bluuebunny/crossref_metadata_2025 huggingface dataset:
GP-Plotter: Flexible Spectral Visualization for Proteomics Data with Emphasis on Glycoproteomics Analysis
Authors: Fang Zheng , Dong Mingming , Qin Hongqiang , Ye Mingliang
Published: October 2024

Identification evaluation and result dissemination are essential components in mass spectrometry-based proteomics analysis. The visualization of fragment ions in mass spectrum provides strong evidence for peptide identification and modification localization. Here, we present an easy-to-use tool, named GP-Plotter, for ion annotation of tandem mass spectra and corresponding image output. Identification result files of common searching tools in the community and user-customized files are supported as input of GP-Plotter. Multiple display modes and parameter customization can be achieved in GP-Plotter to present annotated spectra of interest. Different image formats, especially vector graphic formats, are available for image generation which is favorable for data publication. Notably, GP-Plotter is also well-suited for the visualization and evaluation of glycopeptide spectrum assignments with comprehensive annotation of glycan fragment ions. With a user-friendly graphical interface, GP-Plotter is expected to be a universal visualization tool for the community. GP-Plotter has been implemented in the latest version of Glyco-Decipher (v1.0.4) and the standalone GP-Plotter software is also freely available at https://github.com/DICP-1809.
Healthcare Access for Patients With Inflammatory Bowel Disease in the United States: A Survey by the Crohn’s & Colitis Foundation
Authors: Jordan Ariel A , Bhat Shubha , Ali Tauseef , Brunskill Sarah R , Clusen Nancy A , Maltz Ross M , Moise Ced , Sun Xiaofan , Thomas Harry J , Ray Cassie , Harkins-Schwarz Mary , Ehrlich Orna G
Published: October 2024

Background

A prior survey disseminated in 2017 identified that healthcare access barriers exist and significantly affect patients with inflammatory bowel disease (IBD). We sought to identify, through an updated survey, the healthcare access barriers that patients continue to face, with a focus on socioeconomic factors and patient awareness of resources to navigate existing barriers.

Methods

A 52-question online survey evaluating (1) access to healthcare professionals, medications, and procedures; (2) associated financial challenges; and (3) patient awareness of education and advocacy tools to navigate IBD care barriers, was disseminated through multiple channels to IBD patients and their caregivers.

Results

Of the 2281 completed responses, patients on advanced specialty medications, younger than 65 years of age, or on employer insurance experienced significantly greater issues with insurance barriers to accessing medications and coverage of medically necessary tests/treatments. Patients who live in areas of concentrated poverty were more likely to experience poor health outcomes when subjected to step therapy compared to patients who did not. Additionally, patients were more likely to experience one or more financial barriers or trade-offs if the patient used an advanced specialty medicine or lived in an area with concentrated poverty.

Conclusions

While there have been significant and numerous advancements in IBD treatments, patients with IBD continue to experience barriers to healthcare access and treatment and financial struggles. Ongoing awareness and advocacy efforts focused on healthcare system reform and related policies to further minimize care disparities and barriers remain vital.
COVID-19 Disease Incidence and Severity in Persons Previously Infected and Unvaccinated vs Previously Uninfected and Vaccinated
Authors: Butt Adeel A , Yan Peng , Abou-Samra Abdul-Badi , Shaikh Obaid S
Published: October 2024

Using the national COVID-19 database of the US Department of Veterans Affairs, we matched pairs of individuals who were previously uninfected and vaccinated (≥2 doses of an mRNA vaccine) and previously infected and unvaccinated. The incidence rate of breakthrough infection among vaccinated individuals (per 1000 person-days, 0.30; 95% CI, .29–.32) was similar to the reinfection rate among unvaccinated individuals (0.31; 95% CI, .30–.32; P = .5). The incidence rate of hospitalization/death was higher after reinfection (7.31; 95% CI, 6.66–8.03) as compared with the rate after breakthrough infection (4.69; 95% CI, 4.06–5.42; P < .0001). The incidence of hospitalization/death is significantly higher after reinfection among unvaccinated individuals as compared with breakthrough infection after vaccination.
Nonkin interactions between Bacillus subtilis soil isolates limit the spread of swarming deficient cheats
Authors: Belcijan Pandur Katarina , Kraigher Barbara , Tomac Ana , Stefanic Polonca , Mandic Mulec Ines
Published: October 2024

Cooperative behaviours in human, animal, and even microbial societies are vulnerable to exploitation. Kin discrimination has been hypothesized to help stabilize cooperation. However, the mechanisms that sustain cooperative behaviour remain poorly understood. Here, we investigate the role of kin discrimination in limiting the spread of cheats in adjoining populations during surfactant-dependent cooperative swarming over surfaces using the bacterium Bacillus subtilis as a model organism. We show that mixing surfactant secreting cooperators and cheats that do not produce surfactants at 1:1 initial ratio quickly leads to cooperation collapse. However, when such common swarms encounter nonkin B. subtilis swarms, the proportion of the surfactant nonproducers decreases, suggesting that kinship dependent interactions may limit cheats’ advantage in an adjoining population. To further validate this finding, we subjected wild-type cooperators to multiple transient encounters with kin and nonkin swarms over 20 cycles of experimental evolution. The evolved populations exposed to nonkin swarms less frequently contained defective swarming phenotypes compared to those encountering kin swarms. Altogether, our results support the prediction that the spread of cheats in an adjoining bacterial population is impeded by kin discrimination interactions, which might have a role in stabilizing cooperative behaviour in evolving populations.
A loading dose of clofazimine to rapidly achieve steady-state-like concentrations in patients with nontuberculous mycobacterial disease
Authors: Stemkens Ralf , Lemson Arthur , Koele Simon E , Svensson Elin M , te Brake Lindsey H M , van Crevel Reinout , Boeree Martin J , Hoefsloot Wouter , van Ingen Jakko , Aarnoutse Rob E
Published: October 2024

