bluuebunny/crossref_metadata_2025_split huggingface dataset:
Folded Cymba Concha: Is It Large and Stable Enough for Caudal Septal Extension Graft in Asian Rhinoplasty?
Authors: Namgoong Sik , Kim Soobyn , Kim Hyung-Rok , Jeong Seong-Ho , Han Seung-Kyu , Dhong Eun-Sang 
Published: February 2021

Abstract

Background
Septal extension grafting (SEG) is used for nasal tip projection and positioning. Often, insufficient quadrangular cartilage is available for grafting in Asians, and in most secondary cases the septum is already harvested. We utilized the folded cymba concha as an alternative for caudal SEG (CSEG) by modifying a tongue-in-groove technique.

Objectives
The aim of this study was to evaluate the physical suitability of the cymba concha for CSEG and compare its outcomes with those of septal quadrangular cartilage.

Methods
The mean length and width of 311 harvested consecutive folded cymba conchae were measured from intraoperative photographs. Data from 220 patients with &gt;12 months of follow-up were retrospectively reviewed for clinical outcomes. Clinical demography was determined based on the need for additional spreader grafts. For clinical reliability, anthropometric photographs of patients in whom folded cymba conchae were used were compared with those in whom quadrangular cartilage was used.

Results
Mean [standard deviation] lengths and widths of the folded cymba conchae in men and women were 24.2 [3.9] and 22.4 [3.7] mm, and 7.8 [1.9] and 7.2 [1.9] mm, respectively. Use of the folded cymba concha graft significantly increased nasal tip projection by 28.9% and columellar-labial angle by 9.7%, improving both aspects postoperatively. Anthropometric comparison revealed no significant differences between folded cymba conchae and septal cartilage in terms of nasal tip projection (P = 0.264) and postoperative columellar-labial angle (P = 0.182).

Conclusions
Folded cymba conchal cartilage can be a primary option for CSEG in Asian septorhinoplasty cases or for individuals with insufficient septal cartilage remnants.
NetQuilt: deep multispecies network-based protein function prediction using homology-informed network similarity
Authors: Barot Meet , Gligorijević Vladimir , Cho Kyunghyun , Bonneau Richard 
Published: February 2021

Abstract

Motivation
Transferring knowledge between species is challenging: different species contain distinct proteomes and cellular architectures, which cause their proteins to carry out different functions via different interaction networks. Many approaches to protein functional annotation use sequence similarity to transfer knowledge between species. These approaches cannot produce accurate predictions for proteins without homologues of known function, as many functions require cellular context for meaningful prediction. To supply this context, network-based methods use protein-protein interaction (PPI) networks as a source of information for inferring protein function and have demonstrated promising results in function prediction. However, most of these methods are tied to a network for a single species, and many species lack biological networks.

Results
In this work, we integrate sequence and network information across multiple species by computing IsoRank similarity scores to create a meta-network profile of the proteins of multiple species. We use this integrated multispecies meta-network as input to train a maxout neural network with Gene Ontology terms as target labels. Our multispecies approach takes advantage of more training examples, and consequently leads to significant improvements in function prediction performance compared to two network-based methods, a deep learning sequence-based method and the BLAST annotation method used in the Critial Assessment of Functional Annotation. We are able to demonstrate that our approach performs well even in cases where a species has no network information available: when an organism’s PPI network is left out we can use our multi-species method to make predictions for the left-out organism with good performance.

Availability and implementation
The code is freely available at https://github.com/nowittynamesleft/NetQuilt. The data, including sequences, PPI networks and GO annotations are available at https://string-db.org/.

Supplementary information
Supplementary data are available at Bioinformatics online.
Inference of gene regulatory networks using pseudo-time series data
Authors: Zhang Yuelei , Chang Xiao , Liu Xiaoping 
Published: February 2021

Abstract

Motivation
Inferring gene regulatory networks (GRNs) from high-throughput data is an important and challenging problem in systems biology. Although numerous GRN methods have been developed, most have focused on the verification of the specific dataset. However, it is difficult to establish directed topological networks that are both suitable for time-series and non-time-series datasets due to the complexity and diversity of biological networks.

Results
Here, we proposed a novel method, GNIPLR (Gene networks inference based on projection and lagged regression) to infer GRNs from time-series or non-time-series gene expression data. GNIPLR projected gene data twice using the LASSO projection (LSP) algorithm and the linear projection (LP) approximation to produce a linear and monotonous pseudo-time series, and then determined the direction of regulation in combination with lagged regression analyses. The proposed algorithm was validated using simulated and real biological data. Moreover, we also applied the GNIPLR algorithm to the liver hepatocellular carcinoma (LIHC) and bladder urothelial carcinoma (BLCA) cancer expression datasets. These analyses revealed significantly higher accuracy and AUC values than other popular methods.

