A detailed description of the Materials and Methods is provided in supplementary materials and methods, Supplementary Material online; here, we give a brief overview of the data set and the basic methods used. The 2014 DrosEU data set represents the most comprehensive spatiotemporal sampling of European D. melanogaster populations to date (fig. 1 and supplementary table S1 , Supplementary Material online). It comprises 48 samples of D. melanogaster collected from 32 geographical locations across Europe at different time points in 2014 through a joint effort of 18 research groups. Collections were mostly performed with baited traps using a standardized protocol (see supplementary materials and methods, Supplementary Material online). From each collection, we pooled 33–40 wild-caught males. We used males as they are more easily distinguishable morphologically from similar species than females. Despite our precautions, we identified a low level of D. simulans contamination in our sequences; we computationally filtered these sequences from the data prior to further analysis (see Supplementary Material online). To sequence these samples, we extracted DNA and barcoded each sample, and sequenced the ∼40 flies per sample as a pool (Pool-Seq; Schlötterer et al. 2014 (link)), as paired-end fragments on a Illumina NextSeq 500 sequencer at the Genomics Core Facility of Pompeu Fabra University. Samples were multiplexed in five batches of ten samples, except for one batch of eight samples (supplementary table S1 , Supplementary Material online). Each multiplexed batch was sequenced on four lanes at ∼50× raw coverage per sample. The read length was 151 bp, with a median insert size of 348 bp (range 209–454 bp). Our genomic data set is available under NCBI Bioproject accession PRJNA388788. Sequences were processed and mapped to the D. melanogaster reference genome (v.6.12) and reference sequences from common commensals and pathogens. Our bioinformatic pipeline is available at https://github.com/capoony/DrosEU_pipeline (last accessed May 22, 2020) . To call SNPs, we developed custom software (PoolSNP; see supplementary materials and methods, Supplementary Material online; https://github.com/capoony/PoolSNP, last accessed May 22, 2020 ), using stringent heuristic parameters. In addition, we obtained genome sequences from African flies from the Drosophila Genome Nexus (DGN; http://www.johnpool.net/genomes.html , last accessed May 22, 2020; see supplementary table S14 , Supplementary Material online, for SRA accession numbers). We used data from 14 individuals from Rwanda and 40 from Siavonga (Zambia). We mapped these data to the D. melanogaster reference genome using the same pipeline as for our own data above, and built consensus sequences for each haploid sample by only considering alleles with >0.9 allele frequencies. We converted consensus sequences to VCF and used VCFtools (Danecek et al. 2011 (link)) for downstream analyses. Additional steps in the mapping and variant calling pipeline and further downstream analyses of the data are detailed in supplementary materials and methods, Supplementary Material online.
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Nexus
Nexus
Nexus is a central point or series of connections in a network or web.
It represents a crucial intersection or core that links various elements together.
Nexus refers to a connection, center, or important point that serves as the focal point for multiple relationships or interactions.
This term is commonly used in fields such as computer science, social sciences, and biology to describe the central, interconnected nature of a system or organization.
Understanding the concept of Nexus is essential for analyzing complex systems and identifying the key nodes that facilitate information flow and influence.
Whether in the context of technology, social structures, or biological processes, the Nexus represents a pivotal element that warrants careful consideration and study.
It represents a crucial intersection or core that links various elements together.
Nexus refers to a connection, center, or important point that serves as the focal point for multiple relationships or interactions.
This term is commonly used in fields such as computer science, social sciences, and biology to describe the central, interconnected nature of a system or organization.
Understanding the concept of Nexus is essential for analyzing complex systems and identifying the key nodes that facilitate information flow and influence.
Whether in the context of technology, social structures, or biological processes, the Nexus represents a pivotal element that warrants careful consideration and study.
Most cited protocols related to «Nexus»
Alleles
Consensus Sequence
Diptera
Drosophila
Europeans
Females
Genome
Joints
Males
Negroid Races
Nexus
Pathogenicity
Single Nucleotide Polymorphism
The number of synonymous and non-synonymous substitutions per site was determined using DnaSP 4.0 [45 (link)]. For C. trachomatis, unique sequences were assigned allele numbers using the Non-redundant databases (NRDB) program [46 ]. Allele profile data were analysed in eBurst to define clonal complexes or groups [47 (link),48 (link)]. Groups were defined as sets of related strains containing pairs of strains that share at least six identical alleles at the seven loci.
