bluuebunny/crossref_metadata_2025 huggingface dataset:
Novel Methods for Leveraging Large Cohort Studies for Qualitative and Mixed-Methods Research
Authors: Nguyen Katie Truc Nhat H , Stuart Jennifer J , Shah Aarushi H , Becene Iris A , West Madeline G , Berrill Jane , Gelaye Bizu , Borba Christina P C , Rich-Edwards Janet W
Published: February 2023

Qualitative research methods, while rising in popularity, are still a relatively underutilized tool in public health research. Usually reserved for small samples, qualitative research techniques have the potential to enhance insights gained from large questionnaires and cohort studies, both deepening the interpretation of quantitative data and generating novel hypotheses that might otherwise be missed by standard approaches; this is especially true where exposures and outcomes are new, understudied, or rapidly changing, as in a pandemic. However, methods for the conduct of qualitative research within large samples are underdeveloped. Here, we describe a novel method of applying qualitative research methods to free-text comments collected in a large epidemiologic questionnaire. Specifically, this method includes: 1) a hierarchical system of coding through content analysis; 2) a qualitative data management application; and 3) an adaptation of Cohen’s κ and percent agreement statistics for use by a team of coders, applying multiple codes per record from a large codebook. The methods outlined in this paper may help direct future applications of qualitative and mixed methods within large cohort studies.
From Addressing Aesthetics and Soft Tissue to Visual Performance: Multifaceted Satisfaction Assessment in a Multicenter Study of Patients With Dermatochalasis
Authors: Niazi Feizollah , Foster Jill A , Nahai Foad , Nahai Farzad R , Niazi Sana , Doroodgar Farideh , Salour Soltan Hossein
Published: February 2023

Background

In this study, we seek to answer the question: Does blepharoplasty for dermatochalasis alter visual performance?

Objectives

We seek to determine the impact of blepharoplasty on visual performance (refraction, contrast sensitivity, and visual field) in patients with dermatochalasis.

Methods

A total of 146 eyelids of 74 patients, 48 (64.9%) females and 26 (35.1%) males ranging from 40 to 68 years old, with dermatochalasis were analyzed prospectively. Refraction, contrast sensitivity, visual acuity, higher-order aberrations (HOAs), and mean deviation index (MDI) in the Humphrey visual field were evaluated and recorded before and at 2, 4, and 6 months after upper eyelid blepharoplasty.

Results

At the latest follow-up, uncorrected and corrected distance visual acuity showed no significant differences (P > .05). Patients’ contrast sensitivity increased significantly at all spatial frequencies under both conditions (P < .05) except at 12 cycles per degree in the photopic condition (P = .947). Mean astigmatism significantly decreased from −1.17 ± 0.83 to −0.89 ± 0.66 postoperatively (P ≤ .001). Total HOAs decreased significantly from 0.59 ± 0.13 μm to 0.51 ± 0.09 μm (P < .01) after surgery. The root mean square of the spherical aberration (P < .01), vertical trefoil (P = .018), horizontal trefoil (P < .01), horizontal coma (P < .001), and vertical coma (P < .01) decreased significantly. The MDI of the Humphrey visual field increased significantly postoperatively at all times compared with preoperatively (P < .05). The Blepharoplasty Outcomes Evaluation questionnaire showed significant favorable satisfaction with visual quality indexes (P < .001).

Conclusions

Upper lid blepharoplasty, in addition to its aesthetic effect, is an effective intervention to promote visual function and quality of life.
Postoperative Antibiotics Following Reduction Mammaplasty Does Not Reduce Rates of Surgical Site Infection
Authors: Mookerjee Vikram G , Kammien Alexander J , Prassinos Alexandre J , Grauer Jonathan N , Butler Paris D
Published: February 2023

Background

The efficacy of antibiotic utilization following reduction mammaplasty has not been well studied. Furthermore, there is a lack of data describing subgroups who are historically at high risk for surgical site infection (SSI), specifically the obese population.

Objectives

This study compares SSI rates in reduction mammaplasty patients who received postoperative courses of antibiotics with those who did not. Additional analysis was performed for the subgroup of patients with a body mass index (BMI) ≥30 kg/m2.

Methods

The 2010 to 2021 PearlDiver Mariner data set was reviewed to identify reduction mammaplasty patients. Patients were confirmed to have received perioperative antibiotics. Postoperative antibiotic use was determined based on the presence of postoperative prescriptions, and 1:1 matching was performed for those with and without postoperative antibiotics based on age and the Elixhauser Comorbidity Index. Rates of SSI, emergency department (ED) visits, and readmissions for the 90 days following surgery were recorded and compared. A subgroup analysis was performed on patients with a BMI of ≥30 kg/m2.

Results

Among patients who were confirmed to have received perioperative antibiotics, 2230 patients who also received postoperative antibiotics were identified and matched to 2230 patients who did not. Rates of SSI, ED visits, and readmission were not statistically different. A total of 218 obese patients were identified from this group and matched. Rates of SSI, ED visits, and readmission were not statistically different.

Conclusions

In the current study, no difference in SSI rates between patients who received postoperative antibiotics and those who did not was found. These observations were corroborated in the obese population. These data may assist surgeons when considering postoperative antibiotics following reduction mammaplasty.

