bluuebunny/crossref_metadata_2025 huggingface dataset:
Is Meibomian Gland Dysfunction One Disease? Heterogeneity Among Phenotypes
Authors: Kim Colin K. , Locatelli Elyana V. T. , Prislovsky Amanda , Cabrera Kimberly , Gary Ashlyn A. , Mandal Nawajes , Galor Anat
Published: April 2024

Purpose:

The purpose of this study was to examine ocular surface symptoms, tear metrics, and tear cytokines by Meibomian gland dysfunction (MGD) features.

Methods:

Symptom questionnaires and an ocular surface evaluation were performed on 40 individuals with varied MGD signs (Meibomian gland [MG] plugging, eyelid vascularity, meibum quality, and MG dropout). Tear proteins were extracted off Schirmer strips and analyzed for 23 human inflammation-related proteins. Statistical analysis was performed to examine associations between dry eye metrics inflammatory proteins and MGD features.

Results:

The study involved 40 South Florida veterans with a mean age of 61 ± 13 years; most individuals were male (95%), White (31%), and non-Hispanic (85%). MGD features differentially related to dry eye signs. Eyelid vascularity, meibum quality, and MG dropout, but not MG plugging, correlated with higher corneal staining and lower tear production. MGD features also differentially related to tear cytokines. Eyelid vascularity most closely related to inflammation with significant correlations for interferon-gamma-γ (r = 0.36, P = 0.02), interleukin-4 (IL-4) (r = 0.43, P = 0.006), IL-17A (r = 0.42, P = 0.007), matrix metalloproteinase-2 (r = 0.39, P = 0.01), C-X-C motif chemokine ligand 5 (Regulated upon Activation, Normal T-Cell Expressed and presumably Secreted [RANTES]) (r = 0.32, P = 0.04), and tumor necrosis factor α (r = 0.36, P = 0.02). The other 3 MGD signs were less related to inflammation. Multivariable models revealed IL-4 to be most closely related to eyelid vascularity (standardized β = 0.39, P < 0.0001).

Conclusions:

Eyelid vascularity was the MGD sign most closely related to inflammatory cytokines, suggesting that different MGD features may be driven by different pathophysiological mechanisms.
Mediastinal Nontuberculous Mycobacterial Infection in Children: A Multidisciplinary Approach
Authors: Wiener Jonathan , Wanaguru Dylan , Currie Bruce , Grant Peter , Russell Carolyn , Palasanthiran Pamela , Williams Phoebe , Belessis Yvonne , Soma Marlene
Published: April 2024

Background:

Mediastinal infections due to nontuberculous mycobacteria remain an exceedingly rare entity. Most cases in the published literature do not include pediatric patients. Due to their clinical infrequency, poor response to antimicrobial therapy and often precarious anatomical location, the optimal management of these lesions can be challenging.

Methods:

Retrospective medical record review of 4 pediatric cases of mediastinal nontuberculous mycobacteria infection was undertaken. Each child presented with nonspecific respiratory symptoms, including significant acute airway obstruction and required a range of investigations to confirm the diagnosis. Nonresponsiveness to conservative measures and antimycobacterial therapy ultimately resulted in surgical intervention to obtain clinical improvement.

Results:

All 4 children had extensive evaluation and multidisciplinary involvement in otolaryngology, respiratory medicine, pediatric surgery, infectious diseases and cardiothoracic surgery. They all eventually had their disease debulked via thoracotomy in addition to prolonged antimycobacterial therapy, with successful clinical outcomes.

Conclusions:

Mediastinal nontuberculous mycobacteria infections in the pediatric population are rare and diagnostically challenging. A high clinical suspicion should be maintained, and multidisciplinary input sought. Targeted surgery with adjuvant medical therapy can reduce disease burden with minimal long-term morbidity.
Evaluating the Prognostic Variables for Overall Survival in Patients with Metastatic Renal Cell Carcinoma: A Meta-Analysis Of 29,366 Patients
Authors: Li Bruce , Sood Swati , Huynh Melissa J. , Power Nicholas E.
Published: April 2024

Background:

Scoring systems are a method of risk assessment used to stratify patients with metastatic renal cell carcinoma (mRCC) and guide systemic therapy. The variables are weighed equally when calculating total score. However, the difference of even 1 positive predictor can change one's risk category and therapy.

Objective:

To compare the relative strength of association between predictive variables and overall survival (OS) in mRCC.

Methods:

A search of Medical Literature Analysis and Retrieval System Online (MEDLINE) and Embase was conducted. Clinical studies, retrospective and prospective, were included if the association of at least 1 predictor and OS in patients with mRCC receiving first-line systemic therapy was evaluated. Meta-analysis was performed to generate pooled hazard ratios (HRs) and 95% CIs for OS for predictors with ≥ 5 included studies. Sensitivity analysis identified outlier heterogeneity and publication bias.

Results:

Sixty-six studies containing 29,366 patients were included. Meta-analysis indicated lung metastases, bone metastases, thrombocytosis, time to systemic therapy < 1 year, liver metastases, hypercalcemia, anemia, elevated neutrophil-lymphocyte ratio, multiple metastatic sites, neutrophilia, poor Eastern Cooperative Oncology Group (ECOG) status, no previous nephrectomy, elevated lactate dehydrogenase, Fuhrman grade 3 or 4, central nervous system metastases, elevated C-reactive protein, and Karnofsky Performance Status < 80% were associated with significantly worse OS. The HRs varied from 1.34 to 2.76, representing heterogeneity in predictive strength. The effects of study heterogeneity and publication bias were minimal to moderate across all predictors.

