Miracle-dz/UniFAR-FTUs huggingface dataset:
The ribosomal elongation cycle: tRNA binding, translocation and tRNA release.

Experiments concerning the ribosomal elongation cycle have been performed; the following results were obtained. 1 A measurements of the percentage of tightly coupled ribosomes participating in a tRNA binding reaction is obtained by determining both the stoichiometry of binding and the site location. In the case of AcPhe-tRNA it is sufficient to determine the maximal binding since at moderate Mg2+ concentration (≤ 15 mM) one ribosome cannot bind more than one AcPhe-tRNA molecule, which can be present at either the A or P site (exclusion principle). 2 tRNA binding to poly(U)-programmed ribosomes does not follow the predictions of simple models with rigid tRNA binding sites as postulated by the classical A/P site model. For example, 2.7 molecules of tRNAPhe are found per ribosome at a ribosome concentration of 0.33 μM and a [14C]tRNAPhe excess over ribosomes of about 40-fold, in agreement with our previous report. At a 70S ribosome concentration of 3.3 μM and a sevenfold excess of tRNAPhe a binding of 2.5 tRNA molecules/ribosome would be expected according to the binding constants reported by us, but in fact a binding of only 1.8 molecules/70S ribosome is found. These findings explain the current discrepancies concerning the number of tRNA sites on the ribosome and confirm previous reports that three tRNA molecules can be bound simultaneously to one ribosome. 3 The ternary complex EF-Tu · GTP · Phe-tRNAPhe binds to the A site at 0°C even if the P site is not occupied. Only if the P site is free does the addition of EF-G provoke a translocation to the P site at 0°C, whereas at 37°C the Phe-tRNAPhe‘slides’ from the A to the P site without EF-G. This EF-G-independent sliding is not observed if the P site is filled by a deacylated tRNAPhe. Thus, EF-G is directly involved in the translocation reaction, and its role is not restricted to tRNA release. 4 Kinetics of the puromycin reaction with Phe-tRNA and AcPhe-tRNA, respectively, were compared. The initial rate of AcPhe-puromycin formation exceeds that of Phe-puromycin formation by a factor of 3.6 (0°C, 15 mM Mg2+). 5 Poly(U)-programmed ribosomes carrying only [14C]tRNA release tRNA upon addition of EF-G. tRNA release is observed only if at least two tRNAPhe molecules are present per ribosome. The tRNA bound first is released with a higher probability than that bound second. Such a complex is not related to a classical pretrans-location complex carrying a peptidyl-tRNA at the A site. Therefore, when tRNA release during the course of an EF-G-induced translocation reaction is studied, care must be taken that no significant amounts of the complex 70S · mRNA · (deacylated tRNA) are present.
Identification and Characterization of the Dystrophin Anchoring Site on β-Dystroglycan (*)

Dystrophin, the product of the Duchenne muscular dystrophy gene, is tightly associated with the sarcolemmal membrane to a large glycoprotein complex. One function of the dystrophin-glycoprotein complex is to link the cytoskeleton to the extracellular matrix in skeletal muscle. However, the molecular interactions of dystrophin with the membrane components of the dystrophin-glycoprotein complex are still elusive. Here, we demonstrate and characterize a specific interaction between β-dystroglycan and dystrophin. We show that skeletal muscle and brain dystrophin as well as brain dystrophin isoforms specifically bind to β-dystroglycan. To localize and characterize the dystrophin and β-dystroglycan interaction domains, we reconstituted the interaction in vitro using dystrophin fusion proteins and in vitro translated β-dystroglycan. We demonstrated that the 15 C-terminal amino acids of β-dystroglycan constituted a unique binding site for the second half of the hinge 4 and the cysteine-rich domain of dystrophin (amino acids 3054-3271). This dystrophin binding site is located in a proline-rich environment of β-dystroglycan within amino acids 880-895. The identification of the interaction sites in dystrophin and β-dystroglycan provides further insight into the structure and the molecular organization of the dystrophin-glycoprotein complex at the sarcolemma membrane and will be helpful for studying the pathogenesis of Duchenne muscular dystrophy.
Augmented spontaneous breathing and pulmonary gas exchange during pneumoperitoneum.

