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> Phenomena > Natural Phenomenon or Process > Streams

Streams

Streams are natural or artificial watercourses that flow intermittently or continuously.
They serve a variety of important functions, including drainage, irrigation, and the transport of water, sediment, and nutrients.
Streams can range from small brooks and creeks to large rivers, and they play a crucial role in the hydrological cycle and the overall health of ecosystems.
Researchers studying streams may investigate topics such as hydrology, ecology, water quality, and the impacts of human activities on stream environments.
The study of streams is an important field that contributes to our understanding of freshwater systems and informs efforts to manage and conserve these vital natural resources.

Most cited protocols related to «Streams»

1
Drosophila Genome Analysis Pipeline
Image analysis software was provided as part of the Genome Analyzer analysis pipeline and configured for fully automatic parameter selection. Single-end reads were 76 bases in total length. Quality control was performed using FastQC, showing overall low error rates. The reference genome used was the latest FlyBase version at the time (y1; cn1bw1sp1 strain, Dm5.30). The data was aligned using the BWA algorithm (Li and Durbin, 2009 (link)). A total of 5,234,506 reads were NOT mapped to the genome (i.e., 10.01%). This is usually due to low quality reads or reads have missing base calling information (i.e., “B” in the quality stream). The rest of the reads for X1 and X2 were mapped as indicated. Gap estimation: according to the mapping software, the gap between pair-end reads is 360 ± 20 bp. The distribution percentiles are 345 (25%), 360 (50%), and 375 (75%). The set of6 and to the NCBI’s map of RefSeq and candidate Drosophila genes7.
Reads were filtered using a minimum mapping quality of 20 (MAPQ). Variant calling was performed using SamTools (Li et al., 2009 (link)) and BcfTools. When using individual calls without base alignment quality (BAQ) model, (Li, 2011 (link)) a total of 1,036,435 homozygous SNPs were detected. Using multi-sample calling methods and BAQ model, (Li, 2011 (link)) the number of homozygous SNPs was reduced to 204,250. Variant annotation and filtering was performed using the software SnpEff (Cingolani et al., Fly, in press) and SnpSift, described below.
Cingolani P., Patel V.M., Coon M., Nguyen T., Land S.J., Ruden D.M, & Lu X. (2012). Using Drosophila melanogaster as a Model for Genotoxic Chemical Mutational Studies with a New Program, SnpSift. Frontiers in Genetics, 3, 35.
Publication 2012
A 435 Drosophila Genome Homozygote Single Nucleotide Polymorphism
2
Improving Thread Scaling for Sequencing Data Processing
We also examined how threads coordinate when reading FASTQ (Cock et al., 2010 (link)) input or writing SAM output (Li et al., 2009 (link)). These interactions are synchronized, i.e. protected by locks. The name critical section is given to a portion of the software that only one thread may execute at a time. The critical section for handling input is called the input critical section and is protected by the input lock; likewise for the output critical section and the output lock.
We hypothesized that to improve thread scaling we should restructure the input and output critical sections. Our first goal was to reduce the time spent in the critical section by deferring as much computation until after the critical section as possible. Our second goal was to reduce the total number of times the critical section was entered. This reduces overhead incurred by locking and unlocking upon entering and exiting.
The original strategy (O-parsing) both reads and parses a sequencing read in the critical section (CS). We developed three variants on this approach (Table 1). In deferred (D) parsing, the CS reads a single input record into a buffer. After the CS, the buffer is parsed into the sequencing read data object. Batch deferred (B) parsing is like D-parsing but handles batches of N reads at a time. The B-parsing critical section loops N times, reading each record into a separate buffer. After the CS, another loop parses each buffer into a sequencing read object. This reduces by a factor of N the total number of times the CS is entered. A similar change is made to the output CS: alignment records are written to the output stream in batches of N reads.

Pseudocode for four synchronized parsing strategies

Note: Red code is inside the critical section (CS). Original (O) parsing both reads and parses in the CS. Deferred parsing (D) uses the CS to read the next record into a buffer, counting four newlines to find the record boundary, but defers parsing until after the CS. Batch deferred parsing (B) is like (D) but reads N reads at a time. Block deferred parsing (L) reads a fixed-sized chunk of data (B bytes), assuming that no record spans a B-byte boundary. While the assumption for (L) is violated in practice for formats like FASTQ, it suggests a strategy for making formats more amenable to multithreaded parsing.

