bluuebunny/crossref_metadata_2025 huggingface dataset:
The Effect of Duration of Antibiotic Prophylaxis on Infections Following Open Reduction and Internal Fixation of Mandibular Fractures: A Prospective Randomized Clinical Trial
Authors: Rikhotso Risimati E. , Mohotlhoane Gontse P.
Published: October 2023

Aim:

To evaluate the benefits of a long-term prophylactic antibiotic regimen following treatment of fractured mandibles with open reduction and internal fixation.

Material and Methods:

A prospective, randomized controlled trial was undertaken at Wits Oral Health Centre. Patients with mandibular fractures who were managed with open reduction and internal fixation using miniplates were randomized into 2 groups. The control group, the perioperative antibiotic (POA) group, was composed of patients who received intravenous (IV) antibiotic cover intraoperatively and a further 3 IV doses 24 hours postoperatively. The study group, the extended postoperative antibiotic (EPOA), was composed of patients who received similar doses as the control group but with an additional 5 days of oral antibiotics upon discharge. The patients were then evaluated for evidence of infection 1, 4, and 6 weeks postoperatively.

Results:

A total of 77 patients were included in the study, 41 in the POA and 36 in the EPOA groups. Fourteen patients had evidence of infection noted within the 6-week follow-up period (10 in the POA and 4 in the EPOA groups). Statistical analysis with the Pearson Chi-square and Student t test showed no statistically significant difference (P=0.399) between POA and EPOA groups. There were no significant differences between the groups with respect to site and etiology of fracture, duration of operation, and presence of infection (P>0.05) during the 6-week review period.

Conclusions:

The extended use of antibiotic prophylaxis when managing mandibular fractures with open reduction and internal fixation offers no additional benefit in reducing postoperative infections.
Multicenter Evaluation of Financial Toxicity and Long-Term Health Outcomes After Injury
Authors: Scott John W. , Anderson Geoffrey A. , Conatser Amelia , de Souza Cairo , Evans Emily , Goodwin Zachary , Jakubus Jill L. , Kelm Julia , Mekled Iman , Monahan Janessa , Oh Esther J. , Oliphant Bryant W. , Hemmila Mark R.
Published: October 2023

Background

Despite the growing awareness of the negative financial impact of traumatic injury on patients' lives, the association between financial toxicity and long-term health-related quality of life (hrQoL) among trauma survivors remains poorly understood.

Methods

Patients from nine trauma centers participating in a state-wide trauma quality collaborative had responses from longitudinal survey data linked to inpatient trauma registry data. Financial toxicity was defined based on patient-reported survey responses regarding medical debt, work or income loss, non-medical financial strain, and forgone care due to costs. A financial toxicity score ranging from 0 to 4 was calculated. HrQoL was assessed using the EuroQol 5 Domain (EQ-5D) tool. Multivariable regression models evaluated the association between financial toxicity and hrQoL outcomes while adjusting for patient demographics, injury severity and inpatient treatment intensity, and health systems variables.

Results

Among the 403 patients providing 510 completed surveys, rates of individual financial toxicity elements ranged from 21% to 46%, with 65% of patients experiencing at least one element of financial toxicity. Patients with any financial toxicity had worse summary measures of hrQoL and higher rates of problems in all five EQ-5D domains (p < 0.05 for all). Younger age, lower household income, lack of insurance, more comorbidities, discharge to a facility, and air ambulance transportation were independently associated with higher odds of financial toxicity (p < 0.05 for all). Injury traits and inpatient treatment intensity were not independently associated with financial toxicity.

Conclusion

A majority of trauma survivors in this study experienced some level of financial toxicity, which was independently associated with worse risk-adjusted health outcomes across all hrQoL measures. Risk factors for financial toxicity are not related to injury severity or treatment intensity, but rather to sociodemographic variables and measures of pre- and post-hospital healthcare resource utilization. Targeted interventions and policies are needed to address financial toxicity and ensure optimal recovery for trauma survivors.

Study Type/Level of Evidence

Observational Cohort Study / Level III
Cognitive Intra-individual Variability in the Laboratory Is Associated With Greater Executive Dysfunction in the Daily Lives of Older Adults With HIV
Authors: Ridgely Natalie C. , Woods Steven Paul , Webber Troy A. , Mustafa Andrea I. , Evans Darrian
Published: October 2023

Background:

Executive dysfunction, which is common among persons with HIV (PWH), can have an adverse impact on health behaviors and quality of life. Intra-individual variability (IIV) is a measure of within-person variability across cognitive tests that is higher in PWH and is thought to reflect cognitive dyscontrol.

Objective:

To assess whether cognitive IIV in the laboratory is associated with self-reported executive dysfunction in daily life among older PWH.

Method:

Participants included 71 PWH aged ≥50 years who completed six subtests from the Cogstate battery and two subscales from the Frontal Systems Behavior Scale (FrSBe; self-report version). Cognitive IIV was calculated from the Cogstate as the coefficient of variation derived from age-adjusted normative T scores.

Results:

Cognitive IIV as measured by the Cogstate showed a significant, positive, medium-sized association with current FrSBe ratings of executive dysfunction but not disinhibition.

Conclusion:

Higher cognitive IIV in the laboratory as measured by the Cogstate may be related to the expression of HIV-associated symptoms of executive dysfunction in daily life for older PWH.
Analysis of Conflicts of Interest in Studies Related to Robotics in Gastrointestinal and Abdominal Wall Surgery
Authors: Jafar Uzair , Usama Muhammad , Hase Niklas E , Yaseen Haris , Nayyar Apoorve , Rabinowitz Judy B , Aziz Hassan
Published: October 2023

BACKGROUND:

Industry payments to physicians represent a potential conflict of interest (COI) and can influence the study conclusions. This study aimed to evaluate the accuracy of the COIs reported in major surgical journals.

