bluuebunny/crossref_metadata_2025 huggingface dataset:
Proteomic analysis of the effects of low salinity stress on liver of Naked carp (Gymnocyprinus przewalskii)
Authors: Qu Jiangqi , Yang Jianxin , Qi Hongfang , Chen Li , Zhang Qingjing
Published: August 2021

Naked carp is only distributed widely in Lake Qinghai. A unique feature of this species is its resistance to high salinity, which enables it to survive and adapt to the extreme environment of Lake Qinghai. Since Naked carp is an endangered species, we considered increasing its resources by reproduction and domestication measures in low salinity ponds. To investigate the molecular biological mechanism of the effects of low salinity stress on the liver of the cultured Naked carp, TMT markers combined with high-performance liquid chromatography-mass spectrometry (TMT-LC-MS/MS) were used to compare and analyze the difference in the expression of liver tissue protein between the cultured population (JH) and wild population (QH) in this study. Proteomic analysis results showed that 107 differential proteins were significantly expressed, and 102 of them were up-regulated. Functional and pathway enrichment analysis results found those differential proteins participate in molecular functions such as pyruvate kinase activity, alkali metal ion binding and potassium ion binding, and various biological processes of energy metabolism including glucose metabolism and lipid metabolism. Differential proteins were mainly concentrated in glycolysis and gluconeogenesis, retinol metabolism, linoleic acid metabolism, and steroid biosynthesis and lipid metabolism pathways.
Comprehensive evaluation of transmission network planning scheme for large scale new energy integration
Authors: Lu Yu , Shi Shengyao , Guo Yunfeng , Yang Jingying , Liu Peng , She Xin
Published: August 2021

The demand of large-scale new energy grid connection and transmission promotes the development of transmission network. In order to improve the accuracy of power grid planning scheme evaluation and select a better power grid planning scheme, a power grid planning scheme evaluation and optimization method based on analytic hierarchy process (AHP) is proposed. Firstly, the analytic hierarchy process (AHP) is used to establish the evaluation index system of power grid planning scheme, and the weight of each index is determined. Then, the evaluation index is taken as the input of entropy weight TOPSIS, and the relative paste progress C

i

+ of each scheme and positive ideal, and select the scheme with the largest paste progress as the most appropriate scheme. The results of case analysis show that the method can reasonably determine the weight of evaluation index, accurately evaluate the power grid planning scheme, and provide a scientific basis for the selection of power grid planning scheme.
Power System Planning and Thinking base on China’s “Carbon peak and carbon neutrality” Policy
Authors: Haishan Ke , Huawei He , Jing Ming , Yang Shen
Published: August 2021

China’s “dual-carbon” goal of “carbon peak and carbon neutrality” proposed in 2020 is a historical opportunity to promote the world’s technological revolution. The key to constructing a new power system lies in the diversified development and integration of power supply entities, substantially increasing the proportion of non-fossil energy utilization, building a smart and strong power grid and playing the role of a resource dispatch platform, strengthening technological research and forming a positive cycle of industry, education, research and application. It’s supposed to construct a carbon market system and mechanism for industry upgrading and elimination, while taking into account the issues of efficiency and fairness in the development process.
Study on Type Selection and Head Layout of Zhangzhou Long Crossing Tower
Authors: Xin Ye , Jingfeng Guo , Chengwu Wang , Yinhe Lin , Ming Xie , Xinxin Song
Published: August 2021

By comparing the schemes of combined angle steel and steel tube tower, the tower type of Zhangzhou long crossing tower was optimized, and through different tower head layout, the tower head types of long crossing tower and anchor tower were compared from the technical and economic aspects, in order to provide a certain practical significance for the design and application of long crossing tower.
Sintering behavior and mechanism of tungsten powders prepared by solution combustion synthesis combined with hydrogen reduction
Authors: Zhang Tianhao , Chen Pengqi , Yang Wen , Zhang Xiaodong
Published: August 2021

Nanosized tungsten powders were fabricated by solution combustion synthesis combined with hydrogen reduction. The powder had a size of 20 nm but possessed a large numbers of lattice defects. The fracture surface images at different temperatures show that the as-synthesized tungsten powder could be sintered via a pressureless process to relative density up to 95.78% at 1773 K. Kinetic analysis suggests that grain-boundary diffusion is one of the primary mechanisms of mass transport during the intermediate stage of sintering. The sintering properties are attributed to the ultrafine grain and the high sintering activation caused by the effect of the solution combustion synthesis method. It reveals in detail that the as-synthesized tungsten powder has a lower sintering activation energy compared to commercial nanosized tungsten powder, with a measured hardness of 633 HV.
Nanoparticles influence the herbicide diuron mediated toxicity on marine mussel Mytilus galloprovincialis: single and mixture exposure study
Authors: Bouzidi Imen , Sellami Badreddine , Mezni Amine , Hedfi Amor , Almalki Mohammed , Pacioglu Octvian , Boufahja Fehmi , Mougin Karine , Beyrem Hamouda
Published: August 2021