Blocked deferred (L) parsing reads a chunk of exactly B input bytes into a buffer, assuming that (a) no read spans a B-byte boundary in the input file, such that no B-byte chunk contains a partial input record, and (b) the number of reads per B-byte chunk is N for all chunks (except perhaps the last), known ahead of time. These assumptions do not hold for real FASTQ files, but we can easily modify a FASTQ file to comply by appending extra space characters to every Nth read until the following read begins at an B-byte boundary (Fig. 2). The spaces are ignored by the aligner. This has the effect both of enforcing the L-parsing assumptions and of making it easier to parse paired-end files in a synchronized manner, since a B-sized block taken from the same offset in both files is guaranteed to contain N matching ends. As with B-parsing, the L-parsing output critical section writes alignments in batches of B reads at a time.
Langmead B., Wilks C., Antonescu V, & Charles R. (2018). Scaling read aligners to hundreds of threads on general-purpose processors. Bioinformatics, 35(3), 421-432.
Full text: Click here
Publication 2018
Buffers Character factor A
3
Automated Cortical Surface Reconstruction in FreeSurfer

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Publication 2012
Cortex, Cerebral Gray Matter Tissues White Matter
4
Annotation of Functional SNP Effects
Functional consequences of SNPs on genes are obtained by performing ANNOVAR12 (link) (“gene-based annotation”) using Ensembl genes (build 85). Note that SNPs can be annotated to more than one gene in case of intergenic SNPs which are annotated to the two closest up- and down-stream genes. CADD scores, RegulomeDB scores and 15-core chromatin state are annotated to all SNPs in 1000G phase 3 by matching chromosome, position, reference, and alternative alleles. eQTLs are also extracted by matching chromosome, position and alleles of all independent significant SNPs and SNPs which are in LD with one of the independent significant SNPs for each user-selected tissue type, wherein SNPs can have multiple eQTLs for distinct genes and tissue types (Supplementary Note 2). Information on previously known SNP-trait associations reported in the GWAS catalog is also retrieved for all SNPs of interest by matching chromosome and position.
Watanabe K., Taskesen E., van Bochoven A, & Posthuma D. (2017). Functional mapping and annotation of genetic associations with FUMA. Nature Communications, 8, 1826.
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Publication 2017
Alleles Chromatin Chromosomes Chromosomes, Human, Pair 3 Gene Annotation Genes Genome-Wide Association Study Histocompatibility Testing Single Nucleotide Polymorphism
5
Mitigating Inter-Scanner Variability

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Publication 2012
Brain Cranium Head Microtubule-Associated Proteins Muscle Rigidity

Most recents protocols related to «Streams»

1
Detection of Respiratory Effort and Cerebral Activation from Mandibular Movements
Not available on PMC !

Example 15

In a 15th example, reference is made to FIGS. 12 and 13. FIG. 12 shows an example of the first measurement signal stream F1 and of the second measurement signal stream F2 in the situation where the subject suffers a temporary disappearance of all control of cerebral origin, which is characteristic of central hypopnoea. This disappearance is characterized by the mouth opening passively because it is no longer held up by the muscles. It is therefore seen in the streams F1 and F2 that between the peaks the signal does not indicate any activity. On the other hand at the moment of the peak there is observed a high amplitude of the movement of the mandible. Toward the end of the peaks there is seen a movement that corresponds to a non-respiratory frequency, which is the consequence of cerebral activation that will then result in a micro-arousal. The digit 1 indicates the period of hypopnoea where a reduction of the flow is clearly visible on the stream F5th from the thermistor. The digits 2 and 3 indicate the disappearance of mandibular movement in the streams F1 and F2 during the period of central hypopnoea. FIG. 13 shows an example of the first measurement signal stream F1 and of the second measurement signal stream F2 in the situation where the subject experiences a prolonged respiratory effort that will terminate in cerebral activation. It is seen that the signal from the accelerometer F1 indicates at the location indicated by H a large movement of the head and of the mandible. Thereafter the stream F2 remains virtually constant whereas in that F1 from the accelerometer the level drops, which shows that there is in any event a movement of the mandible, which is slowly lowered. There then follows a high peak I that is a consequence of a change in the position of the head during the activation that terminates the period of effort. The digit 1 indicates this long period of effort marked by snoring. It is seen, as indicated by the digit 2, that the effort is increasing with time. This effort terminates, as indicated by the digit 3, in cerebral activation that results in movements of the head and the mandible, indicated by the letter I.