A distance matrix in Nexus format was generated from the set of allelic profiles using SplitsTree [46 ]. This file was then used for phylogenetic analyses in SplitsTree 4.0 [49 (link)], both by generating an UPGMA tree and by SplitsTree decomposition analyses. Decomposition analysis depicts all the shortest pathways linking sequences, including those that produce an interconnected network.
Phylogenetic evolutionary analyses of the sequences of the different members of Chlamydiales were conducted using MEGA version 3.1 [50 (link)].
A distance matrix in Nexus format was generated from the set of allelic profiles using SplitsTree [46 ]. This file was then used for phylogenetic analyses in SplitsTree 4.0 [49 (link)], both by generating an UPGMA tree and by SplitsTree decomposition analyses. Decomposition analysis depicts all the shortest pathways linking sequences, including those that produce an interconnected network.
Phylogenetic evolutionary analyses of the sequences of the different members of Chlamydiales were conducted using MEGA version 3.1 [50 (link)].
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Alleles
Biological Evolution
Chlamydiales
Chlamydia trachomatis
Clone Cells
Nexus
Strains
Trees
To efficiently formulate target groups that can be used to identify genomic regions with important conservation patterns, it is valuable to get an overview of the overall relationship between the genomes in an alignment. By summarizing all pair-wise average similarities in the alignment into a matrix, such an overview can be obtained. When one genome is compared to another, the average score of all fragments, or alternatively from all fragments over a certain threshold, is used as a measurement of similarity. The data are normalized against the maximum score that can be obtained with the fragment. The threshold is used to obtain a stronger phylogenomic signal since it removes non-conserved regions from the analysis. Thresholds can be set to 5, 10, 15, 20, 25, 30, 35 or 40% of the maximum score value. Also, if no threshold is used, comparing two genomes of different size can sometimes give large differences in values depending on whether the small one is compared to the large one or the other way around.
In Gegenees, the similarity matrix is displayed as a heat-plot. The color profile and the number of decimals can be adjusted so that optimal views of datasets with different properties can be obtained. The size of the “core genome” at a certain threshold can also be viewed as a heat plot. Data can be exported as a plain table, as an HTML heat plot table, or in the Nexus file format for dendrogram production. The HTML heat-plot format can easily be converted to publication-grade quality images.
An important function of the heat plot is to give the user an overview of average similarities. As the datasets get larger, functions for sorting and comparing phylogeny with the definition of the target and background groups become more and more important. Gegenees has therefore been equipped with tools for manual and automated sorting; the composition of the target and the background groups can be directly viewed and modified from the heat-plot.
In Gegenees, the similarity matrix is displayed as a heat-plot. The color profile and the number of decimals can be adjusted so that optimal views of datasets with different properties can be obtained. The size of the “core genome” at a certain threshold can also be viewed as a heat plot. Data can be exported as a plain table, as an HTML heat plot table, or in the Nexus file format for dendrogram production. The HTML heat-plot format can easily be converted to publication-grade quality images.
An important function of the heat plot is to give the user an overview of average similarities. As the datasets get larger, functions for sorting and comparing phylogeny with the definition of the target and background groups become more and more important. Gegenees has therefore been equipped with tools for manual and automated sorting; the composition of the target and the background groups can be directly viewed and modified from the heat-plot.
