Miracle-dz/UniFAR-FTUs huggingface dataset:
Copper Chaperone CupA and Zinc Control CopY Regulation of the Pneumococcal cop Operon

As mechanisms of copper toxicity are emerging, bacterial processing of intracellular copper, specifically inside Streptococcus pneumoniae, remains unclear. In this study, we investigated two proteins encoded by the copper export operon: the repressor, CopY, and the copper chaperone, CupA. Zinc suppressed transcription of the copper export operon by increasing the affinity of CopY for DNA. Furthermore, CupA was able to chelate copper from CopY not bound to DNA and reduce it from Cu2+ to Cu1+. This reduced copper state is essential for bacterial copper export via CopA. In view of the fact that innate immune cells use copper to kill pathogenic bacteria, understanding the mechanisms of copper export could expose new small-molecule therapeutic targets that could work synergistically with copper against pathogenic bacteria. ABSTRACT Any metal in excess can be toxic; therefore, metal homeostasis is critical to bacterial survival. Bacteria have developed specialized metal import and export systems for this purpose. For broadly toxic metals such as copper, bacteria have evolved only export systems. The copper export system (cop operon) usually consists of the operon repressor, the copper chaperone, and the copper exporter. In Streptococcus pneumoniae, the causative agent of pneumonia, otitis media, sepsis, and meningitis, little is known about operon regulation. This is partly due to the S. pneumoniae repressor, CopY, and copper chaperone, CupA, sharing limited homology to proteins of putative related function and confirmed established systems. In this study, we examined CopY metal crosstalk, CopY interactions with CupA, and how CupA can control the oxidation state of copper. We found that CopY bound zinc and increased the DNA-binding affinity of CopY by roughly an order of magnitude over that of the apo form of CopY. Once copper displaced zinc in CopY, resulting in operon activation, CupA chelated copper from CopY. After copper was acquired from CopY or other sources, if needed, CupA facilitated the reduction of Cu2+ to Cu1+, which is the exported copper state. Taken together, these data show novel mechanisms for copper processing in S. pneumoniae. IMPORTANCE As mechanisms of copper toxicity are emerging, bacterial processing of intracellular copper, specifically inside Streptococcus pneumoniae, remains unclear. In this study, we investigated two proteins encoded by the copper export operon: the repressor, CopY, and the copper chaperone, CupA. Zinc suppressed transcription of the copper export operon by increasing the affinity of CopY for DNA. Furthermore, CupA was able to chelate copper from CopY not bound to DNA and reduce it from Cu2+ to Cu1+. This reduced copper state is essential for bacterial copper export via CopA. In view of the fact that innate immune cells use copper to kill pathogenic bacteria, understanding the mechanisms of copper export could expose new small-molecule therapeutic targets that could work synergistically with copper against pathogenic bacteria.
Quantitative serum HBsAg and HBeAg are strong predictors of sustained HBeAg seroconversion to pegylated interferon alfa‐2b in HBeAg‐positive patients

Background and Aim: To evaluate the usefulness of quantitative hepatitis B surface antigen (HBsAg) and hepatitis B e antigen (HBeAg) for predicting HBeAg seroconversion in chronic hepatitis B patients treated with conventional interferon (IFN) alfa‐2b or PegIFN alfa‐2b.
Formation in vitro of complexes between an abnormal fusion protein and the heat shock proteins from Escherichia coli and yeast mitochondria

