Nuclear and magnetic spin structure of the antiferromagnetic triangular lattice compound LiCrTe2 investigated by [Formula: see text]SR, neutron and X-ray diffraction.

Two-dimensional (2D) triangular lattice antiferromagnets (2D-TLA) often manifest intriguing physical and technological properties, due to the strong interplay between lattice geometry and electronic properties. The recently synthesized 2-dimensional transition metal dichalcogenide LiCrTe[Formula: see text], being a 2D-TLA, enriched the range of materials which can present such properties. In this work, muon spin rotation ([Formula: see text]SR) and neutron powder diffraction (NPD) have been utilized to reveal the true magnetic nature and ground state of LiCrTe[Formula: see text]. From high-resolution NPD the magnetic spin order at base-temperature is not, as previously suggested, helical, but rather collinear antiferromagnetic (AFM) with ferromagnetic (FM) spin coupling within the ab-plane and AFM coupling along the c-axis. The value if the ordered magnetic Cr moment is established as [Formula: see text]. From detailed [Formula: see text]SR measurements we observe an AFM ordering temperature [Formula: see text] K. This value is remarkably higher than the one previously reported by magnetic bulk measurements. From [Formula: see text]SR we are able to extract the magnetic order parameter, whose critical exponent allows us to categorize LiCrTe[Formula: see text] in the 3D Heisenberg AFM universality class. Finally, by combining our magnetic studies with high-resolution synchrotron X-ray diffraction (XRD), we find a clear coupling between the nuclear and magnetic spin lattices. This suggests the possibility for a strong magnon-phonon coupling, similar to what has been previously observed in the closely related compound LiCrO[Formula: see text].

Revisiting Goodenough-Kanamori rules in a new series of double perovskites LaSr1-xCaxNiReO6.

The magnetic ground states in highly ordered double perovskites LaSr1-xCaxNiReO6 (x = 0.0, 0.5, 1.0) are studied in view of the Goodenough-Kanamori rules of superexchange interactions in this paper. In LaSrNiReO6, Ni and Re sublattices are found to exhibit curious magnetic states separately, but no long range magnetic ordering is achieved. The magnetic transition at ~255 K is identified with the independent Re sublattice magnetic ordering. Interestingly, the sublattice interactions are tuned by modifying the Ni-O-Re bond angles through Ca doping. Upon Ca doping, the Ni and Re sublattices start to display a ferrimagnetically ordered state at low temperature. The neutron powder diffraction data reveals long range ferrimagnetic ordering of the Ni and Re magnetic sublattices along the crystallographic b-axis. The transition temperature of the ferrimagnetic phase increases monotonically with increasing Ca concentration.

Three-Dimensional Fermi Surface of Overdoped La-Based Cuprates.

We present a soft x-ray angle-resolved photoemission spectroscopy study of overdoped high-temperature superconductors. In-plane and out-of-plane components of the Fermi surface are mapped by varying the photoemission angle and the incident photon energy. No k_{z} dispersion is observed along the nodal direction, whereas a significant antinodal k_{z} dispersion is identified for La-based cuprates. Based on a tight-binding parametrization, we discuss the implications for the density of states near the van Hove singularity. Our results suggest that the large electronic specific heat found in overdoped La_{2-x}Sr_{x}CuO_{4} cannot be assigned to the van Hove singularity alone. We therefore propose quantum criticality induced by a collapsing pseudogap phase as a plausible explanation for observed enhancement of electronic specific heat.

Molecular methods for identification and characterization of novel papillomaviruses.

Papillomaviruses (PV) are a remarkably heterogeneous family of small DNA viruses that infect a wide variety of vertebrate species and are aetiologically linked with the development of various neoplastic changes of the skin and mucosal epithelia. Based on nucleotide similarity, PVs are hierarchically classified into genera, species and types. Novel human PV (HPV) types are given a unique number only after the whole genome has been cloned and deposited with the International HPV Reference Center. As of 9 March 2015, 200 different HPV types, belonging to 49 species, had been recognized by the International HPV Reference Center. In addition, 131 animal PV types identified from 66 different animal species exist. Recent advances in molecular techniques have resulted in an explosive increase in the identification of novel HPV types and novel subgenomic HPV sequences in the last few years. Among PV genera, the γ-PV genus has been growing most rapidly in recent years with 80 completely sequenced HPV types, followed by α-PV and ß-PV genera that have 65 and 51 recognized HPV types, respectively. We reviewed in detail the contemporary molecular methods most often used for identification and characterization of novel PV types, including PCR, rolling circle amplification and next-generation sequencing. Furthermore, we present a short overview of 12 and 10 novel HPV types recently identified in Sweden and Slovenia, respectively. Finally, an update on the International Human Papillomavirus Reference Center is provided.

