bluuebunny/crossref_metadata_2025 huggingface dataset:
DESIGNING OF CUSTOM BARCODES FOR SEQUENCING ON THE MGI PLATFORM
Authors: Bulusheva Irina , Shmitko Anna , Vasiliadis Julia , Suchalko Oleg , Syrko Denis , Belova Vera , Korostin Dmitriy
Published: September 2022

The recently launched MGI platform (DNBSEQ-G50, -G400 and -T7 sequencers) has been gaining popularity for next-generation sequencing. However, the barcode set for library preparation provided by the manufacturer has certain limitations on the number of samples that can be sequenced at a time and the compatibility of barcodes from different or incomplete sets as well as a ratio between the samples.

In this paper, we present a protocol for designing custom barcodes expanding the pre-existing barcode set and demonstrate its performance on the MGI Tech Co. Ltd. (China) machines. We developed a universal “quad method” which allows for simultaneous sequencing of any number of samples up to 252 per lane which is multiple of 4 or 4n+2. Here, we describe this method, its analysis, verification, and integration into the sequencing as well as its validation for sequencing using the DNBSEQ G-400 machine.
Multi-omics analysis reveals distinct non-reversion mechanisms of PARPi resistance in BRCA1- versus BRCA2-deficient mammary tumors
Authors: Bhin Jinhyuk , Dias Mariana Paes , Gogola Ewa , Rolfs Frank , Piersma Sander R. , de Bruijn Roebi , de Ruiter Julian R. , van den Broek Bram , Duarte Alexandra A. , Sol Wendy , van der Heijden Ingrid , Bakker Lara , Kaiponen Taina S. , Lieftink Cor , Morris Ben , Beijersbergen Roderick L. , van de Ven Marieke , Jimenez Connie R. , Wessels Lodewyk F. A. , Rottenberg Sven , Jonkers Jos
Published: September 2022

BRCA1 and BRCA2 both function in DNA double-strand break repair by homologous recombination (HR). Due to their HR-defect, BRCA1/2-deficient cancers are sensitive to poly(ADP-ribose) polymerase inhibitors (PARPi) but they eventually acquire resistance. Preclinical studies yielded several PARPi resistance mechanisms that do not involve BRCA1/2 reactivation, but their relevance in the clinic remains elusive. To investigate which BRCA1/2-independent mechanisms drive spontaneous resistance in vivo, we combined molecular profiling with functional analysis of the HR status of matched PARPi-naïve and PARPi-resistant mouse mammary tumors harboring large intragenic deletions that prevent functional restoration of BRCA1/2. We observed restoration of HR in 64% of PARPi-resistant BRCA1-deficient tumors but none in the PARPi-resistant BRCA2-deficient tumors. Moreover, we found that 53BP1 loss is the prevalent resistance mechanism in HR-proficient BRCA1-deficient tumors, whereas resistance in BRCA2-deficient tumors is mainly induced by the loss of PARG. Our combined multi-omics analysis catalogued additional genes and pathways potentially involved in modulating PARPi response.
Genome-wide metabolite quantitative trait loci analysis (mQTL) in red blood cells from volunteer blood donors
Authors: Moore Amy , Busch Michael P , Dziewulska Karolina , Francis Richard O. , Hod Eldad A. , Zimring James C , D’Alessandro Angelo , Page Grier P
Published: September 2022

The Red Blood Cell (RBC)-Omics study, part of the larger NHLBI-funded Recipient Epidemiology and Donor Evaluation Study (REDS-III), aims to understand the genetic contribution to blood donor RBC characteristics. Previous work identified donor demographic, behavioral, genetic and metabolic underpinnings to blood donation, storage, and - to a lesser extent - transfusion outcomes, but none have yet linked the genetic and metabolic bodies of work. We performed a Genome-Wide Association (GWA) analysis using RBC-Omics study participants with generated untargeted metabolomics data to identify metabolite quantitative trait loci (mQTL) in RBCs. We performed GWA analyses of 382 metabolites in 243 individuals imputed using the 1000 Genomes Project phase 3 all-ancestry reference panel. Analyses were conducted using ProbABEL and adjusted for sex, age, donation center, number of whole blood donations in the past two years, and first ten principal components of ancestry. Our results identified 423 independent genetic loci associated with 132 metabolites (p < 5×10−8). Potentially novel locus-metabolite associations were identified for FLVCR1 and choline, and for LPCAT3 and the lysophosphatidylserine 16.0, 18.0, 18.1, and 18.2; these associations are supported by published rare disease and mouse studies. We also confirmed previous metabolite GWA results for associations including N(6)-Methyl-L-lysine and PYROXD2, and various carnitines and SLC22A16. Association between pyruvate levels and G6PD polymorphisms was validated in an independent cohort and novel murine models of G6PD deficiency (African and Mediterranean variants). We demonstrate that it is possible to perform metabolomics-scale GWA analyses with a modest, trans-ancestry sample size.

