bluuebunny/crossref_metadata_2025_split huggingface dataset:
NEATTILL: A simplified procedure for nucleic acid extraction from arrayed tissue for TILLING and other high-throughput reverse genetic applications
Authors: Sreelakshmi Yellamaraju , Gupta Soni , Bodanapu Reddaiah , Chauhan Vineeta Singh , Hanjabam Mickey , Thomas Sherinmol , Mohan Vijee , Sharma Sulabha , Srinivasan Rajeswari , Sharma Rameshwar 
Published: January 2010

Abstract

Background
TILLING (Targeting Induced Local Lesions in Genomes) is a reverse genetics procedure for identifying point mutations in selected gene(s) amplified from a mutagenized population using high-throughput detection platforms such as slab gel electrophoresis, capillary electrophoresis or dHPLC. One essential pre-requisite for TILLING is genomic DNA isolation from a large population for PCR amplification of selected target genes. It also requires multiplexing of genomic DNA isolated from different individuals (pooling) in typically 8-fold pools, for mutation scanning, and to minimize the number of PCR amplifications, which is a strenuous and long-drawn-out work. We describe here a simplified procedure of multiplexing, NEATTILL (Nucleic acid Extraction from Arrayed Tissue for TILLING), which is rapid and equally efficient in assisting mutation detection.

Results
The NEATTILL procedure was evaluated for the tomato TILLING platform and was found to be simpler and more efficient than previously available methods. The procedure consisted of pooling tissue samples, instead of nucleic acid, from individual plants in 96-well plates, followed by DNA isolation from the arrayed samples by a novel protocol. The three variants of the NEATTILL procedure (vast, in-depth and intermediate) can be applied across various genomes depending upon the population size of the TILLING platform. The 2-D pooling ensures the precise confirmation of the coordinates of the positive mutant line while scanning complementary plates. Choice of tissue for arraying and nucleic acid isolation is discussed in detail with reference to tomato.

Conclusion
NEATTILL is a convenient procedure that can be applied to all organisms, the genomes of which have been mutagenized and are being scanned for multiple alleles of various genes by TILLING for understanding gene-to-phenotype relationships. It is a time-saving, less labour intensive and reasonably cost-effective method. Tissue arraying can cut costs by up to 90% and minimizes the risk of exposing the DNA to nucleases. Before arraying, different tissues should be evaluated for DNA quality, as the case study in tomato showed that cotyledons rather than leaves are better suited for DNA isolation. The protocol described here for nucleic acid isolation can be generally adapted for large-scale projects such as insertional mutagenesis, transgenic confirmation, mapping and fingerprinting which require isolation of DNA from large populations.
Efficacy of Neoadjuvant Cisplatin in Triple-Negative Breast Cancer
Authors: Silver Daniel P. , Richardson Andrea L. , Eklund Aron C. , Wang Zhigang C. , Szallasi Zoltan , Li Qiyuan , Juul Nicolai , Leong Chee-Onn , Calogrias Diana , Buraimoh Ayodele , Fatima Aquila , Gelman Rebecca S. , Ryan Paula D. , Tung Nadine M. , De Nicolo Arcangela , Ganesan Shridar , Miron Alexander , Colin Christian , Sgroi Dennis C. , Ellisen Leif W. , Winer Eric P. , Garber Judy E. 
Published: January 2010