STUDY DESIGN:

Studies with at least one American author published between 2016 and 2021 that discussed observational and intervention studies assessing robotic surgery were included in the analysis. The Centers for Medicare & Medicaid Services’ Open Payments database was used to collect the industry payments. A COI is defined as receiving funding from a robotics company while publishing research directly related to the company’s products. A COI statement was defined as disclosed (or accurate) if the disclosure statement for the study in question acknowledged funding from the robotics companies. A COI was defined as undisclosed (or inaccurate) if the disclosure statement for the study in question did not acknowledge funding from the robotics companies.

RESULTS:

A total of 314 studies and 1978 authors were analyzed. Only 13.6% of the studies had accurate COI statements, whereas the majority (86.4%) had inaccurate COI disclosures. Additionally, 48.9% of the authors who received funding of $10,000 to $100,000 failed to report this amount in their disclosures, and 18% of the authors who received funding of $100,000 or more did not report it in their disclosures.

CONCLUSIONS:

There was a significant discordance between the self-reported COI in gastrointestinal and abdominal wall surgeries. This study calls for continued efforts to improve the definitions of what constitutes a relevant COI and encourages a standardized reporting process. It is imperative for investigators to make accurate disclosure statements.
Finding the Right Balance: Partial REBOA in a Swine Model of Uncontrolled Vascular Injury
Authors: Ho Jessie W , Dawood Zaiba Shafik , Nguyen Jessica , Diaz-Perez Dariel A , Taylor Meredith E , Chtraklin Kiril , Jin Guang , Liu Baoling , Ober Rebecca A , Alam Hasan B
Published: October 2023

BACKGROUND:

We have previously shown that partial REBOA (pREBOA) deployment in the thoracic aorta is safe for 2 to 4 hours, but it is unclear whether the distal blood flow after partial aortic occlusion would lead to ongoing hemorrhage. The objective of this study was to evaluate the hemostatic efficacy of pREBOA in a model of uncontrolled vascular injury.

STUDY DESIGN:

Female Yorkshire swine (n = 10, 40 to 45 kg) were anesthetized and instrumented. A through-and-through injury was created in the common iliac artery. The animals were randomly assigned to: (1) pREBOA-PRO deployment after 3 minutes and (2) control. Both groups were given normal saline resuscitation for hypotension. The pREBOA was adjusted to partial occlusion (distal mean arterial pressure of 30 mmHg), and then left without titration for 2 hours. Then, fresh frozen plasma was transfused and the vessel repaired. The balloon was deflated and the animals were monitored for 2 hours. In the critical care period, 2 L of normal saline was infused, norepinephrine was given for mean arterial pressure ≤55, and electrolytes and acidosis were corrected. Organs were examined for gross and histologic evidence of ischemic injuries. The primary endpoint was post-inflation blood loss.

RESULTS:

All the pREBOA animals survived until the end, whereas control animals had a mean survival time of 38.2 minutes (p < 0.05). The pREBOA group showed significantly less bleeding after balloon deployment (93.8 vs 1,980.0 mL, p < 0.05), and had appropriate lactate clearance, with minimal histologic distal organ ischemia.

CONCLUSIONS:

Partial aortic occlusion with the newly designed balloon can achieve the desired balance between effective hemorrhage control and adequate distal flow, without a need for ongoing balloon titration.
Clinical Utility of Melanoma Sentinel Lymph Node Biopsy Nomograms
Authors: Drebin Harrison M , Hosein Sharif , Kurtansky Nicholas R , Nadelmann Emily , Moy Andrea P , Ariyan Charlotte E , Bello Danielle M , Brady Mary S , Coit Daniel G , Marchetti Michael A , Bartlett Edmund K
Published: October 2023

BACKGROUND:

For patients with melanoma, the decision to perform sentinel lymph node biopsy (SLNB) is based on the estimated risk of lymph node metastasis. We assessed 3 melanoma SLNB risk-prediction models’ statistical performance and their ability to improve clinical decision making (clinical utility) on a cohort of melanoma SLNB cases.

STUDY DESIGN:

Melanoma patients undergoing SLNB at a single center from 2003 to 2021 were identified. The predicted probabilities of sentinel lymph node positivity using the Melanoma Institute of Australia, Memorial Sloan Kettering Cancer Center (MSK), and Friedman nomograms were calculated. Receiver operating characteristic and calibration curves were generated. Clinical utility was assessed via decision curve analysis, calculating the net SLNBs that could have been avoided had a given model guided selection at different risk thresholds.

RESULTS:

Of 2,464 melanoma cases that underwent SLNB, 567 (23.0%) had a positive sentinel lymph node. The areas under the receiver operating characteristic curves for the Melanoma Institute of Australia, MSK, and Friedman models were 0.726 (95% CI, 0.702 to 0.750), 0.720 (95% CI, 0.697 to 0.744), and 0.721 (95% CI, 0.699 to 0.744), respectively. For all models, calibration was best at predicted positivity rates below 30%. The MSK model underpredicted risk. At a 10% risk threshold, only the Friedman model would correctly avoid a net of 6.2 SLNBs per 100 patients. The other models did not reduce net avoidable SLNBs at risk thresholds of ≤10%.

