Miracle-dz/UniFAR-FTUs huggingface dataset:
A Homeostatic Shift Facilitates Endoplasmic Reticulum Proteostasis through Transcriptional Integration of Proteostatic Stress Response Pathways

ABSTRACT Eukaryotic cells maintain protein homeostasis through the activity of multiple basal and inducible systems, which function in concert to allow cells to adapt to a wide range of environmental conditions. Although the transcriptional programs regulating individual pathways have been studied in detail, it is not known how the different pathways are transcriptionally integrated such that a deficiency in one pathway can be compensated by a change in an auxiliary response. One such pathway that plays an essential role in many proteostasis responses is the ubiquitin-proteasome system, which functions to degrade damaged, unfolded, or short half-life proteins. Transcriptional regulation of the proteasome is mediated by the transcription factor Nrf1. Using a conditional knockout mouse model, we found that Nrf1 regulates protein homeostasis in the endoplasmic reticulum (ER) through transcriptional regulation of the ER stress sensor ATF6. In Nrf1 conditional-knockout mice, a reduction in proteasome activity is accompanied by an ATF6-dependent downregulation of the endoplasmic reticulum-associated degradation machinery, which reduces the substrate burden on the proteasome. This indicates that Nrf1 regulates a homeostatic shift through which proteostasis in the endoplasmic reticulum and cytoplasm are coregulated based on a cell's ability to degrade proteins.
Optimization of an hydroxyapatite adhesion assay for Streptococcus sanguis

Previous studies have compared the adhesion of [3H]thymidine-labeled Streptococcus sanguis to saliva-coated hydroxyapatite (SHA) and buffer-coated hydroxyapatite (HA) beads. Although the hypotonic buffer used in these assays was adjusted to simulate saliva, it does not necessarily provide the optimal parameters for the quantitative estimate of adhesion under in vitro conditions. Optimization is necessary to provide the maximum sensitivity of the assay for detecting the effects of various salivas as well as for quantitating the effect of environmental growth conditions on the adhesion of S. sanguis to SHA and HA. A major distinction between the adhesion of S. sanguis to SHA and HA was observed when the bacterial concentration was varied. At high cell concentrations, the number of cells adhering to SHA was twice the number adhering to HA. Such differences were not detected at low cell concentrations. The optimal pH for the adsorption to both SHA and HA was 6. Changes in the ionic strength or addition of mono- or divalent cations found in saliva had little effect on adhesion to HA. In contrast, high concentrations of monovalent cations inhibited adhesion to SHA. Anions such as carbonate, chloride, and sulfate did not have specific effects on adhesion, whereas acetate inhibited adhesion to both SHA and HA. Fluoride inhibited adhesion to both SHA and HA, suggesting an interaction between fluoride and hydroxyapatite. These results indicated that 2 mM phosphate buffer at a pH of 6 containing 5 mM KCl and 1 mM CaCl2 was the optimal buffer for studying the in vitro adhesion of S. sanguis to SHA.
Dispersal of NK homeobox gene clusters in amphioxus and humans

The Drosophila melanogaster genome has six physically clustered NK-related homeobox genes in just 180 kb. Here we show that the NK homeobox gene cluster was an ancient feature of bilaterian animal genomes, but has been secondarily split in chordate ancestry. The NK homeobox gene clusters of amphioxus and vertebrates are each split and dispersed at two equivalent intergenic positions. From the ancestral NK gene cluster, only the Tlx–Lbx and NK3–NK4 linkages have been retained in chordates. This evolutionary pattern is in marked contrast to the Hox and ParaHox gene clusters, which are compact in amphioxus and vertebrates, but have been disrupted in Drosophila.
Microbiological risk from minimally processed packaged salads in the Dutch food chain.

The objective of this study was to evaluate the microbial hazard associated with the consumption of mixed salads produced under standard conditions. The presence of Salmonella, Campylobacter spp. , and Escherichia coli O157 in the Dutch production chain of mixed salads was determined. Microbial prevalence and concentration data from a microbiological surveillance study were used as inputs for the quantitative microbial risk assessment. Chain logistics, production figures, and consumption patterns were combined with the survey data for the risk assessment chain approach. The results of the sample analysis were used to track events from contamination through human illness. Wide 95% confidence intervals around the mean were found for estimated annual numbers of illnesses resulting from the consumption of mixed salads contaminated with Salmonella Typhimurium DT104 (0 to 10,300 cases), Campylobacter spp. (0 to 92,000 cases), or E. coli (0 to 800 cases). The main sources of uncertainty are the lack of decontamination data (i.e., produce washing during processing) and an appropriate dose-response relationship.
The Infrared Imaging Spectrograph (IRIS) for TMT: the science case

