Side Gate Tunable Josephson Junctions at the LaAlO3/SrTiO3 Interface.

Novel physical phenomena arising at the interface of complex oxide heterostructures offer exciting opportunities for the development of future electronic devices. Using the prototypical LaAlO3/SrTiO3 interface as a model system, we employ a single-step lithographic process to realize gate-tunable Josephson junctions through a combination of lateral confinement and local side gating. The action of the side gates is found to be comparable to that of a local back gate, constituting a robust and efficient way to control the properties of the interface at the nanoscale. We demonstrate that the side gates enable reliable tuning of both the normal-state resistance and the critical (Josephson) current of the constrictions. The conductance and Josephson current show mesoscopic fluctuations as a function of the applied side gate voltage, and the analysis of their amplitude enables the extraction of the phase coherence and thermal lengths. Finally, we realize a superconducting quantum interference device in which the critical currents of each of the constriction-type Josephson junctions can be controlled independently via the side gates.

Spin-Orbit Semimetal SrIrO_{3} in the Two-Dimensional Limit.

We investigate the thickness-dependent electronic properties of ultrathin SrIrO_{3} and discover a transition from a semimetallic to a correlated insulating state below 4 unit cells. Low-temperature magnetoconductance measurements show that spin fluctuations in the semimetallic state are significantly enhanced while approaching the transition point. The electronic properties are further studied by scanning tunneling spectroscopy, showing that 4 unit cell SrIrO_{3} is on the verge of a gap opening. Our density functional theory calculations reproduce the critical thickness of the transition and show that the opening of a gap in ultrathin SrIrO_{3} requires antiferromagnetic order.

High-performance Fe(Se,Te) films on chemical CeO2-based buffer layers.

The fabrication of a Fe-based coated conductor (CC) becomes possible when Fe(Se,Te) is grown as an epitaxial film on a metallic oriented substrate. Thanks to the material's low structural anisotropy, less strict requirements on the template microstructure allow for the design of a simplified CC architecture with respect to the REBCO multi-layered layout. This design, though, still requires a buffer layer to promote the oriented growth of the superconducting film and avoid diffusion from the metallic template. In this work, Fe(Se,Te) films are grown on chemically-deposited, CeO2-based buffer layers via pulsed laser deposition, and excellent properties are obtained when a Fe(Se,Te) seed layer is used. Among all the employed characterization techniques, transmission electron microscopy proved essential to determine the actual effect of the seed layer on the final film properties. Also, systematic investigation of the full current transport properties J(θ, H, T) is carried out: Fe(Se,Te) samples are obtained with sharp superconducting transitions around 16 K and critical current densities exceeding 1 MA cm-2 at 4.2 K in self-field. The in-field and angular behavior of the sample are in line with data from the literature. These results are the demonstration of the feasibility of a Fe-based CC, with all the relative advantages concerning process simplification and cost reduction.

P. aeruginosa bloodstream infections among hematological patients: an old or new question?

Pseudomonas aeruginosa is a well-known cause of severe and potentially life-threatening infections among hematological patients. A prospective epidemiological surveillance program ongoing at our Hematology Unit revealed an increase over time of P. aeruginosa bloodstream infections (BSI). Their impact on outcome and antibiotic susceptibility was analyzed. BSI which consecutively occurred at our institution during a 70-month period were evaluated and correlated with type of pathogen, status of underlying disease, neutropenia, previous antibiotic therapy, resistance to antibiotics, and outcome. During the observation period, 441 BSI were recorded. Frequency of Gram-negative BSI was higher than that of other pathogens (57.3%). Overall, 66 P. aeruginosa BSI were recorded; 22 out of 66 were multiresistant (MR P. aeruginosa). Thirty-day mortality for all BSI was 11.3%; it was 27.3% for P. aeruginosa BSI and 36.4% for MR P. aeruginosa. At multivariate analysis, only active hematological disease and P. aeruginosa BSI were associated to an increased risk of death. For MR P. aeruginosa, BSI mortality was 83.3% vs. 18.8% when empiric therapy included or not an antibiotic with in vitro activity against P. aeruginosa (p=0.011). Together with active disease, the emergence of P. aeruginosa BSI, particularly if multiresistant, was responsible for an increased risk of death among hematological patients at our institution. In this scenario, reconsidering the type of combination antibiotic therapy to be used as empiric treatment of neutropenic fever was worthwhile.

