Nanometre imaging of Fe3GeTe2 ferromagnetic domain walls.

Fe3GeTe2 is a layered crystal which has recently been shown to maintain its itinerant ferromagnetic properties even when atomically thin. Here, differential phase contrast scanning transmission electron microscopy is used to investigate the domain structure in a Fe3GeTe2 cross-sectional lamella at temperatures ranging from 95 to 250 K and at nanometre spatial resolution. Below the experimentally determined Curie temperature (T C) of 191 K, stripe domains magnetised along 〈0001〉, bounded with 180◦ Bloch type domain walls, are observed, transitioning to mixed Bloch-Néel type where the cross-sectional thickness is reduced below 50 nm. When warming towards T C, these domains undergo slight restructuring towards uniform size, before abruptly fading at T C. Localised loss of ferromagnetic order is seen over time, hypothesised to be a frustration of ferromagnetic order from ambient oxidation and basal cracking, which could enable selective modification of the magnetic properties for device applications.

Potential clinical implications of HPV status and expressions of p53 and cyclin D1 among oropharyngeal cancer patients.

BACKGROUND: There is increasing evidence that high-risk human papillomavirus plays significant role in oropharyngeal cancer; however, there is lack of knowledge on the interplay between the virus and its downstream-related molecules and their possible prognostic values. The objectives of the study are to better understand the interplay of the HR-HPV and its associated downstream molecules and to evaluate potential biomarkers for patient outcomes. METHODS: We conducted a retrospective study with available formalin-fixed, paraffin-embedded tissue from 244 oropharyngeal cancer patients that received curative radiotherapy or concurrent chemoradiotherapy from 2000 to 2008. In addition to chart review, we performed HPV DNA and RNA in situ hybridization and immunohistochemistry for p53, the retinoblastoma protein, p16, and cyclin D1 analysis. Cox proportional hazard and Kaplan-Meier survival analysis were used to determine the prognostic markers for clinical outcomes. RESULTS: Patients averaged 57.3 ± 9.4 year-old and were mostly males (76.2%) and ever-smokers (76.2%). All patients received curative radiotherapy, and 44.3% received concurrent chemoradiotherapy. We detected the human papillomavirus in 77.9% of study patients. Ever-smokers, more advanced tumor stage, and receiving radiotherapy only had poorer 5-year overall survival, disease-specific survival, and loco-regional recurrence. Cases with positive human papillomavirus and p53 overexpression had poorer disease-specific survival. Cases without human papillomavirus, but cyclin D1 overexpression, were associated with poorer 5-year overall survival. CONCLUSIONS: Our data suggest that additional p53 and cyclin D1 testing may benefit oropharyngeal cancer patients with known human papillomavirus status.

Diagnosis of Ovarian Carcinoma Histotype Based on Limited Sampling: A Prospective Study Comparing Cytology, Frozen Section, and Core Biopsies to Full Pathologic Examination.

Growing insights into the biological features and molecular underpinnings of ovarian cancer has prompted a shift toward histotype-specific treatments and clinical trials. As a result, the preoperative diagnosis of ovarian carcinomas based on small tissue sampling is rapidly gaining importance. The data on the accuracy of ovarian carcinoma histotype-specific diagnosis based on small tissue samples, however, remains very limited in the literature. Herein, we describe a prospective series of 30 ovarian tumors diagnosed using cytology, frozen section, core needle biopsy, and immunohistochemistry (p53, p16, WT1, HNF-1ß, ARID1A, TFF3, vimentin, and PR). The accuracy of histotype diagnosis using each of these modalities was 52%, 81%, 85%, and 84% respectively, using the final pathology report as the reference standard. The accuracy of histotype diagnosis using the Calculator for Ovarian Subtype Prediction (COSP), which evaluates immunohistochemical stains independent of histopathologic features, was 85%. Diagnostic accuracy varied across histotype and was lowest for endometrioid carcinoma across all diagnostic modalities (54%). High-grade serous carcinomas were the most overdiagnosed on core needle biopsy (accounting for 45% of misdiagnoses) and clear cell carcinomas the most overdiagnosed on frozen section (accounting for 36% of misdiagnoses). On core needle biopsy, 2/30 (7%) cases had a higher grade lesion missed due to sampling limitations. In this study, we identify several challenges in the diagnosis of ovarian tumors based on limited tissue sampling. Recognition of these scenarios can help improve diagnostic accuracy as we move forward with histotype-specific therapeutic strategies.

