bluuebunny/crossref_metadata_2025_split huggingface dataset:
The distance and median problems in the single-cut-or-join model with single-gene duplications
Authors: Mane Aniket C. , Lafond Manuel , Feijao Pedro C. , Chauve Cedric 
Published: May 2020

Abstract
Background.
In the field of genome rearrangement algorithms, models accounting for gene duplication lead often to hard problems. For example, while computing the pairwise distance is tractable in most duplication-free models, the problem is NP-complete for most extensions of these models accounting for duplicated genes. Moreover, problems involving more than two genomes, such as the genome median and the Small Parsimony problem, are intractable for most duplication-free models, with some exceptions, for example the Single-Cut-or-Join (SCJ) model.

Results.
We introduce a variant of the SCJ distance that accounts for duplicated genes, in the context of directed evolution from an ancestral genome to a descendant genome where orthology relations between ancestral genes and their descendant are known. Our model includes two duplication mechanisms: single-gene tandem duplication and the creation of single-gene circular chromosomes. We prove that in this model, computing the directed distance and a parsimonious evolutionary scenario in terms of SCJ and single-gene duplication events can be done in linear time. We also show that the directed median problem is tractable for this distance, while the rooted median problem, where we assume that one of the given genomes is ancestral to the median, is NP-complete. We also describe an Integer Linear Program for solving this problem. We evaluate the directed distance and rooted median algorithms on simulated data.

Conclusion.
Our results provide a simple genome rearrangement model, extending the SCJ model to account for single-gene duplications, for which we prove a mix of tractability and hardness results. For the NP-complete rooted median problem, we design a simple Integer Linear Program. Our publicly available implementation of these algorithms for the directed distance and median problems allow to solve efficiently these problems on large instances.
Three-year follow-up of changes of cortical bone thickness after implantation of Endo-Exo-Prosthesis (EEP) for transfemoral amputees
Authors: Örgel Marcus , Liodakis Emmanouil , Jaratjitwilai Pratya , Harb Afif , Wirries Nils , Omar Mohamed , Krettek Christian , Aschoff Horst-Heinrich 
Published: May 2020

Abstract
Introduction
Transcutaneous Osseointegrated Prosthetic Systems (TOPS) offer a good alternative for patients who cannot be satisfactorily rehabilitated by conventional suspension sockets. The Endo-Exo-Prothesis (EEP, ESKA Orthopaedic Handels GmbH®, Deutschland) is the most implanted TOPS in Germany. Previous studies have shown that cortical thickness increases after implantation of TOPS. The aim of this study is to determine changes of cortical thickness in relation to the time after implantation of the Endo-Fix-Stem.

Patients and methods
All transfemoral amputees treated by EEP from 2007 to 2013 were operated by the last author of this study. X-ray images of 4 follow-up intervals (postoperative, 3 months, 12 months, 3 years) were analyzed retrospectively. The femoral residuum was divided into 3 sections (proximal, middle, distal) with 2 measuring points in each section: medial and lateral. Cortical thickness was measured at these 6 points and compared at regular intervals using the Friedman test for non-parametric dependent variables.

Results
Thirty-seven patients with 40 implants were included. The average age was 52.2 years (30–79 years). 83.7% of the patients were male. No statistical significance could be shown for any of the measuring points of the femoral residual (proximal medial, proximal lateral, middle medial, middle lateral, distal medial, distal lateral) among the mean values of the cortical thickness at the different follow-up times (p > 0.05 for all measuring points). Cortical remodeling processes (> 1 millimeter (mm)) occurred in all implants despite a missing statistical significance. Hypertrophy could be confirmed for 42.5% and atrophy for 37.5%. Twenty percent of the cases showed a parallel occurrence of both entities. Cortical changes greater than 5 mm were only observed at the distal end of the femur.

