Miracle-dz/UniFAR-FTUs huggingface dataset:
Modeling and analysis of pneumatic loading system

This paper analyses the fluid dynamic, thermodynamics and kinetic characteristics of a pneumatic loading system, and the detailed nonlinear model is derived and simulated. This model is verified by experiment. The influence of initial pressure and volumn of two champers are studied. The dynamic performances with different supply pressure are compared too. Pneumatic loading system has strong nonlinear, vulnerable to the influence of inertia, friction and disturbances, Study preliminarily the control strategy of pneumatic servo loading system and provides some theoretical basis for future research.
A Scheme for Fast Parallel Communication

Consider $N = 2^n $ nodes connected by wires to make an n-dimensional binary cube. Suppose that initially the nodes contain one packet each addressed to distinct nodes of the cube. We show that there is a distributed randomized algorithm that can route every packet to its destination without two packets passing down the same wire at any one time, and finishes within time $O(\log N)$ with overwhelming probability for all such routing requests. Each packet carries with it $O(\log N)$ bits of bookkeeping information. No other communication among the nodes takes place.The algorithm offers the only scheme known for realizing arbitrary permutations in a sparse N node network in $O(\log N)$ time and has evident applications in the design of general purpose parallel computers.
Regulation of apoptosis by type III interferons

Abstract. Objective: Two types of interferons (IFNs), type I (IFN‐α/β) and type III (IFN‐λs), utilize distinct receptor complexes to induce similar signalling and biological activities, including recently demonstrated for IFN‐λs antitumour activity. However, ability of type III IFNs to regulate cell population growth remains largely uncharacterized.Materials and methods: Intact and modified human colorectal adenocarcinoma HT29 cells were used to study regulation of apoptosis by IFN‐λs. Results and Conclusions: We report that the IFN‐λR1 chain of the type III IFN receptor complex possesses an intrinsic ability to trigger apoptosis in cells. Signalling induced through the intracellular domain of IFN‐λR1 resulted in G1/G0 phase cell cycle arrest, phosphatidylserine surfacing and chromosomal DNA fragmentation. Caspase‐3, caspase‐8 and caspase‐9 were activated; however, pancaspase inhibitor Z‐VAD‐FMK did not prevent apoptosis. In addition, the extent of apoptosis correlated with the level of receptor expression and was associated with prolonged IFN‐λ signalling. We also demonstrated that the ability to trigger apoptosis is a unique intrinsic function of all IFN receptors. However, more robust apoptosis was induced by signalling through type III IFN receptor than through type I or type II (IFN‐γ) receptors, suggesting higher cytotoxic potential of type III IFNs. In addition, we observed that IFN‐γ treatment sensitized HT29 cells to IFN‐λ‐mediated apoptosis. These results provide evidence that type III IFNs, alone or in combination with other stimuli, have the potential to induce apoptosis.
The estranged quotation in Israeli popular music

Abstract Israeli popular music includes many quotations from earlier Israeli songs as well as other Israeliana references. Quotations may take various forms, from cover versions to the mere evocation of song titles. This phenomenon preceded the rockisation of Israeli music, had its apex in the 1970s with early rockisation, and is continuing today, despite a certain decline. The purpose of the quotations is often a mere interaction with traditional materials, but it also sometimes expresses a striving towards an experience of life that is more sincere. Two subtopics of special significance are adolescence and political critique. Since earlier hegemony in Israel was maintained by the old left, the rock music rebellion was not as anti-capitalistic as in the Woodstock Festival, rather manifesting anti-authoritarian trends similar to (but milder than) those encountered in Eastern Europe.
Autonomous Decentralized Semantic Based Traceability Link Recovery Framework

