Miracle-dz/UniFAR-FTUs huggingface dataset:
Expression of trkB in Human Neuroblastoma in Relation to MYCN Expression and Retinoic Acid Treatment

Expression of full-length trkB can be found in some highly malignant neuroblastoma tumors with an amplified MYCN gene. This contrasts sympathetic neuroblasts, from which neuroblastomas are thought to arise, which neither express trkB nor are dependent on the p145trkB ligands, brain-derived neurotrophic factor (BDNF) or neurotrophin-4/5, for their normal development. In this study we show that trkB was expressed in two out of five neuroblastoma tumors with amplified MYCN, while no trkB expression was observed when the MYCN gene was overexpressed in a non–MYCN-amplified neuroblastoma cell line. This shows that MYCN overexpression per se is not sufficient to induce trkB expression. trkB expression and BDNF responsiveness in neuroblastoma cells can be induced by all-trans-retinoic acid (RA). When SH-SY5Y cells were stimulated with a combination of RA and BDNF, norepinephrine and tyrosine hydroxylase levels were unaltered, showing that the cells did not change toward a more catecholaminergic sympathetic phenotype. However, expression of growth-associated protein 43, indicative of a neuronal phenotype, was elevated. Vesicular acetylcholine transporter, choline acetyl transferase, and neuropeptide tyrosine mRNA levels also increased in RA-BDNF–treated cells, which could suggest that these cells develop into a sympathetic cholinergic phenotype. In addition, treatment with RA-induced expression of the platelet-derived growth factor receptor-α. As previously shown for BDNF, platelet-derived growth factor stimulated growth of the RA-treated cells, findings that could have clinical relevance. If these receptors mediate a mitogenic signal in vivo also, this might limit the effect of RA treatment on neuroblastoma patients.
A Geometric take on Metric Learning

Multi-metric learning techniques learn local metric tensors in different parts of a feature space. With such an approach, even simple classifiers can be competitive with the state-of-the-art because the distance measure locally adapts to the structure of the data. The learned distance measure is, however, non-metric, which has prevented multi-metric learning from generalizing to tasks such as dimensionality reduction and regression in a principled way. We prove that, with appropriate changes, multi-metric learning corresponds to learning the structure of a Riemannian manifold. We then show that this structure gives us a principled way to perform dimensionality reduction and regression according to the learned metrics. Algorithmically, we provide the first practical algorithm for computing geodesics according to the learned metrics, as well as algorithms for computing exponential and logarithmic maps on the Riemannian manifold. Together, these tools let many Euclidean algorithms take advantage of multi-metric learning. We illustrate the approach on regression and dimensionality reduction tasks that involve predicting measurements of the human body from shape data.
High pulse energy near-infrared ultrafast optical parametric oscillators

A source-demand in the nearand mid-IR wavelength spectrum exists for various applications such as waveguide inscription, multiphoton imaging, and nonlinear spectroscopy. All of the applications seek for higher repetitions rates for faster processing speed, better signal to noise ratios or to improve the results for applications like laser waveguide inscription. This is in contrast to the high pulse energies, required to drive the nonlinear processes involved with these applications. Available systems are either based on low-energy, high-repetition-rate optical parametric oscillators or highenergy, low-repetition-rate optical parametric amplifiers. In this thesis a sources was developed that can bridge the wide gap between these two extremes, providing sufficient energy to drive nonlinear processes, with repetition rates in the MHz domain. This was achieved by introducing three techniques previously employed for energy scaling in laser cavities. Firstly an exchange from the conventionally used Ti:sapphire pump to a commercial high power Yb:fibre laser system readily scaled the usable pump energy. This was combined with a technique known as cavity-length extension, which allows a lowering of the cavity roundtrip time offering the build-up of pulses with increased energy. In a final stage, cavity-dumping on basis of an acousto-optic modulator was introduced into the a redesigned cavity. The combination of these three techniques, novel to synchronously pumped optical parametric oscillators, enabled the extraction of record-high pulse energies and peak powers.
Enhancements for local feature based image classification

