Boris Dimitrov - Academia.edu (original) (raw)

Papers by Boris Dimitrov

SummaryThe Metagenomic Intra-Species Diversity Analysis System (MIDAS) is a scalable metagenomic ... more SummaryThe Metagenomic Intra-Species Diversity Analysis System (MIDAS) is a scalable metagenomic pipeline that identifies single nucleotide variants (SNVs) and gene copy number variants (CNVs) in microbial populations. Here, we present MIDAS2, which addresses the computational challenges presented by increasingly large reference genome databases, while adding functionality for building custom databases and leveraging paired-end reads to improve SNV accuracy. This fast and scalable reengineering of the MIDAS pipeline enables thousands of metagenomic samples to be efficiently genotyped.Availability and ImplementationThe source code is available at https://github.com/czbiohub/MIDAS2. The documentation is available at https://midas2.readthedocs.io/en/latest/.Supplementary InformationSupplementary data are available at Bioinformatics online.

Nature Biotechnology, 2021

Sequence variation is used to quantify population structure and identify genetic determinants of ... more Sequence variation is used to quantify population structure and identify genetic determinants of phenotypes that vary within species. In the human microbiome and other environments, single nucleotide polymorphisms (SNPs) are frequently detected by aligning metagenomic sequencing reads to catalogs of genes or genomes. But this requires high-performance computing and enough read coverage to distinguish SNPs from sequencing errors. We solved these problems by developing the GenoTyper for Prokaytotes (GT-Pro), a suite of novel methods to catalog SNPs from genomes and use exact k-mer matches to perform ultra-fast reference-based SNP calling from metagenomes. Compared to read alignment, GT-Pro is more accurate and two orders of magnitude faster. We discovered 104 million SNPs in 909 human gut species, characterized their global population structure, and tracked pathogenic strains. GT-Pro democratizes strain-level microbiome analysis by making it possible to genotype hundreds of metagenomes on a personal computer.

Despite progress in the treatment of acute lymphoblastic leukemia (ALL), T-cell ALL (T-ALL) has l... more Despite progress in the treatment of acute lymphoblastic leukemia (ALL), T-cell ALL (T-ALL) has limited treatment options particularly in the setting of relapsed/refractory disease. Using an unbiased genome-scale CRISPR-Cas9 screen we sought to identify pathway dependencies for T-ALL which could be harnessed for therapy development. Disruption of the one-carbon folate, purine and pyrimidine pathways scored as the top metabolic pathways required for T-ALL proliferation. We used a recently developed inhibitor of SHMT1 and SHMT2, RZ-2994, to characterize the effect of inhibiting these enzymes of the one-carbon folate pathway in T-ALL and found that T-ALL cell lines were differentially sensitive to RZ-2994, with a S/G2 cell cycle arrest. The effects of SHMT1/2 inhibition were rescued by formate supplementation. Loss of both SHMT1 and SHMT2 was necessary for impaired growth and cell cycle arrest, with suppression of both SHMT1 and SHMT2 impairing leukemia progressionin vivo. RZ-2994 decr...

Lecture Notes in Computer Science, 1997

We describe three contributions for distributed resource allocation in scienti c applications. Fi... more We describe three contributions for distributed resource allocation in scienti c applications. First, we present an abstract model in which di erent resources are represented as tokens of di erent colors processes acquire resources by acquiring these tokens. Second, we present distributed scheduling algorithms that allow m ultiple resource managers to determine custom policies to control allocation of the tokens representing their particular resources. These algorithms allow m ultiple resource managers, each with its own resource management policy, to collaborate in providing resources for the whole system. Third, we present a n i mplementation of a distributed resource scheduling algorithm framework using our abstract model. This implementation uses Infospheres, which are Internet communication packages written in Java, and shows the bene ts of distributing the task of resource allocation to multiple resource managers. Hierarchical session infrastructure.

Tribology of Abrasive Machining Processes, 2013

Chapter 13 describes a range of loose abrasive processes. Two main processes of lapping and polis... more Chapter 13 describes a range of loose abrasive processes. Two main processes of lapping and polishing are mainly employed in high-precision finishing. Typical examples of various components used in aerospace, automotive, mechanical seals, fluid handling, and many other precision engineering industries are furnished. Advanced abrasive powders often of nanometer sizes are used. Because the abrasives are often of submicron size for ultraprecision processing, the term nanotechnology may be employed. These types of operations are capable of producing fine finishes on both ductile and brittle materials. The relative speeds in lapping and polishing are much lower than in grinding. Consequently, the concentration of energy in the contact area is much lower. The benefit is that average temperatures tend to be lower than in grinding and may be negligible; the disadvantage is that specific energy is higher, although the volumes of material to be removed are small. Types of abrasives and differences between two- and three-body abrasion are discussed. Also discussed are the nature of lapping and polishing tools and process fluids and fluid delivery. References are given to previous work on loose abrasive processes.

