bluuebunny/crossref_metadata_2025 huggingface dataset:
Substance Use Disorder, Opioid Use Disorder, and Symptom Management in Palliative Care
Authors: Huggins Jennifer , Ashley Jennifer , Fasolino Tracy
Published: August 2024

Substance use disorder (SUD) affects more than 1 in 6 Americans older than 12 years and has become an increasingly relevant topic in palliative care. Lack of clear guidelines and fragmented care results in patient safety concerns and poor outcomes. This rapid review aims to present the current literature on opioid contracts/agreements, prescription drug monitoring database access, opioid risk assessment tools, and urine drug screening in the palliative care setting. Through a systematic process, we identified 19 articles published between 2018 and 2023 that pertained to substance use disorder and palliative care.

Current risk mitigation strategies include prescription drug monitoring, opioid use agreements, risk assessment tools, urine drug screening, and the use of buprenorphine to manage pain.

Prescription drug monitoring programs are state-based electronic databases that track controlled substances, and there are numerous risk assessment tools. Urine drug screening involves the use of both immunoassay and confirmatory chromatography to determine the presence or absence of either the prescribed controlled substance or unexpected findings including illicit drugs or prescription-controlled substances that are not prescribed to the patient.

The goal of mitigating risk and reducing harm while providing expert symptom management is the challenge that palliative care transdisciplinary teams face as they continue to care for patients with substance use disorder. This review points to the need for further research on how to incorporate these harm-reducing strategies into clinical practice.
Comparison of IL-6, IL-10, and TNFα Levels Between PLWHIV With and Without Kaposi Sarcoma and Healthy Controls
Authors: Islas-Muñoz Beda , Chávez-Galán Leslie , Ramón-Luing Lucero , Flores-González Julio , Ocaña-Guzmán Ranferi , Cornejo-Juárez Patricia , González-Rodríguez Andrea , Patricia Volkow
Published: August 2024

Introduction:

Kaposi sarcoma (KS) is an angioproliferative disease caused by human herpesvirus 8 and is mediated by cytokines in an immunodeficient environment. This study aimed to compare IL-6, IL-10, and TNFα levels among patients with AIDS with disseminated KS (DKS), treatment naïve patients living with HIV without DKS, and healthy controls. Secondary outcomes were to compare cytokines levels in patients with DKS and unfavorable outcomes, and an analysis of the behavior of cytokines over time.

Methods:

This cohort study was performed at 2 centers in Mexico City. Three groups were included. Group 1: HIV+ treatment naïve with DKS, group 2: HIV+ treatment naïve without KS, and group 3: HIV negative, healthy controls. Plasmatic IL-6, IL-10, and TNFα levels were measured at baseline and over time in groups 1 and 2.

Results:

Seventy-six patients were included: 39 (52%) in group 1, 17 (22%) in group 2, and 20 (26%) in group 3. The median baseline IL-6, IL-10, and TNFα levels were significantly higher in group 1. In group 1, baseline IL-6 was higher in patients who died than in survivors (14.4 vs 5.8 pg/mL P = 0.048). Patients with severe immune reconstitution inflammatory syndrome because of KS had higher IL-6 values than those without it (14.4 vs 5.8 pg/mL P = 0.004). In the repeated measures model in group 1, IL-10 levels were higher in patients who died (P < 0.001) and developed immune reconstitution inflammatory syndrome-KS (P = 0.01).

Conclusions:

IL-6, IL-10, and TNF α levels were markedly higher in patients with DKS. IL-6 and IL-10 levels were higher in patients with unfavorable outcomes.
Blue Ribbon Committee II
Authors: Conrad-Schnetz Kristen , Prabhu Ajita , Johnson Wali Rashad , Jenkins-Turner Megan , Simpson-Mason Bonnie , Terhune Kyla
Published: August 2024

Objective:

Define recommendations for work–life integration and wellness and provide a pathway for supporting, teaching, and strengthening the skills needed to live as an authentic, empathic, compassionate, emotionally intelligent surgeon who provides the best care to patients.

Background:

Burnout is common during surgical residency. It is important to assess how we are addressing the human needs of surgical trainees. We report the recommendations of the work-life integration, wellness, and resilience subcommittee of the Blue Ribbon Committee II.

Methods:

We met monthly via a virtual format and established the needs of the surgical trainee according to Maslow Triangle. Barriers to meeting needs were identified, classified (local, state, national, etc.), and assigned to “easy” or “hard to address.” Recommendations were developed for each Maslow Triangle level and organized into 1- to 2- and 3- to 5-year goals. The Blue Ribbon Committee II (BRCII) narrowed these down to 6 recommendations that were included in a Delphi Analysis with 80% consensus needed to be included in the BRCII paper.

Results:

Six recommendations were developed by the BRCII and 4 met consensus. Final recommendations addressed resident wages, a culture of belonging, workplace safety, and reporting mistreatment.

Conclusions:

Creating a culture of belonging by focusing on program culture through accountability, safety, and collaboration can lead surgical training programs to train highly successful surgeons.
Personality disorders and their association with adverse childhood events
Authors: Crişan Ştefania , Nechita Diana
Published: August 2024

Purpose of review

Theoretical models of personality disorders (PDs) highlight the role of adverse childhood experiences (ACEs) in the development and maintenance of personality pathology. This review presents recent studies on the associations between childhood adversity and PDs, while discussing mechanisms and factors that impact these relationships.