Using local features with nearest neighbor search and direct voting obtains excellent results for various image classification tasks. In this work we decompose the method into its basic steps which are investigated in detail. Different feature extraction techniques, distance measures, and probability models are proposed and evaluated. We show that improvements are possible for each of the investigated enhancements. This shows that the important aspect of the framework is the decomposition of the training images into sets of local features for each class.
Radiographic Evaluation of Monocortical Versus Tricortical Purchase Approaches in Lumbosacral Fixation With Sacral Pedicle Screws: A Prospective Study of Ninety Consecutive Patients

Study Design. Prospective radiographic outcome analysis. Objective. Radiographic evaluation of the rigidity of monocortical and tricortical purchase in lumbosacral fixation. Summary of Background Data. The lumbosacral junction continues to be a difficult region to obtain a successful spinal arthrodesis and is one of the primary regions for construct failure. In inserting sacral screws, 3 types of purchase are known: monocortical, bicortical, and tricortical. Among them no clinical or basic studies have compared monocortical with tricortical purchase. Methods. Ninety consecutive patients diagnosed with spondylolisthesis who underwent lumbosacral fixation were evaluated. Fifty-three patients were treated with a monocortical approach and the other 37 patients were treated with a tricortical approach. Patients underwent surgery for posterolateral fusion or transforaminal lumbar interbody fusion (TLIF) according to their diagnosis. Their radiologic findings, radiolucent zones around sacral screws, and lumbosacral instability of more than 2° flexion just after the surgery and 1 year later were compared. The angulation and length of the inserted screw were also measured and evaluated. Results. There were no significances in the distributions of gender, average age, proportion of fixation method, and fusion range between the monocortical and tricortical groups (P > 0.05). Radiolucent zones and lumbosacral instability were more prevalent in the monocortical group than were in the tricortical group. Smaller angulation also affected the outcome in the monocortical group while screw length did not. Multivariate logistic regression analysis of possible risk factors revealed that female gender (odds ratio [OR]: 3.56, 95% confidence interval [CI]: 1.18–10.8), TLIF operative method (OR: 5.54, 95% CI: 1.08–8.2), number of fusion levels (OR: 1.84, 95% CI: 1.05–3.18), and monocortical purchase (OR: 7.11, 95% CI: 1.58–31.9) were statistically significant. Conclusion. More loosening of sacral screws was radiographically observed in the monocortical purchase group than in the tricortical group 1 year after the lumbosacral fixation surgery. A statistical analysis indicated that the tricortical approach should be used for patients undergoing multilevel fusion including lumbosacral junction by TLIF.
The role of zinc in the stability of the marginally stable IscU scaffold protein

Understanding the factors that determine protein stability is interesting because it directly reflects the evolutionary pressure coming from function and environment. Here, we have combined experimental and computational methods to study the stability of IscU, a bacterial scaffold protein highly conserved in most organisms and an essential component of the iron–sulfur cluster biogenesis pathway. We demonstrate that the effect of zinc and its consequence strongly depend on the sample history. IscU is a marginally stable protein at low ionic strength to the point that undergoes cold denaturation at around −8°C with a corresponding dramatic decrease of enthalpy, which is consistent with the fluxional nature of the protein. Presence of constitutively bound zinc appreciably stabilizes the IscU fold, whereas it may cause protein aggregation when zinc is added back posthumously. We discuss how zinc coordination can be achieved by different side chains spatially available and all competent for tetrahedral coordination. The individual absence of some of these residues can be largely compensated by small local rearrangements of the others. We discuss the potential importance of our findings in vitro for the function in vivo of the protein.
Decreased Apoptosis in the Ileum and Ileal Peyer's Patches: a Feature after Infection with Rabbit EnteropathogenicEscherichia coli O103