The InfraRed Imaging Spectrograph (IRIS) is a first-light instrument being designed for the Thirty Meter Telescope (TMT). IRIS is a combination of an imager that will cover a 16. 4 field of view at the diffraction limit of TMT (4 mas sampling), and an integral field unit spectrograph that will sample objects at 4-50 mas scales. IRIS will open up new areas of observational parameter space, allowing major progress in diverse fields of astronomy. We present the science case and resulting requirements for the performance of IRIS. Ultimately, the spectrograph will enable very well-resolved and sensitive studies of the kinematics and internal chemical abundances of high-redshift galaxies, shedding light on many scenarios for the evolution of galaxies at early times. With unprecedented imaging and spectroscopy of exoplanets, IRIS will allow detailed exploration of a range of planetary systems that are inaccessible with current technology. By revealing details about resolved stellar populations in nearby galaxies, it will directly probe the formation of systems like our own Milky Way. Because it will be possible to directly characterize the stellar initial mass function in many environments and in galaxies outside of the the Milky Way, IRIS will enable a greater understanding of whether stars form differently in diverse conditions. IRIS will reveal detailed kinematics in the centers of low-mass galaxies, allowing a test of black hole formation scenarios. Finally, it will revolutionize the characterization of reionization and the first galaxies to form in the universe.
A Single Point Acupuncture Treatment at Large Intestine Meridian: A Randomized Controlled Trial in Acute Tonsillitis and Pharyngitis

ObjectivesOne out of 4 patients visiting a general practitioner reports of a sore throat associated with pain on swallowing. This study was established to examine the immediate pain alleviating effect of a single point acupuncture treatment applied to the large intestine meridian of patients with sore throat. Patients and MethodsSixty patients with acute tonsillitis and pharyngitis were enrolled in this randomized placebo-controlled trial. They either received acupuncture, or sham laser acupuncture, directed to the large intestine meridian section between acupuncture points LI 8 and LI 10. The main outcome measure was the change of pain intensity on swallowing a sip of water evaluated by a visual analog scale 15 minutes after treatment. A credibility assessment regarding the respective treatment was performed. ResultsThe pain intensity for the acupuncture group before and immediately after therapy was 5.6±2.8 and 3.0±3.0, and for the sham group 5.6±2.5 and 3.8±2.5, respectively. Despite the articulation of a more pronounced improvement among the acupuncture group, there was no significant difference between groups (Δ=0.9, confidence interval: −0.2-2.0; P=0.12; analysis of covariance). Patients' satisfaction was high in both treatment groups. The study was prematurely terminated due to a subsequent lack of suitable patients. DiscussionA single acupuncture treatment applied to a selected area of the large intestine meridian was no more effective in the alleviation of pain associated with clinical sore throat than sham laser acupuncture applied to the same area. Hence, clinically relevant improvement could be achieved. Pain alleviation might partly be due to the intense palpation of the large intestine meridian. The benefit of a comprehensive acupuncture treatment protocol in this condition should be subject to further trials.
Architecture-Based IT Valuation Supporting portfolio management and investment decisions

This paper outlines our architecture-based approach to IT valuation and portfolio management. It sketches how different valuation criteria can be combined and linked to architecture models, and how a first part of this approach is implemented in an architecture modeling tool. In this manner, the value (costs & benefits) of different elements in the architecture can be computed and attributed to the various goals of the organization, thus supporting well-informed IT investment decisions.
The impact of transformational leadership on organizational innovation moderated by organizational culture

This paper attempts to examine the impact of transformational leadership on innovation in the organizational level by looking at moderating role of organizational culture. Based on the literature in many developing countries, innovation is omitted and generally not considered as precedence in organizations though the ability to innovate is accepted as a key factor to future competitiveness of the firms. Previous studies show that, innovation may influenced by various factors and leadership can be one of the most important one. Leadership appears to be an important antecedent of the organizations ability to innovate and transformational leadership style seems to be more appropriate to explore and foster innovation activities. Therefore, this study is based on a critical review of leadership, focusing on transformational leadership theory and on the importance of innovation in the organization introduces a conceptual framework, in order to find the impact of leadership on innovation. The researchers will propose methods for data collection and measuring variables. This study will provide an insight for organizational leaders to develop a suitable leadership style and play an effective role in stimulating innovation and improving organization's capacities to compete and innovate in the challenging business environment.
Coaching: An Approach to Efficiently and Intuitively Create Humanoid Robot Behaviors

