Miracle-dz/UniFAR-FTUs huggingface dataset:
Comparative analysis of different molecular and serological methods for detection of Xylella fastidiosa in blueberry

Bacterial leaf scorch, caused by Xylella fastidiosa, is a major threat to blueberry production in the southeastern United States. Management of this devastating disease is challenging and often requires early detection of the pathogen to reduce major loss. There are several different molecular and serological detection methods available to identify the pathogen. Knowing the efficiency and suitability of these detection techniques for application in both field and laboratory conditions is important when selecting the appropriate detection tool. Here, we compared the efficiency and the functionality of four different molecular detection techniques (PCR, real-time PCR, LAMP and AmplifyRP® Acceler8™) and one serological detection technique (DAS-ELISA). The most sensitive method was found to be real-time PCR with the detection limit of 25 fg of DNA molecules per reaction (≈9 genome copies), followed by LAMP at 250 fg per reaction (≈90 copies), AmplifyRP® Acceler8™ at 1 pg per reaction (≈350 copies), conventional PCR with nearly 1.25 pg per reaction (≈ 440 copies) and DAS-ELISA with 1x105 cfu/mL of Xylella fastidiosa. Validation between assays with 10 experimental samples gave consistent results beyond the variation of the detection limit. Considering robustness, portability, and cost, LAMP and AmplifyRP® Acceler8™ were not only the fastest methods but also portable to the field and didn’t require any skilled labor to carry out. Among those two, AmplifyRP® Acceler8™ was faster but more expensive and less sensitive than LAMP. On the other hand, real-time PCR was the most sensitive assay and required comparatively lesser time than C-PCR and DAS-ELISA, which were the least sensitive assays in this study, but all three assays are not portable and needed skilled labor to proceed. These findings should enable growers, agents, and diagnosticians to make informed decisions regarding the selection of an appropriate diagnostic tool for X. fastidiosa on blueberry.
Selective Feature Generation Method Based on Time Domain Parameters and Correlation Coefficients for Filter-Bank-CSP BCI Systems

This paper presents a novel motor imagery (MI) classification algorithm using filter-bank common spatial pattern (FBCSP) features based on MI-relevant channel selection. In contrast to existing channel selection methods based on global CSP features, the proposed algorithm utilizes the Fisher ratio of time domain parameters (TDPs) and correlation coefficients: the channel with the highest Fisher ratio of TDPs, named principle channel, is selected and a supporting channel set for the principle channel that consists of highly correlated channels to the principle channel is generated. The proposed algorithm using the FBCSP features generated from the supporting channel set for the principle channel significantly improved the classification performance. The performance of the proposed method was evaluated using BCI Competition III Dataset IVa (18 channels) and BCI Competition IV Dataset I (59 channels).
Improved Eating Behaviour and Nutrient Intake in Noncompliant Patients with Phenylketonuria after Reintroducing a Protein Substitute: Observations from a Multicentre Study

Noncompliance is widespread in adults with PKU and is associated with adverse metabolic, nutritional and cognitive abnormalities. Returning to the PKU diet is important for this at-risk population, yet for many this is challenging to achieve. Strategies that ease the return to the PKU diet, while offering nutritional and cognitive advantages, are needed. Twelve PKU adults (33.7 ± 2.6 years), who had been noncompliant for 4.5 years (range: 1 to 11 years), took 33 g of a low-volume, nutrient-enriched, protein substitute daily for 28 days. Outcomes of eating behaviour, nutrient intake and mood were assessed at entry (baseline, days 1–3) and after the intervention period (days 29–31). At baseline, intakes of natural protein and estimated phenylalanine were high (66.4 g and 3318.5 mg, respectively) and intakes of calcium, magnesium, iron, zinc, iodine and vitamin D were below country-specific recommendations. With use of the experimental protein substitute, natural protein and estimated phenylalanine intake declined (p = 0.043 for both). Fat and saturated fat intakes also decreased (p = 0.019 and p = 0.041, respectively), while energy and carbohydrate intake remained unchanged. Micronutrient intake increased (p ≤ 0.05 for all aforementioned) to levels well within reference nutrient intake recommendations. Blood vitamin B12 and vitamin D increased by 19.8% and 10.4%, respectively. Reductions in anxiety and confusion were also observed during the course of the study yet should be handled as preliminary data. This study demonstrates that reintroducing a low-volume, nutrient-enriched protein substitute delivers favourable nutritional and possible mood benefits in noncompliant PKU patients, yet longer-term studies are needed to further confirm this. This preliminary knowledge should be used in the design of new strategies to better facilitate patients’ return to the PKU diet, with the approach described here as a foundation.
Is the efficacy of repetitive transcranial magnetic stimulation influenced by baseline severity of fatigue symptom in patients with myalgic encephalomyelitis

