Miracle-dz/UniFAR-FTUs huggingface dataset:
Tsr–GFP accumulates linearly with time at cell poles, and can be used to differentiate ‘old’ versus ‘new’ poles, in Escherichia coli

In Escherichia coli, the chemotaxis receptor protein Tsr localizes abundantly to cell poles. The current study, utilizing a Tsr–GFP fusion protein and time‐lapse fluorescence microscopy of individual cell lineages, demonstrates that Tsr accumulates approximately linearly with time at the cell poles and that, in consequence, more Tsr is present at the old pole of each cell than at its newborn pole. The rate of pole‐localized Tsr accumulation is large enough that old and new poles can always be reliably distinguished, even for cells whose old poles have had only one generation to accumulate signal. Correspondingly, Tsr–GFP can be reliably used to assign new and old poles to any cell without use of information regarding pole heritage, thus providing a useful tool to analyse cells whose prior history is not available. The absolute level of Tsr–GFP at the old pole of a cell also provides a rough estimate of pole (and thus cell) age.
Large-Scale Mapping and Validation of Escherichia coli Transcriptional Regulation from a Compendium of Expression Profiles

Machine learning approaches offer the potential to systematically identify transcriptional regulatory interactions from a compendium of microarray expression profiles. However, experimental validation of the performance of these methods at the genome scale has remained elusive. Here we assess the global performance of four existing classes of inference algorithms using 445 Escherichia coli Affymetrix arrays and 3,216 known E. coli regulatory interactions from RegulonDB. We also developed and applied the context likelihood of relatedness (CLR) algorithm, a novel extension of the relevance networks class of algorithms. CLR demonstrates an average precision gain of 36% relative to the next-best performing algorithm. At a 60% true positive rate, CLR identifies 1,079 regulatory interactions, of which 338 were in the previously known network and 741 were novel predictions. We tested the predicted interactions for three transcription factors with chromatin immunoprecipitation, confirming 21 novel interactions and verifying our RegulonDB-based performance estimates. CLR also identified a regulatory link providing central metabolic control of iron transport, which we confirmed with real-time quantitative PCR. The compendium of expression data compiled in this study, coupled with RegulonDB, provides a valuable model system for further improvement of network inference algorithms using experimental data.
A facile inhibitor screening of SARS coronavirus N protein using nanoparticle-based RNA oligonucleotide

Hundreds of million people worldwide have been infected with severe acute respiratory syndrome (SARS), and the rate of global death from SARS has remarkably increased. Hence, the development of efficient drug treatments for the biological effects of SARS is highly needed. We have previously shown that quantum dots (QDs)-conjugated RNA oligonucleotide is sensitive to the specific recognition of the SARS-associated coronavirus (SARS-CoV) nucleocapsid (N) protein. In this study, we found that a designed biochip could analyze inhibitors of the SARS-CoV N protein using nanoparticle-based RNA oligonucleotide. Among the polyphenolic compounds examined, (−)-catechin gallate and (−)-gallocatechin gallate demonstrated a remarkable inhibition activity on SARS-CoV N protein. (−)-catechin gallate and (−)-gallocatechin gallate attenuated the binding affinity in a concentrated manner as evidenced by QDs-conjugated RNA oligonucleotide on a designed biochip. At a concentration of 0.05 μg mL−1, (−)-catechin gallate and (−)-gallocatechin gallate showed more than 40% inhibition activity on a nanoparticle-based RNA oligonucleotide biochip system.
Tubular network formation protects mitochondria from autophagosomal degradation during nutrient starvation

Mitochondria are highly dynamic organelles that mediate essential cell functions such as apoptosis and cell-cycle control in addition to their role as efficient ATP generators. Mitochondrial morphology changes are tightly regulated, and their shape can shift between small, fragmented units and larger networks of elongated mitochondria. We demonstrate that mitochondrial elements become significantly elongated and interconnected shortly after nutrient depletion. This mitochondrial morphological shift depends on the type of starvation, with an additive effect observed when multiple nutrients are depleted simultaneously. We further show that starvation-induced mitochondrial elongation is mediated by down-regulation of dynamin-related protein 1 (Drp1) through modulation of two Drp1 phosphorylation sites, leading to unopposed mitochondrial fusion. Finally, we establish that mitochondrial tubulation upon nutrient deprivation protects mitochondria from autophagosomal degradation, which could permit mitochondria to maximize energy production and supply autophagosomal membranes during starvation.
Dietary patterns and colorectal cancer: a case–control study from Portugal

