Assessment of dosimetric impact of interfractional 6D setup error in tongue cancer treated with IMRT and VMAT using daily kV-CBCT

Background

This study aimed to evaluate the dosimetric influence of 6-dimensional (6D) interfractional setup error in tongue cancer treated with intensity-modulated radiation therapy (IMRT) and volumetric modulated arc therapy (VMAT) using daily kilovoltage cone-beam computed tomography (kV-CBCT).

Materials and methods

This retrospective study included 20 tongue cancer patients treated with IMRT (10), VMAT (10), and daily kV-CBCT image guidance. Interfraction 6D setup errors along the lateral, longitudinal, vertical, pitch, roll, and yaw axes were evaluated for 600 CBCTs. Structures in the planning CT were deformed to the CBCT using deformable registration. For each fraction, a reference CBCT structure set with no rotation error was created. The treatment plan was recalculated on the CBCTs with the rotation error (R_Error), translation error (T_Error), and translation plus rotation error (T+R_Error). For targets and organs at risk (OARs), the dosimetric impacts of R_Error, T_Error, and T+R_Error were evaluated without and with moderate correction of setup errors.

Results

The maximum dose variation ΔD (%) for D_98% in clinical target volumes (CTV): CTV-60, CTV-54, planning target volumes (PTV): PTV-60, and PTV-54 was -1.2%, -1.9%, -12.0%, and -12.3%, respectively, in the T+R_Error without setup error correction. The maximum ΔD (%) for D_98% in CTV-60, CTV-54, PTV-60, and PTV-54 was -1.0%, -1.7%, -9.2%, and -9.5%, respectively, in the T+R_Error with moderate setup error correction. The dosimetric impact of interfractional 6D setup errors was statistically significant (p < 0.05) for D_98% in CTV-60, CTV-54, PTV-60, and PTV-54.

Conclusions

The uncorrected interfractional 6D setup errors could significantly impact the delivered dose to targets and OARs in tongue cancer. That emphasized the importance of daily 6D setup error correction in IMRT and VMAT.

Distinguishing Renal Cell Carcinoma From Normal Kidney Tissue Using Mass Spectrometry Imaging Combined With Machine Learning

PURPOSE

Accurately distinguishing renal cell carcinoma (RCC) from normal kidney tissue is critical for identifying positive surgical margins (PSMs) during partial and radical nephrectomy, which remains the primary intervention for localized RCC. Techniques that detect PSM with higher accuracy and faster turnaround time than intraoperative frozen section (IFS) analysis can help decrease reoperation rates, relieve patient anxiety and costs, and potentially improve patient outcomes.

MATERIALS AND METHODS

Here, we extended our combined desorption electrospray ionization mass spectrometry imaging (DESI-MSI) and machine learning methodology to identify metabolite and lipid species from tissue surfaces that can distinguish normal tissues from clear cell RCC (ccRCC), papillary RCC (pRCC), and chromophobe RCC (chRCC) tissues.

RESULTS

From 24 normal and 40 renal cancer (23 ccRCC, 13 pRCC, and 4 chRCC) tissues, we developed a multinomial lasso classifier that selects 281 total analytes from over 27,000 detected molecular species that distinguishes all histological subtypes of RCC from normal kidney tissues with 84.5% accuracy. On the basis of independent test data reflecting distinct patient populations, the classifier achieves 85.4% and 91.2% accuracy on a Stanford test set (20 normal and 28 RCC) and a Baylor-UT Austin test set (16 normal and 41 RCC), respectively. The majority of the model's selected features show consistent trends across data sets affirming its stable performance, where the suppression of arachidonic acid metabolism is identified as a shared molecular feature of ccRCC and pRCC.

CONCLUSION

Together, these results indicate that signatures derived from DESI-MSI combined with machine learning may be used to rapidly determine surgical margin status with accuracies that meet or exceed those reported for IFS.

Rationale for LDH-targeted cancer immunotherapy

Immunotherapies have significantly improved the survival of patients in many cancers over the last decade. However, primary and secondary resistances are encountered in most patients. Unravelling resistance mechanisms to cancer immunotherapies is an area of active investigation. Elevated levels of circulating enzyme lactate dehydrogenase (LDH) have been historically considered in oncology as a marker of bad prognosis, usually attributed to elevated tumour burden and cancer metabolism. Recent evidence suggests that elevated LDH levels could be independent from tumour burden and contain a negative predictive value, which could help in guiding treatment strategies in immuno-oncology. In this review, we decipher the rationale supporting the potential of LDH-targeted therapeutic strategies to tackle the direct immunosuppressive effects of LDH on a wide range of immune cells, and enhance the survival of patients treated with cancer immunotherapies.

