Treatment Outcomes and Toxicity Profile of MRI-Guided Gated-Real Time Online Adaptive Stereotactic Body Radiotherapy to Patients with Pancreatic Tumors

PURPOSE/OBJECTIVE(S)

Stereotactic body radiation therapy (SBRT) to patients with inoperable pancreas cancer has shown promising outcomes. Dose escalation is challenging given the associated risks to nearby organs at risk and requires treatment plan adaptation and motion management. This study reports the treatment related adverse events and treatment outcomes of MRI-guided SBRT utilizing gated-real time online adaptive radiotherapy to patients with pancreatic tumors.

MATERIALS/METHODS

This is a single institution retrospective IRB approved study and included patients with pancreatic tumors who were treated with MRI-guided SBRT utilizing gated-real time online adaptive radiotherapy, consecutively between 2019 and 2022. All patients were treated with 0.35T MRI linear accelerator. All patients' charts and radiation plans were reviewed for this study.

RESULTS

The study included 25 patients treated consecutively to 125 radiation fractions with MRI-guided SBRT. The study included 15 females and 10 males, 19 white, 2 Asians, 1 Latin American and 2 African Americans. The median age was 74, and all patients had pancreatic adenocarcinoma (92%) except two patients who had biopsy proven renal cell carcinoma metastatic to the pancreas without evidence of disease elsewhere. Most patients (68%) received chemotherapy (FOLFIRINOX or Gemcitabine / Protein-bound paclitaxel) prior to SBRT. The median dose to gross target volume (GTV) was 50 Gy, and to planning target volume (PTV) was 35 Gy. All patients were treated in 5 radiation fractions. Thirteen patients (52%) received elective nodal irradiation (ENI). All patients had at least a single real-time online adaptive replanning (median 3 fractions, range 1-5 fractions). All treatment fractions were gated (100%) with MRI guidance. The 1-, 2-, & 3- year local-regional control (LRC) were 81%, 57%, & 57% respectively (Median 16 months). The 1-, 2-, & 3- year Distant Control (DC) were 81%, 74%, & 56% respectively (Median 14 months). The 1-, 2-, 3-year overall survival (OS) were 77%, 35%, & 24% (Median 21 months). Planning Target Volume (PTV) dose ≥40Gy was significantly associated with improved local-regional control (p = 0.02). Gross Target Volume (GTV) dose <50Gy was significantly associated with lower DC (p = 0.03). ENI showed a trend towards improved local-regional control but was not statistically significant (p = 0.1). None of the patients experienced ≥ grade 3 toxicities. Most common adverse event were grades 1 or 2 fatigue (24%), nausea (16%), and abdominal discomfort (12%).

CONCLUSION

In this cohort, MRI-guided SBRT utilizing gated-real time online adaptive radiotherapy was a safe and effective approach for patients with pancreatic tumors who are not surgical candidates. In this study, dose escalation was significantly associated with improved local-regional (PTV ≥40 Gy) and distant control (GTV ≥50Gy). None of the patients experienced grade ≥3 radiation induced adverse events.

Context-aware deep network for coronary artery stenosis classification in coronary CT angiography

Automatic coronary artery stenosis grading plays an important role in the diagnosis of coronary artery disease. Due to the difficulty of learning the informative features from varying grades of stenosis, it is still a challenging task to identify coronary artery stenosis from coronary CT angiography (CCTA). In this paper, we propose a context-aware deep network (CADN) for coronary artery stenosis classification. The proposed method integrates 3D CNN with Transformer to improve the feature representation of coronary artery stenosis in CCTA. We evaluate the proposed method on a multicenter dataset (APOLLO study with NCT05509010). Experimental results show that our proposed method can achieve the accuracy of 0.84, 0.83, and 0.86 for stenosis diagnosis on the lesion, artery, and patient levels, respectively.

Multi-omic longitudinal study reveals immune correlates of clinical course among hospitalized COVID-19 patients

The IMPACC cohort, composed of >1,000 hospitalized COVID-19 participants, contains five illness trajectory groups (TGs) during acute infection (first 28 days), ranging from milder (TG1-3) to more severe disease course (TG4) and death (TG5). Here, we report deep immunophenotyping, profiling of >15,000 longitudinal blood and nasal samples from 540 participants of the IMPACC cohort, using 14 distinct assays. These unbiased analyses identify cellular and molecular signatures present within 72 h of hospital admission that distinguish moderate from severe and fatal COVID-19 disease. Importantly, cellular and molecular states also distinguish participants with more severe disease that recover or stabilize within 28 days from those that progress to fatal outcomes (TG4 vs. TG5). Furthermore, our longitudinal design reveals that these biologic states display distinct temporal patterns associated with clinical outcomes. Characterizing host immune responses in relation to heterogeneity in disease course may inform clinical prognosis and opportunities for intervention.

Single-cell RNA sequencing identifies distinct transcriptomic signatures between PMA/ionomycin- and αCD3/αCD28-activated primary human T cells

Immunologists have activated T cells in vitro using various stimulation methods, including phorbol myristate acetate (PMA)/ionomycin and αCD3/αCD28 agonistic antibodies. PMA stimulates protein kinase C, activating nuclear factor-κB, and ionomycin increases intracellular calcium levels, resulting in activation of nuclear factor of activated T cell. In contrast, αCD3/αCD28 agonistic antibodies activate T cells through ZAP-70, which phosphorylates linker for activation of T cell and SH2-domain-containing leukocyte protein of 76 kD. However, despite the use of these two different in vitro T cell activation methods for decades, the differential effects of chemical-based and antibody-based activation of primary human T cells have not yet been comprehensively described. Using single-cell RNA sequencing (scRNA-seq) technologies to analyze gene expression unbiasedly at the single-cell level, we compared the transcriptomic profiles of the non-physiological and physiological activation methods on human peripheral blood mononuclear cell-derived T cells from four independent donors. Remarkable transcriptomic differences in the expression of cytokines and their respective receptors were identified. We also identified activated CD4 T cell subsets (CD55+) enriched specifically by PMA/ionomycin activation. We believe this activated human T cell transcriptome atlas derived from two different activation methods will enhance our understanding, highlight the optimal use of these two in vitro T cell activation assays, and be applied as a reference standard when analyzing activated specific disease-originated T cells through scRNA-seq.

A coarse-grain reactive model of RDX: Molecular resolution at the μm scale

Predictive models for the thermal, chemical, and mechanical response of high explosives at extreme conditions are important for investigating their performance and safety. We introduce a particle-based, reactive model of 1,3,5-trinitro-1,3,5-triazinane (RDX) with molecular resolution utilizing generalized energy-conserving dissipative particle dynamics with reactions. The model is parameterized with respect to the data from atomistic molecular dynamics simulations as well as from quantum mechanical calculations, thus bridging atomic processes to the mesoscales, including microstructures and defects. It accurately captures the response of RDX under a range of thermal loading conditions compared to atomistic simulations. In addition, the Hugoniot response of the CG model in the overdriven regime reasonably matches atomistic simulations and experiments. Exploiting the model's high computational efficiency, we investigate mesoscale systems involving millions of molecules and characterize size-dependent criticality of hotspots in RDX. The combination of accuracy and computational efficiency of our reactive model provides a tool for investigation of mesoscale phenomena, such as the role of microstructures and defects in the shock-to-deflagration transition, through particle-based simulation.

Comprehensive Characterization of the Multiple Myeloma Immune Microenvironment Using Integrated scRNA-seq, CyTOF, and CITE-seq Analysis

As part of the Multiple Myeloma Research Foundation (MMRF) immune atlas pilot project, we compared immune cells of multiple myeloma bone marrow samples from 18 patients assessed by single-cell RNA sequencing (scRNA-seq), mass cytometry (CyTOF), and cellular indexing of transcriptomes and epitopes by sequencing (CITE-seq) to understand the concordance of measurements among single-cell techniques. Cell type abundances are relatively consistent across the three approaches, while variations are observed in T cells, macrophages, and monocytes. Concordance and correlation analysis of cell type marker gene expression across different modalities highlighted the importance of choosing cell type marker genes best suited to particular modalities. By integrating data from these three assays, we found International Staging System stage 3 patients exhibited decreased CD4+ T/CD8+ T cells ratio. Moreover, we observed upregulation of RAC2 and PSMB9, in natural killer cells of fast progressors compared with those of nonprogressors, as revealed by both scRNA-seq and CITE-seq RNA measurement. This detailed examination of the immune microenvironment in multiple myeloma using multiple single-cell technologies revealed markers associated with multiple myeloma rapid progression which will be further characterized by the full-scale immune atlas project.

Significance

scRNA-seq, CyTOF, and CITE-seq are increasingly used for evaluating cellular heterogeneity. Understanding their concordances is of great interest. To date, this study is the most comprehensive examination of the measurement of the immune microenvironment in multiple myeloma using the three techniques. Moreover, we identified markers predicted to be significantly associated with multiple myeloma rapid progression.

Retrospective Clinical Evaluation of a Decision-Support Software for Adaptive Radiotherapy of Head and Neck Cancer Patients

Purpose

This study aimed to evaluate the clinical need for an automated decision-support software platform for adaptive radiation therapy (ART) of head and neck cancer (HNC) patients.

