Miracle-dz/UniFAR-FTUs huggingface dataset:
Expression, purification, and analysis of unknown translation factors from Escherichia coli: A synthesis approach

New approaches are currently being developed to expose biochemistry and molecular biology undergraduates to a more interactive learning environment. Here, we propose a unique project‐based laboratory module, which incorporates exposure to biophysical chemistry approaches to address problems in protein chemistry. Each of the experiments described herein contributes to the stepwise process of isolating, identifying, and analyzing a protein involved in a central biological process, prokaryotic translation. Students are provided with expression plasmids that harbor an unknown translation factor, and it is their charge to complete a series of experiments that will allow them to develop hypotheses for discovering the identity of their unknown (from a list of potential candidates). Subsequent to the identification of their unknown translation factor, a series of protein unfolding exercises are performed employing circular dichroism and fluorescence spectroscopies, allowing students to directly calculate thermodynamic parameters centered around determining the equilibrium constant for unfolding as a function of denaturant (temperature or chemical). The conclusion of this multi‐part laboratory exercise consists of both oral and written presentations, emphasizing synthesis of the roles of each translation factor during the stepwise process of translation.
MRI evidence of past cerebral microbleeds in a healthy elderly population

Background: Incidental foci of signal loss suggestive of past microbleeds are a frequent finding on gradient-echo T2*-weighted MRI of patients with nontraumatic intracerebral hemorrhage and have been associated with bleeding-prone microangiopathy. If and to what extent such lesions may also occur in the normal population is unclear. Objective: To determine focal hypointensities in asymptomatic elderly individuals and their relation to other clinical and morphologic variables. Methods: T2*-weighted MRI of the brain was performed in a consecutive series of 280 participants (mean age 60 years, range 44 to 79) of the Austrian Stroke Prevention Study. This cohort consisted of randomly selected individuals without history or signs of neuropsychiatric disorder. Results: Past microbleeds ranging from one to five foci of signal loss were seen in 18 (6.4%) individuals. They were strongly associated with higher age, hypertension, and lacunes (p < 0.001), and extensive white matter damage was more frequently noted (p = 0.02). Hypertension was present in all individuals with focal hypointensities in the basal ganglia and infratentorially but in only 5 of 10 volunteers with microbleeds limited to cortico-subcortical sites (p = 0.04). Conclusions: MRI evidence of past microbleeds may be found even in neurologically normal elderly individuals and is related, but not restricted, to other indicators of small vessel disease. The predictive potential of this finding regarding the risk of intracerebral bleeding requires further investigation.
Nutrition education intervention improves vegetable-related attitude, self-efficacy, preference, and knowledge of fourth-grade students.

BACKGROUND Impact of a classroom-based, standardized intervention to address limited vegetable consumption of fourth graders was assessed. METHODS A 4-lesson, vegetable-focused intervention, revised from extant materials was repurposed for Pennsylvania fourth graders with lessons aligned with state academic standards. A reliability-tested survey was modified, then examined for face and content validity and test-retest reliability. Lessons and evaluation materials were modified through an iterative testing process with educator feedback. A nonequivalent control group design was stratified by local Supplemental Nutrition Assistance Program Education (SNAP-Ed) partnering organizations with random assignment of participating elementary schools as control (N = 68) or intervention (N = 72) treatments. Independent t-tests compared control and intervention group changes. A mixed effects model was created to account for classroom effects from the nested sampling method of selecting classrooms within SNAP-Ed partnering organizations. General linear model univariate analyses of variance were conducted to assess intervention effects considering gender, and food preparation/cooking experience. RESULTS During a 3- to 5-week time frame, 57 intervention classrooms (N = 1047 students) and 51 control classrooms (N = 890) completed pre- and post-testing. Intervention students improved in vegetable-related attitude, self-efficacy, preference, and knowledge scores (p < .001). For example, intervention vegetable preference increased 1.56 ± 5.80 points; control group mean increase was only 0.08 ± 4.82 points. Group differences in score changes were not affected by gender or interactions between gender and food preparation/cooking experience with family. CONCLUSIONS A defined intervention delivered in a SNAP-Ed setting can positively impact mediators associated with vegetable intake for fourth-grade students.
Structure of two retrons of Escherichia coli and their common chromosomal insertion site