BACKGROUND AND OBJECTIVE Ventilation of the lungs with positive end-expiratory pressure during pneumoperitoneum has been shown to improve the arterial partial pressure of oxygen. The implications of spontaneous breathing on pulmonary gas exchange remain unknown in this setting. We therefore sought to examine the influence of pressure-support ventilation with spontaneous breathing on gas exchange during simulated laparoscopy. METHODS Ten pigs were subjected to pneumoperitoneum at a pressure of 15 cmH2O. Animals received, in a random order, pressure-support and pressure-controlled ventilation for 60 min per mode. Inert gas and haemodynamic measurements were performed before changing to a subsequent mode. RESULTS Pressure-support ventilation was more efficient than pressure-controlled ventilation regarding perfusion of normal V(A)/Q lung areas (78 +/- 4% vs. 72 +/- 5%) (P < 0.05), alveolar-arterial partial pressure of oxygen difference (9.73 +/- 1.3 vs. 11.2 +/- 1.2 kPa) and arterial partial pressure of oxygen (14.93 +/- 1.6 vs. 13.7 +/- 2.0 kPa) (P < 0.05). CONCLUSIONS Pressure-support ventilation resulted in significantly better gas exchange than pressure-controlled ventilation in this model of simulated laparoscopy.
Optimal placement and sizing of DGs at various load conditions using Shuffled Bat algorithm

In this paper a new and efficient hybrid optimization algorithm is proposed for optimal placement and sizing of the Distributed Generations (DGs). Bus voltage profile improvement, line flow capacity, active and reactive power loss minimization are considered as multi-objectives to optimize under various distribution load conditions. Renewable energy resources such as wind, solar, fuel cell and micro turbines are considered in power system modeling for finding the optimal placement and sizing. Current injection based distribution load flow is considered in DGs modeling in power systems. To optimize the objective function, a new optimization technique called Shuffled Bat algorithm (ShBAT) is proposed. The proposed methodology is tested on 84-bus Taiwan power company distribution systems with 90%, 100% and 120% of base load conditions to demonstrate its performance and effectiveness. Results show that the planned methodology is superior to existing strategies in terms of multi-objectives considered.
What’s So Spatial about Time Anyway?

Skow ([2007]), and much more recently Callender ([2017]), argue that time can be distinguished from space due to the special role it plays in our laws of nature: our laws determine the behaviour of physical systems across time, but not across space. In this work we assess the claim that the laws of nature might provide the basis for distinguishing time from space. We find that there is an obvious reason to be sceptical of the argument Skow submits for distinguishing time from space: Skow fails to pay sufficient attention to the relationship between the dynamical laws and the antecedent conditions required to establish a complete solution from the laws. Callender’s more sophisticated arguments in favour of distinguishing time from space by virtue of the laws of nature presents a much stronger basis to draw the distinction. By developing a radical reading of Callender’s view we propose a novel approach to differentiating time and space that we call temporal perspectivalism. This is the view according to which the difference between time and space is a function of the agentive perspective.
The rocky road of metastasis : the role of cytoskeletal mechanics in cell migratory response to 3 D matrix topography

Bordeleau F, Alcoser TA, Reinhart-King CA. Physical Biology in Cancer. 5. The rocky road of metastasis: the role of cytoskeletal mechanics in cell migratory response to 3D matrix topography. Am J Physiol Cell Physiol 306: C110–C120, 2014. First published November 6, 2013; doi:10.1152/ajpcell.00283. 2013. —The tumor microenvironment is a milieu of heterogeneous architectural features that affect tumor growth and metastatic invasion. Pore size, density, stiffness, and fiber architecture change dramatically from location to location throughout the tumor matrix. While many studies have addressed the effects of two-dimensional extracellular matrix structure and composition on cell migration, less is known about how cancer cells navigate complex, heterogeneous three-dimensional (3D) microenvironments. Mechanical structures such as actin and keratin, part of the cytoskeletal framework, and lamins, part of the nucleoskeletal framework, play a key role in migration and are altered during cancer progression. Recent evidence suggests that these changes in cytoskeletal and nucleoskeletal structures may enable cancer cells to efficiently respond to features such as pore size and stiffness to invade and migrate. Here we discuss the role of cell mechanics and the cytoskeleton in the ability of cells to navigate and respond to 3D matrix features and heterogeneities.
Twizzler: An Operating System for Next-Generation Memory Hierarchies

