bluuebunny/crossref_metadata_2025 huggingface dataset:
Prospective Implementation of Standardized Post-Hepatectomy Care Pathways to Reduce Opioid Prescription Volume after Inpatient Surgery
Authors: DiPeri Timothy P , Newhook Timothy E , Arvide Elsa M , Dewhurst Whitney L , Bruno Morgan L , Chun Yun Shin , Tran Cao Hop S , Lee Jeffrey E , Vauthey Jean-Nicolas , Tzeng Ching-Wei D
Published: June 2022

BACKGROUND:

Among the goals of prospectively implemented post-hepatectomy care pathways was a focus on patient-centric opioid reduction. We sought to evaluate the impact of pathway implementation on opioid volumes in the last 24-hour period and discharge prescriptions.

STUDY DESIGN:

This is a retrospective cohort study comparing a prospective cohort (“POST,” September 2019 through February 2020) treated after pathway implementation to a historical cohort of hepatectomy patients (“PRE,” March 2016 through December 2017) before our 2018 departmental opioid reduction efforts. Opioid volumes in the last 24 hours and prescribed at discharge were converted to oral morphine equivalents (OME) and compared between cohorts.

RESULTS:

There were 276 PRE and 100 POST patients. There was a similar proportion of major (PRE-34.1% vs POST-40%) and minimally invasive hepatectomies (PRE-19.9% vs POST-11%, p = 0.122). Implementation was associated with a shorter length of stay (median 5 d PRE vs 4 d POST, p < 0.001). Standardized opioid weaning was associated with a lower median last 24-hour OME (20 mg PRE vs 10 mg POST, p = 0.001). Using a standardized discharge calculation, median discharge OME were lower (200 mg PRE vs 50 mg POST, p < 0.001). More POST patients were discharged opioid-free (6.9% PRE vs 21% POST, p < 0.001).

CONCLUSIONS:

Implementation of post-hepatectomy care pathways was associated with a 50% reduction in last 24-hour OME, which, combined with a standardized discharge calculation, was associated with an overall 75% reduction in discharge opioid volumes and tripled opioid-free discharges. These data suggest that no-cost, reproducible pathways can be considered in abdominal operations with similar incisions/length of stay to decrease variation in opioid dosing while prioritizing patient-centric opioid needs.
Does Residual Invasive Disease in Wide Local Excision after Diagnosis with Partial Biopsy Technique Influence Survival in Melanoma? Matched-Pair Analysis of Multicenter Selective Lymphadenectomy Trial I and II
Authors: Ramiscal Judi Anne B , Stern Stacey L , Wilson Ana K , Lorimer Patrick D , Lee Nathaniel A , Goldfarb Melanie R , Foshag Leland J , Fischer Trevan D
Published: June 2022

BACKGROUND:

Current guidelines recommend excisional/complete biopsy for melanoma diagnosis, owing to high rates of residual disease found at wide local excision (WLE) after partial biopsy techniques. We sought to determine any survival disadvantage associated with the presence of residual invasive melanoma in the WLE after diagnosis with a partial biopsy technique.

STUDY DESIGN:

Data were examined from Multicenter Selective Lymphadenectomy Trials I and II (MSLT-I and -II), 2 large melanoma trials. Patients diagnosed with excisional/complete biopsy were excluded. Clinicopathologic characteristics, melanoma-specific survival (MSS), distant disease-free survival (DDFS), and disease-free survival (DFS) of those with residual invasive melanoma in the definitive WLE and those with no residual melanoma were compared. Matched pairing was used to reduce variability between groups.

RESULTS:

From 1994 through 2014, 3,939 patients were enrolled in these trials and 874 (22%) were diagnosed using partial biopsy techniques. Of these, 399 (46%) had residual tumor in the WLE. Only 6 patients had residual tumor in their WLE resulting in T-upstaging of their tumor. Match-pairing formed two cohorts (1:1) of patients with and without residual invasive tumor after WLE. A total of 514 patients were paired; 288 (56%) males, 148 (28.8%) aged 60 or older, 192 (37.4%) with truncal melanomas, 214 (41.6%) had Breslow thickness 2 mm or greater, and 376 (73.2%) had positive sentinel nodes. Kaplan-Meier analysis showed no statistical difference in 10-year MSS (73.6% ± 3.3% vs 73.9% ± 3.7%, p = 0.891), DDFS (68.7% ± 3.4% vs 65.3% ± 4.0%, p = 0.548), or DFS (59.6% ± 3.7% vs 59.4% ± 3.9%, p = 0.783).

CONCLUSIONS:

Survival in patients with primary melanoma does not appear to be worse in patients who undergo a partial biopsy technique and are later found to have residual invasive tumor in the WLE specimen.
Modelling methicillin-resistant
Staphylococcus aureus
decolonization: interactions between body sites and the impact of site-specific clearance
Authors: Poyraz Onur , Sater Mohamad R. A. , Miller Loren G. , McKinnell James A. , Huang Susan S. , Grad Yonatan H. , Marttinen Pekka
Published: June 2022

