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De novo assembly is a widely used methodology in bioinformatics. However, the conventional short-readbased de novo assembly is incapable of reliably reconstructing the large-scale structures of human genomes. Recently, a novel optical label-based technology has enabled reliable large-scale de novo assembly. Despite its advantage in large-scale genome analysis, this new technology requires a more computationally intensive alignment algorithm than its conventional counterpart. For example, the runtime of reconstructing a human genome is on the order of 10,000 hours on a sequential CPU. Therefore, in order to practically apply this new technology in genome research, accelerated approaches are desirable. In this article, we present three different accelerated approaches, multicore CPU, GPU, and FPGA. Against the sequential software baseline, our multicore CPU design achieved an 8.4× speedup, while the GPU and FPGA designs achieved 13.6× and 115× speedups, respectively. We also discuss the details of the design space exploration of this new assembly algorithm on these three different devices. Finally, we compare these devices in performance, optimization techniques, prices, and design efforts.

Cerium oxide (ceria, CeO2) is frequently used as a standard in applications such as synchrotron and x-ray free electron lasers for calibrating x-ray wavelengths and offers the potential for understanding the high pressure properties and deformation mechanisms in a wide range of similar face centered cubic (fcc) materials. In this study, the pressure dependence of the strength of ceria was investigated up to 38 GPa using angle dispersive x-ray diffraction in a radial geometry in a diamond anvil cell. In this experiment, the difference in the stress along the axis of compression and perpendicular to the direction of compression can be determined, giving a quantity known as the differential stress. It was found that the differential stress (t), a measure of the lower bound for yield strength, initially increases rapidly from 0.35 ± 0.06 GPa to 2.2 ± 0.4 GPa at pressures of 1.8 and 3.8 GPa, respectively. Above 4 GPa, t increases more slowly to 13.8 ± 2.6 GPa at a pressure of 38 GPa. The changes in the preferred orientation (texture) of CeO2 with pressure were also measured, allowing for the determination of active deformation mechanisms using an elasto-viscoplastic self-consistent model (EVPSC). It was found that as pressure increased, the [001] direction had a slight preferred orientation along the axis of compression. Our EVPSC model of experimental fiber (cylindrically symmetric) textures and lattice strains were most consistent with dominant slip activity along { 111 } ⟨ 1 1 ¯ 0 ⟩. [ABSTRACT FROM AUTHOR]

HFO-1234ze (E) is proposed as a near zero global warming propellant for use in metered dose inhaled (MDI) products. This paper describes the non-clinical safety assessment in mice, rats, and dogs and supplements previously reported data (genetic toxicology, short-term toxicology, and reproductive toxicology). In all species, HFO-1234ze (E) was only detectable in blood for a short period after dosing with no evidence of accumulation. HFO-1234ze (E) was without any toxicological effects at very high doses in subchronic (13-week mouse) and chronic (39-week dog) studies. Chronic (26-week) administration to rats at very high doses was associated with an exacerbation of rodent progressive cardiomyopathy, a well-documented background finding in rodents. In a 2-generation study, extremely high doses were associated with the early euthanasia of some lactating female rats. This finding was considered to be significantly influenced by a state of negative energy balance, reflecting the specific vulnerability of rats during lactation. These findings are considered to not pose a risk to humans with typical MDI use given they occurred at doses which far exceed those expected in patients. Overall, the nonclinical safety data for HFO-1234ze (E) support its further development as an MDI propellant. [ABSTRACT FROM AUTHOR]

The Society of Toxicologic Pathology's Scientific and Regulatory Policy Committee formed a working group to consider the present and future use of digital pathology in toxicologic pathology in general and specifically its use in primary evaluation and peer review in Good Laboratory Practice (GLP) environments. Digital histopathology systems can save costs by reducing travel, enhancing organizational flexibility, decreasing slide handling, improving collaboration, increasing access to historical images, and improving quality and efficiency through integration with laboratory information management systems. However, the resources to implement and operate a digital pathology system can be significant. Given the magnitude and risks involved in the decision to adopt digital histopathology, this working group used pertinent previously published survey results and its members' expertise to create a Points-to-Consider article to assist organizations with building and implementing digital pathology workflows. With the aim of providing a comprehensive perspective, the current publication summarizes aspects of digital whole-slide imaging relevant to nonclinical histopathology evaluations, and then presents points to consider applicable to both primary digital histopathology evaluation and digital peer review in GLP toxicology studies. The Supplemental Appendices provide additional tabulated resources. [ABSTRACT FROM AUTHOR]

