bluuebunny/crossref_metadata_2025 huggingface dataset:
Improving Hypertension Control in the Black Patient Population
Authors: Duckie Charmaine L. , Boston Karen A. , Champagne Brittney , Thompson Julie , Halpern David J. , Granger Bradi B.
Published: October 2023

Background:

Nearly half of American adults have hypertension (HTN), and non-Hispanic Black patients are diagnosed at a higher rate than others.

Local Problem:

Our local clinic population reflected disproportionate rates of uncontrolled HTN among Black patients.

Methods:

A quality improvement pre-/postintervention design was used to evaluate an educational intervention to reduce blood pressure (BP) and improve self-monitoring of BP in Black patients using the Chronic Care Model.

Interventions:

A team-based approach was used to redesign clinic workflows and patient education, prescribe self-paced videos from an electronic health record (EHR) patient portal, and provide home BP cuffs.

Results:

Black participants (n = 79) improved viewing of prescribed videos (7.9% to 68.5%), knowledge scores (67.9 to 75.2), and mean systolic BP (−20.3 mm Hg; P > .001).

Conclusions:

This team-based approach enhanced patient engagement, self-monitoring skills, EHR-reported BP, and overall BP control for a cohort of Black patients with uncontrolled BP.
Structural Equation Modeling of Associations Between Nursing Practice Environment And Missed Nursing Care
Authors: Rivaz Mozhgan , Abbasi Fereshteh , Pasyar Nilofar
Published: October 2023

Background:

Missed nursing care (MNC) negatively impacts the quality of patient care. There may be a relationship between the nursing practice environment (NPE) and MNC; however, this relationship has not been examined in developing countries during the COVID-19 pandemic.

Purpose:

To determine the relationship between the NPE and MNC during the COVID-19 pandemic.

Methods:

A cross-sectional study of 300 participants was conducted in 4 teaching hospitals in Iran. Data were collected using a demographic and clinical form, the Nursing Professional Practice Environment Questionnaire, and MISSCARE survey and analyzed using structural equation modeling.

Results:

The hypothesized model was well fit, showing that 1 unit improvement of the NPE domains of patient-centered care, effective leadership, and policy transparency decreased MNC by 0.18, 0.12, and 0.05, respectively.

Conclusion:

The model confirmed the association between the dimensions of the NPE and MNC. These findings can assist health policymakers and nursing managers in improving the NPE.
Evaluating and Addressing the Diversity, Equity, Inclusion, and Belonging Climate in a School of Nursing
Authors: Rhoten Bethany Andrews , Steed Julia , Johnson Rolanda , Schorn Mavis N.
Published: October 2023

Background:

There is a critical need to prepare a diverse nursing workforce and address issues of structural racism and health inequities.

Problem:

A shortage of underrepresented nurse faculty exacerbates the lack of diversity in nursing education. Microaggressions and discrimination experienced by underrepresented nursing students hinder their personal and professional growth. Evaluating diversity, equity, and inclusion (DEI) and belonging within a school of nursing is crucial for progress.

Approach:

An alumni survey and a faculty/staff survey were conducted to assess DEI perceptions, which informed the development of a strategic plan. Goals focused on monitoring the cultural climate, increasing diversity and inclusivity, and enhancing faculty competencies. Educational offerings and initiatives were implemented to support these goals.

Outcomes:

Ongoing evaluation is essential to sustain progress in this critical area.

Conclusion:

These efforts are necessary for sustainable progress and equitable care provision.
Reverse Mentoring in Nursing Education
Authors: Williams Cheryl
Published: October 2023

Background:

Nurse educators are challenged to prepare an expanding number of diverse students with various sociocultural and generational differences. Whether diversity, sociocultural, and/or generational divides are contributory, a perennial decline exists of historically disenfranchised students finishing nursing programs. Reverse mentoring is an innovative adaption of traditional mentoring. Reverse mentoring is a practice that reverses traditional mentor and mentee roles, which may mitigate diverse and intergenerational misconceptions.

Purpose:

To prepare a diverse nursing workforce, educators should integrate strategies to embrace differences, reduce biases, remove learning barriers, and value learning new teaching methods.

Methods:

A literature review revealed few articles on reverse mentoring in nursing education.

Results:

Reverse mentoring is a successful strategy in many Fortune 500 companies. Therefore, reverse mentoring may demonstrate promise in nursing education.

Conclusion:

Exploring reverse mentoring in nursing education may reveal strategies to elucidate and mitigate biases and barriers in nursing education.
Prognostic Significance of Tumor-associated Stroma in Nasopharyngeal Carcinoma
Authors: Almangush Alhadi , Ruuskanen Miia , Hagström Jaana , Kosma Veli-Matti , Nieminen Pentti , Mäkitie Antti A. , Leivo Ilmo
Published: October 2023