Evaluation of E-cadherin, ß-catenin and vimentin protein expression using quantitative immunohistochemistry in nasopharyngeal carcinoma patients.

PURPOSE: Aberrant expression of proteins involved in epithelial-to-mesenchymal transition have been described in various cancers. In this retrospective study, we sought to evaluate E-cadherin, ß-catenin and vimentin protein expression in non-metastatic nasopharyngeal (NPC) patients treated with curative intent, examine their relationship with each other, and with clinical outcome measures. METHODS: Pre-treatment formalin-fixed paraffin-embedded biopsies of 140 patients treated between January 2000 and December 2007 were assembled into a tissue microarray (TMA). Automated quantitative immunohistochemistry (AQUA®) was performed on sequential TMA sections stained with fluorescent-labeled antibodies against E-cadherin, ß-catenin and vimentin. Cox proportional hazards regression was used to estimate the effect of cytoplasmic vimentin, cytoplasmic E-cadherin, ß-catenin nuclear/cytoplasmic ratio expression on overall survival and disease-free survival. RESULTS: The average age of the patients was 51.7 years (SD=12.1; range 18-85), 66% were male, 71% had a KPS ≥ 90% at the start of treatment and 65% had stage III/IV disease. After adjusting for performance status, WHO and stage, high E-cadherin levels over the 75th percentile were found to produce a significantly increased risk for both a worse overall survival (HR = 2.53, 95% CI 1.21, 5.27) and disease free survival (DFS; HR = 2.14, 95%CI 1.28, 3.59). Vimentin levels over the first quartile produced an increased risk for a worse DFS (HR = 2.21, 95% CI 1.11, 4.38). No association was seen between ß-catenin and survival. CONCLUSION: In this cohort of NPC patients, higher levels of E-cadherin and higher levels of vimentin were associated with worse outcomes. Further work is needed to understand the role of these epithelial mesenchymal transition proteins in NPC.

Determination of sub-ps lattice dynamics in FeRh thin films.

Understanding the ultrashort time scale structural dynamics of the FeRh metamagnetic phase transition is a key element in developing a complete explanation of the mechanism driving the evolution from an antiferromagnetic to ferromagnetic state. Using an X-ray free electron laser we determine, with sub-ps time resolution, the time evolution of the (-101) lattice diffraction peak following excitation using a 35 fs laser pulse. The dynamics at higher laser fluence indicates the existence of a transient lattice state distinct from the high temperature ferromagnetic phase. By extracting the lattice temperature and comparing it with values obtained in a quasi-static diffraction measurement, we estimate the electron-phonon coupling in FeRh thin films as a function of laser excitation fluence. A model is presented which demonstrates that the transient state is paramagnetic and can be reached by a subset of the phonon bands. A complete description of the FeRh structural dynamics requires consideration of coupling strength variation across the phonon frequencies.

Novel biomarkers for prostate cancer including noncoding transcripts.