Key points

Metabolite heterogeneity in fresh (<14 day old) RBCs donated by volunteer donors is linked to genetic polymorphisms;

We report 2,831 high-confidence SNP-metabolite linkages (p < 5.0 × 10−8). Pyruvate levels in fresh RBCs are associated with glucose-6-phosphate dehydrogenase (G6PD) status
MOAHIT: a web tool for visualizing tumor multi-omics data with human anatomy heatmaps
Authors: Zhou Chaozheng , Lin Anqi , Li Mengyao , Qi Chang , Zhang Jian , Luo Peng
Published: September 2022

Multi-omics data plays an important role in cancer research, helping clinicians to better explore drug targets and biomarkers. At present, there exist several databases including TCGA (the Cancer Genome Atlas) and GDSC (Genomics of Drug Sensitivity in Cancer), which contain multi omics data on multiple cancer species, as well as various web tools for analyzing the multi-omics data, which are widely used in oncology research. Tumor heterogeneity is a widespread phenomenon, reflected by differences in multi-omics data of cancers originating from different tissues and organs. However, there is a lack of convenient analysis and visualization tools to explore tumor heterogeneity. As a result, we developed a web tool called Multi-Omics Anatomy Heatmap in Tumors (MOAHIT) based on shiny programming. This tool enables users to analyze and visualize the heterogeneity of human tissues. In addition, MOAHIT enables users to produce a beautiful human anatomy heatmap to visualize the heterogeneity between distinct cancers in the multi-omics data.
Antibiotics that affect translation can antagonize phage infectivity by interfering with the deployment of counter-defences
Authors: Pons Benoit J. , Dimitriu Tatiana , Westra Edze R. , van Houte Stineke
Published: September 2022

It is becoming increasingly clear that antibiotics can both positively and negatively impact the infectivity of bacteriophages (phage), but the underlying mechanisms often remain unclear. Here we demonstrate that antibiotics that target the protein translation machinery can fundamentally alter the outcome of bacteria-phage interactions by interfering with the production of phage-encoded counter-defence proteins. Specifically, using Pseudomonas aeruginosa PA14 and phage DMS3vir as a model, we show that bacteria with CRISPR-Cas immune systems have elevated levels of immunity against phage that encode anti-CRISPR (acr) genes when translation inhibitors are present in the environment. CRISPR-Cas are highly prevalent defence systems that enable bacteria to detect and destroy phage genomes in a sequence-specific manner. In response, many phages encode acr genes that are expressed immediately following infection to inhibit key steps of the CRISPR-Cas immune response. Our data show that while phage carrying acr genes can amplify efficiently on bacteria with CRISPR-Cas immune systems in the absence of antibiotics, the presence of antibiotics that act on protein translation prevents phage amplification, while protecting bacteria from lysis. These results help to understand how antibiotics-phage synergy and antagonism depend on the molecular interactions that define phage infectivity and host immunity.
Epigenetic centromere identity is precisely maintained through DNA replication but is uniquely specified among human cells
Authors: Mahlke Megan A. , Lumerman Lior , Ly Peter , Nechemia-Arbely Yael
Published: September 2022

Centromere identity is defined and maintained epigenetically by the presence of the histone variant CENP-A. How centromeric CENP-A position is specified and precisely maintained through DNA replication is not fully understood. The recently released Telomere-to-Telomere (T2T-CHM13) genome assembly containing the first complete human centromere sequences provides a new resource for examining CENP-A position. Mapping CENP-A position in clones of the same cell line to T2T-CHM13 identified highly similar CENP-A position following multiple cell divisions. In contrast, centromeric CENP-A epialleles were evident at several centromeres of different human cell lines, demonstrating the location of CENP-A enrichment and site of kinetochore recruitment varies among human cells. Across the cell cycle, CENP-A molecules deposited in G1 phase are maintained at their precise position through DNA replication. Thus, despite CENP-A dilution during DNA replication, CENP-A is precisely reloaded onto the same sequences within the daughter centromeres, maintaining unique centromere identity among human cells.
Actin-driven protrusions generate rapid long-range membrane tension propagation in cells
Authors: De Belly Henry , Yan Shannon , da Rocha Hudson Borja , Ichbiah Sacha , Town Jason P. , Turlier Hervé , Bustamante Carlos , Weiner Orion D.
Published: September 2022

Membrane tension is thought to be a long-range integrator of cell physiology. This role necessitates effective tension transmission across the cell. However, the field remains strongly divided as to whether cell membranes support or resist tension propagation, in part due to a lack of adequate tools for locally manipulating membrane tension. We overcome these limitations by leveraging optogenetics to generate localized actinbased protrusions while concurrently monitoring the propagation of membrane tension using dual-trap optical tweezers. Surprisingly, actin-driven protrusions elicit rapid global membrane tension propagation with little to no attenuation, while forces applied to the cell membrane only do not. We present a simple unifying mechanical model in which mechanical forces that act on both the membrane and actin cortex drive rapid, robust membrane tension propagation.

Mechanical perturbations acting on both actin cortex and plasma membrane drive global membrane tension increase within seconds
Oncogenic signals prime cancer cells for toxic cell growth during a G1 cell cycle arrest
Authors: Foy Reece , Crozier Lisa , Pareri Aanchal U , Park Ben Ho , Saurin Adrian T
Published: September 2022