The exposure of habitats to the herbicide diuron, one of the most effective and highly used antifouling agents worldwide, leads to serious environmental toxicity, mainly for marine invertebrates. Moreover, nanoparticles (NPs) act as carriers of organic pollutants in marine ecosystems, thereby influencing their bioaccumulation and toxicity in exposed organisms. This study aimed to investigate the individual and combined toxicity of diuron and two NPs (ZnO NPs and TiO2 NPs) at sub-lethal doses on the marine mussel Mytilus galloprovincialis.
Finite quasi-quantum groups of rank two
Authors: Huang Hua-Lin , Liu Gongxiang , Yang Yuping , Ye Yu
Published: August 2021

This is a contribution to the structure theory of finite pointed quasi-quantum groups. We classify all finite-dimensional connected graded pointed Majid algebras of rank two which are not twist equivalent to ordinary pointed Hopf algebras.
Conflict of Interest in Research and Publication: Has the Pendulum Swung Too Far?
Authors: Glicksman Caroline
Published: August 2021

Traditionally scientists and industry have collaborated to contribute to the development of new drugs, biologics, and medical devices. Conflicts of interest (COI) may develop among surgeons and academic researchers, especially during the process of refinement of techniques and the marketing and sale of devices. Dramatic examples of COI occurred over the last 50 years, leading to strict regulations designed to reduce COI at research institutions. The International Committee of Medical Journal Editors created COI guidelines to help authors and editors ensure clear, reproducible, and unbiased medical articles. The Physician Payments Sunshine Act was designed to increase transparency of financial relationships between physicians and industry. However, in some cases authors and scientists are not obligated to fully disclose their COI. Only direct payments are required to be reported, not indirect payments to faculty at large academic institutions, allowing some to take advantage of the exceptions to the disclosure requirements whereas others must disclose payment for their work effort. Based on prominent scandals, regulations aimed at reducing industry influence in research and publication may fail to recognize the potential benefits of collaboration and produce a narrow-minded view of trust. Where should an editorial board or an academic institution draw the line?
O12 Artificial intelligence-based risk prediction for death after emergency laparotomy using multi slice contrast enhanced computerised tomography
Authors: Rahman S , Body S , Ligthart M , May-Miller P , Pucher P , Curtis N , West M
Published: July 2021

Introduction

Emergency laparotomy has a considerable mortality risk, with more than one in ten patients not surviving to discharge. Preoperative risk prediction using clinical tools is well established, however implemented variably. Preoperative CT is undertaken almost universally and contains granular data beyond diagnostics, including body composition, disease severity and other abstract features with the potential to enhance risk prediction. In this study we established the value of features extracted in an automated fashion from pre-operative CT in predicting 90-day post-surgery mortality.

Method

Anonymised CTs were collated from patients undergoing emergency laparotomy at ten hospitals in Southern England (2016–2017). For each case, axial portal venous abdominal/pelvic series were analysed using a pre-trained neural network, with each image converted into a matrix of numerical features. An elastic-net regression model to predict 90-day mortality was trained using these features and evaluated by bootstrapping with 1000 resampled datasets.

Result

A total of 136,709 images from 274 cases were available for analysis with a mean of 503 per case. Mortality within 90 days occurred in 34 cases (12.4%) with an average NELA mortality prediction of 8.5%. On internal (bootstrap) validation, the elastic net model derived from CT yielded excellent performance (AUC 0.903 95%CI 0.897–0.909), significantly in excess of the NELA risk calculator (AUC 0.809 95%CI 0.736–0.875), with a broader prediction range (0.01%-89.71%).

Conclusion

Artificial intelligence techniques applied to routinely performed cross-sectional imaging predicts emergency laparotomy mortality with greater accuracy than clinical data alone. Integration of these automated tools may be possible in the future.

Take-home Message

Automated analysis of CT can accurately predict risk of mortality after emergency laparotomy.
O16 Development of risk calculators for hand osteoarthritis and invasive treatment
Authors: Shah Karishma , Arden Nigel K , Silman Alan , Collins Gary S , Furniss Dominic
Published: July 2021

Aim

Develop a prediction model for incident radiographic IPJ osteoarthritis when multiple clinical risk factors are present.

Methods

This study used secondary analysis from the Chingford 1000 Women Study, a prospective cohort of women aged 45 to 64 years. At baseline, anthropometric, clinical, and lifestyle measured had been collected. Hand radiographs had been taken at baseline and 10 years, read using the Kellgren-Lawrence atlas. For the current study, participants with osteoarthritis (Kellgren-Lawrence ≥2) in any IPJ at baseline were excluded. Risk factors were selected from baseline based on biological plausibility, a published systematic review, and a Delphi study of Hand Surgeons. Incident osteoarthritis was diagnosed at 10 years if ≥ 1 IPJ was Kellgren-Lawrence ≥2. The model was built with logistic regression and elastic net penalisation, and performance assessed through discrimination (c-statistic) and calibration (c-slope). Complete case analysis was used.

Results

Of 1,003 participants, 459 participants were included in this study (median age: 51 years, 202 (44%) with IPJ osteoarthritis at follow-up). Manual occupation (P < 0.01), base of thumb osteoarthritis (P < 0.03), and older age (using a 3-knot spline) were the most important risk factors. C-statistic was 0.67 (0.62 to 0.72) and C-slope was 1.00 (0.68 to 1.34).

