bluuebunny/crossref_metadata_2025 huggingface dataset:
Course Review: Yorkshire Microsurgery Course 2023
Authors: Bollen Edward , Paul Ganesh
Published: July 2023

Microsurgery is an advanced set of techniques that require a high level of skill to be performed safely. Surgical skills courses offer safe environments for practice in such skills and form a fundamental part of surgical training. The Yorkshire Microsurgery Course is a 3-day course at Bradford Royal Infirmary, United Kingdom. Delivered via short lectures followed by supervised practical sessions, the course aims to provide delegates with the essential knowledge and skills required for microsurgery.

We detail an outline and critical evaluation of the February 2023 iteration of the course, with recommendations for improvement.

Overall, we found the course excellent. It provided delegates with a solid grounding in the fundamentals of microsurgery and the opportunity for personalized practice supervised by experts. We would recommend this course to colleagues interested in a career in plastic surgery.
Regional Anesthesia in Upper-Limb Surgery
Authors: McLennan Lachlan , Haines Morgan , Graham David , Sullivan Timothy , Lawson Richard , Sivakumar Brahman
Published: July 2023

Background

Local and regional anesthesia is associated with numerous clinical and institutional advantages relative to general anesthesia. As anesthesiologists and surgeons increasingly integrate local and regional anesthesia into their clinical practice, an understanding of the principles, evolution, and trends underpinning modern anesthetic techniques continues to be relevant.

Methods

A review of the literature in databases Medline, PubMed, and EMBASE identified recent developments, ongoing trends, and historical milestones in upper-limb regional anesthesia.

Results

Advances in regional anesthetic techniques in the last century have led to reduced postoperative pain, improved safety, and improved outcomes in upper-limb surgery. The development of ultrasound-guided techniques, as well as pharmacological advances in local anesthetic drugs and adjuncts, has further advanced the role of regional anesthesia. Wide-awake local anesthesia with no tourniquet has allowed certain procedures to be performed on select patients in outpatient and low-resource settings.

Conclusions

This review provides an overview of local and regional anesthesia in the upper-limb from its historical origins to its contemporary applications in upper-limb surgery, particularly during the COVID-19 pandemic.
Surgical Treatment of Symptomatic End-Neuroma With a New Bioresorbable Copolyester Nerve Capping Device
Authors: Power Dominic , Curtin Catherine , Bellemère Philippe , Nyman Erika , Pajardi Giorgio , Isaacs Jonathan , Levin Lawrence Scott
Published: July 2023

Background

Neuroma-induced neuropathic pain is associated with loss of function and reduced quality of life. No consistently effective standard-of-care treatment has been defined. Neurocap, a bioresorbable nerve capping device, has been designed to isolate the nerve stump from surrounding tissues to reduce development of symptomatic end-neuromas.

Methods

Patients with peripheral symptomatic end-neuromas were included in a prospective, multicenter, single-arm design. Data were collected presurgery up till 24 months postsurgery. Eligible patients with neuromas were identified based on blocks using anesthetic. Intervention included surgical excision and capping of the transected proximal nerve end with the Neurocap. Main outcome measures were pain, function, recurrence of symptomatic neuroma, use of analgesics, and adverse events.

Results

In total, 73 patients with 50 upper-extremity and 23 lower-extremity end-neuromas were enrolled. End-neuromas were predominately located in the digits and lower leg. Statistical power of the study outcomes was preserved by 46 of 73 patients completing 24-month follow-up. The mean VAS-Pain score at baseline was 70.2 ± 17.8 (scale 0–100) and decreased significantly to 31 ± 32.5 (P < 0.001). Function significantly improved over time. The recurrence rate of confirmed symptomatic neuroma was low (2 of 98 capped nerves). Adverse event rate was low and included pain and infection; there were no unexpected device-related adverse events. Most patients reported lower use of nonsteroidal anti-inflammatory drugs, opioids, and antineuropathic medications at last follow-up compared with baseline.

Conclusions

End-neuroma treatment with excision and capping resulted in long-term significant reduction in reported pain, disability, and analgesic medication use. Adverse event rate was low.
Perioperative Factors Aggravating Pharyngocutaneous Fistula After Total Laryngectomy
Authors: Haga Yoshitaka , Yasunaga Yoshichika , Araki Jun , Nakao Junichi , Mori Hiroaki , Nakagawa Masahiro , Mukaigawa Takashi
Published: July 2023

Background

Pharyngocutaneous fistula formation represents a major postoperative complication following total laryngectomy. We aimed to investigate the risk factors for pharyngocutaneous fistula development after total laryngectomy and to identify factors that lead to severe cases of pharyngocutaneous fistula.

Methods

Patients who underwent total laryngectomy between January 2013 and February 2021 were included in the study and were divided into 2 groups: Those with and without pharyngocutaneous fistula. The severity of pharyngocutaneous fistula was graded using the Clavien-Dindo classification.

Results

Patients with pharyngocutaneous fistula experienced longer operative time, greater intraoperative blood loss, greater decrease in perioperative hemoglobin level, and longer postoperative hospitalization. Unlike in lower-severity cases, patients with grade IIIb pharyngocutaneous fistula underwent preoperative radiotherapy or chemoradiotherapy; preoperative treatment was thus a risk factor for higher severity of pharyngocutaneous fistula (odds ratio, 35; P = 0.004).