Assessment of tumor-associated stroma has shown a reliable prognostic value in recent research. We evaluated the prognostic value of tumor-stroma ratio (TSR) in a large multicenter cohort of nasopharyngeal carcinoma (NPC). We used the conventional hematoxylin and eosin–stained slides of 115 cases of NPC to assess TSR as described in recent guidelines. The amount of tumor-associated stroma was assessed as a percentage and then tumors were classified as stroma-high (>50%) or stroma-low (≤50%). Kaplan-Meier curves, χ2 test, and Cox regression univariable and multivariable analyses were carried out. A total of 48 (41.7%) tumors were stroma-high and 67 (58.3%) tumors were stroma-low. In the Cox regression multivariable analysis, the tumors categorized as stroma-high were associated with a worse overall survival with a hazard ratio of 2.30 (95% CI: 1.27-4.15, P=0.006) and with poor disease-specific survival (hazard ratio=1.87, 95% CI: 1.07-3.28, P=0.029). The assessment of TSR in NPC is simple and cost-effective, and it has a significant prognostic value. TSR can aid in risk stratification and clinical decision-making in NPC.
New Onset Geriatric Syndromes and One-year Outcomes Following Elective Gastrointestinal Cancer Surgery
Authors: Melucci Alexa D. , Loria Anthony , Aquina Christopher T. , McDonald Gabriela , Schymura Maria J. , Schiralli Matthew P. , Cupertino AnaPaula , Temple Larissa K. , Ramsdale Erika , Fleming Fergal J.
Published: October 2023

Objective:

To assess whether older adults who develop geriatric syndromes following elective gastrointestinal surgery have poorer 1-year outcomes.

Summary Background Data:

Within ten years, 70% of all cancers will occur in older adults ≥65 years old. The rise in older adults requiring major surgery has brought attention to age-related complications termed geriatric syndromes. However, whether postoperative geriatric syndromes are associated with long-term outcomes is unclear.

Methods:

A population-based retrospective cohort study using the New York State Cancer Registry and the Statewide Planning and Research Cooperative System was performed including patients >55 years with pathologic stage I-III esophageal, gastric, pancreatic, colon, or rectal cancer who underwent elective resection between 2004-2018. Those aged 55-64 served as the reference group. The exposure of interest was a geriatric syndrome (fracture, fall, delirium, pressure ulcer, depression, malnutrition, failure to thrive, dehydration, or incontinence [urinary/fecal]) during the surgical admission. Patients with any geriatric syndrome within 1 year of surgery were excluded. Outcomes included incident geriatric syndrome, 1-year days alive and out of the hospital, and 1-year all-cause mortality.

Results:

37,998 patients with a median age of 71 years without a prior geriatric syndrome were included. Of those 65 years or more, 6.4% developed a geriatric syndrome. Factors associated with an incident geriatric syndrome were age, alcohol/tobacco use, comorbidities, neoadjuvant therapy, ostomies, open surgery, and upper gastrointestinal cancers. An incident geriatric syndrome was associated with a 43% higher risk of 1-year mortality (hazard ratio, 1.43; 95% confidence interval, 1.27-1.60). For those aged 65+ discharged alive and not to hospice, a geriatric syndrome was associated with significantly fewer days alive and out of hospital (322 vs. 346 d, P<0.0001). There was an indirect relationship between the number of geriatric syndromes and 1-year mortality and days alive and out of the hospital after adjusting for surgical complications.

Conclusions:

Given the increase in older adults requiring major surgical intervention, and the establishment of geriatric surgery accreditation programs, these data suggest that morbidity and mortality metrics should be adjusted to accommodate the independent relationship between geriatric syndromes and long-term outcomes.
TandZ, Partial Seed Coat Patterning Genes in Common Bean, Provide Insight into the Structure and Protein Interactions of a Plant MBW Complex
Authors: McClean Phillip E. , Roy Jayanta , Colbert Christopher L. , Osborne Caroline , Lee Rian , Miklas Phillip N. , Osorno Juan M.
Published: October 2023

Flavonoids are secondary metabolites associated with seed and flower color. A ternary MBW protein complex consisting of interfacingMYB,beta-helix-loop-helix (bHLH), andWD40 repeat (WDR) proteins controls the expression of late biosynthetic genes in the flavonoid pathway.P, the master regulator gene of flavonoid expression in common bean (Phaseolus vulgarisL.) was recently determined to encode a bHLH protein. Two other genes,TandZ, are also historically considered regulators since they determine the distribution of color in seeds and flowers. These two genes were cloned using reverse genetics based on genetic mapping, candidate gene selection, phylogenetic analysis, and mutant analysis. Domain and AlphaFold2 structure analyses determinedTencoded a seven-bladed β-propeller WDR protein, whileZencoded a R2R3 MYB protein. Modeling of the Z MYB/P bHLH/T WDR MBW complex identified interfacing sequence domains and motif in all three genes that are conserved in dicots. One Z MYB motif is a possible β-MoRF that only appears in a structured state when Z MYB is modeled in a MBW complex. Complexes containing mutant T and Z proteins changed the interaction of members of the complex in ways that would alter their role in regulating expression of genes in the flavonoid pathway.

Highlight

The MBW complex of bean comprised of the classicZ,P, andTgenes associated with seed coat patterning defines critical proteins interactions for flavonoid gene expression.
PRCnet: An Efficient Model for Automatic Detection of Brain Tumor in MRI Images
Authors: Farhan Ahmeed Suliman , Khalid Muhammad , Manzoor Umar
Published: October 2023