A long-term goal in cancer research has been to inhibit the cell cycle in tumour cells without causing toxicity in proliferative healthy tissues. The best evidence that this is achievable is provided by CDK4/6 inhibitors, which arrest the cell cycle in G1, are well-tolerated in patients, and are effective in treating ER+/HER2-breast cancer. CDK4/6 inhibitors are effective because they arrest tumour cells more efficiently than some healthy cell types and, in addition, they affect the tumour microenvironment to enhance anti-tumour immunity. We demonstrate here another reason to explain their efficacy. Tumour cells are specifically vulnerable to CDK4/6 inhibition because during the G1 arrest, oncogenic signals drive toxic cell overgrowth. This overgrowth causes permanent cell cycle withdrawal by either preventing exit from G1 or by inducing replication stress and genotoxic damage during the subsequent S-phase and mitosis. Inhibiting or reverting oncogenic signals that converge onto mTOR can rescue this excessive growth, DNA damage and cell cycle exit in cancer cells. Conversely, inducing oncogenic signals in non-transformed cells can drive these toxic phenotypes and sensitize cells to CDK4/6 inhibition. Together, this demonstrates how oncogenic signals that have evolved to stimulate constitutive tumour growth and proliferation can be driven to cause toxic cell growth and irreversible cell cycle exit when proliferation is halted in G1.
The genetics of cortical organisation and development: a study of 2,347 neuroimaging phenotypes
Authors: Warrier Varun , Stauffer Eva-Maria , Huang Qin Qin , Wigdor Emilie M. , Slob Eric A.W. , Seidlitz Jakob , Ronan Lisa , Valk Sofie , Mallard Travis T. , Grotzinger Andrew D. , Romero-Garcia Rafael , Baron-Cohen Simon , Geschwind Daniel H. , Lancaster Madeline , Murray Graham K. , Gandal Michael J. , Alexander-Bloch Aaron , Won Hyejung , Martin Hilary C. , Bullmore Edward T. , Bethlehem Richard A.I.
Published: September 2022

Our understanding of the genetic architecture of the human cerebral cortex is limited both in terms of the diversity of brain structural phenotypes and the anatomical granularity of their associations with genetic variants. Here, we conducted genome-wide association meta-analysis of 13 structural and diffusion magnetic resonance imaging derived cortical phenotypes, measured globally and at 180 bilaterally averaged regions in 36,843 individuals from the UK Biobank and the ABCD cohorts. These phenotypes include cortical thickness, surface area, grey matter volume, and measures of folding, neurite density, and water diffusion. We identified 4,349 experiment-wide significant loci associated with global and regional phenotypes. Multiple lines of analyses identified four genetic latent structures and causal relationships between surface area and some measures of cortical folding. These latent structures partly relate to different underlying gene expression trajectories during development and are enriched for different cell types. We also identified differential enrichment for neurodevelopmental and constrained genes and demonstrate that common genetic variants associated with surface area and volume specifically are associated with cephalic disorders. Finally, we identified complex inter-phenotype and inter-regional genetic relationships among the 13 phenotypes which reflect developmental differences among them. These analyses help refine the role of common genetic variants in human cortical development and organisation.

One sentence summary

GWAS of 2,347 neuroimaging phenotypes shed light on the global and regional genetic organisation of the cortex, underlying cellular and developmental processes, and links to neurodevelopmental and cephalic disorders.
Lattice defects in quinacridone
Authors: Brey Dominik , Scherer Barbara , Schmidt Martin U.
Published: September 2022

Various lattice defects in the αI-phase of quinacridone (C20H12N2O2) were simulated using lattice-energy minimizations. αI-Quinacridone forms a chain structure in P
1, Z = 1. The molecules are connected by hydrogen bonds along [010], by π-stacking along [100] and by weak van der Waals interactions along [001]. αI-Quinacridone is inherently nanocrystalline. Lattice defects were calculated in correspondingly large supercells with up to 4464 atoms, using a previously evaluated force field. Vacancies, vacancy aggregates and interstitial molecules are energetically very unfavourable. A misorientation of a single molecule (flip around [010] by 180°) causes an energy increase of 243.7 kJ mol−1. Various edge and screw dislocations were investigated. A screw dislocation along [010] causes an energy increase of ΔE = 38.0 kJ mol−1 per molecule, all other line dislocations are even worse. In contrast, the rotation of an entire chain around the chain axis [010] by 180° leads to only a very small energy increase (ΔE = 1.6 kJ mol−1) and the real crystals probably contain a high number of such defects. Various planar defects were calculated, including different stacking disorders and misfit-layer structures with two different types of layers having different lateral periodicities. Stacking faults along [001] with herringbone stacking instead of parallel stacking are energetically quite favourable (ΔE = 2.2 kJ mol−1); the same is true for domains with misoriented molecules in the [001] direction. As an example for a bulk defect, domains are calculated in which blocks of 4 × 4 chains are rotated by 180° around [010], which leads to an energy increase of only 1.1 kJ mol−1. Twinning by mirroring at the (001) plane is energetically favourable (ΔE = 0.9 kJ mol−1). This twinning was observed in an HRTEM image. It is probable that the crystallites also contain rotations of chains, layers or blocks around [010] by 180°, but these defects cause only a very slight modification of the molecular packing, which was not observable in the HRTEM image. The lattice defects in αI-quinacridone investigated here provide an insight into lattice defects, their energies and local structures. Similar lattice defects are expected to occur also in other similar organic chain structures.
Crystal structure of MgK0.5[B6O10](OH)0.5·0.5H2O, poly[dimagnesium potassium bis(hexaborate) hydroxide monohydrate]
Authors: Qiu Qi-Ming , Song Jian-Biao
Published: September 2022

The solvothermal reaction of H3BO3, KCF3SO3, Mg(CF3SO3)2 and pyridine led to a new alkali- and alkaline-earth-metal borate, MgK0.5[B6O10](OH)0.5·0.5H2O. Its structure features an intricate three-dimensional framework built from [B6O13]8− clusters, thus resulting in a six-connected achiral net with high symmetry. Each [B6O13]8− building block is composed of three trigonal BO3 and three tetrahedral BO4 units, with these BO4 units being further connected to neighboring BO3 units, giving rise to an oxoboron cluster of the general formula [B6O10]2−.
To what extent have street-level bureaucrats used their discretionary powers during the COVID-19 pandemic in Indonesia?
Authors: Hadna Agus Heruanto , Listyaningsih Umi , Ihwanudin Idris
Published: September 2022

Purpose

The objective of this research is to analyze the extent to which street-level bureaucrats (SLBs) have exercised discretion (low, medium and high) and the contributing factors involved (i.e. the influence of personal, work environment and demographic factors on the exercise of discretion).

