Miracle-dz/UniFAR-FTUs huggingface dataset:
A Stress-Associated Protein, PtSAP13, From Populus trichocarpa Provides Tolerance to Salt Stress

The growth and production of poplars are usually affected by unfavorable environmental conditions such as soil salinization. Thus, enhancing salt tolerance of poplars will promote their better adaptation to environmental stresses and improve their biomass production. Stress-associated proteins (SAPs) are a novel class of A20/AN1 zinc finger proteins that have been shown to confer plants’ tolerance to multiple abiotic stresses. However, the precise functions of SAP genes in poplars are still largely unknown. Here, the expression profiles of Populus trichocarpa SAPs in response to salt stress revealed that PtSAP13 with two AN1 domains was up-regulated dramatically during salt treatment. The β-glucuronidase (GUS) staining showed that PtSAP13 was accumulated dominantly in leaf and root, and the GUS signal was increased under salt condition. The Arabidopsis transgenic plants overexpressing PtSAP13 exhibited higher seed germination and better growth than wild-type (WT) plants under salt stress, demonstrating that overexpression of PtSAP13 increased salt tolerance. Higher activities of antioxidant enzymes were found in PtSAP13-overexpressing plants than in WT plants under salt stress. Transcriptome analysis revealed that some stress-related genes, including Glutathione peroxidase 8, NADP-malic enzyme 2, Response to ABA and Salt 1, WRKYs, Glutathione S-Transferase, and MYBs, were induced by salt in transgenic plants. Moreover, the pathways of flavonoid biosynthesis and metabolic processes, regulation of response to stress, response to ethylene, dioxygenase activity, glucosyltransferase activity, monooxygenase activity, and oxidoreductase activity were specially enriched in transgenic plants under salt condition. Taken together, our results demonstrate that PtSAP13 enhances salt tolerance through up-regulating the expression of stress-related genes and mediating multiple biological pathways.
Transcriptome Analysis of Choke Stroma and Asymptomatic Inflorescence Tissues Reveals Changes in Gene Expression in Both Epichloë festucae and Its Host Plant Festuca rubra subsp. rubra

Many cool-season grasses have symbiotic relationships with Epichloë (Ascomycota, Clavicipitaceae) fungal endophytes that inhabit the intercellular spaces of the above-ground parts of the host plants. The presence of the Epichloë endophytes is generally beneficial to the hosts due to enhanced tolerance to biotic and abiotic stresses conferred by the endophytes. Many Epichloë spp. are asexual, and those infections always remain asymptomatic. However, some Epichloë spp. have a sexual stage and produce a macroscopic fruiting body, a stroma, that envelops the developing inflorescence causing a syndrome termed “choke disease”. Here, we report a fungal and plant gene expression analysis of choke stroma tissue and asymptomatic inflorescence tissue of Epichloë festucae-infected strong creeping red fescue (Festuca rubra subsp. rubra). Hundreds of fungal genes and over 10% of the plant genes were differentially expressed when comparing the two tissue types. The differentially expressed fungal genes in the choke stroma tissue indicated a change in carbohydrate and lipid metabolism, as well as a change in expression of numerous genes for candidate effector proteins. Plant stress-related genes were up-regulated in the stroma tissue, suggesting the plant host was responding to the epiphytic stage of E. festucae as a pathogen.
Dynamic subcellular translocation of V-type H+ -ATPase is essential for biomineralization of the diatom silica cell wall.