Conclusion

Salvage laryngectomy was found to be a predictor of severe pharyngocutaneous fistula development. Prolonged operative time, increased intraoperative blood loss, and decreased postoperative hemoglobin level were found to be predictors of postlaryngectomy pharyngocutaneous fistula formation.
Mitochondria Transplantation Mitigates Damage in an In Vitro Model of Renal Tubular Injury and in an Ex Vivo Model of DCD Renal Transplantation
Authors: Rossi Andrea , Asthana Amish , Riganti Chiara , Sedrakyan Sargis , Byers Lori Nicole , Robertson John , Senger Ryan S. , Montali Filippo , Grange Cristina , Dalmasso Alessia , Porporato Paolo E. , Palles Christina , Thornton Matthew E , Da Sacco Stefano , Perin Laura , Ahn Bumsoo , McCully James , Orlando Giuseppe , Bussolati Benedetta
Published: July 2023

Objectives:

To test whether mitochondrial transplantation (MITO) mitigates damage in two models of acute kidney injury (AKI).

Summary Background Data:

MITO is a process where exogenous isolated mitochondria are taken up by cells. As virtually any morbid clinical condition is characterized by mitochondrial distress, MITO may find a role as a treatment modality in numerous clinical scenarios including AKI.

Methods:

For the in vitro experiments, human proximal tubular cells were damaged and then treated with mitochondria or placebo. For the ex vivo experiments, we developed a non-survival ex vivo porcine model mimicking the donation after cardiac death (DCD) renal transplantation scenario. One kidney was treated with mitochondria, while the mate organ received placebo, before being perfused at room temperature for 24 hours. Perfusate samples were collected at different time points and analyzed with Raman spectroscopy. Biopsies taken at baseline and 24 hours were analyzed with standard pathology, immunohistochemistry and RNA sequencing analysis.

Results:

In vitro, cells treated with MITO showed higher proliferative capacity and ATP production, preservation of physiological polarization of the organelles and lower toxicity and reactive oxygen species production. Ex vivo, kidneys treated with MITO shed fewer molecular species, indicating stability. In these kidneys, pathology showed less damage while RNAseq analysis showed modulation of genes and pathways most consistent with mitochondrial biogenesis and energy metabolism and downregulation of genes involved in neutrophil recruitment, including IL1A, CXCL8, and PIK3R1.

Conclusions:

MITO mitigates AKI both in vitro and ex vivo.
Prognostic Value of Chest CT Findings at BOS Diagnosis in Lung Transplant Recipients
Authors: Van Herck Anke , Beeckmans Hanne , Kerckhof Pieterjan , Sacreas Annelore , Bos Saskia , Kaes Janne , Vanstapel Arno , Vanaudenaerde Bart M. , Van Slambrouck Jan , Orlitová Michaela , Jin Xin , Ceulemans Laurens J. , Van Raemdonck Dirk E. , Neyrinck Arne P. , Godinas Laurent , Dupont Lieven J. , Verleden Geert M. , Dubbeldam Adriana , De Wever Walter , Vos Robin
Published: July 2023

Background.

Bronchiolitis obliterans syndrome (BOS) after lung transplantation is characterized by fibrotic small airway remodeling, recognizable on high-resolution computed tomography (HRCT). We studied the prognostic value of key HRCT features at BOS diagnosis after lung transplantation.

Methods.

The presence and severity of bronchiectasis, mucous plugging, peribronchial thickening, parenchymal anomalies, and air trapping, summarized in a total severity score, were assessed using a simplified Brody II scoring system on HRCT at BOS diagnosis, in a cohort of 106 bilateral lung transplant recipients transplanted between January 2004 and January 2016. Obtained scores were subsequently evaluated regarding post-BOS graft survival, spirometric parameters, and preceding airway infections.

Results.

A high total Brody II severity score at BOS diagnosis (P = 0.046) and high subscores for mucous plugging (P = 0.0018), peribronchial thickening (P = 0.0004), or parenchymal involvement (P = 0.0121) are related to worse graft survival. A high total Brody II score was associated with a shorter time to BOS onset (P = 0.0058), lower forced expiratory volume in 1 s (P = 0.0006) forced vital capacity (0.0418), more preceding airway infections (P = 0.004), specifically with Pseudomonas aeruginosa (P = 0.002), and increased airway inflammation (P = 0.032).

Conclusions.

HRCT findings at BOS diagnosis after lung transplantation provide additional information regarding its underlying pathophysiology and for future prognosis of graft survival.
Loss of Endothelial Glycocalyx During Normothermic Machine Perfusion of Porcine Kidneys Irrespective of Pressure and Hematocrit
Authors: Huijink Tobias M. , van ‘t Hof Cor J. , van Furth L. Annick , de Haan Nora A. , Maassen Hanno , Venema Leonie H. , Lammerts Rosa G.M. , van den Heuvel Marius C. , Hillebrands Jan-Luuk , van den Born Jacob , Berger Stefan P. , Leuvenink Henri G.D.
Published: July 2023

Background.

Normothermic machine perfusion (NMP) is a promising modality for marginal donor kidneys. However, little is known about the effects of NMP on causing endothelial glycocalyx (eGC) injury. This study aims to evaluate the effects of NMP on eGC injury in marginal donor kidneys and whether this is affected by perfusion pressures and hematocrits.

Methods.

