Miracle-dz/UniFAR-FTUs huggingface dataset:
Mutation in phcA Enhanced the Adaptation of Ralstonia solanacearum to Long-Term Acid Stress

Bacterial wilt, caused by the plant pathogen Ralstonia solanacearum, occurs more severely in acidified soil according to previous reports. However, R. solanacearum cannot grow well in acidic environments under barren nutrient culture conditions, especially when the pH is lower than 5. With the worsening acidification of farmland, further determination of how R. solanacearum adapts to the long-term acidic environment is worthwhile. In this study, experimental evolution was applied to evaluate the adaptability and mechanism of the R. solanacearum experimental population responding to long-term acid stress. We chose the CQPS-1 strain as the ancestor, and minimal medium (MM medium) with different pH values as the culture environment to simulate poor soil. After 1500 generations of serial passage experiments in pH 4.9 MM, acid-adapted experimental strains (denoted as C49 strains) were obtained, showing significantly higher growth rates than the growth rates of control experimental strains (serial passage experiment in pH 6.5 MM, denoted as C65 strains). Competition experiments showed that the competitive indices (CIs) of all selected clones from C49 strains were superior to the ancestor in acidic environment competitiveness. Based on the genome variation analysis and functional verification, we confirmed that loss of function in the phcA gene was associated with the acid fitness gain of R. solanacearum, which meant that the inactivation of the PhcA regulator caused by gene mutation mediated the population expansion of R. solanacearum when growing in an acidic stress environment. Moreover, the swimming motility of acid evolution strains and the phcA deletion mutant was significantly enhanced compared to CQPS-1. This work provided evidence for understanding the adaptive strategy of R. solanacearum to the long-term acidic environment.
ESR2 Drives Mesenchymal-to-Epithelial Transition in Triple-Negative Breast Cancer and Tumorigenesis In Vivo

Estrogen receptors (ERs) have pivotal roles in the development and progression of triple-negative breast cancer (TNBC). Interactions among cancer cells and tumor microenvironment are orchestrated by the extracellular matrix that is rapidly emerging as prominent contributor of fundamental processes of breast cancer progression. Early studies have correlated ERβ expression in tumor sites with a more aggressive clinical outcome, however ERβ exact role in the progression of TNBC remains to be elucidated. Herein, we introduce the functional role of ERβ suppression following isolation of monoclonal cell populations of MDA-MB-231 breast cancer cells transfected with shRNA against human ESR2 that permanently resulted in 90% reduction of ERβ mRNA and protein levels. Further, we demonstrate that clone selection results in strongly reduced levels of the aggressive functional properties of MDA-MB-231 cells, by transforming their morphological characteristics, eliminating the mesenchymal-like traits of triple-negative breast cancer cells. Monoclonal populations of shERβ MDA-MB-231 cells undergo universal matrix reorganization and pass on a mesenchymal-to-epithelial transition state. These striking changes are encompassed by the total prevention of tumorigenesis in vivo following ERβ maximum suppression and isolation of monoclonal cell populations in TNBC cells. We propose that these novel findings highlight the promising role of ERβ targeting in future pharmaceutical approaches for managing the metastatic dynamics of TNBC breast cancer.
Using Artificial Intelligence to Establish Chest X-Ray Image Recognition Model to Assist Crucial Diagnosis in Elder Patients With Dyspnea