Tribology of Abrasive Machining Processes, 2013

This chapter introduces and reviews abrasive processes assisted by electrolytic in-process dressi... more This chapter introduces and reviews abrasive processes assisted by electrolytic in-process dressing (ELID) techniques first introduced by Hitoshi Ohmori in 1990. This in situ dressing method is used for metal-bond wheels and is relatively new. This technique is highly successful for fine grain wheels efficiently used to obtain very low surface roughness, and when hard ceramics have to be machined using a very small grain cutting depth in order to avoid failure by cracking. The basic system, principles, and characteristics of ELID abrasion mechanisms are introduced first. Electrical, mechanical and chemical aspects of the process are described. The success and wide application of ELID principles to ceramic grinding are explained. Fourteen applications of the ELID principle to modern abrasive processes are documented to illustrate the scope of application. It is shown how super-finishes can be achieved and greatly increase removal rates through the application of ELID dressing, grinding and polishing processes.

Tribology of Abrasive Machining Processes, 2013

A kinematic analysis defines relationships between removal rate and penetration of the abrasive g... more A kinematic analysis defines relationships between removal rate and penetration of the abrasive grains into the workpiece for the various abrasive machining processes. A kinematic study is an essential precondition for the design of an abrasive machining system. The kinematic process design governs the stresses imposed on the individual grains of the abrasive, which must be neither too small nor too large. Commencing with the speeds and motions of the tool and workpiece, a kinematic analysis proceeds to the physical consequences of the distribution of the cutting edges. This chapter provides measures for the size, duration of contact, and scale of the minute interactions, which take place in the abrasive process. Penetration depth, the length of contact between an abrasive grain and a workpiece, the implications of grain size, grain speed and grain trajectory for grain forces, grain wear, and workpiece roughness are considered. Study of the scale of the grain–workpiece interactions underpins all aspects of abrasive machine process behavior and the tribology of the process. Cutting edge density is analyzed including implications of the stochastic nature of abrasive processes and effects of dressing. A key feature of kinematic analysis is to relate the thickness, width and length of typical grain penetrations to depth of cut and machine variables, such as workspeed and abrasive speed. References are provided to previous work.

Tribology of Abrasive Machining Processes, 2013

Chapter 14 describes the performance of desktop machine tools developed for submicron machining. ... more Chapter 14 describes the performance of desktop machine tools developed for submicron machining. The emphasis is primarily on accuracies that have been achieved and, in particular, the potential for improved productivity and accuracy using the ELID grinding process described in Chapter 12 . Using the ELID process allows the operations to be speeded up and sometimes allows slower polishing processes to be eliminated from a sequence of operations. Typical desktop machine tools developed at Riken include a slicing machine, a lapping machine, a micro-cutting and grinding machine, an injection molding machine, a micro-tool processing machine, and so on. The development of the desktop machine tools was undertaken to meet the individual requirements of particular machines. Aspects of research and development of the desktop machine tool processes and their achievements are described.

Tribology of Abrasive Machining Processes, 2013

Chapter 11 describes the operations to prepare and condition abrasive tools for effective machini... more Chapter 11 describes the operations to prepare and condition abrasive tools for effective machining. First, there is wheel truing to achieve the required precision form of the wheel. Then there is wheel dressing to achieve and to maintain an efficient cutting surface on the grinding wheel . These two distinct conditioning operations are sometimes combined as one. Preparation of grinding wheels also includes ringing to check the integrity of a new abrasive wheel, safe mounting of the abrasive wheel to avoid stress concentrations, and wheel balancing for safety and for effective grinding. Dynamic balancing is also required for high speeds. Other aspects described include cleaning up the wheel surface to remove loading, effects of dressing on grinding performance, self-dressing processes, wheel glazing, and types of grain fracture. Types of dressing tools and their characteristics are described including single-stone, multi-stone, and diamond roll dressers and crush dressers leading to conditioning of super-abrasive wheels. Unconventional dressing methods employed for metal-bond wheels include electrical discharge dressing (EDD) and electrolytic in-process dressing (ELID). A further possibility being researched includes laser dressing. Wear progression of dressing tools is discussed. References are given to previous work on truing and dressing techniques.