Methicillin-resistant
Staphylococcus aureus
(MRSA) can colonize multiple body sites, and carriage is a risk factor for infection. Successful decolonization protocols reduce disease incidence; however, multiple protocols exist, comprising diverse therapies targeting multiple body sites, and the optimal protocol is unclear. Standard methods cannot infer the impact of site-specific components on successful decolonization. Here, we formulate a Bayesian coupled hidden Markov model, which estimates interactions between body sites, quantifies the contribution of each therapy to successful decolonization, and enables predictions of the efficacy of therapy combinations. We applied the model to longitudinal data from a randomized controlled trial (RCT) of an MRSA decolonization protocol consisting of chlorhexidine body and mouthwash and nasal mupirocin. Our findings (i) confirmed nares as a central hub for MRSA colonization and nasal mupirocin as the most crucial therapy and (ii) demonstrated all components contributed significantly to the efficacy of the protocol and the protocol reduced self-inoculation. Finally, we assessed the impact of hypothetical therapy improvements
in silico
and found that enhancing MRSA clearance at the skin would yield the largest gains. This study demonstrates the use of advanced modelling to go beyond what is typically achieved by RCTs, enabling evidence-based decision-making to streamline clinical protocols.
Birds both avoid and control collisions by harnessing visually guided force vectoring
Authors: Chin Diana D. , Lentink David
Published: June 2022

Birds frequently manoeuvre around plant clutter in complex-structured habitats. To understand how they rapidly negotiate obstacles while flying between branches, we measured how foraging Pacific parrotlets avoid horizontal strings obstructing their preferred flight path. Informed by visual cues, the birds redirect forces with their legs and wings to manoeuvre around the obstacle and make a controlled collision with the goal perch. The birds accomplish aerodynamic force vectoring by adjusting their body pitch, stroke plane angle and lift-to-drag ratios beat-by-beat, resulting in a range of about 100° relative to the horizontal plane. The key role of drag in force vectoring revises earlier ideas on how the avian stroke plane and body angle correspond to aerodynamic force direction—providing new mechanistic insight into avian manoeuvring—and how the evolution of flight may have relied on harnessing drag.
A parametric logistic equation with light flux and medium concentration for cultivation planning of microalgae
Authors: Kambe Kazuki , Hirokawa Yasutaka , Koshi Asuka , Hori Yutaka
Published: June 2022

Microalgae are considered to be promising producers of bioactive chemicals, feeds and fuels from carbon dioxide by photosynthesis. Thus, the prediction of microalgal growth profiles is important for the planning of cost-effective and sustainable cultivation–harvest cycles. This paper proposes a mathematical model capable of predicting the effect of light flux into culture and medium concentration on the growth profiles of microalgae by incorporating these growth-limiting factors into a logistic equation. The specific form of the equation is derived based on the experimentally measured growth profiles of
Monoraphidium
sp., a microalgal strain isolated by the authors, under 16 conditions consisting of combinations of incident light fluxes into culture and initial medium concentrations. Using a cross-validation method, it is shown that the proposed model has the ability to predict necessary incident light flux into culture and initial medium concentration for harvesting target biomass at a target time. Finally, model-guided cultivation planning is performed and is evaluated by comparing the result with experimental data.
The absence of alternative stable states in vegetation cover of northeastern India
Authors: Sarania Bidyut , Guttal Vishwesha , Tamma Krishnapriya
Published: June 2022

Globally, forests and savannah are shown to be alternative stable states for intermediate rainfall regimes. This has implications for how these ecosystems respond to changing rainfall conditions. However, we know little about the occurrence of alternative stable states in forest ecosystems in India. In this study, we investigate the possibility of alternative stable states in the vegetation cover of northeastern India, which is a part of the Eastern Himalaya and the Indo-Burma biodiversity hotspots. To do so, we construct the so-called state diagram, by plotting frequency distributions of vegetation cover as a function of mean annual precipitation (MAP). We use remotely sensed satellite data of the enhanced vegetation index (EVI) as a proxy for vegetation cover (at 1 km resolution). We find that EVI exhibits unimodal distribution across a wide range of MAP. Specifically, EVI increases monotonically in the range 1000–2000 mm of MAP, after which it plateaus. This range of MAP corresponds to the vegetation transitional zone (1200–3700 m), whereas MAP greater than 2000 mm covers the larger extent of the tropical forest (less than or equal to 1200 m) of northeast India. In other words, we find no evidence for alternative stable states in vegetation cover or forest states at coarser scales in northeast India.
The war of corals: patterns, drivers and implications of changing coral competitive performances across reef environments
Authors: Kayal Mohsen , Adjeroud Mehdi
Published: June 2022

Amidst global environmental changes, predicting species' responses to future environments is a critical challenge for preserving biodiversity and associated human benefits. We explored the original idea that coral competitive performances, the ability of corals to preempt ecological space on the reef through territorial warfare, serve as indicators of species’ ecological niches and environmental windows, and therefore, responses to future environments. Our surveys indicated that coral performances varied with taxonomic identity, size and position along environmental gradients, highlighting complex interplays between life-history, warfare-strategy and niche segregation. Our results forewarn that growing alterations of coastal environments may trigger shifts in coral dominance, with the decline of major reef-building taxa like acroporids, and emphasize the importance of limiting human impacts for coastal resilience. Our empirical approach untangles the complexity of species' battle-like interactions and can help identify winners and losers in various communities caught in the interplay between ecological niches, environmental windows and global changes.
Ancient DNA from a 2700-year-old goitered gazelle (
Gazella subgutturosa
) supports gazelle hunting in Iron Age Central Asia
Authors: Rodrigues Soares André Elias , Boroffka Nikolaus , Schröder Oskar , Sverchkov Leonid , Benecke Norbert , Günther Torsten
Published: June 2022

