Miracle-dz/UniFAR-FTUs huggingface dataset:
TetAB(46), a predicted heterodimeric ABC transporter conferring tetracycline resistance in Streptococcus australis isolated from the oral cavity

Objectives To identify the genes responsible for tetracycline resistance in a strain of Streptococcus australis isolated from pooled saliva from healthy volunteers in France. S. australis is a viridans Streptococcus, originally isolated from the oral cavity of children in Australia, and subsequently reported in the lungs of cystic fibrosis patients and as a cause of invasive disease in an elderly patient. Methods Agar containing 2 mg/L tetracycline was used for the isolation of tetracycline-resistant organisms. A genomic library in Escherichia coli was used to isolate the tetracycline resistance determinant. In-frame deletions and chromosomal repair were used to confirm function. Antibiotic susceptibility was determined by agar dilution and disc diffusion assay. Results The tetracycline resistance determinant from S. australis FRStet12 was isolated from a genomic library in E. coli and DNA sequencing showed two open reading frames predicted to encode proteins with similarity to multidrug resistance-type ABC transporters. Both genes were required for tetracycline resistance (to both the naturally occurring and semi-synthetic tetracyclines) and they were designated tetAB(46). Conclusions This is the first report of a predicted ABC transporter conferring tetracycline resistance in a member of the oral microbiota.
Probabilistic Implicational Bases in FCA and Probabilistic Bases of GCIs in EL⊥

A probabilistic formal context is a triadic context whose third dimen-sion is a set of worlds equipped with a probability measure. After a formal definition of this notion, this document introduces probability of implications, and provides a construction for a base of implications whose probability satisfy a given lower threshold. A comparison between confidence and probability of implications is drawn, which yields the fact that both measures do not coincide, and cannot be compared. Furthermore, the results are extended towards the light-weight description logic EL ⊥ with probabilistic interpretations, and a method for computing a base of general concept inclusions whose probability fulfill a certain lower bound is proposed.
Visual resonator: interface for interactive cocktail party phenomenon

We present Visual Resonator (VR), an auditory interface that promises to provide an interactive realization of the Cocktail Party Phenomenon. The wearer of this interface can hear a voice or auditory information only from the direction in which he/she is facing, and can send his/her voice only in the direction towards which he/she is facing. In addition, individuals who are within sight of each other can have a conversation, even if they are not close enough to talk directly, since an infrared signal is used to transmit the auditory information.
Geometric Approaches for Top-k Queries

Top-k processing is a well-studied problem with numerous applications that is becoming increasingly relevant with the growing availability of recommendation systems and decision making software. The objective of this tutorial is twofold. First, we will delve into the geometric aspects of top-k processing. Second, we will cover complementary features to top-k queries, with strong practical relevance and important applications, that have a computational geometric nature. The tutorial will close with insights in the effect of dimensionality on the meaningfulness of top-k queries, and interesting similarities to nearest neighbor search.
Microtubule-associated proteins (MAPs) and the organization of actin filaments in vitro

When purified muscle actin was mixed with microtubule-associated proteins (MAPs) prepared from brain microtubules assembled in vitro, actin filaments were organized into discrete bundles, 26 nm in diameter. MAP-2 was the principal protein necessary for the formation of the bundles. Analysis of MAP-actin bundle formation by sedimentation and electrophoresis revealed the bundles to be composed of approximately 20% MAP-2 and 80% actin by weight. Transverse striations were observed to occur at 28-nm intervals along negatively stained MAP- actin bundles, and short projections, approximately 12 nm long and spaced at 28-nm intervals, were resolved by high-resolution metal shadowing. The formation of MAP-actin bundles was inhibited by millimolar concentrations of ATP, AMP-PCP (beta, gamma-methylene- adenosine triphosphate), and pyrophosphate but not by AMP, ADP, or GTP. The addition of ATP to a solution containing MAP-actin bundles resulted in the dissociation of the bundles into individual actin filaments; discrete particles, presumably MAP-2, were periodically attached along the splayed filaments. These results demonstrate that MAPs can bind to actin filaments and can induce the reversible formation of actin filament bundles in vitro.
Classical equations for quantum systems.

