The previously noted methodological decisions will result in many cases of severe pneumonia that will not be captured by PERCH. An inherent limitation of the focus on hospitalized cases is that we will miss cases who never come to hospital or who die at presentation before they can be enrolled. At the Kenya site, approximately two-thirds of children who die do so in the community [4 (link)], and only half of hospitalized children with severe or very severe pneumonia who died during their hospital stay participated in an etiology study [5 ]; thus, missed cases may represent those of greatest interest. This is an inherent paradox in hospital-based pneumonia etiology studies that must be accepted; however, to mitigate the consequences, we aim to collect postmortem specimens at 6 sites that may provide insights into the etiology of those who die at or near the time of presentation to hospital [6 ]. We will also miss the cases who seek care at nonstudy facilities or are not selected for enrollment because of sampling strategies. Although we cannot control the former situation, we will try to minimize the bias in the latter through sampling and analytic methods. The diversity of sites and the large sample size of PERCH will help ensure that we enroll a variety of cases, for which, using subgroup analyses, results can be generalized within these communities and to other similar communities.
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Fish
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Perch
Perch
Perch are a type of freshwater fish typically found in rivers, lakes, and streams.
They belong to the family Percidae and are known for their distinctive spiny fins and vibrant coloration.
Perch play an important role in aquatic ecosystems, serving as both predators and prey.
Their populations are often studied by researchers to understand the health and dynamics of aqueous environments.
Effective research protocols are crucial for accurately assessing perch populations and informing conservation efforts.
PubCompare.ai's AI-driven platform helps optimize perch research protocols, enhanceing reproducibility and accuracy.
Researchers can effortlessly locate the best protocols from literature, pre-prints, and patents using PubCompare.ai's advanced comparison tools, minimizing errors and improving the quality of perch research.
They belong to the family Percidae and are known for their distinctive spiny fins and vibrant coloration.
Perch play an important role in aquatic ecosystems, serving as both predators and prey.
Their populations are often studied by researchers to understand the health and dynamics of aqueous environments.
Effective research protocols are crucial for accurately assessing perch populations and informing conservation efforts.
PubCompare.ai's AI-driven platform helps optimize perch research protocols, enhanceing reproducibility and accuracy.
Researchers can effortlessly locate the best protocols from literature, pre-prints, and patents using PubCompare.ai's advanced comparison tools, minimizing errors and improving the quality of perch research.
Most cited protocols related to «Perch»
Autopsy
Child
Child, Hospitalized
Perch
Pneumonia
Pneumonia, Hospital Acquired
Lake Jyväsjärvi (62° 14′ N, 25° 46′ E) is a moderately eutrophic (total phosphorus concentration around 35–40 µg L−1) urban lake in central Finland with an area of 3.4 km2. Jyväsjärvi is recovering from earlier severe pollution by municipal and industrial waste waters and recent restoration methods have included mass removals of small fish. Perch and roach analysed for this study were collected from these fish removal catches in 2005 and 2006 allowing a random sampling of 202 perch (mean ± SD total length 124±32 mm, range 57–212 mm) and 173 roach (171±73 mm, 57–275 mm) individuals for SIA. A small muscle sample was dissected from each fish, dried in an oven at 60 °C and ground into homogenous powder using a mortar and pestle. A small subsample (0.6 mg) was then accurately weighed into a tin cup for the analysis of δ13C and δ15N in a FlashEA 1112 elemental analyzer coupled to a Thermo Finnigan DELTAplus Advantage mass spectrometer (Thermo Electron Corporation, Waltham, MA, U.S.A.) at the University of Jyväskylä following standard protocols.
Reliable testing for the influence of increasing sample size on the TA, SEA and SEAc in a δ13C–δ15N biplot requires extensive data sets, which are not often available in published ecological stable isotope studies. The 202 perch and 173 roach individuals from Jyväsjärvi were assumed to sufficiently reflect the statistical distributions for the δ13C and δ15N values of these populations and, therefore, could be used for analysing the effect of sample size on TA, SEA and SEAc by bootstrapping (resampling). 5000 random samples of n individuals were drawn from the dataset with replacement and all three metrics were calculated for each draw. The minimum n was set to 5 and maximum to 80 (<50 % of the number of individuals in the original datasets). The same procedure was repeated for the simulated data sets, which were generated for both perch and roach such that sample sizes matched the true data sets. Their sample means were the same as those obtained from the true datasets and the covariance structures of the generated δ13C and δ15N values were the same as in the original data, but the observations followed a multivariate normal distribution.
