bluuebunny/crossref_metadata_2025 huggingface dataset:
What causes simple falls? Trips, slips, and the effects of illness
Authors: Darowski Dr Adam
Published: November 2023

Most falls are due to simple trips and slips of the sort that we all experience from time to time. Most older people who fall do not need any specialist intervention. Most do not ever see a doctor or nurse and find that they have soon forgotten all about it. The problem arises when the falls start to recur and to form a pattern. Those aspects of ageing discussed elsewhere start to play a role. Impaired vision and loss of sensory input from the inner ear and from peripheral nerves, together with a slowing of reaction times, all play a part in turning a stumble into a fall. Other illnesses or disabilities which might have been present for years—the arthritic knee, the mild Parkinson’s disease, the old stroke, the peripheral neuropathy—now contribute to impaired walking or balance in a way that they did not before.
What causes giddiness?
Authors: Darowski Dr Adam
Published: November 2023

Giddiness:

is a very complex and poorly understood symptom when it occurs on standing, can be caused by a drop in the blood supply to the brain occurs when the brain has insufficient information to tell it where it is in space is strongly associated with anxiety and depression is a common side effect of medications needs to be distinguished from vertigo. Where no treatable cause is found, coping strategies help people to manage their problem.Giddiness and unsteadiness are the symptoms most commonly associated with falls. It is very difficult for patients to describe these symptoms, and in particular it is often difficult to distinguish from the patient’s story whether they have giddiness or vertigo—words that are often used interchangeably, even by doctors.
Visual problems that can contribute to falls
Authors: Darowski Dr Adam
Published: November 2023

Having the wrong prescription spectacles is the most common visual problem leading to falls. Eye diseases can lead to impaired vision, and are a major cause of falls. Cataracts can only be treated by surgery. Macular degeneration is a progressive disorder, for which there is usually no effective treatment. Glaucoma is treated with eye drops to prevent an increase in the pressure in the eye. Diabetes has several different effects on the eye. Maintaining good diabetic control slows the progression of diabetic eye disease. New vessels are managed with laser treatment.Spectacles Impaired vision is a major contributory factor for many people who fall. The most common problems are simple short-sightedness, often since youth, or the long-sightedness that occurs once the lens starts to harden after the age of 40. These problems are corrected with glasses. Many people make do with glasses that do not correct their poor vision well enough.
How can walking aids help?
Authors: Darowski Dr Adam
Published: November 2023

A walking stick gives the brain extra information about where the floor is and broadens the base of support to add stability. A Zimmer frame provides support and stability, but has to be lifted at every step. A wheeled Zimmer frame allows support, and is easier for walking.? A delta frame has larger wheels and allows walking at a faster pace, but has limited stability. A trolley may contain a seat and a shopping bag.Walking sticks A walking stick is the most common aid that older people use to help with walking and balance. Some weight can be put through the stick, relieving the burden on a painful or stiff hip or knee joint to a minor extent. The amount of weight that can be transferred onto the stick is small, and a stick is not particularly good for this purpose as it is carried on one side and is not very comfortable to lean on. The walking stick effectively widens the area over which the body is stable.A walking stick gives additional information about body position. Information from the hand holding the stick is much more sensitive than information from the legs.
Working Time And Holidays
Authors: McLynn Lucy
Published: November 2023

Working Time and Holidays: A Practical Legal Guide acts as a concise, affordable, and practical guide to the Working Time Regulations 1998. There were 55,712 claims registered in the Employment Tribunals as "Working Time" claims in 2008, and the area is increasingly one on which almost all employment lawyers will need to advise. The book aims to demystify what is viewed as a difficult and technical area of the law. The book examines topics such as the maximum working week, rest and breaks, annual leave, night work, young workers, and unfair dismissal, detriment and enforcement. The substantial body of case law in the ten years since the implementation of the Regulations, and the amending legislation (including the Working Time (Amendment) Regulations 2007) is brought together and discussed. Working Time and Holidays: A Practical Legal Guide is structured so that answers to questions can be easily found and understood - using case studies, frequently asked questions, and checklists. The book also contains appendices which include both the text of the Regulations, and useful precedents such as an opt out agreement, contractual clauses, annual leave policy, and a record keeping checklist.
Back pain
Authors: Lee John , Brook Suzanne , Daniel Clare
Published: November 2023

Back Pain: The Facts is aimed at people who want to help themselves. Affecting nearly everyone at some time in their lives, 40% of people will have experienced some form of back pain within the last year, with around 5% of sufferers taking time off work within the last month. Long-term back pain causes a great deal of distress and unhappiness, affecting work life, income, home life, relationships, fitness and mood. Back Pain: The Facts uses clear, succinct chapters to give advice about every aspect of managing back pain, as well as answering frequently asked questions from sufferers. A key element is empowerment through understanding why back pain starts and why it persists. There are chapters promoting stretching, exercise, relaxation, communication, and advice on sexual relations, as well as considerable on emphasis on helping with thoughts and feelings.
Disarmament, Demobilization, and Reintegration
Authors: Muggah Robert
Published: November 2023

