bluuebunny/crossref_metadata_2025 huggingface dataset:
Predictive Value of New Onset Versus Primary Meconium-Stained Amniotic Fluid
Authors: Shai Daniel , Mazaki-Tovi Shali , Hendler Israel , Meyer Raanan , Cahan Tal , Shapira Moran , Sivan Eyal , Barzilay Eran , Haas Jigal
Published: June 2023

(Abstracted from Birth 2022;49:805–811

Meconium-stained amniotic fluid (MSAF) occurs in up to 52% of postterm pregnancies, 25% of term pregnancies, and 5% of pregnancies <37 weeks of gestation. As a sign of fetal maturity, MFAS may also help signal fetal distress.
“Urinary Reconstruction in Genital Gender-Affirming Surgery: Checking Our Surgical Complication Blind Spots”
Authors: Blasdel Gaines , Dy Geolani W. , Nikolavsky Dmitriy , Ferrando Cecile A. , Bluebond-Langner Rachel , Zhao Lee C.
Published: June 2023

Background:

Urologic complications in genital gender-affirming surgery (GGAS) are imperfectly measured, with existing evidence limited by “blind spots” which will not be resolved through implementation of patient-reported outcomes alone. Some blind spots are expected in a surgical field with rapidly expanding techniques, and may be exacerbated by factors related to transgender health.

Methods:

We provide a narrative review of systematic reviews published in the last decade to describe the current options for genital gender-affirming surgery and surgeon-reported complications, as well as contrasting peer-reviewed sources with data not reported by primary surgeon. In combination with expert opinion, these findings describe complication rates.

Results:

Eight systematic reviews describe complications in vaginoplasty patients, including 5%-16.3% mean incidence of meatal stenosis and 7%-14.3% mean incidence of vaginal stenosis. Compared to surgeon-reported cohorts, vaginoplasty and vulvoplasty patients in alternate settings report higher rates of voiding dysfunction (47%-66% vs 5.6%-33%), incontinence (23%-33% vs. 4%-19.3%) and misdirected urinary stream (33%-55% vs 9.5%-33%). Outcomes in six reviews of phalloplasty and metoidioplasty included urinary fistula (14%-25%), urethral stricture and/or meatal stenosis (8%-12.2%), and ability to stand to void (73%-99%). Higher rates of fistula (39.5%-56.4%) and stricture (31.8%-65.5%) were observed in alternate cohorts, along with previously unreported complications such as vaginal remnant requiring reoperation.

Conclusion:

The extant literature does not completely describe urologic complications of GGAS. In addition to standardized, robustly validated patient-reported outcome measures, future research on surgeon-reported complications would benefit from using the IDEAL (Idea, Development, Exploration, Assessment, and Long-term Study) framework for surgical innovation.
Distally Based Anterolateral Thigh Flap Algorithm for Unexpected Situations during Soft-Tissue Defect Reconstruction around the Knee
Authors: Du Qingyan , Liu Yuanbo , Zang Mengqing , Zhu Shan , Li Shanshan , Chen Zixiang , Han Tinglu
Published: June 2023

Background:

The distally based anterolateral thigh (dALT) flap is an effective option for soft-tissue reconstruction around the knee; however, unexpected situations may occur intraoperatively, impeding the flap harvest. We proposed an algorithm for surgical conversion for unexpected situations encountered intraoperatively.

Methods:

Between 2010 and 2021, 61 dALT flap harvests were attempted for soft-tissue defect reconstruction around the knee; 25 patients underwent surgical conversion for anomalies, including lack of a suitable perforator, hypoplasia of the descending branch, and compromised reverse flow from the descending branch. After excluding improper cases, 35 flaps were harvested as planned (group A) and 21 surgical conversion cases (group B) were finally enrolled for analysis. An algorithm was developed based on the cases in group B. Outcomes, including complication and flap loss rates, were compared between groups to verify the algorithm’s rationality.

Results:

In group B, the dALT flap was converted to a distally based anteromedial thigh flap (n=8), bi-pedicled dALT flap (n=4), distally based rectus femoris muscle flap (n=3), free anterolateral thigh flap (n=2), or other locoregional flap that required additional incision (n=4). No differences in outcomes were observed between the two groups.

Conclusions:

The proposed contingency planning algorithm for dALT flap surgery proved rational, as surgical conversion could be made via the same incision in most cases, and outcomes generated by the algorithm were acceptable.
Antibiotic Use and Antimicrobial Resistance: KAP survey of medical students to evaluate undergraduate training curriculum
Authors: Saksena Rushika , Parida Annapurna , Jain Madhura , Gaind Rajni
Published: June 2023

Introduction: A better understanding of knowledge, attitude and practices of undergraduate medical students towards antimicrobial resistance (AMR) is necessary to identify gaps in current training curriculum.
Methods: A 20-point Likert scale-based questionnaire divided three parts on knowledge, attitude and practices relating to antibiotic use and resistance was devised. Students attending each year of undergraduate medical program were approached to participate in the study over a one-week-period. KAP scores of each year were compared through logistic ordinal regression and Kruskal-Wallis (KW) test.
Results: Two hundred and eight students participated in the study. Overall, knowledge of about intended use of antibiotics, fixed drug combinations and awareness about AMR was good (average score of 5.9 out of a 8). Steady improvement in knowledge scores was observed from first year (-0.441) to final year (0.00). The medical students had favorable attitude towards rational antimicrobial use (Likert score ³4) including the need to spread awareness about AMR amongst  students and public and following doctor’s prescription. Self-medication was reported by 28.4% of students and hoarding of leftover doses by 49.1%. Attitude score had a direct correlation with the knowledge score on KW test (χ2 =29.6, p≤0.5) but had no significant correlation with antimicrobial practices (χ2 =3.9, p≥0.5).
Conclusion: The gaps identified in students’ practices included self-medication, skipping of dosing, hoarding of leftover medication. As improvement in knowledge did not correlate with that of practices, current curriculum needs to include AMR as a focus area to ensure good antibiotic prescribing practices in future practitioners.
Ramification of Covid-19 pandemic : Occurrence and impact of fungal Infections in a tertiary care hospital
Authors: Kaur Ravinder , Rawat Deepti , William Ashish , Singh Pradeep Kumar , Kandir Neelam S.S , Sharma Akanksha
Published: June 2023