Histopathologic evaluation and peer review using digital whole-slide images (WSIs) is a relatively new medium for assessing nonclinical toxicology studies in Good Laboratory Practice (GLP) environments. To better understand the present and future use of digital pathology in nonclinical toxicology studies, the Society of Toxicologic Pathology (STP) formed a working group to survey STP members with the goal of creating recommendations for implementation. The survey was administered in December 2019, immediately before the COVID-19 pandemic, and the results suggested that the use of digital histopathology for routine GLP histopathology assessment was not widespread. Subsequently, in follow-up correspondence during the pandemic, many responding institutions either began investigating or adopting digital WSI systems to reduce employee exposure to COVID-19. Therefore, the working group presents the survey results as a pre-pandemic baseline data set. Recommendations for use of WSI systems in GLP environments will be the subject of a separate publication. [ABSTRACT FROM AUTHOR]

Pressure generation at cryogenic temperatures presents a problem for a wide array of experimental techniques, particularly neutron studies due to the volume of sample required. We present a novel, compact pressure cell with a large sample volume in which load is generated by a bellow. Using a supply of helium gas up to a pressure of 350 bar, a load of up to 78 kN is generated with leak-free operation. In addition, special fiber ports added to the cryogenic center stick allow for in situ pressure determination using the ruby pressure standard. Mechanical stability was assessed using finite element analysis and the dimensions of the cell have been optimized for use with standard cryogenic equipment. Load testing and on-line experiments using NaCl and BiNiO3 have been done at the WISH instrument of the ISIS pulsed neutron source to verify performance. [ABSTRACT FROM AUTHOR]

N -Phenylanthranilic acid (NPAA) causes renal papillary necrosis (RPN) in the rat following repeated oral dosing. Non-invasive early detection of RPN is difficult, but a number of potential biomarkers have been investigated, including phospholipid and uronic acid excretion. This study used 1 H-nuclear magnetic resonance (NMR) spectroscopic analysis of urine to investigate urinary metabolic perturbations occurring in the rat following exposure to NPAA. Male Alderley Park rats received NPAA (300, 500 or 700 mg kg -1 day -1 orally) for 7 days, and urine was collected on days 7-8, 14-15, 21-22 and 28-29. In a separate study, urine was collected on days 1-2, 3-4, 5-6 and 7-8 from rats receiving 500 mg kg -1 day -1 . Samples were analysed by 1 H NMR spectroscopy combined with multivariate data analysis and clinical chemistry. Histopathology and clinical chemistry analysis of terminal blood samples was carried out following termination on days 4, 6, 8 and 29 (4 week time course) and days 2, 4, 6 and 8 (8 day study). Urine analysis revealed a marked, though variable, excretion of β-hydroxybutyrate, acetoacetate and acetone (ketone bodies) seen on days 3-4, 5-6 and 7-8 of the study. It is postulated that the ketonuria might be secondary to an alteration in fatty acid metabolism due to inhibition of prostaglandin synthesis. In addition, an elevation in urinary ascorbate was observed during the first 8 days of the study. Ascorbate is considered to be a biomarker of hepatic response, probably reflecting an increased hepatic activity due to glucuronidation of NPAA. [ABSTRACT FROM AUTHOR]

Silk is a natural polymer with broad utility in biomedical applications because it exhibits general biocompatibility and high tensile material properties. While mechanical integrity is important for most biomaterial applications, proper function and integration also requires biomaterial incorporation into complex surrounding tissues for many physiologically relevant processes such as wound healing. In this study, we spin silk fibroin into a protein alloy fibre with whole fibronectin using wet spinning approaches in order to synergize their respective strength and cell interaction capabilities. Results demonstrate that silk fibroin alone is a poor adhesive surface for fibroblasts, endothelial cells, and vascular smooth muscle cells in the absence of serum. However, significantly improved cell attachment is observed to silk-fibronectin alloy fibres without serum present while not compromising the fibres' mechanical integrity. Additionally, cell viability is improved up to six fold on alloy fibres when serum is present while migration and spreading generally increase as well. These findings demonstrate the utility of composite protein alloys as inexpensive and effective means to create durable, biologically active biomaterials. [ABSTRACT FROM AUTHOR]

The article discusses the billing of the medical bill's balance to patients after medical insurance payment.

In this report, we present results of high-pressure experiments probing the melt line of zirconium (Zr) up to 37 GPa. This investigation has determined that temperature versus laser power curves provide an accurate method to determine melt temperatures. When this information is combined with the onset of diffuse scattering, which is associated with the melt process, we demonstrate the ability to accurately determine the melt boundary. This presents a reliable method for rapid determination of melt boundary and agrees well with other established techniques for such measurements, as reported in previous works on Zr., (Creative Commons Attribution license.)

