bluuebunny/crossref_metadata_2025 huggingface dataset:
Test-retest reliability of peak location in the sensorimotor network of resting state fMRI for potential rTMS targets
Authors: Hu Yun-Song , Yue Juan , Ge Qiu , Feng Zi-Jian , Wang Jue , Zang Yu-Feng
Published: October 2022

Most stroke repetitive transcranial magnetic stimulation (rTMS) studies have used hand motor hotspots as rTMS stimulation targets; in addition, recent studies demonstrated that functional magnetic resonance imaging (fMRI) task activation could be used to determine suitable targets due to its ability to reveal individualized precise and stronger functional connectivity with motor-related brain regions. However, rTMS is unlikely to elicit motor evoked potentials in the affected hemisphere, nor would activity be detected when stroke patients with severe hemiplegia perform an fMRI motor task using the affected limbs. The current study proposed that the peak voxel in the resting-state fMRI (RS-fMRI) motor network determined by independent component analysis (ICA) could be a potential stimulation target. Twenty-one healthy young subjects underwent RS-fMRI at three visits (V1 and V2 on a GE MR750 scanner and V3 on a Siemens Prisma) under eyes-open (EO) and eyes-closed (EC) conditions. Single-subject ICA with different total number of components (20, 30, and 40) were evaluated, and then the locations of peak voxels on the left and right sides of the sensorimotor network (SMN) were identified. While most ICA RS-fMRI studies have been carried out on the group level, that is, Group-ICA, the current study performed individual ICA because only the individual analysis could guide the individual target of rTMS. The intra- (test-retest) and inter-scanner reliabilities of the peak location were calculated. The use of 40 components resulted in the highest test-retest reliability of the peak location in both the left and right SMN compared with that determined when 20 and 30 components were used for both EC and EO conditions. ICA with 40 components might be another way to define a potential target in the SMN for poststroke rTMS treatment.
Scale-free and oscillatory spectral measures of sleep stages in humans
Authors: Schneider Bence , Szalárdy Orsolya , Ujma Péter P. , Simor Péter , Gombos Ferenc , Kovács Ilona , Dresler Martin , Bódizs Róbert
Published: October 2022

Power spectra of sleep electroencephalograms (EEG) comprise two main components: a decaying power-law corresponding to the aperiodic neural background activity, and spectral peaks present due to neural oscillations. “Traditional” band-based spectral methods ignore this fundamental structure of the EEG spectra and thus are susceptible to misrepresenting the underlying phenomena. A fitting method that attempts to separate and parameterize the aperiodic and periodic spectral components called “fitting oscillations and one over f” (FOOOF) was applied to a set of annotated whole-night sleep EEG recordings of 251 subjects from a wide age range (4–69 years). Most of the extracted parameters exhibited sleep stage sensitivity; significant main effects and interactions of sleep stage, age, sex, and brain region were found. The spectral slope (describing the steepness of the aperiodic component) showed especially large and consistent variability between sleep stages (and low variability between subjects), making it a candidate indicator of sleep states. The limitations and arisen problems of the FOOOF method are also discussed, possible solutions for some of them are suggested.
Motion artifacts removal and evaluation techniques for functional near-infrared spectroscopy signals: A review
Authors: Huang Ruisen , Hong Keum-Shik , Yang Dalin , Huang Guanghao
Published: October 2022

With the emergence of an increasing number of functional near-infrared spectroscopy (fNIRS) devices, the significant deterioration in measurement caused by motion artifacts has become an essential research topic for fNIRS applications. However, a high requirement for mathematics and programming limits the number of related researches. Therefore, here we provide the first comprehensive review for motion artifact removal in fNIRS aiming to (i) summarize the latest achievements, (ii) present the significant solutions and evaluation metrics from the perspective of application and reproduction, and (iii) predict future topics in the field. The present review synthesizes information from fifty-one journal articles (screened according to three criteria). Three hardware-based solutions and nine algorithmic solutions are summarized, and their application requirements (compatible signal types, the availability for online applications, and limitations) and extensions are discussed. Five metrics for noise suppression and two metrics for signal distortion were synthesized to evaluate the motion artifact removal methods. Moreover, we highlight three deficiencies in the existing research: (i) The balance between the use of auxiliary hardware and that of an algorithmic solution is not clarified; (ii) few studies mention the filtering delay of the solutions, and (iii) the robustness and stability of the solution under extreme application conditions are not discussed.
The effect of FTO rs9939609 polymorphism on the association between colorectal cancer and dietary fiber
Authors: Fathi Soroor , Ahmadzadeh Mina , Vahdat Mahsa , Afsharfar Maryam , Roumi Zahra , Hassanpour Ardekanizadeh Naeemeh , Shekari Soheila , Poorhosseini Seyed Mohammad , Gholamalizadeh Maryam , Abdollahi Sepideh , Kheyrani Elham , Doaei Saeid
Published: October 2022

Background

Gene polymorphisms may explain the controversy on the association between colorectal cancer (CRC) and dietary fibers. The purpose of this study was to investigate the effect of fat mass and obesity-associated (FTO) rs9939609 polymorphism on the association between colorectal cancer and dietary fiber.

Methods

This case-control study was conducted on 160 CRC cases and 320 healthy controls in Tehran, Iran. The participants' food intake was assessed using a semi-quantitative food frequency questionnaire (FFQ). The frequency of rs9939609 FTO polymorphism in the case and control groups was determined using the tetra-primer amplification refractory mutation (tetra-ARMS) method.