Conclusions

Osteoarthritis at the base of thumb and IPJs might be a continuum of the same disease. Knowledge of these modifiable and non-modifiable risk factors can inform prevention strategies.
O19 The effect of malnutrition on early outcomes after elective cancer surgery: an international prospective cohort study in 82 countries
Authors: Riad Aya M , Knight Stephen R , Ewen M ,   Harrison on behalf of GlobalSurg Collaborative
Published: July 2021

Introduction

Malnutrition is a key priority on the global health agenda, yet the impact of nutritional state on cancer surgery across income strata remains poorly described. This study aimed to determine the effect of malnutrition on early postoperative outcomes following elective surgery for colorectal or gastric cancer.

Method

Multicentre, international prospective cohort study of consecutive patients undergoing elective surgery for colorectal or gastric cancer. Malnutrition was defined using the Global Leadership Initiative on Malnutrition (GLIM) criteria. The primary outcome was death or major complication within 30 days of surgery. Multilevel logistic regression and three-way mediation analysis determined the relationship between country income group, nutritional status and early postoperative outcomes.

Result

This study included 5709 patients (4593 colorectal; 1116 gastric) from 381 hospitals in 75 countries. Severe malnutrition was present in one third of patients, with a disproportionate burden in upper middle (44%) and low/lower-middle income countries (64%). After adjustment for patient and hospital risk factors, severe malnutrition (aOR 1.62, 95% confidence interval 1.07 to 2.48; P = 0.024) was an independent predictor of 30-day mortality. However, major postoperative complications and surgical site infection rates were similar.

Conclusion

Severe malnutrition represents a high global burden in cancer surgery, particularly within low-income settings. Malnutrition is an independent risk-factor for 30-day mortality following elective surgery for colorectal or gastric cancer, suggesting perioperative nutritional interventions may improve early outcomes following cancer surgery.

Take-home Message

Severe malnutrition affects a large proportion of elective surgical oncology patients, with a significantly higher burden in low and middle income countries. Severe malnutrition is independently associated with increased 30-day mortality after cancer surgery.
O20 Quick, simple and just as effective—comparing pm: L3 ratio to NELA, P-POSSUM and NSQIP scores in assessing mortality risk for emergency laparotomy
Authors: Ming J Y , Holmes M , Pockney P , Gani J
Published: July 2021

Introduction

Multiple tools (NELA, P-POSSUM, ACS-NSQIP) are available to assess mortality risks in patients requiring emergency laparotomy(1–3), but they are time-consuming to perform and have had limited uptake in routine clinical practice in many countries(4). Simpler measures, including psoas muscle: L3 vertebrae (PM: L3) ratio(5,6), may be useful alternates. This measure is quick to perform, requiring no special skills or equipment apart from basic CT viewing software.

Method

We performed an analysis on all patients in the Hunter Emergency Laparotomy Audit (HELA) database, from January 2016 to December 2017. HELA is a retrospective review of all emergency laparotomy undertaken in a discrete area in NSW, Australia. Patients with an available CT abdomen were included (N = 500/562). A single slice axial CT image at the L3 endplate level was analysed using ImageJ® software to measure the area of L3 and bilateral psoas muscles. This can be done using normal PACS software in routine practice.

Result

PM: L3 ratios in this cohort have a mean of 1.082 (95%CI 1.042–1.122; range 0.141–3.934). PM: L3 ratio is significantly lower (P < 0.00001) in those patients who did not survive beyond 30 days (mean 0.865 [95% CI 0.746–0.984]) and 90 days (mean 0.888 [95%CI 0.768–1.008]) compared to patients that survived these periods (30 day mean 1.106 [95% vs. 1.033–1.179], 90 day mean 1.112 [95% CI 1.070–1.154]). These associations are similar to those calculated by established risk assessment models.

Conclusion

PM: L3 ratio is a reliable, quick and easy risk assessment tool to identify high risk patients undergoing emergency laparotomy.

Take-home Message

PM: L3 ratio is a reliable, quick and easy risk assessment tool to identify high risk patients undergoing emergency laparotomy. It is comparable to NELA, P-POSSUM and ACS-NSQIP.
O26 Intertumoural heterogeneity in the structure of the neurovascular unit in glioma: a retrospective observational cohort study
Authors: Keni S , Smith C , Thompson G , Brennan P M
Published: July 2021

Introduction

The neurovascular unit (NVU) is implicated in glioma tumourigenesis and treatment resistance but intertumoural heterogeneity is not well characterised. We evaluated the structure of the glioma NVU across tumour grades, in primary and recurrent disease. We determined association to overall survival.

Method

Ethics approval was obtained (15/ES/0094). A tissue microarray was constructed using biopsies from 137 patients and was immunostained for endothelial cells (CD31), extracellular matrix (collagen-IV), pericytes (PDGFR-β and α-SMA) and tight junctions (claudin-V). The immunostaining was assessed using QuPath software and compared by one-way analysis of variance with Tukey post-hoc testing. Association to overall survival was by univariate Cox regression with hazard ratios (HR).