CONCLUSIONS:

The tested nomograms had comparable performance in our cohort. The only model that achieved clinical utility at risk thresholds of ≤10% was the Friedman model.
Parallel on-chip micropipettes enabling quantitative multiplexed characterization of vesicle mechanics and cell aggregates rheology
Authors: Landiech Sylvain , Elias Marianne , Lapèze Pierre , Ajiyel Hajar , Plancke Marine , Laborde Adrian , Mesnilgrente Fabien , Bourrier David , Berti Debora , Montis Costanza , Mazenq Laurent , Baldo Jérémy , Roux Clément , Delarue Morgan , Joseph Pierre
Published: October 2023

Micropipette aspiration (MPA) is one of the gold standards to quantify biological samples’ mechanical properties, which are crucial from the cell membrane scale to the multicellular tissue. However, relying on the manipulation of individual home-made glass pipettes, MPA suffers from low throughput and difficult automation. Here, we introduce the sliding insert micropipette aspiration (SIMPA) method, that permits parallelization and automation, thanks to the insertion of tubular pipettes, obtained by photolithography, within microfluidic channels. We show its application both at the lipid bilayer level, by probing vesicles to measure membrane bending and stretching moduli, and at the tissue level by quantifying the viscoelasticity of 3D cell aggregates. This approach opens the way to high-throughput, quantitative mechanical testing of many types of biological samples, from vesicles and individual cells to cell aggregates and explants, under dynamic physico-chemical stimuli.
Gene flow throughout the evolutionary history of a polymorphic and generalist clownfish
Authors: Schmid Sarah , Salvy Marianne Bachmann , Jimenez Alberto Garcia , Bertrand Joris A. M. , Cortesi Fabio , Heim Sara , Huyghe Filip , Litsios Glenn , Marcionetti Anna , O’Donnell James , Riginos Cynthia , Tettamanti Valerio , Salamin Nicolas
Published: October 2023

Even seemingly homogeneous on the surface, the oceans display high environmental heterogeneity across space and time. Indeed, different soft barriers structure the marine environment, which offers an appealing opportunity to study various evolutionary processes such as population differentiation and speciation. Here, we focus onAmphiprion clarkii(Actinopterygii; Perciformes), the most widespread of clownfishes that exhibits the highest colour polymorphism. Clownfishes can only disperse during a short pelagic larval phase before their sessile adult lifestyle, which might limit connectivity among populations, thus facilitating speciation events. Consequently, the taxonomic status ofA. clarkiihas been under debate. We used whole-genome resequencing data of 67A. clarkiispecimens spread across the Indian and Pacific Oceans to characterise the species’ population structure, demographic history, and colour polymorphism. We found thatA. clarkiispread from the Indo-Pacific Ocean to the Pacific and Indian Oceans following a stepping-stone dispersal and that gene flow was pervasive throughout its demographic history. Moreover, edge populations exhibited more similar colouration patterns compared to central populations. However, we demonstrate that colour polymorphism is not associated with population structure, thus, colour phenotype is unreliable in assessing the taxonomic status ofA. clarkii. Our study further highlights the power of whole-genome comparative studies to determine the taxonomy of geographically wide-ranging and phenotypically diverse species, supporting the status ofA. clarkiias a single species.
Antidiabetic Drugs May Prevent Kidney Damage
Authors: Vattimo Maria de Fatima Fernandes , Silva Eloiza Oliveira , Ventura Sara , Lima Camila , Garcia Jessica , Maia Alessandra Oliveira , Gusmão Juliana Veloso , Vieira Guilherme Henrique Ferreira , Victoria Carla Djamila de Pina
Published: October 2023

Introduction

Sodium-glucose cotransporter 2 inhibitors (SGLT2i) are a class of drugs that act as glucose reducers in patients with type 2 diabetes mellitus. Recent meta-analyses have shown that SGLT2i also prevent acute kidney injury (AKI) in diabetic patients. The aim of this study was to investigate the protective effect of canagliflozin an SGLT2i on AKI due to ischemia and reperfusion (I/R) in non-diabetic rats.

Methods

Male Wistar rats weighing 250-300 g were divided into four groups: Control; SHAM (rats submitted to surgical simulation of renal ischemia); I/R: rats submitted to renal ischemia (bilateral clamping of the renal hilum for 30 minutes); CANA+I/R: I/R rats that received canagliflozin (30mg/kg, oral, gavage; 5 days before I/R). Renal function parameters were evaluated (serum creatinine [CrS], inulin clearance [Clin]; renal hemodynamics mean arterial pressure [MAP], renal blood flow [RBF], renal vascular resistance [RVR]); oxidative profile (urinary peroxides - FOX, lipid peroxidation - TBARS, urinary nitrate- NO) and thiols in renal tissue and expression of nuclear factor-erythroid 2 related factor 2 [Nrf2] protein.

Results

The I/R group showed an increase in CrS and a reduction in inulin clearance, while the CANA+I/R group showed a reduction in serum creatinine and an increase in inulin clearance compared to the I/R group. In addition, the CANA+I/R group showed a decrease in oxidative metabolites (FOX and TBARS) and an increase in Nrf2 compared to the I/R group.