The metric areas were calculated using a recently published Stable Isotope Bayesian Ellipses in R (SIBER) package [18] (link) for R v.2.10.1 [23] . The original script was modified to include bootstrapping of 5000 isotopic niche areas for each sample size n, which were then stored and their distributions examined using percentile values. The simulated data sets were generated with Multivariate Normal and t Distributions (mvtnorm) package in R.
Reliable testing for the influence of increasing sample size on the TA, SEA and SEAc in a δ13C–δ15N biplot requires extensive data sets, which are not often available in published ecological stable isotope studies. The 202 perch and 173 roach individuals from Jyväsjärvi were assumed to sufficiently reflect the statistical distributions for the δ13C and δ15N values of these populations and, therefore, could be used for analysing the effect of sample size on TA, SEA and SEAc by bootstrapping (resampling). 5000 random samples of n individuals were drawn from the dataset with replacement and all three metrics were calculated for each draw. The minimum n was set to 5 and maximum to 80 (<50 % of the number of individuals in the original datasets). The same procedure was repeated for the simulated data sets, which were generated for both perch and roach such that sample sizes matched the true data sets. Their sample means were the same as those obtained from the true datasets and the covariance structures of the generated δ13C and δ15N values were the same as in the original data, but the observations followed a multivariate normal distribution.
The metric areas were calculated using a recently published Stable Isotope Bayesian Ellipses in R (SIBER) package [18] (link) for R v.2.10.1 [23] . The original script was modified to include bootstrapping of 5000 isotopic niche areas for each sample size n, which were then stored and their distributions examined using percentile values. The simulated data sets were generated with Multivariate Normal and t Distributions (mvtnorm) package in R.
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Electrons
Fishes
Homozygote
Isotopes
Muscle Tissue
Perch
Phosphorus-35
Population Group
Powder
Radionuclide Imaging
The PERCH case definition (Table 2 ) was based on the 2005 World Health Organization (WHO) clinical definition of severe and very severe pneumonia [8 (link)]. The definition relies on the presence of prespecified clinical signs, without information from chest radiograph (CXR) or pulse oximetry. The PERCH enrollment period predated the 2013 reclassification of severe and very severe pneumonia by the WHO [12 ].
Through a series of teleconferences and 2 face-to-face meetings between all PERCH principal investigators (PIs), consensus was achieved on how to elicit, recognize, and interpret each of the signs and symptoms comprising the PERCH clinical case definition (Table 2 ), and on the choice of methods and equipment for obtaining key clinical measurements (pulse oximetry, anthropometry, respiratory rate) and clinical samples (nasopharyngeal [NP] and oropharyngeal [OP] swabs, induced sputum [IS], lung aspirates, blood, urine).
Training materials and advice were sought from a wide variety of sources (see Acknowledgments). Many of the clinical video clips, audio recordings and photographs were recorded at PERCH sites by the principal trainer (J. C.), with written informed consent from the patient’s parents or guardians.
Through a series of teleconferences and 2 face-to-face meetings between all PERCH principal investigators (PIs), consensus was achieved on how to elicit, recognize, and interpret each of the signs and symptoms comprising the PERCH clinical case definition (
Training materials and advice were sought from a wide variety of sources (see Acknowledgments). Many of the clinical video clips, audio recordings and photographs were recorded at PERCH sites by the principal trainer (J. C.), with written informed consent from the patient’s parents or guardians.
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Blood
Clip
Legal Guardians
Lung
Nasopharynx
Oropharynxs
Oximetry, Pulse
Parent
Patients
Perch
Pneumonia
Radiography, Thoracic
RCE1 protein, human
Respiratory Rate
Sputum, Induced
Urine
All laboratory methods were standardized across sites [18 ]. A flocked NP swab (flexible minitip; Copan) and a rayon oropharyngeal (OP) swab specimen were collected from each case and control and were placed into the same vial. The NP/OP specimen was tested for pneumococcus (lytA gene target) as part of a multiplex real-time polymerase chain reaction (PCR) assay (FTD Respiratory Pathogens 33; Fast-track Diagnostics) performed using an Applied Biosystems 7500 (ABI-7500) platform. Standard curves for quantification were generated on an approximately 3-monthly basis and were used to calculate pathogen density (in copies per milliliter) from the sample cycle threshold values. Densities <104 or >108 copies/mL were outside the linear range of the PCR assay, limiting precise density estimation.