Disarmament, demobilization, and reintegration (DDR) is a comparatively new concept. It was adopted by the development and security sectors in the context of so-called ‘post-conflict recovery’ and ‘peace support operations’. As in the case of security sector reform, DDR emerged in conjunction with growing awareness among international donors, agencies, practitioners, and scholars of the linkages between insecurity and under-development in ‘transitional’ environments (Berdal, 1996).
Peace Operations
Authors: White Nigel
Published: November 2023

Historically, the UN has concerned itself in practice with defining and developing the concept of peacekeeping since the first full UN peacekeeping force in the Middle East in 1956. Peacekeeping was defined by the UN at the end of the Cold War in 1991 as an: Generally, peacekeeping operations consist of contributing states’ military contingents under UN command and control, specifically the Secretary-General, acting under delegated authority from the Security Council, exceptionally the General Assembly. This should be contrasted with the enforcement model that emerged out of Chapter VII of the Charter under which a ‘Coalition of the Willing’ is authorized by the Security Council with command and control being vested in the contributing state(s).
Private Sector
Authors: Carbonnier Gilles
Published: November 2023

The concept of the private sector first appeared with the emergence of the market economy and liberal ideology, which emphasized the notions of private property and corporate freedom within a legal and institutional framework provided and guaranteed by the state. Thus the concept, far from being new, has long belonged to everyday parlance.
Genomic Data Analysis of the Nonpathogenic Erwinia amylovora Strain CP200242 Isolated from an Asian Pear Tree
Authors: Ham Hyeonheui , Oh Ga-Ram , Park Dong Suk
Published: November 2023

Erwinia amylovora, the causative phytopathogen for fire blight, is a major threat to apple and pear. A nonpathogenic E. amylovora strain CP200242 was recently isolated from a pear orchard in South Korea. The nonpathogenicity of strain CP200242 was confirmed by inducing a hypersensitive reaction on tobacco leaves and by inoculating immature apple fruits and seedlings with bacterial suspensions. Herein, we report the complete genome sequencing of strain CP200242 data and provide some comparative genomic analysis against strain TS3128 and other closely related Erwinia species. Variant calling indicated that strain CP200242 had 29 variations in the annotated regions compared with strain TS3128, and six gene variants were related to pathogenesis. These genomic data provide valuable information on molecular differences between strains that may be useful for the control of the disease and enhance our understanding of the virulence factors in an E. amylovora reference genome.

[Formula: see text] Copyright © 2023 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license .
Optimal Changes Seen in Patients After Treatment With Poly-l-Lactic Acid: A Retrospective Descriptive Study
Authors: Alcotzer Inbar , Liassidou Aspasia , Hexsel Doris , Tsur Shenhav Leah , Artzi Ofir
Published: November 2023

BACKGROUND

Poly-l-lactic acid (PLLA) is a biostimulator that enhances collagen production and leads to volume restoration. It became popular because of its improvement of facial wrinkles and long-lasting effect, although the specific visible changes it causes in the facial area are not fully described.

OBJECTIVE

To identify and characterize the visible changes resulting from injecting PLLA into the facial area.

METHODS

A list of 678 patients who underwent 2 to 3 treatments with PLLA injections in this center between 2021 and 2022 were retrieved. After 2 rounds of evaluations, 31 independent international evaluators described the 3 main changes they observed in the before-and-after images (taken approximately 7 months after the last injection session) of the 12 patients with the most significant improvement.

RESULTS

A total of 1,015 descriptions were received. They were divided into categories based upon similarity. The main detected changes were better contouring and enhancement of the lateral face, a lifting effect and secondary impact on the nasolabial fold, and improvement of skin texture and skin firmness.

CONCLUSION

Poly-l-lactic acid injections were judged to be effective for contouring, lifting, and improving skin texture in the facial area. Further research is needed to validate these results and create an assessment scale for PLLA injections.
Clonal Relationship and Mutation Analysis in Lymphoplasmacytic Lymphoma/Waldenström Macroglobulinemia Associated With Diffuse Large B-cell Lymphoma
Authors: Berendsen Madeleine R. , van Bladel Diede A.G. , Hesius Eva , Berganza Irusquieta Cristina , Rijntjes Jos , van Spriel Annemiek B. , van der Spek Ellen , Pruijt Johannes F.M. , Kroeze Leonie I. , Hebeda Konnie M. , Croockewit Sandra , Stevens Wendy B.C. , van Krieken J Han J.M. , Groenen Patricia J.T.A. , van den Brand Michiel , Scheijen Blanca
Published: November 2023

Patients with lymphoplasmacytic lymphoma/Waldenström macroglobulinemia (LPL/WM) occasionally develop diffuse large B-cell lymphoma (DLBCL). This mostly results from LPL/WM transformation, although clonally unrelated DLBCL can also arise. LPL/WM is characterized by activating MYD88

L265P
(>95%) and CXCR4 mutations (~30%), but the genetic drivers of transformation remain to be identified. Here, in thirteen LPL/WM patients who developed DLBCL, the clonal relationship of LPL and DLBCL together with mutations contributing to transformation were investigated. In 2 LPL/WM patients (15%), high-throughput sequencing of immunoglobulin gene rearrangements showed evidence of >1 clonal B-cell population in LPL tissue biopsies. In the majority of LPL/WM patients, DLBCL presentations were clonally related to the dominant clone in LPL, providing evidence of transformation. However, in 3 patients (23%), DLBCL was clonally unrelated to the major malignant B-cell clone in LPL, of which 2 patients developed de novo DLBCL. In this study cohort, LPL displayed MYD88

