bluuebunny/crossref_metadata_2025 huggingface dataset:
Association of Insurance Status With Presentation, Treatment, and Survival in Melanoma in the Era of Immune Checkpoint Inhibitors
Authors: Jain Varsha , Venigalla Sriram , Reddy Vishruth K. , Lukens John N. , Mitchell Tara C. , Shabason Jacob E.
Published: September 2019

The effect of health insurance on management and outcomes in melanoma is unclear. Using the National Cancer Database (NCDB), we evaluated the effect of insurance on (1) stage at diagnosis, (2) receipt of immunotherapy, and (3) overall survival (OS) among patients with melanoma. We included patients with stage I–IV melanoma diagnosed from 2011 to 2015. Patients were stratified by age (below 65 vs. 65 y or above) and insurance (commercial, Medicare, Medicaid and uninsured). We evaluated the association between insurance and (1) stage at diagnosis (stage I–III vs. IV) and (2) receipt of immunotherapy (stage IV) using multivariable logistic regression. The association of insurance status with OS in metastatic patients who received immunotherapy was assessed using Kaplan-Meier and Cox proportional hazards analyses. The study included 167,130 patients; 52% had commercial insurance, 43% had Medicare, 3% had Medicaid and 2% were uninsured. In patients below 65 years, those with Medicaid and the uninsured had a higher likelihood of presenting with metastatic melanoma and were less likely to receive immunotherapy compared with those with commercial insurance. Further among those who received immunotherapy, patients with Medicaid (hazard ratio: 1.51, P=0.001) and no insurance (hazard ratio: 1.37, P=0.046) had an inferior OS. In patients 65 years or above, whereas Medicare was associated with an increased likelihood of presenting with metastatic disease, there was no significant difference in receipt of immunotherapy or OS as compared with commercial insurance. In this large modern cohort, insurance was associated with stage at diagnosis, receipt of immunotherapy, and OS for patients below 65 years old with melanoma.
Measuring Self-Reported Cognitive Function Following TBI: Development of the TBI-QOL Executive Function and Cognition-General Concerns Item Banks
Authors: Carlozzi Noelle E. , Tyner Callie E. , Kisala Pamela A. , Boulton Aaron J. , Sherer Mark , Chiaravalloti Nancy , Tulsky David S.
Published: September 2019

Objective:

To develop and calibrate new patient-reported outcome measures of cognitive concerns for individuals with traumatic brain injury (TBI).

Setting:

Five TBI model systems rehabilitation centers in the United States.

Participants:

Adults with medically confirmed history of TBI.

Design:

Cross-sectional survey in interview format.

Main Measures:

Traumatic Brain Injury-Quality of Life (TBI-QOL) Executive Function and TBI-QOL Cognition-General Concerns item banks.

Results:

A total of 569 adults with complicated-mild, moderate, or severe TBI completed preliminary item pools, which included 65 Executive Function items and 56 Cognition-General Concerns items. Confirmatory factor analysis supported the retention of 37 Executive Function and 39 Cognition-General Concerns items. Samejima's graded response model was used to estimate item parameters for associated computer adaptive test administrations, and informed the selection of corresponding static short forms. Data from an independent sample of 77 adults with complicated-mild, moderate, or severe TBI supported the test-retest reliability of these newly developed measures.

Conclusion:

The TBI-QOL Executive Function and Cognition-General Concerns item banks provide researchers and clinicians with reliable tools for assessing patient-reported post-TBI cognitive difficulties as part of the comprehensive TBI-QOL measurement system.
Daily Enemas for Pediatric Bowel Management
Authors: Mantel Connie , Carlin Kristen , Thomas Karen
Published: September 2019

Introduction

Children born with anorectal malformations, Hirschsprung disease, spinal cord defects, and related conditions have problems with constipation and fecal incontinence. In a large pediatric healthcare center, a weeklong outpatient program is offered to families, teaching daily high-volume enema administration. The purpose of this study is to assess the rate of adherence with daily enemas for bowel management and assess problems among children with elimination abnormalities.

Methods

A single-cohort observational study was conducted. Subjects included children ages 3–18 years and their parents who had attended a bowel management training program from April 2012 to December 2017. Data were collected utilizing an anonymous REDCap survey. Survey questions addressed adherence with daily enemas, supports and challenges, and parent-reported satisfaction and child acceptance.

Results

Surveys were sent to 112 parents, and 32 parents had completed the surveys. Approximately half of the sample, with a mean age of 9.9 years (SD = 3.7), adhered to daily enemas for bowel management. Parents reported a variety of problems and barriers to adherence with daily enemas, including child resistance (31.3%), difficulty retaining enema fluid (37.5%), cramping during enema (62.5%), time constraints (40.6%), getting or replacing equipment (28.1%), and bathroom space issues (25.0%). Sixty percent of the sample reported that enema administration requires more than 1 hour.

Discussion

In general, parents reported child acceptance, satisfaction, and limited difficulty with enema management; however, adherence was not as desired, and the rate of reported problems was high. Insight into problems experienced by parents provides nursing opportunity for educational programs that may improve adherence.
Assessment of Health Care Utilization for Dizziness in Ambulatory Care Settings in the United States
Authors: Dunlap Pamela M. , Khoja Samannaaz S. , Whitney Susan L. , Freburger Janet K.
Published: September 2019

Objective:

Describe patient and physician characteristics, and physician recommendations for ambulatory care visits for dizziness in the US.

