bluuebunny/crossref_metadata_2025 huggingface dataset:
Evolution of diverse Hall effects during the successive magnetic phase transitions in Mn2.5Fe0.6Sn0.9 Kagome-lattice alloy
Authors: Liu Z H , Zhang Q Q , Zhang Y J , Zhang H G , Ma X Q , Liu E K
Published: December 2020

Evolution of diverse Hall effects due to successive magnetic transitions has been observed in Mn2.5Fe0.6Sn0.9 by suitable chemical substitution of Fe in Mn3.1Sn0.9. This noncollinear antiferromagnetic alloy exhibits a Neel temperature of 325 K. Upon cooling from 325 K, a magnetic phase transition from noncollinear antiferromagnetism to ferromagnetism occurs at 168 K due to the tilting of magnetization towards c axis. Above this temperature, anomalous Hall resistivity ranged from 0.6 to 1.3 μΩ cm has been observed in noncollinear antiferromagnetic state. Below this temperature, a topological Hall effect (THE) starts to appear due to the non-vanishing scalar spin chirality arising from the noncoplanar spin structure. Further decreasing temperature to 132 K, another magnetic transition happens, resulting in the coexistence of ferromagnetism and antiferromagnetism, so that a Hall plateau with large hysteresis below 70 K is yielded. A hysteresis as high as ∼80 kOe is obtained in ρ

xy
-H at 15 K. However, the Hall plateau disappears and only anomalous Hall effect (AHE) persists when further decreasing the temperature to 5 K. The present study provides a picture of diverse magneto-transport properties correlated to the variable spin structures driven by magnetic phase transitions.
The resistivity of high-Tc cuprates
Authors: Arouca R , Marino E C
Published: December 2020

We show that the resistivity in each phase of the high-Tc cuprates is a special case of a general expression derived from the Kubo formula. We obtain, in particular, the T-linear behavior in the strange metal and upper pseudogap phases, the pure T
2 Fermi liquid behavior observed in the strongly overdoped regime as well as in the mid-pseudogap phase. We also describe the

T

1
+
δ

behavior that interpolates the linear and quadratic behaviors in the crossover regime. We calculate the coefficients: (a) of T in the linear regime and show that it is proportional to the pseudogap transition temperature T
*(x); (b) of the T 
2-term in the Fermi Liquid regime, without adjusting any parameter; and (c) of the T
1.6 term in the crossover regime, all in excellent agreement with the experimental data. From our model, we are able to infer that the resistivity in cuprates is caused by the scattering of holes by excitons, which naturally form as holes are doped into the electron background.
Exceptional points in the one-dimensional Hubbard model
Authors: Rausch Roman , Peters Robert , Yoshida Tsuneya
Published: December 2020

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

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

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

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

Relationship 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

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

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

When 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

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

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 < 0.00001), and the lower esophageal sphincter pressure was significantly reduced by 19.38 mmHg (95% CI, 17.54–21.22, P < 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

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

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

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

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

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.
Electromechanical substrate characterization in arrhythmogenic cardiomyopathy using imaging-based patient-specific computer simulations
Authors: van Osta Nick , Kirkels Feddo , Lyon Aurore , Koopsen Tijmen , van Loon Tim , Cramer Maarten-Jan , Teske Arco J , Delhaas Tammo , Lumens Joost
Published: December 2020

Aims

Arrhythmogenic cardiomyopathy (AC) is an inherited cardiac disease, characterized by life-threatening ventricular arrhythmias and progressive cardiac dysfunction. The aim of this study is to use computer simulations to non-invasively estimate the individual patient’s myocardial tissue substrates underlying regional right ventricular (RV) deformation abnormalities in a cohort of AC mutation carriers.

Methods and results

In 68 AC mutation carriers and 20 control subjects, regional longitudinal deformation patterns of the RV free wall (RVfw), interventricular septum (IVS), and left ventricular free wall (LVfw) were obtained using speckle-tracking echocardiography. We developed and used a patient-specific parameter estimation protocol based on the multi-scale CircAdapt cardiovascular system model to create virtual AC subjects. Using the individual’s deformation data as model input, this protocol automatically estimated regional RVfw and global IVS and LVfw tissue properties. The computational model was able to reproduce clinically measured regional deformation patterns for all subjects, with highly reproducible parameter estimations. Simulations revealed that regional RVfw heterogeneity of both contractile function and compliance were increased in subjects with clinically advanced disease compared to mutation carriers without clinically established disease (17 ± 13% vs. 8 ± 4%, P = 0.01 and 18 ± 11% vs. 10 ± 7%, P < 0.01, respectively). No significant difference in activation delay was found.