Conclusion

Canagliflozin treatment prevented the reduction in renal function induced by ischemia and reperfusion. In addition, there was a reduction in oxidative activity due to a decrease in oxidative metabolites and urinary peroxides and an increase in renal tissue thiols and Nrf-2, which is responsible for transcribing antioxidant activity. Therefore, the current study confirmed a relevant renoprotective effect of canagliflozin in the presence of renal ischemia.
Closed-Loop Estimation of Neurostimulation Strength-Duration Curve Using Fisher Information Optimization and Comparison With Uniform and Random Methods
Authors: Alavi Seyed Mohammad Mahdi
Published: October 2023

Background

Strength-duration (SD) curve, rheobase and chronaxie parameters provide insights about the interdependence between stimulus strength and stimulus duration (or pulse width), and the neural activation dynamics such as the membrane time constant, which are useful for diagnostics and therapeutic applications. The existing SD curve estimation methods are based on open-loop uniform and/or random selection of the pulse widths.

Objective

To develop a method for closed-loop estimation of the SD curve.

Method

In the proposed method, after the selection of each pulse width through Fisher information matrix (FIM) optimization, the corresponding motor threshold (MT) is computed, the SD curve estimation is updated, and the process continues until satisfaction of a stopping rule based on the successive convergence of the SD curve parameters. The results are compared with various uniform methods where pulse widths are chosen in ascending, descending and random orders, and with methods with two and all non-uniform random pulse widths.

Results

160 simulation cases were run. The FIM method satisfied the stopping rule in 144 runs, and estimated the rheobase (chronaxie in parenthesis) with an average absolute relative error (ARE) of 1.73% (2.46%), with an average of 82 samples. At this point, methods with two and all random pulse widths, and uniform methods with descending, ascending and random orders led to 5.66% (20.27%), 2.15% (4.51%), 8.57% (54.96%), 3.52% (5.45%), and 2.19% (4.40%) AREs, which are greater than that achieved through the FIM method. In all 160 runs, The FIM method has chosen the minimum and maximum pulse widths as the optimal pulse widths.

Conclusions

The SD curve is identifiable by acquiring the SD data from the minimum and maximum pulse widths achieved through the FIM optimization. The SD data at random or uniform pulse widths from only the vertical area or lower plateau of the curve might not result in satisfactory estimation.

Significance

This paper provides insights about pulse widths selection in closed-loop and open-loop SD curve estimation methods.
A Markovian dynamics forC. elegansbehavior across scales
Authors: Costa Antonio C. , Ahamed Tosif , Jordan David , Stephens Greg J.
Published: October 2023

How do we capture the breadth of behavior in animal movement, from rapid body twitches to aging? Using high-resolution videos of the nematode wormC. elegans, we show that a single dynamics connects posture-scale fluctuations with trajectory diffusion, and longer-lived behavioral states. We take short posture sequences as an instantaneous behavioral measure, fixing the sequence length for maximal prediction. Within the space of posture sequences we construct a fine-scale, maximum entropy partition so that transitions among microstates define a high-fidelity Markov model, which we also use as a means of principled coarse-graining. We translate these dynamics into movement using resistive force theory, capturing the statistical properties of foraging trajectories. Predictive across scales, we leverage the longest-lived eigenvectors of the inferred Markov chain to perform a top-down subdivision of the worm’s foraging behavior, revealing both “runs-and-pirouettes” as well as previously uncharacterized finer-scale behaviors. We use our model to investigate the relevance of these fine-scale behaviors for foraging success, recovering a trade-off between local and global search strategies.

SIGNIFICANCE STATEMENT

Complex phenotypes, such as an animal’s behavior, generally depend on an overwhelming number of processes that span a vast range of scales. While there is no reason that behavioral dynamics permit simple models, by subsuming inherent nonlinearities and memory into maximally-predictive microstates, we find one forC. elegansforaging. The resulting “Markov worm” is effectively indistinguishable from real worm motion across a range of timescales, and we can decompose our model dynamics both to recover and discover behavioral states. Employing a simple form of substrate interactions, we connect postures to trajectories, illuminating how worms explore the environment. In more complex organisms, our approach can also link behaviors across time, from rapid muscular control to neuromodulation.
Developmentally dynamic changes in DNA methylation in the human pancreas
Authors: MacCalman Ailsa , De Franco Elisa , Franklin Alice , Flaxman Christine S. , Richardson Sarah J. , Murrall Kathryn , Burrage Joe ,   Barts Pancreas Tissue Bank (BPTB), Walker Emma M , Morgan Noel G. , Hattersley Andrew T. , Dempster Emma L. , Hannon Eilis J. , Jeffries Aaron R. , Owens Nick D. L. , Mill Jonathan
Published: October 2023

Development of the human pancreas requires the precise temporal control of gene expression via epigenetic mechanisms and the binding of key transcription factors. We quantified genome-wide patterns of DNA methylation in human fetal pancreatic samples from donors aged 6 to 21 post-conception weeks. We found dramatic changes in DNA methylation across pancreas development, with >21% of sites characterized as developmental differentially methylated positions (dDMPs) including many annotated to genes associated with monogenic diabetes. An analysis of DNA methylation in postnatal pancreas tissue showed that the dramatic temporal changes in DNA methylation occurring in the developing pancreas are largely limited to the prenatal period. Significant differences in DNA methylation were observed between males and females at a number of autosomal sites, with a small proportion of sites showing sex-specific DNA methylation trajectories across pancreas development. Pancreas dDMPs were not distributed equally across the genome, and were depleted in regulatory domains characterized by open chromatin and the binding of known pancreatic development transcription factors. Finally, we compared our pancreas dDMPs to previous findings from the human brain, identifying evidence for tissue-specific developmental changes in DNA methylation. To our knowledge, this represents the most extensive exploration of DNA methylation patterns during human fetal pancreas development, confirming the prenatal period as a time of major epigenomic plasticity.
Unveiling the evolutionary history of lingonberry (Vaccinium vitis-idaeaL.) through genome sequencing and assembly of European and North American subspecies
Authors: Hirabayashi Kaede , Debnath Samir C. , Owens Gregory L.
Published: October 2023