Level of Evidence: 4
Facial Dermal Filler Injection and Vaccination: A 12-Year Review of Adverse Event Reporting and Literature Review
Authors: Sun Alexander H , Tiongco Rafael Felix P , Manahan Michele A
Published: February 2023

Background

Following authorization of 2 COVID-19 vaccines in December 2020, media attention increased towards postvaccine adverse events (AEs) in patients with facial dermal filler injections.

Objectives

The purpose of this study was to characterize vaccine-related facial dermal filler AEs by scrutinizing the FDA's Manufacturer and User Facility Device Experience (MAUDE) database.

Methods

The MAUDE database was queried from January 1, 2011 to January 28, 2023 for facial dermal filler medical device reports (MDRs) discussing vaccination-related AEs. A PubMed (National Institutes of Health, Bethesda, MD) literature review on dermal filler AEs was then conducted. Data were analyzed with descriptive statistics.

Results

Of 10,637 MDRs identified, 33 were included. There were 25 MDRs (75.8%) related to COVID-19 vaccination. Hyaluronic acid–based fillers were described in 31 MDRs (93.9%). AEs were mostly reported within days postinjection (n = 7, 21.2%), but ranged from immediately (n = 2, 6.1%) to months (n = 6, 18.2%) postinjection. Most AEs were reported postvaccine (n = 17, 51.5%) vs postfiller (n = 14, 42.4%). In 26 reports (78.8%), AEs occurred at the site of filler injection. Most MDRs described inflammation/swelling (n = 21, 28.0%). The literature review returned 302 articles, of which 14 were included. Only 1 article (7.1%) was published in a plastic surgery journal.

Conclusions

Although the pandemic brought attention to COVID-19 vaccine–related facial dermal filler AEs, this study shows a low incidence compared with the millions of vaccine and filler injections administered. Reactions with non–COVID-19 vaccines were also documented. Increased awareness may help providers counsel patients undergoing vaccination and dermal filler implantation.

Level of Evidence: 4
Initial Assessment of VECTRA Three-Dimensional Imaging to Accurately Simulate Breast Volume Changes in Transfeminine Patients: A Mannequin Study
Authors: Lopez Ximena , Panton Jasmine , Nagarkar Purushottam , Preston Stephanie , Abramowitz Jessica , Amirlak Bardia
Published: February 2023

Background

Methods that aim to accurately measure and predict breast development can be utilized in gender-affirming treatment planning, patient education, and research.

Objectives

The authors sought to evaluate whether three-dimensional (3D) stereophotogrammetry accurately measures transfeminine breast volume changes on a masculine frame when simulating anticipated changes in soft tissue after gender-affirming surgical therapy. Then, we describe the innovative application of this imaging modality in a transgender patient to illustrate the potential role of 3D imaging in gender-affirming surgical care.

Methods

A 3D VECTRA scanner (Canfield, Fairfield, NJ) was used to measure anthropometric breast measurements. Postoperative changes in breast volume were simulated on a cardiopulmonary resuscitation mannequin using 450 cc MENTOR breast implants (Mentor Worldwide LLC, Irvine, CA). To demonstrate the ability of the VECTRA to accurately simulate transfeminizing augmentation in practice, we describe its use in a 30-year-old transgender female with a 2-year history of gender-affirming hormone therapy, presenting for gender-affirming surgical care.

Results

In the mannequin, mean breast volumes were 382 cc on the right (range 375-388 cc), and 360 cc on the left (range 351-366 cc). The average calculated difference in volume between the 2 sides was 22 cc (range 17-31 cc). There were no instances where the left side was calculated to be larger than the right or where the calculated size was smaller than the actual implant size.

Conclusions

The VECTRA 3D camera is a reliable and reproducible tool for preoperative assessment, surgical planning, and simulating breast volume changes after gender-affirming surgery.

Level of Evidence: 5
baseLess: lightweight detection of sequences in raw MinION data
Authors: Noordijk Ben , Nijland Reindert , Carrion Victor J , Raaijmakers Jos M , de Ridder Dick , de Lannoy Carlos
Published: February 2023

With its candybar form factor and low initial investment cost, the MinION brought affordable portable nucleic acid analysis within reach. However, translating the electrical signal it outputs into a sequence of bases still requires mid-tier computer hardware, which remains a caveat when aiming for deployment of many devices at once or usage in remote areas. For applications focusing on detection of a target sequence, such as infectious disease monitoring or species identification, the computational cost of analysis may be reduced by directly detecting the target sequence in the electrical signal instead. Here, we present baseLess, a computational tool that enables such target-detection-only analysis. BaseLess makes use of an array of small neural networks, each of which efficiently detects a fixed-size subsequence of the target sequence directly from the electrical signal. We show that baseLess can accurately determine the identity of reads between three closely related fish species and can classify sequences in mixtures of 20 bacterial species, on an inexpensive single-board computer.

Availability and implementation

baseLess and all code used in data preparation and validation are available on Github at https://github.com/cvdelannoy/baseLess, under an MIT license. Used validation data and scripts can be found at https://doi.org/10.4121/20261392, under an MIT license.

