bluuebunny/crossref_metadata_2025_split huggingface dataset:
Serum ammonia as a non-invasive marker for early prediction of esophageal varices
Authors: Darweesh Samar K. , Elsabaawy Maha A. , Eltahawy Mahmoud A. , Ghanem Heba S. , Abdel-Razek Wael 
Published: April 2020

Introduction:
There is a growing need for identification of non-endoscopic, non-invasive methods that can accurately predict esophageal varices (EV). Previous studies found an inconclusive correlation between blood ammonia level and the presence and size of EV.

Aim:
We aimed at assessing the value of serum ammonia as a non-invasive method for early prediction of EV.

Patient and methods:
The study included 204 patients with HCV-related cirrhosis. The selected patients were categorized into two groups: patients with EV and those without, also patients with no or small EV and with large EV group. All patients underwent a complete biochemical workup, ultrasound and upper GI endoscopy. Child-Pugh class, Model of End-Stage Liver Disease (MELD) score and platelet count/splenic diameter ratio, and serum ammonia level.

Results:
There was a statistical difference between the two groups of patients regarding the following parameters: serum ammonia, international normalized ratio, portal vein diameter, spleen diameter, Child-Pugh class, MELD score, platelet count/splenic diameter ratio, aspartate aminotransferase-to-platelet ratio index, alanine aminotransferase-to-aspartate aminotransferase ratio, Forns index, FIB-4 and King’s score. Serum ammonia could predict the presence of EV using a cutoff value of 82 (µmol/L) with a sensitivity of 92.3%, specificity 92%. In addition, a cutoff of 95.5 (µmol/L) could predict large EV with a sensitivity of 92.7% and a specificity of 92.3%. Serum Ammonia in cirrhosis with large EV was 143 ± 39 µmol/L and in cirrhosis with small/without EV was 80.7 ± 9.7 µmol/L (P < 0.0001). Platelet/spleen ratio was 555.9 ± 187.3 in cirrhosis with EV and 694.4 ± 74.2 in cirrhosis without EV (P < 0.0001). Platelet/spleen ratio was 407.7 ± 107.1 in cirrhosis with large EV and 690.4 ± 103.7 in cirrhosis with small/without EV (P < 0.0001).

Conclusion:
Serum ammonia can accurately predict the presence and the size of EV in patients with liver cirrhosis with high sensitivity and specificity.
Symptoms and demographic factors associated with early-onset colorectal neoplasia among individuals undergoing diagnostic colonoscopy
Authors: Krigel Anna , Zhou Margaret , Terry Mary Beth , Kastrinos Fay , Lebwohl Benjamin 
Published: April 2020

Background:
The incidence and mortality of colorectal cancer (CRC) are increasing in adults under 50 years. Risk factors associated with early-onset colorectal neoplasia (CRN) are uncertain. We aimed to identify clinical predictors associated with the presence of CRN detected by diagnostic colonoscopy in symptomatic individuals under 50 years of age.

Methods:
We used a single-center endoscopy database to identify symptomatic patients 18–49 years of age who underwent ambulatory colonoscopy between 2007 and 2017. Pathology reports identified CRN as adenomas, advanced adenomas (based on size or histology), or adenocarcinomas. Multivariable analysis was used to determine factors associated with CRN.

Results:
We identified 4333 eligible patients of whom 363 (8.4%) had any CRN and 48 (1.1%) had advanced neoplasia (advanced adenoma or adenocarcinoma). Factors associated with any CRN on multivariable analysis included male sex [odds ratio (OR) 1.50 (1.19–1.88)], older age group [compared to 18–29 years, OR for 30–39: 3.12 (1.93–5.04); OR for 40–49: 4.68 (2.97–7.36)], obesity [OR for BMI 30–34.9 compared to 18–24.9: 1.44 (1.04–2.01)], and any tobacco use [OR 1.63 (1.18–2.23)]. Anemia was associated with advanced neoplasia [OR 3.11 (1.32–7.34)]. Of the advanced neoplastic lesions, 38 of 48 (79.2%) were located in the distal colon.

