bluuebunny/crossref_metadata_2025_split huggingface dataset:
Reliability and validity of the brief dimensional apathy scale
Authors: Radakovic Ratko , Gray Debbie , Dudley Kaitlin , Mioshi Eneida , Dick David , Melchiorre Giulia , Gordon Harry , Newton Judith , Colville Shuna , Pal Suvankar , Chandran Siddharthan , Abrahams Sharon 
Published: January 2020

Abstract

Objective
Apathy is composed of different demotivational subtypes measurable by the dimensional apathy scale (DAS) and can be quickly assessed using the brief DAS (b-DAS). The aim was to determine the reliability and validity of the b-DAS.

Methods
53 amyotrophic lateral sclerosis (ALS) patients and 53 of their informants were recruited. Informants completed the b-DAS, the original informant/carer-rated DAS and behavioral interview about the patients (i.e., presence of behaviors such as apathy/inertia, loss of sympathy/empathy). Patients completed measures of depression, anxiety, emotional lability, cognitive functioning, and functional disability measures.

Results
The b-DAS showed good internal consistency, excellent test–retest reliability, significant positive correlation with the original DAS, and no significant correlations with depression, anxiety, emotional lability, cognitive functioning or functional disability measures. Semi-structured behavior interview showed patients with apathy/inertia had significantly higher b-DAS subscale scores and patients with loss of sympathy/empathy had significantly higher emotional apathy scores only.

Conclusions
The b-DAS is a fast, reliable, and valid instrument for screening apathy subtypes independent of physical disability.
MDEHT: a multivariate approach for detecting differential expression of microRNA isoform data in RNA-sequencing studies
Authors: Amanullah Md , Yu Mengqian , Sun Xiwei , Luo Aoran , Zhou Qing , Zhou Liyuan , Hou Ling , Wang Wei , Lu Weiguo , Liu Pengyuan , Lu Yan 
Published: January 2020

AbstractMotivationmiRNA isoforms (isomiRs) are produced from the same arm as the archetype miRNA with a few nucleotides different at 5 and/or 3 termini. These well-conserved isomiRs are functionally important and have contributed to the evolution of miRNA genes. Accurate detection of differential expression of miRNAs can bring new insights into the cellular function of miRNA and a further improvement in miRNA-based diagnostic and prognostic applications. However, very few methods take isomiR variations into account in the analysis of miRNA differential expression.ResultsTo overcome this challenge, we developed a novel approach to take advantage of the multidimensional structure of isomiR data from the same miRNAs, termed as a multivariate differential expression by Hotelling’s T2 test (MDEHT). The utilization of the information hidden in isomiRs enables MDEHT to increase the power of identifying differentially expressed miRNAs that are not marginally detectable in univariate testing methods. We conducted rigorous and unbiased comparisons of MDEHT with seven commonly used tools in simulated and real datasets from The Cancer Genome Atlas. Our comprehensive evaluations demonstrated that the MDEHT method was robust among various datasets and outperformed other commonly used tools in terms of Type I error rate, true positive rate and reproducibility.Availability and implementationThe source code for identifying and quantifying isomiRs and performing miRNA differential expression analysis is available at https://github.com/amanzju/MDEHT.Supplementary informationSupplementary data are available at Bioinformatics online.
Risk Factors and Predictors of Mortality in Streptococcal Necrotizing Soft-tissue Infections: A Multicenter Prospective Study
Authors: Bruun Trond , Rath Eivind , Madsen Martin Bruun , Oppegaard Oddvar , Nekludov Michael , Arnell Per , Karlsson Ylva , Babbar Anshu , Bergey Francois , Itzek Andreas , Hyldegaard Ole , Norrby-Teglund Anna , Skrede Steinar ,   INFECT Study Group, Nedrebø Torbjørn , Skutlaberg Dag Harald , Hedetoft Morten , Hansen Marco B , Polzik Peter , Rosén Anders , Svensson Mattias , Bergsten Helena , Barrantes Bustinza Walter Israel , Martins dos Santos Vitor A P 
Published: January 2020

Abstract

Background
Necrotizing soft-tissue infections (NSTI) are life-threatening conditions often caused by β-hemolytic streptococci, group A Streptococcus (GAS) in particular. Optimal treatment is contentious. The INFECT cohort includes the largest set of prospectively enrolled streptococcal NSTI cases to date.