Central Asia has been an important region connecting the different parts of Eurasia throughout history and prehistory, with large states developing in this region during the Iron Age. Archaeogenomics is a powerful addition to the zooarchaeological toolkit for understanding the relation of these societies to animals. Here, we present the genetic identification of a goitered gazelle specimen (
Gazella subgutturosa
) at the site Gazimulla-Tepa, in modern-day Uzbekistan, supporting hunting of the species in the region during the Iron Age. The sample was directly radiocarbon dated to 2724–2439 calBP. A phylogenetic analysis of the mitochondrial genome places the individual into the modern variation of
G. subgutturosa
. Our data do represent both the first ancient DNA and the first nuclear DNA sequences of this species. The lack of genomic resources available for this gazelle and related species prevented us from performing a more in-depth analysis of the nuclear sequences generated. Therefore, we are making our sequence data available to the research community to facilitate other research of this nowadays threatened species which has been subject to human hunting for several millennia across its entire range on the Asian continent.
Analytical quality by design based on design space in reversed-phase-high performance liquid chromatography analysis for simultaneous estimation of metformin, linagliptin and empagliflozin
Authors: Marie Aya A. , Salim Mohamed M. , Kamal Amira H. , Hammad Sherin F. , Elkhoudary Mahmoud M.
Published: June 2022

Employing the Quality by Design paradigm through this work helped conclude the method operable design region for optimizing the high performance liquid chromatography (HPLC) assay using Design of Experiments and response surface methodology to obtain a good resolution and determination of all analysed compounds and to achieve a suitable analysis time. A deep understanding of the quality target product profile, analytical target profile and risk assessment for parameters that affect the method performance led to developing an accurate, precise and cost-effective method. Quality risk management principles were applied for determining the critical method parameters affecting the simultaneous determination of metformin hydrochloride (MET), linagliptin (LIN) and empagliflozin (EMP) by reversed-phase HPLC . The ternary mixture was successfully resolved in 5 min with a linearity range of (0.1–600) µg ml
−1
for MET and (0.05–50) µg ml
−1
for LIN and EMP. The newly developed method was validated according to the International Council for Harmonization of Technical Requirements for Registration of Pharmaceuticals for Human Use guidelines. Good agreement was observed with the assay results of the reported UPLC one. To evaluate the greenness of the proposed method, an analytical Eco-Scale method was used.
Finite time blowup of incompressible flows surrounding compressible bubbles evolving under soft equations of state
Authors: Van Gorder Robert A.
Published: June 2022

We explore the dynamics of a compressible fluid bubble surrounded by an incompressible fluid of infinite extent in three dimensions, constructing bubble solutions with finite time blowup under this framework when the equation of state relating pressure and volume is soft (e.g. with volume singularities that are locally weaker than that in the Boyle–Mariotte law), resulting in a finite time blowup of the surrounding incompressible fluid as well. We focus on two families of solutions, corresponding to a soft polytropic process (with the bubble decreasing in size until eventual collapse, resulting in velocity and pressure blowup) and a cavitation equation of state (with the bubble expanding until it reaches a critical cavitation volume, at which pressure blows up to negative infinity, indicating a vacuum). Interestingly, the kinetic energy of these solutions remains bounded up to the finite blowup time, making these solutions more physically plausible than those developing infinite energy. For all cases considered, we construct exact solutions for specific parameter sets, as well as analytical and numerical solutions that show the robustness of the qualitative blowup behaviours for more generic parameter sets. Our approach suggests novel—and perhaps physical—routes to the finite time blowup of fluid equations.
A restatement of the natural science evidence base regarding the source, spread and control of
Campylobacter
species causing human disease
Authors: Goddard Matthew R. , O'Brien Sarah , Williams Nicola , Guitian Javier , Grant Andrew , Cody Alison , Colles Frances , Buffet Jean-Charles , Adlen Ella , Stephens Andrea , Godfray H. Charles J. , Maiden Martin C. J.
Published: June 2022

Food poisoning caused by
Campylobacter
(campylobacteriosis) is the most prevalent bacterial disease associated with the consumption of poultry, beef, lamb and pork meat and unpasteurized dairy products. A variety of livestock industry, food chain and public health interventions have been implemented or proposed to reduce disease prevalence, some of which entail costs for producers and retailers. This paper describes a project that set out to summarize the natural science evidence base relevant to campylobacteriosis control in as policy-neutral terms as possible. A series of evidence statements are listed and categorized according to the nature of the underlying information. The evidence summary forms the appendix to this paper and an annotated bibliography is provided in the electronic supplementary material.
Long walk home: Magellanic penguins have strategies that lead them to areas where they can navigate most efficiently
Authors: Quintana Flavio , Gómez-Laich Agustina , Gunner Richard M. , Gabelli Fabián , Omo Giacomo Dell , Duarte Carlos , Brogger Martín , Wilson Rory P.
Published: June 2022

