bluuebunny/crossref_metadata_2025_split huggingface dataset:
Fecal DNA methylation markers for detecting stages of colorectal cancer and its precursors: a systematic review
Authors: Raut Janhavi R. , Guan Zhong , Schrotz-King Petra , Brenner Hermann 
Published: August 2020

Abstract
Background
DNA methylation biomarkers in stool may have applications in early colorectal cancer (CRC) detection; however, their association with stages of CRC carcinogenesis or their performance in detecting various stages is unclear. We aimed to systematically review the evidence for DNA methylation markers in stool for risk stratification or detection of specific CRC stages, as well as precursors of CRC.

Methods
We conducted a systematic search in line with the Preferred Reporting Items for Systematic Reviews and Meta-Analyses guidelines. We searched PubMed and ISI Web of Knowledge to identify relevant studies published until 14th January 2020. Two reviewers independently extracted data on study population characteristics, candidate genes, methylation measurement methods, odds ratios (ORs), overall and stage-specific sensitivities, specificities, areas under the receiver operating characteristics curve, and p-values for statistical significance for OR and for association of methylation levels with stage.

Results
Twenty-seven studies that reported stage-specific associations or performances of fecal DNA methylation markers for detecting colorectal neoplasms were identified. All studies used methylation-specific polymerase chain reaction for assessing methylation levels in the promoter or exon 1 regions of targeted genes. However, most studies were underpowered and limited by their case-control design. Furthermore, the stage-specific associations or sensitivities were validated for two markers (hypermethylation of GATA4 and VIM) only.

Conclusion
Methylation markers in stool may be useful for detection of CRC precursors or CRC staging, but promising candidate markers need to be validated in longitudinal studies on large screening populations, performing epigenome-wide analyses. Identification of stage-specific DNA methylation biomarkers in stool could boost current strategies towards early detection and enable different approaches to precision medicine for CRC.
Gasping during refractory out-of-hospital cardiac arrest is a prognostic marker for favourable neurological outcome following extracorporeal cardiopulmonary resuscitation: a retrospective study
Authors: Bunya Naofumi , Ohnishi Hirofumi , Wada Kenshiro , Kakizaki Ryuichiro , Kasai Takehiko , Nagano Nobutaka , Kokubu Nobuaki , Miyata Kei , Uemura Shuji , Harada Keisuke , Narimatsu Eichi 
Published: August 2020

Abstract
Background
Gasping during cardiac arrest is associated with favourable neurological outcomes for out-of-hospital cardiac arrest. Moreover, while extracorporeal cardiopulmonary resuscitation (ECPR) performed for refractory cardiac arrest can improve outcomes, factors for favourable neurological outcomes remain unknown. This study aimed to examine whether gasping during cardiac arrest resuscitation during transport by emergency medical services (EMS) was independently associated with a favourable neurological outcome for patients who underwent ECPR. This retrospective study was based on medical records of all adult patients who underwent ECPR due to refractory cardiac arrest. The primary endpoint was neurologically intact survival at discharge. The study was undertaken at Sapporo Medical University Hospital, a tertiary care centre approved by the Ministry of Health, Labour and Welfare, located in the city of Sapporo, Japan, between January 2012 and December 2018.

Results
Overall, 166 patients who underwent ECPR were included. During transportation by EMS, 38 patients exhibited gasping, and 128 patients did not. Twenty patients who exhibited gasping during EMS transportation achieved a favourable neurological outcome (20/38; 52.6%); 14 patients who did not exhibit gasping achieved a favourable neurological outcome (14/128; 10.9%). Gasping during transportation by EMS was independently associated with favourable neurological outcome irrespective of the type of analysis performed (multiple logistic regression analysis, odds ratio [OR] 9.52; inverse probability of treatment weighting using propensity score, OR 9.14).

Conclusions
The presence of gasping during transportation by EMS was independently associated with a favourable neurological outcome in patients who underwent ECPR. The association of gasping with a favourable neurological outcome in patients with refractory cardiac arrest suggests that ECPR may be considered in such patients.
Spatially coupled turbo-coded continuous phase modulation: asymptotic analysis and optimization
Authors: Benaddi Tarik , Poulliat Charly 
Published: August 2020

