Fast Decompression Research Articles

TERSE/PROLIX (TRPX) - a new algorithm for fast and lossless compression and decompression of diffraction and cryo-EM data.

High-throughput data collection in crystallography poses significant challenges in handling massive amounts of data. Here, TERSE/PROLIX (or TRPX for short) is presented, a novel lossless compression algorithm specifically designed for diffraction data. The algorithm is compared with established lossless compression algorithms implemented in gzip, bzip2, CBF (crystallographic binary file), Zstandard(zstd), LZ4 and HDF5 with gzip, LZF and bitshuffle+LZ4 filters, in terms of compression efficiency and speed, using continuous-rotation electron diffraction data of an inorganic compound and raw cryo-EM data. The results show that TRPX significantly outperforms all these algorithms in terms of speed and compression rate. It was 60 times faster than bzip2 (which achieved a similar compression rate), and more than 3 times faster than LZ4, which was the runner-up in terms of speed, but had a much worse compression rate. TRPX files are byte-order independent and upon compilation the algorithm occupies very little memory. It can therefore be readily implemented in hardware. By providing a tailored solution for diffraction and raw cryo-EM data, TRPX facilitates more efficient data analysis and interpretation while mitigating storage and transmission concerns. The C++20 compression/decompression code, custom TIFF library and an ImageJ/Fiji Java plugin for reading TRPX files are open-sourced on GitHub under the permissive MIT license.

BtrBlocks: Efficient Columnar Compression for Data Lakes

Analytics is moving to the cloud and data is moving into data lakes. These reside on object storage services like S3 and enable seamless data sharing and system interoperability. To support this, many systems build on open storage formats like Apache Parquet. However, these formats are not optimized for remotely-accessed data lakes and today's high-throughput networks. Inefficient decompression makes scans CPU-bound and thus increases query time and cost. With this work we present BtrBlocks, an open columnar storage format designed for data lakes. BtrBlocks uses a set of lightweight encoding schemes, achieving fast and efficient decompression and high compression ratios.

Enhancing genomic mutation data storage optimization based on the compression of asymmetry of sparsity.

Background: With the rapid development of high-throughput sequencing technology and the explosive growth of genomic data, storing, transmitting and processing massive amounts of data has become a new challenge. How to achieve fast lossless compression and decompression according to the characteristics of the data to speed up data transmission and processing requires research on relevant compression algorithms. Methods: In this paper, a compression algorithm for sparse asymmetric gene mutations (CA_SAGM) based on the characteristics of sparse genomic mutation data was proposed. The data was first sorted on a row-first basis so that neighboring non-zero elements were as close as possible to each other. The data were then renumbered using the reverse Cuthill-Mckee sorting technique. Finally the data were compressed into sparse row format (CSR) and stored. We had analyzed and compared the results of the CA_SAGM, coordinate format (COO) and compressed sparse column format (CSC) algorithms for sparse asymmetric genomic data. Nine types of single-nucleotide variation (SNV) data and six types of copy number variation (CNV) data from the TCGA database were used as the subjects of this study. Compression and decompression time, compression and decompression rate, compression memory and compression ratio were used as evaluation metrics. The correlation between each metric and the basic characteristics of the original data was further investigated. Results: The experimental results showed that the COO method had the shortest compression time, the fastest compression rate and the largest compression ratio, and had the best compression performance. CSC compression performance was the worst, and CA_SAGM compression performance was between the two. When decompressing the data, CA_SAGM performed the best, with the shortest decompression time and the fastest decompression rate. COO decompression performance was the worst. With increasing sparsity, the COO, CSC and CA_SAGM algorithms all exhibited longer compression and decompression times, lower compression and decompression rates, larger compression memory and lower compression ratios. When the sparsity was large, the compression memory and compression ratio of the three algorithms showed no difference characteristics, but the rest of the indexes were still different. Conclusion: CA_SAGM was an efficient compression algorithm that combines compression and decompression performance for sparse genomic mutation data.