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Genome
Nexus
Kinect data were captured with Motognosis Labs v1.0 (Motognosis UG, Berlin, Germany) with a Kinect for Windows V2 Sensor [10 ] at 30Hz sampling rate. Motognosis Labs used the Software Developer Kit Version 1409 provided by Microsoft [10 ]. The Kinect sensor was placed on a tripod at 1.4m height with a vertical angle of −8°. The sensor was placed to approximately match the orientation of the coordinate system from the gold-standard reference, facing the frontal plane of the test subjects in all tasks. The Kinect skeleton model with its 25 anatomical landmark locations is shown in Fig 1 (left). As gold-standard reference motion tracking system, we used a 16-camera Vicon system (MX13+, Nexus 2.1; Vicon Motion Systems Ltd., Oxford, UK) using 36 attached IR reflecting markers (Fig 1 , middle and right). It was configured to measure marker positions at 100 Hz with 2mm accuracy within an area of 3m by 6m. The Kinect system covered a trapezoid measurement area of roughly 3m by 4m, with a maximum distance of 4.5m to the sensor. Descriptions of all six performed tasks are given in Table 1 . All tasks were recorded simultaneously with both systems. The systems were directly connected from Kinect audio output to Vicon’s audio input via cable. Audio start and stop signals were given for offline temporal synchronization. Each task was performed three to five times before measuring the next. For all tasks except walks, patients started at 2.5m distance to the Kinect sensor for best depth resolution [10 ]. To cover full gait cycles in gait tasks, starting position for these tasks was in 5m distance to the Kinect sensor, which was slightly outside of the sensor range.
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Gold
Nexus
Patients
Skeleton
Trapezoid Bones
Acids
Benzene
Boronic Acids
Carbon-13 Magnetic Resonance Spectroscopy
diphenyl
Esters
Fingers
Gas Chromatography-Mass Spectrometry
Mass Spectrometry
Nexus
NMR, Multinuclear
Palladium
Phenols
Polychlorinated Biphenyls
Spectrometry, Mass, Electrospray Ionization
tetramethylsilane
triphenylphosphine
Workers
Most recents protocols related to «Nexus»
MRI and 3DGA data including marker trajectories and ground reaction forces of twelve children diagnosed with CP (10.4 ± 3.8 years old, height: 133.6 ± 16.1 cm, mass: 30.1 ± 10.8 kg) and thirteen TD children (10 ± 2.2 years old, height: 144.5 ± 8.5 cm, mass: 36.8 ± 9.5 kg) were analyzed for this study. All participants walked without walking aids and with a self-selected speed. The data of all CP children and three TD children was captured during a previous study (Kainz et al., 2017 (link)) while the data of the remaining ten TD children was additionally collected for the purpose of this study. Ethics approval was obtained from the local ethics committees (University of Vienna, reference number 00578). Data collection of the retrospective analyzed data (CP children and three TD children) is described in detail in Kainz et al. (2017) (link).
MRI images of the additionally recorded data (ten TD children) were collected using a 3T magnetic resonance scanner (MAGNETOM Vida, Siemens, Berlin/Munich, Germany) with a T1 vibe sequence with a voxel size of 0.8 × 0.8 × 0.7 mm. 3DGA-data for these ten TD children were captured on the same day as the MRI images using a 12 camera motion capture system (Vicon Motion Systems, Oxford, UK). The used marker set during the motion capturing was based on the Plug-in-Gait marker set (Kadaba et al., 1990 (link); Davis et al., 1991 (link)) with additional clusters of three markers on each thigh and shank segment and an additional marker at the 5th metatarsal head of each foot. Simultaneously, ground reaction forces were acquired using five force plates (Kistler Instrumente, Winterthur, Switzerland). All children performed several gait trials with a self-selected walking speed. Marker trajectories were captured, labelled, and filtered (Butterworth 4th order, 6 Hz low-pass filter) in Nexus 2.12.1 (Vicon Motion System, Oxford, United Kingdom).
MRI images of the additionally recorded data (ten TD children) were collected using a 3T magnetic resonance scanner (MAGNETOM Vida, Siemens, Berlin/Munich, Germany) with a T1 vibe sequence with a voxel size of 0.8 × 0.8 × 0.7 mm. 3DGA-data for these ten TD children were captured on the same day as the MRI images using a 12 camera motion capture system (Vicon Motion Systems, Oxford, UK). The used marker set during the motion capturing was based on the Plug-in-Gait marker set (Kadaba et al., 1990 (link); Davis et al., 1991 (link)) with additional clusters of three markers on each thigh and shank segment and an additional marker at the 5th metatarsal head of each foot. Simultaneously, ground reaction forces were acquired using five force plates (Kistler Instrumente, Winterthur, Switzerland). All children performed several gait trials with a self-selected walking speed. Marker trajectories were captured, labelled, and filtered (Butterworth 4th order, 6 Hz low-pass filter) in Nexus 2.12.1 (Vicon Motion System, Oxford, United Kingdom).
