bluuebunny/crossref_metadata_2025_split huggingface dataset:
A Non-APOE Polygenic Risk Score for Alzheimer’s Disease Is Associated With Cerebrospinal Fluid Neurofilament Light in a Representative Sample of Cognitively Unimpaired 70-Year Olds
Authors: Skoog Ingmar , Kern Silke , Najar Jenna , Guerreiro Rita , Bras Jose , Waern Margda , Zetterberg Henrik , Blennow Kaj , Zettergren Anna 
Published: January 2021

Abstract
The effect of Alzheimer’s disease (AD) polygenic risk scores (PRS) on amyloid and tau pathophysiology and neurodegeneration in cognitively unimpaired older adults is not known in detail. This study aims to investigate non-APOE AD-PRS and APOE ε4 in relation to AD pathophysiology evaluated by cerebrospinal fluid (CSF) biomarkers in a population-based sample of 70-year olds. A total of 303 dementia-free individuals from the Gothenburg H70 Birth Cohort Studies were included. Genotyping was performed using the NeuroChip, and AD-PRS were calculated. CSF levels of amyloid-β (Aβ42), total tau (t-tau), phosphorylated tau (p-tau), neurogranin (Ng), and neurofilament light (NfL) were measured with enzyme-linked immunosorbent assay. Associations were found between non-APOE PRS and both NfL (p = .001) and Aβ42 (p = .02), and between APOE ε4 and Aβ42 (p = 1e−10), t-tau (p = 5e−4), and p-tau (p = .002). Similar results were observed when only including individuals with CDR = 0, except for no evidence of an association between non-APOE PRS and Aβ42. There was an interaction between non-APOE PRS and Aβ42 pathology status in relation to NfL (p = .005); association was only present in individuals without Aβ42 pathology (p = 3e-4). In relation to Aβ42, there was a borderline interaction (p = .06) between non-APOE PRS and APOE ε4; association was present in ε4 carriers only (p = .03). Similar results were observed in individuals with CDR = 0 (n = 246). In conclusion, among cognitively healthy 70-year olds from the general population, genetic risk of AD beyond the APOE locus was associated with NfL in individuals without Aβ42 pathology, and with Aβ42 in APOE ε4 carriers, suggesting these associations are driven by different mechanisms.
FASTQuick: rapid and comprehensive quality assessment of raw sequence reads
Authors: Zhang Fan , Kang Hyun Min 
Published: January 2021

Abstract

Background
Rapid and thorough quality assessment of sequenced genomes on an ultra-high-throughput scale is crucial for successful large-scale genomic studies. Comprehensive quality assessment typically requires full genome alignment, which costs a substantial amount of computational resources and turnaround time. Existing tools are either computationally expensive owing to full alignment or lacking essential quality metrics by skipping read alignment.

Findings
We developed a set of rapid and accurate methods to produce comprehensive quality metrics directly from a subset of raw sequence reads (from whole-genome or whole-exome sequencing) without full alignment. Our methods offer orders of magnitude faster turnaround time than existing full alignment–based methods while providing comprehensive and sophisticated quality metrics, including estimates of genetic ancestry and cross-sample contamination.

Conclusions
By rapidly and comprehensively performing the quality assessment, our tool will help investigators detect potential issues in ultra-high-throughput sequence reads in real time within a low computational cost at the early stages of the analyses, ensuring high-quality downstream results and preventing unexpected loss in time, money, and invaluable specimens.
Ac2-26-Nanoparticles Induce Resolution of Intestinal Inflammation and Anastomotic Healing via Inhibition of NF-κB Signaling in a Model of Perioperative Colitis
Authors: Reischl Stefan , Lee Jong Hyun , Miltschitzky Joseph Raphael Elias , Vieregge Vincent , Walter Robert Leon , Twardy Vanessa , Kasajima Atsuko , Friess Helmut , Kamaly Nazila , Neumann Philipp-Alexander 
Published: January 2021

Abstract

Background
Although in most patients with inflammatory bowel diseases, conservative therapy is successful, a significant proportion of patients still require surgery once in their lifetime. Development of a safe perioperative treatment to dampen colitis activity without disturbance of anastomotic healing is an urgent and unmet medical need. Annexin A1 (ANXA1) has been shown to be effective in reducing colitis activity. Herein, a nanoparticle-based perioperative treatment approach was used for analysis of the effects of ANXA1 on the resolution of inflammation after surgery for colitis.