Brain tumors are the most prevalent and life-threatening cancer; an early and accurate diagnosis of brain tumors increases the chances of patient survival and treatment planning. However, manual tumor detection is a complex, cumbersome and time-consuming task and is prone to errors, which relies on the radiologist’s experience. As a result, the development of accurate and automatic system for tumor detection is critical. In this paper, we proposed a new model called Parallel Residual Convolutional Network (PRCnet) model to classify brain tumors from Magnetic Resonance Imaging. The PCRnet model uses several techniques (such as filters of different sizes with parallel layers, connections between layers, batch normalization layer, and ReLU) and dropout layer to overcome the over-fitting problem, for achieving accurate and automatic classification of brain tumors. The PRCnet model is trained and tested on two different datasets and obtained an accuracy of 94.77% and 97.1% for dataset A and dataset B, respectively which is way better as compared to the state-of-the-art models.
A Library of Electrophysiological Responses in Plants - A Model of Transversal Education and Open Science
Authors: Madariaga Danae , Arro Derek , Irarrázaval Catalina , Soto Alejandro , Guerra Felipe , Romero Angélica , Ovalle Fabián , Fedrigolli Elsa , DesRosiers Tom , Serbe-Kamp Étienne , Marzullo Timothy
Published: October 2023

Electrophysiology in plants is understudied, and, moreover, an ideal model for student inclusion at all levels of education. Here we report on an investigation in “open science”, whereby scientists worked with students and faculty from Chile, Germany, Serbia, South Korea, and the USA. The students recorded the electrophysiological signals of >15 plants in response to a flame or tactile stimulus applied to the leaves. We observed that approximately 60% of the plants studied showed an electrophysiological response with a delay of ∼3-6 seconds after stimulus presentation. In preliminary conduction velocity experiments, we verified that observed signals are indeed biological in origin, with information transmission speeds of ∼2-9 mm/s. Such easily replicable experiments can serve to include more investigators and students in contributing to our understanding of plant electrophysiology.
TRANSPOSABLE ELEMENTS ALTER GENE EXPRESSION AND MAY IMPACT RESPONSE TO CISPLATIN THERAPY IN OVARIAN CANCER
Authors: Mombach Daniela Moreira , Vieira Mercuri Rafael Luiz , da Fontoura Gomes Tiago Minuzzi Freire , Galante Pedro A. F. , Silva Loreto Elgion Lucio
Published: October 2023

Cisplatin is widely employed for cancer treatment; therefore, understanding resistance to this drug is critical for therapeutic practice. While studies have delved into differential gene expression in the context of cisplatin resistance, findings remain somewhat scant. In this study, we employed RNA-seq, ATAC-seq, and in-depth bioinformatics analyses to perform a detailed investigation of the cellular transcriptome, centering on Transposable Elements (TEs) expression in ovarian cancer cell lines both sensitive and resistant to cisplatin treatment. Our results reveal that cisplatin therapy alters the expression of protein-coding genes, but also key TEs, including LINE1,Alu, and endogenous retroviruses, in both cisplatin-sensitive and -resistant cell lines. By co-expressing with downstream genes or by creating chimeric transcripts with host genes at their insertion sites, these TEs seem to control the expression of protein-coding genes, including tumor-related genes. Notably, our model uncovers TEs influencing the expression of cancer genes and cancer pathways. Collectively, our findings indicate that TEs alterations associated with cisplatin treatment occur in critical cancer genes and cellular pathways synergically. In conclusion, this research highlights the importance of considering the entire spectrum of transcribed elements in the genome, especially TE expression, for a complete understanding of complex models like cancer response to treatment.
C4-likeSesuvium sesuvioides(Aizoaceae) exhibits CAM in cotyledons and putative C4+CAM metabolism in adult leaves as revealed by transcriptome analysis
Authors: Siadjeu Christian , Kadereit Gudrun
Published: October 2023

The co-occurrence of C4and CAM photosynthesis in a single species seems to be unusual and rare, probably because of the difficulty to co-regulate both pathways effectively. Nevertheless, it represents a unique chance in gaining new insights into the evolution and regulation of these complex pathways. Comparative transcriptomics using RNA-seq revealed C4-like and CAM photosynthesis inSesuvium sesuvioides(Aizoaceae) leaves and cotyledons, respectively. When compared to cotyledons, phosphoenolpyruvate carboxylase 4 (PEPC4) and some key C4genes were found to be up regulated in leaves. During the day, the expression of NADP-dependent malic enzyme (NADP-ME) was significantly higher in cotyledons than in leaves. The acidity titration confirmed higher acidity in the morning than in the previous evening indicating the induction of weak CAM in cotyledons by environmental conditions. Comparison of the leaves ofS. sesuvioides(C4-like) andS. portulacastrum(C3) revealed that PEPC1 was significantly higher inS. sesuvioides, while PEPC3 and PEPC4 were up-regulated inS. portulacastrum. Finally, potential key regulatory elements involved in the C4and CAM pathways were identified. These findings provide a new species in which C4and CAM co-occur and raises the question if this phenomenon is indeed so rare or just hard to detect and probably more common in succulent C4lineages.

