bluuebunny/crossref_metadata_2025 huggingface dataset:
AEON.py: Python library for attractor analysis in asynchronous Boolean networks
Authors: Beneš Nikola , Brim Luboš , Huvar Ondřej , Pastva Samuel , Šafránek David , Šmijáková Eva
Published: September 2022

AEON.py is a Python library for the analysis of the long-term behaviour in very large asynchronous Boolean networks. It provides significant computational improvements over the state-of-the-art methods for attractor detection. Furthermore, it admits the analysis of partially specified Boolean networks with uncertain update functions. It also includes techniques for identifying viable source-target control strategies and the assessment of their robustness with respect to parameter perturbations.

Availability and implementation

All relevant results are available in Supplementary Materials. The tool is accessible through https://github.com/sybila/biodivine-aeon-py.

Supplementary information

Supplementary data are available at Bioinformatics online.
ScanExitronLR: characterization and quantification of exitron splicing events in long-read RNA-seq data
Authors: Fry Joshua , Li Yangyang , Yang Rendong
Published: September 2022

Exitron splicing is a type of alternative splicing where coding sequences are spliced out. Recently, exitron splicing has been shown to increase proteome plasticity and play a role in cancer. Long-read RNA-seq is well suited for quantification and discovery of alternative splicing events; however, there are currently no tools available for the detection and annotation of exitrons in long-read RNA-seq data. Here, we present ScanExitronLR, an application for the characterization and quantification of exitron splicing events in long-reads. From a BAM alignment file, reference genome and reference gene annotation, ScanExitronLR outputs exitron events at the individual transcript level. Outputs of ScanExitronLR can be used in downstream analyses of differential exitron splicing. In addition, ScanExitronLR optionally reports exitron annotations such as truncation or frameshift type, nonsense-mediated decay status and Pfam domain interruptions. We demonstrate that ScanExitronLR performs better on noisy long-reads than currently published exitron detection algorithms designed for short-read data.

Availability and implementation

ScanExitronLR is freely available at https://github.com/ylab-hi/ScanExitronLR and distributed as a pip package on the Python Package Index.

Supplementary information

Supplementary data are available at Bioinformatics online.
SQuAPP—simple quantitative analysis of proteins and PTMs
Authors: Ergin Enes K , Uzozie Anuli C , Chen Siyuan , Su Ye , Lange Philipp F
Published: September 2022

The comprehensive analysis of the proteome and its modulation by post-translational modification (PTM) is increasingly used in biological and biomedical studies. As a result, proteomics data analysis is ever more carried out by scientists with limited expertise in this type of data. While excellent software solutions for comprehensive and rigorous analysis of quantitative proteomic data exist, most are complex and not well suited for non-proteomics scientists. Integrative analysis of multi-level proteomics data on protein and diverse PTMs, like phosphorylation or proteolytic processing, remains particularly challenging and inaccessible to most biologists. To fill this void, we developed SQuAPP, an R-Shiny web-based analysis pipeline for the quantitative analysis of proteomic data. SQuAPP uses a streamlined workflow model to guide expert and novice users through quality control, data pre-processing, statistical analysis and visualization steps. Processing the protein, peptide and PTM datasets in parallel and their quantitative integration enable rapid identification of protein-level-independent modulation of protein modifications and intuitive interpretation of dynamic dependencies between different protein modifications.

Availability and implementation

SQuAPP is available at http://squapp.langelab.org/. The source code and local setup instructions can be accessed from https://github.com/LangeLab/SQuAPP.
Efficient maximum power point tracker based on neural network and sliding-mode control for buck converters
Authors: Attia Hussain , Hossin Khaled
Published: September 2022

This paper presents detailed design steps of an effective control system aiming to increase the solar energy harvested via photovoltaic power-generation systems. The design of an intelligent maximum power point tracker (MPPT) supported by a robust sliding-mode (SM) controller is discussed in this study. The proposed control scheme is designed to track the MPP and provide a smooth system response by removing the overshoot in the load current during any variation in the connected load. Such a system is suitable for DC–DC buck converter applications. The study begins with modelling the buck converter for a continuous current mode operation. The reference voltage of the tracking system is produced by the proposed neural network (NN) algorithm. The proposed intelligent MPPT integrated with an SM controller is simulated in a MATLAB®/Simulink® platform. The simulation results are analysed to investigate and confirm the satisfaction level of the adopted four-serially connected PV-modules system. The system performance is evaluated at a light intensity of 500 W/m2 and an ambient temperature of 25°C. Applying only the proposed NN algorithm guarantees the MPP tracking response by delivering 100 W at a resistive load of 13 Ω, and 200 W at a load of 6.5 Ω, respectively, with 99.77% system efficiency. However, this simultaneously demonstrates a current spike of ~0.5 A when the load is varied from 50% to 100%. The integrated SM controller demonstrates a robust and smooth response, eliminating the existing current spike.
A neural stem cell paradigm of pediatric hydrocephalus
Authors: Duy Phan Q , Rakic Pasko , Alper Seth L , Robert Stephanie M , Kundishora Adam J , Butler William E , Walsh Christopher A , Sestan Nenad , Geschwind Daniel H , Jin Sheng Chih , Kahle Kristopher T
Published: September 2022

