bluuebunny/crossref_metadata_2025_split huggingface dataset:
High-resolution 3D tractography of fibrous tissue based on polarization-sensitive optical coherence tomography
Authors: Yao Gang , Duan Dongsheng 
Published: December 2019

Fibrous tissues play important roles in many parts of the body. Their highly organized directional structure is essential in achieving their normal biomechanical and physiological functions. Disruption of the typical fiber organization in these tissues is often linked to pathological changes and disease progression. Tractography is a specialized imaging method that can reveal the detailed fiber architecture. Here, we review recent developments in high-resolution optical tractography using Jones matrix polarization-sensitive optical coherence tomography. We also illustrate the use of this new tractography technology for visualizing depth-resolved, three-dimensional fibrous structures and quantifying tissue damages in several major fibrous tissues.Impact statementOrganized fiber structure plays an essential role in realizing normal biological functions in fibrous tissues. A thorough understanding of the structure–function relationship in these tissues is crucial for developing effective technology to diagnose and treat diseases. Tractography imaging is an effective tool in visualizing and quantifying fiber architecture in fibrous tissues. This review describes a recently developed tractography technology that has shown great promise for fast image of 3D fiber organization with microscopic details.
The Cell Cycle G2/M Block Is an Indicator of Cellular Radiosensitivity
Authors: Liu Chang , Nie Jing , Wang Rensheng , Mao Weidong 
Published: December 2019

Background: Determination of the radiosensitivity of a specific tumor is essential to its precision tumor radiotherapy, but the measurement of cellular radiosensitivity with a routine colony forming assay is both labor- and time-consuming. An alternative option allowing rapid and precise prediction of radiosensitivity is necessary. Methods: In this study, we exposed 4 in vitro cultured cell lines to various doses of X-rays or carbon ions and then measured their radiosensitivities with a routine colony-forming assay, and monitored the kinetics of cell cycle distribution with routine propidium iodine staining and flow cytometry. Results: Based on the results, we correlated cellular radiosensitivity with a dynamic assay of cell cycle distribution, specifically, the negative correlation of cellular radiosensitivity with the accumulated G2/M arrested cells at 48 hours after exposure. The higher the proportion of accumulated G2/M arrested cells at 48 hours after exposure, the lower the radiosensitivity of the cell line, that is, the higher radioresistance of the cell line. Conclusion: These findings provide an optional application of regular cell cycle analysis for the prediction of tumor radiosensitivity.
Comparison of outcomes of three surgical approaches for proximal interphalangeal joint arthroplasty using a surface-replacing implant
Authors: Bodmer Elvira , Marks Miriam , Hensler Stefanie , Schindele Stephan , Herren Daniel B. 
Published: December 2019

The objective was to compare outcomes of the volar, Chamay and tendon splitting approaches for proximal interphalangeal joint arthroplasty using a surface-replacing implant (CapFlex-PIP). One-hundred prospectively documented patients with a 2-year follow-up were included. Range of proximal interphalangeal joint motion, the brief Michigan Hand Outcomes Questionnaire and complications were analysed. Between baseline and follow-up, mean proximal interphalangeal joint motion increased for the volar (53° to 54°), Chamay (38° to 53°) and tendon splitting (40° to 61°) approaches. The volar approach yielded the greatest flexion and the highest extension deficit. The mean brief Michigan Hand Outcomes Questionnaire scores at baseline and 2 years were 45 and 74 (volar), 45 and 66 (Chamay) and 41 and 75 (tendon splitting). Seven patients in the Chamay group and two in the volar group required a reoperation consisting of teno-/arthrolysis. The tendon splitting approach tended to result in the best outcomes that were associated with fewer complications compared with the volar and Chamay approaches. Level of evidence: IV
Outcomes of esophagectomy after noncurative endoscopic resection of early esophageal cancer
Authors: Dermine Solène , Leconte Mahaut , Leblanc Sarah , Dousset Bertrand , Terris Benoit , Berger Arthur , Berger Anne , Rahmi Gabriel , Lepilliez Vincent , Plomteux Olivier , Leclercq Philippe , Coriat Romain , Chaussade Stanislas , Prat Frédéric , Barret Maximilien 
Published: December 2019

