bluuebunny/crossref_metadata_2025_split huggingface dataset:
Exceptional points in the one-dimensional Hubbard model
Authors: Rausch Roman , Peters Robert , Yoshida Tsuneya 
Published: December 2020

Abstract
Non-Hermitian phenomena offer a novel approach to analyze and interpret spectra in the presence of interactions. Using the density-matrix renormalization group (DMRG), we demonstrate the existence of exceptional points for the one-particle Green’s function of the 1D alternating Hubbard chain with chiral symmetry, with a corresponding Fermi arc at zero frequency in the spectrum. They result from the non-Hermiticity of the effective Hamiltonian describing the Green’s function and only appear at finite temperature. They are robust and can be topologically characterized by the zeroth Chern number. This effect illustrates a case where temperature has a strong effect in 1D beyond the simple broadening of spectral features. Finally, we demonstrate that exceptional points appear even in the two-particle Green’s function (charge structure factor) where an effective Hamiltonian is difficult to establish, but move away from zero frequency due to a distinct symmetry constraint.
Wafer-level fabrication of alkali vapor cells using in-situ atomic deposition
Authors: Bopp D G , Maurice V M , Kitching J E 
Published: December 2020

Abstract
We demonstrate a new technique for filling mm-scale microfabricated silicon and glass cavities with alkali vapors at the wafer-scale. A single etched silicon wafer contains an array of cavities containing alkali precursor materials offset laterally from the cell array. The wafer is heated to create an array of alkali droplets on an upper glass wafer, which is then translated laterally under vacuum and bonded to create the cells. This technique can be implemented in a commercially available bonding tool, allows the fabrication of cells with arbitrary buffer gas contents and pressures and can potentially produce cells with dimensions below 100 µm.
Ready-to-use paper biofuel cell driven by water
Authors: Shitanda Isao , Momiyama Misaki , Hoshi Yoshinao , Itagaki Masayuki , Tsujimura Seiya 
Published: December 2020

Abstract
A biofuel cell that can generate electricity using only water is expected to be used as a new energy harvester for an emergency power supply. A new 4-series/4-parallel structured paper-substrate biofuel cell was prepared using a fuel supply paper preloaded with glucose and phosphate buffer salts. When a power generation test was conducted by supplying water to the fuel-preloaded paper, the paper-based biofuel cell produced an output approximately 90% (0.84 mW) of that obtained by supplying a phosphate buffer containing glucose as the electrolyte. The open-circuit voltage was 2.1 V, and an LED could be powered by simply supplying water to the cell without using a booster circuit.
A medical history of arterial thrombosis is a strong predictor of post-operative myocardial infarction and stroke in patients with hip fractures—a nationwide cohort study
Authors: Wahlsten Liv Riisager , Zareini Bochra , Smedegaard Lærke , Gislason Gunnar H , Palm Henrik , Brorson Stig 
Published: December 2020

Abstract

Introduction
Hip fractures lead to a substantial burden of disease and mortality among the elderly. Myocardial infarction (MI) and stroke are serious and overlooked complications, and their impact on mortality and morbidity may be underestimated. We investigated; 90-day absolute risk of stroke and MI following hip fracture surgery, and ii) anamnestic risk factors associated with elevated risk of postoperative MI and stroke.

Methods
All Danish patients aged ≥60 undergoing first time hip fracture surgery in 2000–2017 were identified. Outcomes were MI or stroke 90 days after surgery. We performed gender-stratified cumulative incidence functions and multivariate Cox regression models adjusted for age and comorbidities.

Results
124,660 patients were included. Incidence of MI was 2.2% and 1.3%, and incidence of stroke was 3.5% and 2.5%, in men and women, respectively. The most important risk factor for MI and stroke was a previous event. Hazard ratio (HR) of MI associated with previous MI was 2.43 (95% Confidence Interval (CI) 2.02–2.92) in men and 2.65 (95% CI 2.23–3.16) in women, while the HR of stroke associated with previous stroke was 4.17 (95% CI 3.73–4.67) and 3.73 (95% CI 3.43–4.08), respectively. Other risk factors of MI were; sex, age, and a history of heart failure, hypertension, peripheral artery disease or diabetes. For postoperative stroke; sex age, and atrial fibrillation were important risk factors.

