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Study Objectives: Optimal cutoff values of oximetry indices that differentiate obstructive sleep apnea (OSA) from primary snoring (PS) are not well-established. Our study aimed to assess the utility of overnight oximetry indices in differentiating PS from OSA and assessing OSA severity, compared to polysomnography, in children with suspected OSA., Methods: This was a retrospective study of children (1-18 years of age) with snoring who underwent polysomnography. Patients with Down syndrome, craniofacial anomalies, known genetic syndromes, neuromuscular conditions, or a central apnea index ≥ 5 were excluded. Demographic data, polysomnography variables, and oximetry indices (eg, oxygen desaturation index [ODI 3 , defined as number of ≥ 3% desaturation episodes/h of artifact-free recording time, and SpO 2 nadir]) were collected., Results: Of 1,203 children (mean age 9.1 ± 3.9 years, 67.7% males), 91.8% (847/923) ≤ 12 years and 84.3% (236/280) > 12 years of age had OSA. The optimal cutoff of ODI 3 for differentiating PS from OSA was 2.4 (sensitivity [Se]: 78.8% [75.9-81.6%]; specificity [Sp]: 80.5% [69.9-88.7%]) in children ≤ 12 years of age and 3.6 (Se: 71.1% [64.8-76.8%]; Sp: 91.1% [78.8-97.5%]) in children > 12 years of age. The optimal cutoffs of ODI 3 for differentiating PS from mild, moderate, and severe OSA categories were 2.0 (Se: 70.1% [65.3-74.5%]; Sp: 70.1% [58.6-80.0%]), 3.7 (Se: 82.3% [76.6-87.1%]; Sp: 94.8% [87.2-98.6%]), and 4.3 (Se: 99.1% [96.8-99.9%]; Sp: 98.7% [93.0-100.0%]) in children ≤ 12 years of age and 1.9 (Se: 78.8% [75.9-81.6%]; Sp: 80.5% [69.9-88.7%]), 4.1 (Se: 85.4% [72.2-93.9%]; Sp: 91.1% [78.8-97.5%]), and 6.9 (Se: 98.4% [91.2-100.0%]; Sp: 97.8% [88.2-99.9%]) in children > 12 years of age, respectively., Conclusions: This study provides optimal cutoff values for ODI 3 in differentiating PS from OSA and assessing OSA severity in children. Because oximetry is cheaper and widely available, ODI 3 has the potential to be incorporated into cost-effective clinical decision-making algorithms, especially in resource-limited settings., Citation: Koh YQ, Sultana R, Pugalenthi A, et al. Utility of overnight oximetry indices in the evaluation of children with snoring and suspected obstructive sleep apnea. J Clin Sleep Med. 2025;21(1):109-121., (© 2025 American Academy of Sleep Medicine.)

Abstract: Asthma is a major chronic disease affecting children, and children with difficult-to-treat asthma account for a disproportionate share of resource utilisation and healthcare costs. This review presents a comprehensive and up-to-date overview of the treatment strategies in difficult-to-treat paediatric asthma. Mimickers of asthma must first be ruled out, and the diagnosis confirmed with objective tests whenever possible. The effect of comorbid conditions such as obesity, smoking, other atopic conditions and psychosocial factors on asthma control and severity should be considered. Treatment can then be optimised by implementing personalised strategies, including the use of appropriate drug delivery devices and adherence monitoring. Biologics can be an alternative treatment option for selected patients but should not be a substitute for addressing poor adherence. Many patients with difficult-to-treat asthma may not have severe asthma, and the physician should work with patients and families to achieve good asthma control via an individualised approach., (Copyright © 2024 Copyright: © 2024 Singapore Medical Journal.)

Background: Alcohol use disorder (AUD) affects 283 million people worldwide and its prevalence is increasing. Despite the role of the cerebellum in executive control and its sensitivity to alcohol, few studies have assessed its involvement in AUD-relevant functional networks. The goal of this study is to compare resting-state functional connectivity (FC) patterns in abstinent adults with a history of AUD and controls (CTL). We hypothesized that group differences in cerebro-cerebellar FC would be present, particularly within the frontoparietal/executive control network (FPN)., Methods: Twenty-eight participants completed a resting-state functional magnetic resonance imaging (rsfMRI) study. CTL participants had no history of AUD, comorbid psychological conditions, or recent heavy drinking and/or drug use. AUD participants had a history of AUD, with sobriety for at least 30 days prior to data collection. Multivariate pattern analysis, an agnostic, whole-brain approach, was used to identify regions with significant differences in FC between groups. Seed-based analyses were then conducted to determine the directionality and extent of these FC differences. Associations between FC strength and executive function were assessed using correlations with Wisconsin Card Sorting Test (WCST) performance., Results: There were significant group differences in FC in nodes of the FPN, ventral attention network, and default mode network. Post hoc analyses predominantly identified FC differences within the cerebro-cerebellar FPN, with AUD showing significantly less FC within the FPN. In AUD, FC strength between FPN clusters identified in the multivariate pattern analysis (MVPA) analysis (Left Crus II, Right Frontal Cortex) was positively associated with performance on the WCST., Conclusions: Our results show less engagement of the FPN in individuals with AUD than in CTL. FC strength within this network was positively associated with performance on the WCST. These findings suggest that long-term heavy drinking alters cerebro-cerebellar FC, particularly within networks that are involved in executive function., (© 2023 Research Society on Alcohol.)

Competing Interests: Disclosures: The authors disclose no financial or other conflicts of interest.

Objective: Emergency laparotomy (EL) is a major operation performed in critically unwell patients. The National Emergency Laparotomy Audit (NELA), undertaken in the UK since 2013 has shown progressive improvement in clinical outcomes, specifically reduced mortality, and length of stay (LOS) through the implementation of perioperative key performance indicators (KPIs) (ANZ J Surg. 2021;91:2575, Br J Surg. 2015;102:57, Br J Surg. 2017;104:463, JAMA Surg. 2019;154:e190145). The objective is to generate a rural hospital EL audit (MELA) to evaluate local outcomes and clinical standards of practice with regional, national, and international benchmarks., Methods: A review of medical records between January 2014 and December 2021 of patients who undergo an EL. Data collected include patient demographics, clinical information, compliance to KPIs and the primary outcomes of 30-day mortality and LOS., Design: This is a descriptive quantitative study. The inclusion and exclusion criteria were similar to those defined in NELA and ANZELA-QI., Setting and Participants: The general surgeons at the rural hospital provide emergency surgery services for the North-West Queensland community., Main Outcome Measures: To review local clinical outcomes of 30-day mortality, LOS, and adherence to perioperative KPIs., Results: Overall, 84 patients met inclusion criteria. The median age (IQR) was 61 (48.8-70.3) years. The 30-day mortality was 3.6% and mean LOS was 12.8 (±13.4) days which was secondary to the low-risk patients within the data set. Compliance to KPIs (≥80%) was achieved in five of eight standards assessed., Conclusion: Local outcomes appear to be comparable to national and international benchmarks and a similar rural setting. The audited cohort outperformed the national standard in adherence to perioperative KPIs., (© 2023 The Authors. Australian Journal of Rural Health published by John Wiley & Sons Australia, Ltd on behalf of National Rural Health Alliance Ltd.)

Life-threatening airway emergencies and uncontrolled haemorrhage following dental extractions is rarely encountered. Inappropriate handling of dental luxators may lead to unexpected traumatic events resulting from penetrating or blunt trauma to the surrounding soft tissues and vascular damage. Bleeding during or after surgery usually resolves spontaneously or with local haemostatic interventions. Pseudoaneurysms are rare occurrences secondary to blunt or penetrating trauma usually produced by arterial injury leading to extravasation of blood. The rapidly enlarging haematoma with risk of spontaneous pseudoaneurysm rupture is an airway and surgical emergency necessitating urgent intervention. The following case highlights the importance of appreciating the potential complications associated with extractions in the maxilla, significant anatomical relationships and recognizing the clinical signs of a threatened airway., (Published by Oxford University Press and JSCR Publishing Ltd. © The Author(s) 2023.)

