bluuebunny/crossref_metadata_2025 huggingface dataset:
49 Effects of numeracy and literacy on glycemic control and self-perceived efficacy in youth with type 1 diabetes in Haiti
Authors: Leduc Bertrand , Von Oettingen Julia Elisabeth , Duperval Regina , Altenor Ketly , Joseph Mysterline
Published: October 2024

Background

The management of type 1 diabetes (T1D) in low-resource settings remains a challenge in the context of unfavourable social determinants of health. The effects of literacy and numeracy on glycemic control and self-perceived efficacy in youth living with T1D in low-resource settings have been insufficiently investigated.

Objectives

We described literacy and numeracy in Haitian youth with T1D and their caregivers and we evaluated their association with hemoglobin A1c (HbA1c) and perceived diabetes management self-efficacy.

Design/Methods

We conducted a cross-sectional cohort study of youth with T1D treated at the Montrouis clinic in Haiti, between June to December 2017. Inclusion criteria were a diagnosis of T1D at age 0-25 years and at least one parent of Haitian ancestry. One principal caregiver of each youth was also included. Exclusion criteria were inability of informed consent and declined home visit. The study was approved by our Institution Research Ethics Board. Data collection included demographics, clinical data, numeracy questionnaire adapted to the population and the standardized self-efficacy 8-item Perceived Diabetes Self-Management Scale (PDSMS). We used univariate and multivariate linear regression models to evaluate predictors of HbA1c and PDSMS scores.

Results

We included 85 patients (60% female) and 73 caregivers. Median age at diagnosis and diabetes duration were 14.3 and 3.1 years, respectively. Over 90% of patients had suboptimal (HbA1c >7.0%), poor (HbA1c >9%) or very poor (HbA1c >12%) glycemic control. 76 patients (90.5%) self-reported being able to read, 78 (91.8%) to write and 84 (98.8%) to count. Mothers’ and fathers’ median education years were 7.0 and 11, respectively. 54 parents (74.0%) self-reported being able to read and write. Normalized to 100%, median patient numeracy score was 75.0% and the mean PDSMS score was 65.9%. In univariate models, lower HbA1c was predicted by younger age (p=0.013), but not by gender, diabetes duration, numeracy score, mother’s education or PDSMS score. Higher PDSMS score was predicted by higher numeracy scores (p=0.003), marginally by sex (p=0.057), but not by age, diabetes duration, or mother’s education; in a multivariate model adjusted for age, sex and diabetes duration, higher numeracy remained significant (p=0.006).

Conclusion

In youth with T1D in Haiti who have ubiquitously poor glycemic control and suboptimal family literacy and numeracy, numeracy is a predictor of self-perceived efficacy of T1D. Further public health interventions addressing numeracy in youth living with T1D in low-resource settings are advised.
57 Resident education in the NICU: A curriculum innovation project
Authors: Ediger Krystyna , Cormier Sylvie
Published: October 2024

Background

For paediatrics residents, much of newborn care is learned during Neonatal Intensive Care Unit (NICU) rotations. However, the NICU is a high-stress and specialized learning environment. Today’s residents often have less NICU exposure during their training than in the past, leading to concerns from trainees that they are inadequately prepared for neonatal care and resuscitation upon graduation.

Objectives

We aimed to develop, implement and evaluate a paediatric residency NICU curriculum aimed to augment and improve learning on rotation.

Design/Methods

We utilized Kern’s Six Step Approach for Curriculum Development. Step 1: We identified that our paediatric residents consistently expressed dissatisfaction with the quality and quantity of learning opportunities on their NICU rotations. Step 2: A collaborative working group of residents, paediatricians, and neonatologists identified learning needs. Step 3: Needs were mapped to specific general paediatrics educational objectives within the Royal College Competency Based Medical Education (CBME) curriculum. Step 4: Suitable learning strategies were selected including simulation, procedural skill training, embedded time with the neonatal resuscitation team, and lunch and learn seminars. Steps 5 and 6: The curriculum was piloted during the 2021-2022 academic year and resident reactions evaluated.

Results

The detailed curriculum is shown in Table 1. At the start of each NICU rotation, all paediatrics residents on rotation attended a half-day simulation based “boot-camp” consisting of a didactic Neonatal Resuscitation Program (NRP) refresher course, relevant procedural skills stations (intubation, UVC placement, needle thoracocentesis), and simulated neonatal resuscitation scenarios. Junior residents were scheduled for protected time to attend deliveries with a dedicated multidisciplinary resuscitation team to ensure familiarity and begin to solidify skills. Learning was further augmented by weekly, resident-led lunch and learn sessions on topics mapped to level of training. To evaluate this curriculum, resident satisfaction was assessed using surveys post bootcamp and at the end of their rotation. Overall, the curriculum was well received. Bootcamp was the highest rated element; 96% of residents agreed or strongly agreed that the session was useful for their education (Figure 1). Post curriculum implementation, there was significant improvement in resident NICU rotation feedback; residents expressed that the NICU learning environment and resident experience has improved.

Conclusion

We successfully implemented a NICU curriculum for paediatrics residents, with high satisfaction ratings and improved overall rotation feedback. This program shows promise in addressing a long standing educational gap. More research is needed to investigate whether it leads to improved competency in practice.
69 Urinary tract infections in preterm infants: Review in two Canadian tertiary centers
Authors: Nguyen Bao-Nghi , Kuan Mimi , Balay Celine , Shen Ye , Richter Lindsay , Lisonkova Sarka , Wong Jonathan , Ting Joseph
Published: October 2024

Background

Urinary tract infections (UTI) in premature infants are commonly seen in the neonatal intensive care unit (NICU). The reported prevalence of UTI in this population ranges from 1.9-12.2% due to the lack of standardized criteria for UTI among infants less than two months of age. Enterococcus and Enterobacteriaceae are well known to cause UTI and their resistance pattern has been reported to be rising in the neonatal nosocomial infections worldwide.