Methods

We tested RTapp (SegAna), a new ART software platform for deciding when a treatment replan is needed, to investigate a set of 27 HNC patients’ data retrospectively. For each fraction, the software estimated key components of ART such as daily dose distribution and cumulative doses received by targets and organs at risk (OARs) from daily 3D imaging in real-time. RTapp also included a prediction algorithm that analyzed dosimetric parameter (DP) trends against user-specified thresholds to proactively trigger adaptive re-planning up to four fractions ahead. The DPs evaluated for ART were based on treatment planning dose constraints. Warning (V₉₅<95%) and adaptation (V₉₅<93%) thresholds were set for PTVs, while OAR adaptation dosimetric endpoints of +10% (DE₁₀) were set for all D_max and D_mean DPs. Any threshold violation at end of treatment (EOT) triggered a review of the DP trends to determine the threshold-crossing fraction Fx when the violations occurred. The prediction model accuracy was determined as the difference between calculated and predicted DP values with 95% confidence intervals (CI₉₅).

Results

RTapp was able to address the needs of treatment adaptation. Specifically, we identified 18/27 studies (67%) for violating PTV coverage or parotid D_mean at EOT. Twelve PTVs had V₉₅<95% (mean coverage decrease of −6.8 ± 2.9%) including six flagged for adaptation at median Fx= 6 (range, 1–16). Seventeen parotids were flagged for exceeding D_mean dose constraints with a median increase of +2.60 Gy (range, 0.99–6.31 Gy) at EOT, including nine with DP>DE₁₀. The differences between predicted and calculated PTV V₉₅ and parotid D_mean was up to 7.6% (mean ± CI₉₅, −2.7 ± 4.1%) and 5 Gy (mean ± CI₉₅, 0.3 ± 1.6 Gy), respectively. The most accurate predictions were obtained closest to the threshold-crossing fraction. For parotids, the results showed that Fx ranged between fractions 1 and 23, with a lack of specific trend demonstrating that the need for treatment adaptation may be verified for every fraction.

Conclusion

Integrated in an ART clinical workflow, RTapp aids in predicting whether specific treatment would require adaptation up to four fractions ahead of time.

Spatial CRISPR genomics identifies regulators of the tumor microenvironment

While CRISPR screens are helping uncover genes regulating many cell-intrinsic processes, existing approaches are suboptimal for identifying extracellular gene functions, particularly in the tissue context. Here, we developed an approach for spatial functional genomics called Perturb-map. We applied Perturb-map to knock out dozens of genes in parallel in a mouse model of lung cancer and simultaneously assessed how each knockout influenced tumor growth, histopathology, and immune composition. Moreover, we paired Perturb-map and spatial transcriptomics for unbiased analysis of CRISPR-edited tumors. We found that in Tgfbr2 knockout tumors, the tumor microenvironment (TME) was converted to a fibro-mucinous state, and T cells excluded, concomitant with upregulated TGFβ and TGFβ-mediated fibroblast activation, indicating that TGFβ-receptor loss on cancer cells increased TGFβ bioavailability and its immunosuppressive effects on the TME. These studies establish Perturb-map for functional genomics within the tissue at single-cell resolution with spatial architecture preserved and provide insight into how TGFβ responsiveness of cancer cells can affect the TME.

High-dimensional analysis defines multicytokine T-cell subsets and supports a role for IL-21 in atopic dermatitis

BACKGROUND

Flow cytometry is a well-accepted approach for immune profiling; however, its value is restricted by the limited number of markers that can be analyzed simultaneously. Mass cytometry/CyTOF offers broad-scale immune characterization integrating large number of parameters. While partial blood phenotyping was reported in atopic dermatitis (AD), patients' comprehensive profiling, critical for leveraging new targeted treatments, is not available. IL-21 may be involved in inflammatory skin diseases but its role in AD is not well established.

METHODS

We studied T-cell polarization in the blood of 20 moderate-to-severe AD and 15 controls. Using CyTOF and an unsupervised analysis, we measured the frequencies and mean metal intensities of activated polar CD4⁺ /CD8⁺ T-cell subsets. Immunohistochemistry, immunofluorescence, and qRT-PCR were used to analyze skin samples.

RESULTS

Examining 24 surface, intracellular markers, and transcription factors, we identified six CD4⁺ and five CD8⁺ T-cell metaclusters. A CD4⁺ skin-homing IL-13⁺ monocytokine and a novel IL-13⁺ IL-21⁺ multicytokine metaclusters were increased in AD vs. controls (p < .01). While IL-13 signature characterized both clusters, levels were significantly higher in the IL-21⁺ group. Both clusters correlated with AD severity (r = 0.49, p = .029). Manual gating corroborated these results and identified additional multicytokine subsets in AD. Immunohistochemistry and immunofluorescence, validated by mRNA expression, displayed significantly increasedIL-21 counts and colocalization with IL-13/IL-4R in AD skin.

CONCLUSION

A multicytokine signature characterizes moderate-to-severe AD, possibly explaining partial therapeutic responses to one cytokine targeting, particularly in severe patients. Prominent IL-21 signature in blood and skin hints for a potential pathogenic role of IL-21 in AD.

Immune Profiling Mass Cytometry Assay Harmonization: Multicenter Experience from CIMAC-CIDC

PURPOSE

The Cancer Immune Monitoring and Analysis Centers - Cancer Immunologic Data Commons (CIMAC-CIDC) Network is supported by the NCI to identify biomarkers of response to cancer immunotherapies across clinical trials using state-of-the-art assays. A primary platform for CIMAC-CIDC studies is cytometry by time of flight (CyTOF), performed at all CIMAC laboratories. To ensure the ability to generate comparable CyTOF data across labs, a multistep cross-site harmonization effort was undertaken.

EXPERIMENTAL DESIGN

We first harmonized standard operating procedures (SOPs) across the CIMAC sites. Because of a new acquisition protocol comparing original narrow- or new wide-bore injector introduced by the vendor (Fluidigm), we also tested this protocol across sites before finalizing the harmonized SOP. We then performed cross-site assay harmonization experiments using five shared cryopreserved and one lyophilized internal control peripheral blood mononuclear cell (PBMC) with a shared lyophilized antibody cocktail consisting of 14 isotype-tagged antibodies previously validated, plus additional liquid antibodies. These reagents and samples were distributed to the CIMAC sites and the data were centrally analyzed by manual gating and automated methods (Astrolabe).

RESULTS

Average coefficients of variation (CV) across sites for each cell population were reported and compared with a previous multisite CyTOF study. We reached an intersite CV of under 20% for most cell subsets, very similar to a previously published study.

CONCLUSIONS

These results establish the ability to reproduce CyTOF data across sites in multicenter clinical trials, and also highlight the importance of quality control procedures, such as the use of spike-in control samples, for tracking variability in this assay.

Association between mortality risk and the number, location, and sequence of subsequent fractures in the elderly

The mortality risk showed a positive correlation as the number of subsequent fractures increased. Hip fracture showed the greatest association with mortality risk, followed by vertebral fracture. For the combination of hip and vertebral fracture, a hip fracture after a vertebral fracture showed the highest mortality risk.

INTRODUCTION

It is unclear whether subsequent fractures or a certain location and sequence of subsequent fractures are associated with mortality risk in the elderly. We aimed to investigate the relationship between subsequent fractures and mortality risk.

METHODS

Using the Korean National Health Insurance Research Database, we analyzed the cohort data of 24,756 patients aged > 60 years who sustained fractures between 2002 and 2013. Cox regression was used to assess the mortality risk associated with the number, locations, and sequences of subsequent fractures.

RESULTS

Mortality hazard ratios (HRs) for women and men were shown to be associated with the number of subsequent fractures (one, 1.63 (95% confidence interval [CI], 1.48-1.80) and 1.42 (95% CI, 1.28-1.58); two, 1.75 (95% CI, 1.47-2.08) and 2.03 (95% CI, 1.69-2.43); three or more, 2.46(95% CI, 1.92-3.15) and 1.92 (95% CI, 1.34-2.74), respectively). For women, the mortality risk was high when hip (HR, 2.49; 95% CI, 1.80-3.44) or vertebral (HR, 1.40; 95% CI, 1.03-1.90) fracture occurred as a second fracture. Compared with a single hip fracture, there was a high mortality risk in the group with hip fracture after the first vertebral fracture (HR, 2.90; 95% CI, 1.86-4.54), followed by vertebral fracture after the first hip fracture (HR, 1.90; 95% CI, 1.12-3.22).

CONCLUSION

The mortality risk showed a positive correlation as the number of subsequent fractures increased. Hip fracture showed the greatest association with mortality risk, followed by vertebral fracture. For the combination of hip and vertebral fracture, a hip fracture after a vertebral fracture showed the highest mortality risk.