Abstract Objectives: Recently, repetitive transcranial magnetic stimulation (rTMS) has been therapeutically applied for patients with myalgic encephalomyelitis (ME). However, it is still unclear which clinical factors could influence the efficacy of rTMS for ME patients. The purpose of this study is to clarify whether baseline severity of fatigue symptom would influence the efficacy of rTMS applied for ME patients. Methods: Twenty-two patients with ME were studied. Each patient was hospitalized to receive 6–8 sessions of rTMS. In this study, high-frequency rTMS of 10 Hz was applied over prefrontal cortex. To evaluate the severity of fatigue symptom, Brief Fatigue Inventory (BFI) score and Visual Analogue Scale (VAS) rate were applied before and after rTMS application. Based on the BFI score before rTMS, the patients were divided into two groups: ‘severe group’ (n = 9) and ‘mild group’ (n = 13). We compared the extent of the improvements of fatigue symptom between two groups. Results: In severe group, compared to before rTMS, VAS rate was significantly lower not only at discharge but also 2 weeks after discharge. Similarly, mild group also showed significant decrease in VAS rate at the same timepoints. However, the extent of VAS rate change did not differ between two groups. In addition, no significant correlation between baseline score of BFI and the changes in VAS rate was indicated. Conclusions: It can be concluded that rTMS can improve fatigue symptom in ME patients regardless of baseline severity of fatigue symptom. It is expected that rTMS can be a novel therapeutic intervention for ME patients.
CNNDLP: A Method Based on Convolutional Autoencoder and Convolutional Neural Network with Adjacent Edge Attention for Predicting lncRNA–Disease Associations

It is well known that the unusual expression of long non-coding RNAs (lncRNAs) is closely related to the physiological and pathological processes of diseases. Therefore, inferring the potential lncRNA–disease associations are helpful for understanding the molecular pathogenesis of diseases. Most previous methods have concentrated on the construction of shallow learning models in order to predict lncRNA-disease associations, while they have failed to deeply integrate heterogeneous multi-source data and to learn the low-dimensional feature representations from these data. We propose a method based on the convolutional neural network with the attention mechanism and convolutional autoencoder for predicting candidate disease-related lncRNAs, and refer to it as CNNDLP. CNNDLP integrates multiple kinds of data from heterogeneous sources, including the associations, interactions, and similarities related to the lncRNAs, diseases, and miRNAs. Two different embedding layers are established by combining the diverse biological premises about the cases that the lncRNAs are likely to associate with the diseases. We construct a novel prediction model based on the convolutional neural network with attention mechanism and convolutional autoencoder to learn the attention and the low-dimensional network representations of the lncRNA–disease pairs from the embedding layers. The different adjacent edges among the lncRNA, miRNA, and disease nodes have different contributions for association prediction. Hence, an attention mechanism at the adjacent edge level is established, and the left side of the model learns the attention representation of a pair of lncRNA and disease. A new type of lncRNA similarity and a new type of disease similarity are calculated by incorporating the topological structures of multiple bipartite networks. The low-dimensional network representation of the lncRNA-disease pairs is further learned by the autoencoder based convolutional neutral network on the right side of the model. The cross-validation experimental results confirm that CNNDLP has superior prediction performance compared to the state-of-the-art methods. Case studies on stomach cancer, breast cancer, and prostate cancer further show the ability of CNNDLP for discovering the potential disease lncRNAs.
Effects of Tannase and Ultrasound Treatment on the Bioactive Compounds and Antioxidant Activity of Green Tea Extract

