bluuebunny/crossref_metadata_2025 huggingface dataset:
Ocular thermography and clinical measurements in symptomatic and asymptomatic soft contact lens wearers
Authors: Moghadas Maryam , Nosch Daniela S. , Käser Emanuele , Klostermeier Jennifer , Santer Verena , Demian Paul , Bertolini Giovanni , Lamrani Mouad
Published: September 2024

SIGNIFICANCE

Symptoms of dryness and discomfort are the main reasons for contact lens dropout. Clinical tests for this purpose are invasive or subjective. Ocular thermography may help to assess the ocular discomfort and dryness in a noninvasive and objective manner.

PURPOSE

This study aimed to investigate the relationship of ocular thermography with clinical measurements in habitual symptomatic and asymptomatic soft contact lens wearers.

METHODS

Forty habitual contact lens wearers were evaluated in two age- and gender-matched asymptomatic and symptomatic groups (Contact Lens Discomfort Questionnaire scores ≤8 and ≥14, respectively). Clinical measurements took place during visit 1 (with contact lens in situ and after contact lens removal) and at baseline after a 2-week washout period (visit 2). The Ocular Surface Disease Index (OSDI) questionnaire, noninvasive tear breakup time, bulbar conjunctival hyperemia, and corneal staining were assessed. Thermal cooling rate was computed in the central and lower cornea during natural blinking (30 s) and sustained eye opening (10 s).

RESULTS

Dry eye symptoms (OSDI score) were significantly higher in the symptomatic group during contact lens wear (p<0.001) and at baseline (p = 0.001). Thermal cooling rate was significantly higher in the symptomatic group in the lower cornea (10 s, p=0.013) with the contact lens in situ and in the central cornea (30 s, p=0.045) after contact lens removal. At baseline, dry eye symptoms (OSDI score) significantly correlated with cooling rate in the central cornea region for the symptomatic group (30 s: r = −0.5, p=0.03; 10 s: r = −0.63, p=0.005). Noninvasive tear breakup time correlated with cooling rate in the central cornea region at baseline in the symptomatic group (30 s, r = 0.6, p=0.005; 10 s, r = 0.55, p=0.018). Cooling rate in the central cornea region (10-s duration, p<0.0001) and noninvasive tear breakup time (p<0.0001) were identified as significant predictor variables for dry eye symptoms at baseline.

CONCLUSIONS

Noninvasive tear breakup time and thermal cooling rate were identified as significant predictor variables for contact lens–induced dry eye. These findings may suggest the potential for the additional application of ocular thermography in the evaluation of contact lens discomfort.
Higher Expression of Talin-1 is Associated With Less Aggressive Tumor Behavior in Pancreatic Cancer
Authors: Ahmadi Jazi Samira , Tajik Fatemeh , Rezagholizadeh Fereshteh , Taha Seyed Reza , Shariat Zadeh Mahdieh , Bouzari Behnaz , Madjd Zahra
Published: September 2024

Talin-1 is one of the major scaffold proteins in focal adhesions playing a vital role in cell migration, metastasis, and cancer progression. Although studies regarding the importance of Talin-1 in cancer have rapidly developed, its prognostic and diagnostic value still remain unsatisfying in pancreatic cancer (PC). Therefore, the present study aims to investigate the expression, clinical significance, as well as the prognostic and diagnostic value of Talin-1 in different types of PC. Bioinformatic analysis was applied to determine the clinical importance and biological role of Talin-1 expression in PC tumors and the normal adjacent samples. The expression patterns, clinical significance, prognosis, and diagnosis value of Talin-1 were evaluated in tissue microarrays (TMAs) of 190 PC samples including 170 pancreatic ductal adenocarcinoma (PDAC), and 20 pancreatic neuroendocrine tumors (PNET), along with 24 adjacent normal tissues using immunohistochemistry (IHC). The results indicated that the expression of Talin-1 was upregulated in tumor cells compared with adjacent normal tissues. A statistically significant association was observed between the higher cytoplasmic expression of Talin-1 and lower histologic grade (P<0.001) in PDAC samples. Further, our findings indicated an inverse significant correlation between cytoplasmic expression of Talin-1 and recurrence (P=0.014) in PNET samples. No significant association was observed between the cytoplasmic expression of Talin-1 and survival outcomes as well as diagnostic accuracy. In conclusion, our observations demonstrated that a higher cytoplasmic level of Talin-1 protein was significantly associated with less aggressive tumor behaviors in PC samples. Nevertheless, further investigations are required to explore the prognostic plus diagnostic value, and mechanism of action of Talin-1 in pancreatic cancer.
Improved spatial knowledge acquisition through sensory augmentation
Authors: Schmidt Vincent , König Sabine U. , Dilawar Rabia , Sánchez-Pacheco Tracy , König Peter
Published: September 2024

