bluuebunny/crossref_metadata_2025 huggingface dataset:
Acute complications in children with sickle cell disease: Prevention and management
Authors: Beck Carolyn E , Trottier Evelyne D , Kirby-Allen Melanie , Pastore Yves
Published: March 2022

Sickle cell disease (SCD) is a chronic, multi-system disease that requires comprehensive care. The sickling of red blood cells leads to hemolysis and vascular occlusion. Complications include hemolytic anemia, pain syndromes, and organ damage. Patterns of immigration and an increase in newborn screening mean that paediatric health care providers across Canada, in small and large centres alike, need to be knowledgeable about SCD. This statement focuses on principles of prevention, advocacy, and the rapid treatment of common acute complications. Guidance includes the current status of newborn screening, recommendations for immunizations and antibiotic prophylaxis, and an introduction to hydroxyurea, a medication that reduces both morbidity and mortality in children with SCD. Case vignettes demonstrate principles of care for common acute complications of SCD: vaso-occlusive episodes (VOE), acute chest syndrome (ACS), fever, splenic sequestration, aplastic crises, and stroke. Finally, principles of blood transfusion are highlighted, along with indications for both straight and exchange blood transfusions.
Leveraging the power of media to drive cognition: a media-informed approach to naturalistic neuroscience
Authors: Grall Clare , Finn Emily S
Published: March 2022

So-called ‘naturalistic’ stimuli have risen in popularity in cognitive, social and affective neuroscience over the last 15 years. However, a critical property of these stimuli is frequently overlooked: Media—like film, television, books and podcasts—are ‘fundamentally not natural’. They are deliberately crafted products meant to elicit particular human thought, emotion and behavior. Here, we argue for a more informed approach to adopting media stimuli in experimental paradigms. We discuss the pitfalls of combining stimuli that are designed for research with those that are designed for other purposes (e.g. entertainment) under the umbrella term of ‘naturalistic’ and present strategies to improve rigor in the stimulus selection process. We assert that experiencing media should be considered a task akin to any other experimental task(s) and explain how this shift in perspective will compel more nuanced and generalizable research using these stimuli. Throughout, we offer theoretical and practical knowledge from multidisciplinary media research to raise the standard for the treatment of media stimuli in neuroscience research.
Neurotransmitters of sleep and wakefulness in flatworms
Authors: Omond Shauni E T , Hale Matthew W , Lesku John A
Published: March 2022

Study Objectives

Sleep is a prominent behavioral and biochemical state observed in all animals studied, including platyhelminth flatworms. Investigations into the biochemical mechanisms associated with sleep—and wakefulness—are important for understanding how these states are regulated and how that regulation changed with the evolution of new types of animals. Unfortunately, beyond a handful of vertebrates, such studies on invertebrates are rare.

Methods

We investigated the effect of seven neurotransmitters, and one pharmacological compound, that modulate either sleep or wakefulness in mammals, on flatworms (Girardia tigrina). Flatworms were exposed via ingestion and diffusion to four neurotransmitters that promote wakefulness in vertebrates (acetylcholine, dopamine, glutamate, histamine), and three that induce sleep (adenosine, GABA, serotonin) along with the H1 histamine receptor antagonist pyrilamine. Compounds were administered over concentrations spanning three to five orders of magnitude. Flatworms were then transferred to fresh water and video recorded for analysis.

Results

Dopamine and histamine decreased the time spent inactive and increased distance traveled, consistent with their wake-promoting effect in vertebrates and fruit flies; pyrilamine increased restfulness and GABA showed a nonsignificant trend towards promoting restfulness in a dose-dependent manner, in agreement with their sleep-inducing effect in vertebrates, fruit flies, and Hydra. Similar to Hydra, acetylcholine, glutamate, and serotonin, but also adenosine, had no apparent effect on flatworm behavior.

Conclusions

These data demonstrate the potential of neurotransmitters to regulate sleep and wakefulness in flatworms and highlight the conserved action of some neurotransmitters across species.
Absence of Connexin 43 Results in Smaller Retinas and Arrested, Depolarized Retinal Progenitor Cells in Human Retinal Organoids
Authors: Cheng Lin , Cring Matthew R , Wadkins David A , Kuehn Markus H
Published: March 2022

The development of the vertebrate retina relies on complex regulatory mechanisms to achieve its characteristic layered morphology containing multiple neuronal cell types. While connexin 43 (CX43) is not expressed by mature retinal neurons, mutations in its gene GJA1 are associated with microphthalmia and low vision in patients. To delineate how lack of CX43 affects retinal development, GJA1 was disrupted in human induced pluripotent stem cells (hiPSCs) (GJA1−/−) using CRISPR/Cas9 editing, and these were subsequently differentiated into retinal organoids. GJA1−/− hiPSCs do not display defects in self-renewal and pluripotency, but the resulting organoids are smaller with a thinner neural retina and decreased abundance of many retinal cell types. CX43-deficient organoids express lower levels of the neural marker PAX6 and the retinal progenitor cell (RPC) markers PAX6, SIX3, and SIX6. Conversely, expression of the early neuroectoderm markers SOX1 and SOX2 remains high in GJA1−/− organoids throughout their development. The lack of CX43 results in an increased population of CHX10-positive RPCs that are smaller, disorganized, do not become polarized, and possess a limited ability to commit to retinal fate specification. Our data indicate that lack of CX43 causes a developmental arrest in RPCs that subsequently leads to pan-retinal defects and stunted ocular growth.
Insights Regarding Resistance of ‘Nemaguard’ Rootstock to the Bacterium Xylella fastidiosa
Authors: Krugner Rodrigo , Rogers Elizabeth E. , Burbank Lindsey P. , Wallis Christopher M. , Ledbetter Craig A.
Published: March 2022