Result

Primary grade IV tumours had greater CD31+ than grade II tumours (P = 0.046) or recurrent tumours (P = 0.013). After normalising to CD31+, collagen-IV+ was greater in recurrent tumours than in primary grade IV tumours (P = 0.013). PDGFR-β+ was greater in primary grade II tumours than in primary grade III tumours (P = 0.002), primary grade IV tumours (P < 0.001) or recurrent tumours (P < 0.001). Normalised α-SMA+ was greater in recurrent tumours than in primary grade IV tumours (P = 0.021). CD31 + (HR: 1.028, P = 0.004) and collagen-IV + (HR: 1.014, P = 0.008) were negative prognostic factors. After normalisation, PDGFR-β + (HR: 0.975, P = 0.004), α-SMA + (HR: 0.971, P = 0.020) and claudin-V + (HR: 0.994, P = 0.021) were positive prognostic factors.

Conclusion

Neurovascular remodeling is a feature of malignancy and recurrent tumours have altered neurovascular phenotypes. Markers for pericytes, extracellular matrix and tight junctions supplement classical grading features and predict tumour behavior.

Take-home Message

Neurovascular remodeling is a feature of malignancy and recurrent tumours have altered neurovascular phenotypes. Markers for pericytes, extracellular matrix and tight junctions supplement classical grading features and predict tumour behavior.
O28 Can styloid process and internal carotid artery anatomy be used to predict carotid artery dissection?
Authors: Cruddas L , Joffe M , Baker D
Published: July 2021

Introduction

Carotid artery dissection is a common cause of stroke in the young. It has been related to the association of the carotid artery with fixed neighbouring anatomical structures. This study assesses the association between styloid process length, internal carotid artery position and cervical carotid artery dissection (CCAD). This information would provide potential predicative radiological measurements, which could prevent delays in CCAD diagnosis.

Method

Retrospective data was collected from two central London hospitals over five years. CCAD cases were identified from individuals who underwent computer topography angiography (CTA) of the neck for suspected CCAD. The following data was collected: evidence of CCAD; bilateral styloid process length and presence of styloid-hyoid ligament calcification; bilateral styloid process-internal carotid distance; calcification of carotid arteries and whether their position was aberrant. Cases were dissection-side, age and gender matched with two non-dissection controls.

Result

Three hundred and fifty-five individuals were identified. Fifty individuals had CCAD, of which 4 had bilateral dissection. In individuals with CCAD, average styloid process length was 27.5 mm and styloid process-internal carotid distance was 5.14 mm. There was no significant association between styloid process length or styloid process-internal carotid distance, and CCAD when compared with matched controls. Internal carotid artery aberrancy was significant for non-dissection.

Conclusion

In this study, there was no association between styloid process length and styloid process-internal carotid distance with CCAD. These measurements can not be used to predict the possibility of a CCAD following trauma.

Take-home Message

Anatomy of the styloid process and calcification of the styloid-hyoid ligament are highly variable and many independent factors may contribute to the risk of cervical carotid artery dissection. Radiological measurements of the styloid process alone cannot be used to predict risk and likelihood of cervical carotid artery dissection.
Atypical twin atrioventricular nodal re-entrant tachycardia in a congenitally corrected transposition of the great arteries patient with a surgical repair of a ventricular septal defect: a case report
Authors: Gardey Kévin , Thevenard Rémi , Joly Hervé , Bessière Francis
Published: August 2021

Background

Twin atrioventricular (AV) nodal tachycardia is a rare mechanism of supraventricular arrhythmia, only seen in some specific congenital heart defects (CHD). It consists of a re-entrant circuit between two distinct AV nodes (anterior and inferior). Since both nodes have antegrade and retrograde conduction, there is usually two QRS morphologies in sinus rhythm.

Case summary

This case is about an atypical twin AV nodal tachycardia in a 15 years old patient with congenitally corrected transposition of the great arteries and previous history of a ventricular septal defect repair. The surgical closure was probably responsible of a poor antegrade conduction over the inferior AV node, which was responsible for a unique QRS morphology. He finally received a catheter ablation of the inferior AV node. He remained asymptomatic without anti-arrhythmic drugs at 8-months post-ablation.

Discussion

Twin AV nodal re-entrant tachycardia is a rare phenomenon. The presentation and electrophysiological study can be both atypical due to previous surgical repair. The operator should be aware of specific CHD where twin AV nodal re-entrant tachycardias are expected.
Neither cowardly nor greedy? Buying and selling escape from conscription in revolutionary and post-revolutionary France
Authors: Heuer Jennifer Ngaire
Published: August 2021

In late revolutionary and Napoleonic France, arranging for a paid substitute to fight in one’s place could be a straightforward contract. But it was also a vexed relationship; those who avoided fighting could appear cowardly and selfish and those who accepted money to risk their lives foolhardy or greedy. This article examines replacement from its uneasy institution with conscription in the late Revolution, through its apparent banalization under Napoleon, to its end with peace and a new government—and its quiet return as part of a new law on recruitment in 1818. This approach uncovers the centrality of ideas of family, free choice and sacrifice for both proponents and critics of the practice. It also shows how much the consequences of revolution and war reverberated long after peace was declared, as contemporaries wrestled with the ideological and practical legacies of obligatory military service and the contracts that had promised ways of escaping such service.
Quantifying the origin of membrane polarization
Authors: Li Qiuzi , Feng Lang , Cameron Stephen D , Deckman Harry W , Ertaş Deniz
Published: August 2021