Sensory augmentation offers a novel opportunity to broaden our knowledge of human perception through the use of external sensors that record information that humans cannot perceive naturally. This information is then translated in a meaningful way to be presented through an inherent sensory modality. To assess whether such augmented senses affect the acquisition of spatial knowledge during navigation, we trained a group of 26 participants for six weeks with an augmented sense for cardinal directions, called the feelSpace belt. In order to assess perceptual and behavioral changes, we compared the use of spatial strategies and the spatial navigation performance of the belt group to the performance of a control group that did not receive the augmented sense or the training. To this end, all participants explored the virtual reality environment Westbrook for 150 minutes in total. Then, the participants’ spatial knowledge of the virtual reality city was assessed subjectively with the FRS questionnaire and behaviorally in four immersive virtual reality tasks within Westbrook. The belt group reported a significant increase in the use of spatial strategies after training, while the groups’ ratings were comparable at baseline. The finding is consistent with previous studies showing cognitive and subjective changes to space perception as a consequence of wearing the feelSpace belt for an extended time period. Behaviorally, we found that the belt group acquired significantly more accurate knowledge of cardinal directions and of survey knowledge, measured in pointing accuracy, distance and rotation estimates. Finally, we found that the augmented sense also positively affects route knowledge but to a lesser degree. These results suggest that six weeks of training with the feelSpace belt lead to an improved acquisition of survey and route knowledge as reflected by an increased accuracy in survey and route knowledge tasks in a virtual city.
Adjuvant conditioning shapes the adaptive immune response and promotes trained immunotolerance via NLRP3/IL-1
Authors: Boccia Thais , Pan Weikang , Fattori Victor , Cervantes-Díaz Rodrigo , Rogers Michael S. , Zanoni Ivan , Cuenca Alex G.
Published: September 2024

Trained immunity enhances responsiveness of the innate immune system upon restimulation. Although adjuvants are used to enhance immune responses, we showed that repeated administration of alum, termed adjuvant conditioning (AC), establishes an immunosuppressive environment that delays allogeneic graft rejection by expanding myeloid-derived suppressor cells (MDSCs). Here, we show that AC-induced MDSCs suppress antigen specific adaptive responses both in vitro and in vivo, and that the immunosuppression is abolished in the absence of NLRP3 and IL-1 signaling. Allogeneic pancreatic islets transplanted into AC-treated NLRP3-/-mice are not protected, demonstrating that AC requires NLRP3 signaling. Finally, AC also has an immunosuppressive effect on human cells. Overall, our data show that AC establishes an immunosuppressive milieu via the NLRP3/IL-1 axis, leading to trained immunosuppression, or trained tolerance. Our findings give a potent mandate to explore the possibility to target the NLRP3/IL-1 pathway as a new promising strategy to condition transplant recipients and promote allograft tolerance.
Heterosis across environmental and genetic space
Authors: Sandstedt Gabrielle D. , Rushworth Catherine A.
Published: September 2024

When genetically divergent lineages meet again in secondary contact, hybrids may suffer negative, fitness-reducing consequences, or benefit from positive genetic interactions that result in increased fitness. Empirical studies of heterosis, a phenomenon in which hybrids outperform their inbred progenitors, are of great interest in agriculture, but are less often performed in wild systems. In this study, we leverageBoechera retrofracta, a primarily self-fertilizing wildflower species, to explore how population divergence influences fitness effects upon secondary contact. We integrated genomic data and a large-scale fitness experiment to compare fitness and heterozygosity between outbred and inbred progeny ofB. retrofracta. We show that interpopulation hybrids have increased overwintering survival compared to inbred individuals, indicative of heterosis. The magnitude of heterosis varied across genotypes and different environments, with overwintering survival increasing with genetic distance between parents. Sliding window analyses of genotyping by sequencing data show that heterozygosity varies across the genome of two species,B. retrofractaand the commonly co-occurring speciesBoechera stricta. We next compared these data withde novoF2s (intrapopulation, interpopulation, and interspecific crosses), as well as with wild-collected interpopulation crossB. retrofractaand interspecificB. strictaxB. retrofractahybrids. Wild-collected interspecific hybrids appear to be F1s, while wild-collected intraspecificB. retrofractaare consistent with more complex crossing patterns. Because outcrossing is associated with a transition to asexuality in this group, this suggests different mechanisms underlie asexuality in hybrid and non-hybrid lineages. These findings underscore the potential differences in the role of heterosis between genetic groups at different stages of divergence and its relevance following hybridization in nature.
Neoadjuvant androgen deprivation therapy with or without Fc-enhanced non-fucosylated anti-CTLA-4 (BMS-986218) in high risk localized prostate cancer: a randomized phase 1 trial
Authors: Ager Casey R. , Obradovic Aleksandar , McCann Patrick , Chaimowitz Matthew , Wang Alexander L. E. , Shaikh Neha , Shah Parin , Pan Samuel , Laplaca Caroline J. , Virk Renu K. , Hill Jessica C. , Jugler Collin , DeFranco Grace , Bhattacharya Nilika , Scher Howard I. , DeCastro Guarionex Joel , Anderson Christopher B. , McKiernan James M. , Spina Catherine S. , Stein Mark N. , Runcie Karie , Drake Charles G. , Califano Andrea , Dallos Matthew C.
Published: September 2024

