Omics-based characterization of random transgene integration sites from CHO production cell lines

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PLTL in the Developmental Writing Classsroom

Writing placement exam preparation can be broken down into small tasks overseen by Peer Leaders, following (though not precisely) patterns set out by Fred Keller in “Good-bye Teacher” in 1968. The mechanical aspect of writing, however, is never enough for the production of essays that communicate, something that requires audience and a desire to “speak.” Students in developmental classrooms often have problems beyond the writing itself: they may be test shy and may not be prepared to take on even college entry tasks without careful direction. Working with Peer Leaders, the developmental program can address the problems of mechanics and testing demands, the Peer Leaders taking on some of the responsibility for guiding students through the tasks. PLTL can also help address the broader problems of preparation for college and even for critical thinking, the Peer Leaders serving as role models

Challenging games help students learn: an empirical study on engagement, flow and immersion in game-based learning

In this paper, we investigate the impact of flow (operationalized as heightened challenge and skill), engagement, and immersion on learning in game-based learning environments. The data was gathered through a survey from players (N = 173) of two learning games (Quantum Spectre: N = 134 and Spumone: N = 40). The results show that engagement in the game has a clear positive effect on learning, however, we did not find a significant effect between immersion in the game and learning. Challenge of the game had a positive effect on learning both directly and via the increased engagement. Being skilled in the game did not affect learning directly but by increasing engagement in the game. Both the challenge of the game and being skilled in the game had a positive effect on both being engaged and immersed in the game. The challenge in the game was an especially strong predictor of learning outcomes. For the design of educational games, the results suggest that the challenge of the game should be able to keep up with the learners growing abilities and learning in order to endorse continued learning in game-based learning environments.</p

The Lantern Vol. 64, No. 2, Spring 1997

• Year\u27s End, with Resolutions • Addicted • Muerte, Carlos • Motions • At the Wyeth Gallery • Between Contexts • I\u27m Allowed (and More Nonsense) • Wall and Piece • Timekeeper\u27s Workspace • The Process • Second Sex: A Portrait of the Artist as a Woman • On the Side of the Road • Joe • To Matthew Arnold • A Deep Sleep on Hydrocodone • Madness of a Night • Return • The Sudden Grave • A Farce • Twists of Fur • Ambiguity • The Odor of Continuums • My Father\u27s Daughter • The Meaning of Life • I Aim to Tell • Nobody\u27s Fanhttps://digitalcommons.ursinus.edu/lantern/1150/thumbnail.jp

Including neurodiversity in computational thinking

IntroductionThe foundational practices of Computational Thinking (CT) present an interesting overlap with neurodiversity, specifically with differences in executive function (EF). An analysis of CT teaching and learning materials designed for differentiation and support of EF show promise to reveal problem-solving strengths of neurodivergent learners.MethodsTo examine this potential, studies were conducted using a computer-supported, inclusive, and highly interactive learning program named INFACT that was designed with the hypothesis that all students, including neurodivergent learners, will excel in problem solving when it is structured through a variety of CT activities (including games, puzzles, robotics, coding, and physical activities) and supported with EF scaffolds. The INFACT materials were used in 12 treatment classrooms in grades 3–5 for at least 10  h of implementation. Pre-post assessments of CT were administered to treatment classes as well as 12 comparison classes that used 10  h of other CT teaching and learning materials. EF screeners were also used with all classes to disaggregate student results by quartile of EF.FindingsStudents using INFACT materials showed a significant improvement in CT learning as compared to comparison classes. Students with EF scores in the lower third of the sample showed the greatest improvement.DiscussionThis study shows promising evidence that differentiated activities with EF scaffolds situated across several contexts (e.g., games, puzzles, physical activities, robotics, coding) promote effective CT learning in grades 3–5