L265P
mutation in 8 out of eleven patients analyzed (73%), while CXCR4 mutations were observed in 6 cases (55%). MYD88

WT
LPL biopsies present in 3 patients (27%) were characterized by CD79B and TNFAIP3 mutations. Upon transformation, DLBCL acquired novel mutations targeting BTG1, BTG2, CD79B, CARD11, TP53, and PIM1. Together, we demonstrate variable clonal B-cell dynamics in LPL/WM patients developing DLBCL, and the occurrence of clonally unrelated DLBCL in about one-quarter of LPL/WM patients. Moreover, we identified commonly mutated genes upon DLBCL transformation, which together with preserved mutations already present in LPL characterize the mutational landscape of DLBCL occurrences in LPL/WM patients.
A 66-year-old woman with two weeks of distorted vision in the left eye
Authors: Griffin Shane , McDonald H. Richard , Agarwal Anita
Published: November 2023

Purpose:

To report a case of concurrent melanoma metastasis to the orbit and MEK inhibitor-associated retinopathy.

Methods:

Case report of a 66-year-old female patient undergoing mutation targeted MEK-inhibitor treatment for metastatic melanoma with retinal manifestations.

Results:

After initiating MEK-inhibitor therapy our patient presented with bilateral blurred vision. Clinical examination and OCT imaging revealed multifocal bilateral serous retinal detachments consistent with MEKAR. Extrafoveal subretinal fluid foci resolved after discontinuation of MEK-inhibitor therapy, but her foveal lesions persisted for over 18 months. Years after her initial evaluation for MEKAR, our patient developed metamorphopsia in the left eye resulting from chorioretinal folds secondary to intraconal orbital metastasis. MRI revealed additional intracerebral and lung metastases, and the patient expired in 2 months.

Conclusion:

We report a case of prolonged MEKAR with concomitant orbital metastasis from melanoma. Multimodal imaging in conjunction with history and clinical features allows for disease identification and monitoring.
The effect of escalating heat stimulation on top of anesthetized skin
Authors: Riccio Daniele , Lo Vecchio Silvia , Arendt-Nielsen Lars
Published: November 2023

The relationship between itch and heat pain has been vastly explored. A 70-year-old study, showed the development of paradoxical itch following heat stimulation of anesthetized skin. The aim of this study was to re-evaluate, with more modern technologies and systematic approaches, this paradoxical itch effect. Escalating heat stimuli were applied to the local anesthetized skin of 19 healthy subjects, itch, and pain intensities were continuously assessed during the stimulation. As expected, pain sensation was significantly reduced by local intradermal anesthesia, however, no paradoxical itch sensations were observed for any of the stimulation temperatures.
Mangled extremity: limb salvage for reconstruction versus primary amputation
Authors: Tjardes Thorsten , Marche Benedikt , Imach Sebastian
Published: November 2023

Purpose of review

While MESS has historically influenced limb salvage versus amputation decisions, its universal applicability remains uncertain. With trauma systems expanding and advancements in trauma care, the need for a nuanced understanding of limb salvage has become paramount.

Recent findings

Recent literature reflects a shift in the management of mangled extremities. Vascular surgery, plastic surgery, and technological advancements have garnered attention. The MESS's efficacy in predicting amputation postvascular reconstruction has been questioned. Machine learning techniques have emerged as a means to predict peritraumatic amputation, incorporating a broader set of variables. Additionally, advancements in socket design, such as automated adjustments and bone-anchored prosthetics, show promise in enhancing prosthetic care. Surgical strategies to mitigate neuropathic pain, including targeted muscle reinnervation (TMR), are evolving and may offer relief for amputees. Predicting the long-term course of osteomyelitis following limb salvage is challenging, but it significantly influences patient quality of life.

The review underscores the evolving landscape of limb salvage decision-making, emphasizing the need for personalized, patient-centered approaches. The Ganga Hospital Score (GHS) introduces a nuanced approach with a ‘grey zone’ for patients requiring individualized assessments. Future research may leverage artificial intelligence (AI) and predictive models to enhance decision support. Overall, the care of mangled extremities extends beyond a binary choice of limb salvage or amputation, necessitating a holistic understanding of patients’ injury patterns, expectations, and abilities for optimal outcomes.
Incidence and Risk Factors for Brown Adipose Tissue Uptake in PET Imaging in Pediatric Patients
Authors: Smolik Suzanne , Miller Angie L. , Mong David A. , Trenbeath Zachary , Miller Kristen R. , Cost Carrye , Demedis Jenna
Published: November 2023

Background:

Positron emission tomography (PET) scans are used in disease diagnosis and evaluation for pediatric oncology patients. Brown adipose tissue (BAT) 18F-fluorodeoxyglucose-PET uptake is reported in 35% to 47% of pediatric patients. Several risk factors may be associated with BAT uptake.

Objective:

The aim was to determine the incidence and risk factors for BAT in pediatric patients using a consensus-based system and a novel grading scale.

Methods:

A total of 285 PET scans in 154 patients were retrospectively reviewed for the presence of BAT from September 2015 through December 2016. A consensus review was done by 2 radiologists, who graded BAT on a 0 to 3 scale and assessed its impact on PET interpretation.