Methods
Anxa1-knockout mice were used to delineate the effects of ANXA1 on anastomotic healing. A murine model of preoperative dextran sodium sulfate colitis was performed. Collagen-IV-targeted polymeric nanoparticles, loaded with the ANXA1 biomimetic peptide Ac2-26 (Ac2-26-NPs), were synthesized and administered perioperatively during colitis induction. The effects of the Ac2-26-NPs on postoperative recovery and anastomotic healing were evaluated using the disease activity index, histological healing scores, and weight monitoring. Ultimately, whole-genome RNA sequencing of the anastomotic tissue was performed to unravel underlying molecular mechanisms.

Results
Anxa1-knockout exacerbated the inflammatory response in the healing anastomosis. Treatment with Ac2-26-NPs improved preoperative colitis activity (P &lt; 0.045), postoperative healing scores (P &lt; 0.018), and weight recovery (P &lt; 0.015). Whole-genome RNA sequencing revealed that the suppression of proinflammatory cytokine and nuclear factor kappa-light-chain-enhancer of activated B cells (NF-κB) signaling was associated with the treatment effects and a phenotypic switch toward anti-inflammatory M2 macrophages.

Conclusions
Proresolving therapy with Ac2-26-NPs promises to be a potent perioperative therapy because it improves colitis activity and even intestinal anastomotic healing by the suppression of proinflammatory signaling.
Reverse remodelling after aortic valve replacement for chronic aortic regurgitation
Authors: Koga-Ikuta Ayumi , Fukushima Satsuki , Kawamoto Naonori , Saito Tetsuya , Shimahara Yusuke , Yajima Shin , Tadokoro Naoki , Kakuta Takashi , Fukui Toshihiro , Fujita Tomoyuki 
Published: January 2021

Abstract

OBJECTIVES
This study aimed to assess the long-term outcomes and investigate the factors related to left ventricular (LV) reverse remodelling after aortic valve replacement (AVR) in patients with chronic aortic regurgitation (AR).

METHODS
A total of 246 patients who underwent AVR for chronic AR at our institution were included in this retrospective study. Primary end-points included all-cause mortality, cardiac mortality and major adverse cerebral and cardiovascular events. Secondary end-points included cardiac function on echocardiography 1 year after surgery. We explored the predictive factors for reverse remodelling 1 year after surgery.

RESULTS
The 10-year survival rate was 86.0%, with no cardiac deaths in 93.8% and no major adverse cerebral and cardiovascular events in 79.9% of patients. Postoperative LV function and symptoms were significantly improved 1 year after surgery, but 34 patients (13.8%) did not recover normal function and structure. A significant negative correlation was found between the incidence of cardiac death and major adverse cerebral and cardiovascular events and reverse remodelling. Multivariate logistic regression identified preoperative LV ejection fraction (P = 0.001, odds ratio = 1.057) and LV end-systolic dimension index (P = 0.038, odds ratio = 0.912) as significant predictive factors of reverse remodelling 1 year after surgery.