Type- and age-specific distribution of human papillomavirus in women attending cervical cancer screening in Finland.

BACKGROUND: Large-scale data on type-specific HPV prevalences and disease burden are needed to monitor the impact of HPV vaccination and to plan for HPV-based cervical screening. METHODS: 33 043 women (aged 25-65) were screened for HPV by a Hybrid Capture 2 (HC2) in a population-based programme. HPV-positive women (n=2574) were triaged by cytology and HPV genotyped using PCR-Luminex. Type-specific prevalence of HPV infection and its correlation to findings in cytology triage and histology as well as Population Attributable Fractions for a referral to colposcopy and findings in histology were calculated. RESULTS: Among HC2-positive women, 61.5% had normal, 23.1% had ASC-US and 15.5% had LSIL or more severe (LSIL+) results in cytology. Out of HC2-positive samples, 57% contained the 13 Group 1/2A HPV types, which were targeted by the HC2, 15% contained Group 2B types, 8.5% Group 3 types and 30% were found to be negative in HPV genotyping. The proportion of samples positive for HPV by the HC2, but negative in HPV genotyping increased with age and decreased with increasing cytological abnormality. The most frequent types were HPV 16 (0.9% of screened women and 12.1% of the HC2-positive women), HPV 31 (0.7% and 8.9%, respectively) and HPV 52 (0.5% and 6.3%, respectively). The prevalence of Group 1/2A HPV types increased with increasing CIN grade and attributed 78.3% (95% CI 53.4-89.9) of the CIN 3+ lesions, while HPV 16 attributed 55.8% (40.0-67.5) of them. CONCLUSION: The type-specific prevalence of HPV were slightly lower than the average in international meta-analyses. Genotyping for HPV 16 better identified women with CIN 3+ than cytology triage at the threshold of LSIL+. The high proportion of women that were HC2-positive but HPV-negative in genotyping suggests that HPV genotyping may be useful also for validation of results in HPV screening. The large-scale HPV genotyping data were found to be directly useful for planning further preventive efforts for cervical cancer.

Bead-based multiplex genotyping of 58 cutaneous human papillomavirus types.

Cutaneous human papillomaviruses (HPVs) are a heterogeneous, nonmonophyletic assembly, comprising about 50 characterized types and at least 133 isolates putatively representing new types. Their natural history of infection and potential association with nonmelanoma skin cancer are not well understood. Several PCR systems have been developed that amplify a broad spectrum of cutaneous HPVs. However, amplicon genotyping by sequencing or reverse line blot assays are complex and not well suited for high-throughput analyses. We developed a novel multiplex cutaneous papillomavirus genotyping (McPG) assay for 38 defined and 20 putative cutaneous HPVs of the beta, gamma, mu, and nu genera. Viral DNA was amplified by the use of a modified single-tube nested "hanging-droplet" FAP PCR. The amplifiable papillomavirus (PV) spectrum was enlarged by the use of 9 outer and 13 inner primers. Biotinylated PCR products were hybridized to type-specific oligonucleotide probes coupled to fluorescence-labeled polystyrene beads and analyzed using Luminex technology. Analytical sensitivity was analyzed for 38 defined HPVs and was ≤100 genome copies for all types. Integrated ß-globin primers allow for simultaneous DNA quality control. McPG is characterized by high reproducibility (κ= 0.84, 95% confidence interval = 0.79 to 0.88), good concordance with the original nested FAP PCR, followed by sequencing (70.2% complete or partial agreement) when 322 skin biopsy DNA samples were analyzed, and improved ability to detect multiple infections (on average 2.5 HPV types per HPV-positive sample compared to 1.7 HPV types with nested FAP-PCR). In conclusion, McPG is a powerful tool for genotyping multiple cutaneous HPVs in a high-throughput format and is thus suitable for large-scale epidemiological studies.