Results:

The presence of moderate to severe BAT occurred in 11% of PET scans, and 6% of PETs had limited interpretation. Hodgkin lymphoma (n=53) patients had a 3.62-fold increased odds of moderate or severe BAT and a 6.59-fold increased odds of limited interpretation on PET imaging.

Conclusion:

The incidence of BAT was low but impacted radiologic interpretation when present. Further studies with a larger group of Hodgkin lymphoma patients are needed to explore the risk factors associated with moderate or severe BAT.
Non-prescription antibiotics dispensing by community pharmacies: implications for antimicrobial resistance
Authors: Hashmi Furqan K. , Khadka Sitaram , Yadav Gopal K. , Khan Mash’hood Mahmood , Khan Saif Ullah , Saeed Hamid , Saleem Mohammad , Giri Santoshi , Rasool Muhammad Fawad , Mansoor Hussaam-ul-Haq , Riboua Zineb
Published: November 2023

Introduction:

The non-prescription antibiotics dispensing (NPAD) from pharmacies is on the rise in low- and middle-income countries, which contributes to the emergence of antimicrobial resistance (AMR). This study was conducted with the objective to determine the community pharmacy personnel’s perspectives on NPAD and its implications for AMR.

Methods:

A questionnaire-based cross-sectional survey was conducted in Pakistan among 336 pharmacies. The data were analyzed using SPSS v21 and MedCalc for Windows v12.3.0. Modified Bloom’s cut-off point was utilized to categorize the participants’ overall knowledge, attitude, and practice. For univariable logistic regression analyses, odds ratio (OR) was calculated at 95% confidence interval (CI). For multivariable logistic regression analyses, adjusted OR was calculated at 95% CI. Spearman’s rank correlation coefficient test was used to assess the relationships among knowledge, attitude, and/or practice scores.

Results:

The majority of the respondents were staff pharmacists (45.5%). About four-fifths (78.9%) and half (50.9%) of the participants demonstrated moderate to good knowledge and practice, respectively. However, about only one-third (33.1%) had a moderate to good attitude. Staff pharmacists had higher odds of moderate to good knowledge (OR: 2.4, 95% CI: 1.2–4.7) and practice (OR: 2.3, 95% CI: 1.4–3.8). Total knowledge and practice (Spearman’s ρ: 0.280; P <0.001) and total attitude and practice (Spearman’s ρ: 0.299; P <0.001) scores were significantly correlated.

Conclusion:

The qualified pharmacists had satisfactory knowledge, attitude, and practices toward antibiotics. However, non-pharmacist staff lacked knowledge and had probable NPAD practice, which has a negative impact on public health. Regular refresher training, seminars, and strict enforcement of rules and regulations are essential.
Preoperative Role of Superb Microvascular Imaging and Shear-Wave Elastography for Prediction of Axillary Lymph Node Metastasis in Patients With Breast Cancer
Authors: Bulut Iclal Nur , Kayadibi Yasemin , Deger Enes , Kurt Seda Aladag , Velidedeoglu Mehmet , Onur Irem , Ozturk Tulin , Adaletli Ibrahim
Published: November 2023

This study aims to evaluate the role of shearwave elastography (SWE) and superb microvascular imaging (SMI) for preoperative prediction of axillary lymph node metastasis (ALNM) in patients with breast cancer. In a cohort of 214 women with breast cancer, B-Mode ultrasonography (US), SMIvascular-index (SMIvi), and SWE (E-mean, E-ratio) values were recorded before tru-cut biopsy. Axillary fine-needle aspiration biopsy (FNAB) and sentinel lymph node sampling results were collected. Imaging findings and histopathological data were statistically compared. Receiver operating characteristic curve analysis was used to evaluate diagnostic performance. Reverse stepwise logistical regression analysis was conducted. Although ALNM was negative in 111 cases, it was positive in 103 patients. Axillary lymph node metastasis (+) group had larger size (P < 0.001), higher vascularization (SMIvi: 8.0 ± 6.0 versus 5.0 ± 4.3, P < 0.001), and higher elasticity value (E-mean: 129 ± 31 kPa versus 117.3 ± 40 kPa, P = 0.014). Axillary lymph node metastasis was observed statistically more frequently in Her-2 positive cases (P = 0.005). There was no significant difference between other B-mode US findings (P > 0.05), SMI Adler (P = 0.878), and E-ratio (P = 0.212). The most appropriate cutoff value for the prediction of ALNM was 23.5 mm for size, 3.8 for SMIvi, and 138.5 kPa for E-mean. The most sensitive (77%) method was the SMIvi measurement, while the most specific (86%) finding was Her-2 positivity. The combined model (being Her-2 positive, >23.5 cm, and >3.8 SMIvi) increased the specificity (78%), PPV (71%), and accuracy (68%). Although the increased size is a previously studied parameter in predicting the risk of ALNM, Her-2 and data obtained by SWE, and SMI can be used to assist conventional US.
Anthropological Glimpses of Japan in Nineteenth-Century Britain
Authors: Sera-Shriar Efram
Published: November 2023

