bluuebunny/crossref_metadata_2025 huggingface dataset:
Laparoscopic pyelolithotomy in patients with previous ipsilateral renal stone surgery
Authors: Radfar Mohammad Hadi , Dadpour Mehdi , Simforoosh Nasser , Basiri Abbas , Nouralizadeh Akbar , Shakiba Behnam , Valipour Reza , Zare Ali
Published: December 2019

Objectives:

To evaluate the safety and efficacy of transperitoneal laparoscopic pyelolithotomy in renal stone cases with previous renal surgeries.

Patients and methods:

In this prospective study, 190 consecutive patients with renal stones, who were candidates for transperitoneal laparoscopic pyelolithotomy, were enrolled. The patients were divided into two groups. In group A, 163 patients without a history of renal surgery underwent standard laparoscopic pyelolithotomy, whereas in group B laparoscopic pyelolithotomy was performed in 27 patients with a history of kidney stone surgery including percutaneous nephrolithotomy or open stone surgery. All intraoperative data including the operating time and complications such as bleeding requiring transfusion were recorded. Postoperative data such as length of hospitalization, hemoglobin level alteration, and other complications were also recorded.

Results:

There was no significant difference in the preoperative data such as stone size, stone site, age, sex, and stone side between the two groups. There was no significant difference in the stone-free rate between the two groups (p = 0.4). There was no significant difference between the two study groups regarding the operating time, hospital stay, stone-free rate, complications, and transfusion rate.

Conclusion:

Laparoscopic pyelolithotomy can be used as a safe and feasible treatment modality in the setting of previous renal surgery. The complications and stone-free rate of laparoscopic pyelolithotomy in patients with history of renal surgery are acceptable.
The Clinical Journey of Patients with Riboflavin Transporter Deficiency Type 2
Authors: Amir Fatima , Atzinger Carrie , Massey Keith , Greinwald John , Hunter Lisa L. , Ulm Elizabeth , Kettler Margaret
Published: December 2019

Purpose:

To identify symptoms and health care interactions with patients with riboflavin transporter deficiency (RTD) type 2 prior to diagnosis.

Methods:

Parents of children with riboflavin transporter deficiency type 2 (n = 10) were interviewed to collect data on the patient’s clinical journey.

Results:

The average diagnostic delay was 27.6 months. Neurologists were the most commonly visited clinician (90%). Common symptoms during the first year of the patient’s clinical journey included abnormal gait and/or ataxia (70%), nystagmus (50%), and upper body muscle weakness (40%). Prior to diagnosis, optic atrophy, sleep apnea, breath-holding spells, and dysphagia were commonly observed. Hearing loss was only reported in 40% of subjects prior to diagnosis. Riboflavin responsive megaloblastic anemia is reported for the first time. Mitochondrial disease was the most common suspected diagnosis (30%).

Conclusion:

Despite clinical variability, common early symptoms of riboflavin transporter deficiency type 2 exist that can better allow clinicians to more rapidly identify riboflavin transporter deficiency type 2.
Sepsis and Septic Shock Definitions in Patients With Cancer Admitted in ICU
Authors: Nathan Neveux , Sculier Jean-Paul , Ameye Lieveke , Paesmans Marianne , Bogdan-Dragos Grigoriu , Meert Anne-Pascale
Published: December 2019

Introduction:

In 2016, a new definition of sepsis and septic shock was adopted. Some studies based on the general population demonstrated that the Sequential Organ Failure Assessment (SOFA) score is more accurate than the systemic inflammatory response syndrome (SIRS) criteria to predict hospital mortality of infected patients requiring intensive care.

Patients and Method:

We have analyzed all the records of patients with cancer admitted for a suspected infection between January 1, 2013, and December 31, 2016, in our oncological intensive care unit (ICU). Sequential Organ Failure Assessment score and quick SOFA (qSOFA) score as well as SIRS criteria were calculated. We analyzed the accuracy of each score to predict hospital mortality in the setting of the new and old definitions of septic shock.