Men with high-risk localized prostate cancer exhibit high rates of post-surgical recurrence. In these patients, androgen deprivation therapy (ADT) is immunomodulatory, however increased infiltration of regulatory T cells (Tregs) may limit the antitumor immune effects of ADT. We designed a neoadjuvant clinical trial to test whether BMS-986218 – a next-generation non-fucosylated anti-CTLA-4 antibody engineered for enhanced antibody-dependent cellular cytotoxicity or phagocytosis (ADCC/P) – depletes intratumoral Tregs and augments the response to ADT. In this single-center, two-arm, open-label study, 24 men with high-risk localized prostate cancer were randomized to receive a single dose of ADT with or without two pre-operative doses of BMS-986218 (anti-CTLA4-NF) prior to radical prostatectomy. Treatment was well tolerated and feasible in the neoadjuvant setting. A secondary clinical outcome was the rate of disease recurrence, which was lower than predicted in both arms. Mechanistically, anti-CTLA4-NF reduced ADT-induced Treg accumulation through engagement of CD16a/FCGR3Aon tumor macrophages, and depth of Treg depletion was quantitatively associated with clinical outcome. Increased intratumoral dendritic cell (DC) frequencies also associated with lack of recurrence, and pre-clinical data suggest ADCC/P-competent anti-CTLA-4 antibodies elicit activation and expansion of tumor DCs. Patients receiving anti-CTLA4-NF also exhibited phenotypic signatures of enhanced antitumor T cell priming. In total, this study provides the first-in-human evidence of Treg depletion by glycoengineered antibodies targeting CTLA-4 in humans and their potential in combination with ADT in prostate cancer patients with high-risk of recurrence.
Linking ringed seal foraging behaviour to environmental variability
Authors: Nykänen Milaja , Niemi Marja , Biard Vincent , Carter Matt I. D. , Pirotta Enrico , Kunnasranta Mervi
Published: September 2024

Background

Foraging rates directly influence animals’ energetic intake and expenditure and are thus linked to body condition and the ability to survive and reproduce. Further, understanding the underlying processes driving a species’ behaviour and habitat use is important as changes in behaviour could result from changes in environmental conditions.

Methods

In this study, the dives of Saimaa ringed seals (Pusa hispida saimensis) were classified for the first time using hidden Markov models and telemetry data collected on individual dives, and the behavioural states of the diving seals were estimated. In addition, we used generalized additive mixed models on the foraging probability of the seals to identify environmental and temporal drivers of foraging behaviour.

Results

We inferred three (in winter) or four (in summer) different dive types: sleeping/resting dives, shallow inactive dives, transiting dives and foraging dives, based on differences in dive metrics logged by or derived from data from telemetry tags. Long and relatively deep sleeping/resting dives were missing entirely in the winter, compensated by an increased proportion of time used for haul-out. We found profound differences in the behaviour of Saimaa ringed seals during the summer open water season compared to the ice-covered winter, with the greatest proportion of time allocated to foraging during the summer months (36%) and the lowest proportion in the winter (21%). The seals’ foraging probability peaked in summer (July) and was highest during the daytime during both summer and winter months. Moreover, foraging probability was highest at depths of 7-30 m in the winter and at depths >15 m in the summer. We also found some evidence of sex-specific foraging strategies that are adapted seasonally, with females preferring more sheltered water areas during winter.

Conclusions

We suggest that the foraging behaviour of Saimaa ringed seals is largely influenced by diel vertical movements and availability of fish, and that the seals optimize their energy acquisition while conserving energy, especially during the cold winter months. Further, the seals display some flexibility in foraging strategies, a feature that may help this endangered subspecies to cope with ongoing anthropogenic climate change.
External Control Arm with Synthetic Real-world Data for Comparative Oncology using Single Trial Arm Evidence (ECLIPSE): A Case Study using Lung-MAP S1400I
Authors: Gupta Alind , Segars Luke , Singletary David , Hansen Johan Liseth , Geale Kirk , Arora Anmol , Gomes Manuel , Sreeram Ramagopalan , Cheung Winson , Arora Paul
Published: September 2024

2.

Single-arm trials supplemented with external comparator arm(s) (ECA) derived from real-world data are sometimes used when randomized trials are infeasible. However, due to data sharing restrictions, privacy/security concerns, or for logistical reasons, patient-level real-world data may not be available to researchers for analysis. Instead, it may be possible to use generative models to construct synthetic data from the real-world dataset that can then be freely shared with researchers. Although the use of generative models and synthetic data is gaining prominence, the extent to which a synthetic data ECA can replace original data while preserving patient privacy in small samples is unclear.

Objective

To compare the efficacy of nivolumab + ipilimumab combination therapy (“experimental arm”) versus nivolumab monotherapy (“control arm”) in patients with metastatic non-small cell lung cancer (mNSCLC) using real-world data from two real-world databases (“original ECA”), and synthetic data versions of these datasets (“synthetic ECA”), with the aim of validating synthetic data for use in ECA analysis.

Study design

Non-randomized analyses of treatment efficacy comparing the experimental arm to the (i) original ECA and (ii) synthetic ECA, with baseline confounding adjustment.