The automation of traceability links or traceability matrices is important to many software development paradigms. In turn, the efficiency and effectiveness of the recovery of traceability links in the distributed software development is becoming increasingly vital due to complexity of project developments, as this include continuous change in requirements, geographically dispersed project teams, and the complexity of managing the elements of a project time, money, scope, and people. Therefore, the traceability links among the requirements artifacts, which fulfill business objectives, is also critical to reduce the risk and ensures project‘s success. This paper proposes Autonomous Decentralized Semantic based Traceability Link Recovery (AD-STLR) architecture. According to best of our knowledge this is the first architectural approach that uses an autonomous decentralized concept, DBpedia knowledge-base, Babelnet 2.5 multilingual dictionary and semantic network, for finding similarity among different project artifacts and the automation of traceability links recovery. key words: semantic web, NLP, Babelnet, GATE, DBpedia, document similarity
New Approaches for Analysis of Amperometrical Recordings

Abstract: Amperometry is a powerful tool for studying the exocytotic process. Catecholamines released from a single secretory vesicle are oxidized by a carbon fiber microelectrode placed on a chromaffin cell membrane. This phenomenon can be recorded online as an amperometric signal. Each event of exocytosis is called a secretory spike. Several kinetic parameters can be extracted from spikes to get important information about catecholamine storage and to follow the time course of exocytosis. The large amount of data requires the use of computer programs. We describe software, written for Igor Pro (Wavemetrics, Lake Oswego, OR, USA), that allows the offline analysis of amperometric signals. It includes (1) the automatic analysis of a large collection of experiments without user intervention; (2) the visual check of located spikes; (3) data pooling from several experiments to create galleries with hundreds of thousands of spikes. In addition, we have designed a new filtering method for amperometric data. It provides an excellent tool to enhance the signal/noise ratio with minimal artifacts. This filter allows one to obtain more reliable spike parameters.
Analysis of Protein Prenylation and Carboxyl‐Methylation

This unit describes methods for analysis of prenylation and the carboxyl‐methylation that often accompanies it. The two prenoid groups that have been found attached to proteins‐‐farnesyl (C15) and geranylgeranyl (C20)‐‐are both derived from intermediates in the isoprenoid biosynthetic pathway that utilizes mevalonic acid. In the protocols described here, radiolabeled mevalonate is used to label these intermediates in either intact cells or in vitro; the labeled intermediates then become incorporated into proteins. Alternatively, the preformed radioactive prenyl diphosphates can be used for in vitro translations, as described here. Carboxyl‐methylation of C‐terminal prenylated cysteine residues often occurs subsequent to prenylation. Methods are given for radiolabeling of the methyl group with [3H‐methyl]methionine, that is converted intracellularly into S‐adenosylmethionine, and for radiolabeling with preformed S‐adenosyl[3H]methionine.
Wore Representation Analysis of Bio-marker and Disease word

One of the most important processes in a machine learning-based natural language processing module is to represent words by inputting the module. This can be accomplished by representing words in one-hot form with a large vector size without applying the concept of semantic similarity between words, or by word representation (embedding) with vectors to represent lexical similarity. In this study, classification performance of three word representation models (Word2Vec, canonical correlation analysis, and GloVe) is tested on a corpus that established using the abstracts of 204,674 biomedical articles published in PubMed. Categories include disease name, disease symptom, and ovarian cancer marker. The classification performance of each word representation model for each category is visualized by mapping the results in two-dimensional word representations using t-SNE.
The Mechanism of Velocity Modulated Allosteric Regulation in D-3-Phosphoglycerate Dehydrogenase