Levels of 27 transcripts were investigated as potential novel markers for prostate cancer, including genes encoding plasma membrane proteins (ADAM2, ELOVL5, MARCKSL1, RAMP1, TMEM30A, and TMEM66); secreted proteins (SPON2, TMEM30A, TMEM66, and truncated TMEFF2 (called POP4)); intracellular proteins (CAMK2N1, DHCR24, GLO1, NGFRAP1, PGK1, PSMA7, SBDS, and YWHAQ); and noncoding transcripts (POP1 (100 kb) from mRNA AK000023), POP2 (4 kb from mRNA AL832227), POP3 (50 kb from EST CFI40309), POP5 (intron of NCAM2, accession DO668384), POP6 (intron of FHIT), POP7 (intron of TNFAIP8), POP8 (intron of EFNA5), POP9 (intron of DSTN), POP10 (intron of ADAM2, accession DO668396), POP11 (87kb from EST BG194644), and POP12 (intron of EST BQ226050)). Expression of POP3 was prostate specific, whereas ADAM2, POP1, POP4, POP10, ELOVL5, RAMP1, and SPON2 had limited tissue expression. ELOVL5, MARCKSL1, NGFRAP1, PGK1, POP2, POP5, POP8, PSMA7, RAMP1, and SPON2 were significantly differentially expressed between laser microdissected malignant versus benign clinical samples of prostate tissue. PGK1, POP2, and POP12 correlated to clinical parameters. Levels of CAMK2N1, GLO1, SDBS, and TMEM30A transcripts tended to be increased in primary prostate cancer from patients who later had biochemical failure. Expression of GLO1, DHCR24, NGFRAP1, KLK3, and RAMP1 were significantly decreased in metastatic castration-recurrent disease compared with androgen-dependent primary prostate cancer. These novel potential biomarkers may therefore be useful in the diagnosis/prognosis of prostate cancer.

Magnetic response of FeRh to static and dynamic disorder.

Atomic scale defects generated using focused ion as well as laser beams can activate ferromagnetism in initially non-ferromagnetic B2 ordered alloy thin film templates. Such defects can be induced locally, confining the ferromagnetic objects within well-defined nanoscale regions. The characterization of these atomic scale defects is challenging, and the mechanism for the emergence of ferromagnetism due to sensitive lattice disordering is unclear. Here we directly probe a variety of microscopic defects in systematically disordered B2 FeRh thin films that are initially antiferromagnetic and undergo a thermally-driven isostructural phase transition to a volatile ferromagnetic state. We show that the presence of static disorder i.e., the slight deviations of atoms from their equilibrium sites is sufficient to induce a non-volatile ferromagnetic state at room temperature. A static mean square relative displacement of 9 × 10-4 Å-2 is associated with the occurrence of non-volatile ferromagnetism and replicates a snapshot of the dynamic disorder observed in the thermally-driven ferromagnetic state. The equivalence of static and dynamic disorder with respect to the ferromagnetic behavior can provide insights into the emergence of ferromagnetic coupling as well as achieving tunable magnetic properties through defect manipulations in alloys.

Clinical impact of second pathology opinion: a longitudinal study of central genitourinary pathology review before prostate brachytherapy.

PURPOSE: To evaluate the clinical impact of pathology review before prostate brachytherapy. METHODS AND MATERIALS: Original and reviewing pathologists' reports were retrospectively collected from 1323 men treated with prostate brachytherapy between July 1998 and October 2005 at one institution. Statistical analysis was performed pre- and post-January 2002. The clinical impact of pathology review was evaluated. RESULTS: Gleason Score (GS) change (GS(Delta)) occurred in 25.2% (334) of cases; GS increased in 21.6%, decreased in 2.4%, and diagnosed malignancy in 1.2% of cases. Post-2002, concordance in attributed GS improved, with GS(Delta) of 31.9-20.6%, respectively (p<0.001), and a reduction in the average GS(Delta) (p<0.001). The clinical impact was substantial with management changing in 14.8% of cases. CONCLUSION: Concordance between the original and reviewing pathologists' GS has improved during the study period. Nevertheless, discordance persists in one of five cases. Pathology review remains essential, if treatment decisions hinge on GS.

Characterization of the human thyroid epigenome.

The thyroid gland, necessary for normal human growth and development, functions as an essential regulator of metabolism by the production and secretion of appropriate levels of thyroid hormone. However, assessment of abnormal thyroid function may be challenging suggesting a more fundamental understanding of normal function is needed. One way to characterize normal gland function is to study the epigenome and resulting transcriptome within its constituent cells. This study generates the first published reference epigenomes for human thyroid from four individuals using ChIP-seq and RNA-seq. We profiled six histone modifications (H3K4me1, H3K4me3, H3K27ac, H3K36me3, H3K9me3, H3K27me3), identified chromatin states using a hidden Markov model, produced a novel quantitative metric for model selection and established epigenomic maps of 19 chromatin states. We found that epigenetic features characterizing promoters and transcription elongation tend to be more consistent than regions characterizing enhancers or Polycomb-repressed regions and that epigenetically active genes consistent across all epigenomes tend to have higher expression than those not marked as epigenetically active in all epigenomes. We also identified a set of 18 genes epigenetically active and consistently expressed in the thyroid that are likely highly relevant to thyroid function. Altogether, these epigenomes represent a powerful resource to develop a deeper understanding of the underlying molecular biology of thyroid function and provide contextual information of thyroid and human epigenomic data for comparison and integration into future studies.