Conclusion
MI and stroke after hip fractures are overlooked and serious complications. Persons with elevated risk can be identified at admission, based on their medical history.
Exploring associations of non-coding RNAs in human diseases via three-matrix factorization with hypergraph-regular terms on center kernel alignment
Authors: Wang Hao , Tang Jijun , Ding Yijie , Guo Fei 
Published: December 2020

AbstractRelationship of accurate associations between non-coding RNAs and diseases could be of great help in the treatment of human biomedical research. However, the traditional technology is only applied on one type of non-coding RNA or a specific disease, and the experimental method is time-consuming and expensive. More computational tools have been proposed to detect new associations based on known ncRNA and disease information. Due to the ncRNAs (circRNAs, miRNAs and lncRNAs) having a close relationship with the progression of various human diseases, it is critical for developing effective computational predictors for ncRNA–disease association prediction. In this paper, we propose a new computational method of three-matrix factorization with hypergraph regularization terms (HGRTMF) based on central kernel alignment (CKA), for identifying general ncRNA–disease associations. In the process of constructing the similarity matrix, various types of similarity matrices are applicable to circRNAs, miRNAs and lncRNAs. Our method achieves excellent performance on five datasets, involving three types of ncRNAs. In the test, we obtain best area under the curve scores of $0.9832$, $0.9775$, $0.9023$, $0.8809$ and $0.9185$ via 5-fold cross-validation and $0.9832$, $0.9836$, $0.9198$, $0.9459$ and $0.9275$ via leave-one-out cross-validation on five datasets. Furthermore, our novel method (CKA-HGRTMF) is also able to discover new associations between ncRNAs and diseases accurately. Availability: Codes and data are available: https://github.com/hzwh6910/ncRNA2Disease.git. Contact:fguo@tju.edu.cn
MethPanel: a parallel pipeline and interactive analysis tool for multiplex bisulphite PCR sequencing to assess DNA methylation biomarker panels for disease detection
Authors: Luu Phuc-Loi , Ong Phuc-Thinh , Loc Tran Thai Huu , Lam Dilys , Pidsley Ruth , Stirzaker Clare , Clark Susan J 
Published: December 2020

Abstract

Summary
DNA methylation patterns in a cell are associated with gene expression and the phenotype of a cell, including disease states. Bisulphite PCR sequencing is commonly used to assess the methylation profile of genomic regions between different cells. Here we have developed MethPanel, a computational pipeline with an interactive graphical interface to rapidly analyse multiplex bisulphite PCR sequencing data. MethPanel comprises a complete analysis workflow from genomic alignment to DNA methylation calling and supports an unlimited number of PCR amplicons and input samples. MethPanel offers important and unique features, such as calculation of an epipolymorphism score and bisulphite PCR bias correction capabilities, and is designed so that the methylation data from all samples can be processed in parallel. The outputs are automatically forwarded to a shinyApp for convenient display, visualization and remotely sharing data with collaborators and clinicians.

Availabilityand implementation
MethPanel is freely available at https://github.com/thinhong/MethPanel.

Supplementary information
Supplementary data are available at Bioinformatics online.
An open-source high-content analysis workflow for CFTR function measurements using the forskolin-induced swelling assay
Authors: Hagemeijer Marne C , Vonk Annelotte M , Awatade Nikhil T , Silva Iris A L , Tischer Christian , Hilsenstein Volker , Beekman Jeffrey M , Amaral Margarida D , Botelho Hugo M 
Published: December 2020

Abstract

Motivation
The forskolin-induced swelling (FIS) assay has become the preferential assay to predict the efficacy of approved and investigational CFTR-modulating drugs for individuals with cystic fibrosis (CF). Currently, no standardized quantification method of FIS data exists thereby hampering inter-laboratory reproducibility.

Results
We developed a complete open-source workflow for standardized high-content analysis of CFTR function measurements in intestinal organoids using raw microscopy images as input. The workflow includes tools for (i) file and metadata handling; (ii) image quantification and (iii) statistical analysis. Our workflow reproduced results generated by published proprietary analysis protocols and enables standardized CFTR function measurements in CF organoids.

Availability and implementation
All workflow components are open-source and freely available: the htmrenamer R package for file handling https://github.com/hmbotelho/htmrenamer; CellProfiler and ImageJ analysis scripts/pipelines https://github.com/hmbotelho/FIS_image_analysis; the Organoid Analyst application for statistical analysis https://github.com/hmbotelho/organoid_analyst; detailed usage instructions and a demonstration dataset https://github.com/hmbotelho/FIS_analysis. Distributed under GPL v3.0.