The present study investigated the effects of tannase and ultrasound treatment on the bioactive compounds and antioxidant activity of green tea extract. The single-factor experiments and the response surface methodology were conducted to study the effects of parameters on antioxidant activity of green tea extract. The highest antioxidant activity was found under the optimal condition with the buffer solution pH value of 4.62, ultrasonic temperature of 44.12 °C, ultrasonic time of 12.17 min, tannase concentration of 1 mg/mL, and ultrasonic power of 360 W. Furthermore, phenolic profiles of the extracts were identified and quantified by high-performance liquid chromatography. Overall, it was found that tannase led to an increase in gallic acid and a decrease in epigallocatechin gallate, and ultrasounds could also enhance the efficiency of enzymatic reaction.
Etiology-Specific Analysis of Hepatocellular Carcinoma Transcriptome Reveals Genetic Dysregulation in Pathways Implicated in Immunotherapy Efficacy

Immunotherapy has emerged in recent years as arguably the most effective treatment for advanced hepatocellular carcinoma (HCC), but the failure of a large percentage of patients to respond to immunotherapy remains as the ultimate obstacle to successful treatment. Etiology-associated dysregulation of immune-associated (IA) genes may be central to the development of this differential clinical response. We identified immune-associated genes potentially dysregulated by alcohol or viral hepatitis B in HCC and validated alcohol-induced dysregulations in vitro while using large-scale RNA-sequencing data from The Cancer Genome Atlas (TCGA). Thirty-four clinically relevant dysregulated IA genes were identified. We profiled the correlation of all genomic alterations in HCC patients to IA gene expression while using the information theory-based algorithm REVEALER to investigate the molecular mechanism for their dysregulation and explore the possibility of genome-based patient stratification. We also studied gene expression regulators and identified multiple microRNAs that were implicated in HCC pathogenesis that can potentially regulate these IA genes’ expression. Our study identified potential key pathways, including the IL-7 signaling pathway and TNFRSF4 (OX40)- NF-κB pathway, to target in immunotherapy treatments and presents microRNAs as promising therapeutic targets for dysregulated IA genes because of their extensive regulatory roles in the cancer immune landscape.
Effect of Chronic Corticosterone Treatment on Depression-Like Behavior and Sociability in Female and Male C57BL/6N Mice

Depression is a very common psychiatric disorder affecting approximately 300 million people worldwide with the prevalence being twice as high in women as in men. Despite intense research efforts in recent decades, the neurobiological basis underlying depression remains incompletely understood. However, the exposure to chronic stress is widely accepted to constitute a precipitating factor for the development of this mental disorder. Several animal models for the investigation of the pathogenetic link between chronic stress and depression exist and have yielded important insights. The present study aimed at comparing two published protocols for the induction of depression-like behavior in mice based on chronic oral glucocorticoid application. Given the gender distribution in the prevalence of depression, the second goal of this study was to reveal possible differences in the behavioral responses of female and male mice to corticosterone (CORT) treatment. CORT treatment was found to modulate depression-like behavior in selected behavioral paradigms in a sex- and protocol-specific manner. These data are of relevance for the experimental design and interpretation of future studies in the field and further highlight the relevance of “sex as biological variable” to be considered an important parameter for experimental planning and interpretation of results.
FAK-Copy-Gain Is a Predictive Marker for Sensitivity to FAK Inhibition in Breast Cancer