Objectives

Clofazimine is a promising drug for the treatment of nontuberculous mycobacterial (NTM) diseases. Accumulation of clofazimine to reach steady-state plasma concentrations takes months. A loading dose may reduce the time to steady-state-like concentrations. We evaluated the pharmacokinetics (PK), safety and tolerability of a loading dose regimen in patients with NTM disease.

Methods

Adult participants received a 4-week loading dose regimen of 300 mg clofazimine once daily, followed by a maintenance dose of 100 mg once daily (combined with other antimycobacterial drugs). Blood samples for PK analysis were collected on three occasions. A population PK model for clofazimine was developed and simulations were performed to assess the time to reach steady-state-like (target) concentrations for different dosing regimens.

Results

Twelve participants were included. The geometric mean peak and trough clofazimine concentrations after the 4-week loading phase were 0.87 and 0.50 mg/L, respectively. Adverse events were common, but mostly mild and none led to discontinuation of clofazimine. Our loading dose regimen reduced the predicted median time to target concentrations by 1.5 months compared to no loading dose (3.8 versus 5.3 months). Further time benefit was predicted with a 6-week loading dose regimen (1.4 versus 5.3 months).

Conclusion

A 4-week loading dose regimen of 300 mg once daily reduced the time to target clofazimine concentrations and was safe and well-tolerated. Extending the loading phase to 6 weeks could further decrease the time to target concentrations. Using a loading dose of clofazimine is a feasible strategy to optimize treatment of NTM disease.

Clinical Trials Registration

NCT05294146
End user experience of a widely used artificial intelligence based sepsis system
Authors: Owoyemi Ayomide , Okpara Ebere , Salwei Megan , Boyd Andrew
Published: October 2024

Objectives

Research on the Epic Sepsis System (ESS) has predominantly focused on technical accuracy, neglecting the user experience of healthcare professionals. Understanding these experiences is crucial for the design of Artificial Intelligence (AI) systems in clinical settings. This study aims to explore the socio-technical dynamics affecting ESS adoption and use, based on user perceptions and experiences.

Materials and Methods

Resident doctors and nurses with recent ESS interaction were interviewed using purposive sampling until data saturation. A content analysis was conducted using Dedoose software, with codes generated from Sittig and Singh’s and Salwei and Carayon’s frameworks, supplemented by inductive coding for emerging themes.

Results

Interviews with 10 healthcare providers revealed mixed but generally positive or neutral perceptions of the ESS. Key discussion points included its workflow integration and usability. Findings were organized into 2 main domains: workflow fit, and usability and utility, highlighting the system’s seamless electronic health record integration and identifying design gaps.

Discussion

This study offers insights into clinicians’ experiences with the ESS, emphasizing the socio-technical factors that influence its adoption and effective use. The positive reception was tempered by identified design issues, with clinician perceptions varying by their professional experience and frequency of ESS interaction.

Conclusion

The findings highlight the need for ongoing ESS refinement, emphasizing a balance between technological advancement and clinical practicality. This research contributes to the understanding of AI system adoption in healthcare, suggesting improvements for future clinical AI tools.
Concordance of data collected by an app for medical history taking and in-person interviews from patients in primary care
Authors: Joos Carla , Albrink Klara , Hummers Eva , Müller Frank , Antweiler Kai , Schröder Dominik , Noack Eva Maria
Published: October 2024

Objective

This study investigates the concordance of patient information collected using a medical history app compared to in-person interviews.

Materials and Methods

In this cross-sectional study we used an app to collect medical data from patients in family practice in Germany. Collected information included age, height, weight, perceived severity of complaints, and 38 current complaints. Subsequently, in-person interviews based on the query structure of the app were conducted with patients directly after the patient finished filling out the app. Concordance was assessed as exact matches between the data collected app-based and in-person interviews, with the in-person interview as a reference. Regression analysis examined which patient characteristics were associated with mismatching and underreporting of complaints.

Results

Three hundred ninety-nine patients were included in the study. Concordance of reported age, weight, and height, as well as perceived severity of complaints ranged from 76.2% to 96.7%. Across all 38 complaints, 64.4% of participants showed completely identical complaint selection in app-based and in-person interviews; 18.5% of all participants overreported; and 17.0% underreported at least 1 complaint when using the app. Male sex, higher age, and higher number of stated complaints were associated with higher odds of underreporting at least one complaint in the app.

Discussion

App-collected data regarding age, weight, height, and perceived severity of complaints showed high concordance. The discordance shown concerning various complaints should be examined regarding their potential for medical errors.

Conclusion

The introduction of apps for gathering information on complaints can improve the efficiency and quality of care but must first be improved.