Pediatric hydrocephalus, the leading reason for brain surgery in children, is characterized by enlargement of the cerebral ventricles classically attributed to cerebrospinal fluid (CSF) overaccumulation. Neurosurgical shunting to reduce CSF volume is the default treatment that intends to reinstate normal CSF homeostasis, yet neurodevelopmental disability often persists in hydrocephalic children despite optimal surgical management. Here, we discuss recent human genetic and animal model studies that are shifting the view of pediatric hydrocephalus from an impaired fluid plumbing model to a new paradigm of dysregulated neural stem cell (NSC) fate. NSCs are neuroprogenitor cells that comprise the germinal neuroepithelium lining the prenatal brain ventricles. We propose that heterogenous defects in the development of these cells converge to disrupt cerebrocortical morphogenesis, leading to abnormal brain–CSF biomechanical interactions that facilitate passive pooling of CSF and secondary ventricular distention. A significant subset of pediatric hydrocephalus may thus in fact be due to a developmental brain malformation leading to secondary enlargement of the ventricles rather than a primary defect of CSF circulation. If hydrocephalus is indeed a neuroradiographic presentation of an inborn brain defect, it suggests the need to focus on optimizing neurodevelopment, rather than CSF diversion, as the primary treatment strategy for these children.
An Investigative Review for Pharmaceutical Analysis of Fenofibrate
Authors: Saha Moumita , Dhiman Shubham , Gupta G D , Asati Vivek
Published: September 2022

HMG-CoA reductase inhibitors (statins), lipoprotein lipase activators (PPARα agonists) or fibrates are commonly used for controlling increased lipid levels in hyperlipidemia. Fenofibrate (FEN) belongs to the second generation prodrug fibric acid (isobutyric acid) derivative belonging to lipoprotein lipase activator class of drug. Results of clinical studies suggest that FEN can substantially reduce severe acute respiratory syndrome coronavirus 2. alpha and beta variant infection in human cell efficiently. This review article provides an in-depth examination of critical analytical methodologies used in the pharmaceutical analysis of FEN in pure forms, biological samples and pharmaceuticals. According to literature study reports several analytical techniques have been used for determination of FEN alone or in the combined dosage forms. Based on the literature, it was determined that high-performance liquid chromatography and UV/vis-spectrophotometry are the most widely used methods for FEN analysis. Sahoo et al. have developed the best HPLC method in bulk and pharmaceutical dosage form with the retention time of 19.268 min using phosphate buffer (pH 3.0): acetonitrile in the ratio of 30:70 (% v/v) as mobile phase. The information presented here may provide a solid foundation for future research on FEN in the field of drug analysis.
Low BMI and high waist-to-hip ratio are associated with mortality risk among hemodialysis patients: a multicenter prospective cohort study
Authors: Yang Yaya , Zhang Haixia , Lan Xiaolei , Qin Xianhui , Huang Yan , Wang Jieyu , Luo Pei , Wen Zhen , Li Yumin , Kong Yaozhong , Wan Qijun , Wang Qi , Huang Sheng , Liu Yan , Liu Aiqun , Liu Fanna , Yang Shenglin , Lu Yongxin , Zhao Yanhong , Chen Junzhi , Lei Zihan , He Yanhuan , Lin Zizhen , Li Youbao , Liang Min
Published: September 2022

Background

Data are limited on the relationship between waist-to-hip ratio (WHR) and mortality risk among maintenance hemodialysis (MHD) patients. Moreover, the combined association of body mass index (BMI) and WHR with mortality remains uncertain. Therefore, we aimed to explore the individual and combined association of BMI and WHR with the all-cause and cardiovascular disease (CVD) mortality.

Methods

In this multicenter prospective cohort study, we enrolled 1034 MHD patients. The primary outcome was all-cause mortality and secondary outcome was CVD mortality. Multivariable Cox proportional hazards models were used to evaluate the individual and combined association of BMI and WHR with the risk of mortality.

Results

A nonlinear inverse relationship was found between BMI and risk of all-cause mortality (P for nonlinearity <.05). Being underweight (<18.5 kg/m2) was associated with higher all-cause mortality risk (HR 1.45; 95% CI 1.08–1.94) compared with normal weight (18.5–23.9 kg/m2), while being overweight (24–27.9 kg/m2; HR 0.96; 95% CI 0.70–1.31) and obese (≥28 kg/m2; HR 1.19; 95% CI 0.62–2.26) showed no significant differences. Of note, WHR was independently and positively associated with all-cause mortality (per standard deviation increase, HR 1.13; 95% CI 1.00–1.27). When analyzed jointly, patients with low BMI (<18.5 kg/m2) and high WHR (≥0.95) had the highest risk of all-cause mortality. Similar results were obtained for CVD mortality.