ATM, THMS, and RRM1 protein expression in nasopharyngeal carcinomas treated with curative intent.

BACKGROUND: In advanced nasopharyngeal carcinoma (NPC), biomarkers may help predict survival. METHODS: Tumoral expression of ataxia-telangiectasia mutated (ATM), thymidylate synthetase (THMS), and ribonucleotide reductase subunit M1 (RRM1), was correlated with survival in patients with nonmetastatic NPC using quantitative fluorescence immunohistochemistry with automated quantitative digital image analysis. RESULTS: Of the 146 patients included, 58 patients (40%) received concurrent chemoradiation therapy; the remainder was treated with radiation. Overall survival (OS) at 5 years was 71% (95% confidence interval [CI], 62% to 78%); disease-free survival (DFS) was 48% (95% CI, 39% to 57%). OS worsened for increasing values of ATM (hazard ratio [HR], 2.83; 95% CI, 1.01-7.94; p = .049) for values greater than the 75th percentile compared to less than the 25th percentile, but improved for tumors with higher THMS levels (HR, 0.44; 95% CI, 0.20-0.94; p = .033) for values greater than the 25th percentile compared to less than or equal to the 25th percentile. RRM1 was not associated with OS (p = .748). No biomarkers were associated with DFS. CONCLUSION: In our cohort, relative overexpression of ATM and low THMS levels were associated with worse OS. © 2015 Wiley Periodicals, Inc. Head Neck 38: E384-E391, 2016.

Nanoscale switch for vortex polarization mediated by Bloch core formation in magnetic hybrid systems.

Vortices are fundamental magnetic topological structures characterized by a curling magnetization around a highly stable nanometric core. The control of the polarization of this core and its gyration is key to the utilization of vortices in technological applications. So far polarization control has been achieved in single-material structures using magnetic fields, spin-polarized currents or spin waves. Here we demonstrate local control of the vortex core orientation in hybrid structures where the vortex in an in-plane Permalloy film coexists with out-of-plane maze domains in a Co/Pd multilayer. The vortex core reverses its polarization on crossing a maze domain boundary. This reversal is mediated by a pair of magnetic singularities, known as Bloch points, and leads to the transient formation of a three-dimensional magnetization structure: a Bloch core. The interaction between vortex and domain wall thus acts as a nanoscale switch for the vortex core polarization.

Loss of the Notch effector RBPJ promotes tumorigenesis.

Aberrant Notch activity is oncogenic in several malignancies, but it is unclear how expression or function of downstream elements in the Notch pathway affects tumor growth. Transcriptional regulation by Notch is dependent on interaction with the DNA-binding transcriptional repressor, RBPJ, and consequent derepression or activation of associated gene promoters. We show here that RBPJ is frequently depleted in human tumors. Depletion of RBPJ in human cancer cell lines xenografted into immunodeficient mice resulted in activation of canonical Notch target genes, and accelerated tumor growth secondary to reduced cell death. Global analysis of activated regions of the genome, as defined by differential acetylation of histone H4 (H4ac), revealed that the cell death pathway was significantly dysregulated in RBPJ-depleted tumors. Analysis of transcription factor binding data identified several transcriptional activators that bind promoters with differential H4ac in RBPJ-depleted cells. Functional studies demonstrated that NF-κB and MYC were essential for survival of RBPJ-depleted cells. Thus, loss of RBPJ derepresses target gene promoters, allowing Notch-independent activation by alternate transcription factors that promote tumorigenesis.

Assessment of ERCC1 and XPF protein expression using quantitative immunohistochemistry in nasopharyngeal carcinoma patients undergoing curative intent treatment.