Trial registration

The study was registered at the German Clinical Trials Register No. DRKS00026659 registered November 3, 2021. World Health Organization Trial Registration Data Set, https://trialsearch.who.int/Trial2.aspx?TrialID=DRKS00026659
How does anthropogenic food influence the trophic ecology of Rocky Mountain Red Fox?
Authors: Burkholder Emily N , Stephenson John , Hegg Sarah , Gustine David , Robinson Tim , Holbrook Joseph D
Published: October 2024

Providing novel food subsidies to wildlife can influence behavior, resource use, disease dynamics, and food web interactions. Studies examining impacts of anthropogenic food have primarily occurred in urban landscapes where anthropogenic resources are consistently accessible. National parks, however, experience similar issues regarding wildlife exploiting anthropogenic food, but access to anthropogenic food is contingent on human visitation, which can fluctuate dramatically between seasons. We evaluated how fluctuating availability of anthropogenic food and demographic factors influenced the isotopic niche of Rocky Mountain Red Fox (Vulpes vulpes macroura) at the population and individual level in Grand Teton National Park, Wyoming. From 2016 to 2021, we assessed diet-related questions by collecting 55 whisker samples and 52 hair samples from 40 unique individuals and analyzed them using stable isotope analysis (δ13C and δ15N). We discovered that Rocky Mountain red foxes have a broad isotopic niche, with seasonal differences in their consumption of anthropogenic food. Contrary to our expectations, foxes demonstrated increased reliance on anthropogenic food (higher δ13C values) during winter months, whereas natural food consumption or dietary mixing was more prominent in summer months. Natural food scarcity could be driving foxes to seek out more anthropogenic food in the winter, whereas the increased abundance of natural food items in the summer could result in a lower need for foxes to supplement their diet with anthropogenic food. Adults had consistently higher δ13C values relative to juveniles, indicating either intraspecific variation in boldness or dominance leading to increased exploitation of anthropogenic food, which could be a learned behavior coinciding with habituation. Finally, we observed that increasing densities of human features within the home range of a fox was a strong predictor of anthropogenic food reliance at the individual level. Our work provided a deeper understanding of the trophic ecology of Rocky Mountain Red Fox in relation to human activity in a nature preserve, and equipped managers with insight into potential patterns associated with food-conditioned foxes.
Law and Order in Counterinsurgency: The Link between Insurgent Group Characteristics and the Use of Domestic Law Enforcement
Authors: Alakoc Burcu Pinar , Asal Victor
Published: October 2024

Modern-day insurgencies are adaptive, enduring, and increasingly intertwined with criminal elements, and therefore pose serious threats to regional and global security. In response, counterinsurgency strategies have become more diversified. One of the strategies that states can employ toward insurgencies is the use of domestic law enforcement, which includes operations by police and intelligence agencies. Given the predominant focus on military approaches, however, there is little empirical work that examines the use of domestic law enforcement in counterinsurgencies. To address this, we investigate the underlying reasons behind a government’s decision to deploy domestic law enforcement against insurgencies. We argue that specific attributes of insurgent groups significantly shape this decision. Using the BAADI2 dataset, our analysis shows that insurgent groups that participate in cooperative alliances and engage in criminal activities are most likely to motivate a state’s decision to deploy domestic law enforcement as a counterinsurgency strategy against them.
School as a place for Bildung and flourishing
Authors: Lea Kjersti E
Published: October 2024

This article explores the potential of schools to enhance students’ well-being and overall quality of life. The discussion is framed through two distinct perspectives: the Bildung tradition and Aristotelian ethics. In regions where the Bildung tradition is prominent, schools are traditionally viewed as environments conducive to fostering humaneness. However, contemporary educational policies often diverge from the core values of Bildung-oriented education. The article advocates for the continued promotion of Bildung and flourishing within schools. To achieve this, certain foundational conditions must be met. One such condition is acknowledging students’ need for a sense of belonging and purpose, which is essential for their flourishing. This flourishing, in turn, equips students with the courage and resilience to face an uncertain future and contribute to societal change. For schools to foster a sense of belonging, they must be meaningful places of interaction and companionship, both physically and socially. This necessitates recognizing that educational environments are situated within specific geographical and cultural contexts. Consequently, education should not be excessively standardized. The Bildung tradition provides insights into why this is important. When combined with Aristotelian ethics, it becomes possible to develop schools that offer students a sense of belonging and purpose, thereby promoting their flourishing. In this framework, Bildung and flourishing are seen as concepts that embody possibilities and optimism, offering hope and empowerment at both individual and collective levels.
Developmental changes in how pedestrians cross streets in single- vs. dual-lane traffic conditions
Authors: Morrongiello Barbara A , Corbett Michael , Zolis Caroline
Published: October 2024

Objective

Pedestrian injury is a leading contributor to childhood deaths. This study compared the crossing behaviors of children with adults when crossing in virtual single-lane vs. two-lane traffic conditions.

Method

Using a fully immersive virtual reality system, children 7–10 years and adults crossed streets with traffic in one lane (near lane) or in two lanes (near and far lane) with 0 offset so cars from opposing directions arrived at the child’s crossing line at the same time. On each trial, pedestrians made a decision on when to cross and then completed the crossing, with measures of attention and crossing behaviors automatically recorded by the system as they did so.