Conclusions:

Based on the differences in pooled HRs, prognostic strength between the variables is likely not equivalent. Restructuring scoring models, through inclusion of other variables and usage of relative weighting, should be considered to improve accuracy of risk stratification.
Renewing the Nursing Culture
Authors: Porter-O’Grady Tim , Malloch Kathy , Scott Kathy
Published: April 2024

Culture is the driving frame within which all human action takes form. This article explores the elements and characteristics of culture and applies them to the nursing professional community of practice. As it drills down to the work in the cultural context, it argues for the central role of the preceptor in evidencing the influence of culture. For onboarding nurses and the nursing community, the preceptor becomes the carrier of culture, demonstrating the impact of culture in a way that exhibits its influence and impact on nursing practice and patient care.
Does Perceived Scarcity of Money for Food Induce Lower Decline of Enjoyment and Higher Short-term Consumption?
Authors: Tiwari Biplav Babu , Rajbhandari-Thapa Janani , Sevilla Julio , Nayga Rodolfo M.
Published: April 2024

It is known that the decline in enjoyment may be influenced by factors other than the quantity consumed. This study tests the hypothesis that the decline in enjoyment from additional consumption under situational scarcity (more specifically the perceived scarcity of money to buy food) is low compared with the decline in enjoyment when resources are not limited, resulting in higher consumption under situational scarcity. The study followed a between-subjects factorial design with 4 scarcity levels (low [1 level], medium [2 levels], and high [1 level]) in a laboratory-controlled experiment where college students were randomly assigned to different conditions to observe how scarcity perceptions influenced the amount of food consumed and the decline in its enjoyment. As hypothesized, participants in the high scarcity condition consumed more than those in the low or medium conditions. These findings provide preliminary evidence that consumption of energy-dense food may be higher under situational scarcity scenarios. Future research should build on the findings of this study to investigate the relationship between scarcity, declines in enjoyment associated with additional consumption, and food consumption with other food groups and consumer subpopulations.
Social Care Education and Training Among US Pediatric Emergency Medicine Fellowship Programs
Authors: Assaf Raymen Rammy , Assaf Ryan David , Doucet Hannah Barber , Graff Danielle
Published: April 2024

Objective

The aim of the study is to assess the association of social determinants of health (SDOH) education and social needs training on pediatric emergency medicine (PEM) physician perception and practices of social care.

Methods

Data were derived from the 2021 National Social Care Practices Survey of PEM program directors (PDs) and fellows. Ordinal and binary logistic regression modeling were completed for educational/training factors and social care perspective and practice outcomes.

Results

A national sample of 44 PDs (49% response rate) and 109 fellows (28%) participated. A minority of fellows received SDOH education and social needs training during fellowship. Fellows and PDs with SDOH education had a 3.1 odds (95% confidence interval CI, 1.4–6.9) of screening for social needs, with 4.4 odds among fellows (95% CI, 1.2–20.7). Those with social needs training were more comfortable assessing social risk, with 2.4 odds overall (95% CI, 1.2–4.7) and 3.1 odds among fellows (95% CI, 1.4–6.7). They also had 2.4 odds overall (95% CI, 1.1–4.9) of screening for social needs, with a 2.9 odds among fellows (95% CI, 1.3–6.8).

Conclusions

Social care education and training appear to be associated with comfort assessing social risk and social needs screening tendency among both PEM PDs and fellows. Key areas for educational interventions are identified among PEM fellows, who are uniquely positioned as clinical leaders and patient advocates.
Severe Blepharoptosis Correction with the Fixation of Levator Complex and Conjoint Fascial Sheath
Authors: Liu Haipeng , Li Tenghai , Wang Shimeng , Zhang Wei , Li Tian , Liu Bingzhang , Zhang Jiaqi , Shao Ying , Zhang Duo
Published: April 2024

Background:

The correction of severe blepharoptosis is one of the most challenging operations in plastic surgery. This study introduces a novel self-reinforced fixation technique combining the levator complex with conjoint fascial sheath for the correction of severe blepharoptosis and reviews the postoperative results over the preceding 12 years.

Methods:

This retrospective review included all patients who underwent self-reinforced fixation with or without conjoint fascial sheath at the authors’ center between 2010 and 2022. The clinical data of the 2 groups were collected and evaluated.

Results:

All patients were followed up for 6 months to 8 years postoperatively. The mean postoperative marginal reflex distance 1 and levator function increased significantly in both groups. Sufficient correction of ptosis was achieved in 32 (65.31%) and 84 (81.56%) eyelids in groups I and II, respectively. The mean eyelid lagophthalmos was 1.27 ± 0.91 mm and 0.85 ± 0.89 mm in groups I and II, respectively. The most common complication was undercorrection of ptosis, which was observed in 14 eyelids (28.57%) and 15 eyelids (14.56%) in groups I and II, respectively.

Conclusions:

The self-reinforced fixation technique was effective in correcting severe congenital ptosis in Chinese patients. The clinical effect was consistent in the long-term follow-up cases, and the recurrence rate was low. Thus, this technique can enhance the strength of the levator muscle and maintain appropriate elasticity of eye closure.

