Miracle-dz/UniFAR-FTUs huggingface dataset:
Regulation of Escherichia coli Hemolysin E Expression by H-NS and Salmonella SlyA

ABSTRACT The Escherichia coli hlyE gene (also known as clyA or sheA) codes for a novel pore-forming toxin. Previous work has shown that the global transcription factors FNR and CRP positively regulate hlyE expression by binding at the same site. Here in vivo transcription studies reveal that FNR occupies the hlyE promoter more frequently than CRP, providing a mechanism for the moderate upregulation of hlyE expression in response to two distinct environmental signals (oxygen and glucose starvation). It has been reported that H-NS interacts with two large regions of the hlyE promoter (PhlyE), one upstream of the −35 element and one downstream of the −10 element. Here we identify two high-affinity H-NS sites, H-NS I, located at the 3′ end of the extended upstream footprint, and H-NS II, located at the 5′ end of the extended downstream footprint. It is suggested that these high-affinity sites initiate the progressive formation of higher order complexes, allowing a range of H-NS-mediated regulatory effects at PhlyE. Finally, the identification of a SlyA binding site that overlaps the H-NS I site in PhlyE suggests a mechanism to explain how SlyA overproduction enhances hlyE expression by antagonizing the negative effects of H-NS.
Simple, fast and high‐efficiency transformation system for directed evolution of cellulase in Bacillus subtilis

Bacillus subtilis can serve as a powerful platform for directed evolution, especially for secretory enzymes. However, cloning and transformation of a DNA mutant library in B. subtilis are not as easy as they are in Escherichia coli. For direct transformation of B. subtilis, here we developed a new protocol based on supercompetent cells prepared from the recombinant B. subtilis strain SCK6 and multimeric plasmids. This new protocol is simple (restriction enzyme‐, phosphatase‐ and ligase‐free), fast (i.e. 1 day) and of high efficiency (i.e. ∼107 or ∼104 transformants per µg of multimeric plasmid or ligated plasmid DNA respectively). Supercompetent B. subtilis SCK6 cells were prepared by overexpression of the competence master regulator ComK that was induced by adding xylose. The DNA mutant library was generated through a two‐round PCR: (i) the mutagenized DNA fragments were generated by error‐prone PCR and linearized plasmids were made using high‐fidelity PCR, and (ii) the multimeric plasmids were generated based on these two DNA templates by using overlap PCR. Both protein expression level and specific activity of glycoside hydrolase family 5 endoglucanse on regenerated amorphous cellulose were improved through this new system. To our limited knowledge, this study is the first report for enhancing secretory cellulase performance on insoluble cellulose.
Examining the Effects of Lighting Effects on Peripheral Devices for Visual User Notifications

The ubiquitous and pervasive use of lighting effects embedded into peripheral hardware has gained popularity through it's use in Triple-A video game titles such as Call of Duty and the availability of software development kits (SDK) from leading manufacturers. A preliminary NASA TLX experiment was performed to examine the effect that notifications displayed on a peripheral device has, in comparison to traditional dialog notifications. This research will prove useful to create notification design guidance for these devices.
Chest Wall Necrosis and Death Secondary to Hydrochloric Acid Infusion for Metabolic Alkalosis

Central line complications are common, and extravasation injuries related to infusion of caustic substances have been previously described. Although hydrochloric acid has been used for many years to treat metabolic alkalosis, there have been no reported fatal complications. We report the case of a 53-year-old female who received a fatal chemical burn due to extravasation from a subclavian central venous catheter of hydrochloric acid infused to correct severe metabolic alkalosis. This case illustrates the hazards of the infusion of caustic substances through central lines and underscores the importance of constant vigilance regarding line positioning and changes to the surrounding tissues when infusing these substances.
Awakening latency from sleep for meaningful and non-meaningful stimuli.