Supplementary information
Supplementary data are available at Bioinformatics online.
Assessing risk model calibration with missing covariates
Authors: Shin Yei Eun , Gail Mitchell H , Pfeiffer Ruth M 
Published: December 2020

SummaryWhen validating a risk model in an independent cohort, some predictors may be missing for some subjects. Missingness can be unplanned or by design, as in case-cohort or nested case–control studies, in which some covariates are measured only in subsampled subjects. Weighting methods and imputation are used to handle missing data. We propose methods to increase the efficiency of weighting to assess calibration of a risk model (i.e. bias in model predictions), which is quantified by the ratio of the number of observed events, $\mathcal{O}$, to expected events, $\mathcal{E}$, computed from the model. We adjust known inverse probability weights by incorporating auxiliary information available for all cohort members. We use survey calibration that requires the weighted sum of the auxiliary statistics in the complete data subset to equal their sum in the full cohort. We show that a pseudo-risk estimate that approximates the actual risk value but uses only variables available for the entire cohort is an excellent auxiliary statistic to estimate $\mathcal{E}$. We derive analytic variance formulas for $\mathcal{O}/\mathcal{E}$ with adjusted weights. In simulations, weight adjustment with pseudo-risk was much more efficient than inverse probability weighting and yielded consistent estimates even when the pseudo-risk was a poor approximation. Multiple imputation was often efficient but yielded biased estimates when the imputation model was misspecified. Using these methods, we assessed calibration of an absolute risk model for second primary thyroid cancer in an independent cohort.
Spontaneous Emergence of Azithromycin Resistance in Independent Lineages of Salmonella Typhi in Northern India
Authors: Carey Megan E , Jain Ruby , Yousuf Mohammad , Maes Mailis , Dyson Zoe A , Thu Trang Nguyen Hoang , Nguyen Thi Nguyen To , Ho Ngoc Dan Thanh , Nhu Pham Nguyen Quynh , Mahindroo Jaspreet , Thanh Pham Duy , Sandha Kawaljeet Singh , Baker Stephen , Taneja Neelam 
Published: December 2020

Abstract

Background
The emergence and spread of antimicrobial resistance (AMR) pose a major threat to the effective treatment and control of typhoid fever. The ongoing outbreak of extensively drug-resistant Salmonella Typhi (S. Typhi) in Pakistan has left azithromycin as the only remaining broadly efficacious oral antimicrobial for typhoid in South Asia. Ominously, azithromycin-resistant S. Typhi organisms have been subsequently reported in Bangladesh, Pakistan, and Nepal.

Methods
Here, we aimed to understand the molecular basis of AMR in 66 S. Typhi organisms isolated in a cross-sectional study performed in a suburb of Chandigarh in Northern India using whole-genome sequencing and phylogenetic analysis.

Results
We identified 7 S. Typhi organisms with the R717Q mutation in the acrB gene that was recently found to confer resistance to azithromycin in Bangladesh. Six out of the seven azithromycin-resistant S. Typhi isolates also exhibited triple mutations in gyrA (S83F and D87N) and parC (S80I) genes and were resistant to ciprofloxacin. These contemporary ciprofloxacin/azithromycin-resistant isolates were phylogenetically distinct from each other and from those reported from Bangladesh, Pakistan, and Nepal.

Conclusions
The independent emergence of azithromycin-resistant typhoid in Northern India reflects an emerging broader problem across South Asia and illustrates the urgent need for the introduction of typhoid conjugate vaccines in the region.
Clinical outcomes of peroral endoscopic myotomy for achalasia in children: a systematic review and meta-analysis
Authors: Zhong Chunyu , Tan Shali , Huang Shu , Peng Yan , Lü Muhan , Tang Xiaowei 
Published: December 2020