Supplementary information

Supplementary data are available at Bioinformatics Advances online.
Using graph neural networks for site-of-metabolism prediction and its applications to ranking promiscuous enzymatic products
Authors: Porokhin Vladimir , Liu Li-Ping , Hassoun Soha
Published: February 2023

Motivation

While traditionally utilized for identifying site-specific metabolic activity within a compound to alter its interaction with a metabolizing enzyme, predicting the site-of-metabolism (SOM) is essential in analyzing the promiscuity of enzymes on substrates. The successful prediction of SOMs and the relevant promiscuous products has a wide range of applications that include creating extended metabolic models (EMMs) that account for enzyme promiscuity and the construction of novel heterologous synthesis pathways. There is therefore a need to develop generalized methods that can predict molecular SOMs for a wide range of metabolizing enzymes.

Results

This article develops a Graph Neural Network (GNN) model for the classification of an atom (or a bond) being an SOM. Our model, GNN-SOM, is trained on enzymatic interactions, available in the KEGG database, that span all enzyme commission numbers. We demonstrate that GNN-SOM consistently outperforms baseline machine learning models, when trained on all enzymes, on Cytochrome P450 (CYP) enzymes, or on non-CYP enzymes. We showcase the utility of GNN-SOM in prioritizing predicted enzymatic products due to enzyme promiscuity for two biological applications: the construction of EMMs and the construction of synthesis pathways.

Availability and implementation

A python implementation of the trained SOM predictor model can be found at https://github.com/HassounLab/GNN-SOM.

Supplementary information

Supplementary data are available at Bioinformatics online.
Areography, environmental heterogeneity and spatial models explain patterns of past and present diversity inEdraianthus(Campanulaceae)
Authors: Glasnović Peter , Fišer Živa , Jančič Matic , Balant Manica , Surina Boštjan
Published: February 2023

This paper aims to shed light on distribution patterns and the relationship between species diversity and environmental heterogeneity of 17 Edraianthus taxa. We examined present and past distributions (Last Glacial Maximum) by applying ecological niche modelling. The environmental space occupied by the taxa was analysed using niche comparison methods. The results support the idea that the central and southern Dinaric Alps represent a centre of diversity and endemism in the western Balkan Peninsula. Diversity in Edraianthus is best explained by topographic (slope) and bioclimatic predictors (maximum temperature of warmest month, precipitation seasonality, precipitation of warmest quarter, precipitation of coldest quarter), suggesting that mountain areas with the most diversified relief have higher diversity. Niche modelling results suggest considerable range dynamics during the climatically unstable Quaternary. Thermophilic and lowland taxa responded with longitudinal shifts to ecologically suitable areas farther south, whereas high-mountain taxa responded mainly with elevational shifts. The greatest niche similarity is found among phylogenetically closely related taxa and among ecologically similar and often sympatric taxa. The least similarity was observed in species with marked differences in habitat elevation and in more geographically isolated species. Our results suggest that the extent of range and niche overlap varied among some taxa throughout their evolutionary history, which may have led to diversification at both allopatric and sympatric levels. The correlation between the genetic diversity of the most widespread taxon and the richness of taxa could be a consequence of past and present contacts. On the other hand, alternate periods of isolation may have favoured the emergence of taxa that are reproductively isolated and ecologically specialized.
Acute hepatitis of unknown aetiology in children: a clinical update on the recent outbreak with mechanistic insights
Authors: Vimalesvaran Sunitha , Verma Anita , Kyrana Eirini , Deheragoda Maesha , Dhawan Anil
Published: February 2023

Since April 2022, over 1000 children across 35 countries have developed episodes of acute hepatitis of unknown origin. At King’s College Hospital, a total of 65 children were referred with acute hepatitis of unknown etiology, with 10 of these children presenting with acute liver dysfunction leading to acute liver failure. Multiple hypotheses have been proposed and continue to be investigated worldwide. In this review, we explore the current understanding of potential aetiologies for this outbreak. We further characterize the proposed immunological mechanisms of liver injury in these cases.
Cell-free and concentrated ascites reinfusion therapy for refractory massive cardiac ascites in an adult with single ventricle haemodynamics: a case report
Authors: Tsukishiro Yasue , Yamamoto Hiroyuki , Masumoto Akiko , Takaya Tomofumi
Published: February 2023

Background

Cardiac ascites is a classical finding of right-sided heart failure, mainly caused by tricuspid valve disease and constrictive pericarditis. Refractory cardiac ascites, defined as ascites that is uncontrollable with any medication, including conventional diuretics and selective vasopressin V2 receptor antagonists, is a rare but challenging entity. Although cell-free and concentrated ascites reinfusion therapy (CART) is a therapeutic option for refractory ascites in patients with liver cirrhosis and malignancy, its efficacy in cardiac ascites has never been reported. We herein report a case of CART for refractory cardiac ascites in a patient with complex adult congenital heart disease (ACHD).

