Miracle-dz/UniFAR-FTUs huggingface dataset:
Restriction glycosylases: involvement of endonuclease activities in the restriction process.

All restriction enzymes examined are phosphodiesterases generating 3'-OH and 5'-P ends, but one restriction enzyme (restriction glycosylase) excises unmethylated bases from its recognition sequence. Whether its restriction activity involves endonucleolytic cleavage remains unclear. One report on this enzyme, R.PabI from a hyperthermophile, ascribed the breakage to high temperature while another showed its weak AP lyase activity generates atypical ends. Here, we addressed this issue in mesophiles. We purified R.PabI homologs from Campylobacter coli (R.CcoLI) and Helicobacter pylori (R.HpyAXII) and demonstrated their DNA cleavage, DNA glycosylase and AP lyase activities in vitro at 37°C. The AP lyase activity is more coupled with glycosylase activity in R.CcoLI than in R.PabI. R.CcoLI/R.PabI expression caused restriction of incoming bacteriophage/plasmid DNA and endogenous chromosomal DNA within Escherichia coli at 37°C. The R.PabI-mediated restriction was promoted by AP endonuclease action in vivo or in vitro These results reveal the role of endonucleolytic DNA cleavage in restriction and yet point to diversity among the endonucleases. The cleaved ends are difficult to repair in vivo, which may indicate their biological significance. These results support generalization of the concept of restriction-modification system to the concept of self-recognizing epigenetic system, which combines any epigenetic labeling and any DNA damaging.
Exercise training reverses adiponectin resistance in skeletal muscle of patients with chronic heart failure

Background Resistance to the insulin-sensitising adipocytokine, adiponectin, has been described at the level of the skeletal muscle in patients with chronic heart failure (CHF). Objective To investigate whether exercise training (ET) would improve skeletal muscle energy metabolism and adiponectin signalling. Methods In a prospective cohort study, patients with CHF were recruited from the Cardiac Rehabilitation Centre, Antwerp University Hospital. They underwent 4 months' combined endurance–resistance ET. Skeletal muscle mRNA and protein expression of adiponectin, AdipoR1 and downstream metabolic genes were measured. Results Adiponectin mRNA expression in the nine CHF patients was higher than that in 10 matched healthy subjects (p=0.007), whereas AdipoR1 and downstream-located genes involved in lipid (PPAR-α, ACADM) and glucose metabolism (AMPK, hexokinase2) were down-regulated. Skeletal muscle AdipoR1 correlated with VO2 peak (r=0.900; p=0.001), maximal workload (r=0.753; p=0.019) and steady state workload (r=0.928; p<0.001). ET increased maximal workload and muscle strength. In addition, ET lowered adiponectin mRNA expression (p=0.017), whereas the expression of AdipoR1 (p=0.011) and downstream metabolic genes was increased to levels comparable to those in healthy subjects. ELISA confirmed the normalisation of skeletal muscle adiponectin expression at the protein level (p=0.047). Conclusion At the level of the skeletal muscle, CHF patients are characterised by increased adiponectin expression and decreased expression of AdipoR1 and downstream metabolic genes. ET normalises the mRNA expression of adiponectin and AdipoR1 and reverses disorders in lipid and glucose metabolism in skeletal muscle. These alterations in metabolic gene expression may help to understand the beneficial effects of ET in CHF.
Parallel Phylogenies of Pneumocystis Species and their Mammalian Hosts