Phenotypes, genotypes, serotypes and molecular epidemiology of erythromycin-resistant Streptococcus agalactiae in Italy.

The purpose of this investigation was to analyse Streptococcus agalactiae (group B Streptococcus, GBS) isolates collected in Italy from vaginal and urine samples in respect to their clonality, distribution of virulence factors and antimicrobial resistance determinants. Three hundred and eighty-eight GBS were recovered from clinical samples. They were analysed for antibiotic resistance profiling. Erythromycin-resistant strains were further characterised by multilocus sequence typing (MLST), serotyping and the detection of alp genes of the alpha-like protein (Alp) family. GBS isolates represented 40 different sequence types (STs), grouped in five clonal complexes (CCs) and belonged to seven serotypes. Most serotype V strains (81%) possessed alp2-3; serotype Ia carried mainly epsilon, while the serotype III mainly rib. All isolates were susceptible to penicillin, whereas resistance to erythromycin was detected in 15% of isolates. Most erythromycin-resistant GBS strains were of serotype V (56.8%) and belonged to the CC-1 group (50%). Macrolide resistance phenotypes were the cMLS(B) (46.5%) and the M phenotypes (46.5%) due to the presence of ermB and mefA/E genes, respectively. These results provide data which establish a baseline for monitoring erythromycin resistance in this region and also provide an insight into the correlation among clonal types, serotypes, surface protein and resistance genes. The increased prevalence of strains that displayed the M phenotype strengthens the importance of the epidemiological surveillance of macrolide resistance in GBS, which may also represent an important reservoir of resistance genes for other species.

Persistence of human T cell lymphotropic virus type 1 (HTLV-1) sequences in peripheral blood mononuclear cells from patients with mycosis fungoides.

Mycosis fungoides (MF) is a rare form of cutaneous T cell lymphoma suspected of having a viral etiology. As in adult T cell leukemia, the virus involved may be human T lymphotropic virus type 1 (HTLV-1). We cultured the peripheral blood mononuclear cells (PBMC) of 29 patients with MF HTLV-1 seronegative by enzyme-linked immunosorbent assay and Western blot. The presence of reverse transcriptase (RT) and p24 antigen was investigated in the concentrate supernatant of the culture. The DNA of all studied patients was submitted to polymerase chain reaction and Southern blot analysis using primers and probes recognizing the tax region of HTLV-1/2 and the pol region of HTLV-1. 10 of 29 patients were found positive to HTLV-1, whereas they were always negative to RT and p24. The same results were confirmed in double blind after 6 mo. Our findings suggest HTLV-1 may be involved in the etiology of MF, at least in certain cases.

Heterogeneity and penetration of HIV-1 non-subtype B viruses in an Italian province: public health implications.

This study assessed changes in prevalence and distribution of HIV-1 non-subtype B viruses in Italian and immigrant patients over two decades in a province in Italy. All HIV-positive patients who underwent genotypic resistance testing were selected. Prevalence of non-subtype B viruses in 3-year periods was calculated. All sequences of non-subtype B and those provided by REGA as unassigned were analysed for phylogenetic relationships. In total, 250/1563 (16%) individuals were infected with a non-subtype B virus. Prevalence increased over time, reaching a peak (31.5%) in 2004-2006. In Italian patients, the most frequent subtypes were B (92.5%) and F1 (4%). F1 subtype was also prevalent in patients from South America (13.6%); in patients of African origin, CRF02_AG (54.9%) and G (12.3%) were the most frequent. HIV-1 non-subtype B infections in Italians were mostly found in patients who acquired HIV sexually. A phylogenetic relationship between F subtypes in Italian and representative HIV-1 sequences from Brazil was found. C subtypes in Italians were phylogenetically related to subtypes circulating in Brazil. Inter-subtype recombinants were also found in the latest years. The HIV-1 epidemic in Brescia province evolved to the point where about 1/3 patients recently diagnosed harboured non-B HIV subtypes. The distribution of HIV-1 non-B subtypes in Italian patients resembled that in South American patients and phylogenetic relatedness between some Italian and South American HIV-1 strains was found. The possible epidemiological link between these two populations would have been missed by looking only at risk factors for HIV acquisition declared by patients. The evidence of inter-subtype recombinants points to significant genetic assortment. Overall our results support phylogenetic analysis as a tool for epidemiological investigation in order to guide targeted prevention strategies.

