Log In Sign up
The largest database of trusted experimental protocols
> Living Beings > Fungus > Loma

Loma

Loma is an AI-driven platform developed by PubCompare.ai that optimizes research protocols and enhances reproducibility.
The platform helps researchers locate the best protocols from literature, preprints, and patents using intelligent comparisons.
Leveraing AI, Loma identifies the most effective protocols and products to meet research needs.
Expereincing seamless protocol optimization with Loma enables researchers to streamline and improve their studies.

Most cited protocols related to «Loma»

1
Sprague-Dawley Rat Experimental Protocols
One hundred and seventy-eight male adult Sprague-Dawley rats (Harlan, Indianapolis, IN) weighting 300-350 g were used in the present study. All experimental protocols were approved by the Institutional Animal Care and Use Committee of Loma Linda University.
Chen Y., Zhang Y., Tang J., Liu F., Hu Q., Luo C., Tang J., Feng H, & Zhang J.H. (2014). Norrin protected Blood Brain Barrier via Frizzled 4/β-catenin Pathway after Subarachnoid Hemorrhage in Rats. Stroke; a journal of cerebral circulation, 46(2), 529-536.
Publication 2014
Adult Institutional Animal Care and Use Committees Loma Males Rats, Sprague-Dawley
2
Collagenase-Induced Germinal Matrix Hemorrhage

