Matter-Wave Interference versus Spontaneous Pattern Formation in Spinor Bose-Einstein Condensate

We describe effects of matter-wave interference of spinor states in the $^{87}$Rb Bose-Einstein condensate. The components of the F=2 manifold are populated by forced Majorana transitions and then fall freely due to gravity in an applied magnetic field. Weak inhomogeneities of the magnetic field, present in the experiment, impose relative velocities onto different $m_F$ components, which show up as interference patterns upon measurement of atomic density distributions with a Stern-Gerlach imaging method. We show that interference effects may appear in experiments even if gradients of the magnetic field components are eliminated but higher order inhomogeneity is present and the duration of the interaction is long enough. In particular, we show that the resulting matter-wave interference patterns can mimic spontaneous pattern formation in the quantum gas.Comment: 5 pages, 4 figures, version accepted in Phys. Rev.

Critical evaluation of the thermometric performance of ratiometric luminescence thermometers based on Ba3(VO4)2:Mn5+,Nd3+ for deep-tissue thermal imaging

Near-infrared (NIR) luminescence thermometry has been brought to the fore as a reliable approach for remote thermal sensing and imaging. Lanthanide (Ln3+)-based nanophosphors are often proposed as NIR nanothermometers of choice. However, the combination of Ln3+ with transition metal (TM) ions has recently emerged as a strategy to introduce additional emission bands and/or TM ↔ Ln3+ energy transfer pathways whose temperature dependence can be harnessed to increase the sensitivity of the thermometric approach. Yet, the examples of the combination of luminescence nanothermometers working in the NIR and hosting simultaneously TM and Ln3+ are scarce, leaving plenty of space for the exploration of these systems. Herein, we report on the preparation and optimization of the thermometric performance of Ba3(VO4)2:Mn5+,Nd3+ nanophosphors. The different temperature dependences of the emission intensity of the two doped luminescent centers allow using the ratio between Mn5+ and Nd3+ as a reliable thermometric parameter with a relative thermal sensitivity of 1% K−1 close to room temperature. We then showcase the suitability of this nanophosphor for employment in 2D NIR luminescence thermal imaging. Lastly, we critically evaluate the possibility of using this thermal imaging approach through opaque media with the help of phantoms with tissue-like optical properties. As expected, a loss of reliability of the thermometric method is observed due to tissue-induced photon scattering and absorption that differentially affect the emission of Mn5+ and Nd3+. Overall, the reported results underscore the good performance of the newly developed nanothermometer, while consolidating the call for the use of luminescence nanothermometers working in the time-domain (rather than in the spectral domain) for deep-tissue thermal readout/imaging

Hot Nano-particles in Polar or Paramagnetic Liquids Interact as Monopoles.

When neutral nano-particles are heated or cooled in a polar liquid, they will interact with each other as if they carry an electrostatic charge that is proportional to the temperature difference between the particle and the surrounding fluid. The same should hold for suspensions liquids of asymmetric ferromagnetic particles, in which case the heated nano-particles should behave as magnetic monopoles. However, the analogy with electrostatics/magnetostatics is not complete: heated/cooled nano-particles do not move under the influence of an applied homogeneous field. They should, however, interact as monopoles with each other and should move in inhomogeneous fields.This is the author accepted manuscript. The final version is available from the American Chemical Society via https://doi.org/10.1021/acs.jpcb.6b0184

miRNAs as Biomarkers for Diagnosing and Predicting Survival of Head and Neck Squamous Cell Carcinoma Patients

Head and Neck Squamous Cell Carcinoma (HNSCC) is the sixth most common cancer worldwide. These tumors originate from epithelial cells of the upper aerodigestive tract. HNSCC tumors in different regions can have significantly different molecular characteristics. While many microRNAs (miRNAs) have been found to be involved in the regulation of the carcinogenesis and pathogenesis of HNSCC, new HNSCC related miRNAs are still being discovered. The aim of this study was to explore potential miRNA biomarkers that can be used to diagnose HNSCC and prognose survival of HNSCC patients. For this purpose, we chose a panel of 12 miRNAs: miR-146a-5p, miR-449a, miR-126-5p, miR-34a-5p, miR-34b-5p, miR-34c-5p, miR-217-5p, miR-378c, miR-6510-3p, miR-96-5p, miR-149-5p, and miR-133a-5p. Expression of these miRNAs was measured in tumor tissue and neighboring healthy tissue collected from patients diagnosed with HNSCC (n = 79) in either the oral cavity, oropharynx, or larynx. We observed a pattern of differentially expressed miRNAs at each of these cancer locations. Our study showed that some of these miRNAs, separately or in combination, could serve as biomarkers distinguishing between healthy and tumor tissue, and their expression correlated with patients’ overall survival

Microarray-based survey of CpG islands identifies concurrent hyper- and hypomethylation patterns in tissues derived from patients with breast cancer