It has been shown that certain strains of myxobacteria and of Escherichia coli have a genetic element encoding a reverse transcriptase (RT). This element, called a ‘retron’, produces a covalently linked RNA–DNA compound (msDNA–RNA). Here, I report the complete nucleotide sequence of retron EC‐86, the retron in E. coli B, together with its flanking regions. Retron EC‐86 contains genes for msDNA–RNA (msd, and msr), a gene for RT (ret) and a gene for an open reading frame whose function is unknown. The upstream junction is composed of the sequence GCGCGCGC, but there are no direct or inverted repeats at the retron–host junctions. It is also shown that another retron of E. coli, EC‐67, which was isolated originally from the clinical strain CL1 and was later found to be present also in a clinical E. coli isolate from Brazil, is inserted at the same chromosomal site as retron EC‐66. Retron EC‐67 contains only msd, msr, and ret. I suggest that these two retrons were independently inserted into the same site of their host strains via a novel mechanism of integration.
Anthrax Lethal Toxin Increases Superoxide Production in Murine Neutrophils via Differential Effects on MAPK Signaling Pathways1

The combination of lethal factor and its receptor-binding partner, protective Ag, is termed lethal toxin (LT) and has critical pathogenic activity during infection with Bacillus anthracis. We herein report that anthrax LT binds and enters murine neutrophils, leading to the cleavage of mitogen-activated protein kinase kinase/MEK/MAPKK 1–4 and 6, but not mitogen-activated protein kinase kinase 5 and 7. Anthrax LT treatment of neutrophils disrupts signaling to downstream MAPK targets in response to TLR stimulation. Following anthrax LT treatment, ERK family and p38 phosphorylation are nearly completely blocked, but signaling to JNK family members persists in vitro and ex vivo. In contrast to previous reports involving human neutrophils, anthrax LT treatment of murine neutrophils increases their production of superoxide in response to PMA or TLR stimulation in vitro or ex vivo. Although this enhanced superoxide production correlates with effects due to the LT-induced blockade of ERK signaling, it requires JNK signaling that remains largely intact despite the activity of anthrax LT. These findings reveal a previously unrecognized mechanism through which anthrax LT supports a critical proinflammatory response of murine neutrophils.
Growth-differentiation factor 15 as predictor of mortality in acute reperfused ST-elevation myocardial infarction: insights from cardiovascular magnetic resonance

Objective Growth-differentiation factor 15 (GDF-15), a stress-responsive member of the transforming growth factor beta cytokine superfamily, has emerged as a biomarker of increased mortality in cardiovascular disease. However, the exact pathophysiological mechanisms of GDF-15 in the cardiovascular system and in acute ST-elevation myocardial infarction (STEMI) are not well defined. The aim of this study was to determine the relation between GDF-15 and myocardial damage assessed by cardiovascular magnetic resonance (CMR) imaging and to evaluate the prognostic value of GDF-15 in a high-risk STEMI population exclusively reperfused by primary angioplasty. Design, setting, patients GDF-15 concentrations were determined by an ELISA in 238 consecutive patients undergoing primary angioplasty in STEMI less than 12 h after symptom onset. Patients were categorised into two groups defined by the median GDF-15 value on admission. CMR was performed 3 days (IQR 2–4) after infarction for assessment of infarct size, myocardial salvage and microvascular obstruction. The primary clinical endpoint was mortality within 6 months after the index event. Results Elevated GDF-15 concentrations over and above the median on admission were a strong predictor of mortality (19 vs one death, p<0.001) and major adverse cardiac events (27 vs nine events, p=0.001) at 6 months follow-up. Myocardial salvage was an inverse multivariable predictor of GDF-15 concentrations. Conclusions GDF-15 on admission is a strong predictor of mortality in patients with STEMI reperfused by primary angioplasty, which is associated with decreased myocardial salvage and subsequent adverse clinical outcome. Clinical trail registration number http://www.clinicaltrials. gov/ NCT00463749.
Affordance-based 3D feature for generic object recognition