The origin of the phenomenological deterministic laws that approximately govern the quasiclassical domain of familiar experience is considered in the context of the quantum mechanics of closed systems such as the universe as a whole. A formulation of quantum mechanics is used that predicts probabilities for the individual members of a set of alternative coarse-grained histories that decohere, which means that there is negligible quantum interference between the individual histories in the set. We investigate the requirements for coarse grainings to yield decoherent sets of histories that are quasiclassical, i.e., such that the individual histories obey, with high probability, effective classical equations of motion interrupted continually by small fluctuations and occasionally by large ones. We discuss these requirements generally but study them specifically for coarse grainings of the type that follows a distinguished subset of a complete set of variables while ignoring the rest. More coarse graining is needed to achieve decoherence than would be suggested by naive arguments based on the uncertainty principle. Even coarser graining is required in the distinguished variables for them to have the necessary inertia to approach classical predictability in the presence of the noise consisting of the fluctuations that typical mechanisms of decoherence produce. We describe the derivation of phenomenological equations of motion explicitly for a particular class of models. Those models assume configuration space and a fundamental Lagrangian that is the difference between a kinetic energy quadratic in the velocities and a potential energy. The distinguished variables are taken to be a fixed subset of coordinates of configuration space. The initial density matrix of the closed system is assumed to factor into a product of a density matrix in the distinguished subset and another in the rest of the coordinates. With these restrictions, we improve the derivation from quantum mechanics of the phenomenological equations of motion governing a quasiclassical domain in the following respects: Probabilities of the correlations in time that define equations of motion are explicitly considered. Fully nonlinear cases are studied. Methods are exhibited for finding the form of the phenomenological equations of motion even when these are only distantly related to those of the fundamental action. The demonstration of the connection between quantum-mechanical causality and causality in classical phenomenological equations of motion is generalized. The connections among decoherence, noise, dissipation, and the amount of coarse graining necessary to achieve classical predictability are investigated quantitatively. Routes to removing the restrictions on the models in order to deal with more realistic coarse grainings are described.
Zebrafish fgf3 and fgf8 encode redundant functions required for otic placode induction.

Members of the fibroblast growth factor (FGF) family of peptide ligands have been implicated in otic placode induction in several vertebrate species. Here, we have functionally analyzed the roles of fgf3 and fgf8 in zebrafish otic development. The role of fgf8 was assessed by analyzing acerebellar (ace) mutants. fgf3 function was disrupted by injecting embryos with antisense morpholino oligomers (MO) specifically designed to block translation of fgf3 transcripts. Disruption of either fgf3 or fgf8 causes moderate reduction in the size of the otic vesicle. Injection of fgf3-MO into ace/ace mutants causes much more severe reduction or complete loss of otic tissue. Moreover, preplacode cells fail to express pax8 and pax2.1, indicating disruption of early stages of otic induction in fgf3-depleted ace/ace mutants. Both fgf3 and fgf8 are normally expressed in the germring by 50% epiboly and are induced in the primordium of rhombomere 4 by 80% epibloy. In addition, fgf3 is expressed during the latter half of gastrulation in the prechordal plate and paraxial cephalic mesendoderm, tissues that either pass beneath or persist near the prospective otic ectoderm. Conditions that alter the pattern of expression of fgf3 and/or fgf8 cause corresponding changes in otic induction. Loss of maternal and zygotic one-eyed pinhead (oep) does not alter expression of fgf3 or fgf8 in the hindbrain, but ablates mesendodermal sources of fgf signaling and delays otic induction by several hours. Conversely, treatment of wild-type embryos with retinoic acid greatly expands the periotic domains of expression of fgf3, fgf8, and pax8 and leads to formation of supernumerary and ectopic otic vesicles. These data support the hypothesis that fgf3 and fgf8 cooperate during the latter half of gastrulation to induce differentiation of otic placodes.
Facilitating Real-Time Applications in VANETs Through Fast Address Auto-Configuration

Real-time applications are going to play a major role in Vehicular Ad-hoc Networks (VANETs). In this context, nodes' IP addresses need to be automatically configured in a very small time and with a reduced need for re-configurations. Due to the very high mobility of vehicles, however, traditional mechanisms for address auto-configuration fail to perform well. Aimed at solving this problem, we propose a novel Leader-based scheme that exploits the topology of VANETs and a distributed DHCP service to guarantee fast and stable address configuration.
Intracorporeal Anastomosis in Laparoscopic Gastric Cancer Surgery

Laparoscopic gastrectomy has become widely used as a minimally invasive technique for the treatment of gastric cancer. When it was first introduced, most surgeons preferred a laparoscopic-assisted approach with a minilaparotomy rather than a totally laparoscopic procedure because of the technical challenges of achieving an intracorporeal anastomosis. Recently, with improved skills and instruments, several surgeons have reported the safety and feasibility of a totally laparoscopic gastrectomy with intracorporeal anastomosis. This review describes the recent technical advances in intracorporeal anastomoses using circular and linear staplers that allow for totally laparoscopic distal, total, and proximal gastrectomies. Data that demonstrate advantages in early surgical outcomes of a total laparoscopic method compared to laparoscopic-assisted operations are also discussed.
Social Group Modeling with Probabilistic Soft Logic