Liquid respiratory desaturation is a new method of preventing decompression sickness

Introduction. According to the literature data, the method of liquid ventilation for the prevention of decompression sickness (DCS) was proposed only with the condition of its initiation before compression, that excluded the physical basis of the disease - an excess of metabolically indifferent gas in the tissues. However, as the analysis shows, in most cases, the evacuation of the crew of an emergency submarine is aggravated by being in gases’ increased pressure environment. So the casualty tissues become obviously saturated with indifferent gas. Experimental confirmation of the possibility of rapid tissues’ desaturation of nitrogen during respiration by denitrogenizated and oxygenated in a normal conditions respiratory fluid (hereinafter - the method of liquid respiratory desaturation) was obtained on the biological model of DCS of Syrian hamsters. The study aim is an experimental substantiation of the possibility to use liquid respiratory desaturation as a method of preventing the development of decompression disorders. Materials and methods. Scientists have performed a study on 24 mature male Syrian hamsters weighing 165-185g, aged four months, using an experimental laboratory hyperbaric stand for temporary maintenance of small laboratory animals under high pressure of a gas or liquid medium with the possibility of switching from one medium to another in isobaric conditions.The research methodology is based on the assessment of the clinical presentation of decompression disorders and the results of ultrasound examination of gas formations in the heart, large veins and liver after the fast non-stop decompression, in the background of preliminary saturation of the animal's body with indifferent gas (nitrogen) by staying in the air under the pressure 0.6 MPa (60 MWC) for six hours. The effect on experimental groups animals deferens from the control group by the period of immersion and spontaneous breathing in the respiratory fluid (20, 30 and 40 minutes) before decompression. Results. The authors analyzed the clinical picture of acute decompression disorders. The degree of gas formation in small laboratory animals was assessed by researchers using ultrasound using a semi-quantitative method. Spontaneous breathing with the prepared liquid, lasting 30 minutes or more, made it possible to remove excess nitrogen from the body of animals of experimental groups, providing etiopathogenetic prevention of DCS before decompression. The article presents the data of morphological studies. Conclusion. Liquid respiratory desaturation is a method of preventing decompression disorders based on the removal of metabolically indifferent gases from the body during liquid respiration, in the presence of a stress gradient from tissues into the respiratory fluid. The method allows the metabolically indifferent gases' rapid desaturation from the body by liquid ventilation before/or during decompression, thereby creating conditions of ultra-fast decompression modes without the risk of decompression disorders.

A novel method for measuring piezoelectric coefficients

This paper presents a novel method for directly measuring a material’s piezoelectric coefficients based on fast gas decompression. The measured output voltage and the speed of pressure change allow for the calculation of the piezoelectric coefficients. The method is simple, fast, reliable, and easy to apply. It has been used on quartz crystal, PZT ceramic, and antimony sulfoiodide single crystals, where d11 = 2.315(25) pC/N, d33 = 506(16) pC/N, and d31 = 339(16) pC/N were determined, respectively. These values are in good agreement with those reported in the literature. The physical basis of the method and experimental results recorded for different pressures are described.

CMIC: an efficient quality score compressor with random access functionality

BackgroundOver the past few decades, the emergence and maturation of new technologies have substantially reduced the cost of genome sequencing. As a result, the amount of genomic data that needs to be stored and transmitted has grown exponentially. For the standard sequencing data format, FASTQ, compression of the quality score is a key and difficult aspect of FASTQ file compression. Throughout the literature, we found that the majority of the current quality score compression methods do not support random access. Based on the above consideration, it is reasonable to investigate a lossless quality score compressor with a high compression rate, a fast compression and decompression speed, and support for random access.ResultsIn this paper, we propose CMIC, an adaptive and random access supported compressor for lossless compression of quality score sequences. CMIC is an acronym of the four steps (classification, mapping, indexing and compression) in the paper. Its framework consists of the following four parts: classification, mapping, indexing, and compression. The experimental results show that our compressor has good performance in terms of compression rates on all the tested datasets. The file sizes are reduced by up to 21.91% when compared with LCQS. In terms of compression speed, CMIC is better than all other compressors on most of the tested cases. In terms of random access speed, the CMIC is faster than the LCQS, which provides a random access function for compressed quality scores.ConclusionsCMIC is a compressor that is especially designed for quality score sequences, which has good performance in terms of compression rate, compression speed, decompression speed, and random access speed. The CMIC can be obtained in the following way: https://github.com/Humonex/Cmic.

