bluuebunny/crossref_metadata_2025 huggingface dataset:
Management of minimal and overt hepatic encephalopathy with branched-chain amino acids: a review of the evidence
Authors: Swansson Will D. , Anderson Bennett M. , Yeoh Sern Wei , Lewis Diana J.
Published: July 2023

Hepatic encephalopathy (HE) is a challenging complication of liver disease that is associated with substantial morbidity and mortality. Branched-chain amino acid (BCAA) supplementation in the management of HE is a debated topic. This narrative review aims to provide an up-to-date review of the topic and includes studies featuring patients with hepatocellular carcinoma. A review of the literature was performed using the online databases MEDLINE and EMBASE for studies between 2002 and December 2022. Keywords ‘branched-chain amino acids’, ‘liver cirrhosis’ and ‘hepatic encephalopathy’ were used. Studies were assessed for inclusion and exclusion criteria. Of 1045 citations, 8 studies met the inclusion criteria. The main outcomes reported for HE was changed in minimal HE (MHE) (n = 4) and/or incidence of overt HE (OHE) (n = 7). Two of the 4 studies reporting on MHE had improvement in psychometric testing in the BCAA group, but there was no change in the incidence of OHE in any of the 7 papers in the BCAA group. There were few adverse effects of BCAA supplementation. This review found weak evidence for BCAA supplementation for MHE, and no evidence for BCAAs for OHE. However, given the relative paucity and methodological heterogeneity of the current research, there is scope for future studies to examine the effects of varying timing, dosage, and frequency of BCAAs on outcomes such as HE. Importantly, research is also needed to examine BCAAs in conjunction with standard therapies for HE such as rifaximin and/or lactulose.
Mechanism by which oleracein E alleviates TNBS-induced ulcerative colitis
Authors: Huang Yun , Su Yu , Qin Rong , Wang Likun , Zhang Zhibo , Huang Weikang , Fan Xirui , Yao Ying , Wang Hui
Published: July 2023

Objective

This study aimed to investigate the effect of oleracein E (OE) in improving 2,4,6-trinitrobenzene sulfonic acid (TNBS)-induced ulcerative colitis (UC).

Methods

Lipopolysaccharide (LPS) was used to induce a UC cell model, and TNBS was used to induce a UC rat model. ELISA was performed to assess the levels of inflammatory factors (IL-1β, TNF-α, and IL-6). Moreover, the activities of catalase (CAT), myeloperoxidase (MPO), and malonaldehyde (MDA) were detected by kits. Western blotting was performed to assess related proteins of the Nrf2/HO-1 signaling pathway, tight junction protein (ZO-1, Occludin, and claudin-2) expression levels, and apoptosis-related proteins (Bcl2, Bax, and cleaved caspase 3). Flow cytometry was used to analyze ROS levels. The morphology of colon tissues and the apoptosis of cells were detected by HE and TUNEL staining, respectively.

Results

OE significantly increased the activity of CAT and decreased the activity of MPO in LPS-induced Caco-2 cells and TNBS-induced UC rats. However, the levels of IL-1β, IL-6, and TNF-α were markedly reduced both in vivo and in vitro. In addition, OE significantly increased the levels of Nrf2/HO-1 signaling pathway-related proteins and tight junction proteins and inhibited cell apoptosis. HE staining showed that OE significantly decreased the severity of acute TNBS-induced colitis in rats.

Conclusion

OE may exert a regulatory effect on ameliorating intestinal barrier injury and reducing inflammation and oxidative stress levels by activating the Nrf2/HO-1 pathway.
Prevalence of autoimmune, cholestatic and nonalcoholic fatty liver disease in celiac disease
Authors: Hitawala Asif Ali , Almomani Ashraf , Onwuzo Somtochukwu , Boustany Antoine , Kumar Prabhat , Asaad Imad
Published: July 2023

Background

While there is higher prevalence of autoimmune, cholestatic and fatty liver disease in celiac disease (CeD), most data is from small-scale studies. We evaluated the prevalence and risk factors of the same using large cohort data.

Methods

A population-based cross-sectional study was conducted using Explorys, a multi-institutional database. Prevalence and risk factors of autoimmune hepatitis (AIH), primary biliary cholangitis (PBC), primary sclerosing cholangitis (PSC) and nonalcoholic fatty liver disease (NAFLD) in CeD were assessed.

Results

Out of 70 352 325 subjects, 136 735 had CeD (0.19%). The prevalence of AIH (0.32%), PBC (0.15%), PSC (0.004%) and NAFLD (0.7%) were high in CeD. After adjusting for age, gender, Caucasian race and anti-tissue transglutaminase antibody (anti-TTG), CeD subjects had higher odds of AIH [adjusted odds ratio (aOR) 7.06, 95% confidence interval (CI) 6.32–7.89] and PBC (aOR 4.16, 95% CI 3.46–5.0). Even after adjusting for CeD, anti-TTG positivity concurred with higher odds of AIH (aOR 4.79, 95% CI 3.88–5.92) and PBC (aOR 9.22, 95% CI 7.03–12.1). After adjusting for age, gender, Caucasian race, diabetes mellitus (DM), obesity, hypothyroidism and metabolic syndrome, there was higher prevalence of NAFLD in CeD, with the aOR in the presence of DM type 1 being 2.1 (95% CI 1.96–2.25), and in the presence of DM type 2 being 2.92 (95% CI 2.72–3.14).

