bluuebunny/crossref_metadata_2025_split huggingface dataset:
Differential Expression of Long Noncoding RNAs and Their Function-Related mRNAs in the Peripheral Blood of Allergic Rhinitis Patients
Authors: Yang Yanyan , Zhang Yu , Yang Yujuan , Guo Jing , Yang Liping , Li Chenglin , Song Xicheng 
Published: March 2020

Background The mechanism of long noncoding RNAs (lncRNAs) involved in the development of allergic rhinitis (AR) remains unclear. Objective We investigated the mechanism by which differentially expressed lncRNAs contribute to pathogenesis of AR. Methods Expression profiles of lncRNAs and mRNAs were analyzed by microarray detection from the blood samples of 3 AR patients and 3 control subjects, and the main lncRNAs were verified by quantitative real-time polymerase chain reaction (qRT-PCR) in the peripheral blood of 16 AR patients and 18 control subjects. GO (Gene_Ontology), Pathway, and Disease analysis of differentially expressed lncRNAs and mRNAs, and transcription factor prediction analysis were performed to explore synergistic effect of differentially expressed lncRNAs and their function-related mRNAs on AR pathogenesis. Results Thirty-one lncRNAs were differentially expressed in the peripheral blood from AR patients, and 4 of the 5 most differentially expressed lncRNAs had significantly higher levels in AR patients than in control subjects by qRT-PCR analysis. A lncRNA-mRNA coexpression network analysis identified 16 pairs of positive correlations between the 4 lncRNAs and coexpressed mRNAs. GO, Pathway, and Disease analyses indicated that the 4 lncRNAs were correlated with 7 mRNAs enriched in terms of inflammation, immune response, and allergic diseases. Transcription factor prediction results suggested that Oct-1, AP-1, NF-kappaB, and c-Rel play key roles in the pathogenesis of AR mediated by lncRNAs. Conclusion Our results provide new insights into how lncRNAs and their function-related mRNAs might contribute to AR.
Cystic Fibrosis Transmembrane Conductance Regulator Modulator Therapy: A Review for the Otolaryngologist
Authors: Lee Saangyoung E. , Farzal Zainab , Daniels M.Leigh Anne , Thorp Brian D. , Zanation Adam M. , Senior Brent A. , Ebert Charles S. , Kimple Adam J. 
Published: March 2020

Background Cystic fibrosis (CF) is a genetic disease that may result in multiple systemic disorders and potentially fatal severe respiratory compromise. However, the advent of CF transmembrane conductance regulator (CFTR) modulators has changed the management of CF for patients with select mutations. Although clinical trials have highlighted increased pulmonary function and decreased exacerbations as a result of these novel therapies, their effect on the sinuses has not been well-described. Objective Our objective is to review the CFTR modulators to provide otolaryngologists, physicians who frequently care for patients with CF, a basic understanding of these drugs and their effects on chronic rhinosinusitis (CRS) in patients with CF. Methods The clinically approved and available CFTR modulators and specific indications for their use are reviewed. Additionally, a systematic review of these therapies and effects on CRS in CF was performed. Results Four Food and Drug Administration approved CFTR modulators are available for patients with CF. Current drugs are approved for gating, residual function, or F508del mutations. Multiple reports describe CFTR modulators’ increase in transepithelial ion transport in nasal epithelial cultures; however, clinical studies regarding effects of these modulators on sinonasal health are limited to 5 studies that present new data of the effects of CFTR modulators in CRS. Conclusions CFTR modulators have changed management of CF. Initial studies of these medications demonstrate promising results in CF; however, there is a paucity of literature describing the effect of CFTR modulators on CF-associated CRS, although initial results are encouraging.
Movement behaviour patterns in adults with haemophilia
Authors: Timmer Merel A. , Veenhof Cindy , de Kleijn Piet , de Bie Rob A. , Schutgens Roger E. G. , Pisters Martijn F. 
Published: March 2020

