49 research outputs found
Compiler Support for Sparse Tensor Computations in MLIR
Sparse tensors arise in problems in science, engineering, machine learning,
and data analytics. Programs that operate on such tensors can exploit sparsity
to reduce storage requirements and computational time. Developing and
maintaining sparse software by hand, however, is a complex and error-prone
task. Therefore, we propose treating sparsity as a property of tensors, not a
tedious implementation task, and letting a sparse compiler generate sparse code
automatically from a sparsity-agnostic definition of the computation. This
paper discusses integrating this idea into MLIR
Association of Base Excision Repair Gene Polymorphisms with ESRD Risk in a Chinese Population
The base excision repair (BER) pathway, containing OGG1, MTH1 and MUTYH, is a major protector from oxidative DNA damage in humans, while 8-oxoguanine (8-OHdG), an index of DNA oxidation, is increased in maintenance hemodialysis (HD) patients. Four polymorphisms of BER genes, OGG1 c.977C > G (rs1052133), MTH1 c.247G > A (rs4866), MUTYH c.972G > C (rs3219489), and AluYb8MUTYH (rs10527342), were examined in 337 HD patients and 404 healthy controls. And the 8-OHdG levels in leukocyte DNA were examined in 116 HD patients. The distribution of MUTYH c.972 GG or AluYb8MUTYH differed between the two groups and was associated with a moderately increased risk for end-stage renal disease (ESRD) (P = 0.013 and 0.034, resp.). The average 8-OHdG/106 dG value was significantly higher in patients with the OGG1 c.977G, MUTYH c.972G or AluYb8MUTYH alleles (P < 0.001 via ANOVA). Further analysis showed that combination of MUTYH c.972GG with OGG1 c.977GG or AluYb8MUTYH increased both the risk for ESRD and leukocyte DNA 8-OHdG levels in HD patients. Our study showed that MUTYH c.972GG, AluYb8MUTYH, and combination of OGG1 c.977GG increased the risk for ESRD development in China and suggested that DNA oxidative damage might be involved in such process
High pO2 Floating Zone Crystal Growth of the Perovskite Nickelate PrNiO3
Single crystals of PrNiO3 were grown under an oxygen pressure of 295 bar
using a unique high-pressure optical-image floating zone furnace. The crystals,
with volume in excess of 1 mm3, were characterized structurally using single
crystal and powder X-ray diffraction. Resistivity, specific heat, and magnetic
susceptibility were measured, all of which evidenced an abrupt, first order
metal-insulator transition (MIT) at ~130 K, in agreement with previous
literature reports on polycrystalline specimens. Temperature-dependent single
crystal diffraction was performed to investigate changes through the MIT. Our
study demonstrates the opportunity space for high fugacity, reactive
environments for single crystal growth specifically of perovskite nickelates
but more generally to correlated electron oxides.Comment: 19 pages, 6 figures, Supporting Information include
Case report: Rare novel MIPEP compound heterozygous variants presenting with hypertrophic cardiomyopathy, severe lactic acidosis and hypotonia in a Chinese infant
BackgroundMitochondrial intermediate peptidase, encoded by the MIPEP gene, is involved in the processing of precursor mitochondrial proteins related to oxidative phosphorylation. Only a few studies have shown that mutations in MIPEP can cause combined oxidative phosphorylation deficiency-31 (COXPD31), an autosomal recessive multisystem disorder associated with mitochondrial dysfunction. We report herein a rare case of an 8-month-old boy in China with hypertrophic cardiomyopathy (HCM), severe lactic acidosis, and hypotonia caused by novel MIPEP compound heterozygous variants.MethodsTrio-whole-exome sequencing and copy number variation sequencing were performed to identify mutated genetic loci. Sanger sequencing and quantitative real-time PCR were used to validate the candidate single nucleotide variants and copy number variants, respectively.ResultsThe proband was an 8-month-old boy with HCM, severe lactic acidosis, and hypotonia who died 2 months after his first admission. Two novel compound heterozygous variants, c.1081T > A (p. Tyr361Asn) and a whole deletion (Ex1-19 del), were found in the MIPEP gene, which were inherited from his healthy parents respectively. Additionally, his mitochondria DNA copy number was significantly reduced.ConclusionWe are the first to report a patient with rare MIPEP variants in China. Our findings expand the mutation spectrum of MIPEP, and provide insights into the genotype-phenotype relationship in COXPD31
Management of Abnormal Visual Developments
When human beings recognize the external world, more than 80% of the information come from visual function and visual system. Normal visual development and normal binocularity are the fundamental of good visual acuity and visual functions. Any abnormal visual experience would cause abnormality, such as refractive error, strabismus, amblyopia and other diseases. The patients with abnormal visual developments were reported to have abnormal, lonely, and other psycho problems. In this chapter, we will describe the normal developmental of visual function, summarize the abnormal developments and the correction or treatment
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Deleterious ZNRF3 germline variants cause neurodevelopmental disorders with mirror brain phenotypes via domain-specific effects on Wnt/β-catenin signaling
Zinc and RING finger 3 (ZNRF3) is a negative-feedback regulator of Wnt/β-catenin signaling, which plays an important role in human brain development. Although somatically frequently mutated in cancer, germline variants in ZNRF3 have not been established as causative for neurodevelopmental disorders (NDDs). We identified 12 individuals with ZNRF3 variants and various phenotypes via GeneMatcher/Decipher and evaluated genotype-phenotype correlation. We performed structural modeling and representative deleterious and control variants were assessed using in vitro transcriptional reporter assays with and without Wnt-ligand Wnt3a and/or Wnt-potentiator R-spondin (RSPO). Eight individuals harbored de novo missense variants and presented with NDD. We found missense variants associated with macrocephalic NDD to cluster in the RING ligase domain. Structural modeling predicted disruption of the ubiquitin ligase function likely compromising Wnt receptor turnover. Accordingly, the functional assays showed enhanced Wnt/β-catenin signaling for these variants in a dominant negative manner. Contrarily, an individual with microcephalic NDD harbored a missense variant in the RSPO-binding domain predicted to disrupt binding affinity to RSPO and showed attenuated Wnt/β-catenin signaling in the same assays. Additionally, four individuals harbored de novo truncating or de novo or inherited large in-frame deletion variants with non-NDD phenotypes, including heart, adrenal, or nephrotic problems. In contrast to NDD-associated missense variants, the effects on Wnt/β-catenin signaling were comparable between the truncating variant and the empty vector and between benign variants and the wild type. In summary, we provide evidence for mirror brain size phenotypes caused by distinct pathomechanisms in Wnt/β-catenin signaling through protein domain-specific deleterious ZNRF3 germline missense variants
Integrating Scalar Analyses And Optimizations In A Parallelizing And Optimizing Compiler
Scalar analyses and optimizations are indispensable and challenging in parallelizing and optimizing compilers. Scalar analyses statically collect information on how programs manipulate variables. Scalar optimizations, on the other hand, improve the efficiency of the compiled codes and the precision of the analyzed results. Performing scalar analyses and optimizations is challenging, especially when the programming languages being considered support general pointer usage. This is because many existing pointer analysis algorithms are either imprecise or inefficient, and the interactions between analyses and optimizations raise the issue of ordering the analyses and the optimizations. In this dissertation, we propose a new approach to perform scalar analyses and optimizations. We first analyze both pointer and non-pointer variables interprocedurally. The analyzed results are represented by an extended version of the traditional static single assignment (SSA) form. We then perform the opt..