ABSTRACT Significant changes occur in intestinal epithelial cells after infection with enteropathogenic Escherichia coli (EPEC). However, it is unclear whether this pathogen alters rates of apoptosis. By using a naturally occurring weaned rabbit infection model, we determined physiological levels of apoptosis in rabbit ileum and ileal Peyer's patches (PP) and compared them to those found after infection with adherent rabbit EPEC (REPEC O103). Various REPEC O103 strains were first tested in vitro for characteristic virulence features. Rabbits were then inoculated with the REPEC O103 strains that infected cultured cells the most efficiently. After experimental infection, intestinal samples were examined by light and electron microscopy. Simultaneously, ileal apoptosis was assessed by using terminal deoxynucleotidyltransferase-mediated dUTP-biotin nick end labeling (TUNEL) and caspase 3 assays and by apoptotic cell counts based on morphology (hematoxylin-and-eosin staining). The highest physiological apoptotic indices were measured in PP germinal centers (median = 14.7%), followed by PP domed villi (8.1%), tips of absorptive villi (3.8%), and ileal crypt regions (0.5%). Severe infection with REPEC O103 resulted in a significant decrease in apoptosis in PP germinal centers (determined by TUNEL assay; P = 0.01), in the tips of ileal absorptive villi (determined by H&E staining;P = 0.04), and in whole ileal cell lysates (determined by caspase 3 assay; P = 0.001). We concluded that REPEC O103 does not promote apoptosis. Furthermore, we cannot rule out the possibility that REPEC O103, in fact, decreases apoptotic levels in the rabbit ileum.
Common Bile Duct Stone Exploration: T-Tube or Biliary

Introduction: Laparoscopic common bile duct exploration (LCBDE) for choledocholithiasis is a popular option in many surgical institutes. Decompression of biliary system via T-tube post supraduodenal choledochotomy has been the traditional surgical practice. Primary closure of common bile duct (CBD) has been shown to reduce hospital stay but bears a risk of bile leak. We conducted a prospective randomized trial to compare complications and length of stay in patients undergoing biliary stent insertion versus T-tube drainage following LCBDE via choledochotomy. Methods and Procedures: The study involves 52 patients with choledocholithiasis who underwent LCBDE and decompression of the biliary system by either antegrade biliary stent or T-tube insertion. A 7 French biliary stent (9 “10 cm long) have been placed in 27 patients (group I), T-tube insertion have been used for 25 patients (group II). The length of hospital stay and complications were recorded. All transcystic explorations were excluded. Results: There were no significant differences between groups with respect to age, sex, comorbidities, number and size of CBD stones. Postoperative complications have been observed in 4 patients (16%) in the T-tube group (one patient needed reoperation for dislocation of T-tube), and in 1 patient (3.7%) in the biliary stent group (p < 0.05). The mean postoperative hospital stay was 3.2 Â± 1.2 days for group I, and 6.2 Â± 1.7 days for group II (p < 0.05). Conclusions: Our results showed a reduction of length of hospital stay and morbidity following stent insertion compared to T-tube drainage. Also, the use of biliary stent after LCBDE can reduce costs and increase patient satisfaction. The present study is one of the first randomized cohort studies which compares outcomes and length of stay in patients undergoing ante-grade biliary stenting versus T-tube drainage after LCBDE via choledochotomy. The study was performed in a single centre by a group of surgeons experienced in laparoscopic biliary surgery.
Eyelid measurements using digital video processing

The aim of this paper is to present an automatic eyelid measurement system based on digital video processing techniques. Currently, the protocol to measure the palpebral fissure (PF) and the marginal reflex distance (MRD) requires the use of a millimetric ruler. This procedure is subject to error and the accuracy and reproducibility of the results depend on the experience of the examiner. The computer vision system introduced in this paper uses two near infrared light sources synchronized with the camera to robustly detect and track the pupil, and then segment the limbus and the eyelids. The corneal reflection generated by the light sources are used to create a reference point that is used to define the vertical line along which the measurements are taken, and to determine when the patient is actually looking at the camera. Our experimental results show that the system is robust to the presence of eyelashes, glasses, and contact lenses, and the measurements can be accurate to tenths of millimeters.
Extending the Textbook Dynamic AD-AS Framework with Flexible Inflation Expectations, Optimal Policy Response to Demand Changes, and the Zero-Bound on the Nominal Interest Rate