CONCLUSIONS
Preoperative LV ejection fraction and LV end-systolic dimension index were predictive factors for reverse remodelling after surgery, which was associated with late outcomes. Earlier surgery may thus help to restore normal LV function and achieve better late outcomes after AVR for AR.
Biparietal bidirectional bipolar radiofrequency in hybrid cardiac ablation: anin vitroevaluation
Authors: Matteucci Francesco , Maesen Bart , De Asmundis Carlo , Bidar Elham , Micali Linda , Parise Gianmarco , Maessen Jos G , La Meir Mark , Gelsomino Sandro 
Published: January 2021

Abstract OBJECTIVESThe aim of this study was to evaluate the lesion size and depth of radiofrequency (RF) ablation in a simultaneous biparietal bidirectional bipolar (SBB) approach, compared to a simultaneous and staged unipolar and uniparietal bipolar setup [simultaneous uniparietal bipolar (SiUB) and staged uniparietal bipolar (StUB), respectively].METHODSFresh left atrial porcine tissue was mounted into the ABLA-BOX simulator. Different ablation approaches were tested: (i) SBB: a concept consisting of SBB endo-epicardial ablation, (ii) SiUB: simultaneous epicardial uniparietal bipolar and endocardial unipolar ablation and (iii) StUB: staged epicardial uniparietal bipolar and endocardial unipolar ablation. In the StUB setup, a 1-h interval between the epi-endo ablation was respected.RESULTSTransmural lesions were present in 90% of the bipolar biparietal ablations, yet no full transmurality was observed in the simultaneous nor in the staged unipolar with uniparietal bipolar ablation group. In SBB, the area and volume of the ablation lesions were smaller (523.33 mm2/mm and 52.33 mm3/mm, respectively) than in SiUB (588.17 mm2/mm and 58.81 mm3/mm, respectively) and StUB (583.76 mm2/mm and 58.37 mm3/mm, P = 0.044). Also, in SBB, the overall, epicardial and endocardial maximum diameters of the lesions (1.59, 1.57 and 1.52 mm; respectively) were smaller than in SiUB (2.38, 2.26 and 2.33 mm; respectively) and in StUB (2.36, 2.28 and 2.14 mm; respectively, all P &lt; 0.001).CONCLUSIONSAlthough bipolar biparietal bidirectional RF ablation results in smaller lesions than uniparietal bipolar and unipolar ablation, their capacity to penetrate the tissue is much higher. Moreover, in uniparietal RF applications, the energy spreads in the superficial layers of the tissue but fails to penetrate. Therefore, the degree of transmurality is much higher when using such a ‘truly bipolar’ ablation approach.
Incidence of Enteric Fever in a Pediatric Cohort in North India: Comparison with Estimates from 20 Years Earlier
Authors: Sinha Bireshwar , Rongsen-Chandola Temsunaro , Goyal Nidhi , Arya Alok , Kumar Chandra Mohan , Chakravarty Aparna , Aslam Mohammed , More Deepak ,   SEFI tier 1 collaborators, John Jacob , Mohan Venkata Raghava , Bavdekar Ashish , Dutta Shanta , Kang Gagandeep 
Published: January 2021

Abstract

Background
An earlier cohort in 1995–1996 showed a very high burden of typhoid in Delhi. Our aim was to estimate the current overall and age-specific incidence of culture-confirmed enteric fever among children aged 6 months to 15 years in Delhi.

Methods
We enrolled a cohort of 6000 children aged 6 months to &lt;14 years in South Delhi and followed them up weekly for 24 months or until 15 completed years of child age, whichever was earlier. Blood culture to confirm enteric fever was done in children with ≥3 consecutive days of fever.

Results
We recorded a total of 14 650 episodes of fever in the 11 510 person-years (PY) of follow-up. A total of 81 fever episodes were positive for enteric fever. The incidence (95% confidence interval) of all enteric fever was 703.7 (560.5–874.7) per 100 000 PY. The incidences of typhoid and paratyphoid fevers were 608.1 (95% confidence interval, 481.1–768.7) and 111.7 (59.5–191.1) per 100 000 PY, respectively, highest among children aged 10–15 years.

