bluuebunny/crossref_metadata_2025 huggingface dataset:
Assessing the New Norm
Authors: Mehmood Noormah , Nesiama Jo-Ann O. , Yen Kenneth , Dhar Archana , Lowe Geoffrey S.
Published: May 2023

Introduction

Physicians caring for patients with COVID-19 are at high risk for contracting the disease, thus, significant emphasis has been placed on personal protective equipment (PPE). The study aims to assess the impact of advanced PPE across 4 common procedures: endotracheal intubation, bag-valve mask ventilation, intraosseous (IO) insertion, and lumbar puncture (LP) performed by pediatric emergency physicians.

Method

Physicians performed the procedures in a simulated environment. Lumbar puncture and IO were performed with standard precautions versus an air purifying respirator (APR). A direct comparison was drawn for endotracheal intubation and bag-valve mask ventilation between 2 commonly used APRs. Success rate and number of attempts toward successful completion was recorded for all 4 procedures. Physicians filled out a postprocedure survey to assess their ease of use of the APR.

Results

Twenty participants performed IO and LP using an APR and standard precautions. There was no statistical difference in the success rate, number of attempts, average time, or maintenance of sterility (LP only) for both procedures. Twenty total participants divided across 2 types of APR groups performed intubation and BMV. Success rate and number of attempts had no statistical difference for both procedures. Physician feedback surveys to assess the ease of use of APR compared with standard precautions had no statistically significant difference for all 4 procedures.

Conclusions

Wearing increased levels of PPE did not impact procedural success, length of time, sterility, number of attempts, or the physicians' ease in our study. Physicians should be encouraged to wear all appropriate PPE.
How Subjective and Objective Factors in Research and Practice May Perpetuate Health Disparities amongst Patients with Traumatic Brain Injury
Authors: Johnson Karen T. , You HyunBin , Kandel Melissa , Oyesanya Tolu O.
Published: May 2023

Research shows disparities exist in traumatic brain injury (TBI)-related outcomes and are associated with objective and subjective factors. We define objective factors (e.g., age, sex, race/ethnicity, health insurance status, and socioeconomic status) as variables that are frequently measured, not easily modifiable, and not easily influenced by individual perceptions, opinions, or experiences. Conversely, we define subjective factors (e.g., personal health literacy, cultural competence, patient/family-clinician communication, implicit bias, and trust) as variables that may be less frequently measured, more easily modifiable, and more easily influenced by individual perceptions, opinions, or experiences. The purpose of this analysis and perspective is to provide recommendations for further examination of subjective factors within TBI research and practice, with the overarching goal of reducing TBI-related disparities. We recommend establishing reliable and valid measures of subjective factors to allow for further examination of the influence of both objective factors and subjective factors in the TBI population. Providers and researchers must also engage in education and training to recognize their biases and how bias influences decision-making. The influence of subjective factors in practice and research must also be considered to ensure we generate knowledge needed to advance health equity and reduce disparities in outcomes for patients with TBI.
Effect of exercise therapy on cancer-related fatigue in patients with breast cancer: A systematic review and network meta-analysis
Authors: Wu Tong , Yan Fanghong , Wei Yuanyuan , Yuan Chenlu , Jiao Yanxia , Pan Yayan , Zhang Yilin , Zhang Hongyan , Ma Yuxia , Han Lin
Published: May 2023

Objective

This study aimed to explore the efficacy of different exercise therapies in reducing fatigue in patients with breast cancer.

Design

PubMed, Embase, Web of Science, Cochrane Library, CINAHL, CBM, CNKI, VIP, and Wanfang databases were searched from their inception to March 2022. The authors independently screened all randomized controlled trials (RCTs) of exercise therapy in patients with breast cancer. A network meta-analysis was performed using Stata 16.0 software.

Results

Seventy-eight studies were analyzed, with 167 comparisons and 6235 patients. The network results showed that stretching (SMD = -0.74, CI: -1.43, -0.06), yoga (SMD = -0.49, CI: -0.75, -0.22), combined exercise (SMD = -0.47, CI: -0.70, -0.24), aerobic exercise (SMD = -0.46, CI: -0.66, -0.26), and resistance exercise (SMD = -0.42, CI: -0.77, -0.08) significantly reduced fatigue. Pairwise comparisons confirmed that yoga, combined exercise, aerobic exercise, and resistance exercise were positively associated with fatigue relief. However, no significant association was identified between reduced fatigue and traditional Chinese exercises or stretching.

Conclusion

The most effective exercise therapy to relieve cancer-related fatigue in patients with breast cancer was yoga, followed by combined aerobic and resistance exercises. It is expected that more RCTs will be conducted to further explore the efficacy and mechanisms of exercise.
EFFECTS OF AEROBIC AND RESISTIVE EXERCISE ON MUSCLE MEASUREMENTS AND BODY COMPOSITION IN FEMALE PATIENTS WITH RHEUMATOID ARTHRITIS
Authors: Ayyildiz Aylin , Yilmaz Figen , Altindaş Havva , Çiftci Selda , Kuran Banu
Published: May 2023

Objective

This study aimed to show the effects of different exercise types on disease activity, pain, functional status, and quality of life in female patients with rheumatoid arthritis with low disease activity or in remission and supported these findings with body composition and muscle measurements.

Design

This randomized controlled prospective study screened female patients aged 20-50-year-old with rheumatoid arthritis. The patients were randomized into 12-week resistance exercise, aerobic exercise, and control groups.

