A targeted gene panel that covers coding, non-coding and short tandem repeat regions improves the diagnosis of patients with neurodegenerative diseases

Genetic testing for neurodegenerative diseases (NDs) is highly challenging because of genetic heterogeneity and overlapping manifestations. Targeted-gene panels (TGPs), coupled with next-generation sequencing (NGS), can facilitate the profiling of a large repertoire of ND-related genes. Due to the technical limitations inherent in NGS and TGPs, short tandem repeat (STR) variations are often ignored. However, STR expansions are known to cause such NDs as Huntington\u27s disease and spinocerebellar ataxias type 3 (SCA3). Here, we studied the clinical utility of a custom-made TGP that targets 199 NDs and 311 ND-associated genes on 118 undiagnosed patients. At least one known or likely pathogenic variation was found in 54 patients; 27 patients demonstrated clinical profiles that matched the variants; and 16 patients whose original diagnosis were refined. A high concordance of variant calling were observed when comparing the results from TGP and whole-exome sequencing of four patients. Our in-house STR detection algorithm has reached a specificity of 0.88 and a sensitivity of 0.82 in our SCA3 cohort. This study also uncovered a trove of novel and recurrent variants that may enrich the repertoire of ND-related genetic markers. We propose that a combined comprehensive TGPs-bioinformatics pipeline can improve the clinical diagnosis of NDs

Postoperative hyperphosphatemia significantly associates with adverse survival in colorectal cancer patients

BACKGROUND: Hyperphosphatemia has been implicated in the development and treatment of various cancers. However, whether it can be used as a direct prognostic marker of colorectal cancer (CRC) has remained unexplored. Given new insights into the importance of hyperphosphatemia in CRC, we sought to evaluate the association of hyperphosphatemia with the clinical outcomes of this disease. METHODS: In a retrospective analysis of a well-characterized clinic-based cohort with 1,241 CRC patients, we assessed the association of postoperative hyperphosphatemia with patient overall survival. RESULTS: Postoperative hyperphosphatemia measured within the first month after surgery was significantly associated with CRC survival. Compared to patients with a normal phosphate level, those with hyperphosphatemia exhibited a significant unfavorable overall survival with a hazard ratio (HR) of 1.84 (95% confidence interval [CI] 1.49–2.29, P=2.6×10(−8), (log-rank P=1.2×10(−7)). Stratified analyses indicated the association was more pronounced in patients with colon (HR=2.00, 95% CI 1.57–2.56, P=3.17×10(−8)) but not rectal cancer (HR=0.96, 95% CI 0.58–1.59, P=0.889) (P interaction=0.023), as well as in those not receiving chemotherapy (HR=2.15, 95% CI 1.59–2.90, P=6.2×10(−7)) but not in those receiving chemotherapy (HR=1.30, 95% CI 0.92–1.82, P=0.136) (P interaction=0.012). Flexible parametric survival model demonstrated that the increased risk for death conferred by postoperative hyperphosphatemia persisted over 150 months after surgery. CONCLUSION: Our data indicated that postoperative hyperphosphatemia might be used as a prognostic marker of CRC patients after surgery. Since phosphate level is routinely tested in clinics, it may be incorporated into clinical models to predict CRC survival

Your Discomfort Is Valid: Big Feelings and Open Pedagogy

This article explores the affective reactions of 13 community college students engaged in an open pedagogy textbook creation project. The instructor and first author, a human development and family services faculty member and department chair at a community college in Oregon, received feedback from her students that the project impacted them differently than past learning experiences. Student engagement with research and the diverse personal experiences of their classmates fostered both personal challenges and growth. This article groups these experiences into themes and explores different theoretical lenses, including scaffolding (constructivism), transformative learning, threshold concepts and safe spaces/brave spaces. We discuss the support that students and faculty can use in similar learning situations, such as metacognition and cultural humility. Finally, we offer a visual model that open educators can use and adapt to consider how to raise or lower the stakes of an open pedagogy assignment

