Miracle-dz/UniFAR-FTUs huggingface dataset:
Analytical analysis of a discrete MEMS diatomic mass-spring Phononic Band Gap crystal for vibration stabilization applications

This paper presents the use of phononic band gap (PBG) theory for the design of mass-spring networks that can be used for vibration stabilization in MEMS sensors and/or actuators that need to display wideband immunity to vibrations over frequencies at which mechanical noise may be present. A discrete PBG crystal is a mass-spring network designed to satisfy the condition that the masses vary periodically throughout the structure. Discrete PBG crystals display a frequency selective property, both standing and traveling waves may freely vibrate at certain frequencies, yet are strongly attenuated at band gap frequencies. In this paper, the design constraints and governing analytical equations that describe discrete MEMS PBG crystals are presented. A discrete PBG crystal is then designed and fabricated in a multi-user surface micromachining process.
3D IC test scheduling with test pads considered

As the design complexity increases, three-dimensional (3D) integrated circuit (IC) design has become an industry trend. However, the testing of a 3D IC is a design challenge. In addition to minimize the test application time (including pre-bond testing and post-bond testing), the number of test pads of each layer should also be taken into account. In this paper, we propose an integer linear programming (ILP) approach to perform the 3D IC test scheduling with test pads considered. Different from those previous works, our objective is to minimize the weighted sum of the test application time and the number of required test pads. Experimental results consistently show that our approach works well in practice.
Edmund C. Stoner and the Discovery of the Maximum Mass of White Dwarfs

The existence of a mass limit for white dwarfs is usually attributed solely to the late astrophysicist Subrahmanyan Chandrasekhar (1910–95), and this limit is named after him. But as is often the case, the history of this discovery is more nuanced. In this paper I will show that the existence of a maximum mass was first established by Edmund C. Stoner (1899–1968), a physicist who began experimental research under the supervision of Rutherford at the Cavendish in Cambridge, but later switched to theoretical work. Rutherford recommended Stoner to a position at the Physics department of the University of Leeds where he spent his entire career. According to G. Cantor, he was “probably the leading Cavendish-trained theoretical physicist of the 1920’s”, although he learned theory mostly on his own, and became known for his work on magnetism. Unfortunately, Stoner suffered from diabetes and poor health which restricted his travels, and this may account for the fact that he did not receive wider recognition for his achievements. In 1924 Stoner wrote a paper on the distribution of electrons among atomic levels. In the preface of the fourth edition of his classic book, Atomic structure and spectral lines, Arnold Sommerfeld gave special mention to “einen grossen Fortschritt [a great advancement]” brought about by Stoner’s analysis, which then came to the attention of Wolfgang Pauli, and played an important role in his formulation of the exclusion principle in quantum physics. Therefore, it is not surprising that Stoner’s interest in white dwarfs was aroused by Ralph H. Fowler’s suggestion that the exclusion principle could be applied to solve a major puzzle, the origin of the extreme high density of white dwarfs, which could not be explained by classical physics. Arthur Eddington expressed this puzzle as follows: “I do not see how a star which has once got into this compressed state is ever going to go out of it. The star will need energy in order to cool. It would seem that the star will be in an awkward predicament when its supply of subatomic energy fails. Imagine a body continually losing heat but with insufficient energy to grow cold! ” At the time, the conventional wisdom was that the source of internal pressure which maintained all stars in equilibrium against gravitational collapse was the internal pressure of the matter composing the star which had been heated into a gas presumably, according to Eddington, by “subatomic energy”. But when this supply of energy is exhausted and the star cools, Fowler proposed that a new equilibrium would ensue, even at zero temperature, due to the “degeneracy” pressure of the electrons caused by the exclusion principle in quantum mechanics. Fowler, however, did not attempt to determine the equilibrium properties of such a star which he regarded as “strictly JHA, xxxix (2008)
Mutation of WRKY transcription factors initiates pith secondary wall formation and increases stem biomass in dicotyledonous plants