Results

In the participants with the TT genotype of the FTO rs9939609, the cases had higher BMI and lower intake of dietary fiber compared to the controls (P = 0.01). Among A allele carriers of FTO rs9939609 polymorphism, the cases had higher BMI (P = 0.04) and lower intake of total fiber (P = 0.02) and soluble fiber (P = 0.02). An inverse association was found between CRC and dietary fiber intake among those with the AA/AT FTO rs9939609 genotype after adjusting for age, sex, smoking, alcohol consumption, physical activity, BMI, and calorie intake (OR = 0.9, CI 95%:0.84–0.92, P < 0.05).

Conclusion

This study found a link between higher dietary fiber consumption and a lower risk of CRC in A-allele carriers of FTO rs9939609 polymorphism. Future studies are needed to identify the underlying mechanisms of the association between CRC and dietary fibers in people with different FTO genotypes.
Breastfeeding performance index and associated factors among children aged 0–6 months in Ethiopia: Analysis of the 2019 Ethiopia Mini Demographic and Health Survey
Authors: Gessese Getachew Tilahun , Woldeamanuel Berhanu Teshome , Demie Takele Gezahegn , Diriba Biratu Tolesa , Handebo Simegnew
Published: October 2022

Background

Infants under the age of 6 months are commonly affected by malnutrition globally. The higher the breastfeeding performance index (BPI), the greater the advantage of breastfeeding will be. However, there is a lack of literature in the context of Ethiopia. Therefore, this study is aimed at investigating the magnitude and determinants of the breastfeeding performance index score among mothers of children under the age of 6 months in Ethiopia.

Methods

This study was conducted using the 2019 Ethiopia Mini Demographic and Health Survey (EMDHS) dataset. A stratified, two-stage cluster sampling technique was used in the study. The survey data were weighted using the “svy” function in STATA version 16. Descriptive statistics, bivariable and multivariable logistic regression were employed in the analysis. An adjusted odds ratio (AOR) with a 95% confidence interval (CI) was reported. The results were considered statistically significant if the p-value was < 0.05. The goodness of fit of the model was checked using the Hosmer–Lemeshow test.

Results

A total of 4,273 mothers with children under the age of 6 months were included in the analysis. Our analysis revealed that the prevalence of low breastfeeding performance index was 79.05% (95% CI: 78.01, 81.59). A unit increase in child age (AOR = 11.56; 95% CI: 6.97, 19.17), the richest wealth quintile (AOR = 2.76; 95% CI: 1.18, 6.5), a higher level of education (AOR = 5.41; 95% CI: 2.08, 14.05), being married or living with partner (AOR = 2.73; 95% CI: 1.18, 6.27), being women from Somali (AOR = 5.11; 95% CI: 2.08, 12.56), Afar (AOR = 3.03; 95% CI: 1.16, 7.91), Oromia (AOR = 1.88; 95% CI: 1.03, 3.41), Diredawa city administration (AOR = 2.89; 95% CI: 1.04, 8.07), and antenatal care (ANC) visit (AOR = 2.05; 95% CI: 1.31, 3.19) were positively associated with the low breastfeeding performance index.

Conclusion

The prevalence of the low breastfeeding performance index was found to be high. Hence, the findings of the study suggest the need to target interventions aimed at improving breastfeeding performance toward mothers with higher socioeconomic and demographic status and educational status. Antenatal care clients are among the targets of the intervention.
Development and validation of a nomogram model for the prediction of 4L lymph node metastasis in thoracic esophageal squamous cell carcinoma
Authors: Xu Lei , Guo Jia , Qi Shu , Xie Hou-nai , Wei Xiu-feng , Yu Yong-kui , Cao Ping , Zhang Rui-xiang , Chen Xian-kai , Li Yin
Published: October 2022

Objectives

The left tracheobronchial (4L) lymph nodes (LNs) are considered as regional LNs for esophageal squamous cell carcinoma (ESCC), but there is a controversy about routine prophylactic 4L LN dissection for all resectable ESCCs. This study aimed to develop a nomogram for preoperative prediction of station 4L lymph node metastases (LNMs).

Methods

A total of 522 EC patients in the training cohort and 370 in the external validation cohort were included. The prognostic impact of station 4L LNM was evaluated, and multivariable logistic regression analyses were performed to identify independent risk factors of station 4L LNM. A nomogram model was developed based on multivariable logistic regression analysis. Model performance was evaluated in both cohorts in terms of calibration, discrimination, and clinical usefulness.

Results

The incidence of station 4L LNM was 7.9% (41/522) in the training cohort. Patients with station 4L LNM exhibited a poorer 5-year overall survival rate than those without (43.2% vs. 71.6%, p < 0.001). In multivariate logistic regression analyses, six variables were confirmed as independent 4L LNM risk factors: sex (p = 0.039), depth of invasion (p = 0.002), tumor differentiation (p = 0.016), short axis of the largest 4L LNs (p = 0.001), 4L conglomeration (p = 0.006), and 4L necrosis (p = 0.002). A nomogram model, containing six independent risk factors, demonstrated a good performance, with the area under the curve (AUC) of 0.921 (95% CI: 0.878–0.964) in the training cohort and 0.892 (95% CI: 0.830–0.954) in the validation cohort. The calibration curve showed a good agreement on the presence of station 4L LNM between the risk estimation according to the model and histopathologic results on surgical specimens. The Hosmer–Lemeshow test demonstrated a non-significant statistic (p = 0.691 and 0.897) in the training and validation cohorts, which indicated no departure from the perfect fit. Decision curve analysis indicated that the model had better diagnostic power for 4L LNM than the traditional LN size criteria.

