bluuebunny/crossref_metadata_2025_split huggingface dataset:
Chicken manure application alters microbial community structure and the distribution of antibiotic-resistance genes in rhizosphere soil of Cinnamomum camphora forests
Authors: Chen Deqiang , Zou Jiawei , Chen Dexing , He Xin , Zhang Cuili , Li Jinwei , Lan Siren , Liu Zhong-Jian , Zou Shuangquan , Qian Xin 
Published: November 2023

Abstract
The distribution of antibiotic-resistance genes (ARGs) in environmental soil is greatly affected by livestock and poultry manure fertilization, the application of manure will lead to antibiotic residues and ARGs pollution, and increase the risk of environmental pollution and human health. Cinnamomum camphora is an economically significant tree species in Fujian Province, China. Here, through high-throughput sequencing analysis, significant differences in the composition of the bacterial community and ARGs were observed between fertilized and unfertilized rhizosphere soil. The application of chicken manure organic fertilizer significantly increased the relative abundance and alpha diversity of the bacterial community and ARGs. The content of organic matter, soluble organic nitrogen, available phosphorus, nitrate reductase, hydroxylamine reductase, urease, acid protease, β-glucosidase, oxytetracycline, and tetracycline in the soil of C. camphora forests have significant effects on bacterial community and ARGs. Significant correlations between environmental factors, bacterial communities, and ARGs were observed in the rhizosphere soil of C. camphora forests according to Mantel tests. Overall, the findings of this study revealed that chicken manure organic fertilizer application has a significant effect on the bacterial community and ARGs in the rhizosphere soil of C. camphora forests, and several environmental factors that affect the bacterial community and ARGs were identified.
Evaluating the Performance of Widely Used Phylogenetic Models for Gene Expression Evolution
Authors: Dimayacyac Jose Rafael , Wu Shanyun , Jiang Daohan , Pennell Matt 
Published: November 2023

Abstract
Phylogenetic comparative methods are increasingly used to test hypotheses about the evolutionary processes that drive divergence in gene expression among species. However, it is unknown whether the distributional assumptions of phylogenetic models designed for quantitative phenotypic traits are realistic for expression data and importantly, the reliability of conclusions of phylogenetic comparative studies of gene expression may depend on whether the data is well described by the chosen model. To evaluate this, we first fit several phylogenetic models of trait evolution to 8 previously published comparative expression datasets, comprising a total of 54,774 genes with 145,927 unique gene–tissue combinations. Using a previously developed approach, we then assessed how well the best model of the set described the data in an absolute (not just relative) sense. First, we find that Ornstein–Uhlenbeck models, in which expression values are constrained around an optimum, were the preferred models for 66% of gene–tissue combinations. Second, we find that for 61% of gene–tissue combinations, the best-fit model of the set was found to perform well; the rest were found to be performing poorly by at least one of the test statistics we examined. Third, we find that when simple models do not perform well, this appears to be typically a consequence of failing to fully account for heterogeneity in the rate of the evolution. We advocate that assessment of model performance should become a routine component of phylogenetic comparative expression studies; doing so can improve the reliability of inferences and inspire the development of novel models.
Comparison of transcriptome-wide N6-methyladenosine profiles from healthy trio families reveals regulator-mediated methylation alterations
Authors: Li Yini , Liu Hang , He Chuan , Ma Lijia 
Published: November 2023

Abstract
The N6-methyladenosine (m6A) modification is a highly conserved RNA modification found in eukaryotic messenger RNAs (mRNAs). It plays a vital role in regulating various biological processes. Dysregulation of m6A modifications has been linked to a range of complex genetic diseases in humans. However, there has been a lack of comprehensive characterization and comparison of m6A modifications at the transcriptome-wide level within families. To address this gap, we profiled transcriptome-wide m6A methylation in 18 individuals across 6 Yoruba trio families. The m6A methylomes of these 18 individuals revealed that m6A modifications in children showed greater similarity to each other than to their parents. This suggests that m6A modifications are influenced by multiple factors rather than solely determined by genetic factors. Additionally, we found that mRNAs exhibiting m6A modifications specific to children were enriched in cell cycle control processes, while those with m6A modifications specific to parents were associated with chromatin modifications. Furthermore, our analysis on the interactions between differentially expressed m6A-related regulatory genes and age-related genes suggested that age might be one of the factors influencing m6A modifications. In summary, our study provided a valuable dataset that highlighted the differences and functional diversity of m6A modifications within and between trio families.
Differential Impact of Smoking on Methylome and Transcriptome in Crohn’s Disease and Ulcerative Colitis
Authors: Yan Ang Qi , Plichta Damian , Kim Sean , Hyun-A Kim Iris , Gregory Sadie , Xia Yan , Lau Helena , Xavier Ramnik , Ananthakrishnan Ashwin N 
Published: November 2023