The introduction of NVDIMMs (truly non-volatile and directly accessible) requires us to rethink all levels of the system stack, from processor features to applications. Operating systems, too, must evolve to support new I/O models for applications accessing persistent data. We are developing Twizzler, an operating system for next-generation memory hierarchies. Twizzler is designed to provide applications with direct access to persistent storage while providing mechanisms for cross-object pointers, removing itself from the common access path to persistent data, and providing ﬁne-grained security and recoverability. The design of Twizzler is a better ﬁt for low-latency and byte-addressable persistent storage than prior I/O models of contemporary operating systems. We are in the process of building a prototype inside FreeBSD, allowing us to leverage and explore the ideas presented in this report without in-vesting the time to build an operating system from scratch ﬁrst. The purpose of this report is to provide an overview of Twizzler and the design behind it while giving a direction for our upcoming work. We intend to further develop our ideas by extending our FreeBSD prototype, followed by designing a kernel and hardware extensions to make better use of some of our designs (resulting in improved security, simplicity, and improved support for persistent kernel state).
A New Technique for Hepatic Portal Sampling in the Conscious Dog

Abstract A technique for implantation of a silastic catheter into the portal vein is described. The central end of the catheter is passed through a puncture hole into a tributary of the portal vein. The peripheral free end, occluded by a rubber membrane, is passed through the abdominal wall and buried under the skin. Once the catheter is in place it can be kept patent for several weeks. Injection of a substance and withdrawal of blood from the portal vein are carried out by percutaneous puncture of the rubber membrane, a virtually painless procedure that can be carried out in fully conscious nonrestrained dogs.
Reliable screening for zero-defect quality improvement by temperature gradient testing

This paper prevents a new reliable screening for Zero Defect quality improvement of deep sub-micron defects. Applications and results show this method is effective to reject the defective non-outlier dies of abnormal temperature gradient tendency. Challenges of production implementation have been overcome in a multi-step post-processing module including the new screening. Collected wafer-sort mapping data and failure analysis of the rejects have proved the capability of the proposed method in improving product quality and reducing customer returns with very acceptable yield loss.
AMHUSE: a multimodal dataset for HUmour SEnsing

We present AMHUSE (A Multimodal dataset for HUmour SEnsing) along with a novel web-based annotation tool named DANTE (Dimensional ANnotation Tool for Emotions). The dataset is the result of an experiment concerning amusement elicitation, involving 36 subjects in order to record the reactions in presence of 3 amusing and 1 neutral video stimuli. Gathered data include RGB video and depth sequences along with physiological responses (electrodermal activity, blood volume pulse, temperature). The videos were later annotated by 4 experts in terms of valence and arousal continuous dimensions. Both the dataset and the annotation tool are made publicly available for research purposes.
A Flexible KFCI Compensation for Head/Media Optimization in Perpendicular Disk Drives

Head/media matching is one of the key procedures used to ensure an acceptable performance, reliability and areal density of the perpendicular drives with multiple head/media pairs. To achieve the optimal bit error rate (BER) performance, head/media optimization is required to handle the BER variation of each pair within a single drive. Due to a large variation of the head/media performance, the mismatched KFCI slopes often lead the under- and over-compensation issues. In this paper, we derive the mathematical conditions of these problems as a function of the step adjustment size, the initial BER, the target BER and the KFCI slopes. The minimum number of adjustments for the weak and the maximum ones for the strong heads are determined. In addition, we perform an experiment on the perpendicular drives to study the BER variation of head/media. A new graphical explanation is proposed to clearly show how the under- and over-compensation issues occur. Finally, we propose a flexible KFCI compensation method based on the actual KFCI slopes. The experimental results on the failed drives from the current fixed-slope method show that the improvement in the BER performances is achieved using the proposed method.
Measurement of flow using bend sensor

