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A 121

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Most cited protocols related to «A 121»

1
Scaffolding Accuracy of Assemblies
Cited 57 times
Of our 103 A. thaliana assemblies, we highlighted the runtime and scaffolding accuracy of the assembly representing the TFÄ 04 accession (SRR1945711). This assembly was assembled with SPAdes (see below) and had a scaffold N50 of 120,255 bp with a total size of 115,803,138 bp [43 (link)]. Additionally, to demonstrate the scaffolding of a mammalian-sized genome, we used RaGOO to order and orient the mixed haplotype human Canu assembly derived from Pacific Biosciences CCS reads. This human assembly had a contig N50 of 22,778,121 bp and a total size of 3,418,171,375 bp. For both the TFÄ 04 and human assemblies, default RaGOO parameters were used and the software was run with 8 threads (“-t 8”). The TAIR 10 and hs37d5 reference genomes were used to scaffold the TFÄ 04 and human assemblies, respectively. RaGOO completed in 12.576 s and 12 min and 33.090 s for TFÄ 04 and human, respectively. The dotplots for both assemblies were made by aligning RaGOO pseudomolecules to the respective reference genomes with nucmer (-l 200 -c 500). Alignments were filtered with delta filter (-1 -l 20000), and plots were made with Mummerplot (--fat). Only nuclear chromosome and non-alternate sequences are shown in the dotplots.
Alonge M., Soyk S., Ramakrishnan S., Wang X., Goodwin S., Sedlazeck F.J., Lippman Z.B, & Schatz M.C. (2019). RaGOO: fast and accurate reference-guided scaffolding of draft genomes. Genome Biology, 20, 224.
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Publication 2019
A 121 A 778 Chromosomes Genome Haplotypes Homo sapiens Mammals
2
Profiling miRNA Expression in FFPE Tissues
Cited 27 times
RNA (miRNA) was extracted from formalin-fixed paraffin embedded tissues. We assessed slides and tumor blocks that were prepared over the duration of the study prior to the time of miRNA isolation to determine their suitability. The study pathologist (WS) reviewed slides to delineate tumor, normal, and polyp tissue. Cells were dissected from 1–4 sequential sections on aniline blue stained slides using an H&E slide for reference. Total RNA containing miRNA was extracted, isolated, and purified using the RecoverAll Total Nucleic Acid isolation kit (Ambion), RNA yields were determined using a NanoDrop spectrophotometer. 100 ng total RNA was labeled with cy3 and hybridized to Agilent Human miRNA Microarray V19.0 and were scanned on an Agilent SureScan microarray scanner model G2600D. The Agilent Human microarray was generated using known miRNA sequence information compiled in the Sanger miRBASE database v19.0. The microarray contains probes for 2006 unique human miRNAs, with one to four unique probes for each of the known miRNAs. The miRNA array contains 60,000 unique human sequences and averages 30 replicates per probe sequence. Data were extracted from the scanned image using Agilent Feature Extract software v.11.5.1.1. Data were required to pass stringent QC parameters established by Agilent that included tests for excessive background fluorescence, excessive variation among probe sequence replicates on the array, and measures of the total gene signal on the array to assess low signal. If samples failed to meet quality standards for any of these parameters, the sample was re-labeled, hybridized to arrays, and scanned. If a sample failed QC assessment a second time the sample was deemed to be of poor quality and the individual was excluded from down-stream analysis. Of the 1171 initial cases, 30 were excluded at this stage. A quantile normalization across arrays was done using preprocessCore11 (www.bioconductor.org) to minimize differences that could be attributed to the array, amount of RNA, location on array, or other factors that could erroneously influence expression.
We refer to miRNAs using standard nomenclature used in the miRBase database12 (link). Briefly, the first three letters signifies the organism, followed by a unique number. The number is followed by a dash and number (i.e., 1) if more than one loci codes for the miRNA. A lettered suffix denotes closely related miRNAs. If two miRNAs are coded by the same precursor product then the minor product is assigned the suffix (*). If predominant/minor product status is not known then the suffix 5p and 3p are used to denote 5′ and 3′ arm respectively. Many of the miRNAs being replicated in this study were reported prior to current nomenclature. For instance, let-7 may be reported in the literature as being associated with tumor stage, however Let-7 has since been further delineated to several closely related mature sequences and genomic loci, for example let-7a-3p, let-7a-5p, and let-7b-3p. A complete list of the 121 miRNAs previously reported with stage and/or survivals that are being evaluated in this replication is included in Supplemental Table 1.