Highlight

C4and CAM metabolism co-occur in the C4-like speciesSesuvium sesuvioides(Aizoaceae).
Rhythmic lipid and gene expression responses to chilling in panicoid grasses
Authors: Raju Sunil K. Kenchanmane , Zhang Yang , Mahboub Samira , Ngu Daniel W. , Qiu Yumou , Harmon Frank G. , Schnable James C. , Roston Rebecca L.
Published: October 2023

Chilling stress threatens plant growth and development, particularly affecting membrane fluidity and cellular integrity. Understanding plant membrane responses to chilling stress is important for unraveling the molecular mechanisms of stress tolerance. Whereas core transcriptional responses to chilling stress and stress tolerance are conserved across species, the associated changes in membrane lipids appear to be less conserved, as which lipids are affected by chilling stress varies by species. Here, we investigated changes in gene expression and membrane lipids in response to chilling stress during one diurnal cycle in sorghum (Sorghum bicolor), Urochloa (browntop signal grass,Urochloa fusca) (lipids only), and foxtail millet (Setaria italica), leveraging their evolutionary relatedness and differing levels of chilling-stress tolerance. We show that most chilling-induced lipid changes are conserved across the three species, while we observed distinct, time-specific responses in chilling-tolerant foxtail millet, indicating the presence of a finely orchestrated adaptive mechanism. We detected diurnal rhythmicity in lipid responses to chilling stress in the three grasses, which were also present in Arabidopsis (Arabidopsis thaliana), suggesting the conservation of rhythmic patterns across species and highlighting the importance of accounting for diurnal effects. When integrating lipid datasets with gene expression profiles, we identified potential candidate genes that showed corresponding transcriptional changes in response to chilling stress, providing insights into the differences in regulatory mechanisms between chilling-sensitive sorghum and chilling-tolerant foxtail millet.

Significance Statement

Plants respond to low-temperature stress in myriad ways. While core transcriptional changes are conserved across species, specific adaptive strategies do exist. However, membrane lipid responses during chilling do not appear to be conserved. Here, we collected samples from control and chilling stress–treated seedlings [PSC4] to assess gene expression and membrane lipids in three panicoid grasses to show that lipid metabolic changes follow a daily rhythm. Lipid changes in chilling-tolerant foxtail millet occurred at specific time points, partly explaining the difficulty in finding conserved chilling-induced lipid changes in previous reports. We identified specific orthologs in sorghum and foxtail millet that showed a correlation between gene expression and lipid metabolic changes; these orthologs may be used as potential target genes for developing chilling-tolerant sorghum varieties.
Mutation Mechanism In DNA: Non-Hermitian Approach
Authors: Sarısaman Mustafa , Tibatan Mehmet Ali , Uzunal Seval
Published: October 2023

We propose a novel mutation mechanism for points and ordinary or palindromic sequences of DNA and RNA. We adopted non-Hermitian approaches based on quantum mechanics. Hermiticity is in the limelight of any physical structure with quantum character, like DNA, or RNA, as it creates quantum stability in that it yields real eigenvalues and orthonormal states. We show that, through the mutation mechanism we constructed based on non-Hermitian physics, the deterioration of the Hermitian character of the original DNA states, nucleotides, does not create a stability problem. We show that Weyl’s perturbation theory helps us determine the stability of mutated DNA or RNA. We prove that mutations made in the laboratory with conventional nucleotides using non-Hermitian physics methods are not different from mutations that occur spontaneously in nature. This result may help to reveal the quantum nature of genetic diseases in the near future and may shape the molecular approaches.
Mitigation of TDP-43-induced toxic phenotype by expression of RGNEF N-terminal fragment in ALS models
Authors: Droppelmann Cristian A. , Campos-Melo Danae , Noches Veronica , McLellan Crystal , Szabla Robert , Lyons Taylor A. , Amzil Hind , Withers Benjamin , Sonkar Kirti S. , Simon Anne , Buratti Emanuele , Junop Murray , Kramer Jamie M. , Strong Michael J.
Published: October 2023

Aggregation of the RNA-binding protein (RBP) TDP-43 is a hallmark of TDP-proteinopathies including amyotrophic lateral sclerosis (ALS) and frontotemporal dementia (FTD). Since TDP-43 aggregation and dysregulation are causative of neuronal death, there is a special interest in targeting this protein as a therapeutic approach. Previously, we found that TDP-43 extensively co-aggregated with the dual function protein (GEF (guanine exchange factor) and RBP) rho guanine nucleotide exchange factor (RGNEF) in ALS patients. Here, we show that a N-terminal fragment of RGNEF (NF242) interacts directly with the RNA recognition motifs (RRM) of TDP-43 competing with RNA, and that the IPT/TIG domain of NF242 is essential for this interaction. Genetical expression of NF242 in a fruit fly ALS model overexpressing TDP-43 suppressed the neuropathological phenotype increasing lifespan, abolishing motor defects, and preventing neurodegeneration. Intracerebroventricular injections of AAV9/NF242 in a severe TDP-43 murine model (rNLS8) improved lifespan and motor phenotype, and decreased neuroinflammation markers. Our results demonstrate an innovative way to target TDP-43 proteinopathies using a protein fragment with affinity for TDP-43, suggesting a promising therapeutic strategy for TDP-43 proteinopathies such as ALS and FTD.
CellPie: a scalable spatial transcriptomics factor discovery method via joint non-negative matrix factorization
Authors: Georgaka Sokratia , Morgans William Geraint , Zhao Qian , Martinez Diego Sanchez , Ali Amin , Ghafoor Mohamed , Baker Syed-Murtuza , Bristow Robert , Iqbal Mudassar , Rattray Magnus
Published: October 2023

Spatially resolved transcriptomics has enabled the study of expression of genes within tissues while retaining their spatial identity. Most spatial transcriptomics technologies generate a matched histopathological image as part of the standard pipeline, providing morphological information that can complement the transcriptomics data. Here we presentCellPie, a fast, unsupervised factor discovery method, based on joint non-negative matrix factorisation of spatial RNA transcripts and histological image features.CellPieemploys the accelerated hierarchical least squares method to significantly reduce the computational time, enabling efficient application to high-dimensional spatial transcriptomics datasets. We assessedCellPieon two different human cancer types and spatial resolutions, showing an improved performance against published factorisation methods. Additionally, we appliedCellPieto a highly resolved Visium HD dataset, demonstrating its high computational efficiency compared to standard non-negative matrix factorisation and other existing methods.