This paper presents an innovative design and accurate approach to the measurement of flow rate for moderate flow applications. It also deduces linear relationship between flow rate and the change in resistance of the bend sensor used in the setup. The sensor apparatus is very simple to calibrate and install which is a fixed beam cantilever system with one moving end which would give a digital output. The displacement values of free end of the sensor are analysed using ANSYS Finite Element Analysis software.
Globin Gene Silencing in Primary Erythroid Cultures

There are numerous similarities between the erythroid and megakaryocytic lineages which suggest that commitment to either lineage occurs relatively late in hematopoiesis. Commitment toward megakaryocyte development requires obligatory silencing of erythroid-specific genes. Therefore, we investigated the effects of interleukin-6, a known inducer of thrombocyte production, on globin gene expression during erythroid differentiation. Studies in K562 cells demonstrated inhibition of γ globin gene mRNA production and chain biosynthesis in the presence of exogenous interleukin-6 which was abrogated by anti-interleukin-6 monoclonal antibody. Similar studies in primary erythroid progenitors showed inhibition of burst-forming unit-erythroid colony formation when interleukin-6 was added late in cultures with decreased γ and β globin gene mRNA production. Protein binding studies demonstrated an increase in activator protein-1 binding to its consensus sequence by 24 h of interleukin-6 treatment. Inhibition of activator protein-1 gene activity had no effect on γ gene silencing by interleukin-6. A potential interleukin-6 response element was identified in the γ globin gene. Interleukin-6 treatment led to a rapid increase in protein binding to the target DNA sequence. These results suggest that interleukin-6 may play an important role in globin gene silencing during megakaryocytic lineage commitment.
Anti-inflammatory, Analgesic and Antipyretic activities of root of Wattakaka volubilis

Wattakaka volubilis (Family: Asclepiadaceae) has been reported to possess medicinal effects. In the present study, the dried root ethanol extract of W. volubilis designated as 'the extract' was evaluated for pharmacological activity in rats and mice. The anti-inflammatory and antipyretic activities were evaluated in rodents. The analgesic activity was evaluated in mice models. In the acute toxicity study, it was found that the extract was non-toxic up to 1 g/kg, p. o. The extract (100, 200 and 300 mg/kg, p. o.) was found to possess, anti-inflammatory, analgesic and antipyretic activities in a dose-dependent manner and the effect was comparable with that produced by the standard drug, ibuprofen. The extract significantly inhibited the arachidonic acid-induced paw oedema in rats, indicating that the extract inhibited both the cyclo-oxygenase and lipo-oxygenase pathways of arachidonic acid metabolism.
Adaptive Foreground with Cast Shadow Segmentation Using Gaussian Mixture Models and Invariant Color Features

Segmentation of dynamic objects in a scene, often referred to as "foreground segmentation", is a critical early in step in most computer vision applications in domains such as action recognition, image coding, image understanding and human-computer interaction. An approach for modeling the background that uses adaptive Gaussian mixtures in the combined input space of luminance-invariant color is proposed to distinguish moving objects from their moving cast shadows in color image sequences. The proposed technique exploits the background model learning rate based on scene activity, and spectral properties of shadows that are verified by making use of more complex hypotheses on color invariance. Furthermore, the models of background and shadow are adaptively set up and updated. The measurements of observed log-likelihood are employed to perform selective adaptation. Our experiments show that the proposed technique is robust and efficient to problematic phenomena than the prior state-of-the-art. It also has the ability to carry out without sacrificing real-time performance for a wide range of practical applications in video of action recognition.
Identification of an upstream activation sequence and other cis-acting elements required for transcription of COX6 from Saccharomyces cerevisiae

