Miracle-dz/UniFAR-FTUs huggingface dataset:
Ability of Proteus mirabilis to invade human urothelial cells is coupled to motility and swarming differentiation

Proteus mirabilis causes serious kidney infections which can involve invasion of host urothelial cells. We present data showing that the ability to invade host urothelial cells is closely coupled to swarming, a form of cyclical multicellular behavior in which vegetative bacteria differentiate into hyperflagellated, filamentous swarm cells capable of coordinated and rapid population migration. Entry into the human urothelial cell line EJ/28 by P. mirabilis U6450 isolated at different stages throughout the swarming cycle was measured by the antibiotic protection assay method and confirmed by electron microscopy. Differentiated filaments entered urothelial cells within 30 min and were 15-fold more invasive (ca. 0.18% entry in 2 h) than an equivalent dry weight of vegetative cells isolated before differentiation, which attained only ca. 0.012% entry in the 2-h assay. The invasive ability of P. mirabilis was modulated in parallel with flagellin levels throughout two cycles of swarming. Septation and division of intracellular swarm cells produced between 50 and 300 vegetative bacteria per human cell, compared with 4 to 12 intracellular bacteria after incubation with vegetative cells. Transposon (Tn5) mutants of P. mirabilis with specific defects in motility and multicellular behavior were compared with the wild-type for the ability to invade. Mutants which lacked flagella (nonmotile nonswarming) were entirely noninvasive, and those which were motile but defective in swarm cell formation (motile nonswarming) were 25-fold less invasive than wild-type vegetative cells. Mutants with defects in the coordination of multicellular migration and the temporal control of consolidation (cyclical reversion of swarm cells to vegetative cells) were reduced ca. 3- to 12-fold in the ability to enter urothelial cells. In contrast, a nonhemolytic transposon mutant which swarmed normally retained over 80% of wild-type invasive ability. Swarm cells and early consolidation cells were at least 10-fold more cytolytic than vegetative cells as a result of their high-level production of hemolysin.
MazG – a regulator of programmed cell death in Escherichia coli

We have previously reported that mazEF, the first regulatable chromosomal ‘addiction module’ located on the Escherichia coli chromosome, downstream from the relA gene, plays a crucial role in the programmed cell death in bacteria under stressful conditions. It consists of a pair of genes encoding a stable toxin, MazF, and MazE, a labile antitoxin interacting with MazF to form a complex. The cellular target of MazF toxin was recently described to be cellular mRNA, which is degraded by this toxin. On the same operon, downstream to the mazEF genes, we found another open reading frame, which was called mazG. Recently, it was shown that the MazG protein has a nucleotide pyrophosphohydrolase activity. Here we show that mazG is being transcribed in the same polycistronic mRNA with mazEF. We also show that the enzymatic activity of MazG is inhibited by MazEF proteins. When the complex MazEF was added, the enzymatic activity of MazG was about 70% inhibited. We demonstrate that the enzymatic activity of MazG in vivo causes depletion of guanosine 3′,5′‐bispyrophosphate (ppGpp), synthesized by RelA under amino acid starvation conditions. Based on our results, we propose a model in which this third gene, which is unique for chromosomal addiction systems, has a function of limiting the deleterious activity of MazF toxin. In addition, MazG solves a frequently encountered biological problem: how to avoid the persistence of a toxic product beyond the time when its toxicity is useful to the survival of the population.
Predicting gene essentiality from expression patterns in Escherichia coli

Essential genes are genes whose loss of function causes lethality. In the case of pathogen organisms, the identification of these genes is of considerable interest, as they provide targets for the development of novel antibiotics. Computational analyses have revealed that the positions of the encoded proteins in the protein-protein interaction network can help predict essentiality, but this type of data is not always available. In this work, we investigate prediction of gene essentiality from expression data only, using a genome-wide compendium of expression patterns in the bacterium Escherichia coli, by using single decision trees and random forests. We first show that, based on the original expression measurements, it is possible to identify essential genes with good accuracy. Next, we derive, for each gene, higher level features such as average, standard deviation and entropy of its expression pattern, as well as features related to the correlation of expression patterns between genes. We find that essentiality may actually be predicted based only on the two most relevant ones among these latter. We discuss the biological meaning of these observations.
The development of DSM-IV.