The advances in humanoid robots in recent years have given researchers new opportunities to study and create algorithms for generating humanoid behaviors. Not surprisingly, most approaches for creating or modifying behaviors for complex humanoids require specialized knowledge and a large amount of work. Our aim is to provide an alternative, intuitive way to program humanoid behavior. To do this, we examine human-to-human skill transfer, specifically coaching, and adapt it to the humanoid setting. We enable a real-time scenario where a person, acting as a coach, interactively directs humanoid behavior to a desired outcome. This tightly coupled interaction between a person and a humanoid allows efficient, directed learning of new behaviors, where behavior characteristics can be modified on-demand. Communication is realized through demonstration and a coaching vocabulary, and changes are effected by transformation functions acting in the behavior domain
A Study of Local Approximations in Information Theory

The intractability of many information theoretic problems arises from the meaningful but nonlinear definition of Kullback-Leibler (KL) divergence between two probability distributions. Local information theory addresses this issue by assuming all distributions of interest are perturbations of certain reference distributions, and then approximating KL divergence with a squared weighted Euclidean distance, thereby linearizing such problems. We show that large classes of statistical divergence measures, such as f-divergences and Bregman divergences, can be approximated in an analogous manner to local metrics which are very similar in form. We then capture the cost of making local approximations of KL divergence instead of using its global value. This is achieved by appropriately bounding the tightness of the Data Processing Inequality in the local and global scenarios. This task turns out to be equivalent to bounding the chordal slope of the hypercontractivity ribbon at infinity and the Hirschfeld-Gebelein-Renyi maximal correlation with each other. We derive such bounds for the discrete and finite, as well as the Gaussian regimes. An application of the local approximation technique is in understanding the large deviation behavior of sources and channels. We elucidate a source-channel decomposition of the large deviation characteristics of i.i. d. sources going through discrete memoryless channels. This is used to derive an additive Gaussian noise channel model for the local perturbations of probability distributions. We next shift our focus to infinite alphabet channels instead of discrete and finite channels. On this front, existing literature has demonstrated that the singular vectors of additive white Gaussian noise channels are Hermite polynomials, and the singular vectors of Poisson channels are Laguerre polynomials. We characterize the set of infinite alphabet channels whose singular value decompositions produce singular vectors that are orthogonal polynomials by providing equivalent conditions on the conditional moments. In doing so, we also unveil the elegant relationship between certain natural exponential families with quadratic variance functions, their conjugate priors, and their corresponding orthogonal polynomial singular vectors. Finally, we propose various related directions for future research in the hope that our work will beget more research concerning local approximation methods in information theory.
The low molecular weight heparin Enoxaparin inhibits the consumption of factor VII and prothrombin activation in vivo associated with elective knee replacement surgery

Summary. Patients over 40 years of age who undergo elective orthopaedic surgery have a relatively high risk for developing post‐surgical deep vein thrombosis (DVT). Prophylactic use of heparin or low molecular weight heparins can reduce the incidence of post‐operative DVT by up to 80%. It is not known whether prophylaxis is achieved by inhibition of prothrombin activation or catalysis of thrombin inhibition in vivo. We determined the changes in concentrations of factor VII zymogen and thrombin‐antithrombin III (the latter as an index of prothrombin activation) in the plasmas of 129 patients randomized to receive two daily subcutaneous injections of placebo or 30 mg of Enoxaparin after elective knee surgery. Enoxaparin reduced the frequency of post‐surgical DVT by 70%. The concentration of factor VII zymogen had decreased by ∼50% within 24 h after the knee surgery, followed by a gradual increase to near pre‐surgical values. Additionally, post‐Enoxaparin plasmas had statistically significant higher concentrations of factor VII zymogen than post‐placebo plasmas. Post‐Enoxaparin plasmas had significantly lower concentrations of endogenous thrombin‐antithrombin III than comparable post‐placebo plasmas. Finally, post‐Enoxaparin plasmas inactivated exogenous factor Xa and thrombin more effectively than comparable post‐placebo plasmas. As Enoxaparin moderated the generation of endogenous thrombin‐antithrombin III after elective knee surgery, inhibition of prothrombin activation in vivo by Enoxaparin may be important for its prophylactic antithrombotic effect.
Developing prototype of web-based home controlling for teaching trainer

High mobility of people in doing their activities needs a device, which could control electrical appliances from a distance. Connecting a computer over the Internet could realize a distant control system to monitor and control those appliances. This system could also attract students to study the system furthermore. This paper proposed a system, which could be used as a teaching media to introduce a simple distant control system. The systems should be evaluated in both of system working and users' responds when it is used as a teaching media. The results showed that even the speed of uploading and downloading was low, the system still can be updated the current situations. Furthermore, the prototype of web-based home controlling was suitable for a teaching trainer considering the validation result of material and media experts, and also implementation in a real class.
The Chicken Leukocyte Receptor Complex: A Highly Diverse Multigene Family Encoding at Least Six Structurally Distinct Receptor Types1