Factors Associated with Prehospital Delay in Patients with Acute Stroke in South India

Background

Early hospital presentation is critical in the management of acute ischemic stroke. The effectiveness of stroke treatment is highly dependent on the amount of time lapsed between onset of symptoms and treatment. This study was aimed to identify the factors associated with prehospital delay in patients with acute stroke.

Material and Methods

A cross-sectional descriptive study was conducted in Sri Ramachandra University Hospital, India. A total of 210 patients hospitalized in the stroke unit were included. Patients' data were obtained by interviewing the patient and/or accompanying family member and by reviewing their medical records using a standard questionnaire. Associations were determined between prehospital delay (≥4.5 h) and variables of interest by using univariate and multivariate logistic regression analyses.

Results

The prehospital delay was observed in 154 patients (73.3%) and the median prehospital delay was 11.30 h. The following are the factors significantly (P < 0.05) attributed for the delay in presenting to the hospital: contextual factors like using public transport (bus), taxi, time of onset of symptoms, 7 pm-3 am; family history of stroke, perceived cognitive and behavioral factors like, wishing or praying for the symptoms to subside on its own, hesitation to travel due to long distance, delay in arranging transport, and arranging money for admission and wasting time by shopping for general practitioners, nursing homes, and hospitals. The presence of stroke symptom, headache, significantly decreased the prehospital delay.

Conclusions

Prehospital delay is high in South India and influenced by clinical, contextual, and cognitive/behavioral factors.

Evaluation of the dosimetric influence of interfractional 6D setup error in hypofractionated prostate cancer treated with IMRT and VMAT using daily kV-CBCT

INTRODUCTION

Prostate cancer is one of the most common malignant tumors in men and is usually treated with advanced intensity modulated radiation therapy (IMRT) and volumetric modulated arc therapy (VMAT). Significant uncorrected interfractional 6-Dimensional setup errors could impact the delivered dose. The aim of this study was to assess the dosimetric impact of 6D interfractional setup errors in hypofractionated prostate cancer using daily kilovoltage cone-beam computed tomography (kV-CBCT).

METHODS

This retrospective study comprised twenty prostate cancer patients treated with hypofractionated IMRT (8) and VMAT (12) with daily kV-CBCT image guidance. Interfraction 6D setup errors along lateral, longitudinal, vertical, pitch, roll, and yaw axes were evaluated for 400 CBCTs. For targets and organs at risk (OARs), the dosimetric impact of rotational error (R_Error), translational error (T_Error), and translational plus rotational error (T+R_Error) were evaluated on kV-CBCT images.

RESULTS

The single fraction maximum T_Error ranged from 12-20 mm, and the R_Error ranged from 2.8⁰-3.0⁰. The maximum mean absolute dose variation ΔD in D_98% (dose to 98% volume) of CTV-55 and PTV-55 was -0.66±0.82 and -5.94±3.8 Gy, respectively, in the T+R_Error. The maximum ΔD (%) for D_98% and D_0.035cc in CTV-55 was -4.29% and 2.49%, respectively, while in PTV-55 it was -24.9% and 2.36%. The mean dose reduction for D_98% in CTV-55 and D_98% and D_95% in PTV-55 was statistically significant (p<0.05) for T_Error and T+R_Error. The mean dose variation for D_mean and D_50% in the rectum was statistically significant (p<0.05) for T_Error and T+R_Error.

CONCLUSION

The uncorrected interfractional 6D setup error results in significant target underdosing and OAR overdosing in prostate cancer. This emphasizes the need to correct interfractional 6D setup errors daily in IMRT and VMAT.

Instability and rupture of ultrathin freestanding viscoelastic solid films

We analyze the instability of viscoelastic solid freestanding thin films under the influence of van der Waals forces using linear stability analysis and nonlinear simulations. Linear stability analysis shows that the zero-frequency elastic modulus governs the onset of instability and stabilizes the film beyond a critical value analogous to thin supported viscoelastic solid films. However, for freestanding solid films, the critical shear modulus is found to be independent of surface tension, unlike that of thin supported viscoelastic solid films. It is further shown that freestanding viscoelastic solid films with higher moduli can be destabilized for a given film thickness and Hamaker constant compared to supported solid films. In contrast to thin viscoelastic liquid films where the growth rate is enhanced due to elastic effects but length scale is unaltered, freestanding films with solidlike viscoelasticity show a retarded growth rate and enhanced length scale. The presence of solidlike viscoelasticity has a stabilizing effect and affects all the key aspects of instability such as critical wave number, dominant wave number, and maximum growth rate. We numerically solve the set of coupled nonlinear evolution equations for film thickness and tangential displacement in order to elucidate the dynamics of film rupture. Our simulations show that, consistent with the linear stability predictions, an increase in the elastic modulus delays film rupture. The dynamics exhibits self-similarity in the vicinity of film rupture and the film thins as (t_{r}-t)^{3/4}, where t_{r} is the rupture time and t_{r}-t is the time remaining until film rupture. The scaling exponent 3/4 obtained for a thin freestanding viscoelastic solid film is significantly greater than the scaling exponent (1/3) for a thin freestanding viscous film.