Conclusions:
In the largest study to date of symptomatic individuals under 50 years of age undergoing colonoscopy in the USA, advanced CRN was most often detected in the distal colon and was associated with anemia, but not with abnormal bowel habits or abdominal pain. We also found that patients with CRN under 50 years of age were more likely to be male, smokers, and obese. These findings should prompt further investigation of these risk factors alone and in combination.
A systematic review with subset meta-analysis of studies exploring memory recall biases for pain-related information in adults with chronic pain
Authors: Schoth Daniel E. , Radhakrishnan Kanmani , Liossi Christina 
Published: April 2020

Abstract
Pain-related memory biases have been frequently explored in individuals with chronic pain, and along with attentional and interpretation biases are hypothesised to contribute to the onset and/or maintenance of chronic pain. The aim of this review is to provide a systematic review and synthesis of studies exploring memory recall biases for pain-related information in individuals with chronic pain relative to healthy controls and the recall of neutral information. Studies were identified through a search of Medline, PsychINFO, Web of Science, CINAHL, Cochrane Library, and Open Grey databases. Search terms were memory, recall, recognition, and bias*, intersected with pain. Eighteen studies meeting the inclusion criteria were included. Subset meta-analyses are also reported from 12 studies with relevant between-groups data (comparing recall in chronic pain vs healthy control groups) and 12 studies with relevant within-groups data (eg, comparing recall of pain-related/emotional vs neutral words). Between-groups analysis revealed significantly weaker recall bias for affective-pain words in individuals with chronic pain relative to healthy controls, but only when nondepressed chronic pain individuals were included. No significant differences were found between groups in the recall of sensory-pain, illness-related, or depression-related words. Within-groups analysis revealed individuals with chronic pain show a significant recall bias favouring sensory-pain words relative to neutral and affective-pain words, and a bias for illness-related words relative to depression-related words. A recall bias favouring neutral words was found in healthy individuals. Evidence for the presence of pain-related memory biases in patients with chronic pain is inconclusive. Further methodologically rigorous research is required.
Poly-4-Hydroxybutyric Acid Mesh Compares Favorably With Acellular Dermal Matrix in Tissue Expander–Based Breast Reconstruction
Authors: Levy Adam S. , Bernstein Jaime L. , Xia Jimmy J. , Otterburn David M. 
Published: April 2020

Background
Acellular dermal matrix (ADM) is commonly used during immediate expander-based breast reconstruction, with potential advantages of greater intraoperative expansion, decreased time to complete expansion, and decreased rates of capsular contracture. However, ADM is associated with increased infection rate, seroma, and subsequent reconstructive failure. Poly-4-hydroxybutyric acid (P4HB) mesh is a large pore, biosynthetic scaffold shown to fully resorb and incorporate host tissues within 18 months. We sought to compare outcomes between the use of P4HB and ADM in immediate retropectoral expander-based reconstruction.

Methods
One hundred ninety-two consecutive cases (107 patients) of breast reconstruction using ADM were compared with a subsequent cohort of 112 cases (62 patients) using P4HB mesh. In all patients, reconstruction was performed immediately after mastectomy by a single surgeon, and outcomes were compared between groups.

Results
Baseline characteristics were similar between the P4HB and ADM groups. Overall infection rates were lower, but not significantly with P4HB (11% vs 17%, P = 0.18). Time to drain removal was significantly lower with P4HB (15 vs 18 days, P = 0.008), although there was no difference in rates of seroma (0.9% vs 3%, P = 0.43). Similar numbers of patients underwent external beam radiation (22% vs 24%) and received chemotherapy in each group (48% vs 45%). By univariate analysis, all odds ratios were decreased with use of P4HB, including risk of major complications (0.55), seroma (0.17), infection (0.59), need for reoperation (0.78), and skin necrosis (0.77).

Conclusions
Initial findings suggest P4HB mesh to be a safe alternative to ADM in expander-based breast reconstruction, with trends toward decreased rates of infection, seroma, and need for device removal using P4HB mesh. Although our results are limited to a small series of initial patients, P4HB mesh may be a promising novel technique to decrease complications inherent to use of ADM at a reduced material cost.
Fingertip Reconstruction Using a Lateral Flap Based on the Distal Transverse Arch of the Digital Artery
Authors: Cui Manyi , Wang Peiji 
Published: April 2020

Purpose
Fingertip defect is more common in emergency hand trauma in the hospital, and most of them are accompanied by defects of the phalanx and nail bed. There are many methods in clinic for the repair of Yamano zone I fingertip injury. This article reports the repair of this type of injury using a lateral flap based on the distal transverse arch of the digital artery.

Methods
From January 2015 to May 2018, the flap was used in 32 digits of 32 patients who had a fingertip injury. There were 23 men and 9 women with a mean age of 37.6 years. The injured fingers requiring reconstruction included 6 thumb, 11 index fingers, 9 middle fingers, 4 ring fingers, and 2 little fingers. Soft tissue defect range from 1.5 cm × 1.0 cm to 2.5 cm × 2.1 cm. The time of injury to emergency surgery was 1 to 7.5 hours, with a mean time of 3.2 hours. Fingertip reconstruction was performed using a lateral flap based on the distal transverse arch of the digital artery.