ABSTRACT. The single name Pneumocystis carinii consists of an heterogeneous group of specific fungal organisms that colonize a very wide range of mammalian hosts. In the present study, mitochondrial large subunit (mtLSU) and small subunit (mtSSU) rRNA sequences of P. carinii organisms from 24 different mammalian species were compared. The mammals were included in six major groups: Primates (12 species). Rodents (5 species). Carnivores (3 species). Bats (1 species), Lagomorphs (1 species), Marsupials (1 species) and Ungulates (1 species). Direct sequencing of PCR products demonstrated that specific mtSSU and mtLSU rRNA Pneumocystis sequence could be attributed to each mammalian species. No animal harbored P. carinii f. sp. hominis. Comparison of combined mtLSU and mtSSU aligned sequences confirmed cospeciation of P. carinii and corresponding mammalian hosts. P. carinii organisms isolated from mammals of the same zoological group systematically clustered together. Within each cluster, the genetic divergence between P. carinii organisms varied in terms of the phylogenetic divergence existing among the corresponding host species. However, the relative position of P. carinii groups (rodent, carnivore or primate‐derived P. carinii) could not be clearly determined. Further resolution will require the integration of additional sequence data.
DEFICIENCY OF INTERFERON‐ALPHA GENERATING CAPACITY IS ASSOCIATED WITH SUSCEPTIBILITY TO OPPORTUNISTIC INFECTIONS IN PATIENTS WITH AIDS a

Acquired immune deficiency syndrome (AIDS) is a newly described syndrome in which patients are susceptible to certain malignancies and opportunistic infections (OI) usually found only in immunosuppressed individuals. Patients with AIDS have been found to have deficiencies of virtually all of their host defense systems. In this report, the natural resistance systems have been discussed. Although a deficiency of NK-cell function has been found in many patients with AIDS, this deficiency failed to distinguish patients susceptible to OI or malignancy from male homosexual controls. A deficiency of interferon-alpha generation by mononuclear cells upon exposure to HSV-1 infected fibroblasts was the best correlate with susceptibility to OI in AIDS patients. This deficiency failed to correlate with serum levels of acid-labile interferon-alpha in these patients. Although the interferon generating deficiency may be caused by the infections in these patients, it is more likely that the deficiency lays the groundwork for the establishment of the opportunistic infections.
Subcellular proteomics of Trypanosoma cruzi reservosomes

Reservosomes are the endpoint of the endocytic pathway in Trypanosoma cruzi epimastigotes. These organelles have the particular ability to concentrate proteins and lipids obtained from medium together with the main proteolytic enzymes originated from the secretory pathway, being at the same time a storage organelle and the main site of protein degradation. Subcellular proteomics have been extensively used for profiling organelles in different cell types. Here, we combine cell fractionation and LC‐MS/MS analysis to identify reservosome‐resident proteins. Starting from a purified reservosome fraction, we established a protocol to isolate reservosome membranes. Transmission electron microscopy was applied to confirm the purity of the fractions. To achieve a better coverage of identified proteins we analyzed the fractions separately and combined the results. LC‐MS/MS analysis identified in total 709 T. cruzi‐specific proteins; of these, 456 had predicted function and 253 were classified as hypothetical proteins. We could confirm the presence of most of the proteins validated by previous work and identify new proteins from different classes such as enzymes, proton pumps, transport proteins, and others. The definition of the reservosome protein profile is a good tool to assess their molecular signature, identify molecular markers, and understand their relationship with different organelles.
On the Performance of Lateral SiGe Heterojunction Bipolar Transistors With Partially Depleted Base

This paper discusses improvements to a lateral bipolar device capable of integration into the existing CMOS process flow. With the help of simulations, we demonstrate that the emitter transit time limits the cutoff frequency of a lateral bipolar device. We show that with the introduction of a heterojunction and a partially depleted base, we can decrease the emitter transit time and increase the current gain and the cutoff frequency (ft) of the device. For a balanced design, our simulations indicate an n-p-n device with an ft of 812 GHz and an fmax of 1.08 THz; and a p-n-p device with an ft of 635 GHz and an fmax of 1.15 THz. The collector current at cutoff frequency for both n-p-n and p-n-p devices is ~0.03 mA-roughly 100 times lower than commercial vertical heterojunction bipolar transistors.
Testing charged current quasi-elastic and multinucleon interaction models in the NEUT neutrino interaction generator with published datasets from the MiniBooNE and MINERνA experiments

