In vivocharacterization of the optical and hemodynamic properties of the human sternocleidomastoid muscle through ultrasound-guided hybrid near-infrared spectroscopies

Objective.In this paper, we present a detailedin vivocharacterization of the optical and hemodynamic properties of the human sternocleidomastoid muscle (SCM), obtained through ultrasound-guided near-infrared time-domain and diffuse correlation spectroscopies.Approach.A total of sixty-five subjects (forty-nine females, sixteen males) among healthy volunteers and thyroid nodule patients have been recruited for the study. Their SCM hemodynamic (oxy-, deoxy- and total hemoglobin concentrations, blood flow, blood oxygen saturation and metabolic rate of oxygen extraction) and optical properties (wavelength dependent absorption and reduced scattering coefficients) have been measured by the use of a novel hybrid device combining in a single unit time-domain near-infrared spectroscopy, diffuse correlation spectroscopy and simultaneous ultrasound imaging.Main results.We provide detailed tables of the results related to SCM baseline (i.e. muscle at rest) properties, and reveal significant differences on the measured parameters due to variables such as side of the neck, sex, age, body mass index, depth and thickness of the muscle, allowing future clinical studies to take into account such dependencies.Significance.The non-invasive monitoring of the hemodynamics and metabolism of the sternocleidomastoid muscle during respiration became a topic of increased interest partially due to the increased use of mechanical ventilation during the COVID-19 pandemic. Near-infrared diffuse optical spectroscopies were proposed as potential practical monitors of increased recruitment of SCM during respiratory distress. They can provide clinically relevant information on the degree of the patient's respiratory effort that is needed to maintain an optimal minute ventilation, with potential clinical application ranging from evaluating chronic pulmonary diseases to more acute settings, such as acute respiratory failure, or to determine the readiness to wean from invasive mechanical ventilation.

Recipes for diffuse correlation spectroscopy instrument design using commonly utilized hardware based on targets for signal-to-noise ratio and precision

Over the recent years, a typical implementation of diffuse correlation spectroscopy (DCS) instrumentation has been adapted widely. However, there are no detailed and accepted recipes for designing such instrumentation to meet pre-defined signal-to-noise ratio (SNR) and precision targets. These require specific attention due to the subtleties of the DCS signals. Here, DCS experiments have been performed using liquid tissue simulating phantoms to study the effect of the detected photon count-rate, the number of parallel detection channels and the measurement duration on the precision and SNR to suggest scaling relations to be utilized for device design.

The LUCA device: a multi-modal platform combining diffuse optics and ultrasound imaging for thyroid cancer screening

We present the LUCA device, a multi-modal platform combining eight-wavelength near infrared time resolved spectroscopy, sixteen-channel diffuse correlation spectroscopy and a clinical ultrasound in a single device. By simultaneously measuring the tissue hemodynamics and performing ultrasound imaging, this platform aims to tackle the low specificity and sensitivity of the current thyroid cancer diagnosis techniques, improving the screening of thyroid nodules. Here, we show a detailed description of the device, components and modules. Furthermore, we show the device tests performed through well established protocols for phantom validation, and the performance assessment for in vivo. The characterization tests demonstrate that LUCA device is capable of performing high quality measurements, with a precision in determining in vivo tissue optical and dynamic properties of better than 3%, and a reproducibility of better than 10% after ultrasound-guided probe repositioning, even with low photon count-rates, making it suitable for a wide variety of clinical applications.

Samba and CERNBox: Providing online access to Windows-based users at CERN

This paper presents the experience in providing CERN users with direct online access to their EOS/CERNBox-powered user storage from Windows. In production for about 15 months, a High-Available Samba cluster is regularly used by a significant fraction of the CERN user base, following the migration of their central home folders from Microsoft DFS in the context of CERN’s strategy to move to open source solutions.

We describe the configuration of the cluster, which is based on standard components: the EOS-backed CERNBox storage is mounted via FUSE, and an additional mount provided by CephFS is used to share the cluster’s state. Further, we describe some typical shortcomings of such a setup and how they were tackled. Finally, we show how such an additional access method fits in the bigger picture, where the storage is seamlessly accessed by user jobs, sync clients, FUSE/Samba mounts as well as the web UI, whilst aiming at a consistent view and user experience.

MON-488 Technologies of Diffuse Optics in the Diagnosis of Thyroid Cancer

BACKGROUND:

The most common tool to test malignancy in the study of thyroid nodules (NT) is ultrasound and fine needle aspiration biopsy (FNAB). However, the sensitivity and specificity of the method and the effectiveness in thyroid cancer are limited; therefore new methods to study thyroid nodules are required. In this way our goal is to introduce hybrid diffuse optical instruments that are capable to measure and discriminate altered microvascular blood flow, blood volume and tissue scattering coefficients of TN. Near-infrared diffuse optical technologies aim to overcome the shortcomings of present techniques while screening for malignant thyroid nodules for early and fast diagnosis of cancer. This idea was based on the previous experience in breast cancers with diffuse optical techniques.