Protocol full text hidden due to copyright restrictions

Open the protocol to access the free full text link

Publication 2012
Anesthesia Animals Asepsis Betadine Clostridium Collagenase collagenase 1 Cranium Dura Mater Gender Institutional Animal Care and Use Committees Isoflurane Loma Matrix Metalloproteinase 13 Needles Operative Surgical Procedures Oxygen Rats, Sprague-Dawley Reading Frames Scalp Sutures Syringes Trephining
3
Dietary Intake Assessment in the Adventist Health Study-2
The 24 h dietary recalls were unannounced and obtained by telephone. A two-dimensional food portion visual (2D Food Portion Visual; Nutrition Consulting Enterprises, Framingham, MA, USA) was sent to each participant before the first recall to assist with portion size estimates. Trained research dietitians used standard probes and a multiple-pass approach methodology to collect detailed information on all foods, beverages and supplements consumed by each subject during the previous 24 h. Each recall interview was entered using Nutrition Data System for Research (NDS-R) version 4·06 or 5·0 (The Nutrition Coordinating Center, Minneapolis, MN, USA) and the conversation digitally recorded for subsequent quality check. An experienced research dietitian later evaluated randomly selected recall interviews ( ~5 %) and compared them with the recording, as a quality control measure.
The AHS-2 FFQ is a quantitative and comprehensive 22-page instrument consisting of 204 foods, fifty-four questions about food preparation and forty-six fields for open-ended questions. Frequency categories vary with food type to allow respondents to define their daily intake with greater specificity. Thus, the lowest category for most foods and beverages is never or rarely, and for cold cereals and vegetarian protein products, 1–3 per month. The highest frequency category for vegetables, soups, cereals, pasta, dressing, meats, fish, vegetarian protein products and soya milk is 2 or more per day; for nuts and seeds, 4 or more per day; for breads, eggs, dairy products, snacks and beverages, 6 or more per day. Portion sizes include three levels: standard, 12 or less, and 112 or more. Standard portions are based on serving sizes using familiar household units such as cup, tablespoon, slice, patty and others. Pictures of common foods or beverages typically served together were included with the questionnaire to assist subjects in estimating portion sizes. For example, to represent a standard portion, spaghetti, broccoli and steak are arranged on an 11-inch dinner plate, each food measured in a standard portion. Representations of 12 of standard and 112 times the standard portion size are provided as well, using the same foods and dinner plate.
The AHS-2 FFQ was designed to include foods commonly eaten by US Adventists and later modified to accommodate foods specific to black Adventists of US and Caribbean origin(6 (link)). The questionnaire was sent to each subject, completed at home, and then mailed back to AHS-2. Respondents were asked to report on their intake over the previous one year. Upon receipt of the questionnaire, study personnel reviewed the questionnaire for completeness and as necessary followed-up by telephone to clarify any ambiguous or incomplete information.
Completed questionnaires were optically scanned using the NCS 5000i Image Scanner with ScanTools Plus software (Pearson NCS, Bloomington, MN, USA). Standardized processing of open-ended questions was done using the Food Write-In Processing software (Adventist Health Study-2, Loma Linda, CA, USA), a network-based application created in Microsoft® Access (Microsoft Corporation, Redmond, WA, USA).
Nutrient composition of foods reported from 24 h recalls and FFQ were based on the NDS-R 5·0_35 database (The Nutrition Coordinating Center), an analytic database of over 20 000 foods updated annually while maintaining nutrient profiles true to the version used for data collection(7 (link)). Nutrient profiles of foods and supplements not found in the NDS database were obtained from the US Department of Agriculture, manufacturers, and the Caribbean Food and Nutrition Institute. Considerable attention was given to creating recipes for home-cooked vegetarian dishes (n > 500), home-made and commercial soya and nut milks (n > 180) and commercial meat analogues (n 309) frequently consumed among our study population. For the latter we contacted manufacturers or worked with a senior food technologist with experience in this industry, to create recipes.
Jaceldo-Siegl K., Knutsen S.F., Sabaté J., Beeson W.L., Chan J., Herring R.P., Butler T.L., Haddad E., Bennett H., Montgomery S., Sharma S.S., Oda K, & Fraser G.E. (2009). Validation of nutrient intake using an FFQ and repeated 24 h recalls in black and white subjects of the Adventist Health Study-2 (AHS-2). Public health nutrition, 13(6), 812-819.
Publication 2009
Attention Beverages Bread Broccoli Caribbean People Cereals Common Cold Conditioning, Psychology Dairy Products Diet Dietary Supplements Dietitian Eating Eggs Fishes Food Households Hyperostosis, Diffuse Idiopathic Skeletal Loma Meat Mental Recall Milk Nutrients Pastes Plant Embryos Proteins Snacks Soybeans Soy Milk Vegetables Vegetarians
4
Developing the Guideline Implementability Appraisal
The first step in the measurement of implementability was to define its attributes. From a broad-based literature search, we identified several key papers and book chapters that describe the impact of a variety of factors on success of implementation. The report from the Institute of Medicine [9 ] included general definitions and several high level constructs relevant to implementation. Thorsen and Mäkelä [10 ] described critical factors in implementation strategy that facilitate use of guidelines and overcome barriers to adoption. Solberg et al. asked expert implementers about implementation success factors and identified 83 variables grouped into 5 clusters [11 (link)]. Applying diffusion of innovation theory, Grilli and Lomas identified guideline complexity, trialability, and observability as critical factors for successful implementation [12 (link)]. Grol and colleagues found that vagueness, controversy, demand for a change in routines, and absence of an evidence-base differentiated guidelines that were not followed from those that were [13 (link)]. Finally, we examined 3 instruments for appraisal of guideline quality – Cluzeau's 37-item instrument [14 (link)], the AGREE instrument [15 (link)], and Shaneyfelt's Guideline Quality Appraisal Questionnaire [16 (link)]– and extracted factors from each that addressed implementability.
The authors eliminated redundant factors, i.e., those that appeared in several sources or represented concepts that were subsumed by others, through open discussion and consensus. Factors that indicated guideline quality but not implementability were excluded. We decided early on to focus the GLIA on factors that were intrinsic to the guideline, because they could be addressed centrally by a guideline development committee. Thus, we eliminated many factors related to Solberg's medical group characteristics, organizational capability for change, infrastructure for implementation, and external environment. Extrinsic items relating to a recommendation's effect on the process of care and items relating to the novelty or innovation of a guideline statement were retained in the instrument because developers can anticipate these barriers and offer potential strategies for implementation success.
All remaining factors were grouped into categories of related constructs, hereafter referred to as dimensions. We then devised specific questions to characterize each dimension and phrased them so that negative responses identified barriers. These questions ultimately became items of the instrument. We iteratively refined the items, further clarified definitions, and re-categorized items into the most appropriate dimensions.
Shiffman R.N., Dixon J., Brandt C., Essaihi A., Hsiao A., Michel G, & O'Connell R. (2005). The GuideLine Implementability Appraisal (GLIA): development of an instrument to identify obstacles to guideline implementation. BMC Medical Informatics and Decision Making, 5, 23.
Full text: Click here
Publication 2005
Diffusion of Innovation factor A Loma Neuroglia
5
Adventist Health Study-2 Calibration Protocol
The AHS-2 cohort consists of adult members of Seventhday Adventist churches geographically spread throughout the USA and Canada. Over 25 000 cohort members are blacks; the remaining subjects are of other races, mostly white. Recruitment and selection methods of the parent cohort have been described previously(5 (link)). Participants in the calibration study were randomly selected from the parent cohort by church, and then subject-within-church. Because of the special focus on black Adventists as a minority group in the AHS-2, the calibration study was designed such that there would be approximately equal numbers of blacks and whites. No significant differences in the distribution of gender, age, education or vegetarian status between the calibration sub-study sample (n 1011) and the AHS-2 cohort (n 96 592) were observed. When stratifying by ethnicity, only the distributions of mean age and age categories in blacks were nominally significantly different (P = 0·0018 and 0·0032, respectively) between the parent cohort and the calibration study sample (Table 1). This is easily consistent with chance given the multiple testing involved.
The duration of the calibration study was 9–12 months for any one subject (see Fig. 1). We obtained a set of three variably timed 24 h dietary recalls (one Saturday, one Sunday and one weekday intake) during the first two months, which then was duplicated approximately six months later. The aim was to obtain two sets of recalls (a total of six 24 h recalls) from each subject. During the 6-month interval, subjects completed a self-administered food FFQ that was identical to the baseline FFQ and attended a local study clinic. The study was approved by the institutional review board of Loma Linda University, and all subjects gave written informed consent.
Jaceldo-Siegl K., Knutsen S.F., Sabaté J., Beeson W.L., Chan J., Herring R.P., Butler T.L., Haddad E., Bennett H., Montgomery S., Sharma S.S., Oda K, & Fraser G.E. (2009). Validation of nutrient intake using an FFQ and repeated 24 h recalls in black and white subjects of the Adventist Health Study-2 (AHS-2). Public health nutrition, 13(6), 812-819.
Publication 2009
Adult As-A 2 Diet Ethics Committees, Research Ethnicity Food Loma Mental Recall Minority Groups Negroes Parent Vegetarians White Person