Methods
From the INFECT cohort of 409 adults admitted with NSTI to 5 clinical centers in Scandinavia, patients culture-positive for GAS or Streptococcus dysgalactiae (SD) were selected. Risk factors were identified by comparison with a cohort of nonnecrotizing streptococcal cellulitis. The impact of baseline factors and treatment on 90-day mortality was explored using Lasso regression. Whole-genome sequencing of bacterial isolates was used for emm typing and virulence gene profiling.

Results
The 126 GAS NSTI cases and 27 cases caused by SD constituted 31% and 7% of the whole NSTI cohort, respectively. When comparing to nonnecrotizing streptococcal cellulitis, streptococcal NSTI was associated to blunt trauma, absence of preexisting skin lesions, and a lower body mass index. Septic shock was significantly more frequent in GAS (65%) compared to SD (41%) and polymicrobial, nonstreptococcal NSTI (46%). Age, male sex, septic shock, and no administration of intravenous immunoglobulin (IVIG) were among factors associated with 90-day mortality. Predominant emm types were emm1, emm3, and emm28 in GAS and stG62647 in SD.

Conclusions
Streptococcal NSTI was associated with several risk factors, including blunt trauma. Septic shock was more frequent in NSTI caused by GAS than in cases due to SD. Factors associated with mortality in GAS NSTI included age, septic shock, and no administration of IVIG.
Structural and ultrastructural renal lesions in rats fed high-fat and high-phosphorus diets
Authors: Esquinas Paula , Rios Rafael , Raya Ana I , Pineda Carmen , Rodriguez Mariano , Aguilera-Tejero Escolastico , Lopez Ignacio 
Published: January 2020

Abstract

Background
Foods prone to deteriorate renal function are rich in fat and in phosphorus (P), but the interaction between these two factors is not well studied.

Method
Detailed structural and ultrastructural histopathological studies were performed on the kidneys of rats fed different amounts of fat and P: low (4%) fat (LF) and normal (0.6%) P (NP), LF and high (1.2%) P (HP), high (35%) fat (HF) and NP, HF and HP, and HF with low (0.2%) P (LP) for 28 weeks.

Results
Glomeruli of the HF groups showed segmental areas of retraction, sclerosis and thickening of the Bowman’s capsule and basal membranes, which were more accentuated in the HF–HP group. Ultrastructural lesions in the glomeruli also were prominent in rats fed HF, particularly in the HF–HP group, and included thickening of the capillary membrane, endothelial damage, mesangial matrix hypercellularity and podocyte effacement. P restriction reduced the severity of endothelial damage, mesangial matrix hypercellularity, thickening of capillary basement membrane and podocyte effacement. The kidneys of rats fed HP showed significant tubular atrophy and dilatation, focal tubular hyperplasia, thickening of the tubular basal membrane, interstitial edema, inflammation and calcification. All groups fed HF also showed tubular lesions that were more prominent in the HF–HP group. P restriction had a beneficial effect on inflammation and calcification.

Conclusions
Intake of both HF and HP damages the kidneys and their noxious effects are additive. HF intake was preferentially associated with glomerular lesions, while lesions related to HP intake were located mainly in the tubuli and in the interstitium.
Janus Kinase inhibitors in the New Treatment Paradigms of Inflammatory Bowel Disease
Authors: Siegmund Britta 
Published: January 2020

Abstract
This review provides guidance in the decision-making process regarding when to choose a janus kinase [JAK] inhibitor as medical treatment strategy. The focus will be on ulcerative colitis, because the only yet available JAK inhibitor, tofacitinib, has approval for use in ulcerative colitis. The guidance path will include consideration of disease activity, previous treatment, comorbidities, family planning, patient preferences, pharmacology as well as concurrent chronic inflammatory diseases or extraintestinal manifestations. The suggested guidance path illustrates our daily difficulties in the decision-making process regarding best choice for the individual patient. However if predictive biomarkers are lacking, the named criteria can be applied to any other strategy and hence provide support in daily practice.
Utility of double arterial cannulation for surgical repair of acute type A dissection
Authors: Kusadokoro Sho , Kimura Naoyuki , Hori Daijiro , Hattori Masahiro , Matsunaga Wataru , Itagaki Ryo , Yuri Koichi , Mieno Makiko , Nakamura Masanori , Yamaguchi Atsushi 
Published: January 2020

Abstract

OBJECTIVES
Outcomes of planned and unplanned (rescue) double arterial cannulation (DAC) in surgery for acute type A aortic dissection were investigated retrospectively.