Deep Learning Based Real-Time Semantic Segmentation of Cerebral Vessels and Cranial Nerves in Microvascular Decompression Scenes.

Automatic extraction of cerebral vessels and cranial nerves has important clinical value in the treatment of trigeminal neuralgia (TGN) and hemifacial spasm (HFS). However, because of the great similarity between different cerebral vessels and between different cranial nerves, it is challenging to segment cerebral vessels and cranial nerves in real time on the basis of true-color microvascular decompression (MVD) images. In this paper, we propose a lightweight, fast semantic segmentation Microvascular Decompression Network (MVDNet) for MVD scenarios which achieves a good trade-off between segmentation accuracy and speed. Specifically, we designed a Light Asymmetric Bottleneck (LAB) module in the encoder to encode context features. A Feature Fusion Module (FFM) was introduced into the decoder to effectively combine high-level semantic features and underlying spatial details. The proposed network has no pretrained model, fewer parameters, and a fast inference speed. Specifically, MVDNet achieved 76.59% mIoU on the MVD test set, has 0.72 M parameters, and has a 137 FPS speed using a single GTX 2080Ti card.

Pressure-induced structural transformation of clathrate Ge136 via ultrafast recrystallization of an amorphous intermediate

We study the pressure-induced structural transformation of Ge$_{136}$ clathrate by ab initio molecular dynamics and metadynamics. The system under pressure first undergoes amorphization followed by an ultrafast recrystallization to the $\beta$-tin structure on the time scale of 30 ps. The initial pressure-induced amorphization of clathrate is triggered by high pressure while the subsequent fast recrystallization to $\beta$-tin is driven by low temperature. Interestingly, the amorphous intermediate is still diffusive even at room temperature, in spite of very strong undercooling, making the ultrafast recrystallization possible. The system provides an explicit example of structural transformation between two crystalline phases proceeding via non-crystalline intermediate. Upon fast decompression of the amorphous structure with incipient crystalline order the recrystallization is blocked and the system instead proceeds to the tetrahedral LDA amorphous phase.

Supercritical Foaming and Impregnation of Polycaprolactone and Polycaprolactone-Hydroxyapatite Composites with Carvacrol

Polycaprolactone (PCL) and polycaprolactone-hydroxyapatite (PCL-HA) scaffolds were produced by foaming in supercritical carbon dioxide (scCO2) at 20 MPa, as well as in one-step foaming and impregnation process using carvacrol as an antibacterial agent with proven activity against Gram-positive and Gram-negative bacteria. The experimental design was developed to study the influence of temperature (40 °C and 50 °C), HA content (10 and 20 wt.%), and depressurization rate (one and two-step decompression) on the foams’ morphology, porosity, pore size distribution, and carvacrol impregnation yield. The characterization of the foams was carried out using scanning electron microscopy (SEM, SEM-FIB), Gay-Lussac density bottle measurements, and Fourier–transform infrared (FTIR) analyses. The obtained results demonstrate that processing PCL and PCL-HA scaffolds by means of scCO2 foaming enables preparing foams with porosity in the range of 65.55–74.39% and 61.98–67.13%, at 40 °C and 50 °C, respectively. The presence of carvacrol led to a lower porosity. At 40 °C and one-step decompression at a slow rate, the porosity of impregnated scaffolds was higher than at 50 °C and two- step fast decompression. However, a narrower pore size distribution was obtained at the last processing conditions. PCL scaffolds with HA resulted in higher carvacrol impregnation yields than neat PCL foams. The highest carvacrol loading (10.57%) was observed in the scaffold with 10 wt.% HA obtained at 50 °C.