Results

The mean age of the 66 patients was 42.5 ± 5.6 years. In the resistance and aerobic exercise groups compared to the control group, a positive significant difference was found in the pain, disease activity, several sub-parameters of quality of life,M.GastrocnemiusandM.Biceps Femorismuscle thickness measurements, and fat mass in the lower extremities before and after treatment(p < 0.05). Compared to the other groups, the resistance exercise group showed a significant improvement inM.Rectus FemorisandM.Vastus Intermediusmuscle thickness measurements, whole body fat mass, whole body and lower extremity lean body mass, and timed up-and-go test when comparing before and after treatment(p < 0.05).

Conclusion

In rheumatoid arthritis patients, resistance exercises led to a significant increase in muscle thickness, functional status, lean body mass compared to other exercises; resistance exercises also resulted in a significant reduction in pain and disease activity.
Performing Quality Control on Magnetic Resonance Imaging Liver Fat/Iron Quantification Studies: A Critical Requirement
Authors: Hajibonabi Farid , Sharma Puneet , Davarpanah Amir H. , Balthazar Patricia , Moreno Courtney C. , Pectasides Melina , Nandwana Sadhna B.
Published: May 2023

Objective

Nonalcoholic fatty liver and iron overload can lead to cirrhosis requiring early detection. Magnetic resonance (MR) imaging utilizing chemical shift–encoded sequences and multi-Time of Echo single-voxel spectroscopy (SVS) are frequently used for assessment. The purpose of this study was to assess various quality factors of technical acceptability and any deficiencies in technologist performance in these fat/iron MR quantification studies.

Methods

Institutional review board waived retrospective quality improvement review of 87 fat/iron MR studies performed over a 6-month period was evaluated. Technical acceptability/unacceptability for chemical shift–encoded sequences (q-Dixon and IDEAL-IQ) included data handling errors (missing maps), liver field coverage, fat/water swap, motion, or other artifacts. Similarly, data handling (missing table/spectroscopy), curve-fit, fat- and water-peak separation, and water-peak sharpness were evaluated for SVS technical acceptability.

Results

Data handling errors were found in 11% (10/87) of studies with missing maps or entire sequence (SVS or q-Dixon). Twenty-seven percent (23/86) of the q-Dixon/IDEAL-IQ were technically unacceptable (incomplete liver-field [39%], other artifacts [35%], significant/severe motion [18%], global fat/water swap [4%], and multiple reasons [4%]). Twenty-eight percent (21/75) of SVS sequences were unacceptable (water-peak broadness [67%], poor curve-fit [19%] overlapping fat and water peaks [5%], and multiple reasons [9%]).

Conclusions

A high rate of preventable errors in fat/iron MR quantification studies indicates the need for routine quality control and evaluation of technologist performance and technical deficiencies that may exist within a radiology practice. Potential solutions such as instituting a checklist for technologists during each acquisition procedure and routine auditing may be required.
Predicting Breast Cancer Subtypes Using Magnetic Resonance Imaging Based Radiomics With Automatic Segmentation
Authors: Yue Wen-Yi , Zhang Hong-Tao , Gao Shen , Li Guang , Sun Ze-Yu , Tang Zhe , Cai Jian-Ming , Tian Ning , Zhou Juan , Dong Jing-Hui , Liu Yuan , Bai Xu , Sheng Fu-Geng
Published: May 2023

Objective

The aim of the study is to demonstrate whether radiomics based on an automatic segmentation method is feasible for predicting molecular subtypes.

Methods

This retrospective study included 516 patients with confirmed breast cancer. An automatic segmentation—3-dimensional UNet-based Convolutional Neural Networks, trained on our in-house data set—was applied to segment the regions of interest. A set of 1316 radiomics features per region of interest was extracted. Eighteen cross-combination radiomics methods—with 6 feature selection methods and 3 classifiers—were used for model selection. Model classification performance was assessed using the area under the receiver operating characteristic curve (AUC), accuracy, sensitivity, and specificity.

Results

The average dice similarity coefficient value of the automatic segmentation was 0.89. The radiomics models were predictive of 4 molecular subtypes with the best average: AUC = 0.8623, accuracy = 0.6596, sensitivity = 0.6383, and specificity = 0.8775. For luminal versus nonluminal subtypes, AUC = 0.8788 (95% confidence interval [CI], 0.8505–0.9071), accuracy = 0.7756, sensitivity = 0.7973, and specificity = 0.7466. For human epidermal growth factor receptor 2 (HER2)–enriched versus non-HER2–enriched subtypes, AUC = 0.8676 (95% CI, 0.8370–0.8982), accuracy = 0.7737, sensitivity = 0.8859, and specificity = 0.7283. For triple-negative breast cancer versus non–triple-negative breast cancer subtypes, AUC = 0.9335 (95% CI, 0.9027–0.9643), accuracy = 0.9110, sensitivity = 0.4444, and specificity = 0.9865.

Conclusions

Radiomics based on automatic segmentation of magnetic resonance imaging can predict breast cancer of 4 molecular subtypes noninvasively and is potentially applicable in large samples.
Quantitative Assessment of Lipiodol-Related Artifact Reduction for Dual-Energy Computed Tomography After Transcatheter Arterial Chemoembolization: A Phantom Study Evaluating the Use of Metal Artifact Reduction Algorithms
Authors: Ting Yun-Lung , Lin Hsiang-Yi , Huang Tzu-Ting , Hwang Yi-Shuan , Chui Chen-Shou , Li Mei-Rung , Wu Tung-Hsin
Published: May 2023

Objective

This study used metal artifact reduction (MAR) software to examine the computed tomography (CT) number of dual-energy CT (DECT) of hepatocellular carcinoma after transcatheter arterial chemoembolization.