Background: Current guidelines recommend performing esophagectomy after endoscopic resection for early esophageal cancer when the risk of lymph node metastasis or residual cancer is found to be significant and endoscopic treatment is therefore noncurative. Our aim was to assess the safety and oncological outcomes of esophagogastric resection in this specific clinical setting. Patients and methods: A retrospective review from 2012 to 2018 was performed at four tertiary referral centers. All patients had a noncurative endoscopic resection of a clinical T1 esophageal cancer, followed by esophagectomy. Outcome measures were the rates of T0N0 specimens, overall survival, disease-free and cancer-specific survival, postoperative morbidity and mortality. Results: A total of 30 patients (13 with squamous cell carcinoma and 17 with adenocarcinoma) were included. The reasons for noncurative endoscopic resection were: positive vertical margins ( n = 12), squamous cell carcinoma with muscularis mucosae or submucosal layer invasion ( n = 3 and 9), adenocarcinoma with deep submucosal invasion ( n = 11), poorly differentiated tumor ( n = 6) and lymphovascular invasion ( n = 6). Overall, 63% of the esophagi were T0N0: most residual lesions were T1a metachronous lesions, and four (13%) patients had advanced pT status ( n = 3) or lymph node metastases ( n = 2). Overall survival, disease-free survival and cancer-specific survival were 83%, 75%, and 90% respectively. A total of 43% of patients had severe postoperative complications, and postoperative mortality was 7%. Conclusion: In this cohort, esophagectomy allowed the resection of residual advanced cancer or lymph node metastases in 13% of cases, at the cost of 43% severe morbidity and 7% mortality. Therefore, the possibility of close follow up needs to be balanced with a highly morbid surgical management in these patients.
Do Rotation and Measurement Methods Affect Reliability of Anterior Cruciate Ligament Tunnel Position on 3D Reconstructed Computed Tomography?
Authors: Moon Hyun-Soo , Choi Chong-Hyuk , Jung Min , Lee Dae-Young , Chang Hsienhao , Kim Sung-Hwan 
Published: December 2019

Background: The literature has seldom investigated the anterior cruciate ligament (ACL) tunnel position while considering the effect of rotation of 3-dimensional computed tomography (3D-CT) images during measurements. Hypothesis: We hypothesized that (1) measurement of the ACL tunnel position in the femur and tibia through use of 3D-CT is considerably influenced by rotation of the 3D model and (2) there exists a reliable measurement method for ACL tunnel position least affected by rotation. Study Design: Controlled laboratory study. Methods: The 3D-CT images of 30 randomly selected patients who underwent single-bundle ACL reconstruction were retrospectively reviewed. For femoral tunnel assessments, rectangular reference frames were used that involved the highest point of the intercondylar notch and outer margins of the lateral femoral condyle (method 1), the highest point of the intercondylar notch and outer margins of the lateral wall of the intercondylar notch (method 2), and the lowest point of the intercondylar notch and outer margins of the lateral femoral condyle (method 3). For tibial tunnel assessments, rectangular reference frames with the cortical outline at the articular surface of the tibia (method A) and the cortical outline of the proximal tibia (method B) were used. For both femoral and tibial assessments, the tunnel positions at 5°, 10°, and 15° of rotation of the 3D model were compared with that at a neutral position. Results: The values measured by methods 1 and 3 showed significant differences at greater than 5° of rotation compared with the value at the neutral position, whereas method 2 showed relatively consistent results. However, the values measured with both methods A and B showed significant differences at greater than 5° of rotation compared with the value at the neutral position. Conclusion: The tunnel position on 3D-CT images was significantly influenced by rotation during measurements. For femoral tunnel position, measurement with a reference frame using the lateral wall of the intercondylar notch (method 2) was the least affected by rotation, with relatively consistent results. Clinical Relevance: This study demonstrates that measurement using the lateral wall of the intercondylar notch might be a consistent and reliable method for evaluating the ACL femoral tunnel position considering the effect of 3D-CT image rotation during measurements. However, both methods to measure tibial tunnel position described in this study were similarly affected by rotation.
‘Paintings for a Crime’: Composed Cognitive Maps for Measuring Crime and Situation
Authors: Castro Aniyar Daniel 
Published: December 2019