Pneumonia and pulmonary edema are the most common causes of acute respiratory failure in emergency and intensive care. Airway maintenance and heart function preservation are two foundations for resuscitation. Laboratory examinations have been utilized for clinicians to early differentiate pneumonia and pulmonary edema; however, none can provide results as prompt as radiology examinations, such as portable chest X-ray (CXR), which can quickly deliver results without mobilizing patients. However, similar features between pneumonia and pulmonary edema are found in CXR. It remains challenging for Emergency Department (ED) physicians to make immediate decisions as radiologists cannot be on-site all the time and provide support. Thus, Accurate interpretation of images remains challenging in the emergency setting. References have shown that deep convolutional neural networks (CNN) have a high sensitivity in CXR readings. In this retrospective study, we collected the CXR images of patients over 65 hospitalized with pneumonia or pulmonary edema diagnosis between 2016 and 2020. After using the ICD-10 codes to select qualified patient records and removing the duplicated ones, we used keywords to label the image reports found in the electronic medical record (EMR) system. After that, we categorized their CXR images into five categories: positive correlation, negative correlation, no correlation, low correlation, and high correlation. Subcategorization was also performed to better differentiate characteristics. We applied six experiments includes the crop interference and non-interference categories by GoogLeNet and applied three times of validations. In our best model, the F1 scores for pneumonia and pulmonary edema are 0.835 and 0.829, respectively; accuracy rate: 83.2%, Recall rate: 83.2%, positive predictive value: 83.3%, and F1 Score: 0.832. After the validation, the best accuracy rate of our model can reach up to 73%. The model has a high negative predictive value of excluding pulmonary edema, meaning the CXR shows no sign of pulmonary edema. At the time, there was a high positive predictive value in pneumonia. In that way, we could use it as a clinical decision support (CDS) system to rule out pulmonary edema and rule in pneumonia contributing to the critical care of the elderly.
Heterologous Production and Evaluation of the Biological Activity of Cystatin-B From the Red Piranha Pygocentrus nattereri

Cystatin proteins are known to form a superfamily of cysteine protease inhibitors, which play a key role in protein degradation and are related to different physiological processes, such as development and immunity. Currently, numerous immunoregulatory proteins, such as cystatins, are being used in the control and prevention of diseases in aquaculture. Thus, the objective of this study was to produce recombinant cystatin (rCYST-B) from the red piranha Pygocentrus nattereri and to evaluate its effect on bacterial growth. The gene that encodes cystatin-B was isolated from the spleen of P. nattereri and cloned in an expression system. The protein was produced via a heterologous system involving the yeast Pichia pastoris X-33. The inhibitory activity of purified cystatin-B was evaluated on papain using different concentrations (0–80.0 μg/μL) of rCYST-B. The bacteriostatic action of the protein was evaluated using the Kirby-Bauer method on the growth of Escherichia coli and Bacillus subtilis. rCYST-B showed 100% inhibition at a concentration of 60 μg/μL. Moreover, the bacteriostatic activity of E. coli and B. subtilis showed inhibition of 40.36 and 49.08% compared to the negative control (phosphate buffer), respectively. These results suggest that recombinant CYST-B has biotechnological potential for use in aquaculture.
The functional approach to creating the self

Studying consumers is at the heart of the sub-discipline o f consumer behavior; to truly understand the core of said consumers however, the marketing literature has focused on studying the self. The extant literature has discussed the self from several conceptual view points. As such, this study provides a rich theoretical review reaching back into the 19th century literature and extending into more recent developments related to cognitive social psychology. James’ (1890) global tripartite model of the self is adopted, and the various avenues by which consumers create their ‘selves’ are then explored, with particular focus on James’ material self (bodily creation). The latter phase of the study reintroduces Katz’s (1960) functional approach to attitudes as a conceptual lens to examine how matching consumers’ functional profiles to advertising messages, within the context of creating a self, influences the consumers’ overall attitudinal and behavioral responses to the particular message/brands being promoted. A multi-method approach including grounded theoretic and experimental studies is employed, and the findings show that different functions do fuel different individuals’ motives to create their ‘selves,’ and that when viewing an advertisement executed with functions differing from their functional profile, individuals experience mild cognitive dissonance and thus elaborate the message content more; this results in better attitudinal and behavioral responses to stronger over weaker arguments. APPROVAL FOR SCHOLARLY DISSEMINATION The author grants to the Prescott Memorial Library o f Louisiana Tech University the right to reproduce, by appropriate methods, upon request, any or all portions o f this Dissertation. It is understood that “proper request” consists o f the agreement, on the part o f the requesting party, that said reproduction is for his personal use and that subsequent reproduction will not occur without written approval o f the author o f this Dissertation. Further, any portions o f the Dissertation used in books, papers, and other works must be appropriately referenced to this Dissertation. Finally, the author o f this Dissertation reserves the right to publish freely, in the literature, at any time, any or all portions o f this Dissertation.
The Influence of Trait Emotion and Spatial Distance on Risky Choice Under the Framework of Gain and Loss