‘Nemaguard’ is a commonly used rootstock for almond and stone fruits due to resistance to nematodes and enhanced scion vigor. Nemaguard also happens to be resistant to strains of Xylella fastidiosa that cause almond leaf scorch disease. Previous research showed that prior to June-budding, this rootstock can prevent infection of almond nursery stock by X. fastidiosa. Further, the rootstock also promotes recovery from infection in susceptible almond scions. Objectives of this study were to 1) compare movement and bacterial populations of X. fastidiosa in almond and Nemaguard, 2) determine whether the metabolic profile of infected versus noninfected plants of each species correspond with differences in pathogen distribution, and 3) evaluate the impact of feeding on Nemaguard on transmission efficiency and pathogen populations in insects. Results showed limited or no movement of X. fastidiosa beyond the point of mechanical inoculation in Nemaguard, whereas X. fastidiosa was detected in susceptible almond and isolated from plant samples distal to the point of inoculation. Large differences in the concentration of phenolic compounds between Nemaguard and almond were also found, although this was not impacted by infection status. After acquiring X. fastidiosa from infected plants, vector access periods of up to 14 days on Nemaguard neither reduced pathogen populations in vectors nor reduced transmission efficiency of X. fastidiosa to susceptible plants when compared with similar vector-access periods on susceptible grapevines. Results suggest Nemaguard, in spite of having high phenolic concentrations in its xylem, does not directly impact X. fastidiosa survival and that future research should focus on identification of potential physical traits that prevent bacterial attachment, multiplication, or movement within the plant.
Identification and Characterization of Wheat–Aegilops comosa 7M (7A) Disomic Substitution Lines with Stripe Rust and Powdery Mildew Resistance
Authors: Zuo Yuanyuan , Dai Shoufen , Song Zhongping , Xiang Qin , Li Wenjia , Liu Gang , Li Jian , Xu Donghe , Yan Zehong
Published: March 2022

Aegilops comosa (MM, 2n = 2x = 14), an important diploid species from the wheat tertiary gene pool, contains many unique genes/traits of potential use for wheat breeding, such as disease resistance. In this study, three sister lines, NAL-32, NAL-33, and NAL-34, were identified from a wheat–A. comosa distant cross using fluorescence in situ hybridization, simple sequence repeat markers, and PCR-based unique gene markers combined with single nucleotide polymorphism (SNP) array analysis. Genetically, NAL-32 contained neither an alien nor translocation chromosome, whereas NAL-33 and NAL-34 had disomic 7M (7A) substitution chromosomes but differed in the absence or presence of the 1BL/1RS translocation chromosomes, respectively. The absence of 7A in NAL-33 and NAL-34 and the unusual 1B in the latter were verified by wheat 55K SNP arrays. The two 7M (7A) substitution lines had similar levels of resistance to stripe rust and powdery mildew, but better than that of NAL-32 and their common wheat parents, suggesting that the stripe rust and powdery mildew resistance of NAL-33 and NAL-34 were derived from the 7M of A. comosa. This research provides important bridge materials that can potentially be used for transferring stripe rust and powdery mildew resistance.
Association of Blood Biochemical Indexes and Antibiotic Exposure With Severe Immune-related Adverse Events in Patients With Advanced Cancers Receiving PD-1 Inhibitors
Authors: Zhao Lijun , Li Yang , Jiang Ning , Song Xue , Xu Jianhua , Zhu Xiangzhi , Chen Cheng , Kong Cheng , Wang Xiaohua , Zong Dan , Li Luan , Han Cen , Yin Li , He Xia
Published: March 2022

Some patients with cancer treated with programmed death 1 (PD-1) inhibitors experience immune-related severe adverse events (ir-SAEs), however, predictors are limited. The objective was to identify clinicopathologic features that may be associated with a higher ir-SAE risk. This was a nested case-control study. After screening a total of 832 PD-1 inhibitor-treated patients, we identified 42 ir-SAE cases. According to the Common Terminology Criteria for Adverse Events (CTCAE) version 5.0, ir-SAEs were defined as grade ≥3 toxic effects associated with immunotherapy. A total of 126 controls were matched. The crude and adjusted risks of ir-SAEs were estimated by odds ratio (ORs) and 95% CIs using multivariate logistic regression models. Baseline neutrophil-to-lymphocyte ratio (NLR) [per SD increment-adjusted (aOR): 1.16], lactate dehydrogenase (LDH) ≥245 U/L (aOR: 2.39), and antibiotic exposure (aOR: 4.39) were associated with a higher risk of ir-SAEs. When NLR was categorized in 3 groups, significantly higher risks of ir-SAEs (aOR: 4.95) were found in participants in group 3 (>6) than in those in group 1 (<3). Furthermore, NLR (per SD increment-adjusted hazard ratio:1.08) were also significantly associated with shorter overall survival (OS). Baseline LDH ≥245 U/L and antibiotic exposure were no significant association with OS. In conclusion, ir-SAEs were associated between baseline NLR, LDH ≥245 U/L and antibiotic exposure. Lower NLR was correlated with longer OS for cancer.
Breastfeeding Infants in Women with Opioid Use Disorder
Authors: King Cheryl
Published: March 2022