Conclusions

In patients undergoing hemodialysis from China, low BMI and high WHR were individually and jointly associated with higher risk of mortality. Our results emphasize that BMI and WHR may jointly affect the prognosis of MHD patients.
Variation in network evolution through competitive progress via link connection/disconnection
Authors: Sakiyama Tomoko
Published: September 2022

Parameter tuning is a useful method for modelling complex phenomena and replacing one collective pattern with another pattern. However, this approach may not explain how agents in a complex system select an adequate parameter or respond flexibly to a changeable environment. Similar problems are also found in the network evolution where the emergence of characteristic network structures poses a problem. In a previous work, I developed a hawk–dove game on the network where individual players sometimes disconnected links from their partners or connected a link to a new partner in addition to the strategy update. In this game, players coordinated the link connection/disconnection rule by considering the local hierarchy; I found that the coordination of this rule presented the emergence of a scale-free network at one time but not so at another time. Hub nodes may emerge when hawk players are extinct. In this work, I investigated the relationship between the link evolution and the evolution of hub nodes that will be linked to the network structure and found that the network structure could evolve differently according to the competitive progress of the link connection/disconnection.
Identifying the role of preoperative oral/dental health care in post-esophagectomy pulmonary complications: a systematic review and meta-analysis
Authors: Papaconstantinou Dimitrios , Fournaridi Aikaterini-Venedikti , Tasioudi Konstantina , Lidoriki Irene , Michalinos Adamantios , Konstantoudakis Georgios , Schizas Dimitrios
Published: September 2022

Esophageal surgery has traditionally been associated with high morbidity rates. Despite the recent advances in the field of minimally invasive surgery and the introduction of enhanced recovery after surgery (ERAS) protocols, post-esophagectomy morbidity, especially that attributed to the respiratory system, remains a concern. In that respect, preoperative intensification of oral care or introduction of structured oral/dental hygiene regimens may lead to tangible postoperative benefits associated with reduced morbidity (respiratory or otherwise) and length of hospital stay. A systematic literature search of the Medline, Embase, Web of Knowledge and clinicaltrials.gov databases was undertaken for studies reporting use of preoperative oral/dental hygiene improvement regimens in patients scheduled to undergo esophagectomy for esophageal cancer. Meta-analysis was performed using a random-effects model. After screening 796 unique studies, seven were deemed eligible for inclusion in the meta-analysis. Pooled results indicated equivalent postoperative pneumonia rates in the oral pretreatment group and control groups (8.7 vs. 8.5%, respectively); however, the odds for developing pneumonia were reduced by 50% in the pretreatment group (odds ratio 0.5, 95% C.I. 0.37 to 0.69, P < 0.001). No statistically significant difference was detected in the anastomotic leak (odds ratio 0.93, 95% C.I. 0.38 to 2.24, P = 0.87) and length of stay outcomes (mean difference 0.63, 95% C.I. −3.22 to 4.47, P = 0.75). Oral/dental pretreatment reduces the odds for developing post-esophagectomy pneumonia. This finding should be cautiously interpreted given the significant limitations inherent in this meta-analysis. Further investigation via well-designed clinical trials is thus warranted before implementation in routine practice can be recommended.
Harmonization of the American College of Cardiology/American Heart Association and European Society of Cardiology/European Society of Hypertension Blood Pressure/Hypertension Guidelines
Authors: Whelton Paul K , Carey Robert M , Mancia Giuseppe , Kreutz Reinhold , Bundy Joshua D , Williams Bryan
Published: September 2022

The 2017 American College of Cardiology/American Heart Association and 2018 European Society of Cardiology/European Society of Hypertension clinical practice guidelines for management of high blood pressure/hypertension are influential documents. Both guidelines are comprehensive, were developed using rigorous processes, and underwent extensive peer review. The most notable difference between the 2 guidelines is the blood pressure cut points recommended for the diagnosis of hypertension. There are also differences in the timing and intensity of treatment, with the American College of Cardiology/American Heart Association guideline recommending a somewhat more intensive approach. Overall, there is substantial concordance in the recommendations provided by the 2 guideline-writing committees, with greater congruity between them than their predecessors. Additional harmonization of future guidelines would help to underscore the commonality of their core recommendations and could serve to catalyze changes in practice that would lead to improved prevention, awareness, treatment, and control of hypertension, worldwide.
Prenatal exposure to the Chinese famine of 1959–62 and risk of cardiovascular diseases in adulthood: findings from the China PEACE million persons project
Authors: Chen Chaolei , Nie Zhiqiang , Wang Jiabin , Ou Yanqiu , Cai Anping , Huang Yuqing , Yang Qingling , Liu Simin , Li Jie , Feng Yingqing
Published: September 2022

Aims

Much remains unknown about the role of prenatal exposure to environmental stressors in the development of cardiovascular diseases (CVD). The current study aimed to investigate whether exposure to famine early in life was associated with a higher risk of CVD in adulthood.

Methods and results

Among 71 667 men and women participated in the Patient-centred Evaluative Assessment of Cardiac Events (PEACE) Million Persons Project in southern China, specific years of birth were used to define two cohorts: the exposed group (born during the famine of 1959–62) and the non-exposed group [born before the famine (1949–58) or after the famine (1963–72)]. Multivariable-adjusted generalized linear models were used to examine the associations of famine exposure with the risk of developing CVD, as well as with the 10-year CVD risk defined by well-established risk scores. Compared with the non-famine group, early-life exposure to the Chinese famine was significantly associated with increased risks of total CVD (odds ratio, OR = 1.28, 95% confidence interval: 1.16–1.41), coronary heart disease [OR: 1.23 (1.07–1.41)], acute myocardial infarction [OR: 1.32 (1.01–1.70)], heart failure [OR: 2.01 (1.53–2.60)], and stroke [OR: 1.28 (1.12–1.45)] in adulthood. In those without established CVD, early-life exposure to the famine was associated with higher levels of total cholesterol, systolic blood pressure, waist circumference, risk of diabetes, and therefore 10-year CVD risk.