Conclusion

Subjects with CeD are more likely to have AIH, PBC, PSC and NAFLD. AIH and PBC have higher odds in the presence of anti-TTG. The odds of NAFLD in CeD are high regardless of type of DM.
Endoscopic failure for foreign body ingestion and food bolus impaction in the upper gastrointestinal tract: an updated analysis in a European tertiary care hospital
Authors: Calini Giacomo , Ortolan Naima , Battistella Claudio , Marino Marco , Bresadola Vittorio , Terrosu Giovanni
Published: July 2023

Objective

Harmfulness of foreign body ingestion and food bolus impaction (FBIs) varies according to geographical area, population, habits, and diet. Therefore, studies may not draw generalizable conclusions. Furthermore, data regarding FBIs management in Europe are limited and outdated. This study aimed to analyze the endoscopic management and outcomes of FBIs in an Italian tertiary care hospital to identify risk factors for endoscopic failure.

Methods

We retrospectively reviewed patients who underwent upper gastrointestinal endoscopy for FBIs between 2007 and 2017. Baseline, clinical, FBIs, and endoscopic characteristics and outcomes were collected and reported using descriptive statistics and logistic regression analyses.

Results

Of the 381 endoscopies for FBIs, 288 (75.5%) were emergent endoscopy and 135 (35,4%) included underlying upper gastrointestinal conditions. The study population included 44 pediatric patients (11.5%), 54 prisoners (15.8%), and 283 adults (74.2%). The most common type and location of FBIs were food boluses (52.9%) and upper esophagus (36.5%), respectively. While eight patients (2.1%) developed major adverse events requiring hospital admission, the remainder (97.9%) were discharged after observation. No mortality occurred. Endoscopic success was achieved in 263 of 286 (91.9%) verified FBIs endoscopies. Endoscopic failure (8.04%) was associated with age, bone, disk battery, intentional ingestion, razor blade, prisoners, and stomach in the univariate analysis. Multivariate logistic regression revealed that intentional ingestion was associated with endoscopic failure (odds ratio: 7.31; 95% confidence interval = 2.06–25.99; P = 0.002).

Conclusion

Endoscopy for FBIs is safe and successful, with low hospital admission rate in children, prisoners, and adults. Intentional ingestion is a risk factor of endoscopic failure.
Trust and Access: Eye Information-seeking Practices and Preferences among Canadians
Authors: Spafford Marlee M. , Chow Amy H. Y. , Labreche Tammy , Jones Deborah A. , Christian Lisa W. T. , Furtado Nadine M. , MacIver Sarah , Irving Elizabeth L.
Published: July 2023

SIGNIFICANCE

This study highlights the value that the public places on obtaining trusted and accessible health-related information and their preference for obtaining it from their health care practitioners. Previous research has not been specific to Canadians or vision. Findings can be used to increase eye health literacy and eye care utilization.

PURPOSE

Canadians underuse eye care and underestimate the occurrence of asymptomatic eye disease. This study explored eye information-seeking practices and preferences among a group of Canadians.

METHODS

Using snowball sampling, a 28-item online survey collected respondent perceptions about their eye and health information-seeking practices and preferences. Questions examined electronic device access, information source use, and demographics. Two open-ended questions examined information-seeking practices and preferences. Respondents were at least 18 years old and living in Canada. Individuals working in eye care were excluded. Response frequencies and z scores were computed. Written comments were assessed using content analysis.

RESULTS

Respondents searched for less eye than health information (z scores ≥ 2.25, P < .05). For eye and health information, primary care providers were the used and preferred source, and reliance on Internet searches was greater than desired. Trust and access drove information-seeking practices. Respondent comments suggested that a hierarchy of trust operates across My Health Team, My Network, and My External Sources, with a persistent threat posed by Discredited Sources. Access to information sources seemed mediated by enablers (Convenience and Accessible Features) and barriers (Unreachable Health Team and Absent Systems). Eye information was seen as more specialized and harder to find. There was a high regard for health care practitioners who provide their patients with curated trusted information.

CONCLUSIONS

These Canadians value trusted and accessible health-related information. They prefer eye and health information from their health care practitioners and value when their health team provides online curated information, particularly regarding eyes.
Preoperative Botulinum Toxin for Abdominal Wall Reconstruction in Massive Hernia Defects—A Propensity-Matched Analysis
Authors: Niu Ellen F. , Kozak Geoffrey M. , McAuliffe Phoebe B. , Amro Chris , Bascone Corey , Honig Stephanie E. , Elsamaloty Lina H. , Hao Meng , Broach Robyn B. , Kovach Stephen J. , Fischer John P.
Published: July 2023

Purpose

Reconstruction of massive incisional hernias (IHs) poses a significant challenge with high rates of recurrence. Preoperative chemodenervation using botulinum toxin (BTX) injections in the abdominal wall is a technique that has been used to facilitate primary fascial closure. However, there is limited data directly comparing primary fascial closure rates and postoperative outcomes after hernia repair between patients who do and do not receive preoperative BTX injections. The objective of our study was to compare the outcomes of patients who did and did not receive BTX injections before abdominal wall reconstruction.

Methods

This is a retrospective cohort study including adult patients from 2019 to 2021 who underwent IH repair with and without preoperative BTX injections. Propensity score matching was performed based on body mass index, age, and intraoperative defect size. Demographic and clinical data were recorded and compared. The statistical significance level was set at P < 0.05.