FASTAFS: file system virtualisation of random access compressed FASTA files

BackgroundThe FASTA file format, used to store polymeric sequence data, has become a bioinformatics file standard used for decades. The relatively large files require additional files, beyond the scope of the original format, to identify sequences and to provide random access. Multiple compressors have been developed to archive FASTA files back and forth, but these lack direct access to targeted content or metadata of the archive. Moreover, these solutions are not directly backwards compatible to FASTA files, resulting in limited software integration.ResultsWe designed a linux based toolkit that virtualises the content of DNA, RNA and protein FASTA archives into the filesystem by using filesystem in userspace. This guarantees in-sync virtualised metadata files and offers fast random-access decompression using bit encodings plus Zstandard (zstd). The toolkit, FASTAFS, can track all its system-wide running instances, allows file integrity verification and can provide, instantly, scriptable access to sequence files and is easy to use and deploy. The file compression ratios were comparable but not superior to other state of the art archival tools, despite the innovative random access feature implemented in FASTAFS.ConclusionsFASTAFS is a user-friendly and easy to deploy backwards compatible generic purpose solution to store and access compressed FASTA files, since it offers file system access to FASTA files as well as in-sync metadata files through file virtualisation. Using virtual filesystems as in-between layer offers format conversion without the need to rewrite code into different programming languages while preserving compatibility.

Diffusiophoresis driven colloidal manipulation and shortcuts to adiabaticity

While compressing a colloidal state by optical means alone has been previously achieved through a specific time-dependence of the trap stiffness, realizing quickly the reverse transformation stumbles upon the necessity of a transiently expulsive trap. To circumvent this difficulty, we propose to drive the colloids by a combination of optical trapping and diffusiophoretic forces, both time-dependent. Forcing via diffusiophoresis is enforced by controlling the salt concentration at the boundary of the domain where the colloids are confined. The method takes advantage of the separation of time scales between salt and colloidal dynamics, and realizes a fast decompression in an optical trap that remains confining at all times. We thereby obtain a so-called shortcut to adiabaticity protocol where colloidal dynamics, enslaved to salt dynamics, can nevertheless be controlled as desired.

Fast Hyperspectral Image Encoder Based on Supervised Multimodal Scheme

Many compression methods, lossy or lossless, were developed for 3D hyperspectral images, and various standards have emerged and applied to these amounts of data in order to achieve the best rate-distortion performance. However, high-dimensional data volume of hyperspectal images is problematic for compression and decompression time. Nowadays, fast compression and especially fast decompression algorithms are of primary importance in image data applications. In this case, we present a lossy hyperspectral image compression based on supervised multimodal scheme in order to improve the compression results. The supervised multimodal method is used to reduce the amount of data before their compression with the 3D-SPIHT encoder based on 3D wavelet transform. The performance of the Supervised Multimodal Compression (SMC-3D-SPIHT encoder) has been evaluated on AVIRIS hyperspectral images. Experimental results indicate that the proposed algorithm provides very promising performance at low bit-rates while reducing the encoding/decoding time.

Shear zone cooling and fabrics of synkinematic plutons evidence timing and rates of orogenic exhumation in the northwest Borborema Province (NE Brazil)