Coronavirus disease 2019 (Covid-19) pandemic has been prevailing for more than a year associated with increased number of opportunistic invasive fungal infections in patients who have been critically ill or immunocompromised. In this retrospective study, details of various clinical specimens received from suspected patients of fungal infections were processed according to standard protocol were studied. The fungal infections were present in 64% (51/79) COVID-19 positive patients and 43% (163/381) COVID-19 negative patients) during the year 2021 during the second wave of COVID-19. Among Covid infected patients, the fungal infection mostly observed was Candidiasis (63%) followed by Aspergillosis (15% ) and Mucormycosis (6%). The maximum samples positive in Covid patients were urine samples followed by Serum (for Aspergillus Galactomannan). Among the urine and respiratory samples (BAL, Tracheal aspirate, Sputum) in Covid-19 positive patients, maximum positivity of Candida species was seen. Mucormycosis in Covid-19 positive patients was isolated in Nasal samples followed by tissue sample with Rhizopus arrhizus and Rhizopus homothallicus. There has been an increase in fungal co-infections during the COVID-19 pandemic which is a matter of great concern. Early diagnosis is essential for effective management of these patients.
Detection of clinically relevant antibiotic resistant bacteria in shared fomites, waste water, and municipal solid wastes disposed in vicinity of residential areas of Nigerian Urban City
Authors: Yusuf Ibrahim , Muhammad Zainab Damji , Muhammad Amin Binta , Shuaibu Maryam Danladi , Hamza Nafisatu , Isah Hajara Dauda , Abdullahi Nasir Bako , Ene Patience James , Shuaibu Sameera Salisu , Doguwa Nasir , Pedro Shamsudeen Lekan , Muhammad Maryam Adamu
Published: June 2023

Studies on environmental hotspots of antibiotic resistant bacteria (ARB) and antibiotic resistance genes (ARGs) are scanty in Nigeria. A study was designed to assess different environmental wastes and shared fomites for carrying ARB and ARGs of public health concern. A total of 392 samples which include sewage (36), sludge (36), diapers (20), plastics (20), water sachet polythene bags (20), food wastes (20), soil under dump sites (20), and fomites which include restroom floors (80), corridors (24), door handles (56) and room floor and walls (60) were collected and screened for harboring resistant bacteria carrying blaKPC, blaNDM-1, blaCMY-2, blaIMP, blaoxa66 and MecA resistance genes. Further, methicillin resistance Staphylococcus aureus (MRSA) and extended spectrum β-lactamase producing Escherichia coli, Klebsiella pneumoniae, Pseudomonas aeruginosa, and Acinetobacter baumannii were detected using standard techniques. The efficacy of routine disinfection procedures in the elimination of ARB from restroom floors was also evaluated. Sewage, sludge, diapers, food wastes, and restroom floors, are frequently contaminated with high and moderate resistant E. coli, K. pneumoniae, P. aeruginosa and MRSA. Two blaOXA51-like gene variants (blaOXA-66 & blaOXA-180) were identified in A. baumannii recovered from the wastes and shared fomites. Seven ESBL-K. pneumoniae, 5 ESBL-A. baumannii, 2 ESBL-E. coli and 1 ESBL- P. aeruginosa, harboring one or more ARGs (blaKPC, blaNDM-1, blaCMY-2) were detected from isolates colonizing sewage, sludge, restroom floors, and plastics. ARB persisted in restroom floors after disinfection procedures. Environmental wastes indiscriminately discharged within residential areas and fomites shared among people are highly colonized with ARB that harbors ARGs of public health importance.
Clinical impact and public health challenges of a PVL- MRSA bacteraemia outbreak amongst people who inject drugs in South Yorkshire.
Authors: Beaumont Matthew , Subramanian Bala , Agwuh Ken , Pichon Bruno , Ryan Yan
Published: June 2023

Background: Panton-Valentine leukocidin (PVL) Staphylococcus aureus (SA) is an emergent public health concern. PVL toxin has been mostly associated with methicillin-sensitive Staphylococcus aureus (MSSA) related skin and soft tissue infections occurring in high-risk groups such as people who inject drugs (PWID). The emergence of PVL- methicillin resistant Staphylococcus aureus (MRSA) infection is causing severe and life-threatening disease in PWID. 
Clinical cases: we present an outbreak of eight PVL-MRSA bacteraemias at a UK teaching hospital between 2018 and 2022. An additional four patients developed bacteraemias with PVL-negative MRSA of the same multi-locus sequence type (MLST). All patients were PWID and aged between 33- 51 years old. Four patients developed MRSA bacterial endocarditis. Three patients died. These cases represent the initial cases detected at Doncaster and Bassetlaw Teaching Hospitals of what is an ongoing and developing outbreak.  
Management: an outbreak investigation has been undertaken in association with the UK Health Security Agency.  Epidemiological factors have been explored, including via direct contact at a local sheltered accommodation and the possibility of a contaminated drug supply. Whole-genome sequencing confirmed that all isolates were closely related and of the same MLST (sequence type 5). A community substance misuse group disseminated health education on the prevention of PVL-MRSA. Preventing infection in PWID presents a major challenge due to the impact of addiction on engagement with services and the significant barriers faced by our patients to observing infection prevention measures. 
Conclusion: PVL-MRSA is of major public health concern and outbreak investigation and mapping out local epidemiological patterns plays a vital role in preventing further spread throughout the community. Additionally, this work enables targeted and early treatment in patients in high-risk categories for disease. These cases of PVL-MRSA infection in PWID highlights the transmissibility, pathogenic potential and severe clinical disease spectrum within this population. Further work is required to tackle transmission and infection from this pathogenic strain.
Wound infection with Bacteroides fragilis: A case report
Authors: Siddiqui Oves , William Ashish , Gupta Nilakshi , Nirmal Swati , Saxena Sonal
Published: June 2023