Stems of dicotyledonous plants consist of an outer epidermis, a cortex, a ring of secondarily thickened vascular bundles and interfascicular cells, and inner pith parenchyma cells with thin primary walls. It is unclear how the different cell layers attain and retain their identities. Here, we show that WRKY transcription factors are in part responsible for the parenchymatous nature of the pith cells in dicotyledonous plants. We isolated mutants of Medicago truncatula and Arabidopsis thaliana with secondary cell wall thickening in pith cells associated with ectopic deposition of lignin, xylan, and cellulose, leading to an ∼50% increase in biomass density in stem tissue of the Arabidopsis mutants. The mutations are caused by disruption of stem-expressed WRKY transcription factor (TF) genes, which consequently up-regulate downstream genes encoding the NAM, ATAF1/2, and CUC2 (NAC) and CCCH type (C3H) zinc finger TFs that activate secondary wall synthesis. Direct binding of WRKY to the NAC gene promoter and repression of three downstream TFs were confirmed by in vitro assays and in planta transgenic experiments. Secondary wall-bearing cells form lignocellulosic biomass that is the source for second generation biofuel production. The discovery of negative regulators of secondary wall formation in pith opens up the possibility of significantly increasing the mass of fermentable cell wall components in bioenergy crops.
Experimental studies of pathogenecity of Chicken Infectious Anaemia Virus (3 isolates) in Iran

To evaluate pathogenicity of 3 Chicken Anemia Virus isolates-CV1, CV2 and CV3 respectively - the current experiment carried out. After tittering of the viruses, 30 one day old SPF chicks were grouped and intramuscularly inoculated with each isolate in a separate group. Two other groups as positive and control groups were inoculate with a live vaccine virus and normal saline respectively. During the study the birds in first three groups clinically showed raffling feathers, depression and body weight reduction. After 18 days they were weighed, bled and euthanized. Three birds were found dead during the experiment (one in each tested group). Antibodies against CAV in the serum of all 3 groups were detected while no antibody found in negative control group. Hematocrit Values of the three tested groups were under the normal. Grossly the thymus and bursa tissues were severely atrophied. Bone marrow became yellowish and pale. In histopathological study we found aplasia and devoid of erythroid and myeloid cells replacing by fat cells in bone marrow. Severe atrophy and depletion in thymus ,bursa of Fabricius and bone marrow tissues statistically were analyzed and showed that the significance difference in comparing with control groups ( p
Derating of automotive drive systems using model predictive control

Temperature monitoring and derating of electric vehicle (EV) drive trains is of key importance to increase power and torque utilization while preventing thermal damages. Derating by static regulations and standard closed-loop controllers (e.g. PI-type) is not optimal since conservative safety margins have to be chosen to prevent temperature constraint violations. In contrast, model predictive control (MPC) is able to fully utilize the overload capacity of a given drive train and to operate within defined temperature limits. The main contributions of this work is to close the gap between the optimal motion control of EVs and the derating of electrical drive trains. For this goal, simplified vehicle, motor and track models are introduced since the time constants of the mechanical car model are significantly smaller compared to the thermal motor dynamics. A simulative study of a permanent magnet synchronous motor based drive train and the SFTP-US06 drive cycle illustrate the proposed MPC-based derating.
Lysophosphatidic acid acyltransferase-β: a novel target for induction of tumour cell apoptosis

Phosphatidic acid (PA) is a component of cellular membranes that is also a mediator of certain cell signalling functions associated with oncogenesis. These include ras/raf/Erk and Akt/mTor [1-3]. The authors have investigated whether it would be possible to interrupt these known oncogenic pathways through the inhibition of lysophosphatidic acid acyltransferase (LPAAT), an enzyme that catalyses the biosynthesis of PA. The expression and activity of the LPAAT-β isoform are elevated in human tumours, and the respective gene displays transforming capacity when overexpressed in vitro. Inhibition by either genetic means or by isoform-specific small molecules results in a block to cell signalling pathways and apoptosis. Furthermore, the small-molecule inhibitors of LPAAT-β are not cytotoxic to a number of normal cell types, including primary bone marrow progenitors, indicating a differential dependence of tumour cells on LPAAT-β function. These discoveries indicate that LPAAT-β represents a potential novel cancer therapy target.
The structure and aminoacylation of a temperature-sensitive tRNATrp (Escherichia coli).

