bluuebunny/crossref_metadata_2025 huggingface dataset:
Additive pre-diagnostic and diagnostic value of routine bloodbased biomarkers in the detection of colorectal cancer in the UK Biobank cohort
Authors: Tanriver Gizem , Kocagoncu Ece
Published: November 2022

Background

Survival rates from colorectal cancer (CRC) are drastically higher if the disease is detected and treated earlier. Current screening guidelines involve stool-based tests and colonoscopies, whose acceptability and uptake remains low. Routinely collected blood-based biomarkers may offer a low-cost alternative or aid for detecting CRC.

Methods

Here we aimed to evaluate the pre-diagnostic and diagnostic value of a wide-range of multimodal biomarkers in the UK Biobank dataset, including sociodemographic, lifestyle, medical, physical, and blood and urine-based measures in detecting CRC. We performed a Cox proportional hazard and a tree-boosting model alongside feature selection methods to determine optimal combination of biomarkers.

Results

In addition to the modifiable lifestyle factors of obesity, alcohol consumption and cardiovascular health, we showed that blood-based biomarkers that capture the immune response, lipid profile, liver and kidney function are associated with CRC risk. Following feature selection, the final Cox and tree-boosting models achieved a C-index of 0.67 and an AUC of 0.76 respectively.

Conclusions

We show that blood-based biomarkers collected in routine examinations are sensitive to preclinical and clinical CRC. They may provide an additive value and improve diagnostic accuracy of current screening tools at no additional cost and help reduce burden on the healthcare system.
Knowledge and information sources of Helicobacter pylori among Jordanian population: a cross-sectional study
Authors: Alaridah Nader , F. Jarrar Raba’a , Joudeh Rayan M. , Aljarawen Mallak , Jum’ah Mohammad , Nassr Hasan , AlHmoud Raad Riad , Allouzi Abdullah , Wadi Eslam M. , Abu-Humaidan Anas H. A.
Published: November 2022

In 2017, the Jordanian Ministry of Health reported that gastric cancer was one of Jordan’s most commonly diagnosed cancers. Gastric cancer is often linked to Helicobacter pylori, one of the foremost risk factors. Despite the high prevalence of H. pylori in Jordan, no information is available regarding the general population’s awareness of the harmful effects of this pathogen. The study aims to assess the knowledge and the impact of the source of knowledge on H. pylori among the general population in Jordan. A cross-sectional study involving 933 participants was conducted between May and July of 2021. After meeting the inclusion criteria and consenting to participate in this study, participants completed the questionnaire. The questionnaire was conducted interview-based, covering the following sections: sociodemographic data and knowledge related to H. pylori infection. 63% of the participants had a high level of education, 70.5% got their information about H. pylori infection from non-medical sources, and 68.7% had a low level of knowledge. Working in the medical field and attaining information from medical resources showed a significant association with a high level of knowledge, on the other hand, having a history of self-reported or family member of H.pylori infection also showed a significant association with a high level of knowledge. The Mann-Whitney U test showed that the mean ranks of all knowledge items in the medical source group significantly exceed those of the non-medical source group (p-values < 0.05). In Jordan, the awareness of H. pylori was unsatisfying, similar to other countries. Nevertheless, misconceptions in knowledge about H. pylori were identified and further awareness must be spread and advocated. Close observation of the non-medical sources of information is essential for delivering to the general population the sufficient amount of knowledge needed.
Assessing the spatial-temporal risks of SARS-CoV-2 infection for healthcare-workers in the hospital using behavioural indices from routine data
Authors: Wilson-Aggarwal Jared , Gotts Nick , Arnold Kellyn , Spyer Moira J , Houlihan Catherine F , Nastouli Eleni , Manley Ed
Published: November 2022

The COVID-19 pandemic has emphasised the need to rapidly assess infection risks for healthcare workers within the hospital environment. Using data from the first year of the pandemic, we investigated whether an individual’s COVID-19 test result was associated with behavioural markers derived from routinely collected hospital data two weeks prior to a test. The temporal and spatial context of behaviours were important, with the highest risks of infection during the first wave, for staff in contact with a greater number of patients and those with greater levels of activity on floors handling the majority of COVID-19 patients. Infection risks were higher for BAME staff and individuals working more shifts. Night shifts presented higher risks of infection between waves of COVID-19 patients. Our results demonstrate the epidemiological relevance of deriving markers of staff behaviour from electronic records, which extend beyond COVID-19 with applications for other communicable diseases and in supporting pandemic preparedness.
An atlas of genetic regulation and disease associations of microRNAs
Authors: Mustafa Rima , Mens Michelle M.J. , van Hilten Arno , Huang Jian , Roshchupkin Gennady , Huan Tianxiao , Broer Linda , Elliott Paul , Levy Daniel , Ikram M. Arfan , Evangelou Marina , Dehghan Abbas , Ghanbari Mohsen
Published: November 2022