Conclusion

Regional RV deformation abnormalities in AC mutation carriers were related to reduced regional contractile function and tissue compliance. In clinically advanced disease stages, a characteristic apex-to-base heterogeneity of tissue abnormalities was present in the majority of the subjects, with most pronounced disease in the basal region of the RVfw.
Mosaic Evolution of the Phosphopantothenate Biosynthesis Pathway in Bacteria and Archaea
Authors: Thomès Luc , Lescure Alain
Published: December 2020

Phosphopantothenate is a precursor to synthesis of coenzyme A, a molecule essential to many metabolic pathways. Organisms of the archaeal phyla were shown to utilize a different phosphopantothenate biosynthetic pathway from the eukaryotic and bacterial one. In this study, we report that symbiotic bacteria from the group Candidatus poribacteria present enzymes of the archaeal pathway, namely pantoate kinase and phosphopantothenate synthetase, mirroring what was demonstrated for Picrophilus torridus, an archaea partially utilizing the bacterial pathway. Our results not only support the ancient origin of the coenzyme A pathway in the three domains of life but also highlight its complex and dynamic evolution. Importantly, this study helps to improve protein annotation for this pathway in the C. poribacteria group and other related organisms.
Anthropological genetics perspectives on the transatlantic slave trade
Authors: Fortes-Lima Cesar , Verdu Paul
Published: December 2020

During the Trans-Atlantic Slave Trade (TAST), around twelve million Africans were enslaved and forcibly moved from Africa to the Americas and Europe, durably influencing the genetic and cultural landscape of a large part of humanity since the 15th century. Following historians, archaeologists, and anthropologists, population geneticists have, since the 1950’s mainly, extensively investigated the genetic diversity of populations on both sides of the Atlantic. These studies shed new lights into the largely unknown genetic origins of numerous enslaved-African descendant communities in the Americas, by inferring their genetic relationships with extant African, European, and Native American populations. Furthermore, exploring genome-wide data with novel statistical and bioinformatics methods, population geneticists have been increasingly able to infer the last 500 years of admixture histories of these populations. These inferences have highlighted the diversity of histories experienced by enslaved-African descendants, and the complex influences of socioeconomic, political, and historical contexts on human genetic diversity patterns during and after the slave trade. Finally, the recent advances of paleogenomics unveiled crucial aspects of the life and health of the first generation of enslaved-Africans in the Americas. Altogether, human population genetics approaches in the genomic and paleogenomic era need to be coupled with history, archaeology, anthropology, and demography in interdisciplinary research, to reconstruct the multifaceted and largely unknown history of the TAST and its influence on human biological and cultural diversities today. Here, we review anthropological genomics studies published over the past 15 years and focusing on the history of enslaved-African descendant populations in the Americas.
Tobacco smoking and mortality among Aboriginal and Torres Strait Islander adults in Australia
Authors: Thurber Katherine A , Banks Emily , Joshy Grace , Soga Kay , Marmor Alexandra , Benton Glen , White Sarah L , Eades Sandra , Maddox Raglan , Calma Tom , Lovett Raymond
Published: December 2020

Background

Despite generally high smoking prevalences, stemming from colonization, the relationship of smoking to mortality has not been quantified reliably in an Indigenous population. We investigate smoking and mortality among Aboriginal and Torres Strait Islander adults in Australia, where current adult daily smoking prevalence is 40.2%.

Methods

A prospective study of 1388 cardiovascular disease- and cancer-free Aboriginal adults aged ≥45 years, of the 267 153 45 and Up Study participants randomly sampled from the New South Wales general population over 2006–09. Questionnaire and mortality data were linked (through the Centre for Health Record Linkage) to mid-2019. Adjusted hazard ratios (called relative risks, RRs) for all-cause mortality—among current- and past- versus never-smokers—were estimated overall, by smoking intensity and by age at cessation. Smoking-attributable fractions and associated deaths were estimated.

