bluuebunny/crossref_metadata_2025_split huggingface dataset:
Improving the Retention Rate of Fat Grafts in Recipient Areas via Botulinum Toxin A Treatment
Authors: Shi Nian , Su Yingjun , Guo Shuzhong , Zhang Zhaoxiang , Qiu Lihong , Yi Chenggang 
Published: March 2019

Abstract

Background
Improving the retention rate of transplanted fat is, currently, of great concern. Partial immobilization, angiogenesis, and adipose tissue-derived stem cells, all proven to be influenced by botulinum toxin A (BTX-A), are significant in fat graft retention.

Objectives
The authors sought to determine the impact of BTX-A on fat grafts.

Methods
Our study included 12 Sprague Dawley rats and each rat’s hind limbs were randomly designated as the BTX-A side and control side. We injected 0.2 mL of BTX-A-treated fat into the quadriceps femoris and subcutaneous space of the BTX-A sides. This was also done for the control sides but with untreated fat. We performed electroneuromyography of recipient muscles at 1 week post-operation. The rats were euthanized at 12 weeks post-operation and we observed the fat retention rate, the fat’s histologic characteristics, and the density of vessels and mature adipocytes.

Results
The amplitudes of electroneuromyography were smaller for the BTX-A sides than the control sides. For intramuscularly injected fat, the BTX-A sides had better retention rates and histologic characteristics and a higher density of vessels and mature adipocytes than the control sides. For subcutaneously injected fat, the BTX-A sides had better histologic characteristics and a higher density of vessels and mature adipocytes than the control sides, but the retention rates were not significantly different between the 2 sides.

Conclusions
Injecting BTX-A-treated fat grafts can immobilize the surrounding muscles. BTX-A can improve the density of vessels and mature adipocytes, histologic characteristics of fat grafts, and retention rate of fat grafts transplanted into muscles.
Maintenance of deceptive gifts in a natural spider population: ecological and demographic factors
Authors: Albo Maria J , Franco-Trecu Valentina , Wojciechowski Filip J , Toft Søren , Bilde Trine 
Published: March 2019

AbstractAlternative mating tactics are expected to occur predominantly when mate competition is intense, resources are in short supply, or as a result of asymmetric power relationships between individuals. Males of the nuptial gift-giving spider Pisaura mirabilis use a prevailing tactic of offering a nutritive gift (insect prey) and a deceptive tactic of offering a worthless gift (consumed prey) to prospective mates. If the male’s tactic depends on precopulatory male–male competition, worthless gifts should occur primarily late in the season, when the operational sex ratio (OSR) becomes male-biased. If it depends on resource availability and/or postcopulatory sexual selection (sperm competition), worthless gifts should occur mostly early in the mating season, when prey availability is low and most females are unmated (i.e., postcopulatory sexual selection is weak). Nuptial gift construction correlated positively with prey availability and negatively with OSR, suggesting that males increase reproductive effort when resource and mate availability increase. We did not find evidence for body condition affecting male tactic use. Male size had a marked effect on the reproductive tactic employed. Males that matured early in the season were very small and employed mostly the nutritive gift tactic during their short life. Among the males that matured later and persisted through the season, relatively small males employed the worthless gift tactic whereas large males employed the nutritive gift tactic. We suggest that the existence of 2 distinct life-history strategies among males (early small and late large size) interacts with environmental and demographic conditions to maintain the deceptive tactic.
GREP: genome for REPositioning drugs
Authors: Sakaue Saori , Okada Yukinori 
Published: March 2019

Abstract

Summary
Making use of accumulated genetic knowledge for clinical practice is our next goal in human genetics. Here we introduce GREP (Genome for REPositioning drugs), a standalone python software to quantify an enrichment of the user-defined set of genes in the target of clinical indication categories and to capture potentially repositionable drugs targeting the gene set. We show that genes identified by the large-scale genome-wide association studies were robustly enriched in the approved drugs to treat the trait of interest. This enrichment analysis was also highly applicable to other sets of biological genes such as those identified by gene expression studies and genes somatically mutated in cancers. This software should accelerate investigators to reposition drugs to other indications with the guidance of known genomics.

Availability and implementation
GREP is available at https://github.com/saorisakaue/GREP as a python source code.