Data sources

The experimental arm is from the Lung-MAP no-match substudy S1400I (NCT02785952) provided by National Clinical Trials Network (NCTN) in the United States. The real-world data source for the ECA is data from population-based oncology data from the Canadian province of Alberta, and from Nordic countries in Europe, specifically Denmark and Norway.
Clinical Trials for Wolfram Syndrome Neurodegeneration: Novel Design, Endpoints, and Analysis Models
Authors: Wang Guoqiao , Li Zhaolong Adrian , Chen Ling , Lugar Heather , Hershey Tamara
Published: September 2024

Objective

Wolfram syndrome, an ultra-rare condition, currently lacks effective treatment options. The rarity of this disease presents significant challenges in conducting clinical trials, particularly in achieving sufficient statistical power (e.g., 80%). The objective of this study is to propose a novel clinical trial design based on real-world data to reduce the sample size required for conducting clinical trials for Wolfram syndrome.

Methods

We propose a novel clinical trial design with three key features aimed at reducing sample size and improve efficiency: (i) Pooling historical/external controls from a longitudinal observational study conducted by the Washington University Wolfram Research Clinic. (ii) Utilizing run-in data to estimate model parameters. (iii) Simultaneously tracking treatment effects in two endpoints using a multivariate proportional linear mixed effects model.

Results

Comprehensive simulations were conducted based on real-world data obtained through the Wolfram syndrome longitudinal observational study. Our simulations demonstrate that this proposed design can substantially reduce sample size requirements. Specifically, with a bivariate endpoint and the inclusion of run-in data, a sample size of approximately 30 per group can achieve over 80% power, assuming the placebo progression rate remains consistent during both the run-in and randomized periods. In cases where the placebo progression rate varies, the sample size increases to approximately 50 per group.

Conclusions

For rare diseases like Wolfram syndrome, leveraging existing resources such as historical/external controls and run-in data, along with evaluating comprehensive treatment effects using bivariate/multivariate endpoints, can significantly expedite the development of new drugs.
Mapping Selective Oxidations of Unspecific Peroxygenases
Authors: Homann Dominik , Püllmann Pascal , Weissenborn Martin
Published: September 2024

Several unspecific peroxygenases (UPOs) have been identified that perform a broad range of selective oxyfunctionalizations and hence represent a pivotal addition to the biocatalysis ‘toolbox’. To make these ‘oxidation tools’ broadly applicable it is crucial to provide a detailed ‘user manual’ for their substrate preference, chemo- and regioselectivity. We therefore selected 16 different substrates with a panel of 15 diverse UPOs and mapped their preferences. Various UPOs proved to be highly selective — discriminating based on either position or chemical properties of the substrate — with up to 99 % chemo- and regioselectivity while achieving turnover numbers (TONs) of a few hundred up to multiple thousands. This map of UPO selectivity shall serve as a starting point for new chemoenzymatic routes and starting points for protein engineering endeavors..
Antibiotic susceptibility trend estimation for India based on 2018 to 2021 data from GEARS program
Authors: Naik Roshan Ratnakar , Kalita Nehal , Maurya Rajesh Kumar , Rajan Annie
Published: September 2024

Antimicrobial resistance (AMR) continues to be a major public threat due to dwindling supplies of effective antibiotics due to its excessive usage in humans and food producing animals. The objective of our study was to identify and predict future trends in multi-drug resistance amongst enterobacteriaceae and non-enterobacteriaceae family in India for four common broad-spectrum antibiotics. We focussed on four broad spectrum antibiotics levofloxacin, gentamicin, cefepime, and ceftazidime and classified the GEARS program study dataset into sensitive (S), intermediate(I) and resistant (R) isolates based on CLSI breakpoints. Levofloxacin (98.3%) was found to be the most susceptible broad spectrum antibiotic for treatment of non-enterobacteriaceae while it was relatively resistant (56.5%) for enterobacteriaceae treatment. As levofloxacin are among ICMR list of ‘alert antimicrobial agents’,hospitals and clinicans can exercise greater care before prescribing them.
Intergenerational transmission of the structure of the auditory cortex and reading skills
Authors: Kepinska Olga , Bouhali Florence , Degano Giulio , Berthele Raphael , Tanaka Hiroko , Hoeft Fumiko , Golestani Narly
Published: September 2024