Most recents protocols related to «Loma»

1
Haplotype-Resolved Consensus Sequence Generation
Raw reads yielded by ONT are accompanied by substantial sequencing errors. LoMA is a tool to assemble long reads mapped to a region of interest and generates a highly accurate CS that spans the target region (Fig. 1). LoMA detects heterozygous SVs in a target region and outputs haplotype-resolved sequences. In the first step, LoMA constructs a CS spanning the region. This process is initiated by finding overlaps of raw reads using all-to-all pairwise alignment using minimap2 (-x ava-ont) [16 (link)] and then generates a layout of overlapped reads (read layout) (Fig. 1A). Based on the all-to-all pairwise alignment, the read layout is estimated. First, pairs with a dangling read or short overlapping lengths are excluded to remove possible alignment errors (Additional file 2: Fig. S1). Second, the longest read is selected, and pairwise alignments are used to determine the positional relationship between the longest read and other reads. The read layout is divided into overlapped, evenly-spaced divisions of constant length, and read sequences included in each division undergo a multiple alignment using MAFFT [17 (link)]. Based on the multiple alignment, each consensus nucleotide is determined at every position, and a partial CS is generated for each division. Finally, partial CSs of neighboring divisions are aligned using MAFFT and concatenated into a single CS spanning the entire target region.