Supplementary information
Supplementary data are available at Bioinformatics online.
Holistic optimization of an RNA-seq workflow for multi-threaded environments
Authors: Hung Ling-Hong , Lloyd Wes , Agumbe Sridhar Radhika , Athmalingam Ravishankar Saranya Devi , Xiong Yuguang , Sobie Eric , Yeung Ka Yee 
Published: March 2019

Abstract

Summary
For many next generation-sequencing pipelines, the most computationally intensive step is the alignment of reads to a reference sequence. As a result, alignment software such as the Burrows-Wheeler Aligner is optimized for speed and is often executed in parallel on the cloud. However, there are other less demanding steps that can also be optimized to significantly increase the speed especially when using many threads. We demonstrate this using a unique molecular identifier RNA-sequencing pipeline consisting of 3 steps: split, align, and merge. Optimization of all three steps yields a 40% increase in speed when executed using a single thread. However, when executed using 16 threads, we observe a 4-fold improvement over the original parallel implementation and more than an 8-fold improvement over the original single-threaded implementation. In contrast, optimizing only the alignment step results in just a 13% improvement over the original parallel workflow using 16 threads.

Availability and implementation
Code (M.I.T. license), supporting scripts and Dockerfiles are available at https://github.com/BioDepot/LINCS_RNAseq_cpp and Docker images at https://hub.docker.com/r/biodepot/rnaseq-umi-cpp/

Supplementary information
Supplementary data are available at Bioinformatics online.
A novel mouse model of sporadic colon cancer induced by combination of conditional Apc genes and chemical carcinogen in the absence of Cre recombinase
Authors: Souris Jeffrey S , Zhang Hannah J , Dougherty Urszula , Chen Nai-Tzu , Waller Joseph V , Lo Leu-Wei , Hart John , Chen Chin-Tu , Bissonnette Marc 
Published: March 2019

AbstractAlthough valuable insights into colon cancer biology have been garnered from human colon cancer cell lines and primary colonic tissues, and animal studies using human colon cancer xenografts, immunocompetent mouse models of spontaneous or chemically induced colon cancer better phenocopy human disease. As most sporadic human colon tumors present adenomatous polyposis coli (APC) gene mutations, considerable effort has gone into developing mice that express mutant Apc alleles that mimic human colon cancer pathogenesis. A serious limitation of many of these Apc-mutant murine models, however, is that these mice develop numerous tumors in the small intestine but few, if any, in the colon. In this work, we examined three spontaneous mouse models of colon tumorigenesis based upon the widely used multiple intestinal neoplasia (Min) mouse: mice with either constitutive or conditional Apc mutations alone or in combination with caudal-related homeobox transcription factor CDX2P-Cre transgene — either with or without exposure to the potent colon carcinogen azoxymethane. Using the CDX2 promoter to drive Cre recombinase transgene expression effectively inactivated Apc in colonocytes, creating a model with earlier tumor onset and increased tumor incidence/burden, but without the Min mouse model’s small intestine tumorigenesis and susceptibility to intestinal perforation/ulceration/hemorrhage. Most significantly, azoxymethane-treated mice with conditional Apc expression, but absent the Cre recombinase gene, demonstrated nearly 50% tumor incidence with two or more large colon tumors per mouse of human-like histology, but no small intestine tumors — unlike the azoxymethane-resistant C57BL/6J-background Min mouse model. As such this model provides a robust platform for chemoprevention studies.
Variation in ribosomal DNA copy number is associated with lung cancer risk in a prospective cohort study
Authors: Hosgood H Dean , Hu Wei , Rothman Nathaniel , Klugman Madelyn , Weinstein Stephanie J , Virtamo Jarmo R , Albanes Demetrius , Cawthon Richard , Lan Qing 
Published: March 2019