The analysis unit holds in its memory models of these various signals that are the result of processing employing artificial intelligence as described hereinbefore. The analysis unit will process these streams using those results to produce a report on the analysis of those results.

It was found that the accelerometer is particularly suitable for measuring movements of the head whereas the gyroscope, which measures rotation movements, was found to be particularly suitable for measuring rotation movements of the mandible. Thus cerebral activation that leads to rotation of the mandible without the head changing position can be detected by the gyroscope. On the other hand, an IMM type movement will be detected by the accelerometer, in particular if the head moves on this occasion. An RMM type movement will be detected by the gyroscope, which is highly sensitive thereto.

US11864910B2. System comprising a sensing unit and a device for processing data relating to disturbances that may occur during the sleep of a subject (2024-01-09). Sunrise SA [BE]. Inventors: Pierre Martinot [BE].
Full text: Click here
Patent 2024
ARID1A protein, human Arousal Exhaling Fingers Gene Expression Regulation Head Head Movements Mandible Medical Devices Memory Movement Muscle Tissue Oral Cavity Respiratory Rate Sleep Thumb Vision
2
Lantern Cleavage and Analysis
Not available on PMC !

Example 5

Lanterns are placed individually in 96-well plates and treated with 0.5 mL solution of 20% (V/V) HFIP in DCM for 1 h. Lanterns are removed and the cleaved products are concentrated using a stream of N2. Samples were dissolved for UPLC analysis and preparative HPLC.

The following compounds were prepared according to the general procedures of Part A.

US11857565B2. Hydrophobic Auristatin F compounds and conjugates thereof (2024-01-02). SEAGEN INC. [US]. Inventors: Svetlana O. Doronina [US], Philip Moquist [US].
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Patent 2024
Cytokinesis High-Performance Liquid Chromatographies
3
Central Apnoea Respiratory Monitoring
Not available on PMC !

Example 14

In a 14th example, reference is made to FIG. 11. FIG. 11 shows an example of the first measurement signal stream F1 and of the second measurement signal stream F2 in the situation where the subject suffers a central apnoea. The peaks F show a movement of the head and of the mandible on resumption of respiration. It is also seen that between the peaks F there is so to speak no movement of the mandible. The digit 1 indicates an absence of respiratory flow that goes hand in hand with an absence of effort, indicated by the digit 2, and activation and resumption of the effort, indicated by the digit 3.

US11864910B2. System comprising a sensing unit and a device for processing data relating to disturbances that may occur during the sleep of a subject (2024-01-09). Sunrise SA [BE]. Inventors: Pierre Martinot [BE].
Full text: Click here
Patent 2024
Cell Respiration Fingers Head Movements Mandible Medical Devices Movement Respiratory Rate Sleep Sleep Apnea, Central Thumb Vision
4
Detection of Mixed Apnea in Mandibular Movement
Not available on PMC !

Example 13

In a 13th example, reference is made to FIG. 10. FIG. 10 shows an example of the first measurement signal stream F1 and of the second measurement signal stream F2 in the case where the subject suffers a mixed apnoea. As in FIG. 8, there is seen in this FIG. 10 an increase in the angular speed of the mandible at a frequency corresponding to the respiration frequency. The digit 1 indicates an absence of respiratory flow that goes hand in hand with an absence of control and of effort, indicated by the digit 2, followed by restoration of cerebral control and effort, indicated by the digit 3.

US11864910B2. System comprising a sensing unit and a device for processing data relating to disturbances that may occur during the sleep of a subject (2024-01-09). Sunrise SA [BE]. Inventors: Pierre Martinot [BE].
Full text: Click here
Patent 2024
Apnea Fingers Mandible Medical Devices Respiratory Rate Sleep Thumb Vision
5
Catalytic Cracking of Arab Light Crude
Not available on PMC !