Analgesia after thoracotomy is challenging but important as inadequate pain control may result in early postoperative complications and a higher risk for post-thoracotomy pain syndrome. The authors report the successful utilization of an erector spinae plane (ESP) catheter for post-thoracotomy analgesia in a 40-year-old female with two dual-leaded spinal cord stimulators (SCS) in the cervical and thoracic levels. Although thoracic epidural analgesia is the current standard, epidural catheterization may present with obstructive, mechanical, or infectious concerns in patients with SCS. The ESP block may be a preferable approach to postoperative analgesia after thoraco-abdominal surgery over the thoracic epidural for patients with SCS., Competing Interests: The authors have declared that no competing interests exist., (Copyright © 2022, Cheng et al.)

Abiotrophia defectiva or nutritionally variant streptococci (NVS) was first described in 1961 as a rare cause of infectious endocarditis (IE). It is distinct to the Streptococcus genus, pleomorphic, and demonstrates variable Gram-staining characteristics due to poor growth in culture media requiring extended incubation or 16S rRNA sequencing in culture negative situations. 1 NVS has also been implicated in the pathogenesis of culture-negative endocarditis. In comparison with other causes of endocarditis, it has the ability to secrete exopolysaccharide and adheres to fibronectin in the extracellular matrix of endovascular structures. 2 NVS is associated with significant morbidity and mortality, higher rates of multisystem complications ranging from pancreatic abscess, intracranial aneurysms, osteomyelitis, and valvular destruction, despite sensitivity to antibiotics., Competing Interests: The authors declare no conflicts of interest., (Crown Copyright © 2022 Published by Elsevier B.V. on behalf of Craniofacial Research Foundation. All rights reserved.)

Several fMRI studies have shown that the superior cerebellum exhibits load-dependent activations during encoding of letters in a Sternberg verbal working memory (VWM) task. It has been hypothesized that the cerebellum regulates the acquisition of sensory data across all modalities, and thus, that VWM load activations may reflect high- vs low-load differences in sensory acquisition demands. Therefore, increased difficulty in sensory data acquisition should elicit greater activation in the cerebellum. The present fMRI study manipulated sensory acquisition in VWM by presenting visually degraded and non-degraded stimuli with high and low memory loads, thereby identifying load-dependent regions of interest in the cerebellum, and then testing if these regions showed greater activation for degraded stimuli. Results yielded partial support for the sensory acquisition hypothesis in a load-dependent region of the vermis, which showed significantly greater activation for degraded relative to non-degraded stimuli. Because eye movements did not differ for these stimulus types, and degradation-related activations were present after co-varying eye movements, this activation appears to be related to perceptual rather than oculomotor demands. In contrast to the vermis, load-sensitive regions of the cerebellar hemispheres did not show increased activation for degraded stimuli. These findings point to an overall function of association-based prediction that may underlie general cerebellar function, with perceptual prediction of stimuli from partial representations occurring in the vermis, and articulatory prediction occurring in the hemispheres.

Contingency awareness is thought to rely on an intact medial temporal lobe and also appears to be a function of age, as older subjects tend to be less aware. The current investigation used functional magnetic resonance imaging, transcranial direct current stimulation, and eyeblink classical conditioning to study brain processes related to contingency awareness as a function of age. Older adults were significantly less aware of the relationship between the tone-airpuff pairings than younger adults. Greater right parietal functional magnetic resonance imaging activation was associated with higher levels of contingency awareness for younger and older subjects. Cathodal transcranial direct current stimulation over the right parietal lobe led to lower levels of awareness in younger subjects without disrupting conditioned responses. Older adults exhibited hyperactivations in the parietal and medial temporal lobes, despite showing no conditioning deficits. These findings strongly support the idea that the parietal cortex serves as a substrate for contingency awareness and that age-related disruption of this region is sufficient to impair awareness, which may be a manifestation of some form of naturally occurring age-related neglect., (Copyright © 2020 Elsevier Inc. All rights reserved.)

Background: Functional MRI (fMRI) task-related analyses rely on an estimate of the brain's hemodynamic response function (HRF) to model the brain's response to events. Although changes in the HRF have been found after acute alcohol administration, the effects of heavy chronic alcohol consumption on the HRF have not been explored, and the potential benefits or pitfalls of estimating each individual's HRF on fMRI analyses of chronic alcohol use disorder (AUD) are not known., Methods: Participants with AUD and controls (CTL) received structural, functional, and vascular scans. During fMRI, participants were cued to tap their fingers, and averaged responses were extracted from the motor cortex. Curve fitting on these HRFs modeled them as a difference between 2 gamma distributions, and the temporal occurrence of the main peak and undershoot of the HRF was computed from the mean of the first and second gamma distributions, respectively., Results: ANOVA and regression analyses found that the timing of the HRF undershoot increased significantly as a function of total lifetime drinking. Although gray matter volume in the motor cortex decreased with lifetime drinking, this was not sufficient to explain undershoot timing shifts, and vascular factors measured in the motor cortex did not differ among groups. Comparison of random-effects analyses using custom-fitted and canonical HRFs for CTL and AUD groups showed better results throughout the brain for custom-fitted versus canonical HRFs for CTL subjects. For AUD subjects, the same was true except for the basal ganglia., Conclusions: These findings suggest that excessive alcohol consumption is associated with changes in the HRF undershoot. HRF changes could provide a possible biomarker for the effects of lifetime drinking on brain function. Changes in HRF topography affect fMRI activation measures, and subject-specific HRFs generally improve fMRI activation results., (© 2020 by the Research Society on Alcoholism.)

Background: Excessive alcohol consumption produces changes in the brain that often lead to cognitive impairments. One fundamental form of learning, eyeblink classical conditioning (EBC), has been widely used to study the neurobiology of learning and memory. Participants with alcohol use disorders (AUD) have consistently shown a behavioral deficit in EBC. The present functional magnetic resonance imaging (fMRI) study is the first to examine brain function during conditioning in abstinent AUD participants and healthy participants., Methods: AUD participants met DSM-IV criteria for alcohol dependence, had at least a 10-year history of heavy drinking, and were abstinent from alcohol for at least 30 days. During fMRI, participants received auditory tones that predicted the occurrence of corneal airpuffs. Anticipatory eyeblink responses to these tones were monitored during the experiment to assess learning-related changes., Results: Behavioral results indicate that AUD participants showed significant conditioning deficits and that their history of lifetime drinks corresponded to these deficits. Despite this learning impairment, AUD participants showed hyperactivation in several key cerebellar structures (including lobule VI) during conditioning. For all participants, history of lifetime drinks corresponded with their lobule VI activity., Conclusions: These findings suggest that excessive alcohol consumption is associated with abnormal cerebellar hyperactivation and conditioning impairments., (© 2020 by the Research Society on Alcoholism.)

The role of awareness in differential delay eyeblink conditioning (EBC) has been a topic of much debate. We tested the idea that awareness is required for differential delay EBC when two cues are perceptually similar. The present study manipulated frequencies of auditory conditioned stimuli (CS) to vary CS similarity in three groups of participants. Our findings indicate that awareness was not necessary for differential delay EBC when two tones are easily discriminable, awareness was also not needed for relatively similar tones but may facilitate earlier conditioning, and awareness alone was not sufficient for differential delay EBC., (© 2020 Bolaram et al.; Published by Cold Spring Harbor Laboratory Press.)

