Miracle-dz/UniFAR-FTUs huggingface dataset:
The Proteomic Analysis of Maize Endosperm Protein Enriched by Phos-tagtm Reveals the Phosphorylation of Brittle-2 Subunit of ADP-Glc Pyrophosphorylase in Starch Biosynthesis Process

AGPase catalyzes a key rate-limiting step that converts ATP and Glc-1-p into ADP-glucose and diphosphate in maize starch biosynthesis. Previous studies suggest that AGPase is modulated by redox, thermal and allosteric regulation. However, the phosphorylation of AGPase is unclear in the kernel starch biosynthesis process. Phos-tagTM technology is a novel method using phos-tagTM agarose beads for separation, purification, and detection of phosphorylated proteins. Here we identified phos-tagTM agarose binding proteins from maize endosperm. Results showed a total of 1733 proteins identified from 10,678 distinct peptides. Interestingly, a total of 21 unique peptides for AGPase sub-unit Brittle-2 (Bt2) were identified. Bt2 was demonstrated by immunoblot when enriched maize endosperm protein with phos-tagTM agarose was in different pollination stages. In contrast, Bt2 would lose binding to phos-tagTM when samples were treated with alkaline phosphatase (ALP). Furthermore, Bt2 could be detected by Pro-Q diamond staining specifically for phosphorylated protein. We further identified the phosphorylation sites of Bt2 at Ser10, Thr451, and Thr462 by iTRAQ. In addition, dephosphorylation of Bt2 decreased the activity of AGPase in the native gel assay through ALP treatment. Taking together, these results strongly suggest that the phosphorylation of AGPase may be a new model to regulate AGPase activity in the starch biosynthesis process.
Promote Biomarker Discovery by Identifying Homogenous Primary Headache Subgroups

Within‐ and between‐study heterogeneity impede identification of valid primary headache biomarkers. Homogenous subgroup identification and investigation of differential biochemical profiles and networks within and across headache categories, based on statistical techniques, might promote biomarker discovery. When studying common primary headaches with a multifactorial etiology, variability might be captured at different levels (eg, genetics, clinical features, comorbidities, triggers). Moreover, focus on biochemical profiles instead of single compounds is crucial to develop strategies for accurate differential diagnosis.
Addressing the Compartmentalization of Specific Integrin Heterodimers in Mouse Sperm

Integrins are transmembrane cell receptors involved in two crucial mechanisms for successful fertilization, namely, mammalian intracellular signaling and cell adhesion. Integrins α6β4, α3β1 and α6β1 are three major laminin receptors expressed on the surface of mammalian cells including gametes, and the presence of individual integrin subunits α3, α6, β1 and β4 has been previously detected in mammalian sperm. However, to date, proof of the existence of individual heterodimer pairs in sperm and their detailed localization is missing. The major conclusion of this study is evidence that the β4 integrin subunit is expressed in mouse sperm and that it pairs with subunit α6; additionally, there is a detailed identification of integrin heterodimer pairs across individual membranes in an intact mouse sperm head. We also demonstrate the existence of β4 integrin mRNAs in round spermatids and spermatogonia by q-RT-PCR, which was further supported by sequencing the PCR products. Using super-resolution microscopy accompanied by colocalization analysis, we located integrin subunits as follows: α6/β4-inner apical acrosomal membrane and equatorial segment; α3, α6/β1, β4-plasma membrane overlaying the apical acrosome; and α3/β1-outer acrosomal membrane. The existence of α6β4, α3β1 and α6β1 heterodimers was further confirmed by proximity ligation assay (PLA). In conclusion, we delivered detailed characterization of α3, α6, β1 and β4 integrin subunits, showing their presence in distinct compartments of the intact mouse sperm head. Moreover, we identified sperm-specific localization for heterodimers α6β4, α3β1 and α6β1, and their membrane compartmentalization and the presented data show a complexity of membranes overlaying specialized microdomain structures in the sperm head. Their different protein compositions of these individual membrane rafts may play a specialized role, based on their involvement in sperm-epithelium and sperm-egg interaction.
Adenovirus 5 E1A Interacts with E4orf3 To Regulate Viral Chromatin Organization