MicroRNAs (miRNAs) are small non-coding RNAs that post-transcriptionally regulate gene expression. Identification of genetic variants influencing the transcription of miRNAs can provide an understanding of their genetic regulation and implication in human disease. Here we present genome-wide association studies of 2,083 plasma circulating miRNAs measured by next-generation sequencing in 2,178 participants of the Rotterdam Study to identify miRNA-expression quantitative trait loci (miR-eQTLs). We report 4,310 cis- and trans-miR-eQTLs for 64 miRNAs that have been replicated across independent studies. Many of these miR-eQTLs overlap with gene expression, protein, and metabolite-QTLs and with disease-associated variants. The consequences of perturbation in miRNA transcription on a wide range of clinical conditions are systematically investigated in phenome-wide association studies, with their causality tested using Mendelian randomization. Integration of genomics and miRNAs enables interrogation of the genetic architecture of miRNAs, revealing their clinical importance, and providing valuable resources for future studies of miRNAs in human disease.
Intra- and inter-rater reliability, agreement, and minimal detectable change of the handheld dynamometer in individuals with symptomatic hip osteoarthritis
Authors: Vaz Gilvan Ferreira , Freire Felipe Florêncio , Gonçalves Henrique Mansur , de Aviz Marcus Alexandre Brito , Martins Wagner Rodrigues , Durigan João Luiz Quagliotti
Published: November 2022

Introduction

The handheld dynamometer has been validated to measure muscle strength in different muscle groups. However, to date, it has not been tested in individuals who experience pain induced by hip osteoarthritis. The current study aimed to evaluate the intra- and inter-rater reliability, agreement, and minimal detectable change of the Lafayette handheld dynamometer, model 1165, to assess the peak force (Pk) and average peak force (Af) of hip muscles in individuals with symptomatic hip osteoarthritis.

Methods

Twenty participants with hip osteoarthritis (mean ± SD age: 58.7±15.3 years; body mass index: 28.8±4.2 kg/m2) and a pain intensity on the Visual Analogue Scale0020 ≥ 4 (8.05±1.2) were recruited to participate in this study. Pk and Af of hip flexors (seated position), abductors and adductors (supine position), and extensors (prone position) were collected in a single day by two independent raters, each one obtaining test and retest in randomly ordered separate sessions.

Results

The intra-rater intraclass correlation coefficient (ICC) was classified as good (>0.75) or excellent (≥0.90) for all muscle groups, and all inter-rater ICCs were classified as excellent. Rater A had a lower standard error of measurement compared to rater B, ranging from 0.15 to 0.58 kilogram-force (Kgf) compared with 0.34 to 1.25 kg, respectively. However, the inter-rater comparison showed a minimal detectable change < 10% for all Pk and Af measures (except Af for the abductor muscle group). Finally, the inter-rater Bland-Altman analysis demonstrated good agreement for abductors, adductors, and extensors.

Conclusion

Despite pain and dysfunction related to hip osteoarthritis, the handheld dynamometer was shown to be a reliable tool to assess hip muscle strength, with good to excellent intra- and inter-rater ICCs, satisfactory agreement, and small values for minimal detectable change.
Temporal masking and rollover in the neural code for speech with and without hearing loss
Authors: Huang Chengjie G. , Sabesan Shievanie , Lesica Nicholas A.
Published: November 2022

Natural sounds, such as speech, are complex time-varying waveforms containing information critical to how we communicate with each other and navigate the external world. Hearing loss results in a breakdown of this information and causes distortions in the neural code. As a result, perception of complex sounds such as speech is compromised. This problem is further complicated by the fact that sound intensity varies in natural settings, both in quiet and in noisy backgrounds. Somewhat paradoxically, despite increased audibility at high sound intensities, perception and discrimination of speech is actually diminished, especially in the presence of background noise. This phenomenon is known as rollover of speech and its neural basis is poorly understood in both normal-hearing listeners and hearing-impaired listeners. Here we performed in-vivo electrophysiology in awake and anaesthetized Mongolian gerbils(Meriones Unguiculatus)to investigate how hearing loss affects the neural encoding of speech. We presented 22 Vowel-Consonant-Vowel (VCV) syllables to the gerbil and recorded neural responses from the inferior colliculus (IC). We used a k-nearest neighbor neural classifier to investigate whether IC neurons could discriminate between different consonants in normal hearing (NH) and noise-exposed hearing-loss (HL) animals. We found that neural correlates of perceptual rollover were present in the IC and that performance in discrimination decreased when VCVs were presented in background noise when compared to in quiet. Furthermore, we found that forward masking played a prominent role in shaping neural responses and discrimination between various consonants in NH and HL animals. These results suggest there is a critical trade-off in listening between audibility and rollover mediated by temporal masking.
The FXR agonist obeticholic acid does not stimulate liver regeneration in hepatectomized mice
Authors: van Mierlo Kim M.C. , Dahrenmoller Carola , Lebrun Valérie , Jansen Peter L.M. , Dejong Cornelis H.C. , Leclercq Isabelle A. , Olde Damink Steven W.M. , Schaap Frank G.
Published: November 2022

Background

Postresectional liver failure (PLF) is a dreaded complication after partial hepatectomy (PH). Data from animal experiments indicate that endogenous ligands (i.e. bile salts) can stimulate liver regeneration and prevent liver injury after PH, via hepatic Fxr and the ileal Fxr-Fgf15 axis.

Aim

To investigate whether exogenous activation of the Fxr pathway with the semi-synthetic bile acid derivative obeticholic acid (OCA) could stimulate postresectional liver regeneration in mice.

