Miracle-dz/UniFAR-FTUs huggingface dataset:
Plasmids of Carotenoid-Producing Paracoccus spp. (Alphaproteobacteria) - Structure, Diversity and Evolution

Plasmids are components of many bacterial genomes. They enable the spread of a large pool of genetic information via lateral gene transfer. Many bacterial strains contain mega-sized replicons and these are particularly common in Alphaproteobacteria. Considerably less is known about smaller alphaproteobacterial plasmids. We analyzed the genomes of 14 such plasmids residing in 4 multireplicon carotenoid-producing strains of the genus Paracoccus (Alphaproteobacteria): P. aestuarii DSM 19484, P. haeundaensis LG P-21903, P. marcusii DSM 11574 and P. marcusii OS22. Comparative analyses revealed mosaic structures of the plasmids and recombinational shuffling of diverse genetic modules involved in (i) plasmid replication, (ii) stabilization (including toxin-antitoxin systems of the relBE/parDE, tad-ata, higBA, mazEF and toxBA families) and (iii) mobilization for conjugal transfer (encoding relaxases of the MobQ, MobP or MobV families). A common feature of the majority of the plasmids is the presence of AT-rich sequence islets (located downstream of exc1-like genes) containing genes, whose homologs are conserved in the chromosomes of many bacteria (encoding e.g. RelA/SpoT, SMC-like proteins and a retron-type reverse transcriptase). The results of this study have provided insight into the diversity and plasticity of plasmids of Paracoccus spp. , and of the entire Alphaproteobacteria. Some of the identified plasmids contain replication systems not described previously in this class of bacteria. The composition of the plasmid genomes revealed frequent transfer of chromosomal genes into plasmids, which significantly enriches the pool of mobile DNA that can participate in lateral transfer. Many strains of Paracoccus spp. have great biotechnological potential, and the plasmid vectors constructed in this study will facilitate genetic studies of these bacteria.
Incremental semiparametric inverse dynamics learning

This paper presents a novel approach for incremental semiparametric inverse dynamics learning. In particular, we consider the mixture of two approaches: Parametric modeling based on rigid body dynamics equations and nonparametric modeling based on incremental kernel methods, with no prior information on the mechanical properties of the system. The result is an incremental semiparametric approach, leveraging the advantages of both the parametric and nonparametric models. We validate the proposed technique learning the dynamics of one arm of the iCub humanoid robot.
The Effect of “Ischemic” Blood on Transmembrane Potentials of Normal Porcine Ventricular Myocardium

“Ischemic” blood was obtained in pigs from a local coronary vein on release of coronary artery occlusion. The effects of this blood on transmembrane potentials of muscle strips taken from the same heart were compared with control blood. Whereas action potentials remained stable in control blood, ischemic blood collected after more than 15 minutes of coronary occlusion produced shortening of action potential duration, reduction of resting potential, upstroke velocity and amplitude, then postrepolarization refractoriness and finally unresponsiveness. Ischemic blood collected after shorter periods of coronary occlusion produced only mild effects (shortening of action potential and postrepolarization refractoriness). These effects of ischemic blood could not be attributed to increased potassium concentration even in combination with acidosis, hypoxia and hypoglycemia. It appears that during ischemia unidentified factors are released which have potent depressant effects on the excitability of even normal myocardium.
Usefulness of the apparent diffusion coefficient in line scan diffusion-weighted imaging for distinguishing between squamous cell carcinomas and malignant lymphomas of the head and neck.

