bluuebunny/crossref_metadata_2025 huggingface dataset:
Light-strand bias and enriched zones of embedded ribonucleotides are associated with DNA replication and transcription in the human-mitochondrial genome
Authors: Xu Penghao , Yang Taehwan , Kundnani Deepali L , Sun Mo , Marsili Stefania , Gombolay Alli L , Jeon Youngkyu , Newnam Gary , Balachander Sathya , Bazzani Veronica , Baccarani Umberto , Park Vivian S , Tao Sijia , Lori Adriana , Schinazi Raymond F , Kim Baek , Pursell Zachary F , Tell Gianluca , Vascotto Carlo , Storici Francesca
Published: December 2023

Abundant ribonucleoside-triphosphate (rNTP) incorporation into DNA by DNA polymerases in the form of ribonucleoside monophosphates (rNMPs) is a widespread phenomenon in nature, resulting in DNA-structural change and genome instability. The rNMP distribution, characteristics, hotspots and association with DNA metabolic processes in human mitochondrial DNA (hmtDNA) remain mostly unknown. Here, we utilize the ribose-seq technique to capture embedded rNMPs in hmtDNA of six different cell types. In most cell types, the rNMPs are preferentially embedded on the light strand of hmtDNA with a strong bias towards rCMPs; while in the liver-tissue cells, the rNMPs are predominately found on the heavy strand. We uncover common rNMP hotspots and conserved rNMP-enriched zones across the entire hmtDNA, including in the control region, which links the rNMP presence to the frequent hmtDNA replication-failure events. We show a strong correlation between coding-sequence size and rNMP-embedment frequency per nucleotide on the non-template, light strand in all cell types, supporting the presence of transient RNA-DNA hybrids preceding light-strand replication. Moreover, we detect rNMP-embedment patterns that are only partly conserved across the different cell types and are distinct from those found in yeast mtDNA. The study opens new research directions to understand the biology of hmtDNA and genomic rNMPs.
GWAS identifies two important genes involved in Chinese chestnut weight and leaf length regulation
Authors: Zhang Yu , Zhang Weiwei , Liu Yang , Zheng Yi , Nie Xinghua , Wu Qinyi , Yu Wenjie , Wang Yafeng , Wang Xuefeng , Fang Kefeng , Qin Ling , Xing Yu
Published: December 2023

There are many factors that affect the yield of Chinese chestnut (Castanea mollissima), with single nut weight (SNW) being one of the most important. Leaf length is also related to Chinese chestnut yield. However, the genetic architecture and gene function associated with Chinese chestnut nut yield have not been fully explored. In this study, we performed genotyping by sequencing 151 Chinese chestnut cultivars, followed by a genome-wide association study (GWAS) on six horticultural traits. First, we analyzed the phylogeny of the Chinese chestnut and found that the Chinese chestnut cultivars divided into two ecotypes, a northern and southern cultivar group. Differences between the cultivated populations were found in the pathways of plant growth and adaptation to the environment. In the selected regions, we also found interesting tandemly arrayed genes that may influence Chinese chestnut traits and environmental adaptability. To further investigate which horticultural traits were selected, we performed a GWAS using six horticultural traits from 151 cultivars. Forty-five loci that strongly associated with horticultural traits were identified, and six genes highly associated with these traits were screened. In addition, a candidate gene associated with SNW, APETALA2 (CmAP2), and another candidate gene associated with leaf length (LL), CRYPTOCHROME INTERACTING BASIC HELIX-LOOP-HELIX 1 (CmCIB1), were verified in Chinese chestnut and Arabidopsis (Arabidopsis thaliana). Our results showed that CmAP2 affected SNW by negatively regulating cell size. CmCIB1 regulated the elongation of new shoots and leaves by inducing cell elongation, potentially affecting photosynthesis. This study provided valuable information and insights for Chinese chestnut breeding research.
Imagining Out of Hope
Authors: Humbert-Droz Steve , Vazard Juliette
Published: December 2023

Both lay people and philosophers assume that hoping for something implies imagining it. According to contemporary philosophical accounts of hope, hope involves an element of imagination as input, part, or output of hope. However, there is no systematic view of the interaction between hope and the different processes constituting imagination. In this paper we put forward a view of (i) the kind of imaginings typically triggered by hopeful states, (ii) the nature of the interaction between hope and hopeful imaginings, and (iii) the epistemic value of imagining out of hope. We argue that a paradigmatic output of hope is an immersive kind of cognitive imagination. Additionally, justified hopes constrain our immersive imaginings in such a way as to provide them with a specific epistemic value. Hopeful imaginings are not mere fantasies or wishful thinking; they constitute valuable experiences we can learn from and rely on in planning our future.
The new Xpert Mycobacterium tuberculosis/rifampicin (MTB/Rif) Ultra assay in comparison to Xpert MTB/Rif assay for diagnosis of tuberculosis in children and adolescents
Authors: Kaur Harveen , Guglani Vishal , Singhal Lipika , Randev Shivani , Kumar Pankaj , Gupta Varsha
Published: December 2023

Background

Microbiological diagnosis of pediatric tuberculosis (TB) using conventional microbiological techniques has been challenging due to paucibacillary nature of the disease. Molecular methods using cartridge-based tests like Xpert, have immensely improved diagnosis. A novel next-generation cartridge test, Xpert Ultra, incorporates two additional molecular targets and claims to have much lower detection limit. We attempted to compare the two techniques in presumptive pediatric TB patients.

Objectives

The aim of this study was to compare the diagnostic performance of Xpert MTB/Rif Ultra with Xpert MTB/Rif for the detection of pediatric TB.