Conclusion

Early-life exposure to the Chinese famine is associated with an elevated CVD risk later in life, independent of known risk factors.
Corporate political activity in the context of sugar-sweetened beverage tax policy in the WHO European Region
Authors: Lauber Kathrin , Rippin Holly , Wickramasinghe Kremlin , Gilmore Anna B
Published: September 2022

Background

Sugar-sweetened beverage (SSB) taxes have emerged as an effective and increasingly popular tool to reduce added sugar intake, an important contributor to obesity and non-communicable diseases. A common barrier to the implementation of well-designed SSB taxes is the opposition of commercial actors. Focusing on the WHO European Region, this study seeks to map if and how key stakeholders have experienced industry efforts to influence SSB taxes.

Methods

We identified 11 countries in the WHO European Region which have implemented SSB taxes or attempted to do so. Using an online survey informed by the global literature on industry interference with SSB taxation, we approached 70 in-country policymakers, advocates and academics. The data were analysed using an existing framework of corporate political activity.

Results

Twenty-three experts from nine countries responded to the survey. Transnational SSB producers and their business associations were identified as the most active opponents of SSB taxation. Industry claims that the policy would have negative economic effects were identified as the most common and powerful arguments. Direct lobbying was reported in all study countries. Shifts in political activity were recognisable across stages of the policy process, moving from outright opposition to attempts to delay or weaken the policy after its announcement.

Conclusion

Those seeking to introduce effective SSB taxation can use our findings to pre-empt and counter industry opposition. We identify several measures for preventing and mitigating industry interference with SSB tax policy.
Inferring fluid volume during earthquake swarms using seismic catalogues
Authors: Danré Philippe , De Barros Louis , Cappa Frédéric
Published: September 2022

Many studies have pointed out a correlation between either the cumulative or the maximum seismic moment and the injected fluid volume when analysing global data sets of fluid injection-induced earthquake sequences. However, those correlations become quite uncertain when looking at individual episodes, mainly because of the large aseismic component of the induced deformation. If natural swarms are thought to result from the same physical processes as sequences from anthropogenic origin, little is still known about them as observations are limited by the depth of the active zone and the moderate deformations. In this work, we make profit of the similarity between both natural and injection-induced swarms. To this aim, we develop new relations between seismic observables and hydraulic attributes by using a global compilation of injection-induced earthquake catalogues, leading to two methods to estimate the injected fluid volume based solely on earthquake catalogues. Once the precision of our approaches is validated, we estimate the volume and flowrate of fluids circulating in diverse natural swarms, shedding a new light on the fluid dynamics that trigger them.
An LTR retrotransposon in the promoter of a PsMYB10.2 gene associated with the regulation of fruit flesh color in Japanese plum
Authors: Fiol Arnau , García Sergio , Dujak Christian , Pacheco Igor , Infante Rodrigo , Aranzana Maria José
Published: September 2022

Japanese plums exhibit wide diversity of fruit coloration. The red to black hues are caused by the accumulation of anthocyanins, while their absence results in yellow, orange or green fruits. In Prunus, MYB10 genes are determinants for anthocyanin accumulation. In peach, QTLs for red plant organ traits map in an LG3 region with three MYB10 copies (PpMYB10.1, PpMYB10.2 and PpMYB10.3). In Japanese plum the gene copy number in this region differs with respect to peach: there are at least three copies of PsMYB10.1, with the expression of one of them (PsMYB10.1a) correlating with fruit skin color. The objective of this study was to determine a possible role of LG3-PsMYB10 genes in the natural variability of the flesh color trait and to develop a molecular marker for marker-assisted selection (MAS). We explored the variability within the LG3-PsMYB10 region using long-range sequences obtained in previous studies through CRISPR-Cas9 enrichment sequencing. We found that the PsMYB10.2 gene was only expressed in red flesh fruits. Its role in promoting anthocyanin biosynthesis was validated by transient overexpression in Japanese plum fruits. The analysis of long-range sequences identified an LTR retrotransposon in the promoter of the expressed PsMYB10.2 gene that explained the trait in 93.1% of the 145 individuals analyzed. We hypothesize that the LTR retrotransposon may promote the PsMYB10.2 expression and activate the anthocyanin biosynthesis pathway. We propose for the first time the PsMYB10.2 gene as candidate for the flesh color natural variation in Japanese plum and provide a molecular marker for MAS.
Estimating the excess burden of pertussis disease in Australia within the first year of life, that might have been prevented through timely vaccination
Authors: Jayasundara Duleepa , Randall Deborah , Sheridan Sarah , Sheppeard Vicky , Liu Bette , Richmond Peter C , Blyth Christopher C , Wood James G , Moore Hannah C , McIntyre Peter B , Gidding Heather F
Published: September 2022

Background

Previous Australian studies have shown that delayed vaccination with each of the three primary doses of diphtheria-tetanus-pertussis-containing vaccines (DTP) is up to 50 % in certain subpopulations. We estimated the excess burden of pertussis that might have been prevented if (i) all primary doses and (ii) each dose was given on time.

Methods

Perinatal, immunization, pertussis notification and death data were probabilistically linked for 1 412 984 infants born in two Australian states in 2000–12. A DTP dose administered >15 days after the recommended age was considered delayed. We used Poisson regression models to compare pertussis notification rates to 1-year of age in infants with ≥1 dose delayed (Aim 1) or any individual dose delayed (Aim 2) versus a propensity weighted counterfactual on-time cohort.