Results:

Our study includes 241 patients with a solid tumor and 112 with a hematological malignancy. The hospital mortality rate is 37% (68% in patients with septic shock according to the new definition and 60% according to old definition) between 2013 and 2016. To predict hospital mortality, the SOFA score has an area under the receiver operating characteristic curve of 0.74 (95% confidence interval [CI], 0.68-0.79), the qSOFA of 0.65 (95% CI, 0.59-0.70), and the SIRS criteria of 0.58 (95% CI, 0.52-0.63). In multivariate analysis, a higher SOFA score or a higher qSOFA score indicates poor prognosis: odds ratio (OR) per 1-point increase by 1.28 (95% CI, 1.18-1.39) and 1.48 (95% CI, 1.04-2.11), respectively. Complete remission is a good prognostic factor for hospital mortality: OR 0.39 (95% CI, 0.22-0.67).

Conclusion:

The new definition of sepsis and septic shock is applicable in an ICU oncological population with the same reliability as in the general population. The SOFA score is more accurate than qSOFA and SIRS criteria to predict hospital mortality.
Pneumococcal vaccination in adult people living with HIV on suppressive antiretroviral therapy: a case–control study
Authors: Vivancos-Gallego MJ , Muriel Alfonso , Serrano-Villar Sergio , Moreno-Zamora Ana , Pérez-Elías MJ , Quereda Carmen , Casado JL , Sánchez-Conde Matilde , Del Campo Santos , Dronda Fernando , Sánchez-Díaz Ana M , Valencia-Martín Jose Lorenzo , Moreno Santiago
Published: December 2019

There is little information on the effectiveness of the pneumococcal vaccines (PVs), especially for the pneumococcal conjugate vaccines (PCVs), in HIV-infected patients in the modern antiretroviral era. This is a case–control study where cases were people living with HIV (PLWH) with confirmed pneumococcal infection (CPI) and controls were PLWH without CPI matched with cases by gender and year of HIV diagnosis. The selection process was blinded to the study factor (vaccination). Sample size estimation yielded 61 cases and 183 controls. We analyzed the effect of PV on CPI using Cox proportional-hazards regression model with time-dependent covariates. We included 256 subjects: 64 cases, and 192 controls. PVs had been administered to 115 (45%) patients. Only the modified Charlson Comorbidity Index (HR 1.16, 95%CI 1.06–1.27, P = 0.001) and the CD4 nadir (HR 0.99, 95% CI 0.98–0.99, P = 0.001) were independently associated with CPI. Receipt of PV was not associated with CPI after adjusting in the multivariate model with time protection as a dependent covariate (HR 0.65, 95% CI 0.35–1.32 P = 0.250). We also investigated the influence of different immunization schedules. In an adjusted model, we found no evidence of protection against CPI, including double immunization schedules (HR 0.42 95%CI 0.15–1.19 P = 0.102). In this case–control study, we could not show an association between pneumococcal vaccination and confirmed pneumococcal infection, although a protective effect of particular schedules of immunization cannot be ruled out.
N-way partial least squares combined with new self-construction strategy—A promising approach of using near infrared spectral data for quantitative determination of multiple compounds
Authors: Zhang Xiang-Zhi , Ma Ai-Jun , Feng Na , Li Bao Qiong
Published: December 2019

Because of the complexity of near infrared spectral data, effective strategies are necessary proposed for accurate quantitative analysis purpose. This work explores a new self-construction strategy for the arrangement of conventional near infrared two-dimensional spectra into new self-constructed three-dimensional spectra, and investigate the feasibility of N-way partial least squares combined with the new self-constructed three-dimensional near infrared spectra for obtaining accurate quantitative determination results. A proof-of-concept model system, the quantitative analysis of four components (moisture, oil, protein, and starch) in corn samples, was applied to evaluate the performance of the proposed strategy. The ability of the newly proposed approach to predict the target compounds was checked with test samples. The established models have good predictive power for the target compounds with acceptable values of Rp (range from 0.82 to 0.997) and RMSEP (range from 0.03 to 0.47). Compared with partial least squares method on pretreated near infrared spectra and N-way partial least squares method on the basis of near infrared self-constructed three-dimensional spectra, the proposed method is competitive.
End-of-Life Trajectories of Patients With Hematological Malignancies and Patients With Advanced Solid Tumors Visiting the Emergency Department: The Need for a Proactive Integrated Care Approach
Authors: Verhoef Mary-Joanne , de Nijs Ellen J. M. , Ootjers Claudia S. , Fiocco Marta , Fogteloo Anne J. , Heringhaus Christian , Marijnen Corrie A. M. , Horeweg Nanda , der Linden Yvette M. van
Published: December 2019

Purpose:

Patients with hematological malignancies (HM) have more unpredictable disease trajectories compared to patients with advanced solid tumors (STs) and miss opportunities for a palliative care approach. They often undergo intensive disease-directed treatments until the end of life with frequent emergency department (ED) visits and in-hospital deaths. Insight into end-of-life trajectories and quality of end-of-life care can support arranging appropriate care according to patients’ wishes.