CLINICAL QUESTION/LEVEL OF EVIDENCE:

Therapeutic, III.
Reinnervated Serratus Free Flap for a Functional Outcome in Tongue Reconstruction: A Surgical Technique Video
Authors: Baujat Bertrand , Broustaut Nicolas , Dauzier Etienne , Tassart Marc , Wagner Isabelle , Atallah Sarah , Marhic Alix
Published: April 2024

The current benchmark for tongue reconstruction after excision of locally advanced tumors involves the use of free skin or fasciocutaneous flaps, such as the anterolateral thigh flap or forearm free flap. They facilitate the volumetric reconstruction of the tongue, leveraging passive mobility from the remaining native tongue tissue. The challenge in tongue reconstruction surgery remains achieving functional restoration through adequate volume and optimized mobility, using tissue that is both adapted and comparable to native tissue. Although the free serratus muscle flap has been described for various indications, its application in tongue reconstructions remains underexploited. In cases of locally advanced tumors affecting the mobile tongue, typically within the junctional area and without extension to the floor of the mouth or to the tip of the tongue, the serratus free flap has shown positive results. Reinnervation of the flap is achieved connecting the thoracodorsal nerve to the descending branch of the XII nerve. This technique facilitates functional tongue reconstruction, promoting rapid mucosal epithelialization and reinnervation, which, in turn, preserves muscle volume and sustains adequate trophicity without fibrosis. Regarding these considerations, the pure muscle serratus free flap emerges as a valuable and effective alternative in tongue reconstruction. There is a dearth of step-by-step operative technique descriptions for this indication in the literature. The authors present videos demonstrating the surgical technique, showcasing procedures as performed at Tenon Hospital (Paris, France).
Gut permeability is associated with lower insulin sensitivity in youth with perinatally acquired HIV
Authors: Dirajlal-Fargo Sahera , Yu Wendy , Jacobson Denise L. , Mirza Ayesha , Geffner Mitchell E. , Jao Jennifer , McComsey Grace A. ,   for the Pediatric HIV/AIDS Cohort Study (PHACS)
Published: April 2024

The relationships between alterations in the intestinal barrier, and bacterial translocation with the development of metabolic complications in youth with perinatally acquired HIV (YPHIV) have not been investigated.

The PHACS Adolescent Master Protocol enrolled YPHIV across 15 U.S. sites, including Puerto Rico, from 2007 to 2009. For this analysis, we included YPHIV with HIV viral load 1000 c/ml or less, with at least one measurement of homeostatic assessment of insulin resistance (HOMA-IR) or nonhigh density lipoprotein (non-HDLc) between baseline and year 3 and plasma levels of intestinal fatty-acid binding protein (I-FABP), lipopolysaccharide-binding protein (LBP), and zonulin levels at baseline. We fit linear regression models using generalized estimating equations to assess the association of baseline log10 gut markers with log10 HOMA-IR and non-HDLc at all timepoints.

HOMA-IR or non-HDLc was measured in 237, 189, and 170 PHIV at baseline, Yr2, and Yr3, respectively. At baseline, median age (Q1, Q3) was 12 years (10, 14), CD4+ cell count was 762 cells/μl (574, 984); 90% had HIV RNA less than 400 c/ml. For every 10-fold higher baseline I-FABP, HOMA-IR dropped 0.85-fold at baseline and Yr2. For a 10-fold higher baseline zonulin, there was a 1.35-fold increase in HOMA-IR at baseline, 1.23-fold increase in HOMA-IR at Yr2, and 1.20-fold increase in HOMA-IR at Yr3 in adjusted models. For a 10-fold higher baseline LBP, there was a 1.23-fold increase in HOMA-IR at baseline in the unadjusted model, but this was slightly attenuated in the adjusted model. Zonulin was associated with non-HDLc at baseline, but not for the other time points.

Despite viral suppression, intestinal damage may influence downstream insulin sensitivity in YPHIV.
Kaposi sarcoma herpesvirus viral load in bronchoalveolar lavage as a diagnostic marker for pulmonary Kaposi sarcoma
Authors: Saberian Chantal , Lurain Kathryn , Hill Lindsay K. , Marshall Vickie , Castro Elena M. Cornejo , Labo Nazzarena , Miley Wendell , Moore Kyle , Roshan Romin , Ruggerio Margie , Ryan Kerry , Widell Anaida , Ekwede Irene , Mangusan Ralph , Rupert Adam , Barochia Amisha , Whitby Denise , Yarchoan Robert , Ramaswami Ramya
Published: April 2024

Objective:

Kaposi sarcoma is a vascular tumor that affects the pulmonary system. However, the diagnosis of airway lesions suggestive of pulmonary Kaposi sarcoma (pKS) is reliant on bronchoscopic visualization. We evaluated the role of Kaposi sarcoma herpesvirus (KSHV) viral load in bronchoalveolar lavage (BAL) as a diagnostic biomarker in patients with bronchoscopic evidence of pKS and evaluated inflammatory cytokine profiles in BAL and blood samples.

Design:

In this retrospective study, we evaluated KSHV viral load and cytokine profiles within BAL and blood samples in patients who underwent bronchoscopy for suspected pKS between 2016 and 2021.

Methods:

KSHV viral load and cytokine profiles were obtained from both the circulation and BAL samples collected at the time of bronchoscopy to evaluate compartment-specific characteristics. BAL was centrifuged and stored as cell pellets and KSHV viral load was measured using primers for the KSHV K6 gene regions.