Techniques for generic object recognition, which targets everyday objects such as cups and spoons, and techniques for approach vector estimation (e.g. estimating grasp position), which are needed for carrying out tasks involving everyday objects, are considered necessary for the perceptual system of service robots. In this research, we design feature for generic object recognition so they can also be applied to approach vector estimation. To carry out tasks involving everyday objects, estimating the function of the target object is critical. Also, as the function of holding liquid is found in all cups, so a function is shared in each type (class) of everyday objects. We thus propose a generic object recognition method that can estimate the approach vector by expressing an object’s function as feature. In a test of the generic object recognition of everyday objects, we confirmed that our proposed method had a 92% recognition rate. This rate was 11% higher than the mainstream generic object recognition technique of using convolutional neural network (CNN).
An analytical method of channel estimation error for multiple antennas system

In the flat-fading channel (narrow bandwidth channel), the channel coefficients are generally obtained by sending training sequences or pilot signals in the transmitter and estimating them in the receiver. Therefore, some estimation errors are induced in this process. In the paper, we construct a kind of model of channel coefficient estimation error according to the general theory of multiple antennas wireless link, and on the basis of analyzing the statistical characteristics of channel estimation error, and we derive the Cramer-Rao bound of the above estimation error by virtue of the model. It is found that the Cramer-Rao bound given in (V. Tarokh, et al., 2000) is a special case of our result given in the paper. As the ratio of signal to noise is large enough, the former is derived from the latter. Space-time block coding (STBC) is taken as an example, and the loss of system performance is simulated in the presence of channel coefficient estimation error. The simulation results show that the loss of system performance of STBC caused by the channel coefficient estimation error is less than 1 dB, and within the Cramer-Rao bound of estimation error, less than 0.5 dB, which is the minimum in the losses of system performance caused by all of the channel coefficient estimation errors. This conclusion is in accord with the analytical result in theory.
Assessment of geriatric predictors of adherence to Zoledronic acid treatment for osteoporosis: a prospective follow-up study

ABSTRACT Objectives Discontinuation of bisphosphonate treatment remains high even with the long acting parenteral options. Whether there are some unidentified causes of noncompliance more specific to aged individuals is unknown. The aim of this study was to investigate baseline predictors of adherence to Zoledronic acid (ZOL) infusions among non-demented older adults with osteoporosis. Methods Patients aged ≥ 65 years who received a first ever ZOL infusion for osteoporosis were prospectively enrolled. Risk factors for osteoporosis and fractures, comorbidities, geriatric assessment measures, including depression, and anticholinergic burden were determined at baseline. Adherence was defined as taking the next ZOL infusion at 12 months. Results A total of 187 participants were included (mean age: 75.7 ± 6.3 years, female: 77.5%). Adherence to the next ZOL infusion was 66.8% (n = 125). Non-adherent participants (n = 62, 33.2%) had significantly higher frequency of historical height decrease and depression at baseline. Poor adherence was associated with height decrease, presence of depression, and higher anticholinergic burden in univariate analysis. After adjustment for relevant confounders, fragility fracture history (OR: 0.38, 95%CI: 0.17–0.86, p = 0.020), depression (OR: 0.32, 95%CI: 0.12–0.82, p = 0.018), and higher anticholinergic burden (OR: 0.67, 95%CI: 0.49–0.93, p = 0.017) were the predictors of lower adherence to ZOL infusion. Conclusions The rate of adherence to the next ZOL infusion was still suboptimal among older women and men in this study. Past osteoporotic fractures, depression, and higher anticholinergic drug burden predicted poor ZOL adherence. It was a novel finding that drug-related anticholinergic side effects adversely influenced adherence to another medication without anticholinergic properties.
Warped-Linear Models for Time Series Classification

This article proposes and studies warped-linear models for time series classification. The proposed models are time-warp invariant analogues of linear models. Their construction is in line with time series averaging and extensions of k-means and learning vector quantization to dynamic time warping (DTW) spaces. The main theoretical result is that warped-linear models correspond to polyhedral classifiers in Euclidean spaces. This result simplifies the analysis of time-warp invariant models by reducing to max-linear functions. We exploit this relationship and derive solutions to the label-dependency problem and the problem of learning warped-linear models. Empirical results on time series classification suggest that warped-linear functions better trade solution quality against computation time than nearest-neighbor and prototype-based methods.
Financial crisis early-warning based on support vector machine