An interprofessional approach from healthcare professionals can assist the woman with opioid use disorder (OUD) to become free of using opioids during pregnancy and beyond. These vulnerable women and their newborns need extended community support. The purpose of this article is to provide foundational information and standards that support the collaboration of community professionals in providing healthcare and treatment options for the woman with OUD to promote the family unit remaining together, support bonding, and encourage lactation/breastfeeding. Women with OUD need guidance from Christian nurses and the community as they transition to sobriety, motherhood, and breastfeeding.
Teaching Faith Community Nursing on Short-Term Medical Missions in Nigeria
Authors: Otey Tamara D.
Published: March 2022

The purpose of this study was to empower interprofessional Nigerian healthcare volunteers with knowledge and skills to promote community health. The U.S. researcher engaged in community-based participatory research in the context of a long-term partnership of annual short-term medical missions. Using a pre/posttest study design, three Nigerian nurses and the researcher co-taught Foundations of Faith Community Nursing in a 3-day class to 76 participants. The t-test analysis and informal evaluation of participants' performance at a mobile clinic demonstrated strong evidence of learning, suggesting that the teaching was an effective method to empower members of the Nigerian interprofessional team with the knowledge and skill to provide effective culturally congruent community healthcare.
Starting a New Faith Community Nursing Program
Authors: Witherspoon Mary , Stanford Deb
Published: March 2022

Faith community nursing, also known as congregational nursing or parish nursing, is a relatively new addition in the pantheon of nursing subspecialties. Nurses working in this role tailor their services according to the needs of the faith community and often to the community at large. This article describes how one nurse pursued the specialty and helped initiate faith community nursing in her own church.
Patient Expectations for Symptomatic Improvement before Cubital Tunnel Release
Authors: Rogers Miranda J. , Agwuncha Chinelo C. , Kazmers Nikolas H.
Published: March 2022

Background:

Patient expectations before cubital tunnel release (CuTR), a common procedure that leads to incomplete symptom resolution for many patients, are unclear. Study purposes included (1) describing preoperative patient expectations, and (2) identifying factors affecting expectations.

Methods:

Included patients underwent isolated unilateral CuTR between 2015 and 2021 at a single tertiary academic medical center. Expectations regarding the level of symptomatic improvement were queried preoperatively. Univariate and multivariable binary logistic regression was performed to determine factors associated with expecting great improvement.

Results:

Of the 92 included patients, 43 (47%) patients expected great improvement, whereas 27 (29%), four (4%), and five patients (5%) expected some, little, and no improvement, respectively. The remainder (14%) had no expectations. Multivariable modeling demonstrated that retired or unemployed/disabled work status, and commercial insurance status (versus Medicare or Medicaid) were associated with lower expectations independent of the surgeon, surgical technique, revision versus primary CuTR, preoperative atrophy or constant numbness, diabetes, and all studied demographic factors, including social deprivation.

Conclusions:

Roughly half of the patients expect great relief, and a third expect lesser degrees of relief, following CuTR. Preoperative expectations are significantly higher in patients with Medicaid and Medicare insurance, representing an opportunity for education, given the association between public insurance payer status and worse health outcomes in general. Age, BMI, preoperative atrophy and/or numbness, and the presence of medical comorbidities do not influence expectations but have been shown to yield worse outcomes or influence need for revision CuTR, representing an opportunity for intervention to align patient and surgeon expectations.
Recurrent pain in school-aged children: a longitudinal study focusing on the relation to academic achievement
Authors: Ragnarsson Susanne , Johansson Klara , Bergström Erik , Sjöberg Gunnar , Hurtig Anna-Karin , Petersen Solveig
Published: March 2022

Recurrent pain is an increasing public health problem among school-aged children, with potential negative impact on children's daily lives, such as schoolwork. The overall aim of this study was to investigate whether recurrent pain in school year 6 was associated with poorer academic achievement at the end of elementary school in school year 9. The study was a follow-up study based on data from “The Study of Health in School-Aged Children from Umeå”. Participants were 1567 children aged 12 to 13 years who attended school year 6. A follow-up was performed in school year 9, when the children were 16 years old. The children answered a questionnaire about recurrent pain (headache, stomachache, and backache). Information about academic achievement was collected from school registers. The results showed that having weekly recurrent pain in school year 6 predicted lower final overall grade points in school year 9 than in children with no recurrent pain. This applied for recurrent headache, stomachache, backache, and multiple pains and for both girls and boys. Recurrent pain did not predict secondary school eligibility, however. Perceived problems with academic achievement and problems with concentration partly mediated the association between recurrent pain and lower final overall grade points. Sleep problems were not associated with academic achievement and were therefore not a mediator. Thus, the results suggest that recurrent pain may predict later impairment of academic achievement and that problems with concentration and children's perceived achievement in school, but not sleep problems, may partly explain this relationship.
A Systematic Review of Risk Factors for Development, Recurrence, and Progression of Vulvar Intraepithelial Neoplasia
Authors: Jamieson Amy , Tse Samantha S. , Brar Harinder , Sadownik Leslie A. , Proctor Lily
Published: March 2022

Objective

Vulvar intraepithelial neoplasia (VIN) is a premalignant condition with high recurrence rates despite treatment. Vulvar intraepithelial neoplasia develops through separate etiologic pathways relative to the presence or absence of human papillomavirus (HPV) and TP53 mutations. This systematic review was conducted (1) to identify historical risk factors for the development, recurrence, and progression of VIN and (2) to critique these risk factors in the context of advances made in the stratification of VIN based on HPV or TP53 status.

