Observation of Seven Astrophysical Tau Neutrino Candidates with IceCube

We report on a measurement of astrophysical tau neutrinos with 9.7 yr of IceCube data. Using convolutional neural networks trained on images derived from simulated events, seven candidate ν_{τ} events were found with visible energies ranging from roughly 20 TeV to 1 PeV and a median expected parent ν_{τ} energy of about 200 TeV. Considering backgrounds from astrophysical and atmospheric neutrinos, and muons from π^{±}/K^{±} decays in atmospheric air showers, we obtain a total estimated background of about 0.5 events, dominated by non-ν_{τ} astrophysical neutrinos. Thus, we rule out the absence of astrophysical ν_{τ} at the 5σ level. The measured astrophysical ν_{τ} flux is consistent with expectations based on previously published IceCube astrophysical neutrino flux measurements and neutrino oscillations.

Lost gallstones during laparoscopic cholecystectomy as a common but underestimated complication-case report and review of the literature

Introduction

Laparoscopic cholecystectomy (LC) represents one of the most commonly performed routine abdominal surgeries. Nevertheless, besides bile duct injury, problems caused by lost gallstones represent a heavily underestimated and underreported possible late complication after LC.

Methods

Case report of a Clavien-Dindo IVb complication after supposedly straightforward LC and review of all published case reports on complications from lost gallstones from 2000-2022.

Case Report

An 86-year-old patient developed a perihepatic abscess due to lost gallstones 6 months after LC. The patient had to undergo open surgery to successfully drain the abscess. Reactive pleural effusion needed additional drainage. Postoperative ICU stay was 13 days. The patient was finally discharged after 33 days on a geriatric remobilization ward and died 12 months later due to acute cardiac decompensation.

Conclusion

Intraabdominal abscess formation due to spilled gallstones may present years after LC as a late complication. Surgical management in order to completely evacuate the abscess and remove all spilled gallstones may be required, which could be associated with high morbidity and mortality, especially in elderly patients. Regarding the overt underreporting of gallstone spillage in case of postoperative gallstone-related complications, focus need be put on precise reporting of even apparently innocuous complications during LC.

A Comparative Study of Deep Learning Methods for Multi-Class Semantic Segmentation of 2D Kidney Ultrasound Images

Ultrasound (US) imaging is a widely used medical imaging modality for the diagnosis, monitoring, and surgical planning for kidney conditions. Thus, accurate segmentation of the kidney and internal structures in US images is essential for the assessment of kidney function and the detection of pathological conditions, such as cysts, tumors, and kidney stones. Therefore, there is a need for automated methods that can accurately segment the kidney and internal structures in US images. Over the years, automatic strategies were proposed for such purpose, with deep learning methods achieving the current state-of-the-art results. However, these strategies typically ignore the segmentation of the internal structures of the kidney. Moreover, they were evaluated in different private datasets, hampering the direct comparison of results, and making it difficult to determination the optimal strategy for this task. In this study, we perform a comparative analysis of 7 deep learning networks for the segmentation of the kidney and internal structures (Capsule, Central Echogenic Complex (CEC), Cortex and Medulla) in 2D US images in an open access multi-class kidney US dataset. The dataset includes 514 images, acquired in multiple clinical centers using different US machines and protocols. The dataset contains the annotation of two experts, but 321 images with complete segmentation of all 4 classes were used. Overall, the results demonstrate that the DeepLabV3+ network outperformed the inter-rater variability with a Dice score of 78.0% compared to 75.6% for inter-rater variability. Specifically, DeepLabV3Plus achieved mean Dice scores of 94.2% for the Capsule, 85.8% for the CEC, 62.4% for the Cortex, and 69.6% for the Medulla. These findings suggest the potential of deep learning-based methods in improving the accuracy of kidney segmentation in US images.Clinical Relevance- This study shows the potential of DL for improving accuracy of kidney segmentation in US, leading to increased diagnostic efficiency, and enabling new applications such as computer-aided diagnosis and treatment, ultimately resulting in improved patient outcomes and reduced healthcare costs.1.

Observation of high-energy neutrinos from the Galactic plane

The origin of high-energy cosmic rays, atomic nuclei that continuously impact Earth's atmosphere, is unknown. Because of deflection by interstellar magnetic fields, cosmic rays produced within the Milky Way arrive at Earth from random directions. However, cosmic rays interact with matter near their sources and during propagation, which produces high-energy neutrinos. We searched for neutrino emission using machine learning techniques applied to 10 years of data from the IceCube Neutrino Observatory. By comparing diffuse emission models to a background-only hypothesis, we identified neutrino emission from the Galactic plane at the 4.5σ level of significance. The signal is consistent with diffuse emission of neutrinos from the Milky Way but could also arise from a population of unresolved point sources.

peaksat: an R package for ChIP-seq peak saturation analysis

BACKGROUND

Epigenomic profiling assays such as ChIP-seq have been widely used to map the genome-wide enrichment profiles of chromatin-associated proteins and posttranslational histone modifications. Sequencing depth is a key parameter in experimental design and quality control. However, due to variable sequencing depth requirements across experimental conditions, it can be challenging to determine optimal sequencing depth, particularly for projects involving multiple targets or cell types.

RESULTS

We developed the peaksat R package to provide target read depth estimates for epigenomic experiments based on the analysis of peak saturation curves. We applied peaksat to establish the distinctive read depth requirements for ChIP-seq studies of histone modifications in different cell lines. Using peaksat, we were able to estimate the target read depth required per library to obtain high-quality peak calls for downstream analysis. In addition, peaksat was applied to other sequence-enrichment methods including CUT&RUN and ATAC-seq.

CONCLUSION

peaksat addresses a need for researchers to make informed decisions about whether their sequencing data has been generated to an adequate depth and subsequently sufficient meaningful peaks, and failing that, how many more reads would be required per library. peaksat is applicable to other sequence-based methods that include calling peaks in their analysis.