Analyzing the principle of typical financial crisis early-warning model, this study summarizes the limitations of them and their requirement of variance. An empirical research is carried out on how to sample the Chinese listed companies of A-stock market in Shanghai and Shenzhen, and how to determine the core parameters of support vector machine (SVM) as well. This research also studies the predicting accuracy in 1-3 years and the performance on condition that some data are missing. At last the contrastivAnalyzing the principle of typical financial crisis early-warning model, this study summarizes the limitations of them and their requirement of variance. An empirical research is carried out on how to sample the Chinese listed companies of A-stock market in Shanghai and Shenzhen, and how to determine the core parameters of support vector machine (SVM) as well. This research also studies the predicting accuracy in 1-3 years and the performance on condition that some data are missing. At last the contrastive analysis is made between SVM model and the Logistic model. Our experimentation results demonstrate that SVM outperforms the logistic model and SVM also has a sound accuracy under the data missing.e analysis is made between SVM model and the Logistic model. Our experimentation results demonstrate that SVM outperforms the logistic model and SVM also has a sound accuracy under the data missing.
Conserved Cytoplasmic Loops Are Important for both the Transport and Chemotaxis Functions of PcaK, a Protein fromPseudomonas putida with 12 Membrane-Spanning Regions

ABSTRACT Chemotaxis to the aromatic acid 4-hydroxybenzoate (4-HBA) byPseudomonas putida is mediated by PcaK, a membrane-bound protein that also functions as a 4-HBA transporter. PcaK belongs to the major facilitator superfamily (MFS) of transport proteins, none of which have so far been implicated in chemotaxis. Work with two well-studied MFS transporters, LacY (the lactose permease) and TetA (a tetracycline efflux protein), has revealed two stretches of amino acids located between the second and third (2-3 loop) and the eighth and ninth (8-9 loop) transmembrane regions that are required for substrate transport. These sequences are conserved among most MFS transporters, including PcaK. To determine if PcaK has functional requirements similar to those of other MFS transport proteins and to analyze the relationship between the transport and chemotaxis functions of PcaK, we generated strains with mutations in amino acid residues located in the 2-3 and 8-9 loops of PcaK. The mutant proteins were analyzed in 4-HBA transport and chemotaxis assays. Cells expressing mutant PcaK proteins had a range of phenotypes. Some transported at wild-type levels, while others were partially or completely defective in 4-HBA transport. An aspartate residue in the 8-9 loop that has no counterpart in LacY and TetA, but is conserved among members of the aromatic acid/H+ symporter family of the MFS, was found to be critical for 4-HBA transport. These results indicate that conserved amino acids in the 2-3 and 8-9 loops of PcaK are required for 4-HBA transport. Amino acid changes that decreased 4-HBA transport also caused a decrease in 4-HBA chemotaxis, but the effect on chemotaxis was sometimes slightly more severe. The requirement of PcaK for both 4-HBA transport and chemotaxis demonstrates that P. putida has a chemoreceptor that differs from the classical chemoreceptors described for Escherichia coli and Salmonella typhimurium.
Loss of Transcription Factor Nuclear Factor-Erythroid 2 (NF-E2) p45-related Factor-2 (Nrf2) Leads to Dysregulation of Immune Functions, Redox Homeostasis, and Intracellular Signaling in Dendritic Cells*