Conclusions

This model integrated the available clinical and radiological risk factors, facilitating in the precise prediction of 4L LNM in patients with ESCC and aiding in personalized therapeutic decision-making regarding the need for routine prophylactic 4L lymphadenectomy.
The effect of respiratory capacity for dose sparing in left-sided breast cancer irradiation with active breathing coordinator technique
Authors: Chen Hongtao , Piao Ying , Yang Dong , Kuang Peipei , Li Zihuang , Liao Guixiang , Zhong Heli
Published: October 2022

Background and aim

A subsequent cardiac toxicity is deemed to be dose-dependent for left-sided breast cancer irradiation. This study aims to demonstrate the effect of respiratory capacity for dose sparing when the deep inspiration breath hold with Active Breathing Coordinator technique (ABC-DIBH) is used in left-sided breast cancer irradiation.

Methods

74 left-sided breast cancer patients, who received whole breast or post-mastectomy chest wall radiotherapy with ABC-DIBH between 2020 and 2021 in our center, were retrospectively reviewed in this study. CT scans of free breath (FB) and ABC-DIBH were done for each patient, and two treatment plans with a prescription dose of 5000 cGy/25 Fr were designed separately. The dose to heart, left anterior descending artery (LAD) and lungs was compared between FB and ABC-DIBH. The correlation between individual parameters (dose to organs at risk (OARs) and minimum heart distance (MHD)) was analyzed, and the effect of respiratory capacity for dose sparing was assessed.

Results

The plans with ABC-DIBH achieved lower Dmean for heart (34.80%, P < 0.01) and LAD (29.33%, P < 0.01) than those with FB. Regression analysis revealed that both Dmean and D2 of heart were negatively correlated with MHD in the plans with FB and ABC-DIBH, which decreased with the increase in MHD by 37.8 cGy and 309.9 cGy per 1mm, respectively. Besides, a lower Dmean of heart was related to a larger volume of ipsilateral lung in plans with FB. With the increase in volume of ipsilateral lung, the linear correlation was getting weaker and weaker until the volume of ipsilateral lung reached 1700 cc. Meanwhile, a negative linear correlation between Dmean of LAD and MHD in plans with FB and ABC-DIBH was observed, whose slope was 162.5 and 135.9 cGy/mm, respectively. Furthermore, when the respiratory capacity of ABC-DIBH reached 1L, and the relative ratio (ABC-DIBH/FB) reached 3.6, patients could obtain the benefit of dose sparing. The larger difference in respiratory capacity had no significant effect in the larger difference of MHD, Dmean of heart and Dmean of LAD between FB and ABC-DIBH.

Conclusion

This study demonstrates the sufficiently good effect of ABC-DIBH when utilizing for cardiac sparing. It also reveals the correlations among individual parameters and the effect of respiratory capacity for dose sparing. This helps take optimal advantage of the ABC-DIBH technique and predict clinical benefits.
Role of clusters in exclusive breastfeeding practices in Tanzania: A secondary analysis study using demographic and health survey data (2015/2016)
Authors: Jahanpour Ola Farid , Okango Elphas Luchemo , Todd Jim , Mwambi Henry , Mahande Michael Johnson
Published: October 2022

Background

While the benefits of exclusive breastfeeding are widely acknowledged, it continues to be a rare practice. Determinants of exclusive breastfeeding in Tanzania have been studied; however, the existence and contribution of regional variability to the practice have not been explored.

Methods

Tanzania demographic and health survey data for 2015/2016 were used. Information on infants aged up to 6 months was abstracted. Exclusive breastfeeding was defined using a recall of feeding practices in the past 24 h. Enumeration areas and regions were treated as random effects. Models without random effects were compared with those that incorporated random effects using the Akaike information criterion. The determinants of exclusive breastfeeding were estimated using the generalized linear mixed model with enumeration areas nested within the region.

Results

The generalized linear mixed model with an enumeration area nested within a region performed better than other models. The intra-cluster variability at region and enumeration area levels was 3.7 and 24.5%, respectively. The odds of practicing exclusive breastfeeding were lower for older and male infants, for mothers younger than 18, among mothers residing in urban areas, among those who were employed by a family member or someone else, those not assisted by a nurse/midwife, and those who were not counseled on exclusive breastfeeding within 2 days post-delivery. There was no statistical evidence of an association between exclusive breastfeeding practices and the frequency of listening to the radio and watching television. When mapping the proportion of exclusive breastfeeding, a variability of the practice is seen across regions.