Results

In comparison to crossing a single lane of traffic, crossing two-lane roads increased injury risk for all pedestrians, though children experienced significantly greater risk than adults. Children predominantly crossed by stopping before entering the far lane, whereas adults showed greater synchronization of self-movement to traffic flow and more often crossed both lanes without stopping.

Conclusions

Children experience more high-risk outcomes than adults when crossing single-lane roads. Crossing two-lane roads elevates risk for pedestrians of both ages, though this risk is significantly greater for child than adult pedestrians. The predominant strategy used to cross two lanes of traffic shows significant developmental changes. Implications for injury prevention are discussed.
Spontaneous splenic rupture as a primary manifestation of angiosarcoma: a case report
Authors: Awashra Ameer , Sawaftah Zaid , Odah Ali Bani , Sawafta Ahmed , Khatib Amer , Dababat Huthayfa , Yasin Anas , Khamaysa Jehad , Daraghmeh Muath
Published: October 2024

Angiosarcoma, a rare endothelial cell tumor, accounts for < 2% of all sarcomas, typically affecting elderly patients. We present the case of a 62-year-old male with a history of hypertension and ischemic heart disease, who initially presented with severe lower back pain. Subsequent imaging revealed a ruptured splenic lesion and multiple liver lesions, leading to a diagnosis of stage 4 angiosarcoma. Post-splenectomy, the patient exhibited pathological vertebral fractures and elevated liver function tests, consistent with metastatic disease. Despite aggressive surgical intervention and supportive care, the patient’s condition remained critical. The treatment plan included palliative chemotherapy, spine radiotherapy, and ongoing pain management, with close monitoring of disease progression and response to therapy. This case describes the diagnostic challenges and poor prognosis associated with metastatic angiosarcoma.
High water use efficiency due to maintenance of photosynthetic capacity in sorghum under water stress
Authors: Al-Salman Yazen , Cano Francisco Javier , Mace Emma , Jordan David , Groszmann Michael , Ghannoum Oula
Published: October 2024

Environmental change requires more crop production per water use to meet the rising global food demands. However, improving crop intrinsic water use efficiency (iWUE) usually comes at the expense of carbon assimilation. Sorghum is a key crop in many vulnerable agricultural systems with higher tolerance to water stress (WS) than most widely planted crops. To investigate physiological controls on iWUE and its inheritance in sorghum, we screened 89 genotypes selected based on inherited haplotypes from an elite line or five exotics lines, containing a mix of geographical origins and dry versus milder climates, which included different aquaporin (AQP) alleles. We found significant variation among key highly heritable gas exchange and hydraulic traits, with some being significantly affected by variation in haplotypes among parental lines. Plants with a higher proportion of the non-stomatal component of iWUE still maintained iWUE under WS by maintaining photosynthetic capacity, independently of reduction in leaf hydraulic conductance. Haplotypes associated with two AQPs (SbPIP1.1 and SbTIP3.2) influenced iWUE and related traits. These findings expand the range of traits that bridge the trade-off between iWUE and productivity in C4 crops, and provide possible genetic regions that can be targeted for breeding.
A One Health exploration of antimicrobial resistance in Escherichia coli originated from urban and rural lakes ecosystem
Authors: Priyanka Priyanka , Meena Prem Raj , Raj Dharma , Mishra Purnima , Jha Anand Kumar , Duggirala K Siddaardha , Dhanokar Akshay , Kumar Amit , Rana Anuj , Singh Arvind Pratap
Published: October 2024

Antimicrobial resistance (AMR) has become one of the most serious threats to One Health. Aquatic environments are an ideal non-clinical AMR reservoir and can act as a key battlefront for tackling the AMR. However, AMR data using the One Health approach remain scarce in aquatic environments worldwide. Here, we extensively assessed AMR in Escherichia coli isolated from urban and rural lake ecosystems using the One Health perspective. A total of 162 E. coli isolates obtained from lakes were tested against 25 antimicrobials using an in-vitro antimicrobial susceptibility testing method. A low (2%) to moderate (45%) drug resistance rate was found for all antimicrobials used in human/veterinary medicine or animal/plant agriculture. However, <80% E. coli isolates exhibited multidrug resistance (MDR) phenotype to highly important (amikacin, gentamicin, trimethoprim) or critically important (amoxicillin, ampicillin, colistin) drugs of both human and veterinary medicine. Of concern, >50% of E. coli isolates exhibited MDR to drugs used as last-resorts (chloramphenicol, colistin) or as frontline (nitrofurantoin, sulfamethoxazole, ampicillin, gentamicin) against E. coli infections. In conclusion, the presence of MDR E. coli strains in urban or rural lake ecosystems highlights their possible role as AMR reservoirs with potential One Health risks.
More than just the gene: investigating expression using a non-native plasmid and host and its impact on resistance conferred by β-lactamase OXA-58 isolated from a hospital wastewater microbiome
Authors: Wu J , Thompson T P , O'Connell N H , McCracken K , Powell J , Gilmore B F , Dunne C P , Kelly S A
Published: October 2024