Background: Cancers with copy-gain drug-target genes are excellent candidates for targeted therapy. In order to search for new predictive marker genes, we investigated the correlation between sensitivity to targeted drugs and the copy gain of candidate target genes in NCI-60 cells. Methods: For eight candidate genes showing copy gains in NCI-60 cells identified in our previous study, sensitivity to corresponding target drugs was tested on cells showing copy gains of the candidate genes. Results: Breast cancer cells with Focal Adhesion Kinase (FAK)-copy-gain showed a significantly higher sensitivity to the target inhibitor, FAK inhibitor 14 (F14). In addition, treatment of F14 or FAK-knockdown showed a specific apoptotic effect only in breast cancer cells showing FAK-copy-gain. Expression-profiling analyses on inducible FAK shRNA-transfected cells showed that FAK/AKT signaling might be important to the apoptotic effect by target inhibition. An animal experiment employing a mouse xenograft model also showed a significant growth-inhibitory effect of F14 on breast cancer cells showing FAK-copy-gain, but not on those without FAK-copy-gain. Conclusion: FAK-copy-gain may be a predictive marker for FAK inhibition therapy in breast cancer.
Prediction of the development of pulmonary arterial hypertension with Tei Index in congenital heart diseases with left-to-right shunt.

OBJECTIVE The aim of this study was to determine the usefulness of the Tei Index, an echocardiographic parameter, in the early determination of pulmonary artery pressure (PAP) in congenital heart disease (CHD) with a left-to-right shunt. METHODS Right and left ventricular functions were evaluated using Tei Index values determined with tissue Doppler echocardiography. Cardiac catheterization was performed in all cases. The presence of pulmonary arterial hypertension (PAH) was defined as a mean PAP of ≥25 mm Hg and a pulmonary vascular resistance index of >3 WU/m2. Patients with a pulmonary/systemic blood flow ratio of ≥2 were considered candidates for surgery. RESULTS The Tei Index values measured from the left ventricular posterior wall and the right ventricular anterior wall were found to be significantly higher in the patients with PAH (0.68±0.18, 0.67±0.16, respectively) compared with the patients without PAH (0.56±0.16, p=0.027; 0.51±0.12 p=0.001). A significant correlation was detected between the Tei Index value measured from the left ventricular posterior wall and the mean PAP (correlation coefficient: 0.491). CONCLUSION The right ventricular Tei Index values in children with CHD and a left-to-right shunt can be used as a parameter to follow up on the potential development of PAH, to make a diagnosis in the early period, and to make a timely decision about surgery.
Phase II Study of the ALK5 Inhibitor Galunisertib in Very Low-, Low-, and Intermediate-Risk Myelodysplastic Syndromes

Purpose: Overactivation of TGF-β signaling is observed in myelodysplastic syndromes (MDS) and is associated with dysplastic hematopoietic differentiation. Galunisertib, a first-in-class oral inhibitor of the TGF-β receptor type 1 kinase (ALK5) has shown effectiveness in preclinical models of MDS and acceptable toxicity in phase I studies of solid malignancies. Patients and Methods: A phase II multicenter study of galunisertib was conducted in patients with very low-, low-, or intermediate-risk MDS by the Revised International Prognostic Scoring System criteria with hemoglobin ≤ 10.0 g/dL. Patients received oral galunisertib 150 mg twice daily for 14 days on/14 days off. Results: Ten of 41 evaluable patients (24.4%; 95% confidence interval, 12.4–40.3) achieved hematologic improvement erythroid response by International Working Group (IWG) 2006 criteria. A total of 18 of 41 patients (43.9%) achieved erythroid response as per IWG 2000 criteria. Nine of 28 (32.1%) of transfusion-dependent patients had hematologic improvement. A total of 18 of 41 (44%) patients had a significant reduction in fatigue. Overall median duration of response was 90 days in all patients. Rigorous stem and progenitor flow cytometry showed that patients with an early stem cell differentiation block were more likely to respond to galunisertib. The most common treatment-emergent adverse events were grade 1 or 2 in 20 (49%) of 41 patients, including any-grade fatigue (8/41, 20%), diarrhea (7/41, 17%), pyrexia (5/41, 12%), and vomiting (5/41, 12%). Conclusions: In summary, galunisertib treatment has an acceptable safety profile and was associated with hematologic improvements in lower- and intermediate-risk MDS, with responses in heavily transfusion-dependent patients and in those with signs of an early stem cell differentiation block.
Connected Health Services: Framework for an Impact Assessment