A second NP specimen for S. pneumoniae culture was collected simultaneously with the first swab specimen; pneumococcal isolates were serotyped using Quellung reaction or latex agglutination, as described elsewhere [18 ]. Testing was performed at each site, and all sites participated in external quality assurance programs for both pneumococcal PCR and serotyping [18 ].
Cases, but not controls, had blood collected for culture. Some sites (Bangladesh, The Gambia, Mali, and South Africa) collected lung aspirates from children with consolidation on chest radiographs (CXRs) who met clinical and radiologic criteria for the procedure [19 (link)]. Pleural fluid was collected from cases when clinically indicated. Lung aspirate and pleural fluid specimens were tested for pneumococcus by means of culture and PCR; pleural fluid was also tested for pneumococcal antigen (Binax NOW; Alere).
DefinitionsAntibiotic pre-exposure was defined as either a positive serum bioassay result (cases and controls) or documentation of antibiotics administered at the referral or study hospital before specimen collection (cases only) [20 ]. Microbiologically confirmed pneumococcal pneumonia (MCPP) was defined, in PERCH cases, as detection of pneumococcus from a culture of blood, lung aspirate, or pleural fluid; by PCR of lung aspirate or pleural fluid; or by detection of pneumococcal antigen in pleural fluid. A control was considered to have a respiratory tract illness (RTI) if cough or runny nose were reported. RTI was also considered present if a child had (1) ear discharge, wheezing, or difficulty breathing and (2) either fever (temperature ≥38.0°C or reported fever in the past 48 hours) or sore throat.
CXRs were obtained at admission for cases, and each digital image was assessed by 2 members of a panel of 14 radiologists and pediatricians trained in the standardized interpretation of pediatric CXRs; films with discordant conclusions were adjudicated [21 (link), 22 ]. Clinical characteristics, including oxygen saturation, were assessed on the day of enrollment. Case mortality was assessed at hospital discharge and by contact 30 days after discharge.
A second NP specimen for S. pneumoniae culture was collected simultaneously with the first swab specimen; pneumococcal isolates were serotyped using Quellung reaction or latex agglutination, as described elsewhere [18 ]. Testing was performed at each site, and all sites participated in external quality assurance programs for both pneumococcal PCR and serotyping [18 ].
Cases, but not controls, had blood collected for culture. Some sites (Bangladesh, The Gambia, Mali, and South Africa) collected lung aspirates from children with consolidation on chest radiographs (CXRs) who met clinical and radiologic criteria for the procedure [19 (link)]. Pleural fluid was collected from cases when clinically indicated. Lung aspirate and pleural fluid specimens were tested for pneumococcus by means of culture and PCR; pleural fluid was also tested for pneumococcal antigen (Binax NOW; Alere).
DefinitionsAntibiotic pre-exposure was defined as either a positive serum bioassay result (cases and controls) or documentation of antibiotics administered at the referral or study hospital before specimen collection (cases only) [20 ]. Microbiologically confirmed pneumococcal pneumonia (MCPP) was defined, in PERCH cases, as detection of pneumococcus from a culture of blood, lung aspirate, or pleural fluid; by PCR of lung aspirate or pleural fluid; or by detection of pneumococcal antigen in pleural fluid. A control was considered to have a respiratory tract illness (RTI) if cough or runny nose were reported. RTI was also considered present if a child had (1) ear discharge, wheezing, or difficulty breathing and (2) either fever (temperature ≥38.0°C or reported fever in the past 48 hours) or sore throat.
CXRs were obtained at admission for cases, and each digital image was assessed by 2 members of a panel of 14 radiologists and pediatricians trained in the standardized interpretation of pediatric CXRs; films with discordant conclusions were adjudicated [21 (link), 22 ]. Clinical characteristics, including oxygen saturation, were assessed on the day of enrollment. Case mortality was assessed at hospital discharge and by contact 30 days after discharge.
