Miracle-dz/UniFAR-FTUs huggingface dataset:
Flk-1 signalling during ES cell differentiation

Flk-1 (Foetal liver kinase-1), a receptor tyrosine kinase, and its ligand VEGF (vascular endothelial growth factor) are essential for vasculogenesis and haemopoiesis in the early embryo. Flk-1 is expressed initially on the haemangioblast, the common precursor of haemopoietic and endothelial cells, and on subsequent committed endothelial lineages. Flk-1 expression is maintained on adult endothelial cells and mediates angiogenesis, making it an important pharmaceutical target in the pathology of many human diseases including cancer and rheumatoid arthritis. Though involvement of Flk-1 in disease has lead to its extensive study in adult humans little is known about the signals it mediates during development. Using ES cells as a model of development, the aim of this investigation was to identify signals mediated through Flk-1 during early development and to characterise their relative importance in the formation of the haemopoietic, endothelial and cardiomyocyte lineages. Activation of the MAPK and PLC signalling pathways were demonstrated following VEGF treatment of Flk-1-expressing embryoid bodyderived cells, though surprisingly activation of Flk-1 did not appear to mediate activation of the PI3K signalling pathway. Use of an embryoid body-based endothelial sprouting assay demonstrated a requirement for Flk-1 in both endothelial specification and angiogenic expansion. However, this activity was not mediated through either the MAPK or PI3K pathways. The finding that the PI3K pathway is not activated following VEGF stimulation nor required for early vasculogenesis/angiogenesis is surprising given its important role in both homeostatic and pathological angiogenesis in the adult. Previous work had suggested a role for Flk-1 in cardiac differentiation. Investigation of cardiomyocyte differentiation using Flk-1 null ES cells demonstrated a delay in formation of beating cardiomyocytes suggesting that Flk-1 may be involved in, but not required for cardiomyocyte specification. Finally, Flk-1-Tet-on ES cell lines were generated to facilitate investigation of the temporal importance of Flk-1 signalling during different developmental processes. Due to unforeseen difficulties in the maintenance of Flk-1 expression upon ES cell differentiation the full potential of this system was not realised in this study.
13C NMR Relaxation Analysis of Protein GB3 for the Assessment of Sidechain Dynamics Predictions by Current AMBER and CHARMM Force Fields.

Molecular simulations with seven current AMBER- and CHARMM-based force fields yield markedly differing internal bond vector autocorrelation function predictions for many of the 223 methine and methylene H-C bonds of the 56-residue protein GB3. To enable quantification of accuracy, 13C R1, R2, and heteronuclear NOE relaxation rates have been determined for the methine and stereochemically-assigned methylene Cα and Cβ positions. With only three experimental relaxation values for each bond vector, central to this analysis is the accuracy with which MD-derived autocorrelation curves can be represented by a 3-parameter equation which, in turn, maps onto the NMR relaxation values. In contrast to the more widely used extended Lipari-Szabo order parameter representation, 95% of these MD-derived internal autocorrelation curves for GB3 can be fitted to within 1.0% rmsd over the timeframe from 30 ps to 4 ns by a biexponential Larmor frequency-selective representation (LF-S2). Applying the LF-S2 representation to the experimental relaxation rates and uncertainties serves to determine the boundary range for the autocorrelation function of each bond vector consistent with the experimental data. Not surprisingly, all seven force fields predict the autocorrelation functions for the more motionally-restricted 1Hα-13Cα and 1Hβ-13Cβ bond vectors with reasonable accuracy. However, for the 1Hβ-13Cβ bond vectors exhibiting aggregate order parameter S2 values less than 0.85, only 1% of the MD-derived predictions lie with 1 σ of the experimentally determined autocorrelation functions and only 7% within 2 σ. On the other hand, substantial residue type-specific improvements in predictive performance were observed among the recent AMBER force fields. This analysis indicates considerable potential for the use of 13C relaxation measurements in guiding the optimization of the sidechain dynamics characteristics of protein molecular simulations.
Investigation of protein expression dynamics in human tumor cells following pharmacological treatment