BACKGROUND AND PURPOSE Squamous cell carcinoma (SCC) and lymphoma are common malignant tumors of the head and neck. The purpose of this study was to determine whether the apparent diffusion coefficient (ADC) in line scan diffusion-weighted imaging (LSDWI) is useful for distinguishing between SCC and lymphoma of the head and neck. METHODS LSDWI was prospectively performed in 39 patients with SCC and in 14 patients with lymphoma. Images were obtained with a diffusion-weighted factor (b factor) of 5 and 1000 s/mm(2), and ADC maps were generated. ADC values were measured for the two types of tumor. RESULTS Mean ADC values were 0.96 +/- 0.11 x 10(-3) mm(2)/s for SCC and 0.65 +/- 0.09 x 10(-3) mm(2)/s for lymphoma; the difference was significant (P < .001). All but one of the patients with lymphoma had ADC values lower than the lowest ADC (0.76 x 10(-3) mm(2)/s) in patients with SCC. When an ADC of 0.76 x 10(-3) mm(2)/s was used to distinguish between SCC and lymphoma, accuracy was 98% (52 of 53 lesions). CONCLUSION ADC values appear to be useful for distinguishing between SCC and lymphoma in the head and neck.
The effects of civility on advice, leadership, and performance.

Workplace incivility is rampant and on the rise-with costs to individuals and organizations. Despite the increased need for civility, little is known about potential individual benefits of civility, defined as behavior involving politeness and regard for others in the workplace, within workplace norms for respect (Andersson & Pearson, 1999). Recent research has suggested that being civil may be hazardous to influence, power, and income (see Forni, 2002; Judge et al., 2012). Yet, throughout history, civil behavior has been extolled because it paid dividends to the person who behaved well. The focus of this research is whether that holds true in organizations. Using social exchange theory, we developed hypotheses about how civility benefits people, and investigated this in 2 studies. First, in a 2-wave social network study of a research and development department (n = 31) of a biotechnology firm, we found that people who perceived a colleague as civil would be more likely to seek that person out for work advice and to see that person as a leader. The more the individual was perceived as civil by others in his or her network, the better his or her performance. Being sought out for work advice and being viewed as a leader mediated this effect. In the second experiment (n = 162), we extended our understanding of what drove these benefits. We found that people who are civil were perceived as warm and competent, and these positive perceptions, in turn, helped to explain the benefits garnered. We discuss theoretical and practical implications.
Activation of Phosphatidylinositol 3-Kinase and Extracellular Signal-Regulated Kinase Is Required for Glial Cell Line-Derived Neurotrophic Factor-Induced Migration and Invasion of Pancreatic Carcinoma Cells

Pancreatic carcinoma cells exhibit a pronounced tendency to invade along and into intra- and extrapancreatic nerves, even at early stages of the disease. The neurotrophic factor glial cell line-derived neurotrophic factor (GDNF) has been shown to promote pancreatic cancer cell invasion. Here, we demonstrate that pancreatic carcinoma cell lines, such as PANC-1, expressed the RET and GDNF family receptor α receptor components for GDNF and that primary pancreatic tumor samples, derived from carcinomas with regional lymph node metastasis, exhibited marked expression of the mRNA encoding the RET51 isoform. Moreover, GDNF was an efficacious and potent chemoattractant for pancreatic carcinoma cells as examined in in vitro and in vivo model systems. Treatment of PANC-1 cells with GDNF resulted in activation of the monomeric GTPases N-Ras, Rac1, and RhoA, in activation of the mitogen-activated protein kinases extracellular signal-regulated kinase (ERK) and c-Jun NH2-terminal kinase (JNK) and in activation of the phosphatidylinositol 3-kinase/Akt pathway. Both inhibition of the Ras-Raf-MEK (mitogen-activated protein/ERK kinase)-ERK cascade by either stable expression of dominant-negative H-Ras(N17) or addition of the MEK1 inhibitor PD98059 as well as inhibition of the phosphatidylinositol 3-kinase pathway by LY294002 prevented GDNF-induced migration and invasion of PANC-1 cells. These results demonstrate that pancreatic tumor cell migration and possibly perineural invasion in response to GDNF is critically controlled by activation of the Ras-Raf-MEK-ERK and the phosphatidylinositol 3-kinase pathway.
Douala as a “hybrid space”: Comparing online and offline representations of a sub-Saharan city