The Clinical Utility of MRI in Evaluating for Osteomyelitis in Patients Presenting with Uncomplicated Cellulitis

Magnetic resonance imaging (MRI) is vital in the diagnosis of osteomyelitis (OM) in patients presenting with cellulitis. Typically, cellulitis is treated with oral antibiotics; however, patients with concomitant OM may require long-term intravenous antibiotics or surgical intervention. We reviewed lower extremity MRIs in patients presenting with cellulitis and clinical concern for OM. We found 488 patient examinations spanning 5 years (2011 to 2016); 47 patients were excluded (final N = 441). Each MRI was interpreted by a radiologist to determine the rate of OM, abscess, ulceration, and imaging diagnosis of cellulitis. Concurrent assessment of the electronic medical record was performed to review patient demographics, the presence of abscess and/or ulceration, and comorbidities such as diabetes, hyperlipidemia (HLD), atherosclerotic disease, and peripheral vascular disease. Of the 441 lower extremity MRIs included, 170 (39%) were diagnosed with OM, 236 (54%) had ulcers, and 66 (15%) had abscesses. Age, laterality, and reporting physician were not statistically significant independent variables in the rate of reported OM. Diabetes and HLD/atherosclerotic disease were both statistically significant variables with regard to OM rates. Clinical documentation and MRI diagnosis of ulceration were both statistically significant variables in the rate of OM. Regression analysis determined that body part, ulceration, HLD/atherosclerosis, and sex were independent predictors of OM. In our study, of the population of patients with a high clinical suspicion for OM, 39% had OM diagnosed on MRI. However, the incidence of OM in uncomplicated cellulitis was only 11.8% compared with 43.9% in complicated cellulitis. When considering the forefoot alone, patients with ulceration at MRI were 5.6 times more likely to have underlying OM than those without.

A simple dosimetric approach to spatially fractionated GRID radiation therapy using the multileaf collimator for treatment of breast cancers in the prone position

The purpose of this study was to explore the treatment planning methods of spatially fractionated radiation therapy (SFRT), commonly referred to as GRID therapy, in the treatment of breast cancer patients using multileaf collimator (MLC) in the prone position. A total of 12 patients with either left or right breast cancer were retrospectively chosen. The computed tomography (CT) images taken for the whole breast external beam radiation therapy (WB‐EBRT) were used for GRID therapy planning. Each GRID plan was made by using two portals and each portal had two fields with 1‐cm aperture size. The dose prescription point was placed at the center of the target volume, and a dose of 20 Gy with 6‐MV beams was prescribed. Dose‐volume histogram (DVH) curves were generated to evaluate dosimetric properties. A modified linear‐quadratic (MLQ) radiobiological response model was used to assess the equivalent uniform doses (EUD) and therapeutic ratios (TRs) of all GRID plans. The DVH curves indicated that these MLC‐based GRID therapy plans can deliver heterogeneous dose distribution in the target volume as seen with the conventional cerrobend GRID block. The plans generated by the MLC technique also demonstrated the advantage for accommodating different target shapes, sparing normal structures, and reporting dose metrics to the targets and the organs at risks. All GRID plans showed to have similar dosimetric parameters, implying the plans can be made in a consistent quality regardless of the shape of the target and the size of volume. The mean dose of lung and heart were respectively below 0.6 and 0.7 Gy. When the size of aperture is increased from 1 to 2 cm, the EUD and TR became smaller, but the peak/valley dose ratio (PVDR) became greater. The dosimetric approach of this study was proven to be simple, practical and easy to be implemented in clinic.

Dosimetric feasibility of brain stereotactic radiosurgery with a 0.35 T MRI-guided linac and comparison vs a C-arm-mounted linac

PURPOSE

MRI is the gold-standard imaging modality for brain tumor diagnosis and delineation. The purpose of this work was to investigate the feasibility of performing brain stereotactic radiosurgery (SRS) with a 0.35 T MRI-guided linear accelerator (MRL) equipped with a double-focused multileaf collimator (MLC). Dosimetric comparisons were made vs a conventional C-arm-mounted linac with a high-definition MLC.

METHODS

The quality of MRL single-isocenter brain SRS treatment plans was evaluated as a function of target size for a series of spherical targets with diameters from 0.6 cm to 2.5 cm in an anthropomorphic head phantom and six brain metastases (max linear dimension = 0.7-1.9 cm) previously treated at our clinic on a conventional linac. Each target was prescribed 20 Gy to 99% of the target volume. Step-and-shoot IMRT plans were generated for the MRL using 11 static coplanar beams equally spaced over 360° about an isocenter placed at the center of the target. Couch and collimator angles are fixed for the MRL. Two MRL planning strategies (VR1 and VR2) were investigated. VR1 minimized the 12 Gy isodose volume while constraining the maximum point dose to be within ±1 Gy of 25 Gy which corresponded to normalization to an 80% isodose volume. VR2 minimized the 12 Gy isodose volume without the maximum dose constraint. For the conventional linac, the TB1 method followed the same strategy as VR1 while TB2 used five noncoplanar dynamic conformal arcs. Plan quality was evaluated in terms of conformity index (CI), conformity/gradient index (CGI), homogeneity index (HI), and volume of normal brain receiving ≥12 Gy (V_12Gy ). Quality assurance measurements were performed with Gafchromic EBT-XD film following an absolute dose calibration protocol.

RESULTS

For the phantom study, the CI of MRL plans was not significantly different compared to a conventional linac (P > 0.05). The use of dynamic conformal arcs and noncoplanar beams with a conventional linac spared significantly more normal brain (P = 0.027) and maximized the CGI, as expected. The mean CGI was 95.9 ± 4.5 for TB2 vs 86.6 ± 3.7 (VR1), 88.2 ± 4.8 (VR2), and 88.5 ± 5.9 (TB1). Each method satisfied a normal brain V_12Gy  ≤ 10.0 cm³ planning goal for targets with diameter ≤2.25 cm. The mean V_12Gy was 3.1 cm³ for TB2 vs 5.5 cm³ , 5.0 cm³ and 4.3 cm³ , for VR1, VR2, and TB1, respectively. For a 2.5-cm diameter target, only TB2 met the V_12Gy planning objective. The MRL clinical brain plans were deemed acceptable for patient treatment. The normal brain V_12Gy was ≤6.0 cm³ for all clinical targets (maximum target volume = 3.51 cm³ ). CI and CGI ranged from 1.12-1.65 and 81.2-88.3, respectively. Gamma analysis pass rates (3%/1mm criteria) exceeded 97.6% for six clinical targets planned and delivered on the MRL. The mean measured vs computed absolute dose difference was -0.1%.

CONCLUSIONS

The MRL system can produce clinically acceptable brain SRS plans for spherical lesions with diameter ≤2.25 cm. Large lesions (>2.25 cm) should be treated with a linac capable of delivering noncoplanar beams.

Leukocyte-dependent effects of platelet-rich plasma on cartilage loss and thermal hyperalgesia in a mouse model of post-traumatic osteoarthritis

OBJECTIVE

Platelet-rich plasma (PRP) is an emerging therapeutic strategy for treatment of osteoarthritis (OA); however, there is a lack of preclinical and clinical evidence for its efficacy and its mechanism of action is unclear. In the current study, we utilized leukocyte poor-PRP (LP-PRP) and leukocyte rich-PRP (LR-PRP) to mimic clinical point of care formulations and assessed their potential to alter disease progression in a mouse model of post-traumatic OA.

METHOD

Three-month-old wild-type male FVB/N mice received destabilization of the medial meniscus (DMM) surgery to induce OA. To assess the efficacy of LP-PRP and LR-PRP, mice were given intraarticular injections at 2-, 7- and 28-days post-surgery. Mice were then assessed at 5-, 9-, and 13-weeks post-surgery for changes in chronic pain using the hot plate nociceptive assay. At 14-weeks, OA pathogenesis was evaluated using histology and phase-contrast μCT.

RESULTS

Treatment with LP-PRP and to a lesser extent LR-PRP preserved cartilage volume and surface area compared to phosphate-buffered saline (PBS) as measured by phase-contrast μCT. However, both treatments had higher Osteoarthritis Research Society International (OARSI) and synovitis scores compared to sham, and neither substantially improved scores compared to PBS controls. With respect to thermal hyperalgesia, PBS-treated mice displayed reduced latency to response compared to sham, and LR-PRP but not LP-PRP improved latency to response at 5-, 9- and 13-weeks post-surgery compared to PBS.

CONCLUSION

The results of this study suggest that effects of PRP therapy on OA progression and disease-induced hyperalgesia may be leukocyte-dependent. And while LP-PRP and to a lesser extent LR-PRP protect from volume and surface loss, significant pathology is still seen within OA joints. Future work is needed to understand how the different components of PRP effect OA pathogenesis and pain, and how these could be modified to achieve greater therapeutic efficacy.

Accessory Tragus: A Rare Congenital Anomaly in a Dog

Accessory tragus is a congenital malformation of part of the external ear, commonly reported in humans. Clinically, it is a benign, cutaneous mass located anywhere between the tragus of the ear and the angle of the mouth, along the migratory path of the first branchial arch. An accessory tragus was diagnosed in an otherwise healthy six-month-old male castrated American pit bull terrier that had a haired, pedunculated cutaneous mass on the left maxillary region from birth. Histologically, the mass was a polypoid extension of histologically normal haired skin with a central core of subcutaneous adipose tissue and well-differentiated elastic cartilage. To the authors' knowledge, this is the first report of this lesion in a non-human species. Retrospective examination of records from 2008 to 2018 at the Washington Animal Disease Diagnostic Laboratory failed to identify any other case. As accessory tragus in humans is commonly linked with other congenital anomalies and syndromes, recognition of this lesion in animals may aid in early discovery of other congenital defects and inform adequate excision of the lesion to prevent chondrodermatitis.