In the time of the COVID-19 pandemic, people are often faced with uncertain risky choice. Risky choice will be affected by different descriptions of the event’s gain or loss framework, this phenomenon is known as the framing effect. With the continuous expansion and in-depth study of frame effects in the field of risky choice, researchers have found that the are quite different in different situations. People have different interpretations of the same event at different psychological distances, and will also be affected by their own emotions. Therefore, the current study examines the common influence of task frame, spatial distance, and trait emotion on risky choice through two studies. Study 1 used a 2 (framework: gain vs. loss) × 2 (trait sentiment: high vs. low) inter-subject design, and the dependent variable is the choice of the rescue plan for the classic “Asian disease” problem. The results revealed that trait anger did not predict individuals’ risky choice preferences, and high trait anxiety led individuals to be more risk-averse. The framing effect exists in risky choice, and individuals prefer risk seeking in the loss frame. Study 2 used a 2 (spatial distance: distant vs. proximal) × 2 (framework: gain vs. loss) × 2 (trait sentiment: high vs. low) three-factor inter-subject design in which the dependent variable is the choice of rescue plan. The results indicate that the framing effect also exists in risky choice, and individuals prefer risk seeking in a loss frame. High trait anxiety lead individuals to be more risk-averse, while trait anger has no significant predictive effect on risk preference. Distant spatial distance lead individuals to increase their preference for risk-seeking under the gain frame, which leads to the disappearance of the framing effect. In conclusion, trait anxiety and spatial distance have a certain degree of influence on risky choice under the framework of gain and loss.
Inhibiting UCH-L5: Rational Design of a Cyclic Ubiquitin-Based Peptide Inhibitor

The ubiquitin-proteasome system is an essential regulator of many cellular processes including controlling protein homeostasis. The degradation of proteins by the multi-subunit proteasome complex is tightly regulated through a series of checkpoints, amongst which are a set of deubiquitinating proteases (DUBs). The proteasome-associated DUBs, UCH-L5 (Ubiquitin carboxyl-terminal hydrolase isozyme L5) and USP14 (Ubiquitin-specific protease 14), and the integral-DUB in the proteasome, Rpn11, is known to regulate proteasomal degradation by deubiquitination of distinct substrates. Although selective inhibitors for USP14 and Rpn11 have been recently developed, there are no known inhibitors that selectively bind to UCH-L5. The X-ray structure of the Ubiquitin (Ub) bound to UCH-L5 shows a β-sheet hairpin in Ub that contains a crucial hydrophobic patch involved in the interaction with UCH-L5. Herein, we designed and developed both a Ub sequence-based linear- and cyclic- β-sheet hairpin peptide that was found to preferably inhibit UCH-L5. We show that these peptides have low micromolar IC50 values and the cyclic peptide competes with the activity-based UbVME (Ubiquitin-Vinyl-Methyl-Ester) probe for UCH-L5, binding in a concentration-dependent manner. We further establish the selectivity profile of the cyclic peptide for UCH-L5 compared to other members of the UCH-DUB family and other cysteine DUBs in cell lysate. Furthermore, the cyclic peptide infiltrated cells resulting in the accumulation of polyUb chains, and was found to be non-toxic at the concentrations used here. Taken together, our data suggest that the cyclic peptide permeates the cell membrane, inhibits UCH-L5 by possibly blocking its deubiquitinating function, and contributes to the accumulation of polyubiquitinated substrates. The implications of inhibiting UCH-L5 in the context of the 26S proteasome render it an attractive candidate for further development as a potential selective inhibitor for therapeutic purposes.
C1QTNF3 is Upregulated During Subcutaneous Adipose Tissue Remodeling and Stimulates Macrophage Chemotaxis and M1-Like Polarization