Purpose Cisplatin is a chemotherapeutic agent not used routinely for breast cancer treatment. As a DNA cross-linking agent, cisplatin may be effective treatment for hereditary BRCA1-mutated breast cancers. Because sporadic triple-negative breast cancer (TNBC) and BRCA1-associated breast cancer share features suggesting common pathogenesis, we conducted a neoadjuvant trial of cisplatin in TNBC and explored specific biomarkers to identify predictors of response. Patients and Methods Twenty-eight women with stage II or III breast cancers lacking estrogen and progesterone receptors and HER2/Neu (TNBC) were enrolled and treated with four cycles of cisplatin at 75 mg/m2 every 21 days. After definitive surgery, patients received standard adjuvant chemotherapy and radiation therapy per their treating physicians. Clinical and pathologic treatment response were assessed, and pretreatment tumor samples were evaluated for selected biomarkers. Results Six (22%) of 28 patients achieved pathologic complete responses, including both patients with BRCA1 germline mutations;18 (64%) patients had a clinical complete or partial response. Fourteen (50%) patients showed good pathologic responses (Miller-Payne score of 3, 4, or 5), 10 had minor responses (Miller-Payne score of 1 or 2), and four (14%) progressed. All TNBCs clustered with reference basal-like tumors by hierarchical clustering. Factors associated with good cisplatin response include young age (P = .001), low BRCA1 mRNA expression (P = .03), BRCA1 promoter methylation (P = .04), p53 nonsense or frameshift mutations (P = .01), and a gene expression signature of E2F3 activation (P = .03). Conclusion Single-agent cisplatin induced response in a subset of patients with TNBC. Decreased BRCA1 expression may identify subsets of TNBCs that are cisplatin sensitive. Other biomarkers show promise in predicting cisplatin response.
Pharmacogenomic and Pharmacoproteomic Studies of Cetuximab in Metastatic Colorectal Cancer: Biomarker Analysis of a Phase I Dose-Escalation Study
Authors: Tabernero Josep , Cervantes Andres , Rivera Fernando , Martinelli Erika , Rojo Federico , von Heydebreck Anja , Macarulla Teresa , Rodriguez-Braun Edith , Eugenia Vega-Villegas Maria , Senger Stefanie , Ramos Francisco Javier , Roselló Susana , Celik Ilhan , Stroh Christopher , Baselga José , Ciardiello Fortunato 
Published: January 2010

Purpose This study assessed biomarkers for cetuximab efficacy in tissue samples collected during a phase I dose-escalation study exploring every second week administration of cetuximab as first-line therapy in patients with metastatic colorectal cancer (mCRC). Patients and Methods Sixty-two patients received cetuximab monotherapy for 6 weeks, followed by cetuximab plus infusional fluorouracil, leucovorin, and irinotecan until disease progression. Patients in the control arm received cetuximab as a 400 mg/m2 initial dose then 250 mg/m2 per week; patients in the dose-escalation arms received 400 to 700 mg/m2 every second week. Tumor and skin biopsies were taken for immunohistochemical and microarray expression analyses (tumor only) at baseline and week 4. Plasma was collected for proteomic analysis at baseline and week 4. KRAS tumor mutation status was assessed. Results In subsets of paired skin samples from 35 patients, cetuximab treatment was associated with substantial downregulation of phospho(p)-EGFR, p-MAPK and proliferation and substantial upregulation of p27Kip1 and p-STAT3 levels. No marked difference in these effects was noted for different schedules of administration and dose levels. In the cetuximab monotherapy phase, responses were seen only in patients whose tumors were wild-type for KRAS (eight of 29 v zero of 19 for KRAS mutant tumors; P = .015). Progression-free survival was longer for patients with KRAS wild-type compared with KRAS mutant tumors (log-rank P = .048). Genomics/proteomics analyses (42 and 45 patients, respectively) identified candidate biomarkers associated with response. Conclusion Biomarker analysis supported the functional equivalence of weekly and every second week administration of cetuximab and provided further confirmation that patients with KRAS wild-type mCRC were those most likely to benefit from cetuximab treatment.
Randomized, Blinded, Sham-Controlled Trial of Acupuncture for the Management of Aromatase Inhibitor–Associated Joint Symptoms in Women With Early-Stage Breast Cancer
Authors: Crew Katherine D. , Capodice Jillian L. , Greenlee Heather , Brafman Lois , Fuentes Deborah , Awad Danielle , Yann Tsai Wei , Hershman Dawn L. 
Published: January 2010