Methods

Twelve weeks old male C57BL6/J mice were pre-treated with OCA (10 mg/kg/day) or vehicle, and after 7 days subjected to 70% PH. Mice were sacrificed at 24, 48 and 72 hrs after PH, and liver injury, secretory function, and regenerative indices were assessed. In a second study, OCA pre-treated mice received oral sucrose supplementation in the postoperative trajectory, and a group of mice receiving intraperitoneal injection of FGF19 was included as a positive control group. Here, mice were sacrificed at 48 hours after PH.

Results

No effect could be detected on liver mass recovery after PH, although responses ofCyp7a1,Cyp8b1and other Fxr target genes implied general effectiveness of OCA treatment. OCA had no consistent effects on the number of Ki-67+hepatocytes and mitotic figures around the peak of proliferation (i.e. 48 hrs) after PH, having no effect or increasing these regenerative indices in the consecutive experiments. Hepatic bile salt content, an important determinant of PH-induced liver regeneration, at this time point was not affected by OCA. After pretreatment of mice with FGF19, a reduced expression of ileal bile salt-regulated genesFgf15andSlc51bindicating FGF19-mediated repression of bile salt synthesis was seen, but this did not stimulate postresectional liver regeneration in mice.

Conclusion

Despite the activation of hepatic and ileal Fxr as shown by induction of target genes, treatment with OCA or FGF19 did not result in accelerated liver regeneration after PH and liver bile salt content was not influenced. We speculate that bile salt homeostasis and endogenous bile salt signaling is already optimal in unaffected livers for proper progression of regeneration after PH. It will be interesting to study the effects of Fxr agonism on liver regeneration after PH, and prevention of PLF in the context of compromised bile salt homeostasis/signaling prior to PH.
Nucleotide-free structures of Kif20A illuminate the atypical allostery in this mitotic kinesin-6
Authors: Ranaivoson Fanomezana Moutse , Crozet Vincent , Benoît Matthieu P.M.H. , Khalid Amna Abdalla Mohammed , Kikuti Carlos , Sirkia Helena , Marjou Ahmed El , Asenjo Ana B. , Sosa Hernando , Schmidt Christoph F. , Rosenfeld Steven S. , Houdusse Anne
Published: November 2022

KIF20A is a critical kinesin for cell division and a promising anti-cancer drug target. The mechanisms underlying its cellular roles remain elusive. Interestingly, unusual coupling between the nucleotide- and microtubule-binding sites of this kinesin-6 has been reported but little is known about how its divergent sequence leads to atypical motility properties. We present here the first high-resolution structure of its motor domain that delineates the highly unusual structural features of this motor, including a long L6 insertion that integrates into the core of the motor domain and that drastically affects allostery and ATPase activity. Together with the high-resolution cryo-EM microtubule-bound KIF20A structure that reveal the microtubule-binding interface, we dissect the peculiarities of the KIF20A sequence that work to favor fast dissociation of ADP, particularly in contrast to other kinesins. Structural and functional insights from the KIF20A pre-power stroke conformation thus highlight the role of extended insertions in shaping the motor mechanochemical cycle. Essential for force production and processivity is the length of the neck linker in kinesins. We highlight here the role of the sequence preceding the neck linker in controlling its backward docking and show that a neck linker 4-times longer than kinesin-1 is required for the activity of this motor.
Extensive genomic divergence among 61 strains ofChlamydia psittaci
Authors: Sachse Konrad , Hölzer Martin , Vorimore Fabien , Barf Lisa-Marie , Lamkiewicz Kevin , Sachse Carsten , Laroucau Karine , Marz Manja
Published: November 2022

Chlamydia (C.) psittaci, the causative agent of avian chlamydiosis and human psittacosis, is a genetically heterogeneous species. Its broad host range includes parrots and many other birds, but occasionally also humans (via zoonotic transmission), ruminants, horses, swine and rodents. To assess whether there are genetic markers associated with host tropism we comparatively analyzed whole-genome sequences of 61C. psittacistrains. Initially, poorly assembled genomes in public databases were subjected to clean-up, reassembly and polishing. Multiple sequence alignment of the genome sequences revealed four major clades within this species. Clade 1 represents the most recent lineage comprising 40/61 strains and contains 9/10 of the psittacine strains, including type strain 6BC, and 10/13 of human isolates. Clades 2-4 carry strains from different non-psittacine hosts. We found that clade membership correlates with classification schemes based on SNP types,ompAgenotypes, multilocus sequence types as well as plasticity zone (PZ) structure and host preference. Genome analysis also revealed that i) sequence variation in the major outer membrane porin OmpA can result in 3D structural changes of immunogenic domains, ii) past host change of Clade 3 and 4 strains could be associated with loss of MAC/perforin in the PZ, rather than the large cytotoxin, iii) the distinct phylogeny of atypical strains (Clades 3 and 4) is also reflected in their repertoire of inclusion proteins (Inc family) and polymorphic membrane proteins (Pmps). Altogether, our study identified a number of genomic features that can be correlated with the phylogeny and host preference ofC. psittacistrains.
Inhibition of pyruvate dehydrogenase affects the brain protein acylation stronger than PDHA phosphorylation at Ser293
Authors: Aleshin Vasily A. , Sibiryakina Daria A. , Kazantsev Alexey V. , Graf Anastasia V. , Bunik Victoria I.
Published: November 2022