With the escalation of hospital-acquired infections by multidrug resistant bacteria, understanding antibiotic resistance is of paramount importance. This study focuses on the β-lactamase gene, blaOXA-58, an important resistance determinant identified in a patient-facing hospital wastewater system. This study aimed to characterize the behaviour of the OXA-58 enzyme when expressed using a non-native plasmid and expression host. blaOXA-58 was cloned using a pET28a(+)/Escherichia coli BL21(DE3) expression system. Nitrocefin hydrolysis and antimicrobial susceptibility of OXA-58-producing cells were assessed against penicillin G, ampicillin, meropenem, and amoxicillin. blaOXA-58 conferred resistance to amoxicillin, penicillin G, and ampicillin, but not to meropenem. This was unexpected given OXA-58’s annotation as a carbapenemase. The presence of meropenem also reduced nitrocefin hydrolysis, suggesting it acts as a competitive inhibitor of the OXA-58 enzyme. This study elucidates the phenotypic resistance conferred by an antimicrobial resistance gene (ARG) obtained from a clinically relevant setting and reveals that successful functional expression of ARGs is multifaceted. This study challenges the reliability of predicting antimicrobial resistance based solely on gene sequence alone, and serves as a reminder of the intricate interplay between genetics and structural factors in understanding resistance profiles across different host environments.
Medieval reading in the twenty-first century?
Authors: Ward Aengus , He Shiyu
Published: October 2024

Reading practices in medieval manuscripts have often been the subject of critical analysis in the past. Recent technological developments have extended the range of analytical possibilities; one such development is that of eye tracking. In the present article, we outline the results of an experiment using eye tracking technologies which were carried out recently in Spain. The analysis points to particular trends in the ways in which modern readers interact with medieval textual forms and we use this analysis to point to future possibilities in the use of eye tracking to broaden and deepen our understanding of the workings of the medieval page.
Not Quite Yet a Hazy Limbo of Mystery: Intuition in Russell’s An Essay on the Foundations of Geometry
Authors: Nunez Tyke
Published: October 2024

I argue that in Bertrand Russell’s An Essay on the Foundations of Geometry (1897), his forms of externality serve the same fundamental role in grounding the possibility of geometry that Immanuel Kant’s forms of intuition serve in grounding geometry in his critical philosophy. Specifically, both provide knowledge of bare numerical difference, where we have no concept of this difference. Because geometry deals with such conceptually homogeneous magnitudes and their composition on both accounts, forms of intuition or externality (respectively) are at its foundation.
The evolutionary history of GD 1400AB, a white dwarf–brown dwarf binary
Authors: Casewell S L , Burleigh M R , Napiwotzki R , Zorotovic M , Bergeron P , French J R , Hermes J J , Faedi F , Lawrie K L
Published: October 2024

GD1400AB was one of the first known white dwarf $+$ brown dwarf binaries and is the only one of these systems where the white dwarf is a ZZ Ceti pulsator. Here, we present both radial velocity measurements and time-series photometry, analysing both the white dwarf pulsations and the effects of irradiation on the brown dwarf. We find that the brightness temperatures of 1760 $\pm $ 10 K for the nightside and 1860 $\pm$ 10 K for the dayside indicate that the brown dwarf is hotter than spectra have previously suggested, although brightness temperatures calculated using a larger radius for the brown dwarf are consistent with previously determined spectral types. We also discuss the likely evolutionary pathway of this binary and put its common envelope phase into context with the other known systems.
AMIR: a multi-omics data platform for Asteraceae plants genetics and breeding research
Authors: Liu Dongxu , Luo Chengfang , Dai Rui , Huang Xiaoyan , Chen Xiang , He Lin , Mao Hongxia , Li Jiawei , Zhang Linna , Yang Qing-Yong , Mei Zhinan
Published: October 2024

As the largest family of dicotyledon, the Asteraceae family comprises a variety of economically important crops, ornamental plants and numerous medicinal herbs. Advancements in genomics and transcriptomic have revolutionized research in Asteraceae species, generating extensive omics data that necessitate an efficient platform for data integration and analysis. However, existing databases face challenges in mining genes with specific functions and supporting cross-species studies. To address these gaps, we introduce the Asteraceae Multi-omics Information Resource (AMIR; https://yanglab.hzau.edu.cn/AMIR/), a multi-omics hub for the Asteraceae plant community. AMIR integrates diverse omics data from 74 species, encompassing 132 genomes, 4 408 432 genes annotated across seven different perspectives, 3897 transcriptome sequencing samples spanning 131 organs, tissues and stimuli, 42 765 290 unique variants and 15 662 metabolites genes. Leveraging these data, AMIR establishes the first pan-genome, comparative genomics and transcriptome system for the Asteraceae family. Furthermore, AMIR offers user-friendly tools designed to facilitate extensive customized bioinformatics analyses. Two case studies demonstrate AMIR’s capability to provide rapid, reproducible and reliable analysis results. In summary, by integrating multi-omics data of Asteraceae species and developing powerful analytical tools, AMIR significantly advances functional genomics research and contributes to breeding practices of Asteraceae.
Factors Related to the Rise of Congenital Syphilis From the Perspectives of Prenatal Providers and Birthing Parents in Chicago, IL, USA
Authors: Flores John M , Kasal Nikki , Montag Caroline , Dawdani Alicia , Almirol Ellen , Montgomery Jackson M C , Zimmer Daniela , Ridgway Jessica , Schneider John A
Published: October 2024

Background

Rates of congenital syphilis (CS) in the United States have risen sharply in recent years. There has been sparse research centering the voices and experiences of birthing parents who have delivered infants with CS and prenatal providers in Chicago or the surrounding Midwestern United States to date. Additionally, there has been little research on the role of extrinsic factors, such as stigma and attitudes surrounding CS in an individual's community, in their entry into and retention in the CS prevention cascade.