Results
All flaps survived completely after 1 to 1.5 years of follow-up, without evidence of postoperative insufficiency of blood supply or venous congestion. Healing of all donor sites was uncomplicated. No infectious complications were observed. The range of motion of the 32 fingers was excellent; For sweating, 17 fingers were excellent, 10 were good, and 5 were fair (poor sweating was found in the grafting site of the finger). The mean static 2-point discrimination scores on the reconstructed pulp were 5.2 mm (range, 3–9 mm). According to the Cold Intolerance Severity Score, 28 patients reported no cold intolerance, 3 reported mild cold intolerance, and 1 reported moderate cold intolerance. On the basis of the visual analog scale, 30 patients had no pain, 1 reported mild pain, and 1 experienced moderate pain. Positive Tinel sign was found in only 1 reconstructed finger.

Conclusion
It is a new surgical technique that provides good shape and sensory function to the fingers and is simple to operate.
Harnessing the 100,000 Genomes Project whole genome sequencing data - an unbiased systematic tool to filter by biologically validated regions of functionality
Authors: Xiao Sihao , Kai Zhentian , Brown David ,   Genomics England Research Consortium, Shovlin Claire L 
Published: April 2020

SUMMARYWhole genome sequencing (WGS) is championed by the UK National Health Service (NHS) to identify genetic variants that cause particular diseases. The full potential of WGS has yet to be realised as early data analytic steps prioritise protein-coding genes, and effectively ignore the less well annotated non-coding genome which is rich in transcribed and critical regulatory regions. To address, we developed a filter, which we call GROFFFY, and validated in WGS data from hereditary haemorrhagic telangiectasia patients within the 100,000 Genomes Project. Before filter application, the mean number of DNA variants compared to human reference sequence GRCh38 was 4,867,167 (range 4,786,039-5,070,340), and one-third lay within intergenic areas. GROFFFY removed a mean of 2,812,015 variants per DNA. In combination with allele frequency and other filters, GROFFFY enabled a 99.56% reduction in variant number. The proportion of intergenic variants was maintained, and no pathogenic variants in disease genes were lost. We conclude that the filter applied to NHS diagnostic samples in the 100,000 Genomes pipeline offers an efficient method to prioritise intergenic, intronic and coding gDNA variants. Reducing the overwhelming number of variants while retaining functional genome variation of importance to patients, enhances the near-term value of WGS in clinical diagnostics.
Characterization and treatment of SARS-CoV-2 in nasal and bronchial human airway epithelia
Authors: Pizzorno Andrés , Padey Blandine , Julien Thomas , Trouillet-Assant Sophie , Traversier Aurélien , Errazuriz-Cerda Elisabeth , Fouret Julien , Dubois Julia , Gaymard Alexandre , Lescure François-Xavier , Dulière Victoria , Brun Pauline , Constant Samuel , Poissy Julien , Lina Bruno , Yazdanpanah Yazdan , Terrier Olivier , Rosa-Calatrava Manuel 
Published: April 2020

AbstractIn the current COVID-19 pandemic context, proposing and validating effective treatments represents a major challenge. However, the lack of biologically relevant pre-clinical experimental models of SARS-CoV-2 infection as a complement of classic cell lines represents a major barrier for scientific and medical progress. Here, we advantageously used human reconstituted airway epithelial models of nasal or bronchial origin to characterize viral infection kinetics, tissue-level remodeling of the cellular ultrastructure and transcriptional immune signatures induced by SARS-CoV-2. Our results underline the relevance of this model for the preclinical evaluation of antiviral candidates. Foremost, we provide evidence on the antiviral efficacy of remdesivir and the therapeutic potential of the remdesivir-diltiazem combination as a rapidly available option to respond to the current unmet medical need imposed by COVID-19.One Sentence SummaryNew insights on SARS-CoV-2 biology and drug combination therapies against COVID-19.
Intergenerational pathogen-induced diapause inC. elegansis modulated bymir-243
Authors: Gabaldon Carolaing , Legüe Marcela , Palominos M. Fernanda , Verdugo Lidia , Gutzwiller Florence , Calixto Andrea 
Published: April 2020