Results

Twenty patients underwent IH repair with preoperative BTX injections. Twenty patients who underwent IH repair without preoperative BTX injections were selected to comprise a 1:1 propensity-matched control cohort. The average defect size was 663.9 cm2 in the BTX group and 640.7 cm2 in the non-BTX group (P = 0.816). There was no difference in average age (58.6 vs 59.2 years, P = 0.911) and body mass index (33.0 vs 33.2 kg/m2, P = 0.911). However, there was a greater proportion of male patients in the BTX group (85% vs 55%, P = 0.082).

Primary fascial closure was achieved in 95% of BTX patients and 90% of non-BTX patients (P = 1.0). Significantly fewer patients in the BTX group required component separation techniques to achieve primary fascial closure (65% vs 95%, P = 0.044). There was no significant difference in any postoperative surgical and medical outcomes. Hernia recurrence was 10% in the BTX group and 20% in non-BTX group (P = 0.661).

Conclusions

In our study, we observed a lower rate of component separations to achieve primary fascial closure among patients with massive hernia defects who received preoperative BTX injections. These results suggest that preoperative BTX injections may “downstage” the complexity of hernia repair with abdominal wall reconstruction in patients with massive hernia defects and reduce the need for component separation.
Comparative Outcomes of Malar Implants Versus Fat Transfer to Cheeks Among Transfeminine Individuals Undergoing Malar Augmentation
Authors: Chaya Bachar F. , Rodriguez Colon Ricardo , Diep Gustave K. , Brydges Hilliard , Tran David , Laspro Matteo , Onuh Ogechukwu C. , Trilles Jorge , Boczar Daniel , Rodriguez Eduardo D.
Published: July 2023

Background

Malar augmentation is a key procedure sought out by transfeminine individuals seeking to feminize their facial appearance. Different surgical techniques have been described in the literature including fat transfer to the cheeks and malar implant placement. Because of the paucity of information in the literature, there is no consensus on best practices for this procedure. The objective of our study is to determine the effectiveness and safety of malar implants as compared with fat transfer to the cheeks in transfeminine individuals.

Methods

We examined all patients with the diagnosis of gender dysphoria that were referred to the senior author seeking consultation for feminizing facial procedures between June 2017 and August 2022. Patients who underwent fat transfer to the cheeks or malar implant placement were included in our study. We reviewed the electronic medical record of each patient, and we retrieved and analyzed data regarding demographics, medical and surgical history, operative dictations, clinic notes, and postoperative follow-up. Univariate analysis was used to assess for differences in postoperative complications between these 2 groups.

Results

We identified 231 patients underwent feminizing facial gender affirming surgery, with 152 patients receiving malar augmentation through malar implants or fat grafting. One hundred twenty-nine patients (84.9%) underwent malar implant placement and 23 (15.1%) underwent fat grafting to the cheeks. The mean follow-up time was 3.6 ± 2.7 months. Patient satisfaction was greater in the malar implant group (126/129, 97.7%) compared with the fat transfer group (20/23, 87%, P < 0.045). Two patients who received implants (1.8%) experienced postoperative complications. No patient undergoing fat transfer experiences similar adverse outcomes. Nevertheless, the difference was not statistically significant (P = 1.00).

Conclusions

Our findings support the contention that malar implants are a safe alternative for malar augmentation among transfeminine individuals. While autologous fat transfer to the cheek is an indispensable option in patients requiring minor malar enhancement, malar implants offer a more permanent option with a better aesthetic outcome in patients requiring major malar enhancement. To minimize postoperative complications, surgeons should emphasize patient compliance with postoperative directions.
Prognostic Risk Factors of One-stage Surgical Clipping in aSAH Elderly Patients with MIAs
Authors: Chen Cheng , Wang Chao , Zhang Chonghui , Zhou Han , Lu Zhuangzhuang , Feng Yugong
Published: July 2023

Objective:

To discuss the prognostic factors affecting the prognosis of 1-stage surgical clipping in aneurysmal subarachnoid hemorrhage (aSAH) elderly patients with multiple intracranial aneurysms (MIAs).

Materials and Methods:

A total of 84 elderly patients with aSAH who had MIAs and underwent 1-stage surgical clipping were retrospectively analyzed. Follow-up was conducted with patients 30 days after discharge using the Glasgow Outcome Scale (GOS). A GOS score of 1 to 3 was defined as a poor outcome, and a GOS score of 4 to 5 was defined as a good outcome. General information (gender, age, size of aneurysm, location of rupture of the responsible aneurysm, H-H grade, CT characteristics of aSAH, number of subarachnoid hemorrhages, operation opportunity, postoperative complications, and intraoperative rupture) and complications（cerebral infarction, hydrocephalus, electrolyte disturbance, and encephaledema）were recorded. Univariate analysis and multivariate regression analysis were used to analyze factors that may affect outcomes.

Results:

Univariate analysis showed that the number of SAH events (P=0.005), intraoperative rupture (P=0.048) and postoperative complications (P=0.002) were associated with the prognosis of aSAH elderly patients with MIAs undergoing 1-stage surgery. Multivariate analysis showed that the number of SAH events (odds ratio [OR] 4.740, 95% confidence interval [CI] 1.056 to 21.282, P=0.042) and postoperative complications (OR 4.531, 95% CI 1.266 to 16.220, P=0.020) were independently associated with the prognosis of aSAH elderly patients with MIAs undergoing 1-stage surgery.