Clinical implementation, logistics and workflow guide for MRI image based interstitial HDR brachytherapy for gynecological cancers

Interstitial brachytherapy (IBT) is often utilized to treat women with bulky endometrial or cervical cancers not amendable to intracavitary treatments. A modern trend in IBT is the utilization of magnetic resonance imaging (MRI) with a high dose rate (HDR) afterloader for conformal 3D image-based treatments. The challenging part of this procedure is to properly complete many sequenced and co-related physics preparations. We presented the physics preparations and clinical workflow required for implementing MRI-based HDR IBT (MRI-HDR-IBT) of gynecologic cancer patients in a high-volume brachytherapy center. The present document is designed to focus on the clinical steps required from a physicist's standpoint. Those steps include: (a) testing IBT equipment with MRI scanner, (b) preparation of templates and catheters, (c) preparation of MRI line markers, (d) acquisition, importation and registration of MRI images, (e) development of treatment plans and (f) treatment evaluation and documentation. The checklists of imaging acquisition, registration and plan development are also presented. Based on the TG-100 recommendations, a workflow chart, a fault tree analysis and an error-solution table listing the speculated errors and solutions of each step are provided. Our workflow and practice indicated the MRI-HDR-IBT is achievable in most radiation oncology clinics if the following equipment is available: MRI scanner, CT (computed tomography) scanner, MRI/CT compatible templates and applicators, MRI line markers, HDR afterloader and a brachytherapy treatment planning system capable of utilizing MRI images. The OR/procedure room availability and anesthesiology support are also important. The techniques and approaches adopted from the GEC-ESTRO (Groupe Européen de Curiethérapie - European Society for Therapeutic Radiology and Oncology) recommendations and other publications are proven to be feasible. The MRI-HDR-IBT program can be developed over time and progressively validated through clinical experience, this document is expected to serve as a reference workflow guideline for implementing and performing the procedure.

Effect of Scapular Stabilization Exercise during Standing on Upper Limb Function and Gait Ability of Stroke Patients

Background

The purpose of this study was to determine the effect of scapular stabilization exercise during standing on a paretic side on upper limb function and gait ability of stroke patients.

Methods

This study was a hospital-based, randomized controlled trial with a blinded assessor. A total of 17 patients with hemiplegic diagnosis after stroke were divided into two groups (9 patients in a study group and 8 patients in a control group). The study group received physical therapy and scapular stabilization exercise on a paretic side. Participants were subjected to initial evaluation before the treatment. Subjects were subsequently re-evaluated 4 and 8 weeks later to compare the changes. Measurements of hand function and gait ability were performed.

Results

Based on multivariate analysis of variance for repeated-measures, there was a significant time effect for Timed Up and Go test (TUG) (F = 13.816, P = 0.000), Functional Gait Assessment (FGA) (F = 18.613, P = 0.000), and manual function test (MFT) (F = 16.777, P = 0.000). The group × time interaction effect was also significant for FGA (F = 4.966, P = 0.024) and MFT (F = 6.946, P = 0.003), but not for TUG test (F = 3.343, P = 0.069).

Conclusion

Results of the present study indicated that scapular stabilization exercise during standing on a paretic side for 8 weeks had an effect on hand function and gait ability of hemiplegic patients after stroke. Further studies are needed to find the most proper exercise for stroke patients who have gait disability and upper limb dysfunction.

A Modified Injector and Sample Acquisition Protocol Can Improve Data Quality and Reduce Inter-Instrument Variability of the Helios Mass Cytometer

Mass cytometry is a powerful tool for high-dimensional single cell characterization. Since the introduction of the first commercial CyTOF mass cytometer by DVS Sciences in 2009, mass cytometry technology has matured and become more widely utilized, with sequential platform upgrades designed to address specific limitations and to expand the capabilities of the platform. Fluidigm's third-generation Helios mass cytometer introduced a number of upgrades over the previous CyTOF2. One of these new features is a modified narrow bore sample injector that generates smaller ion clouds, which is expected to improve sensitivity and throughput. However, following rigorous testing, we find that the narrow-bore sample injector may have unintended negative consequences on data quality and result in lower median and higher coefficients of variation in many antibody-associated signal intensities. We describe an alternative Helios acquisition protocol using a wider bore injector, which largely mitigates these data quality issues. We directly compare these two protocols in a multisite study of 10 Helios instruments across 7 institutions and show that the modified protocol improves data quality and reduces interinstrument variability. These findings highlight and address an important source of technical variability in mass cytometry experiments that is of particular relevance in the setting of multicenter studies. © 2019 International Society for Advancement of Cytometry.

BAFF-driven B cell hyperplasia underlies lung disease in common variable immunodeficiency

BACKGROUND

Common variable immunodeficiency (CVID) is the most common symptomatic primary immunodeficiency and is frequently complicated by interstitial lung disease (ILD) for which etiology is unknown and therapy inadequate.

METHODS

Medical record review implicated B cell dysregulation in CVID ILD progression. This was further studied in blood and lung samples using culture, cytometry, ELISA, and histology. Eleven CVID ILD patients were treated with rituximab and followed for 18 months.

RESULTS

Serum IgM increased in conjunction with ILD progression, a finding that reflected the extent of IgM production within B cell follicles in lung parenchyma. Targeting these pulmonary B cell follicles with rituximab ameliorated CVID ILD, but disease recurred in association with IgM elevation. Searching for a stimulus of this pulmonary B cell hyperplasia, we found B cell-activating factor (BAFF) increased in blood and lungs of progressive and post-rituximab CVID ILD patients and detected elevation of BAFF-producing monocytes in progressive ILD. This elevated BAFF interacts with naive B cells, as they are the predominant subset in progressive CVID ILD, expressing BAFF receptor (BAFF-R) within pulmonary B cell follicles and blood to promote Bcl-2 expression. Antiapoptotic Bcl-2 was linked with exclusion of apoptosis from B cell follicles in CVID ILD and increased survival of naive CVID B cells cultured with BAFF.

CONCLUSION

CVID ILD is driven by pulmonary B cell hyperplasia that is reflected by serum IgM elevation, ameliorated by rituximab, and bolstered by elevated BAFF-mediated apoptosis resistance via BAFF-R.

FUNDING

NIH, Primary Immune Deficiency Treatment Consortium, and Rare Disease Foundation.

Acquisition, Processing, and Quality Control of Mass Cytometry Data

Mass cytometry uniquely combines the principles of mass spectrometry and flow cytometry for high dimensional profiling of immune cells at a single cell level. Using isotopically conjugated antibodies, mass cytometry overcomes the limitations of spectral overlap associated with flow cytometry and allows for deeper single cell characterization of complex biospecimens using more cellular markers. However, the nature of mass spectrometry-based single cell measurements requires specific considerations in acquiring and processing data. This chapter provides an overview of how to optimally acquire mass cytometry data and how to process this data for subsequent analysis and characterization of cell populations.

Acquisition, Processing, and Quality Control of Mass Cytometry Data

Mass cytometry uniquely combines the principles of mass spectrometry and flow cytometry for high dimensional profiling of immune cells at a single cell level. Using isotopically conjugated antibodies, mass cytometry overcomes the limitations of spectral overlap associated with flow cytometry and allows for deeper single cell characterization of complex biospecimens using more cellular markers. However, the nature of mass spectrometry-based single cell measurements requires specific considerations in acquiring and processing data. This chapter provides an overview of how to optimally acquire mass cytometry data and how to process this data for subsequent analysis and characterization of cell populations.

Increasing G9a automethylation sensitizes B acute lymphoblastic leukemia cells to glucocorticoid-induced death

Synthetic glucocorticoids (GCs) are used to treat lymphoid cancers, but many patients develop resistance to treatment, especially to GC. By identifying genes that influence sensitivity to GC-induced cell death, we found that histone methyltransferases G9a and G9a-like protein (GLP), two glucocorticoid receptor (GR) coactivators, are required for GC-induced cell death in acute lymphoblastic leukemia (B-ALL) cell line Nalm6. We previously established in a few selected genes that automethylated G9a and GLP recruit heterochromatin protein 1γ (HP1γ) as another required coactivator. Here, we used a genome-wide analysis to show that HP1γ is selectively required for GC-regulated expression of the great majority of GR target genes that require G9a and GLP. To further address the importance of G9a and GLP methylation in this process and in cell physiology, we found that JIB-04, a selective JmjC family lysine demethylase inhibitor, increased G9a methylation and thereby increased G9a binding to HP1γ. This led to increased expression of GR target genes regulated by G9a, GLP and HP1γ and enhanced Nalm6 cell death. Finally, the KDM4 lysine demethylase subfamily demethylates G9a in vitro, in contrast to other KDM enzymes tested. Thus, inhibiting G9a/GLP demethylation potentially represents a novel method to restore sensitivity of treatment-resistant B-ALL tumors to GC-induced cell death.