Methods

Hollow columnar acrylic phantoms were filled with lipiodol and inserts of 2 sizes (large and small) were used to simulate liver tumors on a Revolution GSI CT scanner. The CT numbers of a single test object were collected twice: once with and once without the MAR algorithm. Lipiodol beam-hardening artifacts were quantified by measuring CT numbers in a region of interest around the tumor-simulating insert.

Results

The virtual monochromatic CT numbers of large and small tumors were closely related to energy. For small tumors, CT numbers increased with energy. For large tumors, CT numbers increased with energy at 1 cm from the margin but decreased with an increase in energy at 5 cm. Regardless of the size, distance, or location of the tumor, the CT numbers fluctuated more at low energy levels.

Conclusions

At 1 cm from the margin, the CT numbers with MAR were significantly different from those without MAR. Low-energy CT numbers with MAR were near reference values. Metal artifact reduction exhibited superior performance for small tumors. Tumor margin images are affected by artifacts caused by Lipiodol. However, with MAR, CT numbers can be effectively calibrated, thus enabling clinicians to more accurately evaluate hepatocellular carcinoma development and identify residual tumors and recurrent or metastatic lesions.
Implementation of a Multispecialty Geriatric Surgery Pathway Reduces Inpatient Cost for Frail Patients
Authors: Ehrlich April L. , Owodunni Oluwafemi P. , Mostales Joshua C. , Efron Jonthan , Hundt John , Magnuson Tom , Gearhart Susan L.
Published: May 2023

Objective:

The objective of this study was to evaluate the effect of geriatric surgical pathway (GSP) implementation on inpatient cost of care.

Background:

Achieving high-value care for older patients is the goal of the American College of Surgeons Geriatric Verification Program (ACS-GSV). We have previously shown that implementation of our geriatric surgery pathway, which aligns with the ACS-GSV standards, resulted in a reduction in loss of independence and complications.

Methods:

Patients ≥65 years who underwent an inpatient elective surgical procedure included in the American College of Surgeons National Quality Improvement Program (ACS NSQIP) registry from July 2016 through December 2017 were compared with those patients from February 2018 to December 2019 who were cared for on our GSP. An amalgamation of Clinformatics DataMart, the electronic health record, and the ACS NSQIP registry produced the analytical dataset. We compared mean total and direct costs of care for the entire cohort as well as through propensity matching of frail surgical patients to account for differences in clinical characteristics.

Results:

The total mean cost of health care services during hospitalization was significantly lower in the cohort on our GSP ($23,361±$1110) as compared with the precohort ($25,452±$1723), P<0.001. On propensity-matched analysis, cost savings was more evident in our frail geriatric surgery patients.

Conclusions:

This study shows that high-value care can be achieved with the implementation of a GSP that aligns with the ACS-GSV program.
Microbial Contamination During Long-term Ex Vivo Normothermic Machine Perfusion of Human Livers
Authors: Lau Ngee-Soon , Ly Mark , Dennis Claude , Toomath Shamus , Huang Joanna Lou , Huang Joanna , Ly Hayden , Chanda Sumon , Marinelli Tina , Davis Rebecca , Liu Ken , McCaughan Geoff , Crawford Michael , Pulitano Carlo
Published: May 2023

Background.

Normothermic machine perfusion permits the ex vivo preservation of human livers before transplantation. Long-term perfusion for days-to-weeks provides the opportunity for enhanced pretransplant assessment and potential regeneration of organs. However, this risks microbial contamination and infection of the recipient if the organ is transplanted. An understanding of perfusate microbial contamination is required to inform infection control procedures and antimicrobial prophylaxis for this technology.

Methods.

We modified a liver perfusion machine for long-term use by adding long-term oxygenators and a dialysis filter. Human livers that were not suitable for transplantation were perfused using a red-cell-based perfusate under aseptic and normothermic conditions (36 °C) with a goal of 14 d. Cephazolin was added to the perfusate for antimicrobial prophylaxis. Perfusate and bile were sampled every 72 h for microbial culture.

Results.

Eighteen partial human livers (9 left lateral segment grafts and 9 extended right grafts) were perfused using our perfusion system. The median survival was 7.2 d. All organs surviving longer than 7 d (9/18) had negative perfusate cultures at 24 and 48 h. Half of the grafts (9/18) became culture-positive by the end of perfusion. Microbial contaminants included Gram-negative (Pseudomonas species, Proteus mirabilis, Stenotrophomonas maltophilia) and Gram-positive bacteria (Staphylococcus epidermidis, Enterococcus faecalis, and Bacillus species) as well as yeast (Candida albicans).

Conclusions.