Heat shock proteins (HSPs) of the Hsp70 and GroEL families associate with a variety of cell proteins in vivo. However, the formation of such complexes has not been systematically studied. A 31-kDa fusion protein (CRAG), which contains 12 residues of cro repressor, truncated protein A, and 14 residues of beta-galactosidase, when expressed in Escherichia coli, was found in complexes with DnaK, GrpE, protease La, and GroEL. When an E. coli extract not containing CRAG was applied to an affinity column containing CRAG, DnaK, GroEL, and GrpE were selectively bound. These HSPs did not bind to a normal protein A column. DnaK, GrpE, and the fraction of GroEL could be eluted from the CRAG column with ATP but not with a nonhydrolyzable ATP analog. The ATP-dependent release of DnaK and GroEL also required Mg2+, but GrpE dissociated with ATP alone. The binding and release of DnaK and GroEL were independent events, but the binding of GrpE required DnaK. Inactivation of DnaJ, GrpE, and GroES did not affect the association or dissociation of DnaK or GroEL from CRAG. The DnaK and GrpE proteins could be eluted with 10(-6) M ATP, but 10(-4) M was required for GroEL release. This approach allows a one-step purification of these proteins from E. coli and also the isolation of the DnaK and GroEL homologs from yeast mitochondria. Competition experiments with oligopeptide fragments of CRAG showed that DnaK and GroEL interact with different sites on CRAG and that the cro-derived domain of CRAG contains the DnaK-binding site.
Microscopy and Microanalysis of Blood in a Snake Head Fish, Channa gachua Exposed to Environmental Pollution

Abstract Conventional and highly sophisticated analytical methods (Cyria et al., 1989; Massar et al., 2012a) were used to analyze micro-structural and micro-analytical aspects of the blood of snake head fish, Channa gachua, exposed to municipal wastes and city garbage. Red (RBC) and white blood cell (WBC) counts and hemhemoglobin content were found to be higher in pollution affected fish as compared with control. Scanning electron microscopy revealed the occurrence of abnormal erythrocytes such as crenated cells, echinocytes, lobopodial projections, membrane internalization, spherocytes, ruptured cells, contracted cells, depression, and uneven elongation of erythrocyte membranes in fish inhabiting the polluted sites. Energy-dispersive X-ray spectroscopy (EDS) revealed the presence of silicon and lead in the RBCs of pollution affected fish. Significance of the study includes the highly sophisticated analytical approach, which revealed the aforementioned micro-structural abnormalities.
Cloud based big data infrastructure: Architectural components and automated provisioning

This paper describes the general architecture and functional components of the cloud based Big Data Infrastructure (BDI). The proposed BDI architecture is based on the analysis of the emerging Big Data and data intensive technologies and supported by the definition of the Big Data Architecture Framework (BDAF) that defines the following components of the Big Data technologies: Big Data definition, Data Management including data lifecycle and data structures, Big Data Infrastructure (generically cloud based), Data Analytics technologies and platforms, and Big Data security, compliance and privacy. The paper provides example of requirements analysis and implementation of two bioinformatics use cases on cloud and using SlipStream based cloud applications deployment and management automation platform being developed in the CYCLONE project. The paper also refers to importance of standardisation of all components of BDAF and BDI and provides short overview of the NIST Big Data Interoperability Framework (BDIF). The paper discusses importance of automation of all stages of the Big Data applications developments, deployment and management and refers to existing cloud automation tools and new developments in the SlipStream cloud automation platform that allows multi-cloud applications deployment and management.
Proton magnetic resonance spectroscopy of human brain: Applications to normal white matter, chronic infarction, and MRI white matter signal hyperintensities

A modified ISIS method, for image‐selected localized proton magnetic resonance spectroscopy (1H MRS), was used to determine the ratios and T2 relaxation times of proton metabolites in normal subjects and in patients with chronic infarction and MRI white matter signal hyperintensities (WMSH). First, in patients with cerebral infarctions, increased concentrations of lactate were found in the majority of patients, and N‐acetyl aspartate (NAA) was reduced to a significantly greater extent than choline (Cho) or creatine (Cre). For TE = 270 ms, the raw ratios of Cho/NAA, Cre/NAA, and Lac/NAA were significantly (P < 0.05) increased from 0.23 ± 0.02 (mean ± SE), 0.20 ± 0.01, and 0.05 ± 0.01, respectively in the normal group to 0.39 ± 0.08, 0.37 ± 0.05, and 0.48 ± 0.15 in the stroke group. Also, the T2 relaxation time of creatine was significantly (P = 0.007) increased from 136 ms in normal white matter to 171 ms in cerebral infarcts. Second, in patients with WMSH, no significant change of the proton metabolite concentrations could be detected with the exception of the choline which was significantly (P = 0.003) altered. The Cho/NAA ratio, after T2 and excitation profile correction, increased from 0.47 ± 0.02 in the normal group to 0.64 ± 0.05 in the WMSH group. Third, in normal white matter, the concentration of N‐acetyl aspartate, choline, and lactate was estimated to 11.5, 2.0, and 0.6 mM, respectively, by assuming a total creatine concentration of 10 mM.
Interplay between the membrane-associated UhpB and UhpC regulatory proteins