In this work, we show how to model the group affiliations of social media users using probabilistic soft logic. We consider groups of a broad variety, motivated by ideas from the social sciences on groups and their roles in social identity. By modeling group affiliations, we allow the possibility of efficient higher-level relational reasoning about the groups themselves, where the number of groups is relatively small compared to the number of users. We discuss preliminary results from experiments using real social media data collected from Twitter.
A computer-assisted depression intervention in primary care

Background The clinical benefit for depression of an interactive computer-assisted cognitive-behavioral program on CD-ROM, the Wellness Workshop (WW), was evaluated in a randomized controlled trial. Method A total of 191 individuals referred by primary-care physicians were randomly assigned to a control group, where physician-directed treatment as usual (TAU) was provided, or to a treatment group, where TAU was supplemented with the WW CD-ROM, delivered by mail (WW+TAU). Data were collected at baseline, at 6 weeks' post-intervention, and at a 6-month follow-up assessment. Participants were given a strong incentive by a reimbursement of $75 for completion of each assessment. Measures included symptom ratings obtained via structured clinical diagnostic interviews, as well as a battery of self-report questionnaires on symptoms specifically targeted by the intervention. Results Analysis of results demonstrated evidence for skill acquisition for improving dysfunctional thinking and reducing anxiety. Among those who met diagnostic criteria for depression, WW+TAU participants were three times more likely to remit at 6 weeks' post-test than TAU participants. Conclusions The evidence supports the conclusion that the WW intervention added benefit to traditional care for depression. No placebo comparison group was included and the WW+TAU participants received slightly more attention (a supportive telephone contact, ⩽5 min from a psychologist 2 weeks after receiving the program). Overall, the findings add support to the accumulating evidence for the potential clinical benefit of computer-assisted behavioral health interventions.
Relation of cortical areas MT and MST to pursuit eye movements. III. Interaction with full-field visual stimulation.

1. Pursuit eye movements are usually made against a visual background that is moved across the retina by the pursuit movement. We have investigated the effect of this visual stimulation on the response of pursuit cells that lie within the superior temporal sulcus (STS) of the monkey. 2. We assigned these pursuit cells to one of two groups depending on the nature of their preferred visual stimulus. One group of cells, comprising all cells located in the dorsal-medial region of the medial superior temporal area (MSTd) and some cells in lateral-anterior MST (MST1), responded to the motion of a large patterned field but showed little or no response to small spots or slits. The other group, consisting of all foveal middle temporal area (MTf) cells and many MST1 cells, responded preferentially to small spot motion or equally well to small spot motion or large field. 3. For many pursuit cells that preferred large-field stimuli, the visual response showed a reversal of the preferred direction of motion as the size of the stimulus field increased. The reversal usually occurred as the size of the moving random-dot field used as a stimulus increased in size from 20 x 20 degrees to 30 x 30 degrees for motion at approximately 10 degrees/s. The size of the filed stimulus leading to reversal of preferred direction depended on the speed of stimulus motion. Higher speeds of motion required larger stimulus fields to produce a reversal of preferred direction. This reversal (of preferred direction) did not reflect a center-surround organization of the receptive field but seemed to reflect the spatial summation properties of these cells. 4. For three-quarters of the cells that preferred large-field stimulation, the preferred direction of motion for the large field was opposite to the preferred direction of the pursuit response. The remaining cells showed either the same preferred directions for large-field visual stimulation and the pursuit response or had bidirectional visual responses. If we consider only the cells that show a reversal of preferred direction for large- and small-field stimuli, the preferred direction for the large field was always the opposite to that of pursuit, and the preferred direction for the small field was always the same. 5. During pursuit against a lighted background, the cells that showed opposite preferred directions for large-field stimulation and pursuit had synergistic responses--a facilitation of the pursuit response over the response during pursuit in the dark. Slow pursuit speeds (less than 20 degrees/s) produced the greatest facilitation. (ABSTRACT TRUNCATED AT 400 WORDS)
Association of p53 and p21(CDKN1A/WAF1/CIP1) polymorphisms with oral cancer in Taiwan patients.

BACKGROUND The tumor suppressor gene p53 and its downstream effector p21(CDKN1A/WAF1/CIP1) are thought to play major roles in the development of human malignancy. Polymorphic variants of p53, at codon 72, and CDKN1A, at codon 31, have been associated with cancer susceptibility, but few studies have investigated their effect on oral cancer risk. MATERIALS AND METHODS In this hospital-based case-control study, the association of p53 codon 72 and CDKN1A codon 31 polymorphisms with oral cancer risk in a Taiwanese population were investigated. In total, 137 patients with oral cancer and 105 age-matched controls recruited from the Chinese Medical Hospital in Central Taiwan were genotyped. RESULTS We found a significant difference in the frequency of the p53 genotype, but not the CDKN1A genotype, between the oral cancer and control groups. Those who had Arg/Arg at p53 codon 72 showed a 2.68-fold (95% confidence interval = 1.19-6.01) increased risk of oral cancer compared to those with Pro/Pro. The distribution of the combination of p53 codon 72 and CDKN1A codon 31 was different in the oral cancer and control groups. The percentages of three subgroups with the p53 GG homozygote were all higher in the oral cancer group, and the risky double homozygote, p53/CDKN1A GG/CC form, was almost 9-fold higher than the control group. CONCLUSION Our findings suggest that the homozygous Arg allele of the p53 codon 72 may be associated with the development of oral cancer and be a useful marker for primary prevention and anticancer intervention.
Complete androgen ablation suppresses prostate stem cell antigen (PSCA) mRNA expression in human prostate carcinoma