METHODS:

We have developed a device based on near-infrared diffuse correlation spectroscopy (DCS), which is a technology aimed at retrieving the microvascular flow of a certain region of tissue by mean of low power near-infrared laser light, and used in combination with a commercial ultrasound system (US). In order to combine these devices, we have developed a probe enabling multimodal data acquisition and subsequently we have analyzed the optical properties and the blood flow index in the thyroid lobes of eleven subjects who presented a thyroid nodule.

RESULTS:

Four subjects have required FNAB: P4 and P7 were reported as being malignant (Bethesda VI and IV respectively) while P6 and P8 were evaluated as being benign (Bethesda II). Surgical removal confirmed papillary thyroid carcinoma in P4, while denied the result of FNAB for P7 (Multinodular thyroid hyperplasia). We have considered the contralateral lobe as intra-subject reference to validate the feasibility of the DCS system in a very absorbing tissue as thyroid is. The difference between the blood flow index of the nodule and the contralateral lobe is maximum for subject P4, while the difference in benign subjects is lower. T-test showed no significant difference between benign nodules and contralateral lobes. Subject P7 showed a small difference as for other benign subjects despite the FNAB results indicating presence of malignancy.

CONCLUSION:

Apparently diffuse optics technologies would be able to differentiate malignant thyroid nodules from benign thyroid nodules, but more measurements require confirming our preliminary results as that diffuse optical technology can complement the current techniques such as US and FNAB.

A new measurement campaign is being scheduled with a completed, fully integrated device that was developed within the LUCA project (http://www.luca-project.eu).

CERN Disk Storage Services: Report from last data taking, evolution and future outlook towards Exabyte-scale storage

The CERN IT Storage group operates multiple distributed storage systems to support all CERN data storage requirements: the physics data generated by LHC and non-LHC experiments; object and file storage for infrastructure services; block storage for the CERN cloud system; filesystems for general use and specialized HPC clusters; content distribution filesystem for software distribution and condition databases; and sync&share cloud storage for end-user files. The total integrated capacity of these systems exceeds 0.6 Exabyte.

Large-scale experiment data taking has been supported by EOS and CASTOR for the last 10+ years. Particular highlights for 2018 include the special HeavyIon run which was the last part of the LHC Run2 Programme: the IT storage systems sustained over 10GB/s to flawlessly collect and archive more than 13 PB of data in a single month. While the tape archival continues to be handled by CASTOR, the effort to migrate the current experiment workflows to the new CERN Tape Archive system (CTA) is underway.

Ceph infrastructure has operated for more than 5 years to provide block storage to CERN IT private OpenStack cloud, a shared filesystem (CephFS) to HPC clusters and NFS storage to replace commercial Filers. S3 service was introduced in 2018, following increased user requirements for S3-compatible object storage from physics experiments and IT use-cases.

Since its introduction in 2014N, CERNBox has become a ubiquitous cloud storage interface for all CERN user groups: physicists, engineers and administration. CERNBox provides easy access to multi-petabyte data stores from a multitude of mobile and desktop devices and all mainstream, modern operating systems (Linux, Windows, macOS, Android, iOS). CERNBox provides synchronized storage for end-user’s devices as well as easy sharing for individual users and e-groups. CERNBox has also become a storage platform to host online applications to process the data such as SWAN (Service for Web-based Analysis) as well as file editors such as Collabora Online, Only Office, Draw.IO and more. An increasing number of online applications in the Windows infrastructure uses CIFS/SMB access to CERNBox files.

CVMFS provides software repositories for all experiments across the WLCG infrastructure and has recently been optimized to efficiently handle nightlybuilds. While AFS continues to provide general-purpose filesystem for internal CERN users, especially as $HOME login area on central computing infrastructure, the migration of project and web spaces has significantly advanced.

In this paper, we report on the experiences from the last year of LHC RUN2 data taking and evolution of our services in the past year.. We will highlight upcoming changes and future improvements and challenges.

Evolution of the CERNBox platform to support the Malt project

CERNBox is the CERN cloud storage hub for more than 25,000 users at CERN. It allows synchronising and sharing files on all major desktop and mobile platforms (Linux, Windows, MacOSX, Android, iOS) providing universal, ubiquitous, online- and offline access to any data stored in the CERN EOS infrastructure. CERNBox also provides integration with other CERN services for big science: visualisation tools, interactive data analysis and real-time collaborative editing.