Immunodeficiency secondary to anti-interferon-gamma (anti-IFN-γ) autoantibodies was first described in 2004 as an acquired defect in the IFN-γ pathway leading to susceptibility to multiple opportunistic infections, including dimorphic fungi, parasites, and bacteria, especially tuberculosis and non-tuberculous mycobacterium (NTM) species. It has so far only been described in adult patients. We present 2 cases of disseminated NTM infections in otherwise immunocompetent children. A 16-year-old girl with Sweet's syndrome-like neutrophilic dermatosis developed recurrent fever and cervical lymphadenitis secondary to Mycobacterium abscessus. A 10-year-old boy with a history of prolonged fever, aseptic meningitis, aortitis, and arteritis in multiple blood vessels developed thoracic vertebral osteomyelitis secondary to Mycobacterium avium complex. Both patients were found to have positive serum neutralizing anti-IFNγ autoantibodies. Testing for anti-IFNγ autoantibodies should be considered in otherwise healthy immunocompetent hosts with recurrent or disseminated NTM infection. This represents a phenocopy of primary immunodeficiency which has been recently described only in adults. We report the first two cases of this phenomenon to affect children.

The regulation of organelle abundance is critical for cell function and survival; however, the mechanisms responsible are not fully understood. In this study, we characterize a role of the deubiquitinating enzyme USP30 in peroxisome maintenance. Peroxisomes are highly dynamic, changing in abundance in response to metabolic stress. In our recent study identifying the role of USP30 in mitophagy, we observed USP30 to be localized to punctate structures resembling peroxisomes. We report here that USP30, best known as a mitophagy regulator, is also necessary for regulating pexophagy, the selective autophagic degradation of peroxisomes. We find that overexpressing USP30 prevents pexophagy during amino acid starvation, and its depletion results in pexophagy induction under basal conditions. We demonstrate that USP30 prevents pexophagy by counteracting the action of the peroxisomal E3 ubiquitin ligase PEX2. Finally, we show that USP30 can rescue the peroxisome loss observed in some disease-causing peroxisome mutations, pointing to a potential therapeutic target., (© 2019 Riccio et al.)

Aims: Low-grade serous carcinomas (LGSCs) and their precursors serous borderline tumours (SBTs) characteristically harbour mutations in BRAF, KRAS or NRAS but rarely in TP53, whereas high-grade serous carcinomas (HGSCs) are characterised by frequent TP53 mutations but rare BRAF, KRAS or NRAS mutations. In a small subset of cases, LGSCs and/or SBTs develop into high-grade tumours, including HGSCs and poorly differentiated carcinomas (PDCs). Here, we sought to define the repertoire of somatic genetic alterations in low-grade serous tumours and synchronous or metachronous high-grade adnexal carcinomas., Methods and Results: DNA extracted from five SBTs/LGSCs and synchronous or metachronous HGSCs/PDCs and matched normal tissue was subjected to massively parallel sequencing targeting all exons and selected non-coding regions of 341 cancer-related genes. The low-grade and high-grade tumours from a given case were related, and shared mutations and copy number alterations. Progression from low-grade to high-grade lesions was observed, and involved the acquisition of additional mutations and/or copy number alterations, or shifts from subclonal to clonal mutations. Only two (an HGSC and a PDC) of the five high-grade tumours investigated harboured TP53 mutations, whereas NRAS and KRAS hotspot mutations were seen in two HGSCs and one HGSC, respectively., Conclusions: Our results suggest that progression from SBT to HGSC may take place in a subset of cases, and that at least some of the rare HGSCs lacking TP53 mutations may be derived from a low-grade serous precursor., (© 2018 John Wiley & Sons Ltd.)

While mutations affecting protein-coding regions have been examined across many cancers, structural variants at the genome-wide level are still poorly defined. Through integrative deep whole-genome and -transcriptome analysis of 101 castration-resistant prostate cancer metastases (109X tumor/38X normal coverage), we identified structural variants altering critical regulators of tumorigenesis and progression not detectable by exome approaches. Notably, we observed amplification of an intergenic enhancer region 624 kb upstream of the androgen receptor (AR) in 81% of patients, correlating with increased AR expression. Tandem duplication hotspots also occur near MYC, in lncRNAs associated with post-translational MYC regulation. Classes of structural variations were linked to distinct DNA repair deficiencies, suggesting their etiology, including associations of CDK12 mutation with tandem duplications, TP53 inactivation with inverted rearrangements and chromothripsis, and BRCA2 inactivation with deletions. Together, these observations provide a comprehensive view of how structural variations affect critical regulators in metastatic prostate cancer., (Copyright © 2018 Elsevier Inc. All rights reserved.)

Background: Reproductive factors, particularly parity, have differential effects on breast cancer risk according to estrogen receptor (ER) status, especially among African American (AA) women. One mechanism could be through DNA methylation, leading to altered expression levels of genes important in cell fate decisions., Methods: Using the Illumina 450K BeadChip, we compared DNA methylation levels in paraffin-archived tumor samples from 383 AA and 350 European American (EA) women in the Women's Circle of Health Study (WCHS). We combined 450K profiles with RNA-seq data and prioritized genes based on differential methylation by race, correlation between methylation and gene expression, and biological function. We measured tumor protein expression and assessed its relationship to DNA methylation. We evaluated associations between reproductive characteristics and DNA methylation using linear regression., Results: 410 loci were differentially methylated by race, with the majority unique to ER- tumors. FOXA1 was hypermethylated in tumors from AA versus EA women with ER- cancer, and increased DNA methylation correlated with reduced RNA and protein expression. Importantly, parity was positively associated with FOXA1 methylation among AA women with ER- tumors (P = 0.022), as was number of births (P = 0.026), particularly among those who did not breastfeed (P = 0.008). These same relationships were not observed among EA women, although statistical power was more limited., Conclusions: Methylation and expression of FOXA1 is likely impacted by parity and breastfeeding. Because FOXA1 regulates a luminal gene expression signature in progenitor cells and represses the basal phenotype, this could be a mechanism that links these reproductive exposures with ER- breast cancer.

Clear cell carcinoma of the endometrium is a rare type of endometrial cancer that is generally associated with an aggressive clinical behaviour. Here, we sought to define the repertoire of somatic genetic alterations in endometrial clear cell carcinomas (ECCs), and whether ECCs could be classified into the molecular subtypes described for endometrial endometrioid and serous carcinomas. We performed a rigorous histopathological review, immunohistochemical analysis and massively parallel sequencing targeting 300 cancer-related genes of 32 pure ECCs. Eleven (34%), seven (22%) and six (19%) ECCs showed abnormal expression patterns for p53, ARID1A, and at least one DNA mismatch repair (MMR) protein, respectively. Targeted sequencing data were obtained from 30 of the 32 ECCs included in this study, and these revealed that two ECCs (7%) were ultramutated and harboured mutations affecting the exonuclease domain of POLE. In POLE wild-type ECCs, TP53 (46%), PIK3CA (36%), PPP2R1A (36%), FBXW7 (25%), ARID1A (21%), PIK3R1 (18%) and SPOP (18%) were the genes most commonly affected by mutations; 18% and 11% harboured CCNE1 and ERBB2 amplifications, respectively, and 11% showed DAXX homozygous deletions. ECCs less frequently harboured mutations affecting CTNNB1 and PTEN but more frequently harboured PPP2R1A and TP53 mutations than non-POLE endometrioid carcinomas from The Cancer Genome Atlas (TCGA). Compared to endometrial serous carcinomas (TCGA), ECCs less frequently harboured TP53 mutations. When a surrogate model for the molecular-based TCGA classification was used, all molecular subtypes previously identified in endometrial endometrioid and serous carcinomas were present in the ECCs studied, including POLE, MMR-deficient, copy-number high (serous-like)/p53 abnormal, and copy-number low (endometrioid)/p53 wild-type, which were significantly associated with disease-free survival in univariate analysis. These findings demonstrate that ECCs constitute a histologically and genetically heterogeneous group of tumours with varying outcomes. Furthermore, our data suggest that the classification of ECCs as being generally 'high-grade' or 'type II' tumours may not be warranted. Copyright © 2017 Pathological Society of Great Britain and Ireland. Published by John Wiley & Sons, Ltd., (Copyright © 2017 Pathological Society of Great Britain and Ireland. Published by John Wiley & Sons, Ltd.)

