Iterative Soft Decoding Algorithm for DNA Storage Using Quality Score and Redecoding.

Ever since deoxyribonucleic acid (DNA) was considered as a next-generation data-storage medium, lots of research efforts have been made to correct errors occurred during the synthesis, storage, and sequencing processes using error correcting codes (ECCs). Previous works on recovering the data from the sequenced DNA pool with errors have utilized hard decoding algorithms based on a majority decision rule. To improve the correction capability of ECCs and robustness of the DNA storage system, we propose a new iterative soft decoding algorithm, where soft information is obtained from FASTQ files and channel statistics. In particular, we propose a new formula for log-likelihood ratio (LLR) calculation using quality scores (Q-scores) and a redecoding method which may be suitable for the error correction and detection in the DNA sequencing area. Based on the widely adopted encoding scheme of the fountain code structure proposed by Erlich et al., we use three different sets of sequenced data to show consistency for the performance evaluation. The proposed soft decoding algorithm gives 2.3%  âˆ¼  7.0% improvement of the reading number reduction compared to the state-of-the-art decoding method and it is shown that it can deal with erroneous sequenced oligo reads with insertion and deletion errors.

Reducing cost in DNA-based data storage by sequence analysis-aided soft information decoding of variable-length reads.

MOTIVATION: DNA-based data storage is one of the most attractive research areas for future archival storage. However, it faces the problems of high writing and reading costs for practical use. There have been many efforts to resolve this problem, but existing schemes are not fully suitable for DNA-based data storage, and more cost reduction is needed. RESULTS: We propose whole encoding and decoding procedures for DNA storage. The encoding procedure consists of a carefully designed single low-density parity-check code as an inter-oligo code, which corrects errors and dropouts efficiently. We apply new clustering and alignment methods that operate on variable-length reads to aid the decoding performance. We use edit distance and quality scores during the sequence analysis-aided decoding procedure, which can discard abnormal reads and utilize high-quality soft information. We store 548.83 KB of an image file in DNA oligos and achieve a writing cost reduction of 7.46% and a significant reading cost reduction of 26.57% and 19.41% compared with the two previous works. AVAILABILITY AND IMPLEMENTATION: Data and codes for all the algorithms proposed in this study are available at: https://github.com/sjpark0905/DNA-LDPC-codes.

Comparison of histological and molecular features of pediatric-type follicular lymphoma and pediatric nodal marginal zone lymphoma.

Pediatric-type follicular lymphoma and pediatric nodal marginal zone lymphoma are pediatric B cell lymphomas with similar clinical characteristics but distinct histological features. We investigated the differences between pediatric-type follicular lymphoma and pediatric nodal marginal zone lymphoma by comparing their histological and molecular characteristics. A total of 5 pediatric-type follicular lymphoma and 11 pediatric nodal marginal zone lymphoma patients were included in the study. In the histological review, 5 of the 16 cases showed overlapping morphological features of pediatric-type follicular lymphoma and pediatric nodal marginal zone lymphoma; hence, they were reclassified as "mixed type." In molecular analysis, using panel-based massively parallel sequencing, MAP2K1, TNFRSF14, and IRF8 mutations were found in 6, 3, and 2 of the 11 pediatric nodal marginal zone lymphoma patients, respectively, and IRF8 mutation was found in one of the five pediatric-type follicular lymphoma patients. There were no significant differences in genetic alterations established from the histologically reclassified diagnosis as well as the initial diagnosis. Pediatric-type follicular lymphoma and pediatric nodal marginal zone lymphoma showed morphological overlap in some cases, and no difference between the two was found upon molecular analysis. These findings suggest the possibility that pediatric-type follicular lymphoma and pediatric nodal marginal zone lymphoma are single entity pediatric B-cell lymphoma with broad morphological spectrum.

Bacterial Prevalence in Skin, Urine, Diarrheal Stool, and Respiratory Samples from Dogs.