Detection of Ureaplasma biovars and polymerase chain reaction-based subtyping of Ureaplasma parvum in women with or without symptoms of genital infections.

Ureaplasma parvum colonises human mucosal surfaces, primarily in the urogenital and respiratory tracts, causing a wide spectrum of diseases, from non-gonococcal urethritis to pneumonitis in immunocompromised hosts. Although the basis for these diverse clinical outcomes is not yet understood, it has been suggested that only certain strains of these micro-organisms are disease-associated. The aim of this study was to determine the distribution of Ureaplasma biovars and U. parvum serovars and to estimate their possible association with age, absence of lactobacilli, clinical symptoms and antibiotic resistance. DNA was extracted by endocervical, vaginal and urethral samples obtained from 158 women positive for U. urealyticum by culture and were biotyped by polymerase chain reaction (PCR) targeting the multiple-banded gene. Parvo biovar (biovar 1) was found in 136 (86%) and T960 biovar (biovar 2) in 22 (14%) patients. Among the different serovars of U. parvum, we found that serovar 3/14 was present maximally in the 21-25-year-old age group, while T960 biovar was distributed with quite similar frequency in women of 26-30 and >40 years of age. In this study, U. parvum serovar 3/14 and T960 biovar were found to be significantly associated with symptomatic patients and a loss of lactobacilli, while, on the contrary, U. parvum serovar 6 was significantly correlated with asymptomatic women and normal vaginal flora. The most active antibiotic for the majority of Ureaplasma isolates was tetracycline. These preliminary data show the possibility of distinguishing between the more or less virulent strains of Ureaplasma, with important consequences for therapeutic treatment.

Effectiveness of antiretroviral regimens containing abacavir with tenofovir in treatment-experienced patients: predictors of virological response and drug resistance evolution in a multi-cohort study.

BACKGROUND: In treatment-naïve patients, a combination antiretroviral therapy (cART) containing tenofovir (TDF) and abacavir (ABC) with lamivudine leads to unacceptably high virological failure rates with frequent selection of reverse transcriptase mutations M184V and K65R. We explored the efficacy of at least 16 weeks of ABC + TDF-containing cART regimens in 307 antiretroviral-experienced HIV-1-infected individuals included in observational databases. METHODS: Virological failure was defined as an HIV RNA > 400 copies/ml after at least 16 weeks of treatment. Patients had received a median of three prior cART regimens. Of these, 76% concomitantly received a potent or high genetic barrier regimen (with at least one protease inhibitor [PI]) or non-nucleoside reverse transcriptase inhibitor or thymidine analogue) while a third non-thymidine nucleoside analogue was used in the remaining patients. RESULTS: The 1-year estimated probability of virological failure was 34% in 165 patients with HIV RNA > 400 copies/ ml at ABC + TDF regimen initiation. Independent predictors of virological failure were the absence of a potent or high genetic barrier cART, the higher number of cART regimens experienced, and the use of a new drug class. In the subset of 136 patients for whom there were genotypic resistance test results prior to ABC + TDF initiation, the virological failure (1-year estimated probability 46%) was independently predicted by the higher baseline viral load, the concomitant use of boosted PI, and the presence of reverse transcriptase mutation M41L. In 142 patients starting ABC + TDF therapy with HIV RNA pound < or =400 copies/ml, virological failure (1-year estimated probability 17%) was associated only with the transmission category. In a small subset of subjects for whom there were an available paired baseline and follow-up genotype (n = 28), the prevalence of most nucleoside analogue reverse transcriptase inhibitor resistance mutations decreased, suggesting a possible low adherence to treatment. No selection of K65R was detected. CONCLUSION: The virological response to ABC + TDF-containing regimens in this moderately-to-heavily treatment experienced cohort was good. Higher viral load and the presence of M41L at baseline were associated with worse virological responses, while the concomitant prescription of drugs enhancing the genetic barrier of the regimen conveyed a reduced risk of virological failure. The Appendix provides the names of other members of the MASTER cohort.