Conclusion

There is room to improve the proportion of those who practice exclusive breastfeeding in Tanzania. Beyond individual and setting factors, this analysis shows that a quarter of the variability in exclusive breastfeeding practices is at the community level. Further studies may explore the causes of variabilities in regional and enumeration area and how it operates. Interventions to protect, promote, and support exclusive breastfeeding in Tanzania may target the environment that shapes the attitude toward exclusive breastfeeding in smaller geographical areas.
Somatosensory abnormalities after infection with SARS-CoV-2 – A prospective case-control study in children and adolescents
Authors: Eitner Lynn , Maier Christoph , Brinkmann Folke , Schlegtendal Anne , Knoke Leona , Enax-Krumova Elena , Lücke Thomas
Published: October 2022

Background

Long-term neurological complaints after SARS-CoV-2 infection occur in 4–66% of children and adolescents. Controlled studies on the integrity of the peripheral nerve system are scarce. Therefore, we examined the somatosensory function in children and adolescents after SARS-CoV-2 infection in a case-control study compared with age-matched individuals.

Materials and Methods

Eighty-one subjects after SARS-CoV-2 infection (n = 44 female, 11.4 ± 3.5 years, n = 75 SARS-CoV-2 seropositive, n = 6 PCR positive during infection and SARS-CoV-2 seronegative at the time point of study inclusion, n = 47 asymptomatic infection) were compared to 38 controls without SARS-CoV-2 infection (26 female, 10.3 ± 3.4 years, n = 15 with other infection within last 6 months). After standardised interviews and neurological examinations, large fibre (tactile and vibration detection thresholds) and small fibre (cold and warm detection thresholds, paradoxical heat sensation) functions were assessed on both feet following a validated protocol. After z-transformation of all values, all participants were compared to published reference values regarding the number of abnormal results. Additionally, the mean for all sensory parameters values of both study groups were compared to an ideal healthy population (with z-value 0 ± 1), as well as with each other, as previously described. Statistical analyses: t-test, Chi-squared test, and binominal test.

Findings

None of the controls, but 27 of the 81 patients (33%, p < 0.001) reported persistent complaints 2.7 ± 1.9 (0.8–8.5) months after SARS-CoV-2 infection, most often reduced exercise capacity (16%), fatigue (13%), pain (9%), or paraesthesia (6%). Reflex deficits or paresis were missing, but somatosensory profiles showed significantly increased detection thresholds for thermal (especially warm) and vibration stimuli compared to controls. Approximately 36% of the patients after SARS-CoV-2, but none of the controls revealed an abnormal sensory loss in at least one parameter (p < 0.01). Sensory loss was characterised in 26% by large and 12% by small fibre dysfunction, the latter appearing more frequently in children with prior symptomatic SARS-CoV-2 infection. Myalgia/paraesthesia was indicative of somatosensory dysfunction. In all eight re-examined children, the nerve function recovered after 2–4 months.

Interpretation

This study provides evidence that in a subgroup of children and adolescents previously infected with SARS-CoV-2, regardless of their complaints, the function of large or small nerve fibres is presumably reversibly impaired.
Differential effects of ibuprofen and indomethacin on cerebral oxygen kinetics in the very preterm baby
Authors: Stark Michael J. , Crawford Tara M. , Ziegler Nina M. , Hall Anthea , Andersen Chad C.
Published: October 2022

Background

Ibuprofen is preferred to indomethacin for treatment of a significant patent ductus arteriosus (PDA) in preterm babies despite indomethacin being associated with a lower risk of intraventricular haemorrhage. This difference is thought to relate to the discrepant effects of each medication on cerebral oxygen kinetics yet the effect of ibuprofen on cerebral perfusion is uncertain.

Methods

Forty-eight babies < 30 weeks with a significant PDA, defined by echocardiography, were randomly assigned to either indomethacin or ibuprofen (n = 24 per group) and stratified by gestation and chronologic age. Cerebral blood flow [total internal carotid blood flow (TICF)] and oxygen physiology [oxygen delivery (modCerbDO2) and consumption (modCerbVO2)] were measured using cranial Doppler ultrasound and near-infrared spectroscopy, and cerebral oxygen extraction (cFTOE) calculated, immediately before and following administration. Temporal and treatment related changes were analysed.

Results

A fixed effect of time was seen for TICF (p = 0.03) and therefore modCerbDO2 (p = 0.046) and cFTOE (p = 0.04) for indomethacin alone. In the indomethacin group, TICF and modCerbDO2 fell from baseline to 5 and 30 min respectively (TICF p < 0.01, cDO2p = 0.01) before increasing from 5 min to 24 h (p < 0.01) and 30 min and 24 h (p < 0.01) timepoints. cFTOE peaked at 30 min (p = 0.02) returning to baseline at 24 h. There was a parallel increase in arterial lactate.

Conclusion

Indomethacin significantly reduces cerebral blood flow soon after administration, resulting in a parallel increase in oxygen extraction and arterial lactate. This implies that the balance of oxygen kinetics at the time of treatment may be critical in very preterm babies with significant PDA.
Citrullinemia type I in Chinese children: Identification of two novel argininosuccinate synthetase gene mutations
Authors: Xiong Mei , Chen Mingwu
Published: October 2022

Background

In this study, we evaluated the clinical characteristics, prognosis, and gene mutations of five children with citrullinemia type I (CTLN1) diagnosed in our department and identified two novel ASS1 gene mutations.

Methods

We examined the clinical characteristics, prognosis, and gene mutations of the five children through data collection, tandem mass spectrometry, and whole-exon sequencing. MutationTaster, regSNP-intron, and SWISS-MODEL were used for bioinformatic analysis to evaluate the two novel gene mutations. We analyzed differences in blood ammonia and citrulline levels based on clinical phenotypes. Finally, we reviewed the medical literature describing Chinese children with CTLN1.