The emergence of bacterial infections in companion animals is a growing concern as humans can also be infected through the transmission of pathogenic bacteria. Because there have been few studies conducted on companion animals, the extent and significance of prevalence in veterinary practices remain unknown. This is the first nationwide surveillance report aimed at elucidating the prevalence pattern and associated infections of isolated bacteria from dogs in Korea. Bacterial isolates were collected from seven different laboratories participating in the Korean Veterinary Antimicrobial Resistance Monitoring System from 2018 to 2019. The samples were obtained from the diarrheal stool, skin/ear, urine, and respiratory samples of veterinary hospital-visited dogs. Isolation and identification of bacterial species was carried out using a bacterial culture approach and then confirmed with matrix-assisted laser desorption/ionization-time-of-flight mass spectrometry (MALDI-TOF) and polymerase chain reaction (PCR). Out of 3135 isolates in dogs, 1085, 1761, 171, and 118 were extracted from diarrheal stool, skin/ear, urine, and respiratory samples, respectively. The overall prevalence of bacteria was higher among two age groups (1-5 and 6-10 years) with a 66.5 percent prevalence. This study showed that Escherichia coli was the most prevalent species among isolated bacterial species of diarrheal and urine origin, whereas Staphylococcus pseudintermedius was the most prevalent among skin and respiratory sample isolates. The data on the prevalence of bacteria for each dog specimen could provide basic information to estimate the extent of bacterial infection and antimicrobial resistance development and to guide veterinarians in therapeutic decisions in clinical practices throughout Korea.

Prevalence of Bacterial Species in Skin, Urine, Diarrheal Stool, and Respiratory Samples in Cats.

Bacterial infections are a significant cause of illness and death in different animals. However, these bacterial infections could be a source of human disease or illness if these pathogenic bacteria are present in companion animals. This study aimed to investigate the prevalence of pathogenic bacteria associated with different site infections in cats in the Republic of Korea. For this purpose, samples were collected from the skin/ear, urine, respiratory, and diarrheal stool origins of cats obtained between 2018 and 2019 from seven different laboratories and centers participating in the Korean Veterinary Antimicrobial Resistance Monitoring System. These samples were subjected to analysis for the identification and isolation of associated bacterial species using a bacterial culture approach. A total of 609 isolates were identified in four different cat samples. Among them, 267, 184, 57, and 101 were extracted from diarrheal stool, skin, urine, and respiratory samples, respectively. The findings of this study showed that Escherichia coli was the most prevalent species among isolated bacterial species of diarrheal stool and urine origin. Staphylococcus felis and Pasteurella multocida were most prevalent in the skin and respiratory tract, respectively. However, there was no significant difference in bacterial distribution among the different age groups in all samples. This is the first nationwide surveillance report that associates bacterial prevalence with their site of origin and helps in the prevention of bacterial infections in cats. Moreover, the pattern of bacterial prevalence could provide sufficient guidance for the selection of empirical antimicrobial therapy against infections in cats.

Cooperative sequence clustering and decoding for DNA storage system with fountain codes.

MOTIVATION: In DNA storage systems, there are tradeoffs between writing and reading costs. Increasing the code rate of error-correcting codes may save writing cost, but it will need more sequence reads for data retrieval. There is potentially a way to improve sequencing and decoding processes in such a way that the reading cost induced by this tradeoff is reduced without increasing the writing cost. In past researches, clustering, alignment and decoding processes were considered as separate stages but we believe that using the information from all these processes together may improve decoding performance. Actual experiments of DNA synthesis and sequencing should be performed because simulations cannot be relied on to cover all error possibilities in practical circumstances. RESULTS: For DNA storage systems using fountain code and Reed-Solomon (RS) code, we introduce several techniques to improve the decoding performance. We designed the decoding process focusing on the cooperation of key components: Hamming-distance based clustering, discarding of abnormal sequence reads, RS error correction as well as detection and quality score-based ordering of sequences. We synthesized 513.6 KB data into DNA oligo pools and sequenced this data successfully with Illumina MiSeq instrument. Compared to Erlich's research, the proposed decoding method additionally incorporates sequence reads with minor errors which had been discarded before, and thus was able to make use of 10.6-11.9% more sequence reads from the same sequencing environment, this resulted in 6.5-8.9% reduction in the reading cost. Channel characteristics including sequence coverage and read-length distributions are provided as well. AVAILABILITY AND IMPLEMENTATION: The raw data files and the source codes of our experiments are available at: https://github.com/jhjeong0702/dna-storage.