Lingonberry (Vaccinium vitis-idaeaL.) produces tiny red berries that are tart and nutty in flavour. It grows widely in the circumpolar region, including Scandinavia, northern parts of Eurasia, Alaska, and Canada. Although cultivation is currently limited, the plant has a long history of cultural use among indigenous communities. Given its potential as a food source, genomic resources for lingonberry are significantly lacking. To advance genomic knowledge, the genomes for two subspecies of lingonberry (V. vitis-idaeassp.minusand ssp.vitis-idaeavar. ‘Red Candy’) were sequenced andde novoassembled into contig-level assemblies. The assemblies were scaffolded using the bilberry genome (V. myrtillus) to generate chromosome-anchored reference genome consisting of 12 chromosomes each with total length 548.07 Mbp (contig N50 = 1.17 Mbp, BUSCO (C%) = 96.5%) for ssp.vitis-idaea, and 518.70 Mbp (contig N50 = 1.40 Mbp, BUSCO (C%) = 96.9%) for ssp.minus. RNA sequencing based gene annotation identified 27,243 genes on the ssp.vitis-idaeaassembly, and transposable element detection methods found that 45.82% of the genome was repeats. Phylogenetic analysis confirmed that lingonberry is most closely related to bilberry and is more closely related to blueberries than cranberries. Estimates of past effective population size suggested a continuous decline over the past 1–3 MYA, possibly due to the impacts of repeated glacial cycles during Pleistocene leading to frequent population fragmentation. The genomic resource created in this study can be used to identify industry relevant genes (e.g., flavonoid genes), infer phylogeny, and call sequence-level variants (e.g., SNPs) in future research.
Bisphenol S moderately decreases the expression of syncytiotrophoblast marker genes and induces apoptosis in human trophoblast lineages
Authors: Adu-Gyamfi Enoch Appiah , Salamah Joudi , Cheeran Elisha Ann , Lee Bum-Kyu
Published: October 2023

Bisphenol S (BPS) is currently used in the manufacturing of several household equipment such as water pipes and food containers. Hence, its entrance into the human body is almost inevitable. The presence of BPS in body fluids has been reported. However, its potential toxicity, especially on human placenta development and pregnancy progression, has not been explored. In this study, we assessed the impacts of BPS on self-renewal and differentiation potentials of placental stem cells, also known as trophoblast stem cells (TSCs), by exposing them to three different BPS concentrations during both self-renewal and differentiation of TSCs into syncytiotrophoblast (ST), extravillous trophoblast (EVT), and trophoblast organoids. Interestingly, BPS treatment did not affect the stemness, cell cycle and proliferation of the TSCs but it induced apoptosis in each trophoblast lineage. BPS altered the expression of several fusion-related genes. However, this alteration did not translate into significant morphological defects in the STs and organoids. Moreover, BPS did not impair the differentiation of TSCs into EVTs. These findings suggest that the presence of BPS at the feto-maternal interface may exaggerate trophoblast apoptosis and moderately inhibit the trophoblast fusion pathway to affect placenta development and pregnancy. Our study offers valuable insights into the potential toxicity of BPS on human placenta development, emphasizing the need for epidemiological assessment of the relationship between maternal serum levels of BPS and pregnancy complications.
Dissecting signaling regulators driving AXL-mediated bypass resistance and associated phenotypes by phosphosite perturbations
Authors: Creixell Marc , Taylor Scott D. , Gerritsen Jacqueline , Bae Song Yi , Jiang Mingxuan , Augustin Teresa , Loui Michelle , Boixo Carmen , Creixell Pau , White Forest M , Meyer Aaron S
Published: October 2023

Receptor tyrosine kinase (RTK)-targeted therapies are often effective but invariably limited by drug resistance. A major mechanism of acquired resistance involves “bypass” switching to alternative pathways driven by non-targeted RTKs that restore proliferation. One such RTK is AXL whose overexpression, frequently observed in bypass resistant tumors, drives both cell survival and associated malignant phenotypes such as epithelial-to-mesenchymal (EMT) transition and migration. However, the signaling molecules and pathways eliciting these responses have remained elusive. To explore these coordinated effects, we generated a panel of mutant lung adenocarcinoma PC9 cell lines in which each AXL intracellular tyrosine residue was mutated to phenylalanine. By integrating measurements of phosphorylation signaling and other phenotypic changes associated with resistance through multivariate modeling, we mapped signaling perturbations to specific resistant phenotypes. Our results suggest that AXL signaling can be summarized into two clusters associated with progressive disease and poor clinical outcomes in lung cancer patients. These clusters displayed favorable Abl1 and SFK motifs and their phosphorylation was consistently decreased by dasatinib. High-throughput kinase specificity profiling showed that AXL likely activates the SFK cluster through FAK1 which is known to complex with Src. Moreover, the SFK cluster overlapped with a previously established focal adhesion kinase (FAK1) signature conferring EMT-mediated erlotinib resistance in lung cancer cells. Finally, we show that downstream of this kinase signaling, AXL and YAP form a positive feedback loop that sustains drug tolerant persister cells. Altogether, this work demonstrates an approach for dissecting signaling regulators by which AXL drives erlotinib resistance-associated phenotypic changes.