Objectives

To describe the epidemiology, microbiology, and antimicrobial treatment for UTI in premature infants based on different diagnostic criteria.

Design/Methods

This retrospective study (2019-2022) included infants born at <33 weeks of gestational age (GA) with positive urine cultures and ≥5 days of antimicrobials treatment. We collected data from two tertiary level NICUs in Canada, including demographics, microbial susceptibility patterns, urinalysis and imaging results, and antibiotic treatment.

Results

We identified 43 infants managed as UTI based on physicians’ discretions. The median GA at birth was 26-27 weeks, while the median onset of first UTI ranged 39-80 days, with male predominance [Table 2]. Mixed growth of organisms constituted 21-42% of cases of UTI [Table 1]. Among UTI cases with only single growth organism, we found 53.5% and 18.6% cases fulfilled UTI diagnostic criteria based on the concentration of colony forming units (CFU) of >104/mL or >107/L and >105/mL or >108/L, respectively [Table 1]. Of these cases, 67.4% of infants had urinalysis sent with the culture, and the higher the concentration of CFU, the more likely the samples showed positive nitrites on urinalysis, with 100% correlation among those with CFU >105/mL or >108/L. [Table 1] The most common pathogens were Enterococcus species, E.Coli, Klebsiella species, Citrobacter species and Enterobacter cloacae complex [Table 2]. Among gram negative bacilli (E. Coli and Klebsiella species), greater than 42-80% were resistant to 3rd generation cephalosporins (3GC). We did not identify any vancomycin-resistant Enterococcus strains. Median duration of antimicrobial treatment ranged from 8-13 days, depending on the diagnostic criteria applied. At least 10% of infants with UTI showed abnormalities on kidney ultrasound [Table 2].

Conclusion

There exists a large variation in UTI prevalence according to different diagnostic criteria. Abnormal urinalysis with presence of nitrites were frequently associated with UTI of high CFU count. High resistance to 3GC among gram negative bacilli was concerning and carried an impact on the appropriate empirical treatment choice.
74 Reducing unplanned extubations in a level 3 neonatal intensive care unit - the nuts and bolts of UE bundle implementation
Authors: Law Brenda Hiu Yan , Godbout Vanessa
Published: October 2024

Background

Unplanned extubations (UEs) are preventable adverse events that may lead to short term consequences (e.g. cardiopulmonary collapse) and long term sequelae (e.g. acquired airway injury, brain injury) for patients admitted to the Neonatal Intensive Care Unit (NICU). UE prevention care bundles have been demonstrated to reduce UE rates in NICUs; however, implementation of bundle elements is unit dependent.

Objectives

To describe the work of a UE Prevention Team in a Level 3 NICU with rising UE rates despite implementation of UE prevention bundle per Children’s Hospital Solutions for Patient Safety (SPS).

Design/Methods

A neonatologist / respiratory therapist pair was assembled in March 2022 to tackle rising UE rates in a 69 bed NICU. Contributing unit stressors included implementation of a new electronic health record, COVID-19 policies, and nursing shortages. Baseline UE rates were >3x the centerline for SPS network NICUs and likely underreported. Steps undertaken include: 1) daily audit to ensure reporting of all UEs, 2) structured post-event team debriefs, 3) unit education campaign to raise awareness of UE prevention and bundle elements, 4) prominent posting of last UE date and reporting on daily team huddle, 5) rapid UE case reviews and apparent cause analysis with reporting of findings unit-wide, 6) optimize endotracheal tube (ETT) securement methods, 6) enforce T2-T3 ETT tip position, 7) standardize x-ray frequencies and reporting, 8) trial of daily rounds ETT safety checklist.

Results

From rapid case reviews, apparent causes were determined to be incorrect ETT securement device sizing, taping method prone to loss of tape integrity in high humidity, high ETT positions, and inadequate ETT monitoring during high risk activities other than repositioning (invasive/painful procedures, diaper changes). Post-event structured debriefs and unit-wide vigilance increased reporting of UE events to 100%. UE rates fell from a peak of >4 UEs/month, >2.4/100 ventilation days to 1 UE/month, 0.465/100 ventilation days, a 80% reduction.(Figure 1) Most impactful interventions were standard x-ray reporting template in the electronic health record, reinforcing T2-T3 ETT tip positioning, correcting ETT holder sizing, and change in ETT method (Figure 2). Daily rounds checklist was not effective. UE reductions were achieved without changing patient ratios as nurse staffing shortages continued.