Conclusions
Despite a 35% reduction in incidence compared with the 1995–1996 cohort, our study suggested a substantial burden of enteric fever in the population. Continued efforts to improve water, sanitation, and hygiene parameters along with implementation of novel vaccination strategies and disease surveillance can help achieve the goal of disease elimination.
Dysregulated Innate and Adaptive Immune Responses Discriminate Disease Severity in COVID-19
Authors: Janssen Nico A F , Grondman Inge , de Nooijer Aline H , Boahen Collins K , Koeken Valerie A C M , Matzaraki Vasiliki , Kumar Vinod , He Xuehui , Kox Matthijs , Koenen Hans J P M , Smeets Ruben L , Joosten Irma , Brüggemann Roger J M , Kouijzer Ilse J E , van der Hoeven Hans G , Schouten Jeroen A , Frenzel Tim , Reijers Monique H E , Hoefsloot Wouter , Dofferhoff Anton S M , van Apeldoorn Marjan J , Blaauw Marc J T , Veerman Karin , Maas Coen , Schoneveld Arjan H , Hoefer Imo E , Derde Lennie P G , van Deuren Marcel , van der Meer Jos W M , van Crevel Reinout , Giamarellos-Bourboulis Evangelos J , Joosten Leo A B , van den Heuvel Michel M , Hoogerwerf Jacobien , de Mast Quirijn , Pickkers Peter , Netea Mihai G , van de Veerdonk Frank L 
Published: January 2021

Abstract
The clinical spectrum of COVID-19 varies and the differences in host response characterizing this variation have not been fully elucidated. COVID-19 disease severity correlates with an excessive proinflammatory immune response and profound lymphopenia. Inflammatory responses according to disease severity were explored by plasma cytokine measurements and proteomics analysis in 147 COVID-19 patients. Furthermore, peripheral blood mononuclear cell cytokine production assays and whole blood flow cytometry were performed. Results confirm a hyperinflammatory innate immune state, while highlighting hepatocyte growth factor and stem cell factor as potential biomarkers for disease severity. Clustering analysis revealed no specific inflammatory endotypes in COVID-19 patients. Functional assays revealed abrogated adaptive cytokine production (interferon-γ, interleukin-17, and interleukin-22) and prominent T-cell exhaustion in critically ill patients, whereas innate immune responses were intact or hyperresponsive. Collectively, this extensive analysis provides a comprehensive insight into the pathobiology of severe to critical COVID-19 and highlights potential biomarkers of disease severity.
Measurement of the three-axis vibration, temperature, and relative humidity profiles of commercial transport trailers for pigs
Authors: Morris Benjamin K , Davis R Benjamin , Brokesh Edwin , Flippo Daniel K , Houser Terry A , Najar-Villarreal Francisco , Turner Kari K , Williams Jamison G , Stelzleni Alexander M , Gonzalez John M 
Published: January 2021