Schematic overview of LoMA's algorithm. A. The main process to compose a consensus sequence (CS) is shown. Reads are laid out based on all-to-all alignment using minimap2 [16 (link)]. The layout is then subdivided into small divisions for the successive procedure to determine partial CSs based on multiple alignments using MAFFT for each division [17 (link)]. The entire CS is obtained by concatenating these small divisions. B. The read classification process is shown. Reads constituting a CS are aligned to the CS using minimap2 [16 (link)]. LoMA predicts heterozygous loci in the region based on the number of reads supporting a SV, and the reads derived from each estimated haplotype are gathered (Type I and II read sets). Both sets return to the main process (A) after this step

The generated single CS can be a mosaic sequence (pseudo-haplotype) mixing paternal and maternal haplotypes, resulting in the dismissal of one allele of the heterozygous variants. To overcome this problem, we adopted the read-separation step (Fig. 1B). In this step, all input reads are aligned to the first CS recurrently by using minimap2 [16 (link)]. Then, bins (700 bp) with mismatch clusters are detected based on two conditions: the number of discordant reads to the first CS being > 7 and the number of discordant reads being within the mean ± 3σ of a binomial distribution with p = 0.5 (see Additional file 2). Two haplotypes that have multiple heterozygous SVs at different loci are separated using reads that span more than one SV (Fig. 1B). By tracking back all heterozygous bins in a target region, all reads are coherently classified into two individual read sets (Type I and II) in most cases (Fig. 1B). Two CSs are generated from Type I and II. Two read sets will not be produced if a target region does not contain any SV, and the region will be regarded as homozygous.
Ikemoto K., Fujimoto H, & Fujimoto A. (2023). Localized assembly for long reads enables genome-wide analysis of repetitive regions at single-base resolution in human genomes. Human Genomics, 17, 21.
Full text: Click here
Publication 2023
Alleles Consensus Sequence Haplotypes Heterozygote Homozygote Loma Mothers Nucleotides
2
Detecting Large Indels in Genomic Data
To obtain CSs of the unclear regions defined above, we analyzed fastq files by LoMA and constructed CSs with the following parameters:
-b3000 -s2000 -h10 -d3 -r0.5 -m1000
We then called indels (≥ 100 bp) found in the CSs using CAMPHOR [3 (link)].
Ikemoto K., Fujimoto H, & Fujimoto A. (2023). Localized assembly for long reads enables genome-wide analysis of repetitive regions at single-base resolution in human genomes. Human Genomics, 17, 21.
Full text: Click here
Publication 2023
Camphor INDEL Mutation Loma
3
Detecting Structural Variants from WGS Data
To detect SVs from the two samples, we applied LoMA to the WGS data. We first searched for target regions (unclear regions) by scanning all chromosomes from telomere to telomere. We split each autosome and sex chromosome binned per 500 bp, step size 250 bp, and defined an “unclear” region as follows: (1) average coverage between 10 and 200, (2) total number of reads containing indels (≥ 100 bp) or hard- or soft-clipped sequences (≥ 500 bp) > 10, and (3) the proportion of reads containing indels (≥ 100 bp) or hard- or soft-clipped sequences (≥ 500 bp) > 0.2 (Fig. 2A). Then, multiple bins within 10 kbp were merged into one bin. We defined each merged bin as an unclear region in this study. After defining the unclear regions for both NA18943 and NA19240, we collected reads mapped within 10 kbp from both ends of each unclear region using SAMtools [24 (link)].

Whole-genome LoMA analysis. A. The workflow of the whole-genome analysis. Unclear regions were first defined based on the alignment status (indels and clips) of ONT reads. Reads mapped to the regions were separately collected. For each region, LoMA attempted a localized assembly to obtain CSs. CAMPHOR collectively detected structural variants from the CSs for NA18943 and NA19240. B. The relative density of unclear regions of NA18943 and NA19240 are shown in red- and blue-colored heatmaps, respectively. The light-colored regions are dense with unclear regions. The white arrows indicate the autosomal centromeres except chromosome 6. The arrows on chromosome 6 represent the HLA region. C. The precision of indels to the standard SV set was assessed for NA19240. The left vertical axis (bar graphs) shows the number of indels found in each bin (the number of constitutive reads). The right (line graphs) shows the precision of indels in each bin. Both graphs were binned per 2 reads