AbstractFor serially or parallel concatenated communication systems, spatial coupling techniques enable to improve the threshold of these systems under iterative decoding using belief propagation (BP). For the case of low-density parity-check (LDPC) codes, it has been shown that, under some asymptotic assumptions, spatially coupled ensembles have BP thresholds that approach the bitwise maximum a posteriori (MAP) threshold of the related uncoupled ensemble. This phenomenon is often referred to asthreshold saturation, and it has sometimes very important consequences. For example, in the case of regular LDPC code ensembles, spatial coupling enables to achieve asymptotically the capacity for any class of binary memoryless symmetric channels. Since then, this threshold saturation has been conjectured or proved for several other types of concatenations. In this work, we consider a serially concatenated scheme which is the serial concatenation of a simple outer convolutional code and a continuous phase modulator (CPM) separated by an interleaver. Then, we propose a method to do the spatial coupling of several replicas of this serially concatenated scheme, aiming to improve the asymptotic convergence threshold. First, exploiting the specific structure of the proposed system, an original procedure is proposed in order to terminate the spatially coupled turbo-coded CPM scheme. In particular, the proposed procedure aims to ensure the continuity of the transmitted signal among spatially coupled replicas, enabling to keep one of the core characteristics and advantages of coded CPM schemes. Then, based on an asymptotic analysis, we show that the proposed scheme has very competitive thresholds when compared to carefully designed spatially coupled LDPC codes. Furthermore, it is shown how we can accelerate the convergence rate of the designed systems by optimizing the connection distributions in the coupling matrices. Finally, by investigating on different continuous phase modulation schemes, we corroborate the conjecture stating that spatially coupled turbo-coded CPM schemes saturate to a lower bound very close to the threshold given by the extrinsic information transfer (EXIT) area theorem.
CRISPR-Cas system: a potential alternative tool to cope antibiotic resistance
Authors: Aslam Bilal , Rasool Maria , Idris Adi , Muzammil Saima , Alvi Roman Farooq , Khurshid Mohsin , Rasool Muhammad Hidayat , Zhang Derong , Ma Zhongren , Baloch Zulqarnain 
Published: August 2020

AbstractAntibiotic exposure leads to massive selective pressures that initiate the emergence and spread of antibiotic resistance in commensal and pathogenic bacteria. The slow process of developing new antibiotics makes this approach counterintuitive for combatting the rapid emergence of new antibiotic resistant pathogens. Therefore, alternative approaches such as, the development of nucleic acid-based anti-bacterial treatments, anti-bacterial peptides, bacteriocins, anti-virulence compounds and bacteriophage therapies should be exploited to cope infections caused by resistant superbugs. In this editorial, we discuss how the newly popular CRISPR-Cas system has been applied to combat antibiotic resistance.
Heat stress on calves and heifers: a review
Authors: Wang Jingjun , Li Jinghui , Wang Fengxia , Xiao Jianxin , Wang Yajing , Yang Hongjian , Li Shengli , Cao Zhijun 
Published: August 2020

AbstractThe current review is designed with aims to highlight the impact of heat stress (HS) on calves and heifers and to suggest methods for HS alleviation. HS occurs in animals when heat gain from environment and metabolism surpasses heat loss by radiation, convection, evaporation and conduction. Although calves and heifers are comparatively heat resistant due to less production of metabolic heat and more heat dissipation efficiency, they still suffer from HS to some degree. Dry matter intake and growth performance of calves and heifers are reduced during HS because of redistributing energy to heat regulation through a series of physiological and metabolic responses, such as elevated blood insulin and protein catabolism. Enhanced respiration rate and panting during HS accelerate the loss of CO2, resulting in altered blood acid-base chemistry and respiratory alkalosis. HS-induced alteration in rumen motility and microbiota affects the feed digestibility and rumen fermentation. Decreased luteinizing hormone, estradiol and gonadotrophins due to HS disturb the normal estrus cyclicity, depress follicular development, hence the drop in conception rate. Prenatal HS not only suppresses the embryonic development by the impaired placenta, which results in hypoxia and malnutrition, but also retards the growth, immunity and future milk production of newborn calves. Based on the above challenges, we attempted to describe the possible impacts of HS on growth, health, digestibility and reproduction of calves and heifers. Likewise, we also proposed three primary strategies for ameliorating HS consequences. Genetic development and reproductive measures, such as gene selection and embryo transfers, are more likely long-term approaches to enhance heat tolerance. While physical modification of the environment, such as shades and sprinkle systems, is the most common and easily implemented measure to alleviate HS. Additionally, nutritional management is another key approach which could help calves and heifers maintain homeostasis and prevent nutrient deficiencies because of HS.
Abandoned landscape project design
Authors: Biddau Giovanni Maria , Marotta Antonello , Sanna Gianfranco 
Published: August 2020