Recent findings

Studies point to small to moderate associations between childhood adversity and cluster A, cluster B, and cluster C PDs, and some research suggests that childhood adversity could be a predictor for the onset and development of personality pathology. Most research focuses on borderline PD, while research on other PDs is limited. Some mechanisms that explain these associations have been proposed, with the literature investigating emotion dysregulation, dissociation, avoidance, or psychosocial dysfunction as mediators.

The consistent associations between ACEs and PDs seems to point that childhood adversity could be a transdiagnostic risk factor for PDs, but research warrants further prospective investigations for causal conclusions, and calls for future research to investigate potential mediators and moderators more thoroughly.
Genomic analysis of Oceanotoga teriensis strain UFV_LIMV02, a multidrug-resistant thermophilic bacterium isolated from an offshore oil reservoir
Authors: Santos Adriele Jéssica do Carmo , Dias Roberto Sousa , Silva Carlos Henrique Martins da , Vidigal Pedro Marcus Pereira , Sousa Maíra Paula de , Silva Cynthia Canedo da , Paula Sérgio Oliveira de
Published: August 2024

Bacteria of the species Oceanotoga teriensis belong to the family Petrotogaceae, are Gram-negative bacilli, are moderately thermophilic and are included in the group of thiosulfate-reducing bacteria, being capable of significantly accelerating corrosion in metallic structures. However, no in-depth study on the genome, antibiotic resistance and mobile elements has been carried out so far. In this work, the isolation, phenotypic and genotypic characterization of the multi-resistant O. teriensis UFV_LIMV02 strain was carried out, from water samples from an offshore oil extraction platform in Rio de Janeiro (Brazil). We determined that the isolate has a genome of 2 812 778 bp in size, with 26 % GC content, organized into 34 contigs. Genomic annotation using Rapid Annotation using Subsystem Technology revealed the presence of genes related to resistance to antibiotics and heavy metals. By evaluating the antimicrobial resistance of the isolate using the disc diffusion technique, resistance was verified for the classes of antibiotics, beta-lactams, fluoroquinolones, aminoglycosides, sulfonamides, lincosamides and rifamycins, a total of 14 antibiotics. The search for genomic islands, prophages and defence systems against phage infection revealed the presence of five genomic islands in its genome, containing genes related to resistance to heavy metals and antibiotics, most of which are efflux pumps and several transposases. No prophage was found in its genome; however, nine different defence systems against phage infection were detected. When analysing the clustered regularly interspaced short palindromic repeat (CRISPR) systems, four CRISPR arrays, classified as types I-B and III-B, with 272 spacers, can provide the strain with immunity to different mobile genetic elements and bacteriophage infection. The results found in this study show that the isolate UFV_LIVM02 is an environmental bacterium, resistant to different classes of antibiotics, and that the proteins encoded by the predicted genomic islands may be associated with the development of greater resistance to antibiotics and heavy metals. They provide evidence that environmental bacteria found in offshore oil exploration residues may pose a risk for the spread of antibiotic resistance genes. More comprehensive studies on the microbial community present in oil waste are needed to assess the risks of horizontal gene transfer.
Effect of proton pump inhibitors on susceptibility and melanogenesis of Sporothrix species
Authors: Nobre Augusto Feynman Dias , Sousa Alanna Mayara Soares de , Costa Anderson da Cunha , Fernandes Mirele Rodrigues , Kumar Rajender , Ponne Saravanaraman , Rocha Maria Gleiciane , Rodrigues Anderson Messias , Camargo Zoilo Pires de , Brilhante Raimunda Sâmia Nogueira
Published: August 2024

Introduction. Sporotrichosis is a subcutaneous infection caused by dimorphic Sporothrix species embedded in the clinical clade. Fungi have virulence factors, such as biofilm and melanin production, which contribute to their survival and are related to the increase in the number of cases of therapeutic failure, making it necessary to search for new options.

Gap statement. Proton pump inhibitors (PPIs) have already been shown to inhibit the growth and melanogenesis of other fungi.

Aim. Therefore, this study aimed to evaluate the effect of the PPIs omeprazole (OMP), rabeprazole (RBP), esomeprazole, pantoprazole and lansoprazole on the susceptibility and melanogenesis of Sporothrix species, and their interactions with itraconazole, terbinafine and amphotericin B.

Methodology. The antifungal activity of PPIs was evaluated using the microdilution method, and the combination of PPIs with itraconazole, terbinafine and amphotericin B was assessed using the checkerboard method. The assessment of melanogenesis inhibition was assessed using grey scale.

Results. The OMP and RBP showed significant MIC results ranging from 32 to 256 µg ml−1 and 32 to 128 µg ml−1, respectively. Biofilms were sensitive, with a significant reduction (P<0.05) in metabolic activity of 52% for OMP and 50% for RBP at a concentration of 512 µg ml−1 and of biomass by 53% for OMP and 51% for RBP at concentrations of 512 µg ml−1. As for the inhibition of melanogenesis, only OMP showed inhibition, with a 54% reduction.