Prenatal alcohol exposure has been linked to a broad range of developmental deficits, with eyeblink classical conditioning (EBC) among the most sensitive endpoints. This fMRI study compared EBC-related brain activity in 47 children with fetal alcohol syndrome (FAS), partial FAS (PFAS), heavily exposed (HE) non-syndromal children, and healthy controls. All of the children had previously participated in two EBC studies conducted as part of our longitudinal study of fetal alcohol spectrum disorders. Although learning-related behavioral differences were seen in all groups during the scans, controls showed more conditioned responses (CR) than the alcohol-exposed groups. Despite lower conditioning levels relative to controls, the exposed groups exhibited extensive cerebellar activations. Specifically, children with FAS/PFAS showed increased activation of cerebellar lobule VI in session 2, while HE children showed increased activation in session 1. Continuous measures of prenatal alcohol use correlated with learning-related activations in cerebellum and frontal cortices. Only controls showed significant cerebellar activation-CR correlations in the deep nuclei and lateral lobule VI, suggesting that these key regions supporting EBC may be functionally disorganized in alcohol-exposed children. These findings are the first to characterize abnormalities in brain function associated with the behavioral conditioning deficits seen in children with prenatal alcohol exposure., (© The Author 2016. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.)

Purpose: The clinical use of BRAF inhibitors in patients with melanoma is limited by intrinsic and acquired resistance. We asked whether next-generation sequencing of pretreatment tumors could identify coaltered genes that predict for intrinsic resistance to BRAF inhibitor therapy in patients with melanoma as a prelude to rational combination strategies., Patients and Methods: We analyzed 66 tumors from patients with metastatic BRAF -mutant melanoma collected before treatment with BRAF inhibitors. Tumors were analyzed for > 250 cancer-associated genes using a capture-based next-generation sequencing platform. Antitumor responses were correlated with clinical features and genomic profiles with the goal of identifying a molecular signature predictive of intrinsic resistance to RAF pathway inhibition., Results: Among the 66 patients analyzed, 11 received a combination of BRAF and MEK inhibitors for the treatment of melanoma. Among the 55 patients treated with BRAF inhibitor monotherapy, objective responses, as assessed by Response Evaluation Criteria in Solid Tumors (RECIST), were observed in 30 patients (55%), with five (9%) achieving a complete response. We identified a significant association between alterations in PTEN that would be predicted to result in loss of function and reduced progression-free survival, overall survival, and response grade, a metric that combines tumor regression and duration of treatment response. Patients with melanoma who achieved an excellent response grade were more likely to have an elevated BRAF -mutant allele fraction., Conclusion: These results provide a rationale for cotargeting BRAF and the PI3K/AKT pathway in patients with BRAF -mutant melanoma when tumors have concurrent loss-of-function mutations in PTEN . Future studies should explore whether gain of the mutant BRAF allele and/or loss of the wild-type allele is a predictive marker of BRAFi sensitivity., Competing Interests: PTEN Loss-of-Function Alterations Are Associated With Intrinsic Resistance to BRAF Inhibitors in Metastatic MelanomaThe following represents disclosure information provided by authors of this manuscript. All relationships are considered compensated. Relationships are self-held unless noted. I = Immediate Family Member, Inst = My Institution. Relationships may not relate to the subject matter of this manuscript. For more information about ASCO's conflict of interest policy, please refer to www.asco.org/rwc or po.ascopubs.org/site/ifc.Federica CatalanottiNo relationship to discloseDonavan T. ChengEmployment: Illumina, Gilead Sciences (I) Stock and Other Ownership Interests: Illumina, Gilead Sciences (I)Alexander N. ShoushtariConsulting or Advisory Role: Vaccinex, Castle Biosciences, Immunocore Research Funding: Bristol-Myers Squibb, Immunocore Travel, Accommodations, Expenses: Bristol-Myers SquibbDouglas B. JohnsonConsulting or Advisory Role: Bristol-Myers Squibb, Genoptix, Merck Research Funding: Incyte Patents, Royalties, Other Intellectual Property: Intellectual property and patents pending surrounding use of MHC-II and response to immune therapyKatherine S. PanageasNo relationship to discloseParisa MomtazNo relationship to discloseCatherine HighamNo relationship to discloseHelen H. WonNo relationship to discloseJames J. HardingNo relationship to discloseTaha MerghoubNo relationship to discloseNeal RosenStock and Other Ownership Interests: Beigene, Wellspring, Kura Honoraria: Novartis, Eli Lilly, Bayer Consulting or Advisory Role: AstraZeneca, Takeda-Millennium, Daiichi Sankyo, Chugai Pharma Research Funding: Wellspring/Araxes, Chugai Pharma Travel, Accommodations, Expenses: PlexxikonJeffrey A. SosmanHonoraria: Amgen, Merck, Array BioPharma Consulting or Advisory Role: Amgen, Merck, Array BioPharmaMichael F. BergerConsulting or Advisory Role: Cancer Genetics, SequenomPaul B. ChapmanHonoraria: Bristol-Myers Squibb, GlaxoSmithKline, Genentech, Provectus, Momenta Pharmaceuticals, Daiichi Sankyo Consulting or Advisory Role: Bristol-Myers Squibb, GlaxoSmithKline, Genentech, Daiichi Sankyo, Provectus, Momenta Pharmaceuticals Research Funding: GlaxoSmithKline, Genentech, Bristol-Myers Squibb, Pfizer Travel, Accommodations, Expenses: Bristol-Myers SquibbDavid B. SolitHonoraria: Loxo, Pfizer Consulting or Advisory Role: Pfizer, Loxo, (© 2017 by American Society of Clinical Oncology.)

Tumor molecular profiling is a fundamental component of precision oncology, enabling the identification of genomic alterations in genes and pathways that can be targeted therapeutically. The existence of recurrent targetable alterations across distinct histologically defined tumor types, coupled with an expanding portfolio of molecularly targeted therapies, demands flexible and comprehensive approaches to profile clinically relevant genes across the full spectrum of cancers. We established a large-scale, prospective clinical sequencing initiative using a comprehensive assay, MSK-IMPACT, through which we have compiled tumor and matched normal sequence data from a unique cohort of more than 10,000 patients with advanced cancer and available pathological and clinical annotations. Using these data, we identified clinically relevant somatic mutations, novel noncoding alterations, and mutational signatures that were shared by common and rare tumor types. Patients were enrolled on genomically matched clinical trials at a rate of 11%. To enable discovery of novel biomarkers and deeper investigation into rare alterations and tumor types, all results are publicly accessible.

Background: The growing number of Next Generation Sequencing (NGS) tests is transforming the routine clinical diagnosis of hereditary cancers. Identifying whether a cancer is the result of an underlying disease-causing mutation in a cancer predisposition gene is not only diagnostic for a cancer predisposition syndrome, but also has significant clinical implications in the clinical management of patients and their families., Methods: Here, we evaluated the performance of MSK-IMPACT (Memorial Sloan Kettering-Integrated Mutation Profiling of Actionable Cancer Targets) in detecting genetic alterations in 76 genes implicated in cancer predisposition syndromes. Output from hybridization-based capture was sequenced on an Illumina HiSeq 2500. A custom analysis pipeline was used to detect single nucleotide variants (SNVs), small insertions/deletions (indels) and copy number variants (CNVs)., Results: MSK-IMPACT detected all germline variants in a set of 233 unique patient DNA samples, previously confirmed by previous single gene testing. Reproducibility of variant calls was demonstrated using inter- and intra- run replicates. Moreover, in 16 samples, we identified additional pathogenic mutations other than those previously identified through a traditional gene-by-gene approach, including founder mutations in BRCA1, BRCA2, CHEK2 and APC, and truncating mutations in TP53, TSC2, ATM and VHL., Conclusions: This study highlights the importance of the NGS-based gene panel testing approach in comprehensively identifying germline variants contributing to cancer predisposition and simultaneous detection of somatic and germline alterations.