This article explores two early anthropological works on Japan that were produced in Britain during the nineteenth century. The first is James Cowles Prichard's chapter on Japanese culture from the third edition of his
Researches into the physical history of mankind
(1844)
.
It represents the first formative study by a leading ethnologist to tackle the subject. The second is Edward Burnett Tylor's essay on Japanese belief for the
Journal for the Royal Anthropological Institute of Great Britain and Ireland
(1877). During the later decades of the nineteenth century, information about Japanese society still remained relatively incomplete. When Tylor wrote his important essay about Japan in the 1870s, he still drew on the same sources Prichard had used three decades earlier. Very little new ethnographic information had travelled back to England by the second half of the nineteenth century. As a result, researchers continued to struggle when writing about Japanese culture. What we get in these nineteenth-century writings is best described as anthropological ‘glimpses’ of Japan. By exploring these early sketches of Japan, a more textured disciplinary history emerges that helps to complexify and challenge the heroic and teleological narratives of British anthropology's supposed success story.
Food for all? Wildfire ash fuels growth of diverse eukaryotic plankton
Authors: Ladd T. M. , Catlett D. , Maniscalco M. A. , Kim S. M. , Kelly R. L. , John S. G. , Carlson C. A. , Iglesias-Rodríguez M. D.
Published: November 2023

In December 2017, one of the largest wildfires in California history, the Thomas Fire, created a large smoke and ash plume that extended over the northeastern Pacific Ocean. Here, we explore the impact of Thomas Fire ash deposition on seawater chemistry and the growth and composition of natural microbial communities. Experiments conducted in coastal California waters during the Thomas Fire revealed that leaching of ash in seawater resulted in significant additions of dissolved nutrients including inorganic nitrogen (nitrate, nitrite and ammonium), silicic acid, metals (iron, nickel, cobalt and copper), organic nitrogen and organic carbon. After exposure to ash leachate at high (0.25 g ash l
−1
) and low (0.08 g ash l
−1
) concentrations for 4 days, natural microbial communities had 59–154% higher particulate organic carbon concentrations than communities without ash leachate additions. Additionally, a diverse assemblage of eukaryotic microbes (protists) responded to the ash leachate with taxa from 11 different taxonomic divisions increasing in relative abundance compared with control treatments. Our results suggest that large fire events can be important atmospheric sources of nutrients (particularly nitrogen) to coastal marine systems, where, through leaching of various nutrients, ash may act as a ‘food for all’ in protist communities.
BulkECexplorer: a bulk RNAseq compendium of five endothelial subtypes that predicts whether genes are active or leaky
Authors: Brash James T. , Diez-Pinel Guillermo , Fantin Alessandro , Ruhrberg Christiana
Published: November 2023

Transcriptomic data obtained by single cell (sc) RNAseq or bulk RNAseq can be mined to understand the molecular activity of cell types. Yet, lowly expressed but functional genes may remain undetected in RNAseq experiments for technical reasons, such as insufficient read depth or gene drop out in scRNAseq assays. By contrast, bulk RNAseq assays may detect lowly expressed mRNA transcripts thought to be the biologically irrelevant products of leaky transcription. To more accurately represent a cell’s functional transcriptome, we propose compiling many bulk RNAseq datasets into a compendium and applying established classification models to predict whether the detected genes are likely active or leaky in that cell type. Here, we have created such a compendium for vascular endothelial cells from several mouse and human organs, termed the BulkECexplorer.
Selection for dispersal under larval malnutrition results in a non-monotonic kernel inDrosophila melanogaster
Authors: Vibishan B. , Malwade Akshay , Gupta Swaraj Ranjan , Koner Anish , Khodake Vinayak , Dey Sutirth
Published: November 2023

Dispersal is a key strategy for organisms to track favorable conditions and a shifting global climate has necessitated its closer investigation. While the distribution of dispersal distances (i.e. dispersal kernel) influences several aspects of population ecology, it remains unclear how kernel features are themselves affected by environmental factors. The current study addresses this question using laboratory populations ofDrosophila melanogasterselected for greater dispersal under a protein-deficient larval diet. Our results reveal that dispersal-selected populations initiate dispersal more often and travel further on average than unselected controls. Although there is a significant change in the overall kernel shape, selection has not led to a greater tendency for long-distance dispersal (LDD). This is contrary to the results from a previous study on dispersal evolution under standard nutrition. We also find that dispersal evolution under larval malnutrition leads to a non-monotonic dispersal kernel, with the highest frequencies at intermediate distances. The evolved shape of the dispersal kernel and the limited LDD phenotype therefore point to significant qualitative shifts in the evolution of the dispersal kernel due to a change in larval nutrition. Our results thus provide a starting point for further investigation of such context dependence in dispersal evolution.
Super food or super toxic? Turmeric and spirulina as culprits for the toxic effects of food dyes inDrosophila
Authors: von Hellfeld Rebecca , Christie Craig , Derous Davina , Morimoto Juliano
Published: November 2023