Understanding how animals move in dense environments where vision is compromised is a major challenge. We used GPS and dead-reckoning to examine the movement of Magellanic penguins commuting through vegetation that precluded long-distance vision. Birds leaving the nest followed the shortest, quickest route to the sea (the ‘ideal path’, or '
I-path
') but return tracks depended where the birds left the water. Penguins arriving at the beach departure spot mirrored the departure. Most of those landing at a distance from the departure spot travelled slowly, obliquely to the coast at a more acute angle than a beeline trajectory to the nest. On crossing their
I-path
, these birds then followed this route quickly to their nests. This movement strategy saves birds distance, time and energy compared to a route along the beach and the into the colony on the
I-track
and saves time and energy compared to a beeline trajectory which necessitates slow travel in unfamiliar areas. This suggests that some animals adopt tactics that take them to an area where their navigational capacities are enhanced for efficient travel in challenging environments.
Demographic consequences of heterogeneity in conspecific density dependence among mast-fruiting tropical trees
Authors: O'Brien Michael J. , Hector Andy , Kellenberger Roman T. , Maycock Colin R. , Ong Robert , Philipson Christopher D. , Powers Jennifer S. , Reynolds Glen , Burslem David F. R. P.
Published: June 2022

The role of conspecific density dependence (CDD) in the maintenance of species richness is a central focus of tropical forest ecology. However, tests of CDD often ignore the integrated effects of CDD over multiple life stages and their long-term impacts on population demography. We combined a 10-year time series of seed production, seedling recruitment and sapling and tree demography of three dominant Southeast Asian tree species that adopt a mast-fruiting phenology. We used these data to construct individual-based models that examine the effects of CDD on population growth rates (
λ
) across life-history stages. Recruitment was driven by positive CDD for all species, supporting the predator satiation hypothesis, while negative CDD affected seedling and sapling growth of two species, significantly reducing
λ
. This negative CDD on juvenile growth overshadowed the positive CDD of recruitment, suggesting the cumulative effects of CDD during seedling and sapling development has greater importance than the positive CDD during infrequent masting events. Overall, CDD varied among positive, neutral and negative effects across life-history stages for all species, suggesting that assessments of CDD on transitions between just two stages (e.g. seeds seedlings or juveniles mature trees) probably misrepresent the importance of CDD on population growth and stability.
Dynamics in brain activation and behaviour in acute and repeated social defensive behaviour
Authors: de Almeida Alisson P. , Baldo Marcus V. C. , Motta Simone C.
Published: June 2022

In nature, confrontations between conspecifics are recurrent and related, in general, due to the lack of resources such as food and territory. Adequate defence against a conspecific aggressor is essential for the individual's survival and the group integrity. However, repeated social defeat is a significant stressor promoting several behavioural changes, including social defence
per se
. What would be the neural basis of these behavioural changes? To build new hypotheses about this, we here investigate the effects of repeated social stress on the neural circuitry underlying motivated social defence behaviour in male mice. We observed that animals re-exposed to the aggressor three times spent more time in passive defence during the last exposure than in the first one. These animals also show less activation of the amygdalar and hypothalamic nuclei related to the processing of conspecific cues. In turn, we found no changes in the activation of the hypothalamic dorsal pre-mammillary nucleus (PMD) that is essential for passive defence. Therefore, our data suggest that the balance between the activity of circuits related to conspecific processing and the PMD determines the pattern of social defence behaviour. Changes in this balance may be the basis of the adaptations in social defence after repeated social defeat.
Surgical Guidance of Head and Neck Squamous Cell Carcinoma Enabled by a c-MET-Targeting Fluorescent Probe cMBP-ICG
Authors: Wang Jingbo , Li Siyi , Wang Kun , Zhu Ling , Yang Lin , Zhu Yunjing , Zhang Zhen , Hu Longwei , Yuan Yuan , Fan Qi , Ren Jiliang , Yang Gongxin , Ding Weilong , Zhou Xiaoyu , Huang Ruimin , Cui Junqi , Zhang Chunye , Yuan Ying , Tian Jie , Tao Xiaofeng
Published: June 2022

Importance

Head and neck squamous cell carcinoma (HNSCC) is a highly aggressive malignancy which is associated with subtle local invasion and metastasis. Near-infrared (NIR) fluorescence-guided surgical precise resection of the tumor margin and potential metastasis has been appealing.

Objective

To determine whether a peptide-based NIR fluorescence dye, which can be administered via topical application and target tumor tissue via c-MET binding, can improve discrimination of HNSCC from normal tissue.

Design

A nonrandomized controlled trial was conducted between March 2021 and February 2022 at Shanghai Ninth Peoples’ Hospital, China. Study participants were blinded for subjective measurements.

Setting

Exploratory, single-center, open-label, dose-escalation

Participants

Consecutive Asian individuals with clinically suspicious, primary or recurrent HNSCC, who were scheduled for standard-of-care surgery with curative intent, were enrolled.

Interventions

Enrolled patients underwent in vivo fluorescence imaging before surgery, and ex vivo fluorescence imaging was performed on intraoperative specimens using 2.5 μM or 5.0 μM topical applicated fluorescent probes.

Main Outcomes and Measures

Primary analysis compared mean fluorescence intensity (MFI, total fluorescence signal divided by the total number of pixels within the region of interest) of tumor and peritumoral normal tissue. Possible tumor-to-background ratios (TBR, ratio of MFI of tumor over peritumoral normal tissues) may range from 2 to 4.