A temperature-sensitive (t.s.) tRNATrp from Escherichia coli has a single base change from the wild type (w.t.) species, which results in the loss of a base pair at the bottom of the CCA stem of the cloverleaf structure. Thermodynamic studies on this t.s. tRNA show that it is more susceptible to denaturation than the w.t. due to a larger change in the entropy of denaturation. Correlated with this thermodynamic result is the finding that the denatured t.s. tRNA's T psi C loop is more susceptible to digestion by T1 RNase, suggesting that it has greater freedom than the corresponding structure on the denatured w.t. molecule. In contrast, the native form of the t.s. tRNATrp is very similar to the w.t. with regard to aminoacylation, T1 RNase susceptibility, and column chromatographic mobility, despite the fact that it necessarily has one less base pair. In addition, the well known denaturation-dependent shift in column chromatographic mobility, which is observed for both the t.s. and w.t. molecules, depends on a modification in the anticodon loop, since tRNATrp lacking that modification does not shift when denatured. Thus, though it is not usually thought to be implicated, denaturation probably affects the conformation of the anticodon loop. The lethal phenotype of the mutant at high temperature, defective attenuation of the tryptophan biosynthetic operon in the mutant, and some aspects of the denatured state are clarified by these findings.
Empirically detecting the Hype Cycle with the life cycle indicators: An exploratory analysis of three technologies

Hype Cycle is a popular graphic representation of the level of maturity, adoption and business application of a technology, originally introduced by Gartner Research¿s Jackie Fenn. Despite its popularity, the verification or relation to theoretical frameworks is to a large extent missing in current research literature. This paper presents some possible theoretically based conceptualizations and definitions regarding the Hype Cycle. In addition, a bibliometric study of the existence of the Hype Cycle in terms of technology life cycle indicators, specifically in applied research and application phases, was carried out.
Sequence and hydropathy profile analysis of two classes of secondary transporters

A structural class in the MemGen classification of membrane proteins is a set of evolutionary related proteins sharing a similar global fold. A structural class contains both closely related pairs of proteins for which homology is clear from sequence comparison and very distantly related pairs, for which it is not possible to establish homology based on sequence similarity alone. In the latter case the evolutionary link is based on hydropathy profile analysis. Here, we use these evolutionary related sets of proteins to analyze the relationship between E-values in BLAST searches, sequence similarities in multiple sequence alignments and structural similarities in hydropathy profile analyses. Two structural classes of secondary transporters termed ST[3], which includes the Ion Transporter (IT) superfamily and ST[4], which includes the DAACS family (TC# 2.A.23) were extracted from the NCBI protein database. ST[3] contains 2051 unique sequences distributed over 32 families and 59 subfamilies. ST[4] is a smaller class containing 399 unique sequences distributed over 2 families and 7 subfamilies. One subfamily in ST[4] contains a new class of binding protein dependent secondary transporters. Comparison of the averaged hydropathy profiles of the subfamilies in ST[3] and ST[4] revealed that the two classes represent different folds. Divergence of the sequences in ST[4] is much smaller than observed in ST[3], suggesting different constraints on the proteins during evolution. Analysis of the correlation between the evolutionary relationship of pairs of proteins in a class and the BLAST E-value revealed that: (i) the BLAST algorithm is unable to pick up the majority of the links between proteins in structural class ST[3], (ii) ‘low complexity filtering’ and ‘composition based statistics’ improve the specificity, but strongly reduce the sensitivity of BLAST searches for distantly related proteins, indicating that these filters are too stringent for the proteins analyzed, and (iii) the E-value cut-off, which may be used to evaluate evolutionary significance of a hit in a BLAST search is very different for the two structural classes of membrane proteins.
ComEA is a DNA receptor for transformation of competent Bacillus subtilis