Availability

https://github.com/ManchesterBioinference/CellPie
C5aR1 signaling promotes region and age dependent synaptic pruning in models of Alzheimer’s Disease
Authors: Gomez-Arboledas Angela , Fonseca Maria I. , Kramar Enikö , Chu Shu-Hui , Schartz Nicole , Selvan Purnika , Wood Marcelo A. , Tenner Andrea J.
Published: October 2023

INTRODUCTION

Synaptic loss is a hallmark of Alzheimer’s disease (AD) that correlates with cognitive decline in AD patients. Complement-mediated synaptic pruning has been associated with this excessive loss of synapses in AD. Here, we investigated the effect of C5aR1 inhibition on microglial and astroglial synaptic pruning in two mouse models of AD.

METHODS

A combination of super-resolution and confocal and tridimensional image reconstruction was used to assess the effect of genetic ablation or pharmacological inhibition of C5aR1 on the Arctic48 and Tg2576 models of AD.

RESULTS

Genetic ablation or pharmacological inhibition of C5aR1 rescues the excessive pre-synaptic pruning and synaptic loss in an age and region dependent fashion in two mouse models of AD, which correlates with improved long-term potentiation (LTP).

DISCUSSION

Reduction of excessive synaptic pruning is an additional beneficial outcome of the suppression of C5a-C5aR1 signaling, further supporting its potential as an effective targeted therapy to treat AD.
Sex-Specific DNA Methylation and Gene Expression Changes in Mouse Placentas After Early Preimplantation Alcohol Exposure
Authors: Legault Lisa-Marie , Dupas Thomas , Breton-Larrivée Mélanie , Filion-Bienvenue Fannie , Lemieux Anthony , Langford-Avelar Alexandra , McGraw Serge
Published: October 2023

During pregnancy, exposure to alcohol represents an environmental insult capable of negatively impacting embryonic development. This influence can stem from disruption of molecular profiles, ultimately leading to manifestation of fetal alcohol spectrum disorder. Despite the central role of the placenta in proper embryonic development and successful pregnancy, studies on the placenta in a prenatal alcohol exposure and fetal alcohol spectrum disorder context are markedly lacking. Here, we employed a well-established model for preimplantation alcohol exposure, specifically targeting embryonic day 2.5, corresponding to the 8-cell stage. The exposure was administered to pregnant C57BL/6 female mice through subcutaneous injection, involving two doses of either 2.5 g/kg 50% ethanol or an equivalent volume of saline at 2-hour intervals. Morphology, DNA methylation and gene expression patterns were assessed in male and female late-gestation (E18.5) placentas. While overall placental morphology was not altered, we found a significant decrease in male ethanol-exposed embryo weights. When looking at molecular profiles, we uncovered numerous differentially methylated regions (DMRs; 991 in males; 1309 in females) and differentially expressed genes (DEGs; 1046 in males; 340 in females) in the placentas. Remarkably, only 21 DMRs and 54 DEGs were common to both sexes, which were enriched for genes involved in growth factor response pathways. Preimplantation alcohol exposure had a greater impact on imprinted genes expression in male placentas (imprinted DEGs: 18 in males; 1 in females). Finally, by using machine learning model (L1 regularization), we were able to precisely discriminate control and ethanol-exposed placentas based on their specific DNA methylation patterns. This is the first study demonstrating that preimplantation alcohol exposure alters the DNA methylation and transcriptomic profiles of late-gestation placentas in a sex-specific manner. Our findings highlight that the DNA methylation profiles of the placenta could serve as a potent predictive molecular signature for early preimplantation alcohol exposure.

GRAPHICAL ABSTRACT
Relative importance of bacterivorous mixotrophs in an estuary-coast environment
Authors: Li Qian , Dong Kaiyi , Wang Ying , Edwards Kyle F.
Published: October 2023

Mixotrophic eukaryotes are important bacterivores in oligotrophic open oceans, but their significance as grazers in more nutrient-rich waters is less clear. Here we investigated the bacterivory partition between mixotrophs and heterotrophs in a productive, estuary-influenced coastal region in East China Sea. We found ubiquitous, actively feeding phytoplankton populations and taxa with mixotrophic potential, by identifying ingestion of fluorescent prey surrogate and analyzing community 18S rRNA gene amplicons. Potential and active mixotrophs accounted for 10-63% of total eukaryotic community and 17-69% of bacterivores observed, respectively, contributing 6-48% of estimated in situ bacterivory. The much higher mixotroph fitness outside of the turbid plume were potentially driven by increased light and decreased nutrients availability. Our results suggest that, although heterotrophs dominated overall in situ bacterivory, mixotrophs were abundant and important bacterivores in this low-latitude mesotrophic coastal region.