METHODS
The study involved 805 patients who were divided into 4 groups according to the cannulation strategy: single cannulation of the femoral artery (n = 338), axillary artery (n = 256), left ventricular apex (n = 52) or ascending aorta (n = 5) (total, n = 57), and DAC (n = 154). Patients who underwent DAC were divided between planned (n = 132) and rescue (n = 22) usage. Characteristics and outcomes were compared between groups. Both unmatched and propensity score-matched analyses were performed.

RESULTS
Shock (39%, 19%, 33% and 14%, in the femoral artery, axillary artery, left ventricular apex/ascending aorta and DAC, respectively) and leg malperfusion (5%, 16%, 16% and 26%, respectively) differed significantly (P &lt; 0.001), but in-hospital mortality did not (9%, 8%, 18% and 7%, respectively; P = 0.096). The 5-year survival rates were 79.4%, 79.7%, 78.6% and 82.2%, respectively. Propensity score-matched analysis showed no statistically significant differences in in-hospital mortality rates (10%, 12%, 14% and 9%, respectively; P = 0.78) and 5-year survival rates (78.4%, 72.3%, 82.3% and 78.0%, respectively). The leading vessel combination and indications for planned and rescue DAC were the femoral and axillary arteries (98%) and true lumen narrowing and/or leg malperfusion (34%), and the axillary followed by femoral (77%) artery and low cardiopulmonary bypass flow (36%). In-hospital mortality in the planned and rescue DAC groups was 7% and 9%, respectively.

CONCLUSIONS
DAC seems effective for both prevention and management of intraoperative malperfusion.
Prognostic factors of oligometastatic non-small-cell lung cancer following radical therapy: a multicentre analysis
Authors: Opitz Isabelle , Patella Miriam , Payrard Loic , Perentes Jean Yannis , Inderbitzi Rolf , Gelpke Hans , Schulte Sandra , Diezi Maja , Gonzalez Michel , Krueger Thorsten , Weder Walter 
Published: January 2020

Abstract

OBJECTIVES
Patients with oligometastatic non-small-cell lung cancer (NSCLC) may benefit from therapy with curative intent. Our goal was to identify prognostic factors related to better prognosis in a multicentre analysis of patients who underwent surgery of primary tumours in combination with radical treatment of all metastatic sites.

METHODS
We retrospectively reviewed the records of oligometastatic patients who underwent resection of primary tumours at 4 centres (August 2001–February 2018). Oligometastasis was defined as ≤5 synchronous metastases in ≤2 organs. Radical metastatic treatment was surgery, radiotherapy or a combination. The Cox proportional hazards model was used for identification of prognostic factors on overall survival.

RESULTS
We treated 124 patients; 72 (58%) were men, mean age 60 ± 9.8 years, with 87 (70%) adenocarcinoma. Sixty-seven (54%) patients had positive pathologic-N stage (pN). Brain metastases were most common (n = 76; 61%) followed by adrenal (n = 13; 10%) and bone (n = 12; 10%). Systemic therapy was administered in 101 (82%) patients. Median follow-up was 60 months [95% confidence interval (CI) 41–86]. Thirty- and 90-day mortality rates were 0 and 2.4%, respectively. One-, 2-, and 5-year overall survival were 80%, 58% and 36%, respectively. Cox regression analysis showed that patients ≤60 years [hazard ratio (HR) 0.41, 95% CI 0.24, 0.69; P = 0.001] and patients with pN0 (HR 0.38, 95% CI 0.21–0.69; P = 0.002) had a significant survival benefit. The presence of bone metastases negatively affected survival (HR 2.53, 95% CI 1.05–6.09; P = 0.04).