Study Design:

Cross-sectional analysis of visits for dizziness from the National Ambulatory Medical Care Survey (2013–2015).

Setting:

Ambulatory care clinics in the US.

Patients:

20.6 million weighted adult visits [mean age 58.7 (1.0)] for dizziness, identified using ICD-9-CM codes (386.00–386.90, 780.40).

Main Outcome Measures:

Patient, clinical, and physician characteristics and physician diagnostic and treatment recommendations. Prevalence rates for benign paroxysmal positional vertigo (BPPV), unspecified dizziness, and other vestibular disorders were estimated, and descriptive statistics were used to characterize patients, physicians, and physicians’ recommendations.

Results:

The prevalence rate for dizziness visits was 8.8 per 1,000 (95% confidence interval [CI]: 7.5, 10.3). Most visits were for unspecified dizziness (75%), made by women (65%), whites (79%), and were insured by private insurance (50%). Visits for dizziness were to primary care physicians (51.9%), otolaryngologists (13.3%), and neurologists (9.6%). Imaging was ordered and medication prescription was provided in 5.5% and 20.1% of visits. Physical therapy (PT) was used for a higher percentage of BPPV visits (12.9%), than for other diagnoses (<1.0%). Physician treatment recommendations for vestibular diagnoses varied by physician specialty.

Conclusions:

A large percentage of visits had an unspecified diagnosis. A low number of visits for vestibular disorders were referred to PT. There are opportunities to improve care by using specific diagnoses and increasing the utilization of effective interventions for vestibular disorders.
PD-L1 Immunohistochemistry-Discrepant Results Between Synchronous Tumor Samples May Cause More Treatment Choice Dilemmas Than Molecular Heterogeneity in Patients With Advanced Non–Small Cell Lung Cancers
Authors: Lambros Laetitia , Quintin-Roué Isabelle , Bourhis Amélie , Remoué Annabelle , Le Flahec Glen , Marcorelles Pascale , Uguen Arnaud
Published: September 2019

Biomarker analyses have become mandatory for treatment choices in patients with advanced non–small cell lung cancers. PD-L1 expression for immunotherapy as well as oncogenic molecular alterations for targeted therapies must be analyzed in tumor samples. Intersample heterogeneity may cause dilemmas in treatment choices when faced with discrepant biomarker results. We led a retrospective study evaluating the potential impact on guideline-based therapeutic decisions of biomarker analyses performed in several synchronous tumor samples per patient. We collected retrospective data about patients with advanced non–small cell lung cancers, and synchronous tumor paired samples were analyzed for PD-L1 immunohistochemistry (IHC) and oncogene molecular statuses. Among 34 patients, none had a discrepant result between paired samples with respect to oncogene molecular statuses. At the opposite, intersample-discrepant PD-L1 IHC results may have caused treatment choice dilemmas for 6 (17.6%) patients discussing first-line therapy options (ie, immune checkpoint inhibitor therapy versus other systemic therapy with regard to the threshold of ≥50% PD-L1 IHC-positive tumor cells). In addition, for 6 (17.6%) other patients, different PD-L1 IHC results may have also influenced the choice of one therapy or another in second-line therapy (ie, with regard to the threshold of ≥1% PD-L1 IHC-positive tumor cells). In our case series, discrepant results with regard to PD-L1 IHC between paired tumor samples could generate more treatment choice dilemmas than the molecular heterogeneity of oncogenic drivers.
p16 Positive Histologically Bland Squamous Metaplasia of the Cervix
Authors: Goyal Abha , Ellenson Lora H. , Pirog Edyta C.
Published: September 2019

With increasing use of p16 immunohistochemistry (IHC) in diagnosis of premalignant lesions of cervix, we occasionally encounter p16 positivity in squamous metaplasia that lacks morphologic characteristics of “atypical squamous metaplasia” or of squamous intraepithelial lesion (SIL). Our study aims to investigate if transcriptionally active human papilloma virus (HPV) can be identified in such foci and if they have any relationship with squamo-columnar junction (SCJ) cells. Twenty-two cases of cervical specimens with at least a focus of p16 positive bland squamous metaplasia, were selected. HPV E6/E7 mRNA in situ hybridization followed by IHC for CK7 (SCJ biomarker), Ki67, and HPV16 E2, were performed. Follow-up information was obtained. Four cases were excluded due to insufficient tissue. Of the final 18 cases, HPV E6/E7 mRNA in situ hybridization was positive in all. Nine cases showed positivity in >50% cells and the epithelial thickness involved was ≥lower two-thirds in 13 cases. Of the further evaluable 15 cases, CK7 was positive in 14, Ki67 was positive in 10, and HPV16 E2 was negative in all. Concomitant high-grade squamous intraepithelial lesion was identified in 10 cases. On follow-up (duration: 1 to 19 mo), 6 patients showed histologic high-grade squamous intraepithelial lesion. Our study demonstrates that p16 positivity in squamous metaplasia of cervix is associated with the presence of transcriptionally active high-risk HPV even when there are no clear morphologic features of dysplasia. Our results suggest that these lesions are early SILs or SILs that are not yet morphologically evident, most of which arise from SCJ and should be closely followed.
NKX3.1 and Prostein Expression in Testicular Tissue and Sex Cord-stromal Tumors
Authors: Arnesen Christine , Eich Marie-Lisa , Pena Maria D.C. Rodriguez , Cappel Jaclyn R. , Schwartz Lauren , Rais-Bahrami Soroush , Faraj Sheila F. , Prieto Granada Carlos , Gordetsky Jennifer B.
Published: September 2019