Design/methodology/approach

The mixed-methods research uses the embedded design approach. Data were collected during the COVID-19 pandemic through a survey of 2,867 Official Certifier of Title Deeds (Pejabat Pembuat Akta Tanah/PPAT) as SLBs spread across fifty regencies/cities in ten provinces in Indonesia.

Findings

This field study found a significant and positive correlation between SLBs' economic motive and the client's knowledge of land issues with the exercise of discretion. In addition, the study found a significant correlation between the age and gender of SLBs and their practice of discretion.

Practical implications

This study provides insights into that new policies should not further complicate the system but reduce face-to-face interactions between SLBs and their clients by allowing digital technology.

Originality/value

The novelty of this research is the paradox of SLB service during the COVID-19 pandemic differed from the paradoxes identified in earlier studies. SLBs commonly cope with service paradox by limiting their services or focusing solely on the most profitable clientele. However, this study shows that some SLBs actively reach out to clients using a “friendly” service model.
Human herpesvirus 6A and 6B and polyomavirus JC and BK infections in renal cell carcinoma and their relationship with p53, p16INK4a, Ki‐67, and nuclear factor‐kappa B expression
Authors: Namdari Sepide , Chong Pei Pei , Behzad‐Behbahani Abbas , Geramizadeh Bita , Nazhvani Ali Dehghani , Sekawi Zamberi , Farhadi Ali
Published: September 2022

There are a limited number of studies regarding the involvement of viruses in the development and pathogenesis of renal cell carcinoma (RCC). In this study, we aimed to discover whether human herpesvirus 6A (HHV‐6A) and 6B (HHV‐6B) and human polyomavirus JC (JCV) and BK (BKV) are associated with RCC and the expression of p53, p16INK4a, Ki‐67, and nuclear factor‐κB (NF‐κB) in patients with RCC. A total of 122 histologically confirmed RCC tissue specimens and 96 specimens of their corresponding peritumoral tissues were included in this prospective study. Nested PCR was performed to amplify viral DNA sequences. Restriction endonuclease analysis was carried out to discriminate between HHV‐6A and HHV‐6B. p53, p16INK4a, Ki‐67, and NF‐κB immunostaining data of the studied tissue specimens were available from our previous study. Statistical analysis was performed to demonstrate the potential associations. HHV‐6B and JCV were detected in 10.7% and 13.9% of patients with RCC, respectively. We did not detect HHV‐6A and BKV in any of RCC tissue specimens. Moreover, no association was found between either of these viruses and RCC. Our study revealed a significant association between HHV‐6B and p53 overexpression. No other associations were found between cellular biomarkers p53, p16INK4a, Ki‐67, and NF‐κB and the studied viruses. The data of this study, though very limited, disprove the involvement of HHV‐6A, HHV‐6B, BKV, and JCV in the initiation or progression of RCC.
Conserved age‐related increases in hippocampal PDE11A4 cause unexpected proteinopathies and cognitive decline of social associative memories
Authors: Pilarzyk Katy , Porcher Latarsha , Capell William R. , Burbano Steven D. , Davis Jeff , Fisher Janet L. , Gorny Nicole , Petrolle Siena , Kelly Michy P.
Published: September 2022

In humans, associative memories are more susceptible to age‐related cognitive decline (ARCD) than are recognition memories. Reduced cAMP/cGMP signaling in the hippocampus may contribute to ARCD. Here, we found that both aging and traumatic brain injury‐associated dementia increased the expression of the cAMP/cGMP‐degrading enzyme phosphodiesterase 11A (PDE11A) in the human hippocampus. Further, age‐related increases in hippocampal PDE11A4 mRNA and protein were conserved in mice, as was the increased vulnerability of associative versus recognition memories to ARCD. Interestingly, mouse PDE11A4 protein in the aged ventral hippocampus (VHIPP) ectopically accumulated in the membrane fraction and filamentous structures we term “ghost axons.” These age‐related increases in expression were driven by reduced exoribonuclease‐mediated degradation of PDE11A mRNA and increased PDE11A4‐pS117/pS124, the latter of which also drove the punctate accumulation of PDE11A4. In contrast, PDE11A4‐pS162 caused dispersal. Importantly, preventing age‐related increases in PDE11 expression via genetic deletion protected mice from ARCD of short‐term and remote long‐term associative memory (aLTM) in the social transmission of food preference assay, albeit at the expense of recent aLTM. Further, mimicking age‐related overexpression of PDE11A4 in CA1 of old KO mice caused aging‐like impairments in CREB function and remote social—but not non‐social—LTMs. RNA sequencing and phosphoproteomic analyses of VHIPP identified cGMP‐PKG—as opposed to cAMP‐PKA—as well as circadian entrainment, glutamatergic/cholinergic synapses, calcium signaling, oxytocin, and retrograde endocannabinoid signaling as mechanisms by which PDE11A deletion protects against ARCD. Together, these data suggest that PDE11A4 proteinopathies acutely impair signaling in the aged brain and contribute to ARCD of social memories.
In vitro bactericidal efficacy of a new triple antibiotic paste formulation against Enterococcus faecalis biofilm
Authors: Smittiset Benjaporn , Banomyong Danuchit , Ruangsawasdi Nisarat , Kaewprag Jittranan
Published: September 2022

