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Squid

Squids are a diverse group of marine mollusks belonging to the class Cephalopoda.
They are characterized by a streamlined, torpedo-shaped body, eight arms, and two tentacles used for capturing prey.
Squids are found in all the world's oceans and play a crucial role in many marine ecosystems.
They are known for their remarkable abilities, including the capacity to change color and texture for camouflage, expel ink to evade predators, and possess complex nervous systems.
Squids have long been the subject of scientific research, with their unique physiology and behaviors offering insights into evolutionary adaptations and the wonders of the ocean.
Optimizing Squid research with the AI-driven platform of PubCompare.ai can help researchers easily locate and compare protocols from literature, preprints, and patents, identifiying the best procedures and products to improve reproducibility and accuracy in their Squid experiments.

Most cited protocols related to «Squid»

For the construction of reference alignments we used "seed" alignments from the Rfam database version 7.0 [24 (link),23 (link)]. In most cases these alignments are hand-curated and thus of higher quality than Rfam's "full" alignments generated automatically by the INFERNAL RNA profile package [40 (link)]. Alignments with less than 50 sequences were discarded to increase the possibility for creation of subalignments (see below). The SCI (see below) for scoring of structural alignment quality is based on a combination of thermodynamic and covariation measures. Thermodynamic structure prediction becomes increasingly inaccurate with increasing sequence length – e. g. due to kinetic effects – but is widely regarded as sufficiently accurate for sequences not exceeding 300 nt in length [41 (link),42 (link)]. Thus we excluded alignments with an average sequence length above 300 nt to ensure proper thermodynamic scoring.
To each remaining seed alignment we applied a "naive" combinatorial approach that extracts sub-alignments with k ∈ {2, 3, 5, 7, 10, 15} sequences for a given average pairwise sequence identity range (APSI; a measure for sequence homology computed with ALISTAT from the squid package [43 ]). Therefore we computed identities for all sequence pairs from an alignment and selected those pairs possessing the desired APSI ± 10 %. From the remaining list of sequences we randomly picked k unique sequences. Additionally we dropped all alignments with an SCI below 0.6 to assure the structural quality of the alignments and to make sure that the SCI can be applied later to score the test alignments. This way we generated overall 18,990 reference alignments with an average SCI of 0.93; the data-set1 used in [22 (link)] consists of only 388 alignments with an average SCI of 0.89. For further details see Tables 1 and 6.
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Publication 2006
Kinetics Polyglandular Type I Autoimmune Syndrome Sequence Alignment Squid
Using a 151 SQUID (Superconducting QUantum Interference Device) array system, we collected 39 fMCG data between 30 and 37 weeks of gestation from 27 pregnant women who delivered healthy singleton neonates at term. This study was approved by the local Institutional Review Board and all subjects gave their informed written consent to participate in the study. Each study lasted approximately 20–30 min depending on maternal comfort and the data was recorded with a sampling rate of 312.5 Hz. The data was bandpass filtered between 1 and 50 Hz using the Butterworth filter with zero-phase distortion and the interfering maternal cardiac signal was attenuated using the signal space projection technique.30 (link) The fetal R-waves were calculated using the Hilbert transform approach32 (link) and was followed by an adaptive scheme to correct for the missed and extra beats.27 (link)
The different steps involved in the identifying the R-wave are shown in a flowchart (see Fig. 1). After attenuation of the maternal cardiac signals using the orthogonal projection technique, we computed the Fourier transform of the resulting signals from all the sensors and selected only the 10 sensors (C1,10) with the highest Fourier peak power in the 1–60 Hz band. Then, for the data x(t) from a sensor we computed Hilbert transform h(t) using the “Hilbert” function in Matlab (Mathwork, Inc.). We define R(n), the rate of change of Hilbert amplitude (RHA) as follows:
R(n)=[x(n)x(n1)]2+[h(n)h(n1)]2,
R(n) is positive definite and using this property, we linearly combined the RHA from all the 10 sensors with highest spectral content (cRHA).
Publication 2010
Acclimatization Care, Prenatal Ethics Committees, Research Heart Infant, Newborn Medical Devices Pregnancy Pregnant Women Projective Techniques Squid
In this paper, the summed RHA method, FastICA, RHA applied to two or more FastICA components, and simple filtering are considered postprocessing steps designed to simplify the extraction of the fetal R-waves. Since the maternal cardiac signal is dominant over the fetal signal, the maternal MCG was first removed from all SQUID channels by a signal space projection algorithm [31 ] before applying any of the methods tested. To further reduce the influence of the residual maternal MCG, only data from the lower 82 channels of the SARA system, far from the maternal heart but nearer to the fetal heart, were used in our analysis. To be clear, the FastICA was not used to separate the fetal and maternal MCGs in this study, but rather it was only used to separate the fMCG from background signal. After removal of the maternal MCG, each dataset was postprocessed in four ways: 1) compute the RHA of each channel and sum (Hilbert); 2) apply the FastICA and select the dominant fetal component (ICA); 3) compute the RHA of all FastICA components containing fMCG and sum (ICA+Hilbert); and 4) manually select the channel with the largest fMCG signal (filtered). The label “filtered” refers to the 1–100 Hz bandwidth imposed by the initial filtering operations. Ideally, after applying any of the earlier postprocessing methods, the fiducial points may be identified by simply extracting all of the maxima and testing which maxima fall above a selected threshold.