Cancer, the multifactorial disease, resulting in uncontrolled growth of malignant cells, is the second most frequent cause of death worldwide. Despite enormous growth in knowledge on cancer pathology, efficient medication still remains elusive. In recent years, global profiling approaches are increasingly important tools to study complex biological problems, such as cancer. One emerging profiling technology is proteomics, the continuously growing research branch of (bio)analytical chemistry that studies the entire set of proteins in a biological system, their modifications and interactions. However, a variety of computational and technological challenges in proteomics are still limiting the broad application of the technology in cancer research. This thesis contributes in three major topics to new methodological approaches for the analysis of proteomics data and to novel insights of the effects of therapeutical treatment in cancer cells. In the first research part, a new method to analyze 2D-Polyacrylamid Gel Electrophoresis (PAGE) proteomics data is introduced. Although the DIGE (Difference Gel Eletrophoresis) technology greatly influenced the quality of 2D-PAGE experiments through the fluorescent labeling of different samples and their common separation in the same 2D gel, the technology is still accompanied with major challenges. In this thesis we provide a solution to one of the major problems, the accurate and automated mapping of protein spots from different DIGE gels. We implemented a novel scoring method and applied a graph-theoretical approach to solve the assignment problem and to ultimately find the protein spots with reproducible regulation on different gels.
Vibrational stress affects extracellular signal-regulated kinases activation and cytoskeleton structure in human keratinocytes

As the outermost organ, the skin can be damaged following injuries such as wounds and bacterial or viral infections, and such damage should be rapidly restored to defend the body against physical, chemical, and microbial assaults. However, the wound healing process can be delayed or prolonged by health conditions, including diabetes mellitus, venous stasis disease, ischemia, and even stress. In this study, we developed a vibrational cell culture model and investigated the effects of mechanical vibrations on human keratinocytes. The HaCaT cells were exposed to vibrations at a frequency of 45 Hz with accelerations of 0.8g for 2 h per day. The applied mechanical vibration did not affect cell viability or cell proliferation. Cell migratory activity did increase following exposure to vibration, but the change was not statistically significant. The results of immunostaining (F-actin), western blot (ERK1/2), and RT-qPCR (FGF-2, PDGF-B, HB-EGF, TGF-β1, EGFR, and KGFR) analyses demonstrated that the applied vibration resulted in rearrangement of the cytoskeleton, leading to activation of ERK1/2, one of the MAPK signaling pathways, and upregulation of the gene expression levels of HB-EGF and EGFR. The results suggest that mechanical vibration may have wound healing potential and could be used as a mechanical energy-based treatment for enhancing wound healing efficiency.
Fatores associados a um impacto na qualidade de vida pós-revascularização miocárdica

Objective: to analyze the scientific evidence addressing factors associated with impacts on the quality of life of patients submitted to myocardial revascularization. Methods: integrative review, conducted in the databases Medical Literature Analysis and Retrieval System Online/Pubmed, Web of Science, Scopus, Science Direct, Latin American and Caribbean Health Sciences and Scientific Electronic Library Online. Results: eight studies were selected, mostly prospective cohorts, published in the years 2003 to 2013. The worsening of quality of life was determined by the instruments Medical Outcomes Short-Form-36 Health Survey - SF-36 and Item Health Survey – RAND-36, and the impact factors were age above 75, previous history of myocardial infarction or angina pectoris, and association of comorbidities such as diabetes mellitus and depression. Conclusion: factors such as extreme age and female gender were highlighted in the worsening of the quality of life of patients who had undergone myocardial revascularization.
Inter-relationship among nutritional quality parameters of maize (Zea mays) genotypes

The present study was taken up to understand the inter-relationship among various nutritional components of maize (Zea mays L.) kernel. For this purpose, 23 elite maize genotypes received from different centres of All India Coordinated Research Projects on Maize during 2009 and 2010 were used. The samples were ground to powder and processed for the estimation of various nutritional quality parameters such as protein quality, starch, oil and carotenoids and the data was correlated to find the interrelationship between these components. The results showed that the protein content exhibited a significant negative correlation with two important essential amino acids such as tryptophan and lysine. An inverse correlation was found between starch and oil indicating that breeding for high oil maize may lead to lower grain yield. A significant positive correlation was observed between oil content and 100-kernel weight postulating that although increase in oil down-regulate the starch content, the total grain yield, however, would remain unaffected. Protein content showed a non-significant negative correlation with 100-kernel weight. A significant positive correlation was noticed between protein and starch. Another important finding of this study is the positive correlation observed between oil and fat soluble total carotenoids. Breeding for high oil, therefore, would have the added advantage of biofortification of maize. The findings will help to develop improved maize having an answer to better nutrition.
The Role of Atg18 and Atg18-like Proteins in D. melanogaster Autophagy