Ediacaran convergence and collision resulting from amalgamation of West Gondwana are documented in the Borborema Province by high-pressure rock units, contractional tectonics and anatexis. Thermochronological (zircon U-Pb and amphibole-biotite Ar-Ar) and structural (Anisotropy of Magnetic Susceptibility) constraints from shear zone-bounding synkinematic plutons in the Ceará Central Domain provide timing and rates of their subsequent post-collisional evolution. Our results show that: (i) U-Pb ages of zircons of 585–571 Ma record magma crystallisation and a protracted history of assembly for the Tauá batholith, synchronous with deformation in the bounding transcurrent shear zone junction; (ii) AMS fabrics document chamber construction processes and the effect of long-lived strongly localized shear zone deformation; and (iii) 40Ar/39Ar plateau ages of amphibole and biotite from the synkinematic plutons at 577–562 and 559–554 Ma, respectively, yield cooling rates of 20–40 °C/Myr characterising differential cooling paths. Integration of various thermochronometers available for the strike-slip shear zones and the internal high-pressure domain reveals a fast isothermal decompression (long-term unroofing rate of 1.9–5.8 mm/yr), which exhumed high-pressure rock units. Subsequently, fast nearly isobaric cooling (20–40 °C/Myr) occurred in the whole terrane until 590 Ma, with temperatures falling below 320 °C. Due to enhanced magmatic activity during the deformation, the shear zones experienced much higher temperatures at that same depth at 584 Ma followed by fast cooling (20–40 °C/Myr) to temperatures below 320 °C at 560 Ma. These final cooling episodes were accompanied by slow unroofing at an estimated rate of 0.3–0.9 mm/yr, sufficient to bring these rocks close to the surface at 540 Ma, when molassic, pull-apart basins were formed.

Gas‐Pyroclast Motions in Volcanic Conduits During Strombolian Eruptions, in Light of Shock Tube Experiments

AbstractIn a Strombolian volcanic eruption, bursting of a pressurized gas pocket accelerates a mixture of gas and pyroclasts along a conduit and out of a vent. While mixture ejection at the vent is the subject of direct geophysical measurements, and a key to eruption understanding, the dynamics of how the mixture moves in the conduit are not observable and only partly understood. Here, we use analog, transparent shock tube experiments to study the dynamics of gas and particles under fast gas decompression in a vertical tube. Maximum particle exit velocity increases linearly with increasing energy (pressure times volume) of the pressurized gas and, subordinately, with decreasing particle size and depth in the tube. Particles, initially at rest, are at first accelerated and dispersed in the conduit by the expanding gas. When the gas decelerates or even reverses its motion due to pressure changes in the tube, the particles, moving under their inertia, are then decelerated by the gas drag. Deceleration lasts longer for lower initial gas energy and for deeper particle starting position. Experiments and eruptions share two key vent ejection features: (1) particles exit the vent already decelerating, and (2) the exit velocity of the particles decays over time following the same nonlinear law. Friction with slower or even backflowing gas likely causes pyroclast deceleration in volcanic conduits during Strombolian explosions. Pyroclast deceleration, in turn, affects their exit velocity at the vent, as well as estimates of the explosion source depth based on temporal changes in exit velocity.

LCQS: an efficient lossless compression tool of quality scores with random access functionality

BackgroundAdvanced sequencing machines dramatically speed up the generation of genomic data, which makes the demand of efficient compression of sequencing data extremely urgent and significant. As the most difficult part of the standard sequencing data format FASTQ, compression of the quality score has become a conundrum in the development of FASTQ compression. Existing lossless compressors of quality scores mainly utilize specific patterns generated by specific sequencer and complex context modeling techniques to solve the problem of low compression ratio. However, the main drawbacks of these compressors are the problem of weak robustness which means unstable or even unavailable results of sequencing files and the problem of slow compression speed. Meanwhile, some compressors attempt to construct a fine-grained index structure to solve the problem of slow random access decompression speed. However, they solve the problem at the sacrifice of compression speed and at the expense of large index files, which makes them inefficient and impractical. Therefore, an efficient lossless compressor of quality scores with strong robustness, high compression ratio, fast compression and random access decompression speed is urgently needed and of great significance.ResultsIn this paper, based on the idea of maximizing the use of hardware resources, LCQS, a lossless compression tool specialized for quality scores, was proposed. It consists of four sequential processing steps: partitioning, indexing, packing and parallelizing. Experimental results reveal that LCQS outperforms all the other state-of-the-art compressors on all criteria except for the compression speed on the dataset SRR1284073. Furthermore, LCQS presents strong robustness on all the test datasets, with its acceleration ratios of compression speed increasing by up to 29.1x, its file size reducing by up to 28.78%, and its random access decompression speed increasing by up to 2.1x. Additionally, LCQS also exhibits strong scalability. That is, the compression speed increases almost linearly as the size of input dataset increases.ConclusionThe ability to handle all different kinds of quality scores and superiority in compression ratio and compression speed make LCQS a high-efficient and advanced lossless quality score compressor, along with its strength of fast random access decompression. Our tool LCQS can be downloaded from https://github.com/SCUT-CCNL/LCQSand freely available for non-commercial usage.