Availabilityand implementation
The GNIPLR tool is freely available at https://github.com/zyllluck/GNIPLR.

Supplementary information
Supplementary data are available at Bioinformatics online.
Ex vivo normothermic perfusion of isolated segmental porcine bowel: a novel functional model of the small intestine
Authors: Hamed M O , Barlow A D , Dolezalova N , Khosla S , Sagar A , Gribble F M , Davies S , Murphy M P , Hosgood S A , Nicholson M L , Saeb-Parsy K 
Published: February 2021

Abstract

Background
There is an unmet need for suitable ex vivo large animal models in experimental gastroenterology and intestinal transplantation. This study details a reliable and effective technique for ex vivo normothermic perfusion (EVNP) of segmental porcine small intestine.

Methods
Segments of small intestine, 1.5–3.0 m in length, were retrieved from terminally anaesthetized pigs. After a period of cold ischaemia, EVNP was performed for 2 h at 37°C with a mean pressure of 80 mmHg using oxygenated autologous blood diluted with Ringer’s solution. The duration of EVNP was extended to 4 h for a second set of experiments in which two segments of proximal to mid-ileum (1.5–3.0 m) were retrieved from each animal and reperfused with whole blood (control) or leucocyte-depleted blood to examine the impact of leucocyte depletion on reperfusion injury.

Results
After a mean cold ischaemia time of 5 h and 20 min, EVNP was performed in an initial group of four pigs. In the second set of experiments, five pigs were used in each group. In all experiments bowel segments were well perfused and exhibited peristalsis during EVNP. Venous glucose levels significantly increased following luminal glucose stimulation (mean(s.e.m.) basal level 1.8(0.6) mmol/l versus peak 15.5(5.8) mmol/l; P &lt; 0.001) and glucagon-like peptide 1 (GLP-1) levels increased in all experiments, demonstrating intact absorptive and secretory intestinal functions. There were no significant differences between control and leucocyte-depleted animals regarding blood flow, venous glucose, GLP-1 levels or histopathology at the end of 4 h of EVNP.

Conclusions
This novel model is suitable for the investigation of gastrointestinal physiology, pathology and ischaemia reperfusion injury, along with evaluation of potential therapeutic interventions.
Annexin A1 restores cerebrovascular integrity concomitant with reduced amyloid-β and tau pathology
Authors: Ries Miriam , Watts Helena , Mota Bibiana C , Lopez Maria Yanez , Donat Cornelius K , Baxan Nicoleta , Pickering James A , Chau Tsz Wing , Semmler Annika , Gurung Brinda , Aleksynas Robertas , Abelleira-Hervas Laura , Iqbal Soha Jamshed , Romero-Molina Carmen , Hernandez-Mir Gerard , d’Amati Antonio , Reutelingsperger Chris , Goldfinger Marc H , Gentleman Steve M , Van Leuven Fred , Solito Egle , Sastre Magdalena 
Published: February 2021

Abstract
Alzheimer’s disease, characterized by brain deposits of amyloid-β plaques and neurofibrillary tangles, is also linked to neurovascular dysfunction and blood–brain barrier breakdown, affecting the passage of substances into and out of the brain. We hypothesized that treatment of neurovascular alterations could be beneficial in Alzheimer’s disease. Annexin A1 (ANXA1) is a mediator of glucocorticoid anti-inflammatory action that can suppress microglial activation and reduce blood–brain barrier leakage. We have reported recently that treatment with recombinant human ANXA1 (hrANXA1) reduced amyloid-β levels by increased degradation in neuroblastoma cells and phagocytosis by microglia. Here, we show the beneficial effects of hrANXA1 in vivo by restoring efficient blood–brain barrier function and decreasing amyloid-β and tau pathology in 5xFAD mice and Tau-P301L mice. We demonstrate that young 5xFAD mice already suffer cerebrovascular damage, while acute pre-administration of hrANXA1 rescued the vascular defects. Interestingly, the ameliorated blood–brain barrier permeability in young 5xFAD mice by hrANXA1 correlated with reduced brain amyloid-β load, due to increased clearance and degradation of amyloid-β by insulin degrading enzyme (IDE). The systemic anti-inflammatory properties of hrANXA1 were also observed in 5xFAD mice, increasing IL-10 and reducing TNF-α expression. Additionally, the prolonged treatment with hrANXA1 reduced the memory deficits and increased synaptic density in young 5xFAD mice. Similarly, in Tau-P301L mice, acute hrANXA1 administration restored vascular architecture integrity, affecting the distribution of tight junctions, and reduced tau phosphorylation. The combined data support the hypothesis that blood–brain barrier breakdown early in Alzheimer’s disease can be restored by hrANXA1 as a potential therapeutic approach.
Preparation of Monolithic Silica and Polymer Capillary Columns with Ultrahigh Column Efficiencies and Comparisons between van Deemter Plots of Alkylbenzenes on These Two Kinds of Columns
Authors: Ping Guichen , Hou Weiping , Shi Quanquan , Ding Hongjing , Gong Xia , Li Jinmei , Xu Hui 
Published: February 2021