AbstractConversion and transformation of historic buildings and industrial site reclamation projects are becoming topics of renewed interest. Many industrial buildings beckon architecture design theory to revitalize urban areas and make new use of public space. Ruins and historic sites speak to us about the need to rethink settings which belong to long-lost ages and yet are contemporary in the stories they reveal. There are present-day problematic and sensitive areas (abandoned quarries, ex industrial plants, landfills, etc.) which inspire renewed critical thinking; themes of memory and recollection touch us in the here and now. In contrast with the 1970s and 1980 s’ tendency to treat such topics with a mix of lightheartedness and nostalgia, the projects presented in this work regard history as a process of revision and reclamation of profound spatial and social principles. Contact with historic, industrial and modern spaces pushes us to apply new methodological approaches in an effort to re-write the present. In fact, nowadays it is imperative that we engage a relationship with the past which takes into consideration not only ancient legacies but also those entrenched in 20th century crises—uncomfortable memories often embodied in areas of great landscape or historic value. How are we to approach our relationship with these legacies? Critical studies illustrate the value of those projects capable of breathing new life into the fabric of urban space by creating public areas and city parks. Memory, seemingly pushed into a playful, irreverently lighthearted vein for years, is thus allowed once again to speak to us of the human and social desire to reclaim time and provide urban and suburban areas with new opportunities for regeneration and growth.
Coeruptive and posteruptive crustal deformation associated with the 2018 Kusatsu-Shirane phreatic eruption based on PALSAR-2 time series analysis
Authors: Himematsu Yuji , Ozawa Taku , Aoki Yosuke 
Published: August 2020

AbstractCoeruptive deformation helps to interpret physical processes associated with volcanic eruptions. Because phreatic eruptions cause small, localized coeruptive deformation, we sometimes fail to identify plausible deformation signals. Satellite synthetic aperture radar (SAR) data allow us to identify extensive deformation fields with high spatial resolutions. Herein, we report coeruptive crustal deformation associated with the 2018 Kusatsu-Shirane phreatic eruption detected by time series analyses of L-band satellite SAR (ALOS-2/PALSAR-2) data. Cumulative deformation maps derived from SAR time series analyses show that subsidence and eastward displacement dominate the southwestern side of an eruptive crater with a spatial extent of approximately 2 km in diameter. Although we were unable to identify any significant deformation signals before the 2018 eruption, posteruptive deformation on the southwestern side of the crater has been ongoing until the end of 2019. This prolonged deformation implies the progression of posteruptive physical processes within a confined hydrothermal system, such as volcanic fluid discharge, similar to the processes observed during the 2014 Ontake eruption. Although accumulated snow and dense vegetation hinder the detection of deformation signals on Kusatsu-Shirane volcano using conventional InSAR data, L-band SAR with various temporal baselines allowed us to successfully extract both coeruptive and posteruptive deformation signals. The extracted cumulative deformation is well explained by a combination of normal faulting with a left-lateral slip component along a southwest-dipping fault plane and an isotropic deflation. Based on the geological background in which the shallow hydrothermal system develops across Kusatsu-Shirane volcano, the inferred dislocation plane can be considered as a degassing pathway from the shallow hydrothermal system to the surface due to the phreatic eruption. We reconfirmed that SAR data are a robust tool for detecting coeruptive and posteruptive deformations, which are helpful for understanding shallow physical processes associated with phreatic eruptions at active volcanoes.
Implant-supported fixed and removable prostheses in the fibular mandible
Authors: Nguyen Truc Thi Hoang , Eo Mi Young , Myoung Hoon , Kim Myung-Joo , Kim Soung Min 
Published: August 2020

Abstract
Background
To restore the health-related quality of life (HRQoL) of patients who underwent jaw resection and reconstruction surgery, dental rehabilitation is an essential procedure and also one of the most challenging for oral and maxillofacial surgeons. Even though recent studies have reported the possibility and reliability of dental implant rehabilitation with the fibula free flap (FFF), clinical reports of long-term follow-up cases are scarce. We herein reported seven cases of FFF reconstruction and implant rehabilitation. We also discussed implant planning strategy and surgical techniques.

Methods
From 2012 to 2019, seven patients were treated with FFF reconstructive jaw surgery combined with dental implant installation and fabrication of implant-supported prostheses at Seoul National University Dental Hospital, Seoul, Korea. Patient characteristics and FFF treatment results were collected. Records of dental implants were analyzed clinically and radiologically.

Results
Among the seven patients in this report, there were three males and four females, with an average age of 54.4 years. A total of 39 implants were placed in the fibular bone. The mean follow-up period after implant installation was 24 months. Five implants failed and were removed 3 months after installation. The implant success rate was 87.2%. Marginal bone loss at 12 months after loading was 0.23 ± 0.18 mm on the mesial side and 0.25 ± 0.26 mm on the distal side.