Purpose Women with breast cancer (BC) treated with aromatase inhibitors (AIs) may experience joint symptoms that can lead to discontinuation of effective therapy. We examined whether acupuncture improves AI-induced arthralgias in women with early-stage BC. Methods We conducted a randomized, controlled, blinded study comparing true acupuncture (TA) versus sham acupuncture (SA) twice weekly for 6 weeks in postmenopuasal women with BC who had self-reported musculoskeletal pain related to AIs. TA included full body/auricular acupuncture and joint-specific point prescriptions, whereas SA involved superficial needle insertion at nonacupoint locations. Outcome measures included the Brief Pain Inventory–Short Form (BPI-SF), Western Ontario and McMaster Universities Osteoarthritis Index (WOMAC), and Modified Score for the Assessment of Chronic Rheumatoid Affections of the Hands (M-SACRAH) obtained at baseline and at 3 and 6 weeks. Results Of 51 women enrolled, 43 women were randomly assigned and 38 were evaluable. Baseline characteristics were comparable between the two groups. Our primary end point was the difference in mean BPI-SF worst pain scores at 6 weeks, which was lower for TA compared with SA (3.0 v 5.5; P < .001). We also found differences between TA and SA in pain severity (2.6 v 4.5; P = .003) and pain-related interference (2.5 v 4.5; P = .002) at 6 weeks. Similar findings were seen for the WOMAC and M-SACRAH scores. The acupuncture intervention was well-tolerated. Conclusion Women with AI-induced arthralgias treated with TA had significant improvement of joint pain and stiffness, which was not seen with SA. Acupuncture is an effective and well-tolerated strategy for managing this common treatment-related side effect.
Migraine History and Breast Cancer Risk Among Postmenopausal Women
Authors: Li Christopher I. , Mathes Robert W. , Bluhm Elizabeth C. , Caan Bette , Cavanagh Mary F. , Chlebowski Rowan T. , Michael Yvonne , O'Sullivan Mary Jo , Stefanick Marcia L. , Prentice Ross 
Published: January 2010

Purpose Both migraine and breast cancer are hormonally mediated. Two recent reports indicate that women with a migraine history may have a lower risk of postmenopausal breast cancer than those who never suffered migraines. This finding requires confirmation; in particular, an assessment of the influence of use of nonsteroidal anti-inflammatory drugs (NSAID) is needed, because many studies indicate that NSAID use also may confer a reduction in breast cancer risk. Methods We assessed the relationship between self-reported history of migraine and incidence of postmenopausal breast cancer in 91,116 women enrolled on the Women's Health Initiative Observational Study prospective cohort from 1993 to 1998 at ages 50 to 79 years. Through September 15, 2005, there were 4,006 eligible patients with breast cancer diagnosed. Results Women with a history of migraine had a lower risk of breast cancer (hazard ratio [HR], 0.89; 95% CI, 0.80 to 98) than women without a migraine history. This risk did not vary by recent NSAID use. The lower risk was somewhat more pronounced for invasive estrogen-receptor–positive and progesterone-receptor–positive tumors (HR, 0.83; 95% CI, 0.71 to 0.97), as no reduction in risk was observed for invasive ER-negative/PR-negative tumors (HR, 1.16; 95% CI, 0.86 to 1.57), and this difference in risk estimates was borderline statistically significant (P = .06). Conclusion This study supports the hypothesis that a history of migraine is associated with a lower risk of breast cancer and that this relationship is independent of recent NSAID use.
Analysis of Potential Predictive Markers of Cetuximab Benefit in BMS099, a Phase III Study of Cetuximab and First-Line Taxane/Carboplatin in Advanced Non–Small-Cell Lung Cancer
Authors: Khambata-Ford Shirin , Harbison Christopher T. , Hart Lowell L. , Awad Melissa , Xu Li-An , Horak Christine E. , Dakhil Shaker , Hermann Robert C. , Lynch Thomas J. , Weber Martin R. 
Published: January 2010

Purpose The anti–epidermal growth factor receptor (EGFR) antibody cetuximab is efficacious in multiple tumor types. Patient selection with markers predictive of benefit may enhance its therapeutic index. This retrospective, correlative analysis of the phase III trial BMS099 of cetuximab in advanced non–small-cell lung cancer (NSCLC) was conducted to identify molecular markers for the selection of patients most likely to benefit from cetuximab. Methods In BMS099, 676 chemotherapy-naïve patients with stage IIIB (pleural effusion) or stage IV NSCLC of any histology or EGFR expression status were randomly assigned to taxane/carboplatin (T/C) with or without cetuximab. Biomarkers analyzed included K-Ras and EGFR mutations by direct sequencing, EGFR protein expression by immunohistochemistry (IHC), and EGFR gene copy number by fluorescent in situ hybridization (FISH). Relationships between biomarker status and progression-free survival (PFS), overall survival (OS), and overall response rate (ORR) were assessed by log-rank tests per treatment arm for treatment-specific effects and across the total evaluable population. Results Tumor samples were available from 225 randomly assigned patients. K-Ras mutations were found in 17% of evaluable patients (35 of 202 patients), EGFR mutations were found in 10% (17 of 166 patients), EGFR positivity by IHC was found in 89% (131 of 148 patients), and FISH positivity was found in 52% (54 of 104 patients). No significant associations were found between biomarker status and PFS, OS, and ORR in the treatment-specific analyses. Conclusion In contrast with colorectal cancer, and within the limitations of the data set, efficacy parameters did not appear to correlate with K-Ras mutation status or with any of the EGFR-related biomarkers evaluated. Additional exploratory analyses are essential to identify predictive markers and to optimize patient selection for cetuximab therapy in NSCLC.
Children's strategic regulation, metacognitive monitoring, and control processes during test taking
Authors: Krebs Saskia S. , Roebers Claudia M. 
Published: January 2010