Competent cells of Bacillus subtilis efficiently bind and internalize DNA. ComEA and the seven proteins encoded by the comG operon are required in vivo for the binding step. We show here that ComEA, a bitopic membrane protein, is itself capable of high‐affinity DNA binding. A domain necessary for DNA binding is located at the C‐terminus of ComEA. Proteins with similar 60–80 amino acid residue domains are widespread among bacteria and higher organisms. ComEA shows a marked preference for double‐stranded DNA and can bind to oligomers as small as 22 bp in length. DNA binding by ComEA exhibits no apparent base sequence specificity. Using a membrane vesicle DNA‐binding assay system we show that in the absence of cell wall, ComEA is still required for DNA binding, whereas the requirement for the ComG proteins is bypassed. We conclude that the ComG proteins are needed in vivo to provide access of the binding domain of ComEA to exogenous DNA. Possible specific roles for the ComG proteins are discussed.
Cation transport: an example of structural based selectivity.

Through the high-resolution structure of the gramicidin A channel in lamellar phase lipids and the characterization of specific ion peptide interactions, fundamental principles for ion channel selectivity and conductance efficiency are illustrated with atomic resolution detail. Delocalized cation binding in the first turn of the helix reduces the unfavorable entropy contribution upon binding. Stepwise dehydration minimizes the energy barrier for cation entry and provides valence selectivity in this channel. Three or more water molecules in the monovalent cation binding site result in flexibility in the cation solvation environment causing weak cation size selectivity. Lack of cation induced structural modification avoids the formation of a significant energy barrier, thus permitting efficient cation transport.
The Independence of Fuzzy Variables with Applications to Fuzzy Random Optimization

This paper presents the independence of fuzzy variables as well as its applications in fuzzy random optimization. First, the independence of fuzzy variables is defined based on the concept of marginal possibility distribution function, and a discussion about the relationship between the independent fuzzy variables and the noninteractive (unrelated) fuzzy variables is included. Second, we discuss some properties of the independent fuzzy variables, and establish the necessary and sufficient conditions for the independent fuzzy variables. Third, we propose the independence of fuzzy events, and deal with its fundamental properties. Finally, we apply the properties of the independent fuzzy variables to a class of fuzzy random programming problems to study their convexity.
Enhancing Sustainability of the Software Life Cycle via a Generic Knowledge Base

Information technology plays a double-edged part when facing the challenges of sustainable development: On the one hand IT can improve processes, dematerialize physical goods, etc. On the other hand, IT itself is consuming more and more energy and natural resources. In our paper, we present an approach for a generic knowledge database, which helps software developers, managers of data centres, users, and other actors within the hardware and software life cycle in producing, maintaining, and using more sustainable and “greener” software. In detail, we present a model for appropriate articles, and overall system architecture. With some user scenarios we demonstrate, how our system is working.
The use of intravenous albumin in patients at high risk for severe ovarian hyperstimulation syndrome.

Previous experiences in subjects with other forms of third space fluid accumulation have shown that albumin is efficacious in preventing and correcting haemodynamic instability. Using a similar approach in an effort to increase the serum oncotic pressure and to reverse the leakage of fluids from the intravascular space, high risk subjects for severe ovarian hyperstimulation syndrome (SOHS) were treated with albumin. In a recent large study two high risk factors were identified, i.e. the number of oocytes and levels of serum oestradiol. Thirty-six women undergoing assisted reproductive techniques who presented both these factors, received intravenous albumin at a dose of 5% in Ringers lactate in doses of 500 ml during oocyte retrieval and 500 ml immediately thereafter in the recovery room. Daily measurements of urine output, serum and urine electrolytes, weight, abdominal girth, and haematocrit prior to and after oocyte retrieval revealed normal serum and urine electrolyte levels, and no signs of haemoconcentration. No patient in this study developed SOHS, and of course none had to be hospitalized. Vaginal ultrasound performed in the majority of the subjects revealed < or = 100 ml of peritoneal fluid 48-72 h after oocyte retrieval. The only complication from the use of intravenous albumin was the appearance of a 'flu-like condition' (low grade temperature, nausea and muscle pains) developed by 12 women between days 3 and 5 after oocyte collection. Intravenous albumin had thus prevented the development of severe ovarian hyperstimulation syndrome in an assisted reproduction programme. (ABSTRACT TRUNCATED AT 250 WORDS)
Human and Rodent Transcription Elongation Factor P-TEFb: Interactions with Human Immunodeficiency Virus Type 1 Tat and Carboxy-Terminal Domain Substrate

