Miracle-dz/UniFAR-FTUs huggingface dataset:
Patterns and consequences of vertebrate Emx gene duplications

SUMMARY We have cloned and analyzed two Emx genes from the lamprey Petromyzon marinus and our findings provide insight into the patterns and developmental consequences of gene duplications during early vertebrate evolution. The Emx gene family presents an excellent case for addressing these issues as gnathostome vertebrates possess two or three Emx paralogs that are highly pleiotropic, functioning in or being expressed during the development of several vertebrate synapomorphies. Lampreys are the most primitive extant vertebrates and characterization of their development and genomic organization is critical for understanding vertebrate origins. We identified two Emx genes from P. marinus and analyzed their phylogeny and their embryological expression relative to other chordate Emx genes. Our phylogenetic analysis shows that the two lamprey Emx genes group independently from the gnathostome Emx1, Emx2, and Emx3 paralogy groups. Our expression analysis shows that the two lamprey Emx genes are expressed in distinct spatial and temporal patterns that together broadly encompass the combined sites of expression of all gnathostome Emx genes. Our data support a model wherein large‐scale regulatory evolution of a single Emx gene occurred after the protochordate/vertebrate divergence, but before the vertebrate radiation. Both the lamprey and gnathostome lineages then underwent independent gene duplications followed by extensive paralog subfunctionalization. Emx subfunctionalization in the telencephalon is remarkably convergent and refines our understanding of lamprey forebrain patterning. We also identify lamprey‐specific sites of expression that indicate either neofunctionalization in lampreys or sites‐specific nonfunctionalization of all gnathostome Emx genes. Overall, we see only very limited correlation between Emx gene duplications and the acquisition of novel expression domains.
Mucosal immunoglobulins

Summary: Due to their vast surface area, the mucosal surfaces of the body represent a major site of potential attack by invading pathogens. The secretions that bathe mucosal surfaces contain significant levels of immunoglobulins (Igs), which play key roles in immune defense of these surfaces. IgA is the predominant antibody class in many external secretions and has many functional attributes, both direct and indirect, that serve to prevent infective agents such as bacteria and viruses from breaching the mucosal barrier. This review details current understanding of the structural and functional characteristics of IgA, including interaction with specific receptors (such as FcαRI, Fcα/µR, and CD71) and presents examples of the means by which certain pathogens circumvent the protective properties of this important Ig.
The London Congestion Charge

By the 1990s, the average speed of trips across London was below that at the beginning of the twentieth century -- before the car was introduced -- and by the end of that decade, public concern over levels of traffic congestion was high. In early 2003, London imposed a congestion charge -- a daily charge for driving or parking a vehicle on public roads within central London between the hours of 7:00 a.m. and 6:30 p.m. on workdays. Traffic congestion has declined substantially, and the program is largely popular. This article describes the origins of the London congestion charge, how it overcame practical and theoretical difficulties, and what effects it has had. The introduction of the London congestion charge is, in important respects, a triumph of economics. It represents a high-profile public and political recognition of congestion as a distorting externality and of road pricing as an appropriate policy response.
Selective ENG recordings using a multi-contact cuff electrode

This paper describes the design, microfabrication, characterization and experimental validation of a 6-contact cuff electrode embedded in a parylene-based flexible support. This type of electrode is well suited for both peripheral nerve recording and stimulation and offers improved spatial selectivity as compared to conventional ring electrodes. Both measured and modeled impedance spectra are detailed. An experimental validation is performed on an earthworm with both multi-contact cuff (MCC) electrode recording and ring stimulation electrodes. Single fiber action potentials, elicited by the electrical stimulation, are well discriminated on the 6 contacts. Spontaneous activity is also recorded with burst of spikes.
Rhizobium meliloti mutants unable to synthesize anthranilate display a novel symbiotic phenotype