Many popular macroeconomics textbooks have recently adopted the dynamic aggregate demand-aggregate supply framework to analyze business cycle fluctuations and the effects of monetary policy. This brings the textbook treatment much closer to the research frontier, although a major remaining difference is the treatment of inflation expectations. Textbook treatments typically assume adaptive expectations for tractability. In this paper, we extend the model presented in Mankiw [1] by incorporating a more flexible form of expectation formation that is determined as a weighted average of past inflation and the inflation target. This brings the treatment closer to rational expectations and allows for a discussion of costless disinflation. Monetary policy is assumed to follow a Taylorrule, but we allow for deviations from the rule to motivate a discussion regarding optimal monetary policy response to demand shocks. We also include a shock to the risk-premium on the interest rate relevant for demand relative to the policy rate set by the Central Bank, and impose the zero-bound on the nominal interest rate in the solution of the model. These features allow for the analysis of the recent financial crisis, monetary policy falling into a liquidity trap, and the desirability of a temporary increase in the inflation target. Finally, we make available an Excel sheet with which students can analyze the effect of shocks to the economy using impulse responses and dynamic aggregate demand-aggregate supply diagrams.
Performance Optimization Based on Analytical Modeling in a Real-Time System with Constrained Time/Utility Functions

We consider a single-processor firm real-time (FRT) system with exponential interarrival and execution times for jobs with relative deadlines following a general distribution. The scheduling policy of the system is first-come first-served (FCFS) and the capacity of the system is arbitrary. This system is subject to an arbitrary-shaped time/utility function (TUF), which determines the accrued utility of each job according to its completion time. It is considered that the system power consumption at different working states is predetermined for each processor speed. We have proposed an exact analytical method for the calculation of specific performance and power-related measures of the system. The resulting analytical formulations for the performance measures are functions of the processor speed and system capacity. These measures are optimized through appropriate selections of the speed using derivatives and the capacity employing numerical search methods. Some experimental results are presented for different unimodal TUFs in systems with deterministic and exponential relative deadlines. For the latter distribution, the results are compared against similar results obtained through simulation for the nonpreemptive earliest-deadline-first (NP-EDF) scheduling policy. The comparisons show that FCFS is superior to NP-EDF for some measures and TUFs.
Open versus laparoscopy-assisted radical cystectomy: results of a prospective study.

BACKGROUND AND PURPOSE Laparoscopic radical cystectomy is confined to centers where advanced laparoscopy is performed, and its role is not yet well clear. Our aim was to evaluate, through a prospective comparative study, the advantages of the laparoscopic compared with an open approach. PATIENTS AND METHODS From November 2002 to December 2005, all the patients in our center who were found to have muscle-invasive bladder cancer without clinical evidence of lymph-node involvement and an American Society of Anesthesiologists (ASA) score <4 were included in a prospective nonrandomized study. Group A (N = 22) underwent open radical cystectomy, whereas group B (N = 20) underwent laparoscopy-assisted radical cystectomy. The two groups were demographically comparable. We evaluated the mean age, clinical stage, ASA score, operative time, blood loss, intraoperative complications and transfusions, type of diversion, time of catheterization, analgesic consumption, start of oral nutrition, rate of postoperative complications, length of hospital stay, pathologic diagnosis of the specimen, number of lymph nodes removed, and the oncologic outcome. RESULTS No significant statistical difference was observed between the two groups in intraoperative and postoperative parameters except for analgesic consumption and the start of oral nutrition (P < 0.05). The mean operative time was 260 minutes (range 210-290 minutes) for group A and 284 minutes (range 260-305 minutes) for group B. The mean blood loss was 770 mL (range 450-870 mL) in group A and 520 mL (range 400-620 mL) in group B. The rate of autologous transfusion was 18% in group A and 10% in group B. Seventeen ileal diversions and five neobladder creations were performed in group A, whereas the Bricker diversion was used in 10 cases in group B, and a neobladder was chosen in the 10 other cases. CONCLUSION Laparoscopy-assisted radical cystectomy is a safe procedure, like open surgery, but it offers the advantage of minimal invasiveness, represented by reduced analgesic consumption and early recovery of peristalsis with rapid oral nutrition.
Opposite Effects of HIV-1 p17 Variants on PTEN Activation and Cell Growth in B Cells