There has been substantial interest in applying induced polarization phenomena, which broadly include electrode and membrane polarization, to characterize organic contamination and biogeochemical environments. Several phenomenological models, semi-quantitative models and models for particular pore shapes have been proposed for understanding membrane polarization. Here, we present a theoretical framework that directly relates membrane polarization to intrinsic statistical properties of porous materials through a two-point correlation function of fixed charges in the pore space. Our framework provides a new way of modelling complex pore structures with a few statistical parameters and quantifies how two distinct physical processes drive complex conductivity response in the absence of conducting grains. One process is a coupling of the static inhomogeneous conductivity to the induced oscillatory electric field, whereas the second process is a coupling of the static electric field to the induced conductivity modulation. Including both effects, we quantitatively predict the frequency-dependent membrane polarization and show excellent agreement between our predictions and experiments in model porous materials.
Evaluation of three approaches for simulating 3-D time-domain electromagnetic data
Authors: Rochlitz Raphael , Seidel Marc , Börner Ralph-Uwe
Published: August 2021

We implemented and compared the implicit Euler time-stepping approach, the inverse Fourier transform-based approach and the Rational Arnoldi method for simulating 3-D transient electromagnetic data. We utilize the finite-element method with unstructured tetrahedral meshes for the spatial discretization supporting irregular survey geometries and anisotropic material parameters. Both, switch-on and switch-off current waveforms, can be used in combination with direct current solutions of Poisson problems as initial conditions. Moreover, we address important topics such as the incorporation of source currents and opportunities to simulate impulse as well as step response magnetic field data with all approaches for supporting a great variety of applications. Three examples ranging from simple to complex real-world geometries and validations against external codes provide insight into the numerical accuracy, computational performance and unique characteristics of the three applied methods. We further present an application of logarithmic Fourier transforms to convert transient data into the frequency domain. We made all approaches available in the open-source Python toolbox custEM, which previously supported only frequency-domain electromagnetic data. The object-oriented software implementation is suited for further elaboration on distinct modelling topics and the presented examples can serve for benchmarking other codes.
Catholics at Ground Zero: Negotiating (Post) Memory
Authors: McClelland Gwyn
Published: July 2021

As atomic eyewitness memory passes on, and the hibakusha (atomic-bomb survivor) population dwindles, their trauma is increasingly communicated and negotiated by new generations. After the hibakusha, various protagonists are picking up the baton to continue telling the story of Nagasaki, some children of hibakusha and others not. More than seventy-five years after the bomb ‘postmemory’ describes the future of memory after the eyewitnesses are no longer present. Marianne Hirsch introduced this term with the aftermath of the Jewish Holocaust in mind to suggest both continuity and rupture. It has subsequently been used in many other contexts. Here postmemory is applied to the communal memorializing of the atomic bomb event in Nagasaki. Processes of imaginative ‘memory work’ co-create postmemory (in Japanese parlance ni-sei/san-sei or second and third-generation discourse), influencing public history via the Catholic and surrounding community. By observing traces of a multifarious history, including Chinese, Korean, and European influences, and through the lens of emerging postmemory, in this article I reconsider the place of Nagasaki in atomic history.
Fictional Creations
Authors: Steenhagen Maarten
Published: August 2021

Many people assume that fictional entities are encapsulated in the world of fiction. I show that this cannot be right. Some works of fiction tell us about pieces of poetry, music, or theatre written by fictional characters. Such creations are fictional creations, as I call them. Their authors do not exist. But that does not take away that we can perform, recite, or otherwise generate actual instances of such works. This means we can bring such individuals actually into existence, as the works they are. I conclude that the assumption about encapsulation is untenable, unless an exception is made for types.
False detection of rifampicin resistance using Xpert® MTB/RIF Ultra assay due to an A451V mutation in Mycobacterium tuberculosis
Authors: Fitzgibbon Margaret M , Roycroft Emma , Sheehan Gerard , Mc Laughlin Anne-Marie , Quintyne Keith Ian , Brabazon Elaine , O’Meara Mary , Flanagan Peter R , Seagar A -Louise , Laurenson Ian F , Keane Joseph , Rogers Thomas R
Published: July 2021

Background

In a 12 month period, three Irish-born adult cases with pulmonary TB were initially diagnosed by Xpert® MTB/RIF Ultra assay, which detected a rifampicin resistance-conferring mutation prompting treatment as potential MDR cases.

Methods

Further laboratory investigations on the cultured isolates included GenoType MTBDRplus assay, phenotypic drug susceptibility tests using the BD BACTEC MGIT culture system and MIC broth microdilution tests. Sequencing of the rpoB gene was performed using Sanger sequencing and WGS.

Results

Phenotypic drug susceptibility tests determined the isolates to be rifampicin susceptible. Molecular investigations identified an A451V (codon 532) mutation in the Mycobacterium tuberculosis rpoB gene that has not previously been found to cause rifampicin resistance. Genome sequencing revealed that the three isolates’ genomes differed by ≤5 SNPs, indicating a high likelihood of recent transmission events. Furthermore, a cluster of six related M. tuberculosis isolates from our in-house typing database showed four were highly related; all were rifampicin susceptible and lacked this mutation.