Different chromatin and DNA sequence characteristics define glucocorticoid receptor binding sites that are blocked or not blocked by coregulator Hic-5

The glucocorticoid receptor (GR) regulates genes in many physiological pathways by binding to enhancer and silencer elements of target genes, where it recruits coregulator proteins that remodel chromatin and regulate the assembly of transcription complexes. The coregulator Hydrogen peroxide-inducible clone 5 (Hic-5) is necessary for glucocorticoid (GC) regulation of one group of GR target genes, is irrelevant for a second group, and inhibits GR binding to a third gene set, thereby blocking their regulation by GC. Gene-specific characteristics that distinguish GR binding regions (GBR) at Hic-5 blocked genes from GBR at other GC-regulated genes are unknown. Here we show genome-wide that blocked GBR generally require CHD9 and BRM for GR occupancy in contrast to GBR that are not blocked by Hic-5. Hic-5 blocked GBR are enriched near Hic-5 blocked GR target genes but not near GR target genes that are not blocked by Hic-5. Furthermore blocked GBR are in a closed conformation prior to Hic-5 depletion, and require Hic-5 depletion and glucocorticoid treatment to create an open conformation necessary for GR occupancy. A transcription factor binding motif characteristic of the ETS family was enriched near blocked GBR and blocked genes but not near non-blocked GBR or non-blocked GR target genes. Thus, we identify specific differences in chromatin conformation, chromatin remodeler requirements, and local DNA sequence motifs that contribute to gene-specific actions of transcription factors and coregulators. These findings shed light on mechanisms that contribute to binding site selection by transcription factors, which vary in a cell type-specific manner.

Surgical Fixation of a Comminuted Inter-Trochanteric Fracture in a Patient with Bilateral Below Knee Amputation

Surgical fixation of hip fractures in patients with below knee amputation is challenging due to the difficulty in obtaining optimal traction for reduction of the fracture. Surgeons may face difficulty in positioning such patients on the traction table due to the absence of the foot and distal lower limb. There are several techniques described to overcome this technical difficulty. In this case report, we present a case of a 64-year old gentleman with bilateral below knee amputation presenting with a comminuted right intertrochanteric fracture. We highlight a simple and effective method of applying skin traction to obtain adequate reduction for hip fracture fixation.

Randomized clinical trial of antibiotic therapy for uncomplicated appendicitis

Background

Uncomplicated appendicitis may resolve spontaneously or require treatment with antibiotics or appendicectomy. The aim of this randomized trial was to compare the outcome of a non-antibiotic management strategy with that of antibiotic therapy in uncomplicated appendicitis.

Methods

Patients presenting to a university teaching hospital with CT-verified uncomplicated simple appendicitis (appendiceal diameter no larger than 11 mm and without any signs of perforation) were randomized to management with a no-antibiotic regimen with supportive care (intravenous fluids, analgesia and antipyretics as necessary) or a 4-day course of antibiotics with supportive care. The primary endpoint was rate of total treatment failure, defined as initial treatment failure within 1 month and recurrence of appendicitis during the follow-up period.

Results

Some 245 patients were randomized within the trial, and followed up for a median of 19 months. The duration of hospital stay was shorter (mean 3·1 versus 3·7 days; P &lt; 0·001) and the medical costs lower (€1181 versus 1348; P &lt; 0·001) among those randomized to therapy without antibiotics. There was no difference in total treatment failure rate between the groups: 29 of 124 (23·4 per cent) in the no-antibiotic group and 25 of 121 (20·7 per cent) in the antibiotic group (P = 0·609). Eighteen patients (9 in each group) had initial treatment failure, 15 of whom underwent appendicectomy and three received additional antibiotics. Thirty-six patients (20 in the no-antibiotic group, 16 in the antibiotic group) experienced recurrence, of whom 30 underwent appendicectomy and six received further antibiotics.

Conclusion

Treatment failure rates in patients presenting with CT-confirmed uncomplicated appendicitis appeared similar among those receiving supportive care with either a no-antibiotic regimen or a 4-day course of antibiotics. Registration number: KCT0000124 (http://cris.nih.go.kr).

Glucocorticoid receptor binding to chromatin is selectively controlled by the coregulator Hic-5 and chromatin remodeling enzymes

The steroid hormone-activated glucocorticoid receptor (GR) regulates cellular stress pathways by binding to genomic regulatory elements of target genes and recruiting coregulator proteins to remodel chromatin and regulate transcription complex assembly. The coregulator hydrogen peroxide-inducible clone 5 (Hic-5) is required for glucocorticoid (GC) regulation of some genes but not others and blocks the regulation of a third gene set by inhibiting GR binding. How Hic-5 exerts these gene-specific effects and specifically how it blocks GR binding to some genes but not others is unclear. Here we show that site-specific blocking of GR binding is due to gene-specific requirements for ATP-dependent chromatin remodeling enzymes. By depletion of 11 different chromatin remodelers, we found that ATPases chromodomain helicase DNA-binding protein 9 (CHD9) and Brahma homologue (BRM, a product of the SMARCA2 gene) are required for GC-regulated expression of the blocked genes but not for other GC-regulated genes. Furthermore, CHD9 and BRM were required for GR occupancy and chromatin remodeling at GR-binding regions associated with blocked genes but not at GR-binding regions associated with other GC-regulated genes. Hic-5 selectively inhibits GR interaction with CHD9 and BRM, thereby blocking chromatin remodeling and robust GR binding at GR-binding sites associated with blocked genes. Thus, Hic-5 regulates GR binding site selection by a novel mechanism, exploiting gene-specific requirements for chromatin remodeling enzymes to selectively influence DNA occupancy and gene regulation by a transcription factor.

Ligand-binding domains of nuclear receptors facilitate tight control of split CRISPR activity

Cas9-based RNA-guided nuclease (RGN) has emerged to be a versatile method for genome editing due to the ease of construction of RGN reagents to target specific genomic sequences. The ability to control the activity of Cas9 with a high temporal resolution will facilitate tight regulation of genome editing processes for studying the dynamics of transcriptional regulation or epigenetic modifications in complex biological systems. Here we show that fusing ligand-binding domains of nuclear receptors to split Cas9 protein fragments can provide chemical control over split Cas9 activity. The method has allowed us to control Cas9 activity in a tunable manner with no significant background, which has been challenging for other inducible Cas9 constructs. We anticipate that our design will provide opportunities through the use of different ligand-binding domains to enable multiplexed genome regulation of endogenous genes in distinct loci through simultaneous chemical regulation of orthogonal Cas9 variants.

Targeting 6-phosphogluconate dehydrogenase in the oxidative PPP sensitizes leukemia cells to antimalarial agent dihydroartemisinin

The oxidative pentose phosphate pathway (PPP) is crucial for cancer cell metabolism and tumor growth. We recently reported that targeting a key oxidative PPP enzyme, 6-phosphogluconate dehydrogenase (6PGD), using our novel small molecule 6PGD inhibitors Physcion and its derivative S3, shows anti-cancer effects. Notably, humans with genetic deficiency of either 6PGD or another oxidative PPP enzyme, glucose-6-phosphate dehydrogenase (G6PD), exhibit non-immune hemolytic anemia upon exposure to aspirin and various anti-malarial drugs. Inspired by these clinical observations, we examined the anti-cancer potential of combined treatment with 6PGD inhibitors and anti-malarial drugs. We found that stable knockdown of 6PGD sensitizes leukemia cells to anti-malarial agent dihydroartemisinin (DHA). Combined treatment with DHA and Physcion activates AMP-activated protein kinase, leading to synergistic inhibition of human leukemia cell viability. Moreover, our combined therapy synergistically attenuates tumor growth in xenograft nude mice injected with human K562 leukemia cells and cell viability of primary leukemia cells from human patients, but shows minimal toxicity to normal hematopoietic cells in mice as well as red blood cells and mononucleocytes from healthy human donors. Our findings reveal the potential for combined therapy using optimized doses of Physcion and DHA as a novel anti-leukemia treatment without inducing hemolysis.

Molecular Composition and Volatility of Organic Aerosol in the Southeastern U.S.: Implications for IEPOX Derived SOA

We present measurements as part of the Southern Oxidant and Aerosol Study (SOAS) during which atmospheric aerosol particles were comprehensively characterized. We present results utilizing a Filter Inlet for Gases and AEROsol coupled to a chemical ionization mass spectrometer (CIMS). We focus on the volatility and composition of isoprene derived organic aerosol tracers and of the bulk organic aerosol. By utilizing the online volatility and molecular composition information provided by the FIGAERO-CIMS, we show that the vast majority of commonly reported molecular tracers of isoprene epoxydiol (IEPOX) derived secondary organic aerosol (SOA) is derived from thermal decomposition of accretion products or other low volatility organics having effective saturation vapor concentrations <10(-3) μg m(-3). In addition, while accounting for up to 30% of total submicrometer organic aerosol mass, the IEPOX-derived SOA has a higher volatility than the remaining bulk. That IEPOX-SOA, and more generally bulk organic aerosol in the Southeastern U.S. is comprised of effectively nonvolatile material has important implications for modeling SOA derived from isoprene, and for mechanistic interpretations of molecular tracer measurements. Our results show that partitioning theory performs well for 2-methyltetrols, once accretion product decomposition is taken into account. No significant partitioning delays due to aerosol phase or viscosity are observed, and no partitioning to particle-phase water or other unexplained mechanisms are needed to explain our results.