Results:

We evaluated 38 BAL samples from 32 patients (30 with HIV co-infection) of whom 23 had pKS. In patients with airway lesions suggestive of pKS, there was higher KSHV viral load (median 3188 vs. 0 copies/106 cell equivalent; P = 0.0047). A BAL KSHV viral load cutoff of 526 copies/106 cells had a sensitivity of 72% and specificity of 89% in determining lesions consistent with pKS. Those with pKS also had higher IL-1β and IL-8 levels in BAL. The 3-year survival rate for pKS patients was 55%.

Conclusion:

KSHV viral load in BAL shows potential for aiding in pKS diagnosis. Patients with pKS also have evidence of cytokine dysregulation in BAL.
Outcomes of Dermal Regeneration Templates in Irradiated and Nonirradiated Scalp Defects
Authors: Yang Alan Z. , Shelton Eva , Katave Coral , Fruge Seth , Talbot Simon G. , Eberlin Kyle R. , Orgill Dennis P. , Ranganathan Kavitha L.
Published: April 2024

Objectives:

Dermal regeneration templates (DRTs) are frequently used to treat scalp defects. The aim was to compare the time course of healing for DRTs in scalp defects with and without preoperative radiation.

Methods:

The authors conducted a retrospective cohort study of DRT-based scalp reconstruction at 2 academic medical centers between 2013 and 2022. Information was collected on demographic variables, comorbidities, medication use, history of radiation, and DRT outcomes. The primary outcome was DRT loss, defined as exposed calvarium or DRT detachment based on postoperative follow-up documentation. Kaplan-Meier survival analysis and multivariable Cox proportional-hazard regressions were used to compare DRT loss in irradiated and nonirradiated defects. Multivariable logistic regressions were used to compare 30-day postoperative complications (infection, hematoma, or seroma) in irradiated and nonirradiated defects.

Results:

In total, 158 cases were included. Twenty-eight (18%) patients had a preoperative history of radiation to the scalp. The mean follow-up time after DRT placement was 2.6 months (SD: 4.5 mo). The estimated probability of DRT survival at 2 months was 91% (95% CI: 83%–100%) in nonirradiated patients and 65% (95% CI: 48%–88%) in irradiated patients. In the 55 patients with a bony wound base, preoperative head radiation was associated with a higher likelihood of DRT loss (hazard ratio: 11). Half the irradiated defects experienced uncomplicated total wound closure using Integra Wound Matrix Dressing with or without second-stage reconstruction.

Conclusions:

Dermal regeneration template can offer durable coverage in nonirradiated scalp defects. Although DRT loss is more likely in irradiated scalp defects, successful DRT-based reconstruction is possible in select cases.
Spatial versus spatio-temporal approaches for studying metacommunities: a multi-taxon analysis in Mediterranean and tropical temporary ponds
Authors: Gálvez Ángel , Peres-Neto Pedro R. , Castillo-Escrivà Andreu , Bonilla Fabián , Camacho Antonio , García-Roger Eduardo M. , Iepure Sanda , Miralles Javier , Monrós Juan S. , Olmo Carla , Picazo Antonio , Rojo Carmen , Rueda Juan , Sasa Mahmood , Segura Mati , Armengol Xavier , Mesquita-Joanes Francesc
Published: April 2024

Prior research on metacommunities has largely focused on snapshot surveys, often overlooking temporal dynamics. In this study, our aim was to compare the insights obtained from metacommunity analyses based on a spatial approach repeated over time, with a spatio-temporal approach that consolidates all data into a single model. We empirically assessed the influence of temporal variation in the environment and spatial connectivity on the structure of metacommunities in tropical and Mediterranean temporary ponds. Employing a standardized methodology across both regions, we surveyed multiple freshwater taxa in three time periods within the same hydrological year from multiple temporary ponds in each region. To evaluate how environmental, spatial and temporal influences vary between the two approaches, we used nonlinear variation partitioning analyses based on generalized additive models. Overall, this study underscores the importance of adopting spatio-temporal analytics to better understand the processes shaping metacommunities. While the spatial approach suggested that environmental factors had a greater influence, our spatio-temporal analysis revealed that spatial connectivity was the primary driver influencing metacommunity structure in both regions. Temporal effects were equally important as environmental effects, suggesting a significant role of ecological succession in metacommunity structure.
Body mass mediates spatio-temporal responses of mammals to human frequentation across Italian protected areas
Authors: Salvatori Marco , Greco Ilaria , Petroni Luca , Massolo Alessandro , Dorigatti Enrico , Miscioscia Martina , Natucci Luca , Oberosler Valentina , Partel Piergiovanni , Pedrini Paolo , Volcan Gilberto , Rovero Francesco
Published: April 2024