D-3-Phosphoglycerate dehydrogenase (PGDH) (EC) from Escherichia coli is an allosterically regulated enzyme of the Vmax type. It is a tetramer of identical subunits and each subunit is made up of three identifiable domains, the cofactor binding domain, the substrate binding domain, and the regulatory domain. Each subunit contacts two other subunits through adjacent cofactor binding domains and through adjacent regulatory domains. L-Serine, the physiological effector, inhibits catalytic activity by apparently tethering regulatory domains from adjacent subunits together through the formation of hydrogen bonds to each subunit. This investigation demonstrates that cross-linking adjacent regulatory domains with engineered disulfides produces catalytic inhibition in the absence of inhibitor in a manner similar to that produced by the inhibitor. The inhibition due to cross-linking can be completely reversed in a concentration dependent manner by dithiothreitol. The active mutant enzyme, containing the engineered cysteines in the reduced state, retains its ability to be inhibited by L-serine, although at a 100-fold higher concentration. Hill plots of the serine inhibition of mutant and native enzyme indicate that the number of interacting sites remains at 2 in the mutant enzyme. The reversible inhibition of enzyme activity that results from tethering adjacent regulatory domains with engineered disulfides suggests that these domains move in some manner relative to one another during the active to inhibited state transition. These observations support the model which predicts that catalytic activity is regulated by the movement of rigid domains about flexible hinges and that effector binding prevents this by locking the regulatory domains in a state that produces an open active site cleft.
Amikacin pharmacokinetics in patients receiving high-dose cancer chemotherapy

We retrospectively analyzed amikacin pharmacokinetics in 28 patients (mean age, 47.4 +/- 13.6 years) who received high-dose chemotherapy during a neutropenic febrile episode. Patients received an experimental protocol of high-dose anticancer chemotherapy. Amikacin pharmacokinetic parameters were calculated from two or more concentrations in serum around a single dose by the method of Sawchuck and Zaske (J. Pharmacokinet. Biopharm. 4:183-195, 1976). Predicted parameters were calculated by using standard methods. The observed amikacin volume of distribution and clearance were significantly greater and the elimination half-life was longer than predicted (0.38 +/- 0.13 versus 0.25 liter/kg [P = 0.0001], 1.51 +/- 0.92 versus 1.17 +/- 0.38 liters/h/kg [P = 0.012], and 3.8 +/- 2.4 versus 2.9 +/- 1.1 h [P = 0.011], respectively). Multivariate analysis revealed that albumin correlated negatively and creatinine correlated positively with the volume of distribution and the elimination half-life. Creatinine and the percentage below the ideal body weight correlated negatively and hematocrit correlated positively with clearance. Administration of dosage regimens based on predicted pharmacokinetic parameters yielded subtherapeutic amikacin concentrations in serum in our patients. Because of the increased dosage requirements and the need for adequate antibiotic treatment in this population, we suggest guidelines for empiric dosing for patients with advanced cancer receiving intensive chemotherapy.
Contrasting Existence and Robustness of REM/Non-REM Cycling in Physiologically Based Models of REM Sleep Regulatory Networks

Typical human sleep throughout the night consists of alternating periods of rapid eye movement (REM) sleep and non-REM (NREM) sleep. This ultradian rhythm of NREM/REM cycling is thought to be produced by the state-dependent activity of “REM-on” and “REM-off” brainstem and hypothalamic neuronal populations that, respectively, promote or suppress REM sleep. Synaptic interactions among these populations define REM sleep regulatory networks; however, the identity of the key neuronal populations in these networks and the dynamics of interactions among them are disputed and cannot be addressed comprehensively with current experimental techniques. The purpose of this study is to use physiologically based mathematical models to explore the dynamic implications associated with competing hypotheses for network-based REM sleep regulation. Generally, putative REM sleep regulatory networks fall into two categories: a reciprocal interaction network consisting of an excitatory REM-on population interacting with an inhib.
Surface viable counts with nichrome wire loops

A surface viable counting method is described making use of a nichrome wire loop having an external diameter 5 mm, which is streaked on an overdried plate. The loop holds 1/35 ml (0·02857 ml) peptone water. When tried in parallel with pipettes that delivered 1/50 ml (0·02 ml) drops, it gave reproducible results not at all inferior to those obtained with 50-dropping pipettes.
Reflections of ELT Students on Their Progress in Language and Vocabulary Use in Portfolio Process.