Prostate cancer is well known to metastasize to the testis and is not an uncommon finding on castration performed for advanced disease. Although germ cell tumors make up the majority of testis neoplasms, there are more rare tumors, such as rete testis adenocarcinoma, that can mimic metastatic disease. NKX3.1 and prostein (P501S) are antibodies highly specific for prostate origin. Relatively little is known of the expression of these markers in testicular tissue. We investigated the expression of NKX3.1 and P501S in testicular tissues, sex cord-stromal tumors, germ cell tumors, and rete testis adenocarcinoma. We found strong diffuse nuclear staining for NKX3.1 in Sertoli cells of the testis. Expression of NKX3.1 was seen in 0/3 ovarian Sertoli cell tumors, 1/4 testicular Sertoli cell tumors, and in the Sertoli cell component of 1/12 ovarian Sertoli-Leydig cell tumors. We found moderate, diffuse cytoplasmic positivity for P501S in rete testis epithelium and in testicular Leydig cells. P501S also highlighted Leydig cells in 9/12 Sertoli-Leydig cell tumors of the ovary. Two of 3 Leydig cell tumors of the testis showed weak to moderate, diffuse cytoplasmic staining for P501S. All cases of embryonal carcinoma and pure seminoma were negative for both NKX3.1 and P501S. One case of rete testis adenocarcinoma showed patchy positivity for both NKX3.1 and P501S. In conclusion, NKX3.1 shows routine expression in Sertoli cells and P501S shows routine expression in Leydig cells and rete testis epithelium. In addition, these markers can be positive in sex cord-stromal tumors and rete testis adenocarcinoma.
Specificity of Procedure volume and its Association With Postoperative Mortality in Digestive Cancer Surgery
Authors: El Amrani Mehdi , Lenne Xavier , Clement Guillaume , Delpero Jean-Robert , Theis Didier , Pruvot François-René , Bruandet Amelie , Truant Stephanie
Published: September 2019

Objectives:

We aimed to examine whether the improved outcome of a digestive cancer procedure in high-volume hospitals is specific or correlates with that of other digestive cancer procedures, and determine if the discriminant cut-off of hospital volume may influence postoperative mortality (POM) regardless of the procedure.

Background:

Performing complex surgeries in tertiary centers is associated with improved outcome. However, the association between POM and hospital volume of nonspecific procedures is unknown.

Methods:

Patients who underwent colectomy, proctectomy, esophagectomy, gastrectomy, pancreatectomy, and hepatectomy for cancer between 2012 and 2017 were identified in the French nationwide database. Chi-square automatic interaction detector was used to identify the cut-off values of the annual caseload affecting the 90-day POM. A common threshold was estimated by minimization of chi-square distance taking into account the specific mortality of each procedure.

Results:

Overall, 225,752 patients were identified. Hospitals were categorized according to the procedure volume (colectomy: ≥80 cases/yr, proctectomy: ≥35/yr, esophagectomy: ≥41/yr, gastrectomy: ≥16/yr, pancreatectomy: ≥26/yr, and hepatectomy: ≥76/yr). The overall 90-day POM was 5.1% and varied significantly with volume. The benefits of high volume were transferable across procedures. High-volume hospitals for colorectal cancer surgery significantly influenced the risk of death after hepatectomy (P < 0.001) and pancreatectomy (P < 0.001). The common threshold for all procedures that influenced POM was 199 cases/yr (odds ratio 1.29, P < 0.001).

Conclusion:

In digestive cancer surgery, the volume–POM relationship of one procedure was associated with the volume of other procedures. Thus, tertiary hospitals should be defined according to the common threshold of different procedures.
Dynamic biological adhesion: mechanisms for controlling attachment during locomotion
Authors: Federle Walter , Labonte David
Published: September 2019

The rapid control of surface attachment is a key feature of natural adhesive systems used for locomotion, and a property highly desirable for man-made adhesives. Here, we describe the challenges of adhesion control and the timescales involved across diverse biological attachment systems and different adhesive mechanisms. The most widespread control principle for dynamic surface attachment in climbing animals is that adhesion is ‘shear-sensitive’ (directional): pulling adhesive pads towards the body results in strong attachment, whereas pushing them away from it leads to easy detachment, providing a rapid mechanical ‘switch’. Shear-sensitivity is based on changes of contact area and adhesive strength, which in turn arise from non-adhesive default positions, the mechanics of peeling, pad sliding, and the targeted storage and controlled release of elastic strain energy. The control of adhesion via shear forces is deeply integrated with the climbing animals’ anatomy and locomotion, and involves both active neuromuscular control, and rapid passive responses of sophisticated mechanical systems. The resulting dynamic adhesive systems are robust, reliable, versatile and nevertheless remarkably simple.