Establishing ERBB2 [human epidermal growth factor receptor 2 (HER2)] amplification status in breast and gastric carcinomas is essential to treatment selection. Immunohistochemistry (IHC) and fluorescence in situ hybridization (FISH) constitute the current standard for assessment. With further advancements in genomic medicine, new clinically relevant biomarkers are rapidly emerging and options for targeted therapy are increasing in patients with advanced disease, driving the need for comprehensive molecular profiling. Next-generation sequencing (NGS) is an attractive approach for up-front comprehensive assessment, including ERBB2 status, but the concordance with traditional methods of HER2 assessment is not well established. The Memorial Sloan Kettering-Integrated Mutation Profiling of Actionable Cancer Targets (MSK-IMPACT) assay, a hybrid capture-based NGS assay interrogating the coding regions of 410 cancer-related genes, was performed on manually macrodissected unstained sections from formalin-fixed, paraffin-embedded breast (n = 213) and gastroesophageal (n = 39) tumors submitted for clinical mutation profiling. ERBB2 status was assessed using a custom bioinformatics pipeline, and NGS results were compared to IHC and FISH. NGS ERBB2 amplification calls had an overall concordance of 98.4% (248/252) with the combined IHC/FISH results in this validation set. Discrepancies occurred in the context of low tumor content and HER2 heterogeneity. ERBB2 amplification status can be reliably determined by hybridization capture-based NGS methods, allowing efficient concurrent testing for other potentially actionable genomic alterations, particularly in limited material., (Copyright © 2017 American Society for Investigative Pathology and the Association for Molecular Pathology. Published by Elsevier Inc. All rights reserved.)

Elongator is a ~850 kDa protein complex involved in multiple processes from transcription to tRNA modification. Conserved from yeast to humans, Elongator is assembled from two copies of six unique subunits (Elp1 to Elp6). Despite the wealth of structural data on the individual subunits, the overall architecture and subunit organization of the full Elongator and the molecular mechanisms of how it exerts its multiple activities remain unclear. Using single-particle electron microscopy (EM), we revealed that yeast Elongator adopts a bilobal architecture and an unexpected asymmetric subunit arrangement resulting from the hexameric Elp456 subassembly anchored to one of the two Elp123 lobes that form the structural scaffold. By integrating the EM data with available subunit crystal structures and restraints generated from cross-linking coupled to mass spectrometry, we constructed a multiscale molecular model that showed the two Elp3, the main catalytic subunit, are located in two distinct environments. This work provides the first structural insights into Elongator and a framework to understand the molecular basis of its multifunctionality., (© 2016 The Authors.)

It has been argued that cerebellar activations during cognitive tasks may masquerade as cognition, while actually reflecting processes related to movement planning or motor learning. The present study investigated whether the cerebellar load effect for verbal working memory, that is, increased activations in lobule VI/Crus I and lobule VIIB/VIIIA, is related to eye movements and oculomotor processing. Fifteen participants performed an fMRI-based Sternberg verbal working memory task. Oculomotor and cognitive task demands were manipulated by using closely and widely spaced stimuli, and high and low cognitive load. Trial-based quantitative eye movement parameters were obtained from concurrent eye tracking. Conventional MRI analysis replicated the cerebellar load effect in lobules VI and VIIB/VIIIa. With quantitative eye movement parameters as regressors, analysis yielded very similar activation patterns. While load effect and eye regressor generally recruited spatially distinct neocortical and cerebellar regions, conjunction analysis showed that a small subset of prefrontal areas implicated in the load effect also responded to the eye regressor. The present results indicate that cognitive load-dependent activations in lateral superior and posteroinferior cerebellar regions in the Sternberg task are independent of eye movements occurring during stimulus encoding. This is inconsistent with the notion that cognitive load-dependent cerebellar activations merely reflect oculomotor processing., (© The Author 2015. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.)

Translational bioinformatics and clinical research (biomedical) informatics are the primary domains related to informatics activities that support translational research. Translational bioinformatics focuses on computational techniques in genetics, molecular biology, and systems biology. Clinical research (biomedical) informatics involves the use of informatics in discovery and management of new knowledge relating to health and disease. This article details 3 projects that are hybrid applications of translational bioinformatics and clinical research (biomedical) informatics: The Cancer Genome Atlas, the cBioPortal for Cancer Genomics, and the Memorial Sloan Kettering Cancer Center clinical variants and results database, all designed to facilitate insights into cancer biology and clinical/therapeutic correlations., (Copyright © 2016 Elsevier Inc. All rights reserved.)

Importance: Tumor genetic sequencing identifies potentially targetable genetic alterations with therapeutic implications. Analysis has concentrated on detecting tumor-specific variants, but recognition of germline variants may prove valuable as well., Objective: To estimate the burden of germline variants identified through routine clinical tumor sequencing., Design, Setting, and Participants: Patients with advanced cancer diagnoses eligible for studies of targeted agents at Memorial Sloan Kettering Cancer Center are offered tumor-normal sequencing with MSK-IMPACT, a 341-gene panel. We surveyed the germline variants seen in 187 overlapping genes with Mendelian disease associations in 1566 patients who had undergone tumor profiling between March and October 2014., Main Outcomes and Measures: The number of presumed pathogenic germline variants (PPGVs) and variants of uncertain significance per person in 187 genes associated with single-gene disorders and the proportions of individuals with PPGVs in clinically relevant gene subsets, in genes consistent with known tumor phenotypes, and in genes with evidence of second somatic hits in their tumors., Results: The mean age of the 1566 patients was 58 years, and 54% were women. Presumed pathogenic germline variants in known Mendelian disease-associated genes were identified in 246 of 1566 patients (15.7%; 95% CI, 14.0%-17.6%), including 198 individuals with mutations in genes associated with cancer susceptibility. Germline findings in cancer susceptibility genes were concordant with the individual's cancer type in only 81 of 198 cases (40.9%; 95% CI, 34.3%-47.9%). In individuals with PPGVs retained in the tumor, somatic alteration of the other allele was seen in 39 of 182 cases (21.4%; 95% CI, 16.1%-28.0%), of which 13 cases did not show a known correlation of the germline mutation and a known syndrome. Mutations in non-cancer-related Mendelian disease genes were seen in 55 of 1566 cases (3.5%; 95% CI, 27.1%-45.4%). Almost every individual had more than 1 variant of uncertain significance (1565 of 1566 patients; 99.9%; 95% CI, 99.6%-99.9%)., Conclusions and Relevance: Germline variants are common in individuals undergoing tumor-normal sequencing and may reveal otherwise unsuspected syndromic associations.

Implementing a center-wide precision medicine strategy at a major cancer center is a true multidisciplinary effort and requires comprehensive alignment of a broad screening strategy with a clinical research enterprise that can use these data to accelerate development of new treatments. Here, we describe the genomic screening approach at Memorial Sloan Kettering Cancer Center, a hybridization capture-based next-generation sequencing clinical assay for solid tumor molecular oncology designated MSK-IMPACT, and how it enables and supports a large clinical trial portfolio enriched for multi-histology, biomarker-selected, 'basket' studies of targeted therapies., (Copyright © 2015 Elsevier Ltd. All rights reserved.)