One-sentence summary

A systems biology approach elucidates the signaling pathways driving AXL-mediated erlotinib resistance in lung cancer.
Low-cost camera-based estrous tracking enables transgenesis inPeromyscus leucopus, the primary reservoir for Lyme disease
Authors: Buchthal Joanna , Chory Emma J. , Hill Zachary , Dennison Christy , Tu Boqiang , Wierenga Rick P. , Çevrim Çağrı , Golas Stefan , Telford Sam R. , McKinley Kara L. , Jaenisch Rudolf , Markoulaki Styliani , Esvelt Kevin M.
Published: October 2023

CRISPR/Cas9 technology has revolutionized the production of animal models by reducing experimental timelines, slashing costs and streamlining gene editing, leading to a rapid expansion in the number of unique models for the study of human disease and gene function. However, most non-model animals, many of which are important in cancer and aging research, remain recalcitrant to genome engineering due to our limited understanding of their reproductive biology. Many wild rodents that transmit human diseases remain particularly challenging to engineer due to low pregnancy rates, the lack of external copulatory plugs, and susceptibility to premature termination of pregnancy. Here, we present low-cost activity-based estrous tracking for the efficient generation of timed pregnant and pseudopregnant white-footed mice and extend this tracking method to both lab mice and hamsters. Leveraging this technology, we demonstrate the generation of engineeredPeromyscus leucopus, the primary reservoir for Lyme disease-causing bacteria and a putative model organism for studies of aging. These tools have broad implications for biomedical research and ecological engineering.

Abstract Figure
Preventing NK cell activation in the damaged liver induced by cabozantinib/PD-1 blockade increases survival in hepatocellular carcinoma models
Authors: Morita Satoru , Kikuchi Hiroto , Birch Grace , Matsui Aya , Morita Atsuyo , Kobayashi Tatsuya , Ruan Zhiping , Huang Peigen , Hernandez Alexei , Coyne Erin M. , Shin Sarah M. , Yarchoan Mark , Mino-Kenudson Mari , Romee Rizwan , Ho Won Jin , Duda Dan G.
Published: October 2023

The addition of anti-VEGF antibody treatment to immune checkpoint blockade (ICB) has increased the efficacy of immunotherapy in advanced hepatocellular carcinoma (HCC). Despite an initial promise, adding multitargeted kinase inhibitors of VEGFR with ICB has failed to increase survival in HCC. To reveal the mechanisms underlying treatment failure, we studied the effects of cabozantinib/ICB using orthotopic murine HCC models with or without liver damage. We monitored tumor growth and liver function, recorded survival outcomes, and performed immune profiling studies for intra-tumoral and surrounding liver. Cabozantinib/ICB treatment led to tumor regression and significantly improved survival in mice with normal livers. However, consistent with the clinical findings, combination therapy failed to show survival benefits despite similar tumor control when tested in the same models but in mice with liver fibrosis. Moreover, preclinical and clinical data converged, showing that activating immune responses by cabozantinib/ICB treatment induced hepatoxicity. Immune profiling revealed that combination therapy effectively reprogrammed the tumor immune microenvironment and increased NK cell infiltration and activation in the damaged liver tissue. Surprisingly, systemic depletion of NK reduced hepatotoxicity elicited by the combination therapy without compromising its anti-cancer effect, and significantly enhanced the survival benefit even in mice with HCC and underlying liver fibrosis. These findings demonstrate that preventing NK activation allowed for maintaining a favorable therapeutic ratio when combining ICB with cabozantinib in advanced HCC models.
Genome wide association study of Arabidopsis seed mucilage layers at a regional scale
Authors: Viudes Sébastien , Zamar Rémy , Burlat Vincent , Roux Fabrice , Dunand Christophe
Published: October 2023

The myxospermous speciesArabidopsis thalianaextrudes a polysaccharidic mucilage from the seed coat epidermis during imbibition. The whole seed mucilage can be divided into a seed-adherent layer and a fully soluble layer, both layers presenting natural genetic variations. The adherent mucilage is variable in size and composition, while the soluble mucilage is variable in composition and physical properties. Studies reporting both the genetic architecture and the putative selective agents acting on this natural genetic variation are scarce. In this study, we set up a Genome Wide Association study (GWAS) based on 424 natural accessions collected from 166 natural populations ofA. thalianalocated south-west of France and previously characterized for a very important number of abiotic and biotic factors. We identified an extensive genetic variation for both mucilage layers. The adherent mucilage was mainly related to precipitation and temperature whereas the non-adherent mucilage was unrelated to any environmental factors. By combining a hierarchical Bayesian model with a local score approach, we identified 55 and 28 candidate genes, corresponding to 26 and 10 QTLs for the adherent and non-adherent mucilages, respectively. Putative or characterized function and expression data available in the literature were used to filter the candidate genes. Only one gene among our set of candidate genes was already described as a seed mucilage actor, leaving a large set of new candidates putatively implicated inseed mucilage synthesis or release. The present study lay out foundation to understand the influence of regional ecological factors acting on seed mucilage inA. thaliana.
Inhibiting the GPI Transamidase Subunit GPAA1 Abolishes CD24 Surface Localization and Enhances Macrophage-Mediated Phagocytosis of Ovarian Cancer Cells
Authors: Mishra Alok K. , Ye Tianyi , Banday Shahid , Thakare Ritesh P. , Su Chinh Tran-To , Pham Ngoc N. H. , Ali Amjad , Kulshreshtha Ankur , Chowdhury Shreya Roy , Simone Tessa M. , Hu Kai , Zhu Lihua Julie , Eisenhaber Birgit , Deibler Sara K. , Simin Karl , Thompson Paul R. , Eisenhaber Frank , Malonia Sunil K. , Green Michael R.
Published: October 2023