Conclusion. It concludes that the PPIs OMP and RBP have antifungal activity in vitro against planktonic cells and biofilms of Sporothrix species and that, in addition, OMP can inhibit the melanization process in Sporothrix species.
Embracing native diversity to enhance maximum quantum efficiency of photosystem II in maize (Zea maysL.)
Authors: Urzinger Sebastian , Avramova Viktoriya , Frey Monika , Urbany Claude , Scheuermann Daniela , Presterl Thomas , Reuscher Stefan , Ernst Karin , Mayer Manfred , Marcon Caroline , Hochholdinger Frank , Brajkovic Sarah , Ordas Bernardo , Westhoff Peter , Ouzunova Milena , Schön Chris-Carolin
Published: August 2024

Sustainability of maize cultivation would benefit tremendously from early sowing but is hampered by low temperatures during early development in temperate climate. We show that allelic variation of subunit M of NADH-dehydrogenase-like (NDH) complex (ndhm1), discovered in a European maize landrace affects several quantitative traits relevant during early development in cold climates through NDH-mediated cyclic electron transport (CET) around photosystem I, a process crucial for photosynthesis. Starting from a genome-wide association study (GWAS) for maximum potential quantum yield of photosystem II in dark-adapted leaves (Fv/Fm) we capitalized on large phenotypic effects of a hAT transposon insertion inndhm1on quantitative traits early plant height (EPH), Fv/Fm, chlorophyll content and cold tolerance caused by reduced protein levels of NDHM and associated NDH components. Analysis of the native allelic series ofndhm1revealed a rare allele ofndhm1which is associated with small albeit significant effects on maximum potential quantum yield of photosystem II in dark- and light adapted leaves (Fv/Fm, ΦPSII) and early plant height compared to common alleles. Our work showcases the extraction of novel, favorable alleles from locally adapted landraces, offering an efficient strategy for broadening the genetic variation of elite germplasm by breeding or genome editing.
Whole Genome Sequencing Analysis of a Recent Multi-Drug ResistantShigella sonneiOutbreak Among Tunisian Children
Authors: Ferjani Sana , Kanzari Lamia , Hamzaoui Zaineb , Jomni Laila , Ferjani Asma , Fakhfekh Ahmed , Bahri Olfa , Achour Wafa , Zribi Mariem , Trabelsi Sameh , Alya Nissaf Ben , Itani Dana , Bouwazra Safa , Foster-Nyarko Ebenezer , Boubaker Ilhem Boutiba Ben
Published: August 2024

Background

Shigella sonnei, a leading cause of shigellosis, is a global health concern, particularly affecting children under five. The emergence of multidrug-resistant (MDR) strains, including resistance to key antibiotics like ciprofloxacin and third-generation cephalosporins, exacerbates treatment challenges. This study investigates the genetic and antimicrobial resistance profiles ofS. sonneiisolates from Tunisia, focusing on an outbreak of extended-spectrum beta-lactamase (ESBL)-producing strains.

Methods

We analysed nineS. sonneiisolates collected between September 2022 and January 2023 from Tunisian hospitals, using whole genome sequencing (WGS). Standard bacterial identification and serotyping methods were employed alongside antimicrobial susceptibility testing. We examined the genetic relatedness of the isolates, identified resistance genes, and characterised virulence factors.

Results

All the isolates were confirmed asS. sonneiH6, biotype a, and belonged to lineage 3, clade 6 and sub-lineage 3. All harbouredblaCTX-M-15, conferring resistance to third-generation cephalosporins. These were chromosomally integrated, suggesting stable resistance. Five isolates exhibited fluoroquinolone resistance associated with theqnrS1 gene, and all isolates had a single quinolone resistance-determining region mutation (GyrA-D87Y). Additionally, the plasmid-bornemphA gene, conferring resistance to macrolides, was prevalent. Single-linkage hierarchical clustering analysis indicated close genetic relationships withS. sonneistrains from Europe, particularly France and the UK (0 to 31 core genome MLST allele differences), indicating recent international dissemination.

Conclusion

This study provides the first comprehensive molecular characterisation of MDRS. sonneiin Tunisia, highlighting a significant public health threat. The findings underscore the importance of continuous genomic surveillance to track the spread of resistant strains and inform public health interventions.
Microbiota-induced plastic T cells enhance immune control of antigen-sharing tumors
Authors: Najar Tariq A. , Hao Yuan , Hao Yuhan , Romero-Meza Gabriela , Dolynuk Alexandra , Littman Dan R.
Published: August 2024