The adipose tissue undergoes substantial tissue remodeling during weight gain-induced expansion as well as in response to the mechanical and immunological stresses from a growing tumor. We identified the C1q/TNF-related protein family member C1qtnf3 as one of the most upregulated genes that encode secreted proteins in tumor-associated inguinal adipose tissue - especially in high fat diet-induced obese mice that displayed 3-fold larger tumors than their lean controls. Interestingly, inguinal adipose tissue C1qtnf3 was co-regulated with several macrophage markers and chemokines and was primarily expressed in fibroblasts while only low levels were detected in adipocytes and macrophages. Administration of C1QTNF3 neutralizing antibodies inhibited macrophage accumulation in tumor-associated inguinal adipose tissue while tumor growth was unaffected. In line with this finding, C1QTNF3 exerted chemotactic actions on both M1- and M2-polarized macrophages in vitro. Moreover, C1QTNF3 treatment of M2-type macrophages stimulated the ERK and Akt pathway associated with increased M1-like polarization as judged by increased expression of M1-macrophage markers, increased production of nitric oxide, reduced oxygen consumption and increased glycolysis. Based on these results, we propose that macrophages are recruited to adipose tissue sites with increased C1QTNF3 production. However, the impact of the immunomodulatory effects of C1QTNF3 in adipose tissue remodeling warrants future investigations.
Development of an Improved in vitro Model of Bovine Trophectoderm Differentiation

The mechanisms regulating early stages of placentation and trophectoderm differentiation in the ruminant conceptus remain poorly understood. Here we present a model of trophectoderm (TE) differentiation in vitro from outgrowths of individual in vitro derived embryos. Cell outgrowths expressed markers of mononucleate (MNC) and binucleate (BNC) TE cells. The percentage of BNC ranged from 14 to 39% in individual outgrowths as determined by flow cytometry. Pregnancy-associated glycoproteins (PAGs), produced by BNC, were measured in culture media on days 35 to 54. Continuous secretion of PAGs was observed and indicative of BNC functionality. Gene expression was evaluated in 20 embryo cell outgrowths derived from two different sires. Expression of HAND1, which is involved in TE differentiation, and CSH2, a BNC-specific gene, was altered in cell outgrowths between the two sires tested. Single-cell RNA-seq analysis of day 40 TE cell outgrowths revealed 11 distinct cell populations, with specific clusters genes involved in TE lineage specification, proliferation, and differentiation. In addition, whole -RNAseq analysis was performed in day 35 and 40 TE cell outgrowths and confirmed sustained expression of genes expressed by BNC, such as CSH2 and some PAGs. The developed in vitro bovine embryo outgrowth culture found evidence for MNC and BNC differentiation and continuous production of PAGs, recapitulating key features of early bovine placenta development. This model can be used to understand the developmental biology of TE cells, provide insights into paternal influences on TE differentiation, and impact our understanding of early pregnancy loss in cattle.
CD21– CD27– Atypical B Cells in a Pediatric Cohort Study: An Extensive Single Center Flow Cytometric Analysis

Atypical B cells (atBCs) are a distinct B-cell population and represent approximately 5% of B cells in peripheral blood (PB) of healthy adult individuals. However, in adults these cells are expanded in conditions of chronic infections, inflammation, primary immunodeficiencies, autoimmune diseases, and aging. Their immunophenotype is characterized by the lack of CD21 expression and the hallmark human memory B-cell marker CD27. In this study, we investigated the immunophenotype of atBCs in different pediatric pathological conditions and correlated their expansion with the children’s clinical diagnosis. We were able to retrospectively evaluate 1,571 consecutive PB samples, corresponding to 1,180 pediatric patients, by using a 9-color flow-cytometric panel. The results, compared with a pediatric healthy cohort, confirmed an expansion of atBCs in patient samples with percentages greater than 5% of total B cells. Four subpopulations with different expressions of IgM and IgD were discriminated: IgM+IgD+, IgM+-only, IgD+-only, and IgM–IgD–. IgG+ atBCs were predominant in the IgM– IgD– subpopulation. Moreover, the study highlighted some features of atBCs, such as a low CD38 expression, a heterogeneity of CD24, a high expression of CD19 and a large cell size. We also demonstrated that an increase of atBCs in a pediatric cohort is correlated with immunodeficiencies, autoimmune, inflammatory, and hematological disorders, consistent with previous studies mainly performed in adults. Furthermore, our flow cytometric clustering analysis corroborated the recent hypothesis of an alternative B origin for atBCs.
Exhausted PD-1+ TOX+ CD8+ T Cells Arise Only in Long-Term Experimental Trypanosoma cruzi Infection