BackgroundFrom the perspective of self‐regulated learning, the interplay between learners' individual characteristics and the context of testing have been emphasized for assessing learning outcomes.AimsThe present study examined metacognitive processes in children's test‐taking behaviour and explored their impacts on performance. Further, it was investigated whether differences in retrieval processes (operationalized through item difficulty) contribute to performance in strategic regulation skills.Sample and methodsA total of 107 participants (8‐/9‐ and 11‐/12‐year‐olds) solved a cloze test including answerable (easy, medium, and difficult questions) and unanswerable questions about an earlier presented educational film, gave confidence judgments to every answer, and were then allowed to withdraw answers if they wished. Two different scoring schemes for test performance were compared to a control group.ResultsAnalyses revealed relatively adequate monitoring processes when metacognitively distinguishing easy, difficult, and unanswerable items and correct and incorrect answers. At the same time, there was developmental progression in the ability to accurately monitor uncertainty. As to control processes, all children proved to be able to adjust their test‐taking behaviour to the benefit of test accuracy by withdrawing mainly incorrect answers. Controlling was more efficient for easy than for difficult and unanswerable items.ConclusionThe study offers evidence for the impact of metacognitive skills in children's learning outcomes and documents strategic behaviour during test taking, as well as developmental progression in the involved skills. Further, findings underline the importance of memory retrieval for subsequent metacognitive processes.
Epigenetic Contribution to Covariance Between Relatives
Authors: Tal Omri , Kisdi Eva , Jablonka Eva 
Published: January 2010

AbstractRecent research has pointed to the ubiquity and abundance of between-generation epigenetic inheritance. This research has implications for assessing disease risk and the responses to ecological stresses and also for understanding evolutionary dynamics. An important step toward a general evaluation of these implications is the identification and estimation of the amount of heritable, epigenetic variation in populations. While methods for modeling the phenotypic heritable variance contributed by culture have already been developed, there are no comparable methods for nonbehavioral epigenetic inheritance systems. By introducing a model that takes epigenetic transmissibility (the probability of transmission of ancestral phenotypes) and environmental induction into account, we provide novel expressions for covariances between relatives. We have combined a classical quantitative genetics approach with information about the number of opportunities for epigenetic reset between generations and assumptions about environmental induction to estimate the heritable epigenetic variance and epigenetic transmissibility for both asexual and sexual populations. This assists us in the identification of phenotypes and populations in which epigenetic transmission occurs and enables a preliminary quantification of their transmissibility, which could then be followed by genomewide association and QTL studies.
A Genomewide RNA Interference Screen for Modifiers of Aggregates Formation by Mutant Huntingtin in Drosophila
Authors: Zhang Sheng , Binari Richard , Zhou Rui , Perrimon Norbert 
Published: January 2010

AbstractProtein aggregates are a common pathological feature of most neurodegenerative diseases (NDs). Understanding their formation and regulation will help clarify their controversial roles in disease pathogenesis. To date, there have been few systematic studies of aggregates formation in Drosophila, a model organism that has been applied extensively in modeling NDs and screening for toxicity modifiers. We generated transgenic fly lines that express enhanced-GFP-tagged mutant Huntingtin (Htt) fragments with different lengths of polyglutamine (polyQ) tract and showed that these Htt mutants develop protein aggregates in a polyQ-length- and age-dependent manner in Drosophila. To identify central regulators of protein aggregation, we further generated stable Drosophila cell lines expressing these Htt mutants and also established a cell-based quantitative assay that allows automated measurement of aggregates within cells. We then performed a genomewide RNA interference screen for regulators of mutant Htt aggregation and isolated 126 genes involved in diverse cellular processes. Interestingly, although our screen focused only on mutant Htt aggregation, several of the identified candidates were known previously as toxicity modifiers of NDs. Moreover, modulating the in vivo activity of hsp110 (CG6603) or tra1, two hits from the screen, affects neurodegeneration in a dose-dependent manner in a Drosophila model of Huntington's disease. Thus, other aggregates regulators isolated in our screen may identify additional genes involved in the protein-folding pathway and neurotoxicity.
The Impact of Whole Genome Sequencing on Model System Genetics: Get Ready for the Ride
Authors: Hobert Oliver 
Published: January 2010