PURPOSE: We sought to evaluate the prognostic/predictive value of ERCC1 and XPF in patients with nonmetastatic nasopharyngeal carcinoma (NPC) treated with curative intent. METHODS AND MATERIALS: ERCC1 and XPF protein expression was evaluated by immunofluorescence combined with automated quantitative analysis (AQUA) using the FL297 and 3F2 antibodies, respectively. ERCC1 and XPF protein expression levels were correlated with clinical outcomes. RESULTS: Patient characteristics were as follows: mean age 52 years (range, 18-85 years), 67% male, 72% Karnofsky performance status (KPS) ≥ 90%, World Health Organization (WHO) type 1/2/3 = 12%/28%/60%, stage III/IV 65%. With a median follow-up time of 50 months (range, 2.9 to 120 months), the 5-year overall survival (OS) was 70.8%. Median standardized nuclear AQUA scores were used as cutpoints for ERCC1 (n=138) and XPF (n=130) protein expression. Agreement between dichotomized ERCC1 and XPF scores was high at 79.4% (kappa = 0.587, P<.001). Neither biomarker predicted locoregional recurrence, DFS, or OS after adjustment for age and KPS, irrespective of stratification by stage, WHO type, or treatment. CONCLUSIONS: Neither ERCC1 nor XPF, analyzed by quantitative immunohistochemistry using the FL297 and 3F2 antibodies, was prognostic or predictive in this cohort of NPC patients.

Haemophilia B: impact on patients and economic burden of disease.

Worldwide, haemophilia is the most common hereditary bleeding disorder. The incidence of haemophilia B, however, is considerably less than haemophilia A and consequently appears to have received less attention in the research literature. This article aims to summarise the available evidence documenting the patient and economic burden associated with haemophilia B and current methods of disease management. Both the immediate and long-term clinical consequences of haemophilia B can have significant implications for patients in terms of functional limitations and diminished health-related quality of life (HRQOL). Evidence demonstrates that primary prophylaxis is the optimal strategy for replacing missing clotting factor IX (FIX) and managing haemophilia B. Use of recombinant FIX (rFIX) over plasma-derived FIX (pd-FIX) is also generally preferred for safety reasons. Prophylaxis using currently available rFIX products, however, requires a demanding regimen of intravenous infusions 2-3 times a week which may have significant implications for adherence and ultimately the long-term efficacy of such regimens. Only limited assessments of the cost-effectiveness of prophylactic versus on-demand FIX treatment regimens have been conducted to date. Prophylaxis, however, is generally more costly as greater quantities of FIX are consumed. Any reduction in FIX replacement dosing frequency is expected to improve patient adherence and contribute to improved clinical outcomes, further supporting the cost-effectiveness of such interventions. Although a rare disease, as economic constraints for healthcare increase, generating further information regarding the key clinical, patient and economic outcomes associated with haemophilia B will be essential for supporting improvements in care for people with haemophilia B.

Fine-needle aspiration of renal and extrarenal rhabdoid tumors: the experience of the Institut Curie regarding 20 tumors in 13 patients.

BACKGROUND: Rhabdoid tumors (RT) are rare, renal or extrarenal, high-grade malignancies. The cytologic diagnosis may be confirmed if combined with genomic results. In the current study, the authors present the cytologic and ancillary techniques used to diagnose RT in their series of 20 tumors in 13 patients. METHODS: Clinical charts as well as cytologic, histologic, karyotypic, and molecular biology results were reviewed. RESULTS: Twelve fine-needle aspirations (FNAs) were performed for primary diagnosis, 7 were to confirm a metastasis, and 1 was to confirm local recurrence. Primary tumors were in the kidney in 7 cases and 13 were extrarenal. Patient age ranged from 5 months to 26 years. There were 7 females and 6 males. FNAs were cell-rich in 16 cases and cell-poor in 4 cases and revealed a mix of atypical spindle-shaped, round, rhabdoid, or epithelioid cells, singly or in clusters. Mitosis and necrosis occasionally were present. The original cytologic diagnosis was malignant in all cases. There were no unsatisfactory or false-negative samples. In the 12 primary tumors, the preliminary FNA diagnosis was RT in 7 cases (58%), rhabdomyosarcoma in 4 cases (33%), and malignant peripheral nerve sheath tumor in 1 case (8%). Karyotypes were available in 6 cases, 3 of which demonstrated chromosome 22 changes. Fluorescence in situ hybridization revealed loss of probe signals for the SMARCB1 gene locus in 5 cases; DNA sequence analysis performed in 9 cases revealed deletions in codons of the SMARCB1 gene in 7 cases and a mutation in 2 cases. CONCLUSIONS: The primary diagnosis of RT is possible on FNA. In the current study, 12 of 13 cases were diagnosed by FNA with a combination of clinical information, immunocytochemistry, and molecular analysis.

