bluuebunny/crossref_metadata_2025_split huggingface dataset:
Tonsil-derived mesenchymal stem cells enhance allogeneic bone marrow engraftment via collagen IV degradation
Authors: Lee Hyun-Ji , Kim Yu-Hee , Choi Da-Won , Cho Kyung-Ah , Park Joo-Won , Shin Sang-Jin , Jo Inho , Woo So-Youn , Ryu Kyung-Ha 
Published: June 2021

Abstract
Background
Co-transplantation of bone marrow cells (BMCs) and mesenchymal stem cells (MSCs) is used as a strategy to improve the outcomes of bone marrow transplantation. Tonsil-derived MSCs (TMSCs) are a promising source of MSCs for co-transplantation. Previous studies have shown that TMSCs or conditioned media from TMSCs (TMSC-CM) enhance BMC engraftment. However, the factors in TMSCs that promote better engraftment have not yet been identified.

Methods
Mice were subjected to a myeloablative regimen of busulfan and cyclophosphamide, and the mRNA expression in the bone marrow was analyzed using an extracellular matrix (ECM) and adhesion molecule-targeted polymerase chain reaction (PCR) array. Nano-liquid chromatography with tandem mass spectrometry, real-time quantitative PCR, western blots, and enzyme-linked immunosorbent assays were used to compare the expression levels of metalloproteinase 3 (MMP3) in MSCs derived from various tissues, including the tonsils, bone marrow, adipose tissue, and umbilical cord. Recipient mice were conditioned with busulfan and cyclophosphamide, and BMCs, either as a sole population or with control or MMP3-knockdown TMSCs, were co-transplanted into these mice. The effects of TMSC-expressed MMP3 were investigated. Additionally, Enzchek collagenase and Transwell migration assays were used to confirm that the collagenase activity of TMSC-expressed MMP3 enhanced BMC migration.

Results
Mice subjected to the myeloablative regimen exhibited increased mRNA expression of collagen type IV alpha 1/2 (Col4a1 and Col4a2). Among the various extracellular matrix-modulating proteins secreted by TMSCs, MMP3 was expressed at higher levels in TMSCs than in other MSCs. Mice co-transplanted with BMCs and control TMSCs exhibited a higher survival rate, weight recovery, and bone marrow cellularity compared with mice co-transplanted with BMCs and MMP3-knockdown TMSCs. Control TMSC-CM possessed higher collagenase activity against collagen IV than MMP3-knockdown TMSC-CM. TMSC-CM also accelerated BMC migration by degrading collagen IV in vitro.

Conclusions
Collectively, these results indicate that TMSCs enhance BMC engraftment by the secretion of MMP3 for the modulation of the bone marrow extracellular matrix.
Upstream region of OprD mutations in imipenem-resistant and imipenem-sensitive Pseudomonas isolates
Authors: Kiani Masoumeh , Astani Akram , Eslami Gilda , Khaledi Mansoor , Afkhami Hamed , Rostami Soodabeh , Zarei Mohadeseh , Rezaei Khozani Nahid , Zandi Hengameh 
Published: June 2021

AbstractThe current study was aimed at investigating the prevalence of the mutations upstream of the oprD coding region and its promoters among imipenem-resistant and sensitive Pseudomonas aeruginosa isolated from educational hospitals in Yazd City, Iran. All isolates were identified by the conventional biochemical tests. Then, the antibiotic resistance of these isolates was determined using the disk diffusion method according to the CLSI guidelines. Also, the E.test was performed to determine the minimum inhibitory concentrations (MIC) of imipenem. The mutations of this gene were recognized by the amplification of this region and subsequently sequenced. Sequencing of the genomic region upstream of oprD these regions were done in the 29 clinical strains. Statistical analysis was done by the statistical software SPSS-18. Seventy (77.7%) of isolates had MIC ≥ 16 and were resistant to imipenem. Mutations of the upstream of the oprD gene and its promoters were seen in 25 (86.2%) isolates and 4 isolates had no mutation. One isolate had a base substitution A→Cat nt 25 in the coding region and this isolate had a point mutation leading to an amino acid change at positions 9 (I→L). Our study results indicated that none of the strains had mutation in Shine-Dalgarno and the point mutations were the most common mutations upstream of the oprD coding region among P. aeruginosa isolates. Mutations were observed in imipenem-resistant isolates and it seems this mechanism is effective in resistance of isolates to imipenem and this confirmed that the indiscriminate use of antibiotic should be controlled.
Resource sharing of mobile edge computing networks based on auction game and blockchain
Authors: Zhang Xiuxian , Zhu Xiaorong , Chikuvanyanga M.A.M , Chen Meijuan 
Published: June 2021