Expression of the Escherichia coli uhpT gene, encoding the sugar phosphate transport protein, is induced by extracellular glucose-6-phosphate and requires the function of the uhpABC regulatory genes. The UhpA and UhpB proteins are related to the response-regulator and sensor-kinase proteins of two-component regulatory systems, whereas the UhpC protein is related to UhpT and homologous transport proteins. To investigate the role of segments of the membrane-associated UhpB and UhpC regulatory proteins, a series of mutations were constructed in vitro by insertion of a 12- or 24-bp oligonucleotide linker at 44 sites within the uhpABCT locus. The effect of these mutations on regulation of a uhpT-lacZ transcriptional reporter was assayed with the mutated uhp alleles in single copy on the chromosome. All but one of the insertions in uhpA or uhpT were inactive for transcription activation or transport, respectively. In contrast, about half of the insertions in uhpB and uhpC retained Uhp expression, and insertions at four sites in uhpB and at one site in uhpC conferred high-level constitutive expression. The constitutive mutants in UhpB resulted from insertions in the nonpolar amino-terminal half of the protein, and all insertions in that half of UhpB affected Uhp expression in some manner, which suggests that the transmembrane segments of UhpB might negatively regulate the kinase activity of the carboxyl portion. The constitutive behavior of all but one of these uhpB alleles was dependent on the presence of active forms of both UhpA and UhpC, which suggests that UhpB and UhpC act jointly as a complex in the signaling process.
Hypothalamo-hypophysial Dysfunction After Traumatic Brain Injury in Children and Adolescents: A Preliminary Retrospective and Prospective Study

With two study protocols, one retrospective and the other prospective, we evaluated hypothalamo-hypophysial dysfunction (HHD) in paediatric patients treated for traumatic brain injury (TBI) in the neurosurgical or intensive care department at our hospital. The retrospective group comprised 22 patients who had experienced TBI 0.7-7.25 years before the study. The prospective group included 30 patients assessed at TBI (T0), 26 of 30 after 6 months (T6), and 20 of 26 after 12 months (T12). Auxological and hormonal basal parameters of hypothalamo-hypophysial function were evaluated at recall in the retrospective group, and at T0, T6 and T12 in the prospective group. Basal data and standard dynamic tests in selected patients revealed one with precocious puberty, one with total anterior hypopituitarism, one with central hypogonadism, and one with growth hormone (GH) deficiency in the retrospective group; three patients with cerebral salt-wasting syndrome, one with diabetes insipidus and seven with low T3 syndrome at T0 (all transient), one with hypocorticism at T6 confirmed at T12, and one with GH deficiency at T12 in the prospective group. The results of our study show that post-TBI HHD in our paediatric cohort is not uncommon. Of the 48 patients who underwent a complete evaluation (22 retrospective study patients and 26 prospective study patients evaluated at T6) five (10.4%) developed HHD 6 months or more after TBI. HHD was newly diagnosed in one previously normal patient from the prospective group at 12 months after TBI. GH deficiency was the most frequent disorder in our paediatric cohort.
Incorporation of Coenzyme Q10 into Bovine Oocytes Improves Mitochondrial Features and Alleviates the Effects of Summer Thermal Stress on Developmental Competence1

