot length and other biomechanical properties change. Thanks to the simultaneous occurrence of these two oscillatory mechanisms, we are able to reproduce a variety of complex behaviors, including trochoid-like patterns, which evolve into circular orbits as the shoot length increases, and the amplitude of the exogenous oscillations becomes dominant.
Deep Segmentation of Point Clouds of Wheat
Authors: Ghahremani Morteza , Williams Kevin , Corke Fiona M. K. , Tiddeman Bernard , Liu Yonghuai , Doonan John H.
Published: March 2021

The 3D analysis of plants has become increasingly effective in modeling the relative structure of organs and other traits of interest. In this paper, we introduce a novel pattern-based deep neural network, Pattern-Net, for segmentation of point clouds of wheat. This study is the first to segment the point clouds of wheat into defined organs and to analyse their traits directly in 3D space. Point clouds have no regular grid and thus their segmentation is challenging. Pattern-Net creates a dynamic link among neighbors to seek stable patterns from a 3D point set across several levels of abstraction using the K-nearest neighbor algorithm. To this end, different layers are connected to each other to create complex patterns from the simple ones, strengthen dynamic link propagation, alleviate the vanishing-gradient problem, encourage link reuse and substantially reduce the number of parameters. The proposed deep network is capable of analysing and decomposing unstructured complex point clouds into semantically meaningful parts. Experiments on a wheat dataset verify the effectiveness of our approach for segmentation of wheat in 3D space.
Modulation of Abiotic Stress Responses in Rice by E3-Ubiquitin Ligases: A Promising Way to Develop Stress-Tolerant Crops
Authors: Melo Fredilson Veiga , Oliveira M. Margarida , Saibo Nelson J. M. , Lourenço Tiago Filipe
Published: March 2021

Plants are unable to physically escape environmental constraints and have, therefore, evolved a range of molecular and physiological mechanisms to maximize survival in an ever-changing environment. Among these, the post-translational modification of ubiquitination has emerged as an important mechanism to understand and improve the stress response. The ubiquitination of a given protein can change its abundance (through degradation), alter its localization, or even modulate its activity. Hence, ubiquitination increases the plasticity of the plant proteome in response to different environmental cues and can contribute to improve stress tolerance. Although ubiquitination is mediated by different enzymes, in this review, we focus on the importance of E3-ubiquitin ligases, which interact with the target proteins and are, therefore, highly associated with the mechanism specificity. We discuss their involvement in abiotic stress response and place them as putative candidates for ubiquitination-based development of stress-tolerant crops. This review covers recent developments in this field using rice as a reference for crops, highlighting the questions still unanswered.
Final Selection of Quality Protein Popcorn Hybrids
Authors: Parsons Leandra , Ren Ying , Yobi Abou , Angelovici Ruthie , Rodriguez Oscar , Holding David R.
Published: March 2021

Quality Protein Popcorn (QPP) BC2F5inbred lines were produced through an interpopulation breeding system between Quality Protein Maize dent (QPM) and elite popcorn germplasm. In 2019, five QPP F1hybrids were selected for further evaluation due to superior agronomics, endosperm protein quality, and popping quality traits. Though these BC2F5QPP hybrids were phenotypically similar to their popcorn parents, the QPP cultivars conveyed slightly inferior popping characteristics when compared to the original popcorn germplasm. The objective of this study was twofold. First, BC2F5inbred lines were crossed to their popcorn parents and BC3F4inbred lines were produced for hybridization to test the agronomic, protein, and popping trait effects from an additional QPP by popcorn backcross. Second, BC2- and BC3-hybrids were simultaneously evaluated alongside ConAgra Brands®elite cultivars and ranked for potential commercialization in the spring of 2020. These 10 QPP hybrids were grown alongside five ConAgra Brands®elite popcorn cultivars in three locations and agronomic, protein quality, and popping quality traits were evaluated. Significant improvements in popcorn quality traits were observed in the QPP BC3cultivars compared to their BC2counterparts, and yield averages were significantly lower in BC3-derived QPP hybrids compared to the BC2population. Protein quality traits were not significantly different between QPP backcrossing populations and significantly superior to ConAgra elite popcorn varieties. Utilizing a previously published ranking system, six QPP hybrids, three from the BC2F5population and three from the BC3F4population, were evaluated as candidates for final selection. The successful evaluation and ranking system methodology employed is transferable to other hybrid production and testing programs. Incorporating this analysis with concurrent sensory studies, two QPP hybrids were chosen as premier cultivars for potential commercialization.
Similarities and Differences Between Eye and Mouse Dynamics During Web Pages Exploration
Authors: Milisavljevic Alexandre , Abate Fabrice , Le Bras Thomas , Gosselin Bernard , Mancas Matei , Doré-Mazars Karine
Published: March 2021

