bluuebunny/crossref_metadata_2025_split huggingface dataset:
Internet-based self-sampling for
Chlamydia trachomatis
testing: a national evaluation in Sweden
Authors: Söderqvist Joakim , Gullsby Karolina , Stark Lisa , Wikman Maria , Karlsson Roger , Herrmann Bjőrn 
Published: January 2020

Objective

Internet-based testing for
Chlamydia trachomatis
(CT) with self-sampling at home has gradually been implemented in Sweden since 2006 as a free-of-charge service within the public healthcare system. This study evaluated the national diagnostic outcome of this service.

Methods
Requests for data on both self-sampling at home and clinic-based sampling for CT testing were sent to the laboratories in 18 of 21 counties. Four laboratories were also asked to provide data on testing patterns at the individual level for the years 2013–2017.

Results
The proportion of self-sampling increased gradually from 2013, comprising 22.0% of all CT tests in Sweden in 2017. In an analysis of 14 counties (representing 83% of the population), self-sampling increased by 115% between 2013 and 2017 for women, compared with 71% for men, while test volumes for clinic-based sampling were fairly constant for both sexes (1.8% increase for women, 15% increase for men). In 2017 self-sampling accounted for 20.3% of all detected CT cases, and the detection rate was higher than, but similar to, clinic-based testing (5.5% vs 5.1%). The proportion of self-sampling men was also higher, but similar (33.7% vs 30.8%). Analysis of individual testing patterns in four counties over 5 years showed a higher proportion of men using self-sampling only (67%, n=10 533) compared with women (40%, n=8885).

Conclusions
Self-sampling has increased substantially in recent years, especially among women. This service is at least as beneficial as clinic-based screening for detection of CT, and self-sampling reaches men more than clinic-based testing.
Electron acceleration at ELI-Beamlines: Towards high-energy and high-repetition rate accelerators
Authors: Lazzarini C. M. , Goncalves L. V. , Grittani G. M. , Lorenz S. , Nevrkla M. , Valenta P. , Levato T. , Bulanov S. V. , Korn G. 
Published: January 2020

The high energy electron experimental platform * at ELI-Beamlines will give to the users high energy tunable electron beams with low energy spread and divergence, by employing laser-wakefield-acceleration scheme (LWFA) driven by PW-class laser system working at 10 Hz. The platform will offer great flexibility over electron beam parameter space and is foreseen to exploit different targets, acceleration and laser-guiding advanced schemes. In this paper we summarize about more compact accelerators that can be envisioned by the use of really short (near single-cycle) fem-mJ-level laser pulses interacting with nanoparticle and solid targets, as well as with specific near-critical density targets. * Originally developed as H.E.L.L., within the Particle acceleration by Laser program (RP3).
Therapy-Induced Senescence Drives Bone Loss
Authors: Yao Zhangting , Murali Bhavna , Ren Qihao , Luo Xianmin , Faget Douglas V. , Cole Tom , Ricci Biancamaria , Thotala Dinesh , Monahan Joseph , van Deursen Jan M. , Baker Darren , Faccio Roberta , Schwarz Julie K. , Stewart Sheila A. 
Published: January 2020

Abstract

Chemotherapy is important for cancer treatment, however, toxicities limit its use. While great strides have been made to ameliorate the acute toxicities induced by chemotherapy, long-term comorbidities including bone loss remain a significant problem. Chemotherapy-driven estrogen loss is postulated to drive bone loss, but significant data suggests the existence of an estrogen-independent mechanism of bone loss. Using clinically relevant mouse models, we showed that senescence and its senescence-associated secretory phenotype (SASP) contribute to chemotherapy-induced bone loss that can be rescued by depleting senescent cells. Chemotherapy-induced SASP could be limited by targeting the p38MAPK-MK2 pathway, which resulted in preservation of bone integrity in chemotherapy-treated mice. These results transform our understanding of chemotherapy-induced bone loss by identifying senescent cells as major drivers of bone loss and the p38MAPK–MK2 axis as a putative therapeutic target that can preserve bone and improve a cancer survivor's quality of life.