Conclusion

A nimble systems approach is needed to ensure success in implementation of UE prevention care bundles. Simple changes can be made to decrease UEs, guided by rapid case reviews.
Paricalcitol ameliorates diabetic nephropathy by promoting EETs and M2 macrophage polarization and inhibiting inflammation by regulating VDR/CYP2J2 axis
Authors: Tang Shiqi , Tan Jun , Yang Shikun , Li Aimei , Liu Jishi , Zhang Wei , Zhang Hao , Liu Yan
Published: October 2024

Previous studies have shown that paricalcitol (PA) has a protective effect on the kidneys. However, the exact molecular mechanism by which PA affects diabetic nephropathy (DN) progression remains uncertain. PBMCs of patients with DN were isolated, and CYP2J2 and VDR levels were detected by qPCR. Pearson correlation analysis was utilized to detect the relationship between uACR and CYP2J2 and VDR and between CYP2J2 and VDR. The protective effects of PA on DN have been examined by TUNEL, HE staining, ELISA, and Flow cytometry assays in STZ‐induced mice. Moreover, THP‐1 cells were stimulated with HG/LPS for in vitro studies. ELISA, qPCR, western blot, and Flow cytometry assays were utilized to assess the effects of PA on DN progression by regulating CYP2J2. The interaction between CYP2J2 and VDR was analyzed by CHIP‐qPCR and luciferase experiments. CYP2J2 and VDR levels were downregulated and uACR level was upregulated in DN patients. CYP2J2 and VDR were positively correlated in PBMCs. Both CYP2J2 and VDR are inversely correlated with uACR. Moreover, after PA treatment, 11, 12‐EET levels increased, inflammatory factor levels decreased, and M2 macrophage polarization was promoted in STZ‐induced mice and HG/LPS‐triggered THP‐1 cells. Depletion of CYP2J2 and VDR decreased 11, 12‐EET level, enhanced inflammatory factor levels, and inhibited M2 macrophage polarization, which were reversed by CYP2J2 overexpression in HG/LPS‐treated cells. Furthermore, VDR bound to the CYP2J2 promoter and promoted CYP2J2 transcriptional expression. The present work pointed out a new use for PA to inhibit DN progression by increasing EET level, inhibiting inflammatory response, and inducing M2 macrophage polarization via regulating the VDR/CYP2J2 axis.
Association Between Social Determinants of Health and Hearing Loss and Hearing Intervention in Older US Adults
Authors: Terhaar Samantha , Patel Dhruv , Fung Ethan , Mansour Febronia , Wallace Josh F. , Corsten Martin , McDonald James Ted , Johnson-Obaseki Stephanie , Quimby Alexandra E.
Published: October 2024

Objective

Estimate the prevalence of hearing loss and hearing assistance device use among older adults in the United States, and assess for associations with select social determinants of health (SDOH).

Study Design

Cross-sectional US population-based study using National Health and Nutrition Examination Survey (NHANES) 2017–March 2020 (pre-pandemic) data.

Setting

Non-institutionalized civilian adult US population.

Methods

US adults aged ≥70 years who completed NHANES audiometry exams were included. Sample weights were applied to provide nationally representative prevalence estimates of hearing loss and hearing assistance device use. Logistic regression analyses assessed associations between SDOH and both hearing loss and hearing assistance device use.

Results

The overall prevalence of hearing loss was 73.7%. Among those with nonprofound hearing loss, the prevalence of hearing assistance device use was 31.3%. Older individuals (odds ratio [OR], 6.3 [3.668–10.694] comparing ages 80+ versus 70–74 yr) and with lower education (OR, 3.8 [1.455–9.766] comparing <ninth grade versus college graduates or above) experienced a significantly elevated prevalence of hearing loss, whereas females (OR, 0.5 [0.326–0.754] versus males) and Blacks (0.5 [0.295–0.841] versus non-Hispanic Whites) had lower prevalence. Although older individuals with hearing loss had a higher prevalence of hearing assistance device use (OR, 2.1 [1.294–3.553] comparing ages 80+ to 70–74 yr), individuals of Black and other Hispanic races had a significantly lower prevalence of hearing assistance device use than non-Hispanic Whites (OR, 0.4 [0.188–0.671]; OR 0.1 [0.012–0.459], respectively), and those with no health insurance had higher prevalence of use than those who were insured (OR, 4.8 [1.307–17.371]).

Conclusion

The prevalence of hearing loss among older adults in the United States remains roughly stable compared with previous population-based estimates, whereas the prevalence of hearing assistance device use is slightly increased. Population-level disparities exist both in the prevalence of hearing loss and hearing assistance device use across SDOH.
HeartMate III Autonomy Assistant in a Hemiplegic Left Ventricular Assist Device Patient: A Case Report
Authors: Iafrate Manuel , Aviolat Lorraine , Monis Vieira Marques Filipa , Soumille Valentin , Kirsch Matthias
Published: October 2024

Terminal heart failure presents challenges, requiring cardiac transplantation, or mechanical circulatory support. Limited donor organ availability has made mechanical support crucial. Advances in centrifugal-flow systems, compared to axial-flow, have improved patient outcomes by reducing adverse events. Rehabilitation is vital for patient independence postimplantation. We developed a tool to aid hemiplegic patients in managing power sources. A 44 year old male with tritroncular ischemic heart disease and a 15% ejection fraction. He underwent a double bypass and left ventricular assist device (LVAD) implantation while awaiting a transplant. Postsurgery, the patient suffered a stroke, leading to left motor impairments. To assist in managing LVAD power sources, an autonomous tool with a Woodcast support base and antislip surface was developed. The tool improves autonomy and quality of life for motor-impaired patients. It is designed to be portable, adaptable, supporting various mobility levels. Real-world evidence shows it reduces time and alarms for battery changes, proving effective in home settings. The tool significantly enhances hemiparetic patients’ self-care and independence, showing promise for motor-impaired individuals. Further research is needed to evaluate long-term benefits and challenges.
Analytical Validation of a Pan-Cancer NGS Assay for In-House Liquid Biopsy Testing: An International Multicenter Study
Authors: Lescuyer Gaëlle , Harlé Alexandre , Kumar Hari Shankar , Constantoulakis Pantelis , Pfarr Nicole , Heitzer Ellen , Michon Clémence , Russo Gianluca , Speel Ernst-Jan M , Piecyk Marie , Husson Marie , Christopoulou Georgia , Mayr Eva-Maria , Koppermann Mai-Lan , Passot Christophe , Graf Ricarda , Aoul Anes Hadjadj , Bourdon Violaine , Dubbink Hendrikus J , van Marion Ronald , Demers Imke , Dingemans Anne-Marie C , Troncone Giancarlo , Pepe Francesco , Muinelo-Romay Laura , Díaz-Lagares Ángel , Rodriguez-Casanova Aitor , Lago Lestón Ramón Manuel , Pathak Deepak , Shah Parth , Parillaud Romain V , Martínez de Ilarduya Oskar , Behr Jonas , Rapin Alexis , Vetterli Thomas , Boppudi Sanga Mitra , Malapelle Umberto , Payen-Gay Lea
Published: October 2024