The MiniBooNE large axial mass anomaly has prompted a great deal of theoretical work on sophisticated Charged Current Quasi-Elastic (CCQE) neutrino interaction models in recent years. As the dominant interaction mode at T2K energies, and the signal process in oscillation analyses, it is important for the T2K experiment to include realistic CCQE cross section uncertainties in T2K analyses. To this end, T2K's Neutrino Interaction Working Group has implemented a number of recent models in NEUT, T2K's primary neutrino interaction event generator. In this paper, we give an overview of the models implemented, and present fits to published muon neutrino and muon antineutrino CCQE cross section measurements from the MiniBooNE and MINERvA experiments. The results of the fits are used to select a default cross section model for future T2K analyses, and to constrain the cross section uncertainties of the model. We find a model consisting of a modified relativistic Fermi gas model and multinucleon interactions most consistently describes the available data.
Sub-Saharan Africa's Manufacturing Sector: Building Complexity

As Africa's working age population continues to grow rapidly, the region needs to experience both economic growth and high levels of job creation before it can realize the demographic dividend. This paper uses economic complexity analytics to provide product-level insights into sub-Saharan Africa's development path in comparison with that of the Eastern and Southern Asian regions. Specific emphasis is placed on the evolution of the manufacturing sector within these regions. The analysis from this study shows a sub-Saharan African (SSA) productive structure that is disconnected and characterized by products with low levels of economic complexity. The study further shows that the productive structure in SSA is inherently characterized by lower levels of economic complexity, which informed the notion of limited productive capabilities. This stands in contrast to the East and South Asian productive structure, which is connected and complex. This result implies that while the sheer scale and diversity of the manufacturing sector in Asia allows for the generation of a large number and diversity of employment opportunities that of the African manufacturing sector is marginal in nature and points to limited employment opportunities.
Intensive Care Management of Patients in the First 24 Hours After Cardiac Surgery

The cardiac surgery continues having a fundamental roll in the therapeutic arsenal of many heart deseases in spite of the spectacular advances that determined drugs or different forms of interventionist cardiology have experimented during the past few years. The present impact of the heart surgery is due to the constant increase of the cardiovascular risk factors, related to the increase in the life expectancy in last the three decades, the clinical approach of the ischemic cardiopathy towards the repair has taken to the creation and development of techniques and methods at the moment used in the miocardic revascularization surgery; the roll of the coronary surgery initiated by Sabiston in 1962 and popularized by Favaloro in 1967 has had an exponential development with the purpose of to exclude the ill part from the artery by placing a bypass to improve the perfusion of the ischemic area. Nevertheless the other side of the balance is the pharmacological treatment whose objective is to look for the balance between the supply and demands in the ischemic scope at the expense of a smaller consumption of oxygen (VO2), diminution of the inflammatory local metabolism, control of trombotics phenomena, etc. Now on the basis of the knowledge and acquired experience we establish a margin of durability of 90% to 10years in grafts of internal mammary (AMI) and 50-60% of venous grafts (HV), depending on the vascularized area and the type of vein, in relation to the arterial grafts the average life is of 90% to 5 years with sufficient information of early stenosis problems. Most of the post-operated patients recover in a fast and complete form, which depends on the quality of the performed surgery and an opportune and suitable handling as all the symptoms of the organism recover of the effects of: anesthesia, cardiopulmonary derivation (CEC) and surgical stress. Nevertheless some patients who present combinations of indicators of preoperative risk like: age outpost, antecedents of miocardic revascularization, recent and acute miocardic heart attack (IAM), ejection fraction (EF) low or diabetes, have a much greater surgical risk to the one of the habitual patient. At the moment there are certain characteristics that have determined a fast recovery as they are the early extubation, to avoid major sedation, the disconnection of the support devices and the suspension of drugs as rapidly as possible. A fast treatment before a: Low cardiac cost, alteration of the pulmonary function, hemorrhages, coagulopathy and fever is essential to be able to obtain a fast recovery of the patients; at the moment the surgical indications of the miocardiac revascularization (RVM) have been based in relation to the number and degree of affectation of the coronary arteries, decreased ventricular
Prosthodontic Rehabilitation of Arabic Speaking Individuals with Velopharyngeal Incompetence: A Preliminary Study

