Miracle-dz/UniFAR-FTUs huggingface dataset:
Quoted Spreads and Trade Imbalance Dynamics in the European Treasury Bond Market

Using high-frequency transaction data for the three largest European markets (France, Germany and Italy), this paper documents the existence of an asymmetric relationship between market liquidity and trading imbalances: when quoted spreads rise (fall) and liquidity falls (increases) buy (sell) orders tend to prevail. Risk-averse market-makers, with inventory-depletion risk being their main concern, tend to quote wider (narrower) spreads when they think bond appreciation is more (less) likely to occur. It is also found that the probability of being in a specific regime is related to observable bond market characteristics, stock market volatility, macroeconomic releases and liquidity management operations of the monetary authorities.
Low co-existence rates of Lactobacillus spp. and Helicobacter pylori detected in gastric biopsies from patients with gastrointestinal symptoms.

BACKGROUND bacterial diversity of the stomach includes various species. Among them, Helicobacter pylori, a microorganism which has been associated to gastric diseases, is frequently isolated in this habitat. In addition, Lactobacillus spp. , a genus including probiotic strains, has also been documented in this habitat. The co-existence of these two species in the stomach of symptomatic patient needs to be elucidated. AIMS our goal was to establish if Lactobacillus spp. and H. pylori co-exist in the stomach mucosa of symptomatic patients. METHODS gastric biopsies (antrum and/or the body) from 427 Chilean patients with gastrointestinal discomfort were analyzed. The H. pylori infection and/or Lactobacillus spp. colonization status was determined for each patient by standard culture techniques, and statistical correlations between the presence of those species and the age, gender, or the severity of the gastric disease were also established. RESULTS only 6.1% of the samples presented co-existence of Lactobacillus spp. and H. pylori. This former species was isolated in 42.6% of the patients as unique species, while Lactobacillus spp. was isolated as single species in 19.4% of the individuals. Chronic non-atrophic gastritis was prevalent in Lactobacillus spp. non colonized individuals, while chronic non-atrophic and chronic atrophic gastritis diagnosis was similar in Lactobacillus spp. harbouring individuals (p < 0.001). The presence of Lactobacillus spp. Significantly increased with age (p = 0.005), independently of gender. CONCLUSION the negative Pearson correlation between Lactobacillus spp. and H. pylori (r = -0.112, p = 0.020) indicates that the co-existence of both species is low in human gastric mucosa of symptomatic patients.
The Journey of Arsenic from Soil to Grain in Rice

Arsenic (As) is a non-essential toxic metalloid whose elevated concentration in rice grains is a serious issue both for rice yield and quality, and for human health. The rice-As interactions, hence, have been studied extensively in past few decades. A deep understanding of factors influencing As uptake and transport from soil to grains can be helpful to tackle this issue so as to minimize grain As levels. As uptake at the root surface by rice plants depends on factors like iron plaque and radial oxygen loss. There is involvement of a number of transporters viz., phosphate transporters and aquaglyceroporins in the uptake and transport of different As species and in the movement to subcellular compartments. These processes are also affected by sulfur availability and consequently on the level of thiol (-SH)-containing As binding peptides viz., glutathione (GSH) and phytochelatins (PCs). Further, the role of phloem in As movement to the grains is also suggested. This review presents a detailed map of journey of As from soil to the grains. The implications for the utilization of available knowledge in minimizing As in rice grains are presented.
Slow wave activity in the medial prefrontal cortex of the anaesthetised rat : sub-regional characterisation and dopaminergic modulation