Personally significant and non-significant low intensity sound stimuli were used to determine awakening latencies from sleep stages REM and 2. Latency was measured from stimulus onset to a) the sleeper's own acknowledgement of waking, and b) alpha rhythm onset. Both stimuli were presented twice, once in each sleep stage, to 8 Ss. Voluntary response latencies in REM were shorter than in stage 2 (p <.025) but no difference was found for the latency of alpha rhythm onset. The personally significant stimulus, however, caused a significantly shorter awakening latency using both criteria. The results suggest that perceptual thresholds are low in both sleep stages 2 and REM but that the ability or willingness to organize a response is greater in REM sleep.
The Effects of Infliximab or Adalimumab on Vascular Endothelial Growth Factor and Angiopoietin 1 Angiogenic Factor Levels in Inflammatory Bowel Disease: Serial Observations in 37 Patients

Background:Infliximab and adalimumab effectiveness might be related with changes in angiogenic factors. The aim of the study was to compare the concentrations of angiogenic proteins in patients with inflammatory bowel disease (IBD) and healthy controls and to analyze changes in the levels during infliximab and adalimumab treatment. Methods:A prospective case–control study was conducted in 37 patients with IBD starting treatment with infliximab (16 with Crohn’s disease and 6 with ulcerative colitis) or adalimumab (15 with Crohn’s disease) and 40 control subjects. Four samples were taken from IBD patients, one before each of the first 3 doses of infliximab/adalimumab and one at week 14. Serum levels of vascular endothelial growth factor (VEGF), placental growth factor, angiopoietin 1 (Ang1), angiopoietin 2, and Tie2 were measured using enzyme-linked immunosorbent assay. Results:Patients with IBD had higher VEGF levels than control subjects (511.5 ± 255.6 versus 395.5 ± 256.4; P = 0.05). Patients who achieved remission at the third dose of anti–TNF-alpha had lower VEGF levels at baseline (453.5 ± 250.7 versus 667.5 ± 153.9 pg/mL) and before the second (409.7 ± 217 versus 681.3 ± 350.6 pg/mL) and third (400.5 ± 222.8 versus 630.4 ± 243.1 pg/mL) doses compared with those with no remission (P < 0.05). Ang1 levels decreased before each treatment dose in patients who achieved remission (P < 0.05). High baseline VEGF levels predicted for a poor response to anti–TNF-alpha therapy (area under the receiver operating characteristics curve = 0.8), whereas high Ang1 levels were associated with disease remission (area under the receiver operating characteristics curve = 0.7). Concentrations of angiogenic proteins did not correlate with clinical activity scores. Conclusions:Circulating VEGF and Ang1 levels decrease after anti–TNF-alpha therapy and may predict response to treatment. Whether these changes are a direct effect of anti–TNF-alpha therapy or a sign of disease improvement remains to be elucidated.
Fetal lung volume in congenital diaphragmatic hernia

In a retrospective study of 22 neonates with congenital diaphragmatic hernia, fetal lung volume (FLV) measured by magnetic resonance imaging was associated with survival; the best FLV ratio cut-off to predict mortality was 30% of expected FLV. This study supports a correlation between FLV and the chances of survival.
Build Your Own Quadrotor: Open-Source Projects on Unmanned Aerial Vehicles

This article presents a survey on publicly available open-source projects (OSPs) on quadrotor unmanned aerial vehicles (UAVs). Recently, there has been increasing interest in quadrotor UAVs. Exciting videos have been published on the Internet by many research groups and have attracted much attention from the public [1][7]. Relatively simple structures of quadrotors has promoted interest from academia, UAV industries, and radio-control (RC) hobbyists alike. Unlike conventional helicopters, swashplates, which are prone to failure without constant maintenance, are not required. Furthermore, the diameter of individual rotors can be reduced as a result of the presence of four actuators [8].
Polar-localized NPH3-like proteins regulate polarity and endocytosis of PIN-FORMED auxin efflux carriers