Protected area (PA) networks are a pivotal tool to fight biodiversity loss, yet they often need to balance the mission of nature conservation with the socio-economic need of giving opportunity for outdoor recreation. Recreation in natural areas is important for human health in an urbanized society, but can prompt behavioural modifications in wild animals. Rarely, however, have these responses being studied across multiple PAs and using standardized methods. We deployed a systematic camera trapping protocol at over 200 sites to sample medium and large mammals in four PAs within the European Natura 2000 network to assess their spatio-temporal responses to human frequentation, proximity to towns, amount of open habitat and topographical variables. By applying multi-species and single-species models for the number of diurnal, crepuscular and nocturnal detections and a multi-species model for nocturnality index, we estimated both species-specific- and meta-community-level effects, finding that increased nocturnality appeared the main strategy that the mammal meta-community used to cope with human disturbance. However, responses in the diurnal, crepuscular and nocturnal site use were mediated by species' body mass, with larger species exhibiting avoidance of humans and smaller species more opportunistic behaviours. Our results show the effectiveness of standardized sampling and provide insights for planning the expansion of PA networks as foreseen by the Kunming–Montreal biodiversity agreement.
No correlative evidence of costs of infection or immunity on leucocyte telomere length in a wild population of Soay sheep
Authors: Ravindran Sanjana , Underwood Sarah L. , Dorrens Jennifer , Seeker Luise A. , Watt Kathryn , Wilbourn Rachael V. , Sparks Alexandra M. , Sinclair Rona , Chen Zhulin , Pilkington Jill G. , McNeilly Tom N. , Harrington Lea , Pemberton Josephine M. , Nussey Daniel H. , Froy Hannah
Published: April 2024

Telomere length (TL) is a biomarker hypothesized to capture evolutionarily and ecologically important physiological costs of reproduction, infection and immunity. Few studies have estimated the relationships among infection status, immunity, TL and fitness in natural systems. The hypothesis that short telomeres predict reduced survival because they reflect costly consequences of infection and immune investment remains largely untested. Using longitudinal data from a free-living Soay sheep population, we tested whether leucocyte TL was predicted by infection with nematode parasites and antibody levels against those parasites. Helminth parasite burdens were positively associated with leucocyte TL in both lambs and adults, which is not consistent with TL reflecting infection costs. We found no association between TL and helminth-specific IgG levels in either young or old individuals which suggests TL does not reflect costs of an activated immune response or immunosenescence. Furthermore, we found no support for TL acting as a mediator of trade-offs between infection, immunity and subsequent survival in the wild. Our results suggest that while variation in TL could reflect short-term variation in resource investment or environmental conditions, it does not capture costs of infection and immunity, nor does it behave like a marker of an individual's helminth-specific antibody immune response.
Language-like efficiency and structure in house finch song
Authors: Youngblood Mason
Published: April 2024

Communication needs to be complex enough to be functional while minimizing learning and production costs. Recent work suggests that the vocalizations and gestures of some songbirds, cetaceans and great apes may conform to linguistic laws that reflect this trade-off between efficiency and complexity. In studies of non-human communication, though, clustering signals into types cannot be done
a priori
, and decisions about the appropriate grain of analysis may affect statistical signals in the data. The aim of this study was to assess the evidence for language-like efficiency and structure in house finch (
Haemorhous mexicanus
) song across three levels of granularity in syllable clustering. The results show strong evidence for Zipf's rank–frequency law, Zipf's law of abbreviation and Menzerath's law. Additional analyses show that house finch songs have small-world structure, thought to reflect systematic structure in syntax, and the mutual information decay of sequences is consistent with a combination of Markovian and hierarchical processes. These statistical patterns are robust across three levels of granularity in syllable clustering, pointing to a limited form of scale invariance. In sum, it appears that house finch song has been shaped by pressure for efficiency, possibly to offset the costs of female preferences for complexity.
Synthetic coevolution reveals adaptive mutational trajectories of neutralizing antibodies and SARS-CoV-2
Authors: Ehling Roy A. , Minot Mason , Overath Max D. , Sheward Daniel J. , Han Jiami , Gao Beichen , Taft Joseph M. , Pertseva Margarita , Weber Cédric R. , Frei Lester , Bikias Thomas , Murrell Ben , Reddy Sai T.
Published: April 2024

The Covid-19 pandemic showcases a coevolutionary race between the human immune system and SARS-CoV-2, mirroring the Red Queen hypothesis of evolutionary biology. The immune system generates neutralizing antibodies targeting the SARS-CoV-2 spike protein’s receptor binding domain (RBD), crucial for host cell invasion, while the virus evolves to evade antibody recognition. Here, we establish a synthetic coevolution system combining high-throughput screening of antibody and RBD variant libraries with protein mutagenesis, surface display, and deep sequencing. Additionally, we train a protein language machine learning model that predicts antibody escape to RBD variants. Synthetic coevolution reveals antagonistic and compensatory mutational trajectories of neutralizing antibodies and SARS-CoV-2 variants, enhancing the understanding of this evolutionary conflict.
Isolation and Characterization of aHalomonasSpecies for Non-Axenic Growth-Associated Production of Bio-Polyesters from Sustainable Feedstocks
Authors: Woo Sung-Geun , Averesch Nils J. H. , Berliner Aaron J. , Deutzmann Joerg S. , Pane Vince E. , Chatterjee Sulogna , Criddle Craig S.
Published: April 2024

Biodegradable plastics are urgently needed to replace petroleum-derived polymeric materials and prevent their accumulation in the environment. To this end, we isolated and characterized a halophilic and alkaliphilic bacterium from the Great Salt Lake in Utah. The isolate was identified as aHalomonasspecies and designated “CUBES01”. Full-genome sequencing and genomic reconstruction revealed the unique genetic traits and metabolic capabilities of the strain, including the common polyhydroxyalkanoate (PHA) biosynthesis pathway. Fluorescence staining identified intracellular polyester granules that accumulated predominantly during the strain’s exponential growth, a feature rarely found among natural PHA producers. CUBES01 was found to metabolize a range of renewable carbon-feedstocks, including glucosamine and acetyl-glucosamine, as well as sucrose, glucose, fructose, and further also glycerol, propionate, and acetate. Depending on the substrate, the strain accumulated up to ∼60% of its biomass [dry w/w] in poly(3-hydroxbutyrate), while reaching a doubling time of 1.7 h at 30◦C and an optimum osmolarity of 1 M sodium chloride and a pH of 8.8. The physiological preferences of the strain may not only enable long-term aseptic cultivation but can also facilitate the release of intracellular products through osmolysis. Development of a minimal medium also allowed the estimation of maximum PHB production rates, which were projected to exceed 5 gPHB/h. Finally, also the genetic tractability of the strain was assessed in conjugation experiments: two orthogonal plasmid-vectors were stable in the heterologous host, thereby opening the possibility of genetic engineering through the introduction of foreign genes.