Evidence for neutrino emission from the nearby active galaxy NGC 1068

A supermassive black hole, obscured by cosmic dust, powers the nearby active galaxy NGC 1068. Neutrinos, which rarely interact with matter, could provide information on the galaxy’s active core. We searched for neutrino emission from astrophysical objects using data recorded with the IceCube neutrino detector between 2011 and 2020. The positions of 110 known gamma-ray sources were individually searched for neutrino detections above atmospheric and cosmic backgrounds. We found that NGC 1068 has an excess of 79 − 20 + 22 neutrinos at tera–electron volt energies, with a global significance of 4.2σ, which we interpret as associated with the active galaxy. The flux of high-energy neutrinos that we measured from NGC 1068 is more than an order of magnitude higher than the upper limit on emissions of tera–electron volt gamma rays from this source.

Search for Unstable Sterile Neutrinos with the IceCube Neutrino Observatory

We present a search for an unstable sterile neutrino by looking for a resonant signal in eight years of atmospheric ν_{μ} data collected from 2011 to 2019 at the IceCube Neutrino Observatory. Both the (stable) three-neutrino and the 3+1 sterile neutrino models are disfavored relative to the unstable sterile neutrino model, though with p values of 2.8% and 0.81%, respectively, we do not observe evidence for 3+1 neutrinos with neutrino decay. The best-fit parameters for the sterile neutrino with decay model from this study are Δm_{41}^{2}=6.7_{-2.5}^{+3.9}  eV^{2}, sin^{2}2θ_{24}=0.33_{-0.17}^{+0.20}, and g^{2}=2.5π±1.5π, where g is the decay-mediating coupling. The preferred regions of the 3+1+decay model from short-baseline oscillation searches are excluded at 90% C.L.

Strong Constraints on Neutrino Nonstandard Interactions from TeV-Scale ν_{μ} Disappearance at IceCube

We report a search for nonstandard neutrino interactions (NSI) using eight years of TeV-scale atmospheric muon neutrino data from the IceCube Neutrino Observatory. By reconstructing incident energies and zenith angles for atmospheric neutrino events, this analysis presents unified confidence intervals for the NSI parameter ε_{μτ}. The best-fit value is consistent with no NSI at a p value of 25.2%. With a 90% confidence interval of -0.0041≤ε_{μτ}≤0.0031 along the real axis and similar strength in the complex plane, this result is the strongest constraint on any NSI parameter from any oscillation channel to date.

A deep learning method for kidney segmentation in 2D ultrasound images

Ultrasound (US) is a medical imaging modality widely used for diagnosis, monitoring, and guidance of surgical procedures. However, the accurate interpretation of US images is a challenging task. Recently, portable 2D US devices enhanced with Artificial intelligence (AI) methods to identify, in real-time, specific organs are widely spreading worldwide. Nevertheless, the number of available methods that effectively work in such devices is still limited. In this work, we evaluate the performance of the U-NET architecture to segment the kidney in 2D US images. To accomplish this task, we studied the possibility of using multiple sliced images extracted from 3D US volumes to achieve a large, variable, and multi-view dataset of 2D images. The proposed methodology was tested with a dataset of 66 3D US volumes, divided in 51 for training, 5 for validation, and 10 for testing. From the volumes, 3792 2D sliced images were extracted. Two experiments were conducted, namely: (i) using the entire database (WWKD); and (ii) using images where the kidney area is > 500 mm2 (500KD). As a proof-of-concept, the potential of our strategy was tested in real 2D images (acquired with 2D probes). An average error of 2.88 ± 2.63 mm in the testing dataset was registered. Moreover, satisfactory results were obtained in our initial proof-of-concept using pure 2D images. In short, the proposed method proved, in this preliminary study, its potential interest for clinical practice. Further studies are required to evaluate the real performance of the proposed methodology. Clinical Relevance- In this work a deep learning methodology to segment the kidney in 2D US images is presented. It may be a relevant feature to be included in the recent portable US ecosystems easing the interpretation of image and consequently the clinical analysis.

Search for Relativistic Magnetic Monopoles with Eight Years of IceCube Data

We present an all-sky 90% confidence level upper limit on the cosmic flux of relativistic magnetic monopoles using 2886 days of IceCube data. The analysis was optimized for monopole speeds between 0.750c and 0.995c, without any explicit restriction on the monopole mass. We constrain the flux of relativistic cosmic magnetic monopoles to a level below 2.0×10^{-19}  cm^{-2} s^{-1} sr^{-1} over the majority of the targeted speed range. This result constitutes the most strict upper limit to date for magnetic monopoles with β≳0.8 and up to β∼0.995 and fills the gap between existing limits on the cosmic flux of nonrelativistic and ultrarelativistic magnetic monopoles.

Haploflow: Strain-resolved de novo assembly of viral genomes

In viral infections often multiple related viral strains are present, due to coinfection or within-host evolution. We describe Haploflow, a de Bruijn graph-based assembler for de novo genome assembly of viral strains from mixed sequence samples using a novel flow algorithm. We assessed Haploflow across multiple benchmark data sets of increasing complexity, showing that Haploflow is faster and more accurate than viral haplotype assemblers and generic metagenome assemblers not aiming to reconstruct strains. Haplotype reconstructed high-quality strain-resolved assemblies from clinical HCMV samples and SARS-CoV-2 genomes from wastewater metagenomes identical to genomes from clinical isolates.

eV-Scale Sterile Neutrino Search Using Eight Years of Atmospheric Muon Neutrino Data from the IceCube Neutrino Observatory

The results of a 3+1 sterile neutrino search using eight years of data from the IceCube Neutrino Observatory are presented. A total of 305 735 muon neutrino events are analyzed in reconstructed energy-zenith space to test for signatures of a matter-enhanced oscillation that would occur given a sterile neutrino state with a mass-squared differences between 0.01 and 100  eV^{2}. The best-fit point is found to be at sin^{2}(2θ_{24})=0.10 and Δm_{41}^{2}=4.5  eV^{2}, which is consistent with the no sterile neutrino hypothesis with a p value of 8.0%.