Silk is a promising material for biomedical applications, and much research is focused on how application-specific, mechanical properties of silk can be designed synthetically through proper amino acid sequences and processing parameters. This protocol describes an iterative process between research disciplines that combines simulation, genetic synthesis, and fiber analysis to better design silk fibers with specific mechanical properties. Computational methods are used to assess the protein polymer structure as it forms an interconnected fiber network through shearing and how this process affects fiber mechanical properties. Model outcomes are validated experimentally with the genetic design of protein polymers that match the simulation structures, fiber fabrication from these polymers, and mechanical testing of these fibers. Through iterative feedback between computation, genetic synthesis, and fiber mechanical testing, this protocol will enable a priori prediction capability of recombinant material mechanical properties via insights from the resulting molecular architecture of the fiber network based entirely on the initial protein monomer composition. This style of protocol may be applied to other fields where a research team seeks to design a biomaterial with biomedical application-specific properties. This protocol highlights when and how the three research groups (simulation, synthesis, and engineering) should be interacting to arrive at the most effective method for predictive design of their material., Competing Interests: Notes The authors declare no competing financial interest.

Silkworm silk is an attractive biopolymer for biomedical applications due to its high mechanical strength and biocompatibility; as a result, there is increasing interest in scalable devices to spin silk and recombinant silk so as to improve and customize their properties for diverse biomedical purposes (Vepari and Kaplan 2007 Prog. Polym. Sci. 32 ). While artificial spinning of regenerated silk fibroins adds tunability to properties such as degradation rate and surface functionalization, the resulting fibers do not yet approach the mechanical strength of native silkworm silk. These drawbacks reduce the applicability and attractiveness of artificial silk (Kinahan et al 2011 Biomacromolecules 12 ). Here, we used computational fluid dynamic simulations to incorporate shear in tandem with biomimetic ion gradients by coupling a modular novel glass microfluidic device to our previous co-axial flow device. Fibers spun with this combined apparatus demonstrated a significant increase in mechanical strength compared to fibers spun with the basic apparatus alone, with a three-fold increase in Young's modulus and extensibility and a twelve-fold increase in toughness. These results thus demonstrate the critical importance of ionic milieu and shear stress in spinning strong fibers from solubilized silk fibroin.

The International Federation of Societies of Toxicologic Pathologists (IFSTP) proposes a common global framework for training future toxicologic pathologists who will support regulatory-type nonclinical toxicology studies. Trainees optimally should undertake a scientific curriculum of at least 5 years at an accredited institution leading to a clinical degree (veterinary medicine or medicine). Trainees should then obtain 4 or more years of intensive pathology practice during a residency and/or on-the-job "apprenticeship," at least 2 years of which must be focused on regulatory-type toxicologic pathology topics. Possession of a recognized pathology qualification (i.e., certification) is highly recommended. A non-clinical pathway (e.g., a graduate degree in medical biology or pathology) may be possible if medically trained pathologists are scarce, but this option is not optimal. Regular, lifelong continuing education (peer review of nonclinical studies, professional meetings, reading, short courses) will be necessary to maintain and enhance one's understanding of current toxicologic pathology knowledge, skills, and tools. This framework should provide a rigorous yet flexible way to reliably train future toxicologic pathologists to generate, interpret, integrate, and communicate data in regulatory-type, nonclinical toxicology studies.

Proton NMR spectroscopy of urine has previously been used to gain insight into the site and mechanism of toxic injury to the kidney. d-Serine injures the rat kidney, causing selective necrosis of the proximal straight tubules. Damage is accompanied by proteinuria, glucosuria, and amino aciduria, the latter preceding the onset of necrosis. This study has employed (1)H NMR spectroscopy of urine and (1)H NMR and (31)P NMR spectroscopy of kidney extracts to examine the nephrotoxic action of d-serine. Urine was collected 0-8 h (all doses) and 8-24, 24-48, 48-72, 72-96, and 96-120 h (500 mg/kg only) postdosing from Alderley Park rats given d-serine (62.5, 125, 250, and 500 mg/kg ip). (1)H NMR spectra were monitored for markers of tubular damage. Additionally, ATP and ADP were quantitated in kidney perchloric acid extracts, prepared after 0.5, 1, 2, 4, and 8 h (500 mg/kg) to assess energy status; serine was also measured in these samples. At 500 mg/kg, glucosuria, amino aciduria, and reduced citrate, alpha-ketoglutarate, and succinate were observed in urine at 0-8 h. Furthermore, serine and pyruvate levels were elevated at this time. After 8-24 h, similar changes were observed; however, they were more severe reflecting the development of the lesion prior to recovery. These perturbations were dose-related, in particular, for serine and pyruvate, with no alterations seen at 62.5 mg/kg. Kidney serine concentration rapidly increased, where it was maximal after 30 min and cleared by 8 h. A decline in ATP, to approximately 60-70% of control, was observed within the kidney at 2-4 h postdosing, when necrosis first becomes evident suggesting that mitochondrial function might be impaired in the early stages of d-serine-induced nephrotoxicity. The use of NMR spectroscopy has given a comprehensive overview of the effects of d-serine in vivo. Information on the excretion of serine and its effect on renal energy metabolism provides insight into the possible mechanism of renal tubule injury.