AbstractThe edge clouds in mobile edge computing networks are isolate which may belong to different companies or organizations, and hence the communication, computation, and storage resources are not efficiently utilized. To solve this problem, we propose the resource-sharing model of edge clouds which is based on blockchain technology and auction game. In this model, the blockchain platform is regarded as the bridge of the resource sharing, composed of edge clouds, clouds, third-party spectrum and computation management, identity authentication institutions, etc. It is used to record the users’ transaction information and broadcast the intelligent terminals’ resource requirements to all edge clouds in the blockchain platform through smart contracts. Then, an optimization problem of the joint allocation of communication and computation resources is formulated to maximize the utility of intelligent terminals. And an efficient improved sealed second-price auction game is proposed to allocate communication and computation resources and determine the optimal price of resources under the intelligent terminals’ QoS constraints. Simulation results show that the model can effectively improve the system resources utilization and the successful transaction rate.
HTPC: heterogeneous traffic-aware partition coding for random packet spraying in data center networks
Authors: Huang Jiawei , Wang Shiqi , Li Shuping , Zou Shaojun , Hu Jinbin , Wang Jianxin 
Published: June 2021

AbstractModern data center networks typically adopt multi-rooted tree topologies such leaf-spine and fat-tree to provide high bisection bandwidth. Load balancing is critical to achieve low latency and high throughput. Although the per-packet schemes such as Random Packet Spraying (RPS) can achieve high network utilization and near-optimal tail latency in symmetric topologies, they are prone to cause significant packet reordering and degrade the network performance. Moreover, some coding-based schemes are proposed to alleviate the problem of packet reordering and loss. Unfortunately, these schemes ignore the traffic characteristics of data center network and cannot achieve good network performance. In this paper, we propose a Heterogeneous Traffic-aware Partition Coding named HTPC to eliminate the impact of packet reordering and improve the performance of short and long flows. HTPC smoothly adjusts the number of redundant packets based on the multi-path congestion information and the traffic characteristics so that the tailing probability of short flows and the timeout probability of long flows can be reduced. Through a series of large-scale NS2 simulations, we demonstrate that HTPC reduces average flow completion time by up to 60% compared with the state-of-the-art mechanisms.
Understanding the effects of intramuscular injection and feed withdrawal on Salmonella Typhimurium shedding and gut microbiota in pullets
Authors: Joat Nitish Narendra , Khan Samiullah , Chousalkar Kapil 
Published: June 2021

AbstractBackgroundGut microbiota plays a key role in health, immunity, digestion, and production in layers. Factors such as environment, diet, diseases, stress, and flock management significantly affect gut microbiota; however, it is not known how potential stressors such as intramuscular injections or feed withdrawal alter the composition of gut microbiota that result in increased the shedding level of foodborne pathogens. In the current study, the effects of intramuscular corticosterone injection and feed withdrawal were evaluated to understand their role inSalmonellaTyphimurium shedding and changes in the composition of gut microbiota in layers.ResultsSalmonellashedding was observed for 8 weeks post-infection. There was a significant increase inSalmonellaTyphimurium count after intramuscular injection and feed withdrawal. TheSalmonellainfected and the negative control groups showed significant differences in the abundance of different genera in gut microbiota at week 1 and up to week 7 post infection. The infected group showed a significant reduction in alpha diversity of gut microbiota. Firmicutes reduced significantly (P < 0.05) after intramuscular injection, while the feed withdrawal groups did not cause any significant changes in Proteobacteria-Firmicutes ratio. Furthermore, intramuscular injection resulted in a significant change in alpha diversity of gut microbiota.ConclusionsExposure of chicks to relatively low dose ofSalmonellaTyphimurium can lead to persistent shedding in pullets. TheSalmonellaTyphimurium infection disrupted the gut microbiota composition immediately after infection. The potential stress of intramuscular injection and feed withdrawal significantly increased theSalmonellaTyphimurium count in faeces. The intramuscular injection also resulted in a significant alteration of the Proteobacteria-Firmicutes ratio, which could increase the risk of dysbiosis.
Where should police forces target their residential burglary reduction efforts? Using official victimisation data to predict burglary incidences at the neighbourhood level
Authors: Hunter James , Ward Bethany , Tseloni Andromachi , Pease Ken 
Published: June 2021