Abstract This study investigates the complex relationship between the physical and digital spaces of the city of Douala, Cameroon by comparing its online representation with the social representations emerging orally by locals. Using the results of two existing studies reporting on the online image of the city, we investigate the social representations foreigners and locally relevant people have of Douala and uncover similarities and discrepancies of the two resulting representations. Outcomes from the analysis permit reflection on the implications of these and show an unripe, intermediate stage of the “hybrid Douala,” where the virtual space seems still not to be affecting the way the physical space is experienced, as well as where the gaps in the digital divide are perpetuated. At the same time, strong local ownership of certain digital activities suggests how the online image of the city is in the process of being constructed and developed locally. As the spaces of the city start appearing online, the process of hybridization between physical and digital Douala is slowly taking place and offline and online narratives, now rather separated, will possibly communicate a different image of the city to global online narratives.
Collaborative Recurrent Autoencoder: Recommend while Learning to Fill in the Blanks

Hybrid methods that utilize both content and rating information are commonly used in many recommender systems. However, most of them use either handcrafted features or the bag-of-words representation as a surrogate for the content information but they are neither effective nor natural enough. To address this problem, we develop a collaborative recurrent autoencoder (CRAE) which is a denoising recurrent autoencoder (DRAE) that models the generation of content sequences in the collaborative filtering (CF) setting. The model generalizes recent advances in recurrent deep learning from i.i. d. input to non-i.i. d. (CF-based) input and provides a new denoising scheme along with a novel learnable pooling scheme for the recurrent autoencoder. To do this, we first develop a hierarchical Bayesian model for the DRAE and then generalize it to the CF setting. The synergy between denoising and CF enables CRAE to make accurate recommendations while learning to fill in the blanks in sequences. Experiments on real-world datasets from different domains (CiteULike and Netflix) show that, by jointly modeling the order-aware generation of sequences for the content information and performing CF for the ratings, CRAE is able to significantly outperform the state of the art on both the recommendation task based on ratings and the sequence generation task based on content information.
Transmembrane proteins in the Protein Data Bank: identification and classification

MOTIVATION Integral membrane proteins play important roles in living cells. Although these proteins are estimated to constitute 25% of proteins at a genomic scale, the Protein Data Bank (PDB) contains only a few hundred membrane proteins due to the difficulties with experimental techniques. The presence of transmembrane proteins in the structure data bank, however, is quite invisible, as the annotation of these entries is rather poor. Even if a protein is identified as a transmembrane one, the possible location of the lipid bilayer is not indicated in the PDB because these proteins are crystallized without their natural lipid bilayer, and currently no method is publicly available to detect the possible membrane plane using the atomic coordinates of membrane proteins. RESULTS Here, we present a new geometrical approach to distinguish between transmembrane and globular proteins using structural information only and to locate the most likely position of the lipid bilayer. An automated algorithm (TMDET) is given to determine the membrane planes relative to the position of atomic coordinates, together with a discrimination function which is able to separate transmembrane and globular proteins even in cases of low resolution or incomplete structures such as fragments or parts of large multi chain complexes. This method can be used for the proper annotation of protein structures containing transmembrane segments and paves the way to an up-to-date database containing the structure of all known transmembrane proteins and fragments (PDB_TM) which can be automatically updated. The algorithm is equally important for the purpose of constructing databases purely of globular proteins.
Depression, Antidepressants, and Bone Health in Older Adults: A Systematic Review

because both disorders are age related. In the latter study (which evaluated the effect of baseline thyroid function on the subsequent development of atrial fibrillation in older persons), of 2,007 subjects aged 60 and older who did not have atrial fibrillation (AF) at baseline, 183 (142 women) had hypothyroidism and 1,576 (896 women) were euthyroid. In the subsequent 10 years, the cumulative incidence of new-onset AF in the hypothyroid group was 15%, which was comparable with the 11% cumulative incidence of newonset AF in the euthyroid group. The fact that there was no significant difference between the two parameters (15% vs 11%) signified that both groups had developed AF simply as a result of increasing age. In the same study, although only 61 subjects had unequivocal baseline hyperthyroidism, that subgroup was associated with significantly greater risk (P < .001) of subsequent AF than the euthyroid group. In other words, in elderly people with hypothyroidism, older age, rather than thyroid dysfunction, determines subsequent development of AF, whereas in elderly people with hyperthyroidism, baseline thyroid status is the crucial and independent determinant of subsequent AF. Fortuitous associations such as those enumerated above may be consistent and should be taken into account in any analysis that involves evaluation of disease processes that evolve over several years in older persons.
Broadening of Cortical Inhibition Mediates Developmental Sharpening of Orientation Selectivity