Results

Over 14 586 person-years’ follow-up (median 10.6 years), 162 deaths accrued. Mortality RRs [95% confidence interval (CI)] were 3.90 (2.52–6.04) for current- and 1.95 (1.32–2.90) for past- versus never-smokers, with age heterogeneity. RRs increased with smoking intensity, to 4.29 (2.15–8.57) in current-smokers of ≥25 cigarettes/day. Compared with never-smokers, RRs were 1.48 (0.85–2.57) for those quitting at <45 years of age and 2.21 (1.29–3.80) at 45–54 years. Never-smokers lived an average >10 years longer than current-smokers. Around half of deaths among adults aged ≥45 years were attributable to smoking, exceeding 10 000 deaths in the past decade.

Conclusions

In this population, >80% of never-smokers would survive to 75 years, versus ∼40% of current-smokers. Quitting at all ages examined had substantial benefits versus continuing smoking; those quitting before age 45 years had mortality risks similar to never-smokers. Smoking causes half of deaths in older Aboriginal and Torres Strait Islander adults; Indigenous tobacco control must receive increased priority.
Spicy food consumption and risk of gastrointestinal-tract cancers: findings from the China Kadoorie Biobank
Authors: Chan Wing Ching , Millwood Iona Y , Kartsonaki Christiana , Du Huaidong , Guo Yu , Chen Yiping , Bian Zheng , Walters Robin G , Lv Jun , He Pan , Hu Chen , Li Liming , Yang Ling , Chen Zhengming ,   for the China Kadoorie Biobank (CKB) Collaborative Group
Published: December 2020

Background

Previous case–control studies have reported positive associations of spicy food consumption with risks of certain gastrointestinal-tract (GI) cancers. However, there is no prospective evidence on such associations, particularly from China, where there are high incidence rates of GI cancers and spicy food is widely consumed.

Methods

The prospective China Kadoorie Biobank study recruited >512 000 adults aged 30–79 years from 10 areas in China during 2004–2008; 2350 oesophageal, 3350 stomach and 3061 colorectal incident cancer cases were recorded by 1 January 2017, after a median of 10.1 years of follow-up. Cox regression yielded adjusted hazard ratios (HRs) for each cancer associated with spicy food intake.

Results

Overall, 30% of participants reported daily spicy food consumption at baseline. Spicy food consumption was inversely associated with oesophageal cancer risk, with adjusted HRs of 1.00, 0.88, 0.76, 0.84 and 0.81 for those who never/rarely consumed (reference) and consumed monthly, 1–2 days/week, 3–5 days/week and 6–7 days/week, respectively (ptrend < 0.002). The association remained similar after excluding the first 3 years of follow-up but appeared stronger in participants who did not smoke or drink alcohol regularly (ptrend < 0.0001). The corresponding HRs for stomach cancer were 1.00, 0.97, 0.95, 0.92 and 0.89 (ptrend = 0.04), with the association disappearing after excluding the first 3 years of follow-up. For colorectal cancer, the HRs were 1.00, 1.00, 0.95, 0.87 and 0.90, respectively (ptrend = 0.04) and the inverse association appeared to be restricted to rectal rather than colon cancer (pheterogeneity = 0.004). The types and strength of spice used showed little additional effects on these associations.

Conclusion

In Chinese adults, higher spicy food consumption was associated with lower risks of certain GI cancers, particularly among individuals who never smoked or drank alcohol regularly.
Role of new antibiotics for KPC-producingKlebsiella pneumoniae
Authors: Theuretzbacher Ursula , Carrara Elena , Conti Michela , Tacconelli Evelina
Published: December 2020

Klebsiella pneumoniae has accumulated a wide range of resistance determinants and has evolved into a difficult-to-treat pathogen that poses an increasing healthcare threat. KPC is an important marker for extensively drug-resistant (XDR) organisms with limited treatment options. In response to the medical need for new treatment options, several new antibiotics have been developed and registered recently. The β-lactamase inhibitor (BLI) combinations ceftazidime/avibactam, meropenem/vaborbactam and imipenem/relebactam, the cephalosporin–siderophore conjugate cefiderocol, the aminoglycoside derivative plazomicin and the tetracycline derivative eravacycline, focus on carbapenem-resistant Enterobacterales. These modified agents from old antibiotic classes illustrate the challenges of this requirement to address class-specific resistance mechanisms while critical gaps and some cross-resistance within a class, or to unrelated antibiotic classes, remain. The diverse molecular mechanisms and increasing diversification of carbapenem resistance among Klebsiella isolates requires improved rapid molecular diagnostic capabilities and stringent stewardship programmes to preserve the efficacy of new antibiotics for as long as possible.
Association between evidence-based training and clinician proficiency in electronic health record use
Authors: Hollister-Meadows Laura , Richesson Rachel L , Gagne Jennie De , Rawlins Neil
Published: December 2020

Objectives

The purpose of the study was to determine if association exists between evidence-based provider training and clinician proficiency in electronic health record (EHR) use and if so, which EHR use metrics and vendor-defined indices exhibited association.