Maintenance of CpG island methylation in the genome is crucial for cellular homeostasis and this balance is disrupted in cancer. Our rationale was to compare the methylation of CpG islands in tissues (tumor, healthy breast and blood) from patients with breast cancer. We studied 72 genes in 103 samples using microarray hybridization and bisulfite sequencing. We observed tumor specific hyper- or hypomethylation of five genes; COL9A1, MT1A, MT1J, HOXA5 and FLJ45983. A general drop of methylation in COL9A1 was apparent in tumors, when compared with blood and healthy breast tissue. Furthermore, one tumor displayed a complete loss of methylation of all five genes, suggesting overall impairment of methylation. The downstream, evolutionary conserved island of HOXA5 showed hypomethylation in 18 tumors and complete methylation in others. This CpG island also displayed a semimethylated state in the majority of normal breast samples, when compared to complete methylation in blood. Distinct methylation patterns were further seen in MT1J and MT1A, belonging to the metallothionein gene family. The CpG islands of these genes are spaced by 2 kb, which shows selective methylation of two structurally and functionally related genes. The promoters of FLJ45983 and MT1A were methylated above 25% in 18 primary and metastatic tumors. Concurrently, there was also >10% methylation of healthy breast tissue in 11 and 5 samples, respectively. This suggests that the methylation process for the latter two genes takes place already in normal breast cells. Our results also point to a considerable heterogeneity of epigenetic disturbance in breast cancer. This article contains Supplementary Material available at http://www.interscience.wiley.com/jpages/1045-2257/suppmat

Plasma protein changes reflect colorectal cancer development and associated inflammation

Introduction: Colorectal cancer (CRC) is the third most common malignancy and the second leading cause of death worldwide. Efficient non-invasive blood-based biomarkers for CRC early detection and prognosis are urgently needed. Methods: To identify novel potential plasma biomarkers, we applied a proximity extension assay (PEA), an antibody-based proteomics strategy to quantify the abundance of plasma proteins in CRC development and cancer-associated inflammation from few mu L of plasma sample. Results: Among the 690 quantified proteins, levels of 202 plasma proteins were significantly changed in CRC patients compared to age-and-sex-matched healthy subjects. We identified novel protein changes involved in Th17 activity, oncogenic pathways, and cancer-related inflammation with potential implications in the CRC diagnosis. Moreover, the interferon gamma (IFNG), interleukin (IL) 32, and IL17C were identified as associated with the early stages of CRC, whereas lysophosphatidic acid phosphatase type 6 (ACP6), Fms-related tyrosine kinase 4 (FLT4), and MANSC domain-containing protein 1 (MANSC1) were correlated with the late-stages of CRC. Discussion: Further study to characterize the newly identified plasma protein changes from larger cohorts will facilitate the identification of potential novel diagnostic, prognostic biomarkers for CRC

High prevalence of somatic PIK3CA and TP53 pathogenic variants in the normal mammary gland tissue of sporadic breast cancer patients revealed by duplex sequencing

The mammary gland undergoes hormonally stimulated cycles of proliferation, lactation, and involution. We hypothesized that these factors increase the mutational burden in glandular tissue and may explain high cancer incidence rate in the general population, and recurrent disease. Hence, we investigated the DNA sequence variants in the normal mammary gland, tumor, and peripheral blood from 52 reportedly sporadic breast cancer patients. Targeted resequencing of 542 cancer-associated genes revealed subclonal somatic pathogenic variants of: PIK3CA, TP53, AKT1, MAP3K1, CDH1, R81, NCOR1, MED12, CBFB, T8X3, and TSHR in the normal mammary gland at considerable allelic frequencies (9 x 10(-2) - 5.2 x 10(-1)), indicating clonal expansion. Further evaluation of the frequently damaged PIK3CA and TP53 genes by ultra-sensitive duplex sequencing demonstrated a diversified picture of multiple low-level subclonal (in 10(-2)-10(-4) alleles) hotspot pathogenic variants. Our results raise a question about the oncogenic potential in non-tumorous mammary gland tissue of breast-conserving surgery patients

POLCOVID: a multicenter multiclass chest X-ray database (Poland, 2020–2021)

Abstract The outbreak of the SARS-CoV-2 pandemic has put healthcare systems worldwide to their limits, resulting in increased waiting time for diagnosis and required medical assistance. With chest radiographs (CXR) being one of the most common COVID-19 diagnosis methods, many artificial intelligence tools for image-based COVID-19 detection have been developed, often trained on a small number of images from COVID-19-positive patients. Thus, the need for high-quality and well-annotated CXR image databases increased. This paper introduces POLCOVID dataset, containing chest X-ray (CXR) images of patients with COVID-19 or other-type pneumonia, and healthy individuals gathered from 15 Polish hospitals. The original radiographs are accompanied by the preprocessed images limited to the lung area and the corresponding lung masks obtained with the segmentation model. Moreover, the manually created lung masks are provided for a part of POLCOVID dataset and the other four publicly available CXR image collections. POLCOVID dataset can help in pneumonia or COVID-19 diagnosis, while the set of matched images and lung masks may serve for the development of lung segmentation solutions

Indications of post-zygotic copy number variation in a region between <i>IL10Rβ</i> and <i>IFNAR1</i>.

<p>Results from eight Illumina genotyping experiments are shown using blood DNA from two pairs of monozygotic twins (panel A for twin 012_01 versus co-twin 012_02, and in panel B for twin 159201 versus co-twin 159202) and two unrelated individuals, where two different tissues were analyzed from each subject (Panels C and D; subjects ML36 and SK58, respectively). Abbreviations BL, PT and UM indicate peripheral blood DNA, primary breast tumor and healthy morphologically normal breast tissue from a patient affected with breast cancer, respectively. Illumina 610 or 660W SNP arrays were used, which also contain so called “intensity only probes” (often with cvni-prefix), only useful for copy number analyses. Therefore, only Log R Ratio (LRR) windows of Illumina experiments are shown here, since the B Allele Frequency (BAF) values are not informative for this type of probes. LRR values below and above zero suggest a deletion or a gain, respectively. The four array probes showing variation between the studied samples are labeled as red dots in yellow fields.</p