Prostate stem cell antigen (PSCA) is a recently identified glycosylphosphatidylinositol (GPI)‐anchored cell surface protein belonging to the Thy‐1/Ly‐6 family of cell surface antigens. Prior data in prostate cancers indicated that PSCA is directly regulated by androgens and PSCA expression increases with high‐tumor grade, advanced stage, extracapsular invasion, and androgen‐independent progression. The effect of complete androgen ablation (CAA) on tumor PSCA mRNA expression has not been elucidated. The purpose of the present study was to investigate the variations in the expression levels of PSCA mRNA before and after CAA, and further evaluate the clinically prognostic value of PSCA in human prostate carcinoma.
Verification of structural changes of glass when submitted to 17% EDTA

Introduction and objective: This in vitro study verified, through SEM, the structural changes on glass surface when submitted to EDTA. Material and methods: Samples of 4 glass coverslip remained partially (lower half of the sample) immersed in 17% EDTA pH 7.3 for different periods (7 days, 24 hours, 6 hours and 30 minutes). The samples were analyzed by SEM and photographed with x19, 50, 100, 200, 400, 1000, 2000, and 3000 magnification. Results: It was found that the four glass samples submitted to EDTA showed blisters and cracks regardless of time. The control sample showed few defects differing from those in contact with EDTA. Conclusion: EDTA led to changes in the glass structure.
Lack of an association of estrogen receptor alpha gene polymorphisms and transcriptional activity with Alzheimer disease.

BACKGROUND Long-term cognitive decline in postmenopausal women is associated with aging and Alzheimer disease (AD). Estrogen replacement therapy has been reported to reduce the risk of developing AD. The distribution of estrogen receptors (ERs) in neurons overlaps that of the brain neurons known to develop AD. Estrogen increases the secretion and metabolism of amyloid precursor protein, may help synapse formation, and is reported to protect neurons from toxins. Restriction fragment length polymorphisms (RFLPs) of the ERalpha gene at intron 1 and exon 2 were associated with a low bone mineral density in postmenopausal women and also with AD in a Japanese population. OBJECTIVE To determine whether ERalpha gene polymorphisms are associated with transcriptional activity and AD. METHODS A luciferase reporter assay analyzed enhancer activity of the ERalpha gene at intron 1 and exon 2. This activity was evaluated according to the RFLPs. The RFLPs of the ERalpha gene were determined in Japanese patients clinically diagnosed as having AD, white patients diagnosed as having AD at autopsy, and corresponding healthy control subjects. The RFLPs were also evaluated for the contribution of the ERalpha gene RFLPs to AD. RESULTS We found weak (about 2-fold) enhancer activity of the ERalpha gene, which differed among RFLPs. Although there were racial differences in these polymorphisms, we could not confirm the previously reported association between ERalpha gene polymorphisms and AD. CONCLUSION Regulatory element of the ERalpha gene was found in intron 1, but we found no association between ERalpha gene polymorphisms and AD.
Elastoplastic behavior of the metal matrix nanocomposites containing carbon nanotubes: A micromechanics-based analysis

The elastoplastic behavior of aluminum (Al) nanocomposites reinforced with aligned carbon nanotubes (CNTs) is characterized using a unit cell micromechanical model. The interphase zone caused by the chemical reaction between CNT and Al matrix is included in the analysis. To attain the elastoplastic stress–strain curve of the nanocomposites, the successive approximation method together with the von Mises yield criterion is employed. The effects of several important factors including the volume fraction and diameter of CNT, material properties, and size of interphase on the elastoplastic stress–strain curve of the nanocomposites during uniaxial tension are studied. The results indicate that the interphase characteristics significantly affect the elastoplastic behavior of the CNT-reinforced Al nanocomposites. It is also found that the yield stress of the nanocomposites rises with increasing CNT volume fraction or decreasing CNT diameter. Besides, the elastoplastic stress–strain curve of the CNT-reinforced Al nanocomposites is presented for multiaxial tension. The initial yield envelopes of the nanocomposites under longitudinal–transverse biaxial tension are provided too. Comparison between the elastic results of the present model with those of other available micromechanical analyses shows a very good agreement.