To successfully replicate, human adenovirus needs to carry out a rapid yet ordered transcriptional program that executes and drives viral replication. Early in infection, the viral E1A proteins are the key activators and regulators of viral transcription. Here we report, for the first time, that E1A works together with E4orf3 to perfect the viral transcriptional program and identify a novel mechanism by which the virus can adjust viral gene expression by modifying its genome’s nucleosomal organization via cooperation between E1A and E4orf3. ABSTRACT Human adenovirus expresses several early proteins that control various aspects of the viral replication program, including an orchestrated expression of viral genes. Two of the earliest viral transcriptional units activated after viral genome entry into the host cell nucleus are the E1 and E4 units, which each express a variety of proteins. Chief among these are the E1A proteins that function to reprogram the host cell and activate transcription of all other viral genes. The E4 gene encodes multiple proteins, including E4orf3, which functions to disrupt cellular antiviral defenses, including the DNA damage response pathway and activation of antiviral genes. Here we report that E1A directly interacts with E4orf3 via the conserved N terminus of E1A to regulate the expression of viral genes. We show that E4orf3 indiscriminately drives high nucleosomal density of viral genomes, which is restrictive to viral gene expression and which E1A overcomes via a direct interaction with E4orf3. We also show that during infection E1A colocalizes with E4orf3 to nuclear tracks that are associated with heterochromatin formation. The inability of E1A to interact with E4orf3 has a significant negative impact on overall viral replication, the ability of the virus to reprogram the host cell, and the levels of viral gene expression. Together these results show that E1A and E4orf3 work together to fine-tune the viral replication program during the course of infection and highlight a novel mechanism that regulates viral gene expression. IMPORTANCE To successfully replicate, human adenovirus needs to carry out a rapid yet ordered transcriptional program that executes and drives viral replication. Early in infection, the viral E1A proteins are the key activators and regulators of viral transcription. Here we report, for the first time, that E1A works together with E4orf3 to perfect the viral transcriptional program and identify a novel mechanism by which the virus can adjust viral gene expression by modifying its genome’s nucleosomal organization via cooperation between E1A and E4orf3.
Normative values for magnetic resonance elastography–based liver stiffness in a healthy population

INTRODUCTION Chronic liver disease resulting in fibrosis, and ultimately cirrhosis, is a significant cause of morbidity and mortality worldwide. None of the conventional imaging techniques are able to detect early fibrosis and compare its grade with the histopathologic scale. Liver biopsy, as the diagnostic standard for liver fibrosis, also has limitations and is not well accepted by patients. Magnetic resonance elastography is a well-established technique for evaluating liver stiffness and may replace invasive procedures. Detection of liver fibrosis in its early stages, however, requires a detailed knowledge of normal liver stiffness. OBJECTIVES This study aimed to determine normal liver stiffness values in healthy volunteers. PATIENTS AND METHODS A total of 102 volunteers (mean age, 21.6 years; range, 20–28 years) with no history of gastrointestinal, hepatobiliary, or cardiovascular disease were enrolled in the study. Liver stiffness was evaluated by magnetic resonance elastography with a 1.5T clinical magnetic resonance scanner. Images of the induced transverse wave propagation were obtained and converted to tissue stiffness maps (elastograms). RESULTS The mean (SD) liver stiffness for the entire group of volunteers was 2.14 (0.28) kPa (range, 1.37–2.66 kPa). For women, the mean (SD) stiffness value was 2.14 (0.30) kPa (range, 1.37–2.66 kPa), and for men, 2.14 (0.25) kPa (range, 1.54–2.54 kPa). CONCLUSIONS Liver stiffness in a healthy adult cohort did not exceed 2.7 kPa and is not influenced by sex, body mass index, or fat content.
Role of glutathione peroxidase 4 in conjunctival epithelial cells.