Porcine slaughterhouse kidneys (n = 6/group) underwent 35 min of warm ischemia. Thereafter, the kidneys were preserved with oxygenated hypothermic machine perfusion for 3 h. Subsequently, 4 h of NMP was applied using pressure-controlled perfusion with an autologous blood-based solution containing either 12%, 24%, or 36% hematocrit. Pressures of 55, 75, and 95 mm Hg were applied in the 24% group. Perfusate, urine, and biopsy samples were collected to determine both injury and functional parameters.

Results.

During NMP, hyaluronan levels in the perfusate increased significantly (P < 0.0001). In addition, the positivity of glyco-stained glycocalyx decreased significantly over time, both in the glomeruli (P = 0.024) and peritubular capillaries (P = 0.003). The number of endothelial cells did not change during NMP (P = 0.157), whereas glomerular endothelial expression of vascular endothelial growth factor receptor-2 decreased significantly (P < 0.001). Microthrombi formation was significantly increased after NMP. The use of different pressures and hematocrits did not affect functional parameters during perfusion.

Conclusions.

NMP is accompanied with eGC and vascular endothelial growth factor receptor-2 loss, without significant loss of endothelial cells. eGC loss was not affected by the different pressures and hematocrits used. It remains unclear whether endothelial injury during NMP has harmful consequences for the transplanted kidney.
The Association of Tacrolimus Formulation on Cerebral Blood Flow and Cognitive Function
Authors: Mahaparn Irisa , Lepping Rebecca J. , Montgomery Robert N. , Mukherjee Rishav , Billinger Sandra A. , Brooks William M. , Gupta Aditi
Published: July 2023

Background.

Calcineurin inhibitors are inherent vasoconstrictors. Cerebral vasoconstriction can reduce cerebral blood flow (CBF), and negatively impact cerebrovascular response (CVR) to exercise, and cognitive function. The once-daily extended-release (LCP) tacrolimus has fewer side effects than the immediate-release (IR) tacrolimus. The role of calcineurin inhibitors on CBF and the impact of specific formulations of tacrolimus on CBF, CVR, and cognitive function are unknown. In this pilot study, we evaluated whether changing from IR tacrolimus to LCP tacrolimus modulates CBF, CVR, or cognitive function in kidney transplant (KT) recipients.

Methods.

We randomized (2:1) 30 stable KT recipients on IR tacrolimus to intervention (switch to LCP tacrolimus) and control (continue IR tacrolimus) arms. We measured CBF, CVR, and cognitive function at baseline and at 12 wk. We used ANCOVA to evaluate changes in outcome variables, with baseline values and study arm as covariates. We used descriptive statistics with mean changes in outcome variables to compare the 2 groups.

Results.

Participants were 51 ± 13 y old. There was no difference in plasma tacrolimus levels at baseline and at 12 wk in the 2 arms. The changes in CBF, resting middle cerebral artery velocity, CVR, and cognitive function were more favorable in the intervention arm than in the control group.

Conclusions.

Changing IR tacrolimus to LCP tacrolimus may improve CBF, cerebrovascular dynamics, and cognitive function in KT recipients. Larger studies are needed to confirm these results.
A Systematic Review and Meta-analysis of Optimized CMV Preemptive Therapy and Antiviral Prophylaxis for CMV Disease Prevention in CMV High-Risk (D+R-) Kidney Transplant Recipients
Authors: Kumar Lakshin , Murray-Krezan Cristina , Singh Nina , Brennan Daniel C. , Rakita Robert M. , Dasgupta Sayan , Fisher Cynthia E. , Limaye Ajit P.
Published: July 2023

Background.

The optimal strategy for cytomegalovirus (CMV) disease prevention in CMV donor/recipient kidney transplant recipients remains uncertain. Conclusions of prior meta-analyses that CMV disease rates with preemptive therapy (PET) and universal prophylaxis (UP) were comparable may have been affected by inclusion of studies lacking key determinants of efficacy of the respective strategies.

Methods.

We conducted a systematic review and meta-analysis of PET with weekly CMV polymerase chain reaction monitoring for ≥3 mo and UP with 6 mo of valganciclovir. PubMed and Embase databases were reviewed from January 1, 2010, to April 1, 2022. Risk of bias was assessed with 3 instruments (Cochrane RoB, Cochrane RoBINS-I, and an instrument for assessing risk in observational studies). The primary outcome was CMV disease incidence by 1-y posttransplant. Secondary outcomes by 1-y were graft loss, acute allograft rejection, and mortality. Results were synthesized using generalized linear mixed model meta-analysis. PET studies were stratified into low-threshold (LT) and high-threshold (HT) PET based on the viral load threshold for initiation of antiviral therapy.

Results.

Twenty-five studies met inclusion criteria (6 PET, 19 UP). CMV disease incidence was significantly higher in HT (0.30 [95% confidence interval (CI), 0.22-0.39]) versus LT PET (0.06 [95% CI, 0.03-0.12]). LT PET was associated with a significantly lower CMV disease incidence (0.06 [95% CI, 0.03-0.12]) versus UP (0.21 [95% CI, 0.17-0.27]). Incidence of graft loss, acute allograft rejection, or mortality was not significantly different between LT PET and UP (P > 0.05 for all comparisons). Receipt of lymphocyte-depleting antibodies was not associated with a significant difference in CMV disease incidence (odds ratio = 1.34 [95% CI, 0.80-2.25]).

Conclusions.