AbstractExpected crime rates that enable police forces to contrast recorded and anticipated spatial patterns of crime victimisation offer a valuable tool in evaluating the under-reporting of crime and inform/guide crime reduction initiatives. Prior to this study, police forces had no access to expected burglary maps at the neighbourhood level covering all parts of England and Wales. Drawing on analysis of the Crime Survey for England and Wales and employing a population terrain modelling approach, this paper utilises household and area characteristics to predict the mean residential burglary incidences per 1000 population across all neighbourhoods in England and Wales. The analysis identifies distinct differences in recorded and expected neighbourhood burglary incidences at the Output Area level, providing a catalyst for stimulating further reflection by police officers and crime analysts.
Ultra-accurate microbial amplicon sequencing with synthetic long reads
Authors: Callahan Benjamin J. , Grinevich Dmitry , Thakur Siddhartha , Balamotis Michael A. , Yehezkel Tuval Ben 
Published: June 2021

Abstract
Background
Out of the many pathogenic bacterial species that are known, only a fraction are readily identifiable directly from a complex microbial community using standard next generation DNA sequencing. Long-read sequencing offers the potential to identify a wider range of species and to differentiate between strains within a species, but attaining sufficient accuracy in complex metagenomes remains a challenge.

Methods
Here, we describe and analytically validate LoopSeq, a commercially available synthetic long-read (SLR) sequencing technology that generates highly accurate long reads from standard short reads.

Results
LoopSeq reads are sufficiently long and accurate to identify microbial genes and species directly from complex samples. LoopSeq perfectly recovered the full diversity of 16S rRNA genes from known strains in a synthetic microbial community. Full-length LoopSeq reads had a per-base error rate of 0.005%, which exceeds the accuracy reported for other long-read sequencing technologies. 18S-ITS and genomic sequencing of fungal and bacterial isolates confirmed that LoopSeq sequencing maintains that accuracy for reads up to 6 kb in length. LoopSeq full-length 16S rRNA reads could accurately classify organisms down to the species level in rinsate from retail meat samples, and could differentiate strains within species identified by the CDC as potential foodborne pathogens.

Conclusions
The order-of-magnitude improvement in length and accuracy over standard Illumina amplicon sequencing achieved with LoopSeq enables accurate species-level and strain identification from complex- to low-biomass microbiome samples. The ability to generate accurate and long microbiome sequencing reads using standard short read sequencers will accelerate the building of quality microbial sequence databases and removes a significant hurdle on the path to precision microbial genomics.
Diurnal variation in the human skin microbiome affects accuracy of forensic microbiome matching
Authors: Wilkins David , Tong Xinzhao , Leung Marcus H. Y. , Mason Christopher E. , Lee Patrick K. H. 
Published: June 2021

Abstract
Background
The human skin microbiome has been recently investigated as a potential forensic tool, as people leave traces of their potentially unique microbiomes on objects and surfaces with which they interact. In this metagenomic study of four people in Hong Kong, their homes, and public surfaces in their neighbourhoods, we investigated the stability and identifiability of these microbiota traces on a timescale of hours to days.

Results
Using a Canberra distance-based method of comparing skin and surface microbiomes, we found that a person could be accurately matched to their household in 84% of tests and to their neighbourhood in 50% of tests, and that matching accuracy did not decay for household surfaces over the 10-day study period, although it did for public surfaces. The time of day at which a skin or surface sample was taken affected matching accuracy, and 160 species across all sites were found to have a significant variation in abundance between morning and evening samples. We hypothesised that daily routines drive a rhythm of daytime dispersal from the pooled public surface microbiome followed by normalisation of a person’s microbiome by contact with their household microbial reservoir, and Dynamic Bayesian Networks (DBNs) supported dispersal from public surfaces to skin as the major dispersal route among all sites studied.