Background

Liquid biopsy (LBx) assays are transforming precision oncology by the screening of genomic alterations in cfDNA. These assays provide a less invasive alternative to tissue biopsies, which are not always feasible. Molecular pathology laboratories require LBx assays that detect variants at low allele frequencies using standardized methods.

Methods

This study evaluated the Hedera Profiling 2 ctDNA test panel (HP2) (Hedera Dx, Epalinges, Switzerland), a hybrid capture-based NGS assay for the detection of somatic alterations from cfDNA. Covering 32 genes, HP2 enables the detection of SNVs, Indels, Fusions, CNVs, and MSI status from a single DNA-only workflow. The analytical performance was assessed using reference standards and a diverse cohort of 137 clinical samples pre-characterized by orthogonal methods.

Results

In reference standards at 0.5% VAF, detection sensitivity and specificity for SNVs/Indels were 96.92% and 99.67%, respectively, and 100% each for Fusions. For MSI with VAFs of ≥1% and CNVs with VAFs of ≥ 2% both achieved 100% sensitivity.

Conclusion

This international, multicenter analytical performance evaluation study across a large number of hospital laboratories demonstrated high concordance of HP2 assay with orthogonal methods, confirming its significant potential as a highly sensitive, and efficient Pan-Cancer test for future decentralized LBx testing.
Are we in a Big Data era for multiple sclerosis? Lessons from integrating clinical trials and observational studies data into the PRIMUS precision medicine platform
Authors: Demuth Stanislas , Faddeenkov Igor , Paris Julien , Rousseau Olivia , Baciotti Béatrice , Payet Marianne , Casey Romain , Vukusic Sandra , Doyle Senan , Jarre Guillaume , Vince Nicolas , Limou Sophie , Sèze Jérôme De , Kerbrat Anne , Laplaud David , Edan Gilles , Gourraud Pierre-Antoine ,   the PRIMUS Consortium
Published: October 2024

Objective

The “Projections In Multiple Sclerosis” (PRIMUS) project aims to develop a precision medicine platform enabling neurologists to support therapeutic decisions in multiple sclerosis by visualizing similar patient data among a reference database. We present a data integration method to combine randomized clinical trials (RCTs) and observational studies data and optimize their informativeness.

Methods

We developed an extract-transform-load data integration pipeline to combine 13 source databases with 31,786 patients: the “mother” and “high-definition” cohorts from the French MS registry and eleven industrial RCTs. We aimed to inform each treatment class initiation with at least 500 patients with 2-year clinical and MRI follow-up. Our data integration strategy used every patient visit as a potential baseline time point to inform a specific neurologist’ query to the platform, thus tailoring the actual analysis cohort to each patient.

Results

The resulting PRIMUS database had 12,953 patients with at least one informative visit. It could inform 7/8 common treatment initiation scenarios with at least 500 patients (range: 485 for glatiramer acetate; 1,754 for natalizumab). The per-visit integration identified 696 more patients in the high-definition cohort than the classical epidemiological per-patient integration (+114 %). Although the mother cohort’s longitudinal data were deemed to be sparse, we identified 6,128 informative patients (yield: 27.8%; mean: 2.2 visits per patient).

Interpretation

A data integration pipeline and per-visit integration enabled us to build a highly informative reference database to be queried by neurologists through a web application to support discussions with their patients and the selection of disease-modifying treatments.
ENACT: End-to-End Analysis of Visium High Definition (HD) Data
Authors: Kamel Mena , Song Yiwen , Solbas Ana , Villordo Sergio , Sarangi Amrut , Senin Pavel , Mathew Sunaal , Ayestas Luis Cano , Wang Seqian , Classe Marion , Bar-Joseph Ziv , Planas Albert Pla
Published: October 2024

Motivation

Spatial transcriptomics (ST) enables the study of gene expression within its spatial context in histopathology samples. To date, a limiting factor has been the resolution of sequencing based ST products. The introduction of the Visium High Definition (HD) technology opens the door to cell resolution ST studies. However, challenges remain in the ability to accurately map transcripts to cells and in assigning cell types based on the transcript data.

Results

We developed ENACT, the first tissue-agnostic pipeline that integrates advanced cell segmentation with Visium HD transcriptomics data to infer cell types across whole tissue sections. Our pipeline incorporates novel bin-to-cell assignment methods, enhancing the accuracy of single-cell transcript estimates. Validated on diverse synthetic and real datasets, our approach is both scalable and effective offering a robust solution for spatially resolved transcriptomics analysis.