LT PET is associated with a significantly lower incidence of CMV disease compared to UP with similar rates of other clinical outcomes. These findings provide rationale and preliminary data for a randomized superiority trial of optimized LT-PET versus UP in donor seropositive recipient seronegative kidney transplant recipients.
Cross-cultural translation and psychometric validation of the French version of the Fear-Avoidance Components Scale (FACS)
Authors: Duport Arnaud , Bédard Sonia , Raynauld Catherine , Bordeleau Martine , Neblett Randy , Balg Frédéric , Devanne Hervé , Léonard Guillaume
Published: July 2023

Background

The Fear-Avoidance Components Scale (FACS) is a reliable and valid instrument widely used to assess fear-avoidance beliefs related to pain and disability. However, there is a scarcity of validated translations of the FACS in different cultural and linguistic contexts, including the French population. This study aimed to translate and validate the French version of the FACS (FACS-Fr/CF), examining its psychometric properties among French-speaking individuals.

Methods

A cross-cultural translation process – including forward translation, backward translation, expert committee review, and pre-testing – was conducted to develop the FACS-Fr/CF. The translated version was administered to a sample of French-speaking adults (n=55) with musculoskeletal conditions. Internal consistency (including confirmatory analyses of the 2 factors identified in the Serbian version), test-retest reliability and convergent validity were then assessed.

Results

The FACS-Fr/CF demonstrated high global internal consistency (α=0.94, 95% CI: 0.91-0.96) as well as high internal consistency of the 2 factors identified in the Serbian version (α=0.90, 95% CI: 0.86-0.94 and α=0.90, 95% CI: 0.85-0.94, respectively). Test-retest analysis revealed a moderate (close to high) reliability (ICC=0.89; 95% CI: 0.82-0.94 and r=0.89;p<0.005). Convergent validity was supported by significant correlations between the FACS-Fr/CF scores and the Tampa Scale for Kinesiophobia (r=0.82;p< 0.005), the Pain Catastrophizing Scale (r=0.72;p< 0.005) and the Hospital Anxiety and Depression Scale (r=0.66;p< 0.005).

Conclusion

The present study provides evidence for the cross-cultural translation and psychometric validation of the FACS-Fr/CF. The FACS-Fr/CF exhibits a high internal consistency, a moderate (close to high) test-retest reliability, and good construct validity, suggesting its utility in assessing fear-avoidance beliefs in the French-speaking population. This validated tool can enhance the assessment and understanding of fear-avoidance behaviors and facilitate cross-cultural research in pain-related studies.
Higher ultraviolet light exposure is associated with lower mortality: an analysis of data from the UK Biobank cohort study
Authors: Stevenson Andrew C. , Clemens Tom , Pairo-Castineira Erola , Webb David J. , Weller Richard B. , Dibben Chris
Published: July 2023

Objective

To examine to what extent UV exposure is associated with all-cause and cause-specific mortality.

Design

Prospective population-based study.

Setting

UK Biobank.

Participants

376,729 participants with white ancestry and no missing data. Two UV exposures were assessed: sun-seeking behaviour (categorised as less active versus more active) and home latitude.

Main outcome measures

All-cause, cardiovascular disease (CVD), cancer and non-CVD/non-cancer mortality. Risk of residual confounding was examined using three negative control outcomes.

Results

The median follow-up was 12.7 years. Participants with more active sun-seeking behaviour were at a lower risk of all-cause mortality (HR=0.86; 95% confidence interval (CI) 0.80 to 0.93), CVD mortality (HR=0.81; 95% CI 0.68 to 0.95) and cancer mortality (HR=0.86; 95% CI 0.77 to 0.95) compared to participants with less active sun-seeking behaviours, adjusted for demographic, socioeconomic, behavioural and clinical confounders. More active sun seekers had around 50 extra days of survival. Participants whose home latitude was 300km farther south were also at a lower risk of all-cause mortality (HR=0.94; 95% CI 0.92 to 0.96), CVD mortality (HR=0.91; 95% CI 0.86 to 0.95) and cancer mortality (HR=0.93; 95% CI 0.90 to 0.96), adjusted for demographic, socioeconomic, behavioural and clinical confounders. Participants whose home latitude was 300km farther south had around 16 extra days of survival. Sun-seeking behaviour was not associated with two of the three negative controls and home latitude was not associated with any of the negative controls.

Conclusions

Greater behavioural and higher geographically related UV exposures were associated with a lower risk of all-cause, CVD and cancer mortality. This study adds to growing evidence that the benefits of UV exposure may outweigh the risks in low sunlight countries. Tailoring public health advice to both the benefits and hazards of UV exposure may reduce the burden of disease and increase life expectancy in low sunlight countries.
Interpretation of wide confidence intervals in meta-analytic estimates: Is the ‘Absence of Evidence’ ‘Evidence of Absence’?
Authors: Miller Sarah L. , Tuia Jordan , Prasad Vinay
Published: July 2023

Introduction

Recently, a Cochrane review by Jefferson et al. on physical interventions to slow the spread of respiratory viruses concluded that, “Wearing masks in the community probably makes little or no difference to the outcome of laboratory-confirmed influenza/SARS-CoV-2 compared to not wearing masks”, though this finding had a wide confidence interval. Cochrane issued a rare clarifying statement, fueling controversy. We sought to contextualize the findings of the review by Jefferson et al.

Methods

We searched for consecutive reviews by Cochrane published on or before March 9th, 2023. We included studies where a central finding showed an intervention offered no statistically significant benefit, and ascertained the language used by reviewers to describe that result. We compare this to the report by Jefferson et al., and deemed it consistent or inconsistent with the language of their report.