Results

Ten patients (1 female [10%], age = 59.4 ± 12.6 years old) were enrolled. Ex vivo imaging with 5.0 μM fluorescence prob demonstrated TBR of 2.71 ± 0.7, with 2.5 μM fluorescence prob demonstrated TBR of 3.11 ±1.2. To discriminate tumor from normal tissue with MFI, the area under the curve (AUC) was 0.88 (95% CI-0.88 to 1.0) for the 5.0 μM group, and 0.65 (95% CI 0.53 to 0.83) for the 2.5 μM group.

Conclusions and Relevance

This trial demonstrates that topical application of tumor targeting fluorescence probe can differentiate tumor and outlining tumor margins. Further research is currently underway to estimate whether this probe is potent in guiding biopsy and surgical procedure, and assisting long-term follow-up postoperatively.

Trial Registration

Chinese Clinical Trial Registry Identifier: ChiCTR2200058058
RNA-sequencing improves diagnosis for neurodevelopmental disorders by identifying pathogenic non-coding variants and reinterpretation of coding variants
Authors: Dekker Jordy , Schot Rachel , Bongaerts Michiel , de Valk Walter G. , van Veghel-Plandsoen Monique M. , Monfils Kathryn , Douben Hannie , Elfferich Peter , Kasteleijn Esmee , van Unen Leontine M.A. , Geeven Geert , Saris Jasper J. , van Ierland Yvette , Verheijen Frans W. , van der Sterre Marianne L.T. , Niaraki Farah Sadeghi , Huidekoper Hidde H. , Williams Monique , Wilke Martina , Verhoeven Virginie J.M. , Joosten Marieke , Kievit Anneke J.A. , van de Laar Ingrid M.B.H. , Hoefsloot Lies H. , Hoogeveen-Westerveld Marianne , Nellist Mark , Mancini Grazia M.S. , van Ham Tjakko J.
Published: June 2022

Background

For neurodevelopmental disorders (NDD), a molecular diagnosis is key for predicting outcome, treatment and genetic counseling. Currently, in about half of NDD cases, routine DNA-based testing fails to establish a genetic diagnosis. Transcriptome analysis (RNA-seq) improves the diagnostic yield for some groups of diseases, but has not been applied to NDD in a routine diagnostic setting.

Methods

Here, we explored the diagnostic potential of RNA-seq in a cohort of 96 individuals including 67 undiagnosed NDD subjects. We created a user-friendly web-application to analyze RNA-seq data from single individuals’ cultured skin fibroblasts for genic, exonic and intronic expression outliers, based on modified OUTRIDER Z-scores. Candidate pathogenic events were complemented/matched with genomic data and, if required, confirmed with additional functional assays.

Results

We identified pathogenic small genomic deletions, mono-allelic expression, aberrant splicing events, deep intronic variants resulting in pseudo-exon insertion, but also synonymous and nonsynonymous variants with deleterious effects on transcription. This approach increased the diagnostic yield for NDD by 12%. Diagnostic pitfalls during transcriptome analysis include detection of splice abnormalities in putative disease genes caused by benign polymorphisms and/or absence of expression of the responsible gene in the tissue of choice. This was misleading in one case and could have led to the wrong diagnosis in the absence of appropriate phenotyping.

Conclusions

Nonetheless, our results demonstrate the utility of RNA-seq in molecular diagnostics and stress the importance of multidisciplinary team consultation. In particular, the approach is useful for the identification and interpretation of unexpected pathogenic changes in mRNA processing and expression in NDD.
Differential D1 and D2 receptor internalization and recycling induced by amphetamine in vivo
Authors: Hansen Hanne D. , Schain Martin , Deng Helen P. , Mandeville Joseph B. , Rosen Bruce R. , Sander Christin Y.
Published: June 2022

The dopamine system plays a significant role in drug reward and the pathogenesis of addiction. Psychostimulant drugs acutely increase dopamine levels, triggering receptor internalization. In vitro data suggest that dopamine D1 receptors (D1R) recycle, whereas D2 receptors (D2R) degrade in response to activation. Yet, receptor fates in vivo remain unclear. This study bridges in vitro mechanisms and in vivo measurements of stimulant-induced modulation of receptor states using longitudinal multi-modal imaging combined with neuropharmacology. We demonstrate how repeated amphetamine administration differentially modulates D1R vs. D2R signaling in nonhuman primates over 24 hours using simultaneous positron emission tomography and functional magnetic resonance imaging. In contrast to predominantly inhibitory D2R signaling due to an initial amphetamine challenge, excitatory D1R functional signaling prevails three hours later, while D2Rs stay internalized. These results demonstrate differential externalization mechanisms of the D1R and D2R in vivo and a shift in receptor subtype activation after a dopamine surge.
Linking histology and molecular state across human tissues
Authors: Jones Andrew , Gundersen Gregory W. , Engelhardt Barbara E.
Published: June 2022