Bacteroides fragilis is an anaerobic organism which can cause abdominal infections, abscesses, skin and soft tissue infection, and sepsis with high degree of mortality. We present a case of intra-abdominal wound infection after penetrating wound injury caused by B.fragilis. Early diagnosis and treatment has been been critical in the prevention of morbidity and mortality associated with the infection.
Streptomyces zingiberis sp. nov., an endophytic actinobacterium isolated from the root tissue of Zingiber montanum
Authors: Pansomsuay Rawirat , Duangupama Thitikorn , Pittayakhajonwut Pattama , Intaraudom Chakapong , Suriyachadkun Chanwit , He Ya-Wen , Tanasupawat Somboon , Thawai Chitti
Published: June 2023

An endophytic actinobacterium, designated strain PLAI 1-29T, was isolated from the root tissue of Zingiber montanum collected from Pathum Thani province, Thailand. Strain PLAI 1-29T was characterized using a polyphasic taxonomic approach. It typically exhibited morphological and chemotaxonomic properties of the genus

Streptomyces

. Strain PLAI 1-29T produced a spiral spore chain on aerial mycelium and grew at 15–40 °C, pH 6–10 on International

Streptomyces

Project 2 agar. The maximum NaCl concentration for growth was 9 % (w/v). Cells of strain PLAI 1-29T presented
ll
-diaminopimelic acid, arabinose, galactose and ribose. The detected phospholipids were diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol, phosphatidylinositol and phosphatidylinositol mannoside. The major menaquinones were MK-9(H6) and MK-9(H8). The major cellular fatty acids were iso-C16 : 0, anteiso-C15 : 0 and anteiso-C17 : 0. The genome-based taxonomic details revealed the assignment of strain PLAI 1-29T to the genus

Streptomyces

and exhibited low threshold values for the delineation of a novel species by average nucleotide identity–blast (84.0%), average amino acid identity (80.0%) and digital DNA–DNA hybridization (27.6%) with its closest type strain,

Streptomyces xinghaiensis

S187T. Furthermore, several differential physiological and biochemical characteristics were detected between strain PLAI 1-29T and the closest type strain. Based on the combined phenotypic and genomic features, strain PLAI 1-29T (=TBRC 7645T=NBRC 113170T) is considered to represent a new

Streptomyces

species, for which we propose the name Streptomyces zingiberis sp. nov.
Zika virus NS3 and NS5 proteins determine strain-dependent differences in dsRNA accumulation in a host cell type-dependent manner
Authors: Barnard Trisha R. , Landry Breanna N. , Wang Alex B. , Sagan Selena M.
Published: June 2023

For positive-sense RNA viruses, initiation of viral RNA replication represents a major target of antiviral responses to infection. Despite this, the interplay between viral replication and the innate antiviral response at early steps in the Zika virus (ZIKV) life cycle is not well understood. We have previously identified ZIKV isolates with differing levels of dsRNA accumulation, ZIKVPR (high dsRNA per infected cell) and ZIKVCDN (low dsRNA per infected cell), and we hypothesized that we could use reverse genetics to investigate how host and viral factors contribute to the establishment of viral RNA replication. We found that both the ZIKV NS3 and NS5 proteins as well as host factors were necessary to determine the dsRNA accumulation phenotype. Additionally, we show that dsRNA correlates with viral negative-strand RNA measured by strand-specific RT-qPCR, suggesting that dsRNA is an accurate readout of viral RNA replication. Interestingly, although we did not observe NS3- and NS5-dependent differences in cells with defects in interferon (IFN) production, differences in RNA accumulation precede induction of the IFN response, suggesting that RNA sensing pathways or intrinsic restriction factors may differentially restrict ZIKV in an NS3- and NS5-dependent manner. This work expands our understanding of the interplay of early steps of viral RNA replication and the induction of the innate antiviral response to ZIKV infection.
Imageless navigation system (Naviswiss) provides accurate component position in total hip arthroplasty with lateral decubitus position for end-stage hip osteoarthritis: A prospective cohort study with CT-validation
Authors: Scholes Corey , Fatima Manaal , Schwagli Tobias , Liu David
Published: June 2023

Aims

The Naviswiss system (Naviswiss AG, Brugg, Switzerland) is a handheld imageless navigation device used to improve the accuracy of implant positioning in total hip arthroplasty (THA). However, clinical data for leg length discrepancy and femoral offset is lacking, and the validity of the system has not been reported for patients undergoing THA in the lateral decubitus position. This study aimed to report the accuracy of the device in this patient population.

Methods

Patients underwent THA in the lateral decubitus position by a single surgeon. Component positioning measured by the device intraoperatively was compared to postoperative measurements on computed tomography (CT) scans. Agreement between the navigation system and postoperative measurements was reported with respect to acetabular cup inclination, acetabular cup version, femoral offset and leg length discrepancy.