PURPOSE The purpose of the present study was to investigate the role of glutathione peroxidase 4 (GPx4) in conjunctival epithelial cells. METHODS An immortalized human conjunctival epithelial cell line was used. Cells were transfected with catalase, GPx1, GPx4, SOD1, SOD2, or control siRNA. Knockdown was confirmed by RT-PCR and immunoblotting. The cytotoxicity induced by knockdown of these antioxidant enzymes was examined by assay of LDH activity. Furthermore, evaluations of lipid peroxidation, cellular levels of reactive oxygen species, cell proliferation, and apoptosis were conducted in cells treated with GPx4 or control siRNA. In oxidative stress study, cells treated with GPx4 or control siRNA were applied with hydrogen peroxide or ferric sulfide, and their cytotoxicity was evaluated by assay of LDH activity. RESULTS Small interfering RNA of catalase, GPx1, GPx4, SOD1, and SOD2 siRNA remarkably inhibited the mRNA and protein expression of each gene. Knockdown of GPx4 and SOD1 but not catalase, GPx1, and SOD2 significantly induced cytotoxicity. Glutathione peroxidase 4 knockdown increased lipid oxidation and reactive oxygen species. The proliferation of GPx4 siRNA-treated cells was reduced compared with control siRNA-treated cells. Moreover, cell death in GPx4 siRNA-treated cells was characterized by positive staining for annexin V. In an oxidation stress study, GPx4 siRNA knockdown enhanced the cytotoxicity induced by hydrogen peroxide or ferric sulfide. CONCLUSION These results suggest that GPx4 is essential for maintaining oxidative homeostasis and keeping defense against oxidative stress in conjunctival epithelial cells.
Assessing Anxiety Disorders Using Wearable Devices: Challenges and Future Directions

Wearable devices (WD) are starting to increasingly be used for interventions to promote well-being by reducing anxiety disorders (AD). Electrocardiogram (ECG) signal is one of the most commonly used biosignals for assessing the cardiovascular system as it significantly reflects the activity of the autonomic nervous system during emotional changes. Little is known about the accuracy of using ECG features for detecting ADs. Moreover, during our literature review, a limited number of studies were found that involve ECG collection using WD for promoting mental well-being. Thus, for the sake of validating the reliability of ECG features for detecting anxiety in WD, we screened 1040 articles, and only 22 were considered for our study; specifically 6 on panic, 4 on post-traumatic stress, 4 on generalized anxiety, 3 on social, 3 on mixed, and 2 on obsessive-compulsive anxiety disorder articles. Most experimental studies had controversial results. Upon reviewing each of these papers, it became apparent that the use of ECG features for detecting different types of anxiety is controversial, and the use of ECG-WD is an emerging area of research, with limited evidence suggesting its reliability. Due to the clinical nature of most studies, it is difficult to determine the specific impact of ECG features on detecting ADs, suggesting the need for more robust studies following our proposed recommendations.
Overexpression of Transglutaminase from Cucumber in Tobacco Increases Salt Tolerance through Regulation of Photosynthesis

Transglutaminase (TGase) is a regulator of posttranslational modification of protein that provides physiological protection against diverse environmental stresses in plants. Nonetheless, the mechanisms of TGase-mediated salt tolerance remain largely unknown. Here, we found that the transcription of cucumber TGase (CsTGase) was induced in response to light and during leaf development, and the CsTGase protein was expressed in the chloroplast and the cell wall. The overexpression of the CsTGase gene effectively ameliorated salt-induced photoinhibition in tobacco plants, increased the levels of chloroplast polyamines (PAs) and enhanced the abundance of D1 and D2 proteins. TGase also induced the expression of photosynthesis related genes and remodeling of thylakoids under normal conditions. However, salt stress treatment reduced the photosynthesis rate, PSII and PSI related genes expression, D1 and D2 proteins in wild-type (WT) plants, while these effects were alleviated in CsTGase overexpression plants. Taken together, our results indicate that TGase-dependent PA signaling protects the proteins of thylakoids, which plays a critical role in plant response to salt stress. Thus, overexpression of TGase may be an effective strategy for enhancing resistance to salt stress of salt-sensitive crops in agricultural production.
Dynamic vaccination in partially overlapped multiplex network