Microbial contamination of perfusate is common during long-term perfusion of human livers with both exogenous and endogenous sources. Enhanced infection control practices and review of targeted antimicrobial prophylaxis are likely to be necessary for translation into the clinical arena.
Genomic variation during culture adaptation of genetically complex Plasmodium falciparum clinical isolates
Authors: Claessens Antoine , Stewart Lindsay B. , Drury Eleanor , Ahouidi Ambroise D. , Amambua-Ngwa Alfred , Diakite Mahamadou , Kwiatkowski Dominic P. , Awandare Gordon A. , Conway David J.
Published: May 2023

Experimental studies on the biology of malaria parasites have mostly been based on laboratory-adapted lines, but there is limited understanding of how these may differ from parasites in natural infections. Loss-of-function mutants have previously been shown to emerge during culture of some Plasmodium falciparum clinical isolates in analyses focusing on single-genotype infections. The present study included a broader array of isolates, mostly representing multiple-genotype infections, which are more typical in areas where malaria is highly endemic. Genome sequence data from multiple time points over several months of culture adaptation of 28 West African isolates were analysed, including previously available sequences along with new genome sequences from additional isolates and time points. Some genetically complex isolates eventually became fixed over time to single surviving genotypes in culture, whereas others retained diversity, although proportions of genotypes varied over time. Drug resistance allele frequencies did not show overall directional changes, suggesting that resistance-associated costs are not the main causes of fitness differences among parasites in culture. Loss-of-function mutants emerged during culture in several of the multiple-genotype isolates, affecting genes (including AP2-HS, EPAC and SRPK1) for which loss-of-function mutants were previously seen to emerge in single-genotype isolates. Parasite clones were derived by limiting dilution from six of the isolates, and sequencing identified de novo variants not detected in the bulk isolate sequences. Interestingly, several of these were nonsense mutants and frameshifts disrupting the coding sequence of EPAC, the gene with the largest number of independent nonsense mutants previously identified in laboratory-adapted lines. Analysis of genomic identity by descent to explore relatedness among clones revealed co-occurring non-identical sibling parasites, illustrative of the natural genetic structure within endemic populations.
Online Personal Training in Patients with Marfan Syndrome: A Randomized Controlled Study of its Impact on Quality of Life and Physical Capacity
Authors: Jouini Steeve , Milleron Olivier , Eliahou Ludivine , Jondeau Guillaume , Vitiello Damien
Published: May 2023

Background

Marfan syndrome (MFS) is a rare genetic disorder affecting the vascular and musculoskeletal systems. Exercise is classically contraindicated and there are no data on the limitations associated with the syndrome and the benefits of training in this population. This study aimed to characterise the quality of life (QoL) and physical capacity of patients with MFS and to evaluate the benefits of a 3-month online personal training program.

Methods

MFS patients were compared with healthy subjects (H-S) at baseline. They were then randomized 1:1 into a training group (MFS-T) and a control group (MFS-C). The training consisted of 2 supervised online training sessions per week at home for 3 months, and the session program was selected based on the initial assessment. The main outcome measure was QoL as assessed by the MOS SF-36. The evolution of parameters during training was compared between MFS-T and MFS-C.

Results

At baseline, QoL in all dimensions was lower in MFS. Peak oxygen uptake (VDO2peak) was also 25% lower, as was muscle elasticity. Training significantly improved 1) QoL (+20.2±14.3 MFS-Tvs.0.7±0.5 MFS-C), 2) VDO2peak (+34% MFS-Tvs.14% MFS-C), 3) muscle elasticity index (11.5±8.2 MFS-Tvs.+1.2±1. 7 MFS-C), reduced blood pressures during isometric squat (systolic −19±30 MFS-Tvs.0±6 MFS-C; diastolic −27±39 MFS-Tvs.+2±15 MFS-C), reduced pulse wave velocity (PWV) at rest (-1.20±1.89 MFS-Tvs.−0.40±1.61 MFS-C) and after peak exercise (-0.42±0.45 MFS-Tvs.0.08±0.48 MFS-C). Aorta diameter remained stable in both groups (MFS-T −0.19±1.1vs.0.11±0.78 MFS-C). After training, QoL remained lower in MFS-T than in H-S, but peak VDO2, PWV at rest and after exercise were similar to those of H-S.

Conclusions

A 3-month online training program had a beneficial effect on QoL, cardiovascular and muscular parameters in MFS without affecting aortic root diameter.
Molecular Determinants of Calcitriol Signaling and Sensitivity in Glioma Stem-like Cells
Authors: Rehbein Sarah , Possmayer Anna-Lena , Bozkurt Süleyman , Lotsch Catharina , Gerstmeier Julia , Burger Michael , Momma Stefan , Maletzki Claudia , Classen Carl-Friedrich , Freiman Thomas M. , Dubinski Daniel , Lamszus Katrin , Day Bryan W. , Stringer Brett W. , Herold-Mende Christel , Münch Christian , Kögel Donat , Linder Benedikt
Published: May 2023

Glioblastoma is the most common primary brain cancer in adults and represents one of the worst cancer diagnosis for the patients. Suffering from a poor prognosis and limited treatment options, tumor recurrences are virtually inevitable. Additionally, treatment resistance is very common for this disease and worsens the prognosis. These and others factors are hypothesized to be largely due to the fact that glioblastoma cells are known to be able to obtain stem-like traits and thereby driving these phenotypes. Recently, we could show that the in vitro and ex vivo treatment of glioblastoma stem-like cells with the hormonally active form of Vitamin D3, Calcitriol (1α,25(OH)2-vitamin D3) can block stemness in a subset of cell lines and reduce tumor growth. Here, we expanded our cell panel to over 40 different cultures and can show that, while half of the tested cell lines are sensitive, a quarter can be classified as high-responders. Using genetic and proteomic analysis, we further determined that treatment success can be partially explained by specific polymorphism of the Vitamin D3 receptor and that high-responders display a proteome suggestive of blockade of stemness, as well as migratory potential.
Acidification-dependent suppression ofC. difficileby enterococci in vitro
Authors: Smith Holly R. , Wood Alicia K. , Johnson Angus , Stern Avi Z. , Sikander Zainab , Gutierrez Lesly-Hannah , Agosto Addelis A. , McKenney Peter T.
Published: May 2023

Clostridioides difficileand Vancomycin-resistantEnterococcus faecium(VRE) are commonly co-isolated from hospitalized patients. We sought to developin vitroco-culture systems to identify interactions and study biofilm formation by these two opportunistic pathogens. We found that VRE quickly acidifies media containing glucose, fructose and trehalose to a pH that is not compatible with growth ofC. difficile. Acidification was necessary and sufficient for VRE-mediated suppression ofC. difficileand this mechanism is conserved among a panel of enterococci andClostridia. Robust co-culture conditions and biofilm formation were achieved by managing the available carbon source.