Conclusion
Even if our results did not show any significant difference, it can be deduced that the osseointegration process leads to a remodeling of the bone structure, both in terms of increased bone formation and bone resorption. However, it has not yet been conclusively clarified which processes lead to hyper- or atrophy. The force transmission between prosthesis and bone and the facultative bacterial colonization of the stoma are still the main factors which may be responsible for the bone remodeling processes.
Plasma volume expansion and capillary leakage of 20% albumin in burned patients and volunteers
Authors: Zdolsek Markus , Hahn Robert G. , Sjöberg Folke , Zdolsek Joachim H. 
Published: May 2020

AbstractBackgroundBurn injury is associated with a long-standing inflammatory reaction. The use of albumin solutions for plasma volume support is controversial because of concerns of increased capillary leakage, which could aggravate the commonly seen interstitial oedema.MethodsIn the present open controlled clinical trial, an intravenous infusion of 20% albumin at 3 mL/kg was given over 30 min to 15 burn patients and 15 healthy volunteers. Blood samples and urine were collected for 5 h. Plasma dilution, plasma albumin and colloid osmotic pressure were compared. Mass balance calculations were used to estimate plasma volume expansion and capillary leakage of fluid and albumin.ResultsThe patients were studied between 4 and 14 (median, 7) days after the burn injury, which spread over 7–48% (median, 15%) of the total body surface area. The albumin solution expanded the plasma volume by almost 15%, equivalent to twice the infused volume, in both groups. The urinary excretion exceeded the infused volume by a factor of 2.5. Capillary leakage of albumin occurred at a rate of 3.4 ± 1.5 g/h in burn patients and 3.7 ± 1.6 g/h in the volunteers (P = 0.61), which corresponded to 2.4 ± 1.0% and 2.5 ± 1.2% per hour of the intravascular pool (P = 0.85). The median half-life of the plasma volume expansion was 5.9 (25th–75th percentiles 2.7–11.7) h in the burn patients and 6.9 (3.4–8.5) h in the volunteers (P = 0.56).ConclusionsAlbumin 20% was an effective volume expander in patients at 1 week post-burn. No relevant differences were found between burn patients and healthy volunteers.Trial registrationEudraCT 2016-000996-26on May 31, 2016.
The role of baseline BLyS levels and type 1 interferon-inducible gene signature status in determining belimumab response in systemic lupus erythematosus: a post hoc meta-analysis
Authors: Wilkinson Christel , Henderson Robert B. , Jones-Leone Angela R. , Flint Shaun M. , Lennon Mark , Levy Roger A. , Ji Beulah , Bass Damon L. , Roth David 
Published: May 2020

Abstract
Background
Elevated B lymphocyte stimulator (BLyS) levels in patients with systemic lupus erythematosus (SLE) correlate positively with disease activity; BLyS expression is directly linked to interferon (IFN) pathway activation. This post hoc meta-analysis of BLISS-52 and BLISS-76 explored the relationship between baseline BLyS mRNA/protein levels and/or type 1 IFN-inducible gene signature (IFN-1) and responses to the BLyS-targeting monoclonal antibody belimumab in SLE.

Methods
In BLISS-52 and BLISS-76, patients with autoantibody-positive SLE and a SELENA-SLEDAI score ≥ 6 and receiving stable standard SLE therapy were randomised to intravenous belimumab 10 mg/kg or placebo, plus standard of care (SoC), for 52 or 76 weeks. For this post hoc meta-analysis, patients with an appropriate mRNA sample were stratified by BLyS mRNA expression (tertiles: high/medium/low; revised quantiles: high/low), IFN-1 mRNA expression (high/low) and BLyS protein level (high/low). Co-primary endpoints were correlation between baseline BLyS and IFN-1 mRNA levels and SLE Responder Index (SRI)4 response at week 52 within BLyS/IFN-1 subgroups. Secondary endpoints included time to first severe SELENA-SLEDAI Flare Index (SFI) flare.