Results

We found between November 21st, 2022, and March 9th, 2023, there were 20 Cochrane reviews that met the inclusion criteria. We found that 95% (n = 19) of the reviews used language that was consistent with Jefferson’s findings, while 5% (n = 1) used language inconsistent with Jefferson’s conclusion, describing the effect of the intervention on the outcome as “unclear”.

Discussion

Most reviews performed by Cochrane conclude that interventions which fail to show statistically significant benefits make “no difference” have “no effect” or do not “increase or decrease” the outcome, and this occurs despite wide confidence intervals. The conclusions by Jefferson et al. are consistent with Cochrane reporting guidelines and clarification from the organization was unjustified.
ReDirection: a numerically robust R-package to characterize every reaction of a user-defined biochemical network with the probable dissociation constant
Authors: Kundu Siddhartha
Published: July 2023

Biochemical networks integrate enzyme-mediated substrate conversions with non-enzymatic complex formation and disassembly to accomplish complex biochemical and physiological function. The multitude of theoretical studies utilizing empirical/clinical data notwithstanding, the parameters used in these analyses whilst being theoretically sound are likely to be of limited biomedical relevance. There is need for a computational tool which can ascribe functionality to and generate potentially testable hypotheses for a biochemical network. “ReDirection” characterizes every reaction of a user-defined biochemical network with the probable dissociation constant and does so by combinatorially summing all non-redundant and non-trivial vectors of a null space generated subspace from the stoichiometry number matrix of the modelled biochemical network. This is followed by defining and populating a reaction-specific sequence vector with numerical values drawn from each row of this subspace, computing several descriptors and partitioning selected terms into distinct subsets in accordance with the expected outcomes (forward, reverse, equivalent) for a reaction. “ReDirection” computes the sums of all the terms that comprise each outcome-specific subset, maps these to strictly positive real numbers and bins the same to a reaction-specific outcome vector. The p1-norm of this vector is the probable dissociation constant for a reaction and is used to assign and annotate the reaction. “ReDirection” iterates these steps recursively until every reaction of the modelled biochemical network has been assigned an unambiguous outcome. “ReDirection” works on first principles, does not discriminate between enzymatic and non-enzymatic reactions, offers a mathematically rigorous and biochemically relevant environment to explore user-defined biochemical networks under naive and perturbed conditions and can be used to address empirically intractable biochemical problems. The utility and relevance of “ReDirection” is highlighted with an investigation of a constrained biochemical network of human Galactose metabolism. “ReDirection” is freely available and accessible from the comprehensive R archive network (CRAN) with the URL (https://cran.r-project.org/package=ReDirection).
Reconfiguration of Behavioral Signals in the Anterior Cingulate Cortex based on Emotional State
Authors: Lindsay Adrian J , Gallello Isabella , Caracheo Barak F , Seamans Jeremy K
Published: July 2023

Behaviours and their execution depend on the context and emotional state in which they are performed. The contextual modulation of behavior likely relies on regions such as the anterior cingulate cortex (ACC) that multiplex information about emotional/autonomic states and behaviours. The objective of the present study was to understand how the representations of behaviors by ACC neurons become modified when performed in different emotional states. A pipeline of machine learning techniques was developed to categorize and classify complex, spontaneous behaviors from video. This pipeline, termed HUB-DT, discovered a range of statistically separable behaviors during a task in which motivationally significant outcomes were delivered in blocks of trials that created 3 unique ‘emotional contexts’. HUB-DT was capable of detecting behaviors specific to each emotional context and was able to identify and segregate the portions of a neural signal related to a behaviour and to emotional context. Overall, ∼10x as many neurons responded to behaviors in a contextually dependent versus a fixed manner, highlighting the extreme impact of emotional state on representations of behaviors that were precisely defined based on detailed analyses of limb kinematics. This type of modulation may be a key mechanism that allows the ACC to modify behavioral output based on emotional states and contextual demands.
Contact area and tissue growth dynamics shape synthetic juxtacrine signaling patterns
Authors: Dawson Jonathan E. , Bryant Abby , Jordan Trevor , Bhikot Simran , Macon Shawn , Walton Breana , Ajamu-Johnson Amber , Langridge Paul D. , Malmi-Kakkada Abdul N.
Published: July 2023

Cell-cell communication through direct contact, or juxtacrine signaling, is important in development, disease, and many areas of physiology. Synthetic forms of juxtacrine signaling can be precisely controlled and operate orthogonally to native processes, making them a powerful reductionist tool with which to address fundamental questions in cell-cell communicationin vivo. Here we investigate how cell-cell contact length and tissue growth dynamics affect juxtacrine signal responses through implementing a custom synthetic gene circuit inDrosophilawing imaginal discs alongside mathematical modeling to determine synthetic Notch (synNotch) activation patterns. We find that the area of contact between cells largely determines the extent of syn-Notch activation, leading to the prediction that the shape of the interface between signal-sending and signal-receiving cells will impact the magnitude of the synNotch response. Notably, synNotch outputs form a graded spatial profile that extends several cell diameters from the signal source, providing evidence that the response to juxtacrine signals can persist in cells as they proliferate away from source cells, or that cells remain able to communicate directly over several cell diameters. Our model suggests the former mechanism may be sufficient, since it predicts graded outputs without diffusion or long-range cell-cell communication. Overall, we identify that cell-cell contact area together with output synthesis and decay rates likely govern the pattern of synNotch outputs in both space and time during tissue growth, insights that may have broader implications for juxtacrine signaling in general.
DeepETPicker: Fast and accurate 3D particle picking for cryo-electron tomography using weakly supervised deep learning
Authors: Liu Guole , Niu Tongxin , Qiu Mengxuan , Zhu Yun , Sun Fei , Yang Ge
Published: July 2023