In this work we propose and investigate a strategy of vaccination which we call “dynamic vaccination. ” In our model, susceptible people become aware that one or more of their contacts are infected and thereby get vaccinated with probability ω, before having physical contact with any infected patient. Then the nonvaccinated individuals will be infected with probability β. We apply the strategy to the susceptible-infected-recovered epidemic model in a multiplex network composed by two networks, where a fraction q of the nodes acts in both networks. We map this model of dynamic vaccination into bond percolation model and use the generating functions framework to predict theoretically the behavior of the relevant magnitudes of the system at the steady state. We find a perfect agreement between the solutions of the theoretical equations and the results of stochastic simulations. In addition, we find an interesting phase diagram in the plane β-ω, which is composed of an epidemic and a nonepidemic phase, separated by a critical threshold line βc, which depends on q. As q decreases, βc increases, i.e., as the overlap decreases, the system is more disconnected, and therefore more virulent diseases are needed to spread epidemics. Surprisingly, we find that, for all values of q, a region in the diagram where the vaccination is so efficient that, regardless of the virulence of the disease, it never becomes an epidemic. We compare our strategy with random immunization and find that, using the same amount of vaccines for both scenarios, we obtain that the spread of disease is much lower in the case of dynamic vaccination when compared to random immunization. Furthermore, we also compare our strategy with targeted immunization and we find that, depending on ω, dynamic vaccination will perform significantly better and in some cases will stop the disease before it becomes an epidemic.
Change of HER2 status during disease recurrence predicts good prognosis for primary squamous cell carcinoma of the breast

Rationale: Primary squamous cell carcinoma (PSCC) of the breast is one of the least common types of breast cancer. Adjuvant treatment for PSCC remains an unresolved issue. Patient concerns: We reported a case of a 48-year-old postmenopausal female patients with a 2 × 2.5 cm lump presented with no symptoms. Diagnoses: This patient was diagnosed as PSCC of the breast. The original tumor and first recurrence exhibited triple negative phenotype, whereas the second recurrence was HER2-positive. Interventions: A tumorectomy with latissimus dorsi flap reconstruction for the second recurrence was performed followed by targeted therapy with trastuzumab. Outcomes: The patient had a complete remission, which was sustained over the 25 months of follow-up after the tumorectomy. Lessons: This is the first reported case in literature of a breast PSCC patient with switched immunohistochemical phenotypes during disease recurrence. Surgical resection with flap reconstruction and targeted therapy successfully treated the recurrence.
Factors influencing suicide risk assessment clinical practice: protocol for a scoping review

Introduction Every year, suicide accounts for nearly 800 000 deaths worldwide. Appropriate risk assessment and intervention are imperative since evidence demonstrates that a large proportion of those who die by suicide visit health professionals prior to their death. Much previous research has focused on identifying patient-level risk factors that can improve the risk assessment process through scales and algorithms. However, the best practice guidelines emphasise the importance of clinical interviews and prioritise the clinician’s final judgement. The purpose of this review is to (1) understand the clinician and organisational level barriers and facilitators that influence a clinician’s assessment of suicide risk, (2) identify the types of biases that exist within this process and (3) list any evidence-based training protocols and educational initiatives to aid (or support) clinicians with this process. Methods and analysis This scoping review protocol uses the Arksey and O’Malley framework, and Preferred Reporting Items for Systematic Reviews and Meta-Analyses reporting guidelines for scoping reviews. Literature will be identified using a multidatabase search strategy developed in consultation with a medical librarian. The proposed screening process consists of a title and abstract scan, followed by a full-text review by two reviewers to determine the eligibility of articles. Studies outlining any factors that affect a clinician’s suicide risk assessment process, ranging from individual experience and behaviours to organisational level influences, will be included. A tabular synthesis of the general study details will be provided, as well as a narrative synthesis of the extracted data, organised into themes using the Situated Clinical Decision-Making framework. Ethics and dissemination Ethical approval is not required for this review. Results will be translated into educational materials and presentations for dissemination to appropriate knowledge users. Knowledge outputs will also include academic presentations at relevant conferences, and a published, peer-reviewed journal article.
Static and Dynamic 4-Way Handshake Solutions to Avoid Denial of Service Attack in Wi-Fi Protected Access and IEEE 802.11i