CONCLUSIONS
Treatment with curative intent of selected oligometastatic NSCLC, including resection of the primary tumour, can be performed safely and with excellent 5-year survival rates, especially in younger patients with pN0 disease.
Inflamm-ageing: the role of inflammation in age-dependent cardiovascular disease
Authors: Liberale Luca , Montecucco Fabrizio , Tardif Jean-Claude , Libby Peter , Camici Giovanni G 
Published: January 2020

Abstract
The ongoing worldwide increase in life expectancy portends a rising prevalence of age-related cardiovascular (CV) diseases in the coming decades that demands a deeper understanding of their molecular mechanisms. Inflammation has recently emerged as an important contributor for CV disease development. Indeed, a state of chronic sterile low-grade inflammation characterizes older organisms (also known as inflamm-ageing) and participates pivotally in the development of frailty, disability, and most chronic degenerative diseases including age-related CV and cerebrovascular afflictions. Due to chronic activation of inflammasomes and to reduced endogenous anti-inflammatory mechanisms, inflamm-ageing contributes to the activation of leucocytes, endothelial, and vascular smooth muscle cells, thus accelerating vascular ageing and atherosclerosis. Furthermore, inflamm-ageing promotes the development of catastrophic athero-thrombotic complications by enhancing platelet reactivity and predisposing to plaque rupture and erosion. Thus, inflamm-ageing and its contributors or molecular mediators might furnish targets for novel therapeutic strategies that could promote healthy ageing and conserve resources for health care systems worldwide. Here, we discuss recent findings in the pathophysiology of inflamm-ageing, the impact of these processes on the development of age-related CV diseases, results from clinical trials targeting its components and the potential implementation of these advances into daily clinical practice.
Social inequalities in the provision of obstetric services in Norway 1967–2009: a population-based cohort study
Authors: Eriksen Helene Sofie , Høy Susanne , Irgens Lorentz M , Rasmussen Svein , Haug Kjell 
Published: January 2020

Abstract

Background
Socioeconomic (SE) inequalities have been observed in a number of adverse outcomes of pregnancy and many of the risk factors for such outcomes are associated with a low SE level. However, SE inequalities persist even after adjustment for these risk factors. Less well-off women are more vulnerable, but may also get less adequate health services. The objective of the present study was to assess possible associations between SE conditions in terms of maternal education as well as ethnic background and obstetric care.

Methods
A population-based national cohort study from the Medical Birth Registry of Norway. The study population comprised 2 305 780 births from the observation period 1967–2009. Multilevel analysis was used because of the hierarchical structure of the data. Outcome variables included induction of labour, epidural analgesia, caesarean section, neonatal intensive care and perinatal death.

Results
While medical interventions in the 1970s were employed less frequently in women of short education and non-western immigrants, this difference was eliminated or even reversed towards the end of the observation period. However, an excess perinatal mortality in both the short-educated [adjusted relative risk (aRR) = 2.49] and the non-western immigrant groups (aRR = 1.75) remained and may indicate increasing health problems in these groups.

Conclusion
Even though our study suggests a fair and favourable development during the last decades in the distribution across SE groups of obstetric health services, the results suggest that the needs for obstetric care have increased in vulnerable groups, requiring a closer follow-up.
Antibiotic resistome and microbial community structure during anaerobic co-digestion of food waste, paper and cardboard
Authors: Kanger Kärt , Guilford Nigel G H , Lee HyunWoo , Nesbø Camilla L , Truu Jaak , Edwards Elizabeth A 
Published: January 2020

ABSTRACTSolid organic waste is a significant source of antibiotic resistance genes (ARGs) and effective treatment strategies are urgently required to limit the spread of antimicrobial resistance. Here, we studied ARG diversity and abundance as well as the relationship between antibiotic resistome and microbial community structure within a lab-scale solid-state anaerobic digester treating a mixture of food waste, paper and cardboard. A total of 10 samples from digester feed and digestion products were collected for microbial community analysis including small subunit rRNA gene sequencing, total community metagenome sequencing and high-throughput quantitative PCR. We observed a significant shift in microbial community composition and a reduction in ARG diversity and abundance after 6 weeks of digestion. ARGs were identified in all samples with multidrug resistance being the most abundant ARG type. Thirty-two per cent of ARGs detected in digester feed were located on plasmids indicating potential for horizontal gene transfer. Using metagenomic assembly and binning, we detected potential bacterial hosts of ARGs in digester feed, which included Erwinia, Bifidobacteriaceae, Lactococcus lactis and Lactobacillus. Our results indicate that the process of sequential solid-state anaerobic digestion of food waste, paper and cardboard tested herein provides a significant reduction in the relative abundance of ARGs per 16S rRNA gene.
TheShewanellagenus: ubiquitous organisms sustaining and preserving aquatic ecosystems
Authors: Lemaire Olivier N , Méjean Vincent , Iobbi-Nivol Chantal 
Published: January 2020