Picking particles of biological macromolecules from their cryo-electron tomograms is critical to solving their 3D structuresin situ. To reach sub-nanometre resolution, large numbers of particles often need to be picked, a laborious and time-consuming task if performed manually. To date, however, the adoption of automated particle-picking methods remains limited because of the limitations in their accuracy, processing speed and, for those based on learning models, manual annotation cost. To overcome the limitations, we develop DeepETPicker, a deep learning model for fast and accurate picking of 3D particles from cryo-electron tomograms. The training of DeepETPicker requires only weak supervision with low numbers of simplified Gaussian-type labels, reducing the burden of manual annotation of tomograms under very low signal-to-noise ratios. The simplified labels combined with the customized and lightweight model architecture of DeepETPicker as well as GPU-accelerated pooling enable substantially improved accuracy and accelerated processing speed. When tested on simulated as well as real tomograms, DeepETPicker outperforms the competing state-of-the-art methods by achieving the highest overall accuracy and speed, which translate into better quality of picked particles and higher resolutions of final reconstruction maps. DeepETPicker is provided in open source with a user-friendly interface to support automated particle picking for high-resolution cryo-electron tomographyin situ.
EnrichMiner: a biologist-oriented web server for mining biological insights from functional enrichment analysis results
Authors: Liu Xian , Xu Kaikun , Tao Xin , Bo Xiaochen , Chang Cheng
Published: July 2023

Functional enrichment analysis has been widely used to help researchers obtain biological insights from -omics data. However, the results are often redundant and difficult to digest. The key is developing tools to help users explore the relationships between the enriched terms, remove the redundant terms, and finally select representative terms. However, existing tools hardly make a good integration between enrichment analysis and representative terms selection in a biological-friendly manner. Here, we developed a biologist-oriented web server named EnrichMiner to provide a one-stop solution. It is a complete analysis pipeline from a gene list or a ranked gene table to published-style figures. More importantly, it provides user-friendly interfaces and rich interactive operations to help users explore the term relationships and remove redundancy. EnrichMiner has been integrated into the ExpressVis platform, and is freely accessible athttps://omicsmining.ncpsb.org.cn/ExpressVis/EnrichMinerand does not require login.
Radial glia promote microglial development through integrin αVβ8-TGFβ1 signaling
Authors: McKinsey Gabriel L. , Santander Nicolas , Zhang Xiaoming , Kleemann Kilian , Tran Lauren , Katewa Aditya , Conant Kaylynn , Barraza Matthew , Waddell Kian , Lizama Carlos , La Russa Marie , Koo Hyun Ji , Lee Hyunji , Mukherjee Dibyanti , Paidassi Helena , Anton E. S. , Atabai Kamran , Sheppard Dean , Butovsky Oleg , Arnold Thomas D.
Published: July 2023

Microglia diversity emerges from interactions between intrinsic genetic programs and environment-derived signals, but how these processes unfold and interact in the developing brain remains unclear. Here, we show that radial glia-expressed integrin beta 8 (ITGB8) expressed in radial glia progenitors activates microglia-expressed TGFβ1, permitting microglial development. Domain-restricted deletion ofItgb8in these progenitors establishes complementary regions with developmentally arrested “dysmature” microglia that persist into adulthood. In the absence of autocrine TGFβ1 signaling, we find that microglia adopt a similar dysmature phenotype, leading to neuromotor symptoms almost identical toItgb8mutant mice. In contrast, microglia lacking the TGFβ signal transducersSmad2andSmad3have a less polarized dysmature phenotype and correspondingly less severe neuromotor dysfunction. Finally, we show that non-canonical (Smad-independent) signaling partially suppresses disease and development associated gene expression, providing compelling evidence for the adoption of microglial developmental signaling pathways in the context of injury or disease.
In vivosingle-cell CRISPR uncovers distinct TNF-α programs in clonal expansion and tumorigenesis
Authors: Renz Peter F. , Ghoshdastider Umesh , Baghai Sain Simona , Valdivia-Francia Fabiola , Khandekar Ameya , Ormiston Mark , Bernasconi Martino , Kretz Jonas A. , Lee Minkyoung , Hyams Katie , Forny Merima , Pohly Marcel , Ficht Xenia , Ellis Stephanie J. , Moor Andreas E. , Sendoel Ataman
Published: July 2023