ii Acknowledgements . iii Publications . v Table of contents . vi List of figures . x List of tables . xiv List of abbreviations . xv Chapter 1. General introduction . 1 1.1 The mammalian prefrontal cortex . 1 1.2 The rat medial prefrontal cortex . 4 1.2.1 Location and functional homology with the human brain . 4 1.2.2 Laminar structure defines mPFC sub-regions . 4 1.2.3 Connectivity of mPFC sub-regions . 5 1.2. 4 Functions of mPFC sub-regions . 5 1.2. 5 A dorsal-to-ventral division of the mPFC . 8 1.2. 6 Evidence for a differential role of the DP and the underlying dorsal tenia tecta . 8 1.3 Brain rhythms during wakefulness in the prefrontal cortex . 8 1.4 Sleep and associated brain rhythms . 10 1.4. 1 Sleep stages . 10 1.4. 2 Discovery of cortical slow wave activity (SWA) . 12 1.4. 3 Occurrence of SWA/UDS . 13 1.4. 4 UDS – cortical or thalamic origin? 13 1.4. 5 The three-oscillator model of UDS . 14 1.4. 6 SWA as a travelling wave . 17 1.4. 7 Slow waves and nested oscillations . 18 1.4. 8 Function of SWA . 22 1.4. 9 Function of nested fast oscillations during SWA . 25 1.5 Dopamine . 27 1.5. 1 Dopamine pathways of the brain . 27 1.5. 2 Projections from the VTA to the mPFC . 28 1.5. 3 Dopamine receptors . 28 1.5. 4 Effects of dopamine in the brain . 29 1.5. 5 PFC functions regulated by dopamine . 32 1.5. 6 Features of dopamine action . 33 1.5. 7 Dopamine disorders and sleep disturbances . 33 1.6 Thesis overview . 34 Chapter 2. Methods . 35 2.1 Animals . 35 2.2 Electrophysiological recordings under anaesthesia . 35 2.2.1 Anaesthesia . 35 2.2.2 Surgery . 35 2.2.3 Recording electrodes and coordinates . 36 2.2. 4 Data acquisition . 37 2.2. 5 Histological verification of recording site position . 39 2.3 Experimental interventions . 43
Comprehensive identification of translation start sites by tetracycline-inhibited ribosome profiling

Tetracycline-inhibited ribosome profiling (TetRP) provides a powerful new experimental tool for comprehensive genome-wide identification of translation initiation sites in bacteria. We validated TetRP by confirming the translation start sites of protein-coding genes in accordance with the 2006 version of Escherichia coli K-12 annotation record (GenBank U00096.2) and found ∼150 new start sites within 60 nucleotides of the annotated site. This analysis revealed 72 per cent of the genes whose initiation site annotations were changed from the 2006 GenBank record to the newer 2014 annotation record (GenBank U00096.3), indicating a high sensitivity. Also, results from reporter fusion and proteomics of N-terminally enriched peptides showed high specificity of the TetRP results. In addition, we discovered over 300 translation start sites within non-coding, intergenic regions of the genome, using a threshold that retains ∼2,000 known coding genes. While some appear to correspond to pseudogenes, others may encode small peptides or have previously unforeseen roles. In summary, we showed that ribosome profiling upon translation inhibition by tetracycline offers a simple, reliable and comprehensive experimental tool for precise annotation of translation start sites of expressed genes in bacteria.
[Experimental study of pituitary adenylate cyclase activating polypeptide on relieving brain edema induced by ischemia in rats].

AIM In order to study the effects of pituitary adenylate cyclase activating polypeptide(PACAP) on brain edema induced by ischemia in rats and its underlying receptor mechanism. METHODS Brain ischemia model in rats was established by ligaturing four--vessels. The percentage ratio of wet over dry tissue weight, sodium and potassium contents of dry brain tissue were measured by weighing and enzymatic analysis methods. RESULTS The brain water contents significantly increased after rats exposed to 1 h of reperfusion following 30 - minute ischemia. Furthermore, sodium contents in brain tissue increased and potassium contents decreased following perfusion. Changes of brain water contents, sodium and potassium contents were relieved by lateral ventricular injection of PACAP in the concentration of 1 x 10(-9), 1 x 10(-10) or 1 x 10(-11) mol respectively before ischemia. The effect of PACAP could be blocked by MCAP6 - 38 (specific type I PACAP receptor antagonist) lateral ventricular injection prior to PACAP administration. CONCLUSION Exogenous PACAP may act as a protective effect in brain edema induced by ischemia in rats, which is mediated by type I receptor.
Closed-Loop Force Control for Haptic Simulation of Virtual Environments