Adaptation of an organism to metabolic challenges requires mechanisms coupling metabolism to gene expression. Acylations of metabolic and histone proteins acquire significant attention in this regard. We hypothesize that adaptive response to inhibition of a key metabolic process, catalyzed by the acetyl-CoA-generating pyruvate dehydrogenase (PDH) complex, may be mediated by changed protein acylations. The hypothesis is tested by intranasal administration to animals of PDH-specific inhibitors acetylmethylphosphinate (AcMeP) or methyl ester of acetylphosphonate (AcPMe), followed by assessment of physiological parameters, brain protein acylation system and expression/phosphorylation of PDHA subunit. At a fixed dose, AcMeP, but not AcPMe, decreases acetylation and increases succinylation of the brain proteins of apparent molecular mass of 15-20 kDa. Regarding the 30-50 kDa proteins, a strong inhibitor AcMeP affects acetylation only, while a less efficient AcPMe mostly increases succinylation. No increase in the succinylation of the 30-50 kDa proteins by AcMeP coincides with its induction of desuccinylase SIRT5, not observed in the AcPMe-treated animals. The brain PDHA expression or phosphorylation, the animal behavior or ECG do not significantly differ between the studied animal groups. The data indicate that a short-term inhibition of the brain PDH affects acetylation and/or succinylation of the brain proteins, dependent on the inhibitor potency, protein molecular mass and acylation type. Homeostatic nature of these changes is implied by stability of physiological parameters after the PDH inhibition.
Precise identification of cell states altered in disease with healthy single-cell references
Authors: Dann Emma , Teichmann Sarah A. , Marioni John C.
Published: November 2022

Single cell genomics is a powerful tool to distinguish altered cell states in disease tissue samples, through joint analysis with healthy reference datasets. Collections of data from healthy individuals are being integrated in cell atlases that provide a comprehensive view of cellular phenotypes in a tissue. However, it remains unclear whether atlas datasets are suitable references for disease-state identification, or whether matched control samples should be employed, to minimise false discoveries driven by biological and technical confounders. Here we quantitatively compare the use of atlas and control datasets as references for identification of disease-associated cell states, on simulations and real disease scRNA-seq datasets. We find that reliance on a single type of reference dataset introduces false positives. Conversely, using an atlas dataset as reference for latent space learning followed by differential analysis against a matched control dataset leads to precise identification of disease-associated cell states. We show that, when an atlas dataset is available, it is possible to reduce the number of control samples without increasing the rate of false discoveries. Using a cell atlas of blood cells from 12 studies to contextualise data from a case-control COVID-19 cohort, we sensitively detect cell states associated with infection, and distinguish heterogeneous pathological cell states associated with distinct clinical severities. Our analysis provides guiding principles for design of disease cohort studies and efficient use of cell atlases within the Human Cell Atlas.
The effect of wheat genotype on its microbiome is more evident in roots than rhizosphere and is strongly influenced by time
Authors: Quiza Liliana , Tremblay Julien , Pagé Antoine P. , Greer Charles W. , Pozniak Curtis J. , Li Rong , Haug Brenda , Hemmingsen Sean M. , St-Arnaud Marc , Yergeau Etienne
Published: November 2022

Crop breeding has traditionally ignored the plant-associated microbial communities. Consideration of the interactions between plant genotype and associated microbiota is of value since different genotypes of the same crop often harbor distinct microbial communities which can influence the plant phenotype. However, recent studies have reported contrasting results, which led us to hypothesize that the effect of genotype is constrained by time (growth stage, year) and space (plant compartment). To test this hypothesis, we sampled bulk soil, rhizosphere soil and roots of 10 wheat genotypes, twice per year, for 4 years. DNA was extracted and regions of the bacterial 16S rRNA and CPN60 genes and the fungal ITS region were amplified and sequenced. The effect of genotype was highly contingent on the time of sampling and on the plant compartment sampled. Only for a few sampling dates, were the microbial communities significantly different across genotypes. The effect of genotype was most often significant for root microbial communities. The three marker genes used provided a highly coherent picture of the effect of genotype. Taken together, our results confirm that microbial communities in the plant environment strongly vary temporally and spatially and that this can mask the effect of genotype.
DNA-enhanced CuAAC ligand enables live-cell detection of intracellular biomolecules
Authors: Nian Keqing , Liu Yifang , Qiu Yuchen , Zhang Zhuoyu , Brigandi Laura , Wanunu Meni , Rouhanifard Sara H.
Published: November 2022