Conclusions:

The number of SAH events and postoperative complications are independent risk factors for the prognosis of aSAH elderly patients with MIAs undergoing 1-stage surgery. These factors contribute to the timely treatment of potentially related patients.
Nanopore Adaptive Sampling Enriches for Antimicrobial Resistance Genes in Microbial Communities
Authors: Wrenn Danielle C. , Drown Devin M.
Published: July 2023

Antimicrobial resistance (AMR) is a global public health threat. Environmental microbial communities act as reservoirs for AMR, containing genes associated with resistance, their precursors, and the selective pressures to encourage their persistence. Genomic surveillance could provide insight into how these reservoirs are changing and their impact on public health. The ability to enrich for AMR genomic signatures in complex microbial communities would strengthen surveillance efforts and reduce time-to-answer. Here, we test the ability of nanopore sequencing and adaptive sampling to enrich for AMR genes in a mock community of environmental origin. Our setup implemented the MinION mk1B, an NVIDIA Jetson Xavier GPU, and flongle flow cells. We observed consistent enrichment by composition when using adaptive sampling. On average, adaptive sampling resulted in a target composition that was 4x higher than a treatment without adaptive sampling. Despite a decrease in total sequencing output, the use of adaptive sampling increased target yield in most replicates.
Methylphenidate alleviates cognitive dysfunction from early Mn exposure: Role of catecholaminergic receptors
Authors: Beaudin Stephane A. , Howard Shanna , Santiago Nicholas , Strupp Barbara J , Smith Donald R
Published: July 2023

Environmental manganese (Mn) exposure is associated with impaired attention and psychomotor functioning, as well as impulsivity/hyperactivity in children and adolescents. We have shown previously that developmental Mn exposure can cause these same dysfunctions in a rat model. Methylphenidate (MPH) lessens impairments in attention, impulse control, and sensorimotor function in children, but it is unknown whether MPH ameliorates these dysfunctions when induced by developmental Mn exposure. Here, we sought to (1) determine whether oral MPH treatment ameliorates the lasting attention and sensorimotor impairments caused by developmental Mn exposure, and (2) elucidate the mechanism(s) of Mn neurotoxicity and MPH effectiveness. Rats were given 50 mg Mn/kg/d orally over PND 1-21 and assessed as adults in a series of attention, impulse control and sensorimotor tasks during oral MPH treatment (0, 0.5, 1.5, or 3.0 mg/kg/d). Subsequently, selective catecholaminergic receptor antagonists were administered to gain insight into the mechanism(s) of action of Mn and MPH. Developmental Mn exposure caused persistent attention and sensorimotor impairments. MPH treatment at 0.5 mg/kg/d completely ameliorated the Mn attentional dysfunction, whereas the sensorimotor deficits were ameliorated by the 3.0 mg/kg/d MPH dose. Notably, the MPH benefit on attention was only apparent after prolonged treatment, while MPH efficacy for the sensorimotor deficits emerged early in treatment. Selectively antagonizing D1, D2, or α2Areceptors had no effect on the Mn-induced attentional dysfunction or MPH efficacy in this domain. However, antagonism of D2R attenuated the Mn sensorimotor deficits, whereas the efficacy of MPH to ameliorate those deficits was diminished by D1R antagonism. These findings demonstrate that MPH is effective in alleviating the lasting attention and sensorimotor dysfunction caused by developmental Mn exposure, and they clarify the mechanisms underlying developmental Mn neurotoxicity and MPH efficacy. Given that the cause of attention and psychomotor deficits in children is often unknown, these findings have implications for the treatment of environmentally-induced attentional and psychomotor dysfunction in children more broadly.

Highlights

Developmental Mn exposure impaired attention and sensorimotor function

MPH ameliorated the Mn deficits, but the effective dose varied by functional domain

The MPH benefit on attention was only apparent after prolonged treatment

No specific catecholaminergic receptor singly mediates Mn-induced inattention or MPH efficacy in this domain

Dopamine 1 and 2 receptors moderated Mn sensorimotor deficits and MPH efficacy in this domain

MPH can improve behavioral dysfunction induced by an environmental toxicant
Autoimmunity associated allele of tyrosine phosphatase genePTPN22enhances anti-viral immunity
Authors: Orozco Robin C. , Marquardt Kristi , Pratumchai Isaphorn , Mowen Kerri , Domissy Alain , Teijaro John R. , Sherman Linda A.
Published: July 2023

Abstract

The 1858C>T allele of the tyrosine phosphatasePTPN22is present in 5-10% of the North American population and is strongly associated with numerous autoimmune diseases. Although research has been done to define how this allele potentiates autoimmunity, the influencePTPN22and its pro-autoimmune allele has in anti-viral immunity remains poorly defined. Here, we use single cell RNA- sequencing and functional studies to interrogate the impact of this pro- autoimmune allele on anti-viral immunity during Lymphocytic Choriomeningitis Virus clone 13 (LCMV-cl13) infection. Mice homozygous for this allele (PEP- 619WW) clear the LCMV-cl13 virus whereas wildtype (PEP-WT) mice cannot. This is associated with enhanced anti-viral CD4 T cell responses and a more immunostimulatory CD8α-cDC phenotype. Adoptive transfer studies demonstrated that PEP-619WW enhanced anti-viral CD4 T cell function through virus-specific CD4 T cell intrinsic and extrinsic mechanisms. Taken together, our data show that the pro-autoimmune allele ofPtpn22drives a beneficial anti-viral immune response thereby preventing what is normally a chronic virus infection.