Results

The mean difference between intraoperative and postoperative CT measurements was within 2° for angular measurements and 2mm for leg length. Absolute differences for the two indices were within 5° and 4mm. Mean bias was 1-2° overestimation for cup orientation and up to 2mm overestimation for leg length change, but 95% limits of agreement did not exceed absolute thresholds of 10° and 10mm, especially after correction for bias. Four cases (12%) were declared intraoperatively for issues with fixation on the greater trochanter. While inclusion of these cases generated acceptable accuracy overall, their omission improved between-case variability in accuracy and reduced the LOA for both offset and leg length.

Conclusions

The accuracy of the Naviswiss system falls within clinically acceptable recommendations for acetabular cup placement, femoral offset and length length. The system could be further improved with regression-based bias correction.
Investigation ofRFC1tandem nucleotide repeat locus in diverse neurodegenerative outcomes in an Indian cohort
Authors: Tyagi Nishu , Uppili Bharathram , Sharma Pooja , Parveen Shaista , Saifi Sheeba , Jain Abhinav , Sonakar Akhilesh , Ahmed Istaq , Sahni Shweta , Shamim Uzma , Anand Avni , Suroliya Varun , Asokachandran Vivekanand , Srivastava Achal , Sivasubbu Sridhar , Scaria Vinod , Faruq Mohammed
Published: June 2023

Background and Objectives

An intronic bi-allelic pentanucleotide repeat expansion mutation, (AAGGG)400-2000at AAAAG repeat locus inRFC1gene is known as underlying genetic cause in cases with cerebellar ataxia, neuropathy and vestibular areflexia syndrome (CANVAS) and late onset sporadic ataxia. Biallelic positive cases carry a common recessive risk haplotype, ‘AAGA’ spanningRFC1gene. In this study our aim is to find prevalence of bi-allelic (AAGGG)expin Indian ataxia and other neurological disorders and investigate the complexity ofRFC1repeat locus and its potential association with neurodegenerative diseases in Indian population-based cohorts.

Methods

We carried out repeat number and repeat type estimation using flanking PCR and repeat primed PCR (AAAAG/AAAGG/AAGGG) in three Indian disease cohorts and healthy controls. Haplotype assessment of suspected cases was done by genotyping and confirmed by sanger sequencing. Blood samples and consent of all the cases and detailed clinical details of positive cases were collected in collaboration with AIIMS. Further, comprehension ofRFC1repeat locus and risk haplotype analysis in Indian background was performed on the NGS data of Indian healthy controls by ExpansionHunter, ExpansionHunter de novo and PHASE analysis respectively.

Results

Genetic screening ofRFC1-TNR locus in 1998 uncharacterised cases (SCA12: 87; Uncharacterised ataxia: 1818, CMT: 93) and 564 heterogenous controls showed that the frequency of subjects with bi-allelic (AAGGG)expare 1.15%, <0.05%, 2.15% and 0% respectively. TwoRFC1positive sporadic late onset ataxia cases, one bi-allelic (AAGGG)expand another, (AAAGG)exp/(AAGGG)exphad recessive risk haplotype and CANVAS symptoms. Long normal alleles, 15-27, are significantly rare in ataxia cohort. In IndiGen control population (IndiGen; N=1029), long normal repeat range, 15-27, is significantly associated with A3G3and some rare repeat motifs, AGAGG, AACGG, AAGAG, and AAGGC. Risk-associated ‘AAGA’ haplotype of the original pathogenic expansion of A2G3was found associated with the A3G3representing alleles in background population.

Discussion

Apart from bi-allelic (AAGGG)exp, we report cases with a new pathogenic expansion of (AAAGG)exp/(AAGGG)expinRFC1and recessive risk haplotype, ‘AAGA’. We found different repeat motifs atRFC1TNR locus, like, AAAAG, AAAGG, AAAGGG, AAAAGG, AAGAG, AACGG, AAGGC, AGAGG, AAGGG, in Indian background population except ACAGG and (AAAGG)n/(AAGGG)n. Our findings will help in further understanding the role of long normal repeat size and different repeat motifs specifically, AAAGG, AAAGGG and other rare repeat motifs, atRFC1locus.

Abstract Figure

Graphical Abstract:

Genetic heterogenicity atRFC1-TNR locus.
Transfer Learning Enhanced Graph Neural Network for Aldehyde Oxidase Metabolism Prediction and Its Experimental Application
Authors: Xiong Jiacheng , Cui Rongrong , Li Zhaojun , Zhang Wei , Zhang Runze , Fu Zunyun , Liu Xiaohong , Li Zhenghao , Chen Kaixian , Zheng Mingyue
Published: June 2023

Aldehyde oxidase (AOX) is a molybdoenzyme that is primarily expressed in the liver and is involved in the metabolism of drugs and other xenobiotics. AOX-mediated metabolism can result in unexpected outcomes, such as the production of toxic metabolites and high metabolic clearance, which can lead to the clinical failure of novel therapeutic agents. Computational models can assist medicinal chemists in rapidly evaluating the AOX metabolic risk of compounds during the early phases of drug discovery and provide valuable clues for manipulating AOX-mediated metabolism liability. In this study, we developed a novel graph neural network called AOMP for predicting AOX-mediated metabolism. AOMP integrated the tasks of metabolic substrate/non-substrate classification and metabolic site prediction, while utilizing transfer learning from 13C nuclear magnetic resonance data to enhance its performance on both tasks. AOMP significantly outperformed the benchmark methods in both cross-validation and external testing. Using AOMP, we systematically assessed the AOX-mediated metabolism of common fragments in kinase inhibitors and successfully identified four new scaffolds with AOX metabolism liability, which were validated through in vitro experiments. Furthermore, for the convenience of the community, we established the first online service for AOX metabolism prediction based on AOMP, which is freely available athttps://aomp.alphama.com.cn.
Ontogenetic Patterns in Juvenile Blue Crab density: Effects of Habitat and Turbidity in a Chesapeake Bay Tributary
Authors: Hyman A. Challen , Chiu Grace S. , Seebo Michael S. , Smith Alison , Saluta Gabrielle G. , Lipcius Romuald N.
Published: June 2023