Importance

The steady state pH of the colon in humans and mice is below the growth limiting pH forC. difficilefound in this study and others. Following treatment with antibiotics, pH of the colon rises to neutral or slightly alkaline, which correlates with the loss of colonization resistance toC. difficile. These data suggest that manipulation of pH by managing the available carbon source may affect colonization by pathogenic and commensalClostridioides.
SPHINGOLIPIDS AND Δ8-SPHINGOLIPID DESATURASE FROM THE PICOALGAOSTREOCOCCUS TAURIAND INVOLVEMENT IN TEMPERATURE ACCLIMATION
Authors: Ishikawa Toshiki , Domergue Frédéric , Amato Alberto , Corellou Florence
Published: May 2023

Sphingolipids are crucial components of cell membranes. Sphingolipid Δ8-unsaturation is more specific to plants and is involved in the regulation of stress responses. The structure and functions of sphingolipids in microalgae are still poorly understood.Ostreococus tauriis a minimal microalga at the base of the green lineage, and is therefore a key organism for understanding lipid evolution. The present work reports the characterisation as well as the temperature regulation of sphingolipids and Δ8-sphingolipid desaturase fromO. tauri. Complex sphingolipids are glycosylceramides with unique glycosyl moieties encompassing hexuronic acid residues, reminiscent of bacterial glucuronosylceramides, with up to three additional hexose residues. In contrast, the ceramide backbones show limited variety, with dihydroxylated C18/C18:1EΔ8sphingoid bases and C16:0 fatty-acyl chain being the main compounds.

The sphingolipid Δ8-desaturase fromO. tauri, although phylogenetically related to plant homologues has a substrate preference similar to the diatom homologue. Both sphingolipid Δ8-desaturase transcripts and sphingolipid Δ8-unsaturation are regulated in a temperature- dependent manner being higher at 14°C than 24°C. Overexpressing the sphingolipid Δ8- desaturase inO. tauriat 24°C results in higher sphingolipid unsaturation and impairs the increase in cell size, structure and chlorophyll. In particular, the cell-size defect is not detected in cells acclimated to 14°C and is furthermore suppressed upon transfer from 24°C to 14°C. Our work provides the first functional evidence for the involvement of sphingolipid Δ8-unsaturation for temperature acclimation in microalgae, suggesting that this function is an ancestral feature in the green lineage.
The 3’ UTR ofvigRis required for virulence inStaphylococcus aureusand has expanded through STAR sequence repeat insertions
Authors: Mediati Daniel G. , Dan William , Lalaouna David , Dinh Hue , Pokhrel Alaska , Stinear Timothy P. , Cain Amy K. , Tree Jai J.
Published: May 2023

Staphylococcus aureusis an adaptable human pathogen causing life-threatening endocarditis and bacteraemia. Methicillin-resistantS. aureus(MRSA) is alarmingly common, and treatment is confined to last-line antibiotics. Vancomycin is the treatment of choice for MRSA bacteraemia and vancomycin treatment failure is often associated with vancomycin-intermediateS. aureusstrains termed VISA. The regulatory 3’ UTR ofvigRmRNA contributes to vancomycin tolerance in the clinical VISA isolate JKD6008 and upregulates the lytic transglycosylase IsaA. Using MS2-affinity purification coupled with RNA sequencing (MAPS), we find that thevigR3’ UTR also interacts with mRNAs involved in carbon metabolism, amino acid biogenesis, cell wall biogenesis, and virulence. ThevigR3’ UTR was found to repressdapE, a succinyl-diaminopimelate desuccinylase required for lysine and cell wall peptidoglycan synthesis, suggesting a broader role in controlling cell wall metabolism and vancomycin tolerance. Deletion of thevigR3’ UTR increased VISA virulence in a wax moth larvae model, and we find that anisaAmutant is completely attenuated in the larvae model. Sequence and structural analysis of thevigR3’ UTR indicates that the UTR has expanded through the acquisition ofStaphylococcus aureusrepeat insertions (STAR repeats) that partly contribute sequence for theisaAinteraction seed and may functionalise the 3’ UTR. Our findings reveal an extended regulatory network forvigR, uncovering a novel mechanism of regulation of cell wall metabolism and virulence in a clinicalS. aureusisolate.
Microsecond dynamics control the HIV-1 envelope conformation
Authors: Bennett Ashley L. , Edwards R.J. , Kosheleva Irina , Saunders Carrie , Bililign Yishak , Williams Ashliegh , Manosouri Katayoun , Saunders Kevin O. , Haynes Barton F. , Acharya Priyamvada , Henderson Rory
Published: May 2023