Results

Of all infants, 42% had ≥1 delayed DTP dose. We estimated that between 39 to 365 days of age, 85 (95% CI: 61–109) cases per 100 000 infants, could have been prevented if all infants with ≥1 delayed dose had received their three doses within the on-time window. Risk of pertussis was higher in the delayed versus the on-time cohort, so crude rates overestimated the excess burden (110 cases per 100 000 infants (95% CI: 95–125)). The estimated dose-specific excess burden per 100 000 infants was 132 for DTP1, 50 for DTP2 and 19 for DTP3.

Conclusions

We provide robust evidence that improved DTP vaccine timeliness, especially for the first dose, substantially reduces the burden of infant pertussis. Our methodology, using a potential outcomes framework, is applicable to other settings.
Smaller generalization error derived for a deep residual neural network compared with shallow networks
Authors: Kammonen Aku , Kiessling Jonas , Plecháč Petr , Sandberg Mattias , Szepessy Anders , Tempone Raul
Published: September 2022

Estimates of the generalization error are proved for a residual neural network with $L$ random Fourier features layers $\bar z_{\ell +1}=\bar z_\ell + \textrm {Re}\sum _{k=1}^K\bar b_{\ell k}\,e^{\textrm {i}\omega _{\ell k}\bar z_\ell }+ \textrm {Re}\sum _{k=1}^K\bar c_{\ell k}\,e^{\textrm {i}\omega ^{\prime}_{\ell k}\cdot x}$. An optimal distribution for the frequencies $(\omega _{\ell k},\omega ^{\prime}_{\ell k})$ of the random Fourier features $e^{\textrm {i}\omega _{\ell k}\bar z_\ell }$ and $e^{\textrm {i}\omega ^{\prime}_{\ell k}\cdot x}$ is derived. This derivation is based on the corresponding generalization error for the approximation of the function values $f(x)$. The generalization error turns out to be smaller than the estimate ${\|\hat f\|^2_{L^1({\mathbb {R}}^d)}}/{(KL)}$ of the generalization error for random Fourier features, with one hidden layer and the same total number of nodes $KL$, in the case of the $L^\infty $-norm of $f$ is much less than the $L^1$-norm of its Fourier transform $\hat f$. This understanding of an optimal distribution for random features is used to construct a new training method for a deep residual network. Promising performance of the proposed new algorithm is demonstrated in computational experiments.
A quality assurance initiative on improving cefazolin perioperative redose compliance
Authors: Qureshi Faiza , Romeiser Jamie Lee , Murphy Paul F , Go Roderick A , Abola Ramon
Published: September 2022

Objective

Compliance with perioperative antibiotic prophylaxis is crucial for preventing surgical site infection. Anesthesiologists can play a significant role in reducing surgical site infections by following clinical practice guidelines for antibiotic prophylaxis and redosing during surgery. A quality assurance initiative was implemented at a tertiary hospital with the goal of improving cefazolin perioperative antibiotic compliance.

Design

This was a retrospective observational study

Setting

Main operating room of a tertiary care teaching hospital in New York, USA. Our main operating room includes 22 operating rooms that incorporates surgeries from general surgery, vascular surgery, neurology, gynecology, urology, orthopedics, ear, nose and throat (ENT) etc.

Participants

All cases in the main operating room from March 1, 2018 to March 31, 2021 that received first dose of Cefazolin and in which the duration of surgery was more than 4 hrs.

Intervention

A multifaceted intervention was initiated to address low compliance with cefazolin redosing. Multifaceted interventions included the development of a perioperative antibiotic guide for anesthesia providers, automated reminders in anesthesia electronic medical records, grand rounds education, survey and email communications, and regular feedback reports to the anesthesia department.

Main outcome Measures

Cefazolin perioperative redose compliance rate.

Results

Rates of redose compliance were examined in three time periods: preintervention, intervention and postintervention. Cefazolin redosing compliance was 58% in the preintervention period and 90% in the postintervention period. There was a significant positive change in the trend of compliance during the intervention period, indicating that the odds of compliance increased by 13% per month in the intervention period compared to the preintervention period (odds ratio = 1.13, P < 0.001). Redose compliance improvements were sustained a year after the postintervention period (an average of 91%). Surgical site infection rates for colon, coronary artery bypass graft and hip surgeries did not show any significant trend during these time periods.

Conclusion

Multifaceted interventions led to significant and sustained improvements in cefazolin redosing compliance in the main operating room of a tertiary hospital.
Do electronic health record systems “dumb down” clinicians?
Authors: Melton Genevieve B , Cimino James J , Lehmann Christoph U , Sengstack Patricia R , Smith Joshua C , Tierney William M , Miller Randolph A
Published: September 2022

A panel sponsored by the American College of Medical Informatics (ACMI) at the 2021 AMIA Symposium addressed the provocative question: “Are Electronic Health Records dumbing down clinicians?” After reviewing electronic health record (EHR) development and evolution, the panel discussed how EHR use can impair care delivery. Both suboptimal functionality during EHR use and longer-term effects outside of EHR use can reduce clinicians’ efficiencies, reasoning abilities, and knowledge. Panel members explored potential solutions to problems discussed. Progress will require significant engagement from clinician-users, educators, health systems, commercial vendors, regulators, and policy makers. Future EHR systems must become more user-focused and scalable and enable providers to work smarter to deliver improved care.
Determination of the Physiological Age in Two Tephritid Fruit Fly Species Using Artificial Intelligence
Authors: González-López Gonzalo I , Valenzuela-Carrasco G , Toledo-Mesa Edmundo , Juárez-Durán Maritza , Tapia-McClung Horacio , Pérez-Staples Diana
Published: September 2022