IMPORTANCE

The urgent need for renewable replacements for synthetic materials may be addressed through microbial biotechnology. To simplify the large-scale implementation of such bio-processes, robust cell factories that can utilize sustainable and widely available feedstocks are pivotal. To this end, non-axenic growth-associated production could reduce operational costs and enhance biomass productivity, thereby improving commercial competitiveness. Another major cost factor is downstream processing. Especially in the case of intracellular products, such as bio-polyesters. Simplified cell-lysis strategies could also further improve economic viability.
Seq-Scope Protocol: Repurposing Illumina Sequencing Flow Cells for High-Resolution Spatial Transcriptomics
Authors: Kim Yongsung , Cheng Weiqiu , Cho Chun-Seok , Hwang Yongha , Si Yichen , Park Anna , Schrank Mitchell , Hsu Jer-En , Xi Jingyue , Kim Myungjin , Pedersen Ellen , Koues Olivia I. , Wilson Thomas , Jun Goo , Kang Hyun Min , Lee Jun Hee
Published: April 2024

Spatial transcriptomics (ST) technologies represent a significant advance in gene expression studies, aiming to profile the entire transcriptome from a single histological slide. These techniques are designed to overcome the constraints faced by traditional methods such as immunostaining and RNAin situhybridization, which are capable of analyzing only a few target genes simultaneously. However, the application of ST in histopathological analysis is also limited by several factors, including low resolution, a limited range of genes, scalability issues, high cost, and the need for sophisticated equipment and complex methodologies. Seq-Scope—a recently developed novel technology—repurposes the Illumina sequencing platform for high-resolution, high-content spatial transcriptome analysis, thereby overcoming these limitations. Here we provide a detailed step-by-step protocol to implement Seq-Scope with an Illumina NovaSeq 6000 sequencing flow cell that allows for the profiling of multiple tissue sections in an area of 7 mm × 7 mm or larger. In addition to detailing how to prepare a frozen tissue section for both histological imaging and sequencing library preparation, we provide comprehensive instructions and a streamlined computational pipeline to integrate histological and transcriptomic data for high-resolution spatial analysis. This includes the use of conventional software tools for single cell and spatial analysis, as well as our recently developed segmentation-free method for analyzing spatial data at submicrometer resolution. Given its adaptability across various biological tissues, Seq-Scope establishes itself as an invaluable tool for researchers in molecular biology and histology.

KEY POINTS

The protocol outlines a method for repurposing an Illumina NovaSeq 6000 flow cell as a spatial transcriptomics array, enabling the generation of high-resolution spatial datasets.

The protocol introduces a streamlined data analysis pipeline that produces a spatial digital gene expression matrix suitable for various single-cell and spatial transcriptome analysis methods.

The protocol allows for the capture of histology images from the same tissue section subjected to spatial transcriptomics analysis and allows users to precisely align the transcriptome dataset with the histological image using fiducial marks engraved on the flow cell surface.

Leveraging commonly available Illumina equipment, the protocol offers researchers ultra-high submicrometer resolution in spatial transcriptomics analysis with a comprehensive pipeline, rapid turnaround, cost efficiency, and versatility.
Field evidence for the role of plant volatiles induced by caterpillar-derived elicitors in the prey location behavior of predatory social wasps
Authors: Grof-Tisza Patrick , Turlings Ted C.J. , Bustos-Segura Carlos , Benrey Betty
Published: April 2024

One assumed function of herbivore-induced plant volatiles (HIPVs) is to attract natural enemies of the inducing herbivores. Field evidence for this is scarce and often indirect. Also, the assumption that elicitors in insect oral secretions that trigger the volatile emissions are essential for attraction of natural enemies has not yet been demonstrated under field conditions.

After observing social wasps removing caterpillars from maize plants in an agricultural field, we hypothesized that these wasps use HIPVs to locate their prey. To test this, we conducted an experiment that simultaneously explored the importance of caterpillar oral secretions in the interaction.

We found thatSpodopteracaterpillars placed on mechanically damaged plants treated with oral secretion were more likely to be attacked by wasps compared to caterpillars on plants that were only mechanically wounded. Both of the the latter treatments were considerably more attractive than plants that were only treated with oral secretion or left untreated. Subsequent analyses of headspace volatiles confirmed differences in emitted volatiles that likely account for the differential predation events across the treatments.