Author(s): Ngumi, Michael | Abstract: Autophagy describes a conserved process that utilizes a double membrane in isolating cytoplasmic cargo for lysosomal degradation. Nutrient-regulation can be used to control the "off/on" state of the process. In yeast and mammals, the PI(3)P binding protein Atg18, has been determined to localize to the omegasome, isolation membranes and autophagosomes, while positively regulating autophagy. Drosophila melanogaster encodes for three Atg18 family homologues : Atg18, CG11975 and CG8678. Here, I explored their role in autophagy, by analyzing their protein sequences and phylogenetic relationships, autophagy associated phenotypes, and regulated cellular localization. I also investigated the possibility of Atg18, CG11975 or CG8678 being autophagy or PI(3)P markers. Here, I show that the D. melanogaster Atg18 family share conserved sequences and motifs. Phylogenetic analysis revealed close ancestry between the D. melanogaster, yeast and mammal Atg18 family. Overexpression and loss of function studies indicated that Atg18 positively regulates autophagy, and partially localizes to both acidified compartments and autophagosomes. In addition, overexpression of Atg18 induced lysosome acidification in larval fat body. In contrast, overexpression of CG11975 inhibited formation of acidified compartments and autophagosomes. CG11975 also showed low localization to acidified compartments and autophagosomes. Furthermore, coexpression of either Atg18 or CG11975 with the class II PI3-kinase Pi3K68D, mutually altered localizations, suggesting that both Atg18 and CG11975 can detect a Pi3K68D-specific PI(3)P pool. I also show that overexpression of CG8678 does not affect starvation- induced autophagy. These studies showing D. melanogaster Atg18s autophagy phenotypes and PI(3)P localization establish inroads for new markers and functional insights into phosphoinositide-dependent functions in autophagy
Genetic diversity of Rhizoctonia solani isolates (Kuhn) from pepper in Mexico

Resumen Una de las principales limitantes para la produccion de chile son los hongos patogenos causantes de la enfermedad conocida como “marchitez del chile” o “secadera”. Esta enfermedad puede ser devastadora cuando las condiciones climaticas son favorables para el patogeno. A pesar de que se han intentado diferentes medios de control (quimicos y culturales) ninguno ha tenido exito. Una alternativa para su control es producir germoplasma resistente, sin embargo para poder establecer un programa de mejoramiento efectivo es necesario conocer la distribucion y diversidad genetica de los patogenos involucrados, particularmente de Rhizoctonia solani , que por su ubicuidad representa un peligro potencial en todas las zonas productoras. Por ello el objetivo fue caracterizar a R. solani en las zona Centro Norte de Mexico y determinar su diversidad genetica. Para cumplir con este objetivo se consideraron los estados de Chihuahua, Durango, Zacatecas, San Luis Potosi, Colima, Queretaro y Guanajuato donde en 2009 se colectaron plantas adultas de Chile con sintomas de marchitez, se aislo al hongo y se encontro una incidencia del 33%, encontrandose tanto en tallo como en raiz. Las celulas miceliales fueron multinucleadas, caracteristicas de las cepas patogenicas. Las pruebas de anastomosis demostaron la presencia en Mexico de los grupos GA4, GA-2.1, GA-IIB, GA-2IV, GA7, GA11,
Polymorphisms and drug resistance analysis of HIV-1 isolates from patients on first line antiretroviral therapy (ART) in South-eastern Nigeria

