bluuebunny/crossref_metadata_2025_split huggingface dataset:
DensityPath: an algorithm to visualize and reconstruct cell state-transition path on density landscape for single-cell RNA sequencing data
Authors: Chen Ziwei , An Shaokun , Bai Xiangqi , Gong Fuzhou , Ma Liang , Wan Lin 
Published: December 2018

AbstractMotivationVisualizing and reconstructing cell developmental trajectories intrinsically embedded in high-dimensional expression profiles of single-cell RNA sequencing (scRNA-seq) snapshot data are computationally intriguing, but challenging.ResultsWe propose DensityPath, an algorithm allowing (i) visualization of the intrinsic structure of scRNA-seq data on an embedded 2-d space and (ii) reconstruction of an optimal cell state-transition path on the density landscape. DensityPath powerfully handles high dimensionality and heterogeneity of scRNA-seq data by (i) revealing the intrinsic structures of data, while adopting a non-linear dimension reduction algorithm, termed elastic embedding, which can preserve both local and global structures of the data; and (ii) extracting the topological features of high-density, level-set clusters from a single-cell multimodal density landscape of transcriptional heterogeneity, as the representative cell states. DensityPath reconstructs the optimal cell state-transition path by finding the geodesic minimum spanning tree of representative cell states on the density landscape, establishing a least action path with the minimum-transition-energy of cell fate decisions. We demonstrate that DensityPath can ably reconstruct complex trajectories of cell development, e.g. those with multiple bifurcating and trifurcating branches, while maintaining computational efficiency. Moreover, DensityPath has high accuracy for pseudotime calculation and branch assignment on real scRNA-seq, as well as simulated datasets. DensityPath is robust to parameter choices, as well as permutations of data.Availability and implementationDensityPath software is available at https://github.com/ucasdp/DensityPath.Supplementary informationSupplementary data are available at Bioinformatics online.
Evaluation of methods for generative modeling of cell and nuclear shape
Authors: Ruan Xiongtao , Murphy Robert F 
Published: December 2018

Abstract

Motivation
Cell shape provides both geometry for, and a reflection of, cell function. Numerous methods for describing and modeling cell shape have been described, but previous evaluation of these methods in terms of the accuracy of generative models has been limited.

Results
Here we compare traditional methods and deep autoencoders to build generative models for cell shapes in terms of the accuracy with which shapes can be reconstructed from models. We evaluated the methods on different collections of 2D and 3D cell images, and found that none of the methods gave accurate reconstructions using low dimensional encodings. As expected, much higher accuracies were observed using high dimensional encodings, with outline-based methods significantly outperforming image-based autoencoders. The latter tended to encode all cells as having smooth shapes, even for high dimensions. For complex 3D cell shapes, we developed a significant improvement of a method based on the spherical harmonic transform that performs significantly better than other methods. We obtained similar results for the joint modeling of cell and nuclear shape. Finally, we evaluated the modeling of shape dynamics by interpolation in the shape space. We found that our modified method provided lower deformation energies along linear interpolation paths than other methods. This allows practical shape evolution in high dimensional shape spaces. We conclude that our improved spherical harmonic based methods are preferable for cell and nuclear shape modeling, providing better representations, higher computational efficiency and requiring fewer training images than deep learning methods.

Availability and implementation
All software and data is available at http://murphylab.cbd.cmu.edu/software.

Supplementary information
Supplementary data are available at Bioinformatics online.
Comparison of vulnerability to catastrophic wind between Abies plantation forests and natural mixed forests in northern Japan
Authors: Morimoto Junko , Nakagawa Kosuke , Takano Kohei T , Aiba Masahiro , Oguro Michio , Furukawa Yasuto , Mishima Yoshio , Ogawa Kenta , Ito Rui , Takemi Tetsuya , Nakamura Futoshi , Peterson Chris J 
Published: December 2018