AbstractThe objective of this study was to collect and interpret three-axis acceleration, temperature, and relative humidity data from six locations within commercial transport trailers shipping market-weight pigs. Transport was observed in Kansas (n = 15) and North Carolina (n = 20). Prior to loading, three-axis accelerometers were affixed to six locations on the trailers: top fore (TF), top center (TC), top aft (TA), bottom fore (BF), bottom center (BC), and bottom aft (BA) compartments. Data were post-processed to calculate root-mean-square (RMS) accelerations and vibration dose values (VDV) in the vertical direction and the horizontal plane. These values were compared with exposure action values (EAV) and exposure limit values (ELV), vibration levels deemed uncomfortable and potentially dangerous to humans. Additionally, RMS and VDV were compared among the trailer compartments. The vertical RMS accelerations for all compartments exceeded the EAV for loads measured in Kansas, and for the majority of the compartments measured in North Carolina. Many compartments, specifically the BA compartment from all trips, exceeded the vertical ELV. Regardless of where the data were collected, fewer compartments exceeded the EAV in the horizontal orientation. Only BA compartments exceeded the ELV in the horizontal orientation. There were Area × Level interactions for vertical and horizontal RMS and VDV (P &lt; 0.01). The BF compartment had a greater vertical RMS value than the TF, TC, and BC (P &lt; 0.02) compartments, but did not differ (P = 0.06) from the TA compartment. The vertical RMS of the TA compartment did not differ from the TF, TC, and BC compartments (P &gt; 0.13). The BF compartment had a greater (P = 0.02) vertical VDV value than the TC location, but did not differ from the other locations (P &gt; 0.16). All other locations did not differ in vertical VDV (P &gt; 0.12). The BF compartment had greater horizontal RMS than the TC and TA compartments (P &lt; 0.01), but did not differ from TF and BC compartments (P &gt; 0.12). All other compartments did not differ in horizontal RMS (P &gt; 0.34). All compartments, aside from the BA compartment, did not differ in horizontal VDV (P &gt; 0.19). Vibration analyses indicated the BA compartment had the greatest vertical and horizontal vibrations and a large percentage of the compartments exceed the EAV and ELV, which indicated pigs may have experienced uncomfortable trips that could cause discomfort or fatigue.
Nutrient digestibility and fecal characteristics, microbiota, and metabolites in dogs fed human-grade foods
Authors: Do Sungho , Phungviwatnikul Thunyaporn , de Godoy Maria R C , Swanson Kelly S 
Published: January 2021

Abstract
Human-grade (HG) pet foods are commercially available, but they have not been well studied. Our objective was to determine the apparent total tract digestibility (ATTD) of HG pet foods and evaluate their effects on fecal characteristics, microbiota, and metabolites, serum metabolites, and hematology of dogs. Twelve dogs (mean age = 5.5 ± 1.0; BW = 11.6 ± 1.6 kg) were used in a replicated 4 × 4 Latin square design (n = 12/treatment). The diets included 1) Chicken and Brown Rice Recipe (extruded; Blue Buffalo); 2) Roasted Meals Tender Chicken Recipe (fresh; Freshpet); 3) Beef and Russet Potato Recipe (HG beef; JustFoodForDogs); and 4) Chicken and White Rice Recipe (HG chicken; JustFoodForDogs). Each period consisted of 28 d, with a 6-d diet transition phase, 16 d of consuming 100% of the diet, a 5-d phase for fecal collection, and 1 d for blood collection. All data were analyzed using the Mixed Models procedure of SAS 9.4. Dogs fed the extruded diet required a higher (P &lt; 0.05) daily food intake (dry matter basis, DMB) to maintain BW. The ATTD of dry matter (DM), organic matter (OM), energy, and acid-hydrolyzed fat (AHF) were greater (P &lt; 0.05) in dogs fed the HG diets than those fed the fresh diet, and greater (P &lt; 0.05) in dogs fed the fresh diet than those fed the extruded diet. Crude protein ATTD was lower (P &lt; 0.05) for dogs fed the extruded diet than those fed all other diets. Dogs fed the extruded diet had greater (P &lt; 0.05) fecal output (as-is; DMB) than dogs fed fresh (1.5–1.7 times greater) or HG foods (2.0–2.9 times greater). There were no differences in fecal pH, scores, and metabolites, but microbiota were affected by diet. Dogs fed HG beef had higher (P &lt; 0.05) relative abundance of Bacteroidetes and lower (P &lt; 0.05) relative abundance of Firmicutes than dogs fed the fresh or HG chicken diets. The Actinobacteria, Fusobacteria, Proteobacteria, and Spirochaetes phyla were unchanged (P &gt; 0.05), but diet modified the relative abundance of nearly 20 bacterial genera. Similar to previous reports, these data demonstrate that the fecal microbiota of dogs fed HG or fresh diets is markedly different than those consuming extruded diets, likely due to ingredient, nutrient, and processing differences. Serum metabolites and hematology were not greatly affected by diet. In conclusion, the HG pet foods tested resulted in significantly reduced fecal output, were highly digestible, maintained fecal characteristics, serum chemistry, and hematology, and modified the fecal microbiota of dogs.
Identification of Differentially Expressed Long Noncoding RNAs in Mice Intestines After Severe Burns and a Preliminary Study into the Key Gene H19
Authors: Qiu Wei , Deng Yuequ , Zhuang Mengmeng , Wang Peng , Li Cuijie , Li Ye , Zhu Bo , Zhang Pan , Li Dan , Sun Yuan , Yang Juan , Cao Shuqin , Sun Yong 
Published: January 2021