Abstract
Peroral endoscopic myotomy (POEM) is a novel minimally invasive intervention, which has shown to be effective and safe for treating achalasia in adults. Presently, POEM was also reported to be effective for achalasia in children. So we conducted this study to explore the clinical outcomes of POEM for pediatric achalasia. A systematic literature search in PubMed, Embase, and Cochrane databases was performed, which covered the period from January 2009 to June 2020. Selecting studies and collecting data was independently by two reviewers according to predefined criteria. The statistical analysis was carried out using Comprehensive Meta-Analysis software version 2 and Review Manager 5.3. A total of 11 studies with 389 children were identified in the final analysis. Pooled technical success of POEM treatment achalasia was achieved in 385 children (97.4%; 95% confidence interval [CI], 94.7%–98.7%), and the pooled clinical success was achieved in 348 children (92.4%; 95% CI, 89.0%–94.8%). After POEM, the Eckardt score was significantly decreased by 6.76 points (95% CI, 6.18–7.34, P &lt; 0.00001), and the lower esophageal sphincter pressure was significantly reduced by 19.38 mmHg (95% CI, 17.54–21.22, P &lt; 0.00001). The pooled major adverse events rate related to POEM was 12.8% (95% CI, 4.5%–31.5%) and the gastroesophageal reflux rate was 17.8% (95% CI, 14.2%–22.0%). Our current study demonstrated that the POEM was an effective and safe technique for treating achalasia in children. Further randomized comparative studies of POEM and other therapeutic methods are warranted to determine the most effective treatment modality for achalasia in children.
Cannabis induced cardiac arrhythmias: a case series
Authors: Yahud Ella , Paul Gideon , Rahkovich Michael , Vasilenko Lubov , Kogan Yonatan , Lev Eli , Laish-Farkash Avishag 
Published: December 2020

Abstract

Introduction
Cannabis use is known to be associated with significant cardiovascular morbidity. We describe three cases of cannabis-related malignant arrhythmias, who presented to the cardiac department at our institution within the last 2 years. All three patients were known to smoke cannabis on daily basis.

Case summaries
Case 1: A 30-year-old male, presented with recent onset of palpitations. A 12-lead electrocardiogram (ECG), transthoracic echocardiogram (TTE), and blood tests were all normal. During an inpatient exercise treadmill test (ETT) he developed polymorphic ventricular tachycardia (VT), which converted spontaneously to supraventricular tachycardia (SVT) in the recovery phase of the test. Subsequent risk stratification with cardiac magnetic resonance imaging and coronary angiography showed no abnormalities and an electrophysiological study was negative for sustained VT, however, SVT was easily induced with rapid conversion to atrial fibrillation. The patient successfully stopped smoking all tobacco products including cannabis and was treated with beta-blockers, with no further episodes of arrhythmia. Case 2: A 30-year-old male presented to the Emergency Department with palpitations, chest pain, and dizziness that improved during exertion. His initial ECG demonstrated complete atrioventricular block (AVB). Subsequent traces showed Mobitz Type I and second-degree AVB, which converted to atrial flutter after exertion. Routine blood tests, TTE, and an ETT were all normal and he was discharged home with no conduction abnormalities. Case 3: A 24-year-old male presented with two episodes of syncope. Baseline examination was normal, with an ECG showing a low atrial rhythm. Interrogation of his implantable loop recorder showed episodes of early morning bradycardia episodes with no associated symptoms.

Discussion
Cannabis-related arrhythmia can be multiform regarding their presentation. Therefore, ambiguous combinations of arrhythmia should raise suspicion of underlying cannabis abuse, where clinically appropriate. Although causality with regards to cannabis use cannot be proven definitively in these cases, the temporal relationship between drug use and the onset of symptoms suggests a strong association.
Acute liver failure and seizure: a case report of an unusual presentation of acute painless aortic dissection
Authors: Qiu Tian-Yu , See Jason Jia-Hao , Shi Haiyuan , Wong Yu-Jun 
Published: December 2020

Abstract

Background
Painless aortic dissection presenting with seizure and acute liver failure is uncommon. We described a case of early recognition leading to successful treatment of painless aortic dissection with atypical presentation.

Case summary
A young lady presented with generalized tonic-clonic seizures coupled with hepatitic pattern of deranged liver function test. Examination revealed blood pressure of 99/75 mmHg and hepatic flap. Electrocardiography showed sinus tachycardia. Urgent bedside echocardiography showed preserved cardiac function without significant valvular pathology, but noted a moderate pericardial effusion. Abdominal Ultrasound excluded liver cirrhosis or biliary obstructions. Viral hepatitis serologies and anti-liver panel were negative. She was progressively hypotensive with concurrent acute liver failure and oliguric acute kidney injury. Despite no chest pain, her rising serum troponin and widened mediastinum prompted an urgent computed-tomography aortogram, which showed a 4.3 cm dilatation of ascending thoracic aorta with acute haemopericardium and cardiac tamponade. She was diagnosed with malperfusion syndrome from Stanford type A aortic dissection. She underwent emergent ascending aorta and aortic arch repair and dialysis. She experienced complete recovery in her kidney, liver, and neurological function post-operatively.