Conclusions
These results suggest that in addition to considering the decay of microbiota traces with time, diurnal patterns in microbiome exposure that contribute to the human skin microbiome assemblage must also be considered in developing this as a potential forensic method.
Prevalence and spatial distribution patterns of human echinococcosis at the township level in Sichuan Province, China
Authors: He Wei , Wang Li-Ying , Yu Wen-Jie , Zhang Guang-Jia , Zhong Bo , Liao Sha , Wang Qi , Li Rui-Rui , Yang Liu , Yao Ren-Xin , Liu Yang , Danba Zeli , Qin Sheng-Chao , Wang Shi-An , Wang Yan-Xia , Huang Yan , Wang Qian 
Published: June 2021

Abstract
Background
Echinococcosis is a global zoonotic parasitic disease caused by Echinococcus larvae. This disease is highly endemic in Sichuan Province, China. This study investigates the prevalence and spatial distribution characteristics of human echinococcosis at the township level in Sichuan Province, geared towards providing a future reference for the development of precise prevention and control strategies.

Methods
Human prevalence of echinococcosis was evaluated using the B-ultrasonography diagnostic method in Sichuan Province between 2016 and 2019. All data were collected, collated, and analyzed. A spatial distribution map was drawn to intuitively analyze the spatial distribution features. Eventually, the spatial autocorrelation was specified and local indicators of spatial association (LISA) clustering map was drawn to investigate the spatial aggregation of echinococcosis at the township level in Sichuan Province.

Results
The prevalence of echinococcosis in humans of Sichuan Province was 0.462%, among which the occurrence of cystic echinococcosis (CE) was 0.221%, while that of alveolar echinococcosis (AE) was 0.244%. Based on the results of the spatial distribution map, a predominance of echinococcosis in humans decreased gradually from west to east and from north to south. The Global Moran’s I index was 0.77 (Z = 32.07, P < 0.05), indicating that the prevalence of echinococcosis in humans was spatially clustered, exhibiting a significant spatial positive correlation. Further, the findings of local spatial autocorrelation analysis revealed that the “high–high” concentration areas were primarily located in some townships in the northwest of Sichuan Province. However, the “low–low” concentration areas were predominantly located in some townships in the southeast of Sichuan Province.

Conclusions
Our findings demonstrated that the prevalence of echinococcosis in humans of Sichuan Province follows a downward trend, suggesting that the current prevention and control work has achieved substantial outcomes. Nevertheless, the prevalence in humans at the township level is widely distributed and differs significantly, with a clear clustering in space. Therefore, precise prevention and control strategies should be formulated for clusters, specifically strengthening the “high–high” clusters at the township level.

Graphic Abstract
Automatic identification of differences in behavioral co-occurrence between groups
Authors: Tian Yiming , Maekawa Takuya , Korpela Joseph , Amagata Daichi , Hara Takahiro , Matsumoto Sakiko , Yoda Ken 
Published: June 2021

Abstract
Background
Recent advances in sensing technologies have enabled us to attach small loggers to animals in their natural habitat. It allows measurement of the animals’ behavior, along with associated environmental and physiological data and to unravel the adaptive significance of the behavior. However, because animal-borne loggers can now record multi-dimensional (here defined as multimodal) time series information from a variety of sensors, it is becoming increasingly difficult to identify biologically important patterns hidden in the high-dimensional long-term data. In particular, it is important to identify co-occurrences of several behavioral modes recorded by different sensors in order to understand an internal hidden state of an animal because the observed behavioral modes are reflected by the hidden state. This study proposed a method for automatically detecting co-occurrence of behavioral modes that differs between two groups (e.g., males vs. females) from multimodal time-series sensor data. The proposed method first extracted behavioral modes from time-series data (e.g., resting and cruising modes in GPS trajectories or relaxed and stressed modes in heart rates) and then identified two different behavioral modes that were frequently co-occur (e.g., co-occurrence of the cruising mode and relaxed mode). Finally, behavioral modes that differ between the two groups in terms of the frequency of co-occurrence were identified.

Results
We demonstrated the effectiveness of our method using animal-locomotion data collected from male and female Streaked Shearwaters by showing co-occurrences of locomotion modes and diving behavior recorded by GPS and water-depth sensors. For example, we found that the behavioral mode of high-speed locomotion and that of multiple dives into the sea were highly correlated in male seabirds. In addition, compared to the naive method, the proposed method reduced the computation costs by about 99.9%.