Methods

Semistructured interviews seeking to gather perspectives and factors related to the rise of CS were conducted with birthing parents who delivered infants with CS at a major academic medical institution (AMI) and the prenatal providers who served them. This was supplemented by retrospective data of birthing parent outcomes.

Results

Barriers elicited during the interviews included insufficient penicillin uptake, limited transportation, poor communication between providers and patients, gaps in patient understanding or knowledge around CS contraction and treatment, missed appointments, appointment burden for patients, life stressors of patients, housing instability, childcare difficulties, and stigma related to the CS diagnosis. The quantitative data revealed differing proportions of CS outcomes and care between those with care within the AMI, those with care outside the AMI, and those who had no prenatal care.

Conclusions

This study found numerous perspectives and factors that may explain the rise of CS along various stages of the syphilis care continuum through in-depth interviews of prenatal providers and birthing parents.
Controversies in smoldering multiple myeloma: finding the optimal approach for treatment initiation
Authors: Ludwig Heinz , Schreder Martin
Published: October 2024

This commentary focuses on data in favor of early treatment initiation or a cautious wait-and-see strategy in smoldering multiple myeloma.
Charting the course of Sargassum: Incorporating nonlinear elastic interactions and life cycles in the Maxey–Riley model
Authors: Bonner Gage , Beron-Vera F J , Olascoaga M J
Published: October 2024

The surge of pelagic Sargassum in the Intra-America Seas, particularly the Caribbean Sea, since the early 2010s has raised significant ecological concerns. This study emphasizes the need for a mechanistic understanding of Sargassum dynamics to elucidate the ecological impacts and uncertainties associated with blooms. By introducing a novel transport model, physical components such as ocean currents and winds are integrated with biological aspects affecting the Sargassum life cycle, including reproduction, grounded in an enhanced Maxey–Riley theory for floating particles. Nonlinear elastic forces among the particles are included to simulate interactions within and among Sargassum rafts. This promotes aggregation, consistent with observations, within oceanic eddies, which facilitate their transport. This cannot be achieved by the so-called leeway approach to transport, which forms the basis of current Sargassum modeling. Using satellite-derived data, the model is validated, outperforming the leeway model. Publicly accessible codes are provided to support further research and ecosystem management efforts. This comprehensive approach is expected to improve predictive capabilities and management strategies regarding Sargassum dynamics in affected regions, thus contributing to a deeper understanding of marine ecosystem dynamics and resilience.
Statistical estimation of full-sky radio maps from 21 cm array visibility data using Gaussian constrained realizations
Authors: Glasscock Katrine A , Bull Philip , Burba Jacob , Garsden Hugh , Wilensky Michael J
Published: October 2024

An important application of next-generation wide-field radio interferometers is making high dynamic range maps of radio emission. Traditional deconvolution methods like CLEAN can give poor recovery of diffuse structure, prompting the development of wide-field alternatives like Direct Optimal Mapping and m-mode analysis. In this paper, we propose an alternative Bayesian method to infer the coefficients of a full-sky spherical harmonic basis for a drift-scan telescope with potentially thousands of baselines that can precisely encode the uncertainties and correlations between the parameters used to build the recovered image. We use Gaussian constrained realizations (GCR) to efficiently draw samples of the spherical harmonic coefficients, despite the very large parameter space and extensive sky-regions of missing data. Each GCR solution provides a complete, statistically consistent gap-free realization of a full-sky map conditioned on the available data, even when the interferometer’s field of view is small. Many realizations can be generated and used for further analysis and robust propagation of statistical uncertainties. In this paper, we present the mathematical formalism of the spherical harmonic GCR method for radio interferometers. We focus on the recovery of diffuse emission as a use case, along with validation of the method against simulations with a known diffuse emission component.
Regulatory requirements to support a specific regulation of oil norm waste in Brazil
Authors: Lopes Amanda Gomes , Da Silva Francisco Cesar Augusto , Lopes Ricardo Tadeu
Published: October 2024

The oil and natural gas industry is one of the largest producers of Naturally Occurring Radioactive Material (NORM) worldwide. The scale and sludge are NORM wastes with the highest activity concentration levels, reaching 3500 Bq per g of 226Ra (scale). As wastes (sludge, scale, and produced water) are constantly produced in routine activities, a specific regulation for these wastes is necessary. Therefore, this study presents the regulatory requirements that may serve as a basis for the responsible regulatory body to prepare a specific regulation for the NORM waste generated by the oil industry. As a study published showing that the disposal of bulk NORM waste (not packaged wastes) is viable in Brazil, requirements for the management of these wastes and the characteristics of the landfill for disposal were included.
A comparative study of the elevated radioactivity in beach placer deposits of Bangladesh
Authors: Moniruzzaman Md , Łokas Edyta , Mietelski Jerzy , Zhao Qi
Published: October 2024