Characterization of the complete genomes of Camelus dromedarius papillomavirus types 1 and 2.

Camel papillomatosis has been described previously, but the genome of the suspected papillomavirus (PV) has not been identified. An outbreak of papillomatosis occurred in a dromedary farm of 55 animals in Sudan during August 2009. The disease was only present in young animals aged about 3-7 months, of which 44 % (11/25) were affected with lesions, mainly on the lips and lower jaw. This study reports for the first time the complete genomes of Camelus dromedarius papillomavirus types 1 (CdPV1) and 2 (CdPV2), isolated from a cauliflower-like nodule and a round oval raised nodule, respectively. Pairwise comparisons of their L1 nucleotide sequences revealed 69.2 % identity, and phylogenetic analyses suggested that these two PV types are grouped within the genus Deltapapillomavirus. Both viruses were isolated from fibropapillomas, although no putative E5 proteins homologous to that of bovine papillomavirus type 1 were identified. The genetic information will be useful for evolutionary studies of the family Papillomaviridae, as well as for the development of diagnostic methods for surveillance of the disease in dromedaries.

A broad spectrum of human papillomavirus types is present in the skin of Australian patients with non-melanoma skin cancers and solar keratosis.

BACKGROUND: Human papillomavirus (HPV) may play a role in the pathogenesis of non-melanoma skin cancer (NMSC) in epidermodysplasia verruciformis (EV) patients, but in the general population no specific HPV types have been associated with these lesions. Objectives To examine the spectrum of HPV types present in the skin and tumours of Australian patients with NMSC or solar keratosis (SK). METHODS: Biopsies from tumours, and cotton swab samples of perilesional skin and buttock skin from each of 59 Australian patients with basal cell carcinoma (BCC), squamous cell carcinoma (SCC) or SK were tested for HPV DNA by polymerase chain reaction (PCR) using HPV consensus (FAP) primers and by type-specific primers for HPV 38 and candidate HPV 92. The identification of HPV type from consensus PCR was performed by sequencing and comparison with GenBank. RESULTS: In total, 49 of 59 (83%) patients harboured HPV DNA, which was detected in 28 of 64 (44%) biopsies, 48 of 64 (75%; P < 0.001) perilesional swabs and 36 of 59 (61%; P = 0.04) buttock swabs. Forty-five different HPV types/putative types were detected: 15 were previously characterized HPV types, 17 were earlier described putative types and 13 were new putative types. In addition, six subtypes and four variants of HPV sequences were identified. HPV types within the B1 group (EV HPV types) were found in 26 of 64 (40%) lesions, 44 of 64 (69%) perilesional swabs and 35 of 59 (59%) buttock swabs. HPV 38 was detected in 23 of 59 (39%) patients, and was found in seven of 16 (43%) SKs, but was less common in SCCs [three of 23 (13%); P = 0.037] and BCCs [four of 25 (16%); P = 0.056]. Candidate HPV 92 was found in seven of 59 (12%) patients. CONCLUSIONS: A broad spectrum of HPV types, the majority from the B1 group, was found in skin of Australian patients with skin tumours. HPV 38 was found significantly more often in SK than in SCC. However, the role of cutaneous HPV infection in the pathogenesis of NMSC remains elusive.

The ubiquity and impressive genomic diversity of human skin papillomaviruses suggest a commensalic nature of these viruses.

Human papillomaviruses (HPV) are epitheliotropic viruses, with some types suggested to be associated with skin cancer. In this study, swab samples collected from five different sites on the skin of renal transplant recipients, dialysis patients, and age- and sex-matched healthy controls were analyzed for HPV DNA by a newly designed PCR test. Most individuals were found to have asymptomatic HPV infections; more specifically, 94% of the renal transplant patients, 82% of the dialysis patients, and 80% of the healthy controls were positive for HPV DNA. The multiplicity of the HPVs detected was astounding: 20 previously described and 30 putatively new types were identified by cloning and sequencing of 33 samples from 13 individuals. These results demonstrate that normal human skin harbors an array of papillomaviruses, most of them previously unknown.

Mucosal human papillomavirus types in squamous cell carcinomas of the uterine cervix and subsequently on fingers.