Dietary pattern analysis is a powerful technique to study the relationships between diet and cancer, accounting for the specificities of overall dietary intake in each setting. The objective of this study was to quantify the association between dietary patterns and colon and rectum cancers. We evaluated 151 rectum and 102 colon cancer cases selected among surgical patients at the Portuguese Oncology Institute, and 879 community controls. Dietary intake was assessed using a validated food frequency questionnaire. Dietary patterns were defined with principal components and cluster analyses. Age, sex, education, total energy intake, and physical activity-adjusted odds ratios (OR) and 95% confidence intervals (95% CIs) were computed. Three dietary patterns were identified: (i) PI: ‘healthy,’ high consumption of dairy products, wholegrain cereals, vegetables/salads, legumes, fruits and vegetable soup, and low intake of wine; (ii) PII: ‘low consumption of milk and foods containing dietary fiber,’ low intake of dairy products, vegetables/salads, legumes, and fruits; and (iii) PIII: ‘western,’ high consumption of red/processed meat, refined cereals, sugar and sweets, potatoes, alcoholic beverages, and low intake of wholegrain cereals and vegetable soup. Compared with PI, the risk of colon cancer was higher among subjects with PII (OR=2.07; 95% CI: 1.04–4.14) and PIII (OR=2.35; 95% CI: 1.19–4.64). The OR estimates for rectum cancer were 3.12 (95% CI: 1.74–5.61) and 1.41 (95% CI: 0.75–2.63), respectively. Our results confirm the higher risk of colorectal cancer among subjects with ‘western’ diets and ‘low consumption of milk and foods containing foods containing dietary fiber’. At a local level, these results support public health messages based on the accumulated evidence on the relationship between individual food items/groups and colorectal cancer.
Mechanism of 99mTc-d,l-HMPAO Retention in Brain Cells

The intracellular distributions of 99mTc-d,l-HMPAO, 99mTcmeso-HMPAO and 99mTc-PnAO in rat brains were explored in vivo and in vitro. 99mTc-d,l-HMPAO and 99mTcmeso- HMPAO were found to distribute in the mitochondria of rat brain cells with radioactivity prominent throughout the whole brain (ca. 33.1% and 26.5%, respectively) at 10 min post-injection in the in vivo study. Binding to the cerebral mitochondria appeared sensitive to tissue viability or other physiological parameters. This sensitivity was evidenced by the corresponding in vitro study which revealed significantly less radioactivity than that of in vivo in the mitochondria. The binding of both 99mTc-HMPAO diastereomers to the mitochondria was stable after washing with SEH buffer. Extremely low radioactivity of 99mTc-PnAO (~10%) was found in the mitochondria in both in vivo and in vitro studies; the complex proved to be loosely bound and was readily washed out with SEH buffer. The preferential internalization of 99mTc-d,l-HMPAO and 99mTc-meso- HMPAO in the mitochondria could be a step towards an enzymatic degradation in the viable brain cells, for instance through acid hydrolase. The difference in the extent of binding between two 99mTc-HMPAO diastereomers might depend on acid susceptibility, which might be related to the enzymatic acid hydrolysis in the mitochondria. From this study, intracellular binding to mitochondria may be the major mechanism for trapping 99mTc-HMPAO in the brain cells.
The prevalence of ALK rearrangement in pulmonary adenocarcinomas in an unselected Caucasian population from a defined catchment area: impact of smoking

To assess the prevalence of EML4–ALK rearrangement gene measured by immunohistochemistry in an unselected population‐based consecutive cohort of patients with adenocarcinoma of the lung (ACL), and the correlation with smoking history, thyroid transcription factor 1 (TTF1), gender and age.
Experimental Studies of the Hydrodynamics of Liquid Droplet Generation and Transport in Microchannels