Histological imaging and molecular profiling of human tissues both offer information-rich characterizations of biological structure and function. Each of these modalities has been used to characterize the organization and dysregulation of a variety of tissues and cell types. While large-scale studies of each modality in isolation have been conducted, it remains largely unknown the extent to which these two views of a tissue relate to one another. Understanding how cellular states are encoded in cellular morphology would increase the utility and interpretability of imaging data; conversely, understanding the state of the cells within histology images would give deeper insights into the types and states of cells that constitute these tissue samples. To this end, we jointly analyzed 13, 360 human tissue samples with paired bulk gene expression profiles and histology images across 935 donors from the Genotype and Tissue Expression (GTEx) Consortium v8 study. This analysis reveals relationships among gene expression and cellular morphology through shared sources of expression and morphological heterogeneity both within and between tissue types. We describe shared sources of variation including cell-type heterogeneity, sample ischemic time, and donor health and demographics. We find specific correlated effects in both morphology and transcription linked to specific donor characteristics, such as their use of mechanical ventilation. This paired understanding adds value to each data modality on their own by enabling a more precise characterization of the alternative modality in the absence of those data.
Spatial distribution of metabolites in primate retina and its relevance to studies of human metabolic retinal disorders
Authors: Bonelli Roberto , Ansell Brendan R E , Woods Sasha M , Lockwood Sarah , Bishop Paul N , Khan Kamron N , Bahlo Melanie , Fruttiger Marcus
Published: June 2022

The primate retina has evolved regional specialisations for specific visual functions. The macula is specialised towards high acuity vision and is an area that contains an increased density of cone photoreceptors and signal processing neurons. Different regions in the retina display unique susceptibility to pathology, with many retinal diseases primarily affecting the macula. To better understand the properties of different retinal areas we conducted an untargeted metabolomics analysis on full thickness punches from three different regions (macula, temporal peri-macula and periphery) of primate retina. Half of all metabolites identified showed differential abundance in at least one comparison between the three regions. The unique metabolic phenotype of different retinal regions is likely due to the differential distribution of different cell types in these regions reflecting the specific metabolic requirements of each cell type. Furthermore, mapping metabolomics results from macula-specific eye diseases onto the region-specific distributions of healthy primate retina revealed differential abundance defining systemic metabolic dysregulations that were region specific, highlighting how our results may help to better understand the pathobiology of retinal diseases with region specificity.
Securing algal endosymbiont communities for reef-building corals
Authors: Bouwmeester Jessica , Daly Jonathan , Quinn Mariko , Henley E. Michael , Lager Claire , Perry Riley , Page Christopher A. , Hagedorn Mary
Published: June 2022

Photosynthetic dinoflagellates that live in symbiosis with corals (family Symbiodiniaceae) are fundamental for the survival of coral reef ecosystems. During coral bleaching events, it is assumed that these symbionts remain available in the water column, in sediments, or are seeded from unbleached coral colonies. Yet, this hypothesis has not been verified and it remains unclear whether some diversity of Symbiodiniaceae may be lost in the process. Culture methods have been developed for some Symbiodiniaceae, but for the vast majority of these photosynthetic symbionts, known culture methods are not successful at maintaining them for extensive periods. For these unculturable symbionts, cryopreservation, which places cells and tissues in suspended animation for days to decades, offers the best hope for saving the biodiversity of these crucial coral partners. Some cryopreservation processes use slow freezing, but if the cells are sensitive to low temperatures, as is the case for Symbiodiniaceae, then rapid freezing, called vitrification, is needed. We here, tested two published vitrification protocols that had been designed for algal symbionts extracted from Hawaiian corals, but we were unable to recover living symbionts after vitrification and warming. Therefore, we report a successful optimisation of the former vitrification protocols, which we tested on algal symbionts freshly extracted from three Hawaiian coral species, the development of ultra-rapid laser-warming cryopreservation techniques for symbionts, and banking procedures for algal symbionts. We also present some successful uptake of cryopreserved algal symbionts by coral larvae, although at a low rate. It is unclear why the former vitrification protocols failed but we propose that it may have been related to thermal stress and bleaching events that occurred on several occasions throughout the Hawaiian Islands. Maintenance of biodiversity is essential for sustaining functional, productive ecosystems with the adaptability to effectively recover from disturbances. By successfully cryopreserving and banking coral symbionts, we provide a critically needed component for securing Symbiodiniaceae biodiversity into the future.
Maturational networks of human fetal brain activity reveal emerging connectivity patterns prior to ex-utero exposure
Authors: Karolis Vyacheslav R. , Fitzgibbon Sean P. , Cordero-Grande Lucilio , Farahibozorg Seyedeh-Rezvan , Price Anthony N. , Hughes Emer J. , Fetit Ahmed E. , Kyriakopoulou Vanessa , Pietsch Maximilian , Rutherford Mary A. , Rueckert Daniel , Hajnal Joseph V. , Edwards A. David , O’Muircheartaigh Jonathan , Duff Eugene P. , Arichi Tomoki
Published: June 2022

A key feature of the fetal period is the rapid emergence of organised patterns of spontaneous brain activity. However, characterising this process in utero using functional MRI is inherently challenging and requires analytical methods which can capture the constituent developmental transformations. Here, we introduce a novel analytical framework, termed “maturational networks” (matnets), that achieves this by modelling functional networks as an emerging property of the developing brain. Compared to standard network analysis methods that assume consistent patterns of connectivity across development, our method incorporates age-related changes in connectivity directly into network estimation. We test its performance in a large neonatal sample, finding that the matnets approach characterises adult-like features of functional network architecture with a greater specificity than a standard group-ICA approach; for example, our approach is able to identify a nearly complete default mode network. In the in-utero brain, matnets enables us to reveal the richness of emerging functional connections and the hierarchy of their maturational relationships with remarkable anatomical specificity. We show that the associative areas play a central role within prenatal functional architecture, therefore indicating that functional connections of high-level associative areas start emerging prior to exposure to the extra-utero environment.
The F-box cofactor UFO redirects the LEAFY floral regulator to novel cis-elements
Authors: Rieu Philippe , Turchi Laura , Thévenon Emmanuel , Zarkadas Eleftherios , Nanao Max , Chahtane Hicham , Tichtinsky Gabrielle , Lucas Jérémy , Blanc-Mathieu Romain , Zubieta Chloe , Schoehn Guy , Parcy François
Published: June 2022