Analyses of Rhizobium meliloti trp auxotrophs suggest that anthranilate biosynthesis by the R. meliloti trpE(G) gene product is necessary during nodule development for establishment of an effective symbiosis. trpE(G) mutants, as well as mutants blocked earlier along this pathway in aromatic amino acid biosynthesis, form nodules on alfalfa that have novel defects. In contrast, R. meliloti trp mutants blocked later in the tryptophan-biosynthetic pathway form normal, pink, nitrogen-fixing nodules. trpE(G) mutants form two types of elongated, defective nodules containing unusually extended invasion zones on alfalfa. One type contains bacteroids in its base and is capable of nitrogen fixation, while the other lacks bacteroids and cannot fix nitrogen. The trpE(G) gene is expressed in normal nodules. Models are discussed to account for these observations, including one in which anthranilate is postulated to act as an in planta siderophore.
Prospective, multi-institutional pain assessment of 150 women undergoing diagnostic cystoscopy.

BACKGROUND The aim of this study was to prospectively assess women's pain during rigid and flexible diagnostic cystoscopy and afterwards during a one-week follow-up. METHODS Prospective, multi-institutional trial analyzing numeric rating scales (NRS) of women undergoing diagnostic cystoscopy. Pain categories: no (0 points), mild (1-3), moderate (4-6) and severe pain (7-10). Assessing of pain before, during cystoscopy, and at day 1, 4 and 7 of follow-up. RESULTS A total of 150 women undergoing rigid (N.=85) or flexible (N.=65) diagnostic cystoscopy were analyzed. Women undergoing flexible cystoscopy were more frequently pain-free (64.6% vs. 40%, P=0.003) and experienced mild pain less frequently (27.7% vs. 52.9% vs. P=0.002). No significant differences were noted among moderate (6.2% vs. 5.9%, P=0.95) and severe pain (1.5% vs. 1.2%, P=0.85). Patients undergoing their first (P=0.14) and repeat cystoscopy (P=0.08) had similar pain perception. In multivariate logistic regression analyses, women undergoing flexible cystoscopy had a 2.6 increased chance of being pain-free (OR=2.6, CI: 1.28-5.11, P=0.08) and their odds of experiencing mild pain were significantly lower (OR=0.34, CI: 0.17-0.71, P=0.004). The likelihood of experiencing moderate (OR=1.1, CI: 0.28- 4.4, P=0.83) or severe pain (OR=2.42, CI: 0.11-51.79, P=0.57) differed insignificantly. CONCLUSIONS Rigid and flexible cystoscopies were well-tolerated by most women. However, flexible cystoscopy was associated with a higher likelihood of being pain-free and lower chances of experiencing mild pain. Patients' previous experience with cystoscopy did not influence pain perception.
Large-scale analysis of neuroimaging data on commercial clouds with content-aware resource allocation strategies

The combined use of mice that have genetic mutations (transgenic mouse models) of human pathology and advanced neuroimaging methods (such as magnetic resonance imaging) has the potential to radically change how we approach disease understanding, diagnosis and treatment. Morphological changes occurring in the brain of transgenic animals as a result of the interaction between environment and genotype can be assessed using advanced image analysis methods, an effort described as ‘mouse brain phenotyping’. However, the computational methods involved in the analysis of high-resolution brain images are demanding. While running such analysis on local clusters is possible, not all users have access to such infrastructure and even for those that do, having additional computational capacity can be beneficial (e.g. to meet sudden high throughput demands). In this paper we use a commercial cloud platform for brain neuroimaging and analysis. We achieve a registration-based multi-atlas, multi-template anatomical segmentation, normally a lengthy-in-time effort, within a few hours. Naturally, performing such analyses on the cloud entails a monetary cost, and it is worthwhile identifying strategies that can allocate resources intelligently. In our context a critical aspect is the identification of how long each job will take. We propose a method that estimates the complexity of an image-processing task, a registration, using statistical moments and shape descriptors of the image content. We use this information to learn and predict the completion time of a registration. The proposed approach is easy to deploy, and could serve as an alternative for laboratories that may require instant access to large high-performance-computing infrastructures. To facilitate adoption from the community we publicly release the source code.
Filtered-X Affine Projection Algorithms for Active Noise Control Using Volterra Filters