Characteristics of the Diffuse Astrophysical Electron and Tau Neutrino Flux with Six Years of IceCube High Energy Cascade Data

We report on the first measurement of the astrophysical neutrino flux using particle showers (cascades) in IceCube data from 2010-2015. Assuming standard oscillations, the astrophysical neutrinos in this dedicated cascade sample are dominated (∼90%) by electron and tau flavors. The flux, observed in the sensitive energy range from 16 TeV to 2.6 PeV, is consistent with a single power-law model as expected from Fermi-type acceleration of high energy particles at astrophysical sources. We find the flux spectral index to be γ=2.53±0.07 and a flux normalization for each neutrino flavor of ϕ_{astro}=1.66_{-0.27}^{+0.25} at E_{0}=100  TeV, in agreement with IceCube's complementary muon neutrino results and with all-neutrino flavor fit results. In the measured energy range we reject spectral indices γ≤2.28 at ≥3σ significance level. Because of high neutrino energy resolution and low atmospheric neutrino backgrounds, this analysis provides the most detailed characterization of the neutrino flux at energies below ∼100  TeV compared to previous IceCube results. Results from fits assuming more complex neutrino flux models suggest a flux softening at high energies and a flux hardening at low energies (p value ≥0.06). The sizable and smooth flux measured below ∼100  TeV remains a puzzle. In order to not violate the isotropic diffuse gamma-ray background as measured by the Fermi Large Area Telescope, it suggests the existence of astrophysical neutrino sources characterized by dense environments which are opaque to gamma rays.

Time-Integrated Neutrino Source Searches with 10 Years of IceCube Data

This Letter presents the results from pointlike neutrino source searches using ten years of IceCube data collected between April 6, 2008 and July 10, 2018. We evaluate the significance of an astrophysical signal from a pointlike source looking for an excess of clustered neutrino events with energies typically above ∼1  TeV among the background of atmospheric muons and neutrinos. We perform a full-sky scan, a search within a selected source catalog, a catalog population study, and three stacked Galactic catalog searches. The most significant point in the northern hemisphere from scanning the sky is coincident with the Seyfert II galaxy NGC 1068, which was included in the source catalog search. The excess at the coordinates of NGC 1068 is inconsistent with background expectations at the level of 2.9σ after accounting for statistical trials from the entire catalog. The combination of this result along with excesses observed at the coordinates of three other sources, including TXS 0506+056, suggests that, collectively, correlations with sources in the northern catalog are inconsistent with background at 3.3σ significance. The southern catalog is consistent with background. These results, all based on searches for a cumulative neutrino signal integrated over the 10 years of available data, motivate further study of these and similar sources, including time-dependent analyses, multimessenger correlations, and the possibility of stronger evidence with coming upgrades to the detector.

[Waiting list management]

Listing a patient on the Eurotransplant waiting list for a kidney transplantation obliges transplant centers to ensure that an allocated organ can also be transplanted, as long as there are no acute recipient-specific medical or personal contraindications. Assessing the ability for transplantation over a period of up to 10 years between initiation of dialysis and an organ offer represents a major challenge in manpower and logistic efforts. The present article reviews specific aspects regarding waiting list management on the basis of current guideline recommendations and literature data.

Blood CD9+ B cell, a biomarker of bronchiolitis obliterans syndrome after lung transplantation

Bronchiolitis obliterans syndrome is the main limitation for long-term survival after lung transplantation. Some specific B cell populations are associated with long-term graft acceptance. We aimed to monitor the B cell profile during early development of bronchiolitis obliterans syndrome after lung transplantation. The B cell longitudinal profile was analyzed in peripheral blood mononuclear cells from patients with bronchiolitis obliterans syndrome and patients who remained stable over 3 years of follow-up. CD24^hi CD38^hi transitional B cells were increased in stable patients only, and reached a peak 24 months after transplantation, whereas they remained unchanged in patients who developed a bronchiolitis obliterans syndrome. These CD24^hi CD38^hi transitional B cells specifically secrete IL-10 and express CD9. Thus, patients with a total CD9⁺ B cell frequency below 6.6% displayed significantly higher incidence of bronchiolitis obliterans syndrome (AUC = 0.836, PPV = 0.75, NPV = 1). These data are the first to associate IL-10-secreting CD24^hi CD38^hi transitional B cells expressing CD9 with better allograft outcome in lung transplant recipients. CD9-expressing B cells appear as a contributor to a favorable environment essential for the maintenance of long-term stable graft function and as a new predictive biomarker of bronchiolitis obliterans syndrome-free survival.

Trust in Physicians and Regional Brain Volumes: A Population-Based Study

Objective

Trust, a fundamental part of human interpersonal relationships, is known to be associated with specific brain regions and demographic characteristics. Level of trust in medical professionals can alter population health outcomes and influence the nature of the doctor-patient relationship. This study utilized structural magnetic resonance imaging (MRI) and trust data from the Dallas Heart Study (DHS), a large community-based study, to determine brain regions associated with degree of trust in physicians and the medical profession. The first phase of the DHS was conducted from 2000 to 2002 and the second phase from 2007 to 2009.

Methods

The MRI data were analyzed as part of the DHS using automated FreeSurfer software. Forward stepwise binary logistic regression was performed to investigate the association between measures of trust and bilateral brain region volumes and thickness followed by confirmatory multiple regressions of significant brain regions. A total of 1,596 participants were included in the final analysis.

Results

Left caudal anterior cingulate cortex (ACC) thickness was inversely correlated with trust of physicians (P < .01). There were no significant associations between trust in physicians and age, race or ethnicity, or education.

Conclusions

The ACC is an integral part of the salience network, the brain network responsible for communication and social behavior. Trust in physicians did not appear to be influenced by demographic characteristics. The findings suggest there are neuroanatomical correlates of trust in physicians.

Relationship between trust in neighbors and regional brain volumes in a population-based study

Trust is a fundamental part of human interpersonal relationships, and among other complex factors it is shown to be linked with demographic characteristics and specific regions of the brain. The authors utilized a large, community-based database gathered from the Dallas Heart Study to determine specific brain regions associated with an individual's trust in neighbors. A trust questionnaire was taken and regional brain volumes were determined from structural magnetic resonance imaging. Two analyses using logistic regressions in a training set and validation set were performed to investigate the association between measures of trust and bilateral brain region volumes and thickness. A total of 1527 participants were included in the final analysis. Right caudal anterior cingulate cortex thickness and left caudate volume were inversely correlated with neighbor trust, while left amygdala volume was positively correlated with neighbor trust. Greater age and higher level of education were positively correlated with neighbor trust. African Americans showed less neighbor trust than Caucasians and Hispanics. Anterior cingulate cortex, caudate, and amygdala are all integral parts of the salience network; thus, results of this study suggest that the salience network, the brain network responsible for functions such as communication and social behavior, may play a role in the formation of interpersonal trust.