Slattery M.L., Herrick J.S., Mullany L.E., Valeri N., Stevens J., Caan B.J., Samowitz W, & Wolff R.K. (2014). An evaluation and replication of miRNAs with disease stage and colorectal cancer-specific mortality. International journal of cancer. Journal international du cancer, 137(2), 428-438.
Publication 2014
A 121 aniline blue Cells DNA Replication Fluorescence Formalin Genes Genetic Diversity Genome Homo sapiens isolation Microarray Analysis MicroRNAs Neoplasms Nucleic Acids Paraffin Embedding Pathologists Polyps Tissues
3
Nurses' Health Study Cohort Analysis
Cited 17 times
The Nurses’ Health Study (NHS) is a prospective study of a cohort of 121,701 female registered nurses from 11 U.S. states who were enrolled in 1976. The Nurses’ Health Study II (NHS II) is a prospective study of a cohort of 116,686 younger female registered nurses from 14 states who were enrolled in 1989. The Health Professionals Follow-up Study (HPFS) is a prospective study of a cohort of 51,529 male health professionals from all 50 states, enrolled in 1986. Participants were followed with the use of biennial validated questionnaires concerning medical history, lifestyle, and health practices. For this analysis, the baseline year was the first year for which detailed information was available on diet, physical activity, and smoking habits — 1986 in the NHS and HPFS and 1991 in the NHS II. We excluded participants with obesity, diabetes, cancer, or cardiovascular, pulmonary, renal, or liver disease at baseline; those for whom baseline data on lifestyle habits were missing; those with an implausible energy intake (<900 or >3500 kcal per day); those with more than nine blank responses on the diet questionnaire; those who were newly pregnant during follow-up; and those who were over 65 years of age, given possible confounding due to age-related loss of lean muscle mass. The final analyses included 50,422 women in the NHS, 47,898 women in the NHS II, and 22,557 men in the HPFS, all of whom were free of obesity and chronic diseases and for whom data on weight and lifestyle habits at baseline were complete. Cohort members who were excluded because of missing data had characteristics similar to those included in the analysis (data not shown). The funders of this study had no role in its design or conduct; in the collection, management, analysis, or interpretation of the data; or in the preparation, review, or approval of the manuscript.
Mozaffarian D., Hao T., Rimm E.B., Willett W.C, & Hu F.B. (2011). Changes in Diet and Lifestyle and Long-Term Weight Gain in Women and Men. The New England journal of medicine, 364(25), 2392-2404.
Publication 2011
A 121 Cardiovascular System Diabetes Mellitus Diet Disease, Chronic Health Personnel Kidney Liver Diseases Lung Males Malignant Neoplasms Muscle Tissue Nurses Obesity Registered Nurse Woman Youth
4
Healthy Young Females' Fitness Competition Diet
Cited 7 times
A total of 184 healthy, physically active young females, recruited by web page and social media advertisements and who claimed to meet the inclusion criteria volunteered for the study. Out of the females who fulfilled the preliminary criteria, 63 participants were planning on competing under the International Federation of Bodybuilding and Fitness (IFBB) in the year of the study and, thus, would diet accordingly. In addition, a total of 121 volunteers were aiming not to diet now, but would probably diet later in their life or at least try to maintain a fitness lifestyle. An online pre-study questionnaire was sent to the available 44 diet- and 70 randomly chosen control group candidates that fulfilled the preliminary requirements for the study (see below). Females, who were diagnosed with chronic diseases or prescribed medications such as thyroxine, but excluding contraception, and who were younger than 20 or older than 38 years old, whose BMI was below 20 or above 27, or who did not have at least 2 years of resistance training experience were excluded from the study. As a result, the diet group competing in the autumn of 2015 consisted of 30 volunteers. We chose these exclusion criteria because our aim was to investigate normal-weight healthy previously trained females. An equal number of control participants were quasi-randomized by matching based on their age, height, weight, and training experience reported on the pre-study questionnaire. The participants selected for the study filled in an additional questionnaire that was subsequently reviewed by the physician of our study to confirm that they did not meet the exclusion criteria relating to health.