ABSTRACT The human immunodeficiency virus type 1 transcriptional regulator Tat increases the efficiency of elongation, and complexes containing the cellular kinase CDK9 have been implicated in this process. CDK9 is part of the Tat-associated kinase TAK and of the elongation factor P-TEFb (positive transcription elongation factor-b), which consists minimally of CDK9 and cyclin T. TAK and P-TEFb are both able to phosphorylate the carboxy-terminal domain (CTD) of RNA polymerase II, but their relationships to one another and to the stimulation of elongation by Tat are not well characterized. Here we demonstrate that human cyclin T1 (but not cyclin T2) interacts with the activation domain of Tat and is a component of TAK as well as of P-TEFb. Rodent (mouse and Chinese hamster) cyclin T1 is defective in Tat binding and transactivation, but hamster CDK9 interacts with human cyclin T1 to give active TAK in hybrid cells containing human chromosome 12. Although TAK is phosphorylated on both serine and threonine residues, it specifically phosphorylates serine 5 in the CTD heptamer. TAK is found in the nuclear and cytoplasmic fractions of human cells as a large complex (∼950 kDa). Magnesium or zinc ions are required for the association of Tat with the kinase. We suggest a model in which Tat first interacts with P-TEFb to form the TAK complex that engages with TAR RNA and the elongating transcription complex, resulting in hyperphosphorylation of the CTD on serine 5 residues.
Talking about Causing Events

Questions about the nature of the relationship between language and extralinguistic cognition are old, but only recently has a new view emerged that allows for the systematic investigation of claims about linguistic structure, based on how it is understood or utilized outside of the language system. Our paper represents a case study for this interaction in the domain of event semantics. We adopt a transparency thesis about the relationship between linguistic structure and extralinguistic cognition, investigating whether different lexico-syntactic structures can differentially recruit the visual causal percept. A prominent analysis of causative verbs like move suggests reference to two distinct events and a causal relationship between them, whereas non-causative verbs like push do not so refer. In our study, we present English speakers with simple scenes that either do or do not support the perception of a causal link, and manipulate (between subjects) a one-sentence instruction for the evaluation of the scene. Preliminary results suggest that competent speakers of English are more likely to judge causative constructions than non-causative constructions as true of a scene where causal features are present in the scene. Implications for a new approach to the investigation of linguistic meanings and future directions are discussed.
Plasma-enhanced low temperature growth of silicon nanowires and hierarchical structures by using tin and indium catalysts

Plasma-enhanced low temperature growth (<300 °C) of silicon nanowires (SiNWs) and hierarchical structures via a vapor–liquid–solid (VLS) mechanism are investigated. The SiNWs were grown using tin and indium as catalysts prepared by in situ H2 plasma reduction of SnO2 and ITO substrates, respectively. Effective growth of SiNWs at temperatures as low as 240 °C have been achieved, while tin is found to be more ideal than indium in achieving a better size and density control of the SiNWs. Ultra-thin (4–8 nm) silica nanowires, sprouting from the dendritic nucleation patterns on the catalyst’s surface, were also observed to form during the cooling process. A kinetic growth model has been proposed to account for their formation mechanism. This hierarchical structure combines the advantages of the size and position controllability from the catalyst-on-top VLS–SiNWs and the ultra-thin size from the catalyst-on-bottom VLS–ScNWs.