Human papillomavirus (HPV), especially type 16, is causally involved in the pathogenesis of anogenital cancer. There is an increasing number of reports of HPV infections in squamous cell carcinoma (SCC) of the fingers. A search of the Swedish cancer register covering the period 1958-94 inclusive for women with a history of genital and upper extremity SCC revealed 63 cases. Archival material from both cervical and cutaneous lesions was traced and analysed for the presence of HPV DNA in 32 of these patients. A newly developed 'neighbour primer' polymerase chain reaction (PCR) for HPV 16 DNA, aimed at overcoming the obstacle of cross-linked target DNA, was shown to be superior to conventional general and type-specific HPV PCR tests. HPV DNA was significantly more frequently found in digital tumours than in tumours at other cutaneous sites of the upper extremities [67% (10 of 15) vs. 7% (three of 43); P < 0.001]. Among 13 patients with a history of both cervical and finger SCC, HPV 16 was found in cervical samples from seven patients. From five of these seven patients, HPV 16 was also present in the corresponding finger lesions. The results support the hypothesis of a possible transmission of patients' genital HPV infections to fingers.

Asymptomatic penile HPV infection: a prospective study.

The occurrence of human papillomavirus (HPV) among males was analysed with the polymerase chain reaction (PCR) method. Penile brush samples were taken once from 147 males attending for a control or for HPV non-related reasons, and consecutive samples were collected from 88 males re-attending the clinic. Of the males attending once, 13% (19/147) were HPV DNA positive and among the re-attenders 14% (12/88) were initially positive as compared with 33% (29/88) who were positive at least at one visit. Totally, 22 different HPV types were detected of which HPV 16 was most common, found in 6.4% (15/235), followed by HPV 42 found in 3.8% (9/235). Among 14 HPV-positive males with at least one follow-up, 7 had persistent infections with at least one HPV type, and transient HPV types were observed in 9; but in 5 of them new types appeared at follow-up. Among sexually-active males subclinical/latent HPV infection is common and repeated sampling increases its prevalence.

Reliable high risk HPV DNA testing by polymerase chain reaction: an intermethod and intramethod comparison.

BACKGROUND: The development of a reproducible, sensitive, and standardised human papillomavirus (HPV) polymerase chain reaction (PCR) test is required to implement HPV testing in cervical cancer screening programmes and for triaging women with mild to moderate dysplasia. AIMS: To determine the intermethod agreement between different GP5+/6+ and MY09/11 PCR based protocols for the detection and typing of high risk (HR) HPV DNA in cervical smears and to assess the intramethod reproducibility of the GP5+/6+ PCR enzyme immunoassay (EIA) for HR-HPV detection. METHODS: For the intermethod comparison, crude aliquots of 20 well characterised cervical smears comprising five HPV negative samples, and six and nine samples containing single and multiple HPV infections, respectively, were coded and sent from reference laboratory (A) to three other laboratories. One of these (laboratory B) used the GP5+/6+ PCR-EIA and was provided with standard protocols. Another laboratory (C) used GP5+/6+ PCR combined with sequence analysis and type specific PCR, whereas two laboratories (D and E) used MY09/11 PCR followed by restriction fragment length polymorphism (RFLP) analysis for the detection and typing of HR-HPV. The intramethod agreement of GP5+/6+ PCR-EIA was analysed in a subsequent study with four other laboratories (F to I) on crude aliquots of 50 well characterised cervical smears, consisting of 32 HR-HPV positive and 18 HPV negative samples. Standardised protocols, primers, and probes were also provided by the reference laboratory for HR-HPV detection. RESULTS: In the intermethod comparison, pairwise agreement of the different laboratories with reference laboratory A for the detection of HR-HPV varied between 75% and 100% (kappa values: 0.5 to 1). Typing data revealed a broader range in pairwise agreement rates between 32% and 100%. The highest agreement was found between laboratories A and B using standardised protocols and validated reagents. In the intramethod evaluation, pairwise comparison of the laboratories F to I with reference laboratory A revealed excellent agreement rates from 92% to 100% (kappa values: 0.88 to 1.0) with an overall sensitivity of 97.5% (195/200) and specificity of 99.5% (199/200). CONCLUSIONS: The detection of HR-HPV as a group is highly reproducible with GP5+/6+ PCR-EIA provided that standardised protocols and validated reagents are used.