Angiosarcomas are rare malignant mesenchymal tumors of endothelial differentiation. The clinical behavior is usually aggressive and the prognosis for patients with advanced disease is poor with no effective therapies. The genetic bases of these tumors have been partially revealed in recent studies reporting genetic alterations such as amplifications of MYC (primarily in radiation-associated angiosarcomas), inactivating mutations in PTPRB and R707Q hotspot mutations of PLCG1. Here, we performed a comprehensive genomic analysis of 34 angiosarcomas using a clinically-approved, hybridization-based targeted next-generation sequencing assay for 341 well-established oncogenes and tumor suppressor genes. Over half of the angiosarcomas (n = 18, 53%) harbored genetic alterations affecting the MAPK pathway, involving mutations in KRAS, HRAS, NRAS, BRAF, MAPK1 and NF1, or amplifications in MAPK1/CRKL, CRAF or BRAF. The most frequently detected genetic aberrations were mutations in TP53 in 12 tumors(35%) and losses of CDKN2A in9 tumors (26%). MYC amplifications were generally mutually exclusive of TP53 alterations and CDKN2A loss and were identified in 8 tumors (24%), most of which (n = 7, 88%) arose post-irradiation. Previously reported mutations in PTPRB (n = 10, 29%) and one (3%) PLCG1 R707Q mutation were also identified. Our results demonstrate that angiosarcomas are a genetically heterogeneous group of tumors, harboring a wide range of genetic alterations. The high frequency of genetic events affecting the MAPK pathway suggests that targeted therapies inhibiting MAPK signaling may be promising therapeutic avenues in patients with advanced angiosarcomas.

Alcoholism is a debilitating disorder that can take a significant toll on health and professional and personal relationships. Excessive alcohol consumption can have a serious impact on both drinkers and developing fetuses, leading to long-term learning impairments. Decades of research in laboratory animals and humans have demonstrated the value of eyeblink classical conditioning (EBC) as a well-characterized model system to study the neural mechanisms underlying associative learning. Behavioral EBC studies in adults with alcohol use disorders and in children with fetal alcohol spectrum disorders report a clear learning deficit in these two patient populations, suggesting alcohol-related damage to the cerebellum and associated structures. Insight into the neural mechanisms underlying these learning impairments has largely stemmed from laboratory animal studies. In this mini-review, we present and discuss exemplary animal findings and data from patient and neuroimaging studies. An improved understanding of the neural mechanisms underlying learning deficits in EBC related to alcoholism and prenatal alcohol exposure has the potential to advance the diagnoses, treatment, and prevention of these and other pediatric and adult disorders.

Cross-frequency coupling has been shown to be functionally significant in cortical information processing, potentially serving as a mechanism for integrating functionally relevant regions in the brain. In this study, we evaluate the hypothesis that pain-related gamma oscillatory responses are coupled with low-frequency oscillations in the frontal lobe, amygdala and hippocampus, areas known to have roles in pain processing. We delivered painful laser pulses to random locations on the dorsal hand of five patients with uncontrolled epilepsy requiring depth electrode implantation for seizure monitoring. Two blocks of 40 laser stimulations were delivered to each subject and the pain-intensity was controlled at five in a 0-10 scale by adjusting the energy level of the laser pulses. Local-field-potentials (LFPs) were recorded through bilaterally implanted depth electrode contacts to study the oscillatory responses upon processing the painful laser stimulations. Our results show that painful laser stimulations enhanced low-gamma (LH, 40-70 Hz) and high-gamma (HG, 70-110 Hz) oscillatory responses in the amygdala and hippocampal regions on the right hemisphere and these gamma responses were significantly coupled with the phases of theta (4-7 Hz) and alpha (8-1 2 Hz) rhythms during pain processing. Given the roles of these deep brain structures in emotion, these findings suggest that the oscillatory responses in these regions may play a role in integrating the affective component of pain, which may contribute to our understanding of the mechanisms underlying the affective information processing in humans., (Copyright © 2015 IBRO. Published by Elsevier Ltd. All rights reserved.)

Melanotic Schwannomas (MS) are rare tumors that share histological features with melanocytic tumors and schwannomas. However, their genetics are poorly understood. To elucidate the genetic characteristics of MS, we performed genome-wide studies in a series of cases. Twelve MS cases were available for the study. Genomic DNAs extracted from formalin-fixed paraffin embedded tumor tissues were subjected to copy number (CN) and allelic imbalance (AI) analysis by Single Nucleotide Polymorphism (SNP)-array and screened for mutations in coding exons of 341 key cancer-associated genes using a hybrid capture-based next-generation sequencing (NGS) assay. Sanger sequencing was used to further verify recurrent mutations detected by NGS study. SNP-array analysis revealed remarkably stereotypic chromosomal abnormalities in MS. Hypodiploidy was common, typically involving monosomies of chromosomes 1, 2, and 17. All 12 samples showed mutations in PRKAR1A gene, including 2 cases with 2 mutations each. The 14 mutations were scattered across PRKAR1A, and most were inactivating mutations. AI on 17q, presenting as loss of heterozygosity with or without CN losses, combined with a PRKAR1A mutation was observed in 9/12 MS cases. The remaining 3 cases included the two samples harboring two mutations in PRKAR1A. MS exhibits a stereotypic pattern of chromosomal losses. In contrast, melanomas are typically characterized by the presence of multiple CN aberrations, without demonstrable differences in the frequency of losses and gains. Inactivation of both alleles of PRKAR1A by "two hits" observed in almost all cases underscores the central role of PRKAR1A in the pathogenesis of this neoplasm. © 2015 Wiley Periodicals, Inc., (© 2015 Wiley Periodicals, Inc.)

Background: RAF inhibitors are an effective therapy for patients with BRAF-mutant melanoma and brain metastasis. Efficacy data are derived from clinical studies enriched with physiologically fit patients; therefore, it is of interest to assess the real-world experience of vemurafenib in this population. Tumor-specific genetic variants that influence sensitivity to RAF kinase inhibitors also require investigation., Methods: Records of patients with BRAF-mutant melanoma and brain metastases who were treated with vemurafenib were reviewed. Clinical data were extracted to determine extracranial and intracranial objective response rates, progression-free survival (PFS), overall survival (OS), and safety. A bait-capture, next-generation sequencing assay was used to identify mutations in pretreatment tumors that could explain primary resistance to vemurafenib., Results: Among patients with intracranial disease treated with vemurafenib, 27 were included in survival analyses and 22 patients were assessable for response. The extracranial and intracranial objective response rates were 71% and 50%, respectively. Discordant responses were observed between extracranial and intracranial metastatic sites in 4 of 19 evaluable patients. Median PFS was 4.1 months (95% confidence interval [CI]: 2.6-7.9); median intracranial PFS was 4.6 months (95% CI: 2.7-7.9), median OS was 7.5 months (95% CI: 4.3-not reached), with a 30.4% 1-year OS rate. Outcomes were influenced by performance status. Vemurafenib was tolerable, although radiation-induced dermatitis occurred in some patients who received whole-brain radiotherapy. Adequate samples for next-generation sequencing analysis were available for seven patients. Melanomas categorized as "poorly sensitive" (≥20% tumor growth, new lesions, or ≤50% shrinkage for <4 months) harbored co-occurring mutations in genes predicted to activate the phosphatidylinositol 3-kinase-AKT (PI3K-AKT) pathway., Conclusion: Vemurafenib is highly active in BRAF-mutant melanoma brain metastases but has limited activity in patients with poor performance status. The safety and efficacy of concurrent radiotherapy and RAF inhibition requires careful clinical evaluation. Combination strategies blocking the MAPK and PI3K-AKT pathway may be warranted in a subset of patients., Implications for Practice: Vemurafenib is active for BRAF-mutant intracranial melanoma metastases in an unselected patient population typical of routine oncologic practice. Patients with poor performance status appear to have poor outcomes despite vemurafenib therapy. Preliminary data indicate that co-occurring or secondary alterations in the phosphatidylinositol 3-kinase-AKT (PI3K-AKT) pathway are involved in resistance to RAF inhibition, thus providing a rationale for dual MAPK and PI3K-AKT pathway inhibition in this patient population., (©AlphaMed Press.)