Abstract

Background
Smoking is an environmental factor that differentially impacts Crohn’s disease (CD) and ulcerative colitis (UC). The mechanism of impact of smoking on disease risk and clinical outcomes remains to be established.

Methods
This study used a prospective cohort of patients with CD or UC. Self-reported smoking status was validated using serum cotinine measurement. We profiled methylation changes in peripheral blood using the Illumina Methylation BeadChip. Transcriptomic profiling was performed on ileal and colonic tissue using an Illumina TruSeq platform. We compared the methylation and transcriptional changes in current, former, and never smokers stratified by disease type.

Results
Our cohort included 200 patients with CD or UC with methylation profiles and 160 with transcriptomic data. The mean serum cotinine level was higher in current compared with former or never smokers. Epigenetic changes common to both CD and UC included hypomethylation at AHRR. Smoking-associated MGAT3 hypomethylation was associated with severe disease course only in UC, while IER3 hypomethylation was associated with worse course only in CD. Smoking downregulated several inflammatory pathways in UC. Current smoking in CD but not in UC was associated with upregulation of several genes mediating Paneth cell function. Genes with opposite direction of effects in CD and UC include HSD3B2 and GSTA1.

Conclusions
Our findings suggest both common and differential effects of cigarette smoking on CD and UC. Paneth cell dysfunction may mediate adverse impact of smoking on CD. Bile acid and oxidative stress pathways may be relevant for the differential effect of smoking on CD and UC.
Reconstructive surgery for severe breast asymmetry post-paediatric cardiovascular operation by anterolateral thoracotomy
Authors: Ishii Naohiro , Ko Takanori , Shimabukuro Makoto , Matsuzaki Kyoichi 
Published: November 2023

Abstract
Breast maldevelopment is a troublesome long-term complication of anterolateral thoracotomies, and several cases of this event have been reported. However, breast reconstruction in such cases has not yet been reported in detail, and solutions for managing this event remain unexplained. Herein, we present a case of breast maldevelopment after anterolateral thoracotomy, in which symmetrical breasts were successfully obtained by breast reconstruction based on autologous tissue transfer. The surgical approach prior to pleurotomy in anterolateral thoracotomy, particularly when performed on female infant patients, must be modified to prevent postoperative breast malformation.
Impact of lung cancer screening on surgical stage distribution and surgical practice: a regional analysis of patients operated in and out of a screening program
Authors: Gooseman Michael R , Tentzeris Vasileios , Bulliment Kerry L , Qadri Syed S A , Callister Matthew E J , Milton Richard , Chaudhuri Nilanjan , Tcherveniakov Peter , Papagiannopoulos Kostas , Cowen Michael E , Brunelli Alessandro 
Published: November 2023

Abstract

OBJECTIVES
The aim of this study was to assess variations in surgical stage distribution in 2 centres within the same UK region. One centre was covered by an active screening program started in November 2018 and the other was not covered by screening.

METHODS
Retrospective analysis of 1895 patients undergoing lung resections (2018–2022) in 2 centres. Temporal distribution was tested using Chi-squared for trends. A lowess curve was used to plot the proportion of stage 1A patients amongst those operated over the years.

RESULTS
The surgical populations in the 2 centres were similar. In the screening unit (SU), we observed a 18% increase in the proportion of patients with clinical stage IA in the recent phase compared to the early phase (59% vs 50%, P = 0.004), whilst this increase was not seen in the unit without screening. This difference was attributable to an increase of cT1aN0 patients in the SU (16% vs 11%, P = 0.035) which was not observed in the other unit (10% vs 8.2%, P = 0.41). In the SU, there was also a three-fold increase in the proportion of sublobar resections performed in the recent phase compared to the early one (35% vs 12%, P &lt; 0.001). This finding was not evident in the unit without screening.