Constraints on Minute-Scale Transient Astrophysical Neutrino Sources

High-energy neutrino emission has been predicted for several short-lived astrophysical transients including gamma-ray bursts (GRBs), core-collapse supernovae with choked jets, and neutron star mergers. IceCube's optical and x-ray follow-up program searches for such transient sources by looking for two or more muon neutrino candidates in directional coincidence and arriving within 100 s. The measured rate of neutrino alerts is consistent with the expected rate of chance coincidences of atmospheric background events and no likely electromagnetic counterparts have been identified in Swift follow-up observations. Here, we calculate generic bounds on the neutrino flux of short-lived transient sources. Assuming an E^{-2.5} neutrino spectrum, we find that the neutrino flux of rare sources, like long gamma-ray bursts, is constrained to <5% of the detected astrophysical flux and the energy released in neutrinos (100 GeV to 10 PeV) by a median bright GRB-like source is <10^{52.5}  erg. For a harder E^{-2.13} neutrino spectrum up to 30% of the flux could be produced by GRBs and the allowed median source energy is <10^{52}  erg. A hypothetical population of transient sources has to be more common than 10^{-5}  Mpc^{-3}  yr^{-1} (5×10^{-8}  Mpc^{-3}  yr^{-1} for the E^{-2.13} spectrum) to account for the complete astrophysical neutrino flux.

Search for neutrinos from decaying dark matter with IceCube: IceCube Collaboration

With the observation of high-energy astrophysical neutrinos by the IceCube Neutrino Observatory, interest has risen in models of PeV-mass decaying dark matter particles to explain the observed flux. We present two dedicated experimental analyses to test this hypothesis. One analysis uses 6 years of IceCube data focusing on muon neutrino 'track' events from the Northern Hemisphere, while the second analysis uses 2 years of 'cascade' events from the full sky. Known background components and the hypothetical flux from unstable dark matter are fitted to the experimental data. Since no significant excess is observed in either analysis, lower limits on the lifetime of dark matter particles are derived: we obtain the strongest constraint to date, excluding lifetimes shorter than10 28 s at 90% CL for dark matter masses above 10 TeV .

Cross-sectional point prevalence survey to study the environmental contamination of nosocomial pathogens in intensive care units under real-life conditions

BACKGROUND

In intensive care units (ICUs), inanimate surfaces and equipment may be contaminated by nosocomial pathogens, including multi-drug-resistant micro-organisms.

AIMS

To assess the degree of environmental contamination close to and distant from patients, and contamination of healthcare workers' (HCWs) hands with nosocomial pathogens under real-life conditions and to investigate potential transmission events.

METHODS

Over the course of three weeks, agar contact samples were taken close to and distant from patient areas and from HCWs' hands in eight ICUs of a tertiary care hospital in Innsbruck, Austria. Each ICU was visited once without announcement. Species identification and antimicrobial susceptibility testing were performed according to standard methods, and corresponding strains from patient, environment and hand samples were genotyped using pulsed-field gel electrophoresis.

FINDINGS

Among 523 samples, HCWs' hands were most frequently contaminated with potentially pathogenic bacteria (15.2%), followed by areas close to patients (10.9%) and areas distant from patients (9.1%). Gram-positive bacteria were identified most often (67.8%), with Enterococcus spp. being the most prevalent species (70% vancomycin sensitive and 30% vancomycin resistant) followed by Staphylococcus aureus, of which 64% were classified as meticillin-resistant Staphylococcus aureus. Molecular typing documented identical strains among patient, environment and hand isolates.

CONCLUSION

This study found widespread contamination of the ICU environment with clinically relevant pathogens, including multi-drug-resistant micro-organisms, despite cleaning and disinfection. The bioburden might not be restricted to areas close to patients. The role of extended environmental disinfection of areas distant from patients in order to improve infection prevention needs further discussion.

Abstract 1178: Runx1 is obligatory for mammary epithelial cell morphology and phenotype

Introduction: Runx1 belongs to the Runx family of transcription factors. Translocation of Runx1 is well established as a causative factor of leukemia. However the recognition of Runx1 expression in epithelial lining cells of glands suggests that Runx1 functions in maintaining the integrity of that cell layer. Recent studies have identified Runx1 as one of the top genes mutated in breast cancers. Further Runx1 levels are decreased in high-grade primary breast tumors compared to low/mid-grade tumors. Based on these findings, we raise the hypothesis that Runx1 is a tumor suppressor that functions to maintain the normal epithelial phenotype and that loss of Runx1 could promote epithelial to mesenchymal (EMT). Methods and results: We used two human breast cancer cell models systems, the MCF10A to MCF7/T47D and to MDA-MB-231 and the MCF10A progression model from normal-like mammary epithelial cells (MCF10A) to tumorigenic (MCF10AT1) and to metastatic (MCF10CA1a) cells. We observed that the level of Runx1 is decreased in tumorigenic cells. To understand Runx1 function, Runx1 was depleted by shRNA in mammary epithelial cells that resulting in disrupted/altered cellular morphology and suppressed expression of the epithelial gene E-cadherin. To reinforce this observation, EMT was induced by addition of TGFB1 or by growth factor depletion in MCF10A cells. A striking Runx1 decrease resulted suggesting that Runx1 has a crucial role in preventing EMT. Furthermore our analysis of breast tumors and survival data supports the above finding that loss of Runx1 promotes tumor progression.

Conclusion and Impact: Our results highlight an essential role for Runx1 in maintaining normal epithelial phenotype and preventing epithelial to mesenchymal transition as well as tumor progression in breast cancer. Identifying this Runx1 mechanism provides the basis for a novel strategy to treat early stage breast cancer.