In May, 1988, the Board of Trustees of the American Psychiatric Association (APA), Washington, DC, appointed a task force to begin work on the fourth edition of the Diagnostic and Statistical Manual of Mental Disorders (DSM-IV) , scheduled to be published in 1993. In a recent article that appeared in theNEWS AND VIEWSsection of theARCHIVES, Zimmerman 1 suggested that such an endeavor might be premature and expressed concern that any revisions to DSM-III-R would be necessarily rushed and whimsical, would be unresponsive to research, and would contribute to the confusing array of alternative diagnostic criteria sets already available in the literature. Similar concerns have been expressed elsewhere. 2-5 We will provide here the background for the decision to publish DSM-IV in 1993, the rationale for beginning this work in 1988, and the procedural safeguards we have instituted to minimize arbitrary and idiosyncratic revisions. DSM-IV AND ICD-10 The APA
An Optimal Algorithm for the Traveling Salesman Problem with Time Windows

This paper presents the development of new elimination tests which greatly enhance the performance of a relatively well established dynamic programming approach and its application to the minimization of the total traveling cost for the traveling salesman problem with time windows. The tests take advantage of the time window constraints to significantly reduce the state space and the number of state transitions. These reductions are performed both a priori and during the execution of the algorithm. The approach does not experience problems stemming from increasing problem size, wider or overlapping time windows, or an increasing number of states nearly as rapidly as other methods. Our computational results indicate that the algorithm was successful in solving problems with up to 200 nodes and fairly wide time windows. When the density of the nodes in the geographical region was kept constant as the problem size was increased, the algorithm was capable of solving problems with up to 800 nodes. For these problems, the CPU time increased linearly with problem size. These problem sizes are much larger than those of problems previously reported in the literature.
Pyroelectric energy conversion: Optimization principles

In the framework of microgenerators, we present in this paper the key points for energy harvesting from temperature using ferroelectric materials. Thermoelectric devices profit from temperature spatial gradients, whereas ferroelectric materials require temporal fluctuation of temperature, thus leading to different applications targets. Ferroelectric materials may harvest perfectly the available thermal energy whatever the materials properties (limited by Carnot conversion efficiency) whereas thermoelectric material's efficiency is limited by materials properties (ZT figure of merit). However, it is shown that the necessary electric fields for Carnot cycles are far beyond the breakdown limit of bulk ferroelectric materials. Thin films may be an excellent solution for rising up to ultra-high electric fields and outstanding efficiency. Different thermodynamic cycles are presented in the paper: principles, advantages, and drawbacks. Using the Carnot cycle, the harvested energy would be independent of materials properties. However, using more realistic cycles, the energy conversion effectiveness remains dependent on the materials properties as discussed in the paper. A particular coupling factor is defined to quantify and check the effectiveness of pyroelectric energy harvesting. It is defined similarly to an electromechanical coupling factor as k2 = p2thetas0/(epsivthetas 33 CE), where p, thetas0, epsivthetas 33, Ce are pyroelectric coefficient, maximum working temperature, dielectric permittivity, and specific heat, respectively. The importance of the electrothermal coupling factor is shown and discussed as an energy harvesting figure of merit. It gives the effectiveness of all techniques of energy harvesting (except the Carnot cycle). It is finally shown that we could reach very high efficiency using lang111rang0.75Pb(Mg1/3Nb2/3)-0.25PbTiO3 single crystals and synchronized switch harvesting on inductor (almost 50% of Carnot efficiency). Finally, practical implementation key points of pyroelectric energy harvesting are presented showing that the different thermodynamic cycles are feasible and potentially effective, even compared to thermoelectric devices.
A Hierarchical Completeness Proof for Propositional Interval Temporal Logic with Finite Time

We present a completeness proof for Propositional Interval Temporal Logic (PITL) with finite time which avoids certain difficulties of conventional methods. It is more gradated than previous efforts since we progressively reduce reasoning within the original logic to simpler reasoning in sublogics. Furthermore, our approach benefits from being less constructive since it is able to invoke certain theorems about regular languages over finite words without the need to explicitly describe the associated intricate proofs. A modified version of regular expressions called Fusion Expressions is used as part of an intermediate logic called Fusion Logic. Both have the same expressiveness as PITL but are lower-level notations which play an important role in the hierarchical structure of the overall completeness proof. In particular, showing completeness for PITL is reduced to showing completeness for Fusion Logic. This in turn is shown to hold relative to completeness for conventional linear-time temporal logic with finite time. Logics based on regular languages over finite words and ! -words offer a promising but elusive framework for formal specification and verification. A number of such logics and decision procedures have been proposed. In addition, various researchers have obtained complete axiom systems by embedding and expressing the decision procedures directly within the logics. The work described here contributes to this topic by showing how to exploit some interesting links between regular languages and interval-based temporal logics.
Developments of an Efficient Analytical Scheme for Optimal Composition Designs of Tubular Linear Magnetic-Geared Machines