Author Summary

PTPN22and its alternative allele, 1858C>T, has largely been studied in the context of autoimmunity. Through these studies, researchers defined roles for PTPN22 in regulating T lymphocyte activation, myeloid cell cytokine production, and macrophage polarization. Despite these immune pathways being critical for anti-viral immunity, little work has studied how this allele impacts virus infection. In this study, we examine gene expression and function of immune cell subsets to demonstrate how a common allelic variant ofPTPN22,which strongly increases the risk of autoimmune disease, promotes successful clearance of an otherwise chronic viral infection.
Analytical Method Development for Evaluation of Pharmacokinetics and Tissue Distribution of Thiourea-Based Antivirals through nLC/MS-MS
Authors: Kumar Jitendra , Tyagi Purnima , Yadav Manisha , Sharma Deepti , Maras Jaswinder Singh , Kumar Vijay
Published: July 2023

Thiourea-based antivirals are organosulfur chemical compounds. Due to their various medicinal uses, including antiviral, antioxidant, and anticancer properties, they are becoming more popular. In this study, pharmacokinetics, Metabolism, bioavailability, and distribution of thiourea derivatives to organs of rats. Thiourea derivatives, namely DSA-00, DSA-02, and DSA-09, exhibit characteristics similar to those of conventional drugs when evaluated in terms of pharmacokinetics, drug-likeness, and medicinal chemistry throughin-silico analysis. Then a simple and sensitive analytical method was developed for quantified DSA-00, DSA-02, and DSA-09, using prednisolone as an internal standard (IS) and nano liquid chromatography tandem mass spectrometry (nLC-MS/MS). The plasma and tissue samples were preprocessing with acetonitrile before chromatographic separation by C18 column with isocratic elution using a mobile phase of water-methanol (30:70, v/v) at a flow rate of 0.6 mL/min. A triplequadrupole tandem mass spectrometer in multiple-reaction monitoring (MRM) scanning via an electrospray ionization (ESI) source functioning in negative and positive mode detection. For DSA-00, DSA-02, DSA-09 and, internal standard the optimized mass transition ion-pairs (m/z) for quantification were 297.2, 311.2, 309.09, and 361.19 respectively. Each analytic run required only 15 minutes between injections. The calibration curve for thiourea derivatives showed good linear regression coefficient (R2>.99) over a range of 1.00-10000 pg/mL except DSA-09. The lower limit of quantification (LLOQ) was 1.00 ng/mL. The intra- and inter-day precisions were no more than 10.8%, and relative errors (RE) ranged from 0.5 to 5.98%. The validated method was effectively used to explore the pharmacokinetics of orally administrative thiourea derivatives in rats.
Contextualising the developability risk of antibodies with lambda light chains using enhanced therapeutic antibody profiling
Authors: Raybould Matthew I. J. , Turnbull Oliver M. , Suter Annabel , Guloglu Bora , Deane Charlotte M.
Published: July 2023

Antibodies with lambda light chains (λ-antibodies) are generally considered to be less developable than those with kappa light chains (κ-antibodies), leading to substantial systematic biases in drug discovery pipelines. This has contributed to kappa dominance amongst clinical-stage therapeutics. However, the identification of increasing numbers of epitopes preferentially engaged byλ-antibodies shows there is a functional cost to neglecting them as potential lead candidates during discovery campaigns. Here, we update our Therapeutic Antibody Profiler (TAP) tool to use the latest data and machine learning-based structure prediction methods, and apply this new protocol to evaluate developability risk profiles forκ-antibodies andλ-antibodies based on their surface physicochemical properties. We find thatλ-antibodies are on average at a higher risk of poor developability — as an indication, over 40% of single-cell sequenced humanλ-antibodies are flagged by TAP for risk-prone patches of surface hydrophobicity (PSH), compared to around 11% of humanκ-antibodies. Nonetheless, a substantial proportion of naturalλ-antibodies are assigned more moderate risk profiles by TAP and should therefore represent more tractable candidates for therapeutic development. We also analyse the populations of high and low risk antibodies, highlighting opportunities for strategic design that TAP suggests would enrich for more developableλ-based candidates. Overall, we provide context to the differing developability ofκ- andλ-antibodies, enabling a rational approach to incorporate more diversity into the initial pool of immunotherapeutic candidates.
Accounting for Isoform Expression in eQTL Mapping Substantially Increases Power
Authors: LaPierre Nathan , Pimentel Harold
Published: July 2023

A core problem in genetics is eQTL mapping, in which genetic variants associated with changes in expression of genes are identified. It is common in eQTL mapping to compute gene expression by aggregating the expression levels of individual isoforms from the same gene and then performing linear regression between SNPs and this aggregated gene expression level. However, SNPs may regulate isoforms from the same gene in different directions due to alternative splicing, or only regulate the expression level of one isoform, causing this approach to lose power. In this study, we provide a systematic evaluation of methods for accounting for individual isoform expression levels based on generative isoform expression heritability models and real data. Over a range of conditions, we show that these approaches substantially increase the power to map eQTLs in both simulations and commonly analyzed large data sets. We identify settings in which different approaches yield an inflated number of false discoveries or lose power. In particular, we show that calling an eGene if there is a significant association between a SNP and any isoform fails to control False Discovery Rate, even when applying standard False Discovery Rate correction. We show that similar trends are observed in real data from the GEUVADIS and GTEx studies, suggesting the possibility that similar effects are present in these consortia.
Using Drosophila to model a variant of unknown significance in the human cardiogenic geneNkx2.5
Authors: Lovato TyAnna L. , Blotz Brenna , Bileckyj Cayleen , Johnston Christopher A. , Cripps Richard M.
Published: July 2023