Study design

This is an observational comparative analytical study.

Methods

Children under 15 years of age with presumptive TB were enrolled. Appropriate specimens were obtained (sputum, induced sputum or gastric aspirate for suspected pulmonary TB, cerebrospinal fluid for suspected tubercular meningitis and pleural fluid for suspected tubercular pleural effusion), subjected to smear microscopy, mycobacterial culture, Xpert and Xpert ultra tests and other appropriate diagnostic investigations.

Results

Out of 130 enrolled patients, 70 were diagnosed with TB using a composite reference standard (CRS). The overall sensitivity of Xpert was 64.29% [95% confidence interval (CI) 51.93–75.93%] and that of Xpert Ultra was 80% (95% CI 68.73–88.61%) with 100% overall specificity for both. The sensitivity of Xpert and Xpert Ultra in pulmonary specimens (n = 112) was 66.67% and 79.37% and in extrapulmonary specimens (n = 18) was 42.86% and 85.71%, respectively.

Conclusion

Our study found Ultra to be more sensitive than Xpert for the detection of Mycobacterium tuberculosis in children. Our findings support the use of Xpert Ultra as initial rapid molecular diagnostic test in children under evaluation for TB.
A Community-Curated DokuWiki Resource on Diagnostics, Diversity, Pathogenicity, and Genetic Control of Xanthomonads
Authors: Costa Joana , Pothier Joël F. , Bosis Eran , Boch Jens , Kölliker Roland , Koebnik Ralf
Published: December 2023

Xanthomonads, including Xanthomonas and Xylella species, constitute a large and significant group of economically and ecologically important plant pathogens. Up-to-date knowledge of these pathogens and their hosts is essential for the development of suitable control measures. Traditional review articles or book chapters have inherent limitations, including static content and rapid obsolescence. To address these challenges, we have developed a Web-based knowledge platform dedicated to xanthomonads, inspired by the concept of living systematic reviews. This platform offers a dynamic resource that encompasses bacterial virulence factors, plant resistance genes, and tools for diagnostics and genetic diversity studies. Our goal is to facilitate access for newcomers to the field, provide continuing education opportunities for students, assist plant protection services with diagnostics, provide valuable information to breeders on sources of resistance and breeding targets, and offer comprehensive expert knowledge to other stakeholders interested in plant-pathogenic xanthomonads. This resource is available for queries and updates at https://euroxanth.ipn.pt .

[Formula: see text] Copyright © 2024 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license .
The Fungal Diversity and Potential Pathogens Associated with Postharvest Fruit Rot of ‘Huangguan’ Pear (Pyrus bretschneideri) in Hebei Province, China
Authors: Zhang Yang , Zhang Nan , Gao Congcong , Cheng Yudou , Guan Yeqing , Wei Chuangqi , Guan Junfeng
Published: December 2023

Postharvest fruit rot caused by pathogens is a serious problem in the pear industry. This study investigated the fungal diversity and main pathogens and identified a new pathogen in the stored ‘Huangguan’ pear (Pyrus bretschneideri Rehd.), the dominant pear variety in northern China. We sampled 20 refrigeration houses from five main producing regions in Hebei Province and used Illumina sequencing technology to detect the fungal composition. Alternaria (56.3%) was the most abundant fungus, followed by Penicillium (9.2%) and Monilinia (6.2%). We also isolated and identified nine strains of Alternaria and four strains of Penicillium. Moreover, we observed a new postharvest fruit disease in ‘Huangguan’ pear caused by Stemphylium eturmiunum, which was confirmed by phylogenetic analysis by combining the sequences of three conserved genes, including internal transcribed spacer, gapdh, and calmodulin. This study marks the first documentation of S. eturmiunum causing fruit rot in ‘Huangguan’ pears, offering valuable insights for identifying and controlling this newly identified postharvest disease.
Family Integrated Care Shortens the Duration of Home Oxygen Therapy in Infants With Bronchopulmonary Dysplasia
Authors: Shen Fei , Wu Xiao , Chen Xiu-li , Rong Hui , Yang Yang
Published: December 2023

Background:

There have been few reports on whether family integrated care (FIC) can help premature infants with moderate to severe bronchopulmonary dysplasia (BPD) to shorten the duration of home oxygen therapy (HOT).

Purpose:

To investigate the effect of FIC on the duration of HOT in premature infants with moderate to severe BPD.

Methods:

The subjects were retrospectively selected from premature infants with moderate to severe BPD in our center between June 2019 and December 2021. Patients were divided into the FIC group (n = 47) and the non-FIC group (n = 34). For univariate analysis, t test, Mann–Whitney U test, Pearson χ2 test, or Fisher exact test was performed to explore the differences between the 2 groups. For multivariate analysis, simple and multiple linear regression was conducted to explore the effect of FIC on the duration of HOT.

Results:

(1) The duration of HOT and length of stay after grouping were significantly shorter in the FIC group than in the non-FIC group (P < .05). (2) The results of linear regression further revealed that FIC could significantly shorten the duration of HOT (simple linear regression, FIC [A] B: −12.709, 95% confidence interval (CI): −21.665 to −3.753; multiple linear regression, FIC [B] B: −11.419, 95% CI: −18.055 to −4.783).