Conclusions

False detection of rifampicin resistance, albeit rare, should be considered possible with Xpert® MTB/RIF Ultra assay, particularly in low TB incidence settings. Confirmatory sequencing methods should be performed to prevent the unnecessary use of second-line anti-tuberculous drugs.
DOPE: D-Optimal Pooling Experimental design with application for SARS-CoV-2 screening
Authors: Daon Yair , Huppert Amit , Obolski Uri
Published: July 2021

Objective

Testing individuals for the presence of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the pathogen causing the coronavirus disease 2019 (COVID-19), is crucial for curtailing transmission chains. Moreover, rapidly testing many potentially infected individuals is often a limiting factor in controlling COVID-19 outbreaks. Hence, pooling strategies, wherein individuals are grouped and tested simultaneously, are employed. Here, we present a novel pooling strategy that builds on the Bayesian D-optimal experimental design criterion.

Materials and Methods

Our strategy, called DOPE (D-Optimal Pooling Experimental design), is built on a novel Bayesian formulation of pooling. DOPE defines optimal pooled tests as those maximizing the mutual information between data and infection states. We estimate said mutual information via Monte-Carlo sampling and employ a discrete optimization heuristic to maximize it.

Results

We compare DOPE to other, commonly used pooling strategies, as well as to individual testing. DOPE dominates the other strategies as it yields lower error rates while utilizing fewer tests. We show that DOPE maintains this dominance for a variety of infection prevalence values.

Discussion

DOPE has several additional advantages over common pooling strategies: it provides posterior distributions of the probability of infection rather than only binary classification outcomes; it naturally incorporates prior information of infection probabilities and test error rates; and finally, it can be easily extended to include other, newly discovered information regarding COVID-19.

Conclusion

DOPE can substantially improve accuracy and throughput over current pooling strategies. Hence, DOPE can facilitate rapid testing and aid the efforts of combating COVID-19 and other future pandemics.
Electronic health record note review in an outpatient specialty clinic: who is looking?
Authors: Chen Jimmy S , Hribar Michelle R , Goldstein Isaac H , Rule Adam , Lin Wei-Chun , Dusek Haley , Chiang Michael F
Published: July 2021

Note entry and review in electronic health records (EHRs) are time-consuming. While some clinics have adopted team-based models of note entry, how these models have impacted note review is unknown in outpatient specialty clinics such as ophthalmology. We hypothesized that ophthalmologists and ancillary staff review very few notes. Using audit log data from 9775 follow-up office visits in an academic ophthalmology clinic, we found ophthalmologists reviewed a median of 1 note per visit (2.6 ± 5.3% of available notes), while ancillary staff reviewed a median of 2 notes per visit (4.1 ± 6.2% of available notes). While prior ophthalmic office visit notes were the most frequently reviewed note type, ophthalmologists and staff reviewed no such notes in 51% and 31% of visits, respectively. These results highlight the collaborative nature of note review and raise concerns about how cumbersome EHR designs affect efficient note review and the utility of prior notes in ophthalmic clinical care.
FIBER: enabling flexible retrieval of electronic health records data for clinical predictive modeling
Authors: Datta Suparno , Sachs Jan Philipp , FreitasDa Cruz Harry , Martensen Tom , Bode Philipp , Morassi Sasso Ariane , Glicksberg Benjamin S , Böttinger Erwin
Published: August 2021

Objectives

The development of clinical predictive models hinges upon the availability of comprehensive clinical data. Tapping into such resources requires considerable effort from clinicians, data scientists, and engineers. Specifically, these efforts are focused on data extraction and preprocessing steps required prior to modeling, including complex database queries. A handful of software libraries exist that can reduce this complexity by building upon data standards. However, a gap remains concerning electronic health records (EHRs) stored in star schema clinical data warehouses, an approach often adopted in practice. In this article, we introduce the FlexIBle EHR Retrieval (FIBER) tool: a Python library built on top of a star schema (i2b2) clinical data warehouse that enables flexible generation of modeling-ready cohorts as data frames.

Materials and Methods

FIBER was developed on top of a large-scale star schema EHR database which contains data from 8 million patients and over 120 million encounters. To illustrate FIBER’s capabilities, we present its application by building a heart surgery patient cohort with subsequent prediction of acute kidney injury (AKI) with various machine learning models.

Results

Using FIBER, we were able to build the heart surgery cohort (n = 12 061), identify the patients that developed AKI (n = 1005), and automatically extract relevant features (n = 774). Finally, we trained machine learning models that achieved area under the curve values of up to 0.77 for this exemplary use case.