This article is part of the theme issue ‘Transdisciplinary approaches to the study of adhesion and adhesives in biological systems’.
Bidirectional crosstalk between Hypoxia-Inducible Factor and glucocorticoid signalling in zebrafish larvae
Authors: Marchi Davide , Santhakumar Kirankumar , Markham Eleanor , Li Nan , Storbeck Karl-Heinz , Krone Nils , Cunliffe Vincent T. , van Eeden Fredericus J.M.
Published: September 2019

In the last decades in vitro studies highlighted the potential for crosstalk between Hypoxia-Inducible Factor-(HIF) and glucocorticoid-(GC) signalling pathways. However, how this interplay precisely occurs in vivo is still debated. Here, we use zebrafish larvae (Danio rerio) to elucidate how and to what degree hypoxic signalling affects the endogenous glucocorticoid pathway and vice versa, in vivo. Firstly, our results demonstrate that in the presence of upregulated HIF signalling, both glucocorticoid receptor (Gr) responsiveness and endogenous cortisol levels are repressed in 5 days post fertilisation larvae. In addition, despite HIF activity being low at normoxia, our data show that it already impedes both glucocorticoid activity and levels. Secondly, we further analysed the in vivo contribution of glucocorticoids to HIF activity. Interestingly, our results show that both glucocorticoid receptor (GR) and mineralocorticoid receptor (MR) play a key role in enhancing it. Finally, we found indications that glucocorticoids promote HIF signalling via multiple routes. Cumulatively, our findings allowed us to suggest a model for how this crosstalk occurs in vivo.

Author summary

Hypoxia is a common pathophysiological condition to which cells must rapidly respond in order to prevent metabolic shutdown and subsequent death. This is achieved via the activity of Hypoxia-Inducible Factors (HIFs), which are key oxygen sensors that mediate the ability of the cell to cope with decreased oxygen levels.

Although it aims to restore tissue oxygenation and perfusion, it can sometimes be maladaptive and contributes to a variety of pathological conditions including inflammation, tissue ischemia, stroke and growth of solid tumours. In this regard, synthetic glucocorticoids which are analogous to naturally occurring steroid hormones, have been used for decades as anti-inflammatory drugs for treating pathological conditions which are linked to hypoxia (i.e. asthma, rheumatoid arthritis, ischemic injury). Indeed, previous in vitro studies highlighted the presence of a crosstalk between HIF and glucocorticoids. However, how this interplay precisely occurs in an organism and what the molecular mechanism is behind it are questions that still remain unanswered. Here, we provide a thorough in vivo genetic analysis, which allowed us to propose a logical model of interaction between glucocorticoid and HIF signalling. In addition, our results are important because they suggest a new route to downregulate HIF for clinical purposes.
Sex differences in cortisol and memory following acute social stress in amnestic mild cognitive impairment
Authors: Murphy Kelly J. , Hodges Travis E. , Sheppard Paul A.S. , Troyer Angela K. , Hampson Elizabeth , Galea Liisa A.M.
Published: September 2019

Objective

Older adults with amnestic mild cognitive impairment (aMCI) develop Alzheimer’s type dementia approximately ten times faster annually than the normal population. Adrenal hormones are associated with aging and cognition. We investigated the relationship between acute stress, cortisol, and memory function in aMCI with an exploratory analysis of sex.

Method

Salivary cortisol was sampled diurnally and during two test sessions, one session with the Trier Social Stress Test (TSST), to explore differences in the relationship between cortisol and memory function in age-normal cognition (NA) and aMCI. Participants with aMCI (n=6 women, 9 men; mean age=75) or similarly aged NA (n=9 women, 7 men, mean age=75) were given tests of episodic, associative, and spatial working memory with a psychosocial stressor (TSST) in the second session.

Results

The aMCI group performed worse on the memory tests than NA as expected, and males with aMCI had elevated cortisol levels on test days. Immediate episodic memory was enhanced by social stress in NA but not in the aMCI group, indicating that stress-induced alterations in memory are different in individuals with aMCI. High cortisol was associated with impaired performance on episodic memory in aMCI males only. Cortisol in Session 1 moderated the relationship with spatial working memory, whereby higher cortisol was associated with worse performance in NA, but better spatial working memory in aMCI. In addition, effects of aMCI on perceived anxiety in response to stress exposure were moderated by stress-induced cortisol in a sex-specific manner.

Conclusions

We show effects of aMCI on Test Session cortisol levels and effects on perceived anxiety, and stress-induced impairments in memory in males with aMCI in our exploratory sample. Future studies should explore sex as a biological variable as our findings suggests that effects at the confluence of aMCI and stress can be obfuscated without sex as a consideration.
Longitudinal Automatic Segmentation of Hippocampal Subfields (LASHiS) using Multi-Contrast MRI
Authors: Shaw Thomas , York Ashley , Ziaei Maryam , Barth Markus , Bollmann Steffen ,   for the Alzheimer’s Disease Neuroimaging Initiative
Published: September 2019