Force feedback control is investigated for improving the quality of the haptic feedback in virtual reality applications. Advanced control design can increase the transparency of the haptic device at the haptic interface thereby increasing the realism of the simulation. Force feedback also enables the implementation of admittance control approaches heretofore considered the domain of large robotic platforms. The quality of the haptic interface is "rst quanti"ed, and the standard open-loop impedance approach to haptic control is reviewed. Dual-input control schemes with sensory force feedback are then introduced, and the resulting quality of the haptic interface is derived. A four-bar linkage example is used to illustrate the improvement in "delity realized with the various approaches. The tradeoffs encountered in moving to force feedback controllers for haptic applications are also discussed.
How contingent should a lifelike robot be? The relationship between contingency and complexity

We believe that lifelikeness is important to make it possible for a communication robot to interact naturally with people. In this research, the relationship between contingency and complexity in a lifelike robot was investigated. We have developed a robot control system to control experimentally contingency and complexity in interaction by combining a humanoid robot with a motion-capturing system. Two independent experiments were conducted with different levels of interaction complexity: simple interaction and complex interaction. Experiments in the simple interaction situation indicated that subjects felt that the robot behaved autonomously when contingency was low, and there was no significant relationship between contingency and a lifelike impression. On the other hand, experiments in the complex interaction situation showed that the robot gave the subjects the impression of being more autonomous and lifelike when contingency was high.
Identification of Xanthine Oxidase Activity Following Reperfusion in Human Tissue

&NA; In this series of experiments, we surveyed xanthine oxidase activity after microvascular transfer in the venous effluent after reperfusion of human rectus abdominis muscle (n = 8) and jejunum (n = 4). Enzyme activity was correlated with duration of ischemia and biochemical markers of cellular injury. Xanthine oxidase (XO) activity was measured spectrofluorometrically using a pterin assay, whereas cellular injury was measured with commercial creatinine phosphokinase activity assay and lipid peroxidation products using a spectrophotometer. The data demonstrated that XO activity was statistically significantly increased in muscle flaps kept at room temperature during ischemia compared with muscle flaps that were cooled (p < 0.05). Creatinine phosphokinase activity was also increased after 15 minutes of reperfusion in muscle flaps that were not cooled (p < 0.05). Two of the jejunal free flaps had ischemia times of >1 hour and had elevated XO activity after reperfusion despite cooling (p<0.05). Two other jejunal flaps had ischemia times of <1 hour, but in one case, the XO activity was increased before harvest. The other case had no increase in XO activity. Wilkins EG, Rees RS, Smith D, Cashmer B, Punch J, Till GO, Smith DJ Jr. Identification of xanthine oxidase activity following reperfusion in human tissue. Ann Plast Surg 1993;31:60‐65
RelE-Mediated Dormancy Is Enhanced at High Cell Density in Escherichia coli

ABSTRACT Bacteria show remarkable adaptability under several stressful conditions by shifting themselves into a dormant state. Less is known, however, about the mechanism underlying the cell transition to dormancy. Here, we report that the transition to dormant states is mediated by one of the major toxin-antitoxin systems, RelEB, in a cell density-dependent manner in Escherichia coli K-12 MG1655. We constructed a strain, IKA121, which expresses the toxin RelE in the presence of rhamnose and lacks chromosomal relBE and rhaBAD. With this strain, we demonstrated that RelE-mediated dormancy is enhanced at high cell densities compared to that at low cell densities. The initiation of expression of the antitoxin RelB from a plasmid, pCA24N, reversed RelE-mediated dormancy in bacterial cultures. The activation of RelE increased the appearance of persister cells against β-lactams, quinolones, and aminoglycosides, and more persister cells appeared at high cell densities than at low cell densities. Further analysis indicated that amino acid starvation and an uncharacterized extracellular heat-labile substance promote RelE-mediated dormancy. This is a first report on the induction of RelE-mediated dormancy by high cell density. This work establishes a population-based dormancy mechanism to help explain E. coli survival in stressful environments.
Alteration of the sex determining system resulting from structural change of the sex chromosomes in the frog Rana rugosa.