Diatom cell walls, called frustules, are main sources of biogenic silica in the ocean and their intricate morphology is an inspiration for nanoengineering. Here we show dynamic aspects of frustule biosynthesis involving acidification of the silica deposition vesicle (SDV) by V-type H+ ATPase (VHA). Transgenic Thalassiosira pseudonana expressing the VHA B subunit tagged with eGFP (VHAB -eGFP) enabled subcellular protein localization in live cells. In exponentially growing cultures, VHAB -eGFP was present in various subcellular localizations including the cytoplasm, SDVs, and vacuoles. We studied the role of VHA during frustule biosynthesis in synchronized cell cultures of T. pseudonana. During the making of new biosilica components, VHAB -eGFP first localized in the girdle band SDVs, and subsequently in valve SDVs. In single cell time-lapse imaging experiments, VHAB -eGFP localization in SDVs precluded accumulation of the acidotropic silica biomineralization marker PDMPO. Furthermore, pharmacological VHA inhibition prevented PDMPO accumulation in the SDV, frustule biosynthesis, and cell division, as well as insertion of the silicalemma-associated protein SAP1 into the SDVs. Finally, partial inhibition of VHA activity affected the nanoscale morphology of the valve. Altogether, these results indicate VHA is essential for frustule biosynthesis by acidifying the SDVs and regulating the insertion of other structural proteins into the SDV.
Berberine inhibits proliferation and migration of colorectal cancer cells by downregulation of GRP78

Human colorectal cancer (CRC), a highly malignant and metastatic carcinoma, is resistant to many present anticancer therapies. The inhibition of tumor survival and growth through receptor suppression is a promising way to treat CRC. The study aimed to investigate the effect of a natural plant triterpenoid, berberine (BBR), on SW480 cells and whether its role is mediated by Glucose-regulated protein 78 (GRP78). MTT assay, wound healing assay, and Annexin V-FITC assay were used to measure the effect of BBR on the proliferation, migration, and apoptosis of SW480 cells, respectively. Immunofluorescence and western blotting were used to evaluate both the downregulation of BBR on GRP78 and the role of GRP78 in the effect of BBR on SW480 cells. Our results revealed that BBR inhibited the proliferation and migration, as well as induced the apoptosis of SW480 cells, in a dose-dependent manner. BBR induced the dose-dependent inhibition of cell proliferation in HT-29 cells. BBR inhibited the expression of GRP78 and its localization on the cell surface. Moreover, BBR inhibited the expression of Bax, Bcl-2, c-Myc, and Vimentin and up-regulated the cytokeratin expression in SW480 cells. In addition, we found that the effects of BBR on cell proliferation, migration, and apoptosis in SW480 cells were reversed by the overexpression of GRP78. Our findings demonstrated that BBR inhibited the proliferation and migration and induced the apoptosis of SW480 cells by downregulating the expression of GRP78, and targeting GRP78 might be a potential way to develop the effective anticancer therapy.
Prothrombotic and Proinflammatory Activities of the β-Hemolytic Group B Streptococcal Pigment

A prominent feature of severe streptococcal infections is the profound inflammatory response that contributes to systemic toxicity. In sepsis the dysregulated host response involves both immunological and nonimmunological pathways. Here, we report a fatal case of an immunocompetent healthy female presenting with toxic shock and purpura fulminans caused by group B streptococcus (GBS; serotype III, CC19). The strain (LUMC16) was pigmented and hyperhemolytic. Stimulation of human primary cells with hyperhemolytic LUMC16 and STSS/NF-HH strains and pigment toxin resulted in a release of proinflammatory mediators, including tumor necrosis factor, interleukin (IL)-1β, and IL-6. In addition, LUMC16 induced blood clotting and showed factor XII activity on its surface, which was linked to the presence of the pigment. The expression of pigment was not linked to a mutation within the CovR/S region. In conclusion, our study shows that the hemolytic lipid toxin contributes to the ability of GBS to cause systemic hyperinflammation and interferes with the coagulation system.
Silencing of RBP-JK promotes the differentiation of bone marrow mesenchymal stem cells into vascular endothelial cells