Translational bioinformatics and clinical research (biomedical) informatics are the primary domains related to informatics activities that support translational research. Translational bioinformatics focuses on computational techniques in genetics, molecular biology, and systems biology. Clinical research (biomedical) informatics involves the use of informatics in discovery and management of new knowledge relating to health and disease. This article details 3 projects that are hybrid applications of translational bioinformatics and clinical research (biomedical) informatics: The Cancer Genome Atlas, the cBioPortal for Cancer Genomics, and the Memorial Sloan Kettering Cancer Center clinical variants and results database, all designed to facilitate insights into cancer biology and clinical/therapeutic correlations., (Copyright © 2015 Elsevier Inc. All rights reserved.)

The identification of specific genetic alterations as key oncogenic drivers and the development of targeted therapies are together transforming clinical oncology and creating a pressing need for increased breadth and throughput of clinical genotyping. Next-generation sequencing assays allow the efficient and unbiased detection of clinically actionable mutations. To enable precision oncology in patients with solid tumors, we developed Memorial Sloan Kettering-Integrated Mutation Profiling of Actionable Cancer Targets (MSK-IMPACT), a hybridization capture-based next-generation sequencing assay for targeted deep sequencing of all exons and selected introns of 341 key cancer genes in formalin-fixed, paraffin-embedded tumors. Barcoded libraries from patient-matched tumor and normal samples were captured, sequenced, and subjected to a custom analysis pipeline to identify somatic mutations. Sensitivity, specificity, reproducibility of MSK-IMPACT were assessed through extensive analytical validation. We tested 284 tumor samples with previously known point mutations and insertions/deletions in 47 exons of 19 cancer genes. All known variants were accurately detected, and there was high reproducibility of inter- and intrarun replicates. The detection limit for low-frequency variants was approximately 2% for hotspot mutations and 5% for nonhotspot mutations. Copy number alterations and structural rearrangements were also reliably detected. MSK-IMPACT profiles oncogenic DNA alterations in clinical solid tumor samples with high accuracy and sensitivity. Paired analysis of tumors and patient-matched normal samples enables unambiguous detection of somatic mutations to guide treatment decisions., (Copyright © 2015 American Society for Investigative Pathology and the Association for Molecular Pathology. Published by Elsevier Inc. All rights reserved.)

The Spt-Ada-Gcn5 acetyltransferase (SAGA) complex is a highly conserved, 19-subunit histone acetyltransferase complex that activates transcription through acetylation and deubiquitination of nucleosomal histones in Saccharomyces cerevisiae. Because SAGA has been shown to display conformational variability, we applied gradient fixation to stabilize purified SAGA and systematically analyzed this flexibility using single-particle EM. Our two- and three-dimensional studies show that SAGA adopts three major conformations, and mutations of specific subunits affect the distribution among these. We also located the four functional modules of SAGA using electron microscopy-based labeling and transcriptional activator binding analyses and show that the acetyltransferase module is localized in the most mobile region of the complex. We further comprehensively mapped the subunit interconnectivity of SAGA using cross-linking mass spectrometry, revealing that the Spt and Taf subunits form the structural core of the complex. These results provide the necessary restraints for us to generate a model of the spatial arrangement of all SAGA subunits. According to this model, the chromatin-binding domains of SAGA are all clustered in one face of the complex that is highly flexible. Our results relate information of overall SAGA structure with detailed subunit level interactions, improving our understanding of its architecture and flexibility., (© 2015 by The American Society for Biochemistry and Molecular Biology, Inc.)

Amplicon-based methods for targeted resequencing of cancer genes have gained traction in the clinic as a strategy for molecular diagnostic testing. An 847-amplicon panel was designed with the RainDance DeepSeq system, covering most exons of 28 genes relevant to acute myeloid leukemia and myeloproliferative neoplasms. We developed a paired-sample analysis pipeline for variant calling and sought to assess its sensitivity and specificity relative to a set of samples with previously identified mutations. Thirty samples with known mutations in JAK2, NPM1, DNMT3A, MPL, IDH1, IDH2, CEBPA, and FLT3, were profiled and sequenced to high depth. Variant calling using an unmatched Hapmap DNA control removed a substantial number of artifactual calls regardless of algorithm used or variant class. The removed calls were nonunique, had lower variant frequencies, and tended to recur in multiple unrelated samples. Analysis of sample replicates revealed that reproducible calls had distinctly higher variant allele depths and frequencies compared to nonreproducible calls. On the basis of these differences, filters on variant frequency were chosen to select for reproducible calls. The analysis pipeline successfully retrieved the associated known variant in all tested samples and uncovered additional mutations in some samples corresponding to well-characterized hotspot mutations in acute myeloid leukemia. We have developed a paired-sample analysis pipeline capable of robust identification of mutations from microdroplet-PCR sequencing data with high sensitivity and specificity., (Copyright © 2014 American Society for Investigative Pathology and the Association for Molecular Pathology. Published by Elsevier Inc. All rights reserved.)

This study characterized human cerebellar activity during eyeblink classical conditioning (EBC) in children and adults using functional magnetic resonance imaging (fMRI). During fMRI, participants were administered delay conditioning trials, in which the conditioned stimulus (a tone) precedes, overlaps, and coterminates with the unconditioned stimulus (a corneal airpuff). Behavioral eyeblink responses and brain activation were measured concurrently during two phases: pseudoconditioning, involving presentations of tone alone and airpuff alone, and conditioning, during which the tone and airpuff were paired. Although all participants demonstrated significant conditioning, the adults produced more conditioned responses (CRs) than the children. When brain activations during pseudoconditioning were subtracted from those elicited during conditioning, significant activity was distributed throughout the cerebellar cortex (Crus I-II, lateral lobules IV-IX, and vermis IV-VI) in all participants, suggesting multiple sites of associative learning-related plasticity. Despite their less optimal behavioral performance, the children showed greater responding in the pons, lateral lobules VIII, IX, and Crus I, and vermis VI, suggesting that they may require greater activation and/or the recruitment of supplementary structures to achieve successful conditioning. Correlation analyses relating brain activations to behavioral CRs showed a positive association of activity in cerebellar deep nuclei (including dentate, fastigial, and interposed nuclei) and vermis VI with CRs in the children. This is the first study to compare cerebellar cortical and deep nuclei activations in children versus adults during EBC., (Copyright © 2013 Wiley Periodicals, Inc.)

Abstract A multitude of events bombard our sensory systems at every moment of our lives. Thus, it is important for the sensory cortex to gate unimportant events. Tactile suppression is a well-known phenomenon defined as a reduced ability to detect tactile events on the skin before and during movement. Previous experiments found detection rates decrease just prior to and during finger abduction, and decrease according to the proximity of the moving effector. This study examined how tactile detection changes during a reach to grasp. Fourteen human participants used their right hand to reach and grasp a cylinder. Tactors were attached to the index finger, the fifth digit, and the forearm of both the right and left arm and vibrated at various epochs relative to a "go" tone. Results showed that detection rates at the forearm decreased before movement onset; whereas at the right index finger, right fifth digit and at the left index finger, left fifth digit, and forearm sites did not decrease like in the right forearm. These results indicate that the task affects gating dynamics in a temporally- and contextually dependent manner and implies that feed-forward motor planning processes can modify sensory signals.