High-level cognitive skill development relies on genetic and environmental factors, tied to brain structure and function. Inter-individual variability in language and music skills has been repeatedly associated with the structure of the auditory cortex: the shape, size and asymmetry of the transverse temporal gyrus (TTG) or gyri (TTGs). TTG is highly variable in shape and size, some individuals having one single gyrus (also referred to as Heschl’s gyrus, HG) while others presenting duplications (with a common stem or fully separated) or higher-order multiplications of TTG. Both genetic and environmental influences on children’s cognition, behavior, and brain can to some to degree be traced back to familial and parental factors. In the current study, using a unique MRI dataset of parents and children (135 individuals from 37 families), we ask whether the anatomy of the auditory cortex is related to reading skills, and whether there are intergenerational effects on TTG(s) anatomy. For this, we performed detailed, automatic segmentations of HG and of additional TTG(s), when present, extracting volume, surface area, thickness and shape of the gyri. We tested for relationships between these and reading skill, and assessed their degree of familial similarity and intergenerational transmission effects. We found that volume and area of all identified left TTG(s) combined was positively related to reading scores, both in children and adults. With respect to intergenerational similarities in the structure of the auditory cortex, we identified structural brain similarities for parent-child pairs of the 1st TTG (Heschl’s gyrus, HG) (in terms of volume, area and thickness for the right HG, and shape for the left HG) and of the lateralization of all TTG(s) surface area for father-child pairs. Both the HG and TTG-lateralization findings were significantly more likely for parent-child dyads than for unrelated adult-child pairs. Furthermore, we established characteristics of parents’ TTG that are related to better reading abilities in children: fathers’ small left HG, and a small ratio of HG to planum temporale. Our results suggest intergenerational transmission of specific structural features of the auditory cortex; these may arise from genetics and/or from shared environment.
Molecular recording of cellular protein kinase activity with chemical labeling
Authors: Sun De-en , Ng Siu Wang , Zheng Yu , Xie Shu , Schwan Niklas , Breuer Paula , Hoffmann Dirk C. , Michel Julius , Azorin Daniel D. , Boonekamp Kim E. , Winkler Frank , Wick Wolfgang , Boutros Michael , Li Yulong , Johnsson Kai
Published: September 2024

Protein kinases control most cellular processes and aberrant kinase activity is involved in numerous diseases. To investigate the link between specific kinase activities and cellular phenotypes in heterogeneous cell populations andin vivo, we introduce molecular recorders of kinase activities for later analysis. Based on split-HaloTag and a phosphorylation-dependent molecular switch, our recorders become rapidly labeled in the presence of a specific kinase activity and a fluorescent HaloTag substrate. The kinase activity in a given cell controls the degree of fluorescent labeling whereas the recording window is set by the presence of the fluorescent substrate. We have designed specific recorders for four protein kinases, including protein kinase A. We apply our protein kinase A recorder for the sorting of heterogeneous cell populations and subsequent transcriptome analysis, in genome-wide CRISPR screens to discover regulators of PKA activity and for the tracking of neuromodulation in freely moving mice.
Axin1 and Axin2 regulate the WNT-signaling landscape to promote distinct mesoderm programs
Authors: Hernández-Martínez Rocío , Nowotschin Sonja , Harland Luke T.G. , Kuo Ying-Yi , Theeuwes Bart , Göttgens Berthold , Lacy Elizabeth , Hadjantonakis Anna-Katerina , Anderson Kathryn V.
Published: September 2024

How distinct mesodermal lineages – extraembryonic, lateral, intermediate, paraxial and axial – are specified from pluripotent epiblast during gastrulation is a longstanding open question. By investigating AXIN, a negative regulator of the WNT/β-catenin pathway, we have uncovered new roles for WNT signaling in the determination of mesodermal fates. We undertook complementary approaches to dissect the role of WNT signaling that augmented a detailed analysis ofAxin1;Axin2mutant mouse embryos, including single-cell and single-embryo transcriptomics, within vitropluripotent Epiblast-Like Cell differentiation assays. This strategy allowed us to reveal two layers of regulation. First, WNT initiates differentiation of primitive streak cells into mesoderm progenitors, and thereafter, WNT amplifies and cooperates with BMP/pSMAD1/5/9 or NODAL/pSMAD2/3 to propel differentiating mesoderm progenitors into either posterior streak derivatives or anterior streak derivatives, respectively. We propose thatAxin1andAxin2prevent aberrant differentiation of pluripotent epiblast cells into mesoderm by spatially and temporally regulating WNT signaling levels.
Symbiont loss and gain, rather than co-diversification shapes honeybee gut microbiota diversity and function
Authors: Prasad Aiswarya , Pallujam Asha Devi , Siddaganga Rajath , Suryanarayanan Ashwin , Mazel Florent , Brockmann Axel , Yek Sze Huei , Engel Philipp
Published: September 2024

Studying gut microbiota evolution across animals is crucial for understanding symbiotic interactions but is hampered by the lack of high-resolution genomic data. Honeybees, with their specialized gut microbiota and well-known ecology, offer an ideal system to study this evolution. Using shotgun metagenomics on 200 honeybee workers from five species, we recovered thousands of metagenome-assembled genomes, identifying several novel bacterial species. While microbial communities were mostly host-specific, we found both specialist and generalist bacteria, even among closely related species, with notable variation between host species. Some generalists emerged host-specific only at the strain level, suggesting recent host switches. Unexpectedly, we found no evidence of codiversification between hosts and symbionts. Instead, symbiont gains, losses, and replacements led to functional differences, such as the ability to degrade pollen-derived pectin. Our results provide new insights into gut microbiota evolution and uncover the functional potential of the previously underexplored gut microbiota of these important pollinators.
The Role of Thermal Stability in AAV Titration of Engineered Variants
Authors: Zin Emilia A , Desrosiers Melissa , Ocari Tommaso , Labernede Guillaume , Robert Camille , Izabella Charlotte , Saubamea Bruno , Ferrari Ulisse , Dalkara Deniz
Published: September 2024