Significance:
Senescence drives chemotherapy-induced bone loss that is rescued by p38MAPK or MK2 inhibitors. These findings may lead to treatments for therapy-induced bone loss, significantly increasing quality of life for cancer survivors.
A Small Hypoxia Signature Predicted pCR Response to Bevacizumab in the Neoadjuvant GeparQuinto Breast Cancer Trial
Authors: Karn Thomas , Meissner Tobias , Weber Karsten E. , Solbach Christine , Denkert Carsten , Engels Knut , Fasching Peter A. , Sinn Bruno V. , Schrader Iris , Budczies Jan , Marmé Frederik , Müller Volkmar , Holtrich Uwe , Gerber Bernd , Schem Christian , Young Brandon M. , Hanusch Claus , Stickeler Elmar , Huober Jens , van Mackelenbergh Marion , Leyland-Jones Brian , Fehm Tanja , Nekljudova Valentina , Untch Michael , Loibl Sibylle 
Published: January 2020

Abstract

Purpose:
In breast cancer, bevacizumab increased pCR rate but not long-term survival and no predictive markers are available to identify patients with long-term benefit from the drug.

Experimental Design:
We profiled 289 pretherapeutic formalin-fixed, paraffin-embedded (FFPE) biopsies of HER2-negative patients from the GeparQuinto trial of neoadjuvant chemotherapy ± bevacizumab by exome-capture RNA-sequencing (RNA-seq). In a prospectively planned study, we tested molecular signatures for response prediction. IHC validation was performed using tissue microarrays.

Results:
We found strong agreement of molecular and pathologic parameters as hormone receptors, grading, and lymphocyte infiltration in 221 high-quality samples. Response rates (49.3% pCR overall) were higher in basal-like (68.9%) and HER2-enriched (45.5%) than in luminal B (35.7%), luminal A (17.9%), and normal-like (20.0%) subtypes. T-cell (OR = 1.60; 95% confidence interval, 1.21–2.12; P = 0.001), proliferation (OR = 2.88; 95% CI, 2.00–4.15; P &lt; 0.001), and hypoxia signatures (OR = 1.92; 95% CI, 1.41–2.60; P &lt; 0.001) significantly predicted pCR in univariate analysis. In a prespecified multivariate logistic regression, a small hypoxia signature predicted pCR (OR = 2.40; 95% CI, 1.28–4.51; P = 0.006) with a significant interaction with bevacizumab treatment (P = 0.020). IHC validation using NDRG1 as marker revealed highly heterogenous expression within tissue leading to profound loss of sensitivity in TMA analysis, still a significant predictive value for pCR was detected (P = 0.025).

Conclusions:
Exome-capture RNA-seq characterizes small FFPE core biopsies by reliably detecting factors as for example ER status, grade, and tumor-infiltrating lymphocytes levels. Beside molecular subtypes and immune signatures, a small hypoxia signature predicted pCR to bevacizumab, which could be validated by IHC. The signature can have important applications for bevacizumab treatment in different cancer types and might also have a role for novel combination therapies of bevacizumab with immune checkpoint inhibition.
Latest trends, challenges and solutions in security in the era of cloud computing and software defined networks
Authors: Hassan Wajid , Chou Te-Shun , Li Xiaoming , Appiah-Kubi Patrick , Omar Tamer 
Published: January 2020

The emergence of cloud computing has changed perception of all regarding software delivery, development models and infrastructure. Cloud computing has a potential of providing elastic, easily manageable, powerful and cost effective solutions. The rapid transition to cloud computing has fueled concerns on the security issues. The migration of the user’s data and applications in a shared environment of a cloud, where there is a collocation of several users increases security related concerns. Several research efforts have been made in evaluating challenges related to security faced by the cloud computing environments, a number of solutions of such problems have also been proposed. Integrated security solutions should be devised to deal with the increasing security risks. In this paper, a detailed cloud computing survey, key services and concepts are being presented. This paper attempts to evaluate various security threats to cloud computing and a number of security solutions have also been discussed. Furthermore, a brief view of the cloud security regulatory bodies and compliance have also been presented. Despite the research efforts in cloud security field, there are still some open research problems and challenges which are discussed in this paper.
The Effect of Coconut Oil Consumption on Cardiovascular Risk Factors
Authors: Neelakantan Nithya , Seah Jowy Yi Hoong , van Dam Rob M. 
Published: January 2020

Background:
Coconut oil is high in saturated fat and may, therefore, raise serum cholesterol concentrations, but beneficial effects on other cardiovascular risk factors have also been suggested. Therefore, we conducted a systematic review of the effect of coconut oil consumption on blood lipids and other cardiovascular risk factors compared with other cooking oils using data from clinical trials.