CONCLUSIONS
Lung cancer screening is associated with a higher proportion of lung cancers being detected at an earlier stage with a consequent increased practice of sublobar resections.
Unconditionally stable small stencil enriched multiple point flux approximations of heterogeneous diffusion problems on general meshes
Authors: Coatléven Julien 
Published: November 2023

Abstract
We derive new multiple point flux approximations (MPFA) for the finite volume approximation of heterogeneous and anisotropic diffusion problems on general meshes, in dimensions 2 and 3. The resulting methods are unconditionally stable while preserving the small stencil typical of MPFA finite volumes. The key idea is to solve local variational problems with a well-designed stabilization term from which we deduce conservative flux instead of directly prescribing a flux formula and solving the usual flux continuity equations. The boundary conditions of our local variational problems are handled through additional cell-centered unknowns, leading to an overall scheme with the same number of unknowns than first-order discontinuous Galerkin methods. Convergence results follow from well-established frameworks, while numerical experiments illustrate the good behavior of the method.
Associations Between HIV and Severe Mpox in an Atlanta Cohort
Authors: Aldred Bruce , Scott Jane Y , Aldredge Amalia , Gromer Daniel J , Anderson Albert M , Cartwright Emily J , Colasanti Jonathan A , Hall Betsy , Jacob Jesse T , Kalapila Aley , Kandiah Sheetal , Kelley Colleen F , Lyles Robert H , Marconi Vincent C , Nguyen Minh Ly , Rebolledo Paulina A , Sheth Anandi N , Szabo Brittany , Titanji Boghuma K , Wiley Zanthia , Workowski Kimberly , Cantos Valeria D 
Published: November 2023

Abstract

Background
In the Southeastern United States, the 2022 mpox outbreak disproportionately impacted people who are black and people with HIV (PWH).

Methods
We analyzed a cohort of 395 individuals diagnosed with mpox across 3 health care systems in Atlanta, Georgia between 1 June 2022 and 7 October 2022. We present demographic and clinical characteristics and use multivariable logistic regression analyses to evaluate the association between HIV status and severe mpox (per the US Centers for Disease Control and Prevention definition) and, among PWH, the associations between CD4+ T-cell count and HIV load with severe mpox.

Results
Of 395 people diagnosed with mpox, 384 (97.2%) were cisgender men, 335 (84.8%) identified as black, and 324 (82.0%) were PWH. Of 257 PWH with a known HIV load, 90 (35.0%) had &gt; 200 copies/mL. Severe mpox occurred in 77 (19.5%) individuals and there was 1 (0.3%) death. Tecovirimat was prescribed to 112 (28.4%) people, including 56 (72.7%) people with severe mpox. In the multivariable analysis of the total population, PWH had 2.52 times higher odds of severe mpox (95% confidence interval [CI], 1.01–6.27) compared with people without HIV. In the multivariable analysis of PWH, individuals with HIV load &gt; 200 copies/mL had 2.10 (95% CI, 1.00–4.39) times higher odds of severe mpox than PWH who were virologically suppressed. Lower CD4+ T-cell count showed a significant univariate association with severe mpox but was not found to be significantly associated with severe mpox in multivariable analysis.

Conclusions
PWH with nonsuppressed HIV loads had more mpox complications, hospitalizations, and protracted disease courses than people without HIV or PWH with suppressed viral loads. PWH with nonsuppressed HIV loads who are diagnosed with mpox warrant particularly aggressive monitoring and treatment.
Impact of Intravenous Fat Emulsion Choice on Candida Biofilm, Hyphal Growth, and Catheter-Related Bloodstream Infections in Pediatric Patients
Authors: Alvira-Arill Gustavo R , Willems Hubertine M E , Fortwendel Jabez P , Yarbrough April , Tansmore Jessica , Sierra Caroline M , Bashqoy Ferras , Stultz Jeremy S , Peters Brian M 
Published: November 2023

Abstract

Background
Use of mixed-oil (MO) intravenous fat emulsion (IFE) was shown to inhibit Candida albicans biofilm formation and overall rate of catheter-related bloodstream infections (CR-BSIs) compared with soybean-oil (SO) IFE). We aimed to delineate this inhibitory mechanism and impact of IFE choice on distribution of fungal CR-BSIs.