Writing in the target language is an essential skill to be developed, and to this end, reading and writing skills need to be integrated so that students can be engaged in an active and effective learning process in order to help them create a positive change in their progress and achievement. Hence, it should be highly important to see in an integrated reading-writing course, particularly in an ELT context, to what extent students perceive the portfolio-keeping process with respect to language and vocabulary use. This study aimed to explore the reflections of freshmen learners at an ELT department in Turkey on the portfolio process in The Advanced Reading-Writing Course with respect to their progress in language and vocabulary use. Qualitative survey methodology was used to gather the data. The participants were 46 freshman learners attending The Department of English Language Teaching. The data were collected through the reflective essays in which the students reported their views on the portfolio process as well as their development. The data analysis was done by means of content analysis. Unstructured interview technique was also used to capture the students’ perceptions and learning experiences. The findings indicate that the portfolio-keeping process as part of the Advanced Reading-Writing Course gave the students the opportunity to develop their level in writing with respect to language and vocabulary use. The students report that they benefited from the integration of reading and writing skills in spite of the workload, which also reflected into their speaking skill and pronunciation as well. The process also gave the students the opportunity to self-evaluate their progresses in both writing and speaking skill. It is also reported by the students that the portfolio-keeping process helped the students build their self-confidence in language and vocabulary use. Consequently, the findings show that portfolio-keeping enhances the gains throughout the process and helps to create a positive attitude towards writing in the target language.
Reversible small bowel obstruction in the chicken foetus

Background: Ligation of the embryonic gut is an established technique to induce intestinal obstruction and subsequently intestinal atresia in chicken embryos. In this study, we modified this established chicken model of prenatal intestinal obstruction to describe (1) the kinetics of morphological changes, (2) to test if removal of the ligature in ovo is possible in later embryonic development and (3) to describe morphological adaptations following removal of the ligature. Materials and Methods: On embryonic day (ED) 11, small intestines of chick embryos were ligated micro surgically in ovo. In Group 1 (n = 80) gut was harvested proximal and distal to the ligation on ED 12-19. In Group 2 (n = 20) the induced obstruction was released on day 15 and gut was harvested on ED 16-19. Acetyl choline esterase staining was used as to assess resulting morphological changes. Results: A marked intestinal dilatation of the proximal segment can be seen 4 days after the operation (ED 15). The dilatation increased in severity until ED 19 and intestinal atresia could be observed after ED 16. In the dilated proximal segments, signs of disturbed enteric nervous system morphology were obvious. In contrast to this, release of the obstruction on ED 15 in Group 2 resulted in almost normal gut morphology at ED 19. Conclusion: Our model not only allows the description of morphological changes caused by an induced obstruction on ED 11 but also-more important - of morphological signs of adaptation following the release of the obstruction on ED 15.
On microbial states of growth †

It is crucial to the reproducibility of results and their proper interpretation that the conditions under which experiments are carried out be defined with rigour and consistency, in this review we attempt to clarify the differences and interrelationships among steady, balanced and exponential states of culture growth. Basic thermodynamic concepts are used to introduce the idea of steady‐state growth in open, biological systems. The classical, sometimes conflicting, definitions of steady‐state and balanced growth are presented, and a consistent terminology is proposed. The conditions under which a culture in balanced growth is also in exponential growth and in steady‐state growth are indicated. It is pointed out that steady‐state growth always implies both balanced and exponential growth, and examples in which the converse does not hold are described. More complex situations are then characterized and the terminology extended accordingly. This leads to the notion of normal growth and growth that can be synchronous or otherwise unbalanced but still reproducible, and to the condition of approximate steady state manifested by growth in batch culture and by asymmetrically dividing cells, which is analysed in some detail.
Recombinant Probes Reveal Dynamic Localization of CaMKIIα within Somata of Cortical Neurons