Human Coronary Plaque T Cells Are Clonal and Cross-React to Virus and Self

BACKGROUND

Coronary artery disease is an incurable, life-threatening disease that was once considered primarily a disorder of lipid deposition. Coronary artery disease is now also characterized by chronic inflammation' notable for the buildup of atherosclerotic plaques containing immune cells in various states of activation and differentiation. Understanding how these immune cells contribute to disease progression may lead to the development of novel therapeutic strategies.

METHODS

We used single-cell technology and in vitro assays to interrogate the immune microenvironment of human coronary atherosclerotic plaque at different stages of maturity.

RESULTS

In addition to macrophages, we found a high proportion of αβ T cells in the coronary plaques. Most of these T cells lack high expression of CCR7 and L-selectin, indicating that they are primarily antigen-experienced memory cells. Notably, nearly one-third of these cells express the HLA-DRA surface marker, signifying activation through their TCRs (T-cell receptors). Consistent with this, TCR repertoire analysis confirmed the presence of activated αβ T cells (CD4<CD8), exhibiting clonal expansion of specific TCRs. Interestingly, we found that these plaque T cells had TCRs specific for influenza, coronavirus, and other viral epitopes, which share sequence homologies to proteins found on smooth muscle cells and endothelial cells, suggesting potential autoimmune-mediated T-cell activation in the absence of active infection. To better understand the potential function of these activated plaque T cells, we then interrogated their transcriptome at the single-cell level. Of the 3 T-cell phenotypic clusters with the highest expression of the activation marker HLA-DRA, 2 clusters expressed a proinflammatory and cytolytic signature characteristic of CD8 cells, while the other expressed AREG (amphiregulin), which promotes smooth muscle cell proliferation and fibrosis, and, thus, contributes to plaque progression.

CONCLUSIONS

Taken together, these findings demonstrate that plaque T cells are clonally expanded potentially by antigen engagement, are potentially reactive to self-epitopes, and may interact with smooth muscle cells and macrophages in the plaque microenvironment.

CD20-Targeted Therapy Ablates De Novo Antibody Response to Vaccination but Spares Preestablished Immunity

To obtain a deeper understanding of poor responses to COVID-19 vaccination in patients with lymphoma, we assessed blocking antibodies, total anti-spike IgG, and spike-specific memory B cells in the peripheral blood of 126 patients with lymphoma and 20 age-matched healthy controls 1 and 4 months after COVID-19 vaccination. Fifty-five percent of patients developed blocking antibodies postvaccination, compared with 100% of controls. When evaluating patients last treated from days to nearly 18 years prior to vaccination, time since last anti-CD20 was a significant independent predictor of vaccine response. None of 31 patients who had received anti-CD20 treatment within 6 months prior to vaccination developed blocking antibodies. In contrast, patients who initiated anti-CD20 treatment shortly after achieving a vaccine-induced antibody response tended to retain that response during treatment, suggesting a policy of immunizing prior to treatment whenever possible.

SIGNIFICANCE

In a large cohort of patients with B-cell lymphoma, time since anti-CD20 treatment was an independent predictor of neutralizing antibody response to COVID-19 vaccination. Comparing patients who received anti-CD20 treatment before or after vaccination, we demonstrate that vaccinating first can generate an antibody response that endures through anti-CD20-containing treatment. This article is highlighted in the In This Issue feature, p. 85.

Evaluation of kV-CBCT based 3D dose calculation accuracy and its validation using delivery fluence derived dose metrics in Head and Neck Cancer

PURPOSE

The purpose of this study is to evaluate the dosimetric impact of Hounsfield unit (HU) variations in kilovoltage cone-beam computed tomography (kV-CBCT) based 3D dose calculation accuracy in the treatment planning system and its validation using measured treatment delivery dose (MTDD) derived dose metrics for Volumetric Modulated Arc Therapy (VMAT) and Intensity Modulated Radiotherapy (IMRT) plans in Head and Neck (HN) Cancer.

METHODS

CBCT dose calculation accuracy was evaluated for 8 VMAT plans on inhomogeneous phantom and 40 VMAT and IMRT plans of HN Cancer patients and validated using ArcCHECK diode array MTDD derived 3D dose metric on CT and CBCT.