Abstract
The intestine is considered the key organ in stress response to severe burns and injury to the intestine after severe burns can be fatal. However, the injury and subsequent repair of intestinal tissues after severe burns at the genetic level are poorly understood. Long noncoding RNAs (lncRNAs) have important functions in regulating many biological processes, including gene transcription and translation. Autophagy is a process of intracellular degradation and reutilization of cytoplasmic proteins and organelles. We herein analyzed the genome-wide expression profile of lncRNAs and mRNAs after severe burns in the intestines of mice by lncRNA microarray. Quantitative reverse transcription-polymerase chain reaction was performed to verify the reliability of microarray analysis results, and Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis were used for bioinformatics analysis of differentially expressed mRNAs. The common regulatory network between the top 10 differentially expressed lncRNAs and trans-related mRNAs were visualized by Cytoscape (v3.7.2). Next, we hypothesized that H19 is the key gene for intestinal mucosal repair. After H19 was overexpressed, the changes in downstream autophagy protein expression levels were observed. GO and KEGG analysis indicated that the differentially expressed mRNAs were mainly enriched in a cell cycle- and mitosis-related genes. Overexpression of lncRNA-H19 showed that the autophagy-related gene Trim21 was upregulated, while HIF1α was downregulated. LncRNA-H19 played a key role in repairing the intestinal mucosa, and overexpression of lncRNA-H19 activated autophagy and migration of intestinal epithelial cells (IEC-6).
Susceptibility of Four Different Sorghum Varieties to Infestation by the Khapra Beetle
Authors: Gourgouta Marina , Athanassiou Christos G , Arthur Frank H 
Published: January 2021

Abstract
In this study, we evaluated the susceptibility of four different sorghum varieties to infestation by the khapra beetle, Trogoderma granarium Everts (Coleoptera: Dermestidae), as compared with wheat, which served as a ‘control’ commodity. In population growth assays, there was preference for population development on wheat compared to the different sorghum varieties. In contrast, there were no significant differences in total population development among the four varieties of sorghum. However, the proportion of immature stages (larvae, pupae) in relation to the adult stage varied significantly among the different varieties. Moreover, significant differences were noted among the commodities tested regarding the final weight decrease, as well as the amount of frass and kernel damage. Our study clearly demonstrates noticeable differences in the susceptibility of the varieties to T. granarium infestation. These results show that this species can develop on different varieties of sorghum, and variety selection should be further considered in a host-plant resistance-based management program for T. granarium.
Political Connections and White-Collar Crime: Evidence from Insider Trading in France
Authors: Bourveau Thomas , Coulomb Renaud , Sangnier Marc 
Published: January 2021

Abstract
This paper investigates whether political connections affect individuals’ propensity to engage in white-collar crime. We identify connections by campaign donations or direct friendships and use the 2007 French Presidential election as a marker of change in the value of political connections to the winning candidate. We compare the behavior of Directors of publicly listed companies who were connected to the future President to the behavior of other non-connected Directors, before and after the election. Consistent with the belief that connections to a powerful politician can protect someone from prosecution or punishment, we uncover indirect evidence that connected Directors are more likely to engage in suspicious insider trading after the election: Purchases by connected Directors trigger larger abnormal returns, connected Directors are less likely to comply with trading disclosure requirements in a timely fashion, and connected Directors trade closer in time to their firms’ announcements of results. (JEL: D72, G14, G18, G38, K22, K42)