Methods
Transcriptional profiling was conducted on C. albicans grown in SO-IFE, MO-IFE, or SO-IFE with capric acid. Overexpression strains of shared down-regulated genes were constructed using a tetracycline-off system to assess hypha and biofilm formation in IFEs. A 5-year retrospective multicenter cohort study was performed to assess differences in CR-BSIs caused by Candida species based on the IFE formulation received in pediatric patients.

Results
Genes significantly down-regulated in MO-IFE and SO-IFE with capric acid included CDC11, HGC1, and UME6. Overexpression of HGC1 or UME6 enabled filamentation in capric acid and MO-IFE. Interestingly, only overexpression of UME6 was sufficient to rescue biofilm growth in MO-IFE. MO-IFE administration was associated with a higher proportion of non-albicans Candida versus C. albicans CR-BSIs (42% vs 33%; odds ratio, 1.22 [95% confidence interval, .46–3.26]).

Conclusions
MO-IFE affects C. albicans biofilm formation and hyphal growth via a UME6-dependent mechanism. A numerical but not statistically significant difference in distribution of Candida spp. among CR-BSIs was observed.
Utilizing a Quality Improvement Approach to Improve Positioning of Acute Burn Patients
Authors: Freeman Catherine E , Yoo Junhwi , Slater Julia C 
Published: November 2023

Abstract
Patient positioning, using “anti-deformity positioning,” is a standard practice in burn rehabilitation to assist with edema management, scar contracture prevention, and wound healing. Consistently providing proper positioning requires the combined effort of the multidisciplinary burn team. Our primary goal was to increase the frequency that patients were correctly positioned to over 90%. At a medium-sized, academic burn unit, random audits were conducted by burn lead therapists on the compliance of proper patient positioning over 6 months. Using this data as a trigger, a quality improvement project was designed using the Plan-Do-Study-Act (PDSA) cycle. Surveys were distributed to therapy and nursing staff to identify barriers to proper positioning. Effects on positioning compliance postintervention were monitored. In the 6 months prior to intervention, the average correct positioning was 76%. Surveys identified the following barriers to care: nursing needed more education and the approach was too heavily reliant on nursing efforts alone. To address this, therapists provided education to all nurses, communicated daily about positioning expectations, shifted the project to a multidisciplinary approach, and made changes in therapy workflow. The median compliance improved from 79% to 91% (P &lt; .05). Coordinating efforts of the entire burn team improve consistency for positioning in burn patients. Utilizing the PDSA cycle allowed us to identify areas for improvement and develop appropriate interventions to increase education for nursing staff and workflow improvements for therapists. Following the completion of our interventions, we were able to obtain an immediate improvement in our patient positioning compliance.
Transmission accuracy–axial backlash–fatigue life-driven tolerance optimization of planetary roller screw mechanism
Authors: Liu Genshen , Wei Peitang , Liu Huaiju , Du Xuesong , Hu Rui , He Huilin , Zhou Pengliang , Tan Xiaoqing 
Published: November 2023

Abstract
The planetary roller screw mechanism (PRSM) is an advanced linear transmission device. The relationship between tolerance allocation and performance risk still remains elusive, which is a challenge for its future applications. This work proposes a novel transmission accuracy–axial backlash–fatigue life-driven tolerance optimization method for the screw, roller, and nut of PRSM. A computational framework for PRSM transmission accuracy, axial backlash, and fatigue life calculation is developed to work on the parametric variation of design parameters including the eccentric, pitch, nominal diameter, and flank angle. Combinations of parametric variation are obtained by the Latin hypercube sampling-based tolerance statistical model to rapidly evaluate PRSM performance risk under operation conditions and tolerance parameters. The optimal tolerance parameters with the expanded width of tolerance interval and the minimum PRSM performance risk probability are obtained using the non-dominated sorting genetic algorithm. Results reveal that PRSM performance risk probabilities change from 89.25 to 68.72% and 58.1 to 56.86%, with 29.94 and 17.38% tolerance interval width increase under the high-precision and heavy-loading operation cases studied, respectively.
Unveiling the Mind of the Machine
Authors: Clegg Melanie , Hofstetter Reto , de Bellis Emanuel , Schmitt Bernd H 
Published: November 2023

