Rosetta Brains: A Strategy for Molecularly-Annotated Connectomics

We propose a neural connectomics strategy called Fluorescent In-Situ Sequencing of Barcoded Individual Neuronal Connections (FISSEQ-BOINC), leveraging fluorescent in situ nucleic acid sequencing in fixed tissue (FISSEQ). FISSEQ-BOINC exhibits different properties from BOINC, which relies on bulk nucleic acid sequencing. FISSEQ-BOINC could become a scalable approach for mapping whole-mammalian-brain connectomes with rich molecular annotations

Targeted and Genome-Scale Methylomics Reveals Gene Body Signatures in Human Cell Lines

Cytosine methylation, an epigenetic modification of DNA, is a target of growing interest for developing high throughput profiling technologies. Here we introduce two new, complementary techniques for cytosine methylation profiling utilizing next generation sequencing technology: bisulfite padlock probes (BSPPs) and methyl sensitive cut counting (MSCC). In the first method, we designed a set of ~10,000 BSPPs distributed over the ENCODE pilot project regions to take advantage of existing expression and chromatin immunoprecipitation data. We observed a pattern of low promoter methylation coupled with high gene body methylation in highly expressed genes. Using the second method, MSCC, we gathered genome-scale data for 1.4 million HpaII sites and confirmed that gene body methylation in highly expressed genes is a consistent phenomenon over the entire genome. Our observations highlight the usefulness of techniques which are not inherently or intentionally biased in favor of only profiling particular subsets like CpG islands or promoter regions

ShortcutFusion: From Tensorflow to FPGA-based accelerator with reuse-aware memory allocation for shortcut data

Residual block is a very common component in recent state-of-the art CNNs such as EfficientNet or EfficientDet. Shortcut data accounts for nearly 40% of feature-maps access in ResNet152 [8]. Most of the previous DNN compilers, accelerators ignore the shortcut data optimization. This paper presents ShortcutFusion, an optimization tool for FPGA-based accelerator with a reuse-aware static memory allocation for shortcut data, to maximize on-chip data reuse given resource constraints. From TensorFlow DNN models, the proposed design generates instruction sets for a group of nodes which uses an optimized data reuse for each residual block. The accelerator design implemented on the Xilinx KCU1500 FPGA card significantly outperforms NVIDIA RTX 2080 Ti, Titan Xp, and GTX 1080 Ti for the EfficientNet inference. Compared to RTX 2080 Ti, the proposed design is 1.35-2.33x faster and 6.7-7.9x more power efficient. Compared to the result from baseline, in which the weights, inputs, and outputs are accessed from the off-chip memory exactly once per each layer, ShortcutFusion reduces the DRAM access by 47.8-84.8% for RetinaNet, Yolov3, ResNet152, and EfficientNet. Given a similar buffer size to ShortcutMining [8], which also mine the shortcut data in hardware, the proposed work reduces off-chip access for feature-maps 5.27x while accessing weight from off-chip memory exactly once.Comment: 12 page

Accurate Whole-Genome Sequencing and Haplotyping from 10 to 20 Human Cells

Recent advances in whole genome sequencing have brought the vision of personal genomics and genomic medicine closer to reality. However, current methods lack clinical accuracy and the ability to describe the context (haplotypes) in which genome variants co-occur in a cost-effective manner. Here we describe a low-cost DNA sequencing and haplotyping process, Long Fragment Read (LFR) technology, similar to sequencing long single DNA molecules without cloning or separation of metaphase chromosomes. In this study, ten LFR libraries were made using only ~100 pg of human DNA per sample. Up to 97% of the heterozygous single nucleotide variants (SNVs) were assembled into long haplotype contigs. Removal of false positive SNVs not phased by multiple LFR haplotypes resulted in a final genome error rate of 1 in 10 Mb. Cost-effective and accurate genome sequencing and haplotyping from 10-20 human cells, as demonstrated here, will enable comprehensive genetic studies and diverse clinical applications