AbstractThe risk of extreme events due to weather and climate change, such as winds of unprecedented magnitude, is predicted to increase throughout this century. Artificial ecosystems, such as coniferous plantation forests, can suffer irreversible deterioration due to even a slight change in environmental conditions. However, few studies have examined the effects of converting natural forests to plantations on their vulnerability to catastrophic winds. By modelling the 2004 windthrow event of Typhoon Songda in northern Japan using the random forest machine learning method, we answered two questions: do Abies plantation forests and natural mixed forests differ in their vulnerability to strong winds and how do winds, topography and forest structure affect their vulnerability. Our results show that Abies plantation forests are more vulnerable to catastrophic wind than natural mixed forests under most conditions. However, the windthrow process was common to both types of forests, and the behaviour of wind inside the forests may determine the windthrow probability. Future management options for adapting to climate change were proposed based on these findings, including modifications of plantation forest structure to reduce windthrow risk and reconversion of plantations to natural forests.
Influence of fluids on VP/VS ratio: increase or decrease?
Authors: Brantut Nicolas , David Emmanuel C 
Published: December 2018

SUMMARY
The evolution of the ratio between P- and S-wave velocities (VP/VS) with increasing fluid-saturated porosity is computed for isotropic rocks containing spheroidal pores. The ratio VP/VS is shown to either decrease or increase with increasing porosity, depending on the aspect ratio α of the pores, fluid to solid bulk modulus ratio ζ and Poisson’s ratio ν0 of the solid constituents of the rock. A critical initial Poisson’s ratio ν0, crit is computed, separating cases where VP/VS increases (if ν0 &lt; ν0, crit) or decreases (if ν0 &gt; ν0, crit) with increasing porosity. For thin cracks and highly compressible fluids, ν0, crit is approximated by $0.157\, \zeta /\alpha$, whereas for spherical pores ν0, crit is given by 0.2 + 0.8ζ. When ν0 is close to ν0, crit, the evolution of VP/VS with increasing fluid-saturated porosity is near neutral and depends on subtle changes in pore shape and fluid properties. This regime is found to be relevant to partially dehydrated serpentinites in subduction zones (porosity of aspect ratio near 0.1 and ζ in the range 0.01–0.1), and makes detection of these rocks and possibly elevated fluid pressures difficult from VP/VS only.
Evolution of the Yeast Recombination Landscape
Authors: Liu Haoxuan , Maclean Calum J , Zhang Jianzhi 
Published: December 2018

AbstractMeiotic recombination comprises crossovers and noncrossovers. Recombination, crossover in particular, shuffles mutations and impacts both the level of genetic polymorphism and the speed of adaptation. In many species, the recombination rate varies across the genome with hot and cold spots. The hotspot paradox hypothesis asserts that recombination hotspots are evolutionarily unstable due to self-destruction. However, the genomic landscape of double-strand breaks (DSBs), which initiate recombination, is evolutionarily conserved among divergent yeast species, casting doubt on the hotspot paradox hypothesis. Nonetheless, because only a subset of DSBs are associated with crossovers, the evolutionary conservation of the crossover landscape could differ from that of DSBs. Here, we investigate this possibility by generating a high-resolution recombination map of the budding yeast Saccharomyces paradoxus through whole-genome sequencing of 50 meiotic tetrads and by comparing this recombination map with that of S. cerevisiae. We observe a 40% lower recombination rate in S. paradoxus than in S. cerevisiae. Compared with the DSB landscape, the crossover landscape is even more conserved. Further analyses indicate that the elevated conservation of the crossover landscape is explained by a near-subtelomeric crossover preference in both yeasts, which we find to be attributable at least in part to crossover interference. We conclude that the yeast crossover landscape is highly conserved and that the evolutionary conservation of this landscape can differ from that of the DSB landscape.
Stage IV Gestational Choriocarcinoma Diagnosed in the Third Trimester
Authors: Jorgensen Kirsten , Roychowdhury Monika , da Cunha Grace , Kim Young Bae , Schorge John O. 
Published: December 2018

BACKGROUND:
Gestational trophoblastic neoplasia rarely occurs in term pregnancies. Stage IV choriocarcinoma treated with conventional chemotherapy can result in death as a result of hemorrhagic sequelae at tumor sites.

CASE:
A 30-year-old woman at 34 weeks of gestation presented with a persistent cough, worsening dyspnea, and vaginal bleeding. Chest radiograph demonstrated innumerable lung nodules, and quantitative β-hcg concentration exceeded 1.3 million milli-international units/mL. Cesarean delivery was performed for presumed abruption. Placental pathology demonstrated choriocarcinoma, and imaging confirmed stage IV disease with a World Health Organization score of 14. Remission was achieved after two courses of low-dose induction chemotherapy followed by 10 cycles of combination chemotherapy.