Results

ASS1 C773 + 6T > G and c.848 delA as well as c.952_953 del insTT and c.133G > A have not been previously reported in the Human Gene Mutation Database. Using MutationTaster and regSNP-intron, we predicted that these mutations affected protein function. The 3D structure obtained using SWISS-MODEL supported this prediction. Through comparative analysis showed that the ammonia level of the neonatal type was markedly higher than that of other types, whereas citrulline levels did not differ between groups.

Conclusion

We identified two novel mutations that cause disease. The blood ammonia level of neonatal form citrullinemia was markedly higher than that of other types. The genotype-phenotype association in Chinese patients remains unclear and should be further evaluated in genetic studies of larger sample sizes.
Integrating machine learning to construct aberrant alternative splicing event related classifiers to predict prognosis and immunotherapy response in patients with hepatocellular carcinoma
Authors: Liu Wangrui , Zhao Shuai , Xu Wenhao , Xiang Jianfeng , Li Chuanyu , Li Jun , Ding Han , Zhang Hailiang , Zhang Yichi , Huang Haineng , Wang Jian , Wang Tao , Zhai Bo , Pan Lei
Published: October 2022

Introduction: In hepatocellular carcinoma (HCC), alternative splicing (AS) is related to tumor invasion and progression.

Methods: We used HCC data from a public database to identify AS subtypes by unsupervised clustering. Through feature analysis of different splicing subtypes and acquisition of the differential alternative splicing events (DASEs) combined with enrichment analysis, the differences in several subtypes were explored, cell function studies have also demonstrated that it plays an important role in HCC.

Results: Finally, in keeping with the differences between these subtypes, DASEs identified survival-related AS times, and were used to construct risk proportional regression models. AS was found to be useful for the classification of HCC subtypes, which changed the activity of tumor-related pathways through differential splicing effects, affected the tumor microenvironment, and participated in immune reprogramming.

Conclusion: In this study, we described the clinical and molecular characteristics providing a new approach for the personalized treatment of HCC patients.
Identification of cuproptosis-related subtypes in lung adenocarcinoma and its potential significance
Authors: Pan Shize , Song Congkuan , Meng Heng , Li Ning , Li Donghang , Hao Bo , Lu Zilong , Geng Qing
Published: October 2022

Cuproptosis is a novel and unique cell death mode that has attracted significant interest in recent years. Little is currently known about whether cuproptosis-related genes (CRGs) are associated with the pathophysiology and survival of patients with lung adenocarcinoma (LUAD). The present study sought to characterize the transcriptional and genetic alteration of CRGs in LUAD and its potential significance in the tumor microenvironment and predicting the prognosis of LUAD. The secondary eventual aim was to study the role of CRGs in predicting immunotherapy response and its clinical value combined with the TNM stage. We found that several CRGs, including FDX1, DLD, SLC31A1, and MTF1, were enriched in macrophages in our single-cell RNA-seq data. Three distinct molecular subtypes were identified and correlated with clinicopathological characteristics, prognosis, biological pathways, and tumor microenvironment (TME) in LUAD. We developed a cuproptosis-related gene score (CRG_score) and validated it in three independent cohorts and clinical subtypes. The low CRG_score group, characterized by a greater immune score, immunophenoscore (IPS), lower tumor immune dysfunction and exclusion (TIDE) score, and T-cell dysfunction score, had a better prognosis, suggesting that the low CRG_score group responded more favorably to immunotherapy, which was validated in the anti-PD-1/L1 immunotherapy cohort (IMvigor210). In contrast, the high CRG_score group was more sensitive to targeted therapy and chemotherapy, with a higher cancer stem cell (CSC) index and lower half-maximal inhibitory concentration (IC50) for many drugs. Given the established crosstalk between CRG_score and tumor TNM stage, we developed an accurate nomogram for clinical application of the CRG_score. Taken together, our rigorous and comprehensive examination of CRGs in LUAD identified their potential functions in TME, clinicopathological characteristics, drug sensitivity, and prognosis. These findings improve the current understanding of cuproptosis in LUAD, paving the way for more accurate prognosis assessment and tailored treatment for this patient population.
ApoE isoform-dependent effects of xanthohumol on high fat diet-induced cognitive impairments and hippocampal metabolic pathways
Authors: Kundu Payel , Holden Sarah , Paraiso Ines L. , Sudhakar Reetesh , McQuesten Chloe , Choi Jaewoo , Miranda Cristobal L. , Maier Claudia S. , Bobe Gerd , Stevens Jan F. , Raber Jacob
Published: October 2022