The HIV-1 Envelope (Env) glycoprotein facilitates host cell fusion through a complex series of receptor-induced structural changes. Although significant progress has been made in understanding the structures of various Env conformations and transition intermediates that occur within the millisecond timescale, faster transitions in the microsecond timescale have not yet been observed. In this study, we employed time-resolved, temperature-jump small angle X- ray scattering to monitor structural rearrangements in an HIV-1 Env ectodomain construct with microsecond precision. We detected a transition correlated with Env opening that occurs in the hundreds of microseconds range and another more rapid transition that preceded this opening. Model fitting indicated that the early rapid transition involved an order-to-disorder transition in the trimer apex loop contacts, suggesting that conventional conformation-locking design strategies that target the allosteric machinery may be ineffective in preventing this movement. Utilizing this information, we engineered an envelope that locks the apex loop contacts to the adjacent protomer. This modification resulted in significant angle-of-approach shifts in the interaction of a neutralizing antibody. Our findings imply that blocking the intermediate state could be crucial for inducing antibodies with the appropriate bound state orientation through vaccination.
NAC61 regulates late-and post-ripening associated processes in grapes involving a NAC60-dependent regulatory network
Authors: Foresti Chiara , Orduña Luis , Matus José Tomás , Vandelle Elodie , Danzi Davide , Bellon Oscar , Tornielli Giovanni Battista , Amato Alessandra , Zenoni Sara
Published: May 2023

During late-and post-ripening stages, grape berry undergoes profound biochemical and physiological changes whose molecular control is poorly understood. Here, we report the role of NAC61, a grapevine NAC transcription factor, in regulating different processes featuring the berry ripening progression.

NAC61 is highly expressed during post-harvest berry dehydration and its expression pattern is closely related to sugar concentration. The ectopic expression ofNAC61inNicotiana benthamianaleaves determines low stomatal conductance, high leaf temperature, tissue collapse and a higher relative water content. Transcriptome analysis of grapevine leaves transiently overexpressingNAC61,and DNA affinity purification and sequencing analyses allowed us to narrow down a list of NAC61-regulated genes. Direct regulation of the stilbene synthase regulatorMYB14, the osmotic stress-related geneDHN1b, theBotrytis cinereasusceptibility geneWRKY52and theNAC61itself, is validated. We also demonstrate that NAC61 interacts with NAC60, a proposed master regulator of grapevine organ maturation, in the activation ofMYB14andNAC61expression. Overall, our findings establish NAC61 as a key player in a regulative network that governs stilbenoid metabolism and osmotic, oxidative and biotic stress responses in grape berry during late-and post-ripening.

Highlights

NAC61 regulates stilbene biosynthesis and abiotic/biotic stress responses that hallmark late-and post-ripening developmental stages in grapevine berry. NAC61 participates in a NAC60-dependent regulatory network, also triggering its self-activation.
Leveraging longitudinal diffusion MRI data to quantify differences in white matter microstructural decline in normal and abnormal aging
Authors: Archer Derek B. , Schilling Kurt , Shashikumar Niranjana , Jasodanand Varuna , Moore Elizabeth E. , Pechman Kimberly R. , Bilgel Murat , Beason-Held Lori L. , An Yang , Shafer Andrea , Ferrucci Luigi , Risacher Shannon L. , Gifford Katherine A. , Landman Bennett A. , Jefferson Angela L. , Saykin Andrew J. , Resnick Susan M. , Hohman Timothy J. ,   Alzheimer’s Disease Neuroimaging Initiative
Published: May 2023

Abstract

INTRODUCTION

It is unclear how rates of white matter microstructural decline differ between normal aging and abnormal aging.

METHODS

Diffusion MRI data from several well-established longitudinal cohorts of aging [Alzheimer’s Neuroimaging Initiative (ADNI), Baltimore Longitudinal Study of Aging (BLSA), Vanderbilt Memory & Aging Project (VMAP)] was free-water corrected and harmonized. This dataset included 1,723 participants (age at baseline: 72.8±8.87 years, 49.5% male) and 4,605 imaging sessions (follow-up time: 2.97±2.09 years, follow-up range: 1–13 years, mean number of visits: 4.42±1.98). Differences in white matter microstructural decline in normal and abnormal agers was assessed.

RESULTS

While we found global decline in white matter in normal/abnormal aging, we found that several white matter tracts (e.g., cingulum bundle) were vulnerable to abnormal aging.

CONCLUSIONS

There is a prevalent role of white matter microstructural decline in aging, and future large-scale studies in this area may further refine our understanding of the underlying neurodegenerative processes.

HIGHLIGHTS

Longitudinal data was free-water corrected and harmonized

Global effects of white matter decline were seen in normal and abnormal aging

The free-water metric was most vulnerable to abnormal aging

Cingulum free-water was the most vulnerable to abnormal aging
Rapid, efficient auxin-inducible protein degradation inCandidapathogens
Authors: Milholland Kedric L. , Gregor Justin B. , Hoda Smriti , Píriz-Antúnez Soledad , Dueñas-Santero Encarnación , Vu Bao Gia , Patel Krishna P. , Moye-Rowley W. Scott , Vázquez de Aldana Carlos R. , Correa-Bordes Jaime , Briggs Scott D. , Hall Mark C.
Published: May 2023