Rana rugosa in Japan is divided into four geographical races on the basis of the karyotype of the sex chromosomes: one in which heteromorphic sex chromosomes occur in the female sex (ZW/ZZ-system), another in which they are present in males (XX/XY-system), and the remaining two in which no heteromorphism is seen in either sex. The last two inherit the XX/XY sex determining system. Y and Z chromosomes in the former two are of the same karyotype as the no. 7 chromosomes seen in one of the latter two, whereas X and W are caused by two inversions that occurred in the original Xs (no. 7). In this study, we first attempted to detect the structural difference between the resulting X and W by examining their chiasma formation. The chiasma distribution between X and W was closely similar to that between two Xs, suggesting that the W and X are identical in structure. Regarding the change from XX/XY- to ZW/ZZ-system, the simplest explanation is that the putative female-determining gene(s) on the W grew functionally stronger by inversions. Next, we examined the sex of triploids having two Xs and one Z. The data showed that the triploids with two original Xs and a Z were all male, whereas most of those with two resulting Xs and a Z developed into females as expected. We speculated that the female-determining gene(s) on the resulting X grew mildly stronger functionally by position effect, whereas those on the W grew much stronger for some other reason (e.g., duplication). J. Exp. Zool. 286:313-319, 2000.
O-MAP: A per-component online anomaly predicting method for Cloud infrastructure

Virtualized cloud systems are prone to performance anomalies due to various reasons such as resource contentions, software bugs, and hardware failures. It will be a daunting task for system administrators to manually keep track of the execution status of a large number of virtual machines all the time. Anomaly prediction is an effective approach to enhancing availability and reliability of Cloud infrastructures. In this paper, we propose O-MAP, a supervised online anomaly prediction scheme based on Hidden Markov Model (HMM). Our algorithm is basically distributed and runs locally on each computing machine on the Cloud in order to achieve high scalability. Experiments performed on real data sets validate the fact that our algorithm can achieve high prediction accuracy for a range of system anomalies with low overhead to the infrastructure in Cloud.
Entity Extraction is a Boring Solved Problem—Or is it?

This paper presents empirical results that contradict the prevailing opinion that entity extraction is a boring solved problem. In particular, we consider data sets that resemble familiar MUC/ACE data, and report surprisingly poor performance for both commercial and research systems. We then give an error analysis that suggests research challenges for entity extraction that are neither boring nor solved.
Nup358/RanBP2 Attaches to the Nuclear Pore Complex via Association with Nup88 and Nup214/CAN and Plays a Supporting Role in CRM1-Mediated Nuclear Protein Export

ABSTRACT Nuclear pore complexes (NPCs) traverse the nuclear envelope (NE), providing a channel through which nucleocytoplasmic transport occurs. Nup358/RanBP2, Nup214/CAN, and Nup88 are components of the cytoplasmic face of the NPC. Here we show that Nup88 localizes midway between Nup358 and Nup214 and physically interacts with them. RNA interference of either Nup88 or Nup214 in human cells caused a strong reduction of Nup358 at the NE. Nup88 and Nup214 showed an interdependence at the NPC and were not affected by the absence of Nup358. These data indicate that Nup88 and Nup214 mediate the attachment of Nup358 to the NPC. We show that localization of the export receptor CRM1 at the cytoplasmic face of the NE is Nup358 dependent and represents its empty state. Also, removal of Nup358 causes a distinct reduction in nuclear export signal-dependent nuclear export. We propose that Nup358 provides both a platform for rapid disassembly of CRM1 export complexes and a binding site for empty CRM1 recycling into the nucleus.
Selective Attention and Stimulus–Reinforcer Interactions in the Pigeon

The study supplies further evidence that non-associative effects and temporal–spatial similarities between certain combinations of cue and consequence cannot explain all instances of stimulus–reinforcer interactions. Pigeons were trained to press a treadle in the presence of a discriminative compound stimulus either to avoid shock or to obtain a food reinforcer. The compound stimulus was composed of diffuse tone and light cues which had identical temporal patterns of onset, duration and offset. With the avoidance schedule the auditory cue acquired more control than the visual cue; however, when food was the reinforcer, the visual cue exerted more control. This pattern of stimulus control on the appetitive schedule did not change if random shocks were also added, even though these shocks were equal in density to the food presentations and equal in magnitude to those used for the avoidance schedule. Other changes in the appetitive procedure, such as making the tone spatially contiguous with food and removing the light in the food hopper, also failed to alter the relative control by the different cues. Prior training with a food reinforcer did not produce any change in the relative control by the two cues when the birds were retrained on the shock-avoidance schedule. The results suggest that some frequently stated alternatives to selective associability are not adequate explanations of this instance of a stimulus-reinforcer interaction.
Detection of the proto-oncogene eIF4E in larynx and hypopharynx cancers.