Materials and Methods

A systematic search was performed on MEDLINE, Embase, Cochrane Database, PsychInfo, and CINAHL from inception to July 5, 2021. Three gynecologic oncologists independently evaluated the eligibility of studies based on predetermined inclusion and exclusion criteria, abstracted data, and then analyzed the relevant data.

Results

A total of 1,969 studies (involving 6,983 patients) were identified. Twenty-nine studies met inclusion criteria. The quality of evidence was low; primarily level 2b (Oxford Centre for Evidence-Based Medicine). Risk factors associated with the development of VIN include: smoking and coexisting vulvar dermatoses. Risk factors associated with recurrence include: smoking, multifocal disease, and positive surgical margins. Recent studies identified the presence of differentiated VIN/TP53 mutation as the most significant risk factor for both VIN recurrence and malignant progression.

Conclusions

The current body of evidence consists primarily of small retrospective observational studies. Well-designed retrospective case-control series and/or prospective observational studies are urgently needed. Ideally, future studies will collect standardized data regarding associated risk factors and stratify women with VIN based on HPV and TP53 status.
A review of the AURORA and BLISS trials: will it revolutionize the treatment of lupus nephritis?
Authors: Asif Sabaa , Bargman Joanne , Auguste Bourne
Published: March 2022

Purpose of review

Renal involvement in patients with systemic lupus erythematosus can lead to significant complications including end-stage renal disease. Treatment of lupus nephritis has evolved over the last several decades, but despite this evolution, many patients fail to achieve remission and often progress to end-stage kidney disease or carry a burden of adverse side effects related to treatment.

Recent findings

The recent findings from AURORA 1 and BLISS LN trials led the FDA to approve voclosporin and belimumab for the treatment of lupus nephritis. The AURORA 1 trial demonstrated that voclosporin, a second-generation calcineurin inhibitor, effectively lowers proteinuria in patients with lupus nephritis, when added to mycophenolate mofetil with a better safety profile, compared with other calcineurin inhibitors. The BLISS LN trial revealed better control of disease and lower risk of progression to end stage kidney disease (ESKD) and relapses in patients treated with belimumab in addition to standard therapy.

Both voclosporin and belimumab are costly and have not shown any early evidence to revolutionize practice in the management of lupus nephritis. Until more data are made available with future studies or other cost-effective treatment options become available, the widespread adoption and utility of these novel agents remains limited.
Clinical Feasibility of Shear Wave Dispersion Slope for Noninvasive Diagnosis of Nonalcoholic Steatohepatitis in Patients With Morbid Obesity
Authors: Kim Yeonsoo , Hwang Jiyoung , Bae Sung Hwan , Hong Seong Sook , Chang Yun-Woo , Kim Hyun-joo , Kim Sang Hyun , Jin So-Young
Published: March 2022

We aimed to investigate the clinical feasibility of shear wave dispersion slope for assessing nonalcoholic steatohepatitis (NASH) in patients with morbid obesity before bariatric surgery.

This prospective study collected data from 25 participants who received liver biopsy during bariatric surgery between February 2019 and December 2020. All participants underwent ultrasonography shear wave elastography before surgery and shear wave speed and shear wave dispersion slope were measured. Liver specimens were evaluated by 1 pathologist scored histologically for nonalcoholic fatty liver disease (NAFLD). Ultrasonography measurements were compared according to histopathologic findings. Diagnostic performance in differentiating NASH from NAFLD was evaluated using the area under the receiver operating characteristic curve (AUC). Median shear wave speed (1.48 vs 1.62 m/s, P = 0.014) and dispersion slope (8.40 vs 11.80 [m/s]/kHz, P = 0.004) were higher in NASH group than in NAFLD group. Shear wave dispersion slope tended to increase step by step as the severity of activity grade (P = 0.032) and hepatic fibrosis (P = 0.015) increased. The AUC of shear wave dispersion slope for differentiating NASH from NAFLD (AUC, 0.83; 95% confidence intervals, 0.66–1.00) was higher than that of shear wave speed (AUC, 0.78; 95% CI, 0.60–0.97), although it did not reach statistical significance (P = 0.729). Shear wave dispersion slope could be a feasible tool for assessing NASH in patients with morbid obesity.
Comparison of Face-to-Face Education and Multimedia Software Education on Adjustment of Patients With Intestinal Ostomy
Authors: Heidari-Beni Farshad , Esmaeilian Somayeh , Yousefi Fatemeh , Zarei Mohammad Reza , Farahani Mansoureh Ashghali
Published: March 2022

PURPOSE:

The aim of this study was to compare the effect of face-to-face versus multimedia education on the adjustment of patients to an intestinal ostomy.

DESIGN:

Randomized clinical trial.