Prolonged exposure to food dyes, even for those considered safe for consumption, are known to have toxic effects. However, we lack a proper understanding of the underlying compounds that are responsible for the observed toxicity. In this study, we tested the toxic physiological effects of three common commercially available natural food dyes (red, green, blue), and their main ingredients (turmeric and spirulina), onDrosophila melanogasteroviposition, larval development, and larval foraging behaviour. Larval development and egg-to-adult survival was significantly impacted by blue and green dyes. These effects were recapitulated when flies were fed with increasing concentrations of turmeric and spirulina, suggesting that turmeric is a toxic component of the food dye. Red dye, which contains neither turmeric or spirulina, had little impact on fly health and behaviour. Green and blue food dyes decreased egg laying, an effect similar to that observed in increasing concentrations of turmeric and, to a lesser extent, spirulina. When given a choice, larvae preferred to feed as follows: control > red > blue > green diet patches, a pattern inversely correlating with the previously observed toxicity. Our results show that, despite turmeric being often considered a super food, it can have toxic effects that the impact organismal physiology and health.
Nuclear eDNA Metabarcoding Primers for Anthozoan Coral Biodiversity Assessment
Authors: McCartin Luke J. , Saso Emma , Vohsen Samuel A. , Pittoors Nicole C. , Demetriades Penny , McFadden Catherine S. , Quattrini Andrea M. , Herrera Santiago
Published: November 2023

The distributions of anthozoan corals are under-characterized due to their wide bathymetric range, occurrences in remote locales, and difficulties of identification from morphology alone. Environmental DNA (eDNA) sequencing promises to be a non-invasive strategy to complement conventional approaches for mapping and monitoring coral communities. Primers for eDNA meta-barcoding have been designed to amplify nuclear and mitochondrial DNA barcodes in shallow scleractinians and mitochondrialMutSin deep-sea octocorals. However, a comprehensive method for eDNA meta-barcoding from all anthozoan corals, including black corals, has not been developed. We leveraged a sequence database of global coral collections, from shallow water to the deep sea, to design new PCR primers for coral eDNA sequencing that target the28S rRNAgene. We tested the performance of these primers by amplifying and sequencing eDNA from water samples collected in the Gulf of Mexico near mesophotic and deep-sea corals that were also imaged, sampled, and sequenced. Sequencing libraries produced using the primers were highly enriched in coral eDNA, with up to 99.8% of the reads originating from corals. Further, the28Sbarcode amplified using the primers distinguished coral genera. We recovered amplicon sequencing variants (ASVs) identical to DNA barcodes derived from Sanger sequencing and genome skimming of corals sampled at the same field sites. This new eDNA meta-barcoding strategy permits targeted eDNA sequencing of black corals, octocorals, and scleractinians at sites where they co-occur and expands our current toolkit for mapping and monitoring coral communities in shallow coral reefs and the deep sea.
Rapid activation of IL-2 receptor signaling by CD301b+DC-derived IL-2 dictates the outcome of helper T cell differentiation
Authors: Tatsumi Naoya , El-Fenej Jihad , Davila-Pagan Alejandro , Kumamoto Yosuke
Published: November 2023

Effector T helper (Th) cell differentiation is fundamental to functional adaptive immunity. Different subsets of dendritic cells (DCs) preferentially induce different types of Th cells, but the fate instruction mechanism for Th type 2 (Th2) differentiation remains enigmatic, as the critical DC-derived cue has not been clearly identified. Here, we show that CD301b+DCs, a major Th2-inducing DC subset, drive Th2 differentiation through cognate interaction by ‘kick-starting’ IL-2 receptor signaling in CD4T cells. Mechanistically, CD40 engagement induces IL-2 production selectively from CD301b+DCs to maximize CD25 expression in CD4 T cells, which is required specifically for the Th2 fate decision. On the other hand, CD25 in CD301b+DCs facilitates directed action of IL-2 toward cognate CD4T cells. Furthermore, CD301b+DC-derived IL-2 skews CD4T cells away from the T follicular helper fate. These results highlight the critical role of DC-intrinsic CD40–IL-2 axis in bifurcation of Th cell fate.
Near-complete genome assembly of tomato (Solanum lycopersicum) cultivar Micro-Tom
Authors: Shirasawa Kenta , Ariizumi Tohru
Published: November 2023

We present a near-complete genome assembly of tomato (Solanum lycopersicum) cultivar Micro-Tom, which has been recognized as a model cultivar for fruit research. The genome DNA of Micro-Tom, provided by the National BioResource Project (NBRP) Tomato of Japan, was sequenced to obtain 72 Gb of high-fidelity long reads. These reads were assembled into 140 contigs, spanning 832.8 Mb, with an N50 length of 39.6 Mb. The contigs were aligned against the tomato reference genome sequence SL4.0 to establish a chromosome-level assembly. The genome assembly of Micro-Tom contained 98.5% complete BUSCOs and a total of 31,429 genes. Comparative genome structure analysis revealed that Micro-Tom possesses a cluster of rDNA genes spanning a 15 Mb stretch at the short arm of chromosome 2. This region was not found in the genome assemblies of previously sequenced tomato cultivars, possibly because of the inability of previous technologies to sequence such repetitive DNA. In conclusion, the near-complete genome assembly of Micro-Tom reported in this study would advance the genomics and genetics research on tomato and facilitate the breeding of improved tomato cultivars.
The distribution of fitness effects during adaptive walks using a simple genetic network
Authors: O’Brien Nicholas L. V. , Holland Barbara , Engelstädter Jan , Ortiz-Barrientos Daniel
Published: November 2023