Therapies that harness the immune system to target and eliminate tumor cells have revolutionized cancer care. Immune checkpoint blockade (ICB), which boosts the anti-tumor immune response by inhibiting negative regulators of T cell activation1–3, is remarkably successful in a subset of cancer patients, yet a significant proportion do not respond to treatment, emphasizing the need to understand factors influencing the therapeutic efficacy of ICB4–9. The gut microbiota, consisting of trillions of microorganisms residing in the gastrointestinal tract, has emerged as a critical determinant of immune function and response to cancer immunotherapy, with multiple studies demonstrating association of microbiota composition with clinical response10–16. However, a mechanistic understanding of how gut commensal bacteria influence the efficacy of ICB remains elusive. Here we utilized a gut commensal microorganism, segmented filamentous bacteria (SFB), which induces an antigen-specific Th17 cell effector program17, to investigate how colonization with it affects the efficacy of ICB in restraining distal growth of tumors sharing antigen with SFB. We find that anti-PD-1 treatment effectively inhibits the growth of implanted SFB antigen-expressing melanoma only if mice are colonized with SFB. Through T cell receptor clonal lineage tracing, fate mapping, and peptide-MHC tetramer staining, we identify tumor-associated SFB-specific Th1-like cells derived from the homeostatic Th17 cells induced by SFB colonization in the small intestine lamina propria. These gut-educated ex-Th17 cells produce high levels of the pro-inflammatory cytokines IFN-γ and TNF-α, and promote expansion and effector functions of CD8+tumor-infiltrating cytotoxic lymphocytes, thereby controlling tumor growth. A better understanding of how distinct intestinal commensal microbes can promote T cell plasticity-dependent responses against antigen-sharing tumors may allow for the design of novel cancer immunotherapeutic strategies.
PURE-seq identifiesEgr1as a Potential Master Regulator in Murine Aging by Sequencing Long-Term Hematopoietic Stem Cells
Authors: Pan Sixuan , Chang Kai-Chun , Fernández-Maestre Inés , Haver Stéphane Van , Wereski Matthew G. , Bowman Robert L. , Levine Ross L. , Abate Adam R.
Published: August 2024

Single-cell transcriptomics is valuable for uncovering individual cell properties, particularly in highly heterogeneous systems. However, this technique often results in the analysis of many well- characterized cells, increasing costs and diluting rare cell populations. To address this, we developed PURE-seq (PIP-seq for Rare-cell Enrichment and Sequencing) for scalable sequencing of rare cells. PURE-seq allows direct cell loading from FACS into PIP-seq reactions, minimizing handling and reducing cell loss. PURE-seq reliably captures rare cells, with 60 minutes of sorting capturing tens of cells at a rarity of 1 in 1,000,000. Using PURE-seq, we investigated murine long- term hematopoietic stem cells and their transcriptomes in the context of hematopoietic aging, identifyingEgr1as a potential master regulator of hematopoiesis in the aging context. PURE-seq offers an accessible and reliable method for isolating and sequencing cells that are currently too rare to capture successfully with existing methods.
Comprehensive evaluation and practical guideline of gating methods for high-dimensional cytometry data: manual gating, unsupervised clustering, and auto-gating
Authors: Liu Peng , Pan Yuchen , Chang Hung-Ching , Fang Yusi , Xue Xiangning , Zou Jian , Toothaker Jessica M. , Olaloye Oluwabunmi , Santiago Eduardo Gonzalez , McCourt Black , Mitsialis Vanessa , Presicce Pietro , Kallapur Suhas G. , Snapper Scott B. , Liu Jia-Jun , Tseng George C. , Konnikova Liza , Liu Silvia
Published: August 2024

Cytometry is an advanced technique for simultaneously identifying and quantifying many cell surface and intracellular proteins at a single-cell resolution. Analyzing high-dimensional cytometry data involves identifying and quantifying cell populations based on their marker expressions. This study provided a quantitative review and comparison of various ways to phenotype cellular populations within the cytometry data, including manual gating, unsupervised clustering, and supervised auto-gating. Six datasets from diverse species and sample types were included in the study, and manual gating with two hierarchical layers was used as the truth for evaluation. For manual gating, results from five researchers were compared to illustrate the gating consistency among different raters. For unsupervised clustering, 22 tools were quantitatively compared in terms of accuracy with the truth and computing cost. While no method outperformed all others, several tools, including PAC-MAN, CCAST, FlowSOM, flowClust, and DEPECHE, generally demonstrated strong performance. For supervised auto-gating methods, four algorithms were evaluated, where DeepCyTOF and CyTOF Linear Classifier performed the best. We further provided practical recommendations on prioritizing gating methods based on different application scenarios. This study offers comprehensive insights for biologists to understand diverse gating methods and choose the best-suited ones for their applications.
Enzyme family-centred approach identifies helicases as recurrent hemizygous tumour suppressor genes
Authors: Voßgröne Karolin , Favero Francesco , Kashyap Krushanka , Rodríguez-González F. Germán , Olsen André Vidas , Li Xin , Mardin Balca R. , Weischenfeldt Joachim , Sørensen Claus S.
Published: August 2024