The chicken Ig-like receptors (CHIR) have been described as two Ig domain molecules with long cytoplasmic tails containing inhibitory motifs. In this study, we demonstrate that CHIR form a large family, with multiple members showing great sequence variability among members as well as a great diversity in domain organization and properties of the transmembrane and cytoplasmic segments. We characterize various novel receptor types with motifs indicative of inhibitory, activating, or both functions. In addition to the inhibitory receptors with two ITIM, receptors with a single immunoreceptor tyrosine-based switch motif or receptors lacking a cytoplasmic domain were isolated. Activating receptors with a short cytoplasmic domain and a transmembrane arginine assembled with the newly identified chicken FcεRIγ chain. Three bifunctional receptor types were characterized composed of one or two C2-type Ig-like domains, a transmembrane region with a positively charged residue and combinations of cytoplasmic motifs such as ITIM, immunoreceptor tyrosine-based switch motif, and YXXM. RT-PCR revealed distinct expression patterns of individual CHIR. All receptor types shared a conserved genomic architecture, and in single Ig domain receptors a pseudoexon replaced the second Ig exon. Southern blot analyses with probes specific for the Ig1 domain were indicative of a large multigene family. Of 103 sequences from the Ig1 domain of a single animal, 41 unique sequences were obtained that displayed extensive variability within restricted Ig regions. Fluorescence in situ hybridization localized the CHIR gene cluster to microchromosome 31 and identified this region as orthologous to the human leukocyte receptor complex.
Effectiveness of multiplex ligation-dependent probe amplification assay used for detecting deletion of Prader-Willi syndrome.

OBJECTIVE Prader-Willi syndrome (PWS) is characterized by severe hypotonia and feeding difficulties in early infancy, followed by excessive eating and gradual development of morbid obesity in later infancy or early childhood. Patients with PWS are often too young to manifest sufficient features or have atypical findings, making genetic testing important to confirm the diagnosis of PWS. Approximately 99% of patients with PWS have a diagnostic abnormality in the parent-specific methylation imprint within the Prader-Willi critical region (PWCR) at chromosome 15q11.2-q12. Of them, 70% have a paternal deletion; 25% have a maternal uniparental disomy (UPD); and <5% have a mutation in the imprinting center. METHODS Current techniques can identify a diagnostic abnormality, such as paternal deletion or maternal UPD for most of patients with PWS, but they are labor-intensive and cost-expensive. Multiplex ligation-dependent probe amplification (MLPA) is a novel, simple, and cost-effective technique for analysis of relative quantification in a single assay, which has recently been applied for the detection of genomic deletions, duplications, and amplifications in a variety of genes. RESULTS Six out of 20 patients referred for genetic diagnosis of PWS were found to have a deletion by MLPA, confirmed by FISH and DNA methylation analysis with 100% concordance. CONCLUSION MLPA's high sensitivity and specificity for deletion detection is the same as FISH or Southern blot based analysis. Additional collaborative effort for developing and validating the complete MLPA-PWS assay, for not only detecting deletion but also identifying methylation abnormality, is on going.
The problem with tells: lessons learned from absolute dating of Bronze Age mortuary ceramics in Hungary

Abstract Prehistoric population decline is often associated with social collapse, migration and environmental change. Many scholars have assumed that the abandonment of the fortified tell sites of the Great Hungarian Plain c. 1500–1450 BC led to significant regional depopulation. The authors investigate the veracity of this assumption by dating graves from Békés 103—a recently excavated Bronze Age cemetery in eastern Hungary. Using decorative motifs and radiocarbon dates to measure changing ceramic styles over more than 1300 years, they consider the implications for non-tell sites known only through surface survey. The results suggest that, even though people abandoned tell sites, regional populations were maintained.
Compact model for parametric instability under arbitrary stress waveform

A deterministic compact model of instability is presented, capable of simulating reversible parametric drift under any periodic stress waveform and suitable for the implementation in a commercial simulator (Eldo UDRM). The methodology has been applied to NBTI-induced threshold voltage drift; an example is shown, in which recovery simulation is crucial for circuit design.
A Rapid Procedure Suitable to Assess Quantitatively the Endocytosis of Colloidal Gold and Its Conjugates in Cultured Cells

We measured the endocytic uptake of low-density lipoproteins (LDLs) conjugated to colloidal gold in cultured cells, either by counting gold particles on electron micrographs or by inductively coupled plasma (ICP) mass spectrometry (MS). Both procedures are comparable but the latter requires a considerably shorter time and allows analysis of a much larger sample. In addition, ICP MS, compared to alternative radioactive or fluorescent procedures, offers the major advantage of using the same probe to quantify the endocytic uptake and to follow it by electron microscopy. Therefore, ICP MS analysis provides an easy, rapid, and sensitive quantification of endocytosis that complements the electron microscopic studies.