Detection of human papilloma virus DNA in lymph nodes extirpated at radical surgery for cervical cancer is not predictive of recurrence.

In women with recurrent cervical cancer after radical surgery, lymph node metastasis is detectable histologically at the time of surgery in only about 50% of cases. The present study was designed to determine whether the detection of human papilloma virus (HPV) DNA in lymph nodes extirpated at operation, as an indication of micrometastasis, is predictive of recurrence. Using polymerase chain reaction (PCR), a total of 140 lymph nodes from 31 patients with HPV 16 DNA positive primary cervical tumours were tested for the presence of an HPV 16 LCR/E6 gene fragment. HPV 16 DNA was detected in extirpated lymph nodes in 75% (6/8) of patients with recurrence (and who died within 5 years after surgery) and in 70% (16/23) of recurrence-free patients. In only four of the patients with recurrence (three of whom had HPV 16 DNA positive lymph nodes) was metastasis detectable histologically at surgery. HPV DNA positive lymph nodes were found in 91% (10/11) of patients with histologically detectable metastasis at surgery and in 60% (12/20) of patients without metastasis. It is concluded that the presence of HPV DNA in extirpated lymph nodes at cervical cancer operation does not appear to be predictive of tumour recurrence.

DNA analysis indicates patient-specific human papillomavirus type 16 strains in Bowen's disease on fingers and in archival samples from genital dysplasia.

Human papillomavirus (HPV) type 16 is casually involved in the pathogenesis of anogenital cancer and has also been demonstrated in some patients with Bowen's disease (BD) on the fingers. From two women with HPV 16 in BD on the fingers, and in archival samples from genital dysplasia, collected as long as 26 years ago, the non-coding region of the virus was amplified by the polymerase chain reaction and sequenced. The HPV 16 DNA sequences found in the finger lesions and in the genital archival samples showed no diversities within single patients. Compared with an HPV 16R reference sequence, one patient showed a unique T nucleotide at position 78, whereas the other patient exhibited T and A nucleotides at positions 7193 and 7521, respectively. In one of the patients, the same strain of HPV 16 was found in a digital tumour 26 years after its clearance from the genital tract. DNA sequence analysis indicated patient-specific HPV 16 strains. Auto-inoculation from the genital tract was favoured as a plausible explanation of why HPV 16 caused BD on the fingers.

HPV 16 DNA and mRNA in cervical brush samples quantified by PCR and microwell hybridization.

To quantitate HPV 16 DNA and mRNA, biotinylated amplicons from PCR and reverse transcription PCR were captured on streptavidin-coated microtitre plates. The amount of amplicon was determined by colorimetric detection after hybridization with an alkaline phosphatase-labelled probe. Dynamic ranges of between 4 and 6 log10, sufficient to cover the amounts of viral DNA and mRNA prepared from cervical samples were achieved. The reproducibility of the colorimetric detection step was reflected in coefficients of variation (C.V.) below 8%, considerably better than that of chemiluminescence detection. In a series of 89 HPV 16 DNA positive cervical samples, as compared with a CIN I/normal diagnosis subgroup, the number of HPV 16 genome copies per assay was significantly greater in a CIN II subgroup (P = 0.014), and a high-grade neoplasia subgroup (P = 0.040), and the content of HPV 16 mRNA significantly greater in the high-grade neoplasia subgroup (P = 0.0021). The number of mRNA equivalents per copy of viral DNA was higher for E5 than for the other three mRNA species analyzed (P < 0.001), and the concentration of E6*I mRNA was higher than those of the E6 full-length (P < 0.001) and E6*II (P < 0.001) transcripts. Despite these differences, no correlation was found between histological/cytological diagnosis and the amount of viral mRNA relative to the viral load.

Demonstration of Epstein-Barr virus DNA and human papillomavirus DNA in acetowhite lesions of the penile skin and the oral mucosa.

Oral hairy leukoplakia (OHL), thought to be caused by Epstein-Barr virus (EBV), shows similar histological and clinical features to human papillomavirus (HPV)-related acetowhite lesions of the vulva. We thus aimed to investigate the role of both HPV and EBV in men with acetowhite lesions of the penis. HPV but not EBV was significantly associated with penile acetowhite lesions showing koilocytosis compared with normal penile skin (12/20 versus 5/20, P < 0.02). HPV (5/20) and EBV (6/20) was detected in oral mucosa of some of these individuals. These results confirm an aetiological association between HPV and acetowhite penile lesions showing koilocytosis. HPV and EBV carriage in the oral mucosa is relatively common in young sexually active men.