PIN-FORMED (PIN)-dependent auxin transport is essential for plant development and its modulation in response to the environment or endogenous signals. A NON-PHOTOTROPIC HYPOCOTYL 3 (NPH3)-like protein, MACCHI-BOU 4 (MAB4), has been shown to control PIN1 localization during organ formation, but its contribution is limited. The Arabidopsis genome contains four genes, MAB4/ENP/NPY1-LIKE1 (MEL1), MEL2, MEL3 and MEL4, highly homologous to MAB4. Genetic analysis disclosed functional redundancy between MAB4 and MEL genes in regulation of not only organ formation but also of root gravitropism, revealing that NPH3 family proteins have a wider range of functions than previously suspected. Multiple mutants showed severe reduction in PIN abundance and PIN polar localization, leading to defective expression of an auxin responsive marker DR5rev::GFP. Pharmacological analyses and fluorescence recovery after photo-bleaching experiments showed that mel mutations increase PIN2 internalization from the plasma membrane, but affect neither intracellular PIN2 trafficking nor PIN2 lateral diffusion at the plasma membrane. Notably, all MAB4 subfamily proteins show polar localization at the cell periphery in plants. The MAB4 polarity was almost identical to PIN polarity. Our results suggest that the MAB4 subfamily proteins specifically retain PIN proteins in a polarized manner at the plasma membrane, thus controlling directional auxin transport and plant development.
Assessment of heavy metal and radioactivity levels in spinach (Spinacia oleracea) grown at Bahi wetlands in Dodoma Region.

This study reports on the levels of heavy metals and radionuclides in Spinach (Spinacia oleracea) grown in Bahi wetlands in Dodoma Region. The farm soil in Bahi wetland has been reported to contain elevated concentrations of 238 U, 232 Th and 40 K due to the existence of shallow uranium deposit in the area. In this study, spinach (Spinacia oleracea) grown in three zones of Bahi district were analyzed for heavy metals and radioactivity associated with the uranium deposit in the area. The concentrations of elements were determined by Energy Dispersive X-ray Analysis (EDXRF) of Tanzania Atomic Energy Commission, Arusha. The activities of the radionuclides were calculated from their concentration in µg/g. The concentrations of Pb and Cd in all samples were found to be higher than the maximum tolerable limits recommended by Codex 2015. The results show that, the mean activities of 232 Th (10.8 Bq/kg) and 40 K(686.9 Bq/kg)in the samples are lower than the maximum tolerable limits (1000 Bq/kg) recommended by WHO/FAO, yet higher than their activities in samples of spinach collect from a control area. Hence, regular monitoring of heavy metals and radioactivity level in farm soils and agricultural products is recommended Key words: Heavy metals, radioactivity, spinach, Bahi Wetland, EDXRF
Fourier-Resolved Spectroscopy of 4U 1728-34: New Insights into Spectral and Temporal Properties of Low-Mass X-Ray Binaries

Using archival RXTE data we derive the 2-16 keV Fourier-resolved spectra (FRS) of the atoll source 4U 1728-34 in a sequence of its timing states as its low quasi-periodic oscillation (QPO) frequency spans the range between 6 and 94 Hz. The increase in the QPO frequency accompanies a spectral transition of the source from its island to its banana states. The banana-states' FRS are well fitted by a single blackbody component with kT ~ 2-3 keV depending on the source position in the color-color diagram and the Fourier frequency, thus indicating that this spectral component is responsible for the source variability on these timescales. This result is in approximate agreement with similar behavior exhibited by the Z sources, suggesting that, as in that case, the boundary layer—the likely source of the thermal component—is supported by radiation pressure. Furthermore, it is found that the iron line at ~6.6 keV, clearly present in the averaged spectra, not apparent within the limitations of our measurements in the frequency-resolved spectra irrespective of the frequency range. This would indicate that this spectral component exhibits little variability on timescales of 10-2-102 s. In the island state the single blackbody model proved inadequate, particularly notable in our lowest frequency band (0.008-0.8 Hz). An absorbed power law or an additive blackbody plus hard power-law model was required to obtain a satisfactory fit. Statistics do not allow unambiguous discrimination between these possible scenarios.
Bilirubin Promotes De Novo Generation of T Regulatory Cells