Orientation selectivity (OS) of visual cortical neurons is progressively sharpened during development. However, synaptic circuit mechanisms underlying the OS sharpening remain unclear. In the current study, in vivo whole-cell voltage-clamp recordings from layer 4 excitatory neurons in the developing mouse primary visual cortex revealed changes of orientation tuning profiles of their excitatory and inhibitory inputs during a post-eye-opening period when OS of their spiking responses becomes sharpened. In addition to a parallel strengthening of excitation and inhibition during this developmental period, the orientation tuning of excitatory inputs keeps relatively constant, whereas the tuning of inhibitory inputs is broadened, and becomes significantly broader than that of excitatory inputs. Neuron modeling and dynamic-clamp recording demonstrated that this developmental broadening of the inhibitory tuning is sufficient for sharpening OS. Depriving visual experience by dark rearing impedes the normal developmental strengthening of excitation, but a similar broadening of inhibitory tuning, likely caused by a nonselective strengthening of inhibitory connections, results in the apparently normal OS sharpening in excitatory neurons. Our results thus provide the first demonstration that an inhibitory synaptic mechanism can primarily mediate the functional refinement of cortical neurons.
Ontology-Based Knowledge Acquisition for Knowledge Systems

We present a prototype ontology-based knowledge system built with the Protégé-2000 knowledge acquisition tool. Preliminary ideas about the role of ontologies in information systems [1] and its goal of reusing knowledge in information system development [2] are refined. A domain ontology in Protégé and inference rules in Jess are combined into a knowledge system in which the elicitation and the validation of domain facts can be done at the same time. Ontology-based knowledge system development makes it possible to elicit domain facts after the implementation of the ontology-structured knowledge system.
Altered chemotactic response to CXCL12 in patients carrying GATA2 mutations

GATA2 deficiency—formerly described as MonoMAC syndrome; dendritic cells, monocytes, B cells, and natural killer cell deficiency; familial myelodysplastic syndrome/acute myeloid leukemia; or Emberger syndrome—encompasses a range of hematologic and nonhematologic anomalies, mainly characterized by monocytopenia, B lymphopenia, natural killer cell cytopenia, neutropenia, immunodeficiency, and a high risk of developing acute myeloid leukemia. Herein, we present 7 patients with GATA2 deficiency recruited into the French Severe Chronic Neutropenia Registry, which enrolls patients with all kinds of congenital neutropenia. We performed extended immunophenotyping of their whole blood lymphocyte populations, together with the analysis of their chemotactic responses. Lymphopenia was recorded for B and CD4+ T cells in 6 patients. Although only 3 patients displayed natural killer cell cytopenia, the CD56bright natural killer subpopulation was nearly absent in all 7 patients. Natural killer cells from 6 patients showed decreased CXCL12/CXCR4‐dependent chemotaxis, whereas other lymphocytes, and most significantly B lymphocytes, displayed enhanced CXCL12‐induced chemotaxis compared with healthy volunteers. Surface expression of CXCR4 was significantly diminished in the patients’ natural killer cells, although the total expression of the receptor was found to be equivalent to that of natural killer cells from healthy individual controls. Together, these data reveal that GATA2 deficiency is associated with impaired membrane expression and chemotactic dysfunctions of CXCR4. These dysfunctions may contribute to the physiopathology of this deficiency by affecting the normal distribution of lymphocytes and thus potentially affecting the susceptibility of patients to associated infections.
Evaluation of an immunochromatographic test for discrimination between Mycobacterium tuberculosis complex & non tuberculous mycobacteria in clinical isolates from extra-pulmonary tuberculosis