SUBJECT AND SETTING:

The sample comprised 135 patients with new ostomies randomly assigned to 3 groups (control, face-to-face, and multimedia education). Data were collected from November 2018 to May 2019; the study setting was Rasul-e Akram and Imam Khomeini Hospitals, Tehran, Iran.

METHODS:

The control group received no additional ostomy education. The face-to-face education group was educated individually in the hospital environment during four 3-hour sessions delivered over 4 consecutive days. The multimedia group viewed a multimedia educational program using a laptop. Data were collected at baseline and 3 months after the intervention. Data collection forms comprised a demographic questionnaire and the Ostomy Adjustment Inventory-23 (OAI-23).

RESULTS:

Before the intervention, the mean OAI-23 adjustment score did not significantly differ among the 3 groups (P = .752). Three months after the intervention, the mean score of adjustment score in the multimedia software group was significantly higher than those of the face-to-face and control groups (P = .000). In addition, the mean score of adjustment of the face-to-face education group was significantly higher than that of the control group (P = .002).

CONCLUSION:

Findings indicate that multimedia education was associated with higher levels of adjustment when compared to face-to-face teaching.
Acetic Acid Use in Chronic Wound Healing
Authors: Chen Qiuyun , Zhou Kehua
Published: March 2022

BACKGROUND:

Acetic acid is bacteriostatic or bactericidal to many gram-negative and gram-positive microorganisms, especially Pseudomonas. Nevertheless, it has also been found to possess cytotoxic effects in concentrations as low as 0.25% inhibiting the epithelialization process during wound healing.

CASES:

In this multiple case series, we present 2 cases of chronic traumatic leg wounds treated with gauze moistened with acetic acid (0.25%), which were covered with a securing dressing and compression stockinet. Both patients were told to apply gauze moistened with acetic acid (0.25%) twice daily. In both cases, the wound progressed to blue-green drainage and wet yellow slough tissue to near-complete beefy granulation tissue. At this point, acetic acid was replaced with collagen or petrolatum dressing until complete wound closure was achieved. The treatment of these wounds illustrated successful use of acetic acid for chronic wound care.

CONCLUSION:

Our experience with these cases suggests that appearance of blue-green wound drainage and wet yellow slough tissue is a reasonable indication for the use of gauze moistened with acetic acid (0.25%). Further research is needed to test the efficacy of these principles in guiding acetic acid use in wound care.
Evaluating refugia in recent human evolution in Africa
Authors: Blinkhorn James , Timbrell Lucy , Grove Matt , Scerri Eleanor M. L.
Published: March 2022

Homo sapienshave adapted to an incredible diversity of habitats around the globe. This capacity to adapt to different landscapes is clearly expressed within Africa, with Late PleistoceneHomo sapienspopulations occupying savannahs, woodlands, coastlines and mountainous terrain. As the only area of the world whereHomo sapienshave clearly persisted through multiple glacial-interglacial cycles, Africa is the only continent where classic refugia models can be formulated and tested to examine and describe changing patterns of past distributions and human phylogeographies. The potential role of refugia has frequently been acknowledged in the Late Pleistocene palaeoanthropological literature, yet explicit identification of potential refugia has been limited by the patchy nature of palaeoenvironmental and archaeological records, and the low temporal resolution of climate or ecological models. Here, we apply potential climatic thresholds on human habitation, rooted in ethnographic studies, in combination with high-resolution model datasets for precipitation and biome distributions to identify persistent refugia spanning the Late Pleistocene (130–10 ka). We present two alternate models suggesting that between 27% and 66% of Africa may have provided refugia to Late Pleistocene human populations, and examine variability in precipitation, biome and ecotone distributions within these refugial zones.

This article is part of the theme issue ‘Tropical forests in the deep human past’.
Prevotella lacticifex sp. nov., isolated from the rumen of cows
Authors: Shinkai Takumi , Ikeyama Nao , Kumagai Masahiko , Ohmori Hideyuki , Sakamoto Mitsuo , Ohkuma Moriya , Mitsumori Makoto
Published: March 2022

The genus

Prevotella

plays an important role in polysaccharide degradation and fermentation in the rumen. To further understand the function of the phylogenetically diverse genus

Prevotella

, it is necessary to explore the individual characteristics at the species level. In this study, Gram-negative anaerobic bacterial strains isolated from the rumen of Holstein cows were identified. Strain R5019T was classified within the genus

Prevotella

based on 16S rRNA gene sequence-based phylogenetic analysis. The values of 16S rRNA gene sequence similarity, average nucleotide identity and digital DNA–DNA hybridization between strain R5019T and its phylogenetically nearest species

Prevotella multisaccharivorax

PPPA20T were 89.8, 82.6, and 29.3 %, respectively. The genome size of R5019T was estimated to be ca. 4.19 Mb with a genomic G+C content of 49.5 mol%. The major cellular fatty acids and menaquinones were C15 : 0 anteiso and C17 : 0 anteiso and MK-11 and MK-12, respectively. Succinate, lactate, malate, acetate and formate were produced as the fermentation end products using glucose. Based on phylogenetic, physiological, biochemical and genomic differences between 11 strains and other phylogenetically related

Prevotella

species, a novel species, Prevotella lacticifex sp. nov., is proposed within the genus