ABSTRACT Environmental stress-induced alterations in oocyte mitochondria are suggested to deleteriously affect developmental competence of the ovarian pool of oocytes. We examined the association between seasonal effects on oocyte developmental competence and mitochondrial distribution, polarization, mitochondrial DNA (mtDNA) content, and RNA expression, and whether the incorporation of coenzyme Q10 (CoQ10) might improve these effects. Bovine oocytes were collected during the summer (June–August), fall (September–November), and winter (December–May), matured in vitro with or without 50 μM CoQ10, fertilized, and cultured for 8 days. The proportion of developed blastocysts was highest in the winter, intermediate in the fall, and lowest in the summer. Matured oocytes were classified into categories I–IV according to their mitochondrial distribution pattern (MitoTracker green). The proportion of high- and low-polarized mitochondria (JC-1 assay) differed between oocyte categories but was not affected by season. On the other hand, oocyte distribution into categories differed between seasons and was affected by CoQ10, with an increased proportion of category I oocytes in the fall. Oocyte mtDNA did not differ between seasons, but expression of mitochondrion-associated genes involved in the respiratory chain (ND2, SDHD, CYTB, COXII, ATP5B, and TFAM) did. Coenzyme Q10 increased the expression of CYTB, COXII, and ATP5B and the proportions of blastocysts developed in the fall. In summary, season-induced alterations in mitochondrial functions might explain, in part, the reduced oocyte developmental competence. It seems that in the fall, under modest harm, CoQ10 incorporation can alleviate these deleterious effects somewhat.
Teachers' and pupils' definitions of bullying.

BACKGROUND Comparison of teachers' and pupils' definitions of bullying is important for considering the implications for reports of its incidence in schools, for the study of developmental trends in children's and adolescents' perceptions of the phenomenon and for evaluating the effectiveness of interventions designed to combat bullying. AIMS To investigate the effects of gender, teacher/pupil status and, for pupils, bullied/non-bullied (target/non-target) status and age on the definition of bullying. SAMPLES Teachers (N=225: 158 women, 67 men) and pupils (N=1,820: 466 boys, 460 girls were 11-12 years old, year 7, and 415 boys, 479 girls were 13-14 years, year 9) in 51 UK secondary schools participated in a questionnaire survey. A total of 557 of the pupils (117 girls and 117 boys aged 11-12 years, and 197 girls and 126 boys aged 13-14 years) reported that they had been bullied at some time in their present school. METHODS Written questionnaire responses to the question, 'Say what you think bullying is' have been content analysed to derive two sets of categories, one of bullying behaviour and the other of effects of bullying on the target. RESULTS Regarding both bullying behaviour and the effects of bullying on the target, teachers - by comparison with pupils - have been found to express more comprehensive ideas in their definitions. Specifically, pupils compared with teachers are more likely to restrict their definitions to direct bullying (verbal and/or physical abuse) and are less likely to refer to social exclusion, a power imbalance in the bully's favour and the bully's intention to cause the target hurt or harm and to feel threatened. Analysis of definitions on the bases of sex, pupil age and target/non-target status show that: targets are more likely than non-targets are to refer to the bully's physically and verbally abusive behaviour, and for Year 7 compared with Year 9 pupils, to suggest that bullies socially exclude targets; girls are more likely than boys are to mention verbal abuse and the effects on the target of 'Feels hurt/harm', but boys are more likely than girls are to construe bullying as involving repetition; older pupils are more likely than younger ones are to refer to a power imbalance in the bully's favour but, for bully targets, younger ones compared with older ones are more likely to invoke the idea of social exclusion in their definitions. CONCLUSIONS The most important implication of the findings of this study that there are important differences between teachers' and pupils' definitions of bullying is that teachers need to listen carefully to what pupils have to say about bullying and work with and help them to develop their conceptions of the phenomenon. Some teachers, too, need to develop their conceptions of bullying.
Influenza-associated Encephalitis/Encephalopathy Identified by the Australian Childhood Encephalitis Study 2013–2015