The tumor evolution model posits that malignant transformation is preceded by randomly distributed driver mutations in cancer genes, which cause clonal expansions in phenotypically normal tissues. Although clonal expansions occur frequently in human epithelia and can remodel almost entire tissues, the mechanisms behind why only a small number of clones transform into malignant tumors remain enigmatic. Here, we develop an in vivo single-cell CRISPR strategy to systematically investigate tissue-wide clonal dynamics of the 150 most frequently mutated squamous cell carcinoma genes. We couple ultrasound-guided in utero lentiviral microinjections, single-cell RNA sequencing, guide capture and spatial transcriptomics to longitudinally monitor cell type-specific clonal expansions, document their underlying gene programs and contrast clonal expansions from tumor initiation. We uncover a TNF-α signaling module that acts as a generalizable driver of clonal expansions in epithelial tissues. Conversely, during tumorigenesis, the TNF-α signaling module is downregulated, and instead, we identify a subpopulation of invasive cancer cells that switch to an autocrine TNF-α gene program. By analyzing clonally expanded perturbations and their frequency in tumors, we demonstrate that the autocrine TNF-α gene program is associated with epithelial-mesenchymal transition (EMT) and is preexistent in a subpopulation of expanded epidermal stem cells, contributing to the predisposition for tumor initiation. Finally, we provide in vivo evidence that the epithelial TNF-α gene program is sufficient to mediate invasive properties of epidermal stem cells and show that the TNF-α signature correlates with shorter overall survival in human squamous cell carcinoma patients. Collectively, our study demonstrates the power of applying in vivo single-cell CRISPR screening to mammalian tissues and unveils distinct TNF-α programs in tumor evolution. Understanding the biology of clonal expansions in phenotypically normal epithelia and the mechanisms governing their transformation will guide the development of novel strategies for early cancer detection and therapy.
Cancer cell – fibroblast crosstalk via HB-EGF/EGFR/MEK signaling promotes macrophage recruitment in squamous cell carcinoma
Authors: Giangreco Giovanni , Rullan Antonio , Naito Yutaka , Biswas Dhruva , Liu Yun-Hsin , Hooper Steven , Nenclares Pablo , Bhide Shreerang , Cheang Maggie Chon U , Chakravarty Probir , Hirata Eishu , Swanton Charles , Melcher Alan , Harrington Kevin , Sahai Erik
Published: July 2023

Interactions between cells in the tumor microenvironment (TME) shape cancer progression and patient outcomes. To gain new insights into how the TME influences cancer outcomes, we derive gene expression signatures indicative of signaling between stromal fibroblasts and cancer cells, and demonstrate their prognostic significance in multiple and independent squamous cell carcinoma cohorts. By leveraging information within the signatures, we discover that the HB-EGF/EGFR/MEK axis represents a hub of tumor – stroma crosstalk, promoting the expression of CSF2 and LIF and favoring the recruitment of macrophages. Together these analyses demonstrate the utility of our approach for interrogating the extent and consequences of TME crosstalk.
TBP facilitates RNA Polymerase I transcription following mitosis
Authors: Kwan James Z.J. , Nguyen Thomas F. , Teves Sheila S.
Published: July 2023

The TATA-box binding protein (TBP) is the sole transcription factor common in the initiation complexes of the three major eukaryotic RNA Polymerases (Pol I, II, and III). Decades of research have shown that TBP is essential for proper transcription by the three RNA Pols, though the emergence of TBP paralogs throughout evolution have expanded the complexity in RNA Pol initiation. We have previously shown that acute TBP depletion in mouse embryonic stem cells led to a global decrease in Pol III activity, consistent with the requirement of TBP in Pol III inititation. In contrast, Pol II transcription remained unaffected in the absence of TBP and its paralogs. In this report, we show that, in contrast to Pol II-transcribed genes, the TBP paralog TRF2 does not bind to Pol I promoters, and therefore cannot functionally replace TBP upon depletion. Importantly, acute TBP depletion has no major effect on Pol I occupancy or activity on ribosomal RNA genes, but TBP binding in mitosis leads to efficient Pol I reactivation following cell division. These findings provide a more nuanced role for TBP in Pol I transcription in murine embryonic stem cells.

Significance

The TATA-box binding protein (TBP) is a highly conserved and essential protein in eukaryotes. Decades ofin vitroand yeast research have established its role in the initiation of the three main eukaryotic RNA polymerases. However, the ability to rapidly deplete proteinsin vivois revealing more nuance in the function of TBP in mammalian cells. Using this technology, we reassess the role of TBP in RNA Polymerase I (Pol I) transcription in mouse embryonic stem cells. We find that neither TBP nor its paralog TRF2 are required for Pol I recruitment or activity, but TBP binding during mitosis promotes efficient reactivation after cell division. Overall, these findings provide new evidence into the complex function of TBP in eukaryotic transcription.
Molecular epidemiological study of Scrub Typhus in residence, farm and forest habitats from Yunnan Province, China
Authors: Tian Jia-Wei , Kong Yi-Chen , Han Pei-Yu , Xu Fen-Hui , Yang Wei-Hong , Zhang Yun-Zhi
Published: July 2023

The number of people suffering from scrub typhus, which is not of concern, is increasing year by year, especially in Yunnan Province, China. From June 1, 2021 to August 15, 2022, a total of 505 mammalian samples were collected from farm, forest, and residential habitats with high incidence of scrub typhus in Yunnan, China, for nPCR (nested PCR) and qPCR (quantitative real-time PCR) detection ofOrientia tsutsugamushi. A total of 4 orders of murine-like animals, Rodentia (87.52%, n=442), Insectivora (10.29%, n=52), Lagomorpha (1.79%, n=9) and Scandentia (0.40%, n=2) were trapped. Comparing the qPCR infection rates in the three habitats, it was no significant difference that the infection rate of residential habitat (44.44%) and that of the farm habitat (45.05%, P>0.05), which is much larger than that of the forest habitat (3.08%) (P<0.001). Three genotypes (Karp, Kato and TA763) ofO. tsutsugamushiwere found from Yunnan, China in this study. We found a tendency for scrub typhus to migrate from forests to residential habitats.