Conclusion

FIBER is an open-source Python library developed for extracting information from star schema clinical data warehouses and reduces time-to-modeling, helping to streamline the clinical modeling process.
An exploratory data quality analysis of time series physiologic signals using a large-scale intensive care unit database
Authors: Afshar Ali S , Li Yijun , Chen Zixu , Chen Yuxuan , Lee Jae Hun , Irani Darius , Crank Aidan , Singh Digvijay , Kanter Michael , Faraday Nauder , Kharrazi Hadi
Published: August 2021

Physiological data, such as heart rate and blood pressure, are critical to clinical decision-making in the intensive care unit (ICU). Vital signs data, which are available from electronic health records, can be used to diagnose and predict important clinical outcomes; While there have been some reports on the data quality of nurse-verified vital sign data, little has been reported on the data quality of higher frequency time-series vital signs acquired in ICUs, that would enable such predictive modeling. In this study, we assessed the data quality issues, defined as the completeness, accuracy, and timeliness, of minute-by-minute time series vital signs data within the MIMIC-III data set, captured from 16009 patient-ICU stays and corresponding to 9410 unique adult patients. We measured data quality of four time-series vital signs data streams in the MIMIC-III data set: heart rate (HR), respiratory rate (RR), blood oxygen saturation (SpO2), and arterial blood pressure (ABP). Approximately, 30% of patient-ICU stays did not have at least 1 min of data during the time-frame of the ICU stay for HR, RR, and SpO2. The percentage of patient-ICU stays that did not have at least 1 min of ABP data was ∼56%. We observed ∼80% coverage of the total duration of the ICU stay for HR, RR, and SpO2. Finally, only 12.5%%, 9.9%, 7.5%, and 4.4% of ICU lengths of stay had ≥ 99% data available for HR, RR, SpO2, and ABP, respectively, that would meet the three data quality requirements we looked into in this study. Our findings on data completeness, accuracy, and timeliness have important implications for data scientists and informatics researchers who use time series vital signs data to develop predictive models of ICU outcomes.
Comparison of early warning scores for sepsis early identification and prediction in the general ward setting
Authors: Yu Sean C , Shivakumar Nirmala , Betthauser Kevin , Gupta Aditi , Lai Albert M , Kollef Marin H , Payne Philip R O , Michelson Andrew P
Published: August 2021

The objective of this study was to directly compare the ability of commonly used early warning scores (EWS) for early identification and prediction of sepsis in the general ward setting. For general ward patients at a large, academic medical center between early-2012 and mid-2018, common EWS and patient acuity scoring systems were calculated from electronic health records (EHR) data for patients that both met and did not meet Sepsis-3 criteria. For identification of sepsis at index time, National Early Warning Score 2 (NEWS 2) had the highest performance (area under the receiver operating characteristic curve: 0.803 [95% confidence interval [CI]: 0.795–0.811], area under the precision recall curves: 0.130 [95% CI: 0.121–0.140]) followed NEWS, Modified Early Warning Score, and quick Sequential Organ Failure Assessment (qSOFA). Using validated thresholds, NEWS 2 also had the highest recall (0.758 [95% CI: 0.736–0.778]) but qSOFA had the highest specificity (0.950 [95% CI: 0.948–0.952]), positive predictive value (0.184 [95% CI: 0.169–0.198]), and F1 score (0.236 [95% CI: 0.220–0.253]). While NEWS 2 outperformed all other compared EWS and patient acuity scores, due to the low prevalence of sepsis, all scoring systems were prone to false positives (low positive predictive value without drastic sacrifices in sensitivity), thus leaving room for more computationally advanced approaches.
ETV4 mediates the Wnt/β-catenin pathway through transcriptional activation of ANXA2 to promote hepatitis B virus-associated liver hepatocellular carcinoma progression
Authors: Sun Tianfeng , Zhang Jing
Published: August 2021

ETS variant 4 (ETV4) has been implicated in the development of various cancers. However, the molecular events mediated by ETV4 in liver cancer are poorly understood, especially in hepatitis B virus (HBV)-associated liver hepatocellular carcinoma (LIHC). Here, we aimed to identify the target involved in ETV4-driven hepatocarcinogenesis. Bioinformatics analysis revealed that ETV4 was highly expressed in patients with HBV-associated LIHC, and HBV infection promoted the expression of ETV4 in LIHC cells. Inhibition of ETV4 repressed the proliferation, migration, invasion of LIHC cells and suppressed the secretion of HBV and the replication of HBV DNA. ANXA2 expression in LIHC patients was positively correlated with ETV4 expression. Chromatin immunoprecipitation and dual-luciferase reporter assays revealed that ETV4 elevated the ANXA2 expression at the transcriptional level by binding to the ANXA2 promoter. Overexpression of ANXA2 reversed the inhibitory effect of sh-ETV4 on the malignant biological behaviours of HBV-infected LIHC cells by activating the Wnt/β-catenin pathway. In conclusion, ETV4 mediates the activation of Wnt/β-catenin pathway through transcriptional activation of ANXA2 expression to promote HBV-associated LIHC progression.
Traminines A and B, produced by Fusarium concentricum, inhibit oxidative phosphorylation in Saccharomyces cerevisiae mitochondria
Authors: Sakai Katsuyuki , Unten Yufu , Kimishima Aoi , Nonaka Kenichi , Chinen Takumi , Sakai Kazunari , Usui Takeo , Shiomi Kazuro , Iwatsuki Masato , Murai Masatoshi , Miyoshi Hideto , Asami Yukihiro , Ōmura Satoshi
Published: July 2021