Consumption of a high fat diet (HFD) is linked to metabolic syndrome and cognitive impairments. This is exacerbated in age-related cognitive decline (ACD) and in individuals with a genetic risk for Alzheimer’s disease (AD). Apolipoprotein E (apoE) is involved in cholesterol metabolism. In humans, there are three major isoforms, E2, E3, and E4. Compared to E3, E4 increases ACD and AD risk and vulnerability to the deleterious cognitive effects of a HFD. The plant compound Xanthohumol (XN) had beneficial effects on cognition and metabolism in C57BL/6J wild-type (WT) male mice put on a HFD at 9 weeks of age for 13 weeks. As the effects of XN in the context of a HFD in older WT, E3, and E4 female and male mice are not known, in the current study male and female WT, E3, and E4 mice were fed a HFD alone or a HFD containing 0.07% XN for 10 or 19 weeks, starting at 6 months of age, prior to the beginning of behavioral and cognitive testing. XN showed sex- and ApoE isoform-dependent effects on cognitive performance. XN-treated E4 and WT, but not E3, mice had higher glucose transporter protein levels in the hippocampus and cortex than HFD-treated mice. E3 and E4 mice had higher glucose transporter protein levels in the hippocampus and lower glucose transporter protein levels in the cortex than WT mice. In the standard experiment, regardless of XN treatment, E4 mice had nearly double as high ceramide and sphingomyelin levels than E3 mice and male mice had higher level of glycosylated ceramide than female mice. When the differential effects of HFD in E3 and E4 males were assessed, the arginine and proline metabolism pathway was affected. In the extended exposure experiment, in E3 males XN treatment affected the arginine and proline metabolism and the glycine, serine, and threonine metabolism. Myristic acid levels were decreased in XN-treated E3 males but not E3 females. These data support the therapeutic potential for XN to ameliorate HFD-induced cognitive impairments and highlight the importance of considering sex and ApoE isoform in determining who might most benefit from this dietary supplement.
Periplaneta americana extract alleviates steatohepatitis in a mouse model by modulating HMGB1-mediated inflammatory response
Authors: Xiao Yang , Gao Chongqing , Wu Junru , Li Jing , Wang Lijuan , You Yang , Peng Tianqi , Zhang Keke , Cao Mingrong , Hong Jian
Published: October 2022

Alcoholic abuse and obesity are the most common lifestyle implications of chronic liver injury, and always act synergistically to increase the risk of mortality. Periplaneta americana has a long history of being applied in medicine, including wound healing, antitumor, antibacterial, antiviral, antifibrotic, and cardiomyocyte-protecting. Ganlong capsule (GLC), a natural prescription drug extracted from Periplaneta americana, has been widely used in HBV-related symptoms. However, the anti-steatohepatitis efficacy and mechanisms of GLC have not yet been characterized. Here, we found the protective effect of GLC on the development of hepatic steatosis, oxidative stress, and inflammation in vivo under alcohol exposure combined with a high-fat and high-cholesterol diet (HFHC). Consistently, GLC exhibited a hepatoprotective property by preventing hepatocytes from oxidative stress injury and lipid accumulation in vitro. In addition, it exerted an anti-inflammation characteristic by reducing macrophage recruitment and decreasing the expression of pro-inflammatory genes in vivo and in vitro. Mechanically, GLC serum, isolated from GLC-treated mice, reduced extracellular high-mobility group box 1 (HMGB1) of dying hepatocytes; and suppressed subsequent M1 polarization of macrophages in the co-culture system. Furthermore, GLC serum inhibited inflammatory response via suppressing the HMGB1 release and blocking the downstream TLR4/NF-kB pathway. Collectively, GLC alleviates steatohepatitis induced by alcohol consumption and obesity through inhibition of the HMGB1-mediated inflammatory cascade. GLC might be a therapeutic candidate for the treatment of steatohepatitis developed by alcohol abuse and metabolic disorders.
Vlasov simulation of the emissive plasma sheath with energy-dependent secondary emission coefficient and improved modeling for dielectric charging effects
Authors: Sun Guang-Yu , Zhang Shu , Guo Bao-Hong , Sun An-Bang , Zhang Guan-Jun
Published: October 2022

A one-dimensional Vlasov–Poisson simulation code is employed to investigate the plasma sheath considering electron-induced secondary electron emission (SEE) and backscattering. The SEE coefficient is commonly treated as constant in a range of plasma simulations; here, an improved SEE model of a charged dielectric wall is constructed, which includes the wall charging effect on the SEE coefficient and the energy dependency of the SEE coefficient. Pertinent algorithms to implement the previously mentioned SEE model in plasma simulation are studied in detail. It is found that the SEE coefficient increases with the amount of negative wall charges, which in turn reduces the emissive sheath potential. With an energy-dependent SEE coefficient, the sheath potential is a nonlinear function of the plasma electron temperature, as opposed to the linear relation predicted by the classic emissive sheath theory. Simulation combining both wall-charging effect and SEE coefficient’ energy dependency suggests that the space-charged limited sheath is formed at high plasma electron temperature levels, where both sheath potential and surface charging saturate. Additionally, different algorithms to implement the backscattering in the kinetic simulation are tested and compared. Converting backscattered electrons to secondary electrons via an effective SEE coefficient barely affects the sheath properties. The simulation results are shown to be commensurate with the upgraded sheath theory predictions.
Modeling space-resolved ion dynamics in ECR plasmas for predicting in-plasma β-decay rates
Authors: Mishra Bharat , Galatà Alessio , Pidatella Angelo , Biri Sándor , Mauro Giorgio Sebastiano , Naselli Eugenia , Rácz Richárd , Torrisi Giuseppe , Mascali David
Published: October 2022