Of the various conjugation strategies for cellular biomolecules, Cu(I)-catalyzed azide-alkyne cycloaddition (CuAAC) is the preferred click chemistry approach due to its fast reaction rate and the commercial availability of a wide range of conjugates. While extracellular labeling of biomolecules using CuAAC has been widely adopted, intracellular labeling in live cells has been challenging as the high copper concentrations required for CuAAC reaction is toxic to biological systems. As a critical first step towards CuAAC-mediated intracellular labeling, an ultrasensitive CuAAC ligand is needed to reduce cytosolic copper concentrations while maintaining fast reaction kinetics. Here, we developed BTT-DNA, a new DNA oligomer-conjugated CuAAC ligand for click reaction biomolecular labeling. The DNA oligo attachment serves several purposes, including: 1. Increased localization of copper atoms near the ligand, which enables ligation of azide tags with much lower copper concentrations than commercially available CuAAC ligands and without the addition of exogenous copper salt; 2. Allows nucleic acid template-driven proximity ligation by choosing the attached DNA sequence, 3. Enables the liposome encapsulation and delivery of the ligand into live cells, and 4. Facilitates intracellular labeling of nascent phospholipids in live cells. We demonstrate that BTT-DNA mediated labeling has little to no effect on the overall cell health.
Time as a supervisor: temporal regularity and auditory object learning
Authors: Di Tullio Ronald W. , Parthiban Chetan , Piasini Eugenio , Chaudhari Pratik , Balasubramanian Vijay , Cohen Yale E.
Published: November 2022

Sensory systems appear to learn to transform incoming sensory information into perceptual representations, or “objects”, that can inform and guide behavior with minimal explicit supervision. Here, we propose that the auditory system can achieve this goal by using time as a supervisor, i.e., by learning features of a stimulus that are temporally regular. We will show that this procedure generates a feature space sufficient to support fundamental computations of auditory perception. In detail, we consider the problem of discriminating between instances of a prototypical class of natural auditory objects, i.e., rhesus macaque vocalizations. We test discrimination in two ethologically relevant tasks: discrimination in a cluttered acoustic background and generalization to discriminate between novel exemplars. We show that an algorithm that learns these temporally regular features affords better or equivalent discrimination and generalization than conventional feature-selection algorithms, i.e., principal component analysis and independent component analysis. Our findings suggest that the slow temporal features of auditory stimuli may be sufficient for parsing auditory scenes and that the auditory brain could utilize these slowly changing temporal features.
Intranasal self-amplifying RNA SARS-CoV-2 vaccine produces protective respiratory and systemic immunity and prevents viral transmission
Authors: Jennewein Madeleine F. , Schultz Michael D. , Beaver Samuel , Battisti Peter , Bakken Julie , Hanson Derek , Akther Jobaida , Zhou Fen , Mohamath Raodoh , Singh Jasneet , Cross Noah , Kasal Darshan N. , Ykema Matthew , Reed Sierra , Kalange Davies , Cheatwood Isabella R. , Tipper Jennifer L. , Foote Jeremy B. , King R. Glenn , Silva-Sanchez Aaron , Harrod Kevin S. , Botta Davide , Gerhardt Alana , Casper Corey , Randall Troy D. , Lund Frances E. , Voigt Emily A.
Published: November 2022

While mRNA vaccines have been effective in combating SARS-CoV-2, waning of vaccine-induced antibody responses and lack of vaccine-induced respiratory tract immunity contribute to ongoing infection and transmission. In this work, we compare and contrast intranasal (i.n.) and intramuscular (i.m.) administration of a SARS-CoV-2 self-amplifying RNA (saRNA) vaccine delivered by a nanostructured lipid carrier (NLC). Both i.m. and i.n. vaccines induce potent systemic serum neutralizing antibodies, bone marrow-resident IgG-secreting cells, and splenic T cell responses. The i.n. vaccine additionally induces robust respiratory mucosal immune responses, including SARS-CoV-2-reactive lung-resident memory and lung-homing T cell populations. As a booster following previous i.m. vaccination, the i.n. vaccine also elicits the development of mucosal virus-specific T cells. Both the i.m. and i.n. administered vaccines durably protect hamsters from infection-associated morbidity upon viral challenge, significantly reducing viral loads and preventing challenged hamsters from transmitting virus to naïve cagemates. This saRNA-NLC vaccine’s potent systemic immunogenicity, and additional mucosal immunogenicity when delivered i.n., may be key for combating SARS-CoV-2 and other respiratory pathogens.
Parallel phospholipid transfer by Vps13 and Atg2 determines autophagosome biogenesis dynamics
Authors: Dabrowski Rahel , Tulli Susanna , Graef Martin
Published: November 2022

During autophagy, rapid membrane assembly expands small phagophores into large double-membrane autophagosomes. Theoretical modelling predicts the majority of autophagosomal phospholipids is derived from highly efficient non-vesicular phospholipid transfer (PLT) across phagophore-ER contacts (PERCS). Currently, the phagophore-ER tether Atg2 is the only PLT protein known to drive phagophore expansionin vivo. Here, our quantitative live-cell-imaging analysis reveals poor correlation between duration and size of forming autophagosomes and number of Atg2 molecules at PERCS of starving yeast cells. Strikingly, we find Atg2-mediated PLT is non-rate-limiting for autophagosome biogenesis, because membrane tether and PLT protein Vps13 localizes to the rim and promotes expansion of phagophores in parallel with Atg2. In the absence of Vps13, the number of Atg2 molecules at PERCS determines duration and size of forming autophagosomes with an apparentin vivotransfer rate of ~200 phospholipids per Atg2 molecule and second. We propose conserved PLT proteins cooperate in channeling phospholipids across organelle contact sites for non-rate-limiting membrane assembly during autophagosome biogenesis.
The N-terminal domain of the human mitochondrial helicase Twinkle has DNA binding activity crucial for supporting processive DNA synthesis by Polymerase γ
Authors: Johnson Laura C. , Singh Anupam , Patel Smita S.
Published: November 2022