Background & objectives: Accurate diagnosis of tuberculosis (TB) is crucial to facilitate early treatment of the patients, and to reduce its spread. Clinical presentation of Mycobacterium tuberculosis complex (MTBC) and non tuberculous mycobacteria (NTM) may or may not be the same, but the treatment regimen is always different for both the infections. Differentiation between MTBC and NTM by routine laboratory methods is time consuming and cumbersome. This study was aimed to evaluate an immunochromatographic test (ICT), based on mouse monoclonal anti-MPT64, for simple and rapid discrimination between MTBC and NTM in clinical isolates from extra-pulmonary tuberculosis cases. Methods: A total of 800 clinical samples were collected from patients suspected to have extra-pulmonary tuberculosis. Preliminary diagnosis has been done by direct Ziehl–Neelsen (ZN) staining followed by culture in BACTEC system. A total of 150 clinical isolates, which were found positive in BD 460 TB system during September 2009 to September 2010 were selected for the screening by ICT test. p-nitro-α-acetylamino- β-hydroxy propiophenone (NAP) test was performed for differentiation of MTBC and NTM. M. tuberculosis complex was further confirmed by IS6110 PCR of BACTEC culture positive isolates, this served as the reference method for MTBC identification and comparative evaluation of the ICT kit. Results: Of the 150 BACTEC culture positive isolates tested by ICT kit, 101 (67.3%) were found positive for MTBC and remaining 49 (32.7%) were considered as NTM. These results were further confirmed by IS6110 PCR that served as the reference method for detection of MTBC. H37Rv reference strain was taken as a control for ICT test and IS6110 PCR. The reference strain showed the presence of MPT64 antigen band in the ICT test. Similar bands were formed in 101 of 102 MTBC isolates tested, proving 99.1 per cent sensitivity and no bands were detected in 48 (100%) NTM isolates tested, proving 100 per cent specificity of the ICT kit. Interpretation & conclusions: Our findings show that ICT test can be used on direct culture positive specimens. It does not require any special equipment, is simple and less time consuming. It can easily discriminate between MTBC and NTM and thus can help in appropriate management of tuberculosis.
Anti-glomerular basement membrane (GBM)-antibody-mediated disease with normal renal function.

BACKGROUND This study compared the clinical and laboratory characteristics of patients with anti-glomerular basement membrane (GBM) disease and normal renal function, with those of patients with anti-GBM disease where there was renal impairment. METHODS The medical records of the 14 patients who had presented with anti-GBM disease to our hospital in the past 20 years were reviewed. RESULTS Five (36%) had a normal serum creatinine or creatinine clearance at presentation. Other features were haemoptysis (2/5, 40%), macroscopic haematuria (2/5, 40%) or systemic symptoms (1/5, 20%). All five (100%) had some degree of haematuria, four (80%) had proteinuria of at least 1 g/day, and none was hypertensive. Anaemia, a raised WCC, or elevated ESR (> 35 mm/h) occurred less often than in patients with impaired renal function (P<0.05). Two of the five (40%) with normal renal function had circulating anti-GBM antibodies, which were present at low or moderate levels; but seven of the nine with renal impairment (77%) had circulating antibodies, with high levels in five. Renal biopsies from patients with normal renal function were normal (1/5, 20%), showed mesangial proliferation (4/5, 80%) or had more than 20% glomeruli sclerosed (1/5, 20%). Complement deposition was present in 2/4 biopsies (50%). The kidneys from patients with renal impairment had crescents in more than 50% glomeruli (9/9, 100%), and four had more than 20% glomeruli sclerosed (44%). All four kidneys from patients with renal impairment that were examined had complement deposits (100%). Treatment was identical in both groups; patients with normal renal function were followed for a median of 48 months, and those with renal impairment for 180 months. There were no further episodes of haemoptysis, haematuria, or other symptoms of relapse in either group. All five patients with normal renal function are alive, and the serum creatinine is less than 0.2 mmol/l in all (100%), but haematuria persists in one (20%), and proteinuria >1 g/day in two (40%). Eight of the nine (89%) patients with impaired renal function survive, but all are currently being dialysed or have had a renal transplant. CONCLUSION Patients with anti-GBM disease with normal renal function are not uncommon, and often have a good prognosis. There is less renal damage, possibly because of lower levels of circulating anti-GBM antibodies and less glomerular complement deposition.