The CD24-Siglec10 signaling axis is an immune checkpoint pathway that shields ovarian cancer cells from phagocytosis by tumor-associated macrophages (TAMs), making it an appealing immunotherapeutic target. Here, we investigate factors influencing CD24 cell surface expression and assess their suitability as drug targets. Using a CRISPR-based knockout screen, we identify GPAA1 (glycosylphosphatidylinositol anchor attachment-1) as a positive regulator of CD24 cell surface expression. GPAA1 is a crucial component of the multi-subunit GPI transamidase complex, which facilitates the attachment of GPI lipid anchor to the C-terminus of CD24, enabling its surface localization. Reducing the activity of GPAA1 in ovarian cancer cells, either by genetic ablation or targeting with an aminopeptidase inhibitor bestatin, disrupts GPI attachment to CD24. This disruption impairs CD24 cell surface localization, enhances phagocytosis by TAMs, and suppresses tumor growth in mice. Our study highlights the potential of GPAA1 targeting as a therapeutic approach for CD24-positive ovarian cancers.
Multi-Omics Insights into Grapevine Ecodormancy to Budburst Transition: Interplay of Gene Expression, miRNA Regulation, and DNA Methylation
Authors: Shinde Harshraj , Raihan Tajbir , Anand Lakshay , Perry Sharyn E. , Geneve Robert L. , Rodriguez Lopez Carlos M.
Published: October 2023

In grapevine, the transition from a dormant bud to budburst is a critical developmental process related to vegetative and reproductive growth. We generated a time series analysis (five sampling time points) and used transcriptome, small RNA, and whole-genome bisulfite sequencing to characterize this transition. Ecodormant buds took an average of 17 days to budburst. Transcriptome analysis identified a total of 7002 differentially expressed genes across all sampling times and revealed that the brassinosteroid metabolism and the linoleic acid metabolism pathways are upregulated and downregulated respectively across all time points. Gene expression cluster analysis identified the activation of the photosynthesis pathway and photosynthesis related genes during this transition. miRNA expression analysis identified a steady increase in expression of two miRNAs, miR159a and miR159b during the transition from dormancy to budburst. Our analysis suggests that these two miRNAs promote budburst by repressing the expression of auxin responsive genes. Finally, a continued increase in CG methylation levels was observed during the dormancy to budburst transition. Differential methylation analysis, considering dormant buds as the control stage, yielded 6354 differentially methylated regions across the genome. Two glucosidase genes exhibited increases in promoter methylation and a corresponding decrease in gene expression in our analysis. This study provides a multi-omics view of grapevine bud transition from dormancy to bud burst and unveils the interacting genetic and epigenetic networks regulating this process.
Endovascular Thrombectomy versus Intravenous Alteplase for Distal Vessel Occlusions: A Propensity Score-Matched Analysis
Authors: Yoshie Tomohide , Ueda Toshihiro , Hasegawa Yasuhiro , Takeuchi Masataka , Morimoto Masafumi , Tsuboi Yoshifumi , Yamamoto Ryoo , Kaku Shogo , Junichi Ayabe , Akiyama Takekazu , Yamamoto Daisuke , Mori Kentaro , Kagami Hiroshi , Ito Hidemichi , Onodera Hidetaka , Kaga Yasuyuki , Ohtsubo Haruki , Tatsuno Kentaro , Usuki Noriko , Takaishi Satoshi , Yamano Yoshihisa
Published: October 2023

Abstracts

Background

The benefits of endovascular thrombectomy (EVT) for distal medium vessel occlusions (DMVOs) are not well established. This study aimed to evaluate whether EVT is superior to intravenous tissue plasminogen activator (IV tPA) alone in DMVOs.

Methods

This study analyzed data from the K-NET Registry, a prospective, multicenter, observational registry of acute ischemic stroke patients treated with EVT or IV tPA. The study evaluated patients with acute DMVOs who were treated with EVT and/or IV tPA. DMVOs was defined as occlusions in M2-M3 segment of the middle cerebral artery, anterior cerebral artery, or posterior cerebral artery. The analysis included primary DMVOs and excluded secondary DMVOs, such as distal embolism after recanalization of proximal vessel occlusion. Propensity score-matched analysis was conducted to compare the outcomes between EVT and IV tPA alone. A good outcome was defined as a modified Rankin Scale score of 0-2 or no worsening at 90 days. An excellent outcome was defined as an mRS score of 0-1.

Results

The study included 1148 patients with DMVOs, of whom 816 were treated with EVT and 332 were IV tPA alone. Before propensity score matching, the incidence of good and excellent outcomes was significantly lower in EVT group (good outcomes: EVT 50.3% vs. IV tPA 68.0%, p<0.01; excellent outcomes: 39.8% vs. 59.8%, p<0.001). After propensity score matching, there were no significant differences between EVT and IV tPA groups in good outcomes (EVT 57.8% vs. IV tPA 61.3%, p=0.51), excellent outcomes (46.6% vs. 55.0%, p=0.17), all cerebral hemorrhage (11.6% vs. 12.7%, p=0.74), and symptomatic hemorrhage (2.9% vs. 0.6%, p=0.13). Subarachnoid hemorrhage was more frequent in EVT group (14.5% vs. IV tPA 0%).