Methods:
We searched PubMed, SCOPUS, Cochrane Registry, and Web of Science through June 2019. We selected trials that compared the effects of coconut oil consumption with other fats that lasted at least 2 weeks. Two reviewers independently screened articles, extracted data, and assessed the study quality according to the PRISMA guidelines (Preferred Reporting Items for Systematic Reviews and Meta-Analyses). The main outcomes included low-density lipoprotein cholesterol (LDL-cholesterol), high-density lipoprotein cholesterol (HDL-cholesterol), total cholesterol, triglycerides, measures of body fatness, markers of inflammation, and glycemia. Data were pooled using random-effects meta-analysis.

Results:

16 articles were included in the meta-analysis. Results were available from all trials on blood lipids, 8 trials on body weight, 5 trials on percentage body fat, 4 trials on waist circumference, 4 trials on fasting plasma glucose, and 5 trials on C-reactive protein. Coconut oil consumption significantly increased LDL-cholesterol by 10.47 mg/dL (95% CI: 3.01, 17.94;
I
2
= 84%, N=16) and HDL-cholesterol by 4.00 mg/dL (95% CI: 2.26, 5.73;
I
2
= 72%, N=16) as compared with nontropical vegetable oils. These effects remained significant after excluding nonrandomized trials, or trials of poor quality (Jadad score <3). Coconut oil consumption did not significantly affect markers of glycemia, inflammation, and adiposity as compared with nontropical vegetable oils.

Conclusions:
Coconut oil consumption results in significantly higher LDL-cholesterol than nontropical vegetable oils. This should inform choices about coconut oil consumption.
Interdependence of Internal Tide and Lee Wave Generation at Abyssal Hills: Global Calculations
Authors: Shakespeare Callum J. 
Published: January 2020

AbstractThe generation of internal waves at abyssal hills has been proposed as an important source of bottom-intensified mixing and a sink of geostrophic momentum. Using the theory of Bell, previous authors have calculated either the generation of lee waves by geostrophic flow or the generation of the internal tide by the barotropic tide, but never both together. However, the Bell theory shows that the two are interdependent: that is, the presence of a barotropic tide modifies the generation of lee waves, and the presence of a geostrophic (time mean) flow modifies the generation of the internal tide. Here we extend the theory of Bell to incorporate multiple tidal constituents. Using this extended theory, we recalculate global wave fluxes of energy and momentum using the abyssal-hill spectra, model-derived abyssal ocean stratification and geostrophic flow estimates, and the TPX08 tidal velocities for the eight major constituents. The energy flux into lee waves is suppressed by 13%–19% as a result of the inclusion of tides. The generated wave flux is dominated by the principal lunar semidiurnal tide (M2), and its harmonics and combinations, with the strongest fluxes occurring along midocean ridges. The internal tide generation is strongly asymmetric because of Doppler shifting by the geostrophic abyssal flow, with 55%–63% of the wave energy flux (and stress) directed upstream, against the geostrophic flow. As a consequence, there is a net wave stress associated with generation of the internal tide that reaches magnitudes of 0.01–0.1 N m−2 in the vicinity of midocean ridges.
Assessing the Involvement of Users During Development of Lower Limb Wearable Robotic Exoskeletons: A Survey Study
Authors: Ármannsdóttir Anna L. , Beckerle Philipp , Moreno Juan C. , van Asseldonk Edwin H. F. , Manrique-Sancho Maria-Teresa , del-Ama Antonio J. , Veneman Jan F. , Briem Kristín 
Published: January 2020

Objective To explore user-centered design methods currently implemented during development of lower limb wearable robots and how they are utilized during different stages of product development. Background Currently, there appears to be a lack of standardized frameworks for evaluation methods and design requirements to implement effective user-centered design for safe and effective clinical or ergonomic system application. Method Responses from a total of 191 experts working in the field of lower limb exoskeletons were analyzed in this exploratory survey. Descriptive statistics were used to present responses and measures of frequency, and chi-square tests were used to contrast the answers of respondents who identified as clinicians versus engineers. Results A vast majority of respondents involve users in their development, in particular at the initial and iterative stages, although some differences were found between disciplines. A variety of methods and metrics are used to capture feedback from users and test devices, and although valuable, some methods used may not be based on validated measures. Guidelines regarding tests on safety of exoskeletons also lack standardization. Conclusion There seems to be a consensus among experts regarding the importance of a user-centered approach in exoskeleton development; however, standardized frameworks with regard to appropriate testing methods and design approaches are lacking. Such frameworks should consider an interdisciplinary focus on the needs and safety of the intended user during each iteration of the process. Application This exploratory study provides an overview of current practice among engineers and clinicians regarding the user-centered design of exoskeletons. Limitations and recommendations for future directions are identified.
Bilateral Hip Arthroscopy in High-Level Athletes: Results of a Shorter Interval Between Staged Bilateral Hip Arthroscopies
Authors: Hassebrock Jeffrey D. , Chhabra Anikar , Makovicka Justin L. , Economopoulos Kostas J. 
Published: January 2020