Availability and implementation

ENACT source code is available athttps://github.com/Sanofi-Public/enact-pipeline. Experimental data is available athttps://zenodo.org/records/13887921. Supplementary information: Supplementary data are available at BiorXiv online.
Variant calling pipelines for whole exome sequencing in clinical context
Authors: Stepanian Johanna , Saldaña Diego , Mahecha Daniel , Mazabel Laura , Diaz Jorge
Published: October 2024

Introduction Whole exome sequencing (WES) has become a more accessible diagnostic tool in clinical genetic context, leading to the debate of the most accurate and effective bioinformatic pipeline solutions to evaluate variants that explain diseases. Objective This study aimed to evaluate twenty-four pipelines in two samples comparing accuracy, time and computing efficiency. We also contrasted the results based on regions in two of the most common capture kits. Materials and methods We used two accessions ofNA12872whole exome sequencing to contrast four different free access software for mapping using hg38 reference genome, then we used six different software alternatives for variant calling process. Finally, differences in computational resources and efficacy were evaluated. Results Our results showed that the most accurate and fastest pipeline is BWA with Strelka for SNVs detection, and differences in the use of resources and efficacy were proven. Conclusions BWA and Strelka are the most accurate and fastest for detecting SNVs in clinical exomes. Significant differences in efficiency and resource usage exist among the workflows evaluated. These findings aid in selecting the best methods for clinical contexts.
An envelope stress response governs long-chain fatty acid metabolism via a small RNA to maintain redox homeostasis inEscherichia coli
Authors: Shrivastava Megha , Kaur Manmehar , Luke Liz Maria , Kakkar Richa Ashok , Roy Deeptodeep , Singla Shivam , Sharma Vanshika , Sharma Gaurav , Chaba Rachna
Published: October 2024

Long-chain fatty acids (LCFAs) are a tremendous source of energy for several bacteria but are complex to use because they induce redox stress. We previously showed that LCFA degradation impedes oxidative protein folding in theEscherichia colienvelope, an issue that arises due to the insufficiency of ubiquinone, a lipid-soluble electron carrier in the electron transport chain (ETC). To maintain redox homeostasis,E. coliactivates the CpxAR two-component system; however, the nature of feedback imparted by this envelope stress response (ESR) remained unknown. Here, we show that contrary to the well-recognized remedial mode of Cpx restoring envelope integrity by upregulating protein quality control factors, in LCFA-grown cells, it uses a preventive measure to maintain homeostasis. Cpx increases ubiquinone availability for oxidative protein folding by suppressing LCFA metabolism and directly increasing ubiquinone levels. Further, rather than using its conventional mode of imparting regulation via CpxR working as a transcriptional regulator, during LCFA metabolism, Cpx mainly uses its non-coding arm to counteract envelope redox stress. The Cpx-regulated small RNA CpxQ repressesfadgenes involved in LCFA transport and β-oxidation, downregulates components of glyoxylate shunt, gluconeogenesis, and ETC, and increases ubiquinone content. Corroborating with its role in repressing LCFA metabolism and maintaining redox homeostasis, CpxQ overexpression impairs growth ofE. coliin LCFAs and CpxQ deletion renders LCFA-grownE. colihypersensitive to a thiol agent. Our foremost work studying the interconnection between LCFA metabolism, redox stress, and ESR inE. coliprovides a rationale for investigating similar networks in other LCFA-utilizing bacteria.

Significance Statement

Long-chain fatty acids (LCFAs) are energy-rich nutrients forEscherichia coli; however, their utilization hampers disulfide bond (DSB) formation in secreted proteins, an essential process that occurs in the envelope compartment. Here, we show that an envelope stress response manipulates LCFA metabolism inE. coliand uses a small RNA (sRNA) to restore homeostasis. Several bacteria with a huge impact on human health use host-derived LCFAs during infection. Because many virulence factors require DSB formation, the present study offers a basis to examine whether sRNAs play a role in governing envelope redox balance during LCFA metabolism in pathogens. The sRNA-mediated control is likely an ideal strategy both for rapid response to and quick recovery from LCFA-induced stress.
YebC2 resolves ribosome stalling at polyprolines independent of EF-P and the ABCF ATPase YfmR
Authors: Hong Hye-Rim , Prince Cassidy R. , Wu Letian , Lin Isabella N. , Feaga Heather A.
Published: October 2024

Polyproline motifs are essential structural features of many proteins, and recent evidence suggests that EF-P is one of several factors that facilitate their translation. For example, YfmR was recently identified as a protein that prevents ribosome stalling at proline-containing sequences in the absence of EF-P. Here, we show that the YebC-family protein YebC2 (formerly YeeI) functions as a translation factor inB. subtilisthat resolves ribosome stalling at polyprolines. We demonstrate that YebC2, EF-P and YfmR act independently to support cellular fitness. Moreover, we show that YebC2 interacts directly with the 70S ribosome, supporting a direct role for YebC2 in translation. Finally, we assess the evolutionary relationship between YebC2 and other characterized YebC family proteins, and present evidence that transcription and translation factors within the YebC family have evolved separately. Altogether our work identifies YebC2 as a translation factor that resolves ribosome stalling and provides crucial insight into the relationship between YebC2, EF-P, and YfmR, three factors that prevent ribosome stalling at prolines.
Discovery of broad-spectrum bacterial polyamine detoxification inhibitors as potential antivirulence agents and antibiotic adjuvants
Authors: Moulding Peri B. , Flannagan Ronald S. , Wong Jonas , Soliman Ahmed M. , Elhenawy Wael , Heinrichs David E. , El-Halfawy Omar M.
Published: October 2024