Implications for Practice and Research:

FIC improved the optimal target oxygen saturation ratio before discharge and shortened the duration of HOT in premature infants with moderate and severe BPD. FIC should be promoted in China's neonatal intensive care units, though it puts forward new requirements for nursing education and training.
The Role of Shear Stress and Shear Strain in Pressure Injury Development
Authors: Portoghese Caroline , Deppisch Michelle , Sonenblum Sharon , Samson Barbara , Munro Cassendra , Capasso Virginia , Call Evan , Black Joyce , Brienza David
Published: December 2023

Although other patient safety indicators have seen a decline, pressure injury (PI) incidence has continued to rise. In this article, the authors discuss the role of shear stress and shear strain in PI development and describe how accurate assessment and management can reduce PI risk. They provide explanations of shear stress, shear strain, friction, and tissue deformation to support a better clinical understanding of how damaging these forces are for soft tissue. Clinicians must carefully assess each patient’s risk factors regarding shear forces within the contexts of activity and mobility. The authors also provide a toolbox of mitigation strategies, including support surface selection, selection of materials that contact the individual, management of immobility using positioning techniques, and the use of safe patient handling techniques. With a clear understanding of how shear forces affect PI risk and mitigation strategies, clinicians will more accurately assess PI risk and improve PI prevention care plans, ultimately reducing PI incidence to become more aligned with other patient safety indicators.
Chondroid Syringoma on the Tip of the Nose: A Case Report
Authors: Halder Sajal , Ghosh Arushi , Sharma Mona , Hemrajani Priyanka
Published: December 2023

Chondroid syringoma is a benign, rare, asymptomatic, slow-growing mixed tumor. The authors present the case of a 17-year-old adolescent boy who had a tumor on the tip of his nose for a duration of 8 months. An excisional biopsy was performed under local anesthesia. Based on histopathologic analysis, the resected lesion was identified as a chondroid syringoma.
Sagittal Angulation and the Treatment of Geriatric Femoral Neck Fractures: Time to Update our Classification Systems
Authors: Skerrett Duncan , Shefelbine Lara , Coale Max , Unno Florence , Lack William
Published: December 2023

OBJECTIVES:

Inconsistent outcomes have been reported for percutaneous fixation of Garden I/II femoral neck fractures in geriatric patients. It was hypothesized that accounting for variable follow-up would better estimate the failure rate of percutaneous fixation with and without significant sagittal angulation.

METHODS:

Design:

Retrospective.

Setting:

Single academic healthcare system.

Patient Selection Criteria:

Patients ≥ 50 years old treated with percutaneous screw fixation of Garden I/II (OTA/AO B1.1/B1.2) femoral neck fractures from 2010 - 2020 were identified. Pathologic fractures and open approaches were excluded.

Outcome Measures and Comparisons: Sagittal angulation was measured using a previously described method.11 Treatment failure was defined as early fixation failure (within 6 weeks), nonunion and/or avascular necrosis. Potential associations between treatment failure and patient, injury and treatment variables were assessed. Cox proportional hazard analysis accounted for variable follow-up when assessing for event-free survival.

RESULTS:

Of the 240 fractures that met inclusion criteria, there were 20 treatment failures (8%) and 33 fractures with sagittal angulation ≥ 20° on lateral radiographs (14%). Failure-free survival at 2 years was 91% for patients with < 20° posterior angulation and 52% for patients with ≥ 20° of posterior angulation (p < 0.0001). The hazard ratio, which incorporates variable follow-up, for failure with ≥ 20° of posterior angulation was 6.36 (p < 0.0001). No other factors were associated with treatment failure.

CONCLUSIONS:

Significant posterior angulation (≥ 20°) of Garden I/II femoral neck fractures is associated with a high failure rate following screw fixation. The authors suggest characterizing fractures with ≥ 20° of sagittal angulation as Garden III fractures to better support surgical decision-making.
Proteomic Analyses of Plasma from Patients with Fracture Related Infection Reveals Systemic Activation of the Complement and Coagulation Cascades
Authors: Becker Kevin , Sharma Ishani , Slaven James E. , Mosley Amber L. , Doud Emma H. , Malek Sarah , Natoli Roman M.
Published: December 2023

OBJECTIVES:

To compare plasma proteomes of patients with confirmed fracture related infections (FRIs) matched to noninfected controls using liquid chromatography-mass spectrometry (LC-MS)

METHODS:

Design:

Prospective Case-Control Study

Setting:

Single, Academic, Level 1 Trauma Center

Patient Selection Criteria:

Patients meeting confirmatory FRI criteria were matched to controls without infection based on fracture region, age, and time after surgery from June 2019 to January 2022. Tandem Mass Tag LC-MS analysis of patient plasma samples was performed.

Outcome Measures and Comparisons:

Protein abundance ratios in plasma for FRI patients compared to matched controls without infection were calculated.

RESULTS:

Twenty-seven patients meeting confirmatory FRI criteria were matched to 27 controls . Abundance ratios for over 1,000 proteins were measured in the 54 plasma samples. Seventy-three proteins were found to be increased or decreased in FRI patients compared to the matched controls (unadjusted t-test p<0.05). Thirty-two of these proteins were found in all 54 patient samples and underwent subsequent principal component (PC) analysis (PCA) to reduce the dimensionality of the large proteomics data set. A three component PCA accounted for 45.7% of the variation in the data set and had 88.9% specificity for the diagnosis of FRI. STRING protein-protein interaction network analysis of these three PCs revealed activation of the complement and coagulation cascades via the Reactome pathway database (false discovery rates<0.05).

CONCLUSIONS:

Proteomic analyses of plasma from FRI patients demonstrates systemic activation of the complement and coagulation cascades. Further investigation along these lines may help to better understand the systemic response to FRI and improve diagnostic strategies using proteomics.
Cross-Sectional Analysis of Caregiver-Reported Expressive Language Profiles and Associated Covariates in Individuals with Down Syndrome
Authors: Spellun Arielle , Harstad Elizabeth , Hojlo Margaret , Milliken Anna , Pawlowski Katherine , Sideridis Georgios , Baumer Nicole
Published: December 2023

Objective:

To describe the distribution of expressive language abilities of individuals with Down syndrome (DS) in a clinical sample and characterize demographic, environmental, and medical factors associated with varying expressive language profiles.