We have previously demonstrated that bilirubin administration to the recipient induces tolerance towards islet cell transplants across a complete MHC mismatch in a mouse model. Here we assess the mechanisms of such protection. Bilirubin treatment of recipients improved function of islet allografts by suppressing expressions of proinflammatory and proapoptotic genes in those islets and by increasing Foxp3+ T regulatory (Treg) cells at the site of transplanted islets at various days after transplantation. No prolongation of graft survival was observed in recipients treated with bilirubin when CD4+CD25+ T cells were predepleted from those recipients, indicating that Treg cells are necessary for the protective effect of bilirubin. Adoptive transfer of Treg cells from tolerant mice into Rag1-/- recipients resulted in long-term acceptance of skin allografts in an alloantigen-specific manner, suggesting that Treg cells are sufficient to induce tolerance. In addition, bilirubin treatment promoted de novo generation of Treg cells in Rag1-/- recipients. Thus, bilirubin treatment to the recipients prolongs islet allograft survival via a Treg-dependent manner in which CD4+CD25+ Treg cells are both necessary and sufficient for tolerance induction and graft acceptance. Bilirubin treatment promotes de novo generation of Treg cells that might account for the protective effects of bilirubin given to recipients.
Equilibrium Stock Return Dynamics Under Alternative Rules of Learning About Hidden States

We examine the dynamic properties of equilibrium stock returns in an incomplete information economy in which the agents need to learn the hidden state of the endowment process. We consider both the case of optimal Bayesian learning and suboptimal learning, including near-rational learning, over- or under-confidence, optimism or pessimism, adaptive learning, and limited memory. We find that Bayesian learning can quantitatively explain short-run momentum, long-run mean-reversion, predictability, volatility clustering, and leverage effects in stock returns. Only over-confidence can marginally improve some aspects of the model (add short-run momentum) without substantially deteriorating other aspects. We conclude that the success of the incomplete information model is quite dependent on optimally learning agents.
Transcranial direct current stimulation: a remediation tool for the treatment of childhood congenital dyslexia?

Developmental dyslexia (DD) is a neuropsychological condition that is characterized by the persistent difficulty in learning to read amongst people with typical education, motivation, and normal intelligence (Goswami et al., 2006). On the other hand, a recent study (Callens et al., 2012) has pinpointed that when taking the full cognitive profile of students with DD into account, a quite consistent deficiency on a wide range of tasks, predominantly those involving the speed of processing and retrieval of verbal information from long term memory, can be identified. Improved reading by training programs in Childhood Congenital Dyslexia (CDD) leads rarely to full restitution, even in children submitted to intensive interventions. A major progress in the treatment of this disorder could originate from the development of complementary approaches that may enhance existing remediation programs by providing rehabilitation benefits that are larger and stable over time.
Perceptions of UK Based Customers toward Internet Banking in the United Kingdom

Internet banking is becoming increasingly popular due to convenience and flexibility it offers. Banks are forced to promote online banking services to enhance its operations with reduced cost of operations. This particular research has been conducted to evaluate the customer perceptions towards internet banking in the United Kingdom. A sample of 100 UK based banking customers was selected. The sample selection was made by the convenience sampling technique. Qualitative and quantitative methods have been applied to evaluate the research objectives. Through descriptive analysis of research findings, it has been evaluated that customers perceive internet banking services reliable and secure. However, some of the older respondents did not feel convenient to use internet banking and they might have higher security concerns while using internet banking. The dimensions of privacy, security, convenience and time savings was perceived positively by the customers. The research represents future implications for the internet bankers who can attract more online customers by arranging stronger measures of security, and privacy. The results of this particular research are limited to the sample size and questionnaire made. The future researchers have the opportunity to expand the boundary of knowledge of current research by taking a large and diverse sample.
Mechanics of Materials and Structures TURTLE SHELL AND MAMMAL SKULL RESISTANCE TO FRACTURE DUE TO PREDATOR BITES AND GROUND IMPACT

We investigate the relation between the thickness and diameter of naturally occurring shells, such as the carapaces of turtles and the skulls of mammals. We hypothesize that shells used for different protective functions (for example, protection against headbutting or falling on the ground) will exhibit different power-law trends for shell thickness and diameter. To test this hypothesis, we examine over 600 shells from museum collections with diameters between 1 and 100 cm. Our measurements indicate that eggs, turtle shells, and mammalian skulls exhibit clear and distinct allometric trends. We use a theoretical scaling analysis based on elastic thin shell theory to show that the trends observed are consistent with the corresponding protective functions hypothesized. We thus provide theoretical evidence that shells can be classified by their protective function.
Reality check: perceived versus actual performance of community mammographers.