The alarming rise in antimicrobial resistance reinforces an urgent need for new antimicrobial strategies. Chemicals at infection sites, such as polyamines, often influence microbial virulence and antibiotic response. Polyamines are cationic small molecules overproduced by the host during infection, modulating immune responses—the ability of several pathogens to detoxify polyamines correlated with hypervirulence. We sought to uncover inhibitors of polyamine detoxification through a high-throughput whole-cell screen against the community-acquired methicillin-resistantStaphylococcus aureusUSA300, identifying the polyamine analog OES2-0017. This inhibitor synergized with polyamines at the low micromolar range, inhibiting a polyamine detoxification spermine/spermidine acetyltransferase SSAT (SpeG) and another previously uncharacterizedS. aureusSSAT (denoted PaiASaherein). OES2-0017 showed growth-inhibitory effects at higher concentrations, perturbing the bacterial membrane with no detectable effects against eukaryotic membranes at the same concentration range. OES2-0017 showed similar broad-spectrum activities against various Gram-positive and Gram-negative pathogens. OES2-0017 abolished the polyamine-mediated resistance to antibiotics, including vancomycin, in MRSA USA300, phenocopying the ΔspeGmutant and suggesting its potential utility as an antibiotic adjuvant. OES2-0017 eradicated SpeG-expressingSalmonellaTyphimurium inside murine macrophages, suggesting its potential as an antivirulence agent. Small-scale structure-activity relationship, eukaryotic toxicity, and enzymatic inhibition against the human SSAT (SAT1) assays identified analogs with higher bacterial enzyme specificity and no toxicity at the antimicrobial range. Our screen also uncovered additional inhibitors, including the catechol derivative isoproterenol (OES1-1087), showing a similar mode of action and activity as OES2-0017 but with lower potency. This study provides novel antimicrobial compounds with broad-spectrum activity and a novel mode of action for multidrug-resistant priority pathogens.
Semi-automated monitoring of longitudinal microbial metabolic dynamics: A study case for lignin degradation
Authors: Guimarães Ferreira João Vítor , Arini Gabriel Santos , da Rosa-Garzon Nathalia Gonsales , Casanova Turatti Izabel Cristina , Borelli Tiago Cabral , Tsuji Henrique Marcel Yudi de Oliveira , Cabral Hamilton , da Silva Ricardo Roberto
Published: October 2024

This study introduces a low-cost, open-source, semi-automated bioreactor system, developed using Arduino and Raspberry Pi, for longitudinal microbial culture studies. The system protocol includes detailed instructions for custom-designed components, specifications for easily purchasable parts, and open-source code for a web-based control interface. It was validated for sterility and tested in a case study involving the cultivation ofPhanerochaete chrysosporiumandTrichoderma reeseito assess their metabolic dynamics, both in isolation and co-culture, for lignin degradation. Using mass spectrometry coupled with gas chromatography, several lignin degradation intermediates were annotated, including 4-hydroxybenzoic acid, vanillic acid, and ferulic acid, along with their temporal variation profiles over 25 days. The results highlighted potential synergy between the two fungal species in lignin breakdown, while also demonstrating the bioreactor’s flexibility and suitability for diverse biotechnological applications, particularly in the field of bio-degradation and waste valorization.
Morph-specific selection pressures drive phenotypic divergence in a color polymorphic bird
Authors: Passarotto Arianna , Lürig Moritz D. , Aaltonen Esa , Karell Patrik
Published: October 2024

There is a long tradition of using heritable color polymorphisms in natural populations to study selection, gene flow, and other evolutionary processes. However, we still have only limited knowledge on how continuous color variation within genetically discrete morphs affects selective dynamics, which narrows our understanding of how color polymorphisms persist. Our comprehensive analysis of 43 years of plumage color scores from a bi-morphic Finnish population of tawny owls (Strix aluco) reveals that intra-morph variation is substantial, but also unexpectedly dynamic. We show that both morphs recently diverged in their plumage coloration: while the brown morph is on a steady trajectory toward more intense plumage pigmentation, the gray morph has recently shifted toward lighter plumage, following a series of extreme winters. Evidence suggests that this divergence is driven by the brown morph’s higher reproductive success and greater plasticity in response to seasonality, while the gray morph, with its more genetically determined plumage color and limited standing variation, has a reduced capacity to respond to selection and track new phenotypic optima. Our study confirms the presence of substantial and dynamic phenotypic variation within genetically discrete color morphs, and demonstrates its relevance for the evolutionary potential of populations to respond to environmental change.
Packaged delivery of CRISPR-Cas9 ribonucleoproteins accelerates genome editing
Authors: Karp Hannah , Zoltek Madeline , Wasko Kevin , Vazquez Angel Luis , Brim Jinna , Ngo Wayne , Schepartz Alanna , Doudna Jennifer
Published: October 2024

Effective genome editing requires a sufficient dose of CRISPR-Cas9 ribonucleoproteins (RNPs) to enter the target cell while minimizing immune responses, off-target editing and cytotoxicity. Clinical use of Cas9 RNPs currently entails electroporation into cellsex vivo, but no systematic comparison of this method to packaged RNP delivery has been made. Here we compared two delivery strategies, electroporation and enveloped delivery vehicles (EDVs), to investigate the Cas9 dosage requirements for genome editing. Using fluorescence correlation spectroscopy (FCS), we determined that >1300 Cas9 RNPs per nucleus are typically required for productive genome editing. EDV-mediated editing was >30-fold more efficient than electroporation, and editing occurs at least two-fold faster for EDV delivery at comparable total Cas9 RNP doses. We hypothesize that differences in efficacy between these methods result in part from the increased duration of RNP nuclear residence resulting from EDV delivery. Our results directly compare RNP delivery strategies, showing that packaged delivery could dramatically reduce the amount of CRISPR-Cas9 RNPs required for experimental or clinical genome editing.