These findings highlight the importance of HIPVs in prey location by social wasps and provide evidence for the role that elicitors play in inducing attractive odor blends.
Recharacterization of RSL3 reveals that the selenoproteome is a druggable target in colorectal cancer
Authors: DeAngelo Stephen L. , Zhao Liang , Dziechciarz Sofia , Shin Myungsun , Solanki Sumeet , Balia Andrii , El-Derany Marwa O , Castillo Cristina , Qin Yao , Das Nupur K. , Bell Hannah Noelle , Paulo Joao A. , Zhang Yuezhong , Rossiter Nicholas J. , McCulla Elizabeth C. , He Jianping , Talukder Indrani , Ng Billy Wai-Lung , Schafer Zachary T. , Neamati Nouri , Mancias Joseph D. , Koutmos Markos , Shah Yatrik M.
Published: April 2024

Ferroptosis is a non-apoptotic form of cell death resulting from the iron-dependent accumulation of lipid peroxides. Colorectal cancer (CRC) cells accumulate high levels of intracellular iron and reactive oxygen species (ROS) and are thus particularly sensitive to ferroptosis. The compound (S)-RSL3 ([1S,3R]-RSL3) is a commonly used ferroptosis inducing compound that is currently characterized as a selective inhibitor of the selenocysteine containing enzyme (selenoprotein) Gluathione Peroxidase 4 (GPx4), an enzyme that utilizes glutathione to directly detoxify lipid peroxides. However, through chemical controls utilizing the (R) stereoisomer of RSL3 ([1R,3R]-RSL3) that does not bind GPx4, combined with inducible genetic knockdowns of GPx4 in CRC cell lines, we revealed that GPx4 dependency does not always align with (S)-RSL3 sensitivity, questioning the current characterization of GPx4 as the central regulator of ferroptosis. Utilizing affinity pull-down mass spectrometry with chemically modified (S)-RSL3 probes we discovered that the effects of (S)-RSL3 extend far beyond GPx4 inhibition, revealing that (S)-RSL3 is a broad and non-selective inhibitor of selenoproteins. To further investigate the therapeutic potential of broadly disrupting the selenoproteome as a therapeutic strategy in CRC, we employed additional chemical and genetic approaches. We found that the selenoprotein inhibitor auranofin, an FDA approved gold-salt, chemically induced oxidative cell death and ferroptosis in bothin-vitroandin-vivomodels of CRC. Consistent with these data, we found that AlkBH8, a tRNA-selenocysteine methyltransferase required for the translation of selenoproteins, is essential for thein-vitrogrowth and xenograft survival of CRC cell lines. In summary, these findings recharacterize the mechanism of action of the most commonly used ferroptosis inducing molecule, (S)-RSL3, and reveal that broad inhibition of selenoproteins is a promising novel therapeutic angle for the treatment of CRC.
Non-invasive neuromodulation of cerebello-hippocampal volume-behavior relationships
Authors: Magalhães Thamires N. C. , Maldonado Ted , Jackson T. Bryan , Hicks Tracey H. , Herrejon Ivan A. , Rezende Thiago J. R. , Symm Abigail C. , Bernard Jessica A.
Published: April 2024

The study here explores the link between transcranial direct current stimulation (tDCS) and brain-behavior relationships. We propose that tDCS may indirectly influence the complex relationships between brain volume and behavior. We focused on the dynamics between the hippocampus (HPC) and cerebellum (CB) in cognitive processes, a relationship with significant implications for understanding memory and motor skills. Seventy-four young adults (mean age: 22±0.42 years, mean education: 14.7±0.25 years) were randomly assigned to receive either anodal, cathodal, or sham stimulation. Following stimulation, participants completed computerized tasks assessing working memory and sequence learning in a magnetic resonance imaging (MRI) environment. We investigated the statistical interaction between CB and HPC volumes. Our findings showed that individuals with larger cerebellar volumes had shorter reaction times (RT) on a high-load working memory task in the sham stimulation group. In contrast, the anodal stimulation group exhibited faster RTs during the low-load working memory condition. These RT differences were associated with the cortical volumetric interaction between CB-HPC. Literature suggests that anodal stimulation down-regulates the CB and here, those with larger volumes perform more quickly, suggesting the potential need for additional cognitive resources to compensate for cerebellar downregulation. This new insight suggests that tDCS can aid in revealing structure-function relationships, due to greater performance variability, especially in young adults. It may also reveal new targets of interest in the study of aging or in diseases where there is also greater behavioral variability.
NMR study of the interaction between MinC and FtsZ and modeling of the FtsZ:MinC complex
Authors: Machado Luciana E. S. F. , Castellen Patricia , Blasios Valdir , Ribeiro Filho Helder Veras , Bisson-Filho Alexandre W. , Benites-Pariente Jhonatan S. , Nogueira Maria Luiza Caldas , Sforça Mauricio , Honorato Rodrigo Vargas , de Oliveira Paulo Sérgio Lopes , Salinas Roberto K. , Zeri Ana Carolina de Mattos , Gueiros-Filho Frederico J.
Published: April 2024