Hyper-reactive malarial splenomegaly in a patient with human immunodeficiency virus.

Both hyperreactive malarial splenomegaly (HMS) and HIV infection are highly prevalent in sub-Saharan Africa, but the inter-relationships between the two conditions are not clearly defined. Diagnosis of HMS is particularly difficult in HIV-infected patients, and detection of circulating malaria parasites by polymerase chain reaction (PCR) may represent a useful diagnostic tool.

Comparison of the AMPLICOR human papillomavirus test and the hybrid capture 2 assay for detection of high-risk human papillomavirus in women with abnormal PAP smear.

Infection with human papillomavirus (HPV) is a necessary step in the progression to cervical cancer. Many methods for HPV testing are currently available, mostly developed to detect pools of HPV types. Hybrid Capture 2 (HC2) is one of the most widely used. A new PCR-based assay, the Roche AMPLICOR HPV test, has been recently developed. Both assays recognize a group of 13 HR HPV types contemporaneously. This study evaluated the performance of both methods for detecting high-grade cervical lesions as a part of management for abnormal PAP smears. The study population was composed of 213 women, all referred to colposcopy and histologic diagnosis following an abnormal PAP test. Biopsy-confirmed high-grade cervical intraepithelial neoplasia was used as a gold standard. Overall agreement was 84.9% with a kappa value of 0.6. When comparing the ability to detect moderate cervical intraepithelial neoplasia (CIN2+) and high-grade cervical intraepithelial neoplasia (CIN3+/cancer), AMPLICOR proved slightly more sensitive than HC2, a finding that is important when HPV testing is used in a triage of borderline smear results. Genotyping of discordant results showed a prevalence of LR-HPV types in HC2 positive/AMPLICOR negative samples, and a similar prevalence of HR- and LR-HPV types in AMPLICOR positive/HC2 negative samples. In conclusion, the study shows that the AMPLICOR assay is more sensitive than HC2, which makes it a valid alternative for routine clinical use.

Different sequence strains of Streptococcus agalactiae elicit various levels of cytokine production.

Group B streptococcus (GBS) is the most common cause of neonatal and obstetric sepsis and an increasingly important cause of septicemia in elderly subjects and immunocompromised patients. Our aim was to evaluate whether different genotypes of GBS may induce a different production of pro-inflammatory and anti-inflammatory cytokines. We used multilocus sequence typing to identify 71 clones isolated from asymptomatic healthy carriers and symptomatic individuals. All these clinical isolates were used to infect purified human monocytes. TNF-alpha, IL-6, IL-8 and IL-10 secretion was measured. Fifteen allelic sequence types (STs) were identified. The MLST (multilocus sequence typing) analysis grouped the bacteria into four different lineages (clonal cluster) and two of these were closely involved in the infection of symptomatic subjects: CC17 and CC19. Furthermore, CC17 and CC19 stimulated TNF-alpha, IL-6 and IL-8 production significantly more than the other lineages, while CC17 induced a decreased IL-10 production. These results suggest the existence of differences in immune response to infection with particular genotypes of GBS.

Prevalence and distribution of single and multiple HPV infections in cytologically abnormal cervical samples from Italian women.

The prevalence of single and multiple HPV infections was assessed over a cohort of 213 women with cytological abnormalities and its association with cervical neoplasia established. Roche linear array HPV genotyping test was used to identify HPV genotypes. The most prevalent HPV genotypes in cervical cancer samples were HPV16 (61.2%), HPV52 (16.1%), HPV18 (12.9%) and HPV 31 (9.6%). Multiple HR and LR HPV infections, comprising between two and 5+ HPV types, were identified in 49.7% of samples, with a significantly lower number in severe dysplasia and cervical cancer samples (p<0.05). These results seem to indicate that detection of multiple HPV infection with HR-HPV types is not significantly better as a predictor of cervical cancer than single HR-HPV infection, though further longitudinal studies are needed to better clarify the relevance of these infections to the progression of cervical neoplasia.