Prevotella

. The type strain is R5019T (=JCM 34664T=DSM 112675T).
Geobacter benzoatilyticus sp. nov., a novel benzoate-oxidizing, iron-reducing bacterium isolated from petroleum contaminated soil
Authors: Yang Guiqin , Li Yanling , Lin Annian , Zhuang Li
Published: March 2022

A strictly anaerobic bacterial strain, designated Jerry-YXT, was isolated from petroleum-contaminated soil sampled in China. Strain Jerry-YXT was a Gram-stain-negative bacterium forming reddish colonies. It grew optimally at 30 °C and pH 7.0, and tolerated 1.0 % (w/v) NaCl. Strain Jerry-YXT was able to use fumarate, ferric citrate and ferrihydrite as electron acceptors, and ethanol, acetate and benzoate as electron donors. The major fatty acids of this strain were C16 : 0 and C16 : 1
 ω7c/C16 : 1
 ω6c (summed feature 3). The 16S rRNA gene sequence-based phylogenetic analysis placed this strain in the genus

Geobacter

, being most closely related to

Geobacter metallireducens

(98.2 % similarity),

Geobacter hydrogenophilus

(98.1 %) and

Geobacter grbiciae

(98.0 %). The DNA G+C content was 57.6 mol%. The average nucleotide identity and digital DNA–DNA hybridization values between the genomes of strain Jerry-YXT and

G. metallireducens

GS-15T were 81.8 and 35.4 %, respectively. The results of the polyphasic study allowed the genotypic and phenotypic differentiation of strain Jerry-YXT from its closest species, which suggested that strain Jerry-YXT represents a novel species of the genus

Geobacter

. The name for the proposed new species is Geobacter benzoatilyticus sp. nov. The type strain is Jerry-YXT (=MCCC 1K05659T=JCM 39190T).
Gap selection and steering during obstacle avoidance in pigeons
Authors: Antolin Natalia Pérez-Campanero , Taylor Graham K.
Published: March 2022

The ability of birds to fly through cluttered environments has inspired biologists interested in understanding its underlying mechanisms, and engineers interested in applying its underpinning principles. To analyse this problem empirically, we break it down into two distinct, but related, questions: How do birds select which gaps to aim for? And how do they steer through them? We answered these questions by using a combined experimental and modelling approach, in which we released pigeons (Columbia livia domestica) inside a large hall whose open exit was separated from the release point by a curtain creating two vertical gaps—one of which was obstructed by an obstacle. We tracked the birds using a high-speed motion capture system, and found that their gap choice seemed to be biased by their intrinsic handedness, rather than determined by extrinsic cues such as the size of the gap or its alignment with the destination. We modelled the pigeons’ steering behaviour algorithmically by simulating their flight trajectories under a set of six candidate guidance laws, including those used previously to model targeted flight behaviours in birds. We found that their flights were best modelled by delayed proportional navigation commanding turning in proportion to the angular rate of the line-of-sight from the pigeon to the midpoint of the gap. Our results are consistent with this being a two-phase behaviour, in which the pigeon first heads forward from the release point before steering towards the midpoint of whichever gap it chooses to aim for under closed-loop guidance. Our findings have implications for the sensorimotor mechanisms that underlie clutter negotiation in birds, uniting this with other kinds of target-oriented behaviours including aerial pursuit.
Spatial patterning and immunosuppression of glioblastoma immune contexture in hypoxic niches
Authors: Sattiraju Anirudh , Kang Sangjo , Chen Zhihong , Marallano Valerie , Brusco Concetta , Ramakrishnan Aarthi , Shen Li , Hambardzumyan Dolores , Friedel Roland H , Zou Hongyan
Published: March 2022

Glioblastoma (GBM), a highly lethal brain cancer, is notorious for its immunosuppressive microenvironment, yet current immunotherapies are ineffective. Thus, understanding the immune contexture and governing factors of immunosuppression is crucial. Here, we identified a highly dynamic temporospatial patterning of tumor-associated macrophages (TAMs) corresponding to vascular changes in GBM: as tumor vessels transition from an initial dense regular network to later scant engorged vasculature, CD68+ TAMs shift away from perivascular regions to poorly vascularized areas. Remarkably, this process is heavily influenced by the immunocompetency of host animal, as tumor vessels in immunodeficient hosts remained dense and regular while TAMs evenly distributed. Utilizing a sensitive fluorescent reporter to track tumor hypoxia, we revealed that hypoxic niche controls immunosuppression by at least two mechanisms: first, attracting and sequestering activated TAMs in hypoxic zones, and second, reprograming entrapped TAMs towards an immunotolerant state. Indeed, entrapped TAMs also experience hypoxia and upregulate phagocytic marker Cd68 and immunotolerant genes Mrc1 and Arg1, thereby facilitating debris clearing, inflammatory containment, and immunosuppression in hypoxic zones. Mechanistically, we identified Ccl8 and IL-1β as two hypoxic niche factors released by TAMs in response to cues from hypoxic GBM cells, functioning to reinforce TAM retainment. Reciprocally, niche factors also shape the transcriptional responses of hypoxic tumor cells that exhibit quiescence and mesenchymal shift. Moreover, hypoxic niche factors are highly enriched in human GBMs, particularly mesenchymal subtype, and predict poor survival. Importantly, perturbing hypoxic niches resulted in reduced TAM sequestration and better tumor control. Together, understanding the mutual influence of immune contexture and metabolic landscape has important ramifications for improving efficacy of immunotherapies against GBM.
Evaluation of nanopore sequencing for epigenetic epidemiology: a comparison with DNA methylation microarrays
Authors: Flynn Robert , Washer Sam , Jeffries Aaron R , Andrayas Alexandria , Shireby Gemma , Kumari Meena , Schalkwyk Leonard C , Mill Jonathan , Hannon Eilis
Published: March 2022