Staged Surgery for Chronic Primary Aortoduodenal Fistula in a Septic Patient

Aortoenteric fistula is one of the most challenging problems that confront the vascular surgeons. Controversy remains over the optimal treatment because of the continued publication of series with high mortality, amputation, and aortic disruption rates. A positive preoperative blood culture is the best predictor of mortality with increased amputation rates due to infection of the extra-anatomic bypass. Therefore, in selected cases with sepsis, a prudent management protocol is required. We report a 68-yr-old male presenting with a chronic primary aortoduodenal fistula extensively involving the duodenum and Gram-negative sepsis. We planned a staged operation. Initially, an emergency laparotomy and control of the aorta allowed stabilization of the patient, identification of the fistula, and direct in situ placement of the prosthetic graft followed by an en bloc resection of the aneurysm and the surrounding structures. After he recovered from sepsis and had been stabilized, a staged extra-anatomic bypass followed by transabdominal removal of the temporarily placed graft was done. This management plan will allow the highest success rate and may be a prudent management protocol for these difficult cases

The Outcomes of Hypertransfusion in Major ABO Incompatible Allogeneic Stem Cell Transplantation

Major ABO incompatibility may be potentially associated with immediate or delayed hemolysis and delayed onset of erythropoiesis in patients receiving allogeneic hematopoietic stem cell transplantation (HSCT). To determine if hemolysis can be prevented by the inhibition of graft erythropoiesis, we performed hypertransfusion and assessed red cell transfusion requirement and independence. Between October 1995 and December 2001, 28 consecutive patients receiving major ABO incompatible HSCT at Samsung Medical Center were hypertransfused to maintain their hemoglobin levels at 15 g/dL or more. We retrospectively compared the outcomes of these patients with those of 47 patients at Asan Medical Center whose target hemoglobin levels were 10 g/dL. Reticulocyte engraftment was significantly delayed in hypertransfused group (51 days vs. 23 days; p=.001). There was no significant difference in the total amount of red cells transfused within 90 days post-HSCT (25 units vs. 26 units; p=.631). No significant difference in the time to red cell transfusion independence was observed between the two groups (63 days vs. 56 days; p=.165). In conclusion, we failed to improve red cell transfusion requirement and independence in major ABO incompatible HSCT with hypertransfusion

Device modeling of two-steps oxygen anneal-based submicron InGaZnO back-end-of-line field-effect transistor enabling short-channel effects suppression

This work was supported in part by Samsung Electronics Co., Ltd under Grant IO200424-07306-01, in part by the National Research Foundation of Korea (NRF) funded by the Ministry of Science and ICT (MSIT) of Korea Government under Grant 2016R1A5A1012966 and 2020R1A2B5B01001979, and in part by the Institute of Information and Communications Technology Planning and Evaluation (IITP) funded by the Korea government (MSIT) under grant 2021-0-01764. Submicron IGZO FET samples was fabricated by imec. TCAD simulation was supported by SILVACO. The EDA tool was supported by the IC Design Education Center (IDEC), south Korea

Subarachnoid Hemorrhage Misdiagnosed as an Acute ST Elevation Myocardial Infarction

Without significant coronary artery stenosis, ischemic electrocardiographic change including ST segment elevation, segmental wall motion abnormality and elevated serum cardiac-specific markers (creatine kinase-MB, Troponin-T) may develop after central nervous system injuries such as subarachnoid, intracranial or subdural hemorrhage. Misdiagnosing these patients as acute myocardial infarction may result in catastrophic outcomes. By reporting a case of a 55-year old female with subarachnoid hemorrhage mimicking acute ST elevation myocardial infarction, we hope to underline that careful attention of neurologic abnormality is critical in making better prognosis

Ecological connectivity analysis based on the fish community in Jeongan Stream

This study focused on the longitudinal connectivity analysis, based on fish communities in the aspect of spatial variations of 34 sites from upstream to downstream. The Fish Assessment Index (FAI), based on ecological guilds and species composition, was applied to compare the ecological health among the sampling sites. The total number of 35 fish species, were sampled during the study period with dominant species of Zacco platypus (35.4%) and Zacco koreanus (11.8%). Cluster analysis showed that all sites were categorized as 4 distinct group communities (A, B, C, D). Non-metric multidimensional scaling analysis showed distinct difference between upstream (A, B) and downstream groups (C, D). Indicator Value Analysis (IndVal method), conducted to identify indicator species within each group, indicated that the species favoring upstream environments Rhynchocypris oxycephalus for the Group A and Iksookimia koreensis for the Group B. In contrast, the analysis indicated that the species with a preference for downstream habitats Pseudogobio esocinus for the Group C and Carassius auratus for the Group D. Ecological health, based on the FAI scores, showed a declining pattern toward the downstream, along with an increasing proportion of tolerant species and omnivores within the fish community. Overall these findings suggest the compositions of fish communities, as four groups, were modified by the weir structures and organic matter, nutrient pollutions