Materials and Methods

We studied ambulatory clinicians’ EHR use data published in the Epic Systems Signal report to assess proficiency between training participants (n = 133) and nonparticipants (n = 14). Data were collected in May 2019 and November 2019 on nonsurgeon clinicians from 6 primary care, 7 urgent care, and 27 specialty care clinics. EHR use training occurred from August 5 to August 15, 2019, prior to EHR upgrade and organizational instance alignment. Analytics performed were descriptive statistics, paired t-tests, multivariate correlations, and hierarchal multiple regression.

Results

For number of appointments per 30-day reporting period, trained clinicians sustained an average increase of 16 appointments (P < .05), whereas nontrained clinicians incurred a decrease of 8 appointments. Only the trained clinician group achieved postevent improvement in the vendor-defined Proficiency score with an effect size characterized as moderate to large (dCohen = 0.625)

Discussion

Controversies exist on the return of investment from formal EHR training for clinician users. Previously published literature has mostly focused on qualitative data indicators of EHR training success. The findings of our EHR use training study identified EHR use metrics and vendor-defined indices with the capacity for translation into productivity and generated revenue measurements.

Conclusions

One EHR use metric and 1 vendor-defined index indicated improved proficiency among trained clinicians.
Extensive Evaluation via Blinded Testing of an UHPLC-MS/MS Method for Quantitation of Ten Ergot Alkaloids in Rye and Wheat Grains
Authors: Tkachenko Andriy , Benson Kelly , Mostrom Michelle , Guag Jake , Reimschuessel Renate , Webb Brett
Published: December 2020

Background

Ergot alkaloids are mycotoxins produced by the fungus Claviceps, which can contaminate grains and pose a health risk to humans and animals. Validation of an ergot alkaloid method in collaborative projects can be challenging due to instability of analytes, a lack of reliable reference materials, and a fully validated reference method.

Objective

To extensively evaluate performance of a quantitative UHPLC–MS/MS method to detect ten ergot alkaloids at concentrations between 16 and 500 ng/g in grains.

Method

The method performance was evaluated in the Blinded Method Test (BMT) exercise, which allowed organizers to successfully address the challenges. Forty completely blinded test samples were prepared in an independent laboratory and shipped to a participating laboratory to analyze on two separate days.

Results

Precision, accuracy, and HorRatr values met or exceeded the U.S. Food and Drug Administration recommendations. The design of the BMT exercise provided a high degree of confidence in data and conclusions drawn.

Conclusions

The method performed in a manner as expected, and the method can be used by the laboratory for routine testing of wheat and rye grains.

Highlights

BMT of laboratory methods facilitate validation of tests by evaluating performance in an unbiased manner.
PCBP2 Is Downregulated in Degenerating Neurons and Rarely Observed in TDP-43-Positive Inclusions in Sporadic Amyotrophic Lateral Sclerosis
Authors: Yoshimura Motoi , Honda Hiroyuki , Sasagasako Naokazu , Mori Shinichiro , Hamasaki Hideomi , Suzuki Satoshi O , Ishii Takashi , Ninomiya Toshiharu , Kira Jun-Ichi , Iwaki Toru
Published: December 2020