AbstractThe interaction and communication between bacteria and their hosts modulate many aspects of animal physiology and behavior. Dauer entry as a response to chronic exposure to pathogenic bacteria inCaenorhabditis elegansis an example of a dramatic survival response. This response is dependent on the RNAi machinery, suggesting the involvement of sRNAs as effectors. Interestingly, dauer formation occurs after two generations of interaction with two unrelated moderately pathogenic bacteria. Therefore, we sought to discover the identity ofC. elegansRNAs involved in pathogen-induced diapause. Using transcriptomics and differential expression analysis of coding and long and small non-coding RNAs, we found thatmir-243-3pis the only transcript continuously upregulated in animals exposed to both,P. aeruginosaorS. entericafor two generations. Phenotypic analysis of mutants showed thatmir-243is required for dauer formation under pathogenesis but not under starvation. Moreover, DAF-16, a master regulator of defensive responses in the animal and required for dauer formation was found to be necessary formir-243expression. This work highlights the role of a small non-coding RNA in the intergenerational defensive response against pathogenic bacteria and inter-kingdom communication.ImportancePersistent infection of the bacterivore nematodeC. eleganswith bacteria such asP. aeruginosaandS. entericamakes the worm diapause or hibernate. By doing this, the worm closes its mouth avoiding infection. This response takes two generations to be implemented. In this work, we looked for genes expressed upon infection that could mediate the worm diapause triggered by pathogens. We identifymir-243-3pas the only transcript commonly upregulated when animals feed onP. aeruginosaandS. entericafor two consecutive generations. Moreover, we demonstrate thatmir-243-3pis required for pathogen-induced dauer formation, a new function that has not been previously described for this miRNA. We also find that the transcriptional activators DAF-16, PQM-1 and CRH-2 are necessary for the expression ofmir-243under pathogenesis. Here we establish a relationship between a small RNA and a developmental change that ensures the survival of a percentage of the progeny.
Research on the Influence of Information Diffusion on the Transmission of the Novel Coronavirus (COVID-19)
Authors: Lin Shanlang , Ma Chao , Lin Ruofei , Huang Junpei , Xu Ruohan , Yuan Aini 
Published: April 2020

AbstractWith the rapid development of mobile Internet in China, the information of the epidemic is full-time and holographic, and the role of information diffusion in epidemic control is increasingly prominent. At the same time, the publicity of all kinds of big data also provides the possibility to explore the impact of media information diffusion on disease transmission. This paper explores the mechanism of the influence of information diffusion on the spread of the novel coronavirus, develops a model of the interaction between information diffusion and disease transmission based on the SIR model, and empirically tests the role and mechanism of information diffusion in the spread of COCID-19 by using econometric method. The result shows that there was a significant negative correlation between the information diffusion and the spread of the novel coronavirus; The result of robust test shows that the spread of both epidemic information and protection information hindered the further spread of the epidemic.
Importance of suppression and mitigation measures in managing COVID-19 outbreaks
Authors: Hochberg Michael E. 
Published: April 2020

AbstractI employ a simple mathematical model of an epidemic process to evaluate how four basic quantities: the reproduction number (ℛ), the numbers of sensitive (S) and infectious individuals (I), and total community size (N) affect strategies to control COVID-19. Numerical simulations show that strict suppression measures at the beginning of an epidemic can create low infectious numbers, which thereafter can be managed by mitigation measures over longer periods to flatten the epidemic curve. The stronger the suppression measure, the faster it achieves the low numbers of infections that are conducive to subsequent management. Our results on short-term strategies point to a two-step control strategy, following failed mitigation, that begins with suppression of the reproduction number, ℛC, below 1.0, followed by renewed mitigation measures that manage the epidemic by maintaining the effective reproduction number ℛCeff≈ ℛCS/N at approximately 1.0. The objectives of the full sequence of measures observed in a number of countries, and likely to be seen in the longer term, can be symbolically represented as: ℛ0→ ℛC<ℛ0→ℛC<1.0 → ℛCeff≈1.0. We discuss the predictions of this analysis and how it fits into longer-term sequences of measures, including misconceptions about ‘flattening the curve’ and how the herd immunity concept can be used to ‘leverage’ immunity.
Correction of Artifacts Induced by B0 Inhomogeneities in Breast MRI using Reduced Field-of-View Echo-Planar Imaging and Enhanced Reverse Polarity Gradient Method
Authors: Rodríguez-Soto Ana E. , Park Helen , Holland Dominic , Keenan Kathryn E. , Bartsch Hauke , Kuperman Joshua , Wallace Anne M. , Hahn Michael , Ojeda-Fournier Haydee , Dale Anders M. , Rakow-Penner Rebecca 
Published: April 2020