An important goal in cancer research is to identify driver genes and mutations. Reasoning that such mutations often alter enzymatic functions, we investigated the cancer driver role of enzyme families. Using pan-cancer genomic data and established driver mutation catalogues, we found an unexpectedly high rate of mutations in helicases, making helicases the most frequently mutated enzyme family in cancer. Based on both functional perturbation screens and cancer genomic analyses, we provide evidence that cancers with mutated helicases converge on increased genomic instability and faulty DNA repair. We identify a striking phenotype in cells with loss of the helicase Aquarius (AQR). AQR was exclusively hemizygous lost in cancer genomes, which was associated with elevated levels of structural variants and point mutation signatures indicative of homologous recombination deficiency. Finally, we leverage large dependency maps to show that hemizygous loss is a common tumour suppression mechanism among helicases. In summary, we uncover a striking frequency of mutated helicases with key roles in genomic maintenance, and we nominate novel hemizygous cancer driver genes including AQR.
Introgression across narrow contact zones shapes the genomic landscape of phylogenetic variation in an African bird clade
Authors: Rancilhac Loïs , de Souza Stacey G. , Lukhele Sifiso M. , Sebastianelli Matteo , Ogolowa Bridget O. , Moysi Michaella , Nikiforou Christos , Asfaw Tsyon , Downs Colleen T. , Brelsford Alan , vonHoldt Bridgett M. , Kirschel Alexander N.G.
Published: August 2024

Genomic analyses of hybrid zones provide excellent opportunities to investigate the consequences of introgression in nature. In combination with phylogenomics analyses, hybrid zone studies may illuminate the role of ancient and contemporary gene flow in shaping variation of phylogenetic signals across the genome, but this avenue has not been explored yet. We combined phylogenomic and geographic cline analyses in aPogoniulustinkerbird clade to determine whether contemporary introgression through hybrid zones contributes to gene-tree heterogeneity across the species ranges. We found diverse phylogenetic signals across the genome with the most common topologies supporting monophyly among taxa connected by secondary contact zones. Remarkably, these systematic conflicts were also recovered when selecting only individuals from each taxon’s core range. Using analyses of derived allele sharing and “recombination aware” phylogenomics, we found that introgression shapes gene-tree heterogeneity, and the species tree most likely supports monophyletic red-fronted tinkerbirds, as recovered in previous reconstructions based on mitochondrial DNA. Furthermore, by fitting geographic clines across two secondary contact zones, we found that introgression rates were lower in genomic regions supporting the putative species tree compared to those supporting the two taxa in contact as monophyletic. This demonstrates that introgression through narrow contact zones shapes gene-tree heterogeneity even in allopatric populations. Finally, we did not find evidence that mitochondria-interacting nuclear genes acted as barrier loci. Our results show that species can withstand important amounts of introgression while maintaining their phenotypic integrity and ecological separation, raising questions regarding the genomic architecture of adaptation and barriers to gene flow.
Stable isotopic composition of Antarctic and Patagonian marine mammals collected before and during industrial-scale whaling: assessing the baseline for long-term changes in the marine ecosystem
Authors: Genelt-Yanovskiy Evgeny , Genelt-Yanovskaya Anna , Fontanals-Coll Maria , Yamoah Kweku Afrifa , Craig Oliver , Sabin Richard , Scourse James
Published: August 2024

Great Antarctic expeditions, seal hunting and whaling industries left a legacy in natural history collections. To provide the basis for analysing the impact of whaling on marine ecosystem structuring, we conducted the bulk isotope analysis from the specimens of baleen whales (Balaenoptera musculusandB. physalus), and seals(Arctocephalus australisandHydrurga leptonyx) collected between 1843 to 1951 from the South Atlantic, Patagonian waters, Southern Ocean and Antarctic coastal seas, and preserved in the collection of Natural History Museum, London. Analysis of this material indicates the pre-industrial whaling state of these environments, and changes in the trophic position of whales and seals during the period of extensive human pressure. Having controlled for the Suess effect, δ13C values inB. musculus,B. physalusandH. leptonyxwere different before and after the onset of industrial-scale whaling (1904). Bone collagen δ15N values and corresponding trophic position indicate possible trophic changes inA. australis,and variability of the foraging areas ofB. musculus. This study highlights the use of museum specimens for tracing historical trends associated with changes in the population structure and distribution of species and which indicate long- term variability in their foraging ecology.
Statistical estimation of sparsity and efficiency for molecular codes
Authors: Fung Jun Hou , Carrière Mathieu , Blumberg Andrew J.
Published: August 2024

A fundamental biological question is to understand how cell types and functions are determined by genomic and proteomic coding. A basic form of this question is to ask if small families of genes or proteins code for cell types. For example, it has been shown that the collection of homeodomain proteins can uniquely delineate all 118 neuron classes in the nematode C. elegans. However, unique characterization is neither robust nor rare. Our goal in this paper is to develop a rigorous methodology to characterize molecular codes. We show that in fact for information-theoretic reasons almost any sufficiently large collection of genes is able to disambiguate cell types, and that this property is not robust to noise. To quantify the discriminative properties of a molecular codebook in a more refined way, we develop new statistics - partition cardinality and partition entropy - borrowing ideas from coding theory. We prove these are robust to data perturbations, and then apply these in the C. elegans example and in cancer. In the worm, we show that the homeodomain transcription factor family is distinguished by coding for cell types sparsely and efficiently compared to a control of randomly selected family of genes. Furthermore, the resolution of cell type identities defined using molecular features increases as the worm embryo develops. In cancer, we perform a pan-cancer study where we use our statistics to quantify interpatient tumor heterogeneity and we identify the chromosome containing the HLA family as sparsely and efficiently coding for melanoma.
qPRF: A system to accelerate population receptive field decoding
Authors: Waz Sebastian , Wang Yalin , Lu Zhong-Lin
Published: August 2024