BACKGROUND The proto-oncogene eIF4E has been found to be elevated in head and neck squamous cell carcinomas. In an earlier prospective study overexpression of eIF4E, detected by Western blot analysis, in histologically normal surgical margins correlated with an increased local-regional recurrence rate during a 1-year follow-up. OBJECTIVE To test the reverse hypothesis that absence of overexpression of eIF4E in the surgical margins is a predictor for long-term survival in patients with squamous cell carcinoma of the head and neck. DESIGN A retrospective analysis was performed on 31 patients who underwent surgery for squamous cell carcinoma of the larynx or hypopharynx. Immunohistochemical analysis was used to detect eIF4E on paraffin embedded sections of the tumor and the histologically negative surgical margins. RESULTS All 31 patients overexpressed eIF4E in the tumors. Thirteen patients had no detectable level of eIF4E in the margins, and only 1 had a local-regional recurrence. The average disease-free interval in this group of patients was 82.08 months. The remaining 18 patients all overexpressed eIF4E in the surgical margins (eIF4E score range, 5-80). Twelve (67%) of these patients developed a recurrence; the average disease-free interval was 31.95 months. Cox regression analysis showed that eIF4E in the margin (P= .01), nodes (P= .06), site (P= .02), and age (P= .02) had significant effects on the disease-free interval. The Kaplan-Meier survival curves were significantly different for eIF4E-positive and eIF4E-negative margins (P = .002). CONCLUSIONS eIF4E in the surgical margins is an independent prognostic factor and its absence in surgical margins may predict long-term survival. Detecting eIF4E in the margins may improve survival by determining which patients would benefit from further resection or adjuvant therapy.
Biofilms in chronic diabetic foot ulcers—a study of 2 cases

Among the 55 million people in Europe diagnosed as having diabetes mellitus (www.diabetesatlas.org), the lifetime risk of developing a foot complication—often infected wounds—could be as high as 25% (Boulton et al. 2005). Many of the patients with severe infections will require amputation within the foot or above the ankle. Approximately 85% of lower-limb amputations in patients with diabetes are preceded by infected foot ulceration (Adler et al. 1999). Polymicrobial infections predominate in severe diabetic foot infections (Dowd et al. 2008a) and the medical community is now beginning to realize that the diversity of bacterial populations in chronic wounds (Dowd et al. 2008b, James et al. 2008) may be an important contributor to the chronicity of wounds, such as diabetic foot ulcers. In addition, another obstacle to the healing of chronic wounds is the biofilm mode of growth of the infecting organisms (Wolcott and Rhoads 2008). By definition, biofilms are microbial populations that are attached to a surface, or to the surfaces of other organisms, and encase themselves in hydrated extracellular polymeric substance (EPS), which is also referred to as “slime”. The chemical and physical properties of EPS can vary, but it is mainly composed of polysaccharides. EPS is also associated with other macromolecules such as proteins, DNA, lipids, and even humic substances (Nielsen et al. 1996, Tsuneda et al. 2003). Biofilm-related diseases are usually persistent infections that develop slowly. They appear to be rarely cleared by the host immune system and are highly resistant to antimicrobial therapy (Stewart and Costerton 2001). For example, antibiotic resistance in biofilm bacteria of up to 1,000 times that of planktonic bacteria has been extensively documented in experiments in vitro (Stewart and Costerton 2001). Infected diabetic foot ulcers share these characteristics, and it has been hypothesized that biofilms may play a role in these infections (Davis et al. 2006, Dowd et al. 2008a). We evaluated debrided soft tissue from infected diabetic foot ulcers by confocal laser scanning microscopy (CLSM). Part of the debrided tissue was also analyzed using culture methods to evaluate bacterial diversity of the biofilms.