Conclusions

The benefits of EVT for acute DMVOs were similar to IV-tPA alone. Randomized multicenter trials are warranted to establish the superiority of EVT over IV-tPA alone for DMVOs.
New avenues for human blood plasma biomarker discovery via improved in-depth analysis of the low-abundantN-glycoproteome
Authors: Zuniga-Banuelos Frania J. , Hoffmann Marcus , Reichl Udo , Rapp Erdmann
Published: October 2023

To understand implications of protein glycosylation for clinical diagnostic and biopharmaceuticals, innovative glycoproteomic technologies are required. Recently, significant advances were made, particularly toward structure-focusedN-glyco-proteomic analyses. The mass spectrometric analysis of intactN-glycopeptides using stepped collision fragmentation along with glycan oxonium ion profiling now enables to reliably discriminate between differentN-glycan structures. Still, there are weaknesses that currentN-glycoproteomic approaches must overcome: 1) handling of incorrect identifications, 2) identification of rare and modifiedN-glycans, and 3) insufficient glycoproteomic coverage, especially in complex samples. To address these shortcomings, we have developed an innovativeN-glycoproteomic workflow that aims at providing comprehensive site-specific and structuralN-glycoproteomic data on human blood plasma glycoproteins. The workflow features protein depletion plus various fractionation strategies and the use of high-resolution mass spectrometry with stepped collision fragmentation. Furthermore, by including a decision tree procedure established for data validation, we could significantly improve the description of theN-glycan micro-heterogeneity. Our data analysis workflow allows the reliable differentiation of ambiguousN-glycan structures like antenna-versus core-fucosylation plus the modified and rareN-glycans such as sulfated and glucuronidated ones. With this workflow, we were able to advance in the analysis of human blood plasma glycoproteins to concentrations as low as 10 pg/mL. A total of 1,929N-glycopeptides and 942N-glycosites derived from 805 human middle-to low-abundant glycoproteins were identified. Overall, the presented workflow holds great potential to improve our understanding of protein glycosylation and to foster the discovery of blood plasma biomarkers.

Abstract Figure
Unique Binding and Stabilization Mechanisms Employed By and Engineered Into Nanobodies
Authors: Ketaren Natalia E. , Fridy Peter C. , Malashkevich Vladimir , Sanyal Tanmoy , Brillantes Marc , Thompson Mary K. , Oren Deena A. , Bonanno Jeffrey B. , Šali Andrej , Almo Steven C. , Chait Brian T. , Rout Michael P.
Published: October 2023

Nanobodies are single domain antibody variants that bind an antigen with the precision and affinity of a conventional antibody at only a fraction of their size. In solving the crystal structures of our nanobody-GFP complexes and compared with other available structures, we uncover mechanism that enable nanobodies to function so efficiently and effectively as single-domain antibodies. We show that unlike conventional antibodies, a nanobody repertoire maximizes sampling of their antigen surface by binding a single antigen in at least three different orientations which can be predicted by their paratope composition. We also structurally reengineering these nanobodies to improve their antigen affinity, their stability, or both – results which also revealed the strong connection between nanobody stability and affinity. We achieved this by either directly modifying the paratope, or by altering a particular region within their third framework, which is a highly conserved area that we determined plays a role in controlling nanobody stability. Our study suggests that these unique characteristics of nanobodies allow them to interact with antigens as effectively as conventional antibodies, despite their smaller size. This understanding provides methods to facilitate optimizing, humanizing and functionalizing nanobodies, thus paving the way for their utilization in diverse areas such as research, diagnostics, and therapeutic development.

Significance Statement

Nanobodies are a unique type of antibody fragment found in select animals, containing all its antigen binding ability reduced to a single ∼15 kDa protein. There is increasing development of nanobodies for research, diagnostics, and therapeutics, yet how nanobodies function so effectively as single domain antigen binders with the precision and affinity of conventional antibodies is unclear. In this study, we present key observations to help answer this question, where one key finding is the strong relationship between nanobody stability and antigen affinity aided by the identification of a highly conserved region in nanobodies essential for maintaining nanobody stability. This region may have been retained in nanobodies in lieu of stabilizing mechanisms induced by dimerization as seen in conventional antibodies.
Modulating Mesenchymal Stromal Cell Microenvironment Alters Exosome RNA Content and Ligament Healing Capacity
Authors: Chamberlain Connie S. , Prabahar Archana , Kink John A , Mueller Erika , Li Yiyao , Yopp Stephanie , Capitini Christian M. , Hematti Peiman , Murphy William L. , Vanderby Ray , Jiang Peng
Published: October 2023

Although mesenchymal stromal cell (MSC) based therapies hold promise in regenerative medicine, their applications in clinical settings remain challenging due to issues such as immunocompatibility and cell stability. MSC-derived exosomes, small vesicles carrying various bioactive molecules, are a promising cell-free therapy to promote tissue regeneration. However, it remains unknown mainly regarding the ability to customize the content of MSC-derived exosomes, how alterations in the MSC microenvironment influence exosome content, and the effects of such modifications on healing efficiency and mechanical properties in tissue regeneration. In this study, we used anin vitrosystem of human MSC-derived exosomes and anin vivorat ligament injury model to address these questions. We found a context-dependent correlation between exosomal and parent cell RNA content. Under native conditions, the correlation was moderate but heightened with microenvironmental changes.In vivorat ligament injury model showed that MSC-derived exosomes increased ligament max load and stiffness. We also found that changes in the MSCs’ microenvironment significantly influence the mechanical properties driven by exosome treatment. Additionally, a link was identified between altered exosomal microRNA levels and expression changes in microRNA targets in ligaments. These findings elucidate the nuanced interplay between MSCs, their exosomes, and tissue regeneration.

Graphic Abstract