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Acquired Immunodeficiency Syndrome
Child
Foot
Head
Metatarsal Bones
Nexus
Nuclear Magnetic Resonance
Regional Ethics Committees
Thigh
Fourier-transform infrared (FT-IR) spectroscopy was performed on a Nexus 870 spectrometer (Thermo Nicolet) in the mode of attenuated total reflection (ATR) with the range from 4000 to 600 cm−1 and at a resolution of 0.125 cm−1.
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Nexus
Reflex
Spectroscopy, Fourier Transform Infrared
All used chemicals
and solvents are from Merck, Aldrich, and Fluke chemicals in this
work. The spectra of FT-IR were performed with pellets of KBr using
a Nexus 670 FT-IR spectrometer (Daypetronic Company, Tehran, Iran).
TL-chromatography was used to monitor the reaction over silica gel
plates. Particle morphology was investigated using a scanning electron
microscope (Daypetronic Company, Iran-Tehran) through FESEM-TESCAN
MIRA3. The 500 MHz spectra of 1H NMR and 13C
NMR were obtained using a spectrometer of BRUKER NMR (Daypetronic
Company, Iran-Tehran). Energy scattered X-rays of MNPS were
recorded using FESEM-TESCAN MIRA3 (Daypetronic Company, Tehran, Iran).
XRD was performed using Co radiation with a 40 kV wavelength scenting
P AD V X-ray (Beamgostar Taban Company, Tehran, Iran). The samples
were scanned in the ranges of 2θ = 1–10° and 2θ
= 10–80°; a BET isotherm of N2 was recorded
at 77 °K employing a standard gas manifold to explain the features
of materials like average pore diameter, pore-volume, and catalyst
surface (Daypetronic Company, Tehran, Iran). In addition, adsorption
data are presented in Brunauer–Emmett–Teller (BET) method.
In all reactions, CH3COOH with a molecular weight of 400
was applied. The content of Zn was measured by ICP-OES analysis (Tarbiat
Modares University, Tehran, Iran).
and solvents are from Merck, Aldrich, and Fluke chemicals in this
work. The spectra of FT-IR were performed with pellets of KBr using
a Nexus 670 FT-IR spectrometer (Daypetronic Company, Tehran, Iran).
TL-chromatography was used to monitor the reaction over silica gel
plates. Particle morphology was investigated using a scanning electron
microscope (Daypetronic Company, Iran-Tehran) through FESEM-TESCAN
MIRA3. The 500 MHz spectra of 1H NMR and 13C
NMR were obtained using a spectrometer of BRUKER NMR (Daypetronic
Company, Iran-Tehran). Energy scattered X-rays of MNPS were
recorded using FESEM-TESCAN MIRA3 (Daypetronic Company, Tehran, Iran).
XRD was performed using Co radiation with a 40 kV wavelength scenting
P AD V X-ray (Beamgostar Taban Company, Tehran, Iran). The samples
were scanned in the ranges of 2θ = 1–10° and 2θ
= 10–80°; a BET isotherm of N2 was recorded
at 77 °K employing a standard gas manifold to explain the features
of materials like average pore diameter, pore-volume, and catalyst
surface (Daypetronic Company, Tehran, Iran). In addition, adsorption
data are presented in Brunauer–Emmett–Teller (BET) method.
In all reactions, CH3COOH with a molecular weight of 400
was applied. The content of Zn was measured by ICP-OES analysis (Tarbiat
Modares University, Tehran, Iran).
1H NMR
Chromatography
Electromagnetic Radiation
Electron Microscopy
Infrared Spectrophotometry
Nexus
Pellets, Drug
Radiography
Silicon Dioxide
Solvents
Trematoda
The morphological characteristics of O. viverrini (Ov) and minute intestinal flukes (MIFs) eggs are similar. So, the Ov egg was confirmed by specific PCR amplification from genomic DNA using OvNad5 primer as previously described [30 (link)]. PCR amplifications were done by using GoTaq® Colorless Master Mix (Promega, USA) containing 3 µL of genomic DNA, and 25 pmol of each forward and reverse primer (OvNad5-F: TTTGCGGAGGTTTGTTACCT and OvNad5-R: CACCTCACCAATTCAACACG) in a thermal cycler (Mastercycler nexus Eppendorf flexlid, Germany). The amplification steps were including initial denaturation at 95ºC for 5 min, followed by 35 cycles of denaturation at 95ºC for 1 min, annealing at 55 ºC for 1 min, extension at 72 ºC for 1 min, and one cycle of a final extension at 72 ºC for 10 min. The PCR products were size separated on 2% agarose gel containing ViSafe Red Gel Stain (Vivantis, USA) using 1X TBE buffer at 80 V for 2 h. The PCR products were confirmed for their correction by DNA sequencing service (Macrogen, Republic of Korea).