A variety of inducible protein degradation (IPD) systems have been developed as powerful tools for protein functional characterization. IPD systems provide a convenient mechanism for rapid inactivation of almost any target protein of interest. Auxin-inducible degradation (AID) is one of the most common IPD systems and has been established in diverse eukaryotic research model organisms. Thus far, IPD tools have not been developed for use in pathogenic fungal species. Here, we demonstrate that the original AID and the second generation AID2 systems work efficiently and rapidly in the human pathogenic yeastsCandida albicansandCandida glabrata. We developed a collection of plasmids that support AID system use in laboratory strains of these pathogens. These systems can induce >95% degradation of target proteins within minutes. In the case of AID2, maximal degradation was achieved at low nanomolar concentrations of the synthetic auxin analog 5-adamantyl-indole-3-acetic acid (5-Ad-IAA). Auxin-induced target degradation successfully phenocopied gene deletions in both species. The system should be readily adaptable to other fungal species and to clinical pathogen strains. Our results define the AID system as a powerful and convenient functional genomics tool for protein characterization in fungal pathogens.
Differential modulation on neural activity related to flankers during face processing: a visual crowding study
Authors: Qiu Zeguo , Wu Dihua , Muehlebach Benjamin J.
Published: May 2023

The modulations of visual awareness on the processing of emotional faces have been mainly investigated in masking experiments where stimuli were presented for different durations as an integral process to the masking technique. In this visual crowding study, we manipulated the perceivability of a central crowded face (either a fearful or a neutral face) by varying the similarity between the central face and the surrounding flanker stimuli. We presented participants with pairs of visual clutters and recorded their electroencephalography during an emotion judgement task. In an upright flanker condition where both the target face and flanker faces were upright faces (high similarity), participants were less likely to report seeing the central target face, and their P300 was weakened, compared to a scrambled flanker condition where scrambled face images were used as flankers (low similarity). Additionally, at around 120ms post-stimulus, a posterior negativity was found for the upright flanker condition, compared to the scrambled flanker condition, however only for fearful face targets. We concluded that early neural responses seem to be affected by the perceptual characteristics of both target and flanker stimuli whereas neural activity at a later stage is associated with post-perceptual evaluation of the stimuli in this visual crowding paradigm.
Faces capture spatial attention only when we want them to: an inattentional blindness EEG study
Authors: Qiu Zeguo , Lei Xue , Becker Stefanie I. , Pegna Alan J.
Published: May 2023

Previous research on emotional face processing has shown that emotional faces such as fearful faces may be processed without visual awareness. However, evidence for nonconscious attention capture by fearful faces is limited. In fact, studies using sensory manipulation of awareness (e.g., backward masking paradigms) have shown that fearful faces do not attract attention during subliminal viewings nor when they were task-irrelevant. Here, we used a three-phase inattentional blindness paradigm and electroencephalography to examine whether faces (fearful and neutral) capture attention under different conditions of awareness and task-relevancy. We found that the electrophysiological marker for attention capture, the N2-posterior-contralateral (N2pc), was elicited by face stimuli only when participants were aware of the faces and when they were task-relevant (phase 3). When participants were unaware of the presence of faces (phase 1) or when the faces were irrelevant to the task (phase 2), no N2pc was observed. Together with our previous work, we concluded that fearful faces, or faces in general, do not attract attention unless we want them to.
The small acid-soluble proteins ofClostridioides difficileregulate sporulation in a SpoIVB2-dependent manner
Authors: Nerber Hailee N. , Baloh Marko , Brehm Joshua N. , Sorg Joseph A.
Published: May 2023

Clostridioides difficileis a pathogen whose transmission relies on the formation of dormant endospores. Spores are highly resilient forms of bacteria that resist environmental and chemical insults. In recent work, we found thatC. difficileSspA and SspB, two small acid-soluble proteins (SASPs), protect spores from UV damage and, interestingly, are necessary for the formation of mature spores. Here, we build upon this finding and show thatC. difficile sspAandsspBare required for the formation of the spore cortex layer. Moreover, using an EMS mutagenesis selection strategy, we identified mutations that suppressed the defect in sporulation ofC. difficileSASP mutants. Many of these strains contained mutations inCDR20291_0714(spoIVB2) revealing a connection between the SpoIVB2 protease and the SASPs in the sporulation pathway. This work builds upon the hypothesis that the small acid-soluble proteins can regulate gene expression.

Importance

C. difficileis easily spread through the production of highly resistant spores. Understanding how spores are formed could yield valuable insight into how the sporulation process can be halted to render spores that are sensitive to cleaning methods. Here, we identify another protein involved in the sporulation process that is seemingly controlled by the small acid-soluble proteins (SASPs). This discovery allows us to better understand how theC. difficileSASPs may bind to specific sites on the genome to regulate gene expression.
Measuring changes inPlasmodium falciparumcensus population size in response to sequential malaria control interventions
Authors: Tiedje Kathryn E. , Zhan Qi , Ruybal-Pésantez Shazia , Tonkin-Hill Gerry , He Qixin , Tan Mun Hua , Argyropoulos Dionne C. , Deed Samantha L. , Ghansah Anita , Bangre Oscar , Oduro Abraham R. , Koram Kwadwo A. , Pascual Mercedes , Day Karen P.
Published: May 2023