Nursery habitats are characterized by favorable conditions for juveniles, such as higher food availability and lower predation risk, and dispropor-tionately contribute more individuals per unit area to adult segments of the population compared to other habitats. However, nursery habitat inference is complicated by changes in habitat preferences with ontogeny; individuals in early-life stages frequently inhabit different habitats than older juveniles or adults. In this mensurative field experiment, we modeled the density of two juvenile blue crab,Callinectes sapidus, size classes based on carapace width (CW) across multiple habitats at various locations within an estuarine seascape during the blue crab recruitment season. We examined four habi-tat types—unstructured sand, seagrass meadows, salt marsh edge (SME), and shallow detrital habitat (SDH). Results indicated that densities of small ju-venile blue crabs (≤15 mm CW) were highest in seagrass, whereas densities of larger juveniles (16–30 mm CW) were highest in SME. Densities of large juveniles in SME were also greater than those of small juveniles, suggest-ing possible secondary dispersal to SME by small juveniles after settlement and recruitment in seagrass. Turbidity was positively correlated with densi-ties of both size classes, although our model did not address whether this was due to top-down (refuge) or bottom-up (food availability) mechanisms. Ob-served patterns in size-specific habitat utilization may result from changing requirements of juvenile blue crabs with size, as animals minimize mortality-to-growth ratios. Taken together with previous work and patterns observed in SME, these findings emphasize the role of salt marsh habitat within juve-nile blue crab ontogeny and underscore the need to quantify and preserve the complete chain of habitats used by juveniles.
Soluble CTLA-4 raises the threshold for T-cell activation and modulates anti-tumour immunity
Authors: Kennedy Paul T. , Saulters Emma L. , Duckworth Andrew D. , Lim Yeong Jer , Woolley John F. , Slupsky Joseph R. , Cragg Mark S. , Ward Frank J. , Dahal Lekh N.
Published: June 2023

CTLA-4 is a crucial immune checkpoint receptor involved in the maintenance of immune homeostasis, tolerance, and tumour control. Antibodies targeting CTLA-4 have been promising treatment for numerous cancers, but the mechanistic basis of their anti-tumoral immune boosting effects are poorly understood. Although thectla4gene also encodes an alternatively-spliced soluble variant (sCTLA-4), preclinical/clinical evaluation of anti-CTLA-4-based immunotherapies have not considered the contribution of this isoform. Here, we explore the functional properties of sCTLA-4 and evaluate the efficacy of isoform-specific anti-sCTLA-4 antibody targeting in murine cancer model. We show that expression of sCTLA-4 in tumour cells suppresses CD8+T-cellsin vitro, and accelerates growth and experimental metastasis of murine tumoursin vivo. These effects were accompanied by modification of the immune infiltrate, notably restraining CD8+T-cells in a non-effector state. sCTLA-4 blockade with isoform-specific antibody reversed this restraint, enhancing intratumoural CD8+T-cell activation and cytolytic potential, correlating with therapeutic efficacy and tumour control. This previously unappreciated role of sCTLA-4 suggests that better understanding of the biology and function of multi-gene products of immune checkpoint receptors needs to be fully elucidated for improved cancer immunotherapy.
Imaging the pharmacokinetics and therapeutic availability of the bispecific CD3xTRP1 antibody in syngeneic mouse tumor models
Authors: Sandker Gerwin G.W. , Middelburg Jim , Wilbrink Evienne , Molkenboer-Kuenen Janneke , Aarntzen Erik H.J.G. , van Hall Thorbald , Heskamp Sandra
Published: June 2023

Background

CD3 bispecific antibodies (CD3-bsAbs) require binding of both a tumor-associated surface antigen and CD3 for their immunotherapeutic effect. Their efficacy is, therefore, influenced by the absolute tumor uptake and the extracellular dose. To optimize their currently limited efficacy in solid tumors, increased understanding of their pharmacokinetics andin vivointernalization is needed.

Methods

Here were studied the pharmacokinetics andin vivointernalization of CD3xTRP1, a fully murine Fc-inert bsAb, in endogenous TRP1-expressing immunocompetent male C57BL/6J mice bearing TRP1-positive and negative tumors over time. Matching bsAbs lacking TRP1- or CD3-binding capacity served as controls. BsAbs were radiolabeled with111In to investigate their pharmacokinetics, target binding, and biodistribution through SPECT/CT imaging andex vivobiodistribution analyses. Co-injection of111In- and125I-labeled bsAb was performed to investigate thein vivointernalization by comparing tissue concentrations of cellular residing111In versus effluxing125I. Anti-tumor therapy effects were evaluated by monitoring tumor growth and immunohistochemistry.