Bone marrow mesenchymal stem cells (BM-MSCs) are important for postnatal angiogenesis and are suitable for use in construction of blood vessels by tissue engineering. The present study aimed to investigate the influence of recombination signal binding protein for immunoglobulin kappa J region (RBP-JK) on the differentiation of BM-MSCs into vascular endothelial cells, and to assess the underlying mechanisms. BM-MSCs were isolated and identified by flow cytometry. Lentiviral vectors encoding RBP-JK shRNA (shRBPJK) were constructed to knockdown RBP-JK expression and endothelial differentiation of BM-MSCs was induced. The experimental groups were treated with: empty lentiviral vector (vector group), growth factors (bFGF and VEGF; induced group), shRBPJK (shRBPJK group), and growth factors + shRBPJK (induced + shRBPJK group). The expression of endothelial markers, vascular endothelial growth factor receptor 2 (Flk-1), and von Willebrand factor (vWF) were detected by immunofluorescence. Additionally, in vitro blood vessel formation and phagocytosis were assessed using acetylated LDL, Dil complex and the underlying molecular mechanisms evaluated by western blotting. BM-MSCs were separated and transduced with shRBPJK to reduce RBP-JK expression. Compared with the vector group, the expression of the endothelial cell markers, Flk-1 and vWF, in vitro tubule formation, and phagocytosis ability increased, while the expression levels of p-AKT/AKT and p-NF-κB/NF-κB were significantly decreased (P<0.05) in the induced, shRBPJK, and induced + shRBPJK groups. Compared with the induced group, the expression of Flk-1 and vWF, the number of tubules, and phagocytosis were higher in the induced + shRBPJK group, while the expression levels of p-AKT/AKT and p-NF-κB/NF-κB were lower (P<0.05). Collectively, the present data indicated that silencing of RBP-JK promotes the differentiation of MSCs into vascular endothelial cells, and this process is likely regulated by AKT/NF-κB signaling.
A Data Security System Design for Hybrid ( Cloud & Volunteer ) Global Computing

Proceedings/Bildiriler Kitabı 20-21 September /Eylül 2013 | Ankara / TURKEY 3 Abstract In this study; we aimed to develop a data security infrastructure (DSI) for a hybrid global computing system which consists of cloud and volunteer computing. This performed work has put forth potential capacity of a global computing system which is also known as network computing based method, in terms of data security. Each computer performed computing operations on network has named as
Mathematicians ’ Mathematical Thinking for Teaching : Responding to Students ’ Conjectures

Introduction As part of a curriculum development and research project in abstract algebra, we have been investigating teachers’ implementation of an inquiry oriented abstract algebra curriculum (Larsen, 2004, 2009; Larsen, Johnson, Rutherford, and Bartlo, 2009). To understand the ways the instructors might interact with the curriculum, including the challenges they may have during implementation, we have been video taping three mathematicians teaching with our curriculum. In total, we have videotaped four classes over three years. A key feature of the curriculum is that the formal mathematical ideas are developed by building on the students’ informal reasoning and strategies. Thus, the way that the instructor responds to student contributions is of particular importance.
Psychological Well-Being in HIV / AIDS Positive and Negative

This research paper is an attempt to study the level of psychological Well-being in HIV/AIDS patients and normal persons . This study is based on sample of 100 subjects 50 HIV/AIDS patients (25 males and 25 females) and 50 subjects were normal person’s (25 males and 25 females). The psychological well-being of HIV/AIDS positive and negative persons were measured by psychological Well-being scale (PWBS) (HINDI) adopted by S. N. Rai & Deepika Gupta Department of Psychology Chaudhary Charan Singh University Meerut. Three independent variables were studied i.e. gender, normality and HIV/AIDS. Mean, S.D and t-test were applied for data analysis. The results reveal that the all three independent variables i.e. gender, normality and HIV/AIDS are found significant at . 01 level of confidence. This study shows that there is significant difference between the Psychological Well-being of HIV/AIDS patients and normal’s. Significant difference between six areas of psychological Well-being (Self-acceptance, personal growth, purpose in life, environmental mastery, autonomy, positive relations with others) among HIV/AIDS patients and normal’s were found. Also significant difference was found between male and female HIV/AIDS patients.
Patient involvement in Danish health care.