Twinkle is the ring-shaped replicative helicase within the human mitochondria with high homology to bacteriophage T7 gp4 helicase-primase. Unlike many orthologs of Twinkle, the N-terminal domain (NTD) of human Twinkle has lost its primase activity through evolutionarily acquired mutations. The NTD has demonstrated no observed activity thus far, hence its role has remained unclear. In this study, we have biochemically characterized the isolated NTD and C-terminal domain with linker (CTD) to decipher their contributions to the activities of the full-length (FL) Twinkle. This novel CTD construct hydrolyzes ATP, has weak DNA unwinding activity, and assists Polγ-catalyzed strand-displacement synthesis on short replication forks. However, CTD fails to promote multi-kilobase length product formation by Polγ in rolling-circle DNA synthesis. Thus, CTD retains all the motor functions but struggles to implement them for processive translocation. We show that NTD has DNA binding activity, and its presence stabilizes Twinkle oligomerization. The CTD oligomerizes on its own, but loss of NTD results in heterogeneously-sized oligomeric species. The CTD also exhibits weaker and salt-sensitive DNA binding compared to FL Twinkle. Based on these results, we propose that NTD directly contributes to DNA binding and holds the DNA in place behind the central channel of the CTD like a ‘doorstop’, preventing helicase slippages and sustaining processive unwinding. Consistent with this model, mtSSB compensate for the NTD loss and partially restore kilobase length DNA synthesis by CTD and Polγ. The implications of our studies are foundational for understanding the mechanisms of disease-causing Twinkle mutants that lie in the NTD.
Clamp loader processing is important during DNA replication stress
Authors: Tashjian Tommy F. , Chien Peter
Published: November 2022

The DNA clamp loader is critical to the processivity of the DNA polymerase and coordinating synthesis on the leading and lagging strands. In bacteria the major subunit of the clamp loader, DnaX, has two forms: the essential full-length τ and shorter γ. These are conserved across bacterial species and three distinct mechanisms have been found to create them: ribosomal frameshift, transcriptional slippage, and, inCaulobacter crescentus, proteolysis. This conservation suggests that DnaX processing is evolutionarily important, but its role remains unknown.

Here we find a bias against switching from expression of a wild typednaXto a nonprocessableτ-onlyallele inCaulobacter. Despite this bias, cells are able to adapt to theτ-onlyallele with little effect on growth or morphology and only minor defects during DNA damage. Motivated by transposon sequencing, we find that loss of the genesidAin theτ-onlystrain slows growth and increases filamentation. Even in the absence of exogenous DNA damage treatment, theΔsidA τ-onlydouble mutant shows induction of and dependance onrecA, likely due to a defect in resolution of DNA replication fork stalling. We find that some of the phenotypes of theΔsidA τ-onlycan be complemented by expression of γ but that an overabundance of τ-onlydnaXis also detrimental. The data presented here suggest that DnaX processing is important during resolution of replication fork stalling events during DNA replication stress.

IMPORTANCE

Though the presence of DnaX τ and γ forms is conserved across bacteria, different species have developed different mechanisms to make these forms. This conservation and independent evolution of mechanisms suggest that having two forms of DnaX is important. Despite having been discovered more than 30 years ago, the purpose of expressing both τ and γ is still unclear. Here, we present evidence that expressing two forms of DnaX and controlling the abundance and/or ratio of the forms is important during the resolution of replication fork stalling.
Integration of exogenous and endogenous co-stimulatory signals by CAR-Tregs
Authors: Rosado-Sánchez Isaac , Haque Manjurul , Salim Kevin , Speck Madeleine , Fung Vivian , Boardman Dominic , Mojibian Majid , Raimondi Giorgio , Levings Megan K
Published: November 2022

Regulatory T cells (Tregs) expressing chimeric antigen receptors (CAR) are a promising tool to promote transplant tolerance. The relationship between CAR structure and Treg function was studied in xenogeneic, immunodeficient mice, revealing advantages of CD28-encoding CARs. However, these models could underrepresent interactions between CAR-Tregs, antigen-presenting cells (APCs) and donor-specific antibodies. We generated mouse Tregs expressing HLA-A2-specific CARs with different costimulatory domains and compared their function in vitro and in vivo. In vitro assays revealed the CD28-encoding CAR had superior antigen-specific suppression, proliferation and cytokine production. In contrast, in vivo protection from skin allograft rejection and alloantibody production was similar between Tregs expressing CARs encoding CD28, ICOS or PD1, but not GITR, 41BB or OX40, co-stimulatory domains. To reconcile in vitro and in vivo data, we analyzed effects of a CAR encoding CD3ζ but no co-stimulatory domain. These data revealed that exogenous co-stimulation via APCs can compensate for the lack of a CAR-encoded CD28 domain. Thus, Tregs expressing a CAR with or without CD28 are functionally equivalent in vivo. This study reveals a new dimension of CAR-Treg biology and has important implications for the design of CARs for clinical use in Tregs.
Predicting pathological complete response to neoadjuvant chemotherapy in breast cancer from routine diagnostic histopathology biopsies
Authors: Aswolinskiy Witali , Munari Enrico , Horlings Hugo M. , Mulder Lennart , Bogina Giuseppe , Sanders Joyce , Liu Yat-Hee , van den Belt-Dusebout Alexandra W. , Tessier Leslie , Balkenhol Maschenka , Hoven Jeffrey , Wesseling Jelle , van der Laak Jeroen , Lips Esther H. , Ciompi Francesco
Published: November 2022