We consider the use of adaptive Volterra filters, implemented in the form of multichannel filter banks, as nonlinear active noise controllers. In particular, we discuss the derivation of filtered-X affine projection algorithms for homogeneous quadratic filters. According to the multichannel approach, it is then easy to pass from these algorithms to those of a generic Volterra filter. It is shown in the paper that the AP technique offers better convergence and tracking capabilities than the classical LMS and NLMS algorithms usually applied in nonlinear active noise controllers, with a limited complexity increase. This paper extends in two ways the content of a previous contribution published in Proc. IEEE-EURASIP Workshop on Nonlinear Signal and Image Processing (NSIP '03), Grado, Italy, June 2003. First of all, a general adaptation algorithm valid for any order of affine projections is presented. Secondly, a more complete set of experiments is reported. In particular, the effects of using multichannel filter banks with a reduced number of channels are investigated and relevant results are shown.
Retraction in Part: A Genomic Approach to Identify Molecular Pathways Associated with Chemotherapy Resistance

Using previously published annotations for chemotherapy sensitivity in the NCI-60 series of cancer cell lines (2), we performed gene set enrichment analysis on predefined groups of sensitive and resistantNCI-60 cell lines for a range of chemotherapies to identify biological pathways associated with resistance. We purposefully used the annotations for sensitivity and resistance published in the Nature Medicine article and applied a complementary computational approach in order to glean biological insight from the differential gene expression. The article upon which our annotations were based has now been retracted (3). After re-examination, the annotations for the cell lines with respect to chemotherapy sensitivity were erroneous. Thus, our manuscript propagates this error and the results in Table 1 and Supplemental Table 1 from our manuscript are invalid.
Využití peroperačního endonazálního ultrazvukového vyšetření při hodnocení radikality endoskopických operací selární oblasti

Ucel studie: Cilem prace je zhodnoceni prvnich zkusenosti s využitim peroperacniho ultrazvuku při hodnoceni radikality endoskopicke transnazalni exstirpace nadorů selarni krajiny. Použite metody: Od zaři do prosince 2011 bylo provedeno 13 endoskopických transnazalnich operaci selarnich nadorů. Jednalo se o 12 pacientů s makroadenomem hypofýzy a jednoho pacienta s meningeomem. U pacientů bylo provedeno peroperacni transsfenoidalni ultrazvukove vysetřeni. Ultrazvukove nalezy pak byly srovnany s pooperacni magnetickou rezonanci. Výsledky: U 11 pacientů byla peroperacnim ultrazvukem exstirpace hodnocena jako radikalni, u zbylých dvou pak jako parcialni. Na pooperacni MR byla potvrzena radikalni exstirpace u 9 pacientů. U dvou pacientů jsme byli neuspěsni při peroperacnim ultrazvukovem hodnoceni radikality exstirpace. Zavěr: Peroperacni ultrazvukove vysetřeni je relativně levna a dostupna metoda hodnoceni radikality endoskopických transnazalnich operaci. Pro zhodnoceni jeho přinosu ve srovnani s peroperacni magnetickou rezonanci je potřeba dalsich studii.
How Much Should We Invest for Network Facility : Quantitative Analysis on Network ’ Fatness ’ and Machine Learning Performance

Multi-node execution is becoming more and more popular for machine learning because of it’s huge amount of computation. The question we are trying to answer here is that, how should we design computer systems for deep learning, especially in terms of investment for the network. Traditional cluster based ’supercomputers’ require huge amount of investment on network switches since the network ’fatness’ is quite important for the typical applications of super-computers. Do the machine learning workloads share the characteristics with such kinds of applications? To answer this questions, we quantitatively analyze the impact of network fatness on several type of machine learning application types with several network configurations. The results we obtained strongly implies that the network fatness is not important for machine learning applications, and thus we could safely reduce investment on network facilities.
A multicenter trial with a somatostatin analog (99m)Tc depreotide in the evaluation of solitary pulmonary nodules.