Lower urinary tract symptoms in men: The TRIUMPH cluster RCT

Conservative therapies are recommended as initial treatment for male lower urinary tract symptoms. However, there is a lack of evidence on effectiveness and uncertainty regarding approaches to delivery. The objective was to determine whether or not a standardised and manualised care intervention delivered in primary care achieves superior symptomatic outcome for lower urinary tract symptoms to usual care. This was a two-arm cluster randomised controlled trial. The trial was set in 30 NHS general practice sites in England. Participants were adult men (aged ≥ 18 years) with bothersome lower urinary tract symptoms. Sites were randomised 1 : 1 to deliver the TReatIng Urinary symptoms in Men in Primary Health care using non-pharmacological and non-surgical interventions trial intervention or usual care to all participants. The TReatIng Urinary symptoms in Men in Primary Health care using non-pharmacological and non-surgical interventions intervention comprised a standardised advice booklet developed for the trial from the British Association of Urological Surgeons' patient information sheets, with patient and expert input. Patients were directed to relevant sections by general practice or research nurses/healthcare assistants following urinary symptom assessment, providing the manualised element. The healthcare professional provided follow-up contacts over 12 weeks to support adherence to the intervention. The primary outcome was the validated patient-reported International Prostate Symptom Score 12 months post consent. Rather than the minimal clinically important difference of 3.0 points for overall International Prostate Symptom Score, the sample size aimed to detect a difference of 2.0 points, owing to the recognised clinical impact of individual symptoms. A total of 1077 men consented to the study: 524 in sites randomised to the intervention arm ( = 17) and 553 in sites randomised to the control arm ( = 13). A difference in mean International Prostate Symptom Score at 12 months was found (adjusted mean difference of -1.81 points, 95% confidence interval -2.66 to -0.95 points), with a lower score in the intervention arm, indicating less severe symptoms. Secondary outcomes of patient-reported urinary symptoms, quality of life specific to lower urinary tract symptoms and perception of lower urinary tract symptoms all showed evidence of a difference between the arms favouring the intervention. No difference was seen between the arms in the proportion of urology referrals or adverse events. In qualitative interviews, participants welcomed the intervention, describing positive effects on their symptoms, as well as on their understanding of conservative care and their attitude towards the experience of lower urinary tract symptoms. The interviews highlighted that structured, in-depth self-management is insufficiently embedded within general practitioner consultations. From an NHS perspective, mean costs and quality-adjusted life-years were similar between trial arms. The intervention arm had slightly lower mean costs (adjusted mean difference of -£29.99, 95% confidence interval -£109.84 to £22.63) than the usual-care arm, and a small gain in quality-adjusted life-years (adjusted mean difference of 0.001, 95% confidence interval -0.011 to 0.014). The intervention showed a small, sustained benefit for men's lower urinary tract symptoms and quality of life across a range of outcome measures in a UK primary care setting. Qualitative data showed that men highly valued the intervention. Intervention costs were marginally lower than usual-care costs. Limitations of the study included that trial participants were unmasked, with limited diversity in ethnicity and deprivation level. Additional research is needed to assess the applicability of the intervention for a more ethnically diverse population.. This trial is registered as ISRCTN11669964. This award was funded by the National Institute for Health and Care Research (NIHR) Health Technology Assessment programme (NIHR award ref: 16/90/03) and is published in full in ; Vol. 28, No. 13. See the NIHR Funding and Awards website for further award information

Identifying perinatal depression with case-finding instruments : a mixed-methods study (BaBY PaNDA – Born and Bred in Yorkshire PeriNatal Depression Diagnostic Accuracy)