Methods:

Cross-sectional analysis was completed on a sample of 345 individuals with DS between the ages of 4 and 22 years who were enrolled into a longitudinal clinical database between March 2018 and August 2021. Expressive language-related items on a standardized caregiver-reported questionnaire assessing domains of functioning in neurodevelopmental disorders were used to conduct latent variable modeling and determine caregiver-reported expressive language (CREL) classes across the sample. Linear regression was used to explore associations between CREL classes and predictor variables.

Results:

Latent variable modeling revealed 3 distinct classes of CREL abilities representing higher, middle, and lower CREL. Individuals in the lower CREL class were more likely to be female, to use sign language or visual communication systems, have reduced pronunciation, attend private or residential school, and to be in a substantially separate classroom. Membership was not predicted by complex medical histories or co-occurring neurodevelopmental diagnoses.

Conclusion:

Caregiver-reported expressive language abilities in a cohort of individuals with DS were variable, with most of the individuals belonging to higher or middle CREL classes, relative to one another. Additional studies are indicated to understand factors that predict higher expressive language ability and explore how to direct services to individuals who are at risk of more profound language delays.
Food Insecurity Predicts Magnitude of Early BMI Change in a Pediatric Weight Management Intervention
Authors: Frank Miranda L. , Korth Christina X. , Shields Clarissa V. , Hultstrand Kara V. , Putt Geoffrey E. , Walston Marnie W. , Wulkan Mark L. , Perusek Amy K. , Sato Amy F.
Published: December 2023

Objective:

The aim of this study was to estimate the prevalence of food insecurity among children with overweight/obesity presenting for weight management treatment and examine whether food insecurity predicts early change in body mass index (BMI), expressed as a percentage of the 95th percentile (%BMIp95).

Method:

Children (N = 69; ages 3–18 years) presenting to a hospital-based pediatric weight management intervention and 1 parent/guardian per child (N = 69) were included. At the first appointment, parents/guardians completed the US Household Food Security Survey Module: Six-item Short Form and a demographics questionnaire. Height and weight of the children were measured at the first and third appointments to calculate %BMIp95.

Results:

Among participating families, 29.0% reported experiencing food insecurity. Controlling for the ratio of income to poverty, 11.4% of the variance in %BMIp95 change from the first to third appointments was accounted for by food insecurity, ▵F (1, 66) = 8.46, p = 0.01. Children with greater food insecurity demonstrated a smaller magnitude of %BMIp95 decrease, representing a small-to-medium effect size within the context of the regression model (f2 = 0.13).

Conclusion:

A high proportion of families with children receiving weight management treatment reported experiencing food insecurity in comparison with US households with children. There may be unique characteristics of food insecurity, as opposed to household income alone, that explain the smaller magnitude of BMI decrease observed early in treatment. Future research should explore complex associations among food insecurity, income, BMI, and race over time.
The Full Continuum of Robotic Breast Surgery: Robotic-assisted Mastectomy, Robotic DIEP Flap, and Robotic Supermicrosurgery
Authors: Tanna Neil , Sugiyama Gainosuke , Smith Mark L. , Sanchez Susana Benitez , Minasian Raquel A. , Robinson Emma , Silverman Julia , Shuck John W. , Selber Jesse
Published: December 2023

In recent years, robotic surgery has rapidly expanded to improve surgical outcomes in a variety of surgical subspecialties. Although plastic surgery has taken longer to integrate robotic surgery into practice, the advantages of robotic-assisted surgery, including improved visualization and resolution, minimally invasive approaches, and the ability to surpass human precision and scale, have driven its more recent adoption into plastic surgery. Currently, procedures performed with robotic assistance that are considered part of the continuum of surgical treatment of breast cancer include robotic-assisted nipple-sparing mastectomy, reconstruction with the robotic latissimus dorsi flap or the deep inferior epigastric artery perforator flap, and robotic microsurgery for the flap anastomosis and/or the surgical treatment of lymphedema. The authors provide an overview of robotic surgery and how it has been integrated into the field of plastic surgery, as well as a review of the most common procedures within the field where robotic assistance can be incorporated: nipple-sparing mastectomy, robotic latissimus flap, robotic deep inferior epigastric artery perforator flap breast reconstruction, and microvascular anastomoses.
Which lesions are not amenable to tricuspid clipping?
Authors: Bakar Shahrukh N. , Fam Neil P.
Published: December 2023

Purpose of review

Tricuspid transcatheter edge-to-edge repair (T-TEER) has emerged as a well tolerated and effective therapeutic option for many patients with symptomatic severe tricuspid regurgitation at prohibitive surgical risk. However, there remain several important limitations to clip-based technology in the context of other rapidly emerging percutaneous treatment options for tricuspid regurgitation.

Recent findings

Tricuspid lesions pose unique challenges to treatment with the current toolbox of transcatheter clip-based technologies. This review will explore key issues related to patient factors, anatomical factors, and imaging factors that may render lesions to be unsuitable for treatment with T-TEER.