RESULTS

The mean percentage dose difference between CBCT and CT in TPS (ΔD(CBCT-CT)_TPS) and 3DVH (ΔD(CBCT-CT)_3DVH) were compared for the corresponding evaluation dose metrics (D_98%, D_95%, D_50%, D_2%, D_max, D_1cc, D_0.03cc, D_mean) of all PTVs and OARs in phantom and patients. ΔD(CBCT-CT)_TPS and ΔD(CBCT-CT)_3DVH for all evaluation dose points of all PTVs and OARs were less than 2.55% in phantom and 2.4% in HN patients. The Pearson correlation coefficient (r) between ΔD(CBCT-CT)_TPS and ΔD(CBCT-CT)_3DVH for all dose points in all PTVs and OARs showed a strong to moderate correlation in phantom and patients with p < 0.001.

CONCLUSIONS

This study evaluated and validated the potential feasibility of kV-CBCT for treatment plan 3D dose reconstruction in clinical decision making for Adaptive radiotherapy on CT in Head and Neck cancer.

SU086, an inhibitor of HSP90, impairs glycolysis and represents a treatment strategy for advanced prostate cancer

Among men, prostate cancer is the second leading cause of cancer-associated mortality, with advanced disease remaining a major clinical challenge. We describe a small molecule, SU086, as a therapeutic strategy for advanced prostate cancer. We demonstrate that SU086 inhibits the growth of prostate cancer cells in vitro, cell-line and patient-derived xenografts in vivo, and ex vivo prostate cancer patient specimens. Furthermore, SU086 in combination with standard of care second-generation anti-androgen therapies displays increased impairment of prostate cancer cell and tumor growth in vitro and in vivo. Cellular thermal shift assay reveals that SU086 binds to heat shock protein 90 (HSP90) and leads to a decrease in HSP90 levels. Proteomic profiling demonstrates that SU086 binds to and decreases HSP90. Metabolomic profiling reveals that SU086 leads to perturbation of glycolysis. Our study identifies SU086 as a treatment for advanced prostate cancer as a single agent or when combined with second-generation anti-androgens.

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SU086 inhibits prostate cancer growth in preclinical models of prostate cancer

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SU086 targets heat shock protein 90

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SU086 alters prostate cancer glycolysis and decreases intratumoral metabolism

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SU086 in combination with anti-androgens halts prostate cancer growth

Continuous Pathway between the Elasto-Inertial and Elastic Turbulent States in Viscoelastic Channel Flow

Viscoelastic plane Poiseuille flow is shown to become linearly unstable in the absence of inertia, in the limit of high elasticities, for ultradilute polymer solutions. While inertialess elastic instabilities have been predicted for curvilinear shear flows, this is the first ever report of a purely elastic linear instability in a rectilinear shear flow. The novel instability continues up to a Reynolds number (Re) of O(1000), corresponding to the recently identified elasto-inertial turbulent state believed to underlie the maximum-drag-reduced regime. Thus, for highly elastic ultradilute polymer solutions, a single linearly unstable modal branch may underlie transition to elastic turbulence at zero Re and to elasto-inertial turbulence at moderate Re, implying the existence of continuous pathways connecting the turbulent states to each other and to the laminar base state.

In situ DESI-MSI lipidomic profiles of mucosal margin of oral squamous cell carcinoma

Background

Although there is consensus that the optimal safe margin is ≥ 5mm, obtaining clear margins (≥5 mm) intraoperatively seems to be the major challenge. We applied a molecular diagnostic method at the lipidomic level to determine the safe surgical resection margin of OSCC by desorption electrospray ionisation mass spectrometry imaging (DESI-MSI).

Methods

By overlaying mass spectrometry images with hematoxylin-eosin staining (H&E) from 18 recruited OSCC participants, the mass spectra of all pixels across the diagnosed tumour and continuous mucosal margin regions were extracted to serve as the training and validation datasets. A Lasso regression model was used to evaluate the test performance.

Findings

By leave-one-out validation, the Lasso model achieved 88.6% accuracy in distinguishing between tumour and normal regions. To determine the safe surgical resection distance and margin status of OSCC, a set of 14 lipid ions that gradually decreased from tumour to normal tissue was assigned higher weight coefficients in the Lasso model. The safe surgical resection distance of OSCC was measured using the developed 14 lipid ion molecular diagnostic model for clinical reference. The overall accuracy of predicting tumours, positive margins, and negative margins was 92.6%.

Interpretation

The spatial segmentation results based on our diagnostic model not only clearly delineated the tumour and normal tissue, but also distinguished the different status of surgical margins. Meanwhile, the safe surgical resection margin of OSCC on frozen sections can also be accurately measured using the developed diagnostic model.

Funding

This study was supported by Nanjing Municipal Key Medical Laboratory Constructional Project Funding (since 2016) and the Centre of Nanjing Clinical Medicine Tumour (since 2014).