AbstractPurposeDiffusion weighted (DW) echo-planar imaging (EPI) is prone to geometric and intensity distortions due to B0 inhomogeneities. Pulse sequences that excite spins within a reduced field-of-view (FOV) in the phase encoding (PE) direction have been developed to decrease such distortions. In addition, use of the reverse polarity gradient (RPG) method, a retrospective approach to correct distortion artifacts, has been shown to improve the localization of tumor lesions. The purpose of this work was to evaluate the performance of reduced-FOV acquisition and RPG in decreasing distortion artifacts for breast imaging.MethodsEPI data were acquired with full and reduced-FOV in a breast phantom and in a group of 170 women at 3T. The performance of RPG in correcting distortion artifacts in EPI data was evaluated using the mutual information (MI) metric between EPI and anatomical low-distortion images before and after distortion correction.ResultsRPG corrected distortions by 61% in full-FOV EPI and 48% in reduced-FOV EPI in a breast phantom. In patients, MI increased on average 13±8% and 8±6% for both full and reduced-FOV EPI data after distortion correction, respectively. The 95th percentile and maximum displacement between uncorrected and corrected full-FOV EPI datasets were 0.8±0.3cm and 1.9±0.3cm, and for reduced-FOV were 0.4±0.2cm and 1.3±0.3cm.ConclusionMinimal distortion was achieved with RPG applied to reduced-FOV EPI data. RPG improved distortions for full-FOV, but with more modest improvements and limited correction near the nipple.
Knowledge and behaviors toward COVID-19 among U.S. residents during the early days of the pandemic
Authors: Clements John M 
Published: April 2020

AbstractObjectiveTo test the hypothesis that knowledge of COVID-19 influences participation in different behaviors including self-reports of purchasing more goods than usual, attending large gatherings, and using medical masks.MethodsCross-sectional online survey of 1,034 U.S. residents age 18+ conducted on March 17, 2020.ResultsFor every point increase in knowledge, the odds of participation in purchasing more goods (OR=0.88, 95% CI:0.81-0.95), attending large gatherings (OR=0.87, 95%CI: 0.81-0.93), and using medical masks (OR=0.56, 95% CI:0.50-0.62) decreased by 12%, 13%, and 44%, respectively. Gen X and Millennial participants had 56% to 76% higher odds, respectively, of increased purchasing behavior, compared to Baby Boomers. Results suggest politicization of response recommendations. Democrats had 30% lower odds of attending large gatherings (OR=0.70, 95% CI:0.50-0.97), and 48% lower odds of using medical masks (OR=0.52, 95% CI:0.34-0.78), compared to Republicans.ConclusionsThis survey is one of the first attempts to study determinants of knowledge and behaviors in response to the COVID-19 pandemic in the U.S. A national, coordinated effort at pandemic response may ensure better compliance with behavioral recommendations to address this public health emergency.
BAdabouM: a genomic structural variations discovery tool for polymorphism analyses
Authors: Cumer Tristan , Pompanon François , Boyer Frédéric 
Published: April 2020

AbstractGenomic Structural Variations (SVs) are known to impact the evolution of genomes and to have consequences on individual’s fitness. Nevertheless, they remain challenging to detect in whole genome re-sequencing (WGS) data. Lots of methods detecting SVs are described in the literature but they might be hard to install, have non-trivial settings, do not detect all SVs categories and have generally high levels of false positive.Here we introduce BAdabouM, a fast (C written) and easy to install SVs discovery tool. BAdabouM auto evaluates read length, library size and mean coverage to set thresholds specific to each experiment. BAdabouM interprets multiple SVs signatures (reads aligned with a split, non-concordant mapped pairs or uneven coverage) to detect insertions, deletions, copy number variations, inversions, and translocations at single-nucleotide resolution.When compared with two widely used methods on simulated and real datasets, BAdabouM was faster, exhibited a similar accuracy with a good concordance on SVs detected, and detected significantly more insertions. BAdabouM was more reproducible to detect independently SVs across individuals, which is a clear advantage when characterizing population polymorphism. Furthermore, BAdabouM demonstrated a superior ability to detect breakpoints with a base pair resolution.BAdabouM proved to be efficient, fast and accurate to detect SVs, and handle. BAdabouM is a complementary method to be used for a more comprehensive detection of SVs, and is especially suited for studying polymorphism for all types of SVs with a high accuracy.