Scientific Significance Statement

Mixotrophy, the combing of photosynthetic and phagotrophic nutrition, can dramatically increase primary production and alter material movements in aquatic food webs. Understanding the distribution and fitness of phagotrophic mixotrophs in a range of habitats are therefore critical to properly understand the biogeochemical cycles of the ocean. We developed a robust method to estimate active mixotrophs in situ and demonstrate rapid shifts of bacterivory partition between mixotrophs and heterotrophs across an estuary-coast environment in East China Sea. Our results help fill the knowledge gap of mixotroph niches in mesotrophic coastal environments that are impacted by riverine discharge, shedding light on relationships among mixotrophy, light and nutrient conditions.
HIV Infection impairs the Host Response toMycobacterium tuberculosisInfection by altering Surfactant Protein D function in the Human Lung Alveolar Mucosa
Authors: Akhter Anwari , Moliva Juan I. , Azad Abul K. , Olmo-Fontánez Angélica , Garcia-Vilanova Andreu , Scordo Julia M. , Gavrilin Mikhail A. , Diaz Phillip T. , Endsley Janice J. , Weintraub Susan T. , Schlesinger Larry S. , Wewers Mark D. , Torrelles Jordi B.
Published: October 2023

Tuberculosis is the leading cause of death for people living with HIV (PLWH). We hypothesized that altered functions of innate immune components in the human alveolar lining fluid of PLWH (HIV-ALF), drive susceptibility toMycobacterium tuberculosis(M.tb) infection. Our results indicate a significant increase in oxidation of innate proteins and chemokine levels, and significantly lower levels and function of complement components and Th1/Th2/Th17 cytokines in HIV-ALFvs.control-ALF (non-HIV infected people). We further found a deficiency of surfactant protein-D (SP-D) and reduced binding of SP-D toM.tbthat had been exposed to HIV-ALF. Primary human macrophages infected withM.tbexposed to HIV-ALF were significantly less capable of controlling the infection, which was reversed by SP-D replenishment in HIV-ALF. Thus, our data suggest that PLWH without antiretroviral therapy (ART) have declining host innate defense function in their lung mucosa, thereby favoringM.tband potentially other pulmonary infections.
Molecular de-extinction of antibiotics enabled by deep learning
Authors: Wan Fangping , Torres Marcelo D. T. , Peng Jacqueline , de la Fuente-Nunez Cesar
Published: October 2023

Molecular de-extinction is an emerging field that aims to resurrect molecules to solve present-day problems such as antibiotic resistance. Here, we introduce a deep learning approach called Antibiotic Peptide de-Extinction (APEX) to mine the proteomes of all available extinct organisms (the “extinctome”) searching for encrypted peptide (EP) antibiotics. APEX mined a total of 10,311,899 EPs and identified 37,176 sequences predicted to have broad-spectrum antimicrobial activity, 11,035 of which were not found in extant organisms. Chemical synthesis and experimental validation yielded archaic EPs (AEPs) with activity against dangerous bacterial pathogens. Most peptides killed bacteria by depolarizing their cytoplasmic membrane, contrary to known antimicrobial peptides, which target the outer membrane. Notably, lead peptides, including those derived from the woolly mammoth, ancient sea cow, giant sloth, and extinct giant elk, exhibited anti-infective activity in preclinical mouse models. We propose molecular de-extinction, accelerated by deep learning, as a framework for discovering therapeutic molecules.
Reciprocal interactions between the sorghum root microbiome and the parasitic weedStriga hermonthica
Authors: Etalo Desalegn W. , Rybka Dominika , Lombard Lorenzo , Leite Marcio F.A. , Ossowicki Adam , Dini-Andreote Francisco , Arias-Giraldo Luisa , Kuramae Eiko E. , Crous Pedro W. , Tessema Taye , Raaijmakers Jos M.
Published: October 2023

The soil microbiome plays a crucial role in protecting plants against various pests and pathogens. However, its impact on interactions between plants and parasitic weeds, such asStriga hermonthica, is poorly understood. In this study, sorghum plants susceptible toStrigawere grown in 22 different field soils infested with parasite seeds. Significant variations inStrigainfections were observed among the soils. When the mostStriga-suppressive soil was gamma-irradiated, there was a significant increase inStrigaattachments, highlighting the importance of the soil microbiome in disrupting parasite infection. In the presence of the soil microbiome, theStriga-susceptible sorghum plants performed similarly to threeStriga-resistant genotypes. This effect was lost when the soil microbiome was eliminated by gamma-irradiation. Subsequent analysis revealed thatStrigasubstantially affected the sorghum rhizosphere microbiome and that both the sorghum rhizosphere mycobiome and bacteriome composition significantly correlated withStrigaattachment. Interestingly, certain fungal species in the sorghum rhizosphere mycobiome were only detected whenStrigaseeds were present. Further investigation showed that these fungal taxa originated from theStrigaseeds and are known sorghum pathogens, suggesting a potential partnership betweenStrigaand fungal pathogens to invade their shared host. Overall, our study demonstrated that the soil microbiome influencesStrigainfection and sorghum performance in a genotype-dependent manner, and the microbiome ofStrigaseeds affects the composition of the sorghum rhizosphere microbiome.
Neutralisation of SARS-CoV-2 Omicron subvariants BA.2.86 and EG.5.1 by antibodies induced by earlier infection or vaccination
Authors: Lassaunière Ria , Polacek Charlotta , Baig Sharmin , Ellegaard Kirsten , Escobar-Herrera Leandro André , Fomsgaard Anders , Spiess Katja , Schwartz Olivier , Planas Delphine , Simon-Lorière Etienne , Schneider Uffe Vest , Sieber Raphael Niklaus , Stegger Marc , Krause Tyra Grove , Ullum Henrik , Jokelainen Pikka , Rasmussen Morten
Published: October 2023