The Mexican fruit fly (Anastrepha ludens, Loew, Diptera: Tephritidae) and the Mediterranean fruit fly (Ceratitis capitata, Wiedemann, Diptera: Tephritidae) are among the world's most damaging pests affecting fruits and vegetables. The Sterile Insect Technique (SIT), which consists in the mass-production, irradiation, and release of insects in affected areas is currently used for their control. The appropriate time for irradiation, one to two days before adult emergence, is determined through the color of the eyes, which varies according to the physiological age of pupae. Age is checked visually, which is subjective and depends on the technician's skill. Here, image processing and Machine Learning techniques were implemented as a method to determine pupal development using eye color. First, Multi Template Matching (MTM) was used to correctly crop the eye section of pupae for 96.2% of images from A. ludens and 97.5% of images for C. capitata. Then, supervised Machine Learning algorithms were applied to the cropped images to classify the physiological age according to the color of the eyes. Algorithms based on Inception v1, correctly identified the physiological age of maturity at 2 d before emergence, with a 75.0% accuracy for A. ludens and 83.16% for C. capitata, respectively. Supervised Machine Learning algorithms based on Neural Networks could be used as support in determining the physiological age of pupae from images, thus reducing human error and uncertainty in decisions as when to irradiate. The development of a user interface and an automatization process could be further developed, based on the data obtained on this study.
Standardized Field Trials in Cotton and Bioassays to Evaluate Resistance of Tobacco Thrips (Thysanoptera: Thripidae) to Insecticides in the Southern United States
Authors: Krob Jessica L , Stewart Scott D , Brown Sebe A , Kerns Dawson , Graham Scott H , Perkins Clay , Huseth Anders S , Kennedy George G , Reisig Dominic D , Taylor Sally V , Towles Tyler B , Kerns David L , Thrash Benjamin C , Lorenz Gus M , Bateman Nick R , Cook Don R , Crow Whitney D , Gore Jeffrey , Catchot Angus L , Musser Fred R , Catchot Beverly
Published: September 2022

Foliar-applied insecticide treatments may be necessary to manage thrips in cotton (Gossypium hirsutum L.) under severe infestations or when at-planting insecticide seed treatments do not provide satisfactory protection. The most common foliar-applied insecticide is acephate. Field observations in Tennessee suggest that the performance of acephate has declined. Thus, the first objective was to perform leaf-dip bioassays to assess if tobacco thrips, Frankliniella fusca (Hinds) (Thysanoptera: Thripidae), in cotton production regions have evolved resistance to foliar-applied insecticides. A second objective was to assess the performance of commonly applied foliar insecticides for managing thrips in standardized field trials in Arkansas, Tennessee, Mississippi, and Texas. For both objectives, several insecticides were evaluated including acephate, dicrotophos, dimethoate, lambda-cyhalothrin, imidacloprid, and spinetoram. Field trials and bioassays were completed from 2018 to 2021. Dose-response bioassays with acephate were performed on tobacco thrips field populations and a susceptible laboratory population. Bioassay results suggest that tobacco thrips have developed resistance to acephate and other organophosphate insecticides; however, this resistance seems to be most severe in Arkansas, Tennessee, and the Delta region of Mississippi. Resistance to other classes of insecticides were perhaps even more evident in these bioassays. The performance of these insecticides in field trials was variable, with tobacco thrips only showing consistent signs of resistance to lambda-cyhalothrin. However, it is evident that many populations of tobacco thrips are resistant to multiple classes of insecticides. Further research is needed to determine heritability and resistance mechanism(s).
The logic languages of the TPTP world
Authors: Sutcliffe Geoff
Published: September 2022

The Thousands of Problems for Theorem Provers (TPTP) World is a well-established infrastructure that supports research, development and deployment of automated theorem proving systems. This paper provides an overview of the logic languages of the TPTP World, from classical first-order form (FOF), through typed FOF, up to typed higher-order form, and beyond to non-classical forms. The logic languages are described in a non-technical way and are illustrated with examples using the TPTP language.
Orbital angular momentum-resolved convergent-beam electron diffraction by the post-selected injection of electron beam
Authors: Saitoh Koh , Yonezawa Tatsuya , Nambu Hiroki , Tanimura Shogo , Uchida Masaya
Published: September 2022

Recent advances in the production of electron vortex beams carrying orbital angular momentum (OAM) offer unique opportunities to explore materials at the nanoscale level. We present a novel method for observing convergent-beam electron diffraction (CBED) patterns by using an electron vortex beam. In a transmission electron microscope, a series of electron vortex beams generated by a forked grating mask located above the specimen illuminate the specimen, and CBED patterns are imaged onto the observation plane of the microscope, selecting one of the electron vortex beams using an aperture located beneath the specimen. We demonstrate that the post-selection method yields the same OAM-resolved CBED patterns as when a single convergent electron beam is injected. The formation mechanism of the post-selected CBED is also discussed. This post-selection method is general and can be applied to electron energy-loss spectroscopy to probe multipole excitations using electron vortex beams.
The social factors and functions of media use
Authors: Grady Sara M , Tamborini Ron , Eden Allison , Van Der Heide Brandon
Published: September 2022