To illustrate this process, the results from a single recording are presented in Fig. 4. Here, the local maxima from each method were extracted and normalized by the largest positive value, and then, used to build the histograms shown in Fig. 4(A)–(D). For clarity, the histograms were scaled by taking the log(n+1) of each histogram bin. Fig. 4(E)–(H) shows the resulting RR intervals obtained after selecting a threshold between 0 and 1 and then extracting the remaining maxima. For this dataset, the ICA and Hilbert method (RHA) separate the maxima into two nonoverlapping distributions, as shown in Fig. 4(B) and (D), where the histograms indicate a completely resolved distribution of R-wave maxima separated from the distribution of lower amplitude maxima arising from noise and/or other fMCG components. Fig. 4(F) and (H) are the graphs of the corresponding RR intervals for any value of threshold falling between the two resolved distributions. In contrast, Fig. 4(A) and (C) shows overlapping distributions. In these two cases, a single threshold cannot be selected that cleanly separates the maxima of R-waves from maxima originating from other sources. As an example, Fig. 4(E) shows an upward spike in the graph of RR intervals near the beginning of the dataset indicating that at least one true R-wave maxima fell below the threshold. We refer to this case as a “missed” beat. Fig. 4(G) shows several downward spikes indicating that a few maxima were falsely classified as R-waves. We refer to this case as “extra” beat.
Publication 2008
Care, Prenatal Fetal Heart Filtering Surgery Heart Squid
Constructs for bacterial expression of full-length rat Munc18-1, squid Munc18-1, or fragments of rat synaptobrevin-2 (residues 29–93), human SNAP25 (residues 11–82 and 141–203), the cytoplasmic domain (residues 2–253) of rat syntaxin-1A, its N-terminal region (residues 1–180) or its SNARE motif (residues 191–253), as well as the syntaxin-1A(2–253) L165E,E166A mutant (LE mutant), were described previously10 (link), 13 (link), 44 (link), 52 (link). The synaptobrevin(29–93) (S61C), syntaxin-1A(191–253) (R210E), syntaxin-1A(2–253) (R210E), syntaxin-1A(2–253) (C145S, S249C), syntaxin-1A(2–253) (L165E,E166A, C145S, S249C) and syntaxin-1A(2–253) (R210E, C145S, S249C) mutants were generated from the corresponding parent fragments using QuickChange site-directed mutagenesis kit (Stratagene). The vector to express rat Munc13-1(859–1407,1453–1531) fragment (MUN*) was prepared from the previously described Munc13-1(859–1531) fragment32 (link) using standard molecular biology techniques. All proteins were expressed as GST fusions, isolated by affinity chromatography, and purified by gel filtration and/or ion exchange chromatography as described10 (link), 13 (link), 32 (link), 52 (link). Isotopic labeling was performed using well-established procedures9 (link), 58 (link). Protein concentrations were determined by UV absorbance. Most experiments involving Munc18-1 were performed with rat Munc18-1. However, because of the limited solubility of rat Munc18-1, binding experiments where isolated Munc18-1 had to be added at concentrations above 20 μM were performed with squid Munc18-1, which is more soluble and has a 66.4% sequence identity with rat Munc18-1, having very similar biochemical properties44 (link).
Publication 2011
Bacteria Chromatography, Affinity Cloning Vectors Cytoplasm Gel Chromatography Homo sapiens Ion-Exchange Chromatographies Mutagenesis, Site-Directed Parent Proteins SNAP25 protein, human SNAP Receptor Squid Syntaxin-1A UNC13B protein, human Vamp2 protein, rat Vesicle-Associated Membrane Proteins
There are two practical problems with using a single OPM to detect neuromagnetic fields: first, the convoluted shape of the cortex means that, even if the approximate location of the region of interest in the subject's head (somatosensory cortex in our case) is known, the precise orientation of the local normal to the cortical surface is unknown. Since the locations of field maxima outside the head are strongly dependent on the direction of current flow, this means that it is difficult to predict where on the scalp sensors should be optimally placed. Second, in order to mathematically model the measured fields, and hence derive 3D images of changing cortical current flow, the precise location and orientation of the sensors relative to the brain anatomy must be known. We solved both problems via the use of 3D printing (see Fig. 2). We used an anatomical magnetic resonance image (MRI) of the subject's head (as described in Meyer et al. (2017) (link)) (Fig. 2A) in order to extract a 3D mesh, representing the outer surface of the head and face (Fig. 2B). Following this, a nylon cast of the outer head surface was fabricated using 3D printing (http://www.chalkstudios.co.uk/), resulting in a head-cast that is moulded to the shape of the individual subject's head (Fig. 2C/D). As part of the head-cast design, we digitally placed a nominally hexagonal array of slots for 13 radially-oriented OPMs over the subject's right somatosensory cortex. The array was located and oriented so as to sample the field maxima and minima expected at 6.5 mm from the scalp surface due to a dipole in the somatosensory cortex (whose location and orientation was estimated from previous SQUID-based dipole fits to the same subject). Importantly, since the head-cast was generated directly from the subject's MRI, the precise location and orientation of the slots for the sensors, with respect to the brain anatomy, was known. The multiple slots meant that the single OPM could be placed in any one of the 13 locations in order to sample the spatially variation of scalp-level magnetic fields.