Rationale: Emphysema in chronic obstructive pulmonary disease (COPD) can be characterized by high-resolution chest computed tomography (HRCT); however, the repeated use of HRCT is limited because of concerns regarding radiation exposure and cost., Objectives: To evaluate biomarkers associated with emphysema and COPD-related clinical characteristics, and to assess the relationships of soluble receptor for advanced glycation endproducts (sRAGE), a candidate systemic biomarker identified in this study, with single-nucleotide polymorphisms (SNPs) in the gene coding for RAGE (AGER locus) and with clinical characteristics., Methods: Circulating levels of 111 biomarkers were analyzed for association with clinical characteristics in 410 patients with COPD enrolled in the TESRA study. sRAGE was also measured in the ECLIPSE cohort in 1,847 patients with COPD, 298 smokers and 204 nonsmokers. The association between 21 SNPs in the AGER locus with sRAGE levels and clinical characteristics was also investigated., Measurements and Main Results: sRAGE was identified as a biomarker of diffusing capacity of carbon monoxide and lung density in the TESRA cohort. In the ECLIPSE cohort, lower sRAGE levels were associated with increased emphysema, increased Global Initiative for Chronic Obstructive Lung Disease stage, and COPD disease status. The associations with emphysema in both cohorts remained significant after covariate adjustment (P < 0.0001). One SNP in the AGER locus, rs2070600, was associated with circulating sRAGE levels both in TESRA (P = 0.0014) and ECLIPSE (7.07 × 10(-16)), which exceeded genome-wide significance threshold. Another SNP (rs2071288) was also associated with sRAGE levels (P = 0.01) and diffusing capacity of carbon monoxide (P = 0.01) in the TESRA study., Conclusions: Lower circulating sRAGE levels are associated with emphysema severity and genetic polymorphisms in the AGER locus are associated with systemic sRAGE levels. Clinical trial registered with www.clinicaltrials.gov (NCT 00413205 and NCT 00292552).

When the target of a goal-directed reach changes location, people normally respond rapidly and automatically to the target shift. Here, we investigate whether explicit knowledge about a moving target (knowing whether a location change is likely/unlikely) improves responsiveness, with the goal of understanding top-down effects on real-time reaching. In Experiment 1, we presented participants with pre-cues that indicated a 20 or 80% likelihood of a target perturbation on that trial. When participants made pro-pointing responses to the target perturbations, their online response occurred later for 20% trials than for 80% trials, but this effect may have been due to suppression of the online response on 20% trials, rather than enhancement of the response on 80% trials. In Experiment 2, we presented participants with 50 and 100% likelihood pre-cues, and observed no shortening of the latency on 100% trials compared to 50% trials, which suggests that expectation does not enhance the automatic response to a perturbation. However, we did observe more vigorous responses to the perturbation on the 100% trials, and this contributed to shorter movement times relative to the 50% trials. We also examined, in Experiment 2, whether prior knowledge about the direction of the target perturbation would shorten the latency of the online response, but we did not observe any reduction in latency. In sum, the onset of the automatic response appears to be suppressible, but not augmentable by top-down input. The possibility that the forcefulness of the automatic response is modifiable by expectation is examined, but not resolved.

Background: Thymic stromal lymphopoietin (TSLP) pathway blockade is a potential strategy for asthma treatment because the main activities of TSLP are activation of myeloid dendritic cells (mDCs) and modulation of cytokine production by mast cells. TSLP-activated mDCs prime the differentiation of naive T cells into inflammatory TH2 cells., Objective: We sought to investigate mechanisms underlying the development of allergic lung inflammation in cynomolgus monkeys using gene expression profiling and to assess the effect of thymic stromal lymphopoietin receptor (TSLPR) blockade in this model., Methods: An mAb against human TSLPR was generated and confirmed to be cross-reactive to cynomolgus monkey. Animals were dosed weekly with either vehicle or anti-TSLPR mAb for 6 weeks, and their responses to allergen challenge at baseline, week 2, and week 6 were assessed., Results: After 6 weeks of treatment, anti-TSLPR mAb-treated animals showed reduced bronchoalveolar lavage (BAL) fluid eosinophil counts, reduced airway resistance in response to allergen challenge, and reduced IL-13 cytokine levels in BAL fluid compared with values seen in vehicle-treated animals. Expression profiling of BAL fluid cells collected before and after challenge showed a group of genes upregulated by allergen challenge that strongly overlapped with 11 genes upregulated in dendritic cells (DCs) when in vitro stimulated by TSLP (TSLP-DC gene signature). The number of genes differentially expressed in response to challenge was reduced in antibody-treated animals after 6 weeks relative to vehicle-treated animals. Expression of the TSLP-DC gene signature was also significantly reduced in antibody-treated animals., Conclusion: These results demonstrate promising efficacy for TSLPR blockade in an allergic lung inflammation model in which TSLP activation of mDCs might play a key role., (Copyright © 2013 American Academy of Allergy, Asthma & Immunology. Published by Mosby, Inc. All rights reserved.)

Cheng et al. (2008) showed that when goal-directed reaching movements are performed with a 2.5 s inter-trial interval (ITI) under a randomized visual feedback schedule, individuals use online visual information on trial n to perform efficient online corrections on trial n + 1 (i.e., "reminiscence" effect). These results persisted even when participants were given knowledge of the up-coming vision condition. In this study, the ITI was extended to 5 s in an attempt to negate any effects of the preceding trial. Results from this study revealed that trials with vision were always more accurate than trials performed without vision, suggesting that individuals relied significantly on online information. Furthermore, aiming precision improved when participants knew the vision condition before each trial. It is thus suggested that the reminiscence effects are not longer evident with a 5 s ITI, which in turn allows prior knowledge of visual feedback to influence the use of online vision.

Unlabelled: The woodchuck model of hepatitis B virus (HBV) infection displays many characteristics of human infection and has particular value for characterizing the host immune responses during the development of chronic infection. Using the newly developed custom woodchuck microarray platform, we compared the intrahepatic transcriptional profiles of neonatal woodchucks with self-limiting woodchuck hepatitis virus (WHV) infection to those woodchucks progressing to persistent WHV infection. This revealed that WHV does not induce significant intrahepatic gene expression changes during the early-acute stage of infection (8 weeks), suggesting it is a stealth virus. At the mid-acute phase of infection (14 weeks), resolution was associated with induction of a prominent cytotoxic T-cell signature. Strikingly, this was accompanied by high-level expression of PD-1 and various other inhibitory T-cell receptors, which likely act to minimize liver damage by cytotoxic T cells during viral clearance. In contrast to the expression of perforin and other cytotoxic effector genes, the interferon-γ (IFN-γ) signaling response in the mid-acute phase was comparable to that in chronically infected adult animals. The absence of a strong IFN-α/β transcriptional response indicated that type I IFN is not a critical mediator of self-limiting infection. Nevertheless, a number of antiviral genes, including viperin, were differentially expressed during resolving infection, suggesting that a subset of IFN-stimulated genes (ISG) may play a role in the control of WHV replication., Conclusion: We identified new immune pathways associated with the clearance of hepadnavirus infection revealing novel molecular targets with potential for the therapeutic treatment of chronic hepatitis B., (Copyright © 2012 American Association for the Study of Liver Diseases.)

Recently, D. Elliott et al. (2010) asserted that the current control phase of a movement could be segregated in multiple processes, including impulse and limb-target regulation processes. The authors aimed to provide further empirical evidence and determine some of the constraints that govern these visuomotor processes. In 2 experiments, vision was presented or withdrawn when limb velocity was above or below selected velocity criteria. The authors observed that vision provided between 0.8 and 0.9 m/s significantly improved impulse regulation processes while vision provided up to 1.1 m/s significantly increased limb-target regulation processes. These results lend support to D. Elliott et al. and provide evidence that impulse regulation and limb-target regulation can take place at different velocities during a movement.