Method:

Mortality follow-back study to compare of end-of-life trajectories of HM and ST patients who died <3 months after their ED visit. Five indicators based on Earle et al. for quality of end-of-life care were assessed: intensive anticancer treatment <3 months, ED visits <6 months, in-hospital death, death in the intensive care unit (ICU), and in-hospice death.

Results:

We included 78 HM patients and 420 ST patients, with a median age of 63 years; 35% had Eastern Cooperative Oncology Group performance status 3-4. At the ED, common symptoms were dyspnea (22%), pain (18%), and fever (11%). After ED visit, 91% of HM patients versus 76% of ST patients were hospitalized ( P = .001). Median survival was 17 days (95% confidence interval [CI]: 15-19): 15 days in HM patients (95% CI: 10-20) versus 18 days in ST patients (95% CI: 15-21), P = .028. Compared to ST patients, HM patients more often died in hospital (68% vs 30%, P < .0001) and in the ICU or ED (30% vs 3%, P < .0001).

Conclusion:

Because end-of-life care is more aggressive in HM patients compared to ST patients, a proactive integrated care approach with early start of palliative care alongside curative care is warranted. Timely discussions with patients and family about advance care planning and end-of-life choices can avoid inappropriate care at the end of life.
Is Bad News Difficult to Read? A Readability Analysis of Differently Connoted Passages in the Annual Reports of the 30 DAX Companies
Authors: Thoms Claudia , Degenhart Anke , Wohlgemuth Katharina
Published: December 2019

This study examines the strategic use of readability to obfuscate negative news in a German financial communication context. Combining a manual and an automated content analysis, the authors assess the tone and readability of three parts (chairman’s address, share-price development, and development in the fiscal year) of the 2014 annual reports of the 30 companies listed in the German stock index DAX. The results indicate that positively connoted passages in annual reports are not necessarily easier to read than negatively connoted passages. Furthermore, the readability of the annual report varies depending on the part and its function within the report.
Do Medicare and Medicaid Payer-Mix Change After the Privatization of Public Hospitals?
Authors: Ramamonjiarivelo Zo , Weech-Maldonado Robert , McRoy Luceta , Epané Josué Patien , Zengul Ferhat D. , Hearld Larry
Published: December 2019

This study assessed the impact of public hospitals’ privatization on payer-mix. We used a national sample of nonfederal, acute care, public hospitals in 1997 and followed them through 2013, resulting in a cohort of 492 hospitals (8,335 hospital-year observations). Privatization to for-profit (FP) status was associated with a greater increase in Medicare payer-mix (β = 0.13; p ≤ .001), compared with a smaller increase for privatization to not-for-profit (NFP) status (β = 0.02; p ≤ .05). FP privatization was associated with a greater decrease in Medicaid payer-mix (β = −0.09; p ≤ .001), compared with NFP privatization (nonsignificant). There is a larger change in payer-mix after FP privatization than after NFP privatization.
Completing Self-administered Questionnaires: Hmong Older Adults and Their Family Helpers
Authors: Lor Maichou , Schaeffer Nora Cate , Brown Roger L. , Bowers Barbara J.
Published: December 2019

This study describes a method for collecting data from nonliterate, non-English-speaking populations. Our audio computer-assisted self-interview instrument with color-labeled response categories was designed for use with helper assistance. The study included 30 dyads of nonliterate older Hmong respondents and family helpers answering questions about health. Analysis of video recordings identified respondents’ problems and helpers’ strategies to address these problems. Seven dyads displayed the paradigmatic question–answer sequence for all items, while 23 departed from the paradigmatic sequence at least once. Reports and pauses were the most common signs of problems displayed by respondents. Paraphrasing questions or response categories and providing examples were the most common helper strategies. Future research could assess the impact of helpers’ strategies on data quality.
No Republican, No Vote: Undervoting and Consequences of the Top-Two Primary System
Authors: Fisk Colin A.
Published: December 2019