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Eggs
Genome
Intestines
Nexus
Oligonucleotide Primers
Promega
Sepharose
Stains
Trematoda
Tris-borate-EDTA buffer
An 8-video-camera motion capture system and NEXUS 2.8.1 software (Vicon, Oxford, United Kingdom) were used to collect and record the three-dimensional (3D) trajectories of reflective markers at a sampling rate of 150 Hz. The global coordinate system (GCS) was defined by using the right-hand rule when the incline of the treadmill was 0° and was calibrated according to Vicon's specifications. The Y-axis of GCS was defined as the longitudinal axis of the treadmill. The Z-axis of GCS was perpendicular to the ground pointing upward. 15 reflective markers were used in this study. 6 markers were attached onto the roller skis (3 markers each, Figure 1 ) and 6 markers were attached onto the poles (3 markers each, Figure 1 ). Another 3 markers were attached onto the treadmill. Two markers were attached to the front and rear right corners of the treadmill. Another one was attached to the rear left corner of the treadmill. All markers in this study were used to provide the position of roller skis, poles, and the treadmill in the GCS.
Measurements were performed on a motorized treadmill with a belt surface 2.7 m wide and 3.5 m long (Rodby Innovation AB, Vänge, Sweden). A same pair of roller-skis (Marwe SKATING 620 XC, wheel no. 0, Marwe Oy, Hyvinkää, Finland) were used for both techniques and all participants. Two custom-made pole force sensors (VTT MIKES, Technical Research Centre of Finland Ltd., Kajaani, Finland) were used to measure axial ground reaction force (GRF) from poles at a sample rate of 400 Hz. The pole force sensors were mounted below the pole grip and were calibrated in a certified laboratory for force and mass measurements (VTT MIKES, Technical Research Centre of Finland Ltd., Kajaani, Finland). Two custom-made 2D (vertical and medio-lateral) force measurement bindings (Neuromuscular Research Centre, University of Jyväskylä, Finland) (34 (link)) were mounted on the roller-skis to measure the leg forces generated from roller-skis at a sampling rate of 400 Hz. Both pole force sensor and ski measurement bindings have been used in our previous study (35 (link)). The total mass of one equipped pole and one equipped roller ski were 202 g and 664 g greater than the normal ones. A trigger signal was sent from the Coachtech online measurement and feedback system (36 ) (Neuromuscular Research Centre, University of Jyväskylä, Finland) to the motion capture system to mark the start of the force capture. Data from each subject at each incline were collected for at least 30s when the treadmill speed was constant at 10 km/h.
Measurements were performed on a motorized treadmill with a belt surface 2.7 m wide and 3.5 m long (Rodby Innovation AB, Vänge, Sweden). A same pair of roller-skis (Marwe SKATING 620 XC, wheel no. 0, Marwe Oy, Hyvinkää, Finland) were used for both techniques and all participants. Two custom-made pole force sensors (VTT MIKES, Technical Research Centre of Finland Ltd., Kajaani, Finland) were used to measure axial ground reaction force (GRF) from poles at a sample rate of 400 Hz. The pole force sensors were mounted below the pole grip and were calibrated in a certified laboratory for force and mass measurements (VTT MIKES, Technical Research Centre of Finland Ltd., Kajaani, Finland). Two custom-made 2D (vertical and medio-lateral) force measurement bindings (Neuromuscular Research Centre, University of Jyväskylä, Finland) (34 (link)) were mounted on the roller-skis to measure the leg forces generated from roller-skis at a sampling rate of 400 Hz. Both pole force sensor and ski measurement bindings have been used in our previous study (35 (link)). The total mass of one equipped pole and one equipped roller ski were 202 g and 664 g greater than the normal ones. A trigger signal was sent from the Coachtech online measurement and feedback system (36 ) (Neuromuscular Research Centre, University of Jyväskylä, Finland) to the motion capture system to mark the start of the force capture. Data from each subject at each incline were collected for at least 30s when the treadmill speed was constant at 10 km/h.