Antibiotics
Antigens
Biological Assay
Blood
Blood Culture
Child
Conditioning, Psychology
Cough
Diagnosis
Fever
Genes
Latex Fixation Tests
Lung
Oropharynxs
Oxygen Saturation
pathogenesis
Patient Discharge
Pediatricians
Perch
Pleura
Pneumonias, Pneumococcal
Polymerase Chain Reaction
Pulmonal S
Radiography, Thoracic
Radiologist
rayon
Real-Time Polymerase Chain Reaction
Respiratory Rate
Respiratory System
Rhinorrhea
Serum
Sore Throat
Specimen Collection
Streptococcus pneumoniae
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Age Groups
Bronchodilator Agents
Child
Cough
Cyanosis
Dentatorubral-Pallidoluysian Atrophy
Ethics Committees, Research
Haemophilus influenzae type b polysaccharide vaccine
Legal Guardians
Lethargy
Parent
Perch
Pneumococcal Vaccine
Pneumonia
Respiratory Rate
Seizures
Signs and Symptoms, Respiratory
Specimen Collection
Vaccination
Virus Vaccine, Influenza
Wall, Chest
Wheezing
Most recents protocols related to «Perch»
Pigeons were trained and tested in an operant chamber measuring 80 cm (height), 54 cm (width), and 56 cm (depth). The chamber was insulated with acoustic foam to reduce ambient noise. Additionally, a ventilator generated constant background noise in the chamber. The operant chamber was further equipped with copper mesh to shield against electromagnetic noise (a Faraday cage) and a surveillance camera. During the testing sessions, the door of the operant chamber was closed, and an LED strip on the ceiling (“house light”) dimly illuminated the chamber. The birds stood on a wooden perch, facing a 54 by 40 cm acoustic pulse touchscreen monitor (Elo Touch Solutions), which displayed the stimuli and detected responses. A custom pellet feeder, which dropped individual pellets (BioServ) into a small feeding trough, delivered food rewards, which were illuminated during the reward period. All aspects of the behavioral task were controlled by a PC using MATLAB (2016a; MathWorks) and the Biopsychology and Psychophysics Toolboxes (Brainard, 1997 (link); Rose et al., 2008 (link)). We used a custom ethernet-based digital input/output (I/O) device to control the feeder and lights while also sending event codes to the neurophysiology hardware (code and plans are freely available online at https://www.ngl.psy.ruhr-uni-bochum.de/ngl/shareware/index.html.en ).
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Acoustics
Aves
Columbidae
Copper
Electromagnetics
Fingers
Food
Infantile Neuroaxonal Dystrophy
Light
Medical Devices
Pellets, Drug
Perch
Pulse Rate
Touch
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Animals
Diet, High-Protein
Fruit
Humidity
Immunoglobulins
Institutional Animal Care and Use Committees
Macaca mulatta
Males
Monkeys
Nuts
Perch
Secondary Immunization
Vaccination
Vegetables
To quantify the contribution of the different food sources to the isotopic signature of each consumer or functional group of consumers a separate Bayesian mixing model27 (link) with a specific number of putative sources was run over years in MixSiar-package28 (link) in R26 . In European perch (n = 21), a four-source model was run (omnivorous fish, crayfish, zoobenthos and crustacean zooplankton; Table S2 ). In roach (n = 20) and noble crayfish (n = 21), a five-source model was run (zoobenthos, crustacean zooplankton, macrophytes, algae and detritus; Table S3 ). For predatory zoobenthos (n = 20), a two-source model including crustacean zooplankton and zoobenthos was run (Table S4 .). In detritivorous zoobenthos (n = 20), a three-source model was run (macrophytes, algae and detritus, Table S5 ).
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Astacoidea
Crustacea
Europeans
Fishes
Food
Isotopes
Perch
Zooplankton
To estimate the size of the territories (area), we observed the behavior of the owner hummingbird and the locations of the perch, foraging, and chases. Once the observation period was over, we used a GPS (Garmin) to mark points around the perimeter of each activity performed by the territory owner, then calculated the area (square meters) encompassed within the perimeter points. During the observation period, we also counted the number of open flowers contained in each monitored territory.
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Flowers
Perch
Perimetry
We used the following criteria to determine that a floral patch of B. ternifolia was an actively defended feeding territory: (1) the territory owner always returned to the same perch near the patch, (2) foraged within the patch, and (3) actively defended the patch through chases (Camfield, 2006 (link); Mendiola-Islas et al., 2016 (link); Márquez-Luna et al., 2019 (link); Márquez-Luna et al., 2022 (link)). A chase implies persecutions and aggressions towards an intruder to try to force it away from the territory. In our field observations, we did not tag hummingbirds because the tiny size of the permanent bands commonly used to tag hummingbirds makes it impossible to identify them individually (Márquez-Luna et al., 2022 (link)). Instead, during the behavioral recording, each territory owner was recognized based on the fact that chases started from a certain perch and that the same perch was frequented. Twenty-one territories of adult male Broad-tailed hummingbird were monitored in an area of about 50 hectares.