Patterns of BOLD response can be decoded using the population receptive field (PRF) model to reveal how visual input is represented on the cortex (Dumoulin and Wandell, 2008). The time cost of evaluating the PRF model is high, often requiring days to decode BOLD signals for a small cohort of subjects. We introduce the qPRF, an efficient method for decoding that reduced the computation time by a factor of 1436 when compared to another widely available PRF decoder (Kay, Winawer, Mezer and Wandell, 2013) on a benchmark of data from the Human Connectome Project (HCP; Van Essen, Smith, Barch, Behrens, Yacoub and Ugurbil, 2013). With a specially designed data structure and an efficient search algorithm, the qPRF optimizes the five PRF model parameters according to a least-squares criterion. To verify the accuracy of the qPRF solutions, we compared them to those provided by Benson, Jamison, Arcaro, Vu, Glasser, Coalson, Van Essen, Yacoub, Ugurbil, Winawer and Kay (2018). Both hemispheres of the 181 subjects in the HCP data set (a total of 10,753,572 vertices, each with a unique BOLD time series of 1800 frames) were decoded by qPRF in 15.2 hours on an ordinary CPU. The absolute difference inR2reported by Benson et al. and achieved by the qPRF was negligible, with a median of 0.39% (R2units being between 0% and 100%). In general, the qPRF yielded a slightly better fitting solution, achieving a greaterR2on 99.7% of vertices. The qPRF may facilitate the development and computation of more elaborate models based on the PRF framework, as well as the exploration of novel clinical applications.

Highlights

We describe a novel software system, qPRF, which can perform population receptive field (PRF) decoding of BOLD fMRI at speeds about 1400 times faster than the conventional systems designed for PRF decoding.

We show that qPRF yields estimates of PRF model parameters that, in terms of goodness-of-fit, are equivalent to estimates derived using the conventional systems.

An efficient similarity-based search strategy, underlies the accelerated computations of qPRF, supported by a specially designed data structure wherein tens of millions of pre-computed prediction curves are stored.
Heterogeny in cages: Age-structure and timing of attractant availability impacts fertile egg production in the black soldier fly,Hermetia illucens
Authors: Lemke N. B. , Li C. , Dickerson A. J. , Salizar D. A. , Rollinson L. N. , Mendoza J. E. , Miranda C. D. , Crawford S. , Tomberlin J. K.
Published: August 2024

Adult behavior is a growing area of interest for those researching the black soldier fly,Hermetia illucens(L.) (Diptera: Stratiomyidae), which is affected by underlying demography and spatiotemporal patterns. This greenhouse experiment examined the interaction of age-related effects that can accrue within heterogeneous breeding populations and the potential benefits of delaying an oviposition attractant in concert with restricting mean cohort age. The impetus for this investigation was because if flies are introduced into a mating-cage before old flies are removed or culled, this creates a population of mixed-age and mating-status. We hypothesized this potentially reduces quality among available mate choices, especially in small cages where flies might not be able to spatially segregate. Metrics for fitness included copulation frequency, oviposition frequency, weight of eggs produced, and hatch percentage. “Same”-aged cohorts (maximum 4-d-old at introduction) performed better than highly heterogeneous (1-16-d-old) “mixed” cohorts by mating 2.32-times more frequently and laying 6.58-times more eggs that were 1.17-times more fertile, despite 1.41 fewer observed oviposition events. Delaying the attractant had a significant effect on egg collection weight and led to 1.25-times higher egg yields for same- age populations compared to mixed-aged cohorts where the delaying the attractant had no significant effect. These results are likely due in part to an immediate desire to lay eggs by older females as well as haphazard egg laying in cage material, which was 2.09-times higher for mixed cohorts. The results highlight the importance of constraining the age of breeding populations and removing old adults from cages to improve yields and better manipulate behavior. For those for whom this is logistically unfeasible, providing an attractant box initially and continuously may be the preferred method to trap more eggs from heterogeneous populations.
Rapid Parallel Visual Presentation Provides a New Perspective on Relative Clause Processing in Mandarin Chinese
Authors: Dunagan Donald , McLendon Jill , Jordan Tyson , Chacón Dustin A.
Published: August 2024

A fundamental question in language processing research is the degree to which the acceptability and ease of interpretation of a sentence are affected by the moment-by-moment memory encoding and retrieval processes needed to process it in time, vs. the properties of the linguistic representation itself, such as syntactic complexity. This manuscript investigates relative clauses, a crucial testing ground for theories of language processing, using parallel presentation, a technique in which the key elements of the target syntactic dependency are displayed to the visual system at the same time. Compared to serial presentation, parallel presentation mitigates the extent to which complex memory operations must be deployed to process the structure word-by-word. We report on an electroencephalography (EEG) experiment in Mandarin Chinese. Participants were presented with sentences which contained either a subject- or object-modifying subject- or object-extracted relative clause. Sentence presentation was split across two separate screens, with each screen being displayed only for 166ms on average. We find a behavioral preference for subject-extracted relative clauses and distinct EEG signatures for subject- and object-extracted relative clauses. Together, these results – on account of the parallel presentation scheme applied here – provide support for the independent contribution of linguistic representation in processing difficulty and the perspective that relative clause processing involves more than the factors that word by word accounts of this phenomenon would suggest. Further, the EEG result contributes to a growing body of electrophysiology literature attempting to illuminate the processing mechanisms deployed in the context of parallel presentation.
Divergent realized ecological niches of sister species of the Antarctic amphipod genusCharcotia
Authors: Aerts Dorien , Kolder Aaron , Lepoint Gilles , Michel Loïc N. , Schön Isa
Published: August 2024