Highly mutated SARS-CoV-2 Omicron subvariant BA.2.86 emerged in July 2023. We investigated the neutralisation of isolated virus by antibodies induced by earlier infection or vaccination. The neutralisation titres for BA.2.86 were comparable to those for XBB.1 and EG.5.1, by antibodies induced by XBB.1.5 or BA.4/5 breakthrough infection or BA.4/5 vaccination.
The neoliberal multicultural state and the urban Indigenous associative model in Santiago de Chile
Authors: Brablec Dana
Published: October 2023

This article argues that since the recovery of democracy in Chile in the early 1990s, the state has been reshaping the Indigenous socio‐political landscape by adopting neoliberal multiculturalism as a governance model. By not posing significant challenges to the state's neoliberal political and economic priorities, Indigenous cultural activity has been carefully channelled to meet state expectations of what constitutes urban indigeneity. Drawing on the minority and multicultural studies literature and ongoing ethnographic fieldwork, this article analyses how Mapuche civil society navigates the complexities of two relational models of state/ethnic minority interaction: ethno‐bureaucracy and strategic essentialism. Although Mapuche associations have tried to accommodate their interests within the limits of neoliberal multiculturalism, the article argues that this governance model has established incentives for inclusion and exclusion in the socio‐political apparatus, resulting in a fragmentation of the Mapuche associative landscape in urban Chile.
Executive function deficit in betel quid‐dependence: Evidence from functional and effective connectivity of executive control network
Authors: Ban Meiting , Wang Dongcui , He Jincheng , Zhu Xueling , Yuan Fulai
Published: October 2023

Betel quid (BQ) ranks fourth in global self‐administered psychoactive agents, after caffeine, alcohol and nicotine, with 600 million consumers. Patients with BQ dependence (BQD) disorder demonstrate deficits in executive function. However, the neural correlates of the resting‐state executive control network (ECN) and BQD‐related pathopsychological characteristics still remain unclear. The present study aimed to assess the functional and effective connectivity of the ECN using resting‐state functional magnetic resonance imaging (rs‐fMRI). Fifty‐five BQD individuals and 54 healthy controls (HCs) were recruited in this study. The executive function of all participants was tested by three tasks. Independent component and Granger causal analysis were employed to investigate the functional connectivity within ECN and ECN‐related directional effective connectivity, separately. Behavioural results suggested a marked deficit of executive function in BQD individuals. Compared with HCs, BQD individuals showed overall weaker functional connectivity in the ECN, mainly including dorsolateral prefrontal cortex (DLPFC), inferior parietal lobule (IPL) and middle frontal gyrus (MFG). We observed decreased outflow of information from the right DLPFC and IPL to the precentral/pre‐supplement motor area (SMA) and increased outflow of information from the MFG to the middle occipital gyrus in BQD individuals. Correlation analysis revealed that the effective connectivity from IPL to precentral/pre‐SMA was negatively correlated to the BQD scales in BQD individuals. Our findings revealed impaired executive function, functional connectivity of the ECN and causal interaction between networks in patients with BQD. These results could potentially direct future targets for the prevention and intervention of BQD.
Understanding people's experiences of the formal health and social care system for co‐occurring heavy alcohol use and depression through the lens of relational autonomy: A qualitative study
Authors: Jackson Katherine , Kaner Eileen , Hanratty Barbara , Gilvarry Eilish , Yardley Lucy , O'Donnell Amy
Published: October 2023

Background and Aims

Heavy alcohol use and depression commonly co‐occur. However, health and social care services rarely provide coordinated support for these conditions. Using relational autonomy, which recognizes how social and economic contexts and relational support alter people's capacity for agency, this study aimed to (1) explore how people experience formal care provision for co‐occurring alcohol use and depression, (2) consider how this context could lead to adverse outcomes for individuals and (3) understand the implications of these experiences for future policy and practice.

Design

Semi‐structured qualitative interviews underpinned by the methodology of interpretive description.

Setting

North East and North Cumbria, UK.

Participants

Thirty‐nine people (21 men and 18 women) with current or recent experience of co‐occurring heavy alcohol use ([Alcohol Use Disorders Identification Test [AUDIT] score ≥ 8]) and depression ([Patient Health Questionnaire test ≥ 5] screening tools to give an indication of their current levels of alcohol use and mental score).

Measurements

Semi‐structured interview guide supported in‐depth exploration of the treatment and care people had sought and received for heavy alcohol use and depression.

Findings

Most participants perceived depression as a key factor contributing to their heavy alcohol use. Three key themes were identified: (1) ‘lack of recognition’ of a relationship between alcohol use and depression and/or contexts that limit people's capacity to access help, (2) having ‘nowhere to go’ to access relevant treatment and care and (3) ‘supporting relational autonomy’ as opposed to assuming that individuals can organize their own care and recovery. Lack of access to appropriate treatment and provision that disregards individuals’ differential capacity for agency may contribute to delays in help‐seeking, increased distress and suicidal ideation.

Conclusions

Among people with co‐occurring heavy alcohol use and depression, lack of recognition of a relationship between alcohol use and depression and formal care provision that does not acknowledge people's social and economic context, including their intrinsic need for relational support, may contribute to distress and limit their capacity to get well.
Periodontal disease is not associated with risk of inflammatory bowel disease: Results from two prospective cohort studies in the US
Authors: Williams Katherine M. , Challa Prasanna K. , Lopes Emily W. , Burke Kristin E. , Ananthakrishnan Ashwin N. , Richter James M. , Chan Andrew T. , Khalili Hamed
Published: October 2023

Aim

To examine the relationship between periodontal disease and tooth loss and risk of inflammatory bowel disease (IBD).