Determining the concentration of recombinant adeno-associated virus (AAV) productions, also known as titering, is crucial not only for quality control purposes but also for comparative studies of preclinical and clinical gene therapy trials. Recently, several AAVs were engineered by inserting seven amino acids at the outermost tip of the capsid’s protruding VR-VIII loop. These variants have demonstrated increased transduction capabilities over naturally occurring AAV serotypes in several studies. However, they have also been shown to produce lower yields when titered using standard techniques, raising questions about their adequacy for clinical development and use. Here, we investigated why peptide insertion onto AAV capsids reduces their titer by examining viral stocks using electron microscopy and PCR-based titering. We reveal that the DNAse digestion step, performed to eliminate free-floating DNA prior to qPCR or ddPCR, adversely impacts engineered capsid stability due to exposure to heat, artificially lowering viral titers of engineered serotypes. Titering without heating yields significantly higher titers for these variants which have melting temperatures (Tm) close to the DNAse inactivation temperature, while titers for parental serotypes with higher Tmremain unchanged. Our findings provide an important new perspective for titering engineered variants with lower thermostability, especially when comparing their effectiveness to their parental serotypes.
Porosome reconstitution therapy: A biologic rescue from cystic fibrosis
Authors: Won Jin Cho , Vo Ha , Zhao Yongxin , Taatjes Douglas J. , Jena Bhanu P.
Published: September 2024

Cystic fibrosis (CF) is a genetic disorder resulting from mutations in the CF Transmembrane Conductance Regulator (CFTR) gene that codes for a chloride transporting channel at the cell plasma membrane. In CF, highly viscous mucus is secreted in the airways preventing its clearance, leading to lung infections and respiratory failure. A major challenge in treating CF patients has been the presence of more than 2,000 different CFTR mutations or due to the absence of CFTR expression. CFTR is among the 34 major proteins composing the 100 nm porosome secretory machinery in the human airway epithelia, involved in mucin secretion. The airways is coated with a thin film of mucus, composed primarily of mucin MUC5AC and MUC5B. Sputum from patients with CF show a >70% decrease in MUC5B and MUC5AC secretion. Our studies using differentiated 3D cultures of human airway epithelial cell line, also demonstrate loss of both chloride and mucus secretion following exposure to CFTR inhibitors thiazolidinone 172 or the hydrazide GlyH101. Our studies show that human bronchial epithelial (HBE) cells with ΔF508 CFTR mutation, affects nearly a dozen porosome proteins including CFTR. Therefore, we hypothesized that the introduction of normal functional porosomes carrying wild type CFTR into the cell plasma membrane of CF cells would rescue from all forms of CF. Air liquid interface (ALI) 3D differentiated HBE WT-CFTR cells and ΔF508-CFTR CF HBE cell cultures mimicking normal lung physiology, responding to CFTR inhibitors and CF corrector and modulator drugs Tezacaftor, Ivacaftor and TRIKAFTA, was used in the study. Introduction of functional porosome complexes obtained from WT-CFTR HBE cells into the plasma membrane (PM) of ΔF508-CFTR CF cells, was demonstrated by an increase in PM-associated CFTR using Magnify expansion microscopy. Mucin secretion assays demonstrate porosome reconstitution to restore mucin secretion more than twice as effectively as TRIKAFTA. These results are further supported by preliminary nasal potential different studies in ΔF508 mice, where treatment of the nasal passage with porosome isolates from WT-CFTR HBE cells, restore chloride secretion in the nasal passage of mice, a further validation of the highly effective porosome reconstitution therapy for CF.
Genomic approach to studying the relationship between the CRISPR/Cas system and multidrug resistance in clinical isolates ofKlebsiella pneumoniae
Authors: Owaid Hekmat A. , Al-Ouqaili Mushtak T.S. , Al-Marzooq Farah
Published: September 2024

Background

Gene editing techniques have been identified as potential tools to combat antimicrobial resistance (AMR). Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR) and associated sequences (Cas) can be key players in this process. Their presence in bacteria can impact the success of this technology in combating AMR. The aim of this study is to investigate whether CRISPR loci are associated by multidrug, extensive drug, or pan-drug resistance inKlebsiella pneumoniaefrom Iraq.

Methods

Antibiotic susceptibility testing was performed for 100 isolates to detect patterns of resistance. PCR was used to investigate CRISPR/Cas systems. Whole genome sequencing (WGS) was performed on relevant isolates using a DNA nanoball sequencing platform.

Results

Out of 81K. pneumoniaeisolates, 81% were resistant to antibiotics, with 71% producing ESBLs and 21% producing carbapenemases. Additionally, 53% were MDR, 19% XDR, and 9% PDR. Complete CRISPR/Cas systems were found in 38% of isolates, while 78% had incomplete systems. Furthermore, intact CRISPR-1, CRISPR2, and CRISPR3 types were found in 27.0%, 34%, and 18.0% of the isolates, respectively. An inverse correlation was found between antibiotic resistance levels and the presence of CRISPR/Cas systems. Two carbapenemase-producingK. pneumoniae(XDR and PDR) isolates were characterized by WGS. They were found to be carrying blaNDM-5 and blaOXA-181 genes with additional resistance genes against various antibiotic classes, in addition to CRISPR/Cas systems. Phylogenetic analysis indicated relationships with United Kingdom and Chinese strains. Furthermore, the entire genome revealed the presence of unique virulence and antibiotic resistance genes inKlebsiella pneumoniae.