Purpose

Invasive breast cancer patients are increasingly being treated with neoadjuvant chemotherapy, however, only a fraction of the patients respond to it completely. To prevent over-treating patients with a toxic drug, there is an urgent need for biomarkers capable of predicting treatment response before administering the therapy. In this retrospective study, we developed interpretable, deep-learning based biomarkers to predict the pathological complete response (pCR, i.e. the absence of tumor cells in the surgical resection specimens) to neoadjuvant chemotherapy from digital pathology H&E images of pre-treatment breast biopsies.

Experimental Design

Our approach consists of two steps: In the first step, using deep learning, mitoses are detected and the tissue segmented into several morphology compartments including tumor, lymphocytes and stroma. In the second step, computational biomarkers are derived from the segmentation and detection output to encode slide-level relationships between the morphological structures with focus on tumor infiltrating lymphocytes (TILs). We developed and evaluated our method on slides from N=721 patients from three European medical centers with triple-negative and Luminal B breast cancers.

Results

The investigated biomarkers yield statistically significant prediction performance for pCR with areas under the receiver operating characteristic curve between 0.66 and 0.88 depending on the cancer subtype and center.

Conclusion

The proposed computational biomarkers predict pathological complete response, but will require more evaluation and finetuning for clinical application. The results further corroborate the potential role of deep learning to automate TILs quantification, and their predictive value in breast cancer neoadjuvant treatment planning.
Accuracy of left ventricular mechanical dyssynchrony indices for mechanical characteristics of left bundle branch block using cardiovascular magnetic resonance feature tracking
Authors: Loewenstein Daniel E. , Wieslander Björn , Heiberg Einar , Axelsson Jimmy , Klem Igor , Nijveldt Robin , Schelbert Erik B. , Sörensson Peder , Sigfridsson Andreas , Strauss David G. , Kim Raymond J. , Atwater Brett D. , Ugander Martin
Published: November 2022

Aims

More than 90% of patients with left bundle branch block (LBBB) and reduced left ventricular (LV) ejection fraction have LV dyssynchrony and a high probability of response to cardiac resynchronization therapy (CRT). A subgroup of patients with non-specific intraventricular conduction delay (IVCD) have a LBBB-like LV activation pattern when studied using invasive mapping and advanced echocardiographic techniques. These patients also frequently benefit from CRT but these patients have proven difficult to identify using ECG criteria. Cardiovascular magnetic resonance (CMR) imaging indices of dyssynchrony may identify patients with IVCD who may benefit from CRT but their relative accuracies for identification of LV dyssynchrony remains unknown. We compared the LV dyssynchrony classification accuracy of two commonly available CMR indices in a study population of patients with severely reduced LV ejection fraction and no scar, and either LBBB or normal conduction (normal QRS duration and axis, controls).

Methods and results

In LBBB (n=44) and controls (n=36), using CMR feature tracking circumferential strain, dyssynchrony was quantified as the circumferential uniformity ratio estimate (CURE) and the systolic stretch index (SSI). Deidentified CMR image-data were made publicly available. Both CURE and SSI quantified more severe dyssynchrony in LBBB compared to controls (p<0.001 for both). SSI more frequently discriminated LBBB and normal conduction LV activation patterns than CURE (area under the receiver operating characteristics curve [95% confidence interval] 0.98 [0.95-1.00] for SSI vs 0.77 [0.66-0.86] for CURE, p<0.001).

Conclusions

SSI is superior to CURE for discriminating synchronous and dyssynchronous LV activation and should be further studied in the setting of non-LBBB conduction abnormalities.
Pressure cells for in situ neutron total scattering: time and real-space resolution during deuterium absorption
Authors: Ikeda Kazutaka , Ohshita Hidetoshi , Otomo Toshiya , Sakaki Kouji , Kim Hyunjeong , Nakamura Yumiko , Machida Akihiko , Von Dreele Robert B.
Published: November 2022

In situ gas-loading sample holders for two-dimensionally arranged detectors in time-of-flight neutron total scattering experiments have been developed to investigate atomic arrangements during deuterium absorption using time and real-space resolution. A single-crystal sapphire container was developed that allows conditions of 473 K and 10 MPa hydrogen gas pressure. High-resolution transient measurements detected deuterium absorption by palladium that proceeded within a few seconds. A double-layered container with thick- and thin-walled vanadium allowed conditions of 423 K and 10 MPa hydrogen gas pressure. The deuterium occupation sites of a lanthanum–nickel–aluminium alloy are discussed in detail on the basis of real-space high-resolution data obtained from in situ neutron scattering measurements and reverse Monte Carlo structural modeling.
Structure of a hydrophobic leucinostatin derivative determined by host lattice display
Authors: Kiss Cedric , Gall Flavio M. , Dreier Birgit , Adams Michael , Riedl Rainer , Plückthun Andreas , Mittl Peer R. E.
Published: November 2022