Selection for T-TEER must include a detailed clinical evaluation in the context of a ‘heart team’ approach involving multiple subspecialists, with screening for patient/lesion characteristics that make T-TEER suboptimal with current clip-based technologies. Future directions for research include patient-specific 3D modeling techniques, leaflet grasping techniques, clip deployment strategies, and personalized device sizing to increase the spectrum of lesions that may be treated with T-TEER within the context of other emerging transcatheter treatment options.
Biodosimetry Based on Gamma-H2AX Quantification in Human Peripheral Blood Lymphocytes after Partial-body Irradiation
Authors: Ma Li-Ping , Chen Jie , Liu Meng-Meng , Yan Juan , Xiang Jia-Qi , Tian Mei , Gao Ling , Liu Qing-Jie
Published: December 2023

Quantification of gamma-H2AX foci can estimate exposure to ionizing radiation. Most nuclear and radiation accidents are partial-body irradiation, and the doses estimated using the total-body irradiation dose estimation formula are often lower than the actual dose. To evaluate the dose-response relation of gamma-H2AX foci in human peripheral blood lymphocytes after partial-body irradiation and establish a simple and high throughput model to estimate partial-body irradiation dose, we collected human peripheral blood and irradiated with 0-, 0.5-, 1-, 2-, 3-, 4-, 5-, 6-, and 8-Gy gamma rays to simulate total-body irradiation in vitro. Gamma-H2AX foci were quantitated by flow cytometry at 1 h after irradiation, and a dose-response curve was established for total-body irradiation dose estimation. Then, a partial-body irradiation dose-response calibration curve was established by adding calibration coefficients based on the Dolphin method. To reflect the data distribution of all doses more realistically, the partial-body irradiation dose-response calibration curve was divided into two sections. In addition, partial-body irradiation was simulated in vitro, and the PBI data were substituted into curves to verify the accuracy of the two partial-body irradiation calibration curves. Results showed that the dose estimation variations were all less than 30% except the 25% partial-body irradiation group at 1 Gy, and the partial-body irradiation calibration dose-response curves were YF1 = − 3.444 x 2 + 18.532 x + 3.109, R2 = 0.92 (YF ≤ 27.95); YF2 = − 2.704 x 2 + 37.97 x − 56.45, R2 = 0.86 (YF > 27.95). Results also suggested that the partial-body irradiation dose-response calibration curve based on the gamma-H2AX foci quantification in human peripheral blood lymphocytes is a simple and high throughput model to assess partial-body irradiation dose.
An Alternative to Cytology in Triaging Cisgender Men and Transgender Women With HIV for High-Resolution Anoscopy
Authors: Mudrinich Shane M. , Nguyen Minh Ly T. , Blemur Danielle M. , Wang Xinzhu , Wang Yun F. , Krishnamurti Uma , Mosunjac Marina , Flowers Lisa C.
Published: December 2023

Objectives

To evaluate high-risk human papillomavirus testing (hrHPV) as an alternative for anal cytology in screening for high-grade anal neoplasia (AIN2–3) among males with HIV. To identify predictive risk factors for AIN2–3 and develop a clinical tool to triage males with HIV for high-resolution anoscopy (HRA) without cytology.

Design

Retrospective cohort study of 199 adult cisgender men and transgender women with HIV referred to an anal neoplasia clinic in the Southeastern United States between January 2018 and March 2021.

Methods

Each subject underwent cytology, hrHPV, and HRA. Clinical and sociodemographic risk factors were collected for each subject. Significant risk factors for AIN2–3 were identified using logistic regression, and a triage tool incorporating these factors was developed. Screening test characteristics were calculated for cytology with and without adjunct hrHPV, hrHPV alone, and the triage tool.

Results

In multivariate analysis, significant predictors of AIN2–3 were hrHPV positivity (odds ratio [OR] = 11.98, CI = 5.58–25.69) and low CD4 count (OR = 2.70, CI = 1.20–6.11). There was no significant difference in positive or negative predictive values among the tool, stand-alone hrHPV, and anal cytology with adjunct hrHPV. Sensitivity and specificity were not significantly different for stand-alone or adjunctive hrHPV testing. Compared with cytology, stand-alone hrHPV and the novel triage tool reduced unnecessary HRA referrals by 65% and 30%, respectively.

Conclusions

Stand-alone hrHPV would have missed 11 of 74 AIN2–3 and generated 74 fewer unnecessary HRAs than current cytology-based screening patterns, which led to 115 unnecessary HRAs in our cohort. We propose triaging those with low CD4 count, hrHPV positivity, and/or smoking history for HRA.
2019 ASCCP Risk-Based Management Consensus Guidelines: Updates Through 2023
Authors: Perkins Rebecca B. , Guido Richard S. , Castle Philip E. , Chelmow David , Einstein Mark H. , Garcia Francisco , Huh Warner K. , Kim Jane J. , Moscicki Anna-Barbara , Nayar Ritu , Saraiya Mona , Sawaya George F. , Wentzensen Nicolas , Schiffman Mark ,   for the 2019 ASCCP Risk-Based Management Consensus Guidelines Committee
Published: December 2023

This Research Letter summarizes all updates to the 2019 Guidelines through September 2023, including: endorsement of the 2021 Opportunistic Infections guidelines for HIV+ or immunosuppressed patients; clarification of use of human papillomavirus testing alone for patients undergoing observation for cervical intraepithelial neoplasia 2; revision of unsatisfactory cytology management; clarification that 2012 guidelines should be followed for patients aged 25 years and older screened with cytology only; management of patients for whom colposcopy was recommended but not completed; clarification that after treatment for cervical intraepithelial neoplasia 2+, 3 negative human papillomavirus tests or cotests at 6, 18, and 30 months are recommended before the patient can return to a 3-year testing interval; and clarification of postcolposcopy management of minimally abnormal results.
Factors Affecting Medical Residents’ Decisions to Work After Call
Authors: Carr Michele M. , Foreman Anne M. , Friedel Jonathan E. , O’Brien Daniel C. , Wirth Oliver
Published: December 2023

Background

Accreditation Council for Graduate Medical Education (ACGME) work-hour restrictions (WHRs) are intended to improve patient safety by reducing resident fatigue. Compliance with ACGME WHRs is not universal.