ABSTRACTThe Gram-negative Shewanella bacterial genus currently includes about 70 species of mostly aquatic γ­-proteobacteria, which were isolated around the globe in a multitude of environments such as surface freshwater and the deepest marine trenches. Their survival in such a wide range of ecological niches is due to their impressive physiological and respiratory versatility. Some strains are among the organisms with the highest number of respiratory systems, depending on a complex and rich metabolic network. Implicated in the recycling of organic and inorganic matter, they are important components of organism-rich oxic/anoxic interfaces, but they also belong to the microflora of a broad group of eukaryotes from metazoans to green algae. Examples of long-term biological interactions like mutualism or pathogeny have been described, although molecular determinants of such symbioses are still poorly understood. Some of these bacteria are key organisms for various biotechnological applications, especially the bioremediation of hydrocarbons and metallic pollutants. The natural ability of these prokaryotes to thrive and detoxify deleterious compounds explains their use in wastewater treatment, their use in energy generation by microbial fuel cells and their importance for resilience of aquatic ecosystems.
Heterogeneous oceanic mass distribution in GRACE observations and its leakage effect
Authors: Yi Shuang , Heki Kosuke 
Published: January 2020

SUMMARYSignal leakage between the land and ocean is a challenge in using Gravity Recovery and Climate Experiment (GRACE) observation data to study global mass redistributions. Although the leakage occurs in both directions, more attention has been paid to the land-to-ocean leakage and less to the ocean-to-land leakage. Here, we show that the ocean-to-land leakage is non-uniform and non-negligible and propose a new forward modelling method to fully consider bi-directional leakages with the help of the global Ocean ReAnalysis System ORAS5. This observation-driven model could significantly reduce the variations in ocean grids and thus decrease the ocean-to-land leakage. The results with different treatment of the ocean signal leakage are compared. We find that failing to consider the ocean-to-land leakage will cause an underestimation of ∼20 per cent in the seasonal variation and will introduce a bias of several giga-tons in the secular trend. Although the uniform and non-uniform model have similar results in the global average of seasonal mass variations, the non-uniform ocean model is necessary in most places, especially near the Arctic Ocean, the Sea of Japan and the Gulf of Carpentaria. Despite these achievements, we also point out that there is still much room for improvement in ocean mass models, particularly in long-term trends. Our results indicate the importance of the ocean-to-land leakage correction in the mass estimation in coastal land areas using the GRACE data.
Intraoperative identification of major blood supply to Adamkiewicz artery after multistep surgeries in thoraco-abdominal aortic aneurysm repair
Authors: Sakatsume Ko , Kawatsu Satoshi , Adachi Osamu , Saiki Yoshikatsu 
Published: January 2020

Abstract
Herein, we report a case of thoraco-abdominal aortic repair in a 55-year-old man with a multiple treatment history for aortic aneurysm and aortic dissection. A computed tomography scan revealed that the Adamkiewicz artery was connected to an occluded intercostal artery, suggesting that the left inferior epigastric artery was the key artery supplying the Adamkiewicz artery; the key artery was identified through direct monitoring of cerebrospinal fluid temperature and selective hypothermic perfusion. No spinal cord injury was detected during the postoperative period.
GLU: a software package for analysing continuously measured glucose levels in epidemiology
Authors: Millard Louise A C , Patel Nashita , Tilling Kate , Lewcock Melanie , Flach Peter A , Lawlor Debbie A 
Published: January 2020

Abstract
Continuous glucose monitors (CGM) record interstitial glucose levels ‘continuously’, producing a sequence of measurements for each participant (e.g. the average glucose level every 5 min over several days, both day and night). To analyse these data, researchers tend to derive summary variables such as the area under the curve (AUC), to then use in subsequent analyses. To date, a lack of consistency and transparency of precise definitions used for these summary variables has hindered interpretation, replication and comparison of results across studies. We present GLU, an open-source software package for deriving a consistent set of summary variables from CGM data. GLU performs quality control of each CGM sample (e.g. addressing missing data), derives a diverse set of summary variables (e.g. AUC and proportion of time spent in hypo-, normo- and hyper- glycaemic levels) covering six broad domains, and outputs these (with quality control information) to the user. GLU is implemented in R and is available on GitHub at https://github.com/MRCIEU/GLU. Git tag v0.2 corresponds to the version presented here.