Over the last two years, CERNBox has evolved from a pure cloud sync and share platform into a collaborative service, to support new applications such as DrawIO for diagrams and organigrams sketching, OnlyOffice and Collabora Online for documents editing, and DXHTML Gantt for project management, as alternatives to traditional desktop applications. Moving to open source applications has the advantage to reduce licensing costs and enables easier integration within the CERN infrastructure. This move from commercial software to open source solutions is part of the MALT project, led by the IT department at CERN to reduce the dependencies on commercial solutions.

As part of the MALT project, CERNBox is the chosen solution to replace Home directories of the Windows DFS file system. Access to storage from Windows managed devices for end-users is largely covered by synchronization clients. However, online access using standard CIFS/SMB protocol is required for shared use-cases, such as central login services (Terminal Services) and visitor desktop computers. We present recent work to introduce a set of Samba gateways running in High Availability cluster mode to enable direct access to the CERNBox backend storage (EOS).

Systematic study of the effect of ultrasound gel on the performances of time-domain diffuse optics and diffuse correlation spectroscopy

Recently, multimodal imaging has gained an increasing interest in medical applications thanks to the inherent combination of strengths of the different techniques. For example, diffuse optics is used to probe both the composition and the microstructure of highly diffusive media down to a depth of few centimeters, but its spatial resolution is intrinsically low. On the other hand, ultrasound imaging exhibits the higher spatial resolution of morphological imaging, but without providing solid constitutional information. Thus, the combination of diffuse optical imaging and ultrasound may improve the effectiveness of medical examinations, e.g. for screening or diagnosis of tumors. However, the presence of an ultrasound coupling gel between probe and tissue can impair diffuse optical measurements like diffuse optical spectroscopy and diffuse correlation spectroscopy, since it may provide a direct path for photons between source and detector. A systematic study on the effect of different ultrasound coupling fluids was performed on tissue-mimicking phantoms, confirming that a water-clear gel can produce detrimental effects on optical measurements when recovering absorption/reduced scattering coefficients from time-domain spectroscopy acquisitions as well as particle Brownian diffusion coefficient from diffuse correlation spectroscopy ones. On the other hand, we show the suitability for optical measurements of other types of diffusive fluids, also compatible with ultrasound imaging.

Providing large-scale disk storage at CERN

The CERN IT Storage group operates multiple distributed storage systems and is responsible for the support of the infrastructure to accommodate all CERN storage requirements, from the physics data generated by LHC and non-LHC experiments to the personnel users' files.

EOS is now the key component of the CERN Storage strategy. It allows to operate at high incoming throughput for experiment data-taking while running concurrent complex production work-loads. This high-performance distributed storage provides now more than 250PB of raw disks and it is the key component behind the success of CERNBox, the CERN cloud synchronisation service which allows syncing and sharing files on all major mobile and desktop platforms to provide offline availability to any data stored in the EOS infrastructure. CERNBox recorded an exponential growth in the last couple of year in terms of files and data stored thanks to its increasing popularity inside CERN users community and thanks to its integration with a multitude of other CERN services (Batch, SWAN, Microsoft Office).

In parallel CASTOR is being simplified and transitioning from an HSM into an archival system, focusing mainly in the long-term data recording of the primary data from the detectors, preparing the road to the next-generation tape archival system, CTA.

The storage services at CERN cover as well the needs of the rest of our community: Ceph as data back-end for the CERN OpenStack infrastructure, NFS services and S3 functionality; AFS for legacy home directory filesystem services and its ongoing phase-out and CVMFS for software distribution. In this paper we will summarise our experience in supporting all our distributed storage system and the ongoing work in evolving our infrastructure, testing very-dense storage building block (nodes with more than 1PB of raw space) for the challenges waiting ahead.

CERNBox: the CERN cloud storage hub

CERNBox is the CERN cloud storage hub. It allows synchronizing and sharing files on all major desktop and mobile platforms (Linux, Windows, MacOSX, Android, iOS) aiming to provide universal access and offline availability to any data stored in the CERN EOS infrastructure. With more than 16000 users registered in the system, CERNBox has responded to the high demand in our diverse community to an easily and accessible cloud storage solution that also provides integration with other CERN services for big science: visualization tools, interactive data analysis and real-time collaborative editing. Collaborative authoring of documents is now becoming standard practice with public cloud services, and within CERNBox we are looking into several options: from the collaborative editing of shared office documents with different solutions (Microsoft, OnlyOffice, Collabora) to integrating mark-down as well as LaTeX editors, to exploring the evolution of Jupyter Notebooks towards collaborative editing, where the latter leverages on the existing SWAN Physics analysis service. We report on our experience managing this technology and applicable use-cases, also in a broader scientific and research context and its future evolution with highlights on the current development status and future road map. In particular we will highlight the future move to an architecture based on micro services to easily adapt and evolve the service to the technology and usage evolution, notably to unify CERN home directory services.