By adopting the analytical model and magnetic equivalent circuit concepts, a systematic scheme that can be conveniently applied for the optimal component composition designs of an integrated tubular linear magnetic-geared machine (TLM2) will be provided. The TLM2 system can be either adopted to generate electric powers or to supply large mechanical thrust forces. With its complex double-mover and coaxial magnetic gear structures, the associated system performance based on different component parameters and arrangements can be rationally and efficiently evaluated. Based on thorough flux coupling designs and 3-D finite-element analyses, the adequacies of the proposed analytical scheme for assisting the optimal TLM2 system design at specified physical constraints can be confirmed. A laboratory TLM2 prototype has successfully been developed to operate as a generator for demonstration, and it is confident that its linear actuator counterparts can also be conveniently and reasonably designed based on the same scheme.
Short report: Influence of culture and trauma history on autobiographical memory specificity

This study investigated the influence of culture and trauma history on autobiographical memory specificity. Chinese international and British undergraduate university students (N=64) completed the Autobiographical Memory Test, Hopkins Symptom Checklist-25, Twenty Statements Test, Trauma History Questionnaire, and Impact of Events Scale-Revised. The results indicated that the British group provided significantly more specific memories than the Chinese group. The high trauma exposure group provided significantly fewer specific autobiographical memories than the low trauma exposure group. The interaction was not significant. The findings suggest that even in cultures where specificity is not as evident in autobiographical remembering style, trauma exposure appears to exert similar influence on autobiographical memory specificity.
Semiconductor Technology & Manufacturing Status, Challenges, and Solutions — A New Paradigm in the Making

The phenomenal growth of the semiconductor industry has been made possible by our ability to deliver more functionality at a lower and lower cost, with a reduction in cost per function of approximately 25% per year. Technology advancements have also enabled higher performance, lower operating voltages, and associated lower power consumption. Dimensional shrinks based on 248 nm lithography led the revolution in recent years. However, with the fundamental limit for optical lithography at about 1/3rd the wavelength, the limits for 193 nm and 157 nm lithography are about 65 nm and 50 nm respectively. With EUV and most other NGL technologies 7 years in the future the limit for the remainder of the decade is about 50 nm. Technology challenges, whether they are lithographic in nature or based on needed new materials with advanced properties, are summarized in this paper along with suggestions for potential solutions for the remainder of the decade. Even if we meet the technology challenges, continued revenue gro.
Silencing of the Nuclear RPS10 Gene Encoding Mitochondrial Ribosomal Protein Alters Translation in Arabidopsis Mitochondria[W]

This work addresses both mitochondrial translation regulation and coordination of expression of nuclear and mitochondrial genomes in land plants. When the status of mitoribosomes is perturbed, the efficiency of translation of various classes of mitochondrial mRNAs is differently affected. In consequence, ribosomal proteins are oversynthesized, whereas OXPHOS subunits are downregulated. Hardly anything is known about translational control of plant mitochondrial gene expression. Here, we provide evidence for differential translation of mitochondrial transcripts in Arabidopsis thaliana. We found that silencing of the nuclear RPS10 gene encoding mitochondrial ribosomal protein S10 disturbs the ratio between the small and large subunits of mitoribosomes, with an excess of the latter. Moreover, a portion of the small subunits are incomplete, lacking at least the S10 protein. rps10 cells also have an increased mitochondrial DNA copy number per cell, causing an upregulation of all mitochondrial transcripts. Mitochondrial translation is also altered so that it largely overrides the hyperaccumulation of transcripts, and as a consequence, only ribosomal proteins are oversynthesized, whereas oxidative phosphorylation subunits are downregulated. Expression of nuclear-encoded components of mitoribosomes and oxidative phosphorylation system (OXPHOS) complexes seems to be less affected. The ultimate coordination of expression of the nuclear and mitochondrial genomes occurs at the complex assembly level. These findings indicate that mitoribosomes can regulate gene expression by varying the efficiency of translation of mRNAs for OXPHOS and ribosomal proteins.
Conditioning lab on PCB to control temperature and mix fluids at the microscale for biomedical applications