Graphical Abstract
Characterization of Newly Discovered Polyester Polyurethane-degradingMethylobacterium AquaticumStrain A1
Authors: Lee SeongHyeon , Jeong Haemin , Jung Injun , Choi Myounghyun , Kim Ah-Ram
Published: October 2024

In this study, we presentMethylobacterium aquaticumA1, a novel strain capable of degrading polyester polyurethane (PE-PUR). The attachment ofM. aquaticumA1 to PE-PUR and its degradation capabilities were verified using Scanning Electron Microscopy (SEM) and Fourier-Transform Infrared Spectroscopy (FT-IR). Analysis of the reference genome ofM. aquaticumrevealed genes encoding enzymes with potential PE-PUR degrading activity, including esterases, lipase, proteases and amidase such astesA,pgpB,aes,aprE,lon,degQ,andgatA. An esterase activity assay usingp-nitrophenyl acetate (p-NPA) showed increased ester bond-cleaving activity whenM. aquaticumA1 was exposed to polyurethane diol (PU-diol), suggesting inducible enzymatic activity involved in PE-PUR degradation. These findings highlight the potential ofM. aquaticumA1 as a promising biocatalyst for PE-PUR degradation.

IMPORTANCE

Microbial biodegradation is increasingly recognized as a sustainable approach to addressing microplastic pollution. This study introducesM. aquaticumA1, a newly isolated strain capable of adhering to and degrading polyester polyurethane (PE-PUR), one of the most widely utilized plastics. To our knowledge, this is the first report of PE-PUR degradation by a member of theMethylobacteriumgenus. This paper provides a detailed characterization ofM. aquaticumA1 and identifies several enzyme candidates—tesA,pgpB,aes,aprE,lon,degQ,andgatA—as potentially involved in the degradation process. Given thatMethylobacteriumspecies are known to be ecologically beneficial and inhabit diverse environments, the capacity ofM. aquaticumA1 to degrade PE-PUR presents a promising strategy for mitigating microplastic pollution across a range of ecosystems.
Revealing the range of maximum likelihood estimates in the admixture model
Authors: Heinzel Carola Sophia , Baumdicker Franz , Pfaffelhuber Peter
Published: October 2024

Many ancestry inference tools, including STRUCTURE and ADMIXTURE, rely on the admixture model to infer both, allele frequenciespand individual admixture proportionsqfor a collection of individuals relative to a set of hypothetical ancestral populations. We show that under realistic conditions the likelihood in the admixture model is typically flat in some direction around a maximum likelihood estimate (MLE). In particular, the maximum likelihood estimator is non-unique and there is a complete spectrum of possible estimates. Common inference tools typically identify only a few points within this spectrum.

We provide an algorithm which computes the set of equally likely, when starting from. It is analytic forK= 2 ancestral populations and numeric forK> 2. We apply our algorithm to data from the 1000 genomes project, and show that inter-European estimators ofqcan come with a large set of equally likely possibilities. In general, markers with large allele frequency differences between populations in combination with individuals with concentrated admixture proportions lead to small areas with a flat likelihood.

Our findings imply that care must be taken when interpreting results from STRUCTURE and ADMIXTURE if populations are not separated well enough.
Abandoning the Quadrupole for Mass Spectrometry Fragmentation Analysis: Towards 1,000 Hz Speeds with 100% Ion Utilization Using High Resolution Ion Mobility Precursor Isolation
Authors: DeBord Daniel , Rorrer Leonard C. , Deng Liulin , Strathmann Frederick G.
Published: October 2024

In today’s fast-evolving landscape of omics research, tandem mass spectrometry has become a cornerstone for uncovering the complexities of biological systems. Yet, despite its essential role, the technology remains bound by the inherent limitations of quadrupole filters, which throw away up to 99% of the useful ion signal and caps the speed at which fragmentation data can be generated. These deficiencies often force compromises in data depth and accuracy, hindering breakthroughs that tie genomics, proteomics, and metabolomics together. A new technology is poised to break through these performance barriers, unlocking unprecedented capabilities in precision, sensitivity and throughput. This step-change in how mass spectrometry fragmentation analysis is performed will reshape the future of scientific discovery, pushing the boundaries of what’s possible. The solution is high resolution ion mobility (HRIM), which offers a means to quickly and efficiently isolate ions prior to fragmentation and detection by a high resolution mass spectrometer (HRMS) while also resolving challenging isomeric and isobaric compounds that lead to chimeric MS/MS spectra. HRIM isolates ions in time as a result of a high speed separation rather than acting as a filter that discards ion signal like the pervasive quadrupole mass analyzer, allowing higher sensitivity analysis to be achieved. Also, since HRIM eliminates the need to hop or sweep electronics control parameters, as is the case with a quadrupole, fragmentation spectral generation can occur at a much faster rate, upwards of 500 Hz. This whitepaper describes an IM/MS methodology first contemplated over twenty years ago and today being positioned as the fastest method for high resolution fragmentation analysis. Revisiting this concept using the latest generation ion mobility technology based on structures for lossless ion manipulation (SLIM), which is the only HRIM technology that delivers similar resolution and range of analysis as a quadrupole, realizes the full potential of this approach to deliver benefits in both speed and sensitivity for high performance MS/MS measurements. This new way of achieving ion fragmentation in complex samples is set to revolutionize the mass spectrometry space, starting in the growing field of proteomics where all researchers are seeking faster methods to achieve more comprehensive proteomic coverage. Due to the advantages of HRIM physics, we predict this will set the bar for high throughput -omics within the coming years and will eventually be as ubiquitous as the quadrupole is today.
High Prevalence of Latent Tuberculosis Infection among Persons Deprived of Liberty in a Malaysian Prison
Authors: Zhang Lu , Saifi Rumana , Kamarulzaman Adeeba , Ahmad Ahsan , Dhaliwal Sangeeth , Mohd Yukhi Saidatul Hanida , Ibrahim Nor Akma , Koh Hui Moon , Altice Frederick L. , Shenoi Sheela V.
Published: October 2024