Short communication: First detection of Panton-Valentine leukocidin-positive methicillin-resistant Staphylococcus aureus ST30 in raw milk taken from dairy cows with mastitis in South Korea.

We identified 199 Staphylococcus aureus isolates from quarter milk samples of 1,289 dairy cattle between 2014 and 2018. About 66% of the isolates were resistant to at least 1 antimicrobial agent; the highest rate of resistance was to penicillin, followed by resistance to ampicillin, erythromycin, and sulfadimethoxine. We obtained 30 methicillin-resistant S. aureus (MRSA) strains from 6 farms in 3 provinces. The MRSA strains exhibited a significantly higher resistance rate to most of the tested antimicrobials than the oxacillin-susceptible strains. The MRSA strains represented 5 genotypes: ST72-t324-SCCmec IV (n = 14), ST30-t1752-SCCmec IV (n = 8), ST188-t189-SCCmec NT (n = 6), ST188-t2284-SCCmec NT (n = 1), and NT-NT-SCCmec IV (n = 1). One of the ST188 MRSA strains represented a novel staphylococcal protein A (spa) type (t2284). In addition, 7 of the 8 ST30 MRSA strains were Panton-Valentine leukocidin (PVL)-positive and carried various staphylococcal enterotoxin encoding genes. This is the first report of PVL-positive ST30 MRSA-t1752-SCCmec IV from bovine mastitis in Korea. All of ST72-t324-SCCmec IV MRSA strains carried staphylococcal enterotoxin and leukotoxin encoding genes. They were also sensitive to most of the tested non-ß-lactam antimicrobials. In contrast, ST188-t189 MRSA strains were resistant to multiple antimicrobials and predominantly carried the leukotoxin encoding gene. Taken together, these findings may indicate that dairy cows could be a major source for spreading MRSA strains, and contaminated milk could be a vehicle for transmission. Suitable hygienic measures should be established in dairy farms and processing plants to limit the likelihood of introducing MRSA into the food chain.

Short communication: Occurrence and persistence of Prototheca zopfii in dairy herds of Korea.

Bovine mastitis caused by Prototheca has been reported globally, and its incidence is increasing in dairy herds. The present study aimed to investigate the occurrence of Prototheca and persistence of Prototheca zopfii strains in Korean dairy herds. A total of 187 (7.5%) P. zopfii strains were isolated from 2,508 quarter milk samples collected from 50 dairy farms throughout Korea from 2015 to 2017. Prototheca zopfii was isolated from one farm among the 50 farms over the 3-yr period. The P. zopfii isolates belonged to genotype 2. Overall, Prototheca-positive quarter milk samples showed high somatic cell counts with an average value of log 6.48 ± 6.54 cells/mL. Prototheca zopfii was found to be persistent in an infected farm over a 2-yr period. To the best of our knowledge, this is the first report on the presence and persistence of protothecal mastitis caused by P. zopfii genotype 2 in a Korean dairy herd. This disease leads to a significant increase in somatic cell counts in milk, which persists for more than 1 yr in the affected cow udder. These results suggest that P. zopfii could pose a serious risk to dairy herds. Thus, strict surveillance for protothecal mastitis is urgently needed and sanitary conditions regarding the environment and milk collection are essential because of the lack of effective treatment options.

New Binary Locally Repairable Codes with Locality 2 and Uneven Availabilities for Hot Data.

In this paper, a new family of binary LRCs (BLRCs) with locality 2 and uneven availabilities for hot data is proposed, which has a high information symbol availability and low parity symbol availabilities for the local repair of distributed storage systems. The local repair of each information symbol for the proposed codes can be done not by accessing other information symbols but only by accessing parity symbols. The proposed BLRCs with k = 4 achieve the optimality on the information length for their given code length, minimum Hamming distance, locality, and availability in terms of the well-known theoretical upper bound.

A Tree Based Broadcast Scheme for (m, k)-firm Real-Time Stream in Wireless Sensor Networks.

