bluuebunny/crossref_metadata_2025_split huggingface dataset:
Double-Row Repair for Recalcitrant Medial Epicondylitis
Authors: Wu Victor J. , Thon Stephen , Finley Zachary , Bohlen Hunter , Schwartz Zachary , O’Brien Michael J. , Savoie Felix H. 
Published: December 2019

Background: Various techniques have been described for surgical treatment of recalcitrant medial epicondylitis (ME). No single technique has yet to be proven the most effective. Purpose: To evaluate the clinical outcomes of a double-row repair for ME. Study Design: Case series; Level of evidence, 4. Methods: A retrospective review was performed on 31 consecutive patients (33 elbows) treated surgically for ME with a minimum clinical follow-up of 2 years. All patients were initially managed nonoperatively with anti-inflammatories, steroid injections, topical creams, and physical therapy. Outcome measures at final follow-up included visual analog scale (VAS) scores (scale, 0-10), time to completely pain-free state, time to full range of motion (FROM), Mayo Elbow Performance Scores (MEPS), and Oxford Elbow Scores (OES). Patients were contacted by telephone to determine current functional outcomes, pain, activity, functional limitations, and MEPS/OES. Successful and unsuccessful outcomes were determined by the Nirschl grading system. Results: The mean clinical and telephone follow-up periods were 2.3 and 3.6 years, respectively, and 31 of 33 (94%) elbows were found to have a successful outcome. The mean VAS improvement was 4.9 points, from 5.8 preoperatively to 0.9 postoperatively ( P < .001). The mean MEPS and OES at final follow-up were 95.1 and 45.3, respectively. The mean time to pain-free state and time to FROM were 87.4 and 96 days, respectively. Unlike prior studies, no difference in outcome was found between those with and without ulnar neuritis preoperatively ( P = .67). Conclusion: A double-row repair is effective in decreasing pain and improving the overall function for recalcitrant ME. Uniquely, the presence of preoperative ulnar neuritis was associated with higher patient-reported preoperative pain scores but not with poor outcomes using this protocol.
Isolating peripheral effects of endogenous opioids in modulating exertional breathlessness in people with moderate or severe COPD: a randomised controlled trial
Authors: Currow David C. , Hunt Toby , Louw Sandra , Eckert Danny , Allcroft Peter , To Tim H.M. , Greene Aine , Krajnik Malgorzata , Mahler Don , Ekström Magnus 
Published: December 2019

Question addressed by the studyEndogenous opioids (endorphins) have been reported to modulate exercise-induced breathlessness, but the relative contribution of peripheral opioid receptors has not been tested.Materials, participants and methodsThis was a double-blind, randomised, three-arm, cross-over trial in outpatients with spirometry-verified moderate to severe chronic obstructive pulmonary disease. Participants undertook an incremental symptom-limited treadmill test followed by five endurance treadmill tests at 75% of their maximal work rate; two tests for familiarisation and three tests 30 min after intravenous injection of either methylnaltrexone 0.3 mg·kg−1(blocking peripheral opioid receptors only) or naloxone 0.1 mg·kg−1(blocking both central and peripheral opioid receptors) or normal saline, in randomised order. The primary end-point was the regression slope between breathlessness intensity (0–10 numerical rating scale) and oxygen consumption (V′O2) during the walk tests, comparing methylnaltrexone and placebo using a paired t-test.Results17 participants completed the trial: median (range) 66 (55–82) years; 15 males; mean±sdforced expiratory volume (FEV1) 53.8±17.6% predicted; FEV1/forced vital capacity ratio 0.55±15.9. There was no statistically or clinically significant difference in the primary end-point (regression slope of breathlessness intensity andV′O2) for methylnaltrexone (p=0.498) or naloxone (p=0.804), compared to placebo. Secondary outcomes were similar between the three treatment groups, including peak and mean breathlessness intensity and unpleasantness, exercise capacity, endurance time and leg fatigue.Answer to the questionBlocking peripheral opioid receptors (methylnaltrexone) or peripheral and central opioid receptors (naloxone) did not appear to modulate breathlessness intensity nor exercise capacity when compared with placebo (no blockade).
perfectphyloR: An R package for reconstructing perfect phylogenies
Authors: Karunarathna Charith B. , Graham Jinko 
Published: December 2019