Conclusion

An inverse relationship was found between CRISPR/Cas systems and antimicrobial resistance inK. pneumoniae.The discovery of blaNDM-5 and blaOXA-181 genes in Iraqi strains is alarming as this can increase the risk of nosocomial outbreaks. This study elucidates the importance of monitoring CRISPR/Cas systems and antimicrobial resistance for more efficient control and prevention of infection in healthcare settings.
Cardiac Fibroblasts regulate myocardium and coronary vasculature development via the collagen signaling pathway
Authors: Deng Yiting , He Yuanhang , Xu Juan , He Haoting , Zhang Manling , Li Guang
Published: September 2024

The fibroblast (FB), cardiomyocyte (CM), and vascular endothelial cell (Vas_EC) are the three major cell types in the heart, yet their relationships during development are largely unexplored. To address this gap, we employed RNA staining of the FB marker geneCol1a1together with the CM marker geneActn2and the Vas_EC marker geneCdh5at different stages. This approach enabled us to discern the anatomical pattern of cardiac FBs and identify approximately one EC and four CMs directly interacting with each FB. Molecularly, through the analysis of single-cell mRNA sequencing (scRNA-seq) data, we unveiled collagen as the top signaling molecule derived from FBs influencing CM and Vas_EC development. Subsequently, we used a Pdgfra-CreER controlled diphtheria toxin A (DTA) system to ablate the FBs at different stages. We found that the ablation of FBs disrupted myocardium and vasculature development and led to embryonic heart defects. Using scRNA-seq, we further profiled the ablated hearts and identified molecular defects in their ventricular CMs and Vas_ECs compared to control hearts. Moreover, we identified a reduction of collagen in the ablated hearts and predicted collagen as the major signaling pathway regulating the differentially expressed genes in the ablated ventricular CMs. Finally, we performed both short-term and long-term fibroblast ablation at the neonatal stage. We found that short-term ablation caused a reduction in collagen and Vas_EC density, while long-term ablation may induce compensatory collagen expression without causing heart function reduction. In summary, our study has identified the function of fibroblasts in regulating myocardium and vasculature development and implicated an important role for the collagen pathway in this process.
Insights on the obstacles, challenges, and complexities of engaging youth in urban planning in Jordan: assessment and recommendations
Authors: Zeadat Zayed F. , Haddad Naif Adel
Published: September 2024

Purpose

This paper comprehensively investigates the lack of youth involvement in the intricate tapestry of urban policymaking in the Jordanian context. It attempts to present and illustrate the obstacles, challenges, hindrances and complexities facing engaging youth in urban planning in Jordan. Participants aged 18–24 were the primary focus of the investigation, as Jordan's population is predominantly youthful, with approximately 70% of the population under the age of 30.

Design/methodology/approach

The research methodology adopted in this study is a mixed-methods approach, which integrates both qualitative and quantitative data collection and analytical techniques to provide a comprehensive and nuanced understanding of the research problem.

Findings

Youth involvement in Jordan's urban policymaking is limited and inconsistent. Most notably, the prevalence of adultism emerges as the predominant and most substantive impediment, exerting a considerable influence on constraining the agency of young Jordanians in shaping urban policy.

Research limitations/implications

Detailed examples can be developed to offer discerning elucidations relevant to each frame of reference.

Practical implications

A total of 12 discernible barriers emerged from a systematic deductive thematic analysis of primary data.

Originality/value

This comprehensive inquiry highlights the pervasive gaps in support for youth participation in urban policymaking within the administrative framework and across Jordanian society. Subsequent quantitative analysis was employed to strengthen the external validity of the research findings, thereby enhancing the generalizability of the qualitative insights. By employing Jordan as a case study, this paper significantly contributes to the expanding corpus of scholarly work on planning processes and practices within the Global South and the Arab world.
A compound reconfigurable series-fed microstrip antenna for satellite communication applications
Authors: Alsharif Fawzy , Kurnaz Cetin
Published: September 2024

Purpose

This paper aims to present an innovative reconfigurable series-fed microstrip antenna using radiofrequency positive intrinsic negative (RF PIN) diodes for cognitive S-band and C-band satellite communications. The antenna can dynamically reconfigure its frequency, polarization and radiation pattern to meet diverse application needs.

Design/methodology/approach

The design involves a reconfigurable four-element microstrip antenna using FR4 substrate and copper patches. RF PIN diodes enable dynamic frequency, polarization and radiation pattern reconfiguration. Simulations and optimizations are performed using CST and HFSS, using techniques like the Nelder-Mead algorithm, particle swarm optimization, covariance matrix adaptation and trust region framework. An antenna prototype is also fabricated to validate the simulations.

Findings

The proposed antenna demonstrates significant reconfigurability: it switches between S-band (2.45 GHz, 2.52 GHz) and C-band (5.55 GHz, 5.59 GHz) with bandwidths of 120 MHz and 550 MHz, respectively. It transitions between circular and linear polarization in the S-band and modifies the radiation pattern by 45 degrees, providing an alternative radiation direction in the C-band. The antenna achieves a maximum gain of 5.95 dBi at 2.52 GHz and 93% efficiency at 5.55 GHz. Simulated results closely match those from the fabricated prototype, confirming the design’s validity.