Liquid phantoms for near-infrared and diffuse correlation spectroscopies with tunable optical and dynamic properties

We present the recipe and characterization for preparing liquid phantoms that are suitable for both near-infrared spectroscopy and diffuse correlation spectroscopy. The phantoms have well-defined and tunable optical and dynamic properties, and consist of a solution of water and glycerol with fat emulsion as the scattering element. The recipe takes into account the effect of bulk refractive index changes due to the addition of glycerol, which is commonly used to alter the sample viscosity.

Assessment of DICOM Viewers Capable of Loading Patient-specific 3D Models Obtained by Different Segmentation Platforms in the Operating Room

Patient-specific 3D models obtained by the segmentation of volumetric diagnostic images play an increasingly important role in surgical planning. Surgeons use the virtual models reconstructed through segmentation to plan challenging surgeries. Many solutions exist for the different anatomical districts and surgical interventions. The possibility to bring the 3D virtual reconstructions with native radiological images in the operating room is essential for fostering the use of intraoperative planning. To the best of our knowledge, current DICOM viewers are not able to simultaneously connect to the picture archiving and communication system (PACS) and import 3D models generated by external platforms to allow a straight integration in the operating room. A total of 26 DICOM viewers were evaluated: 22 open source and four commercial. Two DICOM viewers can connect to PACS and import segmentations achieved by other applications: Synapse 3D® by Fujifilm and OsiriX by University of Geneva. We developed a software network that converts diffuse visual tool kit (VTK) format 3D model segmentations, obtained by any software platform, to a DICOM format that can be displayed using OsiriX or Synapse 3D. Both OsiriX and Synapse 3D were suitable for our purposes and had comparable performance. Although Synapse 3D loads native images and segmentations faster, the main benefits of OsiriX are its user-friendly loading of elaborated images and it being both free of charge and open source.

Laparoscopic Microwave Liver Ablation and Portal Vein Ligation: An Alternative Approach to the Conventional ALPPS Procedure in Hilar Cholangiocarcinoma

BACKGROUND

Associating liver partition and portal vein ligation for staged hepatectomy (ALPPS) is a new procedure aimed at promoting the overgrowth of small future liver remnants (FLR). The role of ALPPS in hilar cholangiocarcinoma (h-CCA) is currently considered marginal because liver split in the presence of bile duct obstruction increases postoperative morbidity and mortality (Schadde et al. in Ann Surg 260:829-836,2014; Nadalin et al. in Z Gastroenterol 52:35-42,2014). Virtual liver split (Gall et al. in Ann Surg 261:e45-e46,2015) could improve the outcome of ALPPS in h-CCA.

METHODS

A 64-year-old woman with a type IIIA h-CCA without evidence of vascular involvement had a small FLR (FLR/body weight: 0.47 cm³/kg). After bilateral percutaneous biliary drainage (PBD) and bilirubin normalization, the patient was planned for laparoscopic step 1 ALPPS using microwave ablation (MWA). Because of possible challenge in hilar dissection in this tumor type, robotic assistance was preferred to conventional laparoscopy for step 1.

RESULTS

The patient recovered promptly from step 1, with a 68 % increase in the volume of FLR by postoperative day (POD) 10 (FLR/body weight of 0.79 cm³/kg). On POD 15, the patient underwent open right hepatectomy with en bloc resection of the caudate lobe, bile duct bifurcation, and extrahepatic biliary duct (T2N1M0R0). Estimated blood loss was negligible during step 1 and 150 mL during step 2. The patient recovered well. Chemotherapy was started 6 weeks after ALPPS stage 2, and was well tolerated and full course. Twenty months after resection the patient is alive, well, and disease-free.

CONCLUSIONS

Laparoscopic ALPPS (Machado et al. in Ann Surg 256:e13,2012) and MWA on the intended split line (Gringeri and Boetto in Ann Surg 261:e42-e43,2015) have been recently described. The combination of these techniques with PBD allowed successful ALPPS in a patient with h-CCA.

Expression of proto-oncogene C-kit and correlation with morphological evaluations in canine cutaneous mast cell tumors

Canine cutaneous mast cell tumor (MCT) is very common disease in dogs, this is more aggressive than in other species. The biologic behavior of MCT is highly variable and a more accurate prognosis for these tumors needs to performed. The proto-oncogene c-kit is known to play a critical role in development and function of mast cells (MC). The aim of this study was to evaluate the expression of immunohistochemical pattern of c-kit in MCTs and to correlate these results with MC density (MCD) and intratumoral microvessel density (MVD). Our results confirm that a more aggressive biologic behavior of canine MCT is associated with the increased c-kit expression, further suggesting a new role for c-kit, as a useful marker, in diagnostic pathology and in tumor progression.