Head-cast design and fabrication: A) Single sagittal slice from the anatomical MRI. B) Outer head surface extracted from MRI. C) CAD model of the head-cast with slots designed to house the OPM sensors over sensorimotor cortex. Slot positions are based on a-priori prediction of the spatial topography of scalp field pattern, derived from previous SQUID measurements in the same subject. D) 3D-printed head-cast on subject. E) Subject in situ with the OPM attached. Note that the head-cast is not only fixed rigidly to the subject's scalp, but is also fixed relative to the MSR, thus eliminating any sensor motion relative to the subject, and subject motion relative to the MSR.

Fig. 2
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Publication 2017
Brain CD3EAP protein, human Cortex, Cerebral Face Head Magnetic Fields Nylons Scalp Seizures Sensorimotor Cortex Somatosensory Cortex Squid

Most recents protocols related to «Squid»

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Publication 2023
Abdomen Abdominal Cavity Brain Care, Prenatal Fetal Movement Head Heart Infant Magnetic Fields Medical Devices Midwife Reproduction Squid Ultrasonography Woman
The micromorphologies and composition were studied by field emission scanning electron microscopy (SEM, HITACHI, SU8020, Japan) and Flourier transformed infrared spectroscopy (FT-IR, 4000–400 cm−1, Nicolet 6700 apparatus, Thermo Fisher Scientific, U.S.). The ion concentration in solution was measured by ICP-AES (Optima 7300V, PerkinElmer, U.S.). Vibrating sample magnetometry was applied to measure the magnetic properties (VSM, MPMS-SQUID VSM-094, Quantum Design, U.S.). N2 adsorption–desorption analysis was performed for chitosan and MCT using a surface area and porosity analyzer (BET, ASAP 2020, Micromeritics Instrument Corp., U.S.). The enhanced photocatalytic mechanism was studied by X-ray photoelectron spectroscopy (XPS, ESCALAB 250Xi, Thermo Fisher Scientific, U.S.), ultraviolet-visible spectrometry (UV-vis, UV-752N, Shanghai Precision and Scientific Instrument Co., Ltd, China), ultraviolet-visible diffuse reflection spectroscopy (UV-DRS, ESCALAB 250Xi, Thermo Fisher Scientific, U.S.), electron paramagnetic resonance (EPR, Bruker E-500, Switzerland), time-of-flight mass Spectrometry (MS, Orbitrap Fusion™ Tribrid™, Thermo Scientific, U.S.), and liquid chromatography (HPLC, Agilent 1200, U.S.).
Publication 2023
1-methyl-1-piperidinomethane sulfonate Adsorption Chitosan Electron Spin Resonance Spectroscopy High-Performance Liquid Chromatographies Liquid Chromatography Mass Spectrometry Reflex Scanning Electron Microscopy Spectrophotometry, Ultraviolet Spectrum Analysis Squid
CHO-K1 (ATCC CCL-61) and mutant CHO cell lines PgsA-745 (ATCC CRL-2242), PgsB-618 (ATCC CRL-2241), PgsC-605 (ATCC CRL-2245), PgsD-677 (ATCC CRL-2244), and PgsE-606 (ATCC CRL-2246) were obtained from the American Type Culture Collection. The prostate cancer cell line DU145 was kindly provided by Professor Shoko Nishihara, Soka University. The cells were cultured in RPMI 1640 medium (Gibco, Tokyo, Japan) supplemented with 10% v/v FBS (Gibco) or CSS (Gibco), 100 U/ml penicillin G, and 100 µg/ml streptomycin. Purified chondroitin sulfate A (CSA) from whale cartilage, chondroitin sulfate C (CSC) from shark cartilage, dermatan sulfate (DS) from porcine skin, keratan sulfate (KS) from porcine nasal cartilage, and heparan sulfate (HS) from porcine kidney were purchased from PG research (NaCS-A2, NACS-C2, NADS-B2, NSKS2, and NaHS-P2, Tokyo, Japan, http://www.pg-r.com). Hyaluronic acid (HA) from Streptococcus zooepidemicus was provided by Shiseido Co. (Tokyo, Japan). Chemically modified 2-O-ΔS-heparin, 6-O-ΔS-heparin, N-ΔS-heparin, and purified HS