Sequencing of human genome samples has unearthed genetic variants for which functional testing is necessary to validate their clinical significance. We used the Drosophila system to analyze a variant of unknown significance in the human congenital heart disease gene,Nkx2.5. We generated an R321N allele of theNkx2.5orthologtinman(tin) to model a human K158N variant and tested its function in vitro and in vivo. The R321N Tin isoform bound poorly to DNA in vitro and was deficient in activating a Tin-dependent enhancer in tissue culture. Mutant Tin also showed a significantly reduced interaction with a Drosophila Tbox cardiac factor named Dorsocross1. We generated atinR321Nallele using CRISPR/Cas9, for which homozygotes were viable and had normal heart specification, but showed defects in the differentiation of the adult heart that were exacerbated by further loss oftinfunction. We conclude that the human K158N mutation is likely pathogenic through causing both a deficiency in DNA binding and a reduced ability to interact with a cardiac cofactor, and that cardiac defects might arise later in development or adult life.
Reprogramming human B cells with custom heavy chain antibodies
Authors: Rogers Geoffrey L. , Huang Chun , Mathur Atishay , Huang Xiaoli , Chen Hsu-Yu , Stanten Kalya , Morales Heidy , Chang Chan-Hua , Kezirian Eric J. , Cannon Paula M.
Published: July 2023

We describe a genome editing strategy to reprogram the immunoglobulin heavy chain (IgH) locus of human B cells to express custom molecules that respond to immunization. These heavy chain antibodies (HCAbs) comprise a custom antigen-recognition domain linked to an Fc domain derived from the IgH locus and can be differentially spliced to express either B cell receptor (BCR) or secreted antibody isoforms. The HCAb editing platform is highly flexible, supporting antigen-binding domains based on both antibody and non-antibody components, and also allowing alterations in the Fc domain. Using HIV Env protein as a model antigen, we show that B cells edited to express anti-Env HCAbs support the regulated expression of both BCRs and antibodies, and respond to Env antigen in a tonsil organoid model of immunization. In this way, human B cells can be reprogrammed to produce customized therapeutic molecules with the potential forin vivoamplification.
Applying high-resolution spatial transcriptomics to characterize the amyloid plaque cell niche in Alzheimer’s Disease
Authors: Mallach Anna , Zielonka Magdalena , van Lieshout Veerle , An Yanru , Khoo Jia Hui , Vanheusden Marisa , Chen Wei-Ting , Moechars Daan , Arancibia-Carcamo I. Lorena , Fiers Mark , De Strooper Bart
Published: July 2023

The amyloid plaque cell niche is a pivotal hallmark of Alzheimer’s disease (AD). Where early spatial transcriptomics (ST) technologies have provided valuable information on transcriptomic alterations in the small tissue domains overlaying with amyloid plaques, they lacked cellular resolution. Here we compare two novel high-resolution ST platforms, CosMx and Stereo-seq, in their ability to characterize the cellular response in the amyloid plaque niche in an AD mouse model. Combining the results from both techniques empowered us to survey the highly variable microglial-astrocytic response across the amyloid plaque micro-environment and provided a first insight into how these responses could relate to neuronal transcriptomic alterations. This pilot study demonstrates the great potential of high-resolution ST, while simultaneously highlighting limitations that, when addressed, will unleash the full power of these techniques to map the progression of molecular and cellular changes in the brains of AD patients.
Genetics and Environment Distinctively Shape the Human Immune Cell Epigenome
Authors: Wang Wenliang , Hariharan Manoj , Ding Wubin , Bartlett Anna , Barragan Cesar , Castanon Rosa , Rothenberg Vince , Song Haili , Nery Joseph , Aldridge Andrew , Altshul Jordan , Kenworthy Mia , Liu Hanqing , Tian Wei , Zhou Jingtian , Zeng Qiurui , Chen Huaming , Wei Bei , Gündüz Irem B. , Norell Todd , Broderick Timothy J , McClain Micah T. , Satterwhite Lisa L. , Burke Thomas W. , Petzold Elizabeth A. , Shen Xiling , Woods Christopher W. , Fowler Vance G. , Ruffin Felicia , Panuwet Parinya , Barr Dana B. , Beare Jennifer L. , Smith Anthony K. , Spurbeck Rachel R. , Vangeti Sindhu , Ramos Irene , Nudelman German , Sealfon Stuart C. , Castellino Flora , Walley Anna Maria , Evans Thomas , Müller Fabian , Greenleaf William J. , Ecker Joseph R.
Published: July 2023