Abstract
Previous research has shown that consumers respond differently to decisions made by humans versus algorithms. Many tasks, however, are not performed by humans anymore but entirely by algorithms. In fact, consumers increasingly encounter algorithm-controlled products, such as robotic vacuum cleaners or smart refrigerators, which are steered by different types of algorithms. Building on insights from computer science and consumer research on algorithm perception, this research investigates how consumers respond to different types of algorithms within these products. This research compares high-adaptivity algorithms, which can learn and adapt, versus low-adaptivity algorithms, which are entirely pre-programmed, and explore their impact on consumers' product preferences. Six empirical studies show that, in general, consumers prefer products with high-adaptivity algorithms. However, this preference depends on the desired level of product outcome range—the number of solutions a product is expected to provide within a task or across tasks. The findings also demonstrate that perceived algorithm creativity and predictability drive the observed effects. This research highlights the distinctive role of algorithm types in the perception of consumer goods and reveals the consequences of unveiling the mind of the machine to consumers.
“A Vile Custom”: The Strange Career of William Osler’s “Professional Notes”
Authors: Healey Jenna 
Published: November 2023

Abstract:
In 1882, William Osler wrote “Professional Notes among the Indian Tribes about Great Slave Lake, NWT,” a fantastical essay that purportedly described the sexual and obstetric customs of Indigenous peoples residing in the Canadian Northwest. Originally prepared as a prank, “Professional Notes,” along with Osler’s alter ego Egerton Yorrick Davis, became an elaborate inside joke that circulated widely among the medical elite for decades after Osler’s death. In this essay, I trace the history and afterlife of “Professional Notes,” considering both the colonial context of its creation as well as the reasons for its enduring popularity. I argue that “Professional Notes” both reflected and reinforced the anti-Indigenous racism that permeated the medical profession, particularly during its consolidation in the late nineteenth and early twentieth century. I also make a methodological argument for the study of joking within the history of medicine, presenting “Professional Notes” as a powerful example of the role humour has played in shaping medical culture.
Physical activity and checkpoint inhibition: association with toxicity and survival
Authors: Verheijden Rik J , Cabané Ballester Anna , Smit Karel C , van Eijs Mick J M , Bruijnen Cheryl P , van Lindert Anne S R , Suijkerbuijk Karijn P M , May Anne M 
Published: November 2023

Abstract

Background
Although animal experiments suggest beneficial effects of physical activity (PA) on antitumor immunity, little is known about the effects of PA on immune checkpoint inhibitor (ICI) toxicity and effectiveness in humans. We assessed the association of PA with immune-related adverse events (irAE) and survival in patients undergoing ICI.

Methods
Patients receiving ICI who completed the Dutch short questionnaire to assess health enhancing physical activity (SQUASH) questionnaire at the start of treatment as part of the prospective UNICIT study in an academic hospital were included. PA was quantified by calculating total metabolic equivalent task hours per week (total PA) and hours per week of moderate- to vigorous-intensity PA during sport and leisure time (MVPA-SL). Associations of PA with severe irAE occurrence within 1 year and overall survival (OS) were evaluated using logistic regression and Cox proportional hazard regression, respectively, with adjustment for probable confounders.

Results
In total, 251 patients were included, with a median follow-up of 20 months. Moderate and high levels of total PA were associated with lower odds of severe irAE occurrence compared to low levels of total PA (adjusted OR: 0.34 [95% CI = 0.12 to 0.90] and 0.19 [95% CI = 0.05 to 0.55], respectively). Moderate and high levels of total PA were also associated with prolonged survival (adjusted HR: 0.58 [95% CI = 0.32 to 1.04] and 0.48 [95% CI = 0.27 to 0.89], respectively). Similar associations were observed in patients who performed more MVPA-SL.

Conclusions
Higher physical activity levels at the start of ICI treatment are associated with lower risk of severe irAEs and probably prolonged survival. Randomized controlled trials are needed to investigate whether patients indeed benefit from increasing PA levels after diagnosis.