MassExplorer: a computational tool for analyzing desorption electrospray ionization mass spectrometry data

Summary

In the last few years, desorption electrospray ionization mass spectrometry imaging (DESI-MSI) has been increasingly used for simultaneous detection of thousands of metabolites and lipids from human tissues and biofluids. To successfully find the most significant differences between two sets of DESI-MSI data (e.g., healthy vs disease) requires the application of accurate computational and statistical methods that can pre-process the data under various normalization settings and help identify these changes among thousands of detected metabolites. Here, we report MassExplorer, a novel computational tool, to help pre-process DESI-MSI data, visualize raw data, build predictive models using the statistical lasso approach to select for a sparse set of significant molecular changes, and interpret selected metabolites. This tool, which is available for both online and offline use, is flexible for both chemists and biologists and statisticians as it helps in visualizing structure of DESI-MSI data and in analyzing the statistically significant metabolites that are differentially expressed across both sample types. Based on the modules in MassExplorer, we expect it to be immediately useful for various biological and chemical applications in mass spectrometry.

Availability and implementation

MassExplorer is available as an online R-Shiny application or Mac OS X compatible standalone application. The application, sample performance, source code and corresponding guide can be found at: https://zarelab.com/research/massexplorer-a-tool-to-help-guide-analysis-of-mass-spectrometry-samples/.

Supplementary informationMATION

Supplementary data are available at Bioinformatics online.

Intestinal mucormycosis in an adult with H1N1 pneumonia on extracorporeal membrane oxygenation

Gastrointestinal mucormycosis involving ileum is a very rare phenomenon. We present a case of 52-year-old male, known case of diabetes mellitus requiring extracorporeal membrane oxygenation (ECMO) for H1N1 pneumonia with severe acute respiratory distress syndrome (ARDS). The patient had small bowel obstruction with impending perforation requiring emergency bowel resection and ileostomy. The resected bowel segment histopathology showed mucormycosis. He was treated with conventional Amphotericin-B and later changed to Posaconazole. The patient responded very well and was gradually weaned from ventilator and successfully discharged home. This case report highlights rare site of mucormycosis. Early diagnosis and timely intervention can reduce mortality.

Identification of diagnostic metabolic signatures in clear cell renal cell carcinoma using mass spectrometry imaging

Clear cell renal cell carcinoma (ccRCC) is the most common and lethal subtype of kidney cancer. Intraoperative frozen section (IFS) analysis is used to confirm the diagnosis during partial nephrectomy. However, surgical margin evaluation using IFS analysis is time consuming and unreliable, leading to relatively low utilization. In our study, we demonstrated the use of desorption electrospray ionization mass spectrometry imaging (DESI-MSI) as a molecular diagnostic and prognostic tool for ccRCC. DESI-MSI was conducted on fresh-frozen 23 normal tumor paired nephrectomy specimens of ccRCC. An independent validation cohort of 17 normal tumor pairs was analyzed. DESI-MSI provides two-dimensional molecular images of tissues with mass spectra representing small metabolites, fatty acids and lipids. These tissues were subjected to histopathologic evaluation. A set of metabolites that distinguish ccRCC from normal kidney were identified by performing least absolute shrinkage and selection operator (Lasso) and log-ratio Lasso analysis. Lasso analysis with leave-one-patient-out cross-validation selected 57 peaks from over 27,000 metabolic features across 37,608 pixels obtained using DESI-MSI of ccRCC and normal tissues. Baseline Lasso of metabolites predicted the class of each tissue to be normal or cancerous tissue with an accuracy of 94 and 76%, respectively. Combining the baseline Lasso with the ratio of glucose to arachidonic acid could potentially reduce scan time and improve accuracy to identify normal (82%) and ccRCC (88%) tissue. DESI-MSI allows rapid detection of metabolites associated with normal and ccRCC with high accuracy. As this technology advances, it could be used for rapid intraoperative assessment of surgical margin status.

Stability of gravity-driven free-surface flow past a deformable solid: The role of depth-dependent modulus