The epigenomic landscape of human immune cells is dynamically shaped by both genetic factors and environmental exposures. However, the relative contributions of these elements are still not fully understood. In this study, we employed single-nucleus methylation sequencing and ATAC-seq to systematically explore how pathogen and chemical exposures, along with genetic variation, influence the immune cell epigenome. We identified distinct exposure-associated differentially methylated regions (eDMRs) corresponding to each exposure, revealing how environmental factors remodel the methylome, alter immune cell states, and affect transcription factor binding. Furthermore, we observed a significant correlation between changes in DNA methylation and chromatin accessibility, underscoring the coordinated response of the epigenome. We also uncovered genotype-associated DMRs (gDMRs), demonstrating that while eDMRs are enriched in regulatory regions, gDMRs are preferentially located in gene body marks, suggesting that exposures and genetic factors exert differential regulatory control. Notably, disease-associated SNPs were frequently colocalized with meQTLs, providing new cell-type-specific insights into the genetic basis of disease. Our findings underscore the intricate interplay between genetic and environmental factors in sculpting the immune cell epigenome, offering a deeper understanding of how immune cell function is regulated in health and disease.
Laminin γ1-dependent basement membranes are instrumental to ensure proper olfactory placode shape, position and boundary with the brain, as well as olfactory axon development
Authors: Tignard P , Pottin K , Geeverding A , Doulazmi M , Cabrera M , Fouquet C , Liffran M , Fouchard J , Rosello M , Albadri S , Del Bene F , Trembleau A , Breau MA
Published: July 2023

Despite recent progress, the complex roles played by the extracellular matrix in development and disease are still far from being fully understood. Here, we took advantage of the zebrafishslymutation which affects Laminin γ1, a major component of basement membranes, to explore its role in the development of the olfactory system. Following a detailed characterisation of Laminin distribution in the developing olfactory circuit, we analysed basement membrane integrity, olfactory placode and brain morphogenesis, and olfactory axon development inslymutants, using a combination of immunochemistry, electron microscopy and quantitative live imaging of cell movements and axon behaviours. Our results point to an original and dual contribution of Laminin γ1-dependent basement membranes in organising the border between the olfactory placode and the adjacent brain: they maintain placode shape and position in the face of major brain morphogenetic movements, they establish a robust physical barrier between the two tissues while at the same time allowing the local entry of the sensory axons into the brain and their navigation towards the olfactory bulb. This work thus identifies key roles of Laminin γ1-dependent basement membranes in neuronal tissue morphogenesis and axon developmentin vivo.
The importance of input sequence set to consensus-derived proteins and their relationship to reconstructed ancestral proteins
Authors: Nixon Charlotte , Lim Shion A. , Sternke Matt , Barrick Doug , Harms Mike , Marqusee Susan
Published: July 2023

A protein sequence encodes its energy landscape - all the accessible conformations, energetics, and dynamics. The evolutionary relationship between sequence and landscape can be probed phylogenetically by compiling a multiple sequence alignment of homologous sequences and generating common ancestors via Ancestral Sequence Reconstruction or a consensus protein containing the most common amino acid at each position. Both ancestral and consensus proteins are often more stable than their extant homologs - questioning the differences and suggesting that both approaches serve as general methods to engineer thermostability. We used the Ribonuclease H family to compare these approaches and evaluate how the evolutionary relationship of the input sequences affects the properties of the resulting consensus protein. While the overall consensus protein is structured and active, it neither shows properties of a well-folded protein nor has enhanced stability. In contrast, the consensus protein derived from a phylogenetically-restricted region is significantly more stable and cooperatively folded, suggesting that cooperativity may be encoded by different mechanisms in separate clades and lost when too many diverse clades are combined to generate a consensus protein. To explore this, we compared pairwise covariance scores using a Potts formalism as well as higher-order couplings using singular value decomposition (SVD). We find the SVD coordinates of a stable consensus sequence are close to coordinates of the analogous ancestor sequence and its descendants, whereas the unstable consensus sequences are outliers in SVD space.
Uncovering the Vital Role of Lipid Droplets in Coronavirus Replication: A Novel Insight Arising from the Biological Activity of 2-Bromopalmitate
Authors: Liu Dongxiao , Cruz-cosme Ruth , Leibowitz Julian , Wu Yong , Tang Qiyi
Published: July 2023

The emergence of viral infections with global impact highlights the urgent need for broad-spectrum antivirals. In this study, we evaluated the effect of palmitoylation inhibitors [2-bromopalmitate (2-BP), cerulenin, and 2-fluoro palmitic acid (2-FPA)] and the enhancer palmostatin B on the replication of human coronaviruses (hCoV-229E, hCoV-Oc43) and murine hepatitis virus (MHV-A59) at non-cytotoxic concentrations. The results demonstrated that 2-BP strongly suppressed MHV-A59 replication, while cerulenin and 2-FPA only moderately inhibited viral replication. Palmostatin B significantly enhanced viral replication. Notably, 2-BP exhibited superior efficacy. Interestingly, palmostatin B failed to rescue the inhibitory effects of 2-BP but effectively rescued cerulenin and 2-FPA, suggesting additional biological activities of 2-BP beyond palmitoylation inhibition. Furthermore, we discovered that 2-BP specifically disrupted lipid droplets (LDs), and this LD disruption was correlated with viral replication inhibition. Based on our findings, we conclude that the inhibitory effects of 2-BP on viral replication primarily stem from LD disruption rather than palmitoylation inhibition. Therefore, we revealed the crucial role of LDs in the viral replication. Our study provides insights into the development of wide-spectrum antiviral strategies.
Meta-analysis of macrophage nanoparticle targeting across blood and solid tumors using an eLDA Topic modeling Machine Learning approach
Authors: Brown Chloe , Bilynsky Colette , Gainey Melanie , Young Sarah , Kitchin John , Wayne Elizabeth
Published: July 2023

