Automatic bone segmentation in whole-body CT images

PURPOSE

Many diagnostic or treatment planning applications critically depend on the successful localization of bony structures in CT images. Manual or semiautomatic bone segmentation is tedious, however, and often not practical in clinical routine. In this paper, we present a reliable and fully automatic bone segmentation in whole-body CT scans of patients suffering from multiple myeloma.

METHODS

We address this problem by using convolutional neural networks with an architecture inspired by the U-Net [17]. In this publication, we compared three training procedures: (1) training from 2D axial slices, (2) a pseudo-3D approach including axial, sagittal and coronal slices and (3) an approach where the network is pre-trained in an unsupervised manner.

RESULTS

We evaluated the method on an in-house dataset of 18 whole-body CT scans consisting of 6800 axial slices, achieving a dice score of 0.95 and an intersection over union (IOU) of 0.91. Furthermore, we evaluated our method on the dataset used by Peréz-Carrasco et al. (Comput Methods Progr Biomed 156:85-95, 2018). The data and the ground truth have been made publicly available. The proposed method outperformed the other methods, obtaining a dice score of 0.92 and an IOU of 0.85.

CONCLUSION

These promising results could facilitate the evaluation of bone density and the localization of focal lesions in the future, with a potential impact on both disease staging and treatment planning.

Adalimumab versus adalimumab and methotrexate for the treatment of juvenile idiopathic arthritis: long-term data from the German BIKER registry

OBJECTIVE

Adalimumab (ADA) has become a valuable treatment option for juvenile idiopathic arthritis (JIA). The importance of combination with methotrexate (MTX) is unclear.

METHOD

Data from the German Biologics in Paediatric Rheumatology (BIKER) registry are reported. Response to treatment was analysed using JIA American College of Rheumatology (ACR) scores, 10-joint Juvenile Arthritis Disease Activity Score (JADAS10), and improvement of functional status and ACR inactive disease criteria. Compa-risons between rates of adverse events (AEs) and serious adverse events (SAEs) provided data for the safety assessment.

RESULTS

Overall, 584 patients with non-systemic JIA started ADA therapy, 61% of whom received concomitant MTX treatment at baseline. The latter patients were younger (p < 0.001), with shorter disease duration (p = 0.001), more frequently had antinuclear antibodies (p = 0.04), and had higher baseline JADAS10 scores (p = 0.03). In patients with ADA monotherapy, enthesitis-related arthritis (p = 0.004) and presence of human leucocyte antigen-B27 (p = 0.008) were documented more often. Mean treatment duration in both cohorts was 15 months. Comparable last follow-up rates for JIA ACR 30/50/70/90% response, JADAS minimal disease activity, JADAS remission, and ACR inactive disease were, respectively, 75/72/64/49%, 66%, 46%, and 58% for ADA monotherapy, and 77/72/61/45%, 64%, 48%, and 55%, for ADA + MTX. During 1082 patient-years (PY) of ADA exposure, 725 AEs (67/100 PY), including 57 SAEs (5.3/100 PY), were reported. Serious infections were reported in 10 patients (0.9/100 PY) and 11 (1.0/100 PY) had varicella infections/zoster reactivation. Rates of AEs, SAEs, infectious events, and serious infections did not differ between the cohorts. Elevated transaminases (p = 0.005) and gastrointestinal events (p < 0.0001) were reported more often in the combination cohort. Two pregnancies and no deaths were reported.

CONCLUSION

ADA demonstrated an acceptable risk profile and high percentages of patients in both cohorts showed sufficient treatment response. No differences in treatment response or adherence to treatment were found.

Live-cell labeling of endogenous proteins with nanometer precision by transduced nanobodies

Accurate labeling of endogenous proteins for advanced light microscopy in living cells remains challenging. Nanobodies have been widely used for antigen labeling, visualization of subcellular protein localization and interactions. To facilitate an expanded application, we present a scalable and high-throughput strategy to simultaneously target multiple endogenous proteins in living cells with micro- to nanometer resolution. For intracellular protein labeling, we advanced nanobodies by site-specific and stoichiometric attachment of bright organic fluorophores. Their fast and fine-tuned intracellular transfer by microfluidic cell squeezing enabled high-throughput delivery with less than 10% dead cells. This strategy allowed for the dual-color imaging of distinct endogenous cellular structures, and culminated in super-resolution imaging of native protein networks in genetically non-modified living cells. The simultaneous delivery of multiple engineered nanobodies does not only offer exciting prospects for multiplexed imaging of endogenous protein, but also holds potential for visualizing native cellular structures with unprecedented accuracy.