The Ecuadorian State implemented policies to improve the quality and reliability of statistical material. Among these materials, composed cognitive maps were innovated and applied. These materials consist of drawings made by witnesses and victims of perceived hostile and dangerous territories that were analyzed through ethnographic and Grounded Theory Method.  This process allowed for a deeper understanding of hotspots, associated criminal situations and large victimization patterns throughout the national territory, than traditional ones. The composed cognitive maps and resulting spatial dynamics of crime helped to overcome the gap between the micro and macro level problem in criminology and gave important insights to design crime policies. We briefly describe the experience, compare the method to the traditional ones and give an example of its diagnostic potential compared to regular information managed to day by the police.
Patients with FLT3-mutant AML needed to enroll on FLT3-targeted therapeutic clinical trials
Authors: Bucy Taylor , Zoscak John M. , Mori Motomi , Borate Uma 
Published: December 2019

AbstractWe sought to identify the total number of therapeutic trials targeting FLT3-mutant acute myeloid leukemia (AML) to estimate the number of patients needed to satisfy recruitment when compared with the incidence of this mutation in the US AML population. A systematic review of all therapeutic clinical trials focusing on adult FLT3-mutated AML was conducted from 2000 to 2017. An updated search was performed using ClinicalTrials.gov for trials added between October 2017 and December 2018. Analysis was performed for ClinicalTrials.gov search results from 2000 to 2017 to provide descriptive estimates of discrepancies between anticipated clinical trial enrollment using consistently cited rates of adult participation of 1%, 3%, and 5%, as well as 10% participation identified by the American Society of Clinical Oncology in 2008. Twenty-five pharmaceutical or biological agents aimed at treating FLT3-mutant AML were identified. Pharmaceutical vs cooperative group/nonprofit support was 2.3:1, with 30 different pharmaceutical collaborators and 13 cooperative group/nonprofit collaborators. The number of patients needed to satisfy study enrollment begins to surpass the upper bound of estimated participation in 2010, noticeably surpassing projected participation rates between 2015 and 2016. The number of patients needed to satisfy study enrollment surpasses 3% and 5% rates of historical participation for US-only trials in 2017. We estimate that 15% of all US patients with FLT3-mutant AML would have to enroll in US and internationally accruing trials to satisfy requirements in 2017, or approximately 3 times the upper level of historical participation rates in the United States. The current clinical trial agenda in this space requires high percentage enrollment for sustainability.
Genomic analyses of flow-sorted Hodgkin Reed-Sternberg cells reveal complementary mechanisms of immune evasion
Authors: Wienand Kirsty , Chapuy Bjoern , Stewart Chip , Dunford Andrew J. , Wu David , Kim Jaegil , Kamburov Atanas , Wood Timothy R. , Cader Fathima Zumla , Ducar Matthew D. , Thorner Aaron R. , Nag Anwesha , Heubeck Alexander T. , Buonopane Michael J. , Redd Robert A. , Bojarczuk Kamil , Lawton Lee N. , Armand Philippe , Rodig Scott J. , Fromm Jonathan R. , Getz Gad , Shipp Margaret A. 
Published: December 2019

Key Points
Analyses of recurrent mutations, copy number alterations, and structural variants reveal complementary immune evasion mechanisms in cHL. The mutational burden in EBV– cHLs is among the highest reported, potentially contributing to the efficacy of PD-1 blockade.
Editorial focus: understanding off-target effects as the key to successful RNAi therapy
Authors: Bartoszewski Rafal , Sikorski Aleksander F. 
Published: December 2019

AbstractWith the first RNA interference (RNAi) drug (ONPATTRO (patisiran)) on the market, we witness the RNAi therapy field reaching a critical turning point, when further improvements in drug candidate design and delivery pipelines should enable fast delivery of novel life changing treatments to patients. Nevertheless, ignoring parallel development of RNAi dedicated in vitro pharmacological profiling aiming to identify undesirable off-target activity may slow down or halt progress in the RNAi field. Since academic research is currently fueling the RNAi development pipeline with new therapeutic options, the objective of this article is to briefly summarize the basics of RNAi therapy, as well as to discuss how to translate basic research into better understanding of related drug candidate safety profiles early in the process.
Near-Infrared Photoelectric Properties of Multilayer Bi2O2Se Nanofilms
Authors: Yang Hang , Chen Wei , Zheng Xiaoming , Yang Dongsheng , Hu Yuze , Zhang Xiangzhe , Ye Xin , Zhang Yi , Jiang Tian , Peng Gang , Zhang Xueao , Zhang Renyan , Deng Chuyun , Qin Shiqiao 
Published: December 2019