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Epistropheus
Grasp
Nexus
Precipitating Factors
Top products related to «Nexus»
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The Mastercycler nexus is a thermal cycler designed for performing polymerase chain reaction (PCR) experiments in a laboratory setting. It provides precise temperature control and consistent thermal cycling for various molecular biology applications.
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The S-4800 is a high-resolution scanning electron microscope (SEM) manufactured by Hitachi. It provides a range of imaging and analytical capabilities for various applications. The S-4800 utilizes a field emission electron gun to generate high-quality, high-resolution images of samples.
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The Nicolet Nexus 670 is a Fourier transform infrared (FTIR) spectrometer designed for laboratory use. It is capable of performing infrared spectroscopy analysis to identify and characterize various chemical compounds and materials.
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Sephadex LH-20 is a size-exclusion chromatography medium used for the separation and purification of a wide range of molecules, including proteins, peptides, and small organic compounds. It is a hydrophilic, cross-linked dextran polymer with a porous structure that allows for size-based separation. Sephadex LH-20 is commonly used in various applications, such as desalting, fractionation, and purification of samples.
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The Nexus 670 is a high-performance liquid chromatography (HPLC) system designed for a wide range of analytical applications. It features a modular design, advanced electronic controls, and precise flow and gradient delivery.
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Vicon Nexus is a motion capture software solution that provides a comprehensive platform for the acquisition, processing, and analysis of motion data. It serves as the core software for Vicon's motion capture systems, enabling users to capture, visualize, and export precise 3D movement data.
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More about "Nexus"
Nexus is a critical junction or central node in a complex system, acting as a pivotal intersection that links various elements together.
This term is widely used in fields like computer science, social sciences, and biology to describe the interconnected nature of systems and organizations.
The concept of Nexus is crucial for understanding and analyzing complex networks, as it helps identify the key points that facilitate information flow and influence.
Whether in the context of technology, social structures, or biological processes, the Nexus represents a fundamental element that warrants careful consideration and study.
Some related terms and concepts include Mastercycler nexus, a thermal cycler used in molecular biology, and Mastercycler Nexus Gradient, which offers temperature gradient functionality.
MATLAB, a numerical computing environment, can also be used to analyze and visualize nexus-like structures.
The S-4800 and Nicolet Nexus 670 are analytical instruments that may provide insights into nexus-like systems.
Sephadex LH-20, a size-exclusion chromatography medium, can be used to purify and separate compounds in a nexus-like manner.
Nexus 670, a Fourier-transform infrared spectrometer, and Vicon Nexus, a motion capture system, are examples of technologies that may involve nexus-like principles.
Ultimately, the concept of Nexus is a fundamental one that transcends various disciplines, and a deep understanding of its nature can lead to innovative solutions and breakthroughs in complex systems.
This term is widely used in fields like computer science, social sciences, and biology to describe the interconnected nature of systems and organizations.
The concept of Nexus is crucial for understanding and analyzing complex networks, as it helps identify the key points that facilitate information flow and influence.
Whether in the context of technology, social structures, or biological processes, the Nexus represents a fundamental element that warrants careful consideration and study.
Some related terms and concepts include Mastercycler nexus, a thermal cycler used in molecular biology, and Mastercycler Nexus Gradient, which offers temperature gradient functionality.
MATLAB, a numerical computing environment, can also be used to analyze and visualize nexus-like structures.
The S-4800 and Nicolet Nexus 670 are analytical instruments that may provide insights into nexus-like systems.
Sephadex LH-20, a size-exclusion chromatography medium, can be used to purify and separate compounds in a nexus-like manner.
Nexus 670, a Fourier-transform infrared spectrometer, and Vicon Nexus, a motion capture system, are examples of technologies that may involve nexus-like principles.
Ultimately, the concept of Nexus is a fundamental one that transcends various disciplines, and a deep understanding of its nature can lead to innovative solutions and breakthroughs in complex systems.