Case summary

A 43-year-old Japanese female with a history of ACHD involving single ventricle haemodynamics presented with refractory massive cardiac ascites due to progressive heart failure. Because conventional therapy using diuretics could not control her cardiac ascites, abdominal paracentesis was frequently required, resulting in hypoproteinaemia. Therefore, CART was initiated once per month in addition to conventional therapies, which enabled the prevention of hypoproteinaemia and further hospitalizations except to undergo CART. In addition, it helped improve her quality of life without any complications for 6 years until she died from cardiogenic cerebral infarction at the age of 49 years.

Discussion

This case demonstrated that CART can be safely performed in patients with complex ACHD and refractory cardiac ascites due to advanced heart failure. Thus, CART may improve refractory cardiac ascites as effectively as massive ascites caused by liver cirrhosis and malignancy and lead to an improvement in the patients’ quality of life.
A prospective, randomized, controlled, multicentre trial for secondary prevention in patients with chronic coronary syndrome using a smartphone application for digital therapy: the CHANGE study protocol
Authors: Düsing Philip , Eckardt Irina , Schirmer Stephan H , Sinning Jan-Malte , Werner Nikos , Bönner Florian , Krogmann Alexander , Schäfer Sebastian , Sedaghat Alexander , Müller Cornelius , Nickenig Georg , Zietzer Andreas
Published: February 2023

Aims

Coronary artery disease (CAD) remains the leading cause of death worldwide. ‘Stable’ CAD is a chronic progressive condition, which recent European guidelines recommend referring to as ‘chronic coronary syndrome’ (CCS). Despite therapeutic advances, morbidity and mortality among patients with CCS remain high. Optimal secondary prevention in patients with CCS includes optimization of modifiable risk factors with behavioural changes and pharmacological therapy. The CHANGE study aims to provide evidence for optimization of secondary prevention in CCS patients by using a smartphone application (app).

Methods and results

The CHANGE study is designed as a prospective, randomized, controlled trial with a 1:1 allocation ratio, which is currently performed in nine centres in Germany in a parallel group design. 210 patients with CCS will be randomly allocated either to the control group (standard-of-care) or to the intervention group, who will be provided the VantisTherapy* app in addition to standard-of-care to incorporate secondary prevention into their daily life. The study will be performed in an open design. Outcomes will be assessed using objective data from three in-person visits (0, 12, and 24 weeks). Primary outcomes will involve adherence to secondary prevention recommendations and quality of life (QoL). The recruitment process started in July 2022.

Conclusion

The CHANGE study will investigate whether a smartphone-guided secondary prevention app, combined with a monitor function compared with standard-of-care, has beneficial effects on overall adherence to secondary prevention guidelines and QoL in patients with CCS.

Trial registration

The study is listed at the German study registry (DRKS) under the registered number DRKS00028081.
The impact of COVID-19 and COVID vaccination on cardiovascular outcomes
Authors: Akhtar Zubair , Trent Mallory , Moa Aye , Tan Timothy C , Fröbert Ole , MacIntyre C Raina
Published: February 2023

COVID-19 is an independent risk factor for cardiovascular disease. COVID-19 vaccination may prevent this, but in some cases, COVID-19 vaccination may cause myocarditis or pericarditis. Patients with COVID-19 may present with non-specific symptoms that have a cardiac origin. This review examines the cardiovascular complications of COVID-19 infection and the impact of COVID-19 vaccination. COVID-19 cardiovascular complications include myocardial injury, pericarditis, coagulopathy, myocardial infarction, heart failure, arrhythmias, and persistent post-acute risk of adverse cardiovascular outcomes. Diagnostic and referral pathways for non-specific symptoms, such as dyspnoea and fatigue, remain unclear. COVID-19 vaccination is cardioprotective overall but is associated with myopericarditis in young males, though at a lower rate than following SARS-CoV-2 infection. Increased awareness among primary care physicians of potential cardiovascular causes of non-specific post-COVID-19 symptoms, including in younger adults, such as fatigue, dyspnoea, and chest pain, is essential. We recommend full vaccination with scheduled booster doses, optimal management of cardiovascular risk factors, rapid treatment of COVID-19, and clear diagnostic, referral, and management pathways for patients presenting with non-specific symptoms to rule out cardiac complications.
Acute myocardial infarction triggered by physical exertion: a systematic review and meta-analysis
Authors: Čulić Viktor , Alturki Ahmed , Vio Riccardo , Proietti Riccardo , Jerončić Ana
Published: February 2023

Aims

While regular physical activity has clear benefits to cardiovascular health, physical exertion can trigger acute myocardial infarction (AMI). We aimed to estimate how many AMIs may be attributed to bouts of physical exertion and to explore possible modifiers of this association.

Methods and results

MEDLINE, ISI Web of Science, and Scopus databases were searched for case-crossover studies reporting the relative risk (RR) of exertion-related AMI and exposure prevalence in the control periods. We used the random-effects model to pool the RR estimates and the mixed-effects model and random-effects meta-regression for subgroup analyses and estimated the population attributable fraction (PAF) at the population level and in different subgroups. The study met the Preferred Reporting Items for Systematic Reviews and Meta-Analyses requirements. Twelve studies including 19 891 AMI patients met the criteria for inclusion. There was a strong overall association between episodic physical exertion and AMI [RR = 3.46; 95% confidence interval (CI), 3.16–3.78]. The total PAF was 10.6% (95% CI, 9.44–11.83). For each additional year of age, the RR of exertion-related AMI increased by ∼3%, but the PAF decreased by 2%. For each additional time of habitual activity per week, the RR of exertion-related AMI decreased by ∼43%. The impact was greater among those engaged in physical exertion one to three times a week (≥20% of cases) and among those who did not take compared with those who took β-blockers (P = 0.049).