Climate change and resource exploitation in the Southern Ocean are important Anthro-pogenic pressure on Antarctic food webs. Understanding the eco-functional roles of Antarctic communities is essential for ecosystem management and conservation. Amphipods are among the most dominant and ecologically important benthic taxa in the Southern Ocean. The amphipod genusCharcotiais part of the scavenger guild playing a dominant role in nutrient recycling. To study the trophic habits of two sister species,C. amundseniandC. obesa, stable isotope ratios of carbon and nitrogen were investigated along geographical and bathymetrical gradients.Charcotia obesabelongs to the fourth andC. amundsenito the fifth trophic level, based on significant differences in δ15N. Benthic primary producers dominate the diet in both species as derived from their δ13C values.Charcotia obesa, the species with the narrowest depth range, did not show a depth-related pattern in isotopic ratios. An increasing geographic gradient of both δ15N and δ13C values was observed forC. obesa, ranging from the northern most tip of the Western Antarctic Peninsula to the southwestern most part of the Bellings-hausen Sea. This might be linked to nutrient rich glacial meltwater in the latter part of the Southern Ocean. Nitrogen stable isotope ratios ofC. amundsenishowed a significant difference between Crown Bay and the other locations; this might be explained by the close location of the Filchner Area to nutrient rich upwelling in the Weddell Sea Gyre. Our study provides evidence for niche differentiation between two closely related amphipod species. Incorporation of additional samples from other locations and depth ranges in combination with isotope analysis and DNA-based prey identification might clarify the trophic position of benthic amphipods.
Population dynamics in spatial suppression gene drive models and the effect of resistance, density dependence, and life history
Authors: Zhang Xinyue , Sun Weitang , Kim Isabel K. , Messer Philipp W. , Champer Jackson
Published: August 2024

Due to their super-Mendelian inheritance, gene drive systems have the potential to provide revolutionary solutions to critical public health and environmental problems. For suppression drives, however, spatial structure can cause “chasing” population dynamics that may postpone target population elimination or even cause the drive to fail. In chasing, wild-type individuals elude the drive and recolonize previously suppressed areas. The drive can re-enter these recolonized areas, but often is not able to catch up to wild-type and finally eliminate it. Previous methods for chasing detection are only suitable to limited parameter ranges. In this study with expanded parameter ranges, we found that the shift from chasing dynamics to static equilibrium outcomes is continuous as drive performance is reduced. To quantify this, we defined a Weighted Average Nearest Neighbor statistic to assess the clustering degree during chasing, while also characterizing chasing by the per-generation chance of population elimination and drive loss. To detect chasing dynamics in local areas and to detect the start of chasing, we implemented Density-Based Spatial Clustering of Applications with Noise. Using these techniques, we determined the effect of arena size, resistance allele formation rate in both the germline and in the early embryo from maternally deposited Cas9, life history and reproduction strategies, and density-dependent growth curve shape on chasing outcomes. We found that larger real-world areas will be much more vulnerable to chasing and that species with overlapping generations, fecundity-based density dependence, and concave density-dependent growth curves have smaller and more clustered local chasing with a greater chance of eventual population elimination. We also found that embryo resistance and germline resistance hinder drive performance in different ways. These considerations will be important for determining the necessary drive performance parameters needed for success in different species, and whether future drives could potentially be considered as release candidates.
Differential induction ofMedicago truncatuladefence metabolites in response to rhizobial symbiosis and pea aphid infestation
Authors: Benjamin Goodluck , Pacoud Marie , Boutet Stéphanie , Clement Gilles , Brouquisse Renaud , Gatti Jean-Luc , Poirié Marylène , Frendo Pierre
Published: August 2024

Legumes symbiosis with rhizobial nitrogen-fixing bacteria enable them to grow in nitrate-depleted soils. Rhizobial symbioses also induces systemic plant defence against bioagressors.

We investigate how nitrogen-fixing symbiosis (NFS) in the legumeMedicago truncatulacan prime plant defence against the pea aphidAcyrthosiphon pisum. We analysed metabolite modification both by LC-MS and GC-MS and defence pathway gene expression by qPCR in leaves of both NFS and nitrate-fed (non-inoculated; NI) plants after aphid infestation (Amp).

The accumulation of primary and secondary metabolites was modulated by both NFS and aphid infestation. 62 defense-related metabolites such as salicylate, pipecolate, gentisic acid and several soluble sugars were differentially regulated by aphid infestation in both NFS and NI conditions. 19 metabolites, including triterpenoid saponins, accumulated specifically in NFS_Amp conditions. Gene expression analysis showed that aphid-infested plants exhibited significantly higher expression ofChalcone isomerase,flavonol synthase,hydroxyisoflavone-O-methyl transferaseandPterocarpan synthase, whileD-pinitol dehydrogenasewas only significantly induced in NI infested leaves.