were obtained from Iduron (DSH001/2, DSH002/6, and DSH004/NAc, Manchester, U.K.). Purified chondroitin sulfate D (CSD) from shark cartilage (NaCS-D2(Shc)) and biotinylated heparin from porcine intestine (BHHep-Na(PgI)) were obtained from PG Research. Purified chondroitin sulfate E (CSE) from squid cartilage (034-23061) was obtained from Wako Pure Chemicals (Tokyo, Japan). GAGs except for heparin were biotinylated via carboxyl or aldehyde groups by cross-linking. Reaction solutions [1 mg/ml GAG in 100 mM MES-NaOH (pH 5.3), 1.25 mM EZ-link hydrazide biotin (Thermo Fisher Scientific, Tokyo, Japan) and 125 µg/ml 1-ethyl-3-(3-dimethylaminopropyl)carbodiimide (Thermo Fisher Scientific)] were incubated at 20°C for 12 h in the dark. The solution was dialyzed against PBS.
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Publication 2023
4-nitro-4'-aminodiphenyl sulfone Aldehydes Biotin Carbodiimides Cartilage Cell Lines Cells CHO Cells Chondroitin 4-Sulfate Chondroitin 6-Sulfate chondroitin sulfate D Culture Media Dermatan Sulfate Heparin Hyaluronic acid Hydrazide Intestines Keratan Sulfate Kidney Nasal Cartilages Pigs Prostate Cancer shark cartilage extract Skin sodium bisulfide Squid Streptococcus zooepidemicus Streptomycin Sulfate, Heparan Sulfates, Chondroitin Whales
This research study was undertaken by five UCLMS students, four of whom were in Year 5 and one in their Integrated Bachelor of Science (BSc) year. Overseen by a Clinical Associate Lecturer at UCLMS, they were responsible for gaining ethical approval, recruitment, the OSCE design and set up, data collection and analysis. Ethical approval for this study was gained from the UCL Research Ethics Committee (Project ID: 20567/001). Consent for participation was gained from all participants, and all responses were anonymised. The research study was awarded a £500 grant from the Student Quality Improvement and Development fund (SQUID) at UCLMS. This was evenly distributed among the students/doctors acting as OSCE examiners for the virtual mock sessions.
Publication 2023
Ethics Committees, Research Physicians Squid Student
Sea trials to test the new bait were conducted in May 2022 onboard the commercial snow crab fishing vessel “Vima” (LOA 69.2 m) at the snow crab fishing grounds in the Barents Sea. The fishing depth was approximately 300 m.
The treatment pots were baited with the new bait produced by Norbait AS (https://www.norbait.com/), Norway. The production of the bait was performed at a processing line developed by Norbait AS 8. April 2022. The main ingredients were the rest raw materials from the production of seafood products including whitefish and squid offal. The control pots were baited with the standard bait of whole frozen squid (Illex sp.) delivered by the Norwegian seafood company Domstein Fish AS which is normally used in the commercial snow crab fisheries. During the experiments, both treatment and control pots contained similar amount of bait. Specifically, all treatment and control pots were baited with one small mesh bag and one plastic container placed equally in each pot. Each bait bag and container was baited with approximately 320 g of experimental bait and standard bait for the treatment and control pots, respectively.
To compare the catch efficiency of pots using the two bait types, the pots of each bait type were deployed on two separate parallel longlines with approximately 700 m distance (Fig. 2). Such distance was chosen to minimise the potential contamination between the two bait types while the pots were deployed. However, the distance between the pot lines (treatment and control group) also could not be extended much more due to potential variations in snow crab abundance.