The aim of this study was to evaluate the bactericidal efficacy on Enterococcus faecalis biofilm of a novel, low‐concentration triple‐antibiotic paste (TAP‐L2) in propylene glycol/carboxymethylcellulose vehicle (VEH‐2), a ready‐to‐use prototype, compared with two currently used products; a low‐concentration (TAP‐L1) and a high‐concentration paste (TAP‐H1) mixed in macrogol/propylene glycol vehicle (VEH‐1). Sixty‐two root canals were infected with E. faecalis biofilm, medicated with (a) TAP‐L1, (b) TAP‐L2, (c) TAP‐H1, (d) VEH‐1 or (e) VEH‐2 (n = 10) and incubated for 21 days. Live/dead assays were performed using confocal laser scanning microscopy (CLSM), and dead bacteria (%) were calculated. The TAP‐H1 group demonstrated the highest dead bacteria (67.54 ± 2.38%), which was significantly higher than the TAP‐L2 and TAP‐L1 groups (56.85 ± 7.11% and 54.23 ± 10.19%) (p < 0.05). The TAP groups demonstrated significantly higher dead bacteria than the VEH‐1 and VEH‐2 groups (47.51 ± 6.41% and 45.14 ± 8.28%) (p < 0.05). The ready‐to‐use TAP‐L2 had antibacterial activity comparable to TAP‐L1, both of which were lower than TAP‐H1.
Real‐world evidence for the long‐term effect of allergen immunotherapy: Current status on database‐derived European studies
Authors: Vogelberg Christian , Klimek Ludger , Brüggenjürgen Bernd , Jutel Marek
Published: September 2022

Randomized controlled trials (RCTs) are the gold‐standard for benefit–risk assessments during drug approval processes. Real‐word data (RWD) and the resulting real‐world evidence (RWE) are becoming increasingly important for assessing the effectiveness of drug products after marketing authorization showing how RCT results are transferred into real life care. The effectiveness of allergen immunotherapy (AIT) has been assessed in several RWE studies based on large prescription databases. We performed a literature search for retrospective cohort assessments of prescription databases in Europe to provide an overview on the methodology, long‐term effectiveness outcomes, and adherence to AIT. Thirteen respective publications were selected. AIT was more effective in reducing the progression of allergic rhinitis (AR) compared to a non‐AIT control group receiving only symptomatic treatment for AR for up to 6 years. The development and progression of asthma were hampered for most endpoints in patients treated with most preparations compared to the non‐AIT group, receiving only anti‐asthmatic medication. The results for “time to onset” of asthma were inconsistent. Adherence to AIT decreased during the recommended 3‐year treatment period, however, in most studies higher adherence to subcutaneous than to sublingual AIT was shown. The analysis of long‐term effectiveness outcomes of the RWE studies based on prescription databases confirms the long‐term efficacy of AIT demonstrated in RCTs. Progression of rhinitis and asthma symptoms as well as delayed onset of asthma triggered by different allergens, real life adherence to the treatment shows differences in particular application routes.
Caring Housing Futures: A Radical Care Framework for Understanding Rent Control Politics in Seattle, USA
Authors: Thompson Samantha
Published: September 2022

Hegemonic responses to housing crises overwhelmingly rely on liberal economic logics, which preclude understandings of housing inequalities as produced by intersecting structures of racial capitalism and settler colonialism. This creates housing futures that replicate housing injustice, through the reproduction of housing crises that uphold racial capitalism, the settler state, and white property ownership. To address this gap, I develop a radical care framework for analysing responses to housing crises as an approach that emphasises relationality, challenges the commodification of housing, and renders different housing futures possible. Radical care is a collective response to immediate crises and precarious futures. I apply this framework to rent control debates in Seattle, USA, which highlight the complex intersections between care and housing politics in responses to housing crises. I argue that analysing housing politics through a radical care framework helps us to account for more expansive sociopolitical imaginaries and actions that point to housing futures beyond the limits of what is deemed possible in a colonial, racial capitalist housing system.
Molecular physiology of Arc/Arg3.1: The oligomeric state hypothesis of synaptic plasticity
Authors: Eriksen Maria Steene , Bramham Clive R.
Published: September 2022