Background: Joint bleeds are the hallmark of haemophilia, and can lead to disabling haemophilic arthropathy. Consequently, the movement behaviour of adults with haemophilia differs from that of healthy adults. It seems unlikely that a single outcome is able to reflect all relevant information regarding movement behaviour. The aim of the current study was to identify patterns of movement behaviour within persons with haemophilia (PWH) and compare clinical characteristics between patterns of movement behaviour. Methods: A total of 105 PWH [70% severe haemophilia; median age 43 years (30.0–54.0)] were included in the study. Hierarchical cluster analysis was used to identify patterns of movement behaviour. Clustering variables included seven parameters of movement behaviour: sitting, standing, walking, biking, running, frequency of active bouts and length of active bouts. Clinical characteristics included age, severity of haemophilia, joint health, physical functioning and pain. Clinical characteristics were compared between identified clusters by Kruskall–Wallis test. Movement behaviour was assessed with the Activ8 accelerometer, joint health was assessed on the Haemophilia Joint Health Score, physical functioning on the Haemophilia Activity List and the 40 m self-paced walk test and pain on the Numerical Pain Rating Score. Results: Cluster analysis identified three clusters, which were defined as: ‘sedentary’ (57%), ‘bikers and runners’ (22%) and ‘walkers’ (20%). The ‘bikers and runners’ showed better joint health and experienced fewer limitations in activities than the ‘walkers’ and the ‘sedentary’. The ‘walkers’ perceived fewer limitations in activities than the ‘sedentary’, with comparable joint health. We did not identify differences in pain, walking speed and age between the clusters. Conclusions: We identified three patterns of movement behaviour. The majority of PWH was identified as sedentary, whereas less sitting and regular walking during the day seemed to be more beneficial.
Frequency, characteristics and impact of multiple consecutive nosocomial infections in patients with decompensated liver cirrhosis and ascites
Authors: Schultalbers Marie , Tergast Tammo L , Simon Nicolas , Kabbani Abdul‐Rahman , Kimmann Markus , zu Siederdissen Christoph Höner , Gerbel Svetlana , Manns Michael P , Cornberg Markus , Maasoumy Benjamin 
Published: March 2020

BackgroundNosocomial infections are a particular threat for patients with liver cirrhosis. It is not uncommon that individuals develop even several consecutive infections during a single hospital stay. We aimed to investigate the impact and characteristics of multiple, consecutive nosocomial infections.MethodsA total of 514 consecutive patients with liver cirrhosis and ascites were included and followed up for 28 days for nosocomial infection, death or liver transplantation (LTx). Laboratory values were assessed at the time of hospitalization as well as at the onset of each new infectious episode.Results58% (n  = 298) of the patients developed at least one nosocomial infection and in 23% (n  = 119) even multiple infections were documented during a single hospital stay. Consecutive infections usually occurred shortly after the previous episode. Spontaneous bacterial peritonitis (SBP) was the most common infection. However, the proportion of SBP declined from 43% at the first to only 31% at the third nosocomial infection (p  = 0.096). In contrast, the likelihood for other, less common types of infection such as blood stream infections increased. Third nosocomial infections were also more likely to be linked to the detection of fungal pathogens (21% vs. 52%; p  = 0.001). Each additional infectious episode had a dramatic detrimental impact on LTx‐free survival that was independent from the stage of liver disease (adjusted‐HR: 6.76, p  = 0.002 for first nosocomial infection; adjusted‐HR: 14.69, p <0.001 for second nosocomial infection; adjusted‐HR: 24.95, p <0.001 for third nosocomial infection).ConclusionIn patients with decompensated liver cirrhosis LTx‐free survival significantly decreases with every consecutive infectious episode. Development of prevention strategies is urgently required.
Rising incidence of acute pancreatitis in Sweden: National estimates and trends between 1990 and 2013
Authors: Oskarsson Viktor , Hosseini Servah , Discacciati Andrea , Videhult Per , Jans Anders , Ekbom Anders , Sadr‐Azodi Omid 
Published: March 2020