CONCLUSION:
Gestational trophoblastic neoplasia should be considered in a pregnant or postpartum woman presenting with atypical vaginal bleeding. Coexistent pulmonary or neurologic findings may suggest advanced disease.
Efficacy of Misoprostol Alone for First-Trimester Medical Abortion
Authors: Raymond Elizabeth G. , Harrison Margo S. , Weaver Mark A. 
Published: December 2018

OBJECTIVE:
To summarize available data on the effectiveness and safety of single-agent misoprostol for medical abortion in the first trimester.

DATA SOURCES:
We searched MEDLINE, CABI, Cochrane, EMBASE, LILACS, the Web of Science, and ClinicalTrials.gov for English-language studies that evaluated misoprostol alone for abortion of a viable pregnancy in the first trimester.

METHODS OF STUDY SELECTION:
Our search yielded 1,562 citations, of which 38 included data from 53 trial groups that met our inclusion and exclusion criteria.

TABULATION, INTEGRATION, AND RESULTS:
We abstracted data about each trial group, including study characteristics, treatment regimen, clinical protocol, number of women treated and followed, and numbers with outcomes of interest. We used meta-analytic methods and logistic regression to examine factors associated with surgical intervention after treatment. Among all 12,829 evaluable women, 2,536 (meta-analytic estimate 22.0%, 95% CI 18.8–25.5%) had surgical uterine evacuation. Multiple factors were significantly associated with this proportion, including misoprostol amount per dose and route of administration, loss to follow-up rate, publication date, geographic region, number of misoprostol doses, duration of dosing, and time between dosing and evaluation. Of 6,359 evaluable women, 384 (meta-analytic estimate 6.8%, 95% CI 5.3–8.5%) had ongoing pregnancies. At most 26 of 12,184 evaluable women (meta-analytic estimate 0.7%, 95% CI 0.4–1.0%) were transfused or hospitalized for abortion-related reasons. In trials that provided satisfaction data, most women were satisfied or very satisfied with the treatment (meta-analytic estimate 78%, 95% CI 71–85%).

CONCLUSIONS:
Misoprostol alone is effective and safe and is a reasonable option for women seeking abortion in the first trimester. Research is indicated to further refine the regimen and to establish efficacy in the late first trimester.

SYSTEMATIC REVIEW REGISTRATION:
PROSPERO, CRD42018083589.
Stereotactic Pelvic Navigation With Augmented Reality for Transanal Total Mesorectal Excision
Authors: Kwak Jung-Myun , Romagnolo Luis , Wijsmuller Arthur , Gonzalez Cristians , Agnus Vincent , Lucchesi Fabiano R , Melani Armando , Marescaux Jacques , Dallemagne Bernard 
Published: December 2018

INTRODUCTION:
Technical difficulty and unfamiliar surgical anatomy are the main challenges in transanal total mesorectal excision. Precise 3-dimensional real-time image guidance may facilitate the safety, accuracy, and efficiency of transanal total mesorectal excision.

TECHNIQUE:
A preoperative CT was obtained with 10 skin fiducials and further processed to emphasize the border of the anatomical structure by 3-dimensional modeling and pelvic organ segmentation. A forced sacral tilt by placing a 10-degree wedge under the patient’s sacrum was induced to minimize pelvic organ movement caused by lithotomy position. An optical navigation system with cranial software was used. Preoperative CT images were loaded into the navigation system, and patient tracker was mounted onto the iliac bone. Once the patient-to-image paired point registration using skin fiducials was completed, the laparoscopic instrument mounted with instrument tracker was calibrated for instrument tracking. After validating the experimental setup and process of registration by navigating laparoscopic anterior resection, stereotactic navigation for transanal total mesorectal excision was performed in the low rectal neuroendocrine tumor.

RESULTS:
The fiducial registration error was 1.7 mm. The accuracy of target positioning was sufficient at less than 3 mm (1.8 ± 0.9 mm). Qualitative assessment using a Likert scale was well matched between the 2 observers. Of the 20 scores, 19 were judged as 4 (very good) or 5 (excellent). There was no statistical difference between mean Likert scales of the abdominal or transanal landmarks (4.4 ± 0.5 vs 4.3 ± 1.0, p = 0.965).