Results
Of 554 patients included in this analysis, 281 had received belimumab and 273 had received placebo. Baseline BLyS and IFN-1 mRNA levels were highly correlated (Spearman’s rank correlation coefficient 0.7799; 95% confidence interval [CI] 0.7451, 0.8106; p < 0.0001). The proportion of SRI4 responders was higher with belimumab versus placebo in all subgroups, but the difference reached statistical significance in the medium BLyS mRNA tertile (odds ratio [OR] 2.17; 95% CI 1.16, 4.04; p = 0.0153), high BLyS mRNA quantile (OR 1.58; 95% CI 1.02, 2.44; p = 0.0402), high IFN-1 mRNA (OR 1.58; 95% CI: 1.08, 2.31; p = 0.0186) and high BLyS protein (OR 3.57; 95% CI 1.63, 7.83; p = 0.0015) subgroups only. The risk of severe SFI flare was significantly lower with belimumab than placebo in the high BLyS mRNA quantile (hazard ratio [HR] 0.59; 95% CI 0.36, 0.97; p = 0.0371) and high BLyS protein (HR 0.39; 95% CI 0.19, 0.79; p = 0.0090) subgroups.

Conclusions
This post hoc meta-analysis demonstrated a tendency towards improved response to add-on intravenous belimumab 10 mg/kg versus SoC alone in patients with high baseline BLyS protein and IFN-1 mRNA levels and medium/high BLyS mRNA levels.
Fear-avoidance beliefs are associated with exercise adherence: secondary analysis of a randomised controlled trial (RCT) among female healthcare workers with recurrent low back pain
Authors: Taulaniemi Annika , Kankaanpää Markku , Rinne Marjo , Tokola Kari , Parkkari Jari , Suni Jaana H. 
Published: May 2020

Abstract
Background
Exercise is recommended for the treatment and management of low back pain (LBP) and the prevention of chronicity. Exercise adherence has been only modest in intervention studies among people with musculoskeletal pain. Fear-avoidance beliefs (FABs) are known to affect exercise adherence.
The purpose was twofold: to examine which bio-psycho-social factors contributed to exercise adherence during a 6-month neuromuscular exercise intervention among female healthcare workers with recurrent LBP, and to investigate how exercising affects FABs at 6 and 12 months’ follow-up.

Methods
Some 219 healthcare workers aged 30–55 years with mild-to-moderate re-current non-specific LBP were originally allocated into: 1) exercise, 2) counselling, 3) combined exercise and counselling, and 4) control groups. In the present secondary analysis, groups 1 and 3 (exercise only and exercise+counselling) were merged to be exercisers and groups 2 and 4 were merged to be non-exercisers. Baseline variables of the exercise compliers (≥24 times over 24 weeks; n = 58) were compared to those of the non-compliers (< 1 time/week, 0–23 times; n = 52). The effects of the exercise programme on FABs were analysed by a generalised linear mixed model according to the intention-to-treat principle (exercisers; n = 110 vs non-exercisers; n = 109) at three measurement points (baseline, 6, and 12 months). A per-protocol analysis compared the more exercised to the less exercised and non-exercisers.

Results
A low education level (p = 0.026), shift work (p = 0.023), low aerobic (p = 0.048) and musculoskeletal (p = 0.043) fitness, and high baseline physical activity-related FABs (p = 0.019) were related to low exercise adherence. The exercise programme reduced levels of both physical activity- and work-related FABs, and there was a dose response: FABs reduced more in persons who exercised ≥24 times compared to those who exercised 0–23 times.

Conclusion
Healthcare workers who had lower education and fitness levels, worked shifts, and had high physical activity-related FABs had a lower adherence to the 6-month neuromuscular exercise programme. Exercising with good adherence reduced levels of FABs, which have been shown to be linked with prolonged LBP. Motivational strategies should be targeted at persons with low education and fitness levels and high FABs in order to achieve better exercise adherence.
Abundance, diversity, and distribution patterns along with the salinity of four nitrogen transformation-related microbes in the Yangtze Estuary
Authors: Zheng Lei , Liu Tingting , Yuan Dongdan , Wang Huipeng , Zhang Shurong , Ding Aizhong , Xie En 
Published: May 2020

Abstract
Purpose
The abundance and composition of nitrogen transformation-related microbes with certain environmental parameters for living conditions provide information about the nitrogen cycle in the Yangtze Estuary. The aim of this study was to explore the impacts of salinity on four N-related microbes and reveal the phylogenetic characteristics of microorganisms in the Yangtze Estuary ecosystem. A molecular biology method was used for the quantitation and identification of four microbes in the Yangtze River: ammonia-oxidizing bacteria (AOB), ammonia-oxidizing archaea (AOA), denitrifying microbes (nirS-type), and anaerobic ammonia-oxidizing (anammox) bacteria. Sequence identification was performed on the levels of phylum, class, order, family, and genus, and the sequences were then matched to species.