OBJECTIVE Federal regulations mandate that radiologists receive regular albeit limited feedback regarding their interpretive accuracy in mammography. We sought to determine whether radiologists who regularly receive more extensive feedback can report their actual performance in screening mammography accurately. SUBJECTS AND METHODS Radiologists (n = 105) who routinely interpret screening mammograms in three states (Washington, Colorado, and New Hampshire) completed a mailed survey in 2001. Radiologists were asked to estimate how frequently they recommended additional diagnostic testing after screening mammography and the positive predictive value of their recommendations for biopsy (PPV2). We then used outcomes from 336,128 screening mammography examinations interpreted by the radiologists from 1998 to 2001 to ascertain their true rates of recommendations for diagnostic testing and PPV2. RESULTS Radiologists' self-reported rate of recommending immediate additional imaging (11.1%) exceeded their actual rate (9.1%) (mean difference, 1.9%; 95% confidence interval [CI], 0.9-3.0%). The mean self-reported rate of recommending short-interval follow-up was 6.2%; the true rate was 1.8% (mean difference, 4.3%; 95% CI, 3.6-5.1%). Similarly, the mean self-reported and true rates of recommending immediate biopsy or surgical evaluation were 3.2% and 0.6%, respectively (mean difference, 2.6%; 95% CI, 1.8-3.4%). Conversely, radiologists' mean self-reported PPV2 (18.3%) was significantly less than their mean true PPV2 (27.6%) (mean difference, -9.3%; 95% CI, -12.4% to -6.2%). CONCLUSION Despite regular performance feedback, community radiologists may overestimate their true rates of recommending further evaluation after screening mammography and underestimate their true positive predictive value.
Type 2 diabetes mellitus as risk factor for colorectal cancer

Abstract Colorectal cancer occurs more frequently in patients with type 2 diabetes mellitus. The hyperinsulinemia-hypothesis suggests that elevated levels of insulin and free IGF-1 promote proliferation of colon cells and lead to a survival benefit of transformed cells, ultimately resulting in colorectal cancer. In patients with type 2 diabetes mellitus, epidemiological studies show an increased risk for colorectal cancer and an even higher risk if patients are treated with sulphonylureas or insulin. Moreover, tumour progression at hyperinsulinemia is more rapid and tumour-associated mortality is increased. Colorectal cancer can be avoided by screening. Recommendations for colorectal cancer screening should employ the recent epidemiologic evidence. All patients with type 2 diabetes mellitus should be recommended to undergo colonoscopy before starting insulin therapy, and screening intervals should not exceed 5 years. For this concept, a review of the evidence is presented, and a screening algorithm for colorectal cancer in patients with type 2 diabetes mellitus is proposed.
A human-centered approach to robot gesture based communication within collaborative working processes

The increasing ability of industrial robots to perform complex tasks in collaboration with humans requires more capable ways of communication and interaction. Traditional systems use separate interfaces such as touchscreens or control panels in order to operate the robot, or to communicate its state and prospective actions to the user. Transferring human communication, such as gestures to technical non-humanoid robots, creates various opportunities for more intuitive human-robot-interaction. Interaction shall no longer require a separate interface such as a control panel. Instead, it should take place directly between human and robot. To explore intuitive interaction, we identified gestures that are relevant for co-working tasks from human observations. Based on a decomposition approach we transferred them to robotic systems of increasing abstraction and experimentally evaluated how well these gestures are recognized by humans. We created a human-robot interaction use-case in order to perform the task of handling dangerous liquid. Results indicate that several gestures are well perceived when displayed with context information regarding the task.
Context Constrained-Generalized Posterior Probability for Verifying Phone Transcriptions

A new statistical confidence measure, Context ConstrainedGeneralized Posterior probability (CC-GPP), is proposed for verifying phone transcriptions in speech databases. Different from generalized posterior probability (GPP), CC-GPP is computed by considering string hypotheses that bear a focused phone with partially matched left and right contexts. Parameters used for CC-GPP include context window length, a minimal number of matched context phones, and verification thresholds. They are determined by minimizing verification errors in a development set. Evaluated on a test set of 500 sentences that consist of 2.1% phone errors, CCGPP achieves 99.6% accuracy and 78.7% recall when 90% of the phones are accepted.