Rising tuberculosis incidence and mortality necessitate enhanced attention to prevention in neglected high-risk venues like correctional facilities. We sought to identify prevalence and correlates of latent TB infection (LTBI) in Malaysia’s largest prison. From October 2019 to January 2023, people deprived of liberty (PDL) entering Kajang Prison underwent tuberculin skin testing, sputum examination, chest X-ray, and blood tests for HIV, HCV, and C-reactive protein (CRP); PDL with active tuberculosis were excluded. Multivariable logistic regression identified independent correlates of LTBI. Among 601 men without tuberculosis, median age was 42 (IQR 36-50) years with high prevalences of HIV (8.8%) and HCV (43.4%). LTBI prevalence was 68.2% (95%CI[64.4%-71.8%]); independent risk factors included opioid use disorder (OUD, AOR=1.95; 95%CI[1.25-3.05]), pre-incarceration homelessness (AOR=1.89; 95%CI[1.13-2.50]), and HCV (AOR=1.68; 95%CI[1.13-2.50]). Pre-incarceration cannabis use (AOR=0.69; 95%CI[0.39-0.96]) was negatively associated with LTBI, which was also found in people with HIV (AOR=0.10; 95%CI[0.01-0.51]). Among people without HIV, having OUD (AOR=2.32; 95%CI[1.48-3.68]), HCV (AOR=1.64; 95%CI[1.09-2.48]) and CRP ≥5mg/ml (AOR=1.90; 95%CI[1.04-3.65]) were independently associated with LTBI, while methamphetamine use reduced odds of LTBI (AOR=0.58; 95%CI[0.33-0.98]). LTBI prevalence in Malaysia’s largest prison was high, highlighting the need for routine screening and implementation of TB preventive therapy in high-risk settings like prisons.
Enrichment of spermatogonial stem cells and staging of the testis cycle in a dasyurid marsupial, the fat-tailed dunnart
Authors: Tarulli Gerard A. , Tatt Patrick R.S. , Howlett Rhys , Ord Sara , Shapiro Beth , Frankenberg Stephen R. , Pask Andrew J.
Published: October 2024

There is increasing interest in use of marsupial models in research, for use in next-generation conservation by improving fitness through genetic modification, and in de-extinction efforts. Specifically this includes dasyurid marsupials such as the Thylacine, Tasmanian devil, quolls and the small rodent-like dunnarts. Technologies for generating genetically modified Australian marsupials remains to be established. Given the need to advance research in this space, the fat-tailed dunnart (Sminthopsis crassicaudata) is being established as a model for marsupial spermatogonial stem cell isolation, modification and testicular transplantation. This species is small (60-90mm body size), polyovulatory (8-12 pups per birth), and can breed in standard rodent facilities when housed in a 12:12 light cycle. To develop the fat tailed dunnart as a model for next-generation marsupial conservation, this study aimed to enrich dunnart spermatogonial stem cells from whole testis digestions using a fluorescent dye technology and fluorescence-activated cell sorting. This approach is not dependent on antibodies or genetic reporter animals that are limiting factors when performing cell sorting on species separated from human and mouse by large evolutionary timescales. This study also assessed development of spermatogonia and spermatogenesis in the fat-tailed dunnart, by making the first definition of the cycle of the seminiferous epithelium in any dasyurid. Overall, this is the first detailed study to assess the cycle of dasyurid spermatogenesis and provides a valuable method to enrich marsupial spermatogonial stem cells for cellular, functional and molecular analysis.
Dynamic Insights into Hsp90 Inhibitor Binding: Uncovering Intermediate States and Conformational Plasticity
Authors: Sahil Mohammad , Koneru Jaya Krishna , Mondal Jagannath
Published: October 2024

Heat shock protein 90 (Hsp90) is a vital molecular chaperone involved in protein folding, stabilization, and activation, making it a key target in cancer therapy. Tar-geting the N-terminal domain of Hsp90 (N-Hsp90) has emerged as a potential strategy for developing anticancer therapies due to its involvement in the folding and function of oncoproteins. However, the precise molecular details of how inhibitors bind to N-Hsp90 remain elusive due to inherent conformational plasticity involvingloop-inandloop-outstates of loop-4 (L4). In this work, we utilized unbiased molecular dynamics (MD) simulations coupled with Markov state modeling (MSM) and machine learning techniques to investigate the binding dynamics of the inhibitor Geldanamycin (GDM). Our findings reveal a complex two-stage binding mechanism involving the formation of a non-native intermediate state prior to the final bound state. We demonstrate that GDM binding predominantly stabilizes theloop-outconformation of N-Hsp90, chal-lenging prior beliefs and suggesting thatbothconformational selection and induced fit mechanisms are involved. Through a detailed residue-level analysis using Random For-est based ML classifiers, we quantify the relative contributions of these mechanisms, highlighting the dynamic interplay between Hsp90’s conformational states during in-hibitor binding. These findings enhance our understanding of Hsp90’s conformational plasticity and could inform the design of more effective Hsp90 inhibitors.