Ikemoto K., Fujimoto H, & Fujimoto A. (2023). Localized assembly for long reads enables genome-wide analysis of repetitive regions at single-base resolution in human genomes. Human Genomics, 17, 21.
Full text: Click here
Publication 2023
Camphor Centromere Chromosomes Chromosomes, Human, Pair 6 Clip Epistropheus Genome INDEL Mutation Light Loma Sex Chromosomes Telomere
4
Benchmarking LoMA Long-Read Assembly Tool
To estimate the accuracy of LoMA, we compared CSs assembled using the ONT data of NA18943 with GRCh38. We randomly selected 108 positions from the human genome while excluding centromeres and gaps (Additional file 1: Table S1). We collected all reads mapped within 20 kbp of each position from the data of NA18943 and constructed CSs using LoMA. We aligned the generated CSs to GRCh38 using minimap2 [16 (link)] and calculated the error rates from the edit distance. We also aligned all raw reads to GRCh38 and calculated error rates for the raw reads again using the edit distance. For a comparison, we assembled matched regions using lamassemble [15 ]:
-P 8 -a -v -p 2e-3 -m 2*(number of reads) -z 1000 promethion.mat
The error rate of lamassemble was calculated as above.
We also evaluated LoMA using simulated data. We randomly selected one hundred regions from GRCh38 (Additional file 1: Table S2). Simulated reads were generated using NanoSim with the error profile of NA12878 (total error rate, 10.8%) provided by the developers [23 (link)]. Various data sets were generated for each region: coverage 10, 20, 30, 40, and 50 (with a fixed size of 20 kbp), targeted size 20 kbp, 40 kbp, 60 kbp, 80 kbp, and 100 kbp (with a fixed mean coverage of 30×). The error rate, CPU time, and peak memory (RSS) were measured. A computer with M1 chip (Apple) was used to measure the performance. The error rate (edit distance) was calculated as described above.
Ikemoto K., Fujimoto H, & Fujimoto A. (2023). Localized assembly for long reads enables genome-wide analysis of repetitive regions at single-base resolution in human genomes. Human Genomics, 17, 21.
Full text: Click here
Publication 2023
Centromere DNA Chips Genome, Human Loma Memory
5
Validating Insertion Sequences from CSs
To evaluate the accuracy of inserted sequences obtained from CSs, we performed Sanger sequencing. We randomly selected 121 homozygous insertions from NA18943. PCR primers were designed in flanking regions, and the PCR-direct sequence was conducted. We compared the sequences by Sanger sequencing with the matched sequences of CSs generated by LoMA. Since the length of homopolymers was difficult to determine by Sanger sequencing, the stretches of poly(A) were removed from the comparison.
An accurate SV callset of NA19240 was released (the standard SV set) in a previous study leveraging multi-platform data [25 (link)]. We compared the indels of our SV calling result (the LoMA SV set) with those of the standard SV set and assessed the precision. We considered variants from the LoMA SV set as concordant (true positive) with the standard SV set if both were the same variant class and the distance between two breakpoints of the SVs was < 500 bp.
Ikemoto K., Fujimoto H, & Fujimoto A. (2023). Localized assembly for long reads enables genome-wide analysis of repetitive regions at single-base resolution in human genomes. Human Genomics, 17, 21.
Full text: Click here
Publication 2023
Homozygote INDEL Mutation Insertion Mutation Loma Oligonucleotide Primers Poly A

Top products related to «Loma»