Compressed linear algebra for declarative large-scale machine learning

Large-scale Machine Learning (ML) algorithms are often iterative, using repeated read-only data access and I/O-bound matrix-vector multiplications. Hence, it is crucial for performance to fit the data into single-node or distributed main memory to enable fast matrix-vector operations. General-purpose compression struggles to achieve both good compression ratios and fast decompression for block-wise uncompressed operations. Therefore, we introduce Compressed Linear Algebra (CLA) for lossless matrix compression. CLA encodes matrices with lightweight, value-based compression techniques and executes linear algebra operations directly on the compressed representations. We contribute effective column compression schemes, cache-conscious operations, and an efficient sampling-based compression algorithm. Our experiments show good compression ratios and operations performance close to the uncompressed case, which enables fitting larger datasets into available memory. We thereby obtain significant end-to-end performance improvements.

Preliminary results of a novel pure endoscopic procedure in the treatment of degenerative lumbar spinal disorders: double endoscopic technique.

With increased experience and the availability of new technical instrumentations, the surgical endoscopic indications for lumbar spinal pathologies have moved from simple prolapsed disk to canal stenosis. The available endoscopes come in two different sizes (10 mm and 6.3 mm in diameter); however, one is too bulky to use inside the spinal canal and the other is too small to achieve a fast bone decompression. In order to overcome such problems, we developed and used a different surgical technique called: double endoscopic technique. Using this approach, we operated and prospectively collected clinical information on 17 patients (Group A) suffering from a mixed (ligament-bone hypertrophy and prolapsed disk) single segmental lumbar canal stenosis. At a median of 13 months from surgery, all the patients in this group had a very good outcome with an improvement of the VAS and ODI. These clinical results were compared with those from another group of patients who had undergone surgery in the same unit but using standard MIS technique (Group B). Both groups were similar in terms of number, age, symptoms and stenosis location. We compared the pre- and postoperative VAS and ODI values, the amount of postoperative pain killers used during the first week postsurgery, the length of in-hospital stays as well as the blood loss during surgery. Although our aim was only to present a novel surgical endoscopic technique, the results, with all the study limitations including small numbers and short follow-up, have shown that this procedure is safe and effective, yielding an outcome comparable to the standard MIS approach. Furthermore, it is less disruptive towards the involved anatomy, it gives less postoperative pain, it requires a smaller skin incision, and the blood loss is negligible. Thus, this technique may guarantee a faster clinical recovery.

Nucleation stage of multicomponent bubbles of gases dissolved in a decompressed liquid

A new kinetic analysis of degassing and swelling of a decompressed liquid solution with several dissolved gases has been presented. The analysis has been performed for the nucleation stage of formation and growth of supercritical gas bubbles in a closed system under conditions of a limited availability of the dissolved species. The nucleation stage is an important stage of degassing, on which a certain size distribution of gas bubbles is formed, being the starting point for further growth. This stage starts with the appearance of supercritical gas bubbles and is widely completed when the nucleation rate of supercritical gas bubbles diminishes by a decimal order. Neglecting the role of the Laplace pressure in large supercritical bubbles, we were able to introduce the concept of total gas supersaturation and to develop a theory of this stage for liquid solutions with arbitrary number and any values of supersaturations and solubilities of the dissolved gases. First, we have considered slowly growing bubbles within the mean-field approach assuming a stationary diffusion of gases to bubbles at moderate total gas supersaturation. In the case of large total gas supersaturation, we have built a description of fast growing bubbles on the basis of the extended excluded volume approach with nonstationary nonuniform diffusion shells around the bubbles and mean-field mixing of the concentration of gases at the external boundaries of the shells. A main novel feature of the developed theory is its ability to predict the kinetic behavior of the whole ensemble of bubbles with different sizes under changes in the initial gas composition in the liquid solution at its fast decompression. It has been shown that the effects of nonstationary diffusion may be very significant in the growth of multicomponent bubbles and, in particular, are responsible for a significant swelling of a decompressed liquid solution. Distribution of supercritical bubbles in sizes as a function of concentrations of solute gases at any moment of the nucleation stage, the duration of the nucleation stage, and the swelling ratio at the end of the nucleation stage have been determined.