The volumetric and morphometric examination of hippocampus formation subfields in a longitudinal manner using in vivo MRI could lead to more sensitive biomarkers for neuropsychiatric disorders and diseases including Alzheimer’s disease, as the anatomical subregions are functionally specialised. Longitudinal processing allows for increased sensitivity due to reduced confounds of inter-subject variability and higher effect-sensitivity than cross-sectional designs. We examined the performance of a new longitudinal pipeline (Longitudinal Automatic Segmentation of Hippocampus Subfields [LASHiS]) against three freely available, published approaches. LASHiS automatically segments hippocampus formation subfields by propagating labels from cross-sectionally labelled time point scans using joint-label fusion to a non-linearly realigned ‘single subject template’, where image segmentation occurs free of bias to any individual time point. Our pipeline measures tissue characteristics available in in vivo high-resolution MRI scans, at both clinical (3 Tesla) and ultra-high field strength (7 Tesla) and differs from previous longitudinal segmentation pipelines in that it leverages multi-contrast information in the segmentation process. LASHiS produces robust and reliable automatic multi-contrast segmentations of hippocampus formation subfields, as measured by higher volume similarity coefficients and Dice coefficients for test-retest reliability and robust longitudinal Bayesian Linear Mixed Effects results at 7 T, while showing sound results at 3 T. All code for this project including the automatic pipeline is available at https://github.com/CAIsr/LASHiS
Studying functional brain networks from dry electrode EEG set during music and resting states in neurodevelopment disorder
Authors: Sareen Ekansh , Gupta Anubha , Verma Rohit , Achary G. Krishnaveni , Varkey Blessin
Published: September 2019

There has been an emerging interest in the study of functional brain networks in cognitive neuroscience in order to better understand brain responses to different stimuli. Such studies can help in understanding brain connectivity alterations that arise in neurodevelopmental disorders such as intellectual disability (ID). This research contributes to this body of knowledge by studying alterations in brain connectivity in ID compared to the typically developing controls (TDC). Electroencephalography (EEG) data of subjects with ID and TDC is collected through limited channel dry electrode system. Data was analyzed for the auditory and rest state processing along with the study of intra-network connectivity of the brain via clustering coefficients. Research findings indicate evidences for links between the sensory deficits and social impairment in ID individuals.
Reward Evokes Visual Perceptual Learning Following Reinforcement Learning Rules
Authors: Wang Zhiyan , Kim Dongho , Pedroncelli Giorgia , Sasaki Yuka , Watanabe Takeo
Published: September 2019

Visual perceptual learning (VPL) is defined as a long-term performance enhancement as a result of visual experiences. A number of studies have demonstrated that reward can evoke VPL. However, the mechanisms of how reward evoke VPL remain unknown. One possible hypothesis is that VPL is obtained through reward related reinforcement processing. If this hypothesis is true, learning can only occur when reward follows the stimulus presentation. Another interpretation is that VPL is acquired through an enhancement of alertness in association with reward. If the alertness hypothesis is true, learning should occur when reward precedes the stimulus presentation. In our study, we tested the plausibility of the two hypotheses by manipulating the order of reward and stimulus presentation. In Experiment 1, we separated participants into two groups. During training, the ‘Before’ group received water reward 400ms prior to the onset of trained orientation stimulus while the ‘After’ group received water reward 400ms subsequent to the onset of trained orientation stimulus. Both groups were trained using the Continuous Flash Suppression paradigm to render the stimulus imperceptible to the participants by the presentation of dynamic noise in the untrained eye. We found training only in the ‘After’ group indicating that reward may evoke learning through reinforcement-like processing. In Experiment 2, we excluded the possibility that alertness may not be sufficient to elicit learning when presented before stimulus. We presented beep sound prior to the onset of stimulus to increase alertness. Our finding demonstrated that alertness is sufficient enough to evoke learning. In conclusion, our study provided evidence that reward can evoke VPL through reinforcement process.
Visualizing cellular heterogeneity by quantifying the dynamics of MAPK activity in live mammalian cells with synthetic fluorescent biosensors
Authors: Ma Min , Bordignon Pino , Dotto Gian-Paolo , Pelet Serge
Published: September 2019

Mitogen-Activated Protein Kinases (MAPKs) control a wide array of cellular functions by transducing extracellular information into defined biological responses. In order to understand how these pathways are regulated, dynamic single cell measurements are highly needed. Fluorescence microscopy is well suited to perform these measurements, however, more dynamic and sensitive biosensors that allow the quantification of signaling activity in living mammalian cells are required. We have engineered a synthetic fluorescent substrate for human MAPKs that relocates from the nucleus to the cytoplasm when phosphorylated by the kinase. We demonstrate that this reporter provides a better sensitivity relative to other similar biosensors and has allowed the monitoring of ERK MAPK activity pulses upon a single physiological EGF stimulation. In addition, we display its applicability to other MAPKs and in multiple cancer cell lines or primary cells as well as its application in vivo in developing tumors. Using our newly developed biosensors, dynamic single cell measurements with high temporal resolution can be obtained. These reporters can be widely applied to the analysis of molecular mechanisms of MAPK signaling in healthy and diseased state, in cell culture assays or in vivo.
Deep learning models predict regulatory variants in pancreatic islets and refine type 2 diabetes association signals
Authors: Wesolowska-Andersen Agata , Yu Grace Zhuo , Nylander Vibe , Abaitua Fernando , Thurner Matthias , Torres Jason , Mahajan Anubha , Gloyn Anna L , McCarthy Mark I
Published: September 2019

Genome-wide association analyses have uncovered multiple genomic regions associated with T2D, but identification of the causal variants at these remains a challenge. There is growing interest in the potential of deep learning models - which predict epigenome features from DNA sequence - to support inference concerning the regulatory effects of disease-associated variants. Here, we evaluate the advantages of training convolutional neural network (CNN) models on a broad set of epigenomic features collected in a single disease-relevant tissue – pancreatic islets in the case of type 2 diabetes (T2D) - as opposed to models trained on multiple human tissues. We report convergence of CNN-based metrics of regulatory function with conventional approaches to variant prioritization – genetic fine-mapping and regulatory annotation enrichment. We demonstrate that CNN-based analyses can refine association signals at T2D-associated loci and provide experimental validation for one such signal. We anticipate that these approaches will become routine in downstream analyses of GWAS.
CD99 regulates cancer cell transendothelial migration and endothelial cell function via CDC42 and actin remodelling
Authors: Mannion Aarren J. , Odell Adam F. , Taylor Alison , Jones Pamela F. , Cook Graham P
Published: September 2019