Two new tetramic acid derivatives, traminines A (1) and B (2), were isolated from a culture broth of Fusarium concentricum FKI-7550 by bioassay-guided fractionation using multidrug-sensitive Saccharomyces cerevisiae 12geneΔ0HSR-iERG6. The chemical structures of 1 and 2 were elucidated by NMR studies. Compounds 1 and 2 inhibited the growth of the multidrug-sensitive yeast strain on nonfermentable medium containing glycerol, but not on fermentable medium containing glucose. These results strongly suggest that they target mitochondrial machineries presiding over ATP production via oxidative phosphorylation. Throughout the assay monitoring overall ADP-uptake/ATP-release in yeast mitochondria, 1 and 2 were shown to inhibit one or more enzymes involving oxidative phosphorylation. Based on biochemical characterization, we found that the interference with oxidative phosphorylation by 1 is attributable to the dual inhibition of complex III and FoF1-ATPase, whereas that by 2 is solely due to the inhibition of complex III.
Demodex folliculorum (Trombidiformes: Demodicidae) and Demodex brevis Prevalence in an Extreme Environment of Chile
Authors: Gutiérrez Bessy , Soto Rodrigo , Catalán Alejandro , Araya Jorge E , Fuentes Margarita , González Jorge
Published: July 2021

The prevalence of mites of the genus Demodex and their associations with host age, gender, workplace, and comorbid skin and ocular conditions were studied in participants in Antofagasta, Chile, which is in a region with an extreme environment. We examined 680 participants aged 18–88 yr using standardized surface skin biopsies. Among them, Demodex had a prevalence of 13.5 % (95% confidence interval, 10.88–16.17). A slightly higher prevalence was observed in males (51.1%; 95% confidence interval, 40.9–61.3; nonsignificant) and participants in the 69–88 yr age group (50.0%; 95% confidence interval, 23.8–76.2; P < 0.05). Regarding the species involved, Demodex folliculorum was found in 89.1% (CI 82.7–95.5) of cases, while D. brevis was found in the remaining 10.9% of cases. A higher prevalence (25.0% CI 16.1–33.91) was observed in participants who worked indoors in generally enclosed and dust-rich environments (such as theaters, libraries, and administrative offices). There was also a strong association between Demodex prevalence and conjunctival hyperemia, with 35.9% (95% confidence interval, 9.1–35; OR 17.9) of the Demodex positive participants having this pathology compared to 10.3% of the noninfested participants. In summary, the prevalence of Demodex in Antofagasta, Chile (13.5%) was toward the lower end of the range reported among other regions around the world. Environmental factors such as exposure to the sun (including ultraviolet rays) or environmental pollution may affect the mites. In addition, Demodex genetics (related to virulence) and the ocular or skin microbiota may positively or negatively influence infestation and pathology.
Neighborhood-Based Socioeconomic Determinants of Cognitive Impairment in Zambian Children With HIV: A Quantitative Geographic Information Systems Approach
Authors: Buda Alexandra , Dean Owen , Adams Heather R , Mwanza-Kabaghe Sylvia , Potchen Michael J , Mbewe Esau G , Kabundula Pelekelo P , Mweemba Milimo , Matoka Beauty , Mathews Manoj , Menon J Anitha , Wang Bo , Birbeck Gretchen L , Bearden David R
Published: August 2021

Background

Place-based inequalities, such as exposure to violence and access to nutritious food and clean water, may contribute to human immunodeficiency virus (HIV)-associated cognitive impairment. In this study, we investigated neighborhood effects on cognition in children and adolescents with HIV in Lusaka, Zambia.

Methods

We conducted a prospective cohort study of 208 children with perinatally acquired HIV (ages 8–17) and 208 HIV-exposed uninfected controls. Participants underwent neuropsychological testing and interviews assessing socioeconomic status. Geographic regions with clusters of participants with HIV and cognitive impairment were identified using quantitative geographic information systems (QGIS) and SaTScan. Associations between location of residence and cognitive function were evaluated in bivariable and multivariable regression models. Mediation analysis was performed to assess direct and indirect effects of location of the residence on cognitive impairment.

Results

Residence in Chawama, one of the poorest neighborhoods in Lusaka, was significantly associated with cognitive impairment in participants with HIV (odds ratio 2.9; P = .005) and remained significant in a multivariable regression model controlling for potential confounders. Mediation analysis found that 46% of the cognitive effects of residence in Chawama were explained by higher rates of malnutrition, lower school attendance, and poorer self-reported health.

Conclusions

Place-based socioeconomic inequality contributes to cognitive impairment in Zambian children and adolescents with HIV. Neighborhood effects may be mediated by concentrated poverty, malnutrition, limited access to education and health care, and other yet unknown environmental factors that may be potentially modifiable.
The Three Parts of Emotions (3-Component Model)
Authors: Thompson-Brenner Heather , Smith Melanie , Brooks Gayle , Franklin Dee Ross , Espel-Huynh Hallie , Boswell James F.
Published: August 2021

During this session, clients learn about the three components of emotions, which are thoughts, physical sensations, and behaviors/urges. This information is the backbone of the work clients will do to identify their emotions and get ready to change how they approach and experience them. To help clients identify the three parts of an emotional experience, this treatment program uses the 3-Component Model. The three parts interact with one another, and the 3-Component Model uses two-way arrows from each part to the other parts to illustrate how they all affect one another. The EDA form can be useful to identify when strong emotions occurred recently, and the 3-Component Model form is useful to understand and label the thoughts, physical sensations, and behaviors that made up this emotional experience.