Conclusion

Every tenth AMI may be assigned to physical exertion. The impact was more pronounced among younger patients, those exposed to exertion one to three times a week, and those not taking β-blockers.
Salmonella entericaserovar Typhimurium STM1266 encodes a regulator of curli biofilm formation: thebrfSgene
Authors: Kao Sarina , Serfecz Jacquelyn , Sudhakar Architha , Likosky Keely , Romiyo Vineeth , Tursi Sarah , Tükel Çağla , Wilson James W
Published: February 2023

The major biofilm pathway in Salmonella enterica serovar Typhimurium involves specific growth conditions that induce the csgA gene whose product forms surface curli fibers that mediate biofilm formation. We have found that the previously uncharacterized STM1266 gene in S. Typhimurium plays a role in regulating biofilm formation via the curli pathway. S. Typhimurium ΔSTM1266 strains display a biofilm defect, and overexpression of STM1266 results in enhanced biofilm formation. STM1266 deletion resulted in lowered csgA expression using promoter–reporter β-galactosidase assays, and csgA and csgD deletions abrogate the effects of STM1266 overexpression on biofilm formation while deletion of bcsA (encoding an essential enzyme for cellulose formation) has no effect. In a mouse infection model, the ΔSTM1266 strain displayed results similar to those seen for previously reported ΔcsgA strains. The STM1266 gene is predicted to encode a DNA-binding transcriptional regulator of the MerR family and is homologous to the Escherichia coli BluR regulator protein. We respectfully propose to ascribe the name brfS (biofilm regulator for Salmonella Typhimurium) to the STM1266 gene.
Chromosome-scale genome assembly of the pink bollworm, Pectinophora gossypiella, a global pest of cotton
Authors: Stahlke Amanda R , Chang Jennifer , Chudalayandi Sivanandan , Heu Chan C , Geib Scott M , Scheffler Brian E , Childers Anna K , Fabrick Jeffrey A
Published: February 2023

The pink bollworm, Pectinophora gossypiella (Saunders) (Lepidoptera: Gelechiidae), is a major global pest of cotton. Current management practices include chemical insecticides, cultural strategies, sterile insect releases, and transgenic cotton producing crystalline (Cry) protein toxins of the bacterium Bacillus thuringiensis (Bt). These strategies have contributed to the eradication of P. gossypiella from the cotton-growing areas of the United States and northern Mexico. However, this pest has evolved resistance to Bt cotton in Asia, where it remains a critical pest, and the benefits of using transgenic Bt crops have been lost. A complete annotated reference genome is needed to improve global Bt resistance management of the pink bollworm. We generated the first chromosome-level genome assembly for pink bollworm from a Bt-susceptible laboratory strain (APHIS-S) using PacBio continuous long reads for contig generation, Illumina Hi-C for scaffolding, and Illumina whole-genome re-sequencing for error correction. The pseudo-haploid assembly consists of 29 autosomes and the Z sex chromosome. The assembly exceeds the minimum Earth BioGenome Project quality standards, has a low error rate, is highly contiguous at both the contig and scaffold levels (L/N50 of 18/8.26 MB and 14/16.44 MB, respectively), and is complete, with 98.6% of lepidopteran single-copy orthologs represented without duplication. The genome was annotated with 50% repeat content and 14,107 protein-coding genes, further assigned to 41,666 functional annotations. This assembly represents the first publicly available complete annotated genome of pink bollworm and will serve as the foundation for advancing molecular genetics of this important pest species.
Prediction of PGA in earthquake early warning using a long short-term memory neural network
Authors: Wang Ao , Li Shanyou , Lu Jianqi , Zhang Haifeng , Wang Borui , Xie Zhinan
Published: February 2023

Peak ground acceleration (PGA) is a key parameter used in earthquake early warning systems to measure the ground motion strength and initiate emergency protocols at major projects. The traditional P-wave peak displacement-dependent PGA prediction model (Pd-PGA model) tends to underestimate the PGA for large earthquakes because it cannot make full use of the fault continuity rupture information hidden in the time-varying process of ground motion. In this paper, a continuous PGA prediction long short-term memory (LSTM) neural network model is proposed. The model takes eight sequential features of stations that are proxies of the energy and other physical parameters as input and provides the recorded PGA at the station as the target output. A total of 5961 records from 119 earthquakes recorded by the Japanese Strong-Motion Earthquake Network (K-NET) in Japan are used to train the neural network and 3433 records from 73 earthquakes are used as the test set to verify the model’s generalization ability. The results show that within the same data set, the residuals of the predicted PGA for the proposed model are smaller than those of the Pd-PGA model and that the problem of PGA underestimation is resolved. The prediction accuracy also improves with increasing sequence length, which indicates that the LSTM neural network learns the rules hidden in the time series. To further verify the model’s generalization ability, the model performance is analyzed for an M 7.3 earthquake that was not included in the training or test data sets. The results show that the residuals of the predicted PGA for the event are consistent with those for the test data set, indicating that the model has good generalization ability.
Efficient wave type fingerprinting and filtering by six-component polarization analysis
Authors: Sollberger David , Bradley Nicholas , Edme Pascal , Robertsson Johan O A
Published: February 2023