Background: Influenza-associated encephalitis/encephalopathy (IAE) is an important cause of acute encephalitis syndrome in children. IAE includes a series of clinicoradiologic syndromes or acute encephalopathy syndromes that have been infrequently reported outside East Asia. We aimed to describe cases of IAE identified by the Australian Childhood Encephalitis study. Methods: Children ⩽ 14 years of age with suspected encephalitis were prospectively identified in 5 hospitals in Australia. Demographic, clinical, laboratory, imaging, and outcome at discharge data were reviewed by an expert panel and cases were categorized by using predetermined case definitions. We extracted cases associated with laboratory identification of influenza virus for this analysis; among these cases, specific IAE syndromes were identified where clinical and radiologic features were consistent with descriptions in the published literature. Results: We identified 13 cases of IAE during 3 southern hemisphere influenza seasons at 5 tertiary children’s hospitals in Australia; 8 children with specific acute encephalopathy syndromes including: acute necrotizing encephalopathy, acute encephalopathy with biphasic seizures and late diffusion restriction, mild encephalopathy with reversible splenial lesion, and hemiconvulsion-hemiplegia syndrome. Use of influenza-specific antiviral therapy and prior influenza vaccination were infrequent. In contrast, death or significant neurologic morbidity occurred in 7 of the 13 children (54%). Conclusions: The conditions comprising IAE are heterogeneous with varied clinical features, magnetic resonance imaging changes, and outcomes. Overall, outcome of IAE is poor emphasizing the need for optimized prevention, early recognition, and empiric management.
Toward highly efficient cell-type-specific gene transfer with retroviral vectors displaying single-chain antibodies

Recently, we constructed retroviral vector particles derived from spleen necrosis virus (SNV) that display a single-chain antibody (scA) on the viral surface. By transient transfection protocols, we showed that such particles are competent for infection and cell type specific. Efficient infection was dependent on the presence of wild-type envelope, although wild-type SNV was not infectious on target cells (T.-H. T. Chu and R. Dornburg, J. Virol. 69:2659-2663, 1995; T.-H. T. Chu, I. Martinez, W. C. Sheay, and R. Dornburg, Gene Ther. 1:292-299, 1994). In this study, stable packaging lines were constructed and detailed biological and biochemical studies were performed. Chimeric scA-envelope fusion proteins were expressed as efficiently as wild-type envelope and were stable over a period of at least 6 h. Only a fully functional wild-type envelope could act as a helper for efficient virus penetration. The ratio of wild-type envelope protein to chimeric envelope protein appears to determine the efficiency of infection. Virus titers of targeting vectors obtained from stable packaging lines were as high as 10(4) CFU/ml. A 25-fold concentration of vector virus stocks resulted in a 200-fold increase in virus titers (up to 10(6) CFU/ml). These data indicate that an inhibitor of infection was (at least partially) removed by the concentration protocol. Our data show that this technology has several variables for further improvements and, therefore, has the potential to become a powerful tool for cell-type-specific in vivo human gene therapy.
Antimicrobial stewardship: attempting to preserve a strategic resource

Antimicrobials hold a unique place in our drug armamentarium. Unfortunately the increase in resistance among both gram-positive and gram-negative pathogens coupled with a lack of new antimicrobial agents is threatening our ability to treat infections. Antimicrobial use is the driving force behind this rise in resistance and much of this use is suboptimal. Antimicrobial stewardship programs (ASP) have been advocated as a strategy to improve antimicrobial use. The goals of ASP are to improve patient outcomes while minimizing toxicity and selection for resistant strains by assisting in the selection of the correct agent, right dose, and best duration. Two major strategies for ASP exist: restriction/pre-authorization that controls use at the time of ordering and audit and feedback that reviews ordered antimicrobials and makes suggestions for improvement. Both strategies have some limitations, but have been effective at achieving stewardship goals. Other supplemental strategies such as education, clinical prediction rules, biomarkers, clinical decision support software, and institutional guidelines have been effective at improving antimicrobial use. The most effective antimicrobial stewardship programs have employed multiple strategies to impact antimicrobial use. Using these strategies stewardship programs have been able to decrease antimicrobial use, the spread of resistant pathogens, the incidence of C. difficile infection, pharmacy costs, and improved patient outcomes.