BackgroundRecent reports from western countries have indicated an increased incidence and a decreased mortality in acute pancreatitis. However, the incidence assessment has often been hampered by the inclusion of both first‐time and recurrent episodes of acute pancreatitis.MethodsIn this retrospective cohort study, all Swedish residents hospitalized with a first‐time episode of acute pancreatitis between 1990 and 2013 were identified using national registers. Sex‐ and age‐standardized incidence rates per 100,000 individuals and year were calculated, as were annual percent changes (APC) from joinpoint regression models.ResultsOverall, between 1990 and 2013, 66,131 individuals had a first‐time episode of acute pancreatitis in Sweden. Comparing the first five years (1990–1994) to the last four years (2010–2013) of the study period, the overall incidence of acute pancreatitis increased from 25.2 (95% confidence interval (CI): 24.1, 26.3) to 38.3 (95% CI: 37.0, 39.5) cases per 100,000 individuals and year. An increase in incidence was observed irrespective of the subtypes of acute pancreatitis as well as the sex and age of the patients. Although the incidence of complicated acute pancreatitis declined in both men and women between 1990 and 2004, it started to increase in both sexes (APC 3.0; 95% CI: 0.5, 5.5 in men; APC 5.4; 95% CI: 2.6, 8.2 in women) from 2005 onwards.ConclusionBased on nationwide data, the incidence of first‐time acute pancreatitis has increased in Sweden over a period of 24 years. The incidence of disease‐related complications has also been on the rise during the past few years, after declining for more than 15 years before that.
Rapid referral for headache management from emergency department to headache centre: four years data
Authors: Negro Andrea , Spuntarelli Valerio , Sciattella Paolo , Martelletti Paolo 
Published: March 2020

Abstract
Background
Headache is one of the most common reason for medical consultation to emergency department (ED). The inappropriate use of ED for non-emergency conditions is a problem in terms of overcrowding of emergency facilities, unnecessary testing and treatment, increased medical costs, burden on medical service providers and weaker relationships between patient and primary care provider. The aim of this study was to analyze the different stages of ED management of headache to identify those deficiencies that can be overcome by a fast referral to a headache clinic.

Methods
The study is a retrospective analysis of the electronic medical records of patients discharged from an academic ED between January 1, 2015 and December 31, 2018 and referred to the tertiary level headache centre of the same hospital. We analyzed all aspects related to the permanence in ED and also assessed whether there was a match between the diagnosis made in ED and ours.

Results
Among our sample of 244 patients, 76.2% were admitted as “green tag”, 75% underwent a head computed tomography, 19.3% received a neurological consultation, 43% did not receive any pharmacological treatment and 62.7% still had headache at discharge. The length of stay in ED was associated with reporting the first aura ever (p = 0.014) and whether patients received consultations (p < 0.001). The concordance analysis shown a significant moderate agreement only for the diagnosis of migraine and only between triage and headache centre.

Conclusions
Most patients who went to ED complaining of headache received the same treatment regardless of their diagnosis and in many cases the headache had not yet resolved at the time of discharge. Given the many shortcomings in headache management in ED, rapid referral to the headache centre is of paramount importance to help the patient achieve a definiteve diagnosis and appropriate treatment.
Transgenerational effects of different sequential exposure to 2,2′,4,4′-tetra-brominated diphenyl ether (BDE47) and lead (Pb) on Caenorhabditis elegans
Authors: Zhang Jing , Yu ZhenYang 
Published: March 2020

Abstract
Background
Poly-brominated diphenyl ethers (PBDEs) and heavy metals are persistent pollutants in Yangtze River basin, China and also around the globe. In the exposure reality, they may have sequential exposures and long-term outcomes. Yet, the effects combining these two aspects remained largely unexplored. At present, the effects of 2,2′,4,4′-tetra-brominated diphenyl ether (BDE47) and lead (Pb) on Caenorhabditis elegans were studied with two sequential arrangements. One was first exposure to BDE47 and then to Pb (or vice versa) in one generation, and the other one was an early exposure to BDE47 in the parent generation (F0) and then a later exposure to Pb in the offspring (F1) (or vice versa).