In angiosperms, flower patterning requires the localized expression of the APETALA3 (AP3) floral homeotic gene involved in petal and stamen development. AP3 is synergistically induced by the master transcription factor (TF) LEAFY (LFY) and the F-box protein UNUSUAL FLORAL ORGANS (UFO), but the molecular mechanism underlying this synergy has remained unknown. Here we show that the connection to ubiquitination pathways suggested by the F-box domain of UFO is mostly dispensable for its function and that UFO instead acts by forming a transcriptional complex with LFY and binds to newly discovered regulatory elements. Cryo-electron microscopy explains how a LFY-UFO complex forms on these novel DNA sites due to direct interaction of UFO with LFY and DNA. Finally, we show that this complex has a deep evolutionary origin, largely predating flowering plants. This work reveals a novel mechanism of an F-box protein in directly modulating the DNA-binding specificity of a master TF.
Structural features stabilized by divalent cation coordination within hepatitis E virus ORF1 are critical for viral replication
Authors: LeDesma Robert , Biswas Abhishek , Maya Stephanie , Gili Stefania , Higgins John , Ploss Alexander
Published: June 2022

Hepatitis E virus (HEV) is an RNA virus responsible for over 20 million infections annually. HEV’s open reading frame (ORF)1 polyprotein is essential for genome replication, though it is unknown how the different subdomains function within a structural context. Our data show that ORF1 operates as a multifunctional protein, which is not subject to proteolytic processing. Supporting this model, scanning mutagenesis performed on the putative papain-like cysteine protease (pPCP) domain revealed six cysteines essential for viral replication. Our data are consistent with their role in divalent metal ion coordination, which governs local and interdomain interactions that are critical for the overall structure of ORF1; further, the “pPCP” domain can only rescue viral genome replication in trans when expressed in the context of the full-length ORF1 protein but not as an individual subdomain. Taken together our work provides a comprehensive model of the structure and function of HEV ORF1.

Significance Statement

The development of non-teratogenic and potent antiviral therapies against HEV have been hindered by an incomplete understanding of the viral replication cycle. Our work provides a mechanistic insight into the complex replicative cycle of this understudied human pathogen and identifies a novel domain-domain interaction that is vital for replicative fitness.
Characterization of the Rhizophagus irregularis multicopper oxidase family indicates that the iron transporter RiFTR1 does not require a ferroxidase partner
Authors: Tamayo E , Shim C , Castillo AG , Benz JP , Ferrol N
Published: June 2022

The contribution of arbuscular mycorrhizal fungi (AM fungi) to plant iron (Fe) acquisition has been demonstrated in several studies. Recently, it has been shown that AM fungi use a high-affinity reductive pathway for Fe uptake. In the AM fungus Rhizophagus irregularis the ferric reductase RiFRE1 and the Fe permeases RiFTR1 and RiFTR2 have already been characterized. In an attempt to identify the third component of the reductive iron uptake pathway, a genome-wide approach has been used in R. irregularis to find genes encoding ferroxidases of the multicopper oxidase (MCO) gene family. Nine genes putatively encoding MCOs (RiMCO1-9) were identified. A phylogenetic analysis of MCO sequences of fungi from different taxonomic groups revealed that all RiMCOs clustered together in the ferroxidase/laccase group, and none with the Fet3-type ferroxidases. RiMCO1 and RiMCO3 were the only MCO genes displaying a detectable gene expression pattern typical of a high-affinity Fe transport system, indicating that RiMCO1 and RiMCO3 might have a role in the reductive high-affinity Fe uptake system. Moreover, yeast mutant complementation assays showed that the iron permease RiFTR1 can operate without the presence of a ferroxidase, indicating that it is able to transport also ferrous (II) iron.
Development of Top-Down Cortical Propagations in Youth
Authors: Pines Adam , Keller Arielle S. , Larsen Bart , Bertolero Maxwell , Ashourvan Arian , Bassett Dani S. , Cieslak Matthew , Covitz Sydney , Fan Yong , Feczko Eric , Houghton Audrey , Rueter Amanda R. , Tapera Tinashe , Vogel Jacob , Weinstein Sarah M. , Shinohara Russell T. , Fair Damien , Satterthwaite Theodore
Published: June 2022

Hierarchical processing requires activity propagating between higher and lower-order cortical areas. However, studies of brain development have chiefly quantified fluctuations within regions over time rather than propagations occurring over space. Here, we leveraged advances in neuroimaging and computer vision to track cortical activity propagations in a large sample of youth (n=388). We found that propagations robustly ascend and descend the cortical hierarchy, and that top-down propagations become both more prevalent with cognitive control demands and with development in youth.
Structural basis for CDC42 and RAC activation by the dual specificity GEF DOCK10
Authors: Fan Danni , Yang Jing , Cronin Nora , Barford David
Published: June 2022