Background:Hip arthroscopy is a safe and effective mechanism for treating femoroacetabular impingement symptoms in high level athletes. Bilateral symptoms occur in a subset of this population.Purpose:To discuss outcomes of bilateral hip arthroscopy in high-level athletes and compare a standard staged timeline for bilateral hip arthroscopic surgery versus an accelerated timeline.Study Design:Cohort study; Level of evidence, 3.Methods:A retrospective review of all staged bilateral hip arthroscopies was performed on high-level athletes over a 3-year period. Patients were categorized into cohorts based upon when the second procedure was performed (4-6 weeks after the index procedure or >6 weeks after the index procedure). Exclusion criteria included any prior hip surgery, advanced arthritis, previous pelvic or femoral fracture, or inflammatory arthropathy. Demographics, radiographic measurements, operative reports of procedures performed, and patient-reported outcomes (Hip Outcome Score–Activities of Daily Living, Hip Outcome Score–Sport Specific Subscale, modified Harris Hip Score, return to sports, return to same level of play) were compared between groups at 6-month, 1-year, and 2-year intervals, with the Student t test used for continuous data and a chi-square test used for categorical data.Results:50 patients were identified: 22 in the accelerated surgery (AS) group and 28 in the standard surgery (SS) group. Age and number of collegiate participants were greater in the AS group, whereas the number of high school participants and the time away from sports were higher in the SS group. Preoperative alpha angles were significantly larger among the AS group, but no differences were found in postoperative alpha angles, center edge angles, or Tönnis grades. No significant difference was seen in patient-reported outcomes between the 2 groups at 6-month, 1-year, and 2-year follow-up.Conclusion:Bilateral hip arthroscopy performed 4 to 6 weeks apart is a safe and effective treatment option for athletes with bilateral femoroacetabular impingement and labral tears; the procedures entail a high rate of return to sports, return to the same level of sports, and decreased time lost from sports. This information could be useful for an athlete deciding on whether to proceed with bilateral hip arthroscopy and deciding on the timing for the procedures.
Activity of two key toxin groups in Australian elapid venoms show a strong correlation to phylogeny but not to diet
Authors: Tasoulis Theo , Lee Michael S. Y. , Ziajko Manon , Dunstan Nathan , Sumner Joanna , Isbister Geoffrey K. 
Published: January 2020

AbstractBackgroundThe relative influence of diet and phylogeny on snake venom activity is a poorly understood aspect of snake venom evolution. We measured the activity of two enzyme toxin groups – phospholipase A2(PLA2), and L-amino acid oxidase (LAAO) – in the venom of 39 species of Australian elapids (40% of terrestrial species diversity) and used linear parsimony and BayesTraits to investigate any correlation between enzyme activity and phylogeny or diet.ResultsPLA2activity ranged from 0 to 481 nmol/min/mg of venom, and LAAO activity ranged from 0 to 351 nmol/min/mg. Phylogenetic comparative methods, implemented in BayesTraits showed that enzyme activity was strongly correlated with phylogeny, more so for LAAO activity. For example, LAAO activity was absent in both theVermicellaandPseudonaja/Oxyuranusclade, supporting previously proposed relationships among these disparate taxa. There was no association between broad dietary categories and either enzyme activity. There was strong evidence for faster initial rates of change over evolutionary time for LAAO (delta parameter mean 0.2), but no such pattern in PLA2(delta parameter mean 0.64). There were some exceptions to the phylogenetic patterns of enzyme activity: different PLA2activity in the ecologically similar sister-speciesDenisonia devisiandD. maculata; large inter-specific differences in PLA2activity inHoplocephalusandAustrelaps.ConclusionsWe have shown that phylogeny is a stronger influence on venom enzyme activity than diet for two of the four major enzyme families present in snake venoms. PLA2and LAAO activities had contrasting evolutionary dynamics with the higher delta value for PLA2Some species/individuals lacked activity in one protein family suggesting that the loss of single protein family may not incur a significant fitness cost.
First identification and genotyping of Enterocytozoon bieneusi in humans in Myanmar
Authors: Shen Yujuan , Gong Baiyan , Liu Xiaohua , Wu Yanchen , Yang Fengkun , Xu Jie , Zhang Xiaofan , Cao Jianping , Liu Aiqin 
Published: January 2020