Lifetimes of radioactive nuclei are known to be affected by the level configurations of their respective atomic shells. Immersing such isotopes in environments composed of energetic charged particles such as stellar plasmas can result in β-decay rates orders of magnitude different from those measured terrestrially. Accurate knowledge of the relation between plasma parameters and nuclear decay rates are essential for reducing uncertainties in present nucleosynthesis models, and this is precisely the aim of the PANDORA experiment. Currently, experimental evidence is available for fully stripped ions in storage rings alone, but the full effect of a charge state distribution (CSD) as exists in plasmas is only modeled theoretically. PANDORA aims to be the first to verify these models by measuring the β-decay rates of select isotopes embedded in electron cyclotron resonance (ECR) plasmas. For this purpose, it is necessary to consider the spatial inhomogeneity and anisotropy of plasma ion properties as well as the non-local thermodynamic equilibrium (NLTE) nature of the system. We present here a 3D ion dynamics model combining a quasi-stationary particle-in-cell (PIC) code to track the motion of macroparticles in a pre-simulated electron cloud while simultaneously using a Monte Carlo (MC) routine to check for relevant reactions describing the ion population kinetics. The simulation scheme is robust, comprehensive, makes few assumptions about the state of the plasma, and can be extended to include more detailed physics. We describe the first results on the 3D variation of CSD of ions both confined and lost from the ECR trap, as obtained from the application of the method to light nuclei. The work culminates in some perspectives and outlooks on code optimization, with a potential to be a powerful tool not only in the application of ECR plasmas but for fundamental studies of the device itself.
Simulating the Euler equations on multiple GPUs using Python
Authors: Brodtkorb André R. , Sætra Martin L.
Published: October 2022

GPUs have become a household name in High Performance Computing (HPC) systems over the last 15 years. However, programming GPUs is still largely a manual and arduous task, which requires expert knowledge of the physics, mathematics, and computer science involved. Even though there have been large advances in automatic parallelization and GPU execution of serial code, it is still difficult to fully utilize the GPU hardware with such approaches. Many core numeric GPU codes are therefore still mostly written using low level C/C++ or Fortran for the host code. Several studies have shown that using higher level languages, such as Python, can make software development faster and with fewer bugs. We have developed a simulator based on PyCUDA and mpi4py in Python for solving the Euler equations on Cartesian grids. Our framework utilizes the GPU, and can automatically run on clusters using MPI as well as on shared-memory systems. Our framework allows the programmer to implement low-level details in CUDA C/C++, which is important to achieve peak performance, whilst still benefiting from the productivity of Python. We show that our framework achieves good weak and strong scaling. Our weak scaling achieves more than 94% efficiency on a shared-memory GPU system and more than 90% efficiency on a distributed-memory GPU system, and our strong scaling is close to perfect on both shared-memory and distributed-memory GPU systems.
Multiple rather than specific autoantibodies were identified in irritable bowel syndrome with HuProt™ proteome microarray
Authors: Fan Wenjuan , Fang Xiucai , Hu Chaojun , Fei Guijun , Xiao Qiyun , Li Yongzhe , Li Xiaoqing , Wood Jackie D. , Zhang Xuan
Published: October 2022

Immune activation and several autoantibodies might be involved in the pathophysiology of irritable bowel syndrome (IBS). We aimed to identify serum biomarkers for IBS by HuProt™ microarray. IBS patients met Rome III criteria were enrolled. Control groups included healthy controls (HCs) and disease controls (DCs). In stage I, we profiled sera from IBS and control groups with HuProt™ microarrays. Based on significant different proteins in stage I, IBS focused microarrays were constructed and validated in a larger cohort in stage II, then decision tree models were generated to establish a combination of biomarkers. In stage III, 4 purified proteins were verified by ELISA. Finally, we analyzed the correlation of autoantibodies with symptoms. In stage I, we identified 47 significant different proteins including 8 autoantibodies of IgG, 2 of IgA between IBS and HCs; 13 autoantibodies of IgG, 13 of IgA between IBS and DCs. In stage II, we found the positive rates of 14 IgG and IgA autoantibodies in IBS were significantly higher than HCs. Five autoantibodies of IgG and 7 IgA were comprehensively involved in differentiating IBS and HCs with the sensitivity and specificity to diagnose IBS as 40%–46.7% and 79.4%–86.3%. The median optical density value of ELAVL4 (IgG) and PIGP (IgA) were significantly higher in IBS than HCs. Parts of autoantibodies above were related to IBS symptoms. We found a combination of autoantibodies to differentiate IBS with HCs, but no specific autoantibodies could serve as serum biomarkers for IBS.
Flow karyotyping of wheat-Aegilops additions facilitate dissecting the genomes of Ae. biuncialis and Ae. geniculata into individual chromosomes
Authors: Said Mahmoud , Cápal Petr , Farkas András , Gaál Eszter , Ivanizs László , Friebe Bernd , Doležel Jaroslav , Molnár István
Published: October 2022