Results

SPECT/CT and biodistribution analyses showed that CD3xTRP1 specifically targeted TRP1-positive tumors and CD3-rich lymphoid organ and uptake peaked 24 hours pi (KPC3-TRP1: 37.7±5.3 %ID/g, spleen: 29.0±3.9 %ID/g). Studies with control bsAbs demonstrated that uptake of CD3xTRP1 in TRP1-positive tumors and CD3-rich tissues was primarily receptor-mediated. Together with CD3xTRP1 in the circulation being mainly unattached, this indicates that CD3+T cells are generally not traffickers of CD3-bsAbs to the tumor. Additionally, “antigen-sink” effects by TRP1-expressing melanocytes were not observed. We further demonstrated rapid internalization of CD3xTRP1 in KPC3-TRP1 tumors (24h pi: 54.9±2.3% internalized) and CD3-rich tissues (spleen, 24h pi: 79.7±0.9% internalized). Therapeutic effects by CD3xTRP1 were observed for TRP1-positive tumors and consisted of high tumor influx of CD8+T cells and neutrophils, which corresponded with increased necrosis and growth delay.

Conclusions

We show that CD3xTRP1 efficiently targets TRP1-positive tumors and CD3-rich tissues primarily through receptor-mediated targeting. We further demonstrate rapid receptor-mediated internalization of CD3xTRP1 in TRP1-positive tumors and CD3-rich tissues. Even though this significantly decreases the therapeutical available dose, CD3xTRP1 still induced effective anti-tumor T-cell responses and inhibited tumor growth. Together, our data on the pharmacokinetics and mechanism of action of CD3xTRP1 pave the way for further optimization of CD3-bsAb therapies.

Graphical abstract

Imaging the pharmacokinetics and therapeutic availability of the bispecific CD3xTRPl antibody in syngeneic mouse tumor models
Arrest of mouse preterm labor until term delivery by combination therapy with atosiban and mundulone, a natural product with tocolytic efficacy
Authors: Siricilla Shajila , Hansen Christopher J. , Rogers Jackson H. , De Debasmita , Simpson Carolyn L. , Waterson Alex G. , Sulikowski Gary A. , Crockett Stacey L. , Boatwright Naoko , Reese Jeff , Paria Bibhash C. , Newton J , Herington Jennifer L.
Published: June 2023

Currently, there is a lack of FDA-approved tocolytics for the management of preterm labor (PL). In prior drug discovery efforts, we identified mundulone and its analog mundulone acetate (MA) as inhibitors ofin vitrointracellular Ca2+-regulated myometrial contractility. In this study, we probed the tocolytic and therapeutic potential of these small molecules using myometrial cells and tissues obtained from patients receiving cesarean deliveries, as well as a mouse model of PL resulting in preterm birth. In a phenotypic assay, mundulone displayed greater efficacy in the inhibition of intracellular-Ca2+from myometrial cells; however, MA showed greater potency and uterine-selectivity, based IC50and Emaxvalues between myometrial cells compared to aorta vascular smooth muscle cells, a major maternal off-target site of current tocolytics. Cell viability assays revealed that MA was significantly less cytotoxic. Organ bath and vessel myography studies showed that only mundulone exerted concentration-dependent inhibition ofex vivomyometrial contractions and that neither mundulone or MA affected vasoreactivity of ductus arteriosus, a major fetal off-target of current tocolytics. A high-throughput combination screen ofin vitrointracellular Ca2+-mobilization identified that mundulone exhibits synergism with two clinical-tocolytics (atosiban and nifedipine), and MA displayed synergistic efficacy with nifedipine. Of these synergistic combinations, mundulone + atosiban demonstrated a favorablein vitrotherapeutic index (TI)=10, a substantial improvement compared to TI=0.8 for mundulone alone. Theex vivoandin vivosynergism of mundulone and atosiban was substantiated, yielding greater tocolytic efficacy and potency on isolated mouse and human myometrial tissue and reduced preterm birth rates in a mouse model of PL compared to each single agent. Treatment with mundulone 5hrs after mifepristone administration (and PL induction) dose-dependently delayed the timing of delivery. Importantly, mundulone in combination with atosiban (FR 3.7:1, 6.5mg/kg + 1.75mg/kg) permitted long-term management of PL after induction with 30 μg mifepristone, allowing 71% dams to deliver viable pups at term (> day 19, 4-5 days post-mifepristone exposure) without any visible maternal and fetal consequences. Collectively, these studies provide a strong foundation for the future development of mundulone as a stand-alone single- and/or combination-tocolytic therapy for management of PL.
Biased activation of the vasopressin V2 receptor probed by NMR, paramagnetic ligands, and molecular dynamics simulations
Authors: Gaibelet Gérald , Fouillen Aurélien , Riché Stéphanie , Orcel Hélène , Mendre Christiane , Kanso Ali , Lanotte Romain , Nguyen Julie , Dimon Juliette , Urbach Serge , Sounier Rémy , Granier Sébastien , Bonnet Dominique , Cong Xiaojing , Mouillac Bernard , Déméné Hélène
Published: June 2023

G protein-coupled receptors (GPCRs) control critical intercellular communications by responding to extracellular stimuli and undertaking conformational changes to convey signals to intracellular effectors. We combined NMR, molecular pharmacology, and molecular dynamics (MD) simulations to study the conformational diversity of the vasopressin V2 GPCR subtype (V2R) bound to different types of ligands: the antagonist tolvaptan, the endogenous unbiased agonist arginine-vasopressin, and MCF14, a Gs-protein biased agonist. We developed a double-labeling NMR scheme to study the conformational dynamics: V2R was subjected to lysine13CH3methylation, whereas the agonists were tagged with a paramagnetic probe. Paramagnetic relaxation enhancements were used to validate the ligand binding poses in the MD simulations. We found that the bias for the Gs protein over the β-arrestin pathway involves interactions between the conserved NPxxY motif in the transmembrane helix (TM) 7 and a central hydrophobic patch in TM3, which constrains TM7 and likely inhibits β-arrestin signaling. A similar mechanism was observed for the pathogenic mutation, I1303.43N, which constitutively activates the Gs protein without concomitant β-arrestin recruitment. This mechanism resembles to opioid receptors findings indicating common patterns in class A GPCRs.
An R package for ensemble learning stacking
Authors: Nukui Taichi , Onogi Akio
Published: June 2023

We developed an R package for stacking, which is an ensemble approach to supervised learning. Using this package, training and prediction of stacking can be conducted using one-row scripts.