Example 1

An Arab light crude oil with an API gravity of 33.0 and a sulfur content of 1.6 wt. % was fractionated in a distillation column to form a light stream and a heavy stream. Properties of the feed crude oil stream and the resulting fractions (based on their percent composition in the crude oil fractions) are given in Table 1 below.

TABLE 1
Stream NameBoiling RangeNi (ppm)V (ppm)S (wt. %)N (ppm)
Hydrocarbon3.414.521.6444
Feed
Light StreamLess than<1<10.213
370° C.
Heavy StreamGreater than 4.414.21.4431
370° C.

Details of the un-hydrotreated heavy stream are shown below in Table 2, where the heavy stream is designated EX-1(A).

The same Arab light crude oil used in Example 1 was directly cracked in the same cracking reactor and under the same conditions as was used in Example 3(A), results are designated CE-1. Specifically, the temperature was 675° and the TOS was 75 seconds.

TABLE 4
3(A)3(B)3 (Combined)CE-1
(wt. %)(wt. %)(wt. %)(wt. %)
Dry Gas9.876.438.0610.80
Light Olefins39.1151.6743.4634.89
Ethylene11.8210.0610.6910.41
Propylene18.3425.7621.0516.51
Butylene8.9615.8411.727.96
Gasoline Range33.1224.6028.3824.21
Products
Coke4.926.615.5113.86
Conversion91.1494.4689.8687.38

As can be seen in Table 4, the combined yields of total light olefins from the present methods are significantly higher than the yields from the comparative methods. Further, each of examples 3(A), 3(B), and 3(Combined) show significantly decreased levels of coke formation relative to the comparative example CE-1.

Example 2

The heavy stream from Example 1 was hydrotreated in a three-stage hydrotreater. The reaction conditions were: a weighted average bed temperature of 400° C., a pressure of 150 bar, a liquid hourly space velocity (LHSV) of 0.5 h−1, an Hz/oil ratio 1200:1(v/v), an oil flowrate of 300 ml/h, and an H2 flowrate of 360 L/h.

The first stage of the hydrotreater used a KFR-22 catalyst from Albemarle Co. to accomplish hydro-demetallization (HDM). The second stage of the hydrotreater used a KFR-33 catalyst from Albemarle Co. to accomplish hydro-desulfurization (HDS). The third stage of the hydrotreater used a KFR-70 catalyst from Albemarle Co. to accomplish hydro-dearomatization (HDA). The first, second, and third stages were discrete beds placed atop one another in a single reaction zone. The heavy stream flowed downward to the first stage, then to the second stage, and then to the third stage. Properties of this hydrotreated heavy stream are shown in Table 2 below and are designated EX-2.

TABLE 2
EX-1(A)EX-2
Kinematic viscosity at 100° C. (mm2/s)6
Density (g/ml)0.9650.8402
Nitrogen (ppm)120868.5
Sulfur (wt. %)3.10.007
Ni (ppm)10<1
V (ppm)32<1
Aromatics68.625.6

The hydrotreated heavy stream from Example 2 was fed to the advanced cracking evaluation unit. A TOS of 75 seconds, a residence time of from 1 to 2 seconds, and a temperature of 645° C. was used. Characterization of the product is given in Table 5 below.

TABLE 5
CE-13(B)
Temp. ° C.645645
T.O.S.(s)7575
Steaming Cond.810° C. for 6 hours
CAT/OIL6.488.00
Conversion (%)82.7794.46
Yields (wt. %)
H2 (wt. %)0.600.93
C1 (wt. %)4.823.71
C2 (wt. %)2.741.79
C2═ (wt. %)8.0710.06
C3 (wt. %)2.262.25
C3═ (wt. %)17.1625.76
iC4 (wt. %)0.671.58
nC4 (wt. %)0.550.69
t2C4═ (wt. %)2.393.92
1C4═ (wt. %)1.672.78
iC4═ (wt. %)3.596.01
c2C4═ (wt.%)1.903.14
1,3-BD (wt. %)0.010.63
Total Gas (wt. %)46.4463.25
Gasoline (wt. %)18.0924.60
LCO (wt. %)9.843.95
HCO (wt. %)7.381.59
Coke (wt. %)18.246.61
Groups (wt. %)
H2—C2 (dry gas)16.2416.49
C3—C4 (LPG)30.1946.77
C2═−C4═ (Light34.7952.30
olefins)
C3═+C4═26.7142.24
C4═ (Butenes)9.5516.48
Molar Ratios
mol/mol)
C2═/C23.156.03
C3═/C37.9711.97
C4═/C48.067.52
iC4═/C4═0.380.36
iC4═/iC45.513.94