Background Connected health (CH), as a new paradigm, manages individual and community health in a holistic manner by leveraging a variety of technologies and has the potential for the incorporation of telehealth and integrated care services, covering the whole spectrum of health-related services addressing healthy subjects and chronic patients. The reorganization of services around the person or citizen has been expected to bring high impact in the health care domain. There are a series of concerns (eg, contextual factors influencing the impact of care models, the cost savings associated with CH solutions, and the sustainability of the CH ecosystem) that should be better addressed for CH technologies to reach stakeholders more successfully. Overall, there is a need to effectively establish an understanding of the concepts of CH impact. As services based on CH technologies go beyond standard clinical interventions and assessments of medical devices or medical treatments, the need for standardization and for new ways of measurements and assessments emerges when studying CH impact. Objective This study aimed to introduce the CH impact framework (CHIF) that serves as an approach to assess the impact of CH services. Methods This study focused on the subset of CH comprising services that directly address patients and citizens on the management of disease or health and wellness. The CHIF was developed through a multistep procedure and various activities. These included, as initial steps, a literature review and workshop focusing on knowledge elicitation around CH concepts. Then followed the development of the initial version of the framework, refining of the framework with the experts as a result of the second workshop, and, finally, composition and deployment of a questionnaire for preliminary feedback from early-stage researchers in the relevant domains. Results The framework contributes to a better understanding of what is CH impact and analyzes the factors toward achieving it. CHIF elaborates on how to assess impact in CH services. These aspects can contribute to an impact-aware design of CH services. It can also contribute to a comparison of CH services and further knowledge of the domain. The CHIF is based on 4 concepts, including CH system and service outline, CH system end users, CH outcomes, and factors toward achieving CH impact. The framework is visualized as an ontological model. Conclusions The CHIF is an initial step toward identifying methodologies to objectively measure CH impact while recognizing its multiple dimensions and scales.
Fetal exposure to the maternal microbiota in humans and mice.

Previous studies have demonstrated the presence of microbial DNA in the fetal environment. However, it remains unclear whether this DNA represents viable bacteria and how it relates to the maternal microbiota across different body sites. We studied the microbiota of human and mouse dyads to understand these relationships, localize bacteria in the fetus, and demonstrate bacterial viability. In human preterm and full-term mother-infant dyads at the time of Cesarean delivery, the oral cavity and meconium of newborn infants born as early as 24 weeks of gestation contained a microbiota that was predicted to originate from in utero sources including the placenta. Using operative deliveries of pregnant mice under highly controlled, sterile conditions in the laboratory, composition, visualization, and viability of bacteria in the in utero compartment and fetal intestine were demonstrated by 16S rRNA gene sequencing, fluorescence in situ hybridization, and bacterial culture. The composition and predicted source of the fetal gut microbiota shifted between mid- and late gestation. Cultivatable bacteria in the fetal intestine were found during mid-gestation but not late gestation. Our results demonstrate a dynamic, viable mammalian fetal microbiota during in utero development.
The Association between Eating-Out Rate and BMI in Korea

Previous research suggests that adult men consume larger amounts of calories while eating-out than when eating meals prepared at home. Therefore, this study aimed to investigate the association between the daily eating-out rate and body mass index (BMI) in the Korean population. The study used data from 18,019 individuals aged ≥19 years who participated in the Korea National Health and Nutrition Examination Survey (KNHANES) from 2013 to 2016. BMI was measured according to the Asia-Pacific BMI measurement criteria. A multinomial logistic regression analysis was used to examine the validity of the association between the eating-out rate and BMI. In this population, women with higher eating-out rates were found to have higher BMIs. Specifically, the risks of becoming obese or overweight increased among those with a 1%–50% (obesity odds ratio (OR) = 1.28, 95% confidence interval [CI]: 1.09–1.51; overweight OR = 1.38, 95% CI: 1.14–1.64) or 51%–100% daily eating-out rate (obesity OR = 1.51, 95% CI: 1.24–1.84; overweight OR = 1.50, 95% CI: 1.20–1.87), relative to those who reported never eating-out. By contrast, no statistically significant association between the daily eating-out rate and BMI was observed among men. Notably, we observed positive associations of the daily eating-out rate with obesity and being overweight in South Korean women, but not men. Our findings suggest that education about proper habits when eating-out is needed to prevent obesity.