Citation Format: Deli Hong, Terri Messier, Andrew Fritz, Gillian Browne, Janet Stein, Jane Lian, Gary Stein. Runx1 is obligatory for mammary epithelial cell morphology and phenotype. [abstract]. In: Proceedings of the 107th Annual Meeting of the American Association for Cancer Research; 2016 Apr 16-20; New Orleans, LA. Philadelphia (PA): AACR; Cancer Res 2016;76(14 Suppl):Abstract nr 1178.

Chromosomes at Work: Organization of Chromosome Territories in the Interphase Nucleus

The organization of interphase chromosomes in chromosome territories (CTs) was first proposed more than one hundred years ago. The introduction of increasingly sophisticated microscopic and molecular techniques, now provide complementary strategies for studying CTs in greater depth than ever before. Here we provide an overview of these strategies and how they are being used to elucidate CT interactions and the role of these dynamically regulated, nuclear-structure building blocks in directly supporting nuclear function in a physiologically responsive manner.

Alterations in replication timing of cancer-related genes in malignant human breast cancer cells

The replication timing of nine genes commonly involved in cancer was investigated in the MCF10 cell lines for human breast cancer progression. Six of these nine genes are part of a constellation of tumor suppressor genes that play a major role in familial human breast cancer (TP53, ATM, PTEN, CHK2, BRCA1, and BRCA2). Three other genes are involved in a large number of human cancers including breast as either tumor suppressors (RB1 and RAD51) or as an oncogene (cMYC). Five of these nine genes (TP53, RAD51, ATM, PTEN, and cMYC) show significant differences (P < 0.05) in replication timing between MCF10A normal human breast cells and the corresponding malignant MCF10CA1a cells. These differences are specific to the malignant state of the MCF10CA1a cells since there were no significant differences in the replication timing of these genes between normal MCF10A cells and the non-malignant cancer MCF10AT1 cells. Microarray analysis further demonstrated that three of these five genes (TP53, RAD51, and cMYC) showed significant changes in gene expression (≥2-fold) between normal and malignant cells. Our findings demonstrate an alteration in the replication timing of a small subset of cancer-related genes in malignant breast cancer cells. These alterations partially correlate with the major transcriptional changes characteristic of the malignant state in these cells.

Assembly of the SLIP1-SLBP complex on histone mRNA requires heterodimerization and sequential binding of SLBP followed by SLIP1

The SLIP1-SLBP complex activates translation of replication-dependent histone mRNAs. In this report, we describe how the activity of the SLIP1-SLBP complex is modulated by phosphorylation and oligomerization. Biophysical characterization of the free proteins shows that whereas SLIP1 is a homodimer that does not bind RNA, human SLBP is an intrinsically disordered protein that is phosphorylated at 23 Ser/Thr sites when expressed in a eukaryotic expression system such as baculovirus. The bacterially expressed unphosphorylated SLIP1-SLBP complex forms a 2:2 high-affinity (K(D) < 0.9 nM) heterotetramer that is also incapable of binding histone mRNA. In contrast, phosphorylated SLBP from baculovirus has a weak affinity (K(D) ~3 μM) for SLIP1. Sequential binding of phosphorylated SLBP to the histone mRNA stem-loop motif followed by association with SLIP1 is required to form an "active" ternary complex. Phosphorylation of SLBP at Thr171 promotes dissociation of the heterotetramer to the SLIP1-SLBP heterodimer. Using alanine scanning mutagenesis, we demonstrate that the binding site on SLIP1 for SLBP lies close to the dimer interface. A single-point mutant near the SLIP1 homodimer interface abolished interaction with SLBP in vitro and reduced the abundance of histone mRNA in vivo. On the basis of these biophysical studies, we propose that oligomerization and SLBP phosphorylation may regulate the SLBP-SLIP1 complex in vivo. SLIP1 may act to sequester SLBP in vivo, protecting it from proteolytic degradation as an inactive heterotetramer, or alternatively, formation of the SLIP1-SLBP heterotetramer may facilitate removal of SLBP from the histone mRNA prior to histone mRNA degradation.

The prolyl isomerase Pin1 targets stem-loop binding protein (SLBP) to dissociate the SLBP-histone mRNA complex linking histone mRNA decay with SLBP ubiquitination

Histone mRNAs are rapidly degraded at the end of S phase, and a 26-nucleotide stem-loop in the 3' untranslated region is a key determinant of histone mRNA stability. This sequence is the binding site for stem-loop binding protein (SLBP), which helps to recruit components of the RNA degradation machinery to the histone mRNA 3' end. SLBP is the only protein whose expression is cell cycle regulated during S phase and whose degradation is temporally correlated with histone mRNA degradation. Here we report that chemical inhibition of the prolyl isomerase Pin1 or downregulation of Pin1 by small interfering RNA (siRNA) increases the mRNA stability of all five core histone mRNAs and the stability of SLBP. Pin1 regulates SLBP polyubiquitination via the Ser20/Ser23 phosphodegron in the N terminus. siRNA knockdown of Pin1 results in accumulation of SLBP in the nucleus. We show that Pin1 can act along with protein phosphatase 2A (PP2A) in vitro to dephosphorylate a phosphothreonine in a conserved TPNK sequence in the SLBP RNA binding domain, thereby dissociating SLBP from the histone mRNA hairpin. Our data suggest that Pin1 and PP2A act to coordinate the degradation of SLBP by the ubiquitin proteasome system and the exosome-mediated degradation of the histone mRNA by regulating complex dissociation.

GNAS1 T393C polymorphism and disease progression in patients with malignant melanoma

Background

Once metastasized, despite a variety of therapeutic options, the prognosis of patients with malignant melanoma (MM) is still poor. Therefore, the search for reliable markers to identify patients with high risk of disease progression is of high clinical importance. We have recently shown that TT genotypes of the single-nucleotide polymorphism (SNP) T393C in the gene GNAS1 are significantly associated with better outcome in a variety of carcinomas.

Patients

In the present study we assessed whether the T393C SNP is also related to the clinical course in MM. 328 patients with MM were retrospectively genotyped and genotypes were correlated with clinical outcome.