Our data suggest that NFS, in addition to being a plant nitrogen provider, stimulates specific legume defenses upon pest attack and should also be considered as a potential tool in Integrated Pest Management strategy.
Discovering methylated DNA motifs in bacterial nanopore sequencing data with MIJAMP
Authors: Tidwell Alyssa K. , Faust Evelyn , Eckert Carrie A. , Guss Adam M. , Alexander William G.
Published: August 2024

Bacterial DNA methylation is involved in diverse cellular functions ranging from modulation of gene expression, DNA repair, and restriction-modification systems for defense against viruses and other foreign DNA. Methylome analysis determines sites within a bacterial chromosome that are methylated, revealing motifs that may be targeted by native restriction enzymes. Identification of these motifs is therefore critical to making an organism genetically tractable, where mimicking the methylome patterns inEscherichia coliallows plasmid DNA to be protected from restriction in the target organism and can therefore drastically enhance transformation efficiency. Oxford Nanopore Technologies (ONT) sequencing can detect methylated bases during sequencing, but software is needed to identify the corresponding methylated motifs within the data. Here, we develop MIJAMP (MIJAMP Is JustA MethylBED Parser), a software package that was developed to discover methylated motifs from the output of ONT’s Modkit or other data in the methylBED format. MIJAMP employs a human-driven refinement strategy that empirically validates all motifs against genome-wide methylation data, thus eliminating false, under-, or overexplained motifs. MIJAMP can also report methylation data on a specific, user-defined motif. Using MIJAMP, we determined the methylated motifs both in a control strain (wild typeE. coli) and inPicosynecococcussp. strain PCC7002, laying the foundation for improved transformation in this organism. MIJAMP is available athttps://code.ornl.gov/alexander-public/mijamp/.
Common marmosets use body posture as multi-functional signal to solicit, maintain, and modify social play
Authors: Adriaense Jessie E.C. , Ringen Erik J. , Ohashi Atsushi , Burkart Judith M.
Published: August 2024

Social play is a highly active social interaction, characterized by rapid exchanges of various behaviors with multiple partners. Many primates use bodily expressions during social play, yet the potential signaling function of these expressions remains unclear. This study investigated whether common marmosets (Callithrix jacchus)use body posture as signal to regulate play. We recorded play within three captive common marmoset family groups using multiple cameras simultaneously to capture the fast-paced and high frequency behaviors. Three distinct signals (i.e. supine, hide, stalk) and six distinct play types (i.e. wrestle, chase, pounce, touch, catch, pull) were identified. We used a multi-state time-to-event model to analyze the sequences of play, including short-and long-term transitions between different states (i.e. signal, play, or rest/nothing). Our data-driven approach accounted for uncertainty in the duration of play bouts, using probabilistic classification rather than arbitrary bout thresholds. The resulting classifications allowed us to assess the social function of signals by comparing play behavior to a resting state baseline. We found that the presence of a signal: (1) increases the probability to play; (2) extends the duration of play; (3) leads to more diverse play; and (4) increases the probability of play fighting. Marmosets also show turn-taking of signaling and initiating subsequential play. These results show that marmosets use postures as communicative signals to initiate and change play dynamics, and thereby establish a mutual understanding of the joint action. The two-fold contribution of this study concerns novel analytical methods and a deeper conceptual understanding of primate communication. Play and its signals are important elements in the evolution of language, and our research contributes to its further understanding.
Navigating the Landscape of Fear
Authors: Gee Marissa , Gonzalez-Granda Nicolas , Joshi Sunay , Rudrapatna Nagaprasad , Somalwar Anne , Ellner Stephen P. , Vladimirsky Alexander
Published: August 2024

Animals searching for food must navigate through complex landscapes with varying terrain, food availability, predator activity, and shelter. One method for analyzing how foraging animals balance these competing interests is Optimal Foraging Theory, which posits that foragers make decisions that maximize some expected reward or utility. However, models have generally focused on simplified settings, especially regarding animal movement decisions, either ignoring spatial variability entirely or limiting the forager’s options to choosing among a few discrete habitat patches (or patch types) that are modeled as spatially uniform. In this paper, we present a model of optimal foraging in a continuous landscape for an animal that is subject to predation. Foraging animals thus must choose not only where to gather food, but also how to (safely) travel across the landscape. Furthermore, we explicitly model stochastic predator interactions, allowing us to predict optimal foraging trajectories conditional on the presence or absence of an immediate threat from a predator. We illustrate our model with numerical examples, one a hypothetical landscape with two regions of high food abundance and two areas of high predation risk on the direct route between the feeding areas and the forager’s overnight refuge, the other inspired by empirical data on foraging Samango monkeys (Cercopithecus albogularis schwarzi). We find that the shape of a forager’s utility function affects not only where it chooses to feed, but also the paths it takes to and from the optimal feeding ground. Thus, examining predicted optimal trajectories can provide additional information about what quantity, if any, animals optimize while foraging. We also develop and demonstrate a preliminary model for an animal that depletes the food supply in its local environment.