Involvement of thapsigargin- and cyclopiazonic acid-sensitive pumps in the rescue of TMEM165-associated glycosylation defects by Mn2

Congenital disorders of glycosylation are severe inherited diseases in which aberrant protein glycosylation is a hallmark. Transmembrane protein 165 (TMEM165) is a novel Golgi transmembrane protein involved in type II congenital disorders of glycosylation. Although its biologic function is still a controversial issue, we have demonstrated that the Golgi glycosylation defect due to TMEM165 deficiency resulted from a Golgi Mn²⁺ homeostasis defect. The goal of this study was to delineate the cellular pathway by which extracellular Mn²⁺ rescues N-glycosylation in TMEM165 knockout (KO) cells. We first demonstrated that after extracellular exposure, Mn²⁺ uptake by HEK293 cells at the plasma membrane did not rely on endocytosis but was likely done by plasma membrane transporters. Second, we showed that the secretory pathway Ca²⁺-ATPase 1, also known to mediate the influx of cytosolic Mn²⁺ into the lumen of the Golgi apparatus, is not crucial for the Mn²⁺-induced rescue glycosylation of lysosomal-associated membrane protein 2 (LAMP2). In contrast, our results demonstrate the involvement of cyclopiazonic acid- and thapsigargin (Tg)-sensitive pumps in the rescue of TMEM165-associated glycosylation defects by Mn²⁺. Interestingly, overexpression of sarco/endoplasmic reticulum Ca²⁺-ATPase (SERCA) 2b isoform in TMEM165 KO cells partially rescues the observed LAMP2 glycosylation defect. Overall, this study indicates that the rescue of Golgi N-glycosylation defects in TMEM165 KO cells by extracellular Mn²⁺ involves the activity of Tg and cyclopiazonic acid-sensitive pumps, probably the SERCA pumps.-Houdou, M., Lebredonchel, E., Garat, A., Duvet, S., Legrand, D., Decool, V., Klein, A., Ouzzine, M., Gasnier, B., Potelle, S., Foulquier, F. Involvement of thapsigargin- and cyclopiazonic acid-sensitive pumps in the rescue of TMEM165-associated glycosylation defects by Mn²⁺.

Center of Mass Motion of Short-Range Correlated Nucleon Pairs studied via the A(e,e^{'}pp) Reaction

Short-range correlated (SRC) nucleon pairs are a vital part of the nucleus, accounting for almost all nucleons with momentum greater than the Fermi momentum (k_{F}). A fundamental characteristic of SRC pairs is having large relative momenta as compared to k_{F}, and smaller center of mass (c.m.) which indicates a small separation distance between the nucleons in the pair. Determining the c.m. momentum distribution of SRC pairs is essential for understanding their formation process. We report here on the extraction of the c.m. motion of proton-proton (pp) SRC pairs in carbon and, for the first time in heavier and ansymetric nuclei: aluminum, iron, and lead, from measurements of the A(e,e^{'}pp) reaction. We find that the pair c.m. motion for these nuclei can be described by a three-dimensional Gaussian with a narrow width ranging from 140 to 170  MeV/c, approximately consistent with the sum of two mean-field nucleon momenta. Comparison with calculations appears to show that the SRC pairs are formed from mean-field nucleons in specific quantum states.

Effect of patient and nurse ethnicity on emergency department analgesia for children with appendicitis in israeli government hospitals

BACKGROUND

Ethnicity is a risk factor for disparate Emergency Department (ED) analgesia. We aimed to explore ethnic variations in the administration of ED analgesia to children with acute appendicitis in Israeli government hospitals.

METHODS

Children discharged with an International Classification of Disease-Ninth Revision diagnosis of acute appendicitis between 2010 and 2015 were included. The association between patient ethnicity (Jewish, Arab) and analgesia administration (any, opioid) was assessed. Age, gender, triage category, pain score and time of arrival were tested as possible confounders. The effect of patient-nurse ethnic discordance (PNED) was examined.