Droplet microfluidics is a promising field since it overcomes many of the limitations of single phase microfluidic systems. The improved mixing time scale, the increase of number of samples and the isolation of droplets are some of its virtues. The core of droplet microfluidics is a two-phase flow condition that is subjected to scaling of the confining geometry. With the scaling the complexities of the flow phenomena arise. For that reason both the processes of droplet generation and transport are not fully understood for various flow and fluid conditions. The work in this thesis aims to experimentally examine droplet generation and transport in microchannels for flow and fluid conditions that are experimentally challenging to perform. Examination of droplet generation in a T-junction microchannel design was performed with a quantitative velocity field approach known as micro particle image velocimetry (μPIV ). The studies on droplet generation focused on very fast generation regimes, namely transition and dripping that have not been studied for a T-junction design. This achievement was accomplished because of the development of a fast optical detection and triggering system that allowed for acquiring images of different identical droplets at the same position. μPIV results indicate that the quantitative velocity field patterns of different regimes share some similarities. The filling stage in the transition and dripping regimes had some resemblance in their velocity patterns. The velocity patterns for the start of droplet pinch-off were alike for the squeezing and transition regimes. Furthermore, the presence of a surfactant in the droplet phase above the critical micelle concentration (CMC) did not have an effect on the general velocity patterns as long as the capillary number Ca was matched with the no-surfactant condition. The studies of hydrodynamic properties of droplet transport were performed in hard materials to avoid cumulative error sources, such as material pressure compliance and swelling effects. The project had several parts: designing a microchannel network that allowed studying the hydrodynamic properties of small droplets, surface treatments of the channel material for stable droplet generation and examining the hydrodynamics of small liquid droplets with sizes that have not been reported
Brainstorm/J: a Java Framework for Intelligent Agents

Despite the effort of many researchers in the area of multi-agent systems (MAS) for designing and programming agents, a few years ago the research community began to take into account that common features among different MAS exists. Based on these common features, several tools have tackled the problem of agent development on specific application domains or specific types of agents. As a consequence, their scope is restricted to a subset of the huge application domain of MAS. In this paper we propose a generic infrastructure for programming agents whose name is Brainstorm/J. The infrastructure has been implemented as an object oriented framework. As a consequence, our approach supports a broader scope of MAS applications than previous efforts, being flexible and reusable.
FURTHER RESULTS ON NEW STABILITY ANALYSIS FOR UNCERTAIN NEUTRAL SYSTEMS WITH TIME-VARYING DELAY

The delay-dependent and delay-independent conditions are proposed in order to assure the stability for the uncertain neutral system with interval time-varying delays. New additional nonnegative inequalities are introduced to improve the analysis. The solving schemes based on Linear Matrix Inequality (LMI) approach along with the selective examples are presented to demonstrate the improvements achieved.
Stimulated decomposition in peat for engineering applications

Peat deposits are highly compressible, undergoing significant long-term settlement, particularly for fibrous peat. Since decomposition of organic matter can have a significant effect on compression behaviour, the ability to artificially stimulate and pre-decompose a bearing peat stratum prior to the main construction works may mitigate against increased compression rates reported to occur over the design life. This paper presents a feasibility trial of a technique that accelerates the decomposition process in peat prior to entering into full laboratory and field testing. The main decomposition limiting factors of pH and carbon:nitrogen (C:N) ratio are adjusted by adding sufficient amounts of basic and nitrogenous materials. The proposed technique can be tailored for specific peat deposits and can also be achieved in a more sustainable manner. In the trial on moderately decomposed fibrous Sphagnum peat, different peat blends were prepared using additives of peat pulverised fuel ash (PPFA) and urea. Optimum.
MSX1 gene and nonsyndromic oral clefts in a Southern Brazilian population