All of the diet participants were IFBB amateur fitness competitors aiming to lose fat, but maintain their muscle mass in a sport that is tested for prohibited performance enhancing drugs. Out of these participants, 17 were bikini fitness and 9 body fitness competitors and 1 was a fitness competitor. These groups were very similar at the baseline and with regard to the changes during diet (body composition and hormones, data not shown).
The subjects were given comprehensive explanations regarding the study design, protocols, and possible risks. This study was carried out in accordance with the recommendations of Ethical Committee at the University of Jyväskylä with written informed consent from all subjects. All subjects gave written informed consent in accordance with the Declaration of Helsinki. The protocol was approved by the Ethical Committee at the University of Jyväskylä.
Hulmi J.J., Isola V., Suonpää M., Järvinen N.J., Kokkonen M., Wennerström A., Nyman K., Perola M., Ahtiainen J.P, & Häkkinen K. (2017). The Effects of Intensive Weight Reduction on Body Composition and Serum Hormones in Female Fitness Competitors. Frontiers in Physiology, 7, 689.
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Publication 2016
A 121 Body Composition Contraceptive Methods Diet Disease, Chronic Females Hormones Human Body Muscle Tissue Performance-Enhancing Drugs Pharmaceutical Preparations Physicians Thyroxine Voluntary Workers Youth
5
Functional Arm Recovery after Stroke
Cited 7 times
Participants were assessed at baseline (prerandomization), post-intervention (end of therapy), 6 months, and 12 months (end of study) after randomization by clinicians masked to treatment assignment and standardized in administration of primary and secondary outcome assessments.5 (link) A 12-monthchange in the log-transformed Wolf Motor Function Test (WMFT) time score was the primary outcome. The WMFT time score is a mean of 15 hierarchically arranged timed arm movements and hand dexterity tasks.15 (link)–18 (link) If a task could not be completed in 2 minutes (ie, 120 seconds), a time score of 121 seconds was assigned. A log transformation is used to accommodate for the nonnormality in the raw time score.
Secondary outcomes included the 12-month change in WMFT time score (minimum clinically important difference, 19 seconds faster, 16% of the range on the dominant side and unknown on the nondominant side19 (link)) and improvement in participant- reported Stroke Impact Scale (SIS), version 3.0, hand subscale score (percentage with improvement ≥25 points). Because the SIS hand function range is 0 to 100 points, participants with SIS hand function scores of 75 or higher at baseline (n = 15) were excluded from this analysis. The minimal detectable change and minimal clinically important difference for the SIS hand function subscale are 25.9 points and 17.8 points, respectively.20 (link) The primary end point was the end of study (12 months after randomization; mean, 13.5 months after stroke), while end of therapy (16 weeks after randomization; mean, approximately 22 weeks after stroke) was a secondary end point.
Patients (or their designated representatives or caregivers) were contacted by monthly telephone calls to review health status, health care utilization, medications, and adverse events. Adverse events were reported regarding 3 independent characteristics: expectedness, relation to study, and severity.5 (link)
Winstein C.J., Wolf S.L., Dromerick A.W., Lane C.J., Nelsen M.A., Lewthwaite R., Cen S.Y, & Azen S.P. (2016). Effect of a Task-Oriented Rehabilitation Program on Upper Extremity Recovery Following Motor Stroke: The ICARE Randomized Clinical Trial. JAMA, 315(6), 571-581.
Publication 2016
A 121 Cerebrovascular Accident Movement Patient Acceptance of Health Care Patients Pharmaceutical Preparations Therapeutics Wolves

Most recents protocols related to «A 121»

1
Cognitive Bias Modification for Adolescents
Participants were adolescents enrolled in 7th-grade classes from two middle schools in two cities (Xinyang & Jiaxing) of central China. Inclusion criteria were: (1) voluntary participation; (2) familiar with the computer; (3) without mental disorder diagnosis or severe physical problems; (4) not currently receiving treatment with psychotherapy or psychotropic medication. Participants’ recruitment progress through the study is presented in Fig. 1. A total of 121 middle school students were included in the final analysis (53.70% female, mean age = 13.89, SD = 1.09, range = 12–17; CBM-I group: 57.38% female, mean age = 13.74, SD = 1.14; control group: 50.00% female, mean age = 14.05, SD = 1.02), 61 of them were assigned to CBM-I group, 60 of them were assigned to control group.