OBJECTIVE The affinity of various malignant neoplasms including small cell and non-small cell lung cancer for peptide analogs of somatostatin has been well documented. Depreotide is such an analog and can be complexed with technetium-99m ((99m)Tc depreotide) for optimal imaging properties. Using this radiopharmaceutical, solitary pulmonary nodules (SPN) were previously evaluated in a successful phase II/III trial. The results of the larger multicenter phase III study using (99m)Tc depreotide to differentiate malignant and benign etiologies in SPN are now presented. METHODS Patients with SPN </= 6 cm on chest radiograph were referred for evaluation. One hundred fourteen individuals who had an absence of a benign pattern of calcification on CT scan, age > 30 years, and no demonstrable radiographic stability for the prior 2 years were studied. All underwent single-photon emission CT (SPECT) with (99m)Tc depreotide and subsequent tissue histologic examination. Three nuclear medicine specialists blinded to histologic findings examined the SPECT images and scored them as positive or negative based on the presence or absence of activity in the radiographic region of the SPN. The final result was determined by the majority score, which was then compared with the histologic result. RESULTS Of the 114 individuals studied, 88 had a histologic result compatible with malignant neoplasm. (99m)Tc depreotide scintigraphy correctly identified 85 of this group, with three false-negative determinations compared with histology. There were seven false-positive determinations, including six granulomas and one hamartoma. (99m)Tc depreotide scintigraphy correctly excluded malignancy in 19 of 26 patients with benign histologic findings. The sensitivity of this method was 96.6% with a specificity of 73.1%. CONCLUSION (99m)Tc depreotide scintigraphy is a safe and useful method for the noninvasive evaluation of SPN with a sensitivity and accuracy comparable to that reported for fluorine-18 fluorodeoxyglucose positron emission tomography.
Stem Cells in the Epidermis

The epidermis consists of three actively proliferating units, the interfollicular epidermis, the hair follicle, and the sebaceous gland. Stem cells in the epidermis have the capacity to produce all three of these units. The fate of the epidermal stem cells and some of their progeny can be altered, dependent on the environment in which they reside and the genes they express. In this review, we describe the major experiments that have contributed to the understanding of the epidermal stem cells and the control of their fate.
Asymmetries of the balanced SSFP profile. Part I: Theory and observation

The signal in balanced steady‐state free precession has a strong sensitivity to off‐resonance, which is typically described in terms of a signal “profile” over a range of frequencies. This profile has a well‐known form for homogeneous media with a single T1, T2, and resonance frequency, which is symmetric about the on‐resonance frequency. However, a straightforward extension to this established signal model predicts that the profile may become asymmetric in the presence of inhomogeneous frequency content, as would be expected to happen in tissue due to microstructural boundaries, compartments, and chemical shift. The presence of asymmetries in the balanced steady‐state free precession profile may therefore provide a marker of tissue integrity. This manuscript describes the theory behind balanced steady‐state free precession asymmetries, a method for detecting these effects, and the first measurements of balanced steady‐state free precession asymmetries in tissue. Asymmetries are found in gray matter, white matter, and muscle, with excellent reproducibility. A companion paper considers the large white matter asymmetries in more detail. Magn Reson Med, 2010. © 2010 Wiley‐Liss, Inc.
Caring in the wake of the rising tide: Moral distress in residential nursing care of people living with dementia