1
Cd 1 mice by Charles River Laboratories
Sourced in United States, China, Canada, United Kingdom, Germany, Italy, France, Japan, Spain
CD-1 mice are a widely used outbred mouse strain that exhibit genetic diversity. They are suitable for a variety of research applications due to their adaptability and lack of specific genetic modifications.
2
Sprague dawley rat by Charles River Laboratories
Sourced in United States, China, Germany, Canada, United Kingdom, Japan, France, Italy, Morocco, Hungary, New Caledonia, Montenegro, India
Sprague-Dawley rats are an outbred albino rat strain commonly used in laboratory research. They are characterized by their calm temperament and reliable reproductive performance.
3
Hiseq 4000 by Illumina
Sourced in United States, China, United Kingdom, Hong Kong, France, Canada, Germany, Switzerland, India, Norway, Japan, Sweden, Cameroon, Italy
The HiSeq 4000 is a high-throughput sequencing system designed for generating large volumes of DNA sequence data. It utilizes Illumina's proven sequencing-by-synthesis technology to produce accurate and reliable results. The HiSeq 4000 has the capability to generate up to 1.5 terabytes of data per run, making it suitable for a wide range of applications, including whole-genome sequencing, targeted sequencing, and transcriptome analysis.
4
C57bl 6j mice by Jackson ImmunoResearch
Sourced in United States, Montenegro, Japan, Canada, United Kingdom, Germany, Macao, Switzerland, China
C57BL/6J mice are a widely used inbred mouse strain. They are a commonly used model organism in biomedical research.
5
Rpmi 1640 medium by Corning
Sourced in United States, China, Germany
RPMI 1640 medium is a cell culture media formulation commonly used for the in vitro cultivation of various cell types, including human and animal cells. It is a complex mixture of amino acids, vitamins, salts, and other components designed to support cell growth and proliferation.
6
Wistar kyoto wky rats by Charles River Laboratories
Sourced in China, United States, New Caledonia, Canada
The Wistar-Kyoto (WKY) rats are a well-established and widely used laboratory animal model. They are inbred rats derived from the Wistar rat strain. WKY rats are commonly used in research to study various physiological and behavioral processes.
7
Mastercycler pro by Eppendorf
Sourced in Germany, United States
The Mastercycler Pro is a thermal cycler designed for DNA amplification and other temperature-controlled applications in the laboratory. It features a compact design and multiple sample block options to accommodate varying experimental needs. The Mastercycler Pro provides precise temperature control and accurate cycling for consistent and reliable results.
8
Mirneasy kit by Qiagen
Sourced in Germany, United States, United Kingdom, Canada, Netherlands, Spain, France, Australia, Italy, Denmark, Japan, Switzerland, China
The MiRNeasy kit is a product offered by Qiagen for the isolation and purification of microRNA (miRNA) and total RNA from various sample types. The kit utilizes a silica-membrane-based technology to efficiently capture and purify miRNA and other RNA species from cells and tissues.
9
Trizol reagent by Thermo Fisher Scientific
Sourced in United States, China, Japan, Germany, United Kingdom, Canada, France, Italy, Australia, Spain, Switzerland, Netherlands, Belgium, Lithuania, Denmark, Singapore, New Zealand, India, Brazil, Argentina, Sweden, Norway, Austria, Poland, Finland, Israel, Hong Kong, Cameroon, Sao Tome and Principe, Macao, Taiwan, Province of China, Thailand
TRIzol reagent is a monophasic solution of phenol, guanidine isothiocyanate, and other proprietary components designed for the isolation of total RNA, DNA, and proteins from a variety of biological samples. The reagent maintains the integrity of the RNA while disrupting cells and dissolving cell components.
10
Agencourt rnaclean xp beads by Beckman Coulter
Sourced in United States, Germany
The Agencourt RNAClean XP beads are magnetic purification beads used for the removal of RNA from samples. They provide a simple and efficient way to purify RNA from various sample types.

More about "Loma"

Loma, an AI-driven platform developed by PubCompare.ai, is revolutionizing the way researchers optimize their research protocols and enhance reproducibility.
This powerful tool leverages intelligent comparisons to help researchers locate the best protocols from literature, preprints, and patents, ensuring they have access to the most effective methods and products to meet their research needs.
Powered by advanced artificial intelligence, Loma identifies the most suitable protocols and products, enabling researchers to streamline and improve their studies.
Whether you're working with CD-1 mice, Sprague-Dawley rats, or C57BL/6J mice, Loma can help you find the right protocols and reagents, such as RPMI 1640 medium, Wistar-Kyoto (WKY) rats, Mastercycler Pro, MiRNeasy kit, and TRIzol reagent.
By utilizing Loma's seamless protocol optimization features, researchers can experience a more efficient and reproducible research process.
The platform's Agencourt RNAClean XP beads integration ensures high-quality data capture, while its intuitive interface and AI-driven recommendations streamline the workflow, saving time and improving research outcomes.
Discover how Loma, the AI-driven solution from PubCompare.ai, can transform your research experience.
Unlock the power of intelligent protocol comparisons and elevate your studies to new heights of efficiency and reproducibility.