A power analysis with G*Power 3.1.9.2 (Faul et al., 2009 (link)) of repeated measures of ANOVA was used to calculate the required sample size. The results indicated that 56 participants for each condition were needed to yield statistical power of 1-β = 0.90 at α = 0.05 for a medium effect size (f = 0.25). That was to say, 112 participants in total were needed to be capable to detect an effect of this magnitude. The total sample size in the current study exceeded this minimum.

CONSORT flowchart for participants’ recruitment

Zeng K., Cao F., Wu Y., Zhang M, & Ding X. (2023). Effects of interpretation bias modification on hostile attribution bias and reactive cyber-aggression in Chinese adolescents: a randomized controlled trial. Current Psychology (New Brunswick, N.j.).
Publication 2023
A 121 Adolescent Diagnosis Females Mental Disorders neuro-oncological ventral antigen 2, human Physical Examination Psychotherapy Psychotropic Drugs Student
2
Sport Participation Survey in Leiria City
Given that Leiria was chosen as the European City of Sport—2022 (LECS—2022)—a study of the local community’s sport participation was carried out. As a result, during an activity devised in this area, we queried a group of respondents about their sports-related practice. A total of 121 young people were interviewed. Of these, 115 said that they participated in sport by playing football in local clubs. As a result, the local clubs were called in order to gain the necessary authorization to continue this study. After receiving a positive response to continue the investigation, the children’s parents or legal tutors were contacted. During this encounter, the nature, ethical, and data collection procedures of the study were presented. Afterwards, the parents or legal tutors provided an informed consent granting permission for their children to participate in this research. Six potential participants missed the data collection date on the day the surveys were administered and where thus not included in this study. As a result, 109 young male athletes were included in the final sample. On the day of the questionnaire distribution, all information on the nature of this inquiry was delivered to the male athletes. They were also told that they might opt out of the study at any moment. The subjects gave their agreement before completing the questionnaire, and anonymity was maintained. All data collection procedures were in accordance with the Helsinki Declaration [36 (link)]. The data were collected at the beginning of the training session, and the time required for the completion of the questionnaires was approximately 15 min. Before the data collection, ethical approval was obtained from the Polytechnic of Leiria Ethics Committee (PARECER N.º CE/IPLEIRIA/24/2021).
Amaro N., Monteiro D., Rodrigues F., Matos R., Jacinto M., Cavaco B., Jorge S, & Antunes R. (2023). Task-Involving Motivational Climate and Enjoyment in Youth Male Football Athletes: The Mediation Role of Self-Determined Motivation. International Journal of Environmental Research and Public Health, 20(4), 3044.
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Publication 2023
A 121 Athletes Child Ethics Committees Europeans Males Parent
3
Adjuvant FOLFOX Chemotherapy for Stage III Colorectal Cancer
This retrospective study used the medical records of patients with CRC who underwent surgery at Soonchunhyang University, Cheonan Hospital, Cheonan-si, South Korea between January 1, 2014, and July 31, 2018. Patients who were diagnosed with stage III CRC based on the 7th edition Cancer Staging Manual of the American Joint Committee on Cancer and received adjuvant FOLFOX chemotherapy as a first-line treatment were considered for this study. Ethics approval was obtained from the Institutional Review Board of Soonchunhyang University, Cheonan Hospital. A total of 121 patients were selected. The exclusion criteria were as follows: loss of medical records, underlying diseases, such as liver cirrhosis and psychiatric disorders that required medication, the presence of sarcopenia prior to surgery due to intestinal obstruction, and cancer of other organs diagnosed within the last two years. Ultimately, 107 patients were enrolled in our study, and baseline characteristics, including tumor markers, were described.