Recently, various unicast routing protocols have been proposed to deliver measured data from the sensor node to the sink node within the predetermined deadline in wireless sensor networks. In parallel with their approaches, some applications demand the specific service, which is based on broadcast to all nodes within the deadline, the feasible real-time traffic model and improvements in energy efficiency. However, current protocols based on either flooding or one-to-one unicast cannot meet the above requirements entirely. Moreover, as far as the authors know, there is no study for the real-time broadcast protocol to support the application-specific traffic model in WSN yet. Based on the above analysis, in this paper, we propose a new (m, k)-firm-based Real-time Broadcast Protocol (FRBP) by constructing a broadcast tree to satisfy the (m, k)-firm, which is applicable to the real-time model in resource-constrained WSNs. The broadcast tree in FRBP is constructed by the distance-based priority scheme, whereas energy efficiency is improved by selecting as few as nodes on a tree possible. To overcome the unstable network environment, the recovery scheme invokes rapid partial tree reconstruction in order to designate another node as the parent on a tree according to the measured (m, k)-firm real-time condition and local states monitoring. Finally, simulation results are given to demonstrate the superiority of FRBP compared to the existing schemes in terms of average deadline missing ratio, average throughput and energy consumption.

Inhibitory Basal Ganglia Inputs Induce Excitatory Motor Signals in the Thalamus.

Basal ganglia (BG) circuits orchestrate complex motor behaviors predominantly via inhibitory synaptic outputs. Although these inhibitory BG outputs are known to reduce the excitability of postsynaptic target neurons, precisely how this change impairs motor performance remains poorly understood. Here, we show that optogenetic photostimulation of inhibitory BG inputs from the globus pallidus induces a surge of action potentials in the ventrolateral thalamic (VL) neurons and muscle contractions during the post-inhibitory period. Reduction of the neuronal population with this post-inhibitory rebound firing by knockout of T-type Ca2+ channels or photoinhibition abolishes multiple motor responses induced by the inhibitory BG input. In a low dopamine state, the number of VL neurons showing post-inhibitory firing increases, while reducing the number of active VL neurons via photoinhibition of BG input, effectively prevents Parkinson disease (PD)-like motor symptoms. Thus, BG inhibitory input generates excitatory motor signals in the thalamus and, in excess, promotes PD-like motor abnormalities. VIDEO ABSTRACT.

Intravascular large b-cell lymphoma diagnosed via transjugular liver biopsy in a patient with liver dysfunction and thrombocytopenia: A Case Report.

RATIONALE: Intravascular large B-cell lymphoma (IVLBCL) is an extremely rare subtype of large B-cell lymphoma characterized by the presence of lymphoma cells within the lumen of small blood vessels. IVLBCL presents with nonspecific symptoms such as fever, weight loss, and bleeding. Because of its rarity and unremarkable clinical presentation, a timely diagnosis is very challenging. PATIENT CONCERNS: A 71-year-old Korean man complained of fever, but apart from pretibial pitting edema and mild thrombocytopenia, the physical examination and laboratory test findings were unremarkable. DIAGNOSES: A bone marrow biopsy was also nonspecific. The fever persisted and his thrombocytopenia became more pronounced, prompting further laboratory tests that indicated infiltrative liver disease. INTERVENTIONS: Because of coagulopathy, a liver biopsy was performed using a transjugular instead of apercutaneous approach. OUTCOMES: The procedure was performed without complications, and the pathologic examination findings were consistent with IVLBCL. Unfortunately, the patient died because of disease progression before treatment could be administered. LESSONS: Given that an early diagnosis can affect the prognosis of IVLBCL, quickly and safely obtaining a biopsy specimen is very important. The case presented here shows that a liver biopsy obtained via a transjugular approach is safe and could be preferentially considered when there is a high risk for bleeding complications.

Region-Based Collision Avoidance Beaconless Geographic Routing Protocol in Wireless Sensor Networks.

Due to the lack of dependency on beacon messages for location exchange, the beaconless geographic routing protocol has attracted considerable attention from the research community. However, existing beaconless geographic routing protocols are likely to generate duplicated data packets when multiple winners in the greedy area are selected. Furthermore, these protocols are designed for a uniform sensor field, so they cannot be directly applied to practical irregular sensor fields with partial voids. To prevent the failure of finding a forwarding node and to remove unnecessary duplication, in this paper, we propose a region-based collision avoidance beaconless geographic routing protocol to increase forwarding opportunities for randomly-deployed sensor networks. By employing different contention priorities into the mutually-communicable nodes and the rest of the nodes in the greedy area, every neighbor node in the greedy area can be used for data forwarding without any packet duplication. Moreover, simulation results are given to demonstrate the increased packet delivery ratio and shorten end-to-end delay, rather than well-referred comparative protocols.