Peptides comprising many hydrophobic amino acids are almost insoluble under physiological buffer conditions, which complicates their structural analysis. To investigate the three-dimensional structure of the hydrophobic leucinostatin derivative ZHAWOC6027, the previously developed host lattice display technology was applied. Two designed ankyrin-repeat proteins (DARPins) recognizing a biotinylated ZHAWOC6027 derivative were selected from a diverse library by ribosome display under aqueous buffer conditions. ZHAWOC6027 was immobilized by means of the DARPin in the host lattice and the structure of the complex was determined by X-ray diffraction. ZHAWOC6027 adopts a distorted α-helical conformation. Comparison with the structures of related compounds that have been determined in organic solvents reveals elevated flexibility of the termini, which might be functionally important.
Factors affecting the implementation of automated progress monitoring of rebar using vision-based technologies
Authors: Qureshi Abdul Hannan , Alaloul Wesam Salah , Wing Wong Kai , Saad Syed , Alzubi Khalid Mhmoud , Musarat Muhammad Ali
Published: November 2022

Purpose

Rebar is the prime component of reinforced concrete structures, and rebar monitoring is a time-consuming and technical job. With the emergence of the fourth industrial revolution, the construction industry practices have evolved toward digitalization. Still, hesitation remains among stakeholders toward the adoption of advanced technologies and one of the significant reasons is the unavailability of knowledge frameworks and implementation guidelines. This study aims to investigate technical factors impacting automated monitoring of rebar for the understanding, confidence gain and effective implementation by construction industry stakeholders.

Design/methodology/approach

A structured study pipeline has been adopted, which includes a systematic literature collection, semistructured interviews, pilot survey, questionnaire survey and statistical analyses via merging two techniques, i.e. structural equation modeling and relative importance index.

Findings

The achieved model highlights “digital images” and “scanning” as two main categories being adopted for automated rebar monitoring. Moreover, “external influence”, “data-capturing”, “image quality”, and “environment” have been identified as the main factors under “digital images”. On the other hand, “object distance”, “rebar shape”, “occlusion” and “rebar spacing” have been highlighted as the main contributing factors under “scanning”.

Originality/value

The study provides a base guideline for the construction industry stakeholders to gain confidence in automated monitoring of rebar via vision-based technologies and effective implementation of the progress-monitoring processes. This study, via structured data collection, performed qualitative and quantitative analyses to investigate technical factors for effective rebar monitoring via vision-based technologies in the form of a mathematical model.
Interplay of consumer expectation and processing fluency in perception of product innovativeness and product evaluation
Authors: Min Bora
Published: November 2022

Purpose

This study aims to draw on the malleable nature of processing fluency to identify the role of consumer expectation in generating diverging effects of metacognitive experiences on perception of product innovativeness and product evaluation. It also examines critical boundary conditions to offer a more sophisticated understanding of the interactive effect of expectation and processing fluency.

Design/methodology/approach

Studies 1, 2A and 2B recruited 1,922 online participants, and Studies 3 and 4 recruited 644 college students. The authors manipulated product innovativeness expectation by exposing participants to expert reviews of new products, and processing fluency by presenting product detail in either easy-to-read font/color contrast or difficult-to-read font/color contrast. Subsequently, perceived product innovativeness and product evaluation including actual product adoption were measured.

Findings

When a product was expected to be innovative (ordinary), feelings of difficulty with processing its detail increased (decreased) perceived innovativeness and, in turn, interest in purchase. The observation occurred only when a credible external source (vs firms) generated the innovativeness expectation or consumers’ elaboration level was not high. Furthermore, when innovativeness became associated with negative implications, perceived innovativeness no longer enhanced but impaired purchase intention.

Research limitations/implications

Studies used incrementally new products only. Really new products involving a high adoption risk might produce a diverging effect. The findings need to be replicated with higher involvement products. An ideal level of difficulty with comprehending product information was not examined in the present research.

Practical implications

Results carry significant weight for firms who seek to draw consumer attention to their new products by choosing an optimal format of product presentation. The findings suggest that they can proactively administer a proper level of ease/difficulty with comprehending product detail depending on the extent of product innovativeness and target audience.

Originality/value

Extant research has not addressed how the malleable nature of processing fluency systematically affects innovativeness perception and product evaluation. The key contribution of this paper to the metacognition literature is the role of consumer expectation that alters the meaning of metacognitive experiences in relation to innovativeness perception. In addition, this is one of the first to empirically investigate perceptual processing fluency in the elaboration likelihood model theory.
Improving the impact of remote Playing Lean workshops through action inquiry and critical reflexivity
Authors: Pešec Bruno
Published: November 2022

Purpose

The purpose of this study is to share how the learning impact of a remote workshop was improved through action research practices, especially action inquiry and critical reflexivity.

Design/methodology/approach

Research design detailed herein consists of one complete cycle of action and reflection. Methods used include: journaling into four territories of experience, free-form journaling, individual and joint reflection using four parts of speech and extended ways of knowing.

Findings

Action inquiry and critical reflexivity have shown themselves to be a potent means of improving the learning outcomes of remote Playing Lean workshops. Drawing on early insight, the author suggests several venues for further inquiry.

Originality/value

This paper contributes a novel combination of action research practices that can be used for improving other learning initiatives as well, and an example of how to question the veracity of qualitative findings.