Transcription of Saccharomyces cerevisiae COX6, the nuclear gene for subunit VI of cytochrome c oxidase, is activated in heme-proficient cells, requires the HAP2 gene, and is subject to glucose repression. In this study, by deletion mutagenesis of the COX6 promoter, we identified two regions that are important for transcription. The first was an upstream activation site, UAS6. It was found to be contained within an 84-base-pair (bp) sequence, between bp -256 and -340 of the COX6 translational initiation codon, and to contain sequences required for activation by heme and HAP2 and for release from glucose repression. When located upstream of a CYC1-lacZ fusion gene, deleted for both of its UASs, this segment functioned as a UAS element. Although UAS6 could promote expression in either orientation, it showed a marked orientation dependence in its response to HAP2 and the carbon source. The second region lay between bp -255 and -91. It contained two of the three major 5' termini of COX6 mRNAs and a putative TATA box. Deletion analysis of this region demonstrated that the putative TATA box is not required for transcription and that this region is separable into two redundant domains.
Acute sleep restriction increases dietary intake in preschool‐age children

Epidemiological findings suggest short sleep duration is associated with overweight and obesity across the lifespan. In adults, experimental sleep loss increases caloric intake more than total daily energy needs, thus leading to weight gain. To date, little is known about the relationship between sleep restriction and dietary intake in preschool children. Healthy children (n = 10; 41.2 ± 5.4 months; 5 females) followed a strict sleep schedule for 5 days before each experimental condition: 1 day of baseline sleep (nap and scheduled bedtime/wake time) and 1 day of sleep restriction (no‐nap and ~2.3 h bedtime delay). Standardized parent‐report dietary intake measures were obtained on baseline, sleep restriction and sleep recovery (ad libitum sleep opportunity in the 24‐h following sleep restriction) days. As designed, children slept ~3 h less on the sleep restriction than the baseline day (P < 0.001), with no significant differences in sleep between baseline and recovery days (verified with actigraphy). Repeated‐measures anovas indicated differences across conditions in total kilocalories, sugar, carbohydrate and fat intake (all P < 0.05; no differences in protein). Post hoc tests revealed that compared with baseline, children consumed 21% more kilocalories, 25% more sugar and 26% more carbohydrates on the day of sleep restriction, as well as 14% more kilocalories and 23% more fat on the day of sleep recovery (all P < 0.05). Findings suggest that acute sleep loss increases dietary intake in preschoolers both on the day of and the day after sleep restriction. Increased kilocalorie intake may promote weight gain over time and be a mechanism through which short sleep contributes to childhood obesity risk.
Experimental comparative study of an open and completely closed air source heat pump for drying sub-tropical fruits

Heat pump drying (HPD) is an energy efficient and environmentally friendly drying method. Heat pumps (HPs) deliver more heat during the drying process than the work input to the compressor. The performance of HP and the dryer is significantly affected by the surrounding conditions. Therefore, the present study investigates the performance of an open and completely closed air duct HPD systems. Also, the influence of refrigerant charge and condenser fan speed was evaluated. The results demonstrated that, the completely closed air duct HPD system had slightly higher coefficient of performance (COP) and heating capacity than the open HPD system because of the heat from the moist exhausted air from the dryer were recovered at the evaporator. However, the drying air temperatures for the closed HPD system were lower than that of open system. This was due to the circulation of cold air from the evaporator. Also, COP increased with the increase of refrigerant charge in both systems. But, at high refrigerant charge the COP values for both systems were decreased because of the decrease in heating capacity which was possible due to the accumulation of refrigerant in the condenser. Similar trend of results were observed at high condenser fan speed, this was due to the increased fan power consumption. Therefore, for the system developed, the optimum refrigerant charge was observed to be 1650 grams and 840 rpm of condenser fan speed (60% of the full speed) and the obtained COP values at this point were 3.85 and 3.75 for the closed and open HPD system, respectively.
Computer Code for Rational Approximation of Frequency Dependent Admittance Matrices

This paper deals with the problem of approximating with rational functions a matrix whose frequency-dependent elements have been obtained from calculations or from measurements. Based on a previously developed technique (vector fitting), a set of callable routines have been written in the MATLAB language. These routines allow for rational approximation with a common set of stable poles, automatic selection of initial poles, passivity enforcement, and creation of an equivalent electrical network which can be imported into ATP-EMTP. Usage of sparse arithmetic permits the computer code to handle large systems. The methodology is demonstrated by application to a frequency-dependent network equivalent of a radial distribution network (phase domain), for which the accuracy is validated in both the frequency domain and the time domain. The computer code is in the public domain and is available from the author.