Infection with Trypanosoma cruzi remains the most important neglected zoonosis in Latin America. This infection does not lead to specific symptoms in the acute phase, but chronic infection can result in Chagas disease (CD) with cardiac and/or gastrointestinal manifestations that can lead to death. CD8+ T cells are highly effective and essential to control this infection, but fail to eliminate all parasites. In this study, we show that the CD8+ T cells are modulated by the transient induction of co-inhibitory receptors during acute infection of C57BL/6 mice. Therapeutic intervention strategies with blocking antibodies only had a marginal effect on the elimination of parasite reservoirs. Only long-term chronic infection gave rise to dysfunctional CD8+ T cells, which were characterized by high expression of the inhibitory receptor PD-1 and the co-expression of the transcription factor TOX, which plays a crucial role in the maintenance of the exhausted phenotype. PD-1+ TOX+ CD8+ T cells isolated from the site of infection produced significantly less IFN-γ, TNF-α and Granzyme B than their PD-1- TOX- CD8+ T cell counterparts after T. cruzi-specific stimulation ex vivo. Taken together, we provide evidence that, in the context of experimental infection of mice, the magnitude of the CD8+ T cell response in the acute phase is sufficient for parasite control and cannot be further increased by targeting co-inhibitory receptors. In contrast, persistent long-term chronic infection leads to an increase of exhausted T cells within the tissues of persistence. To our knowledge, this is the first description of infection-induced CD8+ T cells with an exhausted phenotype and reduced cytokine production in muscles of T. cruzi-infected mice.
Novel Pharmacology Following Heteromerization of the Angiotensin II Type 2 Receptor and the Bradykinin Type 2 Receptor

The angiotensin type 2 (AT2) receptor and the bradykinin type 2 (B2) receptor are G protein-coupled receptors (GPCRs) that have major roles in the cardiovascular system. The two receptors are known to functionally interact at various levels, and there is some evidence that the observed crosstalk may occur as a result of heteromerization. We investigated evidence for heteromerization of the AT2 receptor and the B2 receptor in HEK293FT cells using various bioluminescence resonance energy transfer (BRET)-proximity based assays, including the Receptor Heteromer Investigation Technology (Receptor-HIT) and the NanoBRET ligand-binding assay. The Receptor-HIT assay showed that Gαq, GRK2 and β-arrestin2 recruitment proximal to AT2 receptors only occurred upon B2 receptor coexpression and activation, all of which is indicative of AT2-B2 receptor heteromerization. Additionally, we also observed specific coupling of the B2 receptor with the Gαz protein, and this was found only in cells coexpressing both receptors and stimulated with bradykinin. The recruitment of Gαz, Gαq, GRK2 and β-arrestin2 was inhibited by B2 receptor but not AT2 receptor antagonism, indicating the importance of B2 receptor activation within AT2-B2 heteromers. The close proximity between the AT2 receptor and B2 receptor at the cell surface was also demonstrated with the NanoBRET ligand-binding assay. Together, our data demonstrate functional interaction between the AT2 receptor and B2 receptor in HEK293FT cells, resulting in novel pharmacology for both receptors with regard to Gαq/GRK2/β-arrestin2 recruitment (AT2 receptor) and Gαz protein coupling (B2 receptor). Our study has revealed a new mechanism for the enigmatic and poorly characterized AT2 receptor to be functionally active within cells, further illustrating the role of heteromerization in the diversity of GPCR pharmacology and signaling.
Multi-Tiered Culturally Responsive Behavior Support: A Qualitative Study of Trauma-Informed Education in an Australian Primary School

There is growing awareness of the impact of intergenerational trauma and community disadvantage on the educational achievement of Aboriginal and Torres Strait Islander (First Nations) children in Australia. Scholars have identified the need for culturally responsive and trauma-informed approaches to complement existing disciplinary and behavior support practices utilized in schools. This pilot research project explored the experiences of primary school teachers who were supported to implement trauma-informed practices in a regional primary school with a large number of First Nations students. Qualitative interviews with eight teachers were conducted after a 3-year (2017–2020) implementation of the Trauma-Informed Behavior Support (TIBS) program. Using a thematic analysis approach, the study identified the following themes: changes in teacher knowledge about the impact of intergenerational trauma, acknowledgment of the multi-systemic influences on student behavior difficulties, increased self-efficacy in providing culturally safe learning environments and strategies for building relationships with First Nations students. The findings offer insights into factors that support the successful and sustainable implementation of culturally responsive and trauma-informed practices in primary school settings.