Beach sediments are mineral deposits formed through weathering and erosion of either igneous or metamorphic rocks. Among the rock constituent minerals are some natural radionuclides that contribute to ionizing radiation exposure on Earth. Kolatoli and Kuakata are the two major beaches with heavy mineral deposits and important tourist sites in Bangladesh. Natural radioactivity in Kolatoli and Kuakata beach sand deposits along the southern coast of Bangladesh was assessed and compared to identify the sources, causes, and possible environmental impact. Result shows most of the radionuclides have higher activity concentrations than the background level, and the activity varies with the sample locations. The dominant radionuclides were found to be the radionuclides of thorium series i.e. Th-232 and Ra-228 followed by uranium series and K-40. The radioactivity in Kolatoli beach sands was observed to be much higher than Kuakata beach due to the presence of a higher content of heavy minerals i.e. illmenite, rutile, zircon, garnet and monazite. Furthermore, monazite and zircon are the two radioactive minerals that are considered to be the main contributors to the radioactivity in Kolatoli beach sand. These minerals are dominated by the activity of thorium series radionuclides i.e. Th-232 and Ra-228 surpass the activity of all other radionuclides such as U-238, U-234, Th-230, Ra-226, Po-210, and K-40. However, major contribution of radioactivity in Kuakata beach sand comes from uranium series radionuclides such as U-238, U-234, Ra-226, and Po-210. Beach morphology, sedimentological, and geochemical evolution of those minerals might be important areas of further study for the radioactivity monitoring activity in those areas.
Dose and timing effects of caffeine on subsequent sleep: a randomized clinical crossover trial
Authors: Gardiner Carissa L , Weakley Jonathon , Burke Louise M , Fernandez Francesca , Johnston Rich D , Leota Josh , Russell Suzanna , Munteanu Gabriella , Townshend Andrew , Halson Shona L
Published: October 2024

Study Objectives

To investigate the effect of a typical dose of caffeine and a high dose of caffeine consumed in the morning, afternoon, and evening on subsequent sleep.

Methods

Using a placebo-controlled, double-blind, randomized crossover design, 23 males (25.3 ± 5.0 years) with a moderate habitual caffeine intake (<300 mg∙day−1) completed seven conditions: placebo, and 100 and 400 mg of caffeine consumed 12, 8, and 4 hours prior to bedtime, with a 48-hour washout. In-home partial polysomnography and sleep diaries were used to assess sleep. Linear mixed models estimated the effect of each condition.

Results

No significant effect on objective or subjective sleep occurred with the 100 mg dose of caffeine compared with the placebo (p > .05), but significant effects occurred with the 400 mg dose (p < .05). Significant delays in sleep initiation and alterations to sleep architecture were observed when 400 mg was consumed within 12 hours of bedtime (p < .05), and significantly greater sleep fragmentation occurred when 400 mg was consumed within 8 hours of bedtime (p < .05). Additionally, perceived sleep quality was significantly reduced when 400 mg was consumed 4 hours prior to bedtime (−34.02%, p = .006) but not at 8 or 12 hours.

Conclusions

A 100 mg dose of caffeine can be consumed up to 4 hours prior to bedtime, but 400 mg may negatively impact sleep when consumed as one dose within 12 hours of bedtime, with the adverse influence on sleep increasing the closer consumption occurs to bedtime. The discrepancy between objective and subjective sleep quality suggests that individuals may have difficulty accurately perceiving the influence of caffeine on sleep quality.

Clinical trial registration

Australian and New Zealand Clinical Trials Registry, registration number: ACTRN12621001625864, https://www.anzctr.org.au/Trial/Registration/TrialReview.aspx?ACTRN=12621001625864.
A Moral Dilemma of “Selling Out”: Race, Class, and Career Considerations among Elite College Students
Authors: Kim Joyce J
Published: October 2024

Research on occupational choice focuses on individualistic work values and emphasizes economic returns. Drawing from 62 in-depth interviews with Asian, Black, and White first-generation, low-income (FGLI), and middle-class students at an elite university, I argue that students’ career decisions comprise a moral dimension. How students contended with this dimension varied based on the intersection of their racial and class backgrounds. Specifically, patterns broadly align with two categories: contingent objections to certain high-prestige, high-paying careers arising from individual priorities or concern for social good, and linked obligations to broader collectivities, such as ethnoracial groups or families. While students across all racial and class backgrounds raised objections based on different individual priorities, FGLI students primarily mentioned objections based on the value of social good. Across class backgrounds, Asian and Black students more often cited obligations based on ethnoracial uplift compared to their White peers. Asian and Black FGLI students prioritized family contributions more strongly than their White FGLI counterparts. Paradoxically, some students used these evaluative logics to justify “selling out” in pursuit of high-prestige, high-paying jobs, whereas others used these justifications to reject them. This study furthers understanding of the cultural processes behind social inequalities and highlights how the intersection of race and class shapes moral understandings.
The balance between alleviating copper damage and maintaining root function during root pruning with excessive copper
Authors: Zhou Yumei , Wu Shiyun , Jia Jingjing , Chen Huan , Zhang Ying , Wu Zejing , Chen Boya , Liu Can , Yang Ming
Published: October 2024