Metastasis requires tumour cells to cross endothelial cell (EC) barriers and this occurs using mechanisms similar to those used by extravasating leucocytes during inflammation. The cell surface receptor CD99 is expressed by leucocytes and EC and participates in inflammatory transendothelial migration (TEM). CD99 is also expressed by tumour cells and we have analysed its role in tumour progression and cancer cell TEM. In a xenograft model, CD99 expression inhibited the metastatic progression of human breast cancer.In vitro, tumour cell CD99 was required for adhesion to ECs. However, tumour cell CD99 inhibited the invasion of the endothelial barrier by breast and prostate cancer cells and TEM itself. Furthermore, tumour cell CD99 depletion was associated with cytoskeletal remodelling. Loss of EC CD99 enhanced endothelial barrier function and reduced tumour cell TEM. Mechanistically, CD99 loss enhanced the expression and activity of CDC42, a known cytoskeletal organiser. CDC42 positively regulates EC angiogenic activity and the enhanced CDC42 activity resulting from loss of EC CD99 increased angiogenesis. As a signal transduction hub, CDC42 activity impacts upon many of the hallmarks of cancer. The functional link between CD99 and CDC42 identified here implicates CD99 in regulating these diverse pathways by modulation of CDC42 activity.
Experience-dependent reorganization drives development of a binocularly unified cortical representation of orientation
Authors: Whitney David , Chang Jeremy T. , Fitzpatrick David
Published: September 2019

Across sensory areas, neural microcircuits consolidate diverse streams of information into unified, representations of the external world. In the carnivore visual cortex, where eye-specific inputs converge, it has been posited that a single, shared columnar representation of orientation develops independent of sensory experience. In this study, in vivo calcium imaging with columnar and cellular resolution reveals a strikingly different developmental process in ferret visual cortex, starting with an early developmental period in which contralateral, ipsilateral or binocular stimulation each yield distinct well-organized representations of orientation that are misaligned at the columnar and cellular scale. Experience-dependent processes drive the reorganization of these three representations towards a single binocularly-aligned representation resembling the early binocular representation through concerted shifts in the preferred orientation of individual neurons. Thus, contrary to previous findings, a unified binocular representation of orientation results from an experience-dependent process that aligns the activity patterns of three distinct neural representations.
A simple method to determine the elimination half-life of drugs displaying noncumulative toxicity
Authors: Nagarajan Deepesh , Venkatesh Preetham , Thakur Chandrani , Datey Akshay , Chandra Nagasuma , Chakravortty Dipshikha
Published: September 2019

The pharmacokinetic characterization of a drug, especially the determination of its biological half-life, is an essential step during the early phases of drug development. An adequate half-life is amongst the many properties needed for selecting a drug candidate for clinical trials. Conversely, drug candidates possessing inadequate half-lives may be modified or eliminated from the drug discovery pipeline altogether. Several methods exist for determining the half-lives of drugs, namely HPLC, fluorescence assays, radioassays, radioimmunoassays, and elemental mass spectrometric assays. However, all these techniques are resource and labor-intensive, and cannot be used for the high-throughput half-life determination of hundreds of drug candidates. Here, we describe TOXHL: a simple technique to determine the half-lives of compounds displaying noncumulative toxicity. To calculate the half life, TOXHLonly relies on the survival outcomes of three experiments performed on an animal model: an acute toxicity experiment, a cumulative toxicity experiment, and a multi-dose experiment at different dosing intervals. As a proof of concept, we use TOXHLto determine the peritoneal half-life of Ω76, an antimicrobial peptide. The half-life of Ω76 determined by TOXHLis in good agreement with results from a standard mass spectrometric method, validating this approach.
Expressed barcodes enable clonal characterization of chemotherapeutic responses in chronic lymphocytic leukemia
Authors: Al’Khafaji Aziz , Gutierrez Catherine , Brenner Eric , Durrett Russell , Johnson Kaitlyn E. , Zhang Wandi , Li Shuqiang , Livak Kenneth J. , Neuberg Donna , Brock Amy , Wu Catherine J.
Published: September 2019