The Min system is a key spatial regulator of cell division in rod-shaped bacteria and the first FtsZ negative modulator to be recognized. Nevertheless, despite extensive genetic and in vitro studies, the molecular mechanism used by MinC to inhibit Z-ring formation remains incompletely understood. The crystallization of FtsZ in complex with other negative regulators such as SulA and MciZ has provided important structural information to corroborate in vitro experiments and establish the mechanism of Z-ring antagonism by these modulators. However, MinC and FtsZ have so far eluded co-crystallization, probably because their complex is too unstable to be crystallized. To gain structural insight into the mechanism of action of MinC, we determined the solution structure of the N-terminal domain ofB. subtilisMinC, and through NMR titration experiments and mutagenesis identified the binding interfaces involved in the MinCN-FtsZ interaction. By using our experimental results as restraints in docking, we also constructed a molecular model for the FtsZ:MinCNcomplex and validated it by molecular dynamics. The model shows that MinCNbinding overlaps with the FtsZ polymerization interface on the C-terminal globular subdomain of FtsZ and, thus, provides a structural basis for MinCNinhibition of FtsZ filament formation. Given that the C-terminal polymerization interface of FtsZ corresponds to the plus end of FtsZ filaments, we propose that capping is the main mechanism employed by MinC to antagonize FtsZ polymerization.
A single strand-based library preparation method for unbiased virome characterization
Authors: Zhai Xichuan , Gobbi Alex , Kot Witold , Krych Lukasz , Nielsen Dennis Sandris , Deng Ling
Published: April 2024

The gut virome is an integral component of the gut microbiome, playing a crucial role in maintaining gut health. However, accurately depicting the entire gut virome is challenging due to the inherent limitations and biases associated with current sequencing library preparation methods. To overcome these problems, we repurposed the ligation-based single-stranded library (SSLR) preparation method for virome studies. We demonstrate that the SSLR method exhibits exceptional efficiency in quantifying viral DNA genomes (both dsDNA and ssDNA) and outperforms existing double-stranded (Nextera) and single-stranded (xGen, MDA+Nextera) library preparation approaches in terms of minimal amplification bias, evenness of coverage, and integrity of assembling viral genomes. The SSLR method can be utilized for the simultaneous library preparation of both DNA and RNA viral genomes. Furthermore, the SSLR method showed its ability to capture highly modified phage genomes, which were often lost using other library preparation approaches.
User Preferences on Long-Acting Pre-Exposure Prophylaxis for HIV Prevention in Sub-Saharan Africa: A Scoping Review
Authors: Pfau Brian , Saravis BA Arden , Cox Sarah N. , Wu Linxuan , Wittenauer Rachel , Callen Emily , Arrouzet Cory , Sharma Monisha
Published: April 2024

Structured Abstract

Background

Novel formulations for PrEP such as injectables, implants, and intravaginal rings are emerging as long-acting alternatives to daily pills for the prevention of HIV. Sub-Saharan Africa has the highest HIV burden as well as the highest PrEP coverage globally. As long-acting formulations continue to become available, it is crucial to understand the product preferences of potential users.

Objective

To conduct a scoping review focused on the region of Sub-Saharan Africa to understand which PrEP products, especially long-acting formulations, different patients and demographic groups prefer as well as the factors that influence their preferences.

Design

We identified 34 publications published between 2014 and 2024 that assessed preferences regarding at least one long-acting PrEP product in the region of Sub-Saharan Africa.

Results

Participants preferred longer-acting products over oral pills when given the choice in almost all studies. On-demand PrEP was commonly preferred over daily dosing, and long-acting products were preferred over on-demand dosing. A majority of studies found injectables to be most commonly preferred compared to daily oral PrEP, implants, and rings. This preference was observed across a range of demographics including men and women, youth, men who have sex with men, and female sex workers. Duration, efficacy, and discretion were the three most important factors influencing participants’ choices.

Conclusions

Long-acting products, especially injectables, are acceptable for a wide range of individuals at risk of HIV in Sub-Saharan Africa and tend to be preferred over daily oral pills. Participants expressed a diversity of values and opinions regarding preferences, emphasizing the benefit of providing multiple formulations to maximize coverage over heterogeneous populations.

Strength and Limitations of this Study

Some key populations, such as transgender women, were underrepresented in the literature. With most studies published before long-acting products became widely available, the hypothetical preferences of non-experienced users may differ from preferences in practice.
Engineering probioticEscherichia coliNissle 1917 to block transfer of multiple antibiotic resistance genes by exploiting a type I CRISPR-Cas system
Authors: Fang Mengdie , Zhang Ruiting , Wang Chenyu , Liu Zhizhi , Fei Mingyue , Tang Biao , Yang Hua , Sun Dongchang
Published: April 2024

Many multidrug-resistant (MDR) bacteria evolved through accumulation of antibiotic-resistance genes (ARGs). Although the potential risk of probiotics as reservoirs of ARGs has been recognized, strategies for blocking transfer of ARGs while using probiotics have rarely been explored. The probioticEscherichia coliNissle 1917 (EcN) has long been used for treating intestinal diseases. Here, we showed frequent transfer of ARGs into EcN bothin vitroandin vivo, raising its potential risk of accumulating antibiotic resistance. Given that no CRISPR-Cas system is found in natural EcN, we integrated the endogenous type I-E CRISPR-Cas system derived fromE. coliBW25113 into EcN, and showed that the engineered EcN was able to efficiently cleave multiple ARGs (i.e.,mcr-1,blaNDM-1andtet(X)). By co-incubation of EcN expressing Cas3-Cascade and that expressing Cas9, we showed that the growth of the former strain outcompeted the latter strain, demonstrating better clinical application prospect of EcN expressing the type I-E CRISPR-Cas system. Finally, the engineered EcN exhibited immunity against transfer of targeted ARGs in the intestine of a model animal (i.e. zebrafish). Our work provides a new strategy for restricting transfer of ARGs in EcN, paving the way for safe use of this probiotic and development of probiotics as living therapeutics.