Abstract
Background
Intestinal pathogen infections are widespread among impoverished populations. Enterocytozoon bieneusi is the most common pathogen of intestinal microsporidian species in humans worldwide. However, no epidemiological information is available on E. bieneusi infection in humans in Myanmar. The present study comprised the first identification and genotyping of E. bieneusi in humans conducted in Myanmar.

Results
A total of 172 fecal specimens were collected from the Wa people (one each) in four villages of Pangsang Township of the Matman District of Shan State, Myanmar, and each participant completed a questionnaire. E. bieneusi was identified and genotyped using polymerase chain reaction (PCR) and sequence analysis of the internal transcribed spacer (ITS) region of the ribosomal RNA (rRNA) gene. The average prevalence of E. bieneusi was 8.72% (15/172), ranging from 3.85 to 13.89% by village. E. bieneusi infection was not related to any of the risk factors studied. Six genotypes were identified, comprising two known genotypes Peru6 (n = 10) and D (n = 1) and four novel genotypes (MMR23, MMR25, MMR86, and MMR87) (one each), and two people infected with genotype Peru6 were from the same family. A phylogenetic analysis based on a neighbor-joining tree of the ITS sequences of E. bieneusi indicated that all the six genotypes were clustered into group 1.

Conclusions
This is the first identification and genotyping of E. bieneusi in humans in Myanmar. The observations that the two people infected with genotype Peru6 were from the same family, and that all six genotypes obtained in the present study fell into zoonotic group 1, showed the potential for anthropogenic and zoonotic transmissions. The present data argue for the importance of epidemiological control and prevention from medical sectors.
Development and characterization of an EMS-mutagenized wheat population and identification of salt-tolerant wheat lines
Authors: Lethin Johanna , Shakil Shahriar S. M. , Hassan Sameer , Sirijovski Nick , Töpel Mats , Olsson Olof , Aronsson Henrik 
Published: January 2020

Abstract
Background
Triticum aestivum (wheat) is one of the world’s oldest crops and has been used for >8000 years as a food crop in North Africa, West Asia and Europe. Today, wheat is one of the most important sources of grain for humans, and is cultivated on greater areas of land than any other crop. As the human population increases and soil salinity becomes more prevalent, there is increased pressure on wheat breeders to develop salt-tolerant varieties in order to meet growing demands for yield and grain quality. Here we developed a mutant wheat population using the moderately salt-tolerant Bangladeshi variety BARI Gom-25, with the primary goal of further increasing salt tolerance.

Results
After titrating the optimal ethyl methanesulfonate (EMS) concentration, ca 30,000 seeds were treated with 1% EMS, and 1676 lines, all originating from single seeds, survived through the first four generations. Most mutagenized lines showed a similar phenotype to BARI Gom-25, although visual differences such as dwarfing, giant plants, early and late flowering and altered leaf morphology were seen in some lines. By developing an assay for salt tolerance, and by screening the mutagenized population, we identified 70 lines exhibiting increased salt tolerance. The selected lines typically showed a 70% germination rate on filter paper soaked in 200 mM NaCl, compared to 0–30% for BARI Gom-25. From two of the salt-tolerant OlsAro lines (OA42 and OA70), genomic DNA was sequenced to 15x times coverage. A comparative analysis against the BARI Gom-25 genomic sequence identified a total of 683,201 (OA42), and 768,954 (OA70) SNPs distributed throughout the three sub-genomes (A, B and D). The mutation frequency was determined to be approximately one per 20,000 bp. All the 70 selected salt-tolerant lines were tested for root growth in the laboratory, and under saline field conditions in Bangladesh. The results showed that all the lines selected for tolerance showed a better salt tolerance phenotype than both BARI Gom-25 and other local wheat varieties tested.

Conclusion
The mutant wheat population developed here will be a valuable resource in the development of novel salt-tolerant varieties for the benefit of saline farming.