AbstractBackgroundA perfect phylogeny is a rooted binary tree that recursively partitions sequences. The nested partitions of a perfect phylogeny provide insight into the pattern of ancestry of genetic sequence data. For example, sequences may cluster together in a partition indicating that they arise from a common ancestral haplotype.ResultsWe present an R package to reconstruct the local perfect phylogenies underlying a sample of binary sequences. The package enables users to associate the reconstructed partitions with a user-defined partition. We describe and demonstrate the major functionality of the package.ConclusionThe package should be of use to researchers seeking insight into the ancestral structure of their sequence data. The reconstructed partitions have many applications, including the mapping of trait-influencing variants.
Antimicrobial peptide identification using multi-scale convolutional network
Authors: Su Xin , Xu Jing , Yin Yanbin , Quan Xiongwen , Zhang Han 
Published: December 2019

Abstract
Background
Antibiotic resistance has become an increasingly serious problem in the past decades. As an alternative choice, antimicrobial peptides (AMPs) have attracted lots of attention. To identify new AMPs, machine learning methods have been commonly used. More recently, some deep learning methods have also been applied to this problem.

Results
In this paper, we designed a deep learning model to identify AMP sequences. We employed the embedding layer and the multi-scale convolutional network in our model. The multi-scale convolutional network, which contains multiple convolutional layers of varying filter lengths, could utilize all latent features captured by the multiple convolutional layers. To further improve the performance, we also incorporated additional information into the designed model and proposed a fusion model. Results showed that our model outperforms the state-of-the-art models on two AMP datasets and the Antimicrobial Peptide Database (APD)3 benchmark dataset. The fusion model also outperforms the state-of-the-art model on an anti-inflammatory peptides (AIPs) dataset at the accuracy.

Conclusions
Multi-scale convolutional network is a novel addition to existing deep neural network (DNN) models. The proposed DNN model and the modified fusion model outperform the state-of-the-art models for new AMP discovery. The source code and data are available at https://github.com/zhanglabNKU/APIN.
Parallel selection on ecologically relevant gene functions in the transcriptomes of highly diversifying salmonids
Authors: Schneider Kevin , Adams Colin E. , Elmer Kathryn R. 
Published: December 2019

AbstractBackgroundSalmonid fishes are characterised by a very high level of variation in trophic, ecological, physiological, and life history adaptations. Some salmonid taxa show exceptional potential for fast, within-lake diversification into morphologically and ecologically distinct variants, often in parallel; these are the lake-resident charr and whitefish (several species in the generaSalvelinusandCoregonus). To identify selection on genes and gene categories associated with such predictable diversifications, we analysed 2702 orthogroups (4.82 Mbp total; average 4.77 genes/orthogroup; average 1783 bp/orthogroup). We did so in two charr and two whitefish species and compared to five other salmonid lineages, which do not evolve in such ecologically predictable ways, and one non-salmonid outgroup.ResultsAll selection analyses are based onCoregonusandSalvelinuscompared to non-diversifying taxa. We found more orthogroups were affected by relaxed selection than intensified selection. Of those, 122 were under significant relaxed selection, with trends of an overrepresentation of serine family amino acid metabolism and transcriptional regulation, and significant enrichment of behaviour-associated gene functions. Seventy-eight orthogroups were under significant intensified selection and were enriched for signalling process and transcriptional regulation gene ontology terms and actin filament and lipid metabolism gene sets. Ninety-two orthogroups were under diversifying/positive selection. These were enriched for signal transduction, transmembrane transport, and pyruvate metabolism gene ontology terms and often contained genes involved in transcriptional regulation and development. Several orthogroups showed signs of multiple types of selection. For example, orthogroups under relaxed and diversifying selection contained genes such asap1m2, involved in immunity and development, andslc6a8, playing an important role in muscle and brain creatine uptake. Orthogroups under intensified and diversifying selection were also found, such as genessyn3, with a role in neural processes, andctsk, involved in bone remodelling.ConclusionsOur approach pinpointed relevant genomic targets by distinguishing among different kinds of selection. We found that relaxed, intensified, and diversifying selection affect orthogroups and gene functions of ecological relevance in salmonids. Because they were found consistently and robustly across charr and whitefish and not other salmonid lineages, we propose these genes have a potential role in the replicated ecological diversifications.
Exploring the antimicrobial resistance profiles of WHO critical priority list bacterial strains
Authors: Havenga Benjamin , Ndlovu Thando , Clements Tanya , Reyneke Brandon , Waso Monique , Khan Wesaal 
Published: December 2019