Background: Nrf2 has been implicated in regulating immune cell signaling and function. Results: Nrf2-deficient murine DCs exhibit enhanced maturation phenotype, increased ROS levels with dysregulation of antigen uptake capabilities, and altered intracellular signaling. Conclusion: Nrf2 regulates DC intracellular redox and immune function. Significance: Defining the role of Nrf2 in DC biology underpins development of potential Nrf2 targeted immunotherapeutics. Dendritic cells (DCs) are critical mediators of immunity and immune tolerance by orchestrating multiple aspects of T cell activation and function. Immature DCs (iDCs) expressing low levels of co-stimulatory receptors are highly efficient at antigen capture but are poor activators of T cells. Maturation of DCs is associated with increased expression of co-stimulatory molecules. Co-stimulatory receptor gene expression is regulated by intracellular redox, NF-κB, and MAPK pathways and by histone deacetylase (HDAC) activity. The transcription factor, Nrf2, is important for maintaining intracellular glutathione (GSH) levels and redox homeostasis and has been implicated in modulating DC co-stimulatory receptor expression. It is unclear whether Nrf2 mediates this effect by GSH-dependent mechanisms and whether it influences DC signaling pathways. Using bone marrow-derived iDCs from Nrf2+/+ and Nrf2−/− mice, we demonstrate that Nrf2−/− iDCs have lower basal GSH levels, enhanced co-stimulatory receptor expression, impaired phagocytic functions, and increased antigen-specific CD8 T cell stimulation capacity. Interestingly, lowering GSH levels in Nrf2+/+ iDCs did not recapitulate the Nrf2−/− iDC phenotype. Loss of Nrf2 resulted in elevated basal levels of reactive oxygen species but did not affect basal NF-κB activity or p38 MAPK phosphorylation. Using pharmacological inhibitors, we demonstrate that enhanced co-stimulatory receptor phenotype of Nrf2−/− iDC does not require ERK activity but is dependent on HDAC activity, indicating a potential interaction between Nrf2 function and HDAC. These results suggest that Nrf2 activity is required to counter rises in intracellular reactive oxygen species and to regulate pathways that control DC co-stimulatory receptor expression.
Evaluation of a group mobility model based on bird flocking for mobile Ad Hoc networks

We evaluate a group mobility model based on bird flocking in comparison with other existing group mobility models for mobile ad hoc networks in this paper. This group mobility model is based on the behavior of a flock of birds which is interpreted by the basic laws of swarming namely cohesion, separation and alignment. While measuring the performance of this group mobility model using AODV routing protocol, the metrics such as average degree of spatial dependence and link duration are proved to be better than that of the existing group mobility models such as RPGM (Reference Point Group mobility model), Nomadic Community model and Pursue mobility model and the Random Waypoint model.
Experimenter-Made vs Subject-Made Mnemonics in Paired-Associate Learning

Two groups of Ss learned 42 pairs of words as a standard paired-associates learning task. One group was provided with mnemonic devices as an aid in learning the pairs and the other group was told to make up their own mnemonic aids. The difference in the number of pairs learned was not significant. Correlation between recall scores and Scholastic Aptitude Test verbal scores approached 0. There was a high correlation between the number of Ss who recalled a given pair correctly in the two groups. This suggests that certain pairs of words are easier to learn than others, regardless of whether S is given a mnemonic aid or has to contrive his own.
College Students' Sexual Consent Communication And Perceptions of Sexual Double Standards: A Qualitative Investigation

CONTEXT Affirmative consent standards adopted by colleges and universities are meant to decrease miscommunication that may lead to sexual assault. However, they may not take into account sociocultural factors that influence consent. In particular, the role of gender norms needs to be better understood. METHODS In-depth interviews about college students' sexual activity, including sexual consent communication, were conducted with 17 female and 13 male students at a large southern university during the spring 2013 semester. The interview protocol and analyses were guided by Carspecken's critical qualitative methodology, which seeks to understand both participants' explicit statements and implied underlying meanings and values. Themes and subthemes were identified through inductive analyses. RESULTS Two overarching themes emerged: Students perceived a sexual double standard, and males viewed obtaining sex as a conquest. Subthemes related to the first theme reflected endorsement of traditional views of women's sexuality (the notions that "good girls" do not have sex, that women should privilege men's sexual needs over their own and that women "owe" men sex once men have "worked" for it). Subthemes related to the second theme reflected males' beliefs that sex is a commodity that pits women and men against one another, and that women can be "convinced" to have sex if they initially refuse. CONCLUSIONS College students' consent communication may be influenced by gender norms that challenge assumptions of affirmative consent standards. Cultural shifts in students' views of sexuality may be necessary for affirmative consent policies to be effective.