The effects of a family-centered psychosocial-based nutrition intervention in patients with advanced cancer: the PiCNIC2 pilot randomised controlled trial

BACKGROUND: Malnutrition in advanced cancer patients is common but limited and inconclusive data exists on the effectiveness of nutrition interventions. Feasibility and acceptability of a novel family-based nutritional psychosocial intervention were established recently. The aims of this present study were to assess the feasibility of undertaking a randomised controlled trial of the latter intervention, to pilot test outcome measures and to explore preliminary outcomes.METHODS: Pilot randomised controlled trial recruiting advanced cancer patients and family caregivers in Australia and Hong Kong. Participants were randomised and assigned to one of two groups, either a family-centered nutritional intervention or the control group receiving usual care only. The intervention provided 2-3 h of direct dietitian contact time with patients and family members over a 4-6-week period. During the intervention, issues with nutrition impact symptoms and food or eating-related psychosocial concerns were addressed through nutrition counselling, with a focus on improving nutrition-related communication between the dyads and setting nutritional goals. Feasibility assessment included recruitment, consent rate, retention rate, and acceptability of assessment tools. Validated nutritional and quality of life self-reported measures were used to collect patient and caregiver outcome data, including the 3-day food diary, the Patient-Generated Subjective Global Assessment Short Form, the Functional Assessment Anorexia/Cachexia scale, Eating-related Distress or Enjoyment, and measures of self-efficacy, carers' distress, anxiety and depression.RESULTS: Seventy-four patients and 54 family caregivers participated in the study. Recruitment was challenging, and for every patient agreeing to participate, 14-31 patients had to be screened. The consent rate was 44% in patients and 55% in caregivers. Only half the participants completed the trial's final assessment. The data showed promise for some patient outcomes in the intervention group, particularly with improvements in eating-related distress (p = 0.046 in the Australian data; p = 0.07 in the Hong Kong data), eating-related enjoyment (p = 0.024, Hong Kong data) and quality of life (p = 0.045, Australian data). Energy and protein intake also increased in a clinically meaningful way. Caregiver data on eating-related distress, anxiety, depression and caregiving burden, however, showed little or no change.CONCLUSIONS: Despite challenges with participant recruitment, the intervention demonstrates good potential to have positive effects on patients' nutritional status and eating-related distress. The results of this trial warrant a larger and fully-powered trial to ascertain the effectiveness of this intervention.TRIAL REGISTRATION: The trial was registered with the Australian &amp; New Zealand Clinical Trials Registry, registration number ACTRN12618001352291 .</p

Src activation by β-adrenoreceptors is a key switch for tumor metastasis

Norepinephrine (NE) can modulate multiple cellular functions important for cancer progression; however, how this single extracellular signal regulates such a broad array of cellular processes is unknown. Here, we identify Src as a key regulator of phosphoproteomic signaling networks activated in response to beta-adrenergic signaling in cancer cells. These results also identify a new mechanism of Src phosphorylation that mediates beta-adrenergic/PKA regulation of downstream networks, thereby enhancing tumor cell migration, invasion and growth. In human ovarian cancer samples, high tumoral NE levels were correlated with high pSrcY419 levels. Moreover, among cancer patients, the use of beta blockers was significantly associated with reduced cancer-related mortality. Collectively, these data provide a pivotal molecular target for disrupting neural signaling in the tumor microenvironment

Differential persistence of foot-and-mouth disease virus in African buffalo is related to virus virulence