Result
The results showed that the dominant species of AOA were crenarchaeote enrichment cultures, thaumarchaeote enrichment cultures, and Nitrosopumilus maritimus cultures, and the dominant AOB species were betaproteobacterium enrichment cultures and Nitrosomona sp. The denitrifying microbes were identified as the phylum Proteobacteria, classes Alphaproteobacteria, Betaproteobacteria, and Gammaproteobacteria, and the species Thauera selenatis. The dominant species of the anammox bacteria was Candidatus Brocadia sp. In the estuarine sediments of the Yangtze River, the nirS gene abundance (1.31 × 107–9.50 × 108 copies g−1 sediments) was the highest among all the detected genes, and the abundance of bacterial amoA, archaeal amoA, and nirS was significantly correlated. Closely correlated with the abundance of the bacterial amoA gene, salinity was an important factor in promoting the abundance and restraining the community diversity of AOB. Moreover, the distribution of the AOB species exhibited regional patterns in the estuarine zone.

Conclusions
The results indicated that salinity might promote abundance while limiting the diversity of AOB and that salinity might have reverse impacts on AOA. Denitrifying microbes, which showed a significant correlation with the other genes, were thought to interact with the other genes during nitrogen migration. The results also implied that AOA has a lower potential nitrification rate than AOB and that both the anammox and denitrification processes (defined by nirS gene) account for N2 production.
Attitudes, knowledge, and preferences of the Israeli public regarding the allocation of donor organs for transplantation
Authors: Elalouf Amir , Pliskin Joseph S. , Kogut Tehila 
Published: May 2020

Abstract
Background
There is a stark disparity between the number of patients awaiting deceased-donor organ transplants and the rate at which organs become available. Though organs for transplantation are assumed to be a community resource, and the organ supply depends on public willingness to donate, current allocation schemes do not explicitly incorporate public priorities and preferences. This paper seeks to provide insights regarding the Israeli public’s preferences regarding criteria for organ (specifically, kidney) allocation, and to determine whether these preferences are in line with current allocation policies.

Methods
A market research company administered a telephone survey to 604 adult participants representing the Jewish-Israeli public (age range: 18–95; 50% male). The questionnaire comprised 39 questions addressing participants’ knowledge, attitudes, and preferences regarding organ donation and criteria for organ allocation, including willingness to donate.

Results
The criteria that respondents marked as most important in prioritizing waitlist candidates were maximum medical benefit (51.3% of respondents) and waiting time (21%). Donor status (i.e., whether the candidate is registered as an organ donor) was ranked by 43% as the least significant criterion. Most participants expressed willingness to donate the organs of a deceased relative; notably, they indicated that they would be significantly more willing to donate if organ allocation policies took their preferences regarding allocation criteria into account. Unlike individuals in other countries (e.g., the UK, the US, and Australia) who responded to similar surveys, Israeli survey respondents did not assign high importance to the candidate’s age (24% ranked it as the least important factor). Interestingly, in some cases, participants’ declared preferences regarding the importance of various allocation criteria diverged from their actual choices in hypothetical organ allocation scenarios.

Conclusions
The findings of this survey indicate that Israel’s citizens are willing to take part in decisions about organ allocation. Respondents did not seem to have a strict definition or concept of what they deem to be just; yet, in general, their preferences are compatible with current policy. Importantly, participants noted that they would be more willing to donate organs if their preferences were integrated into the allocation policy. Accordingly, we propose that allocation systems must strive to respect community values and perceptions while maintaining continued clinical effectiveness.
Functional performance and 30-day postoperative mortality after emergency laparotomy—a retrospective, multicenter, observational cohort study of 1084 patients
Authors: Cihoric Mirjana , Tengberg Line Toft , Foss Nicolai Bang , Gögenur Ismail , Tolstrup Mai-Britt , Bay-Nielsen Morten 
Published: May 2020

Abstract
Background
Despite the importance of predicting adverse postoperative outcomes, functional performance status as a proxy for frailty has not been systematically evaluated in emergency abdominal surgery. Our aim was to evaluate if the Eastern Cooperative Oncology Group (ECOG) performance score was independently associated with mortality following high-risk emergency abdominal surgery, in a multicentre, retrospective, observational study of a consecutive cohort.