The HIV-1 matrix protein p17 is a structural protein that can act in the extracellular environment to deregulate several functions of immune cells, through the interaction of its NH2-terminal region with a cellular surface receptor (p17R). The intracellular events triggered by p17/p17R interaction have been not completely characterized yet. In this study we analyze the signal transduction pathways induced by p17/p17R interaction and show that in Raji cells, a human B cell line stably expressing p17R on its surface, p17 induces a transient activation of the transcriptional factor AP-1. Moreover, it was found to upregulate pERK1/2 and downregulate pAkt, which are the major intracellular signalling components involved in AP-1 activation. These effects are mediated by the COOH-terminal region of p17, which displays the capability of keeping PTEN, a phosphatase that regulates the PI3K/Akt pathway, in an active state through the serin/threonin (Ser/Thr) kinase ROCK. Indeed, the COOH-terminal truncated form of p17 (p17Δ36) induced activation of the PI3K/Akt pathway by maintaining PTEN in an inactive phosphorylated form. Interestingly, we show that among different p17s, a variant derived from a Ugandan HIV-1 strain, named S75X, triggers an activation of PI3K/Akt signalling pathway, and leads to an increased B cell proliferation and malignant transformation. In summary, this study shows the role of the COOH-terminal region in modulating the p17 signalling pathways so highlighting the complexity of p17 binding to and signalling through its receptor(s). Moreover, it provides the first evidence on the presence of a p17 natural variant mimicking the p17Δ36-induced signalling in B cells and displaying the capacity of promoting B cell growth and tumorigenesis.
Neuroscience and Biobehavioral Reviews Theories and Computational Models of Affordance and Mirror Systems: an Integrative Review

Neuroscientific and psychological data suggest a close link between affordance and mirror systems in the brain. However, we still lack a full understanding of both the individual systems and their interactions. Here, we propose that the architecture and functioning of the two systems is best understood in terms of two challenges faced by complex organisms, namely: (a) the need to select among multiple affordances and possible actions dependent on context and high-level goals and (b) the exploitation of the advantages deriving from a hierarchical organisation of behaviour based on actions and action-goals. We first review and analyse the psychological and neuroscientific literature on the mechanisms and processes organisms use to deal with these challenges. We then analyse existing computational models thereof. Finally we present the design of a computational framework that integrates the reviewed knowledge. The framework can be used both as a theoretical guidance to interpret empirical data and design new experiments, and to design computational models addressing specific problems debated in the literature. Open access under CC BY-NC-ND license.
Predicting Predation through Prey Ontogeny Using Size-Dependent Functional Response Models

The functional response is a critical link between consumer and resource dynamics, describing how a consumer’s feeding rate varies with prey density. Functional response models often assume homogenous prey size and size-independent feeding rates. However, variation in prey size due to ontogeny and competition is ubiquitous, and predation rates are often size dependent. Thus, functional responses that ignore prey size may not effectively predict predation rates through ontogeny or in heterogeneous populations. Here, we use short-term response-surface experiments and statistical modeling to develop and test prey size–dependent functional responses for water bugs and dragonfly larvae feeding on red-eyed treefrog tadpoles. We then extend these models through simulations to predict mortality through time for growing prey. Both conventional and size-dependent functional response models predicted average overall mortality in short-term mixed-cohort experiments, but only the size-dependent models accurately captured how mortality was spread across sizes. As a result, simulations that extrapolated these results through prey ontogeny showed that differences in size-specific mortality are compounded as prey grow, causing predictions from conventional and size-dependent functional response models to diverge dramatically through time. Our results highlight the importance of incorporating prey size when modeling consumer-prey dynamics in size-structured, growing prey populations.