The remarkable evolutionary capacity of cancer is a major challenge to current therapeutic efforts. Fueling this evolution is its vast clonal heterogeneity and ability to adapt to diverse selective pressures. Although the genetic and transcriptional mechanisms underlying these responses have been independently evaluated, the ability to couple genetic alterations present within individual clones to their respective transcriptional or functional outputs has been lacking in the field. To this end, we developed a high-complexity expressed barcode library that integrates DNA barcoding with single-cell RNA sequencing through use of the CROP-seq sgRNA expression/capture system, and which is compatible with the COLBERT clonal isolation workflow for subsequent genomic and epigenomic characterization of specific clones of interest. We applied this approach to study chronic lymphocytic leukemia (CLL), a mature B cell malignancy notable for its genetic and transcriptomic heterogeneity and variable disease course. Here, we demonstrate the clonal composition and gene expression states of HG3, a CLL cell line harboring the common alteration del(13q), in response to front-line cytotoxic therapy of fludarabine and mafosfamide (an analog of the clinically used cyclophosphamide). Analysis of clonal abundance and clonally-resolved single-cell RNA sequencing revealed that only a small fraction of clones consistently survived therapy. These rare highly drug tolerant clones comprise 94% of the post-treatment population and share a stable, pre-existing gene expression state characterized by upregulation of CXCR4 and WNT signaling and a number of DNA damage and cell survival genes. Taken together, these data demonstrate at unprecedented resolution the diverse clonal characteristics and therapeutic responses of a heterogeneous cancer cell population. Further, this approach provides a template for the high-resolution study of thousands of clones and the respective gene expression states underlying their response to therapy.
Delineating the rules for structural adaptation of membrane-associated proteins to evolutionary changes in membrane lipidome
Authors: Makarova Maria , Peter Maria , Balogh Gabor , Glatz Attila , MacRae James I. , Mora Nestor Lopez , Booth Paula , Makeyev Eugene , Vigh Laszlo , Oliferenko Snezhana
Published: September 2019

Membrane function is fundamental to life. Each species explores membrane lipid diversity within a genetically predefined range of possibilities. How membrane lipid composition in turn defines the functional space available for evolution of membrane-centered processes remains largely unknown. We address this fundamental question using related fission yeastsSchizosaccharomyces pombeandSchizosaccharomyces japonicus. We show that unlikeS. pombethat generates membranes where both glycerophospholipid acyl tails are predominantly 16-18 carbons long,S. japonicussynthesizes unusual ‘asymmetrical’ glycerophospholipids where the tails differ in length by 6-8 carbons. This results in stiffer bilayers with distinct lipid packing properties. RetroengineeredS. pombesynthesizing theS. japonicus-type phospholipids exhibits unfolded protein response and downregulates secretion. Importantly, our protein sequence comparisons and domain swap experiments indicate that transmembrane helices co-evolve with membranes, suggesting that, on the evolutionary scale, changes in membrane lipid composition may necessitate extensive adaptation of the membrane-associated proteome.
Evidence for incipient alarm signalling in fish
Authors: Wisenden Brian D.
Published: September 2019

In Focus: Bairos‐Novak, K.R., Ferrari, M.C.O., & Chivers, D.P. (2019). A novel alarm signal in aquatic prey: Familiar minnows coordinate group defences against predators through chemical disturbance cues. Journal of Animal Ecology, 88, 1281–1290, https://doi.org/10.1111/1365-2656.12986. Chemicals released during predation have long been studied as cues to nearby prey that predators are active in the vicinity. Until now, these chemicals have been labelled as cues because there was no compelling evidence for the necessary components of a communication system, namely (a) voluntary control of release of information, (b) capacity for graded responses and (c) the presence of specialized structures for the production and release of the signal. New findings by Bairos‐Novak, Ferrari, and Chivers (2019) show that fathead minnows alter the potency of disturbance “cues” when in the presence of other fathead minnows compared to when they are alone and produce either more or different disturbance “cues” when in the presence of familiar conspecifics compared to when they are in the presence of unfamiliar conspecifics. The behavioural response to these cues is shoaling, which would confer fitness benefits to the sender, thereby qualifying as a signal rather than a cue. This is a significant advancement in the field of chemical ecology of aquatic organisms because disturbance “cues” by fathead minnows bear two of the three hallmarks of an incipient disturbance “signal”.
A Meta‐Analysis of School Quality Capitalization in U.S. House Prices
Authors: Turnbull Geoffrey K. , Zheng Minrong
Published: September 2019

School quality capitalization studies report widely mixed results. This article conducts meta‐analysis to identify the data characteristics and research methods that explain this variation. The way the school quality is measured matters but no single measure clearly dominates. Both boundary and neighborhood fixed effects significantly control for the influence of neighborhood amenities. Increasing the number of quality variables reduces the capitalization significance of each. Regional differences also appear to matter; studies using data drawn from the South exhibit weaker capitalization. Also, it is surprising that econometric methods do not appear to be driving results.
Sample Mining and Data Mining: Combined Real‐Time and Retrospective Approaches for the Identification of Emerging Novel Psychoactive Substances
Authors: Krotulski Alex J. , Varnum Susan Jansen , Logan Barry K.
Published: September 2019

Novel psychoactive substances (NPS) are synthetic drugs that pose serious public health and safety concerns. A multitude of NPS have been identified in the United States, often implicated in forensic investigations. The most common and effective manner for identifying NPS is by use of mass spectrometry and the true utility lies within nontargeted acquisition techniques. During this study, a liquid chromatography quadrupole time‐of‐flight mass spectrometry (LC‐QTOF‐MS) assay was developed, validated, and implemented for forensic toxicology testing. A SCIEX TripleTOF™ 5600 + with SWATH® acquisition was used. Resulting data were compared against an extensive library database containing more than 800 compounds. The LC‐QTOF‐MS assay was applied to the reanalysis of biological sample extracts to discover emergent NPS. More than 3,000 sample extracts were analyzed, and more than 20 emerging NPS were detected for the first time. Among these were isopropyl‐U‐47700, 3,4‐methylenedioxy‐U‐47700, fluorofuranylfentanyl, N‐methyl norfentanyl, 2F‐deschloroketamine, 3,4‐methylenedioxy‐alpha‐PHP, eutylone, and N‐ethyl hexedrone.
Impact of nutritional status, muscle mass and oral status on recovery of full oral intake among stroke patients receiving enteral nutrition: A retrospective cohort study
Authors: Nishioka Shinta , Yamasaki Kazumi , Ogawa Kenji , Oishi Kana , Yano Yoko , Okazaki Yuka , Nakashima Ryusei , Kurihara Masaki
Published: September 2019

Aim

To clarify the correlation between malnutrition, muscle mass and oral status, and swallowing function recovery in stroke patients receiving enteral nutrition.