We present a technique to automatically classify the wave type of seismic phases that are recorded on a single six-component recording station (measuring both three components of translational and rotational ground motion) at the Earth’s surface. We make use of the fact that each wave type leaves a unique ’fingerprint’ in the six-component motion of the sensor (i.e. the motion is unique for each wave type). This fingerprint can be extracted by performing an eigenanalysis of the data covariance matrix, similar to conventional three-component polarization analysis. To assign a wave type to the fingerprint extracted from the data, we compare it to analytically derived six-component polarization models that are valid for pure-state plane wave arrivals. For efficient classification, we make use of the supervised machine learning method of support vector machines that is trained using data-independent, analytically derived six-component polarization models. This enables the rapid classification of seismic phases in a fully automated fashion, even for large data volumes, such as encountered in land-seismic exploration or ambient noise seismology. Once the wave-type is known, additional wave parameters (velocity, directionality and ellipticity) can be directly extracted from the six-component polarization states without the need to resort to expensive optimization algorithms. We illustrate the benefits of our approach on various real and synthetic data examples for applications such as automated phase picking, aliased ground-roll suppression in land-seismic exploration and the rapid close-to real-time extraction of surface wave dispersion curves from single-station recordings of ambient noise. Additionally, we argue that an initial step of wave type classification is necessary in order to successfully apply the common technique of extracting phase velocities from combined measurements of rotational and translational motion.
Upadacitinib Induction and Maintenance Therapy Improves Abdominal Pain, Bowel Urgency, and Fatigue in Patients With Ulcerative Colitis: A Post Hoc Analysis of Phase 3 Data
Authors: Danese Silvio , Tran Jacinda , D’Haens Geert , Rubin David T , Aoyama Nobuo , Zhou Wen , Ilo Dapo , Yao Xuan , Sanchez Gonzalez Yuri , Panaccione Remo
Published: February 2023

Background

This post hoc analysis of a large, phase 3 program evaluated the effects of upadacitinib on fatigue, bowel urgency, and abdominal pain in patients with moderately to severely active ulcerative colitis.

Methods

Induction data were pooled from 2 identical studies, the U-ACHIEVE induction and U-ACCOMPLISH studies. Patients in these studies received upadacitinib 45 mg once daily or placebo as induction treatment. Responders to induction treatment were rerandomized in the U-ACHIEVE maintenance study to upadacitinib 15 mg once daily, upadacitinib 30 mg, or placebo. The percentage of patients reporting no abdominal pain and no bowel urgency daily via an electronic diary and a meaningful within-person change (≥5 points) in the Functional Assessment of Chronic Illness Therapy–Fatigue score were evaluated.

Results

The results demonstrated a statistically significantly greater percentage of patients reporting no abdominal pain and absence of bowel urgency observed from week 2 (P < .001), with upadacitinib induction treatment and clinically meaningful improvements in Functional Assessment of Chronic Illness Therapy–Fatigue score observed at week 8 (P < .001), when compared with placebo. The maintenance study showed that significant and meaningful improvements in abdominal pain, bowel urgency, and Functional Assessment of Chronic Illness Therapy–Fatigue score achieved during induction were sustained through 52 weeks of maintenance treatment in upadacitinib- vs placebo-treated patients.

Conclusions

The findings of this study support the additional benefit of upadacitinib in treating moderately to severely active ulcerative colitis by demonstrating a statistically significant impact on clinically meaningful symptoms of fatigue, bowel urgency, and abdominal pain.

(U-ACHIEVE induction and maintenance studies; NCT02819635; U-ACCOMPLISH induction study; NCT03653026).
Proton Pump Inhibitor Use Before and After a Diagnosis of Inflammatory Bowel Disease
Authors: Singh Noreen , Nugent Zoann , Singh Harminder , Shaffer Seth R , Bernstein Charles N
Published: February 2023

Background

Proton pump inhibitors (PPIs) have an impact on the gut microbiome. We investigated whether increased use of PPIs was associated with a diagnosis of inflammatory bowel disease (IBD).

Methods

The University of Manitoba IBD Epidemiology Database includes all Manitobans diagnosed with IBD between 1984 and 2018 with age-, sex-, and geography-matched control subjects and comprehensive prescription drug data from April 1995. Subjects were considered to be users if they received 2 PPI prescriptions. We assessed PPI prescriptions prediagnosis and for 3 years postdiagnosis of IBD. The absolute and relative rates were calculated and compared for PPI use pre– and post–IBD diagnosis.