AbstractThe near-infrared (NIR) photoelectric properties of multilayer Bi2O2Se nanofilms were systematically studied in this paper. Multilayer Bi2O2Se nanofilms demonstrate a sensitive photo response to NIR, including a high photoresponsivity (~ 101 A/W), a quick response time (~ 30 ms), a high external quantum efficiency (~ 20,300%), and a high detection rate (1.9 × 1010 Jones). These results show that the device based on multilayer Bi2O2Se nanofilms might have great potentials for future applications in ultrafast, highly sensitive NIR optoelectronic devices.
flowEMMi: an automated model-based clustering tool for microbial cytometric data
Authors: Ludwig Joachim , zu Siederdissen Christian Höner , Liu Zishu , Stadler Peter F. , Müller Susann 
Published: December 2019

AbstractBackgroundFlow cytometry (FCM) is a powerful single-cell based measurement method to ascertain multidimensional optical properties of millions of cells. FCM is widely used in medical diagnostics and health research. There is also a broad range of applications in the analysis of complex microbial communities. The main concern in microbial community analyses is to track the dynamics of microbial subcommunities. So far, this can be achieved with the help of time-consuming manual clustering procedures that require extensive user-dependent input. In addition, several tools have recently been developed by using different approaches which, however, focus mainly on the clustering of medical FCM data or of microbial samples with a well-known background, while much less work has been done on high-throughput, online algorithms for two-channel FCM.ResultsWe bridge this gap with , a model-based clustering tool based on multivariate Gaussian mixture models with subsampling and foreground/background separation. These extensions provide a fast and accurate identification of cell clusters in FCM data, in particular for microbial community FCM data that are often affected by irrelevant information like technical noise, beads or cell debris. outperforms other available tools with regard to running time and information content of the clustering results and provides near-online results and optional heuristics to reduce the running-time further.Conclusionsis a useful tool for the automated cluster analysis of microbial FCM data. It overcomes the user-dependent and time-consuming manual clustering procedure and provides consistent results with ancillary information and statistical proof.
Genomic insights into mite phylogeny, fitness, development, and reproduction
Authors: Zhang Yan-Xuan , Chen Xia , Wang Jie-Ping , Zhang Zhi-Qiang , Wei Hui , Yu Hai-Yan , Zheng Hong-Kun , Chen Yong , Zhang Li-Sheng , Lin Jian-Zhen , Sun Li , Liu Dong-Yuan , Tang Juan , Lei Yan , Li Xu-Ming , Liu Min 
Published: December 2019

AbstractBackgroundPredatory mites (Acari: Phytoseiidae) are the most important beneficial arthropods used in augmentative biological pest control of protected crops around the world. However, the genomes of mites are far less well understood than those of insects and the evolutionary relationships among mite and other chelicerate orders are contested, with the enigmatic origin of mites at one of the centres in discussion of the evolution of Arachnida.ResultsWe here report the 173 Mb nuclear genome (from 51.75 Gb pairs of Illumina reads) of the predatory mite,Neoseiulus cucumeris, a biocontrol agent against pests such as mites and thrips worldwide. We identified nearly 20.6 Mb (~ 11.93% of this genome) of repetitive sequences and annotated 18,735 protein-coding genes (a typical gene 2888 bp in size); the total length of protein-coding genes was about 50.55 Mb (29.2% of this assembly). About 37% (6981) of the genes are unique toN. cucumerisbased on comparison with other arachnid genomes. Our phylogenomic analysis supported the monophyly of Acari, therefore rejecting the biphyletic origin of mites advocated by other studies based on limited gene fragments or few taxa in recent years. Our transcriptomic analyses of different life stages ofN. cucumerisprovide new insights into genes involved in its development. Putative genes involved in vitellogenesis, regulation of oviposition, sex determination, development of legs, signal perception, detoxification and stress-resistance, and innate immune systems are identified.ConclusionsOur genomics and developmental transcriptomics analyses ofN. cucumerisprovide invaluable resources for further research on the development, reproduction, and fitness of this economically important mite in particular and Arachnida in general.
Bias in estimates of variance components in populations undergoing genomic selection: a simulation study
Authors: Gao Hongding , Madsen Per , Aamand Gert Pedersen , Thomasen Jørn Rind , Sørensen Anders Christian , Jensen Just 
Published: December 2019