Methods

Patients with stroke and dysphagia receiving any amount of enteral nutrition in rehabilitation wards from 2012 to 2016 were eligible for inclusion in this retrospective study. On admission, body composition by bioimpedance analysis, malnutrition confirmed by the European Society for Clinical Nutrition and Metabolism criteria, oral status, functional independence measure and demographic data were collected. Characteristics were compared between “oral intake alone” and “artificial nutrition” groups based on the discharge status. Kaplan‐Meier methods and the Cox proportional hazards model were used to determine explanatory factors for the probability of full oral intake.

Results

Among 174 patients, 113 were analysed (55 women; median age, 77 years). Overall, 61% and 39% were classified as “oral intake alone” and “artificial nutrition,” respectively. Days from onset to admission to rehabilitation wards and motor Functional Independence Measure were higher in the “oral intake alone” group. Kaplan‐Meier analysis demonstrated that patients with lower muscle mass exhibited lower probability of full oral intake (P = .009). The Cox proportional hazards model suggested that lower muscle mass (hazard ratio, 0.493; 95% CI, 0.286‐0.850) and poor oral hygiene (hazard ratio, 0.573; 95% CI, 0.333‐0.987) were independently correlated with “oral intake alone” status. Malnutrition and other oral status are not related to achieving full oral intake.

Conclusions

Skeletal muscle mass and oral hygiene are independently correlated with full oral intake among stroke patients receiving enteral nutrition during the rehabilitation phase.
HLA‐DQ genotypes relative risks for celiac disease in Arabs: A case‐control study
Authors: Al‐Hussaini Abdulrahman , Eltayeb‐Elsheikh Nezar , Alharthi Hanan , Osman Awad , Alshahrani Maram , Sandogji Ibrahim , Alrashidi Sami , Bashir Muhammed Salman
Published: September 2019

Objectives

It remains unknown what degree of risk is conferred by celiac disease (CD)‐predisposing human leukocyte antigen (HLA)‐DQ genotypes in Saudi Arabia compared with in Western countries. In this study, we aimed to determine the CD risk gradient associated with the HLA‐DQ genotypes and to compare HLA‐DQ genotypes between symptomatic patients with CD and screening‐identified asymptomatic CD patients.

Methods

We enrolled three groups of subjects, including 46 CD children diagnosed consecutively over the past 10 years, 54 CD children diagnosed during a mass screening of schoolchildren, and 192 healthy controls. All the participants were typed for the HLA‐DQA1 and HLA‐DQB1 genes by polymerase chain reaction sequence‐specific oligonucleotide probes.

Results

Comparing the patients with CD to controls, we identified 5 groups in the CD risk gradient: (i) very high risk associated with the DQ2.5/DQ8 genotype (odds ratio [OR] 46.93); (ii) high risk (homozygous DQ2.5, DQ2.5/DQ2.2; OR 4.12‐5.04); (iii) intermediate risk (heterozygous DQ2.5, DQ8/DQ2.2; OR 1.61 and 1.67); (iv) low risk (DQ8, DQ2.2); and (v) very low risk (DQ2.x, DQX.5, DQX.x). Heterozygous DQ8 was more common in screening‐identified group compared to symptomatic patients (13.0% vs 2.2%); however, other genotypes were very similar between the two groups.

Conclusion

The highest risk of developing CD in our Saudi Arabia population is associated with the DQ2.5/DQ8 genotype.
Facilitation of glutamate, but not GABA, release in Familial Alzheimer's APP mutant Knock‐in rats with increased β‐cleavage of APP
Authors: Tambini Marc D. , Yao Wen , D'Adamio Luciano
Published: September 2019

Amyloid precursor protein (APP) modulates glutamate release via cytoplasmic and intravesicular interactions with the synaptic vesicle release machinery. The intravesicular domain, called ISVAID, contains the BACE1 cleavage site of APP. We have tested the functional significance of BACE1 processing of APP using App‐Swedish (Apps) knock‐in rats, which carry an App mutation that causes familial Alzheimer's disease (FAD) in humans. We show that in Apps rats, β‐cleavage of APP is favored over α‐cleavage. Apps rats show facilitated glutamate, but not GABA, release. Our data support the notion that APP tunes glutamate release, and that BACE1 cleavage of the ISVAID segment of APP facilitates this function. We define this phenomenon as BACE1 on APP‐dependent glutamate release (BAD‐Glu). Unsurprisingly, Apps rats show no evidence of AD‐related pathology at 15 days and 3 months of age, indicating that alterations in BAD‐Glu are not caused by pathological lesions. The evidence that a pathogenic APP mutation causes an early enhancement of BAD‐Glu suggests that alterations of BACE1 processing of APP in glutamatergic synaptic vesicles could contribute to dementia.