Originality/value

The innovative use of RF PIN diodes enables comprehensive reconfigurability in frequency, polarization and radiation patterns within a single microstrip antenna, meeting the demands of S-band and C-band satellite communications. This study demonstrates superior performance, significant gains and efficiencies across various reconfiguration modes, validated by rigorous simulation and practical fabrication. The simple structural design further distinguishes this study from others in the field.
Traversing the complexity of digital construction and beyond through soft skills: experiences of Malaysian architects
Authors: Shahruddin Syafizal , Sonet Ungku Norani , Azmi Athira , Zainordin Nadzirah
Published: September 2024

Purpose

The evolution of digital construction within Industrial Revolution 5.0 emphasises the harmonious integration of humans and technology, value-driven technology implementation, adaptive leadership and user-centric design solutions. This shift necessitates architects to enhance their soft skills to navigate the transition effectively. Failure to demonstrate these skills may confine architects to passive roles as technology consumers rather than innovative leaders. While existing research predominantly focuses on the technical aspects of digital construction, this study investigates how architects effectively manifest their soft skills within such dynamic contexts, addressing a critical gap in the current literature.

Design/methodology/approach

Employing an interpretive phenomenological approach, the research engaged 14 individual architects practicing in architectural consultancy practices (ACPs) in Malaysia through semi-structured interviews and written exercises to unveil their experiences.

Findings

Thematic analysis revealed six primary themes: “analytical and critical thinking,” “digital communication,” “diversity in leadership styles,” “emotional intelligence,” “ethics and professionalism,” and “curiosity and agility.”

Practical implications

Furthermore, the developed thematic map serves as a foundational resource for human resource practices aiming to design upskilling and reskilling programs that focus on nurturing soft skills. Emphasising soft skills, these programs are designed to thrive in the digital construction era and beyond.

Originality/value

These shared experiences significantly contribute to the theoretical understanding of soft skills within the digital construction context, providing novel insights into their practical application when addressing real-world implications.
A novel approach for integrating BIM and green building rating systems in the construction projects design phase
Authors: Arbabi Alireza , Taherkhani Roohollah , Ansari Ramin
Published: September 2024

Purpose

With the advancement of technology and more attention to environmental issues, building information modeling (BIM) and green building have become two new and growing trends in the construction industry. Therefore, this study proposes a new strategy that integrates BIM and green building rating assessments with an emphasis on Iran Green Building Rating System (IGBRS).

Design/methodology/approach

By creating a Revit-IGBRS project template that includes sheets related to all credits, the project compliance with the IGBRS credits and management of submittal documents for certification has been facilitated. Finally, a case study of the materials and resources category of the IGBRS system was performed to validate the BIM-IGBRS application model. All 8 criteria of this category were examined by using Dynamo programming for the Revit sample project.

Findings

A practical model for BIM and IGBRS integration is presented, which allows designers to be aware of the IGBRS scores obtained before the project’s construction phase and examine different scenarios for the highest scores. Overall, this study showed that integrating BIM and the Iranian rating system is possible with some constraints, and adding some features to BIM software can promote this integration.

Originality/value

Given that no study has been conducted on the integration of BIM with the Iran Green Building Rating System (IGBRS), the present research investigates utilizing building information modeling to meet the credits requirements of this rating system. The results of this research can be generalized and used in other green rating systems.
Blockchain-enhanced computer vision approach for remote safety inspection in construction
Authors: Kim Dohyeong , Yang Jaehun , Lee Doyeop , Lee Dongmin , Rahimian Farzad , Park Chansik
Published: September 2024

Purpose

Computer vision (CV) offers a promising approach to transforming the conventional in-person inspection practices prevalent within the construction industry. However, the reliance on centralized systems in current CV-based inspections introduces a vulnerability to potential data manipulation. Unreliable inspection records make it challenging for safety managers to make timely decisions to ensure safety compliance. To address this issue, this paper proposes a blockchain (BC) and CV-based framework to enhance safety inspections at construction sites.

Design/methodology/approach

This study adopted a BC-enhanced CV approach. By leveraging CV and BC, safety conditions are automatically identified from site images and can be reliably recorded as safety inspection data through the BC network. Additionally, by using this data, smart contracts coordinate inspection tasks, assign responsibilities and verify safety performance, managing the entire safety inspection process remotely.

Findings

A case study confirms the framework’s applicability and efficacy in facilitating remote and reliable safety inspections. The proposed framework is envisaged to greatly improve current safety inspection practices and, in doing so, contribute to reduced accidents and injuries in the construction industry.

Originality/value

This study provides novel and practical guidance for integrating CV and BC in construction safety inspection. It fulfills an identified need to study how to leverage CV-based inspection results for remotely managing the safety inspection process using BC. This work not only takes a significant step towards data-driven decision-making in the safety inspection process, but also paves the way for future studies aiming to develop tamper-proof data management systems for industrial inspections and audits.