Background: Perinatal depression is well recognised as a mental health condition but < 50% of cases are identified in routine practice. A case-finding strategy using the Whooley questions is currently recommended by the National Institute for Health and Care Excellence. Objectives: To determine the diagnostic accuracy, acceptability and cost-effectiveness of the Whooley questions and the Edinburgh Postnatal Depression Scale (EPDS) to identify perinatal depression. Design: A prospective diagnostic accuracy cohort study, with concurrent qualitative and economic evaluations. Setting: Maternity services in England. Participants: A total of 391 pregnant women. Main outcome measures: Women completed the Whooley questions, EPDS and a diagnostic reference standard (Clinical Interview Schedule – Revised) during pregnancy (20 weeks) and postnatally (3–4 months). Qualitative interviews were conducted with health professionals (HPs) and a subsample of women. Results: Diagnostic accuracy results: depression prevalence rates were 10.3% during pregnancy and 10.5% postnatally. The Whooley questions and EPDS (cut-off point of ≥ 10) performed reasonably well, with comparable sensitivity [pregnancy: Whooley questions 85.0%, 95% confidence interval (CI) 70.2% to 94.3%; EPDS 82.5%, 95% CI 67.2% to 92.7%; postnatally: Whooley questions 85.7%, 95% CI 69.7% to 95.2%; EPDS 82.9%, 95% CI 66.4% to 93.4%] and specificity (pregnancy: Whooley questions 83.7%, 95% CI 79.4% to 87.4%; EPDS 86.6%, 95% CI 82.5% to 90.0%; postnatally: Whooley questions 80.6%, 95% CI 75.7% to 84.9%; EPDS 87.6%, 95% CI 83.3% to 91.1%). Diagnostic accuracy of the EPDS (cut-off point of ≥ 13) was poor at both time points (pregnancy: sensitivity 45%, 95% CI 29.3% to 61.5%, and specificity 95.7%, 95% CI 93.0% to 97.6%; postnatally: sensitivity 62.9%, 95% CI 44.9% to 78.5%, and specificity 95.7%, 95% CI 92.7% to 97.7%). Qualitative evaluation: women and HPs were supportive of screening/case-finding for perinatal depression. The EPDS was preferred to the Whooley questions by women and HPs, mainly because of its ‘softer’ wording. Whooley question 1 was thought to be less acceptable, largely because of the terms ‘depressed’ and ‘hopeless’, leading to women not revealing their depressive symptoms. HPs identified a ‘patient-centred’ environment that focused on the mother and baby to promote discussion about mental health. Cost-effectiveness results: screening/case-finding using the Whooley questions or the EPDS alone was not the most cost-effective strategy. A two-stage strategy, ‘Whooley questions followed by the Patient Health Questionnaire’ (a measure assessing depression symptomatology), was the most cost-effective strategy in the range between £20,000 and £30,000 per quality-adjusted life-year in both the prenatal and postnatal decision models. Limitations: Perinatal depression diagnosis was not cross-referenced with women’s medical records so the proportion of new cases identified is unknown. The clinical effectiveness and cost-effectiveness of screening/case-finding strategies was not assessed as part of a randomised controlled trial. Conclusions: The Whooley questions and EPDS had acceptable sensitivity and specificity, but their use in practice might be limited by low predictive value and variation in their acceptability. A two-stage strategy was more cost-effective than single-stage strategies. Neither case-finding instrument met National Screening Committee criteria. Future work: The yield of screening/case-finding should be established with reference to health-care records. The clinical effectiveness and cost-effectiveness of screening/case-finding for perinatal depression needs to be tested in a randomised controlled trial. Funding: The National Institute for Health Research Health Services and Delivery Research programme

The Staphylococcus aureus Response to Unsaturated Long Chain Free Fatty Acids: Survival Mechanisms and Virulence Implications