Formaldehyde production from isoprene oxidation across NOx regimes

The chemical link between isoprene and formaldehyde (HCHO) is a strong, non-linear function of NO_x (= NO + NO₂). This relationship is a linchpin for top-down isoprene emission inventory verification from orbital HCHO column observations. It is also a benchmark for overall photochemical mechanism performance with regard to VOC oxidation. Using a comprehensive suite of airborne in situ observations over the Southeast U.S., we quantify HCHO production across the urban-rural spectrum. Analysis of isoprene and its major first-generation oxidation products allows us to define both a "prompt" yield of HCHO (molecules of HCHO produced per molecule of freshly-emitted isoprene) and the background HCHO mixing ratio (from oxidation of longer-lived hydrocarbons). Over the range of observed NO_x values (roughly 0.1 - 2 ppbv), the prompt yield increases by a factor of 3 (from 0.3 to 0.9 ppbv ppbv^-1), while background HCHO increases by a factor of 2 (from 1.6 to 3.3 ppbv). We apply the same method to evaluate the performance of both a global chemical transport model (AM3) and a measurement-constrained 0-D steady state box model. Both models reproduce the NO_x dependence of the prompt HCHO yield, illustrating that models with updated isoprene oxidation mechanisms can adequately capture the link between HCHO and recent isoprene emissions. On the other hand, both models under-estimate background HCHO mixing ratios, suggesting missing HCHO precursors, inadequate representation of later-generation isoprene degradation and/or under-estimated hydroxyl radical concentrations. Detailed process rates from the box model simulation demonstrate a 3-fold increase in HCHO production across the range of observed NO_x values, driven by a 100% increase in OH and a 40% increase in branching of organic peroxy radical reactions to produce HCHO.

Instrumentation and Measurement Strategy for the NOAA SENEX Aircraft Campaign as Part of the Southeast Atmosphere Study 2013

Natural emissions of ozone-and-aerosol-precursor gases such as isoprene and monoterpenes are high in the southeast of the US. In addition, anthropogenic emissions are significant in the Southeast US and summertime photochemistry is rapid. The NOAA-led SENEX (Southeast Nexus) aircraft campaign was one of the major components of the Southeast Atmosphere Study (SAS) and was focused on studying the interactions between biogenic and anthropogenic emissions to form secondary pollutants. During SENEX, the NOAA WP-3D aircraft conducted 20 research flights between 27 May and 10 July 2013 based out of Smyrna, TN. Here we describe the experimental approach, the science goals and early results of the NOAA SENEX campaign. The aircraft, its capabilities and standard measurements are described. The instrument payload is summarized including detection limits, accuracy, precision and time resolutions for all gas-and-aerosol phase instruments. The inter-comparisons of compounds measured with multiple instruments on the NOAA WP-3D are presented and were all within the stated uncertainties, except two of the three NO₂ measurements. The SENEX flights included day- and nighttime flights in the Southeast as well as flights over areas with intense shale gas extraction (Marcellus, Fayetteville and Haynesville shale). We present one example flight on 16 June 2013, which was a daytime flight over the Atlanta region, where several crosswind transects of plumes from the city and nearby point sources, such as power plants, paper mills and landfills, were flown. The area around Atlanta has large biogenic isoprene emissions, which provided an excellent case for studying the interactions between biogenic and anthropogenic emissions. In this example flight, chemistry in and outside the Atlanta plumes was observed for several hours after emission. The analysis of this flight showcases the strategies implemented to answer some of the main SENEX science questions.

Instrumentation and Measurement Strategy for the NOAA SENEX Aircraft Campaign as Part of the Southeast Atmosphere Study 2013

Natural emissions of ozone-and-aerosol-precursor gases such as isoprene and monoterpenes are high in the southeast of the US. In addition, anthropogenic emissions are significant in the Southeast US and summertime photochemistry is rapid. The NOAA-led SENEX (Southeast Nexus) aircraft campaign was one of the major components of the Southeast Atmosphere Study (SAS) and was focused on studying the interactions between biogenic and anthropogenic emissions to form secondary pollutants. During SENEX, the NOAA WP-3D aircraft conducted 20 research flights between 27 May and 10 July 2013 based out of Smyrna, TN. Here we describe the experimental approach, the science goals and early results of the NOAA SENEX campaign. The aircraft, its capabilities and standard measurements are described. The instrument payload is summarized including detection limits, accuracy, precision and time resolutions for all gas-and-aerosol phase instruments. The inter-comparisons of compounds measured with multiple instruments on the NOAA WP-3D are presented and were all within the stated uncertainties, except two of the three NO₂ measurements. The SENEX flights included day- and nighttime flights in the Southeast as well as flights over areas with intense shale gas extraction (Marcellus, Fayetteville and Haynesville shale). We present one example flight on 16 June 2013, which was a daytime flight over the Atlanta region, where several crosswind transects of plumes from the city and nearby point sources, such as power plants, paper mills and landfills, were flown. The area around Atlanta has large biogenic isoprene emissions, which provided an excellent case for studying the interactions between biogenic and anthropogenic emissions. In this example flight, chemistry in and outside the Atlanta plumes was observed for several hours after emission. The analysis of this flight showcases the strategies implemented to answer some of the main SENEX science questions.

The orally active urotensin receptor antagonist, KR36676, attenuates cellular and cardiac hypertrophy

BACKGROUND AND PURPOSE

Blockade of the actions of urotensin-II (U-II) mediated by the urotensin (UT) receptor should improve cardiac function and prevent cardiac remodelling in cardiovascular disease. Here, we have evaluated the pharmacological properties of the recently identified UT receptor antagonist, 2-(6,7-dichloro-3-oxo-2H-benzo[b][1,4]oxazin-4(3H)-yl)-N-methyl-N-(2-(pyrrolidin-1-yl)-1-(4-(thiophen-3-yl)phenyl) ethyl)acetamide (KR36676).

EXPERIMENTAL APPROACH

Pharmacological properties of KR36676 were studied in a range of in vitro assays (receptor binding, calcium mobilization, stress fibre formation, cellular hypertrophy) and in vivo animal models such as cardiac hypertrophy induced by transverse aortic constriction (TAC) or myocardial infarction (MI).

KEY RESULTS

KR36676 displayed high binding affinity for the UT receptor (Ki : 0.7 nM), similar to that of U-II (0.4 nM), and was a potent antagonist at that receptor (IC50 : 4.0 nM). U-II-induced stress fibre formation and cellular hypertrophy were significantly inhibited with low concentrations of KR36676 (≥0.01 μM). Oral administration of KR36676 (30 mg·kg(-1) ) in a TAC model in mice attenuated cardiac hypertrophy and myocardial fibrosis. Moreover, KR36676 restored cardiac function and myocyte size in rats with MI-induced cardiac hypertrophy.

CONCLUSIONS AND IMPLICATIONS

A highly potent UT receptor antagonist exerted anti-hypertrophic effects not only in infarcted rat hearts but also in pressure-overloaded mouse hearts. KR36676 could be a valuable pharmacological tool in elucidating the complicated physiological role of U-II and UT receptors in cardiac hypertrophy.

PCDHB14- and GABRB1-like nervous system developmental genes are altered during early neuronal differentiation of NCCIT cells treated with ethanol

Ethanol (EtOH) exposure during embryonic development causes dysfunction of the central nervous system (CNS). Here, we examined the effects of chronic EtOH on gene expression during early stages of neuronal differentiation. Human embryonic carcinoma (NCCIT) cells were differentiated into neuronal precursors/lineages in the presence or absence of EtOH and folic acid. Gene expression profiling and pathway analysis demonstrated that EtOH deregulates many genes and pathways that are involved in early brain development. EtOH exposure downregulated several important genes, such as PCDHB14, GABRB1, CTNND2, NAV3, RALDH1, and OPN5, which are involved in CNS development, synapse assembly, synaptic transmission, and neurotransmitter receptor activity. GeneGo pathway analysis revealed that the deregulated genes mapped to disease pathways that were relevant to fetal alcohol spectrum disorders (FASD, such as neurotic disorders, epilepsy, and alcohol-related disorders). In conclusion, these findings suggest that the impairment of the neurological system or suboptimal synapse formation resulting from EtOH exposure could underlie the neurodevelopmental disorders in individuals with FASD.

Biphasic motion of the median nerve in the normal Asian population

BACKGROUND

The biomechanical interaction between the median nerve and the flexor tendons is an important consideration in Carpal tunnel syndrome (CTS). We aim to quantify the displacement and compressive deformation pattern of the median nerve in various stages of finger flexion in the normal population at the inlet of the carpal tunnel.