Cervical mucus antibodies against human papillomavirus type 16, 18, and 33 capsids in relation to presence of viral DNA.

To investigate whether cervical mucus antibodies against human papillomavirus (HPV) capsids are associated with the detection of HPV DNA or HPV-related cytological diagnoses, 611 samples of cervical secretions from 359 women referred to a colposcopy clinic were tested by an enzyme-linked immunosorbent assay for the presence of immunoglobulin A (IgA) antibodies against HPV capsids of HPV type 16, 18, or 33 and for the presence of cervical HPV DNA by PCR. Among subjects with at least one cervical sample positive for HPV type 16 (HPV-16) DNA, 28.1% also had at least one HPV-16 IgA-positive cervical sample (odds ratio [OR] = 2.9; P = 0.0003). IgA to HPV-18 was also more common among HPV-18 DNA-positive subjects (OR = 3.1; P = 0.0325) and IgA to HPV-33 was more common among HPV-33 DNA-positive subjects (OR = 4.2; P = 0.0023). Cervical IgA antibodies to HPV-16 were also more common among patients with cervical intraepithelial neoplasia, particularly among patients with cervical intraepithelial neoplasia grade I (P < 0.0005). The data indicate that an HPV type-restricted IgA antibody response against HPV capsids is detectable in cervical mucus and is associated with a concomitant cervical HPV infection.

Human papillomavirus type 70 genome cloned from overlapping PCR products: complete nucleotide sequence and genomic organization.

The genome of human papillomavirus (HPV) type 70 (HPV 70), isolated from a cervical condyloma, was obtained by cloning overlapping PCR products. By automated DNA sequence analysis, the genome was found to consist of 7,905 bp with a G + C content of 40%. The genomic organization showed the characteristic features shared by other sequenced HPVs. Nucleotide sequence comparison with previously known HPV types demonstrated the closest homology with HPV 68 (82%), HPV 39 (82%), HPV 18 (70%), HPV 45 (70%), and HPV 59 (70%). Comparison with seven other partially sequenced HPV 70 isolates showed homologies of between 100 and 99.5%. Cloning of overlapping PCR products and automated DNA sequence analysis was found to be a feasible method of obtaining full-length sequences of HPVs.

Association of serum antibodies against defined epitopes of human papillomavirus L1, E2, and E7 antigens and of HPV DNA with incident cervical cancer.

In order to provide a large-scale evaluation of the association with cervical cancer of antibodies against human papillomavirus (HPV) antigens, sera from 233 patients with primary, untreated cervical cancer and from 157 healthy age- and sex-matched blood donors were analyzed for IgG and IgA antibodies against HPV-derived peptide antigens and against bovine papillomavirus. Several serological responses were strongly associated with cervical cancer, notably the IgG response against the HPV 16 epitopes L1:13 (Relative risk [RR]: 5.3), E2:9 (RR: 2.9), and E7:5 (RR: 4.3), and the IgA response against an HPV 18 E2-derived antigen (245:18, RR: 3.1). HPV DNA in corresponding cervical tumors was analyzed by Southern blotting (SB) and polymerase chain reaction (PCR) in 47 patients. Sixty-six percent of the patients carried HPV DNA as determined by SB, 91% of patients analyzed by PCR. Neither the antibody responses, nor the presence of HPV DNA were significantly associated with the biological properties of the tumors.

Search for the human papillomavirus in nasal polyps, using a polymerase chain reaction-method.

Viral etiology of nasal polyps was postulated as many as 40 years ago, but so far, no study has shown an association or causal relation between any specific virus and nasal polyps. By using the polymerase chain reaction (PCR) technique, nasal polyps from both 10 patients with intolerance to nonsteroidal anti-inflammatory drugs (NSAID intolerance) (e.g., Aspirin) and from 10 patients with no history of NSAID intolerance were studied for the presence of papillomavirus DNA. Nasal mucosa from 10 patients who had undergone surgery for septoplasty served as controls. The PCR test used covers approximately 30 different types of human papillomaviruses. In this test, all tissue samples studied were found negative for papillomavirus DNA.