Here we introduce a new endpoint “census population size” to evaluate the epidemiology and control ofPlasmodium falciparuminfections, where the parasite, rather than the infected human host, is the unit of measurement. To calculate census population size, we rely on a definition of parasite variation known as multiplicity of infection (MOIvar), based on the hyper-diversity of thevarmultigene family. We present a Bayesian approach to estimate MOIvarfrom sequencing and counting the number of unique DBLα tags (or DBLα types) ofvargenes, and derive from it census population size by summation of MOIvarin the human population. We track changes in this parasite population size and structure through sequential malaria interventions by indoor residual spraying (IRS) and seasonal malaria chemoprevention (SMC) from 2012 to 2017 in an area of high-seasonal malaria transmission in northern Ghana. Following IRS, which reduced transmission intensity by > 90% and decreased parasite prevalence by ∼40-50%, significant reductions invardiversity, MOIvar, and population size were observed in ∼2,000 humans across all ages. These changes, consistent with the loss of diverse parasite genomes, were short lived and 32-months after IRS was discontinued and SMC was introduced,vardiversity and population size rebounded in all age groups except for the younger children (1-5 years) targeted by SMC. Despite major perturbations from IRS and SMC interventions, the parasite population remained very large and retained thevarpopulation genetic characteristics of a high-transmission system (highvardiversity; lowvarrepertoire similarity) demonstrating the resilience ofP. falciparumto short-term interventions in high-burden countries of sub-Saharan Africa.
A Scoping Review of Published and Ongoing Prospective Meta-Analyses in Health Research: Study Protocol
Authors: Love Thomas , Li Xiang , Sotiropoulos James X. , Williams Jonathan G. , Libesman Sol , Hunter Kylie E. , Seidler Anna Lene
Published: May 2023

Background

Prospective meta-analysis (PMA) is an emerging evidence synthesis methodology, in which the study selection criteria, hypotheses and analyses are finalised prior to the knowledge of included study results. This has numerous benefits over retrospective meta-analysis, including a reduction in selection bias, selective outcome reporting and publication bias and improved data harmonisation. Yet, common misunderstandings of the PMA methodology remain, leading to inappropriate and/or suboptimal implementation by researchers.

Objectives

To investigate the landscape of the published and ongoing prospective meta-analyses.

Methods

We will systematically search the International prospective Register of Systematic Reviews (PROSPERO) for PMAs from inception to January 2023 and screen these studies in COVIDENCE. The results of this search will be combined with a search of medical databases (PubMed, Embase, Cochrane Database of Systematic Reviews) up to 2018, to capture PMA that started prior to the launch and subsequently increasingly wide implementation of PROSPERO in February 2011. All PMAs conducted in human health research will be eligible for inclusion. All records will be double-screened, and data will be double extracted, with conflicts resolved through consensus.

Dissemination

Insights from this scoping review will inform adaptions to current PMA guidelines and thus assist researchers in planning future PMAs in their fields.
PCBP1 regulates alternative splicing of AARS2 in congenital cardiomyopathy
Authors: Lu Yao Wei , Liang Zhuomin , Guo Haipeng , Fernandes Tiago , Espinoza-Lewis Ramon A , Wang Tingting , Li Kathryn , Li Xue , Singh Gurinder Bir , Wang Yi , Cowan Douglas , Mably John D , Philpott Caroline C. , Chen Hong , Wang Da-Zhi
Published: May 2023

Alanyl-transfer RNA synthetase 2 (AARS2) is a nuclear encoded mitochondrial tRNA synthetase that is responsible for charging of tRNA-Ala with alanine during mitochondrial translation. Homozygous or compound heterozygous mutations in the Aars2 gene, including those affecting its splicing, are linked to infantile cardiomyopathy in humans. However, how Aars2 regulates heart development, and the underlying molecular mechanism of heart disease remains unknown. Here, we found that poly(rC) binding protein 1 (PCBP1) interacts with the Aars2 transcript to mediate its alternative splicing and is critical for the expression and function of Aars2. Cardiomyocyte-specific deletion of Pcbp1 in mice resulted in defects in heart development that are reminiscent of human congenital cardiac defects, including noncompaction cardiomyopathy and a disruption of the cardiomyocyte maturation trajectory. Loss of Pcbp1 led to an aberrant alternative splicing and a premature termination of Aars2 in cardiomyocytes. Additionally, Aars2 mutant mice with exon-16 skipping recapitulated heart developmental defects observed in Pcbp1 mutant mice. Mechanistically, we found dysregulated gene and protein expression of the oxidative phosphorylation pathway in both Pcbp1 and Aars2 mutant hearts; these date provide further evidence that the infantile hypertrophic cardiomyopathy associated with the disorder oxidative phosphorylation defect type 8 (COXPD8) is mediated by Aars2. Our study therefore identifies Pcbp1 and Aars2 as critical regulators of heart development and provides important molecular insights into the role of disruptions in metabolism on congenital heart defects.
p300 Is an Obligate Integrator of Combinatorial Transcription Factor Inputs
Authors: Ferrie John J. , Karr Jonathan P. , Graham Thomas G.W. , Dailey Gina M. , Zhang Gloria , Tjian Robert , Darzacq Xavier
Published: May 2023

Transcription coactivators are proteins or protein complexes that mediate transcription factor (TF) function. However, they lack DNA binding capacity, prompting the question of how they engage target loci. Three non-exclusive hypotheses have been posited: coactivators are recruited by complexing with TFs, by binding histones through epigenetic reader domains, or by partitioning into phase-separated compartments through their extensive intrinsically disordered regions (IDRs). Using p300 as a prototypical coactivator, we systematically mutated its annotated domains and show by single-molecule tracking in live cells that coactivator– chromatin binding depends entirely on combinatorial binding of multiple TF-interaction domains. Furthermore, we demonstrate that acetyltransferase activity negatively impacts p300–chromatin association and that the N-terminal TF-interaction domains regulate that activity. Single TF-interaction domains are insufficient for both chromatin binding and regulation of catalytic activity, implying a principle that could broadly inform eukaryotic gene regulation: a TF must act in coordination with other TFs to recruit coactivator activity.