In this paper, a Lab on PCB (LOP) for conditioning the medium of cell culture is presented. The target is to control its temperature at 37 °C ± 0.1 °C, to assure the appropriate temperature conditions around the cells. The Lab on PCB is also able to mix other fluids into the medium, if it is necessary. The integration of a PDMS microfluidic circuit over a Printed Circuit Board (PCB) results in a smart platform with a low-cost fabrication process. The microfluidic platform of the system includes three inlet ports, microchannels, a micromixer and one outlet port. The correct operation of the LOP assures that the medium is within the adequate conditions in the outlet port. The PCB incorporates a NTC thermistor to measure the temperature, and microheaters that are activated if the medium temperature is under 36.9 °C. The microheater fabrication process consists of patterning the copper layer of the PCB. The NTC thermistor is welded into copper pads and embedded in PDMS to avoid the contact with the fluid. The system is designed to allow the mixing and heating of fluids and it is connected to a cell culture Lab on PCB, and to an electronic control module, which include the electronic adapting circuit of the NTC and the control of the microheaters. The results of this study concerning the heating and mixing of fluids and the monitoring of temperature are successful.
Secretion by ependymal cells of the neurohypophysis and saccus vasculosus of Polypterus ornatipinnis (osteichthyes)

Electron microscopic studies of the neurohypophysis and saccus vasculosus of the bichir (Polypterus ornatipinnis) reveal an apocrine release of secretory material by ependymal cells (e.g., crown cells). The secretory material appears to migrate along the microtubular apparatus and the ciliary filaments to the cell buds. It is postulated that the formation of the buds and their release is mediated by cilial action. Secretion buds are noted in the cerebrospinal fluid and vascular sinusoids.
Graph-based Model for Topic Detection

In this paper, a novel graph-based model (GBM) is proposed for topic detecting. Different from existing statistical methods, our proposed model considers more semantic factors which combines named entity and dependency relation between words derived from a dependency parse tree. In our model, a graph is constructed for representing words and their association. By utilizing spectral clustering algorithm, we get clusters of words, each cluster represents a topic respectively. Our contribution includes as follows: modeling the topic detection problem as a graph-partitioning problem; proposing a new method of ranking the words association, and based on that, the document collection is represented as an undirected weighted graph. The performance of experiment task for dimensionality reduction and text classification indicates the feasibility and potentiality of our method.
Further discussion on the design of STBC-MLC scheme for different set partitioning

This paper presents the concatenation scheme of space-time block codes (STBC) and multilevel codes/multi-stage decoding (MLC/MSD). We analyze the impact of different set partitionings, namely Ungerboeck's partitioning (UP) and block partitioning (BP), on the concatenation scheme by using product distance. Based on capacity rule, performances of the concatenation schemes with 8-ASK and 8-PSK are given for analyzing.
Mitochondrial Creatine Kinase Binding to Phospholipids Decreases Fluidity of Membranes and Promotes New Lipid-Induced β Structures As Monitored by Red Edge Excitation Shift, Laurdan Fluorescence, and FTIR†

Structural modifications induced by the binding of mitochondrial creatine kinase (mtCK) to saturated and unsaturated phospholipids were monitored by using Laurdan, a membrane probe sensitive to the polarity of the environment. The abrupt change characteristic of a phase transition of lipids alone was attenuated by addition of mtCK. Generalized polarization spectra indicated that mtCK surface binding changed the phospholipid liquid-crystalline state to a more rigid state. Infrared spectra of lipids further strengthened these results: upon mtCK binding, the phospholipid methylene chains had a more rigid conformation than that observed without mtCK at the same temperature. After mtCK binding to vesicles of perdeuterated dimyristoylphosphatidylcholine and nondeuterated dimyristoylphosphatidylglycerol, no lateral phase separation was observed, suggesting that both lipids were rigidified. Moreover, mtCK bound to liposomes exhibited an uncommon red edge excitation shift of 19 nm, while that of the soluble enzym.
‘We have to discuss it’: cancer patients' advance care planning impressions following educational information about cardiopulmonary resuscitation

Most cancer patients desire information about care options at the end of life, including cardiopulmonary resuscitation (CPR). Communicating such care options can be challenging and is part of advance care planning (ACP). Our prior studies with video educational media produced data on patients' categoric preferences (yes/no/unsure) for CPR; however, the thematic underpinnings of these educated preferences in patients treated for advanced cancer aren't well known.
Performance of visible and mid‐infrared scattering‐type near‐field optical microscopes

We describe the principles of two scattering‐type near‐field optical microscopes (s‐SNOMs), one operating at 633 nm wavelength, the other at selectable wavelengths in the range 7.3–11.3 µm, and compare the measurement experience. Both use interferometric detection of scattered radiation, and are therefore capable of amplitude and phase‐contrast imaging. In this study both instruments use the same or even identical commercial probe tips, and measure a single, three‐component, test sample. Our results show that the imaging process of s‐SNOM is wavelength‐independent, namely, that the resolution is determined by the properties of the tip only, and that the contrast is given by the complex refractive index of the sample, predictable from a simple, analytical model of tip–sample interaction. A novel, ‘edge‐darkening’ artefact is described which may appear in s‐SNOM and that is wavelength‐independent.