Abstract
Background
The antimicrobial resistance of clinical, environmental and control strains of the WHO “Priority 1: Critical group” organisms, Acinetobacter baumannii, Escherichia coli, Klebsiella pneumoniae and Pseudomonas aeruginosa to various classes of antibiotics, colistin and surfactin (biosurfactant) was determined.

Methods
Acinetobacter baumannii was isolated from environmental samples and antibiotic resistance profiling was performed to classify the test organisms [A. baumannii (n = 6), P. aeruginosa (n = 5), E. coli (n = 7) and K. pneumoniae (n = 7)] as multidrug resistant (MDR) or extreme drug resistant (XDR). All the bacterial isolates (n = 25) were screened for colistin resistance and the mobilised colistin resistance (mcr) genes. Biosurfactants produced by Bacillus amyloliquefaciens ST34 were solvent extracted and characterised using ultra-performance liquid chromatography (UPLC) coupled to electrospray ionisation mass spectrometry (ESI–MS). The susceptibility of strains, exhibiting antibiotic and colistin resistance, to the crude surfactin extract (cell-free supernatant) was then determined.

Results
Antibiotic resistance profiling classified four A. baumannii (67%), one K. pneumoniae (15%) and one P. aeruginosa (20%) isolate as XDR, with one E. coli (15%) and three K. pneumoniae (43%) strains classified as MDR. Many of the isolates [A. baumannii (25%), E. coli (80%), K. pneumoniae (100%) and P. aeruginosa (100%)] exhibited colistin resistance [minimum inhibitory concentrations (MICs) ≥ 4 mg/L]; however, only one E. coli strain isolated from a clinical environment harboured the mcr-1 gene. UPLC-MS analysis then indicated that the B. amyloliquefaciens ST34 produced C13–16 surfactin analogues, which were identified as Srf1 to Srf5. The crude surfactin extract (10.00 mg/mL) retained antimicrobial activity (100%) against the MDR, XDR and colistin resistant A. baumannii, P. aeruginosa, E. coli and K. pneumoniae strains.

Conclusion
Clinical, environmental and control strains of A. baumannii, P. aeruginosa, E. coli and K. pneumoniae exhibiting MDR and XDR profiles and colistin resistance, were susceptible to surfactin analogues, confirming that this lipopeptide shows promise for application in clinical settings.
Inhibition of autophagy triggers melatonin-induced apoptosis in glioblastoma cells
Authors: Zhou Nan , Wei Zi Xuan , Qi Zeng Xin 
Published: December 2019

Abstract
Background
Autophagy is considered to be another restorative focus for the treatment of brain tumors. Although several research have demonstrated that melatonin induces autophagy in colon cancer and hepatoma cells, there has not been any direct evidence of whether melatonin is capable of inducing autophagy in human glioma cells.

Results
In the present research, we report that melatonin or its agonist, agomelatine, induced autophagy in A172 and U87-MG glioblastoma cells for a concentration-and time-dependent way, which was significantly attenuated by treatment with luzindole, a melatonin receptor antagonist. Furthermore, by suppressing autophagy at the late-stage with bafilomycin A1 and early stage with 3-MA, we found that the melatonin-induced autophagy was activated early, and the autophagic flux was complete. Melatonin treatment alone did not induce any apoptotic changes in the glioblastoma cells, as measured by flow cytometry. Western blot studies confirmed that melatonin alone prominently upregulated the levels of Beclin 1 and LC3 II, which was accompanied by an increase in the expression of Bcl-2, whereas it had no effect on the expression of Bax in the glioblastoma cells. Remarkably, co-treatment with 3-MA and melatonin significantly enhanced the apoptotic cell population in the glioblastoma cells, along with a prominent decrease in the expression of bcl-2 and increase in the Bax expression levels, which collectively indicated that the disruption of autophagy triggers the melatonin-induced apoptosis in glioblastoma cells.