Results

A total of 5920 subjects were diagnosed with IBD after April 1996. Rates of PPI use in control subjects increased gradually from 1.5% to 6.5% over 15 years. Persons with IBD had a higher rate of PPI use, peaking up to 17% within 1 year of IBD diagnosis with a rate ratio (RR) of 3.1 (95% confidence interval [CI], 2.9-3.3). Furthermore, persons with Crohn’s disease (RR, 4.2; 95% CI, 3.7-4.6) were more likely to have been PPI users prediagnosis than persons with ulcerative colitis (RR, 2.4; 95% CI, 2.2-2.7). Important predictors of increased PPI use were older age, year of data collection, and Crohn’s disease diagnosis.

Conclusions

Persons with IBD have higher PPI use preceding their diagnosis. Possibly, the use of a PPI alters the gut microbiome, increasing the risk for IBD diagnosis; or persons with IBD have increased rates of dyspepsia, warranting PPI use; or some IBD symptoms are treated with PPIs whether warranted or not.
Persistence of Antibodies Six Months after Three COVID-19 mRNA Vaccine Doses in Patients with Inflammatory Bowel Disease
Authors: Caldera Freddy , Richard Luke , Almasry Mazen , Phan Hiep , Chun Kelly , Farraye Francis A , Hayney Mary S
Published: February 2023

Lay Summary

We evaluated antibody concentrations 6 months after a third coronavirus disease 2019 messenger RNA vaccine dose in patients with inflammatory bowel diseases. Almost all patients had an antibody response, and those with a previous SARS-CoV-2 infection had higher antibody concentrations.
Verbs and Adjectives to Nouns: The Evolution of Headwords in Encyclopedias from the Late Seventeenth to the Late Nineteenth Century
Authors: Loveland Jeff
Published: February 2023

This article examines the changing forms of headwords in the partial differentiation of encyclopedias away from dictionaries from the late seventeenth century to the late nineteenth century. In the past, this differentiation has mostly been studied as a process of reducing lexical content in encyclopedias and reducing encyclopedic content in dictionaries, but it also manifested itself in the grammatical forms of allowable headwords. Specifically, proto-encyclopedias of the seventeenth and eighteenth centuries tended to accept verbs and adjectives as headwords, whereas many general encyclopedias from the mid-nineteenth century onward virtually eliminated any headwords except nouns. Here I point to three causes for this development in encyclopedias’ headwords: an influx of historical material as general encyclopedias acquired their modern scope, a de-emphasis on terminology and technolects in favor of coverage of concepts, and a rising concern for standardization and making it easier for readers to find what they wanted.
Critical care pharmacist research activity, experience and interests: a 2021 United Kingdom survey
Authors: Jennings Jennifer K , McKenzie Cathrine , Gondongwe Xolani D , Bourne Richard S
Published: February 2023

Background

Research and innovation are essential for effective healthcare service delivery, leading to improvements in patient health and wellbeing. National policy dictates that research delivery is embedded into daily practice of United Kingdom (UK) healthcare professionals, including pharmacists. There is a limited understanding of critical care pharmacist research activities, experiences and interests. It is, therefore, important to describe current practice including barriers and facilitators to enable increased engagement.

Objectives

To describe UK critical care pharmacist research activity, experiences, interests and barriers to better engagement.

Method

An electronic survey was developed, piloted and distributed (June to October 2021) to all critical care pharmacists via UK professional organisations.

Key findings

The survey was completed by 126 pharmacists, providing a 54% response rate. Few pharmacists reported research capability (postgraduate qualification with a research component, 31% (39/126)) and opportunity (dedicated research time, 28.6% (36/126)), only 12.7% (16/126) have both these influencers. Those that did, produced significantly more research outputs (median 4 (0,9) versus 0 (0,1), P = 0.023) and undertook grant funding applications (X2 (1, n = 126) = 25.8, P < 0.001), compared to those without. The most frequently reported barrier to research was the time (opportunity), (71.4%, 90/126). Few pharmacists reported having a research mentor (13.3%, 16/120). Most pharmacists reported an interest in collaborating on research projects across a broad range of areas.

Conclusions

Critical care pharmacists are motivated to participate in the evaluation continuum including research, although most report capability and opportunity barriers to delivery. We suggest policy recommendations to address limitations and increase pharmacist research involvement.
Variants in the Sequence of the Probe Hybridization Site May Affect MLPA Performance in Patients with Duchenne/Becker Muscular Dystrophy
Authors: Buitrago Tatiana , García-Acero Mary , Guerra-Torres Mariana , Pineda Tatiana , Gámez Tatiana , Suárez-Obando Fernando , García-Robles Reggie , Ayala-Ramírez Paola
Published: February 2023

Background

The MLPA (multiplex ligation dependent probe amplification) technique is currently the test most widely used to detect mutations in the Duchenne/Becker muscular dystrophy (DMD) gene in the initial assessment. However, several studies have suggested that MLPA results require implementing other detection methods due to false duplication. Our aim was to evaluate variables that could alter the peak ratio in MLPA in individuals with Duchenne/Becker muscular dystrophy (DMD/BMD) who present sequence variants at the probe hybridization site, such as the location of sequence variants (SVs), melting temperature of the probe, and the type of variant.