Author Summary

Scrub typhus is acute febrile infectious disease caused byOrientia tsutsugamushithat threatens nearly 1 billion people. According to the data we have obtained, the incidence rate of infected people has reached 23.84/100,000 population until December 2022 in Yunnan, China. The incidence rate has increased non-negligibly Compared with 0.65/100,000 population in 2006. Among them, the incidence rate has increased by 71.14% from 2019 to 2022. Scrub typhus is transmitted by the bite of chigger larvae with murine-like animals as the main source of infection Rodentia are the most important reservoir hosts, followed by Insectivora. Therefore, in view of the influencing factor of human habitat, we used qPCR (quantitative real-time PCR) and nPCR (nested PCR) techniques to analyze the prevalence ofO. tsutsugamushiin hosts of different human habitats from June 2021 to August 2022. Our research shows that the diversity ofO. tsutsugamushigenotypes in Yunnan Province provides guidance for the prevention and Control of scrub typhus. And it was found that the infection rate ofO. tsutsugamushiin murine-like animals is quite different in different human habitats, especially the high infection rate in residential habitat and farm habitat, suggesting thatO. tsutsugamushican be infected without wilderness history.
The substrate-binding domains of the osmoregulatory ABC importer OpuA transiently interact
Authors: van den Noort Marco , Drougkas Panagiotis , Paulino Cristina , Poolman Bert
Published: July 2023

Bacteria utilize various strategies to prevent internal dehydration during hypertonic stress. A common approach to countering the effects of the stress is to import compatible solutes such as glycine betaine, leading to simultaneous passive water fluxes following the osmotic gradient. OpuA fromLactococcus lactisis a type I ABC-importer that uses two substrate-binding domains (SBDs) to capture extracellular glycine betaine and deliver the substrate to the transmembrane domains for subsequent transport. OpuA senses osmotic stress via changes in the internal ionic strength and is furthermore regulated by the 2ndmessenger cyclic-di-AMP. We now show, by means of solution-based single-molecule FRET and analysis with multi-parameter photon-by-photon hidden Markov modeling, that the SBDs transiently interact in an ionic strength-dependent manner. The smFRET data are in accordance with the apparent cooperativity in transport and supported by new cryo-EM data of OpuA. We propose that the physical interactions between SBDs and cooperativity in substrate delivery are part of the transport mechanism.
Challenging age-related decline in brain function: Evidence from fast neuroimaging of musical sequence recognition
Authors: Bonetti L. , Fernández Rubio G. , Lumaca M. , Carlomagno F. , Risgaard Olsen E. , Criscuolo A. , Kotz S.A. , Vuust P. , Brattico E. , Kringelbach M.L.
Published: July 2023

Aging is often associated with decline in brain processing power and neural predictive capabilities. To challenge this notion, we used the excellent temporal resolution of magnetoencephalography (MEG) to record the whole-brain activity of 39 older adults (over 60 years old) and 37 young adults (aged 18-25 years) during recognition of previously memorised and novel musical sequences. Our results demonstrate that independent of behavioural measures, older compared to young adults showed increased rapid auditory cortex responses (around 100 and 250 ms after each tone of the sequence) and decreased later responses (around 250 and 350 ms) in hippocampus, ventromedial prefrontal cortex and inferior frontal gyrus. Working memory abilities were associated with stronger brain activity for both young and older adults. Our findings unpick the complexity of the healthy aging brain, showing age-related neural transformations in predictive and memory processes and challenging simplistic notions that non-pathological aging merely diminishes neural predictive capabilities.
Characterising neutrophil subtypes in cancer using human and murine single-cell RNA sequencing datasets
Authors: Fetit Rana , White Mark , Mills Megan L. , Cortes-Lavaud Xabier , McLaren Alistair , Falconer John , Gilroy Kathryn , Nixon Colin , Kirschner Kristina , Jackstadt Rene , Campbell Andrew D. , Sansom Owen J. , Steele Colin W.
Published: July 2023

Neutrophils are a highly heterogenous cellular population. However, a thorough examination of the different transcriptional neutrophil states, between health and malignancy, has not been performed. We utilised single-cell RNA-sequencing of human and murine datasets, both publicly available and independently generated, to identify neutrophil transcriptomic subtypes and their developmental lineages in health and malignancy. Datasets of lung, breast and colorectal cancer (CRC) were integrated to establish and validate the reproducibility of neutrophil gene-signatures. Pseudo-time analysis was used to identify genes driving neutrophil development from health to cancer. Finally, ligand-receptor interactions and signalling pathways between neutrophils and other immune cell populations in primary CRC and metastatic CRC were investigated. We define two main neutrophil subtypes in primary tumours: an activated subtype sharing the transcriptomic signatures of healthy neutrophils; and a tumour-specific subtype. This signature is conserved in murine and human cancer, across different tumour types. In CRC metastases, neutrophils are more heterogenous, exhibiting additional transcriptomic subtypes. Pseudo-time analysis implicates an IL1B/CXCL8/CXCR2 axis in the progression of neutrophils from health to cancer and metastasis, with effects on T-cell effector function. Assessment of global communication signalling identified CD4+ T-cells and macrophages as dominant regulators of the immunosuppressive, metastatic niche, whereas CD8+ T-cells are receivers of signals from other immune cells. We propose that the emergence of metastatic-specific neutrophil subtypes is driven by an IL1/CXCL8/CXCR2 axis, with the evolution of different transcriptomic signals that impair T-cell function at the metastatic site. Thus, a better understanding of the neutrophil transcriptomic programming could optimise immunotherapeutic interventions into early and late interventions, targeting different neutrophil subtypes.