Abstract
Background
After the extensive implementation of genomic selection (GS), the choice of the statistical model and data used to estimate variance components (VCs) remains unclear. A primary concern is that VCs estimated from a traditional pedigree-based animal model (P-AM) will be biased due to ignoring the impact of GS. The objectives of this study were to examine the effects of GS on estimates of VC in the analysis of different sets of phenotypes and to investigate VC estimation using different methods. Data were simulated to resemble the Danish Jersey population. The simulation included three phases: (1) a historical phase; (2) 20 years of conventional breeding; and (3) 15 years of GS. The three scenarios based on different sets of phenotypes for VC estimation were as follows: (1) Pheno1: phenotypes from only the conventional phase (1–20 years); (2) Pheno1 + 2: phenotypes from both the conventional phase and GS phase (1–35 years); (3) Pheno2: phenotypes from only the GS phase (21–35 years). Single-step genomic BLUP (ssGBLUP), a single-step Bayesian regression model (ssBR), and P-AM were applied. Two base populations were defined: the first was the founder population referred to by the pedigree-based relationship (P-base); the second was the base population referred to by the current genotyped population (G-base).

Results
In general, both the ssGBLUP and ssBR models with all the phenotypic and genotypic information (Pheno1 + 2) yielded biased estimates of additive genetic variance compared to the P-base model. When the phenotypes from the conventional breeding phase were excluded (Pheno2), P-AM led to underestimation of the genetic variance of P-base. Compared to the VCs of G-base, when phenotypes from the conventional breeding phase (Pheno2) were ignored, the ssBR model yielded unbiased estimates of the total genetic variance and marker-based genetic variance, whereas the residual variance was overestimated.

Conclusions
The results show that neither of the single-step models (ssGBLUP and ssBR) can precisely estimate the VCs for populations undergoing GS. Overall, the best solution for obtaining unbiased estimates of VCs is to use P-AM with phenotypes from the conventional phase or phenotypes from both the conventional and GS phases.
LRScaf: improving draft genomes using long noisy reads
Authors: Qin Mao , Wu Shigang , Li Alun , Zhao Fengli , Feng Hu , Ding Lulu , Ruan Jue 
Published: December 2019

Abstract
Background
The advent of third-generation sequencing (TGS) technologies opens the door to improve genome assembly. Long reads are promising for enhancing the quality of fragmented draft assemblies constructed from next-generation sequencing (NGS) technologies. To date, a few algorithms that are capable of improving draft assemblies have released. There are SSPACE-LongRead, OPERA-LG, SMIS, npScarf, DBG2OLC, Unicycler, and LINKS. Hybrid assembly on large genomes remains challenging, however.

Results
We develop a scalable and computationally efficient scaffolder, Long Reads Scaffolder (LRScaf, https://github.com/shingocat/lrscaf), that is capable of significantly boosting assembly contiguity using long reads. In this study, we summarise a comprehensive performance assessment for state-of-the-art scaffolders and LRScaf on seven organisms, i.e., E. coli, S. cerevisiae, A. thaliana, O. sativa, S. pennellii, Z. mays, and H. sapiens. LRScaf significantly improves the contiguity of draft assemblies, e.g., increasing the NGA50 value of CHM1 from 127.1 kbp to 9.4 Mbp using 20-fold coverage PacBio dataset and the NGA50 value of NA12878 from 115.3 kbp to 12.9 Mbp using 35-fold coverage Nanopore dataset. Besides, LRScaf generates the best contiguous NGA50 on A. thaliana, S. pennellii, Z. mays, and H. sapiens. Moreover, LRScaf has the shortest run time compared with other scaffolders, and the peak RAM of LRScaf remains practical for large genomes (e.g., 20.3 and 62.6 GB on CHM1 and NA12878, respectively).

Conclusions
The new algorithm, LRScaf, yields the best or, at least, moderate scaffold contiguity and accuracy in the shortest run time compared with other scaffolding algorithms. Furthermore, LRScaf provides a cost-effective way to improve contiguity of draft assemblies on large genomes.