Experimental setup used during the fishing trials. Two mainlines with pots baited with control bait (squid) (blue) and experimental bait (green) were deployed in parallel to each other with 700 m distance between the two. The pots on each mainline had a distance of 25 m. Both mainlines were deployed simultaneously and in the same fishing area. (For interpretation of the references to colour in this figure legend, the reader is referred to the Web version of this article.)

Fig. 2
The distance between the individual pots was 25 m. Both of the parallel longlines were deployed and recovered subsequently; therefore, both lines of pots had similar soaking time. In total, three replicates (experiments) of the parallel lines testing both bait types were deployed during the trials.
After the pots were recovered onboard, the crabs of each pot were sorted into target-sized and undersized individuals and the number of crabs in each fraction was counted for each pot in each line (experimental bait and standard bait) separately. This protocol was followed because of the time constraints and capture rates imposed by sampling during commercial fishing did not enable measuring and registering the precise size for the snow crab captured.
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Publication 2023
Blood Vessel Brachyura Fishes Freezing Illex Louses, Crab Seafood Snow Squid Whitefish

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More about "Squid"

Cephalopods, marine invertebrates, mollusk, ocean dwellers, color-changing abilities, ink defense, complex nervous systems, evolutionary adaptations, SQUID magnetometers, PPMS, VSM, MPMS, scientific research, experimental protocols, reproducibility, accuracy.
Squids are a diverse and fascinating group of marine cephalopods, known for their unique physiological and behavioral traits.
These torpedo-shaped, eight-armed creatures are found in oceans around the world, playing a crucial role in many marine ecosystems.
Squids possess remarkable abilities, such as the capacity to change color and texture for camouflage, expel ink to evade predators, and boast complex nervous systems.
These adaptations have long been the subject of scientific inquiry, offering insights into the wonders of the ocean and the evolutionary processes that have shaped these remarkable creatures.
Optimizing squid research is crucial for advancing our understanding of these enigmatic animals.
The AI-driven platform of PubCompare.ai can greatly assist researchers in this endeavor.
By easily locating and comparing protocols from literature, preprints, and patents, researchers can identify the best procedures and products to improve the reproducibility and accuracy of their squid experiments.
In addition to the PubCompare.ai platform, various SQUID (Superconducting Quantum Interference Device) magnetometers, such as the MPMS-XL, PPMS, SQUID-VSM, and MPMS3, have been instrumental in the study of squid-related phenomena.
These cutting-edge instruments allow researchers to precisely measure the magnetic properties of squid samples, providing invaluable data for understanding their physiology and behavior.
By leveraging the insights gained from the MeSH term description, the metadescription, and the additional SQUID-related information, researchers can optimize their squid studies and uncover new discoveries about these captivating marine creatures.
The combination of advanced tools, such as PubCompare.ai and SQUID magnetometers, along with a deep understanding of squid biology, can lead to breakthroughs in the field of cephalopod research.