Coating high concentrations of copper (Cu) on the inner wall of containers can efficiently inhibit root entanglement of container-grown seedlings. However, how the protective and defensive responses of roots maintain root structure and function during Cu-root pruning is still unclear. Here, Duranta erecta L. seedlings were planted in the containers coated with 40 (T1), 80 (T2), 100 (T3), 120 (T4), 140 (T5) and 160 (T6) g L−1 Cu(OH)2 with containers without Cu(OH)2 as the control. Although T5 and T6 produced the best inhibitory effect on root entanglement, root anatomy structure was damaged. T1 and T2 not only failed to completely control root circling, but also led to decreased root activity and stunted growth. Cu(OH)2 treatments significantly increased lignin concentration of roots with the highest values at T3 and T4. Compared with T3, seedlings at T4 had higher height, biomass and root activity, and no significant root entanglement. Excessive Cu accumulation in Cu(OH)2 treatments changed the absorption of other mineral nutrients and their allocation in the roots, stems and leaves. Overall, Ca was decreased while Mg, Mn, Fe and K were increased, especially K and Mn at T4 which is related to defense capacity. The results indicate that there is a Cu threshold to balance root entanglement control, defense capacity and nutrient uptake function under excessive Cu for container-grown D. erecta seedlings.
Update on hereditary C1q deficiency: pathophysiology, clinical presentation, genotype and management
Authors: Buso Helena , Triaille Clément , Flinn Aisling M. , Gennery Andrew R.
Published: October 2024

Purpose of review

C1q deficiency is a rare inborn error of immunity characterized by susceptibility to severe infections and profound immune dysregulation, with a systemic lupus erythematosus-like phenotype. The management of patients with C1q deficiency is challenged by the rarity of this condition and the wide clinical variability. This review aims to emphasize the importance of a thorough immunological and clinical characterization to help guide a personalized and comprehensive approach to patients.

Recent findings

We focus on the concept of C1q deficiency as a bridge between the monogenic form of systemic lupus erythematosus and the Mendelian type I interferonopathies. Moreover, we explore the role of new treatment strategies such as Janus-associated kinase (JAK) inhibitors and allogeneic stem cell transplantation.

In this narrative review, we provide a systematic overview of C1q deficiency, starting with the description of the pathophysiological background and the variable clinical phenotype, and then exploring the different prognoses, the consequent treatment strategies and future directions.
Conscientious Objection and the Anesthesiologist: An Ethical Dilemma
Authors: Koganti Raghuram , Cohn Moshe M. , Resnicoff Steven H. , Roth Steven
Published: October 2024

Conscientious objection is a legally protected right of medical professionals to recuse themselves from patient care activities that conflict with their personal values. Anesthesiology is different from most specialties with respect to conscientious objection in that the focus is to facilitate safe, efficient, and successful performance of procedures by others, rather than to perform the treatment in question. This could give rise to a unique, somewhat indirect ethical tension between the application of conscientious objection and potential infringement upon patient autonomy and well-being. While some situations have clear grounds and precedent for conscientious objection (e.g., abortion, or futile procedures), newer procedures, such as gender-affirming surgery and xenotransplantation, may trigger conscientious objection for complex reasons. This review discusses ethical, legal, and practical aspects of conscientious objection; challenges to anesthesia groups, departments, and healthcare organizations when conscientious objection is invoked by anesthesiologists; and strategies to help mitigate the ethical dilemmas.
The Role of Cystic Fibrosis Transmembrane Conductance Regulator in Skeletal Muscle Contractile Function
Authors: Wu Kenneth , Michalski Anna , Sykes Jenna , Batt Jane , Stephenson Anne L. , Mathur Sunita
Published: October 2024

Purpose:

Genetic mutations in cystic fibrosis (CF) result in CF transmembrane conductance regulator (CFTR) dysfunction. CFTR is expressed in human skeletal muscle; its effect on skeletal muscle abnormalities is unknown. The study objective is to investigate the role of CFTR in skeletal muscle contractile function.

Methods:

We conducted a prospective, cross-sectional study comparing 34 adults with minimal and 18 with residual function CFTR mutations, recruited from Toronto Adult CF Centre, St. Michael's Hospital, Unity Health Toronto. Quadriceps, biceps brachii, and handgrip strength was measured with dynamometers; leg muscle power with the stair climb power test. Quadriceps muscle contractility was determined by quadriceps muscle strength normalized to quadriceps muscle size, measured with ultrasound images. Multivariable regression was used for analysis.

Results:

People with residual function CFTR mutations had higher quadriceps muscle torque normalized to quadriceps layer thickness and to rectus femoris cross-sectional area by 27.5 Nm/cm [95% CI (2.2, 52.8) Nm/cm, P = .034] and 5.6 Nm/cm2 [95% CI (0.3, 10.9) Nm/cm2, P = .041], respectively, compared with those with minimal function CFTR mutations. There were no differences in quadriceps muscle torque (P = .58), leg muscle power (P = .47), biceps brachii muscle force (P = .14), or handgrip force (P = .12) between the 2 mutation groups.

Conclusions:

CFTR protein may play a role in muscle contractility, implying a limited capacity to exert muscle force per unit of muscle size in people with CF. This suggests that building a greater muscle mass through resistance exercises focusing on muscle hypertrophy in exercise prescription may improve muscle strength in people with CF.