In each territory, the territory owner’s behavior was observed and recorded for a period of four continuous hours (from 8:00 to 12:00 h), when hummingbirds are more active foraging and nectar production is high in this plant species (Torres et al., 2008 (link)). Each territory had the same sampling effort on weekdays and weekends from June to August. Due to the size of the territories (see below), the observations were carried out using binoculars (10 × 42), standing from different points 10 m away from each territory. We detected no apparent approach or avoidance behaviors by birds in response to the observers. We recorded: (1) the number of times the territory owners chased an intruder, and (2) the number of intruders that were not chased and were able to forage in the territory. Additionally, (3) we recorded the number of flowers visited by the owners inside their territories during the entire observation period.
In each territory, the territory owner’s behavior was observed and recorded for a period of four continuous hours (from 8:00 to 12:00 h), when hummingbirds are more active foraging and nectar production is high in this plant species (Torres et al., 2008 (link)). Each territory had the same sampling effort on weekdays and weekends from June to August. Due to the size of the territories (see below), the observations were carried out using binoculars (10 × 42), standing from different points 10 m away from each territory. We detected no apparent approach or avoidance behaviors by birds in response to the observers. We recorded: (1) the number of times the territory owners chased an intruder, and (2) the number of intruders that were not chased and were able to forage in the territory. Additionally, (3) we recorded the number of flowers visited by the owners inside their territories during the entire observation period.
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Adult
Aves
Flowers
Males
Perch
Plant Nectar
Plants
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More about "Perch"
Perch are a type of freshwater fish that belong to the family Percidae.
These vibrant and spiny-finned fish are found in rivers, lakes, and streams, and play a crucial role in aquatic ecosystems as both predators and prey.
Researchers often study perch populations to understand the health and dynamics of aqueous environments, and effective research protocols are essential for accurate assessments and informing conservation efforts.
PubCompare.ai's cutting-edge AI-driven platform helps optimize perch research protocols, enhancing reproducibility and accuracy.
Researchers can effortlessly locate the best protocols from literature, pre-prints, and patents using PubCompare.ai's advanced comparison tools, minimizing errors and improving the quality of perch research.
In addition to perch, researchers may also utilize other tools and media to support their studies, such as Leibovitz's L-15 medium, SASLab Pro, and DMSO.
Statistical analysis software like SAS 9.4 and MATLAB can also be employed to analyze data and draw insights.
Furthermore, Lab Diet 1538 and DMEM (Dulbecco's Modified Eagle Medium) may be used in perch-related experiments, while RNAlater Stabilization Solution can help preserve RNA samples for downstream analysis.
By leveraging the power of PubCompare.ai and integrating these specialized tools and media, researchers can enhance the reproducibility, accuracy, and quality of their perch research, ultimately contributing to a better understanding of these important freshwater fish and their aquatic ecosystems.
Remember, a single typo can add a natural feel to the content: 'reserchers' instead of 'researchers'.
These vibrant and spiny-finned fish are found in rivers, lakes, and streams, and play a crucial role in aquatic ecosystems as both predators and prey.
Researchers often study perch populations to understand the health and dynamics of aqueous environments, and effective research protocols are essential for accurate assessments and informing conservation efforts.
PubCompare.ai's cutting-edge AI-driven platform helps optimize perch research protocols, enhancing reproducibility and accuracy.
Researchers can effortlessly locate the best protocols from literature, pre-prints, and patents using PubCompare.ai's advanced comparison tools, minimizing errors and improving the quality of perch research.
In addition to perch, researchers may also utilize other tools and media to support their studies, such as Leibovitz's L-15 medium, SASLab Pro, and DMSO.
Statistical analysis software like SAS 9.4 and MATLAB can also be employed to analyze data and draw insights.
Furthermore, Lab Diet 1538 and DMEM (Dulbecco's Modified Eagle Medium) may be used in perch-related experiments, while RNAlater Stabilization Solution can help preserve RNA samples for downstream analysis.
By leveraging the power of PubCompare.ai and integrating these specialized tools and media, researchers can enhance the reproducibility, accuracy, and quality of their perch research, ultimately contributing to a better understanding of these important freshwater fish and their aquatic ecosystems.
Remember, a single typo can add a natural feel to the content: 'reserchers' instead of 'researchers'.