Lee S., Kang D.H., Ahn T.S., Kim S.S., Yun J.H., Kim H.J., Seo S.H., Kim T.W., Kong H.J, & Baek M.J. (2023). The Impact of Pre-Chemotherapy Body Composition and Immunonutritional Markers on Chemotherapy Adherence in Stage III Colorectal Cancer Patients. Journal of Clinical Medicine, 12(4), 1423.
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Publication 2023
A 121 Chemotherapy, Adjuvant Ethics Committees, Research Intestinal Obstruction Joints Liver Cirrhosis Malignant Neoplasms Mental Disorders Operative Surgical Procedures Patients Pharmaceutical Adjuvants Pharmaceutical Preparations Pharmacotherapy Sarcopenia Tumor Markers
4
Voxel-based Morphometry of Brain Imaging Data
Brain imaging data were converted from DICOM images to Neuroimaging Informatics Technology Initiative (NIFTI) files using dcm2nii from the MRIcron package (http://people.cas.sc.edu/rorden/mricron/index.html, accessed on 20 December 2022). Images were manually reoriented with the coordinate system’s origin set to the anterior commissure. Voxel-based morphometry analysis was performed on the structural imaging data with the Computational Anatomy Toolbox (CAT12) toolbox (http://www.neuro.uni-jena.de/cat/, accessed on 20 December 2022), an extended toolbox of SPM12 [15 (link)], with default settings. The preprocessing pipeline included realignment, skull stripping, segmentation by tissue type (i.e., gray matter and white matter), and finally, the segmented gray matter images were non-linearly warped to the standard Montreal Neurological Institute (MNI) template [19 (link)], modulated to account for volume changes. Modulated and warped 3D gray matter density maps (GMDMs) were smoothed using a 2-mm full width at half maximum Gaussian kernel. The GMDMs had a dimensionality of 121 × 145 × 121 in the voxel space (a voxel size of 1.5 × 1.5 × 1.5 mm7). The GMDMs were further re-sampled to an isotropic voxel size of 3 × 3 × 3 mm3 to provide an image dimension of 64 × 64 × 64 for an efficient computation.
Lin L., Xiong M., Zhang G., Kang W., Sun S, & Wu S. (2023). A Convolutional Neural Network and Graph Convolutional Network Based Framework for AD Classification. Sensors (Basel, Switzerland), 23(4), 1914.
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Publication 2023
A 121 A 145 Brain Cranium Genitalia Gray Matter Histocompatibility Testing Microtubule-Associated Proteins White Matter
5
Preprocessing of Gray Matter Density Maps for Neuroimaging Analysis
The downloaded data were first converted from DICOM to Neuroimaging Informatics Technology Initiative (NIFTI) format, by using MRIcron software (http://people.cas.sc.edu/rorden/mricron/index.html (accessed on 1 January 2022)). Images were manually reoriented to place their native-space origin at the anterior commissure. Images were then preprocessed by using the Computational Anatomy Toolbox (CAT12) toolbox (http://www.neuro.uni-jena.de/cat/ (accessed on 1 January 2022)), an extended toolbox of SPM12 [27 (link)] with default settings. The preprocessing pipeline included realignment, skull stripping, segmentation into gray matter and white matter, and finally, the segmented gray matter images were spatially normalized into the Montreal Neurological Institute (MNI) space by using diffeomorphic anatomical registration by using exponentiated Lie algebra nonlinear normalization and modulated to preserve volume information. The modulated and warped 3D gray matter density maps (GMDMs) were smoothed by using a 3D Gaussian kernel of 2 mm full width at half maximum. The GMDMs had a dimensionality of 121 × 145 × 121 in the voxel space, with the voxel size of 1.5 × 1.5 × 1.5 mm3. The background voxels increased the computational complexity of model, but they did not contribute to the classification performance. Thus, we established a new bounding box with the dimension of 91 × 115 × 91 (voxel size of 1.5 × 1.5 × 1.5 mm3), which removed most of the background voxels. The complete preprocessing pipeline is summarized in Figure 1.
Shen X., Lin L., Xu X, & Wu S. (2023). Effects of Patchwise Sampling Strategy to Three-Dimensional Convolutional Neural Network-Based Alzheimer’s Disease Classification. Brain Sciences, 13(2), 254.
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Publication 2023
A 121 A 145 Cranium Gray Matter Microtubule-Associated Proteins White Matter

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1
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