The immediate early gene, Arc, is a pivotal regulator of synaptic plasticity, memory, and cognitive flexibility. But what is Arc protein? How does it work? Inside the neuron, Arc is a protein interaction hub and dynamic regulator of intra‐cellular signaling in synaptic plasticity. In remarkable contrast, Arc can also self‐assemble into retrovirus‐like capsids that are released in extracellular vesicles and capable of intercellular transfer of RNA. Elucidation of the molecular basis of Arc hub and capsid functions, and the relationship between them, is vital for progress. Here, we discuss recent findings on Arc structure–function and regulation of oligomerization that are giving insight into the molecular physiology of Arc. The unique features of mammalian Arc are emphasized, while drawing comparisons with Drosophila Arc and retroviral Gag. The Arc N‐terminal domain, found only in mammals, is proposed to play a key role in regulating Arc hub signaling, oligomerization, and formation of capsids. Bringing together several lines of evidence, we hypothesize that Arc function in synaptic plasticity—long‐term potentiation (LTP) and long‐term depression (LTD)—are dictated by different oligomeric forms of Arc. Specifically, monomer/dimer function in LTP, tetramer function in basic LTD, and 32‐unit oligomer function in enhanced LTD. The role of mammalian Arc capsids is unclear but likely depends on the cross‐section of captured neuronal activity‐induced RNAs. As the functional states of Arc are revealed, it may be possible to selectively manipulate specific forms of Arc‐dependent plasticity and intercellular communication involved in brain function and dysfunction.
“They really care about you, they really build relationships”: Care and justice in a community organization
Authors: Dutt Anjali , Toolis Erin , Shi Christine , Moore Claire
Published: September 2022

Contemporary United States society is marked by exacerbated economic inequity and deep sociopolitical polarization, which increases a sense of precarity among marginalized communities. There is growing need to develop and foster practices that promote care and justice for marginalized communities. Organizational settings designed with the intent of supporting marginalized communities may possess unique knowledge related to actualizing care and promoting justice. Through analysis of ethnographic field notes and qualitative interviews conducted with 22 participants at the organization, this study examines organizational policies and practices of everyday decision‐making at a drop‐in center for women and gender non‐conforming people in Washington State, USA. Findings document how policies and practices at the center promote care and justice for diverse marginalized groups. Implications for promoting equitable values in social settings more broadly are discussed.
A closer look at the domain‐specific associations of openness with language achievement: Evidence on the role of intrinsic value from two large‐scale longitudinal studies
Authors: Meyer Jennifer , Schmidt Fabian T. C. , Fleckenstein Johanna , Köller Olaf
Published: September 2022

Background

Many empirical investigations focus on how personality traits and academic motivation are related to academic achievement. Regarding the personality traits described in the five‐factor model, prior research has shown associations between openness to experience and language achievement in particular. Following the principle of trait activation, associations with intrinsic value can explain these domain‐specific relationships of openness with achievement.

Aims

This study investigated whether intrinsic value mediates the associations of openness to experience with language achievement to understand these associations more closely. Based on the principle of trait activation, we combined openness to experience with intrinsic value as a motivational construct more proximal to behaviour.

Samples

We capitalized on two large‐scale longitudinal data sets (N = 1994; M = 16.8 years; 51% female; and N = 2722; M = 17.34 years; 58% female) of German‐speaking students in upper secondary education with two points of measurement, respectively.

Methods

We assessed achievement using report card grades and standardized test scores, capturing three language subskills: reading and listening, measured by standardized tests, and writing competencies, measured by essay assignments. We conducted mediation analysis using bootstrapped confidence intervals and robust standard errors to account for dependencies in the data due to students clustered within classrooms.

Results and Conclusions

Overall, our results show that intrinsic value mediated the relationship between openness and achievement in English as a foreign language. The results remained stable when controlling for prior achievement, predicting achievement gains. Our investigation provides empirical insights into the manifestations of personality in academic contexts. We discuss the limitations of our approach, with a focus on the use of a mediation analysis in this research design.
Association of rs2072446 in the NGFR gene with the risk of Alzheimer's disease and amyloid‐β deposition in the brain
Authors: He Chen‐Yang , Wang Zuo‐Teng , Shen Ying‐Ying , Shi An‐Yu , Li Hui‐Yun , Chen Dong‐Wan , Zeng Gui‐Hua , Tan Cheng‐Rong , Yu Jin‐Tai , Zeng Fan , Wang Yan‐Jiang ,   Alzheimer's Disease Neuroimaging Initiative
Published: September 2022

Introduction and Aims

Alzheimer's disease (AD) is the most common form of dementia with a complex genetic background. The cause of sporadic AD (sAD) remains largely unknown. Increasing evidence shows that genetic variations play a crucial role in sAD. P75 neurotrophin receptor (p75NTR, encoded by NGFR) plays a critical role in the pathogenesis of AD. Yet, the relationship between NGFR gene polymorphisms and AD was less studied. This study aims to analyze the relationship of NGFR gene polymorphism with the risk of AD in the Chinese Han population and amyloid‐β deposition in the ADNI cohort.

Methods

This case–control association study was conducted in a Chinese Han cohort consisting of 366 sporadic AD (sAD) patients and 390 age‐ and sex‐matched controls. Twelve tag‐SNPs were selected and genotyped with a multiplex polymerase chain reaction‐ligase detection reaction (PCR‐LDR) method. The associations between tag‐SNPs and the risk of AD were analyzed by logistic regression. Moreover, another cohort from the Alzheimer's Disease Neuroimaging Initiative (ADNI) database was included to examine the association of one tag‐SNP (rs2072446) with indicators of amyloid deposition. Kaplan–Meier survival analysis and Cox proportional hazards models were used to test the predictive abilities of rs2072446 genotypes for AD progression. The mediation effects of Aβ deposition on this association were subsequently tested by mediation analyses.