PURPOSE The purpose of this paper is to investigate different types of patient involvement in Denmark, and to discuss the potential implications of pursuing several strategies for patient involvement simultaneously. DESIGN/METHODOLOGY/APPROACH The paper presents a preliminary framework for analysis of patient involvement in health care. This framework is used to analyze key governance features of patient involvement in Denmark based on previous research papers and reports describing patient involvement in Danish health care. FINDINGS Patient involvement is important in Denmark at the rhetorical level, and many policies and initiatives have been introduced. All three governance forms (voice, choice and co-production) are used. However, there are important barriers and limitations in translating the rhetoric into practice, and potential synergy and negative synergy effects can be identified when pursuing the strategies at the same time. RESEARCH LIMITATIONS/IMPLICATIONS Because of the chosen research approach, the research results may lack generalizability. Therefore, researchers are encouraged to test the proposed framework further. PRACTICAL IMPLICATIONS The paper includes implications for the development of patient involvement in health care. ORIGINALITY/VALUE This paper fulfills a need to study different types of patient involvement and to develop a theoretical framework for characterizing and analyzing such involvement strategies.
Leveraging technology: creating and sustaining changes for health.

OBJECTIVE The rapid growth and evolution of health-related technology capabilities are driving an established presence in the marketplace and are opening up tremendous potential to minimize and/or mitigate barriers associated with achieving optimal health, performance, and readiness. This article summarizes technology-based strategies that promote healthy habits related to physical activity, nutrition, and sleep. MATERIALS AND METHODS The Telemedicine and Advanced Technology Research Center convened a workshop titled "Leveraging Technology: Creating & Sustaining Changes for Health" (May 29-30, 2013, Fort Detrick, MD). Participants included experts from academia (n=3), government (n=33), and industry (n=16). A modified Delphi method was used to establish expert consensus in six topic areas: (1) physical activity, (2) nutrition, (3) sleep, (4) incentives for behavior change, (5) usability/interoperability, and (6) mobile health/open platform. RESULTS Overall, 162 technology features, constructs, and best practices were reviewed and prioritized for physical activity monitors (n=29), nutrition monitors (n=35), sleep monitors (n=24), incentives for change (n=36), usability and interoperability (n=25), and open data (n=13). CONCLUSIONS Leading practices, gaps, and research needs for technology-based strategies were identified and prioritized. This information can be used to provide a research and development road map for (1) leveraging technology to minimize barriers to enhancing health and (2) facilitating evidence-based techniques to create and sustain healthy behaviors.
Prostate registration using magnetic resonance elastography for cancer localization

Noninvasive detection and localization of prostate cancer in medical imaging is an important, yet difficult task. Benefits range from diagnosis of cancer, to planning and guidance of its treatment. In order to characterize cancer and evaluate its localization in volumetric images, such as ultrasound or magnetic resonance imaging (MRI), their spatial correspondence with the “gold standard” provided by histopathology must be established. In this thesis, we propose a general framework for a multi-slice to volume registration that is applied to register a stack of sparse, unaligned two-dimensional histological slices to a three-dimensional volumetric imaging of the prostate. The approach uses particle filtering that allows deriving optimal pose parameters of the slices in a Bayesian approach. We then propose a novel registration method between in vivo and ex vivo MRI of the prostate to facilitate its registration to histopathology. The method incorporates elasticity information, acquired by magnetic resonance elastography (MRE), to generate a patientspecific biomechanical model of the prostate and periprostatic tissue. Next, we propose a registration method between preoperative MRI and intraoperative transrectal-ultrasound. The method can be incorporated with a robotic surgical system to augment the surgeon’s visualization during robot-assisted prostatectomy. We also study the use of elasticity-based registration of ultrasound elastography and MRE. We then present an image processing approach for enhancing MRE data. The approach employs registration to compensate for motion of patients during the scan to improve the accuracy of the reconstructed elastogram. A super-resolution technique is employed to increase the resolution of the acquired images by utilizing unique properties of MRE. Finally, we develop a theory for optimization-based design of motion encoding in MRE that allows reducing scanning time and increasing signal-to-noise ratio of elasticity reconstruction. We formulate the displacement estimation of the mechanical wave as an experimental design problem, by which we quantify performance of sequences, and optimize multidirectional designs. The proposed methods have been evaluated in simulations and on a diverse set of clinical data. Results may pave the way for a broader clinical deployment of elastography and elastography-based image processing.
Effects of variant gamma chains and sialic acid content of fibrinogen upon its interactions with ADP-stimulated human and rabbit platelets