Objective Moral distress is increasingly being recognized as a concern for health care professionals. The purpose of this study was to explore the nature and prevalence of moral distress among nursing staff who care for people living with dementia. Methods This study was focused on nursing staff caring for people with dementia in long-term care and assisted living sites. The Moral Distress in Dementia Care Survey instrument was distributed to 23 sites and nursing staff rated the frequency and severity of situations that were identified as potentially causing moral distress. Results Moral distress is prevalent in the nursing staff who provide dementia care. Nursing staff reported experiencing moral distress at least daily or weekly. Both frequency and severity of moral distress increased with proximity to (amount of time spent at) the bedside. Moral distress had negative psychological and physiological effects on nursing staff, and affected intention to quit.
Engineering an Efficient Native ASP Solver

Answer set programming (ASP) is a powerful formalism for knowledg e representation and common sense reasoning that allows disjunction in rule heads and non-monotonic negation in b dies. The implementation of efficient ASP systems is an interesting and non-trivial task, which is fu ndamental for the application of this language in practice. The main subjects of our research are the de velopment of evaluation techniques and their implementation in a new ASP solver called WASP. WASP is base d on techniques originally introduced for SAT solving that have been extended to cope with ASP pr ograms. Among them are restarts, conflict-driven constraint learning and backjumping. Moreo ver, WASP combines these SAT-based techniques with optimization methods that have been specifically designed fo r ASP computation, such as source pointers enhancing unfounded-sets computation, forward an d backward inference operators based on atom support, and techniques for stable model checking. The results of a preliminary experiment show that WASP is already comparable in performance with the best solvers tha t participated to the 3rd ASP competition. On the other hand, experiments have also highlighted the weakn esses of the implementation. Ongoing and future work concern the improvement of WASP by both optim izing the implementation and designing new evaluation techniques.
Activation of a Mitogen-activated Protein Kinase (ERK2) by the 5-Hydroxytryptamine1A Receptor Is Sensitive Not Only to Inhibitors of Phosphatidylinositol 3-Kinase, but to an Inhibitor of Phosphatidylcholine Hydrolysis*

A variety of receptors coupled to GTP-binding regulatory proteins (G proteins) initiate signals that culminate in activation of the mitogen-activated protein kinases ERK1 and ERK2. We demonstrate here that the human 5-HT1A receptor expressed in Chinese hamster ovary cells similarly promotes activation of ERK1 and ERK2, but that the pathway used does not conform entirely to those proposed previously for G protein-coupled receptors. Activation of ERK2 by the 5-HT1A receptor-selective agonist 8-hydroxy-N,N-dipropyl-2-aminotetralin hydrobromide (8-OH-DPAT) was inhibited completely by pertussis toxin and substantially by prolonged treatment of cells with phorbol 12-myristate 13-acetate. The implied requirement for protein kinase C, however, was negated in studies with bisindolylmaleimide and Ro-31-8220, which, although completely inhibiting activation of ERK2 by phorbol ester, had no impact on activation by 8-OH-DPAT. The anticipated inhibition by the tyrosine kinase inhibitors genistein and herbimycin A, moreover, was marginal at best. As expected for a Gi-coupled receptor, the inhibitors of phosphatidylinositol 3-kinase wortmannin and LY294002 inhibited activation of ERK2, albeit only partly (70%). Of significance, an inhibitor of a phosphatidylcholine-specific phospholipase C, tricyclodecan-9-yl-xanthogenate (D609), caused a similar degree of inhibition. When the two types of inhibitors were combined, an almost complete inhibition was achieved. Our data suggest that phosphatidylinositol 3-kinase and phosphatidylcholine-specific phospholipase C represent components of different, but partly overlapping pathways that can account almost entirely for the activation of ERK2 by the 5-HT1A receptor.
Global Diffusion of Technological Innovations: A Coupled-Hazard Approach

The authors propose a new methodology called the “coupled-hazard approach” to study the global diffusion of technological innovations. Beyond its ability to describe discontinuous diffusion patterns, the method explicitly recognizes the conceptual difference between the timing of a country's introduction of the new technology (the so-called implementation stage; Rogers 1983) and the timing of the innovation's full adoption in the country (the confirmation stage). To illustrate the method, the authors apply it to the global diffusion of digital telecommunications switches across more than 160 countries.