Breeding of wheat adapted to new climatic conditions and resistant to diseases and pests is hindered by a limited gene pool due to domestication and thousands of years of human selection. Annual goatgrasses (Aegilops spp.) with M and U genomes are potential sources of the missing genes and alleles. Development of alien introgression lines of wheat may be facilitated by the knowledge of DNA sequences of Aegilops chromosomes. As the Aegilops genomes are complex, sequencing relevant Aegilops chromosomes purified by flow cytometric sorting offers an attractive route forward. The present study extends the potential of chromosome genomics to allotetraploid Ae. biuncialis and Ae. geniculata by dissecting their M and U genomes into individual chromosomes. Hybridization of FITC-conjugated GAA oligonucleotide probe to chromosomes suspensions of the two species allowed the application of bivariate flow karyotyping and sorting some individual chromosomes. Bivariate flow karyotype FITC vs. DAPI of Ae. biuncialis consisted of nine chromosome-populations, but their chromosome content determined by microscopic analysis of flow sorted chromosomes indicated that only 7Mb and 1Ub could be sorted at high purity. In the case of Ae. geniculata, fourteen chromosome-populations were discriminated, allowing the separation of nine individual chromosomes (1Mg, 3Mg, 5Mg, 6Mg, 7Mg, 1Ug, 3Ug, 6Ug, and 7Ug) out of the 14. To sort the remaining chromosomes, a partial set of wheat-Ae. biuncialis and a whole set of wheat-Ae. geniculata chromosome addition lines were also flow karyotyped, revealing clear separation of the GAA-rich Aegilops chromosomes from the GAA-poor A- and D-genome chromosomes of wheat. All of the alien chromosomes represented by individual addition lines could be isolated at purities ranging from 74.5% to 96.6% and from 87.8% to 97.7%, respectively. Differences in flow karyotypes between Ae. biuncialis and Ae. geniculata were analyzed and discussed. Chromosome-specific genomic resources will facilitate gene cloning and the development of molecular tools to support alien introgression breeding of wheat.
Genome-wide characterization of C2H2 zinc-finger gene family provides insight into the mechanisms and evolution of the dehydration–rehydration responses in Physcomitrium and Arabidopsis
Authors: Li Xuan , Cao Xubing , Li Jialing , Niu Qinqin , Mo Yuanping , Xiao Lihong
Published: October 2022

Dehydration tolerance is a vital factor for land plant evolution and world agricultural production. Numerous studies enlightened that the plant-specific C2H2-type zinc-finger proteins (C2H2-ZFPs) as master regulators played pivotal roles in the abiotic stress responses of plants. However, a comprehensive understanding of the evolution of C2H2-ZFPs in terrestrial plants and its regulatory mechanism in dehydration and rehydration response remains a mystery. In this study, the genome-wide identification of C2H2-ZFP genes revealed 549 homologs in the representatives of terrestrial plant lineages from liverwort to angiosperms. Based on the characteristics of the conserved C2H2-ZF domains, four major C2H2-ZF types (M-, Z-, Q-, and D-type) were identified in the C2H2-ZFPs, with the dominants of M-type in all selected species and followed by Z-type in non-seed plants and Q-type in seed plants, respectively. Phylogenetic analyses of the identified C2H2-ZFPs supported four major groups in the land plant representatives, among which the members from the desiccation-tolerant Physcomitrium patens and the dehydration-sensitive Arabidopsis thaliana displayed different topological relationships in the phylogenies reconstructed for a single species. C2H2-ZFPs clustered in the same subclades shared similar features in their conserved domains and gene structures. Approximately, 81% of the C2H2-ZFP promoters of all 549 identified C2H2-ZFPs harbored the conserved ABA-responsive elements (ABREs) and/or dehydration-responsive elements (DREs). Comparative transcriptomic analyses showed that 50 PpZFPs and 56 AtZFPs significantly changed their transcripts abundance. Interestingly, most of the dehydration- and rehydration-responsive PpZPFs and AtZFPs had been predicted to contain the ABRE and DRE elements in their promoter regions and with over half of which phylogenetically belonging to group III. The differences in the expression patterns of C2H2-ZFPs in responses to dehydration and rehydration between P. patens and A. thaliana reflected their different strategies to adapt to dehydration. The identified candidate PpZFPs were specifically induced by moderate dehydration and reached the peak transcript abundance in severe dehydration. Our study lays the foundations for further functional investigation of C2H2-ZFPs in dehydration responses from an evolutionary perspective in land plants. The findings will provide us with genetic resources and potential targets for drought tolerance breeding in crops and beyond.
Laticifer growth pattern is guided by cytoskeleton organization
Authors: Medina Maria Camila , Sousa-Baena Mariane S. , Van Sluys Marie-Anne , Demarco Diego
Published: October 2022

Laticifers are secretory structures that produce latex, forming a specialized defense system against herbivory. Studies using anatomical approaches to investigate laticifer growth patterns have described their origin; however, their mode of growth, i.e., whether growth is intrusive or diffuse, remains unclear. Studies investigating how cytoskeleton filaments may influence laticifer shape establishment and growth patterns are lacking. In this study, we combined microtubule immunostaining and developmental anatomy to investigate the growth patterns in different types of laticifers. Standard anatomical methods were used to study laticifer development. Microtubules were labelled through immunolocalization of α-tubulin in three types of laticifers from three different plant species: nonanastomosing (Urvillea ulmacea), anastomosing unbranched with partial degradation of terminal cell walls (Ipomoea nil), and anastomosing branched laticifers with early and complete degradation of terminal cell walls (Asclepias curassavica). In both nonanastomosing and anastomosing laticifers, as well as in differentiating meristematic cells, parenchyma cells and idioblasts, microtubules were perpendicularly aligned to the cell growth axis. The analyses of laticifer microtubule orientation revealed an arrangement that corresponds to those cells that grow diffusely within the plant body. Nonanastomosing and anastomosing laticifers, branched or not, have a pattern which indicates diffuse growth. This innovative study on secretory structures represents a major advance in the knowledge of laticifers and their growth mode.