Washington and California adopted the Top-Two Primary in 2008 and 2012, respectively. Under this new system, all candidates regardless of party affiliation run against each other, narrowing the field down to the top two for the general election. In some jurisdictions, the general election features two candidates from the same party. Ten percent of California voters chose not to vote in the 2016 U.S. Senate election which featured two Democrats. Using data from the Cooperative Congressional Election Study (2012-2016), I find that among those who vote in the national November elections, orphans, or voters without a copartisan candidate on the ballot are more likely to undervote, opting out of voting in their congressional race. Levels of undervoting are nearly 20 percentage points higher for orphaned voters compared to non-orphaned voters. Additionally, voters who abstain perceive more ideological distance between themselves and the candidates compared to voters who cast a vote. These findings support a multi-step framework for vote decisions in same-party matchups: voters are more likely to undervote if they are unable to vote for a candidate from their party (partisan model), but all voters are more likely to vote for a candidate when they perceive ideological proximity (ideological model).
Enabled Players: The Value of Accessible Digital Games
Authors: Cairns Paul , Power Christopher , Barlet Mark , Haynes Gregory , Kaufman Craig , Beeston Jen
Published: December 2019

It is increasingly recognized that there are many players of mainstream digital games who have some form of disability. It is not known which aspects of games are valued by players, regardless of whether they have a disability. We report on a survey of 71 players from the general game community and 123 players with disabilities asking what makes games important to them. We found established motivations to play such as social connection and escapism but additionally that players find games beneficial and provide artistic experiences. Players with disabilities explicitly referred to games helping them to feel enabled or being on a level footing with nondisabled players. The value of accessible games is not just mere play but playing the same games as everyone else. This implies that achieving accessibility through adapting games is an important approach to provide the valued connection and enablement that games provide.
A Nontarget Mechanism to Explain Carcinogenesis Following α-Irradiation
Authors: Priest Nicholas D.
Published: December 2019

This commentary highlights the published data on the metabolic processes that lead to the development of cancer following intakes of asbestos and chemical agents. Following exposure to both, the key initiating event is cell injury leading to cell death that may further lead to inflammation, fibrosis, and cancer. Since α-particle transits also kill cells, it is suggested that cell death and inflammation will also trigger carcinogenesis within tissues irradiated by these particles. Such an explanation would be consistent with the inflammation and fibrosis seen in tumor-bearing tissues irradiated by radon-222, radium-226, thorium-232, plutonium-239, and other α-emitting radionuclides. It would also provide an explanation for dose-related changes in latency and in the similar dose–responses for the same tissue in differently sized species.
Addressing Contextual Challenges in Underserved Indigenous Spaces of the Global South: In Search of an Approach Based on Unlearning, Co-Learning, and Relearning
Authors: Dutta Uttaran
Published: December 2019

Qualitative scholars are increasingly arguing in favor of bridging the gap between emic and etic knowledge as well as to become critically reflexive while conducting research, especially in the underserved contexts. Conducting qualitative research in marginalized spaces of the global South often poses unique challenges. In this case, my research took place in rural eastern India where some of the challenges faced were my ethnocentrism and preconceived baggage, trust building challenges, and situated communicative and structural barriers. My field research experiences taught me the importance of unlearning, co-learning, and relearning to meaningfully engage with the underserved populations and their realities. Unlearning involves critically examining our previously acquired knowledge/assumptions toward exploring purviews and avenues for new learning. Co-learning is a process of collaborative learning with and in grassroots communities toward cocreating culturally meaningful knowledge and opening up avenues for social equality. Intertwined with unlearning and co-learning, the relearning efforts are focused on gaining and embodying new knowledge or ways of seeing. Grounded in the examples from my field research experiences, this article discusses the roles and significance of unlearning, co-learning, and relearning in conducting qualitative research in the underserved context of the global South.
Predictors of Attitudes Toward Gay Men and Lesbian Women in 23 Countries
Authors: Bettinsoli Maria Laura , Suppes Alexandra , Napier Jaime L.
Published: December 2019