Purpose

The purpose of this study was to identify factors that influence residents’ decisions to take a postcall day (PCD) off according to ACGME WHRs.

Methods

Residents (N = 433) at one university were emailed a link to a survey in 2019. The survey included demographic details and a Discrete Choice Experiment examining influences on resident decisions to take a PCD off.

Results

One hundred seventy-five residents (40.4%) responded to the survey; 113 residents (26%) completed the survey. Positive feedback from attending physicians about taking PCDs off in the past had the greatest impact on respondents’ decisions to take a PCD off, increasing the probability by 27.3%, followed by chief resident comments about the resident looking tired (16.6% increase), and having never heard their attendings comment about PCDs off as either positive or negative (13.9% increase). Factors that had the largest effect on decreasing the probability of taking a PCD were negative feedback about taking PCDs off (14.3% decrease), continuity of care concerns (10.8% decrease), and whether the resident was looking forward to an assignment (7.9% decrease).

Conclusions

The most important influencer of residents’ decisions to take a PCD off was related to feedback from their attending physicians, suggesting that compliance with WHRs can be improved by focusing on the residency program’s safety culture.
The Aesthetic Evaluation of the Brow-Eye Continuum After Correction of Severe Congenital Ptosis in Children With Extended Frontalis Muscle Advancement Technique
Authors: Sun Li-Ming , Fan Xiao , Hao Dong-Yue , Cao Jiao , Cang Zheng-Qiang , He Yun-Xia , Qiao Hai-Xia , Song Bao-Qiang , Peng Pai , Liu Chao-Hua
Published: December 2023

Background

Severe congenital ptosis is a common ocular deformity in pediatric patients that can significantly impact visual development and aesthetic appearance, leading to negative psychosocial outcomes. The frontalis muscle advancement technique is a well-established surgical treatment for severe congenital ptosis. Aesthetic changes of the brow-eye continuum often plays an important role in ptosis surgery.

Methods

We conducted a single-center retrospective case series study of patients with severe congenital ptosis who underwent the frontalis muscle advancement technique at the Department of Plastic and Reconstructive Surgery, Xijing Hospital, Fourth Military Medical University between April 2020 and June 2021. The study aimed to evaluate the aesthetic changes of the eyebrow-eyelid continuum after surgery. The main outcome measurements included marginal reflex distance 1, palpebral fissure height, eyebrow position, upper eyelid to lower eyebrow distance, lower eyelid to upper eyebrow distance, and nasal base to lower eyelid distance.

Results

The study included 48 patients (66 eyelids), with 30 unilateral and 18 bilateral patients. Our analysis found that eyebrow height decreased by an average of 4.8% postoperatively relative to preoperatively in all patients.

Conclusions

The frontalis muscle advancement technique has demonstrated effectiveness in achieving aesthetically pleasing outcomes in children with severe ptosis. It is crucial to pay careful attention to the brow-eye continuum during the correction process, as its harmony can greatly impact the final result.
Preventive Effects of Prenatal Folic Acid on Postpartum Depression
Authors: Feng Xueqin , Wang Chunxia , Wang Fuling , Zhang Xiaoyun , Shu Hua , Chen Hui , Duan Liting , Wei Yuxi , Wang Jishui , Man Dongmei , Zhang Fanyong
Published: December 2023

This study was conducted to assess the association of prenatal folic acid (PF) supplements on the onset of postpartum depression (PPD) in Chinese women. Of the 629 subjects, 540 were cases who took PF supplements and 89 were controls who did not take PF. Univariate analysis showed that maternal age and body mass index were the most significant risk factors for developing PPD. Threshold effect analysis showed that maternal age of more than 26 years was an independent determinant of PPD. Current findings with PF supplements are insufficient to attenuate the onset of PPD.
Prospective Study of a System-Wide Adrenal Incidentaloma Quality Improvement Initiative
Authors: Woods Alison P , Feeney Timothy , Gupta Avneesh , Knapp Philip E , McAneny David , Drake Frederick Thurston
Published: December 2023

BACKGROUND:

Appropriate follow-up of incidental adrenal masses (IAMs) is infrequent. We implemented a quality improvement (QI) program to improve management of IAMs.

STUDY DESIGN:

This system-wide initiative targeted primary care providers (PCPs) after IAM detection. It incorporated (1) chart-based messages and emails to PCPs, (2) an evidence-based IAM evaluation algorithm, (3) standardized recommendations in radiology reports, and (4) access to a multispecialty adrenal clinic. Patients diagnosed with an IAM from January 1, 2018, to December 31, 2019, were prospectively included (the “QI cohort”) and compared with a historical, preintervention cohort diagnosed with IAMs in 2016. The primary outcomes were the initiation of an IAM investigation by the PCP, defined as relevant clinical history-taking, laboratory screening, follow-up imaging, or specialist referral.

RESULTS:

The QI cohort included 437 patients and 210 in the historical cohort. All patients had 12 months or more of follow-up. In the QI cohort, 35.5% (155 of 437) met the primary endpoint for PCP-initiated evaluation, compared with 27.6% (58 of 210) in the historical cohort (p = 0.0496). Among the subgroup with a documented PCP working within our health system, 46.3% (74 of 160) met the primary endpoint in the QI cohort vs 33.3% (38 of 114) in the historical cohort (p = 0.035). After adjusting for insurance status, presence of current malignancy, initial imaging setting (outpatient, inpatient, or emergency department), and having an established PCP within our health system, patients in the QI cohort had 1.70 times higher odds (95% CI 1.16 to 2.50) of undergoing a PCP-initiated IAM evaluation. Adrenal surgery was ultimately performed in 2.1% (9 of 437) of QI cohort patients and 0.95% (2 of 210) of historical cohort patients (p = 0.517).