Methods

We conducted a prospective cohort study of 86,602 women from the Nurses' Health Study (1992–2016) and 50,349 men from the Health Professionals Follow‐up Study (1986–2016) with available data on periodontal disease and tooth loss. Cases of IBD were initially reported by participants and then confirmed by medical record review. We used Cox proportional hazards modelling to estimate multivariable‐adjusted hazard ratios (aHRs) and 95% CIs.

Results

Through the end of follow‐up, we documented 175 cases of Crohn's disease (CD) and 209 cases of ulcerative colitis (UC). After adjustment for potential risk factors, there was no association between periodontal disease and risk of CD (pooled aHR: 0.99, 95% CI: 0.65–1.52, p = 0.970) or UC (aHR: 0.99, 95% CI: 0.68–1.45, p = 0.971). Similarly, we did not observe an association between tooth loss and risk of CD (aHR: 0.72, 95% CI: 0.43–1.21, p = 0.218) or UC (aHR: 0.89, 95% CI: 0.58–1.36, p = 0.581) in the pooled analysis. The associations were not modified by sex, age, body mass index (BMI), smoking status or NSAID use (all pinteraction > 0.87).

Conclusion

In two large prospective cohort studies, we did not observe an association between periodontal disease and tooth loss and risk of CD or UC.
Digital instinct—A keyword for making sense of students' digital practice and digital literacy
Authors: Boie Mette Alma Kjærsholm , Dalsgaard Christian , Caviglia Francesco
Published: October 2023

The paper introduces the student‐coined term digital instinct which describes students' disposition to resorting to digital technology for solving problems and doing school assignments. Taking cues from the term digital instinct, the paper describes a student perspective on digital literacy emerging from 100 lived experience descriptions and interviews with 37 Danish upper secondary students. The findings show that students' digital practice is characterised by experience‐based, intuitive and familiar use of technologies. Most notably, students employ digital technologies as cognitive partners that help them carry on with assignments that they initially did not understand, but that they were able to complete with the help of the computer. The study examines the nature of this partnership through the words of the students and identifies how technologies expand student agency but fall short of a reflective use of digital technologies. Recognising the strengths and weaknesses of students' digital practices may inform the concept of digital literacy and encourage teachers to acknowledge the digital instinct as a steppingstone to foster students' reflective use of digital technologies.

Practitioner notes

What is already known about this topic

Students have inadequate command of digital literacies as described in curricular terminology.

Students have positive as well as negative perceptions of the value and usefulness of digital technologies in school.

Students both over‐ and underestimate their own digital literacies.

What this paper adds

Students have a fundamental utilitarian conception of digital technologies that either make schoolwork easier or more difficult, and they do not articulate that their use of digital technologies provides them with digital literacies.

Students' conception of a digital instinct describes an intuitive and familiar, albeit unreflected, use of technologies where students employ experience‐based and self‐taught methods for using digital technologies.

The digital instinct accounts for a feeling of agency among students, manifested in a widespread confidence that they can do assignments and solve problems when they make use of their computer.

Implications for practice and/or policy

Curricular terminologies struggle to capture what students can and cannot do with technology, and how much they understand the underlying technology.

Teachers can involve and build on students' experience‐based digital practices as a starting point for developing digital literacy among students—also as an entry to a curricular perspective.

Teachers should acknowledge students' conception of a ‘digital instinct’ as an important disposition in its own right.
What Can Design Thinkers Learn from Entrepreneurs?
Authors: Nigam Akhil
Published: October 2023

Let's teach designers to be a little more resourceful and a little less deliberate. Sometimes, the best solutions come from unexpected places.

Here are two groups with so much in common and so much to teach each other.
A Digitally Disruptive Supply Chain
Authors: Ady Jacklyn
Published: October 2023

It's inevitable—the traditional supply chain will eventually meet the digital frontier. Imagine today's new community of makers sourcing designers to refine their inventions, and 3D printers to generate first‐round prototypes. What will this brave new world look like?

The future of the supply chain in the digital age…
Modern Infringements: The Unsavory Side of 3D Printing and Digital Replicas
Authors: Katz Robert S.
Published: October 2023

With the advent of cheaper 3D printing and scanning technology comes a host of legal issues. It's best to be prepared for the inevitable.

… and some possible barriers to it.
Creating Design Value Through Understanding Human Cognition and Behavior
Authors: Soken Nelson
Published: October 2023

Groupthink. Egocentrism. Information bias. These are some of the pitfalls that hold us back from the business innovations we hope to achieve. Recognizing them is half the battle.

A thought leader on developing innovation strategies shares his thoughts about the cognitive biases and other human tendencies that keep us from doing truly breakthrough work.
Tips for Building a Successful Design Organization
Authors: Bilson Carole , Aitchison Iain
Published: October 2023

One of your first questions should be: What purpose does design play for the organization? An answer to that question will take you well on the way to understanding your new position.

Good advice for the new manager.
New Technologies: A Transfer of Power
Authors: Brown Liz
Published: October 2023

Like so many other things, new technologies can make our cities better places to live. But they need to be available to everyone.

Emerging technologies in an urban setting: the promise and the problems.