Nonsyndromic oral clefts (NSOC) are the most common craniofacial birth defects in humans. The etiology of NSOC is complex, involving both genetic and environmental factors. Several genes that play a role in cellular proliferation, differentiation, and apoptosis have been associated with clefting. For example, variations in the homeobox gene family member MSX1, including a CA repeat located within its single intron, may play a role in clefting. The aim of this study was to investigate the association between MSX1 CA repeat polymorphism and NSOC in a Southern Brazilian population using a case-parent triad design. We studied 182 nuclear families with NSOC recruited from the Hospital de Clínicas de Porto Alegre in Southern Brazil. The polymorphic region was amplified by the polymerase chain reaction and analyzed by using an automated sequencer. Among the 182 families studied, four different alleles were observed, at frequencies of 0.057 (175 bp), 0.169 (173 bp), 0.096 (171 bp) and 0.67 (169 bp). A transmission disequilibrium test with a family-based association test (FBAT) software program was used for analysis. FBAT analysis showed overtransmission of the 169 bp allele in NSOC (P=0.0005). These results suggest that the CA repeat polymorphism of the MSX1 gene may play a role in risk of NSOC in populations from Southern Brazil.
Microtopography of high-calcium fly ash particle surfaces

Tapping mode atomic force microscopy (TM-AFM) has been used to image the surfaces of glassy spheres from high-calcium fly ash (HCFA). TM-AFM provides high-resolution images of such spheres under ambient conditions (e.g. no vacuum and no conductive coating), showing topographic details which were not accessible with conventional electron microscopy. Combined single-particle X ray diffraction and TM-AFM allows identification of nanometre-sized anorthite, gehlenite, anhydrite and magnetite crystals attached to the glassy spheres. Furthermore, the TM-AFM technique revealed that the glassy matrix is quite inhomogeneous even on the lower nanometre scale. The spatial distribution of reactive and inert mineral phases attached to fly ash particle surfaces provides information about their high-temperature formation, which may be relevant to their subsequent reactivity during hydration.
Estimated prevalence of dengue viremia in Puerto Rican blood donations, 1995 through 2010

BACKGROUND: Dengue virus (DENV) nucleic acid amplification testing of blood donations during epidemics in endemic locations, including Puerto Rico, has suggested possible sizable transfusion transmission risk. Estimates of the long‐term prevalence of DENV viremic donations will help evaluate the potential magnitude of this risk in Puerto Rico.
Widespread utilization of passive energy recapture in swimming medusae

ABSTRACT Recently, it has been shown that some medusae are capable of swimming very efficiently, i.e. with a low cost of transport, and that this is in part due to passive energy recapture (PER) which occurs during bell relaxation. We compared the swimming kinematics among a diverse array of medusae, varying in taxonomy, morphology and propulsive and foraging modes, in order to evaluate the prevalence of PER in medusae. We found that while PER was common among taxa, the magnitude of the contribution to overall swimming varied greatly. The ability of medusae to utilize PER was not related to morphology and swimming performance but was controlled by their swimming kinematics. Utilizing PER required the medusae to pause after bell expansion and individuals could modulate their PER by changing their pause duration. PER can greatly enhance swimming efficiency but there appear to be trade-offs associated with utilizing PER. Summary: The use of passive energy recapture is widespread among medusae and its extent is regulated primarily through the pause duration between swimming cycles.
Annexin 2A sustains glioblastoma cell dissemination and proliferation

Glioblastoma (GBM) is the most devastating tumor of the brain, characterized by an almost inevitable tendency to recur after intensive treatments and a fatal prognosis. Indeed, despite recent technical improvements in GBM surgery, the complete eradication of cancer cell disseminated outside the tumor mass still remains a crucial issue for glioma patients management. In this context, Annexin 2A (ANXA2) is a phospholipid-binding protein expressed in a variety of cell types, whose expression has been recently associated with cell dissemination and metastasis in many cancer types, thus making ANXA2 an attractive putative regulator of cell invasion also in GBM. Here we show that ANXA2 is over-expressed in GBM and positively correlates with tumor aggressiveness and patient survival. In particular, we associate the expression of ANXA2 to a mesenchymal and metastatic phenotype of GBM tumors. Moreover, we functionally characterized the effects exerted by ANXA2 inhibition in primary GBM cultures, demonstrating its ability to sustain cell migration, matrix invasion, cytoskeletal remodeling and proliferation. Finally, we were able to generate an ANXA2-dependent gene signature with a significant prognostic potential in different cohorts of solid tumor patients, including GBM. In conclusion, we demonstrate that ANXA2 acts at multiple levels in determining the disseminating and aggressive behaviour of GBM cells, thus proving its potential as a possible target and strong prognostic factor in the future management of GBM patients.
The glassy wormlike chain