Dedicator of cytokinesis 10 (DOCK10) is a guanine nucleotide exchange factor (GEF) belonging to the DOCK family that activate RHO GTPases. DOCK10 controls amoeboid migration and IL-4 induced B cell activation. Recent structural studies of the catalytic DHR2 domains of DOCK-family GEFs DOCK2 and DOCK9 in the presence of nucleotide-free RAC and CDC42 respectively, have revealed a conserved mechanism of nucleotide exchange distinct from the large family of Dbl homology (DH) GEFs. Less is known from a biochemical and structural perspective, about DOCK10. We have determined the crystal structure of the apo-state of the DHR2 domain of DOCK10 (DOCK10DHR2), which provides the first structural model for the apo-state of a DHR2 domain for the entire DOCK family. It demonstrates the conformational changes within DOCK10DHR2on engaging the GTPase, and associated induced conformational changes of the GTPase required to stimulate nucleotide release. We also report on the unexpected dual specificity of DOCK10DHR2which directly interacts with RAC and CDC42 and induces the nucleotide exchange of bothin vitro. This dual specificity is unique to DOCK10 within its evolutionarily related D subfamily. Structural studies of DOCK10DHR2in complex with RAC revealed an intriguing 2:1 stoichiometry between DOCK10DHR2and the GTPase, that differs from the canonical 1:1 stoichiometry for all other known DOCK-GTPase complexes. This was confirmed in solution using a variety of biophysical techniques. The identification of a novel mode of interaction between DOCK10DHR2and the RAC GTPase provides new insights into how DOCK family GEFs discriminate between CDC42, RAC and RHOA.
Tunable control of insect pheromone biosynthesis inNicotiana benthamiana
Authors: Kallam Kalyani , Moreno-Giménez Elena , Mateos-Fernández Ruben , Tansley Connor , Gianoglio Silvia , Orzaez Diego , Patron Nicola J.
Published: June 2022

Previous work has demonstrated that plants can be used as production platforms for molecules used in health, medicine, and agriculture. Production has been exemplified in both stable transgenic plants and using transient expression strategies. In particular, species ofNicotianahave been engineered to produce a range of useful molecules, including insect sex pheromones, which are valued for species-specific control of agricultural pests. To date, most studies have relied on strong constitutive expression of all pathway genes. However, work in microbes has demonstrated that yields can be improved by controlling and balancing gene expression. Synthetic regulatory elements that provide control over the timing and levels of gene expression are therefore useful for maximizing yields from heterologous biosynthetic pathways. In this study, we demonstrate the use of pathway engineering and synthetic genetic elements for controlling the timing and levels of production of Lepidopteran sex pheromones inNicotiana benthamiana. We demonstrate that copper can be used as a low-cost molecule for tightly regulated inducible expression. Further, we show how construct architecture influences relative gene expression and, consequently, product yields in multigene constructs. We compare a number of synthetic orthogonal regulatory elements and demonstrate maximal yields from constructs in which expression is mediated by dCas9-based synthetic transcriptional activators. The approaches demonstrated here provide new insights into the heterologous reconstruction of metabolic pathways in plants.
Crystal structure of the catalytic domain of human RPTPH
Authors: Kim Myeongbin , Ryu Seong Eon
Published: June 2022

Receptor-type protein tyrosine phosphatases (RPTPs) receive extracellular stimuli and transfer them into cells. They regulate cell growth, differentiation and death via specific signals. They have also been implicated in cancer, diabetes and neurological diseases. RPTPH, a member of the type 3 RPTP (R3-PTP) family, is an important regulator of colorectal cancer and hepatic carcinoma. Despite its importance in drug development, the structure of RPTPH has not yet been resolved. Here, the crystal structure of the catalytic domain of RPTPH was determined at 1.56 Å resolution. Despite similarities to other R3-PTPs in its overall structure, RPTPH exhibited differences in its loop regions and side-chain conformations. Compared with other R3-PTPs, RPTPH has unique side chains near its active site that may confer specificity for inhibitor binding. Therefore, detailed information on the structure of RPTPH provides clues for the development of specific inhibitors.
How does oil price uncertainty affect output in the Central and Eastern European economies? – the Bayesian-based approaches
Authors: Živkov Dejan , Đurašković Jasmina
Published: June 2022

Purpose

This paper aims to investigate how oil price uncertainty affects real gross domestic product (GDP) and industrial production in eight Central and Eastern European countries (CEEC).

Design/methodology/approach

In the research process, the authors use the Bayesian method of inference for the two applied methodologies – Markov switching generalized autoregressive conditional heteroscedasticity (GARCH) model and quantile regression.

Findings

The results clearly indicate that oil price uncertainty has a low effect on output in moderate market conditions in the selected countries. On the other hand, in the phases of contraction and expansion, which are portrayed by the tail quantiles, the authors find negative and positive Bayesian quantile parameters, which are relatively high in magnitude. This implies that in periods of deep economic crises, an increase in the oil price uncertainty reduces output, amplifying in this way recession pressures in the economy. Contrary, when the economy is in expansion, oil price uncertainty has no influence on the output. The probable reason lies in the fact that the negative effect of oil volatility is not strong enough in the expansion phase to overpower all other positive developments which characterize a growing economy. Also, evidence suggests that increased oil uncertainty has a more negative effect on industrial production than on real GDP, whereas industrial share in GDP plays an important role in how strong some CEECs are impacted by oil uncertainty.

Originality/value

This paper is the first one that investigates the spillover effect from oil uncertainty to output in CEEC.