Results

After multiple testing corrections, one tag‐SNP, rs2072446, was associated with an increased risk of sAD (additive model, OR = 1.79, Padjustment = 0.0144). Analyses of the ADNI cohort showed that the minor allele (T) of rs2072446 was significantly associated with the heavier Aβ burden, which further contributed to an increased risk of AD progression in APOE ε4 non‐carrier.

Conclusion

Our study found that rs2072446 in NGFR is associated with both the risk of sAD in the Chinese Han population and the amyloid burden in the ADNI cohort, which reveals the role of p75NTR in AD from a genetic perspective.
Global effects of forest modification on herpetofauna communities
Authors: Iglesias‐Carrasco Maider , Medina Iliana , Ord Terry J.
Published: September 2022

As the area covered by human‐modified environments grows, it is increasingly important to understand the responses of communities to the novel habitats created, especially for sensitive and threatened taxa. We aimed to improve understanding of the major evolutionary and ecological processes that shape the assemblage of amphibian and reptile communities to forest modifications. To this end, we compiled a global data set of amphibian and reptile surveys in natural, disturbed (burned, logged), and transformed (monocultures, polyspecific plantations) forest communities to assess the richness, phylogenetic diversity, and composition of those communities, as well as the morphological disparity among taxa between natural and modified forest habitats. Forest transformations led to a diversity reduction of 15.46% relative to the statistically nonsignificant effect of disturbances. Transformations also led to a community composition that was 39.4% dissimilar to that on natural forests, compared with 16.1% difference in disturbances. Modifications did not affect the morphological disparity of communities (p = 0.167 and 0.744), and we found little evidence of taxon‐specific responses to anthropic impacts. Monocultures and polyspecific plantations detrimentally affected the conservation and ecological value of both amphibian and reptile communities and altered the evolutionary processes shaping these communities, whereas forests with lower impact disturbances might, to some extent, serve as reservoirs of species. Although different mechanisms might buffer the collapse of herpetological communities, preserving remaining natural forests is necessary for conserving communities in the face of future anthropic pressures.
Must‐access prescription drug monitoring programs and retail opioid sales
Authors: Shakya Shishir , Hodges Collin
Published: September 2022

This paper examines the effect of prescription drug monitoring programs (PDMPs) on the retail sales of eight commonly prescribed opioids in the United States. Specifically, we exploit variation in state‐level policies to identify states with “must‐access” versus voluntary PDMPs. Our results suggest that must‐access PDMP implementation does not uniformly reduce prescription retail opioid sales. We also find evidence that must‐access PDMP implementation does not affect the retail sales of two treatment drugs, methadone and buprenorphine. These results suggest that policymakers should consider PDMP implementation as part of a broader response to the opioid crisis rather than a singular policy intervention.
The use of salt substitutes to replace sodium chloride in food products: a review
Authors: Tan Hui‐Ling , Tan Thuan‐Chew , Easa Azhar Mat
Published: September 2022

Sodium chloride (NaCl) has a significant role in food's texture, shelf life, and flavour. The increasing consumption of foods with high amounts of NaCl leads to life‐threatening pathologies. Salt reduction was a cost‐effective strategy. Recent publications on sodium reductions were on fish products, seafoods, meat products, and Asian foods. However, there are no previous reviews on the application effects of salt substitutes (SS) on staple foods. This review article aimed to analyse current application of SS in food products, recent advancements to increase SS intake via food formulation, findings from published literature on various food products, and latest innovations to aid NaCl reduction approach. Approaches that are taken including NaCl reduction based on sensory acceptability of foods, replacing NaCl with low‐sodium blends, and usage of flavour enhancers. The usage of cross‐linking agents, hydrocolloids, and NaCl coating are innovations that reduce NaCl and maintain qualities of food products.
Plasmablastic lymphoma: An update
Authors: Bailly Jenique , Jenkins Nicholas , Chetty Dharshnee , Mohamed Zainab , Verburgh Estelle R. , Opie Jessica J.
Published: September 2022

Plasmablastic lymphoma (PBL) is a highly aggressive B cell non‐Hodgkin lymphoma frequently associated with immunosuppression, particularly human immunodeficiency virus (HIV) infection. Although PBL is rare globally, South Africa has a high burden of HIV infection leading to a higher incidence of PBL in the region. Laboratory features in PBL may overlap with plasmablastic myeloma and other large B cell lymphomas with plasmablastic or immunoblastic morphology leading to diagnostic dilemmas. There are, however, pertinent distinguishing laboratory features in PBL such as a plasma cell immunophenotype with MYC overexpression, expression of Epstein–Barr virus‐encoded small RNAs and lack of anaplastic lymphoma kinase (ALK) expression. This review aims to provide a summary of current knowledge in PBL, focusing on the epidemiology, pathophysiology, laboratory diagnosis and clinical management.
How does employee development affect turnover intention? Exploring alternative relationships
Authors: Martini Mattia , Gerosa Tiziano , Cavenago Dario
Published: September 2022