Foot-and-mouth disease virus (FMDV) circulates as multiple serotypes and strains in many endemic regions. In particular the three Southern African Territories (SAT) serotypes are maintained effectively in their wildlife reservoir, the African buffalo, and individuals may harbour multiple SAT-serotypes for extended periods in the pharyngeal region. However the exact site and mechanism for persistence remain unclear. FMD in buffaloes offers a unique opportunity to study FMDV-persistence, as transmission from carrier ruminants has only convincingly been demonstrated for this species. Following co-infection of naïve African buffaloes with three SAT-serotypes isolated from field buffaloes; palatine tonsil swabs were the sample of choice for recovering infectious FMDV up to 400 days post infection (dpi). Post-mortem examination identified infectious virus for up to 185 dpi and viral genome up to 400 dpi in lymphoid tissue of the head and neck, mainly focussed in germinal centres. Interestingly viral persistence in vivo was not homogenous and the SAT-1 isolate persisted for longer than SAT-2 and SAT-3. Co-infection and passage of these SAT isolates in goat and buffalo cell lines demonstrated a direct correlation between persistence and cell killing capacity. These data suggest FMDV persistence occurs in the germinal centres of lymphoid tissue but the duration of persistence is related to virus replication and cell killing capacity.NJ was funded as a Wellcome Trust Intermediate Clinical Fellow and funding is acknowledged from the Biotechnology and Biological Sciences Research Council (BBS/E/I/00001523 and BBS/E/I/00001717).http://jvi.asm.org2016-11-30hb2016Microbiology and Plant Patholog

Videodensitometric analysis of advanced carotid plaque: correlation with MMP-9 and TIMP-1 expression

<p>Abstract</p> <p>Background</p> <p>Matrix metalloproteinase-9 (MMP-9) and tissue inhibitor of MMP (TIMP) promote derangement of the extracellular matrix, which is ultimately reflected in plaque images seen on ultrasound. Videodensitometry can identify structural disturbances in plaques.</p> <p>Objectives</p> <p>To establish the correlations between values determined using videodensitometry in B-mode ultrasound images of advanced carotid plaques and the total expression of MMP-9 and TIMP-1 in these removed plaques.</p> <p>Methods</p> <p>Thirty patients underwent ultrasonic tissue characterization of carotid plaques before surgery, using mean gray level (MGL), energy, entropy and homogeneity. Each patient was assigned preoperatively to one of 2 groups: group I, symptomatic patients (n = 16; 12 males; mean age 66.7 ± 6.8 years), and group II, asymptomatic patients (n = 14; 8 males; mean age 67.6 ± 6.81 years). Tissue specimens were analyzed for MMP-9 and TIMP-1 expression. Nine carotid arteries were used as normal tissue controls.</p> <p>Results</p> <p>MMP-9 expression levels were elevated in group II and in normal tissues compared to group I (p < 0.001). TIMP-1 levels were higher in group II than in group I, and significantly higher in normal tissues than in group I (p = 0.039). The MGL was higher in group II compared to group I (p = 0.038). Energy had greater values in group II compared to group I (<it>p </it>= 0.02). There were no differences between patient groups in homogeneity and entropy. Energy positively correlated with MMP-9 and TIMP-1 expression (p = 0.012 and p = 0.031 respectively). Homogeneity positively correlated with MMP-9 and TIMP-1 expression (p = 0.034 and p = 0.047 respectively). There were no correlations between protein expression and MGL or entropy.</p> <p>Conclusions</p> <p>Videodensitometric computer analysis of ultrasound scanning images can be used to identify stable carotid plaques, which have higher total expression levels of MMP-9 and TIMP-1 than unstable plaques.</p

The history of Coast Salish “woolly dogs” revealed by ancient genomics and Indigenous Knowledge

Ancestral Coast Salish societies in the Pacific Northwest kept long-haired "woolly dogs" that were bred and cared for over millennia. However, the dog wool-weaving tradition declined during the 19th century, and the population was lost. In this study, we analyzed genomic and isotopic data from a preserved woolly dog pelt from "Mutton," collected in 1859. Mutton is the only known example of an Indigenous North American dog with dominant precolonial ancestry postdating the onset of settler colonialism. We identified candidate genetic variants potentially linked with their distinct woolly phenotype. We integrated these data with interviews from Coast Salish Elders, Knowledge Keepers, and weavers about shared traditional knowledge and memories surrounding woolly dogs, their importance within Coast Salish societies, and how colonial policies led directly to their disappearance

Xバンド電子スピン共鳴によるGaAs;Er,OのEr濃度およびキャリア依存性の研究

博士（理学）神戸大