As can be seen in Table 5, utilizing a hydrotreated heavy stream as the feed to the catalytic reactor results in higher conversion; greater yield of C2, C3, and C4 olefins; greater yield of gasoline; and significantly decreased coke formation, among other advantages.

Example 3

The respective fractions of Arab light crude were cracked at the conditions described below. A catalyst with the composition shown in Table 3 below as used in all of the reactions.

TABLE 3
ComponentWeight %Notes
ZSM-520Phosphorus impregnated at 7.5 wt. %
P2O5 on zeolite
USY21Lanthanum impregnated at 2.5 wt. %
La2O3 on zeolite
Alumina8Pural SB from Sasol
Clay49Kaolin
Silica2Added as colloidal silica Ludox TM-40

An Advanced Cracking Evaluation (ACE) unit was used to simulate a commercial FCC process. The reaction was run two times with fresh catalyst to simulate two separate FCC reaction zones in parallel.

Prior to each experiment, the catalyst is loaded into the reactor and heated to the desired reaction temperature. N2 gas is fed through the feed injector from the bottom to keep catalyst particles fluidized. Once the catalyst bed temperature reaches within ±2° C. of the reaction temperature, the reaction can begin. Feed is then injected for a predetermined time (time-on-stream (TOS)). The desired catalyst-to-feed ratio is obtained by controlling the feed pump. The gaseous product is routed to the liquid receiver, where C5+ hydrocarbons are condensed and the remaining gases are routed to the gas receiver. After catalyst stripping is over, the reactor is heated to 700° C., and nitrogen was replaced with air to regenerate the catalyst. During regeneration, the released gas is routed to a CO2 analyzer. Coke yield is calculated from the flue gas flow rate and CO2 concentration. The above process was repeated for each of Examples 3(A) and 3(B). The weight ratio of catalyst to hydrocarbons was 8.

It should be understood that time-on-stream (TOS) is directly proportional to residence time.

The light stream from Example 1 was fed to the advanced cracking evaluation unit. A time-on-stream (TOS) of 75 seconds, a residence time of from 1 to 2 seconds, and a temperature of 675° C. was used.

The hydrotreated heavy stream from Example 2 was fed to the advanced cracking evaluation unit. A TOS of 75 seconds, a residence time of from 1 to 2 seconds, and a temperature of 645° C. was used. Characterization is shown in both Table 4 and Table 5.

The streams of Examples 3(A) and 3(B) were combined to form a single stream. The single stream simulates the output of processing a whole crude according to the methods of the present disclosure.

Example 3(Combined) is a weighted average of Examples 3(A) and 3(B). Example 3(A) represented 53 wt. % of Example 3(Combined). Example 3(B) represented 44 wt. % of Example 3 (Combined).

US11866659B1. Multi-zone catalytic cracking of crude oils (2024-01-09). Saudi Arabian Oil Company [SA]. Inventors: Mansour Ali Al-Herz [SA], Ali Al Jawad [SA], Qi Xu [SA], Aaron Akah [SA], Musaed Salem Al-Ghrami [SA].
Full text: Click here
Patent 2024
Adjustment Disorders Alkenes Arabs butylene Catalysis Clay Cocaine Distillation ethylene GAS6 protein, human Gravity Hutterite cerebroosteonephrodysplasia syndrome Hydrocarbons Kaolin Lanthanum Light Molar Neoplasm Metastasis Nitrogen Oxide, Aluminum Petroleum phosphoric anhydride Phosphorus Pressure propylene Regeneration Silicon Dioxide Simulate composite resin Sulfur Viscosity Vision Zeolites

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