The study of eye movements is a common way to non-invasively understand and analyze human behavior. However, eye-tracking techniques are very hard to scale, and require expensive equipment and extensive expertise. In the context of web browsing, these issues could be overcome by studying the link between the eye and the computer mouse. Here, we propose new analysis methods, and a more advanced characterization of this link. To this end, we recorded the eye, mouse, and scroll movements of 151 participants exploring 18 dynamic web pages while performing free viewing and visual search tasks for 20 s. The data revealed significant differences of eye, mouse, and scroll parameters over time which stabilize at the end of exploration. This suggests the existence of a task-independent relationship between eye, mouse, and scroll parameters, which are characterized by two distinct patterns: one common pattern for movement parameters and a second for dwelling/fixation parameters. Within these patterns, mouse and eye movements remained consistent with each other, while the scrolling behaved the opposite way.
Revisiting Human-Agent Communication: The Importance of Joint Co-construction and Understanding Mental States
Authors: Kopp Stefan , Krämer Nicole
Published: March 2021

The study of human-human communication and the development of computational models for human-agent communication have diverged significantly throughout the last decade. Yet, despite frequently made claims of “super-human performance” in, e.g., speech recognition or image processing, so far, no system is able to lead a half-decent coherent conversation with a human. In this paper, we argue that we must start to re-consider the hallmarks of cooperative communication and the core capabilities that we have developed for it, and which conversational agents need to be equipped with: incremental joint co-construction and mentalizing. We base our argument on a vast body of work on human-human communication and its psychological processes that we reason to be relevant and necessary to take into account when modeling human-agent communication. We contrast those with current conceptualizations of human-agent interaction and formulate suggestions for the development of future systems.
Systematically Defined Informative Priors in Bayesian Estimation: An Empirical Application on the Transmission of Internalizing Symptoms Through Mother-Adolescent Interaction Behavior
Authors: Schulz Susanne , Zondervan-Zwijnenburg Mariëlle , Nelemans Stefanie A. , Veen Duco , Oldehinkel Albertine J. , Branje Susan , Meeus Wim
Published: March 2021

Background

Bayesian estimation with informative priors permits updating previous findings with new data, thus generating cumulative knowledge. To reduce subjectivity in the process, the present study emphasizes how to systematically weigh and specify informative priors and highlights the use of different aggregation methods using an empirical example that examined whether observed mother-adolescent positive and negative interaction behavior mediate the associations between maternal and adolescent internalizing symptoms across early to mid-adolescence in a 3-year longitudinal multi-method design.

Methods

The sample consisted of 102 mother-adolescent dyads (39.2% girls, Mage T1 = 13.0). Mothers and adolescents reported on their internalizing symptoms and their interaction behaviors were observed during a conflict task. We systematically searched for previous studies and used an expert-informed weighting system to account for their relevance. Subsequently, we aggregated the (power) priors using three methods: linear pooling, logarithmic pooling, and fitting a normal distribution to the linear pool by means of maximum likelihood estimation. We compared the impact of the three differently specified informative priors and default priors on the prior predictive distribution, shrinkage, and the posterior estimates.

Results

The prior predictive distributions for the three informative priors were quite similar and centered around the observed data mean. The shrinkage results showed that the logarithmic pooled priors were least affected by the data. Most posterior estimates were similar across the different priors. Some previous studies contained extremely specific information, resulting in bimodal posterior distributions for the analyses with linear pooled prior distributions. The posteriors following the fitted normal priors and default priors were very similar. Overall, we found that maternal, but not adolescent, internalizing symptoms predicted subsequent mother-adolescent interaction behavior, whereas negative interaction behavior seemed to predict subsequent internalizing symptoms. Evidence regarding mediation effects remained limited.