CONCLUSIONS:

This simple, moderately labor-intensive QI intervention was associated with increased IAM evaluation initiated by PCPs.
The rediscovery of the putative ant social parasite
Manica parasitica
syn. nov. (Hymenoptera: Formicidae) reveals an unexpected endoparasite syndrome
Authors: Prebus Matthew , Georgiev Boyko B. , van de Kamp Thomas , Hamann Elias , Baker Iyla , Rabeling Christian
Published: December 2023

Parasitism is ubiquitous across the tree of life, and parasites comprise approximately half of all animal species. Social insect colonies attract many pathogens, endo- and ectoparasites, and are exploited by social parasites, which usurp the social environment of their hosts for survival and reproduction. Exploitation by parasites and pathogens versus social parasites may cause similar behavioural and morphological modifications of the host. Ants possess two overlapping syndromes: the endo- and social parasite syndromes. We rediscovered two populations of the putative social parasite
Manica parasitica
in the Sierra Nevada, and tested the hypothesis that
M. parasitica
is an independently evolving social parasite
.
We evaluated traits used to discriminate
M. parasitica
from its host
Manica bradleyi,
and examined the morphology of
M. parasitica
in the context of ant parasitic syndromes. We find that
M. parasitica
is not a social parasite. Instead,
M. parasitica
represents cestode-infected
M. bradleyi
. We propose that
M. parasitica
should be regarded as a junior synonym of
M. bradleyi
. Our results emphasize that an integrative approach is essential for unravelling the complex life histories of social insects and their symbionts.
A mixed-method approach to determining contact matrices in the Cox’s Bazar refugee settlement
Authors: Walker Joseph , Aylett-Bullock Joseph , Shi Difu , Kahindo Maina Allen Gidraf , Samir Evers Egmond , Harlass Sandra , Krauss Frank
Published: December 2023

Contact matrices are an important ingredient in age-structured epidemic models to inform the simulated spread of the disease between subgroups of the population. These matrices are generally derived using resource-intensive diary-based surveys and few exist in the Global South or tailored to vulnerable populations. In particular, no contact matrices exist for refugee settlements—locations under-served by epidemic models in general. In this paper, we present a novel, mixed-method approach for deriving contact matrices in populations, which combines a lightweight, rapidly deployable survey with an agent-based model of the population informed by census and behavioural data. We use this method to derive the first set of contact matrices for the Cox’s Bazar refugee settlement in Bangladesh. To validate our approach, we apply it to the UK population and compare our derived matrices with well-known contact matrices collected using traditional methods. Our findings demonstrate that our mixed-method approach successfully addresses some of the challenges faced by traditional and agent-based approaches to deriving contact matrices. It also shows potential for implementation in resource-constrained environments. This work therefore contributes to a broader aim of developing new methods and mechanisms of data collection for modelling disease spread in refugee and internally displaced person (IDP) settlements and better serving these vulnerable communities.
Prior beliefs and the interpretation of scientific results
Authors: Eidels Ami
Published: December 2023

How do prior beliefs affect the interpretation of scientific results? I discuss a hypothetical scenario where researchers publish results that could either support a theory they believe in, or refute that theory, and ask if the two instances carry the same weight. More colloquially, I ask if we should overweigh scientific results supporting a given theory and reported by a researcher, or a team, that initially did not support that theory. I illustrate the challenge using two examples from psychology: evidence accumulation models, and extra sensory perception.
Tenacibaculum tangerinum sp. nov., isolated from a tidal flat sediment
Authors: Lee Sang Hyun , Yoo Yeonjae , Kwon Dae Young , Khim Jong Seong , Xu Xiaoyue , Kim Bogun , Choi In-Geol , Kim Jae-Jin
Published: December 2023

An orange-coloured bacterium, designated as strain GRR-S3-23T, was isolated from a tidal flat sediment collected from Garorim Bay, Chuncheongbuk-do, Republic of Korea. Cells of GRR-S3-23T were aerobic, Gram-stain-negative, rod-shaped and motile. GRR-S3-23T grew at 18–40 °C (optimum, 30 °C), pH 7.0–9.0 (optimum, pH 7.0) and with 2–4 % NaCl (optimum, 2–3 % w/v). Results of 16S rRNA gene sequence analysis indicated that GRR-S3-23T was closely related to

Tenacibaculum aiptasiae

a4T (97.6 %), followed by

Tenacibaculum aestuarii

SMK-4T (97.5 %),

Tenacibaculum mesophilum

MBIC 1140T (97.4 %),

Tenacibaculum singaporense

TLL-A2T (97.3 %),

Tenacibaculum crassostreae

JO-1T (97.2 %),and

Tenacibaculum sediminilitoris

YKTF-3T (97.1 %). The average amino acid identity values between GRR-S3-23T and the related strains were 86.8–72.8 %, the average nucleotide identity values were 83.3–74.1 %, and the digital DNA–DNA hybridization values were 27.0–19.6 %. GRR-S3-23T possessed menaquinone-6 (MK-6) as major respiratory quinone and had summed feature 3 (C16 : 1ω7c and/or C16 : 1ω6c, 20.6 %) and iso-C15 : 1G (10.8 %) as major fatty acids (>10.0 %). The polar lipid profiles of GRR-S3-23T contained phosphatidylethanolamine, one unidentified aminolipid, one unidentified aminophospholipid, three unidentified lipids, one unidentified glycolipid and four unidentified phospholipids. The DNA G+C content of GRR-S3-23T was 33.7%. On the basis of the results of the polyphasic analysis involving phylogenetic, phylogenomic, physiological and chemotaxonomic analyses described in this study, GRR-S3-23T is considered to represent a novel species within the genus