METHODS

Transverse ultrasounds images were taken at the carpal tunnel inlet during full-extension, mid-flexion and full flexion. The displacement, distance, Feret's diameter, and perimeter of the median nerve were calculated and compared between each position.

RESULTS

Biphasic median nerve motion was observed, with a displacement of 2.84 ± 3.49 mm in the ulnar direction from full-extension to mid-flexion (Phase I) and a further 0.93 ± 3.04 mm from mid-flexion to full flexion (Phase II). Of 49 hands, 37 (75.5%) exhibited ulnar displacement in Phase I while 12 (24.5%) exhibited radial displacement. Feret's diameter (5.95 ± 1.08 mm) and perimeter (13.28 ± 2.09) of the median nerve were greatest in the mid-flexed position.

CONCLUSION

In a healthy Asian population, the median nerve has a biphasic motion during finger flexion, with maximal deformation in the mid-flexed position.

Role of distinct surfaces of the G9a ankyrin repeat domain in histone and DNA methylation during embryonic stem cell self-renewal and differentiation

Background

Epigenetic modifications such as histone and DNA methylation are essential for silencing pluripotency genes during embryonic stem cell (ESC) differentiation. G9a is the major histone H3 Lys9 (H3K9) methyltransferase in euchromatin and is required for the de novo DNA methylation of the key regulator of pluripotency Oct3/4 during ESC differentiation. Surprisingly, the catalytic activity of G9a is not required for its role in de novo DNA methylation and the precise molecular mechanisms of G9a in this process are poorly understood. It has been suggested that the G9a ankyrin repeat domain, which can interact with both H3K9me2 and the DNA methyltransferase DNMT3A, could facilitate de novo DNA methylation by bridging the interaction between DNMT3A and H3K9me2-marked chromatin.

Results

Here, we demonstrate that the G9a ankyrin domain H3K9me2-binding function is not required for the de novo DNA methylation of Oct3/4 during ESC differentiation. Moreover, we show that the interaction between the G9a ankyrin domain and DNMT3A is not sufficient to ensure efficient de novo DNA methylation. More importantly, we characterize a specific residue of the G9a ankyrin domain (Asp905) that is critical for both maintaining cellular H3K9me2 levels in undifferentiated ESCs and for the establishment of de novo DNA methylation during differentiation.

Conclusions

These results represent an exciting breakthrough, which reveals 1) an unexpected critical biological function of the G9a ankyrin domain in global histone H3K9 methylation and 2) valuable insights into the molecular mechanisms and interaction surfaces through which G9a regulates de novo DNA methylation of Oct3/4 during ESC differentiation.

Reactive neurogenesis in response to naturally occurring apoptosis in an adult brain

Neuronal birth and death are tightly coordinated to establish and maintain properly functioning neural circuits. Disruption of the equilibrium between neuronal birth and death following brain injury or pharmacological insult often induces reactive, and in some cases regenerative, neurogenesis. Many neurodegenerative disorders are not injury-induced, however, so it is critical to determine if and how reactive neurogenesis occurs under noninjury-induced neurodegenerative conditions. Here, we used a model of naturally occurring neural degradation in a neural circuit that controls song behavior in Gambel's white-crowned sparrows (Zonotrichia leucophrys gambelii) and examined the temporal dynamics between neuronal birth and death. We found that during seasonal-like regression of the song, control nucleus HVC (proper name), caspase-mediated apoptosis increased within 2 d following transition from breeding to nonbreeding conditions and neural stem-cell proliferation in the nearby ventricular zone (VZ) increased shortly thereafter. We show that inhibiting caspase-mediated apoptosis in HVC decreased neural stem-cell proliferation in the VZ. In baseline conditions the extent of neural stem-cell proliferation correlated positively with the number of dying cells in HVC. We demonstrate that as apoptosis increased and the number of both recently born and pre-existing neurons in HVC decreased, the structure of song, a learned sensorimotor behavior, degraded. Our data illustrate that reactive neurogenesis is not limited to injury-induced neuronal death, but also can result from normally occurring degradation of a telencephalic neural circuit.

Effects of feeding levels of starter on weaning age, performance, nutrient digestibility and health parameters in holstein dairy calves

To evaluate the effects of feeding four different levels of starter in male Holstein dairy calves, a completely randomized study was conducted, using 28 calves with initial body weight of 40.5±2.4 kg. The animals were fed iso-nitrogenous starter and were weaned when they consumed 350, 500, 650 and 800 g/d of starter for 3 d consecutively. Starter and water were available ad-libitum throughout the experiment. Body weight at pre-weaning (less than 5 wk) and post-weaning (8 wk) was lower in calves that received 350 g/d of starter than in the other treatments (p<0.05). Feed conversion ratio (FCR) was the highest among all treatments in pre-weaning period (p<0.05). Dry matter intake (DMI) at weaning and total DMI was higher in that calves received 800 g/d of starter compared with other treatments (p<0.05). Calves fed 350 and 500 g/d of starter were weaned earlier (p<0.05) and showed lower milk consumption (kg, DM) compared with other treatments whereas no significant difference was observed between calves fed 350 and 500 g/d of starter (p>0.05). Dry matter, organic matter and crude protein digestibilities were lower in calves that received 350 g/d of starter compared with other treatments (p<0.05). No differences were observed in acid detergent and neutral detergent fiber digestibility among all treatments (p>0.05).Treatments had no significant effect on time of starting rumination, respiratory score, and days of drug administration for pneumonia. There were no meaningful differences in feces, fecal odor scores, body temperature, and days of drug administration for diarrhea among all treatments (p>0.05). Total dry matter intake at the end of experiment showed no significant difference among calves fed 600 and 800 g/d of starter, but calves fed 350 and 500 g/d of starter showed more dry matter (DM) intake than calves in the 600 and 800 g/d groups (p<0.05).

A cross-sectional multicenter study of osteogenesis imperfecta in North America - results from the linked clinical research centers

Osteogenesis imperfecta (OI) is the most common skeletal dysplasia that predisposes to recurrent fractures and bone deformities. In spite of significant advances in understanding the genetic basis of OI, there have been no large-scale natural history studies. To better understand the natural history and improve the care of patients, a network of Linked Clinical Research Centers (LCRC) was established. Subjects with OI were enrolled in a longitudinal study, and in this report, we present cross-sectional data on the largest cohort of OI subjects (n = 544). OI type III subjects had higher prevalence of dentinogenesis imperfecta, severe scoliosis, and long bone deformities as compared to those with OI types I and IV. Whereas the mean lumbar spine area bone mineral density (LS aBMD) was low across all OI subtypes, those with more severe forms had lower bone mass. Molecular testing may help predict the subtype in type I collagen-related OI. Analysis of such well-collected and unbiased data in OI can not only help answering questions that are relevant to patient care but also foster hypothesis-driven research, especially in the context of 'phenotypic expansion' driven by next-generation sequencing.

Failure mode and effects analysis of the universal anaesthesia machine in two tertiary care hospitals in Sierra Leone

Background

Anaesthesia care in developed countries involves sophisticated technology and experienced providers. However, advanced machines may be inoperable or fail frequently when placed into the austere medical environment of a developing country. Failure mode and effects analysis (FMEA) is a method for engaging local staff in identifying real or potential breakdowns in processes or work systems and to develop strategies to mitigate risks.

Methods

Nurse anaesthetists from the two tertiary care hospitals in Freetown, Sierra Leone, participated in three sessions moderated by a human factors specialist and an anaesthesiologist. Sessions were audio recorded, and group discussion graphically mapped by the session facilitator for analysis and commentary. These sessions sought to identify potential barriers to implementing an anaesthesia machine designed for austere medical environments—the universal anaesthesia machine (UAM)—and also engaging local nurse anaesthetists in identifying potential solutions to these barriers.

Results

Participating Sierra Leonean clinicians identified five main categories of failure modes (resource availability, environmental issues, staff knowledge and attitudes, and workload and staffing issues) and four categories of mitigation strategies (resource management plans, engaging and educating stakeholders, peer support for new machine use, and collectively advocating for needed resources).

Conclusions

We identified factors that may limit the impact of a UAM and devised likely effective strategies for mitigating those risks.

Clinical characterization and molecular classification of 12 Korean patients with pseudohypoparathyroidism and pseudopseudohypoparathyroidism

CONTEXT

Pseudohypoparathyroidism (PHP) is defined as resistance toward parathyroid hormones. PHP and pseudopseudohypoparathyroidism (PPHP) are rare disorders resulting from genetic and epigenetic aberrations within or upstream of the GNAS locus. This study investigated the clinical characteristics and performed a molecular analysis of PHP and PPHP.

METHODS

A total of 12 patients with (P)PHP from 11 unrelated families (4 with PHP-Ia, 6 with PHP-Ib, and 2 with PPHP) were characterized using both clinical and molecular methods. Clinical features included the presenting symptoms, Albright hereditary osteodystrophy features, and resistance to hormones. Comprehensive analysis of the GNAS and STX16 loci was undertaken to investigate the molecular defects underlying (P)PHP.