Conclusion

A systematic search for previous information and an expert-built weighting system contribute to a clear specification of power priors. How information from multiple previous studies should be included in the prior depends on theoretical considerations (e.g., the prior is an updated Bayesian distribution), and may also be affected by pragmatic considerations regarding the impact of the previous results at hand (e.g., extremely specific previous results).
Facial and Vocal Expressions During Clinical Interviews Suggest an Emotional Modulation Paradox in Borderline Personality Disorder: An Explorative Study
Authors: Villanueva-Valle Javier , Díaz José-Luis , Jiménez Said , Rodríguez-Delgado Andrés , Arango de Montis Iván , León-Bernal Areli , Miranda-Terres Edgar , Muñoz-Delgado Jairo
Published: March 2021

Videotape recordings obtained during an initial and conventional psychiatric interview were used to assess possible emotional differences in facial expressions and acoustic parameters of the voice between Borderline Personality Disorder (BPD) female patients and matched controls. The incidence of seven basic emotion expressions, emotional valence, heart rate, and vocal frequency (f0), and intensity (dB) of the discourse adjectives and interjections were determined through the application of computational software to the visual (FaceReader) and sound (PRAAT) tracks of the videotape recordings. The extensive data obtained were analyzed by three statistical strategies: linear multilevel modeling, correlation matrices, and exploratory network analysis. In comparison with healthy controls, BPD patients express a third less sadness and show a higher number of positive correlations (14 vs. 8) and a cluster of related nodes among the prosodic parameters and the facial expressions of anger, disgust, and contempt. In contrast, control subjects showed negative or null correlations between such facial expressions and prosodic parameters. It seems feasible that BPD patients restrain the facial expression of specific emotions in an attempt to achieve social acceptance. Moreover, the confluence of prosodic and facial expressions of negative emotions reflects a sympathetic activation which is opposed to the social engagement system. Such BPD imbalance reflects an emotional alteration and a dysfunctional behavioral strategy that may constitute a useful biobehavioral indicator of the severity and clinical course of the disorder. This face/voice/heart rate emotional expression assessment (EMEX) may be used in the search for reliable biobehavioral correlates of other psychopathological conditions.
Subjective Family Socioeconomic Status and Peer Relationships: Mediating Roles of Self-Esteem and Perceived Stress
Authors: Bai Xia , Jiang Liping , Zhang Qi , Wu Ting , Wang Song , Zeng Xiaoying , Li Yanjia , Zhang Li , Li Jingguang , Zhao Yajun , Dai Jing
Published: March 2021

This study explored the relationships between subjective family socioeconomic status (FSES), self-esteem, perceived stress, and perceived peer relationships among Chinese adolescents. A total of 1,353 adolescents (age range: 15–19 years) were asked to complete a questionnaire. Mediation analysis revealed that subjective FSES influenced perceived peer relationships in three ways: first, through the mediating effect of perceived stress; second, through the mediating effect of self-esteem; and third, through the serial mediating effects of perceived stress and self-esteem. The results remained significant after controlling for parental education. In addition, a contrast analysis showed no significant differences in the mediating effects of self-esteem and perceived stress. Thus, we suggest that steps should be taken to improve adolescents' self-esteem and reduce their stress through training interventions and preventive measures, to help them improve their perceived peer relationships and reduce adverse effects associated with low subjective FSES.
Modeling the Interruption of the Transmission of Soil-Transmitted Helminths Infections in Kenya: Modeling Deworming, Water, and Sanitation Impacts
Authors: Okoyo Collins , Medley Graham , Mwandawiro Charles , Onyango Nelson
Published: March 2021

Kenya, just like other countries with endemic soil-transmitted helminths (STH), has conducted regular mass drug administration (MDA) program for the last 5 years among school aged children as a way to reduce STH infections burden in the country. However, the point of interruption of transmission of these infections still remains unclear. In this study, we developed and analyzed an age structured mathematical model to predict the elimination period (i.e., time taken to interrupt STH transmission) of these infections in Kenya. The study utilized a deterministic age structured model of the STH population dynamics under a regular treatment program. The model was applied to three main age groups: pre-school age children (2–4 years), school age children (5–14 years), and adult populations (≥15 years) and compared the impact of two interventions on worm burden and elimination period. The model-simulated results were compared with the 5 year field data from the Kenyan deworming program for all the three types of STH (Ascaris lumbricoides, Trichuris trichiura, and hookworm). The model demonstrated that the reduction of worm burden and elimination period depended heavily on four parameter groups; drug efficacy, number of treatment rounds, MDA and water, sanitation and hygiene (WASH) coverage. The analysis showed that for STH infections to be eliminated using MDA alone in a short time period, 3-monthly MDA plan is desired. However, complementation of MDA with WASH at an optimal (95%) coverage level was most effective. These results are important to the Kenyan STH control program as it will guide the recently launched Breaking Transmission Strategy.