Abstract
Monolithic silica and polymer capillary columns with ultrahigh column efficiencies were prepared. Permeability and electrochromatography performances of these two kinds of columns were compared. Monolithic silica columns bear higher permeability than polymer counterparts by two orders of magnitude. Furthermore, the van Deemter plots of alkylbenzenes on these two kinds of columns demonstrate that monolithic silica columns produce much lower plate heights of alkylbenzes than polymer columns do. Within the range of electroosmotic flow (EOF) velocity investigated, no uptrend of plate height with the increase of EOF was observed suggesting the great capacity of fast separation and high efficiency. The plate height of thiourea on monolithic silica columns is as low as 2.67 μm, representing its corresponding column efficiency is over 430,000 plates/m. As far as we know, it is the highest ever column efficiency reported in the literature. Moreover, the separation of butylbenzene isomers was obtained on the monolithic silica column.
Deficiency of inactive rhomboid protein 2 (iRhom2) attenuates diet-induced hyperlipidaemia and early atherogenesis
Authors: Hannemann Carmen , Schecker Johannes H , Brettschneider Alica , Grune Jana , Rösener Nicole , Weller Andrea , Stangl Verena , Fisher Edward A , Stangl Karl , Ludwig Antje , Hewing Bernd 
Published: February 2021

Abstract

Aims
Atherosclerosis is a chronic inflammatory disease of the arterial vessel wall and anti-inflammatory treatment strategies are currently pursued to lower cardiovascular disease burden. Modulation of recently discovered inactive rhomboid protein 2 (iRhom2) attenuates shedding of tumour necrosis factor-alpha (TNF-α) selectively from immune cells. The present study aims at investigating the impact of iRhom2 deficiency on the development of atherosclerosis.

Methods and results
Low-density lipoprotein receptor (LDLR)-deficient mice with additional deficiency of iRhom2 (LDLR−/−iRhom2−/−) and control (LDLR−/−) mice were fed a Western-type diet (WD) for 8 or 20 weeks to induce early or advanced atherosclerosis. Deficiency of iRhom2 resulted in a significant decrease in the size of early atherosclerotic plaques as determined in aortic root cross-sections. LDLR−/−iRhom2−/− mice exhibited significantly lower serum levels of TNF-α and lower circulating and hepatic levels of cholesterol and triglycerides compared to LDLR−/− mice at 8 weeks of WD. Analyses of hepatic bile acid concentration and gene expression at 8 weeks of WD revealed that iRhom2 deficiency prevented WD-induced repression of hepatic bile acid synthesis in LDLR−/− mice. In contrast, at 20 weeks of WD, plaque size, plaque composition, and serum levels of TNF-α or cholesterol were not different between genotypes.

Conclusion
Modulation of inflammation by iRhom2 deficiency attenuated diet-induced hyperlipidaemia and early atherogenesis in LDLR−/− mice. iRhom2 deficiency did not affect diet-induced plaque burden and composition in advanced atherosclerosis in LDLR−/− mice.
Prevalence and Progression of Incidental Terminal Ileitis on Non-diagnostic Colonoscopy: A Systematic Review and Meta-analysis
Authors: Agrawal Manasi , Miranda Mario Bento- , Walsh Samantha , Narula Neeraj , Colombel Jean-Frederic , Ungaro Ryan C 
Published: February 2021

Abstract

Background
Incidentally diagnosed terminal ileitis [IDTI] has been reported among asymptomatic persons undergoing non-diagnostic colonoscopy. The purpose of our study was to determine the prevalence and long-term outcomes of asymptomatic terminal ileitis.