CONCLUSIONS:
Application of an existing navigation system to transanal total mesorectal excision for a low rectal tumor is feasible. The acceptable accuracy of target positioning justifies its clinical use. Further research is needed to prove the clinical need for the procedure and its impact on clinical outcomes.
Early life exposure to famine and reproductive aging among Chinese women
Authors: Wang Nengying , Huang Yinqiong , Wen Junping , Su Qing , Huang Yanling , Cai Liangchun , Lin Wei , Zong Liyao , Huang Huibin , Qian Xiaofang , Zhu Fengye , Sun Han , Yao Jin , Tang Kaka , Chen Ling , Liang Jixing , Li Liantao , Lin Lixiang , Lu Jieli , Bi Yufang , Wang Weiqing , Zheng Yan , Chen Gang 
Published: December 2018

Abstract

Objective:
To assess the effect of early life exposure to famine, as endured during 1959 to 1961 in China, on reproductive aging in adult women.

Methods:
Between 2011 and 2012, 2,868 women born around the Chinese famine period (1956-1964) were enrolled in this study from three communities in China. Age at natural menopause was obtained retrospectively from a structured questionnaire. The associations of early life famine exposure with reproductive aging during adulthood were estimated, with adjustment of socioeconomic status, lifestyle factors, and body mass index.

Results:
Women exposed to prenatal famine had a higher risk of early menopause (ie, natural menopause <45 years, odds ratio: 1.59, 95% confidence interval [CI]: 1.07, 2.36), and a nonsignificant trend of higher risk of premature ovarian failure (ie, natural menopause <40 y, odds ratio: 1.94, 95% CI: 0.93, 4.00), compared to unexposed women. Exposure to famine during childhood was not significantly associated with reproductive aging. In a secondary analysis focusing on the fetal exposure, prenatal famine exposure was associated with a higher risk of premature ovarian failure (odds ratio: 2.07, 95% CI: 1.08, 3.87), and a nonsignificant trend of higher risk of early menopause (odds ratio: 1.37, 95% CI: 0.98, 1.91), compared to those unexposed to prenatal famine.

Conclusions:
Our study showed that fetal exposure to famine was associated with an increased risk of early menopause. Such findings provided evidence in favor of the thrifty phenotype theory in reproductive aging and helped better understand the etiology of early menopause.
Etiology of Childhood Otorrhea in Luanda, Angola, and a Review of Otitis Media in African Children
Authors: Karppinen Mariia , Bernardino Luis , dos Anjos Elizabete , Pätäri-Sampo Anu , Pitkäranta Anne , Peltola Heikki , Pelkonen Tuula 
Published: December 2018

Background:In resource-poor settings, otorrhea causes a significant burden of disease in children. Etiologic studies and structured data on otorrhea and chronic otitis media among African children remain scarce.Methods:Here, we reviewed 678 bacteriologically analyzed otorrhea samples from Luanda Children’s Hospital from children ≤15 years of age between 2008 and 2015. We then compared these with data from other studies among African children through a literature review of 20 articles published over 2 decades.Results:Overall, 32 different bacteria were identified among 542 isolates from 654 children in Luanda. Gram-negative bacteria constituted the majority of all isolates (85%), wherebyPseudomonasspp. was the most common (n = 158; 29%), followed byProteusspp. (n = 134; 25%). AmongStaphylococcus aureus(n = 54; 10%), 69% of tested isolates were Methicillin-resistantS. aureus, and amongEnterobacteriaceae, 14% were expanded-spectrum β-lactamase isolates. Resistance to quinolones was rare. Furthermore, in a review of the literature, we found a high occurrence of otorrhea and chronic suppurative otitis media in children as well as possible gaps in existing knowledge.Conclusions:In Angola, Gram-negative rods emerged as common causative agents of otorrhea in children followed byS. aureus. The magnitude of chronic otorrhea in Africa represents a cause for public health concern.
Noninvasive approach for de novo acute hypoxemic respiratory failure: noninvasive ventilation, high-flow nasal cannula, both or none?
Authors: García-de-Acilu Marina , Patel Bhakti K. , Roca Oriol 
Published: December 2018

Purpose of review
To summarize the recent evidence regarding the use of noninvasive strategies for de novo acute hypoxemic respiratory failure (AHRF).