Abstract
Disruption of ribosomal DNA (rDNA) has been linked to a variety of diseases in humans, including carcinogenesis. To evaluate the associations between rDNA copy number (CN) and risk of lung cancer, we measured 5.8S and 18S rDNA CN in the peripheral blood of 229 incident lung cancer cases and 1:1 matched controls from a nested case–control study within a prospective cohort of male smokers. There was a dose–response relationship between quartiles of both 18S and 5.8S rDNA CN and risk of lung cancer (odds ratio [OR], 95% confidence interval [CI]: 18S: 1.0 [ref]; 1.2 [0.6–2.1]; 1.8 [1.0–3.4]; 2.3 [1.3–4.1; Ptrend = 0.0002; 5.8S: 1.0 [ref]; 1.6 [0.8–2.9]; 2.2 [1.1–4.2]; 2.6 [1.3–5.1]; Ptrend = 0.0001). The associations between rDNA CN and lung cancer risk were similar when excluding cases diagnosed within 5 years of follow-up, and when stratifying by heavy (>20 cigarettes per day) and light smokers (≤20 cigarettes per day).
We are the first to report that rDNA CN may be associated with future risk of lung cancer. To further elucidate the relationship between rDNA and lung cancer, replication studies are needed in additional populations, particularly those that include non-smokers.
Improving the robustness of scale-free networks by maintaining community structure
Authors: Mozafari Marzieh , Khansari Mohammad 
Published: March 2019

Abstract
Scale-free networks, which play an important role in modelling human activities, are always suffering from intentional attacks which have serious consequences on their functionality. Degree distribution and community structure are two distinguishing characteristics of these networks considered in optimizing network robustness process recently. Since community structure is known as functional modules in some networks, modifying them during the improving network robustness process may affect network performance. We propose a preferential rewiring method to improve network robustness which not only keeps degree distribution unchanged but also preserves community structure and decreases the number of rewired edges at the same time. At first, the robustness of each community is improved by applying a smart rewiring method based on the neighbourhood of nodes. Then, relations between communities are gotten more robust with a preferential rewiring based on degree and betweenness hybrid centrality of nodes. This method was applied to several types of networks including Dolphins, WU-PowerGrid and US-Airline as real-world networks and Lancichinetti–Fortunato–Radicchi benchmark model as an artificial network with the scale-free property. The results show that the proposed method enhances the robustness of all networks against degree centrality attacks between 50% and 80% and betweenness centrality attacks between 30% and 70%. Whereas, in all cases, community structure preserved more than 50%. In comparison with previous studies, the proposed method can improve network robustness more significantly and decrease the number of rewires. It also is not dependent on the attack strategy.
Genetic variation and cryptic lineage diversity of the Nigerian red-headed rock agama Agama agama associate with eco-geographic zones
Authors: Nneji Lotanna M , Adeola Adeniyi C , Yan Fang , Okeyoyin Agboola O , Oladipo Ojo C , Saidu Yohanna , Samuel Dinatu , Nneji Ifeanyi C , Adeyi Akindele O , Onadeko Abiodun B , Olagunju Temidayo E , Omotoso Olatunde , Oladipo Segun O , Iyiola Oluyinka A , Usongo John Y , Auta Timothy , Usman Abbas D , Abdullahi Halima , Ikhimiukor Odion O , Zhou Wei-Wei , Jin Jie-Qiong , Ugwumba Obih A , Ugwumba Adiaha A A , Peng Min-Sheng , Murphy Robert W , Che Jing 
Published: March 2019

AbstractNigeria is an Afrotropical region with considerable ecological heterogeneity and levels of biotic endemism. Among its vertebrate fauna, reptiles have broad distributions, thus, they constitute a compelling system for assessing the impact of ecological variation and geographic isolation on species diversification. The red-headed rock agama, Agama agama, lives in a wide range of habitats and, thus, it may show genetic structuring and diversification. Herein, we tested the hypothesis that ecology affects its genetic structure and population divergence. Bayesian inference phylogenetic analysis of a mitochondrial DNA (mtDNA) gene recovered four well-supported matrilines with strong evidence of genetic structuring consistent with eco-geographic regions. Genetic differences among populations based on the mtDNA also correlated with geographic distance. The ecological niche model for the matrilines had a good fit and robust performance. Population divergence along the environmental axes was associated with climatic conditions, and temperature ranked highest among all environmental variables for forest specialists, while precipitation ranked highest for the forest/derived savanna, and savanna specialists. Our results cannot reject the hypothesis that niche conservatism promotes geographic isolation of the western populations of Nigerian A. agama. Thus, ecological gradients and geographic isolation impact the genetic structure and population divergence of the lizards. This species might be facing threats due to recent habitat fragmentation, especially in western Nigeria. Conservation actions appear necessary.
Role of Faecal Microbiota Transplantation for Maintenance of Remission in Patients With Ulcerative Colitis: A Pilot Study
Authors: Sood Ajit , Mahajan Ramit , Singh Arshdeep , Midha Vandana , Mehta Varun , Narang Vikram , Singh Tarundeep , Singh Pannu Anmol 
Published: March 2019