Results

While the allele frequency in the MM group (fC 0.52) did not significantly differ from that of healthy blood donors, the T393C SNP was associated with tumor progression of MM. Carriers of the C-allele showed a significantly more severe tumor progression as estimated from the time period to develop metastasis (HR 2.2, 95% CI 1.1-3.2, p = 0.017). Proportions of 5-year metastasis-free intervals were 87.1% for TT genotypes and 66.0% for C-allele carriers. Moreover, multivariable Cox regression analysis including tumor stage and melanoma subtype proved the T393C polymorphism to be an independent factor for metastasis (p = 0.012).

Conclusions

In summary, the GNAS1 T393C SNP represents a genetic host factor for predicting tumor progression also in patients with MM; genotyping of this SNP may contribute to better define patients who could benefit from an early individualized therapy.

Prospective, randomized comparison of laryngeal tube and laryngeal mask airway in pediatric patients

BACKGROUND

While reports of the use of laryngeal mask airway (LMA)-Classic in great patient numbers are available, data on the use of the laryngeal tube (LT) in this age group is limited. The two devices are compared in a prospective randomized trial to evaluate success rates and quality of airway seal.

METHODS

Sixty children, aged 2-8 years, scheduled for elective surgical interventions were randomized to be ventilated with LMA or LT. Standardized anesthesia was induced with fentanyl and propofol. Number of insertion attempts, time until first tidal volume and intraoperative tidal volumes, and peak pressures were recorded. Airway leak pressure was measured with cuff pressure adjusted to 60 cmH(2)O.

RESULTS

Demographic data were comparable, average age in the LMA/LT group was 5.2 +/- 1.9/5.3 +/- 1.9 years. Insertion was successful in 29 of 30 patients in the LMA group (second attempt 8) and in all patients in the LT group (second attempt 3). Time until first tidal volume for LMA/LT was 23.1 +/- 7.3/19.2 +/- 8.6 s (P < 0.05). Peak airway pressures for LMA and LT were 15.3 +/- 3.4 and 17.1 +/- 4.0 cmH(2)O (P < 0.05) with tidal volumes of 10.2 +/- 2.2 and 10.2 +/- 1.9 ml.kg(-1), airway leak pressure was 19.2 +/- 8.6 cmH(2)O for LMA and 26.3 +/- 7.3 cmH(2)O for LT (P < 0.001).

CONCLUSION

Insertion success rate is high with both LMA and LT in the age group studied. The airway leak pressure, serving as an estimate to judge quality of airway seal, is higher with the LT.

A study on the prognostic significance of qualitative olfactory dysfunction

We investigated the frequency and prognostic significance of qualitative olfactory dysfunction (parosmia, phantosmia) in a retrospective patient based study. A total of 392 patients with impairment of olfaction were tested at least two times for their olfactory function using the "Sniffin' Sticks". The mean interval between the first and the last test was 11 months. At the first visit 34% of all patients reported parosmia. Parosmia was most frequent in patients with postinfectious olfactory loss (56%), and less frequent in idiopathic, posttraumatic, sinunasal disease with frequencies of 10, 14, and 28%, respectively. In contrast, only 12% of all patients had phantosmias, with no significant differences between the patient groups. Improvement of olfactory function was found in 23% of all patients (n = 90). Pre-existing parosmia or phantosmia had no significant effect on recovery rate. Regarding qualitative olfactory dysfunction, 29% of those patients reporting parosmia reported relief of this symptom after an average of 12 months, whereas 53% of phantosmic patients lost phantosmia during the observation period. Although it has been suggested that olfactory distortion s could be regarded as an indicator of early recovery of decreased olfactory sensitivity, the current data indicate that occurrence of parosmia or phantosmia has little prognostic value. Phantosmia disappears at a faster rate than parosmia. These insights into qualitative olfactory dysfunction are regarded to be significant in the counseling of patients with olfactory loss.

Computer-aided analysis of muscle fibre conduction velocity in neuromuscular diseases

The objective was to measure muscle fibre conduction velocity (MFCV) in the biceps brachii of normal subjects, and patients with mild myopathies and anterior horn cell diseases. Unisolated steel needles served as stimulation and recording electrodes. By aid of a computer program for data acquisition and analysis, up to 1,400 single fibre potentials could be recorded from a single muscle and analysed within 30-45 min. Normal values for mean, minimum, maximum CV and 5%, 25%, 75% and 95% percentiles were established. Females have slower mean and minimal CV than men but maximal MFCV were similar for the two groups. Age has no statistical influence. Myopathic patients showed a MFCV decrease of the already slow muscle fibre population. In neurogenetic diseases the distribution was biphasic with the conduction of the formerly fast conducting fibres either enhanced or reduced. Using different statistical parameters to describe the spectrum of muscle fibre conduction properties provides a sensitive tool to evaluate functional impairment in mild myopathies and to separate them from mild neuropathies.

Inheritance and molecular mapping of new green bug resistance genes in wheat germ plasms derived from Aegilops tauschii

Molecular mapping of genes for crop resistance to the green bug, Schizaphis graminum Rondani, will facilitate selection of green bug resistance in breeding through marker-assisted selection and provide information for map-based gene cloning. In the present study, microsatellite marker and deletion line analyses were used to map green bug resistance genes in five newly identified wheat germ plasms derived from Aegilops tauschii. Our results indicate that the Gb genes in these germ plasms are inherited as single dominant traits. Microsatellite markers X wmc 157 and X gdm 150 flank G bx 1 at 2.7 and 3.3 cM, respectively. Xwmc 671 is proximately linked to G ba, G bb, G bc and G bd at 34.3, 5.4, 13.7, 7.9 cM, respectively. X barc 53 is linked distally to G ba and G bb at 20.7 and 20.2 cM, respectively. X gdm 150 is distal to G bc at 17.9 cM, and X wmc 157 is distal to G bd at 1.9 cM. G bx 1, G ba, G bb, G bc, G bd and the previously characterized G bz are located in the distal 18% region of wheat chromosome 7 DL. G bd appears to be a new green bug resistance gene different from G bx 1 or G bz. G bx 1, G bz G ba, G bb, G bc and G bd are either allelic or linked to Gb 3.