A heuristic model aims to organize and synthesize the substantial body of work examining the social influences that shape media selection, experiences, and effects. The Social Influences and Media Use (SIMU) model describes three broad social forces (users’ internal social needs, their social environment, and the social affordances of media) and their recursive association with media use. This article (a) brings together diverse subdisciplines interested in the social factors and functions of media use, (b) discusses the micro–macro nature of social phenomena and its potential role in future inquires, and (c) illustrates how the model might foster new developments by applying it in a specific area of study. The model may help us identify cohesive patterns (and points of divergence or uniqueness) among existing findings as well as inform future work examining these relationships across a variety of social contexts and media channels.
Cefadroxil Use for Musculoskeletal Infections in an Academic Pediatric Hospital
Authors: Weslander Erin , Thomas Holly , Jeune Ralph , Green Michael , Williams John V
Published: September 2022

Forty-nine of 52 (94.2%) children with musculoskeletal infection (MSKI) were successfully treated with cefadroxil dosed at 30 mg/kg/day over a 10-year time period. Two failures were associated with poor medication adherence. Our study suggests that treatment of MSKI with cefadroxil offers acceptable outcomes. Confirmation through clinical trials is appropriate.
Lessons Learned From the U.S. Military Experience With Hantavirus During the Korean War
Authors: Rouabhia Ramsey , Dinh Dung T , Kua Siang C , Washington Michael A
Published: September 2022

Introduction

The Korean War (1950-1953) consisted of two phases. The first was a rapid mobile phase, and the second was a slow and stationary phase. During the stationary phase, approximately 3,000 UN troops became infected with a then unknown agent. The resulting illness began with flu-like symptoms and often progressed to a severe hemorrhagic fever leading to kidney failure and death. However, the cause was not to be identified until well over 20 years following the conclusion of the war when Dr. Ho Wang Lee succeeded in isolating Hantavirus from field rodents. The U.S. Military experience with Hantavirus during the Korean War is a case study of the potential impact of war-related environmental change on disease transmission. The lessons learned from this experience should inform future military medical planning and serve as a reminder of the impact that an unknown agent can have on military operations.

Materials and Methods

A literature review of all available records with respect to the U.S. Military experience with Hantavirus was conducted. PubMed was the primary search engine used for this review. However, primary literature and historical accounts were also evaluated. All records were examined for environmental, epidemiological, and public health data regarding hemorrhagic fever outbreaks among U.S. forces during the Korean War. The quantitative and qualitative data from these sources were analyzed and evaluated within the context of military medical planning and force health protection to derive lessons learned that should be applied to the management and mitigation of viral disease in future wars.

Results

Widespread deforestation resulting from war-related efforts most likely played a significant role in the outbreaks of Hantavirus among UN forces during the war. A lack of cultural literacy and an overreliance on erroneous assumptions most likely delayed the identification of the true causative agent. It is conceivable that these delays led to an increased casualty rate and that they had a negative impact on military operations during the war.

Conclusions

A basic understanding of the ecological mechanisms that maintain species diversity in the local environment coupled with an appreciation for the impact of environmental change on this diversity is of paramount importance for the prevention and mitigation of viral disease outbreaks in the deployed setting. Military medical planners should become familiar with the medical literature of the region in which they will be operating as this literature often describes the agents that will most likely be encountered by U.S. forces.
A Search for Unbound Stellar Companions to Pulsar J1124−5916
Authors: Kochanek C S
Published: September 2022

We searched for and found no higher mass (${\gtrsim}3{\rm M}_\odot$) unbound binary stellar companions to the progenitor of pulsar J1124−5916. There are lower mass candidates, but they all have high probabilities of being false positives. There are no candidates for it now being a fully unbound triple system. Even if one of the lower mass candidates is an unbound companion, it seems unlikely that it could have contributed to stripping the progenitor prior to the supernova. The stars are too low mass to be significant mass gainers, and they are too slowly moving to be the survivors of a compact, post-common envelope binary. The addition of one more system slightly improves the statistical constraints on the binary and triple status of supernova progenitors just before and after death.
Local Volume dwarf KK242: radial velocity, SF region and metallicity
Authors: Pustilnik S A , Tepliakova A L , Perepelitsyna Y A , Kniazev A Y , Makarova L N , Burenkov A N , Kotov S S , Malygin E A
Published: September 2022