This study explores alternative relationships between perceived investment in employee development (PIED) and turnover intention by including affective commitment, perceived internal employability, and perceived external employability as potential mediators. Data were collected through a structured survey from 337 employees working in two large companies in Italy. The factorial validity and dimensionality of the latent constructs studied were evaluated in a confirmatory factor analysis framework, and the mediation hypotheses were tested in a full structural equation model. Results show that the overall effect of PIED on turnover intention is negative and almost fully mediated by external employability and affective commitment, whereas the path through internal employability is not supported. More specifically, PIED increases commitment, which in turn limits the likelihood of turnover. In addition, although perceived external employability is positively associated with turnover intention, PIED seems to reduce this effect by negatively affecting employee perceptions of their marketability in the labour market. The study supports the assumptions of social exchange theory in explaining turnover behaviour as a consequence of employee development support. Contextually, it questions the existence of the employability paradox because it does not reveal either a retention path via perceived internal employability or a turnover risk via perceived external employability.
Alfred R. Wallace's enduring influence on biogeographical studies of theIndo‐Australianarchipelago
Authors: Ali Jason R. , Heaney Lawrence R.
Published: September 2022

To mark A.R. Wallace's 200th birthday, we review the direct and indirect contributions he made to our understanding of the Indo‐Australian Archipelago's biogeography. He is widely known for his field research (1854–1862) and his 1863 boundary line separating the Oriental and Australasian faunal realms (between Bali and Lombok, Borneo and Sulawesi, and the Philippines and the Moluccas). Notably, though, he never accepted Huxley's ‘Wallace Line’ proposal (1868), whose northern part runs between the main Philippine islands and the Palawan Group to the west. Furthermore, in 1910, which was 3 years prior to his demise, he transferred Sulawesi's fauna to the Oriental realm. In 1924, Merrill introduced the ‘Wallacea’ transition zone. Although the label is today widely used to denote a sub‐region within the Indo‐Australian Archipelago between Wallace's 1863 line and Lydekker's 1896 line (first presented by Darlington in 1957), the western boundary was originally based on Huxley's line, and thus included the Philippine islands minus the Palawan group. Most biogeographers appear to be unaware of Merrill and his intention. Finally, recent attempts to define the faunal break have not led to a consensus view, despite the huge increase in primary data plus the application of modern analytical techniques. This reflects the complexities and diversity of the region's faunal distribution patterns, plus the differences in the ways that researchers choose to process their data.
Impact of uncertainty intolerance on clinical reasoning: A scoping review of the 21st‐century literature
Authors: Brun Clémence , Zerhouni Oulmann , Akinyemi Alexis , Houtin Laurène , Monvoisin Richard , Pinsault Nicolas
Published: September 2022

Rationale, Aims and Objectives

Clinical reasoning is currently extensively studied to find out how to make proper diagnoses. Literature indicates that intolerance of uncertainty (IU) may have a strong negative impact on clinical reasoning. We summarize the various consequences of IU on clinical reasoning.

Methods

A scoping review was conducted using relevant keywords to scientific databases (i.e., Google Scholar, Medline, PsycINFO and PBSC) from September to November 2021. Complementary research included relevant articles and articles retrieved through Google Scholar's alert system. We included articles about healthcare professionals as defined by the French Public Health Code (As defined here: https://www.vie-publique.fr/fiches/37855-categories-de-professionnels-de-sante-code-se-la-sante-publique), and articles reporting on the impact of IU or uncertainty management on clinical reasoning.

Results

We retrieved 1853 articles, of which 8 were kept for final analysis considering our inclusion criteria. Two behaviour categories were affected by uncertainty intolerance: investigative and prescriptive behaviours. Regarding the investigation process, mismanagement of uncertainty appeared to lead to reasoning bias, potentially resulting in diagnostic errors. IU was associated with withholding information, more referrals to peers and less use of new medical interventions. Regarding prescription behaviours, IU among health professionals could lead to overprescribing unnecessary or dangerous tests. IU was also associated with more antibiotic prescriptions for conditions where antibiotics are to be used carefully.

Conclusion

Few studies have yet addressed the impact of IU on clinical reasoning. IU's influence is primarily observed on investigative and prescribing behaviours. More studies are needed to fully understand the impact of IU on clinical reasoning itself, and not only on practical consequences.
Perinatal exposure to tributyltin affects feeding behavior and expression of hypothalamic neuropeptide Y in the paraventricular nucleus of adult mice
Authors: Ponti Giovanna , Bo Elisabetta , Bonaldo Brigitta , Farinetti Alice , Marraudino Marilena , Panzica Giancarlo , Gotti Stefano
Published: September 2022

Organotins such as tributyltin chloride (TBT), are highly diffused environmental pollutants, which act as metabolism disrupting chemicals, i.e. may interfere with fat tissue differentiation, as well as with neuroendocrine circuits, thus impairing the control of energetic balance. We have previously demonstrated that adult exposure to TBT altered the expression of neuropeptides in the hypothalamus. In this study, we orally administered daily a solution containing oil, or TBT (0.25, 2.5, or 25 μg/kg body weight/day) to pregnant females from gestational day 8 until birth, and to their pups from day 0 until post‐natal day 21. Our results showed that TBT exposure of female mice during gestation and of pups during lactation permanently altered the feeding efficiency of pups of both sexes and subcutaneous fat distribution in adult males. In addition, the neuropeptide Y system was affected at the level of the paraventricular nucleus, with a decrease in immunoreactivity in both sexes (significant in females for all TBT doses and in males only for intermediate TBT doses), while no effect was observed in other hypothalamic areas (arcuate, ventromedial and dorsomedial nuclei). Metabolic syndrome, as well as obesity and diabetes, which are significant health issues, are considered multifactorial diseases and may be caused by exposure to metabolic disruptors, both in adults and during perinatal life. In addition, our work indicates that TBT doses defined as the tolerably daily intake had a profound and sex‐specific long‐term effect.