Staphylococcus aureus is an important human commensal and opportunistic pathogen responsible for a wide range of infections. Long chain unsaturated free fatty acids represent a barrier to colonisation and infection by S. aureus and act as an antimicrobial component of the innate immune system where they are found on epithelial surfaces and in abscesses. Despite many contradictory reports, the precise anti-staphylococcal mode of action of free fatty acids remains undetermined. In this study, transcriptional (microarrays and qRT-PCR) and translational (proteomics) analyses were applied to ascertain the response of S. aureus to a range of free fatty acids. An increase in expression of the σB and CtsR stress response regulons was observed. This included increased expression of genes associated with staphyloxanthin synthesis, which has been linked to membrane stabilisation. Similarly, up-regulation of genes involved in capsule formation was recorded as were significant changes in the expression of genes associated with peptidoglycan synthesis and regulation. Overall, alterations were recorded predominantly in pathways involved in cellular energetics. In addition, sensitivity to linoleic acid of a range of defined (sigB, arcA, sasF, sarA, agr, crtM) and transposon-derived mutants (vraE, SAR2632) was determined. Taken together, these data indicate a common mode of action for long chain unsaturated fatty acids that involves disruption of the cell membrane, leading to interference with energy production within the bacterial cell. Contrary to data reported for other strains, the clinically important EMRSA-16 strain MRSA252 used in this study showed an increase in expression of the important virulence regulator RNAIII following all of the treatment conditions tested. An adaptive response by S. aureus of reducing cell surface hydrophobicity was also observed. Two fatty acid sensitive mutants created during this study were also shown to diplay altered pathogenesis as assessed by a murine arthritis model. Differences in the prevalence and clinical importance of S. aureus strains might partly be explained by their responses to antimicrobial fatty acids

Homologous recombination DNA repair defects in PALB2- associated breast cancers

Abstract: Mono-allelic germline pathogenic variants in the Partner And Localizer of BRCA2 (PALB2) gene predispose to a high-risk of breast cancer development, consistent with the role of PALB2 in homologous recombination (HR) DNA repair. Here, we sought to define the repertoire of somatic genetic alterations in PALB2-associated breast cancers (BCs), and whether PALB2-associated BCs display bi-allelic inactivation of PALB2 and/or genomic features of HR-deficiency (HRD). Twenty-four breast cancer patients with pathogenic PALB2 germline mutations were analyzed by whole-exome sequencing (WES, n = 16) or targeted capture massively parallel sequencing (410 cancer genes, n = 8). Somatic genetic alterations, loss of heterozygosity (LOH) of the PALB2 wild-type allele, large-scale state transitions (LSTs) and mutational signatures were defined. PALB2-associated BCs were found to be heterogeneous at the genetic level, with PIK3CA (29%), PALB2 (21%), TP53 (21%), and NOTCH3 (17%) being the genes most frequently affected by somatic mutations. Bi-allelic PALB2 inactivation was found in 16 of the 24 cases (67%), either through LOH (n = 11) or second somatic mutations (n = 5) of the wild-type allele. High LST scores were found in all 12 PALB2-associated BCs with bi-allelic PALB2 inactivation sequenced by WES, of which eight displayed the HRD-related mutational signature 3. In addition, bi-allelic inactivation of PALB2 was significantly associated with high LST scores. Our findings suggest that the identification of bi-allelic PALB2 inactivation in PALB2-associated BCs is required for the personalization of HR-directed therapies, such as platinum salts and/or PARP inhibitors, as the vast majority of PALB2-associated BCs without PALB2 bi-allelic inactivation lack genomic features of HRD

Development and validation of a targeted gene sequencing panel for application to disparate cancers

Next generation sequencing has revolutionised genomic studies of cancer, having facilitated the development of precision oncology treatments based on a tumour’s molecular profile. We aimed to develop a targeted gene sequencing panel for application to disparate cancer types with particular focus on tumours of the head and neck, plus test for utility in liquid biopsy. The final panel designed through Roche/Nimblegen combined 451 cancer-associated genes (2.01 Mb target region). 136 patient DNA samples were collected for performance and application testing. Panel sensitivity and precision were measured using well-characterised DNA controls (n = 47), and specificity by Sanger sequencing of the Aryl Hydrocarbon Receptor Interacting Protein (AIP) gene in 89 patients. Assessment of liquid biopsy application employed a pool of synthetic circulating tumour DNA (ctDNA). Library preparation and sequencing were conducted on Illumina-based platforms prior to analysis with our accredited (ISO15189) bioinformatics pipeline. We achieved a mean coverage of 395x, with sensitivity and specificity of >99% and precision of >97%. Liquid biopsy revealed detection to 1.25% variant allele frequency. Application to head and neck tumours/cancers resulted in detection of mutations aligned to published databases. In conclusion, we have developed an analytically-validated panel for application to cancers of disparate types with utility in liquid biopsy