HIV p17 reverses the anti-inflammatory activity of IL-4 on IL-15 stimulated monocytes and modulates their ability to secrete MIP-1 alpha.

Monocytes play a central role in the immune system by producing and reacting to different soluble factors. Cytokine dysregulation is an hallmark in HIV-infected individuals and it is one of the most significant factors leading to impaired immunity in HIV/AIDS disease. This study investigates the possibility of modulation in the secretion of some inflammatory cytokines and chemokines induced by HIV p17 in monocytes. The results show that p17, while ineffective on resting monocytes, exerts an inflammatory action on IL-4 mediated inhibition of TNF-alpha and IFN-gamma production induced by IL-15 stimulation. In addition, p17 is able to reduce MIP-1alpha secretion, but unable to influence IL-6 production. The ability of HIV p17 to contribute to an altered pattern of secreted soluble factors might imply a key role for this viral protein in the development of AIDS pathogenesis.

Striped nanoscale phase separation at the metal-insulator transition of heteroepitaxial nickelates.

Nucleation processes of mixed-phase states are an intrinsic characteristic of first-order phase transitions, typically related to local symmetry breaking. Direct observation of emerging mixed-phase regions in materials showing a first-order metal-insulator transition (MIT) offers unique opportunities to uncover their driving mechanism. Using photoemission electron microscopy, we image the nanoscale formation and growth of insulating domains across the temperature-driven MIT in NdNiO3 epitaxial thin films. Heteroepitaxy is found to strongly determine the nanoscale nature of the phase transition, inducing preferential formation of striped domains along the terraces of atomically flat stepped surfaces. We show that the distribution of transition temperatures is a local property, set by surface morphology and stable across multiple temperature cycles. Our data provide new insights into the MIT of heteroepitaxial nickelates and point to a rich, nanoscale phenomenology in this strongly correlated material.

Evaluation of the expression of IFN-gamma in lymphocytes using a monoclonal antibody and flow cytometry.

A stable hybridoma cell line secreting specific antibodies against human interferon-gamma (IFN-gamma) and designated IGMB-14 has been established. It belongs to the IgG1, kappa subclass and it reacts in Western blot with the 28 kDa and 56 kDa polypeptides present in two different affinity purified IFN-gamma preparations. Peripheral blood mononuclear cells (PBMC) from a healthy individual, stimulated in vitro by PHA, were analysed for IFN-gamma production both when viable and following fixation. The presence of cytoplasmic or surface IFN-gamma was visualized by an indirect immunofluorescence assay using monoclonal antibody (MAb) IGMB-14 and a single laser FACS-III fluorescence-activated cell sorter. The staining permitted the detection of newly synthesized cytoplasmic IFN-gamma molecules in lymphocytes at day 1 after PHA stimulation and surface IFN-gamma at day 2. IFN-gamma was expressed on almost all the CD4+ lymphocytes as shown by a double staining technique. The specificity of the reaction was confirmed by Western blots and abolishing IFN-gamma staining by pretreatment of MAb IGMB-14 with IFN-gamma. The presence of surface IFN-gamma was also visualized on freshly isolated PBMC from two patients suffering from measles and AIDS but not on PBMC from a healthy individual. The experiments showed that this immunofluorescent method is useful for the detection, enumeration, and phenotypic characterization of IFN-gamma-producing cells in vitro and, in addition, for evaluating the presence of PBMC expressing IFN-gamma on their surface during a viral disease.

Inhibitory effect of papaverine on HIV replication in vitro.