Conclusions
These results provide information indicating that melatonin may act as a common upstream signal between autophagy and apoptosis, which may lead to the development of new therapeutic strategies for glioma.
Herbicide-tolerant endophytic bacteria of rice plants as the biopriming agents for fertility recovery and disease suppression of unhealthy rice seeds
Authors: Rangjaroen Chakrapong , Lumyong Saisamorn , Sloan William T. , Sungthong Rungroch 
Published: December 2019

Abstract
Background
Dirty panicle disease (DPD) caused by several fungal phytopathogens results in damage and depreciation of rice seeds. Unhealthy rice seeds with DPD are potent reservoirs of pathogens and unable to be used as seed stock as they can spread the disease in the paddy fields leading to the severe loss of rice yield and quality. In this study, we aim to search for beneficial endophytes of commercially cultivated rice plants and utilize them as biostimulants in seed biopriming for fertility recovery and disease suppression of unhealthy rice seeds.

Results
Forty-three bacterial endophytes were isolated from rice plants grown in the herbicide-treated paddy fields. Five isolates of these endophytes belonging to the genus Bacillus show excellent antifungal activity against fungal pathogens of DPD. Based on germination tests, biopriming unhealthy rice seeds by soaking in bacterial suspensions for 9 or 12 h was optimal as evidenced by the lowest disease incidence and longer shoot and root lengths of seedlings germinated, compared with controls made of non-treated or hydroprimed healthy and unhealthy seeds. Pot experiments were carried out to evaluate the impact of seed biopriming, in which the percentage of healthy rice yield produced by rice plants emerging from bioprimed seeds was not significantly different, compared to the controls originating respectively from non-treated healthy seeds and chemical fungicide-treated unhealthy seeds.

Conclusion
Biopriming of unhealthy rice seeds with herbicide-tolerant endophytic bacteria could recover seed fertility and protect the full life cycle of emerging rice plants from fungal pests. With our findings, seed biopriming is a straightforward approach that farmers can apply to recover unhealthy rice seed stock, which enables them to reduce the cost and use of agrochemicals in the commercial production of rice and to promote green technology in sustainable agriculture.
Influence of anesthesia methods on surgical outcomes and renal function in retrograde intrarenal stone surgery: a prospective, randomized controlled study
Authors: Kwon Ohseong , Lee Jung-Man , Park Juhyun , Cho Min Chul , Son Hwancheol , Jeong Hyeon , Ryang Seung Hoon , Cho Sung Yong 
Published: December 2019

Abstract
Background
We analyzed the influence of anesthesia methods on surgical outcomes and renal function in retrograde intrarenal surgery (RIRS) in a prospective, randomized controlled study.

Methods
Seventy patients who underwent RIRS from September 2015 to February 2017 were randomly allocated to general anesthesia (GA) or spinal anesthesia (SA) groups. Renal function was assessed using estimated glomerular filtration rate, and separate renal function was evaluated using nuclear medicine tests. Maneuverability and accessibility were evaluated after every surgery. All procedures were performed by a single experienced surgeon (SY Cho).

Results
Stone-free rate was higher in the GA (92.3%, 36 of 39) than the SA (71.0%, 22 of 31) (P = 0.019) group. Pain score was higher in the GA than in the SA group on the first postoperative morning (P = 0.025), but pain scores of the two groups were similar before discharge (P = 0.560). There were no differences in the changes of serum creatinine level (P = 0.792) and changes of estimated glomerular filtration rate (P = 0.807). Differences of separate renal function between operative and contralateral site increased significantly in patients under GA than under SA at postoperative 3 months (P = 0.014). Maneuverability and accessibility were better in SA with sedation than GA (P < 0.001).

Conclusions
RIRS under SA showed advantages in renal function change using renogram at postoperative 3 months and in lower pain score on the first postoperative morning. Performance of operator under SA was worse than that under GA and significantly improved with sedation. RIRS under SA showed advantages in lower pain score at postoperative first day.