Methods

We analyzed patients with clinical suspicion of DMD/BMD through the MLPA technique. The DMD gene was sequenced in patients with normal results in MLPA.

Results

Of 111 patients, 72 had an abnormal MLPA result, of which 10 had a single exon abnormal peak, and 39 had a normal peak ratio. Out of 10 patients, 4 (40%) with a single exon abnormal peak ratio had SV at the hybridization site of the probe. In the other 6, the deletion was confirmed. Out of 39 patients with a normal peak ratio, 11 presented SVs at the hybridization site of the probe, and DMD/BMD was confirmed.

Conclusions

In cases of abnormal peak ratio results of MLPA in a single exon, it would be valuable to sequence the DMD gene to assess whether variants in the probe hybridization site might result in a false positive that could be interpreted as an exon deletion.
On Breaking Functional Fixedness: How the Aha! Moment Enhances Perceived Product Creativity and Product Appeal
Authors: Caprioli Sara , Fuchs Christoph , Van den Bergh Bram
Published: February 2023

How do consumers react to products assembled from existing components? Nine studies in both the lab and the field demonstrate that consumers evaluate products as more creative and more appealing when they consist of components that originally served entirely different functions. When consumers realize that the intended functionality of a component is not fixed, but versatile, they experience an aha! moment, which in turn enhances perceived product creativity and product appeal. This research bridges engineering and consumer research providing theoretical contributions to the product design and creativity literature. The findings of this research have substantive implications for designing sustainable products, especially for product upcycling, the process of transforming old or used components into new products.
Dynamic Economic Thresholds for Insecticide Applications Against Agricultural Pests: Importance of Pest and Natural Enemy Migration
Authors: Keasar Tamar , Wajnberg Eric , Heimpel George , Hardy Ian C W , Harpaz Liora Shaltiel , Gottlieb Daphna , van Nouhuys Saskya
Published: February 2023

In Integrated Pest Management programs, insecticides are applied to agricultural crops when pest densities exceed a predetermined economic threshold. Under conditions of high natural enemy density, however, the economic threshold can be increased, allowing for fewer insecticide applications. These adjustments, called ‘dynamic thresholds’, allow farmers to exploit existing biological control interactions without economic loss. Further, the ability of natural enemies to disperse from, and subsequently immigrate into, insecticide-sprayed areas can affect their biological control potential. We develop a theoretical approach to incorporate both pest and natural enemy movement across field borders into dynamic thresholds and explore how these affect insecticide applications and farmer incomes. Our model follows a pest and its specialist natural enemy over one growing season. An insecticide that targets the pest also induces mortality of the natural enemy, both via direct toxicity and reduced resource pest densities. Pest and natural enemy populations recover after spraying through within-field reproduction and by immigration from neighboring unsprayed areas. The number of insecticide applications and per-season farmer revenues are calculated for economic thresholds that are either fixed (ignoring natural enemy densities) or dynamic (incorporating them). The model predicts that using dynamic thresholds always leads to reduced insecticide application. The benefit of dynamic thresholds in reducing insecticide use is highest when natural enemies rapidly recolonize sprayed areas, and when insecticide efficacy is low. We discuss real-life situations in which monitoring of natural enemies would substantially reduce insecticide use and other scenarios where the presence of beneficial organisms may lead to threshold modifications.
A delayed benign anastomotic stricture after anterior resection for sigmoid adenocarcinoma with concomitant collagenous colitis
Authors: Wallace Lauren , Gallagher James
Published: February 2023

Benign anastomotic strictures most commonly occur within 3–12 months after anterior resection (AR) with chronic symptoms amenable to endoscopic treatment. This case describes an acute large bowel obstruction secondary to a severe delayed benign anastomotic stricture in a 74-year-old female who had previously underwent a laparoscopic AR for sigmoid adenocarcinoma 3 years prior. The pathophysiology of benign anastomotic strictures remains poorly understood. This case was likely multifactorial. Potential contributing factors include anastomotic ischaemia and concomitant collagenous colitis, with inflammation leading to fibrosis and stricture development. Surgical techniques to optimize anastomotic vascularity are important to consider, particularly in older patients with multiple co-morbidities.
Urological Surgery
Authors: Biers Suzanne , Armenakas Noel , Lamb Alastair , Mark Stephen , Reynard John , Sullivan Mark , Turner Kevin , Turney Ben
Published: February 2023

This is a comprehensive handbook providing clear step-by-step guidance through all types of urological operations, and is an essential tool for those whose practice covers urology. Each chapter is written by well-respected sub-specialists in their field, all active and enthusiastic about training and teaching in urology. The handbook includes background information on key urological problems and details about alternative surgical options and risks and complications of procedures, and guides doctors in gaining clear and accurate consent from patients. This is a great resource, and its format allows a quick revision of different procedures, which can be conveniently used in theatres, in clinic, on the ward, and at home, in preparation for surgery. It includes helpful pointers on patient positioning, indications and contraindications for surgery, types of incisions that can be used, important procedure points, the ideal instruments to use, and aftercare of patients and follow-up. It is an excellent reference tool, providing detailed information on all urological operations, with tips and tricks from the experienced contributors.