Results
On growth, sequential Pb-BDE47 exposure caused inhibition in exposure but stimulation in recovery, showing similarity to individual Pb results. Meanwhile, the opposite sequential BDE47-Pb exposure showed inhibition in both exposure and recovery, similar to those of individual BDE47 results. On behavior, the effects of sequential exposure were significantly different from individual results without any similarity. In transgenerational effects, F0 Pb exposure with F1 BDE47 exposure (Pb-F1-BDE47) inhibited growth, similar to the transgenerational results of individual Pb exposure. Meanwhile, the recovery effects were similar to the transgenerational results of individual BDE47. At the same time, Pb-F1-BDE47 exposure significantly hindered the recovery of behavior while the opposite BDE47-F1-Pb exposure resulted in different results. The behavioral effects in F1 showed negative correlation with the contents of γ-aminobutyric acid (GABA), while those in F1 were positively correlated with the activities of acetylcholine esterase (AChE).

Conclusions
Sequential exposure to BDE47 and Pb within one generation or over generations showed significant different effects from individual results. Further studies are still needed to investigate the toxicity patterns and underlying mechanisms.
High-Resolution Confocal Fluorescence Imaging of Serine Hydrolase Activity in Cryosections – Application to Glioma Brain Unveils Activity Hotspots Originating from Tumor-Associated Neutrophils
Authors: Aaltonen Niina , Singha Prosanta K. , Jakupović Hermina , Wirth Thomas , Samaranayake Haritha , Pasonen-Seppänen Sanna , Rilla Kirsi , Varjosalo Markku , Edgington-Mitchell Laura E. , Kasperkiewicz Paulina , Drag Marcin , Kälvälä Sara , Moisio Eemeli , Savinainen Juha R. , Laitinen Jarmo T. 
Published: March 2020

Abstract
Background
Serine hydrolases (SHs) are a functionally diverse family of enzymes playing pivotal roles in health and disease and have emerged as important therapeutic targets in many clinical conditions. Activity-based protein profiling (ABPP) using fluorophosphonate (FP) probes has been a powerful chemoproteomic approach in studies unveiling roles of SHs in various biological systems. ABPP utilizes cell/tissue proteomes and features the FP-warhead, linked to a fluorescent reporter for in-gel fluorescence imaging or a biotin tag for streptavidin enrichment and LC-MS/MS-based target identification. Existing ABPP approaches characterize global SH activity based on mobility in gel or MS-based target identification and cannot reveal the identity of the cell-type responsible for an individual SH activity originating from complex proteomes.

Results
Here, by using an activity probe with broad reactivity towards the SH family, we advance the ABPP methodology to glioma brain cryosections, enabling for the first time high-resolution confocal fluorescence imaging of global SH activity in the tumor microenvironment. Tumor-associated cell types were identified by extensive immunohistochemistry on activity probe-labeled sections. Tissue-ABPP indicated heightened SH activity in glioma vs. normal brain and unveiled activity hotspots originating from tumor-associated neutrophils (TANs), rather than tumor-associated macrophages (TAMs). Thorough optimization and validation was provided by parallel gel-based ABPP combined with LC-MS/MS-based target verification.

Conclusions
Our study advances the ABPP methodology to tissue sections, enabling high-resolution confocal fluorescence imaging of global SH activity in anatomically preserved complex native cellular environment. To achieve global portrait of SH activity throughout the section, a probe with broad reactivity towards the SH family members was employed. As ABPP requires no a priori knowledge of the identity of the target, we envisage no imaginable reason why the presently described approach would not work for sections regardless of species and tissue source.
MoAIMS: efficient software for detection of enriched regions of MeRIP-Seq
Authors: Zhang Yiqian , Hamada Michiaki 
Published: March 2020