This paper focuses on WPA and IEEE 802.11i protocols that represent two important solutions in the wireless environment. Scenarios where it is possible to produce a DoS attack and DoS flooding attacks are outlined. The last phase of the authentication process, represented by the 4-way handshake procedure, is shown to be unsafe from DoS attack. This can produce the undesired effect of memory exhaustion if a flooding DoS attack is conducted. In order to avoid DoS attack without increasing the complexity of wireless mobile devices too much and without changing through some further control fields of the frame structure of wireless security protocols, a solution is found and an extension of WPA and IEEE 802.11 is proposed. A protocol extension with three "static" variants and with a resource-aware dynamic approach is considered. The three enhancements to the standard protocols are achieved through some simple changes on the client side and they are robust against DoS and DoS flooding attack. Advantages introduced by the proposal are validated by simulation campaigns and simulation parameters such as attempted attacks, successful attacks, and CPU load, while the algorithm execution time is evaluated. Simulation results show how the three static solutions avoid memory exhaustion and present a good performance in terms of CPU load and execution time in comparison with the standard WPA and IEEE 802.11i protocols. However, if the mobile device presents different resource availability in terms of CPU and memory or if resource availability significantly changes in time, a dynamic approach that is able to switch among three different modalities could be more suitable.
A Neuroscientific Review of Imagery and Observation Use in Sport

Imagery and observation are multicomponential, involving individual difference characteristics that modify the processes. The authors propose that both imagery and observation function by offering effective routes to access and reinforce neural networks for skilled performance. The neural isomorphism with overt behaviors offers a tempting mechanism to explain the beneficial outcomes of the 2 processes. However, several limitations related to imagery indicate the possibility that imagery may not be as efficacious as the literature would indicate. The authors propose observation-based approaches to offer more valid and effective techniques in sport psychology and motor control.
Reproductive success of cultivated Pyrus calleryana (Rosaceae) and establishment ability of invasive, hybrid progeny.

UNLABELLED • PREMISE OF THE STUDY Pyrus calleryana Decne. , an ornamental tree species introduced from China, is a relatively new invasive that has only recently begun to spread across the United States after intraspecific hybridization between cultivars. The function of such hybridization in the evolution of invasiveness is still relatively understudied, especially with respect to the initial establishment and persistence of invasive genotypes. Multiple introductions of genetically divergent populations or cultivars may benefit from new genetic combinations created during hybridization events and/or release from Allee effects in founder populations. • METHODS We quantified the outcome of intraspecific hybridization between cultivars of P. calleryana in a common garden. Measures of the reproductive success and establishment ability of their early- and advanced-generation hybrid offspring were collected to assess the likelihood of particular cultivar genotypes to establish in invasive populations. These traits also were compared between cultivated and invasive parents to identify any generational differences in invasive potential. • KEY RESULTS Differences were detected in measures of reproductive ability, but no group emerged as consistently more fecund. Advanced-generation hybrids also had significantly less biomass, indicating a reduction in hybrid performance relative to that of the cultivated progeny. • CONCLUSION Ultimately, this study indicates that increased spread of P. calleryana has been initiated by introduction of multiple cultivar types and subsequent widespread planting and is not the result of an inherent fitness advantage of hybrid progeny.
The complete mitochondrial genome of Antheraea pernyi strain 731 (Lepidoptera: Saturniidae)

Abstract In this study, the complete mitochondrial genome of Antheraea pernyi strain 731 (Lepidoptera: Saturniidae) is determined for the first time. It is a circular molecule of 15,570 bp in length, with 37 typical coding genes and one non-coding A T-rich region. Its gene order and content are identical to the common type found in most insect mitogenomes. All protein-coding genes (PCGs) start with a typical ATN initiation codon, except for the cox1 gene, which begins with TTAG codon. Nine genes used standard complete termination codon TAA, whereas the cox1, cox2, nad3, and nad5 genes end with single T. All tRNAs display typical secondary cloverleaf structures as those of other insects. Additionally, the non-coding AT-rich region is 553 bp long, located between rrnS and trnM genes. It contains some structures of repeated motifs and microsatellite-like elements characteristic of the other lepidopterons. Phylogenetic analysis showed that the Antheraea pernyi 731 was close to Saturniidae.