Background: Hypernasality is a frequently encountered problem in the speech of individuals with velopharyngeal incompetence. The use of palatal lift appliance (PLA) is the main treatment option for correction of velopharyngeal incompetence. The literature on the outcomes of using prosthetics treatment for Arabic speaking patients is scarce. Objective: The aim of this study was to investigate the effect of using PLA on hypernasality of Arabic speaking patients with velopharyngeal incompetence. Methods: Six participants with age ranging from 9 to 61 years (4 males and 2 females) were recruited between October 2013 and August 2014. Written informed consents were taken from all the adult participants/the guardians of under-aged participants. All patients exhibited hypernasality with different etiologies for velopharyngeal incompetence (head injury, cerebrovascular accident, and neurological disorders). They were treated with PLAs which were constructed to elevate the dysfunctional soft palate. Nasalance scores and perceptual speech acceptability ratings were measured/evaluated in both situations; with and without appliances. Paired t-test was used to analyze the perceptual ratings and nasalance scores in order to detect any significant change in hypernasality pre and post insertion of PLA. Results: There was a statistically significant decrease (p>0.05) in nasalance scores (Pa, Pi, Ma, Mi, a, i) after PLA insertion. The subtest /u/ showed insignificant change (p= 0.056). Perceptual ratings showed significant reduction in hypernasality which was consistent with nasalance measurements. Conclusion: PLAs can reduce hypernasality in Arabic speaking patients who suffer from velopharyngeal impairment.
Early Experience Determines Song Dialect Responsiveness of Female Sparrows

In a laboratory experiment, female white-crowned sparrows responded almost exclusively to male songs taken from their home dialect region and usually not to songs taken from an alien dialect region. Song dialect populations may represent a level of genetic population structure below that of the subspecies and may play an important role in songbird evolution.
Development of appropriate technology for treatment of molasses-based wastewater

In this study, the performance of a proposed treatment system consisting of an anaerobic process (acidification, methane fermentation) and an aerobic process (trickling filter) was evaluated for treating high concentrations of molasses-based wastewater (43–120 gCOD/L) by a continuous flow experiment. An anaerobic up-flow staged sludge bed (USSB) reactor, equipped with multiple gas solid separators, was used as the main treatment/methane recovery process. The USSB showed good efficiency of both COD removal (80–87%) and methane recovery (70–80%) at an organic loading rate of 11–43 kgCOD/m3 day. As the influent COD concentration was increased, the organic loading rate for stable operation of the USSB was reduced due to cation inhibition. However, the COD removal efficiency of the whole treatment system (including the aerobic post-treatment process) was 96% even at an influent COD concentration of 120 gCOD/L. Use of the treated wastewater as a fertilizer and/or irrigation-water for sugarcane was evaluated by a field cultivation test. Both growth of sugarcane and emission of greenhouse gases from the field soil were measured. A relatively high methane flux (352 μgCH4/m2 h) was observed when the treated wastewater from day 0 was used. By day 3, however, this value was reduced to the same level as the control. In addition, growth of sugarcane was satisfactory when the treated wastewater was used. The treated wastewater was found to be useful for cultivation of sugarcane in terms of both a low risk of greenhouse gas emission from the field soil and effectiveness for growth of sugarcane.
Towards a Pan-European E-Procurement Platform to Aggregate, Publish and Search Public Procurement Notices Powered by Linked Open Data: the Moldeas Approach