Availability and implementation

The R package stacking is available at the GitHub (https://github.com/Onogi/stacking).

Contact

onogiakio@gmail.com

Supplementary information

This manuscript has no supplementary information.
Identification of disulfidptosis-related-ferroptosis associated lncRNAs signature as a novel prognosis model for kidney renal clear cell carcinoma
Authors: Xu Zihan
Published: June 2023

Background:Clear cell renal cell carcinoma (ccRCC) represents 80% of all kidney cancers and has a poor prognosis. Newly discovered types of programmed cell death, ferroptosis and disulfidptosis, could have a direct impact on the outcome of KIRC cancer. Long non-coding RNAs (lncRNAs), which possess stable structures, can influence cancer prognosis and might be potential prognostic prediction factors for KIRC cancer. This study aims to investigate the correlation between disulfidptosis-related ferroptosis-related lncRNA and ccRCC in terms of immunity and prognosis.

Methods:Coexpression analysis was employed to identify disulfidptosis-related ferroptosis-related long non-coding RNAs (DRFRLs). Differential expression analysis of DRFRLs was conducted using the ‘limma’ package in R software, and the ‘ConsensusClusterPlus’ package was utilized to identify molecular subtypes. Prognostic DRFRLs were identified via univariate Cox analysis, and a prognostic model based on eight DRFRLs was constructed through Cox regression analysis and the least absolute shrinkage and selection operator (LASSO) algorithm. Kaplan-Meier (K-M) survival curve analysis and receiver operating characteristic (ROC) curve analysis were utilized to evaluate the prognostic power of this model. Additionally, differences in biological function were investigated using Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG), while immunotherapy response was measured by utilizing tumor mutational burden (TMB) and tumor immune dysfunction and rejection (TIDE) scores. Single-cell analysis from the Tumor Immune Single Cell Center (TISCH) was employed to investigate cells with specific expression of the eight identified lncRNAs.

Results:Two clusters (A and B) of disulfidptosis-related ferroptosis-related long non-coding RNAs (DRFRLs) were identified. Survival analysis revealed that patients with subtype A had a higher probability of survival compared to those in subtype B, suggesting that subtype A predicts better survival. An eight-lncRNA signature was established through LASSO-Cox regression, and Kaplan-Meier curves validated the accuracy of prognostic features prediction (P < 0.001). This signature demonstrated excellent prognostic performance, with an area under the curve (AUC) of 0.762, 0.761, and 0.749 at 1, 3, and 5 years in the training set and 0.790, 0.739, and 0.726 in the testing set, respectively. In the single-cell dataset, LINC01534, FOXD2-AS1, AC002070.1, and AL158212.3 were found to be expressed, with FOXD2-AS1 and AC002070.1 specifically expressing in the KC tumor immune microenvironment.

Conclusions:The proposed signature of eight lncRNAs is a promising biomarker for predicting clinical outcomes and therapeutic responses in patients with ccRCC.
Molecular architecture and conservation of an immature human endogenous retrovirus
Authors: Krebs Anna-Sophia , Liu Hsuan-Fu , Zhou Ye , Rey Juan S. , Levintov Lev , Shen Juan , Howe Andrew , Perilla Juan R. , Bartesaghi Alberto , Zhang Peijun
Published: June 2023

A significant part of the human genome consists of endogenous retroviruses sequences. Human endogenous retrovirus K (HERV-K) is the most recently acquired endogenous retrovirus, is activated and expressed in many cancers and amyotrophic lateral sclerosis and possibly contributes to the aging process. To understand the molecular architecture of endogenous retroviruses, we determined the structure of immature HERV-K from native virus-like particles (VLPs) using cryo-electron tomography and subtomogram averaging (cryoET STA). The HERV-K VLPs show a greater distance between the viral membrane and immature capsid lattice, correlating with the presence of additional peptides, SP1 and p15, between the capsid (CA) and matrix (MA) proteins compared to the other retroviruses. The resulting cryoET STA map of the immature HERV-K capsid at 3.2 Å resolution shows a hexamer unit oligomerized through a 6-helix bundle which is further stabilized by a small molecule in the same way as the IP6 in immature HIV-1 capsid. The HERV-K immature CA hexamer assembles into the immature lattice via highly conserved dimmer and trimer interfaces, whose interactions were further detailed through all-atom molecular dynamics simulations and supported by mutational studies. A large conformational change mediated by the flexible linker between the N-terminal and the C-terminal domains of CA occurs between the immature and the mature HERV-K capsid protein, analogous to HIV-1. Comparison between HERV-K and other retroviral immature capsid structures reveals a highly conserved mechanism for the assembly and maturation of retroviruses across genera and evolutionary time.
Metabolic regulation in erythroid differentiation by systemic ketogenesis in fasted mice
Authors: Ma Wenjuan , Arima Yuichiro , Umemoto Terumasa , Yokomizo Tomomasa , Xu Yuqing , Miharada Kenichi , Tanaka Yosuke , Suda Toshio
Published: June 2023

Systemic ketogenesis affects murine erythroid differentiation under fasting condition, while less ketone body β OHB boosts fatty acid synthesis and mevalonate pathway along with decreased levels of histone acetylation, which are beneficial for erythroid differentiation and maturation undergoing stressed erythropoiesis.