Optimization of core retrieval using a Thermo-Poro-Elastic (T-P-E) approach

One most common cause of damage of the recovered cores occurs during their fast decompression from the bottomhole to the surface. This occurs as sufficient time is not allowed for the pore fluids in the center of the core to dissipate than in the annulus. As a result, excessive pore pressure difference and stresses are induced in the core body. This may cause tensile failure which shows itself as microfractures in its body. These microfractures adversely alter the core rock and mechanical properties.Therefore, the sample should be retrieved/tripped slowly enough so that the induced pore pressure and stress difference do not become excessive and the core does not undergo tensile failure. On the other hand, this slow enough retrieval rate should meet the operational rig costs so that it does not cause invisible lost time. Therefore, the optimal tripping rate should be determined for each case. This should be used as the basis of coring method/tool candidate selection. The industry has so far utilized only generic methods for selecting their core tripping schedules and thus their coring methods (used for coring tool candidate selection). Just recently, there has been some research in this regard which failed to consider the thermal, mechanical, and mud cake effects, they did not also evaluate the induced stresses and the optimal rates.Therefore, in this work, a state-of-the-art T-P-E model is developed and applied to evaluate the optimal tripping rates. This work includes: 1) the modeling, derivation, and evaluation of the hydraulic and thermal effects including the neglected ones in the literature, i.e., the thermal, mud cake, and the mechanical properties, 2) summing-up of all the effects to produce the induced stresses, 3) comparing the induced stresses with the tensile strength, 4) indicating whether tensile failure occurs for a specified tripping rate, and 5) repeating the trial and error process for different tripping rates until the optimal rate can be obtained. Therefore, in this work, a standard procedure is proposed to optimize the retrieval rate by requesting a standard set of inputs and running the model for different tripping rates.In addition, during the modeling process, the contributing parameters have been identified. Having found the contributing parameters, using rig site data including the cuttings analysis (which is used to estimate several input parameters), it is not possible to find the value of the hydraulic diffusivity with certainty. So far, the magnitude of the tripping rate (finding the optimal value of which is the objective of the work) has been controlled just arbitrarily by the drilling crew. Therefore, these two parameters have been introduced as the main uncertain parameters and thus the sensitivity analyses of their effects have been investigated. Using this analysis, some extremes for tripping rates have been introduced, which can be used as a general engineered guideline for coring tool/method candidate selection.

Compression and Conditional Emulation of Climate Model Output

ABSTRACTNumerical climate model simulations run at high spatial and temporal resolutions generate massive quantities of data. As our computing capabilities continue to increase, storing all of the data is not sustainable, and thus it is important to develop methods for representing the full datasets by smaller compressed versions. We propose a statistical compression and decompression algorithm based on storing a set of summary statistics as well as a statistical model describing the conditional distribution of the full dataset given the summary statistics. We decompress the data by computing conditional expectations and conditional simulations from the model given the summary statistics. Conditional expectations represent our best estimate of the original data but are subject to oversmoothing in space and time. Conditional simulations introduce realistic small-scale noise so that the decompressed fields are neither too smooth nor too rough compared with the original data. Considerable attention is paid to accurately modeling the original dataset—1 year of daily mean temperature data—particularly with regard to the inherent spatial nonstationarity in global fields, and to determining the statistics to be stored, so that the variation in the original data can be closely captured, while allowing for fast decompression and conditional emulation on modest computers. Supplementary materials for this article are available online.