The linear stability of a Newtonian liquid layer flowing down an inclined plane lined with a deformable linear elastic solid characterized by a continuously varying modulus is analyzed in this study. A low-wave-number asymptotic analysis is performed to obtain an analytical expression for the complex wavespeed which shows striking similarity with the earlier results of Sahu and Shankar [Sahu and Shankar, Phys. Rev. E 94, 013111 (2016)10.1103/PhysRevE.94.013111] for gravity-driven flow of Newtonian fluid past a solid bilayer having constant shear modulus (in each layer) lined on a rigid inclined plane. This shows that a deformable solid layer having a continuously varying shear modulus can be treated as a generalization of a system having multiple solid layers of constant shear modulus. Also, in the low-wave-number limit, we show that the stability of the free surface is governed by the value of effective shear modulus G_{eff}, and not by the detailed spatial variation of the modulus. Here the effective shear modulus (H/G_{eff}=∫_{1}^{1+H}1/[E_{0}+E[over ¯](z)]dz, where [E_{0}+E[over ¯](z)] represents the modulus gradient function) characterizes the overall modulus of the elastic solid, which is obtained by treating the continuous variation to be the limit of the arrangement of solid layers of infinitesimal thickness (each having a constant shear modulus) in a series. At finite wave numbers, we show that the free-surface and the liquid-solid interface become unstable as we increase the value of Γ, where Γ indicates the ratio of viscous stresses in the fluid to elastic stresses in the solid. When the system is analysed for different types of spatial modulus variations, we find results similar to those of Gkanis and Kumar [Gkanis and Kumar, Phys. Rev. E 73, 026307 (2006)10.1103/PhysRevE.73.026307], i.e., when we have two different configurations of the shear modulus function that have the same spatially averaged modulus, but have different values at the interface, the system is more stable for the configuration having higher shear modulus at the liquid-solid interface. In a similar manner, when we examined systems having the same shear modulus at the liquid-solid interface and same average modulus, the more stable case is the one which has a higher value of shear modulus just below the interface. Thus the use of deformable solids with a depth-dependent modulus potentially offers more control in the passive manipulation of the instabilities.

Viscoelastic Pipe Flow is Linearly Unstable

Newtonian pipe flow is known to be linearly stable at all Reynolds numbers. We report, for the first time, a linear instability of pressure-driven pipe flow of a viscoelastic fluid, obeying the Oldroyd-B constitutive equation commonly used to model dilute polymer solutions. The instability is shown to exist at Reynolds numbers significantly lower than those at which transition to turbulence is typically observed for Newtonian pipe flow. Our results qualitatively explain experimental observations of transition to turbulence in pipe flow of dilute polymer solutions at flow rates where Newtonian turbulence is absent. The instability discussed here should form the first stage in a hitherto unexplored dynamical pathway to turbulence in polymer solutions. An analogous instability exists for plane Poiseuille flow.

The 3D Structure of Human DP Prostaglandin G-Protein-Coupled Receptor Bound to Cyclopentanoindole Antagonist, Predicted Using the DuplexBiHelix Modification of the GEnSeMBLE Method

Prostaglandins play a critical physiological role in both cardiovascular and immune systems, acting through their interactions with 9 prostanoid G protein-coupled receptors (GPCRs). These receptors are important therapeutic targets for a variety of diseases including arthritis, allergies, type 2 diabetes, and cancer. The DP prostaglandin receptor is of interest because it has unique structural and physiological properties. Most notably, DP does not have the 3-6 ionic lock common to Class A GPCRs. However, the lack of X-ray structures for any of the 9 prostaglandin GPCRs hampers the application of structure-based drug design methods to develop more selective and active medications to specific receptors. We predict here 3D structures for the DP prostaglandin GPCR, based on the GEnSeMBLE complete sampling with hierarchical scoring (CS-HS) methodology. This involves evaluating the energy of 13 trillion packings to finally select the best 20 that are stable enough to be relevant for binding to antagonists, agonists, and modulators. To validate the predicted structures, we predict the binding site for the Merck cyclopentanoindole (CPI) selective antagonist docked to DP. We find that the CPI binds vertically in the 1-2-7 binding pocket, interacting favorably with residues R310^7.40 and K76^2.54 with additional interactions with S313^7.43, S316^7.46, S19^1.35, etc. This binding site differs significantly from that of antagonists to known Class A GPCRs where the ligand binds in the 3-4-5-6 region. We find that the predicted binding site leads to reasonable agreement with experimental Structure-Activity Relationship (SAR). We suggest additional mutation experiments including K76^2.54, E129^3.49, L123^3.43, M270^6.40, F274^6.44 to further validate the structure, function, and activation mechanism of receptors in the prostaglandin family. Our structures and binding sites are largely consistent and improve upon the predictions by Li et al. ( J. Am. Chem. Soc. 2007 , 129 ( 35 ), 10720 ) that used our earlier MembStruk prediction methodology.

Status of Cognitive Testing of Adults in India

The assessment of cognitive function is a challenging yet an integral component of psychological, psychiatric, and neurological evaluation. Cognitive assessment tools either can be administered quickly for screening for neurocognitive disorders or can be comprehensive and detailed to identify cognitive deficits for the purpose of localization, diagnosis, and rehabilitation. This article is a comprehensive review of published research that discusses the current challenges for cognitive testing in India, available tools used for the assessment of cognitive function in India, and future directions for cognitive testing in India.

