GPrimer: a fast GPU-based pipeline for primer design for qPCR experiments

Background: Design of valid high-quality primers is essential for qPCR experiments. MRPrimer is a powerful pipeline based on MapReduce that combines both primer design for target sequences and homology tests on off-target sequences. It takes an entire sequence DB as input and returns all feasible and valid primer pairs existing in the DB. Due to the effectiveness of primers designed by MRPrimer in qPCR analysis, it has been widely used for developing many online design tools and building primer databases. However, the computational speed of MRPrimer is too slow to deal with the sizes of sequence DBs growing exponentially and thus must be improved. Results: We develop a fast GPU-based pipeline for primer design (GPrimer) that takes the same input and returns the same output with MRPrimer. MRPrimer consists of a total of seven MapReduce steps, among which two steps are very time-consuming. GPrimer significantly improves the speed of those two steps by exploiting the computational power of GPUs. In particular, it designs data structures for coalesced memory access in GPU and workload balancing among GPU threads and copies the data structures between main memory and GPU memory in a streaming fashion. For human RefSeq DB, GPrimer achieves a speedup of 57 times for the entire steps and a speedup of 557 times for the most time-consuming step using a single machine of 4 GPUs, compared with MRPrimer running on a cluster of six machines. Conclusions: We propose a GPU-based pipeline for primer design that takes an entire sequence DB as input and returns all feasible and valid primer pairs existing in the DB at once without an additional step using BLAST-like tools. The software is available at https://github.com/qhtjrmin/GPrimer.git. © 2021, The Author(s).1

Ameliorating Effects of Ethanol Extract of Fructus mume

We previously reported that Fructus mume (F. mume) extract shows protective effects on memory impairments and anti-inflammatory effects induced by chronic cerebral hypoperfusion. Neurodegeneration of basal cholinergic neurons is also observed in the brain with chronic cerebral hypoperfusion. Therefore, the present study was conducted to examine whether F. mume extracts enhance cognitive function via the action of cholinergic neuron using a scopolamine-induced animal model of memory impairments. F. mume (50, 100, or 200 mg/kg) was administered to C57BL/6 mice for 14 days (days 1–14) and memory impairment was induced by scopolamine (1 mg/kg), a muscarinic receptor antagonist for 7 days (days 8–14). Spatial memory was assessed using Morris water maze and hippocampal level of acetylcholinesterase (AChE) and choline acetyltransferase (ChAT) was examined by ELISA and immunoblotting. Mice that received scopolamine alone showed impairments in acquisition and retention in Morris water maze task and increased activity of AChE in the hippocampus. Mice that received F. mume and scopolamine showed no scopolamine-induced memory impairment and increased activity of AChE. In addition, treatments of F. mume increased ChAT expression in the hippocampus. These results indicated that F. mume might enhance cognitive function via action of cholinergic neurons

A Case of Autoimmune Pancreatitis Manifested by a Pseudocyst and IgG4-Associated Cholangitis

Autoimmune pancreatitis (AIP) is a benign disorder and a unique form of chronic pancreatitis with several characteristic features. A cystic formation that mimics a pseudocyst is a rare finding. There have been a few reports of AIP complicated by pancreatic cysts. We present a case of AIP with multiple pseudocysts and obstructive jaundice caused by IgG4-associated cholangitis. We initially missed the diagnosis due to the pseudocyst. Based on the computed tomography images, laboratory findings and the therapeutic response to steroids, the case was diagnosed as AIP with pseudocysts and associated cholangiopathy

Ninjurin1 positively regulates osteoclast development by enhancing the survival of prefusion osteoclasts

Osteoclasts (OCs) are bone-resorbing cells that originate from hematopoietic stem cells and develop through the fusion of mononuclear myeloid precursors. Dysregulation of OC development causes bone disorders such as osteopetrosis, osteoporosis, and rheumatoid arthritis. Although the molecular mechanisms underlying osteoclastogenesis have been well established, the means by which OCs maintain their survival during OC development remain unknown. We found that Ninjurin1 (Ninj1) expression is dynamically regulated during osteoclastogenesis and that Ninj1(-/-) mice exhibit increased trabecular bone volume owing to impaired OC development. Ninj1 deficiency did not alter OC differentiation, transmigration, fusion, or actin ring formation but increased Caspase-9-dependent intrinsic apoptosis in prefusion OCs (preOCs). Overexpression of Ninj1 enhanced the survival of mouse macrophage/preOC RAW264.7 cells in osteoclastogenic culture, suggesting that Ninj1 is important for the survival of preOCs. Finally, analysis of publicly available microarray data sets revealed a potent correlation between high NINJ1 expression and destructive bone disorders in humans. Our data indicate that Ninj1 plays an important role in bone homeostasis by enhancing the survival of preOCs

MYC and BCL2 overexpression is associated with a higher class of Memorial Sloan-Kettering Cancer Center prognostic model and poor clinical outcome in primary diffuse large B-cell lymphoma of the central nervous system

Table S1. Correlation of BCL6 expression and clinicopathological variables; Table S2. MYC translocation and copy number change in MYC positive cases. (DOCX 24 kb