In vivo inhibition of bone morphogenetic protein-2 on breast cancer cell growth.

STUDY DESIGN: In vitro and in vivo study. OBJECTIVE: To evaluate the role of recombinant human bone morphogenetic protein-2 (rhBMP2) on breast cancer cell (MDA-MB-231 cells) growth. SUMMARY OF BACKGROUND DATA: Bone morphogenetic proteins (BMPs) are expressed in a variety of human carcinoma cell lines and are known to promote tumor invasion and metastasis. However, their roles in tumor progression have not been fully clarified. In addition, there is no in vivo study regarding the inhibitory effect of BMP2 on breast cancer cell proliferation. METHOD: Cell proliferation was determined by BrdU incorporation assay and flow cytometry. BMP2 signal transduction pathways were estimated on Western blot. Fifteen animals were divided into 2 groups; 1 (control = 5) was breast cancer cells alone, while the other (experiment = 5) was rhBMP2 + breast cancer cells. Cancer cells were injected into 2 sites (subcutaneous and femur) of nude mice with or without BMP2. Tumor size was determined by direct measurements for subcutaneous tumor formation and by femur radiographs. Histological and immunohistochemical analyses were performed. RESULTS: RhBMP2 inhibited the proliferation of MDA-MB-231 cells in vitro. Inhibition was associated with changes in both the Smad and Wnt signaling pathways and was ultimately mediated through effects on various cell cycle proteins. Furthermore, rhBMP2 inhibited the growth of MDA-MB-231 cells injected both subcutaneously and intrafemorally. CONCLUSION: In this model using human breast adenocarcinoma cell line, rhBMP2 has no stimulatory effect of tumor growth. Therefore, we can provide the basic science data to support the utilization in the management of patients with spine tumor in the future.

Granular neural networks and their development through context-based clustering and adjustable dimensionality of receptive fields.

In this study, we present a new architecture of a granular neural network and provide a comprehensive design methodology as well as elaborate on an algorithmic setup supporting its development. The proposed neural network relates to a broad category of radial basis function neural networks (RBFNNs) in the sense that its topology involves a collection of receptive fields. In contrast to the standard architectures encountered in RBFNNs, here we form individual receptive fields in subspaces of the original input space rather than in the entire input space. These subspaces could be different for different receptive fields. The architecture of the network is fully reflective of the structure encountered in the training data which are granulated with the aid of clustering techniques. More specifically, the output space is granulated with use of K-means clustering while the information granules in the multidimensional input space are formed by using the so-called context-based fuzzy C-means, which takes into account the structure being already formed in the output space. The innovative development facet of the network involves a dynamic reduction of dimensionality of the input space in which the information granules are formed in the subspace of the overall input space which is formed by selecting a suitable subset of input variables so that this subspace retains the structure of the entire space. As this search is of combinatorial character, we use the technique of genetic optimization [genetic algorithms (GAs), to be more specific] to determine the optimal input subspaces. A series of numeric studies exploiting synthetic data and data coming from the Machine Learning Repository, University of California at Irvine, provide a detailed insight into the nature of the algorithm and its parameters as well as offer some comparative analysis.

Adenomyoma of the small intestine: report of two cases and review of the literature.

Adenomyoma of the small intestine is a rare tumor-like lesion composed of exocrine-type ducts and hypertrophic smooth muscle. We describe two cases of adenomyoma of the small intestine. One was an ileal adenomyoma that presented with intussusception occurring in a 7-month-old boy. The other was a jejunal adenomyoma found incidentally in a 63-year-old man with colon cancer. Histologically, the lesions composed of benign ducts and bundles of smooth muscle. The second case was detected on contrast-enhanced computed tomography scan as a small enhancing polypoid mass. We review the previous literature of adenomyoma of the small intestine.