Tribology of Abrasive Machining Processes, 2013

This chapter introduces typical requirements for energy in modern grinding and other abrasive mac... more This chapter introduces typical requirements for energy in modern grinding and other abrasive machining processes explaining the relationship between machining forces and machining power. Specific energy is introduced as the basic measure of energy required and its use as the basic tool in system design. The rate at which the material can be removed is related to the maximum power available and the ability to usefully employ the power. Accuracy and deflections depend on the machining forces and machine stiffness. Examples of typical work-materials and their grinding conditions including the effect of lubricants are given. Force ratio is introduced as a measure of grain sharpness. Size effect is introduced where specific energy reduces as material removal rates are increased. The size effect is related to equivalent chip thickness. It is also shown that a more detailed understanding can be achieved through the sliced bread analogy, which demonstrates that the energy requirement is related to the extent of new surface area created. Effects of cutting, plowing, and rubbing are analyzed leading to consideration of grain sharpness, wear, and dressing conditions. The latter part of the chapter considers the development of the study of abrasion mechanics and techniques for theoretical modeling. Finally, the chapter describes process limit charts, process optimization, and effects of wheelspeed with practical examples and references.

Tribology of Abrasive Machining Processes, 2004

This chapter focuses on loose abrasive processes that are mainly employed in high-precision finis... more This chapter focuses on loose abrasive processes that are mainly employed in high-precision finishing processes used to generate surfaces of desired characteristics. Abrasive finishing processes are accepted in a wide range of material applications and industries. Advanced abrasive powders available in nanometer sizes are used in a variety of processes including loose abrasives (lapping, polishing), bonded abrasives (grinding wheels), and coated abrasives. Lapping is used primarily to improve form accuracy rather than to reduce surface roughness. The relative speeds in lapping and polishing are much lower than in grinding. Wear is the gradual material removal from a surface due to a mechanical movement and/or chemical process. The common classification of abrasive wear is divided into categories of two-body abrasion and three-body abrasion. Polishing is used as a surface-smoothing operation that mainly consists of removing or smoothing out grinding or lapping lines, scratches, and other surface defects in order to decrease the surface roughness. Chemo-mechanical polishing (CMP) has become an indispensable process for finishing hard, brittle materials for optical, electronic, and structural applications.

Tribology of Abrasive Machining Processes, 2004

Materials used as abrasives include both natural minerals and synthetic products. Abrasive grains... more Materials used as abrasives include both natural minerals and synthetic products. Abrasive grains can be considered as randomly shaped cutting tools characterized by high hardness, sharp edges, and good cutting ability. This chapter discusses the nature of common abrasives and machining characteristics. Standard methods of specifying abrasive wheels are described. Conventional abrasives are described including silicon carbide, aluminium oxide, and garnet. Two superabrasives described include diamond and cubic boron nitride. Abrasives and new abrasive grain developments are discussed in some detail including grains produced by sol gel and related processes. The requirements of an abrasive are discussed in relation to application. Various selection criteria apply depending on workpiece material, work geometry, grinding fluid and removal conditions. The structure of abrasives is discussed and the nature of abrasive tools including types of wheel bonds. Bonded structures include vitrified bonds, organic bonds, and for super-abrasives single layer bonds and metal bonds. Essential calculations methods are provided for the design of grinding wheels. Coated abrasives and abrasive belts are also discussed. References are provided to previous work including a range of abrasive manufacturers.

Tribology of Abrasive Machining Processes, 2004

ABSTRACT To meet the continuously rising demands for high accuracy and high quality products, abr... more ABSTRACT To meet the continuously rising demands for high accuracy and high quality products, abrasive processes like grinding and polishing are playing an important role as finishing processes in manufacturing. However, as abrasive processes are very complex, with a large number of characteristic parameters that influence each other, reproducibility of machining accuracy and quality are the most significant factors for the application of such processes. In order to fulfill the demands, set-up parameters are commonly determined by machining tests that are both time consuming and costly. Consequently, the process quality depends extensively on the experience of the operator.[1][2]

Tribology of Abrasive Machining Processes, 2004

Tribology of Abrasive Machining Processes, 2013

This chapter discusses the size of the contact area between a grinding wheel and a workpiece, tak... more This chapter discusses the size of the contact area between a grinding wheel and a workpiece, taking into account the contact stresses between the grains and the workpiece. Consideration is given to mainly elastic effects of the contact stresses between the grains and the workpiece. The interactions of individual grains with the workpiece causes repeated compressive and tensile loading of the workpiece. The tensile stresses can cause crack propogation in brittle crack-sensitive materials. Elastic deflections of the grinding wheel and workpiece greatly increase the contact length of the grinding zone. It reduces the maximum temperature for a particular grinding force, it reduces the surface roughness, it reduces the fracture wear of the grains, and it increases the dulling wear of the grains. The contact length is further increased with the use of the grinding fluid, which reduces the maximum temperature experienced. There is evidence that elastic deflections in the contact region can help to stabilize the grinding process against self-excited vibrations, although it is important to maximize dynamic stiffnesses to avoid large vibration amplitudes, and irregular wear of the grinding wheel with consequent poor workpiece quality.

Nature Biotechnology, 2021

Lecture Notes in Computer Science, 1997

Tribology of Abrasive Machining Processes, 2013

Tribology of Abrasive Machining Processes, 2004

Tribology of Abrasive Machining Processes, 2013