Various heterogeneous nuclear ribonucleoproteins (hnRNPs) are deposited in pathological inclusions of amyotrophic lateral sclerosis (ALS) and related diseases, such as frontotemporal lobar degeneration (FTLD). Recently, poly (rC)-binding protein 2 (PCBP2, hnRNP-E2), a member of the hnRNP family, was reported to be colocalized with transactivation-responsive DNA-binding protein 43 kDa (TDP-43)-immunopositive inclusions in cases of FTLD-TDP. Here, we used immunohistochemical methods to investigate PCBP1 and PCBP2 expression in the spinal cords of sporadic ALS patients, with special reference to TDP-43-positive inclusions. Thirty autopsy cases of sporadic ALS were examined by immunohistochemistry using antibodies against PCBP1, PCBP2, sequestosome 1 (p62), and TDP-43. In control subjects without neurological disorders, neurons predominantly expressed PCBP2, rather than PCBP1, in their cytoplasm and nuclei. Anterior horn cells of sporadic ALS patients often had various levels of PCBP2 expression, and motor neurons with skein-like inclusions often had reduced or lost cytoplasmic and nuclear PCBP2 staining. Notably, one case with FTLD-TDP subtype B pathology had marked colocalization of TDP-43 and PCBP2 in the cytoplasmic inclusions and dystrophic neurites of the cerebral cortex, hippocampus, and spinal cord. In conclusion, PCBP2 was reduced in anterior horn cells of sporadic ALS, but its occurrence in TDP-43 inclusions was a rare phenomenon.
The physical properties and evolution of the interacting system AM 1204−292
Authors: Rosa D A , Rodrigues I , Krabbe A C , Milone A C , Carvalho S
Published: December 2020

We investigate interaction effects in the stellar and gas kinematics, stellar population, and ionized gas properties of the interacting galaxy pair AM 1204−292,composed of NGC 4105 and NGC 4106. The data consist of long-slit spectra in the range 3000–7050 Å. The massive E3 galaxy NGC 4105 presents a flat stellar velocity profile, while the ionized gas is in strong rotation, suggesting an external origin. Its companion, NGC 4106, shows asymmetries in the radial velocity field, likely due to the interaction. The dynamics of the interacting pair were modelled using the P-Gadget3 treepm/sph code, from which we show that the system has just passed the first perigalacticum, which triggered an outbreak of star formation, currently at full maximum. We characterized the stellar population properties using the stellar population synthesis code starlight and, on average, both galaxies are predominantly composed of old stellar populations. NGC 4105 has a slightly negative age gradient, comparable with that of the most massive elliptical galaxies, but a steeper metallicity gradient. The SB0 galaxy NGC 4106 presents smaller radial variations in both age and metallicity in comparison with intermediate-mass early-type galaxies. These gradients have not been disturbed by interaction, since the star formation happened very recently and was not extensive in mass. Electron density estimates for the pair are systematically higher than those obtained in isolated galaxies. The central O/H abundances were obtained from photoionization models in combination with emission-line ratios, which resulted in 12 + log(O/H) = 9.03 ± 0.02 and 12 + log(O/H) = 8.69 ± 0.05 for NGC 4105 and NGC 4106, respectively.
A deep learning approach to test the small-scale galaxy morphology and its relationship with star formation activity in hydrodynamical simulations
Authors: Zanisi Lorenzo , Huertas-Company Marc , Lanusse François , Bottrell Connor , Pillepich Annalisa , Nelson Dylan , Rodriguez-Gomez Vicente , Shankar Francesco , Hernquist Lars , Dekel Avishai , Margalef-Bentabol Berta , Vogelsberger Mark , Primack Joel
Published: December 2020

Hydrodynamical simulations of galaxy formation and evolution attempt to fully model the physics that shapes galaxies. The agreement between the morphology of simulated and real galaxies, and the way the morphological types are distributed across galaxy scaling relations are important probes of our knowledge of galaxy formation physics. Here, we propose an unsupervised deep learning approach to perform a stringent test of the fine morphological structure of galaxies coming from the Illustris and IllustrisTNG (TNG100 and TNG50) simulations against observations from a subsample of the Sloan Digital Sky Survey. Our framework is based on PixelCNN, an autoregressive model for image generation with an explicit likelihood. We adopt a strategy that combines the output of two PixelCNN networks in a metric that isolates the small-scale morphological details of galaxies from the sky background. We are able to quantitatively identify the improvements of IllustrisTNG, particularly in the high-resolution TNG50 run, over the original Illustris. However, we find that the fine details of galaxy structure are still different between observed and simulated galaxies. This difference is mostly driven by small, more spheroidal, and quenched galaxies that are globally less accurate regardless of resolution and which have experienced little improvement between the three simulations explored. We speculate that this disagreement, that is less severe for quenched discy galaxies, may stem from a still too coarse numerical resolution, which struggles to properly capture the inner, dense regions of quenched spheroidal galaxies.