The ability of papaverine to inhibit human immunodeficiency virus (HIV) replication in H9 cell line and in peripheral blood mononuclear cell (PBMC) culture was examined. HIV-infected H9 cells were exposed to different concentrations of papaverine for 20 days. Reverse transcriptase (RT) activity and the presence of p24 in the supernatant were determined to assess the level of viral replication in treated and control cultures. The most effective concentration of papaverine in the culture medium was 10 micrograms/ml, a dose that did not significantly affect cell proliferation. At this drug concentration the treatment resulted in no RT activity or p24 expression in the supernatant and no virus antigen detection at the cellular level as demonstrated by Western blot (WB) analysis. The activity of the drug occurred in a short period of time (60 hours) as shown by radioimmunoprecipitation (RIP) assay and affected the synthesis of the env precursor protein gp160. The drug was also effective in inhibiting HIV replication in PBMC cultures and influenced specific viral markers, namely, RT and p24. Evidence of the efficacy of papaverine treatment was enforced by the finding in the treated PBMC cultures, compared with the untreated ones, of a reduced percentage of cells forming syncitia and of the inhibition of the virus-induced decrease in the number of cells. When an equal number of virus-infected H9 cells exposed or unexposed to papaverine was analyzed for HIV-specific proteins, a marked decrease in the expression of the viral proteins was observed in the treated cultures. At the same time, one cellular protein of molecular weight 69,000 was not inhibited by papaverine. This may indicate that, at least for one protein, synthesis may not be affected by the drug. Our data suggest that papaverine merits attention as a possible nontoxic candidate for the treatment of HIV infection.

Polymorphism analysis of Epstein-Barr virus isolates of lymphoblastoid cell lines from patients with mycosis fungoides.

In order to determine whether there is an association between the presence of Epstein-Barr virus (EBV) and mycosis fungoides (MF) disease progression, PCR was performed to detect the EBV status of 20 MF patients; six EBV-positive patients were found. EBV variants may differ in their biological properties, such as their ability to transform cells; therefore, the ability of these variants to immortalize B cells in vitro was analysed. Six continuously growing cell lines were obtained from prolonged cultures of unstimulated peripheral blood mononuclear cells that were taken from the six EBV-positive patients with MF. In order to characterize the EBV strains, EBNA-2 and LMP-1/LMP-2 gene polymorphisms in the six cell lines were also analysed. All patients were followed up for 10 years and it was noticed that EBV-positive patients had a poor prognosis with rapid disease progression and high mortality rates, compared to EBV-negative patients. EBV may therefore constitute a co-factor that accelerates the progression of disease.

Liquid competition radioimmunoassay for the detection and quantitation of the HIV p24.

Productive infection of permissive cell cultures by HIV has been detected by different assays of which the measurement of reverse transcriptase (RT) activity has been considered highly specific and sensitive. Here we describe the production and characterization of a mouse hybridoma cell line, MB12, secreting monoclonal antibodies to HIV p24, the major core protein, and the use of this monoclonal antibody to develop a type specific indirect liquid competitive radioimmunoassay (RIA) capable of providing earlier detection of the replicating virus than the RT assay. This assay also provides a quantitative analysis of HIV p24, which can be used to study the viral replication in permissive cell cultures. The ease of methodology and the adaptability of the competitive RIA to various assay conditions make this immunoassay suitable for the study of HIV expression in infected cell cultures.

Prevalence of drug resistance and newly recognised treatment-related substitutions in the HIV-1 reverse transcriptase and protease genes from HIV-positive patients naïve for anti-retrovirals.

The aim of this study was to assess the prevalence of genetic changes in either the HIV reverse transcriptase (RT) or protease (Pro) genes in a cohort of patients naïve for anti-retroviral therapy. Of 61 patients, 43 (70.5%) were infected with HIV strains harbouring at least one resistance-related mutation, with 41 (67.2%) harbouring newly recognised treatment-related mutations. Among the 61 patients, the prevalence of specific mutations in the RT gene was as follows: 39A, 1.6%; 43E, 1.6%; and 228H, 1.6%. The prevalence of specific mutations in the Pro gene was as follows: 11I, 1.6%; 13V, 26.2%; 35D, 19.6%; 45R, 1.6%; 58E, 1.6%; 62V, 31%; 72V, 11.4%; 72M, 6.5%; 72T, 3.2%; 75I, 1.6%; and 89M, 13%. A higher prevalence of newly recognised mutations was found in strains from patients infected through sexual practices (30/36 = 83.4% vs. 11/25 = 44%; p 0.0023; OR 10.91; 95% CI 3.14-40.39). These findings support the use of resistance testing in patients naïve for anti-retroviral therapy, and suggest that the possible impact of newly recognised treatment-related mutations on clinical outcome requires further investigation.