Methods
We performed a systematic review using three biomedical databases [Medline, Embase, and Web of Science] and relevant scientific meeting abstracts. We identified observational studies that reported the prevalence of IDTI in adults undergoing screening or polyp surveillance colonoscopy and/or the long-term outcomes of such lesions. A random-effects meta-analysis was conducted to determine the pooled prevalence rate of IDTI. The progression of IDTI to overt Crohn’s disease [CD] was also described.

Results
Of 2388 eligible studies, 1784 were screened after excluding duplicates, 84 were reviewed in full text, and 14 studies were eligible for inclusion. Seven studies reported the prevalence of IDTI in 44 398 persons undergoing non-diagnostic colonoscopy, six studies reported follow-up data, and one study reported both types of data. The pooled prevalence rate of IDTI was 1.6% (95% confidence interval [CI] 0.1–21.8%) with significant heterogeneity [I2 = 99.7]. Among patients who had undergone non-diagnostic colonoscopy and had follow-up data [range 13–84 months reported in five studies], progression to overt CD was rare.

Conclusions
IDTI is not uncommon on non-diagnostic colonoscopies. Based on limited data, the rate of its progression to overt CD seems low, and watchful waiting is likely a reasonable strategy. Further long-term follow-up studies are needed to inform the natural history of incidental terminal ileitis, factors that predict progression to CD, and therapeutic implications.
The Eclosion of Rhagoletis pomonella (Diptera: Tephritidae) Under Different Chill Durations and Simulated Temperate and Tropical Conditions
Authors: Neven Lisa G , Wakie Tewodros , Yee Wee L 
Published: February 2021

Abstract
The apple maggot fly, Rhagoletis pomonella (Walsh) (Diptera: Tephritidae), is a serious pest of apple in North America that is subject to quarantine measures to prevent its spread to currently pest-free regions, including the tropics. How the fly may survive in warmer climates is unclear. Here, we studied the effects of exposing postchill puparia to simulated temperate and tropical environmental conditions on eclosion of R. pomonella from Washington State, U.S.A. Puparia were chilled for 0–30 wk at 3°C and then held under four postchill conditions: A = 23°C, 16:8 L:D, 40% RH; B = 26°C, 12:12 L:D, 80% RH; C = 26°C, 16:8 L:D, 80% RH; and D = 23°C, 12:12 L:D, 40% RH, with B and D representing tropical conditions and A and C temperate conditions. Within each chill duration, total numbers of flies eclosed were equally high in tropical treatment B and temperate treatment C, while they were lower in treatments A and D. Mean weeks of the first eclosion in treatments B and C were earlier than in treatment D; mean week of peak eclosion and 50% eclosion in treatments A, B, and C were earlier than in treatment D. Eclosion spans in treatments A, B, and D were generally shorter than in treatment C. Results suggest that if introduced into a humid tropical country, R. pomonella puparia from Washington State could produce adult flies, regardless of chill duration or lack of chilling during the pupal stage, but whether flies could establish there would require further study.
Age- and sex-based normal values of layer-specific longitudinal and circumferential strain by speckle tracking echocardiography: the Copenhagen City Heart Study
Authors: Skaarup Kristoffer Grundtvig , Lassen Mats Christian Højbjerg , Johansen Niklas Dyrby , Olsen Flemming Javier , Lind Jannie Nørgaard , Jørgensen Peter Godsk , Jensen Gorm , Schnohr Peter , Prescott Eva , Søgaard Peter , Møgelvang Rasmus , Biering-Sørensen Tor 
Published: February 2021

Abstract

Aims
Technical advancements in 2D-speckle tracking echocardiography (2DSTE) have allowed for quantification of layer-specific global longitudinal strain (GLS) and circumferential strain (GCS) of the left ventricle (LV). The aim of this study was to establish age- and sex-based reference ranges of peak systolic layer-specific GLS and GCS and to assess normal values of regional strain.

Methods and results
We performed 2DSTE analysis of 1997 members of the general population from the fifth round of the Copenhagen City Heart Study, who were free of cardiovascular disease and risk factors. The mean age was 46 ± 16 years (range 21–97) and 62% were female. Mean values for peak systolic whole wall GLS (GLSWW.Sys), endomycardial (GLSEndo.Sys), and epimyocardial (GLSEpi.Sys) were 19.9 ± 2.1% (prediction interval [PI]: 15.8–24.0%), 23.5 ± 2.5% (PI: 18.6–28.4%), and 17.3 ± 1.9% (PI: 13.6–21.1%), respectively. Mean peak systolic whole wall GCS (GCSWW.Sys), was 21.6 ± 3.7% (PI: 14.3–28.9%), endomyocardial (GCSEndo.Sys) was 31.9 ± 4.7% (PI: 22.7–41.1%), and epimyocardial (GCSEpi.Sys) was 14.3 ± 3.8% (PI: 6.8–21.8%). A significant discrepancy in normal strain values between males and females was observed. Men had lower mean values and lower reference limits for all strain parameters. Furthermore, GLS and GCS changed differently with age in males and females. Finally, regional LS decreased from the apical to the basal LV region in both sexes, and regional CS varied significantly by LV segment.