The role of macrophages in regulating the tumor microenvironment has spurned the exponential generation of nanoparticle targeting technologies. With the large amount of literature and the speed at which it is generated it is difficult to remain current with the most up-to-date literature. In this study we performed a topic modeling analysis of the most common usages of nanoparticle targeting of macrophages in solid tumors. The data spans 20 years of literature, providing an extensive meta-analysis of the nanoparticle strategies. Our topic model found 6 distinct topics: Immune and TAMs, Nanoparticles, Imaging, Gene Delivery and Exosomes, Vaccines, and Multi-modal Therapies. We also found distinct nanoparticle usage, tumor types, and therapeutic trends across these topics. Moreover, we established that the topic model could be used to assign new papers into the existing topics, thereby creating a Living Review. This type of meta-analysis provides a useful assessment tool for aggregating data about a large field.
Validating Dynamic Body Acceleration metrics as a measure of energy expenditure in a Neotropical primate
Authors: Rezende Gabriela C. , Cruz-Neto Ariovaldo P. , Börger Luca , Redcliffe James , Hambly Catherine , Speakman John R. , Garbino Guilherme S. T. , Pissinatti Alcides , Moreira Silvia Bahadian , Wilson Rory , Culot Laurence
Published: July 2023

2

Abstract

Quantifying energy expenditure in free-living primates is fundamentally important yet challenging. Acceleration-based metrics such as Dynamic Body Acceleration (DBA), obtained from accelerometers, are potential proxies for energy expenditure, yet have not been previously validated in primates. Here, we validated DBA in black lion tamarins (Leontopithecus chrysopygus) by comparison to doubly labelled water (DLW) in 10 captive tamarins housed at the Rio de Janeiro Primate Centre. Individuals were equipped over 48 hours with a backpack with a tri-axial accelerometer and received an intra-peritoneal DLW injection at the beginning of the experiment, with blood samples taken 1 and 48h later. Daily Energy Expenditure by DLW was 326 (SD=66) kJ/day, close to expected values for primates of their size. The accelerometers recorded at 40 Hz, collecting >6.9 million records per axis for each individual. Individual DBA metrics were calculated and regressed against DLW daily energy measures. From this regression, we found a consistent and significant linear relationship (R2= 0.46) between DLW and DBA, which could be improved by the incorporation of activity and resting time information (R2= 0.52). Our results provide the first estimates of total daily energy expenditure for black lion tamarins and a validation of the method for estimating energy expenditure through accelerometers. Given the similar levels of total energy expenditure of captive and wild primates, this method can now be used in the field to estimate the energy cost of black lion tamarin movements in its natural environment.

1 Summary statement

Dynamic body acceleration was validated against doubly labelled water in black lion tamarins, showing it is a useful tool for measuring free-living energy demands.
Fork in the road: how self-confidence about terrain influences gaze behaviour and path choice
Authors: Eira Silva Vinicius da , Marigold Daniel S.
Published: July 2023

Decisions about where to move occur throughout the day and are essential to life. Different movements may present different challenges and affect the likelihood of achieving a goal. Certain choices may have unintended consequences, some of which may cause harm and bias the decision. Movement decisions rely on a person gathering necessary visual information via shifts in gaze. Here we sought to understand what influences this information-seeking gaze behaviour. We had participants choose between walking across one of two paths that consisted of images of terrain commonly found in either hiking or urban environments. We manipulated the number and type of terrain of each path. We recorded gaze behaviour during the approach to the two paths and had participants rate their self-confidence about walking across each type of terrain as though it was real. Participants did not direct gaze to the path with greater visual information, regardless of how we quantified information. Rather, we show that a person’s self-confidence about their motor abilities predicts how they visually explore the environment with their eyes as well as their choice of action. The greater the self-confidence about walking across one path, the more they directed gaze to it, and the more likely they chose to walk across it. Overall, our results reveal a key role of a cognitive factor (self-confidence) in decision-making during a natural, movement-related behaviour.
A frame and a hotspot in cochlear mechanics
Authors: Strimbu C. Elliott , Chiriboga Lauren A. , Frost Brian L. , Olson Elizabeth S.
Published: July 2023

Auditory sensation is based in nanoscale vibration of the sensory tissue of the cochlea, the organ of Corti complex (OCC). Motion within the OCC is now observable due to optical coherence tomography. In the cochlear base, in response to sound stimulation, the region that includes the electro-motile outer hair cells (OHC) was observed to move with larger amplitude than the basilar membrane (BM) and surrounding regions. The intense motion is based in active cell mechanics, and the region was termed the “hotspot” (Cooper et al., 2018, Nature comm). In addition to this quantitative distinction, the hotspot moved qualitatively differently than the BM, in that its motion scaled nonlinearly with stimulus level at all frequencies, evincing sub-BF activity. Sub-BF activity enhances non-BF motion; thus the frequency tuning of the hotspot was reduced relative to the BM. Regions that did not exhibit sub-BF activity are here defined as the OCC “frame”. By this definition the frame includes the BM, the medial and lateral OCC, and most significantly, the reticular lamina (RL). The frame concept groups the majority OCC as a structure that is largely shielded from sub-BF activity. This shielding, and how it is achieved, are key to the active frequency tuning of the cochlea. The observation that the RL does not move actively sub-BF indicates that hair cell stereocilia are not exposed to sub-BF activity. A complex difference analysis reveals the motion of the hotspot relative to the frame.