Acquisition of resistance mutations by HIV-1 isolates causes treatment failure among infected patients receiving antiretroviral therapy (ART). This study determined patterns of drug-resistance mutations (DRMs) among HIV-1 isolates from patients receiving first-line ART in South-eastern Nigeria. Blood samples were collected from HIV-1 infected patients accessing antiretroviral treatment centers at General Hospital Awo-Omamma, Imo state, State Hospital Asaba, Delta state and St Joseph’s Catholic Hospital Adazi, Anambra state and used for HIV-1 DNA sequencing and phylogenetic analysis. DRMs were scored using combination of Stanford algorithm and the 2015 International Antiviral Society-USA list while drug susceptibility was predicted using Stanford algorithm. Twenty eight of the HIV-1 isolates were sequenced and identified as subtypes G (35.7%), CRF02_AG (57.1%) and unclassifiable, UG (7.1%). Major PI resistance-associated mutations were identified at two sites including M46L (16.7% of subtype G/UG) and V82L (6.3% of CRF02_AG). Minor PI resistance-associated mutations identified among subtype G/UG are L10V/I (8.3%) and K20I (100%) while L10V/I (50%), K20I (100%), L33F (6.3%) and N88D (6.3%) were identified among CRF02_AG. Other polymorphisms found include; I13V/A, E35Q, M36I/L, N37D/S/E/H, R57K/G, L63T/P/S/Q, C67E/S, H69K/R, K70R, V82I and L89M in the range of 28.6% to 100% among the different subtypes. Interpretation based on Stanford algorithm showed that Darunavir/ritonavir is the only regimen whose potency was not compromised by the circulating mutations. Identification of major and minor PI resistance mutations in this study underscores the need for drug resistance testing prior to initiation of second line antiretroviral therapy in Nigeria.
Effect of stimulating waveform and of data processing on respiratory impedance measurement

Objective: Several commercial and custom-made forced oscillation technique (FOT) devices are used to assess respiratory system impedance. The impulse oscillometry system (IOS) is a widespread device, which yields similar but not identical results to those provided by other FOT systems. Differences may be related to the forcing waveform, the device hardware, or the data processing algorithms. We evaluated the agreement between resistance (Rrs) and reactance (Xrs) measurements while alternating between different forcing waveforms and data processing algorithms. Approach: We performed pre- and post-bronchodilator measurements in 20 patients with respiratory complaints. We generated pulse waveforms using an IOS, and sinusoidal oscillations by replacing the IOS loudspeaker with customized loudspeaker providing a 5 Hz sinusoidal pressure signal. Pressure and flow were measured using the IOS sensors and breathing circuit. We developed a data processing algorithm compatible to both forcing signals. We also applied commercial IOS software during pulse waveform and a least mean square (lms) algorithm during sinusoidal waveform. Main results: The median (5th, 95th percentile) differences between Rrs and Xrs were (1) −0.35 (−2.49, 1.23) and 0.16 (−1.63, 3.07 cmH2O*s l−1, when the same algorithm was used during pulse vs sinusoidal stimulus; (2) 0.34 (−2.33, 5.98) and 0.57 (−2.64, 6.09) cmH2O*s l−1, when our algorithm and the IOS software were used during pulse waveform; and (3) 0.33 (−1.20, 6.05) and 0.25 (−4.94, 4.28) cmH2O*s l−1 when the IOS software was used during pulse and the lms algorithm during sinusoidal waveforms. Significance: Both forcing signal and data processing contribute to differences in impedance values measured by different FOT devices.
Game Theory in Mobile CrowdSensing: A Comprehensive Survey

Mobile CrowdSensing (MCS) is an emerging paradigm in the distributed acquisition of smart city and Internet of Things (IoT) data. MCS requires large number of users to enable access to the built-in sensors in their mobile devices and share sensed data to ensure high value and high veracity of big sensed data. Improving user participation in MCS campaigns requires to boost users effectively, which is a key concern for the success of MCS platforms. As MCS builds on non-dedicated sensors, data trustworthiness cannot be guaranteed as every user attains an individual strategy to benefit from participation. At the same time, MCS platforms endeavor to acquire highly dependable crowd-sensed data at lower cost. This phenomenon introduces a game between users that form the participant pool, as well as between the participant pool and the MCS platform. Research on various game theoretic approaches aims to provide a stable solution to this problem. This article presents a comprehensive review of different game theoretic solutions that address the following issues in MCS such as sensing cost, quality of data, optimal price determination between data requesters and providers, and incentives. We propose a taxonomy of game theory-based solutions for MCS platforms in which problems are mainly formulated based on Stackelberg, Bayesian and Evolutionary games. We present the methods used by each game to reach an equilibrium where the solution for the problem ensures that every participant of the game is satisfied with their utility with no requirement of change in their strategies. The initial criterion to categorize the game theoretic solutions for MCS is based on co-operation and information available among participants whereas a participant could be either a requester or provider. Following a thorough qualitative comparison of the surveyed approaches, we provide insights concerning open areas and possible directions in this active field of research.
Pathological mechanism and antisense oligonucleotide-mediated rescue of a non-coding variant suppressing factor 9 RNA biogenesis leading to hemophilia B