: When platelets are stimulated with adenosine diphosphate (ADP), fibrinogen binds to receptors on the platelet membrane, and the platelets aggregate. The primary platelet recognition sites of human fibrinogen are reported to be at the COOH-terminal ends of the gamma chains, with secondary sites in the A alpha chains. Normal human fibrinogen, which consists of three pairs of disulfide-bonded peptide chains, (A alpha, B beta, gamma)2, is heterogeneous with respect to sialic acid content and also contains a small proportion of molecules with a variant gamma chain (designated gamma'), elongated by a peptide extension at the COOH-terminus of the normal gamma chain. We separated fibrinogen into three fractions by chromatography on DEAE cellulose and tested the interactions of these fractions with ADP-stimulated human and rabbit platelets. Two fractions had the normal chain composition, (A alpha B beta, gamma)2, but different sialic acid contents (6.6 and 7.2 mol/mol), and the third fraction had the chain composition (A alpha, B beta)2 gamma gamma' and a sialic acid content of 7.2 mol/mol, which is similar to that of one of the normal fractions. In binding and aggregation experiments, we detected no significant differences between the reactions of the first two fractions, but ADP-stimulated platelets bound only 50% as much of 125I-fibrinogen from the fraction with the gamma' chains and also aggregated less extensively in the presence of this fraction. We conclude that the sialic acid content of fibrinogen does not significantly affect its interactions with platelets, but the elongated gamma' chains bind less effectively to ADP-stimulated platelets, and thus reduce the ability of fibrinogen to support aggregation. This may result from a conformational change caused by the gamma' extension or from the deletion of a portion of the normal gamma chain recognition site.
Is Sociotechnical Thinking Important in Engineering Education?: Survey Perceptions of Male and Female Undergraduates

Research on engineering practice accentuates interplays between the social and technical dimensions of complex engineering problems. Yet within engineering education, relatively little content focuses on such interplays. Content in the engineering curricula often ignores the broader impacts or sociocultural contexts in which engineering designs, products, and services are created and used. As part of a larger study, our research examines whether (compared to males) female undergraduate engineering students indicate similar or different perceptions on the integration of sociotechnical thinking in engineering curricula. The integration of sociotechnical thinking in engineering curricula represents one of several pedagogical techniques that may engage female (and perhaps also male) engineering students as a result of correlation to perceived learning preferences and broader interests. After reviewing relevant literature, this paper analyzes quantitative survey data on student perceptions of the importance of sociotechnical integration in engineering education. Baseline sociotechnical survey data were collected in spring and fall semesters of 2018 in two (spring) and three (fall) engineering classes at two public universities: the Colorado School of Mines and University of Colorado Boulder. Results demonstrate a greater preference for certain forms of sociotechnical thinking in engineering among women. For example, female students assigned greater importance to ‘Ethical’ and ‘Social’ considerations and skills such as ‘Listen to and integrate the perspectives of both engineers and non-engineers’ and ‘Work with people having a diverse set of backgrounds. ’ Also, compared to male students, a higher percentage of female students characterized social responsibility as ‘Engineers’ obligations to the public’ and identified the reason why engineers have special societal obligations as due to the notion that ‘Engineering decisions can impact individuals, communities, and the broader public positively and/or negatively. ’ These results are particularly salient when considered in light of recent research accentuating the importance of contextualized engineering problem-framing and solving processes within a broader sociotechnical context. Finally, we explore ways in which the results open up multiple directions for future research.
Design and FPGA Implementation of Hash Processor

Abstract— Related to the tremendous developments in the wired and wireless communications area, the demand for secure data transmission increases. In order to find solutions for this increasing demand new algorithms and security standards are developed. Among these algorithms and standards, hash functions are widely used. In this paper design and implementation of an FPGA based hash processor is described. The proposed hash processor consists of an arithmetic logic unit, a message computation block, a constants ROM, a register file, a programmable control unit, program memory and standard UART serial interface. Hash processor is configured by the instructions in the program memory and supports SHA1 and SHA-256 hashing. The hardware is described in VHDL and verified on Xilinx FPGAs.