Methods
All patients aged 18 or above undergoing high-risk emergency laparotomy or laparoscopy from four emergency surgical centres in the Capitol Region of Denmark, from January 1 to December 31, 2012, were included. Demographics, preoperative status, ECOG performance score, mortality, and surgical characteristics were registered. The association of frailty with postoperative mortality was evaluated using multiple regression models. Likelihood ratio test was applied for goodness of fit.

Results
In total, 1084 patients were included in the cohort; unadjusted 30-day mortality was 20.2%. ECOG performance score was independently associated with 30-day mortality. Odds ratio for mortality was 1.70 (95% CI (1.0, 2.9)) in patients with ECOG performance score of 1, compared with 5.90 (95% CI (1.8, 19.0)) in patients with ECOG performance score of 4 (p < 0.01). Likelihood ratio test suggests improvement in fit of logistic regression modelling of 30-day postoperative mortality when including ECOG performance score as an explanatory variable.

Conclusions
This study found ECOG performance score to be independently associated with the postoperative 30-day mortality among patients undergoing high-risk emergency laparotomy. The utility of including functional performance in a preoperative risk assessment model of emergency laparotomy should be evaluated.
Determination of the available energy values and amino acid digestibility of Flammulina velutipes stem waste and its effects on carcass trait and meat quality fed to growing-finishing pigs
Authors: Liu Xuzhou , Zhang Bo , Liu Hansuo , Zhang Gang , Zhao Jinbiao , Liu Ling , Piao Xiangshu , Song Hui , Zhang Shuai , Li Yu 
Published: May 2020

Abstract
Background
Flammulina velutipes stem waste (FVS) is the by-product of mushroom industry. The objectives of this study were to determine the available energy and amino acid digestibility of FVS fed to pigs, and to evaluate the effects of dietary FVS inclusion on growth performance, biochemical profile of serum, fecal short chain fatty acid (SCFA) concentration, carcass traits, meat quality, intestinal morphology and microflora of pigs. In Exp. 1, twelve crossbred barrows with initial body weight (IBW) of 37.48 ± 4.31 kg were randomly allotted to 2 dietary treatments, including a corn basal diet and an experimental diet containing 24.35% FVS. In Exp. 2, twelve barrows fitted with an ileal T-cannula (IBW: 32.56 ± 1.67 kg) were randomly allotted to 2 dietary treatments, which included a N-free diet and an experimental diet containing 40.0% FVS. In Exp. 3, ninety growing pigs (IBW: 63.98 ± 6.89 kg) were allotted to 1 of 3 treatment diets for 63 d, including a basal diet and 2 experimental diets with 2.5% and 5% FVS, respectively.

Results
The digestible energy (DE) and metabolizable energy (ME) of FVS were 4.58 and 4.06 MJ/kg on dry matter basis, respectively, and the standardized ileal digestibility (SID) of indispensable AAs ranged from 17.50% to 59.47%. Pigs fed diets with 2.5% FVS showed no difference on average daily gain (ADG) and gain to feed ratio (G/F). Although dietary 5% FVS inclusion impaired apparent total tract digestibility (ATTD) of organic matter and gross energy, it elevated the SCFA concentration (P ≤ 0.04) in gut and antioxidant capacity in serum. In addition, dietary FVS inclusion depressed the backfat thickness (P = 0.03) in pigs. The longissimus dorsi muscle of pigs fed FVS revealed higher n-3 polyunsaturated fatty acid concentration and optimized fatty acid composition. Dietary 2.5% FVS inclusion also improved the intestinal development and health by increasing the villius height to crypt depth ratio (V/C) in jejunum (P < 0.01), and promoting microbial diversity and beneficial microbiota proliferation.

Conclusions
It is feasible to include moderate content of FVS as an unconventional fiber ingredient in diet of growing-finishing pigs.