Trial registration
Clinicaltrials.gov ID is NCT03957109, and registration date is 17th May 2019. This study was retrospectively registered.
Internet use and self-rated health among Swedish 70-year-olds: a cross-sectional study
Authors: Falk Erhag Hanna , Ahlner Felicia , Rydberg Sterner Therese , Skoog Ingmar , Bergström Annika 
Published: December 2019

Abstract
Background
The Internet is increasingly becoming an infrastructure for a number of services, both commercial, public (including health related) and personal. Using the internet have the potential to promote social interaction and social connectedness by upholding social networks and social contacts. However, Internet use is lower in older adults compared to other age groups. This digital divide is considered a risk to the health of older adults since it limits their participation in society, access and use of relevant health related information and services. This study focuses on whether there is an association between Internet use and self-rated health.

Method
A cross-sectional population-based sample of 70-year-olds from The Gothenburg H70 Birth Cohort Study (n = 1136) was examined in 2014–16. All data was collected using structured interviews and questionnaires. Differences in proportions were tested with chi-square test and ordinary least square regression analysis was used to estimate the relationship between Internet use and self-rated health controlling for health factors, hearing and visual impairment, and social contacts.

Results
There is a relationship between more frequent Internet use and good self-rated health (unstandardized β 0.101 p < 0.001), and the effect remained after adjusting for all covariates (unstandardized β 0.082 p < 0.001). Our results also show that, in comparison to health factors, Internet use is of minor importance to the SRH of older adults, since adding these improved the explanatory power of the model by approximately 400% (from 0.04 to 0.18).

Conclusion
Although the direction of the relationship between more frequent interne use and better self-rated health is undetermined in the present study, it can be suggested that using the Internet informs and educates older adults, strengthening their position as active and engaged participants of society. It can also be suggested that those using the Internet report less loneliness and a possibility to establish new computer-mediated relationships within online communities. Further research needs to examine what aspects of Internet use, and in what contexts such positive perceptions arise.
A systematic review: comparative analysis of the effects of propofol and sevoflurane on postoperative cognitive function in elderly patients with lung cancer
Authors: Sun Haitao , Zhang Guohua , Ai Bolun , Zhang Huimin , Kong Xiangyi , Lee Wan-Ting , Zheng Hui , Yan Tao , Sun Li 
Published: December 2019

Abstract
Background
The potential risk for cognitive impairment following surgery and anesthesia is a common concern, especially in the elderly and more fragile patients. The risk for various neurocognitive effects is thus an area of importance. The independent impact of surgery and anesthesia is still not known. Likewise, the independent effect of different drugs used during anesthesia is a matter of debate, as is the number and amounts of drugs used and the “depth of anesthesia.” So, understanding the drug-related phenomenon and mechanisms for postoperative cognitive impairment is essential. This meta-analysis aims to compare the effects of propofol and sevoflurane anesthesia on postoperative cognitive function in elderly patients with lung cancer.

Methods
This study is a systematic review and meta-analysis for controlled clinical studies. Public-available online databases were searched to identify eligible randomized placebo-controlled trials or prospective cohort studies concerning the effects of propofol and sevoflurane on postoperative cognitive function. The primary endpoints are postoperative mini-mental state examination (MMSE) scores at various time points; the secondary endpoint is the serum S100beta concentration 24 h after surgery. Standard mean differences (SMDs) along with 95% confidence intervals (CIs) were extracted and analyzed using random or fixed-effects models. Analyses regarding heterogeneity, risk of bias assessment, and sensitivity were performed.

Results
We searched 1626 eligible publications and 14 studies of 1404 patients were included in the final analysis. The majority of included studies had been undertaken in Asian populations. Results suggested that propofol has a greater adverse effect on cognitive function in the elderly patients with lung cancer than sevoflurane. There were significant differences in issues of MMSE 6 h (11 studies; SMD -1.391, 95% CI -2.024, − 0.757; p < 0.001), MMSE 24 h (14 studies; SMD -1.106, 95% CI -1.588, − 0.624; p < 0.001), MMSE 3d (11 studies; SMD -1.065, 95% CI -1.564, − 0.566; p < 0.001), MMSE 7d (10 studies; SMD -0.422, 95% CI -0.549, − 0.295; p < 0.001), and serum S100beta concentration at 1 day after surgery (13 studies; SMD 0.746, 95% CI 0.475, 1.017; p < 0.001).

Conclusion
Propofol has a more significant adverse effect on postoperative cognitive function in elderly patients with lung cancer than sevoflurane.