Most epigenetic epidemiology to date has utilized microarrays to identify positions in the genome where variation in DNA methylation is associated with environmental exposures or disease. However, these profile less than 3% of DNA methylation sites in the human genome, potentially missing affected loci and preventing the discovery of disrupted biological pathways. Third generation sequencing technologies, including Nanopore sequencing, have the potential to revolutionise the generation of epigenetic data, not only by providing genuine genome-wide coverage but profiling epigenetic modifications direct from native DNA. Here we assess the viability of using Nanopore sequencing for epidemiology by performing a comparison with DNA methylation quantified using the most comprehensive microarray available, the Illumina EPIC array. We implemented a CRISPR-Cas9 targeted sequencing approach in concert with Nanopore sequencing to profile DNA methylation in three genomic regions to attempt to rediscover genomic positions that existing technologies have shown are differentially methylated in tobacco smokers. Using Nanopore sequencing reads, DNA methylation was quantified at 1,779 CpGs across three regions, providing a finer resolution of DNA methylation patterns compared to the EPIC array. The correlation of estimated levels of DNA methylation between platforms was high. Furthermore, we identified 12 CpGs where hypomethylation was significantly associated with smoking status, including 10 within the AHRR gene. In summary, Nanopore sequencing is a valid option for identifying genomic loci where large differences in DNAm are associated with a phenotype and has the potential to advance our understanding of the role differential methylation plays in the aetiology of complex disease.
Drawing the experience dynamics of meditation
Authors: Jachs Barbara , Camino Garcia Manuel , Canales-Johnson Andrés , Bekinschtein Tristan A.
Published: March 2022

Subjective experiences are hard to capture quantitatively without losing depth and nuance, and subjective report analyses are time-consuming, their interpretation contested. We describe Temporal Experience Tracing, a method that captures relevant aspects of the unified conscious experience over a continuous period of time. The continuous multidimensional description of an experience allows us to computationally reconstruct common experience states. Applied to data from 852 meditations – from novice (n=20) and an experienced (n=12) meditators practising Breathing, Loving-Kindness and Open-Monitoring meditation – we reconstructed four recurring experience states with an average duration of 6:46 min (SD = 5:50 min) and their transition dynamics. Three of the experience states assimilated the three meditation styles practiced, and a fourth experience state represented a common low-motivational, ‘off-task’ state for both groups. We found that participants in both groups spent more time in the task-related experience state during Loving Kindness meditation than other meditation styles and were less likely to transition into an ‘off-task’ experience state during Loving Kindness meditation than during Breathing meditation. We demonstrate that drawing the dynamics of experience enables the quantitative analysis of subjective experiences, transforming the time dimension of the stream of consciousness from narrative to measurable.
Campylobacter jejuni modulates reactive oxygen species production and NADPH oxidase 1 expression in human intestinal epithelial cells
Authors: Hong Geunhye , Davies Cadi , Omole Zahra , Liaw Janie , Grabowska Anna D. , Canonico Barbara , Corcionivoshi Nicolae , Wren Brendan , Dorrell Nick , Elmi Abdi , Gundogdu Ozan
Published: March 2022

Campylobacter jejuni is the major bacterial cause of foodborne gastroenteritis worldwide. Mechanistically, how this pathogen interacts with intrinsic defence machinery of human intestinal epithelial cells (IECs) remains elusive. To address this, we investigated how C. jejuni counteracts the intracellular and extracellular reactive oxygen species (ROS) in IECs. Our work shows that C. jejuni differentially regulates intracellular and extracellular ROS production in human T84 and Caco-2 cells. C. jejuni downregulates the transcription and translation of Nicotinamide adenine dinucleotide phosphate (NAPDH) oxidase (Nox1), a key ROS-generating enzyme in IECs and antioxidant defence genes cat and sod1. Furthermore, inhibition of Nox1 by diphenylene iodonium (DPI) and siRNA reduced C. jejuni ability to interact, invade and intracellularly survive within T84 and Caco-2 cells. Collectively, these findings provide mechanistic insight into how C. jejuni modulates the IEC defence machinery.
GenErode: a bioinformatics pipeline to investigate genome erosion in endangered and extinct species
Authors: Kutschera Verena E. , Kierczak Marcin , van der Valk Tom , von Seth Johanna , Dussex Nicolas , Lord Edana , Dehasque Marianne , Stanton David W. G. , Khoonsari Payam Emami , Nystedt Björn , Dalén Love , Díez-del-Molino David
Published: March 2022

Background

Many wild species have suffered drastic population size declines over the past centuries, which have led to ‘genomic erosion’ processes characterized by reduced genetic diversity, increased inbreeding, and accumulation of harmful mutations. Yet, genomic erosion estimates of modern-day populations often lack concordance with dwindling population sizes and conservation status of threatened species. One way to directly quantify the genomic consequences of population declines is to compare genome-wide data from pre-decline museum samples and modern samples. However, doing so requires computational data processing and analysis tools specifically adapted to comparative analyses of degraded, ancient or historical, DNA data with modern DNA data as well as personnel trained to perform such analyses.

