bluuebunny/crossref_metadata_2025_split 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.

Summary
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.
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

AbstractSustainability 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

AbstractBackgroundShigella 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.MethodsWe 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.ResultsAll 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.ConclusionThis 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

ABSTRACTTherapies 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

AbstractSingle-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

ABSTRACTCytometry 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

AbstractAn 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

AbstractGenomic 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

AbstractGreat 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.
qPRF: A system to accelerate population receptive field decoding
Authors: Waz Sebastian , Wang Yalin , Lu Zhong-Lin 
Published: August 2024

ABSTRACTPatterns 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.HighlightsWe 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.