The tempo and mode of adaptation depends on the availability of beneficial alleles. Genetic interactions arising from gene networks can restrict this availability. However, the extent to which networks affect adaptation remains largely unknown. Current models of evolution consider additive genotype-phenotype relationships while often ignoring the contribution of gene interactions to phenotypic variance. In this study, we model a quantitative trait as the product of a simple gene regulatory network, the negative autoregulation motif. Using forward-time genetic simulations, we measure adaptive walks towards a phenotypic optimum in both additive and network models. A key expectation from adaptive walk theory is that the distribution of fitness effects of new beneficial mutations is exponential. We found that both models instead harbored distributions with fewer large-effect beneficial alleles than expected. The network model also had a complex and bimodal distribution of fitness effects among all mutations, with a considerable density at deleterious selection coefficients. This behavior is reminiscent of the cost of complexity, where correlations among traits constrain adaptation. Our results suggest that the interactions emerging from genetic networks can generate complex and multimodal distributions of fitness effects.
Structure-Aware Annotation of Leucine-rich Repeat Domains
Authors: Xu Boyan , Cerbu Alois , Lim Daven , Tralie Christopher J , Krasileva Ksenia
Published: November 2023

Protein domain annotation is typically done by predictive models such as HMMs trained on sequence motifs. However, sequence-based annotation methods are prone to error, particularly in calling domain boundaries and motifs within them. These methods are limited by a lack of structural information accessible to the model. With the advent of deep learning-based protein structure prediction, existing sequenced-based domain annotation methods can be improved by taking into account the geometry of protein structures. We develop dimensionality reduction methods to annotate repeat units of the Leucine Rich Repeat solenoid domain. The methods are able to correct mistakes made by existing machine learning-based annotation tools and enable the automated detection of hairpin loops and structural anomalies in the solenoid. The methods are applied to 127 predicted structures of LRR-containing intracellular innate immune proteins in the model plantArabidopsis thalianaand validated against a benchmark dataset of 172 manually-annotated LRR domains.

Author summary

In immune receptors across various organisms, repeating protein structures play a crucial role in recognizing and responding to pathogen threats. These structures resemble the coils of a slinky toy, allowing these receptors to adapt and change over time. One particularly vital but challenging structure to study is the Leucine Rich Repeat (LRR). Traditional methods that rely just on analyzing the sequence of these proteins can miss subtle changes due to rapid evolution. With the introduction of protein structure prediction tools like AlphaFold 2, annotation methods can study the coarser geometric properties of the structure. In this study, we visualize LRR proteins in three dimensions and use a mathematical approach to ‘flatten’ them into two dimensions, so that the coils form circles. We then used a mathematical concept called winding number to determine the number of repeats and where they are in a protein sequence. This process helps reveal their repeating patterns with enhanced clarity. When we applied this method to immune receptors from a model plant organism, we found that our approach could accurately identify coiling patterns. Furthermore, we detected errors made by previous methods and highlighted unique structural variations. Our research offers a fresh perspective on understanding immune receptors, potentially influencing studies on their evolution and function.
Structural basis of epitope recognition by anti-alpha synuclein antibodies MJFR14-6-4-2
Authors: Liekniņa Ilva , Panteļejevs Teodors , Lends Alons , Reimer Lasse , Jaudzems Kristaps , El-Turabi Aadil , Gram Hjalte , Jensen Poul Henning , Tārs Kaspars
Published: November 2023

Intraneuronal α-synuclein inclusions in the brain are hallmarks of so-called Lewy body diseases - Parkinson’s disease and Dementia with Lewy bodies. Lewy bodies are cytoplasmic inclusions, containing mainly aggregated α-synuclein together with some other proteins including ubiquitin, neurofilament protein, and alpha B crystallin. In its monomeric form, α-synuclein is predominantly localized in nerve terminals, regulating neuronal transmission and synaptic vesicle trafficking. Monomeric α-synuclein lacks a well-defined three-dimensional structure and is considered an intrinsically disordered protein. However, in diseased cells α-synuclein aggregates into oligomeric and fibrillar amyloid species, which can be detected using aggregate-specific antibodies. Here we investigate the aggregate specificity of rabbit monoclonal MJFR14-6-4-2 antibodies, preferentially recognizing aggregated α-synuclein species. We conclude that partial masking of epitope in unstructured monomer in combination with a high local concentration of epitopes instead of distinct epitope conformation is the main reason for apparent selectivity towards various aggregates, including oligomers, fibrils, and artificial virus-like particle constructs bearing multiple copies of the MJFR14-6-4-2 epitope. Based on the structural insight, we were able to express mutant α-synuclein that when fibrillated are unable to bind MJFR14-6-4-2. Using these “stealth” fibrils as a tool for seeding cellular α-synuclein aggregation, provides superior signal/noise ratio for detection of cellular α-synuclein aggregates by MJFR14-6-4-2 immunocytochemistry. Our data provide a molecular level understanding of specific recognition of toxic amyloid oligomers, which is critical for the development of inhibitors against synucleinopathies.
A multilocus perspective on the evolutionary dynamics of multistrain pathogens
Authors: McLeod David V. , Bank Claudia , Gandon Sylvain
Published: November 2023