Genetic analysis and molecular mapping of a wheat gene conferring tolerance to the greenbug (Schizaphis graminum Rondani)

The greenbug, Schizaphis graminum (Rondani), is one of the major pests of wheat worldwide. The efficient utilization of wheat genes expressing resistance to greenbug infestation is highly dependent on a clear understanding of their relationships. The use of such genes will be further facilitated through the use of molecular markers linked to resistance genes. The present study involved several F(2) wheat populations derived from crosses between susceptible cultivars and resistant germplasm carrying different greenbug resistance genes. These populations were used to characterize the inheritance of a wheat gene ( Gbz) conferring tolerance to greenbug biotype I, to identify molecular markers linked to Gbz, and to investigate the relationship between Gbz and Gb3, a previously identified greenbug resistance gene. Our results indicated that Gbz is inherited as a single dominant gene. Microsatellite marker Xwmc157 is completely linked to Gbz, and Xbarc53 and Xgdm46 flank Gbz at distances of 5.1 and 9.5 cM, respectively. Selection of Gbz using marker Xwmc157 alone gives breeders 100% selection accuracy. Gbz may be placed in the distal region of the long arm of the wheat chromosome 7D. The results of allelism tests indicated that Gbz is either allelic or tightly linked to Gb3.

Lr41, Lr39, and a leaf rust resistance gene from Aegilops cylindrica may be allelic and are located on wheat chromosome 2DS

The leaf rust resistance gene Lr41 in wheat germplasm KS90WGRC10 and a resistance gene in wheat breeding line WX93D246-R-1 were transferred to Triticum aestivum from Aegilops tauschii and Ae. cylindrica, respectively. The leaf rust resistance gene in WX93D246-R-1 was located on wheat chromosome 2D by monosomic analysis. Molecular marker analysis of F(2) plants from non-critical crosses determined that this gene is 11.2 cM distal to marker Xgwm210 on the short arm of 2D. No susceptible plants were detected in a population of 300 F(2) plants from a cross between WX93D246-R-1 and TA 4186 ( Lr39), suggesting that the gene in WX93D246-R-1 is the same as, or closely linked to, Lr39. In addition, no susceptible plants were detected in a population of 180 F(2) plants from the cross between KS90WGRC10 and WX93D246-R-1. The resistance gene in KS90WGRC10, Lr41, was previously reported to be located on wheat chromosome 1D. In this study, no genetic association was found between Lr41 and 51 markers located on chromosome 1D. A population of 110 F(3 )lines from a cross between KS90WGRC10 and TAM 107 was evaluated with polymorphic SSR markers from chromosome 2D and marker Xgdm35 was found to be 1.9 cM proximal to Lr41. When evaluated with diverse isolates of Puccinia triticina, similar reactions were observed on WX93D246-R-1, KS90WGRC10, and TA 4186. The results of mapping, allelism, and race specificity test indicate that these germplasms likely have the same gene for resistance to leaf rust.

The effect of leptin treatment on the development of obesity in overfed suckling Wistar rats

OBJECTIVE

To identify the role of hyperleptinaemia in mediating the effects of early postnatal overfeeding in a rat strain known to be prone to manipulations of the early environment which result in predispositions for obesity and associated metabolic and cardiovascular disturbance in later life.

DESIGN

Wistar rats were reared in normal litters (NL, 10--12 pups) or small litters (SL, four pups) from postnatal day 3 and killed for determination of body composition and plasma leptin and insulin concentrations on day 7 or day 21 after having been treated with recombinant leptin (2 x 50 (pmol/g)/day) or saline from day 1.

RESULTS

Rearing in SL doubled the body fat content and plasma leptin levels in comparison to NL pups by 21 days of age. Under leptin-treatment throughout suckling age, NL pups remained leptin responsive, ie the difference in body fat content was progressively reduced relative to the controls. Until 7 days of age, despite the body fat content of untreated SL pups being 2-fold higher and their plasma leptin level 7-fold higher than that of NL pups, leptin treatment caused the same percentage decreases in body fat in SL than in NL pups. But in contrast to NL pups, the SL pups became leptin resistant thereafter. Plasma insulin levels in 7-day-old leptin-treated SL pups were 3-fold higher than in untreated littermates and 5-fold higher than in the NL groups.

CONCLUSION

Prophylactic leptin treatment does not prevent hyperinsulinaemia and excessive fat deposition in SL pups. On the other hand, selective hyperleptinaemia during suckling age does not trigger leptin resistance and obesity in NL pups. Rather than hyperleptinaemia per se, other factors associated with early postnatal overnutrition, for example, the concurrent hyperinsulinaemia, seem to play a pivotal role for the development of leptin-resistance and life-long obesity risk in SL rats.

Frequency distributions of breast cancer characteristics classified by estrogen receptor and progesterone receptor status for eight racial/ethnic groups

BACKGROUND

The National Cancer Institute's Surveillance, Epidemiology, and End Results (SEER) cancer registries have been collecting data regarding estrogen receptor (ER) and progesterone receptor (PR) status in breast cancer since 1990. The current study reports on some of these data for eight racial/ethnic groups.

METHODS

Stratified by ER and PR status, the frequency distributions of 112,588 breast cancer cases diagnosed between 1992--1997 in 11 SEER cancer registries were examined by age at diagnosis, stage at diagnosis, histologic grade, and tumor type for white, black, Hispanic, Japanese, Chinese, Filipino, Native Hawaiian, and American Indian and Alaska Native (AI/AN) females.

RESULTS

For each racial/ethnic group, the percentage of ER positive (+)/PR+ was > ER-PR- > ER+PR- > ER-PR+ tumors. For the two major ER/PR groups, the ER+PR+ tumors were different from the ER-PR- tumors in several ways. For white females, there were differences in the age distributions, stage at diagnosis, and histologic grade. For black females, the differences involved the age distributions and tumor grades. For Hispanic and Japanese females, there were differences with regard to the age distributions and tumor grades. For Filipino, Chinese, and AI/AN females, the tumor stages and grades differed. For Native Hawaiians, the histologic tumor grades were different.

CONCLUSIONS

For each racial/ethnic group, the ER/PR status appeared to divide breast cancer patients into two or more subgroups with unique tumor characteristics. In general, ER status appeared to have the greatest impact on delineating these subgroups, whereas in some cases, PR status was able to modify the subgroups further. It is hoped that reporting these tumor characteristics by ER/PR status for each racial/ethnic group will spur more investigation into the significance of ER/PR status in each racial/ethnic group.