In response to NMDA receptor stimulation, CaMKIIα moves rapidly from a diffuse distribution within the shafts of neuronal dendrites to a clustered postsynaptic distribution. However, less is known about CaMKIIα localization and trafficking within neuronal somata. Here we use a novel recombinant probe capable of labeling endogenous CaMKIIα in living rat neurons to examine its localization and trafficking within the somata of cortical neurons. This probe, which was generated using an mRNA display selection, binds to endogenous CaMKIIα at high affinity and specificity following expression in rat cortical neurons in culture. In ∼45% of quiescent cortical neurons, labeled clusters of CaMKIIα 1–4 μm in diameter were present. Upon exposure to glutamate and glycine, CaMKIIα clusters disappeared in a Ca2+-dependent manner within seconds. Moreover, minutes after the removal of glutamate and glycine, the clusters returned to their original configuration. The clusters, which also appear in cortical neurons in sections taken from mouse brains, contain actin and disperse upon exposure to cytochalasin D, an actin depolymerizer. In conclusion, within the soma, CaMKII localizes and traffics in a manner that is distinct from its localization and trafficking within the dendrites.
The Serum Level of Brain Natriuretic Peptide Increases in Severe Subarachnoid Hemorrhage thereby Reflecting an Increase in Both Cardiac Preload and Afterload

Background: The increase of serum brain natriuretic peptide (sBNP) is well known in patients with severe subarachnoid hemorrhage (SAH). However, the pathophysiology between the clinical severity of SAH and the sBNP secretion is still not clear. The aim of this study is thus to clarify the cardiovascular pathophysiological mechanisms of sBNP secretion in severe SAH patients. Methods: From the database of multicenter prospective study (SAH PiCCO study), sBNP level was compared among initial Hunt and Kosnik (H-K) gradings on the first day. Receiver operating characteristics (ROC) analysis was applied to decide the threshold existing between severe (H-K grade 4-5) and non-severe (H-K grade 2-3) patients. Cardiopulmonary parameters were also measured with thermodilution techniques and compared between low and high sBNP groups. Results: sBNP level was significantly higher in severe patients than in non-severe patients (566.5 ± 204.2 vs. 155.7 ± 32.8 pg/ml, p = 0.034). Based on ROC analysis, the threshold value that divides severe and non-severe was 78.6 pg/ml (AUC = 0.79). In the higher sBNP group (≥78.6 pg/ml), global end-diastolic volume index (GEDI) and intrathoracic blood volume index (ITVI), which indicate the cardiac preload, were significantly higher than in the low sBNP group. The systemic vascular resistance index (SVRI), the indicator for sympathetic activation and cardiac afterload, was also higher in the high BNP group. Conclusions: In severe SAH patients, sBNP elevation was significantly associated with the increase of both cardiac preload and afterload. sBNP may be a good severity biomarker in SAH patients, reflecting the systemic impact it makes on cardiovascular preload and afterload.
Whole-Genome Transcription Profiling Reveals Genes Up-Regulated by Growth on Fucose in the Human Gut Bacterium “Roseburia inulinivorans”

ABSTRACT “Roseburia inulinivorans” is an anaerobic polysaccharide-utilizing firmicute bacterium from the human colon that was identified as a producer of butyric acid during growth on glucose, starch, or inulin. R. inulinivorans A2-194 is also able to grow on the host-derived sugar fucose, following a lag period, producing propionate and propanol as additional fermentation products. A shotgun genomic microarray was constructed and used to investigate the switch in gene expression that is involved in changing from glucose to fucose utilization. This revealed a set of genes coding for fucose utilization, propanediol utilization, and the formation of propionate and propanol that are up-regulated during growth on fucose. These include homologues of genes that are implicated in polyhedral body formation in Salmonella enterica. Dehydration of the intermediate 1,2-propanediol involves an enzyme belonging to the new B12-independent glycerol dehydratase family, in contrast to S. enterica, which relies on a B12-dependent enzyme. A typical gram-positive agr-type quorum-sensing system was also up-regulated in R. inulinivorans during growth on fucose. Despite the lack of genome sequence information for this commensal bacterium, microarray analysis has provided a powerful tool for obtaining new information on its metabolic capabilities.