This paper aims to describe a public procurement information platform which provides a unified pan-European system that exploits the aggregation of tender notices using linking open data and semantic web technologies. This platform requires a step-based method to deal with the requirements of the public procurement sector and the open government data initiative: (1) modeling the unstructured information included in public procurement notices (contracting authorities, organizations, contracts awarded, etc.); (2) enriching that information with the existing product classification systems and the linked data vocabularies; (3) publishing relevant information extracted out of the notices following the linking open data approach; (4) implementing enhanced services based on advanced algorithms and techniques like query expansion methods to exploit the information in a semantic way. Taking into account that public procurement notices contain different kinds of data like types of contract, region, duration, total amount, target enterprise, etc., various methods can be applied to expand user queries easing the access to the information and providing a more accurate information retrieval system. Nevertheless expanded user queries can involve an extra-time in the process of retrieving notices. That is why a performance evaluation is outlined to tune up the semantic methods and the generated queries providing a scalable and time-efficient system. Moreover, this platform is supposed to be especially relevant for SMEs that want to tender in the European Union (EU), easing their access to the information of the notices and fostering their participation in cross-border public procurement processes across Europe. Finally an example of use is provided to evaluate and compare the goodness and the improvement of the proposed platform with regard to the existing ones.
Proinflammatory mediators chronically downregulate the formation of the endothelium-derived hyperpolarizing factor in arteries via a nitric oxide/cyclic GMP-dependent mechanism.

BACKGROUND Endothelium-dependent dilator responses mediated by NO and endothelium-derived hyperpolarizing factor (EDHF) are altered in arteriosclerosis and sepsis. The possibility that proinflammatory mediators that stimulate the expression of inducible NO synthase (NOS II) affect the generation of EDHF was examined in isolated arteries. METHODS AND RESULTS Under combined blockade of NOS and cyclooxygenase, EDHF-mediated relaxation elicited by several agonists was significantly attenuated in rabbit carotid and porcine coronary arteries exposed to cytokines and lipopolysaccharide. The blunted relaxation was coincident with NOS II expression and was prevented by inhibition of NOS II as well as of global protein synthesis. The NO donor CAS 1609 and 8-bromo-cGMP mimicked the proinflammatory mediator effect. In contrast, long-term blockade of endothelial NO generation increased the relaxation in carotid but not in coronary arteries. Proinflammatory mediators reduced the synthesis of EDHF assessed as hyperpolarization of vascular smooth muscle cells elicited by the effluent from bradykinin-stimulated coronary arteries. Proinflammatory mediators induced NOS II expression in cultured endothelial cells and decreased the expression of cytochrome P450 enzymes, which are the most probable candidates for the synthesis of EDHF. CONCLUSIONS Proinflammatory mediators inhibit the formation of EDHF in isolated arteries. This impairment is coincident with NOS II expression in the arterial wall and seems to be mediated through the induced generation of NO, which downregulates the putative EDHF-forming enzyme. Thus, a decreased formation of EDHF may contribute to the endothelial dysfunction in arteriosclerosis and sepsis.
Transitions in men's caring identities: experiences from home-based care to nursing home placement.

Objectives. The aim of this study is to describe, from a gender identity perspective, the experiences of older men involved in the process of caring for a partner at home and the placement into a nursing home. Background. Few studies have paid attention to the importance of gender when considering the social experiences of older men providing care for an ill spouse and finally placing a partner in a nursing home. Further understanding is much needed of how older men experience the process of caring for a spouse from a gender identity perspective. Design. A qualitative constructivist approach was adopted for this study. Participants. Data consists of interviews with seven men that have been informal carers and experienced the placement of their wife in a nursing home. Methods. Interviews were analysed with a constructivist approach. Results. The results indicate that men go through two transitions in their gender identity during the caregiving process and placement. From the mutual loving relationship of being a loving husband, the social responsibility of daily care of their wives changes the situation into that of being a caring husband, and finally with the move to a nursing home there is a transition from intimate care to a relationship based on friendship. Conclusions. The results show that older caregiving men undergo a process involving a reconstruction of gender identity. To formally recognize men's caring activities and to make them sustainable, we believe that men in an informal caring relationship need support. Relevance to clinical practice. Nurses need to recognize the identity struggles resulting in sadness and suffering that are related to changes in men's lives during the caregiving process. Understanding the dynamics and changes that occur when men take on a caring task is important for the development of their role as carers.