We introduce a new model for the dynamics of a wormlike chain (WLC) in an environment that gives rise to a rough free energy landscape, which we name the glassy WLC. It is obtained from the common WLC by an exponential stretching of the relaxation spectrum of its long-wavelength eigenmodes, controlled by a single parameter . Predictions for pertinent observables such as the dynamic structure factor and the microrheological susceptibility exhibit the characteristics of soft glassy rheology and compare favourably with experimental data for reconstituted cytoskeletal networks and live cells. We speculate about the possible microscopic origin of the stretching, implications for the nonlinear rheology, and the potential physiological significance of our results.
Psychometric evaluation of the Cultural Capacity Scale Arabic version for nursing students

Background: With the rising influx of migrants into Saudi Arabia, it becomes necessary to develop a valid and reliable tool that can accurately measure the cultural competence of the Saudi nursing students. Aim: This study evaluated the psychometric properties of the Cultural Capacity Scale Arabic version (CCS-A) for nursing students. Methods: A descriptive, cross-sectional study was conducted among 200 nursing students in Saudi Arabia. The scale reliability was assessed by internal consistency and stability reliability. Scale validity was established by content validity and construct validity. Exploratory factor analysis (EFA) was performed to extract the factors of the CCS-A. Results: The computed Cronbach’s α coefficient was 0.96 and the intra-class correlation was 0.88. The CCS-A exhibited excellent content validity and good construct validity. The EFA revealed a single factor with a cumulative contribution rate of 57.4%. Conclusion: The CCS-A exhibited acceptable reliability and validity, thus supporting its sound psychometric properties.
Quantify Resilience Enhancement of UTS through Exploiting Connected Community and Internet of Everything Emerging Technologies

This work aims at investigating and quantifying the Urban Transport System (UTS) resilience enhancement enabled by the adoption of emerging technology such as Internet of Everything (IoE) and the new trend of the Connected Community (CC). A conceptual extension of Functional Resonance Analysis Method (FRAM) and its formalization have been proposed and used to model UTS complexity. The scope is to identify the system functions and their interdependencies with a particular focus on those that have a relation and impact on people and communities. Network analysis techniques have been applied to the FRAM model to identify and estimate the most critical community-related functions. The notion of Variability Rate (VR) has been defined as the amount of output variability generated by an upstream function that can be tolerated/absorbed by a downstream function, without significantly increasing of its subsequent output variability. A fuzzy-based quantification of the VR based on expert judgment has been developed when quantitative data are not available. Our approach has been applied to a critical scenario as flash flooding considering two cases: when UTS has CC and IoE implemented or not. However, the method can be applied in different scenarios and critical infrastructures. The results show a remarkable VR enhancement if CC and IoE are deployed.
Bond between high strength concrete with recycled coarse aggregate and reinforcing bars

Abstract Recently, natural aggregate resource depletion are being raised due to the pollution issues regarding the construction waste generated during demolition of building deterioration and the supply issues of aggregates. Recycled aggregates are being used as a solution to these issues, but the quality and durability/structural performance issues are the restriction of application. This study conducted a comparative evaluation of bond behaviour according to the reinforcing bar type and substitution rate of recycled coarse aggregate mixed with high strength concrete. That was carried out to verify the applicability of recycled coarse aggregate concrete as a structural member. Seventy-two specimens were manufactured with variables of recycled aggregate substitution rate (0, 30, 50 and 100%), reinforcing bar arrangement direction and reinforcing bar types. The bondstress and the slip relation of reinforcing bar and concrete in high strength concrete using recycled aggregate were found to have little influence on the reinforcing bar arrangement direction, location and substitution rate.