AbstractObjectivesTo study the role of faecal microbiota transplantation [FMT] in maintenance of remission in ulcerative colitis [UC].MethodsIn this pilot study, patients with UC in clinical remission achieved after multi-session FMT were randomly allocated to either maintenance FMT or placebo colonoscopic infusion every 8 weeks, for 48 weeks. The standard of care [SOC] therapy was continued in all patients. The primary endpoint was maintenance of steroid-free clinical remission [Mayo score ≤2, all subscores ≤1] at Week 48. Secondary endpoints were achievement of endoscopic remission [endoscopic Mayo score 0] and histological remission [Nancy grade 0, 1] at Week 48.ResultsIn all, 61 patients in clinical remission were randomised to receive either FMT [n = 31] or placebo [n = 30]. The primary outcome was achieved in 27/31 [87.1%] patients allocated FMT versus 20/30 [66.7%] patients assigned placebo [p = 0.111]. Secondary endpoints of endoscopic remission (FMT: 18/31 [58.1%] versus placebo: 8/30 [26.7%], p = 0.026) and histological remission (FMT: 14/31 [45.2%] versus placebo: 5/30 [16.7%], p = 0. 033) were achieved in a significantly higher number of patients with FMT. Three patients receiving FMT [9.7%] and 8 patients on placebo [26.7%] relapsed. There were no serious adverse events necessitating discontinuation in patients on FMT; one patient who relapsed on placebo required colectomy.ConclusionsMaintenance FMT in patients who are in clinical remission may help sustain clinical, endoscopic and histological remission in patients with UC.
Network topology inference using information cascades with limited statistical knowledge
Authors: Ji Feng , Tang Wenchang , Tay Wee Peng , Chong Edwin K P 
Published: March 2019

AbstractWe study the problem of inferring network topology from information cascades, in which the amount of time taken for information to diffuse across an edge in the network follows an unknown distribution. Unlike previous studies, which assume knowledge of these distributions, we only require that diffusion along different edges in the network be independent together with limited moment information (e.g. the means). We introduce the concept of a separating vertex set for a graph, which is a set of vertices in which for any two given distinct vertices of the graph there exists a vertex whose distance to them is different. We show that a necessary condition for reconstructing a tree perfectly using distance information between pairs of vertices is given by the size of an observed separating vertex set. We then propose an algorithm to recover the tree structure using infection times whose differences have means corresponding to the distance between two vertices. To improve the accuracy of our algorithm, we propose the concept of redundant vertices, which allows us to perform averaging to better estimate the distance between two vertices. Though the theory is developed mainly for tree networks, we demonstrate how the algorithm can be extended heuristically to general graphs. Simulations using synthetic and real networks and experiments using real-world data suggest that our proposed algorithm performs better than some current state-of-the-art network reconstruction methods.
Adaptive control parameterization method by density functions for optimal control problems
Authors: Ejlali Nastaran , Hosseini Seyed Mohammad 
Published: March 2019

AbstractThis paper proposes an efficient adaptive control parameterization method for solving optimal control problems. In this method, mesh density functions are used to generate mesh points. In the first step, the problem is solved by control parameterization on uniform mesh points. Then at each step, the approximate control obtained from the previous step is applied to construct a mesh density function, and consequently a new adapted set of mesh points. Several numerical examples are included to demonstrate that the adaptive control parameterization method is more accurate than a uniform control parameterization one.
Recurrent/Intermittent Vaginal and Rectal Chlamydial Infection Following Treatment: A Prospective Cohort Study Among Female Sexually Transmitted Disease Clinic Patients
Authors: Khosropour Christine M , Soge Olusegun O , Suchland Robert , Leipertz Gina , Unutzer Anna , Pascual Rushlenne , Hybiske Kevin , Barbee Lindley A , Manhart Lisa E , Dombrowski Julia C , Golden Matthew R 
Published: March 2019