Dominant accounts of sexual prejudice posit that negative attitudes toward nonheterosexual individuals are stronger for male (vs. female) targets, higher among men (vs. women), and driven, in part, by the perception that gay men and lesbian women violate traditional gender norms. We test these predictions in 23 countries, representing both Western and non-Western societies. Results show that (1) gay men are disliked more than lesbian women across all countries; (2) after adjusting for endorsement of traditional gender norms, the relationship between participant gender and sexual prejudice is inconsistent across Western countries, but men (vs. women) in non-Western countries consistently report more negative attitudes toward gay men; and (3) a significant association between gender norm endorsement and sexual prejudice across countries, but it was absent or reversed in China, India, and South Korea. Taken together, this work suggests that gender and sexuality may be more loosely associated in some non-Western contexts.
‘I drew the parts of my body in proportion to how much PCOS ruined them’: Experiences of polycystic ovary syndrome through drawings
Authors: Thorpe Cassandra , Arbeau Kelly J , Budlong Benjamin
Published: December 2019

Polycystic ovary syndrome is a chronic endocrine disorder associated with persistent physical symptoms and psychological and lifestyle repercussions. Eighty-nine participants (83 females, 6 non-binary) aged 19–43 years described their experiences of polycystic ovary syndrome through drawings and personal accounts. Four descriptive themes were identified: awareness of visible and invisible symptoms, misshapen self and body, limitations and barriers and resignation. Taken together, participants described a condition with all-encompassing effects: much more than symptom management alone. Findings support the use of drawings as an appropriate method with this population and suggest continuing need for supports for individuals with polycystic ovary syndrome.
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 study

Endogenous 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 methods

This 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.

Results

17 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 question

Blocking 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

Background

A 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.

Results

We 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.

Conclusion

The 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

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

Background

Salmonid 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.

Results

All 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.

Conclusions

Our 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

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

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

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

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

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.
Correction to: Procalcitonin-guided antibiotic therapy in critically ill adults: a meta-analysis
Authors: Zhang Tao , Wang Yan , Yang Qianting , Dong Yalin
Published: December 2019

After publication of the original article [1], the authors have reported that the software developers had used a new amended version of the software called “v0.9.5.10” instead of “v0.9.5.5”, which is referred to in the original article.
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

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.
The chemo-gut study: investigating the long-term effects of chemotherapy on gut microbiota, metabolic, immune, psychological and cognitive parameters in young adult Cancer survivors; study protocol
Authors: Deleemans Julie M. , Chleilat Faye , Reimer Raylene A. , Henning Jan-Willem , Baydoun Mohamad , Piedalue Katherine-Ann , McLennan Andrew , Carlson Linda E.
Published: December 2019

Background

The gut microbiota is an important modulator of immune, metabolic, psychological and cognitive mechanisms. Chemotherapy adversely affects the gut microbiota, inducing acute dysbiosis, and alters physiological and psychological function. Cancer among young adults has risen 38% in recent decades. Understanding chemotherapy’s long-term effects on gut microbiota and psycho-physiological function is critical to improve survivors’ physical and mental health, but remains unexamined. Restoration of the gut microbiota via targeted therapies (e.g. probiotics) could potentially prevent or reverse the psycho-physiological deficits often found in young survivors following chemotherapy, ultimately leading to reduced symptom burden and improved health.

Methods

This longitudinal study investigates chemotherapy induced long-term gut dysbiosis, and associations between gut microbiota, and immune, metabolic, cognitive and psychological parameters using data collected at < 2 month (T1), 3–4 months (T2), and 5–6 months (T3) post-chemotherapy. Participants will be 18–39 year old blood or solid tumor cancer survivors (n = 50), and a healthy sibling, partner or friend as a control (n = 50). Gut microbiota composition will be measured from fecal samples using 16 s RNA sequencing. Psychological and cognitive patient reported outcome measures will include depression, anxiety, post-traumatic stress disorder symptoms, pain, fatigue, and social and cognitive function. Dual-energy X-ray Absorptiometry (DXA) will be used to measure fat and lean mass, and bone mineral concentration. Pro-inflammatory cytokines, C-reactive protein (CRP), lipopolysaccharide (LPS), serotonin, and brain derived neurotrophic factor (BDNF) will be measured in serum, and long-term cortisol will be assayed from hair. Regression and linear mixed model (LMM) analyses will examine associations across time points (T1 – T3), between groups, and covariates with gut microbiota, cognitive, psychological, and physiological parameters.

Conclusion

Knowing what bacterial species are depleted after chemotherapy, how long these effects last, and the physiological mechanisms that may drive psychological and cognitive issues among survivors will allow for targeted, integrative interventions to be developed, helping to prevent or reverse some of the late-effects of treatment that many young cancer survivors face. This protocol has been approved by the Health Research Ethics Board of Alberta Cancer Committee (ID: HREBA.CC-19-0018).