Loss-of-function mutations in the human coagulation factor 9 (F9) gene lead to hemophilia B. Here, we dissected the consequences and the pathomechanism of a non-coding mutation (c.2545A>G) in the F9 3’ untranslated region. Using wild type and mutant factor IX (FIX) minigenes we revealed that the mutation leads to reduced F9 mRNA and FIX protein levels and to lower coagulation activity of cell culture supernatants. The phenotype could not be compensated by increased transcription. The pathomechanism comprises the de novo creation of a binding site for the spliceosomal component U1snRNP, which is able to suppress the nearby F9 poly(A) site. This second, splicing-independent function of U1snRNP was discovered previously and blockade of U1snRNP restored mutant F9 mRNA expression. In addition, we explored the vice versa approach and masked the mutation by antisense oligonucleotides resulting in significantly increased F9 mRNA expression and coagulation activity. This treatment may transform the moderate/severe hemophilia B into a mild or subclinical form in the patients. This antisense based strategy is applicable to other mutations in untranslated regions creating deleterious binding sites for cellular proteins.
The influences of environmental change and development on leaf shape in Vitis

Premise The size and shape (physiognomy) of woody, dicotyledonous angiosperm leaves are correlated with climate. These relationships are the basis for multiple paleoclimate proxies. Here we test whether Vitis exhibits phenotypic plasticity and whether physiognomy varies along the vine. Methods We used Digital Leaf Physiognomy (DiLP) to measure leaf characters of four Vitis species from the USDA Germplasm Repository (Geneva, New York) from the 2012–2013 and 2014–2015 leaf‐growing seasons, which had different environmental conditions. Results Leaf shape changed allometrically through developmental stages; early stages were more linear than later stages. There were significant differences in physiognomy in the same developmental stage between the growing seasons, and species had significant differences in mean physiognomy between growing seasons. Phenotypic plasticity was defined as changes between growing seasons after controlling for developmental stage or after averaging all developmental stages. Vitis amurensis and V. riparia had the greatest phenotypic plasticity. North American species exhibited significant differences in tooth area:blade area. Intermediate developmental stages were most likely to exhibit phenotypic plasticity, and only V. amurensis exhibited phenotypic plasticity in later developmental stages. Conclusions Leaves have variable phenotypic plasticity along the vine. Environmental signal was strongest in intermediate developmental stages. This is significant for leaf physiognomic‐paleoclimate proxies because these leaves are likely the most common in leaf litter and reflect leaves primarily included in paleoclimate reconstructions. Early season and early developmental stages have the potential to be confounding factors but are unlikely to exert significant influence because of differential preservation potential.
Emotions experienced when receiving a temporary deferral: perspectives from staff and donors

Temporary deferrals negatively impact on donor retention. However, little is known about why donors are deterred from returning. One unexplored area is the emotions experienced by donors when deferred. This study investigated these emotions from the perspectives of both the front‐line staff involved in applying deferrals and deferred donors themselves, with the aim of identifying which emotions impact on donors’ intention to return.
Surveying woodland hawks with broadcasts of great horned owl vocalization

Pre-recorded vocalizations of great horned owls (Bubo virginianus) broadcast into predominantly wooded habitat along roadside survey routes resulted in as many detections of resident red-shouldered hawks (Buteo lineatus) and Cooper's hawks (Accipiter cooperi as broadcasts of each conspecific calls. Survey results for 3 species, expressed as average number of contacts/route, were directly related to the number of resident pairs located during systematic searches conducted on foot across the study area. Regression models based on road-transect counts were significant for predicting abundance of red-shouldered hawks, broad-winged hawks (Buteo platypterus), and Cooper's hawks from our study areas.