Many human pathogens, including malaria, dengue, influenza,Streptococcus pneumoniae, and cytomegalovirus, coexist as multiple genetically distinct strains. Understanding how these multistrain pathogens evolve is of critical importance for forecasting epidemics and predicting the consequences of vaccination. One factor believed to play an important role is naturally acquired immunity. Consequently, a large body of research has sought to predict how acquired immunity molds the genomics of pathogen populations (i.e., what shapes pathogen strain structure). The diversity of existing models has resulted in conflicting evolutionary predictions, and has sparked an ongoing debate about which predictions are most broadly applicable. Here, we adopt a multilocus population genetics perspective that unifies the predictions of existing models. We identify three key factors that determine the role of naturally acquired immunity in the evolution of pathogen strain structure: (i) the strength and specificity of immune protections, (ii) the dynamic immunological landscape, and (iii) the number of loci coding for the antigens of the pathogen. Isolating and discussing these three factors clarifies the relationship among previous models of multistrain dynamics, and establishes a solid theoretical foundation for the study of the evolutionary epidemiology of multistrain pathogens.
The actin-associated protein Kaptin modulates F-actin barbed-end dynamics
Authors: Dutta Priyanka , Maiti Ipshita , Ghose Aurnab , Chauhan Radha , Maiti Sankar
Published: November 2023

Living cells require a dynamic and precisely regulated actin cytoskeleton to carry out normal cellular functions. In addition to well-established actin cytoskeleton regulators, such as nucleators, capping proteins, and bundlers, cells likely have uncharacterized modulators that regulate cytoskeleton dynamics, the detailed functions of which are not yet fully understood. In this study, we conducted biochemical exploration to identify the actin-regulatory activity of Kaptin (KPTN), a protein known to co-localize with actin-rich structures at the cell’s periphery. Using single-molecule assays, we demonstrated that KPTN inhibits actin nucleation. Our results revealed that KPTN possesses a novel barbed-end capping activity, which stabilizes and bundles actin filaments. Structural modeling, based on AlphaFold, suggests that KPTN is a member of the WD-repeat-containing protein family. Furthermore, we identified a crucial cationic residue in the putative N-terminal beta-propeller region of KPTN that plays a critical role in modulating actin dynamics. In summary, our data unveil the mechanistic underpinning functions of KPTN and establish its novel role as a regulator of the actin cytoskeleton.
Galectin-9 regulates dendritic cell polarity and uropod contraction by modulating RhoA activity
Authors: Franken Guus , Cuenca-Escalona Jorge , Stehle Isabel , van Reijmersdal Vince , Rodgers Furones Andrea , Gokhale Rohit , Classens René , Di Blasio Stefania , Dolen Yusuf , van Spriel Annemiek B. , Querol Cano Laia
Published: November 2023

Adaptive immunity relies on dendritic cell (DC) migration to transport antigens from tissues to lymph nodes. Galectins, a family of β-galactoside-binding proteins, control cell membrane organisation, exerting crucial roles in multiple physiological processes.

Here, we report a novel mechanism underlying cell polarity and uropod retraction. We demonstrate that galectin-9 regulates chemokine-driven and basal DC migration both in humans and mice, indicating a conserved function for this lectin. We identified the underlying mechanism, namely a deficiency in cell rear contractility mediated by galectin-9 interaction with CD44 that in turn regulates RhoA activity. Analysis of DC motility in the 3D tumour-microenvironment revealed galectin-9 is also required for DC infiltration. Moreover, exogenous galectin-9 rescued the motility of tumour-immunocompromised human blood DCs, validating the physiological relevance of galectin-9 in DC migration and underscoring its implications for DC-based immunotherapies.

Our results identify galectin-9 as a necessary mechanistic component for DC motility and highlight a novel role for the lectin in regulating cell polarity and contractility.
Allele-specific digital PCR enhances precision and sensitivity in the detection and quantification of copy number alterations in heterogeneous DNA samples: anin silicoandin vitrovalidation study
Authors: Nell Rogier J. , Versluis Mieke , Zoutman Willem H. , Luyten Gregorius P.M. , Jager Martine J. , van der Velden Pieter A.
Published: November 2023

The analysis of genetic variation is of crucial importance in cancer care. Measuring copy number alterations, however, remains challenging in heterogenous DNA samples, such as (liquid) biopsies. Using digital PCR, these alterations are classically studied by comparing the abundances of the target of interest to a stable genomic reference. Alternatively, copy numbers may be quantified based on the allelic (im)balance of a heterozygous common single-nucleotide polymorphism (SNP). In this study, the accuracy, practicability, precision and sensitivity of both approaches are evaluatedin silicousing a newly introduced R library ‘digitalPCRsimulations’, andin vitroby analysing control samples and uveal melanoma specimens in duplex and multiplex experimental setups.

Our analyses show that both methodologies are equally effective, as long as a stable reference is identified (classic approach) and the allelic imbalance is caused by the loss or gain/amplification of only one of both alleles (SNP-based approach). Though, heterogeneous copy number alterations can be measured with more precision and sensitivity using the SNP-based approach. In DNA from formalin-fixed and paraffin-embedded samples, the latter approach can also overcome technical artefacts causing inconsistencies between DNA amplicons.

In conclusion, the limits of detecting copy number alterations in heterogeneous DNA can be improved using the SNP-based approach. Consequently, an increasing number of clinical samples may be successfully analysed, providing novel potential for the identification, prognostication and management of cancer.