Conclusion
In this study, we reported age- and sex-based reference ranges of layer-specific GLS and GCS. These reference ranges varied significantly with sex and age.
Clinical impact of PCSK9 inhibitor on stabilization and regression of lipid-rich coronary plaques: a near-infrared spectroscopy study
Authors: Ota Hideaki , Omori Hiroyuki , Kawasaki Masanori , Hirakawa Akihiro , Matsuo Hitoshi 
Published: February 2021

Abstract

Aims
This study aimed to determine the effects of a proprotein convertase subtilisin-kexin type 9 inhibitor (PCSK9i) on coronary plaque volume and lipid components in patients with a history of coronary artery disease (CAD).

Methods and results
This prospective, open-label, single-centre study analysed non-culprit coronary segments using near-infrared spectroscopy-intravascular ultrasound (NIRS-IVUS) at baseline and follow-up angiography. Following changes in the lipid-lowering treatment based on the most recent guideline, the enrolled subjects were divided into two groups: treatment with PCSK9i and statins (PCSK9i: 21 patients and 40 segments) and statins only (control: 32 patients and 50 segments). The absolute and percent LDL-C reductions were significantly greater in the PCSK9i group than in the control group (between group difference: 59.3 mg/dL and 46.4%; P &lt; 0.001 for both). The percent reduction in normalized atheroma volume and absolute reduction in percent atheroma volume (PAV) were also significantly greater in the PCSK9i group (P &lt; 0.001 for both). Furthermore, the PCSK9i group showed greater regression of maximal lipid core burden index for each of the 4-mm segments (maxLCBI4mm) than the control group (57.0 vs. 25.5; P = 0.010). A significant linear correlation was found between the percent changes in LDL-C and maxLCBI4mm (r = 0.318; P = 0.002), alongside the reduction in PAV (r = 0.386; P &lt; 0.001).

Conclusion
The lipid component of non-culprit coronary plaques was significantly decreased by PCSK9i. The effects of statin combined with PCSK9i might be attributed to the stabilization and regression of residual vulnerable coronary plaques in patients with CAD.
Artificial intelligence to diagnose paroxysmal supraventricular tachycardia using electrocardiography during normal sinus rhythm
Authors: Jo Yong-Yeon , Kwon Joon-Myoung , Jeon Ki-Hyun , Cho Yong-Hyeon , Shin Jae-Hyun , Lee Yoon-Ji , Jung Min-Seung , Ban Jang-Hyeon , Kim Kyung-Hee , Lee Soo Youn , Park Jinsik , Oh Byung-Hee 
Published: February 2021

AbstractAimsParoxysmal supraventricular tachycardia (PSVT) is not detected owing to its paroxysmal nature, but it is associated with the risk of cardiovascular disease and worsens the patient quality of life. A deep learning model (DLM) was developed and validated to identify patients with PSVT during normal sinus rhythm in this multicentre retrospective study.Methods and resultsThis study included 12 955 patients with normal sinus rhythm, confirmed by a cardiologist. A DLM was developed using 31 147 electrocardiograms (ECGs) of 9069 patients from one hospital. We conducted an accuracy test with 13 753 ECGs of 3886 patients from another hospital. The DLM was developed based on residual neural network. Digitally stored ECG were used as predictor variables and the outcome of the study was ability of the DLM to identify patients with PSVT using an ECG during sinus rhythm. We employed a sensitivity map method to identify an ECG region that had a significant effect on developing PSVT. During accuracy test, the area under the receiver operating characteristic curve of a DLM using a 12-lead ECG for identifying PSVT patients during sinus rhythm was 0.966 (0.948–0.984). The accuracy, sensitivity, specificity, positive predictive value, and negative predictive value of DLM were 0.970, 0.868, 0.972, 0.255, and 0.998, respectively. The DLM showed delta wave and QT interval were important to identify the PSVT.ConclusionThe proposed DLM demonstrated a high performance in identifying PSVT during normal sinus rhythm. Thus, it can be used as a rapid, inexpensive, point-of-care means of identifying PSVT in patients.