AbstractBackgroundMethylated RNA immunoprecipitation sequencing (MeRIP-Seq) is a popular sequencing method for studying RNA modifications and, in particular, for N6-methyladenosine (m6A), the most abundant RNA methylation modification found in various species. The detection of enriched regions is a main challenge of MeRIP-Seq analysis, however current tools either require a long time or do not fully utilize features of RNA sequencing such as strand information which could cause ambiguous calling. On the other hand, with more attention on the treatment experiments of MeRIP-Seq, biologists need intuitive evaluation on the treatment effect from comparison. Therefore, efficient and user-friendly software that can solve these tasks must be developed.ResultsWe developed a software named “model-based analysis and inference of MeRIP-Seq (MoAIMS)” to detect enriched regions of MeRIP-Seq and infer signal proportion based on a mixture negative-binomial model. MoAIMS is designed for transcriptome immunoprecipitation sequencing experiments; therefore, it is compatible with different RNA sequencing protocols. MoAIMS offers excellent processing speed and competitive performance when compared with other tools. When MoAIMS is applied to studies of m6A, the detected enriched regions contain known biological features of m6A. Furthermore, signal proportion inferred from MoAIMS for m6A treatment datasets (perturbation of m6A methyltransferases) showed a decreasing trend that is consistent with experimental observations, suggesting that the signal proportion can be used as an intuitive indicator of treatment effect.ConclusionsMoAIMS is efficient and easy-to-use software implemented in R. MoAIMS can not only detect enriched regions of MeRIP-Seq efficiently but also provide intuitive evaluation on treatment effect for MeRIP-Seq treatment datasets.
Genus level molecular phylogeny of Aegisthidae Gisbrecht, 1893 (Copepoda: Harpacticoida) reveals morphological adaptations to deep-sea and plagic habitats
Authors: Khodami Sahar , Mercado-Salas Nancy F. , Martìnez Arbizu Pedro 
Published: March 2020

Abstract
Background
The family Aegisthidae is known as typical component of deep-sea hyperbenthic waters that gradually colonized other marine environments. The phylogenetic relationships within this family have been examined here including hyperbenthic, planktonic, benthic forms and two associated Aegisthidae species.

Results
Ninety four specimens belong to 14 genera were studied using 18S and 28S rRNA and COI mtDNA. Bayesian analysis supports the monophyly of 10 genera whereas Andromastax, Jamstecia, Nudivorax and Aegisthus revealed to be paraphyletic. The first offshoot of the phylogenetic tree is a clade consists of the undescribed genus Aegisthidae gen.1 sister to the two monophyletic genera Cerviniella and Hase, whereas the other Cerviniinae members (represented by Cervinia and Expansicervinia) assemble a monophylum, sister to the hyperbenthic and planktonic aegisthid genera, resulting in the paraphyly of the subfamily Cerviniinae. Hence, we defined the new subfamily Cerviniellinae subfam. nov. encompassing the three benthic genera Cerviniella, Hase and Eucanuella. The subfamily Cerviniinae has been re-defined to include Cervinia, Expansicervinia and Paracerviniella. Members of the subfamily Pontostratiotinae were clustered into two clades, one consists of the genus Stratiopontotes sister to an undescribed genus + Cerviniopsis and Siphonis. The second contains Pontostratiotes sister to the members of the planktonic subfamily Aegisthinae, resulting in the paraphyly of the Pontostratiotinae. Therefore, the Pontostratiotinae has been re-defined to include only members of the genus Pontostratiotes; whereas the subfamily Cerviniopseinae has been re-erected and re-defined containing Stratiopontotes, Cerviniopsis, Siphonis, Aegisthidae gen. 2, Herdmaniopsis, Hemicervinia and Tonpostratiotes. Within this subfamily, the associated Siphonis clusters as sister to the Cerviniopsis represents an example of convergent evolution in which the possession of a stylet-like mandible and an oral cone reminiscent of the Siphonostomatoida. The planktonic Aegisthus, Andromastax, Jamstecia, Nudivorax and Scabrantenna confirm the monophylom Aegisthinae, sister to the Pontostratiotinae.

Conclusions
Our DNA based phylogeny reveals the deep-sea origin of Aegisthidae by placing benthic Aegisthidae gen.1 and Cerviniellinae subfam. nov. as the most basal lineages. Secondary adaptations to hyperbenthic and planktonic realms, as well as associated lifestyle were discovered here by the derived positions of Pontostratiotinae, Aegisthinae and Siphonis respectively.