Recent findings
New guidelines for the use of noninvasive ventilation (NIV) in acute respiratory failure have been published. In parallel, high-flow nasal cannula (HFNC) is an emerging noninvasive strategy for AHRF patients. Although some have cautioned against the use of NIV in AHRF, new encouraging data about the use of a helmet interface for NIV in acute respiratory distress syndrome may overcome the limitations of facemask NIV.

Summary
In the last two decades, the use of NIV and HFNC in patients with AHRF has considerably expanded, changing the paradigm of management of AHRF. Choice of each technique should be based according to centre experience and patient tolerability. However, when using noninvasive strategies for AHRF, it is crucial to predefine specific criteria for intubation and monitor patients closely for early detection of clinical deterioration to avoid delayed intubation.
Reconstruction of Large Soft Tissue Defects of the Extremities in Children Using the Kiss Deep Inferior Epigastric Artery Perforator Flap to Achieve Primary Closure of Donor Site
Authors: Luo Zhenhua , Qing Liming , Zhou Zhengbing , Wu Panfeng , Yu Fang , Tang Juyu 
Published: December 2018

Background
The closure of massive skin defects remains challenging, particularly in children. In this report, we describe a technique to achieve primary donor site closure using the kiss deep inferior epigastric perforator (DIEP) flap for the reconstruction of large soft tissue defects located in the extremities of children.

Methods
From May 2011 to May 2016, a retrospective analysis was conducted on 10 pediatric patients with extensive soft tissue defects and reconstruction with double-skin paddle DIEP flap. After harvesting the flap, the skin paddle was divided into 2 separate paddles with a common vascular supply, and then the 2 paddles were sutured side by side through translating 2 paddles or rotating one of the paddles by 90 or 180 degrees, effectively doubling the width of the flap and rejoining it at the recipient site. Data on patient age, medical history, defect size, flap dimensions, recipient vessels, donor site closure, complications, and follow-up were reviewed retrospectively.

Results
Nine children had major soft tissue defects of the lower limb, and the remaining one had an upper limb defect. Only 1 case was complicated by partial necrosis of 1 paddle. Primary donor site closure was accomplished in all cases. The flaps were well matched on texture and contour, except that the 2 flaps were bulky at postoperative follow-up. There was no donor site breakdown, with only a slightly noticeable linear scar.

Conclusion
The kiss DIEP flap could be an alternative for reconstruction of large soft tissue defects of the extremities in children, with lower morbidity and improved cosmetic of the donor site.
Maxillofacial Fractures Associated With Laryngeal Injury
Authors: Wu John Chung-Han , Chen Hsin-Yu , Liao Chien-Hung , Wang Shang-Yu , Fu Chih-Yuan , Chen Chih-Hao , Chen Chien-Tzung 
Published: December 2018

ObjectiveMaxillofacial fractures with concomitant laryngeal injuries put both the quality and maintenance of life in jeopardy. Because of its low incidence, it is often overlooked in the clinical setting. The purpose of this study is to review the incidence, clinical presentations, managements, and outcomes of these patients.MethodsA retrospective analysis of medical records from 2008 to 2015 was conducted at a single institute. A case series (n = 12, which contributed 22.2% of laryngeal injuries in our institute) of these patients was presented, and propensity score matching was applied for further statistical analysis.ResultsWhen comparing patients who sustained maxillofacial fractures with concomitant laryngeal injuries with patients with only maxillofacial fractures and no laryngeal injuries, subcutaneous emphysema (83.3% vs 4.2%,P< 0.001), neck pain (75.0% vs 6.3%,P< 0.001), dyspnea (75.0% vs 0%,P< 0.001), hoarseness (41.7% vs 0%,P< 0.001), neck swelling (66.7% vs 4.2%,P= 0.012), stridor (16.7% vs 0%,P= 0.037), hemoptysis (16.7% vs 0%,P= 0.037), and thoracic trauma (58.3% vs 10.4%,P= 0.001) all showed significant differences. The length of intensive care unit stay (7.42 days vs 3.21 days,P= 0.008), ventilator use (66.7% vs 18.8%,P= 0.002), and tracheostomy (58.3% vs 0%,P< 0.001) were also significantly different.ConclusionsA significant portion of laryngeal injuries is concurrent with maxillofacial fractures. As a craniofacial surgeon, we should be alert to the signs of laryngeal injury. Diagnosis of laryngeal injuries should be established before definitive surgery for maxillofacial fractures.