Discussion
Painless aortic dissection masquerade as acute liver failure is uncommon. We describe a successful early recognition of malperfusion syndrome from painless aortic dissection, thus providing window for timely, life-saving intervention. Clinical challenges in this case include: (i) atypical presentation of aortic dissection, (ii) worsening acute liver failure which could lead to unnecessary liver transplantation, and (iii) risk of contrast-induced nephropathy in the setting of acute renal failure.
Vitamin K deficiency-induced spontaneous haemopericardium and cardiac tamponade in an infant with alpha-1 antitrypsin deficiency: a case report
Authors: Bauer Christoph , Furthner Désirée , Grohmann Eva , Tulzer Gerald 
Published: December 2020

Abstract

Background
Vitamin K deficiency bleeding is a life-threatening complication in early infancy. Exclusive breastfeeding and neonatal cholestasis syndromes, most notable α-1-antitrypsin deficiency, have been reported to be risk factors. Intracranial haemorrhage is most common. No association to haemopericardium has been reported before.

Case summary
We report on an 11 weeks old at term-born infant, who presented with severe anaemia and signs of cardiogenic shock. Immediately echocardiography was done and depicted cardiac tamponade. Pericardiocentesis was performed and a significant amount of haemorrhagic fluid was removed. Further workup revealed deranged coagulation parameters, cholestatic liver disease, and reduced α-1-antitrypsin levels. Despite normal brain sonography, a small cerebral haemorrhage was detected on magnetic resonance imaging. A genetic test finally proofed homozygotic mutation of the SERPINA1-gene and confirmed the diagnosis of α-1-antitrypsin deficiency as the underlaying cause. After initial replacement of coagulation factors, erythrocytes and vitamin K, the infant recovered. Eighteen weeks after discharge, the infant is still on vitamin K supplementation. She did not have any further bleedings and no neurologic or developmental impairment.

Discussion
Alpha-1-antitrypsin deficiency can lead to vitamin K deficiency in young infants even with adequate prophylaxis. Spontaneous haemorrhagic pericardial effusion was a new manifestation of vitamin K deficiency bleeding in our patient and should be considered and ruled out in young infants who present with acute anaemia and poor clinical condition.
Initiatives in primary school for the inclusion of a gender perspective
Authors: Accardo Silvana , Mangini Romina 
Published: December 2020

Abstract
This reflective piece seeks to show how teachers of English as a Foreign Language (EFL) in primary schools can include a gender perspective as a tool to promote and develop social transformation and reflection when integrating Comprehensive Sexuality Education (CSE) in their lessons using different literary materials. The development of a gender perspective involves a critical examination of power and unequal relations between sexed bodies. In the case of Argentina, the passing of Law 26,150 created a National CSE Program, which enforces the teaching of a responsible sexuality education from a gender and human rights perspective. This article describes some of the literary materials and initiatives that we, two EFL primary level teachers, have designed and implemented for the development of such perspective in our lessons following a critical and dialogical pedagogy. We hope these initiatives can help other EFL teachers carry out similar practices according to their contexts.
Choice Architecture in Shakespeare’s Public Meetings: Nudge Theory and Richard III, Coriolanus, and Julius Caesar
Authors: Sullivan Ceri 
Published: December 2020

Abstract
The political and dramatic intentions behind the use of appeals to the early modern public (on and off stage) have already been examined by Shakespeareans. This article points out the technical workings of such appeals by using two new areas of research on decision-making: the ethnography of public meetings and behavioural economics on how to influence choosers. These theories can illuminate the strategies used by the tribunes in handling the citizens of Coriolanus, by Antony in dealing with the plebeians in Julius Caesar, and by Buckingham and Richard when gathering support from the Londoners in Richard III. Using six common psychological biases (anchor-and-adjust, availability, representativeness, priming, arousal, and group norms), Shakespeare’s politicians prompt their hearers to change their minds: a celebrity warrior is recast as a wily tyrant, an execution as a murder, and a regent as the legitimate king.