[Serological certification of the interruption of the vectorial transmission of Chagas disease in Chile]

BACKGROUND

In 1999 an International Commission of Experts evaluated the sanitary interventions that started in 1980 to eliminate Triatoma infestans, the biological vector of Chagas disease, to certify if the conditions needed to interrupt the transmission, were achieved.

AIM

To report the data used by the International certification commission to certify the interruption of vectorial transmission of Chagas disease in Chile.

MATERIAL AND METHODS

A comparative evaluation of the prevalence of Trypanosoma cruzi antibodies in children surveyed between 1994 and 1995 and between 1995 and 1999.

RESULTS

In the first period, 5,948 children were surveyed and in the second, 5,069 children were studied. Twenty children (0.4%) were positive for Trypanosoma cruzi antibodies in the second survey. These figures were significantly lower than the 1.1% prevalence detected between 1994 and 1995. In only three of the 20 cases, the transmission through vectors was confirmed, which represents a 99.4% reduction of this way of transmission.

CONCLUSIONS

Based on these findings, the Commission certified that Chile is the second country in Latin America to interrupt the vector transmission of Chagas disease. The successful public health program for Chagas disease will have a positive impact improving the quality of life of rural populations, that are most exposed to the disease.

Renal oncocytoma of the native kidney after renal transplantation

Patients with acquired cystic kidney disease (ACKD) are at an increased risk of renal neoplasms. Frequent tumors are adenomas and renal cell carcinomas. However, renal oncocytomas may occur in patients with ACKD. Little is known about oncocytomas of the native kidney following renal transplantation. By means of B scan ultrasonography, a solid and echo-inhomogeneous renal mass was incidentically observed in the right native kidney of a 28-year-old female patient with ACKD 4 years following renal transplantation. A nephrectomy was performed. The histological examination revealed a renal oncocytoma. The increased prevalence of neoplasms in the case of ACKD and following renal transplantation requires careful monitoring of the patients concerned. In very rare cases a renal oncocytoma may develop in the native kidney after renal transplantation.

Relation between brain tissue pO2 and dopamine synthesis of basal ganglia--a 18FDOPA-PET study in newborn piglets

Perinatal hypoxic-ischemic cerebral injury is a major determinant of neurologic morbidity and mortality in the neonatal period and later in childhood. There is evidence that the dopaminergic system is sensitive to oxygen deprivation. However, the respective enzyme activities have yet not been measured in the living neonatal brain. In this study, we have used 18F-labelled 6-fluoro-L-3,4-dihydroxyphenylalanine (FDOPA) together with positron emission tomography (PET) to estimate the activity of the aromatic amino acid decarboxylase (AADC), the ultimate enzyme in the synthesis of dopamine, in the brain of newborn piglets under normoxic and moderate asphyxial conditions. The study was performed on 8 newborn piglets (2-5 days old). In each piglet PET studies were performed under control conditions and during 2-hour asphyxia. Simultaneously, brain tissue pO2 was recorded, cerebral blood flow (CBF) was measured with colored microspheres and cerebral metabolic rate of oxygen (CMRO2) was determined. Asphyxia was induced by lowering the inspired fraction of oxygen from 0.35 to 0.10 and adding about 6% CO2 to the inspired gas. Asphyxia elicited a more than 3-fold increase of the CBF (p < 0.01) so that CMRO2 remained unchanged throughout the asphyxial period. Despite this, brain tissue pO2 was reduced from 19 +/- 4 mm Hg to 6 +/- 3 mm Hg (p < 0.01). Blood-brain transfer of FDOPA as well as permeability-surface area product (PS) from striatum were unchanged. Striatal synthesis rate of fluoro-dopamine from FDOPA (k3) was, however, significantly increased (p < 0.01). This increase of the AADC activity is associated with reduced brain tissue pO2. Asphyxia-induced CBF increase impedes an alteration of brain oxidative metabolism.

Zebrafish Mesp family genes, mesp-a and mesp-b are segmentally expressed in the presomitic mesoderm, and Mesp-b confers the anterior identity to the developing somites

Segmentation of a vertebrate embryo begins with the subdivision of the paraxial mesoderm into somites through a not-well-understood process. Recent studies provided evidence that the Notch-Delta and the FGFR (fibroblast growth factor receptor) signalling pathways are required for segmentation. In addition, the Mesp family of bHLH transcription factors have been implicated in establishing a segmental prepattern in the presomitic mesoderm. In this study, we have characterized zebrafish mesp-a and mesp-b genes that are closely related to Mesp family genes in other vertebrates. During gastrulation, only mesp-a is expressed in the paraxial mesoderm at the blastoderm margin. During the segmentation period, both genes are segmentally expressed in one to three stripes in the anterior parts of somite primordia. In fused somites (fss) embryos, in which all early somite boundary formation is blocked, initial mesp-a expression at the gastrula stage remains intact, but the expression of mesp-a and mesp-b is not detected during the segmentation period. This suggests that these genes are downstream targets of fss at the segmentation stage. Comparison with her1 expression (Muller, M., von Weizsacker, E. and Campos-Ortega, J. A. (1996) Development 122, 2071–2078) suggests that, like her1, mesp genes are not expressed in primordia of the first several somites. Furthermore, we found that zebrafish her1 expression oscillates in the presomitic mesoderm. The her1 stripe, which first appears in the tailbud region, moves in a caudal to rostral direction, and it finally overlaps the most rostral mesp stripe. Thus, in the trunk region, both her1 and mesp transcripts are detected in every somite primordium posterior to the forming somites. Ectopic expression of Mesp-b in embryos causes a loss of the posterior identity within the somite primordium, leading to a segmentation defect. These embryos show a reduction in expression of the posterior genes, myoD and notch5, with uniform expression of the anterior genes, FGFR1, papc and notch6. These observations suggest that zebrafish mesp genes are involved in anteroposterior specification within the presumptive somites, by regulating the essential signalling pathways mediated by Notch-Delta and FGFR.