KK242 is a LV dwarf of transition type residing in the void environment. Koda et al. present clear indications on its connection with Scd galaxy NGC6503. This implies the distance to KK242 of ∼6.3 Mpc and its MB=–10.5 mag. Its radial velocity, known from the Effelsberg radio telescope H i observations, reveals, however, the difference with that of NGC6503, ΔV∼400 km s−1. If real, this fact implies the substantial constraints on its origin. To clear-up the issue of KK242 radial velocity, we obtained with the SAO 6-m telescope spectra of its faint star-forming (SF) complex. Hα and Hβ emission is detected in two adjacent compact regions, the southern and northern, separated by ∼2 arcsec (∼60 pc). Their mean radial velocity is Vhel=–66 km s−1, ∼100 km s−1 lower than that of NGC6503. We use the HST Legacy Archive images and photometry of individual stars from the Extragalactic Distance Database, available for KK242, to identify in the SF complex the exciting hot stars, the probable BHeB and RHeB stars and a supernova remnant. We address, based on the possible range of its gas metallicity, the probable evolutionary paths of KK242. Using package Cloudy and parameters of the exciting B0V stars, we conclude that the observed flux ratio of the [S ii] doublet to Hα is consistent with the value of 12+log (O/H) ∼7.35 ±0.18 dex, expected for a stripped void dIrr galaxy.
Genealogy, Evaluation, and Engineering
Authors: Queloz Matthieu
Published: September 2022

Against those who identify genealogy with reductive genealogical debunking or deny it evaluative significance, I argue, first, that while genealogies tend to trace the higher to the lower, they need not reduce the higher to the lower, but can elucidate their relation and help us think more realistically about both relata; second, that if we conceive of genealogy in terms of a triadic model including the addressee, it becomes intelligible how tracing the higher to the lower can facilitate an evaluation of the higher, and how, where the lower is some important practical need rather than some sinister motive, the genealogy can even be vindicatory; and third, that vindicatory genealogies can offer positive guidance on how to engineer better concepts.
IEAtlas: an atlas of HLA-presented immune epitopes derived from non-coding regions
Authors: Cai Yangyang , Lv Dezhong , Li Donghao , Yin Jiaqi , Ma Yingying , Luo Ya , Fu Limei , Ding Na , Li Yongsheng , Pan Zhenwei , Li Xia , Xu Juan
Published: September 2022

Cancer-related epitopes can engage the immune system against tumor cells, thus exploring epitopes derived from non-coding regions is emerging as a fascinating field in cancer immunotherapies. Here, we described a database, IEAtlas (http://bio-bigdata.hrbmu.edu.cn/IEAtlas), which aims to provide and visualize the comprehensive atlas of human leukocyte antigen (HLA)-presented immunogenic epitopes derived from non-coding regions. IEAtlas reanalyzed publicly available mass spectrometry-based HLA immunopeptidome datasets against our integrated benchmarked non-canonical open reading frame information. The current IEAtlas identified 245 870 non-canonical epitopes binding to HLA-I/II allotypes across 15 cancer types and 30 non-cancerous tissues, greatly expanding the cancer immunopeptidome. IEAtlas further evaluates the immunogenicity via several commonly used immunogenic features, including HLA binding affinity, stability and T-cell receptor recognition. In addition, IEAtlas provides the biochemical properties of epitopes as well as the clinical relevance of corresponding genes across major cancer types and normal tissues. Several flexible tools were also developed to aid retrieval and to analyze the epitopes derived from non-coding regions. Overall, IEAtlas will serve as a valuable resource for investigating the immunogenic capacity of non-canonical epitopes and the potential as therapeutic cancer vaccines.
Occupational asthma in teachers
Authors: Burge S , Moore V , Burge C , Robertson A , Huntley C , Walters G
Published: September 2022

Background

Work-related asthma symptoms are common in teachers and teaching assistants, there are few studies evaluating their causes.

Aims

To identify causes of occupational asthma in teachers and teaching assistants referred to the Birmingham Occupational Lung Disease clinic 2000–20 using evaluation of serial Peak Expiratory Flow (PEF) records.

Methods

Teachers and teaching assistants with possible occupational asthma were asked to record PEF 2-hourly at home and work for 4 weeks. Their records were evaluated with the Oasys programme. Those with a positive score for any of the three scores (area between curves (ABC), timepoint and Oasys score from discriminant analysis) were included. Repeat records were made as indicated to help identify the cause and the effects of remedial actions.

Results

Thirty-eight teachers or teaching assistants met the inclusion criteria with all three Oasys scores positive in 24, 2/3 scores in nine and 1/3 in five. The building was the likely cause in 17 (in new builds particularly acrylates from carpet adhesives and in old buildings mould and construction dust), bystander exposure to agents in the schools in 12 (cleaning agents, acrylates from photocopiers and chloramines from indoor pools) and materials used in the classroom in 9 (most commonly MDF in design and technology classes). We illustrate how the PEF records helped identify the cause.

Conclusions

Oasys analysis of PEF records is a useful method of evaluating occupational asthma in teachers and identified difficult to confirm causes where successful remediation or redeployment was achieved.
The antioxidant, tert-butylhydroquinone: a new cause of asthma
Authors: Sherson D L , Jacobsen I B , Thomsen G F
Published: September 2022

The antioxidant, tert-butylhydroquinone (TBHQ), a common additive in food and cosmetics can cause allergic contact dermatitis. A 49-year-old non-atopic male factory worker developed asthma in connection with cleaning mixing drums containing TBHQ. Due to the suspicion that TBHQ might be the cause of asthma, a specific inhalation challenge was carried out. Lactose was used as a control agent. The following day he developed asthma symptoms with a 41% drop in FEV1 after 30-min exposure to small amounts of TBHQ and water. Methacholine reactivity increased 5-fold after TBHQ exposure compared to pre-exposure reactivity. This suggests that TBHQ may be the cause of asthma in this case. Due to this case respirators were introduced in the factory to reduce TBHQ exposure. TBHQ has not previously been shown to cause asthma.