Differences in Gut Metabolites and Microbial Composition and Functions between Egyptian and U.S. Children Are Consistent with Their Diets

Previous studies indicated that populations consuming a Mediterranean diet rich in fiber, vegetables, and fruits have a significantly lower risk of cardiovascular and metabolic diseases than populations of industrialized societies consuming diets enriched in processed carbohydrates, animal proteins, and fats. To explore the potential contributions of gut microbiota to the observed diet-related metabolic effects, we conducted an integrative analysis of distal gut microbiota composition and functions and intestinal metabolites in Egyptian and U.S. teenagers. All Egyptian gut microbial communities belonged to the Prevotella enterotype, whereas all but one of the U.S. samples were of the Bacteroides enterotype. The intestinal environment of Egyptians was characterized by higher levels of short-chain fatty acids, a higher prevalence of microbial polysaccharide degradation-encoding genes, and a higher proportion of several polysaccharide-degrading genera. Egyptian gut microbiota also appeared to be under heavier bacteriophage pressure. In contrast, the gut environment of U.S. children was rich in amino acids and lipid metabolism-associated compounds; contained more microbial genes encoding protein degradation, vitamin biosynthesis, and iron acquisition pathways; and was enriched in several protein- and starch-degrading genera. Levels of 1-methylhistamine, a biomarker of allergic response, were elevated in U.S. guts, as were the abundances of members of Faecalibacterium and Akkermansia, two genera with recognized anti-inflammatory effects. The revealed corroborating differences in fecal microbiota structure and functions and metabolite profiles between Egyptian and U.S. teenagers are consistent with the nutrient variation between Mediterranean and Western diets. IMPORTANCE The human gastrointestinal microbiota functions as an important mediator of diet for host metabolism. To evaluate how consumed diets influence the gut environment, we carried out simultaneous interrogations of distal gut microbiota and metabolites in samples from healthy children in Egypt and the United States. While Egyptian children consumed a Mediterranean diet rich in plant foods, U.S. children consumed a Western diet high in animal protein, fats, and highly processed carbohydrates. Consistent with the consumed diets, Egyptian gut samples were enriched in polysaccharide-degrading microbes and end products of polysaccharide fermentation and U.S. gut samples were enriched in proteolytic microbes and end products of protein and fat metabolism. Thus, the intestinal microbiota might be selected on the basis of the diets that we consume, which can open opportunities to affect gut health through modulation of gut microbiota with dietary supplementations.

Comparative effectiveness and cost-effectiveness of treat-to-target versus benefit-based tailored treatment of type 2 diabetes in low-income and middle-income countries: a modelling analysis

BACKGROUND

Optimal prescription of blood pressure, lipid, and glycaemic control treatments for adults with type 2 diabetes remains unclear. We aimed to compare the effectiveness and cost-effectiveness of two treatment approaches for diabetes management in five low-income and middle-income countries.

METHODS

We developed a microsimulation model to compare a treat-to-target (TTT) strategy, aiming to achieve target levels of biomarkers (blood pressure <130/80 mm Hg, LDL <2·59 mmol/L, and HbA1c <7% [ie, 53·0 mmol/mol]), with a benefit-based tailored treatment (BTT) strategy, aiming to lower estimated risk for complications (to a 10 year cardiovascular risk <10% and lifetime microvascular risk <5%) on the basis of age, sex, and biomarker values. Data were obtained from cohorts in China, Ghana, India, Mexico, and South Africa to span a spectrum of risk profiles.

FINDINGS

The TTT strategy recommended treatment to a larger number of people-who were generally at lower risk of diabetes complications-than the BTT. The BTT strategy recommended treatment to fewer people at higher risk. Compared with the TTT strategy, the BTT strategy would be expected to avert 24·4-30·5% more complications and be more cost-effective from a societal perspective (saving US$4·0-300·0 per disability-adjusted life-year averted in the countries simulated). Alternative treatment thresholds, matched by total cost or population size treated, did not change the comparative superiority of the BTT strategy, nor did titrating treatment using fasting plasma glucose (for areas without HbA1c testing). However, if insulin were unavailable, the BTT strategy would no longer be superior for preventing microvascular events and was superior only for preventing cardiovascular events.

INTERPRETATION

A BTT strategy is more effective and cost-effective than a TTT strategy in low-income and middle-income countries for prevention of both cardiovascular and microvascular complications of type 2 diabetes. However, the superiority of the BTT strategy for averting microvascular complications is contingent on insulin availability.

FUNDING

Rosenkranz Prize for Healthcare Research in Developing Countries and US National Institutes of Health (U54 MD010724, DP2 MD010478).

Management of non-traumatic avascular necrosis of the femoral head-a comparative analysis of the outcome of multiple small diameter drilling and core decompression with fibular grafting

BACKGROUND

The purpose of this study was to compare the clinical and radiological outcomes of multiple small diameter drilling and core decompression with fibular strut grafting in the management of non-traumatic avascular necrosis (AVN) of the femoral head.