Conclusion
Because our method can automatically mine meaningful behavioral modes from multimodal time-series data, it can be potentially applied to analyzing co-occurrences of locomotion modes and behavioral modes from various environmental and physiological data.
The REASON score: an epigenetic and clinicopathologic score to predict risk of poor survival in patients with early stage oral squamous cell carcinoma
Authors: Viet Chi T. , Yu Gary , Asam Kesava , Thomas Carissa M. , Yoon Angela J. , Wongworawat Yan Chen , Haghighiabyaneh Mina , Kilkuts Courtney A. , McGue Caitlyn M. , Couey Marcus A. , Callahan Nicholas F. , Doan Coleen , Walker Paul C. , Nguyen Khanh , Kidd Stephanie C. , Lee Steve C. , Grandhi Anupama , Cheng Allen C. , Patel Ashish A. , Philipone Elizabeth , Ricks Olivia L. , Allen Clint T. , Aouizerat Bradley E. 
Published: June 2021

Abstract
Background
Oral squamous cell carcinoma (OSCC) is a capricious cancer with poor survival rates, even for early-stage patients. There is a pressing need to develop more precise risk assessment methods to appropriately tailor clinical treatment. Genome-wide association studies have not produced a viable biomarker. However, these studies are limited by using heterogeneous cohorts, not focusing on methylation although OSCC is a heavily epigenetically-regulated cancer, and not combining molecular data with clinicopathologic data for risk prediction. In this study we focused on early-stage (I/II) OSCC and created a risk score called the REASON score, which combines clinicopathologic characteristics with a 12-gene methylation signature, to predict the risk of 5-year mortality.

Methods
We combined data from an internal cohort (n = 515) and The Cancer Genome Atlas (TCGA) cohort (n = 58). We collected clinicopathologic data from both cohorts to derive the non-molecular portion of the REASON score. We then analyzed the TCGA cohort DNA methylation data to derive the molecular portion of the risk score.

Results
5-year disease specific survival was 63% for the internal cohort and 86% for the TCGA cohort. The clinicopathologic features with the highest predictive ability among the two the cohorts were age, race, sex, tobacco use, alcohol use, histologic grade, stage, perineural invasion (PNI), lymphovascular invasion (LVI), and margin status. This panel of 10 non-molecular features predicted 5-year mortality risk with a concordance (c)-index = 0.67. Our molecular panel consisted of a 12-gene methylation signature (i.e., HORMAD2, MYLK, GPR133, SOX8, TRPA1, ABCA2, HGFAC, MCPH1, WDR86, CACNA1H, RNF216, CCNJL), which had the most significant differential methylation between patients who survived vs. died by 5 years. All 12 genes have already been linked to survival in other cancers. Of the genes, only SOX8 was previously associated with OSCC; our study was the first to link the remaining 11 genes to OSCC survival. The combined molecular and non-molecular panel formed the REASON score, which predicted risk of death with a c-index = 0.915.

Conclusions
The REASON score is a promising biomarker to predict risk of mortality in early-stage OSCC patients. Validation of the REASON score in a larger independent cohort is warranted.
Key regulators of sensitivity to immunomodulatory drugs in cancer treatment
Authors: Wang Shichao , Li Zhiyue , Gao Shaobing 
Published: June 2021

AbstractImmunomodulatory drugs (IMiDs) include thalidomide, lenalidomide, and pomalidomide, which have shown significant efficacy in the treatment of multiple myeloma (MM), myelodysplastic syndrome (MDS) with deletion of chromosome 5q (del(5q)) and other hematological malignancies. IMiDs hijack the CRL4CRBNubiquitin ligase to target cellular proteins for ubiquitination and degradation, which is responsible for their clinical activity in MM and MDS with del(5q). However, intrinsic and acquired resistance frequently limit the efficacy of IMiDs. Recently, many efforts have been made to explore key regulators of IMiD sensitivity, resulting in great advances in the understanding of the regulatory networks related to this class of drugs. In this review, we describe the mechanism of IMiDs in cancer treatment and summarize the key regulators of IMiD sensitivity. Furthermore, we introduce genome-wide CRISPR-Cas9 screenings, through which the regulatory networks of IMiD sensitivity could be identified.