Results

Here, we present a highly flexible, scalable, and modular pipeline to compare patterns of genomic erosion using samples from disparate time periods. The GenErode pipeline uses state-of-the-art bioinformatics tools to simultaneously process whole-genome re-sequencing data from ancient/historical and modern samples, and to produce comparable estimates of several genomic erosion indices. No programming knowledge is required to run the pipeline and all bioinformatic steps are well-documented, making the pipeline accessible to users with different backgrounds. GenErode is written in Snakemake and Python3 and uses Conda and Singularity containers to achieve reproducibility on high-performance compute clusters. The source code is freely available on GitHub (https://github.com/NBISweden/GenErode).

Conclusions

GenErode is a user-friendly and reproducible pipeline that enables the standardization of genomic erosion indices from temporally sampled whole genome re-sequencing data.
Estimating spatially variable and density-dependent survival using open-population spatial capture-recapture models
Authors: Milleret Cyril , Dey Soumen , Dupont Pierre , Turek Daniel , de Valpine Perry , Bischof Richard
Published: March 2022

Open-population spatial capture-recapture (OPSCR) models use the spatial information contained in individual detections collected over multiple consecutive occasions to estimate occasion-specific density, but also demographic parameters. OPSCR models can also estimate spatial variation in vital rates, but such models are neither widely used nor thoroughly tested. We developed a Bayesian OSPCR model that not only accounts for spatial variation in survival using spatial covariates, but also estimates local density-dependent effects on survival within a unified framework. Using simulations, we show that OPSCR models provide sound inferences on the effect of spatial covariates on survival, including multiple competing sources of mortality, each with potentially different spatial determinants. Estimation of local density-dependent survival was possible but required more data due to the greater complexity of the model. Not accounting for spatial heterogeneity in survival led to positive bias in abundance estimates (up to 10% relative bias). We provide a set of features in R package nimbleSCR that allow computationally efficient fitting of Bayesian OPSCR models with spatially varying survival. The ability to make population-level inferences of spatial variation in survival is an essential step towards a fully spatially-explicit OPSCR model that can disentangle the role of multiple spatial drivers on population dynamics.

Open Research statement

code to reproduce the analysis is available on github;https://github.com/Cyril-Milleret/Public/tree/master/SpatialSurvivalOPSCR
Cholinergic forebrain activation improves cognition, boosts neurotrophin receptors, and lowers Aβ42 levels in the cerebral cortex of 5xFAD mice
Authors: Kumro Jacob , Tripathi Ashutosh , Lei Yun , Sword Jeremy , Callahan Patrick , Terry Alvin , Lu Xin-yun , Kirov Sergei , Pillai Anilkumar , Blake David T
Published: March 2022

The biological basis of Alzheimer’s dementia has been hypothesized in terms of basal forebrain cholinergic decline, and in terms reflecting the neuropathologies surrounding beta amyloid and tau. To shed light on the contributions of these different biological elements, we performed five month intermittent stimulation of the basal forebrain, which projects to the cortical mantle, in 5xFAD Alzheimer’s model mice and wild-type littermates, and subjected mice to behavioral testing and tissue analysis. The 5xFAD mice performed worse in water maze testing than their littermates. Stimulation improved both classes of mice, and removed performance differences between genotypes by the fifth testing day. Stimulated groups had two to four-fold increases in immunoblot measures of each of the neurotrophin receptors tropomyosin receptor kinase A and B. Stimulation also led to lower tissue Aβ42 and beta amyloid cleavage enzyme 1 in 5xFAD mice. Despite the lack of strong direct projections from the basal forebrain stimulation region to the hippocampus, the hippocampal tissues in stimulated mice had more nerve growth factor receptor, and lower levels of beta secretase for amyloid. These data support a causal relation between forebrain cholinergic pathways and cognitive decline dependent on Aβ42. Activation of cholinergic brain pathways improves neurotrophin pathways and reduces Aβ42 accumulation. The recruitment of both classes of neurotrophin receptors in the process suggests a serine protease cleavage intermediary between cholinergic response and neurotrophin activation.
Coexistence in diverse communities with higher-order interactions
Authors: Gibbs Theo , Levin Simon A. , Levine Jonathan M.
Published: March 2022

A central assumption in most ecological models is that the interactions in a community operate only between pairs of species. However, the interaction between two species may be fundamentally changed by the presence of others. Although interactions among three or more species, called higher-order interactions, have the potential to modify our theoretical understanding of coexistence, ecologists lack clear expectations for how these interactions shape community structure. Here, we analytically predict and numerically confirm how the variability and strength of higher-order interactions affect species coexistence. We found that, as higher-order interaction strengths become more variable across species, fewer species coexist, echoing the behavior of pairwise models. If inter-specific higher-order interactions become too harmful relative to self-regulation, coexistence was destabilized, but coexistence was also lost when these interactions were too weak and mutualistic effects became prevalent. Last, we showed that more species rich communities structured by higher-order interactions lose species more readily than their species poor counterparts, generalizing classic results for community stability. Our work provides needed theoretical expectation for how higher-order interactions impact species coexistence in diverse communities.