RESULTS

Overall, 4714 children with acute appendicitis, 3520 Jewish and 1194 Arab, were cared for in the EDs; 1516 (32.2%) received any analgesia and 368 (7.8%) opioid analgesia. Stratified by pain score, no statistical differences were found in the administration of any or opioid analgesia between Jewish and Arab patients with either severe pain or moderate pain. In multivariate modelling adjusted for pain score and triage category, the rates of any analgesia for Arab and Jewish patients were 31.8% (95% CI, 30.9-32.6) and 36.5% (95% CI, 36.0-36.9), adjusted OR (aOR) = 1.16 (95% CI, 0.98-1.38), respectively. The rates of opioid analgesia for Arab and Jewish patients were 8.5% (95% CI, 8.2-8.9) and 7.9% (95% CI, 7.3-8.7), aOR = 0.77; (95% CI, 0.59-1.22), respectively. Jewish and Arab nurses treated proportionally fewer patients from the opposite ethnicity with any analgesia (p < 0.01).

CONCLUSION

Emergency Department analgesia was markedly low, and not associated with patient ethnicity. PNED was associated with decreased rates of analgesia.

SIGNIFICANCE

Emergency Department analgesia for children with acute appendicitis in Israeli government hospitals is markedly low. Patient-provider ethnic discordance may negatively influence the provision of analgesia. Significant efforts should be undertaken in order to increase analgesia provision rates and reduce social inequality.

Measurement of the Q^{2} Dependence of the Deuteron Spin Structure Function g_{1} and its Moments at Low Q^{2} with CLAS

We measured the g_{1} spin structure function of the deuteron at low Q^{2}, where QCD can be approximated with chiral perturbation theory (χPT). The data cover the resonance region, up to an invariant mass of W≈1.9  GeV. The generalized Gerasimov-Drell-Hearn sum, the moment Γ_{1}^{d} and the spin polarizability γ_{0}^{d} are precisely determined down to a minimum Q^{2} of 0.02  GeV^{2} for the first time, about 2.5 times lower than that of previous data. We compare them to several χPT calculations and models. These results are the first in a program of benchmark measurements of polarization observables in the χPT domain.

Physics perspectives with AFTER@LHC (A Fixed Target ExpeRiment at LHC)

AFTER@LHC is an ambitious fixed-target project in order to address open questions in the domain of proton and neutron spins, Quark Gluon Plasma and high-x physics, at the highest energy ever reached in the fixed-target mode. Indeed, thanks to the highly energetic 7 TeV proton and 2.76 A.TeV lead LHC beams, center-of-mass energies as large as [see formula in PDF] = 115 GeV in pp/pA and [see formula in PDF] = 72 GeV in AA can be reached, corresponding to an uncharted energy domain between SPS and RHIC. We report two main ways of performing fixed-target collisions at the LHC, both allowing for the usage of one of the existing LHC experiments. In these proceedings, after discussing the projected luminosities considered for one year of data taking at the LHC, we will present a selection of projections for light and heavy-flavour production.

Supercritical CO2-assisted deposition of NiO on (101)-anatase-TiO2 for efficient facet engineered photocatalysts

Deposition of NiO on the (101) facet of anatase nanocrystals by the SFCD route yields nanocomposites more efficient than pure anatase TiO₂ for the photodecomposition of both anionic and cationic dyes.

First Exclusive Measurement of Deeply Virtual Compton Scattering off ^{4}He: Toward the 3D Tomography of Nuclei

We report on the first measurement of the beam-spin asymmetry in the exclusive process of coherent deeply virtual Compton scattering off a nucleus. The experiment uses the 6 GeV electron beam from the Continuous Electron Beam Accelerator Facility (CEBAF) accelerator at Jefferson Lab incident on a pressurized ^{4}He gaseous target placed in front of the CEBAF Large Acceptance Spectrometer (CLAS). The scattered electron is detected by CLAS and the photon by a dedicated electromagnetic calorimeter at forward angles. To ensure the exclusivity of the process, a specially designed radial time projection chamber is used to detect the recoiling ^{4}He nuclei. We measure beam-spin asymmetries larger than those observed on the free proton in the same kinematic domain. From these, we are able to extract, in a model-independent way, the real and imaginary parts of the only ^{4}He Compton form factor, H_{A}. This first measurement of coherent deeply virtual Compton scattering on the ^{4}He nucleus, with a fully exclusive final state via nuclear recoil tagging, leads the way toward 3D imaging of the partonic structure of nuclei.