Erythroid terminal differentiation and maturation depends on enormous energy supply. During periods of fasting, ketone bodies from the liver are transported into circulation and utilized as crucial fuel for peripheral tissues. However, the effects of fasting or ketogenesis on erythroid behavior remain unknown. Here, we generated a mouse model with insufficient ketogenesis by conditionally knocking out the gene encoding the hepatocyte-specific ketogenic enzyme hydroxymethylglutary-CoA synthase 2 (Hmgcs2KO). Intriguingly, erythroid maturation was enhanced with boosted fatty acid synthesis in bone marrow of hepaticHmgcs2KO mouse under fasting condition, suggesting that systemic ketogenesis has a profound effect on erythropoiesis. Moreover, we observed significantly activated fatty acids synthesis and mevalonate pathway along with reduced histone acetylation in immature erythrocytes under less systemic ketogenesis condition. Our findings revealed an innovative insight to erythroid differentiation, in which metabolic homeostasis and histone acetylation mediated by ketone bodies are essential factors in adaptation towards nutrient deprivation and stressed erythropoiesis.
Microbiome time series data reveal predictable patterns of change
Authors: Karwowska Zuzanna , Szczerbiak Paweł , Kosciolek Tomasz
Published: June 2023

Background

The gut microbiome is crucial for human health and disease. Longitudinal studies are gaining importance in understanding its dynamics over time, compared to cross-sectional approaches. Investigating the temporal dynamics of the microbiome, including individual bacterial species and clusters, is essential for comprehending its functionality and impact on health. This knowledge has implications for targeted therapeutic strategies, such as personalized diets and probiotic therapy.

Results

Here, by adopting a rigorous statistical approach, we aim to shed light on the temporal changes in the gut microbiome and unravel its intricate behavior over time. We leveraged four long and dense time series of the gut microbiome in generally healthy individuals examining how its composition evolves as a community and how individual bacterial species behave over time. We also explore whether specific clusters of bacteria exhibit similar fluctuations, which could provide insights into potential functional relationships and interactions within the microbiome Our study reveals that despite its high volatility, the human gut microbiome is stable in time and can be predicted based solely on its previous states. We characterize the unique temporal behavior of individual bacterial species and identify distinct longitudinal regimes in which bacteria exhibit specific patterns of behavior. Finally, through cluster analysis, we identify groups of bacteria that exhibit coordinated fluctuations over time.

Conclusions

Our findings contribute to our understanding of the dynamic nature of the gut microbiome and its potential implications for human health. The provided guidelines support scientists studying gut microbiome complex dynamics, promoting further research and advancements in microbiome analysis.
Epistolizing accountability: a critical exploration of INGO annual report leaders' letters
Authors: Abnett Helen
Published: June 2023

Purpose

This paper explores how INGOs communicate their activities and achievements. In doing so, the study seeks to increase our understanding of INGOs' accountability practices.

Design/methodology/approach

This paper uses thematic analysis to analyse 90 ‘leaders’ letters' (the letters that many charities include at the beginning of their Annual Reports and Accounts), published by 39 INGOs between 2015 and 2018.

Findings

This paper argues that within the Annual Report letters under consideration, INGOs' accountability practices focus on quantitative, process-driven, output reporting. In doing so, it is the actions and agency of INGOs that are primarily emphasised. INGO constituents are largely excluded from representation. Donors are presented only as contributors of financial capital. Drawing on field theory, the paper argues that this representational practice means INGO constituents are almost irrelevant to INGOs' representational and accountability communication practices.

Originality/value

This paper is indebted to previous important work and, building on such scholarship, seeks to contribute to the ongoing conversation about INGO accountability. While reinforcing some prior knowledge, the findings here also differ in the understanding of how donors are portrayed. The paper extends previous analyses by using field theory to show that the INGO field as considered here is a space in which representations of accountability are based on organisational and transactional factors, and does not value the humanity of INGOs' constituents. This connects to operations of power, between donors, INGOs, and constituents, and reinforces inequitable power within the development system.
Drivers of liking and value perception for a new apple cultivar in Italy
Authors: Rivaroli Sergio , Spadoni Roberta , Tartarini Stefano , Gregori Roberto , Riedel Bettina , Draicchio Paola , Folini Luca , Altintzoglou Themistoklis , Canavari Maurizio
Published: June 2023

Purpose

Combining sensory evaluations and hypothetical valuation mechanisms, this study aims to investigate the impact of consumers' product sensory attributes on willingness to pay (WTP) and overall liking for a new apple cultivar.

Design/methodology/approach

A sample of non-expert participants (n = 122) evaluated the overall liking and just-about-right (JAR) attributes. A variable transformation approach was applied to make linear and interval regression models between the JAR attributes, overall liking scores and participants' WTP.

Findings

The study reveals the high consumer appreciation for the new apple in both hedonic and economic terms. After controlling the anchoring effect's bias, the predicted mean WTP for the new apple cultivar was €3.26 per kilogramme. Crunchiness and flavour significantly affect both participants' overall liking and WTP.

Research limitations/implications

The main limitation is the non-probabilistic sampling procedure, which does not allow for the generalisation of the results. Penalty analysis for JAR attributes in monetary and hedonic terms is beneficial for optimising the product and evaluating its potential in the marketplace.

Practical implications

The findings provide helpful directions for product optimisation in future breeding programmes to ensure the long-term sustainability of the new apple cultivars in the marketplace.

Originality/value

This study provides evidence of the beneficial synergy of mixing sensory-oriented research with the behavioural economics field of study.