Tenacibaculum

, for which the name Tenacibaculum tangerinum is proposed. The type strain is GRR-S3-23T (=KCTC 102029T=KACC 23271T=JCM 36353T).
Pseudomonas cucumis sp. nov., isolated from the rhizosphere of crop plants
Authors: Liao Kaiji , Liu Jianying , Gu Yi-Lin , Wang Can , Wei Hai-Lei
Published: December 2023

Two bacterial strains, FP1935T and FP1962, were isolated from the rhizosphere soil of cucumber and Chieh-qua plants, respectively, in Jilin Province, PR China. These strains were Gram-stain-negative, aerobic, rod-shaped and motile with one or two polar flagella. Analysis of the 16S rRNA gene sequences revealed that they represented members of the genus Pseudomonas, with the highest similarity to Pseudomonas silesiensis A3T (99.45 %), Pseudomonas frederiksbergensis JAJ28T (99.45 %), Pseudomonas mandelii NBRC 103147T (99.38 %), Pseudomonas piscium P50T (99.27 %) and Pseudomonas meliae CFBP 3225T (99.18 %). The DNA G+C contents of FP1935T and FP1962 were 58.99 mol% and 58.98 mol%, respectively. The results of in silico genome-based analyses indicated that these strains were distinct from other species in the genus Pseudomonas, as the average nucleotide identity (ANI) and digital DNA–DNA hybridization (dDDH) values were below the recommended thresholds of 95 % (ANI) and 70 % (dDDH) for prokaryotic species delineation, with no values exceeding 94.1 and 55.8 %, respectively, compared with any other related species. The results of phenotypic and chemotaxonomic tests confirmed their differentiation from their closest relatives. The fatty acid profiles of both strains mainly consisted of summed feature 3 (C16 : 1ω6c and/or C16 : 1ω7c), summed feature 8 (C18 : 1ω7c and/or C18 : 1ω6c), C12 : 0 and C16 : 0. The predominant respiratory quinone was Q-9. Polar lipids include phosphatidylethanolamine, unidentified aminophospholipids, unidentified lipids and an unidentified phospholipid. On the basis of these phenotypic and genotypic results, we propose the name Pseudomonas cucumis sp. nov. for these novel strains. The type strain is FP1935T (=ACCC 62445T=JCM 35690T).
eRNA-IDO: a one-stop platform for identification, interactome discovery and functional annotation of enhancer RNAs
Authors: Zhang Yuwei , Gong Lihai , Ding Ruofan , Chen Wenyan , Rong Hao , Li Yanguo , Shameem Fawziya , Ali Korakkandan Arshad , Li Lei , Liao Qi
Published: December 2023

Increasing evidence proves the transcription of enhancer RNA (eRNA) and its important role in gene regulation. However, we are only at the infancy stage of understanding eRNA interactions with other biomolecules and the corresponding functionality. To accelerate eRNA mechanistic study, we present the first integrative computational platform for humaneRNAidentification, interactome discovery, and functional annotation, termed eRNA-IDO. eRNA-IDO comprises two modules: eRNA-ID and eRNA-Anno. Functionally, eRNA-ID identifies eRNAs fromde novoassembled transcriptomes. The bright spot of eRNA-ID is indeed the inclusion of 8 kinds of enhancer makers, whose combination enables users to personalize enhancer regions flexibly and conveniently. In addition, eRNA-Anno provides cell/tissue specific functional annotation for any novel and known eRNAs through discovering eRNA interactome from the prebuilt or user-defined eRNA-coding gene networks. The pre-built networks include GTEx-based normal co-expression networks, TCGA-based cancer co-expression networks, and omics-based eRNA-centric regulatory networks. Our eRNA-IDO carries sufficient practicability and significance for understanding the biogenesis and functions of eRNAs. The eRNA-IDO server is freely available athttp://bioinfo.szbl.ac.cn/eRNA_IDO/.
Continual improvement of multiplex mutagenesis in Arabidopsis
Authors: Develtere Ward , Decaestecker Ward , Rombaut Debbie , Anders Chantal , Clicque Elke , Vuylsteke Marnik , Jacobs Thomas B.
Published: December 2023

CRISPR/Cas9 is currently the most powerful tool to generate mutations in plant genomes and more efficient tools are needed as the scale of experiments increases. In the model plant Arabidopsis, the choice of promoter driving Cas9 expression is critical to generate germline mutations. Several optimal promoters have been reported. However, it is unclear which promoter is ideal as they have not been thoroughly tested side-by-side. Furthermore, most plant vectors still use one of the two Cas9 nuclear localization sequence (NLS) configurations initially reported and can still be optimized. We genotyped more than 6,000 Arabidopsis T2 plants to test seven promoters and eleven NLS architectures across 14 targets to systematically improve the generation of single and multiplex inheritable mutations. We find that the RPS5A promoter and double-BP NLS architecture were individually the most efficient components. When combined, 99% of T2 plant contained at least one knockout mutation and 84% contained 4-7-plex knock-outs. These optimizations will be useful to generate higher-order knockouts in the germline of Arabidopsis and likely be applicable to other CRISPR systems as well.