MATERIALS AND METHODS

Outcomes of patients with AVN treated by multiple small diameter drilling (group 1) were compared retrospectively with patients treated by core decompression and fibular grafting (group 2). Harris hip score (HHS) was used to assess the clinical status pre- and postoperatively. Modified Ficat and Arlet classification was used to assess the radiological stage pre- and postoperatively.

RESULTS

Forty-six patients (68 hips) were included in this study. Group 1 consisted of 33 hips, and group 2 consisted of 35 hips. In stages I and IIB, there was no statistically significant difference in the final HHS between the two groups. However, in stages IIA and III, hips in group 2 had a better final HHS (P < 0.05). In terms of radiographic progression, there was no statistical difference between hips in stages I, IIA and stage IIB. However, in stage III, hips belonging to group 2 had better results (P < 0.05). Kaplan-Meier survivorship analysis showed better outcome in group 2 in stage III (P < 0.05).

CONCLUSIONS

Hips with AVN in the precollapse stage can be salvaged by core decompression with or without fibular grafting. Multiple small diameter drilling is relatively simple and carries less morbidity and hence preferred in stages I and II. However, in stage III disease, core decompression with fibular strut grafting gives better results.

Passive manipulation of free-surface instability by deformable solid bilayers

This study deals with the elastohydrodynamic coupling that occurs in the flow of a liquid layer down an inclined plane lined with a deformable solid bilayer and its consequences on the stability of the free surface of the liquid layer. The fluid is Newtonian and incompressible, while the linear elastic constitutive relation has been considered for the deformable solid bilayer, and the densities of the fluid and the two solids are kept equal. A temporal linear stability analysis is carried out for this coupled solid-fluid system. A long-wave asymptotic analysis is employed to obtain an analytical expression for the complex wavespeed in the low wave-number regime, and a numerical shooting method is used to solve the coupled set of governing differential equations in order to obtain the stability criterion for arbitrary values of the wave number. In a previous work on plane Couette flow past an elastic bilayer, Neelmegam et al. [Phys. Rev. E 90, 043004 (2014)PLEEE81539-375510.1103/PhysRevE.90.043004] showed that the instability of the flow can be significantly influenced by the nature of the solid layer, which is adjacent to the liquid layer. In stark contrast, for free-surface flow past a bilayer, our long-wave asymptotic analysis demonstrates that the stability of the free-surface mode is insensitive to the nature of the solid adjacent to the liquid layer. Instead, it is the effective shear modulus of the bilayer G_{eff} (given by H/G_{eff}=H_{1}/G_{1}+H_{2}/G_{2}, where H=H_{1}+H_{2} is the total thickness of the solid bilayer, H_{1} and H_{2} are the thicknesses of the two solid layers, and G_{1} and G_{2} are the shear moduli of the two solid layers) that determines the stability of the free surface in the long-wave limit. We show that for a given Reynolds number, the free-surface instability is stabilized when G_{eff} decreases below a critical value. At finite wave numbers, our numerical solution indicates that additional instabilities at the free surface and the liquid-solid interface can be induced by wall deformability and inertia in the fluid and solid. Interestingly, the onset of these additional instabilities is sensitive to the relative placements of the two solid layers comprising the bilayer. We show that it is possible to delay the onset of these additional instabilities, while still suppressing the free-surface instability, by manipulating the ratio of the shear moduli and the thicknesses of the two solid layers in the bilayer. At moderate Reynolds number and finite wave number, we demonstrate that an exchange of modes occurs between the gas-liquid and liquid-solid interfacial modes as the solid bilayer becomes more deformable. We demonstrate further that dissipative effects in the individual solid layers have an important bearing on the stability of the system, and they could also be exploited in suppressing the instability. This study thus shows that the ability to passively manipulate and control interfacial instabilities increases substantially with the use of solid bilayers.

Application of multivariate statistical techniques in microbial ecology

Recent advances in high-throughput methods of molecular analyses have led to an explosion of studies generating large-scale ecological data sets. In particular, noticeable effect has been attained in the field of microbial ecology, where new experimental approaches provided in-depth assessments of the composition, functions and dynamic changes of complex microbial communities. Because even a single high-throughput experiment produces large amount of data, powerful statistical techniques of multivariate analysis are well suited to analyse and interpret these data sets. Many different multivariate techniques are available, and often it is not clear which method should be applied to a particular data set. In this review, we describe and compare the most widely used multivariate statistical techniques including exploratory, interpretive and discriminatory procedures. We consider several important limitations and assumptions of these methods, and we present examples of how these approaches have been utilized in recent studies to provide insight into the ecology of the microbial world. Finally, we offer suggestions for the selection of appropriate methods based on the research question and data set structure.