Conclusion
With the challenges present in FFF-reconstructed patients, an implant-supported prosthesis is a reliable option for stable and functional oral rehabilitation. The implant-supported prosthesis on the FFF has great results regarding restoration of function (mastication, swallowing, and speaking), appearance, and overall HRQoL. Collaboration between surgeons and prosthodontists is essential for a satisfying outcome.
Global Health in Preconception, Pregnancy and Postpartum Alliance: development of an international consumer and community involvement framework
Authors: Bergmeier Heidi J. , Vandall-Walker Virginia , Skrybant Magdalena , Teede Helena J. , Bailey Cate , Baxter Jo-Anna B. , Borges Ana Luiza Vilela , Boyle Jacqueline A. , Everitt Ayesha , Harrison Cheryce L. , Herrera Margely , Hill Briony , Jack Brian , Jones Samuel , Jorgensen Laura , Lim Siew , Montanaro Cynthia , Redman Leanne M. , Stephenson Judith , Sundseth Hildrun , Thangaratinam Shakila , Thynne Paula , Walker Ruth , Skouteris Helen 
Published: August 2020

Abstract
Background
The goal of the Global Health in Preconception, Pregnancy and Postpartum (HiPPP) Alliance, comprising consumers and leading international multidisciplinary academics and clinicians, is to generate research and translation priorities and build international collaboration around healthy lifestyle and obesity prevention among women across the reproductive years. In doing so, we actively seek to involve consumers in research, implementation and translation initiatives. There are limited frameworks specifically designed to involve women across the key obesity prevention windows before (preconception), during and after pregnancy (postpartum). The aim of this paper is to outline our strategy for the development of the HiPPP Consumer and Community (CCI) Framework, with consumers as central to co-designed, co-implemented and co-disseminated research and translation.

Method
The development of the framework involved three phases: In Phase 1, 21 Global HiPPP Alliance members participated in a CCI workshop to propose and discuss values and approaches for framework development; Phase 2 comprised a search of peer-reviewed and grey literature for existing CCI frameworks and resources; and Phase 3 entailed collaboration with consumers (i.e., members of the public with lived experience of weight/lifestyle issues in preconception, pregnancy and postpartum) and international CCI experts to workshop and refine the HiPPP CCI Framework (guided by Phases 1 and 2).

Results
The HiPPP CCI Framework’s values and approaches identified in Phases 1–2 and further refined in Phase 3 were summarized under the following five key principles: 1. Inclusive, 2. Flexible, 3. Transparent, 4. Equitable, and 5. Adaptable. The HiPPP Framework describes values and approaches for involving consumers in research initiatives from design to translation that focus on improving healthy lifestyles and preventing obesity specifically before, during and after pregnancy; importantly it takes into consideration common barriers to partnering in obesity research during perinatal life stages, such as limited availability associated with family caregiving responsibilities.

Conclusion
The HiPPP CCI Framework aims to describe approaches for implementing meaningful CCI initiatives with women in preconception, pregnancy and postpartum periods. Evaluation of the framework is now needed to understand how effective it is in facilitating meaningful involvement for consumers, researchers and clinicians, and its impact on research to improve healthy lifestyle outcomes.
Brassicaceous roots as an unexpected diversity hot-spot of helotialean endophytes
Authors: Maciá-Vicente Jose G. , Piepenbring Meike , Koukol Ondřej 
Published: August 2020

AbstractA high number of fungal strains were isolated from roots of Brassicaceae species collected across western and southern Europe, resulting in an unexpectedly rich collection of Cadophora species. These isolates enable us to present a new and comprehensive view of the ecological, morphological, and phylogenetic traits of root-inhabiting members of this helotialean genus. We provide phylogenetic placement of all of our isolates based on a four-gene dataset, analyze their phenotypic traits in relation to their phylogenetic relationships, and infer the potential distribution ranges of the species by sequence comparisons with available databases. We consider seven well supported phylogenetic lineages as species new to science. Six further lineages probably also represent new species but remain undescribed due to the lack of diagnostic morphological characters. Our results show that Cadophora, as currently circumscribed, is paraphyletic and encompasses a broad spectrum of morphologies and lifestyles. Among the new species, only two (C. ferruginea and C. constrictospora) form phialides and conidia typical of Cadophora, three species (C. echinata, C. gamsii and C. variabilis) produce chains of swollen hyphal segments that may function as holoblastic conidia, and one species (C. fascicularis) produces chains of holoblastic ramoconidia and conidia. Ancestral state reconstruction analysis suggests that phialidic conidiogenesis evolved several times in Cadophora s. lat. from a putatively holoblastic common ancestor. Most Cadophora lineages are rare as estimated from the availability of sequence data, in spite of having relatively wide distribution ranges, whereas five lineages may represent endemic relationships given their restricted distributions. Our dataset, probably the most comprehensive available for Cadophora, nevertheless shows knowledge gaps concerning the phylogenetic relationships within this genus and highlights a need for further investigation.