Tissue microarray for routine clinical breast biomarker analysis. The British Columbia Cancer Agency 2008 experience.

Clinical use of tissue microarrays for immunohistochemical analysis of breast biomarkers, namely estrogen receptor, progesterone receptor, and HER2, was instituted in our laboratory in 2008. The method has proved reliable and cost-effective. We report the results of the initial year of testing with this method.

Evolution of an adenocarcinoma in response to selection by targeted kinase inhibitors.

BACKGROUND: Adenocarcinomas of the tongue are rare and represent the minority (20 to 25%) of salivary gland tumors affecting the tongue. We investigated the utility of massively parallel sequencing to characterize an adenocarcinoma of the tongue, before and after treatment. RESULTS: In the pre-treatment tumor we identified 7,629 genes within regions of copy number gain. There were 1,078 genes that exhibited increased expression relative to the blood and unrelated tumors and four genes contained somatic protein-coding mutations. Our analysis suggested the tumor cells were driven by the RET oncogene. Genes whose protein products are targeted by the RET inhibitors sunitinib and sorafenib correlated with being amplified and or highly expressed. Consistent with our observations, administration of sunitinib was associated with stable disease lasting 4 months, after which the lung lesions began to grow. Administration of sorafenib and sulindac provided disease stabilization for an additional 3 months after which the cancer progressed and new lesions appeared. A recurring metastasis possessed 7,288 genes within copy number amplicons, 385 genes exhibiting increased expression relative to other tumors and 9 new somatic protein coding mutations. The observed mutations and amplifications were consistent with therapeutic resistance arising through activation of the MAPK and AKT pathways. CONCLUSIONS: We conclude that complete genomic characterization of a rare tumor has the potential to aid in clinical decision making and identifying therapeutic approaches where no established treatment protocols exist. These results also provide direct in vivo genomic evidence for mutational evolution within a tumor under drug selection and potential mechanisms of drug resistance accrual.

Tissue microarray for routine analysis of breast biomarkers in the clinical laboratory.

Tissue microarray analysis (TMA) allows multiple analyses on multiple patients on sections from a single paraffin block. Although it is widely used in research and in quality assurance settings, there are few references to its use in clinical practice. This study evaluated TMA assessment of breast biomarkers using immunohistochemical analysis in a clinical histopathology laboratory. Performance parameters, interobserver variability, and concordance between TMA and whole section results were assessed. The arrays had few lost or noninformative cores. A loss of stain intensity occurred in the arrays compared with the whole sections with some but not all antibodies, highlighting the need to validate the staining protocol for each antibody used on TMA sections. With recommended guidelines for specimen selection and reporting, TMA was found to be an economical replacement for whole section analysis for breast biomarkers.

Sinonasal undifferentiated carcinoma: case series and systematic review of the literature.

Sinonasal undifferentiated carcinoma is a rare, highly aggressive malignancy. A number of case series have been published in the literature. Most authors recommend aggressive management with a combination of surgery, radiotherapy, and chemotherapy, but the numbers in the individual studies are too small to produce a definitive opinion on the standard of care. In an attempt to determine the optimal treatment for this condition, we have undertaken a systematic review of the literature to evaluate all cases of sinonasal undifferentiated carcinoma that have been published since its initial description in 1986. Patient demographics, extent of the tumour at presentation, management, and outcomes were evaluated. We also present the experience from our institution.