RESULTS

All PHP-Ib patients displayed hypocalcemic symptoms. All PHP-Ia patients showed resistance toward TSH, in addition to PTH. In most patients with PHP, when the diagnosis of PHP was first established, hypocalcemia and hyperphosphatemia were associated with a significant increase in serum PTH levels. One patient with PHP-Ia was diagnosed with growth hormone deficiency and showed a good response to human recombinant growth hormone therapy. 6 patients with PHP-Ia and PPHP showed 5 different mutations in the GNAS gene. 5 patients with PHP-Ib displayed a loss of differentially methylated region (DMR) imprints of the maternal GNAS. One PHP-Ib patient showed a de novo microdeletion in STX16 and a loss of methylation of exon A/B on the maternal allele. No patients revealed paternal disomy among 4 patients with PHP-Ib.

CONCLUSIONS

Identification of the molecular causes of PHP and PPHP explains their distinctive clinical features and enables confirmation of the diagnosis and exact genetic counseling.

Effect of carbon nanotube addition on the wear behavior of basalt/epoxy woven composites

The effect of acid-treated carbon nanotube (CNT) addition on the wear and dynamic mechanical thermal properties of basalt/epoxy woven composites was investigated in this study. Basalt/CNT/epoxy composites were fabricated by impregnating woven basalt fibers into epoxy resin mixed with 1 wt% CNTs which were acid-treated. Wear and DMA (dynamic mechanical analyzer) tests were performed on basalt/epoxy composites and basalt/CNT/epoxy composites. The results showed that the addition of the acid-treated CNTs improved the wear properties of basalt/epoxy woven composites. Specifically, the friction coefficient of the basalt/epoxy composite was stabilized in the range of 0.5-0.6 while it fell in the range of 0.3-0.4 for basalt/CNT/epoxy composites. The wear volume loss of the basalt/CNT/epoxy composites was approximately 68% lower than that of the basalt/epoxy composites. The results also showed that the glass transition temperature of basalt/CNT/epoxy composites was higher than that of basalt/epoxy composites. The improvement of wear properties of basalt/epoxy composites by the addition of acid-treated CNTs was caused by the homogeneous load transfer between basalt fibers and epoxy matrix due to the reinforcement of CNTs.

Next-generation sequencing for disorders of low and high bone mineral density

To achieve an efficient molecular diagnosis of osteogenesis imperfecta (OI), Ehlers-Danlos syndrome (EDS), and osteopetrosis (OPT), we designed a next-generation sequencing (NGS) platform to sequence 34 genes. We validated this platform on known cases and have successfully identified the causative mutation in most patients without a prior molecular diagnosis.

INTRODUCTION

Osteogenesis imperfecta, Ehlers-Danlos syndrome, and osteopetrosis are collectively common inherited skeletal diseases. Evaluation of subjects with these conditions often includes molecular testing which has important counseling and therapeutic and sometimes legal implications. Since several different genes have been implicated in these conditions, Sanger sequencing of each gene can be a prohibitively expensive and time-consuming way to reach a molecular diagnosis.

METHODS

In order to circumvent these problems, we have designed and tested a NGS platform that would allow simultaneous sequencing on a single diagnostic platform of different genes implicated in OI, OPT, EDS, and other inherited conditions, leading to low or high bone mineral density. We used a liquid-phase probe library that captures 602 exons (~100 kb) of 34 selected genes and have applied it to test clinical samples from patients with bone disorders.

RESULTS

NGS of the captured exons by Illumina HiSeq 2000 resulted in an average coverage of over 900X. The platform was successfully validated by identifying mutations in six patients with known mutations. Moreover, in four patients with OI or OPT without a prior molecular diagnosis, the assay was able to detect the causative mutations.

CONCLUSIONS

In conclusion, our NGS panel provides a fast and accurate method to arrive at a molecular diagnosis in most patients with inherited high or low bone mineral density disorders.

A novel synthetic compound, 3-amino-3-(4-fluoro-phenyl)-1H-quinoline-2,4-dione, inhibits cisplatin-induced hearing loss by the suppression of reactive oxygen species: in vitro and in vivo study

Cisplatin, a chemotherapeutic agent for treating various solid tumors, produces hearing loss in approximately half a million cancer patients annually in the United States. In the course of developing a new protective agent against cisplatin-induced ototoxicity, we have been interested in a novel synthetic compound, 3-amino-3-(4-fluoro-phenyl)-1H-quinoline-2,4-dione (KR-22332). The effect of KR-22332 on cisplatin-induced cytotoxicity was analyzed in vitro in an organ of Corti-derived cell line (HEI-OC1), and in vivo in a zebrafish and rat model. Cisplatin-induced apoptosis, reactive oxygen species (ROS) generation and altered mitochondrial membrane potential (MMP) in HEI-OC1 cells were observed. KR-22332 significantly inhibited cisplatin-induced apoptosis, change of MMP, and intracellular ROS generation. KR-22332 markedly attenuated the cisplatin-induced loss and changes of auditory neuromasts in the zebrafish. Transtympanic administration of KR-22332 in a rat model was protective against cisplatin-induced hearing loss, as determined by click-evoked auditory brainstem response (p<0.01). Tissue terminal deoxynucleotidyl transferase-mediated dUTP-biotin nick end labeling of rat cochlea demonstrated that KR-22332 blocked cisplatin-induced apoptosis. In addition, transtympanic administration of KR-22332 inhibited cisplatin-induced nicotinamide adenine dinucleotide phosphate-oxidase 3 (NOX3) overexpression in the rat cochlea. KR-22332 significantly reduced the expression of p-53, mitogen-activated protein kinases, caspase 3, and tumor necrosis factor-α compared to their significant increase after cisplatin treatment. The results of this study suggest that KR-22332 may prevent ototoxicity caused by the administration of cisplatin through the inhibition of mitochondrial dysfunction and the suppression of ROS generation. These novel findings implicate KR-22332 as a potential candidate for protective agent against cisplatin-induced ototoxicity.

PI3K/Akt and MAPK pathways evoke activation of FoxO transcription factor to undergo neuronal apoptosis in brain of the silkworm Bombyx mori (Lepidoptera: Bombycidae)

The Forkhead box O (FoxO) transcription factors, including FoxO1, FoxO3a, FoxO4, and FoxO6, are implicated in the regulation of cell apoptosis and survival. Here, we examined the role of FoxO transcription factors and the involvement of the PI3K/Akt and mitogen-activated protein kinase (MAPK) pathways in neuronal apoptosis in the brain of the silkworm Bombyx mori following starvation. Starvation inhibited cell proliferation and induced apoptosis through caspase-3 activation. The level of phosphorylated kinase Akt increased when the animals ceased feeding. Starvation conditions reduced extracellular-signal-regulated kinase phosphorylation but increased both c-Jun N-terminal kinase and p38 (MAPK) phosphorylation. FoxO1 and FoxO3a were simultaneously localized in the nuclei. These results provide new insights into the process of apoptosis of brain neurons through the involvement of FoxO transcription factors following starvation of insect species.

AMP-activated kinase links serotonergic signaling to glutamate release for regulation of feeding behavior in C. elegans

Serotonergic regulation of feeding behavior has been studied intensively, both for an understanding of the basic neurocircuitry of energy balance in various organisms and as a therapeutic target for human obesity. However, its underlying molecular mechanisms remain poorly understood. Here, we show that neural serotonin signaling in C. elegans modulates feeding behavior through inhibition of AMP-activated kinase (AMPK) in interneurons expressing the C. elegans counterpart of human SIM1, a transcription factor associated with obesity. In turn, glutamatergic signaling links these interneurons to pharyngeal neurons implicated in feeding behavior. We show that AMPK-mediated regulation of glutamatergic release is conserved in rat hippocampal neurons. These findings reveal cellular and molecular mediators of serotonergic signaling.

Paradoxical response in HIV-negative patients with pleural tuberculosis: a retrospective multicentre study

OBJECTIVE

To evaluate the incidence, clinical characteristics and predicting factors for the development of paradoxical response in human immunodeficiency virus negative patients with isolated pleural tuberculosis (TB).

DESIGN

A multicentre, retrospective cohort study including 458 patients who were diagnosed and treated with isolated pleural TB between March 2005 and February 2010.

RESULTS

Paradoxical response developed in 72 patients (16%) with isolated pleural TB. The mean time to development of paradoxical response was 8.8 ± 6.4 weeks after initiation of anti-tuberculosis treatment. The main presentation of paradoxical response was aggravation of pre-existing pleural effusion in 58 patients (81%). However, the majority of the patients who developed paradoxical response had no associated symptoms (n = 49, 68%). In multiple logistic regression analysis, development of paradoxical response was independently associated with the proportion of eosinophils (adjusted OR 1.293, 95%CI 1.077-1.553) and protein concentrations (adjusted OR 0.590, 95%CI 0.397-0.878) in the pleural fluid at the time of diagnosis.

CONCLUSION

Paradoxical response developed in 16% of the patients approximately 2 months after initiation of anti-tuberculosis treatment, presenting with aggravation of pre-existing pleural effusion. Development of paradoxical response was associated with the proportion of eosinophils and protein concentrations in the pleural fluid at the time of diagnosis.