AbstractBackgroundRectal Chlamydia trachomatis (CT) is common among clinic-attending women, but little is known about clearance and health implications of rectal CT.MethodsAt the municipal sexually transmitted disease clinic in Seattle, Washington, in 2017–2018, we enrolled women at high risk for urogenital CT into an 8-week prospective study. Women received standard CT treatment at enrollment. Women self-collected daily rectal and vaginal specimens for nucleic acid amplification tests (NAATs) and completed weekly sexual exposure diaries. We performed CT culture on the enrollment rectal specimen.ResultsWe enrolled 50 women; 13 (26%) tested positive for vaginal (n = 11) and/or rectal (n = 11) CT. Sixty percent of women with rectal CT per NAAT were also culture positive. Median time to CT clearance after azithromycin treatment was 8.0 days for vaginal CT and 7.0 days for rectal CT. Eight women with rectal CT at enrollment had at least 1 rectal CT-positive NAAT after clearance of the initial infection; none reported anal sex.ConclusionsMost NAAT-positive rectal infections were culture positive, suggesting active infection. Time to NAAT clearance of rectal and genital tract CT was similar, and intermittent rectal CT positivity was common in the absence of anal sexual exposure. The cause of recurrent/intermittent rectal CT and the clinical implications of these infections require further study.
Data, capacity-building, and training needs to address rural health inequities in the Northwest United States: a qualitative study
Authors: Bekemeier Betty , Park Seungeun , Backonja Uba , Ornelas India , Turner Anne M 
Published: March 2019

Abstract

Objective
Rural public health system leaders struggle to access and use data for understanding local health inequities and to effectively allocate scarce resources to populations in need. This study sought to determine these rural public health system leaders’ data access, capacity, and training needs.

Materials and Methods
We conducted qualitative interviews across Alaska, Idaho, Oregon, and Washington with individuals expected to use population data for analysis or decision-making in rural communities. We used content analysis to identify themes.

Results
We identified 2 broad themes: (1) challenges in accessing or using data to monitor and address health disparities and (2) needs for training in data use to address health inequities. Participants faced challenges accessing or using data to address rural disparities due to (a) limited availability or access to data, (b) data quality issues, (c) limited staff with expertise and resources for analyzing data, and (d) the diversity within rural jurisdictions. Participants also expressed opportunities for filling capacity gaps through training—particularly for displaying and communicating data.

Discussion
Rural public health system leaders expressed data challenges, many of which can be aided by informatics solutions. These include interoperable, accessible, and usable tools that help capture, access, analyze, and display data to support health equity efforts in rural communities.

Conclusion
Informatics has the potential to address some of the daunting data-related challenges faced by rural public health system leaders working to enhance health equity. Future research should focus on developing informatics solutions to support data access and use in rural communities.
Ozone as a Potential Fumigant Alternative for the Management of Sitophilus oryzae (Coleoptera: Curculionidae) in Wheat
Authors: Amoah Barbara A , Mahroof Rizana M 
Published: March 2019

AbstractGaseous ozone, an oxidizing agent used as a disinfectant in food processing and preservation, has potential for the control of stored product insects. In this study, we investigated ozone for the management of the rice weevil, Sitophilus oryzae (L.) (Coleoptera: Curculionidae), a serious stored product insect pest. We exposed eggs, immature stages within wheat kernels, and adults of the rice weevil to 200-ppm ozone for 12, 24, 36, 48, and 60 h. Insects were placed at 5, 15, or 25 cm depth within a wheat mass in PVC pipes (10 cm in diameter, 30 cm in height) and exposed to ozone. Egg eclosion was recorded 10 d after treatment (DAT), and immature stages were observed for adult emergence 28 DAT. Adults were observed for survival immediately after ozone exposure and again at 1 and 2 DAT. Egg eclosion was significantly lower at 5 cm compared with 25 cm at all exposure times, but not the 12-h exposure time. For each exposure time tested, significantly lesser adults developed from kernels and none of the adults survived at the 5 cm depth compared with the 15 and 25 cm depths. Survival rate of adults was significantly higher at 25 cm depth than at 15 cm depth at the 24–60 h. The deeper the insect in the grain mass, the higher the survival rate. The work reported suggests that ozone is effective in killing all life stages of S. oryzae; however, the efficacy of the gas is dependent on the concentration, exposure time, depth, and gas loss.