Abstract
Much of our understanding of how organisms develop and function is derived from the extraordinarily powerful, classic approach of screening for mutant organisms in which a specific biological process is disrupted. Reaping the fruits of such forward genetic screens in metazoan model systems like Drosophila, Caenorhabditis elegans, or zebrafish traditionally involves time-consuming positional cloning strategies that result in the identification of the mutant locus. Whole genome sequencing (WGS) has begun to provide an effective alternative to this approach through direct pinpointing of the molecular lesion in a mutated strain isolated from a genetic screen. Apart from significantly altering the pace and costs of genetic analysis, WGS also provides new perspectives on solving genetic problems that are difficult to tackle with conventional approaches, such as identifying the molecular basis of multigenic and complex traits.
Redefining Urinary Tract Infections by Bacterial Colony Counts
Authors: Coulthard Malcolm G. , Kalra Monika , Lambert Heather J. , Nelson Andrew , Smith Terry , Perry John D. 
Published: January 2010

OBJECTIVES:To determine the best urinary bacterial concentration to diagnose urine infections.METHODS:We studied a quantitative culture of paired urine samples from children that were promptly tested together after serial dilution. The initial diagnosis of urinary tract infection made from the result of the first urine culture and subsequently modified according to the second sample result, and then the ratio of their colony counts was considered. A total of 203 children (aged 2.0 weeks to 17.7 years) were screened for urine infection in a hospital setting.RESULTS:The 36 children who had a urinary tract infection, defined as having the same uropathogen in both urine samples at concentrations within 25-fold of each other, had a mean colony count of 1.7 × 107 colony-forming units/mL. Among the 167 children who did not have a urinary tract infection, 12 (7.2%) would have had a false-positive diagnosis made on the first sample, which was revealed because the second sample result was different (n = 7) or had a ≥25-fold different colony count (n = 5). Raising the threshold from 105 to 106 colony-forming units/mL reduces the false-positive rate 4.8%. If 2 samples are cultured, the false-positive rates fall to 3.6% and 0.6%, respectively. All 9 children (5.4% of those without a urinary tract infection) who had a mixed culture with ≥105 colony-forming units/mL of a uropathogen (heavy mixed growth) in the first sample had a urine infection excluded by the second sample result.CONCLUSION:The minimum urinary bacterial concentration that is used to diagnose a urine infection should be increased from ≥105 to ≥106 colony-forming units/mL, because that would reduce the false-positive rate from 7.2% to 4.8% if 1 sample was cultured and from 3.6% to 0.6% if 2 samples were cultured. Urine samples with heavy mixed growths should be considered contaminated.
Parenting Behaviors, Perceptions, and Psychosocial Risk: Impacts on Young Children's Development
Authors: Glascoe Frances Page , Leew Shirley 
Published: January 2010

OBJECTIVE:The goal of this study was to assess which parenting behaviors, perceptions, and risk factors were associated with optimal versus delayed development.METHODS:A total of 382 families from the national Brigance Infant and Toddler Screens standardization and validation study participated. Data sources included parent questionnaires, child testing, and examiner observations of parent-child interactions. Parenting styles research was operationalized with the Brigance Parent-Child Interactions Scale, a brief measure of parenting behaviors and perceptions.RESULTS:Six positive parenting behaviors and perceptions predicted average to above-average development on the Brigance screens. Conversely, &lt;2 positive parenting behaviors and negative perceptions of children indicated child performance nearly 2 SDs below the mean on Brigance screens. Psychosocial risk factors associated with fewer positive parenting behaviors and with negative perceptions included &gt;3 children in the home, multiple moves, limited English, and parental depression.CONCLUSIONS:A dearth of positive parenting behaviors plus negative perceptions of children, with or without psychosocial risk factors, negatively affect child development, which is apparent as early as 6 months of age. The older the child is, the greater the performance gaps are. Language development is particularly at risk when parenting is problematic. Findings underscore the importance of early development promotion with parents, focusing on their talking, playing, and reading with children, and the need for interventions regarding psychosocial risk factors.